title: Paraquat_3

status: Public on Aug 31 2013

city: Leuven

first: Barbara

last: De Coninck

address: Kasteelpark Arenberg 20

institute: KU Leuven

description: paraquat treated A. thaliana leaves (2 replicates) vs control (water) treated A. thaliana leaves (2 replicates), (4 samples in total)

hyb_protocol: A mixture of fragmented biotinylated DNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix GeneChip® Arabidopsis Tiling 1.0R Arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix)

data_processing:
Background correction, log2 transformation and interslide normalization were performed with the Affymetrix Tiling Analysis Software - Version 1.1, Build 2. Since the tiling arrays were based on the A. thaliana genome sequence of the 2007’s version of the TAIR database, the corresponding TAIR7 genome annotation was used for the analysis of the tiling array data. All steps of our strategy are illustrated in Figure S1. In a first step the average log2 intensities of biological replicates were calculated and a threshold value of 8.8 was chosen to identify transcriptionally active probes. This threshold was determined by comparing the log2 intensity distribution of genomic regions with known expression status (expressed and not expressed). Probes with log2 intensities below the threshold that were surrounded by transcriptionally active probes were considered active and vice versa to remove the effect of probes with poor hybridization properties. Secondly, groups of 4-13 successive transcriptionally active probes were combined into short transcriptionally active regions (TARs). Selection of even smaller regions would lead to a high number of false positives and to the identification of very small genes that are difficult to amplify in later stage, while all active regions of 14-15 successive probes were already annotated (TAIR7), supporting our choice of size limits. In a third step, TARs were withheld if the number of transcriptionally active probes was smaller in the control than in the PQ treatment and if the average log2 intensity of all probes in the smallest of the two regions was at least 1.4 higher in the PQ treatment than in the control. Both rules were based on the tiling array results for genomic regions that were known to be induced upon PQ treatment. The former rule was added because of the frequent occurrence of probes having zero intensity in one of the four hybridizations. In small regions these zero values can have substantial influence on the average log2 intensity leading to false positive calls. The threshold for upregulation by PQ was refined by comparing qRT-PCR and tiling array results for 30 selected TARs. All upregulations of 1.4 or more (corresponding to 2.6 fold or more) in the tiling arrays could be confirmed by qRT-PCR supporting our choice of threshold (data not shown). Finally, each selected region was compared to the A. thaliana TAIR7 genome annotation and only regions that were located in intergenic regions, introns or pseudogenes were withheld.
Results file (*signal.txt) descriptions:  first column = position on chromosome (Name: chromosome ID); second column = log transformed, normalized and background corrected intensity.

source_name: A. thaliana leaves (4 weeks old, sprayed with 25 µM paraquat)

label_protocol: Samples were fragmented and labeled with biotin in a terminal labeling reaction according to the Affymetrix WT Double-Stranded DNA Terminal Labeling Kit.

growth_protocol: Seeds of Arabidopsis thaliana wild-type ecotype Columbia-0 (Col-0) were obtained from the European A. thaliana stock Centre (NASC; http://nasc.nott.ac.uk/home.html). They were sown on ‘Zaai- en Stekgrond’ (DCM, Sint-Katelijne-Waver, Belgium) and grown in a growth chamber with 21°C temperature, 75% humidity and a 12h day-light cycle with a light intensity of approximately 120 μmol m-2s-1.

extract_protocol: After 48h treatment, RNA from A. thaliana leaves was isolated by the guanidinium isothiocyanate method (TRIzol reagent; Invitrogen, Carlsbad, USA) followed by purification using the RNeasy Mini Kit (Qiagen, Valencia, USA). First, approximately 100 mg plant material was crushed in liquid nitrogen, 1 ml of TRIzol reagent was added and samples were mixed and incubated for 5 min at room temperature. Following centrifugation (20,000 x g, 10 min, 4°C) the supernatant was transferred to a fresh tube and 200 µl of chloroform was added. The thoroughly mixed samples were incubated for 2 min at room temperature and the upper aqueous phase was transferred to a fresh tube after centrifugation (20,000 x g, 15 min, 4°C). An equal volume of 70% ethanol was added after which the samples were thoroughly shaken and applied onto a Qiagen column. The procedure was continued according to the manufacturer’s instructions. To selectively use mRNA for the tiling array analysis, RNA is converted into cDNA via an oligodT primer and reverse transcriptase. This cDNA was then used as a template for generation of cRNA.

treatment_protocol: Rosette leaves from soil-grown four-week old A. thaliana plants were sprayed with paraquat (25 µM methylviologendichlorodehydrate 98%, Sigma-Aldrich, St. Louis, MO, US) to obtain an equal and proportional distribution. Control plants were mock treated by spraying with H2O. The treated plants were kept at 100% relative humidity for 48h.

value: 4 weeks old

value: leaves

tag: treatment

value: paraquat


title: Genomic DNA from lymph node metastasis 5

status: Public on Sep 19 2013

type: genomic

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

country: USA

institute: Saint John's Cancer Institute

description:
LNM-5
Melanoma lymph node metastasis-5
Cell line derived from patient.

hyb_protocol: Sodium bisulfite modification (SBM) was performed on 1µg of gDNA using the Zymo EZ DNA methylation kit (Zymo Research). An aliquot of SBM-gDNA was analyzed by MethyLight-based quality control to test bisulfite completeness. After correction of SBM-gDNA amount, 200 ng of SBM-gDNA was whole-genome amplified and enzymatically fragmented. Finally, the gDNA was hybridized to Infinium Human Methylation 450K BeadChips.

scan_protocol: The chips were scanned with Illumina iScan using the manufacturer's recommended settings.

data_processing: Data was extracted using the R package methylumi on Bioconductor.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Melanoma lymph node metastasis

label_protocol: Standard Illumina Protocol, run at USC core services.

growth_protocol: Cell lines were grown at 37C in a 5% CO2 humidified atmosphere, in RPMI 1640 (Life Technologies-Bethesda Research Laboratories) supplemented with 10% fetal bovine serum.

extract_protocol: gDNA was extracted from cell lines via the Qiagen DNeasy Kit according to standard instructions and from tissue after microdissection from 10 μm-thick paraffin-embedded archival tissue using Qiagen DNeasy Kit according to standard instructions.

tag: tissue

value: melanoma lymph node metastasis

tag: disease

value: melanoma

tag: clinical stage

value: III


title: Genomic DNA from lymph node metastasis 15

description:
LNM-15
Melanoma lymph node metastasis-15
Tissue


title: Genomic DNA from brain metastasis 4

description:
MBM-4
Melanoma brain metastasis-4
Cell line derived from patient.

source_name: Melanoma brain metastasis

value: melanoma brain metastasis

value: IV


title: Genomic DNA from lymph node metastasis 9

description:
LNM-9
Melanoma lymph node metastasis-9
Cell line derived from patient.


title: Genomic DNA from brain metastasis 3

description:
MBM-3
Melanoma brain metastasis-3
Cell line derived from patient.


title: Subependymal zone from control mice, biological replicate 3

status: Public on Aug 01 2013

type: RNA

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

hyb_protocol: According to the Affymetrix expression protocol (HWS kit)

data_processing: RMA probeset summary with standard settings of the Affymetrix Expression Console software (v.1.2) including median polish and Sketch-Quantile normalisation

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Subependymal zone from control mice

label_protocol: WT Expression Kit (Ambion) and the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Animals per housed under spf conditions

extract_protocol: RNeasy Mini Kit (Qiagen) including DNase treatment

treatment_protocol: No treatment

tag: strain

value: Mixed background (C57BL/6, CD1)

tag: genotype

tag: age

value: 2.5 months

tag: gender

value: not determined

value: Subependymal zone


title: Olfactory bulb from control mice, biological replicate 1

scan_protocol: According to the Affymetrix expression protocol

source_name: Olfactory bulb from control mice

value: Olfactory bulb


title: Genomic DNA from primary melanoma 4

description:
PRM-4
Primary melanoma-4
Tissue

source_name: Primary melanoma

value: primary melanoma

value: II


title: Subependymal zone from control mice, biological replicate 1


title: Genomic DNA from lymph node metastasis 2

description:
LNM-2
Melanoma lymph node metastasis-2
Cell line derived from patient.


title: Subependymal zone from control mice, biological replicate 5


title: Olfactory bulb from control mice, biological replicate 2


title: Olfactory bulb from Brg1 cKO mice, biological replicate 2

source_name: Olfactory bulb from Brg1 cKO mice


title: Subependymal zone from control mice, biological replicate 4


title: Olfactory bulb from Brg1 cKO mice, biological replicate 3


title: Subependymal zone from control mice, biological replicate 2


title: Subependymal zone from Brg1 cKO mice, biological replicate 3

source_name: Subependymal zone from Brg1 cKO mice


title: Subependymal zone from Brg1 cKO mice, biological replicate 2


title: Subependymal zone from Brg1 cKO mice, biological replicate 1


title: ethanol_ethanol_91

city: Durham

first: Jeff

last: Jasper

state: NC

department: Pharmacology and Cancer Biology

institute: Duke University

hyb_protocol: Gene Chip hG-133 plus 2.0 (Affymetrix)

scan_protocol: Affymetrix GeneChip Scanner 7G

data_processing:
Raw data was background corrected with RMA, Log2 transformed, and summarized by median polish using the Affy package (v.1.36.1) in Bioconductor (v.2.15.2).
Log2 RMA, quantile normalization, summary by median polish, adjusted for batch effects.

label: Biotin

label_protocol: Ambion MessageAmp Premier Labeling

growth_protocol: MCF7 cells were plated in 6 well culture dishes at a density of 4x105 cells per well.

extract_protocol: RNA isolation (BioRad, Aurum total RNA mini kit) was performed per kit manufacturer’s instructions.

treatment_protocol: 48 hours after plating, cells were treated with ER ligands using 1 nM final concentration vehicle (ethanol) or E2 in the presence of vehicle (ethanol) or 27HC (1uM).  After 24 hours treatment, cells were washed once in PBS prior to lysis.

tag: cell line

tag: cell type

value: human breast adenocarcinoma cells

tag: treated with

value: 1 nM final conc. vehicle (ethanol) + 1 uM vehicle (ethanol) for 24hr

tag: batch


title: Genomic DNA from primary melanoma 3

description:
PRM-3
Primary melanoma-3
Tissue


title: Genomic DNA from lymph node metastasis 1

description:
LNM-1
Melanoma lymph node metastasis-1
Cell line derived from patient.


title: Olfactory bulb from control mice, biological replicate 4


title: Olfactory bulb from control mice, biological replicate 5


title: Genomic DNA from melanocyte 3

description:
MNC-3
Melanocyte-3
Cell line

source_name: Normal melanocytes

value: melanocytes


title: Olfactory bulb from Brg1 cKO mice, biological replicate 1


title: Genomic DNA from primary melanoma 2

description:
PRM-2
Primary melanoma-2
Tissue


title: Genomic DNA from primary melanoma 1

description:
PRM-1
Primary melanoma-1
Tissue


title: Genomic DNA from lymph node metastasis 3

description:
LNM-3
Melanoma lymph node metastasis-3
Cell line derived from patient.


title: ethanol_ethanol_16


title: E2_ethanol_96

value: 1 nM final conc. E2 + 1 uM vehicle (ethanol) for 24hr


title: E2_27-OH_166

value: 1 nM final conc. E2 + 1 uM 27-Hydroxycholesterol (27HC) for 24hr


title: ethanol_27-OH_164

value: 1 nM final conc. vehicle (ethanol) + 1 uM 27-Hydroxycholesterol (27HC) for 24hr


title: ethanol_27-OH_165


title: ethanol_ethanol_31


title: Genomic DNA from melanocyte 2

description:
MNC-2
Melanocyte-2
Cell line


title: HO-1 PNPase shRNA stable knockdown_3

status: Public on Jul 30 2013

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133A 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GC3000 scanner.

data_processing: After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.

source_name: Human HO-1 melanoma cells transfected with PNPase shRNA_replicate 3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChip® Expression Analysis Technical Manual, Affymetrix).

growth_protocol: The human melanoma cell line HO-1 was maintained in Dulbecco’s Modified Eagle Medium (DMEM; Invitrogen Life Technologies) supplemented with 10% fetal bovine serum (FBS; Sigma) and 5% penicillin/streptomycin (Gibco).

