title: CTCF localization in G2 under CTCF RNAi (ENCODE)

status: Public on Jan 30 2008

first: Katsuhiko

last: Shirahige

department: Research Center for Epigenetic Disease

institute: The University of Tokyo

description: CTCF localization on ENCODE region in HeLa cells in the absence of CTCF. As WCE fraction, the same samples as we used in GSM243278 were used.

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). Washing and scanning protocol provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 450, 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 WCE 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 36). Bandwidth, MaxGap, and MinProbe parameters were set to 250, 1000, and 12, respectively. Cutoff threshold p-values were set to 1.0e-10, 1.0e-8, and 5.0e-8 for ENCODE1.0, 2.0, and Human Tiling 1.0R, respectively.
For ChIP-chip analysis, we use two IP .CEL files and two WCE .CEL files (they are duplicated experiments) to make one profile.

source_name: Chromatin Immuno-precipitated DNA

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‐N11‐ddATP (NEL508).

extract_protocol: Cells at 70-80% confluency were crosslinked with 1% formaldehyde for 10 min and after quenching with 125 mM glycine prepared for ChIP. Chromatin immunoprecipitation was performed using Scc1, Smc3, CTCF, SA2 and control antibodies. The lysate was incubated with the antibodies over night. Then the pre-absorbed protein A Affiprep beads (Bio-Rad) were added and incubated for 2 hours at 4 degree. The beads were washed several times and eluted for 20 min at 65 degree with elution buffer (50 mM Tris, 10 mM EDTA, 1 % SDS). The eluate from the beads was treated with Proteinase K and decrosslinked at 65°C over night. Contaminating RNA was removed by RNAse treatment. Then the sample was further purified by phenol-chloroform extraction and one additional purification step using the PCR purification kit (Qiagen).

tag: HeLa cells. Anti-CTCF antibody was used for Chromatin immuno-precipitation.

source_name: Whole cell extract (WCE) fraction used for the normalization of ChIP fraction.

label_protocol: same as channel 1

extract_protocol: same as channel 1

tag: HeLa cells


title: SA2 distribution in G2 (ENCODE)

type: genomic

city: Bunkyo-ku

state: Tokyo

address: 1-1-1 Yayoi

country: Japan

description: SA2 distribution in G2 phase.

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).

molecule: genomic DNA

organism: Homo sapiens

tag: HeLa cells. Anti-SA2 antibody was used for Chromatin immuno-precipitation.


title: hScc1 localization in G2 in the absence of CTCF (ENCODE)

description: hScc1 localization on ENCODE region in HeLa cells in the absence of CTCF.

tag: HeLa cells. Anti-hScc1 antibody was used for Chromatin immuno-precipitation.


title: hScc1 localization in G2 (Whole Genome #13)

description: hScc1 distribution in G2 phase. Array 13 of 14.


title: CTCF localization in G2 (Whole Genome #10)

description: CTCF distribution in G2 phase. Array 10 of 14. For WCE fraction, the same file as we used for the analysis of hScc1 distribution were used.


title: CTCF localization in G2 under hScc1 RNAi (ENCODE)

description: CTCF localization on ENCODE region in HeLa cells in the absence of hScc1. As WCE fraction, the same samples used for GSM243278 were used for normalization.


title: CTCF localization in G2 (Whole Genome #11)

description: CTCF distribution in G2 phase. Array 11 of 14. For WCE fraction, the same data as we used for the analyses of hScc1 were used.


title: hScc1 localization in G2 (Whole Genome #8)

description: hScc1 distribution in G2 phase. Array 8 of 14.

tag: HeLa cells. Anti-hScc1 atibody was used for Chromatin immuno-precipitation.


title: hScc1 localization in G2 (Whole Genome #6)

description: hScc1 distribution in G2 phase. Array 6 of 14.


title: CTCF localization in G2 (Whole Genome #9)

description: CTCF distribution in G2 phase. Array 9 of 14. For WCE fraction, the same data as we used for the analyses of hScc1 were used.


title: hScc1 distribution in RPE (ENCODE)

description: hScc1 localization in RPE cells.

tag: RPE cells. Anti-hScc1 antibody was used for Chromatin immuno-precipitation.

tag: RPE cells


title: hSmc3 distribution in RPE (ENCODE)

description: hSmc3 localization on ENCODE region in RPE. For the profile analyses, we used the same WCE files used for the analyses of hScc1 in the same cell line.

tag: RPE cells. Anti-hSmc3 antibody was used for Chromatin immuno-precipitation.


title: hScc1 distribution in B-cell (ENCODE)

description: hScc1 distribution in B-cells.

tag: B-cells. Anti-hScc1 antibody was used for Chromatin immuno-precipitation.

tag: B-cells


title: CTCF localization in G2 (Whole Genome #6)

description: CTCF distribution in G2 phase. Array 6 of 14. For WCE fraction, the same data as we used for the analyses of hScc1 were used.


title: CTCF localization in G2 (Whole Genome #2)

description: CTCF distribution in G2 phase. Array 2 of 14. For WCE fraction, the same data as we used for the analyses of hScc1 were used.

tag: HeLa Cells. Anti-CTCF antibody was used for Chromatin immuno-precipitation.

tag: HeLa Cells


title: CTCF localization in G2 (Whole Genome #4)

description: CTCF distribution in G2 phase. Array 4 of 14. For WCE fraction, the same file as we used for the analysis of hScc1 distribution were used.


title: CTCF localization in G2 (Whole Genome #1)

description: CTCF distribution in G2 phase. Array 1 of 14. For WCE fraction, the same data as we used for the analyses of hScc1 were used.


title: CTCF localization in G2 (Whole Genome #3)

description: CTCF distribution in G2 phase. Array 3 of 14. For WCE fraction, the same data as we used for the analyses of hScc1 were used.


title: hScc1 localization in G2 (Whole Genome #2)

description: hScc1 distribution in G2 phase. Array 2 of 14.


title: hScc1 localization in G2 (Whole Genome #11)

description: hScc1 distribution in G2 phase. Array 11 of 14.

tag: HeLa cells. Anti hScc1 antibody was used for Chromatin immuno-precipitation.


title: hScc1 localization in G2 (Whole Genome #1)

description: hScc1 distribution in G2 phase. Array 1 of 14.

tag: HeLa cells samples. Anti-hScc1 atibody was used for Chromatin immuno-precipitation.


title: hScc1 localization in G2 (Whole Genome #10)

description: hScc1 distribution in G2 phase. Array 10 of 14.


title: hSmc3 distribution in M-phase (ENCODE)

description: hSmc3 distribution in M-phase. Wce fraction used for the analyses of SA2 in G2 phase was used for normalization.

tag: HeLa cells. Anti-hSmc3 antibody was used for Chromatin immuno-precipitation.


title: hScc1 localization in G2 (Whole Genome #3)

description: hScc1 distribution in G2 phase. Array 3 of 14.

tag: HeLa cells. Anti-hScc1 atibody was used for Chromatin immuno-precipitation


title: CTCF localization in RPE cells (ENCODE)

description: CTCF localization on ENCODE region in B-cell. For the profile analyses, we used the same WCE files used for the analyses of hScc1 in the same cell line.

tag: RPE cells. Anti CTCF antibody was used for Chromatin immuno-precipitation.


title: CTCF localization in G2 (Whole Genome #13)

description: CTCF distribution in G2 phase. Array 13 of 14. For WCE fraction, the same file as we used for the analysis of hScc1 distribution were used.

tag: HeLa cells. Anti-CTCF antibody was used for Chromatin immuno-precipitation.


title: hSmc3 distribution in G2 (ENCODE)

description: hSmc3 distribution in G2 phase.

tag: HeLa cells


title: hScc1 localization in G2 (Whole Genome #9)

description: hScc1 distribution in G2 phase. Array 9 of 14.

tag: HeLa cells. Antibody against hScc1 was used for Chromatin immuno-precipitation.


title: hSmc3 distribution in G2 (ENCODE) under the depletion of hScc1 by RNAi

description: hSmc3 localization on ENCODE region in HeLa cells in the absence of hScc1.


title: hScc1 distribution in G1 (ENCODE)

description: hScc1 distribution in G1 phase.

tag: HeLa cells. Anti-hScc1 antibody was used for Chromatin immuno-precipitation.


title: hScc1 localization in G2 (Whole Genome #4)

description: hScc1 distribution in G2 phase. Array 4 of 14.

tag: HeLa cells. Anti-hScc1 atibody was used for Chromatin immuno-precipitation.


title: hScc1 localization in G2 (ENCODE)

description: hScc1 distribution in G2 phase.


title: CTCF localization in G2 (ENCODE)

description: CTCF distribution in G2 phase.


title: p53 localization (ENCODE)

description: p53 localization on ENCODE region in HeLa cells.

tag: Hela cells. Anti-p53 antibody was used for Chromatin immuno-precipitation.


title: CTCF localization in G2 (Whole Genome #14)

description: CTCF distribution in G2 phase. Array 14 of 14. For WCE fraction, the same file as we used for the analysis of hScc1 distribution were used.


title: Oligodendroglioma-Odii 284

status: Public on Jan 29 2008

type: RNA

city: Rotterdam

first: Pim

last: French

address: Dr Molewaterplein 50

department: Neurology

country: Netherlands

institute: Erasmus MC

description: examination of differentially regulated splice variants and novel exons in glial brain tumors

hyb_protocol: microarrays were hybridized overnight with 5 g biotin labelled ss-cDNA, and washed in fluidics station wash protocol: MES_EukGE-WS2v5_450

scan_protocol: Genechip scanner 3000 7G

data_processing: GCOS, data extraction in ExACT. Plier data is provided in sample table.

label: biotin

molecule: total RNA

source_name: glioma

label_protocol: labelling was performed according to the Affymetrix (Santa Clara, CA) GeneChip Whole Transcript (WT) Sense Target Labelling Assay manual

extract_protocol: Trizol extraction of total RNA, purification on RNeasy mini columns (Qiagen)

tag: female, 50y, grade II, LOH 1p 19q


title: CTCF localization in B-cell (ENCODE)

description: CTCF localization in B-cells.

tag: B-cell. Anti-CTCF antibody was used for Chromatin immuno-precipitation.


title: Oligodendroglioma-OD 9-b

tag: male, 35y, LOH 1p 19q


title: Oligodendroglioma-Odii 295

tag: male, 34y, grade II, LOH 1p 19q


title: hScc1 localization in G2 (Whole Genome #14)

description: hScc1 distribution in G2 phase. Array 14 of 14.


title: Oligodendroglioma-OD 270b

tag: LOH 1p 19q


title: Oligodendroglioma-Od 275


title: CTCF localization in G2 (Whole Genome #7)

description: CTCF distribution in G2 phase. Array 7 of 14. For WCE fraction, the same file as we used for the analysis of hScc1 distribution were used.


title: Oligodendroglioma-Od 53


title: Oligodendroglioma-Od 293


title: Oligodendroglioma-OD 8-b

tag: female, 45y, LOH 1p, 19q


title: Oligodendroglioma-OD 40b

tag: male, 45y, LOH 1p 19q


title: Oligodendroglioma-OD 266c

tag: male, 46y, LOH 1p 19q


title: CTCF localization in G2 (Whole Genome #12)

description: CTCF distribution in G2 phase. Array 12 of 14. For WCE fraction, the same file as we used for the analysis of hScc1 distribution were used.

