title: SJR4317-sectored_18R

status: Public on Apr 29 2017

city: Durham

first: Yee Fang

last: Hum

address: 381 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University

description: SJR4317 isolate#1 90-minute galactose induction, red sector18

hyb_protocol: Mixed labeled DNA was competitively hybridized to a SNP microarray, and the ratio of Cy5 to Cy3 hybridization to each SNP was determined. Each SNP was represented by four 25-nt oligonucleotides that corresponded to the Watson and Crick strands of each homolog.

scan_protocol: Scanned on an Agilent scanner (GenePix 4000B).

data_processing: The ratio of the medians (635 nm/532 nm) for each probe was used for analysis, and replicate probe medians were averaged (St. Charles et al., 2012).

organism: Saccharomyces cerevisiae

source_name: 90-minute DSB induction

label_protocol: DNA from each sector was labeled with Cy5-dUTP and mixed with control parental DNA labeled with Cy3-dUTP.

growth_protocol: Prior to I-SceI induction, yeast cells were grown overnight at 30°C in 5 ml of non-selective medium containing 1% yeast extract, 2% bacto-peptone and 2% raffinose (YEPR). Following overnight growth, cells were then diluted to an OD of 0.4 in fresh YEPR medium and split into two parallel cultures. When cells reached an OD of 0.8-1, galactose (2% final concentration) was added to one culture of each pair and cells were incubated for an additional 45 or 90 minutes. Following induction for the specified time, yeast cells were pelleted and resuspended in water. Approximately 500 cells/plate were spread on synthetic dextrose medium supplemented with uracil and all amino acids except arginine. Adenine was additionally present at 10 μg/ml, a limiting amount that allows red color development of Ade- cells. Plates were incubated at 30°C overnight and at room temperature for additional 2 days before being moved to 4°C to allow red pigment development.

extract_protocol: Cells in each half of a sectored colony were purified by streaking on YEP-glucose medium, and a single colony from each was used for DNA isolation. Genomic DNA was extracted in agarose plugs and then sheared to 200-400 bp by sonication.

treatment_protocol: 45- or 90-minute of galactose treatment to induce I-SceI cleavage on chromosome IV.

tag: ploidy

value: diploid (W303 x YJM789)

tag: dsb on chromosome iv

value: Yes

source_name: uninduced parental control SJR4317

value: No


title: SJR4317-sectored_19R

type: genomic

state: NC

country: USA

description: SJR4317 isolate#1 90-minute galactose induction, red sector19

molecule: genomic DNA


title: SJR4317-sectored_19W

description: SJR4317 isolate#1 90-minute galactose induction, white sector19


title: SJR4317-sectored_20W

description: SJR4317 isolate#1 90-minute galactose induction, white sector20


title: SJR4317-sectored_20R

description: SJR4317 isolate#1 90-minute galactose induction, red sector20


title: hYAP (5SA/TEAD*) expressing liver

status: Public on May 01 2017

type: RNA

city: Bunkyo-ku

first: Hiroshi

last: Nishina

state: Tokyo

department: Department of Developmental and Regenerative Biology

country: Japan

institute: Medical Research Institute,Tokyo Medical and Dental University (TMDU)

description: oncogene expressing mouse liver

hyb_protocol: Following fragmentation, 0.6 μg cRNA was hybridized for 17 hr at 65°C on the SurePrint G3 Mouse GE 8x60K Microarray using the Gene Expression Hybridization Kit*4. GeneChips were washed using the Gene Expression Wash Buffers Pack

scan_protocol: Genechips scanned using an Agilent DNA Microarray Scanner (G2565CA)

data_processing: standard Agilent protocol

molecule: total RNA

organism: Mus musculus

source_name: 2 days

label_protocol: cDNAs were synthesized by the Low Input Quick Amp Labeling Kit. Cy3-labelled cRNA was synthesized by in vitro transcription with T7 RNA Polymerase.

extract_protocol: Total RNA was extracted from mouse livers using Trizol reagent (Invitrogen) and further purified using RNeasy Mini Kits (Qiagen).

tag: strain

tag: tissue

value: liver


title: SJR4317-sectored_18W

description: SJR4317 isolate#1 90-minute galactose induction, white sector18


title: hYAP (2SA) expressing liver

description: oncogene expressing mouse liver


title: hYAP (WT) expressing liver 1

description: oncogene expressing mouse liver


title: MDA-MB-231-NC,rep3

city: Beijing

first: Jie

last: Wu

address: #5, dongdan 3, dongcheng district

country: China

institute: Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science

description: Gene expression data from MDA-MB-231 cells stably expressing negative control.

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix

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

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

label: biotin

organism: Homo sapiens

source_name: cells, stably expressing negative control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MDA-MB-231 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, GIBCO) and supplemented with 10% fetal bovine serum (Hyclone).

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

treatment_protocol: MDA-MB-231 cells stably expressing CTCF and negative control were established using lentivector-based overexpression system.Then cells were washed 3 times with PBS and lysed with Trizol

tag: cell line

tag: expression

value: negative control


title: MDA-MB-231-NC,rep1


title: hYAP (WT) expressing liver 2

description: oncogene expressing mouse liver


title: MDA-MB-231-CTCF,rep3

description: Gene expression data from MDA-MB-231 cells stably expressing CTCF.

source_name: cells, stably expressing CTCF

value: stably expressing CTCF


title: MDA-MB-231-CTCF,rep1


title: hYAP (1SA) expressing liver

description: oncogene expressing mouse liver


title: hYAP (5SA) expressing liver

description: oncogene expressing mouse liver


title: SJR4317-sectored_17R

description: SJR4317 isolate#1 90-minute galactose induction, red sector17


title: SJR4317-sectored_17W

description: SJR4317 isolate#1 90-minute galactose induction, white sector17


title: SJR4317-sectored_13R

description: SJR4317 isolate#1 90-minute galactose induction, red sector13


title: SJR4317-sectored_16R

description: SJR4317 isolate#1 90-minute galactose induction, red sector16


title: SJR4317-sectored_15R

description: SJR4317 isolate#1 90-minute galactose induction, red sector15


title: SJR4317-sectored_14R

description: SJR4317 isolate#1 90-minute galactose induction, red sector14


title: SJR4317-sectored_15W

description: SJR4317 isolate#1 90-minute galactose induction, white sector15


title: SJR4317-sectored_16W

description: SJR4317 isolate#1 90-minute galactose induction, white sector16


title: SJR4317-sectored_12R

description: SJR4317 isolate#2 90-minute galactose induction, red sector12


title: SJR4317-sectored_14W

description: SJR4317 isolate#1 90-minute galactose induction, white sector14


title: GD9.25 FNP from cyclopamine TX GD8.25, biological rep6

city: Madison

first: Joshua

middle: L

last: Everson

state: WI

address: 2015 Linden Drive, Rm 3217

department: Comparative Biosciences

institute: UW-Madison

description: Gene expression data from GD9.25 cyclopamine-exposed FNP/ventral prosencephalon

hyb_protocol: The end-terminus biotin labeled cDNA is hybridized to an AFX Gene ST 2.0 GeneChip for 16 hours at 45C.  Following hybridization, the GeneChip is washed and stained with Streptavidin-Phycoerythrin (SAPE) on the AFX Fluidics450 Station.

scan_protocol: GeneChips were scanned at 570 nm on a GC3000 G7 scanner

data_processing: Fluorescent signals corresponding to hybridization intensities were analyzed with the Affymetrix GCOS software, and Affymetrix Transcriptome Analysis Console v.2.0 was used to analyze relative expression.

source_name: GD9.25 cyclopamine-exposed pooled FNP and ventral prosencephalon tissues

label_protocol: 100-500ng of total RNA was input into the first strand cDNA synthesis reaction that uses a reverse transcription priming method that specifically primes non-ribosomal RNA, including both poly(A) and non-poly(A) mRNA, which is then followed immediately by second strand cDNA synthesis.  The 2nd cDNA is purified with paramagnetic beads and used for input into an 8 hour IVT reaction creating aRNA.  The aRNA is then used for input into the 2nd cycle cDNA synthesis, the ds cDNA is purified by paramagnetic particles, and finally end-terminus labeled with biotin.

growth_protocol: 1-2 nulliparous female mice were placed with a single male for 1-2 hrs and subsequently examined for the presence of copulation plugs.  The beginning of the mating period was designated as GD0.  Pregnant dams were euthanized at GD9.25 ± 1 hour.  Embryos with 20-24 somite pairs were collected, pooled by litter, and flash frozen.

extract_protocol: Total RNA (DNase treated) was isolated using GE Illustra RNAspin kits (GE Healthcare)

treatment_protocol: Pregnant dams were administered 120 mg kg-1 d-1 cyclopamine (LC Laboratories, CAS #4449-51-8) or vehicle alone (50% w/v 2-hydropropyl-β-cyclodextrin in sodium phosphate/citrate buffer) at GD8.25  via surgically implanted Alzet 2001D microosmotic pumps.  This subcutaneous infusion exposure model yields steady state serum concentrations within a few hours after pump implantation that persist until time of dissection (GD9.25) (PMID: 18411234).

value: FNP and ventral prosencephalon tissues from pooled litter

tag: genotype

value: Wild-type

tag: age

value: Pooled litter of GD9.25 (20-24 somite pairs) embryonic tissues


title: Chronic trametinib plus lapatinib treatment sustained for 3 xenograft generations in UVA366 rep1

status: Public on May 02 2017

city: Charlottesville

first: Edik

middle: Matthew

last: Blais

state: Virginia

address: 415 Lane Road

department: Biomedical Engineering

institute: University of Virginia

description:
biological replicate 1
Gene expression of a human pancreatic tumor orthotopically implanted and grown in a mouse

hyb_protocol: Hybridized to arrays at 45°C for 16 hours

scan_protocol: Affymetrix GeneChip system performed by University of Virginia Core Biomolecular Analysis Facility, which is supported by the University Of Virginia School Of Medicine. Laser GeneArray scanner was used for measuring amounts of bound probes

data_processing: Transcriptomics analyses were performed in the R/Bioconductor programming environment.  Raw gene expression data files (.CEL) were preprocessed using robust multi-array averaging (RMA) as implemented in the oligo package [PMID:20688976], medianpolish summarization for probesets as annotated in the hugene10sttranscriptcluster.db package (version 8.3.1), and quantiles normalization between arrays.

source_name: Chronic trametinib plus lapatinib treatment sustained for 3 xenograft generations in UVA366 PDAC PDX tumors, biological rep1

label_protocol: Biotin labelled according to the standard Affymetrix protocol

extract_protocol: All protect (Qiagen) was used to preserve RNA in all tissue samples. TissueLyzer LT (Qiagen) was used to homogenize tissue. RNA was extracted using the Allprep kit (Qiagen).

