title: Tumor sample GBM.27, glioblastoma

description: tumor profile

value: glioblastoma


title: Hypothalamus-Long-Evans-CornOil-rep3

status: Public on Nov 24 2009

type: RNA

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

hyb_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada

data_processing: Quantitated array data (CEL files) were loaded into the R statistical environment (v2.9.1) using the Affy package (v1.22.1) of the BioConductor library. Data was investigated for spatial and distributional homogeneity, then pre-processed with the RMA algorithm (Irizarry et al. NAR). We employed an updated and remapped mapping of Probes to Entrez Gene IDs as implemented in the R package rat2302rnentrezgcdf (v12.0.0).

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Rat hypothalamus, Long-Evans strain, Corn Oil treated

growth_protocol: Animals were grown in a 12h/12h light/dark cycle housed in groups of 4 rats in suspended stainless-steel wire-mesh cages with pelleted R36 feed and tap water. The temperature was 21 +/- 1 degree Celcius and the relative humidity 50% +/- 10%.

extract_protocol: Total RNA was extracted using Qiagen RNeasy kits according to the manufacturer’s instructions (Qiagen, Mississauga, Canada). Total RNA yield was quantified by UV spectrophotometry and RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: TCDD treated animals were treated with 100 ug/kg TCDD by oral gavage.

tag: strain

value: Long-Evans

tag: gender

value: male

tag: age

value: 16-22 weeks

tag: tcdd dose

value: 0 ug/kg

tag: vehicle

value: Corn Oil

tag: exposure length

value: 23 hours


title: Hemocytes 2 round amplification, biological rep4

status: Public on Oct 30 2009

city: Manhattan

first: Kristin

last: Michel

state: KS

address: 267 Chalmers Hall

department: Biology

country: USA

institute: Kansas State University

description: gene expression data from circulating hemocytes isolated from Anopheles gambiae female adults 1-2 days after eclosion

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Plasmodium/Anopheles Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: GCOS 1.4

organism: Anopheles gambiae

source_name: Hemocytes isolated from 1000 Anopheles gambiae female adults, G3 strain

label_protocol: Total RNA was biotinylated according to the Eukaryotic Target Labeling protocol (Affymetrix), for specific labeling protocol see Samples section

extract_protocol: Total RNA was cleaned up according to the RNeasy Mini protocol for animal cells (Qiagen), for specific extract protocol see Samples section

treatment_protocol: All tissues were isolated from naïve female mosquitoes 1-2 days after eclosion and stored in their respective solutions at -80ºC. For specific treatment protocol, see Samples section

tag: tissue

value: Circulating hemocytes

tag: treatment protocol

value: Hemocytes were harvested from 500 infected females by proboscis clipping and slight thorax-squeezing with dissection forceps. A hemolymph drop from each mosquito was collected directly into RNeasy’s buffer RLT (Qiagen) and stored at -80ºC

tag: rna extraction method

tag: labeling protocol

value: Two cycle Eukaryotic labeling protocol (affymetrix)

tag: starting amount of total rna

value: 80 ng


title: Tumor sample GBM.13, glioblastoma

status: Public on Nov 01 2009

type: genomic

city: New York

first: Cameron

last: Brennan

state: NY

address: 1275 York Avenue

institute: MSKCC

description: tumor profile

hyb_protocol: Microarray hybridization per manufacturer's instructions

scan_protocol: 2um scanner and Feature Extraction 9.5.3.1 (Agilent)

data_processing: Agilent Feature Extraction Software

molecule: genomic DNA

organism: Homo sapiens

source_name: Tumor specimen, snap frozen, -80c stored

label_protocol: Genomic DNA labeling kit PLUS (Agilent), per manufacturer's instructions

extract_protocol: DNeasy Blood and Tissue Kit (Qiagen), per manufacturer's instructions

treatment_protocol: Tumor samples snap-frozen and banked at -80c

tag: disease state

source_name: Pooled normal genomic DNA, male

value: normal tissue


title: Tumor sample GBM.8, glioblastoma

description: tumor profile


title: Tumor sample GBM.17, glioblastoma

description: tumor profile


title: Hemocytes 2 round amplification, biological rep3

value: RNeasy Mini protocol for animal cells (Qiagen)


title: Tumor sample ODG.22, oligodendroglioma (WHO II)

description: tumor profile

value: oligodendroglioma


title: Tumor sample GBM.10, glioblastoma

description: tumor profile


title: Tumor sample GBM.2, glioblastoma

description: tumor profile


title: Hemocytes 2 round amplification, biological rep1


title: Tumor sample GBM.16, glioblastoma

description: tumor profile


title: Hemocytes 2 round amplification, biological rep2


title: Tumor sample GBM.18, glioblastoma

description: tumor profile


title: Tumor sample GBM.4, glioblastoma

description: tumor profile


title: Tumor sample GBM.1, glioblastoma

description: tumor profile


title: Carcasses 1 round amplification, biological rep3

description: gene expression data from carcasses isolated from Anopheles gambiae female adults 1-2 days after eclosion

source_name: carcasses isolated from 20 Anopheles gambiae female adults, G3 strain

value: Carcass

value: Carcasses (mosquito tissues after hemocyte collection and decapitation) were harvested from 20 females on ice. Heads were collected into 200ul Trizol on ice, flash frozen in liquid nitrogen, and stored at -80ºC

value: Trizol extraction, clean-up with RNeasy Mini protocol (Qiagen)

value: One cycle Eukaryotic labeling protocol (affymetrix)


title: Tumor sample GNT.15, high grade glioneuronal tumor

description: tumor profile

value: high grade glioneuronal tumor


title: Carcasses 1 round amplification, biological rep2


title: Tumor sample GBM.19, glioblastoma

description: tumor profile

value: glioblastoma


title: Tumor sample GBM.5, glioblastoma

description: tumor profile


title: Tumor sample GBM.11, glioblastoma

description: tumor profile


title: Tumor sample GBM.14, glioblastoma

description: tumor profile


title: Tumor sample AO.21, anaplastic oligodendroglioma

description: tumor profile

value: anaplastic oligodendroglioma


title: Tumor sample GBM.20, glioblastoma

description: tumor profile


title: Tumor sample GBM.6, glioblastoma

description: tumor profile


title: Carcasses 1 round amplification, biological rep1


title: Tumor sample GBM.9, glioblastoma

description: tumor profile


title: Carcasses 2 round amplification, biological rep1


title: Carcasses 2 round amplification, biological rep2


title: Carcasses 2 round amplification, biological rep3


title: Heads 2 round amplification, biological rep4

description: gene expression data from heads isolated from Anopheles gambiae female adults 1-2 days after eclosion

value: Head

value: Heads were harvested from 40 females at 4C with dissection scissors. Heads were collected into 200ul Trizol on ice, flash frozen in liquid nitrogen, and stored at -80ºC


title: Carcasses 1 round amplification, biological rep4


title: Heads 2 round amplification, biological rep3

source_name: heads isolated from 40 Anopheles gambiae female adults, G3 strain


title: Hemocytes CTRP-ko-EGFP, biological rep1

description: gene expression data from hemocytes isolated from Anopheles gambiae female adults 24-28h after control treatment

data_processing: Analysis of the microarrays was performed using the GCOS 1.4 (Affymetrix).

label_protocol: Total RNA was biotinylated according to the Two-Cycle Eukaryotic Target Labeling protocol (Affymetrix) using 80 ng of total RNA as a starting amount

extract_protocol: Total RNA was extracted according to the RNeasy Mini protocol for animal cells (Qiagen)

treatment_protocol: Hemocytes were harvested from 500 infected females by proboscis clipping and slight thorax-squeezing with dissection forceps. A hemolymph drop from each mosquito was collected directly into RNeasy’s buffer RLT (Qiagen) and stored at -80ºC

tag: infection status

value: non-infected

tag: mean number of oocysts

tag: oocyst prevalence

tag: cell type

value: hemocyte


title: Hemocytes CTRP-ko-EGFP, biological rep2

source_name: hemocytes isolated from Anopheles gambiae female adults 24-28h after control treatment


title: Tumor sample GBM.7, glioblastoma

description: tumor profile


title: Heads 2 round amplification, biological rep2


title: Hemocytes CTRP-ko-EGFP, biological rep3


title: Carcasses 2 round amplification, biological rep4


title: Hemocytes GFP-CON, biological rep2

description: gene expression data from hemocytes isolated from Anopheles gambiae female adults 24-28h after P. berghei infection

value: P. berghei infection


title: O_LS_Wk4

first: Mayte

last: Suarez-Farinas

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

description: Psoriasis patient

hyb_protocol: 15mg of the biotinylated cRNA was hybridized to Affymetrix Human Genome U133A 2.0 Array (22200 probe sets) (Affymetrix Inc.). The chips were washed and stained with streptavidin-phycoerythin.

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing: GCRMA (using gcrma package from R/Bioconductor)

source_name: Patient  O, lesion, 4 week

label_protocol: For each Affymetrix genechip, 4mg total RNA was reverse-transcribed, amplified, and labeled using BioArray High Yield RNA Transcription Labeling Kit (Enzo Biochem Inc.).

extract_protocol: Cells were lysed in RLT with Beta-2-mercaptoethanol. RNA was extracted using the RNeasy Mini Kit (Qiagen), and DNA was removed with on-column DNAse digestion using RNAse-free DNAse Set (Qiagen). RNA was used for either RT-PCR or gene array.

tag: Patient

value: O

tag: Time

value: 4 weeks

tag: Group

value: non-responder

tag: Condition

value: lesional


title: N_LS_Wk4

description: Psoriasis patient

source_name: Patient  N, lesion, 4 week

value: N

value: responder


title: N_LS_Wk12

description: Psoriasis patient

source_name: Patient  N, lesion, 12 week

value: 12 weeks


title: O_LS_Wk12

description: Psoriasis patient

source_name: Patient  O, lesion, 12 week


title: N_NL_Time0

description: Psoriasis patient

source_name: Patient  N, non-lesion, time: 0

value: non-lesional


title: M_LS_Wk12

description: Psoriasis patient

source_name: Patient  M, lesion, 12 week

value: M


title: O_NL_Time0

description: Psoriasis patient

source_name: Patient  O, non-lesion, time: 0


title: M_LS_Wk4

description: Psoriasis patient

source_name: Patient  M, lesion, 4 week


title: O_LS_Wk2

description: Psoriasis patient

source_name: Patient  O, lesion, 2 week

value: 2 weeks


title: M_LS_Wk1

description: Psoriasis patient

source_name: Patient  M, lesion, 1 week

value: 1 week


title: N_LS_Wk2

description: Psoriasis patient

source_name: Patient  N, lesion, 2 week


title: N_LS_Wk1

description: Psoriasis patient

source_name: Patient  N, lesion, 1 week


title: O_LS_Wk1

description: Psoriasis patient

source_name: Patient  O, lesion, 1 week


title: Hemocytes GFP-CON, biological rep1

source_name: hemocytes isolated from Anopheles gambiae female adults 24-28h after P. berghei infection


