title: 13912379 - 20RV421 vs. 20RV043

hyb_protocol: 20RV043 Cy5 / 20RV421 Cy3 : 30pmol.  Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 20RV043:5ug. (Qiagen RNeasy)

extract_protocol: 20RV421:5ug. (Qiagen RNeasy)


title: 13912514 - 20RV507 vs. 20RV355

status: Public on Jun 30 2011

type: RNA

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: To provide quantitative geneticists studying natural variation in our RIL populations with information and resources necessary to speed up QTL cloning and candidate genes identification. This articulates around the creation of two major resources and their integration into databases to make the information accessible to users: A. Whole transcriptome survey, B. Production of complementary material.

hyb_protocol: 20RV355 Cy5 / 20RV507 Cy3 : 30pmol.  Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm, 480V, laser power 35%, Cy5:635nm,pmt voltage 480V, laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

molecule: total RNA

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: aerial - Plants grown in Greenhouse, where temperatures were 20°C/day and 15°C/night. Also in long day conditions (16hr days)with a complement of artificial light 105µE/m²/sec when necessary.

extract_protocol: 20RV355:5ug. (Qiagen RNeasy)

treatment_protocol: no treatment

tag: developmental stage

value: Boyes 1.06 (Boyes et al. Plant Cell 2001)

tag: population

value: ril bur x col-0

tag: harvest date

extract_protocol: 20RV507:5ug. (Qiagen RNeasy)


title: 13912381 - 20RV043 vs. 20RV421

hyb_protocol: 20RV421 Cy5 / 20RV043 Cy3 : 30pmol.  Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13968485 - 20RV133 vs. 20RV281

hyb_protocol: 20RV281 Cy5 / 20RV133 Cy3 : 30pmol.  Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 20RV281:5ug. (Qiagen RNeasy)

extract_protocol: 20RV133:5ug. (Qiagen RNeasy)


title: 13912387 - 20RV302 vs. 20RV497

hyb_protocol: 20RV497 Cy5 / 20RV302 Cy3 : 30pmol.  Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 20RV497:5ug. (Qiagen RNeasy)

extract_protocol: 20RV302:5ug. (Qiagen RNeasy)


title: 13912374 - 20RV530 vs. 20RV117

hyb_protocol: 20RV117 Cy5 / 20RV530 Cy3 : 30pmol.  Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 20RV117:5ug. (Qiagen RNeasy)

extract_protocol: 20RV530:5ug. (Qiagen RNeasy)


title: 13969443 - 8RV285 vs. 8RV183

hyb_protocol: 8RV183 Cy5 / 8RV285 Cy3 : 30pmol.  Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 8RV183:5ug. (Qiagen RNeasy)

value: ril cvi x col-0

extract_protocol: 8RV285:5ug. (Qiagen RNeasy)


title: 13912389 - 20RV497 vs. 20RV302

hyb_protocol: 20RV302 Cy5 / 20RV497 Cy3 : 30pmol.  Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13968470 - 20RV498 vs. 20RV489

hyb_protocol: 20RV489 Cy5 / 20RV498 Cy3 : 30pmol.  Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 20RV489:5ug. (Qiagen RNeasy)

extract_protocol: 20RV498:5ug. (Qiagen RNeasy)


title: 13912373 - 20RV117 vs. 20RV530

hyb_protocol: 20RV530 Cy5 / 20RV117 Cy3 : 30pmol.  Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13969694 - 8RV183 vs. 8RV285

hyb_protocol: 8RV285 Cy5 / 8RV183 Cy3 : 30pmol.  Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13969440 - 8RV424 vs. 8RV009

hyb_protocol: 8RV009 Cy5 / 8RV424 Cy3 : 30pmol.  Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 8RV009:5ug. (Qiagen RNeasy)

extract_protocol: 8RV424:5ug. (Qiagen RNeasy)


title: S2_H3K4me_with_ecdysone

type: genomic

city: Athens

first: Melissa

last: Davis

state: GA

address: 500 DW Brooks Dr S 270C

department: Genetics  and MCG/UGA Medical Partnership

country: USA

institute: University of Georgia

description:
Histone 3 Lysine 4 methylation events in response to hormone in S2 embryonic cell lines
S2E_H3K4me1: S2E_H3K4me1.CEL & S2E_INPUT1.CEL
S2E_H3K4me2: S2E_H3K4me2.CEL & S2E_INPUT2.CEL
S2E_H3K4me3: S2E_H3K4me3.CEL & S2E_INPUT2.CEL

hyb_protocol: Arrays were hybridized using standard operating procedures for the Affymetrix system utilized at the University of Chicago Functional Genomics Facility

scan_protocol: Arrays were scanned on an Affymetrix 6000 Scanner

data_processing: Data was quantile normalized and statistically analyzed using the TAS software program.

label: biotin

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: S2E_H3K4me ChIP DNA [test]

label_protocol: enzymatically processed DNA was nick' end labeled with an SA- bioscience end labelling kit, following the manufacturer's instructions

growth_protocol: cells were grown at normal conditions (25C with no CO2) following the Drosophila Genome Center's instructions for each cell type.

extract_protocol: cells were harvested after hormone treatmentand chromatin was extracted by  published protocol (Negre N, Lavrov S, Hennetin J, Bellis M, Cavalli G (2006) Mapping the distribution of chromatin proteins by ChIP on chip. Methods Enzymol 410: 316–341)

treatment_protocol: cells that were hormone treated were treated with either 3ug of 20-hydroxyecdysone in an isopropanol carrier

tag: hormone

value: ecdysone

tag: cell line

value: embryonic

tag: chip antibody

source_name: S2E_INPUT1 [control]


title: 13969441 - 8RV009 vs. 8RV424

hyb_protocol: 8RV424 Cy5 / 8RV009 Cy3 : 30pmol.  Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: S2_H3K4me_no_ecdysone

description:
Histone 3 Lysine 4 methylation events in response to hormone in S2 embryonic cell lines
S2NOE_H3K4me1: S2NOE_H3K4me1.CEL & S2NOE_INPUT1.CEL
S2NOE_H3K4me2: S2NOE_H3K4me2.CEL & S2NOE_INPUT2.CEL
S2NOE_H3K4me3: S2NOE_H3K4me3.CEL & S2NOE_INPUT2.CEL

source_name: S2NOE_H3K4me ChIP DNA [test]

value: no ecdysone

source_name: S2NOE_INPUT1 [control]


title: Kc_H3K4me_with_ecdysone

description:
Histone 3 Lysine 4 methylation events in response to hormone in Kc embryonic cell lines
KcE_H3K4me1: KcE_H3K4me1.CEL & KcE_INPUT1.CEL
KcE_H3K4me2: KcE_H3K4me2.CEL & KcE_INPUT2.CEL
KcE_H3K4me3: KcE_H3K4me3.CEL & KcE_INPUT3.CEL

source_name: KcE_H3K4me ChIP DNA [test]

value: Kc

source_name: KcE_INPUT1 [control]


title: 13969437 - 8RV299 vs. 8RV170

hyb_protocol: 8RV170 Cy5 / 8RV299 Cy3 : 30pmol.  Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 8RV170:5ug. (Qiagen RNeasy)

extract_protocol: 8RV299:5ug. (Qiagen RNeasy)


title: 13969444 - 8RV170 vs. 8RV299

hyb_protocol: 8RV299 Cy5 / 8RV170 Cy3 : 30pmol.  Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13969438 - 8RV155 vs. 8RV356

hyb_protocol: 8RV356 Cy5 / 8RV155 Cy3 : 30pmol.  Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 8RV356:5ug. (Qiagen RNeasy)

extract_protocol: 8RV155:5ug. (Qiagen RNeasy)


title: Kc_H3K4me_no_ecdysone

description:
Histone 3 Lysine 4 methylation events in response to hormone in Kc embryonic cell lines
KcNOE_H3K4me1: KcNOE_H3K4me1.CEL & KcNOE_INPUT1.CEL
KcNOE_H3K4me2: KcNOE_H3K4me2.CEL & KcNOE_INPUT2.CEL
KcNOE_H3K4me3: KcNOE_H3K4me3.CEL & KcNOE_INPUT3.CEL

source_name: KcNOE_H3K4me ChIP DNA [test]

source_name: KcNOE_INPUT1 [control]


title: 13969436 - 8RV281 vs. 8RV081

hyb_protocol: 8RV081 Cy5 / 8RV281 Cy3 : 30pmol.  Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 8RV081:5ug. (Qiagen RNeasy)

extract_protocol: 8RV281:5ug. (Qiagen RNeasy)


title: 13969435 - 8RV422 vs. 8RV059

hyb_protocol: 8RV059 Cy5 / 8RV422 Cy3 : 30pmol.  Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 8RV059:5ug. (Qiagen RNeasy)

extract_protocol: 8RV422:5ug. (Qiagen RNeasy)


title: 13969439 - 8RV059 vs. 8RV422

hyb_protocol: 8RV422 Cy5 / 8RV059 Cy3 : 30pmol.  Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13969442 - 8RV081 vs. 8RV281

hyb_protocol: 8RV281 Cy5 / 8RV081 Cy3 : 30pmol.  Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13969432 - 8RV356 vs. 8RV155

hyb_protocol: 8RV155 Cy5 / 8RV356 Cy3 : 30pmol.  Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Huh7 DEGS1 siRNA, biological rep3

city: Groton

first: Wanida

last: Ruangsiriluk

state: CT

address: Eastern Point Road

department: CVMED

institute: Pfizer Inc.

description: gene expression from Huh7 cells 72 hours after transfection with siRNA

hyb_protocol: The labeled cRNA was fragmented as recommended by Affymetrix and 10 µg was added to a hybridization cocktail prior to loading onto individual HG-U133_Plus_2 GeneChip®.  The microarrays were hybridized at 45°C for 16- 24 hours and washed and stained on an Affymetrix FS450 fluidics station according to manufacturer recommendations.  This was performed by the vendor Gene Logic Incorporated.

scan_protocol: The microarrays were scanned on a GeneChip® Scanner 3000. This was performed by the vendor Gene Logic Incorporated.

