title: CD8mem_CP_4PCD_Rh23003

status: Public on Aug 09 2012

city: Cleveland

first: Peter

middle: A

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

description: CD8mem T cells sort  from CP animal at 4PCD

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to to Human HT12 V4 BeadChips (Illumina) at 58°C for 20 hours.

scan_protocol: The arrays were scanned using Illumina’s iSCAN and quantified using Genome Studio (Illumina).

data_processing:
Analysis of the GenomeStudio output data was conducted using the R statistical language and various software packages from Bioconductor. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation. Technical replicates were PC225)
software packages and versions: R 2.14.12; Biobase 2.14.0; Limma 3.10.3; impute 1.28.0; bioDist 1.26.0; ComBat (unversioned, downloaded March 2010 from http://www.bu.edu/jlab/wp-assets/ComBat/Download.html)

organism: Macaca mulatta

source_name: Sorted CD8+ and CD4+ memory T cells of mononuclear cell preparation from lymph nodes

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct Hybridization protocol

extract_protocol: RNA was isolated using RNeasy Micro Kits (Qiagen) according to the manufacturer’s protocol.  The isolated total RNA was checked for quantity and quality using a NanoDrop 2000c (Thermo Fisher Scientific) and an Experion Electrophoresis System.  Samples with an RQI classification ≥7.0 were selected to proceed downstream to amplification.   Samples were normalized at 50ng for input and amplified using Illumina TotalPrep RNA amplification kits (Ambion) according to the manufacturer’s protocol.

tag: subject

tag: cohort

tag: lav

tag: protection

value: CP

tag: group

value: B

value: lymph node

tag: sort

tag: time

tag: barcode


title: C_4PCD_Rh24271

type: RNA

country: USA

description: LN from C animal at 4PCD

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to to Human RefSeq-8 V3 BeadChips (Illumina) at 58°C for 20 hours.

data_processing:
Analysis of the GenomeStudio output data was conducted using the R statistical language and various software packages from Bioconductor. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation. Technical replicates were averaged. Batch correction (ComBat) was applied to correct for the cohort effect (PC125 vs. PC225)
software packages and versions: R 2.14.12; Biobase 2.14.0; Limma 3.10.3; impute 1.28.0; bioDist 1.26.0; ComBat (unversioned, downloaded March 2010 from http://www.bu.edu/jlab/wp-assets/ComBat/Download.html)

label: Biotin

molecule: total RNA

source_name: Mononuclear cell preparation from lymph nodes

value: C

tag: tissue

tag: cell type

value: Mononuclear cell preparation


title: CD4mem_CP_4PCD_Rh23789

description: CD4mem T cells sort  from CP animal at 4PCD


title: Primary_HUVEC_HUVEC632_p17_632.1769.1.2

status: Public on Sep 18 2012

type: genomic

city: La Jolla

first: Rathi

middle: D

last: Thiagarajan

state: CA

address: 2880 Torrey Pines Scenic Drive

department: Reproductive Medicine

institute: UCSD

description: SAMPLE 21

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HD Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using IScan using standard recommended Illumina scanner setting

data_processing: Genome Studio software v2010.3

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary human umbilical vein endothelial cell

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: UNKNOWN

tag: passage number

tag: loring pipeline sample id

tag: cell line

value: primary human umbilical vein endothelial cell


title: C_4PCD_Rh22673

description: LN from C animal at 4PCD


title: CD8mem_CP_minus7PCD_Rh23431

description: CD8mem T cells sort  from CP animal at minus7PCD


title: C_14PCD_Rh22673

description: LN from C animal at 14PCD


title: Primary_HUVEC_HUVECBF2_p4_168.249.2.1

description: SAMPLE 19

value: FEMALE


title: hES_WA09_p43_87.521.4.1

description: SAMPLE 23

source_name: Human embryonic stem cell undifferentiated

value: human embryonic stem cell undifferentiated


title: C_minus7PCD_Rh22673

description: LN from C animal at minus7PCD


title: CD4mem_CP_minus7PCD_Rh23166

description: CD4mem T cells sort  from CP animal at minus7PCD


title: CD8mem_CP_4PCD_Rh23434


title: hES.diff_Hues9_pUNK_CD34pos.Angioblasts_628.1760.1.2

description: SAMPLE 12

source_name: differentiated angioblast (CD34+) human embryonic stem cell

value: Unknown


title: hiPS.diff_K633IPS1_p4_endothelial_633.1771.1.2

description: SAMPLE 13

source_name: differentiated endothelial human induced pluripotent stem cell


title: Primary_SMOOTHMUSCLE_HBVSMC266_pUNK_203.556.1.1

description: SAMPLE 16

source_name: Primary human brain vascular smooth muscle cells

value: primary human brain vascular smooth muscle cells


title: hiPS.diff_K633IPS1_pUNK_CD34pos.Angioblasts_633.1770.1.2

description: SAMPLE 11

source_name: differentiated angioblast (CD34+) human induced pluripotent stem cell