title: M_NL_Time0

description: Psoriasis patient

source_name: Patient  M, non-lesion, time: 0


title: L_LS_Wk12

description: Psoriasis patient

source_name: Patient  L, lesion, 12 week

value: L


title: M_LS_Wk2

description: Psoriasis patient

source_name: Patient  M, lesion, 2 week


title: Hemocytes GFP-CON, biological rep3


title: L_LS_Wk1

description: Psoriasis patient

source_name: Patient  L, lesion, 1 week


title: K_NL_Time0

description: Psoriasis patient

source_name: Patient  K, non-lesion, time: 0

value: K


title: K_LS_Wk1

description: Psoriasis patient

source_name: Patient  K, lesion, 1 week


title: L_NL_Time0

description: Psoriasis patient

source_name: Patient  L, non-lesion, time: 0


title: K_LS_Wk12

description: Psoriasis patient

source_name: Patient  K, lesion, 12 week


title: L_LS_Wk2

description: Psoriasis patient

source_name: Patient  L, lesion, 2 week


title: K_LS_Wk2

description: Psoriasis patient

source_name: Patient  K, lesion, 2 week


title: J_LS_Wk12

description: Psoriasis patient

source_name: Patient  J, lesion, 12 week

value: J


title: J_LS_Wk2

description: Psoriasis patient

source_name: Patient  J, lesion, 2 week


title: I_LS_Wk2

description: Psoriasis patient

source_name: Patient  I, lesion, 2 week

value: I


title: I_LS_Wk1

description: Psoriasis patient

source_name: Patient  I, lesion, 1 week


title: J_LS_Wk1

description: Psoriasis patient

source_name: Patient  J, lesion, 1 week


title: I_LS_Wk4

description: Psoriasis patient

source_name: Patient  I, lesion, 4 week


title: J_LS_Wk4

description: Psoriasis patient

source_name: Patient  J, lesion, 4 week


title: H_LS_Wk4

description: Psoriasis patient

source_name: Patient  H, lesion, 4 week

value: H


title: H_LS_Wk12

description: Psoriasis patient

source_name: Patient  H, lesion, 12 week


title: J_NL_Time0

description: Psoriasis patient

source_name: Patient  J, non-lesion, time: 0


title: H_NL_Time0

description: Psoriasis patient

source_name: Patient  H, non-lesion, time: 0


title: I_NL_Time0

description: Psoriasis patient

source_name: Patient  I, non-lesion, time: 0


title: G_LS_Wk4

description: Psoriasis patient

source_name: Patient  G, lesion, 4 week

value: G


title: H_LS_Wk1

description: Psoriasis patient

source_name: Patient  H, lesion, 1 week


title: I_LS_Wk12

description: Psoriasis patient

source_name: Patient  I, lesion, 12 week


title: H_LS_Wk2

description: Psoriasis patient

source_name: Patient  H, lesion, 2 week


title: G_LS_Wk12

description: Psoriasis patient

source_name: Patient  G, lesion, 12 week


title: G_LS_Wk1

description: Psoriasis patient

source_name: Patient  G, lesion, 1 week


title: G_LS_Wk2

description: Psoriasis patient

source_name: Patient  G, lesion, 2 week


title: F_LS_Wk12

description: Psoriasis patient

source_name: Patient  F, lesion, 12 week

value: F


title: F_LS_Wk1

description: Psoriasis patient

source_name: Patient  F, lesion, 1 week


title: G_NL_Time0

description: Psoriasis patient

source_name: Patient  G, non-lesion, time: 0


title: F_LS_Wk4

description: Psoriasis patient

source_name: Patient  F, lesion, 4 week

value: 4 weeks


title: F_NL_Time0

description: Psoriasis patient

source_name: Patient  F, non-lesion, time: 0

value: non-responder


title: E_LS_Wk12

description: Psoriasis patient

source_name: Patient  E, lesion, 12 week

value: E

value: lesional


title: E_LS_Wk4

description: Psoriasis patient

source_name: Patient  E, lesion, 4 week

value: responder


title: E_LS_Wk1

description: Psoriasis patient

source_name: Patient  E, lesion, 1 week


title: E_NL_Time0

description: Psoriasis patient

source_name: Patient  E, non-lesion, time: 0


title: F_LS_Wk2

description: Psoriasis patient

source_name: Patient  F, lesion, 2 week


title: E_LS_Wk2

description: Psoriasis patient

source_name: Patient  E, lesion, 2 week


title: D_LS_Wk4

description: Psoriasis patient

source_name: Patient  D, lesion, 4 week

value: D


title: C_LS_Wk4

description: Psoriasis patient

source_name: Patient  C, lesion, 4 week

value: C


title: D_LS_Wk1

description: Psoriasis patient

source_name: Patient  D, lesion, 1 week


title: C_LS_Wk12

description: Psoriasis patient

source_name: Patient  C, lesion, 12 week

value: 12 weeks


title: D_LS_Wk2

description: Psoriasis patient

source_name: Patient  D, lesion, 2 week

value: 2 weeks


title: D_LS_Wk12

description: Psoriasis patient

source_name: Patient  D, lesion, 12 week


title: C_NL_Time0

description: Psoriasis patient

source_name: Patient  C, non-lesion, time: 0

value: non-lesional


title: B_LS_Wk12

description: Psoriasis patient

source_name: Patient  B, lesion, 12 week

value: B


title: B_LS_Wk4

description: Psoriasis patient

source_name: Patient  B, lesion, 4 week


title: B_LS_Wk2

description: Psoriasis patient

source_name: Patient  B, lesion, 2 week


title: C_LS_Wk1

description: Psoriasis patient

source_name: Patient  C, lesion, 1 week

value: 1 week


title: B_LS_Wk1

description: Psoriasis patient

source_name: Patient  B, lesion, 1 week


title: A_LS_Wk4

description: Psoriasis patient

source_name: Patient  A, lesion, 4 week

value: A


title: B_NL_Time0

description: Psoriasis patient

source_name: Patient  B, non-lesion, time: 0


title: A_LS_Wk12

description: Psoriasis patient

source_name: Patient  A, lesion, 12 week


title: A_NL_Time0

description: Psoriasis patient

source_name: Patient  A, non-lesion, time: 0


title: C_LS_Wk2

description: Psoriasis patient

source_name: Patient  C, lesion, 2 week


title: A_LS_Wk2

description: Psoriasis patient

source_name: Patient  A, lesion, 2 week


title: A_LS_Wk1

description: Psoriasis patient

source_name: Patient  A, lesion, 1 week


title: Murine lung, Apo E (-/-), Diesel Particulate Instillation vs. Control Instillation.Biol. Replicate #3

city: Honolulu

first: John

last: Maresh

state: HI

address: 651 Ilalo

department: Medicine

institute: University of Hawaii

description: The GPR data was analyzed in Acuity. Data was normalized by ratio of medians, and Genepix flags were filtered.

hyb_protocol: The microarrays were hybridized with the Ambion hybridization buffer 16 hours at 50 degrees C. Washing was at room temp: 5 minutes in 2X SSC, 0.1% SDS, then 5 minutes in .1 X SSC, 0.1% SDS, then 5 minutes in .1 X SSC.

scan_protocol: Slides were scanned with Genepix 4000B using standard default settings and autoscan mode

data_processing: The log 2 fold change represents the log 2 of experimental/control ratio of normalized 2 channel feature values (ratio of median normalization determined with the default settings of Acuity).

organism: Mus musculus

source_name: Lungs from ApoE (-/-) mice exposed to diesel particulate intratracheal instillation

label_protocol: RNA was extracted, amplified with the oligodT-T7 amino allyl method (Ambion), Cy-dye labeled with CyDye sulfo NHS dye pack (Amersham).

growth_protocol: In vivo exposure of whole animals.

extract_protocol: Lungs were rapidly frozen after collection. RNA was extracted from homogenized frozen tissues in Trizol pooled from 3 animals. Purification by Qiagen RNeasy columns.

treatment_protocol: RNA from lungs of mice exposed to 100 ug diesel particulate (NIST) suspension by intratracheal instillation under anesthesia, 24 h after exposure. Males. Age 8-12 weeks.

value: lung

tag: gender

value: male

tag: age

value: 8-12 weeks

source_name: Lungs from AooE (-/-)control mice exposed to saline intratracheal instillation

extract_protocol: Trizol and Qiagen columns were used according to each manufacturer's protocols

treatment_protocol: RNA from lungs of control mice exposed to saline, 24 after exposure by intratracheal instillation under anesthesia. Males. Age 8-12 weeks.


title: D_NL_Time0

description: Psoriasis patient

source_name: Patient  D, non-lesion, time: 0


title: Murine lung, Apo E (-/-), Diesel Particulate Instillation vs. Control Instillation, Biol. Replicate #3, dye reversal

source_name: Lungs from ApoE (-/-) mice exposed to control saline intratracheal instillation


title: Murine lung, Diesel Particulate Instillation vs. Control Instillation, biol. replicate #2, dye reversal

source_name: Lungs from mice exposed to diesel particulate intratracheal instillation

source_name: Lungs from control mice exposed to saline intratracheal instillation


title: Murine lung, Diesel Particulate Instillation vs. Control Instillation, biol. replicate #3


title: Murine lung, Diesel Particulate Instillation vs. Control Instillation, biol. replicate #1


title: Murine lung, Apo E (-/-), Diesel Particulate Instillation vs. Control Instillation, dye reversal


title: Murine lung, Diesel Particulate Instillation vs. Control Instillation, biol. replicate #2


title: Ess1 H164R Mutant34-rep5

status: Public on Oct 16 2009

city: Albany

first: Steven

middle: D

last: Hanes

address: 150 New Scotland Ave

department: Developmental Genetics

institute: Wadsworth Center

description: no additional information

hyb_protocol: According to Affymetrix Guidelines

scan_protocol: According to Affymetrix Guidelines

data_processing:
Tiling array software version 1.1 (TAS)
Analysed data provided as signal and p-value .bar files (see supplementary file on Series GSE17638 record).
Comparison of Ess1 H164R mutant vs WT is processed as bar files and can be visualized using IGB

organism: Saccharomyces cerevisiae

source_name: ess1(H164R) ts-mutants after a shift to 34°C for 2 hr

label_protocol: According to Affymetrix Guidelines

growth_protocol: Cells were grown at in YPD at 30c and shifted to 34c for 2 hrs.

extract_protocol: Total RNA was extracted using Epicenter RNA purification kit and Qiagen Rneasy columns

tag: genotype/variation

value: ess1(H164R) ts-mutant


title: Murine lung, Diesel Particulate Instillation vs. Control Instillation, biol. replicate #1, dye reversal

tag: tissue


title: W3031A WT34-rep2

description: no additional information

source_name: wild-type after a shift to 34°C for 2 hr

value: wild-type


title: W3031A WT34-rep1

description: no additional information


title: Ess1 H164R Mutant34-rep4

description: no additional information


title: Murine lung, Apo E (-/-), Diesel Particulate Instillation vs. Control Instillation


title: W3031A WT34-rep3

description: no additional information


title: Ess1 H164R Mutant34-rep3

description: no additional information


title: Murine heart, wild type, Diesel Particulate Instillation vs Control Instillation, biol. replicate #3

description: This is a standard 2 color hybridization to determine transcript-level dysregulation in the heart in response to instillation of diesel engine particulate.

hyb_protocol: Labeled probe plus Cot1, polyA, tRNA combined with 3X SSC plus 25% formamide. 16 hour hybridization with glass coverslips at 42 degrees C. Stringency washing according to manufacturer's protocol.

