title: SCE replicate 2 [DamID]

description: SCE DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing SCE-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pMycDam-SCE was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg SCE-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

value: SCE-Dam


title: PCL replicate 1 [DamID]

status: Public on Oct 01 2010

type: genomic

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description: PCL DamID untreated Kc167 cells

hyb_protocol: 13 µg labeled DNA per, 2.4 µl alignment oligo and 24 µl NimbleGen hybridiziation component A and 1x hybridization buffer in a total volume of 120 µl were heated to 98°C for 5 min and hybridized in a TECAN hybridization station for 16 hrs. at 42°C. Slides were washed sequentially with NimbleGen wash buffers I, II and III with 0.1 mM DTT at 42°C, 25°C, and 23°C, respectively.

scan_protocol: Microarrays were scanned in a DNA Microarray Scanner (Model G2505B, Serial number US22502518) from Agilent Technologies, which uses Scan Control software (Version A.6.11). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were scanned at multiple PMT (100/70/30/10%) for each channel at 5 um resolution using a suitable scan area.

data_processing: Scans were processed with NimbleScan 2.3 using standard settings. Values of all reporters except NimbleGen control reporters were extracted from pair files and represented as log2-ratios, normalized using the the loess() function in R with parameter control=loess.control(trace.hat='approximate') and then median centered. All four scan intensities were processed in that way, and the highest intensity not suffering from overt saturation in either replicate was retained and used for further analyses.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-PCL

label_protocol: 1 µg purified methyl-PCR or ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy dye-coupled nonamers (Trilink Biotech) according to NimbleGen Sample Labeling protocol in NimbleGen Array User's Guide, v4.1 (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pCreDamMyc-PCL was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

extract_protocol: For DamID samples, sample extraction was performed as described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003). All ChIP experiments and the subsequent linear amplification reactions were performed as described in Kind, J. et al., Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila. Cell 133, 813-828, 2008.

treatment_protocol: Cells transfected with 20 μg PCL-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

tag: cell line

tag: dam-fusion

value: Dam-PCL

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-only

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000)  was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: PC replicate 1 [DamID]

description: PC DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-PC

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pDamMyc-PC was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg PC-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

value: Dam-PC


title: RPD3 replicate 1 [DamID]

description: RPD3 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing RPD3-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pMycDam-RPD3 was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg RPD3-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 7


title: PHOL replicate 2 [DamID]

description: PHOL DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-PHOL

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pCreDamMyc-PHOL was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg PHOL-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

value: Dam-PHOL


title: PCAF replicate 1 [DamID]

description: PCAF DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-PCAF

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pGWDamMyc-PCAF was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg PCAF-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

value: Dam-PCAF


title: SIN3A replicate 2 [DamID]

description: SIN3A DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-SIN3A

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pDamMyc-SIN3A was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg SIN3A-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: PROD replicate 2 [DamID]

description: PROD DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-PROD

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pCreDamMyc-PROD was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg PROD-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 7

value: Dam-PROD


title: PHOL replicate 1 [DamID]

description: PHOL DamID untreated Kc167 cells


title: MUS209 replicate 2 [DamID]

description: MUS209 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-MUS209

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pCreDamMyc-MUS209 was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg MUS209-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: PC replicate 2 [DamID]

description: PC DamID untreated Kc167 cells


title: PROD replicate 1 [DamID]

description: PROD DamID untreated Kc167 cells

treatment_protocol: Cells transfected with 20 μg PROD-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 6


title: MUS209 replicate 1 [DamID]

description: MUS209 DamID untreated Kc167 cells


title: MED31 replicate 1 [DamID]

description: MED31 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-MED31

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pCreDamMyc-MED31 was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg MED31-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: MRG15 replicate 2 [DamID]

description: MRG15 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-MRG15

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pCreDamMyc-MRG15 was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg MRG15-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: MNT replicate 1 [DamID]

description: MNT DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing MNT-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pMycDam-MNT was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg MNT-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

value: MNT-Dam


title: MED31 replicate 2 [DamID]

description: MED31 DamID untreated Kc167 cells


title: MRG15 replicate 1 [DamID]

description: MRG15 DamID untreated Kc167 cells


title: JRA replicate 1 [DamID]

description: JRA DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-JRA

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pDamMyc-JRA was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg JRA-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

value: Dam-JRA


title: LHR replicate 1 [DamID]

description: LHR DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-LHR

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pDamMyc-LHR was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg LHR-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

value: Dam-LHR


title: LOLAL replicate 1 [DamID]

description: LOLAL DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-LOLAL

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pCreDamMyc-LOLAL was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg LOLAL-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

value: Dam-LOLAL


title: MAX replicate 2 [DamID]

description: MAX DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing MAX-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pMycDam-MAX was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg MAX-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

value: MAX-Dam


title: JRA replicate 2 [DamID]

description: JRA DamID untreated Kc167 cells


title: MNT replicate 2 [DamID]

description: MNT DamID untreated Kc167 cells


title: LHR replicate 2 [DamID]

description: LHR DamID untreated Kc167 cells


title: LOLAL replicate 2 [DamID]

description: LOLAL DamID untreated Kc167 cells


title: SCE replicate 1 [DamID]

description: SCE DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing SCE-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pMycDam-SCE was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg SCE-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: IAL replicate 1 [DamID]

description: IAL DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-IAL

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pCreDamMyc-IAL was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg IAL-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

value: Dam-IAL

treatment_protocol: Cells transfected with 20 μg Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: HP1c replicate 1 [DamID]

description: HP1c DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing HP1c-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pMycDam-HP1c was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg HP1c-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-only

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000)  was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).


title: HP1c replicate 2 [DamID]

description: HP1c DamID untreated Kc167 cells


title: HP1 replicate 1 [DamID]

description: HP1 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-HP1

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pDamMyc-HP1 was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg HP1-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: IAL replicate 2 [DamID]

description: IAL DamID untreated Kc167 cells


title: HP6 replicate 1 [DamID]

description: HP6 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-HP6

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pDamMyc-HP6 was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg HP6-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: HP6 replicate 2 [DamID]

description: HP6 DamID untreated Kc167 cells


title: HP1 replicate 2 [DamID]

description: HP1 DamID untreated Kc167 cells


title: Unsuccessful subject under HGI/HP diet at CID3 subject 6

type: RNA

city: Toulouse

first: Nathalie

last: Viguerie

address: Avenue Poulhes

country: France

institute: INSERM

description: Labeling and hybridization qualities were verified with Agilent’s spike in kit

hyb_protocol: 850 ng of Cy5 labelled probe was cohybridized the same amount of Cy3 labelled probe. We used the whole human genome oligo microarray from Agilent with the gene expression hybridization kit according to the manufacturer's protocol

scan_protocol: Micro-arrays were scanned on a InnoScan 700 scanner (Innopsys, Carbonne, France, EU) and data were extracted with Mapix software (Innopsys).

data_processing: Data analysis consited in Loess intra-slide normalization followed by quantiles iner-slide normalization by the use of R-bioconductorFeatures with a signal to background ratio strictly below 2 in both color as well as control spots were discarded. Value is the Log2 of normalized Red/Green value ratio.

molecule: total RNA

organism: Homo sapiens

source_name: Human subcutaneous adipose tissue, CID3

label_protocol: Total RNA quality was checked by capillary electrophoresis (Agilent 2100 bioanalyzer and RNA 6000 labChip Kit) and good quality RNA extracts only were used for microarray hybridization. Fluorescent probes were obtained by amplifying and labelling 300ng of RNA with the low RNA input linear amplification kit (Agilent).

extract_protocol: Total RNA was extracted with the RNeasy mini kit (Qiagen) according to manufacturer instructions

tag: gender

value: female

tag: tissue

value: Subcutaneous adipose tissue

tag: clinical intervention day

value: CID3, after dietary intervention

source_name: pool commercial human RNA

value: adipose tissue, liver, skeletal muscle


title: Unsuccessful subject under HGI/HP diet at CID3 subject 5


title: E(Z) replicate 1 [DamID]

description: E(Z) DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-E(Z)

