title: wt 1 mo lv 3 normalization 2

description:
wt 1 mo lv 3.CEL
Gene expression data


title: 3aKO 1 mo lv 1 normalization 2

status: Public on Jul 01 2016

type: RNA

city: Columbus

first: Lindsey

middle: N

last: Kent

state: oh

address: 460 W 12th Ave

department: CCC

country: USA

institute: OSU

description:
3aKO 1 mo lv 1.CEL
Gene expression data

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Affymetrix GeneChip Scanner 3000 was used for data acquisition

data_processing: Data was processed using Affymetrix Expression and Transcriptome analysis consoles

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

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

tag: strain

value: mixed background (FVB/NT, 129S1/Svlmj,C57BL/6NT)

tag: genotype

value: E2f3a knock-out

tag: age

value: 4 weeks (1 month)

tag: tissue

value: liver

tag: normalization


title: 3aKO 1 mo lv 2 normalization 2

description:
3aKO 1 mo lv 2.CEL
Gene expression data


title: wt 1 mo lv 10 normalization 2

description:
wt 1 mo lv 10.CEL
Gene expression data

value: wildtype


title: wt 1 mo lv 8 normalization 2

description:
wt 1 mo lv 8.CEL
Gene expression data


title: wt 1 mo lv 6 normalization 2

description:
wt 1 mo lv 6.CEL
Gene expression data


title: 10C105674

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

organism: Homo sapiens

source_name: cultured cells

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

extract_protocol: Both RUCDR and UCLA extracted RNA from the cultured cells with an RNeasy 96 kit (Qiagen, Venlo, Netherlands), employing either a Qiagen BioRobot Universal System (RUCDR) or a manual procedure (UCLA) using up to 5x105 cells (RUCDR) or 106 cells (UCLA) as the starting material. To quantify RNA yield, we used a Quant-iT RiboGreen (Invitrogen, Waltham, MA) and measured RNA integrity number, reflective of sample quality, using a TapeStation (Agilent, Santa Clara, CA).

tag: rnasource

value: RNA from NIMH repository

tag: cell type

value: Lymphoblastoid cell lines (LCLs)

tag: fid

tag: iid

tag: gender

value: f

tag: age (yrs)


title: 09C87629

value: m


title: 09C86925


title: wt 1 mo lv 2 normalization 2

description:
wt 1 mo lv 2.CEL
Gene expression data


title: wt 1 mo lv 4 normalization 2

description:
wt 1 mo lv 4.CEL
Gene expression data


title: wt 1 mo lv 9 normalization 2

description:
wt 1 mo lv 9.CEL
Gene expression data


title: wt 1 mo lv 5 normalization 2

description:
wt 1 mo lv 5.CEL
Gene expression data


title: 10C116726


title: 10C105288


title: 10C105414


title: 11C121500


title: 10C105405


title: 11C120564


title: 10C106089


title: MH0136583


title: 11C122481


title: 11C120563


title: 10C106187


title: 09C86924


title: 09C82010


title: 1KI 1 mo lv 10 normalization 1

description:
1KI 1 mo lv 10.CEL
Gene expression data

value: E2F1 knock-in


title: 1KI 1 mo lv 8 normalization 1

description:
1KI 1 mo lv 8.CEL
Gene expression data


title: 1KI 1 mo lv 6 normalization 1

description:
1KI 1 mo lv 6.CEL
Gene expression data


title: 1KI 1 mo lv 9 normalization 1

description:
1KI 1 mo lv 9.CEL
Gene expression data


title: 10C116788


title: 10C116789


title: 11C121501


title: 11C119730


title: 1KI 1 mo lv 5 normalization 1

description:
1KI 1 mo lv 5.CEL
Gene expression data


title: wt 1 mo lv 1 normalization 2

description:
wt 1 mo lv 1.CEL
Gene expression data


title: 1KI 1 mo lv 7 normalization 1

description:
1KI 1 mo lv 7.CEL
Gene expression data


title: 10C105819


title: 10C106811


title: 1KI 1 mo lv 3 normalization 1

description:
1KI 1 mo lv 3.CEL
Gene expression data


title: 10C106387


title: 3aKO 1 mo lv 10 normalization 1

description:
3aKO 1 mo lv 10.CEL
Gene expression data


title: 1KI 1 mo lv 1 normalization 1

description:
1KI 1 mo lv 1.CEL
Gene expression data


title: 1KI 1 mo lv 2 normalization 1

description:
1KI 1 mo lv 2.CEL
Gene expression data


title: 254706910100_b4 - fit-3+Fe_1 vs Col0+Fe_1

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Changes in gene expression profiles between fit knock-out, wild-type and FIT overexpressor seedlings under sufficient iron supply and under iron deficiency.

hyb_protocol: Col0+Fe_1 Cy5 / fit-3+Fe_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) 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: seedling - Media: 1X Hoagland agar with 50 µM iron. Hygrometry: 70% Temperature: 21 °C (day), 19 °C (night) Light: 16 h light, 8 h dark

extract_protocol: Col0+Fe_1:100mg. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:iron deficiency - iron deficiency - iron concentration,fe -:quantity 0uM time 6day . 0 µM (-Fe) iron concentration in growth mediaName: - iron sufficiency - iron concentration,fe +:quantity 50uM time 6day . 50 µM (+Fe) iron concentration in growth media

tag: ecotype

value: Columbia

tag: genotype/variation

value: wild type

tag: dev.stage (boyes et al. plant cell 2001)

tag: agent

value: +Fe

extract_protocol: fit-3+Fe_1:100mg. (Qiagen_RNeasy.pdf)

value: mutant (fit-3)


title: 254706910100_b3 - Col0+Fe_1 vs fit-3+Fe_1

hyb_protocol: fit-3+Fe_1 Cy5 / Col0+Fe_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 254706910104_b2 - fit-3-Fe_2 vs Col0-Fe_2

hyb_protocol: Col0-Fe_2 Cy5 / fit-3-Fe_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: Col0-Fe_2:100mg. (Qiagen_RNeasy.pdf)

value: -Fe

extract_protocol: fit-3-Fe_2:100mg. (Qiagen_RNeasy.pdf)


title: 254706910104_b1 - Col0-Fe_2 vs fit-3-Fe_2

hyb_protocol: fit-3-Fe_2 Cy5 / Col0-Fe_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 10C106739


