title: occipital visual neocortex, right, biological rep4

description: exon-level analysis

source_name: occipital visual neocortex, right


title: parietal association neocortex, right, biological rep4

status: Public on May 18 2009

type: RNA

city: New Haven

first: Matthew

middle: Bonser

last: Johnson

state: CT

address: 333 Cedar St., SHM C-316

department: Neurobiology

country: USA

institute: Yale University School of Medicine

description: exon-level analysis

hyb_protocol: Samples were hybridized according to Affymetrix protocols

scan_protocol: Affymetrix Gene Chip Scanner 3000

data_processing: Data were processed using Partek Genomics Suite. Core probesets were imported using RMA defaults with probe GC content correction

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: parietal association neocortex, right

label_protocol: Samples were treated with the RNeasy Mini Kit (Qiagen) to exclude smaller RNAs, and fragmented and labeled using the Affymetrix Whole Transcript Sense Target Labeling Assay.

growth_protocol: not applicable

extract_protocol: Samples were dissected from late 2nd trimester human brains obtained from the Albert Einstein College of Medicine Human Fetal Tissue Repository and total RNA isolated using TRIzol.

treatment_protocol: not applicable

tag: Age

value: 23 weeks gestation

tag: Post-Mortem Interval <1hr


title: hippocampus, right, biological rep4

description: exon-level analysis

source_name: hippocampus, right


title: mediodorsal thalamus, left, biological rep3

description: exon-level analysis

source_name: mediodorsal thalamus, left

value: 21 weeks gestation


title: cerebellum, biological rep4

description: exon-level analysis

source_name: cerebellum


title: dorsolateral prefrontal neocortex, left, biological rep4

description: exon-level analysis

source_name: dorsolateral prefrontal neocortex, left


title: temporal auditory neocortex, right, biological rep4

description: exon-level analysis

source_name: temporal auditory neocortex, right


title: hippocampus, left, biological rep4

description: exon-level analysis

source_name: hippocampus, left


title: ventrolateral prefrontal neocortex, right, biological rep3

description: exon-level analysis


title: ventrolateral prefrontal neocortex, left, biological rep3

description: exon-level analysis


title: dorsolateral prefrontal neocortex, right, biological rep4

description: exon-level analysis


title: medial prefrontal neocortex, left, biological rep4

description: exon-level analysis

source_name: medial prefrontal neocortex, left


title: temporal association cortex, left, biological rep3

description: exon-level analysis

source_name: temporal association cortex, left


title: medial prefrontal neocortex, left, biological rep3

description: exon-level analysis


title: parietal association neocortex, left, biological rep3

description: exon-level analysis

source_name: parietal association neocortex, left


title: motor-somatosensory neocortex, left, biological rep3

description: exon-level analysis

source_name: motor-somatosensory neocortex, left


title: occipital visual neocortex, left, biological rep3

description: exon-level analysis

source_name: occipital visual neocortex, left


title: medial prefrontal neocortex, right, biological rep3

description: exon-level analysis

source_name: medial prefrontal neocortex, right


title: dorsolateral prefrontal neocortex, left, biological rep3

description: exon-level analysis


title: parietal association neocortex, left, biological rep2

description: exon-level analysis

value: 19 weeks gestation


title: striatum: putamen and caudate nucleus, right, biological rep3

description: exon-level analysis


title: hippocampus, left, biological rep3

description: exon-level analysis


title: hippocampus, right, biological rep3

description: exon-level analysis


title: parietal association neocortex, right, biological rep2

description: exon-level analysis


title: mediodorsal thalamus, right, biological rep2

description: exon-level analysis

source_name: mediodorsal thalamus, right


title: cerebellum, biological rep3

description: exon-level analysis


title: occipital visual neocortex, right, biological rep3

description: exon-level analysis


title: mediodorsal thalamus, left, biological rep2

description: exon-level analysis


title: motor-somatosensory neocortex, right, biological rep3

description: exon-level analysis

source_name: motor-somatosensory neocortex, right


title: temporal association cortex, right, biological rep2

description: exon-level analysis

source_name: temporal association cortex, right


title: temporal association cortex, left, biological rep2

description: exon-level analysis


title: ventrolateral prefrontal neocortex, right, biological rep2

description: exon-level analysis


title: striatum: putamen and caudate nucleus, left, biological rep2

description: exon-level analysis


title: orbital prefrontal neocortex, left, biological rep2

description: exon-level analysis

source_name: orbital prefrontal neocortex, left


title: parietal association neocortex, right, biological rep3

description: exon-level analysis

source_name: parietal association neocortex, right


title: striatum: putamen and caudate nucleus, left, biological rep3

description: exon-level analysis


title: ventrolateral prefrontal neocortex, left, biological rep2

description: exon-level analysis


title: striatum: putamen and caudate nucleus, right, biological rep2

description: exon-level analysis


title: temporal auditory neocortex, right, biological rep3

description: exon-level analysis


title: orbital prefrontal neocortex, right, biological rep2

description: exon-level analysis

source_name: orbital prefrontal neocortex, right


title: ventrolateral prefrontal neocortex, right, biological rep4

description: gene-level analysis


title: temporal auditory neocortex, left, biological rep3

description: exon-level analysis

source_name: temporal auditory neocortex, left


title: mediodorsal thalamus, left, biological rep4

description: gene-level analysis

source_name: mediodorsal thalamus, left


title: motor-somatosensory neocortex, right, biological rep2

description: exon-level analysis


title: mediodorsal thalamus, right, biological rep4

description: gene-level analysis


title: striatum: putamen and caudate nucleus, right, biological rep4

description: gene-level analysis


title: temporal association cortex, right, biological rep4

description: gene-level analysis


title: temporal association cortex, left, biological rep4

description: gene-level analysis


title: occipital visual neocortex, right, biological rep4

description: gene-level analysis

source_name: occipital visual neocortex, right


title: striatum: putamen and caudate nucleus, left, biological rep4

description: gene-level analysis


title: occipital visual neocortex, right, biological rep2

description: exon-level analysis


title: occipital visual neocortex, left, biological rep4

description: gene-level analysis


title: parietal association neocortex, left, biological rep4

description: gene-level analysis


title: parietal association neocortex, right, biological rep4

description: gene-level analysis


title: motor-somatosensory neocortex, left, biological rep4

description: gene-level analysis


title: medial prefrontal neocortex, right, biological rep4

description: gene-level analysis


title: motor-somatosensory neocortex, right, biological rep4

description: gene-level analysis


title: ventrolateral prefrontal neocortex, left, biological rep4

description: gene-level analysis


title: medial prefrontal neocortex, right, biological rep2

description: exon-level analysis


title: dorsolateral prefrontal neocortex, right, biological rep3

description: exon-level analysis


title: motor-somatosensory neocortex, left, biological rep2

description: exon-level analysis


title: hippocampus, right, biological rep2

description: exon-level analysis

source_name: hippocampus, right


title: hippocampus, left, biological rep2

description: exon-level analysis

source_name: hippocampus, left


title: medial prefrontal neocortex, left, biological rep2

description: exon-level analysis

source_name: medial prefrontal neocortex, left


title: hippocampus, right, biological rep4

description: gene-level analysis


title: medial prefrontal neocortex, left, biological rep4

description: gene-level analysis


title: hippocampus, left, biological rep4

description: gene-level analysis


title: occipital visual neocortex, left, biological rep2

description: exon-level analysis


title: cerebellum, left, biological rep2

description: exon-level analysis

source_name: cerebellum, left


title: temporal auditory neocortex, right, biological rep2

description: exon-level analysis

source_name: temporal auditory neocortex, right


title: dorsolateral prefrontal neocortex, right, biological rep2

description: exon-level analysis


title: ventrolateral prefrontal neocortex, right, biological rep1

description: exon-level analysis

value: 18 weeks gestation


title: dorsolateral prefrontal neocortex, right, biological rep4

description: gene-level analysis


title: temporal auditory neocortex, right, biological rep4

description: gene-level analysis


title: cerebellum, right, biological rep2

description: exon-level analysis

source_name: cerebellum, right


title: cerebellum, biological rep4

description: gene-level analysis

source_name: cerebellum


title: dorsolateral prefrontal neocortex, left, biological rep2

description: exon-level analysis

source_name: dorsolateral prefrontal neocortex, left


title: temporal auditory neocortex, left, biological rep2

description: exon-level analysis


title: ventrolateral prefrontal neocortex, left, biological rep3

description: gene-level analysis


title: ventrolateral prefrontal neocortex, right, biological rep3

description: gene-level analysis


title: temporal auditory neocortex, left, biological rep4

description: gene-level analysis


title: dorsolateral prefrontal neocortex, left, biological rep4

description: gene-level analysis


title: mediodorsal thalamus, right, biological rep3

description: gene-level analysis

source_name: mediodorsal thalamus, right


title: temporal association cortex, right, biological rep1

description: exon-level analysis


title: ventrolateral prefrontal neocortex, left, biological rep1

description: exon-level analysis


title: temporal association cortex, left, biological rep1

description: exon-level analysis

source_name: temporal association cortex, left


title: mediodorsal thalamus, left, biological rep1

description: exon-level analysis


title: striatum: putamen and caudate nucleus, right, biological rep3

description: gene-level analysis


title: parietal association neocortex, right, biological rep1

description: exon-level analysis


title: temporal association cortex, right, biological rep3

description: gene-level analysis

source_name: temporal association cortex, right


title: temporal association cortex, left, biological rep3

description: gene-level analysis


title: striatum: putamen and caudate nucleus, right, biological rep1

description: exon-level analysis


title: parietal association neocortex, left, biological rep1

description: exon-level analysis

source_name: parietal association neocortex, left


title: striatum: putamen and caudate nucleus, left, biological rep3

description: gene-level analysis


title: mediodorsal thalamus, left, biological rep3

description: gene-level analysis


title: parietal association neocortex, left, biological rep3

description: gene-level analysis


title: occipital visual neocortex, left, biological rep3

description: gene-level analysis

source_name: occipital visual neocortex, left


title: occipital visual neocortex, right, biological rep3

description: gene-level analysis


title: occipital visual neocortex, left, biological rep1

description: exon-level analysis


title: parietal association neocortex, right, biological rep3

description: gene-level analysis

source_name: parietal association neocortex, right


title: motor-somatosensory neocortex, right, biological rep3

description: gene-level analysis

source_name: motor-somatosensory neocortex, right


title: hippocampus, right, biological rep1

description: exon-level analysis


title: medial prefrontal neocortex, left, biological rep1

description: exon-level analysis


title: medial prefrontal neocortex, right, biological rep1

description: exon-level analysis

source_name: medial prefrontal neocortex, right


title: temporal auditory neocortex, right, biological rep1

description: exon-level analysis


title: motor-somatosensory neocortex, left, biological rep3

description: gene-level analysis

source_name: motor-somatosensory neocortex, left


