title: tel1mec1.MMS vs. tel1mec1.UT, rep2

status: Public on Mar 31 2013

city: La Jolla

first: Eric

last: Jaehnig

address: 9500 Gilman Dr

department: Laboratory of Cancer Genetics

institute: Ludwig Institute for Cancer Research

description: US22502657_251507211012_S01_H_flip_3-4.avg

hyb_protocol: According to the protocol recommended by Agilent.

scan_protocol: GenePix 4000A Scanner, Quantitation w/ GenePix 6.0.

data_processing: Lowess normalized, quantile normalized, LIMMA model.

organism: Saccharomyces cerevisiae

source_name: tel1mec1, untreated

label_protocol: As described in Kuo D, Tan K, Zinman G, Ravasi T, Bar-Joseph Z, Ideker T (2010) Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. Genome Biol 11: R77 (PMID 20653936).

growth_protocol: For these experiments, 100 ml cultures for each strain were grown to an OD600 density of 0.8-1.0 at 30oC, split into two 50 ml cultures, and incubated for one additional hour either in the presence (MMS-treated) or absence (untreated) of 0.03% MMS (methyl methanesulfonate; Sigma 129925).

extract_protocol: RNA was isolated by hot phenol/chloroform extraction and enriched for mRNA via the Poly(A) Purist Kit (Ambion     AM1916, Austin, TX, USA).

treatment_protocol: Conditions are untreated (UT) or methyl methanesulfonate (MMS-0.033%) treated.

tag: genetic background

tag: genotype/variation

value: tel1Δ mec1Δ

source_name: tel1mec1, MMS

value: methyl methanesulfonate (MMS)


title: tel1mec1.MMS vs. tel1mec1.UT, rep1

type: RNA

state: CA

country: USA

description: US22502657_251507211012_S01_H_flip_4-4.avg

molecule: total RNA

tag: treatment


title: ste11.UT vs. ste11.MMS, rep1

description: US22502657_251507211009_S01_H_flip_3-4.avg

source_name: ste11, MMS

source_name: ste11, untreated


title: rad53.MMS vs. rad53.UT, rep1

description: US22502657_251507211006_S01_H_flip_2-4.avg

source_name: rad53, untreated

source_name: rad53, MMS


title: dun1.UT vs. dun1.MMS, rep1

description: US22502657_251507211009_S01_H_flip_1-4.avg

source_name: dun1, MMS

source_name: dun1, untreated


title: dun1.MMS vs. dun1.UT, rep1

description: US22502657_251507211009_S01_H_flip_2-4.avg


title: dun1rad53.UT vs. dun1rad53.MMS, rep2

description: US22502657_251507211011_S01_H_flip_1-4.avg

source_name: dun1rad53, MMS

value: dun1Δ rad53Δ

source_name: dun1rad53, untreated


title: dun1rad53.UT vs. dun1rad53.MMS, rep1

description: US22502657_251507211011_S01_H_flip_3-4.avg


title: ste11.MMS vs. ste11.UT, rep2

description: US22502657_251507210130_S01_H_flip_3-4.avg


title: ste11.UT vs. ste11.MMS, rep2

description: US22502657_251507210130_S01_H_flip_2-4.avg


title: chk1rad53.UT vs. chk1rad53.MMS, rep1

description: US22502657_251507211008_S01_H_flip_3-4.avg

source_name: chk1rad53, MMS

value: chk1Δ rad53Δ

source_name: chk1rad53, untreated


title: ste11.MMS vs. ste11.UT, rep1

description: US22502657_251507211009_S01_H_flip_4-4.avg


title: rad53.UT vs. rad53.MMS, rep2

description: US22502657_251507210657_S01_H_flip_3-4.avg


title: crt1.MMS vs. crt1.UT, rep1

description: US22502657_251507211007_S01_H_flip_4-4.avg

source_name: crt1, untreated

source_name: crt1, MMS


title: rad53.UT vs. rad53.MMS, rep1

description: US22502657_251507211006_S01_H_flip_1-4.avg


title: wt.UT vs. wt.MMS, rep1

description: US22502657_251507210128_S01_H_flip_2-4.avg

source_name: wt, MMS

tag: strain

value: wild-type

source_name: wt, untreated


title: chk1.UT vs. chk1.MMS, rep2

description: US22502657_251507211010_S01_H_flip_1-4.avg

source_name: chk1, MMS

source_name: chk1, untreated


title: chk1.MMS vs. chk1.UT, rep1

description: US22502657_251507211010_S01_H_flip_4-4.avg


title: chk1rad53.UT vs. chk1rad53.MMS, rep2

description: US22502657_251507211008_S01_H_flip_1-4.avg


title: chk1dun1.UT vs. chk1dun1.MMS, rep2

description: US22502657_251507211243_S01_H_flip_2-4.avg

source_name: chk1dun1, MMS

value: dun1Δ chk1Δ

source_name: chk1dun1, untreated


title: chk1.UT vs. chk1.MMS, rep1

description: US22502657_251507211010_S01_H_flip_3-4.avg


title: chk1dun1.MMS vs. chk1dun1.UT, rep2

description: US22502657_251507211243_S01_H_flip_1-4.avg


title: chk1.MMS vs. chk1.UT, rep2

description: US22502657_251507211010_S01_H_flip_2-4.avg


title: dun1.MMS vs. dun1.UT, rep2

description: US22502657_251507211176_S01_H_flip_2-4.avg


title: sml1.MMS vs. sml1.UT, rep1

description: US22502657_251507211007_S01_H_flip_2-4.avg

source_name: sml1, untreated

source_name: sml1, MMS


title: chk1rad53.MMS vs. chk1rad53.UT, rep2

description: US22502657_251507211008_S01_H_flip_2-4.avg


title: wt.MMS vs. wt.UT, rep1

description: US22502657_251507210128_S01_H_flip_3-4.avg


title: crt1.UT vs. crt1.MMS, rep1

description: US22502657_251507211007_S01_H_flip_3-4.avg


title: tel1.MMS vs. tel1.UT, rep1

description: US22502657_251507210790_S01_H_flip_2-4.avg

source_name: tel1, untreated

source_name: tel1, MMS


title: sml1.UT vs. sml1.MMS, rep1

description: US22502657_251507211007_S01_H_flip_1-4.avg


title: dun1.UT vs. dun1.MMS, rep2

description: US22502657_251507211176_S01_H_flip_1-4.avg

source_name: dun1, MMS

source_name: dun1, untreated


title: mec1.UT vs. mec1.MMS, rep2

description: US22502657_251507211177_S01_H_flip_4-4.avg

source_name: mec1, MMS

source_name: mec1, untreated


title: chk1rad53.MMS vs. chk1rad53.UT, rep1

description: US22502657_251507211008_S01_H_flip_4-4.avg

source_name: chk1rad53, untreated

source_name: chk1rad53, MMS


title: chk1dun1.MMS vs. chk1dun1.UT, rep1

description: US22502657_251507211243_S01_H_flip_4-4.avg


title: tel1.UT vs. tel1.MMS, rep2

description: US22502657_251507210790_S01_H_flip_1-4.avg


title: wt.UT vs. wt.MMS, rep2

description: US22502657_251507211176_S01_H_flip_4-4.avg


title: sml1.UT vs. sml1.MMS, rep2

description: US22502657_251507211176_S01_H_flip_3-4.avg


title: chk1dun1.UT vs. chk1dun1.MMS, rep1

description: US22502657_251507211243_S01_H_flip_3-4.avg


title: rad53.MMS vs. rad53.UT, rep2

description: US22502657_251507211177_S01_H_flip_1-4.avg

source_name: rad53, untreated

source_name: rad53, MMS


title: mec1.UT vs. mec1.MMS, rep1

description: US22502657_251507211175_S01_H_flip_3-4.avg


title: mec1.MMS vs. mec1.UT, rep2

description: US22502657_251507211175_S01_H_flip_4-4.avg


title: sml1.MMS vs. sml1.UT, rep2

description: US22502657_251507211013_S01_H_flip_3-4.avg


title: tel1mec1.UT vs. tel1mec1.MMS, rep1

description: US22502657_251507211013_S01_H_flip_1-4.avg

source_name: tel1mec1, MMS

source_name: tel1mec1, untreated


title: dun1rad53.MMS vs. dun1rad53.UT, rep2

description: US22502657_251507211177_S01_H_flip_2-4.avg

source_name: dun1rad53, untreated

source_name: dun1rad53, MMS


title: wt.MMS vs. wt.UT, rep2

description: US22502657_251507211013_S01_H_flip_4-4.avg

source_name: wt, untreated

source_name: wt, MMS


title: dun1rad53.MMS vs. dun1rad53.UT, rep1

description: US22502657_251507211011_S01_H_flip_4-4.avg


title: tel1mec1.UT vs. tel1mec1.MMS, rep2

description: US22502657_251507211175_S01_H_flip_2-4.avg


title: tel1.MMS vs. tel1.UT, rep2

description: US22502657_251507210659_S01_H_flip_2-4.avg


title: tel1.UT vs. tel1.MMS, rep1

description: US22502657_251507210659_S01_H_flip_3-4.avg


title: mec1.MMS vs. mec1.UT, rep1

description: US22502657_251507211006_S01_H_flip_4-4.avg


title: crt1.UT vs. crt1.MMS, rep2

description: US22502657_251507210658_S01_H_flip_1-4.avg

source_name: crt1, MMS

source_name: crt1, untreated


title: crt1.MMS vs. crt1.UT, rep2

description: US22502657_251507210658_S01_H_flip_4-4.avg


title: Black 6 - 10

status: Public on Mar 30 2013

city: Toronto

first: Flavia

last: Lakschevitz

state: ON

address: 150 College st room 221

department: Faculty of Dentistry

country: Canada

institute: University of Toronto

description:
Black 6 - 10
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scan protocol

data_processing: Raw data was pre-processed using lumi R package.  Background correction was done in Genomestudio. The quantile normalization method implemented in lumi R package was used to normalize the data

label: biotin

organism: Mus musculus

source_name: Blood

label_protocol: Biotinylated cRNA were prepared with the Ambion Amplification kit:  - Illumina TotalPrep-96 RNA Amplification Kit cat# 4393543

extract_protocol: Following neutrophil isolation, total  RNA was extracted with mirVANA kit from Ambion, followed by clean-up and DNase I treatment with Ambion kit in accordance with protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: genotype

value: WT

tag: gender

value: male

tag: age

value: 6 - 8 weeks

tag: cell type

value: PMN


title: Black 6 - 7

description:
Black 6 - 7
replicate 1

source_name: Peritoneal Exudate


title: Black 6 - 12

description:
Black 6 - 12
replicate 3


title: Black 6 - 9

description:
Black 6 - 9
replicate 3


title: Rac 1 WT - 5

description:
Rac 1 WT - 5
replicate 2

source_name: Bone Marrow


title: Black 6 - 1

description:
Black 6 - 1
replicate 1


title: Rac 1 WT - 4

description:
Rac 1 WT - 4
replicate 1


title: CD4+ D011.10+ CD44 high cells from sOVA immunized sOVA host, 5 days following transfer of D011.10+ T cells rep 3

status: Public on Jan 27 2013

city: San Francisco

first: Andrea

middle: J

last: Barczak

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

hyb_protocol: Cy3-labelled RNA) was fragmented at 60Â°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent UCSF custom 8x15K miRNA arrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned on the Agilent scanner immediately after washing.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.6 (Agilent) using default parameters)

source_name: in vivo activated mouse CD4 T cells

label_protocol: Total RNA was labeled with Cy3-CTP using the miRCURY LNA microRNA power labeling kit (Exiqon, Inc, Woburn, MA), according to manufacturers protocol

extract_protocol: RNA was extracted using Trizol reagent and standard protocol.

