title: JL00005_SDC2_N2_MXemb_ChIP_replicate3

description: SDC-2 ChIP-chip from N2 mixed stage embryos. An affinity purified rabbit polyclonal antibody to SDC-2 was used.

data_processing: ChIP-chip_normalization_standard_zscore_v2. First, the ratio of intensity from sample/reference channel was transformed to log2 space. Second, z-scores were obtained for each probe by standardizing the data by subtracting the mean and dividing by the standard deviation of all probes.

growth_protocol: Worm_embryo_growth_and_harvest_v5. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature followed by quenching with 125mM glycine for 5 minutes. Embryos were then washed twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol: Worm_chromatin_immunoprecipitation_v5. 2mg extract + 1%sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 50 ul of IgG dynabeads (Dyna), and washed 5 minutes with 1.5mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit and concentrated using by Speed vac. For a detailed protocol see http://www.modencode.org/. DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from Ren, R et al (2000) Science 290, 2306-9.

treatment_protocol: Worm_embryo_extraction_v2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4?C and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C. For a detailed protocol see http://www.modencode.org/.


title: ENDOMETRIAL CELLS CONTROL 2

status: Public on Nov 16 2009

type: RNA

city: Vermillion

first: Kathleen

middle: M

last: Eyster

state: SD

address: 414 E. Clark St.

department: Basic Biomedical Sciences

country: USA

institute: University of South Dakota

description: Cells were grown in DMEM/F12 medium supplemented with 1% ITS+, 1% penicillin/streptomycin, and 500 ng/mL puromycin.  2% fetal bovine serum was also added to the medium from days 1-6.

hyb_protocol: see CodeLink application notes and manuals

scan_protocol: CodeLink Bioarrays scanned on Agilent G2565 microarray scanner

data_processing: global median normalization, CodeLink Expression Analysis 4.1.0.4163

molecule: total RNA

organism: Homo sapiens

source_name: CULTURED HUMAN ENDOMETRIAL CELLS (T-HESC) FROM ATCC

extract_protocol: The cultured endometrial cells were rinsed and TRI reagent (MRC) was added.  The cells were scraped into tubes and centrifuged in the presence of bromochloropropane and sodium acetate.  The RNA-containing layer was removed and the RNA purified on an RNeasy extraction column (Qiagen).  The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen).  The purity and quantity was evaluated with the RNA 6000 NanoLabChip in an Agilent Bioanalyzer.

tag: Telomerase immortalized human endometrial cell line (ATCC #CRL-4003), passage 7, treated with vehicle (0.1% ethanol) for 8 days.  Cells were serum starved from days 6-8.


title: MONOCYTES +THESC CONDITIONED MEDIUM 2

description: Cells were grown in RPMI1640 medium supplemented with 1% penicillin/streptomycin and 10% fetal bovine serum.

source_name: CULTURED MONOCYTE CELL LINE (U-937) FROM ATCC

label_protocol: see CodeLink application notes and manuals

extract_protocol: The cultured U-937 monocyte cells were rinsed and TRI reagent (MRC) was added.  The cells were scraped into tubes and centrifuged in the presence of bromochloropropane and sodium acetate.  The RNA-containing layer was removed and the RNA purified on an RNeasy extraction column (Qiagen).  The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen).  The purity and quantity was evaluated with the RNA 6000 NanoLabChip in an Agilent Bioanalyzer.

tag: U-937 monocytes, passage 9, were grown in suspension in RPMI-1640 supplemented with 10% charcoal/dextran treated FBS and 1% penicillin/streptomycin until the cells covered 80% of the flask surface.  The medium was replaced with THESC-conditioned medium for 24 hours.


title: MONOCYTES + THESC CONDITIONED MEDIUM 3

tag: U-937 monocytes, passage 12, were grown in suspension in RPMI-1640 supplemented with 10% charcoal/dextran treated FBS and 1% penicillin/streptomycin until the cells covered 80% of the flask surface.  The medium was replaced with THESC-conditioned medium for 24 hours.


title: JL00003_DPY26_N2_MXemb_ChIP_replicate1

type: genomic

city: Chapel Hill

first: Jason

middle: D

last: Lieb

state: NC

address: 408 Fordham Hall, CB# 3280

department: Biology

institute: University of North Carolina at Chapel Hill

description: DPY-26 ChIP-chip from N2 mixed stage embryos. An affinity purified rabbit polyclonal antibody to DPY-26 was used.

hyb_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42?C.

scan_protocol: ChIP-chip_scanning_nimblegen_v1. Array scanning and raw data extraction were performed at Roche NimbleGen, according to the protocol described in chapter 5 and 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, array signal was scanned by using a GenePix 4000B Scanner with associated software and saved as .tif files of the 532nm and 635nm images individually. Raw signal intensities of the images were extracted  and saved as .pair files by using NimbleScan software according to the NimbleScan v2.4 User?s Guide.

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: Input genomic DNA

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. http://www.nimblegen.com/products/lit/index.html

growth_protocol: Worm_embryo_growth_and_harvest_v1. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature followed by quenching with 125mM glycine for 5 minutes. Embryos were then washed twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol: Worm_chromatin_immunoprecipitation_v5. 2mg extract + 1%sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 50 ul of IgG dynabeads (Dyna), and washed 5 minutes with 1.5mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit and concentrated using by Speed vac. For a detailed protocol see http://www.modencode.org/.DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from Ren, R et al (2000) Science 290, 2306-9.

treatment_protocol: Worm_embryo_extraction_v1. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 7 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4?C and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C. For a detailed protocol see http://www.modencode.org/.

tag: strain

tag: fix

value: 2% CHO, 30 minutes

tag: stage

value: Mixed Embryos

source_name: ChIP DNA


title: JL00004_MIX1_N2_MXemb_ChIP_replicate1

description: MIX-1 ChIP-chip from N2 mixed stage embryos. An affinity purified rabbit polyclonal antibody to MIX-1 was used.


title: JL00005_SDC2_N2_MXemb_ChIP_replicate2


title: Unmigrated Monocytes Incubated Below Stimulated HUVEC - Sample H

city: Snellville

first: Marcie

middle: R

last: Williams

state: GA

address: 2300 Country Walk 3427

department: Biomedical Engineering

institute: Georgia Institute of Technology

hyb_protocol: Hybridization was performed following the Agilent oligonucleotide microarray hybridization users manual and the Agilent in situ Hybridization Plus kit(p/n 5184-3568). Briefly, a total of 250ng of labeled cRNA from each Cy3 and Cy5 sample was combined and mixed with 50 Î¼l of 10x control targets and nuclease-free water to final volume of 240Î¼l. Then 10Î¼l of 25x fragmentation buffer was added to each sample tube and incubated at 60ËšC for 30 minutes in the dark. After the incubation period, a total of 250Î¼l of 2x hybridization buffer was added to terminate the reaction. A volume of 490Î¼l hybridization mix was applied to each 44k 60-mer Human Whole Genome oligo microarray kit(p/n G4112-60510) and hybridized in a hybridization rotation oven (Robbins Scientific 1040-60-1AG) at 60 ËšC for 17h [3-5]. The slides/hybridization chamber was first disassembled in 6xSSC, 0.005% Triton X-102 and washed with 6xSSC, 0.005% Triton X-102 for 10min at room temperature, then washed with 0.1xSSC, 0.005% Triton X-102 for 5 min on ice, and finally dried using a nitrogen-filled air gun.

scan_protocol: The array was scanned using the Agilent dual laser DNA microarray scanner(p/n G2565AA) with SureScan technology. The relative fluorescent intensity values in the Cy3 and Cy5 channels were then extracted from images using the Agilent Feature Extraction software 8.1(p/n G2567AA).

data_processing: Values were normalized per spot (divide by control channel), per chip (normalize to 50th percentile), and per gene (normalize to median) using Genespring 7.

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Kit - according to manufacturer's instructions

extract_protocol: Trizol - according to manufacturer's instructions RNEasy Cleanup Kit - Qiagen - according to manufacturer's instructions

treatment_protocol: Monocytes are incubated for 1.5 hours on an agarose coated dish beneath IL1b stimulated HUVEC grown on a 3 um pore transwell dish.

tag: Monocytes Isolated from Fresh Whole Human Blood

source_name: Human Reference RNA

extract_protocol: Stratagenes Universal Human Reference RNA is composed of total RNA from 10 human cell lines. The reference RNA is designed to be used as a reference for microarray gene-profiling experiments. Since RNA species differ in abundance between cell lines, an ideal reference sample should represent these different RNAs. Equal quantities of DNase-treated total RNA from each cell line were pooled to make the Universal Human Reference RNA.


title: MONOCYTES CONTROL 3

tag: U-937 monocytes, passage 12, were grown in suspension in RPMI-1640 supplemented with 10% charcoal/dextran treated FBS and 1% penicillin/streptomycin until the cells covered 80% of the flask surface.  The medium was replaced with nonconditioned control medium for 24 hours.


title: JL00001_DPY27_N2_L4_ChIP_replicate3

description: DPY-27 ChIP-chip from N2 L4 larval stage. An affinity purified rabbit polyclonal antibody to DPY-27 was used.

growth_protocol: Worm_L4_growth_and_harvest_vSE1. Worms were grown in standard S-basal media liquid culture. The culture was synchronized by starving hatched embryos at L1 stage and grown at 20C in liquid culture until they reach L4 stage. Worms were collected over 34 uM Nitex membrane, and washed with M9 Buffer + protease inhibitors (Calbiochem). Worms were resuspended in 1 pellet volume of M9, frozen as popcorn in liquid N2, and stored at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol: Worm_chromatin_immunoprecipitation_v4.1. 2.2 mg extract was taken and sarkosyl was added to 1% final concentration. 0.2 mg was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 20 uL protein A sepharose (Amersham) and washed 5 minutes with 1 mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit. For a detailed protocol see http://www.modencode.org/.DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from Ren, R et al (2000) Science 290, 2306-9.

treatment_protocol: Worm_germlineless_adult_soma_extract_v2.2. Frozen worms were ground to a powder using mortar and pestle. Worm powder was diluted in M9 + 1% formaldehyde+1mM PMSF and fixed 5 or 10 minutes. Fixing was quenched by the addition of 125 mM glycine for 5 minutes. Cells were collected by centrifuging 5 minutes at 4000 g at 4C. Samples were washed and resuspended in FA Buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4?C and taking the supernatant. Protein concentration was determined by Bradford Assay and 10 mgs were used per ChIP. For a detailed protocol see http://www.modencode.org/.

value: 2% CHO 5 minutes


title: JL00001_DPY27_YPT41_MXemb_ChIP_replicate1

description: DPY-27 ChIP-chip from YPT41 X-II fusion strain mixed stage embryos. An affinity purified rabbit polyclonal antibody to DPY-27 was used.

data_processing: ChIP-chip_normalization_standard_zscore_v2. First, the ratio of intensity from sample/reference channel was transformed to log2 space. Second, z-scores were obtained by standardizing the data for each IP by subtracting the mean and dividing by the standard deviation of all probes. Z-scores were calculated or probes within each physical array and then concatenated for a full-genome dataset (where multiple physical arrays cover the full genome). Replicates were then combined by taking the median/mean probe z-score.

