title: Lung_Gavage_BFUR_1-8

source_name: lung tissue, right lobe, gavage treatment, corn oil vehicle, 13 weeks, 5 days per week, 2,3-benzofuran, 240 mg per kg

treatment_protocol: in vivo Treatment: 2,3-Benzofuran, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 240, Units of Dose or Concentration: mg/kg

value: Excellent


title: Lung_Gavage_BFUR_1-10

status: Public on Feb 14 2007

type: RNA

city: Research Triangle Park

first: Russell

middle: Scott

last: Thomas

state: NC

address: 6 Davis Drive

country: USA

institute: The Hamner Institutes for Health Sciences

description: Sample Type: tissue, Tissue: Lung, Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: affylmGUI, The Walter and Eliza Hall Institute of Medical Research

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: standard Affymetrix protocol

extract_protocol:
Extraction Method: Trizol
Additional Purification Method: Qiagen Rneasy

tag: Array Type

value: Affymetrix Mouse 430_2

tag: Amount to Core

tag: Units of Amount

value: ug

tag: Ratio

tag: RNA Integrity Number

tag: Bioanalyzer Results

value: Good

tag: Sample Preservation

value: RNA later

tag: Strain or Line

tag: NCBI Taxonomy ID

tag: Individual

tag: Developmental State

value: Adult

tag: Sacrifice Method

value: Pentobarbital (5.2 mg/kg) and exsanguination

tag: Sex

value: Female

tag: Age

tag: Units of Age

value: weeks


title: Lung_Feed_NEDD_1-15

source_name: lung tissue, right lobe, feed treatment, 13 weeks, 7 days per week, N-1-naphthyl)ethylenediamine dihydrochloride, 2000 ppm

treatment_protocol: in vivo Treatment: N-(1-naphthyl)ethylenediamine dihydrochloride, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 2000, Units of Dose or Concentration: ppm


title: Lung_Feed_NEDD_1-12


title: Lung_Feed_FCON_1-28

source_name: lung tissue, right lobe, feed treatment, 13 weeks, 7 days per week, rodent chow control

treatment_protocol: in vivo Treatment: Rodent Chow, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 0, Units of Dose or Concentration: ppm


title: Lung_Feed_NAPD_1-2

source_name: lung tissue, right lobe, feed treatment, 13 weeks, 7 days per week, 1,5-naphthalenediamine, 2000 ppm

treatment_protocol: in vivo Treatment: 1,5-Naphthalenediamine, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 2000, Units of Dose or Concentration: ppm


title: Lung_Feed_NEDD_1-14


title: Lung_Feed_FCON_1-29


title: Lung_Gavage_BFUR_1-6


title: Lung_Feed_PCNB_1-16

source_name: lung tissue, right lobe, feed treatment, 13 weeks, 7 days per week, pentachloronitrobenzene, 8187 ppm

treatment_protocol: in vivo Treatment: Pentachloronitrobenzene, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 8187, Units of Dose or Concentration: ppm


title: Lung_Feed_NAPD_1-4


title: Lung_Feed_FCON_2-42

value: ul

tag: Dilution


title: Lung_Feed_FCON_1-27


title: Lung_Gavage_CCON_1-25

source_name: lung tissue, right lobe, gavage treatment, 13 weeks, 5 days per week, corn oil vehicle control

treatment_protocol: in vivo Treatment: Corn Oil, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 0, Units of Dose or Concentration: mg/kg


title: 5_hypothalamus_12hrs_sleep_deprivation_#106

status: Public on Feb 11 2007

city: Philadelphia

first: Miroslaw

last: Mackiewicz

state: PA

address: 2124 TRL 125S 31st Street

department: Medicine

institute: University of Pennsylvania

hyb_protocol: Hybridization and post-hybridization procedures were performed as described by the Affymetrix GeneChip Expression Analysis Technical Manual (http://www.affymetrix.com), and were conducted at the University of Pennsylvania Microarray Core Facility. The cRNA products were fragmented to 200 nucleotides or less, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

data_processing: Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau = 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call. A weighted mean of probe fluorescence (corrected for nonspecific signal by subtracting the mismatch probe value) was calculated using the One-step Tukey's Biweight Estimate. This Signal value, a relative measure of the expression level, was computed for each assayed gene. Global scaling was applied to allow comparison of gene Signals across multiple microarrays: after exclusion of the highest and lowest 2%, the average total chip Signal was calculated and used to determine what scaling factor was required to adjust the chip average to an arbitrary target of 150. All Signal values from one microarray were then multiplied by the appropriate scaling factor.

label: biotin/streptavidin

source_name: hypothalamus; 12 hrs of total sleep deprivation; sacrificed at 7 PM

label_protocol: Target preparation were performed as described by the Affymetrix GeneChip Expression Analysis Technical Manual (http://www.affymetrix.com), and were conducted at the University of Pennsylvania Microarray Core Facility. Briefly, 5 ug of total RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.

growth_protocol: Experiments were performed on male mice (C57/BL6/J), 10 weeks of age ±1 week. Animals were housed in a light/dark cycle of 12 hrs, in a pathogen free, temperature- and humidity-controlled room (22ºC and 45-55%, respectively) with water available ad libitum. Food was accessible for 12 hrs only during the active period. Animals were subjected to 14 days of acclimatization during which a nighttime feeding pattern was established. This was done to avoid differential food intake between mice that were subsequently sleep deprived during the lights on period and those allowed to sleep.

extract_protocol: Mice were sacrificed by cervical dislocation. Brain sectioning was performed according to the mouse brain atlas of Franklin and Paxinos, and broadly defined regions and zones of the hypothalamus were sampled. RNA was isolated with Trizol (Invitrogen) and further purified using RNeasy columns (Qiagen) as per the manufacturer’s instructions.

treatment_protocol: Mice were sacrificed at 7 PM after 12 hrs of total sleep deprivation. Deprivation was initiated at lights on (7 AM), and performed through gentle handling.

tag: Strain

tag: Gender

value: male

value: 10 weeks of age ±1 week

tag: Tissue

value: hypothalamus


title: 4_hypothalamus_12hrs_sleep_deprivation_#105


title: 3_hypothalamus_12hrs_sleep_deprivation_#104


title: 2_hypothalamus_12hrs_sleep_#99

source_name: hypothalamus; 12 hrs of undisturbed sleep; sacrificed at 7 PM

treatment_protocol: Mice were sacrificed at 7 PM after 12 hrs of undisturbed sleep.


title: 2_hypothalamus_12hrs_sleep_deprivation_#103


title: Lung_Gavage_CCON_1-22

tag: Array Type

tag: Amount to Core

tag: Units of Amount


title: 1_hypothalamus_12hrs_sleep_deprivation_#88


title: 1_hypothalamus_9hrs_sleep_deprivation_#81

source_name: hypothalamus; 9 hrs of total sleep deprivation; sacrificed at 4 PM

treatment_protocol: Mice were sacrificed at 4 PM after 9 hrs of total sleep deprivation. Deprivation was initiated at lights on (7 AM), and performed through gentle handling.


title: 1_hypothalamus_12hrs_sleep_#18


title: 2_hypothalamus_9hrs_sleep_deprivation_#82


title: Lung_Feed_NAPD_1-5

tag: Ratio

tag: Bioanalyzer Results


title: 5_hypothalamus_12hrs_sleep_#114


title: 5_hypothalamus_9hrs_sleep_deprivation_#101


title: 5_hypothalamus_9hrs_sleep_#109

source_name: hypothalamus; 9 hrs of undisturbed sleep; sacrificed at 4 PM

treatment_protocol: Mice were sacrificed at 4 PM after 9 hrs of undisturbed sleep.


title: Lung_Gavage_CCON_1-24

tag: RNA Integrity Number

tag: Sample Preservation

tag: Strain or Line


title: 1_hypothalamus_6hrs_sleep_deprivation_#125

source_name: hypothalamus; 6 hrs of total sleep deprivation; sacrificed at 1 PM

treatment_protocol: Mice were sacrificed at 1 PM after 6 hrs of total sleep deprivation. Deprivation was initiated at lights on (7 AM), and performed through gentle handling.


title: 3_hypothalamus_12hrs_sleep_#111


title: 5_hypothalamus_6hrs_sleep_deprivation_#149


title: 2_hypothalamus_6hrs_sleep_deprivation_#126


title: 4_hypothalamus_9hrs_sleep_deprivation_#100


title: 4_hypothalamus_12hrs_sleep_#113


title: 2_hypothalamus_9hrs_sleep_#92


title: 3_hypothalamus_9hrs_sleep_#107


title: 4_hypothalamus_6hrs_sleep_deprivation_#128


title: 3_hypothalamus_9hrs_sleep_deprivation_#83


title: 1_hypothalamus_9hrs_sleep_#12


title: 5_hypothalamus_6hrs_sleep_#157

source_name: hypothalamus; 6 hrs of undisturbed sleep; sacrificed at 1 PM

treatment_protocol: Mice were sacrificed at 1 PM after 6 hrs of undisturbed sleep.


title: 4_hypothalamus_9hrs_sleep_#108


title: 3_hypothalamus_6hrs_sleep_deprivation_#127


title: 4_hypothalamus_6hrs_sleep_#142


title: 2_hypothalamus_6hrs_sleep_#140


title: 4_hypothalamus_3hrs_sleep_deprivation_#145

source_name: hypothalamus; 3hrs of total sleep deprivation; sacrificed at 10 AM

treatment_protocol: Mice were sacrificed at 10 AM after 3 hrs of total sleep deprivation. Deprivation was initiated at lights on (7 AM), and performed through gentle handling.


title: 3_hypothalamus_6hrs_sleep_#141


title: 2_hypothalamus_3hrs_sleep_#136

source_name: hypothalamus; 3 hrs of undisturbed sleep; sacrificed at 10 AM

treatment_protocol: Mice were sacrificed at 10 AM after 3 hrs of undisturbed sleep.


title: 2_hypothalamus_3hrs_sleep_deprivation_#121


title: 5_hypothalamus_3hrs_sleep_#154


title: 3_hypothalamus_3hrs_sleep_#151


title: 5_hypothalamus_time_0_#131

source_name: hypothalamus; sacrificed at lights on  at 7 AM; this is “time 0”

treatment_protocol: Mice were sacrificed at lights on (7AM).


title: 1_hypothalamus_6hrs_sleep_#139


title: 3_hypothalamus_time_0_#119


title: 1_hypothalamus_3hrs_sleep_deprivation_#120


title: 1_hypothalamus_3hrs_sleep_#135


title: 3_hypothalamus_3hrs_sleep_deprivation_#124


title: 4_hypothalamus_3hrs_sleep_#152


title: 4_cerebral_cortex_12hrs_sleep_deprivation_#26

source_name: cerebral cortex; 12 hrs of total sleep deprivation; sacrificed at 7 PM

extract_protocol: Mice were sacrificed by cervical dislocation. Brain sectioning was performed according to the mouse brain atlas of Franklin and Paxinos. The primary and secondary motor areas (M1 and M2) of the cerebral cortex were sampled. RNA was isolated with Trizol (Invitrogen) and further purified using RNeasy columns (Qiagen) as per the manufacturer’s instructions.

