title: p4_06s038b_20070907CRrough

city: Portland

first: Suzy

last: Renn

state: OR

address: 3203 SE Woodstock Blvd

institute: Reed College

description: Cy3= Astatotilapia tweddlei genomic DNA  Cy5= Astatotilapia burtoni genomic DNA hybed by CRL Reilly in 2007

hyb_protocol: The samples were combined with hybridization buffer (3.4X SSC, 0.15% SDS, 1 mM DTT, Cot-1DNA) and hybridized to the microarray at 67.5°C

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=810_770 ScanPower=100_100

data_processing: After removing ""flagged"" and bad spots, only those spots were used whose average intensity was at least two standard deviations above the average background. Arrays were background corrected (method minimal) and normalized in R/Bioconductor with within-arrays loess (using a set of 250 conserved genes) and intensity ratios were calculated.

organism: Haplochromis tweddlei

source_name: Astatotilapia tweddlei

label_protocol: dCTP incorporation with Klenow

growth_protocol: field collections

extract_protocol: ProteinaseK/Phenol Extraction

tag: test

value: Astatotilapia tweddlei

organism: Haplochromis burtoni

source_name: Astatotilapia burtoni

growth_protocol: standard captivity

value: Astatotilapia burtoni


title: wt strain, pGraL, biological rep3, short term

status: Public on Dec 09 2009

type: RNA

city: Bethesda

first: Katarzyna

last: Potrykus

state: MD

address: 6 Center Drive, 6B rm 316

department: NICHD

country: USA

institute: NIH

description: Gene expression data from cells at OD~ 0.5

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on E. coli 2.0 arrays (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Mini_prok2v1_450 protocol.

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

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

label: biotin

molecule: total RNA

organism: Escherichia coli

source_name: E.coli wt cells overexpressing GraL for 15 minutes

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Prokaryotic Traget Preparation in Affymetrix GeneChip® Expression Analysis Technical Manual).

growth_protocol: E.coli cells were grown in LB at 37C, with vigorous shaking

extract_protocol: 5 OD units were removed from the culture and immediately added to an equal volume of ice-cold RNAlater reagent (Ambion). Thus treated samples were stored for 20min on ice. Total RNA was extracted with Trizol reagent (Invitrogen) following manufacturer's instructions.

treatment_protocol: At OD~0.5, GraL overexpression was induced with 1mM IPTG and growth was continued for 15min. The strains emplyed contain lacIq on the chromosome allowing for tight regulation of GraL expression from the plasmid construct.

tag: strain


title: p4_06s035_20070907CR

type: genomic

department: Biology

description: Cy3= Astatotilapia burtoni genomic DNA  Cy5= Rhamphochromis “chilingali” genomic DNA hybed by CRL Reilly in 2007

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=780_730 ScanPower=100_100

molecule: genomic DNA

tag: reference

organism: Rhamphochromis sp. 'chilingali'

source_name: Rhamphochromis “chilingali”

value: Rhamphochromis “chilingali”


title: p4_06s033c_20070907CR

description: Cy3= Astatotilapia burtoni genomic DNA  Cy5= Metriaclima estherae genomic DNA hybed by CRL Reilly in 2007

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=810_790 ScanPower=100_100

organism: Maylandia estherae

source_name: Metriaclima estherae

value: Metriaclima estherae


title: wt strain, pGraL, biological rep2, short term


title: Cythera ES 2

city: La Jolla

first: Alysson

middle: R

last: Muotri

state: CA

address: 9500 Gilman Drive

department: Pediatrics/CMM

institute: University of California San Diego

description: Gene expression data

hyb_protocol: according to Affymetrix protocol

scan_protocol: according to Affymetrix protocol

data_processing: Human Gene U133_2 arrays were analyzed by using affymetrix power tools (apt-probeset-summarize -a rma-sketch -a plier-mm-sketch -d ../../Human/CD_HG-U133_Pl  us_2_Libfiles/HG-U133_Plus_2.cdf -o gene-level-output CM0811101A.CEL CM0811101B.CEL CM0811101C.CEL CM0811102A.CEL CM08111  02B.CEL CM0811102C.CEL CM081110CA.CEL CM081110CB.CEL CM081110CC.CEL CM081110HA.CEL CM081110HB.CEL CM081110HC.CEL CM081110  RA.CEL CM081110RB.CEL CM081110RC.CEL )

organism: Homo sapiens

source_name: Cythera ES

label_protocol: according to Affymetrix protocol

growth_protocol: Human fetal NSCs (ReNCell VM, Chemicon) were cultured on laminin-coated dishes in ReNcell maintenance medium (Chemicon) in the presence of basic fibroblast growth factor 2 (bFGF2), following the manufacturer’s instructions. Human ESC and iPSC were grwon in feeder-free conditions, on matrigel-coated dishes (BD) using mTeSRTM1 .

extract_protocol: Total cellular RNA was extracted from ~5x106 cells using the RNeasy Protect Mini kit (Qiagen, Valencia, CA), according to the manufacturer's instructions, and reverse transcribed using the SuperScript III First-Strand Synthesis System RT-PCR from Invitrogen. The cDNA was amplified by PCR using Accuprime Taq DNA polymerase system (Invitrogene).

treatment_protocol: Cells were collected at 50% confluency. For hESC and hiPSC, we first removed any differentiated cell on the plate by manual microdissociation based on morphology.

tag: cell type

value: Human Embryonic Stem Cells


title: p4_06s032_20070907CR

description: Cy3= Astatotilapia burtoni genomic DNA  Cy5= Protomelas similis genomic DNA hybed by CRL Reilly in 2007

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=770_780 ScanPower=100_100

organism: Protomelas similis

source_name: Protomelas similis

value: Protomelas similis


title: Cythera ES 3

description: Gene expression data


title: HID13 sample 3

city: Nottingham

first: Carey

last: Lambert

state: Notts

address: Queen's Medical Centre

department: Genetics

country: United Kingdom

institute: Nottingham University

description: HID13 sample 3

data_processing: Expression values are generated using quantile normalization (Bolstad et al., 2003, Bioinformatics, 19:185), and Robust Multichip Average (RMA) algorithm (Irizarry et al., 2003, Nucleic Acids Res. 31: e15 and Irizarry et al., 2003, Biostatistics 4:249).

organism: Bdellovibrio bacteriovorus

source_name: Bdellovibrio bacteriovorus HID13 host-independent

extract_protocol: IFR protocol, eluting in 50µl and DNase treating with Ambion DNA-free kit. http://www.ifr.ac.uk/Safety/Microarrays/protocols.html

tag: growth

value: Host-Independent


title: p4_06s034c_20070907CR

description: Cy3= Astatotilapia burtoni genomic DNA  Cy5= Astatotilapia tweddlei genomic DNA hybed by CRL Reilly in 2007

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=780_750 ScanPower=100_100


title: p4_06s039b_20070907CR

description: Cy3= Rhamphochromis “chilingali” genomic DNA  Cy5= Astatotilapia burtoni genomic DNA hybed by CRL Reilly in 2007

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=760_730 ScanPower=100_100


title: wt strain, pGraL, biological rep1, short term


title: wt strain, pvector, biological rep1, short term

source_name: E.coli wt cells with vector control


title: p4_06s40_20071112GJd

description: Cy3= Protomelas similis genomic DNA  Cy5= Astatotilapia burtoni genomic DNA hybed by G Jui in 2007

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=780_690 ScanPower=100_100


title: genomic DNA isolated from C57BL/6 3-month old mice intestine, 1 of 2

city: Houston

first: Jiexin

last: Zhang

state: TX

address: 1515 Holcombe Blvd

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

description: 3m old intestine chr 1 to 8

hyb_protocol: Followed Agilent protocol

scan_protocol: Scanned on an Agilent Technologies Scanner G2505B US23502362 Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1).

data_processing: Agilent Feature Extraction Software (9.1.3.1) was used for background subtraction and normalization.

organism: Mus musculus

source_name: genomic DNA isolated from C57BL/6 3m old mice intestine

label_protocol: Followed Agilent protocol

growth_protocol: C57BL/6 mice (Jackson Laboratories, Bar Harbor, ME) were used.

extract_protocol: Genomic DNA was extracted using a standard phenol–chloroform method

tag: tissue

value: intestine

tag: age


title: Cythera ES 1

description: Gene expression data


title: HID13 sample 2

description: HID13 sample 2


title: genomic DNA isolated from C57BL/6 32-month old mice intestine, 1 of 2

description: 32m old intestine chr 1 to 8

source_name: genomic DNA isolated from C57BL/6 32m old mice intestine


title: HSC-2 mir-146a OE transfected clone S5, P42

status: Public on Dec 08 2009

city: Singapore

first: jinmiao

last: chen

address: Biopolis

country: Singapore

institute: Singapore Immunology Network

description: Gene expression data sample

hyb_protocol: Affymetrix hybridization protocol

scan_protocol: Genechip scanner 3000

data_processing:
The microarray probe set data was summarized using RMA and normalized using the Cross-correlation method using R (Chua et al., 2006).

Chua SW, Vijayakumar P, Nissom PM, Yam CY, Wong VV, Yang H: A novel normalization method for effective removal of systematic variation in microarray data. Nucleic acids research 2006, 34(5):e38.

label: Biotin

organism: Rattus norvegicus

source_name: rno-miR-146a clone S5 transfected passage 42

label_protocol: Affymetrix labeling protocol (one-cycle cDNA synthesis)

growth_protocol: DMEM (high glucose) + 10%FBS + antibiotics

extract_protocol: RNA II kit M&N

value: Wistar

value: hepatic stellate cells

tag: cell line

tag: genome/variation

value: rno-miR-146a clone S5

tag: cell passage


title: HSC-2 mir-146a OE transfected clone S5, P43

description: Gene expression data sample

source_name: rno-miR-146a clone S5 transfected passage 43


title: HID13 sample 1

description: HID13 sample 1


title: HSC-2 mir-146a OE transfected clone S4, P43

description: Gene expression data sample

source_name: rno-miR-146a clone S4 transfected passage 43

value: rno-miR-146a clone S4


title: p4_06s037b_20070907CR

description: Cy3= Metriaclima estherae genomic DNA  Cy5= Astatotilapia burtoni genomic DNA hybed by CRL Reilly in 2007

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=790_770 ScanPower=100_100


title: HSC-2 mir-146a OE transfected clone S4, P42

description: Gene expression data sample

source_name: rno-miR-146a clone S4 transfected passage 42


title: HSC-2 mir-146a OE transfected clone S1, P42

description: Gene expression data sample

source_name: rno-miR-146a clone S1 transfected passage 42

value: rno-miR-146a clone S1


title: HSC-2 scrambled control, 43rd passage

description: Gene expression data control

source_name: scr transfected control

value: scr transfected control


title: HSC-2 mir-146a OE transfected clone S1, P43

description: Gene expression data sample

source_name: rno-miR-146a clone S1 transfected passage 43


title: HSC-2 scrambled control, 42nd passage

description: Gene expression data control


title: HD100 AP sample 3

description: HD100 AP sample 3

source_name: Bdellovibrio bacteriovorus HD100 wild-type attack phase

value: Attack phase


title: HD100 AP sample 2

description: HD100 AP sample 2


title: HSC-2 replicate 2, 43rd passage

description: Gene expression data control

source_name: untransfected control

value: untransfected control


title: HSC-2 replicate 2, 42nd passage

description: Gene expression data control


title: Stratgene Universal Human Reference vs. child_Patient 43

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: This study analyzes gene expression changes associated with a reduction of frataxin from peripheral blood of 28 children and 14 adults with Friedreich's ataxia compared to controls, as well as lymphoblastoid cell lines from patients.

hyb_protocol: 750ng each of Cy3 and Cy5 labeled cRNAs were fragmented and then hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Chips were washed and then scanned with an Agilent Scanner.

data_processing: The data were obtained with the Agilent Feature Extraction software (v9.1), using defaults for all parameters. The Feature Extraction Software performs error modeling before data are loaded into a database system. Images and GEML files, including error and P values, were exported from the Agilent Feature Extraction software and deposited into Rosetta Resolver (version 5.0, build 5.0.0.2.48) (Rosetta Biosoftware, Kirkland, WA).  The ratios (Cy5/Cy3) were generated.

