title: MDA-MB-231 GMB CONTROL DIR

status: Public on May 29 2007

type: RNA

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

description: MDA-MB-231  Control

data_processing: GenePix 6.0

molecule: total RNA

organism: Homo sapiens

source_name: MDA-MB-231  Control

source_name: Universal human reference RNA


title: MCF7 GMB 24H INV

description: MCF7 + GMB 24h

source_name: MCF7 + GMB 24h


title: MDA-MB-231 GMB 24H DIR

description: MDA-MB-231 + GMB 24h

source_name: MDA-MB-231 + GMB 24h


title: MDA-MB-231 GMB 24H INV

description: MDA-MB-231 + GMB 24h


title: GB49

status: Public on May 26 2007

city: Cambridge

first: Lawrence

last: Petalidis

country: United Kingdom

institute: University of Cambridge

description: Glioblastoma (Grade IV) frozen primary human tissue obtained following surgical removal of astrocytic brain tumour. All samples used in this study were collected from brain tumour patients operated on at the neurosurgery departments of the Sahlgrenska Hospital, Göthenburg, Sweden or the Karolinska Hospital, Stockholm, Sweden. This study has been approved by the ethical committee of the Karolinska Hospital, Stockholm, Sweden.  Tumour tissue was stored at -135C until use. Tumours were histopathologically diagnosed by Prof. V.P. Collins according to World Health Organization Brain tumour classification criteria. Total RNA was extracted using CsCl ultracentrifugation and asessed spectrophotometrically and using an Agilent Bioanalyzer 2100. Only RNA with no trace of degradation was used. 7 ug of total RNA were used for preparation of labelled target. Sample preparation, first and second strand cDNA synthesis, in vitro transcription amplification for production of biotin labelled cRNA, fragmentation of cRNA, U133A GeneChip hybridization, staining, washing and scanning were performed exactly as described by the manufacturer (Affymeytrix,Santa Clara). Hybridization was performed using 15 ug of labelled fragmented cRNA for 16 hours using a hybridization oven 640 as described by the manufacturer (Affymetrix, Santa Clara). Post-Hybridization washing and staining of the U133A GeneChips was performed on a  fluidics station 400 (Affymetrix, Santa Clara) and scanning was performed on a GeneArray scanner (Affymetrix, Santa Clara).


title: GB130

description: Glioblastoma (Grade IV)  frozen primary human tissue obtained following surgical removal of astrocytic brain tumour. All samples used in this study were collected from brain tumour patients operated on at the neurosurgery departments of the Sahlgrenska Hospital, Göthenburg, Sweden or the Karolinska Hospital, Stockholm, Sweden. This study has been approved by the ethical committee of the Karolinska Hospital, Stockholm, Sweden.  Tumour tissue was stored at -135C until use. Tumours were histopathologically diagnosed by Prof. V.P. Collins according to World Health Organization Brain tumour classification criteria. Total RNA was extracted using CsCl ultracentrifugation and asessed spectrophotometrically and using an Agilent Bioanalyzer 2100. Only RNA with no trace of degradation was used. 7 ug of total RNA were used for preparation of labelled target. Sample preparation, first and second strand cDNA synthesis, in vitro transcription amplification for production of biotin labelled cRNA, fragmentation of cRNA, U133A GeneChip hybridization, staining, washing and scanning were performed exactly as described by the manufacturer (Affymeytrix,Santa Clara). Hybridization was performed using 15 ug of labelled fragmented cRNA for 16 hours using a hybridization oven 640 as described by the manufacturer (Affymetrix, Santa Clara). Post-Hybridization washing and staining of the U133A GeneChips was performed on a  fluidics station 400 (Affymetrix, Santa Clara) and scanning was performed on a GeneArray scanner (Affymetrix, Santa Clara).


title: AA49

description: Anaplastic Astrocytoma (Grade III) .Forzen primary human tissue obtained following surgical removal of astrocytic brain tumour. All samples used in this study were collected from brain tumour patients operated on at the neurosurgery departments of the Sahlgrenska Hospital, Göthenburg, Sweden or the Karolinska Hospital, Stockholm, Sweden. This study has been approved by the ethical committee of the Karolinska Hospital, Stockholm, Sweden.  Tumour tissue was stored at -135C until use. Tumours were histopathologically diagnosed by Prof. V.P. Collins according to World Health Organization Brain tumour classification criteria. Total RNA was extracted using CsCl ultracentrifugation and asessed spectrophotometrically and using an Agilent Bioanalyzer 2100. Only RNA with no trace of degradation was used. 7 ug of total RNA were used for preparation of labelled target. Sample preparation, first and second strand cDNA synthesis, in vitro transcription amplification for production of biotin labelled cRNA, fragmentation of cRNA, U133A GeneChip hybridization, staining, washing and scanning were performed exactly as described by the manufacturer (Affymeytrix,Santa Clara). Hybridization was performed using 15 ug of labelled fragmented cRNA for 16 hours using a hybridization oven 640 as described by the manufacturer (Affymetrix, Santa Clara). Post-Hybridization washing and staining of the U133A GeneChips was performed on a  fluidics station 400 (Affymetrix, Santa Clara) and scanning was performed on a GeneArray scanner (Affymetrix, Santa Clara).

source_name: Anaplastic Astrocytoma (Grade III) frozen primary human tissue


title: GB35

source_name: Glioblastoma (Grade IV) frozen primary human tissue


title: MCF7 GMB 24H DIR

description: MCF7 + GMB 24h


title: MCF7 GMB 48H INV

description: MCF7 + GMB 48h

source_name: MCF7 + GMB 48h


title: GB245


title: MCF7 GMB 48H DIR

description: MCF7 + GMB 48h


title: MDA-MB-231 GMB 48H DIR

description: MDA-MB-231 + GMB 48h

source_name: MDA-MB-231 + GMB 48h


title: MDA-MB-231 GMB 48H INV

description: MDA-MB-231 + GMB 48h


title: MDA-MB-231 GMB CONTROL INV

description: MDA-MB-231 GMB CONTROL

source_name: MDA-MB-231 GMB CONTROL


title: MCF7 GMB CONTROL DIR

description: MCF7 Control

source_name: MCF7 Control


title: AA14

description: Anaplastic Astrocytoma (Grade III) frozen primary human tissue obtained following surgical removal of astrocytic brain tumour. All samples used in this study were collected from brain tumour patients operated on at the neurosurgery departments of the Sahlgrenska Hospital, Göthenburg, Sweden or the Karolinska Hospital, Stockholm, Sweden. This study has been approved by the ethical committee of the Karolinska Hospital, Stockholm, Sweden.  Tumour tissue was stored at -135C until use. Tumours were histopathologically diagnosed by Prof. V.P. Collins according to World Health Organization Brain tumour classification criteria. Total RNA was extracted using CsCl ultracentrifugation and asessed spectrophotometrically and using an Agilent Bioanalyzer 2100. Only RNA with no trace of degradation was used. 7 ug of total RNA were used for preparation of labelled target. Sample preparation, first and second strand cDNA synthesis, in vitro transcription amplification for production of biotin labelled cRNA, fragmentation of cRNA, U133A GeneChip hybridization, staining, washing and scanning were performed exactly as described by the manufacturer (Affymeytrix,Santa Clara). Hybridization was performed using 15 ug of labelled fragmented cRNA for 16 hours using a hybridization oven 640 as described by the manufacturer (Affymetrix, Santa Clara). Post-Hybridization washing and staining of the U133A GeneChips was performed on a  fluidics station 400 (Affymetrix, Santa Clara) and scanning was performed on a GeneArray scanner (Affymetrix, Santa Clara).


title: GB50


title: GB153


title: AA15


title: GB126


title: A30

description: Diffuse Astrocytoma (Grade II) frozen primary human tissue obtained following surgical removal of astrocytic brain tumour. All samples used in this study were collected from brain tumour patients operated on at the neurosurgery departments of the Sahlgrenska Hospital, Göthenburg, Sweden or the Karolinska Hospital, Stockholm, Sweden. This study has been approved by the ethical committee of the Karolinska Hospital, Stockholm, Sweden.  Tumour tissue was stored at -135C until use. Tumours were histopathologically diagnosed by Prof. V.P. Collins according to World Health Organization Brain tumour classification criteria. Total RNA was extracted using CsCl ultracentrifugation and asessed spectrophotometrically and using an Agilent Bioanalyzer 2100. Only RNA with no trace of degradation was used. 7 ug of total RNA were used for preparation of labelled target. Sample preparation, first and second strand cDNA synthesis, in vitro transcription amplification for production of biotin labelled cRNA, fragmentation of cRNA, U133A GeneChip hybridization, staining, washing and scanning were performed exactly as described by the manufacturer (Affymeytrix,Santa Clara). Hybridization was performed using 15 ug of labelled fragmented cRNA for 16 hours using a hybridization oven 640 as described by the manufacturer (Affymetrix, Santa Clara). Post-Hybridization washing and staining of the U133A GeneChips was performed on a  fluidics station 400 (Affymetrix, Santa Clara) and scanning was performed on a GeneArray scanner (Affymetrix, Santa Clara).


title: GB63


title: GB44


title: AA73


title: GB84


title: PA68

description: Pilocytic Astrocytoma (Grade I). IMPORTANT NOTE: Although upon re-evaluation this tumour was found to be a grade I tumour, in our initial analysis it was considered a grade II DIffuse astrocytoma. Frozen primary human tissue obtained following surgical removal of astrocytic brain tumour. All samples used in this study were collected from brain tumour patients operated on at the neurosurgery departments of the Sahlgrenska Hospital, Göthenburg, Sweden or the Karolinska Hospital, Stockholm, Sweden. This study has been approved by the ethical committee of the Karolinska Hospital, Stockholm, Sweden.  Tumour tissue was stored at -135C until use. Tumours were histopathologically diagnosed by Prof. V.P. Collins according to World Health Organization Brain tumour classification criteria. Total RNA was extracted using CsCl ultracentrifugation and asessed spectrophotometrically and using an Agilent Bioanalyzer 2100. Only RNA with no trace of degradation was used. 7 ug of total RNA were used for preparation of labelled target. Sample preparation, first and second strand cDNA synthesis, in vitro transcription amplification for production of biotin labelled cRNA, fragmentation of cRNA, U133A GeneChip hybridization, staining, washing and scanning were performed exactly as described by the manufacturer (Affymeytrix,Santa Clara). Hybridization was performed using 15 ug of labelled fragmented cRNA for 16 hours using a hybridization oven 640 as described by the manufacturer (Affymetrix, Santa Clara). Post-Hybridization washing and staining of the U133A GeneChips was performed on a  fluidics station 400 (Affymetrix, Santa Clara) and scanning was performed on a GeneArray scanner (Affymetrix, Santa Clara).