scan_protocol: Standard scan methodology with Genepix 4000B device(Molecular Devices)

source_name: Heart from mice exposed to diesel particulate instillation

label_protocol: GE Amersham MicroMAX direct labeling kit with incorporation of dUTP-Cy dye into cDNA. Stringency washing according to manufacturer's protocol.

extract_protocol: Hearts were rapidly frozen after collection. RNA was extracted from homogenized frozen hearts in Trizol pooled from 4 animals. Purification by Qiagen RNeasy columns.

treatment_protocol: RNA from hearts of mice exposed to 100 ug diesel particulate (NIST) suspension, 24 after exposure by intratracheal instillation under anesthesia.

value: heart

source_name: Heart from control mice exposed to saline instillation

extract_protocol: Trizol and Qiagen columns were used according to each manufacturer's protocols.

treatment_protocol: RNA from hearts of control mice exposed to saline, 24 after exposure by intratracheal instillation under anesthesia.


title: Murine heart, wild type, Diesel Particulate Instillation vs Control Instillation, biol. replicate #2, dye reversal


title: High succinic acid tolerance E.coli_rep Up

city: Bucheon

first: Pil

last: Kim

state: Gyunggi

address: 43-1 Yokkok2-dong

country: South Korea

institute: Catholic Univ. of Korea

description: replicate Up

hyb_protocol: 1. Dissolve the dried labeled sample in a reasonable volume of hybridization buffer depending on the area to be covered. (Typically, 22X22mm cover-slip requires 25 ㎕ of hybridization buffer. 22X60mm cover-slip requires 60 ㎕). 2. Heat the labeled sample preparation for 5min at 95℃. 3. Spin down for 30 sec. Do not put on ice!!! 4. Place slide in the hybridization chamber. Put 20㎕ of 3XSSC to the chamber at both ends of the slide. 5. Pipette the labeled target onto the slide surface. 6. Carefully place the cover-slip on top of the slide. Try to reduce the formation of air bubbles. 7. Seal the hybridization chamber and incubate in 42℃. Water-bath or hybridization oven for more than 16 hr.

scan_protocol: DNA chips were scanned using an Axon GenePix 4000B Scanner(Axon Instruments, Union City, CA) with the laser set to 532 and 635 nm, the photomultiplier tube (PMT) voltage to 600 and the scan resolution to 10 µm.

data_processing: Scanned images were analyzed with GenePix Pro 3.0 software (Axon Instruments, Union City, CA) to obtain gene expression ratios. Logged gene expression ratios were normalized by LOWESS regression (Yang et al., 2002) using the GeneSpring GX 7.3 software (Agilent Technologies).

organism: Escherichia coli str. K-12 substr. W3110

source_name: E. coli W3110 (control)

label_protocol:
1. To 20-50ug of total RNA (or 2ug poly(A) RNA), add necessary control RNA mixture and 2ul of oligo(dT) primer (0.5ug/ul ). Make the final volume up to 31ul with RNase-free water. For human and mouse RNA samples, 20ug of total RNA is sufficient for hybridization in ASP. For Drosophila RNA sample, 50 ug of total RNA is needed for ASP. For less amount of RNA, hybridization should be performed mannually in a smaller volume of hybridization buffer.
2. Mix well and incubate at 70 C for 10 minutes. Chill on ice for 1 min. Spin briefly.
3. Add followings to the RNA solution:
5X First Strand buffer 10ul
0.1 M DTT 5ul
Rnasin 1ul
50X aminoallyl-dNTP mix 1ul
SuperScript II (200U/ul) 2ul
4. Mix and incubate at 42 °C for 1 hr. Add additional 1ul of superscript II and incubate for another 1 hr.
5. To hydrolyze RNA, add 16.5ul of 1 M NaOH and 16.5ul of 0.5 M EDTA. Mix and incubate at 65 °C for 15 minutes. Add 16.5ul of 1 M HCl to neutralize pH.
6. Clean-up the cDNA reaction with Microcon YM-30 (Cat No. 42409)
7. Dry sample in a speed vac. Add D.W. and 1M sodium carbonate buffer to resuspend cDNA pellet in 9.0ul of 0.1M sodium carbonate buffer
8. Add 2.0ul of the appropriate NHS-ester Cy dye
9. Incubate the reaction for 1 hour in the dark at room temperature.
10. Clean up the coupling reaction with QIAquick PCR purification kit. Repeat the elution step twice with 30ul elution buffer to get 60ul of elution volumn.
11. Calculate the pmole nucleotide, pmole Cy3, Cy5, and nucleotide/dye ratio. (Determine O.D. at 260nm, 550nm, 650nm, and 700nm.)
12. Dry the Cy3 and Cy5 sample in a speed vac. and proceed to hybridization step.

growth_protocol: The medium for continuous culture contained 3 g glucose medium consisted with 0.8 g NH4Cl, 0.5 g NaCl, 7.5 g Na2HPO4•2H2O, 3 g KH2PO4 with separately added trace element of 0.2 g MgSO4•7H2O, 0.1 g CaCl2, 1 mg thiamine per liter.  The fermentor was maintained at 37℃, 350 rpm with air gas flushing and the feeding and outlet pumps were maintained at flow rate of 0.1 h-1.

extract_protocol: Transcriptome of cells was prepared using a RNA extraction kit (RNeasy mini kit;Qiagen, Hilden, Germany)

tag: sample type

value: control

source_name: Adapted E. coli (DST160, tolerant to high succinic acid concentration)

growth_protocol: The medium for continuous culture contained 3 g glucose medium consisted with 0.8 g NH4Cl, 0.5 g NaCl, 7.5 g Na2HPO4•2H2O, 3 g KH2PO4 with separately added trace element of 0.2 g MgSO4•7H2O, 0.1 g CaCl2, 1 mg thiamine per liter and the concentraiton of added succinate gradually was raised from 30 g/L to 160 g/L during 9 months.  The initial pH of the medium was set to be pH 8. The fermentor was maintained at 37℃, 350 rpm with air gas flushing and the feeding and outlet pumps were maintained at flow rate of 0.1 h-1.

value: test


title: High succinic acid tolerance E.coli_rep Dn

description: replicate Dn


title: Murine heart, wild type, Diesel Particulate Instillation vs Control Instillation, biol. replicate #2


title: Murine heart, Apo E (-/-), Diesel Particulate Instillation vs Control Instillation, biol. replicate #1


title: Ess1 H164R Mutant34-rep1

description: no additional information


title: Murine heart, wild type, Diesel Particulate Instillation vs Control Instillation, biol. replicate #1


title: Murine heart, wild type, Diesel Particulate Instillation vs Control Instillation, biol. replicate #1, dye reversal


title: Murine heart, Apo E (-/-), Diesel Particulate Instillation vs Control Instillation, biol. replicate #1, dye reversal


title: Murine lung, Diesel Particulate Instillation vs. Control Instillation, biol. replicate #3, dye reversal


title: Murine lung, Apo E (-/-), Diesel Particulate Instillation vs. Control Instillation, Biol. Replicate #2, dye reversal


title: Murine heart, wild type, Diesel Particulate Instillation vs Control Instillation, biol. replicate #3, dye reversal


title: Ess1 H164R Mutant34-rep2

description: no additional information


title: Ess1 deletion 0 hormone induced replicate 2

description: no additional information

hyb_protocol: According to standard Affymetrix protocol.

data_processing: The Normalization alogrithm for the microarray data is MAS5.0.

extract_protocol: Total RNA is isolated using Epicenter RNA purification kit and further cleaned and concentrated using Qiagen RNAeasy columns

value: ESS1 deletion mutant carrying ess1(H164R) on a centromeric plasmid


title: Murine lung, Apo E (-/-) Diesel Particulate Instillation vs. Control Instillation, biol. replicate #2


title: Ess1 deletion 0 hormone induced replicate 1

description: no additional information

scan_protocol: According to standard Affymetrix protocol.


title: Ess1 H164R mutant replicate 1 after 2hr at 34 C

description: no additional information

source_name: Ess1 H164 replicate 1 at 34C

label_protocol: According to standard Affymetrix protocol.

value: Ess1 H164 mutant


title: Ess1 H164R mutant replicate 2 after 2hr at 34 C

description: no additional information

source_name: Ess1 H164 replicate 2 at 34C


title: WT 0 hormone induced replicate 1

description: no additional information

source_name: WT 0 hormone induced replicate 1

value: ESS1 deletion mutant carrying wild-type ess1 on a centromeric plasmid


title: PLN24hrno3

status: Public on Oct 15 2009

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: BioArray High Yield RNA transcript labeling T7 kit (Enzo Life Sciences)

scan_protocol: Standard Affymetrix protocol

data_processing: RMA

label: Biotin

source_name: PLN 24 hrs

label_protocol: Standard Affymetrix protocol

extract_protocol: Cells were sorted into Trizol, total RNA was purified according to manufacturer's instructions

treatment_protocol: 4-6 week old female Foxp3-DTR.BDC2.5/NOD transgenic mice were treated with diphtheria toxin and CD3+CD4+CD19-CD8-GFP- T cells were isolated by flow cytometry from pancreas and PLN at 0, 15, and 24 hours after depletion

value: CD4 T cells, pancreas draining lymph node

tag: agent

value: diphtheria toxin

tag: time point

value: 24 hrs

value: female

value: 4-6 weeks

tag: isolation

value: FACS  CD4+CD3+CD19-CD8-GFP-

tag: genotype


title: WT 0 hormone induced replicate 2

description: no additional information

source_name: WT 0 hormone induced replicate 2


title: PLN15hrno4

source_name: PLN 15 hrs

value: 15 hrs


title: WT W3031A replicate 1 after 2hr at 34 C

description: no additional information

source_name: Ess1 WT 34 C rep1


title: PLN24hrno4


title: PLN0hrno3

source_name: PLN 0 hrs

value: 0 hrs


title: PLN15hrno3


title: P0hrno3

source_name: pancreas 0 hrs

value: CD4 T cells, pancreas infiltrating


title: P15hrno4

source_name: pancreas 15 hrs


title: PLN0hrno4


title: P24hrno3

source_name: pancreas 24 hrs


title: P24hrno4


title: P0hrno4


title: P15hrno3


title: WT W3031A replicate 2 after 2hr at 34 C

description: no additional information

source_name: Ess1 WT 34 C rep2


title: Esophageal squamous cell carcinoma sample TE9

status: Public on Oct 04 2009

first: Adam

middle: Joel

last: Bass

address: 44 Binney Street

institute: Dana-Farber Cancer Institute

description: Hybridized to 250K_Sty

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

scan_protocol: Arrays were scanned using the Gene Chip Scanner 3000.

data_processing: DNA from tumor samples were processed and hybridized to Affymetrix StyI 250K SNP arrays using standard protocols.   Normalization of the individual tumor (or tumor cell)'s SNP array data was performed with a newly developed method termed Tangent normalization (full desciption pending in Getz, et al; manuscript in preparation).  For Tangent normalization, SNP array data from as large a pool of non-cancerous normal samples as possible are obtained.  In this analysis, we used data from >1100 normal samples.  The SNP data from these normals are used to generate a  high-dimensional hyperplane that represents all linear combinations of the signal intensities seen in the normal samples; we then project each tumor sample onto this plane to find the 'hypothetical reference' sample that most closely matches that tumor, and use this reference point to infer the copy number.  After the copy-number are inferred from this new technique, we use the GLAD segmentation/smoothing algorithm to further process the data.