source_name: Stratagene Universal Human Reference

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: Purchased Reference RNA

tag: Universal Human Reference total RNA from 10 human cell lines

source_name: child_Patient 43

label_protocol: Starting with 500ng of total RNA, Cy5 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: Total RNA was prepared from total blood using PAXgene™ blood RNA isolation kit (PreAnalytiX/ QIAGEN, Hilden, Germany)

tag: Total peripheral blood from 12 yo female with Friedreich's ataxia; age of onset= 5 yo; age of diagnosis = 6.5 yo; ICARS = 54.5; short GAA = 720; long GAA = 850


title: Stratgene Universal Human Reference vs. child_Patient 7

source_name: child_Patient 7

tag: Total peripheral blood from 14 yo female with Friedreich's ataxia; age of onset= 12 yo; age of diagnosis = 12 yo; ICARS = 36; short GAA = 656; long GAA = 762


title: Stratgene Universal Human Reference vs. child_Patient 45

source_name: child_Patient 45

tag: Total peripheral blood from 16 yo female with Friedreich's ataxia; age of onset= 9 yo; age of diagnosis = 10 yo; ICARS = 36; short GAA = 726; long GAA = 998


title: Stratgene Universal Human Reference vs. child_Patient 62

source_name: child_Patient 62

tag: Total peripheral blood from 15 yo male with Friedreich's ataxia; age of onset= 10 yo; age of diagnosis = 13 yo; ICARS = 27.5; short GAA = 826; long GAA = 1178


title: Stratgene Universal Human Reference vs. child_Patient 63

source_name: child_Patient 63

tag: Total peripheral blood from 17 yo male with Friedreich's ataxia; age of onset= 4 yo; age of diagnosis = 9 yo; ICARS = 48; short GAA = 800; long GAA = 800


title: Stratgene Universal Human Reference vs. child_Patient 29

source_name: child_Patient 29

tag: Total peripheral blood from 9 yo female with Friedreich's ataxia; age of onset= 1 yo; age of diagnosis = 8.5 yo; ICARS = 42; short GAA = 950; long GAA = 1050


title: Stratgene Universal Human Reference vs. child_Patient 25

source_name: child_Patient 25

tag: Total peripheral blood from 14 yo female with Friedreich's ataxia; age of onset= 8 yo; age of diagnosis = 10 yo; ICARS = 55; short GAA = 1079; long GAA = 1266


title: Stratgene Universal Human Reference vs. child_Patient 52

source_name: child_Patient 52

tag: Total peripheral blood from 13 yo female with Friedreich's ataxia; age of onset= 10 yo; age of diagnosis = 12 yo; ICARS = 34; short GAA = 520; long GAA = 1162


title: Stratgene Universal Human Reference vs. child_Patient 24

source_name: child_Patient 24

tag: Total peripheral blood from 10 yo male with Friedreich's ataxia; age of onset= 7 yo; age of diagnosis = 7 yo; ICARS = 56; short GAA = 852; long GAA = 1145


title: Stratgene Universal Human Reference vs. child_Patient 5

source_name: child_Patient 5

tag: Total peripheral blood from 10 yo male with Friedreich's ataxia; age of onset= 7 yo; age of diagnosis = 10 yo; ICARS = 30.5; short GAA = 588; long GAA = 1008


title: Stratgene Universal Human Reference vs. child_Patient 46

source_name: child_Patient 46

tag: Total peripheral blood from 17 yo male with Friedreich's ataxia; age of onset= 8 yo; age of diagnosis = 8 yo; ICARS = 59.5; short GAA = 700; long GAA = 700


title: Stratgene Universal Human Reference vs. child_Patient 26

source_name: child_Patient 26

tag: Total peripheral blood from 10 yo male with Friedreich's ataxia; age of onset= 9 yo; age of diagnosis = 10 yo; ICARS = 30; short GAA = 850; long GAA = 850


title: Stratgene Universal Human Reference vs. child_Patient 64

source_name: child_Patient 64

tag: Total peripheral blood from 16 yo female with Friedreich's ataxia; age of onset= 6 yo; age of diagnosis = 7 yo; ICARS = 56; short GAA = 1000; long GAA = 1400


title: Stratgene Universal Human Reference vs. child_Patient 27

source_name: child_Patient 27

tag: Total peripheral blood from 10 yo male with Friedreich's ataxia; age of onset= 4.5 yo; age of diagnosis = 7 yo; ICARS = 50.5; short GAA = 884; long GAA = 884


title: Stratgene Universal Human Reference vs. child_Patient 51

source_name: child_Patient 51

tag: Total peripheral blood from 15 yo male with Friedreich's ataxia; age of onset= 1.5 yo; age of diagnosis = 13 yo; ICARS = 34.5; short GAA = 782; long GAA = 938


title: Stratgene Universal Human Reference vs. child_Patient 42

source_name: child_Patient 42

tag: Total peripheral blood from 13 yo male with Friedreich's ataxia; age of onset= 5.5 yo; age of diagnosis = 10 yo; ICARS = 47; short GAA = 738; long GAA = 979


title: Stratgene Universal Human Reference vs. child_Patient 49

source_name: Stratagene Universal Human Reference

tag: Universal Human Reference total RNA from 10 human cell lines

source_name: child_Patient 49

tag: Total peripheral blood from 16 yo male with Friedreich's ataxia; age of onset= 6 yo; age of diagnosis = 10 yo; ICARS = 58.5; short GAA = 789; long GAA = 1305


title: Stratgene Universal Human Reference vs. child_Patient 48

source_name: child_Patient 48

tag: Total peripheral blood from 15 yo male with Friedreich's ataxia; age of onset= 10.5 yo; age of diagnosis = 10.5 yo; ICARS = 66; short GAA = 650; long GAA = 950


title: Stratgene Universal Human Reference vs. child_Patient 66

source_name: child_Patient 66

tag: Total peripheral blood from 13 yo female with Friedreich's ataxia; age of onset= 4 yo; age of diagnosis = 5 yo; ICARS = 4; short GAA = 820; long GAA = 1150


title: Stratagene Universal Human Reference vs. GM15851, 251209743133_A01

extract_protocol: Total RNA was prepared from total blood using QIAGEN Rneasy midi kit

tag: Control lymphoblastoid cell line derived from 14 yo


title: Stratgene Universal Human Reference vs. child_Patient 44

source_name: child_Patient 44

tag: Total peripheral blood from 13 yo female with Friedreich's ataxia; age of onset= 12 yo; age of diagnosis = 12 yo; ICARS = 31; short GAA = 799; long GAA = 1208


title: Stratagene Universal Human Reference vs. GM15850, 251209744167_A01

tag: Lymphoblastoid cell line derived from 13 yo patient with Friedreich's ataxia; GAA = 650-1030


title: Stratagene Universal Human Reference vs. GM15850, 251209744166_A01


title: Stratagene Universal Human Reference vs. GM09631, 251209744187_A01

tag: Control lymphoblastoid cell line derived from 29 yo


title: Stratgene Universal Human Reference vs. child_Patient 28

source_name: child_Patient 28

tag: Total peripheral blood from 12 yo male with Friedreich's ataxia; age of onset= 10 yo; age of diagnosis = 12 yo; ICARS = 33.5; short GAA = 827; long GAA = 1229


title: Stratagene Universal Human Reference vs. GM11494, 251209743132_A01

tag: Control lymphoblastoid cell line derived from 23 yo


title: HD100 AP sample 1

description: HD100 AP sample 1

source_name: Bdellovibrio bacteriovorus HD100 wild-type attack phase

tag: growth


title: Stratagene Universal Human Reference vs. GM16205, 251209743012_A01

tag: Lymphoblastoid cell line derived from 30 yo patient with Friedreich's ataxia; GAA = 530-530


title: Stratagene Universal Human Reference vs. GM09631, 251209742756_A01


title: Stratagene Universal Human Reference vs. GM11494, 251209743131_A01


title: Stratagene Universal Human Reference vs. GM16205, 251209743011_A01


title: Stratagene Universal Human Reference vs. GM16197, 251209742754_A01

tag: Lymphoblastoid cell line derived from 14 yo patient with Friedreich's ataxia; GAA = 760-830


title: Stratagene Universal Human Reference vs. GM16197, 251209742755_A01


title: Stratagene Universal Human Reference vs. GM16204B, 251209753038

tag: Lymphoblastoid cell line derived from 53 yo patient with Friedreich's ataxia; GAA = 380-830


title: Stratagene Universal Human Reference vs. GM16204B, 251209753039


title: Stratagene Universal Human Reference vs. GM16243, 251209742750_A01

tag: Lymphoblastoid cell line derived from 23 yo patient with Friedreich's ataxia; GAA = 670-1170


title: Stratagene Universal Human Reference vs. GM16210, 251209752926

tag: Lymphoblastoid cell line derived from 39 yo patient with Friedreich's ataxia; GAA = 580-580


title: Stratagene Universal Human Reference vs. GM09631, 251209753037


title: Stratagene Universal Human Reference vs. GM16203B, 251209752927

tag: Lymphoblastoid cell line derived from 29 yo patient with Friedreich's ataxia; GAA = 670-830


title: Stratagene Universal Human Reference vs. GM16203B, 251209752928

tag: Universal Human Reference total RNA from 10 human cell lines


title: Stratagene Universal Human Reference vs. GM01990C, 251209752969

tag: Control lymphoblastoid cell line derived from 51 yo


title: Stratagene Universal Human Reference vs. GM16210, 251209752925


title: Stratagene Universal Human Reference vs. GM16201, 251209752380

tag: Lymphoblastoid cell line derived from 22 yo patient with Friedreich's ataxia; GAA = 450-640


title: Stratagene Universal Human Reference vs. GM15850, 251209752394


title: Stratagene Universal Human Reference vs. GM10450, 251209752383

tag: Control lymphoblastoid cell line derived from 37 yo


title: Stratagene Universal Human Reference vs. GM15851, 251209752391

tag: Control lymphoblastoid cell line derived from 14 yo


title: Stratagene Universal Human Reference vs. GM16201, 251209752381


title: Stratagene Universal Human Reference vs. GM15850, 251209752393


title: Stratagene Universal Human Reference vs. GM10450, 251209752382


title: Stratagene Universal Human Reference vs. GM14650, 251209752390

tag: Control lymphoblastoid cell line derived from 21 yo


title: Stratagene Universal Human Reference vs. Control 9_FRDA_children

source_name: Control 9_FRDA_children

tag: Total peripheral blood from 22 yo healthy male


title: Stratagene Universal Human Reference vs. Control 10_FRDA_children

source_name: Control 10_FRDA_children

tag: Total peripheral blood from 22 yo healthy female


title: Stratagene Universal Human Reference vs. Control 8_FRDA_children

source_name: Control 8_FRDA_children

tag: Total peripheral blood from 21 yo healthy male


title: Stratagene Universal Human Reference vs. GM15851, 251209752392


title: Stratagene Universal Human Reference vs. Control 5_FRDA_children

source_name: Control 5_FRDA_children

tag: Total peripheral blood from 19 yo healthy male


title: Stratagene Universal Human Reference vs. Control 6_FRDA_children

source_name: Control 6_FRDA children

tag: Total peripheral blood from 21 yo healthy female


title: Stratagene Universal Human Reference vs. Control 7_FRDA_children

source_name: Control 7_FRDA children


title: Stratagene Universal Human Reference vs. Control 4_FRDA_children

source_name: Control 4_FRDA_children


title: Stratagene Universal Human Reference vs. adult_Patient 6

source_name: adult_Patient 6

tag: Total peripheral blood from adult patient with Friedreich's ataxia -- anonymous sample


title: Stratagene Universal Human Reference vs. adult_Patient 5

source_name: adult_Patient 5


title: Stratagene Universal Human Reference vs. control 14_FRDA_adult

source_name: control 14_FRDA_adult


title: Stratagene Universal Human Reference vs. adult_Patient 10

source_name: Stratagene Universal Human Reference

source_name: adult_Patient 10


title: Stratagene Universal Human Reference vs. adult_Patient 13

source_name: adult_Patient 13


title: Stratagene Universal Human Reference vs. adult_Patient 8

source_name: adult_Patient 8


title: Stratagene Universal Human Reference vs. adult_Patient 12

source_name: adult_Patient 12


title: wt strain, pvector, biological rep2, short term

source_name: E.coli wt cells with vector control

tag: strain


title: Stratagene Universal Human Reference vs. control 12_FRDA_adult

source_name: control 12_FRDA_adult

tag: Total peripheral blood from 23 yo healthy male


title: Stratagene Universal Human Reference vs. adult_Patient 9

source_name: adult_Patient 9


title: Stratagene Universal Human Reference vs. control 2_FRDA_adult

source_name: control 2_FRDA_adult

tag: Total peripheral blood from 26 yo healthy male


title: Stratagene Universal Human Reference vs. control 5_FRDA_adult

source_name: control 5_FRDA_adult


title: Stratagene Universal Human Reference vs. control 10_FRDA_adult

source_name: control 10_FRDA_adult


title: Stratgene Universal Human Reference vs. child_Patient 47

source_name: child_Patient 47

tag: Total peripheral blood from 16 yo male with Friedreich's ataxia; age of onset= 5 yo; age of diagnosis = 8 yo; ICARS = 61; short GAA = 700; long GAA = 700


title: Stratagene Universal Human Reference vs. control 11_FRDA_adult

source_name: control 11_FRDA_adult


title: Stratgene Universal Human Reference vs. child_Patient 6

source_name: child_Patient 6

tag: Total peripheral blood from 15 yo female with Friedreich's ataxia; age of onset= 10 yo; age of diagnosis = 12.5 yo; ICARS = 27.5; short GAA = 781; long GAA = 1364