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). Washing and scanning protocol provided by Affymetrix was performed au


title: Oligodendroglioma-Od 259

tag: male, 60y, LOH 1p 19q


title: Oligodendroglioma-Od 257

tag: male, 67y, LOH 1p 19q


title: hScc1 localization in G2 (Whole Genome #12)

description: hScc1 distribution in G2 phase. Array 12 of 14.

tag: HeLa Cells. Antibody against hScc1 was used for Chromatin immuno-precipitation.

tag: HeLa Cells


title: Oligodendroglioma-Od 23

tag: female, 45y, LOH 1p 19q


title: Oligodendroglioma-OD 262b

tag: female, 62y, LOH 1p 19q


title: Oligodendroglioma-Od 170

tag: female, 43y, LOH 1p 19q


title: CTCF localization in G2 (Whole Genome #5)

description: CTCF distribution in G2 phase. Array 5 of 14. For WCE fraction, the same file as we used for the analysis of hScc1 distribution were used.

tag: HeLa cells. Anti-CTCF antibody was used for Chromatin immuno-precipitation.

tag: HeLa cells


title: Oligodendroglioma-Od 144


title: CTCF localization in G2 (Whole Genome #8)

description: CTCF distribution in G2 phase. Array 8 of 14. For WCE fraction, the same file as we used for the analysis of hScc1 distribution were used.


title: Oligodendroglioma-Od 20

tag: male, 50y, LOH 1p 19q


title: Oligodendroglioma-Od 25

tag: male, 51y, LOH 1p 19q


title: hScc1 localization in G2 (Whole Genome #7)

description: hScc1 distribution in G2 phase. Array 7 of 14.

tag: HeLa cells. Anti-hScc1 atibody was used for Chromatin immuno-precipitation


title: hScc1 localization in G2 (Whole Genome #5)

description: hScc1 distribution in G2 phase. Array 5 of 14.


title: Oligodendroglioma-OD 130b

tag: male, 33y, LOH 1p 19q


title: Glioblastoma-Gbm 96

tag: male, 51y, ampl EGFR, expr EGFRvIII


title: Oligodendroglioma-OD 13e-c

tag: male, 40y, LOH 1p 19q


title: Glioblastoma-Gbm 65

tag: male, 49y, ampl EGFR


title: Glioblastoma-Gbm 61

tag: male, 61y, ampl EGFR


title: Oligodendroglioma-Od 21

tag: male, 32y, LOH 1p 19q


title: Oligodendroglioma-Od 11

tag: male, 44y LOH1p 19q


title: Glioblastoma-Gbm 67

tag: male, 58y, ampl EGFR


title: Glioblastoma-Gbm 56

tag: male, 44y


title: Glioblastoma-Gbm 77

tag: male 55y, ampl EGFR, expr EGFRvIII


title: Oligodendroglioma-OD 55b-2

tag: male, 38y, LOH 1p 19q


title: Glioblastoma-Gbm139

tag: male, 35y


title: Glioblastoma-GBM 89-b

tag: female, 54y, ampl EGFR


title: Glioblastoma-Gbm 240

tag: female, 57y


title: Glioblastoma-Gbm 60

tag: male, 38y


title: Glioblastoma-Gbm 254

tag: male, 15y, ampl EGFR


title: Promoter CpG Methylation in Mouse ES Cells (1/2) replicate 5

status: Public on Jan 28 2008

city: Los Angeles

first: Yin

last: Shen

state: CA

address: 695 Charles E. Young Dr.

country: USA

institute: UCLA

description: All cell cultures were maintained at 37 °C with 5% CO2. The culture of mouse ESCs were maintained in DMEM supplemented with 15% heat-inactivated FBS , LIF and penicillin/streptomycin.  mESCs were grown in feeder-free for 2 passages before harvesting of DNA. After genomic DNA isolation, the DNA was RNase treated and 2ug was used for methylated DNA immunoprecipitation (Weber et al., 2005.  Nat Genetics. 37, 853-62. Zhang et al., 2006. Cell. 126:1189-1201.)  Immunoprecipitated DNA was checked with Q-PCR to ensure that it was enriched for methylated DNA.  This DNA was then used for labelling.

hyb_protocol: 250ng of DNA for each channel was labelled using Agilent CGH labelling protocol.   Labelled DNA mixed with mouse Cot-1 DNA, yeast tRNA and Agilent 10x Control targets.  This mix was hybridized to arrays for 40 hours at 65C.  Arrays were washed as per Agilent protocol and scanned immediately

scan_protocol: The arrays were scanned with Agilent DNA microarray scanner (G2565BA), and probe features were extracted using Feature Extraction Software (version 8.5)

data_processing: Arrays were processed using Agilent Feature Extraction (Version 8.5). Log 10 ratio were calculated from processed Cy5/ processed Cy3 signals

organism: Mus musculus

source_name: Wildtype Mouse ES Cell DNA

label_protocol: Cy3 Labelled with Agilent CGH protocol

extract_protocol: Phenol:Chloroform Extracted DNA

tag: Wildtype DNA from J1 Mouse ES Cells

source_name: TKO Mouse ES Cells

label_protocol: Cy5 Labelled with Agilent CGH protocol

tag: Dnmt3a/3b -/-; Dnmt1 KD Mouse ES Cells (Meissner et al., 2005. Nucleic Acid Research. 33:5868-77).


title: Glioblastoma-Gbm 66

tag: male, 32y, ampl EGFR, expr EGFRvIII


title: Promoter CpG Methylation in Mouse ES Cells (1/2) replicate 7


title: Promoter CpG Methylation in Mouse ES Cells (1/2) replicate 4

source_name: TKO Mouse ES Cell

tag: Dnmt3a/3b -/-; Dnmt1 KD Mouse ES Cell (Meissner et al., 2005. Nucleic Acid Research. 33:5868-77).


title: Glioblastoma-Gbm 206

tag: female, 41y


title: Glioblastoma-Gbm 203

tag: male, 56y, ampl EGFR, expr EGFRvIII


title: Promoter CpG Methylation in Mouse ES Cells (1/2) replicate 6


title: Glioblastoma-Gbm 244

tag: female, 62y


title: Glioblastoma-Gbm 157

tag: ampl EGFR


title: Promoter CpG Methylation in Mouse ES Cells (2/2) replicate 6


title: Promoter CpG Methylation in Mouse ES Cells (2/2) replicate 5


title: Promoter CpG Methylation in Mouse ES cells (1/2) replicate 3

description: All cell cultures were maintained at 37 °C with 5% CO2. The culture of mouse ESCs were maintained in DMEM supplemented with 15% heat-inactivated FBS , LIF and penicillin/streptomycin. mESCs were grown in feeder-free for 2 passages before harvesting of DNA. After genomic DNA isolation, the DNA was RNase treated and 2ug was used for methylated DNA immunoprecipitation (Weber et al., 2005. Nat Genetics. 37, 853-62. Zhang et al., 2006. Cell. 126:1189-1201.) Immunoprecipitated DNA was checked with Q-PCR to ensure that it was enriched for methylated DNA. This DNA was then used for labelling.

hyb_protocol: 250ng of DNA for each channel was labelled using Agilent CGH labelling protocol. Labelled DNA mixed with mouse Cot-1 DNA, yeast tRNA and Agilent 10x Control targets. This mix was hybridized to arrays for 40 hours at 65C. Arrays were washed as per Agilent protocol and scanned immediately

source_name: J1 P37 mouse ES Cell Genomic DNA

tag: Wildtype mouse ES Cell Genomic DNA

tag: Dnmt3a/3b -/-; Dnmt1 KD mouse ES Cells (Meissner et al., 2005. Nucleic Acid Research. 33:5868-77)


title: Promoter CpG Methylation in Mouse ES Cells (1/2) replicate 2

tag: Dnmt3a/3b -/-; Dnmt1 KD Mouse ES Cell (Meissner et al., 2005. Nucleic Acid Research. 33:5868-77)


title: Glioblastoma-Gbm 207

tag: female, 67y, ampl EGFR


title: Glioblastoma-GBM 178b

tag: male, 59y, ampl EGFR


title: Glioblastoma-Gbm 152

tag: male, 43y


title: Promoter CpG Methylation in Mouse ES Cells (2/2) replicate 3


title: Promoter CpG Methylation in Mouse ES Cells (2/2) replicate 4


title: Promoter CpG Methylation in Mouse ES Cells (2/2) replicate 1


title: Promoter CpG Methylation in Mouse ES cells (1/2) replicate 1

tag: Dnmt3a/3b -/-; Dnmt1 KD mouse ES Cells (Meissner et al., 2005. Nucleic Acid Research.  33:5868-77)


title: Promoter CpG Methylation in Mouse ES Cells (2/2) replicate 7


title: Glioblastoma-Gbm 161

tag: male, 51y, ampl EGFR


title: Promoter CpG Methylation in Mouse ES Cells (2/2) replicate 2


title: Glioblastoma-GBM 142-c

tag: male, 40y, ampl EGFR, expr EGFRvIII


title: Glioblastoma-Gbm 163

tag: male, 48y, ampl EGFR, expr EGFRvIII


title: Glioblastoma-GBM 149-b

tag: male, 59y, ampl EGFR, expr EGFRvIII


title: Glioblastoma-Gbm 172

tag: female, 63y, ampl EGFR


title: Chordoma_case_24P

status: Public on Jan 25 2008

city: Lund

first: Karolin

middle: H

last: Nord

address: BMC C13

department: Dept of Clinical Genetics

country: Sweden

institute: Lund University

description: Array CGH data on chordoma

hyb_protocol: Arrays were hybridized and washed as described in Knijnenburg et al. (Cytometry A 2007;71:585-91)

scan_protocol: Arrays were scanned in GenePix 4100A scanner

data_processing: Primary data were collected using the GenePix Pro 4.0 software, and the quantified data matrix was deposited into the web-based database BioArray Software Environment (BASE), where filtering and normalization were performed.

source_name: Case 24P

label_protocol: BioPrime DNA Labeling System (Invitrogen, Breda, the Netherlands)

extract_protocol: Standard DNA isolation techniques

tag: Genomic DNA from fresh frozen chordoma biopsy

source_name: Promega reference male/female DNA (Promega, Leiden, the Netherlands)

tag: Pooled lymphoblastoid genomic DNA from multiple individuals


title: Chordoma_case_24R

description: Array CGH data on chordoma

source_name: Case 24R


title: ctr_brain-ctr 345b

source_name: brain sample, non diseased

tag: control brain


title: Chordoma_case_26R1

description: Array CGH data on chordoma

source_name: Case 26R1


title: ctr_brain-ctr 7e

tag: male, 63y


title: Chordoma_case_9

description: Array CGH data on chordoma

hyb_protocol: Arrays were hybridized and washed as described in Heidenblad et al. (Oncogene 2006;25:7106-16)

scan_protocol: Arrays were scanned in Agilent Microarray scanner

source_name: Case 9

label_protocol: BioPrime array CGH labeling module (Invitrogen, Carlsbad, CA, USA)

extract_protocol: DNeasy Tissue Kit (Qiagen, Valencia, CA, USA)

source_name: Promega reference male DNA (Promega, Madison, WI, USA)

tag: Pooled lymphoblastoid genomic DNA from ten male individuals


title: Chordoma_case_8

description: Array CGH data on chordoma

source_name: Case 8


title: Chordoma_case_23

description: Array CGH data on chordoma

source_name: Case 23


title: Chordoma_case_22M

description: Array CGH data on chordoma

source_name: Case 22M


title: ctr_brain-ctr 269


title: Chordoma_case_7

description: Array CGH data on chordoma

source_name: Case 7


title: Chordoma_case_26R2

description: Array CGH data on chordoma

source_name: Case 26R2


title: Chordoma_case_6

description: Array CGH data on chordoma

source_name: Case 6


title: Chordoma_case_22P

description: Array CGH data on chordoma

source_name: Case 22P


title: Chordoma_case_1

description: Array CGH data on chordoma

source_name: Case 1


title: Chordoma_case_3

description: Array CGH data on chordoma

source_name: Case 3


title: Chordoma_case_4

description: Array CGH data on chordoma

source_name: Case 4


title: Chordoma_case_10

description: Array CGH data on chordoma

source_name: Case 10


title: Chordoma_case_21R

description: Array CGH data on chordoma

source_name: Case 21R

source_name: Promega reference male/female DNA (Promega, Leiden, the Netherlands)


title: Wildtype vs DNA Methylation Deficient mESC Gene Expression

description: All cell cultures were maintained at 37 °C with 5% CO2. The culture of mouse ESCs were maintained in DMEM supplemented with 15% heat-inactivated FBS , LIF and penicillin/streptomycin. mESCs were grown in feeder-free for 2 passages before harvesting of RNA.   RNA was isolated using Trizol.

hyb_protocol: 750ng of RNA for each channel was labelled using Agilent Low Input Linear Amplification protocol. Labelled cRNA mixed with Agilent 10x Control targets and Agilent 25x Fragmentation Buffer. This was incubated at 37C for 30 min and the reaction was stopped by the addition of 2x Agilent hybridization buffer.  This mix was hybridized to arrays for 17 hours at 65C at 4rpms. Arrays were washed as per Agilent protocol and scanned immediately

data_processing: Arrays were processed using Agilent Feature Extraction (Version 8.5). Log 10 ratio were calculated from processed Cy5/ processed Cy3 signals.  Replicates 1 and 3 were labeled - J1 with Cy5 and TKO with Cy3.  Replicate 2 was labeled J1 with Cy3 and TKO with Cy5.

label: Cy5 or Cy3

source_name: Wildtype Mouse ES Cell

label_protocol: Cy5 or Cy3 Labelled with Agilent Low Input Linear Amplification Kit

extract_protocol: Trizol Extracted and cleaned with Qiagen RNeasy kit

tag: Wildtype mouse ES Cell (J1) RNA

label: Cy3 or Cy5

source_name: TKO Mouse ES Cell

label_protocol: Cy3 or Cy5 Labelled with Agilent Low Input Linear Amplification Kit


title: Chordoma_case_5

description: Array CGH data on chordoma

source_name: Case 5


title: Chordoma_case_11

description: Array CGH data on chordoma

source_name: Case 11

source_name: Promega reference male DNA (Promega, Madison, WI, USA)


title: Chordoma_case_25

description: Array CGH data on chordoma

source_name: Case 25


title: Chordoma_case_2

description: Array CGH data on chordoma

source_name: Case 2


title: ctr_brain-ctr 278c

source_name: brain sample, non diseased


title: Chordoma_case_21P

description: Array CGH data on chordoma

source_name: Case 21P


title: Glioblastoma-Gbm 180

source_name: glioma

tag: female, 30y


title: ctr_brain-ctr344


title: ctr_brain-ctr 31e

tag: female, 68y


title: Chordoma_case_18

description: Array CGH data on chordoma

source_name: Case 18


title: Chordoma_case_20

description: Array CGH data on chordoma

source_name: Case 20


title: Glioblastoma-Gbm 164

tag: ampl EGFR, expr EGFRvIII


title: Chordoma_case_19

description: Array CGH data on chordoma

source_name: Case 19


title: Chordoma_case_17

description: Array CGH data on chordoma

source_name: Case 17


title: NA19240_C/NA10851

status: Public on Jan 24 2008

city: Santa Clara

first: Peter

last: Tsang

address: 5301 Stevens Creek Blvd.