title: 1KI 1 mo lv 4 normalization 1

description:
1KI 1 mo lv 4.CEL
Gene expression data


title: 10C105794


title: 09C82252


title: 254706910104_b4 - fit-3-Fe_3 vs Col0-Fe_3

hyb_protocol: Col0-Fe_3 Cy5 / fit-3-Fe_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: Col0-Fe_3:100mg. (Qiagen_RNeasy.pdf)

extract_protocol: fit-3-Fe_3:100mg. (Qiagen_RNeasy.pdf)


title: 254706910104_b3 - Col0-Fe_3 vs fit-3-Fe_3

hyb_protocol: fit-3-Fe_3 Cy5 / Col0-Fe_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 09C84343


title: 3aKO 1 mo lv 9 normalization 1

description:
3aKO 1 mo lv 9.CEL
Gene expression data


title: 3aKO 1 mo lv 8 normalization 1

description:
3aKO 1 mo lv 8.CEL
Gene expression data


title: 254706910103_b2 - HA-FIT-8+Fe_3 vs Col0+Fe_3

hyb_protocol: Col0+Fe_3 Cy5 / HA-FIT-8+Fe_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: Col0+Fe_3:100mg. (Qiagen_RNeasy.pdf)

value: mutant (HA-FIT)


title: 3aKO 1 mo lv 4 normalization 1

description:
3aKO 1 mo lv 4.CEL
Gene expression data


title: 254706910103_b3 - Col0-Fe_1 vs fit-3-Fe_1

hyb_protocol: fit-3-Fe_1 Cy5 / Col0-Fe_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: fit-3-Fe_1:100mg. (Qiagen_RNeasy.pdf)

extract_protocol: Col0-Fe_1:100mg. (Qiagen_RNeasy.pdf)


title: 3aKO 1 mo lv 3 normalization 1

description:
3aKO 1 mo lv 3.CEL
Gene expression data


title: 3aKO 1 mo lv 2 normalization 1

description:
3aKO 1 mo lv 2.CEL
Gene expression data


title: 254706910103_b1 - Col0+Fe_3 vs HA-FIT-8+Fe_3

hyb_protocol: HA-FIT-8+Fe_3 Cy5 / Col0+Fe_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 254706910103_b4 - fit-3-Fe_1 vs Col0-Fe_1

hyb_protocol: Col0-Fe_1 Cy5 / fit-3-Fe_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 3aKO 1 mo lv 6 normalization 1

description:
3aKO 1 mo lv 6.CEL
Gene expression data


title: 3aKO 1 mo lv 7 normalization 1

description:
3aKO 1 mo lv 7.CEL
Gene expression data


title: 3aKO 1 mo lv 5 normalization 1

description:
3aKO 1 mo lv 5.CEL
Gene expression data


title: 254706910102_b3 - Col0+Fe_2 vs HA-FIT-8+Fe_2

hyb_protocol: HA-FIT-8+Fe_2 Cy5 / Col0+Fe_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: Col0+Fe_2:100mg. (Qiagen_RNeasy.pdf)


title: 09C90750


title: 09C84342


title: 09C83411


title: MH0136582


title: 254706910102_b2 - HA-FIT-8+Fe_1 vs Col0+Fe_1

hyb_protocol: Col0+Fe_1 Cy5 / HA-FIT-8+Fe_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 09C86269


title: MH0135654


title: wt 1 mo lv 12 normalization 1

description:
wt 1 mo lv 12.CEL
Gene expression data


title: 254706910102_b4 - HA-FIT-8+Fe_2 vs Col0+Fe_2

hyb_protocol: Col0+Fe_2 Cy5 / HA-FIT-8+Fe_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 09C84840


title: 09C84839


title: 09C83412


title: 3aKO 1 mo lv 1 normalization 1

description:
3aKO 1 mo lv 1.CEL
Gene expression data


title: 09C93018


title: 254706910101_b3 - Col0+Fe_3 vs fit-3+Fe_3

hyb_protocol: fit-3+Fe_3 Cy5 / Col0+Fe_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: fit-3+Fe_3:100mg. (Qiagen_RNeasy.pdf)


title: 254706910102_b1 - Col0+Fe_1 vs HA-FIT-8+Fe_1

hyb_protocol: HA-FIT-8+Fe_1 Cy5 / Col0+Fe_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 254706910101_b4 - fit-3+Fe_3 vs Col0+Fe_3

hyb_protocol: Col0+Fe_3 Cy5 / fit-3+Fe_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: wt 1 mo lv 11 normalization 1

description:
wt 1 mo lv 11.CEL
Gene expression data

hyb_protocol: Standard Affymetrix protocol


title: wt 1 mo lv 7 normalization 1

description:
wt 1 mo lv 7.CEL
Gene expression data


title: wt 1 mo lv 10 normalization 1

description:
wt 1 mo lv 10.CEL
Gene expression data


title: 09C82487

hyb_protocol: Standard Illumina hybridization protocol


title: 09C83409


title: 10C107830


title: 254706910101_b2 - fit-3+Fe_2 vs Col0+Fe_2

hyb_protocol: Col0+Fe_2 Cy5 / fit-3+Fe_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: fit-3+Fe_2:100mg. (Qiagen_RNeasy.pdf)


title: 09C83141


title: 09C82810


title: wt 1 mo lv 8 normalization 1

description:
wt 1 mo lv 8.CEL
Gene expression data


title: wt 1 mo lv 3 normalization 1

description:
wt 1 mo lv 3.CEL
Gene expression data


title: 09C83410


title: 254706910100_b1 - fit-3+Fe_3 vs fit-3-Fe_3

hyb_protocol: fit-3-Fe_3 Cy5 / fit-3+Fe_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: wt 1 mo lv 4 normalization 1

description:
wt 1 mo lv 4.CEL
Gene expression data


title: wt 1 mo lv 9 normalization 1

description:
wt 1 mo lv 9.CEL
Gene expression data


title: 09C85177


title: wt 1 mo lv 6 normalization 1

description:
wt 1 mo lv 6.CEL
Gene expression data


title: 254706910101_b1 - Col0+Fe_2 vs fit-3+Fe_2

hyb_protocol: fit-3+Fe_2 Cy5 / Col0+Fe_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 254706910100_b2 - fit-3-Fe_3 vs fit-3+Fe_3

hyb_protocol: fit-3+Fe_3 Cy5 / fit-3-Fe_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: wt 1 mo lv 2 normalization 1