value: cerebral cortex


title: 4_hypothalamus_time_0_#129


title: 1_hypothalamus_time_0_#116


title: 2_hypothalamus_time_0_#118


title: 5_cerebral_cortex_12hrs_sleep_#35

source_name: cerebral cortex; 12 hrs of undisturbed sleep; sacrificed at 7 PM


title: 5_cerebral_cortex_12hrs_sleep_deprivation_#27


title: 5_hypothalamus_3hrs_sleep_deprivation_#146


title: 1_cerebral_cortex_12hrs_sleep_deprivation_#9


title: 4_cerebral_cortex_12hrs_sleep_#34


title: 1_cerebral_cortex_9hrs_sleep_deprivation_#2

source_name: cerebral cortex; 9 hrs of total sleep deprivation; sacrificed at 4 PM


title: 1_cerebral_cortex_9hrs_sleep_#13

source_name: cerebral cortex; 9 hrs of undisturbed sleep; sacrificed at 4 PM


title: 4_cerebral_cortex_9hrs_sleep_deprivation_#21


title: 5_cerebral_cortex_9hrs_sleep_deprivation_#22


title: 5_cerebral_cortex_9hrs_sleep_#30


title: 3_cerebral_cortex_12hrs_sleep_deprivation_#24


title: 1_cerebral_cortex_6hrs_sleep_deprivation_#46

source_name: cerebral cortex; 6 hrs of total sleep deprivation; sacrificed at 1 PM


title: 5_cerebral_cortex_6hrs_sleep_deprivation_#70


title: 2_cerebral_cortex_12hrs_sleep_#20


title: 3_cerebral_cortex_12hrs_sleep_#32


title: 2_cerebral_cortex_9hrs_sleep_#14


title: 2_cerebral_cortex_9hrs_sleep_deprivation_#3


title: 3_cerebral_cortex_9hrs_sleep_#15


title: 2_cerebral_cortex_6hrs_sleep_deprivation_#47


title: 3_cerebral_cortex_6hrs_sleep_deprivation_#48


title: 1_cerebral_cortex_6hrs_sleep_#60

source_name: cerebral cortex; 6 hrs of undisturbed sleep; sacrificed at 1 PM


title: 2_cerebral_cortex_6hrs_sleep_#61


title: 1_cerebral_cortex_12hrs_sleep_#16


title: 3_cerebral_cortex_6hrs_sleep_#62


title: 3_cerebral_cortex_9hrs_sleep_deprivation_#4


title: 2_cerebral_cortex_12hrs_sleep_deprivation_#10


title: 4_cerebral_cortex_9hrs_sleep_#29


title: 4_cerebral_cortex_6hrs_sleep_deprivation_#49


title: 4_cerebral_cortex_6hrs_sleep_#63


title: 5_cerebral_cortex_6hrs_sleep_#64


title: 5_cerebral_cortex_3hrs_sleep_deprivation_#67

source_name: cerebral cortex; 3hrs of total sleep deprivation; sacrificed at 10 AM


title: 4_cerebral_cortex_3hrs_sleep_deprivation_#66


title: 1_cerebral_cortex_3hrs_sleep_#56

source_name: cerebral cortex; 3hrs of undisturbed sleep; sacrificed at 10 AM


title: 4_cerebral_cortex_3hrs_sleep_#72


title: 2_cerebral_cortex_3hrs_sleep_deprivation_#42


title: 3_cerebral_cortex_3hrs_sleep_#58


title: 3_cerebral_cortex_time_0_#40

source_name: cerebral cortex; sacrificed at lights on  at 7 AM; this is “time 0”


title: 1_cerebral_cortex_3hrs_sleep_deprivation_#41


title: 3_cerebral_cortex_3hrs_sleep_deprivation_#45


title: H14.s3 hsr negative rep 1

status: Public on Feb 10 2007

city: Sheffield

first: Duncan

last: Baker

address: Western Bank

department: Department of Biomedical Science

country: United Kingdom

institute: University of Sheffield

description: Gene expression data from human embryonic stem cell line H14.s3 with normal male karyotype.

hyb_protocol: 15µg of cRNA molecules were heat fragmented and applied to the Human U133 plus 2 GeneChips in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45oC for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions.

scan_protocol: The GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL and .CHP files

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Homo sapiens

source_name: Human embryonic stem cell line H14 (WiCell Research Institute) with normal male karyotype.

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

growth_protocol: Cells had been cultured under standard conditions (37oC in media) prior to RNA extraction.

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

tag: Male embryonic stem cell line H14.s3, passage 3, karyotype

tag: Originally human embryonic stem cell line H14 (WiCell Research Institute), H14.s3 maintained at Centre for Stem Cell Biology, University of Sheffield


title: 2_cerebral_cortex_time_0_#39


title: 4_cerebral_cortex_time_0_#50


title: 5_cerebral_cortex_time_0_#52


title: 5_cerebral_cortex_3hrs_sleep_#73


title: developmental sample at T135, rep2

status: Public on Feb 09 2007

city: Boston

first: Hasan

middle: Huseyin

last: Otu

state: MA

address: 4 Blackfan Circle Rm. 238

institute: Harvard Medical School

description: Gene expression data from 10-week-old normal female liver sample.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on Mouse Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with dChip using smoothing spline invariant set method with the model based expression algorithm following the perfect match (PM)-mismatch (MM) difference model. In the dChip analysis, array outliers are not treated as missing expression values and no truncation on signal values is applied.

source_name: Liver sample from mouse embryo liver at 13.5 days post conception (dpc)

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

growth_protocol: All experiments used CD-1 mice obtained from Charles River Laboratories (Wilmington, MA) or our own breeding colony. Animals were maintained in a pathogenfree facility administered by Harvard Medical School in accordance with the institutional guidelines of Harvard Medical School and Beth Israel Deaconess Medical Center. A maximum of five minutes was allowed to elapse between sacrifice and liver harvest to prevent RNA degradation and transcriptional changes.

treatment_protocol: Pregnant CD-1 females were sacrificed with carbon dioxide asphyxiation followed by cervical dislocation. The abdomen was opened and the uterus removed. After removal of the uterine musculature, embryos were removed from the yolk sacs and livers microdissected, taking care to remove all extraneous tissue including the retrohepatic vena cava.

tag: Genotype

value: CD-1 mouse embryo


title: H14 BJI hsr positive rep 2

description: Gene expression data from human embryonic stem cell line H14 BJI with abnormal karyotype, including a homogenous staining region (gene amplification).

source_name: Human embryonic stem cell line H14 (WiCell Research Institute) with abnormal karyotype

treatment_protocol: Cells had been cultured under standard conditions (37oC in media) prior to RNA extraction.

tag: Male embryonic stem cell line, passage 25, karyotype

tag: Originally human embryonic stem cell line H14 (WiCell Research Institute), H14 BJI maintained at Centre for Stem Cell Biology, University of Sheffield


title: 1_cerebral_cortex_time_0_#37

tag: Age


title: 2_cerebral_cortex_3hrs_sleep_#57

tag: Strain


title: H14 BJI hsr positive rep 1

tag: Male embryonic stem cell line, passage 29, karyotype


title: H14.s3 hsr negative rep 2

tag: Male embryonic stem cell line H14.s3, passage 6, karyotype


title: developmental sample at T115, rep1

source_name: Liver sample from mouse embryo liver at 11.5 days post conception (dpc)


title: developmental sample at T105, rep2

source_name: Liver sample from mouse embryo liver at 10.5 days post conception (dpc)


title: developmental sample at T145, rep1

source_name: Liver sample from mouse embryo liver at 14.5 days post conception (dpc)


title: developmental sample at T165, rep2

source_name: Liver sample from mouse embryo liver at 16.5 days post conception (dpc)


title: developmental sample at T115, rep2


title: developmental sample at T125, rep1

source_name: Liver sample from mouse embryo liver at 12.5 days post conception (dpc)


title: developmental sample at T125, rep2


title: developmental sample at T165, rep1


title: developmental sample at T145, rep2


title: developmental sample at T135, rep1


title: regeneration sample at T72, rep2

source_name: 10-week-old normal female liver sample at 72 hours after 2/3 hepatectomy

growth_protocol: All experiments used CD-1 mice obtained from Charles River Laboratories (Wilmington, MA) or our own breeding colony. Animals were maintained in a pathogenfree facility administered by Harvard Medical School in accordance with the institutional guidelines of Harvard Medical School and Beth Israel Deaconess Medical Center.

treatment_protocol: After anesthesia with 100 mg/kg ketamine and 10 mg/kg Xylazine, the abdomen was prepped with alcohol and betadyne. Aftermidline laparotomy, the tip of the xiphoid was resected, and the liver exteriorized. A silk tie was placed around the three anterior lobes of the liver, including the gallbladder, and the 2/3 hepatectomy with cholecystectomy was completed. The liver was returned to the abdominal cavity and the abdomen closed in two layers. Postoperative analgesia consisted of Buprenorphine 0.05-0.1 mg/kg twice daily for 48 hours or until sacrifice. At harvest,mice were sacrificed with carbon dioxide asphyxiation followed by cervical dislocation.

value: Female CD-1 mouse

value: 10 week


title: regeneration sample at T30, rep2

source_name: 10-week-old normal female liver sample at 30 hours after 2/3 hepatectomy


title: regeneration sample at T30, rep1


title: regeneration sample at T24, rep1

source_name: 10-week-old normal female liver sample at 24 hours after 2/3 hepatectomy


title: developmental sample at T105, rep1


title: regeneration sample at T2, rep2

source_name: 10-week-old normal female liver sample at 2 hours after 2/3 hepatectomy


title: regeneration sample at T2, rep1


title: regeneration sample at T48, rep1

source_name: 10-week-old normal female liver sample at 48 hours after 2/3 hepatectomy


title: regeneration sample at T12, rep1

source_name: 10-week-old normal female liver sample at 12 hours after 2/3 hepatectomy


title: regeneration sample at T48, rep2


title: regeneration sample at T18, rep1

source_name: 10-week-old normal female liver sample at 18 hours after 2/3 hepatectomy


title: regeneration sample at T18, rep2


title: regeneration sample at T24, rep2


title: regeneration sample at T6, rep1

source_name: 10-week-old normal female liver sample at 6 hours after 2/3 hepatectomy


title: regeneration sample at T1, rep2

source_name: 10-week-old normal female liver sample at 1 hour after 2/3 hepatectomy


title: regeneration sample at T6, rep2


title: baseline sample at T0, rep1

source_name: 10-week-old normal female liver sample


title: regeneration sample at T12, rep2


title: Dendritic cells generated from blood of donor 1 + A. fumigatus germ tubes

status: Public on Feb 08 2007

city: Würzburg

first: Juergen

last: Loeffler

address: Josef-Schneider-Str. 2

department: Medizinische Klinik & Poliklinik II

country: Germany

institute: Universitätsklinikum Würzburg

description: no additional information

hyb_protocol: Labeled RNA was fragmented and incubated for 16 h at 45°C with a HG-U133 Plus 2.0 human genome array (Affymetrix). The gene chips were automatically washed and stained with streptavidin-phycoerythrin on a fluidics station.

scan_protocol: The probe arrays were scanned by using a GeneChip Scanner 3000 (Affymetrix).

data_processing: For evaluation and analysis of array data, software packages from the Bioconductor project (www.bioconductor.org; Gentleman et al., 2005) were run under R (www.r-project.org). Data were normalized using the function expresso from the affy-package, using variance stabilization normalization (VSN; Huber et al., 2002) and perfect match values only.

label: Biotin

source_name: Immature dendritic cells cultivated together with Aspergillus fumigatus germ tubes for 6h

label_protocol: cRNA was prepared and biotin-labeled by in vitro transcription from 2 µg of total RNA according to the manufacturers protocol without modification (One-Cycle Labeling Kit, Affymetrix, Santa Clara, USA)

growth_protocol: Differentiation of monocytes into immature DCs(iDCs) was achieved by cultivating cells in RPMI 1640 medium (Invitrogen, Karlsruhe, Germany) supplemented with 100 mg/ml Refobacin (Merck, Darmstadt, Germany), 10% fetal calf serum (FCS, Sigma-Aldrich, Taufkirchen, Germany), 100 ng/ml recombinant human granulocyte-macrophage colony-stimulating factor (Leukine, Novartis, Basel, Switzerland) and 20 ng/ml interleukin-4 (R&D Systems, Wiesbaden, Germany). Cultures were fed with fresh medium and cytokines every other day. After culturing for 6 days at 37°C and 5% CO2, iDCs were collected, washed with Hanks buffer and 1x 106 cells were resuspended in 1 ml complete medium. If iDCs were stimulated with fungi, 1 x 106 Aspergillus fumigatus germ tubes were added for 6h.

extract_protocol: Total RNA was isolated using RNeasy Mini kit and QiaShredder spin columns (Qiagen, Hilden, Germany) according to the manufacturer‘s protocol. RNA was eluated with 35 µl RNase-free water and quality and concentration was determined with the 2100 Bioanalyzer (Agilent, Waldbronn, Germany).