title: Stratgene Universal Human Reference vs. child_Patient 50

tag: Universal Human Reference total RNA from 10 human cell lines

source_name: child_Patient 50

tag: Total peripheral blood from 15 yo male with Friedreich's ataxia; age of onset= 13 yo; age of diagnosis = 14 yo; ICARS = 32; short GAA = 800; long GAA = 900


title: Stratgene Universal Human Reference vs. child_Patient 8

source_name: child_Patient 8

tag: Total peripheral blood from 12 yo male with Friedreich's ataxia; age of onset= 8 yo; age of diagnosis = 11 yo; ICARS = 38; short GAA = 800; long GAA = 800


title: Stratgene Universal Human Reference vs. child_Patient 9

source_name: child_Patient 9

tag: Total peripheral blood from 14 yo male with Friedreich's ataxia; age of onset= 11 yo; age of diagnosis = 12 yo; ICARS = 37; short GAA = 241; long GAA = 929


title: Stratagene Universal Human Reference vs. control 15_FRDA_adult

source_name: Stratagene Universal Human Reference

source_name: control 15_FRDA_adult


title: Stratagene Universal Human Reference vs. adult_Patient 11

source_name: adult_Patient 11


title: Stratgene Universal Human Reference vs. child_patient 65

source_name: child_patient 65

tag: Total peripheral blood from 12 yo female with Friedreich's ataxia; age of onset= 6 yo; age of diagnosis = 8 yo; ICARS = 40; short GAA = 900; long GAA = 1200


title: Stratgene Universal Human Reference vs. child_Patient 61

source_name: child_Patient 61

tag: Total peripheral blood from 14 yo female with Friedreich's ataxia; age of onset= 6 yo; age of diagnosis = 14 yo; ICARS = 42; short GAA = 900; long GAA = 900


title: Stratagene Universal Human Reference vs. GM09631, 251209753036

tag: Control lymphoblastoid cell line derived from 29 yo


title: Stratagene Universal Human Reference vs. GM01990C, 251209753035

tag: Control lymphoblastoid cell line derived from 51 yo


title: Stratagene Universal Human Reference vs. GM04079, 251209752968

tag: Lymphoblastoid cell line derived from 30 yo patient with Friedreich's ataxia; GAA = 340-420


title: Stratagene Universal Human Reference vs. Control 3_FRDA_children

source_name: Control 3_FRDA_children

tag: Total peripheral blood from 19 yo healthy male


title: Stratagene Universal Human Reference vs. GM14650, 251209752929

tag: Control lymphoblastoid cell line derived from 21 yo


title: Stratagene Universal Human Reference vs. Control 1_FRDA _children

source_name: Control 1_FRDA _children

tag: Total peripheral blood from 18 yo healthy male


title: Stratagene Universal Human Reference vs. adult_Patient 1

source_name: adult_Patient 1

tag: Total peripheral blood from adult patient with Friedreich's ataxia -- anonymous sample


title: Stratagene Universal Human Reference vs. adult_Patient 2

source_name: adult_Patient 2


title: Stratagene Universal Human Reference vs. adult_Patient 3

source_name: adult_Patient 3


title: Stratagene Universal Human Reference vs. Control 2_FRDA_children

source_name: Control 2_FRDA_children

tag: Total peripheral blood from 21 yo healthy male


title: Stratagene Universal Human Reference vs. adult_Patient 4

source_name: adult_Patient 4


title: Stratagene Universal Human Reference vs. control 7_FRDA_adult

source_name: control 7_FRDA_adult


title: Stratagene Universal Human Reference vs. GM04079, 251209752967


title: Stratagene Universal Human Reference vs. control 13_FRDA_adult

source_name: control 13_FRDA_adult

tag: Total peripheral blood from 50 yo healthy female


title: Stratagene Universal Human Reference vs. control 8_FRDA_adult

source_name: control 8_FRDA_adult

tag: Total peripheral blood from 23 yo healthy male


title: Stratagene Universal Human Reference vs. control 9_FRDA_adult

source_name: control 9_FRDA_adult

tag: Total peripheral blood from 21 yo healthy female


title: Stratagene Universal Human Reference vs. adult_Patient 14

tag: Universal Human Reference total RNA from 10 human cell lines

source_name: adult_Patient 14


title: Stratagene Universal Human Reference vs. adult_Patient 7

source_name: Stratagene Universal Human Reference

source_name: adult_Patient 7


title: Stratagene Universal Human Reference vs. control 4_FRDA_adult

source_name: control 4_FRDA_adult

tag: Total peripheral blood from 33 yo healthy male


title: Stratagene Universal Human Reference vs. control 3_FRDA_adult

source_name: control 3_FRDA_adult

tag: Total peripheral blood from 40 yo healthy female


title: Stratagene Universal Human Reference vs. control 6_FRDA_adult

source_name: control 6_FRDA_adult

tag: Total peripheral blood from 52 yo healthy female


title: Normal human brain DNA - GenomiPhied

city: Los Angeles

first: Albert

last: Lai

address: 635 Charles E. Young Drive S NRB1 555C

department: Neurology

institute: UCLA

description: Only one replicate for this sample.

hyb_protocol: Cy-3 and Cy-5 labeled amplicons were co-hybridized at 65oC for 40 hours to Agilent CpG Island microarrays according to manufacture's instructions.  After hybridization, slides were washed consecutively.

scan_protocol: Scanned by Agilent DNA Microarray Scanner G2505B

data_processing: Agilent Feature Extraction 10.5.3 (FE) was used for extraction only.  Data analysis was done on unnormalize data from FE output (rProcessedSignal and gProcessSignal).  Probes were mapped to corresponding fragment from BfaI digestion.  Loess curve was constructed based on insensitive fragments and Loess correction was applied to the the entire arrays.

source_name: HpaII digestion

label_protocol: HpaII and MspI digests were labeled with Cyanine 5-dUTP and Cyanine 3-dUTP respectively (Perkin-Elmer, Waltham, MA) using Bioprime Array CGH Genomics Labeling Module (Invitrogen, Carlsbad, CA) according to manufacture's instructions.

growth_protocol: U87MG cells were maintained in Dulbecco’s modified Eagle’s medium/F12 (Mediatech, Herndon, VA, USA) supplemented with 10% fetal bovine serum and 100 U/ml penicillin and 100 mg/ml streptomycin, were grown in a 5% CO2 humidified atmosphere. U87MG cells were obtained from Dr. P. Mischel (University of California, Los Angeles, CA, USA).  Normal brain and Glioblastoma specimens has been collected and archived through an IRB approved protocol and obtained from the UCLA Brain Tumor Translational Resource.

extract_protocol: DNA was extracted using Qiagen Dneasy Blood and Tissue Kit (Qiagen, Valencia, CA)

treatment_protocol:
SssI-treated positive control: 4ug of genomic DNA (normal brain) was treated with 16 units of SssI enzyme and 160 nmol S-Adenosylmethione for 6 hours at 37oC twice.
Genomiphied negative control: 10ng of genomic DNA (normal brain) was treated using GenomiPhi V2 Amplification Kit (Amersham Biosciences, Piscataway, NJ) according to manufacture's instructions with unmodified dCTP.
Methylation-specific restriction enzyme: 750 ng of each genomic sample was digested with 25 units of BfaI (NEB, MA) for 6 hours at 37oC.  Digested DNA was then ligated to oligonucleotide linkers consisting of annealed H-12 (5'-TAATCCCTCGGA-3') and H-24 (5'-AGGCAACTGTGCTATCCGAGGGAT - 3') oligonucleotides.  Following ligation, the genomic DNA was divided into two equal portions for separate digestion with 20 units of HpaII (methylation-sensitive isoschizomer) or 40 units of MspI (methylation-insensitive isoschizomer) (NEB).    Each digest was subjected to PCR amplification using the same H-12/H-24 primers with the following conditions: 72°C for 5 minutes, followed by 16 cycles of 97°C for 1 minutes, 62°C for 30 seconds, 72°C for 3 minutes, followed by 72°C for 10 minutes.

tag: cell type

value: normal human brain

source_name: MspI digestion


title: U87MG DNA - rep.2

description: Technical replicate 1 was performed on a different day than technical replicate 2.

value: U87MG cell line


title: Stratagene Universal Human Reference vs. control 1_FRDA_adult

source_name: control 1_FRDA_adult

tag: Total peripheral blood from 26 yo healthy male


title: DNR treated vs non-treated 4h (replicate 1)

city: Barcelona

first: Benjamin

last: Pina

address: Jordi Girona, 18

country: Spain

institute: IDAEA-CSIC

hyb_protocol: Microarray prehybridization was performed in 5x SSC (SSC: 150 mM NaCl, 15mM Na-citrate, pH 7.0), 0.1% SDS, 1%BSA at 42ºC for 45 min. (Fluka, Sigma-Aldrich, Buchs SG, Switzerland). Labeled cDNA was dried in a vacuum trap and used as probe after  resuspension in 110 μl of hybridization solution (50% Formamide, 5xSSC, 0.1% SDS, 100 μg/ml salmon sperm from Invitrogen, Carlsbad, CA, USA). Hybridization and washing were performed in a Lucidea Slide Pro System (GE Healthcare, Uppsala, Sweden).

scan_protocol: GenePix 4000B fluorescence scanner and analyzed by Genepix® Pro 6.0 software (Axon Instruments, MDS Analytical Technologies, Toronto, Canada)

data_processing: Data was filtered according to spot quality. Only those spots with  intensities at least twice the background signal and with at least 75% of pixels with intensities above background plus two standard deviations were selected for further calculations. Following these  criteria, over 70% of spots in each array were usually found suitable for further analysis.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae BY4741 strain

label_protocol: 20 µg of total RNA were used for cDNA synthesis and labeling with Cy3-dUTP and Cy5-dUTP fluorescent nucleotides, following indirect labeling protocol (CyScribe postlabeling kit, GE-Healthcare). Labeling efficiency was evaluated by measuring Cy3 or Cy5 absorbance in Nanodrop Spectrophotometer.

growth_protocol: S. cerevisiae (BY4741 erg6Δ (MATa, his3Δ1, leu2Δ0, met15Δ0, ura3Δ0, YML008c::KanMX4,  from EUROSCARF, Frankfurt, Germany) was grown in 500 ml of YPD medium at 30°C in an environmental shaker (250 rpm) until OD=0.4

extract_protocol: Total RNA extracted by RiboPure RNA extraction kit (Ambion) following manufacturers instructions

treatment_protocol: The culture was divided into three aliquots and diluted four times with fresh YPD medium. Daunorubicin was added to each culture at a final concentration of 12 mM and cultures were allowed to grow for 1 or 4 hours. 500 mL aliquots were taken at times 0 (upon addition of daunorubicin), 1h and 4h.Untraated cultures were grown and samples in parallel

tag: strain

value: BY4741 strain carrying null mutation delta erg6

tag: reference

value: Untreated, incubated for 4h at 30C

tag: time point

tag: temperature

tag: agent

value: 12 mM daunorubicin


title: Normal human brain DNA - rep.2


title: Glioblastoma DNA - rep.2

value: glioblastoma


title: DNR treated vs non-treated 4h (replicate 2)


title: DNR treated vs non-treated 4h (replicate 3)


title: Glioblastoma DNA - rep.1


title: U87MG DNA - rep.1


title: Normal human brain DNA - rep.1


title: Normal human brain DNA - SssI treated - rep.1


title: DNR treated vs non-treated 0h (replicate 2)

value: Initial culture, untreated

value: Initial culture, 0h


title: DNR treated vs non-treated 0h (replicate 3)


title: DNR treated vs non-treated 0h (replicate 1)


title: Normal human brain DNA - SssI treated - rep.2


title: DNR treated vs non-treated 1h (replicate 1)

value: Untreated, incubated for 1h at 30C


title: DNR treated vs non-treated 1h (replicate 2)


title: Stratagene Universal Human Reference vs. GM15851, 251209743134_A01

tag: Control lymphoblastoid cell line derived from 14 yo


title: UCLA_mouse_liver_AXB23_2_222

status: Public on Dec 07 2009

city: los angeles

first: brian

last: bennett

address: Gonda

institute: UCLA-lusis lab

hyb_protocol: All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430A arrays. The HT_MG-430A Array plate consists of 96 single MG-430A arrays arranged into standard SBS 96 well plate format.  All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.

scan_protocol: Scanned images were subjected to visual inspection and a chip quality report was generated by the Affymetrix's GeneChip Operating System (GCOS) and Expression console (Affymetrix). Two of 288 chips were excluded from the final analysis due to low QC scores.

data_processing: The image data was processed using the Affymetrix GCOS algorithm utilizing quantile normalization or the Robust Multiarray method (RMA) to determine the specific hybridizing signal for each gene.