title: medial prefrontal neocortex, right, biological rep3

description: gene-level analysis


title: motor-somatosensory neocortex, right, biological rep1

description: exon-level analysis


title: dorsolateral prefrontal neocortex, left, biological rep1

description: exon-level analysis


title: hippocampus, left, biological rep3

description: gene-level analysis


title: hippocampus, left, biological rep1

description: exon-level analysis


title: hippocampus, right, biological rep3

description: gene-level analysis

source_name: hippocampus, right


title: medial prefrontal neocortex, left, biological rep3

description: gene-level analysis


title: cerebellum, biological rep1

description: exon-level analysis


title: temporal auditory neocortex, right, biological rep3

description: gene-level analysis


title: dorsolateral prefrontal neocortex, left, biological rep3

description: gene-level analysis


title: ventrolateral prefrontal neocortex, left, biological rep2

description: gene-level analysis


title: ventrolateral prefrontal neocortex, right, biological rep2

description: gene-level analysis


title: temporal auditory neocortex, left, biological rep3

description: gene-level analysis

source_name: temporal auditory neocortex, left


title: cerebellum, biological rep3

description: gene-level analysis


title: mediodorsal thalamus, right, biological rep1

description: exon-level analysis


title: dorsolateral prefrontal neocortex, right, biological rep1

description: exon-level analysis


title: temporal auditory neocortex, left, biological rep1

description: exon-level analysis


title: dorsolateral prefrontal neocortex, right, biological rep3

description: gene-level analysis


title: mediodorsal thalamus, right, biological rep2

description: gene-level analysis


title: temporal association cortex, right, biological rep2

description: gene-level analysis


title: temporal association cortex, left, biological rep2

description: gene-level analysis


title: mediodorsal thalamus, left, biological rep2

description: gene-level analysis

source_name: mediodorsal thalamus, left


title: motor-somatosensory neocortex, left, biological rep1

description: exon-level analysis


title: parietal association neocortex, right, biological rep2

description: gene-level analysis


title: striatum: putamen and caudate nucleus, right, biological rep2

description: gene-level analysis


title: striatum: putamen and caudate nucleus, left, biological rep2

description: gene-level analysis


title: orbital prefrontal neocortex, right, biological rep2

description: gene-level analysis

source_name: orbital prefrontal neocortex, right


title: parietal association neocortex, left, biological rep2

description: gene-level analysis


title: orbital prefrontal neocortex, left, biological rep2

description: gene-level analysis

source_name: orbital prefrontal neocortex, left


title: occipital visual neocortex, left, biological rep2

description: gene-level analysis


title: motor-somatosensory neocortex, left, biological rep2

description: gene-level analysis


title: striatum: putamen and caudate nucleus, left, biological rep1

description: exon-level analysis


title: occipital visual neocortex, right, biological rep2

description: gene-level analysis

source_name: occipital visual neocortex, right


title: occipital visual neocortex, right, biological rep1

description: exon-level analysis


title: hippocampus, right, biological rep2

description: gene-level analysis


title: medial prefrontal neocortex, left, biological rep2

description: gene-level analysis

source_name: medial prefrontal neocortex, left


title: dorsolateral prefrontal neocortex, right, biological rep2

description: gene-level analysis


title: medial prefrontal neocortex, right, biological rep2

description: gene-level analysis


title: cerebellum, left, biological rep2

description: gene-level analysis

source_name: cerebellum, left


title: hippocampus, left, biological rep2

description: gene-level analysis

source_name: hippocampus, left


title: ventrolateral prefrontal neocortex, right, biological rep1

description: gene-level analysis


title: temporal auditory neocortex, right, biological rep2

description: gene-level analysis

source_name: temporal auditory neocortex, right


title: motor-somatosensory neocortex, right, biological rep2

description: gene-level analysis


title: dorsolateral prefrontal neocortex, left, biological rep2

description: gene-level analysis

source_name: dorsolateral prefrontal neocortex, left


title: striatum: putamen and caudate nucleus, right, biological rep1

description: gene-level analysis


title: cerebellum, right, biological rep2

description: gene-level analysis

source_name: cerebellum, right


title: temporal association cortex, right, biological rep1

description: gene-level analysis

source_name: temporal association cortex, right


title: mediodorsal thalamus, right, biological rep1

description: gene-level analysis

source_name: mediodorsal thalamus, right


title: ventrolateral prefrontal neocortex, left, biological rep1

description: gene-level analysis


description: gene-level analysis

source_name: striatum: putamen and caudate nucleus, left


title: temporal auditory neocortex, left, biological rep2

description: gene-level analysis


title: parietal association neocortex, right, biological rep1

description: gene-level analysis

source_name: parietal association neocortex, right


description: gene-level analysis


title: temporal association cortex, left, biological rep1

description: gene-level analysis

source_name: temporal association cortex, left


title: parietal association neocortex, left, biological rep1

description: gene-level analysis

source_name: parietal association neocortex, left


title: motor-somatosensory neocortex, left, biological rep1

description: gene-level analysis

source_name: motor-somatosensory neocortex, left


title: motor-somatosensory neocortex, right, biological rep1

description: gene-level analysis

source_name: motor-somatosensory neocortex, right


title: medial prefrontal neocortex, left, biological rep1

description: gene-level analysis


title: occipital visual neocortex, left, biological rep1

description: gene-level analysis

source_name: occipital visual neocortex, left


title: hippocampus, right, biological rep1

description: gene-level analysis

source_name: hippocampus, right


title: hippocampus, left, biological rep1

description: gene-level analysis


title: cerebellum, biological rep1

description: gene-level analysis

source_name: cerebellum


title: dorsolateral prefrontal neocortex, right, biological rep1

description: gene-level analysis


title: temporal auditory neocortex, right, biological rep1

description: gene-level analysis


title: medial prefrontal neocortex, right, biological rep1

description: gene-level analysis

source_name: medial prefrontal neocortex, right


title: HUVEC-Mimic_hypoxia-transcript-rep1

status: Public on Apr 01 2009

city: Beijing

first: Xingyi

last: Hang

address: No. 27 Taiping Road

country: China

institute: Beijing Institute of Radiation Medicine

hyb_protocol: Hybridization to HuEx1.0 microarrays was carried out following the manufacturer’s instructions. 8 μg cRNA were loaded for the second cycle cDNA reaction. Hybridization cocktails containing 3~4 μg fragmented, end-labeled cDNA were applied to GeneChip® Human Exon 1.0 ST arrays. Hybridization was performed for 16 hrs using the MES_EukGE-WS2v5_450-DEV fluidics wash and stain script.

scan_protocol: Scanning of HuEx1.0 microarrays was carried out following the manufacturer’s instructions. Arrays were scanned using the Affymetrix GCS 3000 7G and Gene-Chip Operating Software v1.3 to produce the intensity files.

data_processing: Cell intensity (CEL) file data were quantile-normalized and summarized using the Iterative Probe Logarithmic Intensity Error Estimation (iterPLIER) within Affymetrix Power Tools (APT).

source_name: HUVEC, mimic hypoxia, 24hrs

label_protocol: 1 μg RNA of the sample was processed using the Affymetrix GeneChip® Whole Transcript Sense Target Labeling Assay (Affymetrix, Santa Clara).GeneChip® WT cDNA Synthesis Kit, WT cDNA Amplification Kit, and WT Terminal Labeling Kit (Affymetrix, Inc., Santa Clara, CA) were used for sample preparation.

extract_protocol: Total RNA was extracted from HUVECs using TRIzol reagent according to the manufacturer’s protocols (Invitrogen, Carlsbad, CA).

tag: Human umbilical vein endothelial cells (HUVECs) were treated with cobalt chloride of 300Μm (Sigma) for 24hrs to mimic hypoxia stress.


title: HUVEC-Mimic_hypoxia-transcript-rep2

tag: Human umbilical vein endothelial cells (HUVECs) were treated with cobalt chloride of 300Μm (Sigma) for 24hrs to mimic hypoxia stress. This is one of the three biological replications.


title: dorsolateral prefrontal neocortex, left, biological rep1

description: gene-level analysis


title: temporal auditory neocortex, left, biological rep1

description: gene-level analysis

source_name: temporal auditory neocortex, left


title: HUVEC-normoxia-transcript-rep2

source_name: HUVEC, normoxia, 24hrs

tag: Human umbilical vein endothelial cells (HUVECs) were treated in normoxia for 24hrs as controls. This is one the three biological replications.


title: HUVEC-normoxia-transcript-rep1


title: HUVEC-normoxia-transcript-rep3


title: HUVEC-Mimic_hypoxia-transcript-rep3

tag: Human umbilical vein endothelial cells (HUVECs) were treated with cobalt chloride of 300Μm (Sigma) for 24hrs to mimic hypoxia stress. This is one the three biological replications.


title: 1.0mm Act vs Inact

status: Public on May 01 2009

city: Stanford

first: John

middle: F

last: Fernandes

state: CA

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

description:
Mu active line compared to Mu inactive line at the 1.0mm anther stage
Reps 1-4 (includes 2 dye swaps)
Rep1: Cy3: Anther-1.0mm_2IE1   Cy5: Anther-1.0mm_2AE1
Rep2: Cy3: Anther-1.0mm_2IE2   Cy5: Anther-1.0mm_2AE2
Rep3: Cy3: Anther-1.0mm_2AE3   Cy5: Anther-1.0mm_2IE3
Rep4: Cy3: Anther-1.0mm_2AE4   Cy5: Anther-1.0mm_2IE4

hyb_protocol: 750 ng of each labeled target cRNA were hybridized for 17 h at 60C.

scan_protocol: Slides were scanned on an Agilent G2565AA microarray scanner as indicated in the manual.  Images were processed with the Agilent Feature Extraction software.

data_processing: After removal of spots flagged by Feature Extraction as below background or saturated or outliers, dye normalized values for each channel from Feature Extraction were normalized again to the median array intensity.  Average intensities were then calculated for probes with at least 3 of 4 good intensities.

label: Cy3, Cy5

organism: Zea mays

source_name: Anther-1.0mm MuActive

label_protocol: Total RNA (500 ng) was amplified & labeled with Cy5 using Agilent Low RNA Input Fluorescent Linear Amplification Kit.

growth_protocol: Plants were grown and dissected at the Stanford field; tissues were collected and frozen in liquid nitrogen immediately.

extract_protocol: Total RNA was extracted from 30 - 60 mg of frozen tissues with Qiagen RNeasy Mini kit, digested with DNase I, and cleaned up with RNeasy columns.

tag: Anther-1.0mm MuActive

label: Cy5, Cy3

source_name: Anther-1.0mm MuInactive

tag: Anther-1.0mm MuInactive


title: 1.5mm Act vs Inact

description:
Mu active line compared to Mu inactive line at the 1.5mm anther stage
Reps 1-4 (includes 2 dye swaps)
Rep1: Cy3: Anther-1.5mm_2IF1   Cy5: Anther-1.5mm_2AF1
Rep2: Cy3: Anther-1.5mm_2IF2   Cy5: Anther-1.5mm_2AF2
Rep3: Cy3: Anther-1.5mm_2AF3   Cy5: Anther-1.5mm_2IF3
Rep4: Cy3: Anther-1.5mm_2AF4   Cy5: Anther-1.5mm_2IF4

source_name: Anther-1.5mm MuActive

tag: Anther-1.5mm MuActive

source_name: Anther-1.5mm MuInactive

tag: Anther-1.5mm MuInactive


title: 2.0mm Act vs Inact

description:
Mu active line compared to Mu inactive line at the 2.0mm anther stage
Reps 1-4 (includes 2 dye swaps)
Rep1: Cy3: Anther-2.0mm_2IG1   Cy5: Anther-2.0mm_2AG1
Rep2: Cy3: Anther-2.0mm_2IG2   Cy5: Anther-2.0mm_2AG2
Rep3: Cy3: Anther-2.0mm_2AG3   Cy5: Anther-2.0mm_2IG3
Rep4: Cy3: Anther-2.0mm_2AG4   Cy5: Anther-2.0mm_2IG4

source_name: Anther-2.0mm MuActive

tag: Anther-2.0mm MuActive

source_name: Anther-2.0mm MuInactive

tag: Anther-2.0mm MuInactive


title: HUVEC-normoxia-probeset-rep3

data_processing: Cell intensity (CEL) file data were quantile-normalized and summarized using the Probe Logarithmic Intensity Error Estimation (PLIER) within Affymetrix Power Tools (APT).

label_protocol: 1 μg RNA of the sample was processed using the Affymetrix GeneChip® Whole Transcript Sense Target Labeling Assay (Affymetrix, Santa Clara). GeneChip® WT cDNA Synthesis Kit, WT cDNA Amplification Kit, and WT Terminal Labeling Kit (Affymetrix, Inc., Santa Clara, CA) were used for sample preparation.