tag: host organism

value: Athymic nude mouse

tag: xenograft generation

value: Mouse Passage #8 (F8)

tag: xenograft tissue

value: Human pancreatic tumor explant grown orthotopically on mouse pancreas

tag: xenograft biopsy site

value: Mouse pancreas

tag: treatment condition

tag: treatment summary

tag: trametinib active dosing

value: 0.3 mg/kg trametinib given orally twice per day

tag: lapatinib active dosing

value: 65 mg/kg lapatinib given orally twice per day

tag: trametinib prior dosing

tag: lapatinib prior dosing

tag: trametinib duration

value: Chronic trametinib treatment (3 xenograft generations) sustained prior to sample collection

tag: lapatinib duration

value: Chronic lapatinib treatment (3 xenograft generations) sustained prior to sample collection

tag: sample batch

tag: patient biopsy site

value: Liver

tag: patient cancer type

value: Pancreatic adenocarcinoma

tag: patient tumor stage

value: Metastatic

tag: patient tumor differentiation

value: Poor

tag: patient tumor grade

value: High Grade

tag: patient tumor stromal content

value: Low


title: SJR4317-sectored_10R

description: SJR4317 isolate#2 90-minute galactose induction, red sector10

tag: ploidy

value: diploid (W303 x YJM789)

tag: dsb on chromosome iv

value: Yes

value: No


title: SJR4317-sectored_10W

description: SJR4317 isolate#2 90-minute galactose induction, white sector10


title: SJR4317-sectored_12W

description: SJR4317 isolate#2 90-minute galactose induction, white sector12


title: SJR4317-sectored_9W

description: SJR4317 isolate#2 90-minute galactose induction, white sector9


title: SJR4317-sectored_11W

description: SJR4317 isolate#2 90-minute galactose induction, white sector11


title: GD9.25 FNP from vehicle TX GD8.25, biological rep6

description: Gene expression data from GD9.25 vehicle-exposed FNP/ventral prosencephalon

source_name: GD9.25 vehicle-exposed pooled FNP and ventral prosencephalon tissues

tag: tissue

value: FNP and ventral prosencephalon tissues from pooled litter

tag: genotype

value: Wild-type

tag: strain

tag: age

value: Pooled litter of GD9.25 (20-24 somite pairs) embryonic tissues


title: GD9.25 FNP from vehicle TX GD8.25, biological rep2


title: GD9.25 FNP from cyclopamine TX GD8.25, biological rep4


title: SJR4317-sectored_13W

description: SJR4317 isolate#1 90-minute galactose induction, white sector13


title: GD9.25 FNP from cyclopamine TX GD8.25, biological rep3


title: GD9.25 FNP from cyclopamine TX GD8.25, biological rep5


title: GD9.25 FNP from cyclopamine TX GD8.25, biological rep1


title: GD9.25 FNP from vehicle TX GD8.25, biological rep5


title: SJR4317-sectored_11R

description: SJR4317 isolate#2 90-minute galactose induction, red sector11


title: GD9.25 FNP from vehicle TX GD8.25, biological rep3


title: GD9.25 FNP from cyclopamine TX GD8.25, biological rep2


title: SJR4317-sectored_8W

description: SJR4317 isolate#2 45-minute galactose induction, white sector8

source_name: 45-minute DSB induction


title: SJR4317-sectored_9R

description: SJR4317 isolate#2 90-minute galactose induction, red sector9


title: GD9.25 FNP from vehicle TX GD8.25, biological rep4


title: GD9.25 FNP from vehicle TX GD8.25, biological rep1


title: SJR4317-sectored_8R

description: SJR4317 isolate#2 45-minute galactose induction, red sector8


title: SJR4317-sectored_6R

description: SJR4317 isolate#2 45-minute galactose induction, red sector6


title: SJR4317-sectored_7R

description: SJR4317 isolate#2 45-minute galactose induction, red sector7


title: SJR4317-sectored_7W

description: SJR4317 isolate#2 45-minute galactose induction, white sector7


title: S22

city: New York

first: Weijia

last: Zhang

state: NY

address: 1425 Madison Avenue

department: Department of Medicine

institute: Mount Sinai School of Medicine

description: WT CpG

hyb_protocol: Hybriziation was performed by following Affymetrix standard procedure.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Gene-level intensity data were extracted and normalized by RMA stretch in Affymetrix Expression Console and Batch effects from different labeling protocols were adjusted using the ComBat R package (Johnson WE)

source_name: WT CpG-stimulated DCs

label_protocol: ENCORE amplification and labeling kit (NuGen, San Carlos, CA) was applied to the first batch of samples starting with approximately 100ng of total RNA to generate biotin-labeled RNA fragments for hybridization to the chip.

extract_protocol: We isolated splenic CD11c+DCs (using Miltenyi magnetic beads) from WT or C3ar1-/-C5ar1-/- mice 4hr after injection with CpG 100ug or vehicle control. The cells were immediately placed in in Trizol and sent to SUNY Albany Center for Functional Genomics. Total RNA was isolated by standard techniques (>150pg RNA obtained per sample).  After quality control testing, the samples were processed using standard Affymetrix WT pico protocols, hybridized to Affymetrix Mouse Gene 2.0 ST arrays and the chips were scanned using GeneChip Scanner 7G (Affymetrix Inc.).

value: WT

tag: cell type

value: Splenic CD11C+DC


title: S23

description: DRKO 0

source_name: C3ar1-/-C5ar1-/- unstimulated DCs


title: SJR4317-sectored_5R

description: SJR4317 isolate#2 45-minute galactose induction, red sector5


title: S19

description: DRKO CpG

source_name: C3ar1-/-C5ar1-/- CpG-stimulated DCs


title: S24

description: DRKO CpG


title: SJR4317-sectored_6W

description: SJR4317 isolate#2 45-minute galactose induction, white sector6


title: S18

description: DRKO CpG


title: S17

description: DRKO 0


title: SJR4317-sectored_4R

description: SJR4317 isolate#1 45-minute galactose induction, red sector4


title: SJR4317-sectored_5W

description: SJR4317 isolate#2 45-minute galactose induction, white sector5


title: S14

description: WT CpG


title: SJR4317-sectored_1W

description: SJR4317 isolate#1 45-minute galactose induction, white sector1


title: SJR4317-sectored_3R

description: SJR4317 isolate#1 45-minute galactose induction, red sector3


title: SJR4317-sectored_2R

description: SJR4317 isolate#1 45-minute galactose induction, red sector2


title: SJR4317-sectored_1R

description: SJR4317 isolate#1 45-minute galactose induction, red sector1


title: SJR4317-sectored_3W

description: SJR4317 isolate#1 45-minute galactose induction, white sector3


title: 6b5: 14 day high CEWAF

city: Florence

first: Elizabeth

middle: R.

last: Jones

state: SC

address: 4822 E. Palmetto St.

department: Biology

institute: Francis Marion University

description: Gene expression after 14 days in 15 ppt SW and 10 mg/L CEWAF

hyb_protocol: Hybridization was performed according to Agilent’s One-Color Microarray-Based Gene Expression protocol (Santa Clara, CA, USA).

scan_protocol: Slides were scanned with an Agilent G2505B scanner using one color scan setting for 8 x 15k array slides.

data_processing: Expression data were extracted from TIFF images using Agilent Feature Extraction Software (v10.7.3.1),

organism: Cyprinodon variegatus

source_name: 14 day high CEWAF

label_protocol: Total liver RNA from four biological replicates (one fish per tank) from each treatment was used in Cyanine 3 (Cy3) labeled cRNA synthesis according to Agilent’s One-Color Microarray-Based Gene Expression protocol (Santa Clara, CA, USA).  Dye incorporation for each sample was quantified using a NanoDrop spectrophotometer (Thermo Scientific, Wilmington, DE, USA). Dye specific activity for all samples exceeded 6.0 pmol Cy3/μg, with the exception of two 14-day control samples, which were excluded from further analysis due to low dye incorporation.  .

extract_protocol: Total liver RNA was extracted from four individuals in each treatment (one from each replicate tank) using the Qiagen RNeasy kit (Qiagen, Mississauga, ON, CA) according to the manufacturer’s protocol.  RNA was quantified spectrophotometrically using a NanoDrop 2000 (Thermo Scientific, Wilmington, DE, USA), and RNA integrity assessed using a 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA).  RNA integrity scores for all samples were ≥ 8, therefore all RNA samples were deemed of high quality and appropriate for inclusion in microarray analyses.

treatment_protocol: Adult sheepshead minnows (males and females, 120-d post hatch) were exposed to sewater control, Corexit, low CEWAF, high CEWAF, low HEWAF, and high HEWAF for exposed for 7- or 14-d using a flow-through system.  Each treatment consisted of four replicate tanks with eight individual fish per tank (4 males and 4 females).  Test solutions within each tank were renewed every 15 minutes, and stock solutions renewed every 48 hours to maintain concentrations of PAH compounds.  One individual was sampled from each tank for gene expression analysis.

value: liver

value: 120 d post hatch (adult)

tag: gender

value: F


title: 6c5: 14 day high CEWAF


title: 4d5: 14 day Corexit

description: Gene expression after 14 days in 15 ppt SW and 1mg/L Corexit

source_name: 14 day Corexit


title: 4c5: 14 day Corexit


title: SJR4317-sectored_4W

description: SJR4317 isolate#1 45-minute galactose induction, white sector4


title: SJR4317-sectored_2W

description: SJR4317 isolate#1 45-minute galactose induction, white sector2


title: 3d5: 14 day high HEWAF

description: Gene expression after 14 days in 15 ppt SW and 10 mg/L HEWAF

source_name: 14 day high HEWAF


title: 3c5: 14 day high HEWAF


title: 1c5: 14 day control

description: Gene expression after 14 days in 15 ppt SW

source_name: 14 day control


title: 1b5: 14 day control

value: M


title: 3b5: 14 day high HEWAF


title: 6a5: 14 day high CEWAF


title: S12

description: WT 0

source_name: WT unstimulated DCs


title: 1d5: 14 day control


title: 6d1: 7 day high CEWAF

description: Gene expression after 7 days in 15 ppt SW and 10 mg/L CEWAF

source_name: 7 day high CEWAF


title: S11

description: WT 0


title: S13

description: WT CpG


title: 1a5: 14 day control


title: 6b1: 7 day high CEWAF


title: 3a5: 14 day high HEWAF


title: 6a1: 7 day high CEWAF


title: 5c1: 7 day low CEWAF

description: Gene expression after 7 days in 15 ppt SW and 1mg/L CEWAF

source_name: 7 day low CEWAF


title: 4b1: 7 day Corexit

description: Gene expression after 7 days in 15 ppt SW and 1mg/L Corexit

source_name: 7 day Corexit


title: 5a1: 7 day low CEWAF


title: 4a1: 7 day Corexit


title: 4c1: 7 day Corexit


title: 3c1: 7 day high HEWAF

description: Gene expression after 7 days in 15 ppt SW and 10 mg/L HEWAF

source_name: 7 day high HEWAF


title: 5b1: 7 day low CEWAF


title: 6c1: 7 day high CEWAF


title: 3d1: 7 day high HEWAF


title: 6d5: 14 day high CEWAF


title: 2d1: 7day low HEWAF

description: Gene expression after 7 days in 15 ppt SW and 1mg/L HEWAF

source_name: 7day low HEWAF


title: 4d1: 7 day Corexit


title: 3a1: 7 day high HEWAF


title: 3b1: 7 day high HEWAF


title: 5d1: 7 day low CEWAF


title: 2c1: 7day low HEWAF


title: 1c1: 7 day control

description: Gene expression after 7 days in 15 ppt SW

source_name: 7 day control


title: 2b1: 7day low HEWAF


title: Liver_lncHand2 knockout_rep1

first: Yanying

last: Wang

address: 15 Datun Road, Chaoyang District,Beijing 100101, China

institute: Institute of Biophysics, Chinese Academy of Sciences

description: We deleted lncHand2 by CRISPR/Cas9, then we isolated livers.

