title: RNA polymerase (Beta') ChIP-chip in E. coli K-12 MG1655 cells treated with 20ug/ml bicyclomycin (Dataset 94828)

description: RNA polymerase (Beta') ChIP-chip in E. coli K-12 MG1655 cells treated with 20ug/ml bicyclomycin using monoclonal antibody NT73.

source_name: RNA polymerase (Beta') ChIP in E. coli K-12 MG1655 cells treated with 20ug/ml bicyclomycin

source_name: Genomic DNA control from E. coli K-12 MG1655 cells treated with 20ug/ml bicyclomycin


title: Sigma70 ChIP-chip in E. coli K-12 MG1655 cells (Dataset 56859)

status: Public on Jan 03 2009

type: genomic

city: Madison

first: Rachel

middle: Anne

last: Mooney

state: WI

address: 1550 Linden Drive

department: Biochemistry

country: USA

institute: University of Wisconsin-Madison

description: Sigma70 ChIP-chip in E. coli K-12 MG1655 cells using monoclonal antibody 2G10.

hyb_protocol: Samples were hybridized to arrays by Nimblegen according to established protocols (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Arrays were scanned by Nimblegen according to established protocols (http://www.nimblegen.com/products/lit/lit.html).

molecule: genomic DNA

organism: Escherichia coli

source_name: Sigma70 ChIP in E. coli K-12 MG1655 cells

label_protocol: Samples were labeled by Nimblegen according to established protocols (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Strain MG1655 or isogenic strain MG1655 HA3::nusG cells were grown in MOPS minimal medium supplemented with 0.2% glucose (www.genome.wisc.edu/resources/protocols/mopsminimal.htm).

extract_protocol: Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml) micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. After treatment, a distribution of DNA fragments ranging from 200-600 bp was detected by agarose-gel electrophoretic separation of a small sample that was de-crosslinked by incubation at 65 °C for >4 hr. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then incubated with a 50/50 slurry of Sepharose protein A beads and protein G beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of Sepharose protein A and G beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of 250 mM LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2%SDS), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2%SDS), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes toremove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50ul with EB.

treatment_protocol: Cells were grown with vigorous shaking at 37 °C to mid-log (light scattering at 600 nm equivalent to 0.4 OD). Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the mid-log cultures followed by formaldehyde to 1% final, and shaking was continued for 5 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with agitation for 30 minutes to stop the crosslinking. Cells were spun at 5000 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C.

tag: Monoclonal antibody for Sigma70 (2G10)

source_name: Genomic DNA control from E. coli K-12 MG1655 cells

tag: Genomic DNA control


title: NusG ChIP-chip in E. coli K-12 MG1655 cells (Dataset 70568)

description: NusG ChIP-chip in E. coli K-12 MG1655 cells using anti-NusG polyclonal antibody.

source_name: NusG ChIP in E. coli K-12 MG1655 cells

tag: Polyclonal antibody for NusG (raised for this study)


title: Patient no. 17: control

status: Public on Oct 06 2008

type: RNA

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

description: Gene expression data from primary liposarcom cultures incubated with PBS as control for 24 h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133A  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Liposarcoma culture from tumor 399, untreated

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

growth_protocol: Primary human liposarcoma cultures were isolated by dissecting the tumor and digesting the minced samples enzymatically with 10 ml each of collagenase and dispase (10 mg/ml). The single cell suspension was depleted of red blood cells and cellular debris by centrifugation through a Ficoll-Hypaque density gradient. Liposarcioma cells were diluted and cultured during the whole experiment with Leibovitz's L-15 medium, supplemented with 2.0 mM glutamine and 10% fetal bovine serum in a humidified atmosphere in free air exchange with atmospheric air. Cells were seeded at a density of 2.00E+06 in 25 cm2 flasks.

