title: Project-ST-H@_A4-4_(000vs180)_D4

city: College Station

first: Huaijun

last: Zhou

state: TX

address: Rm 418D Kleberg Center,Texas A&M University

institute: Texas A&M University

description: Four arrays are included in one slide (Agilent 4X44K plateform)

hyb_protocol: A 825 ng of labeled cRNA with specificity over 8 were used for the hybridization reaction using the in situ hybridization kit plus (Agilent Technologies). A 100 ul hybridization solution was loaded on each of array in Agilent 4x44K microarrays. Arrays were incubated at 65 ℃ for 17 h in Agilent’s microarray hybridization chambers. After hybridization, arrays were washed according to the Agilent protocol.

scan_protocol: Slides were scanned at 5-µm resolution using GenePix Personal 4100A (Molecular Devices Corporation, Sunnyvale, CA) and were saved as TIFF images. Auto Photomultiplier tube (PMT) were selected and adjusted to get the ratio of the overall intensities between the two channels (Cy3 and Cy5) was 0.9~1.1. The intensities of the spots on each image were quantified by Genepix pro 6.0 software (Molecular Devices Corporation, Downingtown, PA), and data were saved as .txt files for further analysis.

data_processing: The signal intensity of each gene was globally normalized using LOWESS by R program (Yang et al, 2002).

organism: Gallus gallus

source_name: Chicken Heterophils, treated with Salmonella for 180 min (180M-D4)

label_protocol: A 350 ng of aliquot of total RNA was reverse transcribed into cDNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). The synthesized cDNA was transcribed into cRNA labeled with one of two cyanine-labeled nucleotides (Perkin Elmer, Wellesley, MA). Labeled cRNA was purified with RNeasy Mini columns (Qiagen, Valecia, CA). The quality of each cRNA sample was verified by total yield and specificity measured with ND-100 spectrophotometer (NanoDrop Technologies)

extract_protocol: Heterophils were pelleted, and re-suspended in lysis buffer (Ribopure-Bacteria kit, Ambion Inc., Austin, TX), and frozen. The lysed cells were transferred to Ambion homogenizer columns filled with bead and were vortexed for 10 min at highest speed. Total RNA was extracted from the homogenized lysate according to the manufacturer’s instructions, eluted with 20 µl heated elution buffer and stored at -80°C.

treatment_protocol: Heterophils (1×10^7) were treated with 300 µl Salmonella Typhimurium for 180 min at 39°C on a rotary shaker

tag: Heterophils from 1 wk commercial broiler

source_name: Chicken Heterophils, non-treated (0M-D4)

extract_protocol: Heterophils were pelleted, and re-suspended in lysis buffer (Ribopure-Bacteria kit, Ambion Inc., Austin, TX), and frozen. The lysed cells were transferred to Ambion homogenizer columns filled with bead and vortex for 10 min at highest speed. Total RNA was extracted from the homogenized lysate according to the manufacturer’s instructions, eluted with 20 µl heated elution buffer and stored at -80°C

treatment_protocol: N/A (non-treated)


title: Melanoma cell line MaMel113

status: Public on Apr 13 2010

type: genomic

city: Heidelberg

first: Andreas

last: Gast

state: BW

address: INF 580

department: Division of Molecular Genetic Epidemiology

country: Germany

institute: Gernman Cancer Research Center

description: Hybridized to 250K_StyI

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to the array according to manufacturer's instructions.

scan_protocol: The arrays were washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: CEL files and TXT files (generated by Affymetrix GTYPE) were analyzed by CNAT (Affymetrix) and CNAG (Nannya et al., 2005). Genotype Call (SNP call): AA, AB, BB,  and NoCall; "confidence" = confidence score (rank score for genotype call used)

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Melanoma cell line MaMel113, derived from metastatic tumor

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from cell lines or mononuclear cell preparations obtained from peripheral blood using commercially available DNA or RNA Purification kits (Puregene) according to manufacturer's instructions. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: disease status

value: metastatic melanoma patient

tag: tissue

value: metastatic tumor

tag: cell line


title: Project-ST-H@_A4-2_(000vs180)_D3

type: RNA

country: USA

molecule: total RNA

source_name: Chicken Heterophils, treated with Salmonella for 180 min (180M-D3)

source_name: Chicken Heterophils, non-treated (0M-D3)


title: Melanoma cell line MaMel126

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel126, derived from metastatic tumor


title: Melanoma cell line MaMel107

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel107, derived from metastatic tumor


title: Project-ST-H@_A4-3_(180vs000)_D2

source_name: Chicken Heterophils, non-treated (0M-D2)

source_name: Chicken Heterophils, treated with Salmonella for 180 min (180M-D2)


title: Melanoma cell line MaMel103anew

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel103anew, derived from metastatic tumor


title: L._mex_12h_rep1_2nd_scan

city: San Francisco

first: Sajeev

last: Batra

state: CA

institute: UCSF

hyb_protocol: Cy5 labeled sample was hybridized to the MEEBO array in 3x SSC at 63C overnight.

scan_protocol: MEEBO arrays were scanned with an Axon 4000B scanner (Axon Instruments, Union City, CA, USA) and gridded using SpotReader.

data_processing: Spot analysis was performed with Spotreader and stored in a relational database (Acuity). Data were ratio normalized, and control and poor-quality features (as determined by both visual examination and application of quantitative filters for saturation, feature diameter, and variance) were removed. Data were further filtered for spots that did not exhibit signal in any of the sample channels (based on the percentage of pixels in the feature above background and feature intensity) and for excessive missing data. The ratio of medians of the remaining data was transformed to log2 space, median centered by array, and median centered by gene.

organism: Mus musculus

source_name: Amplified RNA from bone marrow-derived macrophages

label_protocol: RNA extracted from the samples was amplified using Amino Allyl MessageAmp II aRNA kit from Ambion. The amplified material was then coupled to Cy5.

extract_protocol: Qiagen RNeasy Mini Kit

tag: strain

tag: age

value: 8 w

tag: cell type

value: bone marrow derived macrophages

source_name: pool of amplified RNA from each of the 4 timepoints of a given timecourse

label_protocol: RNA extracted from the samples was amplified using Amino Allyl MessageAmp II aRNA kit from Ambion . The amplified material was then coupled to Cy3.


title: L._mex_24h_rep1


title: Melanoma cell line MaMel114new

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel114new, derived from metastatic tumor


title: L._mex_12h_rep1


title: Melanoma cell line MaMel101

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel101, derived from metastatic tumor


title: Melanoma cell line MaMel94

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel94, derived from metastatic tumor


title: Melanoma cell line MaMel79b

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel79b, derived from metastatic tumor


title: Project-ST-H@_A3-3_(120vs000)_D2

source_name: Chicken Heterophils, treated with Salmonella for 120 min (120M-D2)

treatment_protocol: Heterophils (1×10^7) were treated with 300 µl Salmonella Typhimurium for 120 min at 39°C on a rotary shaker


title: L._mex_6h_rep1


title: Project-ST-H@_A3-4_(000vs120)_D4

source_name: Chicken Heterophils, treated with Salmonella for 120 min (120M-D4)


title: Project-ST-H@_A4-1_(180vs000)_D1

source_name: Chicken Heterophils, non-treated (0M-D1)

source_name: Chicken Heterophils, treated with Salmonella for 180 min (180M-D1)


title: Melanoma cell line MaMel73a

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel73a, derived from metastatic tumor


title: Melanoma cell line MaMel80anew

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel80anew, derived from metastatic tumor


title: Melanoma cell line MaMel69

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel69, derived from metastatic tumor


title: Melanoma cell line MaMel76

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel76, derived from metastatic tumor


title: Melanoma cell line MaMel95

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel95, derived from metastatic tumor


title: Melanoma cell line MaMel71new

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel71new, derived from metastatic tumor


title: Project-ST-H@_A3-2_(000vs120)_D3

source_name: Chicken Heterophils, treated with Salmonella for 120 min (120M-D3)

source_name: Chicken Heterophils, non-treated (0M-D3)


title: Melanoma cell line MaMel86a

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel86a, derived from metastatic tumor


title: Melanoma cell line MaMel99new

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel99new, derived from metastatic tumor


title: L._mex_2h_rep1_2nd_scan

source_name: Amplified RNA from bone marrow-derived macrophages

source_name: pool of amplified RNA from each of the 4 timepoints of a given timecourse


title: L._mex_2h_rep1


title: Project-ST-H@_A2-4_(000vs060)_D4

source_name: Chicken Heterophils, treated with Salmonella for 60 min (60M-D4)

label_protocol: A 350 ng of aliquot of total RNA was reverse transcribed into cDNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). The synthesized cDNA was transcribed into cRNA labeled with one of two cyanine-labeled nucleotides (Perkin Elmer, Wellesley, MA). Labeled cRNA was purified with RNeasy Mini columns (Qiagen, Valecia, CA). The quality of each cRNA sample was verified by total yield and specificity measured with ND-100 spectrophotometer (NanoDrop Technologies).

treatment_protocol: Heterophils (1×10^7) were treated with 300 µl Salmonella Typhimurium for 60 min at 39°C on a rotary shaker

source_name: Chicken Heterophils, non-treated (0M-D4)

extract_protocol: Heterophils were pelleted, and re-suspended in lysis buffer (Ribopure-Bacteria kit, Ambion Inc., Austin, TX), and frozen. The lysed cells were transferred to Ambion homogenizer columns filled with bead and vortex for 10 min at highest speed. Total RNA was extracted from the homogenized lysate according to the manufacturer’s instructions, eluted with 20 µl heated elution buffer and stored at -80°C.