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

treatment_protocol: Lentiviral constructs (pGIPZ) expressing GFP were purchased from Open Biosystems that either contained non-silencing short hairpin RNA (shRNA) or shRNAs against hPNPaseold-35. For the overexpression experiments, the Adenovirus empty vector (Ad.vec) was used as a control. For all adenoviral experiments, 1x105 cells were grown in 6 cm dishes and infected after 24 hours with Ad.vec or Ad.hPNPaseold-35 at a final m.o.i of 5000vp/cell diluted in 1ml of serum free media. After 6 hours of infection with shaking every 15 minutes, complete media was added and cells were harvested at the required time points (e.g., 36 hours post-infection) for microarray analysis, RNA or protein isolation.

value: transfected with PNPase shRNA


title: HO-1 Control_scrambled shRNA_2

source_name: Human HO-1 melanoma cells transfected with scrambled shRNA_replicate 2

value: transfected with scrambled shRNA


title: E2_27-OH_168


title: E2_27-OH_167


title: E2_ethanol_36


title: ethanol_27-OH_163


title: HO-1 PNPase shRNA stable knockdown_1

source_name: Human HO-1 melanoma cells transfected with PNPase shRNA_replicate 1


title: HO-1 Control_scrambled shRNA_1

source_name: Human HO-1 melanoma cells transfected with scrambled shRNA_replicate 1


title: E2_ethanol_21


title: HO-1 Control_scrambled shRNA_3

source_name: Human HO-1 melanoma cells transfected with scrambled shRNA_replicate 3


title: HO-1 PNPase shRNA stable knockdown_2

source_name: Human HO-1 melanoma cells transfected with PNPase shRNA_replicate 2


title: Genomic DNA from melanocyte 1

description:
MNC-1
Melanocyte-1
Cell line


title: Olfactory bulb from control mice, biological replicate 3


title: PB CD34+ cells from PMF patient 5793

status: Public on Jul 23 2013

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

description: Peripheral Blood CD34+ cells from PMF patient

hyb_protocol: Fragmented cRNA was hybridized for 16 hr at 45C on Affymetrix HG-U219 array strips in GeneAtlas Hybridization Station. GeneChips were washed and stained using GeneAtlas Hybridization, Wash, and Stain Kit for 3’IVT Arrays.

scan_protocol: GeneChip were finally scanned using GeneAtlas Scanner.

data_processing: Gene expression data were imported into Partek Genomics Suite 6.6 (Partek, St Louis, Mo) as CEL files using default parameters. Raw data were preprocessed, including background correction, normalization, and summarization using robust multiarray average (RMA) analysis.

source_name: Peripheral Blood CD34+ Cells

label_protocol: Biotinylated cRNA were prepared according to the standard GeneAtlas 3’IVT Express Kit protocol from 100ng of  total RNA (P/N 702833 Rev. 4, Affymetrix). Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.

growth_protocol: CD34+ cells were purified from 30–50 ml of Peripheral Blood (PB) collected from primary mielofibrosis (PMF) patients. Mononuclear cells were separated over a Ficoll-Paque gradient (Lymphoprep; Nycomed Pharma, Asker, Norway, http://www.nycomed.com) and processed through two sequential steps of immunomagnetic CD34  selection (Miltenyi Biotec, Bergisch Gladbach,Germany,http://www.miltenyibiotec.com).

extract_protocol: CD34+ cells were purified from Peripheral blood of PMF patients and immediately  lysed in 700uL of QIAZOL Buffer (Qiagen, Valencia, CA, USA). Total RNA from CD34+ cells was extracted using miRNeasy Mini Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations for Purification of Total RNA, Including Small RNAs, from Animal Cells. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.

value: MPD

value: Primary mielofibrosis (PMF)

value: peripheral blood (PB)

tag: v617f jak2

value: neg

tag: asxl1 mut

value: pos

tag: srsf2 mut

tag: ezh2 mut

tag: at least one mutation


title: PB CD34+ cells from PMF patient 5017


title: PB CD34+ cells from PMF patient 4771


title: PB CD34+ cells from PMF patient 5782


title: PB CD34+ cells from PMF patient 5760


title: PB CD34+ cells from PMF patient 5005


title: PB CD34+ cells from PMF patient 5776


title: PB CD34+ cells from PMF patient 5008


title: PB CD34+ cells from PMF patient 5396


title: PB CD34+ cells from PMF patient 5035


title: PB CD34+ cells from PMF patient 5024


title: PB CD34+ cells from PMF patient 5578


title: Pituitary lesion, homozygous for Cdknb1 mutation, biological replicate 16

status: Public on Jul 10 2013

description: Gene expression data from pituitary lesions

data_processing: RMA probeset summary and quantile normalisation (Expression console)

organism: Rattus norvegicus

source_name: Pituitary lesion, sample 09/1122.1

label_protocol: GeneChip® Whole Transcript (WT) Sense Target Labeling Assay (Affymetrix)

value: Sprague–Dawley white eye/Wistar–Kyoto

value: 12 months

value: Female

tag: genotype/variation

value: p27Kip1 (Cdknb1) mutant, homozygous

value: pituitary lesion


title: PB CD34+ cells from PMF patient 5775

tag: tissue


title: PB CD34+ cells from PMF patient 5408

tag: disease


title: Pituitary lesion, homozygous for Cdknb1 mutation, biological replicate 15

source_name: Pituitary lesion, sample 09/1121.1


title: Pituitary lesion, homozygous for Cdknb1 mutation, biological replicate 14

source_name: Pituitary lesion, sample 09/1111.1


title: Pituitary lesion, homozygous for Cdknb1 mutation, biological replicate 08

source_name: Pituitary lesion, sample 08/959

value: 7 months


title: PB CD34+ cells from PMF patient 5196


title: Pituitary lesion, homozygous for Cdknb1 mutation, biological replicate 09

source_name: Pituitary lesion, sample 08/695.1

value: Male


title: Pituitary lesion, homozygous for Cdknb1 mutation, biological replicate 07

source_name: Pituitary lesion, sample 08/592.4

value: 10 months


title: Pituitary lesion, homozygous for Cdknb1 mutation, biological replicate 11

source_name: Pituitary lesion, sample 08/695.3


title: PB CD34+ cells from PMF patient 5566


title: PB CD34+ cells from PMF patient 5757


title: Pituitary lesion, homozygous for Cdknb1 mutation, biological replicate 12

source_name: Pituitary lesion, sample 09/1026.1

value: 8 months


title: Pituitary lesion, homozygous for Cdknb1 mutation, biological replicate 02

source_name: Pituitary lesion, sample 08/666.2

value: 11 months


title: PB CD34+ cells from PMF patient 5415


title: Pituitary lesion, homozygous for Cdknb1 mutation, biological replicate 05

source_name: Pituitary lesion, sample 08/592.2


title: PB CD34+ cells from PMF patient 5719


title: Pituitary lesion, homozygous for Cdknb1 mutation, biological replicate 06

source_name: Pituitary lesion, sample 08/592.3


title: Pituitary lesion, homozygous for Cdknb1 mutation, biological replicate 17

source_name: Pituitary lesion, sample 09/1122.2


title: Pituitary lesion, homozygous for Cdknb1 mutation, biological replicate 10

source_name: Pituitary lesion, sample 08/695.2


title: Pituitary lesion, homozygous for Cdknb1 mutation, biological replicate 03

source_name: Pituitary lesion, sample 08/771.2


title: Pituitary lesion, homozygous for Cdknb1 mutation, biological replicate 04

source_name: Pituitary lesion, sample 08/771.3


title: PB CD34+ cells from PMF patient 4831


title: Pituitary lesion, homozygous for Cdknb1 mutation, biological replicate 01

source_name: Pituitary lesion, sample 08/666.1


title: Pituitary, biological replicate 1

description: Gene expression data from normal pituitary

source_name: Normal pituitary, sample 08/547

value: 6 months

value: wildtype

value: normal pituitary


title: Pituitary, biological replicate 4

source_name: Normal pituitary, sample 09/333


title: Pituitary, biological replicate 2

source_name: Normal pituitary, sample 08/546


title: Pituitary, biological replicate 3

source_name: Normal pituitary, sample 09/782


title: Pituitary, biological replicate 5

source_name: Normal pituitary, sample 09/934


title: SU-DHL-1 cells transfected with empty vector, biological replicate 3

description: Gene expression data from cell line transiently transfected with empty vector

hyb_protocol: According to the Affymetrix expression protocol

data_processing: RMA probeset summary and quantile normalisation performed using CARMAweb RMA package.

source_name: Transient transfection of SU-DHL-1 cell line with empty vector

label_protocol: One-Cycle Eukaryotic Target Labeling Assay (Affymetrix)

growth_protocol: Normal cell culture conditions (according to the Leukemia-Lymphoma Cell line Facts Book and Hans G. Drexler, German Collection of Microorganisms and Cell Cultures Braunschweig, Germany, Academic Press)

treatment_protocol: Transfection with viral particals coding for shRNAs for C/EBPbeta or control particels (or untreated)

value: male


title: SU-DHL-1 cells transfected with shRNA for C/EBPbeta, biological replicate 3

description: Gene expression data from cell line transiently transfected with shRNA for C/EBPbeta

source_name: Transient transfection of SU-DHL-1 cell line with shRNA for C/EBPbeta


title: SU-DHL-1 cells transfected with shRNA for C/EBPbeta, biological replicate 1


title: Ki-JK cells not transfected, biological replicate 1

description: Gene expression data from cell line not transfected

source_name: Ki-JK cell line not transfected

value: Ki-JK


title: SU-DHL-1 cells transfected with empty vector, biological replicate 1


title: SU-DHL-1 cells not transfected, biological replicate 1

source_name: SU-DHL-1 cell line not transfected


title: Ki-JK cells transfected with empty vector, biological replicate 1

source_name: Transient transfection of Ki-JK cell line with empty vector


title: Ki-JK cells transfected with empty vector, biological replicate 2


title: Ki-JK cells transfected with shRNA for C/EBPbeta, biological replicate 2

source_name: Transient transfection of Ki-JK cell line with shRNA for C/EBPbeta


title: WholeBloodRNA_IN0239_Day3

status: Public on Jun 18 2013

city: Bethesda

first: Luis

middle: M

last: Franco

state: MD

address: 9000 Rockville Pike

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol. Scanning was performed on an Illumina iScan system

data_processing:
Raw data underwent background adjustment, variance stabilization transformation, and robust spline normalization using R package lumi (available from Bioconductor) and function lumiExpresso()
The data normalized by background adjustment, variance stabilization transformation, and robust spline normalization in R package lumi

source_name: Whole blood

label_protocol: Biotinylated cRNA was prepared with the Ambion Illumina TotalPrep RNA Amplification Kit

growth_protocol: For each sample, 2.5 mL whole blood was collected directly into PAXgene RNA Stabilization Tubes (QIAGEN), mixed by inverting, incubated at room temperature for at least 2 hours, then frozen at -80C until the time of purification

extract_protocol: RNA was extracted with the QIAGEN PAXgene Blood RNA System, in accordance with the protocol provided with the kit. Quality control was performed on a BioRad Experion microfluidic electrophoresis system

value: whole blood

tag: subject

tag: time

tag: treatment

value: trivalent influenza vaccination


title: WholeBloodRNA_IN0241_Day3


title: WholeBloodRNA_IN0240_Day0

value: baseline


title: WholeBloodRNA_IN0240_Day1


title: WholeBloodRNA_IN0239_Day14


title: Ki-JK cells transfected with shRNA for C/EBPbeta, biological replicate 1


title: SU-DHL-1 cells transfected with empty vector, biological replicate 2


title: WholeBloodRNA_IN0241_Day0


title: WholeBloodRNA_IN0241_Day1


title: Ki-JK cells transfected with empty vector, biological replicate 3

description: Gene expression data from cell line transiently transfected with viral particals coding for control shRNA


title: SU-DHL-1 cells transfected with shRNA for C/EBPbeta, biological replicate 2