source_name: Pilocytic Astrocytoma (Grade I) frozen primary human tissue


title: AA20


title: GB133


title: GB87


title: GB82


title: GB55


title: GB131


title: GB154


title: AA76


title: AA18


title: AA106


title: AA29


title: GB102


title: AA92


title: AA3


title: AA93


title: GB32


title: GB3


title: GB100


title: GB22


title: GB227


title: AA105


title: AA13


title: GB12


title: GB81


title: GB139


title: A26

source_name: Diffuse Astrocytoma (Grade II) frozen primary human tissue


title: AA19


title: A9


title: GB135


title: A36


title: GB28


title: GB136


title: GB101


title: GB238


title: AA2


title: AA100


title: GB17


title: GB213


title: A48


title: GB56


title: GB2


title: GB103


title: slide5final

status: Public on May 14 2007

city: Melbourne

first: Maria

last: Schache

country: Australia

institute: St Vincents Institute

description: control 2 comparison

data_processing: gene pix pro normalisation

source_name: GlycAlb+AG

source_name: control


title: slide7final

description: test comparison

source_name: GlyAlb


title: slide3final

description: control 1 comparison

source_name: GlyAlb+AG


title: slide11final

description: control 2 comparison


title: slide10final

description: control 1 comparison dye-swap

source_name: GlycAlb


title: slide4final

description: control 1 comparison dye swap


title: GB11


title: AA86


title: PA67

description: Pilocytic Astrocytoma (Grade I). IMPORTANT NOTE: Although upon re-evaluation this tumour was found to be a grade I tumour, in our initial analysis it was considered a grade III Anaplastic astrocytoma. Frozen primary human tissue obtained following surgical removal of astrocytic brain tumour. All samples used in this study were collected from brain tumour patients operated on at the neurosurgery departments of the Sahlgrenska Hospital, Göthenburg, Sweden or the Karolinska Hospital, Stockholm, Sweden. This study has been approved by the ethical committee of the Karolinska Hospital, Stockholm, Sweden.  Tumour tissue was stored at -135C until use. Tumours were histopathologically diagnosed by Prof. V.P. Collins according to World Health Organization Brain tumour classification criteria. Total RNA was extracted using CsCl ultracentrifugation and asessed spectrophotometrically and using an Agilent Bioanalyzer 2100. Only RNA with no trace of degradation was used. 7 ug of total RNA were used for preparation of labelled target. Sample preparation, first and second strand cDNA synthesis, in vitro transcription amplification for production of biotin labelled cRNA, fragmentation of cRNA, U133A GeneChip hybridization, staining, washing and scanning were performed exactly as described by the manufacturer (Affymeytrix,Santa Clara). Hybridization was performed using 15 ug of labelled fragmented cRNA for 16 hours using a hybridization oven 640 as described by the manufacturer (Affymetrix, Santa Clara). Post-Hybridization washing and staining of the U133A GeneChips was performed on a  fluidics station 400 (Affymetrix, Santa Clara) and scanning was performed on a GeneArray scanner (Affymetrix, Santa Clara).


title: GB69


title: Dahl(S) replicate 2

status: Public on May 09 2007

city: Suita

first: Kazuaki

last: Kajimoto

state: Osaka

address: 5-7-1 Fujishirodai

department: Department of Epidemiology

country: Japan

institute: National Cardiovascular Center

description: Kidney from Dahl(S) rat 2

data_processing: GeneChip Operating Software ver1.4

label: biotin

organism: Rattus norvegicus

source_name: Dahl(S) kidney

tag: Dahl(S) rat is a salt-sensitive hypertension model animal.


title: GB1

description: Glioblastoma (Grade IV) .Forzen primary human tissue obtained following surgical removal of astrocytic brain tumour. All samples used in this study were collected from brain tumour patients operated on at the neurosurgery departments of the Sahlgrenska Hospital, Göthenburg, Sweden or the Karolinska Hospital, Stockholm, Sweden. This study has been approved by the ethical committee of the Karolinska Hospital, Stockholm, Sweden.  Tumour tissue was stored at -135C until use. Tumours were histopathologically diagnosed by Prof. V.P. Collins according to World Health Organization Brain tumour classification criteria. Total RNA was extracted using CsCl ultracentrifugation and asessed spectrophotometrically and using an Agilent Bioanalyzer 2100. Only RNA with no trace of degradation was used. 7 ug of total RNA were used for preparation of labelled target. Sample preparation, first and second strand cDNA synthesis, in vitro transcription amplification for production of biotin labelled cRNA, fragmentation of cRNA, U133A GeneChip hybridization, staining, washing and scanning were performed exactly as described by the manufacturer (Affymeytrix,Santa Clara). Hybridization was performed using 15 ug of labelled fragmented cRNA for 16 hours using a hybridization oven 640 as described by the manufacturer (Affymetrix, Santa Clara). Post-Hybridization washing and staining of the U133A GeneChips was performed on a  fluidics station 400 (Affymetrix, Santa Clara) and scanning was performed on a GeneArray scanner (Affymetrix, Santa Clara).


title: slide1final

description: test comparison


title: slide9final

description: control 1 comparison


title: slide12final

description: control 2 comparison dye-swap


title: Dahl(S) replicate 3

description: Kidney from Dahl(S) rat 3


title: GB97


title: Lewis replicate 3

description: Kidney from Lewis rat 3

source_name: Lewis kidney

tag: Lewis rat is wild type.


title: CerS injected embryos at St10.5 vs control (B)

status: Public on May 05 2007

first: Joana

middle: Maria

last: Ramis Morey

address: Tennis Court Road

institute: Gurdon Institute

description: Embryos were injected at the one cell stage  with either 5 nL of water (control) or 600pg Cerberus Short mRNA (CerS) dissolved in 5nL of water, Ref: Piccolo, S., E. Agius, et al. (1999).

data_processing: log ratios (Cy5/Cy3) were lowess normalised

organism: Xenopus laevis

source_name: CerS injected embryos St10.5 (B)

tag: see description

source_name: Control (water) injected embryos St10.5 (B)


title: slide6final

description: control 2 comparison dye-swap


title: Post Natally excised Control 5

city: San Francisco

first: Agnes

last: Paquet

state: CA

address: 1550 Fourth Street, RM 545

country: USA

institute: University of California, San Francisco

description: 7 year !Sample_source_name_ch1 = Post Natally excised Human lung tissue

data_processing: RMA

source_name: Post Natally excised Human lung tissue

tag: CCAM subtype Control

tag: Age

value: 7 year

tag: Gender

value: M


title: Pre Natal Control 2

description: 24 week!Sample_source_name_ch1 = Pre Natal Human lung tissue

source_name: Pre Natal Human lung tissue

value: 24 week

value: F


title: Post Natally excised CCAM 3

description: 18 month!Sample_source_name_ch1 = Post Natally excised Human lung tissue

tag: CCAM subtype CCAM- Type I

value: 18 month


title: CerS injected embryos at St10.5 vs control (C)

source_name: CerS injected embryos St10.5 (C)

source_name: Control (water) injected embryos St10.5 (C)


title: Post Natally excised CCAM 4

description: 2 day !Sample_source_name_ch1 = Post Natally excised Human lung tissue

tag: CCAM subtype CCAM- Type II

value: 2 day


title: Dahl(S) replicate 1

description: Kidney from Dahl(S) rat 1

tag: Dahl(S) rat is salt-sensitive hypertension model animal.


title: Lewis replicate 1

description: Kidney from Lewis rat 1


title: CerS injected embryos at St10.5 vs control (A)

description:
Embryos were injected at the one cell stage  with either 5 nL of water (control) or 600pg Cerberus Short mRNA (CerS) dissolved in 5nL of water, Ref: Piccolo, S., E. Agius, et al. (1999). "The head inducer Cerberus is a multifunctional antagonist of Nodal, BMP and Wnt signals." Nature 397(6721): 707-10. Embryos were harvested at Stage 10.5 for RNA analysis. RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) "Single Step Method of RNA Isolation by Acid Guanidinium Thiocyanate-Phenol-Chloroform Extraction." Analytical Biochemistry 162, 156.
50 micrograms of RNA were used for hybridisation.
Probe labelling and hybridization conditions were carried out as detailed in this paper

source_name: CerS injected embryos St10.5 (A)

source_name: Control (water) injected embryos St10.5 (A)


title: Control injected embryos at St10.5 vs CerS (C_swap)


title: Post Natally excised CCAM 1

description: 2 month!Sample_source_name_ch1 = Post Natally excised Human lung tissue

value: 2 month


title: Pre Natal CCAM 4

description: 20 week!Sample_source_name_ch1 = Pre Natal Human lung tissue

tag: CCAM subtype CCAM- Type III

value: 20 week


title: Control injected embryos at St10.5 vs CerS (B_swap)


title: Pre Natal CCAM 3

description: 26 week Pre Natal Human lung tissue

value: 26 weeks


title: Lewis replicate 2

description: Kidney from Lewis rat 2


title: Post Natally excised Control 3

description: 1 year!Sample_source_name_ch1 = Post Natally excised Human lung tissue

value: 1 year


title: slide2final

description: test comparison dye swap


title: Pre Natal CCAM 1

description: 27 week Pre Natal Human lung tissue

value: 27 weeks


title: #149318 48 hour soybean resistant & susceptible response to P. sojae, bio rep 2

status: Public on May 01 2007

city: London

first: Mark

last: Gijzen

state: ON

address: 1391 Sandford St

department: Agriculture & AgriFood Canada

country: Canada

institute: SCPFRC London

description: Etiolated hypocotyl comparison between cultivars with resistant response (Harosoy 63) and susceptible response (Harosoy) to P.sojae

data_processing: Arrayvision LRGC scanner layout, background subtracted intensity

organism: Glycine max

source_name: Harosoy infected with Race 2, 48 hours post inoculation

tag: Harosoy cultivar with susceptible response to P. sojae Race 2 isolate P6497

source_name: Harosoy 63 infected with Race 2, 48 hours post inoculation

tag: Harosoy 63 cutivar with resistant response to P. sojae Race 2 isolate P6497


title: AA101

source_name: Anaplastic Astrocytoma (Grade III) frozen primary human tissue


title: ActivinMO injected embryos at St10.5 vs ControlMO (B)

status: Public on May 04 2007

description:
Embryos were injected at the one cell stage  with 50ng of either Activin antisense morpholino oligonucleotides (MO3) or Control morpholino (mMO1) dissolved in water. Ref: Piepenburg, O., D. Grimmer, et al. (2004). "Activin redux: specification of mesodermal pattern in Xenopus by graded concentrations of endogenous activin B." Development 131(20): 4977-86. Embryos were harvested at Stage 10.5 for RNA analysis.
RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) "Single Step Method of RNA Isolation by Acid Guanidinium Thiocyanate-Phenol-Chloroform Extraction." Analytical Biochemistry 162, 156.
50 micrograms of RNA were used for hybridisation.
Probe labelling and hybridization conditions were carried out as detailed in this paper

source_name: ActivinMO injected embryos St10.5 (B)

source_name: ControlMO injected embryos St10.5 (B)


title: ControlMO injected embryos at St10.5 vs ActivinMO (A_swap)

source_name: ControlMO injected embryos St10.5 (A)

tag: See description

source_name: ActivinMO injected embryos St10.5 (A)


title: ControlMO injected embryos at St10.5 vs ActivinMO (C_swap)

source_name: ControlMO injected embryos St10.5 (C)

source_name: ActivinMO injected embryos St10.5 (C)


title: Post Natally excised CCAM 2

description: 3 week Post Natally excised Human lung tissue

value: 3 weeks


title: #149313 48 hour soybean resistant & susceptible response to P. sojae, bio rep 1


title: Pre Natal Control 1


title: #149319 3 hour soybean water treated, bio rep 2

source_name: Harosoy water treated, 3 hours post inoculation

source_name: Harosoy 63 water treated, 3 hours post inoculation


title: enriched D2 F,liver vs. enriched B6 F,liver, rep1 dye swap

status: Public on Apr 09 2007

city: Hidaka

first: Itoshi

last: NIKAIDO

state: Saitama

address: 1397-1 Yamane

institute: Saitama Medical School

data_processing: After background correction and removal of flagged values, log base 10 expression ratios were normalized using lowess.