growth_protocol: Worm_embryo_growth_and_harvest_vSE1. Embryos were prepared by bleaching from gravid adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature. Embryos were then washed once with 100 mM Tris, twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% TritonX-100, 0.1 % sodium deoxycholate; 150 mM NaCl).  Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.


title: Unmigrated Monocytes Incubated Below Stimulated HUVEC - Sample G

tag: Stratagenes Universal Human Reference RNA is composed of total RNA from 10 human cell lines. The reference RNA is designed to be used as a reference for microarray gene-profiling experiments. Since RNA species differ in abundance between cell lines, an ideal reference sample should represent these different RNAs. Equal quantities of DNase-treated total RNA from each cell line were pooled to make the Universal Human Reference RNA.


title: MONOCYTES CONTROL 2

tag: U-937 monocytes, passage 9, were grown in suspension in RPMI-1640 supplemented with 10% charcoal/dextran treated FBS and 1% penicillin/streptomycin until the cells covered 80% of the flask surface.  The medium was replaced with nonconditioned control medium for 24 hours.


title: JL00003_DPY26_N2_MXemb_ChIP_replicate2

growth_protocol: Worm_embryo_growth_and_harvest_v3. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature followed by quenching with 125mM glycine for 5 minutes. Embryos were then washed twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol: Worm_chromatin_immunoprecipitation_v4.1. 2.2 mg extract was taken and sarkosyl was added to 1% final concentration. 0.2 mg was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 20 uL protein A sepharose (Amersham) and washed 5 minutes with 1 mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit. For a detailed protocol see http://www.modencode.org/. DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from Ren, R et al (2000) Science 290, 2306-9.


title: JL00004_MIX1_N2_MXemb_ChIP_replicate3


title: MONOCYTES + THESC CONDITIONED MEDIUM 1

tag: U-937 monocytes, passage 7, were grown in suspension in RPMI-1640 supplemented with 10% charcoal/dextran treated FBS and 1% penicillin/streptomycin until the cells covered 80% of the flask surface.  The medium was replaced with THESC-conditioned medium for 24 hours.


title: Unmigrated Monocytes Incubated Below Stimulated HUVEC - Sample E

tag: Isolated from Fresh Whole Human Blood


title: JL00004_MIX1_N2_MXemb_ChIP_replicate2


title: JL00001_DPY27_YPT41_MXemb_ChIP_replicate2


title: JL00001_DPY27_N2_L4_ChIP_replicate2B

value: 2% CHO 10 minutes


title: CVMMS126R_8WG16_N2_L4_ChIP_replicate2A

description: PolII ChIP data in N2 L4s. A mouse monoclonal antibody which recognizes primarily the unphosphorylated RNA Pol II CTD (8WG16) obtained from Covance (MMS126R) was used for ChIP.

extract_protocol: Worm_chromatin_immunoprecipitation_v4.1. 2.2 mg extract was taken and sarkosyl was added to 1% final concentration. 0.2 mg was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 20 uL protein A sepharose (Amersham) and washed 5 minutes with 1 mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit. For a detailed protocol see http://www.modencode.org/.


title: JL00001_DPY27_11dh_MXemb_ChIP_replicate1

description: DPY-27 ChIP-chip from 11dh X-I fusion strain mixed stage embryos. An affinity purified rabbit polyclonal antibody to DPY-27 was used.


title: Monocytes Which Failed to Transmigrate - Sample D

source_name: Monocytes Which Failed to Transmigrate

treatment_protocol: Freshly isolated monocytes were incubated above IL1b stimulated HUVEC grown on a 3 um pore transwell assay dish.  Monocytes which failed to transmigrate after 1.5 hours of incubation with stimulated HUVEC were collected from the media above the HUVEC.

extract_protocol: Stratagenes Universal Human Reference RNA is composed of total RNA from 10 human cell lines. The reference RNA is designed to be used as a reference for microarray gene-profiling experiments. Since RNA species differ in abundance between cell lines, an ideal reference sample should represent these different RNAs. Equal quantities of DNase-treated total RNA from each cell line were pooled to make the Universal Human Reference RNA. This Universal Reference RNA is suitable for microarray experiments. Stratagene also supplies a QPCR Human Reference Total RNA, suitable for QRT-PCR, which has undergone further DNase treatment.


title: ENDOMETRIAL CELLS VEHICLE+MONOCYTE-CONDITIONED MEDIUM 3

tag: Telomerase immortalized human endometrial cell line (ATCC #CRL-4003), passage 9, treated with vehicle (0.1% ethanol) for 8 days.  Cells were serum starved days 6-8.  Cells were treated with monocyte-conditioned medium (from U-937 cells) for 24 hours beginning on day 7.


title: CVMMS126R_8WG16_N2_L4_ChIP_replicate2B


title: MONOCYTES CONTROL 1

tag: U-937 monocytes, passage 7, were grown in suspension in RPMI-1640 supplemented with 10% charcoal/dextran treated FBS and 1% penicillin/streptomycin until the cells covered 80% of the flask surface.  The medium was replaced with nonconditioned control medium for 24 hours.


title: Monocytes Which Failed to Transmigrate - Sample C


title: JL00001_DPY27_N2_L4_ChIP_replicate2A


title: ENDOMETRIAL CELLS VEHICLE+MONOCYTE-CONDITIONED MEDIUM 2

tag: Telomerase immortalized human endometrial cell line (ATCC #CRL-4003), passage 7, treated with vehicle (0.1% ethanol) for 8 days.  Cells were serum starved days 6-8.  Cells were treated with monocyte-conditioned medium (from U-937 cells) for 24 hours beginning on day 7.


title: JL00003_DPY26_N2_MXemb_ChIP_replicate3


title: Monocytes which Failed to Transmigrate - Sample A

source_name: Monocytes which Failed to Transmigrate


title: Transmigrated Monocytes - Sample K

source_name: Transmigrated Monocytes

treatment_protocol: Freshly isolated monocytes were allowed to transmigrate for 1.5 across IL1b stimulated HUVEC grown on a 3 um pore transwell assay dish.  Transmigrated monocytes were collected from beneath the transwell dish.

tag: Monocytes Isolated from Fresh Whole Human Bloo


title: JL00005_SDC2_N2_MXemb_ChIP_replicate1


title: JL00001_DPY27_11dh_MXemb_ChIP_replicate2


title: ENDOMETRIAL CELLS ESTRADIOL+MONOCYTE-CONDITIONED MEDIUM 3

tag: Telomerase immortalized human endometrial cell line (ATCC #CRL-4003), passage 9, treated with 17beta estradiol (10-8 M) for 8 days.  Cells were serum starved days 6-8.  Cells were treated with monocyte-conditioned medium (from U-937 cells) for 24 hours beginning on day 7.


title: ENDOMETRIAL CELLS VEHICLE+MONOCYTE-CONDITIONED MEDIUM 1

tag: Telomerase immortalized human endometrial cell line (ATCC #CRL-4003), passage 5, treated with vehicle (0.1% ethanol) for 8 days.  Cells were serum starved days 6-8.  Cells were treated with monocyte-conditioned medium (from U-937 cells) for 24 hours beginning on day 7.


title: JL00001_DPY27_N2_L4_ChIP_replicate1

extract_protocol: Worm_chromatin_immunoprecipitation_v4.1. 2.2 mg extract was taken and sarkosyl was added to 1% final concentration. 0.2 mg was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 20 uL protein A sepharose (Amersham) and washed 5 minutes with 1 mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit. For a detailed protocol see http://www.modencode.org/.NA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from Ren, R et al (2000) Science 290, 2306-9.


title: Transmigrated Monocytes - Sample L


title: Transmigrated Monocytes - Sample I


title: Untreated Monocytes - Sample P

source_name: Untreated Monocytes

treatment_protocol: Freshly isolated monocytes were incubated on agarose coated tissue culture dishes for 1.5 hours in a cell culture incubator.


title: ENDOMETRIAL CELLS ESTRADIOL+MONOCYTE-CONDITIONED MEDIUM 1

tag: Telomerase immortalized human endometrial cell line (ATCC #CRL-4003), passage 5, treated with 17beta estradiol (10-8 M) for 8 days.  Cells were serum starved days 6-8.  Cells were treated with monocyte-conditioned medium (from U-937 cells) for 24 hours beginning on day 7.


title: Untreated Monocytes - Sample O


title: Unmigrated Monocytes Incubated Below Stimulated HUVEC - Sample F


title: Untreated Monocytes - Sample M

hyb_protocol: Hybridization was performed following the Agilent oligonucleotide microarray hybridization user’s manual and the Agilent in situ Hybridization Plus kit(p/n 5184-3568). Briefly, a total of 250ng of labeled cRNA from each Cy3 and Cy5 sample was combined and mixed with 50 μl of 10x control targets and nuclease-free water to final volume of 240μl. Then 10μl of 25x fragmentation buffer was added to each sample tube and incubated at 60˚C for 30 minutes in the dark. After the incubation period, a total of 250μl of 2x hybridization buffer was added to terminate the reaction. A volume of 490μl hybridization mix was applied to each 44k 60-mer Human Whole Genome oligo microarray kit(p/n G4112-60510) and hybridized in a hybridization rotation oven (Robbins Scientific 1040-60-1AG) at 60 ˚C for 17h [3-5]. The slides/hybridization chamber was first disassembled in 6xSSC, 0.005% Triton X-102 and washed with 6xSSC, 0.005% Triton X-102 for 10min at room temperature, then washed with 0.1xSSC, 0.005% Triton X-102 for 5 min on ice, and finally dried using a nitrogen-filled air gun.

scan_protocol: The array was scanned using the Agilent dual laser DNA microarray scanner(p/n G2565AA) with SureScan technology [3]. The relative fluorescent intensity values in the Cy3 and Cy5 channels were then extracted from images using the Agilent Feature Extraction software 8.1(p/n G2567AA) [6].

extract_protocol:
Trizol - according to manufacturer's instructions
RNEasy Cleanup Kit - Qiagen - according to manufacturer's instructions

extract_protocol:
Stratagene’s Universal Human Reference RNA is composed of total RNA from 10 human cell lines. The reference RNA is designed to
be used as a reference for microarray gene-profiling experiments. Since RNA species differ in abundance between cell lines, an ideal
reference sample should represent these different RNAs. Equal quantities of DNase-treated total RNA from each cell line were
pooled to make the Universal Human Reference RNA. This Universal Reference RNA is suitable for microarray experiments.
Stratagene also supplies a QPCR Human Reference Total RNA, suitable for QRT-PCR, which has undergone further DNase treatment.


title: ENDOMETRIAL CELLS ESTRADIOL+PROGESTERONE+MONOCYTE-CONDITIONED MEDIUM 3

tag: Telomerase immortalized human endometrial cell line (ATCC #CRL-4003), passage 9, treated with 17beta estradiol (10-8 M) plus medroxyprogesterone acetate (10-7 M) for 8 days.  Cells were serum starved days 6-8.  Cells were treated with monocyte-conditioned medium (from U-937 cells) for 24 hours beginning on day 7.


