title: Con067

description: set:Training Set

source_name: peripheral blood

value: control

value: Male

value: peripheral blood

value: No

tag: other positive results

tag: corrected gestational age (weeks+days)

tag: birthweight (g)


title: Mock 8 hr FibroS100

status: Public on Apr 14 2011

type: RNA

city: Stanford

first: Patrick

middle: O

last: Brown

state: CA

address: Beckman Center b439

department: Department of biochemistry

country: USA

institute: Stanford university school of medicine

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55167.gif
Figure in article: 1

hyb_protocol: not provided

scan_protocol: scanner model: GenePix 4000B

data_processing: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA). Grids were manually aligned and features were found using the software feature extraction. Features were visually inspected for blemishes and removed from downstream analysis. Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/) and normalized using regression correlation. Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array. Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays. For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples. The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis. The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins

molecule: total RNA

organism: Homo sapiens

source_name: Stratagene UHR RNA, 1 round of amp(Ambion MessageAmp), 6/27/02, spiked in MPX/VAC 8/26/04

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: Stratagene Universal Human Reference RNA

source_name: Mock 8 hr Primary Human Skin Fibroblasts S100 Mock Infected in vitro 7.29.04

label_protocol: Rubins 2003 - Labeling Amplified RNA - Direct Incorporation of Cy Dyes; Preparation of Fluorescent DNA Probe from Amplified mRNA  1. To anneal primer, mix 3-4ug of amplified mRNA with 10ug of random hexamer primer in a total volume of 15.4ul:    mRNA 3-4ug  pdN6 (5 ug/uL) 2uL ddH2O (DEPC) to 15.4 uL Total volume: 15.4 uL  2. Heat to 65oC for 10 min and cool on ice.   3. Add 14.6uL reaction mixture (Master Mix or separate) to each RNA/hexamer mix Reaction mixture  5X first-strand buffer 6.0uL  0.1M DTT 3.0uL Unlabeled dNTPs (low dTTP) 0.6uL Cy3 or Cy5 (1 mM, Amersham) 3.0uL Superscript II (200 U/uL, Gibco BRL) 2.0uL Total volume: 14.6uL   4. Incubate at 42oC for 1 hr.   5. Add 1 uL SSII (RT booster) to each sample. Incubate for an additional 1 hr.   6. Degrade RNA by addition 15uL of 0.1N NaOH and incubate at 65-70oC for 10 min.   7. Neutralize by addition of 15uL of 0.1N HCl.  8. Add 380uL of TE (10mM Tris, 1mM EDTA) to a Microcon YM-30 column.  Next add the 60uL of Cy5 probe and the 60??l of Cy3 probe to the same Microcon.  9. WASH 1: Spin 7-8 min. at 14,000g (=RCF).  Remove flow through and save to a separate tube.  10. WASH 2: Add 450ul 1X TE and spin 7-8 min. at 14,000g. Remove flow through and save to the separate tube.  11.  WASH 3: Add to centricon: 1X TE 450uL 1ug/uL Cot1 human DNA (Gibco-BRL) 20 uL 10ug/uL  polyA RNA (Sigma, #P9403) 2 uL 10ug/uL  tRNA (Gibco-BRL, #15401-011) 2 uL Spin 7-10 min. at 14,000g. Look for nice concentration of the "colored probe" in the centricon. Try to concentrate to a volume of less than 25uL. This volume is attained when the center of the membrane is dry and the probe forms a ring of liquid at the edges of the membrane.  Make sure not to dry the membrane completely!  12. Invert the centricon into a clean tube and spin briefly at 14,000 RPM to recover the probe.; Protocol Type = Labeling; Performer: Kate,,Rubins

extract_protocol:
Rubins 2003 - Trizol Extraction of Total RNA from PBMCs; 1. Make sure the area is clean and free of any RNases.  Keep the samples cold or on ice as much as possible to prevent RNA degradation.   Use only RNase free tubes and RNase free, aerosol-barrier pipette tips throughout the whole experiment.  2. Add 1mL of Trizol to the frozen PBMC pellet.   3. If the Trizol was added to the PBMCs before freezing, thaw the Trizol/PBMCs on the benchtop for 5-10 minutes.  4. Vortex and transfer to 1.5ml microfuge tubes if not already in them.  5. Add 0.2 mls chloroform per 1 ml Trizol.  Vortex or shake vigorously and incubate at room temp. for 2-3 minutes.  6. Centrifuge at 12,000g for 15 minutes at 4C.  7. Transfer the aqueous phase to a fresh tube.  (The volume will be about 60% of the volume of Trizol.)  Note:  If isolating DNA, save the organic phase.  Add 1uL of 1ug/uL Linear Acrylamide if RNA yield is expected to be low.  8. Add 0.5 mLs of isopropanol per 1 ml Trizol used.  Incubate at room temp. for 10 minutes.   9. Centrifuge at top speed (14,000rpm) for 10 minutes at 4C.    10. The RNA pellet will be visible at the bottom of the tube.  Use the vacuum to very carefully aspirate the supernatant. Alternatively, carefully suck off the supernatant with a pipette. Discard supernatant. Check that the pellet is visible at the bottom of the tube.  11. WASH 1: Wash the pellet with 1 ml 70% EtOH.  Centrifuge at top speed 14,000g for 5-7 minutes.  12. Use the vacuum to very carefully aspirate the supernatant. Alternatively, carefully suck off the supernatant with a pipette. Discard supernatant. Check that the pellet is visible at the bottom of the tube.  13. WASH 2:  Wash the pellet with 1 ml 70% EtOH.  Centrifuge at top speed 14,000g for 5-7 minutes.  14. Use the vacuum to very carefully aspirate the supernatant. Alternatively, carefully suck off the supernatant with a pipette. Discard supernatant. Check that the pellet is visible at the bottom of the tube.  15. Air dry pellet shortly, until no EtOH is visible (2-5 minutes).  Do not overdry!  16. Resuspend the pellet in 20uls of DEPC H2O.  Store at ?80C.  17. Check RNA quality and quantity by denaturing gel and OD spec (260nm and 260/280 ratio).; Protocol Type = Extract preparation; Performer: Kate,,Rubins
Rubins 2003 - Ambion Message Amp I; FIRST STRAND CDNA SYNTHESIS: In PCR reaction tube, mix: Amount Reagent 0.1 - 5ug  Total RNA 1uL T7 Oligo (dT) primer 11uL Nuclease free water  70oC for 10 min in a thermocycler with lid on, but not clamped down.   Centrifuge briefly.   Prepare in a Master Mix and keep at room temperature: Amount Reagent 2uL 10X First Strand Buffer 1uL Ribonuclease Inhibitor 4uL dNTP Mix Gently pipette or flick to mix, and then centrifuge briefly.  Incubate master mix at 42oC for 2 minutes prior to adding to reaction tubes.   Add to the master mix: Amount Reagent 1uL Reverse Transcriptase  Quickly transfer 8ul of above Master Mix to each RNA sample, mix by pipetting.   42oC for 2 hours in thermocycler with lid on, but not clamped down.   Centrifuge briefly, place on ice, and immediately proceed to next step  SECOND STRAND SYNTHESIS: Amount Reagent 63uL Nuclease free water 10uL 10X Second Strand Buffer 4uL dNTP Mix 2uL DNA Polymerase 1uL RNase H Add 80uL to each tube. Gently pipette or flick to mix, and then centrifuge briefly.  16oC for 2 hours in thermocycler with lid completely off.    DS cDNA CLEANUP: Preheat the 5mL bottle of water at 50oC for at least 10 minutes. Place filter cartridge in a 2mL tube and add 100ul of cDNA Binding Buffer. Incubate at room temperature for 5 min.  Transfer 100uL reaction from strip-8 PCR tubes into 1.5ml Eppendorf tubes. Add 250uL of cDNA binding buffer to each cDNA sample, mix by pipetting. Add the mix to the filter cartridge. Centrifuge for 1 min at 10,000 x g. Discard flow-through.  Add 650ul of cDNA wash buffer. Centrifuge for 1 min. at 10,000 x g. Discard flow-through. Centrifuge again for 1 min at 10,000 x g to remove trace amounts of ethanol.  Transfer filter cartridge to fresh 2mL tube Add 50uL of preheated water to the center of the column.   Incubate at room temperature for 2 minutes. Centrifuge for 1 minute at 10,000 x g. Repeat elution with a second 50ul of preheated water. Centrifuge for 1 minute at 10,000 x g.   Transfer to strip-8 PCR tubes and mark a line for 8uL Concentrate the purified cDNA to < 8uL by drying in a vacuum centrifuge on high heat.   Resuspend cDNA up to 8uL with H20, mix well, and keep on ice or store at ?20oC.  IN VITRO TRANSCRIPTION  Prepare the following master mix: Amount Reagent 8uL T7 NTP mix (75 mM each) 2uL T7 10X Reaction Buffer 2uL T7 Enzyme Mix Add 12uL to each tube. Gently pipette or flick to mix, and then centrifuge briefly.  37oC for 6 hours in hybridization oven.  Add to each reaction: Amount Reagent 2uL DNaseI  Gently pipette or flick to mix, and then centrifuge briefly.  37oC for 30min in hybridization oven   aRNA PURIFICATION  Preheat 5mL bottle of nuclease free water at 50oC for at least 10 minutes.  Immediately before staring aRNA purification., equilibrate 1 filter cartridge per aRNA sample Place filter cartridge in a 2mL tube and add 100ul of aRNA Binding Buffer. Incubate at room temperature for 5 min.  Add 78uL aRNA Elution Solution to each IVT mix to bring final volume up to 100uL.   Add 350uL of aRNA Binding Buffer to each aRNA sample. Add 250uL of ACS grade 95% ethanol to each sample. Mix by pipetting or gentle vortexing.  Apply entire sample to the equilibrated filter cartridge.  Centrifuge for 1 minute at 10,000 x g.   Discard flow-through but re-use tube.  Add 650uL aRNA Wash Buffer to each filter.   Centrifuge for 1 minute at 10,000 x g.   Discard flow-through but re-use tube. Centrifuge again for 1 min at 10,000 x g Transfer cartridge to a fresh 2mL tube.  Elute aRNA by adding 50uL preheated (50oC) water to center of column.  Incubate at room temperature for 2 min.  Centrifuge for 1 minute at 10,000 x g.  Repeat elution with a second 50uL of preheated water. Centrifuge for 1 minute at 10,000 x g.   Store aRNA at ?80oC.; Protocol Type = Amplification; Performer: Kate,,Rubins