data_processing: All of the array files were normalized using the Robust Multi-Array Average (RMA) method and log2 transformed using the following Bioconductor and R programs: affy (1.18.2), affyio (1.8.1), annaffy (1.12.1), annotate (1.18.0), AnnotationDbi (1.2.2), base (2.7.2), Biobase (2.0.1), chron (2.3-32), contrast (0.11), datasets (2.7.2), DBI (0.2-4), Design (2.3-0), gcrma (2.12.1), genefilter (1.20.1), GO.db (2.2.0), graphics (2.7.2), grDevices (2.7.2), Hmisc (3.7-0), KEGG.db (2.2.0), lattice (0.17-13), limma (2.14.7), MASS (7.2-44), matchprobes (1.12.1), methods (2.7.2), multtest (2.0.0), nlme (3.1-89), odfWeave (0.7.11), preprocessCore (1.2.1), RSQLite (0.7-3), simpleaffy (2.16.1), splines (2.7.2), stats (2.7.2), survival (2.34-1), tools (2.7.2), utils (2.7.2), XML (2.6-0) and xtable (1.5-5).

organism: Homo sapiens

source_name: Huh7 72 hours after DEGS1 siRNA treatment

label_protocol: cDNA was synthesized using 1-2 ug of high quality total RNA. Supercript II™ (Invitrogen) was used to reverse-transcribe the mRNA in the presence of a T7 containing oligo dT24 primer followed by second strand synthesis as recommended by Affymetrix.  cDNA was purified using Agencourt RNAClean magnetic beads and used as a template for in vitro transcription using the GeneChip® One-Cycle Labeling Kit from Affymetrix.  cRNA was purified using Agencourt magnetic beads and the quantity and purity of the cRNA was determined by absorbance at 260 nm and 260/280 absorbance ratio respectively.  The quality of the cRNA was evaluated by assessing the size distribution of the cRNA using a 1.25% MOPS gel.  This was performed by the vendor Gene Logic Incorporated.

growth_protocol: Human hepatocarcinoma cells, Huh7, were maintained at approximately 70-80% confluence in the growing media consisting of high glucose DMEM (Invitrogen, Carlsbad, California), 10% fetal bovine serum (BSA, Sigma-Aldrich, St. Louis, Missouri), 2 mM L-glutamine (Invitrogen), 10mM hepes (Invitrogen) and 1% penicillin-streptomycin (Invitrogen) at 37C, 5% CO2.

extract_protocol: Total RNA was isolated from frozen cell pellet using standard Qiagen Rneasy kit by the vendor Gene Logic Incorporated.

treatment_protocol: Huh7 cells were seeded at 60,000 cells/well in a 12-well plate or 6 millions cells/500 cm2 plate overnight. Next day, Silencer® Select siRNA (Applied Biosystem, Carlsbad, California) against SPTLC1, 2, 3 or DEGS1 gene and siLentFect™ lipid reagent (BIO-RAD, Hercules, California) was prepared in OptiMEM (Invitrogen) according to the manufacturer protocol. Silencer® Select scramble #1 was used as a control. Then, the siRNA-lipid complex was added to each well to yield the final concentration of 20 nM siRNA and incubated for 24 h at 37C, 5% CO2. Media was replaced with the fresh growing media and cells were incubated for another 24 h, before the conditioned media (DMEM + 1% FBS + BSA) was added to the cells at 72 h after siRNA transfection and incubated for another 24 h prior to harvest.

value: Huh7 hepatocarcinoma cell line


title: piPS7_rep3

city: Beijing

first: Yixuan

last: Wang

address: No. 7, Science Park Road, Zhongguancun Life Science Park

country: China

institute: National Institute of Biological Sciences, Beijing, China

hyb_protocol: Labled cDNA was hybridized to Affymetrix GeneChip® Human Genome U133 plus 2.0 Array

scan_protocol: Signals were scaned and analyzed by GeneChip® Scanner 3000 7G3000 (Affymetrix, Inc.).

data_processing: Data were analyzed using GCOS 1.4 software provided by Affymetrix.

source_name: beta-thalassemia patient iPS cells

label_protocol: cDNA was labeled with biotin using WT Terminal Labeling Kit (Affymetrix, Inc.).

extract_protocol: total RNA was isolated using Trizol reagent (Invitrogen). cDNA was synthesized and amplified with WT cDNA Synthesis and Amplification Kit (Affymetrix, Inc.)

tag: derivation

value: beta-thalassemia patient fibroblast cells

tag: gender

value: male

tag: age

value: two years old


title: ciPS5_rep1

source_name: corrected iPS cells

value: beta-thalassemia patient iPS cells


title: hFibro_rep1

source_name: beta-thalassemia patient fibroblast cells

value: beta-thalassemia patient


title: ciPS5_rep3


title: piPS7_rep1


title: Huh7 SPTLC123 siRNA, biological rep1

source_name: Huh7 72 hours after SPTLC123 siRNA treatment


title: Huh7 scramble siRNA, biological rep3

source_name: Huh7 72 hours after scramble siRNA treatment, control


title: Huh7 SPTLC123 siRNA, biological rep2


title: hES_rep3

source_name: human ES cells

value: a Chinese female blastocyst

value: 35 years old


title: hES_rep2


title: Huh7 scramble siRNA, biological rep2


title: hFibro_rep2


title: Huh7 SPTLC123 siRNA, biological rep3


title: hFibro_rep3


title: Huh7 scramble siRNA, biological rep1


title: Huh7 DEGS1 siRNA, biological rep2


title: hES_rep1


title: piPS_rep2


title: ciPS5_rep2


title: Huh7 DEGS1 siRNA, biological rep1


title: MLL_PTD14

city: Taipei

first: Hsi-Che

last: Liu

address: No. 92, Sec. 2, Chung-San North Rd.

country: Taiwan

institute: Mackay Memorial Hospital

description: Gene expression data from bone marrow

hyb_protocol: Standard Affymetrix according to manufacturer's instructions.

data_processing: Probeset intensities were extracted from CEL-files using GeneChip Operating Software (GCOS) (Affymetrix). Probe intensities were normalized. Differentially expressed genes between mixed lineage leukemia translocation (tMLL) and MLL-partial tandem duplication (MLL-PTD) subgroups were calculated using the Student t-test.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. The integrity of the RNA was assessed using the RNA 6000 Nano assay kit on a Bioanalyzer (Agilent Technologies).

tag: genotype

value: MLL partial tandem duplication


title: MLL_PTD10

description: Gene expression data from bone marrow

scan_protocol: Standard Affymetrix according to manufacturer's instructions.


title: MLL_PTD09

description: Gene expression data from bone marrow

label_protocol: Standard Affymetrix according to manufacturer's instructions.


title: MLL_PTD13

description: Gene expression data from bone marrow


title: MLL_PTD15

description: Gene expression data from bone marrow


title: MLL_PTD08

description: Gene expression data from bone marrow


title: MLL_PTD11

description: Gene expression data from bone marrow


title: MLL_PTD12

description: Gene expression data from bone marrow


title: MLL_PTD07

description: Gene expression data from bone marrow


title: MLL_PTD06

description: Gene expression data from bone marrow


title: MLL_PTD02

description: Gene expression data from bone marrow


title: MLL_PTD05

description: Gene expression data from bone marrow


title: MLL_PTD01

description: Gene expression data from bone marrow


title: tMLL05

description: Gene expression data from bone marrow

value: MLL translocation


title: tMLL04

description: Gene expression data from bone marrow


title: tMLL02

description: Gene expression data from bone marrow


title: tMLL10

description: Gene expression data from bone marrow


title: Patient2_339_GH_Day3_GH2_8PM (4 days)

city: Houston

first: Patricia

last: Maningat

state: TX

address: 1100 Bates St

department: CNRC

institute: Baylor College of Medicine

hyb_protocol: 750 ng of labeled cRNAs were hybridized to the Human Ref 8 V2 Beadchip arrays (Illumina  Inc., San Diego, CA) at 55oC overnight (16h) following the Illumina Whole-Genome Gene Expression Protocol for BeadStation (Doc. # 111226048 Rev. B, Illumina Inc)  and stained with 1 ug/ml streptavidin-Cy3 (Amersham Biosciences, Piscataway, NJ) for visualization

scan_protocol: Probe arrays were scanned using the BeadArray reader (Factor 1)

data_processing: Gene expression analysis was performed using the Sentrix BeadChip and BeadStation system from Illumina, Inc

label: Biotin

source_name: Milk Fat Globule

label_protocol: 440 ng total RNA was used for in vitro transcription, overnight for 14h using biotin-11-dUTP for labeling of the cRNA product using the Illumina®TotalPrep RNA amplification kit (Ambion, Inc., Austin, TX)

extract_protocol: RNA was isolated from the milk fat globule using Trizol following the manufacturer's protocol

tag: sample

value: Milk Fat Globule


title: tMLL07

description: Gene expression data from bone marrow


title: tMLL08

description: Gene expression data from bone marrow


title: Patient2_339_GH_Day3_GH2_11PM (4 days)


title: Patient2_339_GH_Day3_GH2_5AM (4 days)


title: Patient2_339_GH_Day4_GH3_8PM (4 days)


title: Patient2_339_GH_Day3_GH2_2AM (4 days)


title: Patient2_339_GH_Day3_GH2_2PM (4 days)


title: tMLL06

description: Gene expression data from bone marrow


title: Patient2_339_GH_Day4_GH3_8AM (4 days)


title: MLL_PTD04

description: Gene expression data from bone marrow


title: Patient2_339_GH_Day3_GH2_11AM (4 days)


title: Patient2_339_GH_Day4_GH3_2PM (4 days)


title: MLL_PTD03

description: Gene expression data from bone marrow


title: tMLL09

description: Gene expression data from bone marrow


title: Patient2_339_GH_Day4_GH3_2AM (4 days)


title: tMLL03

description: Gene expression data from bone marrow


title: tMLL01

description: Gene expression data from bone marrow


title: Patient2_339_GH_Day3_GH2_8AM (4 days)


title: Patient2_339_GH_Day3_GH2_5PM (4 days)


title: Patient2_339_GH_Day2_GH1_2AM (4 days)


title: Patient2_339_GH_Day2_GH1_8PM (4 days)


title: Patient2_339_GH_Day2_GH1_8AM (4 days)


title: Patient2_339_GH_Day2_GH1_5AM (4 days)


title: Patient2_339_GH_Day2_GH1_11AM (4 days)


title: Patient2_339_GH_Day2_GH1_11PM (4 days)


title: Patient2_339_GH_Day2_GH1_5PM (4 days)


title: Patient2_339_GH_Day2_GH1_2PM (4 days)


