title: 5617835071_F

description:
fresh frozen tissue
SAMPLE 53


title: 5617835071_B

status: Public on Mar 20 2012

type: RNA

city: Seoul

first: Cheol-Keun

last: Park

address: 50 Irwon-dong Kangnam-gu

country: South Korea

institute: Samsung Medical Center

description:
fresh frozen tissue
SAMPLE 52

hyb_protocol: RNA was hybridized to Human HT-12 v4 BeadChips from Illumina.

scan_protocol: Standard Illumina scanning protocol

data_processing: The software package to extract raw data was Genomestudio.

molecule: total RNA

organism: Homo sapiens

source_name: Liver Hepatocellular Carcinoma

label_protocol: Standard Illumina labeling protocol

extract_protocol: RNA was extracted using the Rneasy Plus Mini kit - Qiagen.

tag: tissue

value: adjacent non-tumor liver

tag: ajcc stage


title: 5617835105_H

description:
fresh frozen tissue
SAMPLE 50


title: 5617835105_E

description:
fresh frozen tissue
SAMPLE 49


title: n5958040041_B

description:
fresh frozen tissue
SAMPLE 57


title: n5958040041_L

description:
fresh frozen tissue
SAMPLE 59


title: 5617835105_D

description:
fresh frozen tissue
SAMPLE 48


title: 5617835105_K

description:
fresh frozen tissue
SAMPLE 51


title: 5617835105_B

description:
fresh frozen tissue
SAMPLE 47


title: 5617835070_K

description:
fresh frozen tissue
SAMPLE 46


title: 5617835104_F

description:
fresh frozen tissue
SAMPLE 42


title: 5617835069_I

description:
fresh frozen tissue
SAMPLE 40


title: 5617835069_E

description:
fresh frozen tissue
SAMPLE 39


title: 5617835104_D

description:
fresh frozen tissue
SAMPLE 41


title: 5617835069_A

description:
fresh frozen tissue
SAMPLE 38


title: 5617835070_I

description:
fresh frozen tissue
SAMPLE 45


title: 5617835070_C

description:
fresh frozen tissue
SAMPLE 44


title: 5617835103_K

description:
fresh frozen tissue
SAMPLE 37


title: 5617835103_D

description:
fresh frozen tissue
SAMPLE 34


title: 5617835104_I

description:
fresh frozen tissue
SAMPLE 43


title: 5617835068_J

description:
fresh frozen tissue
SAMPLE 32


title: 5617835103_A

description:
fresh frozen tissue
SAMPLE 33


title: 5617835065_K

description:
fresh frozen tissue
SAMPLE 16


title: 5617835092_L

description:
fresh frozen tissue
SAMPLE 19


title: 5617835066_E

description:
fresh frozen tissue
SAMPLE 21


title: 5617835093_J

description:
fresh frozen tissue
SAMPLE 27


title: 5617835066_K

description:
fresh frozen tissue
SAMPLE 23


title: 5617835068_A

description:
fresh frozen tissue
SAMPLE 28


title: 5617835068_E

description:
fresh frozen tissue
SAMPLE 30


title: 5617835103_E

description:
fresh frozen tissue
SAMPLE 35


title: 5617835066_H

description:
fresh frozen tissue
SAMPLE 22


title: 5617835103_I

description:
fresh frozen tissue
SAMPLE 36


title: 5617835092_J

description:
fresh frozen tissue
SAMPLE 18


title: 5617835086_J

description:
fresh frozen tissue
SAMPLE 12


title: 5617835068_C

description:
fresh frozen tissue
SAMPLE 29


title: 5617835068_I

description:
fresh frozen tissue
SAMPLE 31


title: 5617835066_A

description:
fresh frozen tissue
SAMPLE 20


title: 5617835093_E

description:
fresh frozen tissue
SAMPLE 25


title: 5617835093_H

description:
fresh frozen tissue
SAMPLE 26


title: 5617835093_B

description:
fresh frozen tissue
SAMPLE 24


title: 5617835086_K

description:
fresh frozen tissue
SAMPLE 13


title: 5617835086_G

description:
fresh frozen tissue
SAMPLE 11


title: 5617835065_C

description:
fresh frozen tissue
SAMPLE 14


title: 5617835064_K

description:
fresh frozen tissue
SAMPLE 9


title: 5617835086_E

description:
fresh frozen tissue
SAMPLE 10


title: 5617835064_G

description:
fresh frozen tissue
SAMPLE 8


title: 5617835064_B

description:
fresh frozen tissue
SAMPLE 6


title: 5617835064_C

description:
fresh frozen tissue
SAMPLE 7


title: 5617835092_G

description:
fresh frozen tissue
SAMPLE 17


title: 5617835065_H

description:
fresh frozen tissue
SAMPLE 15


title: 5617835179_E

description:
fresh frozen tissue
SAMPLE 5


title: 5617835061_L

description:
fresh frozen tissue
SAMPLE 3


title: HeLa S3 HBO1 control experiment 4

status: Public on Mar 15 2012

city: Lausanne

first: Eric

middle: R

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

description: HeLa S3 transduced with a control siRNA

hyb_protocol: Standard Illumina hybridization protocol

data_processing: Raw bead studio data were processed using R and the BioConductor package lumi. Data were log2 transformed and quantile normalized using subsequently the lumiT and lumiN functions.

label: biotin

source_name: cervical adenocarcinoma

growth_protocol: HeLa S3 cells were grown on 150mm plastic dishes at 37C, 5% CO2 to an approximate confluence of 90%

extract_protocol: Total cellular RNA was extracted with Trizol (Invitrogen) and purified using Macherey-Nagel NucleoSpin RNA II kit.

treatment_protocol: For JADE1 over-expression, HeLa S3 were infected with a retrovirus encoding FLAG-JADE1, and stable clones expressing the FLAG protein were isolated. For HBO1 knock-down, HeLa S3 cells were transiently transfected with siRNA directed against HBO1 using Invitrogen Oligofectamine as per manufacturer's protocol.

tag: cell line

value: HeLa

tag: treatment

value: HBO1 control


title: HeLa S3 HBO1 siRNA rep 4

description: HeLa S3 transiently transfected with HBO1 siRNA

label_protocol: Standard Illumina hybridization protocol

value: HBO1 siRNA


title: 5617835061_J

description:
fresh frozen tissue
SAMPLE 2


title: 5617835061_H

description:
fresh frozen tissue
SAMPLE 1


title: 5617835179_A

description:
fresh frozen tissue
SAMPLE 4


title: HeLa S3 HBO1 control experiment 3

description: HeLa S3 transduced with a control siRNA


title: HeLa S3 HBO1 siRNA rep 3


title: HL60_untreated 6110

status: Public on Mar 14 2012

city: New York

first: Hans-Ulrich

last: Klein

state: NY

department: Neurology

country: USA

institute: Columbia University Medical Center

description:
HL60_untreated
HL-60 cells were established from the peripheral blood of a 35-year-old woman with acute myeloid leukemia (AML FAB M2) in 1976. Collins,S.J., Gallo,R.C. & Gallagher,R.E. (1977). Continuous growth and differentiation of human myeloid leukaemic cells in suspension culture. Nature 270(5635):347-349.

hyb_protocol: Standard Illumina hybridization protocol: qualitative & quantitative quality controls were performed on the labelled cRNA and 750ng of labelled cRNA was hybridized to a Human HT-12(v4) Beadchip.

data_processing: Background values were subtracted and a variance-stabilizing transformation as described by Lin et al. (Nucleic Acids Res. 2008;36(2):e11) was applied. Finally, quantile normalization was applied.

label: Biotin

source_name: HL-60 cells

label_protocol: Samples were normalized to 200ng and were processed according to standard Illumina protocols using a Illumina TotalPrep-96 RNA Amplification Kit (Ambion).

growth_protocol: HL-60 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS, Sigma), 100 U/ml penicillin and 100μg/ml streptomycin. TEX cells were maintained in IMDM supplemented with 15% FBS, 20ng/ml stem cell factor (SCF, Peprotech) and 2ng/ml IL-3 (Peprotech).

extract_protocol: Total RNA stabilized with RNAlater (Ambion) was isolated using the ZR RNA MiniPrep Kit (Zymo Research). The concentration and quality of the total RNA was assessed by spectrophotometry and using a Agilent 2100 BioAnalyzer (Agilent Technologies).

treatment_protocol: Cells were treated with the above described all-trans-retinoic acid (ATRA, 0.1 µM, HL-60; 1µM, TEX), tranycypromine (TCP, 10 µM) or ATRA + tranycypromine drug combinations for 4 days prior to analysis. LSD1 shRNA #1, LSD1 shRNA #2 and scrambled control shRNA was stably transduced and treated with vehicle for 4 days.

value: vehicle

tag: batch


title: TEX_ATRA 6115

description:
TEX_ATRA
TEX cells are derived from primitive human cord blood cells immortalized by expression of the TLS-ERG oncogene. Warner, J.K., et al. Direct evidence for cooperating genetic events in the leukemic transformation of normal human hematopoietic cells. Leukemia 19, 1794-1805 (2005).

source_name: TEX cells

value: TEX

value: all-trans-retinoic acid


title: HL60_TCP 6112

description:
HL60_TCP
HL-60 cells were established from the peripheral blood of a 35-year-old woman with acute myeloid leukemia (AML FAB M2) in 1976. Collins,S.J., Gallo,R.C. & Gallagher,R.E. (1977). Continuous growth and differentiation of human myeloid leukaemic cells in suspension culture. Nature 270(5635):347-349.

value: tranycypromine


title: TEX_ATRA 6099


title: HL60_shScram 6103

description:
HL60_shScram
HL-60 cells were established from the peripheral blood of a 35-year-old woman with acute myeloid leukemia (AML FAB M2) in 1976. Collins,S.J., Gallo,R.C. & Gallagher,R.E. (1977). Continuous growth and differentiation of human myeloid leukaemic cells in suspension culture. Nature 270(5635):347-349.

value: scrambled control shRNA


title: HL60_shLSD1#1 6104

description:
HL60_shLSD1#1
HL-60 cells were established from the peripheral blood of a 35-year-old woman with acute myeloid leukemia (AML FAB M2) in 1976. Collins,S.J., Gallo,R.C. & Gallagher,R.E. (1977). Continuous growth and differentiation of human myeloid leukaemic cells in suspension culture. Nature 270(5635):347-349.

value: LSD1 shRNA #1


title: TEX_untreated 6114

description:
TEX_untreated
TEX cells are derived from primitive human cord blood cells immortalized by expression of the TLS-ERG oncogene. Warner, J.K., et al. Direct evidence for cooperating genetic events in the leukemic transformation of normal human hematopoietic cells. Leukemia 19, 1794-1805 (2005).


title: HL60_ATRA 6111

description:
HL60_ATRA
HL-60 cells were established from the peripheral blood of a 35-year-old woman with acute myeloid leukemia (AML FAB M2) in 1976. Collins,S.J., Gallo,R.C. & Gallagher,R.E. (1977). Continuous growth and differentiation of human myeloid leukaemic cells in suspension culture. Nature 270(5635):347-349.


title: TEX_TCP 6100

description:
TEX_TCP
TEX cells are derived from primitive human cord blood cells immortalized by expression of the TLS-ERG oncogene. Warner, J.K., et al. Direct evidence for cooperating genetic events in the leukemic transformation of normal human hematopoietic cells. Leukemia 19, 1794-1805 (2005).


title: TEX_ATRA+TCP 6101

description:
TEX_ATRA+TCP
TEX cells are derived from primitive human cord blood cells immortalized by expression of the TLS-ERG oncogene. Warner, J.K., et al. Direct evidence for cooperating genetic events in the leukemic transformation of normal human hematopoietic cells. Leukemia 19, 1794-1805 (2005).

value: all-trans-retinoic acid and tranylcypromine


title: HL60_shLSD1#2 6105

description:
HL60_shLSD1#2
HL-60 cells were established from the peripheral blood of a 35-year-old woman with acute myeloid leukemia (AML FAB M2) in 1976. Collins,S.J., Gallo,R.C. & Gallagher,R.E. (1977). Continuous growth and differentiation of human myeloid leukaemic cells in suspension culture. Nature 270(5635):347-349.