title: Melanoma cell line MaMel85

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel85, derived from metastatic tumor


title: Melanoma cell line MaMel66a

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel66a, derived from metastatic tumor


title: Project-ST-H@_A2-3_(060vs000)_D2

source_name: Chicken Heterophils, non-treated (0M-D2)

source_name: Chicken Heterophils, treated with Salmonella for 60 min (60M-D2)


title: Control_0h_for_L._mex_rep1


title: Project-ST-H@_A3-1_(120vs000)_D1

source_name: Chicken Heterophils, non-treated (0M-D1)

source_name: Chicken Heterophils, treated with Salmonella for 120 min (120M-D1)


title: Melanoma cell line MaMel63a

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel63a, derived from metastatic tumor


title: Control_24h_rep1


title: Project-ST-H@_A2-2_(000vs060)_D3

source_name: Chicken Heterophils, treated with Salmonella for 60 min (60M-D3)


title: Control_12h_rep1


title: Melanoma cell line MaMel67

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel67, derived from metastatic tumor


title: Melanoma cell line MaMel57

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel57, derived from metastatic tumor


title: Control_6h_rep1


title: Melanoma cell line MaMel62

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel62, derived from metastatic tumor


title: Project-ST-H@_A2-1_(060vs000)_D1

source_name: Chicken Heterophils, treated with Salmonella for 60 min (60M-D1)


title: Melanoma cell line MaMel61a

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel61a, derived from metastatic tumor


title: Melanoma cell line MaMel60

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel60, derived from metastatic tumor


title: Melanoma cell line MaMel75

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel75, derived from metastatic tumor


title: Project-ST-H@_A1-4_(000vs030)_D4

source_name: Chicken Heterophils, treated with Salmonella for 30 min (30M-D4)

treatment_protocol: Heterophils (1×10^7) were treated with 300 µl Salmonella Typhimurium for 30 min at 39°C on a rotary shaker


title: Melanoma cell line MaMel40

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel40, derived from metastatic tumor


title: Melanoma cell line MaMel59a

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel59a, derived from metastatic tumor


title: Control_0h_for_Control_rep1

source_name: Amplified RNA from bone marrow-derived macrophages

source_name: pool of amplified RNA from each of the 4 timepoints of a given timecourse


title: Control_2h_rep1


title: Project-ST-H@_A1-2_(000vs030)_D3

source_name: Chicken Heterophils, treated with Salmonella for 30 min (30M-D3)

treatment_protocol: Heterophils (1×10^7) were treated with 300 µl Salmonella Typhimurium for 30 min at 39°C on a rotary shaker.

source_name: Chicken Heterophils, non-treated (0M-D3)


title: T._cruzi_24h_rep1


title: Project-ST-H@_A1-3_(030vs000)_D2

source_name: Chicken Heterophils, non-treated (0M-D2)

source_name: Chicken Heterophils, treated with Salmonella for 30 min (30M-D2)


title: Melanoma cell line MaMel58

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel58, derived from metastatic tumor


title: Project-ST-H@_A1-1_(030vs000)_D1

source_name: Chicken Heterophils, non-treated (0M-D1)

source_name: Chicken Heterophils, treated with Salmonella for 30 min (30M-D1)


title: T._cruzi_12h_rep1


title: Melanoma cell line MaMel51

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel51, derived from metastatic tumor


title: Melanoma cell line MaMel39a

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel39a, derived from metastatic tumor


title: T._cruzi_6h_rep1


title: Female human kidney sample No.93 tubulointerstitial fraction

city: Bronx

first: Han

last: Si

state: NY

address: 1300 Morris Park

department: Medicine/Nephrology

institute: AECOM

description: Gene expression data from diseased female tubuli

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG133A 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with ArrayAssist software using gcRMA as normalization method.

source_name: Human kidney sample No.93

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix Two-Cycle target preparation protocol from 10 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNA was prepared using RNAeasy mini columns (Qiagen, Valencia, CA) according to manufacturer’s instruction. RNA quality and quantity was determined using Lab-on-Chip Total RNA PicoKit, Agilent BioAnalyzer. Only samples without evidence of degradation were further used.

treatment_protocol: Kidney tissue was obtained in the operating room immediately after removal from the patient. Tissue was placed into RNALater right after removal from the body and was kept at 4C. 1mmx1mm biopsy tissues were placed under Olympus model SZX12 stereomicroscope using 90 x magnification. The biopsy tissue was manually microdissected at 4C in RNALater for glomerular and tubular compartment using 2 fine tip (1mm) forceps. Dissected tissue was homogenized using Powergen125 (Fisher) homogenizer and stored at -80C.

tag: Diseased tubulointerstitium

tag: Female


title: Melanoma cell line MaMel45a

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel45a, derived from metastatic tumor


title: MB282 LB 4-15-09C technical rep 1

type: mixed

city: Albany

first: Marc

middle: Yi Ming

last: Rehfuss

address: 800 Buchanan St

department: Produce Safety and Microbiology

institute: USDA

description:
Whole genome S. enterica LT2 arrays were prepared at the USDA Western Regional Research Center. Each array contained 4360 PCR-generated ORFs (including 104 from virulence plasmid pSLT).
Reference 1: Eriksson S, Lucchini S, Thompson A, Rhen M, Hinton JC. (2003) Unravelling the biology of macrophage infection by gene expression profiling of intracellular Salmonella enterica. Mol Microbio. 47:103-18.
Reference 2: Kyle JL, Parker CT, Goudeau D, Brandl MT. (2010). Transcriptome Analysis of Escherichia coli 0157:H7 exposed to lysates of lettuce leaves. Appl Environ Microbiol 76:1375-1387.

hyb_protocol: DNA was crossed–linked to slides by UV radiation. All cDNA solutions were adjusted to the same label concentration and were hybridized to the arrays overnight at 42ºC. For each experimental condition, cDNA was prepared from three replicate suspensions (biological replicates) and each cDNA was hybridized to three replicate arrays (technical replicates) at random among several slides.

scan_protocol: Slides were washed and then scanned with a Genepix 4000b scanner and Genepix Pro 4.1 software (Axon Instruments).

data_processing: To address spatial dye effects or any disparity in amounts of spotted cDNA, data were normalized by setting the median log (Cy3/Cy5 ratio) of all of the spots on the same array to zero. Prior to analysis by Genespring, outliers among technical replicates were eliminated from the analysis with Dixon’s Q Test (critical value of 0.1) and remaining data were averaged.

organism: Salmonella enterica

source_name: MB282 grown to mid-log phase in LB broth at 28 deg C 4-15-09C

label_protocol: Preparation of labeled nucleotides and hybridization to arrays was carried out as described previously (Kyle et al., 2010) based on the method developed by Eriksson et al. (2003). Briefly, 20µg RNA from co-cultures and controls was reverse transcribed and Cy3-dCTP (GE Healthcare) incorporated into cDNA using the Fairplay III Microarray Labeling Kit (Stratagene). 2 µg of SL1344 genomic DNA was labeled with Cy5-dCTP (GE Healthcare) using Klenow (New England Biolabs) and served as the reference signal on the arrays. Labeling efficiency was determined with a Nanodrop 2000 Spectrophotometer (Thermo Scientific).

extract_protocol: Eight co-cultures of 50 mL were centrifuged at 800 x g for 2 min. The resulting pellet was enriched for Tetrahymena cells containing ingested SL1344 since most uningested free bacteria were not pelleted and remained in suspension. The supernatant was quickly removed and the pellet was resuspended in ice cold lysis buffer (0.5% SDS, 19% ethanol and 1% phenol in H2O). The suspension containing lysed Tetrahymena was centrifuged at 3200 x g for 5 min at 4 ºC. The bacterial pellet was then stored at -80ºC until RNA extraction. RNA extraction was performed with the Promega SV Total RNA Isolation kit per the manufacturer’s specifications, except that bacterial pellets were first treated with 50 mg/mL of lysozyme (Fisherbrand). RNA from two different sources was used as control. The first control RNA was isolated from 50 mL of SL1344 cells incubated in sterile H2O at an OD600 of 0.2 for 3 h, similarly to the SL1344 cells mixed with Tetrahymena. The second control RNA was isolated from 20 mL of SL1344 cells grown to mid–log phase of growth in LB broth. Both suspensions were centrifuged at 3200 x g for 5 min. at 4 ºC followed by addition of lysis buffer and centrifugation as described above. Bacterial pellets were immediately stored at -80ºC. Three biological replicates were used for each type of suspension. RNA integrity was assessed with the Agilent 2100 Bioanalyzer, and only RNA of high quality was used for microarray hybridizations and RT-qPCR.

tag: subspecies

value: Typhimurium MB282

tag: culture condition

value: MB282 was grown in LB to an OD of 0.4 - 0.6, this served as a control

source_name: MB282 genomic DNA

extract_protocol: 3 mL of Salmonella enterica SL1344 (MB282) was grown overnight in LB broth to stationary phase.  The culture was centrifuged at 11400 x G for 3 minutes in a bench top microcentrifuge. After removing the supernatant, Promega Wizard® Genomic DNA Purification Kit was used to extract DNA from the cell pellet using the manufacturer's protocol.  DNA quality was assessed using the Nanodrop® ND-1000 Spectrophotometer.

tag: reference

value: genomic DNA served as reference signal


title: Melanoma cell line MaMel36new

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel36new, derived from metastatic tumor


title: Melanoma cell line MaMel35

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel35, derived from metastatic tumor


title: T._cruzi_2h_rep1

source_name: Amplified RNA from bone marrow-derived macrophages


title: Melanoma cell line MaMel37a

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel37a, derived from metastatic tumor


title: MB282 LB 4-15-09C technical rep 2


title: MB282 LB 4-15-09B technical rep 2

source_name: MB282 grown to mid-log phase in LB broth at 28 deg C 4-15-09B


title: Control_0h_for_T._cruzi_rep1

source_name: pool of amplified RNA from each of the 4 timepoints of a given timecourse


title: Melanoma cell line MaMel27new

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel27new, derived from metastatic tumor


title: Melanoma cell line MaMel30new

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel30new, derived from metastatic tumor


title: Melanoma cell line MaMel32new

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel32new, derived from metastatic tumor


title: Female human kidney sample No.80 tubulointerstitial fraction

source_name: Human kidney sample No.80


title: Melanoma cell line MaMel19

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel19, derived from metastatic tumor


title: Female human kidney sample No.72 tubulointerstitial fraction

source_name: Human kidney sample No.72


title: Melanoma cell line MaMel26anew

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel26anew, derived from metastatic tumor


title: Female human kidney sample No.88 tubulointerstitial fraction

source_name: Human kidney sample No.88


title: Female human kidney sample No.78 tubulointerstitial fraction

source_name: Human kidney sample No.78


title: MB282 LB 4-15-09B technical rep 1


title: MB282 LB 4-15-09A technical rep 2

source_name: MB282 grown to mid-log phase in LB broth at 28 deg C 4-15-09A


title: Female human kidney sample No.74 tubulointerstitial fraction

source_name: Human kidney sample No.74


title: Melanoma cell line MaMel38

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel38, derived from metastatic tumor


title: Melanoma cell line MaMel17new

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel17new, derived from metastatic tumor


title: Female human kidney sample No.62 tubulointerstitial fraction

source_name: Human kidney sample No.62


title: Female human kidney sample No.70 tubulointerstitial fraction

source_name: Human kidney sample No.70


title: IL4_24h_TM

source_name: Amplified RNA from bone marrow-derived macrophages


title: MB282 LB 4-15-09A technical rep 1

source_name: MB282 genomic DNA


title: IL4_12h_TM

source_name: pool of amplified RNA from each of the 4 timepoints of a given timecourse