title: C_14PCD_Rh24271

description: LN from C animal at 14PCD


title: hES.diff_Hues9_p13_endothelial_628.1761.1.2

description: SAMPLE 14

source_name: differentiated endothelial human embryonic stem cell


title: hiPS.EARLY_HDF51IPS10_p6_161.445.2.1

description: SAMPLE 25

source_name: Human induced pluripotent stem cell undifferentiated

value: human induced pluripotent stem cell undifferentiated


title: hES_WA09_p41_87.304.7.2

description: SAMPLE 22


title: hES.diff_Hues9_p4_Smooth.Muscle_628.1762.1.2

description: SAMPLE 10

source_name: Human embryonic stem cell differentiated smooth muscle

value: human embryonic stem cell differentiated smooth muscle


title: Primary_SMOOTHMUSCLE_HESMC267_pUNK_207.560.1.1

description: SAMPLE 17

source_name: Primary human esophageal smooth muscle cells

value: primary human esophageal smooth muscle cells


title: Primary_HUVEC_HUVECWF8_p4_173.254.2.1

description: SAMPLE 20


title: hiPS.EARLY_HDF51IPS1_p6_153.437.1.1

description: SAMPLE 24


title: hES_Hues9_p49_628.1763.1.2

description: SAMPLE 9


title: C_4PCD_Rh22179

description: LN from C animal at 4PCD


title: C_minus7PCD_Rh22179

description: LN from C animal at minus7PCD


title: C_14PCD_Rh20242

description: LN from C animal at 14PCD


title: CD8mem_CP_minus7PCD_Rh23166


title: CD4mem_CP_4PCD_Rh23048

value: A


title: NP_4PCD_Rh23722

description: LN from NP animal at 4PCD

value: NP


title: CP_4PCD_Rh23434

description: LN from CP animal at 4PCD


title: C_14PCD_Rh22179

description: LN from C animal at 14PCD


title: C_minus7PCD_Rh20242

description: LN from C animal at minus7PCD


title: CD8mem_NP_4PCD_Rh23840

description: CD8mem T cells sort  from NP animal at 4PCD


title: C_minus7PCD_Rh24271

description: LN from C animal at minus7PCD


title: CD8mem_CP_4PCD_Rh23698


title: CP_4PCD_Rh23070

description: LN from CP animal at 4PCD


title: CD4mem_CP_4PCD_Rh23841


title: C_14PCD_Rh24347

description: LN from C animal at 14PCD


title: C_4PCD_Rh20242

description: LN from C animal at 4PCD


title: CD4mem_NP_4PCD_Rh23164

description: CD4mem T cells sort  from NP animal at 4PCD


title: CD4mem_CP_4PCD_Rh24746


title: CD8mem_NP_4PCD_Rh23722


title: PP_4PCD_Rh23026

description: LN from PP animal at 4PCD

value: PP


title: CP_14PCD_Rh23166

description: LN from CP animal at 14PCD

value: CP


title: CD4mem_CP_4PCD_Rh23434

value: B


title: CD8mem_NP_4PCD_Rh23164

value: lymph node


title: CD4mem_CP_4PCD_Rh23431

value: C


title: C_14PCD_Rh24465

description: LN from C animal at 14PCD

value: Mononuclear cell preparation


title: CP_14PCD_Rh23003

description: LN from CP animal at 14PCD


title: CP_14PCD_Rh23434

description: LN from CP animal at 14PCD


title: NP_14PCD_Rh23164

description: LN from NP animal at 14PCD


title: CD4mem_NP_minus7PCD_Rh24761

description: CD4mem T cells sort  from NP animal at minus7PCD


title: CD4mem_CP_minus7PCD_Rh23841


title: CD4mem_CP_minus7PCD_Rh23431


title: CD4mem_CP_minus7PCD_Rh23789


title: CD4mem_NP_4PCD_Rh23722


title: CP_14PCD_Rh23070

description: LN from CP animal at 14PCD


title: CP_14PCD_Rh23009

description: LN from CP animal at 14PCD


title: PP_14PCD_Rh23690

description: LN from PP animal at 14PCD


title: PP_14PCD_Rh23026

description: LN from PP animal at 14PCD


title: CD8mem_CP_4PCD_Rh23048


title: CD8mem_CP_4PCD_Rh23789


title: CD8mem_CP_4PCD_Rh24724


title: CD4mem_CP_4PCD_Rh23166


title: CP_14PCD_Rh23789

description: LN from CP animal at 14PCD


title: CP_4PCD_Rh23003

description: LN from CP animal at 4PCD


title: CD4mem_CP_4PCD_Rh23698


title: CD8mem_CP_minus7PCD_Rh23841


title: PP_4PCD_Rh23690

description: LN from PP animal at 4PCD


title: CD4mem_CP_4PCD_Rh24724


title: CP_4PCD_Rh23048

description: LN from CP animal at 4PCD


title: CP_4PCD_Rh23009

description: LN from CP animal at 4PCD


title: CD8mem_CP_minus7PCD_Rh23789


title: CD8mem_NP_4PCD_Rh23847


title: CP_14PCD_Rh24746

description: LN from CP animal at 14PCD


title: CP_14PCD_Rh24724

description: LN from CP animal at 14PCD


title: NP_4PCD_Rh23840

description: LN from NP animal at 4PCD


title: CD4mem_CP_4PCD_Rh23793


title: CD8mem_CP_4PCD_Rh24746


title: NP_14PCD_Rh24761

description: LN from NP animal at 14PCD


title: C_14PCD_Rh23605

description: LN from C animal at 14PCD


title: CP_4PCD_Rh22741

description: LN from CP animal at 4PCD


title: CD8mem_NP_minus7PCD_Rh24761

description: CD8mem T cells sort  from NP animal at minus7PCD


title: NP_4PCD_Rh24761

description: LN from NP animal at 4PCD


title: NP_4PCD_Rh23847

description: LN from NP animal at 4PCD


title: CD8mem_CP_4PCD_Rh23841


title: CD8mem_CP_4PCD_Rh23431


title: CD4mem_CP_14PCD_Rh24746

description: CD4mem T cells sort  from CP animal at 14PCD


title: CD8mem_CP_minus7PCD_Rh24746


title: CD4mem_NP_4PCD_Rh23840


title: CD8mem_CP_4PCD_Rh23793


title: CD4mem_CP_14PCD_Rh24724


title: PP_4PCD_Rh23657

description: LN from PP animal at 4PCD


title: NP_14PCD_Rh23880

description: LN from NP animal at 14PCD


title: NP_14PCD_Rh23847

description: LN from NP animal at 14PCD


title: CD8mem_CP_4PCD_Rh23166


title: CD4mem_NP_14PCD_Rh23840

description: CD4mem T cells sort  from NP animal at 14PCD


title: NP_14PCD_Rh23840

description: LN from NP animal at 14PCD


title: CP_14PCD_Rh22741

description: LN from CP animal at 14PCD


title: CP_14PCD_Rh23048

description: LN from CP animal at 14PCD


title: CD8mem_CP_minus7PCD_Rh24724


title: CP_4PCD_Rh23698

description: LN from CP animal at 4PCD


title: CP_14PCD_Rh23698

description: LN from CP animal at 14PCD


title: CD4mem_CP_14PCD_Rh23003


title: CD4mem_CP_14PCD_Rh23698


title: C_14PCD_Rh23278

description: LN from C animal at 14PCD


title: C_4PCD_Rh23605

description: LN from C animal at 4PCD


title: CP_4PCD_Rh23789

description: LN from CP animal at 4PCD


title: C_4PCD_Rh24465

description: LN from C animal at 4PCD


title: CD4mem_CP_minus7PCD_Rh23793


title: PP_14PCD_Rh23657

description: LN from PP animal at 14PCD


title: CD8mem_CP_14PCD_Rh23048

description: CD8mem T cells sort  from CP animal at 14PCD


title: CD8mem_CP_minus7PCD_Rh23048


title: CD8mem_NP_14PCD_Rh23722

description: CD8mem T cells sort  from NP animal at 14PCD


title: CD8mem_CP_14PCD_Rh23009


title: CD8mem_NP_14PCD_Rh23164


title: CD4mem_CP_minus7PCD_Rh23009


title: C_minus7PCD_Rh23605

description: LN from C animal at minus7PCD


title: CD8mem_CP_minus7PCD_Rh23793


title: NP_minus7PCD_Rh23722

description: LN from NP animal at minus7PCD


title: C_minus7PCD_Rh23278

description: LN from C animal at minus7PCD


title: CP_minus7PCD_Rh23070

description: LN from CP animal at minus7PCD


title: CD8mem_CP_14PCD_Rh24746


title: CD4mem_NP_14PCD_Rh23164


title: CD4mem_CP_minus7PCD_Rh23003


title: CP_minus7PCD_Rh23793

description: LN from CP animal at minus7PCD


title: NP_4PCD_Rh23880

description: LN from NP animal at 4PCD


title: CD8mem_CP_14PCD_Rh23434


title: C_minus7PCD_Rh24347

description: LN from C animal at minus7PCD


title: CD4mem_CP_minus7PCD_Rh23698


title: CP_minus7PCD_Rh23166

description: LN from CP animal at minus7PCD


title: PP_minus7PCD_Rh23687

description: LN from PP animal at minus7PCD


title: CP_minus7PCD_Rh24724

description: LN from CP animal at minus7PCD


title: CP_minus7PCD_Rh24746

description: LN from CP animal at minus7PCD


title: CD8mem_CP_minus7PCD_Rh23009


title: CD4mem_NP_14PCD_Rh23722


title: CD8mem_NP_14PCD_Rh23880


title: CD4mem_CP_minus7PCD_Rh23048


title: CD8mem_NP_14PCD_Rh24761


title: CD4mem_CP_14PCD_Rh23434


title: CD8mem_CP_minus7PCD_Rh23003


title: NP_minus7PCD_Rh23847

description: LN from NP animal at minus7PCD


title: NP_minus7PCD_Rh23840

description: LN from NP animal at minus7PCD


title: CP_minus7PCD_Rh23048

description: LN from CP animal at minus7PCD


title: CD4mem_CP_14PCD_Rh23793


title: NP_minus7PCD_Rh23880

description: LN from NP animal at minus7PCD


title: CP_minus7PCD_Rh23698

description: LN from CP animal at minus7PCD


title: CP_minus7PCD_Rh22741

description: LN from CP animal at minus7PCD


title: NP_minus7PCD_Rh24761

description: LN from NP animal at minus7PCD


title: CD4mem_CP_14PCD_Rh23048


title: CD4mem_CP_minus7PCD_Rh23434


title: CD8mem_CP_14PCD_Rh23793


title: CP_minus7PCD_Rh23434

description: LN from CP animal at minus7PCD


title: NP_minus7PCD_Rh23164

description: LN from NP animal at minus7PCD


title: CD8mem_NP_14PCD_Rh23840


title: CD8mem_CP_minus7PCD_Rh23698


title: PP_minus7PCD_Rh23690

description: LN from PP animal at minus7PCD


title: PP_minus7PCD_Rh23026

description: LN from PP animal at minus7PCD


title: CP_4PCD_Rh24746

description: LN from CP animal at 4PCD


title: C_4PCD_Rh23278

description: LN from C animal at 4PCD


title: CD4mem_CP_minus7PCD_Rh24724


title: CD4mem_CP_14PCD_Rh23009


title: PP_4PCD_Rh23796

description: LN from PP animal at 4PCD


title: CP_4PCD_Rh23343

description: LN from CP animal at 4PCD


title: CP_4PCD_Rh24724

description: LN from CP animal at 4PCD


title: CD4mem_CP_minus7PCD_Rh24746


title: CD8mem_CP_14PCD_Rh23698


title: CD8mem_CP_14PCD_Rh23003


title: CD4mem_NP_4PCD_Rh23847


title: CD8mem_CP_14PCD_Rh24724


title: CD8mem_CP_minus7PCD_Rh23434


title: C_4PCD_Rh25430

description: LN from C animal at 4PCD


title: C_4PCD_Rh24062

description: LN from C animal at 4PCD


title: PP_4PCD_Rh23709

description: LN from PP animal at 4PCD


title: MCF7 GFP Rep2

status: Public on Aug 07 2012

city: Cambridge

first: Marc

last: Mendillo

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Gene expression data from MCF7 cells transduced with a scramble control GFP shRNAi

hyb_protocol: Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.