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

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).

data_processing: Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization.

source_name: liver, lncHand2 knockout

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

extract_protocol: For wild type and lncHand2 knockout mouse samples, we isolated livers from indicated mouse. Then, total RNA was isolated from livers. For wild type_36h group, we performed 70% partial hepatectomy in wild type mouse. After 36 hours, mouse liver was isolated and total RNA was isolated from livers.

value: male

value: lncHand2 knockout


title: 2a1: 7day low HEWAF


title: Liver_wild type_rep1

description: C57BL/6 mouse, wild type

source_name: liver, wild type

value: wild type


title: 1b1: 7 day control


title: 1d3: 7 day control


title: SAM-treated 01

status: Public on Apr 28 2017

city: Montreal

first: Niaz

last: Mahmood

state: Québec

address: 1001 Decarie Boulevard

country: Canada

institute: McGill University

description:
SAM_1_SRI021A10A10_01
Gene expression data from SAM-treated MDA-MB-231

hyb_protocol: Following fragmentation, 3.5µg DNA target was hybridized on GeneChip® Human Gene 2.0 ST (Affymetrix) and incubated at 450C in the Genechip® Hybridization oven 640 (Affymetrix) for 17 hours at 60 rpm. GeneChips were then washed in a GeneChips® Fluidics Station 450 (Affymetrix) using Affymetrix Hybridization Wash and Stain kit according to the manufacturer’s instructions (Affymetrix).

scan_protocol: GeneChips were scanned on a GeneChip® scanner 3000 (Affymetrix).

data_processing:
Data were normalized using the Robust Multi-array Average (RMA) method
Robust Multi-array Average (RMA) method implemented in the Bioconductor package oligo.

source_name: SAM-treated breast cancer cell line

label_protocol: Sense-strand cDNA was synthesized from 100 ng of total RNA, and fragmentation and labeling were performed to produce ss DNA with the Affymetrix GeneChip® WT Terminal Labeling Kit according to manufacturer’s instructions (Affymetrix).

growth_protocol: cells were maintained in DMEM media supplemented with FBS

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen; Hilden, Germany, Cat#71404)

treatment_protocol: Cells were treated with SAM in the SAM-treated group and compared with non-treated MDA-MB-231 cells

tag: cell line

value: breast cancer cells

tag: treated with

value: S-adenosylmethionine (SAM)


title: Liver_wild type_36h_rep1

description: We performed partial hepatectomy in C57BL/6 mouse, after 36 hours, we isolated livers from the mouse.

source_name: liver, wild type, partial hepatectomy, 36h


title: SAM-treated 03

description:
SAM_3_SRI023A12A12_01
Gene expression data from SAM-treated MDA-MB-231


title: 1a1: 7 day control


title: HCC tissue No.3_before treatment_rep3 for miRNAs microarray

city: Guangzhou

first: Zijun

last: Xie

address: No.106,zhongshan 2nd round

institute: Guangdong General Hospital

description:
microRNA microarray profile of HCC liver tissue No.3
HCC 3(miR)

hyb_protocol: Each slide was hybridized with  1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit  (Cat.# 5188-5242,  Agilent technologies, Santa Clara, CA, US)  in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner  (Cat#G2565CA,  Agilent technologies, Santa Clara, CA, US)  with default settings, Dye channel: Green,  Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: Human liver tissue with HCC

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1561, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: The liver tissue samples were put into liquid nitrogen immediately after the tissues were resected from human bodies. After that, the samples were put into -80℃ icebox for storage until use.

value: 57 years

value: liver with HCC


title: HCC tissue No.2_before treatment_rep2 for miRNAs microarray

description:
microRNA microarray profile of HCC liver tissue No.2
HCC 2(miR)

value: 46 years


title: Control 01

description:
Control_1_SRI018A07A07_01
Gene expression data from control MDA-MB-231

source_name: breast cancer cell line

value: none (untreated control)


title: Normal liver tissue No.1_before treatment_rep1 for miRNAs microarray

description:
microRNA microarray profile of Normal liver tissue No.1
NL 1(miR)

source_name: Human normal liver tissue

value: 39 years

value: female

value: normal liver


title: Normal liver tissue No.3_before treatment_rep3 for miRNAs microarray

description:
microRNA microarray profile of Normal liver tissue No.3
NL 3(miR)

value: 56 years


title: Control 03

description:
Control_3_SRI020A09A09_01
Gene expression data from control MDA-MB-231


title: Normal liver tissue No.2_before treatment_rep2 for miRNAs microarray

description:
microRNA microarray profile of Normal liver tissue No.2
NL 2(miR)

value: 45 years


title: SAM-treated 02

description:
SAM_2_SRI022A11A11_01
Gene expression data from SAM-treated MDA-MB-231


title: Control 02

description:
Control_2_SRI019A08A08_01
Gene expression data from control MDA-MB-231


title: Normal liver tissue No.2_before treatment_rep2 for lncRNAs microarray

description:
lncRNA microarray profile of Normal liver tissue No.2
NL 2(lnc)


title: HCC tissue No.1_before treatment_rep1 for lncRNAs microarray

description:
lncRNA microarray profile of HCC liver tissue No.1
HCC 1(lnc)

value: 35 years


title: cardiac_tissue_Lina5

status: Public on Apr 27 2017

city: Niigata

first: Masayoshi

last: Suda

address: 1-757 Asahimachi-dori, Chuo-ku

department: Department of Cardiovascular Biology and Medicine

institute: Niigata University

description: gene expression of cardiac tissue from a high fat diet fed with DPP-4 inhibitor administration mice

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 10×Blocking buffer and 25×Fragmentation buffer following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays 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 (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 074809_D_F_20150624) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus sp.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) 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 the RNeasy Microarray Tissue Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Mice were fed a high-fat diet or a normal chow for totally 8 weeks from 4 weeks age, and analyzed at 12 weeks of age. A DPP-4 inhibitor was administered within water at the concentration of 10 mg/kg/day for 8 weeks since 4 weeks of age.

value: cardiac tissue

tag: diet

value: high fat diet

tag: agent

value: DPP-4 inhibitor


title: Normal liver tissue No.1_before treatment_rep1 for lncRNAs microarray

description:
lncRNA microarray profile of Normal liver tissue No.1
NL 1(lnc)


title: cardiac_tissue_HF3

description: gene expression of cardiac tissue from a high fat diet fed mice

value: male


title: cardiac_tissue_NC5

description: gene expression of cardiac tissue from a normal chow fed mice

value: normal chow


title: HCC tissue No.3_before treatment_rep3 for lncRNAs microarray

description:
lncRNA microarray profile of HCC liver tissue No.3
HCC 3(lnc)


title: cardiac_tissue_HF1


title: HCC tissue No.1_before treatment_rep1 for miRNAs microarray

description:
microRNA microarray profile of HCC liver tissue No.1
HCC 1(miR)


title: cardiac_tissue_Lina4


title: HCC tissue No.2_before treatment_rep2 for lncRNAs microarray

description:
lncRNA microarray profile of HCC liver tissue No.2
HCC 2(lnc)


title: cardiac_tissue_HF2


title: Normal liver tissue No.3_before treatment_rep3 for lncRNAs microarray

description:
lncRNA microarray profile of Normal liver tissue No.3
NL 3(lnc)


title: Skin-LN_vaccine_24_rep4

status: Public on Apr 26 2017

city: Stockholm

first: Frank

last: Liang

address: Karolinska University Hospital Solna, L2:04

department: Dept. Medicine Solna

country: Sweden

institute: Karolinska Institutet

description: US92603698_252680610776_S01_GE1_107_Sep09_1_4.txt

hyb_protocol: 1.65 ug of Cy3-labelled 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 manufacturer’s instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Rhesus Macaque Gene Expression Microarrays v2 (part number G2519F-026806) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent). Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green, PMT is set to 100%).

data_processing:
Raw microarray images from scanning were processed in Agilent Feature Extraction Software.
Local background adjusted signals (gProcessedSignal) were further quantile normalized using the Bioconductor package to achieve consistency between samples.

organism: Macaca mulatta

source_name: Skin draining lymph node_vaccine injection_24hr

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng Total RNA using the Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Tissue was homogenized in 1 ml Trizol (Ambion) using Tissuelyser (Qiagen) and RNA prepared according to the manufacturers protocol. RNA cleanup was then performed with Qiagen RNeasy mini kit. Total RNA was quality checked on an Agilent Technologies 2200 Tapestation. RNA quantity was measured using NanoDrop ND-1000 Spectrophotometer.

treatment_protocol: Rhesus macaques received intramuscular or intradermal vaccine or saline control injections. Biopsies from the injected muscle and skin plus lymph nodes draining these immunization sites were collected 24hrs post-injection, submergen in RNAlater (Ambion) and stored at -20 ºC until use.

value: Female

tag: injection site/type

value: skin; intradermal (I.D.)

tag: injected with

value: lipid nanoparticle (LNP)-encapsulated mRNA vaccine

value: skin draining lymph node

tag: time point

value: 24hr post-injection


title: cardiac_tissue_Lina3


title: Skin_vaccine_24_rep4

description: US92603698_252680610775_S01_GE1_107_Sep09_1_4.txt

source_name: Skin_vaccine injection_24hr

value: skin


title: Skin-LN_saline_24_rep4

description: US92603698_252680610780_S01_GE1_107_Sep09_1_4.txt

source_name: Skin draining lymph node_saline injection_24hr


title: cardiac_tissue_NC2


title: cardiac_tissue_NC1


title: TGF-β2 Induced HLE B-3_Rep3

city: guilin

first: Bingyu

address: No.2 Around City North RD.109

institute: Guilin Medical University

description:
Biological replicate 3 of 3. TGF-β2 Induced HLE B-3 cells.
TGF-β2.3

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit in Hybridization Oven, according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes with Gene Expression Wash Buffer Kit, followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7.

data_processing: Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1.

source_name: TGF-β2 Induced HLE B-3 cells

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit, following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit.

growth_protocol: HLE B-3 cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 15% fetal bovine serum in humidified air with 5 % CO2 at 37 ℃.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: HLE B-3 cells were stimulated with 10 ng/ml recombinant human TGF-β2 for 24h in serum-free medium.

tag: transformed with

tag: treatment


title: TGF-β2 Induced HLE B-3_Rep2

description:
Biological replicate 2 of 3. TGF-β2 Induced HLE B-3 cells.
TGF-β2.2


title: Control HLE B-3_Rep2

description:
Biological replicate 2 of 3. Control HLE B-3 cells, untreated.
control.2

source_name: HLE B-3 cells

value: control


title: Skin_vaccine_24_rep3

description: US92603698_252680610780_S01_GE1_107_Sep09_1_2.txt


title: Muscle-LN_saline_24_rep3

description: US92603698_252680610775_S01_GE1_107_Sep09_1_2.txt

source_name: Muscle draining lymph node_saline injection_24hr

value: muscle; intramuscular (I.M.)

value: muscle draining lymph node


title: RAW264.7_elaidate

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.38.0).

source_name: RAW264.7_exposed to elaidate coupled to BSA,  FFA:BSA ratio was 2:1

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Murine RAW264.7 macrophages (obtained from the ATCC) were cultured in DMEM supplemented with 10% fetal bovine serum, 100 U/ml penicillin, and 1000 µg/ml streptomycin (Lonza, Verviers, Belgium) in a humidified chamber at 37C  with 5% CO2.

extract_protocol: Total RNA was purified using  the RNeasy Microkit kit (Qiagen, Venlo, the Netherlands). RNA quality was assessed using RNA 6000 nanochips on the Agilent 2100 bioanalyzer (Agilent Technologies, Amsterdam, the Netherlands). RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: RAW264.7 cells were seeded into 6-well plates at 4 x 10^5  cells per well. After overnight incubation, the cells were incubated with 500 µM of the individual fatty acids (oleate, elaidate and palmitate) for 6 hours. Before incubation, fatty acids were reconstituted in ethanol and prepared by dissolving in filter-sterilised 70 mM KOH. The fatty acids were then coupled to FA-free BSA by 30 min incubation at 37C in a pre-warmed DMEM containing FA-free BSA. The final working concentrations of the FAs was 500 μM and the final ratio of FFA:BSA was 2:1.