title: MB282 LB 2-19-09 technical rep 2

source_name: MB282 grown to mid-log phase in LB broth at 28 deg C 2-19-09


title: Female human kidney sample No.59 tubulointerstitial fraction

source_name: Human kidney sample No.59


title: Melanoma cell line MaMel23

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel23, derived from metastatic tumor


title: Melanoma cell line MaMel53

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel53, derived from metastatic tumor


title: Female human kidney sample No.45 tubulointerstitial fraction

source_name: Human kidney sample No.45


title: IL4_6h_TM


title: Melanoma cell line MaMel21

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel21, derived from metastatic tumor


title: Female human kidney sample No.48 tubulointerstitial fraction

source_name: Human kidney sample No.48


title: Melanoma cell line MaMel13

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel13, derived from metastatic tumor


title: Melanoma cell line MaMel12new

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel12new, derived from metastatic tumor


title: MB282 LB 2-19-09 technical rep 1


title: IL4_2h_TM


title: Melanoma cell line MaMel11

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel11, derived from metastatic tumor


title: Female human kidney sample No.44 tubulointerstitial fraction

source_name: Human kidney sample No.44


title: MB282 H2O 4-9-09E technical rep 2

source_name: MB282 incubated in H2O for 3 hours at 28 deg C 4-9-09E

value: MB282 was incubated axenically in H2O, this served as a control


title: Female human kidney sample No.36 tubulointerstitial fraction

source_name: Human kidney sample No.36


title: Melanoma cell line MaMel10

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel10, derived from metastatic tumor


title: IFNG_24h_TM

source_name: Amplified RNA from bone marrow-derived macrophages


title: IFNG_12h_TM


title: MB282 H2O 4-9-09E technical rep 1

source_name: MB282 genomic DNA


title: Male human kidney sample No.94 tubulointerstitial fraction

description: Gene expression data from diseased male tubuli

source_name: Human kidney sample No.94

tag: Male


title: MB282 H2O 4-9-09D technical rep 2

source_name: MB282 incubated in H2O for 3 hours at 28 deg C 4-9-09D


title: MB282 H2O 4-9-09C technical rep 2

source_name: MB282 incubated in H2O for 3 hours at 28 deg C 4-9-09C


title: Male human kidney sample No.51 tubulointerstitial fraction

source_name: Human kidney sample No.51


title: Male human kidney sample No.92 tubulointerstitial fraction

source_name: Human kidney sample No.92


title: MB282 H2O 4-9-09C techical rep 1


title: Male human kidney sample No.95 tubulointerstitial fraction

source_name: Human kidney sample No.95


title: Melanoma cell line MaMel08a

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel08a, derived from metastatic tumor


title: TNF_24h_TM

source_name: pool of amplified RNA from each of the 4 timepoints of a given timecourse


title: Melanoma cell line MaMel05

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel05, derived from metastatic tumor


title: Female human kidney sample No.43 tubulointerstitial fraction

source_name: Human kidney sample No.43


title: Male human kidney sample No.58 tubulointerstitial fraction

source_name: Human kidney sample No.58


title: Melanoma cell line MaMel02

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel02, derived from metastatic tumor


title: Male human kidney sample No.67 tubulointerstitial fraction

source_name: Human kidney sample No.67


title: Male human kidney sample No.56 tubulointerstitial fraction

source_name: Human kidney sample No.56


title: Male human kidney sample No.34 tubulointerstitial fraction

source_name: Human kidney sample No.34


title: IFNG_6h_TM

source_name: Amplified RNA from bone marrow-derived macrophages


title: TNF_12h_TM


title: Melanoma cell line MaMel06

description: Hybridized to 250K_StyI

source_name: Melanoma cell line MaMel06, derived from metastatic tumor


title: IFNG_2h_TM


title: Female human kidney sample No.98 tubulointerstitial fraction

description: Gene expression data from healthy female tubuli

source_name: Human kidney sample No.98

tag: Healthy tubulointerstitium


title: MB282 H2O 4-9-09B technical rep 2

source_name: MB282 incubated in H2O for 3 hours at 28 deg C 4-9-09B

source_name: MB282 genomic DNA


title: Female human kidney sample No.82 tubulointerstitial fraction

source_name: Human kidney sample No.82


title: TNF_6h_TM


title: Control_24h_TM


title: Female human kidney sample No.39 tubulointerstitial fraction

source_name: Human kidney sample No.39


title: Female human kidney sample No.17 tubulointerstitial fraction

source_name: Human kidney sample No.17


title: Male human kidney sample No.81 tubulointerstitial fraction

description: Gene expression data from healthy male tubuli

source_name: Human kidney sample No.81


title: Male human kidney sample No.79 tubulointerstitial fraction

source_name: Human kidney sample No.79


title: MB282 H2O 4-9-09A technical rep 2

source_name: MB282 incubated in H2O for 3 hours at 28 deg C 4-9-09A


title: MB282 H2O 4-9-09A technical rep 1


title: Female human kidney sample No.76 tubulointerstitial fraction

source_name: Human kidney sample No.76


title: Female human kidney sample No.53 tubulointerstitial fraction

source_name: Human kidney sample No.53


title: Male human kidney sample No.50 tubulointerstitial fraction

source_name: Human kidney sample No.50


title: MB282 H2O 4-9-09B technical rep 1


title: Control_12h_TM

source_name: pool of amplified RNA from each of the 4 timepoints of a given timecourse


title: Male human kidney sample No.64 tubulointerstitial fraction

source_name: Human kidney sample No.64


title: TNF_2h_TM


title: MB282 + Tet 2-20-09B technical rep 1

source_name: MB282 co cultured with Tetrahymena in H2O for 3 hours at 28 deg C 2-20-09B

value: MB282 was bound within the Tetrahymena food vacuole (phagosome)


title: MB282 + Tet 2-20-09B technical rep 2


title: Male human kidney sample No.37 tubulointerstitial fraction

source_name: Human kidney sample No.37


title: MB282 + Tet 2-20-09B technical rep 3


title: Control_6h_TM

source_name: Amplified RNA from bone marrow-derived macrophages


title: Male human kidney sample No.77 tubulointerstitial fraction

source_name: Human kidney sample No.77


title: Male human kidney sample No.31 tubulointerstitial fraction

source_name: Human kidney sample No.31


title: Control_2h_TM


title: Female human kidney sample No.98 glomeruli fraction

description: Gene expression data from healthy female glomeruli

source_name: Human kidney sample No.98

tag: Healthy glomeruli


title: MB282 + Tet 2-20-09A technical rep 3

source_name: MB282 co cultured with Tetrahymena in H2O for 3 hours at 28 deg C 2-20-09A

source_name: MB282 genomic DNA


title: Female human kidney sample No.82 glomeruli fraction

source_name: Human kidney sample No.82


title: Female human kidney sample No.83 glomeruli fraction

source_name: Human kidney sample No.83


title: MB282 + Tet 2-20-09A technical rep 2


title: Female human kidney sample No.53 glomeruli fraction


title: L._mex_6h_TM


title: Female human kidney sample No.33 glomeruli fraction

source_name: Human kidney sample No.33


title: L._mex_24h_TM


title: MB282 + Tet 1-29-09 technical rep 3

source_name: MB282 co cultured with Tetrahymena in H2O for 3 hours at 28 deg C 1-29-09


title: Male human kidney sample No.107 glomeruli fraction

description: Gene expression data from healthy male glomeruli

source_name: Human kidney sample No.107


title: MB282 + Tet 1-29-09 technical rep 2


title: Female human kidney sample No.118 glomeruli fraction

source_name: Human kidney sample No.118


title: L._mex_2h_TM


title: L._mex_12h_TM


title: MB282 + Tet 2-20-09A technical rep 1


title: SVZ tissue 4dpl lysolecithin injection

city: Washington

first: Vittorio

last: Gallo

state: DC

address: 111 Michigan Av. NW

department: Center for Neuroscience

institute: CNMC

description: 1ug of cRNA was use to perform the hibridization of spotted cDNA fragments encoding 113 mouse genes for neurotrophic signaling molecules involved in neuronal growth and differentiation, as well as regeneration and survival OMM-031 array.

hyb_protocol: 1ug of cRNA was used for hybridization with the Genearray. Incubation was performed for 12hrs at 60C shaking at 500rpm.

scan_protocol: The arrays were exposed at different time points starting for 1 min and maximum of 10 min to have the largest possible dynamic range for the individual signals and images acquire using x-ray film.  X-ray film were scanned and save as TIFF file format.

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities and ratios lysolecithin vs. NaCl were calculated after values were normalized for each gene. The normalized value for each gene was calculated by dividing the value of each gene by the average value of the housekeeping genes GAPDH, Ppia, and β-actin.

label: Biotin UTP

source_name: Adult mouse lysolecithin injection

growth_protocol: RNA was isolated from 300um fresh brain sections at the level of the SVZ and SVZ was microdissected and used for RNA extraction using Trizol (Invitrogen).

extract_protocol: 1ug of total RNA was reverse-transcribed using oligo-dT primers (Superarray) and reverse transcriptase (Superarray) to perform cDNA. Then cRNA synthesis was performed using the total cDNA reaction in the presence of 10 mM of Biotinylated-UTP (Perlin Elmer) and RNA polymerase according to the instructions for the Gene

treatment_protocol: 1ug of total RNA

value: brain subventricular zone (SVZ)

tag: stage

value: Post natal day 60


title: Female human kidney sample No.21 glomeruli fraction

source_name: Human kidney sample No.21


title: Control_0h_TM_2

source_name: pool of amplified RNA from each of the 4 timepoints of a given timecourse


title: Female human kidney sample No.76 glomeruli fraction

source_name: Human kidney sample No.76


title: Control_0h_TM_1


title: Female human kidney sample No.39 glomeruli fraction

source_name: Human kidney sample No.39


title: MB282 + Tet 1-29-09 technical rep 1


title: Male human kidney sample No.50 glomeruli fraction

source_name: Human kidney sample No.50


title: Male human kidney sample No.81 glomeruli fraction

source_name: Human kidney sample No.81


title: Male human kidney sample No.79 glomeruli fraction

source_name: Human kidney sample No.79


title: SVZ tissue 4dpl NaCl injection

source_name: Adult mouse saline injection

label_protocol: cRNA synthesis was performed using the total cDNA reaction in the presence of 10 mM of Biotinylated-UTP (Perlin Elmer) and RNA polymerase according to the instructions for the Gene