title: ENDOMETRIAL CELLS ESTRADIOL+MONOCYTE-CONDITIONED MEDIUM 2


title: YPT47_totalRNA_replicate3

description: Gene expression data from mixed stage embryos isolated from YPT47, X;V fusion strain.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. http://www.nimblegen.com/products/lit/index.html

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol.http://www.nimblegen.com/products/lit/index.html

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4 (Roche NimbleGen, Inc.).

source_name: mixed stage embryos from X;V fusion strain

label_protocol: Cy3 Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. http://www.nimblegen.com/products/lit/index.html

growth_protocol: Embryos were prepared by bleaching from gravid adults grown in standard S-basal media liquid culture.

extract_protocol: 1V sample in 10V Trizol that was stored at -80C was thawed at 37C, vortexed 30 seconds and re-frozen in liquid nitrogen. Freeze-cracking was repeated a total of four times. 1/5 V chloroform was added and vortexed for 30 seconds. After centrifugation at 13000 rpm for 5 minutes, aqueous phase containing RNA was recovered. RNA was precipitated by mixing with 0.8V isopropanol and incubation on ice, followed by centrifugation at 13000 rpm at 4C for 20 minutes. RNA was washed with 75% ethanol, dissolved in DEPC H2O and cleaned up using Qiagen RNeasy kit.

tag: strain


title: ENDOMETRIAL CELLS ESTRADIOL+PROGESTERONE+MONOCYTE-CONDITIONED MEDIUM 1

tag: Telomerase immortalized human endometrial cell line (ATCC #CRL-4003), passage 5, treated with 17beta estradiol (10-8 M) plus medroxyprogesterone acetate (10-7 M) for 8 days.  Cells were serum starved days 6-8.  Cells were treated with monocyte-conditioned medium (from U-937 cells) for 24 hours beginning on day 7.


title: YPT47_totalRNA_replicate2

tag: stage


title: Untreated Monocytes - Sample N

treatment_protocol: Human Donor

tag: Monocytes Isolated from Fresh Whole Human Blood


title: YPT47_totalRNA_replicate1


title: ENDOMETRIAL CELLS ESTRADIOL+PROGESTERONE 2

tag: Telomerase immortalized human endometrial cell line (ATCC #CRL-4003), passage 7, treated with 17beta estradiol (10-8 M) plus medroxyprogesterone acetate (10-7 M) for 8 days.  Cells were serum starved days 6-8.


title: YPT41_totalRNA_replicate3

description: Gene expression data from mixed stage embryos isolated from YPT41, X;II fusion strain.

source_name: mixed stage embryos from X;II fusion strain


title: ENDOMETRIAL CELLS ESTRADIOL+PROGESTERONE 3

tag: Telomerase immortalized human endometrial cell line (ATCC #CRL-4003), passage 9, treated with 17beta estradiol (10-8 M) plus medroxyprogesterone acetate (10-7 M) for 8 days.  Cells were serum starved days 6-8.


title: ENDOMETRIAL CELLS ESTRADIOL 1

tag: Telomerase immortalized human endometrial cell line (ATCC #CRL-4003), passage 5, treated with 17beta estradiol (10-8M) for 8 days.  Cells were serum starved days 6-8.


title: ADMs vs. donor 3T3-L1 adipocytes 2

city: Tsu

first: Naohito

last: Aoki

address: 1577 Kurimamachiya-cho

department: Graduate School of Bioresources

country: Japan

institute: Mie University

description: Biological replicate 2 of 2.

hyb_protocol: Gene expression Hybridization Kit (5188-5242, Agilent) was used.

scan_protocol: Scanned on an Agilent Microarray scanner.  Images were quantified using Agilent Feature Extraction Software (version 9.5.3).

data_processing: Agilent GeneSpingGX Software was used for data processing.

organism: Mus musculus

source_name: donor 3T3-L1 adipocytes

label_protocol: 250 ng of total RNA was used for cRNA labelling and purification by using low RNA Fluorecent Linear Amplification Puls (for 2-color, 5188-5340, Agilent), RNA Spike in Kit (for 2-color, 5188-5279, Agilent), and RNeasy Mini Kit (Qiagen).

growth_protocol: 3T3-L1 cells were cultured in DMEM (high glucose) containing 10% FCS and  induced into adipocytes with insulin (10µg/ml), dexamethasone (0.25µM) and 3-isobutyl-1-methylxanthine (0.5mM).

extract_protocol: Total RNAs were extracted using Trizol reagenet (invitrogen) following manufacturer's instructions

treatment_protocol: On the Day 11 following differentiation induction, conditioned medium was harvested and the ADMs were prepared by ultracentrifugation followed by RNA preparation.  Cells were harvested on the sama day and subjected to RNA preparation.

tag: cell line

tag: sample type

value: donor 3T3-L1 adipocytes

source_name: 3T3-L1 adipocyte-derived microvesicles

value: 3T3-L1 adipocyte-derived microvesicles


title: ADMs vs. donor 3T3-L1 adipocytes 1

description: Biological replicate 1 of 2.


title: ENDOMETRIAL CELLS ESTRADIOL+PROGESTERONE 1

tag: Telomerase immortalized human endometrial cell line (ATCC #CRL-4003), passage 5, treated with 17beta estradiol (10-8 M) plus medroxyprogesterone acetate (10-7 M) for 8 days.  Cells were serum starved days 6-8.


title: YPT41_totalRNA_replicate2


title: YPT41_totalRNA_replicate1


title: N2_totalRNA_replicate3

description: Gene expression data from mixed stage embryos isolated from N2 strain.

source_name: mixed stage embryos from N2


title: MCC Patient 176

status: Public on Nov 14 2009

city: Nashville

first: Pengcheng

last: Lu

state: TN

address: 2200 Pierce Avenue

institute: Vanderbilt University

description: Gene expression

hyb_protocol: Standard Affymetrix protocols for hybridization to the Affy HGU133 2.0 plus array were used.

scan_protocol: GeneChip Scanner was used for scanning and generating the raw .CEL files.

data_processing: Bioconductor's affy package was used for RMA normalization and raw data processing using default settings for background correction and normalization. Cox regression hazards model was applied to the processed data using the survival package. All analyses were performed using R software.

label: biotin

source_name: Moffitt Cancer Center

label_protocol: Standard Affymetrix protocols were used.

extract_protocol: RNA was extracted using the Qiagen RNeasy kit.

tag: age

tag: gender

value: male

tag: ethnicity

value: caucasian

tag: grade

value: 2 - Moderately differentiated (MD)

tag: overall_event (death from any cause)

value: death

tag: dss_event (disease specific survival; death from cancer)

tag: dfs_event (disease free survival; cancer recurrence)

tag: overall survival follow-up time


title: ENDOMETRIAL CELLS CONTROL 1

tag: Telomerase immortalized human endometrial cell line (ATCC #CRL-4003), passage 5, treated with vehicle (0.1% ethanol) for 8 days.  Cells were serum starved on days 6-8.


title: MCC Patient 166

description: Gene expression

value: female


title: MCC Patient 168

description: Gene expression


title: N2_totalRNA_replicate2

tag: strain

tag: stage


title: ENDOMETRIAL CELLS CONTROL 3

tag: Telomerase immortalized human endometrial cell line (ATCC #CRL-4003), generation 9, treated with vehicle (0.1% ethanol) for 8 days.  Cells were serum starved from days 6-8.


title: ENDOMETRIAL CELLS ESTRADIOL 3

tag: Telomerase immortalized human endometrial cell line (ATCC #CRL-4003), passage 9, treated with 17beta estradiol (10-8 M) for 8 days.  Cells were serum starved days 6-8.


title: N2_totalRNA_replicate1


title: MCC Patient 175

description: Gene expression

value: 3 - Poorly differentiated (PD)


title: ENDOMETRIAL CELLS ESTRADIOL+PROGESTERONE+MONOCYTE-CONDITIONED MEDIUM 2

tag: Telomerase immortalized human endometrial cell line (ATCC #CRL-4003), passage 7, treated with 17beta estradiol (10-8 M) plus medroxyprogesterone acetate (10-7 M) for 8 days.  Cells were serum starved days 6-8.  Cells were treated with monocyte-conditioned medium (from U-937 cells) for 24 hours beginning on day 7.


title: ENDOMETRIAL CELLS ESTRADIOL 2

tag: Telomerase immortalized human endometrial cell line (ATCC #CRL-4003), passage 7, treated with 17beta estradiol (10-8 M) for 8 days.  Cells were serum starved days 6-8.


title: MCC Patient 156

description: Gene expression

value: black

value: recurrence


title: MCC Patient 157

description: Gene expression

value: no death

value: no recurrence


title: CVMMS126R_8WG16_N2_L4_ChIP_replicate1_array2

description: PolII ChIP data in N2 L4s, replicate 1, array part 2. A mouse monoclonal antibody which recognizes primarily the unphosphorylated RNA Pol II CTD (8WG16) obtained from Covance (MMS126R) was used for ChIP.

extract_protocol: Worm_chromatin_immunoprecipitation_v4.1. 2.2 mg extract was taken and sarkosyl was added to 1% final concentration. 0.2 mg was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 20 uL protein A sepharose (Amersham) and washed 5 minutes with 1 mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit. For a detailed protocol see http://www.modencode.org/.Samples were amplified using a modified Whole Genome Amplification Kit protocol (Sigma).

tag: fix


title: CVMMS126R_8WG16_N2_L4_ChIP_replicate1_array1

description: PolII ChIP data in N2 L4s, replicate 1, array part 1. A mouse monoclonal antibody which recognizes primarily the unphosphorylated RNA Pol II CTD (8WG16) obtained from Covance (MMS126R) was used for ChIP.


title: MCC Patient 158

description: Gene expression


title: MCC Patient 152

description: Gene expression


title: MCC Patient 150

description: Gene expression


title: MCC Patient 151

description: Gene expression


title: MCC Patient 149

description: Gene expression


title: MCC Patient 142

description: Gene expression


title: MCC Patient 143

description: Gene expression


title: MCC Patient 140

description: Gene expression


title: MCC Patient 162

description: Gene expression


title: CVMMS126R_8WG16_N2_L4_ChIP_replicate1_array3

description: PolII ChIP data in N2 L4s, replicate 1, array part 3. A mouse monoclonal antibody which recognizes primarily the unphosphorylated RNA Pol II CTD (8WG16) obtained from Covance (MMS126R) was used for ChIP.


