title: PBO treated adults - oligo microarray - slide 6

description: This spotted oligonucleotide microarray is composed of over 14000 transcript specific features as well as a number of controls, including non-Drosophila targets, spotting buffer and empty wells. The oligonucleotides were designed by the International Drosophila Array Consortium (INDAC: details at www.INDAC.net).

hyb_protocol: Microarray pre-hybridisation preparation Microarray slides were prepared for use by incubation for an hour at 42degC in a 50ml centrifuge tube containing the following solution: 0.5g BSA 0.5ml 10% SDS 12.5ml 20x SSC 12.5ml formamide 24.5ml H2O The microarray slide was then immersed in a 50ml centrifuge tube containing H2O and then placed into an empty 50ml centrifuge tube and dried by centrifugation for 5 minutes at 1500rpm. Hybridisation Labeled samples were pooled and made up to a volume of 27ul either by drying down (as described above) or by the addition of NFW. The hybridization mixture was made up by addition of the following: 54ul Pooled sample 14ul 20x SSC 2.4ul 10% SDS 4ul Salmon testes DNA (Sigma) 4ul Cot1 DNA (Invitrogen) 2ul Oligo-dA (Invitrogen) This mixture was incubated for 2 minutes at 98degC and then allowed to reach room temperature for 10 minutes. Lifter slip was placed over the microarray and the hybridisation mix was applied to the microarray. The microarray was then placed into a hybridization chamber, which was wrapped in aluminium foil and then incubated in a 65degC water bath for 20 hours. Washing Wash 1: 1x SSC 0.2% SDS Wash 2: 0.1x SSC 0.2% SDS Wash 3 and 4: 0.1x SSC All washes were performed at room temperature. The microarray was added to 50ml Wash 1 in a tray and agitated until the coverslips floated off, which were then removed. This tray was then placed into a light-tight box and agitated for 5 minutes. The microarray was then transferred to a tray containing 50ml Wash 2, placed into a light-tight box and agitated for 5 minutes. The microarray was then transferred to a tray containing 50ml Wash 3, placed into a light-tight box and agitated for 5 minutes. The microarray was then transferred into a 50ml centrifuge tube wrapped in aluminium foil, containing Wash 4 and agitated for 3 minutes, before being briefly immersed in water and then dried by centrifugation for 5 minutes at 1500rpm in a fresh 50ml centrifuge tube.

value: Four days post emergence from pupa

value: Male


title: Caffeine treated 3rd instar larvae - Array 4

status: Public on Mar 18 2007

type: RNA

city: Parkville

first: Lee

last: Willoughby

state: Victoria

address: 30 Flemington Road

department: Genetics

country: Australia

institute: University of Melbourne

description: The Drosophila melanogaster "detox" microarray contained the cytochrome P450, glutathione-S-transferase and esterase gene families and also incorporated both individual control genes and control dilutions, to account for the large number of "detox" genes that could have potentially been differentially regulated in response to different treatments.

hyb_protocol: Microarray pre-hybridisation preparation Microarray slides were prepared for use by incubation for an hour at 42degC in a 50ml centrifuge tube containing the following solution: 0.5g BSA 0.5ml 10% SDS 12.5ml 20x SSC 12.5ml formamide 24.5ml H2O The microarray slide was then immersed in a 50ml centrifuge tube containing H2O and then placed into an empty 50ml centrifuge tube and dried by centrifugation for 5 minutes at 1500rpm. Hybridisation Labeled samples were pooled and made up to a volume of 27ul either by drying down (as described above) or by the addition of NFW. The hybridization mixture was made up by addition of the following: 27ul Pooled sample 7ul 20x SSC 1.2ul 10% SDS 2ul Salmon testes DNA (Sigma) 2ul Cot1 DNA (Invitrogen) 1ul Oligo-dA (Invitrogen) This mixture was incubated for 2 minutes at 98degC and then allowed to reach room temperature for 10 minutes. 22mm x 25mm Lifter slip was placed over the microarray and the hybridisation mix was applied to the microarray. The microarray was then placed into a hybridization chamber, which was wrapped in aluminium foil and then incubated in a 65degC water bath for 20 hours. Washing Wash 1: 1x SSC 0.2% SDS Wash 2: 0.1x SSC 0.2% SDS Wash 3 and 4: 0.1x SSC All washes were performed at room temperature. The microarray was added to 50ml Wash 1 in a tray and agitated until the coverslips floated off, which were then removed. This tray was then placed into a light-tight box and agitated for 5 minutes. The microarray was then transferred to a tray containing 50ml Wash 2, placed into a light-tight box and agitated for 5 minutes. The microarray was then transferred to a tray containing 50ml Wash 3, placed into a light-tight box and agitated for 5 minutes. The microarray was then transferred into a 50ml centrifuge tube wrapped in aluminium foil, containing Wash 4 and agitated for 3 minutes, before being briefly immersed in water and then dried by centrifugation for 5 minutes at 1500rpm in a fresh 50ml centrifuge tube.

scan_protocol: Microarray slides were scanned using a Genepix 4000B microarray scanner (Axon instruments) and signal quantitation was performed using Genepix pro software (Axon instruments).

data_processing: Data analysis was conducted with LimmaGUI (http://bioinf.wehi.edu.au/limmaGUI/), a graphical interface for Limma (Smyth, G. K. & Speed, T. P. (2003) Methods 31, 265-273). The linear model was computed and the data was normalized with the print-tip loess method. Genes were considered differentially expressed if they had P values < 0.05 after multiple comparison correction (Holm correction) and were greater than 2 fold up or down regulated.

label: Cy3-dCTP (Amersham)

molecule: total RNA

organism: Drosophila melanogaster

source_name: Caffeine treated 3rd instar larvae

label_protocol:
Labeling master mix
6ul 5x Superscript II reaction buffer (Invitrogen)
3ul DTT (Invitrogen)
0.6ul 50x low-C dNTP (see below)
0.5ul RNase OUT (Invitrogen)
1.5ul Superscript II reverse transcriptase enzyme (Invitrogen)
50x low-C dNTP
25ul dATP (100mM)
25ul dGTP (100mM)
25ul dTTP (100mM)
10ul dCTP (100mM)
15ul NFW
2ul of test/control Lucidea Universal Scorecard (Amersham) spike in RNA was added to 14.9ul 4ug/ul RNA sample. 1.5ul oligo dT (Invitrogen) was added to the sample and then incubated at 70degC for 10 minutes.
Samples were immeadiately transferred to ice and cooled for at least one minute.
11.6ul master mix was added to each sample, followed by 3ul Cy3-dCTP (Amersham), which was then incubated at 42degC for 2 hours.
1.5ul 1M NaOH was added to the sample, which was then incubated at 70degC for 10 minutes.
1.5ul 1M HCl was added to the sample and then the reaction mixture was concentrated to under 20ul (required for DyeEx columns). The sample was concentrated by incubation at 80degC for 15-20 minutes, covered by aluminium foil.
Unincorporated Cy-dye was removed using the DyeEx 2.0 kit (QIAGEN), according to the manufacturer's protocol.

growth_protocol: D. melanogaster y; cn bw sp strain adults were allowed to lay eggs for a 6 hour period on petri dishes containing standard fly food with 2x agar. Petri dishes were then collected and incubated at 25degC. Larvae were allowed to develop on the original petri dishes until they were to be exposed, so that all larvae would be 4 1/2 days old when frozen after exposure.

extract_protocol:
RNA extraction
RNA was extracted using trizol reagent (Invitrogen). Eight samples (50 individuals per sample) were used. Frozen samples were crushed on liquid nitrogen and then resuspended in 1ml of trizol reagent. RNA extraction was then performed according to the manufacturer's instructions and the pellet was resuspended in 50ul of nuclease free water (NFW).
RNA clean-up
Samples were pooled to generate four 100ul samples. RNA was cleaned up using the column based RNeasy kit (QIAGEN). RNA clean up was performed according to the manufacturer�s instructions with the RNA being eluted in 80ul NFW. All four samples were pooled, with 5ul set aside for concentration determination using spectrophotometer analysis and an additional 5ul was set aside and run on a 1% agarose gel to assess RNA quality.
RNA concentration
23ul 3M NaOAc (pH 5.2) and 600ul ethanol was added to the RNA sample. This was vortexed and then precipitated for an hour at -20degC. After precipitation, the samples were centrifuged at maximum speed for 15 minutes at 4degC. The pellet was aspirated and 500ul 75% ethanol was added. The sample was vortexed and then centrifuged at maximum speed for 15 minutes at 4degC. The pellet was aspirated and allowed to air dry for 10 minutes in a fume hood. The pellet was then resuspended in NFW to give a final RNA concentration of 4ug/ul.