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

treatment_protocol: 24 h later, after having grown to a subconfluent layer, cell cultures were incubated with doxorubicin (0.5 ug/ml) for 24 h or an equal volume of PBS as control

tag: Sex

value: female

tag: Age at operation

value: 78 years

tag: Site

value: thigh

tag: Size in cm

tag: Histological Subtype

value: atypical lipoma with partly dedifferentiated areas

tag: Responder type

value: high

tag: Grading

tag: Specimen character

value: local recurrence

tag: Previous radiation

value: yes

tag: Previous chemotherapy

value: no


title: Patient no. 13: control

source_name: Liposarcoma culture from tumor 392, untreated

value: 74 years

value: dedifferentiated liposarcoma

value: medium

value: primary tumor


title: NusA ChIP-chip in E. coli K-12 MG1655 cells (Dataset 56226)

description: NusA ChIP-chip in E. coli K-12 MG1655 cells using monoclonal antibody 1NA1.

source_name: NusA ChIP in E. coli K-12 MG1655 cells

tag: Monoclonal antibody for NusA (1NA1)


title: Patient no. 10: control

source_name: Liposarcoma culture from tumor 388, untreated

value: male

value: 76 years


title: Patient no. 19: treated

description: Gene expression data from primary liposarcom cultures incubated with doxorubicin (0.5 µg/ml) for 24 h

source_name: Liposarcoma culture from tumor 401, doxorubicin treated

value: 60 years

value: upper arm


title: Patient no. 4: control

source_name: Liposarcoma culture from tumor 340, untreated


title: Patient no. 4: treated

source_name: Liposarcoma culture from tumor 340, doxorubicin treated


title: Patient no. 15: treated

source_name: Liposarcoma culture from tumor 394, doxorubicin treated

value: 70 years

value: atypical lipoma


title: RNA polymerase (Beta') ChIP-chip in E. coli K-12 MG1655 cells (Dataset 56706)

description: RNA polymerase ChIP-chip in E. coli K-12 MG1655 cells using monoclonal antibody NT73.

source_name: RNA polymerase (Beta') ChIP in E. coli K-12 MG1655 cells

tag: Monoclonal antibody for RNA polymerase Beta' subunit (NT73)


title: Patient no. 14: treated

source_name: Liposarcoma culture from tumor 393, doxorubicin treated

value: female

value: thorax

value: pleomorphic liposarcoma

value: residual tumor


title: Patient no. 14: control

source_name: Liposarcoma culture from tumor 393, untreated


title: Patient no. 17: treated

source_name: Liposarcoma culture from tumor 399, doxorubicin treated

value: 78 years

value: thigh

value: atypical lipoma with partly dedifferentiated areas

value: high

value: local recurrence


title: Patient no. 13: treated

source_name: Liposarcoma culture from tumor 392, doxorubicin treated

value: 74 years

value: dedifferentiated liposarcoma

value: medium

value: no


title: Patient no. 19: control

source_name: Liposarcoma culture from tumor 401, untreated

value: male

value: 60 years

value: yes


title: Patient no. 3: treated

source_name: Liposarcoma culture from tumor 338, doxorubicin treated

value: 70 years

value: upper arm

value: atypical lipoma

value: low

value: primary tumor


title: Patient no. 7: control

source_name: Liposarcoma culture from tumor 385, untreated

value: 37 years

value: myxoid/roundcell liposarcoma


title: Patient no. 5: treated

source_name: Liposarcoma culture from tumor 377, doxorubicin treated

value: 38 years

value: knee

value: myxoid liposarcoma


title: Patient no. 15: control

source_name: Liposarcoma culture from tumor 394, untreated

value: thigh


title: RNA polymerase (Beta') ChIP-chip in E. coli K-12 MG1655 cells treated with 100ug/ml rifampicin (Dataset 81586)

description: RNA polymerase (Beta') ChIP-chip in E. coli K-12 MG1655 cells treated with 100ug/ml rifampicin using monoclonal antibody NT73.

