title: HFF-1

state: CA

value: fibroblasts


title: Rose Bengal 0.5 uM,  biological rep1

status: Public on Mar 13 2014

type: RNA

city: Valencia

first: Francisco

middle: García

last: García

address: Eduardo Primo Yúfera, 3

department: Bionformatics & Biostatistics Unit

country: Spain

institute: CIPF

description: Gene expression data from Arabidopsis Thaliana, Rose Bengal

hyb_protocol: Technical steps as target hybridization, washing and staining of the arrays were performed sequentially as described in the Affymetrix GeneChip expression analysis technical manual using the Affymetrix once-cycle target labelling and control reagents, an Affymetrix GeneChip hybridization oven 640, and Affymetrix Fluidics Station 450

scan_protocol: Microarrays were scanned using Affymetrix GenChip Scanner 3000 7G.

data_processing: Data was standardized from R  using the affy Bioconductor package. Methods: Robust Multi-array Average and quantile normalization.

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Rose Bengal

label_protocol: Biotin-labelled cRNA was produced by in vitro transcription using GeneChip® 3' IVT Express Kit. The biotin-labelled cRNA was degraded by alkaline digestion and used for hybridization with ATH1 arrays.

growth_protocol: Arabidopsis cell suspension culture was maintained in 200 mL of liquid growth medium (Jouannea and Peaudlen, 1967; Axelos et al., 1992) by gentle agitation at 120 rpm at 24 ºC under continuous illumination (50 microE/m2/s) in an incubator shaker. Cells were sub-cultured with a 1/20 dilution factor every 7 days.

extract_protocol: Total RNA was extracted with the acid guanidine isothiocyanate-phenol-chloroform method using Trizol reagent. Total RNA was treated with TURBO DNase  to eliminate traces of contaminating genomic DNA.

treatment_protocol: An incubation of 30 min at high light or 1-h at dark were selected as the optimum time to monitor the changes in the transcription profile in the microarray experiments.

tag: treatment

value: Rose Bengal


title: Hydrogen Peroxide 500 uM,  biological rep3

description: Gene expression data from Arabidopsis Thaliana, Hydrogen Peroxide

source_name: Arabidopsis Thaliana, Hydrogen Peroxide

value: Hydrogen Peroxide


title: Clone#3_mAb225_rep2

city: Richland

first: Katrina

middle: M

last: Waters

state: WA

address: 902 Battelle Blvd; MSIN J4-18

department: Biological Sciences Division

country: USA

institute: Pacific Northwest National Laboratory

description:
TW52
Clone #3 with neutralized autocrine activation

hyb_protocol: Biotin-labeled cRNA (12 µg) was fragmented to a size range between 50-200 bases for array hybridization.  After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: The arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.

data_processing: Raw intensity data were quantile normalized using Genespring software by Robust Multi-Array Analysis (RMA) summarization and probes were subject to quality control to measure the efficiency of transcription, integrity of hybridization, and consistency of qualitative calls.

organism: Homo sapiens

label_protocol: Complementary DNA was synthesized from 1 µg of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to produce biotinylated cRNA from the cDNA template, according to manufacturer’s protocols (Affymetrix One-Cycle Target Labeling Kit).

growth_protocol: hTERT-immortalized normal human keratinocytes (provided by Dr. Jerry Shay, The University of Texas Southwestern Medical Center); Maintained in Keratinocyte serum-free medium (KSF) supplemented with bovine pituitary extract and epidermal growth factor.  Stable RNA transfection of ERK1-green fluorescent protein chimera was achieved using Phoenix retroviral packing cell system and puromycin selection.  Stable subclones were isolated with distinct ERK activation/oscillation patterns: Clone #1 exhibits transient ERK activation with ligand activation but does not oscillate; Clone #2 exhibits persistent ERK oscillations that are dependent on ligand activation; and Clong #3 exhibits spontaneous ERK oscillations in the absence of ligand activation.

extract_protocol: Total RNA was collected using the RNeasy Kit (Qiagen, Valencia, CA).

treatment_protocol: Treatments were performed in KSF supplemented with bovine pituitary extract (no epidermal growth factor). Conditions included 10ng/mL of TGFα used for ligand-activation; 10ug/mL of monoclonal antibody EGF antagonist mAB225 was used to shut down autocrine-activated ERK1; and nonspecific mouse IgG was used as a control for the autocrine-activated ERK1. Cells were harvested for RNA extraction after 24hrs.  Three replicates were collected.

tag: cell type

tag: tranfected with

value: ERK1-green fluorescent protein chimera

tag: clone id

tag: treated with


title: Clone#3_IgG_rep5

description:
TW45
Clone #3 with autocrine activation

value: hTERT-immortalized normal human keratinocytes

value: nonspecific mouse IgG (control)


title: 8-cell embryos_sired by father 7t3RR

city: Montreal

first: Jennifer

last: Maselli

state: Quebec

address: 3655 Prom Sir William Osler

country: Canada

institute: McGill University

data_processing:
The normalization and all the data analysis were performed according to the manufacturer's instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPLP1, LDHA, ACTB; only 3 were used for analysis (ACTB, LDHA, RPLP1) due to variability in expression of the other 2.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)].
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold-Change file reports test/control (i.e., average of all 8-cell embryos sired by BEP-treated males/Average of all 8-cell embryos sired by saline-treated males) ratios.

label: SYBR Green

organism: Rattus norvegicus

source_name: 8-cell embryo, BEP-treated father

label_protocol: RNA was reverse transcribed into cDNA and amplified using the TransPlex Complete Whole Genome Transcriptome Amplification Kit (Sigma, WTA2) according to the manufacturer's protocol. Residual primers and nucleotides were removed using a PCR-clean-up kit (Promega, Madison, WI). Using the cDNA synthesized and the RT2 SYBR Green ROX FAST Mastermix (Qiagen, 330611), according to the manufacturer's protocol, the expression of stem cell transcription factors was determined using the Rat Stem Cell Transcription Factors - RT2 Profiler PCR Array (PARN-501ZC, Qiagen). RT- PCR was done using the ViiA 7 Real-Time PCR System (Life Technologies), on 96-well plates. PCR thermal cycling parameters were: 95ºC for 10 min (one cycle), 95ºC for 15 s, and 60ºC for 1 min (40 cycles); a melting curve program was also done.

extract_protocol: Total RNA was extracted from 25-35 embryos at the eight-cell stage sired by control or BEP-treated males after a 9-wk recovery period (2 females mated per male, n= 4 males/treatment) using the RNeasy Plus Micro kit with on-column DNase digestion (Qiagen, Mississauga, ON, Canada).

tag: sire treatment

value: BEP (bleomycin, etoposide, and cisplatin)

tag: tissue

value: whole embryos

tag: developmental stage

value: 8-cell embryos

tag: strain/background

value: Brown Norway males X Sprague Dawley females


title: 8-cell embryos_sired by father 3T2R


title: 8-cell embryos_sired by father 8T2R


title: 8-cell embryos_sired by father 6T3R


title: genomic DNA from Sample 106

type: genomic

city: Singapore

first: Liang

last: Goh

address: College Road

country: Singapore

institute: Duke-NUS graduate medical school

description: Prostate Cancer Sample

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina GoldenGate array using standard Illumina protocol.

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

data_processing: Illumina GenomeStudio

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Prostate

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from the paraffin embedded tissues using Qiagen DNeasy Kit according to standard instructions.

tag: disease state

value: Prostate Cancer


title: genomic DNA from Sample 104

description: Prostate Cancer Sample


title: 8-cell embryos_sired by father 3C3R

source_name: 8-cell embryo, saline-treated father

value: saline control


title: 8-cell embryos_sired by father 6C3R


title: Control for RB1 and PER1

description: Gene expression data from Arabidopsis Thaliana, Control

source_name: Control for Rose Bengal and Hydrogen Peroxide


title: Clone#3_IgG_rep3

description:
TW43
Clone #3 with autocrine activation


title: Clone#3_mAb225_rep1

description:
TW51
Clone #3 with neutralized autocrine activation

value: 10ug/mL of monoclonal antibody EGF antagonist mAB225


title: Control for RB2 and PER2


title: 8-cell embryos_sired by father 5C2R


title: genomic DNA from Sample 109

description: Prostate Cancer Sample


title: genomic DNA from Sample 108

description: Prostate Cancer Sample


title: genomic DNA from Sample 110

description: Prostate Cancer Sample


title: genomic DNA from Sample 111

description: Prostate Cancer Sample


title: genomic DNA from Sample 107

description: Prostate Cancer Sample


title: genomic DNA from Sample 101

description: Prostate Cancer Sample


title: genomic DNA from Sample 105

description: Prostate Cancer Sample


title: Clone#3_IgG_rep4

description:
TW44
Clone #3 with autocrine activation


title: Clone#3_IgG_rep2

description:
TW42
Clone #3 with autocrine activation


title: Control for RB3 and PER3


title: Clone#1_sham_rep3

description:
TW33
Clone #1, sham

value: none (untreated control)


title: Clone#3_IgG_rep1

description:
TW41
Clone #3 with autocrine activation


title: genomic DNA from Sample 102

description: Prostate Cancer Sample


title: Clone#1_sham_rep4

description:
TW34
Clone #1, sham


title: 8-cell embryos_sired by father 4C2R


title: genomic DNA from Sample 99

description: Prostate Cancer Sample


title: genomic DNA from Sample 103

description: Prostate Cancer Sample


title: genomic DNA from Sample 100

description: Prostate Cancer Sample


title: genomic DNA from Sample 97

description: Prostate Cancer Sample


title: genomic DNA from Sample 98

description: Prostate Cancer Sample


title: genomic DNA from Sample 84

description: Prostate Cancer Sample


title: genomic DNA from Sample 87

description: Prostate Cancer Sample


title: genomic DNA from Sample 90

description: Prostate Cancer Sample


title: genomic DNA from Sample 86

description: Prostate Cancer Sample


title: genomic DNA from Sample 92

description: Prostate Cancer Sample


title: genomic DNA from Sample 95

description: Prostate Cancer Sample


title: genomic DNA from Sample 96

description: Prostate Cancer Sample


title: genomic DNA from Sample 94

description: Prostate Cancer Sample


title: genomic DNA from Sample 89

description: Prostate Cancer Sample


title: genomic DNA from Sample 93

description: Prostate Cancer Sample


title: genomic DNA from Sample 91

description: Prostate Cancer Sample


title: genomic DNA from Sample 85

description: Prostate Cancer Sample


title: genomic DNA from Sample 88

description: Prostate Cancer Sample


title: Clone#1_TGFα_rep4

description:
TW24
Clone #1 with ligand activation

value: 10ng/mL of TGFα (for ligand-activation)