value: murine macrophages

tag: exposed to

value: elaidate (500 µM) coupled to BSA


title: Skin_saline_24_rep4

description: US92603698_252680610779_S01_GE1_107_Sep09_1_1.txt

source_name: Skin_saline injection_24hr

value: saline control


title: Control HLE B-3_Rep3

description:
Biological replicate 3 of 3. Control HLE B-3 cells, untreated.
control.3


title: Skin-LN_vaccine_24_rep3

description: US92603698_252680610780_S01_GE1_107_Sep09_1_1.txt


title: Muscle_vaccine_24_rep4

description: US92603698_252680610777_S01_GE1_107_Sep09_1_4.txt

source_name: Muscle_vaccine injection_24hr

value: muscle


title: Muscle-LN_saline_24_rep4

description: US92603698_252680610778_S01_GE1_107_Sep09_1_1.txt


title: Muscle-LN_vaccine_24_rep3

description: US92603698_252680610777_S01_GE1_107_Sep09_1_1.txt

source_name: Muscle draining lymph node_vaccine injection_24hr


title: RAW264.7_oleate

source_name: RAW264.7_exposed to oleate coupled to BSA,  FFA:BSA ratio was 2:1

value: oleate (500 µM) coupled to BSA


title: Muscle_saline_24_rep4

description: US92603698_252680610781_S01_GE1_107_Sep09_1_1.txt

source_name: Muscle_saline injection_24hr


title: Muscle-LN_vaccine_24_rep4

description: US92603698_252680610778_S01_GE1_107_Sep09_1_2.txt


title: RAW264.7_palmitate

source_name: RAW264.7_exposed to palmitate coupled to BSA,  FFA:BSA ratio was 2:1

value: palmitate (500 µM) coupled to BS


title: Skin_saline_24_rep3

description: US92603698_252680610776_S01_GE1_107_Sep09_1_3.txt


title: TGF-β2 Induced HLE B-3_Rep1

description:
Biological replicate 1 of 3. TGF-β2 Induced HLE B-3 cells.
TGF-β2.1


title: Skin-LN_saline_24_rep3

description: US92603698_252680610778_S01_GE1_107_Sep09_1_4.txt


title: Control HLE B-3_Rep1

description:
Biological replicate 1 of 3. Control HLE B-3 cells, untreated.
control.1


title: Muscle-LN_saline_24_rep2

description: US92603698_252680610780_S01_GE1_107_Sep09_1_3.txt


title: Skin_saline_24_rep2

description: US92603698_252680610781_S01_GE1_107_Sep09_1_4.txt


title: Muscle_saline_24_rep3

description: US92603698_252680610778_S01_GE1_107_Sep09_1_3.txt


title: Muscle_vaccine_24_rep3

description: US92603698_252680610782_S01_GE1_107_Sep09_1_1.txt


title: Skin_vaccine_24_rep2

description: US92603698_252680610775_S01_GE1_107_Sep09_1_1.txt


title: Skin-LN_saline_24_rep2

description: US92603698_252680610782_S01_GE1_107_Sep09_1_2.txt


title: Muscle-LN_vaccine_24_rep2

description: US92603698_252680610776_S01_GE1_107_Sep09_1_1.txt


title: Skin_saline_24_rep1

description: US92603698_252680610777_S01_GE1_107_Sep09_1_3.txt


title: Skin-LN_vaccine_24_rep2

description: US92603698_252680610779_S01_GE1_107_Sep09_1_4.txt


title: Muscle_vaccine_24_rep2

description: US92603698_252680610779_S01_GE1_107_Sep09_1_3.txt


title: Skin_vaccine_24_rep1

description: US92603698_252680610779_S01_GE1_107_Sep09_1_2.txt


title: Muscle_vaccine_24_rep1

description: US92603698_252680610777_S01_GE1_107_Sep09_1_2.txt


title: Muscle_saline_24_rep1

description: US92603698_252680610775_S01_GE1_107_Sep09_1_3.txt


title: Muscle-LN_vaccine_24_rep1

description: US92603698_252680610776_S01_GE1_107_Sep09_1_2.txt


title: Muscle_saline_24_rep2

description: US92603698_252680610782_S01_GE1_107_Sep09_1_3.txt


title: Skin-LN_vaccine_24_rep1

description: US92603698_252680610781_S01_GE1_107_Sep09_1_2.txt


title: Muscle-LN_saline_24_rep1

description: US92603698_252680610782_S01_GE1_107_Sep09_1_4.txt


title: CMP_1

status: Public on Apr 24 2017

first: Shunsuke

last: Kawamura

department: Medical Research Institute

institute: Tokyo Medical and Dental University

hyb_protocol: Two micrograms of Cy3-labeled cDNA was brought up to 50 l with 1x Agilent blocking agent and 1x Agilent hybridization buffer, and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver2.0 (Agilent) for 17 hours at 65 °C in a rotating Agilent hybridization oven. After hybridization, the microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and for 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using the one-color scan setting for 8x60k array slides (scan area 61x21.6 mm, scan resolution 3 m, dye channel set to green, and PMT set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background-subtracted and spatially detrended processed signal intensities.
Gene expression array data were normalized using Subio Platform (ver. 1.18.4667, Subio Inc.)

source_name: Umbilical cord blood

label_protocol: Cyanine-3 (Cy3)-labeled cDNA was prepared from 2.0 g cDNA using the SureTag Complete DNA Labeling Kit (Agilent) according to the manufacturer's instructions, followed by filtering with Amicon Ultra-0.5 mL Centrifugal Filters for DNA Purification and Concentration (Merck Millipore). Dye incorporation and cDNA yield were checked with a NanoDrop ND-2000 Spectrophotometer.

growth_protocol: The PB-Mo, cMoP-Mo, preMo, cMoPs, rGMPs, and CMPs were sorted from at least 20 samples and pooled for one experiment.

extract_protocol: The cDNA from 6.622 ng total RNA was generated and amplified with the Ovation® Pico WTA System V2 (NuGEN Technologies) according to the manufacturer's instructions. The amplified cDNA yield was checked with a NanoDrop ND-2000 Spectrophotometer (Thermo Scientific).

value: Umbilical cord blood

value: CMP


title: Skin-LN_saline_24_rep1

description: US92603698_252680610781_S01_GE1_107_Sep09_1_3.txt

value: Female


title: rGMP_3

value: rGMP


title: cMoP_1

value: cMoP


title: CMP_2


title: rGMP_2


title: cMoP_3


title: CMP_3


title: rGMP_1


title: cMoP_2


title: Pre-monocytes_2

value: Pre-monocytes


title: Peripheral blood CD14+SP monocytes_3

source_name: Peripheral blood

value: Peripheral blood

value: Peripheral blood CD14+SP monocytes


title: cMoP-derived monocytes_2

value: cMoP-derived monocytes


title: Pre-monocytes_1


title: cMoP-derived monocytes_1


title: Pre-monocytes_3


title: Peripheral blood CD14+SP monocytes_2


title: Peripheral blood CD14+SP monocytes_1


title: cMoP-derived monocytes_3


title: P9CTRL - Middle Passage (Control)

city: Barcelona

first: Renuka

last: Kadhaya Pillai

state: Barcelona

address: Passeig Vall d’Hebron

department: Aging Basic Research Group, Molecular Biology and Biochemistry Research Center for Nanomedicine

country: Spain

institute: CIBBIM-Nanomedicine

description:
CTRL
Control Passage 9
Gene expression data from Control or untreated cells

hyb_protocol: The labeled samples were hybridized to Human Gene ST 1.0 Arrays (Affymetrix)

scan_protocol: The arrays were scanned in a GeneChip Scanner 3000 (Affymetrix). CEL files were generated from DAT files using GCOS software (Affymetrix).

data_processing: To generate the log2 expression estimates, overall array intensity was  normalized between arrays and the probe intensity of all probes in a probeset summarized to a single value using RMA (Robust Multichip Average) algorithm .

source_name: HUVEC (Lonza)

label_protocol: Briefly, cDNA library preparation and amplification were performed from 50ng total RNA using WTA2 (Sigma-Aldrich) with 17cycles of amplification. 10 µg cDNA was subsequently fragmented by DNAseI and biotinylated by terminal transferase obtained from GeneChip Mapping 10Kv2 Assay Kit (Affymetrix).

growth_protocol: Human umbilical vein endothelial cells (HUVECs) purchased from Clonetics/Lonza (Bazel, Switzerland) were grown in EGM-2 medium supplemented with growth factors (EGM-2 bullet kit; Clonetics/Lonza).

extract_protocol: RNA was collected using TRIzol.

treatment_protocol: Human umbilical vein endothelial cells (HUVECs) were untreated or treated with TNF (5ng/ml) for 26 days (or Passged until senecence with TNF α).

value: umbilical vein endothelial cells (HUVEC)

tag: phenotype

value: Non-senescent Cells


title: P4CTRL - Early Passage (Young)

description:
CTRL1
Early Passage 4
Gene expression data from Early passage


title: P8CTRL - Middle Passage (Control)

description:
CTRL
Control Passage 8
Gene expression data from control or untreated cells


title: P16 CTRL - Replicative senescence (old passage)

description:
CTRL2
Control Passage 16
Gene expression data from replicative senescence

value: Senescent Cells (Replicative senescence)


title: P1CTRL - Early Passage (Young)

description:
CTRL1
Early Passage 1
Gene expression data from Early passage


title: P9 TNF - TNFα treated (Senescence induced by TNF)

description:
TNF
TNFα Passage 9
Gene expression data from senescent cells or cells treated with TNFα

value: Senescent Cells (upon TNFα treatment)


title: Blood_post_101130760161_R06C02

status: Public on Apr 22 2017

city: Quebec

first: Bénédicte L.

last: Tremblay

state: Quebec

address: Pavillon des Services, 2440 Hochelaga Blvd

department: School of Nutrition

institute: Institute of Nutrition and Functional Foods (INAF), Laval University

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing:
The GenomeStudio® software version 2011.1 (Illumina Inc.) and the Methylation Module were used. Beta values were estimated and data correction (background subtraction and normalization) was applied using internal control probe pairs.
Data correction (background subtraction and normalization) was applied using internal control probe pairs.
the non_normalized.txt contains Unmethylated and methylated signal intensities

label: cy3, cy5

label_protocol: standard Illumina protocol

growth_protocol: Blood samples were collected after an over-night fast from an antecubital vein

extract_protocol: Genomic DNA was isolated from buffy coat using the GenElute™ Blood Genomic DNA kit (Sigma, St Louis, MO, USA)

treatment_protocol: Before (Pre) and after (Post) n-3 fatty acid supplementation

tag: status

value: Post-supplementation

tag: Sex

tag: tissue/cell type

value: blood leukocytes


title: Blood_post_101130760161_R05C02


title: Blood_post_101032560038_R03C02

value: Male


title: Blood_post_101032560036_R05C02


title: Blood_post_101130760161_R02C02


title: Blood_post_101032560038_R01C02


title: Blood_post_101130760161_R04C02


title: Blood_post_101130760161_R03C02


title: Blood_post_101130760161_R01C02


title: Blood_post_101032560023_R04C02


title: Blood_post_101032560006_R06C02


title: Blood_post_101032560036_R03C02


title: Blood_post_101032560038_R04C02


title: Blood_post_101032560023_R05C02


title: Blood_post_101032560036_R04C02


title: Blood_post_101032560036_R06C02


title: Blood_post_101032560036_R02C02


title: Blood_post_101032560038_R05C02


title: Blood_post_101032560006_R05C02


title: Blood_post_101032560023_R06C02


title: Blood_post_101032560005_R05C02


title: Blood_post_101032560006_R02C02


title: Blood_post_101032560006_R03C02


title: Blood_post_101032560006_R04C02


title: Blood_post_101032560023_R03C02


title: Blood_post_101032560006_R01C02


title: Blood_post_101032560036_R01C02


title: Blood_post_101032560023_R01C02


title: Blood_post_101032560023_R02C02


title: Blood_post_101032560005_R06C02


title: Ricolinostat-treated macrophages[DA_34_12.RCC]

city: Boston

first: Ruben

last: Dries

address: 360 Longwood Ave

department: Computational Biology

institute: DFCI

hyb_protocol: nCounter analysis system

scan_protocol: nCounter analysis system

data_processing: nSolver 2.6 software with HumanPanCancerImmunology_1.0.36 analysis module. Individual samples analyzed with different codesets were processed according to standard Nanostring normalization recommendations. In short, the background subtraction step was skipped and housekeeping genes with the counts below 70 were removed from the list. Seven genes with the lowest percent of coefficient of variation were selected for normalization.

