title: HUVEC_siPML2_treated-rep2

city: Cleveland

first: Hung-Ying

last: Kao

state: OH

address: 2123 Adelbert Road, RT400-L

institute: Case Western Reserve University

description: HUVEC cells with passage number less than 5 were transfected with siPML2 for 72 hrs with 20 ng/mL TNFalpha treament for 20 h before total RNA extraction. This is one of the technical replicates located on microarray chip B.

hyb_protocol: Standard protocol as recommended by Illumina.

data_processing: The data was preprocessed by the Bioconductor lumi package (version 2.6.0). It was vst transformed and quantile normalized.

source_name: HUVEC cells, siPML2 transfected for 72hrs with 20ng/mL TNFalpha treatment for 20hrs

tag: cell line

value: HUVEC

tag: transfection

value: PML siRNA

tag: transfection duration

tag: treatment

value: TNFalpha

tag: tnfalpha duration

tag: tnfalpha concentration


title: HUVEC_siPML2_untreated-rep2

status: Public on Jan 10 2013

type: RNA

department: Biochemistry

country: USA

description: HUVEC cells with passage number less than 5 were transfected with siPML2 for 72 hrs without TNFalpha treament before total RNA extraction. This is one of the technical replicates located on microarray chip B.

scan_protocol: Standard protocol as recommended by Illumina.

molecule: total RNA

organism: Homo sapiens

source_name: HUVEC cells, siPML2 transfected for 72hrs without TNFalpha treatment


title: mRNA Abundance +STI 1

city: Stanford

first: Jamie

middle: Geier

last: Bates

state: CA

address: 279 Campus Dr.

institute: Stanford U.

description:
Simple annotation: Leukemia/Lymphoma Cell Lines, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/94430.gif

hyb_protocol: not provided

scan_protocol: GenePix 4000B

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Mus musculus

source_name: Mouse Reference

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: universal mouse reference RNA

source_name: lysate

tag: cell type

value: wildtype v-Abl transformed pre-B cells

tag: compound based treatment

value: IMA


title: HUVEC_siPML1_treated-rep2

description: HUVEC cells with passage number less than 5 were transfected with siPML1 for 72 hrs with 20 ng/mL TNFalpha treament for 20 h before total RNA extraction. This is one of the technical replicates located on microarray chip B.

source_name: HUVEC cells, siPML1 transfected for 72hrs with 20ng/mL TNFalpha treatment for 20hrs

label_protocol: Standard protocol as recommended by Illumina.


title: mRNA Abundance +Rap 1

description:
Simple annotation: Leukemia/Lymphoma Cell Lines, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/94433.gif

value: RAP


title: Longissimus sample Replicate 16

city: saint-gilles

first: marie

last: damon

address: domaine de la prise

country: France

institute: INRA

hyb_protocol: Microarray hybridizations were carried out in Agilent’s SureHyb Hybridization Chambers containing 300 ng of cyanine 3-labeled cRNA sample per hybridization. The hybridization reactions were performed at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit. Slides were disassembled and washed in Gene Expression Wash Buffer 1 for 1 minute at room temperature and then in Gene Expression Wash Buffer 2 for 1 minute at 32°C.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: Raw data from 15198 probes fluorescent hybridization signal intensities were log transformed and centered within sample by subtraction of sample median from all raw values.

organism: Sus scrofa

source_name: skeletal muscle

label_protocol: Total RNA (500 ng) from each animal was labeled individually with Cy3 by using the Quick-Amp Labeling Kit  following the manufacturer’s instructions.

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

tag: pig

tag: muscle type

value: Longissimus

tag: ChIP


title: HUVEC_siPML1_untreated-rep2

description: HUVEC cells with passage number less than 5 were transfected with siPML1 for 72 hrs without TNFalpha treament before total RNA extraction. This is one of the technical replicates located on microarray chip B.

source_name: HUVEC cells, siPML1 transfected for 72hrs without TNFalpha treatment

extract_protocol: Standard protocol as recommended by Illumina.


title: mRNA Abundance +STI 3

description:
Simple annotation: Leukemia/Lymphoma Cell Lines, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/94432.gif


title: mRNA Abundance +Rap 2

description:
Simple annotation: Leukemia/Lymphoma Cell Lines, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/94434.gif


title: Longissimus sample Replicate 11


title: Longissimus sample Replicate 20


title: Longissimus sample Replicate 12


title: HUVEC_siCtrl_treated-rep2

description: HUVEC cells with passage number less than 5 were transfected with non-targeting control siRNA for 72 hrs with 20 ng/mL TNFalpha treament for 20 h before total RNA extraction. This is one of the technical replicates located on microarray chip B.

source_name: HUVEC cells, siCtrl transfected for 72hrs with 20ng/mL TNFalpha treatment for 20hrs

value: control siRNA


title: Longissimus sample Replicate 10


title: HUVEC_siCtrl_untreated-rep2

description: HUVEC cells with passage number less than 5 were transfected with non-targeting control siRNA for 72 hrs without TNFalpha treament before total RNA extraction. This is one of the technical replicates located on microarray chip B.

source_name: HUVEC cells, siCtrl transfected for 72hrs without TNFalpha treatment


title: Gradient Encoding +STI 3

description:
Simple annotation: Leukemia/Lymphoma Cell Lines, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2010-11/91542.gif

source_name: Pool B

source_name: Pool A


title: Gradient Encoding +STI 1

description:
Simple annotation: Leukemia/Lymphoma Cell Lines, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2010-11/91540.gif


title: Gradient Encoding +Rap 2

description:
Simple annotation: Leukemia/Lymphoma Cell Lines, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2010-11/91544.gif


title: HUVEC_siPML2_treated-rep1

description: HUVEC cells with passage number less than 5 were transfected with siPML2 for 72 hrs with 20 ng/mL TNFalpha treament for 20 h before total RNA extraction. This is one of the technical replicates located on microarray chip A.


title: Gradient Encoding Untreated 2

description:
Simple annotation: Leukemia/Lymphoma Cell Lines, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2010-11/91538.gif


title: Gradient Encoding Untreated 1

description:
Simple annotation: Leukemia/Lymphoma Cell Lines, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2010-11/91537.gif


title: Longissimus sample Replicate 14


title: mRNA Abundance Untreated 2

description:
Simple annotation: Leukemia/Lymphoma Cell Lines, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/94428.gif


title: Gradient Encoding +STI 2

description:
Simple annotation: Leukemia/Lymphoma Cell Lines, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2010-11/91541.gif


title: Gradient Encoding +Rap 1

description:
Simple annotation: Leukemia/Lymphoma Cell Lines, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2010-11/91543.gif


title: Longissimus sample Replicate 9


title: Gradient Encoding Untreated 3

description:
Simple annotation: Leukemia/Lymphoma Cell Lines, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2010-11/91539.gif


title: mRNA Abundance Untreated 1

description:
Simple annotation: Leukemia/Lymphoma Cell Lines, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/94427.gif


title: HUVEC_siPML2_untreated-rep1

description: HUVEC cells with passage number less than 5 were transfected with siPML2 for 72 hrs without TNFalpha treament before total RNA extraction. This is one of the technical replicates located on microarray chip A.


title: mRNA Abundance +STI 2

description:
Simple annotation: Leukemia/Lymphoma Cell Lines, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/94431.gif


title: Longissimus sample Replicate 6


title: Gradient Encoding +Rap 3

description:
Simple annotation: Leukemia/Lymphoma Cell Lines, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2010-11/91545.gif


title: Longissimus sample Replicate 7


title: HUVEC_siCtrl_treated-rep1

description: HUVEC cells with passage number less than 5 were transfected with non-targeting control siRNA for 72 hrs with 20 ng/mL TNFalpha treament for 20 h before total RNA extraction. This is one of the technical replicates located on microarray chip A.


title: HUVEC_siPML1_untreated-rep1

description: HUVEC cells with passage number less than 5 were transfected with siPML1 for 72 hrs without TNFalpha treament before total RNA extraction. This is one of the technical replicates located on microarray chip A.


title: Longissimus sample Replicate 5


title: Longissimus sample Replicate 13


title: HUVEC_siCtrl_untreated-rep1

description: HUVEC cells with passage number less than 5 were transfected with non-targeting control siRNA for 72 hrs without TNFalpha treament before total RNA extraction. This is one of the technical replicates located on microarray chip A.


title: Longissimus sample Replicate 4


title: Longissimus sample Replicate 3


title: Longissimus sample Replicate 2


title: Longissimus sample Replicate 18


title: Longissimus sample Replicate 15


title: Longissimus sample Replicate 1


title: BXD38_12

status: Public on Jan 09 2013

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

hyb_protocol: The HT_MG-430A Array plate consists of 96 single MG-430A arrays arranged into standard SBS 96 well plate format.  All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.

scan_protocol: Scanned images were subjected to visual inspection and a chip quality report was generated by the Affymetrix's GeneChip Operating System (GCOS) and Expression console (Affymetrix).

data_processing: The image data was processed using the Affymetrix GCOS algorithm utilizing quantile normalization or the Robust Multiarray method (RMA) to determine the specific hybridizing signal for each gene.

label: biotin

source_name: epididymal adipose tissue

label_protocol: All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430A arrays.

growth_protocol: 16 week male mice maintained on 12 hr light dark cycle fed a chow diet

extract_protocol: Qiazol with homogenization followed by Rneasy spin columns with option Dnase per manufacturers protocol

tag: gender

value: male

tag: age

value: 16 weeks

tag: strain

tag: body fat percentage

tag: tissue

value: epididymal adipose


title: AXB6_13


title: AXB23_12


title: NON_20

value: NON/ShiLtJ


title: NON_21


title: BXD38_11


title: BXD19_12


title: AXB6_14


title: AXB5_10


title: BXD19_13


title: BxH10


title: AXB13_11


title: AXB5_9


title: AXB13_12


title: AXB19_12


title: SEA_15

value: SEA/GnJ


title: BXD6_11


title: AXB23_11


title: BXH4_14


title: BXD19_11


title: BXH4_15


title: BXD19_10


title: BXD6_12


title: BXD32_11


title: BXD32_12


title: Longissimus sample Replicate 8


title: C57_13


title: pituitary tumor_413

type: genomic

first: Fan

last: Gao

state: California

address: 1501 San Pablo St. ZNI 245

department: ZNI

institute: USC

description: array identifier: 6929671097_R06C02

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

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

source_name: genomic DNA from pituitary tumor

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from meningiomas tissues using Qiagen DNeasy Kit according to standard instructions.

tag: tissue type

value: pituitary tumor

tag: subtype


title: pituitary tumor_411

description: array identifier: 6929671097_R05C02


title: AXB19b_10


title: pituitary tumor_266

description: array identifier: 6929671097_R03C02


title: AXB19b_9


title: AXB24_8


title: BXD24a_9


title: BXD24a_10


title: BXD36_10


title: C57_12


title: AXB24_9


title: pituitary tumor_320

description: array identifier: 6929671097_R04C02


title: BXH22_13


title: BXH19_21


title: C58_13


title: BXD36_9


title: BXD28_6


title: BXD12_9


title: BXH22_12


title: BXD12_10


title: BXD21_7


title: C58_14


title: MA_9

value: MA/MyJ


title: BXH19_20


title: B6_20


title: MA_10


title: BXA13_10


title: BXD21_8


title: BXA16_10


title: AXB8_9


title: BXA13_9


title: HUVEC_siPML1_treated-rep1

description: HUVEC cells with passage number less than 5 were transfected with siPML1 for 72 hrs with 20 ng/mL TNFalpha treament for 20 h before total RNA extraction. This is one of the technical replicates located on microarray chip A.

