title: Rep2_Hi-PFOA_Cy3

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping. Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents. Each reaction was spiked with a range of concentrations (0.0049 – 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene). Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label. cDNA from two of the three biological replicates were dye-swapped and hybridized to two slides as technical replicates. cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control. Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation. The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardt’s solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH). Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation. Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays. Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier. Slide# Omy005.P94.13171495


title: Rep1_Hi-PFOA_Cy3

status: Public on Aug 31 2007

type: RNA

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

country: USA

institute: Oregon State University

description:
1800 ppm PFOA treatment - rep1
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping. Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents. Each reaction was spiked with a range of concentrations (0.0049 – 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene). Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label. cDNA from two of the three biological replicates were dye-swapped and hybridized to two slides as technical replicates. cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control. Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation. The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardt’s solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH). Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation. Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays. Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier. Slide# Omy005.P94.13171484

scan_protocol: Scanned images (5 um) were acquired with ScanArray Express (PerkinElmer, Boston, MA) at an excitation of 543 nm for Cy3 and 633 nm for Cy5 and at 90% power. The photomultiplier tube (PMT) settings for each fluor were set based on intensity of spiked internal alien controls to normalize among all slides in the experiment. Image files were quantified in QuantArray (PerkinElmer) and raw median signal and background values were exported to BioArray Software Environment (BASE; Saal et al. 2002) for analysis.

data_processing: Raw mean signal and background values are included. For experiment, data were background subtracted and normalized by LOWESS. Stringent criteria were used to filter for genes that were regulated at least 1.8-fold consistently in all features from biological replicates (n=3 per treatment) and had a p-value <0.05 by Welch’s t-test.

molecule: total RNA

organism: Oncorhynchus mykiss

source_name: 1800 ppm PFOA Liver

label_protocol: Labeled using Genisphere Array 350 kit adapted from manufacturer protocol.

treatment_protocol: Juvenile trout, 12-18 months old, were maintained in separate 375-L tanks (n=3 tanks) for each treatment with 5 fish per tank.  Animals were fed a maintenance ration (2.8% w/w) of experimental diets containing 1800 ppm PFOA for 14 days.  On day 15, fish were euthanized by deep anesthesia with 250 ppm tricaine methanesulfonate.  Approximately 100 mg liver tissue from individual fish was minced, stored in TRIzol Reagent (Invitrogen, Carlsbad, CA) and quick frozen in liquid nitrogen for gene expression analysis.

tag: Strain

value: Mt. Shasta

tag: Age

value: 12-18 months

tag: Tissue

value: liver

tag: Treatment

value: 1800 ppm PFOA

source_name: Reference

treatment_protocol: Juvenile trout, 12-18 months old, were maintained in separate 375-L tanks (n=3 tanks) for each treatment with 5 fish per tank.  Animals were fed a maintenance ration (2.8% w/w) of experimental diets containing 0.15% DMSO for 14 days.  On day 15, fish were euthanized by deep anesthesia with 250 ppm tricaine methanesulfonate.  Approximately 100 mg liver tissue from individual fish was minced, stored in TRIzol Reagent (Invitrogen, Carlsbad, CA) and quick frozen in liquid nitrogen for gene expression analysis.


title: Rep1_E2_Cy5

description:
5 ppm E2 treatment - rep1
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping. Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents. Each reaction was spiked with a range of concentrations (0.0049 – 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene). Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label. cDNA from two of the three biological replicates were dye-swapped and hybridized to two slides as technical replicates. cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control. Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation. The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardt’s solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH). Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation. Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays. Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier. Slide# Omy005.P94.13166412

source_name: 5 ppm E2 Liver

treatment_protocol: Juvenile trout, 12-18 months old, were maintained in separate 375-L tanks (n=3 tanks) for each treatment with 5 fish per tank.  Animals were fed a maintenance ration (2.8% w/w) of experimental diets containing 5 ppm E2 for 14 days.  On day 15, fish were euthanized by deep anesthesia with 250 ppm tricaine methanesulfonate.  Approximately 100 mg liver tissue from individual fish was minced, stored in TRIzol Reagent (Invitrogen, Carlsbad, CA) and quick frozen in liquid nitrogen for gene expression analysis.

value: 5 ppm E2


title: Rep2_E2_Cy5

description:
5 ppm E2 treatment - rep2
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping. Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents. Each reaction was spiked with a range of concentrations (0.0049 – 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene). Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label. cDNA from two of the three biological replicates were dye-swapped and hybridized to two slides as technical replicates. cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control. Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation. The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardt’s solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH). Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation. Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays. Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier. Slide# Omy005.P94.13171488


title: Rep3_Hi-PFOA_Cy5

description:
1800 ppm PFOA treatment - rep3
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping. Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents. Each reaction was spiked with a range of concentrations (0.0049 – 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene). Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label. cDNA from two of the three biological replicates were dye-swapped and hybridized to two slides as technical replicates. cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control. Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation. The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardt’s solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH). Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation. Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays. Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier. Slide# Omy005.P94.13171125


title: Rep1_E2_Cy3

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping. Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents. Each reaction was spiked with a range of concentrations (0.0049 – 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene). Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label. cDNA from two of the three biological replicates were dye-swapped and hybridized to two slides as technical replicates. cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control. Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation. The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardt’s solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH). Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation. Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays. Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier. Slide# Omy005.P94.13166410

extract_protocol: Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.


title: Rep2_Lo-PFOA_Cy3

description:
500 ppm PFOA treatment - rep2
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping. Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents. Each reaction was spiked with a range of concentrations (0.0049 – 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene). Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label. cDNA from two of the three biological replicates were dye-swapped and hybridized to two slides as technical replicates. cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control. Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation. The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardt’s solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH). Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation. Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays. Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier. Slide# Omy005.P94.13171492

source_name: 500 ppm PFOA Liver

treatment_protocol: Juvenile trout, 12-18 months old, were maintained in separate 375-L tanks (n=3 tanks) for each treatment with 5 fish per tank.  Animals were fed a maintenance ration (2.8% w/w) of experimental diets containing 500 ppm PFOA for 14 days.  On day 15, fish were euthanized by deep anesthesia with 250 ppm tricaine methanesulfonate.  Approximately 100 mg liver tissue from individual fish was minced, stored in TRIzol Reagent (Invitrogen, Carlsbad, CA) and quick frozen in liquid nitrogen for gene expression analysis.

value: 500 ppm PFOA


title: Rep3_Lo-PFOA_Cy5

description:
500 ppm PFOA treatment - rep3
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping. Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents. Each reaction was spiked with a range of concentrations (0.0049 – 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene). Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label. cDNA from two of the three biological replicates were dye-swapped and hybridized to two slides as technical replicates. cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control. Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation. The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardt’s solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH). Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation. Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays. Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier. Slide# Omy005.P94.13171502


title: Rep1_Lo-PFOA_Cy3

description:
500 ppm PFOA treatment - rep1
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping. Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents. Each reaction was spiked with a range of concentrations (0.0049 – 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene). Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label. cDNA from two of the three biological replicates were dye-swapped and hybridized to two slides as technical replicates. cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control. Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation. The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardt’s solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH). Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation. Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays. Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier. Slide# Omy005.P94.13166409

value: 2-18 months


title: Rep1_Lo-PFOA_Cy5

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping. Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents. Each reaction was spiked with a range of concentrations (0.0049 – 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene). Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label. cDNA from two of the three biological replicates were dye-swapped and hybridized to two slides as technical replicates. cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control. Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation. The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardt’s solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH). Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation. Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays. Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier. Slide# Omy005.P94.13166411


title: Rep2_Lo-PFOA_Cy5

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping. Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents. Each reaction was spiked with a range of concentrations (0.0049 – 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene). Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label. cDNA from two of the three biological replicates were dye-swapped and hybridized to two slides as technical replicates. cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control. Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation. The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardt’s solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH). Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation. Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays. Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier. Slide# Omy005.P94.13171494


title: ORMES22_ReplicateC

status: Public on Aug 29 2007

city: Beaverton

first: James

middle: Anthony

last: Byrne

address: 505 NW 185th Ave

department: Reproductive Sciences

institute: ONPRC

description: Probe level measurements produced by Affymetrix Microarray Suite 5.0. Analysis performed at level of raw signal. (See Affymetrix Microarray Suite 5.0 reference on web site for description).

