title: Tery_0400_rep2

description:
Sample 23
This is the second of three biological replicates (each from separate cultures) of Trichodesmium erythraeum IMS101 cultures collected at 04:00 (D9) during the 24-hr light-dark cycle.
GenBank Accession NC_008312

source_name: Trichodesmium erythraeum IMS101 sampled at 0400 replicate 2

value: dark


title: Tery_0400_rep3

status: Public on Jun 11 2017

type: RNA

city: Xiamen

first: Tuo

last: Shi

state: Fujian

address: No. 1 South Xiang'an Rd.

country: China

institute: Xiamen University

description:
Sample 24
This is the third of three biological replicates (each from separate cultures) of Trichodesmium erythraeum IMS101 cultures collected at 04:00 (D9) during the 24-hr light-dark cycle.
GenBank Accession NC_008312

hyb_protocol: Hybridization was performed following the standard operating protocol of Roche NimbleGen, Inc., Madison, WI, USA. See www.nimblegen.com.

scan_protocol: Scanning was performed following the standard operating protocol of Roche NimbleGen, Inc., Madison, WI, USA. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to Robust Multi-Array Average (RMA) analysis (Irizarry et al., 2003, Biostatistics 4: 249-264), quantile normalization (Bolstad et al., 2003, Bioinformatics 19: 185-193), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

molecule: total RNA

organism: Trichodesmium erythraeum IMS101

source_name: Trichodesmium erythraeum IMS101 sampled at 0400 replicate 3

label_protocol: Reverse transcription of the total RNA and labeling of cDNA were performed following the standard operating protocol of Roche NimbleGen, Inc., Madison, WI, USA. See www.nimblegen.com.

growth_protocol:
Axenic cultures of Trichodesmium erythraeum IMS101 were maintained at 26 ℃ on a 12h:12h light/dark cycle at 50 μmol quanta m-2 s-1 in YBCII media (Chen et al., 1996, Journal of Phycology 32: 916-923) supplemented with 2.8 μM ferric ammonium citrate. The light was set on at 7:00 and off at 19:00 o′clock. Samples were taken on a 3-hr interval starting at the onset of the light period until the end of the dark period for a total of 24 hr.
At designated time, 200 ml each of triplicate cultures (replicates from different flasks) was filtered onto a 5 μm pore-size 47 mm diameter polycarbonate membrane filter. The filters were immediately frozen in liquid nitrogen and stored at -80 ℃ until processing.

extract_protocol: Total RNA was extracted using the Ambion RiboPure Bacteria kit (Life Technologies, Carlsbad, CA, USA), followed by in-solution DNase digestion with the RNase-Free DNase set and on-column cleanup with the RNeasy MiniElute kit (Qiagen, Valencia, CA, USA). RNA quality and concentration was determined by analysis with a NanoDrop 1000 spectrophotometer (Thermo Scienctific, Waltham, MA, USA) and an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) at the UCSC Microbial Environmental Genomics Applications: Modeling, Experimentation and Remote Sensing (MEGAMER) facility (University of California, Santa Cruz, CA, USA).

tag: light/dark cycle

tag: hours into light (l) /dark (d) period


title: Tery_2200_rep1

description:
Sample 16
This is the first of three biological replicates (each from separate cultures) of Trichodesmium erythraeum IMS101 cultures collected at 22:00 (D3) during the 24-hr light-dark cycle.
GenBank Accession NC_008312

source_name: Trichodesmium erythraeum IMS101 sampled at 2200 replicate 1


title: Tery_2200_rep2

description:
Sample 17
This is the second of three biological replicates (each from separate cultures) of Trichodesmium erythraeum IMS101 cultures collected at 22:00 (D3) during the 24-hr light-dark cycle.
GenBank Accession NC_008312

source_name: Trichodesmium erythraeum IMS101 sampled at 2200 replicate 2


title: Tery_2200_rep3

description:
Sample 18
This is the third of three biological replicates (each from separate cultures) of Trichodesmium erythraeum IMS101 cultures collected at 22:00 (D3) during the 24-hr light-dark cycle.
GenBank Accession NC_008312

source_name: Trichodesmium erythraeum IMS101 sampled at 2200 replicate 3


title: Tery_1600_rep3

description:
Sample 12
This is the third of three biological replicates (each from separate cultures) of Trichodesmium erythraeum IMS101 cultures collected at 16:00 (L9) during the 24-hr light-dark cycle.
GenBank Accession NC_008312

source_name: Trichodesmium erythraeum IMS101 sampled at 1600 replicate 3

value: light


title: Senescent BJ cells transfected with sip21, biological repeat 1

status: Public on Jun 13 2017

city: Rehovot

first: Valery

last: Krizhanovsky

address: Herzel 234

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

description: Expression data of damage-induced senescent human fibroblasts (BJ cells)

hyb_protocol: cDNA was prepared, labeled, and hybridized to Affymetrix GeneChip PrimeView, Human Gene Expression Array, according to standard manufacturer protocols.

scan_protocol: Hybridized chips were stained, washed, and scanned with the Affymetrix GeneChip 3000 7G Plus scanner and converted to cell intensity files by Affymetrix Expression Console SoftwareTM.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.  Transcriptome analysis (processing of raw data, clustering, and creation of correlation matrices) was carried out with Partek Genomics Suite 6.6 (http://www.partek.com/). The raw probe intensities were adjusted according to the numbers of G and C bases in the probe sequence before any probe correction. Preprocessing was performed with the Robust Microarray Averaging algorithm (Irizarry, Hobbs et al., 2003). Genes expressed below background levels (log 1.5 intensity of 6.9) in all examined conditions were excluded from further analyses.

label: biotin

organism: Homo sapiens

source_name: Human senescent primary fibroblasts BJs after transfection with sip21

growth_protocol: Human  BJ fibroblasts were maintained in DMEM supplemented with 2 mM L-glutamine, 100 units/ml of penicillin, 100 µg/ml of streptomycin, and 10% fetal bovine serum (FBS). DNA damage-induced senescence (DIS) was introduced by treatment with etoposide (E1383, Sigma-Aldrich) at a concentration of  50 µM for 48 h.

extract_protocol: Total RNA was extracted from growing and damage-induced senescenct (DIS) BJ cells transfected with siRNA against p21, or with control siRNA, using an RNeasy Mini Kit (QIAGEN). RNA purity was assessed with an ND-1000 NanoDrop Spectrophotometer (Peqlab Biotechnologie) and BioAnalyzer 2100 system (Agilent Technologies).

treatment_protocol: BJ growing and etoposide treated cells (DIS) were plated in 12-well plates. Cells were transfected with ON-TARGETplus SMARTpool small interfering RNA (siRNA) targeting p21 (L-002000-00-0005) or a control, with Non-Targeting siRNA Pool (D-001810-10-20), using DharmaFECT formulation 1 reagent (T-2001-03) according to the instructions of the manufacturer (Thermo Fisher Scientific). After 3 days, total RNA was extracted.

tag: tissue

value: human skin fibroblasts

tag: genotype

value: BJ cell line

tag: age

value: senescent

tag: transfection


title: Tery_1900_rep1

description:
Sample 13
This is the first of three biological replicates (each from separate cultures) of Trichodesmium erythraeum IMS101 cultures collected at 19:00 (L12) during the 24-hr light-dark cycle.
GenBank Accession NC_008312

source_name: Trichodesmium erythraeum IMS101 sampled at 1900 replicate 1


title: Tery_1300_rep1

description:
Sample 7
This is the first of three biological replicates (each from separate cultures) of Trichodesmium erythraeum IMS101 cultures collected at 13:00 (L6) during the 24-hr light-dark cycle.
GenBank Accession NC_008312

source_name: Trichodesmium erythraeum IMS101 sampled at 1300 replicate 1


title: Tery_0700_d1_rep2

description:
Sample 2
This is the second of three biological replicates (each from separate cultures) of Trichodesmium erythraeum IMS101 cultures collected at 07:00 (D12) during the 24-hr light-dark cycle.
GenBank Accession NC_008312

source_name: Trichodesmium erythraeum IMS101 sampled at 0700 replicate 2 (day 1)


title: Tery_1000_rep1

description:
Sample 4
This is the first of three biological replicates (each from separate cultures) of Trichodesmium erythraeum IMS101 cultures collected at 10:00 (L3) during the 24-hr light-dark cycle.
GenBank Accession NC_008312

source_name: Trichodesmium erythraeum IMS101 sampled at 1000 replicate 1


title: Growing BJ cells transfected with siCtrl, biological repeat 1

description: Expression data of growing human fibroblasts (BJ cells)

source_name: Human primary fibroblasts BJs after transfection with siCtrl

label_protocol: cDNA was prepared, labeled, and hybridized to Affymetrix GeneChip PrimeView, Human Gene Expression Array, according to standard manufacturer protocols.

value: primary

value: siCtrl


title: Tery_0700_d1_rep3

description:
Sample 3
This is the third of three biological replicates (each from separate cultures) of Trichodesmium erythraeum IMS101 cultures collected at 07:00 (D12) during the 24-hr light-dark cycle.
GenBank Accession NC_008312

source_name: Trichodesmium erythraeum IMS101 sampled at 0700 replicate 3 (day 1)


title: Tery_0700_d2_rep2

description:
Sample 26
This is the second of three biological replicates (each from separate cultures) of Trichodesmium erythraeum IMS101 cultures collected at 07:00 (2D12) during the 24-hr light-dark cycle.
GenBank Accession NC_008312

source_name: Trichodesmium erythraeum IMS101 sampled at 0700 replicate 2 (day 2)


title: Tery_1000_rep2

description:
Sample 5
This is the second of three biological replicates (each from separate cultures) of Trichodesmium erythraeum IMS101 cultures collected at 10:00 (L3) during the 24-hr light-dark cycle.
GenBank Accession NC_008312

source_name: Trichodesmium erythraeum IMS101 sampled at 1000 replicate 2


title: Tery_0100_rep3

description:
Sample 21
This is the third of three biological replicates (each from separate cultures) of Trichodesmium erythraeum IMS101 cultures collected at 01:00 (D6) during the 24-hr light-dark cycle.
GenBank Accession NC_008312

source_name: Trichodesmium erythraeum IMS101 sampled at 0100 replicate 3


title: Tery_0700_d2_rep3

description:
Sample 27
This is the third of three biological replicates (each from separate cultures) of Trichodesmium erythraeum IMS101 cultures collected at 07:00 (2D12) during the 24-hr light-dark cycle.
GenBank Accession NC_008312

source_name: Trichodesmium erythraeum IMS101 sampled at 0700 replicate 3 (day 2)


title: Tery_0400_rep1

description:
Sample 22
This is the first of three biological replicates (each from separate cultures) of Trichodesmium erythraeum IMS101 cultures collected at 04:00 (D9) during the 24-hr light-dark cycle.
GenBank Accession NC_008312

source_name: Trichodesmium erythraeum IMS101 sampled at 0400 replicate 1


title: Tery_1900_rep2

description:
Sample 14
This is the second of three biological replicates (each from separate cultures) of Trichodesmium erythraeum IMS101 cultures collected at 19:00 (L12) during the 24-hr light-dark cycle.
GenBank Accession NC_008312

source_name: Trichodesmium erythraeum IMS101 sampled at 1900 replicate 2


title: Tery_0100_rep1

description:
Sample 19
This is the first of three biological replicates (each from separate cultures) of Trichodesmium erythraeum IMS101 cultures collected at 01:00 (D6) during the 24-hr light-dark cycle.
GenBank Accession NC_008312

source_name: Trichodesmium erythraeum IMS101 sampled at 0100 replicate 1


title: Tery_0700_d2_rep1

description:
Sample 25
This is the first of three biological replicates (each from separate cultures) of Trichodesmium erythraeum IMS101 cultures collected at 07:00 (2D12) during the 24-hr light-dark cycle.
GenBank Accession NC_008312