scan_protocol: The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.

data_processing: Affymetrix Microarray Suite 5.0. Microarray Suite 5.0 was used to generate a cell intensity file (*.cel). Probe intensities were normalized and summarized using GCRMA (with default settings) with R/Bioconductor.

label: biotin

source_name: MCF7 cells

label_protocol: As per Affymetrix standard instructions

growth_protocol: In vitro cultured according to published conditions

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

tag: treatment


title: BPLER Heat Shock Rep1

description: Gene expression data from BPLER cells after a 1H 42C heat shock

source_name: BPLER cells

value: BPLER

value: 1H 42C heat shock


title: BPLER hA6 Rep1

description: Gene expression data from BPLER cells transduced with hA6 lentiviral shRNAi to deplete HSF1


title: MCF7 GFP Rep1

value: transduced with a scramble control GFP shRNAi


title: BPLER GFP Rep2

description: Gene expression data from BPLER cells transduced with a scramble control GFP shRNAi


title: BPLER GFP Rep1


title: MCF7 hA6 Rep1

description: Gene expression data from MCF7 cells transduced with hA6 lentiviral shRNAi to deplete HSF1


title: HMLER GFP Rep2

description: Gene expression data from HMLER cells transduced with a scramble control GFP shRNAi

source_name: HMLER cells

value: HMLER


title: CP_4PCD_Rh23841

description: LN from CP animal at 4PCD


title: HMLER Scramble Rep1

description: Gene expression data from HMLER cells transduced with a scramble control lentiviral shRNAi


title: BPLER Scramble Rep1

description: Gene expression data from BPLER cells transduced with a scramble control lentiviral shRNAi


title: MCF7 Scramble Rep1

description: Gene expression data from MCF7 cells transduced with a scramble control lentiviral shRNAi


title: MCF7 Scramble Rep2

value: transduced with a scramble control lentiviral shRNAi


title: BPLER hA6 Rep2

value: transduced with hA6 lentiviral shRNAi to deplete HSF1


title: MCF7 hA6 Rep2


title: HMLER hA6 Rep1

description: Gene expression data from HMLER cells transduced with hA6 lentiviral shRNAi to deplete HSF1


title: 11-week-old Npc1+/+, biological replicate 2

status: Public on Jul 12 2012

city: BETHESDA

first: Celine

last: Cluzeau

state: MD

address: 10 Center Drive - room 9D41

department: PDEGEN

institute: NICHD/NIH

description:
Gene expression data
Heterozygous Npc1+/- mice were intercrossed to obtain control (Npc1+/+) and mutant (Npc1-/-) littermates. Pups were weaned 3 weeks after birth and subsequently had free access to water and normal mouse chow. PCR genotyping was performed using tail DNA. Considering that the phenotypic presentation is slightly different between males and females, we chose to work with only females to avoid any gender-specific variations in gene expression [74]. Female pups were sacrificed at 1, 3, 5, 7, 9, and 11 weeks of age. Livers were collected from both mutant and control animals, and immediately frozen on dry ice. Four livers were collected corresponding to each age and genotype, for a total of 48 samples.

hyb_protocol: 200 ng of total RNA was reverse transcribed to obtain labeled cDNA.  Labeled cDNAs was hybridized to the chips.  Chips were washed and stained using standard protocols for the Affymetrix Fluidics Station.

scan_protocol: Arrays were scanned using the Affymetrix Gene Chip Scanner 3000 and gene expression intensities were calculated using the Affymetrix GeneChip Command Console software

data_processing: Affymetrix .CEL files were normalized using the RMA (Robust Multi-Array Analysis) algorithm within Partek Genomics Suite software, version 6.5 (Partek Inc.)

organism: Mus musculus

source_name: BALB/cNctr-Npc1m1N/J, 11-week-old control mouse

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

extract_protocol: Total RNA was extracted from the liver tissue using TRIzol reagent (Invitrogen), followed by purification with Qiagen RNeasy Mini columns (Qiagen). RNA quality and quantity was assessed using both a Bioanalyzer (Agilent Inc.) and NanoDrop (Thermo Scientiﬁc Inc.).

tag: original sample name

tag: strain

value: BALB/c

value: Female

tag: phenotype

value: asymptomatic

tag: genotype/variation

tag: age

value: Liver


title: BPLER Scramble Rep2


title: HMLER hA6 Rep2


title: 1-week-old Npc1+/+, biological replicate 4

source_name: BALB/cNctr-Npc1m1N/J, 1-week-old control mouse


title: 1-week-old Npc1+/+, biological replicate 3


title: 11-week-old Npc1+/+, biological replicate 4


title: 11-week-old Npc1+/+, biological replicate 3


title: HMLER GFP Rep1


title: HMLER Scramble Rep2


title: 11-week-old Npc1+/+, biological replicate 1


title: 5-week-old Npc1+/+, biological replicate 4

source_name: BALB/cNctr-Npc1m1N/J, 5-week-old control mouse

value: DW_34_NPC ++5 wks


title: 9-week-old Npc1+/+, biological replicate 2

source_name: BALB/cNctr-Npc1m1N/J, 9-week-old control mouse

value: DW_40_NPC ++9wks


title: 7-week-old Npc1+/+, biological replicate 1

source_name: BALB/cNctr-Npc1m1N/J, 7-week-old control mouse

value: DW_35_NPC ++7wks


title: 7-week-old Npc1+/+, biological replicate 3

value: DW_37_NPC ++7wks


title: 9-week-old Npc1+/+, biological replicate 4

value: DW_42_NPC ++9wks


title: 9-week-old Npc1+/+, biological replicate 3

value: DW_41_NPC ++9wks


title: 5-week-old Npc1+/+, biological replicate 2

value: DW_32_NPC ++5 wks


title: BPLER Heat Shock Rep2

value: BPLER


title: 7-week-old Npc1+/+, biological replicate 4

value: DW_38_NPC ++7wks


title: 5-week-old Npc1+/+, biological replicate 1

value: DW_31_NPC ++5 wks


title: CP_4PCD_Rh22783

description: LN from CP animal at 4PCD

source_name: Mononuclear cell preparation from lymph nodes

tag: subject

tag: cohort

tag: lav

tag: protection

value: CP

value: C

value: lymph node

value: Mononuclear cell preparation


title: 7-week-old Npc1+/+, biological replicate 2

value: DW_36_NPC ++7wks

value: BALB/c

value: Female


title: 9-week-old Npc1+/+, biological replicate 1

value: DW_39_NPC ++9wks

value: asymptomatic

value: Liver


title: CD4mem_NP_14PCD_Rh23880

source_name: Sorted CD8+ and CD4+ memory T cells of mononuclear cell preparation from lymph nodes