organism: Mus musculus

source_name: "enriched D2 F,liver"

tag: "enriched D2 F,liver"

source_name: "enriched B6 F,liver"

tag: "enriched B6 F,liver"


title: #149315 6 hour soybean resistant & susceptible response to P. sojae, bio rep 2

source_name: Harosoy infected with Race 2, 6 hours post inoculation

source_name: Harosoy 63 infected with Race 2, 6 hours post inoculation


title: ActivinMO injected embryos at St10.5 vs ControlMO (C)


title: ControlMO injected embryos at St10.5 vs ActivinMO (B_swap)


title: BXD27M liver vs. E17.5, rep1

description: BXD27M liver vs. E17.5, rep1

source_name: "BXD-27M, liver"

tag: "BXD-27M, liver"


title: #149317 24 hour soybean resistant & susceptible response to P. sojae, bio rep 2

source_name: Harosoy infected with Race 2, 24 hours post inoculation

source_name: Harosoy 63 infected with Race 2, 24 hours post inoculation


title: #149312 24 hour soybean resistant & susceptible response to P. sojae, bio rep 1


title: #149316 12 hour soybean resistant & susceptible response to P. sojae, bio rep 2

source_name: Harosoy infected with Race 2, 12 hours post inoculation

source_name: Harosoy 63 infected with Race 2, 12 hours post inoculation


title: Post Natally excised CCAM 5

source_name: Post Natally excised Human lung tissue


title: BXD27F liver vs. E17.5, rep1

description: BXD27F liver vs. E17.5, rep1

source_name: "BXD-27F, liver"

tag: "BXD-27F, liver"


title: Tcl1 target genes in embryonic stem cells, biological replicate 1

status: Public on May 10 2007

first: Tatsushi

last: Miyazaki

address: 2-2 Yamadaoka

department: Department of Molecular Therapeutics

institute: Osaka University Graduate School of Medicine

description: A targeting vector replacing parts of exon 2 and exon3 with a PGK-puro cassette was used to disrupt the Tcl1 locus. Clones homozygous for the disrupted Tcl locus were isolated by selecting Tcl1+/- cells with high concentration puromycin. We next transfected Tcl-/- clone 4 with the CAG-Tcl1ireszeopA expression vector.

data_processing: The data processing to obtain the VALUE is as follows. 1. Yield the background-subtracted intensity for each feature.  2. Correct dye biases.  3. In situations when the raw mean signal is less than th background or not signifiicant compared to the background, or the background-subtracted signal is less than its backround standard deviation, the signal is replaced with a surrogate signal.  4. The log ratio of the red over green processed signals is calculated. See Agilent Feature Extraction Software Reference Guide for details.

source_name: Tcl1 stable transformant, clone 1

label_protocol: Low RNA Input Fluorescent Linear Amplification Kit(Agilent) was utilized to obtain Cyanine5 labelled cRNA from 500ng total RNA. The cRNA was purified with a RNeasy mini spin column(QIAGEN). Then 0.75microg each of Cyanine3 and Cyanine5 labelled cRNAs were combined, fragmented and used for hybridization to the microarray.

growth_protocol: Embryonic stem cells were routinely cultured without feeder cells in GMEM supplemented with 10% fetal calf serum, 100microM 2-mercaptoethanol, non-essential amino acid, sodium pyruvate and LIF on gelatin-coated dishes. All assays were carried out before passage 30.

extract_protocol: RNA was isolated using the acid guanidinium-phenol-chloroform (AGPC) method. The denaturing solution was added directly to cell culture dishes washed 3 times with PBS. The quality of purified total RNA was examined by Agilent 2100 Bioanalyzer.

tag: EB3 origin, genotype:(Tcl1-/-,CAG-Tcl1)

source_name: Tcl1 gene disruptant, clone 4

label_protocol: Low RNA Input Fluorescent Linear Amplification Kit(Agilent) was utilized to obtain Cyanine3 labelled cRNA from 500ng total RNA. The cRNA was purified with a RNeasy mini spin column(QIAGEN). Then 0.75microg each of Cyanine3 and Cyanine5 labelled cRNAs were combined, fragmented and used for hybridization to the microarray.

tag: EB3 origin, genotype:Tcl1-/-


title: Pre Natal CCAM 2

description: 28 week Pre Natal Human lung tissue

source_name: Pre Natal Human lung tissue

value: 28 weeks


title: Tcl1 target genes in embryonic stem cells, biological replicate 2

source_name: CAG-EGFP stably transfected Tcl1 gene disruptant, clone 6

tag: EB3 origin, genotype:(Tcl1-/-,CAG-EGFP)

source_name: Tcl1 stable transformant, clone 4


title: #149314 3 hour soybean resistant & susceptible response to P. sojae, bio rep 2

source_name: Harosoy infected with Race 2, 3 hours post inoculation

source_name: Harosoy 63 infected with Race 2, 3 hours post inoculation


title: ActivinMO injected embryos at St10.5 vs ControlMO (A)

source_name: ActivinMO injected embryos St10.5 (A)

tag: see description

source_name: ControlMO injected embryos St10.5 (A)


title: #149311 12 hour soybean resistant & susceptible response to P. sojae, bio rep 1


title: Control injected embryos at St10.5 vs CerS (A_swap)

source_name: Control (water) injected embryos St10.5 (A)

source_name: CerS injected embryos St10.5 (A)


title: slide8final

description: test comparison dye-swap

source_name: control

source_name: GlycAlb


title: #149309 3 hour soybean resistant & susceptible response to P. sojae, bio rep 1


title: BXD8M,liver vs. E17.5, rep1

description: BXD8M,liver vs. E17.5, rep1


title: D2F liver vs. B6F liver, rep2 dye swap

description: D2F liver vs. B6F liver, rep2 dye swap

source_name: "D2F, liver"

tag: "D2F, liver"

source_name: "B6F, liver"

tag: "B6F, liver"


title: BXD31F liver vs. E17.5, rep3

description: BXD31F liver vs. E17.5, rep3

source_name: "BXD-31F, liver"

tag: "BXD-31F, liver"


title: E17.5 vs. BXD21F liver, rep2 dye swap

description: E17.5 vs. BXD21F liver, rep2 dye swap

source_name: "BXD-21F, liver"

tag: "BXD-21F, liver"


title: E17.5 vs. BXD31F liver, rep2 dye swap

description: E17.5 vs. BXD31F liver, rep2 dye swap


title: E17.5 vs. B6M liver, rep1 dye swap

description: E17.5 vs. B6M liver, rep1 dye swap

source_name: "B6M, liver"

tag: "B6M, liver"


title: #149310 6 hour soybean resistant & susceptible response to P. sojae, bio rep 1

source_name: Harosoy 63 infected with Race 2, 6 hours post inoculation

source_name: Harosoy infected with Race 2, 6 hours post inoculation


title: B6M liver vs. E17.5, rep1

description: B6M liver vs. E17.5, rep1


title: BXD32F liver vs. E17.5, rep2

description: BXD32F liver vs. E17.5, rep2

source_name: "BXD-32F, liver"

tag: "BXD-32F, liver"


title: D2M liver vs. B6M liver, rep2 dye swap

description: D2M liver vs. B6M liver, rep2 dye swap

source_name: "D2M, liver"

tag: "D2M, liver"


title: E17.5 vs. BXD28F liver, rep1 dye swap

description: E17.5 vs. BXD28F liver, rep1 dye swap

source_name: "BXD-28F, liver"

tag: "BXD-28F, liver"


title: E17.5 vs. BXD19F liver, rep1 dye swap

description: E17.5 vs. BXD19F liver, rep1 dye swap

source_name: "BXD-19F, liver"

tag: "BXD-19F, liver"


title: enriched D2 M,liver vs. enriched B6 M,liver, rep1 dye swap

source_name: "enriched D2 M,liver"

tag: "enriched D2 M,liver"

source_name: "enriched B6 M,liver"

tag: "enriched B6 M,liver"


title: BXD14M,liver vs. E17.5, rep1

description: BXD14M,liver vs. E17.5, rep1


title: BXD9F,liver vs. E17.5, rep1

description: BXD9F,liver vs. E17.5, rep1


title: Post Natally excised Control 7

description: 1 day!Sample_source_name_ch1 = Post Natally excised Human lung tissue

source_name: Post Natally excised Human lung tissue

tag: CCAM subtype Control

tag: Age

value: 1 day

tag: Gender


title: E17.5 vs. BXD18F liver, rep1 dye swap

description: E17.5 vs. BXD18F liver, rep1 dye swap

source_name: "BXD-18F, liver"

tag: "BXD-18F, liver"


title: BXD12F liver vs. E17.5, rep1

description: BXD12F liver vs. E17.5, rep1

source_name: "BXD-12F, liver"

tag: "BXD-12F, liver"


title: BXD5F liver vs. E17.5, rep1

description: BXD5F liver vs. E17.5, rep1

source_name: "BXD-5F, liver"

tag: "BXD-5F, liver"