source_name: Trichodesmium erythraeum IMS101 sampled at 0700 replicate 1 (day 2)


title: Tery_1300_rep3

description:
Sample 9
This is the third of three biological replicates (each from separate cultures) of Trichodesmium erythraeum IMS101 cultures collected at 13:00 (L6) during the 24-hr light-dark cycle.
GenBank Accession NC_008312

source_name: Trichodesmium erythraeum IMS101 sampled at 1300 replicate 3


title: Tery_1600_rep2

description:
Sample 11
This is the second of three biological replicates (each from separate cultures) of Trichodesmium erythraeum IMS101 cultures collected at 16:00 (L9) during the 24-hr light-dark cycle.
GenBank Accession NC_008312

source_name: Trichodesmium erythraeum IMS101 sampled at 1600 replicate 2


title: Tery_1600_rep1

description:
Sample 10
This is the first of three biological replicates (each from separate cultures) of Trichodesmium erythraeum IMS101 cultures collected at 16:00 (L9) during the 24-hr light-dark cycle.
GenBank Accession NC_008312

source_name: Trichodesmium erythraeum IMS101 sampled at 1600 replicate 1


title: Tery_0100_rep2

description:
Sample 20
This is the second of three biological replicates (each from separate cultures) of Trichodesmium erythraeum IMS101 cultures collected at 01:00 (D6) during the 24-hr light-dark cycle.
GenBank Accession NC_008312

source_name: Trichodesmium erythraeum IMS101 sampled at 0100 replicate 2


title: Tery_1000_rep3

description:
Sample 6
This is the third of three biological replicates (each from separate cultures) of Trichodesmium erythraeum IMS101 cultures collected at 10:00 (L3) during the 24-hr light-dark cycle.
GenBank Accession NC_008312

source_name: Trichodesmium erythraeum IMS101 sampled at 1000 replicate 3


title: Tery_1900_rep3

description:
Sample 15
This is the third of three biological replicates (each from separate cultures) of Trichodesmium erythraeum IMS101 cultures collected at 19:00 (L12) during the 24-hr light-dark cycle.
GenBank Accession NC_008312

source_name: Trichodesmium erythraeum IMS101 sampled at 1900 replicate 3


title: Tery_1300_rep2

description:
Sample 8
This is the second of three biological replicates (each from separate cultures) of Trichodesmium erythraeum IMS101 cultures collected at 13:00 (L6) during the 24-hr light-dark cycle.
GenBank Accession NC_008312

source_name: Trichodesmium erythraeum IMS101 sampled at 1300 replicate 2


title: 27_2_4_Tolvaptan_50

status: Public on Jun 10 2017

city: Chapel Hill

first: Merrie

last: Mosedale

state: North Carolina

address: 301 Pharmacy Lane, Kerr Hall CB#7569

department: Division of Pharmacotherapy and Experimental Therapeutics

country: USA

institute: UNC Eshelman School of Pharmacy

description:
primary human hepatocytes_donor 2
human hepatocyte RNA chiped with mouse fibroblast RNA

hyb_protocol: Fifteen (15) µg of labeled cRNA were fragmented and prepared for hybridization.

scan_protocol: The Affymetrix HT HG-U133+ PM peg arrays were used with the Affymetrix Gene Titan system. Gene Titan robotic instrumentation was used to perform the hybridization, washing, and scanning of the peg arrays.

data_processing: Gene expression analysis was performed in Partek Genomics Suite version 6.6 (Partek, St. Louis, MO). For gene expression profiling, Affymetrix CEL files (54 total, representing N=1 per donor, time point, treatment, and concentration) were normalized using the Robust Multi-array Average method with a log base 2 (log2) transformation. A filtering step was performed to remove control probe sets, probe sets without mRNA annotation, and low expression probe sets. Gene expression differences were identified using analysis of variance models with linear contrasts.

label_protocol: Double-stranded cDNA was synthesized from 150 ng of total RNA, then transcribed to biotin-labeled cRNA using the 3’ Express IVT kit (Affymetrix, Santa Clara, CA).  converted into labeled target antisense RNA (cRNA) using the Single-Round RNA Amplification and Biotin Labeling System (Enzo). Purified cRNA was fragmented using a 5X fragmentation buffer.

growth_protocol: Micropatterned cocultures (MPCCs)  were maintained in HepatoPac® Maintenance Medium (Hepregen) with medium replacement every 2-3 days. The plates were kept in a 37°C humidified incubator with 10% CO2. After shipping, MPCCs were allowed to acclimate for at least 48 h prior to drug treatment.

extract_protocol: Twenty-four (24) hours after the final Total cellular RNA was isolated from MPCCs using an RNeasy total RNA isolation kit and the QIAcube automated system (Qiagen) according to the manufacturer’s instructions. RNA from replicate wells (8 total) was pooled to create N=1 sample per concentration, time, and donor.  mice were sacrificed, livers were excised, and left liver lobe tissue was flash frozen in liquid nitrogen. Total liver RNA was isolated with the RNeasy total RNA isolation kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: On the morning of dosing (Day 0), MPCCs were washed and incubated for 2 h with serum-free HepatoPac® Toxicity Application Medium (Hepregen). The medium then was replaced with dosing solutions (prepared in serum-free HepatoPac® Toxicity Application Medium) and the cells were exposed continuously for 4, 24, or 72 h. Hepatocytes were exposed to either tolvaptan (0.01, 0.1, 1, 20, or 50 µM; Otsuka Pharmaceutical Co. Ltd, Rockville, MD) or vehicle (0.5% v/v DMSO; Sigma, St. Louis, MO).  mice per strain were dosed with vehicle (sterile water) and four with PF-04287881 (600 mg/kg) once daily by oral gavage for seven days.

tag: donor#

tag: time

value: 4 hr

tag: treatment

value: Tolvaptan

tag: dose (um)

value: 50 uM

tag: cell type

value: primary hepatocytes


title: 33_2_24_Tolvaptan_50

value: 24 hr


title: 60_3_72_Tolvaptan_50

description:
primary human hepatocytes_donor 3
human hepatocyte RNA chiped with mouse fibroblast RNA

value: 72 hr


title: Tery_0700_d1_rep1

description:
Sample 1
This is the first of three biological replicates (each from separate cultures) of Trichodesmium erythraeum IMS101 cultures collected at 07:00 (D12) during the 24-hr light-dark cycle.
GenBank Accession NC_008312

source_name: Trichodesmium erythraeum IMS101 sampled at 0700 replicate 1 (day 1)


title: 12_1_24_Tolvaptan_50

description:
primary human hepatocytes_donor 1
human hepatocyte RNA chiped with mouse fibroblast RNA


title: 38_2_72_Tolvaptan_20

value: 20 uM


title: 53_3_24_Tolvaptan_20


title: 18_1_72_Tolvaptan_50


title: 59_3_72_Tolvaptan_20


title: 5_1_4_Tolvaptan_20


title: 48_3_4_Tolvaptan_50


title: 32_2_24_Tolvaptan_20


title: 16_1_72_Tolvaptan_1

value: 1 uM


title: 17_1_72_Tolvaptan_20


title: 6_1_4_Tolvaptan_50


title: 37_2_72_Tolvaptan_1


title: 52_3_24_Tolvaptan_1


title: 4_1_4_Tolvaptan_1


title: 39_2_72_Tolvaptan_50


title: 26_2_4_Tolvaptan_20


title: 25_2_4_Tolvaptan_1


title: 54_3_24_Tolvaptan_50


title: 46_3_4_Tolvaptan_1


title: 47_3_4_Tolvaptan_20


title: 57_3_72_Tolvaptan_0.1


title: 51_3_24_Tolvaptan_0.1


title: 11_1_24_Tolvaptan_20


title: 10_1_24_Tolvaptan_1


title: 15_1_72_Tolvaptan_0.1


title: 58_3_72_Tolvaptan_1


title: 8_1_24_Tolvaptan_0.01


title: 50_3_24_Tolvaptan_0.01


title: 9_1_24_Tolvaptan_0.1


title: 55_3_72_Vehicle_0

value: Vehicle

value: 0 uM


title: 56_3_72_Tolvaptan_0.01


title: 31_2_24_Tolvaptan_1


title: 23_2_4_Tolvaptan_0.01


title: 7_1_24_Vehicle_0


title: 36_2_72_Tolvaptan_0.1


title: 35_2_72_Tolvaptan_0.01


title: 14_1_72_Tolvaptan_0.01


title: 24_2_4_Tolvaptan_0.1


title: 44_3_4_Tolvaptan_0.01


title: 28_2_24_Vehicle_0


title: 30_2_24_Tolvaptan_0.1


title: 3_1_4_Tolvaptan_0.1


title: 43_3_4_Vehicle_0


title: 45_3_4_Tolvaptan_0.1


title: 1_1_4_Vehicle_0


title: 13_1_72_Vehicle_0


title: 34_2_72_Vehicle_0


title: 2_1_4_Tolvaptan_0.01


title: 29_2_24_Tolvaptan_0.01


title: dnTGFbRII DX5- NK2

city: Hefei

first: Zhe-Xiong

last: Lian

state: Anhui

address: Huangshan Road 443, Western Campus of USTC

department: School of Life Sciences and Institution of Immunology

institute: University of Science and Technology of China

description: TG DX5- 2

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

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US).

data_processing: Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. Then raw data were RMA-normalized by Expression Console.

organism: Mus

source_name: dnTGFbRII mice liver

label_protocol: The fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the   Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin. 5.5 μg of single-  stranded cDNA is required for fragmentation and labeling.

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

treatment_protocol: WT and dnTGFbRII mice liver DX5- NK cells were sorted for RNA extraction and hybridization on Affymetrix microarrays.

tag: strain

value: dnTGFbRII

value: liver

value: DX5- NK cell

tag: gender

value: female

tag: old

value: 6-8 week


title: Atf7KO_IVF_Rep3

city: Tsukuba

first: Yang

last: LIU

state: Ibaraki.

address: 3-1-1 Koyadai, Tsukuba, Ibaraki

country: Japan

institute: Riken

description: Gene expression data from liver of 4-weeks old mice

hyb_protocol: Fragmented and labelled cDNA was hybridized to GeneChip Mouse Gene 1.0 ST arrays (Affymetrix)

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000 TG

data_processing: The raw (CEL) data were normalized using the RMA method in the R/ Bioconductor package affy, and the comparisons of gene expression were implemented using the linear models for microarray data (Limma) package

organism: Mus musculus

source_name: Mouse liver

label_protocol: Biotinylated cRNA were prepared by using the WT terminal labeling kit (Ambion) according the manufacturer’s manual.

growth_protocol: Wild-type (WT) and Atf7 mutant mice were produced by IVF or natural mating and maintained in the specific-pathogen-free(SPF), temperature-control mouse facility.