title: MB282 H2O 4-9-09D technical rep 1

source_name: MB282 incubated in H2O for 3 hours at 28 deg C 4-9-09D


title: Male human kidney sample No.37 glomeruli fraction

source_name: Human kidney sample No.37


title: Male human kidney sample No.65 tubulointerstitial fraction

source_name: Human kidney sample No.65


title: Airway-CurrentSmoker-532

status: Public on Apr 12 2010

city: Boston

first: Adam

last: Gustafson

state: MA

address: 44 Cummington St

institute: Boston University

description: transcript-level data

hyb_protocol: Affymetrix Suggested Protocol

scan_protocol: Affymetrix Suggested Protocol

data_processing: RMA-Sketch normalized using Affymetrix Expression Console

label: Biotin

source_name: Bronchial Epithelium

label_protocol: Affymetrix Suggested Protocol

extract_protocol: Affymetrix Suggested Protocol

tag: pyers


title: Airway-dysplasia-after-3473

description: transcript-level data

tag: Myo-inositol treatment

value: Partial Response; Post-treatment measurement; pyers:30; age: 45-50; Current Smoker


title: Airway-CurrentSmoker-534

description: transcript-level data


title: Airway-dysplasia-before-3524

description: transcript-level data

value: Complete Response; Baseline Measurement; pyers:108; age: 65-69; Former Smoker


title: Airway-CurrentSmoker-539

description: transcript-level data


title: Airway-CurrentSmoker-530

description: transcript-level data


title: Airway-CurrentSmoker-462

description: transcript-level data


title: Airway-CurrentSmoker-459-1

description: transcript-level data


title: Airway-dysplasia-before-3472

description: transcript-level data

value: Progressive Disease; Baseline Measurement; pyers:35; age: 70-74; Former Smoker


title: Male human kidney sample No.110 glomeruli fraction

source_name: Human kidney sample No.110


title: Airway-CurrentSmoker-524

description: transcript-level data


title: Airway-CurrentSmoker-546

description: transcript-level data


title: Airway-dysplasia-after-3472

description: transcript-level data

value: Progressive Disease; Post-treatment measurement; pyers:35; age: 70-75; Former Smoker


title: Airway-CurrentSmoker-528

description: transcript-level data


title: Airway-CurrentSmoker-533

description: transcript-level data


title: Airway-dysplasia-before-3473

description: transcript-level data

value: Partial Response; Baseline Measurement; pyers:30; age: 45-49; Current Smoker


title: Airway-CurrentSmoker-526

description: transcript-level data


title: Airway-dysplasia-after-3433

description: transcript-level data

value: Complete Response; Post-treatment measurement; pyers:30; age: 50-54; Former Smoker


title: Airway-dysplasia-after-3434

description: transcript-level data

value: Complete Response; Post-treatment measurement; pyers:50.6; age: 60-65; Current Smoker


title: Airway-dysplasia-after-3382

description: transcript-level data

value: Complete Response; Post-treatment measurement; pyers:32.5; age: 55-60; Former Smoker


title: Airway-dysplasia-after-3344

description: transcript-level data

value: Complete Response; Post-treatment measurement; pyers:35.5; age: 65-70; Former Smoker


title: Airway-dysplasia-before-3434

description: transcript-level data

value: Complete Response; Baseline Measurement; pyers:50.6; age: 60-64; Current Smoker


title: Airway-dysplasia-before-3382

description: transcript-level data

value: Complete Response; Baseline Measurement; pyers:32.5; age: 55-59; Former Smoker


title: Airway-dysplasia-before-3344

description: transcript-level data

value: Complete Response; Baseline Measurement; pyers:35.5; age: 65-69; Former Smoker


title: Male human kidney sample No.77 glomeruli fraction

source_name: Human kidney sample No.77


title: Airway-dysplasia-before-3433

description: transcript-level data

value: Complete Response; Baseline Measurement; pyers:30; age: 50-54; Former Smoker


title: Airway-dysplasia-after-3321

description: transcript-level data

value: Progressive Disease; Post-treatment measurement; pyers:36.8; age: 70-75; Current Smoker


title: Airway-dysplasia-before-3321

description: transcript-level data

value: Progressive Disease; Baseline Measurement; pyers: 36.8; age: 70-74; Current Smoker


title: Airway-dysplasia-2079

description: transcript-level data

value: 52; age:70-74; Current Smoker


title: Airway-dysplasia-before-3304

description: transcript-level data

value: Unknown Response; Baseline Measurement; pyers:40; age: 55-59; Former Smoker


title: Airway-dysplasia-after-3301

description: transcript-level data

value: Complete Response; Post-treatment measurement; pyers:30.8; age: 55-60; Former Smoker


title: Airway-dysplasia-1197

description: transcript-level data

value: 90; age:50-54; Current Smoker


title: Airway-dysplasia-872

description: transcript-level data

value: 57; age:65-69; Current Smoker


title: Airway-dysplasia-1231

description: transcript-level data

value: 39; age:55-59; Current Smoker


title: Airway-dysplasia-before-3301

description: transcript-level data

value: Complete Response; Baseline Measurement; pyers:30.8; age: 55-59; Former Smoker


title: Airway-dysplasia-1761

description: transcript-level data

value: 69; age:60-64; Current Smoker


title: Airway-dysplasia-after-3304

description: transcript-level data

value: Unknown Response; Post-treatment measurement; pyers:40; age: 55-59; Former Smoker


title: SS_D7C

city: New York

first: Stuart

middle: M

last: Chambers

address: 1270 York Ave

institute: Sloan-Kettering Institute

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Array data from BeadStudio was processed using a variance stabilizing transformation and quantile normalization with the LUMI package for Bioconductor in R.

source_name: H9 human embryonic stem cells

label_protocol: Standard Illumina protocol

extract_protocol: Cells were lysed in Trizol LS and standard protocol was used for RNA extraction

tag: agent

value: Noggin + SB431542 +C25II

tag: time point


title: D7A

value: Noggin + SB431542


title: SS_D11C


title: D11B


title: SS_D7A


title: D11A


title: D5B


title: D11C


title: D7C


title: SS_D11A


title: SS_D11B


title: SS_D5B


title: SS_D3C


title: SS_D5A


title: D7B


title: D5A


title: SS_D3A


title: D3C


title: SS_D3B


title: SS_D5C


title: D3B


title: D3A


title: D2C


title: D2B


title: Airway-dysplasia-1842

description: transcript-level data


title: D2A


title: D1B

value: Not applicable


title: Airway-dysplasia-after-3524

description: transcript-level data

value: Complete Response; Post-treatment measurement; pyers:108; age:65-70; Former Smoker


title: Airway-FormerSmoker-LungCancer-SampleBT17

data_processing: MAS5.0 normalized in Affymetrix expression console

tag: Former Smoker; 58 pyers; quit 360 months ago; 70-74 years old


title: Airway-FormerSmoker-NoLungCancer-SampleBT18

tag: Former Smoker; 15 pyers; quit 240 months ago; 45-49 years old


title: Dex AM rep4

city: Indianapolis

first: Chao-Hung

last: Lee

state: IN

address: 1120 South Dr., FH 419

department: Pathology & Lab Medicine

institute: Indiana University

description: gene expression data of alveolar macrophages from dexamethasone-treated rats

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on GeneChip RG-U34A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

organism: Rattus norvegicus

source_name: Alveolar macrophages from dexamethasone-treated rats

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Female Sprague-Dawley rats (Harlan, Indianapolis, IN) of 120-140 g were used.

extract_protocol: Total RNA was isolated from each sample using the RNeasy kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Sprague-Dawley rats were immunosuppressed by giving dexamethasone (1.8 mg/liter) continuously in drinking water for one week and then transtracheally inoculated with 7.5 million P. carinii organisms. Eight weeks after P. carinii infection with continual immunosuppression, alveolar macrophages were isolated. Age-matched normal and dexamethasone-treated rats were used as controls.

value: alveolar macrophage


title: Pc AM rep1

description: gene expression data of alveolar macrophages from Pneumocystis carinii-infected rats

source_name: Alveolar macrophages from Pneumocystis carinii-infected rats


title: Airway-FormerSmoker-NoLungCancer-SampleBT16

tag: Former Smoker; 21 pyers; Quit 1 month ago; 50-54 years old


title: Pc AM rep3

tag: cell type


title: Dex AM rep3


title: Pc AM rep2


title: Airway-CurrentSmoker-LungCancer-SampleBT5

tag: Current Smoker; 20 pyers; 60-64 years old


title: Dex AM rep1


title: D1A


title: Dex AM rep2


title: LLAT 8

city: Stanford

first: Ash

middle: A

last: Alizadeh

address: 269 Campus Drive, CCSR 1145c

department: Medicine, Divisions of Hematology and of Oncology

institute: Stanford University School of Medicine

description:
Simple annotation: T-cell, human tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40714.gif

hyb_protocol: not provided

scan_protocol: Scanner Model: GenePix 4000B

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

source_name: Stratagene common human reference

label_protocol: not provided

extract_protocol: not provided

value: Stratagene common human reference

source_name: LLAT 8

tag: cell line

value: Jurkat

tag: treatment

value: no treatment


title: Normal AM rep4

description: gene expression data of alveolar macrophages from normal rats

source_name: Alveolar macrophages from normal rats


title: Normal AM rep3


title: LLAT 5A

description:
Simple annotation: T-cell, human tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40656.gif

source_name: LLAT 5A

tag: individual


title: Pc AM rep4


title: D5C


title: LLAT 3A

description:
Simple annotation: T-cell, human tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40153.gif

tag: reference

source_name: LLAT 3A


title: D1C


title: Normal AM rep1


title: LLAT 1A

description:
Simple annotation: T-cell, human tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/40060.gif

source_name: LLAT 1A


title: LLAT 7B

description:
Simple annotation: T-cell, human tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40711.gif

source_name: LLAT 7B

value: IFNa/AZT


title: LLAT 4B

description:
Simple annotation: T-cell, human tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40152.gif

source_name: LLAT 4B


title: LLAT 11

description:
Simple annotation: T-cell, human tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40156.gif

source_name: LLAT 11


title: LLAT 4A

description:
Simple annotation: T-cell, human tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/40073.gif

source_name: LLAT 4A


title: Normal AM rep2


title: Airway-COPD-CurrentSmoker-NoLungCancer-SampleXXX

data_processing: RMA normalized using Affymetrix Expression Console

tag: Current Smoker; 74 pyers; 60-64 years old


status: Public on Apr 11 2010

city: Singapore

first: Majid

last: Eshaghi

state: Singapore

address: Biopolis

department: Bilogical Investigation

country: Singapore

institute: Genome Institute of Singapore

description: hybridization of tra1-1 strain and wild-type fission yeast second repeats

hyb_protocol: Samples were mixed with DIG Easy Hyb buffer (Roche) and Herring Sperm DNA (Invitrogen) before applying to MAUI mixer-slide assembly.  The slides were hybridized overnight for 16 hours at 42 degree centigrade under MAUI system (BioMicro). Hybridized slides were washed consecutively in 2¡Á SSC/0.1% SDS for 1 min, 1¡Á SSC for 4 min, 0.2¡Á SSC for 4 min, and 0.05¡Á SSC for 1 min, and then spin-dried before scanning.