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pCreDamMyc-E(Z) was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg E(Z)-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

value: Dam-E(Z)


title: Unsuccessful subject under HGI/HP diet at CID3 subject 4


title: ECR replicate 1 [DamID]

description: ECR DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-ECR

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pDamMyc-ECR was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg ECR-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

value: Dam-ECR


title: EFF replicate 2 [DamID]

description: EFF DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-EFF

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pCreDamMyc-EFF was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg EFF-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

value: Dam-EFF


title: Unsuccessful subject under HGI/HP diet at CID3 subject 3


title: DF31 replicate 1 [DamID]

description: DF31 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-DF31

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pCreDamMyc-DF31 was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg DF31-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: GRO replicate 1 [DamID]

description: GRO DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing GRO-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pMycDam-GRO was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg GRO-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

value: GRO-Dam


title: GRO replicate 2 [DamID]

description: GRO DamID untreated Kc167 cells


title: E(Z) replicate 2 [DamID]

description: E(Z) DamID untreated Kc167 cells


title: D1 replicate 1 [DamID]

description: D1 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-D1

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pGWDamMyc-D1 was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg D1-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: ECR replicate 2 [DamID]

description: ECR DamID untreated Kc167 cells


title: DSP1 replicate 1 [DamID]

description: DSP1 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-DSP1

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pGWDamMyc-DSP1 was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg DSP1-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: D1 replicate 2 [DamID]

description: D1 DamID untreated Kc167 cells


title: Unsuccessful subject under HGI/HP diet at CID3 subject 2


title: DF31 replicate 2 [DamID]

description: DF31 DamID untreated Kc167 cells


title: CG31367 replicate 1 [DamID]

description: CG31367 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-CG31367

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pCreDamMyc-CG31367 was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg CG31367-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: CG31367 replicate 2 [DamID]

description: CG31367 DamID untreated Kc167 cells


title: CTBP replicate 2 [DamID]

description: CTBP DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-CTBP

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pDamMyc-CTBP was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg CtBP-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

value: Dam-CTBP


title: Unsuccessful subject under HGI/HP diet at CID3 subject 1


title: DSP1 replicate 2 [DamID]

description: DSP1 DamID untreated Kc167 cells


title: CTBP replicate 1 [DamID]

description: CTBP DamID untreated Kc167 cells


title: CDK7 replicate 2 [DamID]

description: CDK7 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-CDK7

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pCreDamMyc-CDK7 was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg CDK7-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: EFF replicate 1 [DamID]

description: EFF DamID untreated Kc167 cells


title: Successful subject under HGI/HP diet at CID3 subject 6


title: Successful subject under HGI/HP diet at CID3 subject 5


title: Successful subject under HGI/HP diet at CID3 subject 3


title: CAF1 replicate 2 [DamID]

description: CAF1 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-CAF1

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pGWDamMyc-CAF1 was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg CAF1-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: MAX replicate 1 [DamID]

description: MAX DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing MAX-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pMycDam-MAX was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg MAX-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: CAF1 replicate 1 [DamID]

description: CAF1 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-only


title: Successful subject under HGI/HP diet at CID3 subject 4


title: GH treated for 30 min RKM 05

city: Ann Arbor

first: Ram

last: Menon

state: MI

address: 1500 East Medical Center Drive, D1205 MPB

department: Pediatric Endocrinology

country: USA

institute: University of Michigan

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Background correction, normalization, data analysis and statistical evaluations were performed using the limma and affy Bioconductor packages implemented in the R-statistical language (version 2.3.1, http://www.r-project.org/). RMA was used to normalize the data and fit log2 transformed expression values.

label: biotin

source_name: Human Podocytes (HPC)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Conditionally immortalized hunan podocyte cells (HPC) were cultured in RPMI-1640 under growth permissive conditions for 14 days at 37oC, before experimentation. Under these conditions HPC are completely differentiated.

extract_protocol: Total RNA was extracted from podocytes using Trizol Reagent (Invitrogen) followed by re-purification using a column (Qiagen, RNeasy MiniKit) according to the manufacturer's protocol. In-column DNase digestion was performed for each sample to remove genomic DNA. RNA samples were analyzed for concentration and purity using a Nanodrop ND-1000 spectrophotometer, and integrity was checked using the Agilent 2100 Bioanalyzer.

treatment_protocol: HPC were treated with human Growth hormone (500 ng/ml) for varying perioids of time ranging from 2 min to 30 min.

tag: cell type

value: Human Podocytes (HPC)

tag: treatment group

value: GH treated for 30 min


title: GH treated for 15 min RKM 09

value: GH treated for 15 min


title: CDK7 replicate 1 [DamID]

description: CDK7 DamID untreated Kc167 cells

treatment_protocol: Cells transfected with 20 μg Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: GH treated for 15 min RKM 04


title: GH treated for 5 min RKM 08

value: GH treated for 5 min


title: Successful subject under HGI/HP diet at CID3 subject 2


title: GH treated for 5min RKM 03


title: Successful subject under HGI/HP diet at CID3 subject 1


title: Unsuccessful subject under LGI/HP diet at CID3 subject 5


title: Unsuccessful subject under LGI/HP diet at CID3 subject 4


title: Unsuccessful subject under LGI/HP diet at CID3 subject 3


title: BRM replicate 1 [DamID]

description: BRM DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-BRM

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pDamMyc-BRM was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg BRM-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

value: Dam-BRM


title: GH treated for 2 min RKM 02

value: GH treated for 2 min


title: BCD replicate 1 [DamID]

description: BCD DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-BCD

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pDamMyc-BCD was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg BCD-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

value: Dam-BCD

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000)  was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).


title: BCD replicate 2 [DamID]

description: BCD DamID untreated Kc167 cells


title: BRM replicate 2 [DamID]

description: BRM DamID untreated Kc167 cells


title: ASH2 replicate 1 [DamID]

description: ASH2 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-ASH2

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pCreDamMyc-ASH2 was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg ASH2-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: GH treated for 2 min RKM 07


title: ASH2 replicate 2 [DamID]

description: ASH2 DamID untreated Kc167 cells


title: Unsuccessful subject under LGI/HP diet at CID3 subject 2

source_name: Human subcutaneous adipose tissue, CID3

source_name: pool commercial human RNA


title: Unsuccessful subject under LGI/HP diet at CID3 subject 1


title: Successful subject under LGI/HP diet at CID3 subject 3


title: Control 0 min RKM 01

value: Control 0 min


title: Control 0 min RKM 06


title: CLL cells  LN patient #24

city: Bethesda

first: Adrian

last: Wiestner

state: MD

address: 10 Center Dr

department: Hematology Branch

institute: NHLBI/NIH

description: primary CLL cells

hyb_protocol: Fragmented RNA was assessed for relative length on Agilent 2100 bioanalyzer and hybridized to Affymetrix HG-U133 Plus 2.0 chips for 16 hours.

scan_protocol: Affymetrix GeneChip scanner

data_processing: Intensities were pre-processed with MAS5.0, and further processed with variance stablization transformation

source_name: LN derived CLL cells

label_protocol: Biotin labeled with Affymetrix's IVT labeling kits (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was extracted using Qiagen RNA extraction kit

value: CLL

tag: origin

value: Lymph node

tag: patient

value: patient #24


title: ASF1 replicate 2 [DamID]

description: ASF1L3 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-ASF1L3

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pCreDamMyc-ASF1 was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg ASF1-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: CLL cells  LN patient #26

description: primary CLL cells

value: patient #26


title: CLL cells  LN patient #25

description: primary CLL cells

value: patient #25


title: Successful subject under LGI/HP diet at CID3 subject 4

value: female

value: Subcutaneous adipose tissue

value: CID3, after dietary intervention

value: adipose tissue, liver, skeletal muscle


title: RGC-3-OD

city: Boston

first: Danyi

last: Wang

state: MA

address: 243 Charles St

department: Ophthalmology

institute: Harvard Medical School

description: The NIH Neuroscience Microarray Consortium processed the GeneChip hybridization and scanning.

hyb_protocol: The arrays were hybridized for 16h at 45°C in a rotisserie oven. After hybridization, arrays were washed using the Affymetrix fluidics station and stained with streptavidin-phycoerythrin according to the Affymetrix technical manual.

scan_protocol: Washed arrays were scanned on a Affymetrix GeneChip Scanner 3000.

data_processing: Scanned output files were visually inspected for hybridization artifacts and then analyzed by using Affymetrix GeneChip Operation Software (GCOS). Data obtained were analyzed with DChip.

organism: Rattus norvegicus

source_name: Retinal Ganglion Cells of Normal and Experimental Glaucoma Model of Brown Norway rats

label_protocol: 10 µg of total RNA were used for cRNA labeling according to the recommended Affymetrix protocol.

extract_protocol: Isolated RGCs was processed for RNA extraction using the PicoPure RNA isolation kit (Arcturus, Mountain View, CA) according to the manufacturer’s protocol.    Isolated RNA was amplified using the linear amplification as provided in the RiboAmp HS RNA amplification kit (Arcturus, Mountain View, CA)

treatment_protocol: Retinal ganglion cells were bilaterally back-labeled by stereotaxic injection of Fluorogold into the superior colliculus. Sustained unilateral IOP elevation was produced by hypertonic saline episcleral vein injection in Brown Norway rats with the fellow eye serving as a control (n = 3). After IOP had been elevated for 10 days, the rats were killed by asphyxiation with carbon dioxide, the eyes were rapidly removed. The eyecups were collected and frozen in optimal cutting temperature compound and sectioned. Using laser capture microdissection, 2,000 retinal ganglion cells were captured from each eyes.