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen) based on the manufacturer’s protocol.

treatment_protocol: fresh liver samles were dissected from 4-week-old male mice derived from natural mating or IVF

value: Atf7 mutant


title: WT_IVF_Rep2

value: wild type


title: Atf7KO_IVF_Rep2


title: Atf7KO_IVF_Rep1


title: 49_3_24_Vehicle_0


title: Growing Bj cells transfected with sip21, biological repeat 1

description: Expression data of growing human fibroblasts (BJ cells) after p21 knockdown

source_name: Human primary fibroblasts BJs after transfection with sip21

value: human skin fibroblasts

value: BJ cell line

value: primary


title: Atf7KO_NaturalMating_Rep2


title: WT_IVF_Rep3


title: 22_2_4_Vehicle_0

value: 4 hr

value: primary hepatocytes


title: Scrambled siRNA control biol rep 3B

city: Dortmund

first: Rosemarie

last: Marchan

address: Ardeystrasse 67

department: Systems Toxicology

country: Germany

institute: Ifado

description: Gene expression data from MCF7 cells transfected with Stealth RNA1 scrambled siRNA (med GC)

hyb_protocol: Following fragmentation, 12.5 ug of cRNA was then hybridized to Affymetrix Human Genome U133 plus 2.0 arrays according to the manufacturer’s instructions. The chips were then placed in a GeneChip Hybridization Oven 645 set at 45°C for 16 hours at 60 rpm,stained and washed using the Affymetrix Hybridization, Wash, and Stain Kit on a GeneChip Fluidics Station 450

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

data_processing: For the normalization of the entire set of 16 Affymetrix gene expression arrays, the extrapolation strategy (RMA+) algorithm (Chang, K.-M., Harbron, C., and South, M. (2016): RefPlus: A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods. R package version 1.44.0). was used that applies background correction, log2 transformation, quantile normalization, and a linear model fit to the normalized data in order to obtain a value for each probe set (PS) on each array. As reference, the normalization parameters obtained in earlier analyses were used.

label: Biotin

source_name: RNA from MCF7 cells transfected with scrambled siRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA using the Affymetrix GeneChip IVT Express Kit. A biotinylated nucleotide analog was incorporated during synthesis of amplified RNA (aRNA).used to produce first-strand cDNA u, followed by the complementary second strand cDNA synthesis and in vitro transcription of the double-stranded cDNA molecule, using the Affymetrix GeneChip IVT Express Kit. A biotinylated nucleotide analog was incorporated during synthesis of amplified RNA (aRNA), which was subsequently purified using magnetic beads.

growth_protocol: Cells were maintained in a humidified incubator at 37°C with 5% CO2.

extract_protocol: Total RNA was isolated using the RNeasy Mini extraction kit (Qiagen). RNA concentration was measured using a NanoDrop N-1000 spectrophotometer and RNA integrity assessed using an automated gel electrophoresis system (Experion, Bio-Rad). The RNA was only further used if the RNA quality indicator (RQI) value was higher than 8.

treatment_protocol: Cells were transfected with 20 nM scrambled or EDI3 siRNA using Invitrogen's reverse transfection protocol. After three days, cells were harvested for RNA collection.

tag: cell line

value: breast cancer cell line


title: Edi3 SiRNA_Biol Rep 2B

description: Gene expression data from MCF7 cells transfected with EDI3 Stealth RNAi 1299001-HSS125510

source_name: RNA from MCF7 cells with EDI3 siRNA


title: Scrambled siRNA control biol rep 3C


title: Atf7KO_NaturalMating_Rep3


title: Atf7KO_NaturalMating_Rep1


title: TC03E_93

city: Bologna

first: Daniel

last: Remondini

address: Viale Berti Pichat 6/2

department: Physics and Astronomy - DIFA

country: Italy

institute: Bologna University

description:
Direct labeled file unavailable, thus no merging occurred.
Reverse labeled file (ch1=cy3, ch2(reference)=cy5): E_03_S_E_N.txt

hyb_protocol: Comparative oligonucleotide arrays consisting of more than 19 000 probes were synthesised and utilised as described in Haase et al. Mol. Med. (Tokio), 2007, 13:362. A human universal reference RNA (Stratagene) was used in one channel

scan_protocol: Scanning was performed using a Perkin Elmer Scanarray 4000XL scanner (Buckinghamshire, UK) for both Cy3 and Cy5. Image analysis and data extraction was performed using Bluefuse V3.2 (Bluegnome Ltd, Cambridge, UK).

data_processing: Image analysis and data extraction was performed using Bluefuse V3.2 (Bluegnome Ltd, Cambridge, UK). LOESS fit of Ch1 vs Ch2 for each sample,then merging of direct (D) and swap (S) channels when both were available. Merged data samples were LOESS fitted vs median of first 20 samples (Age<80)

source_name: Human Peripheral Blood T cell

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA. RNAs were isolated by using Rneasy Mini Kit (QIAGEN).

extract_protocol: Peripheral blood mononuclear cells were obtained from 20 ml whole blood by Ficoll gradient separation. CD3+ T lymphocytes were separated by negative magnetic cell sorting (MACS, Miltenyi Biotec) using Pan T-cell Kit II (Miltenyi Biotec) microbeads. Purity and viability of samples were determined by flow cytometry, labelling T-cells respectively with mAb CD3-FITC and propidium iodide. Purity and viability were >95% in all cases. The resulting purified cell population was resuspended in TRIzol Reagent (Invitrogen, Paisley, UK) and stored at -80°C before RNA extraction.

value: male

value: Human Peripheral Blood T cell

tag: age (y)

source_name: Human Universal Reference

value: human universal reference RNA


title: PE05E_94

description:
Direct labeled file (ch1=cy5, ch2(reference)=cy3): E_05_D_E_N.txt
Reverse labeled file (ch1=cy3, ch2(reference)=cy5): E_05_S_E_N.txt


title: Scrambled siRNA control biol rep 2C


title: RM04E_92

description:
Direct labeled file (ch1=cy5, ch2(reference)=cy3): E_04_D_E_N.txt
Reverse labeled file (ch1=cy3, ch2(reference)=cy5): E_04_S_E_N.txt


title: Scrambled siRNA control biol rep 2A


title: Edi3 SiRNA_Biol Rep 3B


title: dnTGFbRII DX5- NK1

description: TG DX5- 1

growth_protocol: WT and dnTGFbRII mice liver DX5- NK cells were sorted


title: WT_IVF_Rep1


title: RG02D_79

description:
Direct labeled file unavailable, thus no merging occurred.
Reverse labeled file (ch1=cy3, ch2(reference)=cy5): D_02_S_E_N.txt


title: MA02E_97

description:
Direct labeled file (ch1=cy5, ch2(reference)=cy3): E_02_D_E_N.txt
Reverse labeled file (ch1=cy3, ch2(reference)=cy5): E_02_S_E_N.txt


title: PA01E_96

description:
Direct labeled file unavailable, thus no merging occurred.
Reverse labeled file (ch1=cy3, ch2(reference)=cy5): E_01_S_E_N.txt


title: Edi3 SiRNA_Biol Rep 3A


title: WT DX5- NK1

description: WT DX5- 1

source_name: C57BL/6 mice liver

value: WT


title: Edi3 SiRNA_Biol Rep 3C


title: Scrambled siRNA control biol rep 3A


title: Edi3 SiRNA_Biol Rep 2A


title: Edi3 SiRNA_Biol Rep 2C


title: Scrambled siRNA control biol rep 1B


title: Scrambled siRNA control biol rep 1C


title: Edi3 SiRNA_Biol Rep 1C


title: SA05D_78

description:
Direct labeled file (ch1=cy5, ch2(reference)=cy3): D_05_D_E_N.txt
Reverse labeled file (ch1=cy3, ch2(reference)=cy5): D_05_S_E_N.txt


title: Edi3 SiRNA_Biol Rep 1B


title: Edi3 SiRNA_Biol Rep 1A


title: GPAM oligo 2 siRNA biol rep 4

description: Gene expression data from MCF7 cells transfected with GPAM Stealth RNAi 1299001-HSS126650

data_processing: For the normalization of the entire set of 16 Affymetrix gene expression arrays, the extrapolation strategy (RMA+) algorithm (Chang, K.-M., Harbron, C., and South, M. (2016): RefPlus: A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods. R package version 1.44.0) was used that applies background correction, log2 transformation, quantile normalization, and a linear model fit to the normalized data in order to obtain a value for each probe set (PS) on each array. As reference, the normalization parameters obtained in earlier analyses were used.

source_name: RNA from MCF7 cells with GPAM siRNA oligo 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA using the Affymetrix GeneChip IVT Express Kit. A biotinylated nucleotide analog was incorporated during synthesis of amplified RNA (aRNA).used to produce first-strand cDNA, followed by the complementary second strand cDNA synthesis and in vitro transcription of the double-stranded cDNA molecule, using the Affymetrix GeneChip IVT Express Kit. A biotinylated nucleotide analog was incorporated during synthesis of amplified RNA (aRNA), which was subsequently purified using magnetic beads.

treatment_protocol: Cells were transfected with 20 nM scrambled or GPAM siRNA using Invitrogen's reverse transfection protocol. After three days, cells were harvested for RNA collection.


title: CF01C_61

description:
Direct labeled file unavailable, thus no merging occurred.
Reverse labeled file (ch1=cy3, ch2(reference)=cy5): C_01_S_E_N.txt


title: NM04C_56

description:
Direct labeled file (ch1=cy5, ch2(reference)=cy3): C_04_D_E_N.txt
Reverse labeled file (ch1=cy3, ch2(reference)=cy5): C_04_S_E_N.txt


title: FM05C_62

description:
Direct labeled file (ch1=cy5, ch2(reference)=cy3): C_05_D_E_N.txt
Reverse labeled file (ch1=cy3, ch2(reference)=cy5): C_05_S_E_N.txt


title: GP03C_57

description:
Direct labeled file (ch1=cy5, ch2(reference)=cy3): C_03_D_E_N.txt
Reverse labeled file (ch1=cy3, ch2(reference)=cy5): C_03_S_E_N.txt


title: BA04D_70

description:
Direct labeled file (ch1=cy5, ch2(reference)=cy3): D_04_D_E_N.txt
Reverse labeled file (ch1=cy3, ch2(reference)=cy5): D_04_S_E_N.txt


title: Scrambled siRNA control biol rep 3


title: GPAM oligo 1 siRNA biol rep 4

description: Gene expression data from MCF7 cells transfected with GPAM Stealth RNAi 1299001-HSS126649

source_name: RNA from MCF7 cells with GPAM siRNA oligo 1


title: DF01D_71

description:
Direct labeled file (ch1=cy5, ch2(reference)=cy3): D_01_D_E_N.txt
Reverse labeled file (ch1=cy3, ch2(reference)=cy5): D_01_S_E_N.txt


title: WT DX5- NK2

description: WT DX5- 2


title: GPAM oligo 1 siRNA biol rep 2


title: Full media control biological rep 3

description: Gene expression data from RNA isolated from MCF7 cells

source_name: RNA from untransfected MCF7 cells


title: Scrambled siRNA control biol rep 4

description: Gene expression data from MCF7 cells transfected with Stealth RNA1 scrambled siRNA (med GC)


title: GPAM oligo 2 siRNA biol rep 3


title: Full media control biological rep 4


title: SL02C_55

description:
Direct labeled file (ch1=cy5, ch2(reference)=cy3): C_02_D_E_N.txt
Reverse labeled file (ch1=cy3, ch2(reference)=cy5): C_02_S_E_N.txt


title: GC04B_44

description:
Direct labeled file (ch1=cy5, ch2(reference)=cy3): B_04_D_E_N.txt
Reverse labeled file (ch1=cy3, ch2(reference)=cy5): B_04_S_E_N.txt


title: ET02B_46

description:
Direct labeled file (ch1=cy5, ch2(reference)=cy3): B_02_D_E_N.txt
Reverse labeled file (ch1=cy3, ch2(reference)=cy5): B_02_S_E_N.txt


title: GPAM oligo 2 siRNA biol rep 2


title: Scrambled siRNA control biol rep 2


title: GPAM oligo 1 siRNA biol rep 3


title: DT01B_43

description:
Direct labeled file (ch1=cy5, ch2(reference)=cy3): B_01_D_E_N.txt
Reverse labeled file (ch1=cy3, ch2(reference)=cy5): B_01_S_E_N.txt


title: RP03B_44

description:
Direct labeled file (ch1=cy5, ch2(reference)=cy3): B_03_D_E_N.txt
Reverse labeled file (ch1=cy3, ch2(reference)=cy5): B_03_S_E_N.txt


title: GPAM oligo 2 siRNA biol rep 1


title: dog uterus with pyometra - biological rep4

city: Poznań

first: Marcin

last: Ruciński

state: Wielkopolska

address: Święcickiego 6

department: Histology and Embryology

country: Poland

institute: Poznań University of Medical Sciences

description: Gene expression data from mongrel dog uterus with pyometra

hyb_protocol: Biotin-labeled fragments of cDNA (5.5 μg) were hybridized to the Affymetrix® Canine Gene 1.1 ST Array Strip (48°C/20 h), washed and stained using the Affymetrix GeneAtlas Fluidics Station according to the manufacturer technical protocol

scan_protocol: The array strips were scanned employing Imaging Station of the GeneAtlas System.