description:
wt 1 mo lv 2.CEL
Gene expression data


title: wt 1 mo lv 5 normalization 1

description:
wt 1 mo lv 5.CEL
Gene expression data


title: 254706910098_b4 - HA-FIT-8-Fe_3 vs HA-FIT-8+Fe_3

hyb_protocol: HA-FIT-8+Fe_3 Cy5 / HA-FIT-8-Fe_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 09C82488


title: 09C95567


title: 254706910099_b3 - fit-3+Fe_2 vs fit-3-Fe_2

hyb_protocol: fit-3-Fe_2 Cy5 / fit-3+Fe_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 254706910099_b1 - fit-3+Fe_1 vs fit-3-Fe_1

hyb_protocol: fit-3-Fe_1 Cy5 / fit-3+Fe_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 09C82809


title: 254706910099_b2 - fit-3-Fe_1 vs fit-3+Fe_1

hyb_protocol: fit-3+Fe_1 Cy5 / fit-3-Fe_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 254706910099_b4 - fit-3-Fe_2 vs fit-3+Fe_2

hyb_protocol: fit-3+Fe_2 Cy5 / fit-3-Fe_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 254706910098_b3 - HA-FIT-8+Fe_3 vs HA-FIT-8-Fe_3

hyb_protocol: HA-FIT-8-Fe_3 Cy5 / HA-FIT-8+Fe_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: wt 1 mo lv 1 normalization 1

description:
wt 1 mo lv 1.CEL
Gene expression data


title: 09C82489


title: 10C101863


title: 254706910098_b1 - HA-FIT-8+Fe_2 vs HA-FIT-8-Fe_2

hyb_protocol: HA-FIT-8-Fe_2 Cy5 / HA-FIT-8+Fe_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 10C101864


title: 3 MT EMF

city: Chongqing

first: Jin-yi

last: liu

address: gaotanyan street

department: College of Preventive Medicine

country: China

institute: Third Military Medical University

description: MicroRNA expression proﬁling in GC-2 cells following 50 Hz ELF-EMF at 3 MT

hyb_protocol: Following fragmentation, 1 ug of LMWRNA were hybridized for 16 hr at 48C on Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Use the free miRNA QC Tool software for data summarization, normalization, and quality control

source_name: 50 Hz ELF-EMF at magnetic field intensities of 3 mT

label_protocol: Biotinylated LMWRNA were prepared according to the standard Affymetrix protocol from 400 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: GC-2 cells were cultured in high-glucose DMEM containing 10% fetal bovine serum at 37°C in a 5% CO2 humidified atmosphere.

treatment_protocol: GC-2 cells were exposed to a 50 Hz ELF-EMF at magnetic intensities of 1 mT, 2 mT and 3 mT for 72 h (5 min on / 10 min off).

tag: cell line

value: spermatocyte-derived GC-2 cells

tag: stress

value: 50 Hz ELF-EMF at 3 MT


title: 10C105063


title: 10C107633


title: 254706910096_b3 - Col0+Fe_2 vs Col0-Fe_2

hyb_protocol: Col0-Fe_2 Cy5 / Col0+Fe_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 254706910097_b3 - HA-FIT-8+Fe_1 vs HA-FIT-8-Fe_1

hyb_protocol: HA-FIT-8-Fe_1 Cy5 / HA-FIT-8+Fe_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 254706910098_b2 - HA-FIT-8-Fe_2 vs HA-FIT-8+Fe_2

hyb_protocol: HA-FIT-8+Fe_2 Cy5 / HA-FIT-8-Fe_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 1 MT EMF

description: MicroRNA expression proﬁling in GC-2 cells following 50 Hz ELF-EMF at 1 MT

source_name: 50 Hz ELF-EMF at magnetic field intensities of 1 mT

value: 50 Hz ELF-EMF at 1 MT


title: 254706910096_b4 - Col0-Fe_2 vs Col0+Fe_2

hyb_protocol: Col0+Fe_2 Cy5 / Col0-Fe_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 09C100068

hyb_protocol: Standard Illumina hybridization protocol


title: 254706910088_b3 - Col0-Fe_3 vs HA-FIT-8-Fe_3

hyb_protocol: HA-FIT-8-Fe_3 Cy5 / Col0-Fe_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: MH0134835


title: 254706910097_b1 - Col0+Fe_3 vs Col0-Fe_3

hyb_protocol: Col0-Fe_3 Cy5 / Col0+Fe_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: SHAM

description: MicroRNA expression proﬁling in GC-2 cells

source_name: SHAM

value: sham


title: 10C108754


title: MH0135619


title: 09C98210


title: 254706910096_b1 - Col0+Fe_1 vs Col0-Fe_1

hyb_protocol: Col0-Fe_1 Cy5 / Col0+Fe_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 254706910096_b2 - Col0-Fe_1 vs Col0+Fe_1

hyb_protocol: Col0+Fe_1 Cy5 / Col0-Fe_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 254706910084_b4 - HA-FIT-8-Fe_2 vs Col0-Fe_2

hyb_protocol: Col0-Fe_2 Cy5 / HA-FIT-8-Fe_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 10C105276


title: MH0141859


title: MH0135229


title: 254706910084_b3 - Col0-Fe_2 vs HA-FIT-8-Fe_2

hyb_protocol: HA-FIT-8-Fe_2 Cy5 / Col0-Fe_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 254706910088_b4 - HA-FIT-8-Fe_3 vs Col0-Fe_3

hyb_protocol: Col0-Fe_3 Cy5 / HA-FIT-8-Fe_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: 254706910097_b2 - Col0-Fe_3 vs Col0+Fe_3

hyb_protocol: Col0+Fe_3 Cy5 / Col0-Fe_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: breast cancer 34

type: genomic

city: Hannover

first: Doris

middle: Johanna

last: Steinemann

department: Institute of Human Genetics

country: Germany

institute: Hannover Medical School

description: hybridized to [OncoScan] Affymetrix OncoScan array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing:
CEL files were generated after scanning by the Affymetrix GeneChip Command Console (AGCC). These CEL files were further processed using OncoScan Console software version 1.3.0.39 to produce OSCHP files.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal. Data was analyzed using Chromosome Analysis Suite (ChAS) version 3.1.0.15.