department: Agilent Labs

institute: Agilent Technologies

hyb_protocol: See manufacturer website: <http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=52010>

scan_protocol: Scanned on an Agilent G2505A Scanner

data_processing: Agilent Feature Extraction v9.1, default CGH parameters

label_protocol: Agilent DNA labeling kit

extract_protocol: genomic DNA was extracted

tag: Coriell sample

tag: Coriell Reference sample


title: NA10851/NA18972_C


title: NA15510_B_3/NA10851


title: NA10851/NA15510_B_2


title: NA11830_C/NA10851


title: NA10851/NA18942_C


title: NA10839_C/NA10851


title: NA12155_C/NA10851


title: NA10851/NA11830_C


title: NA18564_C/NA10851


title: NA18972_C/NA10851


title: NA10851/NA12155_C


title: NA10851/NA10839_C


title: NA12740_A/NA10851


title: NA10851/NA19221_C


title: NA10851/NA07048_A


title: NA10851/NA18860_C


title: NA18942_C/NA10851


title: NA10851/NA18517_A


title: NA15510_B_2/NA10851


title: NA10851/NA15510_B_1


title: NA19221_C/NA10851


title: NA10851/NA12740_A


title: NA15510_B_1/NA10851


title: NA07048_A/NA10851


title: NA18517_A/NA10851


title: NA18860_C/NA10851


title: NA10851/NA18564_C


title: NA10851/NA18504_A


title: NA10851_B/NA10851


title: NA18504_A/NA10851


title: NA10851/NA12802_A


title: NA12802_A/NA10851


title: NA10851/NA07029_A


title: NA07029_A/NA10851


title: NA10851/NA10863_A


title: NA10851/NA18980_A


title: NA10863_A/NA10851


title: NA18537_A/NA10851


title: NA12872_B/NA10851


title: NA10851/NA19132_A


title: NA10851/NA18552_B


title: NA19132_A/NA10851


title: NA10851/NA18572_B


title: NA15510_A/NA10851


title: NA15510_C/NA10851


title: NA10851/NA12872_B


title: NA10851/NA18537_A


title: NA18552_B/NA10851


title: NA10851/NA18975_C


title: NA10851_C/NA10851


title: NA10851/NA10847_B


title: NA10851/NA19007_C


title: NA10851/NA15510_A


title: NA10851_A/NA10851


title: NA18853_B/NA10851


title: NA18572_B/NA10851


title: NA10847_B/NA10851


title: NA18975_C/NA10851


title: NA10851/NA15510_C


title: NA10851/NA19144_B


title: NA19240_C/NA10851


title: NA18980_A/NA10851


title: NA19144_B/NA10851


title: NA10851/NA18502_B


title: NA11830_C/NA10851


title: NA10851/NA11830_C


title: NA18563_B/NA10851


title: NA10851/NA18942_C


title: NA18502_B/NA10851


title: NA19173_B/NA10851


title: NA18942_C/NA10851


title: NA12155_C/NA10851


title: NA10851/NA18853_B


title: NA10851/NA10839_C


title: NA10851_C/NA10851


title: NA10851/NA19173_B


title: NA10851/NA12155_C


title: NA10851/NA15510_C


title: NA10851/NA19240_C


title: NA10851/NA18975_C


title: NA10851/NA19221_C


title: NA10839_C/NA10851


title: NA10851/NA19007_C


title: NA18564_C/NA10851


title: NA19007_C/NA10851


title: NA15510_C/NA10851


title: NA10851/NA18563_B


title: NA18972_C/NA10851


title: NA18860_C/NA10851


title: NA10851/NA18860_C


title: NA18975_C/NA10851


title: NA10851_B/NA10851


title: NA10851/NA18564_C


title: NA15510_B_3/NA10851


title: NA10851/NA15510_B_1


title: NA07048_A/NA10851


title: NA19221_C/NA10851


title: NA18537_A/NA10851


title: PRCC2

city: Houston

first: Federico

middle: A

last: Monzon

state: TX

address: 6565 Fannin St., MS205

department: Pathology

institute: The Methodist Hospital Research Institute

hyb_protocol: Affymetrix Mapping 10K Xba 2.0 Assay

scan_protocol: Affymetrix Mapping 10K Xba 2.0 Assay with an Affymetrix GeneChip 3000 7G scanner

data_processing: Affymetrix GCOS 1.4 and GTYPE 4.0

label: Biotinilated - Fragmented PCR products

source_name: Renal Cell Carcinoma, Papillary Type, genomic DNA from Paraffin Embedded Tissue

label_protocol: Custom labeling protocol for FFPE tissue based on Affymetrix Mapping 10K Assay (Lyons-Weiler MA et al, Mol Diagn Pathol, in press)

extract_protocol: Deparaffinization followed by Qiagen DNeasy Mini kit by manufacturer's instructions

tag: sex

value: M

tag: agedecade

tag: tumor size

tag: furhman nuclear grade

tag: tnm stage

tag: lymphovascular invasion

value: N

tag: gross appearance

value: WC yellow fragile

tag: comment:


title: PRCC3

value: on sectioning the tumor is mostly necrotic


title: PRCC5

value: WC with area of nec

tag: comment

value: Extensive necrosis.


title: NA10851/NA18972_C


title: PRCC1

value: 80% friable caseous white with focal firm tan-white nodular; block B is from caseous

value: Small focus of clear cell; multifocal vs tangential cut.


title: NA10851/NA12740_A


title: NA18517_A/NA10851


title: NA10851/NA18517_A


title: NA15510_B_1/NA10851


title: NA10851/NA07048_A


title: NA10851/NA18504_A


title: NA18504_A/NA10851


title: NA19132_A/NA10851


title: NA10851/NA12802_A


title: NA10851/NA19132_A


title: NA12802_A/NA10851


title: OC4

source_name: Renal Oncocytoma, genomic DNA from Paraffin Embedded Tissue

value: WC golden brown, focally cystic and hem

value: 4cm OC, no ECE, no LVI


title: NA10851/NA15510_B_2


title: OC1

value: ovoid tan

value: IHC: RCC neg, CK7 scat pos and tubules.


title: NA15510_B_2/NA10851


title: OC5

value: WC gold w hem foci; dig images

value: IHC: pos CD10, ecad, inh; neg CI, vim, rcc, EP4; CK7 scat pos; Ki67 1+ of neoplastic cells


title: OC6

value: F

value: mohagany, multinodular, central scar

value: 21cm OC, no ECE, no LVI; FISH not c/w OC.


title: PRCC6

value: M

value: 18 WC yellow-tan nodules


title: CRCC4

source_name: Renal Cell Carcinoma, Clear Cell Type, genomic DNA from Paraffin Embedded Tissue

value: N

value: variegated golden yellow


title: NA10851/NA18980_A


title: CRCC5

value: WC variegated red yellow gold


title: NA18853_B/NA10851


title: CRCC3

value: golden yellow orange


title: NA10863_A/NA10851


title: NA10851/NA12872_B


title: NA18980_A/NA10851


title: NA10851/NA18572_B


title: NA10851/NA10863_A


title: CRCC1

value: lobulated yellow

value: Multifocal; IHC: pos RCC; neg CK7, EP4, vim, inh, IC; CD10 pos memb; ecad focal weak memb


title: CRCC2


title: CHRCC5

description: RenalCellCarcinoma_Chromophobe_FFPE_Rep5

source_name: Renal Cell Carcinoma, Chromophobe Type, genomic DNA from Paraffin Embedded Tissue

value: Bright yellow


title: CHRCC3

description: RenalCellCarcinoma_Chromophobe_FFPE_Rep3

value: WC yellow variegated


title: CHRCC4

description: RenalCellCarcinoma_Chromophobe_FFPE_Rep4

value: Y

value: Tan-brown with central scar and lg areas of hem and nec.

value: .015 cm PRCC


title: CHRCC2

description: RenalCellCarcinoma_Chromophobe_FFPE_Rep2

value: Yellow orange granular lesion with hem foci


title: NA10851/NA18552_B


title: NA10851_A/NA10851


title: CHRCC1

description: RenalCellCarcinoma_Chromophobe_FFPE_Rep1

value: F

value: WC solid, fleshy tan-black

value: IHC: pos CK7, EP4, CI; neg vim, CD10, ecad, inh; Ki67 pos < 10%


title: NA12872_B/NA10851


title: NA10851/NA18537_A


title: Gamendazole 24 hr

city: Kansas City

first: Joseph

middle: S

last: Tash

state: KS

address: 3901 Rainbow Blvd.

department: Center for Male Contraceptive Research and Drug Development

institute: University of Kansas Medical Center

description: Gene expression data

hyb_protocol: Following fragmentation, 15ug of biotin labeled cRNA was hybridized for 16hr 28min at 45C, 60rpm in an Affymetrix Hybridization Oven 640 to a Rat230 2.0 GeneChip expression array. The washing and antibody amplification staining procedure utilizing R phycoerthrin-streptavidin was performed with the Affymetrix Fluidics Station 450 using the EukGE-WS2v5_450 fluidics protocol.

scan_protocol: Single scans were performed using the Affymetrix GeneChip 3000 scanner.

data_processing: The data were analyzed with Gene Chip Operating Software (GCOS 1.1) using Affymetrix default analysis settings as normalization method. http://www.affymetrix.com/support/technical/manual/expression_manual.affx

organism: Rattus rattus

source_name: Rat testis Gamendazole 24 hr

label_protocol: Biotin labeled cRNA targets were prepared from 6.2ug total RNA using Affymetrix's single-cycle eukaryotic target preparation procedure (Expression Analysis Technical Manual, 2001, Affymetrix). Reverse Transcription was performed using Superscipt II Choice System (Invitogen). Invitro-Transcription and labeling was conducted using the GeneChip Expression 3' Amplification Reagent Kit (Affymetrix).

growth_protocol: Adult male Long-Evans rats (60 day old) administered single ip dose of 6mg/kg Gamendazole or 25 mg/kg lonidamine or vehicle control (buffered DMSO) - testes harvested at 0 4 12 and 24 hr

extract_protocol: TriZol, Phase Lock Gel-Heavy

treatment_protocol: Experimental details are found at Tash et al, Gamendazole, an orally active indazole carboxylic acid male contraceptive agent, targets HSP-90, eEF1A, and stimulates IL-1 transcription in Sertoli cells, Biol. Reprod. (2007) under review

tag: rat testis 60 days old


title: NA18552_B/NA10851


title: NA10851/NA15510_A


title: Gamendazole 12 hr

description: Gene expression data

source_name: Rat testis Gamendazole 12 hr


title: NA18572_B/NA10851


title: Control 24 hr

description: Gene expression data

source_name: Rat testis control 24 hr


title: NA15510_A/NA10851


title: NA12740_A/NA10851


title: NA10851/NA07029_A


title: OC2

value: WC brown and yellow, soft; dig images

value: Multifocal; no IHC; no FISH


title: Control 0 hr

description: Gene expression data

source_name: Rat testis control 0 hr


title: Lonidamine 12 hr

description: Gene expression data

source_name: Rat testis lonidamine 12 hr


title: Control 4 hr

description: Gene expression data

source_name: Rat testis control 4 hr


title: NA10851/NA18502_B


title: Lonidamine 24 hr

description: Gene expression data

source_name: Rat testis lonidamine 24 hr


title: NA18502_B/NA10851


title: NA19144_B/NA10851


title: Gamendazole 4 hr

description: Gene expression data

source_name: Rat testis Gamendazole 4 hr


title: NA10851/NA18563_B


title: NA10851/NA19144_B


title: dMyc_null_rep3

status: Public on Jan 22 2008

city: Seattle

first: Robert

last: Eisenman

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: dMyc null Drosophila larvae, analyzed 24hr after egg deposition

hyb_protocol: Experimental and control labeled aRNA targets (4 μg each) were co-hybridized to microarrays for 16 hrs at 63°C and sequentially washed at room temperature in 1 x SSC and 0.03% SDS for 2 min, 1 x SSC for 2 min, 0.2 x SSC with agitation for 20 min, and 0.05 x SSC with agitation for 10 min.  Arrays were immediately centrifuged until dry.

scan_protocol: Arrays were scanned using a GenePix 4000B scanner (Molecular Devices Corporation, Sunnyvale, CA).  Image analysis was performed using GenePix Pro 6.0.