source_name: RNA polymerase (Beta') ChIP in E. coli K-12 MG1655 cells treated with 100ug/ml rifampicin

source_name: Genomic DNA control from E. coli K-12 MG1655 cells treated with 100ug/ml rifampicin


title: Patient no. 12: control

source_name: Liposarcoma culture from tumor 391, untreated

value: female

value: 76 years


title: Patient no. 7: treated

source_name: Liposarcoma culture from tumor 385, doxorubicin treated

value: medium

value: no


title: Rho ChIP-chip in E. coli K-12 MG1655 cells (Dataset 70261)

description: Rho ChIP-chip in E. coli K-12 MG1655 cells using anti-Rho polyclonal antibody.

source_name: Rho ChIP in E. coli K-12 MG1655 cells

tag: Polyclonal antibody for Rho (gift from Jeff Roberts)

source_name: Genomic DNA control from E. coli K-12 MG1655 cells


title: Patient no. 3: control

source_name: Liposarcoma culture from tumor 338, untreated


title: Patient no. 12: treated

source_name: Liposarcoma culture from tumor 391, doxorubicin treated


title: Patient no. 9: control

source_name: Liposarcoma culture from tumor 387, untreated

value: male

value: 53 years

value: atypical liposarcoma

value: local recurrence


title: Patient no. 18: treated

source_name: Liposarcoma culture from tumor 400, doxorubicin treated

value: 67 years

value: atypical lipoma


title: Patient no. 18: control

source_name: Liposarcoma culture from tumor 400, untreated

value: low

value: primary tumor


title: Patient no. 9: treated

source_name: Liposarcoma culture from tumor 387, doxorubicin treated

value: yes


title: Patient no. 1: control

source_name: Liposarcoma culture from tumor 314, untreated

value: 69 years

value: lower arm

value: atypical lipoma with partly dedifferentiated areas


title: NusG ChIP-chip in E. coli K-12 MG1655 HA3::nusG cells (Dataset 62261)

description: NusG ChIP-chip in E. coli K-12 MG1655 HA3::nusG cells using monoclonal antibody 12CA5.

source_name: NusG ChIP in E. coli K-12 MG1655 HA3::nusG cells

tag: Monoclonal antibody for HA (12CA5)

source_name: Genomic DNA control from E. coli K-12 MG1655 HA3::nusG cells


title: Synchronized cells, 120 min, biological replicate I | array yoL_14T

status: Public on Oct 04 2008

city: Worcester

first: Oliver

last: Rando

state: MA

address: 364 Plantation St.

institute: UMass Medical School

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 120 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

hyb_protocol: Labeled samples were combined, concentrated in Microcon YM-30 columns, and hybridized to the microarrays in 3.4X SSC and 0.3% SDS for 16 hours at 65 degrees.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner at 5 micron resolution and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

data_processing: After background correction and removal of flagged values, data was block normalized by dilation and log base 2 expression ratios (Cy5/Cy3) were calculated to produce the values given in the data table.  The Cy5/Cy3 ratio represents the fold change in expression level for the indicated time point relative to unsynchronized cells growing in mid-log phase.

organism: Saccharomyces cerevisiae

source_name: Mid-log mRNA (unsynchronized)

label_protocol: The mRNA was reverse-transcribed, incorporating amino-allyl dUTP and then coupled with Cy3 NHS ester, and cleaned up with the Qiagen MinElute kit.

extract_protocol: Cells were lysed in a buffered SDS solution and extracted twice with hot phenol and once with chloroform, and then precipiated with 0.1 volume sodium acetate and 2.5 volumes of 100% ethanol.  Total RNA pellets were washed and resuspended, and mRNA was purified using the Qiagen Oligotex kit following manuf. instructions.

tag: Strain

source_name: 120 min

label_protocol: The mRNA was reverse-transcribed, incorporating amino-allyl dUTP and then coupled with Cy5 NHS ester, and cleaned up with the Qiagen MinElute kit.


