title: Porcine, control, biological, rep2

city: Wuhan

first: Wang

last: Yang

address: Shizishan street No.1

institute: Huazhong agricultural university

description: Gene expression data from Porcine alveolar Macrophages isolated from control pigs at 6 d.p.i.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. 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 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

organism: Sus scrofa

source_name: Porcine alveolar Macrophages isolated from control pigs, 6 dpi

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Six 27 days old healthy pigs were obtained, Three pigs  were intratracheally challenged with H.parasuis strain 0165 other three pigs were intratracheally challenged with PBS as control. All pigs were slaughtered at 6 dpi

treatment_protocol: Bronchoalveolar lavage of the lungs was performed with 100mL aliguots of sterile PBS containing genamicin at 70 μg/mL(Sigma).Then lavage fluids were centrifuged at 230 ×g for 15 min, and cells were washed twice with Dulbecco’s Modified Eagle’s Medium (DMEM) containing gentamicin (50μg/mL).

value: Alveolar Macrophage

tag: disease state


title: Porcine, HPS infection, biological rep3

status: Public on Jun 28 2011

type: RNA

country: China

description: Gene expression data from Porcine alveolar Macrophages isolated from HPS infection pigs at 6 d.p.i.

label: biotin

molecule: total RNA

source_name: Porcine alveolar Macrophages isolated from HPS infection pigs, 6 dpi

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

tag: tissue

value: HPS infection


title: Ground Sample -  biological replicate 3

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

description: gene expression data from bacteria cultured in ground conditions

hyb_protocol: Samples were hybridized, washed, stained, and scanned as described in the Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol.

data_processing: Raw Affymetrix data were pre-processed using the Affy package in BioConductor as follows: (i) background correction based on the robust multichip average (RMA) convolution model (Irizarry et al., 2003), (ii) quantile normalization to make expression values from different arrays more comparable (Bolstad et al., 2003), (iii) summarization of multiple probe intensities for each probe set to one expression value per gene using RMA (Irizarry et al., 2003). To test for differential expression between the spaceflight and ground control cultures, the Bayesian adjusted t-statistics was used as implemented in the LIMMA package (version 2.5.15) (Smyth, 2004). P-values were corrected for multiple testing using the Benjamini and Hochberg’s method to control the false discovery rate (Benjamini and Hochberg, 1995). Microarray analysis was performed on all three biological replicates.

organism: Pseudomonas aeruginosa PAO1

source_name: Ground sample - control

label_protocol:
Ten micrograms of total RNA was used for cDNA synthesis, fragmentation, and labeling according to the Affymetrix GeneChip P. aeruginosa genome array expression protocol. Briefly, random hexamers (Invitrogen) were added to 10 microgram of RNA along with
in vitro-transcribed Bacillus subtilis control spikes. cDNA was synthesized using Superscript III (Invitrogen) and the following conditions: 25°C for 10 min, 37°C for 60 min, and 70°C for 10 min. RNA was removed by alkaline treatment and subsequent neutralization. The cDNA was purified by using a QIAquick PCR purification kit (QIAGEN) and eluted in 40 microl of elution buffer (QIAGEN). The cDNA was then fragmented by using 0.6 U DNase I (Amersham) per microg cDNA
at 37°C for 10 min. The fragmented cDNA was end labeled with biotin-ddUTP by using a BioArray terminal labeling kit (Enzo) per the manufacturer’s instructions. A gel shift mobility assay was performed using NeutrAvadin (Pierce) on a 5% polyacrylamide gel stained with SYBR green (Roche) to ensure complete fragmentation and labeling.

growth_protocol: P. aeruginosa PAO1 was grown in LB medium containing 25 µg/ml gentamicin in the spaceflight hardware (see below) to avoid growth of any contaminants. The bacterial inoculum 1.5 x 10+8 CFU/ml was suspended in 0.5 ml phosphate buffered saline (PBS)

extract_protocol: Total RNA was isolated using the RNeasy minikit (Qiagen) per the manufacturer’s instructions.

treatment_protocol: A derivative of the wild type P. aeruginosa PAO1 (ATCC 15692) was used for the spaceflight experiment, which contained a gentamicin resistance cassette. The gentamicin-resistant strain was constructed through homologous recombination as described previously (Schweizer, 1993). P. aeruginosa PAO1 was grown in LB medium containing 25 µg/ml gentamicin in the spaceflight hardware (see below) to avoid growth of any contaminants. The bacterial inoculum 1.5 x 108 CFU/ml in the spaceflight hardware was suspended in 0.5 ml phosphate buffered saline (PBS) (Invitrogen), and remained viable but -static during launch and until nine days into the flight. Here after, growth was initiated by the addition of LB as described below. Cells were fixed in-flight using the RNA and protein fixative RNA Later II (Ambion). At 2.5 hours after Shuttle landing at the Kennedy Space Center (KSC), samples were recovered and subsequently used for whole genome transcriptional microarray and proteomic analysis. In each case, the flight culture samples were compared with culture samples grown under identical conditions on the ground at KSC using coordinated activation and termination times (by means of real-time communications with the Shuttle astronauts) in an insulated room that maintained identical temperature and humidity levels as those on the Shuttle (Orbital Environment Simulator).

tag: strain

tag: culture

value: bacteria cultured in normal ground conditions

tag: atcc


title: Porcine, control, biological, rep1


title: M8_Trifxmyd, biological rep4

city: München

first: Olivia

last: Prazeres da Costa

state: Bavaria

address: Trogerstr. 30

department: Medical Microbiology, Immunology and Hygiene

country: Germany

institute: Technische Universität München

description:
M8
TLR-deficient, septic.

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99°C for 5 minutes, then 42°C for 5 minutes, and centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). Transfer 200μl of hyb solution to each array, then tape holes and parafilm. Hybridize 16 hours at 45° at 60rpm. Fluidics washing is FS450_0001.

scan_protocol: Affymetrix GeneChIP Scanner 3000 7G.

data_processing: RMA normalization using Expression Console.

organism: Mus musculus

source_name: Spleen, TLR-deficient, septic

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Shh mutant phenotypes were manually identified as wild-type or mutants. cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

tag: phenotype

value: Toll-like receptor (TLR)-deficient

value: spleen

tag: treatment

value: colon ascendens stent peritonitis (CASP)


title: Hepatocyte

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Division of Organogenesis and Regeneration

country: Japan

institute: Medical Institute of Bioreguration, Kyushu University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

source_name: hepatocytes obtained from adult mouse livers

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labelling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was prepared from cells using an RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

tag: genetic background

tag: cell type


title: Space flight Sample -  biological replicate 2

description: gene expression data from bacteria cultured in space flight conditions

scan_protocol: Samples were hybridized, washed, stained, and scanned as described in the Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol.

source_name: Space flight sample

value: bacteria cultured during space flight


title: Space flight Sample -  biological replicate 1


title: M10_WT_CASP, biological rep2

description:
M10
Wildtype, septic.

source_name: Spleen, wildtype, septic

value: wildtype


title: Porcine, HPS infection, biological rep2


title: M9_WT CASP, biological rep1

description:
M9
Wildtype, septic.


title: M7_Trifxmyd, biological rep3

description:
M7
TLR-deficient, septic.


title: Ground Sample -  biological replicate 1

data_processing: Raw Affymetrix data were pre-processed using the Affy package in BioConductor as follows: (i) background correction based on the robust multichip average (RMA) convolution model (Irizarry et al., 2003), (ii) quantile normalization to make expression values from different arrays more comparable (Bolstad et al., 2003), (iii) summarization of multiple probe intensities for each probe set to one expression value per gene using RMA (Irizarry et al., 2003). To test for differential expression between spaceflight and ground control cultures, the Bayesian adjusted t-statistics was used as implemented in the LIMMA package (version 2.5.15) (Smyth, 2004). P-values were corrected for multiple testing using the Benjamini and Hochberg’s method to control the false discovery rate (Benjamini and Hochberg, 1995). Microarray analysis was performed on all three biological replicates.


title: Porcine, control, biological, rep3


title: M6_Trifxmyd, biological rep2

description:
M6
TLR-deficient, septic.


title: Ground Sample -  biological replicate 2

data_processing: Raw Affymetrix data were pre-processed using the Affy package in BioConductor as follows: (i) background correction based on the robust multichip average (RMA) convolution model (Irizarry et al., 2003), (ii) quantile normalization to make expression values from different arrays more comparable (Bolstad et al., 2003), (iii) summarization of multiple probe intensities for each probe set to one expression value per gene using RMA (Irizarry et al., 2003). To test for differential expression between the spaceflight and ground control cultures,the Bayesian adjusted t-statistics was used as implemented in the LIMMA package (version 2.5.15) (Smyth, 2004). P-values were corrected for multiple testing using the Benjamini and Hochberg’s method to control the false discovery rate (Benjamini and Hochberg, 1995). Microarray analysis was performed on all three biological replicates.


title: Porcine, HPS infection, biological rep1


title: M5_Trifxmyd, biological rep1

description:
M5
TLR-deficient, septic.


title: Sulfolobus solfataricus P2 growth curve. Array 252331010010

status: Public on Jun 27 2011

city: Seoul

first: Sung Ho

last: Yoon

address: 120 Neungdong-ro, Gwangjin-gu

department: Department of Bioscience and Biotechnology

country: South Korea

institute: Konkuk University

description:
ch1:  Sulfolobus solfataricus P2 at OD600=0.312
ch2:  Sulfolobus solfataricus P2 at OD600=0.734, t=32h, Replicate 2

hyb_protocol: 7.5 µg of labeled sample RNA and 7.5 µg of labeled reference RNA were fragmented in total 250 µl mixture (50 µl of 10X blocking agent, 10 µl of 25X fragmentation buffer, H2O) at 60°C for 30 min, then put it on ice for 1 min. 250 µl of fragmentation mix and 250 µl of GE hybridization buffer HI-RPM were mixed and spinned for 1 min at RT at 13,000 rpm, and put on ice. 490 µl of the hybridization mix was applied to the slide in chamber, and put in a hybridization oven at 65°C for 17 hrs. After hybridization, the slide was washed sequentially in GE wash buffer 1 (twice) and 2.

scan_protocol: The arrays were scanned by ScanArray (Perkin Elmer).

data_processing: Signal intensities and local backgrounds were determined by Feature Extraction software (Agilent Technologies). Cy3 and Cy5 intensities were normalized by scaling so that the 75th percentile in the Cy3 and Cy5 channels were equal.

organism: Saccharolobus solfataricus P2

source_name: Sulfolobus solfataricus P2 [reference sample]

label_protocol: 1.5 µg of total RNA were directly labeled with 1.5 µl of Kreatech  dye (Cy3 or Cy5) at 95°C for 5 min, then put it on ice. The solutions were purified by KREApure column.

growth_protocol: Cells were grown aerobically at 80°C in liquid mineral medium pH=3.0 (Arch. Mikrobiol. 84:54-68) containing 0.2% tryptone and 0.1% yeast extract (Difco). One-liter culture flasks containing 400 ml media were inoculated with log phase cells and maintained under constant agitation (230 RPM).