treatment_protocol: Fresh petri dishes containing standard fly food with 2x agar were prepared for exposure, containing either the compound or the appropriate control. A final concentration of 1.5mg/ml Caffeine (Sigma) was used. 50 larvae were transferred to each petri dish. After the appropriate 4 hours, the larvae were frozen in liquid nitrogen and stored at -80degC until RNA extraction.

tag: Strain

value: y cn bw sp

tag: Age

value: Four and a half days post laying, 3rd instar feeding larvae

tag: Treatment

value: exposed to caffeine

label: Cy5-dCTP (Amersham)

source_name: Untreated 3rd instar larvae

label_protocol:
Labeling master mix
6ul 5x Superscript II reaction buffer (Invitrogen)
3ul DTT (Invitrogen)
0.6ul 50x low-C dNTP (see below)
0.5ul RNase OUT (Invitrogen)
1.5ul Superscript II reverse transcriptase enzyme (Invitrogen)
50x low-C dNTP
25ul dATP (100mM)
25ul dGTP (100mM)
25ul dTTP (100mM)
10ul dCTP (100mM)
15ul NFW
2ul of test/control Lucidea Universal Scorecard (Amersham) spike in RNA was added to 14.9ul 4ug/ul RNA sample. 1.5ul oligo dT (Invitrogen) was added to the sample and then incubated at 70degC for 10 minutes.
Samples were immeadiately transferred to ice and cooled for at least one minute.
11.6ul master mix was added to each sample, followed by 3ul Cy5-dCTP (Amersham), which was then incubated at 42degC for 2 hours.
1.5ul 1M NaOH was added to the sample, which was then incubated at 70degC for 10 minutes.
1.5ul 1M HCl was added to the sample and then the reaction mixture was concentrated to under 20ul (required for DyeEx columns). The sample was concentrated by incubation at 80degC for 15-20 minutes, covered by aluminium foil.
Unincorporated Cy-dye was removed using the DyeEx 2.0 kit (QIAGEN), according to the manufacturer's protocol.

value: unexposed control


title: PAO1 on glasswool 1 x hrp + 0.25 % sucrose 48 hr biofilm cells

city: College Station

first: Can

last: Attila

state: TX

address: 524 Jack E. Brown Bldg.

department: Chemical Eng

country: USA

institute: Texas A&M University

description: RNA extracted from biofilm cells of P. aeruginosa PAO1 on glasswool in 1 x hrp + 0.25 % sucrose after 48 hours of contact

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: MAS 5.0 Expression Analysis Default Setting

label: biotin

organism: Pseudomonas aeruginosa

source_name: Channel 1

label_protocol: Affymetrix

extract_protocol: Qiagen RNeasy Protocol

tag: RNA extracted from biofilm cells on glasswool in 1 x hrp + 0.25 % sucrose after 48 hours of growth


title: PBO treated adults - oligo microarray - slide 2

data_processing: Data analysis was conducted with LimmaGUI at The Walter and Eliza Hall Institute (WEHI) bioinformatics web site, a graphical interface for Limma (Smyth, G. K. & Speed, T. P. (2003) Methods 31, 265-273). The linear model was computed and the data was normalized with the print-tip loess method. Genes were considered differentially expressed if they had P values < 0.05 after multiple comparison correction (Holm correction) and were greater than 2 fold up or down regulated.

source_name: PBO treated adult males

growth_protocol: Adult males of the y; cn bw sp strain were collected within a 24 hour window after emergence, sorted into groups of 50 males and then stored at 25oC for four days prior to exposure.

treatment_protocol: 2µl PBO (Aldrich) was added to 150µl of acetone and immediately transferred to a 30ml scintillation vial, which was then rolled until the acetone had evaporated. 50 adult males were transferred to each scintillation vial. After 4 hours, the flies were frozen in liquid nitrogen and stored at -80°C until RNA extraction.

tag: Sex

value: exposed to PBO

source_name: Untreated adult males

treatment_protocol: 150µl of acetone was transferred to a 30ml scintillation vial, which was then rolled until the acetone had evaporated. 50 adult males were transferred to each scintillation vial. After 4 hours, the flies were frozen in liquid nitrogen and stored at -80°C until RNA extraction.

value: unexposed


title: Dicer Wild-type FT3182

status: Public on Mar 16 2007

city: Cambridge

first: Fuchou

last: Tang

state: Cambridgeshire

address: Tennis Court Road

department: Wellcome Trust/Cancer Research UK Gurdon Institute

country: United Kingdom

institute: University of Cambridge

description: Gene expression data from single cell (mouse oocyte) using Applied Biosystems AB1700 Whole Genome Microarray

hyb_protocol: Hybridization was performed according to Applied Biosystems Chemiluminescence Detection Kit Protocol (PN 4339627) using 10 ug fragmented cRNA

scan_protocol: Image was captured using CCD camera came with AB1700 Microarray Analyzer

data_processing: Quantile normalization was performed separately for knockout and wild-type samples. The normalization was performed using ABarray bioconductor package

label: digoxigenin

organism: Mus musculus

source_name: Mouse mature oocyte

label_protocol: Digoxigenin labeled cRNA was prepared according to Applied Biosystems nanoamp RT-IVT protocol

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

tag: Dicer Wild-type


title: Dicer Knock-Out FT3172

tag: Dicer Knock-out


title: PAO1 on poplar root 48 hr

description: RNA extracted from biofilm cells of P. aeruginosa PAO1 on poplar roots after 48 hours of contact

tag: RNA extreacted from biofilm cells of P. aeruginosa PAO1 on poplar roots after 48 hours of contact


title: Dicer Knock-Out FT3175


title: Dicer Knock-Out FT3173


title: Dicer Wild-type FT3179


title: PBO treated adults - oligo microarray - slide 5


title: Dicer Wild-type FT3177


title: PBO treated adults - oligo microarray - slide 1


title: Dicer Knock-Out FT3171


title: PBO treated adults - oligo microarray - slide 4


title: Poplar in 1 x hrp + 0.25 % sucrose no bacteria

description: RNA extracted from poplar roots after 12 hours in 1 x hrp + 0.25 % sucrose

organism: Populus

extract_protocol: Qiagen RNeasy Plant Mini Kit Protocol


title: Dicer Wild-type FT3178


title: Dicer Wild-type FT3181


title: Dicer Knock-Out FT3176


title: PBO treated adults - oligo microarray - slide 3


title: PBMC_S.aureus_MSSA_INF264

city: Dallas

first: Damien

last: Chaussabel

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

description: The subject was infected with S. aureus, MSSA.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 System.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Homo sapiens

source_name: PBMC_S. aureus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: RNeasy mini

value: 13y, when sample taken

tag: Gender

value: M

tag: Race

value: Black

tag: Illness

value: Suppurative arthritis

value: Vancomycin/Cefazolin/Gentamicin

tag: Pathogen

value: S. aureus, MSSA


title: Dicer Knock-Out FT3174


title: PBMC_S.aureus_MSSA_INF271

value: Osteomyelitis

value: Clindamycin


title: Dicer Wild-type FT3180


title: PBMC_S.aureus_MSSA_INF258

value: 8y, when sample taken

value: F

value: Caucasian

value: Osteomyelitis/bacteremia

value: Cefazolin


title: Poplar contacted with P. aeruginosa PAO1 in 1 x hrp + 0.25 % sucrose

description: RNA extracted from poplar roots after 12 hours of contact with P. aeruginosa PAO1 in 1 x hrp + 0.25 % sucrose

extract_protocol: Qiagen RNeasy Plant Mini KIt Protocol

tag: RNA extracted from Poplar roots after 12 hr of contact with P. aeruginosa PAO1 in 1 x hrp + 0.25 % sucrose


title: PBMC_S.aureus_MRSA_INF242

description: The subject was infected with S. aureus, MRSA.

value: 13m, when sample taken

value: Pneumonia/Bacteremia

value: S. aureus, MRSA


title: PBMC_S.aureus_MRSA_INF262

value: 13, when sample taken

value: Hispanic

value: Skin/Soft Tissue Abscess/Bacteremia


title: PBMC_S.aureus_MSSA_INF224

value: 10 y, when sample taken

value: M

value: Oxacillin/Rifampin


title: PBMC_S.aureus_MSSA_INF220

value: 11 y, when sample taken

value: Cefazolin/Rifampin

value: S. aureus, MSSA


title: PBMC_S.aureus_MRSA_INF205

value: 7 y, when sample taken

value: Vancomycin


title: PBMC_S.aureus_MRSA_INF241

value: 0.91y, when sample taken

value: F

value: Black

value: Vancomycin/Rifampin


title: PBMC_S.aureus_MRSA_INF221

value: 6 y, when sample taken

value: Osteomyelitis/bacteremia


title: PBMC_S.aureus_MRSA_INF208

value: Caucasian

value: Osteomyelitis/bacteremia/Pneumonia

value: Vancomycin/Clindamycin/Rifampin

value: S. aureus, MRSA


title: PBMC_S.aureus_MSSA_INF179

hyb_protocol: Standard Affymetrix protocol.

