title: 14269054 - Wild type 1 Repet1 vs SAIL 1 Repet1

hyb_protocol: SAIL 1 Repet1 Cy5 / Wild type 1 Repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: SAIL 1 Repet1

extract_protocol: SAIL 1 Repet1:10ug. (Qiagen_RNeasy.pdf)


title: PSC27_Pre_1, untreated PSC27 cells, replicate #1

status: Public on Jul 23 2012

type: RNA

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

country: USA

institute: Fred Hutchinson Cancer Center

hyb_protocol: Hybridizations to Agilent 44K whole human genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) following the manufacturer’s suggested protocols.

scan_protocol: Fluorescence array images were collected for Cy3 and Cy5 using the Agilent DNA microarray scanner G2505B (Agilent Technologies, Inc., Santa Clara, CA).

data_processing: Agilent Feature Extraction software was used to grid, extract, and LOWESS normalize data (default protocol). Spots of poor quality were replaced by NA (null) values.

molecule: total RNA

organism: Homo sapiens

label_protocol: amplified amino-allyl cDNA from each experimental sample was labeled with Cy3 fluorescent dye (reference amino-allyl cDNA was labeled with Cy5) following the manufacturer’s suggested protocols.

extract_protocol: To provide a reference standard RNA for use on two-color oligo microarrays, we pooled equal amounts of total RNA isolated from LNCaP, DU145, PC3, and CWR22 cell lines (American Type Culture Collection, Manassas, VA) growing at log phase in dye-free RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) (Invitrogen, Carlsbad, CA).  Reference RNA was purified using TRIzol (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol. Reference RNA was then further purified by RNeasy maxi kit and treated with DNAse using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by two rounds of mRNA amplification with amino-allyl incorporation in the second round using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

tag: gender

value: male

tag: cell line

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

extract_protocol: Total RNA was purified by RNeasy maxi kit and treated with DNAse using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by one round of mRNA amplification with amino-allyl incorporation using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

value: PSC27 cells

tag: treatment group

value: untreated


title: 14269065 - SAIL 1 Repet1 vs Wild type 1 Repet1

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: We want to compare the transcriptome of Sg1 insertion mutant to a WT background to understand if this candidate has a role in gene expression regulation at the genome-wide level.

hyb_protocol: Wild type 1 Repet1 Cy5 / SAIL 1 Repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: Wild type 1 Repet1

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: whole plant - Media=Arabidopsis compost  hygrometry=glasshouse condition  Temperature=glasshouse condition  Light=LD glasshouse condition

extract_protocol: Wild type Repet1:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: genotype/variation

value: Wild type

tag: ecotype

value: columbia

tag: developmental stage

value: (boyes et al. plant cell 2001):boyes:1.02

tag: tissue

value: whole plant

value: SAIL 1


title: PSC27_Pre_2, untreated PSC27 cells, replicate #2


title: Pax5KO Fetal liver cells engrafted in BM of an irradiated mice, biological rep1

city: Toronto

first: Sasan

last: Zandi

state: Ontario

address: 101 college St

country: Canada

institute: UHN

description:
Gene expression data
PAXB220+tg+_Rep1

hyb_protocol: cRNA fragments hybridized against MOE430 2.0 Affymetrix gene expression arrays  chip according to manufacturer instructions

scan_protocol: Chips  were scanned  using  a  GeneChip TM Scanner  3000

data_processing: The data were Normalized using RMA method by dCHIP, Limma and GCRMA. unsupervised clustering and other analyses been done in dCHIP

label: biotin

organism: Mus musculus

source_name: Bone marrow of C57Bl6 mice

label_protocol: RNA was labelled  and  amplified  according  to  Affymetrix TM GeneChip Expression  Analysis Technical Manual 2011

growth_protocol: Cells obtained fresh from the bone marrow of wild type mice either after transplanting Pax5KO or wild type fetal liver or without transplantation

extract_protocol: MicroRNeasy kit from qiagene has been used to extract the RNA according to manufacturer instruction

treatment_protocol: No treatment has been used

tag: strain

tag: tissue [transplant]

tag: age

value: Adult 8-12weeks old

tag: cell type

value: B220+ cells sorted out from bone marrow after 4 weeks


title: PSC27_RAD_1, PSC27 cells treated with gamma-irradiation, replicate #1

value: treated with gamma-irradiation


title: NPC Towne 72h

status: Public on Jul 22 2012

city: Newark

first: Saleena

last: Ghanny

address: 185 South Orange Ave

institute: Rutgers University

description: NPC infected with HCMV Towne strain for 72h

hyb_protocol: The Affymetrix Genechip WT Terminal Labeling and Hybridization protocol was used

scan_protocol: Chips were scanned using the Affymetrix 7G Plus scanner and Command Console Software

data_processing: Data was processed by importing CEL files into Partek Software and RMA normalization was performed

label: Biotin

source_name: NPC Towne 72h

label_protocol: The Ambion WT Expression Kit with accompanying protocol was used to label the samples

growth_protocol: Neural precursor cells were grown in DMEM+10%FBS

extract_protocol: RNA was extracted using RNEASY kit from Qiagen

treatment_protocol: HCMV (Towne and TR strains) were added to cells (0.1MOI)

value: Primary neural precursor cells

tag: infection

value: HCMV Towne

tag: time

value: 72 h post-infection


title: NPC Untreated

description: NPC untreated

source_name: NPC Untreated

value: uninfected

value: control


title: LSK cells from control mouse rep3

first: carl

last: virtanen

address: 101 College St

department: Princess Margaret Genomics Centre

institute: University Health Network

description:
Sample 6
replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol (Genome Studio Version 1.7.0)

data_processing: The data were normalised using quantile normalisation in Genespring (version 12.0) followed by median centered normalization

source_name: LSK cells (Lin-Sca1+cKit+)

label_protocol: Biotinylated cDNA were prepared with the WT-Ovation pico RNA amplification system Version 1.0 (Nugen)

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser using RNA 6000 Pico Kit (Agilent).

value: LysMCre

value: 9-16 weeks

value: bone marrow

value: LSK cells (sorted from BM)


title: LSK cells from LysM-KI mouse rep5

description:
Sample 10
replicate 5

value: mutant LysM-KI


title: LSK cells from control mouse rep4

description:
Sample 8
replicate 4


title: LSK cells from LysM-KI mouse rep4

description:
Sample 7
replicate 4


title: LSK cells from control mouse rep5

description:
Sample 9
replicate 5


title: LSK cells from control mouse rep2

description:
Sample 4
replicate 2


title: PSC27_BLEO_1, PSC27 cells treated with bleomycin, replicate #1

value: male

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

value: PSC27 cells

value: treated with bleomycin


title: LSK cells from LysM-KI mouse rep3

description:
Sample 5
replicate 3


title: NPC TR 72h

description: NPC infected with HCMV TR strain, 72h

source_name: NPC TR 72h

value: HCMV TR


title: LSK cells from LysM-KI mouse rep2

description:
Sample 3
replicate 2


title: LSK cells from control mouse rep1

description:
Sample 1
replicate 1


title: LSK cells from LysM-KI mouse rep1

description:
Sample 2
replicate 1


title: B35_miR

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing: After subtracting background signal intensities and set floor value of 0.1, data were normalized by cubic spline normalization (GenePattern, IlluminaNormalizer module, www.broadinstitute.org)

source_name: Human hepatocellular carcinoma

extract_protocol: Using fresh frozen liver and HCC tissues, total RNA was extracted using TRIzol (Invitrogen).

value: Human hepatocellular carcinoma

tag: etiology of liver disease

value: Hepatitis C virus


title: B94_miR


title: M17_miR


title: M104_miR


title: NY34_miR


title: NY79_miR


title: NY228_miR


title: B13_miR


title: NY107_miR

source_name: Human healthy liver

value: Human healthy liver


title: NY108_miR


title: B17_miR


title: Vaccinated Infected 72h Replicate 6

city: Launceston

first: Andrew

last: Bridle

state: Tasmania

address: Old School Road

department: NCMCRS

country: Australia

institute: University of Tasmania

description: Biological replicate 6 of 6

hyb_protocol: Array hybridization was performed using a Tecan Pro HS 4800 Hybridization Station (Tecan, Männedorf, Switzerland) using a Gene Expression Wash Buffer Kit (Agilent, CA, USA) supplemented with triton X-102 as per manufacturer’s instructions. A total of 250 and 400 ng of aRNA and cDNA, respectively were combined and 12 µL 10x blocking agent (Agilent) added to the sample. Before sample loading 60 µL of 2x GEx hybridization buffer (Agilent) was added to the 60 µL sample and incubated at 80oC for 10 min and held at 65oC until loading. Following a 60o C wash with pre-hybridisation buffer (Agilent) 120 µL of the pre-heated sample mixture was injected onto the microarray. Hybridization occurred over 12 h at 60oC using the Tecan Pro HS 4800 set at low agitation frequency. Each sample was hybridised to one single microarray, and 6 biological replicates were used per treatment group (a total of 36 arrays). Following the incubation, arrays were initially washed at 26oC (GE wash buffer 1) then at 37oC (GE was buffer 2) as per Agilent protocol and the slides were dried with 37 psi nitrogen gas and kept dark in a low-ozone environment (≤5 ppb).

scan_protocol: Array scanning was performed on a ScanArray Express (PerkinElmer, MA, USA; 5 μm resolution), adjusting the PMT gain for optimised visualisation of each image.

data_processing: All statistical analyses of the microarray data were conducted using Genespring GX, Signals were normalized per spot and per chip using an intensity-dependent (LOWESS) normalization, then per gene to normalize to the median. Spots were filtered on flags present, and only spots with signals greater or equal to the average base/proportional value of the raw channel were retained.

organism: Salmo salar

source_name: 2nd left gill arch from 6 wk post-vaccinated fish 72 h post-challenge with Y. ruckeri

label_protocol: Amino allyl-modified cDNA was synthesized using a Superscript III Indirect cDNA Labelling System (Invitrogen). In brief, 10 μg total RNA from the gill of each individual fish was reverse transcribed using an anchored oligo(dT)20 primer in cDNA synthesis reactions incorporating amino allyl-modified nucleotides. Reference aRNA was synthesized using 15 μg total RNA pooled from four samples from the six treatments using an Amino Allyl MessageAmp II aRNA amplification Kit (Ambion) as per manufacturer’s instructions. Reference aRNA samples were stored at -80oC as single-use aliquots prior to labelling. Modified cDNA and aRNA were labelled with Mono-Reactive Cy5 and Cy3 dye, respectively (GE Healthcare, NJ, USA). Samples were purified with S.N.A.P. columns (Invitrogen), and quantity and specific activity were determined through spectrophotometry (NanoDrop 1000, Thermo Scientific).

extract_protocol: Total RNA was extracted from gill tissue stored at -20°C in an RNA preservation reagent (25 mM sodium citrate, 10 mM EDTA, 4 M ammonium sulphate, pH 5.2) using a tissue pulveriser cooled in liquid nitrogen. RNA from pulverised tissue samples was further extracted and purified using TRI Reagent (Molecular Research Center, OH, USA) including DNAse treatment (Turbo DNase, Ambion, TX, USA) and a Qiagen RNeasy column-based cleanup according to manufacturer’s instructions (Qiagen, VIC, Australia). Total RNA concentrations were determined using an Invitrogen Qubit fluorometer and Quant-iT RNA assay kit (Invitrogen, VIC, Australia). RNA quality and integrity was estimated from gel electrophoresis and stored at -80°C.

tag: test

value: Gill

source_name: pooled total RNA from 4 samples from each of the six treatments

tag: reference


title: Vaccinated Infected 72h Replicate 5

description: Biological replicate 5 of 6

value: 2nd left gill arch from 6 wk post-vaccinated fish 72 h post-challenge with Y. ruckeri

value: pooled total RNA from 4 samples from each of the six treatments


title: B2-8 vs. B-pool

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization * 60 ul labeled sample is combined with 60 ul 2x-hybmix, containing 50% formamide, 10xSSC, 0.2% SDS, 200 ug/ml herring sperm DNA * Hybridizations of spotted oligo-arrays (Codelink glass) or Agilent microarrays are performed on a HS4800Pro Hybstation (Tecan) * Priming: 5xSSC, 0.1%SDS * Probe injection: pre-hyb, 5xSSC, 25% formamide, 0.1%SDS, 1%BSA, Volume 110ul * Hybridization: 45 min at 42C. * Wash 2x: milliQ * Wash: 5xSSC, 0.1%SDS * Probe injection: sample. Volume 110ul (Agilent 4packs: 55ul) * Hybridization: 16 hours at 42C. * Wash 2x: 1xSSC, 0.2%SDS at 23C * Wash 2x: 0.1xSSC, 0.2%SDS at 23C * Wash 2x: 0.1xSSC at 23C * Drying: blow with nitrogen for 3min at 30C

scan_protocol: Scanning of slides using the Agilent G2565BA scanner.