extract_protocol: Total RNAs were extracted using mirVana miRNA isolation kit (Applied Biosystems, Austin, TX) following manufacturer’s instructions.

treatment_protocol: Samples of 1 x 10^9 cells were taken every 6 hours by pipette, immediately chilled on ice and the cells collected by centrifugation at 1400 x g for 10 minutes at 4°C. Aspirated cell pellets were immediately plunged into liquid nitrogen and stored at -80°C until RNA extraction.

tag: growth phase

value: mid-log phase (OD600=0.312)

source_name: Sulfolobus solfataricus P2 growth curve [test sample]

value: mid-log phase (OD600=0.734)

tag: time

tag: replicate


title: Sulfolobus solfataricus P2 growth curve. Array 252331010009

description:
ch1:  Sulfolobus solfataricus P2 at OD600=0.734, t=32h, Replicate 1
ch2:  Sulfolobus solfataricus P2 at OD600=0.312


title: Sulfolobus solfataricus P2 growth curve. Array 252331010012

description:
ch1:  Sulfolobus solfataricus P2 at OD600=0.312
ch2:  Sulfolobus solfataricus P2 at OD600=0.777, t=38h, Replicate 2

value: mid-log phase (OD600=0.777)


title: Sulfolobus solfataricus P2 growth curve. Array 252331010016

description:
ch1:  Sulfolobus solfataricus P2 at OD600=0.923, t=74h, Replicate 1
ch2:  Sulfolobus solfataricus P2 at OD600=0.312

value: mid-log phase (OD600=0.923)


title: Sulfolobus solfataricus P2 growth curve. Array 252331010015

description:
ch1:  Sulfolobus solfataricus P2 at OD600=0.312
ch2:  Sulfolobus solfataricus P2 at OD600=0.819, t=50h, Replicate 2

value: mid-log phase (OD600=0.819)


title: Pyrococcus furiosus DSM 3638 growth curve. Array 252330910015

description:
ch1:  Pyrococcus furiosus DSM 3638 at OD600=0.23, t=10h, Replicate 1
ch2:  Pyrococcus furiosus DSM 3638 at OD600=0.096

organism: Pyrococcus furiosus DSM 3638

source_name: Pyrococcus furiosus DSM 3638 growth curve [test sample]

growth_protocol: Cells were cultured in standard Pf base media supplemented with 0.1% w/v yeast extract (DIFCO technical grade) and 0.3% w/v maltose (Sigma M2250).

treatment_protocol: Culture samples were removed anaerobically using a sterile syringe and transfered into  sterile 50 ml falcon tubes placed in RT water. Samples were spun at ~300 xg for 25 min (18°C). Spent media was removed and cell pellet was flash frozen in liquid nitrogen before storing at -80°C.

value: mid-log phase (OD600=0.23)

source_name: Pyrococcus furiosus DSM 3638 [reference sample]

value: mid-log phase (OD600=0.096)


title: Sulfolobus solfataricus P2 growth curve. Array 252331010008

description:
ch1:  Sulfolobus solfataricus P2 at OD600=0.312
ch2:  Sulfolobus solfataricus P2 at OD600=0.654, t=26h, Replicate 2

value: mid-log phase (OD600=0.654)


title: Sulfolobus solfataricus P2 growth curve. Array 252331010006

description:
ch1:  Sulfolobus solfataricus P2 at OD600=0.312
ch2:  Sulfolobus solfataricus P2 at OD600=0.353, t=14h, Replicate 2

value: mid-log phase (OD600=0.353)


title: Sulfolobus solfataricus P2 growth curve. Array 252331010017

description:
ch1:  Sulfolobus solfataricus P2 at OD600=0.312
ch2:  Sulfolobus solfataricus P2 at OD600=0.923, t=74h, Replicate 2


title: Sulfolobus solfataricus P2 growth curve. Array 252331010004

description:
ch1:  Sulfolobus solfataricus P2 at OD600=0.312
ch2:  Sulfolobus solfataricus P2 at OD600=0.193, t=8h, Replicate 2

value: mid-log phase (OD600=0.193)


title: Sulfolobus solfataricus P2 growth curve. Array 252331010005

description:
ch1:  Sulfolobus solfataricus P2 at OD600=0.353, t=14h, Replicate 1
ch2:  Sulfolobus solfataricus P2 at OD600=0.312


title: Sulfolobus solfataricus P2 growth curve. Array 252331010007

description:
ch1:  Sulfolobus solfataricus P2 at OD600=0.654, t=26h, Replicate 1
ch2:  Sulfolobus solfataricus P2 at OD600=0.312


title: Pyrococcus furiosus DSM 3638 growth curve. Array 252330910013

description:
ch1:  Pyrococcus furiosus DSM 3638 at OD600=0.124, t=8h, Replicate 1
ch2:  Pyrococcus furiosus DSM 3638 at OD600=0.096

value: mid-log phase (OD600=0.124)


title: Pyrococcus furiosus DSM 3638 growth curve. Array 252330910022

description:
ch1:  Pyrococcus furiosus DSM 3638 at OD600=0.096
ch2:  Pyrococcus furiosus DSM 3638 at OD600=0.354, t=16h, Replicate 2

value: mid-log phase (OD600=0.354)


title: Pyrococcus furiosus DSM 3638 growth curve. Array 252330910019

description:
ch1:  Pyrococcus furiosus DSM 3638 at OD600=0.322, t=13h, Replicate 1
ch2:  Pyrococcus furiosus DSM 3638 at OD600=0.096

value: mid-log phase (OD600=0.322)


title: Pyrococcus furiosus DSM 3638 growth curve. Array 252330910021

description:
ch1:  Pyrococcus furiosus DSM 3638 at OD600=0.354, t=16h, Replicate 1
ch2:  Pyrococcus furiosus DSM 3638 at OD600=0.096


title: Sulfolobus solfataricus P2 growth curve. Array 252331010011

description:
ch1:  Sulfolobus solfataricus P2 at OD600=0.777, t=38h, Replicate 1
ch2:  Sulfolobus solfataricus P2 at OD600=0.312


title: Sulfolobus solfataricus P2 growth curve. Array 252331010013

description:
ch1:  Sulfolobus solfataricus P2 at OD600=0.819, t=50h, Replicate 1
ch2:  Sulfolobus solfataricus P2 at OD600=0.312


title: Pyrococcus furiosus DSM 3638 growth curve. Array 252330910017

description:
ch1:  Pyrococcus furiosus DSM 3638 at OD600=0.292, t=12h, Replicate 1
ch2:  Pyrococcus furiosus DSM 3638 at OD600=0.096

value: mid-log phase (OD600=0.292)


title: Pyrococcus furiosus DSM 3638 growth curve. Array 252330910016

description:
ch1:  Pyrococcus furiosus DSM 3638 at OD600=0.096
ch2:  Pyrococcus furiosus DSM 3638 at OD600=0.23, t=10h, Replicate 2


title: Pyrococcus furiosus DSM 3638 growth curve. Array 252330910018

description:
ch1:  Pyrococcus furiosus DSM 3638 at OD600=0.096
ch2:  Pyrococcus furiosus DSM 3638 at OD600=0.292, t=12h, Replicate 2


title: Pyrococcus furiosus DSM 3638 growth curve. Array 252330910020

description:
ch1:  Pyrococcus furiosus DSM 3638 at OD600=0.096
ch2:  Pyrococcus furiosus DSM 3638 at OD600=0.322, t=13h, Replicate 2


title: Sulfolobus solfataricus P2 growth curve. Array 252331010018

description:
ch1:  Sulfolobus solfataricus P2 at OD600=0.312
ch2:  Sulfolobus solfataricus P2 at OD600=0.095, t=2h, Replicate 2

value: mid-log phase (OD600=0.095)


title: Pyrococcus furiosus DSM 3638 growth curve. Array 252330910014

description:
ch1:  Pyrococcus furiosus DSM 3638 at OD600=0.096
ch2:  Pyrococcus furiosus DSM 3638 at OD600=0.124, t=8h, Replicate 2


title: Pyrococcus furiosus DSM 3638 growth curve. Array 252330910011

description:
ch1:  Pyrococcus furiosus DSM 3638 at OD600=0.041, t=6.5h, Replicate 1
ch2:  Pyrococcus furiosus DSM 3638 at OD600=0.096

treatment_protocol: Culture samples were removed anaerobically using a sterile syringe and transfered into  sterile 50 ml falcon tubes placed in RT water. Samples were spun at ~300 xg for 25 min (18°C). Spent media was removed and cell pellet was flash frozen in liquid nitrogen before storing at -80 °C.

value: mid-log phase (OD600=0.041)


title: Sulfolobus solfataricus P2 growth curve. Array 252331010001

description:
ch1:  Sulfolobus solfataricus P2 at OD600=0.095, t=2h, Replicate 1
ch2:  Sulfolobus solfataricus P2 at OD600=0.312


title: Sulfolobus solfataricus P2 growth curve. Array 252331010003

description:
ch1:  Sulfolobus solfataricus P2 at OD600=0.193, t=8h, Replicate 1
ch2:  Sulfolobus solfataricus P2 at OD600=0.312


title: Pyrococcus furiosus DSM 3638 growth curve. Array 252330910012

description:
ch1:  Pyrococcus furiosus DSM 3638 at OD600=0.096
ch2:  Pyrococcus furiosus DSM 3638 at OD600=0.041, t=6.5h, Replicate 2


title: Pyrococcus furiosus DSM 3638 growth curve. Array 252330910010

description:
ch1:  Pyrococcus furiosus DSM 3638 at OD600=0.096
ch2:  Pyrococcus furiosus DSM 3638 at OD600=0.036, t=5h, Replicate 2

value: mid-log phase (OD600=0.036)


title: Pyrococcus furiosus DSM 3638 growth curve. Array 252330910009

description:
ch1:  Pyrococcus furiosus DSM 3638 at OD600=0.036, t=5h, Replicate 1
ch2:  Pyrococcus furiosus DSM 3638 at OD600=0.096


title: Methanococcus maripaludis MM901 growth curve. Array 252330810007

description:
ch1:  Methanococcus maripaludis MM901 at OD660=0.885, t=649 min, Replicate 1
ch2:  Methanococcus maripaludis MM901 at OD660=0.804

organism: Methanococcus maripaludis S2

source_name: Methanococcus maripaludis MM901 growth curve [test sample]

growth_protocol: Methanococcus maripaludis MM901, wild type Methanococcus maripaludis S2 with an in frame deletion of the uracil phosphoribosyltransferase gene (Proc. Natl. Acad. Sci. U S A 107:11050-11055), was grown in a one-liter fermenter set up as described in (FEMS Microbiol. Lett. 238:85-91), using the modifications to the medium and gases for non-limiting conditions described in (BMC Microbiol. 9:149).

extract_protocol: Total RNA were extracted using mirVana miRNA isolation kit (Applied Biosystems, Austin, TX) following manufacturer’s instructions.

treatment_protocol: Samples were harvested through the sampling port by drawing out with a 20-ml syringe, aliquoted 1.5 ml each into microcentrifuge tubes, and centrifuged at 9800 rpm for 30 sec.  Supernatant was removed and pellets were immediately frozen in an ethanol-dry ice bath and stored at -80°C.

