title: Total Brain RNA from E18.5 Foxf2 mutant embryo rep2

city: Gothenburg

first: Ali

middle: Moussavi

last: Nik

address: Medicinaregatan 9C

department: Chemistry and Molecular Biology

country: Sweden

institute: Gothenburg University

description: E18.5 embryos were dissected in RNase free condition. Brain of the embryos also diddected out in RNase free condition.

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5.0

source_name: Embryonic day E18.5.

label_protocol: standard Affymetrix protocol

extract_protocol:
RNA extraction was performed using the Sigma Mammalian total RNA extraction kit according to the manufacturer protocol.
Extracted RNA was sent to the SWeGene core facility for further analysis.

tag: genetic background

value: Whole brain

value: Foxf2 Mutant


title: SM01R016

status: Public on Mar 02 2015

type: RNA

city: Boston

first: Gabriel

last: Gruionu

state: MA

address: 149 13th Street, Room 3316

department: Radiation Oncology

country: USA

institute: Massachusetts General Hospital

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on RG*34A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the standard Affymetrix protocol.

data_processing: The data were analyzed with Affymetrix Gene Chip Operating Software (GCOS) using the MAS 5.0 algorithm using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: mesenteric artery, F344xBN, 24 mo.

label_protocol: Biotinylated cRNA were prepared from <1ug of total RNA,  see McClintick, J. N., R. E. Jerome, et al. (2003). "Reproducibility of oligonucleotide arrays using small samples." BMC Genomics 4(1): 4.

extract_protocol: Total RNA was purified by using an RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: Collateral artery model created by adjacent arterial occlusion, see Unthank JL, Fath SW, et al. (1996). "Wall remodeling during luminal expansion of mesenteric arterial collaterals in the rat." Circulation Research 79: 1015.

tag: strain

value: Fischer344 x Brown Norway

tag: tissue

value: mesenteric artery

tag: age in months

tag: mass (mg)


title: SM01R008

source_name: mesenteric artery, F344xBN, 15 mo.


title: SM01R020

source_name: mesenteric artery, BN, 15 mo.

value: Brown Norway


title: Total Brain RNA from E18.5 wt embryo rep2

organism: Mus musculus

tag: genotype

value: Wt


title: Total Brain RNA from E18.5 wt embryo rep3


title: SM01R014


title: SM01R018


title: SM01R009


title: SM01R010


title: SM01R015


title: SM01R012


title: Total Brain RNA from E18.5 Foxf2 mutant embryo rep3


title: SM01R013


title: SM01R011


title: SM01R006

source_name: mesenteric artery, F344xBN, 6 mo.


title: Total Brain RNA from E18.5 Foxf2 mutant embryo rep1


title: Total Brain RNA from E18.5 wt embryo rep1


title: SM01R007


title: LPM028_Relapse3

type: genomic

city: Houston

first: Michael

middle: R

last: Green

state: TX

address: 1515 Holcombe Blvd, Unit 903

department: Lymphoma/Myeloma

institute: MD Anderson Cancer Center

hyb_protocol: Overnight hybridization according to Affymetrix Protocol

scan_protocol: Scanned with Affymetrix GeneChip Scanner 3000 and GCOS software

data_processing: Data processed using Affymetrix Genotyping Console software

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: FACS sorted B-cells from tumor at third relapse

label_protocol: Biotin labeling according to Affymetrix Protocol

extract_protocol: Qiagen AllPrep Kit

treatment_protocol: B-cells were identified by CD20 and CD19 and sorted by FACS prior to DNA isolation

tag: patient id

tag: gender

value: male

tag: disease

value: Follicular lymphoma

tag: histology

tag: cell type

value: FACS sorted B-cells


title: LPM029_Relapse1

source_name: FACS sorted B-cells from tumor at first relapse


title: LPM029_Diagnosis_Site1

source_name: FACS sorted B-cells from first site of tumor at diagnosis


title: LPM029_Relapse2

source_name: FACS sorted B-cells from tumor at second relapse


title: LPM029_Diagnosis_Site2

source_name: FACS sorted B-cells from second site of tumor at diagnosis


title: SM01R003


title: LPM028_Relapse2


title: SM01R004


title: SM01R005


title: SM01R033

source_name: mesenteric artery, BN, 6 mo.


title: SM01R002


title: 24_D2

city: buffalo

first: Dan

last: Wang

state: NY

address: Elm & Carlton Streets

institute: RPCI

description: 24 hours post MWF calcitriol treatment, sample 2

hyb_protocol: Samples were hybridized to WT Human Gene 1.0 ST arrays using Affymetrix hybridization kit materials, according to the manufacturrer's instructions. Sample cocktails were heated at 99°C for 5 minutes, then 45°C for 5 minutes, centrifuged at max speed for 1 minute. Eighty ul of hyb solution was transferred to each array, and hybridized 17 hours at 45°C at 60rpm. Fluidics washing protocol used was FS450_0007.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Mouse Gene 1.0 St Arrays were normalized using the RMA function to generate expression summary values through convolution background correction, quantile normalization, and based on multi-array model fitting using the medial polish algorithm

source_name: prostate, 24 hour calcitriol

label_protocol: WT expression kit (Ambion), WT Terminal Labeling Kit (Affymetrix), according to the manufatcturer's instructions

extract_protocol: Total RNA was collected from snap frozen tissue samples kept on dry ice prior to TRIzol extraction. Tissue was homogenized in TRIzol using a Polytron PT 10-35 homogenizer from Kinematica set to 9,000 RPMs. Following homogenization total RNA was extracted using the RiboPure kit (Ambion, #AM1924) following the manufacturer’s protocol. All RNA samples were DNase treated using a DNA-free kit (Ambion, Ca#1906), quantified using a Thermo Scientific Nanodrop 8000, tested for RNA quality by gel electrophoresis, and stored at -80° C until further use.

treatment_protocol: Ventral prostates were harvested from the mouse and flash frozen in liquid nitrogen prior to total RNA extraction.

value: C57BL/6-Tg(TRAMP) x FVB

tag: age

value: 10 weeks

value: ventral prostate


title: 24_D3

description: 24 hours post MWF calcitriol treatment, sample 3


title: LPM028_Diagnosis

source_name: FACS sorted B-cells from tumor at diagnosis


title: LPM027_Relapse3


title: LPM028_Relapse1

value: Not available


title: 24_D1

description: 24 hours post MWF calcitriol treatment, sample 1


title: SM01R001


title: 24_D4

description: 24 hours post MWF calcitriol treatment, sample 4


title: LPM027_Relapse2


title: LPM027_Diagnosis


title: LPM026_Relapse2


title: 24_C4

description: 24 hours post MWF control treatment, sample 4

source_name: prostate, 24 hour control


title: LPM027_Relapse1


title: LPM026_Diagnosis_Site1


title: genomic DNA from Brain Frontal Cortex Sample70

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing:
Unmethylated and methylated signal intensities and detection p values in datSignal.csv supplementary file
BeadStudio software v3.2.

label: Cy3 and Cy5

source_name: Brain Frontal Cortex

label_protocol: Standard Illumina Protocol

growth_protocol: DNA extracted from fresh frozen brain tissue

extract_protocol: genomic DNA was extracted and purified from fresh frozen tissue using AllPrep DNA/RNA mini kit according to standard instructions

treatment_protocol: Standard Illumina Protocol

value: Brain Frontal Cortex

tag: Sex

value: M

value: N

tag: dnamage

tag: ageaccelerationdsvscontrols

tag: ageaccelerationdsvscontrolsincrbm

tag: ageaccelerationdsvscontrolsotherregions

tag: ageaccelerationresidual

tag: postmorteminterval


title: LPM026_Relapse1


title: 24_C3

description: 24 hours post MWF control treatment, sample 3

tag: strain

tag: tissue


title: LPM026_Diagnosis_Site2


title: genomic DNA from Brain Hippocampus Sample71

source_name: Brain Hippocampus

value: Brain Hippocampus


title: 12_D4

description: 12 hours post MWF calcitriol treatment, sample 4

source_name: prostate, 12 hour calcitriol


title: 24_C1

description: 24 hours post MWF control treatment, sample 1


title: 24_C2

description: 24 hours post MWF control treatment, sample 2


title: LPM025_Relapse1


title: 12_D3

description: 12 hours post MWF calcitriol treatment, sample 3


title: LPM025_Diagnosis


title: genomic DNA from Brain Temporal Cortex Sample68

source_name: Brain Temporal Cortex

value: Brain Temporal Cortex

value: F


title: genomic DNA from Brain Occipital Sample66

source_name: Brain Occipital

value: Brain Occipital


title: genomic DNA from Brain Frontal Cortex Sample69


title: LPM024_Diagnosis


title: LPM024_Relapse1


title: 12_D2

description: 12 hours post MWF calcitriol treatment, sample 2


title: genomic DNA from Brain Occipital Sample64

value: DS


title: LPM023_Diagnosis


title: LPM023_Relapse1


title: 12_D1

description: 12 hours post MWF calcitriol treatment, sample 1


title: genomic DNA from Brain Hippocampus Sample65


title: genomic DNA from Brain CRBM Sample63

source_name: Brain CRBM

value: Brain CRBM


title: genomic DNA from Brain Frontal Cortex Sample62


title: 12_C4

description: 12 hours post MWF control treatment, sample 3

source_name: prostate, 12 hour control


title: genomic DNA from Brain Temporal Cortex Sample61


title: Tumor KO8-ID261

city: Copenhagen

first: Anders

middle: H

last: Lund

address: Ole Maaloes Vej 5

department: Biotech Research and Innovation Centre

country: Denmark

institute: University of Copenhagen

description: Gene expression data from EmuMyc tumors. Last 3 numbers of title corresponds to a unique mouse ID

hyb_protocol: Standard hybridization for Affymetrix was performed

scan_protocol: Standard scanning of Affymetrix chips was performed

data_processing: Microarray data was analyzed at gene level in the Gene Array Analyzer webtool [Gellert et al, Nucleic Acids Research, 2012, vol. 40, no.6], which used RMA background correction, normalization and probe set summarization. Probe set “10338063” was excluded from data, as it is currently not mapped to the genome.

source_name: Eμ-MYC mouse, end-stage splenic tumor

label_protocol: Standard labelling for Affymetrix was performed

growth_protocol: The Eμ-MYC mouse strain was crossed to Prdm11 KO mouse strain and survival was evaluated for Eμ-MYC; Prdm11 WT and  Eμ-MYC; Prdm11 KO mice according to standard protocol

extract_protocol: End-stage splenic tumors was taken from euthanized mice and frozen in liquid nitrogen. RNA was extracted from homogenized tumors using RNAeasy + DNAse treatment according to manufacturers instruction (Qiagen)