data_processing:
Features were extracted using Imagene software from Biodiscovery.
genes, no bg corr, hybset spec. dye corr
Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from the hybset itself, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009

label_protocol:
robot amplification and labeling v1.0:
All amplification and labeling procedures are performed in 96 wells plates (4titude, Bioke) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrofotometer (Molecular Devices), and a magnetic bead-locator (Beckman).
mRNA amplification protocol description:
* all RNAs are diluted to 0.6 ug/ul and 5 ul is put in a 96-wells plate (Abgene). All subsequent steps are performed by the robot script.
* mix1 containing 100 ng T7 Mlu VN primer (custom mix) and EC-control RNA per 5 ul is added and mixed in each well.
* plate is incubated @ 70C for 10 mins, cooled to 48C.
* mix2 containing 4ul 5x 1st strand buffer, 2 ul 0.1M DTT (Invitrogen), 1ul RNAse Inhibitor (Boehringer), 1ul 20mM dNTPs (GE Healthcare), 1ul linear acrylamide, and  1ul SuperScriptIII (Invitrogen) per sample is prewarmed to 48C; 10 ul per sample is added and mixed in each well.
* plate is incubated @ 48C for 2 hours and cooled to room temperature.
* 106 ul water and subsequently  mix3 containing 15ul second strand buffer, 3ul 20mM dNTPs (GE Healthcare), 1 ul T4 DNA ligase, 4 ul E.coli DNA polymerase I and 1 ul RNAseH  (Promega) is added and mixed in each well.
* plate is incubated @ 16C for 2 hours, @65C for 10 mins. * ds cDNA product is purified and concentrated with RNAClean (Agencourt, GC biotech) according to manufacturers protocol, to an end volume of 25 ul .
* 8 ul cDNA is put in a 96 wells plate and mixed with 12 ul IVT mix containing 2 ul 10x rxn-buffer, 2 ul each ATP, CTP, GTP, 0.6 ul UTP, 2 ul T7 enzyme mix (MegaScript kit, Ambion, Applied Biosystems), and 2.1 ul 50 mM 5-(3-aminoallyl)-UTP (Ambion, Applied Biosystems).
* Plate is incubated @37C for 4 hours.
* cRNA product is purified with RNAClean (Agencourt, Beckman) according to manufacturers protocol.
* Concentration  is measured (SpectraMax 190) and adjusted to 600 ng/ul by the robot.
* Resulting cRNA plates are sampled for Bioanalyzer QC, snapfrozen and stored at -80C.
Labeling protocol description:
* NHS-ester Cy3 or Cy5 dye (Amersham PA 23001 and 25001): entire tube is resuspended in 100 ul DMSO (Merck 8.02912.10).
All subsequent steps are performed by the robot script :
* 8 ul of each cRNA (0.6 ug/ul) is put in a 96-wells plate (Abgene), the accompanying reference sample is put in the next column (final step combines cy3 and cy5 labeled material ).
* 3 ul 0.5 M NaBicarbonate buffer, pH 9 is added and mixed to all wells.
* 3 ul cy-dye solution is added and mixed to the appropriate wells, plate is incubated at 18C for 1 hour.
* 4.5 ul 5M hydroxylamine is added and mixed, incubated at 18o C for 15 minutes.
* Labeled cRNA product is purified with RNA Clean (Agencourt, GC biotech) according to manufacturers protocol.
* RNA concentration and labeling incorporation are measured (SpectraMax 190).
* 2.5 ug of each labeled sample and reference cRNA are pooled and subjected to fragmentation according to protocol (Ambion, Applied Biosystems), 15 min 70C.
* Samples are stored at -20C until hybridization.

growth_protocol: CP003-grow: Ba/F3 cells were cultured in RPMI-1640 containing glutamax (Invitrogen), 10% fetal bovine serum (Hyclone, Logan, UT), penicillin and streptomycin (Invitrogen), 0.5 mM beta-mercaptoethanol (Merck, Darmstadt, Germany) and recombinant mouse IL-3 produced in Cos cells. For the generation of clonal Ba/F3 cells stably expressing FOXO3(A3)-ER or FOXO4(A3)-ER, the pcDNA3-HA-FOXO3(A3)-ER construct and the pcDNA3-HA-FOXO4(A3)-ER construct were electroporated into Ba/F3 cells. Cells were maintained in the presence of 1 mg/ml G418 (Gibco, Paisley, UK) and clonal lines were generated by limited dilution.

extract_protocol:
RNA extraction:
1. Add 1 ml Trizol per 5x 106 cells in suspension (1 ml trizol per 10 cm culture disk) and mix by pipetting, transfer to 1.5 ml eppendorf tube.   2. Incubate 5 min at room temperature.   3. Add chloroform (200 µl per ml Trizol), mix for 15 seconds by shaking vigorously. Incubate 2-3 min at room temperature.   4. Centrifuge 20 min at 14000 rpm 4°C. After centrifugation, transfer the water-phase to a new 1.5-ml micro centrifuge tube.   5. add isopropanol to precipitate RNA. Use 0.5 ml per 1 ml trizol. Mix by shaking, leave samples at RT for 10 minutes. Centrifuge at 14000 rpm for 15 min.   6. wash pellet with 75% ethanol. Centrifuge at 14000 rpm for 15 min. Carefully pipet off all ethanol (respin briefly and use a P20 for the last microliters). Airdry pellets briefly before dissolving in MilliQ water. Depending on pellet-size, this may take a while. Continue with RNeasy columns (Qiagen) for clean-up of RNA (maximal 100 µg/column)   7. Adjust each sample to a volume of 300 µl with sterile MilliQ water. Add 160 µl buffer RLT to the samples, and mix (= lysis buffer).   8. Add 240 µl ethanol (100% stored at -20 °C) to the lysate, mix well by pipetting and immediately apply the sample to an RNeasy mini spin column sitting in a 2 ml collection tube (use a second P1000 pipet and work as quick as possible). Next lysate, and so on.   9. Centrifuge at 8000 rpm for 15 seconds in an Eppendorf centrifuge. Discard flowthrough, reuse collection tube. All centrifugation steps at roomtemperature! DNAse treatment: D1. Pipet 350 µl Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm to wash. Discard the flow-through. Reuse the collection tube in step D3. D2. Prepare DNase I incubation mix (80 µl/reaction): add 10 µl DNase I stock solution to 70 µl Buffer RDD. Mix by gently inverting the tube. Buffer RDD is supplied with the RNase-Free DNase Set. Note: DNase I is especially sensitive to physical denaturation. Mixing should only be carried out by gently inverting the tube. Do not vortex. D3. Pipet the DNase I incubation mix (80 µl) directly onto the RNeasy silica-gel membrane, and place on the benchtop (20-30°C) for 15 min. Note: Make sure to pipet the DNase I incubation mix directly onto the RNeasy silica-gel membrane. DNase digestion will be incomplete if part of the mix sticks to the walls or the O-ring of the RNeasy column. D4. Pipet 350 µl Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm. Discard the flow-through and collection tube.   10. Transfer the RNeasy column into a new 2 ml collection tube. Add 500 µl buffer RPE, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse the collection tube in next steps.  11. Pipet 500 µl buffer RPE onto the RNeasy column, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse collection tube.   12. Centrifuge at 10,000 rpm for 2 minutes (to dry the RNeasy membrane).   13. Transfer the RNeasy column into a new 1.5 ml collection tube. Pipet 100 µl milliQ directly onto the RNeasy membrane and incubate for 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. Note: When small yields are expected, the elution volume can be lowered to a minimum of 35 µl milliQ.   14. Pipet the eluate of step 13 again onto the RNeasy membrane and incubate for another 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. After elution, put all RNA-samples on ice. 15. Determine RNA concentration by measuring A260, and RNA intactness by Bioanalyzer. Snap-freeze and store eluate at -80 °C.

treatment_protocol: CP003-tr: Ba/F3 cells expressing FOXO3(A3)-ER or FOXO4(A3)-ER were stimulated with 4-OHT for times indicated, after which cells were harvested for RNA isolations.


title: B4-8 vs. B-pool


title: B-pool vs. B3-2


title: NY103_miR


title: B4-2 vs. B-pool


title: B2-2 vs. B-pool


title: B-pool vs. B3-8


title: CLP Ly6D+ CLP cell sorted from BM of B57Bl6 mice, biological rep2

description:
Gene expression data
WT Ly6D+CLP_Rep2

value: Bone marrow

value: Adult 8-12weeks old

value: CLP Ly6D+ CLP cell


title: Vaccinated Infected 72h Replicate 4

description: Biological replicate 4 of 6


title: B-pool vs. B1-8


title: Vaccinated Infected 72h Replicate 3

description: Biological replicate 3 of 6


title: B-pool vs. B1-2


title: B46_miR


title: A4-8 vs. A-pool


title: B44_miR


title: B43_miR


title: NY104_miR


title: B45_miR


title: NY101_miR


title: NY102_miR


title: A-pool vs. A3-8


title: A-pool vs. A1-8


title: A2-8 vs. A-pool


title: Unvaccinated Infected 72h Replicate 6

description: Biological replicate 6 of 6

source_name: 2nd left gill arch from unvaccinated fish 72 h post-challenge with Y. ruckeri


title: Vaccinated Infected 72h Replicate 1

description: Biological replicate 1 of 6


title: A2-2 vs. A-pool


title: Unvaccinated Infected 72h Replicate 2

description: Biological replicate 2 of 6

value: 2nd left gill arch from unvaccinated fish 72 h post-challenge with Y. ruckeri


title: A-pool vs. A1-2


title: Unvaccinated Infected 72h Replicate 3

description: Biological replicate 3 of 6


title: Vaccinated Infected 72h Replicate 2

description: Biological replicate 2 of 6


title: Unvaccinated Infected 8h Replicate 4

description: Biological replicate 4 of 6

source_name: 2nd left gill arch from unvaccinated fish 8 h post-challenge with Y. ruckeri


title: Vaccinated Infected 8h Replicate 3

description: Biological replicate 3 of 6

source_name: 2nd left gill arch from 6 wk post-vaccinated fish 8 h post-challenge with Y. ruckeri