scan_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001).Scanning Hardware – HP GeneArray Scanner

data_processing: MAS 5.0; Data was normalized with Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001). Two .CHP files are provided as supplementary files: one normalized (_GS.CHP) and one not (.CHP).

label: Biotin

organism: Macaca mulatta

source_name: Rhesus monkey IVF-derived embryonic stem cell line ORMES22 biological replicate C

growth_protocol: Embryonic stem cells were grown at 37°C in 5% CO2 atmosphere on mitotically inactivated mouse embryonic fibroblasts (MEF) feeder cells in Dulbecco’s Modified Eagle’s Medium/F12 (DMEM/F12) (Invitrogen) supplemented with 15% foetal bovine serum (FBS) (Hyclone), 0.1 mM ß-mercaptoethanol (Sigma), 1% nonessential amino acids (Invitrogen), 4ng/ml FGF2, 2 mM L-glutamine (Invitrogen) and a pH of 7.2 (altered with 4N NaOH). ES cell colonies were manually passaged every 4-5 days.

extract_protocol: Total RNA was isolated from cell colonies selected for the appropriate ESC morphology (flat monolayer colony with distinctive cobbled stem cell morphology and a high nucleo-cytoplasmic ratio) using the Invitrogen TRIZOL reagent, followed by further purification with the Qiagen RNeasy MinElute Cleanup Kit. The RNA samples were quantified using the NanoDrop ND-1000 UV-Vis spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the quality of the RNA was assessed using Lab-on-a-Chip RNA Pico Chips and the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Embryonic stem cells with good morphology were manually removed from culture for total RNA purification.

tag: Undifferentiated rhesus monkey IVF-derived Oregon Rhesus Macaque Embryonic Stem (ORMES) cell line 22 biological replicate C.


title: CRES2_ReplicateB

hyb_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001)

source_name: Rhesus monkey SCNT-derived embryonic stem cell line CRES2 biological replicate B

tag: Undifferentiated rhesus monkey SCNT-derived Cloned Rhesus Embryonic Stem (CRES) cell line 2 biological replicate B (derived from somatic cell line 19822).


title: ORMES22_ReplicateA

scan_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001). Scanning Hardware – HP GeneArray Scanner

source_name: Rhesus monkey IVF-derived embryonic stem cell line ORMES22 biological replicate A

tag: Undifferentiated rhesus monkey IVF-derived Oregon Rhesus Macaque Embryonic Stem (ORMES) cell line 22 biological replicate A.


title: Geobacter sulfurreducens N2 fixation vs ammonium-amended BR3B

status: Public on Aug 01 2007

city: Amherst

first: Derek

last: Lovley

state: MA

address: University of Massachusetts at Amherst, Dept. of Microbiology, Morrill IV north room 202

department: Microbiology

institute: University of Massachusetts Amherst

description: total RNA was amplified using the Ambion MessageAmp II- Bacteria kit for polyadenylation and subsequent amplification of total RNA.  aRNA was ethanol precipitated and resuspended in nuclease-free water to a total concentration of ~1 ug/ul.

hyb_protocol: Combimatrix 100 ul volume cap.

scan_protocol: Slide was scanned using GenePix software and a GenePix 4000b scanner.

data_processing:
The raw total intensities were treated as follows to generate the M Log2 ratios for this work.  Background signal was calculated from a set of negative control spots incorporated into the array.  As the negative control sequences are not design specific (ie. are found in all of the ESOAs independent of the organism being sampled) some will inevitably demonstrate strong cross hybridization with the sample of interest.  To avoid this issue the negative control spots were ranked according to their total intensity.  The average of the lowest 30% was calculated.  Background signal was calculated as this mean + 2 standard deviations.  The background signal was then subtracted from the total intensity for each spot.  Probes whose signal was not greater than zero after background subtraction were omitted from further analysis.  For the remaining data, the logged ratios [M=log2 (Ex/Ct)] are then calculated and Lowess global normalization is performed. During the data preprocessing, M vs. A plots before and after normalization, and side-by-side box plots for all arrays are used to assess array quality.(3)  LIMMA mixed model analysis (R-package LIMMA(2))is applied to the normalized logged ratios to identify differentially expressed genes.  Specifically, biological replicates are treated as a randomized block to allow for modeling correlations within them. LIMMA calculates a moderated t statistic for each probe, which is the ratio of the estimated mean logged intensity ratio and the Empirical Bayes estimate of its standard error. The P-value of each oligo is then corrected for multiple comparisons according to Benjamini and Hockberg's procedure(1) to control the false discovery rate. Oligos are ranked according to the adjusted P-values and were called differentially expressed if the adjusted P-values are < 0.001.  Note that multiple oligonucleotide probes from the same gene are analyzed separately and a gene is called differentially expressed if at least half of its probes are called differentially expressed.
1.	Benjamini, Y., and Y. Hochberg. 1995. Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B-Methodological 57:289-300.
2.	Smyth, G. K. 2004. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3:Article3.
3.	Smyth, G. K., and T. Speed. 2003. Normalization of cDNA microarray data. Methods 31:265-73.

organism: Geobacter sulfurreducens

source_name: Nitrogen fixation

label_protocol: Micromax ASAP direct RNA labeling protocol

extract_protocol: For reference see:In situ expression of nifD in Geobacteraceae in subsurface sediments. Appl Environ Microbiol. 2004 Dec;70(12):7251-9. PMID: 15574924

tag: Geobacter sulfurreducens was grown anaerobically in chemostats at 0.05 hr-1 in freshwater media with fumarate as the terminal electron acceptor. No ammonia was included in this media.

source_name: Ammonium amended

tag: Geobacter sulfurreducens was grown anaerobically in chemostats at 0.05 hr-1 in freshwater media with fumarate as the terminal electron acceptor. Ammonia was included in this media.


title: Geobacter sulfurreducens N2 fixation vs ammonium-amended BR1B


title: ORMES10_ReplicateB

source_name: Rhesus monkey IVF-derived embryonic stem cell line ORMES10 biological replicate B

label_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001)

tag: Undifferentiated rhesus monkey IVF-derived Oregon Rhesus Macaque Embryonic Stem (ORMES) cell line 10 biological replicate B.


title: CRES1_ReplicateB

source_name: Rhesus monkey SCNT-derived embryonic stem cell line CRES1 biological replicate B

tag: Undifferentiated rhesus monkey SCNT-derived Cloned Rhesus Embryonic Stem (CRES) cell line 1 biological replicate B (derived from somatic cell line 19822).


