title: Gastric Cancer-24-aCGH

description: v

value: female

value: m

value: negative

value: IA


title: Gastric Cancer-12-aCGH

status: Public on Aug 10 2010

type: genomic

city: Sapporo

first: Nobumoto

last: Tomioka

state: Hokkaido

address: Nishi 7 chome, Kita 15 jo, Kita-ku

department: General Surgery

country: Japan

institute: Hokkaido University

description: The array CGH target slide consists of 4015 BAC clones printed in duplicate (MAC Array TM Karyo4K: Macrogen Inc.; http://www.macrogen.com) on aminosilane-coated slide (CMT-GAPS2 Coated Slides, Corning Inc., USA). The Macrogen BAC library is an original library based on the genome of Koreans established in 2000 by Seo of Seoul National University. The average length of insertion is about 100 Kb. Genomic loci of all BAC clones have been verified by end-sequencing and compared to the NCBI public genome map, http://www.ncbi.nlm.nih.gov/mapview/. The genomic positions of all BAC clones were also confirmed by FISH.

hyb_protocol: The pellet was resuspended in 40 μl hybridization solution containing 50% formamide, 10% dextran sulfate, 2x SSC, 4% SDS, and 200 μg yeast tRNA. The hybridization solution was denatured for 10 min at 72 °C and was subsequently incubated for 1 hour at 37 °C to allow blocking of repetitive sequences. Hybridization was performed in slide chambers for 48 hours at 37 °C. After post-hybridization washes, arrays were rinsed, spin-dried.

scan_protocol: Two 16-bit TIFF image files were scanned using a GenePix 4200A two-color fluorescent scanner (Axon Instruments), and individual spots were analyzed with GenePix Pro 3.0 imaging software (Axon Instruments).

data_processing: Data analysis was performed using MacViewer (Macrogen). The log2-transformed fluorescent ratios were calculated from background-subtracted mean intensity values, and these ratios were used to perform normalization according to intensity normalization methods. LOWESS normalization was applied, a smoothing adjustment that removes intensity-dependent variation in dye bias.

molecule: genomic DNA

organism: Homo sapiens

source_name: Human gastric cancer tissue

label_protocol: The labeling and hybridization protocols described by Pinkel et al. were used with some modification to the labeling procedure. Briefly, 21 μl solution containing 500 ng normal DNA (reference DNA) or tumor DNA (test DNA), 20 μl BioPrime DNA Labeling System random primers solution (Invitrogen, Carlsbad, CA, USA), and water were combined and incubated for 5 min at 95 °C, and subsequently cooled on ice. After the addition of 5 μl 10x dNTPs labeling mix (1 mM dCTP, 2 mM dATP, 2 mM dGTP, 2 mM dTTP), 3 μl 1 mM Cy-3 or Cy-5 dCTP (GeneChem Inc., Daejeon, Korea), and 40 U BioPrime DNA Labeling System Klenow fragment (Invitrogen), the mixture was gently mixed and incubated overnight at 37 °C. The addition of 5 μl BioPrime DNA Labeling System Stop Buffer (Invitrogen) ended the reaction. After labeling, unincorporated fluorescent nucleotides were removed using QIAquick Spin columns (Qiagen, Germany). In one tube, Cy3-labeled sample and Cy5-labeled reference DNAs were mixed together, and 50 μg human Cot I DNA (Invitrogen), 20 μl 3M sodium acetate, and 600 μl cold 100% ethanol were added for DNA precipitation.

extract_protocol: DNA was extracted from each cancer tissue sample using the PureGene kit (Gentra Systems Inc., Minneapolis, MN, USA).

tag: tissue

value: gastric cancer tumor

tag: gender

tag: depth of tumor invasion

tag: lymph node metastasis

tag: pathological stage

source_name: Normal human muscle tissue

tag: sample

value: Sex-matched reference normal human muscle DNA


title: Gastric Cancer-14-aCGH

value: male

value: se

value: positive

value: IV


city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: channel ch1 is input DNA

hyb_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.

scan_protocol: Standard Affymetrix Array Scanning Protocol was used

data_processing: M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

label: biotin

organism: Drosophila melanogaster

source_name: Developmental Stage Embryo 2-4hr OR;Antibody H3K36me3 (target is H3K36me3);Strain Oregon-R extraction2_array1 channel_1

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Embryos not older than 16h were collected, bleached in 2.5-3.0% Na-hypochlorite solution, washed two times in cold EWB. Incubated with freshly made 1.8% formaldehyde in X-linking buffer in the presence of of n-heptane.After incubation, embryos were re-suspended in Stop solution Washed at +40C in ChIP wash A solution and then at +40C in ChIP wash B. After sedimentation of the embryos ChIP wash B solution was removed and the embryos were used in an experiment or frozen in liquid N2.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

tag: strain

value: Oregon-R

tag: developmental stage

value: Embryo 2-4hr OR

tag: genotype

value: wild type


title: Gastric Cancer-04-aCGH


title: Gastric Cancer-13-aCGH


title: Gastric Cancer-11-aCGH


title: Gastric Cancer-10-aCGH

value: mp

value: II


title: Gastric Cancer-03-aCGH

value: IIIA


title: Gastric Cancer-02-aCGH

value: ss


description: channel ch1 is input DNA

source_name: Developmental Stage Embryo 14-16hr OR;Antibody H3K36me3 (target is H3K36me3);Strain Oregon-R extraction4_array1 channel_1

label_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.

value: Embryo 14-16hr OR


title: Gastric Cancer-08-aCGH

value: si


title: Gastric Cancer-05-aCGH


title: Gastric Cancer-09-aCGH


title: Gastric Cancer-01-aCGH


title: Gastric Cancer-07-aCGH

value: negative


description: channel ch1 is input DNA

source_name: Developmental Stage Embryo 14-16hr OR;Antibody H3K36me3 (target is H3K36me3);Strain Oregon-R extraction2_array1 channel_1


title: WT_0ISO_1

type: RNA

city: Ann Arbor

first: YU

last: CHEN

state: MI

address: 2300 Hayward

department: Chemical Engineering

country: USA

institute: University of Michigan

description: mRNA enriched from total RNA by removal of 16S and 23S ribosomal RNAs. On the array, there are 12078 probes targeting 4280 CDSs of this strain.

hyb_protocol: Each labeled and fragmented cRNA sample was hybridized individually to one custom 80K microarray by dynamic hybridization as follows. Twenty micrograms of sample was added to hybridization solution (600μl final volume) and incubated at 65°C for 5min and then placed on ice. Hybridization solution contained 6X SSPE (1M NaCl, 6.7mM EDTA, 40mM NaH2PO4 and 27.3mM Na2HPO4), 0.01 μg/μl acetylated BSA (#R3961, Promega), 0.01% Tween-20 (Sigma, #P9416), 10% deionized formamide (#P9037, Sigma).  A large volume of hybridization solution master mix was prepared from which aliquots were removed to prepare each sample.  Hybridizations were performed using a hybridization gasket slide (#G2534-60003, Agilent Technologies) and a Microarray Hybridization Chamber assembly (#G2534A, Agilent Technologies) following the manufacturer’s instructions except that 585μl of hybridization solution was used per gasket slide and both the gasket slide and  microarray slide were preheated to 65°C prior to Hybridization Chamber assembly. The final Hybridization Chamber assembly was incubated at 50°C for 20hrs while rotating at ~5rpm (to assure free movement of the mixing bubble) in a hybridization oven (#G2545A, Agilent Technologies).

scan_protocol: Slides were scanned using an Axon 4000B scanner (Molecular Devices) at 5 micron resolution and 100% laser power. The PMT gain in the 532nm channel was adjusted to appreciate the full dynamic range (0 – 65,000) of signal intensity such that only a few pixels were saturated in a few spots. A signal intensity value for each probe on the array was extracted from the scanned image using Axon GenePixPro 6.1 software (version 6.1.0.4, Molecular Devices).  Fixed diameter (35 microns) circular feature indicators were placed over the centre of each spot (probe) and median pixel intensity was calculated for each feature.

data_processing: First, background fluorescence intensities of individual spots were subtracted directly from foreground intensities for background adjustment. Then variance-stabilizing normalization (vsn) and quantile methods without weight were applied sequentially for normalization with software R (2.11.0, “vsn” and “aroma.light” package). For each strain/isobutanol condition, spots with acceptable signals in at least two out of three biological replicates were chosen for further analysis, which resulted in 4-6 replicates for each probe. Two or three probes for each gene were included on the array. For simplicity, we chose the probe with the smallest overall variation across replicates (measured by the sum of standard deviations across 12-18 technical/biological replicates over all the four strain/isobutanol  conditions) to represent the gene in further analysis. For each chosen probe, the median of the technical replicates on each array was calculated and the log2-transformed value was used to represent the expression level of the corresponding gene for each sample.

molecule: total RNA

organism: Escherichia coli

source_name: WT E.coli EcNR1, no isobutanol

label_protocol: The enriched mRNA (200ng) was converted to cRNA containing aminoallyl-UTP with Message Amp II -Bacteria Prokaryotic RNA amplification kit (#1790, Ambion) following the manufacturer’s instructions. Amino-allyl modified cRNA (45μg) was coupled with amine reactive fluorescent dye (Alexa Fluor-555, #32756, Invitrogen) in a 10μl reaction following the manufacturer's instructions. After fluorescent dye coupling, unincorporated dye was removed with RNEasy Mini Columns (Qiagen) following the manufacturer’s instructions. Labeled cRNA was eluted from RNeasy Mini Columns with RNAse/DNAse free water. The extent of dye incorporation was determined by the Microarray function on a NanoDrop 1000 spectrophotometer (Thermo Scientific). The dye incorporation calculations were performed as described by Invitrogen/Molecular Probes for Alexa Fluor dye products. All samples had dye incorporation between 35 to 43 bases per dye. Fluorescent dye coupled cRNA (20μg) was fragmented by exposure to zinc sulphate (5mM final concentration in a 60μl reaction) at 75°C for 10min and the reaction was stopped by the addition of 500mM EDTA to a final concentration of 20mM. The extent of fragmentation was visualized with a 2100 Bioanalyzer (Agilent Technologies) using a RNA Nano Chip (Agilent Technologies, #5067-1511). Samples with a mean fragment size of 100-200 nucleotides were qualified for hybridization

growth_protocol: Glucose minimal medium (plus 0.5% isobutanol for B1,B2,B3,D1,D2,D3), 30°C with 150 to 200 rpm shaking.

extract_protocol: Total RNA was extracted from early log phase cultures using RNeasy kit (Qiagen). 100 μL RNAase free water was used for final elution; 90 μL aliquot was immediately ethanol precipitated and stored at -80°C. Then, mRNA was enriched from 10μg of total RNA using the MICROBExpressTM Bacterial mRNA Purification Kit (#1905, Ambion) by the removal of 16S and 23S ribosomal RNAs.

treatment_protocol: 0.5% isobutonal for B1,B2,B3,D1,D2,D3 was added at the beginning of cultivation.

value: WT E.coli EcNR1

tag: culture condition

value: No isobutanol


title: WT_5ISO_1

source_name: WT E.coli EcNR1, 0.5% isobutanol

value: 0.5% isobutonal


title: WT_5ISO_3


title: WT_0ISO_3


title: WT_0ISO_2


title: WT_5ISO_2


title: G3.2_0ISO_3

source_name: G3.2 mutant of E.coli EcNR1, no isobutanol

value: G3.2 mutant of E.coli EcNR1


title: G3.2_5ISO_3

source_name: G3.2 mutant of E.coli EcNR1, 0.5% isobutanol


title: G3.2_5ISO_2


title: G3.2_5ISO_1


title: G3.2_0ISO_2


title: G3.2_0ISO_1


title: RNAMCF7p53Knockdown

status: Public on Aug 09 2010

city: Rehovot

first: Efrat

last: Lidor Nili

address: Herzel

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: Array hybridzation was carried out using the Affymetrix HG-U133_Plus_2 array according to manufacturer's instructions.

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 7G per manufacturer's protocol.

data_processing: Algorithm:5.0 ExpressionStat

source_name: RNA from MCF7sip53

label_protocol: Carried out according to manufacturer's instructions

growth_protocol: MCF7 human breast cancer cells, stably transfected with shRNA against p53 or with empty vector were cultured in Dulbecco's modified Eagle's medium plus 10% FBS, 1% P/S and 1µg/ml Puromycin.

extract_protocol: RNA was extracted using the Qiagen Rneasy kit according to the manufacturer's instructions.

treatment_protocol: For p53 activation, MCF7EcoR cells were treated with Neocarzinostatin (NCS (Sigma), 200ng/ml, 4h)

tag: cell line

tag: treatment

value: control


title: VAN_00705

city: San Francisco

first: Huimin

last: Geng

state: CA

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

hyb_protocol: Following fragmentation, 11 micrograms of cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning was performed by the Affymetrix 3000 Scanner.