molecule: genomic DNA

source_name: primary tumor

label_protocol: as given by the manufacturer (Affymetrix)

growth_protocol: primary formalin fixed parafffin embedded tissue

extract_protocol: genomic DANN was extracted from macrodissected with DNAeasy blood and tissue kit (Qiagen)

value: breast tumor


title: 254706910084_b2 - HA-FIT-8-Fe_1 vs Col0-Fe_1

hyb_protocol: Col0-Fe_1 Cy5 / HA-FIT-8-Fe_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: breast cancer 32


title: breast cancer 33


title: breast cancer 31


title: 10C101479


title: 10C107683


title: 10C107558


title: 10C102153


title: 10-H-9

value: RNA from LCL in UCLA


title: 10C101478

value: RNA from NIMH repository


title: 10C101015

value: Lymphoblastoid cell lines (LCLs)


title: 10-H-2

value: f


title: 10C102154


title: 10C102063


title: breast cancer 30


title: 254706910084_b1 - Col0-Fe_1 vs HA-FIT-8-Fe_1

hyb_protocol: HA-FIT-8-Fe_1 Cy5 / Col0-Fe_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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: breast cancer 29


title: breast cancer 28


title: DNA from PBMC purified from a 30 year old female

city: Haifa

first: Ariel

last: Miller

address: Efron 1

department: Medicine

country: Israel

institute: Technion

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation 450 BeadChip  using standard Illumina protocol

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

data_processing:
The methylation BeadChip data was normalized using an R-script pipeline developed by Touleimat and Tost (Epigenomics 4:325-341)
signals.txt reports unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Human blood

label_protocol: Standard Illumina Protocol

extract_protocol: PBMCs were purified from 60 ml blood by Ficoll density gradient centrifugation (U16 NovaMed). Some PBMC's were set aside, and the rest were used for subset isolation. The CD14 subset was isolated using EasySep™ Human Monocyte Enrichment Kit (#19059 Stemcell). B and T cell subsets were purified by FACS ARIA sorting (Becton Dickinson) using anti-CD19 antibody (Ab) (R0808, DAKO), anti-CD4 Ab (556345,BD Pharmingen), and anti-CD8 Ab (F0765,Dako). Recovery was 65-80% with a purity > 95% for all cell-subsets.  FoxpP3+ CD4 cells (Tregs) were also sorted by the FACS ARIA, but not used in this analysis, therefore the CD4 T cells included in the study are Foxp3-. From each sample both RNA and DNA was extracted using AllPrep kit (#80204 QIAGENE) according to manufacturer's protocol. DNA concentration was measured by picogreen and stored at 4°C until use. RNA quantity and quality was measured by NanoDrop and Agilent BioAnalyzer respectively and stored at -80°C until use.

tag: individual

value: 30 years

value: Blood

tag: cell subset

value: PBMC

value: Female


title: 10-H-72


title: breast cancer 27


title: breast cancer 25


title: breast cancer 26


title: DNA fromCD4 T cells purified from a 30 year old female

tag: age

value: CD4 T cells


title: DNA from PBMC purified from a 49 year old female

value: 49 years

tag: tissue


title: DNA from PBMC purified from a 41 year old female

value: 41 years


title: DNA from B cells purified from a 52 year old female

value: 52 years

value: B cells


title: breast cancer 24


title: 254706910097_b4 - HA-FIT-8-Fe_1 vs HA-FIT-8+Fe_1

hyb_protocol: HA-FIT-8+Fe_1 Cy5 / HA-FIT-8-Fe_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) 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.

value: Columbia

value: mutant (HA-FIT)

value: +Fe

value: -Fe


title: DNA from CD4 T cells purified from a 33 year old female

value: 33 years


title: DNA from PBMC purified from a 52 year old female


title: breast cancer 23

value: breast tumor


title: 10C114139

value: RNA from NIMH repository

value: Lymphoblastoid cell lines (LCLs)

value: m


title: 09C82040

value: f


title: breast cancer 22


title: 10C110667


title: 10C113996


title: MH0140831


title: breast cancer 19


title: 10-H-53

value: RNA from LCL in UCLA


title: DNA from CD4 T cells purified from a 52 year old female

value: Blood

value: Female


title: DNA from CD4 T cells purified from a 43 year old female

value: 43 years

value: CD4 T cells


title: DNA from B cells purified from a 49 year old female

value: 49 years


title: DNA from CD8 T cells purified from a 30 year old female

value: 30 years

value: CD8 T cells


title: breast cancer 18


title: 10C113997


title: 10-SM-79


title: DNA from CD8 T cells purified from a 43 year old female


title: breast cancer 17


title: DNA from CD4 T cells purified from a 41 year old female

value: 41 years


title: 10-SM-6


title: 10-SM-7


title: breast cancer 16


title: DNA from CD4 T cells purified from a 49 year old female


title: breast cancer 15


title: 10-J-395


title: 10-SP-74


title: breast cancer 12


title: 10-SM-76


title: breast cancer 13


title: breast cancer 10


title: breast cancer 9


title: DNA from CD8 T cells purified from a 33 year old female


title: breast cancer 7


title: 10-J-396


title: 10-J-105


title: DNA from CD8 T cells purified from a 52 year old female

value: 52 years


title: breast cancer 8


title: breast cancer 6


title: DNA from B cells purified from a 43 year old female

value: B cells


title: 10-E-394


title: DNA from B cells purified from a 30 year old female


title: 10-S-118


title: breast cancer 4


title: DNA from CD8 T cells purified from a 49 year old female


title: breast cancer 3


title: 10-S-397


title: multiple myeloma bone marrow_36

city: Bethesda

first: Weixin

last: Wang

state: MD

address: 9000 Rockville Pike

department: DLM/CC

institute: NIH

description: miRNA profiling

hyb_protocol: Hybridization was done at 56ºC and 20 rpm for 20 h.

scan_protocol: Array images were scanned on Agilent’s G2505C scanner using settings for high-density miRNA arrays.

data_processing:
The scanned images were processed with Agilent’s Feature Extraction software (v.10.7.3.1).
Signal intensity values normalized by all control probes (including spike-ins) on the array.

source_name: multiple myeloma bone marrow_36

label_protocol: Total RNA (100 ng) was reverse transcribed and Cyanine3-pCp labeled using the Agilent microRNA labeling kit according to the manufacturer’s protocol. Labeled cRNA was purified with Micro Bio-Spin 6 columns.