value: mid-log phase (OD660=0.885)

value: 649 min

source_name: Methanococcus maripaludis MM901 [reference sample]

value: mid-log phase (OD660=0.804)


title: Methanococcus maripaludis MM901 growth curve. Array 252330810013

description:
ch1:  Methanococcus maripaludis MM901 at OD660=1.56, t=912 min, Replicate 1
ch2:  Methanococcus maripaludis MM901 at OD660=0.804

value: mid-log phase (OD660=1.56)

value: 912 min


title: 336_rep2

city: Chicago

first: Christopher

middle: David

last: Brown

state: IL

department: Human Genetics

country: USA

institute: University of Chicago

description: Normal human liver gene expression

hyb_protocol: Array hybridizations were performed at The University of Chicago, Argonne National Labs high throughput genome analysis core facility.  1.65 µg of Cy3 labeled cRNA were fragmented, hybridized to Agilent-014850 4x44k array.

scan_protocol: Slides were scanned according the manufacturers instructions.

data_processing: Feature intensity was adjusted by subtracting background intensity using the minimum method (Ritchie, Silver et al. 2007), as implemented in limma (Smythe 2005). The distribution of background subtracted intensities from each array was adjusted by quantile normalization between arrays (Bolstad, Irizarry et al. 2003), as implemented in limma.

organism: Homo sapiens

label_protocol: cRNA was produced using the Agilent Low-Input Linear amplification and labeling kit.  Briefly, reverse transcription was performed on 1 µg of total RNA off an oligo dT primer using a modified MMLV-RT.  Linear amplification and Cy3-CTP labeling were performed with T7 RNA polymerase.  Labeling reactions were cleaned up with RNAeasy columns and total yield and label incorporation were quantified using a nanodrop spectrophotometer.  All reactions were performed after addition of  Agilent one-color spike-in RNA mix.  The spike-in mix contains 10 different in vitro synthesized viral RNAs that are premixed at different concentrations.

extract_protocol: RNA was extracted from tissue homogenized in TRIzol reagent, followed by a clean up on a Qiagen RNAeasy column as per manufacturers’ instructions. The quality of all total RNA samples was assessed with the Agilent Bio-Analyzer.  We required a RNA integrity number (RIN) ≥7 to proceed with labeling.

value: Primary Liver

tag: gender

value: male

tag: age

tag: ancestry


title: Methanococcus maripaludis MM901 growth curve. Array 252330810011

description:
ch1:  Methanococcus maripaludis MM901 at OD660=1.4, t=849 min, Replicate 1
ch2:  Methanococcus maripaludis MM901 at OD660=0.804

value: mid-log phase (OD660=1.4)

value: 849 min


title: 780_rep2

description: Normal human liver gene expression


title: 444_rep2

description: Normal human liver gene expression


title: 788_rep3

description: Normal human liver gene expression


title: 436_rep2

description: Normal human liver gene expression

value: female


title: 423_rep2

description: Normal human liver gene expression


title: 424_rep2

description: Normal human liver gene expression


title: Methanococcus maripaludis MM901 growth curve. Array 252330810015

description:
ch1:  Methanococcus maripaludis MM901 at OD660=1.58, t=1444 min, Replicate 1
ch2:  Methanococcus maripaludis MM901 at OD660=0.804

value: mid-log phase (OD660=1.58)


title: 751_rep2

description: Normal human liver gene expression


title: 152_rep2

description: Normal human liver gene expression


title: Methanococcus maripaludis MM901 growth curve. Array 252330810005

description:
ch1:  Methanococcus maripaludis MM901 at OD660=0.598, t=492 min, Replicate 1
ch2:  Methanococcus maripaludis MM901 at OD660=0.804

value: mid-log phase (OD660=0.598)

value: 492 min


title: 157_rep2

description: Normal human liver gene expression


title: Methanococcus maripaludis MM901 growth curve. Array 252330810016

description:
ch1:  Methanococcus maripaludis MM901 at OD660=0.804
ch2:  Methanococcus maripaludis MM901 at OD660=1.58, t=1444 min, Replicate 2


title: Methanococcus maripaludis MM901 growth curve. Array 252330810003

description:
ch1:  Methanococcus maripaludis MM901 at OD660=0.402, t=334 min, Replicate 1
ch2:  Methanococcus maripaludis MM901 at OD660=0.804

value: mid-log phase (OD660=0.402)

value: 334 min


title: Methanococcus maripaludis MM901 growth curve. Array 252330810012

description:
ch1:  Methanococcus maripaludis MM901 at OD660=0.804
ch2:  Methanococcus maripaludis MM901 at OD660=1.4, t=849 min, Replicate 2


title: 644_rep3

description: Normal human liver gene expression


title: 122_rep2

description: Normal human liver gene expression


title: Methanococcus maripaludis MM901 growth curve. Array 252330810008

description:
ch1:  Methanococcus maripaludis MM901 at OD660=0.804
ch2:  Methanococcus maripaludis MM901 at OD660=0.885, t=649 min, Replicate 2


title: 788_rep2

description: Normal human liver gene expression


title: Methanococcus maripaludis MM901 growth curve. Array 252330810010

description:
ch1:  Methanococcus maripaludis MM901 at OD660=0.804
ch2:  Methanococcus maripaludis MM901 at OD660=1.23, t=783 min, Replicate 2

value: mid-log phase (OD660=1.23)

value: 783 min


title: 750_rep2

description: Normal human liver gene expression


title: Methanococcus maripaludis MM901 growth curve. Array 252330810014

description:
ch1:  Methanococcus maripaludis MM901 at OD660=0.804
ch2:  Methanococcus maripaludis MM901 at OD660=1.56, t=912 min, Replicate 2


title: Methanococcus maripaludis MM901 growth curve. Array 252330810004

description:
ch1:  Methanococcus maripaludis MM901 at OD660=0.804
ch2:  Methanococcus maripaludis MM901 at OD660=0.402, t=334 min, Replicate 2


title: 644_rep2

description: Normal human liver gene expression


title: 345_rep2

description: Normal human liver gene expression


title: 485_rep3

description: Normal human liver gene expression


title: Methanococcus maripaludis MM901 growth curve. Array 252330810002

description:
ch1:  Methanococcus maripaludis MM901 at OD660=0.804
ch2:  Methanococcus maripaludis MM901 at OD660=0.2, t=70 min, Replicate 2

value: mid-log phase (OD660=0.2)

value: 70 min


title: 727_rep3

description: Normal human liver gene expression


title: 792_rep2

description: Normal human liver gene expression


title: 657_rep2

description: Normal human liver gene expression


title: Methanococcus maripaludis MM901 growth curve. Array 252330810006

description:
ch1:  Methanococcus maripaludis MM901 at OD660=0.804
ch2:  Methanococcus maripaludis MM901 at OD660=0.598, t=492 min, Replicate 2

value: mid-log phase (OD660=0.804)


title: 770_rep3

description: Normal human liver gene expression


title: Methanococcus maripaludis MM901 growth curve. Array 252330810001

description:
ch1:  Methanococcus maripaludis MM901 at OD660=0.2, t=70 min, Replicate 1
ch2:  Methanococcus maripaludis MM901 at OD660=0.804


title: 458_rep1

description: Normal human liver gene expression


title: 417_rep2

description: Normal human liver gene expression


title: 401_rep2

description: Normal human liver gene expression


title: 711_rep2

description: Normal human liver gene expression


title: 633_rep2

description: Normal human liver gene expression


title: 464_rep2

description: Normal human liver gene expression


title: 728_rep4

description: Normal human liver gene expression


title: 360_rep2

description: Normal human liver gene expression


title: 624_rep2

description: Normal human liver gene expression


title: 390_rep2

description: Normal human liver gene expression


title: 720_rep4

description: Normal human liver gene expression


title: 458_rep2

description: Normal human liver gene expression


title: 380_rep4

description: Normal human liver gene expression


title: 888_rep2

description: Normal human liver gene expression


title: 724_rep2

description: Normal human liver gene expression


title: 400_rep2

description: Normal human liver gene expression


title: 1_rep2

description: Normal human liver gene expression


title: Methanococcus maripaludis MM901 growth curve. Array 252330810009

description:
ch1:  Methanococcus maripaludis MM901 at OD660=1.23, t=783 min, Replicate 1
ch2:  Methanococcus maripaludis MM901 at OD660=0.804