value: 12 y, when sample taken

value: M

value: Endocarditis/bacteremia

value: Oxacillin/Gentamicin/Rifampin


title: PBMC_S.aureus_MRSA_INF067

scan_protocol: GeneChips were scanned using the Agilent GeneArray 2500 Scanner.


title: PBMC_S.aureus_MSSA_INF005

value: 10 y, when sample taken

value: Hispanic

value: Osteomyelitis

value: Cefazolin

value: S. aureus, MSSA


title: PBMC_S.aureus_MRSA_INF030

value: 15 y, when sample taken

value: Black

value: Bacteremia

value: Vancomycin


title: PBMC_S.aureus_MSSA_INF090

value: 8m, when sample taken

value: Septic arthiritis/bacteremia

value: Oxacillin


title: PBMC_S.aureus_MRSA_INF066

tag: Age:3m, when sample taken

value: F

value: Pneumonia

value: Vancomycin/Gentamicin

value: S. aureus, MRSA


title: Biofilm cells grown on RO membrane

city: New Haven

first: Moshe

last: Herzberg

state: CT

address: 9 Hillhouse avenue

department: Chemical Engineering

institute: Yale University

description: Affymetrix

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Affymetrix Gene@Chip Software

organism: Pseudomonas aeruginosa PAO1

source_name: Cells collected from RO membrane coupon after 20 hours of growth

label_protocol: Affymetrix standard protocol

extract_protocol: Invitrogen RNeasy  kit

tag: Biofilm of Pseudomonas aeruginosa PA01 was grown on RO membrane coupon with defined media in RO unit.


title: PBMC_InfluenzaA_INF542

description: The subject was infected with Influenza A.

hyb_protocol: Hybridize 6-Sample Beadchip

scan_protocol: SentrixScanVersion 2.3.0.13  (This information is in the .XML file)

data_processing: The data were analyzed using BeadStudio version 1.5.1.3 using the average chip normalization method.

label_protocol: Biotynlated cRNA were generated following manufacturer protocols using the Illumina TotalPrep Amplification Kit from Ambion.

value: 0.04y, when sample taken

value: Fever

value: Ampicillin/Gentamicin

value: Influenza A


title: PBMC_S.aureus_MSSA_INF537

value: 9y, when sample taken


title: PBMC_InfluenzaB_INF560

description: The subject was infected with Influenza B.

value: 10y, when sample taken

value: Encephalitis

value: Acyclovir

value: Influenza B


title: PBMC_S.aureus_MRSA_INF062

value: 2 y, when sample taken

value: M

value: Caucasian

value: Osteomyelitis

value: Clindamycin


title: PBMC_S.aureus_MRSA_INF024

value: 3 y, when sample taken

value: Black

value: Vancomycin/Rifampin


title: PBMC_S.aureus_MRSA_INF216

value: 10 y, when sample taken

value: F

value: Hispanic

value: Osteomyelitis/bacteremia

value: S. aureus, MRSA


title: Suspended Pseudomonas aeruginosa in RO unit

description: Affymetrix

source_name: 20 hours of suspended cell growth

tag: Suspended cells of Pseudomonas aeruginosa PA01 grown in defined medium of reverse osmosis membrane unit


title: PBMC_S.aureus_MRSA_INF088

value: 11m, when sample taken

value: Vancomycin


title: PBMC_S.aureus_MRSA_INF529

value: 1.75y, when sample taken

value: Pneumonia/Bacteremia


title: PBMC_S.aureus_MRSA_INF043

value: 7 y, when sample taken

value: Hip abscess/bacteremia


title: PBMC_InfluenzaA_INF530

value: 0.38y, when sample taken

value: M

value: Fever/seizure

value: Influenza A


title: PBMC_S.aureus_MSSA_INF535

value: 0.58y, when sample taken

value: Other

value: Suppurative arthritis

value: Cefazolin

value: S. aureus, MSSA


title: Arp4_Noc

type: genomic

city: Sendai

first: Hideaki

last: Ogiwara

state: Miyagi

address: Aoba 6-3,Aramaki-Aza,Aoba-ku

country: Japan

institute: Tohoku University

description: WCE fraction used for normalization of ChIP fraction.

hyb_protocol: Following denaturation at 100 C for 10 minutes and cooling, 200 micro liter of hybridization mixuter was hybridized for 16 hours at 42 C on GeneChip SC3546a520015F (S. cerevisiae tilling array) using hybridization oven 640 (affymetrix). Each hybridization mixture contains the end-labbeled DNA, 6xSSPE, 0.005% Triton X-100, 0.1 mg/ml herring sperm DNA, oligo B2 (affymetrix) and hybridization control (affymetrix).

scan_protocol: Washing and scanning protocol (EukGE-WS1v3) provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 400, Affymetrix). Arrays were scanned by Hewlett-Packard GeneArray Scanner at an emission wavelength of 560 nm at 7.5 microM resolution.

data_processing:
Single array analysis with MAS 5.0 using default settings.
Data analyses were performed as previously described (Katou et al., 2003, nature). Primary data analyses were carried out with Affymetrix Microarray Suite version 5.0 (MAS 5.0) software using default settings to obtain signal intensity, fold change value, change p-value and detection p-value. To discriminate significant signals for binding to DNA, signals from the ChIP fraction scan were compared to the WCE (whole cell extract) fraction scan using the 3 following criteria: first, the signal reliability was judged by the detection p-value of each locus (p-value ?0.025); secondly, reliability of binding ratio was judged by change p-value (p-value ?0.025); thirdly, only clusters of at least 3 contiguous loci responding to the 2 previous criteria were selected as significantly enriched locus.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Fragmented whole genomic DNA

label_protocol: DNA fragments were end-labelled by addition of terminal transferase and biotin-N6-ddATP as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998).

growth_protocol: Mitotic budding yeast cells were synchronised in G2/M with 15 ug/ml Nocodazole for 180 min.

extract_protocol:
2% of WCE, which is used for IP.
5x10^8 cells were disrupted using Multi-Beads Shocker (MB400U, YASUI KIKAI, Osaka). Whole cell extract was sonicated to obtain average 500 bp genomic DNA fragments. The WCE was used for chromatin immunoprecipitation. The chromatin immunoprecipitated sample and a part of the WCE were eluted and incubated over night at 65ºC to reverse the cross-link. Immunoprecipitated DNA was incubated with proteinase K, extracted with phenol/chloroform/isoamylalcohol, precipitated, resuspended in TE and incubated with RNaseA. The DNA was amplified by PCR after random priming as previously described (Katou et al., 2003, nature). The amplified DNA was digested with Dnase I to a mean size of 100 bp. After DNase I inactivation at 95ºC, fragments were labelled with indicated label protocol.

treatment_protocol: Cells were fixed for 15 min in 1% formaldehyde at room temperature.

tag: W303 background strain expressing FLAG tagged Arp4 protein


title: PBMC_S.aureus_MSSA_INF040

value: 12 y, when sample taken

value: Caucasian

value: Osteomyelitis/bacteremia


title: PBMC_InfluenzaA_INF527

value: 0.13y, when sample taken

value: Black

value: Fever

value: Ampicillin/Ceftriaxone


title: Arp4-FLAG_IP_Noc

description: ChIP-chip data from distribution of Arp4 in G2/M phase

data_processing:
Comparison analysis (ChIP fraction versus WCE fraction) wiht MAS 5.0 using default settings.
Data analyses were performed as previously described (Katou et al., 2003, nature). Primary data analyses were carried out with Affymetrix Microarray Suite version 5.0 (MAS 5.0) software using default settings to obtain signal intensity, fold change value, change p-value and detection p-value. To discriminate significant signals for binding to DNA, signals from the ChIP fraction scan were compared to the WCE (whole cell extract) fraction scan using the 3 following criteria: first, the signal reliability was judged by the detection p-value of each locus (p-value ?0.025); secondly, reliability of binding ratio was judged by change p-value (p-value ?0.025); thirdly, only clusters of at least 3 contiguous loci responding to the 2 previous criteria were selected as significantly enriched locus.

source_name: Chromatin-immunoprecipitated DNA

extract_protocol:
WCE was immunoprecipitated with Anti-Flag monoclonal antibody M2 (Sigma-Aldrich Co., St Louis, MO) coupled to Dynabeads (Dynal, protein A Dynabeads).
5x10^8 cells were disrupted using Multi-Beads Shocker (MB400U, YASUI KIKAI, Osaka). Whole cell extract was sonicated to obtain average 500 bp genomic DNA fragments. The WCE was used for chromatin immunoprecipitation. The chromatin immunoprecipitated sample and a part of the WCE were eluted and incubated over night at 65ºC to reverse the cross-link. Immunoprecipitated DNA was incubated with proteinase K, extracted with phenol/chloroform/isoamylalcohol, precipitated, resuspended in TE and incubated with RNaseA. The DNA was amplified by PCR after random priming as previously described (Katou et al., 2003, nature). The amplified DNA was digested with Dnase I to a mean size of 100 bp. After DNase I inactivation at 95ºC, fragments were labelled with indicated label protocol.