tag: cell line

tag: transfection

tag: transfection duration


title: BXD1_9


title: AXB8_8


title: BXH2_15


title: BXH2_14


title: AXB10_9


title: BXD8_10


title: BXA1_4


title: BXD9_10


title: BXA11_6


title: BXA11_5


title: BXD9_9


title: BXD27_8


title: CE_13

value: CE/J


title: BXA12_12


title: BXD8_9


title: AXB10_8


title: BXA26_10


title: BXD34_9


title: BXA26_9


title: BXA14_10


title: BXD33_9


title: BXA14_9


title: BXA24_10


title: BXD34_10


title: BXA24_9


title: CE_14


title: BXA4_9


title: BXA4_10


title: BXA12_11


title: BXD33_10


title: SEA_16


title: BXD29_9


title: BXH6_14


title: BXD24b_9


title: BXD5_8


title: BXD15_7


title: BXH6_13


title: BXD15_8


title: BXH8_14


title: BXD24b_10


title: BXH7_12


title: BXH20_13


title: BXD29_8


title: BXH7_13


title: BXD42_9


title: BXH9_11


title: BXD28_5


title: BXH20_12


title: BXH8_13


title: BXH9_12


title: BXD13_5


title: BXD5_9


title: BXD39_9


title: Muscle_Day 4_SE rep3

city: Gaithersburg

first: Zheng

last: Liu

address: One Medimmune Way

institute: Medimmune LLC

description:
ACF Study Number: 078-10-007
SAMPLE 130

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on mouse genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Expression Console Software using Affymetrix default analysis settings (RMA) and global scaling as normalization method.

source_name: Muscle

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 400 ng total RNA  (Expression Analysis Technical Manual, Rev 3, Affymetrix).

extract_protocol: Total RNA isolation using RNeasy Mini Kit (Qiagen cat #: 74104) or RNeasy Protect Mini Kit (Qiagen cat #: 74124) followed by GLOBINclear™ Protocol (Invitrogen cat #: AM1981) according to the manufacturer's instructions.