tag: background strain

value: end-stage splenic tumor

tag: genotype/variation

value: Prdm11 KO


title: LPM022_Diagnosis

tag: patient id

value: male

value: Follicular lymphoma


title: 12_C1

description: 12 hours post MWF control treatment, sample 1

value: C57BL/6-Tg(TRAMP) x FVB


title: LPM022_Relapse1

tag: gender

value: FACS sorted B-cells


title: genomic DNA from Brain Frontal Cortex Sample60


title: Tumor KO9-ID357


title: 12_C2

description: 12 hours post MWF control treatment, sample 2

value: 10 weeks

value: ventral prostate


title: LPM021_Relapse1

value: female

tag: disease


title: genomic DNA from Brain Occipital Sample67

value: M


title: Tumor KO7-ID201


title: Tumor KO5-ID131


title: Tumor KO4-ID141


title: Tumor KO3-ID203


title: Tumor KO6-ID291


title: LPM020_Relapse2

tag: histology


title: genomic DNA from Brain Frontal Cortex Sample59

value: Brain Frontal Cortex

value: N


title: LPM021_Diagnosis

tag: cell type


title: Tumor KO2-ID183


title: LPM020_Relapse1


title: LPM019_Relapse2


title: genomic DNA from Brain Temporal Cortex Sample58

value: Brain Temporal Cortex

tag: age


title: genomic DNA from Brain Occipital Sample56

tag: Sex

value: F


title: LPM020_Diagnosis


title: LPM019_Diagnosis


title: Tumor KO1-ID147


title: genomic DNA from Brain Temporal Cortex Sample57

tag: dnamage


title: genomic DNA from Brain CRBM Sample54

tag: ageaccelerationdsvscontrols


title: genomic DNA from Brain Occipital Sample55

value: Brain Occipital

tag: ageaccelerationdsvscontrolsincrbm


title: Tumor WT8 -ID355

value: Prdm11 WT


title: LPM018_Relapse3

source_name: FACS sorted B-cells from tumor at third relapse

value: Not available


title: genomic DNA from Brain Occipital Sample53

tag: ageaccelerationdsvscontrolsotherregions


title: LPM018_Relapse2


title: LPM019_Relapse1

source_name: FACS sorted B-cells from tumor at first relapse


title: genomic DNA from Brain Frontal Cortex Sample50

value: DS

tag: ageaccelerationresidual


title: Tumor WT9 -ID247

value: end-stage splenic tumor


title: genomic DNA from Brain CRBM Sample52

value: Brain CRBM

tag: postmorteminterval


title: Tumor WT6 -ID209


title: LPM018_Relapse1

value: male

value: Follicular lymphoma


title: genomic DNA from Brain Frontal Cortex Sample51


title: genomic DNA from Brain Frontal Cortex Sample49


title: LPM018_Diagnosis

value: FACS sorted B-cells


title: Tumor WT5 -ID375


title: genomic DNA from Brain MidBrain  Sample48

source_name: Brain MidBrain

value: Brain MidBrain


title: Tumor WT4 -ID185


title: LPM016_Diagnosis


title: genomic DNA from Brain Frontal Cortex Sample44


title: genomic DNA from Brain CRBM Sample46


title: Tumor WT1 -ID179


title: LPM016_Relapse1


title: LPM017_Relapse1


title: LPM017_Diagnosis


title: Tumor WT2 -ID287


title: Tumor WT3 -ID119


title: Fft3 ChIP in wt

city: Hamburg

first: Babett

last: Steglich

address: Martinistrasse 52

country: Germany

institute: Universitätsklinikum Hamburg-Eppendorf

description:
Ch1 CEL files: Fft3_anti-myc_1.CEL; Fft3_anti-myc_2.CEL
Ch2 CEL files: wt_anti-myc_1.CEL; wt_anti-myc_2.CEL
Fft3_wt_ChIP

hyb_protocol: Hybridised to Affymetrix GeneChip S. pombe Tiling 1.0FR Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols.

scan_protocol: Scanned at the Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols.

data_processing:
CEL.files were analysed in R (http://www.r-project.org) using the Bioconductor (http://www. bioconductor.org) packages “affy”, “affxparser” and “preprocessCore” with standard parameters. DamID/ChIP sample CEL-files were normalised together with their Dam Control/mock sample CEL-files using quantile normalization with standard parameters. Probe sequences were mapped to the S.pombe genome draft downloaded from ftp://ftp.sanger.ac.uk/ on Nov 19, 2009. Any probes mapping to more than one location in the genome or mapping with more than one mismatch was excluded from further analysis. For DamID, tiling array probe scores were averaged over DpnI/II restriction fragments.
Tab-delimited txt-files contain probe positions and log2 scores for all probes used in this analysis.
Please note that DamID data table contains 29698 data rows. DamID is a method that uses methylation-specific restriction enzymes for the selection of targets. The resolution of DamID is therefore limited to the distance between these restriction sites. When we processed the data, we averaged tiling array probe scores over each restriction fragment. This results in fewer data points, and therefore smaller tables [Steglich et al., Nucleus (2012) or Greil et al., Methods Enzym. (2006)].

organism: Schizosaccharomyces pombe

source_name: wt Fft3-myc anti-myc ChIP

label_protocol: Biotin-labeled according to standard Affymetrix protocols.

growth_protocol: Cultures were grown at 30°C to a density of 7e6 cells/ml.

extract_protocol: Genomic DNA was extracted as described in Moreno et al., Methods Enzym. 1991. ChIP was carried out as described in Durand-Dubief et al., Methods Mol Biol, 2009.

treatment_protocol: For ChIP experiments, DNA was immunoprecipitated as described earlier (Durand-Dubief, 2009) using 2µl of anti-H4K12Ac (ab1761, abcam, Lot: 920722), 2µl of anti-myc (9E10, sigma), 1 µl of anti-GFP (ab290, abcam, Lot: GR76757-1), or 3µl anti-RNA polymerase II CTD repeat (ab5408, abcam, Lot: GR32519-1) antibodies per 100µl chromatin extracts.

tag: strain

value: h+ fft3-myc::hph leu1-32 ade6-210 ura4-D18

tag: molecule subtype

value: immunoprecipitated DNA

source_name: anti-myc ChIP in wt


title: Cnd2 ChIP in fft3D

description:
Ch1 CEL files: cnd2_fft3D_anti-GFP_1.CEL; cnd2_fft3D_anti-GFP_2.CEL
Ch2 CEL files; wt_anti-GFP_1.CEL;  wt_anti-GFP_2.CEL
Cnd2_fft3D_ChIP

source_name: fft3D Cnd2-GFP anti-GFP ChIP

value: cnd2-GFP::NatR fft3D::HygR

source_name: anti-GFP ChIP in wt


title: LPM013_Diagnosis

source_name: FACS sorted B-cells from tumor at diagnosis

value: female


title: LPM012_Relapse2

source_name: FACS sorted B-cells from tumor at second relapse

value: Transformed follicular lymphoma

value: DLC


title: MCF7her2 Cell Line, LBH Treatment, Replicate 3

city: Duarte

first: Shiuan

last: Chen

address: 1500 E Duarte Rd

department: Surgical Research

institute: City of Hope

description:
MCF7her2 Cell Line, LBH Treatment
Gene expression data, continuous culture as indicated in 'characteristics'

hyb_protocol: The chips were hybridized by Affymetrix Hybridization Oven 640 and washed by Affymetrix Fluidics Station 450 according to manufacturer's protocols.

scan_protocol: The chips were scanned by Affymetrix scanner 3000 7G using manufacturer's default settings.

data_processing: Raw Affymetrix intensity measurements of all probe sets were background-corrected, normalized, and summarized into gene level expression measurements using RMA method implemented in Partek Genomic Suite V6.5

source_name: MCF-7her2 - LBH

label_protocol: WT Target Labeling Assay was performed using 100ng of total RNA accorind to Affymetrix's 100 ng Total RNA Labeling Protocol.

growth_protocol: Cells were grown in continuous culture with LBH, depending on the type of cell line indicated above

extract_protocol: TRIzol reagent (Invitrogen, Carlsbad, CA) was used for RNA isolation from cell lines, according to manufacturer’s protocol

treatment_protocol: RNA was harvested from cell lines growing in above-mentioned growth protocol conditions

tag: cell line

tag: treatment


title: LPM013_Relapse1

tag: patient id


title: genomic DNA from Brain CRBM Sample39

tag: tissue

value: M

value: N


title: genomic DNA from Brain CRBM Sample45


title: Cnd2 ChIP in wt

description:
Ch1 CEL files: cnd2_anti-GFP_1.CEL; cnd2_anti-GFP_2.CEL
Ch2 CEL files; wt_anti-GFP_1.CEL;  wt_anti-GFP_2.CEL
Cnd2_wt_ChIP

source_name: wt Cnd2-GFP anti-GFP ChIP

tag: genotype/variation


title: Tumor WT7 -ID245

tag: background strain

value: Prdm11 WT


title: MCF7her2 Cell Line, LBH Treatment, Replicate 2


title: genomic DNA from Brain Frontal Cortex Sample40

source_name: Brain Frontal Cortex

value: Brain Frontal Cortex


title: genomic DNA from Brain Occipital Sample41

value: Brain Occipital

value: F


title: MCF7her2 Cell Line, Control DMSO Treatment, Replicate 3

description:
MCF7her2 Cell Line, Control DMSO Treatment
Gene expression data, continuous culture as indicated in 'characteristics'

source_name: MCF-7her2 - DMSO

value: DMSO


title: genomic DNA from Brain Frontal Cortex Sample42


title: LPM011_Diagnosis

tag: gender

value: male

tag: disease

tag: histology

tag: cell type


title: PolII ChIP in fft3D

description:
Ch1 CEL files: Fft3D_anti-PolII_1.CEL; Fft3D_anti-PolII_2.CEL
Ch2 CEL files: WT_anti-PolII_1.CEL; WT_anti-PolII_2.CEL
PolII_fft3D_ChIP

source_name: fft3D anti-PolII ChIP

value: h+ fft3::hph ade6-M210 uraDS/E leu1-32

source_name: PolII ChIP in wt


title: Man1 DamID in fft3D

description:
Ch1 CEL files: Man1_fft3D_DamID_1.CEL; Man1_fft3D_DamID_2.CEL
Ch2 CEL files: DamCtrl_fft3D_DamID_1.CEL; DamCtrl_fft3D_DamID_2.CEL
Man1_fft3D_DamID

source_name: Man1 fft3D DamID gDNA

value: h? fft3::hph Man1-7myc-Dam:Nat (nmt41 promoter)

source_name: DamCtrl DamID in fft3D

value: fft3::hph 7myc-Dam-NLS:NATr (nmt41 promoter)


title: genomic DNA from Brain Temporal Cortex Sample47

source_name: Brain Temporal Cortex

value: Brain Temporal Cortex

tag: age

tag: Sex

value: DS

tag: dnamage

tag: ageaccelerationdsvscontrols


title: LPM012_Relapse1

source_name: FACS sorted B-cells from tumor at first relapse

value: Follicular lymphoma

value: Not available

value: FACS sorted B-cells


title: genomic DNA from Brain Frontal Cortex Sample37

tag: ageaccelerationdsvscontrolsincrbm

tag: ageaccelerationdsvscontrolsotherregions

tag: ageaccelerationresidual

tag: postmorteminterval


title: Man1 DamID in wt

description:
Ch1 CEL files: Man1_wt_DamID_1.CEL; Man1_wt_DamID_2.CEL
Ch2 CEL files: DamCtrl_wt_DamID_1.CEL; DamCtrl_wt_DamID_2.CEL
Man1_wt_DamID

source_name: Man1 wt DamID gDNA

tag: strain

value: h- Man1-7myc-Dam:NAT (nmt41 promoter)

source_name: DamCtrl DamID in wt

value: h- 7myc-Dam-NLS:NATr (nmt41 promoter)


title: LPM011_Relapse1

tag: patient id

value: Transformed follicular lymphoma

value: DLC


title: genomic DNA from Brain Hippocampus Sample38

source_name: Brain Hippocampus

tag: tissue

value: Brain Hippocampus

value: N


title: MCF7her2 Cell Line, Control DMSO Treatment, Replicate 2

tag: cell line

tag: treatment


title: LPM005_Diagnosis

tag: gender

value: female


title: MCF7her2 Cell Line, Control DMSO Treatment, Replicate 1

value: DMSO


title: LPM005_Relapse1

tag: disease


title: genomic DNA from Brain Frontal Cortex Sample43

value: Brain Frontal Cortex

value: M


title: LPM001_Relapse1

value: male

tag: histology


title: HeLa Cell Line, LBH Treatment, Replicate 2

description:
HeLa Cell Line, LBH Treatment
Gene expression data, continuous culture as indicated in 'characteristics'

source_name: HeLa - LBH

value: HeLa


title: LPM001_Relapse2

tag: cell type


title: HeLa Cell Line, LBH Treatment, Replicate 3


title: siEZH2_3

city: Little Rock

first: Kyounghyun

last: Kim

state: AR

address: Rm 318 CI.3329 4104 Outpatient Circle

department: Pharmacology & Toxicology

institute: University of Arkansas Medical Sciences

description: Raw data file: siEZH2_raw.txt

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V3.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin.  To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.