title: Patient3_339_GH_Day4_GH3_8AM (4 days)


title: Patient2_339_GH_Day1_GH0_8AM (4 days)


title: Patient3_339_GH_Day4_GH3_2AM (4 days)


title: Patient2_339_GH_Day1_GH0_2PM (4 days)


title: Patient3_339_GH_Day2_GH1_8AM (4 days)


title: Patient2_339_GH_Day1_GH0_5PM (4 days)


title: Patient2_339_GH_Day1_GH0_5AM (4 days)


title: Patient3_339_GH_Day4_GH3_2PM (4 days)


title: Patient2_339_GH_Day1_GH0_2AM (4 days)


title: Patient3_339_GH_Day3_GH2_11PM (4 days)


title: Patient3_339_GH_Day3_GH2_2AM (4 days)


title: Patient3_339_GH_Day3_GH2_11AM (4 days)


title: Patient3_339_GH_Day3_GH2_5AM (4 days)


title: Patient3_339_GH_Day3_GH2_5PM (4 days)


title: Patient2_339_GH_Day1_GH0_11AM (4 days)


title: Patient2_339_GH_Day1_GH0_8PM (4 days)


title: Patient3_339_GH_Day3_GH2_8PM (4 days)


title: Patient3_339_GH_Day3_GH2_2PM (4 days)


title: Patient2_339_GH_Day1_GH0_11PM (4 days)


title: Patient3_339_GH_Day4_GH3_8PM (4 days)


title: Patient3_339_GH_Day3_GH2_8AM (4 days)


title: Patient3_339_GH_Day2_GH1_5PM (4 days)


title: Patient3_339_GH_Day1_GH0_8AM (4 days)


title: Patient3_339_GH_Day2_GH1_11PM (4 days)


title: Patient3_339_GH_Day2_GH1_2PM (4 days)


title: Patient3_339_GH_Day2_GH1_8PM (4 days)


title: Patient3_339_GH_Day2_GH1_5AM (4 days)


title: Patient3_339_GH_Day2_GH1_2AM (4 days)


title: E14TG2a ES cells untreated biological rep2

city: Singapore

first: Kian Leong

last: LEE

state: Singapore

address: #07-21, 8 College Road

department: Duke-NUS Medical School

country: Singapore

institute: National University of Singapore (NUS)

description: Biological replicate 2

hyb_protocol: 750ng of each cRNA sample was hybridized to MouseRef-8 v1.1 expression beadchip microarrays (Illumina) as per manufacturer specifications.

scan_protocol: Microarrays were scanned on the BeadArray Reader (Illumina) at scan factor 1 as per manufacturer specifications.

data_processing:
The microarray data was subjected to background subtraction on the BeadStudio Data Analysis software (Illumina) and normalized using the Cross-correlation method (Chua et al., 2006) with MATLAB scripts. Differentially expressed transcripts were identified based on the mean Log2 fold-change in expression values compared to the control DMSO treatment with a cutoff at 1.5-fold change.
Reference: Chua SW, Vijayakumar P, Nissom PM, Yam CY, Wong VV, Yang H: A novel normalization method for effective removal of systematic variation in microarray data. Nucleic acids research 2006, 34(5):e38.

organism: Mus musculus

source_name: HPRT- E14TG2a ES cells

label_protocol: 500ng of total RNA from each sample was reverse transcribed into cDNA and in vitro transcribed into biotin-labelled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion).

growth_protocol: Cells were cultured in 20% ES cell qualified FBS in DMEM containing 100μM non essential amino acids, 100U/ml penicillin, 100μg/ml streptomycin, 2mM GlutaMAX I (Invitrogen), 55μM β mercaptoethanol (Sigma) and 1X homemade Leukemia Inhibitory factor (LIF). Medium was changed daily and cells passaged every second day.

extract_protocol: Total RNA was extracted from 4 biological replicates of HPRT- E14TG2a ES cells subjected to ACT, SB or DMSO/KSR control treatments using the RNeasy Mini kit (Qiagen) according to manufacturer instructions. RNA quality was assessed on the 2100 Bioanalyser (Agilent) using the RNA 6000 Nano Chip kit (Agilent) for intact 18S and 28S ribosomal peaks without significant degradation (RNA Integrity Number >9) for all samples.

treatment_protocol: Cells were pretreated 6h with 20% KSR in DMEM containing 100μM non essential amino acids, 100U/ml penicillin, 100μg/ml streptomycin, 2mM GlutaMAX I (Invitrogen), 55μM β mercaptoethanol (Sigma) supplemented with 10uM SB-431542. This was followed by 18h in the same media supplemented with 25ng/ml Activin (ACT), 10uM SB-431542 (SB), 1/5000 DMSO or unsupplemented (KSR).

tag: cell type

value: E14TG2a ES cells

tag: cell passage

tag: treatment group

value: untreated

tag: treatment duration

value: 18 hours treatment


title: Patient3_339_GH_Day2_GH1_11AM (4 days)


title: E14TG2a ES cells untreated biological rep1

description: Biological replicate 1


title: Patient3_339_GH_Day1_GH0_5AM (4 days)


title: Patient3_339_GH_Day1_GH0_2PM (4 days)


title: E14TG2a ES cells untreated biological rep3

description: Biological replicate 3


title: Patient3_339_GH_Day1_GH0_2AM (4 days)


title: Patient3_339_GH_Day1_GH0_5PM (4 days)


title: Patient3_339_GH_Day1_GH0_8PM (4 days)


title: Patient3_339_GH_Day1_GH0_11PM (4 days)


title: E14TG2a ES cells untreated biological rep4

description: Biological replicate 4


title: NA10851 rep3 genotyping at TCAG (244A)

city: Toronto

first: Stephen

middle: W

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

country: Canada

institute: The Hospital for Sick Children

description: Genomic DNA extracted was analyzed using Illumina's BeadStudio software

hyb_protocol: On each slide, a total combined 55ug of DNA was hybridized according to the 40-hour manual protocol described by manufacturer.

scan_protocol: Arrays were scanned at 5 micron resolution in an Agilent Scanner

data_processing: Images were processed with Agilent Feature Extraction v9.5.1.1, and were required to show derivative Log Ratio spread (DLRS) values < 0.3. CNV detection was performed using Agilent's ADM-2 and also with the Nexus rank segmentation software.

label_protocol: Invitrogen BioPrime CGH labeling kit was used (cat. No. 18094011), according to the manufactures protocol.

extract_protocol: DNA was obtained from Coriell Cell Repositories, extracted from lymphoblastoid cell lines.

value: Male

value: lymphoblastoid cell lines

tag: genotyping center

value: TCAG

tag: cell lline


title: NA18517 rep3 genotyping at TCAG (244A)

value: Female


title: NA15510 rep3 genotyping at TCAG (244A)


title: NA18576 rep2 genotyping at TCAG (244A)


title: NA18980 rep3 genotyping at TCAG (244A)


title: NA12239 rep2 genotyping at TCAG (244A)


title: NA18576 rep3 genotyping at TCAG (244A)


title: NA12239 rep3 genotyping at TCAG (244A)


title: NA18517 rep2 genotyping at TCAG (244A)


title: E14TG2a ES cells +1/5000 DMSO control biological rep4

description: Biological replicate 4

value: +1/5000 DMSO control


title: Patient5_339_GH_Day4_GH3_8AM (4 days)


title: E14TG2a ES cells +10uM SB-431542 biological rep4

description: Biological replicate 4


title: E14TG2a ES cells +1/5000 DMSO control biological rep3

description: Biological replicate 3


title: Patient5_339_GH_Day4_GH3_2AM (4 days)


title: NA18980 rep2 genotyping at TCAG (244A)


title: E14TG2a ES cells +1/5000 DMSO control biological rep2

description: Biological replicate 2


title: Patient5_339_GH_Day4_GH3_2PM (4 days)


title: E14TG2a ES cells +1/5000 DMSO control biological rep1

description: Biological replicate 1


title: NA18517 rep1 genotyping at TCAG (244A)


title: NA10851 rep2 genotyping at TCAG (244A)


title: Patient3_339_GH_Day1_GH0_11AM (4 days)


title: NA18980 rep1 genotyping at TCAG (244A)


title: NA18576 rep1 genotyping at TCAG (244A)


title: Patient5_339_GH_Day4_GH3_8PM (4 days)


title: E14TG2a ES cells +10uM SB-431542 biological rep3

description: Biological replicate 3


title: Patient5_339_GH_Day3_GH2_8AM (4 days)


title: E14TG2a ES cells +10uM SB-431542 biological rep2

description: Biological replicate 2


title: E14TG2a ES cells +10uM SB-431542 biological rep1

description: Biological replicate 1


title: E14TG2a ES cells +25ng/ml Activin biological rep4

description: Biological replicate 4

value: +25ng/ml Activin


title: E14TG2a ES cells +25ng/ml Activin biological rep3

description: Biological replicate 3


title: Patient5_339_GH_Day3_GH2_2AM (4 days)


title: Patient5_339_GH_Day3_GH2_8PM (4 days)


title: Patient5_339_GH_Day3_GH2_5AM (4 days)


title: NA12239 rep1 genotyping at TCAG (244A)


title: Patient5_339_GH_Day3_GH2_11PM (4 days)


title: NA10851 rep1 genotyping at TCAG (244A)


title: NA15510 rep1 genotyping at TCAG (244A)


title: Patient5_339_GH_Day3_GH2_5PM (4 days)


title: E14TG2a ES cells +25ng/ml Activin biological rep2

description: Biological replicate 2


title: Patient5_339_GH_Day3_GH2_2PM (4 days)


title: Patient5_339_GH_Day2_GH1_8AM (4 days)


title: Patient5_339_GH_Day3_GH2_11AM (4 days)


title: E14TG2a ES cells +25ng/ml Activin biological rep1

description: Biological replicate 1


title: Gata4_S105Amut, PE treated whole heart, individual 7

city: Cincinnati

first: Bruce

middle: J

last: Aronow

state: OH

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: Following fragmentation, cRNA were hybridized to theAffymetrix Mouse ST 1.0 genes  GeneChip which was then washed and stained in the Affymetrix Fluidics Station.