title: Clone#1_sham_rep2

description:
TW32
Clone #1, sham


title: Clone#1_TGFα_rep5

description:
TW25
Clone #1 with ligand activation


title: Clone#1_TGFα_rep3

description:
TW23
Clone #1 with ligand activation


title: Clone#2_sham_rep5

description:
TW15
Clone #2, sham


title: genomic DNA from Sample 83

description: Prostate Cancer Sample


title: Clone#1_TGFα_rep2

description:
TW22
Clone #1 with ligand activation


title: Clone#1_TGFα_rep1

description:
TW21
Clone #1 with ligand activation


title: genomic DNA from Sample 82

description: Prostate Cancer Sample


title: Clone#1_sham_rep1

description:
TW31
Clone #1, sham


title: Clone#2_sham_rep4

description:
TW14
Clone #2, sham


title: Clone#2_sham_rep2

description:
TW12
Clone #2, sham


title: genomic DNA from Sample 81

description: Prostate Cancer Sample


title: genomic DNA from Sample 80

description: Prostate Cancer Sample


title: Clone#2_sham_rep3

description:
TW13
Clone #2, sham


title: Clone#1_sham_rep5

description:
TW35
Clone #1, sham


title: genomic DNA from Sample 78

description: Prostate Cancer Sample


title: genomic DNA from Sample 77

description: Prostate Cancer Sample


title: genomic DNA from Sample 75

description: Prostate Cancer Sample


title: genomic DNA from Sample 76

description: Prostate Cancer Sample


title: genomic DNA from Sample 71

description: Prostate Cancer Sample


title: genomic DNA from Sample 73

description: Prostate Cancer Sample


title: genomic DNA from Sample 72

description: Prostate Cancer Sample


title: genomic DNA from Sample 74

description: Prostate Cancer Sample


title: genomic DNA from Sample 70

description: Prostate Cancer Sample


title: Clone#2_TGFα_rep3

description:
TW03
Clone #2 with ligand activation


title: Clone#2_TGFα_rep4

description:
TW04
Clone #2 with ligand activation


title: genomic DNA from Sample 79

description: Prostate Cancer Sample


title: genomic DNA from Sample 69

description: Prostate Cancer Sample


title: Clone#2_TGFα_rep5

description:
TW05
Clone #2 with ligand activation


title: genomic DNA from Sample 66

description: Prostate Cancer Sample


title: genomic DNA from Sample 68

description: Prostate Cancer Sample


title: genomic DNA from Sample 65

description: Prostate Cancer Sample


title: genomic DNA from Sample 67

description: Prostate Cancer Sample


title: genomic DNA from Sample 64

description: Prostate Cancer Sample


title: genomic DNA from Sample 63

description: Prostate Cancer Sample


title: genomic DNA from Sample 58

description: Prostate Cancer Sample


title: genomic DNA from Sample 59

description: Prostate Cancer Sample


title: genomic DNA from Sample 62

description: Prostate Cancer Sample


title: genomic DNA from Sample 61

description: Prostate Cancer Sample


title: Clone#2_sham_rep1

description:
TW11
Clone #2, sham


title: Clone#2_TGFα_rep1

description:
TW01
Clone #2 with ligand activation


title: genomic DNA from Sample 55

description: Prostate Cancer Sample


title: Clone#2_TGFα_rep2

description:
TW02
Clone #2 with ligand activation


title: N2a-AI-4

city: Washington

first: Bi-Dar

last: Wang

state: DC

address: 2300 I street, NW

department: Pharmacology and Physiology

institute: The George Washington University Medical Center

description: Neuro2a anchorage independent tumorspheres (AI), biological rep 4

hyb_protocol: Fragmented and biotin-labeled single strand cDNA amples were hybridized using Affymetrix hybridization kit materials. Hyb cocktails were heated at 99° for 5 min, then incubated at 45° for 5 min and centrifuged at max speed for 1 min. The hyb solution (200μl each sample) was then transferred to each arrays. The hybridizations were performed for 16 hours at 45° at 60rpm, and the washing was performed by GeneChip Fluidics Station 450using using Fluidics transcript FS450_0001.

scan_protocol: Affymetrix GeneChIP Scanner 3000 7G

data_processing: Data were processed using Partek Genomics Suite 6.5 program. GCRMA background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities, then quantile normalized and log2 transformed.

organism: Mus musculus

label_protocol: Samples were enzymatically fragmented and biotinylated using the Affymetrix GeneChip  WT Terminal Labeling Kit.

growth_protocol: AD cells were cultured in DMEM (Gibco) containing 10% fetal bovine serum (Gibco), 0.5% penicillin/streptomycin (Sigma) and 10% L-glutamine (Sigma). AI cells were grown in NeuroCult complete media consisting of NeuroCult Neural Stem Cell (NSC) Basal medium, 1/10 NeuroCult NSC Proliferation supplements, 20ng/ml EGF, 10ng/ml bFGF and 2µg/ml Heparin (medium, supplements and growth factors all from Stem Cell Technologies).

extract_protocol: All RNA samples from AD and AI cells were prepared using RNeasy kit (Qiagen). The 1st- and 2nd-strand cDNA synthesis, and IVT amplification were performed using the Ambion WT expression kit.

treatment_protocol: not applicable.

tag: background strain

value: AJ

value: neuroblastoma

tag: genotype

value: anoikis resistance anchorage independent


title: GFP control cells rep-3

city: Hangzhou

first: Xiaotong

last: Hu

address: Qingchun East Road #3

country: China

institute: Zhejiang University

description: This sample is of control U266 cells. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: After being washed in an ozone-free environment, the slides were scanned using the Agilent Scanner G2505C.

data_processing: Slides were scanned at 5 μm/pixel resolution using an Agilent Scanner G2505C scanner piloted by GenePix Pro 6.0 software (Axon). Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Differentially expressed genes were identified statistical significance were identified through Volcano Plot filtering. Hierarchical clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed using the standard enrichment computation method.

source_name: U266 cells with GFP control

label_protocol: Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA)

growth_protocol: RPMI1640 medium with 15% fetal bovine serum, 100 units/mL penicillin and 100 mg/mL streptomycin

extract_protocol: Total RNA was extracted from cell pellets by Trizol (Invitrogen) and reverse transcribed into cDNA using MultiScribe Reverse Transcriptase (Applied Biosystems, Foster city, CA, USA) according to the manufacturer’s instructions

treatment_protocol: Briefly, when the U266 cells reached 50-60% confluence, the medium was removed and washed twice with PBS. Polybrene was used to increase the infection rate, and the infection was performed with lenti-CD9 and lenti-GFP according to the manufacturer’s instructions. At 2 days post-infection, the percentage of GFP-positive U266 cells was determined using a fluorescence microscope to evaluate the infectivity. GFP-positive cells were selected by flow cytometry.

value: Wild-type


title: GFP control cells rep-2

description: This sample is of control U266 cells. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: genomic DNA from Sample 56

description: Prostate Cancer Sample


title: N2a-AD-4

description: Neuro2a anchorage dependent (AD) cells, biological rep 4

source_name: Neuro2a anchorage dependent (AD) cells

value: anchorage dependent


title: genomic DNA from Sample 57

description: Prostate Cancer Sample


title: N2a-AI-3

description: Neuro2a anchorage independent tumorspheres (AI), biological rep 3


title: genomic DNA from Sample 60

description: Prostate Cancer Sample


title: genomic DNA from Sample 54

description: Prostate Cancer Sample


title: N2a-AI-1

description: Neuro2a anchorage independent tumorspheres (AI), biological rep 1


title: genomic DNA from Sample 52

description: Prostate Cancer Sample


title: genomic DNA from Sample 51

description: Prostate Cancer Sample


title: genomic DNA from Sample 53

description: Prostate Cancer Sample


title: GFP control cells rep-1

description: This sample is of control U266 cells. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: genomic DNA from Sample 50

description: Prostate Cancer Sample


title: genomic DNA from Sample 49

description: Prostate Cancer Sample


title: genomic DNA from Sample 48

description: Prostate Cancer Sample


title: genomic DNA from Sample 47

description: Prostate Cancer Sample


title: CD9 overexpression cells rep-1

description: This sample is of U266 cells with CD9 overexpression. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: U266 cells with CD9 overexpression

value: overexpression of CD9


title: CD9 overexpression cells rep-2

description: This sample is of U266 cells with CD9 overexpression. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: N2a-AI-2

description: Neuro2a anchorage independent tumorspheres (AI), biological rep 2


title: CD9 overexpression cells rep-3

description: This sample is of U266 cells with CD9 overexpression. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: genomic DNA from Sample 37

description: Prostate Cancer Sample


title: N2a-AD-1

description: Neuro2a anchorage dependent (AD) cells, biological rep 1


title: genomic DNA from Sample 39

description: Prostate Cancer Sample


title: genomic DNA from Sample 38

description: Prostate Cancer Sample


title: genomic DNA from Sample 41

description: Prostate Cancer Sample


title: genomic DNA from Sample 46

description: Prostate Cancer Sample


title: genomic DNA from Sample 42

description: Prostate Cancer Sample


title: genomic DNA from Sample 44

description: Prostate Cancer Sample


title: N2a-AD-2

description: Neuro2a anchorage dependent (AD) cells, biological rep 2


title: genomic DNA from Sample 43

description: Prostate Cancer Sample


title: genomic DNA from Sample 40

description: Prostate Cancer Sample


title: genomic DNA from Sample 35

description: Prostate Cancer Sample


title: genomic DNA from Sample 34

description: Prostate Cancer Sample


title: Fresh Frozen Non-Neoplastic Breast Tissue BS_BRN_21

city: Phoenix

first: Bodour

last: Salhia

state: AZ

address: 445 N Fifth Street

department: Integrated Cancer Genomics Division

institute: Translational Genomics Research Institute

hyb_protocol: Approximately 800ng of both Cy5-labeled experimental cRNA and Cy3-labeled universal reference RNA were hybridized to each microarray (adjusting for labeling efficiency).

scan_protocol: Images were captured using an Agilent DNA microarray scanner set at default settings for gene expression.

data_processing: Scanned images were processed using Feature Extractor v. 10.5.1.1. By applying a LOWESS (locally weighted linear regression) correction for dye-bias, background noise was subtracted from spot intensities. To filter the preprocessed data, genes with a background signal higher than feature signal were removed.

label_protocol: A quick-amplification kit (Agilent, Santa Clara, CA) was used to amplify and label 500ng target mRNA species into complementary RNA (cRNA) for oligo microarrays according to the manufacturer's protocol. For each two-color array, experimental samples were compared to commercial universal reference RNA (Stratagene, La Jolla, CA) that was labeled with cyanine 5-CTP and cyanine-3-CTP (Perkin Elmer, Boston, MA), respectively. cRNA concentration and labeling efficiency were measured spectrophotometrically.

extract_protocol: Total RNA, including small RNA, was isolated using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol.  Genomic DNA and total RNA yields were assessed using a NanoDrop 2000c (Thermo Scientific). Total RNA samples were evaluated for integrity using the Bioanalyzer RNA 6000 Nano LabChip Kit (Agilent Technologies, Santa Clara, CA) on a Bioanalyzer 2400 (Agilent Technologies).  Only total RNA samples with RNA integrity number values of at least 7 (RIN ≥ 7) were profiled.