source_name: MDA-MB-231 human breast cancer cells_siEZH2

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

value: MDA-MB-231 breast cancer cells

value: siRNA EZH2


title: HeLa Cell Line, LBH Treatment, Replicate 1


title: HeLa Cell Line, Control DMSO Treatment, Replicate 3

description:
HeLa Cell Line, Control DMSO Treatment
Gene expression data, continuous culture as indicated in 'characteristics'

source_name: HeLa - DMSO


title: LPM012_Diagnosis

source_name: FACS sorted B-cells from tumor at diagnosis

value: Follicular lymphoma


title: siEZH2_2

description: Raw data file: siEZH2_raw.txt


title: siCT_CON_C

description: Raw data file: siEZH2_raw.txt

source_name: MDA-MB-231 human breast cancer cells_siCT_B

value: siRNA Control_B


title: genomic DNA from Brain Hippocampus Sample33

tag: age

value: F


title: genomic DNA from Brain MidBrain  Sample32

source_name: Brain MidBrain

value: Brain MidBrain

tag: Sex


title: HeLa Cell Line, Control DMSO Treatment, Replicate 2


title: LPJ040_Diagnosis_Site2

source_name: FACS sorted B-cells from second site of tumor at diagnosis

value: FACS sorted B-cells


title: LPM001_Diagnosis


title: genomic DNA from Brain Occipital Sample31

source_name: Brain Occipital

value: Brain Occipital

tag: dnamage


title: genomic DNA from Brain Hippocampus Sample34

tag: ageaccelerationdsvscontrols


title: siCT_CON_B

description: Raw data file: siEZH2_raw.txt


title: genomic DNA from Brain MidBrain  Sample30

tag: ageaccelerationdsvscontrolsincrbm


title: LPJ040_Relapse1


title: MCF7her2 Cell Line, LBH Treatment, Replicate 1

source_name: MCF-7her2 - LBH


title: genomic DNA from Brain CRBM Sample26

source_name: Brain CRBM

value: Brain CRBM

tag: ageaccelerationdsvscontrolsotherregions


title: siCT_CON_A

description: Raw data file: siEZH2_raw.txt


title: H295R Cell Line, Control DMSO Treatment, Replicate 3

description:
H295R Cell Line, Control DMSO Treatment
Gene expression data, continuous culture as indicated in 'characteristics'

source_name: H295R - DMSO


title: H295R Cell Line, LBH Treatment, Replicate 2

description:
H295R Cell Line, LBH Treatment
Gene expression data, continuous culture as indicated in 'characteristics'

source_name: H295R - LBH


title: H295R Cell Line, Control DMSO Treatment, Replicate 1


title: H295R Cell Line, LBH Treatment, Replicate 1


title: LPJ040_Diagnosis_Site1

source_name: FACS sorted B-cells from first site of tumor at diagnosis


title: siSp1_3

description: Raw data file: siSp1_raw.txt

source_name: MDA-MB-231 human breast cancer cells_siSp1

value: siRNA Sp1


title: siSp1_2

description: Raw data file: siSp1_raw.txt


title: siSp1_1

description: Raw data file: siSp1_raw.txt


title: genomic DNA from Brain MidBrain  Sample29

value: N

tag: ageaccelerationresidual


title: H295R Cell Line, Control DMSO Treatment, Replicate 2


title: genomic DNA from Brain Hippocampus Sample28

value: Brain Hippocampus

tag: postmorteminterval


title: siCT_CON_2

description: Raw data file: siSp1_raw.txt

source_name: MDA-MB-231 human breast cancer cells_siCT_A

value: siRNA Control_A


title: H295R Cell Line, LBH Treatment, Replicate 3


title: genomic DNA from Brain Hippocampus Sample27


title: siCT_CON_1

description: Raw data file: siSp1_raw.txt


title: Urea_rep3

city: Verona

first: Anita

last: Zamboni

address: Strada Le Grazie, 15

department: Biotechnology

country: Italy

institute: University of Verona

description: Roots of plants treated with urea. It is the third of urea treated biological replicates used in this experiment.

hyb_protocol: Hybridization and washing procedures were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

scan_protocol: Each microarray was scanned using a Axon GenePix 4400 A at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA) according to the manufacturers' instructions.

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), background correction and standard RMA normalization were selected.

organism: Zea mays

source_name: 5-day-old-plants treated with urea

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

growth_protocol:
Maize seed (Zea mays L., cv. PR33T56, Pioneer Hybrid Italia S.p.A.) were germinated over aerated 0.5 mM CaSO4 solution in a dark growth chamber at 25°C. After 3 days, the seedlings were transferred into an aerated hydroponic system in a controlled climatic conditions: day/night photoperiod, 16/8 h;
light intensity, 220 µE m-2 s-1; temperature (day/night) 25/20°C; RH 70 to 80 %. 5-day-old plants were transferred to a nutrient solution containing (µM): KCl 5; CaSO4 500; MgSO4 100; KH2PO4 175; NaFe-EDTA 20; H3BO3 2.5; MnSO4 0.2; ZnSO4 0.2; CuSO4 0.05; Na2MoO4 0.05.
Nitrogen was supplied in form of: 0.5 mM urea (U treatment); 0.5 mM calcium nitrate (N treatment); 0.5 mM urea and 0.5 mM calcium nitrate (UN treatment). As control, plants were exposed to a nitrogen-free nutrient solution (Ctr treatment). The pH of solution was adjusted to pH 6.0 with sodium hydroxide.
After 8 hours (nine hours after the beginning of light phase), six plants from each treatment were pooled together and root samples were frozen in liquid nitrogen and stored at -80°C until further processing.

extract_protocol: Total RNA was isolated using the Invisorb Spin Plant RNA kit (Stratec Molecular, Berlin, Germany)

treatment_protocol:
Roots of 5-d-old maize plants were exposed for 8 hours to nutrient solution containing nitrogen in form of: 0.5 mM urea (U treatment); 0.5 mM calcium nitrate (N treatment); 0.5 mM urea + 0.5 mM calcium nitrate (UN treatment). As control plants were exposed to a nitrogen-free nutrient solution (Ctr).
Roots of six plants were pooled at the end of the experiment.

value: urea

tag: hybrid

value: cv. PR33T56

value: root


title: Urea_rep2

description: Roots of plants treated with urea. It is the second of  urea treated biological replicates used in this experiment.


title: HeLa Cell Line, Control DMSO Treatment, Replicate 1

value: HeLa

value: DMSO


title: genomic DNA from Brain CRBM Sample36


title: siEZH2_1

description: Raw data file: siEZH2_raw.txt

value: MDA-MB-231 breast cancer cells

value: siRNA EZH2


title: genomic DNA from Brain Temporal Cortex Sample23

source_name: Brain Temporal Cortex

value: Brain Temporal Cortex

value: M


title: siCT_CON_3

description: Raw data file: siSp1_raw.txt


title: Urea+nitrate_rep3

description: Roots of plants treated with urea and NO3-. It is the third of urea and  NO3- treated biological replicates used in this experiment.

source_name: 5-day-old-plants treated with urea and NO3-

value: urea + nitrate


title: genomic DNA from Brain Hippocampus Sample25

source_name: Brain Hippocampus

value: F


title: genomic DNA from Brain MidBrain  Sample24

value: Brain MidBrain


title: Urea+nitrate_rep2

description: Roots of plants treated with urea and NO3-. It is the second of  urea and NO3- treated biological replicates used in this experiment.


title: Urea_rep1

description: Roots of plants treated with urea. It is the first of urea treated biological replicates used in this experiment.


title: genomic DNA from Brain Frontal Cortex Sample21

source_name: Brain Frontal Cortex

value: Brain Frontal Cortex


title: genomic DNA from Brain MidBrain  Sample22


title: Urea+nitrate_rep1

description: Roots of plants treated with urea and NO3-. It is the first of urea and  NO3- treated biological replicates used in this experiment.


title: ATDC5 overexpressing HES1

city: TOKYO

first: Taku

last: Saito

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

department: Orthopaedic Surgery, Faculty of Medicine

country: Japan

institute: The University of Tokyo

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray (Agilent) 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 the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: ATDC5 overexpressing HES1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was extracted from the chondrocytes using RNeasy mini kits (Qiagen) according to manufacturer’s protocol.

treatment_protocol: Two stable ATDC5 cell lines were seeded onto 60 mm dishes. RNA was collected from these cells after 3 days monolayer culture.

value: mouse chondrocyte cell line

tag: genotype/variation

value: overexpressing HES1


title: G259: Normal_adjacent_prostate

city: Rotterdam

first: Guido

last: Jenster

department: Urology

country: Netherlands

institute: Erasmus MC

hyb_protocol: Standard hybridization protocol for Affymetrix human exon 1.0 ST

scan_protocol: Standard scanner for Affymetrix human exon 1.0 ST

data_processing:
Cel files were processed using R-package aroma.affymetrix RMA full probeset level
chip-definition_file: HuEx-1_0-st-v2,fullR3,A20071112,EP.cdf

source_name: radical prostatectomy tumor adjacent normal prostate

label_protocol: Standard whole transcript labeling protocol from Affymetrix human exon 1.0 ST

growth_protocol: Samples were directly taken from the patient tissues

extract_protocol: The standard protocol from RNA-Bee (Campro Scientific) was used to extract total RNA

treatment_protocol: Samples were taken from the surgically removed prostate / lymph node and fresh frozen in liq N2-cooled iso-pentane

tag: gleason score

tag: pt-stage

tag: pre-treatment psa (µg/l)

tag: psa progression

value: no

tag: development of metastasis

tag: surgical margins


title: genomic DNA from Brain Frontal Cortex Sample20

tag: tissue

value: N


title: Nitrate_rep3

description: Roots of plants treated with NO3-. It is the third of  NO3- treated biological replicates used in this experiment.

source_name: 5-day-old-plants treated with NO3-

tag: treatment

value: nitrate


title: genomic DNA from Brain Occipital Sample19

value: Brain Occipital

tag: age

tag: Sex


title: G232: Normal_adjacent_prostate

value: yes


title: G277: Normal_adjacent_prostate


title: ATDC5 overexpressing GFP

source_name: ATDC5 overexpressing GFP

tag: cell line

tag: cell type

value: overexpressing GFP


title: genomic DNA from Brain CRBM Sample18

value: Brain CRBM

tag: dnamage

tag: ageaccelerationdsvscontrols

tag: ageaccelerationdsvscontrolsincrbm

tag: ageaccelerationdsvscontrolsotherregions


title: G280: Normal_adjacent_prostate


title: Nitrate_rep2

description: Roots of plants treated with NO3-. It is the second of  NO3- treated biological replicates used in this experiment.

tag: hybrid

value: cv. PR33T56

value: root


title: genomic DNA from Brain Temporal Cortex Sample17

value: Brain Temporal Cortex

tag: ageaccelerationresidual

tag: postmorteminterval


title: G132: Normal_adjacent_prostate

tag: gleason score

tag: pt-stage

tag: pre-treatment psa (µg/l)


title: genomic DNA from Brain Temporal Cortex Sample16

value: M


title: G183: Normal_adjacent_prostate

tag: psa progression

tag: development of metastasis

tag: surgical margins


title: G193: Normal_adjacent_prostate


title: Nitrate_rep1

description: Roots of plants treated with NO3-. It is the first of  NO3- treated biological replicates used in this experiment.

tag: treatment

tag: tissue


title: Control_rep3

description: Roots of control plants. It is the third of control biological replicates used in this experiment.

value: control


title: Control_rep1

description: Roots of control plants. It is the first of control biological replicates used in this experiment.


title: genomic DNA from Brain Frontal Cortex Sample15

tag: age

tag: Sex


title: genomic DNA from Brain Temporal Cortex Sample13

value: F

tag: dnamage


title: G120: Normal_adjacent_prostate


title: genomic DNA from Brain Frontal Cortex Sample14

tag: ageaccelerationdsvscontrols


title: genomic DNA from Brain Occipital Sample10

source_name: Brain Occipital

tag: ageaccelerationdsvscontrolsincrbm


title: genomic DNA from Brain CRBM Sample35

tag: ageaccelerationdsvscontrolsotherregions


title: genomic DNA from Brain CRBM Sample6


title: G122: Normal_adjacent_prostate


title: genomic DNA from Brain Frontal Cortex Sample9


title: G021: Normal_adjacent_prostate


title: Control_rep2

description: Roots of control plants. It is the second of control biological replicates used in this experiment.