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from samples using the Qiagen Puregene kit and quantitated with PicoGreen.

tag: cancer type

value: Esophageal Cancer

tag: cancer sub-type

value: Squamous cell carcinoma

tag: tumor type

value: cell line


title: Esophageal squamous cell carcinoma sample TE4

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample TE15

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample TE6

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample TE5

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample KW16

description: Hybridized to 250K_Sty

value: primary


title: Esophageal squamous cell carcinoma sample KW2

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample KW9

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample TE11

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample KW4

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample TE1

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample TE8

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample KW14

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample KW5

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample KW18

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample TE10

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample KW6

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample T.T

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample KW8

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample KW7

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample KW15

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample KW3

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample KW12

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample KW13

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample KW11

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample KW17

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample KW1

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample HCE7

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample KW10

description: Hybridized to 250K_Sty


title: Tumor sample obtained from Down syndrome ALL case #16

status: Public on Oct 18 2009

city: Memphis

first: Charles

middle: G

last: Mullighan

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

description: Down syndrome ALL case 16

hyb_protocol: Hybridization was carried out in an Agilent oven at 65°C for 40 hours at 20 rpm, followed by standard wash procedures

scan_protocol: Scanned on an Agilent C2565CA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Linear Models for Microarray Analysis was implemented in Bioconductor  was used for background subtraction and LOWESS normalization.

source_name: DNA extracted from ficoll enriched, cryopreserved leukemic cells obtained at diagnosis (tumor sample)

label_protocol: genomic DNA was labeled using the Agilent’s ULS Labeling kit

growth_protocol:
Ficoll enriched, cryopreserved cells were obtained at time of diagnosis of acute lymphoblastic leukemia, and at the time of remission
Samples were over 90% tumor cells (blasts) for the tumor samples, and <1% tumor cells for the remission samples

extract_protocol: Ultra high molecular weight DNA was extracted by column based methods (DNA blood mini kit, Qiagen, Valencia, CA) or phenol-chloroform extraction

tag: sample

value: Diagnostic leukemia

tag: cell type

value: lymphocyte

source_name: DNA extracted from leukocytes obtained at remission from leukemia (normal tissue)

value: Remission leukemia


title: Tumor sample obtained from Down syndrome ALL case #20

description: Down syndrome ALL case 20


title: Esophageal squamous cell carcinoma sample 1777P

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample 1761P

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample 1813P

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample 1819P

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample 1817P

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample 1735P

description: Hybridized to 250K_Sty


title: Lung squamous cell carcinoma sample 2032

description: Hybridized to 250K_Sty

value: Non-small cell lung cancer


title: Lung squamous cell carcinoma sample 1816

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample 1759P

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample 1747P

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample 1749P

description: Hybridized to 250K_Sty


title: Lung squamous cell carcinoma sample 3253

description: Hybridized to 250K_Sty


title: Lung squamous cell carcinoma sample 2727

description: Hybridized to 250K_Sty


title: Lung squamous cell carcinoma sample 2631

description: Hybridized to 250K_Sty


title: Lung squamous cell carcinoma sample 1353

description: Hybridized to 250K_Sty


title: Lung squamous cell carcinoma sample 2345

description: Hybridized to 250K_Sty


title: Lung squamous cell carcinoma sample 3121

description: Hybridized to 250K_Sty


title: Lung squamous cell carcinoma sample 2225

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample 1737P

description: Hybridized to 250K_Sty


title: Lung squamous cell carcinoma sample 3312

description: Hybridized to 250K_Sty


title: Lung squamous cell carcinoma sample 3289

description: Hybridized to 250K_Sty


title: Lung squamous cell carcinoma sample 1707

description: Hybridized to 250K_Sty


title: Lung squamous cell carcinoma sample 3076

description: Hybridized to 250K_Sty


title: Lung squamous cell carcinoma sample 1330

description: Hybridized to 250K_Sty


title: Lung squamous cell carcinoma sample 1673

description: Hybridized to 250K_Sty


title: Lung squamous cell carcinoma sample 2132

description: Hybridized to 250K_Sty


title: Lung squamous cell carcinoma sample 8T

description: Hybridized to 250K_Sty

source_name: Lung squamous cell carcinoma sample 8T


title: Lung squamous cell carcinoma sample 72T

description: Hybridized to 250K_Sty

source_name: Lung squamous cell carcinoma sample 72T


title: Lung squamous cell carcinoma sample 2536

description: Hybridized to 250K_Sty


title: Lung squamous cell carcinoma sample 69T

description: Hybridized to 250K_Sty

source_name: Lung squamous cell carcinoma sample 69T


title: Lung squamous cell carcinoma sample 57T

description: Hybridized to 250K_Sty

source_name: Lung squamous cell carcinoma sample 57T


title: Lung squamous cell carcinoma sample 60T

description: Hybridized to 250K_Sty

source_name: Lung squamous cell carcinoma sample 60T


title: Lung squamous cell carcinoma sample 1669

description: Hybridized to 250K_Sty


title: Lung squamous cell carcinoma sample 2523

description: Hybridized to 250K_Sty


title: Lung squamous cell carcinoma sample 2808

description: Hybridized to 250K_Sty


title: Esophageal squamous cell carcinoma sample 1739P

description: Hybridized to 250K_Sty


title: Lung squamous cell carcinoma sample 71T

description: Hybridized to 250K_Sty

source_name: Lung squamous cell carcinoma sample 71T


title: Lung squamous cell carcinoma sample 40T

description: Hybridized to 250K_Sty

source_name: Lung squamous cell carcinoma sample 40T


title: Lung squamous cell carcinoma sample 38T

description: Hybridized to 250K_Sty

source_name: Lung squamous cell carcinoma sample 38T


title: Lung squamous cell carcinoma sample 3T

description: Hybridized to 250K_Sty

source_name: Lung squamous cell carcinoma sample 3T


title: Lung squamous cell carcinoma sample 47T

description: Hybridized to 250K_Sty

source_name: Lung squamous cell carcinoma sample 47T


title: Lung squamous cell carcinoma sample 33T

description: Hybridized to 250K_Sty

source_name: Lung squamous cell carcinoma sample 33T


title: Lung squamous cell carcinoma sample 51T

description: Hybridized to 250K_Sty

source_name: Lung squamous cell carcinoma sample 51T


title: Lung squamous cell carcinoma sample 43T

description: Hybridized to 250K_Sty

source_name: Lung squamous cell carcinoma sample 43T


title: Lung squamous cell carcinoma sample 32T

description: Hybridized to 250K_Sty

source_name: Lung squamous cell carcinoma sample 32T


title: Lung squamous cell carcinoma sample 2T

description: Hybridized to 250K_Sty

source_name: Lung squamous cell carcinoma sample 2T


title: Lung squamous cell carcinoma sample 21T

description: Hybridized to 250K_Sty

source_name: Lung squamous cell carcinoma sample 21T


title: Lung squamous cell carcinoma sample 24T

description: Hybridized to 250K_Sty

source_name: Lung squamous cell carcinoma sample 24T


title: Family 8 #2 affected

city: Durham

first: Michael

middle: J

last: Kelley

state: NC

address: 508 Fulton St. (111G)

institute: Duke University

description: affected

hyb_protocol: The labeled genomic DNA was hybridized by NimbleGen using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned by NimbleGen per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html)

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan aCGH data extraction

source_name: Family 8 #2

label_protocol: genomic DNA was directly labeled by NimbleGen per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html)

extract_protocol: genomic DNA isolated from whole blood using standard protocols

tag: disease state

value: affected

source_name: NimbleGen Reference DNA

extract_protocol: NimbleGen Reference DNA

value: reference


title: Family 8 #1 affected

description: affected

source_name: Family 8 #1


title: Family 6 #1 affected

description: affected

source_name: Family 6 #1


title: Lung squamous cell carcinoma sample 19T

description: Hybridized to 250K_Sty

source_name: Lung squamous cell carcinoma sample 19T


title: Family 7 #1 affected

description: affected

source_name: Family 7 #1


title: Family 4 #1 affected

description: affected

source_name: Family 4 #1


title: Lung squamous cell carcinoma sample 23T

description: Hybridized to 250K_Sty

source_name: Lung squamous cell carcinoma sample 23T


title: Lung squamous cell carcinoma sample 30T

description: Hybridized to 250K_Sty

source_name: Lung squamous cell carcinoma sample 30T


title: Family 3 #3 affected

description: affected

source_name: Family 3 #3


title: Lung squamous cell carcinoma sample 54T

description: Hybridized to 250K_Sty

source_name: Lung squamous cell carcinoma sample 54T


title: Family 4 #3 affected

description: affected

source_name: Family 4 #3


title: Wild-type

status: Public on Oct 02 2009

city: Worcester

first: Julie

middle: M.

last: Claycomb

address: 373 Plantation Street Biotech2 Suite 219

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

hyb_protocol: Hybridization to the arrays was made using standard Affymetrix protocols and reagents

scan_protocol: Scanning was done with GeneChip Scanner 3000 7G at the University Massachusetts Medical School’s Genomics Core Facility

data_processing:
Signal values for each array probe were calculated using Affymetrix Tiling Analysis Software 1.1.2 (bandwidth: 30; intensities: PM/MM) with three csr-1(tm892) replicates as the experimental datasets and three wild type replicates as the controls.  Probe overlap with annotations was assessed using the Affymerix-provided ce4 coordinate, which indicates the genomic position matching the center of the array probe. Only genes with signal for at least 10 different probes in either the wild type or csr-1(tm892) samples were included for analysis.
Affymetrix probe coordinates (release WS170) were converted to release WS192 coordinates using a Perl script. Gene expression values were defined as the geometric mean of all probe signals within a gene that had a P-value of <0.1. Actin was used to normalize expression values prior to comparison.

organism: Caenorhabditis elegans

source_name: total RNA from wild type animals

label_protocol: Reverse transcritption was performed on 7µg of each sample using the GeneChip WT Double-Stranded cDNA Synthesis Kit.  The dsDNA was then purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified.  7.5µg of each dsDNA sample were used for the subsequent fragmentation and labeling reactions, using the GeneChip WT Double Stranded DNA Terminal Labeling Kit (Affymetrix).

growth_protocol: Synchronous populations of wild type and csr-1(tm892) animals were grown for 54 hours post-hatching at 20 C on OP50 E. coli at a density of approximately 50000 animals per 15cm Petri dish.

extract_protocol: RNA extraction was performed using TRI-Reagent (MRC Laboratories).  Instead of pelleting and resuspending the RNA (as described in the TRI Reagent protocol), RNA was recovered, washed and eluted using the RiboPure total RNA isolation kit (Ambion).