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

data_processing: RMA normalized using MoGene-1_0-st-v1.r3.cdf

source_name: Gata4_S105Amut, PE treated whole heart

label_protocol: Biotinylated cRNA were prepared according to the standard Ambion WT labeling kit.

growth_protocol: 9 week old mice were used to test the effects of Gata4 S105 on response to 5 days of pseudophedrine cardiac stress

extract_protocol: RNA was extracted from snap‐frozen hearts of 9 week-old mice using a Qiagen fibrous tissue RNeasy kit.

treatment_protocol: Animal were treated with saline or PE  injected subcutaneously by continuous osmotic pump (100 mg/kg/day) for five days

tag: background strain

tag: genotype/variation

value: Gata4_S105A_homozygous mutant

value: 9 weeks old

tag: tissue

value: whole heart ventricle


title: Gata4_S105Amut, PE treated whole heart, individual 8


title: NA15510 rep2 genotyping at TCAG (244A)


title: Patient5_339_GH_Day2_GH1_5AM (4 days)


title: Ovarian cancer cell line PEO1

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

state: MI

address: Via Rita Montalcini 4

department: Biomedical Sciences

country: Italy

institute: Humanitas University

description: Genomic DNA extracted from PEO1 was genotyped using Illumina Infinium Human1M-Duo Genotyping BeadChips (Illumina).

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Data was processed in BeadStudio using the standard Illumina protocol.

label: C-Bio and A-DNP

source_name: Ovarian cancer cell line PEO1

label_protocol: standard Illumina protocol

extract_protocol: Extraction of genomic DNA from cell culture was performed using the Gentra Puregene cell kit.

tag: patient number

tag: disease stage

value: Post-treatment


title: Patient5_339_GH_Day2_GH1_2AM (4 days)


title: Gata4_S105Amut, untreated whole heart, individual 6

source_name: Gata4_S105Amut, untreated whole heart


title: Gata4_S105Amut, untreated whole heart, individual 5


title: Patient5_339_GH_Day2_GH1_11PM (4 days)


title: NA18576 rep 3 genotyping at HMS (HumanOmni1-Quad) rev2

hyb_protocol: Standard Illumina protocol for HumanOmni1-Quad Beadchip

data_processing:
Intra-chip normalization was performed using the Illumina's GenomeStudio software v.1.0.1 with a GenCall cutoff of 0.1 and call rate cutoff of 98%. For CNV calling on the Illumina 1M platform we used QuantiSNP, iPattern, PennCNV, cnvPartition and Partek
For CNV detection using different algorithms, various measurements were exported directly from GenomeStudio: the intra-chip normalized X and Y intensity values from the A and B allele-specific probes respectively, and two other measurements derived from X and Y after normalization with respect to reference population, i.e. the Log R ratios (LRR) and B allele frequency (BAF) values. For the algorithms that used LRR, representing the total signal intensity, and BAF, representing the allelic balance, the Illumina’s cluster file made of >120 HapMap was used to generate intensities and genotypes using GenomeStudio.

tag: cell line

value: HMS


title: Patient5_339_GH_Day2_GH1_8PM (4 days)


title: WT, PE treated whole heart, individual 4

source_name: WT, PE treated whole heart

value: WT


title: NA15510 rep 3 genotyping at HMS (HumanOmni1-Quad) rev2

scan_protocol: Standard Illumina protocol for HumanOmni1-Quad Beadchip


title: NA10851 rep 3 genotyping at HMS (HumanOmni1-Quad) rev2

label_protocol: Standard Illumina protocol for HumanOmni1-Quad Beadchip


title: NA18517 rep 3 genotyping at HMS (HumanOmni1-Quad) rev2


title: WT, PE treated whole heart, individual 3


title: NA18980 rep 3 genotyping at HMS (HumanOmni1-Quad) rev2


title: NA12239 rep 3 genotyping at HMS (HumanOmni1-Quad) rev2


title: Patient5_339_GH_Day2_GH1_5PM (4 days)


title: NA10851 rep3 at TCAG (Human1Mv1_C)

hyb_protocol: Standard Illumina protocol for Infinium 1M-single Beadchip


title: NA18576 rep 2 genotyping at HMS (HumanOmni1-Quad) rev2


title: NA18517 rep 2 genotyping at HMS (HumanOmni1-Quad) rev2


title: NA10851 rep2 at TCAG (Human1Mv1_C)

scan_protocol: Standard Illumina protocol for Infinium 1M-single Beadchip


title: NA18980 rep 2 genotyping at HMS (HumanOmni1-Quad) rev2


title: WT, untreated whole heart, individual 2

source_name: WT, untreated whole heart


title: NA10851 rep1 at TCAG (Human1Mv1_C)

label_protocol: Standard Illumina protocol for Infinium 1M-single Beadchip


title: NA15510 rep 2 genotyping at HMS (HumanOmni1-Quad) rev2


title: Patient5_339_GH_Day2_GH1_2PM (4 days)


title: NA18517 rep3 at TCAG (Human1Mv1_C)


title: WT, untreated whole heart, individual 1


title: Patient5_339_GH_Day2_GH1_11AM (4 days)


title: NA18517 rep1 at TCAG (Human1Mv1_C)


title: NA10851 rep 2 genotyping at HMS (HumanOmni1-Quad) rev2


title: NA18980 rep1 genotyping at HMS (HumanOmni1-Quad) rev2


title: NA18517 rep2 at TCAG (Human1Mv1_C)


title: Dexamethasone 4 hours plus tetracycline rep2

city: SEATTLE

first: John

middle: A

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

description:
mouse mammary adenocacinoma tumor with A-fos stably integrated male. The 3134 cell line was derived by transformation of C127, originally isolated from a mammary adenocacinoma tumor of the RIII mouse. A-fos (AP1 dominant negative) and the tetracycline regulator (tTa) were stably integrated into the 3134 cell line., dexamethasone 4 hours
Dexamethasone treated, 4 hours.

hyb_protocol: Hybridizations were carried out according the manufacturer (Affymetrix) protocol.

scan_protocol: Affymterix Gene Chip Scanner 3000

source_name: mammary

treatment_protocol: 4 hour treatment with 100 nM dexamethasone. without tetracycline (1ug/ml) for 48 hours

tag: receptor

tag: source strain

value: RIII

value: female

tag: time

value: 4 hours

tag: treatment

value: Dexamethasone

tag: tet-off

value: plus tetracycline

tag: transgene


title: Patient5_339_GH_Day1_GH0_5AM (4 days)

tag: sample

value: Milk Fat Globule


title: Patient5_339_GH_Day1_GH0_8AM (4 days)


title: NA18517 rep1 genotyping at HMS (HumanOmni1-Quad) rev2

tag: gender

tag: cell type

value: lymphoblastoid cell lines


title: NA18576 rep1 genotyping at HMS (HumanOmni1-Quad) rev2

tag: genotyping center


title: Control 0 hour plus tetracycline rep2

description:
mouse mammary adenocacinoma tumor with A-fos stably integrated male. The 3134 cell line was derived by transformation of C127, originally isolated from a mammary adenocacinoma tumor of the RIII mouse. A-fos (AP1 dominant negative) and the tetracycline regulator (tTa) were stably integrated into the 3134 cell line., dexamethasone 0 hour control
Dexamethasone untreated, 0 hour control.

treatment_protocol: Control, untreated 0 hour without tetracycline (1ug/ml) for 48 hours

value: 0 hour

value: control


title: NA12239 rep 2 genotyping at HMS (HumanOmni1-Quad) rev2

value: Female


title: Control 0 hour no tetracycline rep2

treatment_protocol: Control, untreated 0 hour with tetracycline (1ug/ml)

value: no tetracycline

value: A-fos (AP1 dominant negative) and the tetracycline regulator (tTa)


title: NA15510 rep3 at TCAG (Human1Mv1_C)

value: TCAG


title: Patient5_339_GH_Day1_GH0_11PM (4 days)


title: Patient5_339_GH_Day1_GH0_2AM (4 days)


title: NA15510 rep2 at TCAG (Human1Mv1_C)


title: NA15510 rep1 genotyping at HMS (HumanOmni1-Quad) rev2


title: Dexamethasone 4 hours plus tetracycline rep1


title: NA12239 rep1 genotyping at HMS (HumanOmni1-Quad) rev2


title: Control 0 hour plus tetracycline rep1


title: Patient5_339_GH_Day1_GH0_8PM (4 days)


title: NA15510 rep1 at TCAG (Human1Mv1_C)


title: Dexamethasone 4 hours no tetracycline rep2

treatment_protocol: 4 hour treatment with 100 nM dexamethasone and with tetracycline (1ug/ml)


title: Patient5_339_GH_Day1_GH0_5PM (4 days)


title: Dexamethasone 4 hours no tetracycline rep1


title: Patient5_339_GH_Day1_GH0_2PM (4 days)


title: Control 0 hour no tetracycline rep 1


title: NA18980 rep3 at TCAG (Human1Mv1_C)


title: Patient5_339_GH_Day1_GH0_11AM (4 days)


title: Patient4_339_GH_Day4_GH3_8AM (4 days)


title: NA10851 rep1 genotyping at HMS (HumanOmni1-Quad) rev2

value: Male


title: NA18980 rep 3 genotyping at TCAG (HumanOmni1-Quad) rev2


title: Patient4_339_GH_Day4_GH3_2AM (4 days)


title: NA18517 rep 3 genotyping at TCAG (HumanOmni1-Quad) rev2


title: NA18980 rep2 at TCAG (Human1Mv1_C)


title: NA18980 rep1 at TCAG (Human1Mv1_C)


title: Patient4_339_GH_Day4_GH3_8PM (4 days)


title: NA18576 rep2 at TCAG (Human1Mv1_C)


title: NA10851 rep 3 genotyping at TCAG (HumanOmni1-Quad) rev2


title: NA12239 rep 3 genotyping at TCAG (HumanOmni1-Quad) rev2


title: NA12239 rep2 at TCAG (Human1Mv1_C)


title: NA18517 rep 2 genotyping at TCAG (HumanOmni1-Quad) rev2


title: NA15510 rep 3 genotyping at TCAG (HumanOmni1-Quad) rev2


title: NA18576 rep3 at TCAG (Human1Mv1_C)


title: NA18517 rep3 genotyping at HMS (1X1M)

label_protocol: Invitrogen BioPrime CGH labeling kit was used (cat. No. 18094011), with an extended labeling time and increased cy3/cy5 concentrations compared to the manufactures protocol.