title: HUVEC-normoxia-probeset-rep1


title: HUVEC-Mimic_hypoxia-probeset-rep2


title: HUVEC-normoxia-probeset-rep2


title: HUVEC-Mimic_hypoxia-probeset-rep1


title: Mdr2 KO HCV transgene tumorous tissues sample 6

status: Public on Mar 22 2009

city: Ramat-Gan

first: Mark

last: Katzenellenbogen

address: Ramat-Gan 52900, Israel

department: THE FACULTY OF LIFE SCIENCE, BIOINFORMATICS AND MICROARRAY UNIT

country: Israel

institute: Bar Ilan University

description: According to submitted paper: HCV tumor promoting effect is dependent on host genetic background

hyb_protocol: The sample hybridization was performed according the Affymetrix protocols: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

scan_protocol: The stained array was scanned on the Affymetrix scanner

data_processing: The raw data were processed by the Partek® Genomics SuiteTM (Partek GS) (Partek Inc., St. Louis, MO)  software. The  “extended” subsets of probe-sets was used. RMA  algorithm (Partek defaults) was applied for summarization, and the normalization was performed by the quantile method. The normalized expression values were processed by the Partek batch removing tool.  Probe-set mean was applied for evaluation of transcript cluster expression level.

organism: Mus musculus

source_name: Mdr2 KO HCV transgene tumorous tissues

label_protocol: The sample labeling was performed according the Affymetrix protocols: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

growth_protocol: Mice were maintained under specific pathogen-free conditions at the Specific Pathogen-Free (SPF) unit, Faculty of Medicine, Hebrew University, under a 12 h light/dark cycle, and provided with food and water ad libitum. The Institutional Animal Welfare Committee (NIH approval number OPRR-A01-5011) approved all animal experiments. All animal experiments were performed according to national regulations and institutional guidelines. Founders of the FVB.129P2-Abcb4tm1Bor (Mdr2-KO; old name FVB.129P2-Pgy24tm1Bor) mice were purchased from the Jackson Laboratory (Bar Harbor, USA) 11. Transgenic mice expressing the whole HCV 1b polyprotein were kindly provided by Prof. N. La Monica (IRBM, P. Angeletti, Pomezia, Italy) 9. Double Mdr2-KO/HCV-Tg mice were produced by crossing between homozygous Mdr2-KO and HCV-Tg mice, and by backcrosses of the resulting F1 hybrid (both Mdr2- and HCV-heterozygous) with the parental Mdr2-KO strain. Appearance of tumors was monitored by ultrasound from the age of 10 months, using an ATL 5000 device (ATL, Bothell, WA) with linear transducer (12-15 mHz). Mice were sacrificed at the age of 14 months, when tumor appearance was detected in most Mdr2-KO mice.

extract_protocol: Total RNA was isolated from snap frozen mouse liver tissues with the Trizol® reagent (Invitrogen, Carlsbad, CA) as described by the manufacturer.

treatment_protocol: Non fasting mice were anesthetized with isoflurane and sacrificed by cervical dislocation. Livers were rapidly excised and weighed; part of the liver was fixed in 4% buffered formaldehyde for histological analysis, and the remaining tissue was rapidly frozen in liquid nitrogen and stored at -80ºC until use.

tag: Mdr2 KO

tag: HCV transgene

tag: tumorous tissues

tag: sample 6


title: HUVEC-Mimic_hypoxia-probeset-rep3


title: Mdr2 KO HCV transgene tumorous tissues sample 5

tag: sample 5


title: Mdr2 +/- HCV transgene non tumorous liver tissues sample 5

tag: non tumorous liver tissues


title: Mdr2 +/- no HCV transgene non tumorous liver tissues sample 4

tag: no HCV transgene

tag: sample 4


title: Mdr2 KO no HCV transgene non tumorous liver tissues sample 4

data_processing: The raw data were processed by the Partek® Genomics SuiteTM (Partek GS) (Partek Inc., St. Louis, MO)  software.The  “extended” subsets of probe-sets was used. RMA  algorithm (Partek defaults) was applied for summarization, and the normalization was performed by the quantile method. The normalized expression values were processed by the Partek batch removing tool.


title: Mdr2 +/- no HCV transgene non tumorous liver tissues sample 3

tag: sample 3


title: Mdr2 +/- HCV transgene non tumorous liver tissues sample 4


title: Mdr2 KO HCV transgene non tumorous liver tissues sample 5


title: Mdr2 +/- no HCV transgene non tumorous liver tissues sample 1

tag: sample 1


title: Mdr2 +/- no HCV transgene non tumorous liver tissues sample 2

tag: sample 2


source_name: Mdr2 +/- HCV transgene non tumorous liver tissues


title: Mdr2 KO HCV transgene non tumorous liver tissues sample 1


title: Mdr2 KO HCV transgene tumorous tissues sample 2


source_name: Mdr2 +/- no HCV transgene non tumorous liver tissues


title: Mdr2 KO HCV transgene non tumorous liver tissues sample 4


title: Mdr2 KO no HCV transgene non tumorous liver tissues sample 5


title: Mdr2 KO HCV transgene non tumorous liver tissues sample 3


title: Mdr2 +/- HCV transgene non tumorous liver tissues sample 2


title: Mdr2 KO HCV transgene tumorous tissues sample 1


title: Mdr2 KO HCV transgene tumorous tissues sample 3


title: Mdr2 KO HCV transgene tumorous tissues sample 6


title: Mdr2 KO no HCV transgene non tumorous liver tissues sample 2


title: Mdr2 +/- no HCV transgene non tumorous liver tissues sample 4


title: Mdr2 +/- HCV transgene non tumorous liver tissues sample 3


source_name: Mdr2 KO no HCV transgene non tumorous liver tissues


title: Mdr2 KO HCV transgene non tumorous liver tissues sample 2


title: Mdr2 KO no HCV transgene non tumorous liver tissues sample 3


source_name: Mdr2 KO HCV transgene non tumorous liver tissues


title: Mdr2 KO HCV transgene tumorous tissues sample 4


title: Mdr2 KO HCV transgene non tumorous liver tissues sample 5


title: Mdr2 KO no HCV transgene non tumorous liver tissues sample 1


title: Mdr2 +/- HCV transgene non tumorous liver tissues sample 1


title: Mdr2 KO no HCV transgene non tumorous liver tissues sample 4


title: Mdr2 +/- HCV transgene non tumorous liver tissues sample 4


title: S4 replication in Kc cells

status: Public on Feb 10 2009

type: genomic

city: Vienna

first: Michaela

last: Schwaiger

address: Althanstr. 14

country: Austria

institute: University of Vienna

description: Replicating DNA from cells in the 4th S phase fraction (of 4 fractions) was isolated by BrdU-IP and compared to total genomic DNA.

hyb_protocol: Approximately 6-10μg of DNA was hybridzed per array using the Affymetrix hybridization kit. Arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G.

data_processing: Tiling arrays were analyzed using MAT (Model-based Analysis of Tiling-array) software (Johnson et al. 2006). The bandwith was set to 1000bp for replication timing and nascent DNA analysis, and 300bp for H4K16ac , RNA Polymerase II and transcription data. MAT scores were extracted from the BAR files generated using the Python script ‘Bar2Wig.py’ kindly provided by Wei Li (Harvard University). Data from the Wiggle files were reformatted using Perl for subsequent analysis in R.

label: Biotin

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: replicating DNA from the 4th S phase fraction

label_protocol: Samples (6-10μg of DNA) were enzymatically fragmented and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments

extract_protocol: We sorted cells into S-phase fractions on the basis of DNA content using Fluorescent Activated Cell Sorting (FACS). We collected 60,000 cells from each fraction directly into lysis buffer. DNA was purified, sonicated, denatured and immunoprecipitated with an antibody specific for BrdU (Becton Dickinson) as described (Schubeler et al. 2002), but with two consecutive rounds of immunoprecipitation to increase specificity. olated from cells using Trizol (Invitrogen) and subsequently purified using an RNeasy kit (QIAGEN). For hybridization to Affymetrix tiling arrays, we made double-stranded cDNA by performing two rounds of cDNA synthesis using random primers and addition of 2 mM dUTPs using the GeneChip® WT Double-Stranded cDNA Synthesis Kit (Affymetrix). Nascent strand DNA in a size range of 1000 to 2000 bp was isolated from logarithmically growing Kc cells by alkaline gel electrophoresis as described (Gray et al. 2007). Genomic DNA from Kc cells in G2 phase (isolated by FACS) was used as a control that does not contain nascent strands.ChIP for H4K16 acetylation and RNA Polymerase II was carried out as described (Bell et al. 2007).To obtain sufficient target DNA for microarray hybridization, we amplified the denatured and immunoprecipitated DNA as described (Schubeler et al. 2002).

tag: female, embryonic origin

tag: genomic DNA of cells in the 4th fourth of S phase

source_name: genomic DNA

tag: genomic DNA


title: replication timing of S2 cells

description: The timing of DNA replciation in S2 cells.

source_name: early replicating DNA

tag: male, embryonic origin

tag: genomic DNA of cells in early S phase

source_name: late replicating DNA

tag: genomic DNA of cells in late S phase


title: H4K16 acetylation in early S phase in Kc cells

description: Acetylation of lysine 16 of histone H4 in Kc cells in late S phase (separated based on DNA content using FACS).

source_name: H4K16ac-CHIP DNA

source_name: Input DNA of cells in early S phase


title: S2 replication in Kc cells

description: Replicating DNA from cells in the 2nd S phase fraction (of 4 fractions) was isolated by BrdU-IP and compared to total genomic DNA.

source_name: replicating DNA from the 2nd S phase fraction

tag: genomic DNA of cells in the 2nd fourth of S phase


title: S1 replication in Kc cells

description: Replicating DNA from cells in the 1st S phase fraction (of 4 fractions) was isolated by BrdU-IP and compared to total genomic DNA.

source_name: replicating DNA from the 1st S phase fraction

tag: genomic DNA of cells in the 1st fourth of S phase


title: Mdr2 KO HCV transgene tumorous tissues sample 2

tag: Mdr2 KO

tag: HCV transgene

tag: tumorous tissues


title: Mdr2 KO HCV transgene tumorous tissues sample 5

tag: sample 5


title: H4K16 acetylation in late S phase in Kc cells

description: Acetylation of lysine 16 of histone H4 in Kc cells in early S phase (separated based on DNA content using FACS).

source_name: Input DNA of cells in late S phase


title: Mdr2 KO HCV transgene non tumorous liver tissues sample 4

tag: non tumorous liver tissues


title: H4K16 acetylation in Cl8 cells

description: Acetylation of lysine 16 of histone H4 in Cl8 cells.

tag: male, wing imaginal disc origin

source_name: Input DNA


title: Hypothalamus - B6.CAST-17 short congenics 2

status: Public on Feb 12 2009

city: Baton Rouge

first: Brenda

last: Richards

state: LA

address: 6400 Perkins Rd.

department: Basic Science

institute: Pennington Biomedical Research Center

description: Hypothalamus sample from B6-CAST-17 strain was used

hyb_protocol: Fifteen microgram of DIG labeled fragmented cRNA was used for microarray hybridization and performed according to the Applied Biosystems protocols

scan_protocol: Chemiluminescence detection, imaging, auto girding, and image analysis was done according to the Applied Biosystems protocols and the 1700 Chemiluminescent Microarray Analyzer Software v1.0.3

data_processing: Signal intensities across microarrays were normalized using quantile-quantile normalization method (www.bioconductor.org)

label: DIG-UTP

source_name: Hypothalamus

label_protocol: 1 microgram of total RNA was used to transcribe DIG labeled cRNA using Applied Biosystems Chemiluminescent RT-IVT kit v2.0

extract_protocol: The tissues were removed quickly, frozen in liquid nitrogen and stored at -80 oC. Total RNA was isolated from harvested tissue using TRI-Reagent (Molecular Research Center Inc. Cincinnati, Ohio), and purified using Qiagen RNAeasy columns (Qiagen, Valencia, CA). RNA was stored at -80oC in RNAse free water. Quality and quantity of RNA was determined using Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA)


title: Hypothalamus - Wild type 1


title: RNA Polymerase II in Cl8 cells

description: Total RNA Polymerase II binding in Cl8 cells.

source_name: RNA Polymerase II CHIP DNA


title: nascent strand DNA distribution in Kc cells

description: Nascent strand DNA was isolated from Kc cells.

source_name: nascent strands

tag: nascent strands

tag: genomic DNA of cells in G2 phase


title: transcript levels in Kc and Cl8 cells

description: Total RNA was measured in Kc and Cl8 cells.