title: Unvaccinated Infected 72h Replicate 4

description: Biological replicate 4 of 6


title: CP001-B4-1 vs. CP001-B4-4

hyb_protocol: Hybridization protocol v2.2: PREHYBRIDIZATION: Make 100 ml prehybridization buffer (for a maximum of 4 slides) containing 5xSSC, 25% formamide (Merck Cat# 1.09684.10), 0.1% SDS and 1% bovine serum albumin (BSA; Sigma Cat# A-9418): 25 ml 20x SSC, 25 ml pure formamide, 49 ml ddH2O, 1 ml 10% SDS and 1 g BSA. After BSA has dissolved the solution becomes clear in about 5 minutes. Filter prehybridization buffer through a 0.22 micron syringe filter. Heat the prehybridization solution to 42C in a 100 ml Coplin Jar. Place slides to be analyzed into the preheated prehybridization buffer. Incubate for 45 minutes at 42C. Wash the slides by dipping 5 times in room temperature ddH2O (staining dish). Dip the slides 5 times in room temperature isopropanol (staining dish). Air dry in fume hood (15 ml tube rack upside down). Slides should be used immediately following prehybridization. HYBRIDIZATION: (NOTE: The first steps of the hybridization protocol can be completed during the prehybridization step.) The hybridization volume for a whole slide (25x60mm) is 45 ul. Maximum volume of Cy3 and Cy5 combined target is 25 ul! It could be necessary to concentrate in a speed vac until the volume is below 25 ul. Prepare 2x hybridization buffer containing 50% formamide, 10xSSC and 0.2% SDS: 2.5 ml formamide, 2.5 ml 20xSSC and 0.1 ml 10% SDS. Immediately filter the hybridization buffer through a 0.22 micron filter (before SDS precipitates out of solution). Take 250 ul of the 2x hybridization buffer. Add 5 ul Herring sperm DNA (stock 10 ug/ul, sheared). Final concentration in 2x hybridization buffer is 200 ug/ml. In case of Human Gene Arrays add also 5 ul tRNA (stock 20 ug/ul). Preheat to 42C to overcome SDS precipitation. Combine 25 ul target with 25 ul 2x hybridization buffer (preheated to 42C). Heat at 95C for 5 minutes. Spin at 12K for 2 minutes. DO NOT place on ice after the 2 minute spin. Using standard coverslips: To each array add a total of 45 ul target as 3 to 6 separate dots in the center, along the length of the slide. Put a coverslip (25x60mm) on the array by holding the coverslip in place with your fingertips, toward the bottom of the slide. Gently (!) allow the coverslip to drop onto the array by using a needle. Do not move the coverslip after it is in place. Using LifterSlips (Erie Scientific): Place clean LifterSlip, teflon side down, over the array area. Place the pipette tip along an open edge of the LifterSlip and slowly pipette 45 ul target out of the tip. Capillary action will draw the probe mix under the slip. Place the slide in a Corning Hybridization Chamber (Corning Cat# 2551). Add 20 ul of water to each well in the chamber and clamp the hybridization chamber closed. Gently place the hybridization chamber into a 42C water bath for 16-20 hours. WASHING THE HYBRIDIZED ARRAYS: Remove the slide from the hybridization chamber, taking care not to disturb the coverslip. Perform the following washes: (i) Low-stringency wash: Place the slides in a Coplin Jar containing 100 ml 1xSSC and 0.2% SDS (= 100 ml 1xSSC and 2 ml of 10% SDS). Gently remove the coverslip while the slide is in solution. LifterSlips are reusable and should be washed in 70% EtOH prior to use. Incubate for 4 minutes at room temperature. (ii) High-stringency wash: Place the slides in a Coplin Jar containing 100 ml 0.1xSSC and 0.2% SDS (= 10 ml 1xSSC, 90 ml water and 2 ml of 10% SDS). Incubate for 4 minutes at room temperature. Wash the slide finally in 100 ml 0.1xSSC to remove particles of SDS. Incubate for 4 minutes at room temperature. Allow the slides to dry by centrifuge 1 minute 500 rpm (do this immediately after the third wash).

label_protocol:
aRNA labeling with Cy-dyes:
In dark micro centrifuge tube; dilute/concentrate required aRNA sample (x ng) to 8 µl.  Add 1 µl 0.5 M NaBicarbonate buffer, pH 9. Mix well.  Resuspend monofunctional NHS-ester Cy3 or Cy5 dye (Amersham PA 23001 and 25001): Quickly resuspend entire tube in 10 µl DMSO (Merck 8.02912.10). Add 1.25 µl per sample. Mix immediately and quickly.  Incubate 60 min at RT in the dark.  Add 4.5 µl 4 M hydroxylamine for quenching to prevent cross-coupling.  Incubate 15 min at RT in the dark.    Cleanup using Clontech ChromaSpin-30 columns:  1. Upon removing a CHROMA SPIN Column from the protective plastic bag, invert it several times to resuspend the gel matrix completely. Before removing the top make sure that all the matrix is at the bottom by vigorously flicking the column downwards to remove matrix that is stuck to the top cap.  2. Holding the CHROMA SPIN Column upright, grasp the break-away end between your thumb and index finger and snap off. Place the end of the spin column into one of the 2-ml microcentrifuge (collection) tubes provided, and lift off the top cap. Save the top cap and the white-end cap.  3. Centrifuge at 700 g for 5 min (2700 RPM in Heraeus Megafuge 1.0 Sepatech Centrifuge, 1500 RPM in Eppendorf 5810 centrifuge (prog. 5)). After centrifugation, the column matrix will appear semi-dry. This step purges the equilibration buffer from the column and re-establishes the matrix bed. Make sure that the matrix bed is flat.  4. Remove the spin column and collection tube from the centrifuge rotor, and discard the collection tube and column equilibration buffer.  5. Place the spin column into the second 2-ml microcentrifuge tube. Carefully and slowly apply the sample to the center of the gel bed's flat surface. Drop by drop! Do not allow any sample to flow along the inner wall of the column - this will completely mess up the sample.  6. Centrifuge at 700 g for 5 min.  7. Remove the spin column and collection tube from the rotor and detach them from each other. The purified sample is at the bottom of the collection tube. Immediately keep on ice and in the dark!  Purified sample is about 15-30 µl. Bring sample up to 35 µl with water and take 5 µl eluate for spectrophotometry (190 to 750 nm range).    Samples may be stored at -20 C.

growth_protocol: CP001-grow: Ba/F3 cells were cultured in RPMI-1640 containing glutamax (Invitrogen), 10% fetal bovine serum (Hyclone, Logan, UT), penicillin and streptomycin (Invitrogen), 0.5 mM beta-mercaptoethanol (Merck, Darmstadt, Germany) and recombinant mouse IL-3 produced in Cos cells 44. For the generation of clonal Ba/F3 cells stably expressing myrPI3K-ER or myrPKB-ER, the SRalpha-myrp110 -ER construct and the SRalpha-myrPKB-ER construct were electroporated into Ba/F3 cells together with pSG5 conferring neomycin resistance.

treatment_protocol: CP003-tr: Ba/F3 cells expressing myrPI3K-ER or myrPKB-ER were stimulated with 4-OHT for times indicated, after which cells were harvested for RNA isolations.

value: PKB

value: 30 min


title: Vaccinated Infected 8h Replicate 5

description: Biological replicate 5 of 6

value: 2nd left gill arch from 6 wk post-vaccinated fish 8 h post-challenge with Y. ruckeri


title: Unvaccinated Infected 8h Replicate 5

description: Biological replicate 5 of 6

value: 2nd left gill arch from unvaccinated fish 8 h post-challenge with Y. ruckeri


title: A4-2 vs. A-pool


title: Unvaccinated Infected 72h Replicate 5

description: Biological replicate 5 of 6


title: Vaccinated Infected 8h Replicate 4

description: Biological replicate 4 of 6


title: A-pool vs. A3-2


title: Vaccinated Infected 8h Replicate 2

description: Biological replicate 2 of 6


title: Vaccinated Infected 8h Replicate 6

description: Biological replicate 6 of 6


title: CP001-B4-1 vs. CP001-B4-6

value: 120 min


title: Unvaccinated Infected 8h Replicate 2

description: Biological replicate 2 of 6


title: CP001-B3-3 vs. CP001-B3-1

value: 15 min


title: CP001-B4-1 vs. CP001-B4-7

value: 240 min


title: Unvaccinated Infected 72h Replicate 1

description: Biological replicate 1 of 6


title: CP001-B3-5 vs. CP001-B3-1

value: 60 min


title: Vaccinated Infected 8h Replicate 1

description: Biological replicate 1 of 6


title: Unvaccinated Infected 8h Replicate 6

description: Biological replicate 6 of 6


title: Unvaccinated Infected 8h Replicate 3

description: Biological replicate 3 of 6


title: CP001-B2-1 vs. CP001-B2-7


title: CP001-B3-7 vs. CP001-B3-1


title: CP001-B4-1 vs. CP001-B4-5


title: CP001-B2-1 vs. CP001-B2-6


title: CP001-B3-6 vs. CP001-B3-1


title: CP001-B4-1 vs. CP001-B4-3


title: Unvaccinated Infected 8h Replicate 1

description: Biological replicate 1 of 6


title: CP001-B2-1 vs. CP001-B2-5


title: Vaccinated Uninfected 0h Replicate 5

description: Biological replicate 5 of 6

source_name: 2nd left gill arch from 6 wk post-vaccinated and uninfected fish


title: Vaccinated Uninfected 0h Replicate 2

description: Biological replicate 2 of 6

value: 2nd left gill arch from 6 wk post-vaccinated and uninfected fish


title: Vaccinated Uninfected 0h Replicate 3

description: Biological replicate 3 of 6


title: 72 hr TR treated

description: NPC Untreated vs NPC Treated 72 hr

hyb_protocol: Hybridization protocol   II. Prehybridization  1. Prepare Prehybridization Solution (Fresh Each Time)  **this volume is based on a glass dish with a base measurement of 11x8cm. This dish allows for a pre-hyb of 1-4 slides. Adjust volume accordingly based on size of dish and/or number of slides.  106.0ml dH2O  3.0g BSA  1.2ml 10%SDS  2. Add Prehybridization solution to a glass slide-staining dish and place post-processed slides array side up into solution. Make sure there are no bubbles on the surfaces of the slides.  3. Place the staining jar containing the Prehybridization solution and slides into a waterbath and hybridize for 1 hour at 42oC.  4. Take the prehybridized slides out of the Prehybridization solution and place into a slide holder submerged in a slide-washing tray containing nuclease-free water. Wash slides for 2 minutes with constant shaking up and down.  5. Transfer slide rack to a slide washing tray containing isopropanol and wash for 2 minutes with constant shaking up and down.  6. Take the slides in the isopropanol bath to the centrifuge to keep the slides wet until you can dry them rapidly. Spin at 600 RPM in a 50ml conical for 3 minutes to dry.  **Complete this step within one hour of hybridization  III. Hybridization  1. Add the following to the 4.5µl labeled sample.  0.5µl 10 mg/ml tRNA  0.5ul 10mg/ml Salmon Sperm DNA  1.0µl 20X SSC  2.5ul Formamide  1.0µl 1% SDS  2. Heat to 98 oC for 2 minutes. Spin in centrifuge for 1 min at 12,000 Xg. Let cool for 5 min.  3. Pipette cooled 10µl hybridization solution on microarray. Apply 22 x 22 coverslip to cover array (if bubbles appear under the cover slip, they will slowly migrate to the edges provided that the volume is accurate).  4. OPTIONAL: Apply thin wall of rubber cement around the 4 corners of the coverslip to avoid movement. This step is recommended if your waterbath is not perfectly level.  5. Hybridize in standard hyb. chambers with ~40µl water under each slide (20ul under both ends of each slide) overnight in 50oC water bath  **Bubbles (esp. large ones) can be troublesome for your arrays since they can cause areas of non-hybridization. To avoid bubbles, do not use the blowout feature of the pipette when adding the probe to the slide. Also, clean your coverslips with alcohol and lint-free wipes before placing over probe.  IV. Post Hyb washes (next day)  1. Remove cover slip while array is submerged in first wash solution (2XSSC + 0.1% SDS), transfer to submerged microscope slide staining racks and rinse for 1 min in 1X SSC+0.05% SDS with agitation/shaking.  2. Rinse in 0.06X SSC with shaking. Transfer to another submerged staining rack and wash 2 min in fresh 0.06X SSC with shaking.  3. Centrifuge 3 min at 1000 rpm in a 50ml conical (array edge up) to dry. Scan immediately.

scan_protocol: After washing, the arrays were scanned with a GenePix4200AL scanner (Molecular Devices, Sunnyvale, CA). The images were processed using GenePix 6.1 and the resulting text files were exported to Microsoft Excel.

data_processing: A normalization factor was calculated using 36 human control genes by dividing the median intensity of the Cy5 signal by the median intensity of Cy3 signal of the controls.  The data were normalized by multiplying the Cy3 signal of each spot by the normalization factor.  The ratio of the Cy5 median intensity over the Cy3 median intensity was determined for each spot and the average ratio determined for the replicate spots.

organism: unidentified

source_name: adult neural precursor cells untreated

label_protocol: I. Synthesis and Labeling of cDNA  1. Bring 3.0µg of RNA to a volume of 11µl (in a PCR tube) with nucleotide-free water and add 2.2µl (2mg/ml) random primers (pulse spin to collect contents).  2. Heat 2 min at 98oC, snap cool on ice.  3. (Keep on ice) and add 11.1µl of the following reaction mix:  5.0µl 5X First-Strand buffer  2.5µl 100 mM DTT  2.3µl low dTdNTP mix (5mM A,G,C and 0.2mM T stock)  1.5ul Cy3 or Cy5  Then add 1.2ul Superscript, vortex to mix and spin to collect contents  4. Incubate 10 min at 25oC followed by 90 min at 42oC in PCR machine.  **Can freeze or leave at 4oC overnight if necessary  5. Prime a microcon10 column (YM10 from Millipore) with 400µl TE and spin for 10 min at 10,000 Xg. Empty flow-through in collection tube and return primed column. Add both reactions (cy3 and cy5) to column and centrifuge at 10,000 Xg until ~25µl remaining (~20-30 min). Wash with 200µl TE and spin until almost dry (<5µl).  6. Recover cDNA by inverting microcon into new collection 1.5 ml tube and centrifuge at half max speed 1 min.  7. Bring sample to 4.5µl with TE.  The detailed labeling and hybridization protocol can be obtained at http://www.cag.icph.org/downloads_page.htm#LabelingProtocols.