label: multiple fluorophores

source_name: Macrophages

label_protocol: Nanostring

extract_protocol: Qiagen RNAeasy RNA Isolation Kit utilized to extract RNA from purified T cells and macrophages within tumor cell suspensions

value: Ricolinostat

tag: tissue

value: Lung tumor

tag: strain

value: Mixed background

tag: gemm model


title: Ricolinostat-treated macrophages[DA_19_9.RCC]


title: Blood_pre_101130760161_R03C01

value: Pre-supplementation

value: Female


title: Blood_post_101032560005_R02C02


title: JQ1-treated macrophages[DA_15_7.RCC]


title: JQ1-treated macrophages[DA_16_8.RCC]


title: Blood_post_101032560005_R03C02


title: Blood_pre_101130760161_R02C01


title: Blood_pre_101130760161_R04C01


title: Vehicle-treated macrophages[DA_21_11.RCC]

value: Vehicle


title: MDA-MB-468_suspension_C

city: Halle

last: Posern

address: Hollystrasse 1

department: Institute for Physiological Chemistry

country: Germany

institute: Martin Luther University Halle-Wittenberg

hyb_protocol: Hybridisation to Affimetrix human Gene ST 1.0, according to manufacturers instruction

scan_protocol: Microarray suite MAS5

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. RMA normalisation, MvA quality control. Differentially expressed genes identified by SAM algorithm, using FDR statistics (Reinhard Hoffmann, Augsburg, Germany)

source_name: non-adherent subpopulation C of mammary breast carcinoma cell line MDA-MD-468

label_protocol: according to Affymetrix standard protocol

growth_protocol: RPMI, 10% FBS, antibiotics/antimycotics, at 37 °C, 5% CO2, on uncoated tissue culture dishes

extract_protocol: total RNA extracted by RNeasy Kit (Qiagen) according to instructions; quality checked by RNA gel and 18/28S RNA

treatment_protocol: for selection of stable subpopulations, floating non-adherent cells were collected and re-cultivated on TC dishes for 12-15 passages

tag: adhesiveness

value: unable to adhere


title: Blood_pre_101032560038_R05C01


title: Blood_pre_101130760161_R05C01


title: Blood_pre_101032560038_R06C01


title: Vehicle-treated macrophages[DA_20_10.RCC]


title: MDA-MB-468_suspension_A

source_name: non-adherent subpopulation A of mammary breast carcinoma cell line MDA-MD-468


title: Blood_pre_101032560036_R05C01


title: Blood_pre_101032560038_R03C01


title: MDA-MB-468_suspension_B

source_name: non-adherent subpopulation B of mammary breast carcinoma cell line MDA-MD-468


title: Blood_pre_101032560038_R02C01


title: Ricolinostat-treated T cells[DA_33_06.RCC]

source_name: T cells


title: Blood_pre_101130760161_R01C01


title: MDA-MB-468_parental_ctrl2

source_name: adherent parental mammary breast carcinoma cell line MDA-MD-468

value: adherent


title: Blood_pre_101032560036_R06C01


title: Blood_pre_101032560023_R05C01


title: Ricolinostat-treated T cells[DA_12_03.RCC]


title: Blood_pre_101032560023_R03C01


title: Blood_pre_101032560038_R01C01


title: JQ1-treated T cells[DA_9_02.RCC]


title: Blood_pre_101032560023_R04C01


title: Vehicle-treated T cells [DA_14_05.RCC]


title: Blood_pre_101032560038_R04C01


title: Blood_pre_101032560036_R02C01


title: MDA-MB-468_parental_ctrl1


title: Blood_pre_101032560036_R03C01


title: Vehicle-treated T cells [DA_13_04.RCC]


title: Blood_pre_101130760161_R06C01


title: Blood_pre_101032560036_R01C01


title: Blood_pre_101032560023_R01C01


title: Blood_pre_101032560023_R02C01


title: Blood_post_101032560005_R04C02


title: Blood_pre_101032560006_R06C01


title: liver at pregnant 4

status: Public on Apr 21 2017

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

institute: Iwate University

description:
Gene expression in liver at pregnant
US22502550_251896410070_S01_GE1-v5_95_Feb07_2_4

hyb_protocol: Labeled cRNA probes (600 ng each) were hybridized to the microarray in hybridization buffer (Gene Expression Hybridization Kit, Agilent Technologies) at 65°C for 17 h. After incubation, the arrays were washed with the wash buffer pack (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 018964_D_F_2008110) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Bos taurus

source_name: liver at pregnant

label_protocol: Fluorescence-labeled (Cy3) cRNA probes were prepared from 400 ng of total RNA using a Low RNA Input Linear Amplification Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from the endometrial tissues using Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions.

tag: breed

value: Holstein cow

value: Liver

tag: study

value: In vivo

tag: group

value: pregnant

tag: phase or pregnant day

value: day 162


title: plasma miRNA expression profiles in pregnant women HC2

city: He fei

first: yan

middle: fu

address: 443 huangshan road

institute: University of Science and Technology of China

hyb_protocol: 875 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent 44K Human Whole Genome microarays for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan  (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel Greenis set to Green)

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

source_name: plasma

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Plasma miRNA isolation and enrichment were performed using the miRNeasy Serum/Plasma Kit (Qiagen) following the manufacturer’s protocol.

tag: source

value: plasma

tag: disease state

value: healthy control


title: plasma miRNA expression profiles in GDM women DM1

value: gestational diabetes mellitus


title: liver at pregnant 3

description:
Gene expression in liver at pregnant
US22502550_251896410070_S01_GE1-v5_95_Feb07_2_3

value: day 165


title: Blood_pre_101032560023_R06C01

value: Male

value: blood leukocytes


title: plasma miRNA expression profiles in GDM women DM2


title: liver at pregnant 1

description:
Gene expression in liver at pregnant
US22502550_251896410063_S01_GE1-v5_95_Feb07_1_2

value: day 150


title: mononuclear cells at estrous cycle 2nd 2

description:
Gene expression in mononuclear cells at  estrous cycle
US22502550_251896410096_S01_GE1-v5_95_Feb07_1_1

source_name: mononuclear cells at estrous cycle 2nd

value: mononuclear cells

value: estrous cycle


title: Blood_pre_101032560006_R05C01

value: Pre-supplementation


title: Blood_pre_101032560006_R02C01

value: Female


title: mononuclear cells at estrous cycle 2nd 4

description:
Gene expression in mononuclear cells at  estrous cycle
US22502550_251896410096_S01_GE1-v5_95_Feb07_1_3


title: Blood_pre_101032560006_R03C01


title: JQ1-treated T cells[DA_8_01.RCC]

tag: agent

value: Lung tumor

value: Mixed background


title: mononuclear cells at estrous cycle 1st 4

description:
Gene expression in mononuclear cells at  estrous cycle
US22502550_251896410095_S01_GE1-v5_95_Feb07_2_3

source_name: mononuclear cells at estrous cycle 1st

value: Holstein cow


title: liver at pregnant 2

description:
Gene expression in liver at pregnant
US22502550_251896410070_S01_GE1-v5_95_Feb07_2_2

value: Liver

value: In vivo


title: mononuclear cells at estrous cycle 1st 3

description:
Gene expression in mononuclear cells at  estrous cycle
US22502550_251896410095_S01_GE1-v5_95_Feb07_2_2


title: plasma miRNA expression profiles in pregnant women HC1


title: Blood_post_101032560005_R01C02

value: Post-supplementation


title: mononuclear cells at estrous cycle 2nd 3

description:
Gene expression in mononuclear cells at  estrous cycle
US22502550_251896410096_S01_GE1-v5_95_Feb07_1_2


title: mononuclear cells at pregnant 4

description:
Gene expression in mononuclear cells at pregnant
US22502550_251896410095_S01_GE1-v5_95_Feb07_1_3

source_name: mononuclear cells at pregnant

value: pregnant

value: day 162


title: mononuclear cells at estrous cycle 1st 2

description:
Gene expression in mononuclear cells at  estrous cycle
US22502550_251896410095_S01_GE1-v5_95_Feb07_2_1


title: MDA-MB-468_parental_ctrl3

value: adherent


title: mononuclear cells at estrous cycle 2nd 1

description:
Gene expression in mononuclear cells at  estrous cycle
US22502550_251896410095_S01_GE1-v5_95_Feb07_2_4


title: Blood_pre_101032560006_R01C01


title: mononuclear cells at pregnant 3

description:
Gene expression in mononuclear cells at pregnant
US22502550_251896410095_S01_GE1-v5_95_Feb07_1_2

value: day 165


title: mononuclear cells at pregnant 1

description:
Gene expression in mononuclear cells at pregnant
US22502550_251896410074_S01_GE1-v5_95_Feb07_2_2


title: Granulocytes at estrous cycle 1st 3

description:
Gene expression in granulocytes at estrous cycle
US22502550_251896410074_S01_GE1-v5_95_Feb07_2_3

source_name: Granulocytes at estrous cycle 1st

value: Granulocytes


title: Granulocytes at estrous cycle 1st 4

description:
Gene expression in granulocytes at estrous cycle
US22502550_251896410074_S01_GE1-v5_95_Feb07_2_4


title: Blood_pre_101032560005_R02C01

value: Male

value: blood leukocytes


title: Blood_pre_101032560005_R01C01


title: Granulocytes at estrous cycle 1st 1

description:
Gene expression in granulocytes at estrous cycle
US22502550_251896410065_S01_GE1-v5_95_Feb07_2_1


title: Granulocytes at pregnant 4

description:
Gene expression in granulocytes at pregnant
US22502550_251896410065_S01_GE1-v5_95_Feb07_1_4

source_name: Granulocytes at pregnant


title: Blood_pre_101032560005_R03C01


title: Granulocytes at estrous cycle 1st 2

description:
Gene expression in granulocytes at estrous cycle
US22502550_251896410065_S01_GE1-v5_95_Feb07_2_2


title: Granulocytes at pregnant 2

description:
Gene expression in granulocytes at pregnant
US22502550_251896410065_S01_GE1-v5_95_Feb07_1_2

value: day 150


title: Blood_pre_101032560005_R06C01


title: mononuclear cells at pregnant 2

description:
Gene expression in mononuclear cells at pregnant
US22502550_251896410095_S01_GE1-v5_95_Feb07_1_1

value: mononuclear cells


title: Blood_pre_101032560005_R05C01

value: Pre-supplementation


title: Granulocytes at pregnant 1

description:
Gene expression in granulocytes at pregnant
US22502550_251896410065_S01_GE1-v5_95_Feb07_1_1


