title: Brg1 ChIP-ChIP from HeLaS3 Cells applied to the NimbleGen ENCODE Array Sample 3

description: Red Channel: Brg1 ChIP DNA purified from HeLaS3 cells with monoclonal antibody; Green Channel: Normal mouse IgG ChIP DNA purified from HeLaS3 cells.

source_name: Brg1 ChIP DNA from HeLaS3 cells

label_protocol: ChIP DNA prepared from 1 x 10^8 cells was directly labeled by Klenow (New England Biolabs), random priming with Cy5-coupled nonamers (for Brg1 ChIP DNA) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: HeLaS3 cells were grown in suspension in Joklik's modified minimal essential medium (MEM), supplemented with 5% FBS at 37C in 5% CO2, to a density of 6 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 20 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and cells were washed twice in cold 1x Dulbeccos PBS (Invitrogen), and then swelled on ice in 10 ml hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 10 ml of 1x RIPA buffer per 3 x 10^8 cells (1x RIPA buffer: 10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (power setting 2, 100% duty cycle, six 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with 20 ug of anti-Brg1 mouse monoclonal antibody (Santa Cruz sc-17796) per 1x10^8 cells. Following this incubation Protein G agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol, 2 volumes of 100% ethanol and 1.5 ul of pellet paint (Novagen).

tag: Monoclonal antibody

source_name: normal mouse IgG ChIP DNA from HeLaS3 cells

label_protocol: ChIP DNA prepared from 1 x 10^8 cells was directly labeled by Klenow (New England Biolabs), random priming with Cy3-coupled nonamers (for normal mouse IgG ChIP DNA) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: HeLaS3 cells were grown in suspension in Joklik's modified minimal essential medium (MEM), supplemented with 5% FBS at 37C in 5% CO2, to a density of 6 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 20 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and cells were washed twice in cold 1x Dulbeccos PBS (Invitrogen), and then swelled on ice in 10 ml hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 10 ml of 1x RIPA buffer per 3 x 10^8 cells (1x RIPA buffer: 10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (power setting 2, 100% duty cycle, six 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with 20 ug of normal mouse IgG (Santa Cruz sc-2025) per 1x10^8 cells. Following this incubation Protein G agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol, 2 volumes of 100% ethanol and 1.5 ul of pellet paint (Novagen).

tag: Normal mouse IgG


title: PERH0575_CD4+_t0_aGVHD-_cGVHD+_15

status: Public on Mar 27 2007

type: RNA

city: Cleveland

first: Peter

middle: A

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

country: USA

institute: Case Western Reserve University

description: Peripheral blood was obtained from AHCT donors pre-transplant (referred to as day 0) and from recipients on day 365. Recipients were regarded as negative for acute GVHD (aGVHD) when they lived at least 100 days without presenting GVHD. Recipients were considered negative for chronic GVHD (cGVHD) when they remained cGVHD-free for 365 days post-AHCT. PBMC were isolated from blood by Ficoll separation. CD4 and CD8 T-cell subsets were purified with microbeads.

hyb_protocol: similar to direct labelling protocol lists at UHN Microarray facility web site.

scan_protocol: Scanned at 16 bits using the ScanArray Express Scanner (Packard Bioscience) at 10micro-meter resolution at 635 nm (Cy5) and 532 nm (Cy3) using Genepix Pro 6.0 analysis software (Molecular Divices Corporation)

data_processing: Each quantified output file was run though the following pre-processing steps using R (URL: www.r-project.org)and the Limma package. For Minimum Intensity filtering, R and G values were treated with a surrogate replacement policy for estimating sub-threshold values. For normalization within Arrays, the raw merged R and G channels were lowess-normalized (grouped by print-tip) and transformed to log2 ratios (70).

molecule: total RNA

organism: Homo sapiens

source_name: Universal RNA

tag: Tissue:Universal RNA

source_name: PBMC t0 (donor pre-graft)

extract_protocol: Total RNA was isolated from beads purified CD4 or CD8 T cell populations using TRIzol (Invitrogen/Life Technologies)


title: PERH0531_CD8+_t0_aGVHD-_cGVHD-_17


title: PERH0523_CD4+_t0_aGVHD-_cGVHD-_15


title: Brg1 ChIP-ChIP from HeLaS3 Cells applied to the NimbleGen ENCODE Array Sample 2

status: Public on Mar 28 2007

type: genomic

city: New Haven

first: Guoneng

last: Zhong

state: CT

address: 300 George St

institute: Yale Med

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: value = log_2(Signal for Cy5 / Signal for Cy3)

molecule: genomic DNA


title: SMARCA6 ChIP-ChIP from HeLaS3 Cells applied to the NimbleGen ENCODE Array Sample 3

description: Red Channel: SMARCA6 ChIP DNA purified from HeLaS3 cells with polyclonal antibody; Green Channel: Normal rabbit IgG ChIP DNA purified from HeLaS3 cells

source_name: SMARCA6 ChIP DNA from HeLaS3 cells

label_protocol: ChIP DNA prepared from 1 x 10^8 cells was directly labeled by Klenow (New England Biolabs), random priming with Cy5-coupled nonamers (for SMARCA6 ChIP DNA) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: HeLaS3 cells were grown in suspension in Joklik's modified minimal essential medium (MEM), supplemented with 5% FBS at 37C in 5% CO2, to a density of 6 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 20 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and cells were washed twice in cold 1x Dulbeccos PBS (Invitrogen), and then swelled on ice in 10 ml hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 10 ml of 1x RIPA buffer per 3 x 10^8 cells (1x RIPA buffer: 10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (power setting 2, 100% duty cycle, six 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with 18 ug of anti-SMARCA6 rabbit polyclonal antibody (Abcam ab3851) per 1x10^8 cells. Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol, 2 volumes of 100% ethanol and 1.5 ul of pellet paint (Novagen).

tag: Polyclonal antibody

source_name: normal rabbit IgG ChIP DNA from HeLaS3 cells

label_protocol: ChIP DNA prepared from 1 x 10^8 cells was directly labeled by Klenow (New England Biolabs), random priming with Cy3-coupled nonamers (for normal rabbit IgG ChIP DNA) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: HeLaS3 cells were grown in suspension in Joklik's modified minimal essential medium (MEM), supplemented with 5% FBS at 37C in 5% CO2, to a density of 6 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 20 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and cells were washed twice in cold 1x Dulbeccos PBS (Invitrogen), and then swelled on ice in 10 ml hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 10 ml of 1x RIPA buffer per 3 x 10^8 cells (1x RIPA buffer: 10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (power setting 2, 100% duty cycle, six 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with 18 ug of normal rabbit IgG (Santa Cruz sc-2027) per 1x10^8 cells. Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol, 2 volumes of 100% ethanol and 1.5 ul of pellet paint (Novagen).

tag: Normal rabbit IgG


title: Brg1 ChIP-ChIP from HeLaS3 Cells applied to the NimbleGen ENCODE Array Sample 1


title: PERH0605_CD4+_t0_aGVHD-_cGVHD-_21


title: NRSF ChIP-ChIP from HeLaS3 Cells applied to the NimbleGen ENCODE Array Sample 1

description: Red Channel: NRSF ChIP DNA purified from HeLaS3 cells with polyclonal antibody; Green Channel: Normal rabbit IgG ChIP DNA purified from HeLaS3 cells

source_name: NRSF ChIP DNA from HeLaS3 cells

label_protocol: ChIP DNA prepared from 1 x 10^8 cells was directly labeled by Klenow (New England Biolabs), random priming with Cy5-coupled nonamers (for NRSF ChIP DNA) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: HeLaS3 cells were grown in suspension in Joklik's modified minimal essential medium (MEM), supplemented with 5% FBS at 37C in 5% CO2, to a density of 6 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 20 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and cells were washed twice in cold 1x Dulbeccos PBS (Invitrogen), and then swelled on ice in 10 ml hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 10 ml of 1x RIPA buffer per 3 x 10^8 cells (1x RIPA buffer: 10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (power setting 2, 100% duty cycle, six 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with 20 ug of anti-NRSF rabbit polyclonal antibody (Upstate 07-579) per 1x10^8 cells. Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol, 2 volumes of 100% ethanol and 1.5 ul of pellet paint (Novagen).

extract_protocol: HeLaS3 cells were grown in suspension in Joklik's modified minimal essential medium (MEM), supplemented with 5% FBS at 37C in 5% CO2, to a density of 6 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 20 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and cells were washed twice in cold 1x Dulbeccos PBS (Invitrogen), and then swelled on ice in 10 ml hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 10 ml of 1x RIPA buffer per 3 x 10^8 cells (1x RIPA buffer: 10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (power setting 2, 100% duty cycle, six 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with 20 ug of normal rabbit IgG (Santa Cruz sc-2027) per 1x10^8 cells. Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol, 2 volumes of 100% ethanol and 1.5 ul of pellet paint (Novagen).


title: PERH0516_CD4+_t0_aGVHD+_cGVHD-_4


title: PERH0506_CD8+_t0_aGVHD-_cGVHD+_8


title: PERH0564_CD8+_t0_aGVHD-_cGVHD-_20


title: SMARCA6 ChIP-ChIP from HeLaS3 Cells applied to the NimbleGen ENCODE Array Sample 2


title: PERH0511_CD4+_t0_aGVHD+_cGVHD-_3


title: PERH0524_CD8+_t0_aGVHD-_cGVHD-_16


title: PERH0514_CD4+_t0_aGVHD-_cGVHD+_10


title: PERH0504_CD8+_t0_aGVHD-_cGVHD-_15


title: PERH0520_CD4+_t0_aGVHD-_cGVHD-_14


title: PERH0499_CD8+_t0_aGVHD+_cGVHD-_2


title: PERH0491_CD8+_t0_aGVHD+_cGVHD+_19


title: PERH0485_CD4+_t0_aGVHD-_cGVHD+_8


title: PERH0494_CD4+_t0_aGVHD+_cGVHD-_2


title: PERH0480_CD4+_t0_aGVHD+_cGVHD+_20


title: PERH0475_CD8+_t0_aGVHD+_cGVHD+_16


title: PERH0517_CD8+_t0_aGVHD+_cGVHD-_3


title: PERH0484_CD8+_t0_aGVHD+_cGVHD+_18


title: PERH0486_CD8+_t0_aGVHD-_cGVHD+_7


title: PERH0481_CD8+_t0_aGVHD+_cGVHD+_17


title: PERH0466_CD4+_t0_aGVHD+_cGVHD+_18


title: PERH0455_CD8+_t0_aGVHD-_cGVHD+_6


title: PERH0474_CD4+_t0_aGVHD+_cGVHD+_19


title: PERH0448_CD4+_t0_aGVHD-_cGVHD+_6


title: PERH0454_CD4+_t0_aGVHD-_cGVHD+_7


title: PERH0449_CD8+_t0_aGVHD-_cGVHD+_5


title: PERH0440_CD4+_t0_aGVHD-_cGVHD+_5


title: PERH0434_CD4+_t0_aGVHD-_cGVHD+_4


title: PERH0460_CD8+_t0_aGVHD-_cGVHD-_14


title: PERH0441_CD8+_t0_aGVHD-_cGVHD+_4


title: PERH0435_CD8+_t0_aGVHD-_cGVHD+_3


title: PERH0429_CD8+_t0_aGVHD-_cGVHD-_13


title: PERH0428_CD4+_t0_aGVHD-_cGVHD-_13


title: PERH0373_CD8+_t0_aGVHD+_cGVHD-_7


title: PERH0361_CD8+_t3_aGVHD+_cGVHD-_6

source_name: PBMC t3 (recipient 1 year post-graft)


title: PERH0360_CD4+_t3_aGVHD+_cGVHD-_5


title: PERH0363_CD4+_t0_aGVHD+_cGVHD-_5


title: PERH0372_CD4+_t0_aGVHD+_cGVHD-_6


title: PERH0358_CD8+_t0_aGVHD+_cGVHD-_5


title: PERH0357_CD4+_t0_aGVHD+_cGVHD-_4


title: Lung wt mock repC

city: Munich

first: Joerg

last: Mages

address: Trogerstrasse 30

department: Institute of Medical Microbiology, Immunology and Hygiene

country: Germany

institute: Technical University Munich

description: lung rna from wt mice, 3 days after mock infection, replicate C

hyb_protocol: Affymetrix recommendation

scan_protocol: Affymetrix recommendation

data_processing: Expression VALUES were generated using RMA (Robust Multi-Array Average expression measure) using R 2.4.0; Absolute Detection (ABS_CALL) was generated using the function mas5calls of the affy package for R.

label: biotin

organism: Mus musculus

label_protocol: Affymetrix one round amplification

extract_protocol: Mice were sacrificed by CO2 inhalation three days post infection with C. pneumoniae. The lungs were flushed with 10 ml of PBS applied through the right atrium of the heart to remove blood. Immediately thereafter, lungs were transferred to pre-cooled tubes placed in ethanol/dry ice bath and after homogenization, RNA was isolated using Tri-Reagent ® (T9424, Sigma) as described by the manufacturer.

