title: mutant_with TNF_rep3

city: Portland

first: Grover

middle: C

last: Bagby

state: OR

address: 3181 SW Sam Jackson Park Rd.

department: Dept. of Medicine

institute: Oregon Health & Science University

hyb_protocol: The arrays were hybridized in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) for 18 hours at 45 degrees C, followed by washing, staining with streptavidin-phycoerythrin (SAPE; Molecular Probes, Eugene, OR), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs, Burlingame, CA), and a final staining with SAPE. The staining and washing were performed using two GeneChip Fluidic Station 450s (Affymetrix, Santa Clara, CA) using the FS450_0004 Affymetrix fluidics script. Hybridization date: 01/28/08; Array lot: 4035270

scan_protocol: The distribution of fluorescent material on the processed array was determined using the Affymetrix GS300 Scanner with the 7G upgrade.  The array image scan was processed using Affymetrix Microarray Suite, version 5.0 (MAS 5.0), which resulted in the generation of raw, probe level data in the CEL file format.

data_processing: The data were processed by GeneSifter software using Robust Multichip Analysis (RMA) that includes a background correction, quantile normalization, and median polish as summarization.

source_name: c-Kit+Sca-1+Lin- bone marrow cells from Fancc mutant mouse, cultured in growth factors plus TNF

label_protocol: Total RNA was converted to amplified cDNA using the NuGEN Ovation RNA amplification v.2 System. Using between 5-15ng of total RNA as input, in a three step process, total RNA was converted to cDNA:  (1) First Strand Synthesis: Single stranded cDNA was prepared from total RNA using a chimeric DNA/RNA primers and reverse transcriptase, (Step 2) Second Strand Synthesis: After partial fragmentation of mRNA in the cDNA/mRNA complex, DNA polymerase generated a second strand, (3) SPIA Amplification: The isothermal linear amplification step used an additional DNA/RNA chimeric primer, DNA polymerase and RNase H in an isothermal reaction creating antisense strand cDNA The cDNA was fragmented to produce a uniform distribution of short cDNAs and biotin labeled using the NuGEN Ovation FLv2 reagents. 3.4µg each of labeled target was combined with hybridization control oligomer (Affymetrix, Santa Clara, CA) and control cRNAs (1.5pM BioB, 5.0pM BioC, 25pM BioD, and 100pM Cre; Affymetrix, Santa Clara, CA), in hybridization buffer and applied to the array.

growth_protocol: Freshly-isolated KSL cells were placed into culture dishes at a density of 104 per ml medium.  Medium was RPMI containing 10% fetal bovine serum, 20 ng/ml IL-6, 10 ng/ml IL-11, 50 ng/ml Flt3L, and 10 ng/ml SCF.

extract_protocol: Cells were collected from medium by centrifugation, lysed with 75 ul QIAGEN RLT buffer, then RNA extracted with the QIAGEN Rneasy Micro Kit.

treatment_protocol: Immediately after plating cells, half of the samples were treated with 10 ng/ml TNF alpha for 24 hours before RNA harvest.  The other half of the samples received medium alone.

tag: genotype/variation

value: Fancc-/-

value: 2-4 months

value: hematopoietic progenitor cells


title: N9

status: Public on May 23 2012

type: genomic

city: Ann Arbor

first: Scott

last: Tomlins

state: MI

address: 1400 E. Medical Center Dr., 5410 CCGC

department: Pathology

country: USA

institute: University of Michigan

hyb_protocol: Cy-5 (test channel) and Cy-3 (reference channel) labeled DNA was purified using Microcon YM-30 columns and hybridized for 40 hours at 65o C. Post-hybridization wash was performed with acetonitrile wash and Agilent Stabilization and Drying Solution wash.

scan_protocol: Scanning was performed on an Agilent scanner Model G2505B (5 micron scan with software v7.0).

data_processing: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software (v9.5) using protocol CGH-v4_95_Feb07.  For data analysis, probes on all arrays were limited to those on the 105K array. Log(2) ratios for each probe were determined as rProcessedSignal/gProcessedSignal. To remove copy number variants, all probes with log(2) values >1 or <-1 in any of the 28 benign prostate samples were excluded. The final dataset (consisting of localized prostate cancer and castrate resistant metastatic samples) was uploaded into a custom instance of Oncomine for automated copy number analysis. In Oncomine, circular binary segmentation was performed on the dataset using the DNACopy package (v1.18) available via the Bioconductor project. Agilent Probe IDs are mapped to segments and reporter values are used to generate segment values (mean of reporters). Resulting segments are mapped to hg18 (NCBI 36.1) RefSeq coordinates (UCSC refGene) as provided by UCSC (UCSC refGene, July 2009, hg18, NCBI 36.1, March 2006) and segment values are assigned to each gene. Copy number profiles were visualized using Oncomine Power Tools.

molecule: genomic DNA

organism: Homo sapiens

source_name: normal human male DNA (Promega)

label_protocol: 1.5 - 3 ug of gDNA from prostate specimens (test channel) or Human Male Genomic DNA (Promega, reference channel), was restriction digested with AluI and RsaI, and labeled with Cy-5 (test channel) or Cy-3 (reference channel).

extract_protocol: gDNA was isolated using the Qiagen DNeasy Blood & Tissue Kit according to the manufacturer’s instructions.

tag: sample type

value: reference

source_name: prostate tissue (radical prostatectomy specimen)

tag: tissue

value: benign prostate tissue (N)


title: C21_Normal

city: Chicago

first: Muhammad

middle: Ghulam

last: Kibriya

address: 900 E 57th Street

department: Health Studies

institute: The University of Chicago

hyb_protocol: Illumina

scan_protocol: Illumina

data_processing: Illumina BeadStudio

label: Cy5 and Cy3

source_name: surrounding healthy tissue

label_protocol: Illumina

extract_protocol: Qiagen Puregene Core kit

tag: disease status

value: colorectal carcinoma patient

value: colon tissue

tag: tissue type

value: surrounding healthy colonic mucosa


title: N6


title: C23_Normal


title: WA3

type: RNA

hyb_protocol: 825ng of Cy3 and Cy5 labelled aRNA were hybridized competitively for 17 hrs in a 65 C hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to the manufacturer's recommnded protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent). Arrays were washed according to the manufacturer's recommended protocol including the Stabilization and Drying Solution step (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505B, Agilent) using the default settings for 1x44k or 4x44k format two-color arrays.

data_processing: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software (Version 9.1.3.1).  Spot values were normalized using the default linear-lowess normalization. LogRatio for all probes, which were used for subsequent analysis, were converted to log(2). Although the 1x44k and 4x44k arrays have the same probes, the 4x44k arrays have 10 replicates of some probes. Thus, to generate a final data set, the median value of replicated probes was used for 4x44k arrays. The final data set (including benign prostate, localized prostate cancer and CRPC) was uploaded into a custom instance of Oncomine  for automated analysis. In Oncomine, the dataset was median centered (per array) prior to indicated analyses.

molecule: total RNA

source_name: pooled benign prostate tissue (Clontech)

label_protocol: One ug of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

extract_protocol: Total RNA was isolated with Trizol (Invitrogen Cat. No. 15596-026, Carlsbad, CA), according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNAeasy Mini Kit (Cat. No. 74104) according to the manufacturer's instructions

source_name: metastatic prostate cancer (obtained at rapid [warm] autopsy)

value: metastatic castrate resistant prostate cancer (WA)


title: wild-type_with TNF_rep2

label: biotin

organism: Mus musculus

source_name: c-Kit+Sca-1+Lin- bone marrow cells from wild-type mouse, cultured in growth factors plus TNF

value: wild-type

tag: age

tag: cell type


title: mutant_with TNF_rep2


title: N11


title: mutant_with TNF_rep1


title: C20_Tumour

source_name: Tumour

value: Tumour


title: N8


title: N7


title: N5


title: C20_Normal


title: wild-type_with TNF_rep3


title: wild-type_with TNF_rep1


title: C19_Tumour


title: C17_Tumour


title: T12

value: localized prostate cancer (T)


title: mutant_no TNF_rep3

source_name: c-Kit+Sca-1+Lin- bone marrow cells from Fancc mutant mouse, cultured in growth factors alone


title: N2


title: mutant_no TNF_rep1


title: C19_Normal


title: T6


title: C15_Normal


title: N1


title: N4


title: Myoblast Pax7 Ovexpression - Replicate 1

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

hyb_protocol: 100ng of total RNA was amplified and hybridized to the array.

scan_protocol: According to standard Affymetrix Protocol using an Affymetrix GeneChip Scanner 3000 7G

data_processing: Transcript cluster identifiers (TCID) of the Affymetrix MoGene 1.0 chipset were RMA normalized using the xps Bioconductor package in R-2.10.0  with the Affymetrix provided MoGene-1_0-st-v1.r4 chip layout and scheme files.

source_name: Myoblast Pax7 Ovexpression

label_protocol: Biotin labeled according to standard Affymetrix Protocol

growth_protocol: HAMS's F10 + 20% FBS + bFGF(4ng/ml)

extract_protocol: Total RNA was isolated in triplicates from myoblasts with Pax7 overexpression, Pax3 overexpression and empty vector control using  RNeasy mini kit (Qiagen). The purity of RNA was analyzed by Bioanalyzer (Agilent Technologies, Santa Clara CA). All samples showed RNI > 9.0 and were used for subsequent labeling and hybridization.

tag: strain background

value: Balb/c

tag: tissue origin

value: skeletal muscle

value: myoblasts

value: Pax7 ovexpression


title: T9a


title: Myoblast Pax7 Ovexpression - Replicate 3


title: T10


title: C17_Normal


title: T7


title: wild-type_no TNF_rep3

source_name: c-Kit+Sca-1+Lin- bone marrow cells from wild-type mouse, cultured in growth factors alone


title: T5


title: T8


title: T11


title: Myoblast Pax7 Ovexpression - Replicate 2


title: C16_Normal


title: T1


title: T3


title: Myoblast Pax3 Ovexpression - Replicate 3

source_name: Myoblast Pax3 Ovexpression

value: Pax3 ovexpression


title: C16_Tumour


title: C14_Normal


title: C15_Tumour


title: Myoblast Pax3 Ovexpression - Replicate 2

data_processing: Transcript cluster identifiers (TCID) of the Affymetrix MoGene 1.0 chipset were RMA normalized using the xps Bioconductor package in R-2.10.0  with the Affymetrix provided MoGene-1_0-st-v1.r4 chip layout and scheme files..


title: N16


title: wild-type_no TNF_rep1


title: C7_Normal


title: CTAP Control - Replicate 3

source_name: CTAP Control

value: empty vector control


title: C7_Tumour


title: CTAP Control - Replicate 2


title: Myoblast Pax3 Ovexpression - Replicate 1


title: C14_Tumour


title: N17


title: N15


title: mutant_no TNF_rep2

value: Fancc-/-

value: 2-4 months


title: wild-type_no TNF_rep2

value: hematopoietic progenitor cells


title: C12_Tumour


title: N13

value: reference

value: benign prostate tissue (N)


title: N12


title: C10_Normal

value: colorectal carcinoma patient

value: colon tissue


title: C13_Normal

value: surrounding healthy colonic mucosa


title: N10


title: C13_Tumour


title: C12_Normal


title: Sample07-use04

city: Gdansk

first: Arkadiusz

last: Piotrowski

address: Hallera 107

department: Biology and Pharmaceutical Botany

country: Poland

institute: Medical University of Gdansk

description: Comparative Genomic Hybridization performance on regenerated microarray slides

hyb_protocol: Standard manufacturer's protocol: Roche NimbleGen Arrays User’s Guide: CGH and CNV Arrays v8.1; http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p1.pdf

scan_protocol: MS-200 scanner at 2 µm resolution using high-sensitivity and autogain settings. Separate autogain area was defined for each subarray.