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were separated from 50 ml Buffy Coat blood of healthy donors (DRK-Blutspendedienst, Frankfurt, Germany) by Ficoll-Hypaque density gradient centrifugation (Biochrom AG, Berlin, Germany). Human monocytes were isolated from PBMCs by magnetic-associated cell sorting (MACS) using paramagnetic microbeads conjugated to monoclonal anti-human CD14 antibodies (Miltenyi, Bergisch Gladbach, Germany).

tag: Buffy Coat blood of healthy donors


title: MSREF

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

institute: IGMM MRC Human Genetics Unit

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7395

hyb_protocol: Affymetrix standard protocol Amount labeled  target hybridization to array: 10 ug

scan_protocol: Affymetrix standard protocol

data_processing: Analysis method: Affymetrix GCOS and Gene Spring and Avadis programs GCOS Tgt value: 1500

source_name: postnatal day 1/whole mouse

extract_protocol: Qiagen: RNeasy

treatment_protocol:
pool size:
Pooled sample: yes
Dissection Method: none; whole animals used.
This sample represents the universal standard for cross comparison of microarray data.

tag: gene reported

tag: strain

value: FVB/N

tag: Sex

value: both

tag: developmental stage

value: postnatal day 1

tag: theiler stage

tag: somite count:

tag: developmental landmark:


title: Dendritic cells generated from blood of donor 2 + A. fumigatus germ tubes

description: no additional information


title: baseline sample at T0, rep2


title: Dendritic cells generated from blood of donor 2

description: no additional information

source_name: Immature dendritic cells cultivated in medium for 6h


title: regeneration sample at T1, rep1


title: 51U

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7394

source_name: ureter

treatment_protocol:
pool size:
Pooled sample: no
Dissection Method: whole ureters dissected away from kidney and bladder.
Ureters were dissected away from the kidney & bladder and snap frozen in liquid nitrogen. Samples were briefly stored at -80 °C until total RNA was isolated.

value: SMGA/EGFP transgenic /  PMID:14713859

tag: sex


title: 50U

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7393


title: Dendritic cells generated from blood of donor 1

description: no additional information


title: regeneration sample at T72, rep1


title: A549 Xenograft PCI 5003 C

status: Public on Feb 07 2007

city: Los Angeles

first: Joseph

middle: Gerard

last: Hacia

state: CA

address: 2250 Alcazar Street, IGM 261

department: Biochemistry and Molecular Biology

institute: University of Southern California

description: 1.25 million A549 cells were injected subcutaneously/intramuscularly into the right hind flank of 6 week old CD-1 nude mice that had been irradiated with 4 Gy of total body irradiation from a 137Cs radiation source one day prior to tumor implantation. When the average size of tumors reached approximately 100 mm3, mice were randomized by tumor size to treatment groups, typically containing 6-8 mice per group. Tumor and body weight measurements were performed three times per week. Tumor volume was calculated using the equation V (mm3) = a x b2/2, where a is the largest diameter and b is the smallest diameter. No significant body weight loss was observed. To perform gene expression profiling, mice were treated intravenously with one dose (100 μmol/kg) PCI-5003 (4 mice per group) when the average A549 tumor size reached 500 mm3. After four hours, tumors were harvested and snap frozen immediately on dry ice. Tumor tissue was homogenized, and total RNA was isolated and subjected to analysis using Human Genome U133 Plus 2.0 Arrays.

hyb_protocol: We used the Affymetrix Hybridization Oven 640 and GeneChip® Fluidics Station 450 according to the manufacturer's recomended protocols.

scan_protocol: We used the Affymetrix GeneChip® Scanner 3000 according to the manufacturer's recomended protocols.

data_processing: RMA Normalization

label: Affymetrix single-stage biotin

source_name: A549 human lung cancer cell xenograft in CD-1 nude mice

label_protocol: We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recomended protocols.

extract_protocol: We used the RNA Stat-60 reagent (Tel-Test, Inc.) according to the manufacturer's recomended protocols.


title: A549 Xenograft PCI 5003 A

growth_protocol: 1.25 million A549 cells were injected subcutaneously/intramuscularly into the right hind flank of 6 week old CD-1 nude mice that had been irradiated with 4 Gy of total body irradiation from a 137Cs radiation source one day prior to tumor implantation. When the average size of tumors reached approximately 100 mm3, mice were randomized by tumor size to treatment groups, typically containing 6-8 mice per group. Tumor and body weight measurements were performed three times per week. Tumor volume was calculated using the equation V (mm3) = a x b2/2, where a is the largest diameter and b is the smallest diameter. No significant body weight loss was observed. To perform gene expression profiling, mice were treated intravenously with one dose (100 μmol/kg) PCI-5003 (4 mice per group) when the average A549 tumor size reached 500 mm3. After four hours, tumors were harvested and snap frozen immediately on dry ice. Tumor tissue was homogenized, and total RNA was isolated and subjected to analysis using Human Genome U133 Plus 2.0 Arrays.


title: A549 Xenograft PCI 5002 D

description: 1.25 million A549 cells were injected subcutaneously/intramuscularly into the right hind flank of 6 week old CD-1 nude mice that had been irradiated with 4 Gy of total body irradiation from a 137Cs radiation source one day prior to tumor implantation. When the average size of tumors reached approximately 100 mm3, mice were randomized by tumor size to treatment groups, typically containing 6-8 mice per group. Tumor and body weight measurements were performed three times per week. Tumor volume was calculated using the equation V (mm3) = a x b2/2, where a is the largest diameter and b is the smallest diameter. No significant body weight loss was observed. To perform gene expression profiling, mice were treated intravenously with one dose (100 μmol/kg) PCI-5002 (4 mice per group) when the average A549 tumor size reached 500 mm3. After four hours, tumors were harvested and snap frozen immediately on dry ice. Tumor tissue was homogenized, and total RNA was isolated and subjected to analysis using Human Genome U133 Plus 2.0 Arrays.

source_name: A


title: A549 Xenograft PCI 5003 D

treatment_protocol: 1.25 million A549 cells were injected subcutaneously/intramuscularly into the right hind flank of 6 week old CD-1 nude mice that had been irradiated with 4 Gy of total body irradiation from a 137Cs radiation source one day prior to tumor implantation. When the average size of tumors reached approximately 100 mm3, mice were randomized by tumor size to treatment groups, typically containing 6-8 mice per group. Tumor and body weight measurements were performed three times per week. Tumor volume was calculated using the equation V (mm3) = a x b2/2, where a is the largest diameter and b is the smallest diameter. No significant body weight loss was observed. To perform gene expression profiling, mice were treated intravenously with one dose (100 μmol/kg) PCI-5003 (4 mice per group) when the average A549 tumor size reached 500 mm3. After four hours, tumors were harvested and snap frozen immediately on dry ice. Tumor tissue was homogenized, and total RNA was isolated and subjected to analysis using Human Genome U133 Plus 2.0 Arrays.


title: 49U

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7392

hyb_protocol: Affymetrix standard protocol Amount labeled target hybridization to array: 10 ug


title: A549 Xenograft PCI 5003 B

tag: 1.25 million A549 cells were injected subcutaneously/intramuscularly into the right hind flank of 6 week old CD-1 nude mice that had been irradiated with 4 Gy of total body irradiation from a 137Cs radiation source one day prior to tumor implantation. When the average size of tumors reached approximately 100 mm3, mice were randomized by tumor size to treatment groups, typically containing 6-8 mice per group. Tumor and body weight measurements were performed three times per week. Tumor volume was calculated using the equation V (mm3) = a x b2/2, where a is the largest diameter and b is the smallest diameter. No significant body weight loss was observed. To perform gene expression profiling, mice were treated intravenously with one dose (100 μmol/kg) PCI-5003 (4 mice per group) when the average A549 tumor size reached 500 mm3. After four hours, tumors were harvested and snap frozen immediately on dry ice. Tumor tissue was homogenized, and total RNA was isolated and subjected to analysis using Human Genome U133 Plus 2.0 Arrays.


title: A549 Xenograft Control D

description: 1.25 million A549 cells were injected subcutaneously/intramuscularly into the right hind flank of 6 week old CD-1 nude mice that had been irradiated with 4 Gy of total body irradiation from a 137Cs radiation source one day prior to tumor implantation.  When the average size of tumors reached approximately 100 mm3, mice were randomized by tumor size to treatment groups, typically containing 6-8 mice per group.  Tumor and body weight measurements were performed three times per week.  Tumor volume was calculated using the equation V (mm3) = a x b2/2, where a is the largest diameter and b is the smallest diameter.  No significant body weight loss was observed.  To perform gene expression profiling, mice were treated intravenously with 5% mannitol (4 mice per group) when the average A549 tumor size reached 500 mm3.  After four hours, tumors were harvested and snap frozen immediately on dry ice.  Tumor tissue was homogenized, and total RNA was isolated and subjected to analysis using Human Genome U133 Plus 2.0 Arrays.


title: A549 Xenograft Control B

growth_protocol: 1.25 million A549 cells were injected subcutaneously/intramuscularly into the right hind flank of 6 week old CD-1 nude mice that had been irradiated with 4 Gy of total body irradiation from a 137Cs radiation source one day prior to tumor implantation.  When the average size of tumors reached approximately 100 mm3, mice were randomized by tumor size to treatment groups, typically containing 6-8 mice per group.  Tumor and body weight measurements were performed three times per week.  Tumor volume was calculated using the equation V (mm3) = a x b2/2, where a is the largest diameter and b is the smallest diameter.  No significant body weight loss was observed.  To perform gene expression profiling, mice were treated intravenously with 5% mannitol (4 mice per group) when the average A549 tumor size reached 500 mm3.  After four hours, tumors were harvested and snap frozen immediately on dry ice.  Tumor tissue was homogenized, and total RNA was isolated and subjected to analysis using Human Genome U133 Plus 2.0 Arrays.