tag: strain


title: Lung squamous cell carcinoma sample 15T

description: Hybridized to 250K_Sty

source_name: Lung squamous cell carcinoma sample 15T


title: Family 1 #21 affected

description: affected

source_name: Family 1 #21


title: CSR-1 (tm892)

source_name: total RNA from csr-1tm892 mutant animals

value: csr-1(tm892) mutant strain


title: Family 6 #7 unaffected

description: unaffected

source_name: Family 6 #7

value: unaffected


title: drh-3 tiling array

status: Public on Oct 01 2009

first: Craig

last: Mello

address: 368 Plantatoin Street, Suite AS5-2047

data_processing:
Probe signals were calculated using Affymetrix Tiling Analysis Software 1.1.2 (bandwidth: 30; intensities: PM/MM) with three replicates each drh-3(ne4253) (experimental) and wild-type (control). Affymetrix probe coordinates (release WS170) were converted to release WS192 coordinates using a Perl script. Gene expression values were defined as the geometric mean of all probe signals within a gene that had a P-value of <0.1 and were present in both datasets. Actin was used to normalize expression values prior to comparison.
_signal.bar files are log10; _pvalue.bar are -10Log10

source_name: Total RNA from drh-3(ne4253)

growth_protocol: Synchronous populations were grown in triplicate on E. coli OP50 at 20°C

tag: developmental stage

value: gravid adult


title: Family 2 #1 affected

description: affected

source_name: Family 2 #1

source_name: NimbleGen Reference DNA


title: N2 tiling array

source_name: Total RNA from N2

value: wild type


title: Lung squamous cell carcinoma sample 59T

description: Hybridized to 250K_Sty

source_name: Lung squamous cell carcinoma sample 59T


title: Family 1 #5 affected

description: affected

source_name: Family 1 #5


title: Family 2 #7 affected

description: affected

source_name: Family 2 #7


title: 15422_Gastrictumors_HF-18850_SPR413_Map100kHind

city: San Diego

first: Zhengyan

last: Kan

state: CA

address: 10770 Science Center Drive

department: Computational Biology, Oncology Research & Development

institute: Pfizer

description: GLAD segmented copy number

hyb_protocol: Affymetrix 100K protocol

scan_protocol: Affymetrix 100K protocol

data_processing: Affymetrix 100K Mapping Array intensity signal CEL files were processed by dChip 2005 (Build date Nov 30, 2005). The dChip-normalized signal intensities were converted to log2 ratios. The log2 ratios were centered to a median of zero and segmented using the GLAD package for the R statistical environment.

source_name: Gastric Cancer

label_protocol: Affymetrix 100K protocol

growth_protocol: Tumor samples were acquired from commercial vendors.

extract_protocol: Qiagen AllPrep extraction kit was used according to the manufacturer's instructions

treatment_protocol: Untreated

tag: disease

value: Gastric Cancer


title: 15420_Gastrictumors_HF-18848_SPR413_Map100kHind

description: GLAD segmented copy number


title: Family 7 #1 affected

description: affected

source_name: Family 7 #1


title: Family 2 #19 spouse

description: spouse

source_name: Family 2 #19


title: Family 1 #1 affected

description: affected

source_name: Family 1 #1


title: Family 4 #3 affected

description: affected

source_name: Family 4 #3


title: 15414_Gastrictumors_HF-17266_SPR413_Map100kHind

description: GLAD segmented copy number


title: Family 1 #18 affected

description: affected

source_name: Family 1 #18


title: Lung squamous cell carcinoma sample 52T

description: Hybridized to 250K_Sty

source_name: Lung squamous cell carcinoma sample 52T


title: 15394_Gastrictumors_HF-17152_SPR413_Map100kHind

description: GLAD segmented copy number


title: cde-1 vs wildtype, aged adults

city: Utrecht

first: Rene

last: Ketting

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

hyb_protocol: Standard Agilent protocol

scan_protocol: Standard Agilent protocol

data_processing: Feature Extraction (FE) 9.5 protocol

source_name: wildtype aged adults

label_protocol: RNA was isolated and reverse transcribed with random primers. Each cDNA sample was split and labeled with both Cy3 and Cy5.

growth_protocol: standard C. elegans culture

extract_protocol: 250 gonads were excised and collected in Trizol LS.

tag: stage

value: aged adult

value: gonad

source_name: cde-1 mutant aged adults


title: Lung squamous cell carcinoma sample 12T

description: Hybridized to 250K_Sty

source_name: Lung squamous cell carcinoma sample 12T


title: Lung squamous cell carcinoma sample 13T

description: Hybridized to 250K_Sty

source_name: Lung squamous cell carcinoma sample 13T


title: 15416_Gastrictumors_HF-17579_SPR413_Map100kHind_2

description: GLAD segmented copy number


title: Family 1 #4 spouse

description: spouse

source_name: Family 1 #4


title: 15408_Gastrictumors_HF-17188_SPR413_Map100kHind

description: GLAD segmented copy number


title: 15285_Gastrictumors_HF-19113_SPR413_Map100kHind

description: GLAD segmented copy number


title: 15279_Gastrictumors_HF-18842_SPR413_Map100kHind

description: GLAD segmented copy number


title: Lung squamous cell carcinoma sample 17T

description: Hybridized to 250K_Sty

source_name: Lung squamous cell carcinoma sample 17T


title: cde-1 vs wildtype, young adults

source_name: wildtype young adults

treatment_protocol: 250 gonads were excised and collected in Trizol LS.

value: adult

source_name: cde-1 mutant young adults


title: 15281_Gastrictumors_HF-19107_SPR413_Map100kHind

description: GLAD segmented copy number


title: 15267_Gastrictumors_HF-17566_SPR413_Map100kHind

description: GLAD segmented copy number


title: wildtype vs cde-1, young adults

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential


title: wildtype vs cde-1, aged adults


title: 15263_Gastrictumors_HF-17699_SPR413_Map100kHind

description: GLAD segmented copy number


title: 14847_ColonTumors_HF-18570_SPR404_Map100kHind

description: GLAD segmented copy number

source_name: Colorectal Cancer

value: Colorectal Cancer


title: 14815_ColonTumors_HF-18178_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14805_ColonTumors_HF-18148_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14865_ColonTumors_HF-18604_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14819_ColonTumors_HF-18434_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14853_ColonTumors_HF-18578_SPR404_Map100kHind

description: GLAD segmented copy number


title: 15261_Gastrictumors_HF-17546_SPR413_Map100kHind

description: GLAD segmented copy number


title: 15319_SCLCtumors_HF-18407_SPR414_Map100kHind

description: GLAD segmented copy number

source_name: Non-Small Cell Lung Cancer

value: Non-Small Cell Lung Cancer


title: 14811_ColonTumors_HF-18170_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14837_ColonTumors_HF-18520_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14841_ColonTumors_HF-18534_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14821_ColonTumors_HF-18438_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14835_ColonTumors_HF-18512_SPR404_Map100kHind

description: GLAD segmented copy number


title: 15402_Gastrictumors_HF-17552_SPR413_Map100kHind

description: GLAD segmented copy number

source_name: Gastric Cancer


title: 14843_ColonTumors_HF-18550_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14831_ColonTumors_HF-18478_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14859_ColonTumors_HF-18596_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14807_ColonTumors_HF-18152_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14809_ColonTumors_HF-18158_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14849_ColonTumors_HF-18572_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14813_ColonTumors_HF-18172_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14817_ColonTumors_HF-18190_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14829_ColonTumors_HF-18470_SPR404_Map100kHind

description: GLAD segmented copy number


title: 15291_Gastrictumors_HF-20023_SPR413_Map100kHind

description: GLAD segmented copy number


title: 15303_SCLCtumors_HF-16076_SPR414_Map100kHind

description: GLAD segmented copy number


title: 14803_ColonTumors_HF-18146_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14799_ColonTumors_HF-18138_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14777_ColonTumors_HF-18036_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14801_ColonTumors_HF-18140_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14797_ColonTumors_HF-18118_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14789_ColonTumors_HF-18074_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14791_ColonTumors_HF-18078_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14757_ColonTumors_HF-18263_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14765_ColonTumors_HF-18428_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14785_ColonTumors_HF-18040_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14793_ColonTumors_HF-18084_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14761_ColonTumors_HF-18295_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14773_ColonTumors_HF-18030_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14771_ColonTumors_HF-18026_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14759_ColonTumors_HF-18277_SPR404_Map100kHind

description: GLAD segmented copy number


title: 13869_NSCLC_HF15567_SPR377_Map50KHind

description: GLAD segmented copy number


title: 14158_NSCLC_HF11744_SPR377_Map100kHind

description: GLAD segmented copy number


title: 13817_NSCLC_HF15224_SPR377_Map50KHind

description: GLAD segmented copy number


title: 13891_NSCLC_HF15561_SPR377_Map50KHind

description: GLAD segmented copy number


title: 14775_ColonTumors_HF-18032_SPR404_Map100kHind

description: GLAD segmented copy number


title: 13875_NSCLC_HF15505_SPR377_Map50KHind

description: GLAD segmented copy number


title: 13867_NSCLC_HF15539_SPR377_Map50KHind

description: GLAD segmented copy number


title: 14157_NSCLC_HF11743_SPR377_Map100kHind

description: GLAD segmented copy number


title: 13747_NSCLC_HF11754_SPR377_Map50kHind

description: GLAD segmented copy number


title: 14783_ColonTumors_HF-17998_SPR404_Map100kHind

description: GLAD segmented copy number


title: 13871_NSCLC_HF15570_SPR377_Map50KHind

description: GLAD segmented copy number


title: 13831_NSCLC_HF15355_SPR377_Map50KHind

description: GLAD segmented copy number


title: 13763_NSCLC_HF11730_SPR377_Map50kHind

description: GLAD segmented copy number


title: 13799_NSCLC_HF7980_SPR377_Map50KHind

description: GLAD segmented copy number


title: 13731_NSCLC_HF11765_SPR377_Map50kHind

description: GLAD segmented copy number


title: 13807_NSCLC_HF8025_SPR377_Map50KHind

description: GLAD segmented copy number


title: 14755_ColonTumors_HF-17942_SPR404_Map100kHind

description: GLAD segmented copy number


title: 14749_ColonTumors_HF-17899_SPR404_Map100kHind

description: GLAD segmented copy number


title: 12303_Breasttumors_HF11457_SPR312_Map50kHind

description: GLAD segmented copy number

source_name: Breast Cancer

value: Breast Cancer


title: 12291_Breasttumors_HF11334_SPR312_Map50kHind

description: GLAD segmented copy number


title: 13749_NSCLC_HF11758_SPR377_Map50kHind

description: GLAD segmented copy number


title: 12273_Breasttumors_HF11219_SPR312_Map50kHind

description: GLAD segmented copy number


title: 12295_Breasttumors_HF11356_SPR312_Map50kHind

description: GLAD segmented copy number


title: 13865_NSCLC_HF15535_SPR377_Map50KHind

description: GLAD segmented copy number


title: 13761_NSCLC_HF11785_SPR377_Map50kHind

description: GLAD segmented copy number


title: 12277_Breasttumors_HF11317_SPR312_Map50kHind

description: GLAD segmented copy number


title: 15415_Gastrictumors_HF-17266_SPR413_Map100kXba

description: GLAD segmented copy number


title: 11859_Breasttumors_HF11316_SPR312_Map50kHind

description: GLAD segmented copy number


title: 15403_Gastrictumors_HF-17552_SPR413_Map100kXba

description: GLAD segmented copy number


title: 15409_Gastrictumors_HF-17188_SPR413_Map100kXba

description: GLAD segmented copy number


title: 13769_NSCLC_HF11734_SPR377_Map50kHind

description: GLAD segmented copy number


title: 15264_Gastrictumors_HF-17699_SPR413_Map100kXba

description: GLAD segmented copy number


title: 11849_Breasttumors_HF11221_SPR312_Map50kHind

description: GLAD segmented copy number


title: 15262_Gastrictumors_HF-17546_SPR413_Map100kXba

description: GLAD segmented copy number


title: 15304_SCLCtumors_HF-16076_SPR414_Map100kXba_2

description: GLAD segmented copy number


title: 12279_Breasttumors_HF11322_SPR312_Map50kHind

description: GLAD segmented copy number


title: 15286_Gastrictumors_HF-19113_SPR413_Map100kXba

description: GLAD segmented copy number


title: 15320_SCLCtumors_HF-18407_SPR414_Map100kXba

description: GLAD segmented copy number


title: 15282_Gastrictumors_HF-19107_SPR413_Map100kXba

description: GLAD segmented copy number


title: 15292_Gastrictumors_HF-20023_SPR413_Map100kXba

description: GLAD segmented copy number


title: 14848_ColonTumors_HF-18570_SPR404_Map100kXba

description: GLAD segmented copy number


title: 15421_Gastrictumors_HF-18848_SPR413_Map100kXba

description: GLAD segmented copy number


title: 15423_Gastrictumors_HF-18850_SPR413_Map100kXba

description: GLAD segmented copy number


title: 14860_ColonTumors_HF-18596_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14854_ColonTumors_HF-18578_SPR404_Map100kXba