title: Patient4_339_GH_Day4_GH3_2PM (4 days)


title: NA18576 rep 3 genotyping at TCAG (HumanOmni1-Quad) rev2


title: NA18576 rep1 at TCAG (Human1Mv1_C)


title: Patient4_339_GH_Day3_GH2_8AM (4 days)


title: NA12239 rep1 at TCAG (Human1Mv1_C)


title: NA12239 rep3 at HMS (Human1Mv1_C)


title: NA12239 rep3 at TCAG (Human1Mv1_C)


title: NA18980 rep 2 genotyping at TCAG (HumanOmni1-Quad) rev2


title: Patient4_339_GH_Day3_GH2_5AM (4 days)


title: NA18980 rep3 genotyping at HMS (1X1M)


title: NA15510 rep 2 genotyping at TCAG (HumanOmni1-Quad) rev2


title: Patient4_339_GH_Day3_GH2_11PM (4 days)


title: NA12239 rep2 at HMS (Human1Mv1_C)


title: Patient4_339_GH_Day3_GH2_2AM (4 days)


title: NA10851 rep1 genotyping at TCAG (HumanOmni1-Quad) rev2


title: NA18576 rep 2 genotyping at TCAG (HumanOmni1-Quad) rev2


title: NA12239 rep1 at HMS (Human1Mv1_C)


title: Patient4_339_GH_Day3_GH2_8PM (4 days)


title: NA18517 rep3 at HMS (Human1Mv1_C)


title: NA10851 rep 2 genotyping at TCAG (HumanOmni1-Quad) rev2


title: NA12239 rep3 genotyping at HMS (1X1M)


title: Patient4_339_GH_Day3_GH2_5PM (4 days)


title: NA18517 rep2 at HMS (Human1Mv1_C)


title: Patient4_339_GH_Day3_GH2_11AM (4 days)


title: Patient4_339_GH_Day3_GH2_2PM (4 days)


title: NA18517 rep1 at HMS (Human1Mv1_C)


title: Patient4_339_GH_Day2_GH1_8AM (4 days)


title: NA15510 rep3 genotyping at HMS (1X1M)


title: NA10851 rep3 at HMS (Human1Mv1_C)


title: NA18980 rep2 genotyping at HMS (1X1M)


title: NA18517 rep2 genotyping at HMS (1X1M)


title: NA15510 rep1 genotyping at TCAG (HumanOmni1-Quad) rev2


title: NA18576 rep1 genotyping at TCAG (HumanOmni1-Quad) rev2


title: NA18576 rep3 genotyping at HMS (1X1M)


title: NA10851 rep3 genotyping at HMS (1X1M)


title: NA18517 rep1 genotyping at TCAG (HumanOmni1-Quad) rev2


title: NA12239 rep 2 genotyping at TCAG (HumanOmni1-Quad) rev2


title: Patient4_339_GH_Day2_GH1_11PM (4 days)


title: NA10851 rep1 at HMS (Human1Mv1_C)


title: NA15510 rep3 at HMS (Human1Mv1_C)


title: NA12239 rep2 genotyping at HMS (1X1M)


title: Patient4_339_GH_Day2_GH1_2PM (4 days)


title: Patient4_339_GH_Day2_GH1_11AM (4 days)


title: Patient4_339_GH_Day1_GH0_8AM (4 days)


title: Patient4_339_GH_Day2_GH1_5AM (4 days)


title: Patient4_339_GH_Day2_GH1_8PM (4 days)


title: NA12239 rep1 genotyping at TCAG (HumanOmni1-Quad) rev2


title: NA18576 rep2 genotyping at HMS (1X1M)


title: NA18980 rep1 genotyping at TCAG (HumanOmni1-Quad) rev2


title: Patient4_339_GH_Day1_GH0_5AM (4 days)


title: NA18980 rep1 genotyping at HMS (1X1M)


title: NA10851 rep2 genotyping at HMS (1X1M)


title: Patient4_339_GH_Day1_GH0_2AM (4 days)


title: NA15510 rep2 genotyping at HMS (1X1M)


title: Patient4_339_GH_Day1_GH0_11PM (4 days)


title: NA18980 rep1 at HMS (Human1Mv1_C)


title: NA18576 rep1 genotyping at HMS (1X1M)


title: NA18517 rep1 genotyping at HMS (1X1M)


title: Patient4_339_GH_Day1_GH0_5PM (4 days)


title: Patient4_339_GH_Day1_GH0_8PM (4 days)


title: Patient4_339_GH_Day1_GH0_2PM (4 days)


title: NA18980 rep2 at HMS (Human1Mv1_C)


title: Patient4_339_GH_Day1_GH0_11AM (4 days)


title: Patient4_339_GH_Day2_GH1_5PM (4 days)


title: NA12239 rep1 genotyping at HMS (1X1M)


title: NA15510 rep1 at HMS (Human1Mv1_C)


title: NA18576 rep1 at HMS (Human1Mv1_C)


title: Patient6_339_GH_Day4_GH3_8AM (4 days)


title: Patient6_339_GH_Day4_GH3_2AM (4 days)


title: NA18980 rep3 genotyping at TCAG (1X1M)


title: NA15510 rep2 at HMS (Human1Mv1_C)


title: NA10851 rep1 genotyping at HMS (1X1M)


title: NA18576 rep3 at HMS (Human1Mv1_C)


title: Monocyte replicate 1

type: mixed

city: Minneapolis

first: Xiaoxiao

last: Zhang

address: 312 Church St. SE

institute: University of Minnesota

hyb_protocol: A mixture of labeled RNA and DNA was hybridized to a miRNA microarray (Thomson et al), inside a MAUI mixer in a MAUI hybridization system (BioMicro® System, Inc, Salt Lake City, UT, USA).     Thomson, J.M., Parker, J., Perou, C.M., and S.M. Hammond. 2004. A custom microarray platform for analysis of microRNA gene expression. Nat. Methods 1: 47-53. Epub 2004 Sep 29.

scan_protocol: Slides were scanned with a ScanArray 5000 machine (Perkin Elmer®, Waltham, MA, USA).

data_processing:
BlueFuse (BlueGenome, Cambridge, UK) was used to quantify pixel intensities.  GeneSpring GX 7.3.1 (Agilent Technologies) was used for data normalization.
Data processed by Bluefuse is absolute value, and from GeneSpring is normalized ratio.

source_name: Total RNA  from monocyto

label_protocol: Total RNA was ligated to a synthetic linker, 5’-pCU-DY547-3’.  Reference DNA oligonucleotides (Invitrogen) complementary to a subset of mammalian miRNAs were combined and labeled with a ULYSIS® Alexa Fluor® 647 kit.

growth_protocol: Purified monocytes were cultured at 37°C in 6-well plates (1x106 cells per well) in 3 mL of AIM V medium containing human granulocyte/macrophage colony stimulating factor (GM-CSF, 100 ng/mL) and human interleukin 4 (IL-4, 20 ng/mL).

extract_protocol: Trizol® reagent (Invitrogen) was used to extract total RNA from  cells

treatment_protocol: One mL of fresh medium with GM-CSF and IL-4 was additionally added to the monocyto cell cultures at day 3. Old medium was replaced by 3 mL fresh medium with GM-CSF and IL-4 at day 5.  DCs were stimulated with IL-1β (10 ng/mL), IL-6 (10 ng/ml), TNF-α (10 ng/ml), and PGE2 (1 µg/mL) on day 6, and DCs were harvested on day 8 or the indicated time.

value: monocyte

molecule: other

source_name: Reference DNA

tag: sample type

value: synthetic DNA oligos corrresponding to human miRNAs


title: Patient6_339_GH_Day4_GH3_8PM (4 days)


title: Monocyte replicate 2


title: Patient6_339_GH_Day4_GH3_2PM (4 days)


title: NA15510 rep1 genotyping at HMS (1X1M)

value: HMS


title: NA18576 rep3 genotyping at TCAG (1X1M)


title: Immature Dendritic cells replicate 1

source_name: Total RNA  from immature dendritic cells

value: immature dendritic cell


title: Immature Dendritic cells replicate 2


title: NA18576 rep2 at HMS (Human1Mv1_C)


title: Dendritic cells  replicate 2

source_name: Total RNA  from dendritic cells, control treated

value: dendritic cell


title: NA18980 rep3 at HMS (Human1Mv1_C)


title: Patient6_339_GH_Day3_GH2_8AM (4 days)


title: Patient6_339_GH_Day3_GH2_5AM (4 days)


title: Patient6_339_GH_Day3_GH2_2AM (4 days)


title: Mice uteri-Replicate 3

first: Jing-Pian

last: Peng

address: , #1 Beichen West Rd., Chaoyang

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

description: Analysis used pre-implanted uteri samples for comparison to the post-implanted utreri samples

hyb_protocol: Slides hybridised with Labelled cDNA, placed in shaking water bath for overnight at 42 °C. Arrays then washed in 2x SSC (+0.2 % SDS), at 42 °C for 5 min and 0.2x SSC at room temperature for 5 min prior to drying and scanning.

scan_protocol: Arrays scanned using LuxScan 10KA Microarray Scanner (CapitalBio Corp., Beijing, China).

data_processing: The obtained images were analysed with LuxScan 3.0 software (CapitalBio Corp., Beijing, China). Two hybridizations were performed by using a reverse fluorescence strategy (Cy3, Cy5) for each driver and tester sample. Ratios of each gene from three independent experiments were calculated by SAM software.

source_name: Pre-implanted uteri (Day2, Day3 and Day4)

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using CbcScript RTase. Samples purified using PCR NecleoSpin Extract II Kit (MN) before hybridization.

extract_protocol: Total RNA extracted using Trizol manufacturer's instructions

tag: strain

value: Kunming (Chinese variant of Swiss mice)

source_name: Post-implanted uteri (Day6, Day7 and Day8)


title: Dendritic cells  replicate 1


title: Patient6_339_GH_Day3_GH2_11PM (4 days)


title: Patient6_339_GH_Day3_GH2_8PM (4 days)


title: Mice uteri-Replicate 2


title: CU428 cell exposed to 2, 3, 7, 8-Tetrachlorodibenzo-p-dioxin (TCDD) for 24 hour

city: wuhan

first: Wei

last: Miao

state: hubei

address: donghu south road #7

institute: Institute of hydrobiology, CAS

description: references: Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264.

hyb_protocol: Sample Hybridization protocol provided and performed by NimbleGen.

