title: 1 μM CSPT, Mouse 3

description:
Quality control: approved
125_B05

source_name: Primary mouse hepatocytes, mouse #3, CSPT

value: male

value: Cisplatin (CsPt)

value: CSPT

value: 1 μM CSPT


title: 15E mDNA

status: Public on Oct 23 2014

type: genomic

city: Duarte

first: Marc

last: Jung

state: CA

address: 1500 East Duarte Street

department: Biology

country: USA

institute: City Of Hope

description:
MIRA-chip primary skin fibroblasts, early timepoint mDNA
Sample 47

hyb_protocol: According to standard NimbleGen Protocol

scan_protocol: Follow NimbleScan's default using Agilent Scanner

data_processing: Samples were quantile-normalized and arrays were normalized by Nimblegen's recommended method, tukey-biweight.

molecule: genomic DNA

organism: Homo sapiens

source_name: MIRA DNA_primary skin fibroblast_early

growth_protocol: Primary Skin Fibroblast cells were grown with culture medium (DMEM supplemented with 6% fetal bovine serum) for 2 -3 passages.

extract_protocol: Primary Embryonic Fibroblast cells were grown in a 150 mm dish containing 25 ml of culture medium (DMEM supplemented with 6% fetal bovine serum (FBS) to about 5x107 cells).  Fresh formaldehyde was added directly into media to a final concentration of 1% and incubated at RT for exactly 2 minutes on an orbiting platform. Cross-linking reaction was stopped by adding 2.6 ml of 1.25 M glycine solution. Media was removed and cells were washed twice with 20 ml ice-cold PBS without Ca and Mg. Cells were pelleted by centrifugation for 3 minutes at 250g at 4°C. For sonification, cells were resuspended from each 150 mm dish in 350 µl ChIP Lysis Buffer (1% SDS, 10 mM EDTA and 50 mM Tris-HCl, pH 8.1) containing protease inhibitors (complete protease inhibitor cocktail tablets, Roche applied science, Cat.# 1697498). Sonication was carried out in 1.7 ml Eppendorf tubes using Branson Sonifer with a micro tip. Sonication condition were 10 times at 15sec on, 45sec off, at output 25%. Sheared chromatin was centrifuged at 14,000 rpm for 15 minutes at 4C.  For Methylated-CpG island recovery assay (MIRA), the methylated faction of sonicated genomic DNA from human skin fibroblast cells was captured using recombinant MBD3L1 and MBD2b proteins. Ligation-mediated PCR (LM-PCR) was performed to amplify MIRA-enriched DNA.

tag: donor age (yrs)

tag: cell type

value: primary skin fibroblast

tag: time point

value: early timepoint (E)

tag: chip antibody

value: MIRA

source_name: Input DNA from primary skin fibroblast, early timepoint

value: none, input DNA


title: 16L mDNA

description:
MIRA-chip primary skin fibroblasts, late timepoint mDNA
Sample 56

source_name: MIRA DNA_primary skin fibroblast_late

label_protocol: According to standard NimbleGen Protocol

value: late timepoint (L)

source_name: Input DNA from primary skin fibroblast, late timepoint


title: 16E mDNA

description:
MIRA-chip primary skin fibroblasts, early timepoint mDNA
Sample 48


title: Nuclei proembryo, biological rep 2

type: RNA

city: Tübingen

first: Daniel

last: Slane

state: Baden-Württemberg

address: Spemannstrasse 35

department: Cell Biology

country: Germany

institute: Max Planck Institute for Developmental Biology

description:
nPE #2
Gene expression data from nuclei.

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on ATH1 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip scanner 3000.

data_processing: The data was analyzed with Microarray Suite version 5.0 (MAS 5.0) using "affy" package (v1.32.1).

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Arabidopsis embryos 2-16 cell stage, proembryo, nuclei

label_protocol: Biotinylated cRNA was prepared according to the ENZO BioArray™ Single-round RNA amplification and biotin labeling system.

growth_protocol: Long day 16 hours light/8 hours dark.

extract_protocol: Nuclear extraction with CelLyticTM PN kit (Sigma). RNA extraction with buffer containing proteinase K.

treatment_protocol: Ovules including embryos from 2-16 cell stage were dissected from siliques and fixed with 0.1% PFA (paraformaldeyhde).

tag: ecotype

tag: tissue

value: proembryo

tag: developmental stage

value: embryo (2-16 cell stage)


title: 1 μM CSA, Mouse 3

city: Bilthoven

first: Mirjam

middle: M

last: Schaap

address: Antonie van Leeuwenhoeklaan 9

country: Netherlands

institute: RIVM

description:
Quality control: approved
120_G07

hyb_protocol: According to the protocol provided with the Affymetrix 3' IVT Express Labeling Kit (#901229).

scan_protocol: According to Affymetrix protocols, using a GeneChip HT Array Plate Scanner (Affymetrix).

data_processing: The raw data were subjected to a set of quality control checks. After passing array quality control, the arrays were annotated according to de Leeuw et al. (2008) and expression values were calculated using the robust multi-array average (RMA) algorithm (Affy package, version 1.22.0; Irizarry et al. 2003) available from the Bioconductor project (http://www.bioconductor.org) for the R statistical language (http://cran.r-project.org)). The normalized data was statistically analyzed for differential gene expression using a mixed linear model with coefficients for block (random) and each experimental group (fixed) (Smyth 2004; Wolfinger et al. 2001). A contrast analysis was applied to compare each exposure with the corresponding vehicle control. For hypothesis testing, a permutation-based Fs test was used (Cui et al. 2005). False discovery rate (FDR) correction was performed globally across all contrasts according to Storey and Tibshirani (2003). Only the annotated genes were used for further analysis.

organism: Mus musculus

source_name: Primary mouse hepatocytes, mouse #3, CsA

label_protocol: Biotin-labeled cRNA samples were prepared as described in the Affymetrix GeneChip HT 3' IVT Express Technical Manual (Affymetrix) using 200 ng of purified total RNA as template for the reaction.

growth_protocol: Primary mouse hepatocytes were isolated from 8- to 10-week-old male C57BL/6 mice by a modified two-step collagenase perfusion technique. Cells were cultured in a sandwich configuration in 6-wells at 1.3 x 10^6 cells per well.

extract_protocol: RNA was extracted using QIAzol and purified using the miRNeasy mini kit and the QIAcube (Qiagen), according to the manufacturer's protocol.

treatment_protocol: Hepatocytes were exposed for 24 hours to the 16 non-genotoxic carcinogens. Control cells were vehicle-treated (DMSO or PBS, 0.5%). After 24 hours of exposure, cells were collected in 1 ml RNAprotect (QIAgen) and stored at -80˚C for RNA isolation.

tag: strain

tag: gender

tag: age

value: 8-10 weeks

value: primary mouse hepatocytes

tag: mouse identifier

tag: chemical

value: Cyclosporin A (CsA)

tag: abbreviation

value: CsA

tag: concentration

value: 1 μM CSA


title: Lame 239 Area1

city: Quebec

first: Eric

last: Fournier

state: Quebec

address: 2325 Rue de l'Universite

department: Departement des sciences animales

country: Canada

institute: Universite Laval

hyb_protocol: This document applies to the hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects.

scan_protocol: This is a place holder for the Tecan scanning protocol.

data_processing: Data were normalized with Lowess intra-array and quantile inter-array normalizations using the FlexArray software (Génome Québec, http://www.gqinnovationcenter.com/services/bioinformatics/flexarray)

organism: Bos taurus

label_protocol: This document describes the procedure used for labelling aRNA using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: To initiate a new follicular wave, all follicles larger than 5 mm in diameter were punctured on days 8–11 post-oestrus. Administration of follicle-stimulating hormone (Folltropin-V, Bioniche Animal Health, Belleville, ON, Canada) was begun 36 h after follicular removal. Follicle-stimulating hormone was injected twice a day in doses of 40 mg for a total of 240 mg (six injections). Forty-eight hours after the final injection, the ultrasound-based pick-up procedure was performed using an 18G needle and COOK aspiration device (COOK Medical, Bloomington, IN, USA). Cumulus-oocyte complexes (COC) thus recovered were submitted to in vitro maturation. Cumulus-oocyte complexes were twice washed thoroughly in HEPES-buffered Tyrode's medium containing 10 % bovine serum, 200 μM pyruvate and 50 μg/mL gentamycin to ensure total removal of follicular liquid. Healthy COCs were then placed in maturation medium (groups of 10 per 50 μL droplet) under filtered mineral oil (9 mL) for 24 h at 38.5 °C in a humidified 5 % CO2, 20 % O2 atmosphere. The maturation medium contained TCM199 (Gibco 11150-059, Invitrogen, Burlington, ON, Canada), 10 % foetal calf serum (Sterile Foetal Bovine Serum for Cell Culture, Medicorp, Montreal, QC, Canada), 200 μM pyruvate, 50 μg/mL gentamycin and 0.1 μg/mL folliclestimulating hormone (Gonal-f, Serono Canada Inc., Mississauga, ON, Canada). Washed and matured COCs were placed in groups of five per droplet (50 μL) of modified Tyrode’s lactate medium (containing 0.6 % bovine serum albumin Sigma fraction V and 200 μM gentamycin) under filtered mineral oil. Two μL of a solution containing 1 mM hypotaurine, 2 mM penicillamine and 250 mM epinephrine were then added to each droplet. In vitro fertilization with frozen semen (pooled ejaculate) of the Jersey or Holstein breed (provided by L’Alliance Boviteq) was performed without delay. The semen was thawed at 37 °C in a water bath, laid on a discontinuous Percoll gradient (2 mL of 45 % Percoll over 2 mL of 90 % Percoll) and centrifuged at 700 x g for 30 min at room temperature. The supernatant was discarded and the pellet was re-suspended in modified Tyrode’s lactate medium such that 50,000 spermatozoa (based on count using a haemocytometer) were used to fertilize each group of five COC.

extract_protocol:
This document applies to the total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.
This procedure describes the amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.

treatment_protocol: Presumptive zygotes were stripped of cumulus cells and spermatozoa by gentle pipetting in pre-incubated synthetic oviduct fluid then allocated randomly to two groups for culture in synthetic oviduct fluid (SOF) either with 0.5 mM L-carnitine (the “treated” or “ + LC ” group) or without (the “control” or “ – LC” group). The SOF media was a standard culture medium containing amino acids and 0.4 % fatty-acid-free bovine serum albumin (ICP-Bio, Auckland, New Zealand). Ten zygotes were placed in a single droplet (10 μL) under filtered mineral oil (#8410, Sigma). The culture dishes were incubated at 38.5 °C in a humidified atmosphere containing 6.5 % CO2, 5 % O2 and 88.5 % N2. Ten embryos were transferred to each fresh droplets (10 μL) at 72 h and 120 h (20 μL) after fertilization to prevent ammonia intoxication (from amino acid metabolism) and nutrient depletion. Embryos remained under these conditions until Day 6, when morulas and early blastocysts were categorized according to IETS system for comparison purposes. Samples were produced using seven independent in vitro production runs. The COCs from different donor cows were pooled within respective breed and randomly allocated to treatment or control groups. Morula stage embryos were used for lipid quantification and mitochondrial activity measurement while blastocysts were used for mitochondrial DNA and RNA analyses.

tag: breed (cattle)

value: holstein


title: 15L mDNA

description:
MIRA-chip primary skin fibroblasts, late timepoint mDNA
Sample 55


title: Nuclei proembryo, biological rep 3

description:
nPE #3
Gene expression data from nuclei.


title: DMSO, Mouse 3

description:
Quality control: approved
118_H07

source_name: Primary mouse hepatocytes, mouse #3, DMSO

value: male

value: DMSO control

value: DMSO

value: 0.5% DMSO


title: 13E mDNA

description:
MIRA-chip primary skin fibroblasts, early timepoint mDNA
Sample 45

value: primary skin fibroblast


title: 7E mDNA

description:
MIRA-chip primary skin fibroblasts, early timepoint mDNA
Sample 43

value: early timepoint (E)


title: 9E mDNA

description:
MIRA-chip primary skin fibroblasts, early timepoint mDNA
Sample 44

value: MIRA


title: Lame 238 Area4


title: Nuclei proembryo, biological rep 1

description:
nPE #1
Gene expression data from nuclei.