title: 386_rep2

description: Normal human liver gene expression


title: 665_rep2

description: Normal human liver gene expression


title: 323_rep2

description: Normal human liver gene expression


title: 340_rep2

description: Normal human liver gene expression


title: 478_rep2

description: Normal human liver gene expression


title: 687_rep2

description: Normal human liver gene expression


title: 620_rep2

description: Normal human liver gene expression


title: 334_rep2

description: Normal human liver gene expression


title: 387_rep2

description: Normal human liver gene expression


title: 200_rep2

description: Normal human liver gene expression


title: 444_rep1

description: Normal human liver gene expression


title: 416_rep2

description: Normal human liver gene expression


title: 66_rep2

description: Normal human liver gene expression


title: 431_rep1

description: Normal human liver gene expression


title: 416_rep1

description: Normal human liver gene expression


title: 406_rep2

description: Normal human liver gene expression


title: 434_rep2

description: Normal human liver gene expression


title: 489_rep2

description: Normal human liver gene expression


title: 759_rep4

description: Normal human liver gene expression


title: 751_rep1

description: Normal human liver gene expression


title: 779_rep2

description: Normal human liver gene expression


title: 491_rep2

description: Normal human liver gene expression


title: 431_rep2

description: Normal human liver gene expression


title: 765_rep2

description: Normal human liver gene expression


title: 204_rep2

description: Normal human liver gene expression


title: 350_rep2

description: Normal human liver gene expression


title: 411_rep2

description: Normal human liver gene expression


title: 477_rep2

description: Normal human liver gene expression


title: 368_rep1

description: Normal human liver gene expression


title: 368_rep2

description: Normal human liver gene expression


title: 320_rep2

description: Normal human liver gene expression


title: 404_rep3

description: Normal human liver gene expression


title: 720_rep3

description: Normal human liver gene expression


title: 393_rep2

description: Normal human liver gene expression


title: 792_rep1

description: Normal human liver gene expression


title: 798_rep2

description: Normal human liver gene expression


title: 749_rep4

description: Normal human liver gene expression


title: 177_rep2

description: Normal human liver gene expression


title: 365_rep2

description: Normal human liver gene expression


title: 798_rep1

description: Normal human liver gene expression


title: 343_rep2

description: Normal human liver gene expression


title: 644_rep1

description: Normal human liver gene expression


title: 780_rep1

description: Normal human liver gene expression


title: 640_rep2

description: Normal human liver gene expression


title: 745_rep4

description: Normal human liver gene expression


title: 85_rep2

description: Normal human liver gene expression


title: 759_rep3

description: Normal human liver gene expression


title: 786_rep2

description: Normal human liver gene expression


title: 765_rep1

description: Normal human liver gene expression


title: 469_rep2

description: Normal human liver gene expression


title: 388_rep2

description: Normal human liver gene expression


title: 773_rep2

description: Normal human liver gene expression


title: 369_rep3

description: Normal human liver gene expression


title: 406_rep1

description: Normal human liver gene expression


title: 424_rep1

description: Normal human liver gene expression


title: 177_rep1

description: Normal human liver gene expression


title: 374_rep2

description: Normal human liver gene expression


title: 342_rep2

description: Normal human liver gene expression


title: 365_rep1

description: Normal human liver gene expression


title: 794_rep2

description: Normal human liver gene expression


title: 640_rep1

description: Normal human liver gene expression


title: 491_rep1

description: Normal human liver gene expression


title: 423_rep1

description: Normal human liver gene expression


title: 657_rep1

description: Normal human liver gene expression


title: 618_rep2

description: Normal human liver gene expression


title: 393_rep1

description: Normal human liver gene expression


title: 649_rep2

description: Normal human liver gene expression


title: 318_rep2

description: Normal human liver gene expression


title: 648_rep2

description: Normal human liver gene expression


title: 404_rep2

description: Normal human liver gene expression


title: 350_rep1

description: Normal human liver gene expression


title: 374_rep1

description: Normal human liver gene expression


title: 388_rep1

description: Normal human liver gene expression


title: 469_rep1

description: Normal human liver gene expression


title: 627_rep2

description: Normal human liver gene expression


title: 353_rep2

description: Normal human liver gene expression


title: 417_rep1

description: Normal human liver gene expression


title: 794_rep1

description: Normal human liver gene expression


title: 618_rep1

description: Normal human liver gene expression


title: 321_rep2

description: Normal human liver gene expression


title: 122_rep1

description: Normal human liver gene expression


title: 411_rep1

description: Normal human liver gene expression


title: 85_rep1

description: Normal human liver gene expression


title: 623_rep2

description: Normal human liver gene expression


title: 353_rep1

description: Normal human liver gene expression


title: 221_rep2

description: Normal human liver gene expression


title: 342_rep1

description: Normal human liver gene expression


title: 343_rep1

description: Normal human liver gene expression


title: 477_rep1

description: Normal human liver gene expression


title: 617_rep2

description: Normal human liver gene expression


title: 347_rep2

description: Normal human liver gene expression


title: 648_rep1

description: Normal human liver gene expression


title: 369_rep2

description: Normal human liver gene expression


title: 414_rep2

description: Normal human liver gene expression


title: 786_rep1

description: Normal human liver gene expression


title: 649_rep1

description: Normal human liver gene expression


title: 669_rep2

description: Normal human liver gene expression


title: 669_rep1

description: Normal human liver gene expression


title: 347_rep1

description: Normal human liver gene expression


title: 617_rep1

description: Normal human liver gene expression


title: 221_rep1

description: Normal human liver gene expression


title: 745_rep3

description: Normal human liver gene expression


title: 465_rep2

description: Normal human liver gene expression


title: 321_rep1

description: Normal human liver gene expression


title: 755_rep1

description: Normal human liver gene expression


title: 749_rep3

description: Normal human liver gene expression


title: 733_rep2

description: Normal human liver gene expression


title: 403_rep2

description: Normal human liver gene expression


title: 623_rep1

description: Normal human liver gene expression


title: 795_rep2

description: Normal human liver gene expression


title: 418_rep2

description: Normal human liver gene expression


title: 750_rep1

description: Normal human liver gene expression


title: 318_rep1

description: Normal human liver gene expression


title: 39_rep2

description: Normal human liver gene expression


title: 627_rep1

description: Normal human liver gene expression


title: 773_rep1

description: Normal human liver gene expression


title: 320_rep1

description: Normal human liver gene expression


title: 414_rep1

description: Normal human liver gene expression


title: 378_rep2

description: Normal human liver gene expression


title: 732_rep4

description: Normal human liver gene expression


title: 450_rep2

description: Normal human liver gene expression


title: 754_rep4

description: Normal human liver gene expression


title: 328_rep2

description: Normal human liver gene expression


title: 319_rep2

description: Normal human liver gene expression


title: 332_rep1

description: Normal human liver gene expression


title: 418_rep1

description: Normal human liver gene expression


title: 223_rep2

description: Normal human liver gene expression


title: 754_rep3

description: Normal human liver gene expression


title: 332_rep2

description: Normal human liver gene expression


title: 440_rep2

description: Normal human liver gene expression


title: 450_rep1

description: Normal human liver gene expression


title: 346_rep1

description: Normal human liver gene expression


title: 639_rep2

description: Normal human liver gene expression


title: 346_rep2

description: Normal human liver gene expression


title: 759_rep2

description: Normal human liver gene expression


title: 796_rep1

description: Normal human liver gene expression


title: 470_rep2

description: Normal human liver gene expression


title: 319_rep1

description: Normal human liver gene expression


title: 366_rep2

description: Normal human liver gene expression


title: 639_rep1

description: Normal human liver gene expression


title: 796_rep2

description: Normal human liver gene expression


title: 725_rep1

description: Normal human liver gene expression


title: 366_rep1

description: Normal human liver gene expression


title: 725_rep2

description: Normal human liver gene expression


title: 399_rep2

description: Normal human liver gene expression


title: 642_rep2

description: Normal human liver gene expression


title: 348_rep2

description: Normal human liver gene expression


title: 480_rep2

description: Normal human liver gene expression


title: 620_rep1

description: Normal human liver gene expression


title: 328_rep1

description: Normal human liver gene expression


title: 251_rep2

description: Normal human liver gene expression


title: 378_rep1

description: Normal human liver gene expression


title: 413_rep2

description: Normal human liver gene expression


title: 470_rep1

description: Normal human liver gene expression


title: 403_rep1

description: Normal human liver gene expression


title: 759_rep1

description: Normal human liver gene expression


title: 763_rep4

description: Normal human liver gene expression


title: 333_rep4

description: Normal human liver gene expression


title: 465_rep1

description: Normal human liver gene expression


title: 754_rep2

description: Normal human liver gene expression


title: 413_rep1

description: Normal human liver gene expression


title: 340_rep1

description: Normal human liver gene expression


title: 426_rep2

description: Normal human liver gene expression


title: 156_rep2

description: Normal human liver gene expression


title: 795_rep1

description: Normal human liver gene expression


title: 475_rep2

description: Normal human liver gene expression


title: 426_rep1

description: Normal human liver gene expression


title: 1_rep1

description: Normal human liver gene expression


title: 435_rep2

description: Normal human liver gene expression


title: 791_rep2

description: Normal human liver gene expression


title: 480_rep1

description: Normal human liver gene expression


title: 435_rep1

description: Normal human liver gene expression


title: 440_rep1

description: Normal human liver gene expression


title: 732_rep3

description: Normal human liver gene expression


title: 386_rep1

description: Normal human liver gene expression


title: 775_rep2

description: Normal human liver gene expression


title: 461_rep2

description: Normal human liver gene expression


title: 400_rep1

description: Normal human liver gene expression


title: 732_rep2

description: Normal human liver gene expression


title: 382_rep2

description: Normal human liver gene expression


title: 783_rep1

description: Normal human liver gene expression


title: 337_rep2

description: Normal human liver gene expression


title: 251_rep1

description: Normal human liver gene expression


title: 156_rep1

description: Normal human liver gene expression


title: 382_rep1

description: Normal human liver gene expression


title: 399_rep1

description: Normal human liver gene expression


title: 39_rep1

description: Normal human liver gene expression


title: 223_rep1

description: Normal human liver gene expression


title: 461_rep1

description: Normal human liver gene expression


title: 732_rep1

description: Normal human liver gene expression


title: 754_rep1

description: Normal human liver gene expression


title: 337_rep1

description: Normal human liver gene expression


title: 791_rep1

description: Normal human liver gene expression


title: 733_rep1

description: Normal human liver gene expression


title: 642_rep1

description: Normal human liver gene expression


title: 724_rep1

description: Normal human liver gene expression


title: 333_rep3

description: Normal human liver gene expression


title: 763_rep3

description: Normal human liver gene expression


title: 767_rep2

description: Normal human liver gene expression


title: 438_rep2

description: Normal human liver gene expression


title: 671_rep2

description: Normal human liver gene expression


title: 345_rep1

description: Normal human liver gene expression


title: 348_rep1

description: Normal human liver gene expression


title: 436_rep1

description: Normal human liver gene expression


title: 631_rep2

description: Normal human liver gene expression


title: 157_rep1

description: Normal human liver gene expression


title: 475_rep1

description: Normal human liver gene expression


title: 479_rep1

description: Normal human liver gene expression


title: 619_rep2

description: Normal human liver gene expression


title: 722_rep6

description: Normal human liver gene expression


title: 633_rep1

description: Normal human liver gene expression


title: 200_rep1

description: Normal human liver gene expression


title: 793_rep2

description: Normal human liver gene expression


title: 716_rep4

description: Normal human liver gene expression


title: 634_rep2

description: Normal human liver gene expression


title: 174_rep2

description: Normal human liver gene expression


title: 479_rep2

description: Normal human liver gene expression


title: 238_rep2

description: Normal human liver gene expression


title: 438_rep1

description: Normal human liver gene expression


title: 632_rep2

description: Normal human liver gene expression


title: 476_rep2

description: Normal human liver gene expression


title: 437_rep2

description: Normal human liver gene expression


title: 172_rep2

description: Normal human liver gene expression


title: 376_rep2

description: Normal human liver gene expression


title: 716_rep3

description: Normal human liver gene expression


title: 742_rep4

description: Normal human liver gene expression


title: 352_rep2

description: Normal human liver gene expression


title: 493_rep2

description: Normal human liver gene expression


title: 333_rep2

description: Normal human liver gene expression


title: 476_rep1

description: Normal human liver gene expression


title: 204_rep1

description: Normal human liver gene expression


title: 325_rep4

description: Normal human liver gene expression


title: 757_rep4

description: Normal human liver gene expression


title: 238_rep1

description: Normal human liver gene expression


title: 344_rep2

description: Normal human liver gene expression


title: 216_rep2

description: Normal human liver gene expression


title: 175_rep2

description: Normal human liver gene expression


title: 643_rep2

description: Normal human liver gene expression


title: 730_rep2

description: Normal human liver gene expression


title: 753_rep2

description: Normal human liver gene expression


title: 721_rep4

description: Normal human liver gene expression


title: 775_rep1

description: Normal human liver gene expression


title: 492_rep2

description: Normal human liver gene expression


title: 372_rep2

description: Normal human liver gene expression


title: 335_rep2

description: Normal human liver gene expression


title: 659_rep2

description: Normal human liver gene expression


title: 175_rep1

description: Normal human liver gene expression


title: 643_rep1

description: Normal human liver gene expression


title: 152_rep1

description: Normal human liver gene expression


title: 379_rep2

description: Normal human liver gene expression


title: 753_rep1

description: Normal human liver gene expression


title: 722_rep5

description: Normal human liver gene expression


title: 619_rep1

description: Normal human liver gene expression


title: 757_rep3

description: Normal human liver gene expression


title: 352_rep1

description: Normal human liver gene expression


title: 201_rep2

description: Normal human liver gene expression


title: 335_rep1

description: Normal human liver gene expression


title: 763_rep2

description: Normal human liver gene expression


title: 721_rep3

description: Normal human liver gene expression


title: 629_rep2

description: Normal human liver gene expression


title: 793

type: genomic

hyb_protocol: standard illumina protocols, please see illumina.com

data_processing: One sample was removed because it had a no call rate > 10%. The initial marker set comprised 620,901 markers. 8,300 markers were removed because they showed significant deviation from Hardy-Weinberg equilibrium (HWE, Fischer’s exact test, p<0.001). 29,705 SNPs were removed from the analysis because they had a no call rate in more than > 10% of the samples. Hence, our final marker set is comprised of 583,073 SNPs.  Identity by descent analysis, performed in Plink, revealed 14 pairs of duplicated samples.