tag: RNA

value: whole lung

tag: strain

tag: genotyp

value: wt

tag: infected

value: no

tag: replicate

value: C


title: PERH0354_CD4+_t3_aGVHD+_cGVHD-_4


title: Lung wt inf repC

description: lung rna from wt mice, 3 days after Chlamydia pneumoniae infection, replicate C

treatment_protocol: Mice were infected intranasally with 2.5 x 106 of C. pneumoniae in 30 µl of PBS

value: yes


title: PERH0355_CD8+_t3_aGVHD+_cGVHD-_5


title: Lung wt mock repB

description: lung rna from wt mice, 3 days after mock infection, replicate B

value: B


title: Lung wt mock repA

description: lung rna from wt mice, 3 days after mock infection, replicate A

value: A


title: PERH0364_CD8+_t0_aGVHD+_cGVHD-_6


title: PERH0346_CD8+_t0_aGVHD-_cGVHD-_12


title: Lung myd88 mock repC

description: lung rna from myd88 knockout mice, 3 days after mock infection, replicate C


title: PERH0343_CD8+_t3_aGVHD-_cGVHD-_10


title: PERH0345_CD4+_t0_aGVHD-_cGVHD-_12


title: Lung wt inf repA

description: lung rna from wt mice, 3 days after Chlamydia pneumoniae infection, replicate A


title: Lung wt inf repB

description: lung rna from wt mice, 3 days after Chlamydia pneumoniae infection, replicate B


title: PERH0342_CD4+_t3_aGVHD-_cGVHD-_10


title: Lung myd88 mock repA

description: lung rna from myd88 knockout mice, 3 days after mock infection, replicate A


title: Lung myd88 inf repC

description: lung rna from myd88 knockout mice, 3 days after infection with Chlamydia pneumoniae, replicate C


title: Lung myd88 inf repB

description: lung rna from myd88 knockout mice, 3 days after infection with Chlamydia pneumoniae, replicate B


title: Lung myd88 mock repB

description: lung rna from myd88 knockout mice, 3 days after mock infection, replicate B


title: PERH0337_CD8+_t3_aGVHD-_cGVHD-_9


title: PERH0340_CD8+_t0_aGVHD-_cGVHD-_11


title: PERH0505_CD4+_t0_aGVHD-_cGVHD+_9


title: PERH0339_CD4+_t0_aGVHD-_cGVHD-_11


title: PERH0336_CD4+_t3_aGVHD-_cGVHD-_9


title: PERH0334_CD8+_t0_aGVHD-_cGVHD-_10


title: PERH0333_CD4+_t0_aGVHD-_cGVHD-_10


title: PERH0331_CD8+_t3_aGVHD-_cGVHD-_8


title: PERH0330_CD4+_t3_aGVHD-_cGVHD-_8


title: Lung myd88 inf repA

description: lung rna from myd88 knockout mice, 3 days after infection with Chlamydia pneumoniae


title: sigenae.org:MBA:-570; PF_PigL_Damage_07d

city: Castanet tolosan

first: Laurence

last: Liaubet

address: chemin de borde rouge

department: Animal Genetic

country: France

institute: INRA

scan_protocol: Image scan; BZScan is a free java tool for automatic quantification of DNA microarrays with radioactive labeling.