tag: Retinal Ganglion Cells isolated from adult male Brown Norway rats (300 to 450 g; Charles River, Boston, MA)


title: CLL cells  LN patient #14

description: primary CLL cells

value: patient #14


title: CLL cells  LN patient #13

description: primary CLL cells

value: patient #13


title: Successful subject under LGI/HP diet at CID3 subject 1


title: RGC-3-OS


title: RGC-1-OS


title: Embryonic Drosophila cells, Kc167 cells, Lamin DamID, replicate 2

description:
Lamin DamID untreated Kc167 cells.
Lamin_2

hyb_protocol: Hybridizations were done using standard protocols (see http://microarrays.nki.nl/download/protocols.html).

scan_protocol: Microarrays were scanned in an Agilent scanner.

data_processing: Values of all reporters except NimbleGen control reporters were extracted from pair files, represented as log2-ratios and normalized using the the loess() function in R with parameter control=loess.control(trace.hat='approximate'). Values from 2 replicates were median centered and averaged after which high density probes at chr2L were removed.

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Lamin

label_protocol: 1 µg DamID DNA was directly labeled by Klenow random priming with Cy5/Cy3 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html) at NimbleGen, Reykjavik.

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pNDamMyc-Lamin (Pickersgill H. et al., Characterization of the Drosophila melanogaster genome at the nuclear lamina. Nat Genet. 2006 Sep;38(9):1005-14) was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

extract_protocol: Sample extraction was performed as described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003).

treatment_protocol: Cells transfected with 20 μg Dam-Lamin expression plasmid/2*10e6 cells on day 1; harvested on day 2.

tag: developmental stage

value: embryo

tag: dam fusion

value: lamin

tag: treatment

value: untreated

treatment_protocol: Cells transfected with 20 μg Dam expression plasmid/2*10e6 cells on day 1; harvested on day 2.

value: Dam only


title: RGC-2-OS


title: GH treated for 30 min RKM 10

value: Human Podocytes (HPC)

value: GH treated for 30 min


title: Unsuccessful subject under HGI/LP diet at CID3 subject 6


title: RGC-1-OD

label: Biotin

label_protocol: 10 µg of total RNA was used for cRNA labeling according to the recommended Affymetrix protocol.

extract_protocol: Isolated RGCs were processed for RNA extraction using the PicoPure RNA isolation kit (Arcturus, Mountain View, CA) according to the manufacturer’s protocol.    Isolated RNA was amplified using the linear amplification as provided in the RiboAmp HS RNA amplification kit (Arcturus, Mountain View, CA)

tag: Retinal Ganglion Cells isolated from adult male Brown Norway rats (300 to 450 g; Charles River, Boston, MA).


title: CLL cells  LN patient #12

description: primary CLL cells

value: CLL

value: patient #12


title: Unsuccessful subject under HGI/LP diet at CID3 subject 2


title: Sample_357_current smoker with cancer

first: Avrum

last: Spira

address: 715 Albany Street, R304

department: Pulmonary and Critical Care Medicine

institute: Boston University Medical Center

description: RNA isolated from Bronchial Epithelial cells obtained during time of bronchoscopy

hyb_protocol: Affymetrix Suggested Protocol

scan_protocol: Affymetrix Suggested Protocol

data_processing: MAS5.0 Scaled 100 generated expression value

source_name: current smoker with cancer

label_protocol: Affymetrix Suggested Protocol

extract_protocol: RNA was extracted by using TRIzol Reagent (Invitrogen) according to the manufacturer's protocol

value: Bronchial Epithelium

tag: sex

value: Male

tag: race

value: CAU

tag: age

tag: pkyrs

tag: history

value: current smoker with cancer

tag: status

value: SC


title: RGC-2-OD


title: ACT5C replicate 1 [DamID]

description: ACT5C DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing ACT5C-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pGWMycDam-ACT5C was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg ACT5C-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

tag: cell line

tag: dam-fusion


title: Sample_367_former smoker without cancer

source_name: former smoker without cancer

tag: tissue

value: OTH

value: former smoker without cancer

value: SNC


title: Successful subject under LGI/HP diet at CID3 subject 2

tag: gender

value: female

value: Subcutaneous adipose tissue

tag: clinical intervention day

value: CID3, after dietary intervention

value: adipose tissue, liver, skeletal muscle


title: Successful subject under LGI/HP diet at CID3 subject 5


title: CLL cells  LN patient #9

description: primary CLL cells

tag: cell type

tag: origin

value: Lymph node

tag: patient

value: patient #9


title: ASF1 replicate 1 [DamID]

description: ASF1 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-ASF1


title: Unsuccessful subject under HGI/LP diet at CID3 subject 3


title: ACT5C replicate 2 [DamID]