label_protocol: RNA was isolated from liver samples  from animal that were either normolipidemic or hyperlipidemic through genetic perturbation. 92 strains of mice had three biological replicates, five strains had two biological replicates and two strains with one biological replicate each. All RNA samples were cleaned using a Biosprint96 (Qiagen, Valencia, CA) with RNA cleanup beads (Agencourt Bioscience, Beverly, MA) following manufacturer’s protocol with adaptations for use with the Biosprint. The quality of the total RNA from the those samples were monitored by the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) and RNA quantity was measured with a  NanoDrop (NanoDrop Technologies, Inc. Wilmington, DE) following the manufacturer's instructions. All samples were arrayed into three 96 well microtiter plates following a randomized design format that places samples from the same strain on different plates to better estimate variance across testing strains.

growth_protocol: 16 week old male mice

extract_protocol: Flash frozen samples were weighed and homogenized in Qiazol according to the manufacturer’s protocol.  Following homogenization livers were isolated in RNeasy 96 columns (Qiagen) using the manufacturers protocol.  RNA integrity was confirmed using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

treatment_protocol: no treatment

tag: tissue

value: Liver


title: UCLA_mouse_liver_BXD39_2_340


title: UCLA_mouse_liver_BXD27_1_313


title: UCLA_mouse_liver_FVB_1_82

value: FVB


title: UCLA_mouse_liver_BXD9_4_359


title: UCLA_mouse_liver_NZB_3_171

value: NZB


title: UCLA_mouse_liver_SWR_4_100

value: SWR


title: UCLA_mouse_liver_AXB8_1_235


title: UCLA_mouse_liver_AJ_6_108

value: AJ


title: UCLA_mouse_liver_BXD14_2_288


title: UCLA_mouse_liver_BXA4_1_266


title: UCLA_mouse_liver_BXA16_2_251


title: UCLA_mouse_liver_BXD16_4_294


title: UCLA_mouse_liver_BTBR_1_111

value: BTBR


title: UCLA_mouse_liver_129X1_11_105


title: UCLA_mouse_liver_BXD19_1_296


title: UCLA_mouse_liver_BXH22_4_45


title: UCLA_mouse_liver_AXB13_1_204


title: UCLA_mouse_liver_CBA_10_145

value: CBA


title: UCLA_mouse_liver_BXH19_5_35


title: UCLA_mouse_liver_BXA24_3_259


title: UCLA_mouse_liver_LG_4_155

value: LG


title: UCLA_mouse_liver_MA_3_161

value: MA


title: UCLA_mouse_liver_BXA13_2_245


title: UCLA_mouse_liver_I_2_191

value: I


title: UCLA_mouse_liver_BXD21_1_304


title: UCLA_mouse_liver_BXA25_4_262


title: UCLA_mouse_liver_BXD32_1_325


title: UCLA_mouse_liver_AXB24_2_226


title: UCLA_mouse_liver_BXA8_3_273


title: UCLA_mouse_liver_BXA7_1_269


title: UCLA_mouse_liver_BXD6_1_351


title: UCLA_mouse_liver_BXD1_3_276


title: UCLA_mouse_liver_AXB19a_3_215


title: UCLA_mouse_liver_BXD40_1_342


title: UCLA_mouse_liver_BXA26_4_265


title: UCLA_mouse_liver_NZW_4_176

value: NZW


title: UCLA_mouse_liver_AXB6_2_232


title: UCLA_mouse_liver_NON_13_169

value: NON


title: UCLA_mouse_liver_BXD8_2_355


title: UCLA_mouse_liver_BXD20_1_301


title: UCLA_mouse_liver_AXB4_1_227


title: UCLA_mouse_liver_AXB19b_1_216


title: UCLA_mouse_liver_BXD2_1_299


title: UCLA_mouse_liver_BXD36_1_334


title: UCLA_mouse_liver_BXD28_2_317


title: UCLA_mouse_liver_KK_7_152

value: KK


title: UCLA_mouse_liver_PL_7_179

value: PL


title: UCLA_mouse_liver_AXB1_1_195


title: UCLA_mouse_liver_BXH4_8_128


title: UCLA_mouse_liver_DBA_6_81

value: DBA


title: UCLA_mouse_liver_BXD5_4_350


title: UCLA_mouse_liver_BXH8_1_59


title: UCLA_mouse_liver_AXB15_1_207


title: UCLA_mouse_liver_BXD11_2_279


title: UCLA_mouse_liver_SM_4_94

value: SM


title: UCLA_mouse_liver_C58_5_137


title: UCLA_mouse_liver_BXD24b_1_310


title: UCLA_mouse_liver_B6Cc3-1_6_18


title: UCLA_mouse_liver_RIII_8_188

value: RIII


title: UCLA_mouse_liver_BXD12_3_283

value: Liver


title: UCLA_mouse_liver_BXD29_1_319


title: UCLA_mouse_liver_BXH2_5_124


title: UCLA_mouse_liver_SEA_6_183

value: SEA


title: UCLA_mouse_liver_BXA14_1_248


title: UCLA_mouse_liver_BXD13_3_286


title: UCLA_mouse_liver_AXB10_2_199


title: UCLA_mouse_liver_BXA11_3_240


title: UCLA_mouse_liver_AXB12_4_203


title: UCLA_mouse_liver_BXD42_3_346


title: UCLA_mouse_liver_CE_1_147

value: CE


title: UCLA_mouse_liver_BXH20_5_40


title: UCLA_mouse_liver_AXB19_1_210


title: UCLA_mouse_liver_NOD_6_164

value: NOD


title: UCLA_mouse_liver_CAST_2_142

value: CAST


title: UCLA_mouse_liver_C57_4_131


title: UCLA_mouse_liver_BXH10_6_119


title: UCLA_mouse_liver_AKR_5_5

value: AKR


title: UCLA_mouse_liver_BUB_1_116

value: BUB


title: UCLA_mouse_liver_BXD34_3_333


title: UCLA_mouse_liver_BXH7_2_55


title: UCLA_mouse_liver_BXH9_3_67


title: UCLA_mouse_liver_BXD38_1_336


title: UCLA_mouse_liver_AXB5_1_230


title: UCLA_mouse_liver_BXA2_2_254


title: UCLA_mouse_liver_B6_6_12


title: UCLA_mouse_liver_BalbcJ_3_21

value: BalbcJ


title: UCLA_mouse_liver_BXA12_1_242


title: UCLA_mouse_liver_AXB15_3_209


title: UCLA_mouse_liver_BXD24a_2_308


title: UCLA_mouse_liver_BXH6_1_48


title: UCLA_mouse_liver_LPJ_6_90

value: LPJ


title: UCLA_mouse_liver_BXD33_1_328


title: UCLA_mouse_liver_C3H_4_73


title: UCLA_mouse_liver_BXH14_5_29


title: UCLA_mouse_liver_AXB6_3_233


title: UCLA_mouse_liver_RIII_9_189


title: UCLA_mouse_liver_PL_11_182


title: UCLA_mouse_liver_BXD31_3_324


title: UCLA_mouse_liver_BXH14_2_26


title: UCLA_mouse_liver_BXD42_2_345


title: UCLA_mouse_liver_NZB_4_172

value: NZB


title: UCLA_mouse_liver_BXA13_3_246


title: UCLA_mouse_liver_AXB19_3_211


title: UCLA_mouse_liver_BXA4_4_268


title: UCLA_mouse_liver_BXD16_1_292


title: UCLA_mouse_liver_BXA8_2_272


title: UCLA_mouse_liver_AXB1_2_196


title: UCLA_mouse_liver_AXB8_4_237


title: UCLA_mouse_liver_KK_6_151


title: UCLA_mouse_liver_BXH19_3_33


title: UCLA_mouse_liver_BUB_1_118


title: UCLA_mouse_liver_BXH22_3_44


title: UCLA_mouse_liver_BXH6_5_52


title: UCLA_mouse_liver_BTBR_4_112

value: BTBR


title: UCLA_mouse_liver_NZW_1_175

value: NZW


title: UCLA_mouse_liver_BXD9_1_357


title: UCLA_mouse_liver_BXD14_4_289


title: UCLA_mouse_liver_I_5_193

value: I


title: UCLA_mouse_liver_BXH9_1_65


title: UCLA_mouse_liver_BXD24a_3_309


title: UCLA_mouse_liver_AJ_3_107

value: AJ


title: UCLA_mouse_liver_AXB2_1_219


title: UCLA_mouse_liver_CBA_7_144

value: CBA


title: UCLA_mouse_liver_BXD20_3_303


title: UCLA_mouse_liver_AXB19b_3_218


title: UCLA_mouse_liver_AXB23_3_223


title: UCLA_mouse_liver_BXD13_1_284


title: UCLA_mouse_liver_AXB24_1_225


title: UCLA_mouse_liver_AXB13_3_205


title: UCLA_mouse_liver_BXA16_4_253


title: UCLA_mouse_liver_BXD34_1_331


title: UCLA_mouse_liver_BXD38_2_337


title: UCLA_mouse_liver_BXH4_7_127


title: UCLA_mouse_liver_BXD24b_4_312


title: UCLA_mouse_liver_AXB10_1_198


title: UCLA_mouse_liver_BXD6_4_353


title: UCLA_mouse_liver_129X1_12_106


title: UCLA_mouse_liver_BXD8_1_354


title: UCLA_mouse_liver_AXB4_2_228


title: UCLA_mouse_liver_DBA_4_79

value: DBA


title: UCLA_mouse_liver_SEA_7_184


title: UCLA_mouse_liver_BXA2_4_256


title: UCLA_mouse_liver_AXB2_3_221


title: UCLA_mouse_liver_BXD5_1_348


title: UCLA_mouse_liver_BXA11_4_241


title: UCLA_mouse_liver_BXD12_1_281


title: UCLA_mouse_liver_BalbcJ_2_20


title: UCLA_mouse_liver_BXA24_1_257


title: UCLA_mouse_liver_BXA7_4_271


title: UCLA_mouse_liver_BXD28_3_318


title: UCLA_mouse_liver_CAST_1_141


title: UCLA_mouse_liver_BXD21_3_306


title: UCLA_mouse_liver_B6_5_11


title: UCLA_mouse_liver_BXA1_1_238


title: UCLA_mouse_liver_BXH20_3_38


title: UCLA_mouse_liver_SM_3_93

value: SM


title: UCLA_mouse_liver_AXB19a_1_213

value: Liver


title: UCLA_mouse_liver_BXD39_3_341


title: UCLA_mouse_liver_FVB_2_83

value: FVB


title: UCLA_mouse_liver_AKR_1_1


title: UCLA_mouse_liver_BXD27_4_315


title: UCLA_mouse_liver_BXH7_5_58


title: UCLA_mouse_liver_C58_3_135


title: UCLA_mouse_liver_BXH8_5_63


title: UCLA_mouse_liver_BXD32_4_327


title: UCLA_mouse_liver_AXB12_1_201


title: UCLA_mouse_liver_BXD19_2_297


title: UCLA_mouse_liver_BXD31_2_323


title: UCLA_mouse_liver_C57_11_133


title: UCLA_mouse_liver_CE_5_149

value: CE


title: UCLA_mouse_liver_B6Cc3_4_16


title: UCLA_mouse_liver_BXD2_1_300


title: UCLA_mouse_liver_C3H_2_71


title: UCLA_mouse_liver_BXD33_4_330


title: UCLA_mouse_liver_BXA26_2_264


title: UCLA_mouse_liver_BXD40_3_344


title: UCLA_mouse_liver_SWR_1_97

value: SWR


title: UCLA_mouse_liver_MA_2_160

value: MA


title: UCLA_mouse_liver_BXA12_3_244


title: UCLA_mouse_liver_BXH2_10_125


title: UCLA_mouse_liver_NOD_11_166

value: NOD


title: UCLA_mouse_liver_BXD29_3_321


title: UCLA_mouse_liver_BXD1_1_275


title: UCLA_mouse_liver_NON_17_170

value: NON


title: UCLA_mouse_liver_LPJ_3_87


title: UCLA_mouse_liver_BXD15_1_290


title: UCLA_mouse_liver_BXD11_1_278


title: UCLA_mouse_liver_BXA14_3_250


title: UCLA_mouse_liver_BXA25_3_261


title: UCLA_mouse_liver_LG_7_158

value: LG


title: UCLA_mouse_liver_BXH10_8_120


title: UCLA_mouse_liver_I_3_192


title: UCLA_mouse_liver_BXA13_4_247


title: UCLA_mouse_liver_LG_5_156


title: UCLA_mouse_liver_BXD9_3_358


title: UCLA_mouse_liver_AXB15_2_208


title: UCLA_mouse_liver_BXD8_4_356


title: UCLA_mouse_liver_BXD14_1_287


title: UCLA_mouse_liver_NZW_10_177


title: UCLA_mouse_liver_BXA24_2_258


title: UCLA_mouse_liver_AXB10_3_200


title: UCLA_mouse_liver_BXH6_2_49


title: UCLA_mouse_liver_CE_4_148


title: UCLA_mouse_liver_BXD42_4_347


title: UCLA_mouse_liver_BXA26_1_263


title: UCLA_mouse_liver_BXD20_2_302


title: UCLA_mouse_liver_BXD12_2_282


title: UCLA_mouse_liver_AXB6_6_234


title: UCLA_mouse_liver_AKR_4_4

value: AKR


title: UCLA_mouse_liver_BXH10_7_122


title: UCLA_mouse_liver_NON_8_168


title: UCLA_mouse_liver_BXD39_1_339


title: UCLA_mouse_liver_BXD16_3_293


title: UCLA_mouse_liver_AXB2_2_220