title: Geobacter sulfurreducens N2 fixation vs ammonium-amended BR2B


title: CRES1_ReplicateA

source_name: Rhesus monkey SCNT-derived embryonic stem cell line CRES1 biological replicate A

tag: Undifferentiated rhesus monkey SCNT-derived Cloned Rhesus Embryonic Stem (CRES) cell line 1 biological replicate A (derived from somatic cell line 19822).


title: CRES2_ReplicateC

source_name: Rhesus monkey SCNT-derived embryonic stem cell line CRES2 biological replicate C

tag: Undifferentiated rhesus monkey SCNT-derived Cloned Rhesus Embryonic Stem (CRES) cell line 2 biological replicate C (derived from somatic cell line 19822).


title: Somatic_cell_line_19822_ReplicateA

source_name: Rhesus monkey adult skin fibroblast somatic cell line 19822 biological replicate A

growth_protocol: Somatic cells were grown at 37°C in 5% CO2 atmosphere in Dulbecco’s Modified Eagle’s Medium (DMEM) (Invitrogen) supplemented with 10% foetal bovine serum (FBS).

extract_protocol: Total RNA was isolated from complete dishes of 90% confluent somatic cells using the Invitrogen TRIZOL reagent, followed by further purification with the Qiagen RNeasy MinElute Cleanup Kit. The RNA samples were quantified using the NanoDrop ND-1000 UV-Vis spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the quality of the RNA was assessed using Lab-on-a-Chip RNA Pico Chips and the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Cells were manually removed from culture with a cell scraper without using trypsin.

tag: A differentiated rhesus monkey adult skin fibroblast somatic cell line derived from a nine year old adult male animal (Oregon National Primate Research Center ID:19822).  Biological replicate A.


title: CRES2_ReplicateA

source_name: Rhesus monkey SCNT-derived embryonic stem cell line CRES2 biological replicate A

tag: Undifferentiated rhesus monkey SCNT-derived Cloned Rhesus Embryonic Stem (CRES) cell line 2 biological replicate A (derived from somatic cell line 19822).


title: ORMES10_ReplicateC

source_name: Rhesus monkey IVF-derived embryonic stem cell line ORMES10 biological replicate C

tag: Undifferentiated rhesus monkey IVF-derived Oregon Rhesus Macaque Embryonic Stem (ORMES) cell line 10 biological replicate C.


title: CRES1_ReplicateC

source_name: Rhesus monkey SCNT-derived embryonic stem cell line CRES1 biological replicate C

tag: Undifferentiated rhesus monkey SCNT-derived Cloned Rhesus Embryonic Stem (CRES) cell line 1 biological replicate C (derived from somatic cell line 19822).


title: Prostate_Adenocarcinoma_GOG0301DF1T10

type: genomic

city: Philadelphia

first: Carmen

middle: Elisa

last: Oquendo

state: PA

address: 421 Curie Blvd

institute: University of Pennsylvania

hyb_protocol: Equal amounts of test and reference DNA (1ug each), labeled with opposite dyes, were mixed and precipitated with Cot1-DNA, 3M NaOAc (pH 7.0) and ethanol.  Arrays were hybridized with 50% deionized formamide, 2xSSC, 2% SDS, 10% dextran sulfate and 100μg/μl

scan_protocol: All arrays were scanned in a GenePix 4000B scanner and were analyzed with GenePix Pro 5.0 (Axon instruments, USA).

data_processing: Data was processed through print-tip normalization (lowess) and only consistent within slide and dye swap replicates (with distance to median < 0.4) were averaged and used for further analysis.  The log2 ratios were centered on the mean of each array and copy number aberration (CNA) was determined using a segmentation algorithm called Analysis of Copy Errors (ACE).

molecule: genomic DNA

organism: Homo sapiens

source_name: Genomic DNA from Prostate Adenocarcinoma

label_protocol: DNA samples were hybridized in dye swap to the BAC-CGH array.  Labeling was carried out with either Cy3-dCTP or Cy5-dCTP using the BioPrime labeling Kit.  The reaction was cleaned with Qiagen MiniElute PCR kit.

growth_protocol: Serial sections were cut and preserved in eppendorff tubes (identified as to their origin between levels).  Every 20th section was stained with H&E and only tissue from between levels revealing adequate amounts of tumor was used for further analysis.  The procedure ensured maximum concentration of tumor and minimum intervening stroma.

extract_protocol: Test DNA was extracted from fresh frozen cut tissue sections with Proteinase K and was purified with Phase Lock gels using PCI (25 Phenol: 24 chloroform: 1 isoamyl alcohol) and CI (24 chloroform:1 isoamyl alcohol).  Precipitation of DNA was carried out wi

tag: Organism Part

value: Prostate

tag: Disease State

value: Adenocarcinoma

tag: BioSourceType

tag: Sex

value: Male

tag: BioSource Provider

value: Hospital of the Unversity of Pennsylvania

tag: PSA

tag: Androgen Ablation

value: no

tag: Gleason Score

tag: Pathology Stage

tag: Capsule

value: Extensive

tag: Months to recurrence

tag: Months of follow up

tag: Male Healthy donors

tag: Blood

tag: Periphereal Leukocytes


title: ORMES10_ReplicateA

source_name: Rhesus monkey IVF-derived embryonic stem cell line ORMES10 biological replicate A

tag: Undifferentiated rhesus monkey IVF-derived Oregon Rhesus Macaque Embryonic Stem (ORMES) cell line 10 biological replicate A.


title: Somatic_cell_line_19822_ReplicateB

source_name: Rhesus monkey adult skin fibroblast somatic cell line 19822 biological replicate B

tag: A differentiated rhesus monkey adult skin fibroblast somatic cell line derived from a nine year old adult male animal (Oregon National Primate Research Center ID:19822).  Biological replicate B.


title: ORMES22_ReplicateB

source_name: Rhesus monkey IVF-derived embryonic stem cell line ORMES22 biological replicate B

tag: Undifferentiated rhesus monkey IVF-derived Oregon Rhesus Macaque Embryonic Stem (ORMES) cell line 22 biological replicate B.


title: Prostate_Adenocarcinoma_GOG0231DF1T10

tag: Organism Part

tag: Disease State

value: Intact


title: Somatic_cell_line_19822_ReplicateC

source_name: Rhesus monkey adult skin fibroblast somatic cell line 19822 biological replicate C

tag: A differentiated rhesus monkey adult skin fibroblast somatic cell line derived from a nine year old adult male animal (Oregon National Primate Research Center ID:19822).  Biological replicate C.


title: Prostate_Adenocarcinoma_GOG0304DF1T10

tag: BioSourceType

tag: Sex

tag: BioSource Provider

value: Focal


title: Prostate_Adenocarcinoma_GOG0232DF1T10

tag: PSA

tag: Androgen Ablation

tag: Gleason Score


title: Geobacter sulfurreducens N2 fixation vs ammonium-amended BR3A

tag: Geobacter sulfurreducens was grown anaerobically in chemostats at 0.05 hr-1 in freshwater media with fumarate as the terminal electron acceptor. No ammonia was included in this media.

tag: Geobacter sulfurreducens was grown anaerobically in chemostats at 0.05 hr-1 in freshwater media with fumarate as the terminal electron acceptor. Ammonia was included in this media.