treatment_protocol: LNs and spleens were pooled from DO11 Rag2-/- mice and CD4+ cells purified using magnetic beads. DO11 Rag2-/- cells were used for the transfers but DO11 Rag2+/+ cells were used for the naive group. 2-5 x 10^5 CD4+ cells were then intravenously injected recipients. Donor T cells were transferred into sOVA or WT Balb/c mice and, 24 hours later, these were immunized (IV) with 1-5 x 10^5 bone marrow-derived dendritic cells  that were pre-activated with LPS and loaded with Ova peptide. Naïve or activated D011.10 CD4 T cells were isolated from pooled mouse spleen and lymph nodes using FACS sorting.

tag: tissue

value: spleen/lymph nodes

value: Balb/c

value: 6-8 weeks


title: CD4+ D011.10+ CD44 high cells from sOVA immunized sOVA host, 5 days following transfer of D011.10+ T cells rep 2


title: Black 6 - 8

description:
Black 6 - 8
replicate 2


title: CD4+ D011.10+ CD44 high cells from OVA immunized host, 5 days following transfer of D011.10+ cells rep 2


title: CD4+ D011.10+ CD44 high cells from sOVA immunized sOVA host, 5 days following transfer of D011.10+ T cells rep 1


title: CD4+ D011.10+ CD44 high cells from OVA immunized host, 5 days following transfer of D011.10+ cells rep 1


title: Black 6 - 11

description:
Black 6 - 11
replicate 2


title: Rac 1 WT - 6

description:
Rac 1 WT - 6
replicate 3


title: Black 6 - 2

description:
Black 6 - 2
replicate 2


title: High_CON Rep 2

status: Public on Mar 25 2013

city: Corvallis

first: Robert

middle: L

last: Tanguay

state: OR

department: EMT

institute: Oregon State University

description: 24 hpf zebrafish embryo exposed to High CON Rep 2

hyb_protocol: Hybridization was performed by Nimblegen processing center (Reykjavik, Iceland) following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Nimblegen processing center (Reykjavik, Iceland) following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Danio rerio

source_name: 24 hpf Danio rerio, static waterborne exposed 8-24 hpf, 0.1% DMSO

label_protocol: Labeling was performed by Nimblegen processing center (Reykjavik, Iceland) following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Embryos were incubated in fish water until 8 hpf, then exposed to vehicle control or chemical until 24 hpf, at 28 degrees Celcius

extract_protocol: total RNA was isolated using Trizol protocol (80 uM BPA, 15 uM E2, and vehicle control) or RNAzol protocol (0.1 uM BPA, 0.1 uM E2, and vehicle control)

treatment_protocol: Embryos were static waterborne exposed individually in 96-well microtiter plates (parafilm sealed and covered with foil) to either 0.1% DMSO control, 0.1 uM E2, or 0.1 uM GSK4716

value: whole embryo

tag: agent

value: CON

tag: dose

value: control

tag: developmental stage

value: 24 hpf


title: High_E2 Rep 1

description: 24 hpf zebrafish embryo exposed to High E2 Rep 1

source_name: 24 hpf Danio rerio, static waterborne exposed 8-24 hpf, 15 µM E2

value: High [15 µM E2]


title: High_E2 Rep 2

description: 24 hpf zebrafish embryo exposed to High E2 Rep 2


title: High_CON Rep 1

description: 24 hpf zebrafish embryo exposed to High CON Rep 1


title: High_BPA Rep 2

description: 24 hpf zebrafish embryo exposed to High BPA Rep 2

source_name: 24 hpf Danio rerio, static waterborne exposed 8-24 hpf, 80 µM BPA

value: BPA

value: High [80 µM BPA]


title: Black 6 - 3

description:
Black 6 - 3
replicate 3


title: Low_E2 Rep 2

description: 24 hpf zebrafish embryo exposed to Low E2 Rep 2

source_name: 24 hpf Danio rerio, static waterborne exposed 8-24 hpf, 0.1 µM E2

value: Low [0.1 µM E2]


title: High_BPA Rep 1

description: 24 hpf zebrafish embryo exposed to High BPA Rep 1


title: Low_BPA Rep 2

description: 24 hpf zebrafish embryo exposed to Low BPA Rep 2

source_name: 24 hpf Danio rerio, static waterborne exposed 8-24 hpf, 0.1 µM BPA

value: Low [0.1 µM BPA]


title: Low_CON Rep 2

description: 24 hpf zebrafish embryo exposed to Low CON Rep 2


title: CD4+ D011.10+ CD25- CD44 low cells from DO11.10 Rag2+/+ mice rep 1


title: CD4+ D011.10+ CD25- CD44 low cells from DO11.10 Rag2+/+ mice rep 2


title: Low_E2 Rep 3

description: 24 hpf zebrafish embryo exposed to Low E2 Rep 3


title: Low_BPA Rep 3

description: 24 hpf zebrafish embryo exposed to Low BPA Rep 3


title: Low_CON Rep 3

description: 24 hpf zebrafish embryo exposed to Low CON Rep 3


title: Low_E2 Rep 1

description: 24 hpf zebrafish embryo exposed to Low E2 Rep 1


title: Low_CON Rep 1

description: 24 hpf zebrafish embryo exposed to Low CON Rep 1


title: Low_BPA Rep 1

description: 24 hpf zebrafish embryo exposed to Low BPA Rep 1


title: PBMC_Severe_Disease 15

status: Public on Dec 29 2012

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

description: Severe Disease

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with lumi (lumi_2.4.0) in R version 2.13.2 (2011-09-30)

organism: Homo sapiens

source_name: PBMC, severe disease, mock

label_protocol: Preparation of cDNA, cRNA, and labeling were carried out by the Yale Center for Genomic Analysis using the standard Illumina protocols.   Hybridization buffer from the BeadChip kit (Illumina) was mixed with 1500 ng of biotin-labeled cRNA, heated to 65°C for 5 minutes, and then loaded onto the BeadChip.  The BeadChips were sealed in a hybridization chamber and placed in an oven at 58°C with a rocker for 16-20 hours.  After the hybridization, the BeadChips were washed and stained in a series of washes and stains as outlined in the Illumina protocol.  The BeadChips were scanned on the Illumina Iscan.

extract_protocol: Total RNA from PBMC samples was extracted using the RNeasy mini kit (Qiagen, CA)

value: peripheral blood mononuclear cells (PBMCs)

value: mock

value: Female

tag: batch

tag: disease status

value: Severe Disease

tag: disease severity/outcome

value: Meningitis


title: Maize-SAM-L1

status: Public on Jan 28 2013

type: SRA

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

institute: Iowa State University

description:
L1 layer Specific Gene Expression Profiling in Maize Shoot Apical Meristems
mRNA was amplified from SAM tissue

library_source: transcriptomic

data_processing:
The Illumina reads were aligned to maize gene models (Release 4a.53, http://www.maizesequence.org) with short read aligner NOVOALIGN (http://www.novocraft.com). Two mismatches across 35 bp were allowed and only the reads that uniquely mapped to gene models were considered for further analysis. In total, 4.5 million reads from B73xMo17 and 5.2 million reads from Mo17Xb73 were mapped to 26,394 gene models.
There are two samples in the experiment: L1 cell layer vs. L2 cell layer.
Each sample has two technical Solexa runs. The processed data for each sample is the merged data for final analysis across the technical reps for each sample.

molecule: polyA RNA

organism: Zea mays

source_name: Shoot apical meristem

growth_protocol: kernels planted in growth chambers (PGW-40, Percival Scientific, http://www.percival-scientific.com). Temperature and light cycle were set as 25 degrees for 15 hours of light and 20 degrees for 9 hours of dark. During the light period the light intensity at the surface of the growth medium was maintained between 650 and 800 umol m-2 sec -1.

extract_protocol: Each set of the L1 and the L2 tissues was collected via LCM into the cap of 500-μl microcentrifuge tube filled with 40 μl mineral oil (Ohtsu and Schnable, 2007).  After collection of the tissue, 100 μl of the Extraction Buffer of the PicoPure RNA Isolation Kit (Arcturus, which is now Molecular Devices, Mountain View, CA, USA) was added to the mineral oil including the LCM-collected tissue and mixed thoroughly.  RNA was extracted according to the manual with the RNase-free DNase I treatment (Ohtsu et al., 2007a) as if there were no mineral oil.  For each replication, the same amount of RNA (~1 ng) from the L1 and the L2 was amplified using RiboAmp HS RNA Amplification Kit (Arcturus) according to the manual.  Amounts of the aRNA were determined by measuring OD260 values ç, SPECTRAmax PLUS (Molecular Devices, Sunnyvale, CA, USA).  The yields of the aRNA samples are presented in Table S1.

treatment_protocol: Two tissue types compared without treatment

value: 14 days after planting

tag: stage

value: 14 day old


title: PBMC_Severe_Disease 18

description: Severe Disease

value: Male

value: Encephalitis and Meningitis


title: PBMC_Severe_Disease 7

description: Severe Disease

value: Encephalitis


title: PBMC_Severe_Disease 13

description: Severe Disease


title: PBMC_Severe_Disease 17

description: Severe Disease


title: PBMC_Severe_Disease 16

description: Severe Disease


title: PBMC_Severe_Disease 14

description: Severe Disease


title: Maize-SAM-L2

description:
L2 layer Specific Gene Expression Profiling in Maize Shoot Apical Meristems
mRNA was amplified from SAM tissue


title: PBMC_Asymptomatic 15

description: Asymptomatic

source_name: PBMC, asymptomatic, mock

value: Asymptomatic


title: PBMC_Asymptomatic 17

description: Asymptomatic


title: PBMC_Asymptomatic 19

description: Asymptomatic


title: PBMC_Severe_Disease 4

description: Severe Disease


title: PBMC_Asymptomatic 21

description: Asymptomatic


title: PBMC_Asymptomatic 16

description: Asymptomatic


title: PBMC_Asymptomatic 18

description: Asymptomatic


title: PBMC_Asymptomatic 20

description: Asymptomatic


title: PBMC_Severe_Disease 5

description: Severe Disease


title: PBMC_Severe_Disease 3

description: Severe Disease


title: PBMC_Severe_Disease 1

description: Severe Disease


title: PBMC_Severe_Disease 12

description: Severe Disease


title: PBMC_Severe_Disease 6

description: Severe Disease


title: PBMC_Severe_Disease 9

description: Severe Disease


title: PBMC_Severe_Disease 8

description: Severe Disease


title: PBMC_Asymptomatic 14

description: Asymptomatic


title: PBMC_Severe_Disease 10

description: Severe Disease


title: PBMC_Asymptomatic 10

description: Asymptomatic


title: PBMC_Severe_Disease 2

description: Severe Disease


title: PBMC_Asymptomatic 7

description: Asymptomatic


title: PBMC_Asymptomatic 9

description: Asymptomatic


title: PBMC_Asymptomatic 5

description: Asymptomatic


title: PBMC_Asymptomatic 11

description: Asymptomatic


title: PBMC_Asymptomatic 12

description: Asymptomatic


title: PBMC_Asymptomatic 13

description: Asymptomatic


title: PBMC_Asymptomatic 3

description: Asymptomatic


title: PBMC_Asymptomatic 1

description: Asymptomatic


title: PBMC_Severe_Disease 11

description: Severe Disease


title: PBMC_Asymptomatic 4

description: Asymptomatic


title: PBMC_Asymptomatic 8

description: Asymptomatic


title: PBMC_Asymptomatic 6

description: Asymptomatic


title: PBMC_Asymptomatic 2

description: Asymptomatic


title: LNCaP siEZH2 at DHT rep 1

status: Public on Nov 30 2012

city: San Antonio

first: Kexin

last: Xu

state: TX

address: 7703 Floyd Curl, MC 8257

department: Molecular Medicine

institute: UT Health Science Center at San Antonio

description:
Gene expression data from LNCaP cells after transfection with siRNA against EZH2
LNCaP-DHT-siEZH2-1

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized overnight at 45ºC on Affymetrix human U133 plus 2.0 expression array. The chips were transferred to a fluidics instrument that performs washes and then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE).