tag: time

value: 8 h

tag: infection

value: Mock infection

tag: cell type

value: Primary Human Dermal Fibroblast


title: EBOV 8 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55179.gif
Figure in article: 1

source_name: EBOV 8 hr Primary Human Macrophages infected with Ebola-Zaire in vitro 7.29.04

value: Ebola-Zaire

value: Primary Human Macrophage


title: Mock 0 Pool FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55159.gif
Figure in article: 1

source_name: Mock 0 Pool Primary Human Skin Fibroblasts S100 Mock Infected in vitro 7.29.04

value: 0 h


title: ChIP-Seq analysis of H3K27me3 in human CD45RA CD8 cells; DNA_Lib 666

status: Public on Dec 28 2011

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

description:
sample_term_id: CL_0000625
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 666
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8561
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9463
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM772871_BI.CD8_Naive_Primary_Cells.H3K27me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 666-DNA_Lib 666-DNA_Lib 666.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD8 Naive Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on CD8 Naive Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 2011, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10700
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,053,012
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.01
FINDPEAKS_PERCENTILE: 18
HOTSPOT_SCORE: 0.1038
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.5234
IROC_PERCENTILE: 8
POISSON_SCORE: 0.185
POISSON_PERCENTILE: 18
MAXIMUM_REPLICATE_CORRELATION: 0.94

**********************************************************************

ANALYSIS FILE NAME: GSM772871_BI.CD8_Naive_Primary_Cells.H3K27me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 666-DNA_Lib 666-DNA_Lib 666.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from CD8 Naive Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 2011, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10964
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: CD8N H3K27me3 00 66
BROWSER_TRACK_DESCRIPTION: BI CD8 Naive Primary Cells Histone H3K27me3 Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 666 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,053,012
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.01
FINDPEAKS_PERCENTILE: 18
HOTSPOT_SCORE: 0.1038
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.5234
IROC_PERCENTILE: 8
POISSON_SCORE: 0.185
POISSON_PERCENTILE: 18
MAXIMUM_REPLICATE_CORRELATION: 0.94

**********************************************************************

molecule: genomic DNA

source_name: Naive CD8+ T cells; DNA_Lib 666

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

value: BioSam 184

tag: sample common name

value: CD8 Naive Primary Cells

value: presumed normal

tag: molecule

value: genomic DNA

tag: disease

tag: markers

value: CD8 Naive Primary Cell

value: Unknown

value: Primary Cell

value: Donor 100 7 pooled leukopaks Jan 7 2011

value: Dana Farber

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Millipore

value: Histone H3K27me3

value: Branson


title: EBOV 1 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55219.gif
Figure in article: 1

value: Stratagene Universal Human Reference RNA

source_name: EBOV 1 hr Primary Human Skin Fibroblasts S100 infected with Ebola-Zaire in vitro 7.29.04

value: 1 h

value: Ebola-Zaire

value: Primary Human Dermal Fibroblast


title: EBOV 2 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55173.gif
Figure in article: 1

source_name: EBOV 2 hr Primary Human Macrophages infected with Ebola-Zaire in vitro 7.29.04

value: 2 h

value: Primary Human Macrophage


title: Mock 4 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55165.gif
Figure in article: 1

source_name: Mock 4 hr Primary Human Skin Fibroblasts S100 Mock Infected in vitro 7.29.04

value: 4 h

value: Mock infection


title: Mock 2 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55139.gif
Figure in article: 1

source_name: Mock 2 hr Primary Human Macrophages Mock Infected in vitro 7.29.04


title: Mock 2 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55163.gif
Figure in article: 1

source_name: Mock 2 hr Primary Human Skin Fibroblasts S100 Mock Infected in vitro 7.29.04


title: Mock 1 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55161.gif
Figure in article: 1

source_name: Mock 1 hr Primary Human Skin Fibroblasts S100 Mock Infected in vitro 7.29.04


title: Mock 0 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55157.gif
Figure in article: 1

source_name: Mock 0 hr Primary Human Skin Fibroblasts S100 Mock Infected in vitro 7.29.04

value: 0 h


title: EBOV 0 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55217.gif
Figure in article: 1

source_name: EBOV 0 hr Primary Human Skin Fibroblasts S100 infected with Ebola-Zaire in vitro 7.29.04


title: Mock 12 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55141.gif
Figure in article: 1

source_name: Mock 12 hr Primary Human Macrophages Mock Infected in vitro 7.29.04


title: EBOV 12 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55223.gif
Figure in article: 1

source_name: EBOV 12 hr Primary Human Skin Fibroblasts S100 infected with Ebola-Zaire in vitro 7.29.04


title: Mock 4 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55140.gif
Figure in article: 1

source_name: Mock 4 hr Primary Human Macrophages Mock Infected in vitro 7.29.04


title: EBOV 12 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55182.gif
Figure in article: 1