title: Geobacter sulfurreducens N2 fixation vs ammonium-amended BR2A


title: Prostate_Adenocarcinoma_GOG0223DF1T10

tag: Pathology Stage

tag: Capsule

tag: Months to recurrence

tag: Months of follow up

tag: Male Healthy donors


title: Prostate_Adenocarcinoma_GOG0226DF1T10

tag: Blood

tag: Periphereal Leukocytes


title: Prostate_Adenocarcinoma_GOG0151DF1T10

tag: Organism Part

tag: Disease State


title: Prostate_Adenocarcinoma_GOG0221DF4T10

tag: BioSourceType


title: Prostate_Adenocarcinoma_GOG0157DF1T10

tag: Sex

tag: Months to recurrence:N/A


title: Prostate_Adenocarcinoma_GOG0192DF4T10

tag: BioSource Provider

tag: PSA

value: yes


title: Prostate_Adenocarcinoma_GOG0222DF1T10

tag: Androgen Ablation

tag: Gleason Score


title: Prostate_Adenocarcinoma_GOG0140DF1T10


title: Prostate_Adenocarcinoma_GOG0098DF2T10

tag: Months to recurrence:64


title: Geobacter sulfurreducens N2 fixation vs ammonium-amended BR1A

tag: Geobacter sulfurreducens was grown anaerobically in chemostats at 0.05 hr-1 in freshwater media with fumarate as the terminal electron acceptor. No ammonia was included in this media.

tag: Geobacter sulfurreducens was grown anaerobically in chemostats at 0.05 hr-1 in freshwater media with fumarate as the terminal electron acceptor. Ammonia was included in this media.


title: Prostate_Adenocarcinoma_GOG0155DF1T10

tag: Pathology Stage

tag: Capsule

tag: Months to recurrence


title: Prostate_Adenocarcinoma_GOG0171DF1T10

tag: Months of follow up

tag: Male Healthy donors

tag: Blood


title: Prostate_Adenocarcinoma_GOG0061DF3T10

tag: Organism Part

tag: Disease State

tag: Periphereal Leukocytes


title: Prostate_Adenocarcinoma_GOG0191DF2T10

tag: BioSourceType

tag: Sex


title: Prostate_Adenocarcinoma_GOG0164DF1T10

tag: BioSource Provider

tag: PSA


title: Prostate_Adenocarcinoma_GOG0025DF1T10

tag: Androgen Ablation

tag: Gleason Score

tag: Months to recurrence:99


title: Prostate_Adenocarcinoma_GOG0031DF2T10

tag: Months to recurrence:N/A


title: Prostate_Adenocarcinoma_GOG0041DF1T10

tag: Pathology Stage

tag: Months to recurrence:33


title: su(Hw)v heterozygote wing disc 1

status: Public on Jul 31 2007

city: Cambridge

first: Steve

last: Russell

address: Downing Street

department: Department of Genetics

country: United Kingdom

institute: University of Cambridge

description: An analysis of the effects of loss of Su(Hw) function on gene expression in Drosophila larvae. All comparisons are made against a pool of wild type larval RNA. Due the genetic background issues a su(Hw) null was generated by crossing a null allele with a deletion. Controls compare the heterozgous su(Hw)v and heterozygous deletion larvae with the pool. Timing is synchrionised by collecting soft whitte pre-pupae.

hyb_protocol: Genomics Solution GeneTAC hybridisation station with Ocimum hybridisation buffer. Hybridisation and washing described in detail at http://www.flychip.org.uk/protocols/hybridisation/hyb_oligoMWG.php

scan_protocol: Axon 4000B scanner using standard protocols (http://www.flychip.org.uk/protocols/imaging/scanning2.php)

data_processing:
Spot finding and quantitation via the Dapple package.
Normalisation accross the 4 biological replicates for all 3 conditions (null and both heterozygotes) using VSN. Normalised ratio 'M' (asinh transform functionally equivalent to the log[2] ratio) is given in the VALUE column and the normalised average intensity in the 'A' column. See http://www.flychip.org.uk/services/analysis/ for details and references

organism: Drosophila melanogaster

source_name: wild type wing disc pool

label_protocol: Synthesis of double stranded cDNA followed by klenow labelling as described (http://www.flychip.org.uk/protocols/gene_expression/klenow.php).  2 microgrammes of total RNA were labelled for each reaction.

extract_protocol: 6 wing imaginal discs dissected from wild type soft white prepupae were Trizol extracted using the small scale procedure described at (http://www.flychip.org.uk/protocols/gene_expression/small_extraction.php). RNA from 20 extractions was combined to generate a pooled sample. All wing disc experiments were preformed using this pool.

tag: pool of RNA extracted from wing imaginal discs disected from wild type (Oregon R) soft white prepupae.

source_name: w; Su(Hw)v, cas X/K/Or

extract_protocol: 6 wing imaginal discs dissected from soft white prepupae were Trizol extracted using the small scale procedure described at (http://www.flychip.org.uk/protocols/gene_expression/small_extraction.php). Cross Oregon R with w; su(Hw)v, p[CasX/K]/TM6B, Tb

tag: Wing discs dissected from su(Hw) heterozygotes mutant soft white prepupae.


title: Df(3R)ED5644 heterozygote wing disc 1

extract_protocol: 6 wing imaginal discs dissected from soft white prepupae were Trizol extracted using the small scale procedure described at (http://www.flychip.org.uk/protocols/gene_expression/small_extraction.php). Cross Oregon R with Df(3R)ED5644/TM6B, Tb

tag: Wing discs dissected from Df(3R)ED5644 heterozygotes mutant soft white prepupae.


title: Df(3R)ED5644 heterozygote wing disc 3


title: su(Hw)v heterozygote wing disc 3

tag: wild type wing disc pool

source_name: w; su(Hw)v,


title: su(Hw)v heterozygote wing disc 4


title: Df(3R)ED5644 heterozygote wing disc 2


title: su(Hw) null L3 4

source_name: wild type pool

label_protocol: Standard direct incorporation of Cy dyes during 1st strand cDNA synthesis (http://www.flychip.org.uk/protocols/gene_expression/direct_labelling.php) using 50 microgrammes of total RNA

extract_protocol: arge scale Trizol extraction (http://www.flychip.org.uk/protocols/gene_expression/large_extraction.php). 120 microgrammes of total RNA was taken from each of 18 different collections and pooled yielding a total of 2.1 mg of RNA. This was used for all experiments.

tag: RNA from a pool of Oregon R 3rd instar larvae

extract_protocol: Non-Tubby larvae were collected from bottles with a brush when they just just stopped moving to ensure that they were at the white pre-pupa stage and therefore all of a similar age. Larvae were placed in tubes on ice until there were 10 or 20 larvae (~5mins), Trizol added, the samples were homogenised and stored at -80oC until extraction. Cross Df(3R)ED5644/TM6B, Tb with w; su(Hw)v, p[CasX/K]/TM6B, Tb

tag: RNA from soft white prepupae mutant for supressor of hairy wing (su(Hw))


title: Df(3R)ED5644 heterozygote wing disc 4


title: su(Hw) null wing disc 1

extract_protocol: 6 wing imaginal discs dissected from wild type soft white prepupae were Trizol extracted using the small scale procedure described at (http://www.flychip.org.uk/protocols/gene_expression/small_extraction.php).  RNA from 20 extractions was combined to generate a pooled sample.  All wing disc experiments were preformed using this pool.