description: ACT5C DamID untreated Kc167 cells


title: Unsuccessful subject under HGI/LP diet at CID3 subject 1


title: CLL cells  LN patient #11

description: primary CLL cells

value: patient #11


title: CLL cells  LN patient #10

description: primary CLL cells

value: CLL

value: patient #10


title: Embryonic Drosophila cells, Kc167 cells, Lamin DamID, replicate 1

description:
Lamin DamID untreated Kc167 cells.
Lamin_1

tag: developmental stage

value: embryo

tag: dam fusion

value: lamin

value: untreated

value: Dam only


title: Sample_352_current smoker with cancer

value: Bronchial Epithelium

value: Male

value: CAU

value: current smoker with cancer

value: SC


title: Unsuccessful subject under HGI/LP diet at CID3 subject 4

value: female

value: Subcutaneous adipose tissue


title: CLL cells  LN patient #8

description: primary CLL cells

value: patient #8


title: CLL cells  LN patient #7

description: primary CLL cells

value: Lymph node

value: patient #7


title: Sample_346_current smoker with cancer


title: Sample_338_never smoker

source_name: never smoker

value: Female

value: OTH

value: never smoker

value: NS


title: Successful subject under HGI/LP diet at CID3 subject 5

value: CID3, after dietary intervention

value: adipose tissue, liver, skeletal muscle


title: Sample_334_never smoker

value: HIS


title: Sample_336_current smoker without cancer

source_name: current smoker without cancer

value: Bronchial Epithelium

value: current smoker without cancer

value: SNC


title: CLL cells  LN patient #6

description: primary CLL cells

value: CLL

value: patient #6


title: Successful subject under HGI/LP diet at CID3 subject 2

value: female


title: CLL cells  LN patient #1

description: primary CLL cells

value: patient #1


title: Unsuccessful subject under LGI/LP diet at CID3 subject 3

value: Subcutaneous adipose tissue


title: Sample_333_current smoker without cancer

value: Male


title: CLL cells  LN patient #3

description: primary CLL cells

value: Lymph node

value: patient #3


title: Sample_330_current smoker without cancer

value: AFA


title: CLL cells  LN patient #5

description: primary CLL cells

value: patient #5


title: CLL cells  LN patient #4

description: primary CLL cells

value: patient #4


title: Sample_331_former smoker with cancer

source_name: former smoker with cancer

value: CAU

value: former smoker with cancer

value: SC


title: Unsuccessful subject under LGI/LP diet at CID3 subject 5

value: CID3, after dietary intervention

value: adipose tissue, liver, skeletal muscle


title: Successful subject under HGI/LP diet at CID3 subject 1


title: Unsuccessful subject under LGI/LP diet at CID3 subject 4


title: Sample_325_former smoker with cancer

value: Bronchial Epithelium


title: Unsuccessful subject under LGI/LP diet at CID3 subject 1


title: Unsuccessful subject under LGI/LP diet at CID3 subject 2


title: Successful subject under HGI/LP diet at CID3 subject 3


title: Sample_328_current smoker with cancer

value: current smoker with cancer


title: Unsuccessful subject under HGI/LP diet at CID3 subject 5


title: Sample_321_former smoker with cancer

value: Female


title: Successful subject under HGI/LP diet at CID3 subject 4

value: female


title: Successful subject under LGI/LP diet at CID3 subject 6


title: Sample_316_former smoker without cancer

value: former smoker without cancer

value: SNC


title: CLL cells  LN patient #2

description: primary CLL cells

value: CLL

value: patient #2


title: Successful subject under LGI/LP diet at CID3 subject 4

value: Subcutaneous adipose tissue


title: Successful subject under LGI/LP diet at CID3 subject 5


title: Sample_312_former smoker with cancer

value: Male


title: Sample_304_former smoker without cancer


title: Sample_238_current smoker without cancer

value: current smoker without cancer


title: Unsuccessful subject under HGI/HP diet at CID2 subject 6

source_name: Human subcutaneous adipose tissue, CID2

value: CID2, before dietary intervention


title: Successful subject under LGI/LP diet at CID3 subject 1


title: Sample_251_former smoker without cancer

value: CAU


title: Sample_243_former smoker with cancer

value: former smoker with cancer


title: Sample_287_current smoker without cancer

value: AFA


title: Successful subject under LGI/LP diet at CID3 subject 3

value: CID3, after dietary intervention


title: Sample_226_current smoker without cancer


title: Unsuccessful subject under HGI/HP diet at CID2 subject 3

value: adipose tissue, liver, skeletal muscle


title: Sample_283_current smoker without cancer

value: Bronchial Epithelium


title: Unsuccessful subject under HGI/HP diet at CID2 subject 2


title: Unsuccessful subject under HGI/HP diet at CID2 subject 4


title: Unsuccessful subject under HGI/HP diet at CID2 subject 5


title: Successful subject under HGI/HP diet at CID2 subject 6


title: Sample_225_current smoker without cancer


title: Unsuccessful subject under HGI/HP diet at CID2 subject 1


title: Sample_220_current smoker without cancer


title: Sample_190_current smoker with cancer

value: current smoker with cancer

value: SC


title: Sample_223_current smoker without cancer


title: Sample_197_current smoker with cancer


title: Sample_224_current smoker without cancer


title: Successful subject under HGI/HP diet at CID2 subject 4

value: female


title: Successful subject under HGI/HP diet at CID2 subject 5


title: Sample_185_former smoker without cancer

value: former smoker without cancer


title: Successful subject under HGI/HP diet at CID2 subject 2


title: Sample_184_former smoker with cancer

value: Female


title: Unsuccessful subject under LGI/HP diet at CID2 subject 3


title: Successful subject under HGI/HP diet at CID2 subject 1


title: Sample_160_current smoker with cancer


title: Sample_181_former smoker with cancer


title: Sample_183_current smoker with cancer


title: Successful subject under HGI/HP diet at CID2 subject 3


title: Unsuccessful subject under LGI/HP diet at CID2 subject 2


title: Sample_179_former smoker with cancer


title: Sample_182_current smoker with cancer


title: Sample_178_former smoker with cancer


title: Unsuccessful subject under LGI/HP diet at CID2 subject 4


title: Unsuccessful subject under LGI/HP diet at CID2 subject 5


title: Unsuccessful subject under LGI/HP diet at CID2 subject 1


title: Successful subject under LGI/HP diet at CID2 subject 4


title: Successful subject under LGI/HP diet at CID2 subject 2


title: Sample_159_former smoker with cancer


title: Successful subject under LGI/HP diet at CID2 subject 5


title: Sample_86_current smoker without cancer

value: SNC


title: Sample_85_current smoker without cancer


title: Sample_152_former smoker with cancer


title: Sample_356_former smoker with cancer


title: Successful subject under LGI/HP diet at CID2 subject 1


title: Successful subject under LGI/HP diet at CID2 subject 3


title: Sample_134_current smoker without cancer

value: ASI


title: Sample_66_current smoker without cancer


title: Sample_54_current smoker without cancer


title: Sample_53_current smoker without cancer


title: Unsuccessful subject under HGI/LP diet at CID2 subject 4

value: Subcutaneous adipose tissue


title: Sample_65_current smoker without cancer

value: Male


title: Sample_49_never smoker

value: never smoker

value: NS


title: Sample_15_former smoker without cancer

value: CAU


title: Sample_63_former smoker without cancer


title: Successful subject under HGI/LP diet at CID2 subject 4

value: CID2, before dietary intervention


title: Unsuccessful subject under HGI/LP diet at CID2 subject 6


title: Unsuccessful subject under HGI/LP diet at CID2 subject 2


title: Successful subject under HGI/LP diet at CID2 subject 5


title: Sample_41_former smoker without cancer

value: AFA


title: Unsuccessful subject under HGI/LP diet at CID2 subject 3


title: Unsuccessful subject under HGI/LP diet at CID2 subject 1


title: Successful subject under HGI/LP diet at CID2 subject 2


title: Unsuccessful subject under HGI/LP diet at CID2 subject 5


title: Successful subject under HGI/LP diet at CID2 subject 3


title: Unsuccessful subject under LGI/LP diet at CID2 subject 5


title: Successful subject under HGI/LP diet at CID2 subject 1


title: Unsuccessful subject under LGI/LP diet at CID2 subject 4


title: Unsuccessful subject under LGI/LP diet at CID2 subject 2


title: Unsuccessful subject under LGI/LP diet at CID2 subject 1


title: Successful subject under LGI/LP diet at CID2 subject 4


title: Successful subject under LGI/LP diet at CID2 subject 5


title: Successful subject under LGI/LP diet at CID2 subject 2


title: Unsuccessful subject under LGI/LP diet at CID2 subject 3


title: Successful subject under LGI/LP diet at CID2 subject 3


title: wild-type mouse + 3mg/kg PFOS, biological rep3

city: Research Triangle Park

first: Mitchell

middle: B

last: Rosen

state: NC

department: Reproductive Toxicology

institute: U.S. EPA

description:
WT_3mg/kg-3

Liver gene expression data from wild-type mice treated with 3mg/kg PFOS for 7 days.

hyb_protocol: Following fragmentation, samples were hybridized overnight at 45oC in an Affymetrix Model 640 GeneChip hybridization oven.

scan_protocol: Arrays were washed and stained using an Affymetrix 450 fluidics station, and scanned on an Affymetrix Model 3000 scanner.

data_processing: Microarray data were summarized, background adjusted, and quantile normalized using Robust Multichip Average methodology (RMA Express, ver. 1.0).  Prior to statistical analysis, microarray data were filtered to remove probe sets with weak or no signal.  Data were analyzed for each strain using a one-way ANOVA across dose (Proc GLM, SAS ver. 9.1, Cary, NC).   Individual treatment contrasts were evaluated using a pairwise t-test of the least square means.

organism: Mus musculus

source_name: Wild-type, liver, left lobe, 3mg/kg PFOS, 7 day exposure

label_protocol: Biotin-labeled cRNA was produced from 5 ug total RNA using Enzo Single-Round RNA Amplification and Biotin Labeling System (Cat. No. 42420-10, Enzo Life Sciences Inc, Farmingdale, NY).

growth_protocol: Animals were housed 5 per cage and allowed to acclimate for a period of one week prior to the conduct of the study.  Food and municipal tap water were provided ad libitum.  Animal facilities were controlled for temperature (20-24°C), relative humidity (40-60%), and kept under a 12 hr light-dark cycle.

extract_protocol: Collected tissue (≤ 50 mg) was immediately placed in 1 ml RNAlater and stored at -20◦C.  RNA preparations were then completed by homogenizing the tissue in 1 ml TRI reagent followed by processing according to the manufacturer’s instructions.

treatment_protocol: PPARα-null and wild-type male mice at 6-9 months of age were dosed by gavage for 7 consecutive days with either 0, 3, or 10 mg/kg  PFOS (potassium salt) in 0.5% Tween 20.

tag: strain

tag: genotype

value: wildtype

value: liver

value: male

value: 6-9 months

tag: treatment

value: perfluorooctane sulfonate (PFOS)

tag: treatment dosage

tag: treatment time

value: 7 days


title: Successful subject under LGI/LP diet at CID2 subject 6

value: female

value: adipose tissue, liver, skeletal muscle


title: wild-type mouse +10mg/kg PFOS, biological rep3

description:
WT_10mg/kg-3

Liver gene expression data from wild-type mice treated with 10mg/kg PFOS for 7 days.

source_name: Wild-type, liver, left lobe, 10mg/kg PFOS, 7 day exposure

tag: age


title: wild-type mouse + 10mg/kg PFOS, biological rep1

description:
WT_10mg/kg-1

Liver gene expression data from wild-type mice treated with 10mg/kg PFOS for 7 days.


title: wild-type mouse + 10mg/kg PFOS, biological rep2

description:
WT_10mg/kg-2

Liver gene expression data from wild-type mice treated with 10mg/kg PFOS for 7 days.


title: wild-type mouse + 3mg/kg PFOS, biological rep4

description:
WT_3mg/kg-4

Liver gene expression data from wild-type mice treated with 3mg/kg PFOS for 7 days.