tag: hybrid


title: genomic DNA from Brain Occipital Sample12

tag: ageaccelerationresidual


title: G112: Lymph_node_metastasis

source_name: lymph node metastasis


title: genomic DNA from Brain Frontal Cortex Sample11

tag: postmorteminterval


title: G349: Lymph_node_metastasis

tag: gleason score


title: genomic DNA from Brain CRBM Sample7

source_name: Brain CRBM

value: DS


title: genomic DNA from Brain Temporal Cortex Sample8


title: G033: Normal_adjacent_prostate

tag: pt-stage


title: G300: Lymph_node_metastasis

tag: pre-treatment psa (µg/l)


title: genomic DNA from Brain Temporal Cortex Sample3


title: genomic DNA from Brain Frontal Cortex Sample5

value: Brain Frontal Cortex


title: G055: Lymph_node_metastasis

description: same patient as G054

tag: psa progression


title: G326: Lymph_node_metastasis

tag: development of metastasis


title: G094: Lymph_node_metastasis

tag: surgical margins


title: G295: Lymph_node_metastasis


title: G119: Lymph_node_metastasis


title: genomic DNA from Brain CRBM Sample4


title: G116: Lymph_node_metastasis


title: G039: Normal_adjacent_prostate


title: G342: Prostate_Cancer_TURP

source_name: transurethral resection of prostate tumor


title: G028: Lymph_node_metastasis


title: G348: Prostate_Cancer_TURP


title: G027: Lymph_node_metastasis


title: G304: Prostate_Cancer_TURP


title: G308: Prostate_Cancer_TURP


title: genomic DNA from Brain Frontal Cortex Sample2


title: G054: Lymph_node_metastasis

description: same patient as G055


title: G346: Prostate_Cancer_TURP


title: genomic DNA from Brain Hippocampus Sample1

value: Brain Hippocampus


title: G316: Prostate_Cancer_TURP


title: G344: Prostate_Cancer_TURP


title: G210: Prostate_Cancer_TURP


title: G260: Prostate_Cancer_TURP


title: G247: Prostate_Cancer

source_name: radical prostatectomy prostate tumor


title: G223: Prostate_Cancer

value: positive


title: Mdr2-KO liver tissue_1

status: Public on Mar 01 2015

city: Jerusalem

first: Dr. Daniel

last: Goldenberg

address: Ein-Karem

department: Gene Therapy Institute

country: Israel

institute: Hadassah Medical Center

description: Biological replicate 1 of 3. Mdr2-KO liver tissue.

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.

source_name: Mdr2-KO_MeDIP treated DNA

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

growth_protocol: Mice were grown under ethical committee guidelines with food and water supply unlimited

extract_protocol: Total DNA extracted using phenol-chloroform extraction method

tag: genotype

tag: strain

value: FVB

value: liver


title: LT-HSC d2shSSA rep 3

first: Danika

middle: Mei Po

last: Khong

address: 51 Blossom Street

department: Massachusetts General Hospital

institute: Harvard Medical School

description:
rep3
MIN_Signal-12

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: BM

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

extract_protocol: Total RNA was extracted using Ambion RNAqueuos Micro Kit. Quality control was conducted with Agilent Bioanalyzer.

tag: group

value: sham sex steroid ablation controls

tag: age

tag: gender

value: Male


title: Mdr2-/+ liver tissue control_1

description: Biological replicate 1 of 3. Control Mdr2-/+ liver tissue.

source_name: Mdr2-/+ control_MeDIP treated DNA

tag: tissue

source_name: Mdr2-/+ control_total_DNA


title: G233: Prostate_Cancer

value: yes

value: no


title: G175: Prostate_Cancer

value: negative


title: Male C57BL/6 TCDD 144hours rep3

city: Toronto

first: Stephenie

last: Prokopec

state: Ontario

address: 661 University Avenue, Suite 510

country: Canada

institute: Ontario Institute for Cancer Research

description: HTMoGene11_030512W_PB173_S382_26_RNA.CEL

hyb_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada

data_processing:
Raw array data (CEL files) were loaded into the R statistical environment (v3.0.1) using the affy package (v1.38.1) of the BioConductor library. Data was investigated for distributional homogeneity, then pre-processed using the RMA algorithm. An updated Probe to Entrez Gene ID map, mogene11stmmentrezgcdf (v17.1.0), was used for annotation.
Please note that  7 samples (out of total 65 samples) were identified as outliers and therefore the data were processed without the outliers as well.  The normalized data without outliers were provided in the 'normalized_data_without_outliers.txt' file.

source_name: liver_male C57BL/6_TCDD treated_144 hour exposure

growth_protocol: Animals were housed in Macrolon cages with pelleted Altromin 1314 feed  and tap water available ab libitum. The housing environment was maintained at 21°C with 50 ± 10% relative humidity and artificial illumination on a 12/12 hour light/dark cycle. Animals were housed individually to avoid aggressive behavior.

extract_protocol: Total RNA was extracted using Qiagen RNeasy kits according to the manufacturer’s instructions (Qiagen, Mississauga, Canada). Total RNA yield was quantified by UV spectrophotometry and RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Animals were treated by oral gavage with a single bolus of either TCDD (500 ug/kg) dissolved in corn oil vehicle or corn oil alone (10mL/kg).

tag: Sex

value: adult; 12-15 weeks

tag: treated with

value: 500 ug/kg TCDD

tag: exposure time

value: 144 hours


title: G091: Prostate_Cancer

description: same patient as G032


title: LT-HSC d2SSA rep 2

description:
rep2
MIN_Signal-5

value: 2 days after sex steroid ablation


title: Male C57BL/6 TCDD 144hours rep1

description: HTMoGene11_030512W_PB171_S382_23_RNA.CEL

scan_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada


title: Male C57BL/6 TCDD 144hours rep2

description: HTMoGene11_030512W_PB172_S382_25_RNA.CEL

label_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada


title: Mdr2-/+ liver tissue control_2

description: Biological replicate 2 of 3. Control Mdr2-/+ liver tissue.


title: G. hirsutum L. cv. Bikaneri narma at 10 dpa bollworm infested sample, biological replicate 3

city: New Delhi

first: Mogilicherla

last: Kanakachari

state: Delhi

address: LBS Building, PUSA Campus

department: Molecular Biology and Biotechnology

country: India

institute: National Research Centre on Plant Biotechnology

description: Gene expression profiles of G. hirsutum L. cv. Bikaneri narma at 10 dpa bollworm infested boll, biological replicate 3.

hyb_protocol: Following fragmentation, 12 µg of cRNA were hybridized for 16 hr at 45°C on Affymertix cotton Genechip Genome array. The arrays were washed and stained using streptavidin phycoerythrin on an Affymetrix fluidics station 450.

scan_protocol: The cotton GeneChip Genome arrays were scanned on a GeneChip Scanner 3000.

data_processing: After scannig CEL files were analyzed using GeneSpring GX 11.5 software. The Robust Multiarray Average (RMA) algorithm was used for the back ground correction, quantile normalization and median polished probe set summarization to generate single expression value for each probe set. Normalized expression values were log2-transformed and differential expression analysis was performed using unpaired t-test. The p-values were corrected by applying the false discovery rate (FDR) correction (Benjamini and Hochberg, 2000).

organism: Gossypium hirsutum

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 300ng of total RNA following fragmentation, 12 µg of cRNA were hybridized for 16 hr at 45°C on Affymertix cotton Genechip Genome array. The arrays were washed and stained using streptavidin phycoerythrin on an Affymetrix fluidics station 450.

growth_protocol: The Gossypium hirsutum L. cv. Bikaneri narma were grown in normal agronomic field.

extract_protocol: Total RNA was isolated using Spectrum Plant Total RNA Extraction Kit (Sigma, USA) from control and bollworm infested cotton boll samples.

treatment_protocol: The Gossypium hirsutum L. cv. Bikaneri narma were grown under field condition. Helicoverpa armigera (cotton bollworm) second instar larvae was released at the time of flower opening and covered with polythene bag to prevent insect escape and tagged. The infested flowers were collected after 8 hrs infestations and labeled as 0 dpa. Likewise after two and five day’s infestation the bolls were collected and labelled as 2 and 5 dpa, respectively.  After five days the insect was removed from bolls and left the bolls for up to 10 days and collected then labeled as 10 dpa. Harvested cotton bolls were immediately frozen in liquid nitrogen and stored at -70°C freezer until used for total RNA extraction.

value: cotton bolls

tag: infection

value: bollworm

tag: time

value: 10 dpa

tag: cultivar

value: Bikaneri narma


title: Male C57BL/6 TCDD 144hours rep4

description: HTMoGene11_030512W_PB174_S382_27_RNA.CEL


title: Male C57BL/6 CornOil 144hours rep3

description: HTMoGene11_030512W_PB162_S382_12_RNA.CEL

source_name: liver_male C57BL/6_corn oil treated_144 hour exposure

value: Corn Oil vehicle


title: G. hirsutum L. cv. Bikaneri narma at 10 dpa bollworm infested sample, biological replicate 2

description: Gene expression profiles of G. hirsutum L. cv. Bikaneri narma at 10 dpa bollworm infested boll, biological replicate 2.


title: LT-HSC d2SSA rep 1

description:
rep1
MIN_Signal-4


title: G083: Prostate_Cancer

description: same patient as G082

tag: gleason score

tag: pt-stage


title: LT-HSC d2SSA rep 3

description:
rep3
MIN_Signal-6


title: G051: Prostate_Cancer

tag: pre-treatment psa (µg/l)

tag: psa progression


title: G. hirsutum L. cv. Bikaneri narma at 10 dpa control sample, biological replicate 1.

description: Gene expression profiles of G. hirsutum L. cv. Bikaneri narma at 10 dpa control boll, biological replicate 1.

value: control


title: Male C57BL/6 CornOil 144hours rep2

description: HTMoGene11_030512W_PB161_S382_11_RNA.CEL


title: Mdr2-KO liver tissue_3

description: Biological replicate 3 of 3. Mdr2-KO liver tissue.

value: FVB


title: LT-HSC d2shSSA rep 2

description:
rep2
MIN_Signal-8


title: G. hirsutum L. cv. Bikaneri narma at 10 dpa control sample, biological replicate 3.

description: Gene expression profiles of G. hirsutum L. cv. Bikaneri narma at 10 dpa control boll, biological replicate 3.


title: Male C57BL/6 CornOil 144hours rep1

description: HTMoGene11_030512W_PB160_S382_09_RNA.CEL

value: liver


title: LT-HSC d2shSSA rep 1

description:
rep1
MIN_Signal-7

value: sham sex steroid ablation controls


title: G. hirsutum L. cv. Bikaneri narma at 10 dpa bollworm infested sample, biological replicate 1

description: Gene expression profiles of G. hirsutum L. cv. Bikaneri narma at 10 dpa bollworm infested boll, biological replicate 1.


title: G. hirsutum L. cv. Bikaneri narma at 5 dpa bollworm infested sample, biological replicate 3

description: Gene expression profiles of G. hirsutum L. cv. Bikaneri narma at 5 dpa bollworm infested boll, biological replicate 3.

value: 5 dpa


title: Mdr2-KO liver tissue_2

description: Biological replicate 2 of 3. Mdr2-KO liver tissue.


title: G059: Prostate_Cancer

tag: development of metastasis

tag: surgical margins


title: G. hirsutum L. cv. Bikaneri narma at 10 dpa control sample, biological replicate 2.

description: Gene expression profiles of G. hirsutum L. cv. Bikaneri narma at 10 dpa control boll, biological replicate 2.


title: G104: Prostate_Cancer


title: Female C57BL/6 TCDD 144hours rep4

description: HTMoGene11_022312W_PB87_S380_24LiverB.CEL

source_name: liver_female C57BL/6_TCDD treated_144 hour exposure

tag: strain

value: Female


title: G. hirsutum L. cv. Bikaneri narma at 5 dpa bollworm infested sample, biological replicate 2

description: Gene expression profiles of G. hirsutum L. cv. Bikaneri narma at 5 dpa bollworm infested boll, biological replicate 2.


title: Female C57BL/6 TCDD 144hours rep5

description: HTMoGene11_022312W_PB88_S380_25LiverB.CEL


title: Female C57BL/6 CornOil 144hours rep3

description: HTMoGene11_021512W_PB73_S380_10LiverB.CEL

source_name: liver_female C57BL/6_corn oil treated_144 hour exposure


title: G. hirsutum L. cv. Bikaneri narma at 5 dpa control sample, biological replicate 3.

description: Gene expression profiles of G. hirsutum L. cv. Bikaneri narma at 5 dpa control boll, biological replicate 3.


title: Mdr2-/+ liver tissue control_3

description: Biological replicate 3 of 3. Control Mdr2-/+ liver tissue.