source_name: w; Su(Hw)v, cas X/K/Df(3R)ED5644

extract_protocol: 6 wing imaginal discs dissected from soft white prepupae were Trizol extracted using the small scale procedure described at (http://www.flychip.org.uk/protocols/gene_expression/small_extraction.php). Cross Df(3R)ED5644/TM6B, Tb with w; su(Hw)v,

tag: Wing discs dissected from su(Hw) null mutant soft white prepupae.


title: su(Hw) null wing disc 3

extract_protocol: 6 wing imaginal discs dissected from soft white prepupae were Trizol extracted using the small scale procedure described at (http://www.flychip.org.uk/protocols/gene_expression/small_extraction.php). Cross Df(3R)ED5644/TM6B, Tb with w; su(Hw)v, p[CasX/K]/TM6B, Tb


title: su(hw)-Df heterozygote 4

extract_protocol: Large scale Trizol extraction (http://www.flychip.org.uk/protocols/gene_expression/large_extraction.php). 120 microgrammes of total RNA was taken from each of 18 different collections and pooled yielding a total of 2.1 mg of RNA. This was used for all experiments.

extract_protocol: Non-Tubby larvae were collected from bottles with a brush when they just just stopped moving to ensure that they were at the white pre-pupa stage and therefore all of a similar age. Larvae were placed in tubes on ice until there were 10 or 20 larvae (~5mins), Trizol added, the samples were homogenised and stored at -80oC until extraction. Cross Oregon R with Df(3R)ED5644/TM6B, Tb

tag: RNA from soft white pre-pupae heterozygous for Df(3R)ED5644


title: su(Hw) heterozygote L3 4

extract_protocol: Non-Tubby larvae were collected from bottles with a brush when they just just stopped moving to ensure that they were at the white pre-pupa stage and therefore all of a similar age. Larvae were placed in tubes on ice until there were 10 or 20 larvae (~5mins), Trizol added, the samples were homogenised and stored at -80oC until extraction. Cross Oregon R with w; su(Hw)v, p[CasX/K]/TM6B, Tb

tag: RNA from Soft white prepupae heterozygous for su(hw)v


title: su(Hw)v heterozygote wing disc 2

tag: pool of RNA extracted from wing imaginal discs disected from wild type (Oregon R) soft white prepupae


title: su(Hw) null wing disc 2

extract_protocol: 6 wing imaginal discs dissected from soft white prepupae were Trizol extracted using the small scale procedure described at (http://www.flychip.org.uk/protocols/gene_expression/small_extraction.php). Cross Df(3R)ED5644/TM6B, Tb with w; su(Hw)v,p[CasX/K]/TM6B, Tb


title: su(Hw) null L3 2

source_name: Wild type pool

extract_protocol: Non-Tubby larvae were collected from bottles with a brush when they just just stopped moving to ensure that they were at the white pre-pupa stage and therefore all of a similar age. Larvae were placed in tubes on ice until there were 10 or 20 larvae (~5mins), Trizol added, the samples were homogenised and stored at -80oC until extraction. Cross Df(3R)ED5644/TM6B, Tb with ; su(Hw)v, p[CasX/K]/TM6B, Tb


title: su(hw)-Df heterozygote 2


title: su(hw)-Df heterozygote 3


title: su(Hw) null L3 3


title: su(Hw)v heterozygote L3 1

source_name: w; su(Hw)v, p[CasX/K]/Or


title: su(Hw) null L3 1

description: An analysis of the effects of loss of Su(Hw) function on gene expression in Drosophila larvae.  All comparisons are made against a pool of wild type larval RNA.  Due the genetic background issues a su(Hw) null was generated by crossing a null allele with a deletion.  Controls compare the heterozgous su(Hw)v and heterozygous deletion larvae with the pool.  Timing is synchrionised by collecting soft whitte pre-pupae.

hyb_protocol: Genomics Solution GeneTAC hybridisation station with Ocimum hybridisation buffer.  Hybridisation and washing described in detail at http://www.flychip.org.uk/protocols/hybridisation/hyb_oligoMWG.php

data_processing:
Spot finding and quantitation via the Dapple package.
Normalisation accross the 4 biological replicates for all 3 conditions (null and both heterozygotes) using VSN.  Normalised ratio 'M' (asinh transform functionally equivalent to the log[2] ratio) is given in the VALUE column and the normalised average intensity in the 'A' column.  See http://www.flychip.org.uk/services/analysis/ for details and references

extract_protocol: Non-Tubby larvae were collected from bottles with a brush when they just just stopped moving to ensure that they were at the white pre-pupa stage and therefore all of a similar age.  Larvae were placed in tubes on ice until there were 10 or 20 larvae (~5mins), Trizol added, the samples were homogenised and stored at -80oC until extraction.  Cross Df(3R)ED5644/TM6B, Tb with TM6B, Tb/w; Su(Hw)v, cas X/K/TM6B, Tb

extract_protocol: Large scale Trizol extraction (http://www.flychip.org.uk/protocols/gene_expression/large_extraction.php).  120 microgrammes of total RNA was taken from each of 18 different collections and pooled yielding a total of 2.1 mg of RNA.  This was used for all experiments.


title: su(Hw)v heterozygote L3 2


title: su(Hw) heterozygote L3 3


title: 12 hour Guanosin and Mycophenolic acid (MPA) treated human fibroblasts (MG12h)

status: Public on Jul 29 2007

city: Heidelberg

first: Hendrik

last: Reuter

department: Moleculare Genetics B060

country: Germany

institute: DKFZ

description:
Total RNA was extracted using RNeasy Mini Kit (Quiagen, Hilden, Germany) according to manufacturer's instructions.
2µg total RNA was amplified and labeled using TAcKLE Protocol (PMID: 15718295).

hyb_protocol: aRNA produced by T7 amplification was reversely transcribed and subsequently labeled using Klenow fragment and Cy-dUTPs. Hybridization was carried out at 37 °C in UltraHyb buffer (Ambion) on a GeneTAC hybridization station (Genomic Solutions).

scan_protocol: hybridised arrays werde scaned using an Axon 4000B microarray scanner from Axon Instruments applying GenePix Pro 5.0 software

data_processing: spot replicates were averaged. Spots not recognized by the image analysis software "GenePix Pro 5.0" (Axon Instruments) were excluded from the calculations. Raw fluorescence intensities were normalized applying the variance stabilization method (W. Huber et al., Bioinformatics 18 Suppl. 1, 2002). To eliminate low quality data, the data points were ranked according to spot homogeneity, as assayed by the ratio of median to mean fluorescence intensity, the ratio of spot to local background intensity and the standard deviation of the log2 ratios between spot replicates. Those data points ranked among the lower 20% were removed from the data set. Genes that could not be quantified in more than 33% of all experiments of the experimental series after filtering were excluded as well.

label: Cy3, Cy5

source_name: 2µg total RNA from 12h Guanosin and Mycophenolic acid (MPA) treated human fibroblasts

label_protocol: see Description

extract_protocol: see Description

tag: FCS-stimulated human fibroblasts treated  with Guanosin and Mycophenolic acid (MPA) for 12h

source_name: 2µg total RNA from untreated human fibroblasts

tag: untreated FCS-stimulated human fibroblasts


title: su(hw)-Df heterozygote 1

tag: RNA from soft white prepupae heterozygous for Df(3R)ED5644


title: Gra_F1_A

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

description: The aim of this study was to assess the impact of oocyte competence on subsequent fertility. Based on knowledge already accessible in mammals and on bioinformatics tools including the chicken genome sequence, we focused on the expression of genes involved in the processes of fertilization and of early embryo development. The study was performed using two complementary approaches, a descriptive study of standard laying hens and then a differential study performed with hens from experimental lines expressing broad variations of achieved fertility :approximately 20per cent.A differential kinetic study is performed on INRA lines selected on the basis of their fertility potential in purpose of hopefully access gene markers of fertility performance.