label: C-Bio and A-DNP

molecule: genomic DNA

extract_protocol: Genomic DNA was extracted from frozen tissue samples using standard methods.


title: 632_rep1

description: Normal human liver gene expression


title: 800

scan_protocol: standard illumina protocols, please see illumina.com


title: 791

label_protocol: standard illumina protocols, please see illumina.com


title: 356_rep2

description: Normal human liver gene expression


title: 786


title: 797


title: 631_rep1

description: Normal human liver gene expression


title: 730_rep1

description: Normal human liver gene expression


title: 783


title: 492_rep1

description: Normal human liver gene expression


title: 795


title: 773


title: 794


title: 770


title: 780


title: 798


title: 767


title: 767_rep1

description: Normal human liver gene expression


title: 888


title: 357_rep2

description: Normal human liver gene expression


title: 788


title: 344_rep1

description: Normal human liver gene expression


title: 779


title: 765


title: 323_rep1

description: Normal human liver gene expression


title: 796


title: 778


title: 333_rep1

description: Normal human liver gene expression


title: 174_rep1

description: Normal human liver gene expression


title: 763


title: 759


title: 716_rep2

description: Normal human liver gene expression


title: 775


title: 325_rep3

description: Normal human liver gene expression


title: 754


title: 665_rep1

description: Normal human liver gene expression


title: 357_rep1

description: Normal human liver gene expression


title: 757


title: 216_rep1

description: Normal human liver gene expression


title: 336_rep1

description: Normal human liver gene expression


title: 201_rep1

description: Normal human liver gene expression


title: 753


title: 172_rep1

description: Normal human liver gene expression


title: 750


title: 716_rep1

description: Normal human liver gene expression


title: 379_rep1

description: Normal human liver gene expression


title: 793_rep1

description: Normal human liver gene expression


title: 671_rep1

description: Normal human liver gene expression


title: 659_rep1

description: Normal human liver gene expression


title: 745


title: 372_rep1

description: Normal human liver gene expression


title: 493_rep1

description: Normal human liver gene expression


title: 464_rep1

description: Normal human liver gene expression


title: 755


title: 749


title: 376_rep1

description: Normal human liver gene expression


title: 437_rep1

description: Normal human liver gene expression


title: 748


title: 742


title: 724


title: 489_rep1

description: Normal human liver gene expression


title: 744


title: 636_rep4

description: Normal human liver gene expression


title: 355_rep2

description: Normal human liver gene expression


title: 730


title: 733


title: 727


title: 751


title: 721_rep2

description: Normal human liver gene expression


title: 728


title: 732


title: 687


title: 720


title: 716


title: 721


title: 713_rep2

description: Normal human liver gene expression


title: 788_rep1

description: Normal human liver gene expression


title: 713_rep1

description: Normal human liver gene expression


title: 763_rep1

description: Normal human liver gene expression


title: 722


title: 728_rep3

description: Normal human liver gene expression


title: 662


title: 741


title: 725


title: 665


title: 634_rep1

description: Normal human liver gene expression


title: 721_rep1

description: Normal human liver gene expression


title: 636_rep3

description: Normal human liver gene expression


title: 713


title: 742_rep3

description: Normal human liver gene expression


title: 356_rep1

description: Normal human liver gene expression


title: 629_rep1

description: Normal human liver gene expression


title: 355_rep1

description: Normal human liver gene expression


title: 800_rep2

description: Normal human liver gene expression


title: 624_rep1

description: Normal human liver gene expression


title: 478_rep1

description: Normal human liver gene expression


title: 434_rep1

description: Normal human liver gene expression


title: 439_rep2

description: Normal human liver gene expression


title: 711


title: 381_rep2

description: Normal human liver gene expression


title: 659


title: 669


title: 651


title: 657


title: 360_rep1

description: Normal human liver gene expression


title: 46_rep2

description: Normal human liver gene expression


title: 671


title: 644


title: 459_rep2

description: Normal human liver gene expression


title: 639


title: 642


title: 351_rep2

description: Normal human liver gene expression


title: 220_rep2

description: Normal human liver gene expression


title: 640


title: 383_rep2

description: Normal human liver gene expression


title: 643


title: 632


title: 380_rep3

description: Normal human liver gene expression


title: 745_rep2

description: Normal human liver gene expression


title: 459_rep1

description: Normal human liver gene expression


title: 636


title: 629


title: 634


title: 631


title: 638


title: 433_rep4

description: Normal human liver gene expression


title: 649


title: 624


title: 363_rep4

description: Normal human liver gene expression


title: 633


title: 351_rep1

description: Normal human liver gene expression


title: 439_rep1

description: Normal human liver gene expression


title: 331_rep2

description: Normal human liver gene expression


title: 381_rep1

description: Normal human liver gene expression


title: 619


title: 325_rep2

description: Normal human liver gene expression


title: 727_rep2

description: Normal human liver gene expression


title: 630_rep2

description: Normal human liver gene expression


title: 720_rep2

description: Normal human liver gene expression


title: 648


title: 620


title: 623


title: 662_rep2

description: Normal human liver gene expression


title: 630


title: 618


title: 627


title: 466_rep2

description: Normal human liver gene expression


title: 617


title: 338_rep2

description: Normal human liver gene expression


title: 421_rep2

description: Normal human liver gene expression


title: 613


title: 745_rep1

description: Normal human liver gene expression


title: 492


title: 493


title: 485


title: 800_rep1

description: Normal human liver gene expression


title: 480


title: 484


title: 489


title: 162_rep2

description: Normal human liver gene expression


title: 331_rep1

description: Normal human liver gene expression


title: 485_rep2

description: Normal human liver gene expression


title: 483


title: 220_rep1

description: Normal human liver gene expression


title: 325_rep1

description: Normal human liver gene expression


title: 341_rep4

description: Normal human liver gene expression


title: 491


title: 474


title: 46_rep1

description: Normal human liver gene expression


title: 478


title: 479


title: 741_rep4

description: Normal human liver gene expression


title: 770_rep2

description: Normal human liver gene expression


title: 476


title: 202_rep4

description: Normal human liver gene expression


title: 470


title: 253_rep2

description: Normal human liver gene expression


title: 477


title: 475


title: 484_rep2

description: Normal human liver gene expression


title: 466


title: 151_rep4

description: Normal human liver gene expression


title: 469


title: 722_rep4

description: Normal human liver gene expression


title: 387_rep1

description: Normal human liver gene expression


title: 461


title: 465


title: 457


title: 779_rep1

description: Normal human liver gene expression


title: 464


title: 757_rep2

description: Normal human liver gene expression


title: 749_rep2

description: Normal human liver gene expression


title: 415_rep2

description: Normal human liver gene expression


title: 742_rep2

description: Normal human liver gene expression


title: 459


title: 728_rep2

description: Normal human liver gene expression


title: 450


title: 458


title: 662_rep1

description: Normal human liver gene expression


title: 442


title: 651_rep2

description: Normal human liver gene expression


title: 349_rep2

description: Normal human liver gene expression


title: 448


title: 466_rep1

description: Normal human liver gene expression


title: 445


title: 421_rep1

description: Normal human liver gene expression


title: 439


title: 444


title: 440


title: 217_rep2

description: Normal human liver gene expression


title: 438


title: 435


title: 778_rep2

description: Normal human liver gene expression


title: 744_rep2

description: Normal human liver gene expression


title: 434


title: 390_rep1

description: Normal human liver gene expression


title: 720_rep1

description: Normal human liver gene expression


title: 728_rep1

description: Normal human liver gene expression


title: 446


title: 742_rep1

description: Normal human liver gene expression


title: 433


title: 687_rep1

description: Normal human liver gene expression


title: 431


title: 349_rep1

description: Normal human liver gene expression


title: 436


title: 421


title: 418


title: 423


title: 338_rep1

description: Normal human liver gene expression


title: 749_rep1

description: Normal human liver gene expression


title: 727_rep1

description: Normal human liver gene expression


title: 416


title: 415


title: 409


title: 630_rep1

description: Normal human liver gene expression


title: 419


title: inducible_phrS_gene_repB

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

hyb_protocol: 1. 1ug of fragmented and labeled cDNA were hybridized at 500C onto GeneChip P.aeruginosa Genome arrays, washed and labeled on the fluidic station using the modified fluidic protocol for P. aeruginosa cDNA assay.

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003) for each tissues and each time points separately.

organism: Pseudomonas aeruginosa

source_name: Bacterial RNA

label_protocol: cDNA synthesis was performed according to the Gene Chip P.aeruginosa Array, Expression Analysis protocol (701006rev.2) with the following modification: The cDNA synthesis was performed using 1mM dGTP,dCTP,dATP each, and 0.8mMdTTP, 0.2mM dUTP. I.5ug of cDNA was fragmented using uracil glycosylase and apurinic endonuclease.

growth_protocol: Strain PAO6671 (delta-phrS) carrying either the parental vector pJT19 or the phrS over-expression plasmid pJTphrS were grown in LB medium to an OD600 of 1.0 and then phrS expression was induced with 2 mM toluate. 30 minutes after induction total RNA treated with RNA protect bacteria reagent® (Qiagen) was purified.

extract_protocol: RNA purification was performed by the hot phenol method as described (Leoni et al, 1996). Briefly, the cell pellets of 10 ml culture were mixed with pre-heated (65°C) 2.5 ml lysis buffer (2% sodium dodecyl sulfate, 30 mM Na-acetate and 3 mM EDTA, pH 5.5) and 5 ml phenol (pH 5.5). The mixture was vigorously shaken for 8 min and incubated for 5 min on ice and then centrifuged at 4°C for 15 min at 5000 rpm. Total RNA was obtained by phenol chloroform extraction and precipitated with ethanol and Na-acetate (pH 5.5). To eliminate DNA contamination the total RNA was treated with 40 U of DNAse I (Roche) followed by phenol-chloroform extraction and ethanol precipitation. The quality of the RNA was determined on MOPS-formaldehyde agarose-gels (Sambrook and Russel, 2001).

value: PAO6671 (delta-phrS)

tag: vector

value: pJTphrS

tag: genotype/variation

value: phrS induction


title: 437

value: Primary Liver


title: 426


title: 651_rep1

description: Normal human liver gene expression

value: male


title: 413


title: 411


title: 424


title: 407


title: vector_contol_repB

value: pJT19 (parental vector)

value: control


title: 757_rep1

description: Normal human liver gene expression


title: vector_contol_repA


title: 778_rep1

description: Normal human liver gene expression


title: 162_rep1

description: Normal human liver gene expression


title: 417


title: 408


title: 414


title: 404

value: female


title: 406


title: 711_rep1

description: Normal human liver gene expression


title: small airways, COPD 130

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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.