title: MCC Patient 138

description: Gene expression


title: MCC Patient 136

description: Gene expression


title: MCC Patient 137

description: Gene expression


title: MCC Patient 164

description: Gene expression


title: MCC Patient 155

description: Gene expression


title: MCC Patient 165

description: Gene expression


title: MCC Patient 135

description: Gene expression


title: MCC Patient 131

description: Gene expression


title: MCC Patient 132

description: Gene expression


title: MCC Patient 133

description: Gene expression


title: MCC Patient 130

description: Gene expression


title: MCC Patient 153

description: Gene expression

value: other (not caucasian, black, or hispanic)


title: MCC Patient 141

description: Gene expression

value: 1 - Well differentiated (WD)


title: MCC Patient 134

description: Gene expression


title: MCC Patient 127

description: Gene expression


title: MCC Patient 128

description: Gene expression


title: MCC Patient 120

description: Gene expression


title: MCC Patient 122

description: Gene expression


title: MCC Patient 123

description: Gene expression


title: MCC Patient 124

description: Gene expression


title: MCC Patient 129

description: Gene expression


title: MCC Patient 111

description: Gene expression


title: MCC Patient 126

description: Gene expression


title: MCC Patient 125

description: Gene expression


title: MCC Patient 115

description: Gene expression


title: MCC Patient 110

description: Gene expression


title: MCC Patient 108

description: Gene expression


title: MCC Patient 109

description: Gene expression


title: MCC Patient 105

description: Gene expression


title: MCC Patient 102

description: Gene expression


title: MCC Patient 106

description: Gene expression


title: MCC Patient 98

description: Gene expression


title: MCC Patient 90

description: Gene expression


title: SDQ3146_SDC2_N2_MXemb_ChIP_replicate2

description: SDC-2 ChIP-chip from N2 mixed stage embryos. An affinity purified rabbit polyclonal antibody to SDC-2 obtained from SDI (SDC-2 Q3148). 5 ug used per ChIP.

extract_protocol: Worm_chromatin_immunoprecipitation_v4.1. 2.2 mg extract was taken and sarkosyl was added to 1% final concentration. 2 mg was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 20 uL protein A sepharose (Amersham) and washed 5 minutes with 1 mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit. For a detailed protocol see http://www.modencode.org/. Worm_LM-PCR_Amplification_for_ChIP-chip_v1. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from Ren, R et al (2000) Science 290, 2306-9.

value: 2% CHO, 30 minutes

value: Mixed Embryos


title: MCC Patient 96

description: Gene expression


title: SDQ3148_SDC2_N2_MXemb_ChIP_replicate1


title: MCC Patient 101

description: Gene expression


title: SDQ3146_SDC2_N2_MXemb_ChIP_replicate1


title: MCC Patient 95

description: Gene expression


title: MCC Patient 80

description: Gene expression


title: MCC Patient 76

description: Gene expression


title: MCC Patient 91

description: Gene expression


title: MCC Patient 75

description: Gene expression


title: MCC Patient 71

description: Gene expression


title: MCC Patient 79

description: Gene expression


title: MCC Patient 87

description: Gene expression


title: MCC Patient 82

description: Gene expression


title: MCC Patient 85

description: Gene expression


title: MCC Patient 112

description: Gene expression


title: MCC Patient 72

description: Gene expression


title: MCC Patient 48

description: Gene expression


title: MCC Patient 65

description: Gene expression


title: MCC Patient 49

description: Gene expression


title: MCC Patient 46

description: Gene expression


title: MCC Patient 50

description: Gene expression


title: MCC Patient 45

description: Gene expression


title: MCC Patient 64

description: Gene expression


title: MCC Patient 88

description: Gene expression


title: MCC Patient 74

description: Gene expression


title: MCC Patient 51

description: Gene expression


title: MCC Patient 57

description: Gene expression


title: MCC Patient 44

description: Gene expression


title: Comparative genomic indexing-Campylobacter jejuni strain CNET007-2

city: Albany

first: Craig

middle: T

last: Parker

state: CA

address: 800 Buchanan St

department: PSM

institute: USDA ARS

description: Intensity ratios of DNA (channel 1) divided by DNA (channel 2) signals minus respective background signals. Total array is 16 blocks arranged in 4X4 configuration.

hyb_protocol: Labeled reference and sample DNAs were combined in 45 µl Pronto! cDNA hybridization solution (Corning, Corning, NY) and heated to 95°C for 5 min. Then, 15 µl of the hybridization mixture was put onto a microarray slide and sealed with a cover slip. The microarray slide was placed in a hybridization chamber (Corning) and incubated at 42°C for 18 h. Following hybridization, the slides were washed twice in 2× SSC, 0.1% sodium dodecyl sulfate at 42°C for 10 min, followed by twice in 1× SSC at room temperature for 10 min, and finally twice in 0.2× SSC at room temperature for 5 min. The microarray slides were dried by centrifugation at 300 × g for 10 min before scanning.

scan_protocol: Axon GenePix4000B, 10nm resolution. GenePix software. Optimize intensities manually.

data_processing: Data normalization was performed by bringing the median ratio (Cy5/Cy3) for each of the 16 blocks to 1 using the following equation: (Ti) = (Cy5i/Cy3i) - c, where T is the normalized ratio, i is the gene index, Cy5 and Cy3 are the red and green intensities and c is the 50th percentile of all Cy5/Cy3 ratios. Flagged features are omitted from the data normalization process.

organism: Campylobacter jejuni

source_name: Campylobacter jejuni strains NCTC 11168 and RM1221

label_protocol: Labeling protocol described in Parker et al. J Clin Microbiol 2006, 44(11):4125-4135. PMID: 16943349

extract_protocol: Genomic DNA isolated using protocol described in Parker et al. J Clin Microbiol 2006, 44(11):4125-4135. PMID: 16943349

tag: reference strains

value: NCTC 11168 and RM1221

source_name: Campylobacter jejuni strain CNET007

tag: test strain


title: MCC Patient 47

description: Gene expression

tag: age

tag: gender


title: MCC Patient 43

description: Gene expression

tag: ethnicity

tag: grade


title: MCC Patient 39

description: Gene expression

tag: overall_event (death from any cause)

tag: dss_event (disease specific survival; death from cancer)


title: Comparative genomic indexing-Campylobacter jejuni strain CNET005-2

source_name: Campylobacter jejuni strain CNET005


title: MCC Patient 41

description: Gene expression

tag: dfs_event (disease free survival; cancer recurrence)

tag: overall survival follow-up time


title: MCC Patient 32

description: Gene expression


title: MCC Patient 38

description: Gene expression


title: Comparative genomic indexing-Campylobacter jejuni strain D3226-2

source_name: Campylobacter jejuni strain D3226


title: MCC Patient 42

description: Gene expression


title: Comparative genomic indexing-Campylobacter jejuni strain 07479-2

source_name: Campylobacter jejuni strain 07479


title: Comparative genomic indexing-Campylobacter jejuni strain D3141-2

source_name: Campylobacter jejuni strain D3141


title: Comparative genomic indexing-Campylobacter jejuni strain C356-2

source_name: Campylobacter jejuni strain C356


title: MCC Patient 62

description: Gene expression


title: MCC Patient 30

description: Gene expression


title: MCC Patient 24

description: Gene expression


title: Comparative genomic indexing-Campylobacter jejuni strain C012446-2

source_name: Campylobacter jejuni strain C012446


title: MCC Patient 40

description: Gene expression


title: MCC Patient 28

description: Gene expression


title: MCC Patient 21

description: Gene expression


title: MCC Patient 20

description: Gene expression


title: Comparative genomic indexing-Campylobacter jejuni strain C011300-2

source_name: Campylobacter jejuni strain C011300


title: Comparative genomic indexing-Campylobacter jejuni strain C019165-2

source_name: Campylobacter jejuni strain C019165


title: Comparative genomic indexing-Campylobacter jejuni strain C019168-2

source_name: Campylobacter jejuni strain C019168


title: Comparative genomic indexing-Campylobacter jejuni strain CCUG10950-2

source_name: Campylobacter jejuni strain CCUG10950


title: Comparative genomic indexing-Campylobacter jejuni strain C356-1


title: Comparative genomic indexing-Campylobacter jejuni strain 07479-1


title: MCC Patient 13

description: Gene expression


title: Comparative genomic indexing-Campylobacter jejuni strain D3141-1


title: MCC Patient 18

description: Gene expression


title: Comparative genomic indexing-Campylobacter jejuni strain D3226-1


title: MCC Patient 16

description: Gene expression


title: Comparative genomic indexing-Campylobacter jejuni strain CNET007-1


title: MCC Patient 12

description: Gene expression


title: MCC Patient 11

description: Gene expression


title: Comparative genomic indexing-Campylobacter jejuni strain C012446-1


title: Comparative genomic indexing-Campylobacter jejuni strain CNET005-1


title: MCC Patient 27

description: Gene expression

value: hispanic


title: Comparative genomic indexing-Campylobacter jejuni strain CCUG10950-1


title: MCC Patient 10

description: Gene expression


title: MCC Patient 8

description: Gene expression


title: Comparative genomic indexing-Campylobacter jejuni strain C019165-1


title: Comparative genomic indexing-Campylobacter jejuni strain C011672-1

source_name: Campylobacter jejuni strain C011672


title: Comparative genomic indexing-Campylobacter jejuni strain C012599-1

source_name: Campylobacter jejuni strain C012599


title: Comparative genomic indexing-Campylobacter jejuni strain C019168-1


title: Comparative genomic indexing-Campylobacter jejuni strain D3468-1

source_name: Campylobacter jejuni strain D3468


title: Comparative genomic indexing-Campylobacter jejuni strain D3468-2


title: MCC Patient 3

description: Gene expression


title: Comparative genomic indexing-Campylobacter jejuni strain C011300-1


title: Aerobic vs anaerobic experiment 2, replicate 1

status: Public on Nov 13 2009

city: Richmond

first: Janina

middle: P

last: Lewis

state: VA

address: 521 North 11th Street

department: Philips Institute of OCMB

institute: Virginia Commonwealth University

description: Biological replicate 2 of 3. Technical replicate 1.

hyb_protocol: Labeled cDNA probes were combined and mixed with hybridization buffer and applied to prehybridized array.  Array was placed in hybridization chamber and incubated ON at 42C.

scan_protocol: Scanned on an Axon 4200A microarray scanner. Images were quantified using GenePix software (v 6.0).

data_processing: Normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. LIMMA was used. LIMMA ( Linear Models for Microarray Data) package for statistical inference. LIMMA includes pre-processing capabilities for two-colour spotted arrays such as normalization of cDNA data, and background subtraction.Data were analyzed for significant differences using the Significance Analysis for Oral Pathogen Microarrays (SAOPMD).   SAOPMD combines all the repeats within and between arrays and generates statistics.  Data included were derived from five microarrays.

organism: Porphyromonas gingivalis

source_name: RNA from whole bacteria

label_protocol: 10 µg of total RNA were primed with random DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of ArrayScript reverse transcriptase (Applied Biosystems/Ambion, Austin, TX).  Dyes were incorporated into the reverse transcribed cDNAs (Cy3 and Cy5, GE Healthcare).

growth_protocol: Bacterial cells were grown in the presence of 6% oxygen.

extract_protocol: Total RNA extracted using Qiagen kit following manufacturer's instructions

tag: cell type

value: bacteria

tag: strain

source_name: Total RNA from pooled whole bacteria

growth_protocol: Bacterial cells were grown anaerobically.

value: log phase


title: Aerobic vs anaerobic experiment 2, replicate 2

description: Biological replicate 2 of 3. Technical replicate 2.