value: LSD1 shRNA #2


title: HL60_ATRA+TCP 6113

description:
HL60_ATRA+TCP
HL-60 cells were established from the peripheral blood of a 35-year-old woman with acute myeloid leukemia (AML FAB M2) in 1976. Collins,S.J., Gallo,R.C. & Gallagher,R.E. (1977). Continuous growth and differentiation of human myeloid leukaemic cells in suspension culture. Nature 270(5635):347-349.


title: HL60_TCP 6096


title: TEX_untreated 6098


title: TEX_untreated 5700


title: TEX_TCP 6116


title: HL60_ATRA+TCP 6097


title: HL60_ATRA 6095


title: TEX_ATRA+TCP 6117


title: TEX_ATRA+TCP 5703


title: HL60_shScram 5694


title: HL60_untreated 6094


title: HL60_shLSD1#2 5696


title: HL60_ATRA 5689


title: HL60_untreated 5688


title: TEX_ATRA 5701


title: TEX_TCP 5702


title: HL60_shLSD1#1 5695


title: HL60_TCP 5690


title: MCAS bez235 6hr rep3

status: Public on Mar 13 2012

city: Boston

first: Joan

middle: S.

last: Brugge

state: MA

address: 240 Longwood Avenue

department: Department of Cell Biology

institute: Harvard Medical School

description: replicate 3

hyb_protocol: cRNA was hybridized to the Illumina HumanHT-12 v4 Expression BeadChips and processed according to the manufacturer’s protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data processing was performed using GenomeStudio software (Illumina, Inc.).  Background was subtracted and arrays were normalized using quantile.

source_name: MCAS ovarian cancer cell line

label_protocol: Total RNA was isolated according to manufacturer’s protocol with TRIzol-reagent (Invitrogen).

growth_protocol: Cells were passaged in 1:1 mixture of MCDB105 (Cell Applications Inc.) and 199 (Gibco) media supplemented with inactivated calf serum (Gibco), 2mM L-glutamine (Gibco) and penicillin-streptomycin (Gibco). Cells were routinely cultured in 37°C with 5% CO2.  Cells were seeded on polyHEMA (Sigma #192066) coated (6mg/ml in 95% EtOH and allowed to dry completely) 24-well plates, 20000 cells/well, in 750μl of media supplemented with 2% serum and 2% Matrigel and allowed to grow for 4 days. All samples were prepared in triplicate.

extract_protocol: At the indicated timepoints, six wells for each conditioned were pooled and cells were harvested.

treatment_protocol: Cells were fed with 750μl of media supplemented with 2% serum and 2% Matrigel and 1μm NVP-BEZ235 or DMSO vehicle control.

value: MCAS

value: 1 μM NVP-BEZ235

tag: timepoint

value: 6 hours

tag: culture condition

value: 3D culture (2% serum, 2% matrigel)


title: MCAS bez235 6hr rep1

description: replicate 1


title: MCAS bez235 6hr rep2

description: replicate 2


title: MCAS bez235 24hr rep2

description: replicate 2

value: 24 hours


title: MCAS dmso 24hr rep1

description: replicate 1

value: dmso vehicle control


title: MCAS dmso 6hr rep3

description: replicate 3


title: MCAS dmso 6hr rep1

description: replicate 1


title: OV2008 bez235 24hr rep3

description: replicate 3

source_name: OV2008 ovarian cancer cell line


title: MCAS bez235 24hr rep3

description: replicate 3


title: MCAS dmso 6hr rep2

description: replicate 2


title: HL60_ATRA+TCP 5691


title: MCAS bez235 24hr rep1

description: replicate 1


title: OV2008 bez235 6hr rep3

description: replicate 3


title: MCAS dmso 24hr rep2

description: replicate 2


title: OV2008 bez235 24hr rep2

description: replicate 2


title: OV2008 dmso 24hr rep1

description: replicate 1


title: OV2008 bez235 24hr rep1

description: replicate 1


title: OV2008 dmso 24hr rep2

description: replicate 2


title: MCAS dmso 24hr rep3

description: replicate 3


title: OV2008 bez235 6hr rep1

description: replicate 1


title: OV2008 dmso 24hr rep3

description: replicate 3


title: OV2008 bez235 6hr rep2

description: replicate 2


title: OV2008 dmso 6hr rep1

description: replicate 1


title: HCC_primary_HB10

status: Public on Mar 10 2012

city: Tokyo

first: Tatsuhiro

last: Shibata

address: 5-1-1, Tsukiji, Chuo-ku

country: Japan

institute: National Cancer Center

description: RNA extraction from primary tumor

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

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

source_name: primary HCC

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).

extract_protocol: RNA was prepared using the RNAeasy (Qiagen). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: liver

tag: cell type

value: primary hepatocellular carcinoma


title: HCC_primary_HC10

description: RNA extraction from primary tumor


title: HCC_primary_HB11

description: RNA extraction from primary tumor


title: HCC_primary_HC13

description: RNA extraction from primary tumor


title: HCC_primary_HB7

description: RNA extraction from primary tumor


title: HCC_primary_HC8

description: RNA extraction from primary tumor


title: HCC_primary_HB8

description: RNA extraction from primary tumor


title: Control

status: Public on Mar 09 2012

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

description: Samples collected from Human liver

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

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

data_processing: MAS5 normalization method of Affymetrix

source_name: Control

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

growth_protocol: Primary Human Hepatocytes Were Isolated and Plated on 12 well plates at the University of Pittsburgh in the Laboratory of Dr. Stehphen Strom and provided through the NIH funded Liver Tissue and Cell Distribution System (LTCDS)

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

value: Control

value: primary hepatocyte


title: OV2008 dmso 6hr rep2

description: replicate 2


title: OV2008 dmso 6hr rep3

description: replicate 3


title: IL28B 6 h

description: Samples collected from Human liver

treatment_protocol: RNA was isolated after 6, 12, and 24 h treatment with IFN-α (10 U/mL) or IL28B (25 ng/mL)

tag: time

value: 6 h


title: IFNalpha 6 h

description: Samples collected from Human liver

source_name: IFNalpha

value: IFNalpha


title: IFNalpha 24 h

description: Samples collected from Human liver


title: T Poly IC

description: Samples collected from Human liver

source_name: T Poly IC

value: T Poly IC


title: IL28B 24 h

description: Samples collected from Human liver


title: Harvard Sib CHB1000006581

status: Public on Feb 24 2012

type: genomic

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

description: Harvard.Sib

scan_protocol: Followed the manufacturer's (Illumina) specifications on either a BeadStation 500 or an iScan

data_processing: Avg beta (β), detection value, and signal for Probe A (unmethylated) and Probe B were exported from GenomeStudio v2010.3 Methylation Module 1.8.5. The manufacturer measures methylation through the beta (β) value calculated as probe B signal / (probe A signal + probe B signal + 100). Based on better reproducibility of the controls we calculated the methylation using a metric denoted beta prime (β') which is calculated as probe B signal / (probe A signal + probe B signal).

label: biotin nucleotide or dinitrophenyl labeled

molecule: genomic DNA

source_name: leukocyte

label_protocol: A single nucleotide extension was labeled either with biotin or dinitrophenyl according to the manufacturer's (Illumina) specifications

extract_protocol: DNA was extracted by the Rutgers University Cell and DNA Repository RUCDR

treatment_protocol: Extracted DNA was bisulfite treated with the Zymo bisulfite kit according the manufacturer's specifications

tag: group

tag: gender

value: M

tag: sentrix id

tag: sentrix position

tag: experiment

tag: age at collection months

tag: ethnicity

value: Black

value: leukocyte


title: Harvard Sib CHB1000006607

description: Harvard.Sib

hyb_protocol: Followed the manufacturer's (Illumina) specifications


title: Harvard Sib CHB1000005952

description: Harvard.Sib


title: Harvard Sib CHB1000005894

description: Harvard.Sib


title: Harvard Sib CHB1000005666

description: Harvard.Sib


title: Harvard Sib CHB1000005938

description: Harvard.Sib


title: Harvard Sib CHB1000005854

description: Harvard.Sib


title: Harvard Sib CHB1000005860

description: Harvard.Sib


title: Harvard Sib CHB1000006567

description: Harvard.Sib

value: Asian


title: Harvard Sib CHB1000009633

description: Harvard.Sib


title: Harvard Sib CHB1000006571

description: Harvard.Sib


title: Harvard Sib CHB1000005714

description: Harvard.Sib


title: Harvard Sib CHB1000005670

description: Harvard.Sib


title: Harvard Sib CHB1000005856

description: Harvard.Sib


title: Harvard Sib CHB1000009635

description: Harvard.Sib


title: Harvard Sib CHB1000005690

description: Harvard.Sib


title: Harvard Sib CHB1000006593

description: Harvard.Sib


title: Harvard Sib CHB1000005684

description: Harvard.Sib


title: Harvard Sib CHB1000009609

description: Harvard.Sib


title: Harvard Sib CHB1000005898

description: Harvard.Sib


title: Harvard Sib CHB1000005708

description: Harvard.Sib


title: Harvard Sib CHB1000005662

description: Harvard.Sib


title: Harvard Sib CHB1000006585

description: Harvard.Sib


title: Harvard Sib CHB1000006601

description: Harvard.Sib


title: Harvard Sib CHB1000005700

description: Harvard.Sib


title: Harvard Sib CHB1000006605

description: Harvard.Sib


title: Harvard Sib CHB1000009629

description: Harvard.Sib


title: Harvard Sib CHB1000005702

description: Harvard.Sib


title: Harvard Sib CHB1000005942

description: Harvard.Sib


title: Harvard Sib CHB1000005908

description: Harvard.Sib


title: Harvard Sib CHB1000009631

description: Harvard.Sib


title: Harvard Sib CHB1000005924

description: Harvard.Sib


title: Harvard Sib CHB1000006597

description: Harvard.Sib


title: pristine protocol biopsy pPB10

status: Public on Feb 17 2012

city: Edmonton

first: Konrad

middle: S

last: Famulski

state: Alberta

address: 250 HMRC

country: Canada

institute: University of Alberta

description: Samples with the same initial numbers in the sample names are replicates from the same patient. For the main analysis, only the earliest biopsy per patient was used, and only in those patients with a biopsy taken > 1 year post-transplant

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HGU133 Plus 2.0 Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Gene Array Scanner (Affymetrix) and processed with GeneChip Operating Software Version 1.4.0 (Affynetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

source_name: protocol biopsy

label_protocol: RNA (1-2µg) was labeled using GeneChip HT One-Cycle Target Labeling and Control kit. Quality of labeled cRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to HGU133Plus2.0. GeneChip (Affymetrix, Santa Clara, CA).

growth_protocol: All human renal allograft biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

extract_protocol: Following homogenization of the tissue in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA), total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 4µg/core, (RNA integrity number >7).

treatment_protocol: The immunosuppressive treatment of the patients before the biopsy was based on individual treatment regiments; the treatment after the biopsy was adjusted based on the histopathological diagnosis.

tag: diagnosis

value: pristine protocol biopsy

value: kidney


title: pristine protocol biopsy pPB1

tag: tissue


title: pristine protocol biopsy pPB4


title: PDCCE_FFPE_CRC057

city: Durham

first: David

last: Hsu

state: NC

address: Rm 2167 CIEMAS Bldg, 101 Science Dr.

department: Institute for Genome Sciences and Policy

institute: Duke University

hyb_protocol: The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).

data_processing: The gene expression data were RMA-estimated using the R statistical platform with the Bioconductor affymetrix package.

source_name: mouse derived colorectal explant tumor, colon primary, liver metastasis, formalin-fixed overnight, paraffin-embedded tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Colorectal cancer cells extracted from previously generated explants were injected subcutaneously into the flanks of JAX NOD.CB17-PrkdcSCID-J mice (four-week-old female) and measured every 2-3 days with a vernier caliper until the volume of the tumor (V = L×2W×0.52 (L = longest diameter, W = shortest diameter)) reached approximately 500 mm³. Tumors were grown for three additional weeks then were harvested and placed into formalin overnight and paraffin-embedded the next day.