title: Synchronized cells, 170 min, biological replicate I | array yoL_16B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 170 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 170 min


title: Synchronized cells, 160 min, biological replicate I | array yoL_16T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 160 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 160 min


title: Synchronized cells, 80 min, biological replicate I | array yoL_12T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 80 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 80 min


title: Synchronized cells, 140 min, biological replicate I | array yoL_15T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 140 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 140 min


title: Synchronized cells, 50 min, biological replicate I | array yoL_10B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 50 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 50 min


title: Synchronized cells, 40 min, biological replicate I | array yoL_10T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 40 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 40 min


title: Synchronized cells, 60 min, biological replicate I | array yoL_11T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 60 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 60 min


title: Bcell-lowBMD-7

status: Public on Jun 01 2008

city: Omaha

first: Peng

last: Xiao

state: NE

address: 601 N 30th ST Suite 6730

department: Biomedical Sciences & Osteoporosis Research Center

institute: Creighton University Medical Center

description: Gene expression data from low BMD  postmenopausal females

hyb_protocol: Following fragmentation cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The probe level data generated by Microarray Suite 5.0 (MAS 5.0, Affymetrix) CEL files were converted into expression measures and normalized by Robust Multiarray Algorithm using the Affy package from Bioconductor in R environment.Transformed data were analyzed by Bioconductor's Multtest package to identify differentially expressed genes between the high and the low BMD subgroups using t-statistics. Benjamini and Hochberg (BH) stepwise procedure was used for multiple-testing adjustment and FDR (false discovery rate)<0.05 was used as the significant criterion.

source_name: B cells in blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA from B cells was extracted using Qiagen Rneasy Mini Kit (Qiagen Inc.,CA)

treatment_protocol: B cells isolated from 70mL of whole blood using a B cells positive method Dynabeads CD19 (Pan B)Kit (Invitrogen Life Technologies Dynal Biotech Inc.,CA) following manufacturer's instructions.

tag: postmenopause, age=59,Spine Z-score=-0.52,Hip Z-score=-0.89


title: Bcell-lowBMD-10

tag: postmenopause, age=56,Spine Z-score=-0.73,Hip Z-score=-0.65


title: Synchronized cells, 90 min, biological replicate I | array yoL_12B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 90 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 90 min


title: Synchronized cells, 70 min, biological replicate I | array yoL_11B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 70 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 70 min


title: Synchronized cells, 110 min, biological replicate I | array yoL_13B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 110 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 110 min


title: Synchronized cells, 130 min, biological replicate I | array yoL_14B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 130 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 130 min


title: Synchronized cells, 100 min, biological replicate I | array yoL_13T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 100 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 100 min


title: Bcell-lowBMD-9

tag: postmenopause, age=59,Spine Z-score=-2.26,Hip Z-score=-1.31


title: Synchronized cells, 150 min, biological replicate I | array yoL_15B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 150 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 150 min


title: Patient no. 1: treated

description: Gene expression data from primary liposarcom cultures incubated with doxorubicin (0.5 µg/ml) for 24 h

source_name: Liposarcoma culture from tumor 314, doxorubicin treated

tag: Sex

tag: Age at operation


title: Bcell-lowBMD-8

tag: postmenopause, age=56,Spine Z-score=0.3,Hip Z-score=-0.61


title: Patient no. 6: control

description: Gene expression data from primary liposarcom cultures incubated with PBS as control for 24 h

source_name: Liposarcoma culture from tumor 379, untreated

value: 58 years

tag: Site

value: pelvis retroperitoneal

tag: Size in cm

tag: Histological Subtype

value: myxoid/roundcell liposarcoma

value: high

value: metastasis


title: Bcell-lowBMD-2

tag: postmenopause, age=56,Spine Z-score=-1.62,Hip Z-score=-1.15


title: Bcell-lowBMD-5

tag: postmenopause, age=58,Spine Z-score=-0.7,Hip Z-score=-0.47


title: Synchronized cells, 0 min, biological replicate I | array yoL_08T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were immediately harvested, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: Mid-log mRNA (unsynchronized)