title: A549 Xenograft PCI 5002 C

growth_protocol: 1.25 million A549 cells were injected subcutaneously/intramuscularly into the right hind flank of 6 week old CD-1 nude mice that had been irradiated with 4 Gy of total body irradiation from a 137Cs radiation source one day prior to tumor implantation. When the average size of tumors reached approximately 100 mm3, mice were randomized by tumor size to treatment groups, typically containing 6-8 mice per group. Tumor and body weight measurements were performed three times per week. Tumor volume was calculated using the equation V (mm3) = a x b2/2, where a is the largest diameter and b is the smallest diameter. No significant body weight loss was observed. To perform gene expression profiling, mice were treated intravenously with one dose (100 μmol/kg) PCI-5002 (4 mice per group) when the average A549 tumor size reached 500 mm3. After four hours, tumors were harvested and snap frozen immediately on dry ice. Tumor tissue was homogenized, and total RNA was isolated and subjected to analysis using Human Genome U133 Plus 2.0 Arrays.


title: PCI 5002 B

description: A549 human lung cancer cells (1 x 10^5 cells per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded 8 days prior to treatment of non-cycling plateau phase cultures with drug.  At 4 hours prior to RNA isolation, PCI-5002 (10 μM final concentration) solution was added to the cultures.  After incubation, cultures were washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.

source_name: non-cycling plateau phase A549 lung cancer cell culture


title: A549 Xenograft PCI 5002 B

treatment_protocol: 1.25 million A549 cells were injected subcutaneously/intramuscularly into the right hind flank of 6 week old CD-1 nude mice that had been irradiated with 4 Gy of total body irradiation from a 137Cs radiation source one day prior to tumor implantation. When the average size of tumors reached approximately 100 mm3, mice were randomized by tumor size to treatment groups, typically containing 6-8 mice per group. Tumor and body weight measurements were performed three times per week. Tumor volume was calculated using the equation V (mm3) = a x b2/2, where a is the largest diameter and b is the smallest diameter. No significant body weight loss was observed. To perform gene expression profiling, mice were treated intravenously with one dose (100 μmol/kg) PCI-5002 (4 mice per group) when the average A549 tumor size reached 500 mm3. After four hours, tumors were harvested and snap frozen immediately on dry ice. Tumor tissue was homogenized, and total RNA was isolated and subjected to analysis using Human Genome U133 Plus 2.0 Arrays.


title: PCI 5002 Zinc A

description: A549 human lung cancer cells (1 x 10^5 cells per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded 8 days prior to treatment of non-cycling plateau phase cultures with drug.  At 4 hours prior to RNA isolation, PCI-5002 (10 μM final concentration) + ZnOAc2 (25 μM final concentration) solution was added to the cultures.  After incubation, cultures were washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.


title: PCI 5002 Zinc C

growth_protocol: A549 human lung cancer cells (1 x 10^5 cells per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded 8 days prior to treatment of non-cycling plateau phase cultures with drug.  At 4 hours prior to RNA isolation, PCI-5002 (10 μM final concentration) + ZnOAc2 (25 μM final concentration) solution was added to the cultures.  After incubation, cultures were washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.


title: Zinc C

description: A549 human lung cancer cells (1 x 10^5 cells per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded 8 days prior to treatment of non-cycling plateau phase cultures with drug.  At 4 hours prior to RNA isolation, ZnOAc2 (25 μM final concentration) solution was added to the cultures.  After incubation, cultures were washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.


title: A549 Xenograft Control A

treatment_protocol: 1.25 million A549 cells were injected subcutaneously/intramuscularly into the right hind flank of 6 week old CD-1 nude mice that had been irradiated with 4 Gy of total body irradiation from a 137Cs radiation source one day prior to tumor implantation.  When the average size of tumors reached approximately 100 mm3, mice were randomized by tumor size to treatment groups, typically containing 6-8 mice per group.  Tumor and body weight measurements were performed three times per week.  Tumor volume was calculated using the equation V (mm3) = a x b2/2, where a is the largest diameter and b is the smallest diameter.  No significant body weight loss was observed.  To perform gene expression profiling, mice were treated intravenously with 5% mannitol (4 mice per group) when the average A549 tumor size reached 500 mm3.  After four hours, tumors were harvested and snap frozen immediately on dry ice.  Tumor tissue was homogenized, and total RNA was isolated and subjected to analysis using Human Genome U133 Plus 2.0 Arrays.


title: Control C

description: A549 human lung cancer cells (1 x 10^5 cells per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded 8 days prior to treatment of non-cycling plateau phase cultures with drug.  At 4 hours prior to RNA isolation, control (5% mannitol) solution was added to the cultures.  After incubation, cultures were washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.


title: PCI 5002 Zinc B

treatment_protocol: A549 human lung cancer cells (1 x 10^5 cells per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded 8 days prior to treatment of non-cycling plateau phase cultures with drug.  At 4 hours prior to RNA isolation, PCI-5002 (10 μM final concentration) + ZnOAc2 (25 μM final concentration) solution was added to the cultures.  After incubation, cultures were washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.


title: Control B

growth_protocol: A549 human lung cancer cells (1 x 10^5 cells per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded 8 days prior to treatment of non-cycling plateau phase cultures with drug.  At 4 hours prior to RNA isolation, control (5% mannitol) solution was added to the cultures.  After incubation, cultures were washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.


title: A549 Xenograft Control C

tag: 1.25 million A549 cells were injected subcutaneously/intramuscularly into the right hind flank of 6 week old CD-1 nude mice that had been irradiated with 4 Gy of total body irradiation from a 137Cs radiation source one day prior to tumor implantation.  When the average size of tumors reached approximately 100 mm3, mice were randomized by tumor size to treatment groups, typically containing 6-8 mice per group.  Tumor and body weight measurements were performed three times per week.  Tumor volume was calculated using the equation V (mm3) = a x b2/2, where a is the largest diameter and b is the smallest diameter.  No significant body weight loss was observed.  To perform gene expression profiling, mice were treated intravenously with 5% mannitol (4 mice per group) when the average A549 tumor size reached 500 mm3.  After four hours, tumors were harvested and snap frozen immediately on dry ice.  Tumor tissue was homogenized, and total RNA was isolated and subjected to analysis using Human Genome U133 Plus 2.0 Arrays.


title: PCI 5002 C

growth_protocol: A549 human lung cancer cells (1 x 10^5 cells per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded 8 days prior to treatment of non-cycling plateau phase cultures with drug.  At 4 hours prior to RNA isolation, PCI-5002 (10 μM final concentration) solution was added to the cultures.  After incubation, cultures were washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.


title: PCI 5002 A

treatment_protocol: A549 human lung cancer cells (1 x 10^5 cells per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded 8 days prior to treatment of non-cycling plateau phase cultures with drug.  At 4 hours prior to RNA isolation, PCI-5002 (10 μM final concentration) solution was added to the cultures.  After incubation, cultures were washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.


title: Zinc B

growth_protocol: A549 human lung cancer cells (1 x 10^5 cells per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded 8 days prior to treatment of non-cycling plateau phase cultures with drug.  At 4 hours prior to RNA isolation, ZnOAc2 (25 μM final concentration) solution was added to the cultures.  After incubation, cultures were washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.


title: Control A

treatment_protocol: A549 human lung cancer cells (1 x 10^5 cells per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded 8 days prior to treatment of non-cycling plateau phase cultures with drug.  At 4 hours prior to RNA isolation, control (5% mannitol) solution was added to the cultures.  After incubation, cultures were washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.


title: A549 Xenograft PCI 5002 A

tag: 1.25 million A549 cells were injected subcutaneously/intramuscularly into the right hind flank of 6 week old CD-1 nude mice that had been irradiated with 4 Gy of total body irradiation from a 137Cs radiation source one day prior to tumor implantation. When the average size of tumors reached approximately 100 mm3, mice were randomized by tumor size to treatment groups, typically containing 6-8 mice per group. Tumor and body weight measurements were performed three times per week. Tumor volume was calculated using the equation V (mm3) = a x b2/2, where a is the largest diameter and b is the smallest diameter. No significant body weight loss was observed. To perform gene expression profiling, mice were treated intravenously with one dose (100 μmol/kg) PCI-5002 (4 mice per group) when the average A549 tumor size reached 500 mm3. After four hours, tumors were harvested and snap frozen immediately on dry ice. Tumor tissue was homogenized, and total RNA was isolated and subjected to analysis using Human Genome U133 Plus 2.0 Arrays.


title: mMAPC-2 C Affy

status: Public on Feb 05 2007

city: Leuven

first: Fernando

last: Ulloa Montoya

address: Herestraat 49 bus 804

country: Belgium

institute: Katholieke Universiteit Leuven

description: mMAPC clone 2, bone marrow 2, biological replicate C, Affymetrix

hyb_protocol: Sample was hybridized to Affymetrix mouse 430 2.0 chips, washed, and scanned at the University of Minnesota Affymetrix Microarray Core Facility as described in the Affymetrix GeneChip Expression Analysis Technical Manual. Protocol EukGE-WS2v5_450 .

scan_protocol: Array was scanned at the University of Minnesota Affymetrix Microarray Core Facility as described in the Affymetrix GeneChip Expression Analysis Technical Manual. Pixel Size 1.56. Filter 570. Scanner ID 50209060. Number of Scans 1. Scanner Type M10

data_processing: CEL files were loaded into GeneData Expressionist Refiner (GeneData, San Francisco, CA) to assess overall quality and obtain condensed single intensity values per probeset using the Microarray Analysis Suite Statistical algorithm (MAS 5.0). The mean of mean intensity values for all chips (192) was used to normalize the mean intensity of each chip. Normalization Target: 192, Tau: 0.015, Alpha1: 0.05, Alpha2: 0.065

label_protocol: 100 ng of total cellular RNA was double amplified and labeled with the Two-Cycle Target Labeling and Control Reagents kit P/N 900494 (Affymetrix Inc., Santa Clara, CA) following the manufacturers' protocol.

growth_protocol: BM was plated in 600w glucose DMEM, 40% MCDB-201 containing 10ng/mL mEGF, hPDGF-BB and 1000 units/ml mouse leukemia inhibitory factor (LIF), 2creened fetal calf serum (FCS), 1x selenium-insulin-transferrin-ethanolamine (SITE), 0.2 mg/mL linoleic acid-bovine serum albumin (LA-BSA), 0.8 mg/mL bovine serum albumin, 1x chemically defined lipid concentrate and 1x 2-mercaptoethanol, 100 units of penicillin, 1,000 units of streptomycin in a humidified, 502 and 6% CO2, 37oC incubator. After 4 weeks, CD45+ and Ter119+ cells were depleted using a MACS separation CS column, and cells replated at 10 cells/well. Expansion was done by trypsinizing (0.05% trypsin) the cells and replating them every two days at a density of 100-200 cells/cm2. Cells at population doubling >80 were used for gene arrays.

extract_protocol: Total RNA  was extracted using the RNAeasy microkit (Qiagen, Valencia, CA), DNAse treatment was performed on column

value: C57BL/6, Sex:Female, Age:Adult, Tissue:Bone marrow (cultured cells), Cell type:Multipotent Adult Progenitor Cells


title: Zinc A

treatment_protocol: A549 human lung cancer cells (1 x 10^5 cells per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded 8 days prior to treatment of non-cycling plateau phase cultures with drug.  At 4 hours prior to RNA isolation, ZnOAc2 (25 μM final concentration) solution was added to the cultures.  After incubation, cultures were washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.