extract_protocol: FFPE PDCCE samples were sectioned at 10 μm and placed onto histological slides. An initial section was stained with hematoxylin and eosin for histological characterization of the tissue to ensure > 80% tumor. RNA was then isolated from 8-10m FFPE sections using the RecoverAll-MagMAX Custom Kit and protocol (Applied Biosystems, Foster City, CA) with the following modifications: RNA isolation digestions were incubated at 50°C for 15 minutes and then at 80°C for 15 minutes; Lysis Binding Solution was reconstituted using 22 ml of 100% isopropanol (Mallinckrodt Chemicals, Phillipsburg, NJ); Wash Solution 1H was reconstituted using 12 ml of 100% isopropanol (Mallinckrodt Chemicals); and Wash Solution 2 was reconstituted using 44 ml of 100% ethanol (Pharmco-Aaper, Brookfield, CT).

treatment_protocol: PDCCE FFPE samples were treated with saline by intraperitoneal injection for 2.5 weeks.

tag: primary tumor site

value: Colon

tag: metastatic tumor site

value: Liver


title: pristine protocol biopsy pPB3


title: PDCCE_FFPE_CRC075


title: Harvard Sib CHB1000007287

description: Harvard.Sib


title: PDCCE_FFPE_CRC067


title: PDCCE_FFPE_CRC102


title: PDCCE_FFPE_CRC059

source_name: mouse derived colorectal explant tumor, colon primary, formalin-fixed overnight, paraffin-embedded tissue


title: PDCCE_FFPE_CRC105


title: Harvard Sib CHB1000006611

description: Harvard.Sib


title: PDCCE_FFPE_CRC054

source_name: mouse derived colorectal explant tumor, colon primary, lung metastasis, formalin-fixed overnight, paraffin-embedded tissue

value: Lung


title: Harvard Sib CHB1000006577

description: Harvard.Sib


title: PDCCE_FFPE_CRC034


title: PDCCE_FFPE_CRC039


title: Harvard Sib CHB1000005826

description: Harvard.Sib


title: PDCCE_FFPE_CRC010


title: Harvard Sib CHB1000006573

description: Harvard.Sib


title: Harvard Sib CHB1000005914

description: Harvard.Sib


title: PDCCE_FreshFrozen_CRC105

source_name: mouse derived colorectal explant tumor, colon primary, liver metastasis, fresh frozen tissue

growth_protocol: Colorectal cancer cells extracted from previously generated explants were injected subcutaneously into the flanks of JAX NOD.CB17-PrkdcSCID-J mice (four-week-old female) and measured every 2-3 days with a vernier caliper until the volume of the tumor (V = L×2W×0.52 (L = longest diameter, W = shortest diameter)) reached approximately 500 mm³. Tumors were grown for three additional weeks then were harvested and flash frozen.

extract_protocol: Frozen PDCCE samples were sectioned at 8µm and placed onto histological slides. An initial section was stained with hematoxylin and eosin (Sigma) for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 µg of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, CA). RNA were quantified using a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE), and quality was assessed by spectrophotomeric analysis on an Agilent 2100 Bioanalyzer conductor using the RNA 6000 nano assay Kit (Agilent Technologies, Santa Clara, CA).

treatment_protocol: PDCCE samples were treated with saline by intraperitoneal injection for 2.5 weeks.


title: PDCCE_FFPE_CRC025

source_name: mouse derived colorectal explant tumor, rectal primary, lung metastasis, formalin-fixed overnight, paraffin-embedded tissue

value: Rectal


title: Harvard Sib CHB1000005880

description: Harvard.Sib


title: PDCCE_FreshFrozen_CRC075


title: PDCCE_FFPE_CRC028


title: Harvard Sib CHB1000006609

description: Harvard.Sib


title: Harvard Sib CHB1000005836

description: Harvard.Sib


title: PDCCE_FFPE_CRC007


title: Harvard Sib CHB1000005834

description: Harvard.Sib


title: Harvard Sib CHB1000005864

description: Harvard.Sib


title: Harvard Sib CHB1000005870

description: Harvard.Sib


title: PDCCE_FreshFrozen_CRC059

source_name: mouse derived colorectal explant tumor, colon primary, fresh frozen tissue


title: PDCCE_FreshFrozen_CRC067


title: PDCCE_FreshFrozen_CRC102


title: PDCCE_FreshFrozen_CRC057


title: PDCCE_FreshFrozen_CRC054

source_name: mouse derived colorectal explant tumor, colon primary, lung metastasis, fresh frozen tissue


title: PDCCE_FreshFrozen_CRC010


title: PDCCE_FreshFrozen_CRC039


title: PDCCE_FreshFrozen_CRC034


title: PDCCE_FreshFrozen_CRC012


title: HumanTumor_FreshFrozen_CRC059

source_name: human tumor, colon primary, fresh frozen tissue

extract_protocol: Tumors were flash frozen in OCT at time of surgical resection. An initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca).


title: PDCCE_FreshFrozen_CRC025

source_name: mouse derived colorectal explant tumor, rectal primary, lung metastasis, fresh frozen tissue


title: HumanTumor_FreshFrozen_CRC057

source_name: human tumor, colon primary, liver metastasis, fresh frozen tissue


title: HumanTumor_FreshFrozen_CRC075


title: PDCCE_FreshFrozen_CRC007

description: PDCCE Fresh Frozen CRC007


title: HumanTumor_FreshFrozen_CRC067


title: HumanTumor_FreshFrozen_CRC054

source_name: human tumor, colon primary, lung metastasis, fresh frozen tissue


title: HumanTumor_FreshFrozen_CRC039


title: Harvard Sib CHB1000005896

description: Harvard.Sib


title: PDCCE_FreshFrozen_CRC028


title: HumanTumor_FreshFrozen_CRC034


title: HumanTumor_FreshFrozen_CRC028


title: HumanTumor_FreshFrozen_CRC010


title: HumanTumor_FreshFrozen_CRC007


title: HumanTumor_FreshFrozen_CRC102


title: Untreated cells with Poly(I:C) stimulation rep 2

status: Public on Feb 15 2012

city: new york

first: ivan

last: marazzi

state: ny

address: 1230 York Avenue

institute: rockefeller univeristy

description:
untreated_PolyIC_rep_2
Replicate 2

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Data was analysed using Genespring GX11.0 . To analyze gene expression changes from hPAF1 siRNA treatment, raw data were subject to quantile normalization and baseline transformation was performed to the median of all unstimulated samples. non_normalized.txt = log2-transformed; normalized data matrix = After quantile normalization and baseline transformation performed in Genespring GX11.0

label_protocol: Biotin-labeled RNA was prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems)

growth_protocol: Standard culture techniques

extract_protocol: QIAGEN Rneasy mini kit

treatment_protocol: For siRNA treatments, cells were transfected using Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen) according to the manufacturer’s instructions. siRNA pools targeted to either human PAF1 (L-020349-01, Dharmacon), CHD1 (L-008529-00, Dharmacon) or a control non-targeting pool (D-001810-10-05, Dharmacon) were transfected at a final siRNA concentration of 50 nM. Transfected cells were stimulated with the appropriate stimuli 48 hours post transfection. Gene knockdown efficiency was determined by quantitative PCR and/or Western blotting. For stimulations, cells were infected with A/Puerto Rico/8/1934(ΔNS1) (PR8/∆NS1) at MOI 1 or stimulated with recombinant human IFN beta 1a (IFNβ1) (11415-1, PBL Interferon Source). Where cells were stimulated with IFNβ1, a concentration of 500 units/mL of cytokine was used. For Poly(I:C) stimulations, cells were transfected with Poly(I:C) at a final concentration of 2 µg/ml using the Lipofectamine2000 reagent (Invitrogen).

tag: cell line background

tag: sirna

value: No siRNA

tag: stimulation

value: 2µg/mL Poly(I:C)


title: Control siRNA treated cells with Poly(I:C) stimulation rep 3

description:
siControl_PolyIC_rep_3
Replicate 3

value: Control siRNA


title: Control siRNA treated cells with Poly(I:C) stimulation rep 2

description:
siControl_PolyIC_rep_2
Replicate 2


title: hPAF1 siRNA treated cells with Poly(I:C) stimulation infection rep 2

description:
siPAF_PolyIC_rep_2
Replicate 2

value: hPAF1 siRNA


title: hPAF1 siRNA treated cells with Poly(I:C) stimulation infection rep 1

description:
siPAF_PolyIC_rep_1
Replicate 1


title: Control siRNA treated cells with Poly(I:C) stimulation rep 1

description:
siControl_PolyIC_rep_1
Replicate 1


title: Untreated cells with IFNβ1 stimulation rep 1

description:
untreated_IFNB_rep_1
Replicate 1

value: 500U/mL IFNβ1


title: Untreated cells with IFNβ1 stimulation rep 2

description:
untreated_IFNB_rep_2
Replicate 2


title: hPAF1 siRNA treated cells with IFNβ1 stimulation infection rep 3

description:
siPAF_IFNB_rep_3
Replicate 3


title: Untreated cells with IFNβ1 stimulation rep 3

description:
untreated_IFNB_rep_3
Replicate 3


title: Control siRNA treated cells with IFNβ1 stimulation rep 2

description:
siControl_IFNB_rep_2
Replicate 2


title: Control siRNA treated cells with IFNβ1 stimulation rep 1

description:
siControl_IFNB_rep_1
Replicate 1


title: HumanTumor_FreshFrozen_CRC012


title: Untreated cells with Poly(I:C) stimulation rep 1

description:
untreated_PolyIC_rep_1
Replicate 1


title: hPAF1 siRNA treated cells with Poly(I:C) stimulation infection rep 3

description:
siPAF_PolyIC_rep_3
Replicate 3


title: hPAF1 siRNA treated cells with IFNβ1 stimulation infection rep 1

description:
siPAF_IFNB_rep_1
Replicate 1


title: hPAF1 siRNA treated cells with PR8/∆NS1 infection rep 2

description:
siPAF_dNS1_rep_2
Replicate 2


title: Control siRNA treated cells with IFNβ1 stimulation rep 3

description:
siControl_IFNB_rep_3
Replicate 3


title: Untreated cells with Poly(I:C) stimulation rep 3

description:
untreated_PolyIC_rep_3
Replicate 3


title: hPAF1 siRNA treated cells with PR8/∆NS1 infection rep 1

description:
siPAF_dNS1_rep_1
Replicate 1


title: PDCCE_FFPE_CRC012


title: Control siRNA treated cells with PR8/∆NS1 infection rep 3

description:
siControl_dNS1_rep_3
Replicate 3


title: hPAF1 siRNA treated cells with IFNβ1 stimulation infection rep 2

description:
siPAF_IFNB_rep_2
Replicate 2


title: Control siRNA treated cells with PR8/∆NS1 infection rep 2

description:
siControl_dNS1_rep_2
Replicate 2


title: Control siRNA treated cells with PR8/∆NS1 infection rep 1

description:
siControl_dNS1_rep_1
Replicate 1


title: hPAF1 siRNA treated cells rep 3

description:
siPAF_unstimulated_rep_3
Replicate 3

source_name: A549_hPAF1 siRNA_treated_unstimulated

value: Unstimulated


title: Untreated cells with PR8/∆NS1 infection rep 2

description:
untreated_dNS1_rep_2
Replicate 2


title: Control siRNA treated cells rep 1

description:
siControl_unstimulated_rep_1
Replicate 1

source_name: A549_Control siRNA_treated_unstimulated


title: Control siRNA treated cells rep 3

description:
siControl_unstimulated_rep_3
Replicate 3


title: Untreated cells with PR8/∆NS1 infection rep 1

description:
untreated_dNS1_rep_1
Replicate 1


title: hPAF1 siRNA treated cells rep 2

description:
siPAF_unstimulated_rep_2
Replicate 2


title: Untreated cells rep 3

description:
untreated_unstimulated_rep_3
Replicate 3


title: Control siRNA treated cells with VSV infection rep 1

description:
siControl_VSV_rep_1
Replicate 1

treatment_protocol: For siRNA treatments, cells were transfected using Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen) according to the manufacturer’s instructions. siRNA pools targeted to either human PAF1 (L-020349-01, Dharmacon), CHD1 (L-008529-00, Dharmacon) or a control non-targeting pool (D-001810-10-05, Dharmacon) were transfected at a final siRNA concentration of 50 nM. Transfected cells were stimulated with the appropriate stimuli 48 hours post transfection. Gene knockdown efficiency was determined by quantitative PCR and/or Western blotting. For infections, the A/Puerto Rico/8/1934 influenza virus (H1N1) strain was used at MOI 3.  Infections with vesicular stomatitis virus (Indiana strain) were done at MOI 3.