source_name: 0 min


title: Synchronized cells, 20 min, biological replicate I | array yoL_09T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 20 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 20 min


title: Bcell-lowBMD-3

tag: postmenopause, age=58,Spine Z-score=-1.3,Hip Z-score=-1.16


title: Bcell-highBMD-9

description: Gene expression data from high BMD postmenopausal females

tag: postmenopause, age=55,Spine Z-score=2.74,Hip Z-score=1.19


title: Bcell-lowBMD-4

tag: postmenopause, age=59,Spine Z-score=0.16,Hip Z-score=-0.9


title: Bcell-highBMD-8

tag: postmenopause, age=58,Spine Z-score=1.84,Hip Z-score=0.57


title: Bcell-lowBMD-1

tag: postmenopause, age=58,Spine Z-score=-0.9,Hip Z-score=-0.77


title: Synchronized cells, 10 min, biological replicate I | array yoL_08B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 10 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

tag: Strain

source_name: 10 min


title: Bcell-highBMD-6

tag: postmenopause, age=54,Spine Z-score=2.09,Hip Z-score=3.07


title: Bcell-highBMD-7

tag: postmenopause, age=54,Spine Z-score=2.25,Hip Z-score=2.56


title: Bcell-highBMD-10

tag: postmenopause, age=58,Spine Z-score=1.94,Hip Z-score=1.93


title: Bcell-highBMD-5

tag: postmenopause, age=58,Spine Z-score=1.23,Hip Z-score=0.80


title: Bcell-highBMD-4

tag: postmenopause, age=60,Spine Z-score=1.91,Hip Z-score=2.41


title: L.major LV39 promastigote vs intracellular amastigote_replicate 2

status: Public on May 28 2008

city: Quebec

first: Barbara

last: Papadopoulou

state: Quebec

address: 2705 boulevard Laurier

country: Canada

institute: Centre de Recherche du CHUL

description: Biological replicate 2 of 4  (dye-swap)

hyb_protocol: Prehybridization and hybridization were performed at 42°C. Slides were prehybridized in 5X Denhardt, 30% formamide, 6X SSPE, 0,5% SDS, 100µg/ml salmon sperm DNA. Then, slides were washed . For hybridization, labelled cDNA probes were dried and resuspended in 2,5X Denhardt, 30% formamide, 6X SSPE, 0,5% SDS, 100µg/ml salmon sperm DNA, 750µg/ml Yeast tRNA. then mixed. Mixed probes were applied on the array under a lifterslip. Hybridization was performed for 16h.

scan_protocol: The Perkin Elmer ScanArray 4000XL Scanner was used for image acquisition. GenePix Pro 6.0 image analysis software (Axon Instruments) was used to quantify the fluorescence signal intensities of the array features

data_processing:
Raw data from GenePix were imported in R 2.2.1 for normalization and statistical analyses were performed using the LIMMA (version 2.7.3) package.
Intra-array normalization was carried out using the ‘print-tip loess’ statistical method and inter-array normalization was done by using the ‘quantiles of A’ method for each array (Yang, 2003).
Multiple testing corrections were done using the FDR method with a threshold p-value of 0.05. Only genes statistically significant with an absolute log ratio greater than 0.58 (log2 1.5) were considered as differentially expressed
Data table VALUE column represents normalized log2 (amastigote/promastigote) ratios.

organism: Leishmania major

label_protocol: 10 µg of RNA were converted to aminoallyl-dUTP incorporated cDNA using random hexamers (GEHealthcare) and the SuperScript III RNase H- Reverse Transcriptase (Invitrogen). Probes were thereafter coupled to the fluorescent dye Alexa Fluor555 or Alexa Fluor647 (Invitrogen) following manufacturer recommendations. Fluorescent probes were then purified with MinElute Spin Columns (QIAGEN) and quantified spectrophotometrically.