source_name: random-primed cDNA from total RNA of Kc cells

tag: total RNA

source_name: random-primed cDNA from total RNA from Cl8 cells

tag: total RNA from Cl8 cells


title: replication timing of Cl8 cells

description: The timing of DNA replciation in Cl8 cells.


title: H4K16 acetylation in Kc cells

description: Acetylation of lysine 16 of histone H4 in Kc cells.

tag: female, embryonic origin


title: replication timing of Kc cells

description: The timing of DNA replciation in Kc cells.


title: S3 replication in Kc cells

description: Replicating DNA from cells in the 3rd S phase fraction (of 4 fractions) was isolated by BrdU-IP and compared to total genomic DNA.

source_name: replicating DNA from the 3rd S phase fraction

tag: genomic DNA of cells in the 3rd fourth of S phase

tag: genomic DNA


source_name: Mdr2 KO no HCV transgene non tumorous liver tissues

tag: no HCV transgene

tag: sample 1


title: Hypothalamus - B6.CAST-17 short congenics 3


title: Hypothalamus - Wild type 3


title: Hypothalamus - Wild type 2


title: C7H2-24h-EtOH-Exp2_pri-miRNA

status: Public on Jan 16 2009

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

hyb_protocol: standard Affymetrix procedures

scan_protocol: Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software.

data_processing: preprocessing was performed using the Affymetrix exact tool. Raw CEL files were quantile normalized and probe signals per probeset (defined as all probes mapping to exons of a potential pri-miRNA-transcript) were RMA summarized.

source_name: CCRF-CEM-C7H2 cell line

label_protocol: The chips were stained and washed in an Affymetrix fluidic station 450S.

extract_protocol: Total RNA was depleted of ribosomal RNA and transcribed into cDNA using T7-promoter-tagged hexamer primers. Antisense RNA was produced by T7-polymerase and transcribed into cDNA using random priming in the presence of dUTP which was used to enzymatically fragment the cDNA

tag: homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 24h


title: C7H2-24h-EtOH-Exp3_pri-miRNA

growth_protocol: cultured under standard conditions (37°C, 5% CO2, saturated humidity)


title: C7H2-6h-GC-Exp1_pri-miRNA

tag: homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 6h.


title: C7H2-6h-EtOH-Exp0_pri-miRNA

tag: homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 6h


title: C7H2-24h-GC-Exp2_pri-miRNA

tag: homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 24h.


title: C7H2-24h-EtOH-Exp1_pri-miRNA


title: C7H2-24h-GC-Exp1_pri-miRNA


title: C7H2-6h-EtOH-Exp1_pri-miRNA


title: C7H2-6h-GC-Exp0_pri-miRNA


title: C7H2-6h-EtOH-Exp3_pri-miRNA


title: C7H2-6h-GC-Exp3_pri-miRNA


title: C7H2-24h-GC-Exp3_pri-miRNA


title: Wild type - Skeletal muscle - 3

description: Skeletal muscle sample from B6-CAST-17 strain was used

source_name: Skeletal muscle


title: Congenics - Skeletal muscle - 1


title: Wild type - Skeletal muscle - 2


title: Congenics - Skeletal muscle - 2


title: C7H2-2h-EtOH-ExpV_pri-miRNA

tag: homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 2h


title: C7H2-2h-GC-ExpIII_pri-miRNA

tag: homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 2h.


title: C7H2-2h-GC-ExpV_pri-miRNA


title: C7H2-2h-GC-ExpIV_pri-miRNA


title: Wild type - Skeletal muscle - 1


title: Congenics - Skeletal muscle - 3


title: Hypothalamus - B6.CAST-17 short congenics 1

tag: B6.CAST-17 - Sub congenic


title: C7H2-0.5h-EtOH-ExpIII_pri-miRNA

tag: homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 30 min


title: C7H2-0.5h-EtOH-ExpIV_pri-miRNA


title: C7H2-6h-EtOH-Exp3_pre-miRNA

data_processing: preprocessing was performed using the Affymetrix exact tool. Raw CEL files were quantile normalized and probe signals per probeset (defined as all probes mapping to pre-miRNA sequences) were RMA summarized.


title: C7H2-6h-EtOH-Exp0_pre-miRNA


title: C7H2-24h-EtOH-Exp1_pre-miRNA


title: C7H2-6h-GC-Exp3_pre-miRNA


title: C7H2-2h-GC-ExpV_pre-miRNA


title: C7H2-6h-GC-Exp1_pre-miRNA


title: C7H2-2h-GC-ExpIV_pre-miRNA


title: C7H2-2h-EtOH-ExpIV_pri-miRNA


title: C7H2-2h-EtOH-ExpIII_pri-miRNA

tag: homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 2 h


title: C7H2-6h-GC-Exp0_pre-miRNA


title: C7H2-6h-EtOH-Exp1_pre-miRNA


title: C7H2-0.5h-EtOH-ExpV_pri-miRNA


title: C7H2-0.5h-GC-ExpIV_pri-miRNA

tag: homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 30 min


title: C7H2-0.5h-GC-ExpIII_pri-miRNA


title: C7H2-2h-GC-ExpIII_pre-miRNA


title: RNA Polymerase II in Kc cells

description: Total RNA Polymerase II binding in Kc cells.


title: C7H2-2h-EtOH-ExpV_pre-miRNA


title: C7H2-24h-GC-Exp1_pre-miRNA


title: C7H2-2h-EtOH-ExpIV_pre-miRNA


title: C7H2-0.5h-GC-ExpV_pre-miRNA


title: C7H2-24h-EtOH-Exp3_pre-miRNA


title: C7H2-2h-EtOH-ExpIII_pre-miRNA


title: C7H2-0.5h-EtOH-ExpIV_pre-miRNA


title: C7H2-0.5h-EtOH-ExpV_pre-miRNA


title: C7H2-0.5h-GC-ExpIII_pre-miRNA


title: C7H2-0.5h-EtOH-ExpIII_pre-miRNA


title: C7H2-24h-GC-Exp2_pre-miRNA


title: C7H2-0.5h-GC-ExpIV_pre-miRNA


title: HG_young_male_rep8_Cy5

status: Public on Jan 01 2009

city: Milano

first: Maddalena

last: Fratelli

address: Via La Masa, 19

institute: "Mario Negri" Institute

description: Gene expression of WT mouse.

hyb_protocol: Hybridization and washing were done according to Agilent protocol (SSPE).

scan_protocol: Agilent Technologies Scanner G2505B US45102933, 10 micron resolution using the Agilent scan control software.

data_processing: Image data analysis was performed using the Feature extraction software (v9.1). Detailed description of the protocols used is reported in each raw data file. Vsn normalization (glog - please note: ln) was performed using the vsn package in Bioconductor.

source_name: Harderian gland, young male, wild type

label_protocol: Amino Allyl Labeling Kit (cat 1705, Ambion), following manufacturer's instructions. Samples were then diluted 1:10 and 10 picomoles of each dye was used for hybridization.

growth_protocol: Not applicable.

extract_protocol: Total RNA was extracted using Qiagen RNeasy kit, following manufacturer's instructions.

treatment_protocol: Not applicable.

tag: Strain

tag: Gender

value: male

tag: Age

value: 5 weeks

tag: Tissue

value: Harderian gland

tag: Eartag

tag: wild type


title: C7H2-24h-GC-Exp3_pre-miRNA


title: HG_adult_male_rep3_Cy5

description: Gene expression of WT mouse.

source_name: Harderian gland, adult male, wild type

value: 9 weeks


title: HG_adult_female_rep8_Cy5

description: Gene expression of WT mouse.

source_name: Harderian gland, adult female, wild type

value: female

value: 8 weeks


title: HG_adult_male_rep4_Cy5

description: Gene expression of KO mouse.

source_name: Harderian gland, adult male, Aoh2(-/-)


title: C7H2-0.5h-GC-ExpV_pri-miRNA


title: HG_young_male_rep5_Cy5

description:
Gene expression of KO mouse.

Raw data were used in vsn normalization. Normalized values were excluded from further analyses due to quality reasons and are not included here.

source_name: Harderian gland, young male, Aoh2(-/-)

value: 6 weeks


title: HG_adult_male_rep6_Cy5

description: Gene expression of WT mouse.


title: C7H2-24h-EtOH-Exp2_pre-miRNA


title: HG_young_male_rep10_Cy5

description: Gene expression of KO mouse.


title: HG_adult_male_rep5_Cy5

description: Gene expression of KO mouse.


title: HG_young_male_rep9_Cy5

description: Gene expression of WT mouse.


title: HG_young_female_rep6_Cy5

description: Gene expression of KO mouse.

source_name: Harderian gland, young female, Aoh2(-/-)


title: HG_adult_female_rep7_Cy5

description: Gene expression of KO mouse.

source_name: Harderian gland, adult female, Aoh2(-/-)


title: HG_young_female_rep4_Cy5

description: Gene expression of WT mouse.

source_name: Harderian gland, young female, wild type


title: HG_young_female_rep5_Cy5

description: Gene expression of WT mouse.


title: HG_young_female_rep3_Cy5

description: Gene expression of KO mouse.


title: HG_young_male_rep3_Cy5

description: Gene expression of KO mouse.


title: HG_adult_female_rep3_Cy5

description: Gene expression of WT mouse.


title: HG_adult_female_rep1_Cy5

description: Gene expression of WT mouse.


title: HG_young_male_rep6_Cy5

description: Gene expression of WT mouse.


title: HG_adult_female_rep2_Cy5

description: Gene expression of KO mouse.


title: HG_adult_female_rep5_Cy5

description: Gene expression of WT mouse.

value: 7 weeks


title: HG_young_male_rep7_Cy5

description: Gene expression of KO mouse.


title: HG_young_male_rep2_Cy5

description: Gene expression of WT mouse.


title: HG_adult_female_rep6_Cy5

description: Gene expression of KO mouse.


title: HG_adult_male_rep2_Cy5

description: Gene expression of KO mouse.


title: HG_young_female_rep1_Cy5

description: Gene expression of WT mouse.


title: HG_adult_female_rep4_Cy5

description: Gene expression of KO mouse.


title: HG_young_male_rep4_Cy5

description: Gene expression of WT mouse.


title: HG_young_female_rep2_Cy5

description: Gene expression of KO mouse.


title: HG_young_male_rep1_Cy5

description: Gene expression of KO mouse.


title: H3K4 trimethylation in met1 mutant

status: Public on Feb 01 2009

city: Los Angeles

first: matteo

last: Pellegrini

address: 621 Charles Young Drive South

department: MCD Biology

institute: UCLA

description:
ChIP samples were amplified using whole genome amplification kit before labeling

H3 replicates:
124327-124315.CEL
124328-124316.CEL
124329-124317.CEL

H3k4 replicates:
124336-124324.CEL
124337-124325.CEL
124338-124326.CEL

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Affymetrix scanner

data_processing: Three H3k4 replicates were compared to three H3 antibody replicates using TileMAP.

organism: Arabidopsis thaliana

label_protocol: Standard Affymetrix protocol

extract_protocol: Plants were ground in liquid nitrogen, sonicated and ChIPed with anti H3K4 tri methylation antibody (ab8580)

tag: 3 week old aerial part of seedlings, crosslinked with formaldehyde

source_name: ChIPed with anti H3 antibody (ab1791)

extract_protocol: Plants were ground in liquid nitrogen, sonicated and ChIPed with anti H3 antibody (ab1791)


title: HG_young_male_rep9_Cy3

description: Gene expression of KO mouse.


title: H3K4 trimethylation in wild type (Columbia)

description:
ChIP samples were amplified using whole genome amplification kit before labeling

H3 replicates:
H31.CEL
H32.CEL
H33.CEL

H3k4 replicates:
3K4_1.CEL
3K4_2.CEL
3K4_3.CEL

source_name: ChIPed with anti H3K4 trimethylation antibody (ab8580)


title: HG_young_male_rep10_Cy3

description: Gene expression of WT mouse.


title: HG_adult_male_rep1_Cy5

description: Gene expression of WT mouse.


title: H3K4 dimethylation in wild type (Columbia)

description:
ChIP samples were amplified using whole genome amplification kit before labeling

H3 replicates:
119758-119655.CEL
119759-119656.CEL
119760-119657.CEL
H31.CEL
H32.CEL
H33.CEL

H3k4 replicates:
119764-119661 2K4_1.CEL
119765-119662 2K4_2.CEL
119766-119663 2K4_3.CEL
2K4_1.CEL
2K4_2.CEL
2K4_3.CEL

data_processing: Six H3k4 replicates were compared to six H3 antibody replicates using TileMAP.

source_name: ChIPed with anti H3K4 dimethylation antibody (ab7766)

extract_protocol: Plants were ground in liquid nitrogen, sonicated and ChIPed with anti H3K4 di methylation antibody (ab7766)


title: HG_adult_female_rep6_Cy3

description:
Gene expression of WT mouse.

