title: Embryonic Drosophila cells, Kc167 cells, Lamin DamID after white knockdown, exp2

description:
Lamin DamID Kc167 cells after white RNAi.
Lamin_control_RNAi_exp2

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, white RNAi

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. On day 1, 3 and 5, cells were serum starved for 1h and treated with 15 μg/ml white dsRNA. On day 7, 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 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) and cells were again treated with dsRNA.

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 treated with 15 μg/ml white dsRNA on days 1, 3, 5 and 7 and transfected with 20 μg Dam-Lamin expression plasmid/2*10e6 cells on day 7; harvested on day 8.

tag: cell line

value: embryo

tag: dam fusion

value: lamin

value: white knockdown

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

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. On day 1, 3 and 5, cells were serum starved for 1h and treated with 15 μg/ml white dsRNA. On day 7, 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 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) and cells were again treated with dsRNA.

treatment_protocol: Cells treated with 15 μg/ml white dsRNA on days 1, 3, 5 and 7 and transfected with 20 μg Dam-only expression plasmid/2*10e6 cells on day 7; harvested on day 8.

value: Dam only


title: Ptf1a E10.5 HT dp rep2

status: Public on Jan 24 2011

type: RNA

city: Copenhagen N

first: Anne

last: Grapin-Botton

address: Blegdamsvej3 B

department: DanStem

country: Denmark

institute: University of Copenhagen

description: 3 dp pooled for RNA and 2X linear amplification

hyb_protocol: 12.5 ug of cRNA was fragmented, checked for size on a Bioanalyzer RNA Nanochip. For each sample 11ug were hybridized for 16 hours at 45°C on the Affymetrix Mouse 430_2 . GeneChips were washed and stained in the Afmetrix Fluidics Station.

scan_protocol: Affymetrix's GeneChip Scanner 3000 7G System

data_processing: Probe set summarization was done with GCOS ( GeneChip Operating Software) to enable CEL files to create CHP files. We also used RACE based on RMA to analyze our CEL files for normalization, quality control and expression levels for genes.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Ptf1a mutant mice MGI 1328312

label_protocol: Biotinylated cRNAs were prepared from the amplified cDNA using the IVT Affymetrix Kit and purified with Rneasy Mini Kit and quantified (Nanodrop) and the quality was checked on a Bioanalyer RNA Nanochip

growth_protocol: Adult Ptf1a heterozygote mice were timed mated and embyos were collected at E10.5;midday on the day of vaginal plug appearance was considered E0.5. DNA for genotyping was isolated from the unused embryonic tissue.

extract_protocol: 3 pools of 3 dosal E10.5 pancreatic buds (about 2000 to 3000 cells total) were pooled and total RNA was extracted with the Qiagen Rneasy Mini Kit and DNAsed on the column. After cDNA synthesis with a T7-oligo(dT) primer the material was twice amplified using the AmpTec,Express Art mRNA  Amplification Kit.

treatment_protocol: Dorsal pancreatic buds were dissected and the mesenchyme was removed by mechancal dissection. Individual buds were frozen in 5ul of RNA lysis buffer until the genotype was determined.

tag: strain

tag: age

tag: tissue

value: dorsal pancreas

tag: genotype/variation

value: heterozygote


title: Liver_HS/T+4.5R_rep1

city: Pittsburgh

first: Joyeeta

last: Dutta-Moscato

state: PA

address: 450 Technology Drive, Suite 300

department: Surgery

country: USA

institute: University of Pittsburgh

description: Gene expression data from liver

hyb_protocol: High quality cRNA with yield of more than 10 ug was fragmented and hybridized to arrays for 18 hours. After hybridization, arrays were washed at 46oC for a hour, then stained with CyTM5-Streptavidin conjugate for 30 minutes at room temperature, followed by several non-stringent washing steps to remove unbound conjugate.

scan_protocol: After the final rinse, arrays were spun dry and scanned using ScanArray 5000, using 5 um scan resolution and at preset Cy5 parameters which were 85% Laser power and 55% PMT.

data_processing: Scanned images were processed in batches using Affymetrix MAS 5.0 using default settings

label: biotin

source_name: Liver, 1.5 hour of hemorrhagic shock and severe trauma followed by 4.5 hour resuscitation

label_protocol: 1 ug of total RNA was used for reverse transcription to produce single stranded cDNA (oligo dT primers) followed by second strand synthesis to form double stranded cDNA.  Biotin-labeled cRNA target was produced by in vitro transcription using the cDNA template.

extract_protocol: RNA was isolated from whole liver using TRIzol reagent according to manufacturer's protocol

tag: gender

value: male

value: 8-12 weeks

value: liver


title: Embryonic Drosophila cells, Kc167 cells, Lamin DamID after SU(HW) knockdown_2, exp2

type: genomic

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description:
Lamin DamID Kc167 cells after SU(HW) RNAi.
Lamin_SU(HW)_RNAi_exp2_2

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Lamin, SU(HW) RNAi_2

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. On day 1, 3 and 5, cells were serum starved for 1h and treated with 15 μg/ml SU(HW) dsRNA. On day 7, 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 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) and cells were again treated with dsRNA.

treatment_protocol: Cells treated with 15 μg/ml su(Hw) dsRNA on days 1, 3, 5 and 7 and transfected with 20 μg Dam-Lamin expression plasmid/2*10e6 cells on day 7; harvested on day 8.

tag: developmental stage

tag: treatment

value: SU(HW) knockdown

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-only, SU(HW) RNAi_2

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. On day 1, 3 and 5, cells were serum starved for 1h and treated with 15 μg/ml SU(HW) dsRNA. On day 7, 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 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) and cells were again treated with dsRNA.

treatment_protocol: Cells treated with 15 μg/ml su(Hw) dsRNA on days 1, 3, 5 and 7 and transfected with 20 μg Dam-only expression plasmid/2*10e6 cells on day 7; harvested on day 8.


title: Embryonic Drosophila cells, Kc167 cells, Lamin DamID after control overexpression, exp2

description:
Lamin DamID Kc167 cells after control overexpression.
Lamin_control_oe_2

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

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) together with pAWiresR (this study)  were 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 10 μg Lamin-Dam expression plasmid and 10 ug control overexpression plasmid /2*10e6 cells on day 1; harvested on day 2.

value: control overexpression

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

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) together with pAWiresR (this study)  were 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 10 μg Dam-only expression plasmid and 10 ug control overexpression plasmid /2*10e6 cells on day 1; harvested on day 2.


title: Mo growth minimal medium w/o nitrogen rep1

city: Newark

first: Nicole

middle: M

last: Donofrio

state: DE

address: 531 S. College Ave

department: Plant and Soil Sciences

institute: University of Delaware

hyb_protocol: Dye swap hybridizations of the labeled cRNA samples were performed using 0.5 μg of each sample per hybridization, following Agilent protocol. Each treatment was hybridized with the control (C) sample for 17 h at 60 ºC in the dark. Washes were performed at 25 °C as follows: 10 min in wash #1 (6X SSC) two times; 5 min in wash #2 (0.1X SSC) two times. Slides were immediately dried using a nitrogen gun (Fisher, Pittsburgh, PA) and scanning was immediately followed.

scan_protocol: Scanned on an Agilent Technologies Scanner System (G2565AA) with SureScan technology. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Data pre-processed by the Agilent Feature Extraction Software (version 10.5.1.1) was loaded in R and processed with the Bioconductor package Limma. Microarray spots with background intensity > 100 were not used. Applied background correction with the method “subtract”. Normalization within slides and between channels using the method “loess”. Normalization between slides using the method “Aquantile.

organism: Pyricularia oryzae

source_name: mycelia grown in liquid complete medium 4 days

label_protocol: The isolated RNA was labeled with Cy3 and Cy5 fluorescent dyes using Low RNA Input Fluorescent Linear Amp Kit (Agilent Technologies, Wilmington, DE) following manufacturer’s instructions.

growth_protocol: M. oryzae was grown on oatmeal-agar medium (50 g/L oatmeal, 15 g/L agar) for 10 days, under continuous light at 25ºC. Fungal plugs (5mm) were transferred to flasks containing liquid complete medium (LCM; 10g/L sucrose, 6 g/L casamin acids, 6 g/L yeast extract, 0.1% (v/v) trace elements) and incubated in a shaker at 27ºC and 150 rpm on dark for 4 days. The mycelia were collected using Wattmann filter paper and washed with distilled autoclaved water. The collected mycelia was divided in parts and used as a control (C) and as the start material for all in vitro experiments (heat shock, oxidative, and nutritional limitation).

extract_protocol: Total RNA was extracted using Trizol (Sigma Chemical, St. Louis, MO) following manufacturer's instructions.

treatment_protocol: M. oryzae mycelia grown in liquid complete medium (LCM) on a dark shaker (150 rpm) for four days (set as the control); 72 hours post-incoulated rice (cv. Maratelli) leaves; 72 hours post-incoulated barley (cv. ) leaves; fungal mycelia in LCM on a dark shaker (150 rpm) at 42°C during 45 min; fungal mycelia in LCM plus methyl viologen (Paraquat, 5mM) on a dark shaker (150 rpm) at 27ºC for 24 h; mycelia grown in minimal media (MM; 6g/L NaNO3, 0.5g/L KCl, 0.5g/L MgSO4, 1.5g/L KH2PO4, 0.1% (v/v) trace elements, 10g/L D-glucose), in a dark shaker (150 rpm) for 16 h at 27ºC; fungal mycelia under nitrogen starvation in MM without the nitrogen source (NaNO3; MM-N); fungal mycelia under carbon starvation in MM without the carbon source (D-glucose; MM-C).

tag: sample type

value: mycelia

source_name: mycelia grown in minimal medium without the nitrogen source


title: Liver_HS/T+4.5R_rep2

description: Gene expression data from liver


title: Embryonic Drosophila cells, Kc167 cells, Lamin DamID after SU(HW) overexpression, exp2

description:
Lamin DamID Kc167 cells after SU(HW) overexpression.
Lamin_SU(HW)_oe_2

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Lamin, SU(HW) overexpression

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) together with pA-su(Hw)-iresR (this study)  were 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 10 μg Lamin-Dam expression plasmid and 10 ug SU(HW) overexpression plasmid /2*10e6 cells on day 1; harvested on day 2.

value: SU(HW) overexpression

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-only, SU(HW) overexpression

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) together with pA-su(Hw)-iresR (this study)  were 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 10 μg Dam-only expression plasmid and 10 ug SU(HW) overexpression plasmid /2*10e6 cells on day 1; harvested on day 2.


title: Embryonic Drosophila cells, Kc167 cells, Lamin DamID after white knockdown, exp1

description:
Lamin DamID Kc167 cells after white RNAi.
Lamin_control_RNAi_exp1


title: Control_Patient_6,7,8

city: Dresden

first: Susanne

last: Mende

address: Fetscherstrasse 74

department: Neurology

country: Germany

institute: University Clinic Dresden

description: Pool of whole blood samples from two healthy control individuals. Age- and sex-matched healthy control pool for MELAS patient 6,7,8

hyb_protocol: Following fragmentation, samples of each patients two age- and sex-specific controls were pooled in equal amounts (5 microgramm each). 10 microgramm of cRNA were hybridized to the Affymetrix HG-U133A chip according to the protocols provided by the manufacturer.