title: WholeBloodRNA_IN0239_Day0


title: WholeBloodRNA_IN0238_Day3


title: WholeBloodRNA_IN0241_Day14


title: Ki-JK cells transfected with shRNA for C/EBPbeta, biological replicate 3


title: WholeBloodRNA_IN0240_Day14


title: WholeBloodRNA_IN0240_Day3


title: WholeBloodRNA_IN0238_Day14


title: WholeBloodRNA_IN0237_Day0


title: WholeBloodRNA_IN0238_Day1


title: WholeBloodRNA_IN0236_Day3


title: WholeBloodRNA_IN0236_Day1


title: WholeBloodRNA_IN0237_Day1


title: WholeBloodRNA_IN0238_Day0


title: WholeBloodRNA_IN0237_Day14


title: WholeBloodRNA_IN0236_Day14


title: WholeBloodRNA_IN0234_Day3


title: WholeBloodRNA_IN0236_Day0


title: WholeBloodRNA_IN0232_Day14


title: WholeBloodRNA_IN0230_Day3


title: WholeBloodRNA_IN0234_Day0


title: WholeBloodRNA_IN0239_Day1


title: WholeBloodRNA_IN0234_Day1


title: WholeBloodRNA_IN0234_Day14


title: WholeBloodRNA_IN0230_Day0


title: WholeBloodRNA_IN0232_Day0


title: WholeBloodRNA_IN0229_Day3


title: WholeBloodRNA_IN0230_Day1


title: WholeBloodRNA_IN0232_Day3


title: WholeBloodRNA_IN0228_Day14


title: WholeBloodRNA_IN0228_Day0


title: WholeBloodRNA_IN0232_Day1


title: WholeBloodRNA_IN0229_Day14


title: WholeBloodRNA_IN0237_Day3


title: WholeBloodRNA_IN0229_Day0


title: WholeBloodRNA_IN0229_Day1


title: WholeBloodRNA_IN0228_Day3


title: WholeBloodRNA_IN0227_Day14


title: WholeBloodRNA_IN0227_Day0


title: WholeBloodRNA_IN0227_Day1


title: WholeBloodRNA_IN0226_Day1


title: WholeBloodRNA_IN0227_Day3


title: WholeBloodRNA_IN0226_Day14


title: WholeBloodRNA_IN0226_Day0


title: WholeBloodRNA_IN0225_Day1


title: WholeBloodRNA_IN0226_Day3


title: WholeBloodRNA_IN0225_Day3


title: WholeBloodRNA_IN0222_Day0


title: WholeBloodRNA_IN0221_Day3


title: WholeBloodRNA_IN0224_Day1


title: WholeBloodRNA_IN0225_Day0


title: WholeBloodRNA_IN0220_Day0


title: WholeBloodRNA_IN0230_Day14


title: WholeBloodRNA_IN0224_Day3


title: WholeBloodRNA_IN0222_Day14


title: WholeBloodRNA_IN0223_Day1


title: WholeBloodRNA_IN0223_Day0


title: WholeBloodRNA_IN0221_Day14


title: WholeBloodRNA_IN0222_Day1


title: WholeBloodRNA_IN0224_Day0


title: WholeBloodRNA_IN0219_Day3


title: WholeBloodRNA_IN0221_Day0


title: WholeBloodRNA_IN0219_Day14


title: WholeBloodRNA_IN0221_Day1


title: WholeBloodRNA_IN0223_Day14


title: WholeBloodRNA_IN0220_Day14


title: WholeBloodRNA_IN0220_Day1


title: WholeBloodRNA_IN0219_Day0


title: WholeBloodRNA_IN0220_Day3


title: WholeBloodRNA_IN0223_Day3


title: WholeBloodRNA_IN0218_Day14


title: WholeBloodRNA_IN0219_Day1


title: WholeBloodRNA_IN0218_Day1


title: WholeBloodRNA_IN0222_Day3


title: WholeBloodRNA_IN0218_Day0


title: WholeBloodRNA_IN0217_Day3


title: WholeBloodRNA_IN0217_Day14


title: WholeBloodRNA_IN0311_Day3

value: female


title: WholeBloodRNA_IN0311_Day1


title: WholeBloodRNA_IN0311_Day14


title: WholeBloodRNA_IN0218_Day3


title: WholeBloodRNA_IN0217_Day1


title: WholeBloodRNA_IN0217_Day0


title: WholeBloodRNA_IN0310_Day1


title: WholeBloodRNA_IN0216_Day3


title: WholeBloodRNA_IN0309_Day3


title: WholeBloodRNA_IN0311_Day0


title: WholeBloodRNA_IN0310_Day0


title: WholeBloodRNA_IN0310_Day3


title: WholeBloodRNA_IN0309_Day14


title: WholeBloodRNA_IN0216_Day14


title: WholeBloodRNA_IN0216_Day0


title: WholeBloodRNA_IN0216_Day1


title: WholeBloodRNA_IN0309_Day1


title: WholeBloodRNA_IN0215_Day1


title: WholeBloodRNA_IN0309_Day0


title: WholeBloodRNA_IN0215_Day0


title: WholeBloodRNA_IN0215_Day3


title: WholeBloodRNA_IN0308_Day0


title: WholeBloodRNA_IN0308_Day14


title: WholeBloodRNA_IN0214_Day3


title: WholeBloodRNA_IN0214_Day1


title: WholeBloodRNA_IN0307_Day3


title: WholeBloodRNA_IN0308_Day3


title: WholeBloodRNA_IN0307_Day14


title: WholeBloodRNA_IN0307_Day0


title: WholeBloodRNA_IN0214_Day0


title: WholeBloodRNA_IN0307_Day1


title: WholeBloodRNA_IN0306_Day3


title: WholeBloodRNA_IN0215_Day14


title: WholeBloodRNA_IN0213_Day3


title: WholeBloodRNA_IN0213_Day0


title: WholeBloodRNA_IN0213_Day1


title: WholeBloodRNA_IN0212_Day1


title: WholeBloodRNA_IN0306_Day0


title: WholeBloodRNA_IN0213_Day14


title: WholeBloodRNA_IN0212_Day3


title: WholeBloodRNA_IN0306_Day1


title: WholeBloodRNA_IN0306_Day14


title: WholeBloodRNA_IN0305_Day1


title: WholeBloodRNA_IN0305_Day3


title: WholeBloodRNA_IN0305_Day0


title: WholeBloodRNA_IN0212_Day14


title: WholeBloodRNA_IN0212_Day0


title: WholeBloodRNA_IN0211_Day1


title: WholeBloodRNA_IN0304_Day3


title: WholeBloodRNA_IN0211_Day14


title: WholeBloodRNA_IN0305_Day14


title: WholeBloodRNA_IN0210_Day3


title: WholeBloodRNA_IN0211_Day3


title: WholeBloodRNA_IN0304_Day0


title: WholeBloodRNA_IN0304_Day1


title: WholeBloodRNA_IN0214_Day14


title: WholeBloodRNA_IN0304_Day14


title: WholeBloodRNA_IN0210_Day14


title: WholeBloodRNA_IN0210_Day0


title: WholeBloodRNA_IN0301_Day3


title: WholeBloodRNA_IN0208_Day3


title: WholeBloodRNA_IN0303_Day1


title: WholeBloodRNA_IN0211_Day0


title: WholeBloodRNA_IN0210_Day1


title: WholeBloodRNA_IN0303_Day14


title: WholeBloodRNA_IN0300_Day14


title: WholeBloodRNA_IN0209_Day0


title: WholeBloodRNA_IN0209_Day1


title: WholeBloodRNA_IN0209_Day14


title: WholeBloodRNA_IN0301_Day14


title: WholeBloodRNA_IN0300_Day1


title: WholeBloodRNA_IN0208_Day14


title: WholeBloodRNA_IN0303_Day3


title: WholeBloodRNA_IN0208_Day1


title: WholeBloodRNA_IN0301_Day1


title: WholeBloodRNA_IN0300_Day0


title: WholeBloodRNA_IN0209_Day3


title: WholeBloodRNA_IN0301_Day0


title: WholeBloodRNA_IN0208_Day0


title: WholeBloodRNA_IN0299_Day14


title: WholeBloodRNA_IN0299_Day0


title: WholeBloodRNA_IN0299_Day3


title: WholeBloodRNA_IN0299_Day1


title: WholeBloodRNA_IN0207_Day3


title: WholeBloodRNA_IN0207_Day1


title: WholeBloodRNA_IN0298_Day1


title: WholeBloodRNA_IN0207_Day0


title: WholeBloodRNA_IN0206_Day3


title: WholeBloodRNA_IN0297_Day3


title: WholeBloodRNA_IN0298_Day3


title: WholeBloodRNA_IN0298_Day14


title: WholeBloodRNA_IN0206_Day1


title: WholeBloodRNA_IN0205_Day14


title: WholeBloodRNA_IN0298_Day0


title: WholeBloodRNA_IN0206_Day0


title: WholeBloodRNA_IN0206_Day14


title: WholeBloodRNA_IN0297_Day14


title: WholeBloodRNA_IN0297_Day0


title: WholeBloodRNA_IN0207_Day14


title: WholeBloodRNA_IN0205_Day1


title: WholeBloodRNA_IN0297_Day1


title: WholeBloodRNA_IN0296_Day14


title: WholeBloodRNA_IN0204_Day3


title: WholeBloodRNA_IN0205_Day3


title: WholeBloodRNA_IN0296_Day3


title: WholeBloodRNA_IN0204_Day0


title: WholeBloodRNA_IN0204_Day14


title: WholeBloodRNA_IN0205_Day0


title: WholeBloodRNA_IN0203_Day1


title: WholeBloodRNA_IN0294_Day1


title: WholeBloodRNA_IN0295_Day0


title: WholeBloodRNA_IN0204_Day1


title: WholeBloodRNA_IN0202_Day3


title: WholeBloodRNA_IN0295_Day3


title: WholeBloodRNA_IN0296_Day1


title: WholeBloodRNA_IN0202_Day0


title: WholeBloodRNA_IN0202_Day14


title: WholeBloodRNA_IN0295_Day14


title: WholeBloodRNA_IN0203_Day3


title: WholeBloodRNA_IN0203_Day14


title: WholeBloodRNA_IN0202_Day1


title: WholeBloodRNA_IN0201_Day14


title: WholeBloodRNA_IN0290_Day14


title: WholeBloodRNA_IN0294_Day0


title: WholeBloodRNA_IN0201_Day0


title: WholeBloodRNA_IN0201_Day1


title: WholeBloodRNA_IN0292_Day1


title: WholeBloodRNA_IN0295_Day1


title: WholeBloodRNA_IN0203_Day0


title: WholeBloodRNA_IN0294_Day3


title: WholeBloodRNA_IN0292_Day0


title: WholeBloodRNA_IN0292_Day14


title: WholeBloodRNA_IN0292_Day3


title: WholeBloodRNA_IN0296_Day0


title: WholeBloodRNA_IN0290_Day3


title: WholeBloodRNA_IN0200_Day3


title: WholeBloodRNA_IN0289_Day0


title: WholeBloodRNA_IN0199_Day14


title: WholeBloodRNA_IN0289_Day3


title: WholeBloodRNA_IN0289_Day14


title: WholeBloodRNA_IN0199_Day3


title: WholeBloodRNA_IN0200_Day14


title: WholeBloodRNA_IN0288_Day3


title: WholeBloodRNA_IN0290_Day0


title: WholeBloodRNA_IN0200_Day1


title: WholeBloodRNA_IN0199_Day1


title: WholeBloodRNA_IN0199_Day0


title: WholeBloodRNA_IN0288_Day14


title: WholeBloodRNA_IN0197_Day14


title: WholeBloodRNA_IN0200_Day0


title: WholeBloodRNA_IN0198_Day3


title: WholeBloodRNA_IN0290_Day1


title: WholeBloodRNA_IN0289_Day1


title: WholeBloodRNA_IN0287_Day3


title: WholeBloodRNA_IN0288_Day1


title: WholeBloodRNA_IN0288_Day0


title: WholeBloodRNA_IN0287_Day0


title: WholeBloodRNA_IN0198_Day14


title: WholeBloodRNA_IN0287_Day1


title: WholeBloodRNA_IN0287_Day14


title: WholeBloodRNA_IN0198_Day0


title: WholeBloodRNA_IN0196_Day3


title: WholeBloodRNA_IN0284_Day14


title: WholeBloodRNA_IN0286_Day0


title: WholeBloodRNA_IN0196_Day0


title: WholeBloodRNA_IN0284_Day0


title: WholeBloodRNA_IN0197_Day3


title: WholeBloodRNA_IN0286_Day1


title: WholeBloodRNA_IN0196_Day1


title: WholeBloodRNA_IN0195_Day3


title: WholeBloodRNA_IN0195_Day14


title: WholeBloodRNA_IN0282_Day3


title: WholeBloodRNA_IN0195_Day1


title: WholeBloodRNA_IN0282_Day1


title: WholeBloodRNA_IN0286_Day3


title: WholeBloodRNA_IN0284_Day1


title: WholeBloodRNA_IN0286_Day14


title: WholeBloodRNA_IN0195_Day0


title: WholeBloodRNA_IN0197_Day1


title: WholeBloodRNA_IN0196_Day14


title: WholeBloodRNA_IN0194_Day3


title: WholeBloodRNA_IN0284_Day3


title: WholeBloodRNA_IN0193_Day3


title: WholeBloodRNA_IN0193_Day14


title: WholeBloodRNA_IN0194_Day14


title: WholeBloodRNA_IN0193_Day1


title: WholeBloodRNA_IN0281_Day14


title: WholeBloodRNA_IN0282_Day0


title: WholeBloodRNA_IN0281_Day1


title: WholeBloodRNA_IN0197_Day0


title: WholeBloodRNA_IN0280_Day3


title: WholeBloodRNA_IN0281_Day0


title: WholeBloodRNA_IN0193_Day0


title: WholeBloodRNA_IN0280_Day14


title: WholeBloodRNA_IN0280_Day0


title: WholeBloodRNA_IN0279_Day14


title: WholeBloodRNA_IN0280_Day1


title: WholeBloodRNA_IN0191_Day0


title: WholeBloodRNA_IN0191_Day3