title: Successful subject under LGI/LP diet at CID2 subject 1


title: wild-type mouse + 3mg/kg PFOS, biological rep2

description:
WT_3mg/kg-2

Liver gene expression data from wild-type mice treated with 3mg/kg PFOS for 7 days.


title: wild-type mouse + 3mg/kg PFOS, biological rep1

description:
WT_3mg/kg-1

Liver gene expression data from wild-type mice treated with 3mg/kg PFOS for 7 days.


title: wild-type mouse + 10mg/kg PFOS, biological rep4

description:
WT_10mg/kg-4

Liver gene expression data from wild-type mice treated with 10mg/kg PFOS for 7 days.


title: wild-type mouse + 3mg/kg PFOS, biological rep5

description:
WT_3mg/kg-5

Liver gene expression data from wild-type mice treated with 3mg/kg PFOS for 7 days.


title: wild-type mouse + 10mg/kg PFOS, biological rep5

description:
WT_10mg/kg-5

Liver gene expression data from wild-type mice treated with 10mg/kg PFOS for 7 days.


title: Successful subject under LGI/LP diet at CID3 subject 2

value: CID3, after dietary intervention


title: PPARalpha-null mouse +10mg/kg PFOS, biological rep4

description:
Null_10mg/kg-4

Liver gene expression data from PPARalpa-null mice treated with 10mg/kg PFOS for 7 days.

source_name: PPARalpha-null, liver, left lobe, 10mg/kg PFOS, 7 day exposure

value: PPARalpha-null


title: wild-type mouse + 0mg/kg PFOS, biological rep5

description:
WT_0mg/kg-5

Liver gene expression data from control wild-type mice.

source_name: Wild-type, liver, left lobe, 0mg/kg PFOS, 7 day exposure

value: untreated


title: wild-type mouse + 0mg/kg PFOS, biological rep2

description:
WT_0mg/kg-2

Liver gene expression data from control wild-type mice.


title: wild-type mouse + 0mg/kg PFOS, biological rep3

description:
WT_0mg/kg-3

Liver gene expression data from control wild-type mice.


title: PPARalpha-null mouse +10mg/kg PFOS, biological rep3

description:
Null_10mg/kg-3

Liver gene expression data from PPARalpa-null mice treated with 10mg/kg PFOS for 7 days.


title: wild-type mouse + 0mg/kg PFOS, biological rep1

description:
WT_0mg/kg-1

Liver gene expression data from control wild-type mice.


title: wild-type mouse + 0mg/kg PFOS, biological rep4

description:
WT_0mg/kg-4

Liver gene expression data from control wild-type mice.


title: PPARalpha-null mouse +10mg/kg PFOS, biological rep5

description:
Null_10mg/kg-5

Liver gene expression data from PPARalpa-null mice treated with 10mg/kg PFOS for 7 days.


title: PPARalpha-null mouse +10mg/kg PFOS, biological rep1

description:
Null_10mg/kg-1

Liver gene expression data from PPARalpa-null mice treated with 10mg/kg PFOS for 7 days.


title: PPARalpha-null mouse + 3mg/kg PFOS, biological rep5

description:
Null_3mg/kg-5

Liver gene expression data from PPARalpa-null mice treated with 3mg/kg PFOS for 7 days.

source_name: PPARalpha-null, liver, left lobe, 3mg/kg PFOS, 7 day exposure


title: PPARalpha-null mouse +10mg/kg PFOS, biological rep2

description:
Null_10mg/kg-2

Liver gene expression data from PPARalpa-null mice treated with 10mg/kg PFOS for 7 days.


title: PPARalpha-null mouse + 3mg/kg PFOS, biological rep4

description:
Null_3mg/kg-4

Liver gene expression data from PPARalpa-null mice treated with 3mg/kg PFOS for 7 days.


title: PPARalpha-null mouse + 3mg/kg PFOS, biological rep2

description:
Null_3mg/kg-2

Liver gene expression data from PPARalpa-null mice treated with 3mg/kg PFOS for 7 days.


title: PV16 MSC p4 +MLR 4d 10% HI-FBS

city: rotterdam

first: Mario

last: Pescatori

address: Westplein 11

institute: Health e-genomics

description: PV16 MSC p4 cultured with MLR in transwell culture system for 4days in MEMalpha medium+10% HI-FBS

hyb_protocol: Hybridization to Affymetrix Human Gene 1.0 ST Arrays, staining, washing, and scanning procedures were performed as described by Affymetrix (Affymetrix, Santa Clara, CA, USA)

scan_protocol: GeneChips were scanned using the Scanner 3000 (Affymetrix)

data_processing: To examine the quality of the arrays, measured intensity values were analyzed using Expression Console Software (Affymetrix, Santa Clara, CA). The controls all indicated a high quality of samples and an overall comparability. Probeset annotations were retrieved from Nettafx using Expression Console Software. Probesets differentially expressed among conditions were identified using the class comparison tool implemented in BRB ArrayTools (National Cancer Institute, USA). Principal component analysis was performed using Partek software (Partek Inc., St. Louis, USA). Hierarchical clustering was performed in Spotfire (Spotfire Inc., Somerville, USA)

source_name: Perirenal fat donor 16, passage4

label_protocol: Biotinylated DNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA

growth_protocol: MSC were cultured at 37 degrees Celsius, 5% CO2 and 95% humidity.

extract_protocol: total RNA was isolated using MINI columns (Qiagen, USA).

treatment_protocol: MSC were cultured under the various conditions (see above): control, MLR(transwell) and cytokines

tag: culture conditions

value: MLR 4d


title: PPARalpha-null mouse + 3mg/kg PFOS, biological rep1

description:
Null_3mg/kg-1

Liver gene expression data from PPARalpa-null mice treated with 3mg/kg PFOS for 7 days.


title: PV20 MSC p4 +MLR 4d 10% HI-FBS

description: PV20 MSC p4 cultured with MLR in transwell culture system for 4days in MEMalpha medium+10% HI-FBS

source_name: Perirenal fat donor 20, passage4


title: PV22 MSC p4 +MLR 7d 10% HI-FBS

description: PV22 MSC p4 cultured with MLR in transwell culture system for 7days in MEMalpha medium+10% HI-FBS

source_name: Perirenal fat donor 22, passage4

value: MLR 7d


title: PPARalpha-null mouse + 0mg/kg PFOS, biological rep3

description:
Null_0mg/kg-3

Liver gene expression data from control PPARalpa-null mice.

source_name: PPARalpha-null, liver, left lobe, 0mg/kg PFOS, 7 day exposure


title: PV21 MSC p4 +MLR 4d 10% HI-FBS

description: PV21 MSC p4 cultured with MLR in transwell culture system for 4days in MEMalpha medium+10% HI-FBS

source_name: Perirenal fat donor 21, passage4


title: PPARalpha-null mouse + 3mg/kg PFOS, biological rep3

description:
Null_3mg/kg-3

Liver gene expression data from PPARalpa-null mice treated with 3mg/kg PFOS for 7 days.


title: PPARalpha-null mouse + 0mg/kg PFOS, biological rep4

description:
Null_0mg/kg-4

Liver gene expression data from control PPARalpa-null mice.


title: PV16 MSC p4 +MLR 7d 10% HI-FBS

description: PV16 MSC p4 cultured with MLR in transwell culture system for 7days in MEMalpha medium+10% HI-FBS


title: PV20 MSC p4 +MLR 7d 10% HI-FBS

description: PV20 MSC p4 cultured with MLR in transwell culture system for 7days in MEMalpha medium+10% HI-FBS


title: PPARalpha-null mouse + 0mg/kg PFOS, biological rep2

description:
Null_0mg/kg-2

Liver gene expression data from control PPARalpa-null mice.


title: PPARalpha-null mouse + 0mg/kg PFOS, biological rep1

description:
Null_0mg/kg-1

Liver gene expression data from control PPARalpa-null mice.