value: NP

tag: group

value: A

tag: sort

tag: time

tag: barcode


title: 3-week-old Npc1+/+, biological replicate 4

source_name: BALB/cNctr-Npc1m1N/J, 3-week-old control mouse

value: DW_30_NPC ++3wks

tag: gender

tag: tissue


title: 5-week-old Npc1+/+, biological replicate 3

value: DW_33_NPC ++5 wks


title: 1-week-old Npc1+/+, biological replicate 2

value: DW_26_NPC ++1wk


title: 3-week-old Npc1+/+, biological replicate 1

value: DW_27_NPC ++3wks


title: 3-week-old Npc1+/+, biological replicate 2

value: DW_28_NPC ++3wks


title: 11-week-old Npc1-/-, biological replicate 3

source_name: BALB/cNctr-Npc1m1N/J, 11-week-old mutant mouse

value: DW_23_NPC --11wks

value: post-symptomatic age


title: 3-week-old Npc1+/+, biological replicate 3

value: DW_29_NPC ++3wks


title: 11-week-old Npc1-/-, biological replicate 4

value: DW_24_NPC --11wks


title: 11-week-old Npc1-/-, biological replicate 1

value: DW_21_NPC --11wks


title: 11-week-old Npc1-/-, biological replicate 2

value: DW_22_NPC --11wks

value: BALB/c


title: 9-week-old Npc1-/-, biological replicate 2

source_name: BALB/cNctr-Npc1m1N/J, 9-week-old mutant mouse

value: DW_18_NPC --9wks

value: Female


title: 1-week-old Npc1+/+, biological replicate 1

value: DW_25_NPC ++1wk

value: asymptomatic

value: Liver


title: 9-week-old Npc1-/-, biological replicate 3

value: DW_19_NPC --9wks


title: 9-week-old Npc1-/-, biological replicate 1

value: DW_17_NPC --9wks


title: 7-week-old Npc1-/-, biological replicate 2

source_name: BALB/cNctr-Npc1m1N/J, 7-week-old mutant mouse

value: DW_14_NPC --7wks


title: 3-week-old Npc1-/-, biological replicate 4

source_name: BALB/cNctr-Npc1m1N/J, 3-week-old mutant mouse

value: pre-symptomatic age


title: 7-week-old Npc1-/-, biological replicate 1

value: DW_13_NPC --7wks


title: 5-week-old Npc1-/-, biological replicate 1

source_name: BALB/cNctr-Npc1m1N/J, 5-week-old mutant mouse


title: 1-week-old Npc1-/-, biological replicate 4

source_name: BALB/cNctr-Npc1m1N/J, 1-week-old mutant mouse


title: 9-week-old Npc1-/-, biological replicate 4

value: DW_20_NPC --9wks


title: 3-week-old Npc1-/-, biological replicate 1


title: 5-week-old Npc1-/-, biological replicate 2

value: DW_10_NPC --5wks

value: post-symptomatic age


title: 5-week-old Npc1-/-, biological replicate 3


title: 7-week-old Npc1-/-, biological replicate 4

value: DW_16_NPC --7wks


title: 3-week-old Npc1-/-, biological replicate 2


title: PP_minus7PCD_Rh23796

description: LN from PP animal at minus7PCD

value: PP

value: C

value: lymph node

tag: cell type

value: Mononuclear cell preparation


title: 7-week-old Npc1-/-, biological replicate 3

value: DW_15_NPC --7wks

value: BALB/c

value: Female


title: 5-week-old Npc1-/-, biological replicate 4

value: DW_12_NPC --5wks

value: Liver


title: 3-week-old Npc1-/-, biological replicate 3


title: DGM-01539_sm

status: Public on Jun 20 2012

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, 10 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.

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

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: small airway epithelium from healthy nonsmokers or healthy smokers

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 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: department of genetic medicine id

tag: smoking status

value: NS

tag: serum 25-oh-d

value: high vitamin D


title: 1-week-old Npc1-/-, biological replicate 3

tag: original sample name

tag: strain

tag: phenotype

value: pre-symptomatic age


title: 1-week-old Npc1-/-, biological replicate 1

tag: genotype/variation

tag: age


title: 1-week-old Npc1-/-, biological replicate 2


title: DGM-00914_gt

hyb_protocol: Following labelling, 50 nanograms of DNA were hybridized for 16 hr at 50C on Affymetrix GeneChip Genome-Wide Human SNP Array 5.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing:
The data were analyzed with Partek Genomics Suite software, version 6.2 using default analysis settings and global scaling as normalization method.
CHP files were created from CEL files after running BRLMM_p

source_name: Blood from healthy nonsmokers or healthy smokers

label_protocol: DNA labeling was done according to the standard Affymetrix protocol from 50 nanograms total DNA (Affymetrix® Genome-Wide Human SNP Nsp/Sty Assay 5.0, 702419 Rev.1, Affymetrix).

extract_protocol: DNA was extracted from blood samples using the Autogen FX robotic system in according to the manufacturer's instructions

tag: ethnicity

value: Eur

value: S


title: DGM-01089_gt

value: Afr


title: DGM-00231_gt


title: DGM-00668_gt


title: DGM-00798_gt


title: DGM-00776_gt


title: DGM-00136_gt


title: DGM-00764_gt


title: DGM-00708_gt


title: DGM-00612_gt


title: DGM-00889_gt


title: DGM-00567_gt


title: DGM-00474_gt


title: DGM-00447_gt


title: DGM-00743_gt


title: DGM-00626_gt


title: DGM-00552_gt


title: DGM-00761_gt


title: DGM-00601_gt


title: DGM-00451_gt


title: DGM-00797_gt


title: DGM-00752_gt


title: DGM-00732_gt


title: DGM-00469_gt


title: DGM-00613_gt


title: DGM-00703_gt


title: DGM-00593_gt


title: DGM-00464_gt


title: DGM-00446_gt


title: DGM-00537_gt


title: DGM-00332_gt


title: DGM-00300_gt


title: DGM-00273_gt


title: DGM-00216_gt


title: DGM-00206_gt


title: DGM-00013_gt


title: DGM-00193_gt


title: DGM-00936_gt


title: DGM-01521_gt


title: DGM-01330_gt


title: DGM-00795_gt


title: DGM-01540_gt


title: DGM-01561_gt


title: DGM-01150_gt


title: DGM-01141_gt


title: DGM-00553_gt


title: DGM-00004_gt


title: DGM-00278_gt


title: DGM-00625_gt


title: DGM-00551_gt


title: DGM-00814_gt


title: DGM-00751_gt


title: DGM-00205_gt


title: DGM-00778_gt


title: DGM-00685_gt


title: DGM-00548_gt


title: DGM-00661_gt


title: DGM-00696_gt


title: DGM-00529_gt


title: DGM-00757_gt


title: DGM-00342_gt


title: DGM-00530_gt


title: DGM-00224_gt


title: DGM-00465_gt


title: DGM-00044_gt


title: weak VIA stimulated w/ CM9 AP77

status: Public on Jun 15 2012

description:
Animal AP77 (weak VIA), CM9 peptide stimulated
5937302028_K

hyb_protocol: The biotinylated cRNA was hybridized onto Illumina Human HT-12 BeadChips V4 at 58oC for 20 hrs

scan_protocol: Fluoresent array images were collected using Illumina BeadStation 500GX scanner and image intensity data were extracted using Illumina BeadStudio v3

data_processing: Analysis of the GenomeStudio output data was conducted using the R statistical language and various software packages from Bioconductor. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation

source_name: Gag CM9-specific EM CD8+ T cells

label_protocol: Total RNA was amplified and labeled using the Illumina TotalPrep RNA Amplification kit, which is based on the Eberwine amplification protocol

extract_protocol: RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA quantification was performed using a spectrophotometer (NanoDrop Technologies) and RNA quality was assessed using the Experion automated electrophoresis system (Bio-Rad)