scan_protocol: GeneChips were scanned on an Affymetrix GeneChip Scanner 3000.

data_processing: Chip intensity data were retrieved in cel-files and further proceeded with RMA-Express (www.rmaexpress.bmbolstad.com). Results were exported in log2-scale. In order to reduce inter-experimental variation, all chips scanned on the same day were put into a group. The chips were fitted to a common reference profile by using the median polish procedure. For further analysis, the matched control-chips were subtracted from the individual patient-chips, resulting in age- and sex-corrected profiles.

organism: Homo sapiens

source_name: Human blood from healthy individuals

label_protocol: Biotinylated cRNA was prepared from 3 microgramm of globin-depleted RNA using the GeneChip Expression 3`-Amplification reagents (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was isolated with the PAXgene Blood RNA kit combined with the RNase-free DNase set (both from Qiagen, Hilden, Germany). RNA samples were concentrated with the RNeasy MinElute Cleanup Kit (Qiagen) prior to globin-mRNA depletion using the GLOBINClear Kit from Ambion (Austin, TX).

treatment_protocol: Whole blood samples (7.5ml) were directly collected into PAXgene Blood RNA Tubes of the PAXgene Blood RNA System (Qiagen, Hilden, Germany) to stabilize RNA for gene expression profiling. Blood samples were incubated at room temperature in their PAXgene Blood RNA tubes for at least 2h to ensure complete cell lysis.

value: whole blood


title: Mo growth minimal medium rep2

source_name: mycelia grown in minimal medium

value: mycelia grown in minimal medium

value: mycelia grown in liquid complete medium 4 days


title: Embryonic Drosophila cells, Kc167 cells, Lamin DamID after SU(HW) overexpression, exp1

description:
Lamin DamID Kc167 cells after SU(HW) overexpression.
Lamin_SU(HW)_oe_1


title: Embryonic Drosophila cells, Kc167 cells, Lamin DamID after control overexpression, exp1

description:
Lamin DamID Kc167 cells after control overexpression.
Lamin_control_oe_1


title: Embryonic Drosophila cells, Kc167 cells, Lamin DamID after SU(HW) knockdown_2, exp1

description:
Lamin DamID Kc167 cells after SU(HW) RNAi.
Lamin_SU(HW)_RNAi_exp1_2

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Lamin, SU(HW) RNAi_1

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-only, SU(HW) RNAi_1


title: Mo growth 5mM methyl viologen rep2

source_name: mycelia grown in oxidative burst condition


title: Embryonic Drosophila cells, Kc167 cells, Lamin DamID after SU(HW) knockdown_1, exp1

description:
Lamin DamID Kc167 cells after SU(HW) RNAi.
Lamin_SU(HW)_RNAi_exp1_1


title: Liver_HS/T_rep4

description: Gene expression data from liver

source_name: Liver, 1.5 hour of hemorrhagic shock and severe trauma


title: Embryonic Drosophila cells, Kc167 cells, BEAF32B DamID, replicate 2

description:
BEAF32 DamID untreated Kc167 cells.
BEAF32_2

source_name: Embryonic Drosophila cells, Kc167 cells, expressing BEAF32B-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. pGWC-Beaf32B-MycDam (van Steensel B. et al., Genome Res. [Epub ahead of print]) 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 BEAF32-Dam expression plasmid/2*10e6 cells on day 1; harvested on day 2.

value: untreated

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: Mo growth 42C for 45 minutes rep2

source_name: mycelia grown in heat shock condition

value: mycelia grown in heat shock condition


title: Control_Patient_5

description: Pool of whole blood samples from two healthy control individuals. Age- and sex-matched healthy control pool for MELAS patient 5


title: Liver_HS/T+1.0R_rep2

description: Gene expression data from liver

source_name: Liver, 1.5 hour of hemorrhagic shock and severe trauma followed by 1 hour resuscitation


title: Liver_HS/T+1.0R_rep3

description: Gene expression data from liver


title: Control_Patient_2,3,4

description: Pool of whole blood samples from two healthy control individuals. Age- and sex-matched healthy control pool for MELAS patient 2,3,4


title: Mo growth minimal medium rep1


title: Embryonic Drosophila cells, Kc167 cells, BEAF32B DamID, replicate 1

description:
BEAF32 DamID untreated Kc167 cells.
BEAF32_1

value: embryo


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

description:
DWG DamID untreated Kc167 cells.
DWG_2

source_name: Embryonic Drosophila cells, Kc167 cells, expressing DWG-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. pGWC-Dwg-MycDam (this study) 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 DWG-Dam expression plasmid/2*10e6 cells on day 1; harvested on day 2.

value: DWG


title: Mo growth 5mM methyl viologen rep1

value: mycelia grown in oxidative burst condition


title: Control_Patient_9

description: Pool of whole blood samples from two healthy control individuals. Age- and sex-matched healthy control pool for MELAS patient 9


title: Liver_HS/T_rep3

description: Gene expression data from liver


title: Liver_HS/T+1.0R_rep1

description: Gene expression data from liver


title: Control_Patient_1

description: Pool of whole blood samples from two healthy control individuals. Age- and sex-matched control pool for MELAS patient 1


title: Embryonic Drosophila cells, Kc167 cells, Lamin DamID after SU(HW) knockdown_1, exp2

description:
Lamin DamID Kc167 cells after SU(HW) RNAi.
Lamin_SU(HW)_RNAi_exp2_1

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Lamin, SU(HW) RNAi_2

value: lamin

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-only, SU(HW) RNAi_2

value: Dam only


title: Liver_HS/T_rep2

description: Gene expression data from liver

value: male


title: BMSC-gold - repeat 1 - mAdbID:105994

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: mAdb experiment ID: 105994

hyb_protocol: Hybridization Protocol Other: Hybridization: Combine Cy3 and Cy5 labeled target (adjust the color to purple) and complete dry the sample by speed vacuum . Add 37ul of the following mixture to the dried target (for 20x40mm slide): 1ul 50x Denhardt’s blocking solution (Sigma Cat# 2532) 1ul poly dA (8mg/ml Pharmacia Cat# 27-7988-01) 1ul yeast tRNA (4mg/ml Sigma Cat# R8759) 10ul Human Cot I DNA (1mg/ml Gibco BRL Cat# 15279-011) 3ul 20X SSC 1ul 10% SDS 20ul of DEPC H2O Heat for 2 min at 99oC and Cool to RT. Apply target mixture to array slide, add coverslip, place in humidified hyb chamber, and hybridize at 65oC over night.

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 10 LaserPower: 3.16;; 4.92 Temperature: 34.05

data_processing:
BRB ArrayTool Data Processing
Calculation Method: Analyzed using BRBArrayTools developed by the Biometric Research Branch, National Cancer Institute (http://linus.nci.nih.gov/BRB-ArrayTools.html ). Briefly, the raw data set was filtered according to standard procedure to exclude spots with minimum intensity that arbitrarily was set to an intensity parameter of 200 for in both fluorescence channels. If the fluorescence intensity of one channel was great than 200 and that of the other but was below 200, the fluorescence of the low intensity channel was arbitrarily set to 200. Spots with diameters < 20ìm and flagged spots were also excluded from the analyses. Then, the filtered data were normalized using Lowess Smoother for gene expression microarray.

source_name: Pooled Normal Donor PBMC

label_protocol:
Cy3 Labeling Protocol
Other: Labeled using ULS aRNA Fluorescent Labeling kit (Kreatech).

extract_protocol:
Trizol Extraction Protocol
Other: Cells were lysed with TRIzol reagent (Invitrogen, Carlsbad, CA) and total RNA was isolated according to the manufacturers instructions. RNA integrity was assessed by the presence of 28S and 18S bands using Agilent bioanalyzer and quantified using nanodrop with A260/A280 ratios > 2.0 after dilution in DEPC water.

value: blood

tag: cell type

value: Peripheral Blood Mononuclear Cell (PBMC)

source_name: BMSC-gold

label_protocol:
Cy5 Labeling Protocol
Other: Labeled using ULS aRNA Fluorescent Labeling kit (Kreatech).

growth_protocol:
BMSC culture protocol
Media: alpha-MEM + 20% FBS + 10ug/ml Gentamicin

treatment_protocol:
Treatment type: compound
Agent: Gold Nanoparticle
In-vitro treatment: BMSCs were labeled in serum-free RPMI medium containing 2.25 x 107 gold nanoparticles/mL (British Biocell International, Wales, U.K, particle size-250nm) and 10ng/mL protamine sulfate at 37C. After 4 hours, an equal volume of complete medium was added, and the cells were incubated overnight. The next day, the cells were washed three times with heparinized HBSS (10U/mL) and returned to the incubator in normal medium.

value: Bone marrow

value: bone marrow stromal cell line

value: bone marrow stromal cell


title: Mo growth 42C for 45 minutes rep1

source_name: mycelia grown in liquid complete medium 4 days

value: mycelia


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

description:
DWG DamID untreated Kc167 cells.
DWG_1


title: Liver_HS/T_rep1

description: Gene expression data from liver

value: 8-12 weeks

value: liver


title: Melas_patient_10

description: Whole blood sample from A3243G positive MELAS patient.

hyb_protocol: Following fragmentation, 10 microgramm of cRNA were hybridized to the Affymetrix HG-U133A chip according to the protocols provided by the manufacturer.

data_processing: Chip intensity data were retrieved in cel-files and further proceeded with RMA-Express (www.rmaexpress.bmbolstad.com). Results were exported in log2-scale. In order to reduce inter-experimental variation, all chips scanned on the same day were put into a group. The chips were fitted to a common reference profile by using the median polish procedure.

source_name: Human blood from Melas patient

value: whole blood

tag: patient identifier

tag: sex

tag: age at blood withdrawal

tag: mtdna

value: positive for A3243G Melas mutation

tag: a3243g level of heteroplasmy


title: Melas_patient_7

value: female


title: Mo 72 hours after inoculation in rice rep4

source_name: infected rice leaves after 72 hpi

value: infected rice leaves after 72 hpi

value: infected rice leaves

value: mycelia grown in liquid complete medium 4 days


title: BMSC-control - repeat 2 - mAdbID:105993

description: mAdb experiment ID: 105993

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 10 LaserPower: 3.13;; 4.72 Temperature: 29.9

source_name: BMSC-control


title: Mo 72 hours after inoculation in barley rep1

source_name: infected barley leaves after 72 hpi

value: infected barley leaves after 72 hpi

value: infected barley leaves


title: Melas_patient_6


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

description:
GAF DamID untreated Kc167 cells.
GAF_1

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

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-Gaf (Moorman C. et al., Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):12027-32.) 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-GAF expression plasmid/2*10e6 cells on day 1; harvested on day 2.