title: PV22 MSC p4 10% FBS

description: PV22 MSC p4 in MEMalpha medium+10% FBS

value: Control(FBS)


title: PV22 MSC p4 +cytokines(IFNg/TNFa/IL6) 10%FBS

description: PV22 MSC p4 cultured for 7 days with cytokines(IFNg/TNFa/IL6) in MEMalpha medium+10%FBS

value: Cytokines


title: PV21 MSC p4 10% FBS

description: PV21 MSC p4 in MEMalpha medium+10% FBS


title: PV20 MSC p4 10% FBS

description: PV20 MSC p4 in MEMalpha medium+10% FBS


title: PV21 MSC p4 +MLR 7d 10% HI-FBS

description: PV21 MSC p4 cultured with MLR in transwell culture system for 7days in MEMalpha medium+10% HI-FBS


title: PV20 MSC p4 +cytokines(IFNg/TNFa/IL6) 10%FBS

description: PV20 MSC p4 cultured for 7 days with cytokines(IFNg/TNFa/IL6) in MEMalpha medium+10%FBS


title: PV21 MSC p4 +cytokines(IFNg/TNFa/IL6) 10%FBS

description: PV21 MSC p4 cultured for 7 days with cytokines(IFNg/TNFa/IL6) in MEMalpha medium+10%FBS


title: PV16 MSC p4 10%HI-FBS

description: PV16 MSC p4 cultured for 7 days in MEMalpha medium+10%HI-FBS

value: Control(HI-FBS)


title: PV20 MSC p4 10%HI-FBS

description: PV20 MSC p4 cultured for 7 days in MEMalpha medium+10%HI-FBS


title: PV16 MSC p4 +cytokines(IFNg/TNFa/IL6) 10%FBS

description: PV16 MSC p4 cultured for 7 days with cytokines(IFNg/TNFa/IL6) in MEMalpha medium+10%FBS


title: Young_8_Basal

city: Galveston

first: micah

last: Drummond

state: TX

address: 301 University Boulevard

institute: University of Texas Medical Branch

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate.  The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry.  The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing:
Background is determined using a regression-based background mapping method.  The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots.  Raw data matrix is then subtracted by the background matrix.
Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data.  The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) "A comparison of normalization methods for high density oligonucleotide array data based on variance and bias", Bioinformatics, 19 (2), 185-193].
A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5.  CV is calculated by (standard deviation)/(signal intensity).  When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.
t-Test is performed between “control” and “test” sample groups.   T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution.  miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis.  The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.
All data processes, except clustering plot, are carried out using in-house developed computer programs.  The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

label_protocol: Microarray assay was performed using a service provider (LC Sciences).  The assay started from 4 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in dual-sample experiments.

extract_protocol: Tri-Reagent

value: vastus lateralis basal skeletal muscle

value: 29 years


title: Young_9_Basal

value: 20 years


title: Young_7_Basal

value: male

value: 39 years


title: Young_12_Basal

value: 37 years


title: Young_6_Basal

value: 38 years


title: Young_11_Basal


title: PV21 MSC p4 10%HI-FBS

description: PV21 MSC p4  cultured for 7 days in MEMalpha medium+10%HI-FBS


title: Young_3_Basal

value: 24 years


title: Young_5_Basal

value: 30 years


title: Young_4_Basal

value: 28 years


title: Young_1_Basal


title: Young_2_Basal


title: Young_10_Basal


title: Old_12_Basal

value: 77 years


title: Old_9_Basal

value: 68 years


title: Old_10_Basal

value: 76 years


title: Old_11_Basal


title: Old_8_Basal

value: 72 years


title: PV16 MSC p4 10% FBS

description: PV16 MSC p4 in MEMalpha medium+10% FBS

value: Control(FBS)


title: Old_2_Basal

value: 70 years


title: Old_5_Basal

value: 74 years


title: Old_4_Basal

value: vastus lateralis basal skeletal muscle

value: 71 years


title: Old_3_Basal

value: 66 years


title: Control 38

city: Granada

first: Mª Esther

last: Farez-Vidal

address: Avda Dr. Oloriz s/n

country: Spain

institute: Hospital Universitario San Cecilio

hyb_protocol: Expression Analysis Technical Manual of Affymetrix.

data_processing: RMA.

source_name: Human Lung Control

extract_protocol: RNAeasy Mini Kit (Qiagen).

value: lung

tag: sample type

value: control


title: Old_1_Basal

value: male

value: 67 years


title: Old_7_Basal

value: 86 years


title: Old_6_Basal


title: EPA505_PHE/FLA_6h

city: AUBIERE

first: TERRAT

last: Sebastien

address: 24, avenue des Landais, Campus des Cézeaux

department: Génomique Intégrée des Interactions Microbiennes

institute: UMR CNRS 6023

description: Strain EPA505 with PHE/FLA as sole carbon and energy source. total RNA extracted after 6h of culture

hyb_protocol: For each hybridization experiment, 3.33µg of labeled RNA for kinetics experiments (one sample in Cy3 and another in Cy5) or 12µg of labeled DNA (in Alexa Fluor® 5) for soil were mixed, vacuum dried and resuspended in 5.6 µL of water. Then, the hybridization mix (Roche NimbleGen) was realized according to the manufacturer's protocols. The arrays were hybridized on a 4-bay NimbleGen Hybridization System (Roche NimbleGen) at 42°C for 72 hr. Arrays were washed with NimbleGen wash buffers I, II and III according to vendor protocols.

scan_protocol: Samples were scanned using a Scanner Innoscan 900AL (Innopsys, Carbonne, France) at 2 μm resolution. Individual array images were acquired independently, adjusting the PMT gain (30 for aRNA and 100 for total DNA) for each image as recommended using the software Mapix® (Innopsys). Then, for each array image, raw expression data had been extracted using the NimbleScan software v2.1. (Roche NimbleGen) and feature intensities were exported as .pair files.

data_processing: The background noise was then determined using random probes present on the microarrays (8,863 probes in our experiment) with the method described in the publication Sébastien Terrat, Eric Peyretaillade, Olivier Gonçalves, Eric Dugat-Bony, Fabrice Gravelat, and Pierre Peyret. 2010 - Studying the ‘Unkown’ with Metabolic Design, a new probe design software for explorative functional microarrays development. Nucleic Acids Research (submited). This background noise is defined by two components: the background median intensity (Bposition) and its dispersion (Bdispersion). Finally, a modified signal-to-noise ratio called SNR’ and based on the formula of Verdik (Verdick, D., Handran, S. and Pickett, S. (2002) In LLC, D. P. (ed.), In G. Kamberova (ed.), DNA array image analysis: nuts and bolts. Salem, MA., pp. p. 83-98) is calculated as follow in order to reduce-centralize our data: SNR’ = (probe signal intensity - Bposition)/ Bdispersion. However, spatial effect across array surface is a predominant within-slide experimental artifact that needs to be eliminated before any other normalization procedure (Wang, X., He, H., Li, L., Chen, R., Deng, X.W. and Li, S. (2006) NMPP: a user-customized NimbleGen microarray data processing pipeline. Bioinformatics, 22, 2955-2957). That is why, for all array images obtained in this work, surface was segmented to 16 sub-squares according to probe position (X, Y) indicated in pair report. A Perl script was developed to calculate local background noise in all sub-squares and the median SNR’ retrieved from the three replicates of each probe. Finally, another Perl script was implemented to summarize each replicate probe treated and determine the median value between the three replicates. Positive hybridization was considered significant for probes having an SNR’ > 3 (value to avoid all false positives).

molecule: polyA RNA

organism: Sphingomonas paucimobilis

label_protocol: 10 µg of purified aRNA for each sample was vacuum dried and labeled using the Amersham CyDyeTM Post-Labeling Reactive Dye Packs (GE Healthcare, Little Chalfont, United Kingdom) with Cyanine3 or Cyanine5 dyes as recommended by the supplier. Briefly, the aRNA pellet was resuspended in 20µL of 0.1M bicarbonate buffer (pH 8.7) and incubated for 90 min with 40 nM of dye compound (coupling the dye to amino-allyl-UTP) dissolved in 20 µL of DMSO in the dark at room temperature. Exceeding dye was quenched by addition of 15 μl of 4 M hydroxylamine solution incubated for 15 min in the dark at room temperature. Then, labeled aRNA was purified with NucleoSpin RNA Clean-Up kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s manual.  Total DNA was amplified and labeled using the BioPrime® Total Genomic Labeling System (Invitrogen) following the manufacturer’s instructions. The quantity and quality of labeling were estimated by using the Nanodrop spectrophotometer (Nanodrop) as recommended by protocols.

growth_protocol: Cells were first grown overnight at 37°C on a shaker table (150 rpm) in 70 mL of Luria-Bertani medium (LB) containing streptomycin (100 mg/L) to produce biomass. They were then centrifuged at room temperature for 2 min at 5,000 g and transferred to a sterile minimum mineral medium 457 containing for one liter of distilled water, 2,440 mg of Na2HPO4, 1,520 mg of KH2PO4, 500 mg of (NH4)2SO4, 200 mg of MgSO4.7H2O, 50 mg of CaCl2.2H2O, 200 mg of Tween 80 and 10 mL of SL-4 solution as described by DSMZ. Cultures were prepared as follows, 2 mL of the PAH stock solutions were evaporated in sterile 250-mL Erlenmeyer flasks. Then, 100 mL of sterile medium 457 were added and inoculated with 7.5 × 107 cells prepared as above. Such cultures were incubated at 28°C on a shaker table (150 rpm) for 27 h and bacterial growth was monitored spectrophotometrically at 620 nm. A culture was also grown with glucose (15 g/L) as sole carbon source and energy in order to define basal expression of genes implicated in PAH degradation.