title: WholeBloodRNA_IN0278_Day3


title: WholeBloodRNA_IN0279_Day3


title: WholeBloodRNA_IN0192_Day3


title: WholeBloodRNA_IN0192_Day1


title: WholeBloodRNA_IN0192_Day14


title: WholeBloodRNA_IN0192_Day0


title: WholeBloodRNA_IN0279_Day1


title: WholeBloodRNA_IN0279_Day0


title: WholeBloodRNA_IN0191_Day1


title: WholeBloodRNA_IN0191_Day14


title: WholeBloodRNA_IN0190_Day1


title: WholeBloodRNA_IN0190_Day0


title: WholeBloodRNA_IN0189_Day14


title: WholeBloodRNA_IN0190_Day3


title: WholeBloodRNA_IN0278_Day1


title: WholeBloodRNA_IN0275_Day0


title: WholeBloodRNA_IN0278_Day14


title: WholeBloodRNA_IN0189_Day0


title: WholeBloodRNA_IN0278_Day0


title: WholeBloodRNA_IN0277_Day3


title: WholeBloodRNA_IN0275_Day3


title: WholeBloodRNA_IN0277_Day14


title: WholeBloodRNA_IN0277_Day0


title: WholeBloodRNA_IN0281_Day3


title: WholeBloodRNA_IN0190_Day14


title: WholeBloodRNA_IN0189_Day1


title: WholeBloodRNA_IN0274_Day1


title: WholeBloodRNA_IN0188_Day0


title: WholeBloodRNA_IN0188_Day14


title: WholeBloodRNA_IN0277_Day1


title: WholeBloodRNA_IN0188_Day1


title: WholeBloodRNA_IN0275_Day1


title: WholeBloodRNA_IN0188_Day3


title: WholeBloodRNA_IN0274_Day3


title: WholeBloodRNA_IN0189_Day3


title: WholeBloodRNA_IN0187_Day3


title: WholeBloodRNA_IN0198_Day1


title: WholeBloodRNA_IN0187_Day14


title: WholeBloodRNA_IN0274_Day0


title: WholeBloodRNA_IN0273_Day1


title: WholeBloodRNA_IN0272_Day3


title: WholeBloodRNA_IN0187_Day1


title: WholeBloodRNA_IN0271_Day3


title: WholeBloodRNA_IN0273_Day3


title: WholeBloodRNA_IN0273_Day0


title: WholeBloodRNA_IN0272_Day0


title: WholeBloodRNA_IN0185_Day14


title: WholeBloodRNA_IN0272_Day1


title: WholeBloodRNA_IN0270_Day14


title: WholeBloodRNA_IN0186_Day3


title: WholeBloodRNA_IN0186_Day1


title: WholeBloodRNA_IN0184_Day14


title: WholeBloodRNA_IN0270_Day3


title: WholeBloodRNA_IN0271_Day0


title: WholeBloodRNA_IN0186_Day0


title: WholeBloodRNA_IN0184_Day3


title: WholeBloodRNA_IN0184_Day1


title: WholeBloodRNA_IN0185_Day1


title: WholeBloodRNA_IN0186_Day14


title: WholeBloodRNA_IN0184_Day0


title: WholeBloodRNA_IN0185_Day0


title: WholeBloodRNA_IN0185_Day3


title: WholeBloodRNA_IN0187_Day0


title: WholeBloodRNA_IN0183_Day3


title: WholeBloodRNA_IN0183_Day14


title: WholeBloodRNA_IN0268_Day0


title: WholeBloodRNA_IN0182_Day1


title: WholeBloodRNA_IN0181_Day3


title: WholeBloodRNA_IN0270_Day1


title: WholeBloodRNA_IN0268_Day3


title: WholeBloodRNA_IN0268_Day1


title: WholeBloodRNA_IN0266_Day3


title: WholeBloodRNA_IN0183_Day1


title: WholeBloodRNA_IN0267_Day0


title: WholeBloodRNA_IN0267_Day1


title: WholeBloodRNA_IN0270_Day0


title: WholeBloodRNA_IN0266_Day14


title: WholeBloodRNA_IN0182_Day14


title: WholeBloodRNA_IN0267_Day14


title: WholeBloodRNA_IN0183_Day0


title: WholeBloodRNA_IN0181_Day14


title: WholeBloodRNA_IN0182_Day0


title: WholeBloodRNA_IN0182_Day3


title: WholeBloodRNA_IN0181_Day0


title: WholeBloodRNA_IN0181_Day1


title: WholeBloodRNA_IN0266_Day1


title: WholeBloodRNA_IN0180_Day14


title: WholeBloodRNA_IN0265_Day3


title: WholeBloodRNA_IN0265_Day1


title: WholeBloodRNA_IN0180_Day0


title: WholeBloodRNA_IN0266_Day0


title: WholeBloodRNA_IN0179_Day3


title: WholeBloodRNA_IN0264_Day14


title: WholeBloodRNA_IN0265_Day14


title: WholeBloodRNA_IN0179_Day0


title: WholeBloodRNA_IN0179_Day14


title: WholeBloodRNA_IN0179_Day1


title: WholeBloodRNA_IN0180_Day1


title: WholeBloodRNA_IN0264_Day1


title: WholeBloodRNA_IN0263_Day3


title: WholeBloodRNA_IN0265_Day0


title: WholeBloodRNA_IN0178_Day3


title: WholeBloodRNA_IN0264_Day0


title: WholeBloodRNA_IN0264_Day3


title: WholeBloodRNA_IN0178_Day0


title: WholeBloodRNA_IN0178_Day14


title: WholeBloodRNA_IN0263_Day14


title: WholeBloodRNA_IN0272_Day14


title: WholeBloodRNA_IN0273_Day14


title: WholeBloodRNA_IN0263_Day1


title: WholeBloodRNA_IN0177_Day3


title: WholeBloodRNA_IN0271_Day1


title: WholeBloodRNA_IN0175_Day1


title: WholeBloodRNA_IN0178_Day1


title: WholeBloodRNA_IN0262_Day0


title: WholeBloodRNA_IN0177_Day14


title: WholeBloodRNA_IN0176_Day0


title: WholeBloodRNA_IN0262_Day3


title: WholeBloodRNA_IN0263_Day0


title: WholeBloodRNA_IN0259_Day3


title: WholeBloodRNA_IN0262_Day14


title: WholeBloodRNA_IN0175_Day3


title: WholeBloodRNA_IN0261_Day3


title: WholeBloodRNA_IN0268_Day14


title: WholeBloodRNA_IN0176_Day14


title: WholeBloodRNA_IN0261_Day0


title: WholeBloodRNA_IN0175_Day14


title: WholeBloodRNA_IN0262_Day1


title: WholeBloodRNA_IN0176_Day1


title: WholeBloodRNA_IN0177_Day0


title: WholeBloodRNA_IN0174_Day14


title: WholeBloodRNA_IN0260_Day14


title: WholeBloodRNA_IN0260_Day0


title: WholeBloodRNA_IN0261_Day14


title: WholeBloodRNA_IN0175_Day0


title: WholeBloodRNA_IN0260_Day3


title: WholeBloodRNA_IN0174_Day3


title: WholeBloodRNA_IN0261_Day1


title: WholeBloodRNA_IN0174_Day1


title: WholeBloodRNA_IN0267_Day3


title: WholeBloodRNA_IN0174_Day0


title: WholeBloodRNA_IN0173_Day14


title: WholeBloodRNA_IN0258_Day3


title: WholeBloodRNA_IN0259_Day0


title: WholeBloodRNA_IN0173_Day0


title: WholeBloodRNA_IN0259_Day1


title: WholeBloodRNA_IN0173_Day1


title: WholeBloodRNA_IN0259_Day14


title: WholeBloodRNA_IN0172_Day1


title: WholeBloodRNA_IN0170_Day3


title: WholeBloodRNA_IN0257_Day1


title: WholeBloodRNA_IN0258_Day0


title: WholeBloodRNA_IN0257_Day3


title: WholeBloodRNA_IN0258_Day1


title: WholeBloodRNA_IN0171_Day0


title: WholeBloodRNA_IN0255_Day3


title: WholeBloodRNA_IN0170_Day14


title: WholeBloodRNA_IN0258_Day14


title: WholeBloodRNA_IN0172_Day0


title: WholeBloodRNA_IN0170_Day0


title: WholeBloodRNA_IN0257_Day14


title: WholeBloodRNA_IN0169_Day3


title: WholeBloodRNA_IN0255_Day14


title: WholeBloodRNA_IN0257_Day0


title: WholeBloodRNA_IN0255_Day1


title: WholeBloodRNA_IN0170_Day1


title: WholeBloodRNA_IN0169_Day14


title: WholeBloodRNA_IN0169_Day1


title: WholeBloodRNA_IN0169_Day0


title: WholeBloodRNA_IN0254_Day14


title: WholeBloodRNA_IN0255_Day0


title: WholeBloodRNA_IN0168_Day1


title: WholeBloodRNA_IN0254_Day3


title: WholeBloodRNA_IN0168_Day14


title: WholeBloodRNA_IN0167_Day14


title: WholeBloodRNA_IN0254_Day1


title: WholeBloodRNA_IN0254_Day0


title: WholeBloodRNA_IN0168_Day3


title: WholeBloodRNA_IN0253_Day0


title: WholeBloodRNA_IN0253_Day1


title: WholeBloodRNA_IN0252_Day3


title: WholeBloodRNA_IN0252_Day14


title: WholeBloodRNA_IN0168_Day0


title: WholeBloodRNA_IN0166_Day14


title: WholeBloodRNA_IN0167_Day0


title: WholeBloodRNA_IN0167_Day1


title: WholeBloodRNA_IN0167_Day3


title: WholeBloodRNA_IN0166_Day1


title: WholeBloodRNA_IN0251_Day1


title: WholeBloodRNA_IN0252_Day0


title: WholeBloodRNA_IN0165_Day14


title: WholeBloodRNA_IN0166_Day0


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title: WholeBloodRNA_IN0253_Day14


title: WholeBloodRNA_IN0251_Day3


title: WholeBloodRNA_IN0252_Day1


title: WholeBloodRNA_IN0165_Day1


title: WholeBloodRNA_IN0250_Day3


title: WholeBloodRNA_IN0251_Day0


title: WholeBloodRNA_IN0248_Day0


title: WholeBloodRNA_IN0248_Day3


title: WholeBloodRNA_IN0164_Day1


title: WholeBloodRNA_IN0164_Day0


title: WholeBloodRNA_IN0248_Day14


title: WholeBloodRNA_IN0250_Day14


title: WholeBloodRNA_IN0164_Day14


title: WholeBloodRNA_IN0165_Day0


title: WholeBloodRNA_IN0248_Day1


title: WholeBloodRNA_IN0250_Day0


title: WholeBloodRNA_IN0247_Day3


title: WholeBloodRNA_IN0163_Day14


title: WholeBloodRNA_IN0250_Day1


title: WholeBloodRNA_IN0162_Day3


title: WholeBloodRNA_IN0171_Day1


title: WholeBloodRNA_IN0247_Day14


title: WholeBloodRNA_IN0247_Day1


title: WholeBloodRNA_IN0162_Day14


title: WholeBloodRNA_IN0162_Day0


title: WholeBloodRNA_IN0161_Day14


title: WholeBloodRNA_IN0161_Day1


title: WholeBloodRNA_IN0246_Day3


title: WholeBloodRNA_IN0246_Day1


title: WholeBloodRNA_IN0160_Day14


title: WholeBloodRNA_IN0161_Day0


title: WholeBloodRNA_IN0160_Day1


title: WholeBloodRNA_IN0246_Day14


title: WholeBloodRNA_IN0246_Day0


title: WholeBloodRNA_IN0160_Day0


title: WholeBloodRNA_IN0245_Day14


title: WholeBloodRNA_IN0245_Day1


title: WholeBloodRNA_IN0162_Day1


title: WholeBloodRNA_IN0245_Day0


title: WholeBloodRNA_IN0245_Day3


title: WholeBloodRNA_IN0247_Day0


title: WholeBloodRNA_IN0159_Day1


title: WholeBloodRNA_IN0158_Day14


title: WholeBloodRNA_IN0244_Day3


title: WholeBloodRNA_IN0159_Day0


title: WholeBloodRNA_IN0157_Day14


title: WholeBloodRNA_IN0159_Day14


title: WholeBloodRNA_IN0159_Day3


title: WholeBloodRNA_IN0244_Day1


title: WholeBloodRNA_IN0244_Day14


title: WholeBloodRNA_IN0157_Day1


title: WholeBloodRNA_IN0243_Day3


title: WholeBloodRNA_IN0244_Day0


title: WholeBloodRNA_IN0157_Day0


title: WholeBloodRNA_IN0158_Day0


title: WholeBloodRNA_IN0243_Day14


title: WholeBloodRNA_IN0243_Day1


title: WholeBloodRNA_IN0242_Day3


title: WholeBloodRNA_IN0156_Day14


title: WholeBloodRNA_IN0156_Day1


title: WholeBloodRNA_IN0156_Day0


title: WholeBloodRNA_IN0243_Day0


title: WholeBloodRNA_IN0242_Day14


title: WholeBloodRNA_IN0242_Day0


title: WholeBloodRNA_IN0155_Day14


title: WholeBloodRNA_IN0155_Day0


title: WholeBloodRNA_IN0369_Day1


title: WholeBloodRNA_IN0154_Day14


title: WholeBloodRNA_IN0155_Day3


title: WholeBloodRNA_IN0155_Day1


title: WholeBloodRNA_IN0154_Day1


title: WholeBloodRNA_IN0369_Day14


title: WholeBloodRNA_IN0369_Day0


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title: WholeBloodRNA_IN0164_Day3


title: WholeBloodRNA_IN0153_Day14


title: WholeBloodRNA_IN0153_Day3


title: WholeBloodRNA_IN0154_Day3


title: WholeBloodRNA_IN0368_Day14


title: WholeBloodRNA_IN0153_Day1


title: WholeBloodRNA_IN0368_Day0


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title: WholeBloodRNA_IN0366_Day3