title: UCLA_mouse_liver_BXD19_3_298


title: UCLA_mouse_liver_AXB19_4_212


title: UCLA_mouse_liver_BXH2_7_123


title: UCLA_mouse_liver_BXD29_2_320


title: UCLA_mouse_liver_BalbcJ_5_23

value: BalbcJ


title: UCLA_mouse_liver_B6Cc3_2_14


title: UCLA_mouse_liver_KK_9_154

value: KK


title: UCLA_mouse_liver_BXA14_2_249


title: UCLA_mouse_liver_AXB19b_2_217


title: UCLA_mouse_liver_BXD38_3_338


title: UCLA_mouse_liver_BUB_2_115

value: BUB


title: UCLA_mouse_liver_BXD13_2_285


title: UCLA_mouse_liver_C3H_6_75


title: UCLA_mouse_liver_BXH9_4_68


title: UCLA_mouse_liver_C58_4_136


title: UCLA_mouse_liver_NZB_5_173

value: NZB


title: UCLA_mouse_liver_BXA12_2_243


title: UCLA_mouse_liver_NOD_10_165


title: UCLA_mouse_liver_BXA8_4_274


title: UCLA_mouse_liver_BXA16_3_252


title: UCLA_mouse_liver_BXA7_3_270


title: UCLA_mouse_liver_BXH14_4_28


title: UCLA_mouse_liver_SEA_11_185

value: SEA


title: UCLA_mouse_liver_BXH22_6_47


title: UCLA_mouse_liver_BXH4_10_129


title: UCLA_mouse_liver_BXD5_3_349


title: UCLA_mouse_liver_AJ_9_110

value: AJ


title: UCLA_mouse_liver_BXD21_2_305


title: UCLA_mouse_liver_BXD24b_2_311


title: UCLA_mouse_liver_BXD18_1_295


title: UCLA_mouse_liver_BXA11_1_239


title: UCLA_mouse_liver_BXA25_2_260


title: UCLA_mouse_liver_AXB1_3_197


title: UCLA_mouse_liver_BXD33_2_329


title: UCLA_mouse_liver_CAST_3_139

value: CAST


title: UCLA_mouse_liver_BXD11_3_280


title: TC_MDR-A

city: Bologna

first: Katia

last: Scotlandi

address: Via di Barbiano 1/10

country: Italy

institute: Istituto Ortopedico Rizzoli

description: Cells overexpressing MDR-1 and deprived of metastatic ability were compared with parental cell line to identify a molecular signature associated with chemoresistance and metastasis in EWS.

hyb_protocol: Cot-1 DNA was added to hybridization mixture. Hybridization buffer (AgilentHybridization Kit ) was added, and samples were applied to microarrays enclosed in Agilent hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Hybridized slides were scanned using  PE/Packard Bell   microarray scanner (Perckin Helmer) that acquires data at two wavelenghts  [532nm (green) and 635nm (red)]. Signal and background intensities for both channels were calculated with QuantArray (Perkin Helmer) .

data_processing: Using median over entire array normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. (BRB-ArrayTools http://linus.nci.nih.gov/BRB-ArrayTools.html).

source_name: TC/MDR-A

label_protocol: Total RNA was used to obtain labeled cDNA, according to the manufacturer's instructions (Agilent Direct-Label cDNA synthesis kit protocol, Agilent Technologies).

extract_protocol: Total RNA extracted using Trizol following manifacturer's instructions

tag: EWS cell line

tag: MDR-1 transfected cell line

source_name: parental TC-71

tag: parental TC-71


title: UCLA_mouse_liver_AXB12_3_202


title: UCLA_mouse_liver_BXD6_2_352


title: UCLA_mouse_liver_BXD15_2_291


title: NSCB_expression_380K_229610

type: mixed

city: Madison

first: Melodee

last: Patterson

state: WI

address: 510 Charmany Dr Ste 58 & 59

institute: WiCell

description: Gene expression chip experiments are used to detect the expression level of hESC and differentiation markers in hESC cell lines.

hyb_protocol: 1. Incubate at 95°C (in heat block), 5 min., spin briefly 2. Place at 42°C (in Maui machine), 5-15 min. 3. Prepare microarray: A)pre-heat array on Maui station B) put array into array-holder (with number facing up going in first) carefully remove glue-sticker from lid and put lid onto array C) take array w/ lid out of array-holder thoroughly attach lid using thick slide place array onto Maui station, approx. 2 min. make sure lid is completely attached D) Add 40 µl hyb solution onto microarray and allow to settle (approx. 15 sec.), dry lid thoroughly 4. Place stickers onto lid, press down on both at the same time, make sure are thoroughly attached 5. Squeeze bubbles away from center of array 6. Wet humid cover and place on Maui station 7. Incubate on Maui at 42°C overnight (17 hours) 8. Remove microarray w/lid from Maui and put in array-holder in Wash 1 (at 42°C) 9. Peel lid off chip while submerged 10. Incubate 10-15 sec. w/ gentle agitation 11. Transfer slide into a slide rack in a new container of Wash 1 (r.t.) Incubate 2 min. w/ gentle agitation 12. Transfer to Wash 2 13. Incubate 1 min. w/ gentle agitation 14. Transfer to Wash 3 15. Incubate 15 sec. w/ gentle agitation 16. Spin approx. 1 min. in Array-Go-Round (place arrays such that numbers are facing to the right when rack is placed in front part of wheel) (the rod on slide holder should be on the inside) 17. Blow off any residual liquid 18. Keep slides protected from light and scan as soon as possible

scan_protocol: 1. Turn on the scanner and allow it to warm up for at least 15 minutes before scanning. 2. Open the Gene Pix Scan 6.0 program. 3. Place the chip in the scanner, with the label facing down and outward. 4. Open hardware settings and make sure the pixel size is 5 and the power is 100% for both channels. 5. Do a Preview Scan to adjust the scan frame for the array. Use levels 750 for the 635 (Cy5) channel and 550 for the 532 (Cy3) channel. 6. Perform Data Scans until the PMT levels for the 635 and 532 channels have been adjusted. 7. Adjust the PMT level of the 635 channel so the histogram is leveling off at 1e-5. 8. Adjust the PMT level of the 532 channel so the median (found by the rectangular region measuring tool) is equal to or no more than 30 points higher than the median of the 635 channel. 9. Save image as Single-image TIFF File (*.tif) and make sure both channels are checked. The image files are named chipID_635.tif and chipID_532.tif and stored on the WiCell Iceland server under the scan date (yyyymmdd). 10. The image files are ready for analysis with the NimbleScan software.

data_processing:
1. Image extraction:
NimbleScan provided by NimbleGen is used to extract signal data from image files
(*.TFF). Signals from the scan for Cy3 (green channel) are saved in a file named as chipID_532.pair while signals from the scan for Cy5 (red channel) are saved in a file named as chipID_635.pair.
2. Normalization:
Signal intensities from RNA and gDNA samples are normalized with Robust Multiple-chip Analysis (RMA) algorithm (Irizarry et al., 2003) separately. A median-adjusted ratio is calculated for each gene by dividing its signal intensity from the RNA sample by the sum of the corresponding signal intensity from the gDNA sample and median signal intensity of all genes from the gDNA channel.

source_name: Human ES sample RNA

label_protocol:
1. Dry the sample in the Speed Vac set at 30°C.
2. Resuspend the sample in 4.5μl 0.1M Na2CO3, pH 9.0.
3. Resuspend the Cy5 NHS ester in 4.5μl DMSO
4. Add Cy5 NHS ester to sample
5. Incubate at 22°C in a heat block for 1 hour. Protect the heat block and sample from light.
6. Purify the sample using a Qiaquick PCR purification Kit:
6.1. Add 35μl 100mM NaOAc, pH 5.2 to the sample.
6.2. Add 250μl PB buffer to the sample and load the sample on the column.
6.3. Spin at 13.000 rpm for 1 minute and remove the flow through.
6.4. Add 750μl PE buffer to the column.
6.5. Spin at 13.000 rpm for 1 minute and remove the flow through.
6.6. Spin at 13.000 rpm for 1 minute.
6.7. Transfer the column to new tube.
6.8. Add 30μl EB buffer and incubate for 1 minute on the column.
6.9. Elute once by centrifuging at 13.000 rpm for 1 minute.

extract_protocol:
1. In a hood equipped with an aspirator, remove spent media from the wells of hES cells.
2. Wash each well once with 1ml of PBS. Aspirate the PBS.
3. In the fume hood, add 1 ml of Trizol per well using a 1ml pipetman. Use the pipet tip to scrape the cells into solution and make sure no cells are left behind.
4. Transfer the cells from each well into a separate 1.5ml eppendorf tube.
5. Add 200μl of chloroform into each tube and mix by pipetting up and down. Use a 1ml Pipetman.
6. Spin the tubes at 16000 RCF for 20 minutes at 4°C.
7. Transfer the upper 500μl of the aqueous phase into a new 1.5ml eppendorf tube.
8. Add 500μl of isopropanol to the new tube, and it mix by pipetting up and down.
9. Let the samples sit at room temperature for 15 minutes.
10. Pellet the RNA by spining the tubes at 16000 RCF for 20 minutes at 4°C.
11. Wash the pelleted RNA using 70% ethanol. Slowly add 1ml of 70% ethanol to the RNA, cap the tube, and wash the pellet by flipping the tube twice. If the pellet is dislodged, perform a quick spin and then carefully decant the ethanol.
12. Dry the RNA in a vacuum; however, take care not to over dry it as that makes RNA resuspension difficult.
13. Resuspend the RNA in 25μl of nuclease free water.
14. Use a nanodrop spectrophotometer to measure the concentration and purity of RNA (A260/A280). Record these values for the gene expression submission form.

value: human embryonic stem (hES)

tag: cell line

source_name: hESC H1 DNA

label_protocol:
1. Dry the sample in the Speed Vac set at 30°C.
2. Resuspend the sample in 4.5μl 0.1 M Na2CO3, pH 9.0.
3. Resuspend the Cy3 NHS ester in 4.5μl DMSO
4. Add Cy3 NHS ester to sample
5. Incubate at 22°C in a heat block for 1 hour. Protect the heat block and sample from light.
6. Purify the sample using a Qiaquick PCR purification Kit:
A) Add 35μl 100 mM NaOAc, pH 5.2 to the sample.
B) Add 250μl PB buffer to the sample and load the sample on the column.
C) Spin at 13.000 rpm for 1 minute and remove the flow through.
D) Add 750μl PE buffer to the column.
E) Spin at 13.000 rpm for 1 minute and remove the flow through.
F) Spin at 13.000 rpm for 1 minute.
G) Transfer the column to new tube.
H) Add 30μl H20 and incubate for 1 minute on the column.
I) Elute once by centrifuging at 13.000 rpm for 1 minute.