source_name: EBOV 12 hr Primary Human Macrophages infected with Ebola-Zaire in vitro 7.29.04


title: Mock 24 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55171.gif
Figure in article: 1

source_name: Stratagene UHR RNA, 1 round of amp(Ambion MessageAmp), 6/27/02, spiked in MPX/VAC 8/26/04

source_name: Mock 24 hr Primary Human Skin Fibroblasts S100 Mock Infected in vitro 7.29.04


title: Mock 0 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55137.gif
Figure in article: 1

source_name: Mock 0 hr Primary Human Macrophages Mock Infected in vitro 7.29.04


title: EBOV 24 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55224.gif
Figure in article: 1

source_name: EBOV 24 hr Primary Human Skin Fibroblasts S100 infected with  in vitro 7.29.04


title: Mock 9hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50455.gif
Figure in article: 1

source_name: Stratagene Universal Human Reference RNA, 1 round of amp(Ambion MessageAmp), 6/27/02, spiked in MPX

value: 9 h


title: EBOV 24 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55186.gif
Figure in article: 1

source_name: EBOV 24 hr Primary Human Macrophages infected with Ebola-Zaire in vitro 7.29.04


title: Mock 12 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55169.gif
Figure in article: 1

source_name: Mock 12 hr Primary Human Skin Fibroblasts S100 Mock Infected in vitro 7.29.04


title: EBOV 0 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55168.gif
Figure in article: 1

source_name: EBOV 0 hr Primary Human Macrophages infected with Ebola-Zaire in vitro 7.29.04


title: EBOV 4 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55221.gif
Figure in article: 1

source_name: EBOV 4 hr Primary Human Skin Fibroblasts S100 infected with Ebola-Zaire in vitro 7.29.04


title: DB5L Day 6

status: Public on Nov 30 2010

city: Boston

first: Judy

last: Yen

address: 620 Albany St., Rm 401H

department: NEIDL/Microbiology

institute: Boston University School of Medicine

hyb_protocol: 15 µg of Cy5-labeled sample was mixed with 10 µg of Cy3-labeled reference sample and hybridized using protocols found on http://cmgm.stanford.edu/pbrown/protocols/index.html.  Arrays were hybridized in SciGene Hybex incubators.

scan_protocol: Scanned on Axon 4000B and 4200AL scanners. Images were quantified using GenePix and SpotReader.

data_processing: Normalized using regression correlation, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Data were then filtered for signal intensities greater than or equal to 2 (log2 ratio) in either channel via the Stanford Microarray Database.

organism: Macaca mulatta

source_name: Blood sample taken day 6 post-infection, rhAPC treatment

label_protocol: 500 ng of total RNA were reverse-transcribed, linearly amplified through in vitro transcription, and fluorescently labeled using the Ambion Amino Allyl MessageAmp II kit (Applied Biosystems).  Test samples were labeled with Cy5 and reference samples were labeled with Cy3.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions.

treatment_protocol: rNAPc2 was injected subcutaneously at 30 ug/kg per day.  rhAPC was given to animals intravenously at 48 ug/kg per hour.

tag: tissue

value: blood

value: peripheral blood mononuclear cells (PMBCs)

value: Zaire Ebola Virus (ZEBOV)

tag: drug treatment

value: rhAPC

tag: day collected post-infection

tag: ID

source_name: Universal Human Reference

tag: rna source

value: 10 different human cell lines

tag: vendor

value: Stratagene


title: DB5L Day 3

source_name: Blood sample taken day 3 post-infection, rhAPC treatment


title: DB5L Day -8

source_name: Blood sample taken 8 days pre-infection, rhAPC treatment


title: DB1D Day -8


title: DB1D Day 3


title: CL7C Day 16

source_name: Blood sample taken day 16 post-infection, rhAPC treatment


title: EBOV 2 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55220.gif
Figure in article: 1

source_name: EBOV 2 hr Primary Human Skin Fibroblasts S100 infected with Ebola-Zaire in vitro 7.29.04


title: EBOV 8 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55222.gif
Figure in article: 1

source_name: EBOV 8 hr Primary Human Skin Fibroblasts S100 infected with Ebola-Zaire in vitro 7.29.04

value: 8 h


title: CL7C Day 14

source_name: Blood sample taken day 14 post-infection, rhAPC treatment


title: EBOV 0 Pool FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55218.gif
Figure in article: 1

source_name: Stratagene UHR RNA, 1 round of amp(Ambion MessageAmp), 6/27/02, spiked in MPX/VAC 8/26/04

value: Stratagene Universal Human Reference RNA

source_name: EBOV 0 Pool Primary Human Skin Fibroblasts S100 infected with Ebola-Zaire in vitro 7.29.04


title: EBOV 4 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55175.gif
Figure in article: 1

source_name: EBOV 4 hr Primary Human Macrophages infected with Ebola-Zaire in vitro 7.29.04


title: Mock 0 Pool Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55138.gif
Figure in article: 1

source_name: Mock 0 Pool Primary Human Macrophages Mock Infected in vitro 7.29.04


title: Mock 24 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55142.gif
Figure in article: 1

source_name: Mock 24 hr Primary Human Macrophages Mock Infected in vitro 7.29.04


title: CL7C Day 3


title: CL7C Day -8


title: CL7C Day 6


title: CL4R Day 6


title: CH73 Day 6


title: CL4R Day 10

source_name: Blood sample taken day 10 post-infection, rhAPC treatment


title: CL4R Day 14


title: CL7C Day 10


title: CL4R Day 3


title: CH73 Day 10


title: CH73 Day 0

source_name: Blood sample taken day 0 post-infection, rhAPC treatment


title: CH73 Day 14


title: CL4R Day -8


title: DB1D Day 6


title: DB5L Day 10


title: CH35 Day 14


title: CH04 Day 0


title: CH35 Day 0


title: CH35 Day 3


title: CH04 Day 3


title: BBA Day 22

source_name: Blood sample taken day 22 post-infection, rhAPC treatment

value: BBA


title: CH73 Day 3


title: CH35 Day 6


title: BBA Day 14


title: CH04 Day 6


title: BBA Day 10


title: EBOV 0 Pool Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55170.gif
Figure in article: 1

source_name: EBOV 0 Pool Primary Human Macrophages infected with Ebola-Zaire in vitro 7.29.04