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

data_processing:
The data is processed by RMA with quantile normalization.
Probes are converted to genes by averaging values of probes mapped to the same gene. Combat is used to remove the batch effect.  The Combat-Matrix.txt files are linked as supplementary files on the Series record.

source_name: LNCaP cells depleted of EZH2 in the presence of 10 nM DHT

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8-15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: LNCaP cells were routinely maintained in RPMI-1640 with 10% fetal bovine serum (FBS) plus 1% antibiotics (penicillin and streptomycin). LNCaP-abl (abl) cells were routinely maintained in phenol-red-free RPMI with 10% charcoal-stripped FBS plus 1% antibiotics.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by additional purification using RNeasy Kit (Qiagen, Cat#74104).

treatment_protocol: Cells were transfected with either control siRNA (siCtrl) or siRNAs targeting EZH2 (siEZH2), and maintained in androgen-depleted medium for 24 hours, and then treated with either 10 nM 5α-dihydrotestosterone (DHT, for LNCaP cells) or with ethanol only (for abl cells) for another 24 hours before the RNA was extracted.

tag: cell line

value: LNCaP prostate cancer cells

value: depleted of EZH2

tag: treatment protocol

value: in the presence of DHT


title: LNCaP control at DHT rep 1

description:
Gene expression data from LNCaP cells after transfection with control siRNA
LNCaP-DHT-siCtrl-1

source_name: LNCaP cells transfected with control siRNA in the presence of 10 nM DHT

tag: genotype/variation

value: transfected with control siRNA


title: abl control at VEH rep 2

description:
Gene expression data from abl cells after transfection with control siRNA
abl-VEH-siCtrl-2

source_name: abl cells transfected with control siRNA under hormone depleted conditions

value: LNCaP-abl (abl) prostate cancer cells

value: under hormone depleted conditions


title: LNCaP siEZH2 at DHT rep 2

description:
Gene expression data from LNCaP cells after transfection with siRNA against EZH2
LNCaP-DHT-siEZH2-2


title: LNCaP control at DHT rep 0

description:
Gene expression data from LNCaP cells after transfection with control siRNA
LNCaP-DHT-siCtrl-0


title: LNCaP control at DHT rep 2

description:
Gene expression data from LNCaP cells after transfection with control siRNA
LNCaP-DHT-siCtrl-2


title: abl siEZH2 at VEH rep 2

description:
Gene expression data from abl cells after transfection with siRNA against EZH2
abl-VEH-siEZH2-2

source_name: abl cells depleted of EZH2 under hormone depleted conditions


title: abl control at VEH rep 1

description:
Gene expression data from abl cells after transfection with control siRNA
abl-VEH-siCtrl-1


title: LNCaP siEZH2 at DHT rep 0

description:
Gene expression data from LNCaP cells after transfection with siRNA against EZH2
LNCaP-DHT-siEZH2-0


title: abl siEZH2 at VEH rep 1

description:
Gene expression data from abl cells after transfection with siRNA against EZH2
abl-VEH-siEZH2-1


title: abl control at VEH rep 0

description:
Gene expression data from abl cells after transfection with control siRNA
abl-VEH-siCtrl-0


title: abl siEZH2 at VEH rep 0

description:
Gene expression data from abl cells after transfection with siRNA against EZH2
abl-VEH-siEZH2-0


title: MAI_1_A2 with array type rice from Affymetrix

status: Public on Oct 15 2012

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

country: France

institute: inra

description: The Bacterial Leaf Blight disease of rice is due to Xanthomonas oryzae pv. oryzae. As for many pathogenic bacteria, it relies on a type 3 secretion system (TTSS) that is devoted to the injection of type 3 effectors (T3Es) into the eukaryotic host cell. These proteins are meant to suppress host basal defense responses and/or mimic some host regulatory function promoting bacterial survey in the plant. During an incompatible interaction, T3Es may act as Avr proteins and stimulate Effector-Triggered-Immunity. We aim at evaluating the transcriptomic response of rice leaves challenged with avirulent strains of Xoo BAI3 and MAI1 on resistant lines IR64 and IRBB4 versus the reference susceptible rice line Nipponbare. In addition, we investigated the transcriptomic response of rice leaves upon inoculation of an XoohrcC mutant strain affected in the production of a functional TTSS.

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label: Biotin

organism: Oryza sativa

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: caulin leaf - S2 type greenhouse, 26°C, 80 HR

extract_protocol:
Plant RNeasy kit (Qiagen).
MAI_1_A2:30ug.

treatment_protocol: Name:XOO STRAIN  - syringe-inoculation - pathogen infection,xoo strain bai3:time 24hour . Young leaves of 3 weeks old plantlets are infiltrated with a freshly-grown bacterial suspension at an OD of 0,5 using a syringe.

tag: infection status

value: avirulent strain MAI1

tag: cultivar/strain

tag: harvest date


title: BAID_hrrcC_E2 with array type rice from Affymetrix

extract_protocol:
Plant RNeasy kit (Qiagen).
BAID_hrrcC_E2:30ug.

value: avirulent strain BAID_hrcc

value: nipponbare


title: BAI_3_C2 with array type rice from Affymetrix

extract_protocol:
Plant RNeasy kit (Qiagen).
BAI_3_C2:30ug.

value: avirulent strain BAI3


title: BAI_3_C1 with array type rice from Affymetrix

extract_protocol:
Plant RNeasy kit (Qiagen).
BAI_3_C1:30ug.


title: MAI_1_A1 with array type rice from Affymetrix

extract_protocol:
Plant RNeasy kit (Qiagen).
MAI_1_A1:30ug.


title: MAI_1_B3 with array type rice from Affymetrix

extract_protocol:
Plant RNeasy kit (Qiagen).
MAI_1_B3:30ug.


title: MAI_1_B1 with array type rice from Affymetrix

extract_protocol:
Plant RNeasy kit (Qiagen).
MAI_1_B1:30ug.


title: BAI_3_F2 with array type rice from Affymetrix

extract_protocol:
Plant RNeasy kit (Qiagen).
BAI_3_F2:30ug.


title: BAI_3_F3 with array type rice from Affymetrix

extract_protocol:
Plant RNeasy kit (Qiagen).
BAI_3_F3:30ug.


title: BAID_hrrcC_E1 with array type rice from Affymetrix

extract_protocol:
Plant RNeasy kit (Qiagen).
BAID_hrrcC_E1:30ug.


title: MAI_1_B2 with array type rice from Affymetrix

extract_protocol:
Plant RNeasy kit (Qiagen).
MAI_1_B2:30ug.


title: PGC_shRNA FUS2_rep3

status: Public on Nov 21 2012

city: Nagoya

first: Shinsuke

last: Ishigaki

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Department of Neurology

country: Japan

institute: Nagoya University School of Medicine

description: RMA expression value derived from Expression Console software; all-exon analysis

hyb_protocol: Samples were hybridized with GeneChip mouse exon 1.0 ST Arrays (Affymetrix) and scanned accoding to the manufacture's protocol.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip 3000 7G

data_processing: The data were background corrected and normalized using the robust multiarray average (RMA) procedure implemented in the Affymetrix Expression Console software.  probe group file: MoEx-1_0-st-v1.r2.pgf  meta-probeset file: MoEx-1_0-st-v1.r2.dtl.mm9.full.ps

source_name: primary glial cells, shRNA FUS2

label_protocol: 100ng of total RNA were used to generate labeled cDNA. Biotinylated DNA probes were prepared using Affymetrix WT Expression kit for Affymetrix Whole Transcript Sense Expression arrays and Affymetrix geneChip WT Terminal Labeling kit according to the manufacture's protocol.

growth_protocol: Mouse brains were taken from C57BL/6 strain mouse embryos at E15. Cerebral cortex without meninges were extracted and dissociated into a single-cell suspension by Sumilon dissociation solution (Sumitomo Bakelite, Tokyo Japan). Cells were plated at a density of 1.5 x 106 cells in a 60 mm-well culture plate with D-MEM(Dulbecco's Modified Eagle Medium) containing 10%FBS and 1%Pen-Strep.

extract_protocol: Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen) followed by DnaseI (Qiagen) treatment.

treatment_protocol: On day 11, glial cells were infected with 1.81 x 1010 copies/well (1.36 x 107 copies/µl) of lentivirus expressing shRNA against mouse Fus (shFus1 or shFus2) or control (shCont). After the overnight infection, the virus media was removed. Glia cells were cultured for 5 days after the infection and RNA were extracted on day 16.

tag: strain

value: embryo

value: primary glial cells

value: FUS2 knockdown


title: PGC_control shRNA_rep2

source_name: primary glial cells, control shRNA

tag: age

value: control


title: BAI_3_F1 with array type rice from Affymetrix

extract_protocol:
Plant RNeasy kit (Qiagen).
BAI_3_F1:30ug.


title: PGC_shRNA FUS1_rep2

source_name: primary glial cells, shRNA FUS1

tag: cell type

value: FUS1 knockdown


title: PMN_shRNA FUS2_rep2

source_name: primary motor neurons, shRNA FUS2

growth_protocol: Motor neurons were harvested by gradient centrifugation with Optiprep (Invitrogen). Cells were plated at a density of 1.5 x 106 cells in a 60 mm-well culture plate with the medium containing 0.5x Sumilon nerve-culture medium (Sumitomo Bakelite), 0.5x Neurobasal medium, 1% FBS, 0.5x B27 supplements (Invitrogen), 0.5x Glutamax, 5 µg/ml of BDNF, 5 µg/ml of CNTF, and 0.5% Pen-Strep. A day after plating (day 2), neurons were supplemented with 10 ng/µl of AraC and incubated overnight.

treatment_protocol: On day 5, neurons were infected with 2 x 1010 copies/well (1.5 x 107 copies/µl) of lentivirus expressing shRNA against mouse Fus (shFus1 or shFus2) or control (shCont). After 4 hr of infection, the virus media was removed. Neurons were then cultured for 6 additional days, and were harvested on day 11 followed by RNA extraction and cDNA synthesis.

value: primary motor neurons


title: PGC_control shRNA_rep3


title: BAI_3_C3 with array type rice from Affymetrix

extract_protocol:
Plant RNeasy kit (Qiagen).
BAI_3_C3:30ug.


title: PGC_shRNA FUS2_rep2


title: PGC_shRNA FUS1_rep1


title: MAI_1_A3 with array type rice from Affymetrix

extract_protocol:
Plant RNeasy kit (Qiagen).
MAI_1_A3:30ug.


title: BAI_3_D3 with array type rice from Affymetrix

extract_protocol:
Plant RNeasy kit (Qiagen).
BAI_3_D3:30ug.


title: PGC_control shRNA_rep1


title: BAI_3_D2 with array type rice from Affymetrix

extract_protocol:
Plant RNeasy kit (Qiagen).
BAI_3_D2:30ug.


title: BAI_3_D1 with array type rice from Affymetrix

extract_protocol:
Plant RNeasy kit (Qiagen).
BAI_3_D1:30ug.


title: PGC_shRNA FUS1_rep3


title: 463958A05 - urt1_3 vs WT3

status: Public on Jul 13 2012

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: Identification of mRNA targets of the terminal uridylyltransferase URT1 (AT2G45620) in Arabidopsis thaliana.

hyb_protocol: WT3 Cy5 / urt1_3 Cy3 : 30pmol.