description: GLAD segmented copy number


title: 15268_Gastrictumors_HF-17566_SPR413_Map100kXba

description: GLAD segmented copy number


title: 15280_Gastrictumors_HF-18842_SPR413_Map100kXba

description: GLAD segmented copy number


title: 15417_Gastrictumors_HF-17579_SPR413_Map100kXba_2

description: GLAD segmented copy number


title: 14850_ColonTumors_HF-18572_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14838_ColonTumors_HF-18520_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14832_ColonTumors_HF-18478_SPR404_Map100kXba

description: GLAD segmented copy number


title: 15395_Gastrictumors_HF-17152_SPR413_Map100kXba

description: GLAD segmented copy number


title: 14830_ColonTumors_HF-18470_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14842_ColonTumors_HF-18534_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14814_ColonTumors_HF-18172_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14836_ColonTumors_HF-18512_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14820_ColonTumors_HF-18434_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14822_ColonTumors_HF-18438_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14812_ColonTumors_HF-18170_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14816_ColonTumors_HF-18178_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14798_ColonTumors_HF-18118_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14808_ColonTumors_HF-18152_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14802_ColonTumors_HF-18140_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14794_ColonTumors_HF-18084_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14806_ColonTumors_HF-18148_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14786_ColonTumors_HF-18040_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14804_ColonTumors_HF-18146_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14810_ColonTumors_HF-18158_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14790_ColonTumors_HF-18074_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14772_ColonTumors_HF-18026_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14776_ColonTumors_HF-18032_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14778_ColonTumors_HF-18036_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14792_ColonTumors_HF-18078_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14800_ColonTumors_HF-18138_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14866_ColonTumors_HF-18604_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14774_ColonTumors_HF-18030_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14766_ColonTumors_HF-18428_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14784_ColonTumors_HF-17998_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14756_ColonTumors_HF-17942_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14762_ColonTumors_HF-18295_SPR404_Map100kXba

description: GLAD segmented copy number


title: 13808_NSCLC_HF8025_SPR377_Map50KXba

description: GLAD segmented copy number


title: 13892_NSCLC_HF15561_SPR377_Map50KXba

description: GLAD segmented copy number


title: 13800_NSCLC_HF7980_SPR377_Map50KXba

description: GLAD segmented copy number


title: 13832_NSCLC_HF15355_SPR377_Map50KXba

description: GLAD segmented copy number


title: 14758_ColonTumors_HF-18263_SPR404_Map100kXba

description: GLAD segmented copy number


title: 14750_ColonTumors_HF-17899_SPR404_Map100kXba

description: GLAD segmented copy number


title: 13876_NSCLC_HF15505_SPR377_Map50KXba

description: GLAD segmented copy number


title: 13868_NSCLC_HF15539_SPR377_Map50KXba

description: GLAD segmented copy number


title: 13770_NSCLC_HF11734_SPR377_Map50kXba

description: GLAD segmented copy number


title: 13872_NSCLC_HF15570_SPR377_Map50KXba

description: GLAD segmented copy number


title: 13776_NSCLC_HF11743_SPR377_Map50kXba

description: GLAD segmented copy number


title: 13870_NSCLC_HF15567_SPR377_Map50KXba

description: GLAD segmented copy number


title: 14760_ColonTumors_HF-18277_SPR404_Map100kXba

description: GLAD segmented copy number


title: 13866_NSCLC_HF15535_SPR377_Map50KXba

description: GLAD segmented copy number


title: 13762_NSCLC_HF11785_SPR377_Map50kXba

description: GLAD segmented copy number


title: 14818_ColonTumors_HF-18190_SPR404_Map100kXba

description: GLAD segmented copy number


title: 13748_NSCLC_HF11754_SPR377_Map50kXba

description: GLAD segmented copy number


title: 13778_NSCLC_HF11744_SPR377_Map50kXba

description: GLAD segmented copy number


title: 12296_Breasttumors_HF11356_SPR312_Map50kXba

description: GLAD segmented copy number


title: 13818_NSCLC_HF15224_SPR377_Map50KXba

description: GLAD segmented copy number


title: 13732_NSCLC_HF11765_SPR377_Map50kXba

description: GLAD segmented copy number


title: 13750_NSCLC_HF11758_SPR377_Map50kXba

description: GLAD segmented copy number


title: 12292_Breasttumors_HF11334_SPR312_Map50kXba

description: GLAD segmented copy number


title: 12278_Breasttumors_HF11317_SPR312_Map50kXba

description: GLAD segmented copy number


title: 13764_NSCLC_HF11730_SPR377_Map50kXba

description: GLAD segmented copy number


title: 11850_Breasttumors_HF11221_SPR312_Map50kXba

description: GLAD segmented copy number


title: 14844_ColonTumors_HF-18550_SPR404_Map100kXba

description: GLAD segmented copy number


title: 12280_Breasttumors_HF11322_SPR312_Map50kXba

description: GLAD segmented copy number


title: 12304_Breasttumors_HF11457_SPR312_Map50kXba

description: GLAD segmented copy number


title: 12274_Breasttumors_HF11219_SPR312_Map50kXba

description: GLAD segmented copy number


title: 11860_Breasttumors_HF11316_SPR312_Map50kXba

description: GLAD segmented copy number


title: Nadine_30min_3_PVYNTN_vs_PVYN

city: Ljubljana

first: Polona

last: Kogovsek

address: Vecna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

description: Biological replicate 3 of 5.

hyb_protocol: cDNA synthesis and hybridization was carried out using 3DNA Array 900 kit (Genisphere)

scan_protocol: Microarrays were scanned using a LS200 scanner (TECAN)

data_processing: The TIFF images were quantified using ArrayPro® Analyzer 4.5 software (Media Cybernetics, USA). Quality control was performed and low quality spots: (i) non-uniform spots (mean (signal) / SD (signal) < 1), (ii) spots with low signal/background ratio (mean (signal) / mean (background) < 1.5) or (iii) spots with low signal to noise ratio (SNR) < 3 were downweighted. Additionally empty or non-validated spots were downweighted (weight flag =0). Data analysis was done in R computing environment (http://www.R-project.org). Background was measured locally. For both channels, signal (trimmed mean of the whole variable spot area) and background (trimmed mean of the spot’s local corners) intensities were calculated. Background was subtracted using the option half. Data was then normalized using loess normalization.

organism: Solanum tuberosum

source_name: cv. Nadine, PVYN - inoculated leaves, 30minpi

growth_protocol: Grown in soil in growth chamber using 16 h period of light (21±2 °C) and 8 h of darkness (18±1 °C), light intensity 70-90 mmol m-2 s-2 , 75±2 % humidity

extract_protocol: Total RNA  was isolated by RNeasy Plant Mini kit (Qiagen), treated with DNAse and purified and concentrated with RNeasy MinElute Cleanup Kit (Qiagen).

treatment_protocol: Carborundum-dusted leaves rubbed with sap of PVYNTN and PVYN virus isolate infected plant. Samples (pooled inoculated leaves) collected 30 min, 12 and 48 hours post inoculation

tag: cultivar

value: Nadine

tag: treatment

value: mild virus isolate

tag: time

value: 30min after inoculation

value: pooled leaf material from 6-8 plants, 3-4 leaves per plant

source_name: cv. Nadine, PVYNTN - inoculated leaves, 30minpi

value: aggresive virus isolate


title: Igor_30min_3_PVYNTN_vs_PVYN

description: Biological replicate 3 of 5.

source_name: cv. Igor, PVYN - inoculated leaves, 30minpi

label_protocol: cDNA synthesis and hybridization was carried out using 3DNA Array 900 kit (Genisphere)

value: Igor

tag: tissue

source_name: cv. Igor, PVYNTN - inoculated leaves, 30minpi


title: Igor_48h_4_PVYNTN_vs_PVYN

description: Biological replicate 4 of 5.

source_name: cv. Igor, PVYNTN - inoculated leaves, 48hpi

value: 48h after inoculation

source_name: cv. Igor, PVYN - inoculated leaves, 48hpi


title: Igor_12h_3_PVYNTN_vs_PVYN

description: Biological replicate 3 of 5.

source_name: cv. Igor, PVYN - inoculated leaves, 12hpi

value: 12h after inoculation

source_name: cv. Igor, PVYNTN - inoculated leaves, 12hpi


title: Nadine_48h_3_PVYNTN_vs_PVYN

description: Biological replicate 3 of 5.

source_name: cv. Nadine, PVYN - inoculated leaves, 48hpi

source_name: cv. Nadine, PVYNTN - inoculated leaves, 48hpi


title: Igor_12h_4_PVYNTN_vs_PVYN

description: Biological replicate 4 of 5.


title: Nadine_12h_3_PVYNTN_vs_PVYN

description: Biological replicate 3 of 5.

source_name: cv. Nadine, PVYNTN - inoculated leaves, 12hpi

source_name: cv. Nadine, PVYN - inoculated leaves, 12hpi


title: Igor_30min_4_PVYNTN_vs_PVYN

description: Biological replicate 4 of 5.


title: Aorta, Ang II 28d, #5

city: Stanford

first: Joshua

last: Spin

address: 300 Pasteur Drive

institute: Stanford University

description: no additional information

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples in equimolar concentrations were applied to microarrays, enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version A.9.5.3.1).

data_processing:
Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization.
The Sample data tables report Log base2 (rprocessedsignal/gprocessedsignal) - while raw data files report Log base10 Ratios.
Note: all data included, no missing values imputation performed. Controls spots removed.
Refer to raw data files for additional annotation of matrix table rows.