extract_protocol: Total RNA from pure culture of strain EPA505 was extracted at different times of the PAH degradation kinetics with the RNeasy Mini kit (Qiagen GmbH), treated with 1.5 U of DNase I (Invitrogen) to eliminate DNA contamination. RNA sample concentration and purity was then estimated using the Nanodrop spectrophotometer (Nanodrop). 15 µL of strain EPA505 total RNA were enriched using the MICROBExpress™ Bacterial mRNA Enrichment Kit (Ambion) as recommended by the suppliers. Each enriched mRNA was then amplified using the MessageAmp™ II-Bacteria RNA Amplification Kit (Ambion) with a modified protocol for the in vitro transcription step. Briefly, the purified double-stranded template (~14 µL) was transcribed in vitro with 12 µL of ATP, CTP and GTP mix (25mM each) (Ambion), 3 µL of UTP (75mM) (Ambion), 3 µL of amino-allyl-UTP (50mM) (Ambion), 4 µL of 10X reaction buffer (Ambion) and 4 µL of T7 enzyme mix (Ambion) at 37°C during a 14 h incubation period. Finally, the aRNA was purified using the MessageAmp™ II-Bacteria RNA Amplification Kit (Ambion) as recommended by the manufacturer’s instructions. Total DNA was extracted from 5g of contaminated soil, named S3, following the protocol described by Zhou (Zhou, J., Bruns, M.A. and Tiedje, J.M. (1996) DNA recovery from soils of diverse composition. Applied and Environmental Microbiology, 62, 316-322.). Three extractions were realized and pooled to minimize potential biases. DNA quality was checked on a 0.8% agarose gel.

tag: carbon source

value: PHE/FLA


title: S3_TOTAL_DNA

description: Total DNA extracted from a contaminated soil with various PAHs before bioremediation treatments

organism: uncultured organism


title: EPA505_PHE/FLA_21h

description: Strain EPA505 with PHE/FLA as sole carbon and energy source. total RNA extracted after 21h of culture


title: EPA505_PHE/FLA_10h

description: Strain EPA505 with PHE/FLA as sole carbon and energy source. total RNA extracted after 10h of culture


title: EPA505_PHE/FLA_3h

description: Strain EPA505 with PHE/FLA as sole carbon and energy source. total RNA extracted after 3h of culture


title: EPA505_Phenanthrene_10h

description: Strain EPA505 with Phenanthrene as sole carbon and energy source. total RNA extracted after 10h of culture

value: Phenanthrene


title: EPA505_Phenanthrene_21h

description: Strain EPA505 with Phenanthrene as sole carbon and energy source. total RNA extracted after 21h of culture


title: Tumor 11

scan_protocol: Expression Analysis Technical Manual of Affymetrix.

source_name: Human Lung Tumor

tag: tissue

value: tumor


title: EPA505_Fluoranthene_3h

description: Strain EPA505 with Fluoranthene as sole carbon and energy source. total RNA extracted after 3h of culture

value: Fluoranthene


title: EPA505_Phenanthrene_6h

description: Strain EPA505 with Phenanthrene as sole carbon and energy source. total RNA extracted after 6h of culture


title: EPA505_Phenanthrene_3h

description: Strain EPA505 with Phenanthrene as sole carbon and energy source. total RNA extracted after 3h of culture


title: EPA505_Fluoranthene_21h

description: Strain EPA505 with Fluoranthene as sole carbon and energy source. total RNA extracted after 21h of culture


title: EPA505_Fluoranthene_10h

description: Strain EPA505 with Fluoranthene as sole carbon and energy source. total RNA extracted after 10h of culture


title: EPA505_Glucose_21h

description: Strain EPA505 with Glucose as sole carbon and energy source. total RNA extracted after 21h of culture

value: Glucose


title: EPA505_Glucose_6h

description: Strain EPA505 with Glucose as sole carbon and energy source. total RNA extracted after 6h of culture


title: EPA505_Fluoranthene_6h

description: Strain EPA505 with Fluoranthene as sole carbon and energy source. total RNA extracted after 6h of culture


title: EPA505_Glucose_10h

description: Strain EPA505 with Glucose as sole carbon and energy source. total RNA extracted after 10h of culture


title: EPA505_Glucose_3h

description: Strain EPA505 with Glucose as sole carbon and energy source. total RNA extracted after 3h of culture


title: liver_ethanol_rep1

city: Herston

first: Suyinn

last: Chong

state: Queensland

address: 300 Herston Rd

department: Division of Genetics and Population Health

country: Australia

institute: Queensland Institute of Medical Research

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The dataset was initially analyzed using Illumina's GenomeStudio software and then subjected to additional filtering. Briefly, data normalization and establishment of differential expression using GenomeStudio was performed according to the recommendations of the manufacturer. After normalization based on rank invariant genes, samples were grouped according to treatment into a cohort of offspring of mothers treated with ethanol (ethanol group) and a cohort of offspring of untreated control mothers (control group). Comparing the two groups a confidence value (p value) was then calculated for each probe using the Illumina Custom algorithm. Probes with an unadjusted p-value <0.01 were selected and the resulting datasets were then subjected to the following filtering process: 1) only probes with a ‘detection p-value’ <0.05 in at least one treatment group as determined by the GenomeStudio software and an average signal intensity of >100 in at least one treatment group were included and 2) probes with a change in intensity values above 1.5 fold and below 0.8 fold between the ethanol and control groups were selected.

source_name: liver, ethanol-exposed

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Applied Biosystems)

extract_protocol: RNA was extracted using the QIAGEN Rneasy-Plus kit in accordance with the prescribed protocol. All RNA samples were checked on Agilent’s Bioanalyzer (Agilent RNA 6000 Nano) and had RNA Integrity Numbers (RINs) of at least 9.

treatment_protocol: Maternal ad libitum ingestion of 10% (v/v) ethanol from fertilization to GD 8.5

tag: gender

value: postnatal day 28

value: liver


title: liver_ethanol_rep2

description: replicate 2


title: liver_control_rep3

description: replicate 3

source_name: liver, control


title: liver_ethanol_rep3

description: replicate 3


title: liver_control_rep2

description: replicate 2


title: liver_control_rep4

description: replicate 4


title: liver_control_rep1

description: replicate 1


title: kidney_ethanol_rep6

description: replicate 6

source_name: kidney, ethanol-exposed

label_protocol: Biotinylated cRNA was prepared using the TargetAmp Nano-g Biotin-aRNA Labeling kit for the Illumina system (EPICENTRE Biotechnologies)

extract_protocol: RNA was extracted using the QIAGEN Rneasy-Plus kit in accordance with the prescribed protocol. All RNA samples were checked on Agilent’s Bioanalyzer (Agilent RNA 6000 Nano) and had RNA Integrity Numbers (RINs) of 8-9.

value: kidney


title: Old_16_Basal

value: 65 years


title: Old_14_Basal

value: vastus lateralis basal skeletal muscle

value: 68 years


title: kidney_ethanol_rep4

description: replicate 4


title: kidney_ethanol_rep3

description: replicate 3


title: kidney_ethanol_rep5

description: replicate 5


title: kidney_control_rep6

description: replicate 6

source_name: kidney, control


title: Old_17_Basal


title: Old_15_Basal

value: 66 years


title: kidney_ethanol_rep2

description: replicate 2


title: Young_19_Basal

value: 21 years


title: Old_13_Basal


title: kidney_control_rep4

description: replicate 4


title: Young_18_Basal

value: 33 years


title: kidney_control_rep2

description: replicate 2

value: male


title: Young_13_Basal

value: 31 years


title: kidney_control_rep5

description: replicate 5


title: Young_15_Basal


title: Young_14_Basal

value: 29 years


title: kidney_control_rep1

description: replicate 1


title: Young_17_Basal

value: 40 years


title: PPARalpha-null mouse + 0mg/kg PFOS, biological rep5

description:
Null_0mg/kg-5

Liver gene expression data from control PPARalpa-null mice.