data_processing: For each array result, spot intensity signals were assessed for signal quality and those identified as poor quality were removed from further analysis.  Spot-level ratios were background corrected, log2 transformed, and loess normalized using tools within the GeneTraffic MULTI software package (Stratagene, La Jolla, CA).

organism: Drosophila melanogaster

source_name: dm4 mutant larvae, 24 hr AED

label_protocol: Experimental and control total RNA samples (2 μg) were amplified using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion, Inc., Austin, TX).   The resulting aRNAs were subsequently coupled to either Cy3 or Cy5 fluorophores (GE Healthcare Bio-Sciences Corp., Piscataway, NJ)

extract_protocol: Total RNA was extracted with Trizol Reagent

tag: dm4 Drosophila larvae were collected 24 hours after egg deposition

source_name: control larvae, 24 hr AED

tag: control Drosophila larvae were collected 24 hours after egg deposition


title: NA10847_B/NA10851


title: NA10851/NA10847_B


title: Lonidamine 4 hr

description: Gene expression data

source_name: Rat testis lonidamine 4 hr


title: Control 12 hr

description: Gene expression data

source_name: Rat testis control 12 hr


title: dMyc_null_rep3rev


title: NA10851/NA19173_B


title: NA18563_B/NA10851


title: NA10851/NA18853_B


title: E.coli K-12_MC4100_37˚C and 23˚C M9 glycerol_Rep4

city: Northampton

first: Christine

middle: Ann

last: White-Ziegler

state: MA

address: Clark Science Center

department: Biological Sciences

institute: Smith College

description: This slide is a technical replicate of Rep2 in which the dyes have been flipped.

hyb_protocol: Hybridization was completed as described previously (1). The hybridization solution (10 μl of cDNA mixture, 1 μl of denatured rat Hybloc DNA (1 μg/μl), 20 μl of 2X SDS buffer, 2 μl of dT blocker, and 7 μl of nuclease-free water) was placed over a prewarmed microarray slide and covered with a Corning 22x40 mm coverslip.  The slide was then sealed in a hybridization chamber and submerged for 3 days in a 60˚C water bath.  Microarray slides were washed for 10 minutes in 2X SSC, 0.2% SDS at 37ºC, 10 minutes in 2X SSC at room temperature, and 10 minutes in 0.2X SSC at room temperature.  Slides were dried by centrifugation at 10,000 rpm for two minutes.  For the second hybridization to allow the 3DNA capture reagent to bind to the complementary Cy3 or Cy5 specific 3DNA capture sequences ligated to the cDNAs, each microarray received 42 μl of hybridization solution (2.5 μl of Cy3 capture reagent, 2.5 μl of Cy5 capture reagent, 21 μl of 2X SDS buffer, 0.5 μl anti-fade reagent, and 15.5 μl of nuclease-free water) and hybridized as before via submersion for 3-4 hours in a 61ºC water bath.  The slides were washed, dried , and kept in the dark until they were scanned and analyzed. 1.) White-Ziegler, C. A., A. J. Malhowski, and S. D. Young.  Human body temperature (37˚C) increases the expression of iron, carbohydrate, and amino acid utilization genes in Escherichia coli K-12.  Journal of Bacteriology 2007.  Vol. 189(15):5429-40. Epub 2007 May 25.

scan_protocol: Five slides were used in the analysis with cDNAs, representing three independent growth experiments and two technical replicates (1).  Hybridized slides were scanned using GenePix Pro 4.1 software (Axon Instruments, Inc.).  Photomultiplier tube (PMT) voltage was altered for the initial scanning to ensure proper channel balance and decrease background.  Any gene feature that had a signal-to-background ratio < 2.0 was rejected and not further analyzed.  The ratio of medians values were used for further analysis. 1.) White-Ziegler, C. A., A. J. Malhowski, and S. D. Young.  Human body temperature (37˚C) increases the expression of iron, carbohydrate, and amino acid utilization genes in Escherichia coli K-12.  Journal of Bacteriology 2007.  Vol. 189(15):5429-40. Epub 2007 May 25.

organism: Escherichia coli

source_name: Escherichia coli K-12 MC4100

label_protocol:
Synthesis, labeling of cDNA with Cy3/Cy5, and hybridization was performed using the 3DNA Array 350 RP Expression Array Detection Kit according to the manufacturer’s protocol (Genisphere).  cDNA for each condition was prepared from 2 μg total RNA.  cDNA from both temperatures (37ºC and 23ºC) was cohybridized to slides containing full-length PCR products from all 4,290 annotated open reading frames (ORFs) in E. coli MG1655.
1.) White-Ziegler, C. A., A. J. Malhowski, and S. D. Young.  Human body temperature (37˚C) increases the expression of iron, carbohydrate, and amino acid utilization genes in Escherichia coli K-12.  Journal of Bacteriology 2007.  Vol. 189(15):5429-40. Epub 2007 May 25.

growth_protocol:
Bacterial cultures were inoculated and grown as described previously (1,2).  An inoculum from a 37˚C grown single colony was used to initiate parallel, colony matched 37˚C and 23˚C grown cultures.  The cells from these cultures were harvested at equivalent optical densities after approximately 9-11 generations growth in early-mid exponential phase (OD600= 0.2-0.6).  Cell pellets were subsequently frozen in liquid nitrogen and stored at -80ºC for RNA isolation.
1.) White-Ziegler, C. A., A. M. Black, S. H. Eliades, S. Young, and K. Porter. 2002. The N-acetyltransferase RimJ responds to environmental stimuli to repress pap fimbrial transcription in Escherichia coli. J. Bacteriol. 184:4334-4342.
2.)White-Ziegler, C. A., A. Villapakkam, K. Ronaszeki, and S. D. Young. 2000. H-NS controls pap and daa fimbrial transcription Escherichia coli in response to multiple environmental cues. J. Bacteriol. 182:6391-6400.

extract_protocol:
For microarray analyses, RNA was isolated by phenol: chloroform extraction as described previously (1) with the modifications that the RNA was subjected to a second DNase digestion in solution and cleaned using a RNeasy column per manufacturers directions (Qiagen).
1.)White-Ziegler, C. A., M. L. Angus Hill, B. A. Braaten, M. W. van der Woude, and D. A. Low. 1998. Thermoregulation of Escherichia coli pap transcription: H-NS is a temperature-dependent DNA methylation blocking factor. Mol Microbiol 28:1121-37.

tag: Grown on M9 glycerol medium at 23˚C for ~10 generations to exponential phase (~50 hours)

tag: E. coli K-12 MC4100

tag: Grown on M9 glycerol medium at 37˚C for ~10 generations to exponential phase (~14 hours)


title: dMyc_null_rep2


title: dMyc_null_rep2rev


title: dMyc_null_rep1rev


title: E.coli K-12_MC4100_37˚C and 23˚C M9 glycerol_Rep2

description: Included in other fields

data_processing: Photomultiplier tube (PMT) voltage was altered for the initial scanning to ensure proper channel balance and decrease background.  Any gene feature that had a signal-to-background ratio < 2.0 was rejected and not further analyzed.  The ratio of medians values were used for further analysis.


title: E.coli K-12_MC4100_37˚C and 23˚C M9 glycerol_Rep3

description: Included in other fields


title: NA19173_B/NA10851

tag: Coriell sample


title: E.coli K-12_MC4100_37˚C and 23˚C M9 glycerol_Rep5

description: This slide is a technical replicate of Rep3 in which the dyes have been flipped.


title: NA07029_A/NA10851

tag: Coriell Reference sample


title: dMyc_null_rep1


title: E.coli K-12_MC4100_37˚C and 23˚C M9 glycerol_Rep1

description: Included in other fields


title: A377 vs E18 replicate 2 dye-swap

status: Public on Jan 21 2008

city: Planegg-Martinsried

first: Stephan

last: Hutter

state: Bavaria

address: Grosshaderner Strasse 2

department: Department of Biology II

country: Germany

institute: University of Munich

description: Competitive hybridization between E18 and A377

hyb_protocol: Hybridizations were performed following DGRC protocols (Drosophila Genomics Resource Center Microarrays website) using Corning microarray hybridization chambers (Corning Incorporated, Corning, NY, USA)

scan_protocol: Scanned on an aQuire microarray scanner (Genetix, New Milton, UK), images were quantified using Genetix QScan software (Version 1.1.8.10)

data_processing: Normalized 647/555 ratios were obtained using CARMAweb. Dye-swap replicates were normalized as pairs. Local background effects, within-array variation, and between-array variation was corrected using the "minimum", "printtiploess", and "quantile" methods respectively

label: Alexa Fluor 647

label_protocol: 30 µg of total RNA were reverse transcribed and labeled following DGRC protocols (Drosophila Genomics Resource Center Microarrays website) using SuperScript Plus Indirect cDNA Labeling System and Alexa Flour dyes (Invitrogen, Carlsbad, California, USA)

growth_protocol: Flies were reared on standard cornmeal-molasses medium at 22° C and a 15h-9h light-dark cycle

extract_protocol: TriZol procedure

tag: Strain

tag: Sex

value: male

tag: Age

value: 4-6 days

tag: Tissue

value: whole fly

label: Alexa Fluor 555

label_protocol: 30 µg of total RNA were reverse transcribed and labeled following DGRC protocols (Drosophila Genomics Resource Center Microarrays website) using SuperScript Plus Indirect cDNA Labeling System and Alexa Flour dyes (Invitrogen, Carlsbad, CA, USA)


title: A377 vs E18 replicate 2

description: Competitive hybridization between A377 and E18


title: A398 vs E16 replicate 2

description: Competitive hybridization between A398 and E16


title: A186 vs E17 replicate 1 dye-swap

description: Competitive hybridization between E17 and A186


title: A398 vs E16 replicate 2 dye-swap

description: Competitive hybridization between E16 and A398


title: A82 vs E20 replicate 1

description: Competitive hybridization between A82 and E20


title: A377 vs E18 replicate 1


title: A186 vs E17 replicate 1

description: Competitive hybridization between A186 and E17


title: A377 vs E18 replicate 1 dye-swap


title: A82 vs E20 replicate 1 dye-swap

description: Competitive hybridization between E20 and A82


title: A131 vs E15 replicate 1 dye-swap

description: Competitive hybridization between E15 and A131


title: A131 vs E15 replicate 1

description: Competitive hybridization between A131 and E15


title: A84 vs E01 replicate 2

description: Competitive hybridization between A84 and E01


title: A84 vs E01 replicate 2 dye-swap

description: Competitive hybridization between E01 and A84


title: A384 vs E12 replicate 1 dye-swap

description: Competitive hybridization between E12 and A384


title: A84 vs E01 replicate 1 dye-swap


title: A398 vs E16 replicate 1


title: A398 vs E16 replicate 1 dye-swap


title: A84 vs E01 replicate 1


title: Co-hybridization of E. coli O157:H7 EDL933 with E. coli K-12 M1655 #2

city: Kgs. Lyngby

first: Hanni

last: Willenbrock

address: Kemikalievej, bygning 208

department: Center for Biological Sequence Analysis

country: Denmark

institute: DTU

description: Control co-hybridization of genomic DNA from E. coli O157:H7 EDL933 with E. coli K-12 MG1655

hyb_protocol: NimbleGen standard protocols for CGH (prepared and hybridized by NimbleGen)

data_processing: log2 ratio of isolate/control

source_name: E. coli O157:H7 EDL933

growth_protocol: overnight in Luria-Bertani (LB) broth with continuous agitation

extract_protocol: Genomic DNA isolation according to Grimberg et al. Nucleic acids research 1989, 17(21):8893

tag: control strain O157:H7 EDL933

source_name: E. coli K-12 MG1655

tag: control strain K-12 MG1655


title: A186 vs A95 replicate 1

description: Competitive hybridization between A186 and A95


title: A384 vs A186 replicate 1 dye-swap

description: Competitive hybridization between A186 and A384


title: A384 vs E12 replicate 1

description: Competitive hybridization between A384 and E12


title: A377 vs A384 replicate 1 dye-swap

description: Competitive hybridization between A384 and A377


title: A384 vs A186 replicate 1

description: Competitive hybridization between A384 and A186


title: A82 vs A131 replicate 1 dye-swap

description: Competitive hybridization between A131 and A82


title: A377 vs A384 replicate 1

description: Competitive hybridization between A377 and A384


title: Co-hybridization of E. coli G 4/9 isolate with E. coli K-12 MG1655

description: Co-hybridization of genomic DNA from E. coli isolate G 4/9 from Symbioflor2 with E. coli K-12 MG1655

scan_protocol: NimbleGen standard protocols for CGH (prepared and hybridized by NimbleGen)

source_name: E. coli G4/9

tag: Isolate G 4/9 of Symbioflor2 probiotic product from Symbiopharm


title: A82 vs A131 replicate 1

description: Competitive hybridization between A82 and A131


title: Co-hybridization of E. coli G 1/2 isolate with E. coli K-12 MG1655

description: Co-hybridization of genomic DNA from E. coli isolate G 1/2 from Symbioflor2 with E. coli K-12 MG1655