value: Non-Neoplastic Breast

source_name: Universal reference RNA

tag: sample type

value: Universal reference RNA


title: Fresh Frozen Non-Neoplastic Breast Tissue BS_BRN_20


title: genomic DNA from Sample 33

description: Prostate Cancer Sample


title: genomic DNA from Sample 36

description: Prostate Cancer Sample


title: genomic DNA from Sample 45

description: Prostate Cancer Sample


title: Fresh Frozen Non-Neoplastic Breast Tissue BS_BRN_11


title: Fresh Frozen Non-Neoplastic Breast Tissue BS_BRN_13


title: genomic DNA from Sample 32

description: Prostate Cancer Sample


title: Fresh Frozen Non-Neoplastic Breast Tissue BS_BRN_10


title: Liver cancer xenograft, model ID 03-0252

city: Shanghai

first: Douglas

last: Fang

address: #288 FuTe Zhong Road, WaiGaoQiao Free Trade Zone

institute: WuXi AppTec Co., Ltd.

hyb_protocol: Total RNA was amplified and fragmented using a GeneChip 3’ IVT expression kit (Affymetrix, Santa Clara, CA). Then the samples were hybridized onto a GeneChip PrimeView™ human gene expression array (Affymetrix).

scan_protocol: Scanned on an Affymetrix GeneChip scanner 3000 7G

data_processing: Processed on Affymetrix Expression Console version 1.1, with RMA normalization approach.

source_name: xenograft RNA

extract_protocol: Genomic RNA was isolated using RNeasy protect mini kit (Qiagen). The concentrations were quantified using NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, DE). RNA samples with an RNA integrity number above 8.0 and A260/280 ratios between 1.8 and 2.0 were used for gene expression array.

value: xenograft passage 3

value: xenograft liver tumor


title: N2a-AD-3

description: Neuro2a anchorage dependent (AD) cells, biological rep 3


title: Liver cancer xenograft, model ID 03-0254

label_protocol: Total RNA was amplified and fragmented using a GeneChip 3’ IVT expression kit (Affymetrix, Santa Clara, CA). Then the samples were hybridized onto a GeneChip PrimeView™ human gene expression array (Affymetrix).


title: Liver cancer xenograft, model ID 03-0271

value: xenograft passage 4


title: Fresh Frozen Non-Neoplastic Breast Tissue BS_BRN_14


title: genomic DNA from Sample 30

description: Prostate Cancer Sample


title: genomic DNA from Sample 31

description: Prostate Cancer Sample


title: genomic DNA from Sample 27

description: Prostate Cancer Sample


title: genomic DNA from Sample 26

description: Prostate Cancer Sample


title: Fresh Frozen Non-Neoplastic Breast Tissue BS_BRN_9


title: Fresh Frozen Non-Neoplastic Breast Tissue BS_BRN_6


title: genomic DNA from Sample 29

description: Prostate Cancer Sample


title: genomic DNA from Sample 28

description: Prostate Cancer Sample


title: genomic DNA from Sample 25

description: Prostate Cancer Sample


title: genomic DNA from Sample 24

description: BPH Sample

value: normal


title: Fresh Frozen Non-Neoplastic Breast Tissue BS_BRN_1


title: Liver cancer xenograft, model ID 03-0217


title: Fresh Frozen Non-Neoplastic Breast Tissue BS_BRN_5


title: Liver cancer xenograft, model ID 03-0240


title: genomic DNA from Sample 22

description: BPH Sample


title: genomic DNA from Sample 23

description: BPH Sample


title: genomic DNA from Sample 21

description: BPH Sample


title: Liver cancer xenograft, model ID 03-0209

value: xenograft passage 2


title: Liver cancer xenograft, model ID 03-0243


title: genomic DNA from Sample 20

description: BPH Sample


title: Liver cancer xenograft, model ID 03-0200


title: genomic DNA from Sample 15

description: BPH Sample


title: Liver cancer xenograft, model ID 03-0191


title: Fresh Frozen Non-Neoplastic Brain Tissue NB_17

value: Non-Neoplastic Brain


title: genomic DNA from Sample 14

description: BPH Sample


title: genomic DNA from Sample 12

description: BPH Sample


title: genomic DNA from Sample 19

description: BPH Sample


title: genomic DNA from Sample 13

description: BPH Sample


title: genomic DNA from Sample 18

description: BPH Sample


title: genomic DNA from Sample 17

description: BPH Sample


title: Fresh Frozen Non-Neoplastic Brain Tissue NB_18


title: Liver cancer xenograft, model ID 03-0189


title: genomic DNA from Sample 16

description: BPH Sample


title: genomic DNA from Sample 11

description: BPH Sample


title: Fresh Frozen Non-Neoplastic Brain Tissue NB_10


title: genomic DNA from Sample 10

description: BPH Sample


title: genomic DNA from Sample 9

description: BPH Sample


title: Fresh Frozen Non-Neoplastic Brain Tissue NB_9


title: genomic DNA from Sample 8

description: BPH Sample


title: Fresh Frozen Non-Neoplastic Brain Tissue NB_14


title: Liver cancer xenograft, model ID 03-0164


title: Liver cancer xenograft, model ID 03-0187


title: Liver cancer xenograft, model ID 03-0159


title: Liver cancer xenograft, model ID 03-0185


title: Fresh Frozen Non-Neoplastic Brain Tissue NB_8


title: Fresh Frozen Non-Neoplastic Brain Tissue NB_5


title: Liver cancer xenograft, model ID 03-0147


title: Fresh Frozen Non-Neoplastic Brain Tissue NB_3


title: genomic DNA from Sample 7

description: BPH Sample


title: genomic DNA from Sample 6

description: BPH Sample


title: Fresh Frozen Non-Neoplastic Brain Tissue NB_7


title: Liver cancer xenograft, model ID 03-0149


title: genomic DNA from Sample 5

description: BPH Sample


title: Liver cancer xenograft, model ID 03-0146


title: Fresh Frozen Non-Neoplastic Brain Tissue NB_2


title: genomic DNA from Sample 4

description: BPH Sample


title: genomic DNA from Sample 1

description: BPH Sample


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_55

value: Breast Brain Metastasis


title: Liver cancer xenograft, model ID 03-0141


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_54


title: Liver cancer xenograft, model ID 03-0143


title: genomic DNA from Sample 3

description: BPH Sample


title: genomic DNA from Sample 2

description: BPH Sample


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_52


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_51


title: Liver cancer xenograft, model ID 03-0122


title: KUCaP2 T5-13

city: Kyoto

first: Atsushi

last: Maeno

address: Skyo-ku Shogoin Kawahara-cho 54

department: Urology

country: Japan

institute: Kyoto University Facalty of Medicine

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: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

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. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: xenograft tissue

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

extract_protocol: Small RNAs were extracted from xenograft tissues cut in about 1cm cubes using the mirVana™ miRNA Isolation Kit (Applied Biosystems, Foster City, CA) according to the manufacturer’s protocols.

tag: Stage

value: castration resistant


title: Wild type, biological rep2

city: Utrecht

first: miaomiao

last: Zhou

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: centre of fungal biodiversity, Utrecht, KNAW

description: Gene expression data from A.niger wild type grow on L-rhamnose 2 hours

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized to Affymetrix A. niger Genome Gene chips (GPL6758). GeneChips were washed and stained in an automated process.

scan_protocol: GeneChips were scanned.

data_processing: Affymetrix CEL-data files were preprocessed by using the statistical language and environment R (R Development Core Team, 2007) version 2.6.1. The probe intensities were normalized for background by using the robust multiarray average method (Irizarry, 2003) by using only perfect match (PM) probes. Normalization was performed subsequently by using the quantiles algorithm (Bolstad, 2003). Gene expression values were calculated from the PM probes with the medianpolish summary method (Irizarry, 2003). All statistical preprocessing methods were used by invoking them through the affy package (Gautier, 2004).

organism: Aspergillus niger

source_name: wild type grow on L-rhamnose 2 hours

label_protocol: Biotin-labeled antisense cRNA was produced from 2 μg of total RNA with the Eukaryotic One-Cycle Target Labeling kit (Affymetrix; www.affymetrix.com).

growth_protocol: A. niger N402 (cspA), A. niger N593 (cspA ΔkusA::amdS+, pyrG-) and A. niger FP-304 (cspA ΔkusA::amdS+, pyrG-, ΔrhaR:: pyrG+) were maintained on MM or CM with the addition of L-rhamnose at 30ºC. Sporeplates contained CM + 2% D-glucose, while plates used in the growth experiment contained MM + 25mM L-rhamnose. 1.5% agar was used to solidify the media. Uridine (0.2g L-1) was added to the media to promote growth of the uridine deficient A. niger N593 strain. Liquid cultures were inoculated with 106 spores ml-1 and shaken at 250 rpm.

extract_protocol: RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA) and purified using TRIzol® Plus RNA Purification Kit (Sigma-Aldrich) according to the instructions of the manufacturer.

treatment_protocol: Pre-cultures for RNA isolation were grown for 16 h in 1 L Erlenmeyer flasks that contained 250 ml CM + 2% D-fructose, subsequently the mycelium was washed with MM and transferred for 2 h to 250 ml Erlenmeyer flasks containing 50 ml MM supplemented with 25 mM L-rhamnose. After incubation, the mycelium was harvested by vacuum filtration, dried between towels 14 and immediately frozen in liquid nitrogen.

tag: strain

value: Wild type N402

tag: age

value: 2 hours

value: 25 mM L-rhamnose


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_50


title: Liver cancer xenograft, model ID 03-0117


title: rhaR deletion mutant, biological rep1

description: Gene expression data from A.niger ΔrhaR mutant on L-rhamnose 2 hours

source_name: ΔrhaR mutant grow on L-rhamnose 2 hours

value: ΔrhaR mutant


title: Liver cancer xenograft, model ID 03-0115


title: KUCaP2 T5-8


title: Liver cancer xenograft, model ID 03-0140


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_49


title: rhaR deletion mutant, biological rep2


title: Wild type, biological rep1


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_44


title: Liver cancer xenograft, model ID 03-0086


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_43


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_47


title: Liver cancer xenograft, model ID 03-0061


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_48


title: Liver cancer xenograft, model ID 03-0100


title: KUCaP2 T5-7


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_42


title: Liver cancer xenograft, model ID 03-0097


title: MVT1tumorcells_control_2week_rep1

city: Columbus

first: Haritha

last: Mathsyaraja

address: 460 W12th Ave

institute: The Ohio State University

description:
Gene expression data at macrometastatic stage (2 weeks post injection)
2_week_WT1

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

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

data_processing: Gene expression levels were estimated from GeneChip® probe intensities using WEDGE++ algorithm (WPP), an enhanced integrated version of the published RMA, quantile-normalization and background-correction algorithms.

label: Biotin

source_name: Tumor cells isolated from control mouse lungs 2 week post injection

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: The metastatic mammary tumor cell line MVT1 was maintained in 10% FBS containing DMEM.  3 million GFP tagged MVT1 cells were injected into syngeneic mice. Tumor cells were sorted from metastatic lungs from the various groups.