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title: WholeBloodRNA_IN0153_Day0


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title: WholeBloodRNA_IN0367_Day14


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title: WholeBloodRNA_IN0366_Day14


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title: WholeBloodRNA_IN0151_Day14


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title: WholeBloodRNA_IN0151_Day3


title: WholeBloodRNA_IN0151_Day0


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title: WholeBloodRNA_IN0368_Day3


title: WholeBloodRNA_IN0151_Day1


title: WholeBloodRNA_IN0150_Day14


title: WholeBloodRNA_IN0150_Day3


title: WholeBloodRNA_IN0365_Day14


title: WholeBloodRNA_IN0149_Day1


title: WholeBloodRNA_IN0149_Day14


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title: WholeBloodRNA_IN0148_Day1


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title: WholeBloodRNA_IN0149_Day0


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title: WholeBloodRNA_IN0364_Day3


title: WholeBloodRNA_IN0148_Day3


title: WholeBloodRNA_IN0363_Day14


title: WholeBloodRNA_IN0364_Day1


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title: WholeBloodRNA_IN0363_Day3


title: WholeBloodRNA_IN0148_Day14


title: WholeBloodRNA_IN0362_Day3


title: WholeBloodRNA_IN0363_Day1


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title: WholeBloodRNA_IN0362_Day14


title: WholeBloodRNA_IN0362_Day0


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title: WholeBloodRNA_IN0146_Day14


title: WholeBloodRNA_IN0362_Day1


title: WholeBloodRNA_IN0360_Day1


title: WholeBloodRNA_IN0145_Day0


title: WholeBloodRNA_IN0147_Day0


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title: WholeBloodRNA_IN0146_Day1


title: WholeBloodRNA_IN0363_Day0


title: WholeBloodRNA_IN0143_Day3


title: WholeBloodRNA_IN0146_Day0


title: WholeBloodRNA_IN0360_Day14


title: WholeBloodRNA_IN0144_Day14


title: WholeBloodRNA_IN0145_Day14


title: WholeBloodRNA_IN0365_Day0


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title: WholeBloodRNA_IN0361_Day3


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title: WholeBloodRNA_IN0361_Day14


title: WholeBloodRNA_IN0145_Day1


title: WholeBloodRNA_IN0360_Day0


title: WholeBloodRNA_IN0144_Day0


title: WholeBloodRNA_IN0144_Day1


title: WholeBloodRNA_IN0361_Day0


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title: WholeBloodRNA_IN0359_Day1