data_processing: mean of the duplicate minus mean of the membrane

organism: Sus scrofa

extract_protocol: RNA extraction Qiagen Fibrous Tissue_PF

tag: Origin

value: Longissimus dorsi

value: Muscle


title: sigenae.org:MBA:-568; PF_PigL_Damage_07d


title: PERH0328_CD8+_t0_aGVHD-_cGVHD-_9


title: sigenae.org:MBA:-648; PF_PigL_Damage_02d


title: sigenae.org:MBA:-649; PF_PigL_Damage_02d


title: sigenae.org:MBA:-722; PF_PigL_Control


title: sigenae.org:MBA:-560; PF_PigK_Damage_07d


title: PERH0324_CD4+_t3_aGVHD-_cGVHD-_7


title: PERH0327_CD4+_t0_aGVHD-_cGVHD-_9


title: sigenae.org:MBA:-652; PF_PigL_Damage_06h


title: sigenae.org:MBA:-653; PF_PigL_Damage_06h


title: PERH0325_CD8+_t3_aGVHD-_cGVHD-_7


title: PERH0315_CD4+_t3_aGVHD+_cGVHD-_3


title: PERH0316_CD8+_t3_aGVHD+_cGVHD-_4


title: PERH0321_CD4+_t0_aGVHD-_cGVHD-_8


title: sigenae.org:MBA:-562; PF_PigK_Damage_07d


title: PERH0319_CD8+_t3_aGVHD-_cGVHD-_6


title: PERH0322_CD8+_t0_aGVHD-_cGVHD-_8


title: PERH0313_CD8+_t0_aGVHD-_cGVHD+_17


title: sigenae.org:MBA:-644; PF_PigK_Damage_06h


title: PERH0307_CD8+_t0_aGVHD-_cGVHD+_16


title: sigenae.org:MBA:-719; PF_PigK_Damage_21d


title: sigenae.org:MBA:-718; PF_PigK_Damage_21d


title: sigenae.org:MBA:-720; PF_PigK_Control


title: PERH0318_CD4+_t3_aGVHD-_cGVHD-_6


title: PERH0306_CD4+_t0_aGVHD-_cGVHD+_18


title: sigenae.org:MBA:-640; PF_PigK_Damage_02d


title: sigenae.org:MBA:-639; PF_PigK_Damage_02d


title: sigenae.org:MBA:-721; PF_PigL_Control


title: PERH0304_CD8+_t3_aGVHD-_cGVHD+_12


title: PERH0303_CD4+_t3_aGVHD-_cGVHD+_14


title: sigenae.org:MBA:-643; PF_PigK_Damage_06h


title: PERH0294_CD4+_t0_aGVHD-_cGVHD-_7


title: sigenae.org:MBA:-713; PF_PigJ_Damage_21d


title: PERH0295_CD8+_t0_aGVHD-_cGVHD-_7


title: sigenae.org:MBA:-632; PF_PigJ_Damage_06h


title: PERH0289_CD8+_t0_aGVHD-_cGVHD+_15


title: sigenae.org:MBA:-558; PF_PigJ_Damage_02d


title: PERH0286_CD8+_t3_aGVHD-_cGVHD+_11


title: PERH0288_CD4+_t0_aGVHD-_cGVHD+_17


title: sigenae.org:MBA:-714; PF_PigJ_Damage_21d


title: PERH0291_CD4+_t3_aGVHD-_cGVHD-_5


title: PERH0285_CD4+_t3_aGVHD-_cGVHD+_13


title: PERH0292_CD8+_t3_aGVHD-_cGVHD-_5


title: sigenae.org:MBA:-636; PF_PigJ_Control


title: PERH0272_CD8+_t0_aGVHD+_cGVHD-_4


title: sigenae.org:MBA:-631; PF_PigJ_Damage_06h


title: PERH0271_CD4+_t0_aGVHD+_cGVHD-_3


title: sigenae.org:MBA:-635; PF_PigJ_Control


title: sigenae.org:MBA:-705; PF_PigI_Damage_21d


title: sigenae.org:MBA:-712; PF_PigI_Damage_07d


title: sigenae.org:MBA:-624; PF_PigI_Damage_06h


title: PERH0270_CD8+_t3_aGVHD+_cGVHD-_3


title: sigenae.org:MBA:-711; PF_PigI_Damage_07d


title: PERH0253_CD4+_t0_aGVHD-_cGVHD+_16


title: sigenae.org:MBA:-554; PF_PigI_Damage_02d


title: sigenae.org:MBA:-552; PF_PigI_Damage_02d


title: PERH0269_CD4+_t3_aGVHD+_cGVHD-_2


title: PERH0251_CD4+_t3_aGVHD-_cGVHD+_12


title: PERH0249_CD4+_t0_aGVHD-_cGVHD+_15


title: sigenae.org:MBA:-616; PF_PigH_Damage_21d


title: sigenae.org:MBA:-627; PF_PigI_Control


title: sigenae.org:MBA:-615; PF_PigH_Damage_21d


title: sigenae.org:MBA:-623; PF_PigI_Damage_06h


title: PERH0250_CD8+_t0_aGVHD-_cGVHD+_14


title: PERH0245_CD4+_t0_aGVHD-_cGVHD-_6


title: PERH0310_CD8+_t3_aGVHD-_cGVHD+_13


title: sigenae.org:MBA:-550; PF_PigH_Damage_06h


title: sigenae.org:MBA:-628; PF_PigI_Control


title: PERH0237_CD4+_t0_aGVHD-_cGVHD+_14


title: PERH0240_CD8+_t0_aGVHD-_cGVHD-_5


title: PERH0244_CD8+_t3_aGVHD-_cGVHD-_4


title: PERH0243_CD4+_t3_aGVHD-_cGVHD-_4


title: PERH0246_CD8+_t0_aGVHD-_cGVHD-_6


title: PERH0238_CD8+_t0_aGVHD-_cGVHD+_13


title: sigenae.org:MBA:-704; PF_PigH_Damage_02d


title: sigenae.org:MBA:-549; PF_PigH_Damage_06h


title: sigenae.org:MBA:-700; PF_PigH_Damage_07d


title: PERH0231_CD4+_t0_aGVHD+_cGVHD-_2


title: PERH0232_CD8+_t0_aGVHD+_cGVHD-_3


title: sigenae.org:MBA:-706; PF_PigI_Damage_21d


title: PERH0217_CD4+_t3_aGVHD+_cGVHD+_11


title: PERH0224_CD8+_t3_aGVHD+_cGVHD-_1


title: PERH0212_CD8+_t0_aGVHD-_cGVHD+_12


title: PERH0211_CD4+_t0_aGVHD-_cGVHD+_13


title: PERH0229_CD4+_t3_aGVHD+_cGVHD-_1


title: PERH0209_CD4+_t3_aGVHD-_cGVHD+_11


title: PERH0219_CD4+_t0_aGVHD+_cGVHD+_13


title: sigenae.org:MBA:-609; PF_PigG_Control


title: PERH0230_CD8+_t3_aGVHD+_cGVHD-_2


title: PERH0226_CD8+_t0_aGVHD+_cGVHD-_2


title: sigenae.org:MBA:-610; PF_PigG_Control


title: PERH0239_CD4+_t0_aGVHD-_cGVHD-_5


title: sigenae.org:MBA:-697; PF_PigG_Damage_02d


title: sigenae.org:MBA:-557; PF_PigJ_Damage_02d


title: sigenae.org:MBA:-597; PF_PigF_Damage_21d


title: sigenae.org:MBA:-602; PF_PigF_Damage_07d


title: sigenae.org:MBA:-606; PF_PigG_Damage_21d


title: sigenae.org:MBA:-601; PF_PigF_Damage_07d


title: sigenae.org:MBA:-516; PF_PigG_Damage_06h


title: PERH0210_CD8+_t3_aGVHD-_cGVHD+_10


title: sigenae.org:MBA:-619; PF_PigH_Control


title: sigenae.org:MBA:-620; PF_PigH_Control


title: sigenae.org:MBA:-758; PF_PigG_Damage_07d


title: PERH0207_CD4+_t0_aGVHD+_cGVHD+_12


title: sigenae.org:MBA:-514; PF_PigG_Damage_06h


title: sigenae.org:MBA:-605; PF_PigG_Damage_21d


title: sigenae.org:MBA:-701; PF_PigH_Damage_02d


title: PERH0206_CD8+_t3_aGVHD+_cGVHD+_9


title: PERH0205_CD4+_t3_aGVHD+_cGVHD+_10


title: sigenae.org:MBA:-676; PF_PigE_Damage_06h


title: PERH0196_CD8+_t0_aGVHD+_cGVHD+_10


title: sigenae.org:MBA:-691; PF_PigF_Damage_02d


title: sigenae.org:MBA:-590; PF_PigE_Damage_21d


title: sigenae.org:MBA:-497; PF_PigF_Control


title: sigenae.org:MBA:-677; PF_PigE_Damage_06h


title: PERH0208_CD8+_t0_aGVHD+_cGVHD+_11


title: sigenae.org:MBA:-673; PF_PigE_Damage_02d


title: PERH0193_CD4+_t3_aGVHD+_cGVHD+_9


title: PERH0177_CD4+_t0_aGVHD-_cGVHD+_12


title: PERH0195_CD4+_t0_aGVHD+_cGVHD+_11


title: PERH0194_CD8+_t3_aGVHD+_cGVHD+_8


title: sigenae.org:MBA:-499; PF_PigF_Control


title: sigenae.org:MBA:-693; PF_PigF_Damage_06h


title: sigenae.org:MBA:-593; PF_PigE_Damage_07d


title: PERH0187_CD4+_t3_aGVHD+_cGVHD+_8


title: PERH0190_CD8+_t0_aGVHD+_cGVHD+_9


title: sigenae.org:MBA:-495; PF_PigE_Control


title: PERH0176_CD8+_t3_aGVHD-_cGVHD+_9


title: sigenae.org:MBA:-589; PF_PigE_Damage_21d


title: PERH0178_CD8+_t0_aGVHD-_cGVHD+_11


title: PERH0181_CD4+_t3_aGVHD-_cGVHD-_3


title: PERH0189_CD4+_t0_aGVHD+_cGVHD+_10


title: PERH0188_CD8+_t3_aGVHD+_cGVHD+_7


title: sigenae.org:MBA:-672; PF_PigE_Damage_02d


title: sigenae.org:MBA:-594; PF_PigE_Damage_07d


title: PERH0182_CD8+_t3_aGVHD-_cGVHD-_3


title: sigenae.org:MBA:-493; PF_PigE_Control


title: PERH0172_CD8+_t0_aGVHD+_cGVHD+_8


title: sigenae.org:MBA:-582; PF_PigD_Damage_07d


title: sigenae.org:MBA:-489; PF_PigD_Damage_21d


title: sigenae.org:MBA:-598; PF_PigF_Damage_21d


title: PERH0175_CD4+_t3_aGVHD-_cGVHD+_10


title: sigenae.org:MBA:-585; PF_PigD_Damage_02d


title: sigenae.org:MBA:-486; PF_PigC_Damage_21d


title: sigenae.org:MBA:-664; PF_PigD_Damage_06h


title: sigenae.org:MBA:-668; PF_PigD_Control


title: sigenae.org:MBA:-485; PF_PigC_Damage_21d


title: PERH0171_CD4+_t0_aGVHD+_cGVHD+_9


title: sigenae.org:MBA:-665; PF_PigD_Damage_06h


title: PERH0169_CD4+_t3_aGVHD+_cGVHD+_7


title: sigenae.org:MBA:-572; PF_PigC_Damage_07d


title: PERH0155_CD4+_t3_aGVHD-_cGVHD+_9


title: PERH0170_CD8+_t3_aGVHD+_cGVHD+_6


title: PERH0152_CD8+_t0_aGVHD-_cGVHD+_9


title: sigenae.org:MBA:-574; PF_PigC_Damage_07d


title: sigenae.org:MBA:-491; PF_PigD_Damage_21d


title: PERH0162_CD8+_t3_aGVHD-_cGVHD-_2


title: PERH0164_CD8+_t0_aGVHD-_cGVHD-_4


title: sigenae.org:MBA:-581; PF_PigD_Damage_07d


title: PERH0161_CD4+_t3_aGVHD-_cGVHD-_2


title: PERH0156_CD8+_t3_aGVHD-_cGVHD+_8


title: sigenae.org:MBA:-586; PF_PigD_Damage_02d


title: sigenae.org:MBA:-669; PF_PigD_Control


title: PERH0157_CD4+_t0_aGVHD-_cGVHD+_11


title: PERH0149_CD4+_t3_aGVHD-_cGVHD+_8


title: PERH0163_CD4+_t0_aGVHD-_cGVHD-_4


title: PERH0151_CD4+_t0_aGVHD-_cGVHD+_10


title: PERH0143_CD4+_t0_aGVHD-_cGVHD+_9


title: sigenae.org:MBA:-657; PF_PigC_Damage_06h


title: sigenae.org:MBA:-660; PF_PigC_Control


title: sigenae.org:MBA:-577; PF_PigC_Damage_02d


title: PERH0150_CD8+_t3_aGVHD-_cGVHD+_7


title: PERH0158_CD8+_t0_aGVHD-_cGVHD+_10


title: sigenae.org:MBA:-661; PF_PigC_Control


title: PERH0144_CD8+_t0_aGVHD-_cGVHD+_8


title: germination_rep15-1-2

type: mixed

city: Beijing

first: Qi

last: Jin

address: Rongjing East Road 6#

country: China

institute: State Key Lab of Virus Gene Engineering

description: T.rubrum conidia were collected at 1 hr intervals throught the germination process. The cDNA from  mRNA of the samples were and the genomic DNA of T.rubrum  were coupled with Cy5 or Cy3 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a GenePix 4000B scanner (Axon Instruments, Inc., CA).

data_processing: log2 ratio of Cy3/Cy5

molecule: polyA RNA

organism: Trichophyton rubrum

source_name: mRNA: germination-induced conidia

extract_protocol: Extracted mRNA

tag: T. rubrum conidia induced germination in Sabouraud liquid medium.

source_name: gDNA: BMU01672 genomic DNA (reference)

tag: T. rubrum strain BMU01672 genomic DNA(reference channel )


title: germination_rep14-1-2


title: PERH0142_CD8+_t3_aGVHD-_cGVHD+_6


title: germination_rep13-1-1


title: sigenae.org:MBA:-656; PF_PigC_Damage_06h


title: PERH0132_CD8+_t3_aGVHD-_cGVHD+_4


title: PERH0136_CD8+_t3_aGVHD-_cGVHD+_5


title: PERH0135_CD4+_t3_aGVHD-_cGVHD+_6


title: germination_rep12-1-2


title: germination_rep13-1-2


title: PERH0141_CD4+_t3_aGVHD-_cGVHD+_7


title: PERH0137_CD4+_t0_aGVHD-_cGVHD+_8


title: germination_rep15-1-1


title: PERH0131_CD4+_t3_aGVHD-_cGVHD+_5


title: germination_rep11-1-1

source_name: Characteristics mRNA: germination-induced conidia

tag: Characteristics T. rubrum conidia induced germination in Sabouraud liquid medium.

source_name: T. rubrum genomic DNA labled with Cy5


title: PERH0125_CD4+_t3_aGVHD-_cGVHD-_1


title: PERH0126_CD8+_t3_aGVHD-_cGVHD-_1


title: PERH0119_CD4+_t3_aGVHD-_cGVHD+_4


title: germination_rep12-1-1


title: germination_rep10-1-2


title: germination_rep14-1-1


title: PERH0120_CD8+_t3_aGVHD-_cGVHD+_3


title: germination_rep10-1-1


title: germination_rep9-1-2


title: PERH0114_CD8+_t0_aGVHD-_cGVHD-_3


title: PERH0113_CD4+_t0_aGVHD-_cGVHD-_3


title: sigenae.org:MBA:-578; PF_PigC_Damage_02d


title: germination_rep8-1-2


title: germination_rep9-1-1


title: germination_rep6-1-2


title: PERH0105_CD4+_t3_aGVHD+_cGVHD+_6


title: germination_rep7-1-2


title: germination_rep11-1-2


title: PERH0095_CD4+_t0_aGVHD-_cGVHD-_2


title: germination_rep7-1-1


title: germination_rep5-1-2


title: PERH0107_CD4+_t0_aGVHD+_cGVHD+_8


title: PERH0099_CD4+_t0_aGVHD+_cGVHD+_7


title: PERH0096_CD8+_t0_aGVHD-_cGVHD-_2


title: PERH0092_CD8+_t0_aGVHD+_cGVHD+_6


title: germination_rep5-1-1


title: PERH0100_CD8+_t0_aGVHD+_cGVHD+_7


title: Gene expression during Bacillus subtilis spore germination and outgrowth (t=70)

city: Zeist

first: Bart

last: Keijser

address: Utrechtseweg 48

country: Netherlands

institute: TNO

description: Data supplied is median cy3 value of 4 normalized technical replicates(duplicate spots on the microarray and duplicate hybridization). Raw data and required information is supplied as supplemental file.

hyb_protocol: Automated slide processor (ASP), GE Healthcare

scan_protocol: Microarrays were scanned in an Agilent DNA MicroArray Scanner (Agilent Technologies, Palo Alto, CA,USA) at 100 % PMT and 100% laser power

data_processing: Inconsistent replicate values (duplicate spots on the microarray and duplicate hybridization) were removed if distance to the median was larger than 1 on a log2 scale. Of the remaining replicas, the median value was calculated.

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: germinated spores, 70 minutes into outgrowth

label_protocol: Direct incorporation: Random priming of SSII RT to incorporate cy3-labeled dUTP, followed by NaOH hydrolysis of RNA

extract_protocol: Fast RNA pro Blue - Qbiogene

tag: Strain Bacillus subtilis 168, 1A700

tag: Time

value: 70 minutes into outgrowth


title: Gene expression during Bacillus subtilis spore germination and outgrowth (t=90)

source_name: germinated spores, 90 minutes into outgrowth

value: 90 minutes into outgrowth


title: germination_rep4-1-1


title: Gene expression during Bacillus subtilis spore germination and outgrowth (t=80)

source_name: germinated spores, 80 minutes into outgrowth

value: 80 minutes into outgrowth


title: PERH0090_CD8+_t3_aGVHD+_cGVHD+_5

description: Peripheral blood was obtained from AHCT donors pre-transplant (referred to as day 0) and from recipients on day 365. Recipients were regarded as negative for acute GVHD (aGVHD) when they lived at least 100 days without presenting GVHD. Recipients were considered negative for chronic GVHD (cGVHD) when they remained cGVHD-free for 365 days post-AHCT. PBMC were isolated from blood by Ficoll separation. CD4 and CD8 T-cell subsets were purified with microbeads.


title: Gene expression during Bacillus subtilis spore germination and outgrowth (t=50)

source_name: germinated spores, 50 minutes into outgrowth

value: 50 minutes into outgrowth


title: germination_rep8-1-1


title: germination_rep4-1-2


title: PERH0086_CD8+_t0_aGVHD-_cGVHD+_6


title: Gene expression during Bacillus subtilis spore germination and outgrowth (t=40)

source_name: germinated spores, 40 minutes into outgrowth

value: 40 minutes into outgrowth


title: Gene expression during Bacillus subtilis spore germination and outgrowth (t=100)

source_name: germinated spores, 100 minutes into outgrowth

value: 100 minutes into outgrowth


title: PERH0089_CD4+_t3_aGVHD+_cGVHD+_5


title: PERH0091_CD4+_t0_aGVHD+_cGVHD+_6


title: Gene expression during Bacillus subtilis spore germination and outgrowth (t=30)

source_name: germinated spores, 30 minutes into outgrowth

value: 30 minutes into outgrowth


title: PERH0085_CD4+_t0_aGVHD-_cGVHD+_7

source_name: Universal RNA


title: germination_rep2-3-1


title: germination_rep3-1-1


title: PERH0138_CD8+_t0_aGVHD-_cGVHD+_7

source_name: PBMC t0 (donor pre-graft)


title: germination_rep2-3-2


title: Gene expression during Bacillus subtilis spore germination and outgrowth (t=15)

source_name: germinated spores, 15 minutes into outgrowth

value: 15 minutes into outgrowth


title: Gene expression during Bacillus subtilis spore germination and outgrowth (t=20)

source_name: germinated spores, 20 minutes into outgrowth

value: 20 minutes into outgrowth


title: PERH0081_CD4+_t0_aGVHD+_cGVHD+_5


title: PERH0078_CD8+_t0_aGVHD+_cGVHD+_4


title: PERH0082_CD8+_t0_aGVHD+_cGVHD+_5


title: Gene expression during Bacillus subtilis spore germination and outgrowth (t=25)

source_name: germinated spores, 25 minutes into outgrowth

value: 25 minutes into outgrowth


title: Gene expression during Bacillus subtilis spore germination and outgrowth (t=10)

source_name: germinated spores, 10 minutes into outgrowth

value: 10 minutes into outgrowth


title: PERH0077_CD4+_t0_aGVHD+_cGVHD+_4


title: germination_rep2-1-2

source_name: mRNA: germination-induced conidia


title: germination_rep2-1-1

source_name: gDNA: BMU01672 genomic DNA (reference)


title: Gene expression during Bacillus subtilis spore germination and outgrowth (t=0)

source_name: dormant spores (t=0)

value: 0 minutes into outgrowth (dormant spores); sample is part of time series


title: PERH0076_CD8+_t3_aGVHD+_cGVHD+_4

source_name: PBMC t3 (recipient 1 year post-graft)


title: Gene expression during Bacillus subtilis spore germination and outgrowth (t=5)

source_name: germinated spores, 5 minutes into outgrowth

value: 5 minutes into outgrowth


title: germination_rep1-1-2

source_name: . rubrum mRNA: germination-induced conidia

tag: . rubrum conidia induced germination in Sabouraud liquid medium.

source_name: T. rubrum genomic DNA labled with Cy5


title: germination_rep1-1-1


title: PERH0072_CD8+_t0_aGVHD+_cGVHD-_1


title: germination_rep0-1-2


title: PERH0075_CD4+_t3_aGVHD+_cGVHD+_4


title: PERH0071_CD4+_t0_aGVHD+_cGVHD-_1


title: germination_rep14-2-2

data_processing: log2 ratio of Cy5/Cy3


title: PERH0060_CD8+_t0_aGVHD-_cGVHD+_5


title: PERH0056_CD8+_t0_aGVHD-_cGVHD+_4


title: PERH0053_CD4+_t3_aGVHD-_cGVHD+_3


title: germination_rep13-2-1


title: PERH0059_CD4+_t0_aGVHD-_cGVHD+_6


title: germination_rep14-2-1


title: germination_rep13-2-2


title: Gene expression during Bacillus subtilis spore germination and outgrowth (t=60)

source_name: germinated spores, 60 minutes into outgrowth

value: 60 minutes into outgrowth


title: PERH0054_CD8+_t3_aGVHD-_cGVHD+_2


title: PERH0055_CD4+_t0_aGVHD-_cGVHD+_5


title: germination_rep11-2-2


title: PERH0048_CD8+_t0_aGVHD+_cGVHD+_3


title: germination_rep6-1-1


title: PERH0046_CD8+_t3_aGVHD+_cGVHD+_3


title: germination_re12-2-2


title: Liver_LPI_KOmice_dyeswap_rep3

city: brescia

first: andrea

last: bozzato

address: viale europa 11

country: Italy

institute: university of brescia

description: Dye swap experiment of Liver tissue from Slc7a7 -/- (Cy3 labelled) mice versus normal littermate control (Cy5 labelled) mice. RNA samples extracted from different subjects with the same genotype were pooled into a single RNA mix. Hybridization data were processed using GenePix Pro 4.1 (Axon Instruments). All statistical and graphical analysis were carried out in the R computing environment using Limma (Smyth, 2004) which is part of the Bioconductor project (Gentleman et al., 2004). Within Limma, we performed local background subtraction and global lowess normalization within each slide. Differential gene expression was determined using an empirical Bayes (EB) approach within Limma (Smyth, 2004), computing moderated t-statistics, log-odds ratios of differential expression and adjusted p-values (obtained after FDR adjustment which is Benjamini and Hochberg's method to control the false discovery rate) (Benjamini et al., 2001). After EB analysis, genes were ranked as being differentially expressed in decreasing order of the B-statistic and in conjunction with p-value obtained from moderated t-statistic.