title: PBMC_S.aureus_MRSA_INF522

value: 9.5y, when sample taken

value: F

value: Vancomycin/Rifampin

value: S. aureus, MRSA


title: PBMC_S.aureus_MSSA_INF480

value: 12y, when sample taken

value: M

value: Bacteremia

value: Clindamycin/Doxycycline


title: PBMC_S.pneumoniae_INF523

description: The subject was infected with S. pneumoniae.

source_name: PBMC_S. pneumoniae

value: 3y, when sample taken

value: Hispanic

value: Suppurative arthritis

value: Cefazolin

value: S. pneumoniae


title: PBMC_InfluenzaA_INF519

value: 0.13y, when sample taken

value: Influenza A


title: PBMC_S.aureus_MSSA_INF475

value: 1.33y, when sample taken

value: Black

value: Nafcillin

value: S. aureus, MSSA


title: PBMC_S.aureus_MRSA_INF489

value: 1.08y, when sample taken

value: Caucasian

value: Skin/Soft Tissue Abscess

value: Clindamycin


title: PBMC_S.aureus_MRSA_INF477

value: 6y, when sample taken

value: M

value: Bacteremia/Suppurative arthritis

value: Clindamycin/Rifampin

value: S. aureus, MRSA


title: PBMC_S.aureus_MRSA_INF466

value: 0.5y, when sample taken


title: PBMC_S.pneumoniae_INF471

value: 2y, when sample taken

value: F

value: Meningitis/Bacteremia

value: Ceftriaxone/Vancomycin

value: S. pneumoniae


title: PBMC_S.aureus_MSSA_INF472

value: 0.08y, when sample taken

value: Cefazolin


title: SW48

city: San Francisco

first: Antoine

last: Snijders

state: CA

address: 2340 Sutter Street

department: Cancer Research Institute

institute: University of California San Francisco

description: MMR deficient cell line SW48.txt

hyb_protocol: We combined and precipitated 50 ml Cy3 labeled test DNA, 50 ml Cy5 labeled reference DNA and 100 mg human Cot-1 DNA by adding 0.1 volumes of 3 M sodium acetate (pH 5.2) and 2 volumes of ice-cold ethanol. We collected the precipitate by centrifugation and dissolved the pellet in a final hybridization mixture containing 50% formamide, 2xSSC and 4% SDS. We denatured the hybridization mixture at 75°C for 10-15 min and then incubated the samples at 37°C for 1 hour to block repetitive DNA sequences. We applied a ring of rubber cement closely around the array to form a well, into which we added 50 ml of a pre-incubation solution containing 250 mg salmon sperm DNA, 50% formamide, 2xSSC and 4% SDS.  After a 30 min incubation at room temperature, we removed ~30 ml of the pre-incubation solution and added the denatured and re-annealed hybridization mixture.  We placed a silicone gasket around each hybridization area, placed a microscope slide on top of the gasket, which was thick enough to prevent the microscope slide from contacting the hybridization solution and clamped the whole unit together using binder clips to create an air tight environment.  We carried out the hybridization to the arrays for ~48 hrs on a slowly rocking table at 37°C.  After disassembling the hybridization chamber, we rinsed off the excess hybridization fluid with PN buffer (PN: 0.1 M sodium phosphate, 0.1% nonidet P40, pH 8), then washed the arrays once in a solution containing 50% formamide in 2xSSC for 15 min. at 45°C and finally in PN buffer at room temperature for 15 min.  Subsequently, we removed the ring of rubber cement, drained excess liquid from the arrays, mounted them in a solution containing 90% glycerol, 10% PBS and 1 mM DAPI, and sealed them with a cover slip.

scan_protocol: We acquired 16 bit 1024x1024 pixel DAPI, Cy3 and Cy5 images using a custom built CCD camera system We used “UCSF SPOT” software to automatically segment the spots based on the DAPI images, perform local background correction and to calculate various measurement parameters, including log2ratios of the total integrated Cy3 and Cy5 intensities for each spot.  We used a second custom program SPROC to associate clone identities and a mapping information file with each spot so that the data could be plotted relative to the position of the BACs on the August, 2001 freeze of the draft human genome sequence (http://genome.ucsc.edu).

data_processing: SPROC also implements a filtering procedure to reject data based on a number of criteria, including low reference/DAPI signal intensity and low correlation of the Cy3 and Cy5 intensities with a spot.  The SPROC output consists of averaged ratios of the triplicate spots for each clone, standard deviations of the triplicates and plotting position for each clone on the array, as well as other clone information stored in the database, such as STS content.  We edited the data files to remove ratios on clones for which only one of the triplicates remained after SPROC analysis and/or the standard deviation of the log2ratios of the triplicates was > 0.2.

source_name: Genomic DNA from MMR deficient SW48 cell line labeled with Cyanine-3

label_protocol: We labeled genomic DNA by random priming in a 50 ml reaction by combining 300 ng genomic DNA, 1x random primers solution (BioPrime DNA Labeling System, Gibco BRL), 1x dNTP solution (0.2 mM each of dATP, dTTP, dGTP, 0.05 mM dCTP, 1 mM Tris base (pH 7.6), 0.1 mM EDTA), 40 mM Cy3 or Cy5-dCTP (Amersham) and 40 U Klenow fragment (BioPrime DNA Labeling System, Gibco BRL).  We incubated the DNA and the random primers in a volume of 42 ml at 100°C for 10-15 min, placed the reaction on ice and added the dNTP solution, labeled nucleotides and Klenow fragment. We incubated the random priming reaction overnight at 37°C. We removed unincorporated nucleotides using a Sephadex spin-column.

extract_protocol: We incubated cells from a T75 flask overnight at 55°C in a 3 ml solution containing 0.01 M Tris, pH 7.5, 0.001 M EDTA, pH 8, 0.5% SDS and 0.1 mg/ml proteinase K. We precipitated the DNA with ethanol, recovered it by spooling and then dissolved it in ~300 ml H2O.

tag: cell line DNA

source_name: Genomic DNA isolated from blood

tag: genomic DNA from blood


title: HCT116+chr3_UNTREATED

description: Untreated MMR proficient HCT116+chr3 cell line

source_name: Genomic DNA from MMR proficient HCT116+chr3 cell line labeled with Cyanine-3


title: SKUT1

description: MMR deficient cell line SKUT1.txt

source_name: Genomic DNA from MMR deficient SKUT1 cell line labeled with Cyanine-3


title: DU145

description: MMR deficient cell line DU145.txt

source_name: Genomic DNA from MMR deficient DU145 cell line labeled with Cyanine-3


title: JURKAT

description: MMR deficient cell line JURKAT.txt

source_name: Genomic DNA from MMR deficient JURKAT cell line labeled with Cyanine-3


title: HCT116_I7

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_I7

source_name: Genomic DNA from MMR deficient HCT116 cell line labeled with Cyanine-3


title: PBMC_InfluenzaB_INF320

tag: Age

value: 0.04y, when sample taken

value: Hispanic

value: Fever/URI Sxs

tag: Treatment

value: Ampicillin/Gentamicin

value: Influenza B


title: PBMC_InfluenzaA_INF556

value: 3 1/2y, when sample taken

value: Caucasian

value: Fever/Seizure

value: Ceftriaxone/Oseltamivir

value: Influenza A


title: SKOV3

description: MMR deficient cell line SKOV3.txt

source_name: Genomic DNA from MMR deficient SKOV3 cell line labeled with Cyanine-3


title: DLD1

description: MMR deficient cell line DLD1.txt

source_name: Genomic DNA from MMR deficient DLD1 cell line labeled with Cyanine-3


title: HCT116_B2

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_B2


title: HCT116_Q2

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_Q2


title: LoVo

description: MMR deficient cell line LoVo.txt

source_name: Genomic DNA from MMR deficient LOVO cell line labeled with Cyanine-3


title: PBMC_S.aureus_MSSA_INF459

value: 10y, when sample taken

value: Osteoarthritis/Suppurative arthritis

value: Oxacillin/Rifampin

value: S. aureus, MSSA


title: PBMC_InfluenzaB_INF311

value: 0.1y, when sample taken

value: M

value: Ampicillin/Ceftriaxone


title: PBMC_S.aureus_MRSA_INF465

value: 13y, when sample taken

value: Vancomycin

value: S. aureus, MRSA


title: HCT116_I2

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_I2


title: LS174T

description: MMR deficient cell line LS174T.txt

source_name: Genomic DNA from MMR deficient LS174T cell line labeled with Cyanine-3