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

source_name: DLBCL

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg mRNA.

extract_protocol: Total RNA (3-5 ug) was extracted from fresh frozen tissue using the All Prep RNA/DNA kit (Qiagen, Valencia, CA) according to the manufacturer's protocols.

value: ABC

tag: pathology

value: DLBC

value: lymph node

tag: age

value: M

tag: txprimary

tag: status

value: free of disease after initial treatment

value: alive

tag: overall_survival (years)

tag: progression-free_survival (years)


title: VAN_00697

value: GCB

tag: tissue

tag: gender


title: RNAMCF7ActivatedNCS

source_name: RNA from MCF7EcoR treated with NCS

value: NCS


title: VAN_00675


title: VAN_00648

value: testis


title: VAN_00700

value: COMPOSITE (>50% DLBCL, remaining FL)


title: VAN_00667


title: Gastric Cancer-06-aCGH

value: gastric cancer tumor

value: male

tag: depth of tumor invasion

value: m

tag: lymph node metastasis

value: IA

value: Sex-matched reference normal human muscle DNA


title: VAN_00795

value: F

value: dead


title: VAN_00633


title: VAN_00694


title: VAN_00615


title: VAN_00606


title: VAN_00608

value: With disease, after initial treatment


title: WT_pre-B_cells_Expression_2_(311863)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Expression profiling of wild type CD45+ pre-B cells harvested from the bone marrows of 4 6-week old mice (C57BL/6J).

hyb_protocol: Standard NimbleGen protocol

scan_protocol: Standard NimbleGen protocol

data_processing: RMA normalization by NimbleGen. Gene RMA values calculated from 9 probes per gene by NimbleGen are included as a supplementary file.

organism: Mus musculus

source_name: oligo-dT primed cDNA

label_protocol: Standard NimbleGen protocol

extract_protocol: RNA from 10 million cells was purified using Qiagen's RNeasy mini kit (Qiagen Inc.)  CDNA synthesis and labeling was done in accordance with NimbleGen's instructions.

value: 6 weeks

value: bone marrow

tag: cell type

value: CD45+ pre-B cells


title: VAN_00605

value: ABC

value: DLBC

value: lymph node

value: free of disease after initial treatment


title: Myc_pre-B_cells_Expression_2_(311898)

description: Expression profiling of Myc induced CD45+ pre-B cells harvested from the bone marrows of 3 6-week old mice (B6.Cg-Tg(IghMyc)22Bri/J (Emu-Myc)).

tag: strain

value: (B6.Cg-Tg(IghMyc)22Bri/J (Emu-Myc))


title: NucNcsRep1

description: Mononucleosomal DNA from MCF7EcoR treated with NCS

hyb_protocol: Samples were hybridized at Nimblegen headquarters (http://www.nimblegen.com/products/lit/lit.html) according to their protocol.

scan_protocol: Samples were scanned at Nimblegen headquarters (http://www.nimblegen.com/products/lit/lit.html) according to their protocol.

data_processing: The ratio of experiment/control was calculated and log2 transformed using perl scripts (V5.8.8).

source_name: Mononucleosomal DNA from MCF7EcoR cells treated with NCS

label_protocol: Samples were labeled at Nimblegen headquarters (http://www.nimblegen.com/products/lit/lit.html) according to their protocol.

growth_protocol: Cells were grown in DMEM medium supplememted with 10%FCS, 1µg/ml puromycin and pen-strep

extract_protocol: Mononucleosome preperation: nuclei were isolated from 2.5*10^6 cells in lysis buffer (10mM Tris pH7.4, 10mM NaCl, 3mM MgCl2, 0.5% NP-40, 0.15mM Spermine, 0.5mM Spermidine) for 10 min on ice. Nuclei were washed once in wash buffer (10mM Tris pH7.4, 15mM NaCl, 60mM KCl, 0.15mM Spermine, 0.5mM Spermidine) followed by resuspension in MNase buffer (wash buffer+1mM CaCl2) followed by MNase digestion (1 unit/12 million cells, 10 min at 37ºC), Reaction was stopped by addition of EDTA to 0.01M, SDS and NaCl were added to a final concentration of 2% and 0.2M, respectively. Rnase (0.1mg) was added for 1hr at 37ºC. DNA was extracted using Qiagen PCR purification kit, seperated on a 1.5% agarose gel, and fragments of 150bp were excised and extraction using Qiagen gel extraction kit. In parallel, input DNA was isolated using Qiagen Dneasy Blood and tissue kit and sonicated in TE to ~500bp fragments, 1µg of nucleosomal DNA and input DNA were labeled and hybridized to Nimbelgen custom arrays as above.p53 ChIP was done using CM1 antibody and according to previously published protocol (Weinmann and Farnham,2002).

treatment_protocol: cells were treated with 200ng/ml NCS for 4 hours

value: NCS

source_name: Sonicated genomic DNA from MCF7EcoR treated with NCS


title: VAN_00603

value: M

value: CHOP-RITU

value: alive


title: VAN_00598

value: GCB


title: NucBasalRep2

description: Mononucleosomal DNA from MCF7EcoR

source_name: Mononucleosomal DNA from MCF7EcoR cells

treatment_protocol: no treatment

value: Control

source_name: Sonicated genomic DNA from MCF7EcoR


title: Tumor_B_cells_Expression_2_(311900)

description: Expression profiling of tumor cells harvested from the lymph node of an 8-week old mouse (B6.Cg-Tg(IghMyc)22Bri/J (Emu-Myc)).

value: 8 weeks

value: Tumor B cells


title: Tumor_B_cells_Expression_1_(312091)


title: VAN_00593


title: VAN_00589


title: Nucp53KnockDownRep2

description: Mononucleosomal DNA from MCF7sip53

source_name: Mononucleosomal DNA from MCF7sip53 cells

source_name: Sonicated genomic DNA from MCF7sip53


title: VAN_00596

value: F


title: VAN_00579

value: With disease, after initial treatment


title: VA65


title: VAN_00594

value: ENT


title: VA64


title: VA53

value: toxic death

value: dead


title: VAN_00566

value: DLBC

value: GI


title: VA58

value: ABC

value: lymph node

value: lymphoma death


title: NucBasalRep1

description: Mononucleosomal DNA from MCF7EcoR


title: p53ChIPBasalRep1

description: p53 ChIP-CHIP in MCF7EcoR

source_name: p53 ChIP DNA from MCF7EcoR cells

tag: antibody

value: p53 (Novocastra, NCL-p53-CM1)

source_name: Input DNA from MCF7EcoR


title: VAN_00568

value: NC

value: M

value: free of disease after initial treatment


title: VAN_00132

value: gastric


title: VA57

value: GCB

value: alive


title: p53ChIPActivatedNcsRep2

description: p53 ChIP-CHIP in MCF7EcoR treated with NCS

source_name: p53 ChIP DNA from MCF7EcoR cells treated with NCS

value: NCS

source_name: Input DNA from MCF7EcoR treated with NCS


title: VA52


title: VA59

value: spleen

value: free of disease after treatment for first relapse


title: VAN_00567


title: Myc_pre-B_cells_Expression_1_(311872)

value: (B6.Cg-Tg(IghMyc)22Bri/J (Emu-Myc))

value: 6 weeks

value: bone marrow

value: CD45+ pre-B cells


title: NucNcsRep2


title: p53ChIPActivatedNcsRep1


title: p53ChIPBasalRep2

description: p53 ChIP-CHIP in MCF7EcoR

value: Control


title: Nucp53KnockDownRep1

description: Mononucleosomal DNA from MCF7sip53


title: WT_pre-B_cells_Expression_1_(311399)


title: VA155

value: DLBC

value: lymph node

value: F


title: VA47


title: VA46

value: ABC

value: lymphoma death

value: dead


title: VA152

value: NC

value: free of disease after initial treatment


title: VA49

value: GCB

value: M

value: alive


title: VA156


title: VA44


title: VA43

value: Receiving treatment for first relapse


title: VA41-2


title: VA151

value: ENT

value: free of disease after treatment for first relapse


title: VA148

value: thyroid


title: VA45


title: VA150

value: GI


title: VA48


title: VA146


title: VA50

value: CHOP-RITU-ABVD


title: VAN_00580

value: DLBC

value: breast


title: VA145

value: lymph node


title: VA137

value: F

value: death unrelated


title: WT, rep2

city: Bethesda

first: Lidia

last: Hernandez

state: MD

address: 10 Center Drive

department: CCR/MOB

institute: National Cancer Institute

description: primary cells in culture

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Hu133Plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450/250.

scan_protocol: Affymetrix Gene Chip Scanner

data_processing: BRB-Array Tools version 3.7 (Biometrics Research Branch, NCI, publicly available)

source_name: Wildtype mouse adult fibroblasts

label_protocol: Affymetrix One Cycle Target Labeling kit

growth_protocol: Primary adult mouse fibroblasts in 10% DMEM medium with standard antibiotics

extract_protocol: Trizol extraction according to manufacturer's specifications

treatment_protocol: Primary adult mouse fibroblasts were cultured from the initial derivation in culture as described above and subjected to three passages at confluency, at a passage ratio of 1:3 according to the 3T3 protocol (Todaro and Green, 1963), beginning one passage after derivation.

value: adult primary fibroblasts


title: VA136

value: NC

value: spleen

value: lymphoma death

value: dead


title: VA143

value: GCB

value: M

value: free of disease after initial treatment

value: alive


title: Delta9,rep1

description: primary cells in culture

source_name: Delta9 mouse adult fibroblasts


title: VA147


title: WT, rep1

description: primary cells in culture


title: Delta9,rep3

description: primary cells in culture


title: Delta9,rep2

description: primary cells in culture


title: VA141

value: SPLE-CHOP-RITU-RAD


title: WT, rep3

description: primary cells in culture


title: VA134

value: tonsil


title: R3 t=0 [RAS profiling]

city: Cambridge

first: Mitchell

last: Guttman

state: MA

address: 7 Cambridge Center

institute: Broad Institute

description:
Profiling of p53 inducible KRAS Lung Tumors
Cre Treated for 0hrs

hyb_protocol: Standard Affymetrix protocols

scan_protocol: Standard Affymetrix protocols

data_processing: RMA analysis was performed using the Bioconductor package

label: Biotin

source_name: KRAS P53LSL Lung Tumor Cells

label_protocol: Standard Affymetrix protocols

growth_protocol: Lung tumor-derived cell lines were isolated from individual tumors from KrasLA2/+; Trp53LSL/LSL Rosa26CreERT2 animals and grown in DMEM + 10%FBS

extract_protocol: Trizol

treatment_protocol: For p53 restoration, cultured tumor cell lines were incubated with 500nM 4-hydroxytamoxifen for the indicated times

value: C57BL/6 x 129SvJ

tag: agent

value: untreated

tag: time


title: R2 t=8 [RAS profiling]

description:
Profiling of p53 inducible KRAS Lung Tumors
Cre Treated for 8hrs


title: R2 t=40 [RAS profiling]

description:
Profiling of p53 inducible KRAS Lung Tumors
Cre Treated for 40hrs


title: R2 t=24 [RAS profiling]

description:
Profiling of p53 inducible KRAS Lung Tumors
Cre Treated for 24hrs


title: D50

value: DLBC


title: R2 t=48 [RAS profiling]

description:
Profiling of p53 inducible KRAS Lung Tumors
Cre Treated for 48hrs


title: VA140

value: ABC

value: lymph node

value: CHOP-RITU


title: VA135


title: R1 t=24 [RAS profiling]


title: R1 t=40 [RAS profiling]


title: R2 t=0 [RAS profiling]


title: VA133


title: R1 t=48 [RAS profiling]


title: R1 t=8 [RAS profiling]


title: 487


title: 458


title: D28B


title: D47B

value: COMPOSITE (>50% DLBCL, remaining FL)


title: 444


title: 452

value: F


title: 454


title: siP53_R3 [lincP21KD profiling]

description: RNAi mediated knock-down of specific transcripts

source_name: P53 Restored DNA Damaged LSL MEFs

growth_protocol: Cells were isolated from E13.5 mouse embryos  and grown in DMEM + 10% FBS

treatment_protocol: p53 LSL/LSL MEFs were treated with adenoCRE for p53 restoration for 24h, transfected with siRNA oligos targeting different transcripts for 24h and then treated with 100nM doxorubicin for 13h.