data_processing: Obtained cel files were submitted to bioconductor and R programing lenguage. Each CEL file was merged with a description file.  In order to correct background, normalize, and summarize results, we used the Robust Multiarray Averaging (RMA) algorithm.

organism: Canis lupus familiaris

source_name: mongrel dog uterus (middle of the left horn)

label_protocol: Biotin labeling and fragmentation were performed by Affymetrix GeneChip® WT Terminal Labeling and Hybridization (Affymetrix).

growth_protocol: Pyometra was identified by a fluid-filled uterus and positive bacterial cultures from the uterine content. All animals included in the research were in diestrus, defined using morphological criteria as the examination of vaginal smear and serum progesterone level.

extract_protocol: Total RNA was extracted from samples using TRI Reagent (Sigma, St Louis, MO, USA) and RNeasy MinElute cleanup Kit (Qiagen, Hilden, Germany). Subsequently total RNA (100 ng) from each pooled sample was subjected to two round, sense cDNA amplification (Ambion® WT Expression Kit).

treatment_protocol: mongrel bitches used in this study have undergone a routine ovariohysterectomy in diestrus.

value: uterus

tag: diagnosis

value: Pyometra infection


title: RB05B_43

description:
Direct labeled file (ch1=cy5, ch2(reference)=cy3): B_05_D_E_N.txt
Reverse labeled file (ch1=cy3, ch2(reference)=cy5): B_05_S_E_N.txt


title: TM04A_34

description:
Direct labeled file (ch1=cy5, ch2(reference)=cy3): A_04_D_E_N.txt
Reverse labeled file (ch1=cy3, ch2(reference)=cy5): A_04_S_E_N.txt


title: Full media control biological rep 2


title: GPAM oligo 1 siRNA biol rep 1


title: dog uterus with pyometra - biological rep3


title: DR05A_33

description:
Direct labeled file (ch1=cy5, ch2(reference)=cy3): A_05_D_E_N.txt
Reverse labeled file (ch1=cy3, ch2(reference)=cy5): A_05_S_E_N.txt


title: MM02A_29

description:
Direct labeled file unavailable, thus no merging occurred.
Reverse labeled file (ch1=cy3, ch2(reference)=cy5): A_02_S_E_N.txt


title: Scrambled siRNA control biol rep 1


title: control dog uterus - biological rep3

description: Gene expression data from mongrel dog uterus

value: healthy


title: NR01A_27

description:
Direct labeled file (ch1=cy5, ch2(reference)=cy3): A_01_D_E_N.txt
Reverse labeled file (ch1=cy3, ch2(reference)=cy5): A_01_S_E_N.txt


title: dog uterus with pyometra - biological rep2


title: control dog uterus - biological rep4


title: dog uterus with pyometra - biological rep1


title: MM03A_25

description:
Direct labeled file unavailable, thus no merging occurred.
Reverse labeled file (ch1=cy3, ch2(reference)=cy5): A_03_S_E_N.txt


title: control dog uterus - biological rep2


title: Rockefeller blood fed replicate 2

status: Public on Jun 09 2017

city: Baltimore

first: George

last: Dimopoulos

state: MD

address: 615 N Wolfe St.

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

hyb_protocol: All samples were co-hybridized to the same reference sample, which was formed by pooling 200ng of RNA from 54 midgut samples collected for this experiment. The 18 samples included above were among the 54 samples, which included additional strains not analyzed here. The additonal samples were included in the reference to allow for comparisons across future experiments including additional samples from the total group of 54. All six samples from the same biological replicate were hybridized to six arrays on the same slide, and a different slide was used for each replicate, resulting in a complete block design. Hybridization was performed according to Agilent’s Two-Color Microarray-Based Gene Expression Analysis Protocol.

scan_protocol: Feature extraction was performed using an Agilent Scanner and Agilent Feature Extraction Software

data_processing: Data were analyzed using limma in R. Spots with at least one flag were excluded from analysis (flagged cells are empty in spreadsheet). Background correction was performed using the normexp method. Signals were normalized first within array using loess within-array normalization and then between arrays using quantile normalization.

organism: Aedes aegypti

source_name: Aedes aegypti midgut tissue

label_protocol: Labeling was performed using the Two-Color Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the Two-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technologies). 200ng of RNA from each sample was used for the labeling reaction and labeled cRNA was purified using RNeasy columns (Qiagen).

extract_protocol: Total RNA was extracted using Trizol reagent according to the manufacturer's instructions.

treatment_protocol: Rockefeller and Singapore Aedes aegypti mosquitoes were reared in parallel and provided 3% sucrose + antibiotics [penicillin (100U/ml), streptomycin (100ug/ml), and gentamycin (75ug/ml)] upon eclosion. Five to seven days post eclosion, females from each strain were either (1) maintained on 3% sucrose, (2) given a sterile blood meal or (3) given a blood meal containing a bacterial cocktail. Approximately 12 hours after blood feeding, 15 midguts from all six strain/treatment combinations were dissected in sterile 1X PBS and transferred immediately to TRIzol reagent.

value: Rockefeller

value: Blood fed with sterile blood

source_name: Reference pool

tag: sample type

value: Pool of all midgut samples from experiment (200ng/sample)


title: control dog uterus - biological rep1


title: Singapore sucrose fed replicate 3

value: Singapore

value: Sucrose fed


title: Full media control biological rep 1


title: Rockefeller blood fed replicate 3


title: Singapore blood fed replicate 3


title: Singapore sucrose fed replicate 2


title: Singapore sucrose fed replicate 1


title: Rockefeller blood + bacteria fed replicate 3

value: Blood fed with blood + bacteria


title: Rockefeller sucrose fed replicate 3


title: Rockefeller sucrose fed replicate 1


title: Rockefeller blood + bacteria fed replicate 2


title: Rockefeller sucrose fed replicate 2


title: Singapore blood fed replicate 2


title: Rockefeller blood + bacteria fed replicate 1


title: Singapore blood + bacteria fed replicate 1


title: Rockefeller blood fed replicate 1


title: Singapore blood + bacteria fed replicate 2


title: Singapore blood fed replicate 1


title: AP03D_73

description:
Direct labeled file (ch1=cy5, ch2(reference)=cy3): D_03_D_E_N.txt
Reverse labeled file (ch1=cy3, ch2(reference)=cy5): D_03_S_E_N.txt


title: MYD88_1

status: Public on Jun 08 2017

city: Bethesda

first: James

middle: Q

last: Wang

address: 9000 Rockville Pike

department: National Cancer Institute, Center for Cancer Research

institute: National Institutes of Health

description: MYD88 biological replicate 1

hyb_protocol: Hybridisation performed at 45 degrees for 16 hours according to Affymetrix protocol.

scan_protocol: Affymetrix protocol.

data_processing: Microarray data were subjected to quality control, normalization and differential expression analysis in limma. Quality control reviewed reconstructed array images, distribution of probe intensities, MA plots, fitting of a probe level model in the oligo package to generate box plots of Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE). One of three independent samples of sorted cells and resulting probe weights were used to derive weights for transcript expression estimates on each array suitable for use with limma in a linear model, comparing gene expression in MYD88L265P cells to each of the other groups.  in each experimental group was excluded on the basis of insufficient quality. The final set of 8 samples was normalised using PLM

source_name: Transduced mouse B cells

label_protocol: Biotin followed by streptavidin-PE

growth_protocol: Transduced B cells were cultured without anti-CD40 for 24hr and EGFP+ cells were sorted using FACSAria I and II (BD) cell sorter and washed twice with cold PBS.

extract_protocol: For microarray analysis, sorted EGFP+ transduced cells were resuspended in TRIzol. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Activated B cells were spin-infected with retroviral supernatants containing 10ug/ml DOTAP. Following transduction, the cells were placed back into media containing mitogen for 36 hr. Cells were then washed three times to remove mitogen, and then cultured for 24hr without mitogen before sorting.

value: Mouse mature splenic B cells

value: Retrovirally transduced with MYD88 L265P


title: MYD88_3

description: MYD88 biological replicate 2


title: IKK_3

description: IKK biological replicate 2

value: Retrovirally transduced with IKK K171E


title: EV_3

description: Empty vector biological replicate 2

value: Retrovirally transduced with empty GFP vector


title: CARD11_3

description: CARD11 biological replicate 2

value: Retrovirally transduced with CARD11 L225LI


title: IKK_1

description: IKK biological replicate 1


title: CARD11_1

description: CARD11 biological replicate 1


title: EV_2

description: Empty vector biological replicate 1


title: Singapore blood + bacteria fed replicate 3


title: ATL-derived cell line ED-250knsp

status: Public on Jun 06 2017

type: genomic

city: Kiyotake

first: Shingo

last: Nakahata

state: Miyazaki

address: 5200 Kihara

institute: University of Miyazaki

description:
Hybridized to 250K_Nsp
ED-250knsp

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
CEL files were processed by CNAG 3.0
Algorithm: DynamicModel 3.0

molecule: genomic DNA

source_name: ATL-derived cell line ED

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations from ATL patients and from cell lines by using the standard phenol/chloroform method. DNA quality and quantity were assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

value: ED

value: ATL-derived cell line


title: ATL-derived cell line KK1-250knsp

description:
Hybridized to 250K_Nsp
KK1-250knsp

source_name: ATL-derived cell line KK1


title: Patient 53_5578_SNP6.0

city: Newcastle upon Tyne

first: Claire

middle: Joanne

last: Schwab

state: Tyne and Wear

address: Level 5, Sir James Spence Institute, Queen Victoria Rd

department: Northern Institute for Cancer Research

country: United Kingdom

institute: Newcastle University

description: Hybridized to SNP6.0

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing: CEL and CHP files were generated using Affymetrix Genotyping Console using HapMap collection as reference.

source_name: Patient 53, Diagnostic sample

growth_protocol: Not applicable

extract_protocol: Genomic DNA was extracted from leukemic blasts obtained from peripheral blood or bone marrow at diagnosis or at relapse or using the Qiagen Dneasy Blood and Tissue kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

tag: disease

value: acute lymphoblastic leukemia

tag: Stage

value: Diagnostic sample

value: Bone Marrow


title: HTLV-1-infected T-cell line MT2-250knsp

description:
Hybridized to 250K_Nsp
MT2-250knsp

source_name: HTLV-1-infected T-cell line MT2

value: HTLV-1-infected T-cell line


title: HTLV-1-infected T-cell line HUT102-250knsp

description:
Hybridized to 250K_Nsp
HUT102-250knsp

source_name: HTLV-1-infected T-cell line HUT102


title: Primary ATL cell sample #15-250knsp

description:
Hybridized to 250K_Nsp
ATL#15-250knsp

source_name: Primary ATL cell sample

value: chronic-type adult T-cell leukemia (ATL)


title: Primary ATL cell sample #3-250knsp

description:
Hybridized to 250K_Nsp
ATL#3-250knsp

value: acute-type adult T-cell leukemia (ATL)


title: HTLV-1-infected T-cell line MT4-250knsp

description:
Hybridized to 250K_Nsp
MT4-250knsp

source_name: HTLV-1-infected T-cell line MT4


title: Primary ATL cell sample #7-250knsp

description:
Hybridized to 250K_Nsp
ATL#7-250knsp


title: Primary ATL cell sample #18-250knsp

description:
Hybridized to 250K_Nsp
ATL#18-250knsp


title: Primary ATL cell sample #1-250knsp

description:
Hybridized to 250K_Nsp
ATL#1-250knsp


title: ATL-derived cell line Su9T-250ksty

description:
Hybridized to 250K_Sty
Su9T-250ksty

source_name: ATL-derived cell line Su9T


title: Patient 61_10172_SNP6.0

description: Hybridized to SNP6.0

source_name: Patient 61, Diagnostic sample

tag: tissue


title: Primary ATL cell sample #16-250knsp

description:
Hybridized to 250K_Nsp
ATL#16-250knsp


title: Primary ATL cell sample #17-250knsp

description:
Hybridized to 250K_Nsp
ATL#17-250knsp


title: Primary ATL cell sample #5-250knsp

description:
Hybridized to 250K_Nsp
ATL#5-250knsp


title: Primary ATL cell sample #2-250knsp

description:
Hybridized to 250K_Nsp
ATL#2-250knsp


title: Patient 79_2570_SNP6.0

description: Hybridized to SNP6.0

source_name: Patient 79, Relapse sample

value: Relapse sample


title: ATL-derived cell line KOB-250knsp

description:
Hybridized to 250K_Nsp
KOB-250knsp

source_name: ATL-derived cell line KOB

value: KOB


title: Primary ATL cell sample #19-250knsp

description:
Hybridized to 250K_Nsp
ATL#19-250knsp


title: 14_ESBL019 Filamented Repl 4

city: Örebro

first: Robert

last: Kruse

address: S grevrosengatan

department: Medical Sciences

country: Sweden

institute: Örebro University

description: ESBL019 Filamented Repl 4

hyb_protocol: Labelled samples were hybridised onto G4813A E. coli gene expression Microarray 8×15K glass slides (Agilent) containing 15 208 E. coli probes.