title: mMAPC-2 A Affy

description: mMAPC clone 2, bone marrow 2, biological replicate A, Affymetrix


title: mMAPC-2 B Affy

description: mMAPC clone 2, bone marrow 2, biological replicate B, Affymetrix


title: wnt4_430_mut1

status: Public on Feb 03 2007

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)
Target Amplified protocol: Affymetrix Standard
Rounds of amplification: 1
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7167

hyb_protocol: Amount labeled  target hybridization to array: 15 ug Hybridization/Wash/Stain protocol: EukGE-WS2v4_450

data_processing: Analysis method: Affymetrix GCOS and Rosetta Resolver GCOS Tgt value: 500

source_name: Wnt4 null mutant kidneys

label_protocol: Affymetrix standard protocol

extract_protocol: Disruption in liguid nitrogen, total RNA isolation with Qiagen Rneasy, followed by homogenization with QiaShredder columns (two 30ul elutions).

treatment_protocol:
pool size: 12 Wnt4 null mutant kidneys
Pooled sample: Yes
Dissection Method: Whole organ excision
Experimental Design: Wnt4 is required for renal vesicle (RV) induction.  Therefore, RV and the derivatives (s-shaped body and eventually the mature nephron) are missing in Wnt4 mutants.  At E14.5, these structures are present in wildtype kidneys.  Transcriptional profile comparison between E14.5 wildtype and Wnt4 mutants therefore identify genes expressed in the RV and derivatives. Minimally pooled kidney samples were used as single biological replicates.  CD-1 mice are mated overnight and examined the following morning for the presence of a copulatory plug.  Presence of a plug is taken as day 0.5 post coitum.  Pregnant CD-1 mice are euthanized by standard carbon dioxide asphyxiation.  All fetuses are euthanized by decapitation with scissors.  Fetal kidneys are removed from stage E14.5 embryos and stored in RNAlater at 4°C until RNA isolation (<4 days). Total RNA was isolated from these pools and subjected to a single round of amplification for use on Affymetrix arrays.

value: Wnt4tm1Amc / MGI:1857453

value: unknown

tag: somite count

tag: developmental landmark


title: mMAPC-1 B Affy

description: mMAPC clone 1, bone marrow 1, biological replicate B, Affymetrix

tag: Strain

value: C57BL/6, Sex:Male, Age:Adult, Tissue:Bone marrow (cultured cells), Cell type:Multipotent Adult Progenitor Cells


title: optineurin expression-a01

status: Public on Feb 02 2007

city: Tuebingen

first: Nicole

last: Weisschuh

address: Roentgenweg 11

institute: University Eye Hospital

description: HeLa treated with siRNA specific for optineurin mRNA

hyb_protocol: Standard Affymetrix Protocol

scan_protocol: Standard Affymetrix Protocol

data_processing: GC_RMA normalisation

label: Standard Affymetrix Protocol

label_protocol: Standard Affymetrix Protocol

growth_protocol: DMEM + 10% FCS + 1%PS

extract_protocol: QIAGEN RNEasy

treatment_protocol: Transfection of siRNA duplexes using Oligofectamine according to the manufacturer´s instructions

tag: HeLa cells were transfected with siRNA specific for optineurin mRNA


title: wnt4_430_mut2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)
Target Amplified protocol: Affymetrix Standard
Rounds of amplification: 1
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7168


title: optineurin expression-a02

source_name: HeLa treated with siRNA specific for optineurin mRNA


title: wnt4_430_wt2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)
Target Amplified protocol: Affymetrix Standard
Rounds of amplification: 1
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7166

source_name: wild-type kidney

treatment_protocol:
pool size: 2 wild-type kidneys
Pooled sample: Yes
Dissection Method: Whole organ excision
Experimental Design: Wnt4 is required for renal vesicle (RV) induction.  Therefore, RV and the derivatives (s-shaped body and eventually the mature nephron) are missing in Wnt4 mutants.  At E14.5, these structures are present in wildtype kidneys.  Transcriptional profile comparison between E14.5 wildtype and Wnt4 mutants therefore identify genes expressed in the RV and derivatives. Minimally pooled kidney samples were used as single biological replicates.  CD-1 mice are mated overnight and examined the following morning for the presence of a copulatory plug.  Presence of a plug is taken as day 0.5 post coitum.  Pregnant CD-1 mice are euthanized by standard carbon dioxide asphyxiation.  All fetuses are euthanized by decapitation with scissors.  Fetal kidneys are removed from stage E14.5 embryos and stored in RNAlater at 4°C until RNA isolation (<4 days). Total RNA was isolated from these pools and subjected to a single round of amplification for use on Affymetrix arrays.

value: wild-type


title: optineurin expression-b02

description: HeLa treated with water (mock experiment)


title: mMAPC-1 A Affy

description: mMAPC clone 1, bone marrow 1, biological replicate A, Affymetrix


title: optineurin expression-b01

source_name: HeLa treated with water (mock experiment)


title: optineurin expression-b03


title: Ovary (E16.5-1 dpc)

status: Public on Jan 31 2007

city: Pullman

first: Lizhong

last: Yang

state: WA

address: 531 Fulmer Hall/POB 644660

department: School of Molecular Biosciences

institute: Washington State University

description: All methodology for this dataset is identical to the previously posted dataset generated on the U74 chips.

hyb_protocol: As described by Affymetrix.  Standard protocol.

scan_protocol: Affymetrix GeneChip® Operating Software (GCOS) automates the control of GeneChip® Fluidics Stations and Scanners. In addition, GCOS acquires data, manages sample and experimental information, and performs gene expression data analysis.

data_processing: For each microarray, probe set signal values were initially normalized by scaling to a target intensity of 125.

source_name: Embryonic ovary (E16.5 duplicate 1)

label_protocol: Affymetrix single cycle protocol.

extract_protocol: Trizol

tag: Time course of gene expression in the murine embryonic ovary from the time of the indifferent gonad (11.5dpc) to birth (18.5dpc)


title: optineurin expression-a03


title: wnt4_430_wt1

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)
Target Amplified protocol: Affymetrix Standard
Rounds of amplification: 1
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7165


title: Ovary (E16.5-2 dpc)

source_name: Embryonic ovary (E16.5 duplicate 2)


title: Ovary (E11.5-1 dpc)

source_name: Embryonic Ovary (E11.5 duplicate 1)


title: mMAPC-1 C Affy

description: mMAPC clone 1, isolation 1, biological replicate C, Affymetrix


title: Ovary (E14.5-2 dpc)

source_name: Embryonic ovary (E14.5 duplicate 2)


title: Ovary (E18.5-2 dpc)

source_name: Embryonic ovary (E18.5 duplicate 2)


title: Testis (E18.5-2 dpc)

source_name: Embryonic Testis (E18.5 duplicate 2)

tag: Time course of gene expression in the murine embryonic testis from the time of the indifferent gonad (11.5dpc) to birth (18.5dpc)


title: Ovary (E12.5-2 dpc)

source_name: Embryonic ovary (E12.5 duplicate 2)


title: Ovary (E18.5-1 dpc)

source_name: Embryonic ovary (E18.5 duplicate 1)


title: Testis (E16.5-2 dpc)

source_name: Embryonic Testis (E16.5 duplicate 2)


title: Ovary (E14.5-1 dpc)

source_name: Embryonic ovary (E14.5 duplicate 1)


title: Testis (E14.5-1 dpc)

source_name: Embryonic Testis (E14.5 duplicate 1)


title: Testis (E18.5-1 dpc)

source_name: Embryonic Testis (E18.5 duplicate 1)


title: Testis (E14.5-2 dpc)

source_name: Embryonic Testis (E14.5 duplicate 2)


title: Testis (E16.5-1 dpc)

source_name: Embryonic Testis (E16.5 duplicate 1)


title: Testis (E12.5-2 dpc)

source_name: Embryonic Testis (E12.5 duplicate 2)


title: stimulated embryonic fibroblasts WT, biological rep1

status: Public on Jan 30 2007

city: Cambridge

first: Benjamin

middle: Robert

last: tenOever

address: 7 Divinity Avenue

department: MCB

institute: Harvard University

description: Gene expression data from unstimulated EF cells.

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Hybridization Oven 640.

scan_protocol: GeneChips were scanned using the GeneChip Array Scanner 7G

data_processing: the data were analyzed with GeneChip Operating Software (GCOS) ver 1.3.

source_name: embryonic fibroblast transcription profile 6 hours post interferon treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA

growth_protocol: Cells were grown in DMEM (GibcoBRL) supplemented with 10% Fetal Bovine Serum

treatment_protocol: Fibroblasts were treated with interferon and RNA was extracted using Trizol solution (GibcoBRL).

tag: Genotype

value: wild type BL/6

tag: Primary cell extract


title: Ovary (E11.5-2 dpc)

source_name: Embryonic ovary (E11.5 duplicate 2)


title: stimulated embryonic fibroblasts KO, biological rep3

value: Ikbke-/- BL/6


title: Testis (E12.5-1 dpc)

source_name: Embryonic Testis (E12.5 duplicate 1)


title: unstimulated embryonic fibroblasts WT, biological rep1

source_name: embryonic fibroblast basal transcription

treatment_protocol: Fibroblasts were left untreated and RNA was extracted using Trizol solution (GibcoBRL).


title: unstimulated embryonic fibroblasts KO, biological rep1

value: ikbke -/- BL/6


title: stimulated embryonic fibroblasts KO, biological rep2


title: Ovary (E12.5-1 dpc)

source_name: Embryonic ovary (E12.5 duplicate 1)


title: Testis (E11.5-2 dpc)

source_name: Embryonic Testis (E11.5 duplicate 2)


title: Testis (E11.5-1 dpc)

source_name: Embryonic Testis (E11.5 duplicate 1)


title: stimulated embryonic fibroblasts WT, biological rep3


title: stimulated embryonic fibroblasts WT, biological rep2


title: 85384_CD4+, (delta)FoxP3(EGFP+) mouse cells

status: Public on Jan 26 2007

first: Marc

middle: Richard John

last: Carlson

address: 695 Charles E. Young Dr. S.

department: Department of Human Genetics

institute: UCLA

description: RMA Normalized data.