data_processing: Global lowess normalization by Limma package

source_name: Liver tissue

tag: Liver tissue from two of Slc7a7 -/- adult mice (KO mice)

tag: Liver tissue from two normal littermate control mice (WT mice)


title: germination_rep0-1-1


title: germination_rep10-2-2


title: PERH0040_CD8+_t0_aGVHD-_cGVHD+_3

tag: Tissue:Universal RNA


title: PERH0047_CD4+_t0_aGVHD+_cGVHD+_3


title: Liver_LPI_KOmice_dyeswap_rep4


title: germination_rep3-1-2


title: PERH0045_CD4+_t3_aGVHD+_cGVHD+_3


title: PERH0038_CD8+_t3_aGVHD-_cGVHD+_1


title: germination_rep10-2-4


title: germination_rep12-2-1


title: Liver_LPI_KOmice_rep2

description: Liver tissue from Slc7a7 -/- (Cy5 labelled) mice versus normal littermate control (Cy3 labelled) mice. RNA samples extracted from different subjects with the same genotype were pooled into a single RNA mix. Hybridization data were processed using GenePix Pro 4.1 (Axon Instruments). All statistical and graphical analysis were carried out in the R computing environment using Limma (Smyth, 2004) which is part of the Bioconductor project (Gentleman et al., 2004). Within Limma, we performed local background subtraction and global lowess normalization within each slide. Differential gene expression was determined using an empirical Bayes (EB) approach within Limma (Smyth, 2004), computing moderated t-statistics, log-odds ratios of differential expression and adjusted p-values (obtained after FDR adjustment which is Benjamini and Hochberg's method to control the false discovery rate) (Benjamini et al., 2001). After EB analysis, genes were ranked as being differentially expressed in decreasing order of the B-statistic and in conjunction with p-value obtained from moderated t-statistic.


title: germination_rep9-2-2


title: germination_rep11-2-1


title: Intestine_LPI_KOmice_rep4

description: Intestine tissue from Slc7a7 -/- (Cy5 labelled) mice versus normal littermate control (Cy3 labelled) mice. RNA samples extracted from different subjects with the same genotype were pooled into a single RNA mix. Hybridization data were processed using GenePix Pro 4.1 (Axon Instruments). All statistical and graphical analysis were carried out in the R computing environment using Limma (Smyth, 2004) which is part of the Bioconductor project (Gentleman et al., 2004). Within Limma, we performed local background subtraction and global lowess normalization within each slide. Differential gene expression was determined using an empirical Bayes (EB) approach within Limma (Smyth, 2004), computing moderated t-statistics, log-odds ratios of differential expression and adjusted p-values (obtained after FDR adjustment which is Benjamini and Hochberg's method to control the false discovery rate) (Benjamini et al., 2001). After EB analysis, genes were ranked as being differentially expressed in decreasing order of the B-statistic and in conjunction with p-value obtained from moderated t-statistic.

source_name: Intestine tissue

tag: Intestine tissue from two normal littermate control mice (WT mice)

tag: Intestine tissue from two of Slc7a7 -/-  adult mice (KO mice)


title: Liver_LPI_KOmice_rep1


title: Intestine_LPI_KOmice_dye_swap2

description: Dye swap experiment of Intestine tissue from Slc7a7 -/- (Cy3 labelled) mice versus normal littermate control (Cy5 labelled) mice. RNA samples extracted from different subjects with the same genotype were pooled into a single RNA mix. Hybridization data were processed using GenePix Pro 4.1 (Axon Instruments). All statistical and graphical analysis were carried out in the R computing environment using Limma (Smyth, 2004) which is part of the Bioconductor project (Gentleman et al., 2004). Within Limma, we performed local background subtraction and global lowess normalization within each slide. Differential gene expression was determined using an empirical Bayes (EB) approach within Limma (Smyth, 2004), computing moderated t-statistics, log-odds ratios of differential expression and adjusted p-values (obtained after FDR adjustment which is Benjamini and Hochberg's method to control the false discovery rate) (Benjamini et al., 2001). After EB analysis, genes were ranked as being differentially expressed in decreasing order of the B-statistic and in conjunction with p-value obtained from moderated t-statistic.

source_name: Intestine tissue from two of Slc7a7 -/- adult mice (KO mice)

source_name: Intestine tissue from two normal littermate control mice (WT mice)


title: PERH0037_CD4+_t3_aGVHD-_cGVHD+_2

source_name: Universal RNA


title: PERH0032_CD8+_t0_aGVHD+_cGVHD+_2

source_name: PBMC t0 (donor pre-graft)


title: germination_rep8-2-2


title: germination_rep9-2-1


title: Intestine_LPI_KOmice_rep3

source_name: Intestine tissue from two of Slc7a7 -/-  adult mice (KO mice)


title: Serum treated MEF, polyribosome-associated mRNA, biological rep2

city: Bern

first: Marc

last: Kenzelmann

address: Friedbuhlstrasse 51

department: Molecular Genome Analysis

country: Switzerland

institute: Institute of Medical Microbiology, University of Bern

description: Gene expression data from primary serum treated MEF cells grown to near confluency.

hyb_protocol: Following fragmentation, 10microg of cRNA were hybridized to MU74Av2 GeneChip (Affymetrix) according to manufacturer's instructions.

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

data_processing: The data were analyzed with the SAS MicroArray Solution 1.3, using standard settings except the following: consistence within experimental groups (stimulus and labelling combination) was determined by array group correlation. Loglinear mixed models with Bonferroni corrections were fitted for values of perfect-matches, only with stimulus (10% FBS) and labelling (s4U) considered to be constant and the chip-ID as random.

source_name: 48h serum starved primary mouse embryonic fibroblasts (MEF)

label_protocol: RNA was reverse-transcribed, linearly amplified as described previously (Kenzelmann M. et al. (2004), Genomics 83, 550-558.), and biotin-labelled via a T7-based strategy according to manufacturer's instructions (Affymetrix).

growth_protocol: Cells were grown using high glucose-DMEM (Invitrogen) with 1% Penicillin/Streptomycin (Invitrogen) and 10% dialyzed FBS (cutoff 10,000Da, Sigma) to near confluency. Cells were serum-starved for 48h with 1% dialyzed FBS, and then incubated for 2h with media containing 200uM 4-thiouridine (s4U, Sigma) and 10% FBS, 1uCi 3H-cytidine (20Ci/mmol, Biotrend).

extract_protocol: 100 ug/ml medium of cycloheximide were then added and cells further incubated at 37C for 30min. Cells were washed with PBS containing 100ug/ml cycloheximide, trypsinized (Trypsin-EDTA, 100ug/ml cycloheximide), washed again with PBS and centrifuged at 1000rpm for 6min at 4C. Cells were then lysed by NP-40 lysis buffer (1ml for ~ 107 cells; 10mM Tris-HCl pH 8, 150mM NaCl, 1.5mM MgCl2, 0.1% (v/v) NP-40, 100ug/ml cycloheximide, 0.5mg/ml heparin, 1mM DTT) and douncing. The lysate was centrifuged with 10,000xg at 4C for 10min to remove nuclei and mitochondria. The supernatant was added onto a linear sucrose gradient (15%-50% sucrose) performed in a Beckman SW40 tube using a Biocamp Gradient Master (Nycomed Pharma) based on 10mM Tris-HCl pH 7.5, 140mM NaCl, 1.5mM MgCl2, 1mM DTT and either 15% or 50% sucrose. Gradients were then centrifuged using an SW 40 rotor at 4C with 40,000xg for 2h. The polysomal profile was analyzed at 260nm and fractionated with an ISCO density fractionator (ISCO Inc.) coupled to a UV cell. mRNAs associated with 2 and more ribosomes referred to as 'actively translated' (polyribosome-associated associated. Fractions were collected in Eppendorf tubes containing SDS (final concentration: 1% SDS) and precipitated using PelletPaint (Novagen). Equal fractions of different biological and technical replicates were pooled and RNA eluted using the RNeasy MINI cleanup procedure (QIAGEN) to get rid of the remaining heparin. Samples were then phenol-chloroform (PC, pH 6.6) extracted using PLG heavy 0.5ml Eppendorf tubes, followed by a final precipitation with PelletPaint, 3M NaAcetate and 100% Ethanol and a wash step with 70% Ethanol. The RNA pellet of each fraction was diluted in 10ul water. RNA yield and quality were measured by the RNA6000 Nano assay (Bioanalyzer 2100, Agilent Technologies).

treatment_protocol: Primary mouse embryonic fibroblasts were isolated as described previously (Todaro G.J. and Green H. (1963), J. Cell Biol., 17, 299-313; Brusselbach S.U. et al. (1995), Oncogene, 10, 79-86.)

tag: Genotype

value: C57/BLACK6, ATF1 +/-

tag: Age


title: PERH0039_CD4+_t0_aGVHD-_cGVHD+_4


title: PERH0030_CD8+_t3_aGVHD+_cGVHD+_2


title: PERH0031_CD4+_t0_aGVHD+_cGVHD+_2


title: Intestine_LPI_KOmice_dye_swap1

description: Dye swap experiment of Intestine tissue from Slc7a7 -/- (Cy3 labelled) mice versus normal littermate control (Cy5 labelled) mice. RNA samples extracted from two different subjects with the same genotype were pooled into a single RNA mix. Hybridization data were processed using GenePix Pro 4.1 (Axon Instruments). All statistical and graphical analysis were carried out in the R computing environment using Limma (Smyth, 2004) which is part of the Bioconductor project (Gentleman et al., 2004). Within Limma, we performed local background subtraction and global lowess normalization within each slide. Differential gene expression was determined using an empirical Bayes (EB) approach within Limma (Smyth, 2004), computing moderated t-statistics, log-odds ratios of differential expression and adjusted p-values (obtained after FDR adjustment which is Benjamini and Hochberg's method to control the false discovery rate) (Benjamini et al., 2001). After EB analysis, genes were ranked as being differentially expressed in decreasing order of the B-statistic and in conjunction with p-value obtained from moderated t-statistic.

tag: Intestine tissue from two of Slc7a7 -/- adult mice (KO mice)


title: germination_rep8-2-1


title: germination_rep7-2-2

source_name: Characteristics mRNA: germination-induced conidia

source_name: T. rubrum genomic DNA labled with Cy3


title: germination_rep6-2-1

source_name: mRNA: germination-induced conidia

source_name: gDNA: BMU01672 genomic DNA (reference)


title: Serum starved MEF, polyribosome-associated mRNA, biological rep1

description: Gene expression data from primary serum starved MEF cells grown to near confluency.

growth_protocol: Cells were grown using high glucose-DMEM (Invitrogen) with 1% Penicillin/Streptomycin (Invitrogen) and 10% dialyzed FBS (cutoff 10,000Da, Sigma) to near confluency. Cells were serum-starved for 48h with 1% dialyzed FBS, and then incubated for 2h with media containing 1% FBS (serum starvation control).


title: Serum starved MEF, undertranslated RNA, biological rep1

extract_protocol: 100 ug/ml medium of cycloheximide were then added and cells further incubated at 37C for 30min. Cells were washed with PBS containing 100ug/ml cycloheximide, trypsinized (Trypsin-EDTA, 100ug/ml cycloheximide), washed again with PBS and centrifuged at 1000rpm for 6min at 4C. Cells were then lysed by NP-40 lysis buffer (1ml for ~ 107 cells; 10mM Tris-HCl pH 8, 150mM NaCl, 1.5mM MgCl2, 0.1% (v/v) NP-40, 100ug/ml cycloheximide, 0.5mg/ml heparin, 1mM DTT) and douncing. The lysate was centrifuged with 10,000xg at 4C for 10min to remove nuclei and mitochondria. The supernatant was added onto a linear sucrose gradient (15%-50% sucrose) performed in a Beckman SW40 tube using a Biocamp Gradient Master (Nycomed Pharma) based on 10mM Tris-HCl pH 7.5, 140mM NaCl, 1.5mM MgCl2, 1mM DTT and either 15% or 50% sucrose. Gradients were then centrifuged using an SW 40 rotor at 4C with 40,000xg for 2h. The polysomal profile was analyzed at 260nm and fractionated with an ISCO density fractionator (ISCO Inc.) coupled to a UV cell. mRNAs associated with either no, or one ribosomal subunit, or only 1 full ribosome were referred to as 'undertranslated'. Fractions were collected in Eppendorf tubes containing SDS (final concentration: 1% SDS) and precipitated using PelletPaint (Novagen). Equal fractions of different biological and technical replicates were pooled and RNA eluted using the RNeasy MINI cleanup procedure (QIAGEN) to get rid of the remaining heparin. Samples were then phenol-chloroform (PC, pH 6.6) extracted using PLG heavy 0.5ml Eppendorf tubes, followed by a final precipitation with PelletPaint, 3M NaAcetate and 100% Ethanol and a wash step with 70% Ethanol. The RNA pellet of each fraction was diluted in 10ul water. RNA yield and quality were measured by the RNA6000 Nano assay (Bioanalyzer 2100, Agilent Technologies).