title: HCT116_O1

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_O1


title: HCT116_O3

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_O3


title: PBMC_S.pneumoniae_INF473

value: 2.5y, when sample taken

value: Hispanic

value: Pneumonia/Bacteremia

value: Ceftriaxone

value: S. pneumoniae


title: PBMC_S.aureus_MRSA_INF458

source_name: PBMC_S. aureus

value: 12y, when sample taken

value: Black

value: Disseminated

value: Vancomycin/Rifampin/Linezolid


title: HCT116_O4

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_O4


title: AN3CA

description: MMR deficient cell line AN3CA.txt

source_name: Genomic DNA from MMR deficient AN3CA cell line labeled with Cyanine-3


title: HCT116_CL10

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_CL10.txt


title: HCT116_+chr3_R1

description: Methotrexate treated MMR proficient HCT116+chr3 cell line HCT116_+chr3_R1


title: HCT116_O5

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_O5


title: HCT116_CL5

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_CL5.txt


title: HCT116_+chr3_R2

description: Methotrexate treated MMR proficient HCT116+chr3 cell line HCT116_+chr3_R2


title: HCT116_CL4

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_CL4.txt


title: HCT116_+chr3_M3

description: Methotrexate treated MMR proficient HCT116+chr3 cell line HCT116_+chr3_M3


title: HCT116_CL9

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_CL9.txt


title: HCT116_CL1

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_CL1.txt


title: HCT116_+chr3_P2

description: Methotrexate treated MMR proficient HCT116+chr3 cell line HCT116_+chr3_P2


title: HCT116_+chr3_K1

description: Methotrexate treated MMR proficient HCT116+chr3 cell line HCT116_+chr3_K1


title: HCT116_CL8

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_CL8.txt


title: HCT116_CL3

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_CL3.txt


title: HCT116_CL2

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_CL2.txt


title: HCT116_CL7

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_CL7.txt


title: HCT116_C3

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_C3.txt


title: HCT116_B8

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_B8.txt


title: HCT116_+chr3_L1

description: Methotrexate treated MMR proficient HCT116+chr3 cell line HCT116_+chr3_L1


title: HCT116_+chr3_M1

description: Methotrexate treated MMR proficient HCT116+chr3 cell line HCT116_+chr3_M1


title: HCT116_+chr3_E2

description: Methotrexate treated MMR proficient HCT116+chr3 cell line HCT116_+chr3_E2


title: HCT116_+chr3_M2

description: Methotrexate treated MMR proficient HCT116+chr3 cell line HCT116_+chr3_M2


title: HCT116_C6

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_C6.txt


title: HCT116_B6

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_B6.txt


title: HCT116_CL6

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_CL6.txt


title: HCT116_B3

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_B3.txt


title: HCT116_A11

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_A11.txt


title: HCT116_A10

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_A10.txt


title: HCT116_+chr3_E3

description: Methotrexate treated MMR proficient HCT116+chr3 cell line HCT116_+chr3_E3


title: HCT116_+chr3_E1

description: Methotrexate treated MMR proficient HCT116+chr3 cell line HCT116_+chr3_E1


title: HCT116_A5

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_A5.txt


title: HCT116_A3

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_A3.txt


title: HCT116_CL11

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_CL11.txt


title: granule neuron precursors infected with retroviruses that express N-myc; array A

status: Public on Mar 15 2007

city: Memphis

first: Chunxu

last: Qu

state: TN

address: 262 Danny Thomas Pl

department: Pathology

institute: St Jude Children's Research Institute

description: Gene expression data from mouse brain infected with GNPs infected with retroviruses that express N-myc

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Mus musculus Genome Array MOE430. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GCS 3000

source_name: cerebellum

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

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

tag: Genotype


title: HCT116+chr3_E4

description: Methotrexate treated MMR proficient HCT116+chr3 cell line HCT116+chr3_E4


title: HCT116+chr2

description: Untreated HCT116+chr2 cell line

source_name: Genomic DNA from HCT116+chr2 cell line labeled with Cyanine-3


title: NY1DD Sickle Cell Mouse brains, NLX treated, 10mins. SCNLX-I 817

status: Public on Mar 14 2007

city: Minneapolis

first: Ajay

last: Yekkirala

state: MN

address: 308 Harvard St 8-120

institute: University of Minnesota

description: All info provided.

hyb_protocol: 1) Resuspend dried labeled cDNAs in 7.8ul water 2) Add remaining reagents for Hyb cocktail and mix by pipetting. 3) Heat the probe preparation at 95-100 degrees for 2 minutes. Boiling denatures the sample and makes it accessible for hybridization. 4) Snap cool on ice for 1-3 minutes. 5) Pulse the tubes in the centrifuge to pull down condensation 6) Clean lifterslips with soap and water, then Acetone and dry with Kimwipes. Make sure there are no debris on the array before laying down lifterslip. Place lifterslip on array using either fingers or forceps with dull white strips touching the glass. This creates a platform which allows even distribution of the hybridization solution across the array. Slowly pipette the probe under one corner of the slip until the entire array surface is covered. 7) Put 10-20ul 3XSSC at each little divot at the ends of the Hyb chamber. This is to ensure a constant humidity in the chamber during hybridizations. If the 3XSSC is not applied, the array will dry out. 8) Tightly screw down lid of Hyb chamber and carefully place in incubator. Take caution to keep array completely flat during transfer and hybridizations. 9) Allow hybridization to run for at least 5 hours but not more than 16 hours, in the dark at 42C.

scan_protocol: 1) Prepare wash solutions in glass slide dishes 2) Carefully remove array from incubator or water bath, making sure to keep chamber level. Unscrew chamber and remove array. 3) Keep array level and submerge in 2XSSC to get the lifterslip to fall off. Once submerged tilt array and gently dump off coverslip. It may be necessary to lightly swish array under solution to dislodge the slip. 4) Once slip is off and lying on bottom of slide dish, put array in a slide rack and transfer to the first wash solution. Do not allow the chips to dry out at any point during the washes. 5) Wash hybs. a) 2X SSC, 0.1% SDS (4ml 10%SDS per 400ml) at 37 or 550C for 3 minutes with no agitation b) 2X SSC, RT Let sit 3 minutes in solution then dip up and down 10 times. c) 0.2X SSC RT Let sit 3 minutes in solution then dip up and down 10 times 6) Immediately dry array in room temperature table top centrifuge at 500 rpm for 6 min.

data_processing: Scanned image was processed using the GenePix Pro (Axon Laboratories) software and RAW values were calculated. The data was then updated in the GeneSpring Software (Agilent Tech.) and lowess normalizations were used on all the raw data.

label_protocol: SuperScript Direct labeling system (Invitogen, Cat#: L1015-01) was used and manufacturer's protocol was followed.

extract_protocol:
1) Homogenize brain in 500 microL of TRIzol in a 1.5mL tube with a pestle. Dilute with 500microL.
2)Incubate for 5 mins at RT.
3) Add 200 microL chloroform and vortex. Incubate for 2-3mins and centrifuge at 12000 x g for 15 mins.
4) Transfer upper aqueous portion to a clean tube and precipitate RNA byadding 500 microL of isopropanol. Incubate for 10 mins at RT and centrifuge at 12000 x g for 15 mins.
5) Wash pellet in 75% EtOH and dry pellet for 5-10 mins.
6) Dissolve RNA in 40 microL RNase free water.

tag: Strain:NY1DD Sickle Cell Mice

value: Male

value: 9 wks

tag: Drug

value: Naloxone for 10 mins.

source_name: NY1DD Sickle Cell Mouse brains, Saline treated, 10 mins.

value: Saline for 10 mins.


title: HCT116_+chr3_K5

description: Methotrexate treated MMR proficient HCT116+chr3 cell line HCT116_+chr3_K5


title: granule neuron precursors infected with retroviruses that express N-myc; array B


title: granule neuron precursors, biological replicate 3; array B

description: Gene expression data from purified granule neuron precursors.

source_name: cerebellum of six days old pups


title: granule neuron precursors infected with retroviruses that express Cyclin D1; array A

description: Gene expression data from mouse brain infected with GNPs infected with retroviruses that express Cyclin D1


title: granule neuron precursors, biological replicate 1; array B


title: C57BL/6J wild-type mouse brains, NLX treated, 10mins. 915 WTNLX 1

description: All info provided.

tag: Strain:C57BL/6J Mice

source_name: C57BL/6J wild-type mouse brains, saline treated, 10mins.

tag: Strain:C57BL/6J wild-type mice


title: NY1DD Sickle Cell Mouse brains, NLX treated, 10mins. 825 SCNLX3

description: All info provided.

tag: Gender

source_name: NY1DD Sickle Cell Mouse brains, saline treated control, 10mins.


title: granule neuron precursors, biological replicate 3; array A


title: ns1-R mutant vs wild-type (ns-wt-SAM3-high-rep3)

city: Ithaca

first: Michael

middle: J

last: Scanlon

state: NY

address: 140 Emerson Hall

department: Department of Plant Biology

institute: Cornell University

description: Biological replicate 3 of 6.