data_processing: Arrays were processed using manufacturer's standard settings with NimbleScan v2.6 segMNT, including spatial correction (LOESS) and qspline fit normalization, in order to compensate for differences in signal between the two dyes. SignalMap v.1.9 was used for visual presentation of the resulting data (Roche).

source_name: Peripheral Blood Leukocyte DNA from Sample07

label_protocol: Genomic DNA samples were incubated at 55C for one hour prior to fluorescent labeling of 500 ng of test and reference DNA by random priming with the Nimblegen Dual-Color DNA Labeling kit (Roche NimbleGen Arrays User’s Guide: CGH and CNV Arrays v8.1; (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p1.pdf)) with modifications. We found that the incubation at 55C improves labeling yield. It was therefore possible to use half the amount of the labeling reagents compared to the standard protocol.

extract_protocol: QIAmp DNA Midi Blood Kit (Qiagen).

value: subchromosomal deletion

value: peripheral blood leukocytes

source_name: genomic DNA from a pool of female individuals (Promega)

value: normal


title: Sample01-use01

source_name: Peripheral Blood Leukocyte DNA from Sample01

value: subchromosomal deletion and duplication


title: CTAP Control - Replicate 1

data_processing: Transcript cluster identifiers (TCID) of the Affymetrix MoGene 1.0 chipset were RMA normalized using the xps Bioconductor package in R-2.10.0  with the Affymetrix provided MoGene-1_0-st-v1.r4 chip layout and scheme files. The CHTAP chips were used as controls and Pax7, Pax3 overexpression as the treatment.

value: Balb/c

value: skeletal muscle


title: N8


title: C5_Tumour

value: Tumour


title: Sample01-use04


title: C10_Tumour


title: N9


title: C5_Normal


title: C9_Tumour


title: C9_Normal


title: N6


title: C8_Tumour


title: C8_Normal


title: N5


title: Sample02-use02

source_name: Peripheral Blood Leukocyte DNA from Sample02


title: N14


title: C6_Tumour


title: N2


title: N1


title: Sample04-use01

source_name: Peripheral Blood Leukocyte DNA from Sample04


title: N4


title: C4_Tumour


title: N11


title: N7


title: C4_Normal


title: Sample01-use02


title: Sample06-use03

source_name: Peripheral Blood Leukocyte DNA from Sample06


title: P12_washout-Mock_24h

city: Vancouver

first: Andrew

middle: P

last: Weng

state: BC

address: 675 West 10th Ave

institute: BC Cancer Agency

description:
raw data file ch1: 1_Exiqon_14069970_S01_Cropped.txt
raw data file ch2: 0_Exiqon_14069970_S01_Cropped.txt
Sample name: R85 P12_M

hyb_protocol: Performed as per Exiqon standard procedures.

source_name: Human T-ALL cell line P12 Ichikawa, GSI 4 days, washout, Mock 24h

label_protocol: Individual samples were labelled with Hy3 and compared to a common reference pool of all 4 sampled labelled with Hy5.

growth_protocol: Jurkat and P12 Ichikawa were grown under standard conditions. RPMI 1640 medium supplemented with 10% FCS, 1 mM sodium pyruvate, 2 mM L-glutamine, and antibiotics.

extract_protocol: Total RNA was extracted using standard Trizol protocol.

treatment_protocol: Cells were treated with the gamma-secretase inhibitor (GSI) Compound E (E) at a concentration of 1uM for 4 days followed by washout and resuspension in media containing E or Mock (DMSO).

tag: cell line

value: Human T-ALL cell line P12 Ichikawa

tag: protocol

value: Mock 24hr

source_name: Reference pool (samples R82 J_M, R83 J_E, R85 P12_M, R86 P12_E pooled together)

tag: reference composition


title: Osteosarcoma MNNG/HOS Sarcospheres Hypoxia induced

city: GUANGZHOU

first: haotong

last: wu

address: CHINA GUANGZHOU

country: China

institute: SUN YAT-SEN UNIVERSITY

description: Hypoxia induced sarcospheres come from MNNG/HOS cells cultured in serum-free DMEM/F12 medium under hypoxia  microenvironment

hyb_protocol: Hybridization was performed in NimbleGen Hybridization System.

scan_protocol: Scanning was performed by KangChen Bio-tech Corporation using Axon GenePix 4000B scanner.

data_processing: Data was extracted and normalized using NimbleScan v2.5 Software. Further Data analysis was performed using Agilent GeneSpring GX v11.5.1 software.

source_name: Hypoxia induced Sarcospheres

label_protocol: NimbleGen One-Color DNA Labeling Kit was used for sample labeling.

growth_protocol: Osteosarcoma cells MNNG/HOS were cultured at 37℃ ( 5%CO2 ) in serum- free DMEM/F12 medium.

extract_protocol: Totol RNA was extracted using the RNeasy Mini Kit (Qiagen Inc. Valencia,CA,USA) and the totle RNA was purified by NucleoSpin® RNA clean-up kit (（MACHEREY-NAGEL，Germany).RNA Quantification and Quality Assurance by NanoDrop ND-1000. RNA Integrity and gDNA contamination Test by Denaturing Agarose Gel Electrophoresis.

treatment_protocol: Osteosarcoma cells MNNG/HOS were cultured in serum- free DMEM/F12 medium, and collected suspending sarcospheres after five days.Osteosarcoma cells MNNG/HOS were cultured in serum- free DMEM/F12 medium supplement with 4ng/mL TGF-beta1, and collected suspending TGF-beta1 induced sarcospheres after five days.Osteosarcoma cells MNNG/HOS were cultured in serum- free DMEM/F12 medium under hypoxia microenvironment, and collected suspending hypoxia induced sarcospheres after five days.

value: Human Osteosarcoma cell line MNNG/HOSC

tag: treatment

value: hypoxia

tag: time

value: 5 d


title: Osteosarcoma MNNG/HOS sarcospheres non-treatment

description: Sarcospheres come from MNNG/HOS cells cultured in serum-free DMEM/F12 medium

source_name: Sarcospheres


title: C6_Normal

source_name: surrounding healthy tissue


title: C3_Normal


title: P12_washout-GSI_24h

description:
raw data file ch1: 1_Exiqon_14069971_S01_Cropped.txt
raw data file ch2: 0_Exiqon_14069971_S01_Cropped.txt
Sample name: R86 P12_E

scan_protocol: Performed as per Exiqon standard procedures.

source_name: Human T-ALL cell line P12 Ichikawa, GSI 4 days, washout, GSI 24h

value: GSI 24hr

value: samples R82 J_M, R83 J_E, R85 P12_M, R86 P12_E pooled together


title: Osteosarcoma MNNG/HOS Sarcospheres TGF-beta1 induced

description: TGF-beta1 induced sarcospheres come from MNNG/HOS cells cultured in serum-free DMEM/F12 medium supplement with TGF-beta1

source_name: TGF-beta1 induced Sarcospheres


title: C2_Normal

value: colorectal carcinoma patient


title: C2_Tumour

source_name: Tumour

value: colon tissue


title: Sample04-use04


title: Sample01-use03


title: Jurkat_washout-GSI_24h

description:
raw data file ch1: 1_Exiqon_14069969_S01_Cropped.txt
raw data file ch2: 0_Exiqon_14069969_S01_Cropped.txt
Sample name: R83 J_E

data_processing: Performed as per Exiqon standard procedures.

source_name: Human T-ALL cell line Jurkat, GSI 4 days, washout, GSI 24h

value: Human T-ALL cell line Jurkat


title: Sample03-use04

source_name: Peripheral Blood Leukocyte DNA from Sample03


title: Jurkat_washout-Mock_24h

description:
raw data file ch1: 1_Exiqon_14069968_S01_Cropped.txt
raw data file ch2: 0_Exiqon_14069968_S01_Cropped.txt
Sample name: R82 J_M

source_name: Human T-ALL cell line Jurkat, GSI 4 days, washout, Mock 24h


title: Sample07-use02

source_name: Peripheral Blood Leukocyte DNA from Sample07

value: subchromosomal deletion


title: C3_Tumour


title: Sample05-use04

source_name: Peripheral Blood Leukocyte DNA from Sample05

value: peripheral blood leukocytes

source_name: genomic DNA from a pool of female individuals (Promega)


title: C1_Tumour


title: Osteosarcoma cell line MNNG/HOS TGF-beta1 treatment five days

description: The sample is osteosarcoma cells MNNG/HOS treated by TGF-beta1 for five days.Only collect the suspending sarcospheres.

hyb_protocol: Hybridization was performed by CapitalBio Corporation, beijing, China, according to the NimbleGen’s standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by CapitalBio Corporation, beijing, China, according to the NimbleGen’s standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.6 (Roche NimbleGen, Inc.).

source_name: TGF-beta1 treatment five days_iOSCs

label_protocol: Labeling was performed by a commercial provider,CapitalBio Corporation, beijing, China.See www.capitalbio.com

treatment_protocol: Osteosarcoma cells MNNG/HOS were cultured in serum-free DMEM/F12 medium. After five days, they  spontaneously formed sarcospheres, and then separated the sarcospheres from the residual adherent cells.   Respectively culture the residual adherent cells in serum-free DMEM/F12 medium for five days, or in serum-free DMEM/F12 medium suppliment with 4ng/mL TGF-beta1 for three days (mesophase) or five days (only collect the suspending sarcospheres, iOSCs).

value: human osteosarcoma cell line MNNG/HOS


title: C1_Normal

value: surrounding healthy colonic mucosa


title: Sample03-use01

value: subchromosomal deletion and duplication

value: normal


title: Osteosarcoma cell line MNNG/HOS TGF-beta1 treatment three days

description: The sample is osteosarcoma cells MNNG/HOS treated by TGF-beta1 for three days

source_name: TGF-beta1 treatment three days_mesophase

value: 3 d


title: Sample05-use01


title: Sample06-use04

source_name: Peripheral Blood Leukocyte DNA from Sample06


title: Sample02-use03

source_name: Peripheral Blood Leukocyte DNA from Sample02


title: Sample06-use02


title: Sample06-use01


title: Sample05-use02


title: Sample07-use03


title: Sample04-use02

source_name: Peripheral Blood Leukocyte DNA from Sample04


title: Soy-pool3

status: Public on May 22 2012

city: Little Rock

first: Horacio

last: Gomez-Acevedo

state: Arkansas

address: 4301 W. Markham St

department: Biomedical Informatics

institute: University of Arkansas for Medical Sciences

description: hepatic gene expression

hyb_protocol: Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N = 3/treatment) for 16 h at 45ºC in the hybridization oven set at 60 rpm.

scan_protocol: The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.

data_processing: Cel files were generated using GCOS and utilized for analysis using GeneSpring v 11.0.2.

organism: Rattus norvegicus

source_name: postnatal day 64-rat mammary gland

label_protocol: First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA  reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions.

extract_protocol:
Mammary gland pairs were collected and fresh frozen in liquid nitrogen.
Total mammary glands RNA was isolated from the rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion.

treatment_protocol: Groups of female rats were fed casein or soy protein isolate from post-natal day (PND) 30 until PND 64. On PND 50 all rats were ovariectomized and half of each group underwent E2 replacement via a mini-osmotic pump. At sacrifice (PND 64) abdominal mammary gland pairs were collected and fresh frozen in liquid nitrogen..