data_processing: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.  After background correction and removal of flagged values, features with low intensity (F/B<2 at either 635 or 532 channel) were removed.  Meidans of log base 2 expression ratios were given in the data table.

organism: Schizosaccharomyces pombe

source_name: Fission yeast cells from tra1-1 mutant

label_protocol: Approximately 30 ug of total RNA was used to synthesize cDNA coupled with aa-dUTP by reverse transcriptase. Approximately 1.5 ug of cDNA was coupled with Cy5 fluorescence dye and purified through a Microcon YM-30. Cy5- and Cy3-labeled cDNA were pooled and hybridized to the spotted S. pombe oligonucleotide (oligo)-based DNA microarrays

growth_protocol: Yeast cells were cultured at 30 degree centigrade

extract_protocol: cDNA of the tra1-1 strain generated from total RNA as describled in materials and metholds

tag: cDNA from Schizosaccharomyces pombe tra1-1 strain

source_name: cDNA from WT

label_protocol: Approximately 30 ug of total RNA was used to synthesize cDNA coupled with aa-dUTP by reverse transcriptase. Approximately 1.5 ug of cDNA was coupled with Cy3 fluorescence dye and purified through a Microcon YM-30. Cy5- and Cy3-labeled cDNA were pooled and hybridized to the spotted S. pombe oligonucleotide (oligo)-based DNA microarrays

extract_protocol: total RNA of the WT cells were extracted as describled in materials and metholds

tag: Reference total RNA of the WT


description: hybridization of tra1-1 strain and wild-type fission yeast first repeat

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.


title: Reactive Thrombocytosis Patient platelets THR519

city: Stony Brook

first: Wadie

last: Bahou

department: Hematology

institute: Stony Brook University

hyb_protocol: Hybridization essentially follows that from Pronto! Universal Hybridization Kit (Corning, Corning, NY)

scan_protocol: Scanned using GenePix 4000B (Mol Devices, Sunnyvale, CA). Images were quantified using GenePix Pro Software (ver 6.0)

data_processing: background subtraction data, processed red signal/processed green signal, normalized by positive control genes, normalized by the median of genes across all chips

source_name: Reactive Thrombocytosis  platelets

label_protocol: 20 ng purified platelet or human reference(Stratagene) RNA, spiked with Arabidopsis RNA (internal standard); chimeric DNA/RNA amplification and labeling using Ovation Aminoallyl System (NuGen Technologies, San Carlos, CA); Labeled with Cy3 (human ref RNA) or Cy5 (patient test RNA)

growth_protocol: human platelets purified from 20ml peripheral whole blood

extract_protocol: isolated gel-filtered platelets, platelet RNA extracted using Trizol as described in Gnatenko et al, Blood 2003;3,2,133-144

treatment_protocol: IRB approved protocol at Stony Brook University Medical Center: no treatment of patient/samples; normal healthy adults versus ET, essential thrombocythemia, versus RT, reactive thrombocythemia

source_name: human reference (Stratagene) RNA

tag: human reference (Stratagene) RNA


title: Airway-NoCOPD-CurrentSmoker-NoLungCancer-Sample327

source_name: Bronchial Epithelium

tag: Current Smoker; 88 pyers; 50-54 years old


title: Wild-type fission yeast first repeat

description: Self-self hybridization of Independent sample of wild-type first repeat

source_name: Wild-type fission yeast cells

extract_protocol: cDNA of the WT generated from total RNA as describled in materials and metholds

tag: cDNA from Schizosaccharomyces pombe wild type (WT)


title: Reactive Thrombocytosis Patient platelets THR520


title: Wild-type fission yeast second repeat

description: Self-self hybridization of Independent sample of wild-type second repeats


title: Essential thrombocythemia Patient Platelet THR123

source_name: Essential thrombocythemia  Platelet


title: LLAT 2A

description:
Simple annotation: T-cell, human tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/40070.gif

source_name: Stratagene common human reference

source_name: LLAT 2A


title: LLAT 3B

description:
Simple annotation: T-cell, human tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/40072.gif

source_name: LLAT 3B


title: LLAT 6A

description:
Simple annotation: T-cell, human tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40696.gif

source_name: LLAT 6A


title: Airway-COPD-CurrentSmoker-NoLungCancer-Sample80

tag: Current Smoker; 25 pyers; 40-44 years old


title: Reactive Thrombocytosis Patient platelets THR511


title: Reactive Thrombocytosis Patient platelets THR515


title: Reactive Thrombocytosis Patient platelets THR517


title: Reactive Thrombocytosis Patient platelets THR514


title: Reactive Thrombocytosis Patient platelets THR512


title: LLAT 6B

description:
Simple annotation: T-cell, human tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40713.gif

source_name: LLAT 6B


title: Reactive Thrombocytosis Patient platelets THR510


title: Reactive Thrombocytosis Patient platelets THR516


title: Reactive Thrombocytosis Patient platelets THR507


title: Reactive Thrombocytosis Patient platelets THR508


title: LLAT 10

description:
Simple annotation: T-cell, human tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40724.gif

source_name: LLAT 10


title: Reactive Thrombocytosis Patient platelets THR506


title: Essential thrombocythemia Patient Platelet THR122


title: LLAT 5B

description:
Simple annotation: T-cell, human tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40695.gif

source_name: LLAT 5B


title: Reactive Thrombocytosis Patient platelets THR509


title: LLAT 7A

description:
Simple annotation: T-cell, human tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40712.gif

source_name: LLAT 7A


title: Essential thrombocythemia Patient Platelet THR121


title: Reactive Thrombocytosis Patient platelets THR505


title: Reactive Thrombocytosis Patient platelets THR503


title: LLAT 1B

description:
Simple annotation: T-cell, human tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/40063.gif

source_name: LLAT 1B


title: Reactive Thrombocytosis Patient platelets THR502


title: Reactive Thrombocytosis Patient platelets THR500


title: Reactive Thrombocytosis Patient platelets THR513


title: Reactive Thrombocytosis Patient platelets THR501


title: Reactive Thrombocytosis Patient platelets THR504


title: Normal Patient Platelets N053

source_name: Normal  Platelets

tag: Normal Patient Platelets


title: LLAT 2B

description:
Simple annotation: T-cell, human tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/40071.gif

source_name: LLAT 2B


description: hybridization of tra1-1 strain and wild-type fission yeast third repeats

source_name: Fission yeast cells from tra1-1 mutant

source_name: cDNA from WT


title: Normal Patient Platelets N052

source_name: human reference (Stratagene) RNA


title: Normal Patient Platelets N050


title: Normal Patient Platelets N049


title: Normal Patient Platelets N047


title: Normal Patient Platelets N051


title: Normal Patient Platelets N045


title: Normal Patient Platelets N046


title: Normal Patient Platelets N044


title: Normal Patient Platelets N048


title: Reactive Thrombocytosis Patient platelets THR518

source_name: Reactive Thrombocytosis  platelets


title: Normal Patient Platelets N043


title: Normal Patient Platelets N038


title: Normal Patient Platelets N037


title: Normal Patient Platelets N039


title: Normal Patient Platelets N035


title: Normal Patient Platelets N034


title: Normal Patient Platelets N036


title: Normal Patient Platelets N040


title: Normal Patient Platelets N032


title: Normal Patient Platelets N031


title: PBMC 23 SFA 6 h after intake

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the "Genechip Expression Analysis Technical Manual", section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described n the "Genechip Expression Analysis Technical Manual", section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated using RMA

source_name: Peripheral blood mononuclear cells, SFA shake, 6 hours after intake, individual 23

label_protocol: TThe Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.

extract_protocol: PBMCs were lysed in Qiagen RLT buffer and homogenized using seringes with 0.4 mm needles, whereafter purified total RNA was isolated using Qiagen RNEasy columns

treatment_protocol: Subjects were given a shake containing either SFA or PUFA as the fatty acid source as a single challange consumption

tag: Male, 18-27 years of age


title: Normal Patient Platelets N030


title: LLAT 9

description:
Simple annotation: T-cell, human tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40723.gif

source_name: LLAT 9


title: PBMC 20 SFA 6 h after intake

source_name: Peripheral blood mononuclear cells, SFA shake, 6 hours after intake, individual 20


title: PBMC 25 SFA 6 h after intake

source_name: Peripheral blood mononuclear cells, SFA shake, 6 hours after intake, individual 25


title: PBMC 27 SFA 6 h after intake

source_name: Peripheral blood mononuclear cells, SFA shake, 6 hours after intake, individual 27


title: PBMC 21 SFA 6 h after intake

source_name: Peripheral blood mononuclear cells, SFA shake, 6 hours after intake, individual 21


title: PBMC 24 SFA 6 h after intake

source_name: Peripheral blood mononuclear cells, SFA shake, 6 hours after intake, individual 24


title: PBMC 22 SFA 6 h after intake

source_name: Peripheral blood mononuclear cells, SFA shake, 6 hours after intake, individual 22


title: PBMC 17 SFA 6 h after intake

source_name: Peripheral blood mononuclear cells, SFA shake, 6 hours after intake, individual 17


title: PBMC 16 SFA 6 h after intake

source_name: Peripheral blood mononuclear cells, SFA shake, 6 hours after intake, individual 16


title: AE2_colon

city: Cincinnati

first: Gary

last: Shull

state: OH

address: 231 Albert Sabin Way ML0524

institute: University of Cincinnati

description: 7 wild-type and 7 AE2-null colon RNA samples were compared to identify genes that are differentially expressed in the colon of AE2 knockout mice. Total RNA was collected from both male and female wild-type and AE2-null colons (including both proximal and distal colon) when the mice were 18 days old. All pairs were gender- and aged-matched, and all mice were on a mixed 129 Black Swiss background. To facilitate statistical analysis and reduce any affects of Cy3 and Cy5 labeling, comparisons of two wild-type and two AE2-null samples were repeated using a dye flip.