scan_protocol: Microarrays were scanned with a G2565 CA array laser scanner (Agilent) followed by image analysis and data extraction with Feature Extraction Software version 10.7.3.1 (Agilent).

data_processing: 75th percentile shift normalisation and baseline adjusted

organism: Escherichia coli

source_name: ESBL019 Filamented

label_protocol: The cDNA synthesis was performed by using WT Primer Mix and cDNA Master Mix (Agilent).

growth_protocol: The E. coli isolate ESBL019 was originally isolated from a patient at Örebro University hospital, Sweden and was maintained on tryptic soy agar (TSA) (Becton Dickinson, Le Pont Claix, France). ESBL019 was grown in Luria broth (Difco Laboratories, Detroit, MI, USA) overnight on shake at 200 rpm 37 °C prior to experiments. The bacteria were resuspended in sterile phosphate buffered saline prior to inoculation of CnT-21 cell culture medium (CCM) with or without ceftibuten (480 ng/mL).

extract_protocol: RNA isolation was performed using an RNeasy mini kit (Qiagen Technologies, Hilden, Germany), according to the manufacturer’s protocol. DNA decontamination treatment was performed using Turbo DNase (Qiagen) and the quantity and purity of the purified RNA samples were determined using a spectrophotometer Nanodrop-1000 (Nanodrop Technologies Inc., Wilmington, DE, USA) by measuring the absorbance (A260, 230, 280) and calculating absorbance ratios (A260/A230 and A260/A280). All samples had A260/A230 and A260/A280 ratios above 1.9. The RNA integrity was analysed using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) in conjunction with RNA 6000 Nano LabChip kit (Agilent Technologies) according to the manufacturer’s protocol. RNA integrity number (RIN) values were > 9 for all samples.

treatment_protocol: Four morphologic states of ESBL019 were used during the experiments. A first ESBL019 morphological state was prepared by resuspension of ESBL019 in cell culture medium (CCM) without ceftibuten supplementation prior to its inoculation of primary human bladder epithelial cells (HBEP) (designated; ESBL019 Coliform). A second ESBL019 morphological state was prepared by resuspension in CCM and then used to inoculate HBEP cells with ceftibuten supplementation (480ng/mL) (designated; ESBL019 Transition). This transition from coliform into filamented occurs in the presence of HBEP cells. A third ESBL019 morphological state was prepared by resuspension and pre-incubation for 3 hours in CCM with ceftibuten in a tube, in order to induce complete filamentation of all bacteria. The third pre-filamented ESBL019 fraction was used to inoculate HBEP cells in the presence of ceftibuten to keep the bacteria filamented (designated; ESBL019 Filamented). The CCM of the pre-filamented ESBL019 fraction was replaced with CCM without ceftibuten and the filamented ESBL019 were allowed to revert completely back to its coliform during 1 hour in a tube prior to the inoculation of HBEP cells without ceftibuten (designated; ESBL019 Reverted). Prior to inoculation the bacterial concentrations of all fractions were adjusted in order to inoculate HBEP cells with a multiplicity of infection (MOI) of 10. All inoculated cells were incubated for 4 hours in 5% CO2 at 37oC after which supernatants were collected and centrifuged 5 min at 5000 x g to collect the bacteria.

value: beta-lactamase (ESBL)-producing UPEC (ESBL019)

tag: morphology

value: Filamented


title: 16_ESBL019  Reverted Repl 4

description: ESBL019  Reverted Repl 4

source_name: ESBL019  Reverted

value: Reverted (reverted back from a Filamented shape into a coli shape)


title: 12_ESBL019  Reverted Repl 3

description: ESBL019  Reverted Repl 3


title: Primary ATL cell sample #9-250knsp

description:
Hybridized to 250K_Nsp
ATL#9-250knsp


title: Patient 60_10077_SNP6.0

description: Hybridized to SNP6.0

source_name: Patient 60, Diagnostic sample


title: 11_ESBL019 Transition Repl 3

description: ESBL019 Transition Repl 3

source_name: ESBL019 Transition

value: Transition (from Coli into Filamented)


title: Patient 57_8431_SNP6.0

description: Hybridized to SNP6.0

source_name: Patient 57, Diagnostic sample


title: 13_ESBL019 Coliform Repl 4

description: ESBL019 Coliform Repl 4

source_name: ESBL019 Coliform

value: Coliform


title: 10_ESBL019 Filamented Repl 3

description: ESBL019 Filamented Repl 3


title: 15_ESBL019 Transition Repl 4

description: ESBL019 Transition Repl 4


title: ATL-derived cell line S1T-250ksty

description:
Hybridized to 250K_Sty
S1T-250ksty

source_name: ATL-derived cell line S1T


title: Patient 59_9880_SNP6.0

description: Hybridized to SNP6.0

source_name: Patient 59, Diagnostic sample


title: 8_ESBL019  Reverted Repl 2

description: ESBL019  Reverted Repl 2


title: Patient 47_3393_SNP6.0

description: Hybridized to SNP6.0

source_name: Patient 47, Diagnostic sample


title: 5_ESBL019 Coliform Repl 2

description: ESBL019 Coliform Repl 2


title: 6_ESBL019 Filamented Repl 2

description: ESBL019 Filamented Repl 2


title: 4_ESBL019  Reverted Repl 1

description: ESBL019  Reverted Repl 1


title: 7_ESBL019 Transition Repl 2

description: ESBL019 Transition Repl 2


title: 3_ESBL019 Transition Repl 1

description: ESBL019 Transition Repl 1


title: Primary ATL cell sample #6-250knsp

description:
Hybridized to 250K_Nsp
ATL#6-250knsp


title: 2_ESBL019 Filamented Repl 1

description: ESBL019 Filamented Repl 1


title: 6 non-treatment_6

city: Gifu

first: Akihiro

last: Moriyama

address: 1-1, Yanagido

institute: Gifu University

description: SAMPLE 26

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 min in a reaction volume of 25 μl containing 1x Blocking Agent and 1x Fragmentation Buffer. On completion of the fragmentation reaction, 2x Hybridization Buffer HI-RPM solution was added to the fragmentation mixture containing 0.6 μg of Cy3-labelled cRNA and hybridized for 17 h, at 65C and 10 rpm. After hybridization, microarrays were washed according to Quick Amp Labeling Kit Protocol (Agilent).

scan_protocol: The hybridized microarray slides were washed according to the manufacturer’s instructions and were scanned with an Agilent DNA Microarray Scanner (#G2565CA, Agilent Technologies, CA, USA) at a resolution of 5 μm.

data_processing: These data were normalized by the 25th percentile and quantile methods using Excel.

organism: Saccharomyces cerevisiae

label_protocol: The cDNA was synthesized by Quick Amp Labeling Kit (Agilent) using 0.5 μg total RNA as a template. Cyanine-3 (Cy3) labeled cRNA was prepared from cDNA using the T7 RNA polymerase. Cy3-labeled cRNA was purified by RNeasy Mini Kit (QIAGEN, Hilden, Germany), and checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: The yeast cells after stressed were collected by centrifugation of 15,000 rpm for 1.0 min at 4°C. RNA extraction conformed according to partially modified manufacture protocol of Fast RNA ® Pro Red Kit (MP Biomedicals, CA, USA). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: sample group

value: untreated negative control


title: 1_ESBL019 Coliform Repl 1

description: ESBL019 Coliform Repl 1


title: 6 non-treatment_7

description: SAMPLE 27


title: 6 non-treatment_8

description: SAMPLE 28


title: 6 non-treatment_3

description: SAMPLE 23


title: 6 non-treatment_2

description: SAMPLE 22


title: 6 non-treatment_5

description: SAMPLE 25


title: 6 non-treatment_4

description: SAMPLE 24


title: 6 non-treatment_1

description: SAMPLE 21


title: Primary ATL cell sample #4-250knsp

description:
Hybridized to 250K_Nsp
ATL#4-250knsp


title: 5 UV only_2

description: SAMPLE 18

value: irradiated UV


title: 5 UV only_4

description: SAMPLE 20


title: 5 UV only_3

description: SAMPLE 19


title: ATL-derived cell line SO4-250ksty

description:
Hybridized to 250K_Sty
SO4-250ksty

source_name: ATL-derived cell line SO4


title: 9_ESBL019 Coliform Repl 3

description: ESBL019 Coliform Repl 3


title: 4 non-adTI-Uvx_4

description: SAMPLE 16

source_name: non-adsorbed fraction_8hr_Ti_withoutUV

value: non-adsorbed fraction to TiO2-NOAA without UV


title: 5 UV only_1

description: SAMPLE 17


title: 4 non-adTI-Uvx_1

description: SAMPLE 13


title: 3 adTi- Uvx_3

description: SAMPLE 11

source_name: adsorbed fraction_8hr_Ti_withoutUV

value: adsorbed fraction to TiO2-NOAA without UV


title: Primary ATL cell sample #8-250knsp

description:
Hybridized to 250K_Nsp
ATL#8-250knsp

source_name: Primary ATL cell sample


title: 4 non-adTI-Uvx_2

description: SAMPLE 14


title: 4 non-adTI-Uvx_3

description: SAMPLE 15


title: Primary ATL cell sample #13-250ksty

description:
Hybridized to 250K_Sty
ATL#13-250ksty


title: Primary ATL cell sample #12-250ksty

description:
Hybridized to 250K_Sty
ATL#12-250ksty


title: 3 adTi- Uvx_4

description: SAMPLE 12


title: Primary ATL cell sample #10-250ksty

description:
Hybridized to 250K_Sty
ATL#10-250ksty


title: Patient 64_22339_SNP6.0

description: Hybridized to SNP6.0

source_name: Patient 64, Diagnostic sample

value: acute lymphoblastic leukemia


title: 3 adTi- Uvx_2

description: SAMPLE 10


title: Primary ATL cell sample #11-250ksty

description:
Hybridized to 250K_Sty
ATL#11-250ksty


title: 2 non-adTi-UV_1

description: SAMPLE 5

source_name: non-adsorbed fraction_8hr_Ti_UV

value: non-adsorbed fraction to TiO2-NOAA under UV


title: 2 non-adTi-UV_2

description: SAMPLE 6


title: 2 non-adTi-UV_4

description: SAMPLE 8


title: 3 adTi- Uvx_1

description: SAMPLE 9


title: 1 adTi-UV_4

description: SAMPLE 4

source_name: adsorbed fraction_8hr_Ti_UV

value: adsorbed fraction to TiO2-NOAA under UV


title: 1 adTi-UV_3

description: SAMPLE 3


title: 2 non-adTi-UV_3

description: SAMPLE 7


title: Primary ATL cell sample #14-250ksty

description:
Hybridized to 250K_Sty
ATL#14-250ksty


title: 1 adTi-UV_2

description: SAMPLE 2


title: 1 adTi-UV_1

description: SAMPLE 1


title: Dclk1+ Normal intestinal cells

status: Public on Jun 05 2017

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: Dclk1+ Normal

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: normal small intestines of two Dclk1CreERT2/+ mice