tag: genotype


title: Female C57BL/6 TCDD 144hours rep1

description: HTMoGene11_022312W_PB84_S380_21LiverB.CEL

tag: age


title: Female C57BL/6 TCDD 144hours rep2

description: HTMoGene11_022312W_PB85_S380_22LiverB.CEL


title: Female C57BL/6 CornOil 144hours rep1

description: HTMoGene11_021512W_PB71_S380_08LiverB.CEL


title: G. hirsutum L. cv. Bikaneri narma at 5 dpa control sample, biological replicate 2.

description: Gene expression profiles of G. hirsutum L. cv. Bikaneri narma at 5 dpa control boll, biological replicate 2.


title: Male C57BL/6 TCDD 72hours rep4

description: HTMoGene11_030512W_PB170_S382_21_RNA.CEL

source_name: liver_male C57BL/6_TCDD treated_72 hour exposure

value: Male

value: 72 hours


title: G. hirsutum L. cv. Bikaneri narma at 5 dpa control sample, biological replicate 1.

description: Gene expression profiles of G. hirsutum L. cv. Bikaneri narma at 5 dpa control boll, biological replicate 1.


title: Male C57BL/6 TCDD 72hours rep3

description: HTMoGene11_030512W_PB169_S382_20_RNA.CEL

value: adult; 12-15 weeks


title: Female C57BL/6 CornOil 144hours rep2

description: HTMoGene11_021512W_PB72_S380_09LiverB.CEL


title: Male C57BL/6 TCDD 72hours rep2

description: HTMoGene11_030512W_PB168_S382_19_RNA.CEL

value: 500 ug/kg TCDD


title: G. hirsutum L. cv. Bikaneri narma at 2 dpa bollworm infested sample, biological replicate 3

description: Gene expression profiles of G. hirsutum L. cv. Bikaneri narma at 2 dpa bollworm infested boll, biological replicate 3.

value: 2 dpa


title: G. hirsutum L. cv. Bikaneri narma at 5 dpa bollworm infested sample, biological replicate 1

description: Gene expression profiles of G. hirsutum L. cv. Bikaneri narma at 5 dpa bollworm infested boll, biological replicate 1.


title: Male C57BL/6 TCDD 72hours rep1

description: HTMoGene11_030512W_PB167_S382_18_RNA.CEL


title: G. hirsutum L. cv. Bikaneri narma at 2 dpa bollworm infested sample, biological replicate 2

description: Gene expression profiles of G. hirsutum L. cv. Bikaneri narma at 2 dpa bollworm infested boll, biological replicate 2.


title: Male C57BL/6 CornOil 72hours rep4

description: HTMoGene11_030512W_PB159_S382_08_RNA.CEL

source_name: liver_male C57BL/6_corn oil treated_72 hour exposure


title: G. hirsutum L. cv. Bikaneri narma at 2 dpa bollworm infested sample, biological replicate 1

description: Gene expression profiles of G. hirsutum L. cv. Bikaneri narma at 2 dpa bollworm infested boll, biological replicate 1.


title: Male C57BL/6 CornOil 72hours rep1

description: HTMoGene11_030512W_PB156_S382_05_RNA.CEL


title: Male C57BL/6 CornOil 72hours rep2

description: HTMoGene11_030512W_PB157_S382_06_RNA.CEL


title: G. hirsutum L. cv. Bikaneri narma at 2 dpa control sample, biological replicate 3.

description: Gene expression profiles of G. hirsutum L. cv. Bikaneri narma at 2 dpa control boll, biological replicate 3.


title: Male C57BL/6 CornOil 72hours rep3

description: HTMoGene11_030512W_PB158_S382_07_RNA.CEL


title: G. hirsutum L. cv. Bikaneri narma at 2 dpa control sample, biological replicate 1.

description: Gene expression profiles of G. hirsutum L. cv. Bikaneri narma at 2 dpa control boll, biological replicate 1.


title: G. hirsutum L. cv. Bikaneri narma at 0 dpa bollworm infested sample, biological replicate 1

description: Gene expression profiles of G. hirsutum L. cv. Bikaneri narma at 0 dpa bollworm infested boll, biological replicate 1.

value: 0 dpa


title: G. hirsutum L. cv. Bikaneri narma at 0 dpa bollworm infested sample, biological replicate 3

description: Gene expression profiles of G. hirsutum L. cv. Bikaneri narma at 0 dpa bollworm infested boll, biological replicate 3.

value: cotton bolls


title: G. hirsutum L. cv. Bikaneri narma at 0 dpa bollworm infested sample, biological replicate 2

description: Gene expression profiles of G. hirsutum L. cv. Bikaneri narma at 0 dpa bollworm infested boll, biological replicate 2.

value: bollworm


title: G. hirsutum L. cv. Bikaneri narma at 2 dpa control sample, biological replicate 2.

description: Gene expression profiles of G. hirsutum L. cv. Bikaneri narma at 2 dpa control boll, biological replicate 2.


title: MI-AML291T

city: Ann Arbor

first: Sami

middle: N

last: Malek

state: MI

address: 4410 Cancer Center; 1500 E Medical Center Dr

department: Internal Medicine, Hematology-Oncology

institute: University of Michigan

hyb_protocol: Affymetrix Hybridization Oven 640 for 16 hrs at 50 deg C with rotation at 60 rpm. Washing and staining was done on an Affymetrix Fluidics Station 450.

scan_protocol: Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.

data_processing:
The DNA was prepared for hybridization to SNP 6.0 arrays according to the manufacturer’s recommendations. Affymetrix CEL files for each blast and buccal sample were analyzed using Genotyping Console software for initial quality control, followed by use of the Affymetrix “Birdseed” algorithm to generate tab-delimited SNP call files in text format. Call rates for the entire group of samples included in this report were between 93.64% and 99.45%, with a mean call rate of 98.17%; none of the tumor DNA samples gave out-of-bounds results.
Sample copy number heatmap displays were obtained from CEL files through use of the freely available software dChip, adapted to run on a 64-bit computer environment. To generate functional and practical displays of LOH, a two-step, internally developed, Java-based software analysis system was employed.  The Pre-LOH Unification Tool (PLUT) served to align all individual patient SNP calls to their respective dbSNP rs ID numbers and genomic physical positions prior to incorporation into the LOH tool version 2, an updated version of the LOH tool able to accommodate Affy SNP 6.0 array data
[primary data description] dChip SNP software (www.dchip.org), build date Feb 25, 2009, compatible with 64-bit OS, analyzed the CEL files.  CEL files were normalized using the invariant set method, followed by model-based expression index calculations, and finally inferred copy number data were generated using a median-smoothing algorithm.  See supplementary file linked to Series record.

source_name: primary human: blood or bone marrow, FACS sort-purified AML blasts

label_protocol: The DNA was prepared for hybridization to Affymetrix SNP 6.0 arrays according to the manufacturer's recommendations.

extract_protocol:
[purification protocol] AML blast DNA used for SNP 6.0 profiling was extracted from negatively column enriched AML cell samples as described that were further purified as follows:  post-Miltenyi column samples were washed and stained with FITC-conjugated anti-CD33, PE-conjugated anti-CD13, and APC-conjugated anti-CD45 (all antibodies: eBioscience, San Diego, CA).  After final washing, propidium iodide (PI) was added to a concentration of 1 μg/ml to discriminate dead cells.  Sorting of cells was done on a FACS-ARIA high-speed flow cytometer (Becton Dickinson, Mountain View, CA).  Live cells (PI-negative) were gated for blasts by identifying those cells with intermediate-intensity staining for CD45 and low- to moderate-intensity side scatter. CD33 and CD13 were then used in order to further discriminate myeloid blasts versus contaminating erythroid lineage or other non-myeloid cells.  Cells forming a dense population cloud on the CD33 versus CD13 plots that were either single marker positive or double positive were sorted.  Aliquots of final cell preparations were made for the majority of sorted samples and manually analyzed for cell composition using cytospins and blast counts.
Highly pure blast cells or buccal swabs were digested overnight in 100 mM Tris pH 8.0, 50 mM EDTA, 50 mM NaCl, 0.5% SDS and 100 μg/ml of Proteinase K (Invitrogen) at 560C. DNA was extracted using phenol-chloroform and precipitated using ammonium acetate, ethanol and glycogen.

tag: disease state

value: non-FAB-M3 AML

tag: individual

tag: paired sample

value: tumor

tag: cell type

value: FACS sort-purified AML blasts


title: Female C57BL/6 TCDD 72hours rep5

description: HTMoGene11_022312W_PB83_S380_20LiverB.CEL

source_name: liver_female C57BL/6_TCDD treated_72 hour exposure

tag: Sex

tag: treated with

tag: exposure time

tag: tissue


title: Female C57BL/6 TCDD 72hours rep4

description: HTMoGene11_022312W_PB82_S380_19LiverB_2.CEL


title: MI-AML290T


title: MI-AML290N_BU

source_name: primary human: buccal

value: normal

value: buccal cells


title: MI-AML288N_BU


title: MI-AML288T


title: G. hirsutum L. cv. Bikaneri narma at 0 dpa control sample, biological replicate 2.

description: Gene expression profiles of G. hirsutum L. cv. Bikaneri narma at 0 dpa control boll, biological replicate 2.

tag: infection

value: control

tag: time

tag: cultivar

value: Bikaneri narma


title: MI-AML287T


title: G. hirsutum L. cv. Bikaneri narma at 0 dpa control sample, biological replicate 3.

description: Gene expression profiles of G. hirsutum L. cv. Bikaneri narma at 0 dpa control boll, biological replicate 3.


title: MI-AML287N_BU


title: Female C57BL/6 CornOil 72hours rep4

description: HTMoGene11_021512W_PB70_S380_07LiverB.CEL

source_name: liver_female C57BL/6_corn oil treated_72 hour exposure

value: Corn Oil vehicle

value: liver


title: MI-AML286T


title: G. hirsutum L. cv. Bikaneri narma at 0 dpa control sample, biological replicate 1.

description: Gene expression profiles of G. hirsutum L. cv. Bikaneri narma at 0 dpa control boll, biological replicate 1.