value: Balb/c

value: Muscle

tag: agent

value: SE

tag: time

value: Day 4


title: BXD42_10


title: BXD13_6


title: Muscle_Day 2_SE rep3

description:
ACF Study Number: 078-10-007
SAMPLE 127

value: Day 2


title: Muscle_Day 4_SE rep2

description:
ACF Study Number: 078-10-007
SAMPLE 129


title: Muscle_Day 1_SE rep3

description:
ACF Study Number: 078-10-007
SAMPLE 124

value: Day 1


title: Muscle_Day 4_SE rep1

description:
ACF Study Number: 078-10-007
SAMPLE 128


title: BUB_12

value: BUB/BnJ


title: RIII_13

value: RIIIS/J


title: BXD14_10


title: RIII_12


title: Muscle_6 hr_SE rep3

description:
ACF Study Number: 078-10-007
SAMPLE 121

value: 6 hr


title: Muscle_Day 2_SE rep2

description:
ACF Study Number: 078-10-007
SAMPLE 126


title: Muscle_Day 2_SE rep1

description:
ACF Study Number: 078-10-007
SAMPLE 125


title: BXD14_9

value: male


title: I_13

value: 16 weeks

value: I/LnJ


title: BXA2_10

value: epididymal adipose


title: Muscle_Day 1_SE rep2

description:
ACF Study Number: 078-10-007
SAMPLE 123


title: BXA8_10


title: BXA8_9


title: Muscle_Day 1_SE rep1

description:
ACF Study Number: 078-10-007
SAMPLE 122


title: Muscle_6 hr_SE rep2

description:
ACF Study Number: 078-10-007
SAMPLE 120


title: BXA2_9


title: Muscle_Day 1_PBS rep2

description:
ACF Study Number: 078-10-007
SAMPLE 117

value: PBS


title: Muscle_Day 1_PBS rep3

description:
ACF Study Number: 078-10-007
SAMPLE 118


title: Muscle_Day 4_PBS_rep3-2

description:
ACF Study Number: 078-11-008
SAMPLE 115


title: Muscle_6 hr_SE rep1

description:
ACF Study Number: 078-10-007
SAMPLE 119


title: Muscle_Day 1_PBS rep1

description:
ACF Study Number: 078-10-007
SAMPLE 116


title: BXA7_10


title: BXA7_9


title: Muscle_Day 4_PBS_rep3-1

description:
ACF Study Number: 078-11-008
SAMPLE 114


title: AXB12_10


title: AXB12_9


title: AXB15_7


title: AXB15_8


title: Muscle_Day 4_PBS_rep1-1

description:
ACF Study Number: 078-11-008
SAMPLE 110


title: AXB19b_5


title: LG_9

value: LG/J


title: Muscle_Day 2_PBS_rep3-2

description:
ACF Study Number: 078-11-008
SAMPLE 109


title: Muscle_Day 2_PBS_rep1-2

description:
ACF Study Number: 078-11-008
SAMPLE 105


title: Muscle_Day 4_PBS_rep2-2

description:
ACF Study Number: 078-11-008
SAMPLE 113


title: AXB2_10


title: Muscle_Day 2_PBS_rep3-1

description:
ACF Study Number: 078-11-008
SAMPLE 108


title: Muscle_Day 2_PBS_rep2-2

description:
ACF Study Number: 078-11-008
SAMPLE 107


title: Muscle_Day 4_PBS_rep1-2

description:
ACF Study Number: 078-11-008
SAMPLE 111


title: Muscle_Day 1_PBS_rep3

description:
ACF Study Number: 078-11-008
SAMPLE 103


title: BXD40_7


title: Muscle_Day 1_PBS_rep2

description:
ACF Study Number: 078-11-008
SAMPLE 102


title: Muscle_Day 4_PBS_rep2-1

description:
ACF Study Number: 078-11-008
SAMPLE 112


title: AXB2_9


title: BXA16_8


title: AXB19b_6


title: Muscle_Day 2_PBS_rep2-1

description:
ACF Study Number: 078-11-008
SAMPLE 106


title: Muscle_Day 2_PBS_rep1-1

description:
ACF Study Number: 078-11-008
SAMPLE 104


title: BXD40_8


title: BXD2_8


title: BXD2_7


title: Muscle_Day 1_PBS_rep1

description:
ACF Study Number: 078-11-008
SAMPLE 101


title: Muscle_Day 4_GLA-SE_rep3-2

description:
ACF Study Number: 078-11-008
SAMPLE 97

value: GLA-SE


title: Muscle_Day 4_GLA-SE_rep3-1

description:
ACF Study Number: 078-11-008
SAMPLE 96


title: BTBR_12

value: BTBR T<+> tf/J


title: BXD18_6


title: KK_17

value: KK/HlJ


title: Muscle_6 hr_PBS_rep1

description:
ACF Study Number: 078-11-008
SAMPLE 98

value: Balb/c

value: Muscle


title: KK_16


title: SJL_3

value: SJL/J


title: BXA16_9


title: LG10


title: BTBR_13


title: Muscle_6 hr_PBS_rep3

description:
ACF Study Number: 078-11-008
SAMPLE 100


title: Muscle_Day 4_GLA-SE_rep1-2

description:
ACF Study Number: 078-11-008
SAMPLE 93

value: Day 4


title: Muscle_Day 4_GLA-SE_rep2-1

description:
ACF Study Number: 078-11-008
SAMPLE 94


title: BXA25_9


title: SJL_4


title: Muscle_6 hr_PBS_rep2

description:
ACF Study Number: 078-11-008
SAMPLE 99


title: Muscle_Day 2_GLA-SE_rep3-2

description:
ACF Study Number: 078-11-008
SAMPLE 91

value: Day 2


title: Muscle_Day 4_GLA-SE_rep1-1

description:
ACF Study Number: 078-11-008
SAMPLE 92


title: Muscle_Day 2_GLA-SE_rep1-1

description:
ACF Study Number: 078-11-008
SAMPLE 86


title: Muscle_Day 2_GLA-SE_rep1-2

description:
ACF Study Number: 078-11-008
SAMPLE 87


title: BXD20_10


title: Muscle_Day 2_GLA-SE_rep3-1

description:
ACF Study Number: 078-11-008
SAMPLE 90


title: Muscle_Day 4_GLA-SE_rep2-2

description:
ACF Study Number: 078-11-008
SAMPLE 95


title: AXB4_10


title: AXB19a_9


title: Muscle_Day 2_GLA-SE_rep2-1

description:
ACF Study Number: 078-11-008
SAMPLE 88


title: Muscle_Day 2_GLA-SE_rep2-2

description:
ACF Study Number: 078-11-008
SAMPLE 89


title: AXB4_9


title: Muscle_Day 1_GLA-SE_rep3-2

description:
ACF Study Number: 078-11-008
SAMPLE 85

value: Day 1


title: BXA25_10


title: Muscle_Day 1_GLA-SE_rep2-2

description:
ACF Study Number: 078-11-008
SAMPLE 83


title: AXB19a_8


title: NZW_14

value: NZW/LacJ


title: NZW_13


title: SM_17

value: SM/J


title: BalbcJ_14

value: male

value: BALB/cJ


title: BXH4_13

value: 16 weeks


title: Muscle_Day 1_GLA-SE_rep3-1

description:
ACF Study Number: 078-11-008
SAMPLE 84


title: Muscle_6 hr_GLA-SE_rep3-2

description:
ACF Study Number: 078-11-008
SAMPLE 79

value: 6 hr


title: Muscle_Day 1_GLA-SE_rep1-1

description:
ACF Study Number: 078-11-008
SAMPLE 80


title: LPJ_17

value: LP/J

value: epididymal adipose


title: CAST_8

value: CAST/EiJ


title: LPJ_18


title: SM_18


title: Muscle_6 hr_GLA-SE_rep3-1

description:
ACF Study Number: 078-11-008
SAMPLE 78

value: GLA-SE


title: BXH4_12


title: Muscle_Day 1_GLA-SE_rep2-1

description:
ACF Study Number: 078-11-008
SAMPLE 82


title: BXD22_2


title: Muscle_6 hr_GLA-SE_rep1-1

description:
ACF Study Number: 078-11-008
SAMPLE 74


title: Muscle_6 hr_GLA-SE_rep2-2

description:
ACF Study Number: 078-11-008
SAMPLE 77


title: Muscle_6 hr_GLA-SE_rep1-2

description:
ACF Study Number: 078-11-008
SAMPLE 75


title: BalbcJ_13


title: Muscle_Day 4_GLA_rep3-1

description:
ACF Study Number: 078-11-008
SAMPLE 72

value: GLA


title: Muscle_Day 4_GLA_rep3-2

description:
ACF Study Number: 078-11-008
SAMPLE 73

value: Balb/c


title: Muscle_6 hr_GLA-SE_rep2-1

description:
ACF Study Number: 078-11-008
SAMPLE 76

value: Muscle


title: Muscle_Day 1_GLA-SE_rep1-2

description:
ACF Study Number: 078-11-008
SAMPLE 81


title: SWR_14

value: SWR/J


title: SWR_13


title: BXD11_6


title: Muscle_Day 4_GLA_rep2-2

description:
ACF Study Number: 078-11-008
SAMPLE 71

value: Day 4


title: Muscle_Day 4_GLA_rep1-2

description:
ACF Study Number: 078-11-008
SAMPLE 69


title: AKR_14

value: AKR/J


title: AKR_13


title: Muscle_Day 4_GLA_rep2-1

description:
ACF Study Number: 078-11-008
SAMPLE 70


title: 129X1_13


title: Muscle_Day 2_GLA_rep3-2

description:
ACF Study Number: 078-11-008
SAMPLE 67

value: Day 2


title: CBA_12

value: CBA/J


title: CBA_13


title: 129X1_14


title: Muscle_Day 2_GLA_rep3-1

description:
ACF Study Number: 078-11-008
SAMPLE 66


title: Muscle_Day 4_GLA_rep1-1

description:
ACF Study Number: 078-11-008
SAMPLE 68


title: PL/J_13

value: PL/J


title: C3H_14

value: male


title: Muscle_Day 2_GLA_rep2-2

description:
ACF Study Number: 078-11-008
SAMPLE 65


title: Muscle_Day 1_GLA_rep3-1

description:
ACF Study Number: 078-11-008
SAMPLE 60

value: Day 1


title: Muscle_Day 1_GLA_rep2-2

description:
ACF Study Number: 078-11-008
SAMPLE 59


title: Muscle_Day 1_GLA_rep3-2

description:
ACF Study Number: 078-11-008
SAMPLE 61


title: C3H_13

value: 16 weeks


title: Muscle_Day 2_GLA_rep1-1

description:
ACF Study Number: 078-11-008
SAMPLE 62


title: PL/J_14


title: DBA_14


title: Muscle_Day 2_GLA_rep1-2

description:
ACF Study Number: 078-11-008
SAMPLE 63


title: DBA_13


title: B6_18


title: FVB_11

value: FVB/NJ


title: AJ_15

value: A/J


title: Muscle_Day 1_GLA_rep2-1

description:
ACF Study Number: 078-11-008
SAMPLE 58


title: Muscle_6 hr_GLA_rep2-1

description:
ACF Study Number: 078-11-008
SAMPLE 52

value: 6 hr


title: Muscle_6 hr_GLA_rep3-2

description:
ACF Study Number: 078-11-008
SAMPLE 55


title: Muscle_6 hr_GLA_rep2-2

description:
ACF Study Number: 078-11-008
SAMPLE 53


title: Muscle_Day 1_GLA_rep1-1

description:
ACF Study Number: 078-11-008
SAMPLE 56


title: FVB_10

value: epididymal adipose


title: Muscle_Day 1_GLA_rep1-2

description:
ACF Study Number: 078-11-008
SAMPLE 57


title: Muscle_6 hr_GLA_rep3-1

description:
ACF Study Number: 078-11-008
SAMPLE 54


title: B6_17


title: NOD_18

value: NOD/ShiLtJ


title: Muscle_Day 2_GLA_rep2-1

description:
ACF Study Number: 078-11-008
SAMPLE 64

value: GLA


title: Muscle_Day 4_Alum_rep2-1

description:
ACF Study Number: 078-11-008
SAMPLE 46

value: Balb/c

value: Alum


title: Muscle_Day 4_Alum_rep3-1

description:
ACF Study Number: 078-11-008
SAMPLE 48

value: Muscle


title: Muscle_6 hr_GLA_rep1-2

description:
ACF Study Number: 078-11-008
SAMPLE 51


title: AJ_14


title: Muscle_Day 4_Alum_rep3-2

description:
ACF Study Number: 078-11-008
SAMPLE 49

value: Day 4


title: Muscle_6 hr_GLA_rep1-1

description:
ACF Study Number: 078-11-008
SAMPLE 50


title: Muscle_Day 4_Alum_rep1-2

description:
ACF Study Number: 078-11-008
SAMPLE 45


title: 15 mM lactic acid, 7d

city: Tuebingen

first: Michael

middle: H.

last: Walter

address: Calwer Str. 7

department: Department of Medical Genetics

country: Germany

institute: University of Tuebingen

hyb_protocol: Following fragmentation, 15 ug of cDNA were hybridized for 16 hr at 45°C on GeneChip HuGene-1.0-st-v1 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 gene chip scanner with GCOS 1.4.

data_processing: The data were analysed using Bioconductor package 'affy' under R-2.10.0. Background correction, normalization and probe summarization was performed with RMA using the unsupported CDF environment (package 'hugene10stv1cdf') .

label_protocol: Biotinylated cDNA was prepared according to the Affymetrix Whole Transkript Sense Labelling protocol from100 ng total RNA according to the manufacturer

growth_protocol: The bone marrow was obtained under sterile conditions in steril heparinised syringes. The isolation of the hMSCs was performed with Biotest  Lymphoflot©  (Lymphoflot©, Biotest, Dreireich, Germany). The hMSCs were incubated under standard conditions (37°C,  95% air, 5% CO2) with Lonza Medium MEM Alpha Eagle (MEM Alpha Eagle, Lonza, Walkersville Inc., USA). The medium was changed every 24 hours and non-adherent cells  were removed. The characterisation of the cultivated adherent cells was performed with fluorescence-activated cell sorting (FACS) analysis.

extract_protocol: RNA  was extracted by using RNeasy Midi Kit (Qiagen) following manufacturers instructions for cells.

treatment_protocol: hMSCs were treated with the Lonza MEM Alpha Eagle Medium supplemented with either 5, 10  and 15 mM lactate (pH 7,4) (l-lactate, Sigma Aldrich, Deisenhofen, Germany) for 24 hours. hMSCs incubated in same media without lactate served as controls.

tag: concentration

value: 15 mM

tag: treatment

value: lactic acid

tag: cell type

value: primary bone marrow human mesenchymal stem cells


title: Muscle_Day 4_Alum_rep2-2

description:
ACF Study Number: 078-11-008
SAMPLE 47


title: 5 mM lactic acid, 7d

source_name: bone marrow human mesenchymal stem cells

value: 5 mM


title: Muscle_Day 4_Alum_rep1-1

description:
ACF Study Number: 078-11-008
SAMPLE 44


title: 10 mM lactic acid, 7d

value: 10 mM


title: 5 mM lactic acid, 3d


title: 0 mM lactic acid, 3d

value: 0 mM


title: 0 mM lactic acid, 7d


title: Muscle_Day 2_Alum_rep3-2

description:
ACF Study Number: 078-11-008
SAMPLE 43

value: Day 2


title: Muscle_Day 2_Alum_rep2-1

description:
ACF Study Number: 078-11-008
SAMPLE 40


title: 15 mM lactic acid, 3d


title: Muscle_Day 2_Alum_rep3-1

description:
ACF Study Number: 078-11-008
SAMPLE 42


title: 10 mM lactic acid, 3d


title: Muscle_Day 2_Alum_rep2-2

description:
ACF Study Number: 078-11-008
SAMPLE 41


title: Muscle_Day 2_Alum_rep1-1

description:
ACF Study Number: 078-11-008
SAMPLE 38


title: Muscle_Day 1_Alum_rep2-2

description:
ACF Study Number: 078-11-008
SAMPLE 35

value: Day 1


title: 10 mM lactic acid, 1d


title: Muscle_Day 1_Alum_rep3-2

description:
ACF Study Number: 078-11-008
SAMPLE 37


title: Muscle_Day 1_Alum_rep3-1

description:
ACF Study Number: 078-11-008
SAMPLE 36


title: Muscle_Day 2_Alum_rep1-2

description:
ACF Study Number: 078-11-008
SAMPLE 39


title: 0 mM lactic acid, 1d


title: Cort+RU 6HR #3

city: Ann Arbor

first: Bradley

middle: S

last: Carter

state: MI

address: 109 Zina PItcher Place

department: Molecular and Behavioral Neuroscience Institute

institute: University of Michigan

description: 6 hour steroid+antagonist replicate-3

hyb_protocol: Standard Illumina hybridization protocol (MouseWG-6 v2.0 Expression BeadChip)

scan_protocol: Standard Illumina scanning protocol (BeadArray reader)

data_processing: Data normalised using quantile normalization with Illumina GenomeStudio software; for each time point, the Cort/Cort+RU data was normlized to the corresponding vehicle control data (e.g. Matrix normalized data is representative for 2 hour data; normalized to 2 hour vehicle data)

label: Biotin

source_name: Cortical astrocyte culture

label_protocol: Biotinylated cRNA were prepared with the Ambion's TotalPrep RNA Amplification kit for Illumina arrays

growth_protocol: Primary cultures derived from P0-P2 mouse pups (cortex or hippocampus), plated 250,000-500,000/well in 6-well dishes, grown 9-11 days until ~confluent (grown in 37C incubator with DMEM+10%FBS media; 100% media changed 24 hours post-plating, 50% media replaced every 2-3 days afterward)

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: 100nM corticosterone with or without 500nM RU486  in media for given time period (returned to incubator)

value: Brain

tag: developmental stage

value: 6 hour 100nM corticosterone + 500nM RU486


title: 5 mM lactic acid, 1d


title: RU486 6HR #3

description: 6 hour antagonist replicate-3

value: 6 hour 500nM RU486


title: Cort+RU 6HR #1

description: 6 hour steroid+antagonist replicate-1


title: Muscle_Day 1_Alum_rep2-1

description:
ACF Study Number: 078-11-008
SAMPLE 34


title: Cort+RU 6HR #2

description: 6 hour steroid+antagonist replicate-2


title: 15 mM lactic acid, 1d


title: Muscle_6 hr_Alum_rep2-2

description:
ACF Study Number: 078-11-008
SAMPLE 29

value: 6 hr


title: RU486 6HR #1

description: 6 hour antagonist replicate-1


title: Muscle_Day 1_Alum_rep1-1

description:
ACF Study Number: 078-11-008
SAMPLE 32


title: Muscle_6 hr_Alum_rep3-2

description:
ACF Study Number: 078-11-008
SAMPLE 31


title: Veh 6HR #2

description: 6 hour vehicle replicate-2

value: 6 hour vehicle


title: Muscle_Day 1_Alum_rep1-2

description:
ACF Study Number: 078-11-008
SAMPLE 33

value: Balb/c


title: Muscle_6 hr_Alum_rep1-2

description:
ACF Study Number: 078-11-008
SAMPLE 27

value: Alum


title: Muscle_6 hr_Alum_rep3-1

description:
ACF Study Number: 078-11-008
SAMPLE 30

value: Muscle


title: Muscle_6 hr_Alum_rep2-1

description:
ACF Study Number: 078-11-008
SAMPLE 28


title: RU486 6HR #2

description: 6 hour antagonist replicate-2


title: Muscle_6 hr_Alum_rep1-1

description:
ACF Study Number: 078-11-008
SAMPLE 26


title: Cort 6HR #3

description: 6 hour steroid replicate-3

value: 6 hour 100nM corticosterone


title: Veh 6HR #1

description: 6 hour vehicle replicate-1


title: Lymphnode_Day 1_PBS_rep1

description:
ACF Study Number: 078-11-008
SAMPLE 23

source_name: Lymphnode

value: Lymphnode

value: PBS


title: 2nd Water deficit stress 6h

city: Beijing

first: Junping

address: Department of Ornamental Horticulture, China Agricultural University

department: Ornamental Horticulture

country: China

institute: China Agricultural University

description: Analysis used total RNA samples of petals taken from flowers treated by WDS comparison to those from control flowers

hyb_protocol: The washes of prehybridization, hybridization, and posthybridization were carried out according to UltraGAPS coated slides instruction manual (Corning, NY, USA).

scan_protocol: The slides were scanned by using an Axon Genepix 4000B scanner (Molecular Devices, Union City, CA, USA) at a resolution of 10 μm. Laser and photomultiplier tube voltages were adjusted manually to minimize background and the number of spots that had saturated signal values.

data_processing: Spot intensities were quantified using GenePix pro 6.0 (Axon Instruments). Spots with mean signal intensities less than local background intensities plus two standard deviations of the local background in both channels were regarded as empty spots and not included in the downstream statistical analysis. A Print-tip Lowess Normalization strategy was applied to normalize the ratio values for each array using the marray package in Bioconductor (Yang et al, 2002).