value: embryo

value: GAF

value: untreated

value: Dam only


title: Melas_patient_8


title: Mo 72 hours after inoculation in rice rep3


title: Liver_MT_rep3

description: Gene expression data from liver

source_name: Liver, minor trauma

value: male


title: BMSC-FePro - repeat 1 - mAdbID:105995

description: mAdb experiment ID: 105995

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 10 LaserPower: 3.16;; 5.07 Temperature: 32.61

value: blood

value: Peripheral Blood Mononuclear Cell (PBMC)

source_name: BMSC-FePro

treatment_protocol:
Treatment type: compound
Agent: FePro
Treatment dose: 50:3 ug/ml
Treatment time: overnight
Treatment temperature: 37
In-vitro treatment: Culture media was aspirated from the flasks containing BMSCs and replaced with media containing FePro complexes. After 2 hours of incubation at 37C, an equal amount of complete medium was added for a final concentration of Fe to Pro, 50 ug/ml to 3 ug/mL, respectively. Cells were incubated overnight (~16 hours), and washed three times with sterile PBS containing 10 U/mL heparin sulfate. Complete medium was added to each flask and labeled cells were kept in culture for 2 days to ensure all FePro complexes were endocytosed.
Other: Two FDA-approved agents, ferumoxides (Fe), a suspension of superparamagnetic iron oxide nanoparticles (SPION), and protamine sulfate (Pro), a drug used to reverse heparin anticoagulation, have been combined to produce the FePro complex.

value: Bone marrow

value: BMSC cell line

value: Bone marrow stromal cell (BMSC)


title: Mo 72 hours after inoculation in rice rep2

value: mycelia


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

description:
CTCF DamID untreated Kc167 cells.
CTCF_2

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

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. pGWNDamMyc-CTCF (this study) 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-CTCF expression plasmid/2*10e6 cells on day 1; harvested on day 2.

value: CTCF


title: Mo 72 hours after inoculation in barley rep2


title: Melas_patient_9

value: whole blood

value: female

value: positive for A3243G Melas mutation


title: Liver_MT_rep1

description: Gene expression data from liver

value: 8-12 weeks

value: liver


title: BMSC-FePro - repeat 3 - mAdbID:105992

description: mAdb experiment ID: 105992

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 10 LaserPower: 3.15;; 5.06 Temperature: 32.71


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

description:
GAF DamID untreated Kc167 cells.
GAF_2

value: embryo

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


title: BMSC-control - repeat 1 - mAdbID:105991

description: mAdb experiment ID: 105991

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 10 LaserPower: 3.15;; 5.08 Temperature: 32.37

value: bone marrow stromal cell line

value: bone marrow stromal cell


title: Melas_patient_5


title: Liver_MT_rep2

description: Gene expression data from liver


title: Mo 72 hours after inoculation in rice rep1

value: mycelia grown in liquid complete medium 4 days

value: infected rice leaves after 72 hpi

value: infected rice leaves


title: Liver_C_rep5

description: Gene expression data from liver

source_name: Liver, control

value: male


title: Melas_patient_4


title: BMSC-gold - repeat 3 - mAdbID:105990

description: mAdb experiment ID: 105990

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 10 LaserPower: 3.15;; 5.03 Temperature: 33.13

value: blood

value: Peripheral Blood Mononuclear Cell (PBMC)

value: Bone marrow


title: EtOH control PAO1 (Sample 2)

city: Gainesville

first: Jason

middle: Christopher

last: Kwan

state: FL

address: 2000 SW Archer Road

department: Medicinal Chemistry

institute: University of Florida

description: Overnight cultures of P. aeruginosa PAO1 were diluted 100-fold then incubated at 37 °C with shaking for 2 h in LB, then diluted 100-fold again and incubated for a further 2 h.  Cultures were diluted 10-fold and 10 μL EtOH was added (total culture volume 1 mL).  The culture was incubated for 6 h at 37 °C with shaking before RNA was stabilized and extracted.

hyb_protocol: Samples were hybridized with rotation at 50 °C for 16 h to the Affymetrix GeneChip® P. aeruginosa Genome Arrays.  The arrays were washed and stained with the reagents supplied in GeneChip® Hybridization Wash and Stain Kit (Affymetrix, Inc.) on an Affymetrix Fluidics Statino 450.

scan_protocol: Chips were scanned with a GeneChip® 7G Scanner (Affymetrix, Inc.).

data_processing: Statistical tests were performed using Bioconductor statistical software (http://www.bioconductor.org) and R program (R: A language and environment for statistical computing).  Raw data were normalized by Robust Multichip Analysis (RMA) approach.  Then the probe set’s detection call was estimated using the Wilcoxon signed rank-based algorithm.  Probe sets that were absent in all the study samples were removed from further analysis.  A linear modeling approach and the empirical Bayes statistics as implemented in the limma package in the R software were employed for differential expression analysis.  The p-values obtained were controlled for multiple testing (FDR, false discovery rate) using Benjamini-Hochberg method.

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa treated with EtOH, 6h

label_protocol: Reverse transcription and terminal labeling of cDNA was carried out according to Affymetrix's protocol.

extract_protocol: RNA was stabilized in vivo by use of RNAprotect bacteria reagent (Qiagen) according to the manufacturer’s instructions.  RNA was extracted using the RNeasy Kit (Qiagen) according to the manufacturer’s instructions.RNA samples were quantified by UV absorbance (Nanodrop 8000, Thermo), and DNA contamination was quantified by RT-PCR of the samples using a primer/probe set for rpsL (PA4268). To reduce DNA contamination, Turbo DNA-free (1907, Ambion) was used according to the manufacturer’s “stringent” treatment protocol.  RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).


title: Embryonic Drosophila cells, Kc167 cells, SU(HW) DamID, replicate 2

description:
SU(HW) DamID untreated Kc167 cells.
SU(HW)_2

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-SU(HW)

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. pGWNDamMyc-su(Hw) (van Steensel B. et al., Genome Res. [Epub ahead of print] ) 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-SU(HW) expression plasmid/2*10e6 cells on day 1; harvested on day 2.

value: SU(HW)

value: untreated

value: Dam only


title: Lyngbyoic acid treated PAO1 (Sample 2)

description: Overnight cultures of P. aeruginosa PAO1 were diluted 100-fold then incubated at 37 °C with shaking for 2 h in LB, then diluted 100-fold again and incubated for a further 2 h.  Cultures were diluted 10-fold and lyngbyoic acid was added (total culture volume 1 mL, final lyngbyoic acid concentration 1 mM, added as 100 mM stock in 10 μL EtOH).  The culture was incubated for 6 h at 37 °C with shaking before RNA was stabilized and extracted.

source_name: Pseudomonas aeruginosa treated with Lyngbyoic Acid 1 mM, 6h


title: Embryonic Drosophila cells, Kc167 cells, SU(HW) DamID, replicate 1

description:
SU(HW) DamID untreated Kc167 cells.
SU(HW)_1


title: Liver_C_rep4

description: Gene expression data from liver


title: BMSC-control - repeat 3 - mAdbID:105989

description: mAdb experiment ID: 105989

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 10 LaserPower: 3.16;; 5.05 Temperature: 32.92


title: Melas_patient_3

value: whole blood


title: EtOH Control PAO1 (Sample 1)


title: Liver_C_rep3

description: Gene expression data from liver


title: BMSC-FePro - repeat 2 - mAdbID:105987

description: mAdb experiment ID: 105987

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 10 LaserPower: 3.09;; 4.69 Temperature: 27.49

value: BMSC cell line

value: Bone marrow stromal cell (BMSC)


title: Lyngbyoic acid treated PAO1 (Sample 1)

scan_protocol: Chips were scanned with a GeneChip® 7G Scanner (Affymetrix, Inc.)


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

description:
CTCF DamID untreated Kc167 cells.
CTCF_1

value: CTCF


title: Liver_C_rep2

description: Gene expression data from liver

value: 8-12 weeks

value: liver


title: Melas_patient_2

value: positive for A3243G Melas mutation


title: Melas_patient_1

value: 22 years


title: Liver_C_rep1

description: Gene expression data from liver


title: HFD_C57BL/6J_E28

status: Public on Jan 23 2011

city: Chapel Hill

first: Ivan

last: Rusyn

state: NC

address: 0031 Michael Hooker Research Center

department: Gillings School of Global Public Health

institute: University of North Carolina

description:
Batch2
E28

hyb_protocol: Labeled samples and reference were hybridized to the microarray at 65 degrees for 17 hours and washed with washing solutions.

scan_protocol: Arrays were scanned with Agilent Microarray Scanner (Agilent), and the obtained images were analyzed with Agilent Feature Extraction software (v8.5, Agilent Technologies).

data_processing: Normalization and filtering were performed with UNC Microarray Database (https://genome.unc.edu/). Inter-batch normalization was carried out using the ComBat procedure.

source_name: liver sample from C57BL/6J, HFD

label_protocol: 2.0 ug of total RNA from each sample, or 2.5 ug from mouse reference RNA (Icoria, Inc., RTP, NC), was labeled with fluorescent dye (Cy5 and Cy3, respectively).

extract_protocol: Total RNA was isolated using an RNeasy plus mini kit (Qiagen, Valencia, CA).

treatment_protocol: A high-fat diet or EtOH-containing high-fat diet was administered via gastric tube for 28 days.

value: WSB/EiJ

tag: diet

value: high fat diet

source_name: mouse liver RNA (reference)


title: BMSC-gold - repeat 2 - mAdbID:105986

description: mAdb experiment ID: 105986

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 10 LaserPower: 3.09;; 4.48 Temperature: 28.34

source_name: Pooled Normal Donor PBMC

source_name: BMSC-gold

tag: cell line

value: bone marrow stromal cell line

value: bone marrow stromal cell


title: HFD_C57BL/6J_E29

description:
Batch3
E29


title: EtOH_C57BL/6J_E22

description:
Batch5
E22

source_name: liver sample from C57BL/6J, EtOH

value: ethanol-containing high fat diet


title: EtOH_C57BL/10J_379

description:
Batch5
379

source_name: liver sample from C57BL/10J, EtOH

value: PWD/PhJ


title: HFD_C57BL/6J_E27

description:
Batch1
E27


title: EtOH_C57BL/6J_E30

description:
Batch1
E30


title: HFD_KK/HlJ_381

description:
Batch3
381

source_name: liver sample from KK/HlJ, HFD


title: HFD_C57BL/10J_377

description:
Batch1
377

source_name: liver sample from C57BL/10J, HFD

value: NZW/LacJ


title: HFD_WSB/EiJ_401

description:
Batch5
401

source_name: liver sample from WSB/EiJ, HFD


title: HFD_PWD/PhJ_398

description:
Batch5
398

source_name: liver sample from PWD/PhJ, HFD


title: HFD_KK/HlJ_385

description:
Batch4
385


title: EtOH_C57BL/10J_371

description:
Batch4
371


title: HFD_PWD/PhJ_393

description:
Batch4
393


title: HFD_C57BL/10J_378

description:
Batch2
378


title: HFD_MOLF/EiJ_360

description:
Batch3
360

source_name: liver sample from MOLF/EiJ, HFD


title: HFD_PWD/PhJ_399

description:
Batch1
399


title: HFD_C57BL/10J_364

description:
Batch5
364


title: EtOH_PWD/PhJ_336

description:
Batch4
336

source_name: liver sample from PWD/PhJ, EtOH

value: MOLF/EiJ


title: EtOH_C57BL/10J_370

description:
Batch3
370


title: EtOH_PWD/PhJ_327

description:
Batch2
327


title: HFD_MOLF/EiJ_357

description:
Batch2
357


title: EtOH_PWD/PhJ_335

description:
Batch3
335


title: HFD_MOLF/EiJ_356

description:
Batch1
356


title: HFD_WSB/EiJ_315

description:
Batch3
315

value: KK/HlJ


title: HFD_WSB/EiJ_318

description:
Batch4
318


title: EtOH_WSB/EiJ_309

description:
Batch2
309

source_name: liver sample from WSB/EiJ, EtOH


title: EtOH_WSB/EiJ_308

description:
Batch1
308


title: EtOH_MOLF/EiJ_288

description:
Batch5
288

source_name: liver sample from MOLF/EiJ, EtOH

value: FVB/NJ


title: EtOH_MOLF/EiJ_286

description:
Batch4
286


title: EtOH_KK/HlJ_304

description:
Batch2
304

source_name: liver sample from KK/HlJ, EtOH


title: EtOH_KK/HlJ_296

description:
Batch5
296


title: HFD_129S1SvImJ_281

description:
Batch4
281

source_name: liver sample from 129S1SvImJ, HFD


title: HFD_129S1SvImJ_280

description:
Batch3
280


title: HFD_129S1SvImJ_278

description:
Batch2
278


title: EtOH_MOLF/EiJ_292

description:
Batch1
292


title: HFD_BTBR T+tf/J_267

description:
Batch1
267

source_name: liver sample from BTBR T+tf/J, HFD


title: HFD_BALB/cByJ_276

description:
Batch5
276

source_name: liver sample from BALB/cByJ, HFD


title: EtOH_NZW/LacJ_223

description:
Batch4
223

source_name: liver sample from NZW/LacJ, EtOH

source_name: mouse liver RNA (reference)