title: Granulocytes at estrous cycle 2nd 1

description:
Gene expression in granulocytes at estrous cycle
US22502550_251896410064_S01_GE1-v5_95_Feb07_2_1

source_name: Granulocytes at estrous cycle 2nd

value: estrous cycle


title: liver at estrous cycle 2nd 2

description:
Gene expression in liver at estrous cycle
US22502550_251896410064_S01_GE1-v5_95_Feb07_1_2

source_name: liver at estrous cycle 2nd


title: Granulocytes at estrous cycle 2nd 2

description:
Gene expression in granulocytes at estrous cycle
US22502550_251896410064_S01_GE1-v5_95_Feb07_2_2


title: liver at estrous cycle 1st 4

description:
Gene expression in liver at estrous cycle
US22502550_251896410061_S01_GE1-v5_95_Feb07_2_4

source_name: liver at estrous cycle 1st


title: Granulocytes at estrous cycle 2nd 3

description:
Gene expression in granulocytes at estrous cycle
US22502550_251896410064_S01_GE1-v5_95_Feb07_2_3


title: liver at estrous cycle 2nd 3

description:
Gene expression in liver at estrous cycle
US22502550_251896410064_S01_GE1-v5_95_Feb07_1_3


title: liver at estrous cycle 2nd 1

description:
Gene expression in liver at estrous cycle
US22502550_251896410064_S01_GE1-v5_95_Feb07_1_1


title: Blood_pre_101032560006_R04C01


title: Granulocytes at estrous cycle 2nd 4

description:
Gene expression in granulocytes at estrous cycle
US22502550_251896410064_S01_GE1-v5_95_Feb07_2_4


title: Pax5_6

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

description: Leukemic Bone Marrow cells of Pax5+/- mouse, biological replicate 6

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450)

data_processing: The RMA function provided by the package oligo from R/Bioconductor was applied to the raw expression data.

source_name: Pax5+/- bone marrow leukemic cells

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Ambion)

growth_protocol: Animals were housed in conventional facility and they have been exposed to common pathogens.

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

treatment_protocol: Not applicable

value: Total Bone marrow

tag: genotype

tag: cell type

value: bone marrow leukemic cells


title: Pax5_1

description: Leukemic Bone Marrow cells of Pax5+/- mouse, biological replicate 1


title: Pax5_3

description: Leukemic Bone Marrow cells of Pax5+/- mouse, biological replicate 3


title: WT4

description: Bone Marrow proB and preB cells of WT mouse, biological replicate 4

source_name: WT bone marrow proB and preB cells

value: Bone marrow:proB and preB

value: WT


title: Pax5_5

description: Leukemic Bone Marrow cells of Pax5+/- mouse, biological replicate 5


title: Pax5_4

description: Leukemic Bone Marrow cells of Pax5+/- mouse, biological replicate 4


title: WT2

description: Bone Marrow proB and preB cells of WT mouse, biological replicate 2


title: Bank1Pax5_6

description: Leukemic Bone Marrow cells of Bank1+/- + Pax5+/- mouse, biological replicate 6

source_name: Bank1+/- + Pax5+/- bone marrow leukemic cells


title: Bank1Pax5_4

description: Leukemic Bone Marrow cells of Bank1+/- + Pax5+/- mouse, biological replicate 4


title: liver at estrous cycle 1st 3

description:
Gene expression in liver at estrous cycle
US22502550_251896410061_S01_GE1-v5_95_Feb07_2_3

value: Holstein cow

value: Liver

value: In vivo


title: Bank1Pax5_3

description: Leukemic Bone Marrow cells of Bank1+/- + Pax5+/- mouse, biological replicate 3


title: Pax5_2

description: Leukemic Bone Marrow cells of Pax5+/- mouse, biological replicate 2


title: Bank1Pax5_5

description: Leukemic Bone Marrow cells of Bank1+/- + Pax5+/- mouse, biological replicate 5


title: Bank1Pax5_1

description: Leukemic Bone Marrow cells of Bank1+/- + Pax5+/- mouse, biological replicate 1


title: WT1

description: Bone Marrow proB and preB cells of WT mouse, biological replicate 1


title: liver at estrous cycle 1st 1

description:
Gene expression in liver at estrous cycle
US22502550_251896410061_S01_GE1-v5_95_Feb07_2_1


title: Bank1Pax5_2

description: Leukemic Bone Marrow cells of Bank1+/- + Pax5+/- mouse, biological replicate 2


title: liver at estrous cycle 1st 2

description:
Gene expression in liver at estrous cycle
US22502550_251896410061_S01_GE1-v5_95_Feb07_2_2


title: Granulocytes at pregnant 3

description:
Gene expression in granulocytes at pregnant
US22502550_251896410065_S01_GE1-v5_95_Feb07_1_3

value: pregnant


title: Blood_pre_101032560005_R04C01


title: Normal_Prostate_HSPH0401

status: Public on Mar 01 2017

first: Ericka

last: Ebot

state: MA

address: 677 Huntington Avenue

department: Epidemiology

institute: Harvard T.H. Chan School of Public Health

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: For the expression profiles generated, we regressed out technical variables including mRNA concentration, age of the block, batch (96-well plate), percent of the probes on the array detectable above the background, log transformed average background signal, and the median of the perfect match probes for each probe intensity of the raw data. The residuals were then shifted to have the original mean expression values and normalized using the RMA method. We mapped gene names to Affymetrix transcript cluster IDs using the NetAffx annotations as implemented in Bioconductor annotation package pd.hugene.1.0.st.v1; this resulted in 20,254 unique named genes.  As gene names were used in the final analysis, this is what we have included in the sample tables.

source_name: FFPE normal_prostate

label_protocol: standard Affymetrix protocol

extract_protocol: RNA was extracted using the Biomek FXP automated platform with the Agencourt FormaPure FFPE kit (Beckman Coulter). cDNA synthesis and amplification was performed using the WT-Ovation FFPE System V2 (NuGEN). Amplified cDNA was then fragmented and labeled with a terminal deoxynucleotidyl transferase covalently linked to biotin to prepare for micrarray hybridization. The labeled cDNA was hybridized to a GeneChip Human Gene 1.0 ST micraorray (Affymetrix).

value: FFPE normal_prostate

tag: bmi


title: Normal_Prostate_HSPH0398


title: Normal_Prostate_HSPH0417


title: Normal_Prostate_HSPH0395


title: Normal_Prostate_HSPH0386


title: Normal_Prostate_HSPH0388


title: liver at estrous cycle 2nd 4

description:
Gene expression in liver at estrous cycle
US22502550_251896410064_S01_GE1-v5_95_Feb07_1_4


title: Normal_Prostate_HSPH0407


title: Normal_Prostate_HSPH0387


title: Normal_Prostate_HSPH0394


title: WT3

description: Bone Marrow proB and preB cells of WT mouse, biological replicate 3

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G


title: Normal_Prostate_HSPH0371


title: Normal_Prostate_HSPH0374


title: Normal_Prostate_HSPH0370


title: Normal_Prostate_HSPH0360


title: mononuclear cells at estrous cycle 1st 1

description:
Gene expression in mononuclear cells at  estrous cycle
US22502550_251896410095_S01_GE1-v5_95_Feb07_1_4