extract_protocol:
1. Determine When to Harvest hES cells for DNA Extraction
A) At least 1x10^6 hES cells should be harvested for DNA extraction, depending on the quantity
required.
B) Yields of genomic DNA will vary from sample to sample depending on the amount and type of cells processed. In addition, the quality of starting material will affect DNA yield.
C) Estimated yield for hES cells: 5pg of DNA per cell (5μg DNA per 10^6 cells). One well of a 6-well plate will normally have between 1-4x106 hES cells by day 5 after passage.
2. Trypsinize the Cells
A) The following steps should be performed in a sterile biosafety cabinet while wearing personal protective equipment.
B) Add 1.5ml of 1X trypsin-EDTA working solution (pre-warmed to 37oC) to each well of a 6- well plate.
C) Return the plate to the 37C incubator for 2-3 minutes.
D) Remove the plate from the incubator and observe cell detachment with an inverted phase contrast microscope. Proceed to next step when colony edges begin to lift off the plate.
E) Using a sterile glass serological pipet, gently pipet up and down to detach the cells and break up the cell clumps.
F) Pool the detached cells in a 15ml centrifuge tube containing 5ml of trypsin stop solution within 5-7 minutes of adding the trypsin-EDTA solution.
G) Gently pipet the solution up and down to mix thoroughly.
H) Centrifuge the tube for 5 minutes at 1000 RPM.
3. RNA Digestion
A) Aspirate the supernatant and gently flick the tube until the pellet is resuspended.
B) Slowly add 200μl PBS to the cells while tapping gently on the tube to ensure good mixing.
C) Add 4μl RNase A (100mg/ml) and incubate at room temperature (RT) for 2 minutes.
4. Protein Digestion
A) Add 20μl Proteinase K and 200μl Buffer AL to the sample, mixing thoroughly by
vortexing. It is important that the solution is immediately and thoroughly mixed by
vortexing and pipetting to yield a homogenous solution.
NOTE: Do not add proteinase K directly to buffer AL.
B) Incubate the cell solution in a 70°C waterbath for 10 minutes.
5. DNA Precipitation and Separation of Cellular Components
A) Add 200μl ethanol (96-100%) to the sample, and mix thoroughly by vortexing.
B) A white precipitate may form on addition of ethanol. This precipitate does not interfere with the DNeasy procedure.
C) Pipet the mixture (including all of the precipitate) into the DNeasy Mini spin column placed in a 2ml collection tube. Centrifuge at ≥6000 x g (8000 rpm) for 1 minute. Discard flowthrough and collection tube.
NOTE: In order to obtain optimum DNA yield and quality, it is important not to overload
the spin column. The maximum number of hES cells that should be used in a DNA
extraction is 5x106 (normally, 2 wells of a 6-well plate). For larger amounts of starting material use multiple spin columns.
6. Wash the DNA
A) Place the DNeasy spin column in a new collection tube and add 500μl of Buffer AW1.
B) Centrifuge at ≥6000 x g (8000rpm) for 1 minute. Discard flow-through and collection tube.
C)Place the DNeasy spin column in a new collection tube and add 500μl of buffer AW2.
D) Centrifuge at 20,000 x g (14,000 rpm) for 3 minutes to dry the DNeasy membrane. Discard flow-through and collection tube.
NOTE: It is important to dry the membrane of the DNeasy Mini spin column, since
residual ethanol may interfere with subsequent reactions. This centrifugation step ensures that no residual ethanol will be carried over during the following elution.
E) Following the centrifugation step, remove the DNeasy Mini spin column carefully so the column does not come into contact with the flow-through, since this will result in carryover of ethanol. If carryover of ethanol occurs, place the spin column in a new collection tube and centrifuge again for 1 minute at 20,000 x g (14,000 rpm). Again discard the flow-through and collection tube.
7. Elution
A) Place the DNeasy Mini spin column in a clean 1.5ml or 2ml microcentrifuge tube and pipet 50-200μl Buffer AE directly onto the DNeasy membrane. Incubate the column at room temperature for 1 minute and then centrifuge for 1 minute at ≥6000 x g (8000rpm) to elute.
NOTE: Elution with less than 200μl of Buffer AE increases the final DNA concentration in the elute, but also decreases the overall DNA yield.
B) Repeat elution step as described in 7 A).
NOTE: A new microcentrifuge tube can be used for the second elution step to prevent dilution of the first elute. Alternatively, to combine the two elutes, the microcentrifuge tube from step 4.7.1 can be reused for the second elution step.
NOTE: More than 200μl should not be eluted into a 1.5 ml microcentrifuge tube because the DNeasy spin column will come into contact with the elute.


title: TC_MDR-D

source_name: TC/MDR-D

tag: Cells resistant to Yondelis 12nM


title: UCLA_mouse_liver_DBA_5_80

value: DBA

value: Liver


title: TC_MDR-C

source_name: TC/MDR-C

tag: Cells resistant to Yondelis 6nM


title: UCLA_mouse_liver_AXB5_2_231


title: UCLA_mouse_liver_RIII_10_190

value: RIII


title: UCLA_mouse_liver_FVB_3_84

value: FVB


title: TC_MDR-B

source_name: TC/MDR-B


title: UCLA_mouse_liver_BXA4_3_267


title: NSCB_expression_380K_229652

extract_protocol:
. Determine When to Harvest hES cells for DNA Extraction
A) At least 1x10^6 hES cells should be harvested for DNA extraction, depending on the quantity
required.
B) Yields of genomic DNA will vary from sample to sample depending on the amount and type of cells processed. In addition, the quality of starting material will affect DNA yield.
C) Estimated yield for hES cells: 5pg of DNA per cell (5μg DNA per 10^6 cells). One well of a 6-well plate will normally have between 1-4x106 hES cells by day 5 after passage.
2. Trypsinize the Cells
A) The following steps should be performed in a sterile biosafety cabinet while wearing personal protective equipment.
B) Add 1.5ml of 1X trypsin-EDTA working solution (pre-warmed to 37oC) to each well of a 6- well plate.
C) Return the plate to the 37C incubator for 2-3 minutes.
D) Remove the plate from the incubator and observe cell detachment with an inverted phase contrast microscope. Proceed to next step when colony edges begin to lift off the plate.
E) Using a sterile glass serological pipet, gently pipet up and down to detach the cells and break up the cell clumps.
F) Pool the detached cells in a 15ml centrifuge tube containing 5ml of trypsin stop solution within 5-7 minutes of adding the trypsin-EDTA solution.
G) Gently pipet the solution up and down to mix thoroughly.
H) Centrifuge the tube for 5 minutes at 1000 RPM.
3. RNA Digestion
A) Aspirate the supernatant and gently flick the tube until the pellet is resuspended.
B) Slowly add 200μl PBS to the cells while tapping gently on the tube to ensure good mixing.
C) Add 4μl RNase A (100mg/ml) and incubate at room temperature (RT) for 2 minutes.
4. Protein Digestion
A) Add 20μl Proteinase K and 200μl Buffer AL to the sample, mixing thoroughly by
vortexing. It is important that the solution is immediately and thoroughly mixed by
vortexing and pipetting to yield a homogenous solution.
NOTE: Do not add proteinase K directly to buffer AL.
B) Incubate the cell solution in a 70°C waterbath for 10 minutes.
5. DNA Precipitation and Separation of Cellular Components
A) Add 200μl ethanol (96-100%) to the sample, and mix thoroughly by vortexing.
B) A white precipitate may form on addition of ethanol. This precipitate does not interfere with the DNeasy procedure.
C) Pipet the mixture (including all of the precipitate) into the DNeasy Mini spin column placed in a 2ml collection tube. Centrifuge at ≥6000 x g (8000 rpm) for 1 minute. Discard flowthrough and collection tube.
NOTE: In order to obtain optimum DNA yield and quality, it is important not to overload
the spin column. The maximum number of hES cells that should be used in a DNA
extraction is 5x106 (normally, 2 wells of a 6-well plate). For larger amounts of starting material use multiple spin columns.
6. Wash the DNA
A) Place the DNeasy spin column in a new collection tube and add 500μl of Buffer AW1.
B) Centrifuge at ≥6000 x g (8000rpm) for 1 minute. Discard flow-through and collection tube.
C)Place the DNeasy spin column in a new collection tube and add 500μl of buffer AW2.
D) Centrifuge at 20,000 x g (14,000 rpm) for 3 minutes to dry the DNeasy membrane. Discard flow-through and collection tube.
NOTE: It is important to dry the membrane of the DNeasy Mini spin column, since
residual ethanol may interfere with subsequent reactions. This centrifugation step ensures that no residual ethanol will be carried over during the following elution.
E) Following the centrifugation step, remove the DNeasy Mini spin column carefully so the column does not come into contact with the flow-through, since this will result in carryover of ethanol. If carryover of ethanol occurs, place the spin column in a new collection tube and centrifuge again for 1 minute at 20,000 x g (14,000 rpm). Again discard the flow-through and collection tube.
7. Elution
A) Place the DNeasy Mini spin column in a clean 1.5ml or 2ml microcentrifuge tube and pipet 50-200μl Buffer AE directly onto the DNeasy membrane. Incubate the column at room temperature for 1 minute and then centrifuge for 1 minute at ≥6000 x g (8000rpm) to elute.
NOTE: Elution with less than 200μl of Buffer AE increases the final DNA concentration in the elute, but also decreases the overall DNA yield.
B) Repeat elution step as described in 7 A).
NOTE: A new microcentrifuge tube can be used for the second elution step to prevent dilution of the first elute. Alternatively, to combine the two elutes, the microcentrifuge tube from step 4.7.1 can be reused for the second elution step.
NOTE: More than 200μl should not be eluted into a 1.5 ml microcentrifuge tube because the DNeasy spin column will come into contact with the elute.


title: NSCB_expression_380K_229542


title: NSCB_expression_380K_229649


title: UCLA_mouse_liver_BXD1_4_277


title: NSCB_expression_380K_229428


title: NSCB_expression_380K_229643


title: NSCB_expression_380K_229414


title: RTSV infected TN1 15DAI replication3

city: Sapporo

first: Kouji

last: Satoh

state: Hokkaido

address: Hitsujigaoka 1

country: Japan

institute: NARO/HARC

description: Biological replication 3 of 3, RTSV infected TN1 at 15DAI

hyb_protocol: hybridization_Kit: in situ hybridization plus hybridization_Manufacturer: Agilent Technologies hybridization_Manual: Agilent Technologies

scan_protocol: Scanner: Agilent DNA microarray Scaner Manufacturer: Agilent Technologies Software: Scanner Control software Manufacturer: Agilent Technologies Manual: Agilent Technologies

data_processing:
Software: Feature Extraction ver 9.5
Manufacturer: Agilent Technologies
Manual: Agilent Technologies

organism: Oryza sativa Indica Group

source_name: RTSV TN1 15DAI rep 3

label_protocol:
Kit: Low RNA Input Linear Amplification kit
Manufacturer: Agilent Technologies
Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol:
Growth environment: greenhouse
Growth: pot culture (D: 120mm x H: 150mm)
Growth media :Soil collected fielf of International Rice Research Institute, Philippines. Alutoclaved prior to use
No of seedling per pot : 5
Light condition: Natural conditions
Tempareture: 28±3℃
Growth environment: greenhouse
Light condition: Natural conditions
Tempareture: 28±3℃
Growth length: 15 DAI

extract_protocol:
separation: trimming
extraction source: frozen
extraction source: shoots pooled from 5 individual plants
kit: Qiagen RNeasy maxi kit
manual: Qiagen

treatment_protocol:
treatment method: tube method (Cabauatan et al.1995)
growth stage:  9-day old plant
Light condition: Natural conditions
Tempareture: 28±3℃
virus inoculation: rice tungro spherical virus (RTSV)
virus inoculation: three viruliferous green leafhoppers (Nephotettix virescence) per 1 seedling
Virus inoculation: 24hours
Light condition: Natural conditions
Tempareture: 28±3℃

tag: infection

value: RTSV TN1 15DAI

tag: replicate

value: Taichung Native 1

value: whole plant 5 cm above ground

source_name: Mock TN1 15DAI rep 3

treatment_protocol:
treatment method: tube method (Cabauatan et al.1995)
growth stage:  9-day old plant
Light condition: Natural conditions
Tempareture: 28±3℃
virus inoculation: mock inoculation
virus inoculation: three virus-free green leafhoppers (Nephotettix virescence) per 1 seedling
virus inoculation: 24hours
Light condition: Natural conditions
Tempareture: 28±3℃

value: Mock TN1 15DAI


title: UCLA_mouse_liver_SM_1_91

value: SM


title: UCLA_mouse_liver_MA_1_159

value: MA


title: UCLA_mouse_liver_AXB4_3_229


title: NSCB_expression_380K_229255

tag: cell type


title: RTSV infected TN1 15DAI replication2

description: Biological replication 2 of 3, RTSV infected TN1 at 15DAI

source_name: RTSV TN1 15DAI rep 2

source_name: Mock TN1 15DAI rep 2


title: UCLA_mouse_liver_BXD40_2_343


title: RTSV infected TN1 12DAI replication3

description: Biological replication 3 of 3, RTSV infected TN1 at 12DAI

source_name: RTSV TN1 12DAI rep 3

growth_protocol:
Growth environment: greenhouse
Growth: pot culture (D: 120mm x H: 150mm)
Growth media :Soil collected fielf of International Rice Research Institute, Philippines. Alutoclaved prior to use
No of seedling per pot : 5
Light condition: Natural conditions
Tempareture: 28±3℃
Growth environment: greenhouse
Light condition: Natural conditions
Tempareture: 28±3℃
Growth length: 12 DAI

value: RTSV TN1 12DAI

source_name: Mock TN1 12DAI rep 3

value: Mock TN1 12DAI


title: UCLA_mouse_liver_BXH20_2_37


title: UCLA_mouse_liver_SWR_3_99

value: SWR


title: NSCB_expression_380K_225459


title: UCLA_mouse_liver_BXD31_1_322


title: NSCB_expression_380K_225461


title: NSCB_expression_380K_221426


title: NSCB_expression_380K_229402


title: NSCB_expression_380K_229359


title: NSCB_expression_380K_225467


title: NSCB_expression_380K_229205


title: NSCB_expression_380K_221424


title: NSCB_expression_380K_225460


title: RTSV infected TN1 12DAI replication2

description: Biological replication 2 of 3, RTSV infected TN1 at 12DAI

source_name: RTSV TN1 12DAI rep 2

source_name: Mock TN1 12DAI rep 2


title: NSCB_expression_380K_229254


title: NSCB_expression_380K_229260


title: RTSV infected TN1 15DAI replication1

description: Biological replication 1 of 3, RTSV infected TN1 at 15DAI

source_name: RTSV TN1 15DAI rep 1

source_name: Mock TN1 15DAI rep 1


title: NSCB_expression_380K_221399

source_name: Human ES sample total RNA


title: NSCB_expression_380K_225474


title: Sample 28 Ovary Normal patient 14

city: Petach Tikva

first: Roy

last: Navon

address: 94 Em Hamoshavot Road

country: Israel

institute: Agilent Technologies

description: SAMPLE 28

hyb_protocol: miRNA Microarray System Protocol v.1.5. See Agilent Technologies website.