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

treatment_protocol: The CSF1R inhibitor GW2580 was resuspended in 0.5% hydroxypropylmethylcellulose and 0.05% Tween-80 solution and mice were gavaged at a dose of 160mg/kg daily

value: FVB/N

value: control

value: lung

tag: time

value: 2 week post injection

value: Tumor epithelial cell


title: MVT1tumorcells_GW2580treated_2week_rep2

description:
Gene expression data at macrometastatic stage (2 weeks post injection) treated with CSF1R inhibitor
2_week_GW2

source_name: Tumor cells isolated from GW2580 treated mouse lungs 2 week post injection

tag: treatment

value: CSF1R inhibitor GW2580


title: KUCaP2 T5-5


title: MVT1tumorcells_control_2week_rep2

description:
Gene expression data at macrometastatic stage (2 weeks post injection)
2_week_WT2

tag: cell type


title: KUCaP2 T5-6

value: androgen dependent


title: KUCaP2 T5-4


title: MVT1tumorcells_GW2580treated_2week_rep1

description:
Gene expression data at macrometastatic stage (2 weeks post injection) treated with CSF1R inhibitor
2_week_GW1


title: MVT1tumorcells_control_1week_rep2

description:
Gene expression data at micrometastatic stage (1 week post injection)
1_week_WT2

source_name: Tumor cells isolated from control mouse lungs 1 week post injection

value: 1 week post injection


title: Liver cancer xenograft, model ID 03-0020

value: xenograft passage 3

value: xenograft liver tumor


title: Liver cancer xenograft, model ID 03-0021


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_35

value: Universal reference RNA


title: Liver cancer xenograft, model ID 03-0022


title: MVT1tumorcells_control_1week_rep1

description:
Gene expression data at micrometastatic stage (1 week post injection)
1_week_WT1


title: KUCaP2 T5-9


title: KUCaP2 T5-2


title: Primary murine microglia - PBS Stimulated rep3

city: Boston

first: Tsuneya

last: Ikezu

state: MA

address: 72 East Concord St

department: BUSM - Department of Pharmacology and Experimental Therapeutics

institute: Boston University School of Medicine

description: Brains from pooled litter

hyb_protocol: The labeled, fragmented DNA was hybridized to the miRNA 2.0 Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: Data was normalized using the Affymetrix miRNA QC Tool (version 1.1.1.0), with default background detection, RMA global background correction, quantile normalization, and median polish summarization.

source_name: Wild-type CD-1 mice

label_protocol: Biotin labeling was performed using the Affymetrix FlashTag Biotin HSR RNA Labeling Kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: Primary Microglia from P0 CD-1 mice were cultured for 5-7 days in DMEM/FBS/Penn-Strep with 10 ng/ml of both M-CSF and GM-CSF

extract_protocol: Total RNA was isolated by using QIAzol and miRNeasy Minikit per supplier's protocol

treatment_protocol: Media was changed the night before to serum free media (DMEM/Pen-Strep only) and then stimulated with 100 ng/ml of LPS, 20 ng/ml of IL-4 or equivalent volume of PBS for 4 hours

value: primary microglia

tag: stimulation

value: PBS

value: P0-P1 pups


title: Primary murine microglia - PBS Stimulated rep2

description: Brains from pooled litter


title: Primary murine microglia - PBS Stimulated rep1

description: Brains from pooled litter


title: Liver cancer xenograft, model ID 03-0019


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_26

value: Breast Brain Metastasis


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_33


title: Liver cancer xenograft, model ID 03-0018


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_27


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_24


title: Primary murine microglia - LPS Stimulated rep2

description: Brains from pooled litter

value: LPS


title: Primary murine microglia - LPS Stimulated rep1

description: Brains from pooled litter


title: Primary murine microglia - LPS Stimulated rep3

description: Brains from pooled litter


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_22


title: MDA-MB-231_24hr_50μM_rep1

first: Ting

last: Li

address: No.270 Dong’an Road

department: Department of Medical Oncology

institute: Fudan University Shanghai Cancer Center

description: The ID column includes the Agilent Probe Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL10332.

hyb_protocol: The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols. Briefly, total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies).

scan_protocol: The labeled cRNAs were hybridized onto the Whole Human Genome Oligo Microarray (4x44K, Agilent Technologies). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that have flags in 'Detected' in both samples were chosen for differentially expressed genes screening.

source_name: MDA-MB-231 cell lines, 24hr, 50μM fenofibrate, replicate 1

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies). Cyanine-3 (Cy3) labeled cRNA was prepared from 1 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: The total RNA was extracted by TRIzol after harvesting cells treated with fenofibrate.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: MDA-MB-231 cells were seeded into 10cm culture dishes (Corning) at a density of 2×10^5 cells/mL in a volume of 10 ml. These cells were cultured as a monolayer in 5% CO2 and 95% air in a humidified incubator at 37°C for 24 h after cell attachment. The cells were treated with fenofibrate at different concentrations (0 and 50μM, DMSO in each group was balanced) and then incubated for 24 hours.

tag: cell lines

value: MDA-MB-231 cell line

value: 50μM Fenofibrate for 24hr


title: Liver cancer xenograft, model ID 03-0017


title: Liver cancer xenograft, model ID 03-0014

value: xenograft passage 4


title: Liver cancer xenograft, model ID 03-0016


title: Liver cancer xenograft, model ID 03-0012


title: Primary murine microglia - IL-4 Stimulated rep3

description: Brains from pooled litter


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_16


title: MDA-MB-231_24hr_0μM_rep1

source_name: MDA-MB-231 cell lines, 24hr, 0μM fenofibrate, replicate 1

tag: treated with

value: 0 μM Fenofibrate (control) for 24hr


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_20


title: Primary murine microglia - IL-4 Stimulated rep1

description: Brains from pooled litter


title: Primary murine microglia - IL-4 Stimulated rep2

description: Brains from pooled litter


title: Liver cancer xenograft, model ID 03-0010


title: Liver cancer xenograft, model ID 03-0007


title: Liver cancer xenograft, model ID 03-0011


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_21


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_15


title: Liver cancer xenograft, model ID 03-0009


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_13


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_14


title: Liver cancer xenograft, model ID 03-0005


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_12


title: Liver cancer xenograft, model ID 03-0004


title: Liver cancer xenograft, model ID 03-0006


title: Liver cancer tumor, model ID 03-0141

source_name: tumor RNA

value: Liver cancer tumor

value: primary liver tumor


title: Liver cancer tumor, model ID 03-0097


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_10


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_9


title: Liver cancer tumor, model ID 03-0100


title: Liver cancer tumor, model ID 03-0022


title: Liver cancer tumor, model ID 03-0020


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_6


title: Liver cancer tumor, model ID 03-0021


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_2


title: Liver cancer tumor, model ID 03-0018


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_7


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_8


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_5


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_11


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_4


title: Liver cancer tumor, model ID 03-0019


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_1


title: 60min: Block + ActD, Biological Replicate 3

status: Public on Mar 12 2014

city: Bethesda

first: Philip

last: Lee

address: 35 Lincoln Drive

department: NICHD

institute: NIH

description: BlockD 60min

hyb_protocol: Illumina hybridization protocol

scan_protocol: Illumina scanning protocol

data_processing: Normalised using quantile normalisation with IlluminaGUI in R

source_name: Hippocampal cell culture

label_protocol: Standard Illumina protocol

growth_protocol: Cultures were grown for 12 days prior to treatments

extract_protocol: Trizol extraction followed by cleancup using Qiagen RNeasy column.  Quality control by Agilent Bioanalyser

treatment_protocol: Treatments were for 5 minutes, 30 minutes and 60 minutes

value: Sprague Dawley

value: Embryonic day 18.5

value: hippocampal neurons


title: 60min: Block, Biological Replicate 3

description: Block 60min


title: 5min: Block + ActD, Biological Replicate 3

description: BlockD 5min


title: 30min: BiC/4AP, Biological Replicate 3

description: Activity 30min


title: 60min: BiC/4AP, Biological Replicate 3

description: Activity 60min


title: 30min: Block + ActD, Biological Replicate 3

description: BlockD 30min


title: 60min: BiC/4AP + ActD, Biological Replicate 3

description: ActivityD 60min


title: 30min: Block, Biological Replicate 3

description: Block 30min


title: Liver cancer tumor, model ID 03-0012


title: 5min: BiC/4AP, Biological Replicate 3

description: Activity 5min


title: 5min: Block, Biological Replicate 3

description: Block 5min


title: CS_wt13

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

country: France

institute: INSERM-UGA

hyb_protocol: Hybridization, staining and detection of cRNAs on Illumina Mouse WG-6 v2 Expression BeadChips were performed according to the manufacturer’s protocol.

scan_protocol: The Illumina I-Scan system was used to scan Expression BeadChips, according to Illumina recommendations.

data_processing: The data were normalised using quantile normalisation.

source_name: adult mouse condensing spermatids

label_protocol: The starting amount of total RNA used for the reactions was 200 nanograms per sample. The Illumina Total Prep RNA Amplification Kit (Applied Biosystems / Ambion, Austin, USA) was used to generate biotinylated, amplified cRNA according to the manufacturer recommendations.

extract_protocol: 0.5-1 μg RNA was reverse transcribed with the SuperScriptTM III First-Strand Synthesis SuperMix (Invitrogen). Total RNA quantification was performed using the Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific Incorporation, Waltham, USA). Integrity of the extracted RNAs was assessed with the Bioanalyzer 2100 and the RNA6000 Nano kit (Agilent Technologies Incorporation, Santa Clara, USA). A RNA integrity number (RIN) greater or equal to 7.00 was achieved for all samples.

tag: genotype (cbp/p300)

value: wild type

value: 7 weeks


title: 30min: BiC/4AP + ActD, Biological Replicate 3

description: ActivityD 30min


title: CS_mut23

value: Cbp/p300 post-meiotic knock down


title: CS_mut21


title: CS_wt18


title: 5min: BiC/4AP + ActD, Biological Replicate 3

description: ActivityD 5min


title: CS_wt17


title: RS_mut11

source_name: adult mouse round spermatids


title: RS_mut9


title: CS_mut22


title: CS_mut24


title: CS_mut20


title: CS_wt15


title: CS_wt16


title: CS_wt14


title: RS_mut12


title: RS_mut10


title: CS_mut19


title: Fresh Frozen Breast Brain Metastasis Tissue BBM_23

tag: tissue

value: Universal reference RNA


title: RS_mut7


title: RS_wt5


title: RS_wt4


title: Control mouse

city: Madrid

first: Simón

last: Méndez-Ferrer

address: Calle Melchor Fernández Almagro, 3

institute: CNIC

description:
Control
Gene expression profiling of bone marrow stromal nestin+ cells isolated 10 weeks after transplantation with control bone marrow cells.

hyb_protocol: The hybridisation cocktail containing fragmented biotin-labeled target DNA was transferred into Affymetrix GeneChip Mouse Gene 1.0 ST Arrays and incubated at 45 degrees on a rotator in a hybridisation oven 640 (Affymetrix) for 17 hours at 60rpm. The arrays were washed and stained on a Fluidics Station 450 by using Hybridisation Wash and Stain Kit (Affymetrix, cat. nu. 900720) using fluidics procedure FS450_0007.

scan_protocol: The GeneChips were processed with an Affymetrix GeneChip Scanner 3000 7G. DAT image files of the microarrays were generated using Affymetrix GeneChip Command Console (AGCC, version 0.0.0.676).