extract_protocol: Total RNA was isolated from the bone marrow supernatant of multiple myeloma using miRNeasy Mini Kit (Qiagen, Germantown, MD). RNA concentration and quality was determined using an Agilent Bioanalyzer 2100 (Agilent, Wilmington, DE) and NanoDrop 2000 instrument (Thermo Scientific, Wilmington, DE).

value: bone marrow

tag: phenotype

value: multiple myeloma


title: breast cancer 2

value: breast tumor


title: DNA from Monocyte purified from a 30 year old female

value: Monocyte


title: multiple myeloma bone marrow_35

description: miRNA profiling

source_name: multiple myeloma bone marrow_35


title: 260-31147-V

city: Chicago

first: Silvia

last: Kariuki

state: IL

department: Human Genetics

institute: University of Chicago

data_processing: quantile normalized and variance transformed using LUMI package in R

source_name: PBMCs

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

extract_protocol: RNA was extracted with QIAGEN RNeasy Plus mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: PBMCs were treated with phytohemagglutinin with 1,25-dihydroxyvitamin D3, or vehicle control (EtOH) for 6hours

value: PBMC

tag: ethnic group

value: African American

tag: treatment

value: 1,25 dihydroxyvitamin D3 + phytohemagglutinin


title: multiple myeloma bone marrow_34

description: miRNA profiling

source_name: multiple myeloma bone marrow_34


title: 264-31149-E

tag: cell type

value: vehicle (EtOH) + phytohemagglutinin


title: multiple myeloma bone marrow_33

description: miRNA profiling

source_name: multiple myeloma bone marrow_33


title: 255-31131-E


title: DNA from Monocyte purified from a 49 year old female

value: Blood

value: Female


title: multiple myeloma bone marrow_31

description: miRNA profiling

source_name: multiple myeloma bone marrow_31


title: 259-31147-E


title: DNA from Monocyte purified from a 53 year old female


title: 257-31146-E


title: multiple myeloma bone marrow_32

description: miRNA profiling

source_name: multiple myeloma bone marrow_32


title: DNA from Monocyte purified from a 33 year old female


title: DNA from Monocyte purified from a 41 year old female


title: 253-31131-V


title: 262-31149-V


title: 258-31146-V


title: multiple myeloma bone marrow_30

description: miRNA profiling

source_name: multiple myeloma bone marrow_30


title: 251-31100-V


title: multiple myeloma bone marrow_29

description: miRNA profiling

source_name: multiple myeloma bone marrow_29


title: multiple myeloma bone marrow_28

description: miRNA profiling

source_name: multiple myeloma bone marrow_28


title: multiple myeloma bone marrow_27

description: miRNA profiling

source_name: multiple myeloma bone marrow_27


title: multiple myeloma bone marrow_26

description: miRNA profiling

source_name: multiple myeloma bone marrow_26


title: 250-31100-E


title: multiple myeloma bone marrow_25

description: miRNA profiling

source_name: multiple myeloma bone marrow_25


title: multiple myeloma bone marrow_24

description: miRNA profiling

source_name: multiple myeloma bone marrow_24


title: multiple myeloma bone marrow_23

description: miRNA profiling

source_name: multiple myeloma bone marrow_23


title: multiple myeloma bone marrow_22

description: miRNA profiling

source_name: multiple myeloma bone marrow_22


title: 248-31090-E


title: multiple myeloma bone marrow_21

description: miRNA profiling

source_name: multiple myeloma bone marrow_21


title: multiple myeloma bone marrow_5

description: miRNA profiling

source_name: multiple myeloma bone marrow_5


title: breast cancer 11

source_name: primary tumor


title: 10C112679

source_name: cultured cells

extract_protocol: Both RUCDR and UCLA extracted RNA from the cultured cells with an RNeasy 96 kit (Qiagen, Venlo, Netherlands), employing either a Qiagen BioRobot Universal System (RUCDR) or a manual procedure (UCLA) using up to 5x105 cells (RUCDR) or 106 cells (UCLA) as the starting material. To quantify RNA yield, we used a Quant-iT RiboGreen (Invitrogen, Waltham, MA) and measured RNA integrity number, reflective of sample quality, using a TapeStation (Agilent, Santa Clara, CA).

tag: rnasource

value: RNA from NIMH repository

value: Lymphoblastoid cell lines (LCLs)

tag: fid

tag: iid

value: f


title: 249-31090-V

source_name: PBMCs


title: 246-31029-E


title: 241-31025-E


title: multiple myeloma bone marrow_4

description: miRNA profiling

source_name: multiple myeloma bone marrow_4


title: 233-30942-V


title: 230-30925-V


title: multiple myeloma bone marrow_2

description: miRNA profiling

source_name: multiple myeloma bone marrow_2


title: 229-30925-E


title: 244-31029-V


title: 242-31025-V


title: 239-31019-E


title: 240-31019-V


title: control bone marrow_9

description: miRNA profiling

source_name: control bone marrow_9

value: control


title: 226-30814-V


title: multiple myeloma bone marrow_3

description: miRNA profiling

source_name: multiple myeloma bone marrow_3


title: control bone marrow_8

description: miRNA profiling

source_name: control bone marrow_8


title: control bone marrow_6

description: miRNA profiling

source_name: control bone marrow_6


title: 228-30814-E


title: control bone marrow_7

description: miRNA profiling

source_name: control bone marrow_7


title: Liver_60Fat_rep4

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

hyb_protocol: 600ng of labeled cRNA were hybridized on the array using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: Scannedusing  Agilent Technologies G2505C scanner

data_processing: Images were quantified using Feature Extraction Software (Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift

organism: Rattus norvegicus

source_name: Liver_HFD treated

label_protocol: The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using Qiagen RNeasy columns(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop. Samples that pass the QC for specific activity were taken for hybridization.

extract_protocol: RNA isolation was done by using TRIzol method as per the manufacturer’s instructions.

treatment_protocol: Freshly excised liver were snap frozen in liquid nitrogen followed by storage in -80C till furthur processing.