value: Ebola-Zaire


title: BBA Day 0


title: AA016 Day 6

source_name: Blood sample taken day 6 post-infection, rhAPC treatment


title: AA016 Day 0

source_name: Universal Human Reference


title: W7K Day 9

source_name: Blood sample taken day 9 post-infection, rNAPc2 treatment


title: L201-2 Day 10

source_name: Blood sample taken day 10 post-infection, rNAPc2 treatment


title: DB1L Day 3

source_name: Blood sample taken day 3 post-infection, rhAPC treatment


title: L201-2 Day 7

source_name: Blood sample taken day 7 post-infection, rNAPc2 treatment


title: DB1L Day -8

source_name: Blood sample taken 8 days pre-infection, rhAPC treatment


title: 94E120 Day 6


title: GKP Day 7

value: GKP


title: GKP Day 13

source_name: Blood sample taken day 13 post-infection, rNAPc2 treatment


title: L201-2 Day 17

source_name: Blood sample taken day 17 post-infection, rNAPc2 treatment


title: BBA Day 6


title: L201-2 Day 3

source_name: Blood sample taken day 3 post-infection, rNAPc2 treatment


title: W7K Day 0

source_name: Blood sample taken day 0 post-infection, rNAPc2 treatment


title: GDK Day 6

source_name: Blood sample taken day 6 post-infection, rNAPc2 treatment

value: GDK


title: W7K Day 6


title: GKP Day 3


title: 94E120 Day 0


title: L201-2 Day 0


title: GKP Day 0


title: 94E120 Day 10


title: W7K Day 3


title: L201-2 Day 6


title: DBF Day 6

value: DBF


title: DBF Day 7


title: GKP Day 6


title: DBF Day 3


title: CH49 Day 6


title: GDK Day 3


title: CH49 Day 3


title: GDK Day 0


title: AXX Day 17

value: AXX


title: CH49 Day 0


title: DBF Day 0


title: CH49 Day 8

source_name: Blood sample taken day 8 post-infection, rNAPc2 treatment


title: AXX Day 6


title: AXX Day 0


title: AXX Day 10


title: 94E136 Day 6


title: 94E136 Day 3


title: AXX Day 3


title: DB7U Day -8

source_name: Blood sample taken 8 days pre-infection, no drug treatment

value: untreated


title: DB7U Day 3

source_name: Blood sample taken day 3 post-infection, no drug treatment


title: 94E136 Day 0


title: 94E136 Day 7


title: CH52 Day 6

source_name: Blood sample taken day 6 post-infection, no drug treatment


title: CH52 Day 3


title: CH52 Day 0

source_name: Blood sample taken day 0 post-infection, no drug treatment


title: GTX Day 0

value: GTX


title: CH78 Day 9

source_name: Blood sample taken day 9 post-infection, no drug treatment


title: DB7U Day 6

source_name: Universal Human Reference


title: Bisulfite-Seq analysis of RRBS677 derived from human H1 cells; RRBS677

status: Public on Nov 11 2010

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS677/RRBS678
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3901
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3907
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM621765_BI.H1.RRBS.RRBS677-678.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS677-RRBS678.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of H1 Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the H1 Cell Line, Libraries RRBS677-678 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5244
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 RRBS 77
BROWSER_TRACK_DESCRIPTION: BI H1 Cell Line RRBS Libraries RRBS677-678 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.8

**********************************************************************

source_name: H1 (WA01) embryonic stem cells; NIH Approval # NIHhESC-10-0043; RRBS677

extract_protocol: Library construction protocol: Smith et al., Methods 48, 226-232

tag: lineage

value: embrionic stem cell

tag: medium

value: TESR

value: genomic DNA

tag: passage

tag: line

tag: batch

value: Cell Line

value: undifferentiated

tag: Sex

value: Male

value: Cellular Dynamics

value: 2x5hrs Epitect Kit

value: 20 ng

value: T4 Ligase (2,000U/ul) 16C o/n

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: Gel size selection

value: Pfu Turbo Cx hot start


title: ChIP-Seq analysis of WCE in human Memory CD4 cells; Lib:RI:20100324:12--ChIP:MA:20100319:12:Memory CD4:WCE

status: Public on Nov 12 2010

description:
sample_term_id: CL_0000897
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20100324:12--ChIP:MA:20100319:12:Memory CD4:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3787
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3884
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM621447_BI.CD4_Memory_Primary_Cells.Input.20.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100324:12--ChIP:MA:20100319:12:Memory CD4:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of CD4 Memory Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on CD4 Memory Primary Cells, Donor 20 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4829
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0094
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.0599
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3463
POISSON_PERCENTILE: 85

**********************************************************************

ANALYSIS FILE NAME: GSM621447_BI.CD4_Memory_Primary_Cells.Input.20.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100324:12--ChIP:MA:20100319:12:Memory CD4:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Memory Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from CD4 Memory Primary Cells, Donor 20 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5103
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CD4M Input 20
BROWSER_TRACK_DESCRIPTION: BI CD4 Memory Primary Cells ChIP-Seq Input Donor 20 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0094
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.0599
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3463
POISSON_PERCENTILE: 85

**********************************************************************

source_name: "Memory CD4 cells derived from fom pooled leukopacks by Ficoll sedimentation, magnetic bead purification, and FACS"; Lib:RI:20100324:12--ChIP:MA:20100319:12:Memory CD4:WCE

value: CD45RO CD4

value: Unknown

value: Primary Cell

value: Whitehead Institute

value: standard

value: SDS lysis

value: ChIP-Seq Input

value: Input

value: Bioruptor


title: Bisulfite-Seq analysis of RRBS776 derived from human H1 cells; RRBS776

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS776/RRBS777/RRBS778/RRBS779
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3924
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3970
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM621705_BI.H1.RRBS.RRBS776-779.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS776-RRBS777-RRBS778-RRBS779.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of H1 Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the H1 Cell Line, Libraries RRBS776-779 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5221
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 RRBS 76
BROWSER_TRACK_DESCRIPTION: BI H1 Cell Line RRBS Libraries RRBS776-779 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.65

**********************************************************************

source_name: H1 (WA01) embryonic stem cells; NIH Approval # NIHhESC-10-0043; RRBS776

value: embrionic stem cell

value: TESR

value: genomic DNA

value: p37 or p38

value: Cell Line

value: undifferentiated

value: Male

value: Cellular Dynamics

value: 2x5hrs Epitect Kit

value: 20 ng

value: T4 Ligase (2,000U/ul) 16C o/n


title: Bisulfite-Seq analysis of RRBS524 derived from human hiPS-18c cells; RRBS524

description:
sample_term_id: NTR_0001167
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS524/RRBS525
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3944
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3956
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM621725_BI.iPS-18c.RRBS.RRBS524-525.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS524-RRBS525.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of iPS-18c Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the iPS-18c Cell Line, Libraries RRBS524-525 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5239
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS18c RRBS 24
BROWSER_TRACK_DESCRIPTION: BI iPS-18c Cell Line RRBS Libraries RRBS524-525 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.9

**********************************************************************

source_name: IPS cell line 18c; RRBS524

value: induced pluripotent stem cells

value: induced pluripotent cells

value: KSR

value: Female

value: Harvard University

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: Gel size selection

value: Pfu Turbo Cx hot start


title: Bisulfite-Seq analysis of RRBS398 derived from human hiPS-18a cells; RRBS398

description:
sample_term_id: NTR_0001165
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS398/RRBS399
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3915
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3962
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM621696_BI.iPS-18a.RRBS.RRBS398-399.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS398-RRBS399.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of iPS-18a Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the iPS-18a Cell Line, Libraries RRBS398-399 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5251
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS18a RRBS 98
BROWSER_TRACK_DESCRIPTION: BI iPS-18a Cell Line RRBS Libraries RRBS398-399 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.52

**********************************************************************

source_name: induced pleuripotent 18a stem cell line; RRBS398

value: genomic DNA

value: Cell Line

value: undifferentiated


title: Bisulfite-Seq analysis of RRBS366 derived from human hiPS-18b cells; RRBS366

description:
sample_term_id: NTR_0001166
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS366/RRBS367
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3914
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3971
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM621695_BI.iPS-18b.RRBS.RRBS366-367.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS366-RRBS367.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of iPS-18b Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the iPS-18b Cell Line, Libraries RRBS366-367 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5222
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS18b RRBS 66
BROWSER_TRACK_DESCRIPTION: BI iPS-18b Cell Line RRBS Libraries RRBS366-367 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 97.74

**********************************************************************

source_name: IPS cell line 18b; RRBS366

value: 2x5hrs Epitect Kit

value: 20 ng


title: Bisulfite-Seq analysis of RRBS396 derived from human hiPS-18c cells; 42LR0AAXX091002-8-S

description:
sample_term_id: NTR_0001167
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: Solexa-13943
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2323
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2305
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM621564_BI.iPS-18c.RRBS.RRBS396.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LR0AAXX091002-8-S.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of iPS-18c Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the iPS-18c Cell Line, Library RRBS396 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5233
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS18c RRBS 96
BROWSER_TRACK_DESCRIPTION: BI iPS-18c Cell Line RRBS Library RRBS396 EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.0