tag: treatment

value: no infection

value: control

organism: Human betaherpesvirus 5

source_name: adult neural precursor cells infected with HCMV TR strain, 72h

value: TR

value: infection


title: Vaccinated Uninfected 0h Replicate 6

description: Biological replicate 6 of 6

value: Gill

value: pooled total RNA from 4 samples from each of the six treatments


title: CP001-B2-1 vs. CP001-B2-4


title: Vaccinated Uninfected 0h Replicate 4

description: Biological replicate 4 of 6


title: CP001-B2-1 vs. CP001-B2-3


title: CP001-B1-7 vs. CP001-B1-1


title: CP001-B1-3 vs. CP001-B1-1


title: CP001-B1-5 vs. CP001-B1-1


title: CP001-A4-1 vs. CP001-A4-4


title: Unvaccinated Uninfected 0h Replicate 4

description: Biological replicate 4 of 6

source_name: 2nd left gill arch from unvaccinated and uninfected control fish


title: Unvaccinated Uninfected 0h Replicate 5

description: Biological replicate 5 of 6

value: 2nd left gill arch from unvaccinated and uninfected control fish


title: CP001-A3-7 vs. CP001-A3-1


title: Unvaccinated Uninfected 0h Replicate 2

description: Biological replicate 2 of 6


title: CP001-A4-1 vs. CP001-A4-7


title: CP001-A4-1 vs. CP001-A4-5


title: Unvaccinated Uninfected 0h Replicate 6

description: Biological replicate 6 of 6


title: CP001-B1-4 vs. CP001-B1-1


title: Unvaccinated Uninfected 0h Replicate 1

description: Biological replicate 1 of 6


title: Unvaccinated Uninfected 0h Replicate 3

description: Biological replicate 3 of 6


title: CP001-A4-1 vs. CP001-A4-6


title: CP001-B1-6 vs. CP001-B1-1


title: CP001-A4-1 vs. CP001-A4-3


title: 72 hr Towne infection

description: NPC Untreated vs Towne 72 hr

source_name: adult neural precursor cells infected with HCMV Towne strain for 72h

value: Towne


title: Vaccinated Uninfected 0h Replicate 1

description: Biological replicate 1 of 6


title: hip1D, Severe stress alone

city: Kyoto

first: Fuyuki

last: Ishikawa

address: Yoshida-Konoe-cho, Sakyo-ku

country: Japan

institute: Kyoto University

description: Gene expression data from hip1D cells exposed to 25 mM H2O2 for 1 h

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Yeast Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with RMA algorithm (Affymetrix Expression Console version 1.1).

organism: Schizosaccharomyces pombe

source_name: Fission yeast hip1D cells exposed to 25 mM H2O2 for 1 h

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

growth_protocol: Fission yeast cells were grown to the logarithmic phase in YES medium at 32°C.

extract_protocol: Total RNA was isolated as previously described (Kanoh et al. 1995) and treated with 0.625 U/g RNA of DNase I to digest genomic DNA.

tag: genotype


title: WT, Priming stress and Severe stress

description: Gene expression data from WT cells exposed to 40°C for 1 h followed by 25 mM H2O2 for 1 h

source_name: Fission yeast WT cells exposed to 40°C for 1 h followed by 25 mM H2O2 for 1 h


title: slm9D, Priming stress and Severe stress

description: Gene expression data from slm9D cells exposed to 40°C for 1 h followed by 25 mM H2O2 for 1 h

source_name: Fission yeast slm9D cells exposed to 40°C for 1 h followed by 25 mM H2O2 for 1 h


title: hip1D, Priming stress and Severe stress

description: Gene expression data from hip1D cells exposed to 40°C for 1 h followed by 25 mM H2O2 for 1 h

source_name: Fission yeast hip1D cells exposed to 40°C for 1 h followed by 25 mM H2O2 for 1 h


title: CP001-A2-1 vs. CP001-A2-7


title: WT, Severe stress alone

description: Gene expression data from WT cells exposed to 25 mM H2O2 for 1 h

source_name: Fission yeast WT cells exposed to 25 mM H2O2 for 1 h


title: CP001-A3-6 vs. CP001-A3-1


title: slm9D, Severe stress alone

description: Gene expression data from slm9D cells exposed to 25 mM H2O2 for 1 h

source_name: Fission yeast slm9D cells exposed to 25 mM H2O2 for 1 h


title: hip1D, Priming stress alone

description: Gene expression data from hip1D cells exposed to 40°C for 1 h

source_name: Fission yeast hip1D cells exposed to 40°C for 1 h


title: CP001-A3-4 vs. CP001-A3-1


title: CP001-A2-1 vs. CP001-A2-6


title: WT, No stress

description: Gene expression data from WT cells without stress

source_name: Fission yeast WT cells without stress


title: CP001-A2-1 vs. CP001-A2-4


title: WT, Priming stress alone

description: Gene expression data from WT cells exposed to 40°C for 1 h

source_name: Fission yeast WT cells exposed to 40°C for 1 h


title: CP001-A2-1 vs. CP001-A2-3


title: CP001-A3-3 vs. CP001-A3-1


title: CP001-A3-5 vs. CP001-A3-1


title: hip1D, No stress

description: Gene expression data from hip1D cells without stress

source_name: Fission yeast hip1D cells without stress


title: slm9D, Priming stress alone

description: Gene expression data from slm9D cells exposed to 40°C for 1 h

source_name: Fission yeast slm9D cells exposed to 40°C for 1 h


title: slm9D, No stress

description: Gene expression data from slm9D cells without stress

source_name: Fission yeast slm9D cells without stress


title: CP001-A2-1 vs. CP001-A2-5


title: hMSC - Unknown - 61F (022255_h)

status: Public on Jul 21 2012

city: Enschede

first: Nathalie

last: Groen

address: Drienerlolaan 5

department: Tissue Regeration

institute: University of Twente - MIRA – Institute for Biomedical Technology and Technical Medicine

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Unknown - 61F

hyb_protocol: The RNA was hybridized to the Human Genome U133A 2.0 Array (Affymetrix).

scan_protocol: GeneChips were scanned with a GeneChip G3000 scanner (Affymetrix)

data_processing: The data was processed as described in Hulsman et al. (2010; Delineation of amplification, hybridization and location effects in microarray data yields better-quality normalization. BMC Bioinformatics 11: 156) using Matlab, quantile-quantile normalization).

source_name: Female donor 61

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

growth_protocol: Bone marrow aspirates (5-20 ml) were obtained from donors with written informed consent and were approved by the medical ethical committee of the University medical Centre Utrecht, and hMSCs were isolated and proliferated in vitro. Briefly, aspirates were resuspended using a 20-gauge needle, plated at a density of 500,000 nucleated cells/cm2 and cultured in hMSC proliferation medium containing α-minimal essential medium, 10% fetal bovine serum, 0.2 mM ascorbic acid, 2 mM L-glutamine, 100 U/mL penicillin with 100 µg/mL streptomycin and 1 ng/mL basic fibroblast growth factor (bFGF). When confluence was reached, cells were further subcultured at 1000 cell/cm2 on tissue culture poly styrene flasks.

extract_protocol: RNA was isolated using an RNeasy mini kit (Qiagen).

treatment_protocol: Bone marrow-derived hMSCs from different donors aging from 17 - 89 years were compared.

tag: gender

value: Female

tag: aspiration site

value: Unknown


title: hMSC - Unknown - 66F (022256_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Unknown - 66F

source_name: Female donor 66


title: CP001-A1-5 vs. CP001-A1-1


title: hMSC - Iliac crest - 54F (022253_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Iliac crest - 54F

source_name: Female donor 54

value: Iliac crest


title: CP001-A1-6 vs. CP001-A1-1


title: hMSC - Unknown - 58M (022257_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Unknown - 58M

source_name: Male donor 58

value: Male


title: hMSC - Iliac crest - 42F (022249_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Iliac crest - 42F

source_name: Female donor 42


title: hMSC - Acetabulum - 68F (022247_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Acetabulum - 68F

source_name: Female donor 68

value: Acetabulum


title: CP001-A1-7 vs. CP001-A1-1


title: hMSC - Acetabulum - 66F (022254_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Acetabulum - 66F


title: CP001-B3-4 vs. CP001-B3-1

value: PKB

value: 30 min


title: hMSC - Acetabulum - 65F (022243_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Acetabulum - 65F

source_name: Female donor 65


title: hMSC - Acetabulum - 80F (022248_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Acetabulum - 80F

source_name: Female donor 80


title: hMSC - Iliac crest - 21M (022246_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Iliac crest - 21M

source_name: Male donor 21


title: hMSC - Unknown - 51F (022258_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Unknown - 51F

source_name: Female donor 51


title: CP001-A1-3 vs. CP001-A1-1

value: 15 min


title: hMSC - Unknown - 76F (022250_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Unknown - 76F

source_name: Female donor 76


title: hMSC - Acetabulum - 76F (022245_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Acetabulum - 76F


title: CP001-A1-4 vs. CP001-A1-1


title: hMSC - Iliac crest - 40M (022252_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Iliac crest - 40M

source_name: Male donor 40


title: hMSC - Unknown - 59F (017747_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Unknown - 59F

source_name: Female donor 59


title: hMSC - Iliac crest - 54F (017745_h)


title: hMSC - Acetabulum - 81F (022242_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Acetabulum - 81F

source_name: Female donor 81


title: hMSC - Unknown - 44M (022251_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Unknown - 44M

source_name: Male donor 44


title: hMSC - Iliac crest - 37F (017746_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Iliac crest - 37F

source_name: Female donor 37


title: hMSC - Acetabulum - 75M (022240_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Acetabulum - 75M

source_name: Male donor 75


title: hMSC - Acetabulum - 42M (017744_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Acetabulum - 42M

source_name: Male donor 42


title: hMSC - Acetabulum - 69F (017742_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Acetabulum - 69F

source_name: Female donor 69


title: hMSC - Acetabulum - 76F (017740_h)


title: 188 dpn liver LP 58

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Leibniz Institute for Farm Animal Biology (FBN)

description: Gene expression data from liver sample of offspring

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42C on Affymetrix GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and BioConductor.

organism: Sus scrofa

source_name: Liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

value: 188 dpn

tag: sample type

value: offspring of German Landrace gilts fed a gestational low protein diet

value: gestational low protein diet

value: liver

tag: genetic background

value: German Landrace


title: 188 dpn liver LP 57


title: hMSC - Acetabulum - 71F (017741_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Acetabulum - 71F

source_name: Female donor 71


title: 188 dpn liver LP 60


title: 188 dpn liver LP 61


title: hMSC - Acetabulum - 70F (022241_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Acetabulum - 70F

source_name: Female donor 70


title: 188 dpn liver LP 54


title: hMSC - Iliac crest - 47M (017738_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Iliac crest - 47M

source_name: Male donor 47


title: 188 dpn liver LP 55


title: hMSC - Iliac crest - 61F (017734_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Iliac crest - 61F

source_name: Female donor 61


title: hMSC - Iliac crest - 34F (017737_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Iliac crest - 34F

source_name: Female donor 34


title: hMSC - Iliac crest - 53F (017732_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Iliac crest - 53F

source_name: Female donor 53


title: hMSC - Iliac crest - 71F (017735_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Iliac crest - 71F


title: hMSC - Iliac crest - 24F (017733_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Iliac crest - 24F

source_name: Female donor 24


title: hMSC - Acetabulum - 57F (017743_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Acetabulum - 57F

source_name: Female donor 57


title: 188 dpn liver LP 53


title: 188 dpn liver LP 59


title: hMSC - Acetabulum - 75F (022244_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Acetabulum - 75F

source_name: Female donor 75


title: 188 dpn liver LP 56


title: 188 dpn liver LP 51


title: hMSC - Iliac crest - 46F (017730_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Iliac crest - 46F

source_name: Female donor 46


title: 188 dpn liver LP 52


title: hMSC - Iliac crest - 64F (017731_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Iliac crest - 64F

source_name: Female donor 64


title: hMSC - Acetabulum - 19F (017728_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Acetabulum - 19F

source_name: Female donor 19


title: hMSC - Iliac crest - 56F (017729_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Iliac crest - 56F

source_name: Female donor 56


title: hMSC - Iliac crest - 36M (017727_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Iliac crest - 36M

source_name: Male donor 36


title: 188 dpn liver LP 49


title: 188 dpn liver LP 50


title: hMSC - Iliac crest - 35F (013931_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Iliac crest - 35F