tag: strain

value: Sprague Dawley

tag: gender

value: male

tag: weight

tag: fed with

value: 60% high fat diet (HFD) for 12 wks

value: liver


title: control bone marrow_4

description: miRNA profiling

source_name: control bone marrow_4

value: bone marrow


title: 236-30942-E


title: 223-30809-E


title: control bone marrow_3

description: miRNA profiling

source_name: control bone marrow_3


title: Liver_Control_rep3

value: normal diet for 12 wks


title: 222-29929-V


title: Liver_60Fat_rep3


title: Liver_60Fat_rep2


title: Liver_Control_rep4


title: Liver_Control_rep2


title: control bone marrow_2

description: miRNA profiling

source_name: control bone marrow_2


title: 221-29929-E


title: 217-29928-V


title: 224-30809-V


title: e6/e7 Silenced CaSki cell Replicate 3

city: Guangzhou

first: Fei

last: LIU

address: North of Guangzhou avenue No,1838, Baiyun District

department: Department of Laboratory Medicine

institute: Nanfang Hospital, Southern Medical University

hyb_protocol: The array used is: Exiqon miRCURY LNA microRNA array, 7th gen (hsa, miRBase 18). Prepare the hybridization mix in a PCR tube (Labeled sample 12.5ul, 2×Hybridization buffer 90ul, Nuclease-free Buffer 77.5ul). Incubate at 95°C for 2 min. During the incubation the target preparation should be protected from light. Leave on ice for at least 2 min. Briefly spin the reaction after ice incubation.Take cover slide out of the package. Carefully laid the miRCURYTM Array on top of the assembly of cover slide and spacer, where the printed side of array should be facing toward the cover slide, to form a hybridization assembly. The printed side of array is on the side of the label. Insert the hybridization assembly into a (3.1 x 9cm) heat-shrank hybridization (hyb.) bag. Sample loading side of the hybridization assembly should face the opening side of film bag. Lower the assembly to the end of the bag. Clip the bag with a clipper “securely” from the opening end. Immerse the assembly to the rim of the slide in 95℃ hot water swiftly (approximately 2~5 sec). Do not dip the assembly too far into the water to avoid water leaking into the assembly. The hyb. bag will shrink and tightly wrap around the assembly. Remove the assembly from water and wipe off the water from the assembly. Trim off the excess film from the top of the assembly. Keep the assembly in a 50℃ oven for at least 10 minutes. Load the180ul target hybridization mix into the assembly through the sample loading opening. Fill up the hybridization space with 1X Hybridization buffer till the liquid level reaches to approximately 5 mm (0.5cm) away from the top rim. Cut the second Hyb. Bag to approximately one-half of its original length. Keep the assembly vertical and slip on the shortened hyb. bag from step 11 all the way until the assembly reaches the end of the hyb. bag. Use a pair of forceps to hold onto the top of the assembly. Immerse the entire assembly into 95℃ hot water with the assembly in upright position. Place the hybridization assembly into a 56℃ oven and set it on a rotator. Remember to rotate the assembly at 2 rotations per minute (RPM) for overnight. After hybridization, disassembled the hybridization assembly, and wash the slides at 56℃ for 2min. using Wash buffer A. Wash briefly at room temperature in Wash buffer B. Wash for 2min. at room temperature in Wash buffer B. Wash for 2min. at room temperature in Wash buffer C. Wash briefly in water. Dry the slides by centrifugation for 5 min. at 200* g(1000rpm). Scan slides immediately after drying.

scan_protocol: Scanning is performed with the Axon GenePix 4000B microarray scanner

data_processing: GenePix pro V6.0 is used to read the raw intensity of the image. The intensity of green signal is calculated after background subtraction and four Replicated spots of each probe on the same slide have been averaged. We use Median Normalization Method to obtain “Normalized Data”, Normalized Data= (Foreground-Background)¬/¬median, the median is 50 percent quantile of microRNA intensity which is larger than 30 in all samples after background correction. After normalization, the statistical significance of differentially expressed miRNA was analyzed by T-test. Unsupervised hierarchical clustering and Correlation analysis was performed on miRNA data.

source_name: e6/e7 Silenced CaSki cell

label_protocol: Thaw all kit components.Combine reagents on ice (Total RNA: 1ug in 3ul H2O, CIP buffer 0.5 ul, CIP enzyme 0.5 ul). Incubate 30 min.at 37℃, using a PCR cycler with heated lid. Stop the enzyme reaction and denaturate the RNA by incubation at 95℃ followed by snap cooling on ice. Leave on ice for at least 2 min. and up to 15min. Briefly spin the reaction after incubation on ice. Combine reagents on ice(4ul CIP reaction, Labeling buffer 3ul, Fluorescent label(Hy3TM) 1.5ul, DMSO 2ul, Labeling enzyme 2ul). Mix the reagents by gentle vortexing or by pipetting up and down to ensure that all reagents are mixed thoroughly. Incubate at 16°C for 1hour, using a PCR cycler with heated lid. Protect the reaction from light. Incubate for 15 min. at 65°C. After stopping the labeling procedure, briefly spin the reaction and leave it at 4°C. The labeled sample is now ready for hybridization on the array.

growth_protocol: HPV16-positive human cervical cancer cell lines CaSki was grown in RPMI1640 medium with 10% FBS at 37 °C and 5% CO2.

extract_protocol: Lyse cells directly in a culture dish by adding 1 ml of TRIzol Reagent, Incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIzol Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at 12,000 × g for 15 minutes at 4°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIzol Reagent used for homogenization. Transfer the upper, aqueous phase to a new collection tube. Add 1.5 volume of 100% ethanol, and mix thoroughly by pipitting up and down several times. Pipet up to 700 μl of the sample, including any precipitate that may have formed, into an RNeasy Mini spin column in a 2 ml collection tube. Close the lid gently, and centrifuge for 15 s at ≥8000 x g at room temperature. Discard the flow-through. Add 700ul Buffer RWT to the RNeasy Mini spin column. Close the lid gently and centrifuge for 15s at ≥8000 x g at room temperature to wash the column. Discard the flow-through. Add 500 μl Buffer RPE to the spin column. Close the lid gently, and centrifuge for 15 s at ≥8000 x g to wash the spin column membrane. Discard the flow-through. Add another 500ul Buffer RPE onto the spin column. Close the lid gently and centrifuge for 2min at ≥8000 x g to dry the RNeasy Mini spin column membrane. Place the RNeasy Mini spin column into a new 2ml collection tube, and discard the old collection tube with the flow-through. Centrifuge in a microcentrifuge at full speed for 1min. Transfer the RNeasy Mini spin column to a new 1.5ml collection tube. Pipet 20ul RNase-free water directly onto the RNeasy Mini spin column membrane. Close the lid gently and centrifuge for 1min at ≥8000 x g to elute the RNA.