title: MI-AML286N_BU


title: Female C57BL/6 TCDD 72hours rep2

description: HTMoGene11_021512W_PB80_S380_17LiverB.CEL

value: Female


title: Female C57BL/6 CornOil 72hours rep1

description: HTMoGene11_021512W_PB79_S380_16LiverB.CEL

value: 72 hours


title: Female C57BL/6 TCDD 72hours rep3

description: HTMoGene11_022312W_PB81_S380_18LiverB.CEL

value: adult; 12-15 weeks


title: Female C57BL/6 TCDD 72hours rep1

description: HTMoGene11_021512W_PB67_S380_04LiverB.CEL

value: 500 ug/kg TCDD


title: MI-AML285T


title: Female C57BL/6 CornOil 72hours rep3

description: HTMoGene11_021512W_PB69_S380_06LiverB.CEL


title: MI-AML285N_BU


title: Female C57BL/6 CornOil 72hours rep2

description: HTMoGene11_021512W_PB68_S380_05LiverB.CEL


title: MI-AML284T


title: Male C57BL/6 TCDD 24hours rep4

description: HTMoGene11_030512W_PB166_S382_17_RNA.CEL

source_name: liver_male C57BL/6_TCDD treated_24 hour exposure

value: Male

value: 24 hours


title: Female C57BL/6 TCDD 144hours rep3

description: HTMoGene11_022312W_PB86_S380_23LiverB.CEL

value: 144 hours


title: MI-AML284N_BU


title: MI-AML283T


title: Male C57BL/6 TCDD 24hours rep2

description: HTMoGene11_030512W_PB164_S382_14_RNA.CEL


title: MI-AML279T


title: MI-AML279N_BU


title: Male C57BL/6 CornOil 24hours rep1

description: HTMoGene11_030512W_PB153_S382_02_RNA.CEL

source_name: liver_male C57BL/6_corn oil treated_24 hour exposure


title: Male C57BL/6 TCDD 24hours rep3

description: HTMoGene11_030512W_PB165_S382_16_RNA.CEL


title: MI-AML275N_BU


title: MI-AML273T


title: Male C57BL/6 CornOil 24hours rep2

description: HTMoGene11_030512W_PB154_S382_03_RNA.CEL


title: MI-AML283N_BU


title: MI-AML275T_022411


title: MI-AML274N_BU_1


title: Female C57BL/6 TCDD 24hours rep4

description: HTMoGene11_021512W_PB77_S380_14LiverB.CEL

source_name: liver_female C57BL/6_TCDD treated_24 hour exposure


title: Male C57BL/6 TCDD 24hours rep1

description: HTMoGene11_030512W_PB163_S382_13_RNA.CEL


title: Male C57BL/6 CornOil 24hours rep3

description: HTMoGene11_030512W_PB155_S382_04_RNA.CEL


title: Female C57BL/6 TCDD 24hours rep5

description: HTMoGene11_021512W_PB78_S380_15LiverB.CEL


title: Female C57BL/6 CornOil 24hours rep1

description: HTMoGene11_021512W_PB64_S380_01LiverB.CEL

source_name: liver_female C57BL/6_corn oil treated_24 hour exposure


title: Female C57BL/6 TCDD 24hours rep3

description: HTMoGene11_021512W_PB76_S380_13LiverB.CEL


title: MI-AML267N_BU


title: MI-AML267T


title: Female C57BL/6 TCDD 24hours rep2

description: HTMoGene11_021512W_PB75_S380_12LiverB.CEL


title: Female C57BL/6 CornOil 24hours rep2

description: HTMoGene11_021512W_PB65_S380_02LiverB.CEL


title: Male C57BL/6 TCDD 6hours rep5

description: HTMoGene11_030812W_PB187_S383_13_RNA.CEL

source_name: liver_male C57BL/6_TCDD treated_6 hour exposure

value: 6 hours


title: Female C57BL/6 TCDD 24hours rep1

description: HTMoGene11_021512W_PB74_S380_11LiverB.CEL


title: MI-AML274T

value: non-FAB-M3 AML


title: MI-AML263T

value: tumor


title: Male C57BL/6 TCDD 6hours rep4

description: HTMoGene11_030812W_PB186_S383_12_RNA.CEL


title: Male C57BL/6 TCDD 6hours rep3

description: HTMoGene11_030812W_PB185_S383_11_RNA.CEL


title: MI-AML263N_RE


title: MI-AML273N_BU


title: MI-AML260T

value: FACS sort-purified AML blasts


title: MI-AML260N_BU_091411

value: normal


title: Female C57BL/6 CornOil 24hours rep3

description: HTMoGene11_021512W_PB66_S380_03LiverB.CEL


title: Male C57BL/6 TCDD 6hours rep2

description: HTMoGene11_030812W_PB184_S383_10_RNA.CEL


title: Male C57BL/6 CornOil 6hours rep1

source_name: liver_male C57BL/6_corn oil treated_6 hour exposure


title: Male C57BL/6 CornOil 6hours rep4


title: Male C57BL/6 CornOil 6hours rep3


title: Male C57BL/6 CornOil 6hours rep2


title: Male C57BL/6 TCDD 6hours rep1


title: MI-AML257N_BU

value: buccal cells


title: MI-AML254T


title: MI-AML255T


title: Female C57BL/6 TCDD 6hours rep5

description: HTMoGene11_030812W_PB192_S383_18_RNA.CEL

source_name: liver_female C57BL/6_TCDD treated_6 hour exposure


title: MI-AML255N_BU


title: MI-AML254N_BU


title: MI-AML252N_BU


title: MI-AML253N_BU


title: Female C57BL/6 TCDD 6hours rep4

description: HTMoGene11_030812W_PB191_S383_17_RNA.CEL


title: MI-AML252T


title: MI-AML251T


title: MI-AML257T


title: Female C57BL/6 TCDD 6hours rep2

description: HTMoGene11_030812W_PB189_S383_15_RNA.CEL


title: Female C57BL/6 TCDD 6hours rep1

description: HTMoGene11_030812W_PB188_S383_14_RNA.CEL


title: Female C57BL/6 CornOil 6hours rep3

source_name: liver_female C57BL/6_corn oil treated_6 hour exposure


title: Female C57BL/6 CornOil 6hours rep4


title: MI-AML253T


title: MI-AML250N_BU


title: MI-AML248T


title: MI-AML251N_BU


title: MI-AML250T


title: MI-AML248N_REMISSION_BM


title: MI-AML244N_BU_091411


title: Female C57BL/6 CornOil 6hours rep2


title: MI-AML243T


title: MI-AML243N_BU


title: MI-AML241T


title: Female C57BL/6 TCDD 6hours rep3

description: HTMoGene11_030812W_PB190_S383_16_RNA.CEL


title: Female C57BL/6 CornOil 6hours rep1


title: Ly-6D-CLPs_CpG_ rep2

city: Philadelphia

first: Edward

middle: M

last: Behrens

state: Pennsylvania

institute: The Children's Hospital of Philadelphia

hyb_protocol: 2ug of fragmented and labeled SPIA cDNA was hybridized to an Affymetrix Mouse Gene 2.0ST Array for 17 hours at 50C and 60rpm. Arrays were washed on an Affymetrix GeneChip Fluidics Station 450 using fluidics protocol FS450_0007.

scan_protocol: Chips were scanned with an Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with Partek Genomics Suite using RMA normalization.

source_name: Ly-6D- CLPs from bone marrow, CpG treated

label_protocol: 5ug of SPIA cDNA was fragmented and labeled using the NuGen Encore Biotin Module

growth_protocol: Mice were treated every other day for 10 days with PBS or 50ug CpG1826.  Bone marrow CLPs were sorted by flow cytometry on day 10.

extract_protocol: RNAeasy (Qiagen) was used as per manufacures protocol. Further amplification was done using the The NuGen Ovation Pico WTA System V2 kit as per manufacturers instructions to generate single stranded SPIA cDNA from  5 ng of total RNA

treatment_protocol: Cells were sorted directly into RNAeasy buffer for extraction.

value: bone marrow common lymphoid progenitors

value: negative

tag: treatment

value: CpG


title: Ly-6D-CLPs_CpG_ rep3


title: Ly-6D-CLPs_PBS_ rep2

source_name: Ly-6D- CLPs from bone marrow, PBS treated

value: PBS


title: Ly-6D+CLPs_CpG_ rep3

source_name: Ly-6D+ CLPs from bone marrow, CpG treated

value: positive


title: Ly-6D+CLPs_PBS_ rep2

source_name: Ly-6D+ CLPs from bone marrow, PBS treated


title: Ly-6D+CLPs_PBS_ rep1


title: Ly-6D-CLPs_PBS_ rep1


title: Ly-6D+CLPs_CpG_ rep1


title: MI-AML237N_BU


title: MI-AML239N_BU_091411


title: Ly-6D-CLPs_PBS_ rep3


title: MI-AML244T


title: MI-AML238T


title: MI-AML239T_AML_from_MDS


title: Ly-6D-CLPs_CpG_ rep1


title: MI-AML237T


title: Ly-6D+CLPs_CpG_ rep2


title: MI-AML235T


title: MI-AML233T


title: MI-AML235N_BU


title: MI-AML291N_BU


title: MI-AML232N_BU


title: MI-AML236N_RE


title: MI-AML236T


title: MI-AML229T


title: MI-AML241N_BU_091411


title: MI-AML229N_BU


title: MI-AML227N_BU


title: MI-AML225N_BU


title: MI-AML223T


title: MI-AML223N_BU


title: MI-AML222T


title: MI-AML233N_BU


title: MI-AML222N_BU_091411


title: MI-AML221T


title: MI-AML217T


title: MI-AML217N_BU


title: MI-AML215T


title: MI-AML216T


title: MI-AML214N_BU


title: MI-AML221N_BU


title: MI-AML210T


title: MI-AML232T


title: MI-AML210N_BU


title: MI-AML212T


title: MI-AML204N_BU


title: MI-AML212N_BU


title: MI-AML203T


title: MI-AML203N_BU


title: MI-AML227T


title: MI-AML202T


title: MI-AML225T


title: MI-AML202N_BU


title: MI-AML201N_BU


title: MI-AML201T


title: MI-AML200N_BU


title: MI-AML216N_BU_031910


title: MI-AML215N_BU


title: MI-AML214T


title: MI-AML199T


title: MI-AML197T


title: MI-AML198T


title: MI-AML195N_BU


title: MI-AML204T


title: MI-AML197N_BU


title: MI-AML198N_BU


title: MI-AML194N_BU


title: MI-AML191T


title: MI-AML193T


title: MI-AML193N


title: MI-AML238N_BU


title: MI-AML192T


title: MI-AML192N


title: MI-AML189N_BU_031910


title: MI-AML191N


title: MI-AML200T


title: MI-AML188N_092109


title: MI-AML188T_092809


title: MI-AML184T_031910


title: MI-AML189T_092109


title: MI-AML184N_031910


title: MI-AML182T


title: MI-AML182N_032009


title: MI-AML180T_031910


title: MI-AML180N_BU_031910


title: MI-AML179T


title: MI-AML199N_BU


title: MI-AML195T


title: MI-AML194T


title: MI-AML179N


title: MI-AML174N_031910


title: MI-AML169N


title: MI-AML176T


title: MI-AML169T


title: MI-AML164T


title: MI-AML167T


title: MI-AML167N_BU


title: MI-AML163N


title: MI-AML164N


title: MI-AML163T


title: MI-AML161N


title: MI-AML161T


title: MI-AML160T


title: MI-AML159N


title: MI-AML160N


title: MI-AML158T


title: MI-AML157N


title: MI-AML153T


title: MI-AML157T


title: MI-AML159T


title: MI-AML158N


title: MI-AML153N


title: MI-AML174T


title: MI-AML176N


title: MI-AML151T


title: MI-AML145N


title: MI-AML150T


title: MI-AML142T


title: MI-AML147N


title: MI-AML145T


title: MI-AML151N


title: MI-AML147T


title: MI-AML150N


title: MI-AML140T


title: MI-AML138T


title: MI-AML142N


title: MI-AML140N


title: MI-AML138N


title: MI-AML137T


title: MI-AML136T


title: MI-AML136N


title: MI-AML133T


title: MI-AML137N


title: MI-AML132T


title: MI-AML132N


title: MI-AML133N_BU


title: MI-AML128T


title: MI-AML131T


title: MI-AML128N


title: MI-AML127T


title: MI-AML127N


title: MI-AML126T


title: MI-AML125N_BU


title: MI-AML124T


title: MI-AML125T


title: MI-AML126N


title: MI-AML123T_021709


title: MI-AML123N_031910


title: MI-AML131N


title: MI-AML122T


title: MI-AML124N


title: MI-AML120T


title: MI-AML122N


title: CAST/EiJ-3003

city: Chapel Hill

first: Samir

last: Kelada

state: NC

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina

hyb_protocol: The hybridization cocktail containing the Biotin labeled microRNAs was hybridized to the Affymetrix GeneChip® miRNA 2.0 Arrays. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix. The probe arrays were stained with streptavidin phycoerythrin solution (Molecular Probes, Carlsbad, CA) and enhanced by using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA).