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: Normal epithelia of small intestine were freshly isolated from the small intestines of Dclk1CreERT2/+ mice at the age of 26 weeks. Mouse intestinal tumors were freshly isolated from the small intestines of Dclk1CreERT2/+; ApcMin/+ mice at the age of more than 16 weeks. These tissues were minced and incubated with digestion buffer (DMEM with 10% FCS, penicillin-streptomycin, Invitrogen, Carlsbad, CA, USA), 1 mg/ml collagenase type XI (Sigma-Aldrich, St.Louis, MO, USA) and 0.1 mg/ml DNase I for 15 min at 37°C. After incubation, cells were filtered through a 40-µm mesh, shaken vigorously and incubated with PBS containing 2 mM EDTA for 20min at 4°C. To obtain Dclk1+ tumor cells, GFP-expressing cells were sorted by FACSAria II (BD Biosciences, San Jose, CA, USA). RNA was extracted from the sorted cells using the RNeasy Micro kit or RNeasy Mini kit according to the manufacturer’s instructions (Qiagen, Hilden, Germany).

value: male

tag: genotype/variation

tag: histology

value: normal small intestines


title: Dclk1- Normal intestinal cells

description: Dclk1- Normal

source_name: normal small intestine of a Dclk1CreERT2/+ mouse

value: normal small intestine


title: Dclk1- Tumor cells

description: Dclk1- Tumor

source_name: intestinal tumors of a Dclk1CreERT2/+; ApcMin/+ mouse

value: Dclk1CreERT2/+; ApcMin/+

value: intestinal tumor


title: pmp0 (0μg/ml PMP)

city: Yangzhou

first: Wenwen

state: Jiangsu

address: 11 Huaihai Road

institute: Clinical Medical College and 2School of Medicine, Yangzhou University, Yangzhou, P.R. China

description: RA-FLSs treated with 0μg/ml PMPs

hyb_protocol: Following fragmentation, aRNA were hybridized for 16 hr at 45℃ on GeneChip Hybridization Oven  645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing: The data were analyzed with rma using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Third generation RA-FLSs

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from total RNA.

growth_protocol: RA-FLS were maintained in DMEM containing 15% FBS, 100 U/ml penicillin and 100 μg/ml streptomycin in an incubator at 37℃ with 5% CO2.

treatment_protocol: RA-FLS were treated with (50μg/ml) or without PMPs (0μg/ml) for 48 h.

value: female

value: synovial tissue


title: Dclk1+ Tumor cells

description: Dclk1+ Tumor

source_name: intestinal tumors of seven Dclk1CreERT2/+; ApcMin/+ mice


title: pmp50 (50μg/ml PMPs)

description: RA-FLSs treated with 50μg/ml PMPs


title: Intermediate spinal cord, Animal 2

status: Public on Jun 03 2017

city: New York

first: Jarret

last: Weinrich

state: New York

address: 1233 York Ave 16G

institute: Weill Cornell Graduate School of Medical Sciences

hyb_protocol: 10 ug of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by Affymetrix GeneChip Command Console as CEL files.

source_name: Intermediate spinal cord

label_protocol: 500 ng total RNA converted to cRNA using Affymetrix GeneChip®3' IVT Kit and in vitro transcription resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).

extract_protocol: RNA extraction plus kit was used to isolate RNA, and cDNA was made with invitrogen superscriptase.

value: spinal cord

tag: region

value: Intermediate

tag: age

tag: genotype


title: Ventral spinal cord, Animal 2

source_name: Ventral spinal cord

value: Ventral


title: Intermediate spinal cord, Animal 3


title: Dorsal spinal cord, Animal 1

source_name: Dorsal spinal cord

value: Dorsal


title: Intermediate spinal cord, Animal 1


title: Ventral spinal cord, Animal 1


title: mCSF treated cells-replicate 5

city: Frederick

first: Dennis

last: Klinman

state: Maryland

address: 1050 Boyles St

department: Cancer and Inflammation Program

description: biological replicate donor 5

hyb_protocol: Cy dyed aRNA of control and target samples were combined, denaturated by heating for 2 min at 98o C, and mixed with 18 ul hybridization solution at 42̊C (Ambion, Austin, TX, USA).  Microarrays were overlaid with this solution and hybridized for 18 h at 42̊C using an actively mixing MAUI hybridization system (BioMicro Systems, Salt Lake City, UT) then washed sequentially.

scan_protocol: Arrays were scanned on an Axon genepix 4000B scanner and images were quantified using GenePix software v 5.1

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. GenePix ans BRB arraytools software was used.

source_name: FACS sorted human DR+ monocytes

label_protocol: 200-500 ng of total RNA was amplified through the Amino Allyl MessageAmp II aRNA Kit (Ambion, Life Technologies).  Total RNA is reverse transcribed into cDNA followed by in vitro transcription with T7 RNA polymerase into antisense amplified RNA (aRNA). Aminoallyl modified UTPs are incorporated during in vitro transcription for Cy-dye coupling.  aRNA from mMDSC samples were labeled with Cy5 monoreactive dye (Amersham Biosciences, Piscataway, NJ) .  A reference human sample (Stratagene) was processed in parallel and labeled with Cy3.  For the coupling reaction up to 10ul of aRNA (2000-4000ng) was added to 0.1M sodium bicarbonate buffer (pH 8.7) to a total volume of 20 ul and then added to either Cy3 or Cy5 dissolved in 20ul DMSO for 120 minutes in the dark.  To quench unreacted Cy-dye, 18ul of 4M hydroxylamine was added for 15 minuted in the dark before cleaning up using the Rneasy MinElute kit (Qiagen).

growth_protocol: PBMC were separated from fresh buffy coats from healthy volunteers and separated using density gradient and ficol reagent.  Cells were stained and FACS sorted to isolate monocytes that were CD14+ and HLA-DR+

extract_protocol: total RNA was extracted using Qiagen's Rneasy minikit, following the instuction booklet

treatment_protocol: FACS sorted monocytes are stimuated with 1ug/ml pam3 or 500ng/ml m-csf for 4 hours then cells are collected and stored in RNA later for RNA extraction

tag: cell type

value: DR+ monocytes

tag: stimulation

value: 500ng/ml m-csf for 4 hours

source_name: total RNA from Stratagene universal reference RNA

tag: source

value: universal RNA


title: pam3-treated cells replicate -4

description: biological replicate donor 4

value: 1ug/ml pam3 for 4 hours


title: pam3-treated cells replicate -5

description: biological replicate donor 5


title: mCSF treated cells-replicate 6

description: biological replicate donor 6


title: pam3-treated cells replicate -3

description: biological replicate donor 3


title: mCSF treated cells-replicate 4

description: biological replicate donor 4


title: pam3-treated cells replicate -1

description: biological replicate donor 1


title: pam3-treated cells replicate -6

description: biological replicate donor 6


title: Ventral spinal cord, Animal 3


title: Normoxia rat pup 13-13, technical replicate 2

city: Rotterdam

first: Jennifer

last: Collins

address: Wytemaweg 80

department: Pediatric Surgery

country: Netherlands

institute: Erasmus University Medical Center

description: Gene expression data from passage 2 primary CD146+ lung mesenchymal stromal cells, cultured at 5% O2 for 10-12 days

hyb_protocol: Labeled samples were hybridized to Rat 2.1 ST Arrays overnight in Affymetrix hybridization oven 640 at 45°C and  60 rpm, for 17 hours ± 1 hour. The arrays then were washed and stained in Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned with Affymetrix Scanner 3000 to acquire images and raw data.

data_processing: Significant up- and down-regulated genes were identified by significance analysis of microarrays (SAM), followed by gene-set enrichment analysis (GSEA software V2.1.0, Broad Institute). A default false discovery rate (FDR) of 0.25 identified differential gene set enrichment. Pathway interactions were visualized using Cytoscape software V3.1.129, using the following cut-offs: p-value 0.05, Q-value 0.25, Jaccard and overlap combined similarity 0.25.

organism: Rattus norvegicus

source_name: Rat lung CD146+ mesenchymal stromal cells, isolated at postnatal day 12 from control (normoxia) rat pups

label_protocol: For each Sample 300 ng of total RNA was labeled with Whole Transcript (WT) Sense Target Labeling kit following protocol from Affymetrix

growth_protocol: Cells were grown at 5% O2, 5% CO2 on tissue culture treated plastic until 80-90% confluency, at which point the cells were passaged or frozen. All samples were frozen once after initial expansion at P0, thawed and expanded for CD146+ cell selection at P1, and CD146+ cells were expanded further after selection (P2) for RNA isolation.

extract_protocol: RNA was isolated from CD146+ L-MSCs (n=3 per group) using a Qiashredder (79656, Qiagen, Hilden, Germany) and RNeasy Plus Mini kit (74136, Qiagen), according to manufacturer’s instructions. RNA quality was ensured using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Rat pups received either 10-day exposure to 95% O2 (hyperoxia) directly after birth, or room air. All samples were treated equally from primary cell isolation onward.

tag: strain

value: Sprague-Dawley rat

value: postnatal day 12.5

value: Lung tissue

value: CD146+ lung mesenchymal stromal cells

tag: treatment group

value: 10-day exposure to room air


title: Normoxia rat pup 13-13, technical replicate 1


title: Normoxia rat pup 13-11, technical replicate 3


title: Dorsal spinal cord, Animal 3


title: Dorsal spinal cord, Animal 2


title: mCSF treated cells-replicate 3

description: biological replicate donor 3


title: Normoxia rat pup 13-13, technical replicate 3


title: mCSF treated cells-replicate 2

description: biological replicate donor 2


title: Normoxia rat pup 13-11, technical replicate 1


title: Normoxia rat pup 13-11, technical replicate 2


title: Normoxia rat pup 13-10, technical replicate 1


title: Normoxia rat pup 13-10, technical replicate 2


title: untreated cells-replicate 4

description: biological replicate donor 4

value: untreated


title: Hyperoxia rat pup 13-3, technical replicate 3

source_name: Rat lung CD146+ mesenchymal stromal cells, isolated at postnatal day 12 from hyperoxia exposed rat pups

value: 10-day exposure to 95% O2 (hyperoxia)


title: Hyperoxia rat pup 13-3, technical replicate 1


title: untreated cells-replicate 6

description: biological replicate donor 6


title: Hyperoxia rat pup 13-3, technical replicate 2


title: untreated cells-replicate 5

description: biological replicate donor 5


title: Normoxia rat pup 13-10, technical replicate 3


title: Hyperoxia rat pup 13-2, technical replicate 3


title: untreated cells-replicate 1

description: biological replicate donor 1


title: untreated cells-replicate 3

description: biological replicate donor 3


title: Hyperoxia rat pup 13-2, technical replicate 1


title: untreated cells-replicate 2

description: biological replicate donor 2


title: Hyperoxia rat pup 13-1, technical replicate 1


title: Hyperoxia rat pup 13-1, technical replicate 3


title: mCSF treated cells-replicate 1

description: biological replicate donor 1


title: Hyperoxia rat pup 13-1, technical replicate 2


title: Hyperoxia rat pup 13-2, technical replicate 2


title: Mef2c shRNA rep3

status: Public on Jun 02 2017

city: La Jolla

first: Andrew

middle: P.