value: vesicular stomatitis virus (VSV)


title: Control siRNA treated cells rep 2

description:
siControl_unstimulated_rep_2
Replicate 2


title: Control siRNA treated cells with VSV infection rep 3

description:
siControl_VSV_rep_3
Replicate 3


title: Untreated cells with VSV infection rep 2

description:
untreated_VSV_rep_2
Replicate 2


title: hPAF1 siRNA treated cells with VSV infection infection rep 2

description:
siPAF_VSV_rep_2
Replicate 2


title: Untreated cells rep 1

description:
untreated_unstimulated_rep_1
Replicate 1


title: hPAF1 siRNA treated cells with VSV infection infection rep 1

description:
siPAF_VSV_rep_1
Replicate 1


title: hPAF1 siRNA treated cells with VSV infection infection rep 3

description:
siPAF_VSV_rep_3
Replicate 3


title: hPAF1 siRNA treated cells rep 1

description:
siPAF_unstimulated_rep_1
Replicate 1


title: Untreated cells with VSV infection rep 3

description:
untreated_VSV_rep_3
Replicate 3


title: Control siRNA treated cells with VSV infection rep 2

description:
siControl_VSV_rep_2
Replicate 2


title: Untreated cells with PR8/∆NS1 infection rep 3

description:
untreated_dNS1_rep_3
Replicate 3


title: hPAF1 siRNA treated cells with PR8/∆NS1 infection rep 3

description:
siPAF_dNS1_rep_3
Replicate 3


title: Untreated cells rep 2

description:
untreated_unstimulated_rep_2
Replicate 2


title: Untreated cells with VSV infection rep 1

description:
untreated_VSV_rep_1
Replicate 1


title: HumanTumor_FreshFrozen_CRC105


title: hPAF1 siRNA treated cells with H1N1 infection rep 3

description:
siPAF_H1N1_rep_3
Replicate 3

value: A/Puerto Rico/8/1934 influenza virus (H1N1)


title: hPAF1 siRNA treated cells with H1N1 infection rep 2

description:
siPAF_H1N1_rep_2
Replicate 2


title: Control siRNA treated cells with H1N1 infection rep 3

description:
siControl_H1N1_rep_3
Replicate 3


title: hPAF1 siRNA treated cells with H1N1 infection rep 1

description:
siPAF_H1N1_rep_1
Replicate 1


title: Control siRNA treated cells with H1N1 infection rep 1

description:
siControl_H1N1_rep_1
Replicate 1


title: Control siRNA treated cells with H1N1 infection rep 2

description:
siControl_H1N1_rep_2
Replicate 2


title: Untreated cells with H1N1 infection rep 3

description:
untreated_H1N1_rep_3
Replicate 3


title: hPAF1 siRNA treated cells rep 1

description:
siPAF_unstimulated_rep_1
Replicate 1


title: Untreated cells rep 3


title: hPAF1 siRNA treated cells rep 2

description:
siPAF_unstimulated_rep_2
Replicate 2


title: Untreated cells rep 1


title: Control siRNA treated cells rep 1

source_name: A549_control siRNA_treated_unstimulated


title: Control siRNA treated cells rep 2


title: hPAF1 siRNA treated cells rep 3

description:
siPAF_unstimulated_rep_3
Replicate 3


title: Control siRNA treated cells rep 3


title: hPAF1 siRNA treated cells rep 3

description:
siPAF_unstimulated_rep_3
Replicate 3

data_processing: Data was analysed using Genespring GX11.0 . To analyze gene expression changes from hPAF1 siRNA treatment, raw data were subject to quantile normalization and baseline transformation was performed to the median of all unstimulated samples. non_normalized.txt = log2-transformed ; normalized data matrix = After quantile normalization and baseline transformation performed in Genespring GX11.0

treatment_protocol: For siRNA treatments, cells were transfected using Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen) according to the manufacturer’s instructions. siRNA pools targeted to either human PAF1 (L-020349-01, Dharmacon), CHD1 (L-008529-00, Dharmacon) or a control non-targeting pool (D-001810-10-05, Dharmacon) were transfected at a final siRNA concentration of 50 nM. Transfected cells were used for further experiments 48 hours post transfection. Gene knockdown efficiency was determined by quantitative PCR and/or Western blotting.

value: unstimulated


title: hPAF1 siRNA treated cells rep 1

description:
siPAF_unstimulated_rep_1
Replicate 1


title: Untreated cells rep 2


title: HumanTumor_FreshFrozen_CRC025

source_name: human tumor, rectal primary, lung metastasis, fresh frozen tissue


title: Untreated cells rep 1


title: Untreated cells with H1N1 infection rep 1

description:
untreated_H1N1_rep_1
Replicate 1


title: OxPAPC-treated

status: Public on Feb 14 2012

city: Los Angeles

first: James

middle: Robert

last: Springstead

state: CA

address: 3210 MRL, 10833 Le Conte Ave

department: Medicine-Cardiology

institute: UCLA

scan_protocol: Standard Illumina scan protocol

data_processing: Data were analyzed using the Genome Studio software package.  During data analysis, data were analyzed using background subtraction, quantile normalization, and the content descriptor file ‘HumanHT-12_V4_0_R1_15002873_B.bgx’ in the Genome Studio files.  The data were filtered for results with either the detection p value less than 0.001 for the 15dPGJ2/OxPAPC RNA measurement or for the control measurement.  The fold changes in probes were calculated as the average probe level for each treatment divided by the average probe level for control treatment and converted to log 2 values to analyze for gene regulation.  Upregulated / downregulated genes were identified as those which changed at least 1.25 fold from control values in the presence of lipids.

source_name: HAEC

label_protocol: Illumina protocol

extract_protocol: Wash w/PBS, RNA lysis buffer

treatment_protocol: Duplicate wells of HAECs were treated with 1% M199 media or media containing 64µM OxPAPC, 5µM PEIPC or 5µM 15dPGJ2 for 4 hours at 37C and RNA was extracted.

tag: treatment

value: OxPAPC

value: human aorta endothelial cell


title: Untreated cells rep 2


title: Control

label_protocol:
Illumina protocol
Illumina protocol

value: none, media (1%FBS, 99%M199)

tag: cell type


title: Untreated cells rep 3


title: 15dPGJ2-treated


title: Control siRNA treated cells rep 3


title: hPAF1 siRNA treated cells rep 2

description:
siPAF_unstimulated_rep_2
Replicate 2


title: Control siRNA treated cells rep 1


title: MDA436_cell_line_10nMAG_rep1

status: Public on Jan 19 2012

city: Lund

first: Ida

last: Johansson

address: Department of Oncology Clinical Sciences Lund University BMC C13

department: Oncology

country: Sweden

institute: Lund University

description: replicate 5

data_processing: The data were normalised using qQuantile and probes with a p-value large than 0.01 were filter out in BASE2.

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

extract_protocol: Total RNA was extracted using the Qiagen RNA Mini kit (Qiagen, Valencia, CA)

tag: cell line

tag: replicate


title: MDA436_cell_line_DMSO_rep2

description: replicate 1

value: DMSO


title: Control siRNA treated cells rep 2


title: MDA436_cell_line_DMSO_rep3

description: replicate 1


title: MDA436_cell_line_LY_rep1

description: replicate 2

value: LY


title: MDA436_cell_line_100nMAG_LY_rep1

description: replicate 4

value: 100nMAG LY


title: MDA436_cell_line_DMSO_rep1

description: replicate 1


title: MDA436_cell_line_LY_rep2

description: replicate 2


title: MDA436_cell_line_100nMAG_rep1

description: replicate 3


title: MDA436_cell_line_100nMAG_rep3

description: replicate 3


title: MDA436_cell_line_100nMAG_LY_rep2

description: replicate 4


title: MDA436_cell_line_100nMAG_LY_rep3

description: replicate 4


title: MDA436_cell_line_10nMAG_rep2

description: replicate 5


title: MDA436_cell_line_100nMAG_rep2

description: replicate 3


title: Compound 1-14(1uM) 6h

status: Public on Jan 17 2012

city: Dallas

first: liang

last: zhang

state: Texas

address: 5323 harry hines blvd k2.202

institute: utsw

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

source_name: HBEC_Compound 1-14_1uM_6h

label_protocol: Biotinylated cRNA were prepared according  to UT Southwestern Microarray protocol for Illumina arrays

growth_protocol: HBEC cells were plated in 10 cm diameter dishes in keratinocyte serum-free medium and grown overnight to just reach confluency.

extract_protocol: For each sample total RNA was isolated with RNeasy Mini Kit and RNA was delivered to the UT Southwestern Microarray Core Facility.

treatment_protocol: Reagents were added at the concentrations and for the times listed on each sample.

value: HBEC

tag: tissue origin

value: bronchial


title: nuclear RNA after NS1 transfection (16h) and DMSO treatment(24h)

source_name: nuclear RNA_NS1 transfection_DMSO

growth_protocol: 293T cells were plated in 10 cm diameter dishes in DMEM containing 10% fetal calf serum.

extract_protocol: For each sample total/cytoplasmic/nuclear RNA was isolated with Trizol and RNA was delivered to the UT Southwestern Microarray Core Facility.

tag: tissue source

value: kidney


title: nuclear RNA after empty vector transfection (16h) and compound 1(5uM) treatment(24h)

source_name: nuclear RNA_empty vector transfection_compound 1 (5uM)


title: nuclear RNA after NS1 transfection (16h) and compound 1(5uM) treatment(24h)

source_name: nuclear RNA_NS1 transfection_compound 1 (5uM)


title: Compound 1-14(1uM) 12h

source_name: HBEC_Compound 1-14_1uM_12h


title: Compound 1(5uM) 6h

source_name: HBEC_Compound 1_5uM_6h


title: DMSO 12h

source_name: HBEC_DMSO 12h


title: nuclear RNA after empty vector transfection (16h) and DMSO treatment(24h)

source_name: nuclear RNA_empty vector transfection_DMSO


title: DMSO 6h

source_name: HBEC_DMSO 6h


title: Compound 1(5uM) 12h

source_name: HBEC_Compound 1_5uM_12h


title: total RNA after NS1 transfection (16h) and compound 1(5uM) treatment(24h)

source_name: total RNA_NS1 transfection_compound 1 (5uM)


title: MDA436_cell_line_LY_rep3

description: replicate 2


title: Untreated cells with H1N1 infection rep 2

description:
untreated_H1N1_rep_2
Replicate 2

value: No siRNA


title: nuclear RNA after NS1 transfection (16h) and DMSO treatment (24h)


title: total RNA after empty vector transfection (16h) and compound 1(5uM) treatment(24h) rep2

source_name: total RNA_empty vector transfection_compound 1 (5uM)


title: cytoplasmic RNA after M transfection (16h) and DMSO treatment(24h) rep2

source_name: cytoplasmic RNA_M transfection_DMSO


title: MDA436_cell_line_10nMAG_rep3

description: replicate 5


title: total RNA after empty vector transfection (16h) and DMSO treatment(24h)

source_name: total RNA_empty vector transfection_DMSO


title: total RNA after NS1 transfection (16h) and DMSO treatment (24h)

source_name: total RNA_NS1 transfection_DMSO


title: nuclear RNA after M transfection (16h) and compound 1(5uM) treatment(24h) rep2

source_name: nuclear RNA_M transfection_compound 1 (5uM)


title: nuclear RNA after empty vector transfection (16h) and compound 1(5uM) treatment(24h) rep2


title: cytoplasmic RNA after empty vector transfection (16h) and DMSO treatment(24h) rep2

source_name: cytoplasmic RNA_empty vector transfection_DMSO


title: total RNA after M transfection (16h) and compound 1(5uM) treatment(24h) rep2

source_name: total RNA_M transfection_compound 1 (5uM)


title: cytoplasmic RNA after NS1 transfection (16h) and compound 1(5uM) treatment (24h)

source_name: cytoplasmic RNA_NS1 transfection_compound 1(5uM)


title: nuclear RNA after M transfection (16h) and DMSO treatment(24h) rep1

source_name: nuclear RNA_M transfection_DMSO


title: nuclear RNA after NS1 transfection (16h) and compound 1(5uM) treatment (24h)