title: Normal_Prostate_HSPH0361


title: Normal_Prostate_HSPH0368


title: Normal_Prostate_HSPH0366


title: Normal_Prostate_HSPH0357


title: Normal_Prostate_HSPH0353


title: Normal_Prostate_HSPH0350


title: Normal_Prostate_HSPH0351


title: Normal_Prostate_HSPH0348


title: Normal_Prostate_HSPH0347


title: Normal_Prostate_HSPH0341


title: Normal_Prostate_HSPH0344


title: Normal_Prostate_HSPH0336


title: Normal_Prostate_HSPH0338


title: Normal_Prostate_HSPH0326


title: Normal_Prostate_HSPH0342


title: Normal_Prostate_HSPH0324


title: Normal_Prostate_HSPH0327


title: Normal_Prostate_HSPH0322


title: Normal_Prostate_HSPH0333


title: Normal_Prostate_HSPH0320


title: Normal_Prostate_HSPH0311


title: Normal_Prostate_HSPH0310


title: Normal_Prostate_HSPH0313


title: Normal_Prostate_HSPH0315


title: Normal_Prostate_HSPH0317


title: Normal_Prostate_HSPH0305


title: Normal_Prostate_HSPH0295


title: Normal_Prostate_HSPH0312


title: Normal_Prostate_HSPH0318


title: Prostate_Tumor_HSPH0417

source_name: FFPE prostate tumor

value: FFPE prostate tumor


title: Normal_Prostate_HSPH0274


title: Normal_Prostate_HSPH0280


title: Normal_Prostate_HSPH0294


title: Normal_Prostate_HSPH0292


title: Prostate_Tumor_HSPH0416


title: Prostate_Tumor_HSPH0415


title: Normal_Prostate_HSPH0304


title: Prostate_Tumor_HSPH0412


title: Prostate_Tumor_HSPH0408


title: Prostate_Tumor_HSPH0409


title: Prostate_Tumor_HSPH0414


title: Prostate_Tumor_HSPH0406


title: Prostate_Tumor_HSPH0405


title: Prostate_Tumor_HSPH0413


title: Normal_Prostate_HSPH0319


title: Prostate_Tumor_HSPH0407


title: Prostate_Tumor_HSPH0402


title: Prostate_Tumor_HSPH0404


title: Prostate_Tumor_HSPH0401


title: Prostate_Tumor_HSPH0403


title: Prostate_Tumor_HSPH0400


title: Prostate_Tumor_HSPH0411


title: Prostate_Tumor_HSPH0395


title: Prostate_Tumor_HSPH0392


title: Prostate_Tumor_HSPH0394


title: Prostate_Tumor_HSPH0389


title: Prostate_Tumor_HSPH0387


title: Prostate_Tumor_HSPH0398


title: Prostate_Tumor_HSPH0393


title: Normal_Prostate_HSPH0307


title: Prostate_Tumor_HSPH0386


title: Prostate_Tumor_HSPH0410


title: Prostate_Tumor_HSPH0396


title: Prostate_Tumor_HSPH0397


title: Prostate_Tumor_HSPH0391


title: Prostate_Tumor_HSPH0390


title: Prostate_Tumor_HSPH0381


title: Prostate_Tumor_HSPH0385


title: Prostate_Tumor_HSPH0382


title: Prostate_Tumor_HSPH0384


title: Prostate_Tumor_HSPH0399


title: Prostate_Tumor_HSPH0379


title: Prostate_Tumor_HSPH0380


title: Prostate_Tumor_HSPH0388


title: Prostate_Tumor_HSPH0383


title: Prostate_Tumor_HSPH0378


title: Prostate_Tumor_HSPH0377


title: Prostate_Tumor_HSPH0376


title: Prostate_Tumor_HSPH0375


title: Prostate_Tumor_HSPH0364


title: Prostate_Tumor_HSPH0372


title: Prostate_Tumor_HSPH0368


title: Prostate_Tumor_HSPH0374


title: Prostate_Tumor_HSPH0365


title: Prostate_Tumor_HSPH0371


title: Prostate_Tumor_HSPH0373


title: Prostate_Tumor_HSPH0369


title: Prostate_Tumor_HSPH0367


title: Prostate_Tumor_HSPH0366


title: Prostate_Tumor_HSPH0361


title: Prostate_Tumor_HSPH0363


title: Prostate_Tumor_HSPH0358


title: Prostate_Tumor_HSPH0370


title: Prostate_Tumor_HSPH0360


title: Prostate_Tumor_HSPH0356


title: Prostate_Tumor_HSPH0352


title: Prostate_Tumor_HSPH0353


title: Prostate_Tumor_HSPH0346


title: Prostate_Tumor_HSPH0362


title: Prostate_Tumor_HSPH0348


title: Prostate_Tumor_HSPH0351


title: Prostate_Tumor_HSPH0354


title: Prostate_Tumor_HSPH0349


title: Prostate_Tumor_HSPH0350


title: Prostate_Tumor_HSPH0359


title: Prostate_Tumor_HSPH0347


title: Prostate_Tumor_HSPH0342


title: Prostate_Tumor_HSPH0344


title: Prostate_Tumor_HSPH0355


title: Prostate_Tumor_HSPH0345


title: Prostate_Tumor_HSPH0337


title: Prostate_Tumor_HSPH0340


title: Prostate_Tumor_HSPH0333


title: Prostate_Tumor_HSPH0339


title: Prostate_Tumor_HSPH0343


title: Prostate_Tumor_HSPH0341


title: Prostate_Tumor_HSPH0335


title: Prostate_Tumor_HSPH0338


title: Prostate_Tumor_HSPH0334


title: Prostate_Tumor_HSPH0328


title: Prostate_Tumor_HSPH0326


title: Prostate_Tumor_HSPH0331


title: Prostate_Tumor_HSPH0325


title: Prostate_Tumor_HSPH0324


title: Prostate_Tumor_HSPH0332


title: Prostate_Tumor_HSPH0327


title: Prostate_Tumor_HSPH0330


title: Prostate_Tumor_HSPH0317


title: Prostate_Tumor_HSPH0329


title: Prostate_Tumor_HSPH0323


title: Prostate_Tumor_HSPH0322


title: Prostate_Tumor_HSPH0318


title: Prostate_Tumor_HSPH0320


title: Prostate_Tumor_HSPH0312


title: Prostate_Tumor_HSPH0313


title: Prostate_Tumor_HSPH0314


title: Prostate_Tumor_HSPH0307


title: Prostate_Tumor_HSPH0308


title: Prostate_Tumor_HSPH0309


title: Prostate_Tumor_HSPH0311


title: Prostate_Tumor_HSPH0310


title: Prostate_Tumor_HSPH0303


title: Prostate_Tumor_HSPH0306


title: Prostate_Tumor_HSPH0336


title: Prostate_Tumor_HSPH0302


title: Prostate_Tumor_HSPH0301


title: Prostate_Tumor_HSPH0304


title: Prostate_Tumor_HSPH0300


title: Prostate_Tumor_HSPH0299


title: Prostate_Tumor_HSPH0319


title: Prostate_Tumor_HSPH0293


title: Prostate_Tumor_HSPH0292


title: Prostate_Tumor_HSPH0295


title: Prostate_Tumor_HSPH0298


title: Prostate_Tumor_HSPH0291


title: Prostate_Tumor_HSPH0297


title: Prostate_Tumor_HSPH0290


title: Prostate_Tumor_HSPH0289


title: Prostate_Tumor_HSPH0316


title: Prostate_Tumor_HSPH0305


title: Prostate_Tumor_HSPH0288


title: Prostate_Tumor_HSPH0285


title: Prostate_Tumor_HSPH0287


title: Prostate_Tumor_HSPH0283


title: Prostate_Tumor_HSPH0294


title: Prostate_Tumor_HSPH0286


title: Prostate_Tumor_HSPH0280


title: Prostate_Tumor_HSPH0279


title: Prostate_Tumor_HSPH0281


title: Prostate_Tumor_HSPH0321


title: Prostate_Tumor_HSPH0284


title: Prostate_Tumor_HSPH0296


title: Prostate_Tumor_HSPH0278


title: Prostate_Tumor_HSPH0282


title: Prostate_Tumor_HSPH0272


title: Prostate_Tumor_HSPH0269


title: Prostate_Tumor_HSPH0271


title: Prostate_Tumor_HSPH0357


title: Prostate_Tumor_HSPH0266


title: Prostate_Tumor_HSPH0277


title: Prostate_Tumor_HSPH0276


title: Prostate_Tumor_HSPH0274


title: Prostate_Tumor_HSPH0268


title: Prostate_Tumor_HSPH0267


title: Diagnostic_DLBCL_sample_H447 [re-analysis]

status: Public on Oct 05 2016

city: Aalborg

first: Julie

middle: Støve

last: Bødker

address: Sdr. Skovvej 15

department: Department of Heamatology

country: Denmark

institute: Aalborg University Hospital

hyb_protocol: Included in the label protocol.

scan_protocol: Gene Chips were scanned using the Affymetrix GeneChip scanner 3000 7G

data_processing:
Data were analyzed using R version 3.0.2 and several R and Bioconductor packages and Partek Genomics Suite version 6.6. The .CEL files were pre-processed in Partek using the Robust Multichip Average procedure (RMA) and scan date and labelling kit were set as random effects.
The .CEL files were pre-processed in Partek Genomics Suite version 6.6. RMA normalization was used and scan date and labelling kit were set as random effects.

source_name: diagnostic diffuse large B-cell lymphoma sample

label_protocol: Biotinylated cRNA were prepared using the GeneChip 3' IVT Express Kit (#P/N901229, Affymetrix) from 100 ng total RNA using manual P/N702646 Rev.4.

extract_protocol: Total RNA was purified from frozen diagnostic DLBCLs by homogenizing the sample in Trizol and incubating for 5 minutes at RT. 200µl chloroform was added and incubated 2 minutes at RT, the mixture was centrifuged at 12,000 g for 10 minutes at 4°C. The aqueous phase was transferred to a new tube and 100 % ethanol added in 1.25X the volume. Mix well and transfer to mirVANA columns (#1561, Ambion) and follow the manufacturer’s instruction from this point.

treatment_protocol: Diagnostic samples of diffuse large B-cell lymphoma (DLBCL)

value: diagnostic diffuse large B-cell lymphoma (DLBCL)

tag: abc/gcb class

value: Unclassified

tag: bags class

value: Plasmablast

tag: the regs probability of resistance towards doxorubicin (h)

tag: ipi status

tag: treatment

value: R-CHOP


title: Diagnostic_DLBCL_sample_H457 [re-analysis]

tag: tissue

value: GCB

value: Centroblast


title: Diagnostic_DLBCL_sample_H448 [re-analysis]


title: Diagnostic_DLBCL_sample_H442 [re-analysis]

value: ABC


title: Prostate_Tumor_HSPH0273


title: Prostate_Tumor_HSPH0265


title: Diagnostic_DLBCL_sample_H452 [re-analysis]


title: Diagnostic_DLBCL_sample_H449 [re-analysis]

value: R-CEOP


title: Diagnostic_DLBCL_sample_H454 [re-analysis]


title: Diagnostic_DLBCL_sample_H438 [re-analysis]


title: F9_H3K4me3_6h_ATRA

status: Public on Sep 15 2016

type: SRA

city: Illkirch; Strasbourg

first: Marco Antonio

last: Mendoza-Parra

address: 1, rue Laurent Fries

country: France

institute: IGBMC

library_source: genomic

data_processing:
ChIP-seq and related datasets (FAIRE-seq; Input control) were quality certified with NGS-QC Generator tool (www.ngs-qc.org). Specifically, this methodology allows providing enrichment quality descriptors discretized in a scale ranging from “AAA” (Best) to “DDD” (worst).
Relevant binding sites in all ChIP-Seq and FAIRE-Seq datasets were identified with MeDiChISeq, a regression-based approach which after a learning process defines a representative binding pattern from the dataset under analysis (Mendoza-Parra et al; BMC Genomics 2013). Specifically a P-value confidence cutoff of 1x10-2.5 complemented by a peak intensity threshold based on a Poisson distribution background model.
Genome-wide quantile normalization prior multiprofiles comparison has been performed with EPImetheus (Saleem MA; unpublished).
Genome_build: mm9
Supplementary_files_format_and_content: peaks (MeDiChISeq) and quality report (pdf)

source_name: F9 embryonal carcinoma cells

growth_protocol: F9 EC cells were cultures in Dubelcco’s modified Eagle’s medium supplemented with 10% fetal Calf serum. In a similar manner, P19 cell’s medium was supplemented with 5% fetal Calf serum and 5% delipidated Calf serum. In both cases the medium was complemented with 40ug/ml Gentamicin. F9 or P19 EC cells were cultured in monolayer conditions seeded in gelatine-coated tissue culture plates (0.1%).

extract_protocol:
F9 or P19 EC cells were fixed with 1% para-formaldehyde (Electron Microscopy Sciences) for 30 minutes at room temperature. ChIP assays were performed following previously described conditions: chromatin sonication and immunoprecipitation in lysis buffer (50mM Tris–Cl pH=8, 140mM NaCl, 1mM EDTA, 1% Triton, 0.1% Na-deoxycholate) complemented with protease inhibitor cocktail (Roche 11873580001); 2x washes with lysis buffer; 2x washes with lysis buffer containing 360mM NaCl; 2x washes with washing buffer (10mM Tris–Cl pH=8, 250mM LiCl, 0.5% NP-40, 1mM EDTA, 0.5% Na-deoxycholate); 2x washes with 1x TE; elution at 651C; 15 min in elution buffer (50mM Tris–Cl pH=8, 10mM EDTA, 1% SDS). RXRa has been immunoprecipitated with purified polyclonal antibodies generated by immunization of rabbits with the following peptide:mRXRa: PB105 (MDTKHFLPLDFSTQVNSSSLNSPTGRGC). RXRa ChIP assays were performed with 6x106 cells per time point; while histone modification marks were evaluated with 2x106 cells. FAIRE assays were performed as described previously (Giresi et al, 2007; Simon et al, 2012).
qPCR-qualified ChIP assays were quantified (Qubit dsDNA HS assay kit; Invitrogen); then 10 ng of the ChIPed material was used for preparing Illumina sequencing libraries following a multiplexing approach (NEXTflexTM ChIP-seq Bioo Scientific;  ref: 514120). Prepared sequencing libraries were sequenced on the Illumina instrument HiSeq2000 (4 ChIP samples per lane). Regular Illumina pipelines were used for image processing and base calling. Sequence files were then aligned to the mouse genome assembly following by default parameters (mm9; Bowtie).

treatment_protocol: For cell differentiation induction, ATRA was added to plates in a final concentration of 1x10-6 M at different time points. For RAR subtype-specific agonists’ treatment, cells were incubated with BMS961 (RARg specific; final concentration 1x10-7 M), BMS753 (RARa specific; final concentration 1x10-6 M) or BMS641 (RARb specific; final concentration 1x10-7 M).

value: ATRA

tag: time point

value: 6 hours

tag: chip antibody

value: Abcam ab8580


title: Diagnostic_DLBCL_sample_H456 [re-analysis]


title: Diagnostic_DLBCL_sample_H444 [re-analysis]


title: Diagnostic_DLBCL_sample_H437 [re-analysis]

value: Centrocyte


title: spleen_stroke_MTC26

status: Public on Jul 19 2016

city: Edinburgh

first: Barry

middle: W

last: McColl

address: 49 Little France Crescent

department: Centre for Discovery Brain Sciences

country: United Kingdom

institute: University of Edinburgh

description: gene expression data from experimental stroke mouse spleen

hyb_protocol: Following fragmentation, 3 ug of cRNA were hybridized to the Affymetrix MoGene 1.0 ST array plate using Gene Titan was and stain kit for WT array plates using affymetrix standard protocols . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Gene chips were scanned by edinburgh genomics

data_processing: The resulting CEL files were used for analysis in Partek Genomics Suite (Partek Incorporated, St. Louis, Missoiri, USA) by ANOVA

source_name: spleen 5 d after experimental stroke surgery

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix) and labelled using affymetrix Genechip WT terminal labelling kit .