title: EtOH_NZW/LacJ_231

description:
Batch5
231


title: EtOH_BTBR T+tf/J_200

description:
Batch4
200

source_name: liver sample from BTBR T+tf/J, EtOH


title: EtOH_BALB/cByJ_181

description:
Batch3
181

source_name: liver sample from BALB/cByJ, EtOH


title: HFD_NZW/LacJ_228

description:
Batch1
228

source_name: liver sample from NZW/LacJ, HFD


title: EtOH_BALB/cByJ_174

description:
Batch2
174


title: HFD_NZW/LacJ_229

description:
Batch2
229


title: HFD_BALB/cByJ_272

description:
Batch4
272


title: EtOH_BALB/cByJ_171

description:
Batch1
171


title: HFD_BTBR T+tf/J_266

description:
Batch5
266


title: EtOH_129S1SvImJ_160

description:
Batch2
160

source_name: liver sample from 129S1SvImJ, EtOH


title: EtOH_BTBR T+tf/J_189

description:
Batch2
189


title: EtOH_BTBR T+tf/J_196

description:
Batch3
196


title: HFD_BALB/cByJ_179

description:
Batch3
179


title: HFD_BTBR T+tf/J_265

description:
Batch4
265


title: HFD_FVB/NJ_151

description:
Batch3
151

source_name: liver sample from FVB/NJ, HFD


title: EtOH_129S1SvImJ_159

description:
Batch1
159


title: EtOH_129S1SvImJ_156

description:
Batch5
156


title: HFD_FVB/NJ_150

description:
Batch2
150

value: BTBR T+tf/J


title: HFD_FVB/NJ_149

description:
Batch1
149


title: HFD_NZW/LacJ_227

description:
Batch5
227


title: EtOH_NZW/LacJ_217

description:
Batch3
217


title: EtOH_FVB/NJ_146

description:
Batch1
146

source_name: liver sample from FVB/NJ, EtOH


title: HFD_AKR/J_65

description:
Batch5
65

source_name: liver sample from AKR/J, HFD

value: BALB/cByJ


title: EtOH_AKR/J_49

description:
Batch2
49

source_name: liver sample from AKR/J, EtOH

value: AKR/J


title: EtOH_BALB/cJ_85

description:
Batch4
85

source_name: liver sample from BALB/cJ, EtOH

value: BALB/cJ


title: HFD_AKR/J_63

description:
Batch3
63

value: liver


title: HFD_AKR/J_64

description:
Batch4
64


title: EtOH_FVB/NJ_141

description:
Batch4
141


title: EtOH_DBA/2J_134

description:
Batch5
134

source_name: liver sample from DBA/2J, EtOH


title: EtOH_FVB/NJ_142

description:
Batch5
142


title: EtOH_DBA/2J_126

description:
Batch4
126


title: HFD_DBA/2J_124

description:
Batch1
124

source_name: liver sample from DBA/2J, HFD


title: EtOH_DBA/2J_121

description:
Batch3
121


title: HFD_DBA/2J_132

description:
Batch2
132


title: EtOH_C3H/HeJ_40

description:
Batch2
40

source_name: liver sample from C3H/HeJ, EtOH


title: EtOH_AKR/J_50

description:
Batch3
50


title: EtOH_BALB/cJ_84

description:
Batch3
84


title: HFD_BALB/cJ_76

description:
Batch1
76

source_name: liver sample from BALB/cJ, HFD


title: HFD_DBA/2J_123

description:
Batch5
123


title: EtOH_BALB/cJ_79

description:
Batch2
79


title: HFD_BALB/cJ_75

description:
Batch5
75


title: EtOH_AKR/J_43

description:
Batch1
43


title: EtOH_C57BL/6J_19

description:
Batch4
19

source_name: liver sample from C57BL/6J, EtOH


title: HFD_BALB/cJ_27

description:
Batch4
27


title: HFD_C3H/HeJ_7

description:
Batch3
7

source_name: liver sample from C3H/HeJ, HFD


title: HFD_C3H/HeJ_38

description:
Batch4
38


title: EtOH_C3H/HeJ_32

description:
Batch5
32


title: EtOH_C3H/HeJ_36

description:
Batch1
36


title: MINR GMP

status: Public on Jan 22 2011

city: Groningen

first: JJ

last: Schuringa

address: Hanzeplein 1

department: Experimental Hematology

institute: UMCG

description: MINR GMP

hyb_protocol: Standard Illumina scanning protocol

scan_protocol: Illumina i-Scan reader

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

source_name: cord blood

label_protocol: Standard Illumina hybridization protocol

growth_protocol: Cord blood (CB) CD34+ cells were isolated by Miltenyi miniMACS column. Cells were prestimulated in HPGM with 100 ng/ml KITL, FLT#L and TPO for 48 hrs. Cells were transduced with control MiNR1 or STAT5A-ER in three rounds over 48 hrs. Hematopoietic stem cells (HSCs), common myeloid progenitors (CMPs), granulocyte/macrophage progenitors (GMPs), and megakaryocyte/erythroid progenitors (MEPs) were sorted (for details see Blood 2011, Fatrai et al). cells were stimulated with 100 ng/ml 4OHT for 24 hrs after which RNA was isolated for Illumina beadhchiop arrays HT12 v3

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

treatment_protocol: Transduced cells were treated with 100 ng/ml 4OHT for 24 hrs

value: cord blood

value: granulocyte/macrophage progenitors


title: HFD_C3H/HeJ_6

description:
Batch2
6

source_name: mouse liver RNA (reference)


title: STAT5-ER CMP

description: STAT5-ER CMP

value: common myeloid progenitors


title: STAT5-ER MEP

description: STAT5-ER MEP

value: megakaryocyte/erythroid progenitors


title: MINR1 MEP

description: MINR1 MEP


title: p190B transgenic biological replicate 4 (TV01M010)

city: South Bend

first: Tracy

last: Vargo-Gogola

state: IN

address: 1234 Notre Dame Avenue

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on GeneChip RG-U34A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

source_name: p190B expressing mammary epithelial cells, Doxycycline treated 7 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 5 week old female mice were treated for 7 days with doxycycline containing chow (2 g/kg)

extract_protocol: Trizol extraction of total RNA followed by purification using a RNeasy column according to manufacturer's instructions.

treatment_protocol: mammary epithelial cells were isolated as previously described (McHenry PR et al., 2010, Breast Cancer Research)

value: FVB/N

value: female


title: MINR1 CMP

description: MINR1 CMP


title: p190B transgenic biological replicate 1 (TV01M007)


title: p190B transgenic biological replicate 5 (TV01M011)


title: STAT5-ER GMP

description: STAT5-ER GMP


title: p190B transgenic biological replicate 3 (TV01M009)


title: MMTV-rtTA biological replicate 6 (TV01M006)

source_name: Control mammary epithelial cells, Doxycycline treated 7 days

value: MMTV-rtTA


title: MMTV-rtTA biological replicate 1 (TV01M001)


title: MINR1 HSC

description: MINR1 HSC

value: Hematopoietic stem cells


title: p190B transgenic biological replicate 6 (TV01M012)


title: RT4E05

city: Clamart

first: Nathalie

last: Lédée

address: 157 rue de la porte de trivaux

department: Hopital Antoine Béclère, Pavillon Jean Dalsace

country: France

institute: INSERM UMRS-783, université Paris XI

description: rsa 4

hyb_protocol: double-stranded cDNA was synthesized from 4 µg of total RNA primed with a poly-(dT)-T7 oligonucteotide. The cDNA was used in an in vitro transcription reaction (IVT) in the presence of T7 RNA polymerase and biotyin-labeled modified nucleotides during 16 hours at 37°C. Biotinylated cRNA was purified and then fragmented (35-200 nucleotides) together with hybridization controls and hybridized to the microarrays for 16 hours at 45°C. Using Fluidics Station (Affymetrix), the hybridized biotin-labeled cRNA was revealed by successive reactions with streptavidin R-phycoerythrin conjugate, biotinylated anti-strepatvidine antibody and streptavidine R-phycoerythrin conjugate.

scan_protocol: The arrays were finally scanned with an affymetrix/Hewlett-Packard GeneChip Scanner 3000 7G.

data_processing: Data were read and pre-processed using the R sofware (http://www.R-project.org/) and especially using packages from the Bioconductor project (http://www.bioconductor.org). CEL data files were read using the affy package. Data were normalized by condition using the GC-RMA method implemented in the gcrma package. This method performs a Background Adjustment Using Sequence Information before normalized the data using the rma method (which is a quantile normalisation followed by a summarization of probes by median polish). Differential analysis was performed with the anapuce package of R2 [ http://www.agroparistech.fr/mia/doku.php?id=productions:logiciels]. A double-sided, unpaired t-test was computed for each gene between the two conditions. Variance of the difference in gene expression was split between subgroups of genes with homogeneous variance [7]. The raw P values were adjusted by the Bonferroni method, which controls the Family Wise Error Rate (FWER). A gene is declared differentially expressed if the Bonferroni-corrected P-Value is less than 0.01.