source_name: E. coli G 1/2

label_protocol: NimbleGen standard protocols for CGH (prepared and hybridized by NimbleGen)

tag: Isolate G 1/2 of Symbioflor2 probiotic product from Symbiopharm


title: Co-hybridization of E. coli O157:H7 EDL933 with E. coli K-12 M1655 #1


title: Co-hybridization of E. coli G5 isolate with E. coli O157:H7 EDL933

description: Co-hybridization of genomic DNA from E. coli isolate G5 from Symbioflor2 with E. coli O157:H7 EDL933

source_name: E. coli G5

tag: Isolate G5 of Symbioflor2 probiotic product from Symbiopharm


title: A384 vs A398 replicate 2

description: Competitive hybridization between A384 and A398


title: A377 vs A131 replicate 2 dye-swap

description: Competitive hybridization between A131 and A377


title: A384 vs A398 replicate 1


title: Co-hybridization of E. coli G 3/10 isolate with E. coli O157:H7 EDL933

description: Co-hybridization of genomic DNA from E. coli isolate G 3/10 from Symbioflor2 with E. coli O157:H7 EDL933

source_name: E. coli isolate G3/10

tag: Isolate G 3/10 of Symbioflor2 probiotic probiotic from Symbiopharm


title: A82 vs A95 replicate 2

description: Competitive hybridization between A82 and A95


title: A384 vs A398 replicate 1 dye-swap

description: Competitive hybridization between A398 and A384


title: A186 vs A95 replicate 1 dye-swap

description: Competitive hybridization between A95 and A186


title: A82 vs A95 replicate 1 dye-swap

description: Competitive hybridization between A95 and A82


title: A384 vs A398 replicate 2 dye-swap


title: A82 vs A95 replicate 1


title: A84 vs A186 replicate 1 dye-swap

description: Competitive hybridization between A186 and A84


title: A84 vs A186 replicate 1

description: Competitive hybridization between A84 and A186


title: A398 vs A82 replicate 2

description: Competitive hybridization between A398 and A82


title: A398 vs A82 replicate 2 dye-swap

description: Competitive hybridization between A82 and A398


title: A377 vs A131 replicate 1

description: Competitive hybridization between A377 and A131


title: A398 vs A82 replicate 1 dye-swap


title: A377 vs A131 replicate 2


title: Co-hybridization of E. coli G 1/2 isolate with E. coli O157:H7 EDL933

description: Co-hybridization of genomic DNA from E. coli isolate G 1/2 from Symbioflor2 with E. coli O157:H7 EDL933

source_name: E. coli isolate G 1/2

growth_protocol: overnight in Lurie-Bertani (LB) broth with continuous agitation


title: Co-hybridization of E. coli isolate G 4/9 with E. coli O157:H7 EDL933

description: Co-hybridization of genomic DNA from E. coli isolate G 4/9 from Symbioflor2 with E. coli O157:H7 EDL933

source_name: E. coli isolate G4/9

tag: Isolate G 4/9 of Symbioflor2 probiotic product from Symbiopham


title: A84 vs A186 replicate 2


title: A84 vs A131 replicate 1 dye-swap

description: Competitive hybridization between A131 and A84


title: A84 vs A186 replicate 2 dye-swap


title: A398 vs A82 replicate 1


title: Co-hybridization of E. coli isolate G 3/10 with control strain K-12 MG1655

description: Co-hybridization of genomic DNA from E. coli isolate G 3/10 from Symbioflor2 with E. coli K-12 MG1655

source_name: E. coli isolate G 3/10

tag: Isolate G 3/10 of Symbioflor2 probiotic product from Symbiopharm


title: A84 vs A131 replicate 1

description: Competitive hybridization between A84 and A131


title: Co-hybridization of E. coli G5 isolate with E. coli K-12 MG1655

description: Co-hybridization of genomic DNA from E. coli isolate G5 from Symbioflor2 with E. coli K-12 MG1655

source_name: E. coli isolate G5


title: A82 vs A95 replicate 2 dye-swap


title: E12 vs E17 replicate 2 dye-swap

description: Competitive hybridization between E17 and E12


title: E17 vs E18 replicate 1 dye-swap

description: Competitive hybridization between E18 and E17


title: E18 vs E20 replicate 1 dye-swap

description: Competitive hybridization between E20 and E18


title: E12 vs E17 replicate 1 dye-swap


title: E18 vs E20 replicate 1

description: Competitive hybridization between E18 and E20


title: E12 vs E17 replicate 2

description: Competitive hybridization between E12 and E17


title: E16 vs E17 replicate 2

description: Competitive hybridization between E16 and E17


title: E16 vs E17 replicate 1 dye-swap

description: Competitive hybridization between E17 and E16


title: E15 vs E20 replicate 1

description: Competitive hybridization between E15 and E20


title: E16 vs E17 replicate 1


title: E15 vs E20 replicate 1 dye-swap

description: Competitive hybridization between E20 and E15


title: E16 vs E17 replicate 2 dye-swap


title: A377 vs A131 replicate 1 dye-swap

description: Competitive hybridization between A131 and A377


title: E15 vs E16 replicate 2 dye-swap

description: Competitive hybridization between E16 and E15


title: E15 vs E16 replicate 2

description: Competitive hybridization between E15 and E16


title: E20 vs E01 replicate 1

description: Competitive hybridization between E20 and E01


title: E17 vs E18 replicate 1

description: Competitive hybridization between E17 and E18


title: E14 vs E15 replicate 2 dye-swap

description: Competitive hybridization between E15 and E14


title: E15 vs E16 replicate 1


title: E14 vs E15 replicate 2

description: Competitive hybridization between E14 and E15


title: E12 vs E14 replicate 2 dye-swap

description: Competitive hybridization between E14 and E12


title: E12 vs E14 replicate 1 dye-swap


title: E12 vs E14 replicate 1

description: Competitive hybridization between E12 and E14


title: E14 vs E15 replicate 1


title: E01 vs E12 replicate 1

description: Competitive hybridization between E01 and E12


title: E01 vs E12 replicate 1 dye-swap

description: Competitive hybridization between E12 and E01


title: E14 vs E15 replicate 1 dye-swap


title: E15 vs E16 replicate 1 dye-swap


title: E12 vs E17 replicate 1


title: E12 vs E14 replicate 2


title: SNU_Breast_CGH_G17

status: Public on Jan 17 2008

city: Seoul

first: Wonshik

last: Han

address: 28 Yongon-dong, Chongno-gu

department: Dept. of Surgery

country: South Korea

institute: Seoul National University College of Medicine

hyb_protocol: The pellet was resuspended in 40 μl hybridization solution containing 50% formamide, 10% dextran sulfate, 2x SSC, 4% SDS, and 200 μg yeast tRNA. The hybridization solution was denatured for 10 min at 72 °C and was subsequently incubated for 1 hour at 37 °C to allow blocking of repetitive sequences. Hybridization was performed in slide chambers for 48 hours at 37 °C. After post-hybridization washes, arrays were rinsed, spin-dried.

scan_protocol: Arrays were scanned into two 16-bit TIFF image files using a GenePix 4200A two-color fluorescent scanner (Axon Instruments), and individual spots were analyzed with GenePix Pro 3.0 imaging software (Axon Instruments).

data_processing: The log2-transformed fluorescent ratios were calculated from background-subtracted median intensity values, and these ratios were used to perform normalization according to intensity normalization methods. We applied LOWESS normalization, a smoothing adjustment that removes intensity-dependent variation in dye bias.

source_name: Human breast cancer tissue

label_protocol: The labeling and hybridization protocols described by Pinkel et al. were used with some modification to the labeling procedure. Briefly, 21 μl solution containing 500 ng normal DNA (reference DNA) or tumor DNA (test DNA), 20 μl BioPrime DNA Labeling System random primers solution (Invitrogen, Carlsbad, CA, USA), and water were combined and incubated for 5 min at 95 °C, and subsequently cooled on ice. After the addition of 5 μl 10x dNTPs labeling mix (1 mM dCTP, 2 mM dATP, 2 mM dGTP, 2 mM dTTP), 3 μl 1 mM Cy-3 or Cy-5 dCTP (GeneChem Inc., Daejeon, Korea), and 40 U BioPrime DNA Labeling System Klenow fragment (Invitrogen), the mixture was gently mixed and incubated overnight at 37 °C. The addition of 5 μl BioPrime DNA Labeling System Stop Buffer (Invitrogen) ended the reaction. After labeling, unincorporated fluorescent nucleotides were removed using QIAquick Spin columns (Qiagen, Germany). In one tube, Cy3-labeled sample and Cy5-labeled reference DNAs were mixed together, and 50 μg human Cot I DNA (Invitrogen), 20 μl 3M sodium acetate, and 600 μl cold 100% ethanol were added for DNA precipitation.

extract_protocol: DNA was extracted from each breast cancer tissue sample using the PureGene kit (Gentra Systems Inc., Minneapolis, MN, USA).

tag: Human breast cancer tissue

source_name: Normal human female whole blood

tag: Normal human female whole blood


title: SNU_Breast_CGH_G25


title: SNU_Breast_CGH_G23


title: SNU_Breast_CGH_G24


title: SNU_Breast_CGH_G31


title: SNU_Breast_CGH_G28


title: SNU_Breast_CGH_G26


title: SNU_Breast_CGH_G29


title: SNU_Breast_CGH_G18


title: SNU_Breast_CGH_G21


title: SNU_Breast_CGH_G19


title: SNU_Breast_CGH_G22


title: SNU_Breast_CGH_G30


title: SNU_Breast_CGH_G16


title: SNU_Breast_CGH_G34


title: SNU_Breast_CGH_G33


title: SNU_Breast_CGH_G32


title: SNU_Breast_CGH_G15


title: SNU_Breast_CGH_G13


title: SNU_Breast_CGH_S26

extract_protocol: Channel 2 DNA was purchased from Promega Corporation: Human Genomic DNA, Female (#G1521)


title: SNU_Breast_CGH_S27


title: SNU_Breast_CGH_G14


title: SNU_Breast_CGH_S22


title: SNU_Breast_CGH_S21


title: SNU_Breast_CGH_G27


title: SNU_Breast_CGH_S24


title: SNU_Breast_CGH_S23


title: SNU_Breast_CGH_S25


title: SNU_Breast_CGH_G12


title: SNU_Breast_CGH_S20


title: SNU_Breast_CGH_S14


title: SNU_Breast_CGH_S17


title: SNU_Breast_CGH_S18


title: SNU_Breast_CGH_S7


title: SNU_Breast_CGH_S15


title: SNU_Breast_CGH_S13


title: SNU_Breast_CGH_S19


title: SNU_Breast_CGH_S5


title: SNU_Breast_CGH_G54


title: SNU_Breast_CGH_G53


title: SNU_Breast_CGH_S6


title: SNU_Breast_CGH_S11


title: SNU_Breast_CGH_S10


title: SNU_Breast_CGH_G55


title: SNU_Breast_CGH_S8


title: SNU_Breast_CGH_G57


title: SNU_Breast_CGH_G56


title: SNU_Breast_CGH_S16


title: SNU_Breast_CGH_S12


title: SNU_Breast_CGH_G52


title: SNU_Breast_CGH_S9


title: SNU_Breast_CGH_G48


title: SNU_Breast_CGH_G51


title: SNU_Breast_CGH_G50


title: SNU_Breast_CGH_G49


title: SNU_Breast_CGH_S50


title: SNU_Breast_CGH_G47


title: SNU_Breast_CGH_G46


title: SNU_Breast_CGH_S48


title: SNU_Breast_CGH_G45


title: SNU_Breast_CGH_S47


title: SNU_Breast_CGH_G43


title: SNU_Breast_CGH_G44


title: SNU_Breast_CGH_S42


title: SNU_Breast_CGH_G41


title: SNU_Breast_CGH_G42


title: SNU_Breast_CGH_G39


title: SNU_Breast_CGH_S44


title: SNU_Breast_CGH_S39


title: SNU_Breast_CGH_G36


title: SNU_Breast_CGH_S43


title: SNU_Breast_CGH_G40


title: SNU_Breast_CGH_S46


title: SNU_Breast_CGH_S41


title: SNU_Breast_CGH_G37


title: SNU_Breast_CGH_G38


title: SNU_Breast_CGH_S40


title: SNU_Breast_CGH_S49


title: SNU_Breast_CGH_S45


title: SNU_Breast_CGH_S34


title: SNU_Breast_CGH_S35


title: SNU_Breast_CGH_S38


title: SNU_Breast_CGH_S37


title: SNU_Breast_CGH_S36


title: SNU_Breast_CGH_G35


title: E20 vs E01 replicate 1 dye-swap

description: Competitive hybridization between E01 and E20


title: SNU_Breast_CGH_S33


title: SNU_Breast_CGH_S31


title: SNU_Breast_CGH_S30


title: SNU_Breast_CGH_G10


title: SNU_Breast_CGH_G8


title: SNU_Breast_CGH_S29


title: SNU_Breast_CGH_G3


title: SNU_Breast_CGH_G1


title: SNU_Breast_CGH_G5


title: SNU_Breast_CGH_G9


title: SNU_Breast_CGH_G11


title: SNU_Breast_CGH_G7


title: SNU_Breast_CGH_S58


title: SNU_Breast_CGH_S32


title: SNU_Breast_CGH_G2


title: SNU_Breast_CGH_G4


title: SNU_Breast_CGH_S60


title: SNU_Breast_CGH_S61


title: SNU_Breast_CGH_S62


title: SNU_Breast_CGH_S59


title: SNU_Breast_CGH_S57


title: SNU_Breast_CGH-S56


title: RPS14_Pt_B_3

city: La Jolla

first: Pablo

last: Tamayo

address: 3855 Health Sciences Drive MC 0658

department: Moores Cancer Center

institute: UCSD

description: Patient sample 2 infected with a lentivirus expressing RPS19

hyb_protocol: cDNA was hybridized to HG_U133AAofAv2 microarrays following standard Affymetrix procedure.