growth_protocol: Promastigote cells were grown in SDM-79 medium supplemented with 10% heat-inactivated fetal bovine serum and 5 µg/ml hemin at 25 °C. Amastigote cells were isolated from mice infected.

extract_protocol: Total RNA was isolated from 108 Leishmania cells during the mid-log phase (promastigote) or after 6 weeks of mice infection (amastigote) using RNeasy Plus Mini Kit (QIAGEN) as described by the manufacturer. The RNA preparation was treated with TURBO DNase (Ambion) to avoid any genomic contamination

tag: strain

tag: promastigote stage, replicate 2

tag: intracellular amastigote stage, replicate 2


title: L. infantum MOHM/MA/67/ITMAP-263 promastigote vs intracellular amastigote_replicate 1

description: Biological replicate 1 of 6

hyb_protocol: Prehybridization and hybridization were performed at 42°C. Slides were prehybridized in 5X Denhardt, 30% formamide, 6X SSPE, 0,5% SDS, 100µg/ml salmon sperm DNA. Then, slides were washed . For hybridization, labelled cDNA probes were dried and resuspended in 2,5X Denhardt, 30% formamide, 6X SSPE, 0,5% SDS, 100µg/ml salmon sperm DNA, 750µg/ml Yeast tRNA, and then mixed. Mixed probes were applied on the array under a lifterslip. Hybridization was performed for 16h.

scan_protocol: The Perkin Elmer ScanArray 4000XL Scanner was used for image acquisition. GenePix Pro 6.0 image analysis software (Axon Instruments) was used to quantify the fluorescence signal intensities of the array features.

data_processing:
Raw data from GenePix were imported in R 2.2.1 for normalization, and statistical analyses were performed using the LIMMA (version 2.7.3) package.
Intra-array normalization was carried out using the ‘print-tip loess’ statistical method and inter-array normalization was done by using the ‘quantiles of A’ method for each array (Yang, 2003).
Multiple testing corrections were done using the FDR method with a threshold p-value of 0.05. Only genes statistically significant with an absolute log ratio greater than 0.75 (log2 1.7) were considered as differentially expressed
Data table VALUE column represents normalized log2 (amastigote/promastigote) ratios.

organism: Leishmania infantum

growth_protocol: Promastigote cells were grown in SDM-79 medium supplemented with 10% heat-inactivated fetal bovine serum and 5 µg/ml hemin at 25 °C. Amastigote cells were grown in THP-1 macrophage in RMPI 1640 medium supplemented with 10% heat-inactivated fetal bovine.

extract_protocol: Total RNA was isolated from 108 Leishmania cells during the mid-log phase (promastigote) or after 4 days macrophage infection (amastigote) using RNeasy Plus Mini Kit (QIAGEN) as described by the manufacturer. The RNA preparation was treated with TURBO DNase (Ambion) to avoid any genomic contamination

tag: promastigote stage, replicate 1

tag: intracellular amastigote stage, replicate 1


title: L.major LV39 promastigote vs intracellular amastigote_replicate 3

description: Biological replicate 3 of 4

tag: promastigote stage, replicate 3

tag: intracellular amastigote stage, replicate 3


title: L. infantum MOHM/MA/67/ITMAP-263 promastigote vs intracellular amastigote_replicate 2

description: Biological replicate 2 of 6  (dye-swap)


title: Exon4_3

status: Public on Mar 20 2006

city: Cincinnati

first: James

middle: Patrick

last: Bridges

state: OH

address: 3333 Burnet Avenue

department: Pulmonary Biology

institute: Cincinnati Children's Hospital Medical Center

description: stably transfected with delta exon4 mutant of surfactant protein C

hyb_protocol: accroding to manufacture's protocol (Affymetrix)