value: Gag CM9-specific EM CD8+ T cells

tag: animal

tag: via

value: weak

tag: stimulation

value: CM9 peptide


title: DGM-00052_gt


title: DGM-00416_gt


title: DGM-10152_gt


title: DGM-10132_gt


title: strong VIA stimulated w/ CM9 ZD51

description:
Animal ZD51 (strong VIA), CM9 peptide stimulated
5491099043_F

value: strong


title: DGM-00029_gt


title: strong VIA unstimulated ZD51

description:
Animal ZD51 (strong VIA), CM9 peptide unstimulated
5491099043_D

value: unstimulated


title: DGM-00041_gt


title: DGM-00073_gt


title: DGM-00069_gt


title: DGM-10139_gt


title: DGM-00072_gt


title: DGM-00262_gt


title: DGM-00030_gt


title: DGM-00078_gt


title: DGM-00035_gt


title: strong VIA stimulated w/ CM9 ZD46

description:
Animal ZD46 (strong VIA), CM9 peptide stimulated
5491099043_E


title: DGM-00632_gt


title: strong VIA unstimulated ZD46

description:
Animal ZD46 (strong VIA), CM9 peptide unstimulated
5491099043_C


title: strong VIA stimulated w/ CM9 AR96

description:
Animal AR96 (strong VIA), CM9 peptide stimulated
5483347147_L


title: DGM-00249_gt


title: weak VIA stimulated w/ CM9 AR81

description:
Animal AR81 (weak VIA), CM9 peptide stimulated
5483347147_I


title: DGM-00171_gt


title: Homozygous pool-15 generations-100uM zinc-replicate5-Down

status: Public on Apr 17 2012

city: Berkeley

first: Chris

last: Vulpe

state: Ca

address: 119 Morgan Hall

department: Nutritional Sciences and Toxicology

institute: UC Berkeley

description: Down tag data processing

hyb_protocol: Reactions hybridized overnight to custom-built TAG4 microarrays (Affymetrix)

scan_protocol: After hybridization, arrays were stained and scanned at an emission wavelength of 560 nm using a GeneChip scanner (Affymetrix).

data_processing:
Robust mean Log2 intensity for replicate features calculated with S-plus/R function.
Up and down tags are processed separately and output reported as separate data sets.
Note: Platform GPL8633 contains the array design which will be helpful for users who do not want to use our preprocessing strategy.

organism: Saccharomyces cerevisiae

label_protocol: The strain-specific barcodes contained in the DNA were amplified by PCR using a set of biotinylated primers

growth_protocol: Growth in zinc defined media (LZM), 30 °C, 200 rpm. Measurements of optical density at 595 nm (OD595) to monitor growth

extract_protocol: Cells were collected and genomic DNA was extracted using the YDER kit (Pierce Biotechnology)

treatment_protocol: Zinc concentration incorporated into growth media, 2 concentrations with 6 biological replicates each, for 5 and 15 generations (g) of growth

tag: pool

value: Homozygous deletion mutants

tag: growth stage

value: 15 generations

tag: agent

value: zinc

tag: concentration


title: Homozygous pool-15 generations-100uM zinc-replicate6-Down

description: Down tag data processing


title: Homozygous pool-15 generations-100uM zinc-replicate4-Down

description: Down tag data processing


title: strong VIA unstimulated AC1

description:
Animal AC1 (strong VIA), CM9 peptide unstimulated
5491099043_A

tag: cell type


title: Homozygous pool-15 generations-100uM zinc-replicate2-Down

description: Down tag data processing


title: DGM-00036_gt

tag: department of genetic medicine id


title: Homozygous pool-15 generations-1uM zinc-replicate6-Down

description: Down tag data processing


title: Homozygous pool-15 generations-100uM zinc-replicate1-Down

description: Down tag data processing


title: Homozygous pool-15 generations-1uM zinc-replicate5-Down

description: Down tag data processing


title: DGM-10131_gt

tag: smoking status


title: Homozygous pool-15 generations-1uM zinc-replicate4-Down

description: Down tag data processing


title: strong VIA unstimulated ZD12

description:
Animal ZD12 (strong VIA), CM9 peptide unstimulated
5491099043_B


title: DGM-00244_gt


title: DGM-00060_gt


title: Homozygous pool-15 generations-1uM zinc-replicate3-Down

description: Down tag data processing


title: DGM-00313_gt


title: DGM-00061_gt


title: DGM-10404_gt


title: DGM-00791_gt


title: Homozygous pool-5 generations-100uM zinc-replicate2-Down

description: Down tag data processing

value: 5 generations


title: Homozygous pool-15 generations-1uM zinc-replicate1-Down

description: Down tag data processing


title: Homozygous pool-5 generations-1uM zinc-replicate6-Down

description: Down tag data processing


title: Homozygous pool-5 generations-100uM zinc-replicate1-Down

description: Down tag data processing


title: Homozygous pool-5 generations-100uM zinc-replicate5-Down

description: Down tag data processing


title: Homozygous pool-5 generations-1uM zinc-replicate5-Down

description: Down tag data processing


title: Homozygous pool-5 generations-100uM zinc-replicate3-Down

description: Down tag data processing


title: Homozygous pool-5 generations-1uM zinc-replicate4-Down

description: Down tag data processing


title: Homozygous pool-5 generations-100uM zinc-replicate4-Down

description: Down tag data processing


title: Homozygous pool-5 generations-1uM zinc-replicate1-Down

description: Down tag data processing


title: Homozygous pool-5 generations-1uM zinc-replicate2-Down

description: Down tag data processing


title: Homozygous pool-5 generations-1uM zinc-replicate3-Down

description: Down tag data processing


title: DGM-00471_gt


title: DGM-00028_gt


title: DGM-00038_gt


title: strong VIA unstimulated AR96

description:
Animal AR96 (strong VIA), CM9 peptide unstimulated
5483347147_K


title: NMFH1

status: Public on Feb 02 2012

city: Tainan

first: Chien-Feng

last: Li

address: 901 Chunghwa Road

department: Pathology/Medical Research

country: Taiwan

institute: Chi-Mei Medical Center

hyb_protocol: The samples were rehydrated in Roche NimbleGen Hybridization Buffer (Roche NimbleGen Inc.), denatured at 95oC for 5 min, and then cooled to 42oC. Hybridizations were carried out for 18 hr (16~20 hr) at 42oC in the NimbleGen Service Laboratory.

scan_protocol: Arrays were scanned on a GenePix 4000B scanner (Axon Instruments, Molecular Devices Corp., Sunnyvale, CA) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html). Data were extracted from scanned images using NimbleScan 2.3 extraction software (Roche NimbleGen, Inc.).

data_processing:
Arrays were processed using NimbleGen's standard protocol for NimbleGen 385K Whole-Genome Tiling v1.0 array data extraction. The data were qspline normalized using the Bioconductor package.

The supplementary *.txt file includes the ID numbers and positions of probes, signal intensities for the tumor and reference samples, and corrected (normalized) ratios.

source_name: Myxofibrosarcoma cell line (NMFH1)

label_protocol: DNA samples were labeled using Roche Nimblegen's standard protocol. Total genomic DNA from each tumor were directly labeled by random primer extension labeling (Cy3) without an intervening whole-genome amplification step. The reference DNA samples were labeled with Cy5.

extract_protocol: Based on H&E sections, regions suitable for DNA extraction were dissected from 12 fresh specimens after trimming necrotic and fibrous areas to assure higher than 80% of tumor content. For each case, 1 μg of total genomic DNA at a concentration of 500 ng/μl was extracted from fresh tissue by using "recoverall DNA Purification Kits" (Ambion, Austin, TX) for hybridization against oligonucleotide microarrays. To ensure DNA integrity, each sample should have an A260/280 ratio of 1.7 to 2.0 and no sign of degradation, as evaluated by gel electrophoresis.