title: WholeBloodRNA_IN0358_Day3


title: WholeBloodRNA_IN0358_Day14


title: WholeBloodRNA_IN0142_Day3


title: WholeBloodRNA_IN0359_Day0


title: WholeBloodRNA_IN0358_Day1


title: WholeBloodRNA_IN0357_Day3


title: WholeBloodRNA_IN0143_Day1


title: WholeBloodRNA_IN0141_Day3


title: WholeBloodRNA_IN0357_Day1


title: WholeBloodRNA_IN0142_Day0


title: WholeBloodRNA_IN0143_Day0


title: WholeBloodRNA_IN0357_Day14


title: WholeBloodRNA_IN0356_Day0


title: WholeBloodRNA_IN0141_Day1


title: WholeBloodRNA_IN0140_Day3


title: WholeBloodRNA_IN0358_Day0


title: WholeBloodRNA_IN0354_Day14


title: WholeBloodRNA_IN0141_Day14


title: WholeBloodRNA_IN0359_Day3


title: WholeBloodRNA_IN0356_Day14


title: WholeBloodRNA_IN0142_Day14


title: WholeBloodRNA_IN0141_Day0


title: WholeBloodRNA_IN0357_Day0


title: WholeBloodRNA_IN0356_Day1


title: WholeBloodRNA_IN0142_Day1


title: WholeBloodRNA_IN0356_Day3


title: WholeBloodRNA_IN0354_Day1


title: WholeBloodRNA_IN0139_Day3


title: WholeBloodRNA_IN0140_Day14


title: WholeBloodRNA_IN0140_Day0


title: WholeBloodRNA_IN0140_Day1


title: WholeBloodRNA_IN0353_Day14


title: WholeBloodRNA_IN0353_Day0


title: WholeBloodRNA_IN0353_Day1


title: WholeBloodRNA_IN0139_Day0


title: WholeBloodRNA_IN0352_Day0


title: WholeBloodRNA_IN0139_Day14


title: WholeBloodRNA_IN0138_Day1


title: WholeBloodRNA_IN0351_Day1


title: WholeBloodRNA_IN0351_Day3


title: WholeBloodRNA_IN0138_Day14


title: WholeBloodRNA_IN0350_Day3


title: WholeBloodRNA_IN0137_Day14


title: WholeBloodRNA_IN0351_Day0


title: WholeBloodRNA_IN0138_Day0


title: WholeBloodRNA_IN0352_Day14


title: WholeBloodRNA_IN0350_Day1


title: WholeBloodRNA_IN0354_Day0


title: WholeBloodRNA_IN0352_Day3


title: WholeBloodRNA_IN0138_Day3


title: WholeBloodRNA_IN0137_Day3


title: WholeBloodRNA_IN0139_Day1


title: WholeBloodRNA_IN0137_Day1


title: WholeBloodRNA_IN0349_Day3


title: WholeBloodRNA_IN0352_Day1


title: WholeBloodRNA_IN0353_Day3


title: WholeBloodRNA_IN0350_Day0


title: WholeBloodRNA_IN0350_Day14


title: WholeBloodRNA_IN0137_Day0


title: WholeBloodRNA_IN0349_Day1


title: WholeBloodRNA_IN0349_Day14


title: WholeBloodRNA_IN0348_Day3


title: WholeBloodRNA_IN0349_Day0


title: WholeBloodRNA_IN0136_Day3


title: WholeBloodRNA_IN0348_Day1


title: WholeBloodRNA_IN0136_Day0


title: WholeBloodRNA_IN0347_Day0


title: WholeBloodRNA_IN0347_Day1


title: WholeBloodRNA_IN0136_Day14


title: WholeBloodRNA_IN0348_Day0


title: WholeBloodRNA_IN0345_Day1


title: WholeBloodRNA_IN0348_Day14


title: WholeBloodRNA_IN0346_Day0


title: WholeBloodRNA_IN0347_Day3


title: WholeBloodRNA_IN0347_Day14


title: WholeBloodRNA_IN0136_Day1


title: WholeBloodRNA_IN0135_Day0


title: WholeBloodRNA_IN0346_Day3


title: WholeBloodRNA_IN0135_Day3


title: WholeBloodRNA_IN0346_Day14


title: WholeBloodRNA_IN0135_Day1


title: WholeBloodRNA_IN0345_Day14


title: WholeBloodRNA_IN0346_Day1


title: WholeBloodRNA_IN0344_Day14


title: WholeBloodRNA_IN0134_Day3


title: WholeBloodRNA_IN0135_Day14


title: WholeBloodRNA_IN0345_Day3


title: WholeBloodRNA_IN0344_Day1


title: WholeBloodRNA_IN0345_Day0


title: WholeBloodRNA_IN0134_Day1


title: WholeBloodRNA_IN0344_Day3


title: WholeBloodRNA_IN0134_Day14


title: WholeBloodRNA_IN0134_Day0


title: WholeBloodRNA_IN0133_Day1


title: WholeBloodRNA_IN0343_Day3


title: WholeBloodRNA_IN0342_Day0


title: WholeBloodRNA_IN0343_Day14


title: WholeBloodRNA_IN0344_Day0


title: WholeBloodRNA_IN0133_Day14


title: WholeBloodRNA_IN0342_Day3


title: WholeBloodRNA_IN0343_Day1


title: WholeBloodRNA_IN0133_Day3


title: WholeBloodRNA_IN0132_Day3


title: WholeBloodRNA_IN0342_Day14


title: WholeBloodRNA_IN0338_Day3


title: WholeBloodRNA_IN0337_Day14


title: WholeBloodRNA_IN0338_Day0


title: WholeBloodRNA_IN0338_Day1


title: WholeBloodRNA_IN0132_Day14


title: WholeBloodRNA_IN0337_Day1


title: WholeBloodRNA_IN0337_Day0


title: WholeBloodRNA_IN0132_Day0


title: WholeBloodRNA_IN0343_Day0


title: WholeBloodRNA_IN0336_Day3


title: WholeBloodRNA_IN0132_Day1


title: WholeBloodRNA_IN0336_Day1


title: WholeBloodRNA_IN0336_Day0


title: WholeBloodRNA_IN0336_Day14


title: WholeBloodRNA_IN0338_Day14


title: WholeBloodRNA_IN0335_Day3


title: WholeBloodRNA_IN0337_Day3


title: WholeBloodRNA_IN0131_Day1


title: WholeBloodRNA_IN0334_Day3


title: WholeBloodRNA_IN0131_Day14


title: WholeBloodRNA_IN0335_Day1


title: WholeBloodRNA_IN0335_Day0


title: WholeBloodRNA_IN0131_Day3


title: WholeBloodRNA_IN0334_Day14


title: WholeBloodRNA_IN0335_Day14


title: WholeBloodRNA_IN0342_Day1


title: WholeBloodRNA_IN0130_Day14


title: WholeBloodRNA_IN0330_Day1


title: WholeBloodRNA_IN0129_Day1


title: WholeBloodRNA_IN0131_Day0


title: WholeBloodRNA_IN0334_Day1


title: WholeBloodRNA_IN0331_Day0


title: WholeBloodRNA_IN0130_Day1


title: WholeBloodRNA_IN0129_Day3


title: WholeBloodRNA_IN0330_Day0


title: WholeBloodRNA_IN0129_Day0


title: WholeBloodRNA_IN0330_Day3


title: WholeBloodRNA_IN0333_Day0


title: WholeBloodRNA_IN0329_Day1


title: WholeBloodRNA_IN0329_Day14


title: WholeBloodRNA_IN0331_Day1


title: WholeBloodRNA_IN0333_Day1


title: WholeBloodRNA_IN0333_Day14


title: WholeBloodRNA_IN0329_Day0


title: WholeBloodRNA_IN0331_Day14


title: WholeBloodRNA_IN0130_Day3


title: WholeBloodRNA_IN0129_Day14


title: WholeBloodRNA_IN0130_Day0


title: WholeBloodRNA_IN0328_Day14


title: WholeBloodRNA_IN0328_Day1


title: WholeBloodRNA_IN0128_Day3


title: WholeBloodRNA_IN0330_Day14


title: WholeBloodRNA_IN0329_Day3


title: WholeBloodRNA_IN0128_Day14


title: WholeBloodRNA_IN0328_Day3


title: WholeBloodRNA_IN0327_Day1


title: WholeBloodRNA_IN0327_Day3


title: WholeBloodRNA_IN0128_Day1


title: WholeBloodRNA_IN0326_Day0


title: WholeBloodRNA_IN0327_Day14


title: WholeBloodRNA_IN0127_Day3


title: WholeBloodRNA_IN0324_Day3


title: WholeBloodRNA_IN0326_Day3


title: WholeBloodRNA_IN0328_Day0


title: WholeBloodRNA_IN0128_Day0


title: WholeBloodRNA_IN0324_Day14


title: WholeBloodRNA_IN0326_Day14


title: WholeBloodRNA_IN0127_Day1


title: WholeBloodRNA_IN0127_Day14


title: WholeBloodRNA_IN0126_Day14


title: WholeBloodRNA_IN0127_Day0


title: WholeBloodRNA_IN0126_Day3


title: WholeBloodRNA_IN0326_Day1


title: WholeBloodRNA_IN0327_Day0


title: WholeBloodRNA_IN0324_Day1


title: WholeBloodRNA_IN0322_Day3


title: WholeBloodRNA_IN0323_Day3


title: WholeBloodRNA_IN0323_Day1


title: WholeBloodRNA_IN0323_Day0


title: WholeBloodRNA_IN0322_Day1


title: WholeBloodRNA_IN0126_Day0


title: WholeBloodRNA_IN0324_Day0


title: WholeBloodRNA_IN0125_Day3


title: WholeBloodRNA_IN0322_Day0


title: WholeBloodRNA_IN0321_Day14


title: WholeBloodRNA_IN0126_Day1


title: WholeBloodRNA_IN0321_Day1


title: WholeBloodRNA_IN0321_Day0


title: WholeBloodRNA_IN0321_Day3


title: WholeBloodRNA_IN0320_Day3


title: WholeBloodRNA_IN0125_Day0


title: WholeBloodRNA_IN0320_Day1


title: WholeBloodRNA_IN0320_Day0


title: WholeBloodRNA_IN0320_Day14


title: WholeBloodRNA_IN0319_Day3


title: WholeBloodRNA_IN0316_Day14


title: WholeBloodRNA_IN0123_Day3


title: WholeBloodRNA_IN0123_Day14


title: WholeBloodRNA_IN0317_Day1


title: WholeBloodRNA_IN0319_Day1


title: WholeBloodRNA_IN0123_Day1


title: WholeBloodRNA_IN0319_Day0


title: WholeBloodRNA_IN0316_Day3


title: WholeBloodRNA_IN0316_Day0


title: WholeBloodRNA_IN0125_Day1


title: WholeBloodRNA_IN0316_Day1


title: WholeBloodRNA_IN0317_Day0


title: WholeBloodRNA_IN0315_Day1


title: WholeBloodRNA_IN0315_Day3


title: WholeBloodRNA_IN0123_Day0


title: WholeBloodRNA_IN0312_Day3


title: WholeBloodRNA_IN0124_Day0


title: WholeBloodRNA_IN0315_Day14


title: WholeBloodRNA_IN0312_Day14


title: WholeBloodRNA_IN0312_Day1


title: female_DR_rep1

status: Public on May 01 2013

city: Cologne

first: Julia

last: Hoffmann

address: Joseph-Stelzmann-Str. 9b

department: Partridge

institute: MPI for Biology of Ageing

hyb_protocol: 200 pmol of the labelled samples (corresponding to approx. 2-3 µg cRNA) in hybridisation buffer containing salmon testes DNA and yeast tRNA were hybridized to the array at 42°C overnight. After hybridization, slides were washed twice with1 × SSC at RT for 1 h; 1 × SSC, 0.1% Triton-X- 100 at 60°C for 30 minutes and with 0.1 × SSC, 0.1% Tri- ton-X-100 at 37°C for 30 min. Subsequently, they were washed with 0.1 × SSC for 30 seconds at RT and rinsed with water before dried.

scan_protocol: The slides were scanned with the GenePixTM 4000B scanner (Axon Instruments, Molecular Devices, Munich, Germany). For spot finding and generating preliminary result files, the raw scanned image files were analyzed using GenePixPro version 6.0 (Axon Instruments), whereas data normalization and further data filtering were performed with Acuity 4.1 (Axon Instruments).

data_processing: Ratio-based normalization using default settings in Acuity. Criteria for inclusion of data in further analysis: Signal-to noise-ratio for at least one of the wavelengths > 3; -10 > log2 ratio ch2/ch1> 10; features is not flagged bad or absent in previous GenePix analysis.

label: Alexa Fluor 555

organism: Drosophila melanogaster

source_name: fat body, control food, 7 d

label_protocol: In brief, cDNA synthesis from RNA isolated from fat bodies was performed with Prime Script RT (Takara) using the following primers: OdT T7 I (5’-GAG AGA GGA TCC AAG TAC TAA TAC GAC TCA CTA TAG GGA GAT TTT TTT TTT TTT TTT TTT TTT T G/A/C-3’) and CapFinder Sp6rG (5’-CAG CGG CCG CAG ATT TAG GTG ACA CTA TAG A rGrGrG-3’). cDNA was amplified with OdT T7 II (5’-GAG AGA GGA TCC AAG TAC TAA TAC GAC TCA CTA TAG G-3’) and Adaptor Sp6rG (5’-GAC GCC TGC AGG CGA TGA ATT TAG G-3’) and LA Taq polymerase. cDNA was transcribed with MEGAscript® T7 (Ambion) including aminoallyl-UTP (Ambion) and subsequently labeled with Alexa Fluor 555 or 647 (Invitrogen) for control or experimental sample, respectively.

growth_protocol: Fly stocks were raised on standard cornmeal-agar medium at 25 °C under a 12 h/12 h light/dark cycle.

extract_protocol: Isolation of total RNA with Trizol (RNAmagic, Biobudget).

value: fat body

tag: strain

tag: genotype

value: wild-type

tag: age at start of treatment

value: 2 d

value: 7 d control food

label: Alexa Fluor 647

source_name: fat body, dietary restriction food, 7d

value: 7 d dietary restriction food


title: female_sir2up_rep3

source_name: fat body, ethanol, 24 h

tag: gender

value: 24 h ethanol (control)

source_name: fat body, RU486, 24 h

value: 24 h RU486 (Sir2 overexpression in fat body)


title: female_DR_rep3


title: female_DR_rep2


title: female_sir2up_rep1


title: male_sir2up_rep2


title: female_sir2up_rep2


title: male_sir2up_rep1


title: male_sir2up_rep3


title: Embryonic cerebral cortex, Trnp1 knockdown, biological replicate 2

status: Public on Apr 26 2013

description: Gene expression data from embryonic cerebral cortex, Trnp1 knockdown

hyb_protocol: According to the Affymetrix expression protocol (HWS kit).

scan_protocol: According to the Affymetrix expression protocol.

data_processing: RMA probeset summary with standard settings of the Affymetrix Expression Console software (v.1.2) including median polish and Sketch-Quantile normalisation.

source_name: Trnp1 knockdown tissue

label_protocol: Ovation PicoSL WTA System V2 and Encore Biotin Module (Nugen).

extract_protocol: RNeasy Mini or Micro Kit (Qiagen) including DNase treatment.

treatment_protocol: Briefly, E13 cortices were electroporated with the constructs for overexpression and knockdown including GFP as transfection control. 24h after transfection GFP positive cells were isolated by FACS.

value: cerebral cortex

tag: age

value: not determined

value: Trnp1 knockdown


title: Embryonic cerebral cortex, Trnp1 knockdown, biological replicate 3


title: Embryonic cerebral cortex, control, biological replicate 1

description: Gene expression data from embryonic cerebral cortex, control

source_name: control tissue

value: WT


title: ulcerative colitis colon mucosa Kelle41

status: Public on Jun 01 2013

city: Houston

first: R.

middle: Alan

last: Harris

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: Ulcerative colitis before treatment with 6-mercaptopurine and mesalamine colon mucosa sample.

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to the Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol

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

data_processing: GenomeStudio software version 2010.3.0.30128

source_name: colon mucosa Kelle41, before treatment with 6-mercaptopurine and mesalamine

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted and purified from colon mucosa samples using QIAamp DNA Mini Kit (Qiagen, Valencia, CA) starting at step 5 of the Tissue Protocol following bead beating and Qiagen TissueLyser treatment. All samples were quality tested with PicoGreen prior to proceeding with the microarrays.

value: Male

tag: age (y)

value: Colon mucosa

tag: disease state

value: ulcerative colitis


title: Control rostral cerebral cortex at embryonic day E14 (littermate of Pax6 Leca4 mutants), biological replicate 2 [WT_2]

status: Public on Mar 19 2013

description: Gene expression data from embryonic rostral cerebral cortex from wildtype mice

data_processing: RMA analysis with CARMAweb standard settings (University Graz)

source_name: Rostral cerebral cortex from WT control mice

label_protocol: MessageAmp Premier RNA Amplification Kit (Ambion AM1792)

growth_protocol: Animals housed under spf conditions

extract_protocol: RNeasy Micro Kit (Qiagen) including DNase treatment

value: Embryonic day E14

value: nd

value: Wild type


title: Control rostral cerebral cortex at embryonic day E14 (littermate of Pax6 Leca4 mutants), biological replicate 1 [WT_1]


title: Pax6 mutant (Leca4) rostral cerebral cortex at embryonic day E14, biological replicate 3

description: Gene expression data from embryonic rostral cerebral cortex from Leca4 mice

source_name: Rostral cerebral cortex from Leca4 mice

value: Pax6 Leca4 mutant


title: Embryonic cerebral cortex, control, biological replicate 2


title: Control rostral cerebral cortex at embryonic day E14 (littermate of Pax6 Leca4 mutants), biological replicate 3 [WT_3]


title: Embryonic cerebral cortex, control, biological replicate 4


title: WholeBloodRNA_IN0317_Day3

value: female

value: whole blood

value: trivalent influenza vaccination


title: Embryonic cerebral cortex, Trnp1 knockdown, biological replicate 1


title: Pax6 mutant (Leca4) rostral cerebral cortex at embryonic day E14, biological replicate 1


title: Crohn's disease colon mucosa Kelle40

description: Crohn's disease colon mucosa sample

source_name: colon mucosa Kelle40

value: Female

value: Crohn's disease


title: Control rostral cerebral cortex at embryonic day E14 (littermate of Pax6 Leca2 mutants), biological replicate 1 [WT_5]


title: Pax6 mutant (Leca2) rostral cerebral cortex at embryonic day E14, biological replicate 4

description: Gene expression data from embryonic rostral cerebral cortex from Leca2 mice

source_name: Rostral cerebral cortex from Leca2 mice

value: Pax6 Leca2 mutant


title: Pax6 mutant (Leca4) rostral cerebral cortex at embryonic day E14, biological replicate 2


title: Control rostral cerebral cortex at embryonic day E14 (littermate of Pax6 Leca2 mutants), biological replicate 3 [WT_7]


title: Pax6 mutant (Leca2) rostral cerebral cortex at embryonic day E14, biological replicate 3


title: Pax6 mutant (Leca2) rostral cerebral cortex at embryonic day E14, biological replicate 2


title: Control rostral cerebral cortex at embryonic day E14 (littermate of Pax6 Sey mutants), biological replicate 2 [WT_9]

value: C57BL/6J x DBA/2J (B6D2F1)


title: Pax6 mutant (Small-eye; Sey) rostral cerebral cortex at embryonic day E14, biological replicate 3

description: Gene expression data from embryonic rostral cerebral cortex from Sey mice

source_name: Rostral cerebral cortex from Sey mice

value: Pax6 Sey mutant


title: Control rostral cerebral cortex at embryonic day E14 (littermate of Pax6 Sey mutants), biological replicate 3 [WT_10]


title: Pax6 mutant (Small-eye; Sey) rostral cerebral cortex at embryonic day E14, biological replicate 4


title: Control rostral cerebral cortex at embryonic day E14 (littermate of Pax6 Sey mutants), biological replicate 1 [WT_8]


title: 4016 lesional

status: Public on Jan 28 2013

city: Seattle

first: Jeannette

last: Bigler

state: WA

address: 3200 NE 92nd Street

institute: BJ Group, LLC

hyb_protocol: Procedure used standard Affymetrix protocol.

data_processing: Scans were imported into Rosetta Resolver and pre-processed using the 'Resolver Affymetrix Rosetta Intensity Profile Builder (saves reporters)' pipeline

source_name: Lesional skin biopsy from psoriasis patient

label_protocol: Total RNA was reverse-transcribed and amplified using the NuGen Ovation™ RNA amplification system V2 with Ovation™WB reagent. Amplified RNA was fragmented and labeled using the NuGen FL-Ovation™ cDNA Biotin Module V2. Amplification and labeling were performed on a Beckman-Coulter ArrayPlex.

extract_protocol: The frozen biopsies were homogenized using a TissueRuptor and RNA extracted using the mirVana™ kit with on-column DNase treatment

tag: tissue type

value: Lesional skin


title: Pax6 mutant (Small-eye; Sey) rostral cerebral cortex at embryonic day E14, biological replicate 1


title: Fourth ventricular choroid plexus from Otx2ko mice at E13, biological replicate 3

status: Public on Feb 05 2013

description: Gene expression data from fourth ventricular choroid plexus of Otx2 k.o. mice

data_processing: RMA probeset summary and quantile normalisation

source_name: Otx2 deficient mouse strain (Puelles et al., 2003, Nature Neuroscience Vol 6(5))

label_protocol: MessageAmp Premier labeling kit (Ambion)

tag: strain background

value: Mixed background

value: Otx2 k.o.

tag: developmental stage

value: not determined


title: Fourth ventricular choroid plexus from wildtype mice at E13, biological replicate 2

description: Gene expression data from fourth ventricular choroid plexus of wildtype mice

source_name: Wildtype mice

value: Wildtype


title: Pax6 mutant (Leca2) rostral cerebral cortex at embryonic day E14, biological replicate 1

value: Embryonic day E14


title: Fourth ventricular choroid plexus from wildtype mice at E13, biological replicate 1


title: 1156 lesional

scan_protocol: Procedure used standard Affymetrix protocol.