title: Aerobic vs anaerobic experiment 3, replicate 1

description: Biological replicate 3 of 3. Technical replicate 1.


title: Aerobic vs anaerobic experiment 1, replicate 2

description: Biological replicate 1 of 3. Technical replicate 2.


title: Comparative genomic indexing-Campylobacter jejuni strain C011338-1

source_name: Campylobacter jejuni strains NCTC 11168 and RM1221

source_name: Campylobacter jejuni strain C011338


title: Comparative genomic indexing-Campylobacter jejuni strain C011338-2


title: MCC Patient 6

description: Gene expression

source_name: Moffitt Cancer Center


title: Aerobic vs anaerobic experiment 1, replicate 1

description: Biological replicate 1 of 3. Technical replicate 1.


title: 01-10-08_Philpott_MS_Yeast2_8

city: Bethesda

first: Caroline

last: Philpott

state: MD

address: 10 Center Dr, Bldg.10-Rm.9B-05

department: NIDDK

institute: National Institutes of Health

description: 3839 -Strain grown under high iron conditions, 300 uM Fe

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Affymetrix Microarray Suite version 5.0

organism: Saccharomyces cerevisiae

source_name: yeast grown under high iron conditions

label_protocol: Standard Affymetrix protocol

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

tag: dose


title: 01-10-08_Philpott_MS_Yeast2_5

description: 3842- Strain grown under high iron conditions, 300 uM Fe


title: MCC Patient 2

description: Gene expression

value: male

value: caucasian


title: 01-10-08_Philpott_MS_Yeast2_3

description: 3841- Strain grown under low iron conditions 10 uM Fe

source_name: yeast grown under low iron conditions


title: 01-10-08_Philpott_MS_Yeast2_4

description: 3838 - Strain grown under low iron conditions, 10 uM Fe


title: 01-10-08_Philpott_MS_Yeast2_2

description: 3837-Strain grown under 10 uM Fe (low iron) conditions


title: 01-10-08_Philpott_MS_Yeast2_6

description: 3843- Strain grown under high iron conditions, 300 uM Fe


title: MCC Patient 1

description: Gene expression

value: 2 - Moderately differentiated (MD)


title: MCC Patient 97

description: Gene expression

value: death


title: 01-10-08_Philpott_MS_Yeast2_1

description: 3840- Gene expression data from  strain grown under low  iron conditions

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


title: 01-10-08_Philpott_MS_Yeast2_7

description: 3844 - Strain grown under high iron conditions, 300 uM Fe


title: Comparative genomic indexing-Campylobacter jejuni strain C012599-2


title: MCC Patient 33

description: Gene expression


title: MCL6505_N_Mapping250K_Nsp

city: Tokyo

first: Motohiro

last: Kato

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

institute: University of Tokyo

description: We have used anonymous normal references (own-lab-generated) for SNP array analysis.

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing:
CNAG/AsCNAR 3.0
After appropriate normalization of mean array intensities, signal ratios between tumours and anonymous normal references were calculated in an allele-specific manner, and allele-specific copy numbers were inferred from the observed signal ratios based on the hidden Markov model using CNAG/AsCNAR 3.0 software (http://www.genome.umin.jp).

label: biotin phytoerythrin

source_name: mantle cell lymphoma specimens

label_protocol: Affymetrix standard

extract_protocol: standard DNA extraction using PUREGENE DNA extracting kit (Gentra, USA)

tag: disease state

value: mantle cell lymphoma


title: MCL-LL1002_N_Mapping250K_Nsp


title: MCL-REC1_N_Mapping250K_Nsp


title: MCL3810_N_Mapping250K_Nsp


title: MCL-L616-99_N_Mapping250K_Nsp


title: MCL11787_N_Mapping250K_Nsp


title: MCL-L70-95_N_Mapping250K_Nsp


title: MCC Patient 4

description: Gene expression

value: female


title: MCL-NCEB1_N_Mapping250K_Nsp


title: MCL-SP49_N_Mapping250K_Nsp


title: MCL-HBL2_N_Mapping250K_Nsp


title: MCL10593_N_Mapping250K_Nsp


title: MCL8460_N_Mapping250K_Nsp


title: MCL-L340-99_N_Mapping250K_Nsp


title: MCL-L10-93_N_Mapping250K_Nsp


title: MCL-993_N_Mapping250K_Nsp


title: MCL10656_N_Mapping250K_Nsp


title: MCL-866_N_Mapping250K_Nsp


title: MCL-655_N_Mapping250K_Nsp


title: MCL8234_N_Mapping250K_Nsp


title: MCL-L151-98_N_Mapping250K_Nsp


title: MCL11527_N_Mapping250K_Nsp


title: MCL-L193-58_N_Mapping250K_Nsp


title: Microvinification UCD522/P29, 2

city: Barcelona

first: Benjamin

last: Pina

address: Jordi Girona, 18

country: Spain

institute: IDAEA-CSIC

description: High-sulfide (UCD522) vs low-sulfide (P29) yeast strains.

hyb_protocol: Hybridization was peformed using the Febit Geniom One synthesizer/hybridizer/reader apparatus according to manufacturer's specifications.

scan_protocol: In-situ scanning in the Febit Geniom One synthesizer/hybridizer/reader apparatus.

data_processing: Merlin software (Abecasis GR., Cherny SS., Cookson WO. and Cardon LR. 2002. Merlin - rapid analysis of dense genetic maps using sparse gene flow trees. Nature genetics 30: 3-49). Each analyzed gene was tested using five oligonucleotides. Fluorescence higher than 2500 units was considered significant.

label: phycoerythrin

label_protocol: Total RNA was labelled using an indirect protocol. Biotin-labelled cRNA was synthesized in vitro from each yeast RNA sample. The samples were then labelled separately with either streptavidin-phycoerythrin or streptavidin-Cy3. Merlin software.

growth_protocol: Yeast strains used in this study were Saccharomyces cerevisiae UCD522 and P29. Fermentation media was pasteurized grape juice in 1 L glass bottle. Fermentation temperature was controlled by a HotCold Incubator (Selecta, Barcelona, Spain), set at 18ºC, and continuous rotation was provided by a Rotabit from Selecta. Wine analysis was done by official or equivalent methods. Fermentation was monitored by weight loss in a 2000g scale (Precisa, Madrid, Spain).

extract_protocol: Yeast cells (approximately 2 X 10e8 cells) were harvested from liquid culture by centrifugation, snap frozen, and immediately physically disrupted in liquid nitrogen by mortar and pestle. RNA was extracted and purified from the resulting powder using the RNAeasy kit (Qiagen, Valencia, CA) following the manufacturers’ recommendations.

tag: sulfide production

value: low

value: high


title: MCL-40287_N_Mapping250K_Nsp


title: Diabetic diaphragm #3

city: Cleveland

first: Erik

last: van Lunteren

state: OH

address: 10701 East Boulevard

department: Pulmonary 111J(W)

institute: Cleveland VA Medical Center

description: Standard affy

data_processing: MAS5.0; Standard affy

label: Standard affy

organism: Rattus norvegicus

source_name: Diaphragm

tag: Diaphragm from diabetic rats, injected with streptozotocin at 8 weeks, tissue obtained at 12 weeks


title: Diabetic diaphragm #1

description: Standard affy


title: MCL-512_N_Mapping250K_Nsp


title: Diabetic diaphragm #2

description: Standard affy


title: MCL-40005_N_Mapping250K_Nsp


title: Normal diaphragm #3

description: Standard affy

tag: Diaphragm from control rats, injected with buffer at 8 weeks, tissue obtained at 12 weeks


title: MCL-31686_N_Mapping250K_Nsp


title: Tolerogenic (IL-10) vs. Control dendritic cells

city: Mexico City

first: Carmen

last: Sánchez-Torres

department: Molecular Biomedicine

country: Mexico

institute: CINVESTAV-IPN

hyb_protocol: Equal quantities of labeled cDNA were hybridized using hybridization solution UniHyb (TeleChem International INC), to the Human arrays for 14 h at 42 ºC.

scan_protocol: Acquisition and quantification of array images was performed in ScanArray 4000 with its accompanying software ScanArray 4000 from Packard BioChips. All images were captured using 65% PMT gain, 70 to 75% laser power and 10µm resolution at 50% scan rate. For each spot the Cy3 and Cy5 density mean value and the Cy3 and Cy5 background mean value were calculated with software ArrayPro Analyzer from Media Cibernetics.

data_processing:
Data analysis was performed with free software GenArise, developed in the Computing Unit of Cellular Physiology Institute of UNAM (http://www.ifc.unam.mx/genarise/). LOWESS normalization, filter by intensity (each Cy3 value in the spot must be greater than two standard deviations from Cy3 background values, the same criterion for Cy5) and replicate analysis of data obtained from log2 of processed Red signal/processed Green signal. Differentially expressed genes was selected by calculating an intensitydependent z-score, using a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point, and define a z-score.
Intensity-dependent z-score. z measures the number of SD a data point is from the mean. zi = (Ri – mean(R)) / sd(R), where zi is the z-score for each element, Ri is the log-ratio for each element, and sd(R) is the standard deviation of the log-ratio. The elements with a z-score > 2 standard deviation would be the significantly differentially expressed genes.

source_name: Monocyte-derived dendritic cells

label_protocol: 30 mg of total RNA (pool of 7.5 mg of total RNA per donor) were used for cDNA synthesis incorporating dUTP-Cy3 (N) or dUTP-Cy5 (TA) employing the CyScribe Firs-Strand cDNA labeling kit (Amersham), following manufactures's instructions

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

treatment_protocol: Monocyte-derived dendritic cells cultured for 6 days with GM-CSF (1000 U/ml), IL-4 (15 ng/ml) and IL-10 (20 ng/ml), and matured for 12 hours with TNF-alpha (40 ng/ml) and PGE2 (0,1 mg/ml). The culture medium was RPMI 1640 supplemented with 10% heat-inactivated autologous serum, 2 mM L-glutamine, 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 100 U/ml penicillin, 100 ug/ml streptomycin, and 50 uM 2-ME.

tag: treatment

value: With IL-10

value: dendritic cells

treatment_protocol: Monocyte-derived dendritic cells cultured for 6 days with GM-CSF (1000 U/ml) and IL-4 (15 ng/ml), and matured for 12 hours with TNF-alpha (40 ng/ml) and PGE2 (0,1 mg/ml). The culture medium was RPMI 1640 supplemented with 10% heat-inactivated autologous serum, 2 mM L-glutamine, 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 100 U/ml penicillin, 100 ug/ml streptomycin, and 50 uM 2-ME.

value: Without IL-10


title: Pooled retinal RNA from room air-exposed post-natal day 3 SD rats, biological replicate 3

city: Adelaide

first: Melinda

middle: N

last: Tea

state: South Australia

address: Flinders Medical Centre, Carpark Building

department: Ophthalmology

country: Australia

institute: Flinders University

description: Gene Expression Data

hyb_protocol: As per Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual (P/N 701880 Rev4) using Affymetrix Genechip Hybridization, Wash and Stain Kit (P/N 900720)

scan_protocol: As per Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual (P/N 701880 Rev4) using Affymetrix Genechip Scanner 3000 7G

data_processing: CEL files generated from DAT files automatically by Affymetrix AGCC software.  CEL files processed using Partek Genomics Suite v 6.4 using RMA background correction and Partek GC content correction.