tag: diet

value: Soy protein isolate

tag: gender

value: female

tag: strain

value: Sprague-Dawley


title: Sample03-use03

tag: genotype/variation


title: Soy-pool2

description: hepatic gene expression


title: Casein-pool1

description: hepatic gene expression

value: Casein


title: Sample05-use03


title: Estradiol-pool1

description: hepatic gene expression

value: 17-b estradiol


title: Sample02-use01


title: Osteosarcoma cell line MNNG/HOS non-treatment

description: The sample is non-treatment osteosarcoma cells MNNG/HOS

source_name: non-treatment_residual adherent cells

value: control


title: Estradiol-Soy-pool3

description: hepatic gene expression

value: 17-b estradiol and SPI


title: Estradiol-pool2

description: hepatic gene expression


title: Estradiol-Soy-pool2

description: hepatic gene expression


title: Estradiol-Soy-pool1

description: hepatic gene expression


title: Soy-pool1

description: hepatic gene expression


title: Sample02-use04


title: Casein-pool3

description: hepatic gene expression


title: Epiblast stem cells

city: Toronto

first: Brian

middle: Joseph

last: Cox

state: Ontario

address: 1 King's College Circle, Rm 3360

department: Physiology

institute: University of Toronto

description: Gene expression of mouse epiblast stem cells.

hyb_protocol: As per Affymetrix protocol.

scan_protocol: As per Affymetrix protocol.

data_processing: Used the limma package in R. Applied RMA.

source_name: epiblast stem cells

label_protocol: As per Affymetrix protocol.

growth_protocol: EpiSC were cultured in N2B27 media (Ying and Smith, 2003) supplemented with 10 ng/ml Activin A and 12 ng/ml bFGF on fibronectin.

extract_protocol: Trizol extraction protocol and RNeasy columns.

value: ICR

value: male

value: E5.5 mouse epiblast

tag: passage

tag: embryo stage

value: late post-implantation epiblast


title: Estradiol-pool3

description: hepatic gene expression


title: CD133-, rep1

city: Vienna

first: Alexandra

last: Graf

address: Spitalgasse 23

country: Austria

institute: Medical University of Vienna

hyb_protocol: Affymetrix, according to manufacturers protocols (Affymetrix, Santa Clara, CA, USA, https://www.affymetrix.com)

scan_protocol: Affymetrix 3000, Software Command Console

data_processing: Statistical analyses were performed with R-Bioconductor. First, data was normalized using R-Bioconductor function RMA. For further analyses, we filtered genes with an expression level greater than log2 (100) in at least 2 of the 6 samples and an inter quartile range larger than 0.3.

source_name: CD133 negative HCT 116 cell line, repetition 1

label_protocol: Affymetrix WT labeling kit (Biotin)

growth_protocol: The identity of HCT116 was confirmed by flow cytometrie.

extract_protocol: RNeasy mini kit (Qiagen)

treatment_protocol: Phenotyping and mutation analysis were repeated after multiple passages and after cell sorting into CD133+ and CD133- cells


title: Casein-pool2

description: hepatic gene expression


title: Wild type Retina Rep2

city: Boston

first: Jing

last: Chen

state: MA

address: 300 Longwood Ave.

department: Ophthalmology

institute: Children's Hospital Boston/Harvard Medical School

description: WT replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using Rank Invariant normalisation with Bead Studio

source_name: Retina RNA

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

extract_protocol: RNA was extracted with  with QIAGEN RNeasy  kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Retinas were isolated from P8 Lrp5 KO and wild type mice.

tag: source

value: JAX stock # 000664

tag: tissue

value: retina

tag: genotype

value: wild type


title: CD133+, rep2

source_name: CD133 positive HCT 116 cell line, repetition 2

tag: cell type


title: Lrp5 Retina Rep2

description: Lrp5 replicate 2

value: JAX stock # 005823

tag: age

value: Lrp5 KO


title: MSC_AT_24_leg_P19_48

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

hyb_protocol: The HumanMethylation27 BeadChip (Illumina, San Diego, USA) was hybridized with 200ng DNA.

scan_protocol: The HumanMethylation27 BeadChip (Illumina, San Diego, USA) was scanned using the BeadArray Reader.

data_processing: Initial data analysis was performed with the BeadStudio Methylation software from Illumina (ie, BeadStudio Methylation Analysis Module 3.2.0). Raw data were background normalized.

source_name: human mesenchymal stem cells (MSC) from adipose tissue - passage 19

label_protocol: Genomic DNA (600 ng) from each sample was bisulfite converted using the EpiTect Bisulfite Kit (Qiagen, Hilden, Germany). This step leads to the deamination of non-methylated cytosines to uracils, while methylated cytosines are refractory to the effects of bisulfite and remain cytosine. After bisulfate conversion each sample was whole genome amplified and enzymatically fragmented.

extract_protocol: Genomic DNA of approximately 10(6) human mesenchymal stem cells (MSC) from adipose tissue was isolated using the QIAGEN DNA Blood Midi-Kit. DNA quality was assessed with a NanoDrop ND-1000 spectrometer (NanoDrop Technologies, Wilmigton, Del) and average fragment length was assessed by gel electrophoresis.

treatment_protocol: Cells were harvested by trypsination after early or late passages.

value: human mesenchymal stem cells derived from leg adipose tissue


title: Wild type Retina Rep1

description: WT replicate 1


title: Fib_D_VIII_abdomen_P31_43

source_name: human dermal fibroblasts - passage 31

extract_protocol: Genomic DNA of approximately 10(6) dermal fibroblasts was isolated using the QIAGEN DNA Blood Midi-Kit. DNA quality was assessed with a NanoDrop ND-1000 spectrometer (NanoDrop Technologies, Wilmigton, Del) and average fragment length was assessed by gel electrophoresis.

value: human dermal fibroblasts from abdomen


title: MSC_AT_23_breast_P35_43

source_name: human mesenchymal stem cells (MSC) from adipose tissue - passage 35

value: human mesenchymal stem cells derived from breast adipose tissue

value: female


title: MSC_AT_23_breast_P2_43

source_name: human mesenchymal stem cells (MSC) from adipose tissue - passage 2


title: Lrp5 Retina Rep3

description: Lrp5 replicate 3


title: CD133-, rep2

source_name: CD133 negative HCT 116 cell line, repetition 2


title: Wild type Retina Rep3

description: WT replicate 3


title: Fib_D_VIII_abdomen_P2_43

source_name: human dermal fibroblasts - passage 2


title: Sample04-use03

value: subchromosomal deletion and duplication

value: peripheral blood leukocytes

source_name: genomic DNA from a pool of female individuals (Promega)

value: normal


title: Fib_D_VII_leg_P2_48

value: human dermal fibroblasts from leg


title: MSC_AT_24_leg_P2_48


title: CD133+, rep1

source_name: CD133 positive HCT 116 cell line, repetition 1


title: CD133-, rep3

source_name: CD133 negative HCT 116 cell line, repetition 3


title: Fib_D_VI_breast_P2_43

value: human dermal fibroblasts from breast


title: Lrp5 Retina Rep1

description: Lrp5 replicate 1


title: Fib_D_VI_breast_P33_43

source_name: human dermal fibroblasts - passage 33


title: Fib_D_VII_leg_P34_48

source_name: human dermal fibroblasts - passage 34


title: Fib_D_III_abdomen_P39_62

source_name: human dermal fibroblasts - passage 39


title: IRF9-RNAi and IFN-alpha2c OVCAR3 - repeat 2 - mAdbID:91036

city: Bethesda

first: Joseph

last: Bekisz

state: MD

address: 50 South Drive

department: NIAID

institute: NIH

description: mAdb experiment ID: 91036

hyb_protocol: Hybridization Protocol Other: Using MinElute PCR Purification columns, dye coupled cDNA samples were purified and then respective samples were mixed together, heated at 95°C for 5 min followed by incubation at 42°C for 5 min. SlideHyb Buffer #1 (Ambion; Austin, TX) was added to the combined samples, and then samples were loaded onto ~21K 70mer oligonucleotide microarrays (printed by Genomics Technology Section RTB/NIAID) sealed with MAUI Mixer FL hybridization chambers (BioMicro Systems; Salt Lake City, UT) and incubated overnight at 42°C. Arrays were then washed for 5 min each in buffers; Buffer #1: 1× saline sodium citrate (SSC) with 0.05% SDS; Buffer #2: 0.1× SSC. Arrays were then dried.

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 20;; 10 LaserPower: 3.17;; 2.78 Temperature: 22.25 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices; Sunnyvale, CA).

data_processing:
Data Processing Protocol
Calculation Method: Array data was normalized via 50th percentile normalization and spot intensity was calculated by subtracting local median background from mean foreground intensity.

source_name: Negative RNAi OVCAR3

label_protocol:
Cy3 Labeling Protocol
Other: Amino allyl-oligo-dT (5’ amino-modified) primer (1µg/µl) (31) was incubated with 5 µg total RNA and then reverse transcription (RT) labeling reaction mixture from FairPlay Microarray Labeling Kit (Agilent Technologies) was added to each sample. Following incubation at 42°C for 90 min, cDNA was purified using MinElute PCR Purification columns (Qiagen). After eluting and drying cDNA samples, they were resuspended in 5µl 2× Coupling Buffer. Following, 5µl of Cy3 mono-reactive dye (GE Healthcare/Amersham Biosciences; Piscataway, NJ) was added to the samples and incubated in the dark at room temperature for 90 min.

extract_protocol:
Sample Extraction Protocol
Other: Total RNA was purified using RNeasy Kit (Qiagen; Valencia, CA).

treatment_protocol:
Treatment type: small molecule
Agent: Stealth RNAi Negative Control Low GC (Invitrogen)
Treatment dose: 100 nM
Treatment time: 4 hours
Treatment temperature: 37C
In-vitro treatment: Stealth RNAi Negative Control Low GC (Invitrogen) was used as negative-RNAi. The RNAi oligos (100nM) were mixed with Lipofectamine (Invitrogen) in OPTI-MEM medium (Invitrogen), and the mixture was added to the medium on cells. The cells were incubated for 4 h at 37°C then the medium was replaced with medium containing antibiotics.

value: ovary

value: human ovarian adenocarcinoma cells

tag: disease state

value: human ovarian adenocarcinoma

source_name: IRF9-RNAi and IFN-aplha2c OVCAR3

label_protocol:
Cy5 Labeling Protocol
Other: Amino allyl-oligo-dT (5’ amino-modified) primer (1µg/µl) (31) was incubated with 5 µg total RNA and then reverse transcription (RT) labeling reaction mixture from FairPlay Microarray Labeling Kit (Agilent Technologies) was added to each sample. Following incubation at 42°C for 90 min, cDNA was purified using MinElute PCR Purification columns (Qiagen). After eluting and drying cDNA samples, they were resuspended in 5µl 2× Coupling Buffer. Following, 5µl of Cy5 mono-reactive dye (GE Healthcare/Amersham Biosciences; Piscataway, NJ) was added to the samples and incubated in the dark at room temperature for 90 min.

treatment_protocol:
Treatment type: small molecule
Agent: human interferon (IFN-apha2c)
Treatment dose: 10 ng/ml
Treatment time: 24 hours
Treatment temperature: 37C
In-vitro treatment: OVCAR3 cells were plated and adhered overnight at 37°C. 10 ng/ml of IFN-apha2c was then added into the medium. After incubation for 24 hours at 37°C, the cells were harvested and used for microarray analysis.
Treatment type: small molecule
Agent: IFN regulatory factor (IRF) 9 RNA interference (IRF9-RNAi)
Treatment dose: 100 nM
Treatment time: 4 hours
Treatment temperature: 37C
In-vitro treatment: Duplex RNAi, 25 base pair (bp) and 21 bp, were purchased from Invitrogen and Dharmacon (Lafayette, CO), respectively. The RNAi oligos (100 nM) were mixed with Lipofectamine (Invitrogen) in OPTI-MEM medium (Invitrogen), and the mixture was added to the medium on cells. The cells were incubated for 4 h at 37°C then the medium was replaced with medium containing antibiotics.


title: IFN-alpha2c OVCAR3 - repeat 8 - mAdbID:91360

description: mAdb experiment ID: 91360

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 30;; 10 LaserPower: 3.46;; 2.79 Temperature: 22.63 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices; Sunnyvale, CA).