tag: transfection

value: AdenoCRE

tag: treatment protocol

value: siRNA targetting P53


title: 476

source_name: DLBCL

tag: pathology

value: free of disease after treatment for first relapse

value: dead


title: siLincP21_R2 [lincP21KD profiling]

value: siRNA targetting lincP21


title: siLincP21_R3 [lincP21KD profiling]


title: R2 t=16 [RAS profiling]

description:
Profiling of p53 inducible KRAS Lung Tumors
Cre Treated for 16hrs


title: R1 t=16 [RAS profiling]


title: siP53_R2 [lincP21KD profiling]


title: siP53_R1 [lincP21KD profiling]


title: siRNA p53 R3 [hnRNPKKD profiling]

treatment_protocol: p53 LSL/LSL MEFs were treated with adenoCRE for p53 restoration for 24h, transfected with siRNA oligos targeting different transcripts for 24h and then treated with 100nM doxorubicin for 13h


title: siRNA control R3 [hnRNPKKD profiling]

value: siRNA non-targetting pool


title: siRNA lincp21 R2 [hnRNPKKD profiling]


title: siRNA hnRNPK R3 [hnRNPKKD profiling]

value: siRNA targetting hnRNPK


title: siRNA p53 R2 [hnRNPKKD profiling]


title: siRNA lincp21 R3 [hnRNPKKD profiling]


title: siRNA control R2 [hnRNPKKD profiling]


title: 464

value: GCB

tag: age

value: free of disease after initial treatment

value: alive


title: siLincP21_R1 [lincP21KD profiling]

value: C57BL/6 x 129SvJ


title: R1 t=0 [RAS profiling]

value: untreated


title: siScramble_R1 [lincP21KD profiling]


title: CRE9hrs [MEF profiling]

description: Profiling of p53 inducible MEFs after DNA Damage

source_name: P53 Inducible Mouse Embryonic Fibroblasts

growth_protocol: Cells were isolated from E13.5 mouse embryos and grown in DMEM + 10% FBS

treatment_protocol: p53 LSL/LSL MEFs were treated with adenoCRE for p53 restoration or adenoGFP as control for 24h and treated with 500nM doxorubicin for the indicated times.

value: doxorubicin

tag: time (doxorubicin)


title: siScramble_R2 [lincP21KD profiling]


title: siRNA p53 R1 [hnRNPKKD profiling]


title: CRE1hrs [MEF profiling]


title: CRE3hrs [MEF profiling]


title: siRNA hnRNPK R1 [hnRNPKKD profiling]


title: D63

value: DLBC

value: GI

value: M

tag: txprimary

tag: status


title: GFP9hrs [MEF profiling]

value: AdenoGFP (control)


title: siRNA lincp21 R1 [hnRNPKKD profiling]

value: AdenoCRE


title: CRE0hrs [MEF profiling]


title: siRNA hnRNPK R2 [hnRNPKKD profiling]


title: CRE6hrs [MEF profiling]


title: Aorta_cMycOFF_26days_biological rep3

city: Coventry

first: Yi-Fang

last: Wang

address: Gibbet Hill Road

department: Biological Sciences

country: United Kingdom

institute: Warwick University

description: Adult female mice, 3-6 months of age, inbred into CBA-C57Bl/6 background and maintained under barrier conditions, were treated with TAM for up to 7 days (Myc ON) and then monitored during recovery for more than 4 months (140 days) (Myc OFF).

hyb_protocol: A two-cycle protocol was performed at the beginning of our gene array analysis. 10µg double-amplified biotin-labelled cRNA were hybridised to Affymetrix MOE430 2.0 GeneChips (Affymetrix UK Ltd, High Wycombe, UK)) together with pre-labelled hybridisation controls as described in the Affymetrix GeneChip Expression Analysis Technical Manual.

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

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

source_name: Whole aorta, Untreated, 26 days

label_protocol: Biotin

growth_protocol: Pelengaris S, Khan M, Evan G (2002) Suppression of Myc-induced apoptosis in beta cells exposes multiple innate oncogenic properties of Myc sufficient to trigger immediate carcinogenic progression. Cell 109: 321-334.

extract_protocol: The thoracic part of the aorta was snap-frozen in liquid nitrogen for RNA extraction. Frozen mouse aortas were homogenised and total RNA was extracted using RNEasy Plus Mini-Kit (Qiagen, Crawley, UK), according to the manufacturer’s protocol. RNA concentration was estimated using a spectrophotometer (ND-1000 Nanodrop, Labtech International Ltd, East Sussex, UK) prior to further quality control check by a bioanalyzer (2100 Bioanalyzer, Agilent Technologies, Cheshire, UK). For this purpose, n=3 mice were used per timepoint, each mouse was analysed individually without pooling of RNA .

treatment_protocol: c-MycERTAM protein is activated in pancreatic beta cells of adult transgenic mice, by daily intraperitoneal (IP) administration of tamoxifen (TAM; Sigma-Aldrich, Dorset, UK) (1 mg/0.2 ml in peanut oil). Inactivation of c-MycERTAM protein was achieved following withdrawal of TAM.  All protocols conformed with the Home Office (UK) laws and regulations, and transgenic mice were registered with the University of Warwick, Biological Sciences Committee for Genetically Modified. Mice were killed by cervical dislocation. The thoracic cavity was opened rapidly and saline was perfused through the mouse heart while the aorta was intact. All remaining blood was washed off the aorta before isolation.

value: Whole aorta

tag: genotype

value: CBA-C57BL/6 pIns-c-MycERTAM

value: female

value: 3-6 months


title: siRNA control R1 [hnRNPKKD profiling]

value: siRNA non-targetting pool


title: Aorta_cMycOFF_26days_biological rep2

tag: tissue


title: GFP3hrs [MEF profiling]


title: Aorta_cMycOFF_26days_biological rep1

tag: gender


title: Aorta_cMycOFF_11days_biological rep1

source_name: Whole aorta, Untreated, 11 days


title: Aorta_cMycOFF_11days_biological rep2


title: GFP1hrs [MEF profiling]


title: Aorta_cMycON_7days_biological rep2

source_name: Whole aorta, Tamoxifen treated, 7 days


title: GFP6hrs [MEF profiling]


title: GFP0hrs [MEF profiling]


title: Aorta_cMycOFF_11days_biological rep3


title: Aorta_cMycON_7days_biological rep3


title: Aorta_cMycON_7days_biological rep1


title: Aorta_cMycON_2days_biological rep3

source_name: Whole aorta, Tamoxifen treated, 2 days


title: Aorta_cMycON_4days_biological rep3

source_name: Whole aorta, Tamoxifen treated, 4 days


title: Aorta_cMycON_4days_biological rep2


title: Aorta_cMycON_4days_biological rep1


title: Aorta_cMycON_2days_biological rep1


title: Aorta_cMycON_2days_biological rep2


title: Aorta_cMycOFF_0days_biological rep1

source_name: Whole aorta, Untreated, 0 days


title: U87ctrl cells replicate 3

status: Public on Aug 08 2010

city: Talence

first: Michel

last: Moenner

address: Avenue des Facultés

department: Université Bordeaux 1

country: France

institute: Inserm U920

description: U87dn cells expressing a dominant negative transgene of IRE1alpha were compared to U87ctrl cells transfected with the corresponding empty plamid to identify genes associated to tumor invasion and angiogenesis.

hyb_protocol: Hybridization and washing was carried out on a GeneChip (Affymetrix) station, washing according to the manufacturer’s protocol.

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

data_processing: Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.

source_name: Human glioblastoma cell (U87) clones: empty plasmid U87 (U87 ctrl) cells.

label_protocol: Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) 'standard protocol'

growth_protocol: Cells were incubated for 16h in DMEM supplemented with 10% FBS and glutamine

extract_protocol: Total RNA was isolated using RNeasy mini kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer

treatment_protocol: U87 IRE1 dominant negative cells and U87 control  cells were  grown for 16 hours in culture dishes prior mRNA isolation

tag: cell line

value: U87 glioblastoma cell line

tag: genotype/variation

value: control


title: Clostridium difficile at 120 min post-infection - replicate 1

status: Public on Aug 07 2010

type: mixed

city: Ithaca

first: Tavan

last: Janvilisri

state: NY

address: Veterinary Research Tower, College of Veterinary Medicine, Cornell University

institute: Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University

description: Biological replicate 1 of 3: C. difficile 120 min post-infection

hyb_protocol: The Cy5-labeled cDNA and Cy3-labeled genomic DNA probes were hybridized on C. difficile spotted array. The microarray slides were prehybridized using a solution containing 25% formamide, 5x SSC (1x SSC consists of 0.15M NaCl with 0.015M sodium citrate), 0.2% (w/v) sarcosyl, and 10 mg/ml bovine serum albumin at 42 °C for 1 h. The slides were then washed in MilliQ water and blow dried using compressed nitrogen gas. Equivalent amounts of labeled probes from reference and tested strains were pooled, lyophilized, and resuspended in 70 µl of hybridization buffer (25% formamide, 5x SSC, 0.2% sodium dodecyl sulfate (SDS), 1 mg/ml salmon sperm DNA, and 1 mg/ml yeast tRNA). The probes were then denatured at 99 °C for 5 min, centrifuged briefly at 13,800 x g and applied to the microarray under a 22 x 60mm LifterSlip (Erie Scientific Co.). Hybridizations were performed at 42 °C for 16 h in a sealed humidified hybridization chamber (Corning). Following the hybridization, excess hybridization solution and unbound probes were washed away during four washing steps including 5 min in 2x SSC, 1% SDS at 42 °C and 5 min in 0.1% SSC at room temperature for three times. The slides were then dried and scanned immediately.

scan_protocol: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments).

data_processing: The Cy3 and Cy5 signals and the local background intensities were quantified using GenePix Pro 6.1 software. The local background value was subtracted from the intensity of each spot. Spots were examined manually, and poor spots were flagged for elimination from the analysis. All subsequent data analyses were performed by using Microsoft Excel and TM4 suite softwares.

organism: Clostridioides difficile

source_name: Clostridium difficile RNA

label_protocol: 5 µg of RNA were reverse-transcribed using SuperScript III reverse transcriptase with random hexamers (Invitrogen) according to the manufacturer’s instructions. The corresponding cDNA was labeled with 25 U of Klenow fragment (New England Biolabs, Ipswich, MA), 10 µg of exo-resistant random primers (Fermentas, Glen Burnie, MD), dNTP mix (0.12 mM each dATP, dCTP, and dGTP and 0.03 mM dTTP), and 0.1 mM of Cy5-dUTP (Amersham Biosciences, Piscataway, NJ) at 37C for 24 h. Genomic DNA (2 µg) from C. difficile 630 was fragmented by DraI digestion, labeled with Cy3-dUTP under the same condition and used as the reference channel on each slide to allow comparison of each timepoint and different samples.

extract_protocol: RNA extraction was performed using RNeasy mini-prep kit (Qiagen) according to the manufacturer’s instructions. Genomic DNA was isolated from C. difficile by using DNeasy Blood and Tissue Mini Kit (Qiagen) as described in the manufacturer’s protocol for gram-positive bacteria.

tag: infection time (min)

organism: Clostridioides difficile 630

source_name: Genomic DNA from Clostridium difficile reference strain 630


title: Clostridium difficile at 30 min post-infection - replicate 3

description: Biological replicate 3 of 3: C. difficile 30 min post-infection


title: U87 IRE1dn cells replicate 3

source_name: Human glioblastoma cell (U87) clone: U87 IRE1.NCK DN (U87dn)

value: expression of dominant negative transgene of IRE1alpha


title: Clostridium difficile control (uninfected) - replicate 3

description: Biological replicate 3 of 3: C. difficile Control


title: Clostridium difficile control (uninfected) - replicate 1

description: Biological replicate 1 of 3: C. difficile Control


title: Clostridium difficile at 60 min post-infection - replicate 1

description: Biological replicate 1 of 3: C. difficile 60 min post-infection


title: Clostridium difficile at 30 min post-infection - replicate 1

description: Biological replicate 1 of 3: C. difficile 30 min post-infection


title: Clostridium difficile at 30 min post-infection - replicate 2

description: Biological replicate 2 of 3: C. difficile 30 min post-infection


title: U87ctrl cells replicate 1


title: Clostridium difficile at 120 min post-infection - replicate 3

description: Biological replicate 3 of 3: C. difficile 120 min post-infection


title: Clostridium difficile at 120 min post-infection - replicate 2

description: Biological replicate 2 of 3: C. difficile 120 min post-infection


title: Clostridium difficile at 60 min post-infection - replicate 2

description: Biological replicate 2 of 3: C. difficile 60 min post-infection


title: Clostridium difficile at 60 min post-infection - replicate 3

description: Biological replicate 3 of 3: C. difficile 60 min post-infection


title: Aorta_cMycOFF_0days_biological rep2


title: Clostridium difficile control (uninfected) - replicate 2

description: Biological replicate 2 of 3: C. difficile Control


title: Aorta_cMycOFF_0days_biological rep3


title: U87ctrl cells replicate 2


title: Caco-2 at 30 min post-infection - replicate 3

description: Biological replicate 3 of 3: Caco-2 cells 30 min post-infection

hyb_protocol: Ten micrograms of Cy5-labeled aRNA were hybridized to the Human Whole Genome OneArray (Phalanx Biotech Group, Palo Alto, CA) in accordance with the company’s recommendations.