source_name: suprarenal aorta, aneurysm, Ang II treated 28d

label_protocol: Five hundred nanograms of extracted total RNA were labeled using Cyanine-5-CTP in a T-7 transcription reaction via Agilent's Low Input Linear RNA Amplification/Labeling System per manufacturer's protocol.

extract_protocol: Flash-frozen suprarenal aortic tissue was homogenized for RNA extraction, and isolated using the RNeasy Fibrous Tissue Mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol:
Alzet osmotic minipumps were subcutaneously implanted into apoE-/- mice at 12-14 weeks of age anesthetized with isoflurane. Pumps contained either angiotensin II solution delivering a concentration of 1000 ng/kg/min, or saline vehicle. Mice were treated for 7 days, 14 days or 28 days.
At the end of the treatment period, anesthetized mice (isoflurane) were sacrificed and exsanguinated by perfusion with saline at a pressure of approximately 100 mm Hg.  Aortic samples consisting of the entire suprarenal aorta were surgically isolated and immediately flash-frozen in liquid nitrogen.

tag: sample type

value: test

tag: gender

value: male

value: ApoE-/-

value: suprarenal aorta, aneurysm

tag: agent

value: Ang II

source_name: Stratagene Universal Mouse Reference

label_protocol: For ch 2., 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label.

treatment_protocol: not applicable

value: reference


title: Aorta, Ang II 28d, #3

description: no additional information


title: Aorta, Ang II 28d, #4

description: no additional information


title: Aorta, Ang II 28d, #1

description: no additional information


title: Aorta, Ang II 28d, #2

description: no additional information


title: Aorta, Ang II 28d, #6

description: no additional information


title: Aorta, Ang II 14d, #5

description: no additional information

source_name: suprarenal aorta, aneurysm, Ang II treated 14d


title: Aorta, Ang II 14d, #2

description: no additional information


title: Aorta, Ang II 14d, #3

description: no additional information


title: Aorta, Ang II 14d, #1

description: no additional information


title: Dissected aneurysm, Ang II 7d #3

description: no additional information

source_name: suprarenal aorta, dissected aneurysm, Ang II treated 7d

value: suprarenal aorta, dissected aneurysm


title: Aorta, Ang II 7d, #4

description: no additional information

source_name: suprarenal aorta, non-dissected aneurysm, Ang II treated 7d


title: Aorta, Ang II 14d, #4

description: no additional information


title: Dissected aneurysm, Ang II 7d #1

description: no additional information


title: Dissected aneurysm, Ang II 7d #2

description: no additional information


title: Aorta, Ang II 7d, #2

description: no additional information

value: suprarenal aorta, non-dissected aneurysm


title: Aorta, Ang II 7d, #1

description: no additional information


title: Aorta, saline 28d, #5

description: no additional information

source_name: suprarenal aorta, control, saline treated 28d

value: suprarenal aorta

value: control (saline)


title: Aorta, saline 28d, #3

description: no additional information


title: Aorta, saline 28d, #1

description: no additional information


title: Aorta, saline 14d, #5

description: no additional information

source_name: suprarenal aorta, control, saline treated 14d


title: Aorta, saline 28d, #2

description: no additional information


title: Aorta, saline 14d, #2

description: no additional information


title: Aorta, saline 28d, #4

description: no additional information


title: Aorta, Ang II 7d, #3

description: no additional information


title: Aorta, saline 14d, #3

description: no additional information


title: Aorta, saline 7d, #5

description: no additional information

source_name: suprarenal aorta, control, saline treated 7d


title: Aorta, saline 7d, #4

description: no additional information


title: Aorta, saline 7d, #6

description: no additional information


title: Aorta, saline 7d, #3

description: no additional information


title: Aorta, saline 14d, #1

description: no additional information


title: Aorta, saline 14d, #6

description: no additional information


title: Aorta, saline 14d, #4

description: no additional information


title: Aorta, saline 7d, #1

description: no additional information


title: Aorta, saline 7d, #2

description: no additional information


title: estrogen treated endometrium at day 15, biological rep2

city: new haven

first: morgan

middle: dean

last: ashworth

state: CT

address: 333 cedar street

department: OB/GYN reproductive immunology

institute: yale school of medicine

description: Gene expression from endometrium

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

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

data_processing: [1] dChip’s method of invariant set normalization in which the chip with the median intensity value was used as the baseline against which the brightnesses of the remaining chips were adjusted in order to be of a comparable level.  [2] Standardization was conducted by calculating model-based expression indices (MBEI) using dChip’s Perfect-Match (PM)-only model.  This additional modeling reduces the variance of expression level estimates by accounting for probe differences.  [3] Data were log transformed to improve statistical performance by approximating a normal distribution within each gene.  The log base2 scale is favorable because each unit difference represents a 2-fold difference.

organism: Sus scrofa

source_name: estrogen treated endometrium at day 15, collected on day 15 of psuedo pregnancy

label_protocol: cRNA were prepared by the GeneChip One-Cycle target labeling kit according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Gilts were group housed.  Estrus detection was conducted twice daily.  Gilts were treated with estrogen or corn oil at the onset of their second estrus following a normal estrous cycle, and again 24 hours later.

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

treatment_protocol: Endometrium was collected on either days 13 or 15 of pseudo pregnancy following a flushing of the uteri with 20 mL of physiological saline.  Endometrium was placed into a wirl pouch, snap-frozen in liquid nitrogen and then placed in the -80C until utilized.

value: Endometrium

tag: age

value: 8-10 months

tag: genotype

value: cross bred cyclic gilts

tag: time of pseudo-pregnancy

value: 15 days


title: estrogen treated endometrium at day 15, biological rep1

description: Gene expression from endometrium


title: Non estrogen treated endometrium at day 15, biological rep 2

description: Gene expression from endometrium

source_name: Non estrogen treated endometrium at day 15, collected on day 15 of psuedo pregnancy


title: estrogen treated endometrium at day 15, biological rep3

description: Gene expression from endometrium


title: estrogen treated endometrium at day 13, biological rep4

description: Gene expression from endometrium

source_name: estrogen treated endometrium at day 13, collected on day 13 of psuedo pregnancy

value: 13 days


title: estrogen treated endometrium at day 13, biological rep3

description: Gene expression from endometrium


title: estrogen treated endometrium at day 13, biological rep2

description: Gene expression from endometrium


title: Non estrogen treated endometrium at day 13, biological rep3

description: Gene expression from endometrium

source_name: Non estrogen treated endometrium at day 13, collected on day 13 of psuedo pregnancy


title: Non estrogen treated endometrium at day 15, biological rep 3

description: Gene expression from endometrium


title: Non estrogen treated endometrium at day 15, biological rep 1

description: Gene expression from endometrium


title: estrogen treated endometrium at day 13, biological rep1

description: Gene expression from endometrium


title: Non estrogen treated endometrium at day 13, biological rep4

description: Gene expression from endometrium


title: Non estrogen treated endometrium at day 13, biological rep1

description: Gene expression from endometrium


title: Non estrogen treated endometrium at day 13, biological rep2

description: Gene expression from endometrium


title: SN1091687

city: los angeles

first: Brian

last: O'Connor

address: 2018 Griffith Park Blvd

institute: UCLA

description: Group 4

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data was normalized using the justRMA algorithm from the Bioconductor group following the methods of the Celsius project.

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

extract_protocol: Total RNA was isolated by Trizol extraction and was furher purified by Qiagen Rneasy spin columns following the manufacturer's specifications


title: SN1091688

description: Group 4


title: SN1091694

description: Group 3


title: SN1091692

description: Group 4


title: SN1091691

description: Group 4


title: SN1091686

description: Group 4


title: SN1091689

description: Group 4


title: SN1091690

description: Group 4


title: SN1087697

description: Group 4


title: SN1091693

description: Group 4


title: SN1085853

description: Group 3


title: SN1091695

description: Group 3


title: SN1085854

description: Group 3


title: SN1085870

description: Group 4


title: phospho-mimic, biological rep2

city: Dallas

first: Zain

last: Paroo

state: TX

address: 5323 Harry Hines Blvd

department: Biochemistry

institute: UT Southwestern Medical Center

description: miRNA expression from Flp-In 293 cells stably expressing phopsho-mimic TRBP

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate.  The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 ?L 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression)

source_name: 293 phospho-mimic

label_protocol: Microarray assay was performed using a service provider (LC Sciences).  The assay started from 4 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.  The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry.  After RNA hybridization, tag-conjugating Cy5 was circulated through the microfluidic chip for dye staining.

growth_protocol: Cells were cultured at 37 degrees Celsius under 5% CO2 in DMEM containing 10% FBS and 4 mM L-glutamine.  Cells were split before reaching 80% confluency.  Total RNA was harvested at ~50% confluency.

treatment_protocol: RNA extraction for miRNA microarray analysis was performed two weeks following establishment of monoclonal, isogenic cell lines.

tag: cell line

value: 293 phospho-mimic


title: phospho-mimic, biological rep3


title: SN1091684

description: Group 2


title: SN1085872

description: Group 2


title: SN1085875

description: Group 3


title: Nadine_48h_5_PVYNTN_vs_PVYN

description: Biological replicate 5 of 5.

source_name: cv. Igor, PVYN - inoculated leaves, 30minpi

value: Nadine

value: mild virus isolate

value: 48h after inoculation

value: pooled leaf material from 6-8 plants, 3-4 leaves per plant

source_name: cv. Igor, PVYNTN - inoculated leaves, 30minpi

value: aggresive virus isolate


title: SN1085855

description: Group 3


title: Nadine_12h_5_PVYNTN_vs_PVYN

description: Biological replicate 5 of 5.

value: 12h after inoculation


title: SN1085874

description: Group 3


title: phospho-mimic, biological rep1


title: SN1085871

description: Group 4


title: SN1091685

description: Group 2


title: SN1085873

description: Group 2


title: Nadine_48h_4_PVYNTN_vs_PVYN

description: Biological replicate 4 of 5.


title: Nadine_30min_5_PVYNTN_vs_PVYN

description: Biological replicate 5 of 5.

value: 30min after inoculation


title: SN1085877

description: Group 1


title: SN1085857

description: Group 1


title: SN1085876

description: Group 3


title: phospho-mutant, biological rep3

description: miRNA expression from Flp-In 293 cells stably expressing phopsho-mutant TRBP

source_name: 293 phospho-mutant

value: 293 phospho-mutant


title: SN1085878

description: Group 1


title: SN1085856

description: Group 1


title: SN1085879

description: Group 1


title: phospho-mutant, biological rep2


title: Igor_48h_5_PVYNTN_vs_PVYN

description: Biological replicate 5 of 5.

value: Igor


title: Nadine_12h_4_PVYNTN_vs_PVYN

description: Biological replicate 4 of 5.


title: phospho-mutant, biological rep1


title: SN1087698

description: Group 2


title: Nadine_30min_4_PVYNTN_vs_PVYN

description: Biological replicate 4 of 5.


title: Igor_12h_5_PVYNTN_vs_PVYN

description: Biological replicate 5 of 5.


title: Igor_30min_5_PVYNTN_vs_PVYN

description: Biological replicate 5 of 5.