label: Biotin

source_name: Retinae, exposed to room air to post-natal day 3

label_protocol: As per Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual (P/N 701880 Rev4) using Affymetrix WT cDNA Synthesis and Amplification Kit (Part# 900673) and  Affymetrix WT Terminal Labeling and Control Regents (Part# 901524). The rRNA reduction step is not recommended by Affymetrix for the Genearrays and was not performed.

extract_protocol: Total RNA was extracted from the retinae of individual rats using TRIzol according to the manufacturer's method. Total RNA was further purified using a Qiagen Rneasy Micro column purification kit according to the manufacturer's protocol.

treatment_protocol: Within 12 hours of birth, female rats and their litters were placed in a humidified oxygen chamber and exposed to alternating 24 hour cycles of hyperoxia (80% oxygen in air) and normoxia (21% oxygen in air) until the rats were euthansed at post-natal day 3. Age-matched room air-exposed rats were used as controls.

value: Sprague Dawley


title: Pooled retinal RNA from room air-exposed post-natal day 3 SD rats, biological replicate 2

description: Gene Expression Data


title: Tolerogenic (IL-10 and IL-6) vs Control dendritic cells

treatment_protocol: Monocyte-derived dendritic cells cultured for 6 days with GM-CSF (1000 U/ml), IL-4 (15 ng/ml), IL-10 (20 ng/ml) and IL-6 (25 ng/ml), and matured for 12 hours with TNF-alpha (40 ng/ml) and PGE2 (0,1 mg/ml). The culture medium was RPMI 1640 supplemented with 10% heat-inactivated autologous serum, 2 mM L-glutamine, 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 100 U/ml penicillin, 100 μg/ml streptomycin, and 50 μM 2-ME.

value: With IL-10 and IL-6

treatment_protocol: Monocyte-derived dendritic cells cultured for 6 days with GM-CSF (1000 U/ml) and IL-4 (15 ng/ml), and matured for 12 hours with TNF-alpha (40 ng/ml) and PGE2 (0,1 mg/ml). The culture medium was RPMI 1640 supplemented with 10% heat-inactivated autologous serum, 2 mM L-glutamine, 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 100 U/ml penicillin, 100 μg/ml streptomycin, and 50 μM 2-ME.

value: Without IL-10 or IL-6


title: Pooled retinal RNA from cyclic hyperoxia-exposed post-natal day 3 SD rats, biological replicate 1

description: Gene Expression Data

source_name: Retinae, exposed to cyclic hyperoxia to post-natal day 3


title: Pooled retinal RNA from cyclic hyperoxia-exposed post-natal day 3 SD rats, biological replicate 2

description: Gene Expression Data


title: Tolerogenic (IL-10 and TGF-b1) vs. Control dendritic cells

treatment_protocol: Monocyte-derived dendritic cells cultured for 6 days with GM-CSF (1000 U/ml), IL-4 (15 ng/ml), IL-10 (20 ng/ml) and TGF-b1 (20 ng/ml), and matured for 12 hours with TNF-alpha (40 ng/ml) and PGE2 (0,1 mg/ml). The culture medium was RPMI 1640 supplemented with 10% heat-inactivated autologous serum, 2 mM L-glutamine, 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 100 U/ml penicillin, 100 ug/ml streptomycin, and 50 uM 2-ME.

value: With IL-10 and TGF-b1

value: Without IL-10 or TGF-b1


title: Pooled retinal RNA from room air-exposed post-natal day 3 SD rats, biological replicate 1

description: Gene Expression Data


title: Pooled retinal RNA from room air-exposed post-natal day 3 F344 rats, biological replicate 1

description: Gene Expression Data

value: Fischer 344


title: Pooled retinal RNA from cyclic hyperoxia-exposed post-natal day 3 F344 rats, biological replicate 3

description: Gene Expression Data


title: Anaerobic carbon-limited chemostat culture with 0.2 g/l hop acids of pdr1,pdr3,yrr1,yrm1 mutant -2

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

hyb_protocol: Microarray analysis. Sampling of cells from chemostats, total RNA extraction, cDNA synthesis and hybridization on the arrays were performed as previously described [3]. Reference List 3. De Nicola R, Hazelwood LA, De Hulster EA, Walsh MC, Knijnenburg TA, Reinders MJ et al.: Physiological and transcriptional responses of Saccharomyces cerevisiae to zinc limitation in chemostat cultures. Appl Environ Microbiol 2007, 73: 7680-7692.

data_processing:
GCOS software
CHP file targetted at 150

label: biotin, streptavidin phycoerythrin (SAPE)

source_name: Chemostat culture

growth_protocol:
Media. The composition of the synthetic medium [1] for shake-flask and chemostat cultivation was as follows: 5 g.l-1 (NH4)2SO4, 3 g.l-1 KH2PO4, 0.5 g.l-1 MgSO4 and trace elements. The media was sterilized by autoclaving at 120 oC. Glucose (25 g.l-1 for chemostat cultivation), vitamins and the anaerobic growth factors Tween-80 and ergosterol, were supplemented after sterilization [1]. The glucose was autoclaved separately at 110 oC, and the vitamins were filter sterilized.
Chemostat cultivation. Anaerobic glucose-limited steady-state chemostat cultures at a dilution rate of 0.10 h-1 of S. cerevisiae CEN.PK113-7D were performed as previously described [2]. Iso-α-acid enriched hop extracts were filter sterilized and added at a concentration of 0.2 g.l-1. Medium reservoirs containing iso-α-acid enriched hop extracts were stored at 4ºC and protected from light.
Reference List
1. Verduyn C, Postma E, Scheffers WA, van Dijken JP: Energetics of Saccharomyces cerevisiae in anaerobic glucose-limited chemostat cultures. J Gen Microbiol 1990, 136: 405-412.
2. Tai SL, Boer VM, Daran-Lapujade P, Walsh MC, de Winde JH, Daran JM et al.: Two-dimensional transcriptome analysis in chemostat cultures. Combinatorial effects of oxygen availability and macronutrient limitation in Saccharomyces cerevisiae. J Biol Chem 2005, 280: 437-447.

treatment_protocol: Quenching in liquid nitrogen

tag: description

value: Saccharomyces cerevisiae prototrophic strain

tag: genotype

value: mata mal2-8c suc2 ura3 pdr3::loxP pdr1::loxP-kanMX-loxP yrm1::hphNT1 yrr1::natNT2 p426GPD (URA3)


title: Normal diaphragm #2

description: Standard affy


title: Normal diaphragm #1

description: Standard affy


title: Anaerobic carbon-limited chemostat culture with 0.2 g/l hop acids of pdr1,pdr3,yrr1,yrm1 mutant-1

scan_protocol: Microarray analysis. Sampling of cells from chemostats, total RNA extraction, cDNA synthesis and hybridization on the arrays were performed as previously described [3]. Reference List 3. De Nicola R, Hazelwood LA, De Hulster EA, Walsh MC, Knijnenburg TA, Reinders MJ et al.: Physiological and transcriptional responses of Saccharomyces cerevisiae to zinc limitation in chemostat cultures. Appl Environ Microbiol 2007, 73: 7680-7692.


title: Pooled retinal RNA from cyclic hyperoxia-exposed post-natal day 3 F344 rats, biological replicate 2

description: Gene Expression Data


title: Pooled retinal RNA from room air-exposed post-natal day 3 F344 rats, biological replicate 2

description: Gene Expression Data


title: MCL-1173_N_Mapping250K_Nsp


title: MCL-21699_N_Mapping250K_Nsp


title: Anaerobic carbon-limited chemostat culture with 0.2 g/l hop acids of pdr1,pdr3 mutant -2

label_protocol:
Microarray analysis. Sampling of cells from chemostats, total RNA extraction, cDNA synthesis and hybridization on the arrays were performed as previously described [3].
Reference List
3. De Nicola R, Hazelwood LA, De Hulster EA, Walsh MC, Knijnenburg TA, Reinders MJ et al.: Physiological and transcriptional responses of Saccharomyces cerevisiae to zinc limitation in chemostat cultures. Appl Environ Microbiol 2007, 73: 7680-7692.

value: mata mal2-8c suc2 ura3 pdr3::loxP pdr1::loxP-kanMX-loxP p426GPD(URA3)


title: MCL-22073_N_Mapping250K_Nsp


title: Anaerobic carbon-limited chemostat culture with 0.2 g/l hop acids of pdr1,pdr3 mutant-1

extract_protocol:
Microarray analysis. Sampling of cells from chemostats, total RNA extraction, cDNA synthesis and hybridization on the arrays were performed as previously described [3].
Reference List
3. De Nicola R, Hazelwood LA, De Hulster EA, Walsh MC, Knijnenburg TA, Reinders MJ et al.: Physiological and transcriptional responses of Saccharomyces cerevisiae to zinc limitation in chemostat cultures. Appl Environ Microbiol 2007, 73: 7680-7692.


title: Wild type +SU5402 (5μM) rep3

city: Singapore

first: Kian Leong

last: LEE

state: Singapore

address: #07-21, 8 College Road

department: Duke-NUS Medical School

country: Singapore

institute: National University of Singapore (NUS)

description: Biological replicate 3

hyb_protocol: 750ng of each cRNA sample was hybridized to MouseRef-8 v2.0 Expression BeadChip microarrays (Illumina, USA) as per manufacturer specifications.

scan_protocol: Microarrays were scanned on the BeadArray Reader (Illumina, USA) at scan factor 1 as per manufacturer specifications.

data_processing: The microarray data was subjected to background subtraction on the BeadStudio Data Analysis software (Illumina, USA) and normalized using the Cross-correlation method (Chua et al., 2006). Differentially expressed transcripts were identified based on the mean Log2 fold change in expression values compared to the wild type ES cell controls with a cutoff at 1.5-fold change. Reference: Chua SW, Vijayakumar P, Nissom PM, Yam CY, Wong VV, Yang H: A novel normalization method for effective removal of systematic variation in microarray data. Nucleic acids research 2006, 34(5):e38.

source_name: Wild type +SU5402 (5μM)

label_protocol: 500ng of total RNA from each sample was reverse transcribed into cDNA and in vitro transcribed into biotin-labelled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion, USA).

growth_protocol: Cells were cultured on gelatin coated plates in Glascow MEM (Sigma-Aldrich) supplemented with 15% FBS (Hyclone), 1000 IU/ml LIF, 2-mercaptoethanol, and Non-Essential Amino Acids (Gibco). Medium was changed daily and cells passaged every second day.

extract_protocol: Total RNA was extracted from 3 biological replicates of wild-type and Ndst1/2 - /- ES cells subjected to NaCIO3-, SU5402 or control treatments using the RNeasy Mini kit (Qiagen, Germany) according to manufacturer instructions. RNA quality was assessed on the 2100 Bioanalyser (Agilent, USA) using the RNA 6000 Nano Chip kit (Agilent, USA) for intact 18S and 28S ribosomal peaks without significant degradation (RNA Integrity Number >9) for all samples.