scan_protocol: InnoScan900_MAPIX, Cy3:pmt voltage 532nm,650V,laser power 5%, Cy5:635nm,pmt voltage 700V,laser power 5%

data_processing:
For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.
We used the arrays with 73228 probes but we didn't exploit all the probe. Indeed half of the probes are "no gene" probes.

organism: Arabidopsis thaliana

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

growth_protocol: rosette - Media=soil hygrometry=50-80% Temperature=22/18 Light=16/8 10,000 lux/day

treatment_protocol: no treatment

tag: ecotype

value: Columbia (Col0)

value: (Boyes et al. Plant Cell 2001):boyes:6.00-6.50

tag: tissue

value: rosette

value: WT


title: PMN_control shRNA_rep3

source_name: primary motor neurons, control shRNA


title: Primary cerebellar neurons_shRNA FUS2_rep1

source_name: primary cerebellar neurons, shRNA FUS2

growth_protocol: Primary cerebellar neurons were taken from mouse cerebellum of C57BL/6 strain mouse embryos at E15. Cerebellum without meninges were extracted and dissociated by Sumilon dissociation solution (Sumitomo Bakelite). Cells were plated at a density of 1.7 x 106 cells in a 60 mm-well culture plate with Sumilon nerve-culture medium (Sumitomo Bakelite).

treatment_protocol: On the day 5 cerebellar neurons were infected with 2.5x1010 copies/well (1.25 x 107 copies/ul) of the lentivirus expressing shRNA against mouse Fus (shFus1 or shFus2) or control (shCont). After 4 hr of infection, the media containing the virus was removed. Neurons were then cultured for 4 additional days, and were harvested on day 9 followed by RNA extraction and cDNA synthesis.

value: primary cerebellar neurons


title: PMN_shRNA FUS1_rep1

source_name: primary motor neurons, shRNA FUS1


title: Primary cerebellar neurons_control shRNA_rep3

source_name: primary cerebellar neurons, control shRNA


title: Primary cerebellar neurons_shRNA FUS1_rep2

source_name: primary cerebellar neurons, shRNA FUS1


title: 463958A09 - WT3 vs urt1_3

hyb_protocol: urt1_3 Cy5 / WT3 Cy3 : 30pmol.


title: 463958A01 - WT2 vs urt1_2

hyb_protocol: urt1_2 Cy5 / WT2 Cy3 : 30pmol.


title: PMN_shRNA FUS1_rep2


title: 463792A05 - WT1 vs urt1_1

hyb_protocol: urt1_1 Cy5 / WT1 Cy3 : 30pmol.


title: 463792A01 - urt1_1 vs WT1

hyb_protocol: WT1 Cy5 / urt1_1 Cy3 : 30pmol.


title: BAID_hrrcC_E3 with array type rice from Affymetrix

extract_protocol:
Plant RNeasy kit (Qiagen).
BAID_hrrcC_E3:30ug.


title: PGC_shRNA FUS2_rep1


title: PMN_shRNA FUS1_rep3


title: ZT16 gi-2 3

status: Public on Jul 01 2012

city: Pohang

first: Hee Jung

last: Koo

address: Hyojadong San 31

country: South Korea

institute: Pohang University of Science and Technology

description: 7-day-old seedlings of gi-2 mutant grown under LD were harvested at ZT16 [rep3]

hyb_protocol: Standard Agilent  hybridization protocols

scan_protocol: Agilent Technologies Scanner G2505C

data_processing: The data were treated using MATLAB 7.10.0 (R2010a)

source_name: Arabidopsis 7-day-old seedlings

label_protocol: Refer to the Agilent Gene Expression System Manual

growth_protocol: 16L/8D-grown seedlings for 7 days

extract_protocol: Total mRNA was extracted using WelPrepTM (JOIN BIO-INNOVATION, Daegu, Korea), and DNA was digested by treatment with DNase I (Ambion, Austin, TX).

treatment_protocol: Seven-day-old seedlings grown under LD were harvested at ZT1 and ZT16.

value: seedling

value: 7 d

tag: cultivar

tag: genotype

value: gi-2 mutant

tag: sampling time


title: Primary cerebellar neurons_shRNA FUS2_rep2

tag: developmental stage


title: ZT16 gi-2 2

description: 7-day-old seedlings of gi-2 mutant grown under LD were harvested at ZT16 [rep2]


title: Primary cerebellar neurons_shRNA FUS2_rep3


title: Primary cerebellar neurons_shRNA FUS1_rep1


title: ZT16 col 3

description: 7-day-old seedlings of WT(col-0) grown under LD were harvested at ZT16 [rep3]

value: wild type


title: PMN_shRNA FUS2_rep3


title: Primary cerebellar neurons_control shRNA_rep2


title: PMN_shRNA FUS2_rep1


title: ZT16 col 1

description: 7-day-old seedlings of WT(col-0) grown under LD were harvested at ZT16 [rep1]


title: ZT16 gi-2 1

description: 7-day-old seedlings of gi-2 mutant grown under LD were harvested at ZT16 [rep1]


title: ZT1 gi-2 3

description: 7-day-old seedlings of gi-2 mutant grown under LD were harvested at ZT1 [rep3]


title: ZT1 col 1

description: 7-day-old seedlings of WT(col-0) grown under LD were harvested at ZT1 [rep1]


title: Primary cerebellar neurons_shRNA FUS1_rep3


title: ZT1 gi-2 1

description: 7-day-old seedlings of gi-2 mutant grown under LD were harvested at ZT1 [rep1]


title: ZT1 col 3

description: 7-day-old seedlings of WT(col-0) grown under LD were harvested at ZT1 [rep3]


title: PMN_control shRNA_rep1


title: 463792A09 - urt1_2 vs WT2

hyb_protocol: WT2 Cy5 / urt1_2 Cy3 : 30pmol.


title: Primary cerebellar neurons_control shRNA_rep1


title: vegetative buds_rep6

status: Public on Feb 08 2012

city: Québec

first: John

last: MacKay

state: Québec

address: 1030, avenue de la Médecine, Pavillon C.-E. Marchand

department: Centre d'étude de la forêt

institute: Université Laval

description:
JF003-8041.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.

hyb_protocol: Each microarray was hybridized with one sample labelled with one dye. The samples were mixed and the volume was reduced to ~10 µl by evaporating excess water in a DNA 120 speedvac (Thermo Fisher Scientific). Labelled aRNAs were fragmented for 15 minutes at 70°C using Ambion’s ”RNA Fragmentation Reagents“, placed on ice for 1 minute, denatured for 2 minutes at 95°C, put on ice for 2 min and resuspended in 120 µl hybridization buffer (50% formamide, 5X SSC, 0,1% SDS, 0,1 mg/mL Herring sperm DNA) preheated to 55°C. Samples were kept in a heating block at 50°C until hybridization. Hybridizations were performed in HS400Pro hybridization stations (Tecan Group Ltd., Männedorf, Switzerland). The slides were heated at 80°C for 10 minutes, then washed once at 37°C with 0.5X SSC, 0.1% SDS for 20 seconds and once at 50°C with 2X SSC, 0.5% SDS for 20 seconds, and prehybridized for 1 hour at 65°C in 5X SSC, 0.1% SDS, 0.1 mg/ml BSA, 0.1 mg/ml Herring Sperm DNA. Next the slides were washed at 55°C with 2X SSC, 0.5% SDS for 1 minute with a 30 seconds soak and washed again at 45°C for 1 minute with the same solution. The resuspended labelled targets were injected into the chambers and hybridized for 16 hours at 45°C with sample agitation. The slides were then washed as follows: 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 2X SSC, 0.5% SDS, 1 time 1 minute at 45° in 2X SSC, 0.5% SDS, 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 37°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 23°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute 30 seconds at 23°C with 30 seconds soaking in 0.1X SSC, 1 time 30 seconds at 23°C in 0.1X SSC and 2 times 30 seconds at 23°C in milliQ filtered water. Finally slides were dried for 2 minutes 30 seconds with nitrogen gaz.

scan_protocol: Microarray Scanner: ScanArray Express (Perkin Elmer, Waltham MA, USA) Image Analysis Program: QuantArray v3.0 (Packard BioChip Technologies, Billerica, MA, USA) Slide scanning was performed at 5 micron resolution.

data_processing: Data analyses were performed using customized scripts for R and Bioconductor (http://www.r-project.org and http://www.bioconductor.org). Spots that were flagged as presenting abnormal morphology during the image processing were replaced by mean value of the remaining spots of the same probe from the other slides from the same sample type. Background intensities were subtracted from the foreground intensities. Background-subtracted data were log2-transformed and normalized using quantile correction approach.   A filtering step was applied to select positive genes to be used for further analysis. The mean intensity of spots containing buffer only was calculated for each row of sub-grids, and was taken as the minimum intensity of probes for that subgrid. A probe was called positive (detected above background) when its signal intensity was above the buffer intensity on at least 50% of slides within a given sample type. When determining differential expression, positive probes were probes that were detected according to this criterion in at least one of the tissues (e.g. phelloderm and xylem juvenile). Mean probe intensity was determined for genes represented by more than one positive probe.   The average signal intensity was determined from all of the slides available for a sample type. The genes were then ranked based on their average signal intensities within a tissue type and equally divided into 10 separate classes according to their signal intensity. Genes from class 1 or class 10 were the 10% with lowest and highest signal intensities, respectively.

organism: Picea glauca

source_name: vegetative buds

label_protocol: Total RNA (1 µg) or mRNA (10 ng) was transcribed in-vitro by using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion by Life Technologies, Austin, TX, USA), following the manufacturer’s instructions. The aaRNA (5 ug per sample) was labeled using Alexa Fluor 555 or 647 dyes (Invitrogen, Carlsbad, CA, USA), and purified as per the manufacturer’s instructions. Dye incorporation efficiency was determined by using a Nanodrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer’s instructions.

growth_protocol: Buds were collected from branches of several clonal replicates of 9-year-old trees of P. glauca regenerated from two genetically distinct somatic embryogenesis lines as described (Klimaszewska et al. 2011) during the mid-Spring when the buds were just beginning to grow. For each genotype, five biological samples each consisting of 6 buds (approximately 80 mg fresh weight) were used for analysis.

extract_protocol: All of the tissue samples were frozen in liquid nitrogen immediately after removal from the trees, the seed or tissue culture vessels, and stored at -80°C. Tissues were ground under liquid nitrogen and total RNA was extracted following Chang et al. (1993) as described in Pavy et al. (2008) for all of the sample types, except for megagametophytes where poly A+ RNA was extracted directly by using the Dynabeads mRNA Mikro kit (Dynal/Invitrogen, Oslo, Norway) following manufacturers instructions.

value: vegetative buds

tag: age of trees

tag: replicate

tag: slide batch


title: vegetative buds_rep9

description:
JF003-8044.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: vegetative buds_rep8

description:
JF003-8043.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: vegetative buds_rep5

description:
JF003-8039.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: ZT16 col 2

description: 7-day-old seedlings of WT(col-0) grown under LD were harvested at ZT16 [rep2]


title: vegetative buds_rep4

description:
JF003-8036.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: vegetative buds_rep3

description:
JF003-8032.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: ZT1 gi-2 2

description: 7-day-old seedlings of gi-2 mutant grown under LD were harvested at ZT1 [rep2]


title: vegetative buds_rep2

description:
JF003-8030.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: vegetative buds_rep1

description:
JF003-8028.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: vegetative buds_rep7

description:
JF003-8042.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: hOE-MCSs_FD1_spheres_rep1

status: Public on Jan 01 2012

city: MARSEILLE

first: El Chérif

last: Ibrahim

address: 27 Bd Jean Moulin

institute: Aix Marseille Université-CNRS

description: Gene expression of FD hOE-MSC-derived spheres

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. All data were normalized by quantile normalization.