organism: Rosa hybrid cultivar

source_name: Petal samples from flowers exposed to air again for 6h for 2nd WDS treatment after 12h water recovery

label_protocol: Cy3- and cy5-labeled cDNA probes were generated using SuperScript direct cDNA Labeling System (Invitrogen, Carlsbad, USA) according to established protocols. Cy3 and Cy5 probes were mixed with equivalent quantity, and purified by spin columns (Minipore, Eschborn, Germany) to 20 µL volume.

growth_protocol: The flowers were placed in a climate-controlled room at 23–25 oC, 30–40% relative humidity (RH), and a 12 h/12 h light/dark photoperiod with light intensity of 40 µmol m−2 s−1 to simulate water deficit stress (WDS).

extract_protocol: Total RNA of samples were extracted using the hot borate method

treatment_protocol: The flowers were subjected to a repeated WDS treatment. They were exposed to air for 24 h on test-beds as 1st WDS, and their stems were recut off 1 cm stem base under water and placed in water for 12 h as WR (water recovery), then the flowers were re-exposed to air for 12 h as 2nd WDS. All control flowers had been placed in water.

value: flower petals

value: stage 2

tag: stress

value: 2nd Water deficit stress

source_name: Petal samples from flowers placed in water for 42h as control

value: control


title: Lymphnode_Day 1_PBS_rep3

description:
ACF Study Number: 078-11-008
SAMPLE 25


title: Cort 6HR #1

description: 6 hour steroid replicate-1


title: Veh 6HR #3

description: 6 hour vehicle replicate-3


title: Water recovery 12h

source_name: Petal samples from flowers placed in water for 1h followed 25h WDS treatment

value: Water recovery

source_name: Petal samples from flowers placed in water for 36h as control


title: Water recovery 1h

source_name: Petal samples from flowers placed in water for 12h followed 24h WDS treatment

source_name: Petal samples from flowers placed in water for 25h as control


title: Lymphnode_Day 1_PBS_rep2

description:
ACF Study Number: 078-11-008
SAMPLE 24

value: Day 1


title: BXD22_1

tag: gender

value: male

value: 16 weeks

value: epididymal adipose


title: Lymphnode_Day 4_GLA-SE_rep3

description:
ACF Study Number: 078-11-008
SAMPLE 22

value: GLA-SE

value: Day 4


title: 1st Water deficit stress 24h

source_name: Petal samples from flowers exposed to air for 24h for WDS treatment

value: 1st Water deficit stress

source_name: Petal samples from flowers placed in water for 24h as control


title: Cort+RU 4HR #3

description: 4 hour steroid+antagonist replicate-3

value: Brain

value: 4 hour 100nM corticosterone + 500nM RU486


title: Cort 6HR #2

description: 6 hour steroid replicate-2

value: 6 hour 100nM corticosterone


title: 1st Water deficit stress 12h

source_name: Petal samples from flowers exposed to air for 12h for WDS treatment

source_name: Petal samples from flowers placed in water for 12h as control


title: Lymphnode_Day 2_GLA-SE_rep2

description:
ACF Study Number: 078-11-008
SAMPLE 18

value: Balb/c

value: Lymphnode

value: Day 2


title: 1st Water deficit stress 6h

source_name: Petal samples from flowers exposed to air for 6h for WDS treatment

value: flower petals

value: stage 2

source_name: Petal samples from flowers placed in water for 6h as control


title: Lymphnode_Day 1_GLA-SE_rep3

description:
ACF Study Number: 078-11-008
SAMPLE 16


title: Lymphnode_Day 4_GLA-SE_rep2

description:
ACF Study Number: 078-11-008
SAMPLE 21


title: Lymphnode_Day 2_GLA-SE_rep3

description:
ACF Study Number: 078-11-008
SAMPLE 19


title: Lymphnode_Day 4_GLA-SE_rep1

description:
ACF Study Number: 078-11-008
SAMPLE 20


title: Lymphnode_Day 1_GLA-SE_rep1

description:
ACF Study Number: 078-11-008
SAMPLE 14


title: RU486 4HR #3

description: 4 hour antagonist replicate-3

value: 4 hour 500nM RU486


title: Lymphnode_Day 2_GLA-SE_rep1

description:
ACF Study Number: 078-11-008
SAMPLE 17


title: Cort+RU 4HR #2

description: 4 hour steroid+antagonist replicate-2


title: Cort+RU 4HR #1

description: 4 hour steroid+antagonist replicate-1


title: Lymphnode_Day 1_GLA-SE_rep2

description:
ACF Study Number: 078-11-008
SAMPLE 15


title: 1st Water deficit stress 3h

source_name: Petal samples from flowers exposed to air for 3h for WDS treatment

source_name: Petal samples from flowers placed in water for 3h as control

value: control


title: RU486 4HR #2

description: 4 hour antagonist replicate-2


title: Blood_6 hr_PBS_pulled

description:
ACF Study Number: 078-11-008
SAMPLE 10

source_name: Blood

value: Blood

value: PBS

value: 6 hr


title: RU486 4HR #1

description: 4 hour antagonist replicate-1

source_name: Cortical astrocyte culture


title: Lymphnode_6 hr_GLA-SE_rep1

description:
ACF Study Number: 078-11-008
SAMPLE 11

source_name: Lymphnode


title: Lymphnode_6 hr_GLA-SE_rep2

description:
ACF Study Number: 078-11-008
SAMPLE 12


title: iP-MSC donor2 cloneC

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 Beadchip using standard Infinium HD Methylation Assay protocol.

scan_protocol: Standard Infinium HD Methylation Assay protocol

data_processing: Initial analysis was performed by the Genomestudio 2010.3 (Modul M Version 1.8.5). Data were normalized with internal controls according to Illumina´s standard procedures. Methylation level at each locus was calculated with the GenomeStudio Methylation module as beta-value (ranging from 0 to 1). The number of beads per feature varies between chips and beta-values were calculated as average of at least three technical replica.

source_name: bone marrow-derived MSC (iP-MSC)

growth_protocol: MSC from three donors were infected on two consecutive days with equal amounts of pMXs based retroviruses (Addgene, Cambridge, MA, USA) carrying the OCT3/4, SOX2, KLF4 and c-MYC genes. On day 3, medium was changed to high glucose DMEM (Gibco), 20% FCS, 1% nonessential amino acids (NAA), 1x penicillin/streptomycin, 1x L-glutamine, 0.1 mM β-mercaptoethanol (βME) and 50 ng/ml basic fibroblast growth factor (bFGF) (Peprotech, Hamburg, Germany). On day 6 the cells were plated on gelatin-coated dishes containing irradiated CF1 murine embryonic fibroblasts (MEFs), and on day 7 the culture medium was supplemented with 20 μg/ml vitamin C (Sigma) and 1mM valproic acid (Sigma). Between days 21–30 the ESC-like colonies were observed and mechanically isolated. Established iP-MSC were maintained on MEFs in DMEM/F12 medium supplemented with Glutamax, 20% knockout serum replacer, 1% NAA, 0.1 mM βME and 50 ng/ml bFGF. Cells were passaged by manual dissection of cell clusters every 5-6 days.

extract_protocol: Genomic DNA was isolated from 10(6) cells using the Qiagen DNA Blood Midi Kit.

treatment_protocol: MSC were isolated from tibia plateau of patients undergoing orthopaedic surgery. All samples were taken after written consent using guidelines approved by the Ethic Committee on the Use of Human Subjects at the University of Aachen (Permit number: EK128/09). MSC were culture-expanded in standard medium consisting of DMEM (PAA; 1g/L glucose) supplemented with glutamine (PAA), penicillin/streptomycin (PAA) and 10% human platelet lysate (hPL).

tag: donor

value: donor2, cloneC

value: iPSC


title: Veh 4HR #3

description: 4 hour vehicle replicate-3

tag: strain

value: 4 hour vehicle


title: 1st Water deficit stress 1h

source_name: Petal samples from flowers exposed to air for 1h for WDS treatment

value: 1st Water deficit stress

source_name: Petal samples from flowers placed in water for 1h as control


title: Lymphnode_6 hr_GLA-SE_rep3

description:
ACF Study Number: 078-11-008
SAMPLE 13

value: GLA-SE


title: iP-MSC donor5 cloneC

label_protocol: Standard Infinium HD Methylation Assay protocol

value: donor5, cloneC


title: Blood_Day2_GLA-SE_rep2

description:
ACF Study Number: 078-11-008
SAMPLE 8


title: 17-TM2

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: LM

hyb_protocol: A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s procedures.

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

data_processing: Data were normalized using RMA as implemented in the Affy package of Bioconductor. Expression values are represented on a log2-scale.

source_name: PaCa, liver metastasis

label_protocol: RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).

growth_protocol: Biopsies were taken peroperatively and stored in RNAlater (-80°C) until RNA extraction.

extract_protocol: RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the instructions of the manufacturer.

value: male

tag: age

value: 67 years

value: liver metastasis from pancreatic cancer

tag: tumor stage

value: M+


title: Placenta_villi_weeks8_4

city: New Delhi

first: Meraj

middle: Alam

last: Khan

state: Delhi

address: Room No.2029

department: Physiology

country: India

institute: All India Institute of Medical Sciences

description:
Fertile_hpv8w_SP22_23 years
This placental sample is of first  trimester normal pregnancy, underwent elective surgical termination. It is the fourth of eight, 8 weeks biological replicates sample, each from different individual woman.

hyb_protocol: The labeled cDNA probes were hybridized to the NimbelGen Human Gene Expression 12x135K (60-mer probes per target for latest 45,033 human genome builds) microarray in glass format (070925_HG18_expr_HX12) using the NimbleGen Expression protocol. See http://www.nimblegen.com/products/ expression/ eukarya/ human/ 12x135k/ index.html.

scan_protocol: Scanning was performed by Agilent G2505B microarray scanner system at 5 micron resolution, following the standard operating protocol.

data_processing:
The scanned images were processed to normalize the expression data using quantile normalization and Robust Multi-array analysis (RMA) algorithm using the NimbleScan2.5 software (Roche NimbleGen, Inc.).
The RMA  files containing normalized image analysis values for each detected probe along with accession number were imported into the GeneSpring11.5.0 software (Agilent Technologies) for further analysis on log transformed data and averaged gene-level signal intensity.

source_name: 8 weeks placental villi

label_protocol: Microarray experiments with individual samples were performed according to standard methodological guide lines (http://www.mged.org/ Workgroups/MIAME/miame.html). Total RNA (10 µg/sample) with RIN score >8.0 was converted to cDNA by reverse transcriptase enzymes and labeled with Cy3 dye. See www.nimblegen.com.

extract_protocol: Placental samples were collected in sterile ice-cold phosphate buffered saline (PBS, pH 7.4). The tissue samples were quickly washed in ice-cold PBS to remove blood and debris, and separated from surrounding membranes, and villous portions were dissected from decidual and embryonic tissue under a dissecting microscope and further washed with sterile, cold PBS. The total RNA was extracted using Trizol (Agilent Technologies Singapore Pvt. Ltd., Shung Avenue, Singapore) and cleaned up with DNase I (Sigma Chemical Co., St. Louis, Missouri, USA) and subjected to re-extraction when it was necessary. The yield and purity of the extracted RNA was checked using standard spectrophotometric method and 1% agarose gel electrophoresis. Furthermore, RIN score of individual sample was determined using Bioanalyzer, RNA Chip kit and Software from Agilent Technologies (Santa Clara, CA, USA).