Raw data were used in vsn normalization. Normalized values were excluded from further analyses due to quality reasons and are not included here.


title: HG_young_male_rep5_Cy3


title: HG_adult_male_rep6_Cy3

description: Gene expression of KO mouse.


title: HG_adult_female_rep5_Cy3


title: H3k4 monomethylation in met1 mutant

description:
ChIP samples were amplified using whole genome amplification kit before labeling

H3 replicates:
124327-124315
124328-124316
124329-124317

H3k4 replicates:
124330-124318.CEL
124331-124319.CEL
124332-124320.CEL

extract_protocol: Plants were ground in liquid nitrogen, sonicated and ChIPed with anti H3K4 mono methylation antibody (ab8895)


title: HG_adult_female_rep8_Cy3

description: Gene expression of KO mouse.


title: H3K4 monomethylation in wild type (Columbia)

description:
ChIP samples were amplified using whole genome amplification kit before labeling

H3 replicates:
119758-119655.CEL
119759-119656.CEL
119760-119657.CEL

H3k4 replicates:
119761-119658.CEL
119762-119659.CEL
119763-119660.CEL

source_name: ChIPed with anti H3K4 mono methylation antibody (ab8895)


title: HG_young_male_rep8_Cy3

description: Gene expression of KO mouse.


title: HG_adult_male_rep4_Cy3

description: Gene expression of WT mouse.


title: HG_adult_male_rep3_Cy3

description: Gene expression of KO mouse.


title: HG_adult_male_rep5_Cy3

description: Gene expression of WT mouse.


title: HG_young_female_rep3_Cy3

description: Gene expression of WT mouse.


title: HG_young_male_rep1_Cy3


title: HG_young_male_rep7_Cy3

description: Gene expression of WT mouse.


title: HG_adult_female_rep3_Cy3

description: Gene expression of KO mouse.


title: HG_young_female_rep1_Cy3

description: Gene expression of KO mouse.


title: HG_adult_male_rep1_Cy3


title: HG_young_female_rep4_Cy3

description: Gene expression of KO mouse.


title: HG_adult_female_rep1_Cy3

description: Gene expression of KO mouse.


title: HG_adult_male_rep2_Cy3

description: Gene expression of WT mouse.


title: HG_young_male_rep6_Cy3

description: Gene expression of KO mouse.


title: HG_adult_female_rep7_Cy3

description: Gene expression of WT mouse.


title: HG_young_male_rep3_Cy3

description: Gene expression of WT mouse.


title: H3K4 dimethylation in met1 mutant

description:
ChIP samples were amplified using whole genome amplification kit before labeling

H3 replicates:
124327-124315.CEL
124328-124316.CEL
124329-124317.CEL

H3k4 replicates:
124333-124321.CEL
124334-124322.CEL
124335-124323.CEL

source_name: ChIPed with anti H3K4 di methylation antibody (ab7766)


title: HG_young_male_rep4_Cy3

description: Gene expression of KO mouse.


title: HG_young_male_rep2_Cy3

description: Gene expression of KO mouse.


title: Skin_adult_female_rep4

description: Gene expression of WT vs. KO mouse.

hyb_protocol: Hybridization and washing were done according to Agilent protocol (GE version 5.5).

scan_protocol: Agilent Technologies Scanner G2505B US45102933, 5 micron resolution and XDR protocol using the Agilent scan control software.

data_processing: Image data analysis was performed using the Feature extraction software (v9.1). Detailed description of the protocols used is reported in each raw data file. Log ratios are derived by the 'Per Spot and Per Chip: Intensity dependent (Lowess) normalization' of the Genespring GX 7.3 software (Agilent Technologies).

source_name: Skin, adult female, Aoh2 (-/-)

value: Skin

source_name: Skin, adult female, wild type


title: HG_young_female_rep2_Cy3

description: Gene expression of WT mouse.


title: HG_young_female_rep5_Cy3

description: Gene expression of KO mouse.


title: Skin_adult_female_rep1

description: Gene expression of WT vs. KO mouse.


title: Skin_adult_female_rep2

description: Gene expression of WT vs. KO mouse.


title: HG_adult_female_rep2_Cy3

description: Gene expression of WT mouse.


title: Skin_adult_female_rep3

description: Gene expression of WT vs. KO mouse.


title: HG_adult_female_rep4_Cy3

description: Gene expression of WT mouse.


title: thu1_mem_CD8

status: Public on Dec 31 2008

city: Canberra

first: Zuopeng

last: Wu

state: ACT

address: Garren Rd

department: Dept. of Immunology & Genetics

country: Australia

institute: John Curtin School of Medical Research

description: exon-level analysis

hyb_protocol: Affymetrix Gene Chip Fluidics station 450

scan_protocol: Affymetrix GCS3000 7G

data_processing: Exon- and gene-level data were generated using Partek Genomic Suite 6.3 software, with the defult algorithm of RMA.

label_protocol: Affymetrix Mouse Exon Array labeling system

growth_protocol: RPMI+10 FCS

extract_protocol: RNeasy plus Mini kit (Qiagen)

treatment_protocol: anti-CD4, anti-CD8, and anti-CD44 staining

tag: C57BL/6, Female, 8-12weeks,

tag: Spleen, excised, 60min


title: wt1_naive_CD8

description: exon-level analysis


title: wt2_naive_CD8

description: exon-level analysis


title: thu4_mem_CD8

description: exon-level analysis


title: wt3_mem_CD4

description: exon-level analysis


title: thu3_naive_CD8

description: exon-level analysis


title: wt4_naive_CD8

description: exon-level analysis


title: thu4_naive_CD8

description: exon-level analysis


title: thu2_mem_CD8

description: exon-level analysis


title: wt2_mem_CD8

description: exon-level analysis


title: wt3_naive_CD4

description: exon-level analysis


title: wt2_mem_CD4

description: exon-level analysis


title: thu3_mem_CD8

description: exon-level analysis


title: wt2_naive_CD4

description: exon-level analysis


title: wt4_mem_CD8

description: exon-level analysis


title: thu4_mem_CD4

description: exon-level analysis


title: thu3_mem_CD4

description: exon-level analysis


title: wt4_naive_CD4

description: exon-level analysis


title: wt1_naive_CD4

description: exon-level analysis


title: thu4_naive_CD4

description: exon-level analysis


title: thu2_naive_CD8

description: exon-level analysis


title: wt3_naive_CD8

description: exon-level analysis


title: wt1_mem_CD4

description: exon-level analysis


title: wt1_mem_CD8

description: exon-level analysis


title: thu1_mem_CD4

description: exon-level analysis


title: thu2_mem_CD4

description: exon-level analysis


title: wt3_mem_CD8

description: exon-level analysis


title: wt4_mem_CD4

description: exon-level analysis


title: thu1_naive_CD8

description: exon-level analysis


title: HG_young_female_rep6_Cy3

description: Gene expression of WT mouse.


title: thu3_naive_CD4

description: exon-level analysis


title: thu2_naive_CD4

description: exon-level analysis


title: Thu_Thymus_CD8-2D

description: exon-level analysis

tag: Thymus, excised, 60min


title: WT_Thymus_CD8-1D

description: exon-level analysis


title: Thu_Thymus_CD8-2B

description: exon-level analysis


title: Thu_Thymus_CD8-2C

description: exon-level analysis


title: WT_Thymus_CD8-1C

description: exon-level analysis


title: Thu_Thymus_CD4-2D

description: exon-level analysis


title: Thu_Thymus_CD4-2C

description: exon-level analysis


title: WT_Thymus_CD4-1A

description: exon-level analysis


title: WT_Thymus_CD8-1B

description: exon-level analysis


title: Thu_Thymus_CD4-2B

description: exon-level analysis


title: WT_Thymus_CD8-1A

description: exon-level analysis


title: WT_Thymus_CD4-1D

description: exon-level analysis


title: WT_Thymus_CD4-1B

description: exon-level analysis


title: Thu_Thymus_CD4-2A

description: exon-level analysis


title: BLKSJ-high glucose-3

city: Thousand Oaks

first: Dan

last: Baker

address: 1 Amgen Center Drive

department: Molecular Sciences

institute: Amgen Inc.

description:
Agilent's Whole Mouse Genome Oligo microarray is comprised of 41,534 60-mer oligonucleotide probes representing over 41,000 mouse genes and transcripts
Cy3 data from: 060806_251269420835_S01_44k_Feature_Extraction.txt
Cy5 data from: 060806_251269420804_S01_44k_Feature_Extraction.txt

hyb_protocol: Purified cRNA was quantified and similar amounts of Cy3- and Cy5-labeled cRNA were combined, fragmented, hybridized, and washed following Agilent Two-Color Microarray-Based Gene Expression Analysis Protocol v4.0.2.

scan_protocol: Arrays were scanned at 10um, 100% PMT Green, 100% PMT Red on the Agilent Microarray Scanner G2505B.

data_processing: Array data was extracted using Agilent Feature Extraction Software v8.1, and analyzed as dye normalized relative fluorescence units (RFUs.)  Dye normalization was accomplished by pairing Cy-3 and Cy-5 values, and determining the effect of dye on RFU magnitude by including dye as a factor in an ANOVA analysis of the binary logarithm transformed probe intensities, including all two factor interactions.  The other factors in the ANOVA were strain and glucose pretreatment.  Found to be significant, the effect of reporter dye was subtracted in a least-squares manner, followed by channel averaging for each probe.

source_name: C57BLKS/J pancreatic islets

label_protocol: Two hundred nanograms of total RNA from each sample was separately amplified and labeled with Cy3- and Cy5-labeled CTP using the Agilent low input linear amplification kit Labeled cRNA was purified using the Qiagen RNeasy Mini kit protocol for liquid samples.

growth_protocol: Pancreatic islets were isolated from 12 week old mice.  Prior to all experiments islets were cultured for 48 h in RPMI-1640 media containing 11 mM glucose.

extract_protocol: At the end of the culture pretreatment the islets were picked from the culture vessel, rinsed briefly in HBSS/FBS buffer and homogenized in RLT buffer. RNA was prepared using the micro-RNAeasy kit.

treatment_protocol: Islets were then cultured separately for 24 h in RPMI-1640 media containing either 5 mM or 20 mM glucose.