source_name: Untreated OVCAR3

tag: cell line

source_name: IFN-alpha2c OVCAR3

treatment_protocol:
Treatment type: small molecule
Agent: human interferon (IFN-apha2c)
Treatment dose: 10 ng/ml
Treatment time: 24 hours
Treatment temperature: 37C
In-vitro treatment: OVCAR3 cells were plated and adhered overnight at 37°C. 10 ng/ml of IFN-apha2c was then added into the medium. After incubation for 24 hours at 37°C, the cells were harvested and used for microarray analysis.


title: CD133+, rep3

source_name: CD133 positive HCT 116 cell line, repetition 3


title: Sample07-use01

source_name: Peripheral Blood Leukocyte DNA from Sample07

value: subchromosomal deletion


title: Fib_D_III_abdomen_P2_62


title: IRF9-RNAi and IFN-alpha2c OVCAR3 - repeat 1 - mAdbID:91035

description: mAdb experiment ID: 91035

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 30;; 10 LaserPower: 3.16;; 2.79 Temperature: 22.31 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices; Sunnyvale, CA).


title: IFN-alpha2c OVCAR3 - repeat 7 - mAdbID:91359

description: mAdb experiment ID: 91359

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 30;; 10 LaserPower: 3.41;; 2.78 Temperature: 22.63 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices; Sunnyvale, CA).


title: Negative RNAi and IFN-alpha2c OVCAR3 - repeat 3 - mAdbID:90208

description: mAdb experiment ID: 90208

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 20;; 15 LaserPower: 3.18298;; 2.79846 Temperature: 24.625 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices; Sunnyvale, CA).

source_name: Negative RNAi and IFN-alpha2c OVCAR3

treatment_protocol:
Treatment type: small molecule
Agent: human interferon (IFN-apha2c)
Treatment dose: 10 ng/ml
Treatment time: 24 hours
Treatment temperature: 37C
In-vitro treatment: OVCAR3 cells were plated and adhered overnight at 37°C. 10 ng/ml of IFN-apha2c was then added into the medium. After incubation for 24 hours at 37°C, the cells were harvested and used for microarray analysis.
Treatment type: small molecule
Agent: Stealth RNAi Negative Control Low GC (Invitrogen)
Treatment dose: 100 nM
Treatment time: 4 hours
Treatment temperature: 37C
In-vitro treatment: Stealth RNAi Negative Control Low GC (Invitrogen) was used as negative-RNAi. The RNAi oligos (100nM) were mixed with Lipofectamine (Invitrogen) in OPTI-MEM medium (Invitrogen), and the mixture was added to the medium on cells. The cells were incubated for 4 h at 37°C then the medium was replaced with medium containing antibiotics.


title: IFNAR2-RNAi and IFN-alpha2c OVCAR3 - repeat 4 - mAdbID:91033

description: mAdb experiment ID: 91033

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 30;; 10 LaserPower: 3.16;; 2.78 Temperature: 22.19 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices; Sunnyvale, CA).

source_name: IFNAR2-RNAi and IFN-alpha2c OVCAR3

treatment_protocol:
Treatment type: small molecule
Agent: human interferon (IFN-apha2c)
Treatment dose: 10 ng/ml
Treatment time: 24 hours
Treatment temperature: 37C
In-vitro treatment: OVCAR3 cells were plated and adhered overnight at 37°C. 10 ng/ml of IFN-apha2c was then added into the medium. After incubation for 24 hours at 37°C, the cells were harvested and used for microarray analysis.
Treatment type: small molecule
Agent: IFN-alpha receptor RNA interference (IFNAR2-RNAi)
Treatment dose: 100 nM
Treatment time: 4 hours
Treatment temperature: 37C
In-vitro treatment: Duplex RNAi, 25 base pair (bp) and 21 bp, were purchased from Invitrogen and Dharmacon (Lafayette, CO), respectively. The RNAi oligos (100 nM) were mixed with Lipofectamine (Invitrogen) in OPTI-MEM medium (Invitrogen), and the mixture was added to the medium on cells. The cells were incubated for 4 h at 37°C then the medium was replaced with medium containing antibiotics.


title: Negative RNAi and IFN-alpha2c OVCAR3 - repeat 2 - mAdbID:91024

description: mAdb experiment ID: 91024

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 20;; 10 LaserPower: 3.06;; 2.72 Temperature: 21.88 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices; Sunnyvale, CA).


title: IFNAR1-RNAi and IFN-alpha2c OVCAR3 - repeat 4 - mAdbID:90203

description: mAdb experiment ID: 90203

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 15;; 15 LaserPower: 3.21;; 2.83 Temperature: 24.56 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices; Sunnyvale, CA).

source_name: IFNAR1-RNAi and IFN-alpha2c OVCAR3

treatment_protocol:
Treatment type: small molecule
Agent: human interferon (IFN-apha2c)
Treatment dose: 10 ng/ml
Treatment time: 24 hours
Treatment temperature: 37C
In-vitro treatment: OVCAR3 cells were plated and adhered overnight at 37°C. 10 ng/ml of IFN-apha2c was then added into the medium. After incubation for 24 hours at 37°C, the cells were harvested and used for microarray analysis.
Treatment type: small molecule
Agent: IFN-alpha receptor RNA interference (IFNAR1-RNAi)
Treatment dose: 100 nM
Treatment time: 4 hours
Treatment temperature: 37C
In-vitro treatment: Duplex RNAi, 25 base pair (bp) and 21 bp, were purchased from Invitrogen and Dharmacon (Lafayette, CO), respectively. The RNAi oligos (100 nM) were mixed with Lipofectamine (Invitrogen) in OPTI-MEM medium (Invitrogen), and the mixture was added to the medium on cells. The cells were incubated for 4 h at 37°C then the medium was replaced with medium containing antibiotics.


title: IFNAR2-RNAi and IFN-alpha2c OVCAR3 - repeat 5 - mAdbID:90204

description: mAdb experiment ID: 90204

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 20;; 15 LaserPower: 3.22571;; 2.84119 Temperature: 24.5625 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices; Sunnyvale, CA).


title: IFN-alpha2c OVCAR3 - repeat 5 - mAdbID:82932

description: mAdb experiment ID: 82932

scan_protocol: Creator: GenePix Pro 5.1.0.0 Scanner: GenePix 4200A 01 [99052] ScanPower: 11;; 7 LaserPower: 3.37;; 2.9 Temperature: 23.25 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices; Sunnyvale, CA).


title: IFN-alpha2c OVCAR3 - repeat 6 - mAdbID:83026

description: mAdb experiment ID: 83026

scan_protocol: Creator: GenePix Pro 5.1.0.0 Scanner: GenePix 4200A 01 [99052] ScanPower: 11;; 8 LaserPower: 3.38;; 2.94 Temperature: 23.63 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices; Sunnyvale, CA).


title: Rhodobacter capsulatus DE442 late stationary growth phase

city: St. John's

first: Ryan

middle: G

last: Mercer

state: Newfoundland

address: 232 Elizabeth Avenue

department: Biology

institute: Memorial University

description: Target preparation, labeling, hybridization and scanning performed at Michael Smith Genome Science Center, Vancouver, BC

hyb_protocol: As per described in Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232 Rev. 2) - Chapter 6: Prokaryotic Target Hybridization, page 119-126

scan_protocol: As per described in Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232 Rev. 2) - Chapter 7: Prokaryotic Arrays: Washing, Staining and Scanning page 127-152.

data_processing:
Raw data was RMA normalized after scanning
Analyzed using GeneSpring v7.2 (Agilent Technologies)
Further normalized in GeneSpring (per chip) to the 50th percentile

organism: Rhodobacter capsulatus

source_name: DE442, Late Stationary, Photoheterotrophic

label_protocol: As per described in Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232 Rev. 2) - Chapter 5: Prokaryotic Target Preparation, page 101-118

growth_protocol: Growth Conditions: YPS medium, Photosynthetic

extract_protocol: As per described in RNeasy Mini Handbook (Qiagen Inc.), Protocol for Isolation of Total RNA from Bacteria, pages 56-60.

tag: growth phase

value: late stationary


title: Rhodobacter capsulatus DE442 GTA DNA

hyb_protocol: As per described in Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232 Rev. 2) - Chapter 6: Prokaryotic Target Hybridization, page 119-126 Changes - denatured at 99 degrees C for 5min then cooled to 50 degrees C for 5 min before injecting into array for 16 hour hybridization.

data_processing: Raw data was MAS5 normalized

source_name: R. capsulatus DE442 GTA

extract_protocol: Cultures of strain DE442 were grown for 48 hours. The cells were then centrifuged at 5855 x g, the supernatant filtered through a 0.45-μm polyvinylidene fluoride (PVDF) filter (Millipore, Bedford, MA), and the filtrate ultracentrifuged at 184000 x g for 5 hours. The resulting pellet was resuspended by shaking at 100 RPM in G buffer (Solioz & Marrs, 1977) overnight at 4°C. The resuspensions were treated with 2 units RNase-free DNase I (New England Biolabs, Pickering, Canada) and 1.2 units RNase A (Sigma-Aldrich, Oakville, Canada) in 1X DNase Buffer (New England Biolabs) at 37°C for 30 minutes to remove any free nucleic acids, and then incubated at 75°C in the presence of 5 mM EDTA (pH 8). DNA was purified by phenol:chloroform:isoamyl alcohol (25:24:1) extraction and ethanol precipitation. The sample was subjected to agarose gel electrophoresis and the ~4-kb RcGTA DNA band extracted using the QIAEX II Gel Extraction Kit (Qiagen, Mississauga, Canada).

value: GTA particles


title: Rhodobacter capsulatus SB1003 late stationary growth phase

source_name: R. capsulatus SB1003 late stationary


title: Ex-vivo CD4+ T cells healthy control H

city: Darlinghurst

first: Sanjay

last: Swaminathan

state: New South Wales

address: 405 Liverpool St

country: Australia

institute: St Vincent's Centre for Applied Medical Centre

description: 100ng total RNA put onto Agilent microarray

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

scan_protocol: Scanning was performed using an Agilent G2505B scanner

data_processing: 22 arrays were imported into GeneSpring GX 10 and pre-processed using default settings: threshold raw signals to 1.0, followed by log-base-2 transformation, then percentile shift normalization, setting the 75th percentile on each array to 0.

source_name: Unstimulated ex-vivo isolated CD4+ T cells

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

growth_protocol: CD4+ T cells isolated from PBMCs using MACS CD4+ positive selection. PBMCs  were frozen down from peripheral blood using Ficoll Paque density centrifugation.

extract_protocol: Total RNA was extracted from CD4+ T cells using Qiagen miRNeasy kit; RNA quality was checked using a spectrophotometer and an Agilent Bioanalyzer Nano Chip and Small RNA chip

treatment_protocol: Cells were separated from PBMCs and not stimulated in any way prior to RNA extraction

value: CD4+ T cells

value: Normal


title: IRF9-RNAi and IFN-alpha2c OVCAR3 - repeat 3 - mAdbID:90205

description: mAdb experiment ID: 90205

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 20;; 15 LaserPower: 3.2428;; 2.84973 Temperature: 24.5625 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices; Sunnyvale, CA).


title: IFN-alpha2c OVCAR3 - repeat 4 - mAdbID:82884

description: mAdb experiment ID: 82884

scan_protocol: Creator: GenePix Pro 5.1.0.0 Scanner: GenePix 4200A 01 [99052] ScanPower: 11;; 7 LaserPower: 3.25;; 2.9 Temperature: 22.63 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices; Sunnyvale, CA).


title: IFNAR1-RNAi and IFN-alpha2c OVCAR3 - repeat 3 - mAdbID:91028

description: mAdb experiment ID: 91028

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 20;; 10 LaserPower: 3.11;; 2.75 Temperature: 22.44 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices; Sunnyvale, CA).