**********************************************************************

source_name: IPS cell line 18c; 42LR0AAXX091002-8-S

value: induced pluripotent stem cells

value: T4 Ligase (2,000U/ul) 16C o/n


title: ChIP-Seq analysis of H3K4me3 in human hiPS-18c cells; 42MNCAAXX100106-8-S

status: Public on Apr 28 2010

description:
sample_term_id: NTR_0001167
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-15173
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2209
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2208
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM537671_BI.iPS-18c.H3K4me3.Solexa-15173.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42MNCAAXX100106-8-S.hg19.level.1
ANALYSIS TITLE: Mapping of iPS-18c Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the iPS-18c Cell Line, Library Solexa-15173 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4638
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.1726
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.1963
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.9958
IROC_PERCENTILE: 18
POISSON_SCORE: 0.3429
POISSON_PERCENTILE: 13

**********************************************************************

ANALYSIS FILE NAME: GSM537671_BI.iPS-18c.H3K4me3.Solexa-15173.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42MNCAAXX100106-8-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-18c Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the iPS-18c Cell Line, Library Solexa-15173 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4912
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS18c H3K4me3 73
BROWSER_TRACK_DESCRIPTION: BI iPS-18c Cell Line Histone H3K4me3 Library Solexa-15173 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.1726
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.1963
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.9958
IROC_PERCENTILE: 18
POISSON_SCORE: 0.3429
POISSON_PERCENTILE: 13

**********************************************************************

source_name: IPS cell line 18c; 42MNCAAXX100106-8-S

value: induced pluripotent cells

value: KSR

value: Histone H3K4me3

value: SDS lysis

value: Bioruptor

value: 10 million cells

value: Protein A-Sepharose 4B

value: 70 ul bed volume

value: Millipore


title: GTX Day 6

value: blood

tag: cell type

value: peripheral blood mononuclear cells (PMBCs)

tag: infection

value: Zaire Ebola Virus (ZEBOV)

value: untreated

value: GTX

value: 10 different human cell lines

value: Stratagene


title: CH78 Day 3


title: CH78 Day 6


title: CH78 Day 0


title: CH78 Day 7

source_name: Blood sample taken day 7 post-infection, no drug treatment


title: CH78 Day 8

source_name: Blood sample taken day 8 post-infection, no drug treatment


title: E2 vs. Con

status: Public on May 09 2008

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Total RNA was labeled using the Agilent Fluorescent Direct Label Kit protocol with a slight modification in the starting amount (10 ?g of starting material was used, rather than 20 ?g).  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol. Slides were washed as indicated in this protocol and then scanned with an Agilent Scanner.

hyb_protocol: Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol. Slides were washed as indicated in this protocol.

scan_protocol: Chips were scanned with an Agilent Scanner and processed with the Agilent Feature Extraction Software (v7.1).

data_processing: Agilent Feature Extraction protocol for the Agilent Human1A array, log2ratio Treated/Control

extract_protocol: Total RNA was prepared from MCF-7 cells treated for 24 h with 10nM 17b-estradiol using Rneasy Midi Kits (Invitrogen).

tag: MCF-7 cells stably expressing the GR and endogenous estrogen receptor.

source_name: Con

extract_protocol: Total RNA was prepared from MCF-7 cells treated for 24 h with vehicle using Rneasy Midi Kits (Invitrogen).


title: Dex (2) vs. Con (2)

source_name: Dex (2)

label_protocol: Total RNA was labeled using the Agilent Fluorescent Direct Label Kit protocol with a slight modification in the starting amount (10 ?g of starting material was used, rather than 20 ?g).

extract_protocol: Total RNA was prepared from MCF-7 cells treated for 24 h with 1nM dexamethasone using Rneasy Midi Kits (Invitrogen).

source_name: Con (2)


title: Con vs. E2+ MG132

extract_protocol: Total RNA was prepared from MCF-7 cells treated for 24 h with MG132 (1uM) and 17b-estradiol (10nM) using Rneasy Midi Kits (Invitrogen).


title: E2 (2) vs. Con (2)


title: Con (2) vs. Dex (2)


title: MG132 (2) vs. Con (2)

extract_protocol: Total RNA was prepared from MCF-7 cells treated for 24 h with 1uM MG132 using Rneasy Midi Kits (Invitrogen).


title: Con (2) vs. MG132 (2)


title: E2 + MG132 (2) vs. Con (2)


title: Dex vs. Con

source_name: Dex


title: E2+ MG132 vs. Con


title: Con (2) vs. MG132 + Dex (2)

extract_protocol: Total RNA was prepared from MCF-7 cells treated for 24 h with dexamethasone (1nM) and MG132 (1uM) using Rneasy Midi Kits (Invitrogen).


title: Con vs. MG132 + Dex

source_name: MG132 + Dex


title: Con vs. Dex


title: Con (2) vs. E2 (2)


title: MG132 vs. Con


title: MG132 + Dex vs. Con


title: Con vs. E2


title: Con (2) vs. E2 + MG132 (2)


title: Con vs. MG132


title: LIVER_DIPYRONE_1636mg/kg_3days_exp6098_rep1_85829

status: Public on Mar 28 2008

city: Mountain View

first: Jeremy

last: Gollub

address: 325 E. Middlefield Rd.

institute: Iconix Biosciences

description:
HybID: 85829
treated sample for experiment (RepID) 6098
replicate 1 of 3
Experimental sample
Replicate experimental sample: GSM221715: LIVER_DIPYRONE_1636mg/kg_3days_exp6098_rep2_85830
Replicate experimental sample: GSM221716: LIVER_DIPYRONE_1636mg/kg_3days_exp6098_rep3_85831
Matched control sample: GSM204808: LIVER_vehicle_NA_5days_control_NA_85526
Matched control sample: GSM204874: LIVER_vehicle_NA_5days_control_NA_85536
Matched control sample: GSM204676: LIVER_vehicle_NA_1days_control_NA_85576
Matched control sample: GSM204767: LIVER_vehicle_NA_3days_control_NA_85579
Matched control sample: GSM204829: LIVER_vehicle_NA_5days_control_NA_85582
Matched control sample: GSM204702: LIVER_vehicle_NA_1days_control_NA_85602
Matched control sample: GSM204653: LIVER_vehicle_NA_1days_control_NA_85604
Matched control sample: GSM204749: LIVER_vehicle_NA_3days_control_NA_85605
Matched control sample: GSM204788: LIVER_vehicle_NA_3days_control_NA_85607
Matched control sample: GSM204841: LIVER_vehicle_NA_5days_control_NA_85609
Matched control sample: GSM204668: LIVER_vehicle_NA_1days_control_NA_85835
Matched control sample: GSM204709: LIVER_vehicle_NA_1days_control_NA_85837
Matched control sample: GSM204734: LIVER_vehicle_NA_3days_control_NA_85839
Matched control sample: GSM204822: LIVER_vehicle_NA_5days_control_NA_85841
Matched control sample: GSM204864: LIVER_vehicle_NA_5days_control_NA_85843
Matched control sample: GSM204848: LIVER_vehicle_NA_5days_control_NA_85885
Matched control sample: GSM204605: LIVER_vehicle_NA_.25days_control_NA_85890
Matched control sample: GSM204628: LIVER_vehicle_NA_.25days_control_NA_85892
Matched control sample: GSM204710: LIVER_vehicle_NA_1days_control_NA_85897
Matched control sample: GSM204646: LIVER_vehicle_NA_1days_control_NA_85899
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