value: PPARalpha-null

value: 6-9 months

value: untreated

value: 7 days


title: kidney_control_rep3

description: replicate 3

value: postnatal day 28


title: kidney_ethanol_rep1

description: replicate 1


title: Kidney_WT_baseline_rep1

status: Public on Sep 30 2010

city: Durham

first: Natalia

middle: A

last: Makhanova

address: 106 Research Drive

department: Nephrology

institute: Duke University

description: wild type mice on NS diet

hyb_protocol: 20 micrograms of  biotin-labeled target complementary RNA (cRNA) were fragmented and hybridized for 16 hr at 45 C to each GeneChip Mouse Genome 430 2.0 Arrays  according to the manufacturer's instructions

scan_protocol: Gene Chips were scanned using GeneChip® Scanner 3000 7G (Affymetrix)

data_processing: The expression data were processed with robust multiarray analysis (RMA) algorithms with GeneSpring GX version 7.3.1 (Agilent Technologies, Santa Clara, CA) and per-gene normalization to the median was applied with using cross-error model to enhance the statistical power of  the analysis.

source_name: Kidney, wild type mice, control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA

extract_protocol: Total RNA from snap-frozen kidneys was extracted with RNeasy Mini Kit (Qiagen) according to manufacturer’s protocols

treatment_protocol: analysis of RNA from kidneys of wild-type (WT) and AT1A receptor-deficient mice (KOs) at baseline and after 2 days of angiotensin II  (ANG II) infusion (1 μg/kg/min)

value: wild type mice

value: NS diet


title: Kidney_WT_baseline_rep3

description: wild type mice on NS diet

value: kidney


title: Kidney_WT_ANG II_rep1

description: wild type with ANG II

source_name: Kidney, wild type mice, ANG II

value: ANG II +NS diet


title: Kidney_KO_baseline_rep2

description: AGTR1A -KO on NS diet

source_name: Kidney, AGTR1A-KO mice, control

value: AGTR1A-KO mice


title: Kidney_WT_baseline_rep2

description: wild type mice on NS diet


title: Kidney_KO_baseline_rep1

description: AGTR1A -KO on NS diet


title: Kidney_KO_ANG II_rep3

description: AGTR1A -KO mice with ANG II

source_name: Kidney, AGTR1A-KO mice, ANG II


title: Kidney_KO_baseline_rep3

description: AGTR1A -KO on NS diet


title: Kidney_WT_ANG II_rep3

description: wild type with ANG II


title: Kidney_KO_ANG II_rep2

description: AGTR1A -KO mice with ANG II


title: Kidney_KO_ANG II_rep1

description: AGTR1A -KO mice with ANG II


title: Kidney_WT_ANG II_rep2

description: wild type with ANG II


title: MTB_pafA_CDC1551_Samples 4

status: Public on Sep 29 2010

city: Rockville

first: PFGRC

last: JCVI

address: 9704 Medical Center Drive

department: PFGRC

institute: J. Craig Venter Institute

description: Channel 1 (cy3): M. tuberculosis pafA strain Cy3 cell culture growing in the suplemented with Cu. Channel 2 (cy5): M. tuberculosis CDC1551 strain Cy5 cell culture growing in the suplemented with Cu

hyb_protocol: Slide was hybridized for 12 hours at 42 in Water Bath with volume of 100 in solution of 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin, and blocked in 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate. After hybridization, the slide was washed with 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature, then dried in air. Aminosilane-coated slides were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42 C degree for 60 min.  The slides then were washed at room temperature with distilled water, dipped in isopropanol, and allowed to dry.  Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate.  Resuspended probes were heated to 95 C degree  prior to hybridization.  The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42 C degree.   Hybridized slides were washed sequentially in solutions of 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature, then dried in air.

scan_protocol: Hybridized slides were scanned with an Axon GenePix 4000 scanner

data_processing: Individual TIFF images from each channel were analyzed with TIGR Spotfinder (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html). Microarray data were normalized by LOWESS normalization and with in-slide replicate analysis using TM4 software MIDAS (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html)

organism: Mycobacterium tuberculosis

source_name: Mtb mpa mutant cells

label_protocol: DNA probes for microarray experiments were generated by adding 2 ug of total RNA in a mixture containing 6 ug of random hexamers (Invitrogen), 0.01 M dithiothreitol, an aminoallyl-deoxynucleoside triphosphate mixture containing 25 mM each dATP, dCTP, and dGTP, 15 mM dTTP, and 10 mM amino-allyl-dUTP (aa-dUTP) (Sigma), reaction buffer, and 400 units of SuperScript III reverse transcriptase (Invitrogen) at 42 C degree overnight. The RNA template then was hydrolyzed by adding NaOH and EDTA to a final concentration of 0.2 and 0.1 M, respectively, and incubating at 70 C degree for 15 min. Unincorporated aa-dUTP was removed with a Minelute column (Qiagen). The probe was eluted with a phosphate elution buffer (4 mM KPO4, pH 8.5, in ultrapure water), dried, and resuspended in 0.1 M sodium carbonate buffer (pH 9.0). To couple the amino-allyl cDNA with fluorescent labels, normal human serum-Cy3 or normal human serum-Cy5 (Amersham) was added at room temperature for 1h. Uncoupled label was removed using the Qiagen Minelute column (Valencia, CA).

growth_protocol: The wildtype cells were grown in 7H9 minimal media to stationary phase (OD580 = 4). The mutant cells were grown in 7H9 minimal media to stationary phase (OD580 = 4)

extract_protocol: RNA was extracted from Mtb as follows: an equal volume of 4 M guanidinium isothiocyanate (GTC), 0.5% sodium N-lauryl sarcosine, 25 mM trisodium citrate) was added to cultures to arrest transcription, and cells were collected by centrifugation at 2,885 x g. Bacterial were resuspended in 1 ml TRIzol reagent (Invitrogen) and bead beat with zirconia silica beads (BioSpec Products) in a BioSpec Mini Bead Beater two times for 30 s, with 1 min cooling on ice in between. Samples were either stored at -80 C degree or used immediately. Samples were centrifuged for 5 min at 16,100 5 g at 4 C degree to pellet cellular debris. 300 ml of chloroform was added to PhaseLock tubes (Heavy 2 ml, 5Prime) after which the TRIzol samples were added. Tubes were vigorously inverted for 15 s and allowed to rest at RT for 5 min. Tubes were centrifuged for 10 min at 10,500 g at 4 C degree. The aqueous phases were added to microfuge tubes containing 270 ml isopropanol and 270 ml high salt solution (0.8 M  trisodium citrate, 1.2 M NaCl) and vortexed for 5 s. After a 10 min incubation at RT, tubes were microcentrifuged at 16,100 g for 10 min at 4 C degree to pellet RNA. RNA pellets were washed with 1 ml of 75% ethanol and centrifuged at 7,500 g for 5 min at 4 C degree. Pellets were allowed to dry by air and resuspended in 50 µl of RNA storage buffer (Ambion). 2 µl were used for quantification and another 2 µl were added to 80% formamide/ 20% loading dye to check RNA integrity on an (1.6%) agarose gel. The purification process was repeated two times to obtain DNA-free RNA. RNA aliquots were stored at -80 C degree.

value: mpa

source_name: Mtb CDC1551 cells

growth_protocol: The wildtype cells were grown in 7H9 minimal media to  stationary phase (OD580 = 4); The mutant cells were grown in 7H9 minimal media to stationary phase (OD580 = 4)


title: MTB_pafA_CDC1551_Samples 2

description: Channel 1 (cy3): M. tuberculosis CDC1551 strain Cy3 cell culture growing in the suplemented with Cu. Channel 2 (cy5): M. tuberculosis pafA strain Cy5 cell culture growing in the suplemented with Cu

growth_protocol: The wildtype cells were grown in 7H9 minimal media to stationary phase (OD580 = 2). The mutant cells were grown in 7H9 minimal media to stationary phase (OD580 = 2)

source_name: Mtb pafA mutant cells

growth_protocol: The wildtype cells were grown in 7H9 minimal media to stationary phase (OD580 = 2), The mutant cells were grown in 7H9 minimal media to stationary phase (OD580 = 2)

value: pafA


title: MTB_pafA_CDC1551_Samples 3


title: MTB_mpa_CDC1551_Samples 2

description: Channel 1 (cy3): M. tuberculosis CDC1551 strain Cy3 cell culture growing in the suplemented with Cu. Channel 2 (cy5): M. tuberculosis mpa strain Cy5 cell culture growing in the suplemented with Cu

growth_protocol: The wildtype cells were grown in 7H9 minimal media to stationary phase (OD580 = 2)      The mutant cells were grown in 7H9 minimal media to stationary phase (OD580 = 2)


title: MTB_mpa_CDC1551_Samples 3

description: Channel 1 (cy3): M. tuberculosis mpa strain Cy3 cell culture growing in the suplemented with Cu. Channel 2 (cy5): M. tuberculosis CDC1551 strain Cy5 cell culture growing in the suplemented with Cu