title: cohesin (Mcd1-6HA) distribution in nocodazole-arrested cells

city: Aurora

first: Paul

last: Megee

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado Denver School of Medicine

hyb_protocol: Performed in-house at Nimblegen

scan_protocol: Performed in-house at Nimblegen

data_processing: log2 ratios were calculated by Nimblegen

source_name: PMY515 HA immunoprecipitated DNA

label_protocol: Samples were processed in-house at Nimblegen

growth_protocol: Cells were first staged in the G1 period of the cell cycle with alpha factor. Cells were then washed twice in media containing Pronase (0.1 mg/ml final concentration) to remove alpha factor and then released into fresh media containing 0.1 mg/ml Pronase and 15 ug/ml nocodazole to arrest cells in G2/M. Arrests were scored microscopically and cell morphologies were scored to determine arrests (greater than 90% unbudded plus shmoos or large-budded for the G1 and G2/M arrests, respectively).

extract_protocol: see Dedon et al. 1991 and Braunstein et al. 1993

value: pmy515 [trp1 ade2-1 his3 mcd1-6ha:his5+ ura3 leu2 ∆bar1::LEU2 can1-100 GAL psi+ (W303 background)]

source_name: PMY515 Total Genomic DNA

growth_protocol: as described above


title: GM06690 replicate 2

city: Cambridge

first: Erez

last: Lieberman-Aiden

address: 7 Cambridge Center

institute: Broad Institute

description: mRNA Expression

hyb_protocol: standard Affymetrix protocol

scan_protocol: The washing and staining were performed on the GeneChip® Fluidics Station and the GeneChip® Scanner 3000 was used for scanning.

data_processing: After scanning, the expression value for each gene was calculated using RMA (Robust Multi-Array) normalization. The average intensity difference values were normalized across the sample set. Probe sets that were absent in all samples according to Affymetrix flags were removed. All values lower than 50 were replaced by 50.

label_protocol: All samples were normalized to 125 ng/uL The Affymetrix One-Cycle Target labeling assay (P/N 900687) was used to synthesize hybridization target.  Labeled cRNA hybridization target was produced using a 3-day, semi-automated workflow designed to maximize efficiency and reduce processing times. Samples were hybridized on GeneChip® Human Genome U133 Plus 2.0 arrays (P/N 900467).

growth_protocol: Human cell line GM06990, an EBV-transformed lymphoblastoid cell line (Coriell, Camden, NJ), was cultured in RPMI1640, 15% fetal calf serum, 1% penicillin-streptomycin, and 2mM L-glutamine.

extract_protocol: Total RNA was extracted using QIAzol reagent and following the miRNeasy kit's procedure (Qiagen) and sample quality was controlled on a 2100 Bioanalyzer (Agilent).


title: GM06690 replicate 1

description: mRNA Expression


title: HD-1dim 1

city: Melbourne

first: Holger

last: Schlueter

state: Victoria

address: Locked Bag 1

department: Research

country: Australia

institute: Peter Mac Callum cancer Centre

description: Gene expression data from human FACS seperated subpopulations of dermal cell isolates of neonatal foreskins

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on GeneChip Affymetrix HG-U133 2.0plus expression array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GS300-7G scanner

data_processing: The data were analyzed with Gene Chip Operating Software Version 1.4 using Affymetrix default analysis settings. The CEL files generated was later normalized using the RMA method

source_name: Dermal cell isolate from 4 neonatal foreskin, HD-1dim

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol two-cycles target labeling kit from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Qiagen Rneasy kit protocol

treatment_protocol: Enzyme digested foreskin to isolate dermal cells

value: foreskin

tag: cell type

value: primary dermal cells

tag: facs-sorted cell subpopulation

value: HD-1dim cells

value: neonatal


title: HD-1dim 2


title: HD-1dim 4


title: Igor_48h_3_PVYNTN_vs_PVYN

description: Biological replicate 3 of 5.

source_name: cv. Igor, PVYN - inoculated leaves, 48hpi

source_name: cv. Igor, PVYNTN - inoculated leaves, 48hpi


title: HD-1bri 3

source_name: Dermal cell isolate from 4 neonatal foreskin, HD-1bri

value: HD-1bri cells


title: HD-1dim 3


title: Normal liver N13_E-AFMX-11-448274985

city: Napoli

first: Lucio

last: Nitsch

address: Via Pansini 5

department: Biologia e Patologia Cellulare e Molecolare

country: Italy

institute: Unversity of Naples Federico II

description: Gene expression data from a frozen liver biopsy obtained from a healthy adult subject who suffered sudden death

data_processing: Affymetrix CEL files were imported into GeneSping 7.2 software (Agilent Technologies Inc.) and normalized by RMA algorithm

source_name: Frozen biopsy from normal liver

label_protocol: In vitro transcription was performed to obtain biotin labeled cRNA according to Affymetrix protocols described at http://www.affymetrix.com/support/technical/manuals.affx

extract_protocol: Total RNA was extracted by Trizol

value: normal liver

tag: arrayexpress repository sample id

value: data retrieved from arrayexpress database, E-AFMX-11-448274985

value: Not available

value: male


title: HD-1bri 4

tag: developmental stage


title: HD-1bri 2


title: HD-1bri 1


title: wildtype_1a versus asense_mutant_1a

city: London

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

country: United Kingdom

institute: Imperial College London

description: Material is derived from a population of neuroblast and GMC cells.

hyb_protocol: Hybridisation to amino-modified long oligonucleotide microarrays using a Genomic Solutions hybridisation station with the Biosolutions hybridisation buffer (http://www.flychip.org.uk/protocols/hybridisation/)

scan_protocol: Operating instructions for the Genepix 4000B dual laser scanner (http://www.flychip.org.uk/protocols/imaging/).

data_processing: Spot finding and quantitation via the Dapple package. Normalization was done using variance stabilising normalization (VSN).

organism: Drosophila melanogaster

label_protocol: Klenow Labelling: Random primers are annealed to denatured DNA templates and extended by Klenow fragment using the Bioprime DNA Labeling System (Invitrogen) while fluorescent dyes Cy3-dCTP or Cy5-dCTP (GE Healthcare) are incorporated. (http://www.flychip.org.uk/protocols/gene_expression/)

growth_protocol: Embryos developed at 25oC

extract_protocol: 50-100 cells were lysed, RNA reverse transcribed, cDNA tailed using terminal transferase and amplified using PCR

tag: strain

value: ventral nerve cord

value: embryo stage 11


title: asense_mutant_5b versus wildtype_5b


title: prospero mutant_1 versus common reference

description: Material is derived from a population of neuroblast and GMC cells

extract_protocol: 50-100 cells were lysed, RNA was reverse transcribed, cDNA tailed using terminal transferase and amplified using PCR

source_name: TDSCR

extract_protocol: RNA from ~30 embryos was extracted using Trizol, RNA was reverse transcribed, cDNA tailed using terminal transferase and amplified using PCR

value: whole embryo

value: embryo stage 10-12

value: reference


title: prospero mutant_4 versus common reference


title: HaloCHIP CREB + Forskolin biological rep 2, technical rep 1

city: Madison

first: Danette

last: Hartzell

state: WI

address: 2800 Woods Hollow Road

institute: Promega

description: no additional information

hyb_protocol: Standard Nimblegen protocol

scan_protocol: Standard Nimblegen protocol

data_processing: The raw data from the arrays were analyzed as follows: the log2 ratio (enriched-cy5/total input-cy3) was calculated for each probe and data were then smoothed by averaging across a sliding window of 3 neighbouring probes shifting 1 probe at a time, minimizing noise from single probes. The median and standard deviation were calculated from the smoothed ratios for each sample. The median was subtracted from each ratio and divided by the standard deviation to center and normalize the data from each array.  To summarize the enrichment for an entire promoter, the top 4 probe values were averaged for a given promoter region to approximate the 75th  percentile value.  The raw data, normalized data, and collapsed data for each array are available as supplemental at the following site: www.switchgeargenomics.com/creb_supp_data/.

source_name: Hela Cells transfected with the HaloTag-CREB fusion constructs

label_protocol: Standard Nimblegen protocol

growth_protocol: HeLa cells (2-4 x 105) were plated in a single well of a standard 6-well plate. After reaching 70-80% confluency, typically 18-24 hours later, cells were transfected with the HaloTag-CREB fusion constructs.

extract_protocol: ChIP assays were performed as described in http://www.usbweb.com/proto/78460a.pdf. HaloCHIP experiments were performed as described in  http://www.promega.com/tbs/tm075/tm075.pdf.

treatment_protocol: Cell were treated with 10uM Forskolin at 37C for 45 minutes, then crosslinked with 0.75% formaldehyde for 10min at 22C.

value: HeLa cells

tag: genome/variation

value: HaloTag-CREB fusion construct

source_name: Hela Cells


title: prospero mutant_2 versus common reference


title: asense_mutant_4a versus wildtype_4a


title: asense_mutant_5a versus wildtype_5a


title: wildtype_3a versus asense_mutant_3a


title: ChIP-chip CREB + Forskolin biological rep 2, technical rep 1

description: no additional information

source_name: Hela cell extract immunoprecipitated with anti-CREB1 antibody

growth_protocol: HeLa cells (4 x 106) were plated in several 150mm plates and grown to 80-90% confluency.

treatment_protocol: Cell were treated with 10uM Forskolin at 37C for 45 minutes, then crosslinked with 1% formaldehyde for 10min at 22C.

tag: antibody

value: CREB

source_name: Hela cell extract immunoprecipitated with a control anybody


title: wildtype_1b versus asense_mutant_1b


title: asense_mutant_6a versus wildtype_6a


title: prospero mutant_3 versus common reference


title: HaloCHIP CREB + Forskolin biological rep 1, technical rep 1

description: no additional information

growth_protocol: HeLa cells (2-4 x 105) were plated in a single well of a standard 6-well plate.


title: asense_mutant_4b versus wildtype_4b


title: wildtype_6 versus common reference


title: prospero mutant_5 versus common reference


title: prospero mutant_6 versus common reference


title: wildtype_5 versus common reference


title: HaloCHIP CREB + Forskolin biological rep 3, technical rep 1

description: no additional information


title: wildtype_4 versus common reference


title: wildtype_2 versus common reference


title: HaloCHIP CREB + Forskolin biological rep 1, technical rep 2

description: no additional information


title: ChIP-chip CREB + Forskolin biological rep 1, technical rep 1

description: no additional information


title: HaloCHIP CREB (no Forskolin) biological rep 2

description: no additional information

treatment_protocol: Cells were crosslinked with 0.75% formaldehyde for 10min at 22C.


title: HaloCHIP CREB (no Forskolin) biological rep 3

description: no additional information


status: Public on Sep 30 2009

city: Rockville

first: Maryanne

last: Vahey

state: MD

address: 1600 East Gude Drive

institute: Walter Reed Army Institute of Research

description: Gene expression data from a volunteer V56 ;it belongs to InfectivityControl group

hyb_protocol: Follow Affymetrix's protocol

scan_protocol: GeneChips were scanned using the GeneArray Scanner

data_processing: CEL files were normalized using RMA method. This dataset was further normalized with a dataset from Plus2.0 Genechip using quantiles normalization method available in the affy package of bioconductor. Probesets that are absent in all samples are eliminated in the later stage of analysis

source_name: A PBMC sample from volunteer V56, challenged without vaccine

treatment_protocol: PBMC samples are collected at various time points during a malaria vaccine trial

tag: group

value: InfectivityControl

value: PBMC