hyb_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. 12.5 ug of cRNA sample was fragmented in 40 mM Tris-acetate (TrisOAc) pH7.9, 100 mM KOAc and 31.5 mM MgOAc at 94oC for 20 min. This typically resulted in a fragmented cRNA with a size range between 100 to 200 bases. 10 ug of the fragmented cRNA was used for hybridization of each Rat-Uniset I (RU1) Expression BioArray (Amersham Biosciences, Piscataway, NJ) in a volume of 260 ul, containing 78 ul of CodeLink Hyb buffer component A and 130 ul of CodeLink Hyb buffer component B (Amersham Biosciences, Piscataway, NJ). The hybridization solution was denatured at 90oC for 5 min then chilled on ice. The sample was vortexed at maximum speed for 5 sec and centrifuged at maximum speed for 5 min before 250 ul of the solution was injected into the inlet port of the flex-hybridization chamber, and placed in a CodeLink 12-slide shaker tray. The hybridization ports were sealed with 1 cm sealing strips (Amersham Biosciences, Piscataway, NJ), and the shaker tray(s) containing the slides was loaded into a New Brunswick Innova 4080 shaking incubator, with the hybridization chambers facing up. Slides were incubated for 20 hr at 37oC, while shaking at 300 rpm. The 12-slide shaker tray was removed from the shaker, and the hybridization chamber removed from each slide. Each slide was placed into the BioArray Rack of the Parallel Processing Tool (Amersham Biosciences, Piscataway, NJ) and incubated with 0.75x TNT (0.075 M Tris-HCl, pH7.6, 0.1125 M NaCl, 0.0375 % Tween-20) at 46oC for 1hr. The BioArray Rack was moved from the TNT containing reservoir to the small reagent reservoir containing 1:500 dilution of streptavidin-Alexa 647 (Molecular Probes, Eugene, OR). The signal was developed for 30 min at room temperature, before the reaction was stopped and slides were washed four times for 5 min each in TNT buffer (0.1 M Tris-HCl, pH7.6, 0.15 M NaCl, 0.05% Tween-20) using a large reagent reservoir. The slides were rinsed in ddH2O with 0.05% Tween-20 twice for 5 sec each before they were dried by centrifugation with a Qiagen Sigma 4-15C centrifuge (Valencia, CA) using a swinging bucket rotor (2x96) for exactly 3 min at 2000rpm (acceleration at position 9 and deceleration at position 9). The dried slides were stored in light protective slide boxes at room temperature prior to scanning.

scan_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. The Axon GenePix Scanner (Axon Instrument, Union City, CA) was calibrated using the Calibration Slide supplied by Axon Instrument with GenePix 4.0 at 635 nm using the Calibration System. After calibration of the scanner, all processed slides were scanned with the laser set to 635 nm, the photomultiplier tube (PMT) voltage to 600 and the scan resolution to 10 microns. For consistency all slides were scanned the same day of color development, within an hour after dry spinning them and the data was analyzed using the CodeLink Expression Analysis Software version 2.2.25 (Amersham Biosciences, Piscataway, NJ).

data_processing: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44, supplemental methods.  Prior to statistical computation, the spot reading data was normalized. For this purpose a new nonlinear normalization procedure, similar to the centralization approach reported in the literature (Zien et al., 2001) was developed for the CodeLink array platform. The normalization procedure uses proprietary algorithm that assumes that in general, for an array with many probes, the majority of the signal represents genes that have unchanged expressions compared to controls, with the extreme values representing the true biology of the process and not some artifact due to measurement noise. The algorithm does not make the assumption that the true mRNA abundance being measured is linearly proportional to the spot reading signal or any assumption about the error distribution of such signals or their differential. Rather, the assumption of unchanged signals representing the bulk of the signal measurements is used to center a nonlinear curve fit to a reference template. This reference template is constructed for a large set of time matched, same tissue and same vehicle, control arrays, computing a median log signal for each probe. The replicate size of this set is adequate to ensure very small random error in the ensemble signal level for each reference probe. The curve fit corrects for some array processing problems, such as partial signal saturation, and improves the overall quality of the data compared to simple linear normalization methods. Essentially the curve tracks the mode of the signal distribution for sets of genes against the expected value for that set.

label: biotin

molecule: polyA RNA

organism: Rattus norvegicus

source_name: LIVER, DIPYRONE, 1636mg/kg, 3 days

label_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. The methods used for cRNA preparation (cDNA synthesis, cRNA preparation, and cRNA purification) are essentially as described in the CodeLink™ manual v2.1 as supplied by Amersham Biosciences (Piscataway, NJ) using the Qiagen BioRobot 9604 (Valencia, CA). cDNA synthesis, cRNA preparation, and cRNA purification were completely processed in a 96-well format using the automated Qiagen BioRobot 9604 procedure. 0.6 – 20 ìg of enriched RNA from different tissue sources were added to a reaction mixture in a final volume of 12 ìl, containing bacterial control RNA (1.5pg FixA, 5pgYjeK, 5pg AraB, 15pg EntF, 50pg FixB, 150pg HisB, 500pg LeuB, 1500pg gnd) and 1.0 ìl of 100 pmol ìl-1 T7-(dT)24 oligonucleotide primer (Proligo, Boulder, CO). The T7-(dT)24 oligonucleotide primer used, is an HPLC purified 63-mer with the sequence : 5'-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3'. The mixture was incubated for 10 min at 70oC and chilled on ice. On ice, 4 ul of 5x first-strand buffer, 2 ul 0.1 M DTT, 1 ul of 10 mM dNTP mix and 1 ul Superscript™II RNaseH-reverse transcriptase (200 U/ul) were added to the mixture to make a final volume of 20 ul. The mixture was incubated for 1 hr at 37oC. Second-strand cDNA was synthesized in a volume of 150 ul, containing 92 ul nuclease-free water, 30 ul of 5x second-strand buffer, 3 ul of 10 mM dNTP mix, 4 ul of Escherichia coli DNA polymerase I (10 U/ìl) and 1 ul of RNase H (2 U/ul) for 2 hr at 16oC. The cDNA was purified using a Qiagen QIAquick purification kit, and completely dried down using a Speed-Vac concentrator (45oC) for 2 hr. The dried product was resuspended in IVT reaction mix containing 3.0 ul of nuclease-free water, 4.0 ul 10x reaction buffer, 4.0 ul 75 mM ATP, 4.0 ul 75 mM GTP, 3.0 ul 75 mM CTP, 3.0 ul 75 mM UTP, 7.5 ul 10 mM Biotin 11-CTP, 7.5 ul 10 mM Biotin 11-UTP and 4.0 ul enzyme mix. The reaction mix was incubated for 14 hr at 37oC using an MJ Research 96-well PTC-200 Thermal Cycler (MJ Research, Waltham, MA), before the cRNA was purified using a Qiagen RNeasy® kit. The resulting cRNA yield was quantified using the 96-well ìQuan Universal Microplate Spectrophotometer Model MQX200 (BIO-TEK Instruments Inc., Winooski, VT) at a wavelength of 260 nm. Conformance of the cRNA sample to historical size distributions (the bulk of the cRNA product should be between 500 and 3,000 bases in size) was confirmed using the Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). Samples not near the historical norm were reprocessed starting from tissue or RNA.

growth_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44.  Sprague-Dawley (Crl:CD®(SD)|GS BR) rats (aged 6-8 weeks and weighing 200 - 260 g), were purchased from Charles River Laboratories (Wilmington, MA). They were housed in plastic cages for 1 week for acclimation to the laboratory environment of a ventilated room (temperature, 22oC ±3oC; humidity, 30 - 70%; light/dark cycle, 12 h d-1, 6:00am - 6:00pm) until use. Certified Rodent Diet #5002 (PMI Feeds Inc.) and chlorinated tap water was available ad libitum.