scan_protocol: Scanned on an Agilent G2565AA Scanner

data_processing: GeneView files were generated using Agilent's Feature Extraction software version 9.5.3.1

source_name: Ovary Normal

label_protocol: miRNA Microarray System Protocol v.1.5. See Agilent Technologies website for miRNA labeling protocol.

extract_protocol: Total RNA was purchased from ABI (Ambion) as FirstChoice(R) Human Tumor/Normal Adjacent Tissue RNA.

value: Ovary

tag: origin

value: Normal


title: Sample 30 Ovary Normal patient 4

description: SAMPLE 30


title: Sample 29 Ovary Tumor patient 4

description: SAMPLE 29

source_name: Ovary Tumor

value: Tumor


title: Sample 31 Testes Tumor patient 10

description: SAMPLE 31

source_name: Testes Tumor

value: Testes


title: Sample 27 Ovary Tumor patient 14

description: SAMPLE 27


title: Sample 26 Testes Normal patient 13

description: SAMPLE 26

source_name: Testes Normal


title: Sample 25 Testes Tumor patient 13

description: SAMPLE 25


title: UCLA_mouse_liver_BXH19_2_32

tag: strain


title: RTSV infected TN1 12DAI replication1

description: Biological replication 1 of 3, RTSV infected TN1 at 12DAI

source_name: RTSV TN1 12DAI rep 1

source_name: Mock TN1 12DAI rep 1


title: UCLA_mouse_liver_BXD32_3_326


title: Sample 24 Lung Normal patient 12

description: SAMPLE 24

source_name: Lung Normal

value: Lung


title: UCLA_mouse_liver_AXB19a_2_214

value: Liver


title: NSCB_expression_380K_221396

source_name: Human ES sample mRNA

value: human embryonic stem (hES)

source_name: hESC H1 DNA


title: Sample 23 Lung Tumor patient 12

description: SAMPLE 23

source_name: Lung Tumor


title: Sample 22 Lung Normal patient 11

description: SAMPLE 22


title: UCLA_mouse_liver_129X1_7_103


title: UCLA_mouse_liver_AXB23_4_224


title: UCLA_mouse_liver_B6_4_10


title: RTSV infected TN1 9DAI replication2

description: Biological replication 2 of 3, RTSV infected TN1 at 9DAI

source_name: RTSV TN1 9DAI rep 2

growth_protocol:
Growth environment: greenhouse
Growth: pot culture (D: 120mm x H: 150mm)
Growth media :Soil collected fielf of International Rice Research Institute, Philippines. Alutoclaved prior to use
No of seedling per pot : 5
Light condition: Natural conditions
Tempareture: 28±3℃
Growth environment: greenhouse
Light condition: Natural conditions
Tempareture: 28±3℃
Growth length: 9 DAI

value: RTSV TN1 9DAI

source_name: Mock TN1 9DAI rep 2

value: Mock TN1 9DAI


title: RTSV infected TN1 9DAI replication3

description: Biological replication 3 of 3, RTSV infected TN1 at 9DAI

source_name: RTSV TN1 9DAI rep 3

value: Taichung Native 1

source_name: Mock TN1 9DAI rep 3


title: UCLA_mouse_liver_C57_5_132


title: UCLA_mouse_liver_AXB8_2_236


title: RTSV infected TN1 6DAI replication3

description: Biological replication 3 of 3, RTSV infected TN1 at 6DAI

source_name: RTSV TN1 6DAI rep 3

growth_protocol:
Growth environment: greenhouse
Growth: pot culture (D: 120mm x H: 150mm)
Growth media :Soil collected fielf of International Rice Research Institute, Philippines. Alutoclaved prior to use
No of seedling per pot : 5
Light condition: Natural conditions
Tempareture: 28±3℃
Growth environment: greenhouse
Light condition: Natural conditions
Tempareture: 28±3℃
Growth length: 6 DAI

value: RTSV TN1 6DAI

value: whole plant 5 cm above ground

source_name: Mock TN1 6DAI rep 3

value: Mock TN1 6DAI


title: RTSV infected TN1 9DAI replication1

description: Biological replication 1 of 3, RTSV infected TN1 at 9DAI

source_name: RTSV TN1 9DAI rep 1

source_name: Mock TN1 9DAI rep 1


title: RTSV infected TN1 6DAI replication1

description: Biological replication 1 of 3, RTSV infected TN1 at 6DAI

source_name: RTSV TN1 6DAI rep 1

source_name: Mock TN1 6DAI rep 1


title: RTSV infected TW16 15DAI replication3

description: Biological replication 3 of 3, RTSV infected TW16 at 15DAI

source_name: RTSV TW16 15DAI rep 3

value: RTSV TW16 15DAI

value: TW16 is an RTSV-resistant near-isogenic line (BC5) made by cross between Taichung Native 1 (recurrent parent) and Utri Merah (donor parent).

source_name: Mock TW16 15DAI rep 3

value: Mock TW16 15DAI


title: RTSV infected TN1 6DAI replication2

description: Biological replication 2 of 3, RTSV infected TN1 at 6DAI

source_name: RTSV TN1 6DAI rep 2

source_name: Mock TN1 6DAI rep 2


title: Sample 20 Testes Normal patient 10

description: SAMPLE 20

source_name: Testes Normal


title: Sample 19 Testes Tumor patient 10

description: SAMPLE 19

source_name: Testes Tumor


title: Sample 16 Liver Normal patient 8

description: SAMPLE 16

source_name: Liver Normal


title: UCLA_mouse_liver_AXB13_4_206


title: Sample 15 Liver Tumor patient 8

description: SAMPLE 15

source_name: Liver Tumor


title: Sample 18 Liver Normal patient 9

description: SAMPLE 18


title: Sample 17 Liver Tumor patient 9

description: SAMPLE 17


title: Sample 14 Colon Normal patient 7

description: SAMPLE 14

source_name: Colon Normal

value: Colon


title: Sample 21 Lung Tumor patient 11

description: SAMPLE 21

source_name: Lung Tumor


title: Sample 11 Colon Tumor patient 6

description: SAMPLE 11

source_name: Colon Tumor


title: Sample 12 Colon Normal patient 6

description: SAMPLE 12


title: UCLA_mouse_liver_BXH8_3_61


title: UCLA_mouse_liver_LPJ_1_85

value: LPJ


title: UCLA_mouse_liver_BXA2_3_255


title: UCLA_mouse_liver_BTBR_11_114

value: BTBR


title: RTSV infected TW16 15DAI replication2

description: Biological replication 2 of 3, RTSV infected TW16 at 15DAI

source_name: RTSV TW16 15DAI rep 2

source_name: Mock TW16 15DAI rep 2


title: RTSV infected TW16 9DAI replication3

description: Biological replication 3 of 3, RTSV infected TW16 at 9DAI

source_name: RTSV TW16 9DAI rep 3

value: RTSV TW16 9DAI

source_name: Mock TW16 9DAI rep 3

value: Mock TW16 9DAI


title: Sample 10 Colon Normal patient 5

description: SAMPLE 10

value: Normal


title: Sample 9 Colon Tumor patient 5

description: SAMPLE 9

value: Tumor


title: RTSV infected TW16 15DAI replication1

description: Biological replication 1 of 3, RTSV infected TW16 at 15DAI

source_name: RTSV TW16 15DAI rep 1

source_name: Mock TW16 15DAI rep 1


title: RTSV infected TW16 9DAI replication2

description: Biological replication 2 of 3, RTSV infected TW16 at 9DAI

source_name: RTSV TW16 9DAI rep 2

source_name: Mock TW16 9DAI rep 2


title: Sample 13 Colon Tumor patient 7

description: SAMPLE 13


title: RTSV infected TW16 9DAI replication1

description: Biological replication 1 of 3, RTSV infected TW16 at 9DAI

source_name: RTSV TW16 9DAI rep 1

source_name: Mock TW16 9DAI rep 1


title: UCLA_mouse_liver_BXD27_3_314

value: Liver


title: Sample 8 Ovary Normal patient 4

description: SAMPLE 8

source_name: Ovary Normal

value: Ovary


title: Sample 7 Ovary Tumor patient 4

description: SAMPLE 7

source_name: Ovary Tumor


title: Sample 32 Testes Normal patient 10

description: SAMPLE 32

source_name: Testes Normal

value: Testes


title: Sample 6 Lymphoma Normal patient 3

description: SAMPLE 6

source_name: Lymphoma Normal

value: Lymphoma


title: Sample 5 Lymphoma Tumor patient 3

description: SAMPLE 5

source_name: Lymphoma Tumor


title: Sample 3 Prostate Tumor patient 2

description: SAMPLE 3

source_name: Prostate Tumor

value: Prostate


title: Colo320DMvHDFA_50form

status: Public on Dec 05 2009

city: Seattle

first: Scott

middle: J.

last: Diede

state: WA

address: 1100 Fairview Avenue North, Mailstop c3-168

institute: Fred Hutchinson Cancer Research Center

description: Colo320DM DAMD + 50% formamide, Tiling Array A

hyb_protocol: Approximately 7.5μg of DNA was hybridzed per array using the Affymetrix hybridization kit. Arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing: Affymetrix Human Tiling 2.0R Arrays and 1.0R Promoter Arrays were analyzed using Tiling Array Software (v 1.1.02, Affymetrix). Raw data were scaled to a target intensity of 100 and normalized by quantile normalization. For probe analysis, a bandwidth of 250 bp was used and perfect match (PM) probes were used in a Wilcoxon Rank Sum two-sided test.

source_name: Colo320DM DAMD Assay + 50% formamide

label_protocol: Samples (7.5μg of DNA) were enzymatically fragmented and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments.

extract_protocol: Genomic DNA was extract from cell lines, primary medulloblastoma and adult cerebellum using a QIAGEN Blood & Cell Culture DNA kit per manufacturer's instructions. The DAMD assay and variations of denaturation conditions were performed as described (Diede et al., 2009). A total of 2 µg of genomic DNA was used as starting material for the DAMD assay. The sample was split into two tubes such that 1 µg was digested with KpnI (10 Units, NEB) and 1 µg was digested with SbfI (10 Units, NEB) for at least 8 hours in a total volume of 20 µl for each digestion. The restriction enzymes were then heat inactivated at 65˚C for 20 minutes. The KpnI and SbfI digests were combined, and then split evenly into two tubes. To the 20 µl of the DNA mixture, 27.36 µl of water and 1.64 µl of 3M NaCl was added such that the final concentration of NaCl was 100 mM and the total volume was 49 µl. For the formamide variation of the protocol to more specifically enrich for DNA palindromes, formamide was added to a final concentration of 50% before DNA denaturing. Denaturation was performed by boiling samples in a water bath for 7 minutes followed by rapid renaturation by immersing samples in an ice-water bath for at least 3 minutes. S1 (Invitrogen) digestion was performed by adding 6 µl 10x S1 nuclease buffer, 4 µl 3M NaCl, and 1 µl of S1 (diluted to 100 Units/µl using S1 Dilution buffer). Samples were then incubated for 60 minutes at 37˚C. S1 was inactivated by extraction with phenol followed by a phenol:chloroform extraction. DNA was ethanol precipitated in the presence of 20 µg of glycogen, and the DNA pellet was resuspended in 80 µl of 1/10 TE. The sample was then divided evenly into two tubes, with one tube subjected to digestion with MseI (40 Units, NEB) and the other tube with MspI (40 Units, NEB) for at least 6 hours at 37˚C (final volume of each digestion was 50 µl). Restriction enzymes were subsequently heat inactivated at 65˚C for 20 minutes. For ligation-mediated PCR, linkers were first created by combining 100 µl of a 100 pmol/µl solution of each oligo with 6.9 µl of 3M NaCl (final concentration 100 mM) and boiling in a water bath for 7 minutes. The water bath was then allowed to slowly cool to 25˚C to allow for annealing. Linkers were recovered by ethanol precipitation and the DNA pellet was resuspended in 500 µl of water. For the MseI linker, JW-102g was annealed to JW103pcTA. For the MspI linker, JW-102g was annealed to JW103pc-2. Linkers were then ligated onto the MseI or MspI digested DNA by adding 5 µl of the appropriate linker to the 50 µl digest, then 7 µl 10x T4 DNA ligase buffer, 1 µl T4 DNA ligase (400 Units, NEB) and 7 µl water for a final volume of 70 µl. Ligation was performed at 16˚C for at least 8 hours and then heat inactivated at 65˚C for 10 minutes. Linkers were then removed using a YM-50 Microcon (Amicon) filter by adding the 70 µl ligation mixture to the column followed by the addition of 160 µl of 1/10 TE. Columns were spun at 12000xg in a microcentrifuge for 5 minutes to almost dryness. 20 µl of 1/10 TE was then added to the membrane, incubated at room temperature for 5 minutes, and then the DNA was recovered by spinning at 1000xg for 3 minutes per the manufacturer’s protocol. 4 µl of this DNA was used as template for a PCR using the appropriate MseI (JW-102gMse) or MspI (JW-102gMsp) primer (4 µl DNA, 10 µl 10x PCR buffer, 10 µl 2mM dNTPs, 20 µl 5x GC-rich solution, 12 µl primer (10 pmol/µl), 1 µl Taq, 43 µl water (reagents from Roche FastStart Taq kit). PCR conditions were as follows: 96˚C 6 minutes, 30 cycles of 96˚C 30 seconds, 55˚C 30 seconds, 72˚C 30 seconds, with final extension of 72˚C for 7 minutes. MseI and MspI PCR products were combined and purified using a YM-30 Microcon (Amicon) filter. The 200 µl of PCR reaction was placed on the column and 300 µl of 1/10 TE was added. The column was spun at 14000xg until sample was concentrated to ~25 µl, and DNA was recovered into a new tube (1000xg for 3 minutes). This DNA was used as the input for biotin labeling.