source_name: Female donor 35


title: 188 dpn liver LP 48

description: Gene expression data from liver sample of offspring


title: 28 dpn liver LP 45

value: 28 dpn


title: hMSC - Acetabulum - 61F (013933_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Acetabulum - 61F


title: 188 dpn liver LP 47


title: hMSC - Acetabulum - 69M (017739_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Acetabulum - 69M

source_name: Male donor 69


title: 188 dpn liver LP 46

source_name: Liver


title: hMSC - Iliac crest - 27F (013930_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Iliac crest - 27F

source_name: Female donor 27


title: hMSC - Acetabulum - 38F (013929_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Acetabulum - 38F

source_name: Female donor 38


title: hMSC - Acetabulum - 74F (013932_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Acetabulum - 74F

source_name: Female donor 74


title: 28 dpn liver LP 43


title: 28 dpn liver LP 40


title: 28 dpn liver LP 37


title: hMSC - Iliac crest - 38F (013927_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Iliac crest - 38F


title: hMSC - Iliac crest - 61M (013934_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Iliac crest - 61M

source_name: Male donor 61


title: 28 dpn liver LP 39


title: 28 dpn liver LP 44


title: 28 dpn liver LP 41


title: 28 dpn liver LP 38


title: hMSC - Acetabulum - 63F (013928_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Acetabulum - 63F

source_name: Female donor 63


title: 28 dpn liver LP 42


title: 28 dpn liver LP 36


title: hMSC - Iliac crest - 42M (013925_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Iliac crest - 42M

source_name: Male donor 42


title: hMSC - Acetabulum - 61F (013924_h)

source_name: Female donor 61


title: hMSC - Iliac crest - 17M (017736_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Iliac crest - 17M

source_name: Male donor 17


title: hMSC - Iliac crest - 52F (013926_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Iliac crest - 52F

source_name: Female donor 52


title: hMSC - Acetabulum - 59F (013919_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Acetabulum - 59F

source_name: Female donor 59


title: 28 dpn liver LP 33


title: 28 dpn liver LP 34


title: hMSC - Acetabulum - 67M (013922_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Acetabulum - 67M

source_name: Male donor 67


title: 1 dpn liver LP 30

value: 1 dpn


title: hMSC - Iliac crest - 76F (013918_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Iliac crest - 76F

source_name: Female donor 76


title: 28 dpn liver LP 31


title: hMSC - Acetabulum - 66M (013923_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Acetabulum - 66M

source_name: Male donor 66


title: hMSC - Acetabulum - 79F (013920_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Acetabulum - 79F

source_name: Female donor 79


title: 28 dpn liver LP 35

description: Gene expression data from liver sample of offspring


title: hMSC - Acetabulum - 49M (013921_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Acetabulum - 49M

source_name: Male donor 49


title: 28 dpn liver LP 32


title: hMSC - Acetabulum - 29F (013915_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Acetabulum - 29F

source_name: Female donor 29


title: 1 dpn liver LP 27

source_name: Liver


title: 1 dpn liver LP 29


title: hMSC - Acetabulum - 49F (013917_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Acetabulum - 49F

source_name: Female donor 49


title: 1 dpn liver LP 25


title: 1 dpn liver LP 28


title: hMSC - Iliac crest - 84F (013916_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Iliac crest - 84F

source_name: Female donor 84


title: 1 dpn liver LP 22


title: 1 dpn liver LP 26


title: 1 dpn liver LP 21


title: hMSC - Acetabulum - 28F (013914_h)

description:
Gene expression data from hMSCs isolated from donors of different age
hMSC - Acetabulum - 28F

source_name: Female donor 28


title: 1 dpn liver LP 24


title: rESC-/- 2

city: Cambridge

first: Harry

middle: G

last: Leitch

address: Tennis Court Road

country: United Kingdom

institute: University of Cambridge

description: BL2 rES

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw data were filtered remove any non expressed genes from the set to avoid adding noise to the analysis. The data were then transform using VST (Variance Stabilizing Transform) and normalised by quantile normalisation

source_name: rESC-/-

label_protocol: Total Prep 96-RNA amplification kit from Ambion (Applied Biosystems)

extract_protocol: QIAGEN Rneasy kit

tag: strain background

tag: genotype/variation

value: Blimp1 null (-/-)

value: reversion of EpiSC to ESC (rESC)


title: rESC-/- 3

description: BL6 rES


title: rESC-/- 1

description: J2.3 rES


title: rESC+/- 2

description: BL7 rES

source_name: rESC+/-

value: Blimp1 heterozygous (+/-)


title: EpiSC-/- 3

description: BL6 Epi

source_name: EpiSC-/-

value: epiblast stem cells (EpiSC)


title: 1 dpn liver LP 18

tag: tissue


title: 1 dpn liver LP 23


title: 1 dpn liver LP 20


title: EpiSC+/- 3

description: BL7 Epi

source_name: EpiSC+/-


title: rESC+/- 1

description: BL3 rES


title: 94 dpc liver LP 14

value: 94 dpc


title: 94 dpc liver LP 15


title: EpiSC+/- 1

description: BL3 Epi


title: 94 dpc liver LP 12


title: 94 dpc liver LP 11


title: ESC-/- 2_2i

value: embryonic stem cells (ESC)

tag: growth condition

value: in the presence of 2i/LIF


title: 1 dpn liver LP 19

tag: age


title: 94 dpc liver LP 16


title: 1 dpn liver LP 17


title: MEF

description: MEF

source_name: MEF

value: wild type

tag: cell type

value: Mouse Embryonic Fibroblast (MEF)


title: ESC-/- 3_2i


title: EpiSC+/- 2

description: BL4 Epi


title: 94 dpc liver LP 13


title: 94 dpc liver LP 10


title: EpiSC-/- 2

description: BL2 Epi


title: ESC+/- 3_2i


title: 94 dpc liver LP 08


title: ESC+/- 2_2i


title: ESC+/- 1_2i


title: 94 dpc liver LP 07


title: ESC-/- 1_2i


title: 94 dpc liver LP 09


title: ESC-/- 3

source_name: ESC-/-


title: ESC-/- 2


title: 94 dpc liver LP 06


title: 94 dpc liver LP 04


title: ESC+/- 3

source_name: ESC+/-


title: ESC+/- 2


title: ESC+/- 1


title: IMR90-DAPT-1

status: Public on Jul 20 2012

city: Tucson

first: Megha

last: Padi

state: AZ

address: 1071 East Lowell St.

department: Molecular and Cellular Biology

institute: University of Arizona

hyb_protocol: Samples were hybridized to Human Gene 1.0 ST arrays according to the manufacturer's instructions.

scan_protocol: Scanning of microarrays was performed by following Affymetrix protocols at the Dana-Farber Cancer Institute microarray core facility.

data_processing: The data in Batches 1-8 were normalized by RMA with a custom CDF from the Michigan Microarray group (Version 13), using the R/Bioconductor package affy. ComBat was applied to this dataset with the batch variable as annotated above. Batch 9 was normalized separately by RMA with the custom CDF from the Michigan Microarray group (Version 13), using the R/Bioconductor package affy.

source_name: IMR-90 cells expressing GFP, treated with DAPT

label_protocol: RNA was converted into cDNA, then amplified and labeled with biotinylated nucleotides by in vitro transcription to produce biotinylated cRNA, according to the standard Affymetrix protocol.

growth_protocol: IMR-90 cells were cultured in DMEM (Cellgro) supplemented with 15% FBS (Omega Scientific), 1% Pen Strep (GIBCO), 1% Glutamax (GIBCO) and 1% MEM NEAA (GIBCO).

extract_protocol: viORF-expressing IMR-90 cell lines at passage 9 were seeded into five replicates at a density of 1 x 10^6 cells per 10-cm plates and harvested after 48 hr in RNAlater (Ambion). After isolation of total RNA (RNeasy, Qiagen) RNA integrity was determined using a Bioanalyzer (Agilent).