source_name: hOE-MCSs, FD1, spheres, rep1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The medium used to generate spheres contained DMEM/F12 supplemented with ITS, 50ng/ml EGF and 50ng/ml bFGF. The neural differentiation was obtained in the presence of 1µM all-trans retinoic acid, 5µM forskolin and 15nM Sonic Hedgehog (rafnshh) for 7 days.

extract_protocol: Total RNA was isolated using the Rneasy Mini  Kit (Qiagen) with DNAse treatment on the column according to manufacturer's recommantation RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Kinetin was added the last 2 days of rafnshh-treated cells at 100µM.

tag: status

value: FD

tag: culture conditions

value: spheres

tag: treatment

tag: gender

value: Female


title: hOE-MCSs_C4_rafnshh_rep1

description: Gene expression of control rafnshh-treated hOE-MSCs

source_name: hOE-MCSs, C4, rafnshh, rep1

value: rafnshh


title: hOE-MCSs_C1_rafnshh_rep1

source_name: hOE-MCSs, C1, rafnshh, rep1

value: control


title: ZT1 col 2

description: 7-day-old seedlings of WT(col-0) grown under LD were harvested at ZT1 [rep2]


title: hOE-MCSs_FD1_rafnshh_kinetin_rep1

description: Gene expression of FD rafnshh- and kinetin-treated hOE-MSCs

source_name: hOE-MCSs, FD1, rafnshh, kinetin, rep1

value: kinetin


title: hOE-MCSs_FD2_spheres_rep1

source_name: hOE-MCSs, FD2, spheres, rep1


title: hOE-MCSs_C1_spheres_rep1

description: Gene expression of control hOE-MSC-derived spheres

source_name: hOE-MCSs, C1, spheres, rep1


title: hOE-MCSs_FD2_rafnshh_kinetin_rep1

source_name: hOE-MCSs, FD2, rafnshh, kinetin, rep1


title: PMN_control shRNA_rep2

description: RMA expression value derived from Expression Console software; all-exon analysis

value: embryo

value: primary motor neurons

tag: genotype/variation


title: hOE-MCSs_C3_spheres_rep1

source_name: hOE-MCSs, C3, spheres, rep1

value: Male


title: hOE-MCSs_FD4_rafnshh_rep1

description: Gene expression of FD rafnshh-treated hOE-MSCs

source_name: hOE-MCSs, FD4, rafnshh, rep1


title: hOE-MCSs_FD3_spheres_rep1

source_name: hOE-MCSs, FD3, spheres, rep1


title: hOE-MCSs_FD3_rafnshh_rep1

source_name: hOE-MCSs, FD3, rafnshh, rep1


title: hOE-MCSs_FD2_rafnshh_rep1

source_name: hOE-MCSs, FD2, rafnshh, rep1


title: hOE-MCSs_FD4_rafnshh_kinetin_rep1

source_name: hOE-MCSs, FD4, rafnshh, kinetin, rep1


title: hOE-MCSs_FD1_rafnshh_rep1

source_name: hOE-MCSs, FD1, rafnshh, rep1


title: hOE-MCSs_C2_rafnshh_rep1

source_name: hOE-MCSs, C2, rafnshh, rep1


title: hOE-MCSs_FD4_spheres_rep1

source_name: hOE-MCSs, FD4, spheres, rep1


title: hOE-MCSs_FD3_rafnshh_kinetin_rep1

source_name: hOE-MCSs, FD3, rafnshh, kinetin, rep1


title: hOE-MCSs_C4_spheres_rep1

source_name: hOE-MCSs, C4, spheres, rep1


title: hOE-MCSs_C3_rafnshh_rep1

source_name: hOE-MCSs, C3, rafnshh, rep1


title: Affy_TALL_2_bm

status: Public on Dec 20 2011

city: Uppsala

first: Jessica

last: Nordlund

address: Academic Hospital, Entrance 70, 3rd floor

department: Medical Sciences

country: Sweden

institute: Uppsala University

hyb_protocol: Biotinylated cRNAs were hybridized to the gene chips for 16 hours in a 45°C incubator, rotated at 60 rpm.

scan_protocol: The GeneChips were then washed and stained using the Fluidics Station 450 and scanned using the GeneChip® Scanner 3000 7G

data_processing: The data was normalized using the robust multi-array average (RMA) method  (Irizarry et al. 2003)

source_name: Bone marrow

label_protocol: Biotinylated cRNA were prepared from two micrograms of total RNA

extract_protocol: AllPrep DNA/RNA Mini Kit (Qiagen)

tag: disease state

value: acute lymphoblastic leukemia

value: bone marrow

tag: subtype

value: T-cell lineage ALL (T-ALL)


title: Affy_HeH_4_bm

value: High Hyperploidy (HeH)


title: Affy_t12-21_2_bm


title: Affy_t9-22_2_bm


title: hOE-MCSs_C2_spheres_rep1

source_name: hOE-MCSs, C2, spheres, rep1

tag: age


title: Affy_t9-22_1_bm


title: Affy_HeH_6_bm


title: HB_17_96

status: Public on Oct 27 2011

city: Baltimore

first: Carlo

last: Colantuoni

state: MD

address: 733 N Broadway

department: Neurology

institute: Johns Hopkins Univ. School of Medicine

hyb_protocol: After purification, the labeled antisense RNAs are hybridized overnight to the oligo chips in 5X SSC, 25% Formamide and 0.2% SDS buffer at 45 oC using Maui Mixer FL hybridization chambers (BioMicro Systems, Salt Lake City, UT). The slides are then washed at room temperature in a series of SSC/SDS buffers and dried by centrifugation.

scan_protocol: A laser confocal scanner (Agilent Technologies, Palo Alto, CA) was used to scan the hybridized Cy3and Cy5 probes on the chips. The fluorescent intensities at the target locations on the array were measured using the DEARRAY software (www.scanalytics.com).

data_processing: Two color intensity data was imported, background subtracted, low intensities dropped, intensities converted to log2(sample/ref), ratios loess normalized, outliers dropped (>6 MADs), missing data from low intesity cut-off were imputed. Only the 30,176 probes (out of the total 49,152 on GPL4611) that passed all quality control and other filters were used. No "cleaning" procedure has been applied to these data - see "Overall design" and "Supplemental Files" for additional data.

source_name: Postmortem dorsolateral prefrontal cortex (DLPFC BA 46/9)

label_protocol: 500 ng of each total RNA sample or Reference is reverse transcribed with an oligo dT-T7 and amplified (T7) using the Ambion MessageAmp II Kit (Cat#1753, Ambion, Austin, TX). The generated aminoallyl UTP labeled RNAs are then coupled with either Cy3 or Cy5 mono NHS ester CyDyes from GE Healthcare, Piscataway, NJ.

extract_protocol: Total RNA was extracted from ~ 100 mg of tissue using the RNeasy Kit (Qiagen) according to manufacturer’s protocol.

treatment_protocol: Total RNA was extracted from dissected frozen postmortem human brain tissue.

tag: array batch

tag: Sex

value: F

tag: race

value: AS

tag: postmortem interval (pmi)

tag: ph

tag: rna integrity number (rin)

tag: smoking history

value: No

tag: smoke at death

tag: blood ethanol

value: Negative

tag: highest education

tag: brain bank source

value: NIMH

tag: medical examiner office

value: DC

tag: surrogate variable 1 (sv1)

tag: surrogate variable 2 (sv2)

source_name: Reference RNA pooled from all samples

tag: description

value: Reference RNA pooled from all samples


title: Affy_TALL_3_bm

tag: disease state

tag: tissue

tag: subtype


title: Affy_HeH_2a_bm


title: Affy_dic9-20_3_bm


title: HB_18_53

tag: array batch

tag: age

tag: Sex

value: M

value: CAUC


title: HB_18_29

tag: race

value: AA

tag: postmortem interval (pmi)

tag: ph


title: HB_18_65

tag: rna integrity number (rin)

tag: smoking history

value: Yes

tag: smoke at death


title: Affy_t12-21_3_bm


title: HB_18_85

tag: blood ethanol

tag: highest education

tag: brain bank source

value: VA


title: Affy_HeH_7_bm


title: HB_16_18

tag: medical examiner office

tag: surrogate variable 1 (sv1)

tag: surrogate variable 2 (sv2)


title: HB_22_24

tag: description


title: HB_16_31


title: HB_20_91


title: HB_16_69


title: Affy_dic9-20_1_bm

tag: disease state

tag: tissue

tag: subtype


title: HB_17_15

tag: array batch

tag: age

tag: Sex


title: HB_16_25

tag: race

tag: postmortem interval (pmi)

tag: ph


title: HB_17_99

tag: rna integrity number (rin)

tag: smoking history

tag: smoke at death


title: HB_22_33

tag: blood ethanol

value: Positive

tag: highest education

tag: brain bank source


title: HB_17_28

tag: medical examiner office

tag: surrogate variable 1 (sv1)

tag: surrogate variable 2 (sv2)