source_name: nuclear RNA_NS1 transfection_compound 1(5uM)


title: cytoplasmic RNA after NS1 transfection (16h) and compound 1(5uM) treatment(24h)

source_name: cytoplasmic RNA_NS1 transfection_compound 1 (5uM)


title: nuclear RNA after M transfection (16h) and compound 1(5uM) treatment(24h) rep1


title: nuclear RNA after empty vector transfection (16h) and DMSO treatment(24h) rep1


title: cytoplasmic RNA after empty vector transfection (16h) and compound 1(5uM) treatment(24h) rep1

source_name: cytoplasmic RNA_empty vector transfection_compound 1 (5uM)


title: cytoplasmic RNA after M transfection (16h) and DMSO treatment(24h) rep1


title: nuclear RNA after empty vector transfection (16h) and compound 1(5uM) treatment(24h) rep1

source_name: nuclear RNA_empty vector transfection_compound 1 (5uM)


title: total RNA after M transfection (16h) and DMSO treatment(24h) rep2

source_name: total RNA_M transfection_DMSO


title: cytoplasmic RNA after M transfection (16h) and compound 1(5uM) treatment(24h) rep2

source_name: cytoplasmic RNA_M transfection_compound 1 (5uM)


title: total RNA after NS1 transfection (16h) and compound 1(5uM) treatment (24h)

source_name: total RNA_NS1 transfection_compound 1(5uM)


title: cytoplasmic RNA after empty vector transfection (16h) and compound 1(5uM) treatment(24h)


title: total RNA after empty vector transfection (16h) and compound 1(5uM) treatment(24h) rep1


title: total RNA after M transfection (16h) and DMSO treatment(24h) rep1


title: total RNA after M transfection (16h) and compound 1(5uM) treatment(24h) rep1


title: total RNA after NS1 transfection (16h) and DMSO treatment(24h)


title: total RNA after empty vector transfection (16h) and compound 1(5uM) treatment(24h)


title: nuclear RNA after M transfection (16h) and DMSO treatment(24h) rep2


title: cytoplasmic RNA after NS1 transfection (16h) and DMSO treatment(24h)

source_name: cytoplasmic RNA_NS1 transfection_DMSO


title: cytoplasmic RNA after empty vector transfection (16h) and DMSO treatment(24h)


title: cytoplasmic RNA after empty vector transfection (16h) and DMSO treatment(24h) rep1


title: cytoplasmic RNA after M transfection (16h) and compound 1(5uM) treatment(24h) rep1


title: cytoplasmic RNA after empty vector transfection (16h) and compound 1(5uM) treatment(24h) rep2


title: total RNA after empty vector transfection (16h) and DMSO treatment(24h) rep1


title: cytoplasmic RNA after NS1 transfection (16h) and DMSO treatment (24h)


title: nuclear RNA after empty vector transfection (16h) and DMSO treatment(24h) rep2

source_name: nuclear RNA_empty vector transfection_DMSO


title: RMA Control_16

status: Public on Jan 10 2012

city: Roskilde

first: Vibe

last: Skov

address: Koegevej 7-13

department: Hematology

country: Denmark

institute: Roskilde Hospital

description: Gene expression data from control subjects

hyb_protocol: Fragmented aRNA was hybridized to Affymetrix HG-U133 Plus 2.0 chips

scan_protocol: Standard Affymetrix protocol

data_processing: Data were analyzed in Bioconductor/R using RMA

source_name: Control

label_protocol: total RNA was converted to amplified RNA (aRNA) and fragmented using the MessageAmpTM III RNA amplification kit

extract_protocol: Total RNA was extracted from whole-blood using the Paxgene Blood RNA Kit

tag: disease

value: Control subject

value: Whole blood


title: total RNA after empty vector transfection (16h) and DMSO treatment(24h) rep2

source_name: total RNA_empty vector transfection_DMSO


title: RMA Control_17


title: RMA Control_18


title: RMA Control_21


title: RMA Control_19


title: RMA Control_20


title: RMA Control_13


title: RMA Control_15


title: RMA Control_12


title: RMA Control_10


title: RMA Control_6


title: RMA Control_11


title: RMA Control_4


title: RMA Control_14


title: RMA Control_8


title: RMA Control_7


title: RMA Control_1


title: RMA Control_5


title: MPD

description: Gene expression data from a patient with Myeloproliferative Disorder

value: Myeloproliferative Disorder (MPD)


title: RMA Control_2


title: RMA PMF_8

description: Gene expression data from patients with Primary Myelofibrosis (PMF)

source_name: Primary Myelofibrosis (PMF)


title: RMA PMF_6


title: RMA PMF_9


title: RMA PV_37

description: Gene expression data from patients with Polycythemia Vera (PV)

source_name: Polycythemia Vera (PV)


title: RMA PMF_1


title: RMA PMF_3


title: RMA Control_9


title: RMA PMF_5


title: RMA PV_40


title: RMA PMF_4


title: RMA PV_32


title: RMA PV_41


title: RMA PV_35


title: RMA PMF_2


title: RMA PV_27


title: RMA PV_38


title: RMA PV_30


title: RMA PV_36


title: RMA PV_33


title: RMA PV_25


title: RMA PV_31


title: RMA PV_39


title: RMA PMF_7


title: RMA PV_24


title: RMA PV_28


title: RMA PV_29


title: RMA PV_34


title: RMA PV_26


title: RMA PV_20


title: RMA PV_21


title: RMA PV_22


title: RMA PV_23


title: RMA PV_18


title: RMA PV_16


title: RMA PV_11


title: RMA PV_15


title: RMA PV_9


title: RMA PV_19


title: RMA Control_3


title: RMA PV_17


title: RMA PV_13


title: RMA PV_4


title: RMA PV_3


title: RMA PV_12


title: RMA PV_8


title: RMA PV_6


title: RMA PV_1


title: RMA ET_18

description: Gene expression data from patients with Essentiel Thrombocythemia (ET)

source_name: Essentiel Thrombocythemia (ET)


title: RMA PV_2


title: RMA ET_16


title: RMA PV_7


title: RMA PV_5


title: RMA ET_19


title: RMA PV_10


title: RMA ET_14


title: RMA ET_13


title: RMA ET_3


title: RMA ET_15


title: RMA ET_9


title: RMA ET_12


title: RMA ET_8


title: RMA ET_10


title: RMA ET_11


title: RMA ET_2


title: RMA ET_4


title: RMA ET_1


title: RMA ET_5


title: RMA ET_6


title: RMA ET_7


title: RMA ET_17


title: myoblasts-expt3_controlMedia-rep4

status: Public on Jan 03 2012

city: Seattle

first: Janet

middle: M.

last: Young

state: WA

address: 1100 Fairview Avenue N., C3-168,  P.O. Box 19024

department: Division of Human Biology

institute: Fred Hutchinson Cancer Research Center

description: Sample name: MB_d

data_processing:
Probe intensities were corrected, normalized, and summarized by the Lumi package of Bioconductor (Du et al., 2008). Differentially expressed genes were identified by the LIMMA package of Bioconductor (Wettenhall and Smyth, 2004).
Data from the DUX-overexpression and the defensin experiments were normalized separately.

source_name: myoblasts grown in control media

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit (Applied Biosystems) for Illumina arrays

growth_protocol: Primary human myoblasts were collected and cultured as previously described (Snider et al., 2010, PubMed ID 21060811).

extract_protocol: RNA was extracted with Qiagen RNeasy kit according to manufacturer's instruction. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol:
Overexpression experiment: control human primary myoblasts were transduced with lentivirus carrying DUX4-fl, DUX4-s or GFP (MOI = 15) for 24h.
Defensin experiment: cultured control myoblasts were grown at 50% confluence and treated with 1 µM human β-defensin 3. Equivalent volume of vehicle (water) was added to myoblasts for the control condition.

value: myoblast

tag: growth medium

value: controlMedia


title: myotubes-expt3_controlMedia-rep1

description: Sample name: MT_a

source_name: myotubes grown in control media

value: myotube


title: myotubes-expt3_defensinMedia-rep3

description: Sample name: MT_DEF_c

source_name: myotubes grown in media containing human beta-defensin 3 peptide

value: defensinMedia


title: myoblasts-expt3_defensinMedia-rep4

description: Sample name: MB_DEF_d

source_name: myoblasts grown in media containing human beta-defensin 3 peptide


title: myotubes-expt3_controlMedia-rep3

description: Sample name: MT_c


title: myoblasts-expt3_controlMedia-rep1

description: Sample name: MB_a


title: myotubes-expt3_defensinMedia-rep2

description: Sample name: MT_DEF_b


title: myotubes-expt3_defensinMedia-rep4

description: Sample name: MT_DEF_d


title: myoblasts-expt3_defensinMedia-rep1

description: Sample name: MB_DEF_a


title: myoblasts-expt3_defensinMedia-rep3

description: Sample name: MB_DEF_c


title: myoblasts-expt3_controlMedia-rep2

description: Sample name: MB_b


title: myotubes-expt3_defensinMedia-rep1

description: Sample name: MT_DEF_a


title: myotubes-expt3_controlMedia-rep2

description: Sample name: MT_b


title: myoblasts-expt2_lentiGFP-rep4

description: Sample name: GFP_12_new

source_name: myoblasts transduced with lentivirus carrying GFP

tag: transduction

value: lentiGFP


title: myoblasts-expt3_controlMedia-rep3

description: Sample name: MB_c


title: myoblasts-expt2_lentiGFP-rep3

description: Sample name: GFP_11_new


title: myoblasts-expt3_defensinMedia-rep2

description: Sample name: MB_DEF_b


title: myoblasts-expt2_lentiDUX4short-rep1

description: Sample name: Short_5_new

source_name: myoblasts transduced with lentivirus carrying DUX4-s


title: myoblasts-expt2_lentiGFP-rep2

description: Sample name: GFP_10_new


title: myoblasts-expt2_lentiDUX4short-rep2

description: Sample name: Short_6_new


title: myoblasts-expt2_lentiDUX4fl-rep1

description: Sample name: Full_1_new

source_name: myoblasts transduced with lentivirus carrying DUX4-fl


title: myoblasts-expt2_lentiDUX4fl-rep4

description: Sample name: Full_4_new


title: myoblasts-expt2_lentiDUX4short-rep4

description: Sample name: Short_8_new


title: myotubes-expt3_controlMedia-rep4

description: Sample name: MT_d


title: myoblasts-expt2_lentiDUX4short-rep3

description: Sample name: Short_7_new


title: myoblasts-expt2_lentiDUX4fl-rep2

description: Sample name: Full_2_new


title: myoblasts-expt1_untransduced-rep4

description: Sample name: cntrlA_8_old

source_name: control untransduced myoblasts

value: untransduced


title: myoblasts-expt2_lentiGFP-rep1

description: Sample name: GFP_9_new


title: myoblasts-expt1_untransduced-rep3

description: Sample name: cntrlA_7_old


title: myoblasts-expt1_untransduced-rep2

description: Sample name: cntrlFL_4_old


title: myoblasts-expt2_lentiDUX4fl-rep3

description: Sample name: Full_3_new


title: myoblasts-expt1_untransduced-rep1

description: Sample name: cntrlFL_3_old


title: myoblasts-expt1_lentiDUX4fl-rep1

description: Sample name: pLentiFL_1_old


title: RMA PV_14


title: 270_82

status: Public on Dec 31 2011

first: Brian

last: Denton

address: 307 E. 63rd Street

department: Epidemiology and Biostatistics

institute: Memorial Sloan-Kettering Cancer Center

hyb_protocol: Per manufacturer's instructions

scan_protocol: scanned on the BeadArray Reader, iScan system.

data_processing: Signal intensity generated with Illumina iScan Control software and expression was quantile normalized using the preprocessCore library in R (R 2.10.1, preprocessCore version 1.8.0).