data_processing: RMA normalization, Permutation and ANOVA

source_name: HEK293 cell line


title: L. infantum MOHM/MA/67/ITMAP-263 promastigote vs intracellular amastigote_replicate 5

description: Biological replicate 5 of 6  (dye-swap)

tag: promastigote stage, replicate 5

tag: intracellular amastigote stage, replicate 5


title: Bcell-highBMD-1

tag: postmenopause, age=57,Spine Z-score=2.28,Hip Z-score=1.46


title: EVcontrol1

description: stably transfected with empty vector (pTRE2-Hyg)

scan_protocol: accroding to manufacture's protocol (Affymetrix)


title: L. infantum MOHM/MA/67/ITMAP-263 promastigote vs intracellular amastigote_replicate 6

description: Biological replicate 6 of 6

tag: promastigote stage, replicate 6

tag: intracellular amastigote stage, replicate 6


title: Bcell-highBMD-2

tag: postmenopause, age=57,Spine Z-score=2.37,Hip Z-score=0.97


title: L.major LV39 promastigote vs intracellular amastigote_replicate 1

description: Biological replicate 1 of 4


title: L. infantum MOHM/MA/67/ITMAP-263 promastigote vs intracellular amastigote_replicate 4

description: Biological replicate 4 of 6  (dye-swap)

tag: promastigote stage, replicate 4

tag: intracellular amastigote stage, replicate 4


title: EVcontrol2

label_protocol: accroding to manufacture's protocol (Affymetrix)

tag: stably transfected with empty vector (pTRE2-Hyg)


title: EVcontrol3

extract_protocol: accroding to manufacture's protocol (Affymetrix)


title: L.major LV39 promastigote vs intracellular amastigote_replicate 4

description: Biological replicate 4 of 4  (dye-swap)


title: Exon4_2

tag: stably transfected with delta exon4 mutant of surfactant protein C


title: Exon4_1


title: L. infantum MOHM/MA/67/ITMAP-263 promastigote vs intracellular amastigote_replicate 3

description: Biological replicate 3 of 6


title: Bcell-highBMD-3

tag: postmenopause, age=57,Spine Z-score=1.66,Hip Z-score=1.29


title: Bcell-lowBMD-6

tag: postmenopause, age=60,Spine Z-score=-0.2,Hip Z-score=-0.88


title: WT3

description: stably transfected with wild-type surfactant protein C


title: Exon4_2B

description: stably transfected with delta exon 4 mutant of surfactant protein C


title: Exon4_3B

tag: stably transfected with delta exon 4 mutant of surfactant protein C


title: WT2

tag: stably transfected with wild-type surfactant protein C


title: WT1

data_processing: RMA Normalization, Permutation and Anova


title: EVcontrol3_B


title: EVcontrol2_B


title: Exon4_1B


title: EVcontrol1_B


title: WT2_B


title: WT3_B


title: WT1_B


title: nHR4

status: Public on Feb 24 2005

city: Boston

first: Wenzhong Xiao

address: 55 Fruit Street, GRV 1302

department: Department of Surgery

institute: Massachusetts General Hospital

description: T Cell and monocyte populations, leukocyte or leukocyte subpopulations

source_name: Stratagene Human Reference RNA


title: nHC1


title: 8779590


title: nHR3


title: 10750331


title: nHC2


title: 24057954


title: 35017567


title: Synchronized cells, 30 min, biological replicate I | array yoL_09B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 30 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

tag: Strain

source_name: 30 min


title: control patient 1, chip A

status: Public on Jan 27 2009

city: Glasgow

first: Suzanne

last: Hagan

state: Lanarkshire

address: Cowcaddens Road

department: Biological Sciences

country: United Kingdom

institute: Glasgow Caledonian University

description: Gene expression data from PBMC.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C onto GeneChip HG-U133A and HG-U133B chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Arrays were scanned using the GeneChip Scanner 2500.