treatment_protocol: Cells were treated 24h with either heparan sulfation inhibitor (NaClO3-, 20mM) or FGFR inhibitor (SU5402, 5μM)

tag: cell line

value: Wild type ES cells

value: SU5402 (5μM) 24 hours


title: MCL-1143_N_Mapping250K_Nsp

value: mantle cell lymphoma


title: Wild type +SU5402 (5μM) rep3r

description: Technical replicate of Biological replicate 3


title: Anaerobic carbon-limite chemostat with 0.2 g/l hop acids-2

value: MATa MAL2-8c SUC2


title: MCL-1153_N_Mapping250K_Nsp


title: Wild type +SU5402 (5μM) rep2

description: Biological replicate 2


title: Jeko1_N_Mapping250K_Nsp


title: Anaerobic carbon-limited chemostat culture with 0.2 g/l hop acids-3


title: MCL-22601_N_Mapping250K_Nsp


title: Ndst1/2-/- ES cells Untreated rep3r

source_name: Ndst1/2-/- ES cells Untreated

value: Ndst1/2-/- ES cells

value: Untreated


title: Ndst1/2-/- ES cells Untreated rep3

description: Biological replicate 3


title: Pooled retinal RNA from cyclic hyperoxia-exposed post-natal day 3 F344 rats, biological replicate 1

description: Gene Expression Data


title: Wild type +SU5402 (5μM) rep1

description: Biological replicate 1


title: Ndst1/2-/- ES cells Untreated rep2

description: Biological replicate 2


title: Male corneal epithelial cells, biological rep 1 (Affymetrix)

city: Boston

first: David

middle: A

last: Sullivan

state: MA

address: 20 Staniford Street

institute: Schepens Eye Research Institute

description: Corneoscleral rim scrappings from a male donor age 34.

hyb_protocol: Following fragmentation, 20 microg of cRNA were hybridized for 18 hr at 45C on an Affymetrix GeneChip Human Genome U133A 2.0 Array in an Affymetrix hybridization oven. GeneChips were washed and stained with streptavidin-Alexa 647 and washed again using a Model 450 Fluidics station and Affymetrix GeneChip Operating Software (GCOS) .

scan_protocol: GeneChips were scanned with a Affymetrix Model 7000 scanner running GCOS v1.3 software.

data_processing: Data were analyzed with GCOS software using the default settings.  The default scaling produced a trimmed mean intensity of 500.

label_protocol: Biotinylated cRNA were prepared according to the standard Codelink protocol from 2 microg total RNA using a CodeLink Expression Assay Reagent Kit.

extract_protocol: RNA was twice purified with Trizol following the manufacturer's instructions.

tag: gender

value: Male

value: corneal epithelial cells

tag: cell age


title: Female corneal epithelial cells, biological rep 3 (Affymetrix)

description: Corneoscleral rim scrappings from a female donor age 50.

value: Female


title: Ndst1/2-/- ES cells Untreated rep1

description: Biological replicate 1


title: MCL-1132_N_Mapping250K_Nsp


title: Wild type + NaClO3- (20mM)  rep3r

source_name: Wild type + NaClO3- (20mM)

value: NaClO3- (20mM) 24 hours


title: Wild type + NaClO3- (20mM)  rep3

description: Biological replicate 3


title: Cultured male corneal epithelial cells, biological rep 2 (Codelink 18.5K)

description: Cultured male corneal epithelial cells from a male donor age 60.  Outgrowths were cultured from cornea rims in keratinocyte serum-free medium containing 50 µg/ml bovine pituitary extract and 5 ng/ml epidermal growth factor.  At 70% confluence the corneal epithelial cells were lifted with trypsin and seeded onto collagen coated plates.  This first passage was then grown to confluence in the medium above and the RNA isolated.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 18 hr at 37C on GE Healthcare/Amersham Biosciences CodeLink UniSet Human 20K I Bioarray. Bioarrays were washed and stained with streptavidin-Alexa 647 and washed again.

scan_protocol: Bioarrays were scanned with a ScanArray Express HT scanner using ScanArray Express software.

data_processing: Data were analyzed with the CodeLink Image Analysis software using the default settings and normalized using global scaling to a median target intensity  on each array of 1.0.

value: male

value: cultured corneal epithelial cells


title: Female corneal epithelial cells, biological rep 1 (Affymetrix)

description: Corneoscleral rim scrappings from a female donor age 31.


title: Male corneal epithelial cells, biological rep 1 (Codelink 19.2K)

source_name: Corneoscleral rim scrappings from a male donor age 34.


title: Male corneal epithelial cells, biological rep 3 (Codelink 19.2K)

description: Corneoscleral rim scrappings from a male donor age 52.


title: Cultured male corneal epithelial cells, biological rep 1 (Codelink 18.5K)

description: Cultured male corneal epithelial cells from a male donor age 56.  Outgrowths were cultured from cornea rims in keratinocyte serum-free medium containing 50 µg/ml bovine pituitary extract and 5 ng/ml epidermal growth factor.  At 70% confluence the corneal epithelial cells were lifted with trypsin and seeded onto collagen coated plates.  This first passage was then grown to confluence in the medium above and the RNA isolated.


title: WT-4 versus WS-4

city: Lausanne

first: Eric

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

description: WS biological replicate 2 of 2.

hyb_protocol: Hybridization and washing was performed using the in situ Hybridization Plus kit (Agilent) and following the manufactures instructions.

scan_protocol: The arrays were scanned using a dual-laser DNA microarray scanner (Agilent). The data was then extracted from images by the Feature Extraction software 6.1 (Agilent).

data_processing: The data were background subtracted and normalized using the loess method all included in the limma package of BioConductor(www.bioconductor.org)

source_name: Mouse embryonic fibroblasts from wild type animals

label_protocol: Protocol from Agilent

growth_protocol: Cells were maintained in DMEM with 50 microg/ml streptomycin and 10% fetal bovine serum.

extract_protocol: Sambrook et al., 1989. Molecular cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press.

treatment_protocol: Cells were treated for one hour with 0.5 mM hydrogen peroxide and fed with fresh media without hydrogen peroxide before total RNA extraction 24hours later

tag: developmental stage

source_name: Mouse WS embryonic fibroblasts


title: Female corneal epithelial cells, biological rep 3 (Codelink 19.2K)

source_name: Corneoscleral rim scrappings from a female donor age 50.


title: Female corneal epithelial cells, biological rep 2 (Affymetrix)

description: Corneoscleral rim scrappings from a female donor age 44.

hyb_protocol: Following fragmentation, 20 microg of cRNA were hybridized for 18 hr at 45C on a Affymetrix GeneChip Mouse Expression Array 430A using a Affymetrix hybridization oven. GeneChips were washed and stained with streptavidin-Alexa 647 and washed again using a Model 450 Fluidics station and Affymetrix GeneChip Operating Software (GCOS) .


title: Male corneal epithelial cells, biological rep 2 (Codelink 19.2K)

description: Corneoscleral rim scrappings from a male donor age 44.


title: Wild type + NaClO3- (20mM)  rep1

description: Biological replicate 1


title: WS-H2O2 treated-2 versus WS-untreated-2

description: WS biological replicate 2 of 2.

source_name: Mouse WS embryonic fibroblasts treated with H2O2


title: WT-3 versus WS-3

description: WS biological replicate 1 of 2.


title: Female corneal epithelial cells, biological rep 2 (Codelink 19.2K)

source_name: Corneoscleral rim scrappings from a female donor age 44.


title: Cultured female corneal epithelial cells, biological rep 2 (Codelink 18.5K)

description: Cultured female corneal epithelial cells from a female donor age 53.  Outgrowths were cultured from cornea rims in keratinocyte serum-free medium containing 50 µg/ml bovine pituitary extract and 5 ng/ml epidermal growth factor.  At 70% confluence the corneal epithelial cells were lifted with trypsin and seeded onto collagen coated plates.  This first passage was then grown to confluence in the medium above and the RNA isolated.


title: Wild type CCE ES cells Control rep3r

source_name: Wild type CCE ES cells


title: Wild type CCE ES cells Control rep3

description: Biological replicate 3


title: WS-H2O2 treated-1 versus WS-untreated-1

description: WS biological replicate 1 of 2.


title: WT-H2O2 treated-2 versus WT-untreated-2

description: WT biological replicate 2 of 2.

source_name: Mouse embryonic fibroblasts from wild type animals treated with H2O2


title: Female corneal epithelial cells, biological rep 1 (Codelink 19.2K)

source_name: Corneoscleral rim scrappings from a female donor age 31.


title: Wild type CCE ES cells Control rep2

description: Biological replicate 2


title: Cultured female corneal epithelial cells, biological rep 1 (Codelink 18.5K)

description: Cultured female corneal epithelial cells from a female donor age 42.  Outgrowths were cultured from cornea rims in keratinocyte serum-free medium containing 50 µg/ml bovine pituitary extract and 5 ng/ml epidermal growth factor.  At 70% confluence the corneal epithelial cells were lifted with trypsin and seeded onto collagen coated plates.  This first passage was then grown to confluence in the medium above and the RNA isolated.


title: Wild type CCE ES cells Control rep1

description: Biological replicate 1


title: WT-H2O2 treated-1 versus WT-untreated-1

description: WT biological replicate 1 of 2.


title: Male corneal epithelial cells, biological rep 2 (Affymetrix)

source_name: Corneoscleral rim scrappings from a male donor age 44.


title: Anaerobic carbon-limited chemostat with 0.2 g/l hop acids-1


title: mH2A1 ChIP-chip (replicate A)

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: no additional information

hyb_protocol: According to standard NimbleGen protocol.

data_processing: Genomic data analysis was performed using the statistical programming language R (R Development Core Team). All data processing scripts are available upon request. The log2 ratio data from each of the arrays was subjected to lowess normalization.

source_name: Input DNA from IMR90 cells

extract_protocol: IMR90 human embryonic lung fibroblasts were grown to ~80 to 90% confluence, cross-linked with 1% paraformaldehyde in PBS for 10 min. at 37°C, and quenched in 125 mM glycine in PBS for 5 min at 4°C. The cells were collected by centrifugation and sonicated in lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris•HCl, pH 7.9, 1x protease inhibitor cocktail) to generate chromatin fragments of ~500 bp in length. The material was clarified by centrifugation, diluted 10-fold in dilution buffer (0.5% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris•HCl, pH 7.9, 1x protease inhibitor cocktail), and pre-cleared with protein A-agarose beads. The pre-cleared, chromatin-containing supernatant was used in immunoprecipitation reactions with antibodies against macroH2A1. The immunoprecipitated genomic DNA and a sample of input material were cleared of protein and residual RNA by digestion with proteinase K and RNase H, respectively. The DNA was then extracted with phenol:chloroform:isoamyl alcohol and precipitated with ethanol. The material was then amplified with LM-PCR.

value: IMR90, primary embryonic lung fibroblasts

tag: antibody

source_name: MacroH2A1 ChIP DNA


title: mH2A1 ChIP-chip (replicate B)

description: no additional information

scan_protocol: According to standard NimbleGen protocol.