title: 14E mDNA

description:
MIRA-chip primary skin fibroblasts, early timepoint mDNA
Sample 46

value: none, input DNA


title: 13L mDNA

description:
MIRA-chip primary skin fibroblasts, late timepoint mDNA
Sample 53

value: late timepoint (L)


title: 10 μM TCPOBOP, Mouse 3

description:
Quality control: approved
119_D07

source_name: Primary mouse hepatocytes, mouse #3, TCPOBOP

value: TCPOBOP

value: 10 μM TCPOBOP


title: Lame 238 Area1


title: 14L H3K27me3

description:
Chip-chip primary skin fibroblasts, late timepoint H3K27me3
Sample 38

source_name: H3K27me3 ChIP DNA_primary skin fibroblast_late

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #

tag: chip antibody lot #


title: 16L H3K27me3

description:
Chip-chip primary skin fibroblasts, late timepoint H3K27me3
Sample 40

tag: donor age (yrs)

tag: cell type


title: 2E mDNA

description:
MIRA-chip primary skin fibroblasts, early timepoint mDNA
Sample 41

tag: time point

tag: chip antibody


title: 30 μM ARO, Mouse 3

description:
Quality control: approved
116_D05

source_name: Primary mouse hepatocytes, mouse #3, ARO

value: 8-10 weeks

value: primary mouse hepatocytes

value: Aroclor 1254

value: ARO

value: 30 μM ARO


title: 6L mDNA

description:
MIRA-chip primary skin fibroblasts, late timepoint mDNA
Sample 50


title: 13L H3K27me3

description:
Chip-chip primary skin fibroblasts, late timepoint H3K27me3
Sample 37


title: 1 mM CF, Mouse 3

description:
Quality control: approved
115_G05

source_name: Primary mouse hepatocytes, mouse #3, CF

value: male

value: Clofibrate

value: CF

value: 1 mM CF


title: 15L H3K27me3

description:
Chip-chip primary skin fibroblasts, late timepoint H3K27me3
Sample 39

value: primary skin fibroblast


title: Array 244 Area4

value: Jersey


title: 3 μM MEN, Mouse 3

description:
Quality control: approved
113_H07

source_name: Primary mouse hepatocytes, mouse #3, MEN

value: Menadion

value: MEN

value: 3 μM MEN


title: 1 mM PB, Mouse 3

description:
Quality control: approved
114_E05

source_name: Primary mouse hepatocytes, mouse #3, PB

value: Phenobarbital (Pb)

value: PB

value: 1 mM PB


title: 0.3 μM TBTO, Mouse 3

description:
Quality control: approved
111_G07

source_name: Primary mouse hepatocytes, mouse #3, TBTO

value: 8-10 weeks

value: Tributyltinoxide (TBTO)

value: TBTO

value: 0.3 μM TBTO


title: Array 244 Area3


title: Array 244 Area2


title: Lame 238 Area2

value: holstein


title: Array 244 Area1


title: 10 μM BPA, Mouse 3

description:
Quality control: approved
109_D07

source_name: Primary mouse hepatocytes, mouse #3, BPA

value: male

value: primary mouse hepatocytes

value: Bisphenol A (BPA)

value: BPA

value: 10 μM BPA


title: 1 mM TCE, Mouse 3

description:
Quality control: approved
110_F07

source_name: Primary mouse hepatocytes, mouse #3, TCE

value: Methyl chloroform (1,1,1-TCE)

value: TCE

value: 1 mM TCE


title: Array 243 Area4

value: Jersey


title: 30 μM ETP, Mouse 3

description:
Quality control: approved
108_C05

source_name: Primary mouse hepatocytes, mouse #3, ETP

value: Etoposide

value: ETP

value: 30 μM ETP


title: Array 243 Area3


title: Array 243 Area2


title: Lame 239 Area3


title: 11L H3K27me3

description:
Chip-chip primary skin fibroblasts, late timepoint H3K27me3
Sample 36

value: primary skin fibroblast

value: late timepoint (L)

value: Millipore

value: none, input DNA


title: 1 nM OA, Mouse 3

description:
Quality control: approved
107_H05

source_name: Primary mouse hepatocytes, mouse #3, OA

value: 8-10 weeks

value: Okadaic Acid (OA)

value: OA

value: 1 nM OA


title: 100 μM HCH, Mouse 3

description:
Quality control: approved
117_H05

source_name: Primary mouse hepatocytes, mouse #3, HCH

value: male

value: primary mouse hepatocytes

value: beta-Hexachlorocyclohexane (HCH)

value: HCH

value: 100 μM HCH


title: Lame 238 Area3

value: holstein


title: Array 243 Area1

value: Jersey


title: 1 mM MNU, Mouse 3

description:
Quality control: approved
105_C07

source_name: Primary mouse hepatocytes, mouse #3, MNU

value: N-Nitroso-N-Methylurea (MNU)

value: MNU

value: 1 mM MNU


title: 16_BTBR T+ tf/J_female_Autism-4

city: Jefferson

first: Volodymyr

last: Tryndyak

address: 3900 NCTR Rd

department: Division of Biochemical Toxicology

institute: US-FDA National Center for Toxicological Research

description: Gene expression in the cerebellum of female BTBR T+ tf/J mice

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent 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 SurePrint G3 Mouse GE Oligo Microarrays (G4858A-028005) 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 (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, 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 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The raw data were normalized using ArrayTrack software (USFDA National Center for Toxicological Research, Jefferson, AR).

source_name: 16, BTBR T+ tf/J, female, Autism-4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick-Amp Labeling kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from a cerebellum tissue using RNeasy Mini kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000C spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The frozen cerebellum from male and female BTBR T+tf/J and C57BL/6J mice (8 weeks of age, n=5 per gender/strain) were obtained from the Jackson Laboratory (Bar Harbor, ME, USA).

tag: strain/genotype

value: BTBR T+tf/J

tag: tissue

value: Cerebellum

value: Female

value: 8 weeks


title: 0.3 μM MMC, Mouse 3

description:
Quality control: approved
101_A07

source_name: Primary mouse hepatocytes, mouse #3, MMC

tag: strain

value: 8-10 weeks

value: Mitomycine C (MMC)

value: MMC

value: 0.3 μM MMC


title: 5L H3K27me3

description:
Chip-chip primary skin fibroblasts, late timepoint H3K27me3
Sample 32

value: primary skin fibroblast

value: late timepoint (L)

value: Millipore

source_name: Input DNA from primary skin fibroblast, late timepoint

value: none, input DNA


title: 15_BTBR T+ tf/J_female_Autism-3

source_name: 15, BTBR T+ tf/J, female, Autism-3

tag: gender


title: 10 nM TCDD, Mouse 3

description:
Quality control: approved
103_D05

source_name: Primary mouse hepatocytes, mouse #3, TCDD

value: male

tag: age

value: primary mouse hepatocytes

value: TCDD

value: 10 nM TCDD


title: 14_BTBR T+ tf/J_female_Autism-2

source_name: 14, BTBR T+ tf/J, female, Autism-2


title: 1 mM DM, Mouse 3

description:
Quality control: approved
102_B05

source_name: Primary mouse hepatocytes, mouse #3, DM

tag: mouse identifier

value: D-mannitol

value: DM

value: 1 mM DM


title: 100 μM WY, Mouse 3

description:
Quality control: approved
104_F05

source_name: Primary mouse hepatocytes, mouse #3, WY

tag: chemical

value: WY

value: 100 μM WY


title: 13_BTBR T+ tf/J_female_Autism-1

source_name: 13, BTBR T+ tf/J, female, Autism-1

value: BTBR T+tf/J

value: Cerebellum

value: Female

value: 8 weeks


title: 30 μM HCE, Mouse 3

description:
Quality control: approved
100_A05

source_name: Primary mouse hepatocytes, mouse #3, HCE

value: 8-10 weeks

value: Heptachlor epoxide (HCE)

tag: abbreviation

value: HCE

value: 30 μM HCE


title: 12_BTBR T+ tf/J_male_Autism-4

description: Gene expression in the cerebellum of male BTBR T+ tf/J mice

source_name: 12, BTBR T+ tf/J, male, Autism-4

value: Male


title: 2L H3K27me3

description:
Chip-chip primary skin fibroblasts, late timepoint H3K27me3
Sample 31

source_name: H3K27me3 ChIP DNA_primary skin fibroblast_late

value: primary skin fibroblast

value: late timepoint (L)

value: Millipore

value: none, input DNA


title: 300 μM DEM, Mouse 5

description:
Quality control: approved
09_B05

source_name: Primary mouse hepatocytes, mouse #5, DEM

value: male

value: primary mouse hepatocytes

value: Diethyl maleate (Dem)

value: DEM

tag: concentration

value: 300 μM DEM


title: 10 μM LAC, Mouse 5

description:
Quality control: approved
10_F07

source_name: Primary mouse hepatocytes, mouse #5, LAC

value: Lead Acetate (LAc)

value: LAC

value: 10 μM LAC


title: 10_BTBR T+ tf/J_male_Autism-2

source_name: 10, BTBR T+ tf/J, male, Autism-2

value: BTBR T+tf/J

value: Cerebellum

value: 8 weeks


title: 11_BTBR T+ tf/J_male_Autism-3

source_name: 11, BTBR T+ tf/J, male, Autism-3


title: 9L H3K27me3

description:
Chip-chip primary skin fibroblasts, late timepoint H3K27me3
Sample 35


title: 9_BTBR T+ tf/J_male_Autism-1

source_name: 9, BTBR T+ tf/J, male, Autism-1


title: 13E H3K27me3

description:
Chip-chip primary skin fibroblasts, early timepoint H3K27me3
Sample 27

source_name: H3K27me3 ChIP DNA_primary skin fibroblast_early

value: early timepoint (E)

source_name: Input DNA from primary skin fibroblast, early timepoint


title: 14E H3K27me3

description:
Chip-chip primary skin fibroblasts, early timepoint H3K27me3
Sample 28


title: 1 nM CA, Mouse 5

description:
Quality control: approved
08_C05

source_name: Primary mouse hepatocytes, mouse #5, CA

value: 8-10 weeks

value: Calyculin A (CA)

value: CA

value: 1 nM CA


title: DMSO, Mouse 5

description:
Quality control: approved
04_H05

source_name: Primary mouse hepatocytes, mouse #5, DMSO

value: DMSO control

value: DMSO

value: 0.5% DMSO


title: 8_C57BL/6J_female_Control-4

description: Gene expression in the cerebellum of female C57BL/6J mice

source_name: 8, C57BL/6J, female, Control-4

value: Female


title: 16E H3K27me3

description:
Chip-chip primary skin fibroblasts, early timepoint H3K27me3
Sample 30

value: primary skin fibroblast

value: Millipore

value: none, input DNA


title: 6E mDNA

description:
MIRA-chip primary skin fibroblasts, early timepoint mDNA
Sample 42

source_name: MIRA DNA_primary skin fibroblast_early

value: MIRA


title: 1 nM OA, Mouse 5

description:
Quality control: approved
03_B07

source_name: Primary mouse hepatocytes, mouse #5, OA

value: male

value: primary mouse hepatocytes

value: Okadaic Acid (OA)

value: OA

value: 1 nM OA


title: 5E H3K27me3

description:
Chip-chip primary skin fibroblasts, early timepoint H3K27me3
Sample 22

value: early timepoint (E)


title: 6L H3K27me3

description:
Chip-chip primary skin fibroblasts, late timepoint H3K27me3
Sample 33

value: late timepoint (L)

source_name: Input DNA from primary skin fibroblast, late timepoint


title: 15E H3K27me3

description:
Chip-chip primary skin fibroblasts, early timepoint H3K27me3
Sample 29


title: 1 mM TCE, Mouse 5

description:
Quality control: approved
02_G05

source_name: Primary mouse hepatocytes, mouse #5, TCE

value: 8-10 weeks

value: Methyl chloroform (1,1,1-TCE)

value: TCE

value: 1 mM TCE


title: 1 mM DIDP, Mouse 5

description:
Quality control: approved
06_C07

source_name: Primary mouse hepatocytes, mouse #5, DIDP

value: Diisodecyl phthalate (DIDP)

value: DIDP

value: 1 mM DIDP


title: 4_C57BL/6J_male_Control-4

description: Gene expression in the cerebellum of male C57BL/6J mice

source_name: 4, C57BL/6J, male, Control-4

value: Cerebellum

value: Male

value: 8 weeks


title: 3_C57BL/6J_male_Control-3

source_name: 3, C57BL/6J, male, Control-3


title: 9E H3K27me3

description:
Chip-chip primary skin fibroblasts, early timepoint H3K27me3
Sample 25

value: primary skin fibroblast

value: Millipore

value: none, input DNA


title: 11E H3K27me3

description:
Chip-chip primary skin fibroblasts, early timepoint H3K27me3
Sample 26


title: 5_C57BL/6J_female_Control-1

source_name: 5, C57BL/6J, female, Control-1

value: Female


title: 7L H3K27me3

description:
Chip-chip primary skin fibroblasts, late timepoint H3K27me3
Sample 34

source_name: H3K27me3 ChIP DNA_primary skin fibroblast_late


title: 6E H3K27me3

description:
Chip-chip primary skin fibroblasts, early timepoint H3K27me3
Sample 23


title: 1_C57BL/6J_male_Control-1

source_name: 1, C57BL/6J, male, Control-1


title: 7E H3K27me3

description:
Chip-chip primary skin fibroblasts, early timepoint H3K27me3
Sample 24


title: 14L H3K4me3

description:
Chip-chip primary skin fibroblasts, late timepoint H3K4me3
Sample 18

source_name: H3K4me3 ChIP DNA_primary skin fibroblast_late

value: Active Motif

tag: chip antibody cat.#


title: 2E H3K27me3

description:
Chip-chip primary skin fibroblasts, early timepoint H3K27me3
Sample 21

value: early timepoint (E)

tag: chip antibody vendor


title: 7_C57BL/6J_female_Control-3

source_name: 7, C57BL/6J, female, Control-3


title: LCM-MMTV-wnt1 tumor stromal Rarb wt-3

city: Montréal

first: Xingxing

last: LIU

state: QC

address: 1160 Pine Ave

department: Biochemistry, GCC

institute: McGill University

description: Gene expression data from MMTV-wnt1 tumor stroma.