source_name: recurrent spontaneous abortion

label_protocol: Four micrograms of total RNA were labeled using the GeneChip® Expression 3’ Amplification One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA).The cRNA was hybridized to Genechip Human Genome U133 Plus 2.0 Array (Affymetrix)

extract_protocol: Total RNA was isolated with the Qiagen RNeasy mini kit (Qiagen, Courtabeuf, France)  including the RNase-Free DNAse set.Genomic DNA contamination was eliminated with RNAse inhibitor.RNA quantity and quality were confirmed by the analysis with an Experion system and RNA StdSens analysis kit (Bio-Rad)

value: endometrium


title: RT5E36

description: rsa 5


title: MMTV-rtTA biological replicate 4 (TV01M004)


title: STAT5-ER HSC

description: STAT5-ER HSC


title: RT6E07

description: rsa 3


title: p190B transgenic biological replicate 2 (TV01M008)


title: MMTV-rtTA biological replicate 3 (TV01M003)


title: MMTV-rtTA biological replicate 2 (TV01M002)


title: RT5E03

description: rsa 2


title: MMTV-rtTA biological replicate 5 (TV01M005)


title: HFD_KK/HlJ_306

description:
Batch2
306

source_name: liver sample from KK/HlJ, HFD

value: high fat diet


title: EtOH_KK/HlJ_302

description:
Batch1
302

source_name: liver sample from KK/HlJ, EtOH

value: ethanol-containing high fat diet


title: RT5E47

description: echec 5

source_name: implantation failure


title: EtOH_WSB/EiJ_314

description:
Batch3
314

source_name: liver sample from WSB/EiJ, EtOH

value: KK/HlJ


title: RT3E35

description: Fertiles 5

source_name: fertile


title: RT4E11

description: rsa 1


title: Control Replicate 3

city: San Francisco

first: Andrew

last: Jheon

state: CA

address: 513 Parnassus Ave HSE1501

institute: UCSF

description: Biological replicate 3 of 3. Gene expression in wild-type teeth at P0.

hyb_protocol: Equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays (Agilent). Hybridizations were performed for 14 hrs, according to the manufacturers protocol (Agilent).

scan_protocol: Arrays were scanned using the Agilent microarray scanner (Agilent).

data_processing: Raw signal intensities were extracted with Feature Extraction v10.3 software (Agilent). Agilent Feature Extraction Software (v10.3) was used for background subtraction and LOWESS normalization.

source_name: WT P0 lower 1st molar

label_protocol: RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol (Agilent).

extract_protocol: Tooth germs of the 1st lower molars were isolated. Total RNA extraction performed using Rneasy (Qiagen).

value: Male

value: wild-type


title: RT5E35

description: echec 4


title: RT2E10

description: echec 1


title: RT4E10

description: echec 3


title: KO HSC_secondary recipient_replicate2

city: Drexel Hill

first: Qi

last: Yang

address: 82 Ferne Blvd, Apt6

institute: University of Pennsylvania

hyb_protocol: The labeled cDNAs were hybridized overnight at 65°C to an Agilent Whole Murine Genome Oligo Microarrays 4 x 44K.

scan_protocol: Fluorescence signals were scanned by Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing: The data were processed by the Agilent Feature Extraction Software (FES)

source_name: donor derived knockout murine HSC in secondary recipient mice

label_protocol: The cDNAs were labelled with Cy3 by Miltenyi Biotec.

extract_protocol: RNA were extracted and amplified by Miltenyi Biotec using  a global PCR protocol with mRNA-derived cDNA. The amplified mRNA was isolated by magnetic bead.

treatment_protocol: Donor derived wild-type or E47 Knockout murine HSC in primary or secondary recipient mice were sorted by flow cytometry cell sorting. The cells were lysed using SuperAmp™ Lysis Buffer and stored appropriately by the customer according to the instructions of the SuperAmp Preparation Kit. The samples sent on dry ice to Miltenyi Biotec.

value: haematopoietic stem cell (HSC)

value: E47 knock out

tag: derivation

value: secondary recipient mouse


title: WT HSC_secondary recipient_replicate2

source_name: donor derived wild-type murine HSC in secondary recipient mice

value: wild type


title: Perp-null Replicate 3

description: Biological replicate 3 of 3. Gene expression in Perp-null teeth at P0.

source_name: Perp-null P0 lower 1st molar

tag: strain

value: Perp-null


title: WT HSC_primary recipient_replicate2

source_name: donor derived wild-type murine HSC in primary recipient mice

value: primary recipient mouse


title: WT HSC_secondary recipient_replicate1


title: KO HSC_secondary recipient_replicate1


title: KO HSC_primary recipient_replicate2

source_name: donor derived knockout murine HSC in primary recipient mice


title: RT4E01

description: echec 2


title: RT5E01

description: Fertiles 2


title: Perp-null Replicate 1

description: Biological replicate 1 of 3. Gene expression in Perp-null teeth at P0.


title: Control Replicate 2

description: Biological replicate 2 of 3. Gene expression in wild-type teeth at P0.


title: RT3E10

description: Fertiles 1


title: Perp-null Replicate 2

description: Biological replicate 2 of 3. Gene expression in Perp-null teeth at P0.


title: RT5E21

description: Fertiles 3


title: WT HSC_primary recipient_replicate1


title: RT5E27

description: Fertiles 4


title: gacA_repa

city: Boston

first: Suresh

last: Gopalan

state: MA

address: 185 Cambridge Street, CPZN 7250

department: Molecular Biology

institute: Massachusetts General Hosptal & Harvard Medical School

description: Arabidopsis seedlings (10 day old) infected with P. aeruginosa (PA14) gacA mutant, and gene expression analyzed 1 day post infection

hyb_protocol: Chips were hybridized according standard Affymetrix protocol, and washed in GeneChip 450 fluidics station.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) in GCOS environment using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings, PA14DgacA treated, 24h pi

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Strelilized Arabidopsis seeds Col-0 expressing hRluc under the CaMV 35S promoter were grown for 10 days in MS medium with vitamins (Phytotechnologies, CA) with 0.5 % sucrose (adjusted in the beginning to pH 5.8) with 75 microE light, 18 h photoperiod and 80% humidity at 22oC. Bacteria were grown to mid-exponential phase in LB.

extract_protocol: RNA was extracted using RNeasy Plant mini kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: 10 day old seedlings in 100 microliter medium were infected with 10 microliter of 0.0002 ABS600 bacteria, continued incubation at 25oC for 24 h, and flash frozen in liquid N2.

value: seedlings

tag: infection

value: P. aeruginosa PA14DgacA

tag: cultivar


title: gacA_repc

tag: tissue


title: KO HSC_primary recipient_replicate1

tag: genotype/variation


title: Control Replicate 1

description: Biological replicate 1 of 3. Gene expression in wild-type teeth at P0.

tag: gender


title: PA14_repc

description: Arabidopsis seedlings (10 day old) infected with P. aeruginosa (PA14), and gene expression analyzed 1 day post infection

source_name: Arabidopsis seedlings, PA14 treated, 24h pi

value: P. aeruginosa PA14


title: PA14_repa


title: aCGH tumor T103

status: Public on Jan 21 2011

first: Rinske

last: Drost

institute: The Netherlands Cancer Institute

description: aCGH Palb2GT/+;p53-/- lymphoma

hyb_protocol: Hybridizations were carried out for 18 hr at 428C in the NimbleGen Service Laboratory. The arrays were washed using a NimbleGen Wash Buffer System (NimbleGen Systems, Inc.) and immediately dried down by centrifugation.

scan_protocol: Arrays were scanned at 5-lm resolution using the GenePix4000B scanner (Axon Instruments, Molecular Devices Corp., Sunnyvale, CA). Data were extracted from scanned images using NimbleScan 2.0 extraction software (NimbleGen Systems, Inc.), which allows for automated grid alignment, extraction, and generation of data files.

data_processing: Deletion and amplification breakpoints were determined by automated segmentation analysis of data sets as follows: each array data set was  imported into R (www.r-project.org; Ihaka et al., 1996) for normalization. The normalize.qspline method from the affy Bioconductor package (www.bioconductor.org; Gentleman et al., 2004) was used to normalize the signal intensities of the test vs. reference.

source_name: DNA from Palb2GT/+;p53-/- lymphoma

label_protocol: The labeling of genomic DNA samples for oligonucleotide microarray CGH analysis was performed using the method of Brennen et al., (2004) with modifications. Genomic DNA was randomly fragmented by sonication to a size range of 500–2,000 bp. For labeling, each DNA sample (1 lg) was denatured at 988C in the presence of 1 O.D. of 50-Cy3- or 50-Cy5-labeled random nonamer (TriLink Biotechnologies, SanDiego, CA) in 62.5 mM Tris-HCl, pH 7.5, 6.25 mM MgCl2, and 0.0875% b-mercaptoethanol. The denatured sample was chilled on ice, and then incubated with 100 units (exo-) Klenow fragment (NEB, Ipswich, MA) and dNTP mix (6 mM each in Tris, EDTA (TE), Invitrogen, Carlsbad, CA) for 2 hr at 378C. Reactions were terminated by addition of 0.5 M EDTA (pH 8.0); the end products were precipitated with isopropanol and resuspended in water. Fifty-fold amplification was typically achieved. The Cy-labeled test sample (Cy3) and reference sample (Cy5) were combined (15 lg each) and dried down by vacuum centrifugation. The reference sample was a pool of six male individuals (Promega, Madison, WI). The sample was rehydrated in 40 ll of NimbleGen Hybridization Buffer (NimbleGen Systems, Inc.), denatured at 958C for 5 min, and then cooled to 428C.

extract_protocol: Genomic DNA was isolated from tissue by proteinase K lysis and organic extraction with phenol-chloroform.

value: lymphoma

source_name: DNA from Palb2GT/+;p53-/- spleen

value: Spleen


title: aCGH tumor T176

description: aCGH Palb2GT/+;p53-/- lymphoma

source_name: DNA from Palb2GT/+;p53-/- liver

value: Liver


title: aCGH tumor T111

description: aCGH Palb2+/+;p53-/- lymphoma

source_name: DNA from Palb2+/+;p53-/- lymphoma

source_name: DNA from Palb2+/+;p53-/- spleen


title: aCGH tumor T068

description: aCGH Palb2GT/+;p53-/- lymphoma


title: aCGH tumor T102

description: aCGH Palb2GT/+;p53-/- lymphoma


title: aCGH tumor T104

description: aCGH Palb2+/+;p53-/- lymphoma


title: aCGH tumor T98

description: aCGH Palb2+/+;p53-/- lymphoma


title: aCGH tumor T254

description: aCGH Palb2GT/+;p53-/- lymphoma


title: aCGH tumor T107

description: aCGH Palb2+/+;p53-/- lymphoma


title: aCGH tumor T095

description: aCGH Palb2GT/+;p53-/- lymphoma


title: aCGH tumor T126

description: aCGH Palb2GT/+;p53-/- lymphoma


title: aCGH tumor T143

description: aCGH Palb2+/+;p53-/- lymphoma


title: aCGH tumor T61

description: aCGH Palb2+/+;p53-/- lymphoma


title: aCGH tumor T100

description: aCGH Palb2+/+;p53-/- lymphoma


title: aCGH tumor T071

description: aCGH Palb2+/+;p53-/- lymphoma


title: aCGH tumor T82

description: aCGH Palb2GT/+;p53-/- lymphoma


title: aCGH tumor T093

description: aCGH Palb2GT/+;p53-/- lymphoma


title: aCGH tumor T50

description: aCGH Palb2GT/+;p53-/- lymphoma


title: aCGH tumor T105

description: aCGH Palb2+/+;p53-/- lymphoma


title: aCGH tumor T115

description: aCGH Palb2+/+;p53-/- lymphoma


title: aCGH tumor T083

description: aCGH Palb2GT/+;p53-/- lymphoma


title: aCGH tumor T276

description: aCGH Palb2GT/+;p53-/- lymphoma


title: aCGH tumor T174

description: aCGH Palb2+/+;p53-/- lymphoma

source_name: DNA from Palb2+/+;p53-/- liver


title: aCGH tumor T113

description: aCGH Palb2GT/+;p53-/- lymphoma


title: aCGH tumor T560

description: aCGH Palb2GT/+;p53-/- lymphoma


title: aCGH tumor T665

description: aCGH Palb2GT/+;p53-/- lymphoma


title: irradiated C57BL/6 mouse 3

city: Pune

first: Sanjay

last: Mukherjee

state: Maharashtra

address: Ganeshkhind

department: Department of Zoology

country: India

institute: University of Pune

description: Mouse 22.4k cDNA microarray.There were total 23040 spots on the array out of them 176 were blank spots and 209 were control spots(A. thaliana DNA,these spots were eliminated from final data but the intensity of these spots was used to calculate true positive spots (Intensity higher than the control spot intensity).