title: Male corneal epithelial cells, biological rep 3 (Affymetrix)

description: Corneoscleral rim scrappings from a male donor age 50.


title: 4426-LMS-soft tissue-CGH_US45102891

status: Public on Nov 12 2009

city: Stanford

first: Andrew

last: Beck

address: Stanford

institute: Stanford University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84360.gif

hyb_protocol: not provided

scan_protocol: Agilent G2505B scanner

data_processing: VALUE is Log ratio Cy5/Cy3

source_name: normal gender-matched human leukocytes

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: normal gender-matched human leukocytes

source_name: 4426-LMS-soft tissue-CGH_US45102891

tag: simple annotation

value: aCGH, tumor tissue

tag: phenotype

value: Conventional

tag: measurement

value: time(change) 21 years

tag: individual

tag: compound based treatment

value: No

tag: organism part

value: ST - retroperitoneum

value: P

tag: sex/mating type

value: M

tag: experiment type

value: aCGH


title: STT222_control_US45102891

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84373.gif

value: Normal Colon


title: 4453-LMS-soft tissue-CGH_US45102891

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84370.gif

source_name: 4453-LMS-soft tissue-CGH_US45102891

value: time(change) 62 years

value: ST - right buttock

tag: disease state

value: F


title: STT1096_control_US45102891

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84372.gif

value: Normal Muscle


title: 4445-LMS-soft tissue-CGH_US45102891

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84367.gif

source_name: 4445-LMS-soft tissue-CGH_US45102891

value: Pleomorphic

value: time(change) 52* years

value: ST - left thigh


title: 4446-LMS-soft tissue-CGH_US45102891

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84368.gif

value: normal gender-matched human leukocytes

source_name: 4446-LMS-soft tissue-CGH_US45102891

value: time(change) 39 years

value: ST - left che wall


title: 4424-LMS-soft tissue-CGH_US45102891

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84361.gif

source_name: 4424-LMS-soft tissue-CGH_US45102891

value: aCGH, tumor tissue

value: Conventional

value: time(change) 76 years

value: ST -  right inguinal


title: 4431-LMS-soft tissue-CGH_US45102891

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84366.gif

source_name: 4431-LMS-soft tissue-CGH_US45102891

value: time(change) 58 years

value: CT+RT

value: ST - right upper arm


title: 4399-LMS-soft tissue-CGH_US45102891

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84364.gif

source_name: 4399-LMS-soft tissue-CGH_US45102891

value: time(change) 65 years

value: No

value: ST - retroperitoneum

value: P

value: aCGH


title: 4427-LMS-soft tissue-CGH_US45102891

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84365.gif

source_name: 4427-LMS-soft tissue-CGH_US45102891

value: Pleomorphic/Conventional

value: time(change) 48 years

value: ST - chest wall

value: M


title: 4403-LMS-soft tissue-CGH_US45102891

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84353.gif

value: normal gender-matched human leukocytes

source_name: 4403-LMS-soft tissue-CGH_US45102891

value: time(change) 69 years

value: RT

value: ST - left scrotum


title: 4415-LMS-Lung-CGH_US45102891

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84358.gif

value: aCGH, tumor tissue

value: Conventional

value: time(change) 57 years

value: ST - Epididymis


title: 4451-LMS-soft tissue-CGH_US45102891

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84369.gif

source_name: 4451-LMS-soft tissue-CGH_US45102891

value: Pleomorphic

value: time(change) 58* years

value: ST - right shoulder

value: F


title: 4409-LMS-Lung-CGH_US45102891

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84354.gif

value: time(change) 55 years

value: No

value: ST - Retrocoecal tumor

value: aCGH


title: 4410-LMS-soft tissue-CGH_US45102891

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84355.gif

source_name: 4410-LMS-soft tissue-CGH_US45102891

value: time(change) 50 years

value: ST - left upper leg

value: P

value: M


title: STT4722-LMS-m-HG-ST-M(same pt as 4723)-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64534.gif

source_name: Universal human reference

value: Universal human reference

value: Primary tumor, tumor tissue

value: time(change) 49 years

value: C1-2 spine

value: Expression


title: 4430-LMS-soft tissue-CGH_US45102891

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84363.gif

value: normal gender-matched human leukocytes

source_name: 4430-LMS-soft tissue-CGH_US45102891

value: aCGH, tumor tissue

value: Conventional

value: time(change) 58 years

value: ST - right upper arm


title: STT315_control_US45102891

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84371.gif

value: Normal Muscle


title: 2679-LMS-Uterus-CGH_US45102891

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84352.gif

value: Pleomorphic

value: time(change) 48 years

value: No

value: UT

value: F


title: 4411-LMS-soft tissue-CGH_US45102891

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84356.gif

source_name: 4411-LMS-soft tissue-CGH_US45102891

value: ST - retroperitoneum

value: P

value: aCGH


title: STT146_control_US45102891

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84374.gif

value: Normal Colon


title: 4420-LMS-soft tissue-CGH_US45102891

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84359.gif

source_name: 4420-LMS-soft tissue-CGH_US45102891

value: time(change) 63 years

value: M


title: 4398-LMS-soft tissue-CGH_US45102891

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84362.gif

value: normal gender-matched human leukocytes

source_name: 4398-LMS-soft tissue-CGH_US45102891

value: time(change) 45 years

value: ST - right upper leg


title: STT4600-LMS-f-HG-UT-M-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63399.gif

value: Universal human reference

value: Primary tumor, tumor tissue

value: Conventional

value: time(change) 47 years

value: Expression


title: 516-LMS-Uterus-CGH_

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84351.gif

source_name: normal gender-matched human leukocytes

value: aCGH, tumor tissue

value: time(change) 68 years

value: No


title: STT4453-LMS-f-IG-ST-P-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55560.gif

value: time(change) 62 years

value: ST - right buttock

value: F


title: STT4577-LMS-f-LG-UT-R1-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62266.gif

value: UT


title: STT4604-LMS-f-IG-ST?-R2-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63654.gif

value: time(change) 57 years

value: CT

value: ST - Left chest wall


title: STT4608-LMS-f-HG-UT-R1-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63400.gif


title: STT4611-LMS-f-pleomorphic-HG-UT-R2-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63651.gif

value: Pleomorphic

value: time(change) 58 years

value: RT


title: STT4613-LMS-f-LG-UT?-M2-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63650.gif

value: Universal human reference

value: Primary tumor, tumor tissue

value: UT**


title: STT4399-LMS-f-HG-ST-P-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/52133.gif

value: Conventional

value: time(change) 65 years

value: ST - retroperitoneum

value: P

value: Expression


title: STT4606-LMS-f-HG-UT-M2-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63653.gif

value: time(change) 56 years


title: STT4446-LMS-m-IG-ST-P-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53441.gif

value: time(change) 39 years

value: No

value: ST - left che wall

value: M


title: STT4578-LMS-f-HG-UT?-M4-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62268.gif

value: time(change) 62 years

value: F


title: STT4605-LMS-f-HG-UT-M1-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63396.gif

value: time(change) 55 years

value: UT


title: STT4612-LMS-f-IG-UT-R3-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63397.gif

value: Universal human reference

value: Pleomorphic

value: time(change) 66 years


title: STT4723-LMS-m-HG-ST-M(same pt as 4722)-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64533.gif

value: Primary tumor, tumor tissue

value: time(change) 49 years

value: C1-2 spine


title: STT4601-LMS-f-HG-UT-P-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63655.gif

value: Pleomorphic/Conventional

value: P


title: STT4579-LMS-f-pleomorphic-HG-UT?-M1-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63347.gif

value: time(change) 52 years

value: Expression


title: STT4423-LMS-m-HG-ST-P-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/55945.gif

value: time(change) 67 years

value: No

value: ST - left inguinal


title: STT4571-LMS-f-HG-UT-P-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/61585.gif

value: time(change) 28 years


title: 4412-LMS-Lung-CGH_US45102891

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-08/84357.gif

value: normal gender-matched human leukocytes

value: aCGH, tumor tissue

value: Conventional

value: time(change) 48 years

value: RT

value: ST - retroperioneum

value: F

value: aCGH


title: STT4603-LMS-f-HG-UT-M5-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63657.gif

value: Universal human reference

value: Primary tumor, tumor tissue

value: Pleomorphic

value: time(change) 32 years

value: CT+RT

value: UT


title: STT4408-LMS-f-HG-ST-R4(same pt as 4409)-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53442.gif

value: time(change) 55 years

value: CT

value: ST - Retrocoecal tumor

value: Expression


title: STT4401-LMS-f-HG-?-M?-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52681.gif

value: time(change) 49 years

value: No

value: Unknown


title: STT4425-LMS-f-IG-ST-P-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56488.gif

value: Conventional

value: time(change) 54 years

value: ST - right upper leg

value: P


title: Human_line6_2

first: Genevieve

last: Konopka

department: Neuroscience

description: SY5Y cells overexpressing FOXP2 human

hyb_protocol: Manufacturer's instructions

scan_protocol: Manufacturer's instructions

data_processing: Quantile normalization; please see associated published manuscript

source_name: SY5Y cells, line 6, FOXP2 human 2

label_protocol: Manufacturer's instructions

extract_protocol: Qiagen RNeasy kit


title: Human_line7_1

description: SY5Y cells overexpressing FOXP2 human

source_name: SY5Y cells, line 7, FOXP2 human 1


title: Human_line7_4

description: SY5Y cells overexpressing FOXP2 human

source_name: SY5Y cells, line 7, FOXP2 human 4


title: Human_line7_3

description: SY5Y cells overexpressing FOXP2 human

source_name: SY5Y cells, line 7, FOXP2 human 3


title: Human_line7_2

description: SY5Y cells overexpressing FOXP2 human

source_name: SY5Y cells, line 7, FOXP2 human 2


title: Human_line6_4

description: SY5Y cells overexpressing FOXP2 human

source_name: SY5Y cells, line 6, FOXP2 human 4


title: Human_line6_3

description: SY5Y cells overexpressing FOXP2 human

source_name: SY5Y cells, line 6, FOXP2 human 3


title: Human_line1_2

description: SY5Y cells overexpressing FOXP2 human

source_name: SY5Y cells, line 1, FOXP2 human 2


title: Human_line1_3

description: SY5Y cells overexpressing FOXP2 human

source_name: SY5Y cells, line 1, FOXP2 human 3


title: STT4396-LMS-f-HG-ST-P-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56484.gif

value: Universal human reference

value: Pleomorphic/Conventional

value: time(change) 56 years

value: F


title: Human_line1_4

description: SY5Y cells overexpressing FOXP2 human

source_name: SY5Y cells, line 1, FOXP2 human 4


title: STT4410-LMS-m-pleomorphic-HG-ST-P-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54145.gif

value: Primary tumor, tumor tissue

value: Pleomorphic

value: time(change) 50 years

value: ST - left upper leg

value: M


title: STT4430-LMS-f-IG-ST-P(same pt as 4431)-tRNA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55933.gif

value: time(change) 58 years

value: ST - right upper arm

value: Expression