data_processing: Data normalisation was performed using the Robust Multi-array Average (RMA) algorithm. To perform principal component analysis (PCA) comparison with previously published data, GEO data sets were downloaded and pre-processed using the GEOquery Bioconductor package. Normalised data sets were adjusted to the same intensity range, and batch effect correction was performed using ComBat.

source_name: Bone marrow stromal nestin+ cells, control

label_protocol: cDNA target was synthesized, fragmented, biotin-labeled using WT target labeling and Control Reagents (Affymetrix, vat. num. 900652), according to the procedure described in the GeneChip Whole Transcript Sense Target labeling Assay Manual, Version 4 (Affymetrix, Santa Clara, USA). cDNA was fragmented and the resulting fragments of approximately 40-70 nucleoides were monitored with Bioanalyzer using the RNA nano 6000 Chip.

extract_protocol: RNA was obtained using Picopure RNA isolation kit (Arcturus).

tag: genotype/variation

value: Nes-gfp

value: bone marrow CD45- CD31- Ter119- Nes-GFP+ cells


title: slt2 2.5/7 A and B

city: Recife

first: Rodrigo

middle: Mendonça

last: Lucena

state: Pernambuco

address: Av. Jorn. Aníbal Fernandes

department: Genetics

country: Brazil

institute: Federal University of Pernambuco

hyb_protocol: RNA from lab strains BY4741, hog1 and slt2 mutants that had grown in YPD medium pH 7, were labelled with Cy3 and mixed with Cy5-labelled RNA from BY4741, hog1 and slt2 mutants that had grown in YPD medium pH 2.5. Target and reference cRNA samples were mixed and the hybridizations were performed on yeast gene expression 8x15K spots slides (cat. nr. G4813A-016322, Agilent, USA) at 65 ºC for 17 hours at 10 r.pm. in the Microarray Hybridization Oven (cat. nr. G2545A, Agilent, USA).

scan_protocol: The slides were placed into the High-Resolution Microarray Scanner (cat. nr. G2505-60502, Agilent, USA). The fluorescence data were extracted (.txt files) for each spot  by using Scan Control 8.5.1 software (Agilent, USA)

data_processing: Data were then analyzed using specific packages from the R statistical language with the specific LIMMA and MArray  packages. Background correction was done with normexp method. Robust spline and quantile methods were used for normalization within and between arrays, respectively. A list of differentially expressed genes was generated by applying adjusted p-values for multiple tests. Groups of genes with statistical significance (Adj.p<0.05) were utilized.

organism: Saccharomyces cerevisiae

source_name: slt2 2.5 A and B

label_protocol: Synthesis of cDNA and labelling was performed by Two-Color Low Input Quick Amp Labeling Kit (cat. nr. 5190-2306, Agilent, USA), with Two-Color RNA spike-in kit for internal control (cat. nr. 5188-5279, Agilent, USA). For yeast samples, 100 ng of purified RNA was used for labelling.

growth_protocol: Cell from BY4741 strain (EUROSCARF collection) and their derivate mutants hog1∆ and slt2∆ were growth overnight and were transferred to fresh neutral YPD medium (20 g/l glucose, 20 g/l yeast extract and 10 g/l peptone) at 30ºC and 150 rpm in a rotatory shaker  at an initial cell density of OD600 0.1 and cultivated to OD600 0.5.

extract_protocol: total RNA in the lysates was purified by using RNAspin Mini RNA Isolation Kit (cat. nr. 25-0500-71, GE HealthCare, USA) following manufacturer´s instructions and suspended in 25 μl nuclease-free water.

treatment_protocol: The cultures were centrifuged and each one was re-suspended with YPD medium pH 2.5 adjusted with sulfuric acid. After incubation for 1 h at 30°C with orbital agitation (150 rpm), the cells were recovered by centrifugation and immediately used to RNA extraction

value: Lab strain BY4741 (EUROSCARF collection)

tag: developmental stage

value: stress YPD pH 2.5 - sulfuric acid

source_name: slt2 7 A and B


title: RS_wt2


title: RS_wt3


title: RS_wt6


title: hog1 2.5/BY4741 2.5


title: slt2 2.5/BY4741 2.5


title: MPN mouse 1

description:
01_MxCre-JAK2V617F
Gene expression profiling of bone marrow stromal nestin+ cells isolated 10 weeks after transplantation with Mx1-cre;JAK2-617F bone marrow cells.

source_name: Bone marrow stromal nestin+ cells, Mx1-cre;JAK2-V617F

tag: strain/background


title: MPN mouse 2

description:
02_MxCre-JAK2V617F
Gene expression profiling of bone marrow stromal nestin+ cells isolated 10 weeks after transplantation with Mx1-cre;JAK2-617F bone marrow cells.


title: BY4741 2.5/7 A and B

source_name: BY4741 2.5 A and B

source_name: BY4741 7 A and B


title: RS_wt1


title: MPN mouse 3

description:
03_MxCre-JAK2V617F
Gene expression profiling of bone marrow stromal nestin+ cells isolated 10 weeks after transplantation with Mx1-cre;JAK2-617F bone marrow cells.


title: amiEBB1_Apex_rep1

city: Charleston

first: Yordan

middle: S

last: Yordanov

state: IL

address: 600 Lincoln ave

department: Department of Biological Sciences

institute: Eastern Illinois University

description: Gene expression data from apex of amiEBB1

hyb_protocol: Following fragmentation, 12.5 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Poplar Genome Array. GeneChips were washed and stained in the  Affymetrix GeneChip(r) Fluidics Station 450

scan_protocol: Arrays were scanned with an Affymetrix GeneChip(r) Scanner 3000 at 570nm. The Affymetrix eukaryotic hybridization control kit and Poly-A RNA control kit were used to ensure efficiency of hybridization and cRNA amplification. All cRNA was synthesized at the same time. Hybridizations were conducted with one replicate of all times and treatments concurrently. Each array image was visually screened to discount for signal artifacts, scratches or debris.

data_processing: The data were processed with RMAExpress (http://rmaexpress.bmbolstad.com/) using default analysis settings, Quantile normalization and median polish.

organism: Populus tremula x Populus alba

source_name: Apices from amiEBB1 expressing plant

label_protocol: Biotinylated cRNA was prepared according to the 3' IVT Express Affymetrix protocol from 100ng total RNA.

growth_protocol: Greenhouse conditions

extract_protocol: We isolated RNA from about 0.3g tissue. RNA was extracted as previously described (Busov VB,at al, 2003, Plant Physiol 132: 1283-1291) using QIAGEN kits.

treatment_protocol: Apices from amiEBB1 expressing plant about 0.5 cm, was fixed in liquid Nitrogen and stored  at -80oC until RNA extraction.

tag: plant info

value: P. tremula x P. alba INRA 717-IB4

value: Apices


title: 20th week ch M Aorta_29/12_1

city: Bangalore

first: Vrushali

middle: Umakant

last: Deshpande

state: Karnataka

address: No. 258/A, Bommasandra Industrial Area,

department: Molecular Immunology

country: India

institute: Thrombosis Research Institute

description: Gene expression at 20W kept on Chow diet

hyb_protocol: The labeled cRNA samples were hybridized on to a Agilent Custom Whole Genome Mouse 8x60k designed by Genotypic Technology Private Limited (AMADID: 026986). 600ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: Slides were scanned using the Agilent Microarray Scanner G2505C at 3 micron resolution

data_processing: Data extraction from Images was done using Agilent Feature Extraction software Version 10.5

source_name: ascending aorta

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP (Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Invitrogen) according to the manufacturer protocol. Total RNA integrity was assessed using RNA 6000 Nano Lab Chip on the 2100 Bioanalyzer (Agilent, Palo Alto, CA) following the manufacturer’s protocol. Total RNA purity was assessed by the NanoDrop® ND-1000 UV-Vis Spectrophotometer (Nanodrop technologies, Rockland, USA). We considered RNA to be good quality based on the rRNA 28S/18S ratios and RNA integrity number (RIN

treatment_protocol: Double knockout mice were kept on High fat diet and chow diet for 0, 4, 8, 14 and 20 weeks

value: ascending aorta with atherosclerotic lesion

tag: gender

value: Male

tag: diet

value: chow diet


title: 20th week_HF M Aorta_28/12

description: Gene expression at 20W kept on High fat diet

value: high fat diet


title: Te_3d_rep 1

city: Potsdam-Golm

first: Majken

last: Pagter

address: Am Mühlenberg 1

country: Germany

institute: Max Planck Intitute of Molecular Plant Physiology

description: Gene expression data from detached leaves of cold acclimation Arabidopsis Tenela sub-zero acclimated for 3d at -3°C

hyb_protocol: Hybridization solution was prepared according to Affymetrix´GeneChip Expression Analysis Technical Manual. The final cRNA concentration was 60 ng/µl. Hybridization was performed for 16-18 h at 45°C and 60 rpm in a rotating hybridization oven (Hybridization Oven 640, Affymetrix). Washing and staining was performed with a fluidics station (GeneChip Fluidics Station 450, Affymetrix), controlled by GCOS v1.4.

scan_protocol: Scanning was performed with the geneChip Scanner 3000 7G (Affymetrix), controlled by GCOS v1.4.

data_processing:
The raw ATH1 hybridization intensities were imported into the Robin software to perform quality assessment and data normalization and to identify genes, which were differentially expressed between cold acclimated samples and samples subjected to different durations of sub-zero acclimation. Principal components analysis (PCA) indicated that one of the Col-0 replicates sub-zero acclimated for 8 h or 3 d (replicate 3 i both cases) were outliers. Hence, these replicates were excluded from further analysis. Data normalization was performed using the RMA method. Statistical analysis of differential gene expression between cold acclimated and sub-zero acclimated samples was carried out using a linear model-based approach, applying a 0.05 P-values and log2 fold ratio greater than 1 and lower than -1 cut-off. P-values were corrected for multiple testing using the Benjamin-Hochberg correction.
Expression estimated for each each probe on each chip after normalization.

source_name: Tenela sub-zero acclimated at -3° for 3 days, replicate 1

label_protocol: Biotin-labelled aRNA was synthesised from 1 µg total RNA using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Ambion, Carlsbad, CA, USA)

growth_protocol: Seeds from the Arabidopsis thaliana accessions Columbia-0, Rschew and Tenela were sown in soil and grown in the greenhouse at 16-h day length, with light supplementation to reach at least 200 µmol m-2 s-1, and a temperature of 20°C during the day, 18°C during the night until 42 days after sowing.

extract_protocol: Total RNA was isolated from a pool of three leaves from three different plants for each sample, using the RNeasy Mini Kit (Qiagen)

treatment_protocol: For cold acclimation, plants were transferred to a 4°C growth cabinet at 16-h day length with 90 µmol m-2 s-1 for an additional 14 days. For sub-zero acclimation, detached leaves from cold acclimated plants were transferred into glass tubes containing 200 µl of distilled water and placed in a temperature-controlled silicon oil bath at -3°C in darkness. In the absence of active ice nucleation, the leaves stayed supercooled during the entire incubation period. Leaves of cold acclimated plants and leaves sub-zero acclimated for 8h, 1d or 3d were collected for RNA extraction and hybridization on Affymetrix ATH1 microarrays.