title: Ex-vivo CD4+ T cells healthy control C


title: Ex-vivo CD4+ T cells healthy control G


title: Ex-vivo CD4+ T cells healthy control F


title: Ex-vivo CD4+ T cells healthy control E


title: Ex-vivo CD4+ T cells healthy control D


title: Ex-vivo CD4+ T cells healthy control B


title: IFNAR2-RNAi and IFN-alpha2c OVCAR3 - repeat 3 - mAdbID:80139

description: mAdb experiment ID: 80139

scan_protocol: Creator: GenePix Pro 5.1.0.0 Scanner: GenePix 4200A 01 [99052] ScanPower: 10;; 5 LaserPower: 3.18;; 2.91 Temperature: 22.75 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices; Sunnyvale, CA).


title: IFNAR1-RNAi and IFN-alpha2c OVCAR3 - repeat 2 - mAdbID:80138

description: mAdb experiment ID: 80138

scan_protocol: Creator: GenePix Pro 5.1.0.0 Scanner: GenePix 4200A 01 [99052] ScanPower: 10;; 5 LaserPower: 3.17;; 2.89 Temperature: 22.81 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices; Sunnyvale, CA).


title: Ex-vivo CD4+ T cells Chronic HIV F

value: Chronic HIV


title: Sample03-use02

scan_protocol: MS-200 scanner at 2 µm resolution using high-sensitivity and autogain settings. Separate autogain area was defined for each subarray.

source_name: Peripheral Blood Leukocyte DNA from Sample03

source_name: genomic DNA from a pool of female individuals (Promega)


title: Ex-vivo CD4+ T cells Chronic HIV E


title: Ex-vivo CD4+ T cells Chronic HIV G


title: Ex-vivo CD4+ T cells Chronic HIV D


title: Ex-vivo CD4+ T cells healthy control A


title: IFNAR2-RNAi and IFN-alpha2c OVCAR3 - repeat 1 - mAdbID:79635

description: mAdb experiment ID: 79635

scan_protocol: Creator: GenePix Pro 5.1.0.0 Scanner: GenePix 4200A 01 [99052] ScanPower: 10;; 5 LaserPower: 3.15;; 2.87 Temperature: 21.69 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices; Sunnyvale, CA).


title: IFN-alpha2c OVCAR3 - repeat 3 - mAdbID:80136

description: mAdb experiment ID: 80136

scan_protocol: Creator: GenePix Pro 5.1.0.0 Scanner: GenePix 4200A 01 [99052] ScanPower: 8;; 8 LaserPower: 3.28;; 2.82 Temperature: 21.5 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices; Sunnyvale, CA).


title: IFN-alpha2c OVCAR3 - repeat 1 - mAdbID:79807

description: mAdb experiment ID: 79807

scan_protocol: Creator: GenePix Pro 5.1.0.0 Scanner: GenePix 4200A 01 [99052] ScanPower: 10;; 9 LaserPower: 3.14;; 2.85 Temperature: 22.5 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices; Sunnyvale, CA).


title: Negative RNAi and IFN-alpha2c OVCAR3 - repeat 1 - mAdbID:79637

description: mAdb experiment ID: 79637

scan_protocol: Creator: GenePix Pro 5.1.0.0 Scanner: GenePix 4200A 01 [99052] ScanPower: 10;; 5 LaserPower: 3.2;; 2.89 Temperature: 22.25 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices; Sunnyvale, CA).


title: IFNAR1-RNAi and IFN-alpha2c OVCAR3 - repeat 1 - mAdbID:79634

description: mAdb experiment ID: 79634

scan_protocol: Creator: GenePix Pro 5.1.0.0 Scanner: GenePix 4200A 01 [99052] ScanPower: 10;; 5 LaserPower: 3.13;; 2.81 Temperature: 21.38 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices; Sunnyvale, CA).


title: IFN-alpha2c OVCAR3 - repeat 2 - mAdbID:80132

description: mAdb experiment ID: 80132

scan_protocol: Creator: GenePix Pro 5.1.0.0 Scanner: GenePix 4200A 01 [99052] ScanPower: 5;; 7 LaserPower: 3.15;; 2.87 Temperature: 22.44 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices; Sunnyvale, CA).


title: Ex-vivo CD4+ T cells RNA LTNP G

value: long term non-progressor (LTNP)


title: Biotin-HSR labeled synthetic miRNA spike in, 5000 attomoles

type: other

city: Duarte

first: John

middle: S.

last: Kaddis

state: CA

address: 1500 East Duarte Road

department: Diabetes and Cancer Discovery Science

institute: City of Hope

description:
Synthetic human, rat, and mouse miRNAs.
miRNA-1_0_2Xgain library file used for scanning.

hyb_protocol: The quantity of miRNA spike in varied from 5000 to 4.88 attomoles.

scan_protocol: Standard Affymetrix protocol.

data_processing: Prior to analysis, raw signal intensity values were Robust Multichip Average (RMA) background corrected, quantile normalized, median polish summarized, and log2 transformed separately for FlashTag biotin-only and FlashTag biotin-HSR chip data.

label: biotin-HSR

molecule: other

organism: synthetic construct

source_name: Synthetic oligos, 5000 attomoles

label_protocol: The Genisphere FlashTag Biotin-HSR Kit was used. The protocol is available for download at the product website (www.genisphere.com) or by contacting the kit manufacturer.

extract_protocol: The synthetic miRNAs were obtained from the Ambion mirVana miRNA Reference Panel v9.1 (Lot number 072307).

tag: miRNA spike in amount

value: 5000 attomoles


title: IFNAR2-RNAi and IFN-alpha2c OVCAR3 - repeat 2 - mAdbID:80134

description: mAdb experiment ID: 80134

scan_protocol: Creator: GenePix Pro 5.1.0.0 Scanner: GenePix 4200A 01 [99052] ScanPower: 9;; 7 LaserPower: 3.19;; 2.88 Temperature: 22.63 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices; Sunnyvale, CA).


title: Ex-vivo CD4+ T cells RNA LTNP E


title: Ex-vivo CD4+ T cells RNA LTNP D


title: Biotin-HSR labeled synthetic miRNA spike in, 1250 attomoles

source_name: Synthetic oligos, 1250 attomoles

value: 1250 attomoles


title: Ex-vivo CD4+ T cells RNA LTNP F


title: HOB-01 transwell JJN3, replicate 3

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

hyb_protocol: Following fragmentation, 15 micrograms of cRNA were hybridized for 16 hr at 45°C on the GeneChip HG-U133 Plus 2.0 Array. The arrays were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The probe level data were converted to expression values using default GCOS1.1 scaling. Natural-scaled data are provided.

source_name: HOB-01 pre-osteocytes cells, transwell JJN3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: Extraction of total RNA was performed by the RNeasy Kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Human pre-osteocytic cell line HOB-01 were detached with EDTA 2mM and washed twice with PBS solution.

value: pre-osteocytes cells

tag: treatment

value: co-cultured with the JJN3 human myeloma cell line


title: EGFP-NC

city: Hangzhou

first: cheng

last: jun

state: Zhejiang Province

address: 79 Qingchun Road

department: Department of Surgery

institute: Division of Hepatobiliary and Pancreatic Surgery

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

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software (Agilent technologies, Santa Clara, CA, US).

source_name: protect HCC cells

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: DMEM medium supplemented with 10% fetal bovine serum (FBS)

extract_protocol: Total RNA was extracted and purified using RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US)

treatment_protocol: the stably transfected HepG2 cells with Hsp27 ORF vectors, Hsp27 shRNA or control vectors

tag: transfection

value: control vector


title: HOB-01 transwell JJN3, replicate 2


title: Biotin-HSR labeled synthetic miRNA spike in, 2500 attomoles

source_name: Synthetic oligos, 2500 attomoles

value: 2500 attomoles


title: Biotin-HSR labeled synthetic miRNA spike in, 4.88 attomoles

source_name: Synthetic oligos, 4.88 attomoles

value: 4.88 attomoles


title: IRES2-HSP27

value: Hsp27 ORF vector


title: Biotin-HSR labeled synthetic miRNA spike in, 78.13 attomoles

source_name: Synthetic oligos, 78.13 attomoles

value: 78.13 attomoles


title: HOB-01 transwell JJN3, replicate 1


title: Biotin-HSR labeled synthetic miRNA spike in, 625 attomoles

source_name: Synthetic oligos, 625 attomoles

value: 625 attomoles


title: HOB-01, replicate 1

source_name: HOB-01 pre-osteocytes cells, control

value: control


title: Biotin-HSR labeled synthetic miRNA spike in, 156.25 attomoles

source_name: Synthetic oligos, 156.25 attomoles

value: 156.25 attomoles


title: Biotin-HSR labeled synthetic miRNA spike in, 9.77 attomoles

source_name: Synthetic oligos, 9.77 attomoles

value: 9.77 attomoles


title: Biotin-HSR labeled synthetic miRNA spike in, 312.5 attomoles

source_name: Synthetic oligos, 312.5 attomoles

value: 312.5 attomoles


title: Biotin-HSR labeled synthetic miRNA spike in, 39.06 attomoles

source_name: Synthetic oligos, 39.06 attomoles

value: 39.06 attomoles


title: Ex-vivo CD4+ T cells Chronic HIV C

scan_protocol: Scanning was performed using an Agilent G2505B scanner

value: CD4+ T cells

value: Chronic HIV


title: Ex-vivo CD4+ T cells Chronic HIV B


title: HOB-01, replicate 3


title: Biotin-HSR labeled synthetic miRNA spike in, 19.53 attomoles

source_name: Synthetic oligos, 19.53 attomoles

value: 19.53 attomoles


title: Ex-vivo CD4+ T cells RNA LTNP C

source_name: Unstimulated ex-vivo isolated CD4+ T cells

value: long term non-progressor (LTNP)


title: Ex-vivo CD4+ T cells Chronic HIV A


title: HOB-01, replicate 2

value: pre-osteocytes cells


title: Biotin-HSR labeled synthetic miRNA spike in, 0 attomoles

source_name: Synthetic oligos, 0 attomoles

value: 0 attomoles


title: Biotin-Only labeled lung samples, 1000ng total RNA, technical rep1

description: miRNA-1_0 library file used for scanning.

hyb_protocol: The quantity of labeled extract used varied from 100 to 1000 ng of labeled total RNA (amount of RNA used was an experimental factor).  The protocol is available for download from the manufacturer website at www.genisphere.com or www.affymetrix.com.

source_name: Lung, 1000ng RNA, biotin-only label

label_protocol: The Genisphere FlashTag Biotin Kit was used. The protocol is available for download at the product website (www.genisphere.com) or by contacting the kit manufacturer.

extract_protocol: Total RNA was obtained from Ambion FirstChoice Total Brain (Lot number 0906005) and Ambion FirstChoice Total Lung (Lot number 0904002). RNA extraction was performed by Ambion using a proprietary modification of the Ambion AM1910 totally RNA Kit.

value: lung

tag: rna amount


title: HSP27-SiRNA

value: Hsp27 shRNA vector


title: BF1

city: wuhan

first: Qiu

last: wen-ming

state: hubei

address: shizishan street

institute: Key Laboratory of Horticultural Plant Biology (Ministry of Education)

description: Analysis used RNA of Qianyang seedless Ponkan mandarin as control for comparision to RNA of Qianyang seedless Ponkan mandarin at four developmental stages (SF, MF, BF and OV).

hyb_protocol: Cy5/Cy3-labelled cDNA was hybridized with the microarray at 42 °C overnight. Hybridization was performed in duplicate by dye swap. And then the arrays were washed with 0.2% SDS, 2×SSC at 42 °C for 5 min, and 0.2% SSC for 5 min at room temperature.

scan_protocol: Arrays were scanned with a confocal laser scanner, LuxScanTM-scanner (CapitalBio Corp.)