hyb_protocol: Agilent-028005 SurePrint G3 Mouse Genome 8x60 K arrays (Agilent Technologies, product G4852A) were used for all experiments. RNA samples (500 ng) were subjected to fragmentation followed by 18 h hybridization, washing, and scanning (Agilent Technologies, model G2505B) according to the manufacturer's protocol (manual ID #G4140-90030). Samples were hybridized against Universal Mouse Reference RNA.

scan_protocol: Microarray data were feature extracted using Feature Extraction Software (v. 7.11) from Agilent with the default parameters.

data_processing:
Outlier features on arrays were flagged by the software. Arrays were required to have an average raw signal intensity of 1,000 in each channel, and a signal to noise ratio above 16 per channel. MvA plots were examined for signs of hybridization or labeling problems. FlexArray and VSN were used to normalize the data.
Replicate arrays were required to have a concordance above 0.944. This level was established empirically using sets of known good replicate arrays in our database.

source_name: wild type mammary stroma

label_protocol: Test samples were labeled with Cy3 dye, and Universal Mouse Reference RNA (Stratagene, ID #750600, La Jolla, California, USA) was labeled with Cy5 dye, according to the manufacturer's procedure. Prior to microarray hybridizations, amplified products were quantified using a spectrophotometer (Nanodrop, Wilmington, Delaware, USA) and subjected to BioAnalyzer to assay for quality (Agilent Technologies, Santa Clara, California, USA).

extract_protocol: Total RNA was extracted from each population of microdissected cells using a GITC (guanidinium isothiocyanate) extraction protocol.

treatment_protocol: Tissue specimens were microdissected into epithelium and stroma using a PixCell IIe LCM system (Arcturus). All microdissections were performed within two hours following tissue staining.

tag: strain/background

value: FVB

tag: genotype/variation

value: Rarb +/+ (WT)

value: wnt1-mammary gland tumors

tag: cell population

value: stroma

source_name: Universal Mouse Reference RNA

tag: sample type

value: reference


title: 2_C57BL/6J_male_Control-2

source_name: 2, C57BL/6J, male, Control-2


title: LCM-MMTV-wnt1 tumor stroma Rarb wt-2


title: 13L H3K4me3

description:
Chip-chip primary skin fibroblasts, late timepoint H3K4me3
Sample 17

tag: donor age (yrs)

tag: cell type

tag: time point

value: late timepoint (L)

tag: chip antibody lot #


title: 15L H3K4me3

description:
Chip-chip primary skin fibroblasts, late timepoint H3K4me3
Sample 19

tag: chip antibody


title: LCM-MMTV-wnt1 tumor stroma Rarb KO-4

source_name: Rarb-null mammary stroma

value: Rarb -/-

tag: tissue


title: 6_C57BL/6J_female_Control-2

description: Gene expression in the cerebellum of female C57BL/6J mice

source_name: 6, C57BL/6J, female, Control-2

tag: strain/genotype

tag: gender

tag: age


title: 7L H3K4me3

description:
Chip-chip primary skin fibroblasts, late timepoint H3K4me3
Sample 14


title: LCM-MMTV-wnt1 tumor stroma Rarb KO-3


title: LCM-MMTV-wnt1 tumor stromal Rarb wt-1


title: 16L H3K4me3

description:
Chip-chip primary skin fibroblasts, late timepoint H3K4me3
Sample 20


title: LCM-MMTV-wnt1 tumor cell Rarb wt-2

description: Gene expression data from MMTV-wnt1 tumor cells.

source_name: wild type mammary epithelia

value: epithelia


title: LCM-MMTV-wnt1 tumor stroma Rarb KO-1


title: LCM-MMTV-wnt1 tumor cell Rarb KO-4

source_name: Rarb-null mammary epithelia


title: LCM-MMTV-wnt1 tumor cell Rarb wt-1


title: 6L H3K4me3

description:
Chip-chip primary skin fibroblasts, late timepoint H3K4me3
Sample 13

source_name: Input DNA from primary skin fibroblast, late timepoint


title: LCM-MMTV-wnt1 tumor cell Rarb KO-3


title: 11L H3K4me3

description:
Chip-chip primary skin fibroblasts, late timepoint H3K4me3
Sample 16


title: 2L H3K4me3

description:
Chip-chip primary skin fibroblasts, late timepoint H3K4me3
Sample 11


title: LCM-MMTV-wnt1 tumor cell Rarb KO-1


title: 121613-HCC1428-rep2

status: Public on Oct 22 2014

city: Dallas

first: Xiaoyu

last: Wang

state: Texas

address: ND3 200, 6001 Forest Park Rd

department: Cancer Center

institute: Ut Southwestern Medical Center

description:
biological replicate 2
gal_208520,208521,208522_lot35100-35100_hsa-and-related-vira_from_mb190

hyb_protocol: Hybridization using an Agilent Hybridization  SureHyb Chamber Kit and Gasket Slide Kit according to the  manufacturer’s instructions.

scan_protocol: The microarray slides were scanned   using a Tecan’s PowerScanner (Tecan, Austria) with Exiqon miRNA array parameters

data_processing: Image analysis was carried out using the ImaGene® 9.0  software of the miRCURY LNA™ microRNA Array Analysis  Software package.

source_name: Cell line

label_protocol: The RNA was labeled using the miRCURY LNA™ microRNA   Hi-Power Labeling Kit (Exiqon, Denmark) according to the   manufacturer’s instructions

growth_protocol: Cells were grown in the recomended culture media for 48 h.

extract_protocol: Total RNA was extracted following manufacturer's protocol for Qiagen Rneasy Plus, Cat. No. 74134, Appendix D: Purification of Total RNA containing small RNAs from cells

treatment_protocol: Cells were approx 70% confluent at the time of lysis and RNA extraction.

tag: phenotype

value: Non-motile

tag: cell line


title: 229 Area2

description: Array 6

hyb_protocol: Hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects.

scan_protocol: Scan on a PowerScanner (Tecan) using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)

label_protocol:
Amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.
Labelling aRNA was done using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: The cows received a super-ovulating treatment: Follicles of diameter larger than 8 mm were aspirated on day 8-12 post-oestrus. Administration of FSH (Folltropin-V, Bioniche Animal Health) was begun 36 hours later (twice daily in doses decreasing from 60 mg to 20 mg for a total of 400 mg over four days). Prostaglandin F2α analogue (Estrumate, Intervet, Kirkland, QC, Canada) was administrated in doses of 500 μg with each of the two final FSH injections to initiate luteolysis. Cows appearing oestrus at 36 h after the final FSH/Estrumate injection were inseminated twice with pooled semen (12 and 24 h later). On day 6 after insemination, embryos were recovered by uterine flushing and categorized according to the IETS system.

extract_protocol: Total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.

tag: breed (cattle)

value: Jersey

tag: cryotolerance

value: poor performance post-freezing

value: holstein

value: good cryotolerance


title: 229 Area3

description: Array 7


title: 228 Area1

description: Array 1


title: 229 Area4

description: Array 8


title: 229 Area1

description: Array 5


title: RBP2 ChIP dye swap (chip-2)

city: Barcelona

first: Anna

last: Bigas

state: Barcelona

address: Dr. Aiguader 88

department: Cancer Research

country: Spain

institute: Institut Hospital del Mar d'Investigacions Mèdiques

hyb_protocol: Scanned on an Agilent G2565AA scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Probes are are divided in to two different chips; chip-1 and chip-2.

source_name: AGM_anti-RBPj ChIP

label_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

extract_protocol: AGM cells were crosslinked in 0.5% formaldehyde for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for 30 min on ice. The crosslinked chromatin was sheared to an average size of 1000 bp by ten 30-second pulses using a Dr. Hielscher sonicator (GmbH). The lysate was then centrifuged to remove cell debris, and the chromatin was visualized in an agarose gel. The chromatin was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and pre-cleared with 25 µl protein A sepharose beads (pre-absorbed with salmon sperm DNA and BSA) for 2 h at 4C. The chromatin supernatant was then incubated overnight with 2 µg of the different antibodies at 4C. After incubation with protein A sepharose beads (50 µl) for 2h at 4C, the immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4C; RIPA buffer (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer (500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS, 1% NP40) LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and 2x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 500 µl elution buffer (1% SDS, 100 mM NaHCO3) for 1 h at RT. After centrifugation the soluble chromatin was incubated overnight at 65C, followed by a 2 hour treatment with proteinase K to 500 µg/ml at 55C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/100 of the material used for ChIP) by phenol extraction and ethanol precipitation.

tag: strain

tag: developemetal stage

value: E11.5 embryo

value: Aorta/Gonad/Mesonephros (AGM) cells

value: anti-RBPj antibody

tag: chip antibody reference

value: ChIP DNA

value: input DNA


title: 121613-MCFDCIS-rep2

value: Motile

value: MCFDCIS


title: 228 Area4

description: Array 4


title: 228 Area2

description: Array 2


title: 9L H3K4me3

description:
Chip-chip primary skin fibroblasts, late timepoint H3K4me3
Sample 15

value: primary skin fibroblast

tag: chip antibody vendor

value: Active Motif

tag: chip antibody cat.#

value: none, input DNA


title: 228 Area3

description: Array 3


title: LCM-MMTV-wnt1 tumor cell Rarb wt-3

tag: strain/background

value: FVB

tag: genotype/variation

value: Rarb +/+ (WT)

value: wnt1-mammary gland tumors

tag: cell population

tag: sample type

value: reference


title: 16E H3K4me3

description:
Chip-chip primary skin fibroblasts, early timepoint H3K4me3
Sample 10

source_name: H3K4me3 ChIP DNA_primary skin fibroblast_early

tag: donor age (yrs)

tag: cell type

tag: time point

value: early timepoint (E)

tag: chip antibody

tag: chip antibody lot #

source_name: Input DNA from primary skin fibroblast, early timepoint


title: CD8 Relapse (2992ONTC83)

city: Ramat-Gan

first: Michael

last: Gurevich

address: Tel-Hashomer

department: Multiple Sclerosis Center

country: Israel

institute: Sheba Medical Center

description: Gene expression of CD8+ blood cells from ON patient in relapse

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. 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: Summarized/scaled/normalized probeset data generated by GC-RMA

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

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

treatment_protocol: PBMC were purified using Ficoll hypaque gradient (Invitrogen, USA). Cell subsets of CD4+, CD8+ T lymphocytes , CD19+ B cells and CD14+ macrophages sub-populations were isolated using FITC-conjugated magnetic microbeads (Pharmigen, USA)(purity >95%) Microarray gene expression was performed separately for each cell sub-population.