hyb_protocol: Fluorescent targets were hybridized as described in the “cDNA microarray protocol” file at Schnable Lab website at Iowa State University.

scan_protocol: Scanned on an ScanArray 5000™  scanner. Images were quantified using Digital Genome™ software

data_processing: LOWESS normalized, followed by median centering so that expression measures would be comparable across slides. The lowess normalized data from each scan was used for a mixed linear model analysis (Wolfinger et al., 2001).

organism: Zea mays

source_name: RNA from ns1-R

label_protocol: 2µg of amplified RNA were indirectly labeled by amino allyl incorporation as described (Nakazono et al, 2003).  To remove dye bias, Cy dyes were swapped between the RNA samples

growth_protocol: Maize seedlings of the highly introgressed ns 1:1 line (segregation ratio at 50% ns1-R and 50% nonmutant) were grown under the same controlled condition and harvested for laser microdissection at two weeks after germination.

extract_protocol: Total RNA were extracted using the PicoPure™ RNA extraction kit, and two rounds of RNA amplification were performed using T7-RNA polymerase as described (Nakozano et al., 2003) with changes described in Moll et al., 2004.

tag: scan with high laser power and PMT gain settings

source_name: RNA from nonmutant


title: granule neuron precursors, biological replicate 2; array A


title: ns1-R mutant vs wild-type (ns-wt-SAM3-high-rep2)

description: Biological replicate 2 of 6.


title: granule neuron precursors, biological replicate 1; array A


title: HCT116_UNTREATED

description: Untreated MMR deficient HCT116 cell line

source_name: Genomic DNA isolated from blood


title: ns1-R mutant vs wild-type (ns-wt-SAM3-high-rep5)

description: Biological replicate 5 of 6.


title: ns1-R mutant vs wild-type (ns-wt-SAM3-high-rep4)

description: Biological replicate 4 of 6.


title: NY1DD Sickle Cell Mouse brains, NLX treated, 10mins. 819 SCNLX2

description: All info provided.

source_name: NY1DD Sickle Cell Mouse brains, Saline treated control, 10mins.


title: ns1-R mutant vs wild-type (ns-wt-SAM3-high-rep6)

description: Biological replicate 6 of 6.


title: C57BL/6J wild-type mouse brains, NLX treated, 10mins. 915 WTNLX 2

description: All info provided.


title: granule neuron precursors infected with retroviruses that express Cyclin D1; array B


title: C57BL/6J wild-type mouse brains, NLX treated, 10mins. 921 WTNLX 3

description: All info provided.


title: ns1-R mutant vs wild-type (ns-wt-SAM3-high-rep1)

description: Biological replicate 1 of 6.


title: ns1-R mutant vs wild-type (ns-wt-SAM3-mid-rep4)

description: Biological replicate 4 of 6.

tag: scan with median laser power and PMT gain settings


title: ns1-R mutant vs wild-type (ns-wt-SAM3-mid-rep5)

description: Biological replicate 5 of 6.


title: ns1-R mutant vs wild-type (ns-wt-SAM3-mid-rep6)

description: Biological replicate 6 of 6.


title: ns1-R mutant vs wild-type (ns-wt-SAM3-low-rep6)

description: Biological replicate 6 of 6.

tag: scan with low laser power and PMT gain settings


title: ns1-R mutant vs wild-type (ns-wt-SAM3-mid-rep1)

description: Biological replicate 1 of 6.


title: ns1-R mutant vs wild-type (ns-wt-SAM3-mid-rep3)

description: Biological replicate 3 of 6.


title: ns1-R mutant vs wild-type (ns-wt-SAM3-low-rep3)

description: Biological replicate 3 of 6.


title: ns1-R mutant vs wild-type (ns-wt-SAM3-low-rep4)

description: Biological replicate 4 of 6.


title: ns1-R mutant vs wild-type (ns-wt-SAM3-low-rep2)

description: Biological replicate 2 of 6.


title: granule neuron precursors, biological replicate 2; array B


title: ns1-R mutant vs wild-type (ns-wt-SAM3-low-rep1)

description: Biological replicate 1 of 6.


title: ns1-R mutant vs wild-type (ns-wt-sam1-rep5)

description: Biological replicate 5 of 6.


title: ns1-R mutant vs wild-type (ns-wt-SAM3-low-rep5)

description: Biological replicate 5 of 6.


title: ns1-R mutant vs wild-type (ns-wt-sam1-rep2)

description: Biological replicate 2 of 6.


title: ns1-R mutant vs wild-type (ns-wt-SAM2-rep4)

description: Biological replicate 4 of 6.


title: ns1-R mutant vs wild-type (ns-wt-SAM2-rep5)

description: Biological replicate 5 of 6.


title: ns1-R mutant vs wild-type (ns-wt-sam1-rep6)

description: Biological replicate 6 of 6.


title: ns1-R mutant vs wild-type (ns-wt-sam1-rep1)

description: Biological replicate 1 of 6.


title: ns1-R mutant vs wild-type (ns-wt-sam1-rep3)

description: Biological replicate 3 of 6.


title: ns1-R mutant vs wild-type (ns-wt-SAM2-rep3)

description: Biological replicate 3 of 6.


title: ns1-R mutant vs wild-type (ns-wt-SAM2-rep1)

description: Biological replicate 1 of 6.


title: RDV_3

city: Tsukuba

first: Takumi

last: SHIMIZU

address: Kannondai 3-1-1

institute: National Agricultural Research Center

description:
Keyword : Oryza sativa
Keyword : Rice Dwarf virus

hyb_protocol: Kit : in situ hybridization kit plus Manufacture : Agilent Technologies

scan_protocol: Scanner : Agilent DNA microarray scanner Manufacture: Agilent Technologies

data_processing: Feature Extraction ver 8.1.1.1 (Agilent Technologies)

organism: Oryza sativa

label_protocol:
kit : Low input RNA linear amplification kit
Manufacture : Agilent Technologies

growth_protocol: Ten rice seeds (Oryza sativa L. cv. Nipponbare) were sown in a pot that has been filled with a commercial soil mixture (Bonsol; Sumitomo Chemical, Osaka, Japan). The pot was then submerged in water inside a container and was kept in a growth chamber at 25?3?C under natural sunlight for 9 days.

extract_protocol:
kit : RNeasy maxi kit
Manufacture : Qiagen

treatment_protocol: Nine-day-old rice seedlings were exposed to approximately fifty virus-free insects (leafhoppers)

tag: cultivar

value: Nipponbare

value: 18 days

tag: Tissue

value: shoot

treatment_protocol: Nine-day-old rice seedlings were exposed to approximately fifty viruliferous insects (leafhoppers)


title: ns1-R mutant vs wild-type (ns-wt-sam1-rep4)

description: Biological replicate 4 of 6.


title: RDV_4


title: RDV_2


title: ns1-R mutant vs wild-type (ns-wt-SAM2-rep2)

description: Biological replicate 2 of 6.


title: HCT116_Q1

description: Methotrexate treated MMR deficient HCT116 cell line HCT116_Q1

source_name: Genomic DNA from MMR deficient HCT116 cell line labeled with Cyanine-3


title: IgM FO B cells HEL-stimulated exp2

status: Public on Mar 13 2007

city: Acton

first: Keisuke

last: Horikawa

state: ACT

address: Garran Rd

department: DIG

institute: JCSMR, ANU

description: 1 sort, total 2 mice

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: MAS 5.0, scaled to 150

label: Biotin followed by streptavidin-PE

source_name: FO B cells

label_protocol: Affymetrix protocol

extract_protocol: Trizol

tag: CD21medCD23hi B cells were sorted from anti-HEL IgM:RAG2KO:H2KK B10.BR mice 1 hr after HEL injection (5 mg/head, ip).


title: ns1-R mutant vs wild-type (ns-wt-SAM2-rep6)

description: Biological replicate 6 of 6.


title: IgM FO B cells unstimulated exp2

description: 2 separate sorts, total 4 mice

tag: CD21medCD23hi B cells were sorted from anti-HEL IgM:RAG2KO:H2KK B10.BR mice.


title: IgMG FO B cells unstimulated exp2

description: 2 separate sorts, total 6 mice

tag: CD21medCD23hi B cells were sorted from anti-HEL IgMG:RAG2KO:H2KK B10.BR mice.


title: ns1-R mutant vs wild-type (ns-wt-SAM3-mid-rep2)

description: Biological replicate 2 of 6.


title: IgM FO B cells unstimulated exp1

description: 1 sort, total 2 mice


title: IgMG FO B cells HEL-stimulated exp1

description: 3 separate sorts, total 8 mice

tag: CD21medCD23hi B cells were sorted from anti-HEL IgMG:RAG2KO:H2KK B10.BR mice 1hr after HEL injection (5 mg/head, ip).