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

organism: Gallus gallus

label_protocol: labelling Biotin direct, amplification=yes, RNAa 20 ug.

growth_protocol: ovary - light 14 L _ 10 D - 14h and dark during 10h food : ad libitum aliment standard, pondeuse 5S temperature: 20degreeC

treatment_protocol: no treatment

tag: Gallus gallus  - age:55weekdev.stage (Boyes et al. Plant Cell 2001):gra f1 1 (granulosa cells collected at the f1 stage)


title: 12 hour Mycophenolic acid (MPA) treated human fibroblasts (M12h)

source_name: 2µg total RNA from 12h Mycophenolic acid (MPA) treated human fibroblasts

tag: FCS-stimulated human fibroblasts treated  with Mycophenolic acid (MPA) for 12h


title: 12 hour Guanosin treated human fibroblasts (G12h)

source_name: 2µg total RNA from 12h Guanosin treated human fibroblasts

tag: FCS-stimulated human fibroblasts treated  with Guanosin for 12h


title: 20 minute Guanosin and Mycophenolic acid (MPA) treated human fibroblasts (MG20min)

source_name: 2µg total RNA from 20 minutes Guanosin and Mycophenolic acid (MPA) treated human fibroblasts

tag: FCS-stimulated human fibroblasts treated  with Guanosin and Mycophenolic acid (MPA) for 20 minutes


title: ov

source_name: ov

tag: Gallus gallus  - age:55weekdev.stage (Boyes et al. Plant Cell 2001):just ovulated oocyte


title: 1 hour Mycophenolic acid (MPA) treated human fibroblasts (M1h)

source_name: 2µg total RNA from 1h Mycophenolic acid (MPA) treated human fibroblasts

tag: FCS-stimulated human fibroblasts treated  with Mycophenolic acid (MPA) for 1h


title: 36 hour Guanosin and Mycophenolic acid (MPA) treated human fibroblasts (MG36h)

source_name: 2µg total RNA from 36h Guanosin and Mycophenolic acid (MPA) treated human fibroblasts

tag: FCS-stimulated human fibroblasts treated  with Guanosin and Mycophenolic acid (MPA) for 36h


title: su(Hw) null wing disc 4

tag: pool of RNA extracted from wing imaginal discs disected from wild type (Oregon R) soft white prepupae.


title: F1_A

tag: Gallus gallus  - age:55weekdev.stage (Boyes et al. Plant Cell 2001):f1-a (24 hours before ovulation)


title: 36 hour Mycophenolic acid (MPA) treated human fibroblasts (M36h)

source_name: 2µg total RNA from 36h Mycophenolic acid (MPA) treated human fibroblasts

tag: FCS-stimulated human fibroblasts treated  with Mycophenolic acid (MPA) for 36h


title: 1 hour Guanosin treated human fibroblasts (G1h)

source_name: 2µg total RNA from 1h Guanosin treated human fibroblasts

tag: FCS-stimulated human fibroblasts treated  with Guanosin for 1h


title: ov_A


title: F1


title: 20 minute Mycophenolic acid (MPA) treated human fibroblasts (M20min)

source_name: 2µg total RNA from 20 minutes Mycophenolic acid (MPA) treated human fibroblasts

tag: FCS-stimulated human fibroblasts treated  with Mycophenolic acid (MPA) for 20 minutes


title: 1 hour Guanosin and Mycophenolic acid (MPA) treated human fibroblasts (MG1h)

source_name: 2µg total RNA from 1h Guanosin and Mycophenolic acid (MPA) treated human fibroblasts

tag: FCS-stimulated human fibroblasts treated  with Guanosin and Mycophenolic acid (MPA) for 1h


title: Gra_F1


title: 20 minute Guanosin treated human fibroblasts (G20min)

source_name: 2µg total RNA from 20 minutes Guanosin treated human fibroblasts

tag: FCS-stimulated human fibroblasts treated  with Guanosin for 20 minutes


title: 36 hour Guanosin treated human fibroblasts (G36h)

source_name: 2µg total RNA from 36h Guanosin treated human fibroblasts

tag: FCS-stimulated human fibroblasts treated  with Guanosin for 36h


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 33 of 37

status: Public on Jul 28 2007

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Drive

department: Department of Cellular and Molecular Medicine

institute: Ludwig Institute for Cancer Research

description: Chromatin immunoprecipitation was performed using antibodies against Pol2 and formaldehyde crosslinked chromatin from kidney cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5) that contains non-overlapping 50-mer oligonucleotides, positioned at every 100 basepairs (bp)

hyb_protocol: NimbleGen hybridization protocol

scan_protocol: NimbleGen scan protocol

data_processing: Genome-wide array sets (1-37) for all tissues were loess normalized using the R package limma.

organism: Mus musculus

source_name: Chromatin immunoprecipitated DNA from kidney cells using Pol2 antibody

extract_protocol: immunoprecipitated chromatin

tag: cells

value: kidney immunoprecipitated chromatin

source_name: Input Chromatin kidney cells.

extract_protocol: input chromatin

value: kidney input chromatin


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 33 of 37

description: Chromatin immunoprecipitation was performed using antibodies against Pol2 and formaldehyde crosslinked chromatin from liver cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5) that contains non-overlapping 50-mer oligonucleotides, positioned at every 100 basepairs (bp)

source_name: Chromatin immunoprecipitated DNA from liver cells using Pol2 antibody

value: liver immunoprecipitated chromatin

source_name: Input Chromatin liver cells.

value: liver input chromatin


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 31 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 35 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 35 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 31 of 37

description: Chromatin immunoprecipitation was performed using antibodies against Pol2 and formaldehyde crosslinked chromatin from ES cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5) that contains non-overlapping 50-mer oligonucleotides, positioned at every 100 basepairs (bp)

source_name: Chromatin immunoprecipitated DNA from ES cells using Pol2 antibody

value: ES immunoprecipitated chromatin

source_name: Input Chromatin ES cells.

value: ES input chromatin


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 27 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 35 of 37

description: Chromatin immunoprecipitation was performed using antibodies against Pol2 and formaldehyde crosslinked chromatin from heart cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5) that contains non-overlapping 50-mer oligonucleotides, positioned at every 100 basepairs (bp)

source_name: Chromatin immunoprecipitated DNA from heart cells using Pol2 antibody

value: heart immunoprecipitated chromatin

source_name: Input Chromatin heart cells.

value: heart input chromatin


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 33 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 35 of 37

description: Chromatin immunoprecipitation was performed using antibodies against Pol2 and formaldehyde crosslinked chromatin from brain cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5) that contains non-overlapping 50-mer oligonucleotides, positioned at every 100 basepairs (bp)

source_name: Chromatin immunoprecipitated DNA from brain cells using Pol2 antibody

value: brain immunoprecipitated chromatin

source_name: Input Chromatin brain cells.