title: HB_17_65

tag: description


title: HB_16_89


title: HB_17_47


title: HB_22_25


title: HB_16_58


title: HB_17_31


title: HB_16_83


title: HB_18_40


title: HB_22_27


title: HB_17_46


title: HB_17_79


title: HB_17_32


title: HB_18_49


title: HB_18_73

value: Other


title: HB_17_61


title: HB_22_49


title: HB_20_30


title: HB_17_76


title: HB_17_49


title: HB_16_24

value: HISP


title: HB_18_22


title: HB_22_28

value: Unknown


title: HB_18_37


title: HB_16_41


title: HB_17_19


title: HB_18_42


title: HB_18_44


title: HB_18_84


title: HB_22_29


title: HB_19_49


title: HB_20_95


title: HB_18_61


title: HB_18_13


title: HB_16_85


title: HB_18_52


title: HB_17_12


title: HB_18_26


title: HB_22_23


title: HB_16_82


title: HB_18_20


title: HB_17_68


title: HB_16_74


title: HB_17_52


title: HB_16_51


title: HB_22_32


title: HB_22_22


title: HB_20_31


title: HB_16_22


title: HB_16_34


title: HB_17_16


title: HB_17_86


title: HB_18_60


title: HB_18_80


title: HB_17_37


title: HB_16_70


title: HB_16_16


title: HB_22_31


title: HB_17_50


title: HB_16_73


title: HB_16_57


title: HB_18_72


title: HB_22_26


title: HB_17_71


title: HB_20_74


title: HB_18_28


title: HB_18_24


title: HB_16_55


title: HB_18_14


title: HB_16_46


title: HB_22_51


title: HB_18_79


title: HB_16_68


title: HB_18_25


title: HB_17_30


title: HB_18_45


title: HB_17_18


title: HB_20_92


title: HB_17_64


title: HB_16_17


title: HB_16_67


title: HB_20_94


title: HB_20_98


title: HB_16_37


title: HB_20_32


title: HB_18_41


title: HB_20_81


title: HB_20_85


title: HB_16_64


title: HB_20_77


title: HB_17_20


title: HB_22_30


title: HB_17_34


title: HB_20_96


title: HB_17_29


title: HB_17_54


title: HB_18_39


title: HB_20_90


title: HB_16_87


title: HB_17_51


title: HB_16_79


title: HB_18_12


title: HB_22_34


title: HB_18_88


title: HB_17_69


title: HB_17_14


title: HB_16_65


title: HB_16_21


title: HB_20_70


title: HB_16_53


title: HB_18_51


title: HB_17_84


title: HB_17_60


title: HB_16_63


title: HB_17_35


title: HB_18_59


title: HB_20_72


title: HB_18_36


title: HB_16_19


title: HB_17_82


title: HB_18_23


title: HB_18_78


title: HB_16_71


title: HB_17_77


title: HB_20_71


title: HB_18_82


title: HB_20_78


title: HB_20_89


title: HB_18_57


title: HB_18_19


title: HB_17_21


title: HB_18_21


title: HB_18_11


title: HB_16_14


title: HB_20_59

value: BTB


title: HB_18_50

value: F


title: HB_18_69


title: HB_17_62


title: HB_18_70


title: HB_20_37


title: HB_16_30


title: HB_20_35


title: HB_18_90


title: HB_20_41


title: HB_22_50


title: HB_17_67


title: HB_20_68


title: HB_19_52


title: HB_22_54


title: HB_22_53


title: HB_18_67


title: HB_17_45


title: HB_17_36


title: HB_20_58


title: HB_18_76


title: HB_20_79


title: HB_22_66


title: HB_20_40


title: HB_20_49


title: HB_20_55


title: HB_22_60


title: HB_20_65


title: HB_22_52


title: HB_17_17


title: HB_17_11


title: HB_20_43


title: HB_20_66


title: HB_20_53


title: HB_20_57


title: HB_20_52


title: HB_20_38


title: HB_22_56


title: HB_20_64


title: HB_20_46


title: HB_22_38


title: HB_22_36


title: HB_16_20


title: HB_17_66


title: HB_22_37


title: HB_22_46


title: HB_18_43


title: HB_16_72


title: HB_16_66


title: HB_20_63

value: Unavailable


title: HB_22_55


title: HB_19_50

value: No


title: HB_16_90

value: Negative


title: HB_20_67


title: HB_22_40


title: HB_22_47

value: NIMH


title: HB_18_81


title: HB_20_60


title: HB_20_62


title: HB_20_39


title: HB_17_27

value: DC


title: HB_18_86

value: Reference RNA pooled from all samples


title: HB_16_23


title: HB_20_44

value: M


title: HB_20_33

value: CAUC


title: HB_22_45


title: HB_17_78

value: AA


title: HB_22_39


title: HB_18_46


title: HB_18_15


title: HB_17_94


title: HB_20_47


title: HB_16_33


title: HB_19_51


title: HB_22_58


title: HB_20_73


title: HB_18_54


title: HB_17_63


title: HB_18_71


title: HB_16_56


title: HB_16_77


title: HB_22_67


title: HB_20_34


title: HB_16_27

value: Yes


title: HB_20_42


title: HB_16_61


title: HB_22_41


title: HB_17_25


title: HB_18_33


title: HB_22_43


title: HB_20_83


title: HB_18_89


title: HB_17_59


title: HB_20_75


title: HB_17_26


title: HB_16_28


title: HB_18_17


title: HB_18_68


title: HB_16_76


title: HB_20_86


title: HB_17_58


title: HB_20_97


title: HB_20_82


title: HB_20_88


title: HB_18_64


title: HB_16_62


title: HB_20_84


title: HB_18_35


title: HB_17_75


title: HB_20_76


title: HB_20_27


title: HB_22_42


title: HB_17_74


title: HB_20_80


title: HB_18_58


title: HB_18_16


title: HB_20_29


title: HB_22_35


title: HB_17_91


title: HB_16_29


title: HB_18_34


title: Chlamydomonas reinhardtii 2137 - Copper sufficient - TAP - 4

status: Public on Oct 24 2011

city: Los Angeles

first: Sabeeha

last: Merchant

state: California

address: 607 Charles E. Young Drive East

department: Department of Chemistry and Biochemistry

institute: University of California Los Angeles

data_processing:
Processed sequence files from the Solexa pipeline output were aligned against the v.3.1 assembly of the Chlamydomonas genome. The SOAP alignment program (Li et al., 2008) was used to map the short reads in two steps. In a first alignment round, the raw sequences were aligned to the genomic sequence with a tolerance of up to two mismatches and no indels. For those sequences that did not align to the genome a second round alignment was performed in which we recursively trim one base at a time (up to 21-mers or half of the read length) at either the 5’ or 3’ end of the reads until we found a (perfect) match to the genome.
Alignments from both rounds were tagged as either unique or not unique and combined. The most 5’ position of each alignment is recorded along with the length of the alignment. For differential expression analysis, per-base unique hits from both strands were pooled and summed across the genome to obtain gene counts. Additional normalization was performed to estimate gene expression levels.

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas cultured cells

growth_protocol: Cultures were grown in Tris-acetate-phosphate (TAP), or minimal medium (TP) at 24 C with shaking (180 rpm), and under continuous light (~90x10-6mol/m2/s)

extract_protocol: Nucleic acids were isolated and analyzed according to standard procedures by hybridization or on an Agilent 2100 Bioanalyzer. For quantitative transcriptomes, RNAs were sequenced at Illumina by either the NlaIII tag protocol or by whole transcriptome analysis.

treatment_protocol: Inoculum cultures were maintained under copper-deficient conditions. The minimal medium cultures were under constant aeration. Cells were collected at a density of 3x106 cell ml-1 (steady-state).

tag: genetic background

value: Chlamydomonas reinhardtii 2137

tag: genotype

value: wt

tag: treatment

value: copper sufficient

tag: medium

value: TAP

tag: analysis

value: Illumina's RNA-Seq whole transcriptome analysis

tag: sequencing cycles / read length

tag: library type

value: paired-end

tag: mean/std insert size


title: Chlamydomonas reinhardtii 2137 - Copper sufficient - Minimal media - 4

value: Minimal media


title: Chlamydomonas reinhardtii 2137 - Copper sufficient - Minimal media - 2


title: Chlamydomonas reinhardtii 2137 - Copper deficient - TAP - 4

value: copper deficient


title: Chlamydomonas reinhardtii 2137 - Copper deficient - Minimal media - 2


title: Chlamydomonas reinhardtii 2137 - Copper deficient - Minimal media - 4


title: 315T rep3

status: Public on Jul 07 2011

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

description: 315T replicate 3

hyb_protocol: A total hybridisation volume of 15ul is prepared for each sample and    15ul loaded into a single array on the Sentrix Human-HT12v4 Beadchip.     A total of 12 different labelled samples can be loaded into 12    individual arrays per beadchip.  The chip is hybridised at 58C for 16    hours in an oven with a rocking platform.  After hybridisation, the    chip is washed using the appropriate protocols as outlined in the    illumina manual.  Upon completion of the washing, the chips are then    coupled with Cy3 and scanned in the illumina BeadArray Reader.

scan_protocol: Arrays were scanned in the Illumina BeadArray Reader.

data_processing: The scanner operating software, GenomeStudio, converts the signal on the    array into a TXT file for analysis. The data were then calibrated and quantile normalized using the neqc method of Shi et al. (2010) [PMID:20929874]. This analysis was was carried out in R using the limma package.

source_name: xenograft tumor

label_protocol: Human total RNA was quality ascertained using the Agilent Bioanalyser    2100 using the NanoChip protocol.  A total of 500ng was labelled using    the Ambion Total Prep RNA amplification kit (Cat. No. IL1791).  The    quantity of labelled product was ascertained using the Agilent    Bioanalyser 2100 using the NanoChip protocol.  A total of 750ng of    labelled cRNA was then prepared for hybridisation to the Sentrix Human-   HT12v4 Beadchip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that    includes GEX-HYB Hybridisation Buffer (supplied with the beadchip).

extract_protocol: RNA was extracted using Invotrogen Trizol Reagent    in accordance with the prescribed protocol provided with the kit.    DNase treatment was performed using the QIAGEN RNase free DNase Set    prior to RNA purification using the QIAGEN RNAeasy kit in accordance    with the prescribed protocol provided with the kit. Quality control    was performed with Agilent Bioanalyser.

tag: tumor id

tag: tumor type

value: human breast tumor xenograft


title: EmbryoPairedEnd114nt_2

status: Public on Jun 16 2011

city: Aurora

first: Jianbin

last: Wang

state: CO

address: 12801 East 17th Ave

department: Biochemistry and Molecular Genetics

institute: University of Colorado Denver

description: Ascaris mixed samples from 0 - 64 hr embryos

data_processing: Following removal of the adaptor sequences from the sequence reads, high quality reads with >= 36 nt in length were selected.

organism: Ascaris suum

source_name: Ascaris sample

growth_protocol: For the germinal zone of the testis and ovary, the distal 5 cm of the gonad was isolated from live worms and stored at -80°C. Other regions of the gonads were dissected from live worms and either frozen immediately at -80°C or lysed by homogenization in Trizol and then frozen. Ascaris fertilized eggs were harvested from 4 regions of female uteri (Zygote 1-4) by treatment with 0.5 N NaOH, followed by extensive washing in water, and then stored at 4 °C with 5 volumes of PBS (pH 2.0). For embryonation, the fertilized eggs from final proximal region of the uterus (Zygote-4 = 0 hr embryos) were incubated at 30 °C in PBS (pH 2.0) with constant (100 rpm) shaking for the desired time. The outer shell/membranes were de-coated with 0.4 N KOH/1.4% sodium hypochlorite at 4 °C (zygotes from regions 1-4) or 30°C (developing embryos and larvae) for 180 or 90 minutes, respectively, prior to RNA preparation. RNA from fertilized eggs in the uterus and early embryos (0 hr to 8 days) were extracted directly with Trizol (Invitrogen). Frozen L1, L2, testis and ovary samples were first ground with a mortar and pestle in liquid nitrogen and then extracted with Trizol.

extract_protocol: cDNA libraries were prepared from polyadenylated RNA (2x oligo-dT purified using μMACS™ mRNA Isolation Kit, Miltenyi Biotec). Two types of libraries were prepared: 1) sheared, full-length cDNA synthesized using a combination of oligo-dT and random hexamer priming and 2) cDNA prepared from RNA first chemically sheared and then double-stranded cDNA prepared using ramom hexamer priming. For the chemically sheared library, RNA was treated for 75-150 sec with RNA fragmentation buffer (Ambion) at 70°C to generate RNA fragments 150-400 nt in length. First stand cDNA was prepared by random priming (3-6 µg random hexamers/1 µg of A+ RNA) and second stranded cDNA synthesis was carried out using a SuperScript® Double-Stranded cDNA Synthesis Kit (Invitrogen).  Solexa paired-end adaptors were added to the blunt cDNA as described by Illumina, cDNA fragments of 300-400 bp in length were gel purified, the fragments amplified using 17 PCR cycles, and paired-end, 76-120 nt reads were generated as described on the Illumina GAII.

tag: library preparation

value: Paired-end 114 nt (insert:200-300 nt)

tag: library id

tag: tissue

value: mixed samples from 0 - 64 hr embryos


title: OvaryPairedEnd120nt_2

description: Ascaris ovary germinal zone

value: Paired-end 120 nt (insert:200-300 nt)

value: ovary germinal zone


title: LarvaePairedEnd120nt_2

description: Ascaris mixed samples from 128 cells - L2

value: mixed samples from 128 cells - L2


title: FemaleReproductivePairedEnd120nt_2

description: Ascaris complete female reproductive system

value: complete female reproductive system


title: MixedSamplesPairedEnd120nt_2

description: Ascaris mixed samples of germlines and embryos, full length cDNA sheared


title: TestisPairedEnd114nt_2

description: Ascaris testis germinal zone

value: testis germinal zone


title: EmbryoPairedEnd76nt_2

value: Paired-end 76 nt (insert:200-300 nt)


title: TestisPairedEnd76nt_2

description: Ascaris testis germinal zone


title: WholeMalePairedEnd120nt_2

description: Ascaris whole male

value: whole male


title: 838T rep2

description: 838T replicate 2


title: 838T rep1

description: 838T replicate 1


title: 838T rep3

description: 838T replicate 3


title: Lonely 5392306056_D

status: Public on Mar 16 2011

first: Steve

last: Cole

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

hyb_protocol: Standard Illumina beadarray hybridization protocol for gene expression profiling (carried out in UCLA Southern California Genotyping Consortium Core Laboratory).