scan_protocol: Affymetrix

data_processing: Raw expression values were normalized using Robust Multiarray Averaging (RMA)

label_protocol: Linear amplification of 20 ng of total RNA was performed using the Ovation Biotin RNA Amplification and Labeling System (Nugen, Inc.).

growth_protocol: CD34+ cells were induced to differentiate for 10 days along the erythroid and megakaryocytic lineages.

extract_protocol: RNA was purified from mononuclear cells using Trizol (Invitrogen).

treatment_protocol: shRNAs were introduced into normal CD34+ human hematopoietic progenitor cells,


title: SNU_Breast_CGH_S28


title: RPS14_Pt_B_1

description: Patient sample 2 infected with a lentivirus expressing RPS17


title: Empty_Pt_B_3

description: Patient sample 2 infected with a lentivirus expressing an empty vector


title: RPS14_Pt_A_2

description: Patient sample 1 infected with a lentivirus expressing RPS15


title: SNU_Breast_CGH_G6


title: RPS14_Pt_A_3

description: Patient sample 1 infected with a lentivirus expressing RPS16


title: RPS14_Pt_A_1

description: Patient sample 1 infected with a lentivirus expressing RPS14


title: SNU_Breast_CGH_S55


title: RPS14_Pt_B_2

description: Patient sample 2 infected with a lentivirus expressing RPS18


title: SNU_Breast_CGH_S54


title: stationary phase phase biological replicate 3 technical replicate 2

city: Lausanne

first: Emmanuel

last: Denou

state: vaud

address: vers chez les blancs

department: Nutrition & Health

country: Switzerland

institute: Nestlé Research Center

hyb_protocol: Total RNA was hybridized onto DNA-arrays together with RNA extracted from mid-exponential phase cells

scan_protocol: array slides were scanned with a Scanarray 4000 machine (Packard Biochip Technologies, Billerica, U.S.A)

data_processing:
Data were extracted from the scanned images using the software Imagene 5.6 (Biodiscovery, El Segundo, U.S.A).
Spots displaying low intensity (i.e. less than three fold the local background standard deviation) were considered empty (value=0)
For all technical replicates, the control for fluorescence labeling by dye-swap was done. As the method is based on qualitative detection, negative and positive controls were used to confirm the absence of cross and/or non-specific hybridization.
the absolute expression pattern was determined at least from three independent biological samples.
A gene was called as “expressed” (value=1) when it was detected in all three experiments.

organism: Lactobacillus johnsonii

source_name: Total RNA bacterial growth in sixfors fermentor 3

label_protocol:
2 μg of total RNA was labeled using the 3DNA Array 350RP Genisphere kit (Genisphere Inc., Hatfield, U.S.A)
Luciferase control mRNA (10 ng) (Promega, Zurich, Switzerland) was mixed with total RNA before labeling to balance the two channels during scanning

growth_protocol:
Grown in MRS with 2% of glucose as carbon source to which filter-sterilized cysteine was added after autoclaving (at a final concentration of 0.05% w/v) as redox buffer.
Cultures were incubated at 37°C under anaerobic conditions
cells were grown in a Sixfors fermentor system, composed of four individual 500 ml vessels (Infors, Bottmingen, Switzerland)
Four separate fermentation vessels (fermentor 1 to 4), which were inoculated at 0.4% (v/v) with four individual overnight cultures in order to reach a starting optical density (OD600nm) of 0.05.

extract_protocol:
Cell pellets were crushed and suspended in equal volumes of TE buffer (pH 8) and phenol (pH 4.2)
total RNA was extracted by the Macaloid method
The cells were disrupted at maximum speed using a Mini-Bead Beater-8 (BioSpec Products, Bartlesville, USA) at 4°C, during 1 min for three cycles with a resting period of 1 min on ice between each cycle
RNA was purified by phenol/chloroform extraction followed by ethanol precipitation
Pellets were re-suspended in nucleotide free water and 100 μg of total RNA was treated with 200 units of DNase I (Ambion, Huntingdon, United Kingdom) during 2 hours at 37°C to eliminate contaminating DNA.
The Rneasy mini-kit (Qiagen, Basel, Switzerland) that was used for further purification includes an additional on-column DNase digestion.
RNA concentrations were determined spectrophotometrically.
RNA integrity for all samples was tested using the Agilent RNA 6000 Nano assay (Agilent, Waldbronn, Germany).

treatment_protocol:
Aliquots of 15 ml for mid-exponential phases and 10 ml for adaptation and mid-stationary phases
Centrifuged for 5 min at 10,000 x g at 4°C.
Cell pellets were snap frozen in liquid nitrogen and stored at –80°C until further use.

tag: stationary phase 3

source_name: Total RNA bacterial growth reference (exponential phase)

tag: exponential phase 1


title: SNU_Breast_CGH_S52


title: stationary phase phase biological replicate 2 technical replicate 1

source_name: Total RNA bacterial growth in sixfors fermentor 2

tag: stationary phase 2

tag: exponential phase 2


title: stationary phase phase biological replicate 2 technical replicate 2

tag: Strain


title: Empty_Pt_B_2

source_name: Patient sample 2 infected with a lentivirus expressing an empty vector


title: SNU_Breast_CGH_S3


title: SNU_Breast_CGH_S4


title: SNU_Breast_CGH_S2

scan_protocol: Two 16-bit TIFF image files were scanned using a GenePix 4200A two-color fluorescent scanner (Axon Instruments), and individual spots were analyzed with GenePix Pro 3.0 imaging software (Axon Instruments).


title: SNU_Breast_CGH_S53


title: SNU_Breast_CGH_S1


title: Empty_Pt_B_1

tag: Patient sample 2 infected with a lentivirus expressing an empty vector


title: stationary phase phase biological replicate 3 technical replicate 1


title: Empty_Pt_A_3

description: Patient sample 1 infected with a lentivirus expressing an empty vector


title: adaptation phase phase biological replicate 3 technical replicate 2

tag: adaptation phase 3


title: adaptation phase phase biological replicate 3 technical replicate 1


title: stationary phase phase biological replicate 1 technical replicate 2

source_name: Total RNA bacterial growth in sixfors fermentor 1

tag: stationary phase 1

tag: exponential phase 4


title: RPS14_G8_72_hr_B

description: CD34+ cells infected with lentivirus expressing RPS14_G8 shRNA, harvested 72 hours after infection


title: Empty_Pt_A_2

source_name: Patient sample 1 infected with a lentivirus expressing an empty vector


title: SNU_Breast_CGH_S51


title: Empty_Pt_A_1

tag: Patient sample 1 infected with a lentivirus expressing an empty vector


title: adaptation phase phase biological replicate 2 technical replicate 2

tag: adaptation phase 2

tag: exponential phase 3


title: RPS14_G8_72_hr_A

source_name: CD34+ cells infected with lentivirus expressing RPS14_G8 shRNA, harvested 72 hours after infection


title: RPS14_G6_72_hr_A

description: CD34+ cells infected with lentivirus expressing RPS14_G6 shRNA, harvested 72 hours after infection


title: stationary phase phase biological replicate 1 technical replicate 1


title: RPS14_G8_72_hr_C

tag: CD34+ cells infected with lentivirus expressing RPS14_G8 shRNA, harvested 72 hours after infection


title: RPS14_G6_72_hr_B

source_name: CD34+ cells infected with lentivirus expressing RPS14_G6 shRNA, harvested 72 hours after infection


title: adaptation phase phase biological replicate 1 technical replicate 2

tag: adaptation phase 1


title: exponential phase phase biological replicate 3 technical replicate 1


title: exponential phase phase biological replicate 2 technical replicate 1


title: exponential phase phase biological replicate 3 technical replicate 2


title: adaptation phase phase biological replicate 1 technical replicate 1


title: exponential phase phase biological replicate 1 technical replicate 1


title: exponential phase phase biological replicate 1 technical replicate 2


title: RPS14_G6_72_hr_C

tag: CD34+ cells infected with lentivirus expressing RPS14_G6 shRNA, harvested 72 hours after infection


title: adaptation phase phase biological replicate 2 technical replicate 1


title: RPS14_G4_72_hr_B

description: CD34+ cells infected with lentivirus expressing RPS14_G4 shRNA, harvested 72 hours after infection


title: RPS14_G4_72_hr_A

source_name: CD34+ cells infected with lentivirus expressing RPS14_G4 shRNA, harvested 72 hours after infection


title: exponential phase phase biological replicate 2 technical replicate 2


title: Luc_72_hr_A

description: CD34+ cells infected with lentivirus expressing luciferase shRNA, harvested 72 hours after infection


title: Yeast_sporulation_2.0hr

status: Public on Jan 16 2008

first: Michael

last: Baitaluk

address: 9500 Gilman dr

department: SDSC

description: Each Sample represents the cross-slide replicate analysis (A and B). For time point T, replicate A has Cy3 for 0 time point and Cy5 for time point T: A(T)= f(Cy30,Cy5T) and replicate B has Cy3 for T and Cy5 for 0: B(T)=f(Cy3T,Cy50).

scan_protocol: Microarrays were scanned on Biorad VersArray scanner using manufacturer’s instructions.

data_processing: Modified algorithm for cell detection using image segmentation was used to determine spot boundaries.Algorithm description

label: Cy3, Cy5

organism: Saccharomyces cerevisiae

source_name: Total RNA from yeast cells 2.0 hr and 0.0 hr

extract_protocol: Total RNA


title: Yeast_sporulation_4.5hr

source_name: Total RNA from yeast cells 4.5 hr and 0.0 hr


title: Yeast_sporulation_5.5hr

source_name: Total RNA from yeast cells 5.5 hr and 0.0 hr


title: Yeast_sporulation_5.0hr

source_name: Total RNA from yeast cells 5.0 hr and 0.0 hr


title: Luc_72_hr_B

source_name: CD34+ cells infected with lentivirus expressing luciferase shRNA, harvested 72 hours after infection


title: Yeast_sporulation_2.5hr

source_name: Total RNA from yeast cells 2.5 hr and 0.0 hr


title: Yeast_sporulation_4.0hr

source_name: Total RNA from yeast cells 4.0 hr and 0.0 hr


title: Yeast_sporulation_3.5hr

source_name: Total RNA from yeast cells 3.5 hr and 0.0 hr


title: Yeast_sporulation_1.0hr

source_name: Total RNA from yeast cells 1.0 hr and 0.0 hr


title: Yeast_sporulation_0.0hr

source_name: Total RNA from yeast cells 0.0 hr


title: Yeast_sporulation_0.5hr

source_name: Total RNA from yeast cells 0.5hr and 0.0 hr


title: Luc_72_hr_C

tag: CD34+ cells infected with lentivirus expressing luciferase shRNA, harvested 72 hours after infection


title: Yeast_sporulation_6.0hr

source_name: Total RNA from yeast cells 6.0 hr and 0.0 hr


title: Yeast_sporulation_1.5hr

source_name: Total RNA from yeast cells 1.5 hr and 0.0 hr


title: 51481-10-8 Deoxynivalenol 3rd

status: Public on Jan 15 2008

city: Tsukuba

first: Emiko

last: Kitagawa

state: Ibaraki

address: Onogawa 16-1

institute: National Institute of Advanced Industrial Science and Technology

description: Data with flag value 0 were used for LOWESS normalization processing.

hyb_protocol: Hybridized for 16-18 h at 65 C

scan_protocol: Scan Array 4000 (PerkinElmer Japan Co., Ltd) was used for scanning. Array images were analyzed with Gene Pix Pro 4.0 (Axon Instrument).

data_processing: GeneSpring ver 7.3.1 (Agilent Technologies Inc.)

molecule: polyA RNA

source_name: DON treated for 2 h, Cy5

label_protocol: Cyscribe first-strand cDNA labelling kit (Amersham Biosciences)

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in 50 ml YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 10,000 ppm (final concentration).