hyb_protocol: Genomic DNA fragmented to an average size of 2kb was alllowed to hybridize on to the array for 16hrs. At 42 dg.celcius, the bound DNA to the array was detected using antibodies.

scan_protocol: the array was scanned at 573nm using scan array express scanner (Perkin Elmer USA) at 70 PMT gain.

data_processing: data normalized using LOWESS method using R-Package 2.5. The true signals for methylation were determined and normalized using control spots (blank spots+A. Thaliana DNAspots) present on the array(ref-Kelkar et al., 2009, Epigenetics 6(4):1-7).

source_name: irradiated liver tissue

label_protocol: The methylation was detected using antibodies against 5-methyl cytosine (5mC) of DNA. A secondary antibody labelled with Cy3 was used to detect the bound anti-5mC antibodies.

extract_protocol: Total genomic DNA was isolated from liver tissue using phenol chloroform method

tag: age

value: 4 weeks old

value: female

tag: developmental stage

value: Adult


title: irradiated C57BL/6 mouse 2


title: irradiated C57BL/6 mouse1


title: 09_Pol2_rep2

city: Worcester

first: Richard

middle: E

last: Baker

address: 55 Lake Avenue North

department: Microbiology & Physiological Systems

institute: University of Massachusetts Medical School

description: ChIP-chip wild-type splenic B cells Pol2

hyb_protocol: Arrays were hybridized in Maui hybridization stations following Nimblegen protocols (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Hybridized arrays were scanned on an Agilent Technologies DNA Micraarray Scanner model G2505B.  Two-channel fluorescence intensities were extracted from the resulting TIFF files using NimbleScan v2.4  (Nbs1) or Nimblescan v2.6 (Pol2) software.

data_processing: MA2C (Robust, C=2)

source_name: Pol2 ChIP DNA from wild-type splenic B cells induced to undergo CSR

label_protocol: DNA samples were amplified using the WGA2 kit (Sigma Corp) according to the provided protocol, except the first fragmentation step was omitted. ChIP samples were amplified undiluted, whereas input control samples were amplified at a starting concentration of 1-2 ng/µl. After amplification, IP and input DNAs were labeled with Cy5 and Cy3 nonamers, respectively (TriLink Biotechnologies) using random primers and linear amplification with Klenow fragment of E. coli DNA Polymerase I (eBioscience Biotechnologies).

growth_protocol: Single-cell suspensions were prepared from spleens of 6 to 12 week old mice

extract_protocol: Cells were washed in PBS and fixed for 10 min at 37°C with 1% formaldehyde. Fixation was quenched by incubating with glycine at a final concentration of 125 mM for 5 minutes at room temperature. Fixed cells were then washed 3 times with PBS and the dried pellet was stored at -80°C. To perform ChIP, the pellet was thawed in Lysis buffer as per the Upstate protocol in the presence of protease and phosphatase inhibitors, and then sonicated 20 times for 10 sec bursts using a VibraCell (Sonics) sonicator at a medium setting. Aliquots containing 2 million cell equivalents of lysate were incubated overnight at 4°C with a mixture of Protein A/Protein G Dynabeads (Invitrogen) coupled with specific antibody. Beads were then washed according to the Upstate protocol and DNA was de-crosslinked and eluted by overnight incubation in elution buffer at 65°C. Eluted DNA and an aliquot of the input DNA were treated with Proteinase K and RNase A (final concentrations of 125 µg/ml) at 55°C overnight. DNA was precipitated in ethanol after phenol/chloroform extraction and resuspended in Tris-EDTA (10/0.1) pH 7 buffer.

treatment_protocol: Cultures induced for 2 days with 50 μg/ml LPS, 100 ng/ml human BLyS, and 25 ng/ml anti–δ-dextran

tag: genotype

tag: cell type

value: cultured splenic B cells

tag: chip antibody

tag: chip antibody manufacturer

value: Upstate

tag: chip antibody catalog #

tag: chip antibody lot #

source_name: input DNA from wild-type splenic B cells induced to undergo CSR

treatment_protocol: Cultures were induced for 2 days with 50 μg/ml LPS, 100 ng/ml human BLyS, and 25 ng/ml anti–δ-dextran

value: none, input DNA


title: 09_Pol2_rep1

value: wild-type


title: 09_Nbs1_aid_rep1

description: ChIP-chip aid-/- splenic B cells Nbs3

data_processing: NimbleScan v2.4

source_name: Nbs1 ChIP DNA from aid-/- splenic B cells induced to undergo CSR

value: aid-/-

value: Abcam

source_name: input DNA from aid-/- splenic B cells induced to undergo CSR


title: control C57BL/6 mouse 3

source_name: control liver tissue

tag: sex


title: 09_Nbs1_aid_rep2

description: ChIP-chip aid-/- splenic B cells Nbs4


title: control C57BL/6 mouse 1


title: 09_Nbs1_WT_rep2

description: ChIP-chip wild-type splenic B cells Nbs2

source_name: Nbs1 ChIP DNA from wild-type splenic B cells induced to undergo CSR


title: 08_Pol2_rep2


title: 09_Nbs1_WT_rep1

description: ChIP-chip wild-type splenic B cells Nbs1


title: control C57BL/6 mouse 2


title: 08_Nbs1_aid_rep2

description: ChIP-chip aid-/- splenic B cells Nbs4


title: 03_Nbs1_aid_rep1

description: ChIP-chip aid-/- splenic B cells Nbs3


title: 08_Pol2_rep1


title: 05_Nbs1_WT_rep1


title: 05_Nbs1_WT_rep2


title: 08_Nbs1_WT_rep2


title: 05_Nbs1_aid_rep2

description: ChIP-chip aid-/- splenic B cells Nbs4


title: EMF3_cy3 vs MSC_cy5

city: Beijing

first: Antican

last: Wang

state: Beijing

address: #17 Pan Jia Yuan Nan Li, Chao Yang District.

department: State Key Lab of Molecular Oncology, Department of Etiology and Carcinogenesis

country: China

institute: Cancer Institute and Hosital, Chinese Academy of Medical Sciences.

description: supplement experiment, dye reversed

hyb_protocol: Standard Capitalbio Methods, http://www.capitalbio.com/marticle/Manual400010-Human_22k_oligo_array-070620.pdf

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. To make comparisons between the three cell lines, the “Separate Channel Analysis of Two-Color Data” model of  LIMMA package within the R 2.11.0 was used to analyze the red and green channels log-intensities separately.

source_name: Hybrid strain 3 from EC9706 fused with MSC

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: EC9706 was maintained in RPMI-1640 (Gibco, USA) supplemented with 10% fetal bovine serum (Gibco, Cat.16000), 100 U/ml penicillin G, and 100 μg/ml streptomycin at 37°C in a humidified 5% CO2 incubator, refreshed with complete medium every 3 days, and subcultured when cell confluence reached 90%. Both hMSC and fusion cells were cultured in MSCM (Tianjin, China, AmCellGene Co. Ltd.) and changed every 3 days; cells were trypsinized with TrpLE (Gibco, Cat. 12605) and split when 80% confluence was achieved. All hMSCs were used at passage 3-12 for all experiments.

extract_protocol: Total RNA isolation was isolated by TRIZOL (Invitrogen, CA) and purified by Nucleospin RNA clean-up (MN, USA).

treatment_protocol: Heterokaryons (EMFs) were generated by fusing hMSC and EC9706 using 50% polyethylene glycol, pH7.4 (PEG 1500; Roche, Cat.783641) according to the method on “Current Protocols in Stem Cell Biology”

tag: sample type

source_name: Human umbilical cord mesenchymal stem cells derived from human full term umbilical cord tissues

value: MSC


title: 03_Pol2_rep2


title: 05_Nbs1_aid_rep1

description: ChIP-chip aid-/- splenic B cells Nbs3


title: 08_Nbs1_WT_rep1


title: MSC_cy3 vs EMF2_cy5

value: Human umbilical cord mesenchymal stem cells derived from human full term umbilical cord tissues

source_name: Hybrid strain 2 from EC9706 fused with MSC


title: EC9706_cy3 vs EMF3_cy5

source_name: Esophageal carcinoma cell line EC9706

tag: cell line

value: Hybrid strain 3 from EC9706 fused with MSC


title: 03_Pol2_rep1

tag: strain


title: EMF1_cy3 vs MSC_cy5

description: supplement experiment, dye reversed

source_name: Hybrid strain 1 from EC9706 fused with MSC


title: 07_Pol2_rep1


title: 07_Nbs1_aid_rep1

description: ChIP-chip aid-/- splenic B cells Nbs3


title: 05_Pol2_rep2


title: 07_Nbs1_WT_rep1


title: EC9706_cy3 vs EMF2_cy5

value: Hybrid strain 2 from EC9706 fused with MSC


title: 03_Nbs1_WT_rep2


title: 07_Pol2_rep2


title: EC9706_cy3 vs EMF1_cy5

value: Hybrid strain 1 from EC9706 fused with MSC


title: 05_Pol2_rep1


title: 08_Nbs1_aid_rep1

description: ChIP-chip aid-/- splenic B cells Nbs3


title: normal_5

city: Frederick

first: Stephanie

middle: Kaye

last: Watkins

state: MD

address: 1050 Boyles St.

department: CIP/LMI

institute: NCI-Frederick

description: Dendritic cells normal human prostate patient 5

hyb_protocol: replicates of each group were hybridized to Affymetrixhuman Gene ST 1.0 GeneChip in Affymetrix hybridization oven at 45C, 60rpm for 16 hrs

scan_protocol: Wash and stain were performed on Affymetrix Fluidics Station 450 and scanned on Affymetrix GeneChip scanner 3000

data_processing: Data were collected using Affymetrix AGCC software,Statistical and clustering analysis was performed with Partek Genomics Suite software using RMA normalization algorithm.

source_name: normal Patient 5

label_protocol: 200 ng of RNA was reverse transcribed with random hexamer primer, amplified and terminal labeled with biotin using Affymetrix Whole Transcript Sense Target Labeling kit according to manufacturer’s protocol

extract_protocol:
RNA was isolated using the qiagen RNAeasy mini spin colomn according to manufacturer's instuctions. All samples used for microarray analysis have high quality score (RIN >9).
RNA quality was checked on Agilent Bioanalyzer

treatment_protocol: Cells were purified from digested prostates by magnetic beads >90% purity was confirmed

value: male

value: normal prostate

tag: cell-type

value: dendritic cells


title: Btaf1_mutant vs Wt age matched dye swap

city: Utrecht

first: Frits

last: Meijlink

address: Uppsalalaan 8

institute: Hubrecht Institute

hyb_protocol: according to Agilent guidelines

scan_protocol: according to Agilent guidelines

data_processing: Microarray signal and background information were retrieved using Feature Extraction (V.9.5.3, Agilent Technologies).  LOWESS normalized.