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Genechip Scanner and GCOS software.

data_processing: RMA using justRMA from Bioconductor.

source_name: CD4 positive, (delta) FOXP3 (EGFP+) T-Cells

label_protocol: Affymetrix biotin labelling method

extract_protocol: RNEasy

tag: FACS sorted T-Cells.


title: iDC normoxia 8

status: Public on Jan 27 2007

city: Genoa

first: Paolo

last: Fardin

address: Largo G. Gaslini 5

department: Molecular Biology

country: Italy

institute: Istiuto Giannina Gaslini

description:
Human peripheral blood mononuclear cells (PBMC) were isolated from venous blood of voluntary healthy donors. All cultures were maintained in RPMI 1640 medium supplemented with 10% FBS heat inactivated, 50μg/ml gentamycin. Monocytes were purified by negative selection. To generate IDC the monocytes were incubated in six-well culture plates for 4 days under normoxic conditions.
The monocytes were incubated in six-well culture plates for 4 days under normoxic conditions.

hyb_protocol: Fragmented cRNA was used for hybridization to Affymetrix HG-U133 plus 2.0 arrays according to the Affymetrix’s instructions.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Expression values were quantified and array quality control was performed with the statistical algorithms implemented in Affymetrix Microarray Suite 5.0.

source_name: Monocyte derived dendritic cells under normoxic conditions

label_protocol: The RNA was reverse-transcribed into cDNA and biotin labeled according to the Affymetrix’s instructions.

extract_protocol: Total RNA was independently isolated from DCs derived from the Mn of three different donors using RNeasy mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

tag: Monocyte derived from PBMC of healthy donor


title: iDC hypoxia 7

description:
Human peripheral blood mononuclear cells (PBMC) were isolated from venous blood of voluntary healthy donors. All cultures were maintained in RPMI 1640 medium supplemented with 10% FBS heat inactivated, 50μg/ml gentamycin. Monocytes were purified by negative selection. To generate IDC the monocytes were incubated in six-well culture plates for 4 days under hypoxic conditions.
The monocytes were incubated in six-well culture plates for 4 days under hypoxic conditions.

source_name: Monocyte derived dendritic cells under hypoxia conditions


title: 76091_CD4+, FoxP3(EGFP+) mouse cells

description: RMA Normalized data.

source_name: CD4 positive, FOXP3 (EGFP+) T-Cells


title: iDC normoxia 7


title: iDC normoxia 6


title: 82430_CD4+, (delta)FoxP3(EGFP+) mouse cells

description: RMA Normalized data.


title: iDC hypoxia 8


title: 85382_CD4+, FoxP3(EGFP+) mouse cells

description: RMA Normalized data.


title: iDC hypoxia 6


title: 76093_CD4+, (delta)FoxP3(EGFP+) mouse cells

description: RMA Normalized data.


title: 76092_CD4+, (delta)FoxP3(EGFP-) mouse cells

description: RMA Normalized data.

source_name: CD4 positive, (delta) FOXP3 (EGFP-) T-Cells


title: wild-type P9 hair follicle, biological rep2

city: Cincinnati

first: Raphael

last: Kopan

state: Ohio

address: 3333 Burnet Avenue

department: Developmental Biology

institute: Cincinnati Children's Hospital

description: Gene expression data from wild-type hair bulb.

hyb_protocol: refer to Washington University Genechip Core Facility

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: hair follicles from wild-type

extract_protocol: RNeasy mini kit (Qiagen, CA)

tag: hair bulbs only from 9-day-old mice


title: endothelial cell_UFP treatment_rep3(59)

city: RTP

first: Edward

last: Karoly

address: MD 58D

department: HSD

institute: U.S. EPA

description: We profiled gene expression of human pulmonary artery endothelial cells exposed to ultrafine Chapel Hill particles (100ug/ml) or vehicle for 4h.

hyb_protocol: see affymetrix manual

scan_protocol: see affymetrix manual

data_processing: GCOS; raw value no transformation

label: enzo biotin label

source_name: human pulmonary artery endothelial cell

label_protocol: see affymetrix manual

extract_protocol: RNA was extracted with Trizol reagent (GIBCO BRL Life Technologies, Gaithersburg, MD) and purified with Qiagen RNeasy mini columns (Qiagen, Valencia, CA) according to manufacturer’s protocols.  Total RNA was resuspended in RNase free water and assessed with the Agilent 2100 Bioanalyzer and RNA 6000 Nano assay (Agilent Technologies, Palo Alto, CA).  All RNA samples had a 28S/18S ratio ≥ 1.8 and were stored at -80°C prior to shipment on dry ice to Expression Analysis Inc, (Durham, NC).

tag: human pulmonary artery endothelial cell culture.  Treatment

value: 4h Ultrafine particle (100ug/ml)


title: endothelial cell_UFP treatment_rep2(58)

tag: Human pulmonary artery endothelial cell cultrure.  Treatment

value: 4h ultrafine particle (100ug/ml)


title: endothelial cell_control_rep4(56)

description: We profiled gene expression of human pulmonary artery endothelial cells exposed to ultrafine Chapel Hill particles (100ugt/ml) or vehicle for 4h.

tag: Human pulmonary artery endothelial cell culture.  Treatment

value: 4h control


title: endothelial cell_UFP treatment_rep4(60)

hyb_protocol: see affymetrix protocol

scan_protocol: see affymetrix protocol

label_protocol: see affymetrix protocol


title: endothelial cell_control_rep2(54)

tag: human pulmonary artery endothelial cells

tag: treatment


title: 82428_CD4+, FoxP3(EGFP+) mouse cells.txt

description: RMA Normalized data.


title: 76090_CD4+, FoxP3(EGFP-) mouse cells

description: RMA Normalized data.

source_name: CD4 positive, FOXP3 (EGFP-) T-Cells


title: emN1 P9 hair follicle, biological rep2

description: Gene expression data from Notch1-deficient hair bulb.

scan_protocol: refer to Washington University Genechip Core Facility

source_name: hair follicles from embryo-deleted area (absence of functional Notch1)


title: endothelial cell_UFP treatment_rep1(57)

tag: human pulmonary artery endothelial cell.  Treatment

value: Ultrafine particle treatment (100ug/ml).


title: anN1 P9 hair follicle, biological rep1

description: Gene expression data from anN1 hair bulb.

source_name: hair follicles from anagen-deleted area (presence of functional Notch1)

label_protocol: refer to Washington University Genechip Core Facility


title: endothelial cell_control_rep1(53)

source_name: human pulmonary artery endothelial cell control

tag: Human pulmonary artery endothelial cells.


title: endothelial cell_control_rep3(55)


title: anN1 P9 hair follicle, biological rep2


title: wild-type P9 hair follicle, biological rep1


title: YFP+Foxp3+ r1

status: Public on Jan 25 2007

city: Seattle

first: Alexander

last: Rudensky

address: 1959 Pacific St

department: Immunology

institute: University of Washington

description: Sample isolated from wild type Foxp3 CD4+YFP+Ly5.2+ T cells following treatment with HR-MMPCreGFP and six week adoptive transfer.

hyb_protocol: According to established procedure at the Center for Expression Array. Seattle, WA

data_processing: GCRMA v 1.1.3, default settings

source_name: CD4+YFP+Ly5.2+ from Foxp3+

label_protocol: Ambion Message Amp II

extract_protocol: Qiagen RNeasy


title: YFP+Foxp3delta r1

description: Sample isolated from loxP flanked Foxp3 CD4+YFP+Ly5.2+ T cells following treatment with HR-MMPCreGFP and six week adoptive transfer.

scan_protocol: According to established procedure at the Center for Expression Array. Seattle, WA

source_name: CD4+YFP+Ly5.2+ from Foxp3delta


title: emN1 P9 hair follicle, biological rep1


title: YFP+Foxp3+ r2

tag: Sample isolated from wild type Foxp3 CD4+YFP+Ly5.2+ T cells following treatment with HR-MMPCreGFP and six week adoptive transfer.


title: Wild type myeloid progenitors (7)

first: Christopher

last: Sears

address: 300 Longwood Avenue

institute: HMS/CHB

description: Study the effect of the deficiency of FoxO1, FoxO3, and FoxO4 in murine bone marrow hematopoietic stem cells and myeloid progenitors on expression of genes involved in reactive oxygen species (ROS) metabolism.

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: Tothova Z, Kollipara R, Huntly BJ, Lee BH, Castrillon DH, Cullen DE, McDowell EP, Lazo-Kallanian S, Williams IR, Sears C, Armstrong SA, Passegue E, DePinho RA, Gilliland DG. (2006) FoxO are critical mediators of hematopoietic stem cell resistance to physiologic oxidative stress. Cell 2007

source_name: wt myeloid progenitors

label_protocol: NuGen Ovation Biotin labeling system

extract_protocol: Bone marrow hematopoietic stem cells or myeloid progenitors from pooled Mx-Cre-; FoxO1/O3/O4LoxP/LoxP or Mx-Cre+; FoxO1/O3/O4LoxP/LoxP mice were sorted and RNA was prepared using the Qiagen RNeasy micro kit. Amplification and biotin labeling of fragmented amplified cDNA was carried out using the NuGen Ovation Biotin labeling system (NuGEN Technologies, Inc) in triplicate. Labeled probes were hybridized to Affymetrix Mouse Genome 430 2.0 (MOE430_2) GeneChip arrays.

tag: Prospectively purified bone marrow hematopoietic stem cells (LSK, defined as Lineage- Sca-1+ c-Kit+) and myeloid progenitors (defined as Lineage- Sca-1- c-Kit+) from Mx-Cre-; FoxO1/O3/O4LoxP/LoxP and Mx-Cre+; FoxO1/O3/O4LoxP/LoxP mice 4 weeks after induction of excision with polyinosine-polycyticylic acid (pIpC, 300ug)


title: FoxO deficient myeloid progenitors (11)

source_name: FoxO deficient myeloid progenitors


title: Wild type LSK (2)

source_name: wt LSK


title: Wild type LSK (3)


title: FoxO deficient LSK (6)

source_name: FoxO deficient LSK


title: FoxO deficient myeloid progenitors (10)


title: Wild type LSK (1)


title: FoxO deficient LSK (5)


title: YFP+Foxp3delta r2

tag: Sample isolated from loxP flanked Foxp3 CD4+YFP+Ly5.2+ T cells following treatment with HR-MMPCreGFP and six week adoptive transfer.


title: Sakakibara_1-9_DMSO-treatment-wild_Rep3_ATH1

status: Public on Jan 22 2007

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

description:
sterilisation: Sterilized by treatment with bleach.
Growth protocol: Arabidopsis seedlings were grown vertically on MS agar plates for 2 weeks.
Location: Growth chamber
growth substrate type: Agar
medium: Murashige and Skoog basal salt mixture

hyb_protocol: standard NASC hybridization protocol

scan_protocol: standard NASC scanning protocol

data_processing: The data were analysed using Affymetrix Microarray Suite 5.0 (MAS5)

organism: Arabidopsis thaliana

label_protocol: standard NASC labeling protocol

extract_protocol: standard NASC extraction protocol

treatment_protocol: The Arabidopsis were treated with 0.02% DMSO by spraying for 1h.

tag: Stock Code

tag: Tissue

value: aerial parts


title: FoxO deficient myeloid progenitors (12)


title: Wild type myeloid progenitors (8)


title: Sakakibara_1-7_DMSO-treatment-wild_Rep1_ATH1

institute: Nottingham Arabidopsis Stock Centre (NASC)


title: Wild type myeloid progenitors (9)


title: Sakakibara_1-10_DMSO-treatment-mutant_Rep1_ATH1


title: Sakakibara_1-5_TZ-treatment-mutant_Rep2_ATH1

treatment_protocol: The Arabidopsis were treated with 20 µM trans-zeatin by spraying for 1h


title: Sakakibara_1-8_DMSO-treatment-wild_Rep2_ATH1


title: Sakakibara_1-3_TZ-treatment-wild_Rep3_ATH1


title: Sakakibara_1-11_DMSO-treatment-mutant_Rep2_ATH1


title: Sakakibara_1-2_TZ-treatment-wild_Rep2_ATH1


title: stimulated embryonic fibroblasts KO, biological rep1

source_name: embryonic fibroblast transcription profile 6 hours post interferon treatment

tag: Genotype


title: Sakakibara_1-6_TZ-treatment-mutant_Rep3_ATH1


title: Sakakibara_1-4_TZ-treatment-mutant_Rep1_ATH1


title: Sakakibara_1-12_DMSO-treatment-mutant_Rep3_ATH1


title: Truman_1-8_Pst-DC3000(hrpA)-4hpi_Rep3_ATH1

description:
Location: Growth Room
Growth substrate: A 4:1 mixture of Levingtons F2 compost (Fisons, Ipswich, UK) and vermiculite
stratification: 2 days in fridge at 4oCA
Growth protocol: Arabidopsis thaliana genotypes were sown in Levingtons F2 compost (Fisons, Ipswich, UK) and vernalized for 2 days at 4oC. Plants were grown under short day conditions in a controlled environment chamber (12 h light, 100?150 uE at 22oC day, 20oC night) for 5 weeks before use

treatment_protocol: Leaves were inoculated with Pseudomonas syringae pv tomato DC3000::hrpA- mutant. DC3000::hrpA- cultures were grown overnight in 10 ml of Kings B solution (King et al., 1954) supplemented with antibiotics. Plants were inoculated with DC3000::hrpA- containing the empty vector plasmid pVSP61 (Innes et al., 1993) Antibiotics rifampicin(50 lg ml)1) and kanamycin (25 lg ml)1) were used for selection of the bacterium and plasmid, respectively. Overnight cultures were washed once in 10 mM MgCl2 and final cell densities were adjusted to OD600 0.2. Both sides of a leaf were infiltrated on their abaxial surface with a needleless 1ml syringe. At least 5 leaves per plant were inoculated and 16 plants were pooled to make this sample.