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

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

data_processing: See: Sartor, et al. BMC Bioinformatics. 2006 Dec 19;7:538.  To test for differentially expressed genes, a hierarchical Bayes procedure, IBMT (Sartor et al., BMC Bioinf, 2006) was used.

source_name: total RNA from whole colon

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

extract_protocol: Total RNA was extracted from whole colon using Tri-Reagent as per the manufacturer's instructions.

tag: strain

value: 129 Black Swiss (mixed)

value: 2614 WT female

value: 2625 WT male

value: 2561 WT male

value: 1976 KO female

value: 2017 WT female

value: 2053 KO male

value: 1952 KO female

value: 2054 WT male

value: 1978 WT female

value: 2615 KO female

value: 2027 KO male

value: 2564 KO male

value: 2018 KO female

value: 2056 WT female


title: Normal Patient Platelets N033

source_name: Normal  Platelets


title: PBMC 15 SFA 6 h after intake

source_name: Peripheral blood mononuclear cells, SFA shake, 6 hours after intake, individual 15


title: Normal Patient Platelets N029


title: PBMC 14 SFA 6 h after intake

source_name: Peripheral blood mononuclear cells, SFA shake, 6 hours after intake, individual 14


title: Normal Patient Platelets N027


title: Normal Patient Platelets N026


title: PBMC 11 SFA 6 h after intake

source_name: Peripheral blood mononuclear cells, SFA shake, 6 hours after intake, individual 11


title: Normal Patient Platelets N024

source_name: human reference (Stratagene) RNA


title: Normal Patient Platelets N025


title: Normal Patient Platelets N028


title: Normal Patient Platelets N023


title: Normal Patient Platelets N022


title: Normal Patient Platelets N021


title: Normal Patient Platelets N020


title: Normal Patient Platelets N019


title: PBMC 10 SFA 6 h after intake

source_name: Peripheral blood mononuclear cells, SFA shake, 6 hours after intake, individual 10


title: PBMC 04 SFA 6 h after intake

source_name: Peripheral blood mononuclear cells, SFA shake, 6 hours after intake, individual 04


title: PBMC 05 SFA 6 h after intake

source_name: Peripheral blood mononuclear cells, SFA shake, 6 hours after intake, individual 05


title: PBMC 12 SFA 6 h after intake

source_name: Peripheral blood mononuclear cells, SFA shake, 6 hours after intake, individual 12


title: PBMC 02 SFA 6 h after intake

source_name: Peripheral blood mononuclear cells, SFA shake, 6 hours after intake, individual 02


title: PBMC 07 SFA 6 h after intake

source_name: Peripheral blood mononuclear cells, SFA shake, 6 hours after intake, individual 07


title: PBMC 06 SFA 6 h after intake

source_name: Peripheral blood mononuclear cells, SFA shake, 6 hours after intake, individual 06


title: PBMC 03 SFA 6 h after intake

source_name: Peripheral blood mononuclear cells, SFA shake, 6 hours after intake, individual 03


title: Normal Patient Platelets N018


title: Normal Patient Platelets N016


title: PBMC 25 SFA baseline

source_name: Peripheral blood mononuclear cells, SFA shake, baseline, individual 25


title: PBMC 27 SFA baseline

source_name: Peripheral blood mononuclear cells, SFA shake, baseline, individual 27


title: PBMC 01 SFA 6 h after intake

source_name: Peripheral blood mononuclear cells, SFA shake, 6 hours after intake, individual 01


title: PBMC 24 SFA baseline

source_name: Peripheral blood mononuclear cells, SFA shake, baseline, individual 24


title: SS_D7B

source_name: H9 human embryonic stem cells

tag: agent

value: Noggin + SB431542 +C25II

tag: time point


title: Normal Patient Platelets N015

source_name: Normal  Platelets


title: PBMC 23 SFA baseline

source_name: Peripheral blood mononuclear cells, SFA shake, baseline, individual 23


title: Normal Patient Platelets N014


title: Normal Patient Platelets N012


title: PBMC 22 SFA baseline

source_name: Peripheral blood mononuclear cells, SFA shake, baseline, individual 22


title: Salt stress vs. reference DvH_mid-log_phasemin._250_null_Salt:NaCl_set2073

city: Berkeley

middle: P.

last: Arkin

address: 1 Cyclotron Road

department: Physical Biosciences Division

institute: Virtual Institute for Microbial Stress and Survival

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Salt:NaCl. This sample was treated with 250 null Salt:NaCl.  Treatment time point = mid-log phase min.

hyb_protocol: He, Z., Wu, L., Li, X., Fields, M., and Zhou, J. 2005.  Empirical Establishment of Oligonucleotide Probe Design Criteria. Appl. Environ. Microbiol. 71:3753-3760.

scan_protocol: ImaGene software

data_processing: See Methods in: S. R. Chhabra, Q. He, K. H. Huang, S. P. Gaucher, E. J. Alm, Z. He, M. Z. Hadi, T. C. Hazen, J. D. Wall, J. Zhou, A.  . Arkin, and A. K. Singh, Global Analysis of Heat Shock Response in Desulfovibrio vulgaris Hildenborough, J Bacteriol. 2006 March; 188(5): 1817-1828. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16484192

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, mid-log phasemin. 250 null Salt:NaCl

growth_protocol: Three 250-ML bottles containing 100 mL of  defined PIPES buffered medium LS4D (13, 27), amended with 60mM lactate and 50mM sulfate were inoculated with exponentially grown cultures (1:10) to generate three biological replicates for the control. Similarly, three 250 mM NaCl-added replicates were generated but the additional 250 mM NaCl was added into the LS4D medium for the treatment. The head space of the vessels was 5% H2, 5% CO2, and 90% N2. Biomass (50 ml culture) for each sample of three replicates was harvested at the mid exponential phase (ca. 0.25 OD600) by centrifuging at 11,000  g for 5 min at 4 degrees C.  Cell pellets were immediately frozen in liquid N2 and stored at -80 degrees C until RNA isolation.

treatment_protocol: mid-log phasemin. 250 null Salt:NaCl.

value: Hildenborough

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, genomic DNA.


title: Normal Patient Platelets N013

source_name: human reference (Stratagene) RNA


title: PBMC 15 SFA baseline

source_name: Peripheral blood mononuclear cells, SFA shake, baseline, individual 15


title: Normal Patient Platelets N011


title: PBMC 16 SFA baseline

source_name: Peripheral blood mononuclear cells, SFA shake, baseline, individual 16


title: Normal Patient Platelets N010


title: PBMC 17 SFA baseline

source_name: Peripheral blood mononuclear cells, SFA shake, baseline, individual 17


title: PBMC 21 SFA baseline

source_name: Peripheral blood mononuclear cells, SFA shake, baseline, individual 21


title: Normal Patient Platelets N009


title: dwarf event of rgl1 transgenic, biological rep2

city: Houghton

first: Jiqing

last: Gou

email: jgou@mtu.edu, vbusov@mtu.edu

state: MI

address: 1400 Townsend Dr.

institute: Michigan Tech University

description: Gene expression data from rgl1 transgenic poplar root

hyb_protocol: Combine 225 µl 1cycle hybridization cocktail and 25 µl of cRNA (6 µg) to each array and place in hyb oven at 45˚C, rotate at 60rpm overnight in an Affymetrix GeneChip® Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned with an Affymetrix GeneChip® Scanner 3000 at 570nm.

data_processing: CEL files were processed by GC-RMA implemented in GeneSpring GX10.0

organism: Populus sp.

source_name: root of dwarf event of rgl1 transgenic poplar

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Plants were grown in hormone-free ½MS media containing 0.7% Phytagar (Gibco–BRL) and 1% sucrose, and maintained at 26°C under 16/8h photoperiod.

extract_protocol: Total RNA was isolated according to the manufacturer's instruction of Qiagen RNeasy Plant Kit

treatment_protocol: Roots from seven-week-old in vitro grown plants were carefully removed form media, washed, snap-frozen in liquid nitrogen and stored at -80oC until processed.

tag: genotype

value: rgl1 transgenic poplar

tag: tissue

value: poplar root


title: PBMC 12 SFA baseline

source_name: Peripheral blood mononuclear cells, SFA shake, baseline, individual 12


title: PBMC 14 SFA baseline

source_name: Peripheral blood mononuclear cells, SFA shake, baseline, individual 14


title: PBMC 20 SFA baseline

source_name: Peripheral blood mononuclear cells, SFA shake, baseline, individual 20


title: PBMC 06 SFA baseline

source_name: Peripheral blood mononuclear cells, SFA shake, baseline, individual 06


title: PBMC 11 SFA baseline

source_name: Peripheral blood mononuclear cells, SFA shake, baseline, individual 11


title: PBMC 10 SFA baseline

source_name: Peripheral blood mononuclear cells, SFA shake, baseline, individual 10


title: PBMC 07 SFA baseline

source_name: Peripheral blood mononuclear cells, SFA shake, baseline, individual 07


title: dwarf event of rgl1 transgenic, biological rep1


title: PBMC 05 SFA baseline

source_name: Peripheral blood mononuclear cells, SFA shake, baseline, individual 05


title: wt-like event of rgl1 transgenic, biological rep1

source_name: root of wt-like event of rgl1 transgenic poplar


title: wt-like event of rgl1 transgenic, biological rep2


title: wt-like event of GA2ox1 transgenic, biological rep1

description: Gene expression data from GA2ox1 transgenic poplar root

source_name: root of wt-like event of GA2ox1 transgenic poplar

value: GA2ox1 transgenic poplar


title: Normal Patient Platelets N008

source_name: Normal  Platelets


title: wt-like event of GA2ox1 transgenic, biological rep2


title: Normal Patient Platelets N007

source_name: human reference (Stratagene) RNA


title: PBMC 03 SFA baseline

source_name: Peripheral blood mononuclear cells, SFA shake, baseline, individual 03


title: PBMC 04 SFA baseline

source_name: Peripheral blood mononuclear cells, SFA shake, baseline, individual 04


title: Normal Patient Platelets N006


title: NSCLC tumor 181T

city: L´Hospitalet de Llobregat

first: Sandra

last: Castillo

address: Avda. Gran Via 199-203

country: Spain

institute: IDIBELL-PEBC

description:
Genomic DNA extracted from lung tumors was genotyped using Infinium HumanOmni1-Quad Genotyping BeadChips (Illumina).
181T

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48ºC, single-base extension and allele-specific staining was performed (XC1, XC2, TEM, STM, ATM, XC3, PB1) on a Teflow chamber rack system.

scan_protocol: After allele-specific staining, BeadChip arrays were coated with PB1/XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Beadstudio 3.1.3 with GT module 3.2.33 (Illumina).

label: C-Bio and A-DNP

source_name: non-small cell lung carcinoma

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37ºC using amplification master mix (WG-MSM) and primer/neutralization mix (WG-MA2). After incubation, the amplified DNA was fragmented with fragmentation mix (WG-FMS) and precipitated with 2-propanol and precipitation mix (PM1). The precipitated DNA was resuspended using RA1.