tag: cell line

tag: batch

value: Batch 9


title: ESC-/- 1


title: IMR90-3553-4

source_name: IMR-90 cells expressing shMAML1


title: IMR90-DMSO-3

source_name: IMR-90 cells expressing GFP, treated with DMSO


title: 94 dpc liver LP 01


title: IMR90-DAPT-3


title: IMR90-3553-1


title: IMR90-PLKO-2

source_name: IMR-90 cells expressing empty PLKO vector


title: IMR90-DAPT-2


title: IMR90-PLKO-4


title: IMR90-PLKO-3


title: IMR90-DMSO-1


title: 94 dpc liver LP 05


title: IMR90-EBV-BSRF1-E

source_name: IMR-90 cells expressing EBV-BSRF1

value: Batch 8


title: IMR90-EBV-BGLF3.5-E

source_name: IMR-90 cells expressing EBV-BGLF3.5


title: 94 dpc liver LP 02

source_name: Liver

value: offspring of German Landrace gilts fed a gestational low protein diet


title: IMR90-3553-3


title: IMR90-DMSO-2


title: IMR90-PLKO-1


title: IMR90-EBV-BFLF2-E

source_name: IMR-90 cells expressing EBV-BFLF2


title: IMR90-3553-2


title: IMR90-EBV-BNLF2B-E

source_name: IMR-90 cells expressing EBV-BNLF2B


title: IMR90-ADENO5-E3GP19K-E

source_name: IMR-90 cells expressing ADENO5-E3GP19K


title: IMR90-EBV-BLRF2-E

source_name: IMR-90 cells expressing EBV-BLRF2


title: IMR90-ADENO5-E4ORFB-E

source_name: IMR-90 cells expressing ADENO5-E4ORFB


title: IMR90-ADENO5-E4ORF1-E

source_name: IMR-90 cells expressing ADENO5-E4ORF1


title: IMR90-ADENO5-E4ORF3-E

source_name: IMR-90 cells expressing ADENO5-E4ORF3


title: IMR90-EBV-BNLF2A-E

source_name: IMR-90 cells expressing EBV-BNLF2A


title: 94 dpc liver LP 03

value: gestational low protein diet


title: IMR90-POLYOMCV-LST-E

source_name: IMR-90 cells expressing POLYOMCV-LST


title: IMR90-EBV-BNLF2B-D


title: IMR90-HPV16-E7-C-E

source_name: IMR-90 cells expressing HPV16-E7-C


title: IMR90-POLYOHPYV607A-LST-E

source_name: IMR-90 cells expressing POLYOHPYV607A-LST


title: IMR90-POLYOJCMAD1-LST-E

source_name: IMR-90 cells expressing POLYOJCMAD1-LST


title: IMR90-POLYOTSPY-LST-E

source_name: IMR-90 cells expressing POLYOTSPY-LST


title: IMR90-EBV-BFRF0.5-D

source_name: IMR-90 cells expressing EBV-BFRF0.5


title: IMR90-EBV-BNLF2A-D


title: IMR90-POLYOJCCY-LST-E

source_name: IMR-90 cells expressing POLYOJCCY-LST


title: IMR90-EBV-BSRF1-D

source_name: IMR-90 cells expressing EBV-BSRF1


title: IMR90-EBV-BGLF3.5-D

source_name: IMR-90 cells expressing EBV-BGLF3.5


title: IMR90-POLYOHPYV713A-LST-E

source_name: IMR-90 cells expressing POLYOHPYV713A-LST


title: IMR90-EBV-BFRF0.5-E


title: IMR90-ADENO5-E4ORF3-D


title: IMR90-ADENO5-E4ORF1-D


title: IMR90-ADENO5-E4ORFB-D


title: IMR90-ADENO5-E3GP19K-D


title: IMR90-POLYOSV40-LT-rep6-E

source_name: IMR-90 cells expressing POLYOSV40-LT


title: IMR90-POLYOHPYV713A-LST-D


title: IMR90-POLYOTSPY-LST-D


title: IMR90-EBV-BLRF2-D


title: IMR90-POLYOWU-LST-E

source_name: IMR-90 cells expressing POLYOWU-LST


title: IMR90-EBV-BFLF2-D

source_name: IMR-90 cells expressing EBV-BFLF2


title: IMR90-GFP-rep7-E

source_name: IMR-90 cells expressing GFP


title: IMR90-POLYOHPYV607A-LST-D


title: IMR90-POLYOJCCY-LST-D


title: IMR90-HPV16-E7-C-D


title: IMR90-POLYOJCMAD1-LST-D


title: IMR90-GFP-rep7-D


title: IMR90-EBV-BNLF2A-C


title: IMR90-POLYOSV40-LT-rep6-D


title: IMR90-EBV-BNLF2B-C

source_name: IMR-90 cells expressing EBV-BNLF2B


title: IMR90-EBV-BGLF3.5-C


title: IMR90-EBV-BSRF1-C


title: IMR90-ADENO5-E3GP19K-C

source_name: IMR-90 cells expressing ADENO5-E3GP19K


title: IMR90-POLYOWU-LST-D


title: IMR90-EBV-BLRF2-C

source_name: IMR-90 cells expressing EBV-BLRF2


title: IMR90-ADENO5-E4ORF3-C

source_name: IMR-90 cells expressing ADENO5-E4ORF3


title: IMR90-POLYOMCV-LST-D

source_name: IMR-90 cells expressing POLYOMCV-LST


title: IMR90-HPV16-E7-C-C

source_name: IMR-90 cells expressing HPV16-E7-C

value: Batch 7


title: IMR90-POLYOWU-LST-C


title: IMR90-ADENO5-E4ORFB-C

source_name: IMR-90 cells expressing ADENO5-E4ORFB


title: IMR90-ADENO5-E4ORF1-C

source_name: IMR-90 cells expressing ADENO5-E4ORF1


title: IMR90-POLYOHPYV713A-LST-C


title: IMR90-EBV-BFRF0.5-C

source_name: IMR-90 cells expressing EBV-BFRF0.5


title: IMR90-POLYOJCCY-LST-C

source_name: IMR-90 cells expressing POLYOJCCY-LST


title: IMR90-POLYOMCV-LST-C


title: IMR90-EBV-BFLF2-C


title: IMR90-GFP-rep7-C


title: IMR90-EBV-BFLF2-B


title: IMR90-POLYOHPYV607A-LST-C

source_name: IMR-90 cells expressing POLYOHPYV607A-LST


title: IMR90-POLYOSV40-LT-rep6-C


title: IMR90-POLYOTSPY-LST-C

source_name: IMR-90 cells expressing POLYOTSPY-LST


title: IMR90-EBV-BGLF3.5-B

source_name: IMR-90 cells expressing EBV-BGLF3.5


title: IMR90-EBV-BNLF2A-B

source_name: IMR-90 cells expressing EBV-BNLF2A


title: IMR90-EBV-BSRF1-B

source_name: IMR-90 cells expressing EBV-BSRF1


title: IMR90-EBV-BFRF0.5-B


title: IMR90-EBV-BLRF2-B


title: IMR90-ADENO5-E4ORFB-B


title: IMR90-ADENO5-E3GP19K-B


title: IMR90-ADENO5-E4ORF3-B


title: IMR90-POLYOHPYV713A-LST-B

source_name: IMR-90 cells expressing POLYOHPYV713A-LST


title: IMR90-POLYOSV40-LT-rep6-B

source_name: IMR-90 cells expressing POLYOSV40-LT


title: IMR90-ADENO5-E3GP19K-A


title: IMR90-EBV-BNLF2B-A

source_name: IMR-90 cells expressing EBV-BNLF2B


title: IMR90-POLYOHPYV607A-LST-B


title: IMR90-EBV-BLRF2-A


title: IMR90-EBV-BFRF0.5-A


title: IMR90-EBV-BNLF2A-A


title: IMR90-POLYOJCCY-LST-B


title: IMR90-EBV-BGLF3.5-A


title: IMR90-GFP-rep7-B

source_name: IMR-90 cells expressing GFP


title: IMR90-EBV-BSRF1-A


title: IMR90-ADENO5-E4ORF1-B


title: IMR90-EBV-BFLF2-A

source_name: IMR-90 cells expressing EBV-BFLF2


title: IMR90-EBV-BNLF2B-B


title: IMR90-POLYOJCMAD1-LST-C

source_name: IMR-90 cells expressing POLYOJCMAD1-LST


title: IMR90-HPV16-E7-C-B


title: IMR90-POLYOJCMAD1-LST-B


title: IMR90-POLYOWU-LST-B

source_name: IMR-90 cells expressing POLYOWU-LST


title: IMR90-POLYOMCV-LST-B

source_name: IMR-90 cells expressing POLYOMCV-LST


title: IMR90-POLYOTSPY-LST-B


title: IMR90-POLYOHPYV713A-LST-A


title: IMR90-ADENO5-E4ORF3-A

source_name: IMR-90 cells expressing ADENO5-E4ORF3


title: IMR90-ADENO5-E4ORFB-A

source_name: IMR-90 cells expressing ADENO5-E4ORFB


title: IMR90-POLYOHPYV607A-LST-A


title: IMR90-POLYOJCMAD1-LST-A


title: IMR90-EBV-BILF1-E

source_name: IMR-90 cells expressing EBV-BILF1

value: Batch 6


title: IMR90-ADENO5-E4ORF1-A

source_name: IMR-90 cells expressing ADENO5-E4ORF1


title: IMR90-ADENO5-E1B19K-E

source_name: IMR-90 cells expressing ADENO5-E1B19K


title: IMR90-GFP-rep6-E


title: IMR90-POLYOTSPY-LST-A

source_name: IMR-90 cells expressing POLYOTSPY-LST


title: IMR90-EBV-BXLF1-E

source_name: IMR-90 cells expressing EBV-BXLF1


title: IMR90-POLYOMCV-LST-A


title: IMR90-POLYOJCCY-LST-A

source_name: IMR-90 cells expressing POLYOJCCY-LST


title: IMR90-HPV18E7-technical replicate7

source_name: IMR-90 cells expressing HPV18-E7


title: IMR90-POLYOMCV-LTTRUNC-E

source_name: IMR-90 cells expressing POLYOMCV-LTTRUNC


title: IMR90-POLYOWU-LST-A


title: IMR90-POLYOSV40-LT-rep6-A

source_name: IMR-90 cells expressing POLYOSV40-LT


title: IMR90-POLYOSV40-LT-rep5-E


title: IMR90-EBV-BALF1-E

source_name: IMR-90 cells expressing EBV-BALF1


title: IMR90-HPV16-E6XX-E

source_name: IMR-90 cells expressing HPV16-E6XX


title: IMR90-GFP5-E

source_name: IMR-90 cells expressing GFP


title: IMR90-GFP-rep7-A


title: IMR90-HPV16-E7-C-A

source_name: IMR-90 cells expressing HPV16-E7-C


title: IMR90-ADENO5-E1B19K-D


title: IMR90-HPV16-E6NOXI128T-E

source_name: IMR-90 cells expressing HPV16-E6NOXI128T


title: IMR90-GFP-rep6-D


title: IMR90-HPV18-E6NOX-E

source_name: IMR-90 cells expressing HPV18-E6NOX


title: IMR90-HPV18-E6X-E

source_name: IMR-90 cells expressing HPV18-E6X


title: IMR90-EBV-BALF1-D


title: IMR90-POLYOMCV-LTTRUNC-D


title: IMR90-EBV-BILF1-D


title: IMR90-HPV5-E7-rep2-E

source_name: IMR-90 cells expressing HPV5-E7


title: IMR90-EBV-BXLF1-D


title: IMR90-HPV16-E6NOX-E

source_name: IMR-90 cells expressing HPV16-E6NOX


title: IMR90-HPV5-E7-rep2-D


title: IMR90-HPV16-E6NOXI128T-D


title: IMR90-HPV18-E6NOX-D


title: IMR90-HPV18-E6X-D


title: IMR90-EBV-BALF1-C


title: IMR90-HPV16-E6XX-D


title: IMR90-GFP5-D


title: IMR90-EBV-BILF1-C

source_name: IMR-90 cells expressing EBV-BILF1


title: IMR90-HPV16-E6NOX-D


title: IMR90-POLYOSV40-LT-rep5-D


title: IMR90-EBV-BXLF1-C


title: IMR90-GFP-rep6-C


title: IMR90-HPV5-E7-rep2-C


title: IMR90-ADENO5-E1B19K-C

source_name: IMR-90 cells expressing ADENO5-E1B19K


title: IMR90-POLYOMCV-LTTRUNC-C


title: IMR90-HPV16-E6NOXI128T-C


title: IMR90-HPV18-E6NOX-C


title: IMR90-POLYOSV40-LT-rep5-C


title: IMR90-HPV16-E6XX-C


title: IMR90-EBV-BXLF1-B


title: IMR90-GFP-rep6-B


title: IMR90-POLYOMCV-LTTRUNC-B


title: IMR90-EBV-BALF1-B


title: IMR90-HPV16-E6NOX-C


title: IMR90-HPV18-E6X-C


title: IMR90-HPV5-E7-rep2-B


title: IMR90-HPV18-E6X-B


title: IMR90-EBV-BILF1-B


title: IMR90-GFP5-C


title: IMR90-HPV18-E6NOX-B


title: IMR90-HPV16-E6NOXI128T-B


title: IMR90-HPV16-E6NOX-B


title: IMR90-HPV16-E6XX-B


title: IMR90-EBV-BALF1-A


title: IMR90-EBV-BILF1-A


title: IMR90-POLYOMCV-LTTRUNC-A


title: IMR90-HPV5-E7-rep2-A


title: IMR90-GFP-rep6-A


title: IMR90-EBV-BXLF1-A


title: IMR90-HPV16-E6XX-A


title: IMR90-ADENO5-E1B19K-B


title: IMR90-GFP5-B


title: IMR90-POLYOSV40-LT-rep5-B


title: IMR90-HPV18-E6X-A


title: IMR90-HPV16-E6NOXI128T-A


title: IMR90-HPV16-E6NOX-A


title: IMR90-POLYOSV40-LT-rep5-A


title: IMR90-GFP5-A


title: IMR90-HPV18-E6NOX-A


title: IMR90-EBV-BDLF4-E

source_name: IMR-90 cells expressing EBV-BDLF4

value: Batch 5


title: IMR90-SV40LT-technical replicate6

source_name: IMR-90 cells expressing SV40-LT


title: IMR90-HPV18E7-technical replicate6


title: IMR90-HPV18E7-technical replicate5


title: IMR90-SV40LT-technical replicate5


title: IMR90-EBV-BDLF3.5-E

source_name: IMR-90 cells expressing EBV-BDLF3.5


title: IMR90-EBV-BGLF3-E

source_name: IMR-90 cells expressing EBV-BGLF3


title: IMR90-EBV-BFRF2-E

source_name: IMR-90 cells expressing EBV-BFRF2


title: IMR90-ADENO5-E1B19K-A


title: IMR90-EBV-BVLF1-E

source_name: IMR-90 cells expressing EBV-BVLF1


title: IMR90-EBV-BTRF1-E

source_name: IMR-90 cells expressing EBV-BTRF1


title: IMR90-EBV-BRRF2-E

source_name: IMR-90 cells expressing EBV-BRRF2


title: IMR90-POLYOSV40-LT-rep4-E

source_name: IMR-90 cells expressing POLYOSV40-LT


title: IMR90-EBV-EBNA1-E