value: 23 years

tag: gestation stage

value: 8 weeks

tag: gestational history

value: term pregnancy_1; preterm_0; abortion_1; living children_1


title: Blood_Day1_GLA-SE_rep3

description:
ACF Study Number: 078-11-008
SAMPLE 6

value: Balb/c

tag: tissue

value: Day 1


title: Blood_Day2_GLA-SE_rep3

description:
ACF Study Number: 078-11-008
SAMPLE 9

value: Blood

value: Day 2


title: Veh 4HR #2

description: 4 hour vehicle replicate-2

value: Brain


title: Placenta_villi_weeks8_5

description:
Fertile_hpv8w_SP12_28 years
This placental sample is of first  trimester normal pregnancy, underwent elective surgical termination. It is the fifth of eight, 8 weeks biological replicates sample, each from different individual woman.

value: 28 years


title: Placenta_villi_weeks8_6

description:
Fertile_hpv8w_SP5.5_26 years
This placental sample is of first  trimester normal pregnancy, underwent elective surgical termination. It is the sixth of eight, 8 weeks biological replicates sample, each from different individual woman.

value: 26 years

value: term pregnancy_1; preterm_0; abortion_2; living children_1


title: Placenta_villi_weeks8_7

description:
Fertile_hpv8w_SP1.1_20 years
This placental sample is of first  trimester normal pregnancy, underwent elective surgical termination. It is the seventh of eight, 8 weeks biological replicates sample, each from different individual woman.

value: 20 years


title: Cort 4HR #1

description: 4 hour steroid replicate-1

value: 4 hour 100nM corticosterone


title: D-7730/A1-BT

description: good

source_name: PaCa, good prognosis

value: male

value: 32 years

value: pancreatic ductal adenocarcinoma (PDAC)

tag: tumor grade

tag: Stage

tag: prognosis

value: good


title: Blood_Day1_GLA-SE_rep1

description:
ACF Study Number: 078-11-008
SAMPLE 4

tag: agent

value: GLA-SE

tag: time


title: 11-179

description: LM

value: 69 years

value: liver metastasis from pancreatic cancer

value: M+


title: Cort 4HR #2

description: 4 hour steroid replicate-2

tag: treatment


title: Blood_Day2_GLA-SE_rep1

description:
ACF Study Number: 078-11-008
SAMPLE 7

value: Balb/c


title: Cort 4HR #3

description: 4 hour steroid replicate-3


title: Placenta_villi_weeks8_3

description:
Fertile_hpv8w_SP14_28 years
This placental sample is of first  trimester normal pregnancy, underwent elective surgical termination. It is the third of eight, 8 weeks biological replicates sample, each from different individual woman.

value: 8 weeks

value: term pregnancy_2; preterm_0; abortion_1; living children_2


title: Veh 4HR #1

description: 4 hour vehicle replicate-1

value: Brain

value: 4 hour vehicle


title: Blood_Day1_GLA-SE_rep2

description:
ACF Study Number: 078-11-008
SAMPLE 5

value: Blood

value: Day 1


title: D-12411/1-BT

description: bad

source_name: PaCa, bad prognosis

value: female

value: 78 years

value: bad


title: D-12928/2-BT

description: bad

value: male

value: 59 years


title: D-5115-BT

description: good

value: 55 years

value: pancreatic ductal adenocarcinoma (PDAC)

value: good


title: Blood_6 hr_GLA-SE_rep3

description:
ACF Study Number: 078-11-008
SAMPLE 3

value: GLA-SE

value: 6 hr


title: 12-180

description: LM

value: 47 years

value: liver metastasis from pancreatic cancer

value: M+


title: Cort+RU 2HR #2

description: 2 hour steroid+antagonist replicate-2

value: Brain

value: 2 hour 100nM corticosterone + 500nM RU486


title: Placenta_villi_weeks8_2

description:
Fertile_hpv8w_SP8_26 years
This placental sample is of first  trimester normal pregnancy, underwent elective surgical termination. It is the second of eight, 8 weeks biological replicates sample, each from different individual woman.

value: 26 years

value: 8 weeks

value: term pregnancy_1; preterm_0; abortion_1; living children_1


title: 14-210

description: PM

source_name: PaCa, peritoneal metastasis

value: 79 years

value: peritoneal metastasis from pancreatic cancer


title: Blood_6 hr_GLA-SE_rep1

description:
ACF Study Number: 078-11-008
SAMPLE 1

value: Balb/c

value: Blood


title: Blood_6 hr_GLA-SE_rep2

description:
ACF Study Number: 078-11-008
SAMPLE 2


title: 9-167

description: LM

value: female

value: 62 years


title: Placenta_villi_weeks7_9

description:
Fertile_hpv7w_SP30_22 years
This placental sample is of first  trimester normal pregnancy, underwent elective surgical termination. It is the nineth of nine, 7 weeks biological replicates sample, each from different individual woman.

source_name: 7 weeks placental villi

value: 22 years

value: 7 weeks


title: Cort+RU 2HR #1

description: 2 hour steroid+antagonist replicate-1


title: RU486 2HR #2

description: 2 hour antagonist replicate-2

value: 2 hour 500nM RU486


title: Placenta_villi_weeks8_1

description:
Fertile_hpv8w_SP3_30 years
This placental sample is of first  trimester normal pregnancy, underwent elective surgical termination. It is the first of eight, 8 weeks biological replicates sample, each from different individual woman.

value: 30 years

value: term pregnancy_2; preterm_0; abortion_2; living children_2


title: Veh 2HR #3

description: 2 hour vehicle replicate-3

value: 2 hour vehicle


title: Placenta_villi_weeks7_8

description:
Fertile_hpv7w_SP27_24 years
This placental sample is of first  trimester normal pregnancy, underwent elective surgical termination. It is the eighth of nine, 7 weeks biological replicates sample, each from different individual woman.

value: 24 years

value: term pregnancy_1; preterm_0; abortion_2; living children_1


title: Placenta_villi_weeks7_7

description:
Fertile_hpv7w_SP2.2_25 years
This placental sample is of first  trimester normal pregnancy, underwent elective surgical termination. It is the seventh of nine, 7 weeks biological replicates sample, each from different individual woman.

value: 25 years


title: RU486 2HR #3

description: 2 hour antagonist replicate-3

value: Brain


title: EVI_GFP positive Lin- cells replicate 3

city: Hannover

first: Adrian

last: Schwarzer

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

institute: Hannover Medical School

description: Gene expression data from untransduced Lin- hematopoietic progenitors cultured in S3F11 medium

hyb_protocol: 12.5 ug of fragmented and biotin labeled aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix 3000 7G Scanner

data_processing: CEL files were background corrected, quantile normalized and summarized using the RMA package (Bioconductor). QC was performed with ArrayQualityMetrics (Bioconductor)

source_name: Lin- Rosa26rtTA cells transduced with pRRL.TET.EVI1.IRES.EGFP

label_protocol: Biotin GeneChip 3 IVT Express Kit (Affymetrix)

growth_protocol: S3F11 medium:  murine stem cell factor (mSCF) 50 ng/ml, murine interleukin 3 (mIL-3) 20 ng/ml, human FMS like tyrosine kinase 3 ligand (hFlt-3) 50 ng/ml, and human interleukin 11 (hIL-11) 50 ng/ml

extract_protocol: Qiagen Rneasy Micro Kit followed by linear RNA amplification with GeneChip 3 IVT Express Kit (Affymetrix)

treatment_protocol: Flow sorted transduced and untransduced Lin- hematopoietic progenitors were pelleted and total RNA extracted with Qiagen Rneasy Micro Kit

tag: background strain

tag: cell type

value: Lin- hematopoietic progenitors


title: Cort+RU 2HR #3

description: 2 hour steroid+antagonist replicate-3

tag: developmental stage

value: 2 hour 100nM corticosterone + 500nM RU486


title: Placenta_villi_weeks7_5

description:
Fertile_hpv7w_SP25_26 years
This placental sample is of first  trimester normal pregnancy, underwent elective surgical termination. It is the fifth of nine, 7 weeks biological replicates sample, each from different individual woman.

value: 26 years

value: term pregnancy_2; preterm_0; abortion_1; living children_2


title: Veh 2HR #2

description: 2 hour vehicle replicate-2


title: RU486 2HR #1

description: 2 hour antagonist replicate-1


title: Veh 2HR #1

description: 2 hour vehicle replicate-1


title: Placenta_villi_weeks7_6

description:
Fertile_hpv7w_SP29_25 years
This placental sample is of first  trimester normal pregnancy, underwent elective surgical termination. It is the sixth of nine, 7 weeks biological replicates sample, each from different individual woman.

value: term pregnancy_1; preterm_0; abortion_1; living children_1


title: Placenta_villi_weeks7_4

description:
Fertile_hpv7w_SP11_25 years
This placental sample is of first  trimester normal pregnancy, underwent elective surgical termination. It is the fourth of nine, 7 weeks biological replicates sample, each from different individual woman.


title: D-12341/2-BT

description: bad

tag: gender

value: male

value: 52 years

value: pancreatic ductal adenocarcinoma (PDAC)

value: bad


title: EVI_GFP positive Lin- cells replicate 2


title: D-11719*-BT

description: good

value: female

value: 62 years

value: good


title: 8-M3

description: PM

value: 49 years

value: peritoneal metastasis from pancreatic cancer

value: M+


title: D-10865-BT

description: good

value: 61 years


title: Cort 2HR #3

description: 2 hour steroid replicate-3

value: Brain

value: 2 hour 100nM corticosterone


title: EVI_GFP negative Lin- cells replicate 2

source_name: Lin- Rosa26rtTA cells untransduced

value: Lin- hematopoietic progenitors


title: 6-M2

description: LM

value: 65 years

value: liver metastasis from pancreatic cancer


title: Cort 2HR #2

description: 2 hour steroid replicate-2


title: Placenta_villi_weeks7_3

description:
Fertile_hpv7w_SP5_26 years
This placental sample is of first  trimester normal pregnancy, underwent elective surgical termination. It is the third of nine, 7 weeks biological replicates sample, each from different individual woman.

value: 26 years

value: 7 weeks

value: term pregnancy_1; preterm_0; abortion_1; living children_1


title: EVI_GFP negative Lin- cells replicate 3


title: Placenta_villi_weeks7_2

description:
Fertile_hpv7w_SP3.3_24 years
This placental sample is of first  trimester normal pregnancy, underwent elective surgical termination. It is the second of nine, 7 weeks biological replicates sample, each from different individual woman.

value: 24 years


title: D-11993-BT

description: bad

value: male

value: 72 years

value: pancreatic ductal adenocarcinoma (PDAC)

value: bad


title: 4-M1

description: LM

value: 69 years


title: D-10578/1-BT

description: bad

value: female

value: 75 years


title: EVI_GFP positive Lin- cells replicate 1


title: 7-M2

description: PM

value: peritoneal metastasis from pancreatic cancer

value: M+


title: EVI_GFP negative Lin- cells replicate 1


title: D-10342-BT

description: good

value: 53 years

value: good


title: Placenta_villi_weeks6_7

description:
Fertile_hpv6w_SP13_21 years
This placental sample is of first  trimester normal pregnancy, underwent elective surgical termination. It is the seventh of eight, 6 weeks biological replicates sample, each from different individual woman.

source_name: 6 weeks placental villi

value: 21 years

value: 6 weeks


title: Gene expression in DX5+ NK

city: Hefei

first: Hui

last: Peng

address: 443 Huangshan Road

institute: University of Science and Technology of China

description: Gene expression in DX5+ NK

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Mouse430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Raw data were normalized by MAS 5.0 algorithm,GCOS1.4.

source_name: Liver DX5+ NK cells

label_protocol: cRNA were labeled by using One-Cycle Target Labeling and Control Reagents, Affymetrix, P/N 900493,and then purified by using QIAGEN RNeasy Total RNA Isolation kit.