tag: age (years)

tag: gender

value: female

tag: disease state

value: ON patient in relapse

value: CD8+ blood cells


title: CD8 Relapse (4608ONTC90)

source_name: CD8+ blood cells from ON patient in relapse


title: RBP2 ChIP (chip-2)

tag: strain

value: E11.5 embryo

value: Aorta/Gonad/Mesonephros (AGM) cells


title: CD8 Relapse (3703ONTC90)


title: CD8 Relapse (2856ONTC70)

value: male


title: 11E H3K4me3

description:
Chip-chip primary skin fibroblasts, early timepoint H3K4me3
Sample 6


title: 13E H3K4me3

description:
Chip-chip primary skin fibroblasts, early timepoint H3K4me3
Sample 7


title: CD8 Control (4767ONTC90)

description: Gene expression of CD8+ blood cells from healthy subject

source_name: CD8+ blood cells from healthy subject

value: healthy subject


title: CD8 Control (4766ONTC90)


title: CD8 Control (3859C70)


title: 5L H3K4me3

description:
Chip-chip primary skin fibroblasts, late timepoint H3K4me3
Sample 12

value: late timepoint (L)


title: 7E H3K4me3

description:
Chip-chip primary skin fibroblasts, early timepoint H3K4me3
Sample 4


title: CD8 Control (set673892CONTC67)


title: CD8 Control (4695ONTC83)


title: CD8 Control (4692ONTC83)


title: CD14 Relapse (3539ONM66)

description: Gene expression of CD14+ blood cells from ON patient in relapse

value: CD14+ blood cells


title: CD14 Relapse (2856ONM66)

source_name: CD14+ blood cells from ON patient in relapse


title: CD8 Control (3857C70)


title: 6E H3K4me3

description:
Chip-chip primary skin fibroblasts, early timepoint H3K4me3
Sample 3

value: primary skin fibroblast


title: CD14 Control (set673893CONM67)

description: Gene expression of CD14+ blood cells from healthy subject

source_name: CD14+ blood cells from healthy subject


title: CD14 Relapse (3703ONM87)


title: CD14 Relapse (2992ONM81)


title: CD14 Relapse (3608ONM87)


title: 2E H3K4me3

description:
Chip-chip primary skin fibroblasts, early timepoint H3K4me3
Sample 1

value: Active Motif


title: CD8 Control (set673893CONTC67)


title: CD14 Control (3859C66)


title: CD14 Control (4695ONM81)


title: CD14 Control (set673892CONM67)


title: 5E H3K4me3

description:
Chip-chip primary skin fibroblasts, early timepoint H3K4me3
Sample 2

value: none, input DNA


title: CD14 Control (4692ONM81)


title: CD8 Relapse (3539ONTC70)


title: 15E H3K4me3

description:
Chip-chip primary skin fibroblasts, early timepoint H3K4me3
Sample 9


title: CD8 Relapse (4479ONTC83)


title: CD19 Relapse (4608ONBC88)

description: Gene expression of CD19+ blood cells from ON patient in relapse

value: CD19+ blood cells


title: CD19 Relapse (2992ONBC82)

source_name: CD19+ blood cells from ON patient in relapse


title: CD19 Relapse (4479ONBC82)


title: CD14 Control (3857C66)


title: CD14 Control (3767ONM87)


title: CD14 Control (3768ONM87)


title: CD19 Control (set673893CONB67)

description: Gene expression of CD19+ blood cells from healthy subject

source_name: CD19+ blood cells from healthy subject


title: CD14 Control (3766ONM87)


title: CD19 Relapse (3539ONBC71)


title: CD19 Control (4767ONBC88)


title: CD19 Control (4768ONBC88)


title: CD19 Control (4695ONBC82)


title: 14E H3K4me3

description:
Chip-chip primary skin fibroblasts, early timepoint H3K4me3
Sample 8


title: CD19 Relapse (2856ONBC71)


title: CD19 Relapse (3703ONBC88)


title: CD19 Control (set673892CONB67)


title: CD19 Control (4692ONBC82)


title: CD19 Control (3859C71New2)


title: CD4 Relapse (4608ONTH89)

description: Gene expression of CD4+ blood cells from ON patient in relapse

value: CD4+ blood cells


title: CD19 Control (3857C71)


title: CD4 Relapse (2856ONTH68)

source_name: CD4+ blood cells from ON patient in relapse


title: CD4 Relapse (3539ONTH68)


title: CD4 Relapse (4479ONTH84)


title: CD4 Relapse (2992ONTH84)


title: CD4 Control (4766ONTH89)

description: Gene expression of CD4+ blood cells from healthy subject

source_name: CD4+ blood cells from healthy subject


title: CD4 Relapse (3703ONTH89)


title: CD4 Control (4768ONTH89)


title: CD4 Control (4692ONTH84)


title: CD4 Control (4767ONTH89)


title: CD4 Control (set673892CONTH67)


title: CD4 Control (3859ONC68)


title: CD19 Control (4766ONBC88)


title: 062112-HCC1806-rep1

description: biological replicate 1

hyb_protocol: Direct Hybridization Assay Protocols in Illumina Whole-Genome Gene Expression Direct Hybridization Assay Guide

scan_protocol: illumina HiScan®SQ System User Guide

data_processing: Raw data were generated by GenomeStudioTM Gene Expression Module v1.0 without background subtraction and normalization

label_protocol: Ambion Illumina TotalPrep RNA Amplification Kit protocol

tag: majority phenotype

value: Motile

tag: cell line


title: CD4 Control (3857ONC68)


title: CD4 Control (4695ONTH84)


title: 062112-HCC1806-rep2

description: biological replicate 2


title: CD4 Control (set673893CONTH67)


title: 062112-MCFDCIS-rep1

description: biological replicate 1

value: MCFDCIS


title: 062112-HCC1428-rep2

description: biological replicate 2

value: Non-motile


title: 062112-MCFDCIS-rep2

description: biological replicate 2


title: 062112-MCF-7-rep1

description: biological replicate 1


title: 062112-MCF-7-rep2

description: biological replicate 2


title: 061014-MCFDCIS Slug siRNA-rep2

description: biological replicate 2

value: Slug siRNA, non-motile

tag: treatment

value: Slug siRNA


title: 062112-HCC1428-rep1

description: biological replicate 1


title: 9E H3K4me3

description:
Chip-chip primary skin fibroblasts, early timepoint H3K4me3
Sample 5

value: early timepoint (E)

tag: chip antibody vendor

tag: chip antibody cat.#


title: 061014-MCFDCIS Control-rep2

description: biological replicate 2

value: Control, motile

value: Control


title: 061014-MCFDCIS Slug siRNA-rep1

description: biological replicate 1


title: CD14 Relapse (4479ONM81)

value: female

value: ON patient in relapse


title: 091813-MCFDCIS miR203-rep2

description: biological replicate 2

value: miR203a, non-motile


title: CD8 Control (4768ONTC90)

value: healthy subject

value: CD8+ blood cells


title: 091813-HCC1806 p63 siRNA-rep2

description: biological replicate 2

value: p63 siRNA, non-motile

value: p63 siRNA


title: 061014-MCFDCIS Control-rep1

description: biological replicate 1


title: 091813-HCC1806 Control-rep2

description: biological replicate 2


title: 091813-MCFDCIS miR203-rep1

description: biological replicate 1


title: 091813-MCFDCIS p63 siRNA-rep2

description: biological replicate 2


title: 8106854082_D

city: New Haven

first: Jaekwang

last: Jeong

address: 1 Gilbert St.

department: Internal Medicine

institute: Yale University

description: replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: SKBR3 NHERF1 kd

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

growth_protocol: The human cell lines, SKBR3 cells were obtained from  ATCC and maintained in culture in DMEM +GlutaMAX-1 (Gibco-life  Technologies) containing 10% fetal bovine serum (FBS) and pen/strep (Gibco-life  Technologies) at 37°C in 5% CO2.

extract_protocol: Total RNA was prepared using TRIzol reagent (Invitrogen). The isolated  RNA was purified using the Qiagen RNeasy cleanup kit (Valencia, CA).

treatment_protocol: Cells were cultured in 12-well plates and infected by adding the various  shRNA lentiviral particles to the culture for 48 hours as per the manufacturers  instructions.

tag: genotype/variation

value: SKBR3 NHERF1 kd


title: 8106854082_F

description: replicate 6


title: 091813-MCFDCIS Control-rep1

description: biological replicate 1


title: 8106854082_B

description: replicate 5

source_name: SKBR3 control

value: SKBR3 control


title: 8106854082_L

description: replicate 6

source_name: SKBR3HER2 kd

value: SKBR3HER2 kd


title: 8106854082_A

description: replicate 4


title: 8106854082_H

description: replicate 5

source_name: SKBR3 PMCA2 kd

value: SKBR3 PMCA2 kd


title: 091813-HCC1806 p63 siRNA-rep1

description: biological replicate 1


title: 091813-HCC1806 Control-rep1

description: biological replicate 1


title: 8106854082_E

description: replicate 5


title: 8106854082_I

description: replicate 6


title: 8106854082_C

description: replicate 6


title: 091813-MCFDCIS p63 siRNA-rep1

description: biological replicate 1

value: MCFDCIS


title: 8106854082_G

description: replicate 4


title: 8106854082_K

description: replicate 5


title: 8106854082_J

description: replicate 4


title: 091813-MCFDCIS Control-rep2

description: biological replicate 2


title: 8106854060_K

description: replicate 2


title: 8106854060_L

description: replicate 3


title: 8106854060_F

description: replicate 3


title: 8106854060_E

description: replicate 2


title: 8106854060_G

description: replicate 1


title: 8106854060_J

description: replicate 1


title: 121613-HCC1428-rep1

description:
biological replicate 1
gal_208500,208501,208502,208510_lot35014-35014_hsa-and-related-vira_from_mb190,miRPlus

tag: phenotype

value: Non-motile


title: 121613-MCFDCIS-rep1

value: Motile


title: 8106854060_C

description: replicate 3


title: 8106854060_B

description: replicate 2


title: 8106854060_H

description: replicate 2


title: 8106854060_D

description: replicate 1


title: Math1-nGFP + Cells RepC

city: Stanford

first: Byron

middle: H

last: Hartman

address: 300 Pasteur Drive Edwards R219

department: Otolaryngology - Head and Neck Surgery

institute: Stanford University School of Medicine

description:
Sample HC_C
5624779027_A
Hair Cells RepC

data_processing: The data were log2 transformed and normalized using quantile normalization with IlluminaGUI in R

source_name: Mouse Cochlea

extract_protocol: RNA was extracted with Machery Nagel RNA XS kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: age

value: 3 Days

value: FACS isolated cochlea cells

tag: cell population

value: Hair Cells


title: Math1-nGFP + Cells RepA

description:
Sample HC_A
5624779015_H
Hair Cells RepA

tag: cell type


title: Math1nGFP-/CD271L/CD146L/CD326+ (Deiters’ & Claudius cells) RepB

description:
Sample SC_B
5624779015_F
Deiters' & Claudius Rep B

value: Deiters' & Claudius Cells


title: Math1nGFP-/CD271H (Suspected Cochlear Macrophage Cells) RepA

description:
Sample Mac_A
5624779027_F
Macrophages RepA

value: Macrophages


title: Math1nGFP-/CD271L/CD146H/CD326+ (GER cells) RepC

description:
Sample GER_C
5624779027_D
GER Cells RepA

value: GER Cells


title: Math1-nGFP + Cells RepB

description:
Sample HC_B
5624779027_H
Hair Cells RepB


title: Math1nGFP-/CD271L/CD326- (Below basilar membrane cells) RepB

description:
Sample BM_B
5624779015_E
Below Basilar Membrane Cells Rep B

value: Below Basilar Membrane Cells


title: Math1nGFP-/CD271H (Suspected Cochlear Macrophage Cells) RepC

description:
Sample Mac_C
5624779015_C
Macrophages RepC


title: PBMC_17D vaccinated_day3_rep3

city: Riverside

first: Ilhem

last: Messaoudi

address: 3401 Watkins Dr.

department: Biomedical Science

institute: UC Riverside

hyb_protocol: Labelled hybridization targets were mixed with hybridization solution containing hybridization controls (Affymetrix) according to NuGEN Technologies protocol and hybridized with the GeneChip® Rhesus Macaque Genome Array (Affymetrix)

scan_protocol: Image processing was performed using Affymetrix GeneChip Command Console (AGCC) v3.1.1

data_processing: Absolute expression analysis was performed using the Affymetrix analysis algorithm, MAS 5.0 (Microarray Suite 5.0). Absolute analyses were rerun using global scaling to an average target intensity of 200.

organism: Macaca mulatta

source_name: Rhesus PBMC 3 days after vaccination with YFV 17D

label_protocol: Labeled target cDNA was prepared from total RNA samples. Samples were amplified and labeled using NuGEN Ovation v2 with whole blood reagent and Encore Biotin Module protocol (3'IVT assay).