source_name: Uveal melanoma

label_protocol: Per manufacturer's instructions

growth_protocol: RPMI 10% FBS

extract_protocol: Total RNA was extracted from cells using Trizol lysis reagent

treatment_protocol: Untreated versus 8h Selumetinib

value: GNAQ mutant

value: post treatment


title: 290_03

value: GNAQ WT & BRAF WT, pre treatment

value: pre treatment


title: myoblasts-expt1_lentiDUX4short-rep2

description: Sample name: pLentiA_6_old


title: 270_81


title: 270_83


title: 270_03


title: OMMI_01


title: 290_01


title: 290_02


title: myoblasts-expt1_lentiDUX4fl-rep2

description: Sample name: pLentiFL_2_old


title: 270_01


title: OMMI_82


title: myoblasts-expt1_lentiDUX4short-rep1

description: Sample name: pLentiA_5_old


title: 92.1_83


title: OMMI_81


title: 270_02


title: 92.1_03


title: 92.1_82


title: 92.1_01


title: OMMI_03


title: 92.1_81


title: OCMIA_83

value: BRAF mutant, pre treatment


title: OMMI_83


title: 92.1_02


title: OCMIA_82


title: OCMIA_01


title: OCMIA_02


title: OCMIA_81


title: OCMIA_03


title: ethanol-treated during early gestation 1

status: Public on Dec 16 2011

city: London

first: Katarzyna

last: Janus

state: ON

address: 1151 Richmond Street

institute: University of Western Ontario

hyb_protocol: 5.5 ug of single-stranded cDNA was hybridized for 16 hours at 45 degrees C to the array.  Liquid handling steps were performed by a GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 using Command Console v1.1

data_processing: The data were analyzed with Partek Genomics Suite software v6.6.  Probes  were quantile-normalized using the GeneChip-Robust Multiarray Averaging and log2 transformed. All other settings were left as default.

organism: Mus musculus

source_name: brain, ethanol-treated, P70 male

label_protocol: Single-stranded cDNA was synthesized using 200 ng of total RNA using Ambion WE Expression Kit for Affymetrix GeneChip Whole Transcript WT Expression Arrays and labelled using the Affymetrix GeneChip WT Terminal Labeling kit.

growth_protocol: Mice were raised in standard same-sex housing conditions (14/10-hour light/dark cycle, 40-60% humidity,21°C to 24°C temperature).  Mice were sacrificed at postnatal day 70.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions and cleaned using Rneasy Mini kit (QIAGEN).

treatment_protocol: At postntatal day 70, mice were sacrificed by CO2 asphyxiation and whole brain tissue were dissected using RNAse-free tools.  Brains were snap-frozen in liquid nitrogen and stored at -80 degrees C until RNA isolation.

tag: strain

tag: Sex

value: male

tag: age

value: postnatal day 70

value: brain

value: ethanol on gestational days 8 and 11


title: ethanol-treated during early gestation 2

tag: tissue


title: C4-2B siNS_16hr DHT rep3

status: Public on Dec 15 2011

first: Dai-Ying

last: Wu

address: 1441 Eastlake Ave, NOR 6314

department: Biochemistry

institute: University of Southern California

description:
5491021084_K
replicate 3

hyb_protocol: Hybridization was performed by the Southern California Genotyping Consortium at UCLA as per their standard protocol.

scan_protocol: Scanning was performed by the Southern California Genotyping Consortium at UCLA as per their standard protocol.

data_processing: The data were normalized using neqc with limma in R and batch corrected using ComBat

source_name: C4-2B siNS_16hr_DHT

label_protocol: Labeling was performed by the Southern California Genotyping Consortium at UCLA as per their standard protocol.

growth_protocol: Cells were plated and grown in RPMI 1640 phenol red-free medium supplemented with 5% charcoal stripped serum for 3 days prior to hormone treatment

extract_protocol: RNA was extracted using the TRIzol method as per the manufacturer's instructions

treatment_protocol: Cells were treated with 10nM dihydrotestosterone for 16 hours

value: prostate cancer cells

tag: genotype/variation

value: transfected with siRNA against a non-specific (NS) sequence


title: C4-2B sip300_0hr DHT rep4

description:
5491021084_J
replicate 4

source_name: C4-2B sip300_0hr_DHT

value: transfected with siRNA specifically targeting EP300


title: control for early gestation ethanol treatment 2

source_name: brain, saline-treated, P70 male

value: saline on gestational days 8 and 11


title: C4-2B siCBP_0hr DHT rep1

description:
5445316054_K
replicate 1

source_name: C4-2B siCBP_0hr_DHT

value: transfected with siRNA pecifically targeting CREBBP.


title: C4-2B siCBP_0hr DHT rep2

description:
5491021084_F
replicate 2


title: C4-2B siNS_0hr DHT rep2

description:
5491021084_L
replicate 2

source_name: C4-2B siNS_0hr_DHT


title: C4-2B sip300_16hr DHT rep2

description:
5491021084_C
replicate 2

source_name: C4-2B sip300_16hr_DHT


title: C4-2B siNS_0hr DHT rep4

description:
5491021084_I
replicate 4


title: control for early gestation ethanol treatment 1


title: C4-2B siCBP_16hr DHT rep3

description:
5491021084_B
replicate 3

source_name: C4-2B siCBP_16hr_DHT


title: C4-2B siNS_16hr DHT rep1

description:
5491021084_D
replicate 1


title: C4-2B sip300_16hr DHT rep3

description:
5491021084_E
replicate 3


title: C4-2B siCBP_16hr DHT rep1

description:
5491021084_G
replicate 1


title: C4-2B siCBP_0hr DHT rep3

description:
5491021084_H
replicate 3


title: C4-2B sip300_16hr DHT rep4

description:
5445316054_L
replicate 4


title: C4-2B sip300_0hr DHT rep1

description:
5491021084_A
replicate 1


title: C4-2B sip300_16hr DHT rep1

description:
5445316054_G
replicate 1


title: C4-2B siCBP_16hr DHT rep4

description:
5445316054_J
replicate 4


title: LNCaP cells treated with siRNA targeting EZH2

status: Public on Dec 11 2011

city: Chicago

first: Jindan

last: Yu

state: IL

address: 303 E. Superior St.

department: Medicine - Hem/Onc

institute: Northwestern University

description:
5701666055_D
LNCaP_siEZH2
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

data_processing: The bead-level data were preprocessed using GenomeStudio (Illumina) and the expression data was analyzed using the beadarray package in Bioconductor, log2 transformed and quantile normalized using the beadarray package.

source_name: LNCaP cells grown in 10%FBS subjected to siRNA against EZH2

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

value: LNCaP

value: EZH2 siRNA


title: C4-2B sip300_0hr DHT rep3

description:
5445316054_I
replicate 3


title: C4-2B siNS_16hr DHT rep2

description:
5445316054_F
replicate 2


title: C4-2B siNS_0hr DHT rep3

description:
5445316054_C
replicate 3


title: C4-2B siNS_0hr DHT rep1

description:
5445316054_A
replicate 1


title: C4-2B siCBP_16hr DHT rep2

description:
5445316054_D
replicate 2


title: C4-2B siNS_16hr DHT rep4

description:
5445316054_H
replicate 4


title: C4-2B sip300_0hr DHT rep2

description:
5445316054_B
replicate 2


title: C4-2B siCBP_0hr DHT rep4

description:
5445316054_E
replicate 4


title: 290_82


title: LNCaP cells hormone deprived and treated with R1881 for 48 hours

description:
5701666055_B
LNCaP_R1881
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

source_name: LNCaP cells grown in 10%FCS for 2 days before treated with 1nM R1881

value: 1nM synthetic androgen R1881


title: LnCaP cells treated with control non-targeting siRNA

description:
5701666055_C
LNCaP_siCtrl
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

source_name: LNCaP cells grown in 10%FBS subjected to non-targeting siRNA

value: control siRNA


title: LNCaP_abl cells treated with ethanol for 48 hours

description:
5701666057_A
LNCaP_abl_Ethl
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

source_name: LNCaP_abl cells grown in 10%FCS treated with vehicle

value: LNCaP-abl

value: vehicle (Ethanol)


title: LNCaP cells hormone deprived and treated with ethanol for 48 hours

description:
5701666055_A
LNCaP_Ethl
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

source_name: LNCaP cells grown in 10%FCS for 2 days before treated with vehicle


title: lymphoma7050_untreated_rep1

status: Public on Nov 21 2011

city: Berlin

first: Maja

last: Milanovic

address: Augustenburgerplatz 1

department: Hematology and Oncology

country: Germany

institute: Charite University Medicine, Berlin

description:
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; untreated.
7050.CEL

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on MOE430 2.0 Arrays (Affymetrix). GeneChips were washed and stained with standard protocols in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scanner G3000

data_processing: Affymetrix CEL files were imported into Partek Genomic Suite Software (Version 6.5, Partek Inc., St. Louis, USA) and processed by the implemented RMA workflow (median polish probe set summarization, RMA background correction, quantile normalization).

source_name: primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice with palpable lymphadenopathy

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (One Cycle Target labeling protocol) from 3 ug total RNA.

growth_protocol: Primary Emu-myc lymphoma cells were cultivated in B-cell medium (DMEM and IMDM in 1:1 ratio, 10%FBS, 4mM L-glutamine, 25µM beta-mercaptoethanol, 100U/ml penicilin/streptamycin) on gamma-irradiated (20Gy) NIH 3T3 cells as feeder.

extract_protocol: The total RNA from untreated or 5 days ADR treated Myc;Bcl2 lymphomas was prepared using an RNeasy Mini kit (QIAGEN, Valencia, California) according to the manufacturer's instruction.

treatment_protocol: Freshly isolated lymphoma cells were retrovirally transduced by Bcl2 (MSCVpuro) and selected with Puromycin for 48h. These Myc;Bcl2 cells were either left untreated or treated in vitro with 0.05µg/ml Adriamycin for 5 days

tag: senescence induction

value: no


title: lymphoma5560_untreated_rep1

description:
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; untreated.
5560.CEL


title: lymphoma3769_untreated_rep1

description:
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; untreated.
3769.CEL


title: lymphoma403_untreated_rep1

description:
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; untreated.
403.CEL


title: lymphoma3594_ADR_rep1

description:
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; treated 5 days in vitro with 0.05µg/ml Adriamycin.
3594_DOX.CEL

value: TIS


title: lymphoma403_ADR_rep1

description:
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; treated 5 days in vitro with 0.05µg/ml Adriamycin.
403 sen.CEL


title: lymphoma5766_untreated_rep1

description:
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; untreated.
5766.CEL


title: lymphoma7050_ADR_rep1

description:
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; treated 5 days in vitro with 0.05µg/ml Adriamycin.
7050_DOX.CEL


title: 290_83

value: GNAQ WT & BRAF WT, pre treatment

value: post treatment


title: LNCaP_abl cells treated with R1881 for 48 hours

description:
5701666057_B
LNCaP_abl_R1881
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

source_name: LNCaP_abl cells grown in 10%FCS treated with 1nM 1881


title: OMMI_02

value: GNAQ mutant

value: pre treatment


title: lymphoma3769_ADR_rep1

description:
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; treated 5 days in vitro with 0.05µg/ml Adriamycin.
3769_DOX.CEL


title: lymphoma2949_untreated_rep1

description:
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; untreated.
2949.CEL


title: lymphoma5560_ADR_rep1

description:
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; treated 5 days in vitro with 0.05µg/ml Adriamycin.
5560 sen.CEL


title: lymphoma3594_untreated_rep1

description:
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; untreated.
3594.CEL


title: lymphoma2581_untreated_rep1

description:
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; untreated.
2581.CEL


title: lymphoma6054_ADR_rep1

description:
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; treated 5 days in vitro with 0.05µg/ml Adriamycin.
6054_DOX.CEL


title: lymphoma6054_untreated_rep1

description:
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; untreated.
6054.CEL


title: lymphoma2949_ADR_rep1

description:
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; treated 5 days in vitro with 0.05µg/ml Adriamycin.
2949_DOX.CEL


title: lymphoma1570_untreated_rep1

description:
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; untreated.
1570.CEL


title: lymphoma5766_ADR_rep1

description:
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; treated 5 days in vitro with 0.05µg/ml Adriamycin.
5766_DOX.CEL


title: lymphoma1570_ADR_rep1

description:
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; treated 5 days in vitro with 0.05µg/ml Adriamycin.
1570 sen.CEL


title: lymphoma2581_ADR_rep1

description:
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; treated 5 days in vitro with 0.05µg/ml Adriamycin.
2581 sen.CEL


title: U2OS with DMSO, biological rep5

status: Public on Nov 18 2011

first: Lars

last: Anders

address: 44 Binney Street

department: Cancer Biology

institute: Dana-Farber Cancer Institute

hyb_protocol: The fragmented cDNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to GeneChip Human Gene 1.0 ST Array chips overnight at 45°C (performed by the Dana Farber Cancer Institute Microarray Core). A fluidics instrument was used by the core to perform washes to remove cDNA that had not hybridized to its complementary oligonucleotide probe. The bound cDNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were subsequently added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: A confocal laser scanner was used for excitation and measurement of cDNAs bound to complementary oligonucleotides by the Dana Farber Cancer Institute Microarray Core.