source_name: whole embryo

label_protocol: 300 ng of total RNA was labeled using low RNA Input Linear Amp kit (Agilent Technologies, Pato Alto, CA, USA).

extract_protocol: Embryos were stored in RNAlater (Ambion) and RNA was purified using a Qiagen kit.

treatment_protocol: Btaf1 V1330M mutant were compared to WT embryos

value: wild type

value: C57BL/6J *FVB/NJ

value: Btaf1 mutant


title: 03_Nbs1_aid_rep2

description: ChIP-chip aid-/- splenic B cells Nbs4

value: cultured splenic B cells


title: normal_3

description: Dendritic cells normal human prostate patient 3

source_name: normal Patient 3


title: Btaf1_mutant vs Wt age matched


title: 07_Nbs1_aid_rep2

description: ChIP-chip aid-/- splenic B cells Nbs4


title: 01_Pol2_rep2

value: Upstate


title: Btaf1_mutant vs Wt stage matched dye swap


title: normal_1

description: Dendritic cells normal human prostate patient 1

source_name: normal Patient 1


title: 03_Nbs1_WT_rep1

value: none, input DNA


title: tumor_4

description: Dendritic cells tumor human prostate patient 4

source_name: Tumor Patient 4

value: tumor bearing prostate


title: Btaf1_mutant vs Wt stage matched


title: tumor_3

description: Dendritic cells tumor human prostate patient 3

source_name: Tumor Patient 3


title: tumor_5

description: Dendritic cells tumor human prostate patient 5

source_name: Tumor Patient 5


title: tumor_2

description: Dendritic cells tumor  human prostate patient 2

source_name: Tumor Patient 2


title: 07_Nbs1_WT_rep2

value: wild-type

source_name: input DNA from wild-type splenic B cells induced to undergo CSR


title: tumor_1

description: Dendritic cells tumor human prostate patient 1

source_name: Tumor Patient 1


title: 01_Pol2_rep1

source_name: Pol2 ChIP DNA from wild-type splenic B cells induced to undergo CSR


title: normal_4

description: Dendritic cells normal human prostate patient 4

source_name: normal Patient 4


title: Strain_ypT49_vs_N2

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

country: Canada

institute: University of British Columbia

hyb_protocol: The sample was rehydrated in 40 l of NimbleGen Hybridization Buffer (NimbleGen Systems, Inc.), denatured at 95°C for 5 min, and then cooled to 42°C. Hybridizations were carried out for 18 hr at 42°C in the NimbleGen Service Laboratory. The arrays were washed using a NimbleGen Wash Buffer System (NimbleGen Systems, Inc.) and immediately dried down by centrifugation. See Selzer, R.R., T.A. Richmond, N.J. Pofahl, R.D. Green, P.S. Eis, P. Nair, A.R. Brothman, and R.L. Stallings. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319 (PMID 16075461).

scan_protocol: The scanner used was an Axon Scanner (Model # 4000B) . See Selzer, R.R., T.A. Richmond, N.J. Pofahl, R.D. Green, P.S. Eis, P. Nair, A.R. Brothman, and R.L. Stallings. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319 (PMID 16075461).

data_processing: The raw log2 intensity ratio were normalized with the LOESS regression.

organism: Caenorhabditis elegans

label_protocol: Cy3 dye-labeled random 9mers (TriLink BioTechnologies, Inc.) were diluted to 1 O.D./42 µl of buffer containing 0.125M Tris-HCl (pH 8.0), 0.125M MgCl2, 1.75 µl/ml β-Mercaptoethanol. 1 µg of genomic DNA was added to each random 9mer buffer solution, denatured at 95 ºC and then chilled on ice in 0.2 ml PCR tubes. 10 µl of 50X dNTP mixture (1X TE buffer, 10 mM each of dATP, dCTP, dGTP and dTTP), 8 µl DI water and 100 U Klenow fragment (exo-) was added to each tube and mixed well with a pipet. Samples were centrifuged and incubated at 37 ºC for 2 hours. 10 µl 0.5 M EDTA was added and mixed well to stop the labeling reaction. DNA was precipitated by adding 11.5 µl 0.5 M NaCl and 110 µl isopropanol, vortexing, incubating in the dark for 10 minutes at room temperature, and centrifuging at 12,000X G for 10 minutes. The supernatant was removed and the DNA pellet was washed with 500 µl 80% ethanol. After centrifugation at 12,000X G for 2 minutes, the supernatant was removed and the pellet was dried in a SpeedVac on low heat for 5 minutes before being rehydrated in 25 µl DI water. DNA concentration was measured using a spectrophotometer.

extract_protocol: DNA was prepared either by standard phenol-chloroform extraction followed by ethanol precipitation, or with the Puregene DNA Purification Kit (D-7000A, Gentra Systems) using the solid tissue protocol.

value: hermaphrodite

value: whole animals

source_name: Wild-type N2

label_protocol: Cy5 dye-labeled random 9mers (TriLink BioTechnologies, Inc.) were diluted to 1 O.D./42 µl of buffer containing 0.125M Tris-HCl (pH 8.0), 0.125M MgCl2, 1.75 µl/ml β-Mercaptoethanol. 1 µg of genomic DNA was added to each random 9mer buffer solution, denatured at 95 ºC and then chilled on ice in 0.2 ml PCR tubes. 10 µl of 50X dNTP mixture (1X TE buffer, 10 mM each of dATP, dCTP, dGTP and dTTP), 8 µl DI water and 100 U Klenow fragment (exo-) was added to each tube and mixed well with a pipet. Samples were centrifuged and incubated at 37 ºC for 2 hours. 10 µl 0.5 M EDTA was added and mixed well to stop the labeling reaction. DNA was precipitated by adding 11.5 µl 0.5 M NaCl and 110 µl isopropanol, vortexing, incubating in the dark for 10 minutes at room temperature, and centrifuging at 12,000X G for 10 minutes. The supernatant was removed and the DNA pellet was washed with 500 µl 80% ethanol. After centrifugation at 12,000X G for 2 minutes, the supernatant was removed and the pellet was dried in a SpeedVac on low heat for 5 minutes before being rehydrated in 25 µl DI water. DNA concentration was measured using a spectrophotometer.


title: Strain_ypT50_vs_N2


title: Strain_ypT48_vs_N2


title: Strain_ypT45_vs_N2


title: Strain_ypT43_vs_N2


title: Strain_ypT50_outcrossed_vs_N2


title: normal_2

description: Dendritic cells normal human prostate patient 2

source_name: normal Patient 2


title: Strain_ypT37_vs_N2


title: Strain_ypT46_vs_N2


title: 01_Nbs1_aid_rep2

description: ChIP-chip aid-/- splenic B cells Nbs4

source_name: Nbs1 ChIP DNA from aid-/- splenic B cells induced to undergo CSR

value: aid-/-

value: Abcam

source_name: input DNA from aid-/- splenic B cells induced to undergo CSR


title: Strain_ypT40_vs_N2


title: Strain_ypT40_outcrossed_vs_N2


title: Strain_ypT47_vs_N2


title: Strain_ypT42_vs_N2


title: Strain_ypT38_vs_N2


title: Strain_ypT44_vs_N2


title: Strain_ypT35_vs_N2


title: Strain_ypT33_vs_N2


title: Strain_ypT41_vs_N2


title: Strain_ypT36_vs_N2


title: Strain_ypT29_outcrossed_vs_N2


title: Strain_ypT30_vs_N2


title: Strain_ypT34_vs_N2


title: Strain_ypT29_vs_N2


title: Strain_ypT28_vs_N2


title: Strain_ypT34_outcrossed_vs_N2


title: Strain_ypT27_vs_N2


title: Strain_ypT32_vs_N2


title: Strain_ypT52_vs_N2


title: Strain_ypT25_vs_N2


title: strain_ypT23_outcrossed_vs_N2


title: 01_Nbs1_WT_rep1

source_name: Nbs1 ChIP DNA from wild-type splenic B cells induced to undergo CSR


title: Strain_ypT23_vs_N2

source_name: wild-type N2


title: 01_Nbs1_aid_rep1

description: ChIP-chip aid-/- splenic B cells Nbs3


title: Strain_ypT21_vs_N2


title: pBabe_puro_38_0C_7d_rep_1

city: London

first: Parmjit

last: Jat

address: Queen Square

department: Institute of Neurology

country: United Kingdom

institute: UCL

description: pBabe puro (control vector for the pLXIPGSEp53 rescue) grown for 7 days at 38oC

hyb_protocol: According to Affymetrix

scan_protocol: According to Affymetrix

data_processing: The data were analyzed with Bioconductor R packages affy and limma using RMA as normalisation method.

source_name: pBabe puro (control vector) at 38oC for 7 days

label_protocol: Invitrogen + Enzo

growth_protocol: HMF3A cells and derivatives thereof were maintained in DMEM supplemented with 10% heat inactivated fetal bovine serum, 2mM glutamine, 100 units per ml penicillin and 100 micrograms per ml streptomcyin and cultured in atmosphere of 5% CO2 and 20% O2.

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

treatment_protocol: HMF3A cells were cultured at 34°C ±0.5°C and temperature shift experiments performed at 38°C ±0.5°C. Cells were incubated at 38°C ±0.5°C for 7 days before RNA was extracted.  HMF3A cells were serum starved by culturing in DMEM supplemented with 0.25% heat inactivated fetal bovine serum, 2mM glutamine, 100 units per ml penicillin and 100 micrograms per ml streptomycin.  Cultures were fed with fresh medium the day prior to RNA extraction and were harvested at no greater than 80% confluence.