value: brain input chromatin


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 27 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 27 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 25 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 25 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 18 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 35 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 27 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 25 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 18 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 27 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 33 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 31 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 25 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 31 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 18 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 18 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 25 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 16 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 18 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 33 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 16 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 31 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 11 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 16 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 11 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 9 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 11 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 16 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 9 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 16 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 7 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 7 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 9 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 7 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 9 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 2 of 37


title: mes H3K4me3 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 3 of 4

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3 and formaldehyde crosslinked chromatin from mes cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5) that contains non-overlapping 50-mer oligonucleotides, positioned at every 100 basepairs (bp)

data_processing: Condensed array sets (1-4) for all tissues were either loess normalized or median normalized using the R package limma with the normalization using the RANDOM_GC probes.

source_name: Chromatin immunoprecipitated DNA from mes cells using H3K4me3 antibody

value: mes immunoprecipitated chromatin

source_name: Input Chromatin mes cells.

value: mes input chromatin


title: mes Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 3 of 4

description: Chromatin immunoprecipitation was performed using antibodies against Pol2 and formaldehyde crosslinked chromatin from mes cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5) that contains non-overlapping 50-mer oligonucleotides, positioned at every 100 basepairs (bp)

source_name: Chromatin immunoprecipitated DNA from mes cells using Pol2 antibody


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 9 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 7 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 2 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 2 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 2 of 37


title: liver H3Ac Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 3 of 4

description: Chromatin immunoprecipitation was performed using antibodies against H3Ac and formaldehyde crosslinked chromatin from liver cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5) that contains non-overlapping 50-mer oligonucleotides, positioned at every 100 basepairs (bp)

source_name: Chromatin immunoprecipitated DNA from liver cells using H3Ac antibody


title: mes H3Ac Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 3 of 4

description: Chromatin immunoprecipitation was performed using antibodies against H3Ac and formaldehyde crosslinked chromatin from mes cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5) that contains non-overlapping 50-mer oligonucleotides, positioned at every 100 basepairs (bp)

source_name: Chromatin immunoprecipitated DNA from mes cells using H3Ac antibody


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 11 of 37


title: liver H3K4me3 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 3 of 4

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3 and formaldehyde crosslinked chromatin from liver cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5) that contains non-overlapping 50-mer oligonucleotides, positioned at every 100 basepairs (bp)

source_name: Chromatin immunoprecipitated DNA from liver cells using H3K4me3 antibody


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 3 of 4


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 2 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 11 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 7 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 3 of 4


title: heart H3K4me3 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 3 of 4

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3 and formaldehyde crosslinked chromatin from heart cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5) that contains non-overlapping 50-mer oligonucleotides, positioned at every 100 basepairs (bp)

source_name: Chromatin immunoprecipitated DNA from heart cells using H3K4me3 antibody


title: kidney H3K4me3 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 3 of 4

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3 and formaldehyde crosslinked chromatin from kidney cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5) that contains non-overlapping 50-mer oligonucleotides, positioned at every 100 basepairs (bp)

source_name: Chromatin immunoprecipitated DNA from kidney cells using H3K4me3 antibody


title: kidney H3Ac Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 3 of 4

description: Chromatin immunoprecipitation was performed using antibodies against H3Ac and formaldehyde crosslinked chromatin from kidney cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5) that contains non-overlapping 50-mer oligonucleotides, positioned at every 100 basepairs (bp)

source_name: Chromatin immunoprecipitated DNA from kidney cells using H3Ac antibody

source_name: Input Chromatin kidney cells.


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 3 of 4


title: brain H3Ac Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 3 of 4

description: Chromatin immunoprecipitation was performed using antibodies against H3Ac and formaldehyde crosslinked chromatin from brain cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5) that contains non-overlapping 50-mer oligonucleotides, positioned at every 100 basepairs (bp)

source_name: Chromatin immunoprecipitated DNA from brain cells using H3Ac antibody


title: brain H3K4me3 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 3 of 4

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3 and formaldehyde crosslinked chromatin from brain cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5) that contains non-overlapping 50-mer oligonucleotides, positioned at every 100 basepairs (bp)

source_name: Chromatin immunoprecipitated DNA from brain cells using H3K4me3 antibody


title: mes Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 1 of 4


title: kidney H3Ac Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 1 of 4


title: liver H3K4me3 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 1 of 4

source_name: Input Chromatin liver cells.


title: heart H3Ac Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 3 of 4

description: Chromatin immunoprecipitation was performed using antibodies against H3Ac and formaldehyde crosslinked chromatin from heart cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5) that contains non-overlapping 50-mer oligonucleotides, positioned at every 100 basepairs (bp)

source_name: Chromatin immunoprecipitated DNA from heart cells using H3Ac antibody


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 1 of 4

source_name: Chromatin immunoprecipitated DNA from kidney cells using Pol2 antibody


title: liver H3Ac Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 1 of 4


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 1 of 4

source_name: Chromatin immunoprecipitated DNA from liver cells using Pol2 antibody


title: liver H3K4me3 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 4 of 4


title: mes H3K4me3 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 1 of 4


title: mes Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 4 of 4


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 4 of 4


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 1 of 4

source_name: Chromatin immunoprecipitated DNA from heart cells using Pol2 antibody

source_name: Input Chromatin heart cells.


title: heart H3Ac Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 1 of 4


title: mes H3Ac Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 4 of 4

source_name: Input Chromatin mes cells.


title: mes H3Ac Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 1 of 4


title: kidney H3K4me3 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 1 of 4


title: brain H3Ac Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 1 of 4

source_name: Input Chromatin brain cells.


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 1 of 4

source_name: Chromatin immunoprecipitated DNA from brain cells using Pol2 antibody


title: mes H3K4me3 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 4 of 4

source_name: Chromatin immunoprecipitated DNA from mes cells using H3K4me3 antibody


title: liver H3Ac Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 4 of 4

source_name: Chromatin immunoprecipitated DNA from liver cells using H3Ac antibody


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 4 of 4


title: brain H3K4me3 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 1 of 4


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 4 of 4


title: heart H3K4me3 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 1 of 4

source_name: Chromatin immunoprecipitated DNA from heart cells using H3K4me3 antibody


title: kidney H3Ac Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 4 of 4


title: kidney H3K4me3 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 4 of 4

source_name: Chromatin immunoprecipitated DNA from kidney cells using H3K4me3 antibody


title: mes Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 2 of 4

source_name: Chromatin immunoprecipitated DNA from mes cells using Pol2 antibody


title: brain H3Ac Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 4 of 4


title: heart H3Ac Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 4 of 4


title: brain H3K4me3 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 4 of 4


title: liver H3K4me3 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 2 of 4

source_name: Chromatin immunoprecipitated DNA from liver cells using H3K4me3 antibody


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 4 of 4


title: mes H3K4me3 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 2 of 4


title: heart H3K4me3 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 4 of 4


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 37 of 37

source_name: Input Chromatin kidney cells.


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 2 of 4


title: liver H3Ac Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 2 of 4


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 2 of 4


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 37 of 37


title: kidney H3K4me3 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 2 of 4


title: kidney H3Ac Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 2 of 4

source_name: Chromatin immunoprecipitated DNA from kidney cells using H3Ac antibody


title: heart H3K4me3 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 2 of 4


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 36 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 37 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 2 of 4


title: heart H3Ac Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 2 of 4


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 37 of 37

source_name: Chromatin immunoprecipitated DNA from ES cells using Pol2 antibody

source_name: Input Chromatin ES cells.