last: Hodges

state: California

address: 10901 N Torrey Pines Rd

department: Bioinformatics Shared Resource

institute: SBP

description: Gene expression from Mef2C shRNA expressing cells

hyb_protocol: GeneChip WT Terminal Labeling and Control Kit (Affymetrix) were used for amplifying and labeling 150 ng of total

scan_protocol: Samples were scanned with the Affymetrix GeneChip Scanner 7G

data_processing: Statistical Analysis of normalized data was made at the Bioinformatics & Data Management core at SBP using Partek Genomics Suite software. Analysis of gene expression was performed with Partek® Genomics Suite® software (version 6.6; 2016). RMA background correction, quantile normalization, log2 transformation and median polished probeset summarization was performed to generate intensity values. After the initial preprocessing, one-way ANOVA using Method of Elements and Fisher’s Least Significant Difference (LSD) (Tamhane, 2000) was run on the data to identify significantly-changing microarray features and corresponding genes for either MEF2C or Nup210 versus the scramble control.  Filters were applied for gene prioritization and Venn diagram overlaps (e.g. significant p-value, p<0.05, and/or absolute fold-change, abs(FC) > 1.25 ).

source_name: Mef2c shRNA, differentiated C2C12 myotubes

label_protocol: Total RNA was purifiedwith Trizol following the manufacturer specifications. After the addition of ethanol 70% the RNA was loaded on an RNeasy purification column and further purified following the kit instructions. RNA quality and concentration were determined using Pico chips on a Bioanalyzer 2100 (Agilent Technologies).

growth_protocol: Proliferating C2C12myoblasts weremaintained in DMEM + 20% FBS. Differentiation was induced by shifting to DMEM + 2% horse serum.

extract_protocol: C2C12 cells were infected with Control, Nup210 or Mef2C specific shRNA36h after initiation of differentiation with 2x108 TU. 48 hours post-infection myotubes were collected for RNA isolation.

value: C2C12 cells

value: Mef2C depleted


title: Mef2c shRNA rep2


title: Control scramble shRNA rep1

description: Gene expression from scramble shRNA expressing cells

source_name: Control scramble shRNA, differentiated C2C12 myotubes

value: control


title: Control scramble shRNA rep2


title: Control scramble shRNA rep5


title: Mef2c shRNA rep4


title: Control scramble shRNA rep3


title: Control scramble shRNA rep4


title: Mef2c shRNA rep5


title: Nup210 shRNA rep5

description: Gene expression from Nup210 shRNA expressing cells

source_name: Nup210 shRNA, differentiated C2C12 myotubes

value: Nup210 depleted


title: Mef2c shRNA rep6


title: Mef2c shRNA rep1


title: Nup210 shRNA rep4


title: Nup210 shRNA rep2


title: High oxygen supply_24h

city: Nanjing

first: Huanqing

last: Niu

address: No.30, Puzhu South Road

institute: Nanjing Tech University

description: Gene expression in 24h-grown Arthrobacter sp. CGMCC 3584 under high oxygen supply

hyb_protocol: each Slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US). After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

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

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

organism: Arthrobacter sp. CGMCC 3584

source_name: High oxygen supply, 24h

label_protocol: Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany). Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: The seed culture medium contained in grams per liter: glucose 10, peptone 10, beef extract 10, and NaCl 3. The fermentation medium contained in grams per liter: glucose 50, urea 8, K2HPO4 18, KH2PO4 5, MgSO4 0.1, biotin 0.01, hypoxanthine 8, NaF 0.4 and CoCl2 0.005. The initial pH was adjusted to 7.0 by NaOH and the medium was autoclaved for 20 min at 115 ◦C. The seed cultures were incubated at 30 ◦C and 300 rpm for 18 h. Then the seed medium was transferred into a 5-L fermenter (NBS Bioflo-110) containing 3L of fermentation medium at an inoculum dose of 10% (v/v). The fermentation parameters were controlled by a digital measurement and control system. The cultivation was carried out at 30 ◦C and aeration rate was 8 L/min. The pH was automatically controlled to within 7.0–7.2 with 2.0 M NaOH and 2.0 M HCl. Peanut oil (0.1%, v/v) added as an antifoaming agent.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: The cells were pelleted by centrifugation at 5000 × g for 10 min at 4 °C and rinsed twice with ice-cold PBS buffer (137 mM NaCl, 2.7 mM KCl, 8 mM Na2HPO4, and 2 mMKH2PO4, pH 7.40). All the cells were frozen immediately using liquid nitrogen and then stored at -80 °C.

tag: growth phase

value: cAMP production


title: High oxygen supply_36h

description: Gene expression in 36h-grown Arthrobacter sp. CGMCC 3584 under high oxygen supply

source_name: High oxygen supply, 36h


title: Nup210 shRNA rep1


title: High oxygen supply_12h

description: Gene expression in 12h-grown Arthrobacter sp. CGMCC 3584 under high oxygen supply

source_name: High oxygen supply, 12h

value: Cell growth


title: Low oxygen supply_48h

description: Gene expression in 48h-grown Arthrobacter sp. CGMCC 3584 under low oxygen supply

source_name: Low oxygen supply, 48h


title: High oxygen supply_48h

description: Gene expression in 48h-grown Arthrobacter sp. CGMCC 3584 under high oxygen supply

source_name: High oxygen supply, 48h


title: Nup210 shRNA rep3


title: WAP-Cre:PTEN tumor PW96

city: Toronto

first: Sharon

state: Ontario

address: 67 College Street Room 456

country: Canada

institute: University of Toronto

description:
PW96
Gene expression data from Wap-Cre:PTEN tumor

hyb_protocol: Affymetrix Mouse Gene 1.0 st microarray experiment were performed by the Centre of Applied Genomics (HSC, Toronto)

data_processing: Microarray Data were normalized using RMA method via Partek software and absolute expression values were obtained. Batch-correction was performed by Partek

source_name: Mouse Mammary Tumor

growth_protocol: Samples from independent primary mammary tumors from MMTV-Neu,WAP-Cre:PTEN models and wild-type mammary glands were frozen and kept in -80 degree.

extract_protocol: Total RNA was extracted with Trizol reagent twice. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Total RNA obtained from primary tumors were used for microarray analysis to determine differentially regulated genes among different mouse models.  Cluster analysis and pathway analysis based on gene expression were then performed to determine significant genes/pathways

value: Primary Tumor

tag: sample dimension

value: Mammary Tumor less than 1.0 cm diameter

value: Well Differentiated


title: WAP-Cre:PTEN tumor PW266B

description:
PW266B
Gene expression data from Wap-Cre:PTEN tumor

scan_protocol: Affymetrix Mouse Gene 1.0 st microarray experiment were performed by the Centre of Applied Genomics (HSC, Toronto)


title: Low oxygen supply_36h

description: Gene expression in 36h-grown Arthrobacter sp. CGMCC 3584 under low oxygen supply

source_name: Low oxygen supply, 36h


title: Low oxygen supply_24h

description: Gene expression in 24h-grown Arthrobacter sp. CGMCC 3584 under low oxygen supply

source_name: Low oxygen supply, 24h


title: Control scramble shRNA rep6


title: WAP-Cre:PTEN tumor PW293R5

description:
PW293R5
Gene expression data from Wap-Cre:PTEN tumor

label_protocol: Affymetrix Mouse Gene 1.0 st microarray experiment were performed by the Centre of Applied Genomics (HSC, Toronto)

value: Poorly Differentiated


title: WAP-Cre:PTEN tumor J191R

description:
J191R
Gene expression data from Wap-Cre:PTEN tumor


title: Low oxygen supply_12h

description: Gene expression in 12h-grown Arthrobacter sp. CGMCC 3584 under low oxygen supply

source_name: Low oxygen supply, 12h


title: WAP-Cre:PTEN tumor PW3

description:
PW3
Gene expression data from Wap-Cre:PTEN tumor


title: WAP-Cre:PTEN tumor PW28

description:
PW28
Gene expression data from Wap-Cre:PTEN tumor


title: WAP-Cre:PTEN tumor PW104

description:
PW104
Gene expression data from Wap-Cre:PTEN tumor


title: WAP-Cre:PTEN tumor PW83

description:
PW83
Gene expression data from Wap-Cre:PTEN tumor


title: WAP-Cre:PTEN tumor PW105

description:
PW105
Gene expression data from Wap-Cre:PTEN tumor


title: WAP-Cre:PTEN tumor PW153

description:
PW153
Gene expression data from Wap-Cre:PTEN tumor


title: WAP-Cre:PTEN tumor PW19

description:
PW19
Gene expression data from Wap-Cre:PTEN tumor


title: MMTV-Neu tumor N240

description:
N240
Gene expression data from primary MMTV-Neu tumor

value: MMTV-Neu

value: Epithelial


title: Nup210 shRNA rep6

description: Gene expression from Nup210 shRNA expressing cells


title: MMTV-Neu tumor N222

description:
N222
Gene expression data from primary MMTV-Neu tumor


title: WAP-Cre:PTEN tumor P196

description:
P196
Gene expression data from Wap-Cre:PTEN tumor


title: Wap-Cre:PTEN tumor PW160

description:
PW160
Gene expression data from Wap-Cre:PTEN tumor


title: Wap-Cre:PTEN tumor PW152L2

description:
PW152L2
Gene expression data from Wap-Cre:PTEN tumor


title: Wap-Cre:PTEN tumor PW261

description:
PW261
Gene expression data from Wap-Cre:PTEN tumor


title: Wap-Cre:PTEN tumor J186R

description:
J186R
Gene expression data from Wap-Cre:PTEN tumor


title: MMTV-Neu Tumor N362

description:
N362-2
Gene expression data from primary MMTV-Neu tumor


title: Wap-Cre:PTEN tumor PW191

description:
PW191
Gene expression data from Wap-Cre:PTEN tumor


title: Wap-Cre:PTEN tumor PW154

description:
PW154
Gene expression data from Wap-Cre:PTEN tumor


title: MMTV-Neu Tumor N348

description:
N348
Gene expression data from primary MMTV-Neu tumor


title: Wild Type Mammary Gland FvB6L

description:
FvB6L
Gene expression data from wild type mammary gland

source_name: Mouse Mammary Gland

value: Mammary Epithelial

value: Wild Type

value: Mammary glands less than 1.0 cm diameter


title: MMTV-Neu Tumor N334

description:
N334
Gene expression data from primary MMTV-Neu tumor


title: Wap-Cre:PTEN tumor PW123L

description:
PW123L
Gene expression data from Wap-Cre:PTEN tumor


title: Wap-Cre:PTEN tumor J76R

description:
J76R
Gene expression data from Wap-Cre:PTEN tumor


title: Wild Type Mammary Gland FvB5L

description:
FvB5L
Gene expression data from wild type mammary gland


title: Slc51a knockout mouse ileum, biological rep 3

city: Atlanta

first: Paul

last: Dawson

state: GA

address: 1760 Haygood Drive

department: Division of Pediatric GI/Hepatology

institute: Emory University

description: Gene expression data from mouse ileal tissue

hyb_protocol: 6 ug of biotynylated cRNA was hybridized for 16 h at 45 °C with the Affymetrix GeneAtlas Mouse MG-430 PM Array Strips. Strips were washed and stained using the GeneAtlas Fluidics Station according to standard Affymetrix operating procedures (GeneAtlas™ System User’s Guide; P/N 08-0306 Rev A January 2010)

scan_protocol: Strips were scanned using the GeneAtlas Imager system.

data_processing: Fluidics Control, Scan control and data collection was performed using the GeneAtlas Instrument Control Software version 1.0.5.267. The raw data generated were normalized using the robust multi-array average (RMA) method.