title: BXD14F,liver vs. E17.5, rep1

description: BXD14F,liver vs. E17.5, rep1


title: BXD8F,liver vs. E17.5, rep1

description: BXD8F,liver vs. E17.5, rep1


title: BXD9M,liver vs. E17.5, rep1

description: BXD9M,liver vs. E17.5, rep1


title: E17.5 vs. BXD32F liver, rep1 dye swap

description: E17.5 vs. BXD32F liver, rep1 dye swap


title: E17.5 vs. BXD31F liver, rep1 dye swap

description: E17.5 vs. BXD31F liver, rep1 dye swap


title: E17.5 vs. BXD6F liver, rep1 dye swap

description: E17.5 vs. BXD6F liver, rep1 dye swap

source_name: "BXD-6F, liver"

tag: "BXD-6F, liver"


title: BXD31F liver vs. E17.5, rep2

description: BXD31F liver vs. E17.5, rep2


title: BXD21F liver vs. E17.5, rep1

description: BXD21F liver vs. E17.5, rep1


title: BXD21F liver vs. E17.5, rep2

description: BXD21F liver vs. E17.5, rep2


title: BXD31F liver vs. E17.5, rep1

description: BXD31F liver vs. E17.5, rep1


title: E17.5 vs. BXD15F liver, rep2 dye swap

description: E17.5 vs. BXD15F liver, rep2 dye swap

source_name: "BXD-15F, liver"

tag: "BXD-15F, liver"


title: E17.5 vs. BXD5M liver, rep1 dye swap

description: E17.5 vs. BXD5M liver, rep1 dye swap

source_name: "BXD-5M, liver"

tag: "BXD-5M, liver"


title: BXD6F liver vs. E17.5, rep1

description: BXD6F liver vs. E17.5, rep1


title: E17.5 vs. BXD5F liver, rep1 dye swap

description: E17.5 vs. BXD5F liver, rep1 dye swap


title: BXD16M liver vs. E17.5, rep1

description: BXD16M liver vs. E17.5, rep1

source_name: "BXD-16M, liver"

tag: "BXD-16M, liver"


title: BXD28F liver vs. E17.5, rep1

description: BXD28F liver vs. E17.5, rep1


title: BXD18F liver vs. E17.5, rep1

description: BXD18F liver vs. E17.5, rep1


title: BXD19F liver vs. E17.5, rep1

description: BXD19F liver vs. E17.5, rep1


title: BXD12M liver vs. E17.5, rep1

description: BXD12M liver vs. E17.5, rep1

source_name: "BXD-12M, liver"

tag: "BXD-12M, liver"


title: E17.5 vs. BXD2F liver, rep1 dye swap

description: E17.5 vs. BXD2F liver, rep1 dye swap

source_name: "BXD-2F, liver"

tag: "BXD-2F, liver"


title: BXD5M liver vs. E17.5, rep1

description: BXD5M liver vs. E17.5, rep1


title: BXD2F liver vs. E17.5, rep1

description: BXD2F liver vs. E17.5, rep1


title: E17.5 vs. BXD12F liver, rep1 dye swap

description: E17.5 vs. BXD12F liver, rep1 dye swap


title: E17.5 vs. BXD32F liver, rep2 dye swap

description: E17.5 vs. BXD32F liver, rep2 dye swap

tag: "BXD-32F, liver"


title: E17.5 vs. BXD21F liver, rep1 dye swap

description: E17.5 vs. BXD21F liver, rep1 dye swap

source_name: "BXD-21F, liver"

tag: "BXD-21F, liver"


title: BXD31M liver vs. E17.5, rep1

description: BXD31M liver vs. E17.5, rep1

source_name: "BXD-31M, liver"

tag: "BXD-31M, liver"


title: E17.5 vs. BXD16F liver, rep1 dye swap

description: E17.5 vs. BXD16F liver, rep1 dye swap

source_name: "BXD-16F, liver"

tag: "BXD-16F, liver"


title: BXD32F liver vs. E17.5, rep1

description: BXD32F liver vs. E17.5, rep1

source_name: "BXD-32F, liver"


title: BXD18M liver vs. E17.5, rep1

description: BXD18M liver vs. E17.5, rep1

source_name: "BXD-18M, liver"

tag: "BXD-18M, liver"


title: BXD32M liver vs. E17.5, rep1

description: BXD32M liver vs. E17.5, rep1

source_name: "BXD-32M, liver"

tag: "BXD-32M, liver"


title: E17.5 vs. BXD31M liver, rep1 dye swap

description: E17.5 vs. BXD31M liver, rep1 dye swap


title: BXD15F liver vs. E17.5, rep1

description: BXD15F liver vs. E17.5, rep1


title: BXD16F liver vs. E17.5, rep1

description: BXD16F liver vs. E17.5, rep1


title: E17.5 vs. BXD15M liver, rep1 dye swap

description: E17.5 vs. BXD15M liver, rep1 dye swap

source_name: "BXD-15M, liver"

tag: "BXD-15M, liver"


title: E17.5 vs. BXD18M liver, rep1 dye swap

description: E17.5 vs. BXD18M liver, rep1 dye swap


title: E17.5 vs. BXD16M liver, rep1 dye swap

description: E17.5 vs. BXD16M liver, rep1 dye swap


title: E17.5 vs. BXD19M liver, rep1 dye swap

description: E17.5 vs. BXD19M liver, rep1 dye swap

source_name: "BXD-19M, liver"

tag: "BXD-19M, liver"


title: E17.5 vs. BXD12M liver, rep1 dye swap

description: E17.5 vs. BXD12M liver, rep1 dye swap


title: BXD28M liver vs. E17.5, rep1

description: BXD28M liver vs. E17.5, rep1

source_name: "BXD-28M, liver"

tag: "BXD-28M, liver"


title: E17.5 vs. BXD6M liver, rep2 dye swap

description: E17.5 vs. BXD6M liver, rep2 dye swap

source_name: "BXD-6M, liver"

tag: "BXD-6M, liver"


title: BXD21M liver vs. E17.5, rep1

description: BXD21M liver vs. E17.5, rep1

source_name: "BXD-21M, liver"

tag: "BXD-21M, liver"


title: BXD19M liver vs. E17.5, rep1

description: BXD19M liver vs. E17.5, rep1


title: E17.5 vs. BXD2M liver, rep1 dye swap

description: E17.5 vs. BXD2M liver, rep1 dye swap

source_name: "BXD-2M, liver"

tag: "BXD-2M, liver"


title: BXD15F liver vs. E17.5, rep2

description: BXD15F liver vs. E17.5, rep2

source_name: "BXD-15F, liver"

tag: "BXD-15F, liver"


title: APAP mouse hepatotoxicity 6F

status: Public on Feb 27 2007

city: Lucknow

first: Sanjeev

last: Noel

state: Uttar Pradesh

address: M G Marg

department: Toxicology

country: India

institute: Central Drug Research Institute

description:
Mice (Mus musculus) were sacrificed and livers were snap frozen in liquid nitrogen, and subsequently stored at -80 degree C till further use. Liver samples were mechanically homogenized and total RNA was extracted with TRI reagent (Sigma). 25 ug of total RNA was converted into
labelled cDNA using CyScribe first strand cDNA labelling kit(Amersham). Briefly, a reaction mixture of 25uL contained 1uL oligo(dT) primers, 1uL dCTP mix, 1uL labelled CTPs, 2Ul; 0.1M DTT, 4UL; 5X RT buffer and 1uL CyScribe reverse transcriptase. Primer annealing was done at 70 degree C for 10 minutes followed by incubation at room temperature for
15 minutes. Primer extention was carried out at 42 degree C for 2 hours. Template RNA was degraded by 2uL; 2.5M NaOH at 37 degree C for 15 minutes. Reaction mixture was neutralized by adding 10uL; 2M HEPES buffer before purifying it from unincorporated nucleotides through GFX columns(Amersham). Purified labelled cDNA was concentrated by evaporation under vacuum after estimating the percent incorporation of the dyes spectrophotometrically.

hyb_protocol: The Cy5 and Cy3 labelled cDNAs were resuspended in Cyscribe Hyb buffer(Amersham) containing 10ug/ml sheared Salmon sperm DNA, and 10ug/ml Yeast tRNA.The samples were heated at 95 degree C for 3 minutes and immediately chilled to avoid secondary structures. The labelled samples were hybridized to the arrays and incubated for 16-18hrs at 42 degree C.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with Molecular dynamics III scanner supported with ImageQuant v5.0.

data_processing: Image intensity data were extracted and analyzed with ArrayVision v8.0 analysis software. Background correted data was LOWESS normalized and log ratios were calculated using Avadis v4.3. Further, the data was processed to calculate mean log ratios for duplicate spots and analysed statistically either using Avadis v4.3 or Microsoft Excel to find differentially expressed genes. Multiple experiments were analysed with either Avadis v4.3 or TMEV v3.1(TIGR).

source_name: Liver

label_protocol: CyScribe first strand cDNA labelling kit protocol (Amersham)

growth_protocol: Mice were kept under optimal conditions of light and temperature

extract_protocol: TRI reagent (sigma)

treatment_protocol: Control mice

tag: Swiss mice, Male, 10-12 weeks

source_name: Liver, Drug treated

treatment_protocol: Mice were treated with a single dose of hepatotoxicant


title: BXD6M liver vs. E17.5, rep2

description: BXD6M liver vs. E17.5, rep2


title: LV153(BXD11F liver vs. E17.5, rep1 dye swap


title: E17.5 vs. BXD15F liver, rep1 dye swap

description: E17.5 vs. BXD15F liver, rep1 dye swap


title: BXD2M liver vs. E17.5, rep1

description: BXD2M liver vs. E17.5, rep1


title: E17.5 vs. BXD32M liver, rep1 dye swap

description: E17.5 vs. BXD32M liver, rep1 dye swap


title: D2F liver vs. B6F liver, rep1 dye swap

description: D2F liver vs. B6F liver, rep1 dye swap

source_name: "D2F, liver"

tag: "D2F, liver"

source_name: "B6F, liver"

tag: "B6F, liver"


title: Apap mouse hepatotoxicity 24F


title: Apap mouse hepatotoxicity 24R

source_name: Liver. Drug treated


title: E17.5 vs. BXD11F liver, rep1 dye swap

description: E17.5 vs. BXD11F liver, rep1 dye swap

source_name: "BXD-11F, liver"

tag: "BXD-11F, liver"


title: E17.5 vs. BXD6M liver, rep1 dye swap

description: E17.5 vs. BXD6M liver, rep1 dye swap


title: E17.5 vs. BXD11M liver, rep1 dye swap

description: E17.5 vs. BXD11M liver, rep1 dye swap

source_name: "BXD-11M, liver"

tag: "BXD-11M, liver"