scan_protocol: After hybridization, the slides were scanned with Axon 4000B, and the raw data were generated by Genepix 6.0. Two gpr files linked below as supplementary files: In the gpr filename, Rep# represents biological replicate and _# represents technical replicate (e.g., Rep1_1.gpr represents biological rep 1, technical rep 1)

data_processing: The signal intensity of each spot was corrected by subtracting background signals in the immediate surrounding. Spots were examined manually, and poor spots were flagged for elimination from the analysis. The net intensities were log2 transformed, within-chip normalized using lowess algorithm, and quantile normalized across all chips. The mean normalized log2 ratio and standard deviation were calculated from all replicates. All subsequent data analyses were performed using Microsoft Excel and TM4 suite of programs

source_name: Caco-2 cells

label_protocol: Five microgram of total RNA were used as a template for antisense RNA amplification using MessageAmp aRNA Kit (Ambion, Austin, TX). The resulting aRNA was then labeled with Cy5-dUTP using Amino Allyl cDNA Labeling Kit (Ambion) according to the manufacturer’s instructions.

extract_protocol: RNA extraction was performed using RNeasy mini-prep kit (Qiagen) according to the manufacturer’s instructions. For Caco-2 cells, the pellets were resuspended in lysis buffer and were subjected to QIAshredder homogenizer columns (Qiagen) before proceeding with RNeasy kit. Contaminated DNA was removed by adding 20 units RNase-free DNase in DNA digesting buffer (Qiagen) for 15 min at room temperature. RNA was quantified by NanoDrop-1000 spectrophotometer (Thermo Scientific, Wilmington, DE) and its integrity was evaluated using Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). RNA samples with a RNA integrity number of >8 were labeled and used in microarray or qRT-PCR experiments.


title: S1H1_non_SZ_control

status: Public on Aug 06 2010

city: Atlanta

first: Jennifer

middle: Gladys

last: Mulle

state: GA

address: 615 Michael Street, Room 375, Whitehead Bldg

department: Department of Human Genetics

institute: Emory Univeristy School of Medicine

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
CEL files were analyzed using affymetrix power tools software, apt-copynumber-workflow, version apt1.10.0.  Log2Ratio data were extracted and analyzed using GLAD (Hupe 2004) GADA (Pique-Regi, 2008) and BEAST (G.A. Satten, personal communication) for deletions > 500 kb.
primary data description: Log2 Ratio data for all probes generated by apt-copynumber-workflow (affymetrix powertools software).

source_name: DNA extraced from blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was extraced from blood using theGentra PureGene DNA extraction kit or the Qiagen DNA extraction kit

tag: group


title: S1H3_non_SZ_control


title: S1H9_non_SZ_control


title: S1H4_non_SZ_control


title: S1H2_non_SZ_control


title: S1H7_non_SZ_control


title: S1H8_non_SZ_control


title: S1H10_non_SZ_control


title: S1H5_non_SZ_control


title: S1G9_non_SZ_control


title: S1G6_non_SZ_control


title: S1G7_non_SZ_control


title: S1H11_non_SZ_control


title: S1H6_non_SZ_control


title: S1G5_non_SZ_control


title: Caco-2 at 30 min post-infection - replicate 2

description: Biological replicate 2 of 3: Caco-2 cells 30 min post-infection


title: S1G4_non_SZ_control


title: S1G3_non_SZ_control


title: Caco-2 at 120 min post-infection - replicate 2

description: Biological replicate 2 of 3: Caco-2 cells 120 min post-infection


title: S1G11_non_SZ_control


title: Caco-2 at 60 min post-infection - replicate 3

description: Biological replicate 3 of 3: Caco-2 cells 60 min post-infection


title: S1G2_non_SZ_control


title: S1G10_non_SZ_control


title: S1G12_non_SZ_control


title: Caco-2 at 120 min post-infection - replicate 1

description: Biological replicate 1 of 3: Caco-2 cells 120 min post-infection


title: Caco-2 control (uninfected) - replicate 1

description: Biological replicate 1 of 3: Caco-2 cells Control


title: S1G1_non_SZ_control


title: S1F12_non_SZ_control


title: S1F9_non_SZ_control


title: Caco-2 at 30 min post-infection - replicate 1

description: Biological replicate 1 of 3: Caco-2 cells 30 min post-infection


title: S1E9_non_SZ_control


title: U87 IRE1dn cells replicate 1

description: U87dn cells expressing a dominant negative transgene of IRE1alpha were compared to U87ctrl cells transfected with the corresponding empty plamid to identify genes associated to tumor invasion and angiogenesis.