title: Serum treated MEF, polyribosome-associated mRNA, biological rep1

growth_protocol: Cells were grown using high glucose-DMEM (Invitrogen) with 1% Penicillin/Streptomycin (Invitrogen) and 10% dialyzed FBS (cutoff 10,000Da, Sigma) to near confluency. Cells were serum-starved for 48h with 1% dialyzed FBS, and then incubated for 2h with media containing 10% FBS (stimulation control).


title: PERH0029_CD4+_t3_aGVHD+_cGVHD+_2

source_name: PBMC t3 (recipient 1 year post-graft)


title: PERH0021_CD4+_t0_aGVHD+_cGVHD+_1


title: PERH0022_CD8+_t0_aGVHD+_cGVHD+_1


title: Serum starved MEF, undertranslated RNA, biological rep2

growth_protocol: Cells were grown using high glucose-DMEM (Invitrogen) with 1% Penicillin/Streptomycin (Invitrogen) and 10% dialyzed FBS (cutoff 10,000Da, Sigma) to near confluency. Cells were serum-starved for 48h with 1% dialyzed FBS, and then incubated for 2h with media containing 200uM 4-thiouridine (s4U, Sigma) and 1% FBS, and 1uCi 3H-cytidine (20Ci/mmol, Biotrend).


title: Serum starved MEF, cytoplasmic RNA, biological rep1

extract_protocol: Cells were washed with PBS, trypsinized (Trypsin-EDTA), washed again with PBS and centrifuged at 1000rpm for 6min at 4C. Cells were then lysed by the help of NP-40 lysis buffer (1ml for ~ 107 cells; 10mM Tris-HCl pH 8, 150mM NaCl, 1.5mM MgCl2, 0.1% (v/v) NP-40, 0.5mg/ml heparin, 1mM DTT) and douncing. The lysate was centrifuged with 10,000xg at 4C for 10min to seperate nuclei from the cytoplasm. The supernatant was stored, and the remaining nuclei were further and fully lysed. Both lysates were then processed according to the RNeasy MINI cleanup procedure (QIAGEN) to get rid of the remaining heparin. Samples were then phenol-chloroform (PC, pH 6.6) extracted using PLG heavy 0.5ml Eppendorf tubes, followed by a final precipitation with PelletPaint, 3M NaAcetate and 100% Ethanol and a wash step with 70% Ethanol. The RNA pellet of each fraction was diluted in 10ul water. RNA yield and quality were measured by the RNA6000 Nano assay (Bioanalyzer 2100, Agilent Technologies).


title: Serum treated MEF, undertranslated RNA, biological rep1


title: PERH0019_CD4+_t3_aGVHD+_cGVHD+_1


title: germination_rep6-2-2


title: PERH0015_CD4+_t3_aGVHD-_cGVHD+_1


title: Serum treated MEF, undertranslated RNA, biological rep2


title: germination_rep5-2-2


title: germination_rep5-2-1


title: germination_rep4-2-1


title: germination_rep3-2-2


title: germination_rep7-2-1


title: PERH0012_CD8+_t0_aGVHD-_cGVHD+_2


title: germination_rep4-2-2


title: PERH0020_CD8+_t3_aGVHD+_cGVHD+_1


title: PERH0017_CD4+_t0_aGVHD-_cGVHD+_3


title: Serum treated MEF, cytoplasmic RNA, biological rep1

growth_protocol: Cells were grown using high glucose-DMEM (Invitrogen) with 1% Penicillin/Streptomycin (Invitrogen) and 10% dialyzed FBS (cutoff 10,000Da, Sigma) to near confluency. Cells were serum-starved for 48h with 1% dialyzed FBS, and then incubated for 2h with media containing  10% FBS (stimulation control).


title: ANA-1 macrophage inf repB

description: total RNA from ANA-1 macrophages, 8 hours after Chlamydia pneumoniae infection, replicate B

extract_protocol: Trizol, as recommended by the manufacturer

tag: ANA-1 macrophages, 8 h, Chlamydia pneumoniae infected, M.O.I 10


title: ANA-1 macrophage inf repA

description: total RNA from ANA-1 macrophages, 8 hours after Chlamydia pneumoniae infection, replicate A

tag: ANA-1 macrophages, 8 h, Chlamydia pneumoniae infected, M.O.I. 10


title: ANA-1 macrophage mock repB

description: total RNA from ANA-1 macrophages, 8 hours after mock infection, replicate B

tag: ANA-1 macrophages, 8 h, not infected


title: PERH0011_CD4+_t0_aGVHD-_cGVHD+_2


title: germination_rep3-2-1

tag: T. rubrum conidia induced germination in Sabouraud liquid medium.


title: germination_rep1-2-2

tag: T. rubrum strain BMU01672 genomic DNA(reference channel )


title: PERH0004_CD8+_t0_aGVHD-_cGVHD-_1


title: germination_rep1-2-1


title: PERH0008_CD8+_t0_aGVHD-_cGVHD+_1


title: PERH0007_CD4+_t0_aGVHD-_cGVHD+_1


title: germination_rep0-2-2


title: ANA-1 macrophage mock repA

description: total RNA from ANA-1 macrophages, 8 hours after mock infection, replicate A


title: germination_rep1

description:
 T.rubrum conidia were collected at 1 hr intervals throught the germination process. The cDNA from  mRNA of the samples were and the genomic DNA of T.rubrum  were coupled with Cy5 or Cy3 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a GenePix 4000B scanner (Axon Instruments, Inc., CA).
Data processing Images were processed using GenePix 6.0 (Axon Instruments, Inc., CA)

tag: T. rubrum strain BMU01672 genomic DNA(reference channel)


title: Human_umbilical_cord_reticulocyte_transcriptome_CB13_HG-U133B

status: Public on Mar 26 2007

city: Bethesda

first: Jeffery

middle: Lynn

last: Miller

state: MD

address: 10 Center Drive

department: Molecular Medicine Branch

institute: NIH/NIDDK

description: Sample was filtered through Leukoreduction filter to remove white blood cells.

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

label: Biotin

source_name: Normal human umbilical cord red blood cells

label_protocol: Affymetrix protocol

extract_protocol: Affymetrix protocol


title: Human_umbilical_cord_reticulocyte_transcriptome_CB12_HG-U133B

tag: Normal human umbilical cord red blood cells


title: PERH0003_CD4+_t0_aGVHD-_cGVHD-_1


title: Human_umbilical_cord_reticulocyte_transcriptome_CB12_HG-U133A

extract_protocol: Total RNA extraction using Trizol-LS, then purified w/ Qiagen RNeasy cloumn.


title: Serum starved MEF, polyribosome-associated mRNA, biological rep2


title: Human_umbilical_cord_reticulocyte_transcriptome_CB09_HG-U133B


title: Human_umbilical_cord_reticulocyte_transcriptome_CB13_HG-U133A


title: Human_umbilical_cord_reticulocyte_transcriptome_CB11_HG-U133A


title: Human_umbilical_cord_reticulocyte_transcriptome_CB08_HG-U133A


title: germination_rep15-2-1


title: Human_umbilical_cord_reticulocyte_transcriptome_CB10_HG-U133B


title: Human_umbilical_cord_reticulocyte_transcriptome_CB10_HG-U133A


title: Human_umbilical_cord_reticulocyte_transcriptome_CB11_HG-U133B


title: Adult_human_reticulocyte_transcriptome_AB14_HG_U133B

source_name: Normal human adult red blood cells

tag: Normal human adult red blood cells


title: Adult_human_reticulocyte_transcriptome_AB13_HG_U133B


title: Human_umbilical_cord_reticulocyte_transcriptome_CB14_HG-U133A


title: Human_umbilical_cord_reticulocyte_transcriptome_CB04_HG-U133A


title: Adult_human_reticulocyte_transcriptome_AB10_HG_U133B


title: Human_umbilical_cord_reticulocyte_transcriptome_CB09_HG-U133A


title: Human_umbilical_cord_reticulocyte_transcriptome_CB05_HG-U133B


title: Human_umbilical_cord_reticulocyte_transcriptome_CB07_HG-U133A


title: Human_umbilical_cord_reticulocyte_transcriptome_CB03_HG-U133B


title: Adult_human_reticulocyte_transcriptome_AB12_HG_U133B


title: Human_umbilical_cord_reticulocyte_transcriptome_CB05_HG-U133A


title: Adult_human_reticulocyte_transcriptome_AB09_HG_U133B


title: Human_umbilical_cord_reticulocyte_transcriptome_CB01_HG-U133B


title: Adult_human_reticulocyte_transcriptome_AB14_HG-U133A


title: Human_umbilical_cord_reticulocyte_transcriptome_CB14_HG-U133B


title: Adult_human_reticulocyte_transcriptome_AB09_HG-U133A


title: Human_umbilical_cord_reticulocyte_transcriptome_CB06_HG-U133B


title: Human_umbilical_cord_reticulocyte_transcriptome_CB08_HG-U133B


title: Human_umbilical_cord_reticulocyte_transcriptome_CB06_HG-U133A


title: Human_umbilical_cord_reticulocyte_transcriptome_CB04_HG-U133B


title: Adult_human_reticulocyte_transcriptome_AB07_HG-U133B


title: Human_umbilical_cord_reticulocyte_transcriptome_CB01_HG-U133A


title: Adult_human_reticulocyte_transcriptome_AB06_HG-U133B


title: Adult_human_reticulocyte_transcriptome_AB11_HG-U133A


title: Adult_human_reticulocyte_transcriptome_AB03_HG_U133B


title: Human_umbilical_cord_reticulocyte_transcriptome_CB07_HG-U133B


title: Human_umbilical_cord_reticulocyte_transcriptome_CB02_HG-U133A


title: Adult_human_reticulocyte_transcriptome_AB11_HG-U133B


title: Human_umbilical_cord_reticulocyte_transcriptome_CB03_HG-U133A


title: Adult_human_reticulocyte_transcriptome_AB10_HG-U133A


title: Adult_human_reticulocyte_transcriptome_AB07_HG-U133A


title: Adult_human_reticulocyte_transcriptome_AB06_HG-U133A


title: Adult_human_reticulocyte_transcriptome_AB08_HG_U133B


title: Adult_human_reticulocyte_transcriptome_AB12_HG-U133A


title: Adult_human_reticulocyte_transcriptome_AB05_HG-U133B


title: Adult_human_reticulocyte_transcriptome_AB01_HG_U133B


title: Adult_human_reticulocyte_transcriptome_AB05_HG-U133A


title: Human_umbilical_cord_reticulocyte_transcriptome_CB02_HG-U133B


title: Adult_human_reticulocyte_transcriptome_AB13_HG-U133A


title: Adult_human_reticulocyte_transcriptome_AB08_HG-U133A


title: Adult_human_reticulocyte_transcriptome_AB04_HG-U133A


title: Adult_human_reticulocyte_transcriptome_AB03_HG-U133A


title: Adult_human_reticulocyte_transcriptome_AB02_HG-U133A


title: Adult_human_reticulocyte_transcriptome_AB04_HG-U133B


title: Adult_human_reticulocyte_transcriptome_AB02_HG-U133B


title: UACC-257 hg133b21

first: Uma

middle: T

last: Shankavaram

address: 9000 Rockville Pike

department: NCI

institute: NIH

description:
Background Avg = 53.25
Background Max = 55.4
Background Min = 51.8
Background Stdev = 0.70
Central- Avg = 1667
Central- Count = 9
Corner+ Avg = 53
Corner+ Count = 32
Corner- Avg = 1640
Corner- Count = 32
Noise Avg = 2.72
Noise Max = 3.5
Noise Min = 2.3
Noise Stdev = 0.18
RawQ = 2.32
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: skin

scan_protocol: Affymetrix CEL analysis (Percentile); Protocol Type = feature_extraction; Parameter CellMargin = 2; Parameter OutlierHigh = 1.500; Parameter OutlierLow = 1.004; Parameter Percentile = 75; Software: Affymetrix MicroArraySuite, type: feature_extraction_software; Protocol Type = image_acquisition; Software: Affymetrix MicroArraySuite, type: image_acquisition_software; Hardware: ;

data_processing: ExpressionStat; Protocol Type = bioassay_data_transformation; Parameter Alpha1 = 0.05; Parameter Alpha2 = 0.065; Parameter BG = 4; Parameter Epsilon = 0.5; Parameter Gamma1H = 0.0045; Parameter Gamma1L = 0.0045; Parameter Gamma2H = 0.006; Parameter Gamma2L = 0.006; Parameter HZ = 4; Parameter NF = 1.000000000000; Parameter Perturbation = 1.1; Parameter SF = 1.000000000000; Parameter SmoothFactorBG = 100; Parameter Tau = 0.015; Parameter VZ = 4; Software: Affymetrix GeneChip Operating Software, type: bioassay_data_transformation_software;

source_name: melanoma-melanotic

label_protocol: Affymetrix Labeling Protocol; The exact protocol is not available. But Standard Operating Proceadure can be found at          http://www.affymetrix.com/support/technical/manual/expression_manual.affx         or         http://www.affymetrix.com/Auth/support/downloads/manuals/expression_ever_manual.zip         Manual number: 701025 Revision 6, page 2.1.3; Protocol Type = labeling;