title: Apap mouse hepatotoxicity 12R


title: E17.5 vs. BXD21M liver, rep1 dye swap

description: E17.5 vs. BXD21M liver, rep1 dye swap


title: BXD15M liver vs. E17.5, rep1

description: BXD15M liver vs. E17.5, rep1


title: E17.5 vs. BXD28M liver, rep1 dye swap

description: E17.5 vs. BXD28M liver, rep1 dye swap


title: BXD11F liver vs. E17.5, rep1

description: BXD11F liver vs. E17.5, rep1


title: Apap mouse hepatotoxicity 6R


title: CT mouse hepatotoxicity 6F


title: CT mouse hepatotoxicity 24R

description: Mice (Mus musculus) were sacrificed and livers were snap frozen in liquid nitrogen, and subsequently stored at -80 degree C till further use. Liver samples were mechanically homogenized and total RNA was extracted with TRI reagent (Sigma). 25 ug of total RNA was converted into labelled cDNA using CyScribe first strand cDNA labelling kit(Amersham). Briefly, a reaction mixture of 25uL contained 1uL oligo(dT) primers, 1uL dCTP mix, 1uL labelled CTPs, 2Ul; 1M DTT, 4UL; 5X RT buffer and 1uL CyScribe reverse transcriptase. Primer annealing was done at 70 degree C for 10 minutes followed by incubation at room temperature for 15 minutes. Primer extention was carried out at 42 degree C for 2 hours. Template RNA was degraded by 2uL; 2.5M NaOH at 37 degree C for 15 minutes. Reaction mixture was neutralized by adding 10uL; 2M HEPES buffer before purifying it from unincorporated nucleotides through GFX columns(Amersham). Purified labelled cDNA was concentrated by evaporation under vacuum after estimating the percent incorporation of the dyes spectrophotometrically.


title: Apap mouse hepatotoxicity 12F

source_name: Liver, drug treated


title: BXD11M liver vs. E17.5, rep1

description: BXD11M liver vs. E17.5, rep1


title: BXD6M liver vs. E17.5, rep1

description: BXD6M liver vs. E17.5, rep1


title: #150551 Soybean embryo, RCAT-Angora & Harovinton, Delhi 2003 time course

status: Public on Jan 01 2007

first: Sangeeta

last: Dhaubhadel

department: Agriculture & Agrifood Canada

description: Embryo comparison between cultivars of low (Harovinton) and high (RCAT-Angora) seed isoflavonoid content

data_processing: Arrayvision LRGC scanner layout, background subtracted intensity"

source_name: RCAT  70dap D03

tag: RCAT-Angora, soybean cultivar with high seed isoflavonoid content

source_name: Hvtn 70dap D03

tag: Harovinton, soybean cultivar with low seed isoflavonoid content


title: CT mouse hepatotoxicity 6R

description: Mice (Mus musculus) were sacrificed and livers were snap frozen in liquid nitrogen,  and subsequently stored at -80 degree C till further use. Liver samples were mechanically homogenized and total RNA was extracted with TRI  reagent (Sigma). 25 ug of total RNA was converted into labelled cDNA using CyScribe first strand cDNA labelling kit(Amersham). Briefly, a reaction mixture of 25uL contained 1uL oligo(dT) primers, 1uL dCTP mix, 1uL labelled CTPs, 2Ul; 1M DTT, 4UL; 5X RT buffer and 1uL CyScribe reverse transcriptase. Primer annealing was done at 70 degree C for 10 minutes followed by incubation at room temperature for 15 minutes. Primer extention was carried out at 42 degree C for 2 hours. Template RNA was degraded by 2uL; 2.5M NaOH at 37 degree C for 15 minutes. Reaction mixture was      neutralized by adding 10uL; 2M HEPES buffer before purifying it from unincorporated nucleotides through GFX columns(Amersham). Purified labelled  cDNA was concentrated by evaporation under vacuum after estimating the percent incorporation of the dyes spectrophotometrically.

hyb_protocol: The Cy5 and Cy3 labelled cDNAs were resuspended in Cyscribe Hyb buffer(Amersham) containing 10ug/ml sheared Salmon sperm DNA, and 10ug/ml Yeast tRNA.The samples were heated at 95 degree C for 3 minutes and immediately chilled to avoid secondary structures.     The labelled samples were hybridized to the arrays and incubated for 16-18hrs at 42 degree C.


title: D2M liver vs. B6M liver, rep1 dye swap

description: D2M liver vs. B6M liver, rep1 dye swap

source_name: "D2M, liver"

tag: "D2M, liver"

source_name: "B6M, liver"

tag: "B6M, liver"


title: CT mouse hepatotoxicity 12F


title: CT mouse hepatotoxicity 12R


title: CT mouse hepatotoxicity 24F


title: B6F liver vs. D2F liver, rep1

description: B6F liver vs. D2F liver, rep1


title: #150803 Soybean embryo, RCAT-Angora & Harovinton, Delhi 2003 time course

source_name: Hvtn  50dap D03

source_name: RCAT 50dap D03


title: #150801 Soybean embryo, RCAT-Angora & Harovinton, Delhi 2003 time course

source_name: Hvtn  40dap D03

source_name: RCAT 40dap D03


title: B6M liver vs. D2M liver, rep1

description: B6M liver vs. D2M liver, rep1


title: #150572 Soybean embryo, RCAT-Angora & Harovinton, Delhi 2004 time course

source_name: Hvtn 70 dap D04

source_name: RCAT 70dap D04


title: #150574 Soybean embryo, RCAT-Angora & Harovinton, Delhi 2003 time course

source_name: Hvtn  30dap D03

source_name: RCAT 30dap D03


title: #150575 Soybean embryo, RCAT-Angora & Harovinton, Delhi 2003 time course

source_name: RCAT  40dap D03

source_name: Hvtn 40dap D03


title: #150573 Soybean embryo, RCAT-Angora & Harovinton, Delhi 2003 time course

source_name: RCAT  30dap D03

source_name: Hvtn 30dap D03


title: #149324 Soybean embryo, RCAT-Angora & Harovinton, Delhi 2003 time course

source_name: RCAT 70dap D03


title: #150569 Soybean embryo, RCAT-Angora & Harovinton, Delhi 2004 time course

source_name: RCAT 60 dap D04

source_name: Hvtn 60 dap D04


title: #150567 Soybean embryo, RCAT-Angora & Harovinton, Delhi 2004 time course

source_name: RCAT 50 dap D04

source_name: Hvtn 50 dap D04


title: #150568 Soybean embryo, RCAT-Angora & Harovinton, Delhi 2004 time course


title: #150570 Soybean embryo, RCAT-Angora & Harovinton, Delhi 2004 time course


title: #150552 Soybean embryo, RCAT-Angora & Harovinton, Delhi 2003 time course

source_name: Hvtn 70dap D03


title: #150802 Soybean embryo, RCAT-Angora & Harovinton, Delhi 2003 time course

source_name: RCAT  50dap D03

source_name: Hvtn 50dap D03


title: #149325 Soybean embryo, RCAT-Angora & Harovinton, Delhi 2003 time course

source_name: RCAT  70dap D03


title: #150565 Soybean embryo, RCAT-Angora & Harovinton, Delhi 2004 time course

source_name: RCAT  40dap D04

source_name: Hvtn 40dap D04


title: #149323 Soybean embryo, RCAT-Angora & Harovinton, London 2003 time course

source_name: Hvtn 60dap L03

source_name: RCAT 60dap L03


title: #150571 Soybean embryo, RCAT-Angora & Harovinton, Delhi 2004 time course

source_name: RCAT 70 dap D04

source_name: Hvtn 70 dap D04


title: #150805 Soybean embryo, RCAT-Angora & Harovinton, London 2003 time course

source_name: Hvtn  70 dap L03

source_name: RCAT 70 dap L03


title: #150564 Soybean embryo, RCAT-Angora & Harovinton, Delhi 2004 time course

source_name: Hvtn  30dap D04

source_name: RCAT 30dap D04


title: #150566 Soybean embryo, RCAT-Angora & Harovinton, Delhi 2004 time course

source_name: Hvtn  40dap D04

source_name: RCAT 40dap D04


title: #150563 Soybean embryo, RCAT-Angora & Harovinton, Delhi 2004 time course

source_name: RCAT  30dap D04

source_name: Hvtn 30dap D04


title: #149322 Soybean embryo, RCAT-Angora & Harovinton, London 2003 time course

source_name: RCAT  60dap L03


title: #150811 Soybean embryo, RCAT-Angora & Harovinton, London 2003 time course

source_name: Hvtn  50dap L03

source_name: RCAT 50dap L03


title: #150809 Soybean embryo, RCAT-Angora & Harovinton, London 2003 time course

source_name: Hvtn 40dap L03

source_name: RCAT 40dap L03


title: Hsrc12

status: Public on Dec 31 2006

city: Leipzig

first: Friedemann

last: Horn

address: Johannisalle 30

department: Institute of Clinical Immunology and Transfusion Medicine

country: Germany

institute: University of Leipzig

description: This sample is part of a experiment series addressing the role of coactivator SRC-1/NcoA-1 for the induction of interleukin-6 (IL-6) target genes in HepG2 cells. Either control HepG2 cells or HepG2 cells manipulated to stably express an shRNA that knocks down SRC-1 expression were treated with IL-6 for 1 or 4 h or left untreated.

data_processing: Affymetrix MAS5.0

label: Phycoerythrin

growth_protocol: HepG2 cells were cultured in a 2:1 (v/v) mixture of Dulbecco's minimal essential medium (DMEM) and Ham's F12 medium with 10% (v/v) fetal calf serum and 1% (w/v) antibiotics (penicillin and streptomycin), at 37 degrees C and 5 % CO2.

extract_protocol: Total RNA was prepared using the Qiagen RNeasy Mini Kit according to the manufacturer’s instructions. RNA quality was examined by the RNA 6000 LabChip Kit on the Agilent 2100 bioanalyzer.

treatment_protocol: cells treated with 10 ng/ml interleukin-6 for 4 hour

tag: HepG2-∆Src1 cells were generated by lentiviral infection of the HepG2 human hepatocellular carcinoma cell line with a vector coding for a small-hairpin RNA that knocks down expression of the coactivator SRC-1/NcoA-1 (nuclear receptor coactivator 1). Cells were treated with interleukin-6 for 4 h.


title: Hsrc11


title: #150808 Soybean embryo, RCAT-Angora & Harovinton, London 2003 time course

source_name: RCAT  40dap L03


title: Hsrc10

treatment_protocol: cells treated with 10 ng/ml interleukin-6 for 1 hour

tag: HepG2-∆Src1 cells were generated by lentiviral infection of the HepG2 human hepatocellular carcinoma cell line with a vector coding for a small-hairpin RNA that knocks down expression of the coactivator SRC-1/NcoA-1 (nuclear receptor coactivator 1). Cells were treated with interleukin-6 for 1 h.