extract_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. Following sacrifice, 6 mm disposable biopsy punches (#REF 33-36 Miltex, Inc. Bethpage, NY) were used to obtain tissue samples of approximately 100 mg. Samples were placed in cryogenic tubes and snap frozen. Poly A(+)-RNA from tissue samples was isolated using the MagNA Pure LC robot (Roche, Basel, Switzerland) in combination with the MagNA Pure LC mRNA Isolation kit I and II (Roche, Basel, Switzerland) for cells (see supplemental methods section) and tissues, respectively. Tissue samples were completely homogenized directly from ~100 mg punches stored on dry ice prior to application of lysis buffer to a final concentration of 65 mg tissue per ml of buffer. After complete homogenization, using disposable Omni Tip Disposable Generator Probes (Omni Inc, Warrenton, VA) and before loading of the samples into the 32-well MagNA Pure plate, the samples were drawn up 5-6 times through a 20-gauge needle attached to a 3-ml syringe to ensure any tissue pieces or clumps were removed from the lysate prior to robotic processing. Tissue sample processing was performed in duplicate wells (loading 150 ul of homogenized sample to each well) of the MagNA Pure LC, which is programmed to extract mRNA using the oligo-dT selection method into a final elution volume of 100 ul. Poly A(+) RNA sample concentration was performed manually using a standard ethanol precipitation protocol in the presence of glycogen (50 ug/ml). After precipitation the final purified RNA sample was resuspended in 7 ìl DEPC-H2O and quantified using a Ribogreen high-range assay (Molecular Probes) on the Wallac Victor2 Fluorometer (Perkin-Elmer, Fremont, CA). Additionally, the integrity of each RNA sample was determined, by comparison to historical standards (no gross degradation should be visible as suggested by clear 18S and 28S peaks on top of a hump of complex RNA, with lower amounts of RNA below 18S than under and above the 18S peak), using the Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA) in combination with the RNA 6000 Nano Lab Chip kit (Agilent Technologies).

treatment_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44.  Compounds were administered via the route of administration (ROA) that corresponds to that by which humans receive the drug. Compounds were typically administered orally (PO) (83%), intravenously (IV) (9.4%), subcutaneously (SC) (5.7%), or intraperitoneally (IP) (2%). If the compound is a toxicant or a biochemical standard, it was administered orally. For oral dosing, the vehicle choice largely depends on the solubility of the compound in water. Water-soluble compounds were administered in water. Insoluble compounds are administered in either corn oil or 0.5% carboxymethylcellulose (CMC) using the best literature recommendation as a guide. IV administered compounds were usually dissolved in saline and SC administered compounds in corn oil. The highest dose the rats receive is the Maximum Tolerated Dose (MTD). The dosing of animals was staggered based on intended harvest order to ensure that sacrifice occurred within 30 minutes of the recorded time point. Dosing frequency was as described in Sample_characteristics for the particular treatment.

tag: Sprague-Dawley

tag: age

value: 6 to 8 weeks

tag: sex

value: male

value: LIVER

tag: treatment compound

value: DIPYRONE

tag: dose

tag: solvent

value: WATER

tag: administration route

value: ORAL GAVAGE

tag: frequency of dosing

value: DAILY

tag: treatment duration

value: 3 days

tag: experiment date


title: MG132 + Dex (2) vs. Con (2)


title: LIVER_ETOPOSIDE_100mg/kg_.25days_exp2987_rep1_15391

description:
HybID: 15391
treated sample for experiment (RepID) 2987
replicate 1 of 3
Experimental sample
Replicate experimental sample: GSM221959: LIVER_ETOPOSIDE_100mg/kg_.25days_exp2987_rep2_13540
Replicate experimental sample: GSM221960: LIVER_ETOPOSIDE_100mg/kg_.25days_exp2987_rep3_14055
Matched control sample: GSM204626: LIVER_vehicle_NA_.25days_control_NA_13650
Matched control sample: GSM204603: LIVER_vehicle_NA_.25days_control_NA_13655
Matched control sample: GSM204679: LIVER_vehicle_NA_1days_control_NA_13657
Matched control sample: GSM204743: LIVER_vehicle_NA_3days_control_NA_13660
Matched control sample: GSM204617: LIVER_vehicle_NA_.25days_control_NA_13855
Matched control sample: GSM204756: LIVER_vehicle_NA_3days_control_NA_13867
Matched control sample: GSM204825: LIVER_vehicle_NA_5days_control_NA_13875
Matched control sample: GSM204615: LIVER_vehicle_NA_.25days_control_NA_13923
Matched control sample: GSM204658: LIVER_vehicle_NA_1days_control_NA_13925
Matched control sample: GSM204736: LIVER_vehicle_NA_3days_control_NA_13932
Matched control sample: GSM204846: LIVER_vehicle_NA_5days_control_NA_14006
Matched control sample: GSM204614: LIVER_vehicle_NA_.25days_control_NA_14066
Matched control sample: GSM204661: LIVER_vehicle_NA_1days_control_NA_14072
Matched control sample: GSM204762: LIVER_vehicle_NA_3days_control_NA_14076
Matched control sample: GSM204612: LIVER_vehicle_NA_.25days_control_NA_14190
Matched control sample: GSM204818: LIVER_vehicle_NA_5days_control_NA_14279
Matched control sample: GSM204655: LIVER_vehicle_NA_1days_control_NA_14288
Matched control sample: GSM204823: LIVER_vehicle_NA_5days_control_NA_14298
Matched control sample: GSM204645: LIVER_vehicle_NA_1days_control_NA_14306
Matched control sample: GSM204735: LIVER_vehicle_NA_3days_control_NA_14311
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

source_name: LIVER, ETOPOSIDE, 100mg/kg, .25 days

tag: tissue

value: ETOPOSIDE

value: 100 mg/kg

value: CORN OIL

value: .25 days


title: human iPS cells

status: Public on Nov 22 2007

city: Kyoto

first: Shinya

last: Yamanaka

address: 53 Kawahara-machi, Shogoin, Sakyo-ku

country: Japan

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

description: human iPS cells

hyb_protocol: Agilent protocol

scan_protocol: Agilent protocol

data_processing: GeneSpring GX

source_name: induced pluripotent stem cells derived from HDF (clone 201B7)

label_protocol: Agilent protocol

extract_protocol: Trizol

tag: clone 201B7


title: LIVER_CYTARABINE_23mg/kg_.25days_exp3043_rep2_13877

description:
HybID: 13877
treated sample for experiment (RepID) 3043
replicate 2 of 3
Experimental sample
Replicate experimental sample: GSM221541: LIVER_CYTARABINE_23mg/kg_.25days_exp3043_rep1_13878
Replicate experimental sample: GSM221543: LIVER_CYTARABINE_23mg/kg_.25days_exp3043_rep3_13879
Matched control sample: GSM204626: LIVER_vehicle_NA_.25days_control_NA_13650
Matched control sample: GSM204603: LIVER_vehicle_NA_.25days_control_NA_13655
Matched control sample: GSM204679: LIVER_vehicle_NA_1days_control_NA_13657
Matched control sample: GSM204743: LIVER_vehicle_NA_3days_control_NA_13660
Matched control sample: GSM204617: LIVER_vehicle_NA_.25days_control_NA_13855
Matched control sample: GSM204756: LIVER_vehicle_NA_3days_control_NA_13867
Matched control sample: GSM204825: LIVER_vehicle_NA_5days_control_NA_13875
Matched control sample: GSM204615: LIVER_vehicle_NA_.25days_control_NA_13923
Matched control sample: GSM204658: LIVER_vehicle_NA_1days_control_NA_13925
Matched control sample: GSM204736: LIVER_vehicle_NA_3days_control_NA_13932
Matched control sample: GSM204846: LIVER_vehicle_NA_5days_control_NA_14006
Matched control sample: GSM204614: LIVER_vehicle_NA_.25days_control_NA_14066
Matched control sample: GSM204661: LIVER_vehicle_NA_1days_control_NA_14072
Matched control sample: GSM204762: LIVER_vehicle_NA_3days_control_NA_14076
Matched control sample: GSM204612: LIVER_vehicle_NA_.25days_control_NA_14190
Matched control sample: GSM204818: LIVER_vehicle_NA_5days_control_NA_14279
Matched control sample: GSM204655: LIVER_vehicle_NA_1days_control_NA_14288
Matched control sample: GSM204823: LIVER_vehicle_NA_5days_control_NA_14298
Matched control sample: GSM204645: LIVER_vehicle_NA_1days_control_NA_14306
Matched control sample: GSM204735: LIVER_vehicle_NA_3days_control_NA_14311
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