extract_protocol: For total genomic DNA extraction, sections of approximate thickness of 10-20 μm were collected from tumor samples and placed in 1% SDS/proteinase K (10 mg/ml) at 58ºC overnight. The samples were then subjected to phenol-chloroform extraction and ethanol precipitation.

tag: gender

value: male

value: lung tumor

tag: histological type

value: squamous cell carcinoma


title: Normal Patient Platelets N003


title: Normal Patient Platelets N004


title: PBMC 27 PUFA 6 h after intake

source_name: Peripheral blood mononuclear cells, PUFA shake, 6 hours after intake, individual 27


title: Normal Patient Platelets N002


title: Essential thrombocythemia Patient Platelet THR120

source_name: Essential thrombocythemia  Platelet


title: semidwarf event of GA2ox1 transgenic, biological rep1

source_name: root of semidwarf event of GA2ox1 transgenic poplar


title: PBMC 24 PUFA 6 h after intake

source_name: Peripheral blood mononuclear cells, PUFA shake, 6 hours after intake, individual 24


title: PBMC 01 SFA baseline

source_name: Peripheral blood mononuclear cells, SFA shake, baseline, individual 01


title: PBMC 02 SFA baseline

source_name: Peripheral blood mononuclear cells, SFA shake, baseline, individual 02


title: PBMC 25 PUFA 6 h after intake

source_name: Peripheral blood mononuclear cells, PUFA shake, 6 hours after intake, individual 25


title: PBMC 23 PUFA 6 h after intake

source_name: Peripheral blood mononuclear cells, PUFA shake, 6 hours after intake, individual 23


title: PBMC 22 PUFA 6 h after intake

source_name: Peripheral blood mononuclear cells, PUFA shake, 6 hours after intake, individual 22


title: PBMC 20 PUFA 6 h after intake

source_name: Peripheral blood mononuclear cells, PUFA shake, 6 hours after intake, individual 20


title: NSCLC tumor 276T

description:
Genomic DNA extracted from lung tumors was genotyped using Infinium HumanOmni1-Quad Genotyping BeadChips (Illumina).
276T


title: semidwarf event of GA2ox1 transgenic, biological rep2


title: PBMC 17 PUFA 6 h after intake

source_name: Peripheral blood mononuclear cells, PUFA shake, 6 hours after intake, individual 17


title: dwarf event of GA2ox1 transgenic, biological rep2

source_name: root of dwarf event of GA2ox1 transgenic poplar


title: dwarf event of GA2ox1 transgenic, biological rep1


title: wild type, biological rep2

description: Gene expression data from wildtype poplar root

source_name: root of wildtype poplar (7171B4 genotyp)

value: wildtype poplar (7171B4 genotype)


title: wild type, biological rep1


title: NSCLC tumor 143T

description:
Genomic DNA extracted from lung tumors was genotyped using Infinium HumanOmni1-Quad Genotyping BeadChips (Illumina).
143T


title: Essential thrombocythemia Patient Platelet THR119

source_name: human reference (Stratagene) RNA


title: NSCLC tumor 110T

description:
Genomic DNA extracted from lung tumors was genotyped using Infinium HumanOmni1-Quad Genotyping BeadChips (Illumina).
110T


title: PBMC 16 PUFA 6 h after intake

source_name: Peripheral blood mononuclear cells, PUFA shake, 6 hours after intake, individual 16


title: Essential thrombocythemia Patient Platelet THR118


title: PBMC 14 PUFA 6 h after intake

source_name: Peripheral blood mononuclear cells, PUFA shake, 6 hours after intake, individual 14


title: PBMC 15 PUFA 6 h after intake

source_name: Peripheral blood mononuclear cells, PUFA shake, 6 hours after intake, individual 15


title: PBMC 12 PUFA 6 h after intake

source_name: Peripheral blood mononuclear cells, PUFA shake, 6 hours after intake, individual 12


title: Essential thrombocythemia Patient Platelet THR116

source_name: Essential thrombocythemia  Platelet


title: Reactive Thrombocytosis Patient platelets THR521

source_name: Reactive Thrombocytosis  platelets


title: Essential thrombocythemia Patient Platelet THR115


title: Essential thrombocythemia Patient Platelet THR117


title: PBMC 10 PUFA 6 h after intake

source_name: Peripheral blood mononuclear cells, PUFA shake, 6 hours after intake, individual 10


title: Reactive Thrombocytosis Patient platelets THR522


title: PBMC 06 PUFA 6 h after intake

source_name: Peripheral blood mononuclear cells, PUFA shake, 6 hours after intake, individual 06


title: PBMC 05 PUFA 6 h after intake

source_name: Peripheral blood mononuclear cells, PUFA shake, 6 hours after intake, individual 05


title: PBMC 03 PUFA 6 h after intake

source_name: Peripheral blood mononuclear cells, PUFA shake, 6 hours after intake, individual 03


title: PBMC 11 PUFA 6 h after intake

source_name: Peripheral blood mononuclear cells, PUFA shake, 6 hours after intake, individual 11


title: Essential thrombocythemia Patient Platelet THR114


title: PBMC 04 PUFA 6 h after intake

source_name: Peripheral blood mononuclear cells, PUFA shake, 6 hours after intake, individual 04


title: mature leaf,mannitol, biological rep2

city: Gent

first: aleksandra

last: skirycz

address: Technologiepark 927

department: Plant System Biology

country: Belgium

institute: Ghent University

description: leaf size around 40mm2

hyb_protocol: Standard affymetrix protocol

scan_protocol: Standard affymetrix protocol

data_processing: Expression data were processed using RMA (background correction, normalization and summarization) in BioConductor (Gentleman et al. 2004; Irizarry et al. 2003a; 2003b). An alternative CDF (tinesath1cdf) was used, where each probe is assigned uniquely to one transcript and is excluded if it aligns to a different transcript with 24 or more perfect matches (Casneuf et al. 2007; http://www.bioconductor.org/packages/release/data/experiment/html/tinesath1cdf.html)

organism: Arabidopsis thaliana

source_name: Wild type, mature leaf, stress

label_protocol: Standard affymetrix protocol

growth_protocol: plant were grown on MS medium under 16 h light/ 8 h dark cycle at 22°C

extract_protocol: Biosources were dissected in RNAlater, Trizol extraction (Invitrogen) followed by clean-up by RNeasy plant mini kit (Qiagen) , according to manufacturer protocol

treatment_protocol: plant were grown on MS medium with 25mM mannitol under 16 h light/ 8 h dark cycle at 22°C

tag: stress

value: osmotic stress

tag: ecotype

value: mature leaf (3rd true leaf)

tag: developmental stage

value: leaf 3_22DAS plants

value: wild-type


title: PBMC 07 PUFA 6 h after intake

source_name: Peripheral blood mononuclear cells, PUFA shake, 6 hours after intake, individual 07


title: mature leaf,mannitol, biological rep3

description: leaf size around 40mm2


title: PBMC 02 PUFA 6 h after intake

source_name: Peripheral blood mononuclear cells, PUFA shake, 6 hours after intake, individual 02


title: PBMC 27 PUFA baseline

source_name: Peripheral blood mononuclear cells, PUFA shake, baseline, individual 27


title: human_adipocyte_ROSI_186

city: Toulouse

first: Nathalie

last: Viguerie

address: Avenue Poulhes

country: France

institute: INSERM

description: Labeling and hybridization qualities were verified with Agilent’s spike in kit.

hyb_protocol: 1µg of Cy5 labelled probe was cohybridized the same amount of Cy3 labelled control probe. We used the whole human genome oligo microarray from Agilent with the gene expression hybridization kit according to the manufacturer’s protocol.

scan_protocol: Micro-arrays were scanned on a 4000A Axon scanner and data were extracted with Feature Extraction (9.5.1.1, Agilent).

data_processing: The data extracted with Feature Extraction were normalized with the Lowess procedure without background subtraction by use of R. Features with a signal to background ratio strictly below 1,5 in both color as well as control spots were discarded. Value is the Log2 of normalized Red / Green value ratio.

source_name: human differentiated preadipocyte, DMSO, 48h

label_protocol: RNA quality was checked by capillary electrophoresis (Experion, BioRad)  and good quality RNA extracts only were used for microarray hybridization. Fluorescent probes were obtained by amplifying and labelling 500ng of RNA with the low RNA input linear amplification kit (Agilent).

extract_protocol: Total RNA was extracted with the RNeasy mini kit (Qiagen) according to manufacturer instructions.

treatment_protocol: Subcutaneous abdominal WAT was obtained from female subjects undergoing plastic surgery in agreement with French laws on biomedical research. Human adipocytes in primary culture were differentiated. At day 12 or 13, culture media was replaced and cells were treated with Rosiglitazone (1µM). After 48 h of treatment, cells were lysed for mRNA extraction. Vehicle was added to control cells.

value: female

value: subcutaneous abdominal white adipose tissue

tag: cell type

value: adipocyte

source_name: human differentiated preadipocyte, Rosiglitazone, 48h


title: PBMC 01 PUFA 6 h after intake

source_name: Peripheral blood mononuclear cells, PUFA shake, 6 hours after intake, individual 01


title: mature leaf, control, biological rep3

description: leaf size around 40mm2

source_name: Wild type, mature leaf, control

value: control


title: Essential thrombocythemia Patient Platelet THR113

source_name: human reference (Stratagene) RNA

tag: human reference (Stratagene) RNA


title: mature leaf,mannitol, biological rep1

description: leaf size around 40mm2


title: human_adipocyte_ROSI_191


title: human_adipocyte_ROSI_183


title: mature leaf, control, biological rep2

description: leaf size around 40mm2


title: PBMC 25 PUFA baseline

source_name: Peripheral blood mononuclear cells, PUFA shake, baseline, individual 25


title: human_adipocyte_GW7647_191

treatment_protocol: Subcutaneous abdominal WAT was obtained from female subjects undergoing plastic surgery in agreement with French laws on biomedical research. Human adipocytes in primary culture were differentiated. At day 12 or 13, culture media was replaced and cells were treated with GW7647 (1µM). After 48 h of treatment, cells were lysed for mRNA extraction. Vehicle was added to control cells.