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 2 of 4


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 36 of 37

source_name: Chromatin immunoprecipitated DNA from kidney cells using Pol2 antibody


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 37 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 34 of 37

source_name: Chromatin immunoprecipitated DNA from liver cells using Pol2 antibody

source_name: Input Chromatin liver cells.


title: brain H3K4me3 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 2 of 4

source_name: Chromatin immunoprecipitated DNA from brain cells using H3K4me3 antibody


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 36 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 34 of 37


title: brain H3Ac Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 2 of 4

source_name: Chromatin immunoprecipitated DNA from brain cells using H3Ac antibody


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 34 of 37

source_name: Chromatin immunoprecipitated DNA from heart cells using Pol2 antibody

source_name: Input Chromatin heart cells.


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 34 of 37

source_name: Chromatin immunoprecipitated DNA from brain cells using Pol2 antibody

source_name: Input Chromatin brain cells.


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 36 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 32 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 30 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 23 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 30 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 32 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 36 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 34 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 30 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 23 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 32 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 30 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 23 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 23 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 29 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 23 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 22 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 30 of 37


title: mes H3Ac Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 2 of 4

source_name: Chromatin immunoprecipitated DNA from mes cells using H3Ac antibody

source_name: Input Chromatin mes cells.


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 26 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 22 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 26 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 29 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 22 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 32 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 32 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 29 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 29 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 28 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 26 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 21 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 26 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 29 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 24 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 21 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 24 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 28 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 22 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 22 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 24 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 28 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 28 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 21 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 21 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 15 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 26 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 15 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 21 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 24 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 20 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 19 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 24 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 20 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 28 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 19 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 15 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 19 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 20 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 20 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 15 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 19 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 19 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 17 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 17 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 6 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 14 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 14 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 17 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 15 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 17 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 5 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 13 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 14 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 14 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 6 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 20 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 5 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 5 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 10 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 14 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 13 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 13 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 10 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 13 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 10 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 10 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 6 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 6 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 12 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 5 of 37


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 17 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 6 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 13 of 37


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 8 of 37


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 8 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 12 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 12 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 8 of 37


title: BCL6 ChIP replicate 2

status: Public on Jul 07 2007

city: Bronx

first: Ari

last: Melnick

state: NY

address: 1300 Morris Park Ave - Chanin 302

department: Developmental and Molecular Biology

institute: Albert Einstein College of Medicine

description: BCL6 ChIP performed in Ramos cells

hyb_protocol: Samples were hybridized by NimbleGen Systems, Reykjavik, Iceland

scan_protocol: Scan protocol Arrays were scanned and analyzed by NimbleGen Systems, Reykjavik, Iceland

data_processing: The fold enrichment for each probe was calculated as the ratio of Cy5 vs. Cy3 and Any peaks involving >5 probes and with > 2.5 fold enrichment were considered potentially positive hits

source_name: Input DNA

label_protocol: Samples were labeled by NimbleGen Systems, Reykjavik, Iceland

extract_protocol: As described in: Polo, J.M. et al. Specific peptide interference reveals BCL6 transcriptional and oncogenic mechanisms in B-cell lymphoma cells. Nat Med 10, 1329-35 (2004)

tag: Total DNA extracted from Ramos Cells

tag: BCL6 ChIP performed in Ramos cells.


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 12 of 37


title: BCL6 ChIP replicate 1

description: BCL6 ChIP performed in Ramos cells

tag: BCL6 ChIP performed in Ramos


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 4 of 37


title: heart Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 4 of 37


title: MEFF Expression Biological Replicate 1

status: Public on Jul 01 2007

type: mixed

city: Vienna

first: Denise

middle: P.

last: Barlow

address: Dr. Bohrgasse 9/4

department: Austrian Academy of Sciences

country: Austria

institute: Center of Molecular Medicine (CeMM)

description: The input and Poly-A RNA were hybridized to the same microarray. Microarrays were scanned with a Genepix 4000B scanner (Axon Instruments).

data_processing: The unnormalized values represent the 'Ratio of Medians' of each ID on the platform. The average 'Ratio of Medians' was calculated for each PCR_FRAG_ID on the platform and plotted.

label: Alexa 647

molecule: polyA RNA

source_name: Poly-A RNA

tag: 13.5dpc female mouse embryo fibroblast cell line (MEFF). The cells have a maternal deletion of the imprinted Igf2r cluster.

label: Alexa 555

molecule: other

source_name: Input DNA (whole cell extract)


title: kidney Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 1 of 37

description: Chromatin immunoprecipitation was performed using antibodies against Pol2 and formaldehyde crosslinked chromatin from kidney cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5) that contains non-overlapping 50-mer oligonucleotides, positioned at every 100 basepairs (bp)

source_name: Input Chromatin kidney cells.


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 5 of 37


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 3 of 37

description: Chromatin immunoprecipitation was performed using antibodies against Pol2 and formaldehyde crosslinked chromatin from liver cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5) that contains non-overlapping 50-mer oligonucleotides, positioned at every 100 basepairs (bp)


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 10 of 37

description: Chromatin immunoprecipitation was performed using antibodies against Pol2 and formaldehyde crosslinked chromatin from ES cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5) that contains non-overlapping 50-mer oligonucleotides, positioned at every 100 basepairs (bp)

source_name: Chromatin immunoprecipitated DNA from ES cells using Pol2 antibody


title: MEFB1 Expression Biological Replicate 1

tag: 13.5dpc female mouse embryo fibroblast cell line (MEFB1). The cells have a paternal deletion of the imprinted Igf2r cluster.


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 4 of 37


title: Actin ChIP replicate 2

description: Actin ChIP performed in Ramos cells

source_name: Actin Chip product

tag: Actin Chip performed in Ramos cells.


title: MEFF Expression Biological Replicate 2


title: ES Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 12 of 37

source_name: Input Chromatin ES cells.


title: brain Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 1 of 37


title: Murine embyonic pancreas stem cells

status: Public on Jul 11 2007

city: Kobe

first: Yuichi

last: Hori

state: Hyogo

address: 7-5-1 Kusunoki-cho, Chuo-ku

department: Surgery

country: Japan

institute: Kobe University School of Medicine

description: CD133negPDGFRb- cells _CD133highPDGFRb- cells

hyb_protocol: Performed using Gene Expression Hybridization Kit (5188-5242 : Agilent)

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1.3).

data_processing: Dye biases between two signals, Red and Green, were corrected using Lowess normalization, subtracted background and converted to log10 of processed Red signal/processed Green signal.

source_name: Total RNA from murine CD133negPDGFRb- cells labeled with Cyanine-5 (red).

label_protocol: Sample labeling was done using Agilent’s Low RNA Fluorescent Linear Amplification Kit PLUS (5188-5340: Agilent) following manufacture’s instructions. Amplified cRNAs were quantified using the Agilent 2100 bioanalyzer and RNA 6000 Nano kit.

extract_protocol: Total RNAs were extracted using RNAeasy Micro Kit (QIAGEN) following manufacturer’s instructions.

treatment_protocol: To isolate CD133highPDGFRb- cells and CD133negPDGFRb- cells, 500 of embryonic day 13.5 fetal pancreases were obtained, digested in 0.04 units Liberase Blenzyme 3 (Roche) at 37℃ for 5 min, then triturated in low glucose DMEM media containing 0.2% bovine serum albumin. After staining with monoclonal antibodies, these cells were subjected to FACS cell sorting and each fraction was collected to extract total RNA.

tag: Pancreas

source_name: Total RNA from murine CD133highPDGFRb- cells labeled with Cyanine-3 (green).


title: Actin ChIP replicate 3

description: Actin ChIP performed in Ramos cells

tag: Actin ChIP performed in Ramos cells.


title: BCL6 ChIP replicate 3

description: BCL6 ChIP performed in Ramos cells