title: #150807 Soybean embryo, RCAT-Angora & Harovinton, London 2003 time course

source_name: Hvtn  30dap L03

source_name: RCAT 30dap L03


title: #150810 Soybean embryo, RCAT-Angora & Harovinton, London 2003 time course

source_name: RCAT  50dap L03

source_name: Hvtn 50dap L03


title: #149321 Soybean cultivars, RCAT-Angora & Harovinton

type: genomic

molecule: genomic DNA

source_name: Harovinton

source_name: RCAT


title: #150804 Soybean embryo, RCAT-Angora & Harovinton, London 2003 time course

source_name: RCAT  70dap L03

source_name: Hvtn 70dap L03


title: #150558 Soybean embryo, RCAT-Angora & Harovinton, London 2004 time course

source_name: Hvtn 40dap L04

source_name: RCAT 40dap L04


title: #150559 Soybean embryo, RCAT-Angora & Harovinton, London 2004 time course

source_name: RCAT  50dap L04

source_name: Hvtn 50dap L04


title: #150555 Soybean embryo, RCAT-Angora & Harovinton, London 2004 time course

source_name: RCAT  70dap L04

source_name: Hvtn 70dap L04


title: #149320 Soybean cultivars, RCAT-Angora & Harovinton


title: #150806 Soybean embryo, RCAT-Angora & Harovinton, London 2003 time course

source_name: RCAT  30dap L03

source_name: Hvtn 30dap L03


title: #150553 Soybean embryo, RCAT-Angora & Harovinton, London 2004 time course

source_name: RCAT  60dap L04

source_name: Hvtn 60dap L04


title: #150560 Soybean embryo, RCAT-Angora & Harovinton, London 2004 time course

source_name: RCAT 50dap L04


title: #150556 Soybean embryo, RCAT-Angora & Harovinton, London 2004 time course

source_name: RCAT 70dap L04


title: Hsrc6

treatment_protocol: cells treated with 10 ng/ml interleukin-6 for 4 hours

tag: HepG2 human hepatocellular carcinoma cell line

tag: treated with interleukin-6 for 4 hours


title: Hsrc7

treatment_protocol: Untreated control cells.

tag: HepG2-∆Src1 cells were generated by lentiviral infection of the HepG2 human hepatocellular carcinoma cell line with a vector coding for a small-hairpin RNA that knocks down expression of the coactivator SRC-1/NcoA-1 (nuclear receptor coactivator 1).


title: #150557 Soybean embryo, RCAT-Angora & Harovinton, London 2004 time course

source_name: RCAT  40dap L04


title: Hsrc8


title: #150554 Soybean embryo, RCAT-Angora & Harovinton, London 2004 time course

source_name: Hvtn  60dap L04

source_name: RCAT 60dap L04


title: Hsrc9


title: #150562 Soybean embryo, RCAT-Angora & Harovinton, London 2004 time course

source_name: Hvtn  30dap L04

source_name: RCAT 30dap L04


title: Hsrc4

tag: treated with interleukin-6 for 1 hour


title: Hsrc3

tag: HepG2 human hepatocellular carcinoma cell line treated with interleukin-6 for 1 hour


title: HUVEC_nickel_experiment 4

city: Hannover

first: Dorothee

last: Viemann

state: Deutschland

address: Carl-Neuberg-Straße 1

department: Department of Pediatric Pulmonology, Allergy and Neonatology

institute: Hannover Medical School

description: HUVEC cultured under standard conditions, stimulated for 5h with 1.5 mM NiCl2

data_processing: MAS 5.0, scaled to 180

label: SAGE

source_name: human umbilical vein endothelial cells (HUVEC)

tag: HUVEC treated for 5h with 1.5 mM NiCl2


title: Hsrc5


title: HUVEC_control_experiment 3

description: HUVEC cultured under standard conditions, unstimulated

tag: HUVEC unstimulated


title: #150561 Soybean embryo, RCAT-Angora & Harovinton, London 2004 time course

source_name: RCAT  30dap L04

source_name: Hvtn 30dap L04


title: HUVEC_control_experiment 2


title: HUVEC_control_experiment 4


title: HUVEC_nickel_experiment 3

tag: HUVEC stimulated for 5h with 1.5 mM NiCl2


title: HUVEC_nickel_experiment 1

description: HUVEC cultured as described and stimulated for 5h with 1.5 mM NiCl2


title: NZB Bio Replicate No.3

status: Public on Nov 03 2006

city: Bar Harbor

first: Ioannis

middle: M

last: Stylianou

state: ME

address: 600 Maine Street

institute: The Jackson Laboratory

description: Female Liver 8wk old mice from strain NZB/BinJ provided by the Jackson Lab.

hyb_protocol: See Jackson Lab Website

data_processing: Values are Normalised RMA data

source_name: Liver

growth_protocol: Chow diet - Weaned at 3Wks, Sac at 8Wks.

extract_protocol: Trizol by Invitrogen Protocol

treatment_protocol: Mice were fasted for 4 hours prior to dissection. Mice were perfused with 50mL sterile PBS. Samples snap frozen in liquid nitrogen.

tag: NZB/BinJ

tag: Liver

tag: Female

tag: 8 WK old - 4hr fast


title: HUVEC_control_experiment 1

description: HUVEC cultured in standard medium

treatment_protocol: 5h treament of HUVEC with 1.5 mM NiCl2

tag: unstimulated HUVEC


title: Hsrc1

treatment_protocol: untreated control cells


title: NZB Bio Replicate No.2

tag: 8wk old - 4hr fast


title: SM Bio replicate No.2

description: Female Liver 8wk old mice from strain SM/J provided by the Jackson Lab.

tag: SM

tag: Chow diet


title: HsfA2KO_seedling_HS44_rep2

status: Public on Nov 01 2006

city: Taipei

first: Yee-yung

last: Charng

address: 128, Academia Rd. Sec. 2

department: Agric. Biotech. Res. Center

country: Taiwan

institute: Academia Sinica

description: 3-d old seedlings were heat treated for 1 h at 37 degree C, recovered for 2 d at 24 degree C, and heat treated for 45 min at 44 degree C

data_processing: normalized by global scaling

organism: Arabidopsis thaliana

source_name: seedling, heat shock 37C 1h, recover 24C 2d, and heat shock 44C 45min

tag: Ecotype

value: Col-0 HsfA2 T-DNA knockout line (SALK_008978)

tag: Stage

value: 5-d old

tag: Tissue

value: whole seedling


title: Hsrc2

tag: HepG2 human hepatocellular carcinoma cell line


title: Wt_seedling_HS44_rep1

source_name: seedling, heat shock 37C 1h, recover 24C 2d, and heat shock 44C 45 min

value: Col-0 wild type


title: NZB Bio Replicate No.1


title: HUVEC_nickel_experiment 2


title: HsfA2KO_seedling_HS37_rep2

description: 5-d old seedlings were heat treated for 1 h at 37 degree C

source_name: seedling, heat shock 37C 1h

value: seedling


title: HsfA2KO_seedling_HS44_rep1


title: SM Bio replicate No.1

tag: SM/J

tag: 8wk old


title: SM Bio replicate No.3

tag: 8 wk old

tag: Chow diet - 4hr fast


title: Wt_seedling_HS44_rep2


title: HsfA2KO_seedling_HS37_rep1

tag: HsfA2 T-DNA knockout line (SALK_008978)


title: HsfA2KO_seedling_control_rep2

description: seedling, heat shock, control

source_name: seedling, heat shock, control


title: Wt_seedling_HS37_rep2

value: Col-0 wildtype


title: Wt_seedling_control_rep2

description: seedling, heat shock, control


title: Wt_seedling_HS37_rep1


title: Mental retardation patient 1

status: Public on Oct 22 2006

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

institute: MPIMG

description:
DNA isolated from blood of a mentally retarded patient with facial dysmorphism
Gender: male

hyb_protocol: Hybridization was done overnight at 42°C in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

scan_protocol: Slides were scanned using an Axon 4000B scanner (Axon Instruments, Union City, CA)

data_processing: TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen et al., 2005). Background intensities were not subtracted. Signal intensities were normalized by subgrid LOWESS. Aberrant ratios involving three or more neighbouring clones were considered as genomic aberrations, unless they coincided with a known polymorphism as listed in the Database of Genomic Variants ( version Dec 2005)

source_name: DNA isolated from blood

label_protocol: Probes were labelled by random priming. Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

extract_protocol: DNA was extracted from peripheral blood by means of Qiagen Genomic Tip columns

tag: Gender

value: male

source_name: male reference DNA

tag: male reference DNA isolated from blood of a healthy donor


title: Mental retardation patient 2

description:
DNA isolated from blood of a mentally retarded patient
Gender: male

tag: DNA isolated from blood of a healthy male donor


title: Mental retardation patient 21

description:
DNA isolated from blood of a mentally retarded patient with minor facial dysmorphism
Gender: male

extract_protocol: cell lysis and salting out

tag: DNA isolated from an EBV transformed cell line derived from peripheral blood lymphocytes of a healthy male donor


title: HsfA2KO_seedling_control_rep1

description: seedling, heat shock, control


title: Mental retardation patient 23

tag: DNA isolated from blood of a mentally retarded patient with facial dysmorphism


title: Mental retardation patient 20

description:
DNA isolated from blood of a mentally retarded patient with facial dysmorphism and congenital malformation
Gender: female

value: female

source_name: female reference DNA

tag: DNA isolated from an EBV transformed cell line derived from peripheral blood lymphocytes of a healthy female donor


title: Mental retardation patient 22

tag: DNA isolated from blood of a mentally retarded patient


title: Mental retardation patient 24


title: Mental retardation patient 17

description:
DNA isolated from blood of a mentally retarded patient
Gender: female

tag: DNA isolated from blood of a healthy female donor


title: Wt_seedling_control_rep1

description: seedling, heat shock, control

tag: Ecotype


title: Mental retardation patient 9


title: Mental retardation patient 12

extract_protocol: DNA was extracted by cell lysis and salting out


title: Mental retardation patient 19


title: Mental retardation patient 14


title: Mental retardation patient 13

description:
DNA isolated from blood of a mentally retarded patient with CHARGE syndrome
Gender: female


title: Mental retardation patient 18


title: Mental retardation patient 15

description:
DNA isolated from blood of a mentally retarded patient with Prader Willi/ Angelman syndrome
Gender: male


title: Mental retardation patient 8


title: Mental retardation patient 11

description:
DNA isolated from blood of a mentally retarded patient with facial dysmorphism and congenital malformation
Gender: male


title: Mental retardation patient 25


title: Mental retardation patient 10

description: DNA isolated from blood of a mentally retarded patient

extract_protocol: DNA was extracted from peripheral blood of a healthy male donor by means of Qiagen Genomic Tip columns

tag: DNA isolated from peripheral blood of a healthy male donor


title: Mental retardation patient 4


title: Mental retardation patient 3


title: Mental retardation patient 6


title: Mental retardation patient 7

description:
DNA isolated from blood of a patient with 22q11 deletion syndrome
Gender: male


title: Mental retardation patient 16

description:
DNA isolated from blood of patient with Smith Magenis Syndrome
Gender: male


title: Mental retardation patient 5

tag: DNA isolated from blood of a mentally retarded patient with minor facial dysmorphism


title: Microarray gene expression analysis in atrophying rainbow trout muscle 4

status: Public on Oct 04 2006

city: Morgantown

first: Mohamed

last: Salem

state: WV

address: Division of Animal and Nutritional Sciences, West Virginia University

institute: West Virginia University

scan_protocol: ScanArray Lite microarray scanner was used to scan arrays and ScanArray Express software (PerkinElmer, Wellesley, MA) was used to process array images, align spots, integrate robot-spotting files with the microarray images and quantify spots.