data_processing:
The resulting images were analyzed with LuxScanTM 3.0 software (CapitalBio Corp.).
A spatial and intensity-dependent (LOWESS) normalization method was employed and normalized ratio data were then log2 transformed.

organism: Citrus reticulata

source_name: flower bud at full bloom stage (BF)

label_protocol: An aliquot of 5 μg total RNA was used to produce Cy5/Cy3-labelled cDNA employing an RNA amplification combined with Klenow enzyme labeling strategy.

growth_protocol: Plants were grown in the same orchard, and the flowers were bagged to prevent cross-pollination. All the samples were harvested and frozen in liquid nitrogenthen stored at -80°C until needed.

extract_protocol: Total RNA from flower samples at four stages (SF, MF, BF and OV) were extracted with modified Trizol method.

treatment_protocol: No treatment

value: Qianyang seedless Ponkan mandarin (mutant)

value: Egan NO.1 Ponkan mandarin (wildtype)


title: Biotin-Only labeled lung samples, 1000ng total RNA, technical rep2


title: Biotin-Only labeled lung samples, 500ng total RNA, technical rep2

source_name: Lung, 500ng RNA, biotin-only label


title: OV1

source_name: young ovaries of 2-3 days after flowering (OV)


title: Ex-vivo CD4+ T cells RNA LTNP B


title: Ex-vivo CD4+ T cells RNA LTNP A


title: Biotin-Only labeled lung samples, 500ng total RNA, technical rep1


title: MF1

source_name: flower bud medium bud stage (MF)


title: Biotin-Only labeled lung samples, 100ng total RNA, technical rep2

source_name: Lung, 100ng RNA, biotin-only label


title: Biotin-Only labeled lung samples, 200ng total RNA, technical rep1

source_name: Lung, 200ng RNA, biotin-only label


title: Biotin-Only labeled lung samples, 200ng total RNA, technical rep2


title: Biotin-Only labeled brain samples, 500ng total RNA, technical rep2

source_name: Brain, 500ng RNA, biotin-only label

value: brain


title: SF1

source_name: flower bud at quaring stage (SF)


title: Biotin-Only labeled brain samples, 1000ng total RNA, technical rep2

source_name: Brain, 1000ng RNA, biotin-only label


title: Biotin-Only labeled lung samples, 100ng total RNA, technical rep1


title: Biotin-Only labeled brain samples, 1000ng total RNA, technical rep1


title: Biotin-Only labeled brain samples, 200ng total RNA, technical rep1

source_name: Brain, 200ng RNA, biotin-only label


title: Biotin-Only labeled brain samples, 200ng total RNA, technical rep2


title: Biotin-Only labeled brain samples, 500ng total RNA, technical rep1


title: Biotin-Only labeled brain samples, 100ng total RNA, technical rep2

source_name: Brain, 100ng RNA, biotin-only label


title: Biotin-Only labeled brain samples, 100ng total RNA, technical rep1


title: Biotin-HSR labeled lung samples, 500ng total RNA, technical rep1

description: miRNA-1_0_2Xgain library file used for scanning.

source_name: Lung, 500ng RNA, biotin-HSR label


title: 13.5 WT limbs rep 2

city: Loma Linda

first: Kerby

last: Oberg

address: 24785 Stewart St

institute: Loma Linda University

description:
Wild Type - 13.5 - 2
0407A-02_C2-13.5.CEL
Gene expression from limbs of normal mice at 13.5

hyb_protocol: Hypbrization for 16 hrs by UCI Genomics using standard Affymetrix protocols

scan_protocol: Completed by UCI Genomics using a scanner controlled by GeneChip Operating Software

data_processing: The data was normalized using RMA and analyzed using the Comprehensive R and Bioconductor based web service for microarray data analysis (CARMAweb - Rainer et al., 2006)

label: Biotin

source_name: WT embryos in finger separation phase of limb development

label_protocol: Submitted to UCI Genomics for Biotin labeling of cRNA using standard Afffymetrix protocols

growth_protocol: Limbs were harvested from embryos at the specified day of development and genotyped.

extract_protocol: Total RNA for each sample (6 limbs pooled) was extracted using RNA easy (Qiagen).

treatment_protocol: Limbs were placed in RNA later (Qiagen), shifted to -80c as per manufacturers protocol, and stored until all of the limbs could be processed.

value: Handplate

tag: developmental stage

value: Lmx1b +/+


title: Biotin-HSR labeled lung samples, 1000ng total RNA, technical rep2

source_name: Lung, 1000ng RNA, biotin-HSR label


title: Biotin-HSR labeled lung samples, 100ng total RNA, technical rep2

source_name: Lung, 100ng RNA, biotin-HSR label


title: 13.5 WT limbs rep 1

description:
Wild Type - 13.5 - 1
0407A-02_C1-13.5.CEL
Gene expression from limbs of normal mice at 13.5

tag: strain


title: Biotin-HSR labeled lung samples, 500ng total RNA, technical rep2


title: Biotin-HSR labeled lung samples, 1000ng total RNA, technical rep1


title: Biotin-HSR labeled lung samples, 200ng total RNA, technical rep2

source_name: Lung, 200ng RNA, biotin-HSR label


title: Biotin-HSR labeled brain samples, 500ng total RNA, technical rep2

source_name: Brain, 500ng RNA, biotin-HSR label


title: Biotin-HSR labeled brain samples, 500ng total RNA, technical rep1


title: Biotin-HSR labeled brain samples, 1000ng total RNA, technical rep1

source_name: Brain, 1000ng RNA, biotin-HSR label


title: Zic3 NPC 3

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: BJ1 fibroblast transduced with OCT4, SOX2, KLF4 and Zic3

hyb_protocol: A mixture of fragmented biotinylated cDNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix  GeneChip Human Gene 1.1 ST Array Plate followed by staining and washing in the GeneTitan® Instrument (Affymetrix) according to the manufacturer's procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using the GeneTitan® HT Array Plate Scanner (Affymetrix).

data_processing: RMA-normalized expression values as obtained with the xps package (version 1.10.2) of BioConductor

source_name: ZiNPC

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Using the Ambion WT Expression Kit, per sample, an amount of 100 ng of total RNA spiked with bacterial poly-A RNA positive controls (Affymetrix) was converted to double stranded cDNA in a reverse transcription reaction. Next the sample was converted and amplified to antisense cRNA in an in vitro transcription reaction which was subsequently converted to single stranded sense cDNA. Finally, samples were fragmented and labeled with biotin in a terminal labeling reaction according to the Affymetrix WT Terminal Labeling Kit.

growth_protocol: mTESR medium

extract_protocol: Rneasy (Qiagen)

treatment_protocol: The coding region of the mouse Zic3 gene was amplified by RT-PCR and cloned in pMIG-IRES-GFP plasmid (Addgene). The pMXs plasmids encoding for OCT4, SOX2 and KLF4 were purchased from Addgene. pMXs and pMIG-based retroviral vectors  were  transfected individually along with the viral packaging genes gag-pol  (Addgene) and VSVG (Addgene)  into 293T cells  (ATCC) using Fugene HD reagent (Roche) according to the manufacturer's directions. Human BJ1 cells (Lonza) were seeded at 1.5 x 105 cells/well in 6-well plates (Sigma) without feeders. Cells were transduced with Zic3, KLF4, OCT4 and SOX2 retroviral vector containing supernatants mixed equally. To achieve maximum transduction efficiency, cells were transduced twice with the viral supernatant.  Four days after transduction, the transduced cells were reseeded at 1.5 x 105 cells per 100-mm dish containing MEF and cultured with hESC medium.  ZiNPC were picked in 15-20 days post transduction.

value: ZiNPC derived from BJ1 fibroblasts

tag: gender

value: male

value: Zic3, KLF4, OCT4 and SOX2


title: hESC NSC 3

description: neurospeheres derived from hESC

source_name: neurosphere from hESC H9

growth_protocol: neurosphere medium

treatment_protocol: hESC cultures were disaggregated using accutase for 10 min and plated on Matrigel-coated dishes in mTESR medium. hESC were allowed to expand for 3 d or until they were nearly confluent. The differentiation towards neural progenitors was performed in hESC media lacking bFGF with 10 µM TGF-b inhibitor (Tocris) and 500 ng/ml of Noggin (R&D). Upon day 5 of differentiation, the TGF-ß inhibitor was withdrawn while maintaining 500 ng/ml of Noggin and increasing amounts of N2 media (25%, 50%, 75%) was added for further 6 days with changing media for every 2 d.

tag: sample type

value: neurosphere from hESC H9

value: female

value: hESC media lacking bFGF with TGF-b inhibitor and Noggin


title: 12.5 KO limbs rep 2

description:
Lmx1b KO - 12.5 - 2
071904A_M2-12.5.CEL
Gene expression from limbs of Lmx1b KO mice at 12.5

source_name: KO embryos in handplate phase of development

value: Limb bud and girdle

tag: genotype/variation

value: Lmx1b -/-


title: 13.5 KO limbs rep 1

description:
Lmx1b KO - 13.5 - 1
0407A-02_M1-13.5.CEL
Gene expression from limbs of Lmx1b KO mice at 13.5

source_name: KO embryos in finger separation phase of limb development


title: 12.5 WT limbs rep 1

description:
Wild Type - 12.5 - 1
071904A_C1-12.5.CEL
Gene expression from limbs of normal mice at 12.5

source_name: WT embryos in handplate phase of development


title: hESC 2

description: hESC

source_name: hESC H9

treatment_protocol: cultured for two passages on matrigel in mTESR medium

value: hESC H9


title: 12.5 KO limbs rep 1

description:
Lmx1b KO - 12.5 - 1
071904A_M1-12.5.CEL
Gene expression from limbs of Lmx1b KO mice at 12.5


title: Biotin-HSR labeled lung samples, 100ng total RNA, technical rep1


title: Biotin-HSR labeled brain samples, 1000ng total RNA, technical rep2


title: hESC NSC 2

description: neurospeheres derived from hESC


title: hESC 3

description: hESC


title: Biotin-HSR labeled lung samples, 200ng total RNA, technical rep1


title: Zic3 NPCc2


title: 13.5 KO limbs rep 2

description:
Lmx1b KO - 13.5 - 2
0407A-02_M2-13.5.CEL
Gene expression from limbs of Lmx1b KO mice at 13.5


title: 12.5 WT limbs rep 2

description:
Wild Type - 12.5 - 2
071904A_C2-12.5.CEL
Gene expression from limbs of normal mice at 12.5


title: 11.5 WT limbs rep 2

description:
Wild Type - 11.5 - 2
0706A-02_C2-11.5.CEL
Gene expression from limbs of normal mice at 11.5

source_name: WT embryos in limb bud phase of development


title: Biotin-HSR labeled brain samples, 200ng total RNA, technical rep1

source_name: Brain, 200ng RNA, biotin-HSR label


title: hESC NSC 1

description: neurospeheres derived from hESC


title: LS_001_bC

city: Tuebingen

first: Felix

last: Ott

address: Spemannstr. 35-39

institute: Max Planck Institute for Developmental Biology

hyb_protocol: Probes were hybridized to Arabidopsis Tiling 1.0R arrays for 14 h at 42°C. Arrays were washed using a Fluidics Station 450, wash protocol FS450_0001.

scan_protocol: Tiling arrays were scanned using a GeneChip® Scanner 3000 7G.

data_processing: All probes that were not identically conserved in the genomes of Col-0, Bur-0 and C24 were excluded. If less than three conserved probes composed a probe set the complete set was completely excluded. For expression measurements for probe set definitions RMA normalization was applied (see Laubinger et al., Genome Biol. 2008, and Zeller et al., Plant J., 2009, for details)

organism: Arabidopsis thaliana

source_name: WT, Col-0 16°C, LL, whole inflorescenses, replicate C

label_protocol: 7.5 µg dsDNA was fragmented and labeled using the GeneChip® WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix).