source_name: LIVER, CYTARABINE, 23mg/kg, .25 days

value: CYTARABINE

value: 23 mg/kg

value: SALINE

value: INTRAVENOUS


title: 717 Day 1, in-vivo Cyno Ebola Inf, PBMC

status: Public on Jun 28 2007

first: Kate

last: Rubins

address: Nine Cambridge Center

institute: Whitehead Institute for Biomedical Research

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41278.gif

scan_protocol: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA).  Grids were manually aligned and features were found using the software feature extraction.  Features were visually inspected for blemishes and removed from downstream analysis.    Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/)  and normalized using regression correlation.  Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array.    Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays.    For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples.    The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis.    The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Stratagene Universal Human Reference RNA, 1 round of amplification (Ambion MessageAmp), 6/27/02

organism: Macaca fascicularis

source_name: 717 Day 1, in-vivo Cyno Ebola Inf, PBMC

tag: 717 Day 1, in-vivo Cyno Ebola Inf, PBMC


title: 9028 Day 1, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41311.gif

tag: Stratagene Universal Human Reference RNA, 1 round of amplification (Ambion MessageAmp), 6/27/02


title: 9028 Day 2 #1, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41312.gif


title: 9108 Day -6a Preebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41314.gif


title: 9108 Day -6b Preebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41315.gif


title: 48-143 Day -6b Preebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41349.gif


title: 9028 Day 2 last, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41313.gif


title: 9878 Day -6a Preebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41331.gif


title: 9093 Day 3, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41330.gif


title: 9093 Day 1, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41328.gif


title: 9093 Day -6b Preebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41327.gif


title: 9028 Day -6b Preebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41292.gif


title: 9028 Day -6a Preebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41290.gif


title: 28-332 Day 6, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41347.gif


title: 32q Day -1a Prebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41271.gif


title: 9093 Day 2, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41329.gif


title: 717 Day -4b Preebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41276.gif


title: 32q Day -1b Prebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41272.gif


title: 28-332 Day -6b Preebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41343.gif


title: 359 Day 5, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41270.gif

source_name: 359 Day 5, in-vivo Cyno Ebola Inf, PBMC

tag: 359 Day 5, in-vivo Cyno Ebola Inf, PBMC


title: 717 Day -4a Preebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41275.gif


title: 28-332 Day -6a Preebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41342.gif


title: 28-332 Day 2, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41345.gif


title: 323 Day -6b Prebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41258.gif


title: 9093 Day -6a Preebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41326.gif


title: 32q Day 3, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41273.gif

source_name: 32q Day 3, in-vivo Cyno Ebola Inf, PBMC

tag: 32q Day 3, in-vivo Cyno Ebola Inf, PBMC


title: 323 Day -6a Prebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41257.gif


title: 28-332 Day 3, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41346.gif


title: 323 Day 2, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41259.gif

source_name: 323 Day 2, in-vivo Cyno Ebola Inf, PBMC

tag: 323 Day 2, in-vivo Cyno Ebola Inf, PBMC


title: 48-143 Day -6a Preebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41348.gif


title: 9877 Day 1, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41325.gif


title: 28-221 Day 2, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41340.gif


title: 9112 Day 2, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41322.gif


title: 28-221 Day 5, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41341.gif


title: 8667 Day 2, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41286.gif


title: 9112 Day -6b Preebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41321.gif


title: 9877 Day -6a Preebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41323.gif


title: 8667 Day 3, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41288.gif


title: 28-221 Day -1a Preebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41338.gif


title: 8667 Day 1, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41284.gif


title: 331 Day 2, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41265.gif

source_name: 331 Day 2, in-vivo Cyno Ebola Inf, PBMC

tag: 331 Day 2, in-vivo Cyno Ebola Inf, PBMC


title: 28-221 Day -1b Preebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41339.gif


title: 331 Day 1, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41264.gif

source_name: 331 Day 1, in-vivo Cyno Ebola Inf, PBMC

tag: 331 Day 1, in-vivo Cyno Ebola Inf, PBMC


title: 8667 Day -6b Preebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41282.gif


title: 359 Day -6b Prebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41267.gif


title: 359 Day 3, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41269.gif

source_name: 359 Day 3, in-vivo Cyno Ebola Inf, PBMC

tag: 359 Day 3, in-vivo Cyno Ebola Inf, PBMC


title: 331 Day -6a Prebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41262.gif


title: 9877 Day -6b Preebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41324.gif


title: 359 Day -6a Prebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41266.gif


title: 9878 Day 6 #1, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41337.gif


title: 359 Day 2, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41268.gif

source_name: 359 Day 2, in-vivo Cyno Ebola Inf, PBMC

tag: 359 Day 2, in-vivo Cyno Ebola Inf, PBMC


title: 9878 Day 4, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41335.gif


title: 9112 Day -6a Preebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41320.gif


title: 323 Day 5, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41261.gif

source_name: 323 Day 5, in-vivo Cyno Ebola Inf, PBMC

tag: 323 Day 5, in-vivo Cyno Ebola Inf, PBMC


title: 331 Day -6b Prebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41263.gif


title: 8667 Day -6a Preebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41280.gif


title: 48-143 Day 2, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41350.gif


title: 48-143 Day 5, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41351.gif


title: 9878 Day 6 last, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41336.gif


title: 9878 Day 2, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41333.gif


title: 9108 Day 4, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41319.gif


title: 323 Day 3, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41260.gif

source_name: 323 Day 3, in-vivo Cyno Ebola Inf, PBMC

tag: 323 Day 3, in-vivo Cyno Ebola Inf, PBMC


title: 9108 Day 3, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41317.gif


title: HCMV-infected foreskin fibroblasts

status: Public on Sep 28 2000

type: SAGE

anchor: NlaIII

city: Bern

first: Marc

last: Kenzelmann

address: Friedbuhlstrasse 51

department: Molecular Genome Analysis

country: Switzerland

institute: Institute of Medical Microbiology, University of Bern

description:
Primary human foreskin fibroblasts at passages 15-18, cultured in Eagles Minimal Essential Medium (MEM) supplemented with penicillin and 10% fetal calf serum (FCS).
Confluent cells serum starved for 3 days with MEM containing 1% FCS.
85% of cells in G0/G1 cell cycle phase.
Cells infected at a multiplicity of infection (m.o.i.) of 5 with human cytomegalovirus (HCMV) strain AD169 infectious particles (virions) for 90 min at 37°Celsius.
mRNA isolated using a direct mRNA extraction kit.
Keywords = human cytomegalovirus, AD169, virions, HCMV-infected foreskin fibroblasts

source_name: mRNA of HCMV-infected human foreskin fibroblasts


title: 9108 Day 1, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41316.gif


title: 9878 Day -6b Preebleed, in-vivo Cyno Ebola Inf, PBMC

description:
Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41332.gif