extract_protocol: Hot-phenol and oligotex dt mRNA purification kit (TaKaRa)

treatment_protocol: Deoxynivalenol (Wako, 048-18631)

tag: strain S288C

source_name: control (without treatment), Cy3

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking until OD=1, then grown for 2 h.

treatment_protocol: without treatment


title: 51481-10-8 Deoxynivalenol 4th


title: 21259-20-1 T-2 Toxin 3rd

source_name: T2 treated for 2 h, Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in 50 ml YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 108 ppm (final concentration).

treatment_protocol: T-2 Toxin Standard (Wako, 209-08251)


title: 1162-65-8 Aflatoxin B1 4th

source_name: Aflatoxin B1 treated for 2 h, Cy5

treatment_protocol: Aflatoxin B1 (ACROS organics, 227340100)


title: 1165-39-5 Aflatoxin G1 3rd

source_name: Aflatoxin G1 treated for 2 h, Cy5

treatment_protocol: Aflatoxin G1 (ACROS organics, 227360100)


title: 51481-10-8 Deoxynivalenol 2nd


title: 51481-10-8 Deoxynivalenol 1st


title: 1162-65-8 Aflatoxin B1 2nd


title: 1165-39-5 Aflatoxin G1 1st


title: 1165-39-5 Aflatoxin G1 4th


title: 1165-39-5 Aflatoxin G1 2nd


title: 1162-65-8 Aflatoxin B1 3rd


title: 21259-20-1 T-2 Toxin 2nd


title: Microarrays N2 L4 stage C. elegans control(RNAi) vs. mdt-15(RNAi) (40hr RNAi) Replicate #3

city: San Francisco

first: Stefan

last: Taubert

department: CMP

institute: UCSF

description: Fred Hutchinson Cancer Research Center Microarray facility

data_processing:
We used limma, a BioConductor package.
To normalize the data:
Read in data, setting weight to zero if flag<0
Use background correction method rma
normalizeWithinArrays, default method (print tip loess). This generates normalized values for M (log(R/G)) and A (1/2*log(R*G)).
Flipped the sign of M, to make M = log(test/reference)
To find differentially expressed genes:
Removed genes that did not have at least 3 unflagged spots with A > 2e6
Ran lmFit, eBayes, and topTable (number=500) with the default parameters. In particular, the default multiple hypothesis correction method is "BH"
We selected all the genes with p-value <.05, and considered these differentially regulated.

organism: Caenorhabditis elegans

source_name: Whole animal RNA extract control RNAi

growth_protocol: RNAi treatment with HT1115 bacteria; carrying L4440 clone for 40 hrs; 4mM IPTG on NGM lite plates

treatment_protocol: ~20'000 animals harvested, washed 5x in M9, flash-frozen in liquid N2, stored at -70oC

tag: N2 Strain L4 Stage

source_name: Whole animal RNA extract MDT15 RNAi

growth_protocol: RNAi treatment with HT1115 bacteria; carrying mdt-15 RNAi clone (Julie Ahringer library) for 40 hrs; 4mM IPTG on NGM lite plates

tag: N2 strain L4 stage


title: Microarrays N2 L4 stage C. elegans control(RNAi) vs. mdt-15(RNAi) (40hr RNAi) Replicate #4

hyb_protocol: Fred Hutchinson Cancer Research Center Microarray facility

data_processing:
We used limma, a BioConductor package.
To normalize the data:
Read in data, setting weight to zero if flag<0
Use background correction method rma
normalizeWithinArrays, default method (print tip loess). This generates normalized values for M (log(R/G)) and A (1/2*log(R*G)).
To find differentially expressed genes:
Removed genes that did not have at least 3 unflagged spots with A > 2e6
Ran lmFit, eBayes, and topTable (number=500) with the default parameters. In particular, the default multiple hypothesis correction method is "BH"
We selected all the genes with p-value <.05, and considered these differentially regulated.


title: 21259-20-1 T-2 Toxin 1st


title: Microarrays N2 L4 stage C. elegans control(RNAi) vs. mdt-15(RNAi) (40hr RNAi) Replicate #5

scan_protocol: Fred Hutchinson Cancer Research Center Microarray facility


title: Microarrays N2 L4 stage C. elegans control(RNAi) vs. mdt-15(RNAi) (40hr RNAi)

label_protocol: Fred Hutchinson Cancer Research Center Microarray facility

tag: Strain N2 Stage L4


title: HMLE_DNEcad_rep3

city: Boston

first: Tamer

middle: T

last: Onder

address: One Blackfan Circle

institute: Children's Hospital Boston

description: Gene expression changes induced by knockdown of E-cadherin, expression of dominant-negative E-cadherin and double knockdown of E-cadherin and Beta-catenin in immortalized human mammary epithelial cells

hyb_protocol: Standard Affymetrix protocol; hybridization was performed with high-throughput HT_HG-U133A arrays in 96-well format

scan_protocol: Scanned using an HT Scanner

data_processing: Raw data files (.CEL) were converted into probe-set values using RMA normalization.

label: Biotin

source_name: HMLE cells (Immortalized human mammary epithelial cells, SV40 - largeT/smallT, hTERT-immortalized) expressing dominant-negative E-cadherin

label_protocol: Standard Affymetrix protocol

growth_protocol: in vitro cultured in MEGM medium on regular culture plates

extract_protocol: Total RNA was extracted from culture plates for each cell type using an RNeasy Mini kit coupled with an RNase-free DNase set (Qiagen).

treatment_protocol: Immortalized by SV40 - largeT/smallT in MEGM medium

tag: Gender

value: female, Age:Premenopausal, Tissue:Normal Breast


title: HMLE_DNEcad_rep2


title: Microarrays N2 L4 stage C. elegans control(RNAi) vs. mdt-15(RNAi) (40hr RNAi) Replicate #2

extract_protocol: Fred Hutchinson Cancer Research Center Microarray facility


title: HMLE_shEcad+shBcat_rep3

source_name: HMLE cells (Immortalized human mammary epithelial cells, SV40 - largeT/smallT, hTERT-immortalized), expressing shRNA against E-cadherin and shRNA against Beta-catenin


title: 1162-65-8 Aflatoxin B1 1st


title: HMLE_shEcad+shBcat_rep1


title: HMLE_shEcad_rep2

source_name: HMLE cells (Immortalized human mammary epithelial cells,  SV40 - largeT/smallT, hTERT-immortalized), exressing shRNA against E-cadherin


title: HMLE_shEcad_rep1


title: HMLE_shEcad_rep3


title: 1243502_CGH

first: Arthur

last: Lee

address: 221 Longwood Ave.

institute: Harvard Medical School

description: see other fields

hyb_protocol: Hybridization was performed using the MAUI Hybridization System (BioMicro Systems, Salt Lake City, UT) at 42º C for 16 hr.

scan_protocol: Arrays were scanned with a GenePix 4000B 5µm microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Signal intensities were extracted using NimbleScan software (NimbleGen Systems, Inc.), and relative intensity log2 ratios were normalized using the Qspline method.

organism: Macaca mulatta

source_name: GENOMIC DNA SELF

label_protocol: Sample was labeled and hybridized using standard NimbleGen aCGH protocols in Reykjavik, Iceland. Briefly, 1µg of genomic DNA was labeled with random 9-mer “wobble”-Cy3 or Cy5 (TriLink BioTechnologies, San Diego, CA) using Exo-Klenow DNA polymerase (New England Biolabs, Ipswich, MA), at 37° C for 2 hr.

growth_protocol: Macaques were housed at the New England Primate Research Center prior to whole venous blood extraction.

extract_protocol: Whole venous blood was collected during routine health evaluations at the New England Primate Research Center. DNA was isolated from peripheral leukoctyes with the Puregene DNA isolation kit (Gentra, Minneapolis, MN) and purified using the Wizard DNA Cleanup System (Promega, Madison, WI).

tag: sex

value: female

tag: individual

tag: ancestry

value: Indian


title: HMLE_DNEcad_rep1


title: HMLE_shCntrl_rep3

source_name: HMLE cells (Immortalized human mammary epithelial cells,  SV40 - largeT/smallT, hTERT-immortalized), expressing Control shRNA


title: 1255202_CGH

description: see other fields

treatment_protocol: Whole venous blood was collected during routine health evaluations at the New England Primate Research Center. DNA was isolated from peripheral leukoctyes with the Puregene DNA isolation kit (Gentra, Minneapolis, MN) and purified using the Wizard DNA Cleanup System (Promega, Madison, WI).

value: MALE


title: 103642_CGH

description: see other fields

source_name: GENOMIC DNA REFERENCE

source_name: GENOMIC DNA TEST


title: HMLE_shCntrl_rep1


title: 75% restricted rat number 11

status: Public on Jan 14 2008

city: Angers

first: Matthieu

last: Arvier

address: 4 rue larrey

department: UMR 694

country: France

institute: INSERM

hyb_protocol: Samples were applied to microarrays enclosed in Telechem hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Perkinhelmer 4000 Scanner. Images were quantified using Perkin elmer ScanArray® Express Software

data_processing: LOWESS normalized. Genspring GX 7.3 software was used.

organism: Rattus norvegicus

source_name: Total RNA from 75% restricted rats labelled with Cyanine-5 (red).

label_protocol: tRNA extractions were prepared using the Amino Allyl MessageAmpII aRNA Amplification Kit (Ambion, 1753) and  labeled individually with Cy3 or Cy5 (Amersham).

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

tag: Age

value: week 13

source_name: Total RNA from pooled control rats tRNA labeled with Cyanine-3 (green).


title: HMLE_shEcad+shBcat_rep2


title: 75% restricted rat number 9


title: HMLE_shCntrl_rep2


title: 75% restricted rat number 10


title: 75% restricted rat number 12


title: 103243_CGH

description: see other fields


title: 103244_cgh

description: see other fields


title: 103632_CGH

description: see other fields


title: RPS14_G4_72_hr_C

source_name: CD34+ cells infected with lentivirus expressing RPS14_G4 shRNA, harvested 72 hours after infection


title: 75% restricted rat number 7


title: 102487_CGH

description: see other fields


title: 101681_cgh

description: see other fields

source_name: genomic DNA reference

source_name: genomic DNA test


title: 75% restricted rat number 6


title: 75% restricted rat number 5


title: 102253_CGH

description: see other fields


title: 103631_CGH

description: see other fields


title: 50% restricted rat number 11

source_name: Total RNA from 50% restricted rats labelled with Cyanine-5 (red).


title: 75% restricted rat number 3


title: 75% restricted rat number 2


title: 50% restricted rat number 7


title: 50% restricted rat number 9


title: 50% restricted rat number 10


title: 50% restricted rat number 6


title: 50% restricted rat number 3


title: 75% restricted rat number 4


title: 25% restricted rat number 12

source_name: Total RNA from 25% restricted rats labelled with Cyanine-5 (red).


title: 50% restricted rat number 2


title: 102192_cgh

description: see other fields


title: 50% restricted rat number 4


title: 25% restricted rat number 11


title: 25% restricted rat number 10


title: 50% restricted rat number 5


title: 50% restricted rat number 1


title: 25% restricted rat number 8


title: 25% restricted rat number 9


title: 25% restricted rat number 3


title: 25% restricted rat number 7


title: 25% restricted rat number 6


title: 25% restricted rat number 4


title: 25% restricted rat number 5


title: 25% restricted rat number 2


title: 25% restricted rat number 1


title: Fasted rat number 12

source_name: Total RNA from fasted rats labelled with Cyanine-5 (red).


title: Fasted rat number 11


title: Fasted rat number 10


title: Fasted rat number 5


title: Fasted rat number 8


title: Fasted rat number 6


title: Fasted rat number 7


title: Control rat 12

source_name: Total RNA from control rats labelled with Cyanine-5 (red).


title: Fasted rat number 1


title: Fasted rat number 2


title: Fasted rat number 3


title: Control rat 11


title: Control rat 5


title: Control rat 8


title: Control rat 9


title: Control rat 10


title: Control rat 6


title: Control rat 1


title: Control rat 3


title: Control rat 4


title: Control rat 2


title: Fasted rat number 9


title: NA12874 growth 3.

status: Public on Jan 13 2008

city: Montreal

first: Tony

last: Kwan

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

country: Canada

institute: McGill University

description: Probeset expression data from NA12874 growth 3

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16-20 hr at 45C on GeneChip Human Exon 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data were analyzed with Affymetrix Power Tools package using Affymetrix default analysis settings and sketch quantile as normalization method.

source_name: CEU NA12874 Biological Growth 3

label_protocol: Biotinlabelled target for the microarray experiment were prepared using 1 ug 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).

growth_protocol: Cells were grown at 37°C and 5% CO2 in RPMI 1640 medium supplemented with 15% heat-inactivated fetal bovine serum, 2 mM L-glutamine and penicillin/streptomycin

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

treatment_protocol: Cells were harvested at a density of 0.8-1.1 x 10e6 cells/mL. Cells were then resuspended and lysed in TRIzol reagent

value: male, Cell-type:lymphoblasts

tag: Coriell cell line repository identifier:GM12874


title: NA12874 growth 2.