treatment_protocol: Cells were seeded in six-well plate at 1×106 cells/well and cultured overnight. After washed three times with PBS, cells were transfected with siRNA-e6/e7 or negative control at a final concentration of 100nM using Lipofectamine RNAiMaX (Invitrogen). Six hours later, the medium was replaced with complete medium which containing 10% FBS. After 48h incubation, cell were harvested for RNA extraction.

tag: cell line

value: CaSki

value: cervical cancer cells with HPV16 positive


title: control bone marrow_1

description: miRNA profiling

source_name: control bone marrow_1


title: e6/e7 Silenced CaSki cell Replicate 2


title: 219-29928-E

hyb_protocol: Standard Illumina hybridization protocol

value: PBMC

value: African American


title: e6/e7 Silenced CaSki cell Replicate 1


title: 214-29787-E

value: vehicle (EtOH) + phytohemagglutinin


title: PHOX2B+ #1

city: Baltimore

first: Gabsang

last: Lee

address: 733 North Broadway

department: School of Medicine

institute: The Johns Hopkins University

hyb_protocol: 18hrs at 45°C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix' GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing: Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform. RMA normalization was used to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.

source_name: PHOX2B-2A-eGFP+ sorted cells from PHOX2B::eGFP reporter hESC line, LSB (day 0-3/4) - m3i (day 2-7) - SP (day 3-10)

label_protocol: NuGen Ovation RNA-Seq System V2, with the Encore Biotin Module as per manufacturer's protocol.

growth_protocol: We cultured undifferentiated OCT4::eGFP, SOX10::eGFP, ASCL1::eGFP, and PHOX2B::eGFP genetic reporter H9 hESC lines on mitotically inactivated mouse embryonic fibroblasts, in a medium containing DMEM/F12, 20% knockout serum replacement, 0.1 mM MEM-NEAA, 1 mM L-glutamine, 55 μM β-mercaptoethanol and 4 ng/mL FGF2. All cells were maintained at 37°C and 5% CO2 in a humidified incubator.

extract_protocol: Cells lysed in TRIzol and frozen at -80°C were thawed and homogenized at 0°C, then incubated at R.T. for 5min and centrifuged at 12,000g for 10min. at 4°C. The supernatants were chloroform extracted, incubated for 15min., again centrifuged at 12,000g for 15min. at 4°C and the aqueous layer treated with 0.5ml isopropanol per 1.0ml of TRIzol solution at 20°C for 10min then centrifuged at 12,000g for 10min at 4°C. The pellets were washed with 1ml 75% EtOH at 0°C, centrifuged at 12,000g for 10min. at 4°C and resuspended in 20μl H20.

treatment_protocol: Dissociated hESCs were plated on Geltrex at a density of 20,000-25,000 cells/cm2 in MEF-conditioned hESC medium containing 10 ng/mL FGF2 and 10 μM ROCK-inhibitor (Y-27632). Cells were allowed to reach 70%–80% confluence over 2 days. Differentiation was initiated by switching to medium that included KSR medium with 500 nM LDN193189 and 10 μM SB431542 (LSB). Beginning at day 4, the KSR medium was gradually replaced with increasing amounts of N2 medium (25% increments every other day). SOX10::eGFP line: LSB (day 0-3/4) - CHIR (day 2-6.5). ASCL1::eGFP line: LSB (day 0-3/4) - CHIR (day 2-7) - SP (day 3-8). PHOX2B::eGFP line: LSB (day 0-3/4) - m3i (day 2-7) - SP (day 3-10). The eGFP positive samples were collected by cell sorting at the specific time points: OCT4+, day -2; SOX10+, day 6.5; ASCL1+, day 8; PHOX2B+, day 10. m3i, CHIR (CHIR99021), DAPT, and PD173074; SP, Shh plus PMP (purmorphamine).

tag: originating cell line

tag: differentiation stage

value: putative sympathetic neuronal precursors


title: Control CaSki cell Replicate 3

source_name: CaSki cell


title: 215-29787-V

value: 1,25 dihydroxyvitamin D3 + phytohemagglutinin


title: Liver_Control_rep1


title: 213-29786-V


title: PHOX2B+ #2


title: Control CaSki cell Replicate 2


title: Control CaSki cell Replicate 1


title: ASCL1+ #1

source_name: ASCL1-2A-eGFP+ sorted cells from ASCL1::eGFP reporter hESC line, LSB (day 0-3/4) - CHIR (day 2-7) - SP (day 3-8)

value: putative sympathoadrenal progenitors


title: ASCL1+ #2


title: 212-29786-E

source_name: PBMCs


title: OCT4+ #2

source_name: OCT4-2A-eGFP+ sorted cells from OCT4::eGFP reporter hESC line

value: undifferentiated hESCs


title: 210-29784-E


title: SOX10+ #3

source_name: SOX10-2A-eGFP+ sorted cells from SOX10::eGFP reporter hESC line, LSB (day 0-3/4) - CHIR (day 2-6.5)

value: multi-potent neural crest cells


title: OCT4+ #1


title: SOX10+ #2


title: IGFR_IR_100nM_IGF-1_Clone_2

city: Boston

first: Grace

last: Daher

address: 1 Joslin Place

institute: Joslin Diabetes Center

description:
IGFR_IR_stimulated_Clone_2
s22

hyb_protocol: 3.5ug of fragmented and labeled cDNA was used to make 150ul hyb cocktail, of which 130ul was injected into GeneChip Mouse Gene 2.0 ST arrays and hybridized for 16 hours at 45°C. Arrays were washed and stained using Affymetrix Fluidics Station 450 with reagents from Affymetrix.