growth_protocol: 40 minute occlusion of the middle cerebral artery was performed on male 8-10 week old C57BL/6J mice.   Sham-surgery was performed on age and sex matched control animals.  Animals were allowed to recover for 5 d before perfusion with saline + 0.01% DEPC and harvesting of spleens.

extract_protocol: Extraction of RNA was carried out using the Qiagen Rneasy mini kit according to the manufacturers instructions

treatment_protocol: 1/4 of the spleen was manually homogenised in 350 ml RLT buffer from Qiagen Rneasy mini kit (Qiagen, Manchester, UK) with 3.5 ml b-mercaptoethanol

tag: strain

value: spleen

value: stroke


title: Diagnostic_DLBCL_sample_H446 [re-analysis]


title: Diagnostic_DLBCL_sample_H440 [re-analysis]


title: spleen_stroke_MTC9


title: spleen_stroke_MTC11


title: spleen_sham_MTC45

description: control gene expression data from sham-operated mouse spleen

source_name: spleen 5 d after sham surgery

value: sham


title: spleen_sham_MTC44


title: Prostate_Tumor_HSPH0270

tag: group


title: Striatal microglia at 22month, biological rep2

status: Public on Dec 10 2015

description: Gene expression data from striatal microglia of 4 month old mice

hyb_protocol: Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C to the Affymetrix HT_MG-430_PM-16 plate array in the Gene Titan using the Affymetrix standard protocols.

scan_protocol: GeneChips were scanned using the Gene Titan Multi-channel  instrument from Affymetrix.

data_processing: The data were analyzed with Affymetric Expression Console built-in Robust Multiarray Averaging (RMA) method using Affymetrix default analysis settings and global scaling as normalization method. Samples were normalized within subsets. Text files on the series record include the RMA signal intensity for the different normalizations.

source_name: Microglia extracted from striatum at 22 month of age

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: C57BL/6J mice maintained under standard conditions.

extract_protocol: Rneasy Plus Micro Kit (isolated microglia) and Rneasy Midi Kit (regional homogenates) extraction of total RNA was performed according to the manufacturer's instructions.

value: brain

tag: age


title: Hippocampal microglia at 22month, biological rep4

description: Gene expression data from hippocampal microglia of 4 month old mice

source_name: Microglia extracted from hippocampus at 22 month of age


title: Striatal microglia at 22month, biological rep3


title: Hippocampal microglia at 22month, biological rep3


title: Striatal microglia at 22month, biological rep1


title: Cortical microglia at 22month, biological rep3

description: Gene expression data from cortical microglia of 4 month old mice

source_name: Microglia extracted from cortex at 22 month of age


title: Hippocampal microglia at 22month, biological rep1


title: Prostate_Tumor_HSPH0315

value: FFPE prostate tumor


title: Cerebellar microglia at 22month, biological rep4

description: Gene expression data from cerebellar microglia of 4 month old mice

source_name: Microglia extracted from cerebellum at 22 month of age


title: Cerebellar microglia at 22month, biological rep1


title: Hippocampal microglia at 22month, biological rep2


title: Cortical microglia at 22month, biological rep2


title: Striatal microglia at 22month, biological rep4


title: Cortical microglia at 12month, biological rep3

source_name: Microglia extracted from cortex at 12 month of age


title: Hippocampal microglia at 12month, biological rep1

source_name: Microglia extracted from hippocampus at 12 month of age


title: Hippocampal microglia at 12month, biological rep2


title: Cortical microglia at 12month, biological rep4


title: Cortical microglia at 12month, biological rep2


title: Cerebellar microglia at 22month, biological rep2


title: Cortical microglia at 22month, biological rep4


title: Striatal microglia at 12month, biological rep4

source_name: Microglia extracted from striatum at 12 month of age


title: Cortical microglia at 12month, biological rep1


title: Striatal microglia at 12month, biological rep3


title: Cortical microglia at 22month, biological rep1


title: Striatal microglia at 12month, biological rep2


title: Striatal microglia at 12month, biological rep1


title: Hippocampal microglia at 12month, biological rep4


title: Luminal-K8YFP-8w-1

status: Public on Aug 13 2015

city: Bruxelles

first: Alexandra

last: Van Keymeulen

address: 808, route de Lennik CP602

department: IRIBHM

country: Belgium

institute: Université Libre de Bruxelles

description: Gene expression of YFP+ luminal cells of K8CREERT2/RosaYFP mice 8w following tamoxifen administration, replicate 1

hyb_protocol: A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix MG-430 PM arrays  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: The data were analyzed with R (version 2.14.0) Bioconductor fRMA (version 1.6) package with default analysis settings.

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent).  All following steps were carried out at the IRB Functional Genomic Core (Barcelona) according to the manufacturers protocol (Affymetrix)

growth_protocol: Mice were maintained in a certified animal house according to European guidelines

extract_protocol: Qiagen Rneasy Micro

treatment_protocol: Female mice were injected with 3 times with 5 mg of tamoxifen every three days starting at age of 4-5 week. Mice were sacrified at the indicated time point and mammary gland was digested in Collagenase+hyaluronidase. Single cells were stained with the appropriate antibodies and FACS sorted before RNA extraction.

value: Mouse mammary gland FACS purified luminal cells


title: Cerebellar microglia at 12month, biological rep4

source_name: Microglia extracted from cerebellum at 12 month of age


title: PBS LY6C+ : PBS injected LY6C+ monocytes [JS_9_PBS3]

status: Public on Apr 01 2015

city: London

first: Stephen

last: Henderson

address: Paul O'Gorman Building

department: Cancer Institute

institute: UCL

description: Gene expression data from primary monocytes

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mogene 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were preprocessed and normalised initially using the Bioconductor oligo package (RMA algorithm). (In Publication data were further merged with other public datasets and renormalised)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Not applicable

extract_protocol: Extraction of total RNA was performedusing the RNAeasy Microkit (Qiagen, UK)

treatment_protocol: Monocytes populations were purified fromCD11c-DTR mice which were injected with PBS or diphtheria toxin 48 hours previously. Common monocyte progenitors (cMoP) were isolated from untreated C57BL/6 mice.

value: monocyte

value: 8-12 weeks


title: Cerebellar microglia at 12month, biological rep2


title: Cerebellar microglia at 12month, biological rep3


title: Hippocampal microglia at 12month, biological rep3


title: Basal-K5YFP-8w-1

description: Gene expression of YFP+ basal cells of K5CREERT2/RosaYFP mice 8w following tamoxifen administration, replicate 1

value: Mouse mammary gland FACS purified basal cells


title: PBS LY6C+ : PBS injected LY6C+ monocytes [G32_PBS1]


title: root -N, biological rep 2

status: Public on Jun 30 2015

city: Taipei

first: Ming-Hsiun

last: Hsieh

address: 128 Academia Road, Section 2

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

description: Gene expression data from rice roots without gln treatment

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

scan_protocol: The arrays were scanned on the Affymetrix GeneChip Scanner 3000.

data_processing: The Affymetrix CEL data were generated from GCOS and normalized using RMA algorithm in Genespring 11.5 software. Baselines were transformed to median of control samples. Expression value of probeset that >100 was defined as present. Unpaired t-test was performed to examine the reproducibility of the data sets. Probesets with P-value <0.05 and at least two-fold change between control and treatment groups were selected into the final list.

organism: Oryza sativa Japonica Group

source_name: rice roots without gln treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Rice (Oryza sativa L. ssp. Japonica cv. TNG67) seeds were germinated in continuous dark at 30°C for 3 days and then transferred to hydroponic solution (Yoshida et al., 1976) without NH4NO3 (-N) and grown under controlled conditions (30°C, 12-h photoperiod, 200 µmol photons m-2 s-1, 70% relative humidity) for 2 weeks.

extract_protocol: Total RNA from –N and + Gln-treated roots was extracted using a phenol extraction protocol.

treatment_protocol: 17-day-old rice seedlings grown in –N hydroponic solution were transferred to -N or +2.5 mM Gln solution for 30 min.

tag: variety

value: root

tag: growth stage

value: 17 day-old seedling


title: PBS LY6C+ : PBS injected LY6C+ monocytes [JS_8_PBS2]


title: CON_LON_test045

status: Public on Aug 11 2010

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

description: Whole Blood from healthy control recruited in London. The subject was negative for skin test and IGRA test.

hyb_protocol: Hybridize 12-Sample Beadchip

scan_protocol: SentrixScanVersion 2.3.0.13  (This information is in the .XML file)

data_processing: The data were analysed using BeadStudio version 1.5.1.3 using the average chip normalization method.

source_name: Whole Blood from healthy control

label_protocol: Biotinylated cRNA were generated following manufacturer protocols using the Illumina TotalPrep Amplification Kit from Ambion

extract_protocol: RNA was isolated using the MagMAX™-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA) according to the manufacturer's instructions

tag: gender

value: Male

tag: ethnicity

value: Black

tag: illness

value: Control (BCG+)

tag: geographical region

value: London

tag: bcg vaccinated

value: Yes

tag: region of birth

tag: tst

tag: smear of index case

tag: modal x-ray grade


title: PBS LY6C+ : PBS injected LY6C+ monocytes [JS_7_PBS1]

tag: tissue

tag: cell type


title: Basal-K5YFP-8w-2

description: Gene expression of YFP+ basal cells of K5CREERT2/RosaYFP mice 8w following tamoxifen administration, replicate 2


title: PTB_LON_test042

description: Whole Blood from patient with active TB recruited in London. The subject was infected with Mycobacterium tuberculosis and confirmed as culture positive.

source_name: Whole Blood from patient with Active TB

value: Female

value: White

value: PTB

value: Minimal

value: tuberculosis


title: LTB_LON_test029

description: Whole Blood from patient with Latent TB  recruited in London .  The subject was an asymptomatic household contact of an active patient or a new entrant from an endemic country and tested positive by both IGRA and tuberculin skin test.

source_name: Whole Blood from patient with Latent TB

value: Asian other

value: Latent

value: pulm

value: Sm+

value: No disease


title: Cerebellar microglia at 12month, biological rep1

value: brain

tag: genotype


title: CON_LON_test048


title: CON_LON_test047

value: South Asian


title: root -N, biological rep 1

value: root

value: 17 day-old seedling


title: Luminal-K8YFP-8w-2

description: Gene expression of YFP+ luminal cells of K8CREERT2/RosaYFP mice 8w following tamoxifen administration, replicate 2

value: Mouse mammary gland FACS purified luminal cells


title: LTB_LON_test030

value: London


title: PTB_LON_test051

value: Male

value: Moderate


title: LTB_LON_test043

value: Female

value: Yes


title: PTB_LON_test052

value: White

value: PTB

value: Minimal


title: Prostate_Tumor_HSPH0275

source_name: FFPE prostate tumor

value: FFPE prostate tumor

tag: bmi


title: PTB_LON_test006

value: Advanced

value: scanty

value: tuberculosis


title: Cerebellar microglia at 22month, biological rep3

value: brain


title: CON_LON_test046

value: Asian other

value: Control (BCG+)


title: LTB_LON_test008

value: Black

value: Latent

value: pulm

value: Sm+

value: No disease


title: CON_LON_test041

value: Female

value: London


title: PTB_LON_test050

value: White

value: Yes


title: LTB_LON_test033


title: LTB_LON_test011

value: Other


title: LTB_LON_test025

value: unknown