tag: accession

value: Tenela

tag: stress

value: sub-zero acclimated at -3°

value: 3 days

value: Leaves


title: hog1 2.5/7 A and B

source_name: hog1 2.5 A and B

tag: strain

source_name: hog1 7 A and B


title: Te_3d_rep 3

source_name: Tenela sub-zero acclimated at -3° for 3 days, replicate 3

tag: time


title: F_Ch 20WF

value: Female

tag: age


title: Te_1d_rep 3

description: Gene expression data from detached leaves of cold acclimation Arabidopsis Tenela sub-zero acclimated for 1d at -3°C

source_name: Tenela sub-zero acclimated at -3° for 1 day, replicate 3

value: 1 day


title: Te_3d_rep 2

source_name: Tenela sub-zero acclimated at -3° for 3 days, replicate 2


title: 20W_HFF

description: Gene expression at 8W kept on High fat diet


title: 14th week HF M Aorta 2_1

description: Gene expression at 14W kept on High fat diet


title: amiEBB1_Apex_rep2


title: F_Ch 4WF

description: Gene expression at 4W kept on chow diet


title: 8W_cHF

description: Gene expression at 8W kept on Chow diet


title: Te_1d_rep 1

source_name: Tenela sub-zero acclimated at -3° for 1 day, replicate 1


title: 4WCh_M1_30/11

description: Gene expression at 4W kept on chow diet


title: 14th week_chow M1 Aorta_22/12_1

description: Gene expression at 14W kept on Chow diet


title: Te_8h_rep 3

description: Gene expression data from detached leaves of cold acclimation Arabidopsis Tenela sub-zero acclimated for 8h at -3°C

source_name: Tenela sub-zero acclimated at -3° for 8 hours, replicate 3

value: 8 hours


title: Te_1d_rep 2

source_name: Tenela sub-zero acclimated at -3° for 1 day, replicate 2


title: 8th week HF M Aorta_3/1_2


title: Te_8h_rep 1

source_name: Tenela sub-zero acclimated at -3° for 8 hours, replicate 1


title: 0 week_Aorta M_chow_2

description: Gene expression at 0W kept on chow diet


title: 8th week_ch M Aorta_1

description: Gene expression at 8W kept on Chow diet


title: 4W_HFF

description: Gene expression at 4W kept on High fat diet


title: Te_CA_rep 2

description: Gene expression data from leaves of intact Arabidopsis Tenela cold acclimation at 4°C for two weeks

source_name: Tenela cold acclimated at 4° for two weeks, replicate 2

value: cold acclimated at 4°

value: two weeks


title: Te_CA_rep 3


title: F_Ch ZERO

description: Gene expression at 0W kept on chow diet


title: 8W_HFF

description: Gene expression at 4W kept on High Fat diet


title: 4W_A_HF_M_Aorta_4W_29/11


title: Te_CA_rep 1

source_name: Tenela cold acclimated at 4° for two weeks, replicate 1


title: Te_8h_rep 2

source_name: Tenela sub-zero acclimated at -3° for 8 hours, replicate 2


title: 26972c GmbHLHM1 rep2

city: Urrbrae

first: Brent

middle: N

last: Kaiser

state: SA

address: Waite Campus

department: School of Agriculture Food and Wine

country: Australia

institute: The University of Adelaide

hyb_protocol: RNA hybridization to the Affymetrix GeneChip Yeast Genome 2.0 Arrays was performed by the Ramaciotti Centre for Gene Function Analysis (University of New South Wales, Sydney, Australia).

scan_protocol: Scanning was performed by the Ramaciotti Centre for Gene Function Analysis (University of New South Wales, Sydney, Australia.

data_processing: Raw CEL data files were imported into GeneSpring software and pre-processed using Robust Multichip Average (RMA) algorithm where the variation between the chips was normalized at the probe set level to obtain the ratio of expression to the median expression for each sample.

source_name: 26972c GmbHLHM1

label_protocol: RNA labeling was performed by the Ramaciotti Centre for Gene Function Analysis (University of New South Wales, Sydney, Australia).

growth_protocol: Starter yeast cultures were initially prepared to ensure uniform cell growth. The 26972c yeast strain (mep1-1, mep2∆, Mep3, ura-) harboring GmbHLHm1-pYES3 or the pYES3 empty vector was inoculated in 20 ml of Grenson’s minimal yeast media supplemented with 2% w/v glucose and 0.1% (w/v) L-proline. The cultures were grown in 50 ml falcon tubes and incubated at 28°C and shaken at 200 rpm for 24 h. Ten replicate sterile 50 ml falcon tubes containing identical media were spiked with 1 ml of each yeast starter culture and incubated at 28°C at 200 rpm for 2 days. Log-phase cells were pelleted, washed in sterile Milli Q H2O twice and then resuspended in 20 ml of Grenson’s minimal yeast media supplemented with 2% (w/v) galactose and 0.5 mM (NH4)2SO4. The cells were incubated at 28°C and shaken at 200 rpm. The cell cultures were harvested after 12 h of incubation and washed once in 20 ml of ice-cold sterile Milli Q water.

extract_protocol: Total RNA was extracted using hot acidified phenol according to: Collart MA & Oliviero S (2001) Preparation of yeast RNA. Current protocols in molecular biology:13.12. 11-13.12. 15.

treatment_protocol: 12 hour exposure to 1 mM ammonium and 2% galactose

tag: strain/genotype

value: ammonium transport mutant (26972c)

tag: transfection

value: pYES3 containing GmbHLHm1


title: Rsch_3d_rep 3

description: Gene expression data from detached leaves of cold acclimation Arabidopsis Rschew sub-zero acclimated for 3d at -3°C

source_name: Rschew sub-zero acclimated at -3° for 3 days, replicate 3

value: Rschew


title: 26972c GmbHLHM1 rep1


title: Rsch_3d_rep 2

source_name: Rschew sub-zero acclimated at -3° for 3 days, replicate 2


title: Rsch_1d_rep 2

description: Gene expression data from detached leaves of cold acclimation Arabidopsis Rschew sub-zero acclimated for 1d at -3°C

source_name: Rschew sub-zero acclimated at -3° for 1 day, replicate 2


title: Rsch_1d_rep 3

source_name: Rschew sub-zero acclimated at -3° for 1 day, replicate 3


title: 26972c pYES3 rep1

value: empty vector control (pYES3)


title: 26972c pYES3 rep2


title: 26972c pYES3 rep3


title: 26972c GmbHLHM1 rep3


title: Rsch_1d_rep 1

source_name: Rschew sub-zero acclimated at -3° for 1 day, replicate 1


title: Rsch_8h_rep 2

description: Gene expression data from detached leaves of cold acclimation Arabidopsis Rschew sub-zero acclimated for 8h at -3°C

source_name: Rschew sub-zero acclimated at -3° for 8 hours, replicate 2


title: Rsch_8h_rep 3

source_name: Rschew sub-zero acclimated at -3° for 8 hours, replicate 3


title: Rsch_CA_rep 2

description: Gene expression data from leaves of intact Arabidopsis Rschew cold acclimation at 4°C for two weeks

source_name: Rschew cold acclimated at 4° for two weeks, replicate 2


title: No stimulation cell body compartment

description: 3 replicate coverslips pooled

hyb_protocol: The nylon filters were prehybridized for 2 h at 60C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham Bioscience) and then hybridized for 17 h at 60C with the denatured probes

scan_protocol: Filters were scanned using Storm phosphoimager

data_processing: Scanned images processed using phosphoimager software

source_name: DRG Cell culture

label_protocol: 3 ug of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 100 mCi of [33P]dCTP (Amersham Bioscience, Piscataway, NJ)

growth_protocol: Cultures were grown for 3 weeks prior to stimulation

treatment_protocol: Stimulation was for 2 hours

value: NIH Swiss

value: Embryonic day 13.5

tag: cell type

value: Dorsal Root Ganglion (DRG)


title: RS_mut8

source_name: adult mouse round spermatids

value: Cbp/p300 post-meiotic knock down

value: 7 weeks


title: Rsch_CA_rep 1

source_name: Rschew cold acclimated at 4° for two weeks, replicate 1


title: CT26_macrophage_coculture_rep2

city: Bronx

first: Leonard

middle: H

last: Augenlicht

state: NY

address: 1300 Morris Park Ave

department: Medicine and Cell Biology

institute: Albert Einstein College of Medicine

description: 2nd CT26+RAW

hyb_protocol: Fragmented cRNA was hybridized on the Affymetrix Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: cel files were processed using RMA with the R/Bioconductor, affy package.  Replicates were averaged, and difference on the log scale calculated between CT26 expression and expression in CT26 cells cultured with RAW macrophages. This log difference was expressed as fold change on a linear scale for publication figures.

label_protocol: Biotinylated cRNA were prepared from 5 ug total RNA following the procedures in the Affymetrix Expression Analysis Technical Manual.

growth_protocol: Routinely cultured in RPMI 1640 medium

extract_protocol: CT26 cells were digested from plates using Trypsin/EDTA and total RNA isolated with TRIzol. RAW cells were directly disrupted in TRIzol from transwell inserts and total RNA isolated. TRIzol was from Invitrogen. RNA was cleaned up by RNeasy Mini Kit from Qiagen.

treatment_protocol: CT26 cells (1×104 cells in 1.5ml per well) and RAW cells (1×104 cells in 0.5ml per insert) were added to 12 well plates and transwell inserts (3401, Corning, Lowell, MA), respectively. The inserts were placed into the wells 8 hours after seeding the cells, a period to allow cell attachment.  In this transwell co-culture system, the two cell types can  exchange soluble factors although direct contact is eliminated.