extract_protocol: Total RNA was extracted from each sample using Trizol (Qiagen) according to the manufacturer's protocol. RNA was then further purified using  RNeasy Mini Kit (Qiagen).

treatment_protocol: DX5-NK1.1+CD3- cells and DX5+NK1.1+CD3- cells were sorted from the liver of naive B6 wild-type mice by  FACS Aria.

value: liver


title: Placenta_villi_weeks6_8

description:
Fertile_hpv6w_SP23_26 years
This placental sample is of first  trimester normal pregnancy, underwent elective surgical termination. It is the eighth of eight, 6 weeks biological replicates sample, each from different individual woman.

value: 26 years

value: term pregnancy_2; preterm_0; abortion_1; living children_2


title: 3-149

description: PM

value: 76 years


title: Gene expression in DX5- NK

description: Gene expression in DX5- NK

source_name: Liver DX5- NK cells


title: Placenta_villi_weeks7_1

description:
Fertile_hpv7w_SP2_26 years
This placental sample is of first  trimester normal pregnancy, underwent elective surgical termination. It is the first of nine, 7 weeks biological replicates sample, each from different individual woman.

value: 7 weeks

value: term pregnancy_1; preterm_0; abortion_1; living children_1


title: Placenta_villi_weeks6_6

description:
Fertile_hpv6w_SP26_30 years
This placental sample is of first  trimester normal pregnancy, underwent elective surgical termination. It is the sixth of eight, 6 weeks biological replicates sample, each from different individual woman.

value: 30 years

value: term pregnancy_3; preterm_0; abortion_1; living children_3


title: Cort 2HR #1

description: 2 hour steroid replicate-1

value: Brain

value: 2 hour 100nM corticosterone


title: liver from wildtype mouse embryo at 17dpc, biological rep1

city: Tokyo

first: Mami

last: Uemura

address: Yayoi 1-1-1, Bunkyo-ku

department: Veterinary Anatomy

country: Japan

institute: The University of Tokyo

description:
Gene expression data from liver in wildtype mouse at 17dpc
Mouse_WT-1
080207_WT.CEL

hyb_protocol: RNA samples were hybridized to Affymetrix Mouse 430 2.0 DNA microarray chips using the GeneChip® Hybridization Oven 640 (Affymetrix,Clara, CA). Washing and staining of the hybridized chips were conducted using the GeneChip® Fluidics Station 450 (Affymetrix). Santa

scan_protocol: Chips were scanned using the Affymetrix GeneChip® Scanner 3000 (Affymetrix) with autoloader.

data_processing: Expression data sets were analyzed using the R statistics software (http://www.r-project.org/) with BioConductor software (http://www.bioconductor.org/) packages.  The MAS5 method from the BioConductor software was used for background correction and normalization of the DNA microarray data.

source_name: liver in wildtype mouse embryo

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

growth_protocol: Virgin female mice 6–8 wk of age for C57BL6 strain were cohabited with adult Sox17+/- males (>3 mo of age) of the same strain. Mating was assessed by daily vaginal plug check. The presence of the vaginal plug was considered as day 0.5 of pregnancy.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was quantified by spectrophotometry (nano drop 2000 ThermoScientific) and quality was verified using  spectrophotometry  (nano drop 2000 Thermo Scientific).

treatment_protocol: On gestation day 17, female mice were sacrificed and liver with biliary system collected. Liver tissues were dissected from liver with biliary system.

tag: genotype/variation

value: wildtype

tag: gestational stage

value: day 17 of pregnancy


title: 2-45

description: LM

value: male

tag: age

value: 69 years

value: liver metastasis from pancreatic cancer

value: M+


title: Placenta_villi_weeks6_4

description:
Fertile_hpv6w_SP17_27 years
This placental sample is of first  trimester normal pregnancy, underwent elective surgical termination. It is the fourth of eight, 6 weeks biological replicates sample, each from different individual woman.

value: 27 years

value: 6 weeks

value: term pregnancy_1; preterm_0; abortion_2; living children_1


title: Placenta_villi_weeks6_5

description:
Fertile_hpv6w_SP21_26 years
This placental sample is of first  trimester normal pregnancy, underwent elective surgical termination. It is the fifth of eight, 6 weeks biological replicates sample, each from different individual woman.

value: 26 years

value: term pregnancy_2; preterm_0; abortion_1; living children_2


title: liver from wildtype mouse embryo at 17dpc, biological rep2

description:
Gene expression data from liver in wildtype mouse at 17dpc
Mouse_WT-2
080418-WT.CEL

value: liver

tag: strain


title: liver from Sox17+/- mouse embryo at 17dpc, biological rep2

description:
Gene expression data from liver in Sox17+/- mouse at 17dpc
Mouse_MUT-2
080418-Mts.CEL

source_name: liver in sox17+/- mouse embryo


title: D-10167-BT

description: good

value: 78 years

value: pancreatic ductal adenocarcinoma (PDAC)

tag: tumor stage

value: good


title: G1-phase 096042A 201104081116 S01 BOTTOM

status: Public on Jan 08 2013

first: Niels

last: Van der Aa

address: Herestraat 49 bus 602

institute: KU Leuven

description: whole genome amplified single-cell DNA

hyb_protocol: Hybridization and washing of 24sure arrays followed the protocol provided by the manufacturer.

scan_protocol: Scanning was performed using a DNA-microarray scanner (Agilent Technologies)

data_processing: GenePix Pro 6.0 software (Axon - Molecular Devices) was used  for feature extraction and to normalize the data so the ratio of means for all features equals 1. All further analyses were performed in R (version 2.13.2 – www.r-project.com). Log2 intensity ratios with a signal/noise ratio of less than 2 were excluded from the analyses. The remaining intensities were made consistent within each array using median correction as implemented in R using the limma package. Next, the log2 intensity ratios of replicate probes were averaged using the R-package snapCGH. Technical GC-bias correction was performed by subtracting from each probe’s log2 intensity ratio the corresponding value from a mean locally weighted regression between the log2 intensity ratios and the %GC-content of the corresponding micro-array probe locus for all G- and G2/M-phase samples per batch. Using the spline function in R missing data in this mean lowess regression curve were filled in before it was used for the correction of log2 intensity ratios.

source_name: EBV-transformed lymphoblast cell

label_protocol: 150ng of test-samples and reference were labeled for 2h by random primer labeling (BioPrime aCGH Genomic Labeling System; Invitrogen) using respectively Cy5- and Cy3-dCTPs (GE Healthcare).

growth_protocol: Epstein-Barr virus (EBV) immortalized lymphoid cells were cultured in DMEM/F12 medium (Gibco) with 10% fetal bovine Serum (Thermo Scientific) at 37°C at 5%CO2.

extract_protocol: The genome of collected single cells was amplified using the Sureplex amplification system (BlueGnome).

treatment_protocol: Cells were stained with DyeCycle Orange (Invitrogen) according to the manufacturer’s protocol. In short, cells were washed with 1xPBS and incubated at a concentration of 10^6 cells/ml at 37°C for 30 minutes after adding DyeCycle orange at 2µl/10^6 cells. Cells of lymphoblastoid cell lines at ~5*10^6cells/ml were sorted using a FACS Vantage SE or a FACSAria III with FACS DiVa software (BD Biosciences).

value: EBV-transformed lymphoblast cell line

value: female

tag: cell cycle phase

tag: origin

value: female normal control cell line 2

source_name: SureRef male reference DNA (BlueGnome

tag: sample type

value: SureRef male reference DNA (BlueGnome


title: S-phase 096042A 201104081116 S01 TOP

description: whole genome amplified single-cell DNA

value: S-phase

value: male


title: S-phase 118071B bottom S3 agi

description: whole genome amplified singl-cell DNA

value: male carrying 750kb amplification on the short arm of chromosome 4

value: Kreatech male reference DNA


title: S-phase 118077B Top S6 agi

description: whole genome amplified singl-cell DNA


title: Placenta_villi_weeks6_1

description:
Fertile_hpv6w_SP1_42 years
This placental sample is of first  trimester normal pregnancy, underwent elective surgical termination. It is the first of eight, 6 weeks biological replicates sample, each from different individual woman.

value: 42 years

tag: gestation stage

tag: gestational history

value: term pregnancy_3; preterm_0; abortion_2; living children_3


title: G2/M-phase 118076B Top M4 agi

description: whole genome amplified singl-cell DNA


title: S-phase 118070B Top S2 agi

description: whole genome amplified singl-cell DNA


title: G2/M-phase 096046A 201104291113 S01 TOP

description: whole genome amplified single-cell DNA


title: G2/M-phase 096046A 201104291113 S01 BOTTOM

description: whole genome amplified single-cell DNA


title: liver from Sox17+/- mouse embryo at 17dpc, biological rep1

description:
Gene expression data from liver in Sox17+/- mouse at 17dpc
Mouse_MUT-1
080207_MU.CEL

tag: tissue

value: day 17 of pregnancy


title: G2/M-phase 118076B bottom M5 agi

description: whole genome amplified singl-cell DNA


title: Placenta_villi_weeks6_2

description:
Fertile_hpv6w_SP4_26 years
This placental sample is of first  trimester normal pregnancy, underwent elective surgical termination. It is the second of eight, 6 weeks biological replicates sample, each from different individual woman.

value: 26 years

value: 6 weeks

value: term pregnancy_1; preterm_0; abortion_1; living children_1


title: 16-TM1

description: bad

value: 67 years

value: M+

tag: prognosis

value: bad


title: Placenta_villi_weeks6_3

description:
Fertile_hpv6w_SP4.4_25 years
This placental sample is of first  trimester normal pregnancy, underwent elective surgical termination. It is the third of eight, 6 weeks biological replicates sample, each from different individual woman.

value: 25 years


title: S-phase 118072B top S4 agi

description: whole genome amplified singl-cell DNA

value: EBV-transformed lymphoblast cell line

tag: treatment


title: G1-phase 118072B bottom G4 agi

description: whole genome amplified singl-cell DNA


title: G1-phase 118074B bottom G5 agi

description: whole genome amplified singl-cell DNA


title: G2/M-phase 118075B bottom M3 agi

description: whole genome amplified singl-cell DNA


title: G1-phase 118071B top G3 agi

description: whole genome amplified singl-cell DNA


title: S-phase 118073B bottom Smulticell agi

data_processing: GenePix Pro 6.0 software (Axon - Molecular Devices) was used for feature extraction and to normalize the data so the ratio of means for all features equals 1. All further analyses were performed in R (version 2.13.2 – www.r-project.com). Log2 intensity ratios with a signal/noise ratio of less than 2 were excluded from the analyses. The remaining intensities were made consistent within each array using median correction as implemented in R using the limma package. Next, the log2 intensity ratios of replicate probes were averaged using the R-package snapCGH. Technical GC-bias correction was performed by subtracting from each probe’s log2 intensity ratio the corresponding value from a mean locally weighted regression between the log2 intensity ratios and the %GC-content of the corresponding micro-array probe locus for all G- and G2/M-phase samples per batch. Using the spline function in R missing data in this mean lowess regression curve were filled in before it was used for the correction of log2 intensity ratios.

source_name: EBV-transformed lymphoblast cell line

source_name: Kreatech male reference DNA


title: G1-phase 118070B bottom G1 agi

description: whole genome amplified singl-cell DNA


title: G1-phase 118073B Top Gmulticell agi


title: G2/M-phase 118077B bottom Mmulticell agi


title: RNF2040 knockdown Rif 1 cells, 2-1

first: Sophia

last: Chernikova

email: sophiac1@stanford.edu, sbcher@gmail.com

address: 269 Campus Dr

department: Radiation Oncology

institute: Stanford University

description:
Simple annotation: DNA damage, Histone modifiers
Image: http://smd.stanford.edu/MicroArray/gifs/2009-03/82972.gif
Knock down by RNA interference: Bre1b vs no knockdown

source_name: no knockdown

value: RIF-1 cells

source_name: Bre1b knockdown in RIF-1 cells


title: controlpool vs. Lmx1a-1

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: scanning of slides using Agilent G256BA Features were extracted using Imagene software from Biodiscovery.