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing: Expression intensities were calculated using GeneChip® Command Console® Software (AGCC version 4.1.2) and Expression Console™ Software (version 1.3.1).

source_name: mouse lung

label_protocol: 500 nanograms  of total RNA (including small RNAs) was used in conjunction with the Affymetrix recommended protocol Affymetrix® FlashTag™ Biotin HSR RNA Labeling Kits (Cat#901911).

extract_protocol: Lung tissue was homogenized in Trizol and RNA was isolated according to manufacturer's instructions.

treatment_protocol: Mice were  i.p. sensitized with 10 ug Der p 1 on days 1 and 7, then challenged with 50 ug Der p 1 on day 15.  All mice were harvested on day 18 (72 hours after challenge). The right lower lobe was flash frozen in liquid nitrogen.

value: CAST/EiJ


title: C57BL/6J-2006


title: MI-AML118N_BU


title: MI-AML120N_060908


title: MI-AML118T_AML_from_MDS

source_name: primary human: blood or bone marrow, FACS sort-purified AML blasts


title: PWK/PhJ-6008

value: PWK/PhJ


title: C57BL/6J-2001


title: NOD/ShiLtJ-4010

value: NOD/ShiLtJ


title: PWK/PhJ-6006


title: CAST/EiJ-3001


title: A/J-1008

value: A/J


title: NOD/ShiLtJ-4008


title: CAST/EiJ-3006


title: MI-AML115T


title: MI-AML115N


title: NZO/HILtJ-5008

value: NZO/HILtJ


title: WSB/EiJ-7005

value: WSB/EiJ


title: MI-AML113T


title: C57BL/6J-2002


title: A/J-1010


title: MI-AML113N


title: A/J-1009


title: NOD/ShiLtJ-4011


title: MI-AML112T


title: MI-AML112N


title: 129S1/SvImJ-12911


title: WSB/EiJ-7009


title: 129S1/SvImJ-12912


title: MI-AML110N


title: 129S1/SvImJ-12914


title: MI-AML110T


title: MI-AML109T_072208


title: A/J-1007


title: MI-AML109N_032009


title: C57BL/6J-2003


title: MI-AML108N


title: MI-AML108T


title: MI-AML107N


title: MI-AML107T


title: MI-AML105N


title: MI-AML105T


title: WSB/EiJ-7008


title: MI-AML103T


title: MI-AML103N


title: CAST/EiJ-3002


title: 129S1/SvImJ-12913


title: MI-AML102T


title: MI-AML102N


title: WSB/EiJ-7007


title: PWK/PhJ-6009


title: MI-AML100T


title: PWK/PhJ-6007


title: MI-AML100N


title: MI-AML101N


title: MI-AML099N


title: MI-AML098T


title: MI-AML097T


title: MI-AML098N


title: MI-AML097N


title: NOD/ShiLtJ-4012


title: NZO/HILtJ-5007


title: NZO/HILtJ-5006


title: MI-AML096T


title: MI-AML095N


title: MI-AML095T


title: MI-AML093T


title: NZO/HILtJ-5005


title: MI-AML093N


title: MI-AML101T


title: MI-AML092T


title: MI-AML099T


title: MI-AML092N


title: MI-AML091N


title: Caco2_Cholesterol_250µM_48h_rep4

city: Madrid

first: Lidia

middle: Ángeles

last: Daimiel-Ruiz

state: Madrid

address: Ctra. Cantoblanco, Km 8

department: Nutritional Genomics of Cardiovascular Disease and Obesity

country: Spain

institute: Institute IMDEA Food

description:
miRNAs contained in the miRBase version 17 were in situ synthesized in microfluidic chips
S18 - IMDEA 219

hyb_protocol: Performed in the LC Sciences miRNA microarray service

scan_protocol: Axon GenePix 4000B Microarray Scanner, 10 µm

data_processing: Background substraction, LOWESS Normalization, Treatment/Control ratio; log2 transformation, ANOVA test and correction for multiple testing.

source_name: Caco-2 cells

growth_protocol: Caco-2 cells were mantained in DMEM supplemented with antibiotics and 10% fetal bovine serum. For experiments, cells were differentiated in transwell plates for 21 days

extract_protocol: miRNA-enriched total RNA was extracted with miRNeasy mini kit (Qiagen) following manufacturer's instructions

treatment_protocol: 24 hours before treatment, cells were changed to medium supplemented with delipidized serum. Micelles were prepared with the appropiate doses of the tested lipids combined wuth lyso-PC (150 µM) and sodium taurocholate (2-5 mM). 24 and 48 hours after treatmens, cells were harvested with QiAzol (Qiagen)

tag: cell line

value: Cholesterol 250µM 48h


title: MI-AML090T

value: non-FAB-M3 AML


title: Caco2_Cholesterol_250µM_48h_rep3

description:
miRNAs contained in the miRBase version 17 were in situ synthesized in microfluidic chips
S09 - IMDEA 152

label_protocol: Performed in the LC Sciences miRNA microarray service


title: Caco2_Control_rep2

description:
miRNAs contained in the miRBase version 17 were in situ synthesized in microfluidic chips
S15 - IMDEA 159

value: Control


title: MI-AML096N_BU_070610

source_name: primary human: buccal


title: MI-AML090N


title: MI-AML089N_031910


title: Caco2_CLA_200µM_24h_rep2

description:
miRNAs contained in the miRBase version 17 were in situ synthesized in microfluidic chips
S06 - IMDEA 146

value: CLA 200µM 24h


title: Caco2_Cholesterol_250µM_48h_rep1

description:
miRNAs contained in the miRBase version 17 were in situ synthesized in microfluidic chips
S07 - IMDEA 150


title: Caco2_CLA_200µM_24h_rep1

description:
miRNAs contained in the miRBase version 17 were in situ synthesized in microfluidic chips
S05 - IMDEA 144


title: Caco2_DHA_200µM_24h_rep3

description:
miRNAs contained in the miRBase version 17 were in situ synthesized in microfluidic chips
S04 - IMDEA 143

value: DHA 200µM 24h


title: MI-AML089T

value: tumor

value: FACS sort-purified AML blasts


title: Caco2_Control_rep3

description:
miRNAs contained in the miRBase version 17 were in situ synthesized in microfluidic chips
S16 - IMDEA 160


title: MI-AML087N

value: normal

value: buccal cells


title: Caco2_Control_rep4

description:
miRNAs contained in the miRBase version 17 were in situ synthesized in microfluidic chips
S17 - IMDEA 210


title: MI-AML091T


title: Caco2_DHA_200µM_24h_rep1

description:
miRNAs contained in the miRBase version 17 were in situ synthesized in microfluidic chips
S02 - IMDEA 141


title: MI-AML081T


title: MI-AML080T


title: MI-AML081N


title: Caco2_Control_rep1

description:
miRNAs contained in the miRBase version 17 were in situ synthesized in microfluidic chips
S01 - IMDEA 137


title: Caco2_Cholesterol_250µM_48h_rep2

description:
miRNAs contained in the miRBase version 17 were in situ synthesized in microfluidic chips
S08 - IMDEA 151


title: IL-10- B cells from HDM 3

city: Nantes

first: Faouzi

last: Braza

address: 30 boulevard Jean Monnet

country: France

institute: Inserm

hyb_protocol: Cy3 labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays (8x60K, Design ID 028005) using Agilent’s recommended hybridization chamber and oven. Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

source_name: Activated spleen B cells with CD40 agonist and LPS in the 5 final hours

label_protocol: 250 ng of each of the amplified cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

growth_protocol: Purified B cells from spleen of control and HDM mice have been activated with CD40 agonist during two days. LPS was added to the culture in the last five hours

extract_protocol: Cell samples were lysed using SuperAmp Lysis Buffer following manufacturer’s instructions. SuperAmplification was performed according to Miltenyi Biotec’s undisclosed protocol. Briefly, the amplification is based on a global PCR protocol of mRNA-derived cDNA. mRNA was isolated via magnetic bead technology.

treatment_protocol: Staining of IL-10 producing B cells with the IL-10 secretion assay (Miltenyi Biotec) and sorting of IL-10+ and IL-10- B cells by FACS AriaIII (BD bisocience)

tag: gender

value: Female

value: Spleen

value: Balb/c


title: IL-10- B cells from HDM 2

tag: strain


title: Caco2_DHA_200µM_24h_rep2

description:
miRNAs contained in the miRBase version 17 were in situ synthesized in microfluidic chips
S03 - IMDEA 142


title: IL-10- B cells from HDM 1


title: MI-AML080N


title: IL-10- B cells from control mice 3


title: IL-10- B cells from control mice 2


title: MI-AML087T


title: IL-10+ B cells from HDM 2


title: IL-10+ B cells from HDM 3


title: IL-10- B cells from control mice 1


title: MI-AML078T


title: IL-10+ B cells from control mice 3


title: hearts_bR3

city: Cologne

first: Julia

last: Hoffmann

address: Joseph-Stelzmann-Str. 9b

department: Partridge

institute: MPI for Biology of Ageing

description: Sample 3

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

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

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

label: Alexa Fluor 555

organism: Drosophila melanogaster

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

growth_protocol: Wild type (w1118) and homozygous mutant (Hand173) flies were raised at low population density on standard medium at 22 °C.

extract_protocol: About 100 heart tubes including associated tissue (pericardial cells, longitudinal ventral muscles) from both genotypes were carefully extracted and directly collected in Trizol (Invitrogen - Life technologies, Frankfurt, Germany) for subsequent RNA preparations.

treatment_protocol: Wandering 3rd instar larvae were collected, transferred into a tea basket and anesthetized by incubating the larvae at 60 °C for 15 seconds in a water bath. Such treatment induces immediate stretching of the larvae with a relaxed muscle contraction state, which facilitates the subsequent heart preparation.

tag: genotype/variation

value: wild type

value: Approx. 100 heart tubes including associated tissue (pericardial cells, longitudinal ventral muscles)

tag: develop. stage

value: wandering 3rd instar larvae

label: Alexa Fluor 647

value: homozygous hand null mutant


title: IL-10+ B cells from control mice 2


title: IL-10+ B cells from HDM 1


title: IL-10+ B cells from control mice 1


title: MI-AML077T

tag: disease state


title: hearts_bR2

description: Sample 2


title: MDA-MB-231 cells treated with TGFb for 24h

city: Guangzhou

first: Bodu

last: Liu

state: State...

address: School of Life Sciences, Sun Yat-sen U East Camp, High. Edu. Meg. Cntr.

country: China

institute: Sun Yat-sen University

description: Double-Stranded cDNA was labeled and hybridized to Arraystar (Rockville, MD) 12x135K LncRNA Expression microarray in NimbleGen Hybridization System. After hybridization and washing, the processed slides were scanned with the Axon GenePix 4005B microarray

hyb_protocol: Double-Stranded cDNA was labeled and hybridized to Arraystar (Rockville, MD) 12 x 135K LncRNA Expression microarray in NimbleGen Hybridization System.

scan_protocol: The processed slides were scanned with the Axon GenePix 4000B microarray scanner.

data_processing: Raw data were extracted as paired files by NimbleScan software (version 2.5), which offers quantile normalization and background correction. Files of probe level (norm_RMA.pair) and gene summary (RMA.calls) were produced,and the latter were imported into Agilent GeneSpring Software (version11.0) and was normalized using quantile method.

source_name: breast cancer cell line

label_protocol: 1ug of total RNA were reversely transcribed into first-strand cDNA using Superscript First-Strand cDNA Synthesis Kit (18080-051, Invitrogen, Carlsbad, CA).

extract_protocol: Total RNA was extracted using TRIzol (15596-026, Invitrogen, Carlsbad, CA)

value: TGFb


title: hearts_bR1

description: Sample 1


title: MI-AML077N

tag: individual


title: C2 Control T=240

city: Lyngby

first: Federico

last: De Masi

address: Kemitorvet 208

department: Institute of Systems Biology

institute: Technical University of Denmark

hyb_protocol: Samples were prepared and hybridized to GeneChip Yeast 2.0 Expression Array according to Affymetrix specifications. Specifically, 5 ug of biotin-labelled and fragmented aRNAs were mixed with the hybridization cocktail indicated by Affymetrix, subsequently heated in different temperatures and finally introduced into the mini (169) array format. For array hybridization, the hybridization oven 640 was used.

scan_protocol: The arrays were washed and stained using the microfluidics station 450 and the fluidics protocol FS450_0006, which is compatible with the 169 microarray format. Then, the arrays were scanned using an Affymetrix GeneChip Scanner 3000 according to manufacturer's instruction

data_processing: The scanned probe array images (.DAT files) were converted into CEL files using the default values of the Affymetrix GeneChip operating software v1.4.

source_name: JB50, no H2O2

label_protocol: RNA target preparation for microarray expression analysis was performed using the GeneChip 3' IVT Express kit. Reverse transcription for cDNA synthesis, dsDNA synthesis, in vitro transcription and biotin-labeling of aRNAs were completed according to Affymetrix specifications.

growth_protocol: The fission yeast Schizosaccharomyces pombe JB50 strain (homothallic, h90) was grown at 32°C in batch cultures prepared in shake flasks (500 mL Erlenmeyer flasks, R.B.M. Lab) containing YES broth (Formedium, PCM0305). Two independent batch cultures were grown to a cell concentration of ~8 x 106 cell/mL (OD595nm = 0.4) and a third to a cell density of ~1.4 x 107 cell/mL (OD595nm = 0.7). Cells were shaken at 160 rpm throughout the cultivation and samples were collected at 0, 5, 10, 15, 30, 50, 60, 90, 120, 180 and 240 minutes after treatment with 0.5 mM HP. Reference samples from unstressed, exponentially growing cells were collected in two more independent batch cultures. Samples collected at 0, 60, 120, 180 and 240 minutes were used for mRNA quantification.