growth_protocol: NCI60Adherent; RNA harvesting protocol for adherent cells           Media used:         RPMI 1640 500 ml          FBS 25 ml -use the DTP serum if possible, from Bio Whittaker, not heat         inactivated          200 mM Glutamine 5 ml           1 flask = ~15 x 106 cells yields ~ 100 ugr RNA. Grow 10 flasks.                    Cells: start from growing cells from Frederick (not frozen). Started before at         passage #8-12. Do not use past passage 20.                    Growth schedule prior to harvest: Grow cells to         ~80 confluencey. Trypsinize cells with 5 ml try-EDTA per T162, 15 min., 370C. Pipet up and         down several times w 10 ml pipet to get good dispersment of cells. Count cells. Pass cells         to as many flasks as there are cells for. When passing cells, combine flasks into a single         pool. Pass 1x106 cells into each T162 w 30 ml media.  Repeat growth cycle until 10 flasks         are available.   Refeed Refeed cells the day prior to harvest without harvesting).  Draw off         media (wo cells). Add back media, 30 ml per T162. Add back to T-162âs. 37 deg C, ON  Harvest         Target confluency 80%  # of flasks = 10   Draw off media from 1st flask. Lyse cells in 15         ml lysis buffer (w 10 ul fresh BME per ml). Scrape cells. Draw off media from 2nd flask.         Pipet lysis buffer from flask 1 into flask 2. Repeat lysis with up to 4 T162âs. Pipet into         50 ml tube.  Repeat w next set of 4 flasks.  When done, vortex 10 sec.. Draw lysate thru a         20 guage needle 12xâs. Freeze at ö800C.  Purify using Quiagen Midi Kit.  Use a maximun of         100 x 106 cells per column. More will not bind to the column.                           Company Info         ------------           Quiagen Midi Kit Cat # 75144  RLT Buffer (lysis buffer) Cat. # 79216 $60-list, $51- discounted 1-800-362-7737                    Fetal Bovine Serum 500 ml, list $261- Cat #14-502F Lot # 9S083F Cambrex (old Bio Whittaker) 1-800-638-8174                   1x PBS pH 7.3-7.5 Bio Whittaker cat #17-516F $5.30 per 500 ml bottle (1-11)                    250 ml conical tubes Corning cat #25350-250                    RPMI-1640 wo L-glutamine cat # 12-167F  $13.25 per 500 ml bottle (for 1-11 bottles) Cambrex (old Bio Whittaker) Walkersville, Md. 21793 301-898-7025 1-800-638-8174                  Trypsin (0.05%)-EDTA (0.1%) In phosphate buffered saline without calcium and magnesium. cat # 118-087-061 $4.20 per 100 ml bottle Quality Biological, Inc. 301-840-9331                    L-glutamine 200 mM, 100x Gibco-BRL cat # 25030-149 20 ml 1-800-828-6686                    162 cm2 flask cat # 3150                    Costar Tissue Culture Cell Scrapper, 25 cm Sarstedt Cat. # 83.1830                    Cells are received from Nick Scudiero,  E-mail: SCUDIERO@dtpax2.ncifcrf.gov          Also trypsin, FBS and glutamine have been coming from there as well.; Protocol Type = grow;

extract_protocol: NCI60 Extraction Protocol; Harvest         Target confluency  80%            # of flasks = 10                  Draw off media from 1st flask.         Lyse cells in 15 ml lysis buffer (w 10 ul fresh BME per ml).         Scrape cells.         Draw off media from 2nd flask.         Pipet lysis buffer from flask 1 into flask 2.         Repeat lysis with up to 4 T162’s.         Pipet into 50 ml tube.                  Repeat w next set of 4 flasks.                  When done, vortex 10 sec..         Draw lysate thru a 20 guage needle 12x’s.         Freeze at –800C.                  Purify using Quiagen Midi Kit.          Use a maximun of 100 x 106 cells per column. More will not bind to the column.         ; Protocol Type = nucleic_acid_extraction;

tag: age

value: unknown

value: melanoma-melanotic

tag: sex


title: Adult_human_reticulocyte_transcriptome_AB01_HG-U133A


title: K-562 hg133b21

description:
Background Avg = 33.50
Background Max = 38.0
Background Min = 32.0
Background Stdev = 1.28
Central- Avg = 3080
Central- Count = 9
Corner+ Avg = 51
Corner+ Count = 32
Corner- Avg = 3338
Corner- Count = 32
Noise Avg = 1.31
Noise Max = 2.0
Noise Min = 1.1
Noise Stdev = 0.15
RawQ = 1.44
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: blood

source_name: myelogenous leukemia

growth_protocol: NCI60Suspended; RNA harvesting protocol for suspended cells:           Media used:          RPMI 1640 500 ml          FBS 25 ml          200 mM Glutamine 5 ml                    Cells:          start from growing cells from Frederick (not frozen). Started before at passage #8-12. Do not use past passage 20. Grow 10         flasks. 1 flask = ~15 x 106 cells yields ~ 100 ugr RNA.  Growth schedule prior to harvest         Count cells as necessary to follow growth. Grow cells to ~0.52 x 106 cells /ml  Pass 1x106         cells into each T162 w 30 ml media. Pass cells to as many flasks as there are cells for.         When passing cells, combine into a single pool.  Repeat growth cycle until 10 flasks are         available.  Refeed Refeed cells the day prior to harvest (without passsing). To do so: Spin         down cells 1.7k rpm, 10 min., in a 50 ml tube. Draw off media. Resuspend in 30 ml media.         Return to flask.  Harvest Harvest at 0.52 x 106cells per ml when 10 flasks are available.         Spin  4 flasks of cells at  1.7k rpm (~ 500 x g), 10 min (speed setting at 3.5), in a 250 ml         centrifuge tube.   Draw off media, leaving ~0.5 ml behind. Flick centirifuge tube to break         up cells. Lyse cells in 15 ml lysis buffer (w 10 ul fresh BME per ml) per 4 T162âs.  Vortex         10 sec. Draw thru a 20 guage needle 12xâs. Freeze at ö800C.   Purify using Quigen Midi         Kit.Use a maximum of 100 x 106 cells per column. More will not bind to the column.                  Company Info:           Fetal bovine serum Do not heat inactivate. Bio Whittaker Cat# 14-501F Lot #9S083F 301-898-7025                    Quiagen Midi Kit Cat # 75144                    DTT Fluka or Gallard  1x PBS pH 7.3-7.5                  Bio Whittaker cat #17-516F $5.30 per 500 ml bottle (1-11)                    250 ml conical centrifuge tubes Corning cat # 25350-250                    RPMI-1640 wo L-glutamine cat # 12-167F  $13.25 per 500 ml bottle         (for 1-11 bottles) Cambrex (old Bio Whittaker) Walkersville, Md. 21793 301-898-7025         1-800-638-8174                    Trypsin (0.05%)-EDTA (0.1%) In phosphate buffered saline without calcium and         magnesium. cat # 118-087-061 Quality Biological, Inc. 301-840-9331                    L-glutamine 200 mM, 100x Gibco-BRL cat # 25030-081  162 cm2 flask cat # 3150                   Costar Tissue Culture Cell Scrapper, 25cm Sarstedt Cat. # 83.1830                    Cells are recieved from Nick Scudiero,  E-mail:SCUDIERO@dtpax2.ncifcrf.gov          Also trypsin, FBS and glutamine have been coming from there as well.; Protocol Type = grow;

value: myelogenous leukemia

value: chronic myelogenous leukemia

value: female


title: HT29 hg133b21

description:
Background Avg = 56.91
Background Max = 59.8
Background Min = 53.8
Background Stdev = 1.35
Central- Avg = 1536
Central- Count = 9
Corner+ Avg = 44
Corner+ Count = 32
Corner- Avg = 1514
Corner- Count = 32
Noise Avg = 2.45
Noise Max = 2.8
Noise Min = 2.2
Noise Stdev = 0.10
RawQ = 2.48
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: colon

source_name: adenocarcinoma

value: adenocarcinoma


title: MCF7 hg133b21

description:
Background Avg = 43.97
Background Max = 46.1
Background Min = 40.6
Background Stdev = 0.94
Central- Avg = 1578
Central- Count = 9
Corner+ Avg = 26
Corner+ Count = 32
Corner- Avg = 1549
Corner- Count = 32
Noise Avg = 1.46
Noise Max = 1.7
Noise Min = 1.3
Noise Stdev = 0.05
RawQ = 1.87
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: breast

source_name: breast epithelial adenocarcinoma

value: breast epithelial adenocarcinoma


title: SF-295 hg133b21

description:
Background Avg = 50.52
Background Max = 52.9
Background Min = 48.4
Background Stdev = 0.90
Central- Avg = 1291
Central- Count = 9
Corner+ Avg = 50
Corner+ Count = 32
Corner- Avg = 1418
Corner- Count = 32
Noise Avg = 2.24
Noise Max = 2.6
Noise Min = 2.1
Noise Stdev = 0.09
RawQ = 2.30
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: central nervous system

source_name: glioblastoma undifferentiated

value: glioblastoma undifferentiated


title: MALME-3M hg133b21

description:
Background Avg = 43.20
Background Max = 44.1
Background Min = 42.3
Background Stdev = 0.36
Central- Avg = 791
Central- Count = 9
Corner+ Avg = 37
Corner+ Count = 32
Corner- Avg = 768
Corner- Count = 32
Noise Avg = 1.74
Noise Max = 2.1
Noise Min = 1.6
Noise Stdev = 0.09
RawQ = 1.94
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: skin

source_name: malignant melanoma

value: malignant melanoma

value: male


title: SK-MEL-5 hg133b21

description:
Background Avg = 59.05
Background Max = 63.0
Background Min = 55.9
Background Stdev = 1.16
Central- Avg = 1874
Central- Count = 9
Corner+ Avg = 49
Corner+ Count = 32
Corner- Avg = 2004
Corner- Count = 32
Noise Avg = 2.30
Noise Max = 2.6
Noise Min = 2.0
Noise Stdev = 0.10
RawQ = 2.21
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: skin

source_name: melanoma

value: melanoma

value: melanoma-premelanotic


title: HCC-2998 hg133b21

description:
Background Avg = 70.92
Background Max = 78.2
Background Min = 66.0
Background Stdev = 2.74
Central- Avg = 1593
Central- Count = 9
Corner+ Avg = 85
Corner+ Count = 32
Corner- Avg = 1615
Corner- Count = 32
Noise Avg = 3.66
Noise Max = 4.3
Noise Min = 3.2
Noise Stdev = 0.19
RawQ = 2.81
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: colon

source_name: carcinoma

value: carcinoma


title: PC-3 hg133b21

description:
Background Avg = 41.49
Background Max = 43.1
Background Min = 40.1
Background Stdev = 0.52
Central- Avg = 1204
Central- Count = 9
Corner+ Avg = 28
Corner+ Count = 32
Corner- Avg = 1137
Corner- Count = 32
Noise Avg = 1.80
Noise Max = 2.1
Noise Min = 1.6
Noise Stdev = 0.07
RawQ = 1.99
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: prostate

source_name: prostate adenocarcinoma

value: prostate adenocarcinoma


title: OVCAR-5 hg133b21

description:
Background Avg = 60.52
Background Max = 65.5
Background Min = 57.1
Background Stdev = 1.59
Central- Avg = 2429
Central- Count = 9
Corner+ Avg = 85
Corner+ Count = 32
Corner- Avg = 2891
Corner- Count = 32
Noise Avg = 2.75
Noise Max = 3.1
Noise Min = 2.4
Noise Stdev = 0.12
RawQ = 2.84
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: ovary

value: adenocarcinoma-wd


title: SW-620 hg133b21

description:
Background Avg = 44.27
Background Max = 47.8
Background Min = 41.1
Background Stdev = 1.39
Central- Avg = 1392
Central- Count = 9
Corner+ Avg = 28
Corner+ Count = 32
Corner- Avg = 1374
Corner- Count = 32
Noise Avg = 1.87
Noise Max = 2.2
Noise Min = 1.6
Noise Stdev = 0.11
RawQ = 2.11
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: colon


title: HOP-62 hg133b21

description:
Background Avg = 42.68
Background Max = 44.3
Background Min = 39.6
Background Stdev = 0.82
Central- Avg = 1588
Central- Count = 9
Corner+ Avg = 42
Corner+ Count = 32
Corner- Avg = 1459
Corner- Count = 32
Noise Avg = 1.92
Noise Max = 2.2
Noise Min = 1.7
Noise Stdev = 0.09
RawQ = 1.95
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: lung

source_name: adenocarcinoma-undifferentiated

value: adenocarcinoma-undifferentiated


title: A549/ATCC hg133b21

description:
Background Avg = 42.65
Background Max = 45.2
Background Min = 40.3
Background Stdev = 0.86
Central- Avg = 1883
Central- Count = 9
Corner+ Avg = 40
Corner+ Count = 32
Corner- Avg = 1779
Corner- Count = 32
Noise Avg = 1.93
Noise Max = 2.2
Noise Min = 1.7
Noise Stdev = 0.09
RawQ = 1.83
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: lung

source_name: adenocarcinoma-poor or moderately differentiated


title: SK-OV-3 hg133b21

description:
Background Avg = 50.68
Background Max = 55.9
Background Min = 41.1
Background Stdev = 3.56
Central- Avg = 3046
Central- Count = 9
Corner+ Avg = 42
Corner+ Count = 32
Corner- Avg = 2760
Corner- Count = 32
Noise Avg = 2.14
Noise Max = 2.6
Noise Min = 1.9
Noise Stdev = 0.12
RawQ = 2.33
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: ovary


title: 786-0 hg133b21

description:
Background Avg = 27.88
Background Max = 29.1
Background Min = 26.0
Background Stdev = 0.65
Central- Avg = 1420
Central- Count = 9
Corner+ Avg = 18
Corner+ Count = 32
Corner- Avg = 1377
Corner- Count = 32
Noise Avg = 1.11
Noise Max = 1.2
Noise Min = 1.0
Noise Stdev = 0.04
RawQ = 1.44
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: kidney