data_processing: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve.

source_name: wt-control

label_protocol: robot amplification and labeling v1.0

growth_protocol: EH001-growth; Complete Lmx1a coding sequence was amplified from cDNA of E16.5 whole brain RNA, by using the primers: Lmx1a-forward 5'-CACGGGAAGCTAGACTCAAC-3' and Lmx1a-reverse 5'-CCCTTCACACAGTATGGTTG-3'. Lmx1a was ligated into pGEM-t-easy vector (Promega), and after sequence analysis (Baseclear) cloned into the expression vector pcDNA3.1(-) (Invitrogen). MN9D cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% (v/v) heat-inactivated fetal calf serum (hiFCS), 100 units/mL penicillin, 100 units/mL streptomycin and 2 mM L-Glutamine, in a standard incubator with 5% CO2 at 37°C. Cells were grown on 10 cm dishes, additionally coated with poly-L-lysine. At least 2 hours before transfection, culture medium was replaced by antibiotics free medium. Transfection was performed with Lipofectamine 2000 (Invitrogen), according to manufacturer's protocol. Expression vector pcDNA3.1(-)-Lmx1a was transfected in an amount of 6 ug DNA. Control (empty) vector was transfected in equimolar amounts. Cloning vector pBluescript SKII(+) was added as carrier DNA. 5 – 6 hours post transfection, the cells were split (1:3) and cultured in fresh medium with antibiotics. Cells were harvested when the plates were 90 – 95% confluent and RNA was isolated for microarray analysis.

extract_protocol: 1. Add 1 ml Trizol per 5x 106 cells in suspension (1 ml trizol per 10 cm culture disk) and mix by pipetting, transfer to 1.5 ml eppendorf tube. 2. Incubate 5 min at room temperature. 3. Add chloroform (200 µl per ml Trizol), mix for 15 seconds by shaking vigorously. Incubate 2-3 min at room temperature. 4. Centrifuge 20 min at 14000 rpm 4°C. After centrifugation, transfer the water-phase to a new 1.5-ml micro centrifuge tube. 5. add isopropanol to precipitate RNA. Use 0.5 ml per 1 ml trizol. Mix by shaking, leave samples at RT for 10 minutes. Centrifuge at 14000 rpm for 15 min. 6. wash pellet with 75% ethanol. Centrifuge at 14000 rpm for 15 min. Carefully pipet off all ethanol (respin briefly and use a P20 for the last microliters). Airdry pellets briefly before dissolving in MilliQ water. Depending on pellet-size, this may take a while. Continue with RNeasy columns (Qiagen) for clean-up of RNA (maximal 100 µg/column) 7. Adjust each sample to a volume of 300 µl with sterile MilliQ water. Add 160 µl buffer RLT to the samples, and mix (= lysis buffer). 8. Add 240 µl ethanol (100% stored at -20 °C) to the lysate, mix well by pipetting and immediately apply the sample to an RNeasy mini spin column sitting in a 2 ml collection tube (use a second P1000 pipet and work as quick as possible). Next lysate, and so on. 9. Centrifuge at 8000 rpm for 15 seconds in an Eppendorf centrifuge. Discard flowthrough, reuse collection tube. All centrifugation steps at roomtemperature. DNAse treatment: D1. Pipet 350 µl Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm to wash. Discard the flow-through. Reuse the collection tube in step D3. D2. Prepare DNase I incubation mix (80 µl/reaction): add 10 µl DNase I stock solution to 70 µl Buffer RDD. Mix by gently inverting the tube. Buffer RDD is supplied with the RNase-Free DNase Set. Note: DNase I is especially sensitive to physical denaturation. Mixing should only be carried out by gently inverting the tube. Do not vortex. D3. Pipet the DNase I incubation mix (80 µl) directly onto the RNeasy silica-gel membrane, and place on the benchtop (20-30°C) for 15 min. Note: Make sure to pipet the DNase I incubation mix directly onto the RNeasy silica-gel membrane. DNase digestion will be incomplete if part of the mix sticks to the walls or the O-ring of the RNeasy column. D4. Pipet 350 µl Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm. Discard the flow-through and collection tube. 10. Transfer the RNeasy column into a new 2 ml collection tube. Add 500 µl buffer RPE, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse the collection tube in next steps. 11. Pipet 500 µl buffer RPE onto the RNeasy column, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse collection tube. 12. Centrifuge at 10,000 rpm for 2 minutes (to dry the RNeasy membrane).   13. Transfer the RNeasy column into a new 1.5 ml collection tube. Pipet 100 µl milliQ directly onto the RNeasy membrane and incubate for 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. Note: When small yields are expected, the elution volume can be lowered to a minimum of 35 µl milliQ. 14. Pipet the eluate of step 13 again onto the RNeasy membrane and incubate for another 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. After elution, put all RNA-samples on ice. 15. Determine RNA concentration by measuring A260, and RNA intactness by Bioanalyzer. Snap-freeze and store eluate at -80°C.

tag: cell line

value: dopaminergic cells

value: wild type-control

tag: transfected with

value: empty pcDNA3.1(-)

value: Mus musculus


title: Non-Cancer Urothelia-39

city: Orlando

first: Virginia

last: Urquidi

state: FL

address: 6900 Lake Nona Blvd

department: CRI

institute: MD Anderson Cancer Center Orlando

description:
NC-000039
Gene expression data from human urothelial cells in urine sediment.

hyb_protocol: Fragmented, biotinylated cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 microarrays. The Affymetrix GeneChip system used  includes an Affymetrix 450 fluidics station, 3000 scanner, hybridization oven and GeneChip Operating Software.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data was normalized using the MAS5 algorithm provided in Expression Console 1.1 of Affymetrix. The output are positive values.

source_name: Bladder barbotage, non-cancer

label_protocol: Preparation of labeled cRNA was performed according to the Affymetrix Two-Cycle Target Labeling Assay.

extract_protocol: Total RNA was  extracted from urothelial cells using the Qiagen RNeasy protocol.

tag: cell type

value: non-cancer urothelial cells

tag: disease status

value: no bladder cancer


title: RNF2040 knockdown Rif 1 cells, 2-2

description:
Simple annotation: DNA damage, Histone modifiers
Image: http://smd.stanford.edu/MicroArray/gifs/2009-03/82973.gif
Knock down by RNA interference: Bre1b vs mock (GFP) knockdown

hyb_protocol: not provided

scan_protocol: GenePix 4000B

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: mock (GFP) knockdown

label_protocol: not provided

extract_protocol: not provided


title: GFP/control 2

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: WM115 cells transduced with GFP control

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized on U133_Plus2 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-WS2v5 (for FS400) or FS450_0001 (for FS450).

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner (Agilent).

data_processing: The data were analyzed with dChip version2006 using Affymetrix default analysis settings and quantile normalization method.

source_name: WM115 cells transduced with GFP control

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

growth_protocol: All cell lines were propagated at 37°C and 5% CO2 in humidified atmosphere in RPMI 1640 Medium (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (FBS).

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (Invitrogen) and then cDNA was made from total RNA with SuperScript II (Invitrogen) using random primers. cDNA was treated with RNase H (Invitrogen) to remove RNA.

treatment_protocol: Full-length cDNA encoding HOXA1 (NM_005522.4) was obtained from the human ORFeome collection and transferred to viral vectors via Gateway recombination. The WM115 melanoma cell lines was transduced with either control or HOXA1 vector.

tag: protocol

value: transduced with GFP control


title: GFP/control 3

description: WM115 cells transduced with GFP control


title: Non-Cancer Urothelia-40

description:
NC-000040
Gene expression data from human urothelial cells in urine sediment.


title: HOXA1 1

description: WM115 cells transduced with HOXA1

source_name: WM115 cells transduced with HOXA1

value: transduced with HOXA1


title: controlpool vs. Lmx1a-3

tag: genotype/variation


title: HOXA1 3

description: WM115 cells transduced with HOXA1


title: controlpool vs. Lmx1a-2


title: HOXA1 2

description: WM115 cells transduced with HOXA1


title: Lmx1a-2 vs. controlpool


title: Lmx1a-1 vs. controlpool


title: Lmx1a-3 vs. controlpool


title: Non-Cancer Urothelia-38

description:
NC-000038
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-36

description:
NC-000036
Gene expression data from human urothelial cells in urine sediment.


title: GFP/control 1

description: WM115 cells transduced with GFP control


title: RNF2040 knockdown Rif 1 cells, 1-1

description:
Simple annotation: DNA damage, Histone modifiers
Image: http://smd.stanford.edu/MicroArray/gifs/2009-02/82891.gif
Knock down by RNA interference: Bre1a vs no knockdown

source_name: Bre1a knockdown in RIF-1 cells


title: Non-Cancer Urothelia-35

description:
NC-000035
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-37

description:
NC-000037
Gene expression data from human urothelial cells in urine sediment.


title: RNF2040 knockdown Rif 1 cells, 1-2

description:
Simple annotation: DNA damage, Histone modifiers
Image: http://smd.stanford.edu/MicroArray/gifs/2009-02/82892.gif
Knock down by RNA interference: Bre1a vs mock (GFP) knockdown


title: Non-Cancer Urothelia-33

description:
NC-000033
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-31

description:
NC-000031
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-32

description:
NC-000032
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-29

description:
NC-000029
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-30

description:
NC-000030
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-25

description:
NC-000025
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-24

description:
NC-000024
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-19

description:
NC-000019
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-18

description:
NC-000018
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-22

description:
NC-000022
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-20

description:
NC-000020
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-21

description:
NC-000021
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-26

description:
NC-000026
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-17

description:
NC-000017
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-27

description:
NC-000027
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-16

description:
NC-000016
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-11

description:
NC-000011
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-13

description:
NC-000013
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-15

description:
NC-000015
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-7

description:
NC-000007
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-23

description:
NC-000023
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-14

description:
NC-000014
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-9

description:
NC-000009
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-12

description:
NC-000012
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-10

description:
NC-000010
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-3

description:
NC-000003
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-5

description:
NC-000005
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-6

description:
NC-000006
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-1

description:
NC-000001
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-8

description:
NC-000008
Gene expression data from human urothelial cells in urine sediment.


title: Non-Cancer Urothelia-28

description:
NC-000028
Gene expression data from human urothelial cells in urine sediment.


title: Cancer Urothelia-49

description:
C-000049
Gene expression data from human urothelial cells in urine sediment.

source_name: Bladder barbotage, cancer

value: urothelial cancer cells

value: bladder cancer


title: Non-Cancer Urothelia-2

description:
NC-000002
Gene expression data from human urothelial cells in urine sediment.


title: Cancer Urothelia-50

description:
C-000050
Gene expression data from human urothelial cells in urine sediment.


title: Cancer Urothelia-48

description:
C-000048
Gene expression data from human urothelial cells in urine sediment.


title: Cancer Urothelia-43

description:
C-000043
Gene expression data from human urothelial cells in urine sediment.


title: Cancer Urothelia-51

description:
C-000051
Gene expression data from human urothelial cells in urine sediment.


title: Cancer Urothelia-46

description:
C-000046
Gene expression data from human urothelial cells in urine sediment.