source_name: IMR-90 cells expressing EBV-EBNA1


title: IMR90-EBV-BDLF3.5-D


title: IMR90-EBV-BDLF4-D


title: IMR90-GFP4-E

source_name: IMR-90 cells expressing GFP


title: IMR90-EBV-BTRF1-D


title: IMR90-EBV-BNRF1-rep2-E

source_name: IMR-90 cells expressing EBV-BNRF1


title: IMR90-EBV-BFRF2-D


title: IMR90-EBV-BVLF1-C


title: IMR90-EBV-BGLF3-D


title: IMR90-EBV-BVLF1-D


title: IMR90-POLYOSV40-LT-rep4-D


title: IMR90-EBV-BNRF1-rep2-D


title: IMR90-EBV-BDLF4-C


title: IMR90-EBV-BDLF3.5-C


title: IMR90-EBV-EBNA1-D


title: IMR90-EBV-BTRF1-C


title: IMR90-GFP4-D


title: IMR90-EBV-BRRF2-D


title: IMR90-POLYOSV40-LT-rep4-C


title: IMR90-EBV-BRRF2-C


title: IMR90-GFP4-C


title: IMR90-EBV-BFRF2-C


title: IMR90-EBV-BVLF1-B


title: IMR90-EBV-EBNA1-C


title: IMR90-EBV-BDLF4-B


title: IMR90-EBV-BGLF3-B


title: IMR90-EBV-BTRF1-B


title: IMR90-EBV-BFRF2-B


title: IMR90-EBV-BNRF1-rep2-C


title: IMR90-EBV-EBNA1-B


title: IMR90-EBV-BRRF2-B


title: IMR90-EBV-BGLF3-C


title: IMR90-GFP4-B


title: IMR90-EBV-BDLF3.5-A


title: IMR90-POLYOSV40-LT-rep4-B


title: IMR90-EBV-BTRF1-A


title: IMR90-EBV-BGLF3-A


title: IMR90-EBV-EBNA1-A


title: IMR90-EBV-BFRF2-A


title: IMR90-HPV18E7-technical replicate4

source_name: IMR-90 cells expressing HPV18-E7


title: IMR90-EBV-BVLF1-A


title: IMR90-GFP4-A


title: IMR90-SV40LT-technical replicate4


title: IMR90-EBV-BNRF1-rep2-A


title: IMR90-POLYOSV40-LT-rep4-A


title: IMR90-HPV18E7-technical replicate3

value: Batch 4


title: IMR90-EBV-BHRF1-E

source_name: IMR-90 cells expressing EBV-BHRF1


title: IMR90-EBV-BRRF2-A


title: IMR90-EBV-LF2-E

source_name: IMR-90 cells expressing EBV-LF2


title: IMR90-EBV-LMP2A-E

source_name: IMR-90 cells expressing EBV-LMP2A


title: IMR90-EBV-BNRF1-rep1-E


title: IMR90-EBV-BNRF1-rep2-B


title: IMR90-SV40LT-technical replicate3


title: IMR90-EBV-BDLF4-A


title: IMR90-POLYOSV40-ST-E

source_name: IMR-90 cells expressing POLYOSV40-ST


title: IMR90-HPV18-E5-E

source_name: IMR-90 cells expressing HPV18-E5


title: IMR90-EBV-BRLF1-E

source_name: IMR-90 cells expressing EBV-BRLF1


title: IMR90-HPV5-E6-rep2-E

source_name: IMR-90 cells expressing HPV5-E6


title: IMR90-HPV6B-E5A-E

source_name: IMR-90 cells expressing HPV6B-E5A


title: IMR90-HPV11-E5B-E

source_name: IMR-90 cells expressing HPV11-E5B


title: IMR90-HPV6B-E5B-E

source_name: IMR-90 cells expressing HPV6B-E5B


title: IMR90-HPV16-E5-E

source_name: IMR-90 cells expressing HPV16-E5


title: IMR90-POLYOMCV-ST-E

source_name: IMR-90 cells expressing POLYOMCV-ST


title: IMR90-Vec-rep5-E

source_name: IMR-90 cells expressing empty MSCV vector


title: IMR90-GFP-rep2-E


title: IMR90-POLYOSV40-LT-rep3-E

source_name: IMR-90 cells expressing POLYOSV40-LT


title: IMR90-Vec-rep4-E


title: IMR90-EBV-BNRF1-rep1-D


title: IMR90-EBV-BHRF1-D


title: IMR90-EBV-BRLF1-D


title: IMR90-EBV-LF2-D


title: IMR90-EBV-LMP2A-D


title: IMR90-HPV5-E6-rep2-D


title: IMR90-HPV8-E6-rep2-D

source_name: IMR-90 cells expressing HPV8-E6


title: IMR90-HPV18-E5-D


title: IMR90-HPV16-E5-D


title: IMR90-POLYOMCV-ST-D


title: IMR90-Vec-rep5-D


title: IMR90-GFP-rep3-D

source_name: IMR-90 cells expressing GFP


title: IMR90-POLYOSV40-LT-rep3-D


title: IMR90-HPV11-E5B-D


title: IMR90-Vec-rep4-D


title: IMR90-HPV6B-E5A-D


title: IMR90-EBV-LMP2A-C

value: Batch 3


title: IMR90-EBV-BHRF1-C


title: IMR90-POLYOSV40-ST-C


title: IMR90-POLYOMCV-ST-C


title: IMR90-EBV-LF2-C


title: IMR90-GFP-rep2-D


title: IMR90-POLYOSV40-ST-D


title: IMR90-EBV-BRLF1-C


title: IMR90-HPV6B-E5B-D


title: IMR90-HPV6B-E5B-C


title: IMR90-HPV11-E5B-C


title: IMR90-HPV18-E5-C


title: IMR90-EBV-BNRF1-rep1-C

source_name: IMR-90 cells expressing EBV-BNRF1


title: IMR90-HPV16-E5-C


title: IMR90-HPV5-E6-rep2-C


title: IMR90-HPV6B-E5A-C


title: IMR90-HPV8-E6-rep2-C


title: IMR90-Vec-rep4-C


title: IMR90-GFP-rep2-C


title: IMR90-POLYOSV40-LT-rep3-C


title: IMR90-Vec-rep5-C


title: IMR90-GFP-rep3-C


title: IMR90-EBV-LMP2A-B


title: IMR90-POLYOMCV-ST-B


title: IMR90-HPV6B-E5B-B


title: IMR90-EBV-BRLF1-B


title: IMR90-EBV-BHRF1-B

source_name: IMR-90 cells expressing EBV-BHRF1


title: IMR90-HPV16-E5-B


title: IMR90-HPV11-E5B-B


title: IMR90-GFP-rep2-B


title: IMR90-POLYOSV40-ST-B


title: IMR90-HPV18-E5-B


title: IMR90-HPV8-E6-rep2-B


title: IMR90-GFP-rep3-B


title: IMR90-Vec-rep5-B


title: IMR90-HPV6B-E5A-B


title: IMR90-Vec-rep4-B


title: IMR90-HPV5-E6-rep2-B


title: IMR90-EBV-BNRF1-rep1-B


title: IMR90-EBV-BRLF1-A


title: IMR90-EBV-LF2-B

source_name: IMR-90 cells expressing EBV-LF2


title: IMR90-EBV-BHRF1-A


title: IMR90-EBV-LMP2A-A

source_name: IMR-90 cells expressing EBV-LMP2A


title: IMR90-POLYOSV40-LT-rep3-B


title: IMR90-HPV11-E5B-A


title: IMR90-HPV6B-E5B-A


title: IMR90-EBV-BNRF1-rep1-A


title: IMR90-POLYOSV40-ST-A

source_name: IMR-90 cells expressing POLYOSV40-ST


title: IMR90-EBV-LF2-A


title: IMR90-HPV6B-E5A-A


title: IMR90-HPV5-E6-rep2-A


title: IMR90-HPV11-E6-E

source_name: IMR-90 cells expressing HPV11-E6

value: Batch 2


title: IMR90-HPV18-E6-E

source_name: IMR-90 cells expressing HPV18-E6


title: IMR90-HPV16-E6-E

source_name: IMR-90 cells expressing HPV16-E6


title: IMR90-POLYOSV40-LT-rep3-A


title: IMR90-HPV6B-E7-E

source_name: IMR-90 cells expressing HPV6B-E7


title: IMR90-Vec-rep5-A


title: IMR90-GFP-rep3-A


title: IMR90-HPV18-E5-A

source_name: IMR-90 cells expressing HPV18-E5


title: IMR90-HPV8-E6-rep1-E


title: IMR90-HPV5-E7-rep1-E

source_name: IMR-90 cells expressing HPV5-E7


title: IMR90-HPV11-E7-E

source_name: IMR-90 cells expressing HPV11-E7


title: IMR90-SV40LT-technical replicate2

source_name: IMR-90 cells expressing SV40-LT


title: IMR90-HPV8-E6-rep2-A


title: IMR90-Vec-rep4-A

source_name: IMR-90 cells expressing empty MSCV vector


title: IMR90-HPV16-E7-N-E

source_name: IMR-90 cells expressing HPV16-E7-N


title: IMR90-SV40LT-technical replicate1


title: IMR90-HPV18E7-technical replicate2

source_name: IMR-90 cells expressing HPV18-E7


title: IMR90-HPV18E7-technical replicate1


title: IMR90-HPV6B-E6-E

source_name: IMR-90 cells expressing HPV6B-E6


title: IMR90-POLYOSV40-LT-rep2-E

source_name: IMR-90 cells expressing POLYOSV40-LT


title: IMR90-HPV8-E7-E

source_name: IMR-90 cells expressing HPV8-E7


title: IMR90-GFP-rep2-A

source_name: IMR-90 cells expressing GFP


title: IMR90-POLYOMCV-LT-E

source_name: IMR-90 cells expressing POLYOMCV-LT


title: IMR90-Vec-rep2-E


title: IMR90-Vec-rep3-E


title: IMR90-HPV5-E6-rep1-E

source_name: IMR-90 cells expressing HPV5-E6


title: IMR90-Vec-rep1-E


title: IMR90-POLYOMCV-ST-A

source_name: IMR-90 cells expressing POLYOMCV-ST


title: IMR90-HPV11-E6-D

source_name: IMR-90 cells expressing HPV11-E6


title: IMR90-HPV8-E6-rep1-D

source_name: IMR-90 cells expressing HPV8-E6


title: IMR90-HPV11-E7-D


title: IMR90-EBV-EBNALP-E

source_name: IMR-90 cells expressing EBV-EBNALP


title: IMR90-HPV6B-E6-D


title: IMR90-POLYOSV40-LT-rep1-E


title: IMR90-HPV5-E6-rep1-D


title: IMR90-HPV16-E6-D

source_name: IMR-90 cells expressing HPV16-E6


title: IMR90-HPV18-E6-D

source_name: IMR-90 cells expressing HPV18-E6


title: IMR90-HPV8-E7-D


title: IMR90-HPV6B-E7-D

source_name: IMR-90 cells expressing HPV6B-E7


title: IMR90-GFP-rep1-E


title: IMR90-POLYOSV40-LT-rep1-D


title: IMR90-POLYOSV40-LT-rep2-D


title: IMR90-Vec-rep2-D


title: IMR90-POLYOMCV-LT-D


title: IMR90-HPV16-E7-N-D


title: IMR90-HPV18-E6-C

value: Batch 1


title: IMR90-GFP-rep1-D


title: IMR90-HPV5-E7-rep1-D

source_name: IMR-90 cells expressing HPV5-E7


title: IMR90-Vec-rep1-D

source_name: IMR-90 cells expressing empty MSCV vector


title: IMR90-Vec-rep3-D


title: IMR90-HPV18-E7-D


title: IMR90-EBV-EBNALP-D


title: IMR90-HPV11-E6-C


title: IMR90-HPV16-E6-C


title: IMR90-HPV8-E6-rep1-C


title: IMR90-HPV6B-E6-C


title: IMR90-HPV5-E6-rep1-C


title: IMR90-HPV16-E7-N-C

source_name: IMR-90 cells expressing HPV16-E7-N


title: IMR90-HPV18-E7-C

source_name: IMR-90 cells expressing HPV18-E7


title: IMR90-HPV11-E7-C

source_name: IMR-90 cells expressing HPV11-E7


title: IMR90-HPV6B-E7-C


title: IMR90-Vec-rep3-C


title: IMR90-Vec-rep1-C


title: IMR90-POLYOMCV-LT-C


title: IMR90-HPV5-E6-rep1-B


title: IMR90-POLYOSV40-LT-rep1-C

source_name: IMR-90 cells expressing POLYOSV40-LT


title: IMR90-HPV6B-E6-B

source_name: IMR-90 cells expressing HPV6B-E6


title: IMR90-GFP-rep1-C

source_name: IMR-90 cells expressing GFP


title: IMR90-HPV5-E7-rep1-C


title: IMR90-HPV11-E6-B


title: IMR90-EBV-EBNALP-C


title: IMR90-HPV8-E6-rep1-B


title: IMR90-HPV18-E7-B


title: IMR90-HPV11-E7-B


title: IMR90-EBV-EBNALP-B


title: IMR90-Vec-rep2-C


title: IMR90-HPV18-E6-B


title: IMR90-HPV8-E7-B

source_name: IMR-90 cells expressing HPV8-E7


title: IMR90-HPV6B-E7-B


title: IMR90-HPV5-E7-rep1-B


title: IMR90-HPV8-E7-C


title: IMR90-POLYOMCV-LT-B

source_name: IMR-90 cells expressing POLYOMCV-LT


title: IMR90-POLYOSV40-LT-rep1-B


title: IMR90-HPV16-E6-B


title: IMR90-Vec-rep3-B


title: IMR90-HPV16-E7-N-B


title: IMR90-Vec-rep2-B


title: IMR90-POLYOSV40-LT-rep2-B


title: IMR90-GFP-rep1-B


title: IMR90-HPV11-E6-A


title: IMR90-HPV18-E6-A


title: IMR90-HPV16-E7-N-A


title: IMR90-HPV6B-E6-A


title: IMR90-HPV8-E6-rep1-A


title: IMR90-Vec-rep1-B


title: IMR90-HPV11-E7-A


title: IMR90-POLYOMCV-LT-A


title: IMR90-HPV18-E7-A


title: IMR90-HPV5-E7-rep1-A


title: IMR90-Vec-rep1-A


title: IMR90-Vec-rep2-A


title: IMR90-HPV16-E5-A

source_name: IMR-90 cells expressing HPV16-E5


title: IMR90-HPV5-E6-rep1-A

source_name: IMR-90 cells expressing HPV5-E6


title: IMR90-POLYOSV40-LT-rep2-C


title: IMR90-POLYOSV40-LT-rep1-A


title: IMR90-HPV16-E6-A


title: IMR90-HPV8-E7-A


title: IMR90-HPV6B-E7-A


title: IMR90-HPV18-E7-E


title: IMR90-POLYOSV40-LT-rep2-A


title: IMR90-EBV-EBNALP-A


title: IMR90-GFP-rep1-A


title: IMR90-Vec-rep3-A


title: Stellate/Basket cells at P35, biological rep2

city: Hershey

first: Anirban

last: Paul

state: PA

address: 500 University Drive

department: Neural and Behavioral Sciences

institute: Penn State College of Medicine

description:
SB_P35_2
Gene expression data from GABAergic Stellate/Basket cells

hyb_protocol: Hybridization performed byCold Spring Harbor Microarray Core Facility with their standard protocol. Samples were hybridized to Affymetrix MOE430.2 array.