title: K-562 hg133a21

description:
Background Avg = 35.24
Background Max = 36.5
Background Min = 33.0
Background Stdev = 0.71
Central- Avg = 1748
Central- Count = 9
Corner+ Avg = 42
Corner+ Count = 32
Corner- Avg = 1785
Corner- Count = 32
Noise Avg = 1.57
Noise Max = 1.9
Noise Min = 1.3
Noise Stdev = 0.09
RawQ = 1.59
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: blood


title: RPMI-8226 hg133b21

description:
Background Avg = 45.30
Background Max = 48.2
Background Min = 42.4
Background Stdev = 1.30
Central- Avg = 1020
Central- Count = 9
Corner+ Avg = 27
Corner+ Count = 32
Corner- Avg = 1010
Corner- Count = 32
Noise Avg = 1.85
Noise Max = 2.4
Noise Min = 1.5
Noise Stdev = 0.12
RawQ = 2.01
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: blood

source_name: myeloma

value: myeloma


title: NCI-H322M hg133b21

description:
Background Avg = 49.45
Background Max = 51.5
Background Min = 46.9
Background Stdev = 0.85
Central- Avg = 2275
Central- Count = 9
Corner+ Avg = 35
Corner+ Count = 32
Corner- Avg = 1955
Corner- Count = 32
Noise Avg = 2.29
Noise Max = 2.7
Noise Min = 2.0
Noise Stdev = 0.11
RawQ = 2.36
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: lung

source_name: small cell bronchioalveolar carcinoma

value: small cell bronchioalveolar carcinoma


title: SR hg133b21

description:
Background Avg = 44.72
Background Max = 47.9
Background Min = 42.8
Background Stdev = 0.95
Central- Avg = 4320
Central- Count = 9
Corner+ Avg = 94
Corner+ Count = 32
Corner- Avg = 5675
Corner- Count = 32
Noise Avg = 1.62
Noise Max = 1.9
Noise Min = 1.4
Noise Stdev = 0.10
RawQ = 1.85
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: blood

source_name: lymphoma

value: lymphoma


title: SNB-75 hg133b21

description:
Background Avg = 32.76
Background Max = 34.8
Background Min = 30.0
Background Stdev = 0.95
Central- Avg = 1631
Central- Count = 9
Corner+ Avg = 20
Corner+ Count = 32
Corner- Avg = 1658
Corner- Count = 32
Noise Avg = 1.44
Noise Max = 1.6
Noise Min = 1.3
Noise Stdev = 0.06
RawQ = 1.64
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: central nervous system

source_name: astrocytoma

value: unknown

value: astrocytoma


title: germination_rep15-2-2

description: T.rubrum conidia were collected at 1 hr intervals throught the germination process. The cDNA from  mRNA of the samples were and the genomic DNA of T.rubrum  were coupled with Cy5 or Cy3 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a GenePix 4000B scanner (Axon Instruments, Inc., CA).

source_name: mRNA: germination-induced conidia

source_name: gDNA: BMU01672 genomic DNA (reference)


title: OVCAR-8 hg133b21

description:
Background Avg = 54.12
Background Max = 56.1
Background Min = 52.1
Background Stdev = 0.80
Central- Avg = 1653
Central- Count = 9
Corner+ Avg = 30
Corner+ Count = 32
Corner- Avg = 1294
Corner- Count = 32
Noise Avg = 1.91
Noise Max = 2.3
Noise Min = 1.6
Noise Stdev = 0.13
RawQ = 2.09
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: ovary

value: carcinoma-undifferentiated

value: female


title: CCRF-CEM hg133b21

description:
Background Avg = 33.34
Background Max = 34.9
Background Min = 31.9
Background Stdev = 0.67
Central- Avg = 1590
Central- Count = 9
Corner+ Avg = 21
Corner+ Count = 32
Corner- Avg = 1654
Corner- Count = 32
Noise Avg = 1.33
Noise Max = 1.5
Noise Min = 1.2
Noise Stdev = 0.05
RawQ = 1.66
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: blood

source_name: lymphoblastic leukemia

value: lymphoblastic leukemia

value: acute lymphoblastic leukemia


title: EKVX hg133b21

description:
Background Avg = 40.52
Background Max = 41.8
Background Min = 39.0
Background Stdev = 0.49
Central- Avg = 907
Central- Count = 9
Corner+ Avg = 20
Corner+ Count = 32
Corner- Avg = 926
Corner- Count = 32
Noise Avg = 1.28
Noise Max = 1.4
Noise Min = 1.2
Noise Stdev = 0.04
RawQ = 1.74
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: lung

value: adenocarcinoma


title: NCI-ADR-RES hg133b21

description:
Background Avg = 28.89
Background Max = 31.3
Background Min = 27.5
Background Stdev = 0.76
Central- Avg = 2584
Central- Count = 9
Corner+ Avg = 38
Corner+ Count = 32
Corner- Avg = 2684
Corner- Count = 32
Noise Avg = 1.06
Noise Max = 1.2
Noise Min = 1.0
Noise Stdev = 0.04
RawQ = 1.35
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: ovary


title: SR hg133a21

description:
Background Avg = 52.44
Background Max = 61.7
Background Min = 46.4
Background Stdev = 2.61
Central- Avg = 2654
Central- Count = 9
Corner+ Avg = 43
Corner+ Count = 32
Corner- Avg = 2597
Corner- Count = 32
Noise Avg = 2.34
Noise Max = 3.0
Noise Min = 1.8
Noise Stdev = 0.19
RawQ = 2.19
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: blood

value: male


title: HOP-92 hg133b21

description:
Background Avg = 57.50
Background Max = 60.1
Background Min = 53.7
Background Stdev = 1.28
Central- Avg = 1234
Central- Count = 9
Corner+ Avg = 78
Corner+ Count = 32
Corner- Avg = 1282
Corner- Count = 32
Noise Avg = 3.15
Noise Max = 3.6
Noise Min = 2.6
Noise Stdev = 0.19
RawQ = 2.45
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: lung

source_name: large cell-undifferentiated

value: large cell-undifferentiated


title: HL-60 hg133a21

description:
Background Avg = 36.60
Background Max = 39.2
Background Min = 35.2
Background Stdev = 0.69
Central- Avg = 914
Central- Count = 9
Corner+ Avg = 30
Corner+ Count = 32
Corner- Avg = 1033
Corner- Count = 32
Noise Avg = 1.47
Noise Max = 1.7
Noise Min = 1.3
Noise Stdev = 0.07
RawQ = 1.64
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: blood

source_name: promyelocytic leukemia

value: promyelocytic leukemia

value: acute promyelocytic leukemia


title: SK-MEL-28 hg133b21

description:
Background Avg = 38.07
Background Max = 41.0
Background Min = 35.2
Background Stdev = 1.01
Central- Avg = 931
Central- Count = 9
Corner+ Avg = 33
Corner+ Count = 32
Corner- Avg = 845
Corner- Count = 32
Noise Avg = 1.98
Noise Max = 2.4
Noise Min = 1.7
Noise Stdev = 0.11
RawQ = 1.91
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: skin

value: melanoma

value: malignant melanoma


title: OVCAR-3 hg133b21

description:
Background Avg = 55.16
Background Max = 59.1
Background Min = 53.0
Background Stdev = 1.10
Central- Avg = 1469
Central- Count = 9
Corner+ Avg = 61
Corner+ Count = 32
Corner- Avg = 1651
Corner- Count = 32
Noise Avg = 2.12
Noise Max = 2.5
Noise Min = 1.9
Noise Stdev = 0.10
RawQ = 2.14
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: ovary

source_name: adenocarcinoma


title: A498 hg133b21

description:
Background Avg = 41.55
Background Max = 45.6
Background Min = 38.1
Background Stdev = 1.66
Central- Avg = 1378
Central- Count = 9
Corner+ Avg = 19
Corner+ Count = 32
Corner- Avg = 1395
Corner- Count = 32
Noise Avg = 1.55
Noise Max = 1.8
Noise Min = 1.3
Noise Stdev = 0.08
RawQ = 1.95
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: kidney


title: IGROV1 hg133b21

description:
Background Avg = 53.24
Background Max = 55.5
Background Min = 50.9
Background Stdev = 0.79
Central- Avg = 5302
Central- Count = 9
Corner+ Avg = 77
Corner+ Count = 32
Corner- Avg = 5698
Corner- Count = 32
Noise Avg = 2.33
Noise Max = 2.6
Noise Min = 2.0
Noise Stdev = 0.09
RawQ = 2.24
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: ovary

source_name: cystoadenocarcinoma

value: cystoadenocarcinoma


title: SK-MEL-2 hg133b21

description:
Background Avg = 33.78
Background Max = 36.1
Background Min = 30.9
Background Stdev = 1.08
Central- Avg = 1184
Central- Count = 9
Corner+ Avg = 24
Corner+ Count = 32
Corner- Avg = 1088
Corner- Count = 32
Noise Avg = 1.61
Noise Max = 1.9
Noise Min = 1.4
Noise Stdev = 0.09
RawQ = 1.71
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: skin


title: MDA-MB-435 hg133b21

description:
Background Avg = 29.96
Background Max = 31.6
Background Min = 28.2
Background Stdev = 0.65
Central- Avg = 1962
Central- Count = 9
Corner+ Avg = 19
Corner+ Count = 32
Corner- Avg = 2015
Corner- Count = 32
Noise Avg = 0.99
Noise Max = 1.1
Noise Min = 0.8
Noise Stdev = 0.04
RawQ = 1.35
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: skin

source_name: ductal breast carcinoma

value: ductal breast carcinoma

value: ductal breast carcinoma; metastatic site:pleural effusion; In a recent study using cDNA microarrays, the parent line (MD A-MB-435) of MDA-MB-435S clustered with cell lines of melanoma origin. Ross DT et al. Nature Genetics 24:227-235, 2000 )


title: RPMI-8226 hg133a21

description:
Background Avg = 44.71
Background Max = 46.5
Background Min = 43.1
Background Stdev = 0.64
Central- Avg = 552
Central- Count = 9
Corner+ Avg = 27
Corner+ Count = 32
Corner- Avg = 524
Corner- Count = 32
Noise Avg = 2.08
Noise Max = 2.5
Noise Min = 1.8
Noise Stdev = 0.14
RawQ = 2.00
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: blood

value: myeloma


title: KM12 hg133b21

description:
Background Avg = 45.22
Background Max = 46.5
Background Min = 43.9
Background Stdev = 0.52
Central- Avg = 913
Central- Count = 9
Corner+ Avg = 23
Corner+ Count = 32
Corner- Avg = 764
Corner- Count = 32
Noise Avg = 1.23
Noise Max = 1.4
Noise Min = 1.1
Noise Stdev = 0.05
RawQ = 1.70
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: colon

value: unknown


title: UACC-62 hg133a21

description:
Background Avg = 51.31
Background Max = 54.7
Background Min = 47.2
Background Stdev = 1.34
Central- Avg = 1255
Central- Count = 9
Corner+ Avg = 30
Corner+ Count = 32
Corner- Avg = 1086
Corner- Count = 32
Noise Avg = 2.50
Noise Max = 3.1
Noise Min = 2.2
Noise Stdev = 0.16
RawQ = 2.08
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: skin

source_name: melanoma


title: HCT-15 hg133b21

description:
Background Avg = 49.63
Background Max = 51.7
Background Min = 46.3
Background Stdev = 1.15
Central- Avg = 1333
Central- Count = 9
Corner+ Avg = 33
Corner+ Count = 32
Corner- Avg = 1247
Corner- Count = 32
Noise Avg = 2.13
Noise Max = 2.5
Noise Min = 1.9
Noise Stdev = 0.12
RawQ = 2.30
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: colon


title: BT-549 hg133b21

description:
Background Avg = 43.09
Background Max = 45.4
Background Min = 41.4
Background Stdev = 0.63
Central- Avg = 1664
Central- Count = 9
Corner+ Avg = 26
Corner+ Count = 32
Corner- Avg = 1780
Corner- Count = 32
Noise Avg = 1.53
Noise Max = 1.7
Noise Min = 1.4
Noise Stdev = 0.04
RawQ = 1.86
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: breast

source_name: papillary infiltrating ductal carcinoma

value: papillary infiltrating ductal carcinoma

value: invasive papillary breast carcinoma


title: NCI-H226 hg133b21

description:
Background Avg = 60.01
Background Max = 62.8
Background Min = 57.4
Background Stdev = 1.01
Central- Avg = 2336
Central- Count = 9
Corner+ Avg = 40
Corner+ Count = 32
Corner- Avg = 1935
Corner- Count = 32
Noise Avg = 2.23
Noise Max = 2.7
Noise Min = 2.0
Noise Stdev = 0.13
RawQ = 2.27
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: lung

source_name: squamous cell carcinoma

value: squamous cell carcinoma

value: carcinoma


title: NCI-H522 hg133b21

description:
Background Avg = 46.47
Background Max = 49.6
Background Min = 44.4
Background Stdev = 0.93
Central- Avg = 1042
Central- Count = 9
Corner+ Avg = 28
Corner+ Count = 32
Corner- Avg = 1002
Corner- Count = 32
Noise Avg = 2.16
Noise Max = 2.5
Noise Min = 1.9
Noise Stdev = 0.10
RawQ = 2.18
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: lung