tag: high glucose


title: WT_Thymus_CD4-1C

description: exon-level analysis


title: B6-high glucose-3

description:
Agilent's Whole Mouse Genome Oligo microarray is comprised of 41,534 60-mer oligonucleotide probes representing over 41,000 mouse genes and transcripts
Cy3 data from: 060806_251269420804_S01_44k_Feature_Extraction.txt
Cy5 data from: 060806_251269420835_S01_44k_Feature_Extraction.txt

source_name: C57BL/6 pancreatic islets


title: B6-high glucose-4

description:
Agilent's Whole Mouse Genome Oligo microarray is comprised of 41,534 60-mer oligonucleotide probes representing over 41,000 mouse genes and transcripts
Cy3 data from: 060806_251269420836_S01_44k_Feature_Extraction.txt
Cy5 data from: 060806_251269420837_S01_44k_Feature_Extraction.txt


title: BLKSJ-low glucose-5

description:
Agilent's Whole Mouse Genome Oligo microarray is comprised of 41,534 60-mer oligonucleotide probes representing over 41,000 mouse genes and transcripts
Cy3 data from: 060806_251269420764_S01_44k_Feature_Extraction.txt
Cy5 data from: 060806_251269420763_S01_44k_Feature_Extraction.txt

tag: low glucose


title: Thu_Thymus_CD8-2A

description: exon-level analysis


title: BLKSJ-high glucose-2

description:
Agilent's Whole Mouse Genome Oligo microarray is comprised of 41,534 60-mer oligonucleotide probes representing over 41,000 mouse genes and transcripts
Cy3 data from: 060806_251269420803_S01_44k_Feature_Extraction.txt
Cy5 data from: 060806_251269420802_S01_44k_Feature_Extraction.txt


title: B6-high glucose-1

description:
Agilent's Whole Mouse Genome Oligo microarray is comprised of 41,534 60-mer oligonucleotide probes representing over 41,000 mouse genes and transcripts
Cy3 data from: 060806_251269420800_S01_44k_Feature_Extraction.txt
Cy5 data from: 060806_251269420801_S01_44k_Feature_Extraction.txt


title: BLKSJ-high glucose-1

description:
Agilent's Whole Mouse Genome Oligo microarray is comprised of 41,534 60-mer oligonucleotide probes representing over 41,000 mouse genes and transcripts
Cy3 data from: 060806_251269420801_S01_44k_Feature_Extraction.txt
Cy5 data from: 060806_251269420800_S01_44k_Feature_Extraction.txt


title: B6-high glucose-2

description:
Agilent's Whole Mouse Genome Oligo microarray is comprised of 41,534 60-mer oligonucleotide probes representing over 41,000 mouse genes and transcripts
Cy3 data from: 060806_251269420802_S01_44k_Feature_Extraction.txt
Cy5 data from: 060806_251269420803_S01_44k_Feature_Extraction.txt


title: BLKSJ-low glucose-3

description:
Agilent's Whole Mouse Genome Oligo microarray is comprised of 41,534 60-mer oligonucleotide probes representing over 41,000 mouse genes and transcripts
Cy3 data from: 060806_251269420760_S01_44k_Feature_Extraction.txt
Cy5 data from: 060806_251269420745_S01_44k_Feature_Extraction.txt


title: B6-low glucose-4

description:
Agilent's Whole Mouse Genome Oligo microarray is comprised of 41,534 60-mer oligonucleotide probes representing over 41,000 mouse genes and transcripts
Cy3 data from: 060806_251269420761_S01_44k_Feature_Extraction.txt
Cy5 data from: 060806_251269420762_S01_44k_Feature_Extraction.txt


title: BLKSJ-high glucose-4

description:
Agilent's Whole Mouse Genome Oligo microarray is comprised of 41,534 60-mer oligonucleotide probes representing over 41,000 mouse genes and transcripts
Cy3 data from: 060806_251269420837_S01_44k_Feature_Extraction.txt
Cy5 data from: 060806_251269420836_S01_44k_Feature_Extraction.txt


title: B6-high glucose-5

description:
Agilent's Whole Mouse Genome Oligo microarray is comprised of 41,534 60-mer oligonucleotide probes representing over 41,000 mouse genes and transcripts
Cy3 data from: 061306_251269420952_S01_44k_Feature_Extraction.txt
Cy5 data from: 061306_251269420953_S01_44k_Feature_Extraction.txt


title: BLKSJ-low glucose-4

description:
Agilent's Whole Mouse Genome Oligo microarray is comprised of 41,534 60-mer oligonucleotide probes representing over 41,000 mouse genes and transcripts
Cy3 data from: 060806_251269420762_S01_44k_Feature_Extraction.txt
Cy5 data from: 060806_251269420761_S01_44k_Feature_Extraction.txt


title: B6-low glucose-1

description:
Agilent's Whole Mouse Genome Oligo microarray is comprised of 41,534 60-mer oligonucleotide probes representing over 41,000 mouse genes and transcripts

Cy3 data from:
061306_251269420953_S01_44k_Feature_Extraction.txt
060806_251269420741_S01_44k_Feature_Extraction.txt

Cy5 data from:
061306_251269420952_S01_44k_Feature_Extraction.txt
060806_251269420742_S01_44k_Feature_Extraction.txt


title: BLKSJ-low glucose-2

description:
Agilent's Whole Mouse Genome Oligo microarray is comprised of 41,534 60-mer oligonucleotide probes representing over 41,000 mouse genes and transcripts
Cy3 data from: 060806_251269420744_S01_44k_Feature_Extraction.txt
Cy5 data from: 060806_251269420743_S01_44k_Feature_Extraction.txt


title: BLKSJ-low glucose-1

description:
Agilent's Whole Mouse Genome Oligo microarray is comprised of 41,534 60-mer oligonucleotide probes representing over 41,000 mouse genes and transcripts
Cy3 data from: 060806_251269420742_S01_44k_Feature_Extraction.txt
Cy5 data from: 060806_251269420741_S01_44k_Feature_Extraction.txt


title: B6-low glucose-5

description:
Agilent's Whole Mouse Genome Oligo microarray is comprised of 41,534 60-mer oligonucleotide probes representing over 41,000 mouse genes and transcripts
Cy3 data from: 060806_251269420763_S01_44k_Feature_Extraction.txt
Cy5 data from: 060806_251269420764_S01_44k_Feature_Extraction.txt


title: B6-low glucose-3

description:
Agilent's Whole Mouse Genome Oligo microarray is comprised of 41,534 60-mer oligonucleotide probes representing over 41,000 mouse genes and transcripts
Cy3 data from: 060806_251269420745_S01_44k_Feature_Extraction.txt
Cy5 data from: 060806_251269420760_S01_44k_Feature_Extraction.txt


title: B6-low glucose-2

description:
Agilent's Whole Mouse Genome Oligo microarray is comprised of 41,534 60-mer oligonucleotide probes representing over 41,000 mouse genes and transcripts
Cy3 data from: 060806_251269420743_S01_44k_Feature_Extraction.txt
Cy5 data from: 060806_251269420744_S01_44k_Feature_Extraction.txt


title: wt2_mem_CD8

description: gene-level analysis; MoEx-1_0-st-v1.r2.dt1.mm8.core.mps


title: wt1_mem_CD8


title: wt3_mem_CD8


title: thu3_mem_CD8


title: wt3_mem_CD4


title: thu2_mem_CD8


title: thu1_mem_CD8


title: wt4_mem_CD4


title: wt4_mem_CD8


title: thu2_mem_CD4


title: thu4_mem_CD4


title: thu1_mem_CD4


title: wt2_mem_CD4


title: wt1_mem_CD4


title: thu2_naive_CD8


title: wt4_naive_CD4


title: wt3_naive_CD4


title: thu3_naive_CD4


title: thu1_naive_CD8


title: thu4_naive_CD4


title: wt4_naive_CD8


title: thu3_naive_CD8


title: thu4_naive_CD8


title: thu3_mem_CD4


title: wt1_naive_CD8


title: wt2_naive_CD4


title: wt3_naive_CD8


title: thu2_naive_CD4


title: wt1_naive_CD4


title: thu1_naive_CD4

description: exon-level analysis


title: wt2_naive_CD8


title: thu1_naive_CD4


title: WT_Thymus_CD8-1B


title: WT_Thymus_CD8-1A


title: WT_Thymus_CD8-1C


title: Thu_Thymus_CD8-2C


title: Thu_Thymus_CD8-2D


title: Thu_Thymus_CD8-2B


title: WT_Thymus_CD4-1C


title: Thu_Thymus_CD8-2A


title: WT_Thymus_CD8-1D


title: WT_Thymus_CD4-1A


title: Thu_Thymus_CD4-2A


title: Thu_Thymus_CD4-2B


title: Thu_Thymus_CD4-2C


title: Thu_Thymus_CD4-2D


title: WT_Thymus_CD4-1B


title: WT_Thymus_CD4-1D


title: S404AGR(Dex)::3

status: Public on Nov 24 2008

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Cells were grown in DMEM-F12 medium, supplemented with 10% Fetal Bovine Serum. 48 hour before treatments, cells were placed in DMEM-F12 medium supplemented with 10% charcoal-dextran-treated FBS.  Cells were not treated or were treated with 100 nM dexamethasone for 6 hr.

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data were obtained and processed with the Agilent Feature Extraction Software (v9.5).  The Agilent Feature Extraction Software performed error modeling, adjusting for additive and multiplicative noise.  The resulting data were imported into Rosetta Resolver (v7.1) and log2 intensities were exported.

source_name: S404A Glucocorticoid receptor alpha treated for 6 hr, replicate 3

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: The RNeasy RNA extraction kit, with on column DNAse digestion (Qiagen) was used, according to manufacturer's protocol.

tag: Human osteosarcoma, female


title: S404AGR(Dex)::1

source_name: S404A Glucocorticoid receptor alpha treated for 6 hr, replicate 1


title: S404AGR(-)::2

source_name: S404A Glucocorticoid receptor alpha treated for 0 hr, replicate 2


title: WTGR(-)::3

source_name: WT Glucocorticoid receptor alpha treated for 0 hr, replicate 3


title: WTGR(Dex)::2

source_name: WT Glucocorticoid receptor alpha treated for 6 hr, replicate 2


title: WTGR(Dex)::3

source_name: WT Glucocorticoid receptor alpha treated for 6 hr, replicate 3


title: S404AGR(-)::1

source_name: S404A Glucocorticoid receptor alpha treated for 0 hr, replicate 1


title: mMSC-NCP secretome

status: Public on Oct 18 2008

type: protein

city: Louisville

last: Li

state: KY

address: 580 S. Preston st.,

institute: Gheens Center on Aging

description:
separation: the tryptic peptides were quantified by a QSTAR® XL hybrid liquid tandem mass spectrometry system (Applied Biosystems) interfaced with an 1100 Series Capillary LC system (Agilent).

digestion: 20 µg of trypsin

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing:
software: MS and MS/MS data were analyzed for protein identification using ProteinPilotTM software 2.0.1 (Applied Biosystems) with the Paragon Algorithm.

parameters: A peptide was considered unique if it had a unique raw peptide sequence; peptides identified with unmodified and oxidized forms of methionine were only counted once. All data were searched against NCBI sequence database released on 04-22, 2008. All searches were performed with MMTS for Cys Alykylation, Trypsin digestion. Species are Mus musculus.

quantification: The search parameters were 95% confidence for protein identification threshold, trypsin as enzyme,  and thorough ID as search method, as described in the manufacturer’s protocol

label: not applicable

molecule: protein

source_name: Secretome

label_protocol: not applicable

growth_protocol: Mouse primary marrow stromal cells (MSCs) were isolated according to the method described by Azizi et al. from GFP adult mice. Mouse MSCs were cultured in neural cell differentiation media (Neurobasal medium, (Invitrogen) supplemented with 0.5 µmol/L all-trans-retinoic acid (Sigma), 1% FBS (Thermo Fisher Scientific), 5% horse serum (Hyclone), 1% N2 supplement (Invitrogen), 1% penicillin/streptomycin (Thermo Fisher Scientific), and 10 ng/mL rh-BDNF (Promega)) for 14 days.

extract_protocol: 20 µg of trypsin was added to 150 µg of mMSC-NPC secretome proteins, incubated overnight at 37 °C, purified by a BioCAD HPLA system, and peak fractions were selected.