data_processing: Pre-processing and normalization of data was accomplished using R-project statistical environment and Bioconductor through the GenePix AutoProcessor (GPAP) website.

molecule: polyA RNA

organism: Oncorhynchus mykiss

source_name: Contol muscle

extract_protocol: Muscle deterioration as a physiological response to the energetic demands of fish spawning represents a unique model for studying the mechanisms of muscle degradation in non-mammalian animals. A salmonid microarray, containing 16,006 cDNAs, was used to study the transcriptome response to atrophying fast-switch muscles from gravid rainbow trout in comparison to sterile fish. Total RNA was isolated using the Trizol reagent (Invitrogen) according to manufacturer’s instruction. Concentrations of isolated RNA were determined by measuring absorbance at 260 nm. The integrity of RNA was determined by agarose gel electrophoresis. Poly(A)+ RNA was purified using Oligotex mRNA Mini Kit (Qiagen) according to manufacturer’s instruction. A salmonid microarray containing cDNAs representing 16,006 genes selected from atlantic salmon and rainbow trout expressed sequence tag databases was used to profile changes of gene expression in spawning-induced atrophying muscles. mRNA (0.8 μg) from trout muscles were used as templates in reverse transcription reactions incorporating amino-allyl dUTP into the cDNA using oligo-d(T) primer and Superscript II reverse transcriptase (Invitrogen). The synthesized cDNAs from atrophying (fertile fish) and non-atrophying muscles (sterile fish) were differentially labeled using N-hydroxysuccinate-derived Cy3 and Cy5 dyes, respectively (GE Health). Labeled cDNAs were purified using a PCR purification kit (Qiagen) to remove unincorporated dyes. The Cy3 and Cy5 labeled cDNAs were then combined and concentrated down to 20 μl using a Microcon-30 concentrator (Millipore) followed by addition of 130 µl of Slidehyb 3 of solution (Ambion, Inc. Austin, TX). Microarray hybridizations were performed on a Tecan HS400 automated microarray hybridization station (Tecan US, Durham, NC). The slides were placed on the machine at 60°C for 2 minutes followed by a pre-hybridization at 55°C for 30 minutes with pre-hybridization solution (5XSSC, 1% SDS, 1% BSA) under medium agitation. After brief washing at 60°C for 1 minute, differentially labeled cDNAs in hybridization buffer (~145 µl) were injected into the hybridization chamber. The hybridizations were carried out for 3 hours at 60°C followed by another 13 hours at 55°C. Arrays were washed 2x in 2XSSC, 01% SDS, followed by 2x in 0.1XSSC, 0.1% SDS at room temperature. Following 2 more washes in 0.1XSSC, the slides were rinsed in water and dried by centrifugation.

tag: white muscle from sterile fish

source_name: Atrophying muscle

tag: white muscle atrophying from fertile fish


title: Microarray gene expression analysis in atrophying rainbow trout muscle 2

department: Division of Animal and Nutritional Sciences

description: A salmonid microarray, containing 16,006 cDNAs, was used to study the transcriptome response to atrophying fast-switch muscles from gravid rainbow trout in comparison to sterile fish.

scan_protocol: ScanArray Lite microarray scanner was used to scan arrays and ScanArray Express software (PerkinElmer, Wellesley, MA) was used to process array images, align spots, integrate robot-spotting files with the microarray images and quantify spots


title: Microarray gene expression analysis in atrophying rainbow trout muscle 3


title: Microarray gene expression analysis in atrophying rainbow trout muscle 1

extract_protocol: Muscle deterioration as a physiological response to the energetic demands of fish spawning represents a unique model for studying the mechanisms of muscle degradation in non-mammalian animals. A salmonid microarray, containing 16,006 cDNAs, was used to study the transcriptome response to atrophying  fast-switch muscles from gravid rainbow trout in comparison to sterile fish. Total RNA was isolated using the Trizol reagent (Invitrogen) according to manufacturer’s instruction. Concentrations of isolated RNA were determined by measuring absorbance at 260 nm. The integrity of RNA was determined by agarose gel electrophoresis. Poly(A)+ RNA was purified using Oligotex mRNA Mini Kit (Qiagen) according to manufacturer’s instruction. A salmonid microarray containing cDNAs representing 16,006 genes selected from atlantic salmon and rainbow trout expressed sequence tag databases was used to profile changes of gene expression in spawning-induced atrophying muscles. mRNA (0.8 μg) from trout muscles were used as templates in reverse transcription reactions incorporating amino-allyl dUTP into the cDNA using oligo-d(T) primer and Superscript II reverse transcriptase (Invitrogen). The synthesized cDNAs from atrophying (fertile fish) and non-atrophying muscles (sterile fish) were differentially labeled using N-hydroxysuccinate-derived Cy3 and Cy5 dyes, respectively (GE Health). Labeled cDNAs were purified using a PCR purification kit (Qiagen) to remove unincorporated dyes. The Cy3 and Cy5 labeled cDNAs were then combined and concentrated down to 20 μl using a Microcon-30 concentrator (Millipore) followed by addition of 130 µl of Slidehyb 3 of solution (Ambion, Inc. Austin, TX). Microarray hybridizations were performed on a Tecan HS400 automated microarray hybridization station (Tecan US, Durham, NC). The slides were placed on the machine at 60°C for 2 minutes followed by a pre-hybridization at 55°C for 30 minutes with pre-hybridization solution (5XSSC, 1% SDS, 1% BSA) under medium agitation. After brief washing at 60°C for 1 minute, differentially labeled cDNAs in hybridization buffer (~145 µl) were injected into the hybridization chamber. The hybridizations were carried out for 3 hours at 60°C followed by another 13 hours at 55°C. Arrays were washed 2x in 2XSSC, 01% SDS, followed by 2x in 0.1XSSC, 0.1% SDS at room temperature. Following 2 more washes in 0.1XSSC, the slides were rinsed in water and dried by centrifugation.


title: X-ray irradiated male mouse array 83

status: Public on Oct 01 2006

city: Augusta

first: Yutao

last: Liu

state: GA

address: 1120 15th Street

department: Cellular Biology and Anatomy

institute: Augusta University

description: Male mice 10-14 weeks of age were exposed in vivo to 10 rad X-ray. Control mice were sham-exposed.  Spleen was harvested 3.5 hrs post-irradiation.  Each hybridization consists of one control mouse and one exposed mouse randomly paired to form a biological replicate.  Each biological replicate was hybridized in duplicate, incorporating a dye swap to control for dye-specific effects.

data_processing: Spots flagged for poor quality or low expression were omitted from the dataset, as were outliers.  The remaining data were normalized using Lowess, with independent normalization for each printtip.

source_name: sham control

tag: Strain

tag: Age:10 -14 weeks

tag: Tissue

value: spleen

source_name: irradiated sample


title: X-ray irradiated male mouse array 97


title: X-ray irradiated male mouse array 70


title: X-ray irradiated male mouse array 95


title: X-ray irradiated male mouse array 54


title: X-ray irradiated male mouse array 47


title: X-ray irradiated male mouse array 84

value: BalbxJ


title: X-ray irradiated male mouse array 68


title: X-ray irradiated male mouse array 46

value: A/J


title: X-ray irradiated male mouse array 86


title: Microarray gene expression analysis in atrophying rainbow trout muscle 5

source_name: Control muscle


title: X-ray irradiated male mouse array 50


title: X-ray irradiated male mouse array 89


title: X-ray irradiated male mouse array 52


title: X-ray irradiated male mouse array 34


title: X-ray irradiated male mouse array 48


title: X-ray irradiated male mouse array 45


title: X-ray irradiated male mouse array 51


title: X-ray irradiated male mouse array 88


title: X-ray irradiated male mouse array 96


title: X-ray irradiated male mouse array 36


title: X-ray irradiated male mouse array 90


title: X-ray irradiated male mouse array 35


title: X-ray irradiated male mouse array 87


title: X-ray irradiated male mouse array 53


title: X-ray irradiated male mouse array 29


title: X-ray irradiated male mouse array 27


title: X-ray irradiated male mouse array 28


title: X-ray irradiated male mouse array 11


title: X-ray irradiated male mouse array 26


title: X-ray irradiated male mouse array 25


title: Neuroblastoma tumor 96170 (GPL96)

status: Public on Sep 06 2006

city: Los Angeles

first: Shahab

last: Asgharzadeh

address: 4650 Sunset Boulevard, Mail Stop #57

department: Hematology-Oncology

institute: Childrens Hospital Los Angeles

description: Neuroblastoma tumor

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: dCHIP (PM-MM model)

source_name: Neuroblastoma tumor obtained at diagnosis

label_protocol: Approximately 15 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Approximately 15 sections were obtained from snap frozen tissue (at diagnosis or relapse) and total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: Patient with disease relapse


title: 3 hours macrophage exposure 3

city: Madrid

first: Concha

last: Gil

state: Madrid

address: Pza. Ramón y Cajal s/n

department: Departamento Microbiología II

country: Spain

institute: Universidad Complutense de Madrid

description: 18-24 h prior to initiation of the co-culture experiment, macrophages were collected and counted with a Neubauer chamber (hemocytometer). A total of 3,5 x 107 cells were plated in complete culture media in 750-ml cell culture flask and grown overnight at 37ºC in a humidified atmosphere with 5% CO2. C. albicans strain SC5314 was grown overnight at 30ºC on solid YED medium (to maintain cells in the yeast form). On day 1, these yeast cells were harvested, washed twice with phosphate buffered saline (PBS), counted and diluted to the desired density in 50 ml of complete culture media. 5 x 107 yeast cells were added per flask to obtain a fungus-macrophage ratio 1:1, (since repeated cell counts of the overnight macrophage cultures indicated a growth rate of 1,4) and incubated for 1.5 h. (for microarray experiments) and 3h. at 37°C and 5% CO2 . Non ingested and unbound Candida cells were removed by washing 3 times with ice-cold PBS. The macrophages and bounded/ingested yeast cells were dislodged by scraping the flask with rubber scrapers in ice-cold water, and pooled by centrifugation for 10 min at 4000 rpm.The resulting cell pellet was resuspended in a 0.25 % Triton X114 solution (50 mM Tris-HCl, 2mM EDTA, pH 7.5), vortexed 3 times and left/chilled on ice in order to eliminate most of the lysated macrophages. After 30 min, the sample was washed 4-6 times with ice-cold MilliQ water, in order to eliminate any trace of the detergent employed.