title: Cancer Urothelia-52

description:
C-000052
Gene expression data from human urothelial cells in urine sediment.


title: Cancer Urothelia-44

description:
C-000044
Gene expression data from human urothelial cells in urine sediment.


title: Cancer Urothelia-47

description:
C-000047
Gene expression data from human urothelial cells in urine sediment.


title: Spleen_B10_TBI_900cGy_rep1

city: Salt Lake City

first: Thai

last: Cao

state: UT

address: 30 North 1900 East, SOM5C402

institute: University of Utah

description: TBI - 900 cGy

hyb_protocol: Agilent One-color Heterologous GE Hybridization and Wash Protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 um resolution.

data_processing: Array images were processed with Agilent Feature Extraction software version 10.5.1.1. Array data files were filtered to remove positive and negative control features and any features flagged as non-uniform outliers or population outliers, as recommended by Agilent.  Log-transformed signal intensity values were then globally normalized using the percentile shift algorithm, shifting to the 75th percentile of each sample, followed by baseline shifting to the median of all samples.

source_name: Spleen

label_protocol: Agilent One-Color Quick Amp Labeling Protocol

growth_protocol: Total RNA was extracted from the spleens immediately after harvesting from mice 24 hours after total body irradiation, or from resting mice for un-irradiated controls.

extract_protocol: Total RNA was isolated from whole splenocytes homogenized with a rotor-stator device in TRIzol (Invitrogen) followed by RNeasy purification.  Samples quality was checked using an Agilent 2100 Bioanalyzer.

treatment_protocol: Mice were treated with total body irradiation using an XRAD320 Biological Irradiator (Precision X-Ray, North Branford, CT).

tag: total body irradiation dose

value: 900 cGy


title: Spleen_B10_TBI_500cGy_rep3

description: TBI - 500 cGy

value: 500 cGy

tag: strain


title: Cancer Urothelia-41

description:
C-000041
Gene expression data from human urothelial cells in urine sediment.


title: Spleen_B10_TBI_300cGy_rep3

description: TBI - 300 cGy

value: 300 cGy


title: Spleen_B10_TBI_900cGy_rep2

description: TBI - 900 cGy


title: Cancer Urothelia-45

description:
C-000045
Gene expression data from human urothelial cells in urine sediment.


title: Spleen_B10_TBI_500cGy_rep1

description: TBI - 500 cGy


title: renal cortex, vehicle treated 4

city: Shanghai

first: Yi

last: Fang

address: No 180 Fenglin Road

department: nephrology

institute: Zhongshan Hospital

description: microRNA expression after vehicle treatment in remnant kidney cortex

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US)and Feature Extraction software (Agilent technologies, Santa Clara, CA, US)with default settings.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software (Agilent technologies, Santa Clara, CA, US).

organism: Rattus norvegicus

source_name: 5/6 Nx rat, vehicle treated

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

growth_protocol: All experiments were performed in male Sprague-Dawley rats weighing 180 to 200 g obtained from the Animal Centre, Shanghai Medical College, Fudan University (Shanghai, China). Rats were allowed free access to water and rodent food. All protocols were approved by the Institutional Animal Care Use Committee of Fudan University

extract_protocol: Total RNA was extracted and purified using RNAqueous® Kit(Cat#AM1912, Ambion, Austin, TX, US) | mirVana™ miRNA Isolation Kit(Cat#AM1560, Ambion, Austin, TX, US)| mirVana™ PARIS™ Kit(Cat#AM1556, Ambion, Austin, TX, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100(Agilent technologies, Santa Clara, CA, US)

treatment_protocol: kidney tissue was dissected in ice-cold PBS to, remove medulla, and then snap-frozen in liquid nitrogen before transferring to storage at -80°C until further analysis

value: Sprague-Dawley

tag: gender

value: male

value: renal cortex

tag: agent

value: vehicle


title: renal cortex, vehicle treated 3


title: Spleen_B10_TBI_500cGy_rep2

description: TBI - 500 cGy


title: Non-Cancer Urothelia-34

description:
NC-000034
Gene expression data from human urothelial cells in urine sediment.


title: Cancer Urothelia-42

description:
C-000042
Gene expression data from human urothelial cells in urine sediment.


title: renal cortex, vehicle treated 2


title: Spleen_B10_TBI_900cGy_rep3

description: TBI - 900 cGy


title: Spleen_B10_TBI_300cGy_rep2

description: TBI - 300 cGy


title: renal cortex, vehicle treated 1


title: Cancer Urothelia-40

description:
C-000040
Gene expression data from human urothelial cells in urine sediment.


title: Cancer Urothelia-39

description:
C-000039
Gene expression data from human urothelial cells in urine sediment.


title: renal cortex, L-mim treated 4

description: microRNA expression after L-mim treatment in remnant kidney cortex

source_name: 5/6 Nx rat, L-mim treated

value: L-mimosine


title: renal cortex, L-mim treated 3


title: Spleen_B10_TBI_0cGy_rep3

description: TBI - 0 cGy

value: 0 cGy


title: renal cortex, L-mim treated 2


title: renal cortex, L-mim treated 1


title: Spleen_B10_TBI_300cGy_rep1

description: TBI - 300 cGy


title: Spleen_B10_TBI_0cGy_rep1

description: TBI - 0 cGy


title: Spleen_B10_TBI_0cGy_rep2

description: TBI - 0 cGy


title: Cancer Urothelia-38

description:
C-000038
Gene expression data from human urothelial cells in urine sediment.


title: Spleen_BALB_TBI_800cGy_rep2

description: TBI - 800 cGy

value: 800 cGy


title: Spleen_BALB_TBI_800cGy_rep3

description: TBI - 800 cGy


title: wild type strain grown to OD600 0,5 plus epinephrine

city: Sao PAulo

first: Fernanda

middle: Maria

last: Franzin

state: Sao Paulo

address: 1210 Joaquim Tavora st

department: Laboratory of Genetics

country: Brazil

institute: Butantan Institute

description: Laboratory of Bacteriology, Butantan Institute, Sao Paulo, Brazil

hyb_protocol: hyb protocol was done according to manufacturer's specifications: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

scan_protocol: scan protocol was done according to manufacturer's specifications: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

data_processing: data has  been processed by protocols within GCOSv1.4

organism: Escherichia coli O55:H7

source_name: wild type epi

label_protocol: label protocol was done according to manufacturer's specifications: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

growth_protocol: grown to OD600 0,5

extract_protocol: Ambion Ribopure RNA isolation

treatment_protocol: no epinephrine, 50µM epinephrine

value: atypical EPEC

value: wild type

tag: growth condition

value: grown to OD600 0,5 with 50µM epinephrine


title: Cancer Urothelia-37

description:
C-000037
Gene expression data from human urothelial cells in urine sediment.


title: Cancer Urothelia-36

description:
C-000036
Gene expression data from human urothelial cells in urine sediment.


title: Cancer Urothelia-35

description:
C-000035
Gene expression data from human urothelial cells in urine sediment.


title: delta qseC strain grown to OD600 0,5 plus epinephrine

source_name: delta qseC epi

value: delta qseC


title: delta qseC strain grown to OD600  0,5

source_name: delta qseC

value: grown to OD600 0,5


title: Cancer Urothelia-34

description:
C-000034
Gene expression data from human urothelial cells in urine sediment.

value: urothelial cancer cells


title: WT 2 hr refeed

city: Dallas

first: Yingfeng

last: Deng

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center at Dallas

description: pooled sample

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalised with Illumina GenomeStudio GX version 1.9.0.

source_name: WT 2 hr refeed control

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

value: FVB

tag: age

value: 10 wks

value: liver slice


title: wild type strain grown to OD600 0,5

source_name: wild type


title: WT  24 hr Dox

description: pooled sample

source_name: WT  24 hr Dox

tag: induced with

value: Doxycycline for 24hr


title: LIXs 48 hr Dox

description: pooled sample

source_name: LIXs 48 hr Dox

value: LIXs

value: Doxycycline for 48hr


title: WT 24 hr fast

description: pooled sample

source_name: WT 24 hr fast control


title: Cancer Urothelia-32

description:
C-000032
Gene expression data from human urothelial cells in urine sediment.

value: bladder cancer


title: Spleen_BALB_TBI_400cGy_rep3

description: TBI - 400 cGy

value: 400 cGy


title: WT  48 hr Dox

description: pooled sample

source_name: WT  48 hr Dox


title: Cancer Urothelia-33

description:
C-000033
Gene expression data from human urothelial cells in urine sediment.


title: Spleen_BALB_TBI_800cGy_rep1

description: TBI - 800 cGy


title: LIXs 24 hr Dox

description: pooled sample

source_name: LIXs 24 hr Dox


title: Spleen_BALB_TBI_400cGy_rep2

description: TBI - 400 cGy


title: Spleen_BALB_TBI_300cGy_rep3

description: TBI - 300 cGy

value: 300 cGy


title: Spleen_BALB_TBI_400cGy_rep1

description: TBI - 400 cGy


title: Cancer Urothelia-30

description:
C-000030
Gene expression data from human urothelial cells in urine sediment.


title: Cancer Urothelia-29

description:
C-000029
Gene expression data from human urothelial cells in urine sediment.


title: Cancer Urothelia-31

description:
C-000031
Gene expression data from human urothelial cells in urine sediment.


title: control 1

city: London

first: Katarzyna

last: Janus

state: ON

address: 1151 Richmond Street

country: Canada

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.

source_name: brain, saline-treated

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: Dams were raised in standard same-sex housing conditions (14/10-hour light/dark cycle, 40-60% humidity,21°C to 24°C temperature).  Dams were sacrificed at gestational day 16, and fetuses were extracted.

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 gestational day 16, dams were sacrificed by CO2 asphyxiation and whole brain tissue from fetuses were dissected using RNAse-free tools.  Brains were snap-frozen in liquid nitrogen and stored at -80 degrees C until RNA isolation.

value: control

tag: Sex

value: unknown

value: embryonic day 16

value: brain


title: ethanol-treated 2

source_name: brain, ethanol-treated

value: ethanol

tag: tissue


title: ethanol-treated 1


title: control 2


title: Muscle_PGC-1alpha-mTg_rep3

city: Basel

first: Joaquín

last: Pérez-Schindler

address: Klingelbergstrasse 50 / 70

department: Biozentrum

country: Switzerland

institute: University of Basel

description: Gene expression data from gastrocnemius muscle of adult male mice.

hyb_protocol: 85µl cocktail (containing 2µg labeled DNA) was loaded on Mouse Gene 1.0 ST Array (Affymetrix) and hybridized for 17 hours (45°C, 60rpm) in Hybridization oven 645 (Affymetrix).  The arrays were washed and stained on Fluidics Stations 450 (Affymetrix) by using the Hybridization Wash and Stain Kit (Affymetrix) under FS450_0007 protocol.

scan_protocol: GeneChips were scanned with an Affymetrix GeneChip Scanner 3000 7G.

data_processing:
DAT images and CEL files of the microarrays were generated using Affymetrix GeneChip Command Control 3.0.0.1214.
Affymetrix CEL files were normalized according to RMA method (Irizarry, 2003) and data were log 2.0 transformed. To select differently expressed genes a 1-way ANOVA model by using Method of Moments (Eisenhart, 1947) was applied using Partek Genomic Suite (version 6.6).

source_name: Gastrocnemius muscle from PGC-1alpha mTg mouse

label_protocol: Target synthesis was prepared starting from 250ng total RNA using the WT Expression kit (Ambion). Fragmentation and labeling of amplified cDNA were performed using the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: RNA from gastrocnemius was isolated with miRNeasy Mini Kit (QIAGEN)

value: Male


title: Muscle_PGC-1alpha-mTg_rep5