treatment_protocol: After 14 days’ induction, neural progenitor cells (90% confluent) from both mouse MSCs were washed in plain DMEM medium (without serum) 3 times. 5 ml plain DMEM medium (Manassas) were added to each plate (50,000 cells/plate). Twenty-four hours later, culture supernatant was collected as secretome, and centrifuged (1000 × g, 4 ºC ) for 10 minutes, filtered with 0.22-µm low protein binding membrane (Millipore), then stored in aliquots in -80 ºC

tag: gender


title: S404AGR(Dex)::2

source_name: S404A Glucocorticoid receptor alpha treated for 6 hr, replicate 2


title: WTGR(-)::1

source_name: WT Glucocorticoid receptor alpha treated for 0 hr, replicate 1


title: S404AGR(-)::3

source_name: S404A Glucocorticoid receptor alpha treated for 0 hr, replicate 3


title: WTGR(Dex)::1

source_name: WT Glucocorticoid receptor alpha treated for 6 hr, replicate 1


title: WTGR(-)::2

source_name: WT Glucocorticoid receptor alpha treated for 0 hr, replicate 2


title: VT reference technical replicate 2

status: Public on Oct 07 2008

city: Montréal

first: Amandine

last: Bemmo

state: Québec

address: 740, Dr Penfield Avenue

department: Human Genetics

country: Canada

institute: McGill University

description:
Meta-probeset expression data (transcript cluster ids)
apt-probeset-summarize -p ../../LIBRARY_FILES/HuEx-1_0-st-v2.pgf -c ../../LIBRARY_FILES/HuEx-1_0-st-v2.clf -b ../../LIBRARY_FILES/antigenomic.bgp -a plier-gcbg-sketch -a dabg --use-feat-effect plier-gcbg-sketch.feature-response.txt --rm-probes probe_mask_list_maqc2_2SD.txt --probeset-ids meta-probeset.core.txt.mask

hyb_protocol: Hybridization was performed using 5 micrograms of biotinylated target, which was incubated with the GeneChip® Human Exon 1.0 ST array (Affymetrix) at 45˚C for 16-20 hours. Following hybridization, non-specifically bound material was removed by washing and detection of specifically bound target was performed using the GeneChip® Hybridization, Wash and Stain kit, and the GeneChip® Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix) and raw data was extracted from the scanned images and analyzed with the Affymetrix Power Tools software package (Affymetrix).

data_processing: The Affymetrix Power Tools software package (Affymetrix) was used to quantile normalize the probe fluorescence intensities and to summarize the probe set (representing exon expression) and meta-probe set (representing gene expression) intensities.

source_name: Brain Reference RNA

label_protocol: Biotin-labelled target for the microarray experiment were prepared using 1µg of total RNA. The RNA was subjected to a rRNA removal procedure with the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen) and cDNA was synthesized using the GeneChip® WT (Whole Transcript) Sense Target Labeling and Control Reagents kit as described by the manufacturer (Affymetrix)

extract_protocol: total RNA was extracted

tag: Brain Reference RNA

tag: catalog no. 6050


title: VT brain technical replicate 5

source_name: Universal Human Reference RNA

tag: Universal Human Reference RNA

tag: catalog no. 740000


title: VT reference technical replicate 3


title: VT brain technical replicate 4


title: VT reference technical replicate 1


title: VT reference technical replicate 4


title: VT reference technical replicate 5


title: VT brain technical replicate 2


title: VT brain technical replicate 1


title: thu4_mem_CD8


title: VT brain technical replicate 3


title: MU brain technical replicate 5


title: MU brain technical replicate 4


title: MU brain technical replicate 3


title: MU brain technical replicate 2


title: MU reference technical replicate 4


title: MU reference technical replicate 3


title: MU reference technical replicate 2


title: MU reference technical replicate 5


title: MU brain technical replicate 1


title: MU reference technical replicate 1


title: VT reference technical replicate 4

description:
Probeset expression data
apt-probeset-summarize -p ../../LIBRARY_FILES/HuEx-1_0-st-v2.pgf -c ../../LIBRARY_FILES/HuEx-1_0-st-v2.clf -b ../../LIBRARY_FILES/antigenomic.bgp -a plier-gcbg-sketch -a dabg --feature-effects --rm-probes probe_mask_list_maqc2_2SD.txt


title: VT reference technical replicate 3


title: VT reference technical replicate 5


title: VT brain technical replicate 5


title: VT brain technical replicate 1


title: VT reference technical replicate 1


title: MU brain technical replicate 5


title: VT brain technical replicate 4


title: 05-050 gDNA, 40C-Wpa, 5ng, experiment ID 94902

status: Public on Sep 24 2008

first: Xinghua

last: Pan

address: 300 Cedar Street, TAC-S320

department: Department of Genetics

description: HR-CGH was performed in order to demonstrate the detectability of the breakpoints and size of known large aberrations (Copy Number Variations). This particular array was applied for judging the possible locus-by-locus bias and distortion (if any) existed with the products resulted from the process of whole genome amplification (40C-Wpa) with an input of the original gDNA.

hyb_protocol: Hybridization performed by NimbleGen Inc. using NimbleGen protocol.

scan_protocol: Scan performed by NimbleGen Inc. using NimbleGen protocol and NimbleScan software.

data_processing: The data were processed in genomic region bins of a number of varying sizes. Using NimbleScan software, data were qspline-normalized. The normalized data, representing log2 (test/reference) ratios, are provided in the .gff files.

source_name: 5 ng of sample 05-050 genomic DNA, amplified using 40C-Wpa

label_protocol: Labeling performed by NimbleGen Inc. using NimbleGen protocol.

extract_protocol: QiaGen QIAEXII kit with the option for >4 kb DNA

tag: Genomic DNA sample originally with large-scale deletions in Cs22.

tag: 40C-Wpa was started from 5 ng of the gDNA.

source_name: 5 ng genomic DNA from 7 normal male individuals (Promega), amplified using 40C-Wpa

tag: Pooled genomic DNA from 7 normal male individuals (Promega).

tag: Used as control.


title: 05-050 gDNA, Wpa, 5ng, experiment ID 141539

description: HR-CGH was performed in order to demonstrate the detectability of the breakpoints and size of known large aberrations (Copy Number Variations). This particular array was applied for judging the possible locus-by-locus bias and distortion (if any) existed with the products resulted from the process of whole genome amplification (Wpa) with an input of the original gDNA.

source_name: 5 ng of sample 05-050 genomic DNA, amplified using Wpa

tag: Wpa was started from 5 ng of the gDNA.

source_name: 5 ng genomic DNA from 7 normal male individuals (Promega), amplified using Wpa


title: 04-018 gDNA, Wpa, 0.5ng, experiment ID 145381

source_name: 0.5 ng of sample 04-018 genomic DNA, amplified using Wpa

tag: Wpa was started from 0.5 ng of the gDNA.

source_name: 0.5 ng genomic DNA from 7 normal male individuals (Promega), amplified using Wpa


title: MU brain technical replicate 1


title: MU brain technical replicate 2


title: C17_IP_2280_NOC

status: Public on Jul 18 2008

city: London

first: claudio

last: d'ambrosio

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: Cancer Research UK

description: comparison of condensin Brn1-9PK subunit (C15 and C16 averaged) with TopoII-9PK (comparison of TopoII-9PK with the cohesin subunit Scc1-9PK in the supplementary Figure 4)

hyb_protocol: Hybridization was performed as previously described (Katou et al. 2003). Samples were hybridized for 16 hours at 42ºC in a hybridization oven (GeneChip Hybridization Oven 640, Affymetrix)

scan_protocol: The washing and scanning protocol, provided by Affymetrix, was performed automatically on a fluidics station (GeneChip fluidics station 450, Affymetrix)

data_processing: Data were processed following the protocol provided by Affymetrix (GCOS ver 1.4)

organism: Saccharomyces cerevisiae

source_name: ChIP DNA from yeast Saccharomyces cerevisiae cells

label_protocol: DNA was labeled with biotin-N6-ddATP using terminal transferase TdT (Roche, 400U/µl).

growth_protocol: Cells in YP + 2% glucose were synchronized in metaphase with the spindle depolymerising drug nocodazole

extract_protocol: Extraction was performed as previously described (Katou et al. 2003).

tag: Genotype

value: MATa TopoII-9PK

tag: 2 hours nocodazole arrested cells

tag: Strain

tag: Antibody

value: anti-PK


title: M9.IPA.

label: DNA was labeled with biotin-N6-ddATP using terminal transferase TdT (Roche, 400U/µl)

treatment_protocol: Extraction was performed as previously described (Katou et al. 2003)

value: MATa Scc1-9PK


title: 04-018 gDNA, 40C-Wpa, 5ng, experiment ID 98690

source_name: 5 ng of sample 04-018 genomic DNA, amplified using 40C-Wpa


title: VT reference technical replicate 2


title: C15_SUP_2200_NOC

source_name: Input DNA from Saccharomyces cerevisiae cells from unbound fraction

value: MATa Brn1-9PK


title: 05-050 gDNA, experiment ID 42762

description: HR-CGH was performed in order to demonstrate the detectability of the breakpoints and size of large aberrations (Copy Number Variations). This particular array was used as the control as the native DNA pair for judging the possible locus-by-locus bias and distortion (if any) existed with the products resulted from the process of whole genome amplification with an input of the same original gDNA.

source_name: Genomic DNA for sample 05-050

extract_protocol: Standard protocol for genomic DNA.

tag: Genomic DNA sample with large-scale deletions in Cs22.

source_name: Genomic DNA from 7 normal male individuals (Promega)


title: C16_IP_2200_NOC


title: 04-018 gDNA, Wpa, 0.1ng, experiment ID 141565

source_name: 0.1 ng of sample 04-018 genomic DNA, amplified using Wpa

tag: Wpa was started from 0.1 ng of the gDNA.

source_name: 0.1 ng genomic DNA from 7 normal male individuals (Promega), amplified using Wpa


title: MU reference technical replicate 4


title: C15_IP_2200_NOC


title: 04-018 gDNA, Wpa, 5ng, experiment ID 141542

source_name: 5 ng of sample 04-018 genomic DNA, amplified using Wpa


title: MU reference technical replicate 1


title: MU brain technical replicate 4


title: MU reference technical replicate 5


title: 04-018 gDNA, experiment ID 36320

source_name: Genomic DNA for sample 04-018


title: MU reference technical replicate 3


title: MU reference technical replicate 2


title: MG-thymoma-female (transcript)

status: Public on Jul 03 2008

first: Lilach

last: Soreq

address: Queen Square

department: Molecular  Neuroscience

institute: UCL

description: transcript cluster id summary data generated from A12Exon.CEL

hyb_protocol: Each sample was hybridized to a GeneChip® Exon 1.0 ST Array (Affymetrix, Santa Clara, CA, USA) according to manufacturer's instructions

scan_protocol: Affymetrix GCS 3000 7G scanner

data_processing: scanning through GeneChip® Operating Software  (GCOS)

source_name: MG-thymoma

label_protocol: Whole transcripts sense targeting labeling assay

extract_protocol: RNeasy lipid tissue kit (Qiagen, Valencia, CA)

tag: Thymus

tag: Gender

value: Female, age:53


title: intestine_nhe3

status: Public on Aug 08 2008

city: Cincinnati

first: Gary

last: Shull

state: OH

address: 231 Albert Sabin Way ML0524

institute: University of Cincinnati

hyb_protocol: The microarrayed DNA probes were incubated in Prehybridization Buffer (5X SSC, 0.1% SDS, and 1% bovine serum albumin) at 42oC for 90 min.  For hybridization, the microarray slides are spotted with 42 ml Hybridization Buffer  (25% formamide, 5X SSC, 0.1% SDS, 5 mg/ml COT1-DNA, 5 mg/ml poly(A)-DNA, and 2 mg/ml yeast tRNA) and the fluorescence-labeled target cDNA; covered with glass coverslips (Fisher; Pittsburgh, PA), and placed in humidified hybridization chambers (Corning; Acton, MA).  The hybridization chambers were placed in a water bath at 48°C for 66 hr.  The slides were placed in a slide rack set in a staining dish and washed in 1X SSC with 0.2% SDS for 4 min at 48°C with agitation and transferred to a staining dish with 0.1X SSC and 0.2% SDS and washed with agitation for 4 min at room temperature and two times for 4 min each in 0.1X SSC at room temperature.  The slides were spun-dried immediately after washing.