title: COLO205 hg133b21

description:
Background Avg = 38.84
Background Max = 41.0
Background Min = 36.2
Background Stdev = 1.05
Central- Avg = 1533
Central- Count = 9
Corner+ Avg = 31
Corner+ Count = 32
Corner- Avg = 1471
Corner- Count = 32
Noise Avg = 1.78
Noise Max = 2.1
Noise Min = 1.6
Noise Stdev = 0.07
RawQ = 1.91
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: colon


title: SF-539 hg133b21

description:
Background Avg = 50.20
Background Max = 52.3
Background Min = 47.9
Background Stdev = 0.84
Central- Avg = 1517
Central- Count = 9
Corner+ Avg = 35
Corner+ Count = 32
Corner- Avg = 1429
Corner- Count = 32
Noise Avg = 2.10
Noise Max = 2.4
Noise Min = 1.8
Noise Stdev = 0.11
RawQ = 1.98
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: central nervous system

source_name: glial neoplasm

value: glial neoplasm

value: female


title: CAKI-1 hg133b21

description:
Background Avg = 45.28
Background Max = 47.1
Background Min = 43.7
Background Stdev = 0.63
Central- Avg = 3103
Central- Count = 9
Corner+ Avg = 57
Corner+ Count = 32
Corner- Avg = 3311
Corner- Count = 32
Noise Avg = 1.66
Noise Max = 1.9
Noise Min = 1.5
Noise Stdev = 0.07
RawQ = 1.93
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: kidney

source_name: clear cell carcinoma

value: clear cell carcinoma

value: male


title: DU-145 hg133b21

description:
Background Avg = 40.58
Background Max = 42.7
Background Min = 37.2
Background Stdev = 1.10
Central- Avg = 1226
Central- Count = 9
Corner+ Avg = 23
Corner+ Count = 32
Corner- Avg = 1022
Corner- Count = 32
Noise Avg = 1.54
Noise Max = 1.7
Noise Min = 1.4
Noise Stdev = 0.05
RawQ = 1.58
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: prostate

source_name: carcinoma


title: SNB-19 hg133b21

description:
Background Avg = 52.67
Background Max = 56.1
Background Min = 49.3
Background Stdev = 1.60
Central- Avg = 1251
Central- Count = 9
Corner+ Avg = 50
Corner+ Count = 32
Corner- Avg = 1201
Corner- Count = 32
Noise Avg = 2.32
Noise Max = 2.8
Noise Min = 2.0
Noise Stdev = 0.15
RawQ = 2.23
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: central nervous system

source_name: glioblastoma undifferentiated

value: glioblastoma undifferentiated


title: HS578T hg133b21

description:
Background Avg = 90.17
Background Max = 108.2
Background Min = 70.8
Background Stdev = 6.93
Central- Avg = 6872
Central- Count = 9
Corner+ Avg = 122
Corner+ Count = 32
Corner- Avg = 6599
Corner- Count = 32
Noise Avg = 8.89
Noise Max = 12.8
Noise Min = 7.3
Noise Stdev = 0.80
RawQ = 3.81
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: breast

source_name: breast epithelial carcinosarcoma

value: breast epithelial carcinosarcoma

value: carcinosarcoma


title: T47D hg133b21

description:
Background Avg = 35.99
Background Max = 37.6
Background Min = 33.6
Background Stdev = 0.81
Central- Avg = 3326
Central- Count = 9
Corner+ Avg = 30
Corner+ Count = 32
Corner- Avg = 3255
Corner- Count = 32
Noise Avg = 1.30
Noise Max = 1.5
Noise Min = 1.1
Noise Stdev = 0.05
RawQ = 1.65
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: breast

source_name: breast epithelial carcinoma

value: breast epithelial carcinoma

value: infiltrating ductal carcinoma


title: NCI-H460 hg133b21

description:
Background Avg = 35.02
Background Max = 37.5
Background Min = 33.4
Background Stdev = 0.77
Central- Avg = 2384
Central- Count = 9
Corner+ Avg = 28
Corner+ Count = 32
Corner- Avg = 2336
Corner- Count = 32
Noise Avg = 1.56
Noise Max = 1.7
Noise Min = 1.4
Noise Stdev = 0.05
RawQ = 1.88
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: lung

source_name: large cell carcinoma-undifferentiated

value: large cell carcinoma-undifferentiated


title: HOP-92 hg133a21

description:
Background Avg = 100.43
Background Max = 107.6
Background Min = 86.2
Background Stdev = 4.32
Central- Avg = 868
Central- Count = 9
Corner+ Avg = 97
Corner+ Count = 32
Corner- Avg = 721
Corner- Count = 32
Noise Avg = 4.61
Noise Max = 5.3
Noise Min = 3.9
Noise Stdev = 0.27
RawQ = 3.05
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: lung

value: large cell-undifferentiated


title: MOLT-4 hg133b21

description:
Background Avg = 32.63
Background Max = 34.4
Background Min = 30.7
Background Stdev = 0.70
Central- Avg = 939
Central- Count = 9
Corner+ Avg = 17
Corner+ Count = 32
Corner- Avg = 890
Corner- Count = 32
Noise Avg = 1.34
Noise Max = 1.5
Noise Min = 1.2
Noise Stdev = 0.05
RawQ = 1.66
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: blood

value: lymphoblastic leukemia

value: acute lymphoblastic leukemia


title: U251 hg133b21

description:
Background Avg = 57.41
Background Max = 61.0
Background Min = 55.1
Background Stdev = 1.08
Central- Avg = 2272
Central- Count = 9
Corner+ Avg = 43
Corner+ Count = 32
Corner- Avg = 1920
Corner- Count = 32
Noise Avg = 2.22
Noise Max = 2.8
Noise Min = 1.9
Noise Stdev = 0.15
RawQ = 2.25
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: central nervous system


title: UO-31 hg133b21

description:
Background Avg = 34.76
Background Max = 36.9
Background Min = 33.2
Background Stdev = 0.86
Central- Avg = 1188
Central- Count = 9
Corner+ Avg = 47
Corner+ Count = 32
Corner- Avg = 1321
Corner- Count = 32
Noise Avg = 1.51
Noise Max = 1.7
Noise Min = 1.3
Noise Stdev = 0.08
RawQ = 1.67
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: kidney

source_name: renal cell carcinoma

value: unknown

value: renal cell carcinoma

value: renal cell carcinoma-very poorly differentiated


title: TK-10 hg133b21

description:
Background Avg = 38.82
Background Max = 40.0
Background Min = 37.7
Background Stdev = 0.46
Central- Avg = 1525
Central- Count = 9
Corner+ Avg = 28
Corner+ Count = 32
Corner- Avg = 1200
Corner- Count = 32
Noise Avg = 1.17
Noise Max = 1.3
Noise Min = 1.1
Noise Stdev = 0.04
RawQ = 1.70
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: kidney

source_name: renal spindle cell carcinoma

value: renal spindle cell carcinoma


title: MOLT-4 hg133a21

description:
Background Avg = 52.65
Background Max = 56.2
Background Min = 48.3
Background Stdev = 1.53
Central- Avg = 655
Central- Count = 9
Corner+ Avg = 27
Corner+ Count = 32
Corner- Avg = 912
Corner- Count = 32
Noise Avg = 1.77
Noise Max = 2.1
Noise Min = 1.6
Noise Stdev = 0.10
RawQ = 1.96
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: blood

source_name: lymphoblastic leukemia


title: RXF-393 hg133b21

description:
Background Avg = 43.26
Background Max = 45.6
Background Min = 41.9
Background Stdev = 0.74
Central- Avg = 1501
Central- Count = 9
Corner+ Avg = 47
Corner+ Count = 32
Corner- Avg = 1651
Corner- Count = 32
Noise Avg = 1.86
Noise Max = 2.1
Noise Min = 1.6
Noise Stdev = 0.10
RawQ = 1.80
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: kidney

source_name: hypernephroma

value: hypernephroma

value: hypernephroma-poorly differentiated


title: Diseased 8

city: Catania

first: Sebastiano

last: Cavallaro

address: Viale Regina Margherita, 6

department: Institute of Neurological Sciences

institute: Italian National Research Council

description: Complementary RNAs (cRNAs) labelled with Cy5-CTP (Perkin-Elmer) were synthesized from 1 µg of total RNA of each sample using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies) following the manufacturer’s protocol. A reference cRNA, labelled with Cy3-CTP (Perkin-Elmer), was synthesized from 1 µg of sample Diseased 2 RNA. Aliquots (750 ng) of Cy3 and Cy5 labelled cRNA targets were co-hybridized on Whole Human Genome Oligo Microarrays (Agilent Technologies). Microarray hybridization and washing were performed using reagents and instruments (hybridization chambers and rotating oven) as indicated by the manufacturer (Agilent Technologies). Microarrays were scanned at 10-μm resolution using a GenePix Personal 4100A microarray scanner and the GenePix Pro 6.0 acquisition and data-extraction software (Molecular Devices, Corp.).

data_processing: No Normalization

source_name: motor cortex, reference

tag: Sample ID

value: Diseased 2; Sample Type:tissue; Order Code:BTB3292 [Brain and Tissue Bank for Developmental Disorders (Miami, FL, USA)]; Chief Disease:ALS; Cause of Death:ALS; Age [years / days]:76 / 197; Gender:Male; Race:Caucasian; PMI [h]:24.

source_name: motor cortex, diseased 8

value: Diseased 8; Sample Type:tissue; Order Code:BTB3611 [Brain and Tissue Bank for Developmental Disorders (Miami, FL, USA)]; Chief Disease:ALS; Cause of Death:n/a; Age [years / days]:69 / 90; Gender:Female; Race:Caucasian; PMI [h]:13.


title: SF-268 hg133b21

description:
Background Avg = 39.52
Background Max = 40.7
Background Min = 38.2
Background Stdev = 0.52
Central- Avg = 1105
Central- Count = 9
Corner+ Avg = 24
Corner+ Count = 32
Corner- Avg = 1130
Corner- Count = 32
Noise Avg = 1.54
Noise Max = 1.8
Noise Min = 1.4
Noise Stdev = 0.05
RawQ = 1.70
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: central nervous system

source_name: glioblastoma undifferntiated

value: glioblastoma undifferntiated

value: glioblastoma undifferentiated

value: female


title: Diseased 6

source_name: motor cortex, diseased 6

value: Diseased 6; Sample Type:tissue; Order Code:BTB3590 [Brain and Tissue Bank for Developmental Disorders (Miami, FL, USA)]; Chief Disease:ALS; Cause of Death:pneumonia; Age [years / days]:75 / -; Gender:Male; Race:Caucasian; PMI [h]:24.


title: Diseased 10

source_name: motor cortex, diseased 10

value: Diseased 10; Sample Type:tissue; Order Code:BTB3713 [Brain and Tissue Bank for Developmental Disorders (Miami, FL, USA)]; Chief Disease:ALS; Cause of Death:ALS; Age [years / days]:66 / 252; Gender:Male; Race:Caucasian; PMI [h]:13.


title: A549/ATCC hg133a21

description:
Background Avg = 43.61
Background Max = 45.9
Background Min = 41.0
Background Stdev = 0.86
Central- Avg = 626
Central- Count = 9
Corner+ Avg = 25
Corner+ Count = 32
Corner- Avg = 711
Corner- Count = 32
Noise Avg = 1.90
Noise Max = 2.2
Noise Min = 1.7
Noise Stdev = 0.09
RawQ = 1.87
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: lung

source_name: adenocarcinoma-poor or moderately differentiated

value: adenocarcinoma

value: male


title: SN12C hg133b21

description:
Background Avg = 45.38
Background Max = 47.1
Background Min = 43.3
Background Stdev = 0.68
Central- Avg = 1426
Central- Count = 9
Corner+ Avg = 37
Corner+ Count = 32
Corner- Avg = 1676
Corner- Count = 32
Noise Avg = 1.76
Noise Max = 2.0
Noise Min = 1.4
Noise Stdev = 0.08
RawQ = 1.93
Columns = 712
Number of Cells = 506944
Rows = 712
OrganismPart: kidney

value: renal cell carcinoma-poorly differentiated


title: Diseased 4

source_name: motor cortex, diseased 4

value: Diseased 4; Sample Type:tissue; Order Code:BTB3580 [Brain and Tissue Bank for Developmental Disorders (Miami, FL, USA)]; Chief Disease:ALS; Cause of Death:respiratory failure; Age [years / days]:58 / 83; Gender:Male; Race:Caucasian; PMI [h]:22.


title: Diseased 7

source_name: motor cortex, diseased 7

value: Diseased 7; Sample Type:tissue; Order Code:BTB3603 [Brain and Tissue Bank for Developmental Disorders (Miami, FL, USA)]; Chief Disease:ALS; Cause of Death:n/a; Age [years / days]:67 / 325; Gender:Female; Race:Caucasian; PMI [h]:17.


title: Diseased 9

source_name: motor cortex, diseased 9

value: Diseased 9; Sample Type:tissue; Order Code:BTB3689 [Brain and Tissue Bank for Developmental Disorders (Miami, FL, USA)]; Chief Disease:ALS; Cause of Death:n/a; Age [years / days]:61 / 141; Gender:Female; Race:Caucasian; PMI [h]:22.


title: Diseased 2

source_name: motor cortex, diseased 2


title: Diseased 3

source_name: motor cortex, diseased 3

value: Diseased 3; Sample Type:tissue; Order Code:BTB3461 [Brain and Tissue Bank for Developmental Disorders (Miami, FL, USA)]; Chief Disease:ALS; Cause of Death:ALS; Age [years / days]:77 / 53; Gender:Male; Race:Caucasian; PMI [h]:7.5.