data_processing:
Partek Genomic Suite was used for gene-level analysis of the exon array primary data (CEL files). Gene-level expressions were summarized using the robust multi-array average (RMA) method from Partek Genomic Suite.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: U2OS cells

label_protocol: The Dana Farber Cancer Institute Microarray Core synthesized single-stranded cDNA through a multi-step process from the extracted RNA, and fragmented single-stranded cDNA was end-labeled with a biotinylated nucleotide-analog.

growth_protocol: Cells were maintained according to the guidelines of the American Type Culture Collection (ATCC). Cells (viability >90%) were transferred to 10 cm dishes to a cell density to 25% and grown in McCoy medium supplemeted with 10% FBS for 30h, followed by compound treatment for 4 h.

extract_protocol: Following compound/vehicle treatement, U2OS cells were immediately washed in PBS, trypsinized and subjected to total RNA extraction using the RNeasy Plus Kit (Qiagen) according to the manufacturers protocol.

treatment_protocol: Cells were treated either with 1mM PD0332991 or vehicle (DMSO) for 4h.

value: osteosarcoma

value: U2OS cells

value: vehicle (DMSO) for 4h


title: U2OS with PD0332991, biological rep5


title: U2OS with DMSO, biological rep4


title: U2OS with PD0332991, biological rep1


title: U2OS with DMSO, biological rep3


title: U2OS with DMSO, biological rep2


title: U2OS with PD0332991, biological rep2


title: U2OS with PD0332991, biological rep4


title: U2OS with DMSO, biological rep1


title: U2OS with PD0332991, biological rep3


title: ZnD-10d_GRP_sub9

status: Public on Nov 15 2011

city: Gainesville

first: Robert

middle: J.

last: Cousins

state: Florida

address: 359 FSHN Bldg. Newell Dr. PO Box 110370

department: Food Science and Human Nutrition Department, Center for Nutritional Sciences

institute: University of Florida

description: Subject 9

data_processing: Probes with detection P-values above 0.05 in all samples were excluded from the dataset by the Illumina GenomeStudio software. Absolute signal intensities of the filtered probes were quantile normalized using EXPANDER 5.2 (Ulitsky I et al. 2010, Nat Protoc. 2010;5:303-22).

source_name: Human peripheral blood, zinc depleted, 10 d

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification kit (Ambion)

extract_protocol: Total RNA from whole blood collected in PAXgene tubes (BD) was extracted using the Qiagen Rneasy kit according to manufactuer's instructions. Globin RNA contents in the isolated whole blood RNA was reduced by the GLOBINclear kit (Ambion). Purity and integrity of yielded RNA were assessed with the NanoDrop spectrophotometer and Agilent Bioanalyzer, respectively.

treatment_protocol: In order to establish a defined baseline condition prior to dietary zinc depletion, subjects consumed meals composed of a mixed diet providing ~11 mg Zn/d for 7 d. An egg white-based liquid formula which provided <0.5 mg Zn/d was consumed during the following 10 d for acute dietary zinc depletion.

tag: gender

value: Male

value: Adult

value: Zinc-Depleted for 10 d

value: Whole blood

tag: sampling method

value: PAXgene system

tag: rna subtype

value: Globin RNA-reduced RNA


title: Baseline_GRP_sub9

description: Subject 9

source_name: Human peripheral blood, baseline, 0 d

tag: treatment

value: Baseline


title: ZnD-10d_GRP_sub8

description: Subject 8


title: Baseline_GRP_sub7

description: Subject 7


title: Baseline_GRP_sub8

description: Subject 8


title: Baseline_GRP_sub6

description: Subject 6


title: Baseline_GRP_sub4

description: Subject 4


title: Baseline_GRP_sub5

description: Subject 5


title: ZnD-10d_GRP_sub3

description: Subject 3


title: ZnD-10d_GRP_sub7

description: Subject 7


title: ZnD-10d_GRP_sub6

description: Subject 6


title: ZnD-10d_GRP_sub2

description: Subject 2


title: Baseline_GRP_sub3

description: Subject 3


title: ZnD-10d_GRP_sub4

description: Subject 4


title: Baseline_GRP_sub2

description: Subject 2


title: ZnD-10d_GRP_pooled

description: Pooled


title: ZnD-6d_GRP_pooled

description: Pooled

source_name: Human peripheral blood, zinc depleted, 6 d

value: Zinc-Depleted for 6 d


title: Baseline_GRP_sub1

description: Subject 1


title: ZnD-10d_GRP_sub1

description: Subject 1


title: Baseline_GRP_pooled

description: Pooled


title: Baseline_PAX_pooled

description: Pooled

value: Total RNA


title: ZnD-6d_PAX_pooled

description: Pooled


title: D25 LSB/S/F8/CHIR biological rep 4

status: Public on Nov 07 2011

city: New York

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description:
Gene expression data from Day25 of LSB/S/F8/CHIR condition
D25_3_4

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX human HT12 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using Illumina iScanner

data_processing: The data were analyzed with GenomeStudio V2011.1 using Illumina default analysis settings. No normalization and background correction are performed.

source_name: Differentiated hESCs

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

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

treatment_protocol: Differentiated hESC with three conditions (LSB, LSB/S/F8, LSB/S/F8/CHIR) were subjected to RNA extraction in specific timepoint (day 0, 1, 3, 5, 7, 11, 13, 25) and hybridization on Illumina microarrays. Each sample has 3 or 4 biological repeats.

tag: cell type

value: Differentiated hESCs

tag: agent

tag: time


title: ZnD-10d_PAX_pooled

description: Pooled


title: D25 LSB/S/F8/CHIR biological rep 3

description:
Gene expression data from Day25 of LSB/S/F8/CHIR condition
D25_3_3


title: D25 LSB biological rep 2

description:
Gene expression data from Day25 of LSB condition
D25_1_2

value: LSB


title: D25 LSB/S/F8 biological rep 1

description:
Gene expression data from Day25 of LSB/S/F8 condition
D25_2_1


title: D25 LSB/S/F8 biological rep 2

description:
Gene expression data from Day25 of LSB/S/F8 condition
D25_2_2


title: D25 LSB/S/F8/CHIR biological rep 2

description:
Gene expression data from Day25 of LSB/S/F8/CHIR condition
D25_3_2


title: D25 LSB/S/F8 biological rep 3

description:
Gene expression data from Day25 of LSB/S/F8 condition
D25_2_3


title: D25 LSB biological rep 3

description:
Gene expression data from Day25 of LSB condition
D25_1_3


title: D13 LSB/S/F8/CHIR biological rep 3a

description:
Gene expression data from Day13 of LSB/S/F8/CHIR condition for late stage comparison
D13_3_3a

value: LSB/S/F8/CHIR  (for late stage comparison)


title: D25 LSB biological rep 1

description:
Gene expression data from Day25 of LSB condition
D25_1_1


title: D13 LSB/S/F8 biological rep 4a

description:
Gene expression data from Day13 of LSB/S/F8 condition for late stage comparison
D13_2_4a

value: LSB/S/F8  (for late stage comparison)


title: D25 LSB/S/F8 biological rep 4

description:
Gene expression data from Day25 of LSB/S/F8 condition
D25_2_4


title: D13 LSB/S/F8 biological rep 3a

description:
Gene expression data from Day13 of LSB/S/F8 condition for late stage comparison
D13_2_3a


title: D13 LSB/S/F8 biological rep 1a

description:
Gene expression data from Day13 of LSB/S/F8 condition for late stage comparison
D13_2_1a


title: D13 LSB/S/F8 biological rep 2a

description:
Gene expression data from Day13 of LSB/S/F8 condition for late stage comparison
D13_2_2a


title: D13 LSB/S/F8/CHIR biological rep 4a

description:
Gene expression data from Day13 of LSB/S/F8/CHIR condition for late stage comparison
D13_3_4a


title: D13 LSB/S/F8/CHIR biological rep 1a

description:
Gene expression data from Day13 of LSB/S/F8/CHIR condition for late stage comparison
D13_3_1a


title: D13 LSB biological rep 4a

description:
Gene expression data from Day13 of LSB condition for late stage comparison
D13_1_4a

value: LSB  (for late stage comparison)


title: D25 LSB biological rep 4

description:
Gene expression data from Day25 of LSB condition
D25_1_4


title: D25 LSB/S/F8/CHIR biological rep 1

description:
Gene expression data from Day25 of LSB/S/F8/CHIR condition
D25_3_1


title: D13 LSB biological rep 3a

description:
Gene expression data from Day13 of LSB condition for late stage comparison
D13_1_3a


title: D13 LSB biological rep 2a

description:
Gene expression data from Day13 of LSB condition for late stage comparison
D13_1_2a


title: D13 LSB biological rep 1a

description:
Gene expression data from Day13 of LSB condition for late stage comparison
D13_1_1a


title: D13 LSB/S/F8 biological rep 3

description:
Gene expression data from Day13 of LSB/S/F8 condition
D13_2_3


title: D13 LSB/S/F8/CHIR biological rep 3

description:
Gene expression data from Day13 of LSB/S/F8/CHIR condition
D13_3_3


title: D13 LSB/S/F8/CHIR biological rep 2

description:
Gene expression data from Day13 of LSB/S/F8/CHIR condition
D13_3_2


title: D13 LSB/S/F8/CHIR biological rep 1

description:
Gene expression data from Day13 of LSB/S/F8/CHIR condition
D13_3_1


title: D13 LSB/S/F8/CHIR biological rep 2a

description:
Gene expression data from Day13 of LSB/S/F8/CHIR condition for late stage comparison
D13_3_2a