title: S1F2_non_SZ_control


title: S1F8_non_SZ_control


title: S1F7_non_SZ_control


title: U87 IRE1dn cells replicate 2


title: S1F6_non_SZ_control


title: S1F11_non_SZ_control


title: S1E8_non_SZ_control


title: S1E7_non_SZ_control


title: S1E6_non_SZ_control


title: Caco-2 at 120 min post-infection - replicate 3

description: Biological replicate 3 of 3: Caco-2 cells 120 min post-infection


title: Caco-2 at 60 min post-infection - replicate 1

description: Biological replicate 1 of 3: Caco-2 cells 60 min post-infection


title: S1F1_non_SZ_control


title: S1E4_non_SZ_control


title: S1E5_non_SZ_control


title: S1E3_non_SZ_control


title: S1F3_non_SZ_control


title: S1E11_non_SZ_control


title: S1E10_non_SZ_control


title: S1D9_non_SZ_control


title: S1E12_non_SZ_control


title: S1D8_non_SZ_control


title: S1E1_non_SZ_control


title: Caco-2 control (uninfected) - replicate 2

description: Biological replicate 2 of 3: Caco-2 cells Control


title: Caco-2 control (uninfected) - replicate 3

description: Biological replicate 3 of 3: Caco-2 cells Control


title: S1D2_non_SZ_control


title: S1D12_MSSM_non_SZ_control


title: S1D10_non_SZ_control


title: S1D1_non_SZ_control


title: S1C9_non_SZ_control


title: S1C7_non_SZ_control


title: S1C8_non_SZ_control


title: S1D4_non_SZ_control


title: S1C6_non_SZ_control


title: S1C5_non_SZ_control


title: S1C4_non_SZ_control


title: S1D3_non_SZ_control


title: S1E2_non_SZ_control


title: S1C12_non_SZ_control


title: S1C3_non_SZ_control


title: S1B9_non_SZ_control


title: S1C1_non_SZ_control


title: S1D11_non_SZ_control


title: S1C10_non_SZ_control


title: S1C2_non_SZ_control


title: S1C112_non_SZ_control


title: S1B6_non_SZ_control


title: S1B3_non_SZ_control


title: S1B7_non_SZ_control


title: S1B8_non_SZ_control


title: S1B2_non_SZ_control


title: S1D5_non_SZ_control


title: S1B12_non_SZ_control


title: S1B11_non_SZ_control


title: S1B5_non_SZ_control


title: S1A8_non_SZ_control


title: S1B1_non_SZ_control


title: S1A5_non_SZ_control


title: S1A7_non_SZ_control


title: S1A3_non_SZ_control


title: S1B4_non_SZ_control


title: RP2D5_SZ_case

value: schizophrenia case


title: S1A2_non_SZ_control


title: S1A1_non_SZ_control


title: S1A10_non_SZ_control


title: S1A11_non_SZ_control


title: RP2D6_SZ_case


title: RP2C7_SZ_case


title: RP2C8_SZ_case


title: RP2C4_SZ_case


title: S1A4_non_SZ_control


title: Caco-2 at 60 min post-infection - replicate 2

description: Biological replicate 2 of 3: Caco-2 cells 60 min post-infection


title: RP2C2_SZ_case


title: RP1G7_SZ_case


title: RP2B6_SZ_case


title: RP2A2_SZ_case


title: RP1E8_SZ_case


title: RP2B10_SZ_case


title: RP2A3_SZ_case


title: RP1F11_SZ_case


title: RP2D9_SZ_case


title: S1A12_non_SZ_control


title: RP1E5_SZ_case


title: RP1D5_SZ_case


title: RP1D2_SZ_case


title: RP1H11_SZ_case


title: RP1E2_SZ_case


title: P1E7_SZ_case


title: MU2_RP2E5_SZ_case


title: RP1C8_SZ_case


title: RP1B4_SZ_case


title: RP1A4_SZ_case


title: RP1B1_SZ_case


title: MU2_RP2E8_SZ_case


title: MU2_RP2E2_SZ_case


title: MU1_AP3G7_SZ_case


title: MU2_AP4H3_SZ_case


title: MU1_AP3G8_SZ_case


title: RP2C5_SZ_case


title: P1E4_SZ_case


title: MU1_AP3G1_SZ_case


title: MU1_AP2H9_SZ_case


title: MU1_AP2H3_SZ_case


title: MS7H12_non_SZ_control


title: MS7H7_non_SZ_control


title: MU1_AP2H6_SZ_case


title: MS7H10_non_SZ_control


title: MS7H1_non_SZ_control


title: MS7H9_non_SZ_control


title: MS7H11_non_SZ_control


title: MS7H8_non_SZ_control


title: MS7F6_non_SZ_control


title: MS7G9_non_SZ_control


title: MS7F7_non_SZ_control


title: MS7G2_non_SZ_control


title: MS7F11_non_SZ_control


title: MS7F3_non_SZ_control


title: MS7G3_non_SZ_control


title: MS7F12_non_SZ_control


title: MS7G10_non_SZ_control


title: MS7G6_non_SZ_control


title: MS7G5_non_SZ_control


title: MS7G4_non_SZ_control


title: MS7F5_non_SZ_control


title: MS7F4_non_SZ_control


title: MS7F10_non_SZ_control


title: MS7F2_non_SZ_control


title: MS7F8_non_SZ_control


title: MS7F9_non_SZ_control


title: MS7G1_non_SZ_control


title: MS7G11_non_SZ_control


title: MU1_AP2G12_SZ_case


title: MS7F1_non_SZ_control


title: MS7E9_non_SZ_control


title: MS7E7_non_SZ_control


title: MS7E8_non_SZ_control


title: MS7E3_non_SZ_control


title: MS7E5_non_SZ_control


title: MS7E4_non_SZ_control


title: MS7E6_non_SZ_control


title: MS7E1_non_SZ_control


title: MS7E11_non_SZ_control


title: MS7D8_non_SZ_control


title: MS7D9_non_SZ_control


title: MS7D6_non_SZ_control


title: MS7D7_non_SZ_control


title: MS7E2_non_SZ_control


title: MS7D5_non_SZ_control


title: MS7C11_non_SZ_control


title: MS7C12_non_SZ_control


title: MS7C2sl_non_SZ_control


title: MS7C7_non_SZ_control


title: MS7C1sl_non_SZ_control


title: MS7D1_non_SZ_control


title: MS7D11_non_SZ_control


title: MS7D2_non_SZ_control


title: MS7C8_non_SZ_control


title: MS7C6_non_SZ_control


title: MS7C3_non_SZ_control


title: MS7D3_non_SZ_control


title: MS7C9_non_SZ_control


title: MS7C5_non_SZ_control


title: MS7C4_non_SZ_control


title: MS7D12_non_SZ_control


title: MS7D10_non_SZ_control


title: MS7B8_non_SZ_control


title: MS7B7_non_SZ_control


title: MS7B5_non_SZ_control


title: MS7B11_non_SZ_control


title: MS7B12_non_SZ_control


title: MS7B2_non_SZ_control


title: MS7B10_non_SZ_control


title: MS7B1_non_SZ_control


title: MS7C10_non_SZ_control


title: MS7B9_non_SZ_control


title: MS7A9_non_SZ_control


title: MS7A6_non_SZ_control


title: MS7B6_non_SZ_control


title: MS7A7_non_SZ_control


title: MS7A4_non_SZ_control


title: MS7A12_non_SZ_control


title: MS7A10_non_SZ_control


title: MS6A7_non_SZ_control


title: MS6A6_non_SZ_control


title: MS7A1_non_SZ_control


title: MS6A3_non_SZ_control


title: MS7A3_non_SZ_control


title: MS7A11_non_SZ_control


title: MS7A2_non_SZ_control


title: MS6A4_non_SZ_control


title: MS6A8_non_SZ_control


title: MS7B3_non_SZ_control


title: MS6A12_non_SZ_control


title: MS6A5_non_SZ_control


title: MS7B4_non_SZ_control


title: MS6A11_non_SZ_control


title: MS5H9_non_SZ_control


title: MS6A10_non_SZ_control


title: MS6A9_non_SZ_control


title: MS6A1_non_SZ_control


title: MS6A2_non_SZ_control


title: MS5H7_non_SZ_control


title: MS5H5_non_SZ_control


title: MS5H4_non_SZ_control


title: MS5H3_non_SZ_control


title: MS5H12_non_SZ_control


title: MS5H11_non_SZ_control


title: MS5G9_non_SZ_control


title: MS5G6_non_SZ_control


title: MS5G12_non_SZ_control


title: MS5G5_non_SZ_control


title: MS5H10_non_SZ_control


title: MS5F6_non_SZ_control


title: MS5G2_non_SZ_control


title: MS5G4_non_SZ_control


title: MS5F12_non_SZ_control


title: MS5H6_non_SZ_control


title: MS5F4_non_SZ_control


title: MS5G11_non_SZ_control


title: MS5F3_non_SZ_control


title: MS5F7_non_SZ_control


title: MS5G10_non_SZ_control


title: MS5F1_non_SZ_control


title: MS5E9_non_SZ_control


title: MS5E2_non_SZ_control


title: MS5E3_non_SZ_control


title: MS5E11_non_SZ_control


title: MS5E6_non_SZ_control


title: MS5D9_non_SZ_control


title: MS5H2_non_SZ_control


title: MS5D8_non_SZ_control


title: MS5F9_non_SZ_control


title: MS5D10_non_SZ_control


title: MS5C7_non_SZ_control


title: MS5C6_non_SZ_control


title: MS5E7_non_SZ_control


title: MS5B5_non_SZ_control


title: MS5B4_non_SZ_control


title: MS5B6_non_SZ_control


title: MS5B3_non_SZ_control


title: MS5B2_non_SZ_control


title: MS5B8_non_SZ_control


title: MS5C5_non_SZ_control


title: MS5C3_non_SZ_control


title: MS5C2_non_SZ_control


title: MS5B7_non_SZ_control


title: MS5B9_non_SZ_control


title: MS5B11_non_SZ_control


title: MS5B1_non_SZ_control


title: MS5B10_non_SZ_control


title: MS5C10_non_SZ_control


title: MS5C1_non_SZ_control


title: MS5A5_non_SZ_control


title: MS5A6_non_SZ_control


title: MS5A8_non_SZ_control


title: MS5A3_non_SZ_control


title: MS5A4_non_SZ_control


title: MS5A2_non_SZ_control


title: MS5A12_non_SZ_control


title: MS5A11_non_SZ_control


title: MS4H8_non_SZ_control


title: MS4H9_non_SZ_control


title: MS5B12_non_SZ_control


title: MS4H6_non_SZ_control


title: MS4H3_non_SZ_control


title: MS4H2_non_SZ_control


title: MS4H11_non_SZ_control


title: MS4H5_non_SZ_control


title: MS4G2_non_SZ_control


title: MS4G8_non_SZ_control


title: MS4G3_non_SZ_control


title: MS4H4_non_SZ_control


title: MS4H1_non_SZ_control


title: MS4G11_non_SZ_control


title: MS4G6_non_SZ_control


title: MS4G10_non_SZ_control


title: MS4H7_non_SZ_control


title: MS4G5_non_SZ_control


title: MS4G12_non_SZ_control


title: MS4H10_non_SZ_control


title: MS4F4_non_SZ_control


title: MS4G1_non_SZ_control


title: MS4F12_non_SZ_control


title: MS4F7_non_SZ_control


title: MS4F6_non_SZ_control


title: MS4F8_non_SZ_control


title: MS4F3_non_SZ_control


title: MS4F5_non_SZ_control


title: MS4F11_non_SZ_control


title: MS4F10_non_SZ_control


title: MS4E4_non_SZ_control


title: MS4E7_non_SZ_control


title: MS4E2_non_SZ_control


title: MS4E12_non_SZ_control


title: MS4E10_non_SZ_control


title: MS4E3_non_SZ_control


title: MS4E11_non_SZ_control


title: MS4E9_non_SZ_control


title: MS4E8_non_SZ_control


title: MS4D2_non_SZ_control


title: MS4D5_non_SZ_control


title: MS4D9_non_SZ_control


title: MS4D3_non_SZ_control


title: MS4D10_non_SZ_control


title: MS4C1_non_SZ_control


title: MS4C5_non_SZ_control


title: MS4E1_non_SZ_control


title: MS4C4_non_SZ_control


title: MS4C9_non_SZ_control


title: MS4D4_non_SZ_control


title: MS4C2_non_SZ_control


title: MS4C11_non_SZ_control


title: MS4D12_non_SZ_control


title: MS4D8_non_SZ_control


title: MS4C3_non_SZ_control


title: MS4C7_non_SZ_control


title: MS4D6_non_SZ_control


title: MS4D7_non_SZ_control


title: MS4C6_non_SZ_control


title: MS4C12_non_SZ_control


title: MS4B8_non_SZ_control


title: MS4C8_non_SZ_control


title: MS4B7_non_SZ_control


title: MS4B9_non_SZ_control


title: MS4B6_non_SZ_control


title: MS4B5_non_SZ_control


title: MS4B4_non_SZ_control


title: MS4B2_non_SZ_control


title: MS4B11_non_SZ_control


title: MS4B10_non_SZ_control


title: MS4A6_non_SZ_control


title: MS3H3_non_SZ_control


title: MS4A2_non_SZ_control


title: MS4A5_non_SZ_control


title: MS3H9_non_SZ_control


title: MS3H10_non_SZ_control


title: MS3H6_non_SZ_control


title: MS3H5_non_SZ_control


title: MS4A8_non_SZ_control


title: MS3H11_non_SZ_control


title: MS4A12_non_SZ_control


title: MS4A4_non_SZ_control


title: MS3G7_non_SZ_control


title: MS3G6_non_SZ_control


title: MS3H7_non_SZ_control


title: MS3H2_non_SZ_control


title: MS3G8_non_SZ_control


title: MS5G1_non_SZ_control


title: MS4A1_non_SZ_control


title: MS4A7_non_SZ_control


title: MS4B1_non_SZ_control


title: MS3H1_non_SZ_control


title: MS3G5_non_SZ_control


title: MS3G4_non_SZ_control


title: MS3G2_non_SZ_control


title: MS3G12_non_SZ_control


title: MS3G3_non_SZ_control


title: MS3G1_non_SZ_control


title: MS3F8_non_SZ_control


title: MS3F3_non_SZ_control


title: MS3F7_non_SZ_control


title: MS3F4_non_SZ_control


title: MS5C4_non_SZ_control


title: MS3F1_non_SZ_control


title: MS3E9_non_SZ_control


title: MS3F12_non_SZ_control


title: MS3F10_non_SZ_control


title: MS3F2_non_SZ_control


title: MS3G10_non_SZ_control


title: MS3F11_non_SZ_control


title: MS3E2_non_SZ_control


title: MS3E8_non_SZ_control


title: MS3E4_non_SZ_control


title: MS3E12_non_SZ_control


title: MS3E6_non_SZ_control


title: MS3F6_non_SZ_control


title: MS3E5_non_SZ_control


title: MS3D11_non_SZ_control


title: MS3D12_non_SZ_control


title: MS3D5_non_SZ_control


title: MS3D7_non_SZ_control


title: MS3E10_non_SZ_control


title: MS3D8_non_SZ_control


title: MS3D6_non_SZ_control


title: MS3D3_non_SZ_control


title: MS3E11_non_SZ_control


title: MS3D4_non_SZ_control


title: MS3D1_non_SZ_control


title: MS3C7_non_SZ_control


title: MS3C9_non_SZ_control


title: MS3C8_non_SZ_control


title: MS3C2_non_SZ_control


title: MS3B8_non_SZ_control


title: MS3B7_non_SZ_control


title: MS3C11_non_SZ_control


title: MS3C10_non_SZ_control


title: MS3C4_non_SZ_control


title: MS3C12_non_SZ_control


title: MS3B9_non_SZ_control


title: MS3D10_non_SZ_control


title: MS3D2_non_SZ_control


title: MS3F9_non_SZ_control


title: MS3B11_non_SZ_control


title: MS3B3_non_SZ_control


title: MS3B2_non_SZ_control


title: MS3B6_non_SZ_control


title: MS3B4_non_SZ_control


title: MS3B12_non_SZ_control


title: MS3A9_non_SZ_control


title: MS3B1_non_SZ_control


title: MS3B10_non_SZ_control


title: MS3C6_non_SZ_control


title: MS3C5_non_SZ_control


title: MS3C1_non_SZ_control


title: MS3D9_non_SZ_control


title: MS3A5_non_SZ_control


title: MS3A8_non_SZ_control


title: MS3A11_non_SZ_control


title: MS3A6_non_SZ_control


title: MS3A3_non_SZ_control


title: MS2H8_non_SZ_control


title: MS2H9_non_SZ_control


title: MS3A2_non_SZ_control


title: MS2H7_non_SZ_control


title: MS3A7_non_SZ_control


title: MS2H4_non_SZ_control


title: MS3B5_non_SZ_control


title: MS3A12_non_SZ_control


title: MS3A10_non_SZ_control


title: MS2H12_non_SZ_control


title: MS2H10_non_SZ_control


title: MS2G9_MSSM_non_SZ_control


title: MS2G6_non_SZ_control


title: MS2H1_non_SZ_control


title: MS2G8_non_SZ_control


title: MS2G5_non_SZ_control


title: MS2H2_non_SZ_control


title: MS2G2_non_SZ_control


title: MS2G12_MSSM_non_SZ_control


title: MS2G3_non_SZ_control


title: MS2G10_non_SZ_control


title: MS2F9_non_SZ_control


title: MS2G4_non_SZ_control


title: MS2F6_non_SZ_control


title: MS2H11_non_SZ_control


title: MS3H4_non_SZ_control