title: Pax6 mutant (Small-eye; Sey) rostral cerebral cortex at embryonic day E14, biological replicate 2

value: nd


title: Control rostral cerebral cortex at embryonic day E14 (littermate of Pax6 Leca2 mutants), biological replicate 2 [WT_6]

value: Wild type


title: Fourth ventricular choroid plexus from wildtype mice at E13, biological replicate 4


title: 4008 lesional


title: Fourth ventricular choroid plexus from Otx2ko mice at E13, biological replicate 1


title: 1156 non-lesional

source_name: Non-lesional skin biopsy from psoriasis patient

value: Non-lesional skin


title: 4006 lesional


title: 4016 non-lesional


title: 4006 non-lesional


title: Fourth ventricular choroid plexus from Otx2ko mice at E13, biological replicate 2


title: 4008 non-lesional


title: Fourth ventricular choroid plexus from Otx2ko mice at E13, biological replicate 4


title: Fourth ventricular choroid plexus from wildtype mice at E13, biological replicate 3


title: 4007 non-lesional


title: 4013 non-lesional


title: 4013 lesional


title: 4003 non-lesional


title: WholeBloodRNA_IN0312_Day0

source_name: Whole blood

value: female

value: baseline


title: Control rostral cerebral cortex at embryonic day E14 (littermate of Pax6 Leca4 mutants), biological replicate 4 [WT_4]


title: 3016 non-lesional


title: 3021 lesional


title: 4002 lesional


title: 1153 non-lesional


title: 4007 lesional


title: 1148 non-lesional


title: 3019 lesional


title: 1147 non-lesional


title: 4002 non-lesional


title: 1147 lesional


title: 3002 lesional


title: 3016 lesional


title: 3008 lesional


title: 3021 non-lesional


title: Embryonic cerebral cortex, control, biological replicate 3

value: cerebral cortex

value: WT


title: 3003 lesional


title: 1145 lesional


title: 3019 non-lesional


title: 1148 lesional


title: 3003 non-lesional


title: 1145 non-lesional


title: 3008 non-lesional


title: 3005 non-lesional


title: 3002 non-lesional


title: 1153 lesional


title: 4003 lesional


title: 1139 lesional


title: 1139 non-lesional


title: 1138 non-lesional


title: 1134 lesional


title: 1134 non-lesional


title: 1141 lesional


title: 12108-5

status: Public on Oct 31 2012

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

institute: University Medical Center Hamburg-Eppendorf

description:
G34-NP8
Gene expression data from mammary carcinoma developed in WAP-SV40 NP8 mouse line

hyb_protocol: Following fragmentation, cRNA was hybridized on Mouse Genome 430 2.0 GeneChip, washed and stained following the manufacturer’s recommendation.

scan_protocol: Microarrays were scanned with the GeneChip Scanner 3000 7G.

data_processing: An alternative probe set mapping is published by the AffyProbeMiner project [remapped gene consistent cdf-file, using validated complete coding sequences in GenBank, version 1.0.0; AffyProbeMiner cdf (mouse4302geneccds) version 1.8.0]. Note: The R/Bioconductor version of the CDF file was used to calculate probe set signals. RMA background correction and quantile normalization were used.

source_name: WAP-NP8 Mouse Mammary Carcinoma, Grade 3

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

extract_protocol: Total RNA was extracted using Trizol Reagent (Invitrogen) followed by DNA digestion (TURBO DNA-free; Ambion) according to the manufacturer’s instructions. Total RNA from tumor samples and normal mammary gland was cleaned up using RNeasy mini kit according to the manufacturer’s instructions (Qiagen).

tag: tumor

value: WAP-NP8 Mouse Mammary Carcinoma

value: Balb/c

tag: tumour grade

value: Grade 3


title: 12212-2


title: 1141 non-lesional


title: 1138 lesional


title: 3005 lesional


title: 1135 lesional


title: 1135 non-lesional


title: 12109-1


title: 11304-3


title: 12192-8


title: E2_Raloxifene_145

status: Public on May 09 2012

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

description: 2060_4367_24150_145.0_HG-U133+Plus+2.CEL

data_processing:
GC-RMA (JMP Genomics 4.1), adjustment for batch effects (Distance-weighted discrimination)
Log2 GC-RMA, quantile normalization, summary by median polish, adjusted for batch effects.

source_name: MCF-7 cells

treatment_protocol: 48 hours after plating, cells were treated with ER ligands using 1 nM final concentration vehicle (ethanol) or E2 in the presence or absence of vehicle (DMSO) or SERM (100 nM).  After 24 hours treatment, cells were washed once in PBS prior to lysis.

tag: cell line

tag: agonist

tag: antagonist

value: Raloxifene

tag: co-treatment


title: E2_Lasofoxifene_156

description: 2060_4367_24161_156.0_HG-U133+Plus+2.CEL

value: Lasofoxifene


title: ethanol_Lasofoxifene_152

description: 2060_4367_24157_152.0_HG-U133+Plus+2.CEL

value: ethanol


title: ethanol_Lasofoxifene_153

description: 2060_4367_24158_153.0_HG-U133+Plus+2.CEL


title: E2_4OHT_142

description: 2060_4367_24147_142.0_HG-U133+Plus+2.CEL


title: E2_ethanol_141

description: 2060_4367_24146_141.0_HG-U133+Plus+2.CEL


title: E2_Bazedoxifene_144

description: 2060_4367_24149_144.0_HG-U133+Plus+2.CEL

value: Bazedoxifene


title: E2_Lasofoxifene_154

description: 2060_4367_24159_154.0_HG-U133+Plus+2.CEL


title: ethanol_Bazedoxifene_139

description: 2060_4367_24144_139.0_HG-U133+Plus+2.CEL


title: E2_Raloxifene_130

description: 2060_4367_24135_130.0_HG-U133+Plus+2.CEL


title: ethanol_ICI_182_780_138

description: 2060_4367_24143_138.0_HG-U133+Plus+2.CEL

value: ethanol_ICI 182,780


title: ethanol_Lasofoxifene_151

description: 2060_4367_24156_151.0_HG-U133+Plus+2.CEL


title: ethanol_ICI_182_780_123

description: 2060_4367_24128_123.0_HG-U133+Plus+2.CEL


title: ethanol_ethanol_136

description: 2060_4367_24141_136.0_HG-U133+Plus+2.CEL


title: ethanol_ethanol_121

description: 2060_4367_24126_121.0_HG-U133+Plus+2.CEL


title: 12192-2

source_name: WAP-NP8 Mouse Mammary Carcinoma, Grade 4

value: Grade 4


title: E2_ICI_182_780_143

description: 2060_4367_24148_143.0_HG-U133+Plus+2.CEL


title: E2_ICI_182_780_128

description: 2060_4367_24133_128.0_HG-U133+Plus+2.CEL


title: E2_Raloxifene_115

description: 2060_4367_24120_115.0_HG-U133+Plus+2.CEL


title: ethanol_Raloxifene_140

description: 2060_4367_24145_140.0_HG-U133+Plus+2.CEL


title: E2_Lasofoxifene_155

description: 2060_4367_24160_155.0_HG-U133+Plus+2.CEL


title: ethanol_Bazedoxifene_124

description: 2060_4367_24129_124.0_HG-U133+Plus+2.CEL


title: E2_4OHT_127

description: 2060_4367_24132_127.0_HG-U133+Plus+2.CEL


title: ethanol_Raloxifene_125

description: 2060_4367_24130_125.0_HG-U133+Plus+2.CEL


title: ethanol_ethanol_106

description: 2060_4367_24111_106.0_HG-U133+Plus+2.CEL


title: E2_Raloxifene_100

description: 2060_4367_24105_100.0_HG-U133+Plus+2.CEL


title: E2_4OHT_112

description: 2060_4367_24117_112.0_HG-U133+Plus+2.CEL


title: E2_ICI_182_780_113

description: 2060_4367_24118_113.0_HG-U133+Plus+2.CEL


title: E2_ICI_182_780_98


title: ethanol_4OHT_107

description: 2060_4367_24112_107.0_HG-U133+Plus+2.CEL


title: ethanol_ICI_182_780_108

description: 2060_4367_24113_108.0_HG-U133+Plus+2.CEL


title: E2_Bazedoxifene_129

description: 2060_4367_24134_129.0_HG-U133+Plus+2.CEL


title: ethanol_Raloxifene_110

description: 2060_4367_24115_110.0_HG-U133+Plus+2.CEL


title: E2_Bazedoxifene_114

description: 2060_4367_24119_114.0_HG-U133+Plus+2.CEL


title: E2_Bazedoxifene_99


title: ethanol_Raloxifene_95


title: ethanol_ethanol_91


title: E2_ethanol_126

description: 2060_4367_24131_126.0_HG-U133+Plus+2.CEL


title: ethanol_4OHT_122

description: 2060_4367_24127_122.0_HG-U133+Plus+2.CEL


title: E2_4OHT_97


title: E2_ethanol_111

description: 2060_4367_24116_111.0_HG-U133+Plus+2.CEL


title: E2_Raloxifene_85


title: E2_Bazedoxifene_84

description: 2060_4367_24089_84.0_HG-U133+Plus+2_2.CEL


title: ethanol_4OHT_92


title: ethanol_Bazedoxifene_109

description: 2060_4367_24114_109.0_HG-U133+Plus+2.CEL


title: ethanol_Bazedoxifene_94


title: E2_ethanol_96


title: ethanol_4OHT_137

description: 2060_4367_24142_137.0_HG-U133+Plus+2.CEL


title: ethanol_Bazedoxifene_79

description: 2060_4367_24084_79.0_HG-U133+Plus+2_2.CEL


title: E2_4OHT_82

description: 2060_4367_24087_82.0_HG-U133+Plus+2_2.CEL


title: E2_ethanol_81

description: 2060_4367_24086_81.0_HG-U133+Plus+2_2.CEL


title: ethanol_ICI_182_780_93


title: E2_Bazedoxifene_69


title: E2_4OHT_67


title: ethanol_4OHT_77


title: E2_ICI_182_780_68


title: E2_ICI_182_780_53


title: ethanol_ethanol_76


title: E2_Raloxifene_70


title: ethanol_Raloxifene_80

description: 2060_4367_24085_80.0_HG-U133+Plus+2_2.CEL


title: ethanol_Raloxifene_65


title: ethanol_ethanol_46


title: ethanol_ICI_182_780_63


title: ethanol_Bazedoxifene_64


title: ethanol_ICI_182_780_78


title: E2_Raloxifene_55


title: E2_ethanol_51


title: E2_ethanol_66


title: ethanol_4OHT_62


title: E2_ICI_182_780_83

description: 2060_4367_24088_83.0_HG-U133+Plus+2_2.CEL


title: ethanol_ethanol_61


title: ethanol_ICI_182_780_48


title: E2_4OHT_52


title: E2_Bazedoxifene_54


title: ethanol_4OHT_47


title: ethanol_Raloxifene_50


title: E2_Raloxifene_40


title: ethanol_Bazedoxifene_49


title: E2_ICI_182_780_38


title: ethanol_Bazedoxifene_34


title: ethanol_ICI_182_780_33


title: E2_Raloxifene_25


title: E2_4OHT_37


title: E2_4OHT_22


title: ethanol_Raloxifene_35


title: ethanol_ethanol_31


title: ethanol_ethanol_16


title: E2_Raloxifene_10


title: ethanol_ICI_182_780_18


title: E2_Bazedoxifene_39


title: E2_Bazedoxifene_24


title: E2_ICI_182_780_8


title: E2_4OHT_7


title: PolII_80mMsalt_DRB_HS_(IP4_DRB_HS_20110313_4)

status: Public on Nov 15 2011

type: SRA

first: Jorja

last: Henikoff

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: supplementary protocol file: Solexa_library_protocol_GEO.pdf

library_source: genomic

data_processing: 1. We used Novoalign to map paired-end 25bp reads to release r5.30 of the D.melanogaster genomic sequence obtained from FlyBase. The genomic sequence was unmasked and chrU, chr2RHet, chr2LHet, chr3RHet, chr3LHet, chrXHet and chrYHet were omitted from the reference sequence. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file PolII_80mMsalt_DRB_HS_20110313_4.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file PolII_80mMsalt_DRB_HS_20110313_4.bedgraph) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

source_name: Pol II ChIP

extract_protocol: ChIP was done as described in CM Weber, JG Henikoff & S Henikoff, H2A.Z nucleosomes enriched over active genes are homotypic, Nat Struct Mol Bio 2010 Dec;17(12):1500-7, PMID 21057526 and supplementary file ChIP_protocol.rtf. A modified Illumina Solexa library protocol was used as described in supplementary file Solexa_library_protocol_GEO.pdf.