value: 3 days after vaccination with YFV 17D

value: Peripheral Blood Mononuclear Cells

tag: Sex

value: Female


title: Math1nGFP-/CD271L/CD146H/CD326+ (GER cells) RepA

description:
Sample GER_A
5624779015_A
GER Cells RepA


title: Math1nGFP-/CD271L/CD146H/CD326+ (GER cells) RepB

description:
Sample GER_B
5624779015_G
GER Cells Reb B


title: Math1nGFP-/CD271H (Suspected Cochlear Macrophage Cells) RepB

description:
Sample Mac_B
5624779015_B
Macrophages RepB


title: Math1-nGFP + Cells RepD

description:
Sample HC_D
5624779027_G
Hair Cells RepD


title: PBMC_YFVwt infected_day3_rep2

source_name: Rhesus PBMC 3 days after infection with YFV wild type


title: PBMC_YFVwt infected_day0_rep1

source_name: Rhesus PBMC before infection with YFV wild type

value: before infection with YFV wild type


title: PBMC_17D vaccinated_day3_rep1


title: PBMC_17D vaccinated_day0_rep3

source_name: Rhesus PBMC before vaccination with YFV 17D

value: before vaccination with YFV 17D


title: Math1nGFP-/CD271L/CD146L/CD326+ (Deiters’ & Claudius cells) RepA

description:
Sample SC_A
5624779015_D
Deiters' & Claudius Rep A


title: PBMC_YFVwt infected_day0_rep3


title: PBMC_YFVwt infected_day3_rep3

value: 3 days after infection with YFV wild type


title: PBMC_17D vaccinated_day3_rep2


title: PBMC_YFVwt infected_day0_rep2


title: CCRF-CEM Tubercidin 5xIC50 3 hours treated, biological replicate 2

city: Olomouc

first: Petr

last: Dzubak

address: Hnevotinska 5

department: Institute of Molecular and Translational Medicine

country: Czech Republic

institute: Palacky University, Faculty of Medicine and Dentistry

description:
Sample name: CCRF-CEM_Tubercidin_11-2
Gene expression data from Tubercidin treated CCRF-CEM cancer cell line

hyb_protocol: Following fragmentation, DNA was hybridized for 16 hr at 45C on GeneChip Human Exon 1.0 ST Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing:
The data were analysed using R/Bioconductor freeware and additional Bioconductor package. All arrays were preprocessed by RMA method (robust multi-array average) on the gene level using the oligo package. Ther processed gene expression levels were analysed for their differential expression between the AB61-treated and control cells. Initially, the raw p values of moderated t-test were calculated by the limma package.
Supplementary files: Log Fold Change of Control vs. Treated sample intensity (mean of three replicates)

source_name: CCRF-CEM cancer cell line, treated by Tubercidin at 5xIC50 for 3 hours

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (GeneChip Whole Transcript (WT) Sense Target Labeling Assay P/N 701880 Rev. 5 .

growth_protocol: CCRF-CEM cancer cell line was cultivated in RPMI medium, supplemented by 10% FCSI and antibiotics according to ATCC recommendations

treatment_protocol: Cells were treated by AB61 (250 nM), Tubercidin (550 nM) or actinomycin D (1 nM) which is 5x IC50 for 3 hours.

value: CCRF-CEM cancer cell line

tag: agent

value: Tubercidin


title: CCRF-CEM Actinomycin D 5xIC50 3 hours treated, biological replicate 3

description:
Sample name: CCRF-CEM_ActD_9-3
Gene expression data from Actinomycin D treated CCRF-CEM cancer cell line

source_name: CCRF-CEM cancer cell line, treated by Actinomycin D at 5xIC50 for 3 hours

value: Actinomycin D


title: PBMC_17D vaccinated_day0_rep1


title: CCRF-CEM Tubercidin 5xIC50 3 hours treated, biological replicate 3

description:
Sample name: CCRF-CEM_Tubercidin_12-3
Gene expression data from Tubercidin treated CCRF-CEM cancer cell line


title: Senescence Day 10, replicate 3

city: Poznan

first: Agnieszka

last: Zmienko

address: Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry PAS

description: Biological replicate 3 of 3. Samples collected 10 days after senescence induction by placing the leaves in the dark.

hyb_protocol: All of the hybridization, washing and drying steps were performed in A4x44k Quad Chambers in an HS 4800 Pro (Tecan) automatic hybridization station according to the manufacturer’s guidelines regarding Agilent microarrays treatment. A Gene Expression Hybridization Kit (Agilent) and Gene Expression Wash Buffer Kit solutions (Agilent) were used for the hybridization and washing steps, respectively.

scan_protocol: The intensity data were collected with 4200AL GenePix scanner and GenePix Pro 6.1 software at 5 µm resolution, at green and red channel. Each microarray was scanned twice with auto PMT adjusted at low (0.01 %) or high (1%) spot saturation levels.

data_processing: The scans were processed with GenePix Pro 6.1 software using morphological opening background method. Intensity data were analyzed with R/Bioconductor limma package. Background was subtracted (offset 10) and the scans with low and high intensity were merged with mergeScansRG function. Loess within-array normalization and Aquantile between-array normalization was applied.

organism: Hordeum vulgare

source_name: primary leaf-Dark-Day 10

label_protocol: Labeled cRNA samples were prepared from 200 ng RNA each, using Quick Amp Labeling Kit (Agilent). The labeling efficiency was monitored with Nanodrop 2000.

growth_protocol: Seedlings were grown for 7 days in soil under controlled conditions (day/night 16/8 h, 23 °C, light intensity 150 μmol m-2 s-1, 60% humidity).

extract_protocol: Samples from 3 biological replicates (independent cultivations) were obtained, and each sample was a pool of ~15 plants. Total RNA was extracted from frozen barley leaves with spin-columns (RNeasy Plant Mini Kit, QIAGEN) and DNase-digested with TURBO DNA-free kit (Ambion) according to the manufacturers’ standard protocols. RNA quality was determined using Nanodrop 2000 and 2100 Bioanalyzer (Agilent). All of the samples used for the study were pure (A260/A280 ≥ 1.9; A260/A230 ≥ 2) and showed no visible signs of degradation.

treatment_protocol: The senescence process was induced by placing the seedlings in the dark. Leaves were collected at day 0 (before senescence induction) day 3, day 5, day 7, day 10 and day 12, and the samples were named accordingly

tag: variety

value: Nagrad

source_name: pooled RNA from all samples


title: PBMC_17D vaccinated_day0_rep2


title: CCRF-CEM Tubercidin 5xIC50 3 hours treated, biological replicate 1

description:
Sample name: CCRF_CEM_Tubercidin_10-1
Gene expression data from Tubercidin treated CCRF-CEM cancer cell line


title: CCRF-CEM Actinomycin D 5xIC50 3 hours treated, biological replicate 2

description:
Sample name: CCRF-CEM_ActD_8-2
Gene expression data from Actinomycin D treated CCRF-CEM cancer cell line


title: CCRF-CEM Actinomycin D 5xIC50 3 hours treated, biological replicate 1

description:
Sample name: CCRF-CEM_ActD_7-1
Gene expression data from Actinomycin D treated CCRF-CEM cancer cell line


title: Senescence Day 10, replicate 1

description: Biological replicate 1 of 3. Samples collected 10 days after senescence induction by placing the leaves in the dark.


title: Senescence Day 3, replicate 2

description: Biological replicate 2 of 3. Samples collected 3 days after senescence induction by placing the leaves in the dark.

source_name: primary leaf-Dark-Day 3


title: Senescence Day 10, replicate 2

description: Biological replicate 2 of 3. Samples collected 10 days after senescence induction by placing the leaves in the dark.


title: PBMC_YFVwt infected_day3_rep1


title: Senescence Day 5, replicate 3

description: Biological replicate 3 of 3. Samples collected 7 days after senescence induction by placing the leaves in the dark.

source_name: primary leaf-Dark-Day 7


title: CCRF-CEM AB61 5xIC50 3 hours treated, biological replicate 3

description:
Sample name: CCRF-CEM_AB61_6-3
Gene expression data from AB61 treated CCRF-CEM cancer cell line

source_name: CCRF-CEM cancer cell line, treated by AB61 compound at 5xIC50 for 3 hours

value: AB61 compound


title: CCRF-CEM AB61 5xIC50 3 hours treated, biological replicate 2

description:
Sample name: CCRF-CEM_AB61_5-2
Gene expression data from AB61 treated CCRF-CEM cancer cell line


title: Senescence Day 0, replicate 3

description: Biological replicate 3 of 3. Samples collected before the induction of senescence.

source_name: primary leaf-Dark-Day 0


title: Senescence Day 5, replicate 1

description: Biological replicate 1 of 3. Samples collected 7 days after senescence induction by placing the leaves in the dark.


title: Senescence Day 0, replicate 1

description: Biological replicate 1 of 3. Samples collected before the induction of senescence.


title: CCRF-CEM AB61 5xIC50 3 hours treated, biological replicate 1

description:
Sample name: CCRF-CEM_AB61_4-1
Gene expression data from AB61 treated CCRF-CEM cancer cell line


title: Senescence Day 3, replicate 1

description: Biological replicate 1 of 3. Samples collected 3 days after senescence induction by placing the leaves in the dark.


title: CCRF-CEM non-treated, biological rep3

description:
Sample name: CCRF-CEM_Control_3-3
Gene expression data from non treated CCRF-CEM cancer cell line

source_name: CCRF-CEM cancer cell line, non-treated, control

value: non-treated control


title: Senescence Day 0, replicate 2

description: Biological replicate 2 of 3. Samples collected before the induction of senescence.


title: CCRF-CEM non-treated, biological rep1

description:
Sample name: CCRF-CEM_Control_1-1
Gene expression data from non treated CCRF-CEM cancer cell line


title: CCRF-CEM non-treated, biological rep2

description:
Sample name: CCRF-CEM_Control_2-2
Gene expression data from non treated CCRF-CEM cancer cell line


title: Chronic_Control_d16 (n=4)

city: Groningen

first: Jourik

middle: A

last: Gietema

address: Hanzeplein 1

department: Medical Oncology

institute: UMCG

description: 1_Controle d16_5 vs Controle d16_3 gl12963811

hyb_protocol: After labeling, samples were randomly hybridised to the custom-made 18K cDNA microarrays.

scan_protocol: Fluorescent images of the microarray slides were obtained with the Affymetrix GMS428 scanner (Affymetrix) for both fluorophores, signal intensities for each spot were quantified by dedicated IMAGENE 5.6 software (Biodiscovery).

data_processing: Quantile normalisation was applied to log2 transformed signal intensities

source_name: HMEC-1 control after 16 days culturing

label_protocol: After purification (Qiaquick PCR purification kit, Qiagen), amplified RNA (cRNA) samples were transformed to cDNA with reverse transcriptase, and independently labelled with Cy3 (green) and Cy5 (red).

growth_protocol: HMEC-1 cells were grown a monolayer in MCDB-131 medium supplemented with 10% FCS, 10mM L-Glutamine, 1 μg/ml hydrocortisone, 10 ng/ml human EGF and cultured at 37⁰C in a humified atmosphere containing 5% CO2. Experiments were performed between passages 15-30.

extract_protocol: Total RNA was isolated from HMEC-1 by a RNeasy kit (Qiagen) and pooled for each time-point and drug from 2 independent experiments.

treatment_protocol: In an “acute”-exposure setting, HMEC-1 were left untreated as controls, or were treated with 0.3 or 1.5 μg/mL bleomycin and 2.6 or 12.9 μM cisplatin for 6, 24, and 48 hrs. In a “chronic”-exposure setting, lower doses were administered 0.06 μg/mL bleomycin or 0.52 μM cisplatin two times a week; cells were collected for analysis at day 30. Administration of cisplatin had to be withheld at the 7th administration because of considerable cell death, but was continued at full dose thereafter. Bleomycin could be administered without interruption.

value: human microvascular endothelial cell line


title: 8106854060_I

description: replicate 3

value: SKBR3 PMCA2 kd


title: Chronic_Control_d2 (n=6)

description: 1_Controle d30_5 vs Controle d2_3 gl12966821

source_name: HMEC-1 control after 2 days culturing


title: M_Control_30_None

city: Indianapolis

first: Jeanette

middle: Nance

last: McClintick

state: IN

address: 635 Barnhill Dr.

department: Biochemistry & Molecular Biology

institute: Indiana University School of Medicine

hyb_protocol: Samples were hybridized to Affymetrix HG U133 Plus 2 GeneChips® for 17 h, then washed and stained using the standard Affymetrix protocols.

scan_protocol: GeneChips® were scanned using an Affymetrix Model 3000 scanner controlled by GCOS software (Affymetrix, Santa Clara, CA).

data_processing: MAS5 signals and detection calls were generated by GCOS and scaled to 1000.

source_name: LCLs from non-alcoholic_no treatment

label_protocol: Reverse transcription and labeling used the Affymetrix 3’ IVT labeling kit and protocols (GeneChip® Expression Analysis Technical Manual, Affymetrix, Santa Clara). Samples were labeled in groups balanced by sex and phenotype to the extent possible; pairs of treated and untreated samples from the same individual were labeled and hybridized at the same time.

growth_protocol: 2 x 10^6 LCLs from each of 21 alcoholics and 21 non-alcoholics were seeded in 10 ml of RPMI1640 medium supplemented with 15% FBS, 2 mM glutamine, 50 U/ml penicillin, and 50 µg/ml streptomycin.