data_processing: The raw data were generated with GeneChip Operating Software (GCOS). Data was normalised with Robust Multichip Average (RMA) method using Bioconductor module Affy implemented into the automated FunAlyse pipeline in the Sir Henry Wellcome Functional Genomics Facility. Differential expression was calculated using RankProducts method, separately for each A and B chip.

source_name: PBMC, control

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

extract_protocol: Total RNA was isolated from PBMC pellets following the detailed manufacturer’s protocols in the Promega RNAgents Total Isolation System.

treatment_protocol: Patients with CFS and normal healthy controls underwent venous blood sample collection (prior to 11am) in 2x5ml EDTA tubes. PBMC were isolated immediately and stored within 2 hours of sampling. EDTA-treated whole blood was diluted 1:1 with phosphate-buffered saline (PBS). Two volumes of blood were overlaid onto one volume Histopaque-1077 (Sigma) and centrifuged at 20oC, 500g for 30 min. The PBMC interfaces were washed twice with PBS and the pellets were re-suspended in PBS. Aliquots were counted and dry pellets (2x105 cells) were stored under liquid nitrogen.

tag: Male, healthy normal control


title: Pancreatic Islets_18h culture_30 mmol/l glucose_rep4

status: Public on Jan 26 2009

city: Brussels

first: Jean-Christophe

last: Jonas

address: Av. Hippocrate, 55

department: Physiology and Pharmacology

country: Belgium

institute: UCL, Faculty of Medicine

description: Before the experiment, the islets were precultured for 1 week in serum-free RPMI medium containing 5 g/l BSA and 10 mmol/l glucose

hyb_protocol: Fragmented cRNA was hybridized 16h at 45°C to a Rat Genome 230 2.0 array.

scan_protocol: After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin and scanned using the Affymetrix 3000 GeneScanner.

data_processing: Raw data were analyzed using the Affymetrix GCOS software. Signal intensities were scaled using the global scaling method of the statistical expression algorithm taking 150 as target intensity value. Scaling factors were less than 3 times different from each other in all used arrays.

organism: Rattus norvegicus

source_name: Pancreatic islets, 18h culture, 30 mmol/l glucose

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

growth_protocol: After isolation, the islets were precultured for 1 week in serum-free RPMI medium containing 5 g/l BSA and 10 mmol/l glucose. The medium was renewed after 24h, then every 48h.

extract_protocol: Islet total RNA was extracted using the Absolutely microprep kit (Stratagene, city, CA, USA) following manufacturer’s instructions.

treatment_protocol: After preculture, the islets were cultured 18h in serum-free RPMI medium containing 5 g/l BSA and 2, 5, 10 or 30 mmol/l glucose (1000 islets per condition).

value: Wistar (male)

tag: Weight


title: H3K4me2 patterns in DKO

status: Public on Jan 20 2009

city: Ghent

first: Leander

last: Van Neste

address: Coupure Links 653

department: Molecular Biotechnology

institute: Ghent University

hyb_protocol: Labeled DNA was mixed (5 – 6 µg each of immunoenriched and whole cell extract DNA) and hybridized to arrays in Agilent hybridization chambers for 20 hours at 40°C.

scan_protocol: Hybridized microarrays were scanned using an Agilent G2565BA microarray scanner.

data_processing: Median blanks subtraction followed by an inter-array median normalization and a dye-bias median normalization. Downstream analysis in R.

source_name: DKO Immunoprecipitated DNA

label_protocol: Bioprime random primer labeling kits

growth_protocol: McCoy’s 5A modified medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol: Multiple phenol:chloroform:isoamyl alcohol extractions

treatment_protocol: ChIP DNA using a H3K4me2 specific antibody

tag: Immunoprecipitation using a specific antibody for H3K4me2 of the DKO human colorectal cancer cell line

source_name: DKO WCE

treatment_protocol: Whole cell extract

tag: Whole cell extract of the DKO human colorectal cancer cell line