tag: cell type

value: S2 cells


title: E2_Bazedoxifene_9


title: Total_control_(Nuc1_20110223_1)

data_processing: 1. We used Novoalign to map paired-end 25bp reads to release r5.30 of the D.melanogaster genomic sequence obtained from FlyBase. The genomic sequence was unmasked and chrU, chr2RHet, chr2LHet, chr3RHet, chr3LHet, chrXHet and chrYHet were omitted from the reference sequence. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file Total_control_20110223_1.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file Total_control_20110223_1.bedgraph) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

source_name: total nuclei

extract_protocol: Salt extraction was done as described in S Henikoff, JG Henikoff, A Sakai, GB Loeb, K Ahmad, Genome-wide profiling of salt fractions maps physical properties of chromatin. Genome Research, March 2009, 19:460-469, PMID 19088306 and supplementary file Salt_protocol.rtf. A modified Illumina Solexa library protocol was used as described in supplementary file Solexa_library_protocol_GEO.pdf.


title: E2_ethanol_36


title: E2_ethanol_21


title: ethanol_ICI_182_780_3


title: ethanol_Bazedoxifene_19


title: PolII_80mMsalt_HS_(IP2_HS_20110313_2)

data_processing: 1. We used Novoalign to map paired-end 25bp reads to release r5.30 of the D.melanogaster genomic sequence obtained from FlyBase. The genomic sequence was unmasked and chrU, chr2RHet, chr2LHet, chr3RHet, chr3LHet, chrXHet and chrYHet were omitted from the reference sequence. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file PolII_80mMsalt_HS_20110313_2.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file PolII_80mMsalt_HS_20110313_2.bedgraph) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.


title: PolII_80mMsalt_DRB_(IP3_DRB_20110313_3)

data_processing: 1. We used Novoalign to map paired-end 25bp reads to release r5.30 of the D.melanogaster genomic sequence obtained from FlyBase. The genomic sequence was unmasked and chrU, chr2RHet, chr2LHet, chr3RHet, chr3LHet, chrXHet and chrYHet were omitted from the reference sequence. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file PolII_80mMsalt_DRB_20110313_3.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file PolII_80mMsalt_DRB_20110313_3.bedgraph) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.


title: PolII_80mMsalt_control_(IP1_Ctl_20110313_1)

data_processing: 1. We used Novoalign to map paired-end 25bp reads to release r5.30 of the D.melanogaster genomic sequence obtained from FlyBase. The genomic sequence was unmasked and chrU, chr2RHet, chr2LHet, chr3RHet, chr3LHet, chrXHet and chrYHet were omitted from the reference sequence. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file PolII_80mMsalt_control_20110313_1.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file PolII_80mMsalt_control_20110313_1.bedgraph) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.


title: ethanol_Raloxifene_20


title: E2_ethanol_6


title: ethanol_4OHT_32


title: ethanol_Bazedoxifene_4


title: CATCH-IT_DRB_(CST7_20110519_6)

description:
CATCH-IT after 10 minute DRB treatment
library_strategy: CATCH-IT-Seq
library_selection: CATCH-IT
supplementary protocol file: CATCH-IT.protocol.doc
supplementary protocol file: Solexa_libarary_protocol_GEO.pdf

data_processing: 1. We used Novoalign to map paired-end 25bp reads to release r5.30 of the D.melanogaster genomic sequence obtained from FlyBase. The genomic sequence was unmasked and chrU, chr2RHet, chr2LHet, chr3RHet, chr3LHet, chrXHet and chrYHet were omitted from the reference sequence. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file CATCH-IT_DRB_20110519_6.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file CATCH-IT_DRB_20110519_6.bedgraph) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

source_name: CATCH-IT

extract_protocol: RB Deal, JG Henikoff and S Henikoff, Genome-wide kinetics of nucelosome turnover determined by metabolic labeling of histones. Science 2010 May 28;328(5982):1161-4. Supplementary file CATCH-IT.protocol.doc.


title: CATCH-IT_HS_(CST6_20110519_5)

description:
CATCH-IT after 15 minute heat shock at 37 degrees C
library_strategy: CATCH-IT-Seq
library_selection: CATCH-IT
supplementary protocol file: CATCH-IT.protocol.doc
supplementary protocol file: Solexa_libarary_protocol_GEO.pdf

data_processing: 1. We used Novoalign to map paired-end 25bp reads to release r5.30 of the D.melanogaster genomic sequence obtained from FlyBase. The genomic sequence was unmasked and chrU, chr2RHet, chr2LHet, chr3RHet, chr3LHet, chrXHet and chrYHet were omitted from the reference sequence. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file CATCH-IT_HS_20110519_5.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file CATCH-IT_HS_20110519_5.bedgraph) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.


title: ethanol_Raloxifene_5


title: ethanol_4OHT_17


title: ethanol_4OHT_2


title: 80mMsalt_DRB_HS_(Input4_20110223_8)

description:
Salt extraction after 15 minutes of heat shock at 37 degrees C and DRB treatment for 10 min.
supplementary protocol file: Solexa_library_protocol_GEO.pdf

data_processing: 1. We used Novoalign to map paired-end 25bp reads to release r5.30 of the D.melanogaster genomic sequence obtained from FlyBase. The genomic sequence was unmasked and chrU, chr2RHet, chr2LHet, chr3RHet, chr3LHet, chrXHet and chrYHet were omitted from the reference sequence. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file 80mMsalt_DRB_HS_20110223_8.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file 80mMsalt_DRB_HS_20110223_8.bedgraph) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

source_name: 80mM salt fraction

tag: treatment

value: Heat shock for 15min at 37C, and DRB for 10min


title: CATCH-IT_control_(CST5_20110519_4)

description:
CATCH-IT under normal conditions
library_strategy: CATCH-IT-Seq
library_selection: CATCH-IT
supplementary protocol file: CATCH-IT.protocol.doc
supplementary protocol file: Solexa_libarary_protocol_GEO.pdf

data_processing: 1. We used Novoalign to map paired-end 25bp reads to release r5.30 of the D.melanogaster genomic sequence obtained from FlyBase. The genomic sequence was unmasked and chrU, chr2RHet, chr2LHet, chr3RHet, chr3LHet, chrXHet and chrYHet were omitted from the reference sequence. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file CATCH-IT_control_20110519_4.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file CATCH-IT_control_20110519_4.bedgraph) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.


title: 80mMsalt_control_(Input1_20110223_5)

data_processing: 1. We used Novoalign to map paired-end 25bp reads to release r5.30 of the D.melanogaster genomic sequence obtained from FlyBase. The genomic sequence was unmasked and chrU, chr2RHet, chr2LHet, chr3RHet, chr3LHet, chrXHet and chrYHet were omitted from the reference sequence. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file 80mMsalt_control_20110223_5.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file 80mMsalt_control_20110223_5.bedgraph) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.


title: 80mMsalt_DRB_(Input3_20110223_7)

description:
Salt extraction after 10 minute DRB treatment.
supplementary protocol file: Solexa_library_protocol_GEO.pdf

data_processing: 1. We used Novoalign to map paired-end 25bp reads to release r5.30 of the D.melanogaster genomic sequence obtained from FlyBase. The genomic sequence was unmasked and chrU, chr2RHet, chr2LHet, chr3RHet, chr3LHet, chrXHet and chrYHet were omitted from the reference sequence. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file 80mMsalt_DRB_20110223_7.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file 80mMsalt_DRB_20110223_7.bedgraph) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

value: DRB for 10min


title: 80mMsalt_HS_(Input2_20110223_6)

description:
Salt extraction after 15 minutes of heat shock at 37 degrees C.
supplementary protocol file: Solexa_library_protocol_GEO.pdf

data_processing: 1. We used Novoalign to map paired-end 25bp reads to release r5.30 of the D.melanogaster genomic sequence obtained from FlyBase. The genomic sequence was unmasked and chrU, chr2RHet, chr2LHet, chr3RHet, chr3LHet, chrXHet and chrYHet were omitted from the reference sequence. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file 80mMsalt_HS_20110223_6.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file 80mMsalt_HS_20110223_6.bedgraph) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

value: heat shock for 15min at 37C


title: 350mMsalt_DRB_(CST3_20110519_3)

description:
350mM input after 10 minute DRB treatment
supplementary protocol file: Solexa_libarary_protocol_GEO.pdf
supplementary protocol file: CATCH-IT.protocol.doc

data_processing: 1. We used Novoalign to map paired-end 25bp reads to release r5.30 of the D.melanogaster genomic sequence obtained from FlyBase. The genomic sequence was unmasked and chrU, chr2RHet, chr2LHet, chr3RHet, chr3LHet, chrXHet and chrYHet were omitted from the reference sequence. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file 350mMsalt_DRB_20110519_3.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file 350mMsalt_DRB_20110519_3.bedgraph) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

source_name: 350mM salt extraction


title: ethanol_ethanol_1


title: 350mMsalt_control_(CST1_20110519_1)

description:
350mM input under normal conditions
supplementary protocol file: Solexa_libarary_protocol_GEO.pdf
supplementary protocol file: CATCH-IT.protocol.doc

data_processing: 1. We used Novoalign to map paired-end 25bp reads to release r5.30 of the D.melanogaster genomic sequence obtained from FlyBase. The genomic sequence was unmasked and chrU, chr2RHet, chr2LHet, chr3RHet, chr3LHet, chrXHet and chrYHet were omitted from the reference sequence. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file 350mMsalt_control_20110519_1.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file 350mMsalt_control_20110519_1.bedgraph) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.


title: UtE-iPS-11_p18_3

status: Public on Mar 07 2011

city: Tsukuba

first: Makoto

last: Asashima

state: Ibaraki

address: 1-1-1 Higashi

department: Tsukuba Central 4

country: Japan

institute: National Institute of Advanced Industrial Science Technology (AIST)

description: Gene expression in human iPS cell

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x HiRPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using default parameters (protocol GE1-v5_95 and Grid: 014850_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: UtE-iPS-11, passage  18

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using the Quick-Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using ISOGEN (Nippon Gene, Toyama, Japan) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Human iPS cells were maintained in an undifferentiated state in the presence of bFGF. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

tag: provenance somatic cell

value: human uterine endometrium (hUtE) cell

tag: iPS cell-line name

tag: passage number


title: UtE-iPS-11_p18_1

description: Gene expression in human iPS cell


title: 350mMsalt_HS_(CST2_20110519_2)

description:
350mM input after 15 minute heat shock at 37 degrees C
supplementary protocol file: Solexa_libarary_protocol_GEO.pdf
supplementary protocol file: CATCH-IT.protocol.doc

data_processing: 1. We used Novoalign to map paired-end 25bp reads to release r5.30 of the D.melanogaster genomic sequence obtained from FlyBase. The genomic sequence was unmasked and chrU, chr2RHet, chr2LHet, chr3RHet, chr3LHet, chrXHet and chrYHet were omitted from the reference sequence. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file 350mMsalt_HS_20110519_2.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file 350mMsalt_HS_20110519_2.bedgraph) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.


title: UtE-iPS-11_p13_2

description: Gene expression in human iPS cell

source_name: UtE-iPS-11, passage  13


title: Wild type EBV-transformed B-cells, biological replicate 1

status: Public on Nov 19 2010

description:
Gene expression data from a B-cell line derived from a healthy donor
wt_minusVitD_1

hyb_protocol: According to the GeneChip Whole Transcript (WT) Sense Target Labeling Assay

data_processing: RMA probeset summary and quantile normalisation (Expression console)

source_name: Wild type EBV-transformed B-cells

label_protocol: MessageAmp II-Biotin Enhanced 1-cycle protocoll (Ambion)

growth_protocol: Cells were maintained in RPMI 1640 medium, 37°C in 5% CO2

treatment_protocol: Vitamin D treatment (1,25(OH)2D3 (Biomol, USA))

tag: individual

value: Healthy donor

tag: gender

value: female

value: B-cell

tag: agent


title: UtE-iPS-11_p13_3

description: Gene expression in human iPS cell


title: UtE-iPS-11_p13_1

description: Gene expression in human iPS cell


title: UtE-iPS-11_p18_2

description: Gene expression in human iPS cell


title: HVDRR EBV-transformed B-cells, biological replicate 1

description:
Gene expression data from a B-cell line derived from a patient with hereditary vitamin D resistant rickets
JK_minusVitD_1

source_name: HVDRR EBV-transformed B-cells

value: Patient with hereditary vitamin D resistant rickets


title: Wild type EBV-transformed B-cells treated with vitamin D, biological replicate 1

description:
Gene expression data from a B-cell line derived from a healthy donor
wt_plusVitD_3

value: vitamin D


title: Wild type EBV-transformed B-cells treated with vitamin D, biological replicate 2

description:
Gene expression data from a B-cell line derived from a healthy donor
wt_plusVitD_4


title: HVDRR EBV-transformed B-cells treated with vitamin D, biological replicate 2

description:
Gene expression data from a B-cell line derived from a patient with hereditary vitamin D resistant rickets
JK_plusVitD_4