growth_protocol: Plants were grown on soil at 16°C and LL until flowering.

extract_protocol: For synthesis of targets, 1 µg of total RNA was used as template for generation of cRNA using the MessageAmp II-Biotin Enhanced Kit (Ambion, Austin, TX, USA). We followed the manufacturer’s instruction with one exception: For tiling arrays, biotinylated NTPs were replaced by unmodified NTPs (stock solution 25 mM each).7 µg unmodified cRNA (for tiling arrays) was converted into dsDNA (GeneChip® WT Double-Stranded cDNA Synthesis Kit, Affymetrix, Santa Clara, CA, USA) and dsDNA was purified using the MinElute Reaction Cleanup Kit (Qiagen, Hilden, Germany).

treatment_protocol: none.

tag: cultivar


title: LS_001_bB

source_name: WT, Col-0 16°C, LL, whole inflorescenses, replicate B


title: Biotin-HSR labeled brain samples, 200ng total RNA, technical rep2

tag: tissue


title: Biotin-HSR labeled brain samples, 100ng total RNA, technical rep2

source_name: Brain, 100ng RNA, biotin-HSR label


title: Biotin-HSR labeled brain samples, 100ng total RNA, technical rep1


title: Zic3 NPC1


title: 11.5 WT limbs rep 1

description:
Wild Type - 11.5 - 1
0706A-02_C1-11.5.CEL
Gene expression from limbs of normal mice at 11.5

source_name: WT embryos in early limb bud phase of development


title: 293T-mock

status: Public on May 21 2012

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: mock-treated 293T cells

hyb_protocol: Before hybridization, 1650 ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction, LOWESS normalization, and dye-normalization .

source_name: nonhepatic cells

label_protocol: 100 ng of total RNA was labeled using Low Input Quick-Amp Labeling Kit (Agilent Technologies, Pato Alto, CA, USA). In brief, cDNA was reverse transcribed from 100 ng of total RNA with an oligo-dT-T7 promoter primer and AffinityScript MT -RT. Fluorescent antisense cRNA was synthesized with cyanine 3-CTP (Cy3-CTP), and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with miRNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).

growth_protocol: Cells were cultured at 37 °C under the condition of a humidified atmosphere and 5% CO2 and maintained in Dulbecco's modified Eagle's minimal essential medium (DMEM) supplemented with 10% fetal bovine serum (FBS).

extract_protocol: Total RNAs were extracted from cancer cell lines in RNA later (Ambion), derived from Hep3B, Huh7, Hec1B and 293T using miRNeasy extraction kit (Qiagen) following manufacturer's instructions.

treatment_protocol: Infected cell (HCV+): By using lentiviral vector, microRNA 122 was expressed in the cells. The cells were infected with cell cultured HCV (HCVcc) at an MOI of 10. RNA was collected 24 hours post-infection.

tag: infection status

value: Mock-treatment


title: 11.5 KO limbs rep 1

description:
Lmx1b KO - 11.5 - 1
0706A-02_M1-11.5.CEL
Gene expression from limbs of Lmx1b KO mice at 11.5

source_name: KO embryos in early limb bud phase of development


title: 11.5 KO limbs rep 2

description:
Lmx1b KO - 11.5 - 2
0706A-02_M2-11.5.CEL
Gene expression from limbs of Lmx1b KO mice at 11.5


title: hESC 1

description: hESC

hyb_protocol: A mixture of fragmented biotinylated cDNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix GeneChip Human Gene 1.1 ST Array Plate followed by staining and washing in the GeneTitan® Instrument (Affymetrix) according to the manufacturer's procedures.

tag: cell type


title: Hep3B-mock

description: mock-treated Hep3B cells

source_name: hepatic cells


title: LS_001_bA

source_name: WT, Col-0 16°C, LL, whole inflorescences, replicate A


title: F verticillioides total RNA_48 hr_rep1

city: Peoria

first: Robert

last: Butchko

state: IL

address: 1815 N. University St.

institute: U.S. Dept. of Agriculture

description:
Raw data file: 30648_532.ftr
This sample is of wild-type Fusarium verticillioides M3125. It is the first of two biological replicates used in this experiment, each from separate cultures.

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

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

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

organism: Fusarium verticillioides

source_name: F verticillioides, liquid media, 48 hr

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

growth_protocol: F verticillioides was grown in liquid fumonisin media (GYAM) for 2, 5 days, shaking at 250 rpm at 27 degrees celcius following Proctor et al, Co-expression of 15 contiguous genes delineates a fumonisin biosynthetic gene cluster in Gibberella moniliformis, Fungal Genetics and Biology, 38:237-249

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA).  DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

value: wild-type (fumonisin producer)

tag: time

value: 48 hr


title: Pi0.1+U200 [Olga35]

city: Chicago

first: Olga

middle: Y

last: ZABORINA

address: 5841 S Maryland

department: Surgery

institute: University of Chicago

description:
gene expression of P. aeruginosa PAO1 in 0.1xTY supplemented with kappa-opioid
Gene Chip Pseudomonas aeruginosa genome array
JA8.CEL

hyb_protocol: 1.5 µg of fragmented  and biotin labeled targets was hybridized to array for 16 h at 50°C and 60 rpm in an Affymetrix Hybridization Oven 640.

scan_protocol: After hybridization, arrays were washed and stained with Streptavidin Phycoerythrin. The fluorescent signals were amplified using a biotinylated antistreptavidin antibody in a Affymetrix GeneChip Fluidics Station (Affymetrix, Inc.) and the signals were detected in a GeneChip Scanner 3000 7G. The expression data were extracted using the Gene Chip Operating Software (MicroArray Suite 5.0 software, Affymetrix).

data_processing: Data were normalized data using RMA backround correction and Quantile normaliztion technique. The cel file were used for data analysis using ANOVA to identify differentially expressed genes [P-value <0.01 , Fold change >1.25]. dChip was used for analysis.

organism: Pseudomonas aeruginosa PAO1

source_name: liquid culture 7 hrs 0.1xTY+200 uM U-50,488

label_protocol: Ten μg of each total RNA was processed  for biotin labeled target preparation for hybridization to Pseudomonas aeruginosa expression arrays according to Genechip Expression analysis technical manual (Affymetrix, Inc).

growth_protocol: P. aeruginosa PAO1 grew in 0.1xTY supplemented when needed with 25 mM potassium phosphate buffer pH 6.0 hrs and/or 200 uM U-50,488, 7 hrs, 37C

extract_protocol: Cells were suspended in RNA protector solution (Bio-Rad), centrifuged 5,000 rpm, 10 min, 4C, lyzed in lysozyme TE solution followed by TRIzol. Total RNA was separated using PLG Phase lock gel followed by precipitation with isopropanol. DNA was removed with DNA-free kit

tag: growth stage

value: P. aeruginosa liquid culture of OD around 0.25 at 600 nm


title: Pi0.1+U200 [Olga36]

description:
gene expression of P. aeruginosa PAO1 in 0.1xTY supplemented with kappa-opioid
Gene Chip Pseudomonas aeruginosa genome array
JA9.CEL


title: Pi25 [Olga39]

description:
gene expression of P. aeruginosa PAO1 in 0.1xTY Pi 25 mM
Gene Chip Pseudomonas aeruginosa genome array
JA12.CEL

source_name: liquid culture 7 hrs 0.1xTY+Pi 25 mM


title: Pi25 [Olga38]

description:
gene expression of P. aeruginosa PAO1 in 0.1xTY Pi 25 mM
Gene Chip Pseudomonas aeruginosa genome array
JA11.CEL


title: Pi25 [Olga37]

description:
gene expression of P. aeruginosa PAO1 in 0.1xTY Pi 25 mM
Gene Chip Pseudomonas aeruginosa genome array
JA10.CEL


title: F verticillioides total RNA_120 hr_rep2

description:
Raw data file: 32083_532.ftr
This sample is of wild-type Fusarium verticillioides M3125. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: F verticillioides, liquid media, 120 hr


title: Pi0.1+U200 [Olga34]

description:
gene expression of P. aeruginosa PAO1 in 0.1xTY supplemented with kappa-opioid
Gene Chip Pseudomonas aeruginosa genome array
JA7.CEL


title: Pi 0.1 [Olga22]

description:
gene expression of P. aeruginosa PAO1 in 0.1xTY
Gene Chip Pseudomonas aeruginosa genome array
JA2.CEL

source_name: liquid culture 7 hrs 0.1xTY


title: Pi 0.1 [Olga23]

description:
gene expression of P. aeruginosa PAO1 in 0.1xTY
Gene Chip Pseudomonas aeruginosa genome array
JA3.CEL


title: F verticillioides total RNA_120 hr_rep1

description:
Raw data file: 32069_532.ftr
This sample is of wild-type Fusarium verticillioides M3125. It is the first of two biological replicates used in this experiment, each from separate cultures.


title: F verticillioides total RNA_48 hr_rep2

description:
Raw data file: 30646_532.ftr
This sample is of wild-type Fusarium verticillioides M3125. It is the second of two biological replicates used in this experiment, each from separate cultures.


title: PI25 + U200 [Olga31]

description:
gene expression of P. aeruginosa PAO1 in 0.1xTY Pi 25 mM supplemented with kappa-opioid
Gene Chip Pseudomonas aeruginosa genome array
JA4.CEL

source_name: liquid culture 7 hrs 0.1xTY+Pi 25 mM+200 uM U-50,488


title: PI25 + U200 [Olga33]

description:
gene expression of P. aeruginosa PAO1 in 0.1xTY Pi 25 mM supplemented with kappa-opioid
Gene Chip Pseudomonas aeruginosa genome array
JA6.CEL


title: PI25 + U200 [Olga32]

description:
gene expression of P. aeruginosa PAO1 in 0.1xTY Pi 25 mM supplemented with kappa-opioid
Gene Chip Pseudomonas aeruginosa genome array
JA5.CEL


title: Huh7-mock

description: mock-treated Huh7 cells

tag: cell line


title: Hec1B-mock

description: mock-treated Hec1B cells


title: 4hr WT rep3

city: Reno

first: Tong

last: Zhou

state: NV

address: 1664 N Virginia St

institute: University of Nevada School of Medicine

description: Gene expression data from lung tissue of mouse infected with WT S. aureus at 4-hour time point.

hyb_protocol: Samples were hybridized with Affymetrix Mouse Genome 430 2.0 Arrays per manufacturer’s instructions.