scan_protocol: Nimblegen. Sample scan protocol provided and performed by NimbleGen.

data_processing: Array normalization was performed using the quantile normalization method of Bolstad et al. (2003). Normalized expression values for the individual probes were used to obtain the expression values for a given open reading frame (ORF) by using the robust multiarray average (RMA) procedure as previously described by Irizarry et al. (2003).

organism: Tetrahymena thermophila

label_protocol: Sample labeling protocol provided and performed by NimbleGen.

growth_protocol: 1XSPP, 30 degree, 100 rpm shaking, until 300,000 cells/ml.

extract_protocol: Homogenization was done using a Qiashredder spin column and total RNA was extracted using the RNeasy Protect Cell Mini Kit (Qiagen, Valenica, CA) according to manufacturer’s instructions. The concentration of total RNA was determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Rockland, DE) and RNA integrity was verified using a Bioanalyzer 1000 (Agilent, Palo Alto, CA).

treatment_protocol: Cells at 300,000 cells/ml was incubated in SPP medium with 1 ppb TCDD treatment for 25 hours, taking DMSO as control.

value: tcdd


title: Mice uteri-Replicate 1


title: NA10851 rep3 genotyping at TCAG (1X1M)


title: NA18517 rep2 genotyping at TCAG (1X1M)


title: CU428 cell exposed to Dichlorodiphenyltrichloroethane (DDT) for 24 hour

treatment_protocol: Cells at 300,000 cells/ml was incubated in SPP medium with 4ppm DDT treatment for 24 hours, using DMSO as solvent.

value: dichlorodiphenyltrichloroethane


title: Mus Musculus_Hsf2 mutant fully-grown oocyte_rep2

city: Toulouse

first: Florent

last: LE MASSON

address: 118 route de Narbonne Bat4R3b3

institute: CNRS

description: This sample is of Hsf2 mutant oocytes. It is the second of two Hsf2 mutant technical replicates used in this experiment.

hyb_protocol: Labelled cDNA were hybridized to a NimbleGen Mus musculus Gene Expression 385K microarray, containing 42,586 probe sets with up to 9 probes of 60mer oligonucleotides per gene, following the protocol by Roche NimbleGen, Inc. (Madison, USA). The microarrays were incubated on the NimbleGen Hybridization System 4 (Roche NimbleGen) for 16 hours at 42 °C. The hybridized slides were washed at 10× wash buffer I, II and III (Roche NimbleGen) and dried by nitrogen gas at room temperature.

scan_protocol: Slides were scanned with an Axon GenePix Pro 4200A microarray scanner at 5μm resolution, 532 nm and 635nm wavelengths software using associated software GenePix Pro software (Molecular Devices, Sunnyvale, CA). The scanned images of the arrays were quantified using NimbleScan software (Roche NimbleGen).

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: Mus musculus oocyte Hsf2 mutant

label_protocol: The cDNA of each sample (3.5μg) was synthesized as probe and labeled with Cy3- or Cy5-conjugated random nonamers (TriLink Biotechnologies, San Diego, CA).

growth_protocol: Fully grown oocytes (GV) were collected from ovaries of 8-12 week-old mice (WT, Hsf1 mutant or Hsf2 mutant) in M2 medium (SIGMA).

extract_protocol: Total RNA from 200 to 400 fully grown oocytes (GV) from each genotype (WT, Hsf1 mutant or Hsf2 mutant) were extracted using Qiagen RNeasy micro kit and 10ng samples of RNA were amplified using NuGen WT ovation Pico RNA amplification system to obtain about 10µg of single-strand (ss) cDNA. Two micrograms of ss cDNA was converted to double-strand cDNA using Klenow fragment of the DNA polymerase I and the synthesized cDNAs were then incubated with 1μl of 4 mg/ml RNase A at 37 °C for 10 minutes, precipitated and the pellet dissolved with 20μl of nuclease-free water.

tag: age

value: 8-12 weeks-old mice

value: Oocyte

tag: developmental stage

value: Fully-grown, GV germinal vesicule stage

tag: genetic background

value: Hsf2 mutant

tag: genotype

value: mixed 129XI/SvJ and C57BL/6


title: Patient6_339_GH_Day3_GH2_5PM (4 days)

value: Milk Fat Globule


title: Patient6_339_GH_Day3_GH2_2PM (4 days)


title: NA18576 rep2 genotyping at TCAG (1X1M)

value: Female

value: lymphoblastoid cell lines

tag: cell line


title: OsPDCD-3D5B

city: Shanghai

first: Fan

last: Sun

address: 220 Handan Road

institute: Fudan University

description: 4µg RNAs were labeled and 1µg of Cy3- and Cy5-labeled cRNAs were used.

hyb_protocol: Agilent protocol G4140-90040

scan_protocol: Agilent Technologies Scanner G2505C

data_processing: Data was analyzed by Feature Extraction software (Agilent)

organism: Oryza sativa

source_name: 18-day-old Zhonghua 11 seedlings, heat-shocked

label_protocol: Low RNA inout Lineat Amplification/Labeling Kit (Agilent)

growth_protocol: seedlings were grown in half-strength Murashige and Skoog medium under a 16/8 h light/dark cycle at 26°C, heat-shocked for 6 h

extract_protocol: QIAGEN RNeasy® Mini Kit

value: 18-day-old seedlings

tag: cultivar

value: Zhonghua 11

source_name: 18-day-old Zhonghua 11 seedlings, untreated


title: CU428 cell exposed to DMSO for 24 hour

source_name: CU428 cell exposed to DMSO for 24 hour

treatment_protocol: Cells at 300,000 cells/ml was incubated in SPP medium, with 4.02μlDMSO  per ml SPP as the control of Dichlorodiphenyltrichloroethane (DDT) and 2, 3, 7, 8-Tetrachlorodibenzo-p-dioxin (TCDD) treatment.

value: dmso


title: OsPDCD-3B5D

growth_protocol: seedlings were grown in half-strength Murashige and Skoog medium under a 16/8 h light/dark cycle at 26°C


title: Mus Musculus_Hsf2 mutant fully-grown oocyte_rep1

description: This sample is of Hsf2 mutant oocytes. It is the first of two Hsf2 mutant technical replicates used in this experiment.


title: NA12239 rep3 genotyping at TCAG (1X1M)

value: TCAG

value: Male


title: NA12239 rep2 genotyping at TCAG (1X1M)


source_name: Tetrahymena thermophila CU428 cell exposed to Tributyltin (TBT) for 24 hour

treatment_protocol: CU428 cells at 300,000 cells/ml was incubated in SPP medium, with 5 ppb TBT treatment for 24 hour, using DMSO as solvent.

value: tributyltin


title: NA18517 rep3 genotyping at TCAG (1X1M)


title: NA10851 rep2 at HMS (Human1Mv1_C)

value: HMS


title: Mus Musculus_Hsf1 mutant fully-grown oocyte_rep2

description: This sample is of Hsf1 mutant oocytes. It is the second of two Hsf1 mutant technical replicates used in this experiment.

source_name: Mus musculus oocyte Hsf1 mutant

value: Hsf1 mutant


title: Patient6_339_GH_Day2_GH1_5AM (4 days)

source_name: Milk Fat Globule


title: Patient6_339_GH_Day3_GH2_11AM (4 days)


title: NA15510 rep2 genotyping at TCAG (1X1M)


title: OsPDCD-3A5C

source_name: 24-day-old Zhonghua 11 seedlings, untreated

value: 24-day-old seedlings

source_name: 24-day-old Zhonghua 11 seedlings, heat-shocked


title: Patient6_339_GH_Day2_GH1_8AM (4 days)


title: NA18517 rep1 genotyping at TCAG (1X1M)


title: Mus Musculus_wild-type fully-grown oocyte_rep2

description: This sample is of wild-type oocytes. It is the second of two wild-type technical replicates used in this experiment.

source_name: Mus musculus oocyte wild-type

value: 8-12 weeks-old mice

value: wild-type


title: NA18980 rep1 genotyping at TCAG (1X1M)


title: CU428 cell exposed to DMSO

source_name: Tetrahymena thermophila CU428 cell exposed to dimethyl sulfoxide (DMSO) for 24 hour

treatment_protocol: CU428 cells at 300,000 cells/ml was incubated in SPP medium, with 4.02μL DMSO per ml SPP, as a control of Tributyltin (TBT) treatment.


title: NA18980 rep2 genotyping at TCAG (1X1M)


title: Patient6_339_GH_Day2_GH1_2AM (4 days)


title: Mus Musculus_wild-type fully-grown oocyte_rep1

description: This sample is of wild-type oocytes. It is the first of two wild-type technical replicates used in this experiment.

value: Oocyte

value: Fully-grown, GV germinal vesicule stage


title: OsPDCD-3C5A


title: Patient6_339_GH_Day2_GH1_8PM (4 days)


title: Patient6_339_GH_Day2_GH1_5PM (4 days)


title: Patient6_339_GH_Day2_GH1_2PM (4 days)


title: MammaryTissue-48h-Ecoli-BiologicalRep2

city: Kearneysville

first: Roger

middle: Luis

last: Vallejo

state: WV

address: 11861 Leetown Rd.

department: NCCCWA

institute: USDA-ARS

description: gene expression data in mammary tissue sampled at 48 hr post Ecoli injection

hyb_protocol: The fragmented cRNA target was hybridized to the probe array (GeneChip® Mouse Expression Set 430A) in the Microarray Core Facility at Pennsylvania State University (University Park, PA). One tissue sample or population of mRNAs was hybridized to one GeneChip® array using the Affymetrix System (Affymetrix, Santa Clara, CA) and a Microfluidcs Agilent System (Agilent Technologies, Santa Clara, CA).

scan_protocol: according to Affymetrix protocol

data_processing: For the pre-processing of the raw gene expression data, we wrote an R script using functions from the R package version 2.7.0 (Gentleman et al., 2004). We performed a data background correction using the robust multichip average (RMA) procedure suggested by Irizarry et al. (2005). Briefly, this procedure included a log2 transformation of the perfect match signal expression, quantile data normalization and a median Polish summary method. After running these functions in the raw expression data, we obtained an expression “score” for each of the 22,690 gene entries.

source_name: Mouse right mammary gland tissue at 48hr post Ecoli injection

label_protocol: The target (biotin labeled cRNA) was prepared and fragmented in accordance with instructions in the GeneChip® Mouse Expression Set 430A expression analysis technical manual (Affymetrix, Santa Clara, CA).