scan_protocol: Scanning were performed by Cold Spring Harbor Microarray Core Facility with their standard protocol.

data_processing: R 2.9.1 was used with Bioconductor packages to process the CEL files using GCRMA; dCHIP was used for differential expression analysis and data visualization

molecule: polyA RNA

source_name: Stellate/Basket cells sorted from postnatal day 35

label_protocol: polyA RNA was amplified using two rounds of MessageAmp II aRNA amplification kit (Ambion, USA), labeled with biotin.

growth_protocol: Animals were maintained in normal light dark cycles on generic rodent chow and water.

extract_protocol: RNA isolated using spin columns; Picopure from Applied Biosystems Cat#KIT0202 using manufacturers protocol, RNA was Dnase treated before amplification.

treatment_protocol: Cerebellum was vibratome sectioned in artificial cerebrospinal fluid; slices were blocked with a cocktail of AP5, CNQX and TTX and mildly digested with bacterial protease type XIV (0.01mg/ml), triturated and manually sorted based on GFP expression and cell soma size.

tag: strain

value: CB6-Tg(Gad1-EGFP)G42Zjh/J (G42)

value: Gad67-GFP bac transgenic

value: male

tag: developmental stage

value: postnatal day 35

value: Cerebellum

value: Stellate/Basket cells


title: Stellate/Basket cells at P56, biological rep2

description:
SB_P56_2
Gene expression data from GABAergic Stellate/Basket cells

source_name: Stellate/Basket cells sorted from postnatal day 56

value: postnatal day 56


title: Stellate/Basket cells at P56, biological rep1

description:
SB_P56_1
Gene expression data from GABAergic Stellate/Basket cells


title: Stellate/Basket cells at P56, biological rep3

description:
SB_P56_3
Gene expression data from GABAergic Stellate/Basket cells


title: Stellate/Basket cells at P28, biological rep4

description:
SB_P28_4
Gene expression data from GABAergic Stellate/Basket cells

source_name: Stellate/Basket cells sorted from postnatal day 28

value: postnatal day 28


title: Stellate/Basket cells at P35, biological rep3

description:
SB_P35_3
Gene expression data from GABAergic Stellate/Basket cells


title: Stellate/Basket cells at P28, biological rep3

description:
SB_P28_3
Gene expression data from GABAergic Stellate/Basket cells


title: Stellate/Basket cells at P35, biological rep1

description:
SB_P35_1
Gene expression data from GABAergic Stellate/Basket cells


title: Purkinj cells at P56, biological rep4

description:
Pkj_P56_4
Gene expression data from GABAergic Purkinje cells

source_name: Purkinje cells sorted from postnatal day 56

value: Purkinje cells


title: Stellate/Basket cells at P21, biological rep2

description:
SB_P21_2
Gene expression data from GABAergic Stellate/Basket cells

source_name: Stellate/Basket cells sorted from postnatal day 21

value: postnatal day 21


title: Stellate/Basket cells at P28, biological rep2

description:
SB_P28_2
Gene expression data from GABAergic Stellate/Basket cells


title: Purkinj cells at P35, biological rep1

description:
Pkj_P35_1
Gene expression data from GABAergic Purkinje cells

source_name: Purkinje cells sorted from postnatal day 35


title: Stellate/Basket cells at P28, biological rep1

description:
SB_P28_1
Gene expression data from GABAergic Stellate/Basket cells


title: Purkinj cells at P35, biological rep2

description:
Pkj_P35_2
Gene expression data from GABAergic Purkinje cells


title: Purkinj cells at P56, biological rep1

description:
Pkj_P56_1
Gene expression data from GABAergic Purkinje cells


title: Stellate/Basket cells at P21, biological rep1

description:
SB_P21_1
Gene expression data from GABAergic Stellate/Basket cells


title: Purkinj cells at P56, biological rep3

description:
Pkj_P56_3
Gene expression data from GABAergic Purkinje cells


title: Purkinj cells at P28, biological rep4

description:
Pkj_P28_4
Gene expression data from GABAergic Purkinje cells

source_name: Purkinje cells sorted from postnatal day 28


title: Purkinj cells at P35, biological rep4

description:
Pkj_P35_4
Gene expression data from GABAergic Purkinje cells


title: Stellate/Basket cells at P14, biological rep3

description:
SB_P14_3
Gene expression data from GABAergic Stellate/Basket cells

source_name: Stellate/Basket cells sorted from postnatal day 14

value: postnatal day 14


title: Stellate/Basket cells at P14, biological rep1

description:
SB_P14_1
Gene expression data from GABAergic Stellate/Basket cells


title: Purkinj cells at P56, biological rep2

description:
Pkj_P56_2
Gene expression data from GABAergic Purkinje cells


title: Purkinj cells at P35, biological rep3

description:
Pkj_P35_3
Gene expression data from GABAergic Purkinje cells


title: Stellate/Basket cells at P14, biological rep4

description:
SB_P14_4
Gene expression data from GABAergic Stellate/Basket cells


title: High IL-2:IFN index derived CD8+ T cell clone #2

city: Bethesda

first: Udai

last: Kammula

state: MD

address: 9000 Rockville Pike

institute: NIH

description: Gene expression data from High IL-2:IFN index derived CD8+ T cell clone

hyb_protocol: Biotin-labeled cDNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 Array (Santa Clara, CA) according to manufacturer's instructions.

scan_protocol: Washing, staining, and scanning of the microarray were carried out under strictly controlled conditions with the Affymetrix Fluidics Station and Scanner.

data_processing: Raw data from the generated cell-intensity files (.cel' extension) were imported into Partek Genomics Suite with normalization performed by robust multichip analysis (RMA) algorithm.

label_protocol: About 100 ng of total RNA samples were reverse transcribed and labeled by biotin according to the standard Affymetrix protocol.

extract_protocol: Total RNA was isolated from resting high index and low index derived T cell clones (Qiagen RNeasy kit) and quality was validated with Agilent Bioanalyzer.

value: High IL-2 IFN index derived CD8+ T cell clone

tag: il-2 ifn index

value: High


title: Stellate/Basket cells at P21, biological rep3

description:
SB_P21_3
Gene expression data from GABAergic Stellate/Basket cells


title: High IL-2:IFN index derived CD8+ T cell clone #1


title: Low IL-2:IFN index derived CD8+ T cell clone #1

description: Gene expression data from Low IL-2:IFN index derived CD8+ T cell clone

value: Low IL-2 IFN index derived CD8+ T cell clone

value: Low


title: Purkinj cells at P28, biological rep3

description:
Pkj_P28_3
Gene expression data from GABAergic Purkinje cells


title: Purkinj cells at P28, biological rep2

description:
Pkj_P28_2
Gene expression data from GABAergic Purkinje cells


title: Stellate/Basket cells at P14, biological rep2

description:
SB_P14_2
Gene expression data from GABAergic Stellate/Basket cells


title: Low IL-2:IFN index derived CD8+ T cell clone #2


title: High IL-2:IFN index derived CD8+ T cell clone #3


title: DMSO_TP3

city: Singapore

first: Zbynek

last: Bozdech

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

hyb_protocol: Microarray hybridizations were carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, hybridizations were performed for 16 hours at 65°C using a Maui hybridization system (BioMicro Systems, Salt Lake City, Utah, USA).

scan_protocol: Scanning as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, scanning was performed with an Axon GenePix 4000B microarray scanner and associated GenePix Pro v6.0 software (Axon Instruments, Union City, California, USA).

data_processing: Data processing as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, Lowess normalization and subsequent filtering for quality control were carried out using Acuity 4.0 (Axon Instruments). Spots were considered of good quality when they were unflagged and had a median intensity greater than the local background plus 2 times the standard deviation of the background for each dye channel. The values presented in the sample data represent log2-transformed ratios of the measurement in the sample channel (Cy5) divided by the corresponding measurement in the reference channel (Cy3, P. falciparum RNA reference pool).

organism: Plasmodium falciparum

source_name: Early schizonts (32 hours postinvasion) P. falciparum parasites treated with DMSO for 4h

label_protocol: Labeling  carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5.

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

treatment_protocol: Treatment of P. falciparum infected erythrocytes with ACT-213165 at IC50 concentration and DMSO controls: treated and untreated(DMSO): 5 timepoints each: 1h, 2h, 4h, 6h, 8h; cultures: each sample: 2.5ml infected RBC pellets, 2% parasitaemia, t0: 32h p.i., 6h sync window

tag: agent

value: DMSO control

tag: time point

source_name: reference pool

tag: reference

value: P. falciparum reference pool consisting of even mass of 11 parts of RNA 11 = 4x (0-10h p.i.) + 3x (10-20h) + 2x (20-30h) + 1x (30-40h) + 1x (38-48h); 10h sync window


title: H460-ADPGK knockout-2

city: Auckland

first: Cris

last: Print

address: Grafton Campus, Park Rd

country: New Zealand

institute: Auckland University

description: ADPGK gene knockout H460 cells replicate 2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on U133A and U133B Affymetrix GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were normalised with the RMA algorithm using default settings apart from no background correction.

source_name: H460 cultured cells in which the ADPGK gene has been knocked out

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Both H460 and HCT116 cell lines were obtained from the American Type Culture Collection (ATCC), and used within 90 days passage from frozen stocks confirmed to be mycoplasma negative.  All cell lines were grown in alphaMEM (Invitrogen, CA), supplemented with 5% foetal bovine serum.

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

treatment_protocol: Plasmids for expression of a pair of custom-designed CompoZrTM Fok1 Zinc finger nucleases (ZFNs) against two 18 base pair target sites in the first exon of the human ADPGK gene (chromosome 15: 73,043,636-73,076,126) were purchased from Sigma Aldrich, MO. The targeted region is: 5'-CCGGGACCCGTCTCCCCCgagggCCGGTTGGCGGCAGCCTGG-3', where the lower case bases indicate the untargeted Fok1 nuclease site. Plasmids were transfected into cells using LipofectamineTM LTX and Plus reagent (Invitrogen, CA) according to the manufacturer’s instructions (for generation of HCT116 C3), or alternatively by nucleofection (Lonza, Switzerland) using NucleofectorTM solution V and programs D-032 for HCT116 and T-030 for H460. Co-transfection with a GFP-coding plasmid (pEGFP-N1, Clontech) and subsequent fluorescence-activated cell sorting (Becton Dickinson FACSVantage Cell Sorter) was used in some cases to enrich for positively transfected cells (for generation of clones HCT116 C3, H460 ID10 and IIE5). ZFN-transfected cells were cloned by limiting dilution in 96 well plates, and after growing for 7 days wells containing a single colony were trypsinized and expanded in duplicate wells, one of which was trypsinized and extracted (Laemmli buffer, Bio-Rad Laboratories, CA) for screening by western immunoblotting.

tag: genotype

value: ADPGK KO


title: H460-wild type-2

description: wild type H460 cells replicate 2

source_name: Wild type H460 cultured cells

value: Wild type


title: H460-wild type-1

description: wild type H460 cells replicate 1


title: DMSO_TP1

source_name: Early schizonts (32 hours postinvasion) P. falciparum parasites treated with DMSO for 1h