title: MS2F7_non_SZ_control


title: MS2E5_non_SZ_control


title: MS2E4_non_SZ_control


title: MS2F10_non_SZ_control


title: MS2F2_non_SZ_control


title: MS2E8_non_SZ_control


title: MS2E9_non_SZ_control


title: MS2E3_non_SZ_control


title: MS2F5_non_SZ_control


title: MS2E6_non_SZ_control


title: MS2E2_non_SZ_control


title: MS2D9_non_SZ_control


title: MS2E11_non_SZ_control


title: MS2E12_non_SZ_control


title: MS2E10_non_SZ_control


title: MS2D8_non_SZ_control


title: MS2D7_non_SZ_control


title: MS2D4_non_SZ_control


title: MS2D11_non_SZ_control


title: MS2D3_non_SZ_control


title: MS2D12_non_SZ_control


title: MS2e1_non_SZ_control


title: MS2F8_non_SZ_control


title: MS2F3_non_SZ_control


title: MS2F11_non_SZ_control


title: MS2F4_2_non_SZ_control


title: MS2D1_non_SZ_control


title: MS2C9_non_SZ_control


title: MS2C8_non_SZ_control


title: MS2C7_non_SZ_control


title: MS2C2_non_SZ_control


title: MS2C10_non_SZ_control


title: MS2C3_non_SZ_control


title: MS2C6_non_SZ_control


title: MS2C11_non_SZ_control


title: MS2B9_non_SZ_control


title: MS2B4_non_SZ_control


title: MS2B8_non_SZ_control


title: MS2B7_non_SZ_control


title: MS2B3_non_SZ_control


title: MS2B6_non_SZ_control


title: MS2B2_non_SZ_control


title: MS2B5_non_SZ_control


title: MS2A9_non_SZ_control


title: MS2B11_non_SZ_control


title: MS2B10_non_SZ_control


title: MS2B12_non_SZ_control


title: MS2B1_non_SZ_control


title: MS2A7_non_SZ_control


title: MS2A8_non_SZ_control


title: MS2D10_non_SZ_control


title: MS2D2_non_SZ_control


title: MS2A6_non_SZ_control


title: MS2C5_non_SZ_control


title: MS2A5_non_SZ_control


title: MS2C1_non_SZ_control


title: MS2A3_non_SZ_control


title: MS2A4_non_SZ_control


title: MS2A2_non_SZ_control


title: MS2A1_non_SZ_control


title: APH8_SZ_case


title: MS2A10_non_SZ_control


title: MS2A11_non_SZ_control


title: APG8_SZ_case


title: APG5_SZ_case


title: APH2_SZ_case


title: APG11_SZ_case


title: APE5_SZ_case


title: APF11_SZ_case


title: APF8_SZ_case


title: APF5_SZ_case


title: APE2_SZ_case


title: APD8_SZ_case


title: APD5_SZ_case


title: MS2A12_non_SZ_control


title: APD2_SZ_case


title: APC5_SZ_case


title: APH5_SZ_case


title: APE8_SZ_case


title: APE11_SZ_case


title: APB4_SZ_case


title: AP9F1_SZ_case


title: AP9C10_SZ_case


title: AP9C1_SZ_case


title: AP9E7_SZ_case


title: APB1_SZ_case


title: APB10_SZ_case


title: AP9D12_SZ_case


title: AP9A10_SZ_case


title: APC1_SZ_case


title: AP9A1_SZ_case


title: AP9D4_SZ_case


title: AP9A4_SZ_case


title: AP9C7_SZ_case


title: APA7_SZ_case


title: AP8H10_SZ_case


title: AP8G4_SZ_case


title: AP8H1_SZ_case


title: AP8G10_SZ_case


title: AP8G7_SZ_case


title: AP9A7_SZ_case


title: AP8F7_SZ_case


title: AP9D7_SZ_case


title: APA10_SZ_case


title: AP9B1_SZ_case


title: APC11_SZ_case


title: AP8F10_SZ_case


title: AP8F4_SZ_case


title: APB7_SZ_case


title: AP8E7_SZ_case


title: AP8E10_SZ_case


title: AP8F1_SZ_case


title: AP8E4_SZ_case


title: AP8E1_SZ_case


title: AP7C4_h2_SZ_case


title: AP7H3_SZ_case


title: AP7D5_h2_SZ_case


title: AP7E5_h2_SZ_case


title: AP7H9_SZ_case


title: AP8_2_C4_SZ_case


title: AP7F9_SZ_case


title: AP8_2_C9_SZ_case


title: AP8_2_D9_SZ_case


title: AP8_2_B10_SZ_case


title: AP8A1_SZ_case


title: AP7E9_h2_SZ_case


title: AP8_2_D10_SZ_case


title: APA4_SZ_case


title: AP8_2_D4_SZ_case


title: AP7G9_SZ_case


title: AP7C1_h2_SZ_case


title: AP7C7_h2_SZ_case


title: AP7G5_SZ_case


title: AP8_2_C10_SZ_case


title: AP7D11_h2_SZ_case


title: AP7B7_h2_SZ_case


title: AP7B10_h2_SZ_case


title: AP6H9_SZ_case


title: AP7B1_h2_SZ_case


title: AP7F3_SZ_case


title: AP7A1_SZ_case


title: AP8_2_B1_SZ_case


title: AP6H5_SZ_case


title: AP6F9_SZ_case


title: AP6G8_SZ_case


title: AP6G3_SZ_case


title: AP6G12_SZ_case


title: AP6F12_SZ_case


title: AP6G9_SZ_case


title: AP6F6_SZ_case


title: AP6F5_SZ_case


title: AP6E4_SZ_case


title: AP6D3_SZ_case


title: AP6C2_SZ_case


title: AP6C9_SZ_case


title: AP6B9_SZ_case


title: AP6D6_SZ_case


title: AP6A7_SZ_case


title: AP6D2_SZ_case


title: AP6C6_SZ_case


title: AP6E12_SZ_case


title: AP6D10_SZ_case


title: AP6D12_SZ_case


title: AP6A4_SZ_case


title: AP5H5_SZ_case


title: AP6A10_SZ_case


title: AP7A4_SZ_case


title: AP5G5_SZ_case


title: AP5G11_SZ_case


title: AP5F7_SZ_case


title: AP5F10_SZ_case


title: AP5E1_SZ_case


title: AP5E10_SZ_case


title: AP5E4_SZ_case


title: AP5D7_SZ_case


title: AP5D4_SZ_case


title: AP5F1_SZ_case


title: AP5D1_SZ_case


title: AP5C1_SZ_case


title: AP5A10_SZ_case


title: AP4D8_SZ_case


title: AP5A7_SZ_case


title: AP4D5_SZ_case


title: AP4F3_SZ_case


title: AP5B7_SZ_case


title: AP4G6_SZ_case


title: AP5A1_SZ_case


title: AP4F9_SZ_case


title: AP4C5_SZ_case


title: AP5C4_SZ_case


title: AP4E12_SZ_case


title: AP4G3_SZ_case


title: AP4G9_SZ_case


title: AP4F6_SZ_case


title: AP5C7_SZ_case


title: AP4D11_SZ_case


title: AP4F12_SZ_case


title: AP4C8_SZ_case


title: AP5E7_SZ_case


title: AP4E2_SZ_case


title: AP4C11_SZ_case


title: AP4B2_SZ_case


title: AP4C2_SZ_case


title: AP4B11_SZ_case


title: AP4H2_SZ_case


title: AP4A8_SZ_case


title: AP4A7_SZ_case


title: AP3_2_H8_SZ_case


title: AP3_2_F4_SZ_case


title: AP3_2_H5_SZ_case


title: AP3_2_H2_SZ_case


title: AP4A11_SZ_case


title: AP3_2_F7_SZ_case


title: AP4B6_SZ_case


title: AP3_2_F10_SZ_case


title: AP2E11_SZ_case


title: AP3_2_D10_SZ_case


title: AP3_2_C7_SZ_case


title: AP2G6_SZ_case


title: AP2F5_SZ_case


title: AP3_2_D4_SZ_case


title: AP2G3_SZ_case


title: AP3_2_A1_SZ_case


title: AP3_2_E7_SZ_case


title: AP2E5_SZ_case


title: AP2F9_SZ_case


title: AP2D8_SZ_case


title: AP3_2_E4_SZ_case


title: AP3_2_E1_SZ_case


title: AP3_2_E10_SZ_case


title: AP2E2_SZ_case


title: AP2G9_SZ_case


title: AP3_2_B4_SZ_case


title: AP3_2_C4_SZ_case


title: AP3_2_C10_SZ_case


title: AP2D5_SZ_case


title: AP2D2_SZ_case


title: AP2D11_SZ_case


title: AP2C11_SZ_case


title: AP2C2_SZ_case


title: AP3_2_F1_SZ_case


title: 2D01_SZ_case


title: AP2B4_SZ_case


title: AP2A1_SZ_case


title: AP2A4_SZ_case


title: AP2A7_SZ_case


title: AP2B8_SZ_case


title: 1H7_SZ_case


title: AP2B11_SZ_case


title: 2A01_SZ_case


title: 2B01_SZ_case


title: 1B4_SZ_case


title: 1B10_SZ_case


title: 1D1_SZ_case


title: 1D4_SZ_case


title: 1D7_SZ_case


title: 1G7_SZ_case


title: 1F4_SZ_case


title: 1G10_SZ_case


title: 1F10_SZ_case


title: 1D10_SZ_case


title: 1H10_SZ_case


title: 1F7_SZ_case


title: 1B1_SZ_case


title: 1G4_SZ_case


title: 1H4_SZ_case


title: 1A4_SZ_case


title: 1B7_SZ_case


title: 1C10_SZ_case


title: 1A7_SZ_case


title: 1A1_SZ_case


title: tumor  47

city: Chapel Hill

first: Matthew

middle: D

last: Wilkerson

state: NC

address: 450 West Drive

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description: tumor  47

hyb_protocol: Microarrays were hybridized in an Robbins Scientific hybridization oven with 850ng of labeled Cy3 Reference and 850ng of Cy5 experimental samples using the Agilent hybridization kit as described by the manufacturer. The arrays were incubated overnight and then washed once for 10 minutes in 2X SSC and 0.0005% triton X-102, twice for 5 minutes in 0.1XSSC, and then immersed into Agilent Stabilization and Drying solution for 20 seconds.

scan_protocol: Microarrays were scanned with Agilent Scanner and intensity was recorded using Agilent Feature Extraction Software.

data_processing: Agilent feature extraction output was processed by normexp background correction and loess normalization using Bioconductor library limma.

source_name: lung squamous cell carcinoma tumor RNA

label_protocol: The total RNA labeling and hybridization protocol used is described in the Agilent low RNA input linear amplification kit (http://www.chem.agilent.com/Scripts/PDS.asp?lPage=10003 ), with the following two changes: 1) a Qiagen PCR purification kit was used to clean up the cRNA instead of the LiCl precipitation, and 2) all regents volumes were reduced by one half.

extract_protocol: Total RNA was extracted using RNeasy kit from Qiagen following manufacturer's instructions. These total RNA samples were run on an Agilent Bioanalyzer 2100 (Agilent Technologies, Inc) to ensure RNA quality.

tag: subtype

value: secretory

tag: sex

value: Male

tag: stage

value: IIb

tag: grade

value: poor

source_name: Stratagene Human Universal Reference

tag: contents

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs


title: tumor  53

description: tumor  53

value: Ib

value: mod

value: minimal


title: tumor  48

description: tumor  48

value: primitive

value: Female


title: tumor  52

description: tumor  52

value: basal

value: Ia

value: marked


title: Reprogrammed iPSC line (hiPSC 3975 p9)

city: Los Angeles

first: Kathrin

last: Plath

address: 615 Charles E. Young Drive South

department: Biological Chemistry

institute: UCLA

description: Gene expression data from hiPSC line 3975

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on human expression arrays

scan_protocol: Gene chips were analyzed using GeneChip® Scanner 3000.

data_processing:
The raw data was processed using the RMA algorithm and was implemented using R (Bioconductor).
The data is presented as a summary of the highest confidence probesets for each given RefSeq identifier. (See Materials and Methods, Chin, et al. Cell Stem Cell, 2009)

source_name: hiPSC line 3975 (p9)

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

growth_protocol: Cell lines were cultured in hESC cell media for hESC and hiPSC lines (Lowry, et al. PNAS, 2008) and DMEM for the fibroblast line.

extract_protocol: Total RNA was extracted using Stratagene's Lysis Buffer and extracted according to the manufacturer's instructions.

treatment_protocol: Reprogrammed Cell lines were treated as described in Lowry, et al. (PNAS, 2008)

tag: cell type

value: hiPSC

value: hiPSC line 3975


title: tumor  38

description: tumor  38

tag: age


title: Fibroblast cell line (NHDF3284)

description: Gene expression data from NHDF fibroblasts

source_name: NHDF 3284 fibroblasts

value: fibroblast

value: NHDF 3284


title: human ES cell line (H1 p56)

description: Gene expression data from H1

value: embryonic stem cells


title: tumor  39

description: tumor  39

value: Male


title: tumor  44

description: tumor  44

value: secretory


title: tumor  54

description: tumor  54

value: classical


title: tumor  49

description: tumor  49

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs


title: tumor  40

description: tumor  40

value: Ib


title: human ES cell line (Hsf1 p51)

description: Gene expression data from HSF1


title: Reprogrammed iPSC line (hiPSC 3975 p6)

source_name: hiPSC line 3975 (p6)


title: Fibroblast cell line (NHDF3535a)

source_name: NHDF 3535 fibroblasts

value: NHDF 3535


title: Fibroblast cell line (NHDF17430)

source_name: NHDF 17430 fibroblasts


title: tumor  43

description: tumor  43

value: IIb

value: poor

value: minimal


title: tumor  42

description: tumor  42

value: Female

value: mod


title: tumor  37

description: tumor  37


title: Reprogrammed iPSC line (hiPSC IMR90 p9)

description: Gene expression data from IMR90 hiPSC line

source_name: hiPSC line IMR90 (p9)

value: hiPSC line IMR90


title: Fibroblast cell line (NHDF3535b)


title: tumor  46

description: tumor  46


title: tumor  41

description: tumor  41

value: basal

value: marked


title: tumor  51

description: tumor  51


title: tumor  36

description: tumor  36

value: primitive


title: tumor  56

description: tumor  56


title: tumor  50

description: tumor  50

value: IIIa


title: tumor  55

description: tumor  55


title: tumor  45

description: tumor  45


title: tumor  33

description: tumor  33


title: tumor  35

description: tumor  35


title: tumor  30

description: tumor  30

value: Ia


title: tumor  34

description: tumor  34


title: tumor  29

description: tumor  29

value: Male


title: tumor  28

description: tumor  28

value: secretory


title: tumor  24

description: tumor  24

value: classical


title: tumor  32

description: tumor  32

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs


title: tumor  27

description: tumor  27


title: tumor  31

description: tumor  31

value: Ib


title: tumor  26

description: tumor  26


title: tumor  25

description: tumor  25


title: tumor  19

description: tumor  19


title: tumor  22

description: tumor  22


title: tumor  17

description: tumor  17


title: tumor  20

description: tumor  20

value: IIa


title: tumor  12

description: tumor  12


title: tumor  16

description: tumor  16


title: tumor  21

description: tumor  21

value: IIb


title: tumor  15

description: tumor  15


title: tumor  10

description: tumor  10

value: poor


title: tumor  11

description: tumor  11


title: tumor  7

description: tumor  7


title: tumor  23

description: tumor  23

value: minimal


title: tumor  13

description: tumor  13

value: Female


title: tumor  18

description: tumor  18

value: mod


title: tumor  6

description: tumor  6


title: tumor  14

description: tumor  14


title: tumor  8

description: tumor  8


status: Public on Aug 05 2010

hyb_protocol: For array hybridization, 2ug of the labeled DNA material was hybridized per chip for 18 h at 45C in a 3 M tetramethyl ammonium chloride/1x MES-based solution containing 100?g/mL Herring Sperm DNA, 0.02% Triton and 30pM of biotinylated control oligo B2 (Affymetrix). All reagents were from Invitrogen, except where noted otherwise.