extract_protocol: cells were harvested and lysed with buffer RLT, supplied in the Qiagen RNeasy kit, and RNA extractions were conducted per the manufacturer’s protocol

treatment_protocol: Cells were cultured in the absence or presence of 75 mM ethanol for 24 h

tag: source subject id

tag: subject status

value: non-alcoholic (control)

tag: subject gender

value: male

value: lymphoblastoid cell line (LCL)

tag: treated with

value: none (untreated control)

tag: labelling batch


title: M_Alcoholic_40_ethanol

source_name: LCLs from alcoholic_ethanol treatment

value: Alcoholic

tag: cell line

value: 75mM ethanol for 24h


title: M_Control_24_None


title: Chronic_Control_d30 (n=4)

description: 1_Controle d16_5 vs Controle d30_3 gl12966818

source_name: HMEC-1 control after 30 days culturing


title: Chronic_Control_d2 (n=5)

description: 1_Controle d2_5 vs Controle d2_3 gl12966825


title: Chronic_CDDP_d2 (n=4)

description: 1_Controle d2_5 vs CDDP d2_3 gl12966819

source_name: HMEC-1 after 2 days contiunous exposure to IC10 CDDP


title: M_Control_24_ethanol

source_name: LCLs from non-alcoholic_ethanol treatment


title: M_Alcoholic_40_None

source_name: LCLs from alcoholic_no treatment


title: RBP2 ChIP dye swap (chip-1)

source_name: AGM_anti-RBPj ChIP

tag: strain

tag: developemetal stage

value: E11.5 embryo

value: Aorta/Gonad/Mesonephros (AGM) cells

tag: chip antibody

value: anti-RBPj antibody

tag: chip antibody reference

tag: sample type

value: ChIP DNA

value: input DNA


title: RBP2 ChIP (chip-1)


title: Chronic_Bleo_d30 (n=6)

description: 1_CDDP d30_5 vs Bleo d30_3 gl12964200

source_name: HMEC-1 after 30 days contiunous exposure to IC10 Bleo


title: M_Alcoholic_32_ethanol


title: Chronic_CDDP_d2 (n=3)

description: 1_Controle d2_5 vs CDDP d2_3 gl12963816


title: M_Alcoholic_32_None


title: Chronic_Control_d2 (n=4)

description: 1_CDDP d2_5 vs Controle d2_3 gl12966824


title: 8106854060_A

description: replicate 1

source_name: SKBR3 control

tag: genotype/variation

value: SKBR3 control


title: M_Control_30_ethanol


title: Chronic_Bleo_d2 (n=4)

description: 1_CDDP d30_5 vs Bleo d2_3 gl12963817

source_name: HMEC-1 after 2 days contiunous exposure to IC10 Bleo


title: Chronic_CDDP_d16 (n=3)

description: 1_CDDP d16_5 vs CDDP d16_3 gl12966817

source_name: HMEC-1 after 16 days contiunous exposure to IC10 CDDP


title: Chronic_Bleo_d2 (n=3)

description: 1_CDDP d2_5 vs Bleo d2_3 gl12966820


title: M_Control_3_ethanol


title: Chronic_Bleo_d30 (n=5)

description: 1_Bleo d30_5 vs Bleo d30_3 gl12963810


title: Chronic_Bleo_d16  (n=4)

description: 1_CDDP d16_5 vs Bleo d16_3 gl12966826

source_name: HMEC-1 after 16 days contiunous exposure to IC10 Bleo


title: Chronic_CDDP_d30 (n=4)

description: 1_Bleo d30_5 vs CDDP d30_3 gl12963814

source_name: HMEC-1 after 30 days contiunous exposure to IC10 CDDP


title: M_Alcoholic_2_ethanol


title: M_Control_3_None


title: M_Alcoholic_4_ethanol


title: Chronic_Bleo_d16 (n=3)

description: 1_Bleo d30_5 vs Bleo d16_3 gl12966822


title: M_Alcoholic_2_None


title: M_Control_22_ethanol


title: M_Alcoholic_4_None


title: Chronic_Bleo_d30 (n=4)

description: 1_Bleo d2_5 vs Bleo d30_3 gl12963812


title: Chronic_CDDP_d30 (n=3)

description: 1_Bleo d2_5 vs CDDP d30_3 gl12966823


title: Chronic_Control_d30 (n=3)

description: 1_Bleo d16_5 vs Controle d30_3 gl12963815


title: F_Control_16_ethanol

value: female


title: Chronic_Control_d16 (n=3)

description: 1_Bleo d16_5 vs Controle d16_3 gl12966816


title: M_Control_22_None


title: Acute_CDDP_IC50_t=24 (n=6)

description: 1_acuut Controle t=6_5 vs CDDP IC50 t=24_3 gl12964194

source_name: HMEC-1 after 24 hours exposure to IC50 CDDP


title: F_Control_16_None


title: Acute_CDDP_5xIC50_t=24 (n=4)

description: 1_acuut Controle t=48_5 vs CDDP 5xIC50 t=24_3 gl12964198

source_name: HMEC-1 after 24 hours exposure to 5x IC50 CDDP


title: M_Alcoholic_44_None


title: M_Alcoholic_44_ethanol


title: Acute_Control_t=24 (n=6)

description: 1_acuut Controle t=24_5 vs Controle t=24_3 gl12964203

source_name: HMEC-1 control after 24 hours


title: Acute_Bleo_5xIC50_t=6 (n=4)

description: 1_acuut Controle t=24_5 vs Bleo 5xIC50 t=6_3 gl12964195

source_name: HMEC-1 after 6 hours exposure to 5x IC50 Bleo


title: Chronic_CDDP_d16 (n=4)

description: 1_Controle d30_5 vs CDDP d16_3 gl12966827


title: Acute_Control_t=24 (n=5)

description: 1_acuut CDDP IC50 t=48_5 vs Controle t=24_3 gl12964201


title: F_Alcoholic_11_ethanol


title: F_Alcoholic_11_None


title: Acute_Bleo_5xIC50_t=24 (n=4)

description: 1_acuut CDDP IC50 t=24_5 vs Bleo 5xIC50 t=24_3 gl12964196

source_name: HMEC-1 after 24 hours exposure to 5x IC50 Bleo


title: Acute_CDDP_5xIC50_t=48 (n=4)

description: 1_acuut CDDP 5xIC50 t=6_5 vs CDDP 5xIC50 t=48_3 gl12964410

source_name: HMEC-1 after 48 hours exposure to 5x IC50 CDDP


title: Acute_Bleo_IC50_t=48 (n=4)

description: 1_acuut CDDP 5xIC50 t=24_5 vs Bleo IC50 t=48_3 gl12964197

source_name: HMEC-1 after 48 hours exposure to IC50 Bleo


title: Acute_CDDP_5xIC50_t=6 (n=4)

description: 1_acuut CDDP IC50 t=6_5 vs CDDP 5xIC50 t=6_3 gl12964193

source_name: HMEC-1 after 6 hours exposure to 5x IC50 CDDP


title: M_Control_17_None

source_name: LCLs from non-alcoholic_no treatment


title: M_Alcoholic_31_ethanol

source_name: LCLs from alcoholic_ethanol treatment


title: Acute_Control_t=48 (n=4)

description: 1_acuut CDDP 5xIC50 t=48_5 vs controle t=48_3 gl12964407

source_name: HMEC-1 control after 48 hours


title: F_Control_41_None


title: M_Control_17_ethanol

source_name: LCLs from non-alcoholic_ethanol treatment


title: F_Control_41_ethanol


title: Acute_Bleo_IC50_t=6 (n=4)

description: 1_acuut Bleo IC50 t=6_5 vs Bleo IC50 t=6_3 gl12964411

source_name: HMEC-1 after 6 hours exposure to IC50 Bleo


title: M_Alcoholic_31_None

source_name: LCLs from alcoholic_no treatment


title: Acute_Bleo_5xIC50_t=48 (n=4)

description: 1_acuut Bleo 5xIC50 t=48_5 vs Bleo 5xIC50 t=48_3 gl12964199

source_name: HMEC-1 after 48 hours exposure to 5x IC50 Bleo


title: Acute_CDDP_IC50_t=48 (n=4)

description: 1_acuut Bleo 5xIC50 t=6_5 vs CDDP IC50 t=48_3 gl12964190

source_name: HMEC-1 after 48 hours exposure to IC50 CDDP


title: Acute_CDDP_IC50_t=6 (n=4)

description: 1_acuut Bleo IC50 t=48_5 vs CDDP IC50 t=6_3 gl12964192

source_name: HMEC-1 after 6 hours exposure to IC50 CDDP


title: F_Alcoholic_14_ethanol


title: M_Control_28_ethanol


title: M_Control_28_None


title: F_Alcoholic_14_None


title: F_Control_13_ethanol


title: Acute_Bleo_IC50_t=24 (n=4)

description: 1_acuut Bleo 5xIC50 t=24_5 vs Bleo IC50 t=24_3 gl12964191

source_name: HMEC-1 after 24 hours exposure to IC50 Bleo


title: F_Control_13_None


title: Acute_Control_t=6 (n=3)

description: 1_2 Controle t=6_5 vs Controle t=6_3 gl12964805

source_name: HMEC-1 control after 6 hours


title: M_Alcoholic_23_ethanol


title: Acute_Control_t=6 (n=4)

description: 1_acuut Bleo IC50 t=24_5 vs Controle t=6_3 gl12964414


title: Acute_Control_t=48 (n=3)

description: 1_2 CDDP IC50 t=6_3 vs Controle t=48_5 gl12964813


title: F_Alcoholic_36_ethanol


title: M_Alcoholic_23_None


title: Acute_CDDP_IC50_t=48 (n=3)

description: 1_2 Controle t=24_3 vs CDDP IC50 t=48_5 gl12964815


title: Acute_CDDP_IC50_t=6 (n=3)

description: 1_2 CDDP IC50 t=24_3 vs CDDP IC50 t=6_5 gl12964811


title: Acute_Bleo_5xIC50_t=48 (n=3)

description: 1_2 CDDP 5xIC50 t=6_5 vs Bleo 5xIC50 t=48_3 gl12964803


title: Acute_CDDP_IC50_t=24 (n=5)

description: 1_2 CDDPxIC50 t=24_5 vs CDDP IC50 t=24_3 gl12964814

source_name: HMEC-1 after 24 hours exposure to IC50 CDDP


title: Acute_CDDP_IC50_t=24 (n=4)

description: 1_2 CDDP 5xIC50 t=48_3 vs CDDP IC50 t=24_5 gl12964808


title: F_Alcoholic_36_None


title: F_Control_5_ethanol


title: Acute_Control_t=24 (n=4)

description: 1_2 CDDP 5xIC50 t=6_3 vs Controle t=24_5 gl12964812

source_name: HMEC-1 control after 24 hours


title: Acute_Bleo_5xIC50_t=6 (n=3)

description: 1_2 CDDP 5xIC50 t=24_5 vs Bleo 5xIC50 t=6_3 gl12964204

source_name: HMEC-1 after 6 hours exposure to 5x IC50 Bleo


title: Acute_CDDP_IC50_t=48 (n=2)

description: 1_2 CDDP 5xIC50 t=48_5 vs CDDP IC50 t=48_3 gl12964205


title: Acute_Bleo_IC50_t=24 (n=3)

description: 1_2 Controle t=48_3 vs Bleo IC50 t=24_5 gl12964809


title: M_Control_39_None


title: M_Control_39_ethanol


title: M_Control_25_None


title: F_Alcoholic_10_ethanol


title: F_Alcoholic_10_None


title: M_Control_25_ethanol


title: Acute_Bleo_5xIC50_t=48 (n=2)

description: 1_2 Bleo IC50 t=48_3 vs Bleo 5xIC50 t=48_5 gl12964806


title: Acute_Bleo_IC50_t=48 (n=3)

description: 1_2 Bleo IC50 t=6_3 vs Bleo IC50 t=48_5 gl12964807


title: Acute_Bleo_IC50_t=6 (n=3)

description: 1_2 Bleo IC50 t=24_3 vs Bleo IC50 t=6_5 gl12964810


title: Acute_CDDP_5xIC50_t=24 (n=3)

description: 1_2 Bleo 5xIC50 t=6_5 vs CDDP 5xIC50 t=24_3 gl12964202

source_name: HMEC-1 after 24 hours exposure to 5x IC50 CDDP


title: Acute_Bleo_5xIC50_t=24 (n=3)

description: 1_2 Bleo 5xIC50 t=24_5 vs Bleo 5xIC50 t=24_3 gl12964804

source_name: HMEC-1 after 24 hours exposure to 5x IC50 Bleo


title: Chronic_Control_d30 (n=2)

description: 0_Controle d30_5 vs Controle d2_3 gl12966821

source_name: HMEC-1 control after 30 days culturing


title: F_Control_35_ethanol


title: Chronic_Control_d30 (n=1)