tag: cell line

value: myxofibrosarcoma cells

source_name: Lymphocytes from gender-matched donor 08

tag: tissue

value: lymphocytes from gender-matched donor


title: strong VIA unstimulated 4251

description:
Animal 4251 (strong VIA), CM9 peptide unstimulated
5483347147_J


title: OH931

source_name: Myxofibrosarcoma cell line (OH931)

source_name: Lymphocytes from gender-matched donor 09


title: MFS11

source_name: Myxofibrosarcoma sample 11

value: myxofibrosarcoma tumor

source_name: Lymphocytes from gender-matched donor 06


title: MFS12

source_name: Myxofibrosarcoma sample 12

source_name: Lymphocytes from gender-matched donor 07


title: MFS10

source_name: Myxofibrosarcoma sample 10

source_name: Lymphocytes from gender-matched donor 05


title: MFS08

source_name: Myxofibrosarcoma sample 08

source_name: Lymphocytes from gender-matched donor 03


title: MFS07

source_name: Myxofibrosarcoma sample 07

source_name: Lymphocytes from gender-matched donor 02


title: Homozygous pool-15 generations-100uM zinc-replicate3-Down

description: Down tag data processing


title: MFS06

source_name: Myxofibrosarcoma sample 06

source_name: Lymphocytes from gender-matched donor 01


title: MFS09

source_name: Myxofibrosarcoma sample 09

source_name: Lymphocytes from gender-matched donor 04


title: MFS03

source_name: Myxofibrosarcoma sample 03

source_name: Tumor-adjacent normal soft tissue 03

value: tumor-adjacent normal soft tissue


title: MFS04

source_name: Myxofibrosarcoma sample 04

source_name: Tumor-adjacent normal soft tissue 04


title: CD25+CD45RA-FOXP3+_donor4

status: Public on Dec 14 2011

city: Regensburg

first: Christian

last: Schmidl

address: Franz-Josef-Strauss-Allee 11

country: Germany

institute: Rengensburg Center for Interventional Immunology

hyb_protocol: 600 ng labeled cRNA were fragmented and hybridized on the Whole Human Genome Expression Array G4851A (8x60K, Agilent) according to the manufacturer's instructions (Version 6.5 May 2010). In brief, 600ng labeled cRNA were combined with 5 µl 10x blocking agent, brought to 24µl with ddH2O and 1µl of 25x fragmentation buffer was added. The cRNA was the fragmented for exactly 30 minutes at 60°C, cooled on ice for one minute, and 25µl of 2x GEx Hybridisation Buffer HI-RPM were mixed with each sample by pipetting. The mix was centrifuged briefly and hybrydised immediately to  the microarrays. Arrays were rotated over night for 17 hours at 65°C at HI-RPM.

scan_protocol: GE Wash Buffers were all supplied with 0.005% Triton X-102; Arrays were disassembled in an ozone-filtered room in GE Wash Buffer I, washed in Wash Buffer I for one minute at room temperature and the for another minute with GE Wash Buffer II at elevated temperature (buffer was prewarmed overnight at 37°C).  The arrays were scanned immediately: Dye channel: Green; Scan Region: Scan Area (61 x 21.6mm); Scan Resolution: 3 µm; Tiff: 20 bit;

data_processing: Images were processed using Feature Extraction Software 10.7.3.1 (Agilent) and further analyzed using GeneSpring GX 11.0.2 software. Fluorescence signals were normalized (75 percentile) and baseline transformed to the median of all samples. Probes were discarded when: Feature is not positive and significant; Feature is not above background

source_name: memory Treg cells expanded in vitro

label_protocol: 50 to 200 ng of high-quality RNA were amplified and Cyanine 3-CTP labeled with the One Color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions (Version 6.5 May 2010).  Labeled and amplified RNA was purified with Qiagen RNeasy mini spin columns.  RNALabeling efficiency was controlled using the NanoDrop spectrophotometer.

growth_protocol: PBMCs were isolated from leukapheresis products of healthy volunteers by density gradient centrifugation. CD4+CD25highCD45RA+ “naïve” Treg cells and CD4+CD25highCD45RA- “memory” Treg cells were isolated by FACS (BD FACSAria, BD Biosciences, Heidelberg, Germany) and expanded in vitro. T cells were cultured on irradiated, huCD32-expressing L929 cells with anti-CD3 (OKT3; Orthoclone, Ortho Biotech (Neuss, Germany)) and anti-CD28 antibodies (CD28.2, BD Biosciences; 100 ng/mL each) in the presence of high-dose IL-2 (Proleukin, Chiron, Amsterdam, Netherlands; 300 U/mL) and restimulated once per week. Cultures were continued for 11-12 days and rested for 3-4 days in medium containing IL-2.

extract_protocol: For FOXP3 staining and subsequent RNA-extraction we composed an own staining buffer comprising PBS, 2 % Tryptone (Roth, Karlsruhe, Germany) and 0.1 % DEPC (Roth). The buffer was autoclaved, cooled to 4 °C prior to use and will in the following be referred to as “staining buffer”. After 11 days of culture and resting for 4 days in IL-2 containing medium, surface staining with CD4-FITC (BD Biosciences) was carried out according to the manufacturer’s instructions. Up to 7 E07 cells were one time washed in staining buffer and subsequently resuspended in 2 ml ice-cold 70 % ethanol (J.T. Baker, Deventer, The Netherlands) on a vortex. For fixation, cells were incubated for 15’ at -20 °C. After two times washing in 20 ml staining buffer, the cells were resuspended in 1000 µl staining buffer containing 20 µl rat-serum (eBioscience) and 400-800 U recombinant RNasin (Promega, Madison, WI). Following 5’ incubation at 4 °C 50 µl anti-human FOXP3-APC (clone PCH101, eBioscience) were added and incubated for another 25’ at 4 °C in the dark. Finally, cells were washed in 20 ml staining buffer and resuspended in 600 µl staining buffer for FACS-sort. RNA was isolated from FACS sorted cells using the RNeasy Micro Kit (Qiagen, Hilden, Germany) or TRizol® Reagent (Invitrogen, Darmstadt, Germany) according to the manufacturer’s instructions. When RNA was extracted from less than 1 E06 cells, 20 µg glycogen (Glycogen for molecular biology, Roche GmbH, Mannheim, Germany) were added during the TRizol® procedure. Quality was checked with the Agilent Bioanalyzer RNA 6000 Nano Kit according to the manufacturer's instructions.

tag: days of expansion

value: 11 (+4 rested)

tag: foxp3 status


title: MFS05

source_name: Myxofibrosarcoma sample 05

source_name: Tumor-adjacent normal soft tissue 05


title: Homozygous pool-5 generations-100uM zinc-replicate6-Down

description: Down tag data processing


title: Homozygous pool-15 generations-1uM zinc-replicate2-Down

description: Down tag data processing


title: CD25+CD45RA-FOXP3+_donor3


title: CD25+CD45RA-FOXP3-_donor5


title: MFS02

source_name: Myxofibrosarcoma sample 02

source_name: Tumor-adjacent normal soft tissue 02


title: CD25+CD45RA-FOXP3-_donor4


title: lymphoma1467_ADR_rep1

status: Public on Nov 21 2011

city: Berlin

first: Maja

last: Milanovic

address: Augustenburgerplatz 1

department: Hematology and Oncology

institute: Charite University Medicine, Berlin

description:
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; treated 5 days in vitro with 0.05µg/ml Adriamycin.
1467 sen.CEL

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on MOE430 2.0 Arrays (Affymetrix). GeneChips were washed and stained with standard protocols in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scanner G3000

data_processing: Affymetrix CEL files were imported into Partek Genomic Suite Software (Version 6.5, Partek Inc., St. Louis, USA) and processed by the implemented RMA workflow (median polish probe set summarization, RMA background correction, quantile normalization).

source_name: primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice with palpable lymphadenopathy

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (One Cycle Target labeling protocol) from 3 ug total RNA.

growth_protocol: Primary Emu-myc lymphoma cells were cultivated in B-cell medium (DMEM and IMDM in 1:1 ratio, 10%FBS, 4mM L-glutamine, 25µM beta-mercaptoethanol, 100U/ml penicilin/streptamycin) on gamma-irradiated (20Gy) NIH 3T3 cells as feeder.

extract_protocol: The total RNA from untreated or 5 days ADR treated Myc;Bcl2 lymphomas was prepared using an RNeasy Mini kit (QIAGEN, Valencia, California) according to the manufacturer's instruction.

treatment_protocol: Freshly isolated lymphoma cells were retrovirally transduced by Bcl2 (MSCVpuro) and selected with Puromycin for 48h. These Myc;Bcl2 cells were either left untreated or treated in vitro with 0.05µg/ml Adriamycin for 5 days

tag: senescence induction

value: yes


title: CD25+CD45RA-FOXP3+_donor1


title: CD25+CD45RA-FOXP3-_donor1


title: lymphoma1467_untreated_rep1

description:
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression; untreated.
1467.CEL

value: no


title: col100

status: Public on Nov 05 2011

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix)

source_name: Primary tumor resection

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.