scan_protocol: Scanned at 0.7 microns/pixel.

data_processing: Data_Normalization_for_Expression_Arrays protocol. Three biological replicates were hybridized for this experiment. The data from replicate arrays were quantile-normalized (Bolstad et al., 2003) and all arrays were scaled to a median array intensity given (e.g. 361).  Processed data are obtained using following parameters: median value is 361   Signal Graph generation protocol. The sliding window approach (bandwidth 50) has been used to estimate RNA abundance (signal which is listed in column #2). It was found by calculating the median of all pairwise average PM-MM values, where PM is a perfect match and MM is a mismatch.  Processed data are obtained using following parameters: bandwidth is 50

source_name: adult female,eclosion + 30 days (Celniker/RNA:400) extraction2_array1 channel_1

label_protocol: Double-stranded cDNA was treated with RNase H (Epicentre Technologies) and RNases A/T1 (Ambion), extracted by using a QIAquick PCR purification kit (Qiagen), and subjected to further fragmentation to 50-100 bp by DNase I (1 unit/ul; Epicentre Technologies; size distribution of fragmented DNA was verified on a 2% agarose gel).The fragmented cDNA was then end-labeled with 2.5mM biotinylated DNA labeling reagent (Affymetrix) by using 100 units of terminal deoxynucleotidyltransferase (TdT; Roche Diagnostics) in 1x TdT buffer (Roche Diagnostics) and 5 mM CoCl2 (Roche Diagnostics) for 2 h at 37C. TdT LABELING; Perform in 20 ul for 5 ug of DNA, 35 ul for 10 ug of DNA, and 70 ul for 10-15 ug of DNA.  - 40 ul of fragmented DNA  - 14 ul of 5X TdT buffer (Roche)  - 7 ul of 20mM CoCl2 (Roche)  - 2.3 ul of DNA Labeling Reagents (Affymetrix)  - 0.5 ul of Terminal deoxytransferase, 8000U (Roche)  - 6.2 ul of diH2OIncubate at 37C for 2 hours in water bath.The labeled cDNA is now ready to be hybridized.

growth_protocol:
Fly population cages contained the sequenced D. melanogaster isogenic strain with the mutations; yellow (y1), cinnabar (cn1), brown (bw1), and speck (sp1) [1]. Two homemade Plexiglas cages approximately 25cm x 25cm x 25cm, were used for staged embryo collections. These population cages were constructed from ¼ inch solid Plexiglas except for the open front panel. The fronts of the cages were covered with sleeves constructed of muslin cloth that were attached to the Plexiglas sides using Velcro strips. Each muslin sleeve was then twisted and held closed with a hose clamp. Flies were fed with three hard egg lay collection plates made in 150 X 15 mm Petri dishes containing a substrate of 3.3% agar, 13% unsulfured molasses, and 0.15% Tegasept. The hard egg lay plates were completely covered with a thin layer of moist yeast paste (Fleischmann?s Baker?s Dry Yeast) and placed horizontally on a short 1cm raised Plexiglas bar in the bottom of each cage to avoid crushing flies. The two population cages were maintained at 24? C in a controlled environment on a 24-hour light cycle (14 hours light / 10 hours dark) using three 60W bulbs on a timer. Flies were introduced to the cages at least four days prior to collections and fertility counts. These animals were initially grown in bottles at the same controlled environment described above. Each population cage was established from four trays with 35 bottles per tray containing newly eclosed adult flies. Each 250ml (pint) bottle contained approximately 40ml standard Drosophila medium in use at Bloomington (http://flystocks.bio.indiana.edu/Fly_Work/media-recipes/media-recipes.htm). The isogenic Drosophila mutant strain was propagated in bottles (A) starting with approximately 40-50 adults per bottle on day zero. New bottles (B) were generated from these bottles (A) on day 14. Cages were established by clearing the ?A? bottles into an empty bottle (without food) and transferring the newly eclosed adult flies in the ?A? bottles into the two population cages on day 18. The next round of cages and bottles (C) were established from the ?B? bottles in the same manner. Two-hour embryo collections were made during the light cycles following at least one two-hour pre-lay.
Protocol for staging adult flies for RNA isolation.

extract_protocol:
RNA extraction: TRIzol procedure for Insects followed by DNase and RNeasyNote: This protocol is used to prepare RNA that will be used for microarray hybridization or RT-PCR.
cDNA Synthesis and Labeling: Note that this protocol gives you labeled dsDNA, as such the array results are not stranded.* ug cDNA hybed per chip: 10 ug if template was total RNA or Poly-A-, 2.5 ug if Poly-A+ RNAFIRST-STRAND SYNTHESIS  - 10 ug of Total RNA (DNAsed,Cleaned-up and ETOH precipitated)  - 1.25 ug of 250ng/ul random primers (Invitrogen)  - diH2O to 60 ul Vf.Incubate at 70C for 10 mins (fast ramp) then cool to 15C over the course of 20 minutes. Once it reaches 15C add:  - 20 ul of 5X First-Strand Buffer (Invitrogen)  - 10 ul of 100mM DTT (Invitrogen)  - 5 ul of 10mM dNTPs (Invitrogen)Incubate at 15C for 30 minutes then heat to 42C over the course of 20 minutes.  Once it reaches 42C add:  - 10 ul Superscript RT II (Invitrogen)Incubate at 42C for 60 minutes, then heat rapidly to 70C and incubate for 15 minutes, then park it at 4C.SECOND-STRAND SYNTHESISTo the First strand synthesis reaction above add while at 4C:  - 450 ul diH2O  - 150 ul 5X Second-Strand Buffer (Invitrogen)  - 15 ul 10mM dNTPs (Invitrogen)  - 5 ul 10U/ul E. coli DNA Ligase (Invitrogen)  - 20 ul 10U/ul E. coli DNA Polymerase (Invitrogen)  - 5 ul 2U/ul E. coli RNAseH (Invitrogen)Incubate at 16C for 120 minutes, then 70C for 15 minutes, then park it at 4C.RNA REMOVAL and cDNA PURIFICATIONAdd:  - 3 ul of 10U/ul RNaseH (Ambion)  - 3 ul of 5 and 20U/ul RNAseA/T1 (Ambion)Incubate at 37C for 20 minutesUse a Qiagen PCR Clean-up kit (two columns per reaction), ETOH precipitate the eluate and 70% ETOH rinse.  Redissolve in 35 ul diH2O.  Measure the OD600 on a Nanodrop.cDNA FRAGMENTATION*** NEED TO ADD ***Check the fragmentation on an agarose gel. Want it to be around 100 nucleotides.

tag: strain

value: Y cn bw sp

tag: developmental stage

value: Adult female, eclosion + 30 days


title: Celniker/RNA:515 extraction1_array1

label_protocol: Double-stranded cDNA was treated with RNase H (Epicentre Technologies) and RNases A/T1 (Ambion), extracted by using a QIAquick PCR purification kit (Qiagen), and subjected to further fragmentation to 50-100 bp by DNase I (1 unit/ul; Epicentre Technologies; size distribution of fragmented DNA was verified on a 2% agarose gel).The fragmented cDNA was then end-labeled with 2.5mM biotinylated DNA labeling reagent (Affymetrix) by using 100 units of terminal deoxynucleotidyltransferase (TdT; Roche Diagnostics) in 1x TdT buffer (Roche Diagnostics) and 5 mM CoCl2 (Roche Diagnostics) for 2 h at 37C.

growth_protocol:
Fly population cages contained the sequenced D. melanogaster isogenic strain with the mutations; yellow (y1), cinnabar (cn1), brown (bw1), and speck (sp1) [1]. Two homemade Plexiglas cages approximately 25cm x 25cm x 25cm, were used for staged embryo collections. These population cages were constructed from ¼ inch solid Plexiglas except for the open front panel. The fronts of the cages were covered with sleeves constructed of muslin cloth that were attached to the Plexiglas sides using Velcro strips. Each muslin sleeve was then twisted and held closed with a hose clamp. Flies were fed with three hard egg lay collection plates made in 150 X 15 mm Petri dishes containing a substrate of 3.3% agar, 13% unsulfured molasses, and 0.15% Tegasept. The hard egg lay plates were completely covered with a thin layer of moist yeast paste (Fleischmann?s Baker?s Dry Yeast) and placed horizontally on a short 1cm raised Plexiglas bar in the bottom of each cage to avoid crushing flies. The two population cages were maintained at 24? C in a controlled environment on a 24-hour light cycle (14 hours light / 10 hours dark) using three 60W bulbs on a timer. Flies were introduced to the cages at least four days prior to collections and fertility counts. These animals were initially grown in bottles at the same controlled environment described above. Each population cage was established from four trays with 35 bottles per tray containing newly eclosed adult flies. Each 250ml (pint) bottle contained approximately 40ml standard Drosophila medium in use at Bloomington (http://flystocks.bio.indiana.edu/Fly_Work/media-recipes/media-recipes.htm). The isogenic Drosophila mutant strain was propagated in bottles (A) starting with approximately 40-50 adults per bottle on day zero. New bottles (B) were generated from these bottles (A) on day 14. Cages were established by clearing the ?A? bottles into an empty bottle (without food) and transferring the newly eclosed adult flies in the ?A? bottles into the two population cages on day 18. The next round of cages and bottles (C) were established from the ?B? bottles in the same manner. Two-hour embryo collections were made during the light cycles following at least one two-hour pre-lay.
Protocol for the separation of heads from adult flies (aged 1-20 days post-eclosion). Note that this protocol typically results in loss of antennal and maxillary organs but retention of mouthparts.

extract_protocol:
Protocol for isolating total RNA from dissected tissues of Drosophila.
First-strand cDNA synthesis was performed by using SuperScript II reverse transcriptase in the reaction volume of 105 ul for 15 ug of starting RNA material. The RNA was mixed with random hexamers (83.3 ng/g mRNA), heated to 70C for 10 min, and cooled to 15C after which 5x SuperScript II First Strand buffer, DTT (10 mM), and dNTPs (0.5 mM) were added. SuperScript II was added after a 20-min incubation (200 units/ug RNA) followed by a 20-min ramp to 42C and 60-min incubation at 420C. SuperScript II was inactivated at 75C for 15 min.The second-strand cDNA was synthesized by addition of 50 units of Escherichia coli DNA ligase, 200 units of E. coli DNA polymerase I, 10 units of E. coli RNase H, and 0.2 mM dNTPs to the first-strand synthesis reaction at 16C for 2 h.

value: Oregon-R

value: Female heads

value: Adult female, eclosion + 1 day

value: wild type


title: Celniker/RNA:516 extraction2_array1


title: tumor  5

description: tumor  5

value: Ia


title: Celniker/RNA:498 extraction2_array1


source_name: adult male,eclosion + 30 days (Celniker/RNA:396) extraction3_array1 channel_1

value: Adult male, eclosion + 30 days

value: Male


source_name: adult male,eclosion + 30 days (Celniker/RNA:394) extraction2_array1 channel_1


source_name: adult female,eclosion + 30 days (Celniker/RNA:402) extraction3_array1 channel_1


source_name: adult female,eclosion + 30 days (Celniker/RNA:398) extraction1_array1 channel_1


title: Celniker/RNA:497 extraction1_array1


title: Celniker/RNA:531 extraction1_array1

growth_protocol:
Fly population cages contained the sequenced D. melanogaster isogenic strain with the mutations; yellow (y1), cinnabar (cn1), brown (bw1), and speck (sp1) [1]. Two homemade Plexiglas cages approximately 25cm x 25cm x 25cm, were used for staged embryo collections. These population cages were constructed from ¼ inch solid Plexiglas except for the open front panel. The fronts of the cages were covered with sleeves constructed of muslin cloth that were attached to the Plexiglas sides using Velcro strips. Each muslin sleeve was then twisted and held closed with a hose clamp. Flies were fed with three hard egg lay collection plates made in 150 X 15 mm Petri dishes containing a substrate of 3.3% agar, 13% unsulfured molasses, and 0.15% Tegasept. The hard egg lay plates were completely covered with a thin layer of moist yeast paste (Fleischmann?s Baker?s Dry Yeast) and placed horizontally on a short 1cm raised Plexiglas bar in the bottom of each cage to avoid crushing flies. The two population cages were maintained at 24? C in a controlled environment on a 24-hour light cycle (14 hours light / 10 hours dark) using three 60W bulbs on a timer. Flies were introduced to the cages at least four days prior to collections and fertility counts. These animals were initially grown in bottles at the same controlled environment described above. Each population cage was established from four trays with 35 bottles per tray containing newly eclosed adult flies. Each 250ml (pint) bottle contained approximately 40ml standard Drosophila medium in use at Bloomington (http://flystocks.bio.indiana.edu/Fly_Work/media-recipes/media-recipes.htm). The isogenic Drosophila mutant strain was propagated in bottles (A) starting with approximately 40-50 adults per bottle on day zero. New bottles (B) were generated from these bottles (A) on day 14. Cages were established by clearing the ?A? bottles into an empty bottle (without food) and transferring the newly eclosed adult flies in the ?A? bottles into the two population cages on day 18. The next round of cages and bottles (C) were established from the ?B? bottles in the same manner. Two-hour embryo collections were made during the light cycles following at least one two-hour pre-lay.
Protocol for dissection of gonads (male: accessory gland and testes separately; female: ovaries) from Oregon R adults aged 1, 4, or 20 days post-eclosion.