growth_protocol: The saline and E. coli challenged mammary glands were excised aseptically after at 24 and 48 hr post-injection.

extract_protocol: total RNA was isolated using Lipid Tissue Midi Kit following the manufacturer's instructions (Qiagen, Valencia, CA).

treatment_protocol: The tissue samples were stored in RNA Later (Ambion, Austin, TX).

tag: Strain

value: Balb/cJ, Gender:female, Parturition:first, Age:5th to 8th day after pups delivery, Tissue:right-side mammary gland, Treatment:Ecoli injected, Time post-injection:48hr


title: Patient6_339_GH_Day2_GH1_11PM (4 days)

value: Milk Fat Globule


title: NA12239 rep1 genotyping at TCAG (1X1M)

value: Female


title: Mus Musculus_Hsf1 mutant fully-grown oocyte_rep1

description: This sample is of Hsf1 mutant oocytes. It is the first of two Hsf1 mutant technical replicates used in this experiment.

value: mixed 129XI/SvJ and C57BL/6


title: Patient6_339_GH_Day1_GH0_8AM (4 days)


title: MammaryTissue-48h-Ecoli-BiologicalRep1


title: Patient6_339_GH_Day2_GH1_11AM (4 days)


title: NA10851 rep2 genotyping at TCAG (1X1M)

value: lymphoblastoid cell lines


title: MammaryTissue-48h-Saline-BiologicalRep1

description: gene expression data in mammary tissue sampled at 48 hr post saline injection

source_name: Mouse left mammary gland tissue at 48hr post saline injection

value: Balb/cJ, Gender:female, Parturition:first, Age:5th to 8th day after pups delivery, Tissue:left-side mammary gland, Treatment:Saline injected, Time post-injection:48hr


title: MammaryTissue-48h-Saline-BiologicalRep2


title: MammaryTissue-24h-Ecoli-BiologicalRep2

description: gene expression data in mammary tissue sampled at 24 hr post Ecoli injection

source_name: Mouse right mammary gland tissue at 24hr post Ecoli injection

value: Balb/cJ, Gender:female, Parturition:first, Age:5th to 8th day after pups delivery, Tissue:right-side mammary gland, Treatment:Ecoli injected, Time post-injection:24hr


title: NA15510 rep3 genotyping at TCAG (1X1M)

value: TCAG


title: Patient6_339_GH_Day1_GH0_2AM (4 days)


title: Patient6_339_GH_Day1_GH0_11PM (4 days)


title: Patient6_339_GH_Day1_GH0_5AM (4 days)


title: NA18576 rep1 genotyping at TCAG (1X1M)

value: Male


title: NA10851 rep1 genotyping at TCAG (1X1M)


title: MammaryTissue-24h-Ecoli-BiologicalRep1


title: MammaryTissue-24h-Saline-BiologicalRep2

description: gene expression data in mammary tissue sampled at 24 hr post saline injection

source_name: Mouse left mammary gland tissue at 24hr post saline injection

value: Balb/cJ, Gender:female, Parturition:first, Age:5th to 8th day after pups delivery, Tissue:left-side mammary gland, Treatment:Saline injected, Time post-injection:24hr


title: Patient6_339_GH_Day1_GH0_8PM (4 days)


title: NA15510 rep1 genotyping at TCAG (1X1M)

description: Genomic DNA extracted was analyzed using Illumina's BeadStudio software


title: Patient6_339_GH_Day1_GH0_5PM (4 days)


title: NA15510 rep 3 genotyping at HMS (Human660W-Quad) rev2

hyb_protocol: Standard Illumina protocol for Human660W-Quad Beadchip

value: HMS


title: NA12239 rep 2 genotyping at TCAG (Illumina_650Y) rev2

hyb_protocol: Standard Illumina protocol for Illumina_650Y Beadchip


title: NA12239 rep1 genotyping at TCAG (Illumina_650Y) rev2

scan_protocol: Standard Illumina protocol for Illumina_650Y Beadchip


title: NA18980 rep 3 genotyping at HMS (Human660W-Quad) rev2

scan_protocol: Standard Illumina protocol for Human660W-Quad Beadchip


title: MammaryTissue-24h-Saline-BiologicalRep1


title: Patient6_339_GH_Day1_GH0_2PM (4 days)


title: NA10851 rep 3 genotyping at TCAG (Illumina_650Y) rev2

label_protocol: Standard Illumina protocol for Illumina_650Y Beadchip


title: NA10851 rep1 genotyping at TCAG (Illumina_650Y) rev2


title: NPS regions from 3 stage-matched Wnt3a wildtype  embryos (biological replicate 3)

city: Frederick

first: Terry. P

last: Yamaguchi

state: MD

address: 1050 Boyles St, Bldg 539,Rm218

department: Cancer and Developmental Biology

institute: National Cancer Institute-Frederick

hyb_protocol: Array hybridizations were performed per manufacturer's protocols (701027 Rev.5) in triplicate per genotype. Subsequent washing, staining, and array scanning were carried out according to manufacturer’s protocols (701028 Rev.5).  Affymetrix GeneChips MOE430 2.0 39K microarrays were used for this study.

scan_protocol: Array scanning were carried out according to Affymetrix protocols (701028 Rev.5).

data_processing: Statistical analysis was performed on probe-intensity level data (CEL files) using BRB ArrayTools v.3.2.  Initial filtering and preprocessing was achieved using the robust multi-array analysis (RMA) algorithm. Class comparison analysis was conducted using a random-variance F-test. Genes were considered statistically significant if their parametric p-value was less than 0.05. Moreover, a Multivariate Permutation Test was performed to control for false discoveries such that with 90% confidence the gene list so obtained had a false discovery rate of less than 10%. Hierarchical clustering was carried out for statistically-significant genes using normalized log base 2 of the signal values using BRB ArrayTools.

source_name: Microdissect node and primitive streaks (NPS)

label_protocol: Protocols for synthesis of cDNA and cRNA were performed using the Affymetrix Two-Cycle Target Labeling Kit (P/N 900494; Affymetrix, Santa Clara, CA) according to manufacturer’s recommendations (701025 Rev.6). Briefly, 30-50ng of total RNA from individual embryos was used as template for first cycle cDNA synthesis. For second cycle cDNA synthesis, equivalent amounts of cRNA from three stage-matched embryos per genotype were pooled (600ng total) to generate labeled-target per array. Following in-vitro transcription, biotin-labeled cRNA was hybridized to GeneChip® Mouse Genome 430 2.0 Arrays (Affymetrix).

extract_protocol: Total RNA was isolated with TRIzol reagent (Invitrogen) from dissected node and primitive streak regions of E7.75-E8 wildtype and Wnt3a mutant embryos as previously described (Dunty et al., 2008, Development Jan;135(1): 85-94).

value: C57BL/6 and 129/Sv mixed

value: E7.75-8 embryos (0-2 somites)

tag: genotype/variation

value: Wnt3a wild type


title: Patient6_339_GH_Day1_GH0_11AM (4 days)

hyb_protocol: 750 ng of labeled cRNAs were hybridized to the Human Ref 8 V2 Beadchip arrays (Illumina  Inc., San Diego, CA) at 55oC overnight (16h) following the Illumina Whole-Genome Gene Expression Protocol for BeadStation (Doc. # 111226048 Rev. B, Illumina Inc)  and stained with 1 ug/ml streptavidin-Cy3 (Amersham Biosciences, Piscataway, NJ) for visualization

scan_protocol: Probe arrays were scanned using the BeadArray reader (Factor 1)


title: NA18576 rep 3 genotyping at HMS (Human660W-Quad) rev2

label_protocol: Standard Illumina protocol for Human660W-Quad Beadchip


title: NA12239 rep 3 genotyping at TCAG (Illumina_650Y) rev2


title: NA10851 rep 2 genotyping at TCAG (Illumina_650Y) rev2


title: NA18517 rep 2 genotyping at TCAG (Illumina_650Y) rev2


title: NA18517 rep 3 genotyping at HMS (Human660W-Quad) rev2


title: NPS regions from 3 stage-matched Wnt3a wildtype  embryos (biological replicate 2)


title: NPS regions from 3 stage-matched Wnt3a wildtype  embryos (biological replicate 1)


title: NA18517 rep1 genotyping at TCAG (Illumina_650Y) rev2


title: A172_Neg.cntrl_24h

city: Turku

first: Saija

middle: M

last: Haapa-Paananen

address: Itäinen Pitkäkatu 4C

department: Medical Biotechnology

country: Finland

institute: VTT Technical Research Centre of Finland

hyb_protocol: Standard Illumina hybridization protocol: 750 ng of biotin-labeled cRNA was hybridized.

scan_protocol: Standard Illumina scanning protocol: The arrays were scanned with the Illumina BeadArray Reader and raw data was produced with GenomeStudio v. 2010.2; Gene Expression Module v.1.7.0 (Illumina).

data_processing: The numerical results were extracted with Bead Studio without any normalization or background subtraction. The data was preprocessed by Bioconductor beadarray and lumi (Du,P. et al. 2008) packages. The data were vst transformed and quantile normalized. Gene expression after siRNA transfections was compared to the siRNA negative control to calculate fold changes (ratios) after HES6 silencing. For HES6 overexpression the expression of pEYFP-HES6wt stable LN405 cell line was compared to pEYFP-mock transfected stable LN405 cell line to calculate log2 fold changes.

source_name: A172 cell line, negative siRNA transfection 24 hrs

label_protocol: Three hundred ng of purified total RNA was amplified with the Illumina Total Prep RNA Amplification kit (Ambion, Austin, TX).

growth_protocol: DMEM (4500 mg/l glucose), 10% FBS, 2mM L-Glutamine, 1xPen-Strep. Additionally for or pEYFP-mock and pEYFP-HES6wt stable cell lines 400 µg/ml G418 (Sigma).

extract_protocol: Total RNA was isolated with RNeasy (Qiagen) or MiRVana™ Total RNA Isolation kit (Ambion). RNA quality was evaluated by using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: A172 and LN405 cells (240 000 per well on 6-well plates) were transfected for 12-24 h with siHES6 pool, or three individual siRNAs (HES6_1, HES6_2, HES6_3 from Qiagen) or AllStars negative control siRNA (Qiagen) at 30 nM using SiLentFect (Bio-Rad Laboratories, Hercules, CA). One to two biological replicate transfections were performed. LN405 cells were also used for creating stable cell lines by transfecting either pEYFP-C1 mock (BD Biosciences Clontech) or pEYFP-HES6wt (Eun et al. 2008) with Fugene6 (Roche) and selecting the positive cells with 600ug/ml of G418 (Sigma). The cells were kept in culture in the presence of 400ug/ml of G418.