tag: disease status

value: AJCC stage II CRC

value: primary tumor resection

tag: age at diagnosis

tag: Sex

value: f

tag: meta or recurrence within 3 years

tag: time to meta or recurrence


title: col102


title: col101


title: MFS01

source_name: Myxofibrosarcoma sample 01

source_name: Tumor-adjacent normal soft tissue 01


title: CD25+CD45RA-FOXP3+_donor2


title: col094

value: m


title: col097


title: col098


title: CD25+CD45RA-FOXP3-_donor3


title: col099


title: CD25+CD45RA-FOXP3-_donor2


title: CD25+CD45RA-FOXP3+_donor5


title: col085


title: col096


title: col090


title: col086


title: col084


title: col091


title: col083


title: col095


title: col080


title: col093


title: col089


title: col092


title: col082


title: col072


title: col075


title: col077


title: col073


title: col063


title: col076


title: col068


title: col069


title: col074


title: col081


title: col078


title: col070


title: col067


title: col065


title: col066


title: col058


title: col064


title: col062


title: col079


title: col060


title: col059


title: col061


title: col052


title: col057


title: col049


title: col050


title: col054


title: col051


title: col041


title: col044


title: col047


title: col045


title: col034


title: col048


title: col036


title: col035


title: col055


title: col040


title: col022


title: col038


title: col046


title: col026


title: col021


title: col024


title: col053


title: col020


title: col019


title: col037


title: col039


title: col023


title: col033


title: col056


title: col015


title: col017


title: col012


title: col013


title: col014


title: col007


title: col002


title: col005


title: col006


title: col016


title: col008


title: col009


title: col018


title: col010


title: JM109 GLY-1, biological rep1

status: Public on Jul 22 2011

city: Bei Jing

first: Liang

state: Bei Jing

address: Zhongguan Cun Nanda Jie No.12

department: Biotechnology Research Institute

country: China

institute: Chinese Academy of Agricultural Sciences

description: RNA extracted from cells of E. coli K-12 JM109 after 200 mM glyphosate shock for 1 h

hyb_protocol: The biotin-labeled target was hybridized to the Affymetrix GeneChip E. coli 2.0 array at 45ºC for 16 hour at 60 rpm using the Hybridization Oven 640 (Affymetrix), then a three-step fluorescent staining was conducted using the Fluidics Station 450 (Affymetrix) during the washing and staining procedure.

scan_protocol: The data were collected by using Affymetrix GeneChip Scanner 3000.

data_processing: Affymetrix GeneChip Operating Software (GCOS) Version 1.4  Details: Intra-chip normalizations were performed using Affymetrix Gene Chip Operating Software (GCOS). Default statistical parameters were used to normalize each chip to the same target intensity (1500) as described in the Affymetrix GeneChip Expression Analysis manual. All nine possible inter-chip comparisons were performed in GCOS. The data were subsequently exported to a Microsoft Excel spreadsheet for manipulation. Consensus “detection p-value”, “change p-value”, and “signal log ratios” were calculated, and the default E. coli array p-value cutoff parameters were applied to these consensus values to estimate the transcript change between two conditions and the transcript presence under each condition. Background-subtracted data sets were used to calculate up-regulated and down-regulated genes based on fold changes of greater than 2.

organism: Escherichia coli

source_name: E. coli K12 strain JM109

label_protocol: Affymetrix Technical Manual, Prokaryotic Sample and Array Processing

growth_protocol: E.coli cells  grown with aeration in LB media at 37º C until early log phase (0.4) and were treated with/without 200 mM glyphosate for 1 h, after that the cells were harvested to extract RNA. LB medium recipe is as follow: 10g tryptone, 5g yeast extract, 10g NaCl per 1 liter.

extract_protocol: Total RNA was extracted using the commercial product TRIzol Reagent (Invitrogen, Carlsbad, CA).Disrupt about 107cells with a homogenizer with 1ml TRIzol Reafent on ice. Store the homogenate for 5 minutes at room temperature to permit the complete dissociation of nucleoprotein complexes. Next, supplement the homogenate with 0.2 ml chloroform per 1 ml of TRI Reagent, cover the samples tightly and shake vigorously for 15 seconds. Store the resulting mixture at room temperature for 2-15 minutes and centrifuge at 12,000 g for 15 minutes at 4 C. Following centrifugation, the mixture separates into a lower red phenol-chloroform phase, interphase and the colorless upper aqueous phase. Transfer the aqueous phase to a fresh tube. Precipitate RNA from the aqueous phase by mixing with isopropanol. Use 0.5 ml of isopropanol per 1 ml of TRI Reagent used for the initial homogenization. Store samples at room temperature for 5-10 minutes and centrifuge at 12,000 g for 8 minutes at 4 - 25 C. Remove the supernatant and wash the RNA pellet ( by vortexing) with 75% ethanol and subsequent centrifugation at 7,500 g for 5 minutes at 4 - 25 C. Add at least 1 ml of 75% ethanol per 1 ml TRI Reagent used for the initial homogenization. Remove the ethanol wash and briefly air-dry the RNA pellet for 3 - 5 min. Dissolve RNA in DEPC-treated water by passing solution a few times through a pipette tip. Using an on-column DNase digestion with RNase-free DNase I (Qiagen) to purify the total RNA.

treatment_protocol: Treatment protocol- E.coli cells grown in LB media with  at 37C until early log phase (0.4), then were treated with 200 mM glyphosate for 1 h,after that the cells were harvested to extract RNA.

tag: treatment

value: 200 mM glyphosate shock for 1 h


title: JM109-3, biological rep3

description: RNA extracted from cells of E. coli K-12 JM109 without 200 mM glyphosate shock

value: without salt shock


title: col004


title: col011


title: JM109 GLY-2, biological rep2


title: col001


title: JM109 GLY-3, biological rep3


title: Vehicle_Control_Rep2

status: Public on Aug 03 2011

city: Gainesville

first: Maria

middle: Belen

last: Rabaglino

state: FL

address: 326 University Village Apt 6

institute: University of Florida

description:
Gene expression in fetal hypothalamus untreated-Replicate 2
Raw data file: E2S_Ctrl_02.txt

hyb_protocol: 600 ng of each labeled cRNA was fragmented and then mixed with hybridization buffer using the Agilent gene expression hybridization kit. These were applied to a sheep 8 X 15 K array slide (Agilent  019921), containing 8 arrays with 15,744  oligomers with a length of 60 bases corresponding to 15,744 ovine genetic sequences published in the NCBI data base and  hybridized at 65 °C for 17 h at 10 rpm.  After hybridization, the slides were washed for 1 minute at room temperature with Wash Buffer 1 (Agilent) and for 1 minute with 37 °C Wash buffer 2 (Agilent). After dry the excess of liquid, the slides were washed for 30 seconds in the stabilization and drying solution.

scan_protocol: The slides were scanned with an Agilent 2-dye G2505B scanner that is compatible with any 1' x 3' glass slide.

data_processing: Features were extracted with Agilent Feature extraction 9.1 software. Raw data was analyzed with JMP Genomic 5.1 software. Features flagged as Feature Non-uniform outliers were excluded from the analysis. Probes with less than two Features were excluded as well.  Processed signal data for each array was log2 transformed and normalized by the median.

organism: Ovis aries

source_name: Hypothalamus, infused with vehicle solution

label_protocol: One µg of the DNase-treated RNA was labeled with Cyanine 3 (Cy3) CTP with the Agilent Quick Amp kit (5190-0442, New Castle, DE) according to their methodology, purified with the Qiagen RNeasy kit (Valencia, CA) according to Agilent’s revision of the Qiagen protocol as shown in the Quick Amp kit protocol except that the microcentrifugation spins were performed at room temperature instead of 4 °C. The resulting labeled cRNA was analyzed with the Nanodrop spectrophotometer, and the specific activities and the yields of the cRNAs were calculated; these ranged from 10.41 to 19.73 pmol Cy3/µg RNA and from 5.0 to 12.8 µg, respectively. The labeled cRNA was stored at -80oC until use.