title: IgM FO B cells HEL-stimulated exp1

description: 2 separate sorts, toal 4 mice


title: RDV_1

growth_protocol: Ten rice seeds (Oryza sativa L. cv. Nipponbare) were sown in a pot that has been filled with a commercial soil mixture (Bonsol; Sumitomo Chemical, Osaka, Japan). The pot was then submerged in water inside a container and was kept in a growth chamber at 25±3°C under natural sunlight for 9 days.

tag: Age


title: 9299c_hd

status: Public on Mar 12 2007

city: Vancouver

first: BCGSC

last: BC Cancer Agency

state: BC

address: 675 West 10th Avenue

department: Gene Expression

country: Canada

institute: Canada's Michael Smith Genome Sciences Centre

description: 50K Hind Array data

hyb_protocol: Hybridization, washes and staining were performed as described in the Affymetrix GeneChip® Mapping 100K Assay Manual (www.affymetrix.com). Samples were hybridized to GeneChip® Human Mapping 50K Xba240 or Hind240 arrays in an Affymetrix Hybridization Oven 640. Washes and staining of the arrays were performed with an Affymetrix Fluidics Station 450.

scan_protocol: Array images were obtained using an Affymetrix GeneChip® Scanner 3000, as described in the Affymetrix GeneChip® Mapping 100K Assay Manual (www.affymetrix.com).

data_processing: Mapping algorithm settings: Gtype(dm) heterozygote call threshold= 0.25, homozygote call threshold=0.25

label: Biotin with Streptavidin, R-phycoerythrin conjugate (SAPE).

source_name: Mentally retarded child of unaffected biological parents 9299m (mother) and 9299f (father).

label_protocol: Labeling was performed according to the Affymetrix GeneChip® Mapping 100K Assay Manual (www.affymetrix.com).

extract_protocol: Genomic DNA was isolated from whole blood using the Puregen Gentra® DNA Purification Kit following the manufacturer's protocol.

value: whole blood


title: 9236f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 9236c (child).


title: IgMG FO B cells unstimulated exp1

description: 2 separate sorts, total 5 mice


title: 9236c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 9236m (mother) and 9236f (father).


title: 9923m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 9923c (child).


title: 9923c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 9923m (mother) and 9923f (father).


title: 9299f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 9299c (child).


title: 9042m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 9042c (child).


title: 8939m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 8939c (child).


title: 9143f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 9143c (child).


title: 9962c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 9962m (mother) and 9962f (father).


title: 9962f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 9962c (child).


title: 9042f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 9042c (child).


title: 9263f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 9263c (child).


title: 8939s_hd

description: 50K Hind Array data

source_name: Unaffected sibling of mentally retarded child 8939c (child).


title: 9143c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 9143m (mother) and 9143f (father).


title: 9299m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 9299c (child).


title: 8565s_hd

description: 50K Hind Array data

source_name: Unaffected sibling of mentally retarded child 8565c (child).


title: 9042c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 9042m (mother) and 9042f (father).


title: 9962m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 9962c (child).


title: 8939c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 8939m (mother) and 8939f (father).


title: 8785c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 8785m (mother) and 8785f (father).


title: 9923f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 9923c (child).


title: 9143m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 9143c (child).


title: 9236m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 9236c (child).


title: 9263m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 9263c (child).


title: 9263c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 9263m (mother) and 9263f (father).


title: 8785f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 8785c (child).


title: 8785m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 8785c (child).


title: 8565f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 8565c (child).


title: 8552f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 8552c (child).


title: 8565c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 8565m (mother) and 8565f (father).


title: 8552m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 8552c (child).


title: 8939f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 8939c (child).


title: 8531m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 8531c (child).


title: 8552c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 8552m (mother) and 8552f (father).


title: 8531c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 8531m (mother) and 8531f (father).


title: 8565m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 8565c (child).


title: 7807f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 7807c (child).


title: 8379f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 8379c (child).


title: 8326c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 8326m (mother) and 8326f (father).


title: 7807c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 7807m (mother) and 7807f (father).


title: 8326m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 8326c (child).


title: 8005c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 8005m (mother) and 8005f (father).


title: 7690f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 7690c (child).


title: 8379c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 8379m (mother) and 8379f (father).


title: 8005f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 8005c (child).


title: 8379m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 8379c (child).


title: 7551m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 7551c (child).


title: 8005m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 8005c (child).


title: 8305f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 8305c (child).


title: 8326f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 8326c (child).


title: 8531f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 8531c (child).


title: 7690m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 7690c (child).


title: 7690c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 7690m (mother) and 7690f (father).


title: 7551c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 7551m (mother) and 7551f (father).


title: 7807m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 7807c (child).


title: 7551f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 7551c (child).


title: 7415c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 7415m (mother) and 7415f (father).


title: 7415m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 7415c (child).


title: 7353m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 7353c (child).


title: 7415f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 7415c (child).


title: 7048m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 7048c (child).


title: 7353f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 7353c (child).


title: 7353c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 7353m (mother) and 7353f (father).


title: 7047m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 7047c (child).


title: 7048c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 7048m (mother) and 7048f (father).


title: 6789m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 6789c (child).


title: 7048f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 7048c (child).


title: 6913c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 6913m (mother) and 6913f (father).


title: 6607m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 6607c (child).


title: 7047f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 7047c (child).


title: 6913m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 6913c (child).


title: 6545s_hd

description: 50K Hind Array data

source_name: Unaffected sibling of mentally retarded child 6545c (child).


title: 6545f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 6545c (child).


title: 6913f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 6913c (child).


title: 6607f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 6607c (child).


title: 7047c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 7047m (mother) and 7047f (father).


title: 6434m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 6434c (child).


title: 6434c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 6434m (mother) and 6434f (father).


title: 6789c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 6789m (mother) and 6789f (father).


title: 6607c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 6607m (mother) and 6607f (father).


title: 6789f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 6789c (child).


title: 6545m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 6545c (child).


title: 6434s_hd

description: 50K Hind Array data

source_name: Unaffected sibling of mentally retarded child 6434c (child).


title: 6168f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 6168c (child).


title: 6168m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 6168c (child).


title: 6349m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 6349c (child).


title: 6128c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 6128m (mother) and 6128f (father).


title: 6545c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 6545m (mother) and 6545f (father).


title: 6349f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 6349c (child).


title: 5994m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 5994c (child).


title: 6128m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 6128c (child).


title: 6128f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 6128c (child).


title: 5994f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 5994c (child).


title: 6434f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 6434c (child).


title: 5923c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 5923m (mother) and 5923f (father).


title: 5566f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 5566c (child).


title: 5994c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 5994m (mother) and 5994f (father).


title: 5566m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 5566c (child).


title: 5923f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 5923c (child).


title: 5495f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 5495c (child).


title: 5495m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 5495c (child).


title: 5434m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 5434c (child).


title: 5495c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 5495m (mother) and 5495f (father).


title: 5434f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 5434c (child).


title: 5434c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 5434m (mother) and 5434f (father).


title: 5358f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 5358c (child).


title: 5923m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 5923c (child).


title: 5358m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 5358c (child).


title: 5358c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 5358m (mother) and 5358f (father).


title: 4840c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 4840m (mother) and 4840f (father).


title: 6168c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 6168m (mother) and 6168f (father).


title: 5202m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 5202c (child).


title: 5003m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 5003c (child).


title: 4840f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 4840c (child).


title: 5566c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 5566m (mother) and 5566f (father).


title: 4818f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 4818c (child).


title: 5003f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 5003c (child).


title: 5202f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 5202c (child).


title: 5202c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 5202m (mother) and 5202f (father).


title: 4794c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 4794m (mother) and 4794f (father).


title: 5003c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 5003m (mother) and 5003f (father).


title: 4818m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 4818c (child).


title: 4840m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 4840c (child).


title: 4794m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 4794c (child).


title: 4535c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 4535m (mother) and 4535f (father).


title: 4794f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 4794c (child).


title: 4484m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 4484c (child).


title: 4818c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 4818m (mother) and 4818f (father).


title: 4462c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 4462m (mother) and 4462f (father).


title: 4395f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 4395c (child).


title: 4484f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 4484c (child).


title: 4484c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 4484m (mother) and 4484f (father).


title: 4357m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 4357c (child).


title: 4395m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 4395c (child).


title: 4535m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 4535c (child).


title: 4462f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 4462c (child).


title: 4395c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 4395m (mother) and 4395f (father).


title: 4357c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 4357m (mother) and 4357f (father).


title: 4268c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 4268m (mother) and 4268f (father).


title: 4287f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 4287c (child).


title: 4268m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 4268c (child).


title: 4535f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 4535c (child).


title: 4287c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 4287m (mother) and 4287f (father).


title: 4287m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 4287c (child).