value: Adult ovaries

value: Adult female eclosion+4 day


title: Celniker/RNA:532 extraction2_array1


title: tumor  3

description: tumor  3

value: secretory

value: marked

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs


title: tumor  2

description: tumor  2

value: IIb

value: poor


title: tumor  9

description: tumor  9

value: classical

value: Female

value: mod

value: minimal


title: tumor  1

description: tumor  1

value: basal

value: Ib


title: tumor  4

description: tumor  4


title: Mouse retina_3 days_ rep2

city: Acton

first: Riccardo

last: Natoli

state: ACT

address: Sullivans Creek Road

department: CMBE

country: Australia

institute: ANU

description: Gene expression data from mouse retina exposued to 3 days 75% hyperoxia

hyb_protocol: Standard Affymetrix protocols were followed in the hybridisation, blocking and washing (GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 3)).

scan_protocol: The arrays were scanned on the GCS 3000 Affymetrix high resolution scanner and analyzed using the GeneChip Operating Software v1.4 (GCOS; Affymetrix) and GeneSpring v 7.3.1 (Agilent Technologies).

data_processing: RMA normalization performed in GeneSpring v 7.3.1. Log2 RMA data was quantile transformed to median sample baseline.

source_name: retina, 3 days exposure to 75% hyperoxia

label_protocol: Biotin-labeled cRNA was prepared according to the standard Affymetrix protocol from 500ng total RNA (Affymetrix manual, P/N 702646 Rev. 7).

growth_protocol: Animals were raised in cyclic light conditions using 12hrs dim (5 lux) and 12hrs dark (no light).

extract_protocol: Total RNA was extracted from each retinal biopsy using Trizol and chloroform to separate the RNA from other cell components. The RNA was then purified and isolated using RNAqueous-Micro RNA isolation kit (Ambion, Inc., Austin, TX). In some cases where genomic DNA contamination was a concern, the RNA was DNAse treated.

treatment_protocol: Animals were placed in an oxygen chamber and exposed to 75% oxygen for a period of either 3, 7 or 14 days.

value: Retina

value: Adult P80 - 120


title: Mouse retina_14 days_ rep2

description: Gene expression data from mouse retina exposued to 14 days 75% hyperoxia

source_name: retina, 14 days exposure to 75% hyperoxia


title: Mouse retina_14 days_ rep1


title: Mouse retina_7 days_ rep2

description: Gene expression data from mouse retina exposued to 7 days 75% hyperoxia

source_name: retina, 7 days exposure to 75% hyperoxia


molecule: polyA RNA

source_name: CME-W1 Cl.8+ (Celniker/RNA:493) extraction3_array1 channel_1

growth_protocol: Describes growth and care of Cl.8 cell line for modENCODE RNA isolation.

extract_protocol:
Protocol for extraction of polyA RNA starting with cell cultures from D. melanogaster.
cDNA Synthesis and Labeling: Note that this protocol gives you labeled dsDNA, as such the array results are not stranded.* ug cDNA hybed per chip: 10 ug if template was total RNA or Poly-A-, 2.5 ug if Poly-A+ RNAFIRST-STRAND SYNTHESIS  - 10 ug of Total RNA (DNAsed,Cleaned-up and ETOH precipitated)  - 1.25 ug of 250ng/ul random primers (Invitrogen)  - diH2O to 60 ul Vf.Incubate at 70C for 10 mins (fast ramp) then cool to 15C over the course of 20 minutes. Once it reaches 15C add:  - 20 ul of 5X First-Strand Buffer (Invitrogen)  - 10 ul of 100mM DTT (Invitrogen)  - 5 ul of 10mM dNTPs (Invitrogen)Incubate at 15C for 30 minutes then heat to 42C over the course of 20 minutes.  Once it reaches 42C add:  - 10 ul Superscript RT II (Invitrogen)Incubate at 42C for 60 minutes, then heat rapidly to 70C and incubate for 15 minutes, then park it at 4C.SECOND-STRAND SYNTHESISTo the First strand synthesis reaction above add while at 4C:  - 450 ul diH2O  - 150 ul 5X Second-Strand Buffer (Invitrogen)  - 15 ul 10mM dNTPs (Invitrogen)  - 5 ul 10U/ul E. coli DNA Ligase (Invitrogen)  - 20 ul 10U/ul E. coli DNA Polymerase (Invitrogen)  - 5 ul 2U/ul E. coli RNAseH (Invitrogen)Incubate at 16C for 120 minutes, then 70C for 15 minutes, then park it at 4C.RNA REMOVAL and cDNA PURIFICATIONAdd:  - 3 ul of 10U/ul RNaseH (Ambion)  - 3 ul of 5 and 20U/ul RNAseA/T1 (Ambion)Incubate at 37C for 20 minutesUse a Qiagen PCR Clean-up kit (two columns per reaction), ETOH precipitate the eluate and 70% ETOH rinse.  Redissolve in 35 ul diH2O.  Measure the OD600 on a Nanodrop.cDNA FRAGMENTATION*** NEED TO ADD ***Check the fragmentation on an agarose gel. Want it to be around 100 nucleotides.

value: dorsal mesothoracic disc

value: third instar larval stage


source_name: CME-W1 Cl.8+ (Celniker/RNA:491) extraction1_array1 channel_1

value: Male


source_name: S2-DRSC (Celniker/RNA:479) extraction1_array1 channel_1

growth_protocol: Description of the growth and maintenance of S2-DRSC cells used by modENCODE for RNA preparations.

value: embryo-derived cell-line

value: late embryonic stage


source_name: S2-DRSC (Celniker/RNA:480) extraction2_array1 channel_1


molecule: nuclear RNA

source_name: ML-DmBG3-c2 (Celniker/RNA:490) extraction3_array1 channel_1

growth_protocol: instructions for growth of BG3-c2 cells for RNA isolation.

extract_protocol:
For isolation of nuclear RNA from cell cultures.  Nuclei are isolated by differential centrifugation and RNA is collected using the TRIzol protocol for cell lines. This protocol is modified from Zimmerman et al 1982 (PNAS 79:3148) and used to prepare nuclear RNA from cell lines
cDNA Synthesis and Labeling: Note that this protocol gives you labeled dsDNA, as such the array results are not stranded.* ug cDNA hybed per chip: 10 ug if template was total RNA or Poly-A-, 2.5 ug if Poly-A+ RNAFIRST-STRAND SYNTHESIS  - 10 ug of Total RNA (DNAsed,Cleaned-up and ETOH precipitated)  - 1.25 ug of 250ng/ul random primers (Invitrogen)  - diH2O to 60 ul Vf.Incubate at 70C for 10 mins (fast ramp) then cool to 15C over the course of 20 minutes. Once it reaches 15C add:  - 20 ul of 5X First-Strand Buffer (Invitrogen)  - 10 ul of 100mM DTT (Invitrogen)  - 5 ul of 10mM dNTPs (Invitrogen)Incubate at 15C for 30 minutes then heat to 42C over the course of 20 minutes.  Once it reaches 42C add:  - 10 ul Superscript RT II (Invitrogen)Incubate at 42C for 60 minutes, then heat rapidly to 70C and incubate for 15 minutes, then park it at 4C.SECOND-STRAND SYNTHESISTo the First strand synthesis reaction above add while at 4C:  - 450 ul diH2O  - 150 ul 5X Second-Strand Buffer (Invitrogen)  - 15 ul 10mM dNTPs (Invitrogen)  - 5 ul 10U/ul E. coli DNA Ligase (Invitrogen)  - 20 ul 10U/ul E. coli DNA Polymerase (Invitrogen)  - 5 ul 2U/ul E. coli RNAseH (Invitrogen)Incubate at 16C for 120 minutes, then 70C for 15 minutes, then park it at 4C.RNA REMOVAL and cDNA PURIFICATIONAdd:  - 3 ul of 10U/ul RNaseH (Ambion)  - 3 ul of 5 and 20U/ul RNAseA/T1 (Ambion)Incubate at 37C for 20 minutesUse a Qiagen PCR Clean-up kit (two columns per reaction), ETOH precipitate the eluate and 70% ETOH rinse.  Redissolve in 35 ul diH2O.  Measure the OD600 on a Nanodrop.cDNA FRAGMENTATION*** NEED TO ADD ***Check the fragmentation on an agarose gel. Want it to be around 100 nucleotides.

value: CNS-derived cell-line

value: y v f mal

value: Unknown


source_name: S2-DRSC (Celniker/RNA:481) extraction3_array1 channel_1


source_name: ML-DmBG2-c3 (Celniker/RNA:485) extraction1_array1 channel_1


source_name: ML-DmBG3-c2 (Celniker/RNA:489) extraction2_array1 channel_1


source_name: ML-DmBG2-c3 (Celniker/RNA:487) extraction3_array1 channel_1


source_name: CME-W1 Cl.8+ (Celniker/RNA:492) extraction2_array1 channel_1


source_name: WPP + 12 hr (Celniker/RNA:336) extraction3_array1 channel_1

growth_protocol:
Fly population cages contained the sequenced D. melanogaster isogenic strain with the mutations; yellow (y1), cinnabar (cn1), brown (bw1), and speck (sp1) [1]. Two homemade Plexiglas cages approximately 25cm x 25cm x 25cm, were used for staged embryo collections. These population cages were constructed from ¼ inch solid Plexiglas except for the open front panel. The fronts of the cages were covered with sleeves constructed of muslin cloth that were attached to the Plexiglas sides using Velcro strips. Each muslin sleeve was then twisted and held closed with a hose clamp. Flies were fed with three hard egg lay collection plates made in 150 X 15 mm Petri dishes containing a substrate of 3.3% agar, 13% unsulfured molasses, and 0.15% Tegasept. The hard egg lay plates were completely covered with a thin layer of moist yeast paste (Fleischmann?s Baker?s Dry Yeast) and placed horizontally on a short 1cm raised Plexiglas bar in the bottom of each cage to avoid crushing flies. The two population cages were maintained at 24? C in a controlled environment on a 24-hour light cycle (14 hours light / 10 hours dark) using three 60W bulbs on a timer. Flies were introduced to the cages at least four days prior to collections and fertility counts. These animals were initially grown in bottles at the same controlled environment described above. Each population cage was established from four trays with 35 bottles per tray containing newly eclosed adult flies. Each 250ml (pint) bottle contained approximately 40ml standard Drosophila medium in use at Bloomington (http://flystocks.bio.indiana.edu/Fly_Work/media-recipes/media-recipes.htm). The isogenic Drosophila mutant strain was propagated in bottles (A) starting with approximately 40-50 adults per bottle on day zero. New bottles (B) were generated from these bottles (A) on day 14. Cages were established by clearing the ?A? bottles into an empty bottle (without food) and transferring the newly eclosed adult flies in the ?A? bottles into the two population cages on day 18. The next round of cages and bottles (C) were established from the ?B? bottles in the same manner. Two-hour embryo collections were made during the light cycles following at least one two-hour pre-lay.
Protocol for collecting pre-pupal, pupal and pharate adult stages from the sequenced D. melanogaster isogenic strain with the mutations; yellow (y1), cinnabar (cn1), brown (bw1), and speck (sp1) [1].

value: Y cn bw sp

value: WPP + 12 hr


title: Mouse retina_7 days_ rep1


source_name: WPP + 12 hr (Celniker/RNA:332) extraction1_array1 channel_1


source_name: S2-DRSC (Celniker/RNA:483) extraction2_array1 channel_1


source_name: WPP + 12 hr (Celniker/RNA:334) extraction2_array1 channel_1