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

data_processing: Data were analyzed using RMA, on Affymetrix Expression Console.

label_protocol: 5.5 ug of ss-cDNA was fragmented then labeled with biotin using the WT PLUS protocol from Affymetrix.

growth_protocol: The IR/IGFR double floxed mouse pups were used to collect brown preadipocytes, immortalized by SV40, and infected with adenoviral Cre to induce recombination and endogenous IR and IGF1R deletion (DKO). Normal receptors as well as chimeric receptors were then reconstituted into the DKO cells using retroviral expression system.

extract_protocol: Total RNA was extracted using an RNeasy mini kit (Qiagen) following manufacturer’s manual.

treatment_protocol: Cells were serum starved overnight with DMEM + 0.1% BSA. Cells were then treated with insulin or IGF-1 (100 nM) for 6 h and then washed once with cold 1 × PBS and resuspended in RLT lysis buffer (Qiagen).

value: brown preadipocytes

tag: genotype

value: IR and IGF1R DKO

tag: reconstituted with


title: 205-29779-E


title: 206-29779-V


title: SOX10+ #1


title: IGFR_IR_100nM_IGF-1_Clone_1

description:
IGFR_IR_stimulated_Clone_1
s20


title: Liver_60Fat_rep1

value: Sprague Dawley

value: male

tag: tissue


title: MNCL2.CEL,biological rep2

city: Nagpur

first: Dr. saravana

last: devi

state: Maharashtra

department: Environmental Health Division

institute: CSIR-National Environmental Engineering Research Institute

description: MNCL 2.rma-Signal

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

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

data_processing: The data were analyzed with Expression Console  using Affymetrix default analysis settings and RMA as normalization method used. The probes of   intensities less than the 20.0 percentile in the raw data were excluded.

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

growth_protocol: SHSY5Y cells grown in MEM:F12 (1:1) media cointaning 10 % Fetal bovin serum

extract_protocol: Total RNA prepared using Rneasy mini kit

treatment_protocol: Treated with  100 μM of manganese (1/5of LC50) for 24hrs.

value: Neuroblastoma cell line

tag: treated with


title: 208-29784-V

tag: ethnic group


title: IGFR_IR_nostimulated_Clone_1

description:
IGFR_IR_nostimulated_Clone_1
s19

tag: treatment

value: not stimulated


title: OCT4+ #3


title: IGFR_IR_nostimulated_Clone_3

description:
IGFR_IR_nostimulated_Clone_3
s23

tag: cell type


title: IGFR_IR_100nM_IGF-1_Clone_3

description:
IGFR_IR_stimulated_Clone_3
s24


title: IGFR_100nM_IGF-1_Clone_2

description:
IGFR_stimulated_Clone_2
s16

value: IGFR


title: ASCL1+ #3


title: Lung_C3H_P56_r3

city: Bar Harbor

first: Carol

last: Bult

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description:
Sample name: C3H_P56_559_m559_b4
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

hyb_protocol: As per standard Affymetrix protocol for the Mouse 1.0ST arrays.

scan_protocol: GeneChips were scanned by the GeneChip® Scanner 3000 7G (Affymetrix) using the AGCC Scan Control software program.

data_processing:
First data was processed using DeSNPer, a tool developed at the Center for Genome Dynamics (Jackson Laboratory) which removes probes with single nucleotide polymorphisms within the three strains of interest to reduce hybridization bias. Then a custom probe annotation pipeline was used to align probe sequences with the Ensembl Release 70 Mus musculus transcriptome. Next, data was log2-transformed, then probe-level hybridization intensities were quantile normalized and median polished to generate summarized expression values. Finally, transcriptome-alignment locations from the remaining probe sequences were converted to genomic locations for gene-level annotation.
RMA log2 expression values.
See supplementary files linked to the Series record.

source_name: Lung, C3H, P56

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol for the Mouse 1.0ST arrays from 250-300ng total RNA.

growth_protocol: Mice were fed regular lab chow diet ad libitum until time of tissue harvest.

extract_protocol: RNA was extracted using mirVana isolation kits (Ambion) following manufacturer's instructions. An additional DNAse I (Promega) step was added before organic extraction. RNA quality was assessed using RNA 6000 LabChip assays and 2100 Bioanalyzer (Agilent Technologies). OD 260/280 and OD 260/230 ratios were also measured using nanodrop spectrophotometer (Thermo Fisher Scientific).

treatment_protocol: Immediately following dissection, whole lung tissues (or whole embryos for time point e9.5) were placed in RNAlater and stored at -80C.

value: Lung

tag: stock

tag: age

tag: stage1 (canonical stages of lung development)

tag: stage2 (molecular divisions of lung development)


title: Lung_C3H_P56_r2

description:
Sample name: C3H_P56_268_m268_b2
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

tag: strain


title: Lung_C3H_P56_r1

description:
Sample name: C3H_P56_267_m267_b2
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: IGFR_IR_nostimulated_Clone_2

description:
IGFR_IR_nostimulated_Clone_2
s21


title: IGFR_nostimulated_Clone_3

description:
IGFR_nostimulated_Clone_3
s17


title: 201-29633-E


title: 196-29628-E


title: 203-29776-E


title: 199-29633-V


title: MNCL1.CEL,biological rep1

description: MNCL 1.rma-Signal

value: 100 μM of manganese (1/5of LC50) for 24hrs


title: IGFR_nostimulated_Clone_1

description:
IGFR_nostimulated_Clone_1
s13


title: 197-29628-V

value: PBMC


title: IGFR_nostimulated_Clone_2

description:
IGFR_nostimulated_Clone_2
s15


title: Lung_C3H_P30_r3

description:
Sample name: C3H_P30_523_m523_b4
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C3H, P30


title: 195-29623-V

value: African American


title: 192-29554-E

value: vehicle (EtOH) + phytohemagglutinin


title: MNCL3.CEL,biological rep3

description: MNCL 3.rma-Signal


title: 194-29623-E


title: Lung_C3H_P30_r1

description:
Sample name: C3H_P30_159_m159_b2
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: 204-29776-V


title: C2.CEL,biological rep2

value: none (untreated control)


title: C1.CEL,biological rep1


title: IR_IGFR_100nM_Insulin_Clone_3

description:
IR_IGFR_stimulated_Clone_3
s12

value: insulin


title: Lung_C3H_P30_r2

description:
Sample name: C3H_P30_160_m160_b2
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: IGFR_100nM_IGF-1_Clone_1

description:
IGFR_stimulated_Clone_1
s14


title: Lung_C3H_P24_r3

description:
Sample name: C3H_P24_504_m504_b2
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, C3H, P24


title: Lung_C3H_P24_r2

description:
Sample name: C3H_P24_503_m503_b2
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: C3.CEL,biological rep3


title: Lung_C3H_P24_r1

description:
Sample name: C3H_P24_502_m502_b2
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: IR_IGFR_nostimulated_Clone_2

description:
IR_IGFR_nostimulated_Clone_2
s9