description: Probeset expression data from NA12874 growth 2

source_name: CEU NA12874 Biological Growth 2


title: NA12892 growth 2.

description: Probeset expression data from NA12892 growth 2

source_name: CEU NA12892 Biological Growth 2

value: female, Cell-type:lymphoblasts

tag: Coriell cell line repository identifier:GM12892


title: NA12873 growth 1.

description: Probeset expression data from NA12873 growth 1

source_name: CEU NA12873 Biological Growth 1

tag: Coriell cell line repository identifier:GM12873


title: NA12875 growth 3.

description: Probeset expression data from NA12875 growth 3

source_name: CEU NA12875 Biological Growth 3

tag: Coriell cell line repository identifier:GM12875


title: NA12891 growth 1.

description: Probeset expression data from NA12891 growth 1

source_name: CEU NA12891 Biological Growth 1

tag: Coriell cell line repository identifier:GM12891


title: NA12875 growth 1.

description: Probeset expression data from NA12875 growth 1

source_name: CEU NA12875 Biological Growth 1


title: NA12892 growth 3.

description: Probeset expression data from NA12892 growth 3

source_name: CEU NA12892 Biological Growth 3


title: NA12872 growth 3.

description: Probeset expression data from NA12872 growth 3

source_name: CEU NA12872 Biological Growth 3

tag: Coriell cell line repository identifier:GM12872


title: NA12872 growth 2.

description: Probeset expression data from NA12872 growth 2

source_name: CEU NA12872 Biological Growth 2


title: NA12875 growth 2.

description: Probeset expression data from NA12875 growth 2

source_name: CEU NA12875 Biological Growth 2


title: NA12815 growth 3.

description: Probeset expression data from NA12815 growth 3

source_name: CEU NA12815 Biological Growth 3

tag: Coriell cell line repository identifier:GM12815


title: NA12874 growth 1.

description: Probeset expression data from NA12874 growth 1

source_name: CEU NA12874 Biological Growth 1


title: NA12892 growth 1.

description: Probeset expression data from NA12892 growth 1

source_name: CEU NA12892 Biological Growth 1


title: NA12873 growth 2.

description: Probeset expression data from NA12873 growth 2

source_name: CEU NA12873 Biological Growth 2


title: NA12891 growth 3.

description: Probeset expression data from NA12891 growth 3

source_name: CEU NA12891 Biological Growth 3


title: NA12872 growth 1.

description: Probeset expression data from NA12872 growth 1

source_name: CEU NA12872 Biological Growth 1


title: NA12814 growth 2.

description: Probeset expression data from NA12814 growth 2

source_name: CEU NA12814 Biological Growth 2

tag: Coriell cell line repository identifier:GM12814


title: NA12814 growth 3.

description: Probeset expression data from NA12814 growth 3

source_name: CEU NA12814 Biological Growth 3


title: NA12873 growth 3.

description: Probeset expression data from NA12873 growth 3

source_name: CEU NA12873 Biological Growth 3


title: NA12815 growth 2.

description: Probeset expression data from NA12815 growth 2

source_name: CEU NA12815 Biological Growth 2


title: NA12815 growth 1.

description: Probeset expression data from NA12815 growth 1

source_name: CEU NA12815 Biological Growth 1


title: 50% restricted rat number 8

source_name: Total RNA from 50% restricted rats labelled with Cyanine-5 (red).

source_name: Total RNA from pooled control rats tRNA labeled with Cyanine-3 (green).


title: NA12891 growth 2.

description: Probeset expression data from NA12891 growth 2

source_name: CEU NA12891 Biological Growth 2


title: NA12814 growth 1.

description: Probeset expression data from NA12814 growth 1

source_name: CEU NA12814 Biological Growth 1


title: 75% restricted rat number 8

source_name: Total RNA from 75% restricted rats labelled with Cyanine-5 (red).


title: NA12813 growth 3.

description: Probeset expression data from NA12813 growth 3

source_name: CEU NA12813 Biological Growth 3

tag: Coriell cell line repository identifier:GM12813


title: NA12812 growth 1.

description: Probeset expression data from NA12812 growth 1

source_name: CEU NA12812 Biological Growth 1

tag: Coriell cell line repository identifier:GM12812


title: NA12763 growth 2.

description: Probeset expression data from NA12763 growth 2

source_name: CEU NA12763 Biological Growth 2

tag: Coriell cell line repository identifier:GM12763


title: NA12750 growth 2.

description: Probeset expression data from NA12750 growth 2

source_name: CEU NA12750 Biological Growth 2

tag: Coriell cell line repository identifier:GM12750


title: NA12760 growth 2.

description: Probeset expression data from NA12760 growth 2

source_name: CEU NA12760 Biological Growth 2

tag: Gender

tag: Coriell cell line repository identifier:GM12760


title: NA12761 growth 2.

description: Probeset expression data from NA12761 growth 2

source_name: CEU NA12761 Biological Growth 2

tag: Coriell cell line repository identifier:GM12761


title: NA12750 growth 1.

description: Probeset expression data from NA12750 growth 1

source_name: CEU NA12750 Biological Growth 1


title: NA12264 growth 3.

description: Probeset expression data from NA12264 growth 3

source_name: CEU NA12264 Biological Growth 3

tag: Coriell cell line repository identifier:GM12264


title: NA12760 growth 1.

description: Probeset expression data from NA12760 growth 1

source_name: CEU NA12760 Biological Growth 1


title: NA12761 growth 3.

description: Probeset expression data from NA12761 growth 3

source_name: CEU NA12761 Biological Growth 3


title: NA12762 growth 1.

description: Probeset expression data from NA12762 growth 1

source_name: CEU NA12762 Biological Growth 1

tag: Coriell cell line repository identifier:GM12762


title: NA12264 growth 2.

description: Probeset expression data from NA12264 growth 2

source_name: CEU NA12264 Biological Growth 2


title: NA12812 growth 3.

description: Probeset expression data from NA12812 growth 3

source_name: CEU NA12812 Biological Growth 3


title: NA12762 growth 3.

description: Probeset expression data from NA12762 growth 3

source_name: CEU NA12762 Biological Growth 3


title: NA12813 growth 1.

description: Probeset expression data from NA12813 growth 1

source_name: CEU NA12813 Biological Growth 1


title: NA12762 growth 2.

description: Probeset expression data from NA12762 growth 2

source_name: CEU NA12762 Biological Growth 2


title: NA12751 growth 2.

description: Probeset expression data from NA12751 growth 2

source_name: CEU NA12751 Biological Growth 2

tag: Coriell cell line repository identifier:GM12751


title: NA12763 growth 3.

description: Probeset expression data from NA12763 growth 3

source_name: CEU NA12763 Biological Growth 3


title: NA12813 growth 2.

description: Probeset expression data from NA12813 growth 2

source_name: CEU NA12813 Biological Growth 2


title: NA12761 growth 1.

description: Probeset expression data from NA12761 growth 1

source_name: CEU NA12761 Biological Growth 1


title: NA12750 growth 3.

description: Probeset expression data from NA12750 growth 3

source_name: CEU NA12750 Biological Growth 3


title: NA12760 growth 3.

description: Probeset expression data from NA12760 growth 3

source_name: CEU NA12760 Biological Growth 3


title: NA12812 growth 2.

description: Probeset expression data from NA12812 growth 2

source_name: CEU NA12812 Biological Growth 2


title: NA12763 growth 1.

description: Probeset expression data from NA12763 growth 1

source_name: CEU NA12763 Biological Growth 1


title: NA12751 growth 3.

description: Probeset expression data from NA12751 growth 3

source_name: CEU NA12751 Biological Growth 3


title: Fasted rat number 4

source_name: Total RNA from fasted rats labelled with Cyanine-5 (red).

tag: Age

source_name: Total RNA from pooled control rats tRNA labeled with Cyanine-3 (green).


title: NA12751 growth 1.

description: Probeset expression data from NA12751 growth 1

source_name: CEU NA12751 Biological Growth 1


title: 50% restricted rat number 12

source_name: Total RNA from 50% restricted rats labelled with Cyanine-5 (red).


title: 75% restricted rat number 1

source_name: Total RNA from 75% restricted rats labelled with Cyanine-5 (red).


title: NA12264 growth 1.

description: Probeset expression data from NA12264 growth 1

source_name: CEU NA12264 Biological Growth 1


title: NA12239 growth 3.

description: Probeset expression data from NA12239 growth 3

source_name: CEU NA12239 Biological Growth 3

tag: Coriell cell line repository identifier:GM12239


title: NA12249 growth 2.

description: Probeset expression data from NA12249 growth 2

source_name: CEU NA12249 Biological Growth 2

tag: Coriell cell line repository identifier:GM12249


title: NA12248 growth 3.

description: Probeset expression data from NA12248 growth 3

source_name: CEU NA12248 Biological Growth 3

tag: Coriell cell line repository identifier:GM12248


title: NA12234 growth 2.

description: Probeset expression data from NA12234 growth 2

source_name: CEU NA12234 Biological Growth 2

tag: Coriell cell line repository identifier:GM12234


title: NA12249 growth 3.

description: Probeset expression data from NA12249 growth 3

source_name: CEU NA12249 Biological Growth 3


title: NA12239 growth 1.

description: Probeset expression data from NA12239 growth 1

source_name: CEU NA12239 Biological Growth 1


title: NA12234 growth 3.

description: Probeset expression data from NA12234 growth 3

source_name: CEU NA12234 Biological Growth 3


title: NA12239 growth 2.

description: Probeset expression data from NA12239 growth 2

source_name: CEU NA12239 Biological Growth 2


title: NA12248 growth 1.

description: Probeset expression data from NA12248 growth 1

source_name: CEU NA12248 Biological Growth 1


title: NA12154 growth 3.

description: Probeset expression data from NA12154 growth 3

source_name: CEU NA12154 Biological Growth 3

tag: Coriell cell line repository identifier:GM12154


title: NA12234 growth 1.

description: Probeset expression data from NA12234 growth 1

source_name: CEU NA12234 Biological Growth 1


title: NA12155 growth 1.

description: Probeset expression data from NA12155 growth 1

source_name: CEU NA12155 Biological Growth 1

tag: Coriell cell line repository identifier:GM12155


title: NA12156 growth 1.

description: Probeset expression data from NA12156 growth 1

source_name: CEU NA12156 Biological Growth 1

tag: Coriell cell line repository identifier:GM12156


title: NA12248 growth 2.

description: Probeset expression data from NA12248 growth 2

source_name: CEU NA12248 Biological Growth 2


title: NA12249 growth 1.

description: Probeset expression data from NA12249 growth 1

source_name: CEU NA12249 Biological Growth 1


title: NA12156 growth 2.

description: Probeset expression data from NA12156 growth 2

source_name: CEU NA12156 Biological Growth 2


title: NA12155 growth 3.

description: Probeset expression data from NA12155 growth 3

source_name: CEU NA12155 Biological Growth 3


title: NA12146 growth 2.

description: Probeset expression data from NA12146 growth 2

source_name: CEU NA12146 Biological Growth 2

tag: Coriell cell line repository identifier:GM12146


title: NA12145 growth 1.

description: Probeset expression data from NA12145 growth 1

source_name: CEU NA12145 Biological Growth 1

tag: Coriell cell line repository identifier:GM12145


title: NA12146 growth 3.

description: Probeset expression data from NA12146 growth 3

source_name: CEU NA12146 Biological Growth 3


title: NA12156 growth 3.

description: Probeset expression data from NA12156 growth 3

source_name: CEU NA12156 Biological Growth 3


title: NA12145 growth 2.

description: Probeset expression data from NA12145 growth 2

source_name: CEU NA12145 Biological Growth 2


title: NA12145 growth 3.

description: Probeset expression data from NA12145 growth 3

source_name: CEU NA12145 Biological Growth 3


title: NA12144 growth 3.

description: Probeset expression data from NA12144 growth 3

source_name: CEU NA12144 Biological Growth 3

tag: Coriell cell line repository identifier:GM12144


title: NA12146 growth 1.

description: Probeset expression data from NA12146 growth 1

source_name: CEU NA12146 Biological Growth 1

tag: Gender


title: NA12154 growth 2.

description: Probeset expression data from NA12154 growth 2

source_name: CEU NA12154 Biological Growth 2


title: NA12155 growth 2.

description: Probeset expression data from NA12155 growth 2

source_name: CEU NA12155 Biological Growth 2


title: NA12154 growth 1.

description: Probeset expression data from NA12154 growth 1

source_name: CEU NA12154 Biological Growth 1


title: Control rat 7

source_name: Total RNA from control rats labelled with Cyanine-5 (red).

source_name: Total RNA from pooled control rats tRNA labeled with Cyanine-3 (green).


title: NA12006 growth 3.

description: Probeset expression data from NA12006 growth 3

source_name: CEU NA12006 Biological Growth 3

tag: Coriell cell line repository identifier:GM12006