tag: Developmental stage

value: whole leaves from the inner rosette (systemic/ uninoculated leaves)


title: Sakakibara_1-1_TZ-treatment-wild_Rep1_ATH1


title: Truman_1-6_Pst-DC3000(avrRpm1)-4hpi_Rep2_ATH1

treatment_protocol: Leaves were inoculated with avirulent Pseudomonas syringae pv tomato DC3000(avrRpm1). DC3000(avrRpm1) cultures were grown overnight in 10 ml of Kings B solution (King et al., 1954) supplemented with antibiotics. Plants were inoculated with DC3000 containing the vector plasmid pVSP61 (Innes et al., 1993) carrying the avirulence gene avrRpm1. Antibiotics rifampicin(50 lg ml)1) and kanamycin (25 lg ml)1) were used for selection of the bacterium and plasmid, respectively. Overnight cultures were washed once in 10 mM MgCl2 and final cell densities were adjusted to OD600 0.2. Both sides of a leaf were infiltrated on their abaxial surface with a needleless 1ml syringe. At least 5 leaves per plant were inoculated and 16 plants were pooled to make this sample.


title: Truman_1-9_Pst-DC3000(avrRpm1)-4hpi_Rep3_ATH1


title: Truman_1-7_Pst-DC3000-4hpi_Rep3_ATH1

treatment_protocol: Leaves were inoculated with virulent Pseudomonas syringae pv tomato DC3000. DC3000 cultures were grown overnight in 10 ml of Kings B solution (King et al., 1954) supplemented with antibiotics. Plants were inoculated with DC3000 containing the empty vector plasmid pVSP61 (Innes et al., 1993) Antibiotics rifampicin(50 lg ml)1) and kanamycin (25 lg ml)1) were used for selection of the bacterium and plasmid, respectively. Overnight cultures were washed once in 10 mM MgCl2 and final cell densities were adjusted to OD600 0.2. Both sides of a leaf were infiltrated on their abaxial surface with a needleless 1ml syringe. At least 5 leaves per plant were inoculated and 16 plants were pooled to make this sample.


title: Truman_1-5_Pst-DC3000(hrpA)-4hpi_Rep2_ATH1


title: Ulker_1-6_WRKY-KO-30_Rep1_ATH1

description:
location: Growth chamber
Atmosphere: Normal
Humidity: 70%
Temperature: 22C day 19C night
Lighting: 14 hours light and 8 hour dark
Medium: Special substrate from Stender Germany containing 70%white turf 20%vermiculite (3-6mm) and 10% sand.  The substrate is autoclaved two times with 2 days interval.
Treatment: Confidor WG70 Bayer Germany  containing 70% imidacloprid (12g/m3 soil)
Nutrients: Osmocote Plus mini containing 16%N 8%P 11%K and 2% micronutrients (100ml/m3 soil)
Water: When necesssary.  Soil was never let to completely dry.

source_name: WRKY T-DNA knockout

value: 35 days old.  Plants just started bolting.

value: Entire rosette excluding the stem and flowers


title: Truman_1-4_Pst-DC3000-4hpi_Rep2_ATH1


title: Truman_1-3_Pst-DC3000(avrRpm1)-4hpi_Rep1_ATH1


title: Ulker_2-6_WRKY-KO-13-Pst-DC3000_Rep1_ATH1

description:
location: Growth chamber
Humidity: 70%
Temperature: 22C day 19C night
Lighting: 10 hours light and 14 hours dark
Medium: Special substrate from Stender Germany containing 70%white turf 20%vermiculite (3-6mm) and 10% sand.  The substrate is autoclaved two times with 2 days interval.
Treatment: Confidor WG70 Bayer Germany  containing 70% imidacloprid (12g/m3 soil)
Nutrients: Osmocote Plus mini containing 16%N 8%P 11%K and 2% micronutrients (100ml/m3 soil)
Water: When necesssary.  Soil was never let to completely dry.

source_name: WRKY53 T-DNA knockout

value: 14 day old plants

value: Entire rosette


title: Ulker_1-7_WRKY-KO-56_Rep1_ATH1


title: Ulker_2-5_WRKY-KO-40-Pst-DC3000_Rep1_ATH1

source_name: WRKY18/40 T-DNA double knockout


title: Truman_1-1_Pst-DC3000-4hpi_Rep1_ATH1


title: Ulker_1-1_WT-Col-0-L_Rep1_ATH1


title: Ulker_1-3_WRKY-KO-07_Rep1_ATH1


title: Ulker_1-4_WRKY-KO-54_Rep1_ATH1


title: Ulker_2-4_WRKY-KO-30-Pst-DC3000_Rep1_ATH1

source_name: WRKY60 T-DNA knockout


title: Ulker_1-2_WRKY-KO-02_Rep1_ATH1


title: Garnier_1-12_C24-TET_Rep3_ATH1

description:
Location: Growth chamber
stratification: Overnight in water at 4C in the dark Transfer to MS plate 72h at 4C in the dark Tranfer to growth chamber
sterilisation: 15 mn 1.7% Sodium Hypochloride 1% Triton X100 Rince at least three times in dds water
Growth protocol: 16h day(10Klux) 21C; 8h night 18C
Growth substrate type: Agar
Growth medium: Murashige and Skoog basal salt mixture

source_name: Tetraploid C24 obtained by Colchicine treatment

value: whole plant


title: Garnier_1-11_C24-TET_Rep2_ATH1


title: Garnier_1-9_C24-TME_Rep3_ATH1

source_name: triploid C24 from 4x per 2x cross


title: Ulker_2-3_WRKY-KO-07-Pst-DC3000_Rep1_ATH1

source_name: WRKY18 T-DNA knockout


title: Ulker_2-1_WT-Col-0-L-MgCl2_Rep1_ATH1


title: Ulker_2-2_WRKY-KO-02-Pst-DC3000_Rep1_ATH1

source_name: WRKY40 T-DNA knockout


title: Garnier_1-10_C24-TET_Rep1_ATH1


title: Truman_1-2_Pst-DC3000(hrpA)-4hpi_Rep1_ATH1


title: Ulker_2-7_WT-Col-0-L-Pst-DC3000_Rep1_ATH1


title: Ulker_1-8_WT_Col-0-S_Rep1_ATH1


title: Garnier_1-5_C24-TFE_Rep2_ATH1


title: Garnier_1-8_C24-TME_Rep2_ATH1


title: Garnier_1-6_C24-TFE_Rep3_ATH1


title: Durrant_1-5_sni1_Rep2_ATH1

description:
Stratification: Cold treated 3 days at 4 degrees
Location: Growth room
Growth substrate: Commercial soil
Average temperature: 22oC

tag: Genetic background

tag: Genetic variation

value: induced mutation by radiation (At4g18460)


title: Garnier_1-7_C24-TME_Rep1_ATH1


title: Durrant_1-6_sni1_Rep3_ATH1


title: Garnier_1-1_C24-DIP_Rep1_ATH1


title: Coates_1-5_Col-0_Rep2_ATH1

description:
location: Growth Room
Temperature: 24oC
Lighting: 16h day/8h night
Medium: 0.5 x Murashige and Skoog 1% agar
Stratification: sterilise seed 15 min parozone  rinse 3x distilled water  2 days at 4oC before germination

tag: developmental stage

value: between 1.0 and 1.02 (7 days)

tag: tissue

value: roots


title: Garnier_1-4_C24-TFE_Rep1_ATH1


title: Durrant_1-4_sni1_Rep1_ATH1


title: Coates_1-11_Col-3_Rep3_ATH1

tag: stock code


title: Coates_1-10_ara1OX_Rep3_ATH1

tag: genetic background


title: Coates_1-4_ara1/2mut_Rep1_ATH1


title: Coates_1-6_ara1OX_Rep2_ATH1


title: Durrant_1-1_wild-type_Rep1_ATH1

value: wild-type


title: Hammond_3-12_Caesium-treated-root_Rep2_ATH1

description:
location: Growth Room
Atmosphere: Normal
Humidity: 80 %
Temperature: 22 °C
Lighting: 16 hour day
Medium: 0.8 % (w/v) agar containing 1 % (w/v) sucrose and a 1/10 MS salt  mix
Stratification: imbibed for 3-5 days at 4 °C

value: all root material


title: Hammond_3-11_Potassium-starved-root_Rep2_ATH1


title: Durrant_1-3_wild-type_Rep3_ATH1


title: Coates_1-3_Col-3_Rep1_ATH1


title: Coates_1-12_ara1/2mut_Rep3_ATH1


title: Coates_1-9_Col-0_Rep3_ATH1


title: Coates_1-2_ara1OX_Rep1_ATH1


title: Durrant_1-2_wild-type_Rep2_ATH1


title: Coates_1-8_ara1/2mut_Rep2_ATH1


title: Coates_1-1_Col-0_Rep1_ATH1


title: Hammond_3-10_Control-root_Rep2_ATH1


title: FoxO deficient LSK (4)


title: Garnier_1-2_C24-DIP_Rep2_ATH1


title: Coates_1-7_Col-3_Rep2_ATH1


title: Hammond_3-14_Potassium-starved-shoot_Rep3_ATH1

value: shoots


title: Hammond_3-18_Caesium-treated-root_Rep3_ATH1


title: Hammond_3-16_Control-root_Rep3_ATH1


title: Hammond_3-8_Potassium-starved-shoot_Rep2_ATH1


title: Hammond_3-17_Potassium-starved-root_Rep3_ATH1


title: Hammond_3-9_Caesium-treated-shoot_Rep2_ATH1


title: Hammond_3-15_Caesium-treated-shoot_Rep3_ATH1


title: Hammond_3-4_Control-root_Rep1_ATH1


title: Hammond_3-2_Potassium-starved-shoot_Rep1_ATH1


title: Hammond_3-5_Potassium-starved-root_Rep1_ATH1


title: Gan_1-6_mutant-nitrate-continuous(ANC)_Rep1_ATH1

description:
Humidity: 55 to 75%
Temperature: 20oC
Lighting: 8h light/16h dark
Medium: hydropony
Nutrients: holgand medium