description: 0_Controle d30_5 vs CDDP d16_3 gl12966827


title: F_Control_5_None

source_name: LCLs from non-alcoholic_no treatment


title: F_Control_35_None


title: M_Alcoholic_6_None


title: Chronic_Control_d2 (n=3)

description: 0_Controle d2_5 vs Controle d2_3 gl12966825

source_name: HMEC-1 control after 2 days culturing


title: F_Alcoholic_7_None


title: M_Alcoholic_6_ethanol

source_name: LCLs from alcoholic_ethanol treatment


title: F_Alcoholic_7_ethanol


title: M_Control_9_None


title: Chronic_Control_d16 (n=1)

description: 0_Controle d16_5 vs Controle d16_3 gl12963811

source_name: HMEC-1 control after 16 days culturing


title: Chronic_Control_d2 (n=2)

description: 0_Controle d2_5 vs CDDP d2_3 gl12966819


title: M_Control_9_ethanol

source_name: LCLs from non-alcoholic_ethanol treatment


title: Chronic_CDDP_d2 (n=2)

description: 0_CDDP d2_5 vs Controle d2_3 gl12966824

source_name: HMEC-1 after 2 days contiunous exposure to IC10 CDDP


title: Chronic_Control_d16 (n=2)

description: 0_Controle d16_5 vs Controle d30_3 gl12966818


title: F_Control_15_ethanol


title: F_Alcoholic_33_ethanol


title: Chronic_CDDP_d2 (n=1)

description: 0_CDDP d2_5 vs Bleo d2_3 gl12966820


title: M_Alcoholic_26_None

source_name: LCLs from alcoholic_no treatment


title: F_Control_15_None


title: M_Control_34_None


title: F_Alcoholic_33_None


title: M_Alcoholic_26_ethanol


title: Chronic_Control_d2 (n=1)

description: 0_Controle d2_5 vs CDDP d2_3 gl12963816


title: M_Control_34_ethanol


title: Chronic_CDDP_d16 (n=2)

description: 0_CDDP d16_5 vs CDDP d16_3 gl12966817

source_name: HMEC-1 after 16 days contiunous exposure to IC10 CDDP


title: Chronic_CDDP_d30 (n=2)

description: 0_CDDP d30_5 vs Bleo d30_3 gl12964200

source_name: HMEC-1 after 30 days contiunous exposure to IC10 CDDP


title: Chronic_CDDP_d16 (n=1)

description: 0_CDDP d16_5 vs Bleo d16_3 gl12966826


title: Chronic_Bleo_d30 (n=3)

description: 0_Bleo d30_5 vs CDDP d30_3 gl12963814

source_name: HMEC-1 after 30 days contiunous exposure to IC10 Bleo


title: F_Control_29_ethanol


title: Chronic_Bleo_d30 (n=2)

description: 0_Bleo d30_5 vs Bleo d30_3 gl12963810


title: Chronic_CDDP_d30 (n=1)

description: 0_CDDP d30_5 vs Bleo d2_3 gl12963817


title: Chronic_Bleo_d30 (n=1)

description: 0_Bleo d30_5 vs Bleo d16_3 gl12966822


title: Chronic_Bleo_d2 (n=1)

description: 0_Bleo d2_5 vs Bleo d30_3 gl12963812

source_name: HMEC-1 after 2 days contiunous exposure to IC10 Bleo


title: Chronic_Bleo_d16 (n=2)

description: 0_Bleo d16_5 vs Controle d30_3 gl12963815

source_name: HMEC-1 after 16 days contiunous exposure to IC10 Bleo


title: F_Control_29_None


title: M_Alcoholic_42_ethanol


title: Chronic_Bleo_d2 (n=2)

description: 0_Bleo d2_5 vs CDDP d30_3 gl12966823


title: F_Alcoholic_20_None


title: F_Alcoholic_20_ethanol


title: M_Control_12_ethanol


title: M_Alcoholic_42_None


title: Chronic_Bleo_d16 (n=1)

description: 0_Bleo d16_5 vs Controle d16_3 gl12966816


title: Acute_Control_t=48 (n=2)

description: 0_acuut Controle t=48_5 vs CDDP 5xIC50 t=24_3 gl12964198

source_name: HMEC-1 control after 48 hours


title: Acute_Control_t=24 (n=2)

description: 0_acuut Controle t=24_5 vs Bleo 5xIC50 t=6_3 gl12964195

source_name: HMEC-1 control after 24 hours


title: M_Control_12_None


title: Acute_Control_t=24 (n=3)

description: 0_acuut Controle t=24_5 vs Controle t=24_3 gl12964203


title: Acute_CDDP_IC50_t=48 (n=1)

description: 0_acuut CDDP IC50 t=48_5 vs Controle t=24_3 gl12964201

source_name: HMEC-1 after 48 hours exposure to IC50 CDDP


title: Acute_Control_t=6 (n=2)

description: 0_acuut Controle t=6_5 vs CDDP IC50 t=24_3 gl12964194

source_name: HMEC-1 control after 6 hours


title: F_Control_19_None


title: M_Alcoholic_8_None


title: M_Alcoholic_8_ethanol


title: M_Control_1_ethanol


title: F_Control_19_ethanol


title: F_Alcoholic_43_None


title: Acute_CDDP_IC50_t=6 (n=2)

description: 0_acuut CDDP IC50 t=6_5 vs CDDP 5xIC50 t=6_3 gl12964193

source_name: HMEC-1 after 6 hours exposure to IC50 CDDP


title: Acute_CDDP_IC50_t=24 (n=3)

description: 0_acuut CDDP IC50 t=24_5 vs Bleo 5xIC50 t=24_3 gl12964196

source_name: HMEC-1 after 24 hours exposure to IC50 CDDP


title: Acute_CDDP_5xIC50_t=24 (n=2)

description: 0_acuut CDDP 5xIC50 t=24_5 vs Bleo IC50 t=48_3 gl12964197

source_name: HMEC-1 after 24 hours exposure to 5x IC50 CDDP


title: M_Control_1_None

source_name: LCLs from non-alcoholic_no treatment


title: Acute_CDDP_5xIC50_t=48 (n=3)

description: 0_acuut CDDP 5xIC50 t=48_5 vs controle t=48_3 gl12964407

source_name: HMEC-1 after 48 hours exposure to 5x IC50 CDDP


title: F_Alcoholic_43_ethanol

source_name: LCLs from alcoholic_ethanol treatment


title: Acute_CDDP_5xIC50_t=6 (n=3)

description: 0_acuut CDDP 5xIC50 t=6_5 vs CDDP 5xIC50 t=48_3 gl12964410

source_name: HMEC-1 after 6 hours exposure to 5x IC50 CDDP


title: Acute_Bleo_IC50_t=48 (n=2)

description: 0_acuut Bleo IC50 t=48_5 vs CDDP IC50 t=6_3 gl12964192

source_name: HMEC-1 after 48 hours exposure to IC50 Bleo


title: Acute_Bleo_IC50_t=6 (n=2)

description: 0_acuut Bleo IC50 t=6_5 vs Bleo IC50 t=6_3 gl12964411

source_name: HMEC-1 after 6 hours exposure to IC50 Bleo


title: F_Control_18_ethanol

source_name: LCLs from non-alcoholic_ethanol treatment


title: M_Alcoholic_27_ethanol


title: Acute_Bleo_IC50_t=24 (n=2)

description: 0_acuut Bleo IC50 t=24_5 vs Controle t=6_3 gl12964414

source_name: HMEC-1 after 24 hours exposure to IC50 Bleo


title: F_Alcoholic_37_ethanol


title: F_Control_18_None


title: Acute_Bleo_5xIC50_t=48 (n=1)

description: 0_acuut Bleo 5xIC50 t=48_5 vs Bleo 5xIC50 t=48_3 gl12964199

source_name: HMEC-1 after 48 hours exposure to 5x IC50 Bleo


title: Acute_Bleo_5xIC50_t=6 (n=2)

description: 0_acuut Bleo 5xIC50 t=6_5 vs CDDP IC50 t=48_3 gl12964190

source_name: HMEC-1 after 24 hours exposure to 5x IC50 Bleo


title: M_Alcoholic_27_None

source_name: LCLs from alcoholic_no treatment


title: Acute_CDDP_IC50_t=6 (n=1)

description: 0_2 CDDP IC50 t=6_3 vs Controle t=48_5 gl12964813


title: Acute_Control_t=6 (n=1)

description: 0_2 Controle t=6_5 vs Controle t=6_3 gl12964805


title: cell-si-NC-03

city: Nanjing

first: Yongguo

last: Shi

state: Jiangsu

address: Nanjing xiaguan district jiangjiayuan 121

country: China

institute: The Second Affiliated Hospital of Nanjing Medical University

hyb_protocol: The labeled cRNAs were hybridized onto the microarray according to the manufacturer’s standard protocols.

scan_protocol: After washing, arrays were scanned using GenePix 4000B scanner (Molecular Devices) according to the manufacturer’s protocol.

data_processing: Feature Extraction software (GenePix® Pro 7, Axon Instruments, Inc. ) was used to analyze array  images  to get  raw data. To  begin  with,  the  raw  data  was  normalized  with  the quantile algorithm. The probes that at least 1 out of all samples have flags in Detected were  chosen  for  further  data  analysis.  Differentially  expressed  genes  were  then identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05.   expression pattern among samples.

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were transcribed  to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

extract_protocol: Total RNA from each sample was extracted using TRK1001（LC Sciences, Cat. TRK-1001, Total RNA Purification Kit）according to the manufacturer’s instructions. Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Small interfering RNA (siRNA) and nonspecific control siRNA was synthesised (Carlsbad, California, USA) Cells were plated and cultured in growth media until cell density reached 50   60% prior to siRNA transfection using Lipofectamine2000 (Invitrogen, Shanghai, China) according to the manufacturer's instructions. Cells were harvested after 48 h for microarray analysis.

value: cell line

tag: transfection

value: nonspecific control siRNA


title: cell-si-SPRY4-IT1-01

value: small interfering RNA


title: Acute_CDDP_IC50_t=24 (n=2)

description: 0_2 CDDP IC50 t=24_5 vs CDDP IC50 t=24_3 gl12964814

tag: cell type

value: human microvascular endothelial cell line


title: Acute_Control_t=48 (n=1)

description: 0_2 Controle t=48_3 vs Bleo IC50 t=24_5 gl12964809

source_name: HMEC-1 control after 48 hours


title: Acute_CDDP_5xIC50_t=6 (n=1)

description: 0_2 CDDP 5xIC50 t=6_3 vs Controle t=24_5 gl12964812


title: cell-si-NC-01


title: cell-si-SPRY4-IT1-03


title: Acute_CDDP_5xIC50_t=48 (n=2)

description: 0_2 CDDP 5xIC50 t=48_5 vs CDDP IC50 t=48_3 gl12964205


title: cell-si-NC-02


title: Acute_CDDP_5xIC50_t=6 (n=2)

description: 0_2 CDDP 5xIC50 t=6_5 vs Bleo 5xIC50 t=48_3 gl12964803


title: Acute_CDDP_5xIC50_t=48 (n=1)

description: 0_2 CDDP 5xIC50 t=48_3 vs CDDP IC50 t=24_5 gl12964808


title: Acute_CDDP_5xIC50_t=24 (n=1)

description: 0_2 CDDP 5xIC50 t=24_5 vs Bleo 5xIC50 t=6_3 gl12964204


title: F_Alcoholic_37_None


title: Acute_CDDP_IC50_t=24 (n=1)

description: 0_2 CDDP IC50 t=24_3 vs CDDP IC50 t=6_5 gl12964811


title: 11Aneg_HSC_rep3

city: Irvine

first: Matthew

middle: Arthur

last: Inlay

address: 845 Health Sciences Rd. Gross Hall Rm. 2010

department: Molecular Biology & Biochemistry

institute: UC Irvine

description:
sorted 04-30-2012, 1803 cells
Bone marrow from 1-2 mice per experiment was crushed, stained with anti-KIT microbeads, and KIT-enriched by AutoMACS.  KIT-enriched BM was stained with antibodies for 15 min on ice in PBS + 2% serum then washed and filtered
CD11A- and CD11A+ HSCs were sorted on a BD FACS Aria II in yield mode into individual tubes, then resorted directly into Trizol in purity mode and stored at -80 degrees C until purification
RNA was amplified by the two-cycle amplification kit (Invitrogen) according to the manufacturer's protocol. Amplification performed by the Stanford PAN Gene Expression Core

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip 3000 7G with GCOS version 1.4.0.036.