value: colo320DM colon cancer cell line

source_name: HDF DAMD Assay + 50% formamide

value: primary fibroblast culture


title: Sample 4 Prostate Normal patient 2

description: SAMPLE 4

source_name: Prostate Normal


title: Colo320DMvHDFA_DAMD

description: Colo320DM DAMD, Tiling Array A

source_name: Colo320DM DAMD Assay

source_name: HDF DAMD Assay


title: UCLA_mouse_liver_BXH7_3_56


title: Colo320DMvHDFD_50form


title: UCLA_mouse_liver_PL_8_180

value: PL


title: Sample 2 Breast Normal patient 1

description: SAMPLE 2

source_name: Breast Normal

value: Breast


title: Sample 1 Breast Tumor patient 1

description: SAMPLE 1

source_name: Breast Tumor


title: RTSV infected TW16 6DAI replication2

description: Biological replication 2 of 3, RTSV infected TW16 at 6DAI

source_name: RTSV TW16 6DAI rep 2

value: RTSV TW16 6DAI

value: TW16 is an RTSV-resistant near-isogenic line (BC5) made by cross between Taichung Native 1 (recurrent parent) and Utri Merah (donor parent).

value: whole plant 5 cm above ground

source_name: Mock TW16 6DAI rep 2

value: Mock TW16 6DAI


title: UCLA_mouse_liver_BXD28_1_316


title: UCLA_mouse_liver_BXD24a_1_307


title: UCLA_mouse_liver_BXD34_2_332


title: UCLA_mouse_liver_BXD36_2_335


title: UCLA_mouse_liver_CBA_6_143

value: CBA


title: WRKY6 knockout mutant seedling

city: Beijing

first: Wei-Hua

last: Wu

state: Beijing

address: No.2 Yuanmingyuan West Road

department: College of Biological Sciences

country: China

institute: China Agricultural University

description: Gene expression analysis of seven-day-old wrky6-1 knockout seedlings.

hyb_protocol: Fifteen ug of fragmented cRNA was added in 300 ul hybridization solutions and 200 ul of this mixture was used for hybridization on Arabidopsis ATH1 Genome Arrays for 16 h at 45 ℃. The standard wash and double-stain protocols (EukGE-WS2v5-450) were applied using an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The arrays were scanned on an Affymetrix GeneChip scanner 3000. The scanned arrays were analyzed with Affymetrix GCOS 1.0 (MAS 5.0) software to generate both the CEL and CHP files.

data_processing: One biological experiment was conducted. The scanned arrays were analyzed with Affymetrix GCOS 1.0 (MAS 5.0) software.

organism: Arabidopsis thaliana

source_name: wrky6-1 knockout seedling

label_protocol: Eight ug of purified total RNA was used to generate first-strand cDNA in a reverse transcription reaction (One-Cycle Target Labeling and Control Reagents, Affymetrix). After second-strand synthesis, the double-stranded cDNA were used to generate cRNA via in vitro transcriptional reaction. The cRNA was labeled with biotin and 20 ug of this cRNA was fragmented. Size distribution of the cRNA and fragmented cRNA was assessed using an Eppendorf Biophotometer (Eppendorf) and electrophoresis.

growth_protocol: The seeds were surface sterilized with the mixed solutions of NaClO (0.5%) and Triton X-100 (0.01%) for 10 min followed by washing with sterilized distilled water for 4 times.  The sterilized seeds were first incubated on Petri dishes containing MS agar medium at 4℃ for 2 days before germination.  The seeds were germinated at 22℃ under constant illumination at 40 μmol•m-2•s-1 and the 7-day-old seedlings were harvested for RNA extraction.

extract_protocol: The total RNA was extracted using the TRIzol reagent (Invitrogen). RNA concentration, purity and integrity were determined and confirmed by using an Eppendorf Biophotometer (Eppendorf) and electrophoresis. The total RNA was further purified using RNeasy Mini Kit (Qiagen).

tag: genotype

value: wrky6-1 knockout

tag: age

value: 7 days

value: seedling


title: Wild-type Arabidopsis seedling

description: Gene expression analysis of seven-day-old wild-type seedlings.

source_name: wild-type seedling

tag: ecotype

value: Columbia

value: wild-type


title: RTSV infected TW16 6DAI replication1

description: Biological replication 1 of 3, RTSV infected TW16 at 6DAI

source_name: RTSV TW16 6DAI rep 1

source_name: Mock TW16 6DAI rep 1


title: Colo320DMvHDFD_DAMD

description: Colo320DM DAMD, Technical Rep 1-3, Tiling Array A


title: 35S:WRKY6 seedling

description: Gene expression analysis of seven-day-old 35S:WRKY6 overexpressing seedlings.

source_name: 35S:WRKY6 overexpressing seedling


title: H-NS SL1344 pSfR27 sfh minus biological rep 1

city: Dublin

first: Shane

last: Dillon

address: Trinity College

department: Department of Microbiology

country: Ireland

institute: Moyne Institute of Preventive Medicine

description: biological replicate 1

hyb_protocol: Cy3 labeled ChIP DNA and Cy5 labeled control genomic DNAs were co-precipitated using standard sodium acetate/ethanol procedures and resuspended in hybridization buffer (Oxford Gene Technologies), and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridiized for 24 hours at 55oC in an Agilent hybiridization oven at 5 rpm. After hybridization, slides were washed according to instructions provided by Oxford Gene Technologies

scan_protocol: The microarray slides were scanned using a GenePix 4100A scanner (Axon Instruments). Cy3 and Cy5 images were acquired at 10 um resolution using a laser power of 100%. Scanned images were analyzed using GenePix Pro 6.1 software

data_processing: median normalization of mean of ratios (532/635) values

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: H-NS ChIP DNA from SL1344 (pSfR27)sfh- cells

label_protocol: Fluorescent labeling of DNA samples were carried out using the BioPrime Random Labeling kit (Invitrogen) as follows: 60 ul of 2.5 x random primer solution, x* ul DNA, and (70.5-x) ul sterile water were heated at 100oC for 10 minutes, snap chilled on ice and following were then added – 15 ul dNTP mix (1mM dCTP, 2mM dGTP, dTTP, dATP), 1.5 ul 1 mM Cy3/Cy5 labeled dCTP (GE healthcare) and 3 ul Klenow fragment (40 U/ ul). *[20 ul of ChIP DNA and 300 ng of Input DNA were fluorescently labeled with Cy3 d-CTP and Cy5-dCTP respectively]. The Labeling reactions wereas carried out at 37 oC overnight and 15 ml of stop buffer added to terminate the reaction. Labeled DNAs were purified using G-50 columns (GE-healthcare), according to manufacturers instructions.

growth_protocol: SL1344 (pSfR27) sfh- cells were inoculated 1:100 into 25 ml fresh Lennox broth and grown at 37degrees celsius in a shaking waterbath until OD600 0.2

extract_protocol: 25 ml of culture were harvested and re-suspended in 50 ml of PBS.  DNA-protein interactions were cross-linked by adding formaldehyde to a final concentration of 1% for 30 minutes. Glycine was then added to a final concentration of 0.125M to stop the cross-linking. The cells were pelleted, re-suspended in 0.6 ml of lysis buffer (50 mM Tris-HCl pH 8.1, 10 mM EDTA, 1% SDS, Roche protease inhibitor cocktail). 1.4 ml of IP dilution buffer (20 mM Tris-HCl pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.01% SDS, Roche protease inhibitor cocktail) was added and the chromatin was sonicated on ice in a 5ml tube to reduce the DNA length to an average size of approximately 500 bp using the Sanyo/MES Soniprep sonicator (8 bursts at an amplitude 10 microns for 30 seconds, with 1 minute cooling between bursts). 1.0 ml of IP dilution buffer was added to the chromatin, which was then pre-cleared by adding 50 ul of normal rabbit IgG for 1 hour at 4°C on a rotating wheel. 100 ul of homogeneous Protein G-agarose suspension was added to the pre-cleared chromatin and the samples were incubated for 3 hours at 4°C on a rotating wheel. The samples were centrifuged at 7500 rpm for 2 minutes at 4°C to pellet the protein G-agarose beads and the supernatant was used to set up various immunoprecipitation conditions in 2 ml microfuge tubes. An aliquot of 200 ul of chromatin was stored at -20°C to be used as input DNA. Experimental ChIP conditions – 1350 ul chromatin + 5μl of monoclonal H113 anti-H-NS antibodies (Lucchini et al., 2006) or 10 ug of FLAG monoclonal antibodies (Sigma-Aldrich, Cat. No. F3165). The samples were incubated at 4°C overnight on a rotating wheel. 50 ul homogeneous protein G-agarose suspension was added to each sample and the samples were incubated at 4°C for at least 3 hours on a rotating wheel. The samples were centrifuged at 7,500 rpm for 2 minutes at 4°C to pellet the protein G-agarose beads. The supernatant was removed and the protein G-agarose beads were washed twice with 750 ul of cold IP wash buffer 1 (20 mM Tris-HCl pH 8.1, 50 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), once with 750 ul of cold IP wash buffer 2 (10 mM Tris-HCl pH 8.1, 250 mM LiCl, 1 mM EDTA, 1% NP-40, 1% deoxycholic acid) and twice with 750 ul of cold TE pH 8.0. DNA-protein-antibody complexes were eluted from the protein G-agarose beads by twice washing the beads with 225 ul of IP elution buffer (100 mM NaHCO3, 1% SDS) and both eluates were combined. 0.2 ul of RNase A (10 mg/ml) and NaCl (to a final concentration of 0.3 M) were added to each of the IP test and input samples and incubated at 65ºC for 6 hours to reverse the cross-links. 9 ul of Proteinase K (10 mg/ml) was then added to each sample and incubated at 45ºC for at least 3 hours. DNA was purified and recovered by performing a standard phenol-chloroform extraction, followed by ethanol precipitation with 5 ug of glycogen and 5 ug of yeast tRNA. The DNA pellets of the IP samples were re-suspended in 50 ul of sterile filtered water and 100 ul for the Input DNA samples

value: SL1344 (pSfR27) sfh-

tag: chip antibody

value: H-NS

source_name: Input DNA from SL1344

growth_protocol: SL1344 cells were inoculated 1:100 into 25 ml fresh Lennox broth and grown at 37degrees celsius in a shaking waterbath until OD600 0.2


title: H-NS SL1344 BR1

description: biological replicate 1

source_name: H-NS ChIP DNA from SL1344 cells


title: Sfh 3xFLAG SL1344 hns minus pSfR27 biological rep 1

description: biological replicate 1

source_name: Sfh ChIP DNA from SL1344 hns- (pSfR27) cells

growth_protocol: SL1344 hns- (pSfR27) cells were inoculated 1:100 into 25 ml fresh Lennox broth and grown at 37degrees celsius in a shaking waterbath until OD600 0.2

value: SL1344 hns- (pSfR27)


title: H-NS SL1344 BR2

description: biological replicate 2


title: R147vH114_50form

description: Medulloblastoma R147 DAMD + 50% formamide, Promoter Array

source_name: Medulloblastoma R147 DAMD Assay + 50% formamide

value: Primary medulloblastoma sample

source_name: H114 DAMD Assay + 50% formamide

value: Adult normal cerebellum


title: H-NS SL1344 pSfR27 biological rep 1

description: biological replicate 1

source_name: H-NS ChIP DNA from SL1344 (pSfR27) cells

growth_protocol: SL1344 (pSfR27) cells were inoculated 1:100 into 25 ml fresh Lennox broth and grown at 37degrees celsius in a shaking waterbath until OD600 0.2