source_name: human differentiated preadipocyte, GW7647, 48h


title: hop059|MDA157

first: Jonathan

last: Pollack

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University

description:
Simple annotation: Breast, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71092.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1560, 6080; Software: type: feature extraction; Performer: Yun La,,Choi Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-11-03; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 400; Parameter Laser on time = 91083; Parameter Laser Power = 3.74; Parameter Scan Time = 13:02:37; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.62; Performer: Yun La,,Choi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-11-03; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 460; Parameter Scan Power = 100; Parameter Laser on time = 91127; Parameter Laser Power = 3.36; Parameter Scan Time = 13:02:37; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.62; Performer: Yun La,,Choi

source_name: Common Reference RNA

tag: reference

value: Common Reference RNA

tag: cell line

value: fibroblast-like


title: hop064|MDA468

description:
Simple annotation: Breast, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71095.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1800, 5720; Software: type: feature extraction; Performer: Yun La,,Choi Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-11-10; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 400; Parameter Laser on time = 91978; Parameter Laser Power = 3.75; Parameter Scan Time = 17:30:47; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.04; Performer: Yun La,,Choi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-11-10; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 500; Parameter Scan Power = 100; Parameter Laser on time = 92023; Parameter Laser Power = 3.39; Parameter Scan Time = 17:30:47; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.04; Performer: Yun La,,Choi

value: epithelial-like


title: Essential thrombocythemia Patient Platelet THR111

source_name: Essential thrombocythemia  Platelet


title: hop102|HS578T

description:
Simple annotation: Breast, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71116.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1620, 5400; Software: type: feature extraction; Performer: Yun La,,Choi Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-11-10; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 410; Parameter Laser on time = 91960; Parameter Laser Power = 3.75; Parameter Scan Time = 17:14:40; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.86; Performer: Yun La,,Choi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-11-10; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 500; Parameter Scan Power = 100; Parameter Laser on time = 92005; Parameter Laser Power = 3.37; Parameter Scan Time = 17:14:40; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.86; Performer: Yun La,,Choi


title: mature leaf, control, biological rep1

description: leaf size around 40mm2


title: human_adipocyte_ROSI_180


title: PBMC 23 PUFA baseline

source_name: Peripheral blood mononuclear cells, PUFA shake, baseline, individual 23


title: Essential thrombocythemia Patient Platelet THR112


title: expanding leaf,mannitol, biological rep3

description: leaf size around 7mm2

source_name: Wild type, expanding leaf, stress

value: expanding leaf (3rd true leaf)

value: leaf 3_15DAS plants


title: human_adipocyte_GW7647_186


title: Essential thrombocythemia Patient Platelet THR108


title: PBMC 20 PUFA baseline

source_name: Peripheral blood mononuclear cells, PUFA shake, baseline, individual 20


title: PBMC 22 PUFA baseline

source_name: Peripheral blood mononuclear cells, PUFA shake, baseline, individual 22


title: Essential thrombocythemia Patient Platelet THR107


title: hop085|EFM19

description:
Simple annotation: Breast, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71106.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1560, 6080; Software: type: feature extraction; Performer: Yun La,,Choi Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-11-03; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 380; Parameter Laser on time = 91106; Parameter Laser Power = 3.74; Parameter Scan Time = 13:26:41; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.29; Performer: Yun La,,Choi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-11-03; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 420; Parameter Scan Power = 100; Parameter Laser on time = 91151; Parameter Laser Power = 3.37; Parameter Scan Time = 13:26:41; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.29; Performer: Yun La,,Choi


title: human_adipocyte_GW7647_183

extract_protocol: Total RNA was extract with the RNeasy mini kit (Qiagen) according to manufacturer instructions.


title: expanding leaf,mannitol, biological rep2

description: leaf size around 7mm2


title: Essential thrombocythemia Patient Platelet THR110


title: Essential thrombocythemia Patient Platelet THR106


title: Essential thrombocythemia Patient Platelet THR109


title: Essential thrombocythemia Patient Platelet THR105


title: PBMC 21 PUFA baseline

source_name: Peripheral blood mononuclear cells, PUFA shake, baseline, individual 21


title: 334630, mytotubes #172, BHLHB2 vs GFP

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

description:
Human primary myotubes culture #172 infected with BHLHB2 for 48hours vs Human primary myotubes culture #172 infected with GFP for 48hours
Date:2007/12/06

hyb_protocol: Agilent : 1500.0 ng of labelled nucleic acid was hybridized at 62 degree_C during 17 hours.

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Normalized using a global Lowess method.

label_protocol: Fluorescent probes were synthesized by chemical coupling of 5ug aminoallyl aRNA with cyanine 3 (Cy3) or Cy5 dyes and purified using Rneasy Mini Kit (Qiagen).

growth_protocol: Myotubes were prepared from a human skeletal muscle biopsy.

extract_protocol: Trizol

treatment_protocol: After 7 days of differentiation, myotubes were infected for 48 hours with recombinant adenovirus expressing BHLHB2.

value: subject #172

tag: Tissue

value: Human primary myotubes culture

treatment_protocol: After 7 days of differentiation, myotubes were infected for 48 hours with recombinant adenovirus expressing GFP.


title: PBMC 17 PUFA baseline

source_name: Peripheral blood mononuclear cells, PUFA shake, baseline, individual 17


title: expanding leaf, control, biological rep2

description: leaf size around 7mm2

source_name: Wild type, expanding leaf, control


title: 334632, mytotubes #184, BHLHB2 vs GFP

description:
Human primary myotubes culture #184 infected with BHLHB2 for 48hours vs Human primary myotubes culture #184 infected with GFP for 48hours
Date:2007/12/06

value: subject #184


title: 334631, mytotubes #172, BHLHB3 vs GFP

description:
Human primary myotubes culture #172 infected with BHLHB3 for 48hours vs Human primary myotubes culture #172 infected with GFP for 48hours
Date:2007/12/06

treatment_protocol: After 7 days of differentiation, myotubes were infected for 48 hours with recombinant adenovirus expressing BHLHB3.


title: PBMC 16 PUFA baseline

source_name: Peripheral blood mononuclear cells, PUFA shake, baseline, individual 16


title: Essential thrombocythemia Patient Platelet THR104


title: proliferating leaf,mannitol, biological rep3

description: leaf size around 0.1mm2

source_name: Wild type, proliferating leaf, stress

value: proliferating leaf (3rd true leaf)

value: leaf 3_9DAS plants


title: PBMC 24 PUFA baseline

source_name: Peripheral blood mononuclear cells, PUFA shake, baseline, individual 24


title: hop137|NF|1219

description:
Simple annotation: Breast, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71118.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1800, 5720; Software: type: feature extraction; Performer: Yun La,,Choi Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-11-10; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 410; Parameter Laser on time = 91970; Parameter Laser Power = 3.74; Parameter Scan Time = 17:22:20; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.95; Performer: Yun La,,Choi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-11-10; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 500; Parameter Scan Power = 100; Parameter Laser on time = 92015; Parameter Laser Power = 3.38; Parameter Scan Time = 17:22:20; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.95; Performer: Yun La,,Choi

value: normal breast fibroblasts


title: expanding leaf, control, biological rep3

description: leaf size around 7mm2


title: human_adipocyte_GW7647_180

source_name: human differentiated preadipocyte, DMSO, 48h

treatment_protocol: Subcutaneous abdominal WAT was obtained from female subjects undergoing plastic surgery in agreement with French laws on biomedical research. Human adipocytes in primary culture were differentiated. At day 12 or 13, culture media was replaced and cells were treated with GW7647 (1µM). After 48 h of treatment, cells were either lysed for mRNA extraction. Vehicle was added to control cells.


title: PBMC 14 PUFA baseline

source_name: Peripheral blood mononuclear cells, PUFA shake, baseline, individual 14


title: 334647, mytotubes #170, BHLHB3 vs GFP

description:
Human primary myotubes culture #170 infected with BHLHB3 for 48hours vs Human primary myotubes culture #170 infected with GFP for 48hours
Date:2007/12/10

value: subject #170


title: proliferating leaf,mannitol, biological rep2

description: leaf size around 0.1mm2

value: osmotic stress

value: wild-type


title: Essential thrombocythemia Patient Platelet THR102

source_name: human reference (Stratagene) RNA


title: Essential thrombocythemia Patient Platelet THR103


title: 334645, mytotubes #170, BHLHB2 vs GFP

description:
Human primary myotubes culture #170 infected with BHLHB2 for 48hours vs Human primary myotubes culture #170 infected with GFP for 48hours
Date:2007/12/10


title: Essential thrombocythemia Patient Platelet THR101


title: PBMC 15 PUFA baseline

source_name: Peripheral blood mononuclear cells, PUFA shake, baseline, individual 15


title: PBMC 12 PUFA baseline

source_name: Peripheral blood mononuclear cells, PUFA shake, baseline, individual 12


title: proliferating leaf,mannitol, biological rep1

description: leaf size around 0.1mm2


title: 334648, mytotubes #165, BHLHB2 vs GFP

description:
Human primary myotubes culture #165 infected with BHLHB2 for 48hours vs Human primary myotubes culture #165 infected with GFP for 48hours
Date:2007/12/10

value: subject #165


title: PBMC 10 PUFA baseline

source_name: Peripheral blood mononuclear cells, PUFA shake, baseline, individual 10


title: proliferating leaf, control, biological rep3

description: leaf size around 0.1mm2

source_name: Wild type, proliferating leaf, control


title: PBMC 11 PUFA baseline

source_name: Peripheral blood mononuclear cells, PUFA shake, baseline, individual 11


title: Essential thrombocythemia Patient Platelet THR100

source_name: Essential thrombocythemia  Platelet


title: proliferating leaf, control, biological rep2

description: leaf size around 0.1mm2


title: 334650, mytotubes #184, GFP vs BHLHB3

description:
Human primary myotubes culture #184 infected with GFP for 48hours vs Human primary myotubes culture #184 infected with BHLHB3 for 48hours
Date:2007/12/18


title: 20D +/- pool vs F57

description: Biological replicate 3 dye swap

hyb_protocol: 1µg of labelled nucleic acid was hybridized in 2X Agilent Hybridation Buffer at 67 degree_C during 17 hours

scan_protocol: Scanned on Axon Genepix 4000B scanner. Images were quantified using Genepix pro 6.0

data_processing: Lowess normalization.

source_name: 20D +/- pool

label_protocol: One microgram of total RNA  was amplified with the Amino Allyl MessageAmp II aRNA kit (Ambion) according to the manufacturer’s instructions. Fluorescent probes were synthesized by chemical coupling of 5 µg of aminoallyl aRNA with cyanine (Cy)3 or Cy5 dyes, following a dye switch experimental plan. Fluorescent probes were purified using Rneasy minikit (Qiagen)

extract_protocol: Total RNA extracted using Rneasy Mini Kit (Qiagen) following manufacturer's instructions

value: testis


title: PBMC 06 PUFA baseline

source_name: Peripheral blood mononuclear cells, PUFA shake, baseline, individual 06


title: PBMC 07 PUFA baseline

source_name: Peripheral blood mononuclear cells, PUFA shake, baseline, individual 07


title: 20D +/- pool vs F56

description: Biological replicate 2 dye swap