data_processing: Each data was normalized individually using RMA method against the common reference on Gene Expression Commons system (http://gexc.stanford.edu/)

source_name: bone marrow

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

value: CD11A negative HSC

tag: age

value: 10 weeks

tag: gender


title: 11Apos_HSC_rep2

description:
sorted 04-30-2012, 2293 cells
Bone marrow from 1-2 mice per experiment was crushed, stained with anti-KIT microbeads, and KIT-enriched by AutoMACS.  KIT-enriched BM was stained with antibodies for 15 min on ice in PBS + 2% serum then washed and filtered
CD11A- and CD11A+ HSCs were sorted on a BD FACS Aria II in yield mode into individual tubes, then resorted directly into Trizol in purity mode and stored at -80 degrees C until purification
RNA was amplified by the two-cycle amplification kit (Invitrogen) according to the manufacturer's protocol. Amplification performed by the Stanford PAN Gene Expression Core

value: CD11A positive HSC

value: male


title: 11Apos_HSC_rep1

description:
sorted 10-31-2011, 1274 cells
Bone marrow from 1-2 mice per experiment was crushed, stained with anti-KIT microbeads, and KIT-enriched by AutoMACS.  KIT-enriched BM was stained with antibodies for 15 min on ice in PBS + 2% serum then washed and filtered
CD11A- and CD11A+ HSCs were sorted on a BD FACS Aria II in yield mode into individual tubes, then resorted directly into Trizol in purity mode and stored at -80 degrees C until purification
RNA was amplified by the two-cycle amplification kit (Invitrogen) according to the manufacturer's protocol. Amplification performed by the Stanford PAN Gene Expression Core

value: 8-12 weeks


title: 11Aneg_HSC_rep2

description:
sorted 10-31-2011, 1300 cells
Bone marrow from 1-2 mice per experiment was crushed, stained with anti-KIT microbeads, and KIT-enriched by AutoMACS.  KIT-enriched BM was stained with antibodies for 15 min on ice in PBS + 2% serum then washed and filtered
CD11A- and CD11A+ HSCs were sorted on a BD FACS Aria II in yield mode into individual tubes, then resorted directly into Trizol in purity mode and stored at -80 degrees C until purification
RNA was amplified by the two-cycle amplification kit (Invitrogen) according to the manufacturer's protocol. Amplification performed by the Stanford PAN Gene Expression Core


title: Acute_Control_t=24 (n=1)

description: 0_2 Controle t=24_3 vs CDDP IC50 t=48_5 gl12964815

source_name: HMEC-1 control after 24 hours


title: Acute_Bleo_IC50_t=6 (n=1)

description: 0_2 Bleo IC50 t=6_3 vs Bleo IC50 t=48_5 gl12964807


title: 11Aneg_HSC_rep1

description:
sorted 04-08-2012, 1011 cells
Bone marrow from 1-2 mice per experiment was crushed, stained with anti-KIT microbeads, and KIT-enriched by AutoMACS.  KIT-enriched BM was stained with antibodies for 15 min on ice in PBS + 2% serum then washed and filtered
CD11A- and CD11A+ HSCs were sorted on a BD FACS Aria II in yield mode into individual tubes, then resorted directly into Trizol in purity mode and stored at -80 degrees C until purification
RNA was amplified by the two-cycle amplification kit (Invitrogen) according to the manufacturer's protocol. Amplification performed by the Stanford PAN Gene Expression Core

value: 6 weeks


title: Acute_Bleo_IC50_t=48 (n=1)

description: 0_2 Bleo IC50 t=48_3 vs Bleo 5xIC50 t=48_5 gl12964806


title: Acute_Bleo_IC50_t=24 (n=1)

description: 0_2 Bleo IC50 t=24_3 vs Bleo IC50 t=6_5 gl12964810


title: Wnt3A 2

city: Shanghai

first: Qing Cissy

last: Yu

address: 320 Yue Yang Road

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institute of Biological Sciences

description: Gene expression data from isolated,Wnt3A treated mammary gland stem cell cultured as colony for 2 passages.

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

data_processing: The data were analyzed with GeneSpring GX10.0 using Affymetrix default analysis settings and global scaling (RMA) as normalization method.

source_name: Wnt3A treated mammary stem cells in culture for 2 passages

growth_protocol: Mammary glands from 8- to 12-week-old virgin female mice (CD1) were isolated. The minced tissue was placed in culture medium (RPMI 1640 with 25 mM HEPES, 5% fetal bovine serum, 1% PSQ, 300U ml-1 Collagenase III [Worthington]) and digested for 2 hrs at 37°C. After lysis of the red blood cells in NH4Cl, a single-cell suspension was obtained by sequential incubation with 0.25% trypsin-EDTA at 37°C for 5 min and 0.1 mg/ml DNase I (Sigma) for 5 mins with gentle pipetting, followed by filtration through 40 mm cell strainers.Cells were pelleted and resuspended for antibody incubation performed on ice for 15 min in HBSS with 10% fetal bovine serum. The following antibodies in 1:200 dilutions were used: FITC conjugated CD31, CD45, TER119 (BD PharMingen), CD24-PE/cy7, CD29-APC (Biolegend). Mammary stem cell enriched population (Lin-, CD24+, CD29hi) cells were isolated using BD FACSAria. The purity of sorted population was routinely checked and ensured to be more than 95%.FACS-sorted cells were resuspended at a density of 4×105 cells ml-1 in chilled 100% growth factor reduced Matrigel (BD Bioscience), and the mixture was allowed to polymerized before covering with culture medium (DMEM/F12, ITS (1:100, Sigma), 50 ng ml-1EGF, plus either vehicle [1% CHAPS in PBS] or 200 ng ml-1Wnt3A 25). Culture medium was changed every 24 hrs. Primary colony numbers were scored after 6–7 days in culture. To passage colonies, media was aspirated and Matrigel was digested by incubation in 500 ul of Matrigel recovery solution (BD Bioscience) for 1 hr on ice. Colonies released from Matrigel were harvested after pelleting. Single cells were obtained through incubation with 0.25% trypsin-EDTA at 37 °C for 5 min, followed by gentle pipetting. Single cells were then replated in Matrigel as described above. 2nd colonies were harvested after 6-7 days in culture as described above.

extract_protocol: Total RNA from 2nd colonies cultured in the presence of vehicle and Wnt3A was extracted with PicoPure (Arcturs) in accordance with the manufacturer’s protocol. RNA concentration was determined with NanoDrop ND-1000, and quality was determined using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies)

treatment_protocol: Purified Wnt3A protein or control vesicle were supplemented into growth medium throughout the course of culturing period.

tag: tissue

value: mammary gland

value: mammary stem cells

tag: agent


title: Wnt3A 1


title: Control 2

description: Gene expression data from isolated,vesicle treated mammary gland stem cell cultured as colony for 2 passages.

source_name: Vesicle treated mammary stem cells in culture for 2 passages

value: control


title: Acute_Bleo_5xIC50_t=24 (n=1)

description: 0_2 Bleo 5xIC50 t=24_5 vs Bleo 5xIC50 t=24_3 gl12964804


title: mouse lung infected 5 days, biological rep2

status: Public on Oct 21 2014

city: beijing

first: yanyan

last: bao

address: Dongzhimen South Street

institute: Biosafety Laboratory, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences

description:
13～15g
microRNA expression data

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip miRNA 4.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: mouse lung infected 5 days with PR8 H1N1 influenza virus

growth_protocol: Mice were anesthetized with ether and were intranasally inoculated with 104 TCID50 of PR8 virus in physiological saline.For the total RNAs extraction, entire lungs from mice infected by PR8 virus were randomly selected and harvested on the 2th and 5th day.

extract_protocol: Total RNAs were extracted from mouse lungs using QIAGEN RNeasy Mini Kit,according to the manufacturer's instructions.

treatment_protocol: Whole mouse lung tissues were homogenized in liquid nitrogen. Total RNAs were extracted from mouse lungs using QIAGEN RNeasy Mini Kit.

value: lung

value: ICR


title: mouse lung infected 5 days, biological rep3

description:
13～15g
microRNA expression data


title: Acute_Bleo_5xIC50_t=6 (n=1)

description: 0_2 Bleo 5xIC50 t=6_5 vs CDDP 5xIC50 t=24_3 gl12964202

source_name: HMEC-1 after 6 hours exposure to 5x IC50 Bleo


title: mouse lung infected 5 days, biological rep1

description:
13～15g
microRNA expression data


title: Control 1


title: SEQC NB patient 493

first: Leming

address: 2005 Songhu Road

department: School of Life Sciences

institute: Fudan University

hyb_protocol: Hybridization was performed following the manufacturer's protocol. In brief, 1650 ng of Cy3-labeled cRNA was hybridized on 4x44K custom microarrays using Agilent's High-RPM Gene Expression Hyb Kit. Hybridization was performed for 17 hours at 65°C in a rotating hyb oven at 10 rpm according the company's recommendations.

scan_protocol: After washing, scanning was performed at an Agilent scanner G2505C according to the manufacturer's protocol.

data_processing: Resulting TIFF-images were processed using Agilent's Feature Extraction software Version 9.5.1.

source_name: neuroblastoma

label_protocol: Labeling was performed according to Agilent's recommentdations. In brief, 1µg total of tumor RNA was linearily amplified and labeled with Cy3 using Agilent's one-color Quick Amp Labeling Kit following the instructions of the protocol.

extract_protocol: 30-60mg of snap-frozen neuroblastoma specimen was cryo-sectioned and were homogenized in TRIzol reagent (Invitrogen, Karlsruhe, Germany) using the FastPrep FP120 cell disruptor (Qbiogene, Inc, Carlsbad, CA, USA).Total RNA was isolated following the TRIzol protocol (Invitrogen) and RNA integrity was assessed using the 2100 Bioanalyzer (Agilent, Waldbronn, Germany). Only samples with an RNA Integrity Number >7.5 were taken for further analysis.

treatment_protocol: All neuroblastoma samples of this set were obtained prior to any cytotoxic treatment and were snap-frozen immediately after surgery. Prior to RNA extraction tumor cell content was checked by a pathologist and only samples with >60% tumor content were processed further.

value: Neuroblastoma

tag: dataset

tag: Sex

value: M

tag: age at diagnosis

tag: mycn status

tag: high risk

tag: inss stage

tag: class label

tag: progression

tag: death from disease


title: mouse lung infected 2 days, biological rep3

description:
13～15g
microRNA expression data

source_name: mouse lung infected 2 days with PR8 H1N1 influenza virus

tag: strain


title: mouse lung infected 2 days, biological rep1

description:
13～15g
microRNA expression data


title: mouse lung infected 2 days, biological rep2

description:
13～15g
microRNA expression data


title: mouse lung of control, biological rep3

description:
13～15g
microRNA expression data

source_name: mouse lung uninfected with PR8 H1N1 influenza virus


title: mouse lung of control, biological rep2

description:
13～15g
microRNA expression data


title: SEQC NB patient 492


title: SEQC NB patient 497

value: F


title: mouse lung of control, biological rep1

description:
13～15g
microRNA expression data


title: SEQC NB patient 494


title: SEQC NB patient 496


title: SEQC NB patient 495


title: SEQC NB patient 498


title: Senescence Day 5, replicate 2

description: Biological replicate 2 of 3. Samples collected 7 days after senescence induction by placing the leaves in the dark.

source_name: primary leaf-Dark-Day 7

tag: variety

value: Nagrad

source_name: pooled RNA from all samples


title: SEQC NB patient 488


title: SEQC NB patient 486


title: SEQC NB patient 489


title: SEQC NB patient 490


title: SEQC NB patient 484


title: SEQC NB patient 487


title: SEQC NB patient 491


title: SEQC NB patient 476


title: SEQC NB patient 483


title: SEQC NB patient 475


title: SEQC NB patient 482


title: SEQC NB patient 474


title: SEQC NB patient 480


title: SEQC NB patient 470


title: SEQC NB patient 473


title: SEQC NB patient 469


title: SEQC NB patient 479


title: SEQC NB patient 485


title: SEQC NB patient 471


title: 2012-T17-RMS_N

city: Tokyo

first: Riki

last: Nishimura

address: 7-3-1, Hongo, Bunkyo-ku

country: Japan

institute: University of Tokyo

description: Hybridized to 250K_Nsp

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: CEL files and CHP files (generated by Affymetrix GTYPE using the DM algorithm) were processed by CNAG/AsCNAR 3.0

label: Biotin

source_name: ERMS tumor specimen

label_protocol: Affymetrix standard protocol

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from resected fresh tumor blocks or freeze tumor blocks.

tag: disease

value: RMS

tag: histology subtype

value: ERMS


title: SEQC NB patient 477


title: SEQC NB patient 481


title: SEQC NB patient 468


title: SEQC NB patient 466


title: SEQC NB patient 472


title: SEQC NB patient 467


title: SEQC NB patient 478