value: Human mammary fibroblasts (HMF3A)

tag: treatment


title: Strain_ypT18_vs_N2

tag: tissue


title: Strain_ypT2_outcrossed_vs_N2


title: pBabe_puro_38_0C_7d_rep_2

value: pBabe puro (control vector) at 38oC for 7 days


title: 01_Nbs1_WT_rep2


title: C38_0C_7d_33_5C_7d_rep_1

description: Control for temperature by growing HMF3A cells at 38oC for 7 days and then shifting back to 33.5oC: IGNORE

source_name: HMF3A cells at  38oC for 7 days + back to 33.5oC

value: 38oC for 7 days + back to 33.5oC


title: C38_0C_7d_33_5C_7d_rep_3

source_name: HMF3A cells at 38oC for 7 days + back to 33.5oC


title: Strain_ypT24_vs_N2


title: Strain_ypT6_vs_N2


title: pBabe_puro_38_0C_7d_rep_3


title: C38_0C_7d_33_5C_7d_rep_2


title: pRS_p21_38_0C_rep_3

description: pRS p21 (p21) grown at 38oC

source_name: pRS p21 at 38oC

value: pRS p21 (p21) grown at 38oC


title: pRS_p53_38_0C_rep_3

description: pRS p53 (p53) grown at 38oC

source_name: pRS p53 at 38oC

value: pRS p53 (p53) grown at 38oC


title: Strain_ypT7_vs_N2


title: Strain_ypT13_vs_N2


title: Strain_ypT3_vs_N2


title: Strain_ypT6_outcrossed_vs_N2


title: pRS_p53_38_0C_rep_1

description: pRS p53 (p53) grown at 38oC


title: Strain_ypT14_vs_N2


title: pRS_p53_38_0C_rep_2

description: pRS p53 (p53) grown at 38oC


title: pLPC_E2F_DB_38_0C_rep_3

description: pLPC E2F-DB (dominant negative mutant of E2F) grown at 38oC

source_name: pLPC E2F-DB at 38oC


title: Strain_ypT17_vs_N2


title: pLPC_E2F_DB_38_0C_rep_1

value: pLPC E2F-DB (dominant negative mutant of E2F) grown at 38oC


title: pLPC_E2F_DB_38_0C_rep_2


title: pLPC_wt_E7_38_0C_rep_2

description: pLPC wt E7 (viral protein HPV16 E7) grown at 38oC

source_name: pLPC wt E7 at 38oC


title: Strain_eT6_vs_N2


title: Strain_unc-1_vs_N2


title: pLXIP_GSE_p53_38_0C_rep_2

description: pLXIP GSE p53 (genetic suppressor element of p53) grown at 38oC

source_name: pLXIP GSE p53 at 38oC


title: Strain_ypT2_vs_N2


title: Strain_unc-3_vs_N2


title: pLPC_12S_E1A_38_0C_rep_3

description: pLPC 12S E1A (viral protein Adenovirus 5 12S E1A) grown at 38oC

source_name: pLPC 12S E1A at 38oC


title: pLPC_wt_LT_38_0C_rep_3

description: pLPC wt LT (wild type LT antigen) grown at 38oC

source_name: pLPC wt LT at 38oC


title: pLPC_12S_E1A_38_0C_rep_1

value: pLPC 12S E1A (viral protein Adenovirus 5 12S E1A) grown at 38oC


title: pLPC_wt_LT_38_0C_rep_2

value: pLPC wt LT (wild type LT antigen) grown at 38oC


title: pLPC_wt_E7_38_0C_rep_1

value: pLPC wt E7 (viral protein HPV16 E7) grown at 38oC


title: pLXIP_GSE_p53_38_0C_rep_1

value: pLXIP GSE p53 (genetic suppressor element of p53) grown at 38oC


title: pLXIP_GSE_p53_38_0C_rep_3


title: pLPC_12S_E1A_38_0C_rep_2


title: pLPC_wt_LT_38_0C_rep_1


title: pLPCX_38_0C_7d_rep_3

description: pLPCX (empty vector for introducing genes that can overcome the growth arrest) grown for 7 days at 38oC

source_name: pLPCX vector at 38oC for 7 days


title: pRS_p21_38_0C_rep_1

description: pRS p21 (p21) grown at 38oC


title: pRS_p21_38_0C_rep_2

description: pRS p21 (p21) grown at 38oC


title: Strain_eT5_vs_N2

source_name: Wild-type N2


title: pRS_LAMIN_38_0C_7d_rep_1

description: pRS LAMIN (vector used for silencing genes expression and expresses lamin A) grown for 7days at 38oC

source_name: pRS LAMIN vector at 38oC for 7 days


title: pLPCX_38_0C_7d_rep_1

value: pLPCX (empty vector for introducing genes that can overcome the growth arrest) grown for 7 days at 38oC


title: Quiescence_rep_3

description: Quiescence

source_name: Quiescence


title: pLPC_wt_E7_38_0C_rep_3


title: Quiescence_rep_1

description: Quiescence


title: HMF3S_38_0C_7d_rep_1

description: Gene expression data from HMF3S cells grown for 7 days at 38oC

source_name: HMF3A cells at 38oC for 7 days

value: 7 days at 38oC


title: HMF3S_33_5C_7d_rep_2

description: Gene expression data from HMF3S cells grown for 7 days at 33.5oC

source_name: HMF3A cells at 33.5oC for 7 days

value: 7 days at 33.5oC


title: C38_0_rep_2

description: Gene expression data from HMF3A cells grown for 7 days at 38oC


title: HMF3S_38_0C_7d_rep_3


title: JFP41_induced_30.0min_rep2

city: Richmond

first: Alejandro

last: Rodriguez

state: VA

address: 521 North 11th Street

department: Dentistry

institute: Virginia Commonwealth University

description: Biological replicate 2 of 3. Induced cells 30 min. after competence induction. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.

hyb_protocol: Slides were pretreated for 2 – 3 h at 42ºC in 50µl of prehybridization solution (5x SSC, 0.1% SDS, 1% BSA). Slides were maintained in hybridization cassettes (ArrayIt®, Sunnyvale, CA) throughout the incubation phase. The slides were then washed three times with MilliQ water in a High Throughput Wash Station (ArrayIt®) followed with one wash in isopropanol and dried using a mini-slide centrifuge (Labnet International, Edison, NJ). Dried probes were then resuspended in 50µl hybridization buffer (40% formamide, 5x SSC, 0.1% SDS, 0.6µg/µl salmon sperm DNA). The solution was heated at 95ºC for 10 min while vortexing intermittently and then transferred onto pretreated slides under a LifterSlip™ (Erie Scientific, Portsmouth, NH). The probes were allowed to hybridize for 16 – 20 h at 42ºC in a hybridization cassette. Humidity was maintained with the addition of 15µl of unused hybridization buffer in each well. Slides were washed twice in 2x SSC, 0.1% SDS, 0.1 mM DTT at 55ºC for 10 min, twice at room temperature in 0.1x SSC, 0.1% SDS, 0.1 mM DTT for 5 min, and twice at room temperature in 0.1x SSC, 0.1 mM DTT for 5 min. The slides were then dipped in MilliQ water before being dried in a mini-slide centrifuge. Microarrays were immediately scanned in an Axon GenePix® 4200 scanner (MDS Analytical Technologies).

scan_protocol: Scanned on an Axon Genepix 4200 Scanner Images were quantified using Genepix Pro software (version 5.1)

data_processing: Median normalization of the intensity distributions obtained from log2 of processed Red signal/processed Green signal. Data processed through the Ramhorn Array Database

organism: Streptococcus sanguinis

source_name: 30 min. post-competence induction

label_protocol: 2µg total RNA was annealed to 6µg random hexamers (Invitrogen, Carlsbad, CA) in a total volume of 18.5µl and incubated at 70ºC for 10 min. Samples were snap frozen in ethanol at -80ºC for 30s before addition of 6µl of 5x First Strand Buffer (250 mM Tris-Cl, pH 8.3, 375 mM KCl, 15 mM MgCl2), 3µl 0.1M DTT, and 0.6µl of dNTP solution (25 mM each dATP, dCTP, and dGTP, 15 mM dTTP (Invitrogen) and 10 mM amino allyl-dUTP (Sigma)). The solution was then incubated overnight at 42ºC with 300 U of Superscript III (Invitrogen). The RNA template was then hydrolyzed via the addition of 10µl 0.5 M EDTA and 10µl 1 M NaOH and incubation at 65ºC for 15 min. The mixture was neutralized with 25µl 1 M Tris pH 7.0 and 10µl 3 M NaOAc, and purified using MiniElute® PCR Purification Kit (Qiagen) replacing the Tris buffers with phosphate buffers (5 mM KPO4, pH 8, 80% EtOH) and (4 mM KPO4, pH 8.5) for the wash and elution steps, respectively. The reaction was then dried in a Speed-Vac centrifuge before being resuspended in 4.5µl 0.1 M Na2HCO3, pH 9.3 and 4.5µl of the ester dye (Cy3 or Cy5 (Amersham) for the control and experimental samples, respectively). The coupling reaction proceeded for 1.5 - 2 h at room temperature in the dark before being stopped via the addition of 35µl 100 mM NaOAc pH 5.2 and then purified over Qiagen MiniElute PCR purification columns per the manufacturer's protocol and supplied buffers.

growth_protocol: Overnight cultures of JFP41 grown in Todd Hewitt (TH) broth (Bacto, Sparks, MD) supplemented with 2.5% (v/v) horse serum (TH-HS) (Invitrogen, Grand Island, NY) at 37ºC were diluted 1:200 in pre-warmed TH-HS (7.6). The culture was allowed to incubate until the optical density at 660 nm reached ~0.07.

extract_protocol: Twenty ml of culture was removed and mixed with an equal volume of hot acid phenol containing 0.1 M citrate buffer (pH 4.3, Sigma) and 0.1% (v/v) sodium dodecyl sulfate (SDS, Ambion, Austin, TX). Samples were incubated in a boiling water bath for 10 min, cooled in an ice bath and transferred to Phase Lock Gel™ (PLG) tubes (5 Prime Inc., Gaithersburg, MD). After centrifugation at 1500 x g for 5 min, the supernatant was removed and extracted with an equal volume of acid phenol:chloroform  (1:1), then chloroform. RNA was precipitated from the supernatant by NaOAc/isopropanol precipitation, followed by centrifugation. The resulting RNA pellet was washed with 70% ethanol, dried via tube inversion, and dissolved in 100µl DEPC-treated water. Samples were then treated with DNase I and purified over RNeasy columns (Qiagen, Valencia, CA) according to protocols supplied by the manufacturer.

treatment_protocol: Once an optical density at 660 nm reached ~0.07, cells were treated with Streptococcus sanguinis synthetic CSP (NH2-DLRGVPNPWGWIFGR-COOH) at a concentration of 220 ng/ml and incubated for the appropriate time.

source_name: uninduced cells


title: C38_0_rep_3


title: pRS_LAMIN_38_0C_7d_rep_3

value: pRS LAMIN (vector used for silencing genes expression and expresses lamin A) grown for 7days at 38oC


title: JFP41_induced_20.0min_rep3

description: Biological replicate 3 of 3. Induced cells 20 min. after competence induction. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.

source_name: 20 min. post-competence induction


title: C33_5_rep_1

description: Gene expression data from HMF3A cells grown at 33.5oC

source_name: HMF3A cells at 33.5oC


title: JFP41_induced_20.0min_rep2

description: Biological replicate 2 of 3. Induced cells 20 min. after competence induction. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.


title: Quiescence_rep_2

description: Quiescence


title: JFP41_induced_15.0min_rep3

description: Biological replicate 3 of 3. Induced cells 15 min. after competence induction. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.

source_name: 15 min. post-competence induction


title: HMF3S_38_0C_7d_rep_2


title: JFP41_induced_17.5min_rep2

description: Biological replicate 2 of 2. Induced cells 17.5 min. after competence induction. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.

source_name: 17.5 min. post-competence induction


title: JFP41_induced_30.0min_rep1

description: Biological replicate 1 of 3. Induced cells 30 min. after competence induction. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.


title: JFP41_induced_17.5min_rep1

description: Biological replicate 1 of 2. Induced cells 17.5 min. after competence induction. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.


title: JFP41_induced_15.0min_rep2

description: Biological replicate 2 of 3. Induced cells 15 min. after competence induction. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.


title: JFP41_induced_30.0min_rep3

description: Biological replicate 3 of 3. Induced cells 30 min. after competence induction. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.


title: pRS_LAMIN_38_0C_7d_rep_2


title: C33_5_rep_3


title: HMF3S_33_5C_7d_rep_3


title: HMF3S_33_5C_7d_rep_1