tag: cell line

value: mouse colon tumor epithelial cells

tag: culture condition

value: cocultured with macrophage RAW264


title: CT26_macrophage_coculture_rep1

description: 1st CT26+RAW

source_name: CT26 cells cultured with RAW macrophages


title: CT26_cells_alone_rep2

description: 2nd CT26 alone

source_name: CT26 cultured cells

value: cultured alone


title: RAW_macrophage_alone_rep2

description: 2nd RAW alone

source_name: RAW cultured macrophages

value: mouse macrophage cells


title: Rsch_8h_rep 1

source_name: Rschew sub-zero acclimated at -3° for 8 hours, replicate 1

value: sub-zero acclimated at -3°

tag: tissue

value: Leaves


title: Rsch_CA_rep 3

value: cold acclimated at 4°


title: CT26_cells_alone_rep1

description: 1st CT26 alone


title: RAW_macrophage_CT26_coculture_rep1

description: 1st RAW+CT26

source_name: RAW macrophages cultured with CT26 cells

value: cocultured with CT26 cells


title: DRG Cell Bodies 2 hours activity

description: 3 replicate coverslips pooled


title: No stimulation axons only

description: 3 replicate coverslips pooled


title: RAW_macrophage_CT26_coculture_rep2

description: 2nd RAW+CT26


title: Rsch_3d_rep 1

source_name: Rschew sub-zero acclimated at -3° for 3 days, replicate 1

value: 3 days


title: DRG Axons Only 2 hours activity

description: 3 replicate coverslips pooled


title: 60min: BiC/4AP + ActD, Biological Replicate 2

description: 60min- #92-ActivityD

source_name: Hippocampal cell culture

value: Sprague Dawley

value: Embryonic day 18.5

value: hippocampal neurons


title: 60min: BiC/4AP, Biological Replicate 2

description: 60min- #91-Activity


title: 30min: BiC/4AP, Biological Replicate 2

description: 30min- #88-Activity


title: 30min: BiC/4AP + ActD, Biological Replicate 2

description: 30min- #87-ActivityD


title: Col_3d_rep 1

description: Gene expression data from detached leaves of cold acclimation Arabidopsis Columbia-0 sub-zero acclimated for 3d at -3°C

source_name: Columbia-0 sub-zero acclimated at -3° for 3 days, replicate 1


title: 60min: Block + ActD, Biological Replicate 2

description: 60min- #89-BlockD


title: 60min: Block, Biological Replicate 2

description: 60min- #90-Block


title: RAW_macrophage_alone_rep1

description: 1st RAW alone


title: Col_3d_rep 2

source_name: Columbia-0 sub-zero acclimated at -3° for 3 days, replicate 2


title: 30min: Block + ActD, Biological Replicate 2

description: 30min- #86-BlockD


title: 5min: BiC/4AP, Biological Replicate 2

description: 5min- #83-Activity


title: Col_1d_rep 1

description: Gene expression data from detached leaves of cold acclimation Arabidopsis Columbia-0 sub-zero acclimated for 1d at -3°C

source_name: Columbia-0 sub-zero acclimated at -3° for 1 day, replicate 1

value: 1 day


title: 5min: BiC/4AP + ActD, Biological Replicate 2

description: 5min- #82-ActivityD


title: Col_1d_rep 3

source_name: Columbia-0 sub-zero acclimated at -3° for 1 day, replicate 3


title: 60min: BiC/4AP, Biological Replicate 1

description: 77-Activity 60min


title: 60min: Block, Biological Replicate 1

description: 80-Block 60min


title: 60min: BiC/4AP + ActD, Biological Replicate 1

description: 79-ActivityD 60min


title: Col_8h_rep 2

description: Gene expression data from detached leaves of cold acclimation Arabidopsis Columbia-0 sub-zero acclimated for 8h at -3°C

source_name: Columbia-0 sub-zero acclimated at -3° for 8 hours, replicate 2

value: 8 hours


title: 60min: Block + ActD, Biological Replicate 1

description: 78-BlockD 60min


title: Col_1d_rep 2

source_name: Columbia-0 sub-zero acclimated at -3° for 1 day, replicate 2


title: 30min: BiC/4AP + ActD, Biological Replicate 1

description: 76-ActivityD 30min


title: 30min: Block, Biological Replicate 2

description: 30min- #85-Block


title: 30min: Block + ActD, Biological Replicate 1

description: 75-BlockD 30min


title: 30min: Block, Biological Replicate 1

description: 73-Block 30min


title: Col_CA_rep 2

description: Gene expression data from leaves of intact Arabidopsis Columbia-0 cold acclimation at 4°C for two weeks

source_name: Columbia-0 cold acclimated at 4° for two weeks, replicate 2

value: two weeks


title: 5min: BiC/4AP + ActD, Biological Replicate 1

description: 70-ActivityD 5min


title: 30min: BiC/4AP, Biological Replicate 1

description: 74-Activity 30min


title: 5min: Block + ActD, Biological Replicate 2

description: 5min- #81-BlockD


title: Col_8h_rep 1

source_name: Columbia-0 sub-zero acclimated at -3° for 8 hours, replicate 1


title: 5min: Block, Biological Replicate 2

description: 5min- #84-Block


title: Col_CA_rep 3


title: 5min: Block, Biological Replicate 1

description: 72-Block 5min


title: IL-10-deficient_Uninfected

city: La Jolla

first: Lars

last: Eckmann

address: 9500 Gilman Drive

department: Gastroenterology

institute: University of San Diego

description: Gene expression in whole colonic tissue from uninfected IL10-deficient mice

hyb_protocol: 1650ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarray Kit, 4x44K (G4122F) 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). 5 µm scanning in green at 10% and 100% PMT

data_processing: the protocol used for extraction was GE1_107_Sep09. Version 10.7.3.1. of feature extraction. The data were normalized using the multi-loess method described in this paper: Microarray truths and consequences, R. Sasik, C. H. Woelk and J. Corbeil, J. Mol. Endocrinology, 33, 1 (2004)

source_name: IL-10-deficient_Uninfected_whole colon

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150ng RNA using the Quick Amplification 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: Total RNA (isolated with TRIzol reagent) was prepared from whole colonic tissue of WT and IL-10-/- mice before or 2 weeks after infection with Citrobacter rodentium.

treatment_protocol: 8-wk-old mice were infected by oral gavage with 200 µl of Citrobacter rodentium strain DBS100  (5 x 10^8 CFU/mouse).

tag: strain background

tag: genotype/variation

value: IL-10-/-; IL-10 deficient

value: female

value: 10 weeks

tag: infected  with

value: none (uninfected control)

value: whole colon


title: IL-10-deficient_Infected

description: Gene expression in whole colonic tissue from infected IL-10-deficient mice

source_name: IL-10-deficient_Infected_whole colon

value: 200 µl of C. rodentium DBS100  (5 x 10^8 CFU/mouse)


title: 5min: Block + ActD, Biological Replicate 1

description: 71-BlockD 5min


title: C57BL/6_Infected

description: Gene expression in whole colonic tissue from infected C57BL/6 mice

source_name: WT_infected_whole colon

value: wild type


title: C57BL/6_Uninfected

description: Gene expression in whole colonic tissue from uninfected C57BL/6 mice

source_name: WT_Uninfected_whole colon


title: 5min: BiC/4AP, Biological Replicate 1

description: 69-Activity 5min


title: Col_CA_rep 1

source_name: Columbia-0 cold acclimated at 4° for two weeks, replicate 1

value: Leaves


title: monocytes_SLE_patient3_rep1

city: Cordoba

first: Rosario

last: Lopez Pedrera

address: Avda. Menendez Pidal s/n

institute: IMIBIC

description:
Sample name: 10NG216
Gene expresion of monocytes from SLE patient

hyb_protocol: 1,5 ug of Cy3-labelled cRNA (specific activity >10,0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25 x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55ul of 2x Hi-RPM Agilent hybridization buffer was added to the fragmentation mixture and hybridized to 4x44k Agilent Whole Human Genome Oligo Microarrays (AMADID 14850) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were dissasembled in GE Wash buffer 1 (Agilent) and 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 immediatly by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44 array slides (Scan Area 61x21,6mm, Scan resolution 5 um, Dye channel is set to Green and Green PMI gain is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10,1 (Agilent) using default parameters (protocol GE1-v1_101 and Grid: 014850_D_F_20120130) to obtain bacground subtracted and spatially detrended Processes Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Data analysis (performed with GeneSpring GX version 10.0 -Agilent Technologies-) compared each disease (primary antiphospholipid syndrome (APS), systemic lupus erythematosus (SLE), and lupus with antiphospholipid syndrome or secondary antiphospholipid syndrome (SAPS)) with healthy donors or with the other two diseases. See supplementary files linked to Series record.

source_name: Monocytes from SLE patient donor 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500ng RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) 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: Total RNA from monocytes was extracted using TRIzol reagent (Invitrogen)  according to the manufacturer's instructions.

value: Monocytes

tag: disease state

value: Systemic lupus erythematosus


title: monocytes_SLE_patient2_rep1

description:
Sample name: 09NG476
Gene expresion of monocytes from SLE patient

source_name: Monocytes from SLE patient donor 2


title: lung_O3_24hpost_rep4

city: Denver

first: Kelsa

last: Gabehart

state: CO

address: 1400 Jackson St

department: Pediatrics

institute: National Jewish Health

hyb_protocol: Labeled cRNA was fragmented and 1.65 micrograms from each sample were hybridized to each array using the Hybridization Kit (Agilent Technologies). Hybridization was performed at 65˚C for 17 h with constant rotation. Arrays were washed in a two-step process using buffers from Agilent Technologies.

scan_protocol: Arrays were scanned on the Agilent DNA Micoarray G2505B scanner (Agilent Technologies) using one color scan setting for 1x44k array slides.

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

source_name: lung, ozone, 24 h post, replicate 4

label_protocol: Labeling was performed using the Quick-Amp Labeling Kit (5190-0442, Agilent Technologies). First strand cDNA was transcribed from 600-1000 ng of total RNA using a T7-Oligo(dT) promoter primer. Subsequent synthesis of cRNA generated between 7.0 and 22.0 ng of Cy-3 labeled cRNA. Unincorporated nucleotides were removed from the labeled cRNA using RNeasy spin columns (Qiagen). Quality control parameters (cRNA yield and specific activity of labeled RNA) were assessed using the NanoDrop 1000 (Thermo Scientific) as recommended by Agilent Technologies.

growth_protocol: Mice were bred and maintained under specific pathogen-free conditions in the animal facility of the Biological Resource Center at National Jewish Health (Denver, CO).

extract_protocol: Total RNA was isolated from whole lung using TRIzol RNA isolation reagent (Invitrogen, Carlsbad, CA) and cleaned up using miRCURY RNA Isolation Kit (Exiqon, Woburn, MA), following the manufacturers’ instructions. RNA quantity was determined with a NanoDrop ND-100 Spectrophotometer (NanoDrop, Wilington, DE). RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  RNA integrity values ranged between 8.6-9.1, and 28S/18S ratios ranged between 1.0-1.4.

treatment_protocol: Three-day old BALB/c mice were exposed to ozone (1000 parts per billion) or filtered normal air for 3 h. Six and 24 h after completion of exposure, the mice were euthanized by intraperitoneal injection of pentobarbital (Nembutal®, 100 mg/kg body weight) and exsanguinated by severing the aorta. The lungs were isolated immediately after and stored in RNAlater for 24 h at 4˚C, before RNA extraction.

value: lung

value: BALB/c

value: 3 days old

tag: exposure

value: 1000 ppb Ozone 3 h

tag: time post exposure


title: lung_FA_24hpost_rep4

source_name: lung, filtered air, 24 h post, replicate 4

value: Filtered Air


title: THP1_VitD3

data_processing: cel files were processed using RMA with the R/Bioconductor, affy package.  Differences in expression between samples were calculated on a log scale, and converted to fold change on a linear scale for supplemental publication figures.

source_name: THP1 cell treated with Vitamin D3

growth_protocol: HCT116 and Hke-3 cells were cultured in MEM, 10%FBS and THP1 macropahges were cultured in RPMI, 10%FBS.

extract_protocol: cRNA was prepared from 5Ug total RNA.

treatment_protocol: Tumor cells were co-cultured with macropahges and were treated with VitD3 for 24hours.