source_name: airway epithelial cells obtained by bronchoscopy and brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: Age

tag: Sex

value: F

tag: Ethnic group

value: white

tag: Smoking status

value: COPD, GOLD-II, 38.5 pack-years


title: 403

tag: tissue


title: 66_rep1

description: Normal human liver gene expression


title: 170

city: Huntsville

first: Greg

last: Cooper

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description: This Sample consists of two replicates

hyb_protocol: Labeled RNA was hybridized to Illumina HumanRef-8 v.2 beadchips (GPL6104), washed, and stained with Cy3-Streptavidin.

scan_protocol: Scanning was performed on an Illumina BeadArray Reader.

data_processing: All liver samples were analyzed with two technical replicates that were randomized between processed batches of 24 arrays performed on different days.  Raw signal intensity measurements from each sample were processed using the Illumina BeadStudio software v. 2.3.41 using the ‘average’ normalization function.  Replicate data from each liver was averaged prior to statistical (eQTL) analysis.

label_protocol: 750 ng of cRNA was amplified and labeled with biotin.

extract_protocol: Expression analysis was performed using standard Illumina array protocols.  Briefly, total total RNA was extracted using Trizol reagent and quality assessed with the Agilent BioAnalyzer.

tag: ancestry (pc 1)

tag: ancestry (pc 2)


title: 171

description: This Sample consists of two replicates


title: 744_rep1

description: Normal human liver gene expression


title: 359_rep1

description: Normal human liver gene expression


title: 217_rep1

description: Normal human liver gene expression


title: inducible_phrS_gene_repA

tag: strain


title: 386


title: 390


title: 169

description: This Sample consists of two replicates

value: M


title: 888_rep1

description: Normal human liver gene expression


title: 168

description: This Sample consists of two replicates


title: 393


title: 399


title: 741_rep3

description: Normal human liver gene expression


title: 381


title: 388


title: 379


title: 380


title: 166

description: This Sample consists of two replicates


title: 378


title: 167

description: This Sample consists of two replicates


title: 741_rep1

description: Normal human liver gene expression


title: 165

description: This Sample consists of two replicates


title: 741_rep2

description: Normal human liver gene expression


title: 387


title: 722_rep3

description: Normal human liver gene expression


title: 376


title: 365


title: 372


title: 368


title: 172

description: This Sample consists of two replicates


title: 366


title: 164

description: This Sample consists of two replicates


title: 363


title: 722_rep2

description: Normal human liver gene expression


title: 162

description: This Sample consists of two replicates


title: 163

description: This Sample consists of two replicates


title: 433_rep3

description: Normal human liver gene expression


title: 383


title: 362


title: 359


title: 161

description: This Sample consists of two replicates


title: 360


title: 433_rep2

description: Normal human liver gene expression


title: 722_rep1

description: Normal human liver gene expression


title: 159

description: This Sample consists of two replicates


title: 160

description: This Sample consists of two replicates


title: 369


title: 358


title: 380_rep2

description: Normal human liver gene expression


title: 158

description: This Sample consists of two replicates


title: 400


title: 357


title: 356


title: 157

description: This Sample consists of two replicates


title: 380_rep1

description: Normal human liver gene expression


title: 433_rep1

description: Normal human liver gene expression


title: 363_rep3

description: Normal human liver gene expression


title: 156

description: This Sample consists of two replicates


title: 351


title: 382


title: 374


title: 352


title: 389


title: 354


title: 155

description: This Sample consists of two replicates


title: 363_rep2

description: Normal human liver gene expression


title: 363_rep1

description: Normal human liver gene expression


title: 348


title: 401


title: 154

description: This Sample consists of two replicates


title: 341_rep3

description: Normal human liver gene expression


title: 353


title: 341_rep2

description: Normal human liver gene expression


title: 355


title: 153

description: This Sample consists of two replicates


title: 347


title: 342


title: 341_rep1

description: Normal human liver gene expression


title: 150

description: This Sample consists of two replicates


title: 345


title: 349


title: 152

description: This Sample consists of two replicates


title: 149

description: This Sample consists of two replicates


title: 202_rep3

description: Normal human liver gene expression


title: 350


title: 202_rep2

description: Normal human liver gene expression


title: 343


title: 202_rep1

description: Normal human liver gene expression


title: 341


title: 337


title: 147

description: This Sample consists of two replicates


title: 340


title: 148

description: This Sample consists of two replicates


title: 336


title: 344


title: 151_rep3

description: Normal human liver gene expression


title: 346


title: 146

description: This Sample consists of two replicates


title: 151_rep2

description: Normal human liver gene expression


title: 335


title: 334


title: 145

description: This Sample consists of two replicates


title: 144

description: This Sample consists of two replicates


title: 332


title: 143

description: This Sample consists of two replicates


title: 333


title: 320


title: 770_rep1

description: Normal human liver gene expression


title: 328


title: 484_rep1

description: Normal human liver gene expression


title: 485_rep1

description: Normal human liver gene expression


title: 253


title: 142

description: This Sample consists of two replicates


title: 141

description: This Sample consists of two replicates


title: 151_rep1

description: Normal human liver gene expression


title: 251


title: 415_rep1

description: Normal human liver gene expression


title: 139

description: This Sample consists of two replicates


title: 248


title: 321


title: 401_rep1

description: Normal human liver gene expression


title: 318


title: 138

description: This Sample consists of two replicates


title: 238


title: 383_rep1

description: Normal human liver gene expression


title: 223


title: 331


title: 216


title: 204


title: 323


title: 202


title: 217


title: 137

description: This Sample consists of two replicates


title: 338


title: 325


title: 220


title: 201


title: 319


title: 221


title: 135

description: This Sample consists of two replicates


title: 253_rep1

description: Normal human liver gene expression


title: 136

description: This Sample consists of two replicates


title: 200


title: 457_rep2

description: Normal human liver gene expression


title: 334_rep1

description: Normal human liver gene expression


title: MT2_L-GMP 3

city: Cambridge

first: Brian

last: Huntly

address: Wellcome Trust/MRC Building, Hills Road

department: Cambridge Institute for Medical Research

country: United Kingdom

institute: University of Cambridge

description:
Gene expression data from murine leukemic stem cells (LSC), with GMP surface phenotype
K_MT2 L-GMP 3.CEL

hyb_protocol: Gene expression levels were measured using Affymetrix (Santa Clara, CA) GeneChip Mouse Genome 430A 2.0 arrays (22,690 probesets) with hybridisation and washes as per the manufacturers specifications.

scan_protocol: As per Affymetrix specifications.

data_processing:
The starting point for all analyses was the ''.CEL'' files from the MAS5 software. Data was analyzed using the R statistical package bioconductor. Data quality was assessed using functions in the affy and affyPLM packages and outlier arrays were removed from subsequent analysis.
The GCRMA algorithm (ver. 2.4.1) was used to obtain normalized expression estimates.

source_name: Murine leukemic stem cells (LSC), with GMP surface phenotype

label_protocol: As per the manufacturer's instructions and as previously published, with one modification: biotinylated CTP and UTP (Enzo Diagnostics, Farmingdale, NY) in a 2.5:1 proportion to non-biotinylated CTP and UTP. All RNA populations were simultaneously amplified.

extract_protocol: 36 hours after spininoculation of oncogene or empty-vector transduced GMP, GFP positive cells were homogenized with TRIzol® Reagent (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions. RNA isolated from the above populations along with sorted normal LSK, GMP, and MOZ-TIF2 leukemic GMP were quantitated with the Quant-iT™ RiboGreen® RNA Reagent and Kit (Invitrogen) according to manufacturer’s specifications, and used for RNA amplification and hybridization as previously published.

tag: cell type

value: leukemic stem cells (LSC)

tag: transduction protocol


title: 134

description: This Sample consists of two replicates


title: MT2_L-GMP 2

description:
Gene expression data from murine leukemic stem cells (LSC), with GMP surface phenotype
J_MT2 L-GMP 2.CEL


title: 404_rep1

description: Normal human liver gene expression


title: CRM-stimulated PBMC from vaccinated newborns, RNA pool/group 5

city: Subiaco

first: Anthony

last: Bosco

state: WA

address: 100 Roberts Road

country: Australia

institute: Telethon Kids Institute

hyb_protocol: The samples were hybridized to HuGene ST1.0 microarrays according to standardized protocols and reagents from Affymetrix.

scan_protocol: The samples were scanned on a GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed in Expression Consol software (Affymetrix) employing the probe logarithmic intensity error algorithm (PLIER, parameters - PM-GCBG background subtraction, quantile normalization, iterPLIER summarization).

source_name: Recall responses to CRM antigen in PBMC collected at 9 months of age from infants who were vaccinated at birth.

label_protocol: The samples were labelled according to standardized protocols and reagents from Affymetrix.

growth_protocol: PBMC were cultured in RPMI/5% HI-human AB seruem for 72 hours.

extract_protocol: PBMC samples were extracted with TRIzol followed by Rneasy.

treatment_protocol: PBMC were cultured in the presence or absence of CRM197 antigen.

value: PBMC

value: 9 months

tag: age at vaccination

value: newborn

tag: treatment group

value: CRM-stimulated


title: 133

description: This Sample consists of two replicates

tag: gender


title: 636_rep2

description: Normal human liver gene expression

tag: age


title: Unstimulated PBMC from vaccinated newborns, RNA pool/group 5

source_name: Unstimulated PBMC collected at 9 months of age from infants who were vaccinated at birth.