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

data_processing: The expression level was summarized by gcrma package in Bioconductor with GC robust multichip average (GCRMA) normalization.

source_name: 4hr WT

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

extract_protocol: Total mouse lung RNA was isolated by directly solubilizing lung tissue in Trizol LS (Life Technologies) using a Brinkman Polytron tissue disruptor.

treatment_protocol: Seven-week-old female C57BL/6J mouse (Jackson Laboratories, Wilmington, MA) was inoculated via the intranasal route with Staphylococcus aureus Newman wild-type (WT).

value: lung


title: Pi 0.1 [Olga21]

description:
gene expression of P. aeruginosa PAO1 in 0.1xTY
Gene Chip Pseudomonas aeruginosa genome array
JA1.CEL


title: 4hr Hla- rep3

description: Gene expression data from lung tissue of mouse infected with Hla- S. aureus at 4-hour time point.

source_name: 4hr Hla-

treatment_protocol: Seven-week-old female C57BL/6J mouse (Jackson Laboratories, Wilmington, MA) was inoculated via the intranasal route with Staphylococcus aureus isogenic toxin-deficient mutant (Hla-).


title: 4hr WT rep1


title: 4hr WT rep2


title: 4hr PBS rep1

description: Gene expression data from lung tissue of mouse treated with PBS at 4-hour time point.

source_name: 4hr PBS

treatment_protocol: Seven-week-old female C57BL/6J mice (Jackson Laboratories, Wilmington, MA) were inoculated via the intranasal route with phosphate-buffered saline (PBS).


title: 4hr Hla- rep1


title: 4hr Hla- rep2


title: 24hr WT rep3

description: Gene expression data from lung tissue of mouse infected with WT S. aureus at 24-hour time point.

source_name: 24hr WT


title: 4hr PBS rep2


title: KO CFU-E

city: Saint Louis

first: Ansuman

last: Satpathy

state: MO

address: 660 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University in St. Louis

hyb_protocol: Hybed onto Mouse Gene 1.0 (Affymetrix)

scan_protocol: Standard Affymetrix procedures

data_processing: Data was analyzed using Arraystar software (DNASTAR) with Quantile RMA normalization

source_name: Zbtb46gfp/gfp mice

label_protocol: Ambion/Affymetrix WT Expression Kit

growth_protocol: Cells from bone marrow were harvested by crushing bones with a mortal and pestel and isolating cells with Histopaque 1119 gradient.  Cells were Ack lysed, filtered through a 70um strainer and stained with the appropriate antibodies.

extract_protocol: Pre MegE cells were sorted as Lin- CD117+ CD150+ CD105-CD41-CD16/32-. Pre CFU-E cells were sorted as Lin- CD117+ CD150+ CD105lo CD41- CD16/32-.  CFU-E cells were sorted as Lin- CD117+ CD150- CD105+ Cd41- CD16/32-.  Splenic CD4+ DCs were sorted as B220- CD11c+ MHCII+ CD8- CD172+ CD11b+ CD4+.

treatment_protocol: Mice were analyzed at steady-state.

tag: background strain

value: CFU-E


title: Wildtype pupa vs. dicer-2 mutant pupa replicate 3

city: Seoul

first: Do-hwan

last: Lim

address: Anam-dong 5-ga, seongbuk-gu

department: college of life sciences and biotechnology

country: South Korea

institute: Korea Univ.

hyb_protocol: Fragmented cRNA was added into hybridization buffer from in situ hybridization kit (Agilent). Hybridization solution was applied onto Agilent oligo microarray, and then microarray was hybridizatied for 16h at 60°C. Microarray was washed with wash solution I(6X SSC, 0.00005% Triton-X 102) and solution II (0.1X SSC, 0.00005% Triton-X 102) for 10 min at R.T and 4°C, respectively.

scan_protocol: Scanned on a Agilent scanner G2505B

data_processing: The scaned image was analyzed using Agilent Feature Exraction software. Raw data was normalized by LOWESS normalization method.

organism: Drosophila melanogaster

source_name: Pupa

label_protocol: 1 µg of total RNA were primed with T7 oligo dT primer at 70°C for 10 min, then reversed transcribed at 42°C for 2 h using SuperScript II. Follwing cDNA synthesis, in vitro transcription was performed with T7 RNA polymerase at 37°C for 14h. cRNA for each sample was coupled with Cy-dye. Cy-dye labeled cRNA was fragmented for hybridization.

extract_protocol:
Flies were maintained on standard cornmeal/agar media under non-crowded condition at 25°C
Total RNA extracted using Trizol following manufacturer's instructions

tag: genotype

value: y w eyFLP; FRT42D

value: y w eyFLP; FRT42Ddcr-2L811fsX/FRT42Ddcr-2R416X


title: 4hr PBS rep3


city: Los Angeles

first: Vasu

last: Punj

address: Biggy Street

institute: USC

description: Gene expression data from BCBL1 cells stably expressing empty vector-treated with 4OHT

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16hr on Affymetrix GeneChip HG-U133 Plus 2 (whole genome) as recommended by manufacturer

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

data_processing: The data were analyzed with Gene Spring GX 11.5.1

source_name: BCBL1 cells from American Type Culture Collection

label_protocol: Starting from 5 µg total RNA, labeled cRNA was prepared using the Roche Microarray cDNA Synthesis, Microarray RNA Target Synthesis (T7) and Microarray Target Purification Kit, according to the manufacturer's instructions

growth_protocol: BCBL1 were grown in RPMI medium containing 10% FBS (fetal bovine serum) .  Cells were stably transduced with either a MSCVneo vector or MSCVneo expressing a 4-Hydroxytamoxifen (4-OHT)-inducible K13-ERTAM.

extract_protocol: RNA was extracted from the cells using  RNeasy mini kit (Qiagen Valenica, CA)

treatment_protocol: Cells were grown in presence or absence of 4OHT.

value: PEL Cell line

tag: transgene

value: control

tag: treatment


title: chiPS-1T(SCID)

city: La Jolla

first: Tongbiao

last: Zhao

address: 9500 Gilman Dr

department: Biological Sciences

institute: University of California San Diego

description: Gene expression data from chiPS formed terotama in SCID

hyb_protocol: Following digestion, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array

scan_protocol: GeneChips were scanned using a GeneArray Scanner.

data_processing: The data were analyzed with the Affymetrix software Command Console and Expression Console using MAS5.0 Analysis Algorithms.

source_name: Teratoma formed in SCID

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: The integration free human iPS lines chiPS was subcutaneously transplanted into the SCID and HuSCID mice

extract_protocol: Total RNAs were extracted using a Rneasy total RNA isolation kit (Qiagen) according to the mannual.

treatment_protocol: Tumors were surgically removed around 6-8 weeks after transplantation.

value: reprogrammed iPSCs (chiPS)

tag: chips transplanted into

value: SCID mice

tag: resulting tumor

value: Teratoma


title: Het Pre CFU-E

source_name: Zbtb46 gfp/+ mice

value: Zbtb46 gfp/+

value: Pre CFU-E


title: Wildtype pupa vs. dicer-2 mutant pupa replicate 1


title: KO Pre MegE

value: Pre MegE


title: Het CFU-E


description: Gene expression data from BCBL1 cells stably expressing empty vector-untreated


title: Het Pre MegE


title: congenital GBM tumor sample (CBGM_ID00692)

city: Aurora

first: Diane

middle: K

last: Birks

state: CO

department: Neurosurgery

institute: University of Colorado, Denver - Anschutz Medical Campus

description:
congenital GBM tumor sample
GBMI_ID00692_1.CEL

hyb_protocol: For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to  the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).

scan_protocol: All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).

data_processing: Data were background corrected and normalized using the gcRMA algorithm in R, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale.

source_name: patient tumor sample

label_protocol: For all samples other than PBGM_ID00089, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer.  For sample PBGM_ID00089, limited amount of starting RNA precluded use of this protocol. Instead PBGM_ID00089 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.

extract_protocol: RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions

treatment_protocol: all samples were collected at time of surgery

value: M

tag: age at diagnosis (years)

tag: disease state

value: congenital GBM tumor


title: KO Pre CFU-E


description: Gene expression data from BCBL1 cells stably expressing K13-ER with 4OHT-inducible ER system-untreated


title: congenital GBM tumor sample (CBGM_ID00531)

description:
congenital GBM tumor sample
GBMI_ID00531_1.CEL

tag: gender

value: F


title: Wildtype pupa vs. dicer-2 mutant pupa replicate 2


description: Gene expression data from BCBL1 cells stably expressing K13-ER with 4OHT-inducible ER system-treated with 4OHT


title: 24hr WT rep1

tag: strain

value: female


title: 24hr WT rep2


title: chiPS-1T(HuSCID)

description: Gene expression data from chiPS formed terotama in HuSCID

source_name: Teratoma formed by HuSCID

value: HuSCID mice


title: 24hr Hla- rep3

description: Gene expression data from lung tissue of mouse infected with Hla- S. aureus at 24-hour time point.

source_name: 24hr Hla-

value: lung


title: 24hr PBS rep3

description: Gene expression data from lung tissue of mouse treated with PBS at 24-hour time point.

source_name: 24hr PBS


title: 24hr Hla- rep2


title: vehicle 12h treatment, replicate 4 polysome-associated RNA

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

description: MCF7 treated with vehicle for 12h follwed by extraction of polysome-associated RNA.

hyb_protocol: The resulting labelled samples were hybridized to the Human Genome U133 Plus 2.0 gene arrays from Affymetrix according the instructions of the manufacturer

scan_protocol: Arrays were scanned using the GeneArray Scanner 3000 according to the instructions from the manufacturer.

data_processing: Data was extracted and normalized using a custom CDF and Robust Multi-array Average (RMA) in R (r-project.org) with default settings.

label_protocol: 500 µg cytoplasmic or polysome-associated RNA was used as starting material for the 3’ IVT Express Kit (Affymetrix).

growth_protocol: MCF7 cells were obtained from ATCC and grown in RPMI (Invitrogen), supplemented with 10% fetal bovine serum (FBS; Invitrogen), 2 mM L-glutamine, and 100 units/ml penicillin/streptomycin (all from Invitrogen) at 37oC and 5% CO2.

extract_protocol: Polysome profile analysis was carried out as previously described (Dowling RJ, Zakikhani M, Fantus IG, Pollak M, & Sonenberg N (2007) Cancer Res 67, 10804-10812). A parallel sample was collected from post-nuclear lysates that are loaded onto the sucrose gradient and RNA was isolated using Trizol (Invitrogen) (“cytoplasmic mRNA”). Polysome fractions with mRNA associated with >3 ribosomes were pooled (“polysome-associated” mRNA) and RNA was isolated using Trizol.

treatment_protocol: Cells were treated with vehicle, rapamycin (100nM), PP242 (1M) and metformin (10mM) for 12h

tag: tumor type

value: Breast cancer

tag: rna source

value: polysome-associated

value: vehicle

tag: experiment


title: 24hr Hla- rep1

tag: tissue


title: rapamycin 12h treatment, replicate 4 cytosolic RNA

description: MCF7 treated with rapamycin for 12h follwed by extraction of cytosolic RNA.

value: cytosolic

value: rapamycin


title: KO CD4+ DC

tag: genotype/variation

tag: cell type

value: CD4+ DC


title: 24hr PBS rep2


title: metformin 12h treatment, replicate 4 polysome-associated RNA

description: MCF7 treated with metformin for 12h follwed by extraction of polysome-associated RNA.

tag: cell line

value: metformin


title: adult GBM tumor sample (ABGM_xB00056)

description:
adult GBM tumor sample
GBM_xB00056_1.CEL

value: adult GBM tumor


title: WT Pre CFU-E

source_name: Zbtb46+/+ mice

tag: background strain


title: WT2 CDP

hyb_protocol: Hybed onto Mouse 430 2.0 (Affymetrix)

data_processing: Data was analyzed using dCHIP software.

source_name: WT CDP

label_protocol: 3' IVT Express Kit (Affymetrix)

extract_protocol:
BM progenitor sorts: CMPs were sorted as PI- Lin- IL7R- MHCII- CD16/32- CD11c- Cd117hi CD135+, CDPs were sorted as PI-Lin-IL7R-MHCII- CD16/32- CD11c- CD117int CD135+, pre-cDCs were sorted as PI- Lin-IL7R-. BM G MHCII- CD16/32- CD117lo CD135+ CD11c+, GMPs were sorted as PI-IL7R-IL7R-MHCII-CD11c-CD117hiCD16/32+ CD135-.
BM GM-CSF and M-CSF cultures:  whole BM was harvested as described and cultured in either 20ng/ml of GM-CSF or M-CSF for 7 days.  Non-adherent CD11c+ cells from GM-CSF were purified and analyzed.  Adherent cells from GM-CSF and M-CSF were isolated following PBS washes to remove non-adherent cells and analyzed.
BM monocytes were purified by negative selection using antibodies for Ly6G, B220, CD4, CD8a, DX5, CD11c, Ter119, and CD117, resulting in a fraction of cells that were greater than 90% pure for expression of  CD11b and Ly6C.  Cells were cultured with 20 ng/ml of GM-CSF for the indicated number of hours (Hr), harvested and microarray analysis performed.

value: bone marrow progenitor


title: WT2 PrecDC BM

source_name: WT PrecDC BM