source_name: Mouse Ileal tissue Slc51a knockout mouse ileum

label_protocol: 250 ng of purified total RNA was reverse transcribed and biotin labeled to produce biotynylated cRNA tagets according to the standard Affymetrix GeneAtlas 3'-IVT Express labeling protocol (GeneAtlas 3' IVT Expression Kit User Manual, P/N 702833 Rev. 4, Affymetrix).

growth_protocol: Wild type and Slc51a knockout mice (males, C57BL/6 background; ~2 months of age)

extract_protocol: Trizol extraction of total RNA was performed. The RNA was further purified using an Rneasy MinElute Cleanup Kit (Qiagen #74204)

treatment_protocol: Mice described above were fasted for 4 hours,  anesthetized with ketamine-xylazine, and then  sacrificed by decapitation. Ileal tissue was collected and stored in liquid nitrogen until used to isolate RNA.

value: ileal

value: Slc51a knockout

value: C57BL/6 background

tag: gender

value: male


title: Wild Type Mammary Gland FvB4L

description:
FvB4L
Gene expression data from wild type mammary gland


title: MMTV-Neu tumor N242

description:
N242
Gene expression data from primary MMTV-Neu tumor


title: Slc51a knockout mouse ileum, biological rep 1


title: Wild type mouse ileum, biological rep 4

source_name: Mouse Ileal tissue from Wild Type mice

value: wild type


title: Wild type mouse ileum, biological rep 1


title: Slc51a knockout mouse ileum, biological rep 4


title: Wild type mouse ileum, biological rep 2


title: THP-1 Control Repeat 2

status: Public on Jun 01 2017

city: Boston

first: Athalia

middle: Rachel

last: Pyzer

state: MA

address: 3 Blackfan Circle CLS 724

institute: BIDMC

hyb_protocol: As per NanoString Manufacturers protocol

data_processing: Data obtained were then normalized to positive miRNA ligation reaction controls and background noise was subtracted. Correction for multiple comparisons was perfored using the False Discovery Rate.

source_name: THP-1 CTL

extract_protocol: Qiagen RNAEasy kit was used to isolate RNA from 1 million successfully transduced cells

treatment_protocol: The human acute myeloid leukemia cell lines MOLM-14 and THP-1 were silenced for MUC1 expression by  lentiviral transduction of MUC1 specific shRNA or scrambled control. RNA was extracted and NanoString array for microRNAs was performed.

tag: cell line

tag: transduction

value: scrambled control


title: Arabidopsis_Col0_DCMU.HLvsHL_rep4

city: Colchester

first: Ruben

last: Alvarez-Fernandez

address: Wivenhoe Park

department: Biological Sciences

institute: University of Essex

scan_protocol: Genepix 4000B scanner

data_processing: limma for R (see attached Rscript and SpotTypes file)

organism: Arabidopsis thaliana

label_protocol: Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) Protocol (manual part number G4140-90050), 500 ng of starting RNA

growth_protocol: Plants were grown in a growth chamber for 5 weeks in short day (8h/16 lighth/dark cycle) at 22°C, 150 µmol m-2 s-1 photosynthetically active photon flux density (PPFD) and 55% RH in 100-ml pots with Levington's L2+S growing medium.

extract_protocol: The outer leaves from four biological replicates were ground and RNA purified with Trizol (Life Technologies). RNA was resuspended in water and DNAse-treated (TurboDNAse, Life Technologies), then column-purified (Qiagen RNAeasy cleanup protocol) and eluted in water. Integrity tested on a Bioanalyzer (QuickRNA600nano kit), concentration re-assessed on a nanodrop and DNA contamination assessed by PCR with RNA template against a DNA template control.

treatment_protocol: At the beginning of the dark cycle a set of 8 plants were sprayed with 50 µM DCMU (water dilution from a 1 mM methanol stock) until the leaves were evenly wet. Control plants (8) were sprayed with solvent only. They were kept covered overnight and into 1h in their light cycle, then uncovered for 1h in normal growth conditions, and finally subjected alongside the controls to high light (1000 µmol m-2 s-1) for 30 min using a white LED array as the high light source. All 16 plants were immediately snap-frozen in liquid nitrogen after finishing the high light treatment. Expression of the APX2 gene was determined by qPCR and was used as a marker of the response to  high light. Four plants with the most even expression of this gene in each of the treatments were selected for microarray analysis.

tag: ecotype

tag: tissue

value: fully developed leaves

value: 5 weeks post germination

tag: treatment

value: HL


title: THP-1 Control Repeat 3

scan_protocol: As per NanoString Manufacturers protocol


title: Slc51a knockout mouse ileum, biological rep 2

tag: genotype/variation


title: Arabidopsis_Col0_DCMU.HLvsHL_rep3

hyb_protocol: Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) Protocol (manual part number G4140-90050)


title: Arabidopsis_Col0_DCMU.HLvsHL_rep2


title: Arabidopsis_Col0_DCMU.HLvsHL_rep1


title: Wild type mouse ileum, biological rep 3


title: Wap-Cre:PTEN tumor PW157

description:
PW1574R
Gene expression data from Wap-Cre:PTEN tumor

value: Primary Tumor

value: Mammary Tumor less than 1.0 cm diameter

tag: histology


title: MOLM-14 MUC1 Silenced Repeat 3

source_name: MOLM-14 MUC3

label_protocol: As per NanoString Manufacturers protocol

value: MUC1 specific shRNA


title: THP-1 Control Repeat 1


title: THP-1 MUC1 Silenced Repeat 3

source_name: THP-1 MUC1


title: MOLM-14 Control Repeat 3

source_name: MOLM-14 CTL


title: MOLM-14 Control Repeat 1


title: MOLM-14 Control Repeat 2


title: THP-1 MUC1 Silenced Repeat 2


title: MOLM-14 MUC1 Silenced Repeat 1

source_name: MOLM-14 MUC1


title: THP-1 MUC1 Silenced Repeat 1


title: MOLM-14 MUC1 Silenced Repeat 2

source_name: MOLM-14 MUC2


title: Aspirin 2

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

hyb_protocol: Following fragmentation, 4.2 ug of cDNA were hybridized for 16 hr at 45C on Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000 7G

data_processing: Raw Affymetrix intensity measurements of all probe sets were background-corrected, normalized, and summarized into gene level expression measurements using RMA method implemented in Partek Genomics Suite.

source_name: lung tissue

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (wt_sensetarget_label_manual).

extract_protocol: The lung tissues were isolated from mice and total RNA was extracted using Qiagen RNeasy kit.

treatment_protocol: The aspirin solution and/or triptolide suspension were gavaged into mice five days a week for two months. The treatment groups include: 1) PBS buffer, 2) aspirin (4 mg/kg body weight), 3) triptolide (1 mg/kg body weight), and 4) aspirin (4 mg/kg body weight)/triptolide (1 mg/kg body weight) disolved or suspended in PBS.

value: aspirin (4 mg/kg body weight)


title: Aspirin and Triptolide 1

value: aspirin (4 mg/kg body weight)/triptolide (1 mg/kg body weight) disolved or suspended in PBS


title: Aspirin and Triptolide 3


title: Untreated control 1

value: untreated


title: Triptolide 1

value: triptolide (1 mg/kg body weight)


title: CDP_Normal_4

city: Saint Louis

first: David

last: DeNardo

state: MO

address: 660 South Euclid Avenue

institute: Washington University School of Medicine

description: Age-matched control non-tumor bearing mice

hyb_protocol: 1.5 ug of Cy5-labelled cRNA (specific activity >10.0 pmol Cy5/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 Mouse 8x60K Expression Microarrays 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: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Raw data values were log2-transformed and quantile normalized across all samples. Detectable genes were defined as those with a detected call in at least 1 of 16 samples studied. R software package “limma” was used to detect differentially expressed genes. Significant genes were determined at p<0.05 and absolute fold-change >=1.5.

source_name: Bone Marrow CDP

label_protocol: Cyanine-5 (Cy5) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: To Total RNA from MDPs and CDPs from tumor bearing (PyMT) and non-tumor bearing (normal) mouse bone marrow was isolated using E.Z.N.A. Total RNA Kit according to the manufactory's instruction.

treatment_protocol: Tumors were established in the mammary fat using the PyMT B6 cell line, a cell line derived from the MMTV-PyMT genetic mammary tumor model on the C57/Bl6 background. Tumors were grown to 1.5 cm diameter. Bone marrow was harvested from tumor bearing (PyMT) and non-tumor bearing (normal) mice. MDPs and CDPs were selected through cell sorting.

tag: geneder

value: female

tag: tumor


title: Triptolide 2


title: CDP_Normal_5


title: MDP_PyMT_4

description: Mice bearing 1.5cm diameter orthotopic mammary tumor derived from the PyMT B6 cell line

source_name: Bone Marrow MDP

value: PyMT B6


title: Aspirin 1


title: MDP_Normal_3


title: Untreated control 2


title: CDP_PyMT_2


title: MDP_PyMT_3


title: Triptolide 3


title: MDP_PyMT_5


title: CDP_PyMT_4


title: 002_GWB

city: Detroit

first: Guojun

last: Wu

state: Michigan

address: 4100 John R Street, HWCRC,Room 824, None

department: Oncology

institute: Karmanos Cancer Institute

hyb_protocol: Following labeling procedure, 2.76 ug of cDNA were hybridized at 48C on human ST 2.1 arrays, and were washed and stained using the Affymetrix Gene Atlas system (software version 2.0.0.460).

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system (software version 2.0.0.460).

data_processing: Data was analyzed using the oligo Bioconductor package implemented in the R-statistical language version 3.3.0. RMA was used to fit log2 transformed expression values.

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA.

growth_protocol: All four cell models ((MCF10A/LacZ, MCF10A/Her2, MCF10A/mutant PIK3CA, and MCF10A/Her2+mutant PIK3CA) were cultured in SFIHE medium in 37C with 5% CO2.

extract_protocol: RNA was extracted and purified using the RNeasy plus mini kit.

treatment_protocol: We did not perform any treatment on these cells.

tag: stable transfection


title: MDP_Normal_4


title: MDP_Normal_5


title: 003_GWC

source_name: MCF10A/mutant PIK3CA


title: CDP_Normal_3


title: Aspirin 3


title: CDP_PyMT_3


title: MDP_PyMT_2


title: CDP_Normal_2


title: CDP_PyMT_5


title: Aspirin and Triptolide 2


title: 001_GWA

value: LacZ


title: 004_GWD

source_name: MCF10A/Her2+mutant PIK3CA

value: Her2 and PIK3CA-H1047R


title: THP-1 LPS 2 miR-204-3p

city: Nagasaki

first: Tomohiro

last: Koga

address: 1-7-1 Sakamoto

institute: Nagasaki University

description:
AR2377_11
Gene expression after 18hr LPS stimulation in macrophages derived from THP-1 cells.

hyb_protocol: 2.0ug of Cy3-labelled cDNA was filled up to 50 ul containing 1x Agilent blocking agent and 1x Agilent hybridization buffer, and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver2.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: macrophages derived from THP-1 cells

label_protocol: cDNA were amplified by Ovation® Pico WTA System V2（NuGEN Technologies) from 3ng total RNA according to the manufacturer's instructions. Amplified cDNA yield were checked with the NanoDrop ND-2000 Spectrophotometer. Cyanine-3 (Cy3) labeled cDNA was prepared with SureTag Complete DNA Labeling Kit (Agilent) according to the manufacturer's instructions, followed by Amicon Ultra-0.5 mL Centrifugal Filters for DNA Purification and Concentration (Merck Millipore). Dye incorporation and cDNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: The RNA was obtained from macrophages from THP-1 cells after LPS stimulation. Total cellular RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) following the manufacturer's recommendations. The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Macrophages derived from THP-1 cells were stimulated with 100ng/ml of LPS for 18 hours.

value: THP-1 (ATCC TIB-202)

tag: cell type

value: macrophages

value: LPS

tag: miRNA


title: MDP_Normal_2

tag: strain