value: Unstimulated


title: 132

description: This Sample consists of two replicates


title: 174

tag: ancestry


title: MT2_L-GMP 1

description:
Gene expression data from murine leukemic stem cells (LSC), with GMP surface phenotype
11_MT2 L-GMP 1_020407.CEL


title: Unstimulated PBMC from vaccinated newborns, RNA pool/group 4


title: 130

description: This Sample consists of two replicates


title: 457_rep1

description: Normal human liver gene expression


title: CRM-stimulated PBMC from vaccinated newborns, RNA pool/group 3


title: 369_rep1

description: Normal human liver gene expression


title: 636_rep1

description: Normal human liver gene expression


title: GMP GFP 3

description:
Gene expression data from murine granulocyte monocyte progenitor (GMP); transduced with GFP (empty-vector)
E_GFP 3_020407.CEL

source_name: Murine granulocyte monocyte progenitor (GMP); transduced with GFP (empty-vector)

value: granulocyte monocyte progenitor (GMP)

value: transduced with GFP (empty-vector)


title: 175

value: Primary Liver


title: GMP GFP 2

description:
Gene expression data from murine granulocyte monocyte progenitor (GMP); transduced with GFP (empty-vector)
6_GFP 2_020407.CEL


title: CRM-stimulated PBMC from vaccinated newborns, RNA pool/group 4


title: 131

description: This Sample consists of two replicates


title: 162

value: male


title: 172


title: 177


title: 128

description: This Sample consists of two replicates


title: GMP GFP 1

description:
Gene expression data from murine granulocyte monocyte progenitor (GMP); transduced with GFP (empty-vector)
5_GFP 1_020407.CEL


title: Unstimulated PBMC from vaccinated newborns, RNA pool/group 3


title: 407_rep1

description: Normal human liver gene expression


title: CRM-stimulated PBMC from vaccinated newborns, RNA pool/group 2


title: 157


title: 125

description: This Sample consists of two replicates


title: 127

description: This Sample consists of two replicates


title: 124

description: This Sample consists of two replicates


title: AE-GMP 3

description:
Gene expression data from murine granulocyte monocyte progenitor (GMP); transduced with AML1-ETO oncogene
M_AE 3_062007.CEL

source_name: Murine granulocyte monocyte progenitor (GMP); transduced with AML1-ETO oncogene

value: transduced with AML1-ETO oncogene


title: 358_rep2

description: Normal human liver gene expression


title: Unstimulated PBMC from vaccinated newborns, RNA pool/group 2


title: CRM-stimulated PBMC from vaccinated newborns, RNA pool/group 1


title: 121

description: This Sample consists of two replicates


title: 358_rep1

description: Normal human liver gene expression


title: AE-GMP 2

description:
Gene expression data from murine granulocyte monocyte progenitor (GMP); transduced with AML1-ETO oncogene
L_AE 2_062007.CEL


title: 152


title: 87


title: 120

description: This Sample consists of two replicates


title: Unstimulated PBMC from vaccinated newborns, RNA pool/group 1


title: 85


title: NHA9-GMP 3

description:
Gene expression data from murine granulocyte monocyte progenitor (GMP); transduced with NUP98-HOXA9 oncogene
I_NHA9 3.CEL

source_name: Murine granulocyte monocyte progenitor (GMP); transduced with NUP98-HOXA9 oncogene

value: transduced with NUP98-HOXA9 oncogene


title: Unstimulated PBMC from vaccinated infants, RNA pool/group 5

source_name: Unstimulated PBMC collected at 9 months of age from infants who were vaccinated at 1 month.

value: 1 month


title: 119

description: This Sample consists of two replicates


title: MT2-GMP 4

description:
Gene expression data from murine granulocyte monocyte progenitor (GMP); transduced with MOZ-TIF2 oncogene
G_MT2 4_062007.CEL

source_name: Murine granulocyte monocyte progenitor (GMP); transduced with MOZ-TIF2 oncogene

value: transduced with MOZ-TIF2 oncogene


title: CRM-stimulated PBMC from vaccinated infants, RNA pool/group 5

source_name: Recall responses to CRM antigen in PBMC collected at 9 months of age from infants who were vaccinated at 1 month.


title: 151


title: 115

description: This Sample consists of two replicates

value: F


title: CRM-stimulated PBMC from vaccinated infants, RNA pool/group 4


title: NHA9-GMP 1

description:
Gene expression data from murine granulocyte monocyte progenitor (GMP); transduced with NUP98-HOXA9 oncogene
9_NHA9 1_020407.CEL


title: 122


title: 407_rep2

description: Normal human liver gene expression


title: AE-GMP 4

description:
Gene expression data from murine granulocyte monocyte progenitor (GMP); transduced with AML1-ETO oncogene
12_AE 4_062007.CEL


title: 39


title: 156


title: 114

description: This Sample consists of two replicates


title: 118

description: This Sample consists of two replicates


title: Unstimulated PBMC from vaccinated infants, RNA pool/group 3


title: Sf301_LB+Con_Sta_rep1

city: Beijing

first: Junping

last: Peng

address: No 6, Rongjing Eastern Street, BDA

institute: Chinese center for disease control and prevention

description: This sample is of wild-type Shigella flexneri 2a strain 301  at 37℃ in LB+0.01% congo red medium, in stationary phase. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Labeled cDNA samples were individually hybridized to the microarray according to the NimbleGen standard operating procedure. Competitive hybridization was done three times for the sample from one condition.

scan_protocol: Microarrays were scanned at a 5μm resolution using a GenePix 4000B scanner (Axon Instruments). Data were extracted using NimbleScan (NimbleGen).

organism: Shigella flexneri 2a str. 301

source_name: Shigella flexneri 2a strain 301 wild-type

label_protocol: The separate labeling reactions were pooled after each respective Cy dye incorporation step and then again divided into aliquots to minimize inconsistencies in probe generation. cDNA was purified with a QIAquick PCR Purification kit (QIAGEN) according to the QIAquick Spin handbook.

growth_protocol: S. flexneri 2a strain 301(Sf301) was routinely grown at 37℃ overnight on Luria-Bertani(LB) agar plate containing 0.01% congo red. A single red colony was inoculated into LB medium without antibiotics and grown overnight at 37℃ and 250 r.p.m. For RNA extraction, an overnight culture of bacteria was diluted 1: 50 into 100 ml fresh medium with aeration by rotary shaking (250 r.p.m.)

extract_protocol: Total RNA was isolated using a Promega SV total RNA purification kit according to the manufacturer’s instructions.

tag: genotype

value: Wild-type

tag: phenotype

value: normal

tag: growth condition


title: 38


title: Sf301_LB+Con_Sta_rep2

description: This sample is of wild-type Shigella flexneri 2a strain 301  at 37℃ in LB+0.01% congo red medium, in stationary phase. It is the seond of three wild-type biological replicates used in this experiment, each from separate cultures.


title: 46

value: female


title: 111

description: This Sample consists of two replicates

value: M


title: 113

description: This Sample consists of two replicates


title: NHA9-GMP 2

description:
Gene expression data from murine granulocyte monocyte progenitor (GMP); transduced with NUP98-HOXA9 oncogene
10_ NHA9 2_020407.CEL


title: 1


title: Unstimulated PBMC from vaccinated infants, RNA pool/group 4

value: PBMC

value: 9 months


title: 66


title: MT2-GMP 3

description:
Gene expression data from murine granulocyte monocyte progenitor (GMP); transduced with MOZ-TIF2 oncogene
H_MT2 3_020407.CEL


title: Sf301_LB+Con_Sta_rep3

description: This sample is of wild-type Shigella flexneri 2a strain 301  at 37℃ in LB+0.01% congo red medium, in stationary phase. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: MT2-GMP 2

description:
Gene expression data from murine granulocyte monocyte progenitor (GMP); transduced with MOZ-TIF2 oncogene
8_MT2 2_020407.CEL


title: CRM-stimulated PBMC from vaccinated infants, RNA pool/group 2

value: CRM-stimulated


title: Unstimulated PBMC from vaccinated infants, RNA pool/group 2

value: Unstimulated


title: MT2-GMP 1

description:
Gene expression data from murine granulocyte monocyte progenitor (GMP); transduced with MOZ-TIF2 oncogene
7_MT2 1_020407.CEL

value: granulocyte monocyte progenitor (GMP)


title: CRM-stimulated PBMC from vaccinated infants, RNA pool/group 3


title: GMP 4

description:
Gene expression data from murine granulocyte monocyte progenitor (GMP); untransduced
4_ GMP 4_062007.CEL

source_name: Murine granulocyte monocyte progenitor (GMP); untransduced

value: untransduced


title: 109

description: This Sample consists of two replicates

value: Primary Liver


title: Sf301_LB+Con_Log_rep3

description: This sample is of wild-type Shigella flexneri 2a strain 301  at 37℃ in LB+0.01% congo red medium, in log phase. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: Sf301_LB+Con_Log_rep2

description: This sample is of wild-type Shigella flexneri 2a strain 301  at 37℃ in LB+0.01% congo red medium, in log phase. It is the seond of three wild-type biological replicates used in this experiment, each from separate cultures.


title: 108

description: This Sample consists of two replicates


title: GMP 2

description:
Gene expression data from murine granulocyte monocyte progenitor (GMP); untransduced
17_GMP 2_020407.CEL


title: CRM-stimulated PBMC from vaccinated infants, RNA pool/group 1


title: Unstimulated PBMC from vaccinated infants, RNA pool/group 1


title: Seed (Sl) vs mesocarp (Ml) at late development phase

city: Legnaro

first: claudio

last: Bonghi

state: Padova

address: Viale dell'UNiversità, 16

country: Italy

institute: University of Padova

description: Analysis used to compare transcript levels in seed (Sl) and mesocarp (Ml) at late development.

hyb_protocol: Pre-hybridisations were carried out by soaking whole glass slides in a solution containing 5X SSC, 0.1% SDS, 5X Denhardt’s solution and 100ng/μL DNA carrier at 48°C for at least 2 h. Then the slides were washed once with a 0.2X SSC solution and dried by centrifuging for 4 min at 1000 rpm. Hybridisations were carried out in 250 µL of hybridisation solution (5X SSC, 0.1% SDS, 25% formamide) containing 100-150 pmol of Cy3- and Cy5-labelled target cDNAs.  The glass slides were placed in a hybridisation chamber (Corning, USA) kept on a water bath at 48°C  at least 36 h. Then the slides were briefly rinsed with 1X SSC 0.1% SDS and washed once the same solution for 5 min. Three additional washes (one with 0.2XSSC 0.1% SDS and two with 0.2X SSC, for 5 min each) at room temperature were performed before drying the glass slides with a brief centrifugation. The probe design and these hybridisation/washing conditions allow the detection of specific genes even within gene families.

scan_protocol: The microarray was scanned with a two channel confocal microarray scanner (ScanArray® Lite, Perkin Elmer, USA) using its dedicated software (ScanArray Express 3.0.0., Perkin Elmer). The laser power and the photomultiplier tube (PMT) were set between 75 and 85 % of maximum. The excitation/emission settings were 543/570 nm for Cy3 and 633/670 nm for Cy5. After laser focusing and balancing of the two channels, scans were conducted at a resolution of 5 μm. For any scan, two separate 16-bit TIFF images were produced.

data_processing:
Software from the TM4 (www.tm4.org) package developed at TIGR (www.tigr.org, Saeed et al., 2003) was used to analyze microarray data. Images were processed using the Spotfinder 2.2.3. software by means of the Otsu algorithm. Spots were also visually examined to delete the non-uniform ones.
The expression data extracted by Spotfinder were normalized by MIDAS 2.18 using the LOWESS (Locally Weighted Regression Scatter Plot Smoothing, Cleveland, 1979) algorithm with the “block mode”, keeping as reference the Cy3 channel. The “IA” and “IB” values have been used to determine log2(IB/IA) reported in the “VALUE column of the data table. The data from the technical replicates have been averaged.
Normalized split data were loaded in MeV 4.3 and subjected to SAM (Significance Analysis of Microarrays, Tusher et al., 2001) analyses.  Lists of clones with significant changes in expression were identified at delta values that gave a false discovery rate (FDR) of 0% (90th percentile).