scan_protocol: Standard Illumina beadarray scan protocol for gene expression profiling (carried out in UCLA Southern California Genotyping Consortium Core Laboratory).

data_processing: Gene expression values derived from Illumina GenomeStudio software.

source_name: Peripheral blood mononuclear cells

label_protocol: Standard Illumina beadarray probe synthesis for gene expression profiling (carried out in UCLA Southern California Genotyping Consortium Core Laboratory).

extract_protocol: Human peripheral blood leukocytes were isolated and total RNA was extracted using Qiagen RNEasy.

tag: lonely

tag: age

tag: female

tag: black

tag: hispanic

tag: married

tag: logincome

tag: bmi

tag: granpct

tag: lymphpct

tag: monopct


title: 315T rep2

description: 315T replicate 2


title: NonLonely 5412581001_A


title: NonLonely 5392306044_G


title: NonLonely 5412581031_G


title: NonLonely 5412581020_A


title: NonLonely 5412581075_D


title: NonLonely 5392306037_B


title: Lonely 5392306056_A


title: NonLonely 5412581001_H


title: NonLonely 5412581075_C


title: NonLonely 5412581031_A


title: NonLonely 5412581001_E


title: NonLonely 5392306004_G


title: NonLonely 5412581024_H


title: Lonely 5412581001_B


title: Lonely 5412581077_H


title: NonLonely 5262667043_H


title: NonLonely 5392306037_F


title: NonLonely 5412581020_H


title: NonLonely 5412581077_C


title: 315T rep1

description: 315T replicate 1


title: NonLonely 5392306059_C


title: Lonely 5412581031_H


title: NonLonely 5412581024_C


title: NonLonely 5412581077_E


title: NonLonely 5262667043_C


title: Lonely 5412581001_G


title: NonLonely 5262667043_A


title: NonLonely 5262667043_G


title: NonLonely 5392306059_B


title: Lonely 5412581001_D


title: Lonely 5392306037_A


title: NonLonely 5392306004_D


title: NonLonely 5412581024_F


title: NonLonely 5392306044_H


title: NonLonely 5412581077_F


title: NonLonely 5412581020_D

value: missing


title: NonLonely 5392306059_D


title: NonLonely 5412581024_A


title: Lonely 5412581024_G


title: Lonely 5392306056_B


title: NonLonely 5412581001_F


title: NonLonely 5392306004_B


title: NonLonely 5392306044_E


title: Lonely 5412581075_E


title: NonLonely 5392306056_C


title: NonLonely 5392306056_H


title: Lonely 5412581020_B


title: NonLonely 5412581075_A


title: NonLonely 5392306044_F


title: Lonely 5392306004_H


title: Lonely 5412581020_C


title: NonLonely 5392306044_D


title: Lonely 5392306037_E


title: Lonely 5392306004_C


title: NonLonely 5412581031_F


title: NonLonely 5412581031_E


title: NonLonely 5392306044_C


title: NonLonely 5412581031_B


title: NonLonely 5392306056_E


title: NonLonely 5412581024_D


title: NonLonely 5412581020_F


title: NonLonely 5262667043_E


title: NonLonely 5412581024_B


title: NonLonely 5392306037_G


title: NonLonely 5392306059_A


title: NonLonely 5392306037_C


title: NonLonely 5412581077_D


title: Lonely 5412581031_D


title: Lonely 5412581075_B


title: NonLonely 5392306056_G


title: NonLonely 5392306059_G


title: Lonely 5392306059_H


title: Lonely 5412581077_A


title: Lonely 5412581077_B


title: NonLonely 5392306037_D


title: NonLonely 5412581020_G


title: NonLonely 5262667043_F


title: NonLonely 5392306059_F


title: NonLonely 5412581024_E


title: Lonely 5392306004_E


title: NonLonely 5412581031_C


title: NonLonely 5392306059_E


title: NonLonely 5392306004_A


title: NonLonely 5412581020_E


title: NonLonely 5392306037_H


title: NonLonely 5262667043_B


title: NonLonely 5392306044_B


title: NonLonely 5392306004_F


title: NonLonely 5392306056_F


title: Lonely 5392306044_A


title: NonLonely 5262667043_D


title: NonLonely 5412581077_G


title: NonLonely 5412581001_C


title: histologically normal breast epithelium from prophylactic mastectomy patient sample 2

status: Public on Jun 01 2010

city: Boston

first: Kelly

last: Graham

state: MA

address: 650 Albany Street

department: Hematology/Oncology

institute: Boston University School of Medicine

description: Gene Expression data from case 276P:Histologically Normal Epithelium from Prophylactic Mastectomy Patient

hyb_protocol: 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)

scan_protocol: The stained arrays were scanned using a G2500 Scanner (Agilent)

data_processing: .cel files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.

label_protocol: T7-based RNA ampliﬁcation was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).

extract_protocol: RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).

treatment_protocol: Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most HN samples were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells. Some HN lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions.

tag: specimen

value: Prophylactic Mastectomy

tag: disease state

value: control

value: breast epithelium


title: histologically normal breast epithelium from prophylactic mastectomy patient sample 3

description: Gene Expression data from case 451P:Histologically Normal Epithelium from Prophylactic Mastectomy Patient


title: histologically normal breast epithelium from ER- breast cancer patient sample 2

description: Gene Expression data from case 289H:Histologically Normal Epithelium from ER- Breast Cancer Patient

value: ER- Breast Cancer

value: breast cancer


title: histologically normal breast epithelium from prophylactic mastectomy patient sample 4

description: Gene Expression data from case 242P:Histologically Normal Epithelium from Prophylactic Mastectomy Patient


title: histologically normal breast epithelium from ER- breast cancer patient sample 7

description: Gene Expression data from case 272H:Histologically Normal Epithelium from ER- Breast Cancer Patient


title: histologically normal breast epithelium from ER- breast cancer patient sample 1

description: Gene Expression data from case 319H:Histologically Normal Epithelium from ER- Breast Cancer Patient


title: reduction mammoplasty breast epithelium sample 15

description: Gene Expression data from case 361R:Reduction Mammoplasty Epithelium

source_name: Reduction Mammoplasty Epithelium

value: Reduction Mammoplasty


title: histologically normal breast epithelium from ER+ breast cancer patient sample 2

description: Gene Expression data from case 379H:Histologically Normal Epithelium from ER+ Breast Cancer Patient

value: ER+ Breast Cancer


title: histologically normal breast epithelium from ER+ breast cancer patient sample 7

description: Gene Expression data from case 237H:Histologically Normal Epithelium from ER+ Breast Cancer Patient


title: histologically normal breast epithelium from ER- breast cancer patient sample 6

description: Gene Expression data from case 322H:Histologically Normal Epithelium from ER- Breast Cancer Patient


title: histologically normal breast epithelium from ER- breast cancer patient sample 3

description: Gene Expression data from case 364H:Histologically Normal Epithelium from ER- Breast Cancer Patient


title: histologically normal breast epithelium from ER- breast cancer patient sample 8

description: Gene Expression data from case 226H:Histologically Normal Epithelium from ER- Breast Cancer Patient


title: histologically normal breast epithelium from ER+ breast cancer patient sample 5

description: Gene Expression data from case 380H:Histologically Normal Epithelium from ER+ Breast Cancer Patient


title: reduction mammoplasty breast epithelium sample 18

description: Gene Expression data from case 305R:Reduction Mammoplasty Epithelium


title: histologically normal breast epithelium from prophylactic mastectomy patient sample 1

description: Gene Expression data from case 395P:Histologically Normal Epithelium from Prophylactic Mastectomy Patient


title: histologically normal breast epithelium from ER+ breast cancer patient sample 9

description: Gene Expression data from case 232H:Histologically Normal Epithelium from ER+ Breast Cancer Patient


title: histologically normal breast epithelium from ER+ breast cancer patient sample 4

description: Gene Expression data from case 304BH:Histologically Normal Epithelium from ER+ Breast Cancer Patient


title: histologically normal breast epithelium from prophylactic mastectomy patient sample 6

description: Gene Expression data from case 249P:Histologically Normal Epithelium from Prophylactic Mastectomy Patient


title: histologically normal breast epithelium from ER+ breast cancer patient sample 6

description: Gene Expression data from case 446BH:Histologically Normal Epithelium from ER+ Breast Cancer Patient


title: histologically normal breast epithelium from ER+ breast cancer patient sample 1

description: Gene Expression data from case 316H:Histologically Normal Epithelium from ER+ Breast Cancer Patient


title: histologically normal breast epithelium from ER- breast cancer patient sample 5

description: Gene Expression data from case 273H:Histologically Normal Epithelium from ER- Breast Cancer Patient


title: histologically normal breast epithelium from ER+ breast cancer patient sample 3

description: Gene Expression data from case 251H:Histologically Normal Epithelium from ER+ Breast Cancer Patient


title: histologically normal breast epithelium from ER+ breast cancer patient sample 8

description: Gene Expression data from case 388AH:Histologically Normal Epithelium from ER+ Breast Cancer Patient


title: histologically normal breast epithelium from ER- breast cancer patient sample 4

description: Gene Expression data from case 342H:Histologically Normal Epithelium from ER- Breast Cancer Patient


title: histologically normal breast epithelium from ER- breast cancer patient sample 9

description: Gene Expression data from case 333H:Histologically Normal Epithelium from ER- Breast Cancer Patient


title: histologically normal breast epithelium from prophylactic mastectomy patient sample 5

description: Gene Expression data from case 446AP:Histologically Normal Epithelium from Prophylactic Mastectomy Patient


title: reduction mammoplasty breast epithelium sample 16

description: Gene Expression data from case 419R:Reduction Mammoplasty Epithelium


title: reduction mammoplasty breast epithelium sample 17

description: Gene Expression data from case 310R:Reduction Mammoplasty Epithelium


title: N2_B_l1 (454)

status: Public on Mar 04 2010

first: Lukas

last: Habegger

address: 266 Whitney Ave

description: RNA-Seq; polyA selected mRNA

data_processing: Reads were obtained and aligned to the human reference genome (hg18) using BOWTIE for Illumina single-end reads, ELAND for Illumina paired-end reads, and BLAT for the long 454 reads.  Subsequently, the mapped reads were converted into signal track (WIG) files by counting the number of mapped reads at each nucleotide position.  The counts were then normalized by the total number of mapped reads per million.

source_name: Neural differentiation; neural progenitors

growth_protocol: Two neural differentiation strategies were used. In one approach (A) hESC H1 line was differentiated and cultured using feeder-free chemically defined adherent cell culture system through three stages: N1, an initiation stage; N2, a Neural Progenitor Cell (NPC) stage which produces only neurons upon further differentiation; and N3 which produces both neurons and glial cells. In the second approach (B), neural progenitors (N2-B) were generated from undifferentiated H1 hESCs via embryoid body like neurosphere formation. In each case, standard protocols involving bone morphogenic protein (BMP) signaling antagonists (Noggin) and basic fibroblast growth factor (bFGF) were used

extract_protocol: Solexa sequencing: mRNA was fragmented using 10X Fragmentation Buffer (Ambion) and double-stranded cDNA was synthesized using SuperScript II (invitrogen) reverse transcriptase and random primers. DNA sequencing followed the instructions of the mRNA-Sequencing Sample Prep Kit (Illumina). 454 sequencing: Single-stranded cDNA library was synthesized and adapters were ligated (Supporting Information Appendix) and sequenced using the emPCR II Kit (Amplicon A) and on the 454 Genome Sequencer FLX instrument following the manufacturer’s instructions.  GS FLX Titanium cDNA Libraries were prepared and sequenced at the 454 Life Sciences Sequencing Centre (Branford, CT).

tag: developmental stage

value: neural progenitors


title: hESC_B_l1 (454)

description: RNA-Seq; polyA selected mRNA

source_name: Embryonic stem cells

value: Embryonic stem cells


title: reduction mammoplasty breast epithelium sample 13

description: Gene Expression data from case 406R:Reduction Mammoplasty Epithelium


title: reduction mammoplasty breast epithelium sample 14

description: Gene Expression data from case 396R:Reduction Mammoplasty Epithelium


title: reduction mammoplasty breast epithelium sample 12

description: Gene Expression data from case 383R:Reduction Mammoplasty Epithelium


title: koryakE84

status: Public on Nov 30 2010

type: genomic

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

description: Genomic DNA extracted from blood was genotyped using Human660W-Quad v1.0   Genotyping BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing:
Genomic DNA extracted from blood was genotyped using Infinium  Human660W-Quad v1.0 Genotyping BeadChips (Illumina).
Image data was analyzed using Genomestudio v2009.2 with GT module 1.5.16 (Illumina).