hyb_protocol: cDNA was synthesized from 20-30 microgrammes of total RNA by reverse transcription using CyScribe Post-Labeling kit, incorporating Cy3-cUTP or Cy5-dUTP (Amersham Biosciences) into the cDNA corresponding to each sample to be compared. The amount of cDNA as well as the incorporation of Cy3 and Cy5 dyes into cDNA targets was quantified on an Ultrospec 3300 Pro UV/ Visible spectrophotometer (Amersham Biosciences). Both labeled cDNA populations were combined, dried in a vacuum trap, and used as a hybridization probe after resuspension in hybridization solution and 100 micrograms Salmon Sperm. Slides were hybridized overnight with labeled probe at42 degrees in a water bath. Before scanning, the chips were washed and dried following the manufactures instructions

scan_protocol: Microarrays were scanned with a GenePix 4000B scanner (Axon Instruments. Union City, CA) at a resolution of 5m (PMT values ranging from 550 to 700 and laser power 100%)

data_processing: GenePix Pro 4.0 analysis software (Axon Instruments) was used to locate spots in the microarray with the appropriate grid and to obtain the two Cy3/Cy5 image TIFF files. All images were further processed using GenePix 4.0 software according to manufacturer instructions. Flagged spots and spots with an average intensity minus background below the media of the intensity minus background for all the non flagged spots in any channel (Cy3 or Cy5) were not retained for further analysis. Within this group those spots which showed in at least one channel a value of intensity minus background higher than 5 times the media of the background for all spots in the microarray for this channel were recovered.

organism: Candida albicans

source_name: candida not exposed

source_name: candida exposed to macrophages

tag: The C. Albicans strain used in this study was SC5314. The strain was maintained on solid YED medium and incubated at 30 degrees for at least 2 days.

tag: RAW 264.7 murine macrophages were obtained from the American Type Culture Collection (Rockville, Md) and maintained in complete culture media at 37ºC in a humidified atmosphere with 5% CO2. Cells were maintained at low densities (75% confluence) and passed until reaching the confluent state, usually every 3-4 days on sterile culture plates. RAW cells were plated at the indicated density 18-24 h prior to initiation of the experiments.


title: X-ray irradiated male mouse array 24

tag: Gender


title: X-ray irradiated male mouse array 3


title: Neuroblastoma tumor 96051 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 96036 (GPL96)

description: Neuroblastoma tumor

tag: Patient without disease relapse (minimum of 5 years from diagnosis)


title: Neuroblastoma tumor 96051 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 96170 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 95277 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 95277 (GPL97)

description: Neuroblastoma tumor


title: 3 hours macrophage exposure 1


title: X-ray irradiated male mouse array 4


title: Neuroblastoma tumor 96029 (GPL96)

description: Neuroblastoma tumor


title: X-ray irradiated male mouse array 2


title: X-ray irradiated male mouse array 5


title: Neuroblastoma tumor 96052 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 96036 (GPL97)

description: Neuroblastoma tumor


title: X-ray irradiated male mouse array 6


title: Neuroblastoma tumor 96052 (GPL97)

description: Neuroblastoma tumor


title: 3 hours macrophage exposure 2


title: 3 hours macrophage exposure 4


title: Neuroblastoma tumor 96029 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 95259 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 95228 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 95108 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 95259 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 95218 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 95218 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 95089 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 95088 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 95026 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 95003 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 95108 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 95089 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 95086 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94271 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 95088 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 95228 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 95086 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94272 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 95082 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 95029 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 95026 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94272 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94256 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94283 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 95003 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 95029 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94271 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94283 (GPL97)

description: Neuroblastoma tumor


title: X-ray irradiated male mouse array 85


title: Neuroblastoma tumor 95082 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94254 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94256 (GPL97)

description: Neuroblastoma tumor


title: X-ray irradiated male mouse array 49


title: Neuroblastoma tumor 94220 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94189 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94254 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94211 (GPL97)

description: Neuroblastoma tumor

source_name: Neuroblastoma tumor obtained at disease relapse

tag: Tumor obtained at disease relapse


title: Neuroblastoma tumor 94178 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94178 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94152 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94168 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94164 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94189 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94181 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94140 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94220 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94176 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94176 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94097 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94140 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94087 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94164 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94097 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94153 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94087 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94181 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94153 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94168 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94078 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94078 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94050 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94049 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94048 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94049 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93291 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94034 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94050 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94048 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 94034 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93225 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93177 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93225 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93291 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93239 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93134 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93246 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93253 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93146 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93239 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93162 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93246 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93162 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93134 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93146 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93133 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93177 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93253 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93130 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93133 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93116 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93094 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93094 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93130 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93074 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93053 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93079 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93086 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93079 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93116 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93073 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93073 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93007 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 92283 (GPL96)

description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


title: Neuroblastoma tumor 92282 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93007 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93074 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93082 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 93048 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 92283 (GPL97)

description: Neuroblastoma tumor


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description: Neuroblastoma tumor


title: Neuroblastoma tumor 92226 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 92290 (GPL96)

description: Neuroblastoma tumor


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description: Neuroblastoma tumor


title: Neuroblastoma tumor 92223 (GPL97)

description: Neuroblastoma tumor


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description: Neuroblastoma tumor


title: Neuroblastoma tumor 92216 (GPL97)

description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


title: Neuroblastoma tumor 92175 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 92199 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 92216 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 92174 (GPL97)

description: Neuroblastoma tumor


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description: Neuroblastoma tumor


title: Neuroblastoma tumor 92119 (GPL97)

description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


title: Neuroblastoma tumor 92143 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 92122 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 92223 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 92028 (GPL97)

description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


title: Neuroblastoma tumor 91207 (GPL97)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 91207 (GPL96)

description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


title: Neuroblastoma tumor 91141 (GPL96)

description: Neuroblastoma tumor


title: Neuroblastoma tumor 91036 (GPL97)

description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


title: Neuroblastoma tumor 90204 (GPL96)

description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


title: Neuroblastoma tumor 90126 (GPL97)

description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


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description: Neuroblastoma tumor


title: Neuroblastoma tumor 86120 (GPL97)

description: Neuroblastoma tumor


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title: Sigma1278b_ureaVSthr_rep2

status: Public on Sep 01 2006

city: gosselies

first: Patrice

last: Godard

address: rue des professeurs Jeener et Brachet, 12

department: IBMM

country: Belgium

institute: Université Libre de Bruxelles

description: comparison of Sigma1278b transcriptome during growth on urea and on threonine

scan_protocol: The hybridized microarray was scanned with a GMS418 fluorescence reader (Genetic MicroSystems, Woburn, MA) having a resolution of 10 µm; the laser power was set at 100%. The slide was scanned twice to get the Cy5 and Cy3 signals, once with the PMT (Photo Multiplier Tube) gain set at 80% and once with it set at 20%. Signal quantification for each probe on the microarray was performed with GenePix 4.01.17 image acquisition software (Axon Instruments, Union City, CA). Spots with a diameter greater than 210 µm or smaller than 80 were considered low-quality spots as were spots having (median pixel intensity - mean pixel intensity)> 40% of the median pixel intensity for each channel and spots having less than 95% of their spot pixels more than two standard deviations above background in either the green or the red channel. Low-quality spots were excluded from further analysis.

data_processing: Intensity values from high-PMT-gain pictures were used, except in the case of saturated spots. In the latter case, intensity values from low-PMT-gain pictures were used after scale correction. Intensity-dependent within-tip-group and scale normalization were applied as described by Yang et al. 2002 (PMID = 11842121) using Bioconductor tools (Gentleman et al. 2004 : PMID = 15461798).  Fluorescence ratios were computed on the basis of hybridization signals normalized with background corrections.

organism: Saccharomyces cerevisiae

source_name: Sigma1278b ; minimum medium ; NS = urea

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229); Carbon source = glucose 3%; Nitrogen source = urea (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)

source_name: Sigma1278b ; minimum medium ; NS = threonine

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229); Carbon source = glucose 3%; Nitrogen source = threonine (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_ureaVSasp_rep2

description: comparison of Sigma1278b transcriptome during growth on urea and on aspartate

source_name: Sigma1278b ; minimum medium ; NS = aspartate

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229); Carbon source = glucose 3%; Nitrogen source = aspartate (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_ureaVSpro_rep2

description: comparison of Sigma1278b transcriptome during growth on urea and on proline

source_name: Sigma1278b ; minimum medium ; NS = proline

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229); Carbon source = glucose 3%; Nitrogen source = proline (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_ureaVSphe_rep2

description: comparison of Sigma1278b transcriptome during growth on urea and on phenylalanine

source_name: Sigma1278b ; minimum medium ; NS = phenylalanine

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229); Carbon source = glucose 3%; Nitrogen source = phenylalanine (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_ureaVSval_rep2

description: comparison of Sigma1278b transcriptome during growth on urea and on valine

source_name: Sigma1278b ; minimum medium ; NS = valine

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229); Carbon source = glucose 3%; Nitrogen source = valine (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_ureaVSam_rep2

description: comparison of Sigma1278b transcriptome during growth on urea and on ammonium

source_name: Sigma1278b ; minimum medium ; NS = ammonium

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229); Carbon source = glucose 3%; Nitrogen source = ammonium sulfate (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_ureaVSglt_rep2

description: comparison of Sigma1278b transcriptome during growth on urea and on glutamate

source_name: Sigma1278b ; minimum medium ; NS = glutamate

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229); Carbon source = glucose 3%; Nitrogen source = glutamate (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_ureaVSmet_rep2

description: comparison of Sigma1278b transcriptome during growth on urea and on methionine

source_name: Sigma1278b ; minimum medium ; NS = methionine

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229); Carbon source = glucose 3%; Nitrogen source = methionine (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_ureaVSleu_rep2

description: comparison of Sigma1278b transcriptome during growth on urea and on leucine

source_name: Sigma1278b ; minimum medium ; NS = leucine

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229); Carbon source = glucose 3%; Nitrogen source = leucine (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)