scan_protocol: Imaging and data generation were carried out using a GenePix 4000A and GenePix 4000B (Axon Instruments; Union City, CA) and associated software from Axon Instruments, Inc. (Foster City, CA).  The microarray slides were scanned with dual lasers with wavelength frequencies to excite Cy3 and Cy5 fluorescence emittance.  Images were captured in JPEG and TIFF files, and DNA spots captured by the adaptive circle segmentation method.  Information extraction for a given spot is based on the median value for the signal pixels minus the median value for the background pixels to produce a gene set data file for all the DNA spots.  The Cy3 and Cy5 fluorescence signal intensities were normalized.

data_processing: See: Sartor, et al. BMC Bioinformatics. 2006 Dec 19;7:538.

source_name: total RNA from whole small intestine

label_protocol: Fluorescence-labeled cDNAs were synthesized from total RNA using an indirect amino allyl labeling method via an oligo(dT)-primed, reverse transcriptase reaction.  The cDNA was decorated with monofunctional reactive Cy3 and Cy5 dyes.

growth_protocol: Adult mice.

extract_protocol: Total RNA was extracted from whole small intestine using Tri-Reagent according to the manufacturer's instructions.

tag: strain

value: FVBN mice, variable:WT

value: FVBN mice, variable:NHE3 KO


title: Normal Thymus-female (transcript)

description: transcript cluster id summary data generated from A13Exon.CEL

source_name: Normal Thymus

value: Female, age:46


title: Normal Thymus-male (transcript)

description: transcript cluster id summary data generated from A14Exon.CEL

value: Male, age:43


title: 04-018 vs. 04-018 gDNA (self), experiment ID 47750

institute: Yale University School of Medicine

description: HR-CGH was performed in order to demonstrate the detectability of the breakpoints and size of large aberrations (Copy Number Variations). This particular array was accomplished to show the ratio of a DNA sample against itself on array, which was to demonstrate the variability/noise of the array hybridization itself. Theoretically the ratio should be 1 (or log2 ratio = 0).


title: SMAD2/3 localization in TGF-beta-treated HaCaT cells

status: Public on Oct 29 2008

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

country: Japan

institute: University of Tokyo

description: HaCaT cells treated with TGF-beta3 were used for Smad2/3 ChIP. Sheared input genomic DNA was used for control. Both Smad2/3 ChIP and input samples were prepared as biological duplicate.

hyb_protocol: Each sample was hybridized to the array in 200 ul containing 1XHybridization buffer (Affymetrix), 50pM Control oligonucleotide (oligo B2, Affymetrix), Herring Sperm DNA (0.1mg/ml), Acetylated BSA (0.5mg/ml), and 7% DMSO. Samples were denatured at 100C for 10 minutes, and then put on ice before being hybridized for 16 hours at 45C in an hybridization oven (GeneChip Hybridization Oven 640, Affymetrix).

scan_protocol: Arrays were scanned using the Genechip Scanner3000 7G following the library array description.

data_processing: Array intensity data from duplicated experiments of ChIP and input fraction were compared by MAT (Model-based Analysis of Tiling-array) algorithm, using the software provided by the laboratory of X.Shirley Liu (http://chip.dfci.harvard.edu/~wli/MAT/). We calculated MAT score and mapped the results to genomic positions in human genome assembly hg 17 (NCBI Build 35). Bandwidth and MaxGap parameters were set to 275 and 275, respectively. We use two Smad2/3 ChIP .CEL files (2HaCaT_Smad2_3_promR.CEL and 5HaCaT_Smad2_3_promR.CEL) and two input .CEL files (2HaCaT_input_promR.CEL and 5HaCaT_input_promR.CEL)(they are biologically duplicated experiments) to make one profile.

label_protocol: DNA was amplified by IVT (In vitro transcription) method. For the labeling, DNA was fragmented by DNaseI. DNA was end-labeled by Terminal Transferase with biotin-11-ddATP.

growth_protocol: HaCaT cells were maintained in Dulbecco's modified Eagle's (DMEM 11965, GIBCO/Invitrogen, CA) supplemented with 10% fetal bovine serum (FBS), 100 U/ml of penicillin G, and 100 microgram/ml of streptomycin. Cells were grown in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol: Cells were fixed with 1% formaldehyde for 10 min at room temperature with swirling. Glycine was added to a final concentration of 0.125 M, and the incubation was continued for an additional 5 min. Cells were washed twice with ice-cold PBS, harvested by scraping, pelleted, and resuspended in 1 ml of SDS lysis buffer [50 mM Tris-HCl (pH 8.1), 1% SDS, 10 mM EDTA, and protease inhibitors (P8340)]. Samples were sonicated four times 15 sec each with an interval of 30 sec with a UH-50 sonicator (SMT, Japan). Samples were centrifuged at 14,000 rpm at 8C for 10 min. After removal of a control aliquot (Input_DNA), supernatants were diluted ten-fold in ChIP dilution buffer [20 mM Tris-HCl (pH 8.0), 150 mM NaCl, 2 mM EDTA, 1% TritonX-100, and Complete EDTA-free protease inhibitors (Roche Diagnostics, Switzerland)]. Samples were incubated at 4C overnight in 2-methacryloyloxyethyl phosphorylcholine polymer-treated 15 ml polypropylene tubes (Assist, Japan) with anti-mouse IgG-Dynabeads that had been pre-incubated with 10 microgram of anti-Smad2/3 in PBS / 0.5% bovine serum albumin (BSA). Beads were then moved to 1.7 ml siliconized tubes (#3207, Corning, NY), and were washed five times with ChIP wash buffer [50 mM HEPES-KOH (pH 7.0), 0.5 M LiCl, 1 mM EDTA, 0.7% DOC, 1% Igepal CA630] and once with TE buffer (pH 8.0). Immunoprecipitated samples were eluted and reverse-crosslinked by incubation overnight at 65C in elution buffer [50 mM Tris-HCl (pH 8.0), 10 mM EDTA, 1% SDS]. Genomic DNA was then extracted with a PCR purification kit (Qiagen).

treatment_protocol: Cells were stimulated with 3ng/ml (120pM) of TGF-beta3 in growth medium for 1.5 hours.

tag: immmortalized keratinocyte cell line

extract_protocol: Cells were fixed with 1% formaldehyde for 10 min at room temperature with swirling. Glycine was added to a final concentration of 0.125 M, and the incubation was continued for an additional 5 min. Cells were washed twice with ice-cold PBS, harvested by scraping, pelleted, and resuspended in 1 ml of SDS lysis buffer [50 mM Tris-HCl (pH 8.1), 1% SDS, 10 mM EDTA, and protease inhibitors (P8340)]. Samples were sonicated four times 15 sec each with an interval of 30 sec with a UH-50 sonicator (SMT, Japan). Samples were centrifuged at 14,000 rpm at 8C for 10 min. Aliquot of the supernatant was reverse-crosslinked by incubation overnight at 65C in elution buffer [50 mM Tris-HCl (pH 8.0), 10 mM EDTA, 1% SDS]. Genomic DNA was then extracted with a PCR purification kit (Qiagen).


title: VT brain technical replicate 2

source_name: Universal Human Reference RNA

tag: Universal Human Reference RNA

tag: catalog no. 740000


title: MU brain technical replicate 3

source_name: Brain Reference RNA

tag: Brain Reference RNA

tag: catalog no. 6050


title: intestine_nhe3cftr

value: FVBN, variable:double KO


title: VT brain technical replicate 3


title: RNA exosome depletion reveals ubiquitous transcriptional activity upstream of active human promoters

status: Public on Aug 15 2008

city: Århus

first: Pascal

last: Preker

address: C. F. Møllers Alle, Bldg 1130

country: Denmark

institute: Århus University

description: Labeling, hybridization to hg17 ENCODE 50mer tiling arrays (catalog number C1980001), analysis of primary data and data processing were all paid services by Roche NimbleGen (http://www.nimblegen.com/).

hyb_protocol: Hybridization to hg17 ENCODE 50mer tiling arrays (catalog number C1980001) by Roche NimbleGen (http://www.nimblegen.com/).

scan_protocol: NimbleScan version=2.3.78 by Roche NimbleGen (http://www.nimblegen.com/).

data_processing:
Analysis of primary data and data processing were all paid services by Roche NimbleGen (http://www.nimblegen.com/).
The log2-ratio is computed and scaled to center the ratio data around zero. Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value.

molecule: polyA RNA

source_name: HeLa cells treated with siRNA against eGFP (control)

label_protocol: Labeling with Cy3 and Cy5, respectively, by Roche NimbleGen (http://www.nimblegen.com/).

extract_protocol: RNA was extracted using Trizol (Invitrogen) according to the manufacturers protocol. Double-stranded cDNA was generated from 20 μg of total RNA from eGFP and hRrp40 siRNA-treated cells using Invitrogens double-stranded cDNA synthesis kit and an anchored primer (T20VN).

treatment_protocol: HeLa cells were grown in DMEM medium supplemented with 10% fetal bovine serum at 37°C and 5% CO2. Transfections were done with 20 nM siRNA for 3 days and repeated for another 3 days both times using Lipofectamin20000 as transfecting agent according to the manufacturers instructions (Invitrogen).

tag: HeLa cells cultured in DMEM medium

source_name: HeLa cells hRrp40 siRNA-treated (test)


title: H3K4me2 normalized to Input DNA

status: Public on Feb 12 2008

city: New York

first: Neri

last: Minsky

state: NY

address: 1230 York Avenue

institute: Rockefeller University

description: This single channel data is submitted as 2 channel in order to represent the ChIP-chip nature of the experiment. Analysis was performed using Hs_PromPR_v02-3_NCBIv34.bpmap, but probe coordinates were mapped to NCBIv35 (hg17) using the LiftOver tool (UCSC). Subsequent analysis was done relative to hg17.

hyb_protocol: Array hybridization was carried out using the Affymetrix Chromatin Immunoprecipitation (ChIP) Assay kit according to the manufacturer’s instructions.

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 7G per manufacturer's protocol.

data_processing: Processed values (normalized log-ratios) for ChIP-chip "Samples" were calculated by (1) taking logs of raw intensities, (2) scaling probes with the same G/C content in each array to have a median zero, (3) and taking the difference between the H2B (or H3K4me2) and a specific control (one of H3/Control-Input/Control-Ab). Probe locations refer to the hg17 version of the human genome (UCSC).

source_name: H3K4me2 ChIP DNA from HCT116

label_protocol: DNA amplification and labeling were carried out using the Affymetrix Chromatin Immunoprecipitation (ChIP) Assay kit according to the manufacturer’s instructions.

growth_protocol: HCT116 cells were grown in McCoy's 5A medium supplemented with 10% FCS and antibiotics

extract_protocol: 5x10E6 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of Cell lysis buffer (5mM PIPES, pH=8, 85mM KCL, 0.5% NP-40). Nuclei were pelleted (4000rpm, 5min) and resuspended in Nuclei Lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0). The crosslinked chromatin was then sheared to an average size of 500 bp. The lysate was then centrifuged to remove cell debris. The chromatin was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and pre-cleared with 25 µl protein A sepharose beads (pre-absorbed with salmon sperm DNA and BSA) for 2 h at 4C. The chromatin supernatant was then incubated overnight with the antibody and with protein A sepharose beads (30 µl) at 4C. The immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4C; Dilution buffer (see above), dialysis buffer (2mM EDTA. 50mM TRIS pH=8) LiCl buffer (500 mM LiCl, 100 mM Tris pH=8.0, 1% Na deoxycholate, 1% NP40) and TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in elution buffer (1% SDS, 100 mM NaHCO3) followed by the addition of RNAse A (37C 1hr) and proteinaseK to 500 µg/ml (45C 3hr). Samples were then subjected to overnight incubaton at 65C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input by the PCR product purification kit (QIAGEN). RNA was extracted using the QIAGEN RNeasy kit according to the manufacturer's protocol.

treatment_protocol: Treatment: no treatment

tag: Age

value: cell line

tag: Human colorectal cancer

source_name: Input DNA from HCT116

tag: no antibody


title: H3K4me2 normalized to non-specific antibody

source_name: Control antibody ChIP DNA from HCT116

value: Control antibody


title: MG-thymoma-male (probe set)

description: probe set (exon) summary data generated from A11Exon.CEL

value: Male, age:44