value: Whole root system

value: knock-out mutant


title: Hammond_3-1_Control-shoot_Rep1_ATH1


title: Gan_1-5_wildtype-nitrate-continuous(WNC)_Rep1_ATH1


title: Hammond_3-6_Caesium-treated-root_Rep1_ATH1


title: Gan_1-1_wildtype-nitrate-minus(WNM)_Rep1_ATH1


title: Gan_1-2_mutant-nitrate-minus(ANM)_Rep1_ATH1


title: Gan_1-3_wildtype-nitrate-minus(WNM)_Rep2_ATH1


title: JPritchard_A-2_CTR_Rep2_ATH1

description:
location: Growth Room
Humidity: 70%
Temperature: 22oC
Lighting: 18 hour days
Medium: compost
Nutrients: osmocote slow release fertiliser mixed in compost
Water: 3 x per week
treatment: none

value: 2 mature rosette leaves


title: JPritchard_A-3_CTR_Rep3_ATH1


title: JPritchard_A-1_CTR_Rep1_ATH1


title: JPritchard_A-5_API_Rep2_ATH1

description:
location: Growth Room
Humidity: 70%
Temperature: 22oC
Lighting: 18 hour days
Medium: compost
Nutrients: osmocote slow release fertiliser mixed in compost
Water: 3 x per week
treatment: 10 aphids caged on 2 rosette leaves for 8 hours


title: JPritchard_A-6_API_Rep3_ATH1


title: MW001_ATH1_A2-Wheel-w05

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 86.40
Background Stdev (float) = 2.54
Background Max (float) = 96.0
Background Min (float) = 82.5
Noise Avg (float) = 4.59
Noise Stdev (float) = 0.24
Noise Max (float) = 5.5
Noise Min (float) = 4.1
RawQ (float) = 3.32
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 505
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: MW001_ATH1_A2-Wheel-w05.DAT

hyb_protocol: EukGE-WS2v4; Protocol Type = Hybridization; Parameter Wash A1 Recovery Mixes = 0 (type integer); Parameter Wash A1 Temperature (C) = 25 (type integer); Parameter Number of Wash A1 Cycles = 10 (type integer); Parameter Mixes per Wash A1 Cycle = 2 (type integer); Parameter Wash B Recovery Mixes = 0 (type integer); Parameter Wash B Temperature (C) = 50 (type integer); Parameter Number of Wash B Cycles = 4 (type integer); Parameter Mixes per Wash B Cycle = 15 (type integer); Parameter Stain Temperature (C) = 25 (type integer); Parameter First Stain Time (seconds) = 600 (type integer); Parameter Wash A2 Recovery Mixes = 0 (type integer); Parameter Wash A2 Temperature (C) = 25 (type integer); Parameter Number of Wash A2 Cycles = 10 (type integer); Parameter Mixes per Wash A2 Cycle = 4 (type integer); Parameter Second Stain Time (seconds) = 600 (type integer); Parameter Third Stain Time (seconds) = 600 (type integer); Parameter Wash A3 Recovery Mixes = 0 (type integer); Parameter Wash A3 Temperature (C) = 30 (type integer); Parameter Number of Wash A3 Cycles = 15 (type integer); Parameter Mixes per Wash A3 Cycle = 4 (type integer); Parameter Holding Temperature (C) = 25 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Fluidics Station, Parameter: Parameter Station Number = 1 (type integer), Parameter: Parameter Position = 2 (type integer); Performers: John,Y,Okyere, , Janet,,Higgins

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 231 (type integer); Parameter Upper left corner y coordinate = 230 (type integer); Parameter Upper right corner x coordinate = 4497 (type integer); Parameter Upper right corner y coordinate = 221 (type integer); Parameter Lower right corner x coordinate = 4507 (type integer); Parameter Lower right corner y coordinate = 4491 (type integer); Parameter Lower left corner x coordinate = 241 (type integer); Parameter Lower left corner y coordinate = 4500 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.537659 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

label_protocol: Preparation of biotin-labeled cRNA; RNA samples were quality controlled using the Agilent 2100 Bioanalyzer. 100 pmol T7-(dT)24 primer (5'-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(dT)24-3')  was hybridized with the Total RNA ( 8 - 12ug) at 70°C for 10 minutes. First strand cDNA was synthesized by reverse transcription using 400 units SuperScript II Reverse Transcriptase in a reaction containing 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2, 10 mM dithiothreitol (DTT) and 0.5 mM dNTPs at 42C for 1 hour.  The reaction was then put on ice for 2 mins, followed by second strand cDNA synthesis.  130ul of the second strand reaction mix was added to the 20ul  first strand synthesis reaction. The second strand reaction mix  contained 40 units E. coli DNA polymerase I, 10 units E. coli DNA ligase, 2 units  E. coli RNase H and 0.2 mM dNTPs in a buffer containing 20 mMTris-HCl (pH 6.9), 90 mM KCl, 4.6 mM MgCl2, 10mM (NH4)SO4 and 0.15 mM ß-NAD+. The reaction was incubated at 16 C for 2 hours.  10 units T4 DNA Polymerase was added and the reaction incubated for a further 5 minutes at 16 C, then the reaction was terminated using EDTA.  The double-stranded cDNA was cleaned up using the cDNA Cleanup Spin Column supplied in the Affymetrix GeneChip Sample Cleanup Module.  The double-stranded cDNA was used as a template for in Vitro transcription of biotin-labeled cRNA using the ENZO BioArray RNA Transcript Labeling Kit supplied by Affymetrix.  The Transcript Labeling kit produces large amounts of hybridizable biotin-labeled RNA targets by in Vitro transcription from bacteriophage T7 RNA polymerase promoters.  The reaction mixture containing Biotin-Labeled ribonucleotides (ATP, GTP, CTP, UTP with Bio-UTP and Bio-CTP), DTT, RNase inhibitor mix and T7 RNA polymerase was incubated at 37 C for 5 hrs, gently mixing every 30 minutes during the incubation. This produced an average of 40ug biotin-labeled cRNA . The biotin-labeled cRNA  was cleaned up using the cRNA Cleanup Spin Column supplied in the Affymetrix GeneChip Sample Cleanup Module.  The quantity and quality of the cRNA was measured using the Agilent 2100 Bioanalyzer. The total amount of cRNA was calculated, the starting quantity of RNA subtracted to give the quantity of adjusted cRNA.  The cRNA was fragmented by metal-induced hydrolysis to break down full-length cRNA to 35-200 base fragments.  15ug of adjusted cRNA was used to prepare 300ul of hybridization cocktail of which 200ul was hybridized with the GeneChip.   ; Protocol Type = labeling; Performers: John,Y,Okyere, Janet,,Higgins

growth_protocol: unknown; Parameter location = Greenhouse; Parameter Atmosphere = Normal; Parameter Humidity = 80%; Parameter Temperature = 20C; Parameter Lighting = 16h photoperiod; Parameter Medium = compost; Parameter Treatment = Intersept; Parameter Nutrients = John Innes compost and perlite; Parameter Water = daily from below; Parameter Stratification = 4 days at 4C; Performer: Mike,,Wheeler

extract_protocol: Wheeler Trizol Protocol; Protocol:  Centrifuged at 12000g for 10 min at 4C, SN transferred to fresh 50ml tube. 3ml chloroform added, vortex 15s. RT for 2 min. Centrifuged at 10000g 15min at 4C. Aq. phase collected and placed in new 50ml tube. RNA precipitated using 0.5 vol isopropanol and 0.5 vol 0.8M Na citate/1.2M NaCl. Mixed and set at Rt for 10 min. Centrifuged at 10,000g for 10 min at 4C. SN discarded, pellet washed with 20ml 75% ethanol. Vortexed 10s. Centrifuged at 10000g, 10 min at 4C. Pellet dried in air for 10 min. 300 microlitres of DEPC-water added + 1 microlitre of RNase Inhibitor. Concentration checked by spec and by gel electrophoresis. Cleaned up using QIAgen RNA minikits. Frozen on dry ice. ; Protocol Type = nucleic_acid_extraction; Performer: Mike,,Wheeler

tag: OrganismPart

value: rosette leaves

tag: Ecotype

tag: NASC:Growth Stage


title: MW001_ATH1_A3-Wheel-w05

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 115.34
Background Stdev (float) = 4.87
Background Max (float) = 126.8
Background Min (float) = 104.4
Noise Avg (float) = 6.02
Noise Stdev (float) = 0.37
Noise Max (float) = 7.5
Noise Min (float) = 5.3
RawQ (float) = 4.28
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 572
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: MW001_ATH1_A3-Wheel-w05.DAT

hyb_protocol: EukGE-WS2v4; Protocol Type = Hybridization; Parameter Wash A1 Recovery Mixes = 0 (type integer); Parameter Wash A1 Temperature (C) = 25 (type integer); Parameter Number of Wash A1 Cycles = 10 (type integer); Parameter Mixes per Wash A1 Cycle = 2 (type integer); Parameter Wash B Recovery Mixes = 0 (type integer); Parameter Wash B Temperature (C) = 50 (type integer); Parameter Number of Wash B Cycles = 4 (type integer); Parameter Mixes per Wash B Cycle = 15 (type integer); Parameter Stain Temperature (C) = 25 (type integer); Parameter First Stain Time (seconds) = 600 (type integer); Parameter Wash A2 Recovery Mixes = 0 (type integer); Parameter Wash A2 Temperature (C) = 25 (type integer); Parameter Number of Wash A2 Cycles = 10 (type integer); Parameter Mixes per Wash A2 Cycle = 4 (type integer); Parameter Second Stain Time (seconds) = 600 (type integer); Parameter Third Stain Time (seconds) = 600 (type integer); Parameter Wash A3 Recovery Mixes = 0 (type integer); Parameter Wash A3 Temperature (C) = 30 (type integer); Parameter Number of Wash A3 Cycles = 15 (type integer); Parameter Mixes per Wash A3 Cycle = 4 (type integer); Parameter Holding Temperature (C) = 25 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Fluidics Station, Parameter: Parameter Station Number = 1 (type integer), Parameter: Parameter Position = 3 (type integer); Performers: John,Y,Okyere, , Janet,,Higgins

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 233 (type integer); Parameter Upper left corner y coordinate = 229 (type integer); Parameter Upper right corner x coordinate = 4500 (type integer); Parameter Upper right corner y coordinate = 205 (type integer); Parameter Lower right corner x coordinate = 4525 (type integer); Parameter Lower right corner y coordinate = 4475 (type integer); Parameter Lower left corner x coordinate = 258 (type integer); Parameter Lower left corner y coordinate = 4499 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.389096 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: MW001_ATH1_A3-Wheel-w14

description:
Rows (integer) = 712
Cols (integer) = 712
Number of Probe Sets (integer) = 22810
Background Avg (float) = 71.31
Background Stdev (float) = 1.72
Background Max (float) = 76.2
Background Min (float) = 67.7
Noise Avg (float) = 4.22
Noise Stdev (float) = 0.31
Noise Max (float) = 5.7
Noise Min (float) = 3.7
RawQ (float) = 2.83
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 832
Number Cells Modified (integer) = 0
Rows (integer) = 712
Cols (integer) = 712
Number of Cells (integer) = 506944
Image: MW001_ATH1_A3-Wheel-w14.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 234 (type integer); Parameter Upper left corner y coordinate = 230 (type integer); Parameter Upper right corner x coordinate = 4501 (type integer); Parameter Upper right corner y coordinate = 199 (type integer); Parameter Lower right corner x coordinate = 4533 (type integer); Parameter Lower right corner y coordinate = 4469 (type integer); Parameter Lower left corner x coordinate = 266 (type integer); Parameter Lower left corner y coordinate = 4499 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.377728 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;