extract_protocol: Total RNA from the collected biomass samples was isolated using a hot-phenol protocol.

treatment_protocol: Cells were harvested by gentle centrifugation at 2000 rpm for 3 minutes at room temperature, and pellets were frozen immediately in liquid nitrogen.

tag: treatment(s)

value: no H2O2


title: MDA-MB-231 cells treated with IL6 for 24h

description: Double-Stranded cDNA was labeled and hybridized to Arraystar (Rockville, MD) 12x135K LncRNA Expression microarray in NimbleGen Hybridization System. After hybridization and washing, the processed slides were scanned with the Axon GenePix 4004B microarray


title: C2 Control T=180


title: C2 Control T=120


title: MI-AML076T

value: non-FAB-M3 AML

tag: paired sample

tag: cell type


title: MDA-MB-231 cells treated with TNFa for 24h

description: Double-Stranded cDNA was labeled and hybridized to Arraystar (Rockville, MD) 12x135K LncRNA Expression microarray in NimbleGen Hybridization System. After hybridization and washing, the processed slides were scanned with the Axon GenePix 4003B microarray

value: TNFa


title: C2 Control T=0


title: MDA-MB-231 cells treated with LPS for 24h

description: Double-Stranded cDNA was labeled and hybridized to Arraystar (Rockville, MD) 12x135K LncRNA Expression microarray in NimbleGen Hybridization System. After hybridization and washing, the processed slides were scanned with the Axon GenePix 4001B microarray

value: LPS


title: C2 Control T=60


title: MI-AML076N


title: C1 Control T=240


title: C1 Control T=180


title: MI-AML078N


title: MDA-MB-231 cells treated with IL1b for 24h

description: Double-Stranded cDNA was labeled and hybridized to Arraystar (Rockville, MD) 12x135K LncRNA Expression microarray in NimbleGen Hybridization System. After hybridization and washing, the processed slides were scanned with the Axon GenePix 4002B microarray


title: BE2C_shMEIS2_rep3

city: Augusta

first: Justin

last: Choi

state: GA

address: 1410 Laney Walker Blvd.

department: Cancer Center

institute: Georgia Regents University

description: RNA expression value

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Data were normalized, significance determined by ANOVA, and fold change calculated with the Partek Genomics Suite (Partek Inc., St. Louis, MO). Gene annotation enrichment analysis was performed with the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 for all significantly changed genes (≥ ±1.5 fold, P < 0.01) and Gene Set Enrichment Analysis (GSEA).

source_name: BE(2)-C/pLKO.1-shMEIS2-43 48h

label_protocol: TdT-labled cRNA were prepared with an Affymetrix GeneChip WT Terminal labeling kit

growth_protocol: BE(2)-C cells were infected with pLKO.1-based lentiviruses expressing either shGFP or shMEIS2-43 for 48 hours

extract_protocol: Total RNA was isolated from the cell samples using Trizol (Invitrogen), and RNA quality and quantity was assessed using a Agilent BioAnalyzer and a Nanodrop Spectrophotometer.

value: MEIS2 depletion


title: C1 Control T=120


title: MI-AML073T_ENROLL_26JUL2006

value: tumor


title: MDA-MB-231 cells treated with PBS for 24h

description: Double-Stranded cDNA was labeled and hybridized to Arraystar (Rockville, MD) 12x135K LncRNA Expression microarray in NimbleGen Hybridization System. After hybridization and washing, the processed slides were scanned with the Axon GenePix 4000B microarray scanner.

value: PBS


title: C1 Control T=60


title: BE2C_shMEIS2_rep2

description: RNA expression value


title: MI-AML073N_BU

value: normal


title: C1 Control T=0


title: MI-AML068T

value: FACS sort-purified AML blasts


title: MI-AML068N

value: buccal cells


title: BE2C_shMEIS2_rep1

description: RNA expression value


title: MI-AML064T


title: R2 Stress induced T=240


title: MI-AML064N


title: BE2C_shGFP_rep3

description: RNA expression value

source_name: BE(2)-C/pLKO.1-shGFP 48h

value: control


title: R2 Stress induced T=50


title: MI-AML063T


title: R2 Stress induced T=30


title: R2 Stress induced T=120


title: MI-AML063N


title: R2 Stress induced T=90


title: R2 Stress induced T=15


title: BE2C_shGFP_rep2

description: RNA expression value


title: BE2C_shGFP_rep1

description: RNA expression value


title: R2 Stress induced T=10


title: MI-AML062T


title: R2 Stress induced T=180


title: R1 Stress induced T=240


title: R1 Stress induced T=120


title: R1 Stress induced T=90


title: MI-AML062N


title: R2 Stress induced T=60


title: R1 Stress induced T=180


title: R1 Stress induced T=30


title: MI-AML060T


title: R1 Stress induced T=60


title: R1 Stress induced T=50


title: MI-AML060N


title: R1 Stress induced T=15


title: R2 Stress induced T=0


title: R1 Stress induced T=10


title: MI-AML059T


title: MI-AML059N


title: MI-AML057T


title: R1 Stress induced T=0


title: MI-AML057N


title: MI-AML056T


title: MI-AML056N


title: MI-AML053T


title: R1 Stress induced T=5


title: MI-AML053N


title: MI-AML050T


title: FL_Ctrl.2

first: Kyoko

last: Hayakawa

state: PA

address: 333 Cottman Avenue

institute: Fox Chase Cancer Center

description: mRNA expression of fetal liver Pro-B cells transduced with empty vector retrovirus, replicate 2

hyb_protocol: Follow Agilent 60-mer oligo array hybridization protocol.

scan_protocol: Arrays were scanned by following scanning protocol recommended by Agilent, and spot quantifications were done using feature extraction software

data_processing: data were quantile normalized

source_name: Fetal liver Pro-B cells transduced with empty vector retrovirus, replicate 2

label_protocol: Amplified RNAs were labeled with cy3 or cy5 dye

extract_protocol: RNA was extracted using the acid phenol method. 100ng of total RNA was used for RNA amplification following Ambion RNA amplification protocol.

treatment_protocol:
For each bone marrow sort, two BALB/c Rag1 null mice were sacrificed and a single cell suspension was prepared from bone marrow after flushing femur and tibia using a 1ml syringe and a 25 gauge needle. Bone marrow Pro-B cells were sorted into wells of a 24-well plate containing OP9 stromal cells and IL-7; the next day 12 wells were transduced with Lin28b retrovirus and 12 were transduced with empty vector (pMIG). 4 days later, GFP+ cells were isolated by cell sorting for preparation of mRNA.
For each fetal liver sort, BALB/c Rag1 null mouse with embryos at day 16 of gestation was sacrificed, embryos (average of 8) were sacrificed, and a single cell suspension was prepared from liver by gentle dissociation between 2 frosted glass slides. Pro-B cells were sorted from a pool of fetal liver into wells of a 24-well plate containing OP9 stromal cells and IL-7; the next day 12 wells were transduced with Let-7b retrovirus and 12 were transduced with empty vector (MSCV). 4 days later, GFP+ cells were isolated by cell sorting for preparation of mRNA.

value: BALB/c Rag1 null

tag: developmental stage

value: Fetus

value: Fetal Liver


title: Let7.2

description: mRNA expression of fetal liver Pro-B cells transduced with Let7 containing retrovirus, replicate 2

source_name: Fetal liver Pro-B cells transduced with Let7 containing retrovirus, replicate 2


title: BM_Ctrl.2

description: mRNA expression of bone marrow Pro-B cells transduced with empty vector retrovirus, replicate 2

source_name: Bone marrow Pro-B cells transduced with empty vector retrovirus, replicate 2

value: Adult

value: Bone Marrow


title: benign pancreatic or biliary tract diseases I19

city: Kamakura

first: Ichikawa

last: Makiko

state: Kanagawa

institute: Toray Industries, Inc.

description: miRNA profiling

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing: Mean and standard deviation (SD) of the 5% trimmed signals of the negative controls were calculated. Signals of miRNAs over mean+2SD of the negative controls were subtracted with the mean of the negative controls. The undetected signal was replaced with the value that was the least signal intensity on each DNA chip minus 0.1 in log2 scale followed by quantile normalization.

source_name: Serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.). Total RNA was also obtained from the FFPE sections using the Arcturus® Paradise® Extraction and Isolation kit (Life Technologies) in accordance with the manufacturer's instructions.

value: serum

value: Male

tag: tumor stage

value: uncertain

tag: age

tag: operability


title: benign pancreatic or biliary tract diseases I14

description: miRNA profiling

tag: tissue

value: Female


title: benign pancreatic or biliary tract diseases I20

description: miRNA profiling


title: R2 Stress induced T=5


title: benign pancreatic or biliary tract diseases I15

description: miRNA profiling


title: benign pancreatic or biliary tract diseases I12

description: miRNA profiling


title: benign pancreatic or biliary tract diseases I13

description: miRNA profiling


title: Let7.1

description: mRNA expression of fetal liver Pro-B cells transduced with Let-7 containing retrovirus, replicate 1

source_name: Fetal liver Pro-B cells transduced with Let-7 containing retrovirus, replicate 1


title: FL_Ctrl.1

description: mRNA expression of fetal liver Pro-B cells transduced with empty vector retrovirus, replicate 1

source_name: Fetal liver Pro-B cells transduced with empty vector retrovirus, replicate 1


title: benign pancreatic or biliary tract diseases I17

description: miRNA profiling


title: benign pancreatic or biliary tract diseases I21

description: miRNA profiling


title: Lin28.2

description: mRNA expression of bone marrow Pro-B cells transduced with Lin28b-containing retrovirus, replicate 2

source_name: Bone marrow Pro-B cells transduced with Lin28b-containing retrovirus, replicate 2


title: benign pancreatic or biliary tract diseases I11

description: miRNA profiling


title: benign pancreatic or biliary tract diseases I10

description: miRNA profiling


title: MI-AML050N

value: non-FAB-M3 AML


title: benign pancreatic or biliary tract diseases I18

description: miRNA profiling


title: benign pancreatic or biliary tract diseases I07

description: miRNA profiling


title: Lin28.1

description: mRNA expression of bone marrow Pro-B cells transduced with Lin28b-containing retrovirus, replicate 1

source_name: Bone marrow Pro-B cells transduced with Lin28b-containing retrovirus, replicate 1


title: benign pancreatic or biliary tract diseases I16

description: miRNA profiling


title: MI-AML049T


title: benign pancreatic or biliary tract diseases I09

description: miRNA profiling


title: BM_Ctrl.1

description: mRNA expression of bone marrow Pro-B cells transduced with empty vector retrovirus, replicate 1

source_name: Bone marrow Pro-B cells transduced with empty vector retrovirus, replicate 1


title: MI-AML047T

source_name: primary human: blood or bone marrow, FACS sort-purified AML blasts


title: MI-AML049N


title: MI-AML047N_010908


title: MI-AML045N


title: benign pancreatic or biliary tract diseases I04

description: miRNA profiling


title: benign pancreatic or biliary tract diseases I05

description: miRNA profiling


title: MI-AML044T


title: MI-AML044N


title: benign pancreatic or biliary tract diseases I02

description: miRNA profiling


title: MI-AML043T


title: liver cancer HC49

description: miRNA profiling

value: liver cancer


title: MI-AML043N


title: benign pancreatic or biliary tract diseases I01

description: miRNA profiling


title: liver cancer B34

description: miRNA profiling


title: liver cancer B70

description: miRNA profiling


title: MI-AML041T

value: tumor


title: liver cancer HC50

description: miRNA profiling


title: liver cancer HC47

description: miRNA profiling


title: MI-AML045T


title: liver cancer HC45

description: miRNA profiling


title: liver cancer HC46

description: miRNA profiling


title: liver cancer HC43

description: miRNA profiling


title: benign pancreatic or biliary tract diseases I03

description: miRNA profiling


title: liver cancer HC42

description: miRNA profiling


title: liver cancer HC41

description: miRNA profiling


title: MI-AML040T


title: liver cancer HC40

description: miRNA profiling


title: liver cancer HC48

description: miRNA profiling


title: liver cancer HC39

description: miRNA profiling