The labeling scheme for each channel of the supplementary files is available in the 'GSE22582_readme.txt' file, which is linked to the Series GSE22582 record.

organism: Prunus persica

source_name: seed late development (Sl)

label_protocol: Total RNA (20 μg) was converted into target cDNA by reverse transcription using the SuperScriptTM Indirect cDNA Labeling System (Invitrogen, USA) following manufacturer instruction. The amino-modified cDNA was coupled to a monoreactive N-hydroxysuccinimide (NHS)-ester fluorescent dyes: the red-fluorescent cyanine5 (Cy5) and the green-fluorescent cyanine3 (Cy3) (GE Healthcare, USA). A final purification step using Microcon-PCR centrifugal filter devices (Millipore, USA) removed any unincorporated dye. The purity and yield of the labelled cDNA was calculated from the OD values obtained by means of a spectrophotometer using the formulas reported in the SuperScriptTM Indirect cDNA Labeling System instruction manual.

growth_protocol: Peach of cv 'Fantasia’  were collected at 42, 60, 106 and 123 days after full bloom (DAFB), corresponding to the first exponential growth phase (S1), the onset (S2I) of pit hardening, the second exponential growth phase (S3) and the ripening (S4), respectively. Mesocarp and seed were excised from fruit and immediately frozen in liquid nitrogen and stored at -80°C until use. To monitor seed development, seeds were excised from fruit starting from late S1 up to ripening at weekly intervals, dissected and viewed by stereomicroscopy.

extract_protocol: Frozen mesocarp and seed were ground in liquid nitrogen to a fine powder and total RNA was extracted as described by Ruperti and co-workers (2001, Physiol Plant 2001, 111(3):336-344). Fifty μg of total RNA were treated with 10 units of RQ1 RNase-Free DNAse (Promega) and 1 unit of RNAguard (RNase INHIBITOR) (Amersham) for 30 min, and then purified by phenol-chlorophorm according to the manufacturer’s instructions. The concentration of RNA was quantified by measuring the absorbance at 260 nm and its integrity was checked electrophoretically on agarose gels.

treatment_protocol: No treatment was performed.

tag: cultivar

value: Fantasia

value: seed

tag: developmental stage

value: late

source_name: Mesocarp late development (Ml)

value: mesocarp


title: AE-GMP 1

description:
Gene expression data from murine granulocyte monocyte progenitor (GMP); transduced with AML1-ETO oncogene
13_AE 1_020407.CEL

value: transduced with AML1-ETO oncogene


title: GMP 1

description:
Gene expression data from murine granulocyte monocyte progenitor (GMP); untransduced
3_ GMP 1_020407.CEL


title: 106

description: This Sample consists of two replicates

value: F


title: Sf301_LB_Sta_rep3

description: This sample is of wild-type Shigella flexneri 2a strain 301  at 37℃ in LB medium, in stationary phase. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.

value: Wild-type


title: 104

description: This Sample consists of two replicates


title: 105

description: This Sample consists of two replicates


title: GMP 3

description:
Gene expression data from murine granulocyte monocyte progenitor (GMP); untransduced
C_GMP 3_020407.CEL


title: Sf301_LB_Sta_rep1

description: This sample is of wild-type Shigella flexneri 2a strain 301  at 37℃ in LB medium, in stationary phase. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.

value: normal


title: HSC 3

description:
Gene expression data from murine hematopoietic stem cells (HSC), (LSK phenotype); untransduced
1_HSC 3.CEL

source_name: Murine hematopoietic stem cells (HSC), (LSK phenotype); untransduced

value: hematopoietic stem cells (HSC)


title: HSC 1

description:
Gene expression data from murine hematopoietic stem cells (HSC), (LSK phenotype); untransduced
A_HSC 1_020407.CEL


title: HSC 2

description:
Gene expression data from murine hematopoietic stem cells (HSC), (LSK phenotype); untransduced
B_HSC 2_020407.CEL


title: Sf301_LB_Sta_rep2

description: This sample is of wild-type Shigella flexneri 2a strain 301  at 37℃ in LB medium, in stationary phase. It is the seond of three wild-type biological replicates used in this experiment, each from separate cultures.


title: 5m_rep2

status: Public on Jun 26 2011

city: Milano

first: Riccardo

middle: Lorenzo

last: Rossi

state: MI

address: Via Trivulzio 10

department: Integrative Biology

institute: Fondazione INGM

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation (no background subtraction) with BeadStudio 3.0

source_name: Memory CD4+ T cells, sample#5, replica2

label_protocol: Biotinylated cRNA were prepared with the MessageAmp kit for Illumina arrays (Ambion)

extract_protocol: RNA was extracted with  miRVANA kit (Ambion), in accordance with the standard protocol (miRNA preserving one) provided with the kit. Quality control was performed with 2100 Bioanalyser from Agilent.

value: periperhal blood

tag: tag

value: memory CD4+T lymphocytes


title: 6m_rep2

source_name: Memory CD4+ T cells, sample#6, replica2

tag: tissue


title: 7m_rep1

source_name: Memory CD4+ T cells, sample#7, replica1


title: 5m_rep1

source_name: Memory CD4+ T cells, sample#5, replica1


title: Mesocarp late development (Ml) vs early development (Me)

description: Analysis used to compare transcript levels in mesocarp at late (Ml) and early (Me) development.

source_name: mesocarp late development (Ml)

source_name: Mesocarp early development (Me)

value: early


title: 102

description: This Sample consists of two replicates

value: M

tag: ancestry (pc 1)


title: Seed late development (Sl) vs early development (Se)

description: Analysis used to compare transcript levels in seed at late (Sl) and early (Se) development.

source_name: Seed early development (Se)


title: Sf301_LB_Log_rep3

description: This sample is of wild-type Shigella flexneri 2a strain 301  at 37℃ in LB medium, in log phase. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.

value: at 37℃ in LB medium, in log phase.


title: Sf301_LB_Log_rep2

description: This sample is of wild-type Shigella flexneri 2a strain 301  at 37℃ in LB medium, in log phase. It is the seond of three wild-type biological replicates used in this experiment, each from separate cultures.


title: 7m_rep2

source_name: Memory CD4+ T cells, sample#7, replica2


title: 026N

source_name: Naive CD4+ T cells, sample#026

value: naive CD4+T lymphocytes


title: 7N_rep2

source_name: Naive CD4+ T cells, sample#7, replica2


title: 3m_rep2

source_name: Memory CD4+ T cells, sample#3, replica2


title: 7N_rep1

source_name: Naive CD4+ T cells, sample#7, replica1


title: 6m_rep1

source_name: Memory CD4+ T cells, sample#6, replica1


title: Sf301_LB_Log_rep1

description: This sample is of wild-type Shigella flexneri 2a strain 301  at 37℃ in LB medium, in log phase. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Shigella flexneri 2a strain 301 wild-type


title: 3m_rep1

source_name: Memory CD4+ T cells, sample#3, replica1


title: Sf301_LB_Lag_rep3

description: This sample is of wild-type Shigella flexneri 2a strain 301  at 37℃ in LB medium, in lag phase. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.

value: at 37℃ in LB medium, in lag phase.


title: 065N

source_name: Naive CD4+ T cells, sample#065


title: Sf301_LB+Con_Log_rep1

description: This sample is of wild-type Shigella flexneri 2a strain 301  at 37℃ in LB+0.01% congo red medium, in log phase. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: Sf301_LB_Lag_rep2

description: This sample is of wild-type Shigella flexneri 2a strain 301  at 37℃ in LB medium, in lag phase. It is the seond of three wild-type biological replicates used in this experiment, each from separate cultures.


title: 5N_rep2

source_name: Naive CD4+ T cells, sample#5, replica2


title: 3N_rep1

source_name: Naive CD4+ T cells, sample#3, replica1


title: 6N_rep1

source_name: Naive CD4+ T cells, sample#6, replica1


title: 6N_rep2

source_name: Naive CD4+ T cells, sample#6, replica2


title: E. coli virF vs virFdel rep 1

status: Public on Jun 25 2011

city: Rome

first: Gianni

last: Prosseda

address: via dei sardi 70

department: Biology and Biotechology C. Darwin

institute: Saoienza , University of Rome

hyb_protocol: The labeled cDNA (Cy3 sample and Cy5 sample mixed) were added to 50 µl of hybridization buffer containing 50% formamide, 10X SSC, 0.2% SDS. After hybridization, slides were washed sequential

scan_protocol: Scanned on an PerkinElmer ScanArray Lite scanner. Images were quantified using ScanArray Express and GenePix Pro 6.1 software

data_processing: Global Lowess normalized, with J-Express software. We filtered the data to exclude artifacts, and low signal spots

organism: Escherichia coli

source_name: E. coli MG1655 pMYSH6504 (virF)

label_protocol: 80 µg of total RNA was labeled with Cy3 or Cy5 using LabelStar Array Kit (Qiagen)

growth_protocol: Bactera were grown in Luria Broth medium (LB) and allowed to growth to OD600 = 0,6-0,8.

extract_protocol: Total RNA was isolated by hot phenol extraction. Than RNA was treated with DNAse I for 30 minutes at 37°C

source_name: E. coli MG1655 pMY6504R


title: 5N_rep1

source_name: Naive CD4+ T cells, sample#5, replica1


title: 3N_rep2

source_name: Naive CD4+ T cells, sample#3, replica2


title: MCL71

city: Kurume

first: Yoshizo

last: Kimura

department: Pathology

institute: Kurume university

data_processing: The data were normalised using quantile normalisation with lumi package in R.

source_name: MCL in situ

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit

extract_protocol: RNA from whole tissue was extracted with Trizol reagent. RNA, which was laser-microdissected from tissue, was isolated according to Ambion RNAqueous-Micro protocal for LCM. Quality control was performed with Experion BIO-RAD automated electrophoresis system.

value: lymph node

tag: diagnosis

value: mantle cell lymphoma in situ

tag: growth pattern

value: mantle zone

value: male

tag: sample type

value: laser microdissection


title: MCL107

source_name: aggressive MCL

value: aggressive mantle cell lymphoma

value: diffuse

value: whole tissue


title: Seed (Se) vs Mesocarp (Me) at early development phase

description: Analysis used to compare transcript levels in seed (Se) and mesocarp (Me) at early development.

source_name: seed early development (Se)

value: Fantasia

value: seed

source_name: Mesocarp early development (Me)

value: mesocarp


title: MCL200

source_name: classical MCL

value: classical mantle cell lymphoma

value: nodular


title: MCL98


title: MCL132_A

source_name: aggressive areas in iMCL

value: intermediate mantle cell lymphoma (aggressive region)

value: not done


title: MCL80_A

value: female


title: MCL135


title: MCL40


title: MCL5


title: MCL126


title: MCL114


title: MCL141


title: MCL132_C

source_name: classical areas in iMCL

value: intermediate mantle cell lymphoma (classical region)


title: MCL102

value: lymph node


title: MCL113

value: mantle cell lymphoma in situ


title: Sf301_LB_Lag_rep1

description: This sample is of wild-type Shigella flexneri 2a strain 301  at 37℃ in LB medium, in lag phase. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Shigella flexneri 2a strain 301 wild-type

value: Wild-type

value: normal

value: at 37℃ in LB medium, in lag phase.


title: MCL80_C

value: laser microdissection


title: MCL112

value: mantle zone

value: male


title: R4

source_name: normal mantle zone B-lymphocytes

value: benign lymphadenitis


title: R3


title: 103

description: This Sample consists of two replicates

value: Primary Liver

value: F

tag: ancestry (pc 2)


title: R1