title: 4246c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 4246m (mother) and 4246f (father).


title: 4268f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 4268c (child).


title: 4246f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 4246c (child).


title: 3890f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 3890c (child).


title: 3890c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 3890m (mother) and 3890f (father).


title: 3811m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 3811c (child).


title: 3811s_hd

description: 50K Hind Array data

source_name: Unaffected sibling of mentally retarded child 3811c (child).


title: 3923m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 3923c (child).


title: 3923f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 3923c (child).


title: 3855c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 3855m (mother) and 3855f (father).


title: 4246m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 4246c (child).


title: 3811f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 3811c (child).


title: 3595c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 3595m (mother) and 3595f (father).


title: 3717f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 3717c (child).


title: 3588f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 3588c (child).


title: 3553c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 3553m (mother) and 3553f (father).


title: 3595m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 3595c (child).


title: 3595f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 3595c (child).


title: 3553f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 3553c (child).


title: 3811c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 3811m (mother) and 3811f (father).


title: 3855f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 3855c (child).


title: 3588m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 3588c (child).


title: 3890m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 3890c (child).


title: 3588c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 3588m (mother) and 3588f (father).


title: 3553m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 3553c (child).


title: 3476m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 3476c (child).


title: 3476f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 3476c (child).


title: 3855m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 3855c (child).


title: 3717c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 3717m (mother) and 3717f (father).


title: 3717m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 3717c (child).


title: 3923c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 3923m (mother) and 3923f (father).


title: 3202m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 3202c (child).


title: 3202f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 3202c (child).


title: 3025s_hd

description: 50K Hind Array data

source_name: Unaffected sibling of mentally retarded child 3025c (child).


title: 3153f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 3153c (child).


title: 3202c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 3202m (mother) and 3202f (father).


title: 3476c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 3476m (mother) and 3476f (father).


title: 2926m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 2926c (child).


title: 3153m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 3153c (child).


title: 3025f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 3025c (child).


title: 3153c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 3153m (mother) and 3153f (father).


title: 2890m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 2890c (child).


title: 3025c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 3025m (mother) and 3025f (father).


title: 2806f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 2806c (child).


title: 2926c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 2926m (mother) and 2926f (father).


title: 3025m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 3025c (child).


title: 2711m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 2711c (child).


title: 2806m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 2806c (child).


title: 2926f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 2926c (child).


title: 2890c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 2890m (mother) and 2890f (father).


title: 2472m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 2472c (child).


title: 2738m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 2738c (child).


title: 2890f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 2890c (child).


title: 2738f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 2738c (child).


title: 2806c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 2806m (mother) and 2806f (father).


title: 2738c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 2738m (mother) and 2738f (father).


title: 2472c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 2472m (mother) and 2472f (father).


title: 2346m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 2346c (child).


title: 1895m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 1895c (child).


title: 1978f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 1978c (child).


title: 1978m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 1978c (child).


title: 2135c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 2135m (mother) and 2135f (father).


title: 1895f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 1895c (child).


title: 2346c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 2346m (mother) and 2346f (father).


title: 2711f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 2711c (child).


title: 2472f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 2472c (child).


title: 2711c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 2711m (mother) and 2711f (father).


title: 1978c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 1978m (mother) and 1978f (father).


title: 1889f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 1889c (child).


title: 1895c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 1895m (mother) and 1895f (father).


title: 2346f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 2346c (child).


title: 1765f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 1765c (child).


title: 1605m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 1605c (child).


title: 1889m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 1889c (child).


title: 1538m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 1538c (child).


title: 1605f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 1605c (child).


title: 1605c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 1605m (mother) and 1605f (father).


title: 1523c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 1523m (mother) and 1523f (father).


title: 1608m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 1608c (child).


title: 1889c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 1889m (mother) and 1889f (father).


title: 1765c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 1765m (mother) and 1765f (father).


title: 1523f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 1523c (child).


title: 1467m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 1467c (child).


title: 1523m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 1523c (child).


title: 1538f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 1538c (child).


title: 1492c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 1492m (mother) and 1492f (father).


title: 1360m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 1360c (child).


title: 1492m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 1492c (child).


title: 1538c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 1538m (mother) and 1538f (father).


title: 1608f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 1608c (child).


title: 1467f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 1467c (child).


title: 1492f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 1492c (child).


title: 1360f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 1360c (child).


title: 1360c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 1360m (mother) and 1360f (father).


title: 1765s_hd

description: 50K Hind Array data

source_name: Unaffected sibling of mentally retarded child 1765c (child).


title: 1608c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 1608m (mother) and 1608f (father).


title: 1252m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 1252c (child).


title: 1280m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 1280c (child).


title: 1252f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 1252c (child).


title: 1280c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 1280m (mother) and 1280f (father).


title: 1252c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 1252m (mother) and 1252f (father).


title: 1234c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 1234m (mother) and 1234f (father).


title: 1234m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 1234c (child).


title: 1467c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 1467m (mother) and 1467f (father).


title: 1097m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 1097c (child).


title: 1097f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 1097c (child).


title: 1234f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 1234c (child).


title: 0899c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 0899m (mother) and 0899f (father).


title: 1014c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 1014m (mother) and 1014f (father).


title: 0899f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 0899c (child).


title: 1014m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 1014c (child).


title: 0674m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 0674c (child).


title: 1097c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 1097m (mother) and 1097f (father).


title: 0866m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 0866c (child).


title: 1014f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 1014c (child).


title: 0866f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 0866c (child).


title: 0866c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 0866m (mother) and 0866f (father).


title: 0674f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 0674c (child).


title: 0674c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 0674m (mother) and 0674f (father).


title: 0899m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 0899c (child).


title: 1280f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 1280c (child).


title: 0674s_hd

description: 50K Hind Array data

source_name: Unaffected sibling of mentally retarded child 0674c (child).


title: 0517c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 0517m (mother) and 0517f (father).


title: 0491m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 0491c (child).


title: 0621c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 0621m (mother) and 0621f (father).


title: 0648f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 0648c (child).


title: 0648c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 0648m (mother) and 0648f (father).


title: 0621f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 0621c (child).


title: 0648m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 0648c (child).


title: 0491f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 0491c (child).


title: 0517f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 0517c (child).


title: 0491c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 0491m (mother) and 0491f (father).


title: 0451m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 0451c (child).


title: 0421c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 0421m (mother) and 0421f (father).


title: 0451f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 0451c (child).


title: 0621m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 0621c (child).


title: 0421m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 0421c (child).


title: 0395c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 0395m (mother) and 0395f (father).


title: 0421f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 0421c (child).


title: 0517m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 0517c (child).


title: 0392f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 0392c (child).


title: 0395m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 0395c (child).


title: 0392c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 0392m (mother) and 0392f (father).


title: 0392s_hd

description: 50K Hind Array data

source_name: Unaffected sibling of mentally retarded child 0392c (child).


title: 0167m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 0167c (child).


title: 0231m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 0231c (child).


title: 0231c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 0231m (mother) and 0231f (father).


title: 0337m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 0337c (child).


title: 0337f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 0337c (child).


title: 0231f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 0231c (child).


title: 0337c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 0337m (mother) and 0337f (father).


title: 0392m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 0392c (child).


title: 0162f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 0162c (child).


title: 0167f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 0167c (child).


title: 0162c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 0162m (mother) and 0162f (father).


title: 0134c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 0134m (mother) and 0134f (father).


title: 0091f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 0091c (child).


title: 0091s_hd

description: 50K Hind Array data

source_name: Unaffected sibling of mentally retarded child 0091c (child).


title: 0134f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 0134c (child).


title: 1765m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 1765c (child).


title: 0091c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 0091m (mother) and 0091f (father).


title: 9962m_xb

description: 50K Xba Array data

source_name: Unaffected biological mother of mentally retarded child 9962c (child).


title: 9923f_xb

description: 50K Xba Array data

source_name: Unaffected biological father of mentally retarded child 9923c (child).


title: 0162m_hd

description: 50K Hind Array data

source_name: Unaffected biological mother of mentally retarded child 0162c (child).


title: 9299m_xb

description: 50K Xba Array data

source_name: Unaffected biological mother of mentally retarded child 9299c (child).


title: 0395f_hd

description: 50K Hind Array data

source_name: Unaffected biological father of mentally retarded child 0395c (child).


title: 9923m_xb

description: 50K Xba Array data

source_name: Unaffected biological mother of mentally retarded child 9923c (child).


title: 0451c_hd

description: 50K Hind Array data

source_name: Mentally retarded child of unaffected biological parents 0451m (mother) and 0451f (father).


title: 9962c_xb

description: 50K Xba Array data

source_name: Mentally retarded child of unaffected biological parents 9962m (mother) and 9962f (father).


title: 9923c_xb

description: 50K Xba Array data

source_name: Mentally retarded child of unaffected biological parents 9923m (mother) and 9923f (father).