tag: ecacc no.

tag: tissue derivation

value: brain

value: glioblastoma

value: male

tag: sirna

value: Negative Control siRNA

tag: plasmid

tag: transfection time

value: 24 hrs


title: NA18517 rep 3 genotyping at TCAG (Illumina_650Y) rev2

tag: gender

value: Female

tag: cell type


title: NA18980 rep 2 genotyping at HMS (Human660W-Quad) rev2

tag: genotyping center


title: A172_Hes6_1_24h

source_name: A172 cell line, HES6_1 siRNA transfection 24 hrs

value: Hs_HES6_1 siRNA


title: A172_Neg.cntrl_12h

source_name: A172 cell line, negative siRNA transfection 12 hrs

value: 12 hrs


title: NPS regions from 3 stage-matched Wnt3a null embryos (biological replicate 3)

tag: strain

value: Wnt3a null


title: IL4_T24

city: Hanover

first: Jennifer

middle: L

last: Sargent

state: NH

address: Dartmouth College; HB7400

department: Genetics

institute: Dartmouth Medical School

hyb_protocol: Agilent Protocols and Hybridization Kits

scan_protocol: GenePix 400B scanner (Axon Instruments)

data_processing: Feature extraction with GenePix 5.1 software

label_protocol: Agilent Linear Amplification Low RNA Input Kit

growth_protocol: primary human dermal fibroblasts were cultured under standard conditions (DMEM + 10% FBS)

extract_protocol: total RNA isolated using Trizol methods; cleaned up with Qiagen RNeasy mini-columns

treatment_protocol: cells were exposed to 50nM IL4 for 24 hours, and RNA isolated at 0, 2, 4, 8, 12 and 24 hours

tag: tissue

value: dermal fibroblasts

tag: time point (hours)

source_name: universal human reference

tag: manufacturer

value: stratagene


title: NA12239 rep 3 genotyping at HMS (Human660W-Quad) rev2

value: lymphoblastoid cell lines


title: NPS regions from 3 stage-matched Wnt3a null embryos (biological replicate 2)

tag: age


title: NA10851 rep 3 genotyping at HMS (Human660W-Quad) rev2

value: Male

tag: cell line


title: NPS regions from 3 stage-matched Wnt3a null embryos (biological replicate 1)


title: A172_Hes6_3_12h

source_name: A172 cell line, HES6_3 siRNA transfection 12 hrs

value: Hs_HES6_3 siRNA


title: IL4_T12


title: LN405_Neg.cntrl_12h

source_name: LN405 cell line, negative siRNA transfection 12 hrs

tag: dsmz no.

value: ACC 189

value: glioblastoma-astrocytoma

value: female


title: NA18576 rep 2 genotyping at HMS (Human660W-Quad) rev2

value: HMS


title: NA15510 rep 3 genotyping at TCAG (Illumina_650Y) rev2

value: TCAG


title: NA18517 rep 2 genotyping at HMS (Human660W-Quad) rev2


title: IL4_T4


title: A172_Hes6_2_12h

source_name: A172 cell line, HES6_2 siRNA transfection 12 hrs

value: brain

value: glioblastoma

value: male

value: Hs_HES6_2 siRNA


title: LN405_Hes6_3_12h

source_name: LN405 cell line, HES6_3 siRNA transfection 12 hrs


title: NA18980 rep 3 genotyping at TCAG (Illumina_650Y) rev2

value: Female


title: NA15510 rep1 genotyping at TCAG (Illumina_650Y) rev2


title: NA15510 rep 2 genotyping at HMS (Human660W-Quad) rev2


title: LN405_Hes6_2_12h

source_name: LN405 cell line, HES6_2 siRNA transfection 12 hrs

value: 12 hrs


title: IL4_T2


title: IL4_T03


title: LN405pEYFPhes6wt_2

source_name: LN405 pEYFP-HES6wt transfected stable cell line

value: pEYFP-C1+HES6wt (Eun et al. 2008)


title: IL4_T02

value: dermal fibroblasts


title: LN405pEYFPmock_2

source_name: LN405 pEYFP-mock transfected stable cell line

value: pEYFP-C1 mock (BD Biosciences Clontech)


title: IL4_T8

value: stratagene


title: NA15510 rep 2 genotyping at TCAG (Illumina_650Y) rev2

value: lymphoblastoid cell lines


title: IL4_T01


title: LN405pEYFPhes6wt_1


title: LN405pEYFPmock_1


title: NA10851 rep 2 genotyping at HMS (Human660W-Quad) rev2

value: Male


title: NA18980 rep1 genotyping at HMS (Human660W-Quad) rev2


title: NA12239 rep 2 genotyping at HMS (Human660W-Quad) rev2


title: NA18980 rep1 genotyping at TCAG (Illumina_650Y) rev2


title: NA18980 rep 2 genotyping at TCAG (Illumina_650Y) rev2


title: LN405_siHes6_b

description: Biological replicate 2 of 2.

scan_protocol: Standard Illumina scanning protocol: The arrays were scanned with the Illumina BeadArray Reader and raw data was produced with GenomeStudio (version 2008.1; Illumina).

data_processing: The numerical results were extracted with Bead Studio without any normalization or background subtraction. The data was preprocessed by Bioconductor beadarray (version 1.12.1) and lumi (version 1.10.2)/lumiHumanAll.db (version 1.6.1) (Du, P. et al. 2008) packages (R 2.9.2). The data were vst transformed and quantile normalized. Gene expression after siRNA transfections was compared to the siRNA negative control to calculate fold changes (ratios) after HES6 silencing and a mean was calculated from two biological replicate samples.

source_name: LN405 cell line, HES6 siRNA pool transfection, 12 hrs

label_protocol: Three hundred ng of purified total RNA was amplified with the Illumina Total Prep RNA Amplification kit  (Ambion, Austin, TX).

growth_protocol: DMEM (4500 mg/l glucose), 10% FBS, 2mM L-Glutamine, 1xPen-Strep.

extract_protocol: Total cellular RNAs were isolated with MiRVana™ Total RNA Isolation kit (Ambion, Austin, TX). RNA quality was evaluated by using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol:
A172 (European Collection of Cell Cultures (ECACC) no. 88062428) and LN-405 (DSMZ no. ACC 189) cells (240,000 per well on 6-well plates) were transfected with siHES6 pool or AllStars negative control siRNA (Qiagen, GmbH, Germany) at 30 nM using SiLentFect (Bio-Rad). Two biological replicate transfections were performed with 12 h incubation.

HES6 siRNA pool: 10 nM each, 30 nM total:
Hs_HES6_1: TTGGAGTTAGTTACCCTTGAA (SI00435792)
Hs_HES6_2: TTCCATTGACATCAAATGTGA (SI00435799)
Hs_HES6_3: AAGCTTGAACTTGCCACTTCA (SI00435806).

value: ACC 189

value: HES6 siRNA pool


title: NA18576 rep1 genotyping at HMS (Human660W-Quad) rev2


title: IL13_T8

treatment_protocol: cells were exposed to 50nM IL13 for 24 hours, and RNA isolated at 0, 2, 4, 8, 12 and 24 hours


title: NA18517 rep1 genotyping at HMS (Human660W-Quad) rev2


title: IL13_T4


title: NA18576 rep 3 genotyping at TCAG (Illumina_650Y) rev2


title: IL13_T24


title: IL13_T12


title: IL13_T03


title: IL13_T2


title: LN405_siHes6_a

description: Biological replicate 1 of 2.

value: glioblastoma-astrocytoma

value: female


title: NA18576 rep 2 genotyping at TCAG (Illumina_650Y) rev2

value: TCAG


title: NA18576 rep1 genotyping at TCAG (Illumina_650Y) rev2


title: LN405_siNEG_a

description: Biological replicate 1 of 2.

source_name: LN405 cell line, negative siRNA transfection, 12 hrs

value: brain

value: negative control siRNA


title: LN405_siNEG_b

description: Biological replicate 2 of 2.


title: A172_siHes6_b

description: Biological replicate 2 of 2.

source_name: A172 cell line, HES6 siRNA pool transfection, 12 hrs

value: glioblastoma

value: male


title: A172_siHes6_a

description: Biological replicate 1 of 2.


title: A172_siNEG_b

description: Biological replicate 2 of 2.

source_name: A172 cell line, negative siRNA transfection, 12 hrs


title: IL13_T01


title: A172_siNEG_a

description: Biological replicate 1 of 2.


title: Vac__day 7_rep18

city: Kingswood

first: Grant

last: Parnell

state: NSW

address: Nepean Hospital

department: Nepean Clinical School

country: Australia

institute: University of Sydney

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was normalised using cubic spline algorithm in Illumina BeadStudio V2.0

source_name: Vaccine_day 7_rep18

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

extract_protocol: RNA was extracted using PAXgene RNA

treatment_protocol: Whole blood samples collected using PAXgene RNA tubes and stored at -20 degrees Celcius until processing

value: Paxgene Whole Blood RNA Samples


title: Muscle WT-1

city: Rahway

first: Oscar

last: Puig

state: NJ

address: 126 East Lincoln Ave

department: Molecular Profiling Research Informatics

institute: Merck Research Laboratories

description: Mice overexpressing reverse tetracycline-transactivator (rtTA) exhibited all four sequelae of metabolic syndrome (visceral obesity, insulin resistance, dyslipidemia, and hypertension), a pro-inflammatory state and marked hepatic steatosis. Gene expression profiling of the adipose tissue, muscle and liver revealed changes in gene expression of key factors involved in lipid metabolism, insulin resistance, and inflammation.

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

source_name: Muscle

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

value: Muscle

tag: genotype

value: WT

tag: genetic background

value: FVB


title: IL13_T02

value: dermal fibroblasts


title: NA10851 rep1 genotyping at HMS (Human660W-Quad) rev2

value: HMS


title: Vac__baseline_rep18


title: Vac__day 7_rep17

source_name: Vaccine_day 7_rep17


title: Muscle WT-3


title: Muscle WT-2