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

tag: gender

value: Male

tag: population

value: Koryaks

tag: region

value: Siberia

value: blood


title: alveolar macrophages, smoker 230

status: Public on Aug 10 2009

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: alveolar macrophages obtained from bronchoalveolar lavage

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: Age

tag: Sex

value: F

tag: Ancestry

value: African

tag: Smoking status

value: smoker, 20 pack-years


title: reduction mammoplasty breast epithelium sample 5

description: Gene Expression data from case 373R:Reduction Mammoplasty Epithelium

tag: tissue


title: reduction mammoplasty breast epithelium sample 9

description: Gene Expression data from case 368R:Reduction Mammoplasty Epithelium


title: chukchi113

value: Female

value: Chukchis


title: reduction mammoplasty breast epithelium sample 6

description: Gene Expression data from case 350R:Reduction Mammoplasty Epithelium

value: control


title: reduction mammoplasty breast epithelium sample 1

description: Gene Expression data from case 360R:Reduction Mammoplasty Epithelium

value: breast epithelium


title: reduction mammoplasty breast epithelium sample 2

description: Gene Expression data from case 352R:Reduction Mammoplasty Epithelium


title: reduction mammoplasty breast epithelium sample 11

description: Gene Expression data from case 402R:Reduction Mammoplasty Epithelium


title: alveolar macrophages, smoker 195

value: European

value: smoker, 16 pack-years


title: reduction mammoplasty breast epithelium sample 8

description: Gene Expression data from case 357R:Reduction Mammoplasty Epithelium

value: Reduction Mammoplasty


title: alveolar macrophages, smoker 183

value: M


title: alveolar macrophages, smoker 206

value: Hispanic

value: smoker, 51 pack-years


title: alveolar macrophages, smoker 159

value: smoker, 3.8 pack-years


title: alveolar macrophages, smoker 177

value: smoker, 38 pack-years


title: reduction mammoplasty breast epithelium sample 7

description: Gene Expression data from case 309R:Reduction Mammoplasty Epithelium


title: alveolar macrophages, smoker 155

value: smoker, 7.6 pack-years


title: alveolar macrophages, smoker 164

value: smoker, 44.3 pack-years


title: alveolar macrophages, smoker 161

value: smoker, 5 pack-years


title: alveolar macrophages, smoker 136

value: smoker, 26 pack-years


title: alveolar macrophages, smoker 134

value: F

value: smoker, 20 pack-years


title: alveolar macrophages, smoker 120

value: African

value: smoker, 30 pack-years


title: alveolar macrophages, smoker 130

value: smoker, 12 pack-years


title: reduction mammoplasty breast epithelium sample 3

description: Gene Expression data from case 347R:Reduction Mammoplasty Epithelium

value: control

value: breast epithelium


title: B140H_B

status: Public on Mar 01 2010

city: Minneapolis

first: David

middle: A.

last: Largaespada

state: MN

address: 2231 6th Street SE

department: Dept. of Genetics, Cell Biology and Development, Cancer Center

institute: The University of Minnesota

description: Gene expression in an Ara-C-resistant AML cell line.

hyb_protocol: 15 micrograms labeled cRNA under standard conditions (Affymetrix, Santa Clara, CA).

scan_protocol: Standard (Affymetrix, Santa Clara, CA).

data_processing: Data generated using robust multiarray average (RMA).

source_name: B140H murine leukemia cell line derived from BXH-2 mice

label_protocol: MessageAmpTM III RNA Amplification Kit (Ambion, Austin, TX).

growth_protocol: Passaged in ASM media in absence of Ara-C.

extract_protocol: RNeasy Midi Kit (QIAGEN, Valencia, CA).

treatment_protocol: Exposed to increasing concentrations of Ara-C.

tag: cell line

tag: cell type

value: murine leukemia cells

tag: ara-c sensitivity

value: resistant


title: alveolar macrophages, smoker 087

value: M

value: Hispanic


title: alveolar macrophages, non-smoker 083

value: non-smoker


title: B117P_B

description: Gene expression in an Ara-C-sensitive AML cell line.

source_name: B117P murine leukemia cell line derived from BXH-2 mice

value: sensitive


title: B140P_B

source_name: B140P murine leukemia cell line derived from BXH-2 mice


title: alveolar macrophages, non-smoker 064


title: alveolar macrophages, smoker 129

value: smoker, 11 pack-years


title: alveolar macrophages, non-smoker 071


title: B117H_B

source_name: B117H murine leukemia cell line derived from BXH-2 mice


title: alveolar macrophages, smoker 103

value: smoker, 15 pack-years


title: alveolar macrophages, smoker 122

value: smoker, 3 pack-years


title: alveolar macrophages, smoker 125

value: smoker, 19 pack-years


title: alveolar macrophages, non-smoker 059_089

value: F


title: alveolar macrophages, non-smoker 076


title: alveolar macrophages, smoker 094

value: smoker, 45 pack-years


title: alveolar macrophages, non-smoker 045

value: African


title: alveolar macrophages, smoker 114

value: smoker, 22 pack-years


title: alveolar macrophages, smoker 112

value: European

value: smoker, 23 pack-years


title: ec_stat_4

status: Public on Nov 04 2009

city: La Jolla

first: Bernhard

last: Palsson

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

description: This sample is of wild-type E. coli MG1655 under stationary condition. It is the fourth of three biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by UCSD GeneChip Core, following Nimblegen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scan was performed with an Axon GenePix 4000B scanner by UCSD GeneChip Core, following Nimblegen standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli K12 MG1655, M9 complete medium, stationary phase

label_protocol: Labeling was performed with an amino-allyl indirect labeling protocol followed by a Dnase I fragmentation step.

growth_protocol: E. coli MG1655 strain was cultured in M9 complete medium at 37 °C with constant agitation and harvested at stationary phase. (OD600nm ~ 1.5)

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Thermo NanoDrop 1000.

tag: medium

value: M9 complete medium

tag: growth phase

value: stationary phase

tag: genotype

value: Wild type


title: alveolar macrophages, non-smoker 059

value: M


title: alveolar macrophages, smoker 119

value: smoker, 33 pack-years


title: alveolar macrophages, non-smoker 060

value: non-smoker


title: alveolar macrophages, non-smoker 029


title: alveolar macrophages, non-smoker 066


title: alveolar macrophages, non-smoker 023


title: alveolar macrophages, non-smoker 042


title: ec_stat_5

description: This sample is of wild-type E. coli MG1655 under stationary condition. It is the fifth of three biological replicates used in this experiment, each from separate cultures.


title: brain, adrenal medulla: 2-Foggy_12_som_e1_le1

status: Public on Oct 28 2008

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

description: Foggy(DelCter) RNA injected 12-somite embryos

source_name: brain, adrenal medulla


title: brain, adrenal medulla: 3-Control_12_som_e1_le1

description: control RNA injected 12-somite embryos


title: brain, adrenal medulla: 6-Foggy36_e1_le1

description: embryonic brain


title: ec_stat_3

description: This sample is of wild-type E. coli MG1655 under stationary condition. It is the third of three biological replicates used in this experiment, each from separate cultures.


title: brain, adrenal medulla: 4-WT36_e1_le1

description: embryonic brain


title: brain, adrenal medulla: 5-Foggy36_e1_le1

description: embryonic brain


title: alveolar macrophages, non-smoker 022


title: brain, adrenal medulla: 2-Control_12_som_e1_le1

description: control RNA injected 12-somite embryos


title: brain, adrenal medulla: 3-Foggy_12_som_e1_le1


title: brain, adrenal medulla: 5-WT36_e1_le1

description: embryonic brain


title: brain, adrenal medulla: 1-Control_12_som_e1_le1

description: control RNA injected 12-somite embryos


title: brain, adrenal medulla: 1-Foggy36_e1_le1

description: embryonic brain


title: brain, adrenal medulla: 2-Foggy36_e1_le1

description: embryonic brain


title: brain, adrenal medulla: 4-Foggy36_e1_le1

description: embryonic brain


title: brain, adrenal medulla: 1-WT36h_e1_le1

description: embryonic brain


title: brain, adrenal medulla: 1-Foggy_12_som_e1_le1


title: brain, adrenal medulla: 6-WT36_e1_le1

description: embryonic brain


title: HighLonely 2

status: Public on Nov 02 2007

description: Affymetrix U133A

hyb_protocol: Standard Affymetrix hybridization protocol for gen expression profiling (carried out in UCLA DNA Microarray Core).

scan_protocol: Standard Affymetrixscan protocol for gene expression profiling (carried out in UCLA DNA Microarray Core).

data_processing: RMA (RMAExpress) processing of Affymetrix .CEL files generated by UCLA DNA Microarray Core.

source_name: Peripheral blood leukocytes from individuals with high levels of social isolation

label_protocol: Standard Affymetrix probe synthesis for gene expression profiling (carried out in UCLA DNA Microarray Core).

extract_protocol: Peripheral blood leukocytes were isolated from fresh whole blood by ficol density gradient, and total RNA was extracted using Qiagen RNEasy.

tag: HighLonely


title: LowLonely 3

description: Affymetrix U133A

source_name: Peripheral blood leukocytes from individuals with low levels of social isolation

tag: LowLonely


title: LowLonely 2

description: Affymetrix U133A


title: HighLonely 4

description: Affymetrix U133A


title: alveolar macrophages, smoker 023

status: Public on Aug 01 2008

tag: age

tag: sex

tag: ancestry

tag: smoking status

value: smoker, 20 pack-years


title: LowLonely 1

description: Affymetrix U133A


title: brain, hippocampus: C-1-2_e1_le1

status: Public on Jun 24 2008

description:
rat hippocampus
Treatment, type=pharmacogenomic_treatment, description=Control diet, CFC training

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5

organism: Rattus norvegicus

source_name: brain, hippocampus

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

tag: hippocampus


title: HighLonely 6

description: Affymetrix U133A


title: LowLonely 6

description: Affymetrix U133A


title: LowLonely 8

description: Affymetrix U133A


title: Embryonic Stem Cells, Cell line: H9 hES cell derived d17 definitive neural epithelial pool #1_e1_le1

status: Public on Apr 19 2008

source_name: Embryonic Stem Cells, Cell line


title: HighLonely 3

description: Affymetrix U133A


title: LowLonely 4

description: Affymetrix U133A


title: HighLonely 1

description: Affymetrix U133A


title: brain, adrenal medulla: 3-Foggy36_e1_le1

description: embryonic brain


title: brain, hippocampus: C-3-1_e1_le1

description:
rat hippocampus
Treatment, type=pharmacogenomic_treatment, description=Control diet, naive animals


title: LowLonely 7

description: Affymetrix U133A


title: LowLonely 5

description: Affymetrix U133A


title: HighLonely 5

description: Affymetrix U133A


title: blood, Blood: 24h-control-1_e1_le1

status: Public on Apr 12 2008

description:
no nicotine treatment
Treatment, type=incubate

source_name: blood, Blood