title: D13 LSB/S/F8 biological rep 1

description:
Gene expression data from Day13 of LSB/S/F8 condition
D13_2_1


title: D13 LSB/S/F8 biological rep 2

description:
Gene expression data from Day13 of LSB/S/F8 condition
D13_2_2


title: ZnD-10d_GRP_sub5

description: Subject 5


title: D11 LSB/S/F8 biological rep 3

description:
Gene expression data from Day11 of LSB/S/F8 condition
D11_2_3


title: D13 LSB biological rep 3

description:
Gene expression data from Day13 of LSB condition
D13_1_3


title: D11 LSB biological rep 2

description:
Gene expression data from Day11 of LSB condition
D11_1_2


title: D11 LSB/S/F8 biological rep 1

description:
Gene expression data from Day11 of LSB/S/F8 condition
D11_2_1


title: D13 LSB biological rep 2

description:
Gene expression data from Day13 of LSB condition
D13_1_2


title: D11 LSB/S/F8/CHIR biological rep 1

description:
Gene expression data from Day11 of LSB/S/F8/CHIR condition
D11_3_1


title: D7 LSB/S/F8 biological rep 3

description:
Gene expression data from Day7 of LSB/S/F8 condition
D7_2_3


title: D11 LSB biological rep 3

description:
Gene expression data from Day11 of LSB condition
D11_1_3


title: D11 LSB biological rep 1

description:
Gene expression data from Day11 of LSB condition
D11_1_1


title: D7 LSB/S/F8 biological rep 2

description:
Gene expression data from Day7 of LSB/S/F8 condition
D7_2_2


title: D7 LSB/S/F8/CHIR biological rep 3

description:
Gene expression data from Day7 of LSB/S/F8/CHIR condition
D7_3_3


title: D11 LSB/S/F8 biological rep 2

description:
Gene expression data from Day11 of LSB/S/F8 condition
D11_2_2


title: D7 LSB biological rep 2

description:
Gene expression data from Day7 of LSB condition
D7_1_2


title: D7 LSB/S/F8/CHIR biological rep 2

description:
Gene expression data from Day7 of LSB/S/F8/CHIR condition
D7_3_2


title: D13 LSB biological rep 1

description:
Gene expression data from Day13 of LSB condition
D13_1_1


title: D11 LSB/S/F8/CHIR biological rep 2

description:
Gene expression data from Day11 of LSB/S/F8/CHIR condition
D11_3_2


title: D7 LSB biological rep 3

description:
Gene expression data from Day7 of LSB condition
D7_1_3


title: D5 LSB/S/F8/CHIR biological rep 3

description:
Gene expression data from Day5 of LSB/S/F8/CHIR condition
D5_3_3


title: D7 LSB/S/F8 biological rep 1

description:
Gene expression data from Day7 of LSB/S/F8 condition
D7_2_1


title: D7 LSB biological rep 1

description:
Gene expression data from Day7 of LSB condition
D7_1_1


title: D7 LSB/S/F8/CHIR biological rep 1

description:
Gene expression data from Day7 of LSB/S/F8/CHIR condition
D7_3_1


title: D5 LSB/S/F8 biological rep 2

description:
Gene expression data from Day5 of LSB/S/F8 condition
D5_2_2


title: D5 LSB/S/F8/CHIR biological rep 2

description:
Gene expression data from Day5 of LSB/S/F8/CHIR condition
D5_3_2


title: D5 LSB/S/F8 biological rep 3

description:
Gene expression data from Day5 of LSB/S/F8 condition
D5_2_3


title: D11 LSB/S/F8/CHIR biological rep 3

description:
Gene expression data from Day11 of LSB/S/F8/CHIR condition
D11_3_3


title: D5 LSB biological rep 2

description:
Gene expression data from Day5 of LSB condition
D5_1_2


title: D5 LSB/S/F8/CHIR biological rep 1

description:
Gene expression data from Day5 of LSB/S/F8/CHIR condition
D5_3_1


title: D5 LSB/S/F8 biological rep 1

description:
Gene expression data from Day5 of LSB/S/F8 condition
D5_2_1


title: D5 LSB biological rep 3

description:
Gene expression data from Day5 of LSB condition
D5_1_3


title: D5 LSB biological rep 1

description:
Gene expression data from Day5 of LSB condition
D5_1_1


title: D3 LSB/S/F8 biological rep 3

description:
Gene expression data from Day3 of LSB/S/F8 condition
D3_2_3


title: D3 LSB/S/F8 biological rep 2

description:
Gene expression data from Day3 of LSB/S/F8 condition
D3_2_2


title: D3 LSB biological rep 3

description:
Gene expression data from Day3 of LSB condition
D3_1_3


title: D1 LSB biological rep 1

description:
Gene expression data from Day1 of LSB condition
D1_1


title: D1 LSB biological rep 3

description:
Gene expression data from Day1 of LSB condition
D1_3


title: D0 LSB biological rep 3

description:
Gene expression data from Day0 of LSB condition
D0_3


title: D0 LSB biological rep 2

description:
Gene expression data from Day0 of LSB condition
D0_2


title: D1 LSB biological rep 2

description:
Gene expression data from Day1 of LSB condition
D1_2


title: D3 LSB/S/F8 biological rep 1

description:
Gene expression data from Day3 of LSB/S/F8 condition
D3_2_1


title: D3 LSB biological rep 2

description:
Gene expression data from Day3 of LSB condition
D3_1_2


title: D3 LSB biological rep 1

description:
Gene expression data from Day3 of LSB condition
D3_1_1


title: 8hr, vehicle injected - 21V8

status: Public on Nov 03 2011

first: Kathryn

last: Graham

address: 11560 University Ave

description: 8hr, vehicle injected

hyb_protocol: Samples were hybridized using the Affymetrix Gene Chip Hybridization Control Kit and the Genechip Hybridization, Wash and Stain Kit. Cocktails wew heated at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute. 200μl of hyb solution was transferred to each array, then the holes were taped with Tough Spots. Arrays were hybridized for  17 hours at 45° at 60rpm• The fluidics washing used was FS450_0001.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using GeneSpring 11.5. Using a Core analysis, the  data was summarized using RMA 16, log transformed and baselined to the median in all samples.
MoEx-1_0-st-v1_na30_mm9_2009-11-09

source_name: 8hr, vehicle injected

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

extract_protocol: Total muscle RNA was extracted using the RNeasy fibrous tissue mini kit (Qiagen, Valencia, CA).

treatment_protocol: Mice were injected intracerebroventrivularly with interleukin 1b and the animals were sacrificed 2, 4, or 8 hours after injection. Skeletal muscle was isloated for use in this analysis.

value: skeletal muscle


title: 8hr, vehicle injected - 17V8

description: 8hr, vehicle injected


title: 8hr, Il-1b injected - 26I8

description: 8hr, Il-1b injected

source_name: 8hr, Il-1b injected


title: 8hr, vehicle injected - 13V8

description: 8hr, vehicle injected


title: 8hr, Il-1b injected - 14I8

description: 8hr, Il-1b injected


title: 4hr, vehicle injected - 3V4

description: 4hr, vehicle injected

source_name: 4hr, vehicle injected


title: 4hr, Il-1b injected - 15I4

description: 4hr, Il-1b injected

source_name: 4hr, Il-1b injected


title: 8hr, Il-1b injected - 22I8

description: 8hr, Il-1b injected


title: 4hr, Il-1b injected - 22I4

description: 4hr, Il-1b injected


title: 4hr, Il-1b injected - 4I4

description: 4hr, Il-1b injected


title: 4hr, Il-1b injected - 1814

description: 4hr, Il-1b injected


title: D0 LSB biological rep 1

description:
Gene expression data from Day0 of LSB condition
D0_1


title: 4hr, Il-1b injected - 13I4

description: 4hr, Il-1b injected


title: 8hr, vehicle injected - 9V8

description: 8hr, vehicle injected


title: 4hr, vehicle injected - 7V4

description: 4hr, vehicle injected


title: 4hr, vehicle injected - 17V4

description: 4hr, vehicle injected


title: 4hr, vehicle injected - 1V4

description: 4hr, vehicle injected


title: 2hr, Il-1b injected - 12I2

description: 2hr, Il-1b injected

source_name: 2hr, Il-1b injected


title: 8hr, vehicle injected - 1V8

description: 8hr, vehicle injected


title: 4hr, vehicle injected - 5V4

description: 4hr, vehicle injected


title: 2hr, vehicle injected - 11V2

description: 2hr, vehicle injected

source_name: 2hr, vehicle injected


title: 2hr, Il-1b injected - 2I2

description: 2hr, Il-1b injected


title: 2hr, Il-1b injected - 10I2

description: 2hr, Il-1b injected


title: 2hr, vehicle injected - 9V2

description: 2hr, vehicle injected


title: 2hr, vehicle injected - 7V2

description: 2hr, vehicle injected


title: 2hr, Il-1b injected - 8I2

description: 2hr, Il-1b injected


title: 2hr, vehicle injected - 5V2

description: 2hr, vehicle injected


title: 2hr, Il-1b injected - 4I2

description: 2hr, Il-1b injected


title: Cultured chicken embryonic hepatocytes: 1 nM TCDD replicate 3

status: Public on Oct 29 2011

city: Ottawa

first: Jason

last: O'Brien

address: 1125 Colonel By Drive, Raven Road

institute: Environment Canada

description: 1 nM TCDD replicate 3

hyb_protocol: Labelled sample and reference cRNA (825 ng each) was fragmented and then hybridized to arrays for 17 hours using Agilent Hybridization kits as per manufacturer’s direction

scan_protocol: Arrays scanned on an Agilent G2505B scanner at 5 um resolution. Data were acquired using Agilent Feature Extraction software version 9.5.3.1.

data_processing: A reference design was used to analyse gene expression data. The design was blocked on the slide as Agilent slides contain four arrays per slide. Background fluorescence was measured using the (-)3xSLv1 probes. Probes with median signal intensities less than the trimmed mean (trim = 5%) plus three trimmed standard deviations of the (-)3xSLv1 probe were flagged as absent. Data were pre-processed using R (http://www.R-project.org).  The median signal intensities were normalized by the global LOWESS method using the transform.madata function in the microarray analysis of variance (MAANOVA) library. Ratio intensity plots, using complete and single linkages, were generated to identify arrays with poor quality. Differentially expressed genes were identified using the MAANOVA library.  The analysis of variance (ANOVA) model included the main effect of treatment and block effect of the microarray.  The Fs statistic, a shrinkage estimator, was used for the gene-specific variance components and the associated p-values for all the statistical tests were estimated using the permutation method (30,000 permutations with residual shuffling). These p-values were then adjusted for multiple comparisons using the false discovery rate approach (FDR). The least-squares means was used to estimate the fold changes for each pairwise comparison.

organism: Gallus gallus

source_name: Cultured chicken embryonic heaptocytes: 1 nM TCDD treated

label_protocol: Complementary RNA (cRNA) for each microarray hybridization was prepared from 150 ng of total RNA. cRNA from experimental samples was labelled with Cy5 and reference cRNA with Cy3 using Agilent Quick Amp labelling kits as per manufacturer’s instructions

extract_protocol: Total RNA was isolated from CEH using RNeasy 96 kits (Qiagen), including the on-column DNase treatment according to the manufacturer’s instructions

value: 1 nM TCDD

tag: age of embryo

value: day 19

value: hepatocytes

tag: exposure time

value: 24 hrs

source_name: Cultured chicken embryonic hepatocytes: reference pool

tag: reference

value: pool of equal parts of all control and treated samples


title: Cultured chicken embryonic hepatocytes: 1 nM TCDD replicate 4

description: 1 nM TCDD replicate 4


title: Cultured chicken embryonic hepatocytes: 1 nM TCDD replicate 2

description: 1 nM TCDD replicate 2


title: Cultured chicken embryonic hepatocytes: 1 nM TCDD replicate 1

description: 1 nM TCDD replicate 1


title: 2hr, vehicle injected - 1V2

institute: University of Alberta

description: 2hr, vehicle injected


title: Cultured chicken embryonic hepatocytes: 0.03 nM TCDD replicate 4

description: 0.03 nM TCDD replicate 4

source_name: Cultured chicken embryonic heaptocytes: 0.03 nM TCDD treated

value: 0.03 nM TCDD


title: Cultured chicken embryonic hepatocytes: 0.03 nM TCDD replicate 2

description: 0.03 nM TCDD replicate 2


title: Cultured chicken embryonic hepatocytes: 0.03 nM TCDD replicate 5

description: 0.03 nM TCDD replicate 5


title: Cultured chicken embryonic hepatocytes: 40 uM L-PFOS replicate 5

description: 40 uM L-PFOS replicate 5

source_name: Cultured chicken embryonic heaptocytes: 40 uM L-PFOS treated

value: 40 uM L-PFOS


title: Cultured chicken embryonic hepatocytes: 10 uM T-PFOS replicate 4

description: 10 uM T-PFOS replicate 4

source_name: Cultured chicken embryonic heaptocytes: 10 uM T-PFOS treated

value: 10 uM T-PFOS


title: Cultured chicken embryonic hepatocytes: 0.03 nM TCDD replicate 3

description: 0.03 nM TCDD replicate 3


title: Cultured chicken embryonic hepatocytes: 10 uM T-PFOS replicate 3

description: 10 uM T-PFOS replicate 3


title: Cultured chicken embryonic hepatocytes: 10 uM T-PFOS replicate 5

description: 10 uM T-PFOS replicate 5


title: Cultured chicken embryonic hepatocytes: 0.03 nM TCDD replicate 1

description: 0.03 nM TCDD replicate 1


title: Cultured chicken embryonic hepatocytes: 40 uM L-PFOS replicate 1

description: 40 uM L-PFOS replicate 1


title: Cultured chicken embryonic hepatocytes: 40 uM L-PFOS replicate 2

description: 40 uM L-PFOS replicate 2


title: Cultured chicken embryonic hepatocytes: 10 uM T-PFOS replicate 1

description: 10 uM T-PFOS replicate 1


title: Cultured chicken embryonic hepatocytes: 10 uM L-PFOS replicate 5

description: 10 uM L-PFOS replicate 5

source_name: Cultured chicken embryonic heaptocytes: 10 uM L-PFOS treated

value: 10 uM L-PFOS