value: macropahges

tag: cultured with

value: VitD3 for 24h


title: monocytes_SLE_patient1_rep1

description:
Sample name: 09NG456
Gene expresion of monocytes from SLE patient

source_name: Monocytes from SLE patient donor 1


title: monocytes_lupus_with_APS_patient5_rep1

description:
Sample name: 09NG465
Gene expresion of monocytes from Lupus with APS patient

source_name: Monocytes from lupus with APS patient donor 5

value: Lupus with Antiphospholipid syndrome


title: monocytes_lupus_with_APS_patient6_rep1

description:
Sample name: 09NG475
Gene expresion of monocytes from Lupus with APS patient

source_name: Monocytes from lupus with APS patient donor 6


title: lung_FA_24hpost_rep3

source_name: lung, filtered air, 24 h post, replicate 3


title: monocytes_lupus_with_APS_patient4_rep1

description:
Sample name: 09NG464
Gene expresion of monocytes from Lupus with APS patient

source_name: Monocytes from lupus with APS patient donor 4


title: monocytes_control1_rep1

description:
Sample name: 09NG449
Gene expresion of monocytes from healthy donor

source_name: Monocytes from healthy donor 1

value: Healthy


title: lung_FA_24hpost_rep1

source_name: lung, filtered air, 24 h post, replicate 1


title: Hke3_THP1_coculture

source_name: Hke3_co-cultured with THP1 macrophages

value: Colorectal carcinoma cells

value: THP1 macrophages


title: monocytes_control3_rep1

description:
Sample name: 10NG210
Gene expresion of monocytes from healthy donor

source_name: Monocytes from healthy donor 3


title: 5KB3-6

city: Hong Kong

first: Kenneth

middle: R

last: Boheler

address: 5 Sassoon Road

institute: The University of Hong Kong

description: Replica 5 Gene expression data from KB3 human induced pluripotent stem cells (origin Foreskin Fibroblasts) - passage number 15 (plate #556)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using log2 transformation and quantile normalization

source_name: Human induced pluripotent stem cell line KB3 (prepared as part of this paper)

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

growth_protocol: Human embryonic stem cells (hESCs, line H9) or human induced pluripotent stem cells (hiPSC, line KB3) were passaged with dispase and plated onto matrigel coated dishes and cultivated in the presence of mTeSR1 media for 5-8 days, until the cultures were approximately (70-80%) confluent. mTeSR1 media was changed daily.  Cells were then washed with DPBS (no Mg, no Ca) and used for subsequent RNA extraction.

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

tag: treatment

value: KB3 hiPSC cultivated in mTeSR1 and on Matrigel coated plates


title: lung_FA_24hpost_rep2

source_name: lung, filtered air, 24 h post, replicate 2

tag: strain


title: 1KB3 REPEAT

description: Technical Replica 1 repeat Gene expression data from KB3 human induced pluripotent stem cells (origin Foreskin Fibroblasts) - passage 13 (plate # 530)


title: THP1_alone

description: THP1 alone

source_name: THP1 cell_no treatment

value: none (cultured alone)


title: lung_O3_24hpost_rep3

source_name: lung, ozone, 24 h post, replicate 3


title: Hke3_VitD3

source_name: Hke3 cells_no treatment


title: Hke3_THP1_coculture_VitD3

source_name: Hke3_co-cultured with THP1 macrophages and Vit D3

value: THP1 macrophages and Vitamin D3


title: 4KB3-8

description: Replica 4 Gene expression data from KB3 human induced pluripotent stem cells (origin Foreskin Fibroblasts) - passage 15 (plate #558)


title: monocytes_APS_patient9_rep1

description:
Sample name: 09NG477
Gene expresion of monocytes from APS patient

source_name: Monocytes from APS patient donor 9

value: Antiphospholipid syndrome


title: monocytes_control2_rep1

description:
Sample name: 10NG209
Gene expresion of monocytes from healthy donor

source_name: Monocytes from healthy donor 2

value: Monocytes


title: lung_O3_24hpost_rep2

source_name: lung, ozone, 24 h post replicate 2


title: lung_O3_24hpost_rep1

source_name: lung, ozone, 24 h post, replicate 1


title: 2KB3

description: Replica 2 Gene expression data from KB3 human induced pluripotent stem cells (origin Foreskin Fibroblasts) - passage 14 (Plate #539)


title: 3KB3

description: Replica 3 Gene expression data from KB3 human induced pluripotent stem cells (origin Foreskin Fibroblasts) - passage 11 (plate number appears to be #526)


title: 1-H9 REPEAT

description: Technical Replica 1 repeat - Gene expression data from H9 human embryonic stem cells (WiCell) (plate #543)

source_name: Human embryonic stem cell line H9 - WiCell

value: H9 hESC cultivated in mTeSR1 and on Matrigel coated plates


title: 1KB3

description: Replica 1 Gene expression data from KB3 human induced pluripotent stem cells (origin Foreskin Fibroblasts) passage 13 (Plate #530)


title: lung_FA_6hpost_rep4

source_name: lung, filtered air, 6 h post, replicate 4

value: lung

value: 6 h


title: monocytes_APS_patient8_rep1

description:
Sample name: 09NG474
Gene expresion of monocytes from APS patient

source_name: Monocytes from APS patient donor 8


title: HCT116_THP1_coculture_VitD3

source_name: HCT116_co-cultured with THP1 macrophages and Vit D3


title: monocytes_APS_patient7_rep1

description:
Sample name: 09NG467
Gene expresion of monocytes from APS patient

source_name: Monocytes from APS patient donor 7


title: lung_FA_6hpost_rep3

source_name: lung, filtered air, 6 h post, replicate 3

value: BALB/c

value: 3 days old


title: HCT116_THP1_coculture

source_name: HCT116_co-cultured with THP1 macrophages


title: lung_O3_6hpost_rep4

source_name: lung, ozone, 6 h post, replicate 4

value: 1000 ppb Ozone 3 h


title: lung_O3_6hpost_rep3

source_name: lung, ozone, 6 h post, replicate 3


title: HCT116_alone

description: HCT116 alone

source_name: HCT116_no treatment


title: Hke3_alone

description: Hke3 alone


title: 5H9

description: Replica 5 Gene expression data from H9 human embryonic stem cells (WiCell) - passage 50 (plate #547)


title: 2H9

description: Replica 2 Gene expression data from H9 human embryonic stem cells (WiCell) - passage 46 (plate # 521)


title: 4H9

description: Replica 4 Gene expression data from H9 human embryonic stem cells (WiCell) - passage 49 (pooled plates #541+#542)


title: lung_FA_6hpost_rep2

source_name: lung, filtered air, 6 h post, replicate 2

value: Filtered Air


title: Fresh BM

status: Public on Mar 11 2014

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

institute: Nanjing University

description: without GM-CSF and IL-6 treatment

data_processing: Data were analyzed using RQ Manager Software version 1.2 and 7900 Sequence Detection System 2.4 (Applied Biosystems). For the normalization it uses MammU6 as endogenous control miRNA.

label: FAM

source_name: bone marrow

growth_protocol: BM cells were cultured in RPMI1640 medium supplemented with 2 mM L-glutamine, 10mM HEPES, 20µM 2-mercaptoethanol, 150 U/ml streptomycin, 200 U/ml penicillin and 10% FBS   Cells were cultured at 37°C in 5% CO2-humidified atmosphere

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: BM cells were treated with 40 ng/ml GM-CSF and 40 ng/ml IL-6  for 4 days

value: without GM-CSF and IL-6 treatment


title: SLE_treated_patient5_rep1

description: Gene expression after treatment with Fluvastatin

data_processing: The scanned images were analyzed with Feature Extraction Software 10,1 (Agilent) using default parameters (protocol GE1-v1_101 and Grid: 014850_D_F_20120130) to obtain bacground subtracted and spatially detrended Processes Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Monocytes from SLE patients after fluvastatin treatment

treatment_protocol: Twenty seven SLE patients were given 20mg/day fluvastatin for one month. Blood samples were obtained before the starting of the treatment and at the end of treatment. Monocytes were isolated by immunomagnetic depletion of non-monocytes.Complementary RNAs from monocyte-RNA isolated of six SLE patients (four before treatment and two after treatment) were prepared for hybridization in an Agilent G4112F platform (Whole human Genome microarray 44K) using the One-color gene expression system (Agilent technologies).

tag: gender

value: Female


title: HCT116_VitD3

description: HCT116 +D3

source_name: HCT116 treated with Vitamin D3

value: VitD3 for 24h


title: SLE_treated_patient6_rep1

tag: age


title: SLE_untreated_patient4_rep1

description: Gene expression before treatment

source_name: Monocytes from SLE patients without treatment

value: Male


title: 3H9-4

description: Replica 3 Gene expression data from H9 human embryonic stem cells (WiCell) - passage 49 (plate number 544)


title: SLE_untreated_patient3_rep1

description: Gene expression before treatment


title: Induced BM

description: with GM-CSF and IL-6 treatment

value: with GM-CSF and IL-6 treatment


title: lung_FA_6hpost_rep1

source_name: lung, filtered air, 6 h post, replicate 1


title: Reference_DASL_P0 rep2

first: Maggie

last: Chow

address: 8110 La Jolla Shores Dr. Ste 201

department: Neuroscience

institute: NIH-UC San Diego Autism Center of Excellence

description: Reference RNA

data_processing: Data not normalized

source_name: Stratagene Universal Reference pooled RNA

label_protocol: DASL- and IVT-based protocols

extract_protocol: Ambion MELT kit for frozen brain samples and Roche High Pure FFPE RNA Micro Kit for formalin fixed samples

tag: assay

value: DASL

tag: heat treatment

value: Heating at 95C for 0 min


title: SLE_untreated_patient1_rep1

description: Gene expression before treatment


title: lung_O3_6hpost_rep2

source_name: lung, ozone, 6 h post replicate 2


title: lung_O3_6hpost_rep1

source_name: lung, ozone, 6 h post, replicate 1


title: Reference_DASL_P30 rep2

description: Reference RNA

value: Stratagene Universal Reference pooled RNA

value: Heating at 95C for 30 min


title: Reference_DASL_P10 rep1

description: Reference RNA

value: Heating at 95C for 10 min


title: 1-H9-3

description: Replica 1 Gene expression data from H9 human embryonic stem cells (WiCell), passage 49 (plate #543)

source_name: Human embryonic stem cell line H9 - WiCell

value: H9 hESC cultivated in mTeSR1 and on Matrigel coated plates


title: Reference_DASL_B25+P75 rep1

description: Reference RNA

source_name: Ambion FirstChoice Human Brain Reference and Stratagene Universal Reference pooled RNA

value: 25% Brain 75% Pooled


title: Reference_DASL_B75+P25 rep1

description: Reference RNA

value: 75% Brain 25% Pooled


title: Reference_DASL_B25+P75 rep2

description: Reference RNA


title: Reference_DASL_B75+P25 rep2

description: Reference RNA


title: Reference_DASL_P60 rep1

description: Reference RNA

value: Heating at 95C for 60 min


title: Reference_DASL_B60 rep2

description: Reference RNA

source_name: Ambion FirstChoice Human Brain Reference RNA

value: brain


title: Reference_DASL_P0 rep1

description: Reference RNA


title: Reference_DASL_P10 rep2

description: Reference RNA


title: Reference_DASL_P60 rep2

description: Reference RNA


title: Reference_DASL_B30 rep2

description: Reference RNA


title: Reference_DASL_B60 rep1

description: Reference RNA