extract_protocol: RNA was extracted from the hypothalamus using Trizol (Invitrogen, Carlsbad, CA) and following the manufacturer’s directions. The RNA was resuspended in RNAsecure, and stored at -80oC in aliquots until use. For microarray analysis 20 ug of these RNAs, which had been stored for seven years, were DNase treated using the Turbo RNase-free DNase kit (Ambion, Foster City, CA),  the concentration determined with a Nanodrop spectrophotometer (ND-1000, ThermoFisher, Wilmington DE) and the integrity of the RNA was measured using an Agilent Bioanalyzer, 2100 model.

treatment_protocol: Estradiol-3-sulfate was infused in the treated ovine fetus employing an osmotic mini-pump attached to a small catheter and placed into the lateral cerebral ventricle. The same procedure was performed in the twin fetus but using vehicle saline infusion instead (control). The gestational age at the time of surgery was around 125 days. After 7-10 days of infusion, fetuses were euthanized and hypothalami collected for mRNA extraction. The protocol was applied to 4 set of twin fetuses.

tag: developmental stage

value: fetus

tag: gestational age

value: control

value: brain (hypothalamus)


title: EstradiolSulfate_Treatment_Rep4

description:
Gene expression in fetal hypothalamus treated with Estradiol Sulfate-Replicate 4
Raw data file: E2S_Trt_04.txt

source_name: Hypothalamus, infused with Estradiol Sulfate

tag: agent

value: Estradiol Sulfate


title: col003


title: Vehicle_Control_Rep1

description:
Gene expression in fetal hypothalamus untreated-Replicate 1
Raw data file: E2S_Ctrl_01.txt


title: Vehicle_Control_Rep4

description:
Gene expression in fetal hypothalamus untreated-Replicate 4
Raw data file: E2S_Ctrl_04.txt


title: EstradiolSulfate_Treatment_Rep1

description:
Gene expression in fetal hypothalamus treated with Estradiol Sulfate-Replicate 1
Raw data file: E2S_Trt_01.txt


title: Vehicle_Control_Rep3

description:
Gene expression in fetal hypothalamus untreated-Replicate 3
Raw data file: E2S_Ctrl_03.txt


title: EstradiolSulfate_Treatment_Rep3

description:
Gene expression in fetal hypothalamus treated with Estradiol Sulfate-Replicate 3
Raw data file: E2S_Trt_03.txt


title: EstradiolSulfate_Treatment_Rep2

description:
Gene expression in fetal hypothalamus treated with Estradiol Sulfate-Replicate 2
Raw data file: E2S_Trt_02.txt


title: JM109-1, biological rep1

description: RNA extracted from cells of E. coli K-12 JM109  without 200 mM glyphosate shock


title: JM109-2, biological rep2

description: RNA extracted from cells of E. coli K-12 JM109 without 200 mM glyphosate shock.


title: CTRLb_11b_04

status: Public on May 18 2011

first: Reyna

middle: Cristina

last: Colli-Dula

state: Florida

address: Mowry Drive 471

department: CEHT

description:
Replicate 4
Gene expression after 14 days of exposure to Primary and Secondary Treated Effluents in male liver of Fathead Minnow (FHM).

scan_protocol: Microarrays were kept in the dark until scanning on an Agilent G2505B microarray scanner.

data_processing: Agilent Feature Extraction Software (v9.5) formed a composite of the two scans and calculated parameters for Extended Dynamic Range. Data extraction was performed using Agilent Feature Extraction software. Background-subtracted raw expression data (gProcessedSignal) were imported into JMP Genomics v5 (SAS, Cary, NC). During import, data were log2-transformed and all control and non-uniform spots were removed prior to the final analysis. Raw intensity data for each microarray were normalized by median centering before performing ANOVA. Differentially regulated transcripts were identified using a one-way analysis of variance.

organism: Pimephales promelas

source_name: Liver, 14 d, CTRLb

label_protocol: Agilent protocol titled One-color microarrays-based  gene expression analysis (document no. G4140-90040 v6.5) was used.

growth_protocol: Adult fathead minnow were provided by the USEPA laboratory (Cincinnati, OH).  The fish had already developed secondary sexual characteristics.  The fish were acclimated for one week prior to treatment exposure.  During acclimation, three male and three female fathead minnow were placed in a 12 L aquarium that contained 10 L of moderately hard water.  The water temperature was maintained at 25+1oC with a photoperiod of 16 hours light: 8 hours dark.  The fish were fed frozen adult brine shrimp twice a day.

extract_protocol: Total RNA was extracted using the RNA STAT-60 reagent (Tel-Test, Friendswood, TX, USA), reconstituted in RNAsecure (Ambion), and DNase-treated with Turbo DNA-free (Ambion). In all cases, the manufacturers’ protocols were followed.  RNA quantity for microarray analysis was measured using the NanoDrop ND-1000 (Nanodrop Technologies, Wilmington, DE), and RNA quality was evaluated using the Agilent 2100 BioAnalyzer with the RNA 6000 Nanochip. RNA integrity values (RIN) were >8.0 for all samples used in the analysis.

treatment_protocol: Eighteen fish were exposed per treatment.  The aquaria received 10 L of moderately hard water or treatment solution and were aerated.  Water temperature was maintained at 25+1oC with a photoperiod of 16 hours light: 8 hours dark.  Each treatment was renewed daily by replacing fifty percent of the volume in each tank.  Fish were fed frozen adult brine shrimp twice daily (approximately 0.1g of food per gram-fish weight).  Water quality was recorded three times a week during the experiment (total ammonia, dissolved oxygen, conductivity, pH and temperature).  During the 14-day exposures, water quality averages were as follows: dissolved oxygen 7.64±0.35 mg/L, ammonia 1.49±1.3 mg/L, conductivity 340.29±33.2 µS and pH 7.42±0.1.  The percentage survival of fish per treatment ranged between 88 and 100%. Throughout exposure to POTW effluents and control treatments, the fish remained in their original acclimation tanks, and received treatment solutions by static renewal.  Daily 50% static renewals consisted of removing 5 L of water from each tank and then adding a 5 L of treatment solution.  Water controls received moderately hard water during water renewals with similar methods and equipment used for other treatments.  Photoperiod, temperature, salinity and feeding regimes were kept similar to acclimation conditions.

value: liver

tag: gender

value: male

value: sexually mature

value: moderately hard water

tag: treatment duration

value: 14 days


title: 5%EFFHb_36b_06

description:
Replicate 6
Gene expression after 14 days of exposure to Primary and Secondary Treated Effluents in male liver of Fathead Minnow (FHM).

hyb_protocol: gilent protocol titled One-color microarrays-based  gene expression analysis (document no. G4140-90040 v6.5) was used.

source_name: Liver, 14 d, 5%EFFHb

value: 5% secondary treated effluent


title: 5%EFFHb_35b_05

description:
Replicate 5
Gene expression after 14 days of exposure to Primary and Secondary Treated Effluents in male liver of Fathead Minnow (FHM).


title: E2b_39b_01

description:
Replicate 1
Gene expression after 14 days of exposure to Primary and Secondary Treated Effluents in male liver of Fathead Minnow (FHM).

source_name: Liver, 14 d, E2b

value: estradiol


title: E2b_38b_06

description: Gene expression after 14 days of exposure to Primary and Secondary Treated Effluents in male liver of Fathead Minnow (FHM).


title: 5%EFFHa_59_10

description:
Replicate 10
Gene expression after 14 days of exposure to Primary and Secondary Treated Effluents in male liver of Fathead Minnow (FHM).

source_name: Liver, 14 d, 5%EFFHa

value: 5% primary treated effluent


title: 5%EFFHa_58_09

description:
Replicate 9
Gene expression after 14 days of exposure to Primary and Secondary Treated Effluents in male liver of Fathead Minnow (FHM).


title: E2b_41b_03

description:
Replicate 3
Gene expression after 14 days of exposure to Primary and Secondary Treated Effluents in male liver of Fathead Minnow (FHM).


title: 5%EFFHa_44_02

description:
Replicate 2
Gene expression after 14 days of exposure to Primary and Secondary Treated Effluents in male liver of Fathead Minnow (FHM).


title: 5%EFFHb_30b_03


title: CTRLb_4b_01


title: 5%EFFHa_53_06


title: 5%EFFHa_51_05


title: E2b_40b_02


title: CTRLb_5b_02


title: E2b_42b_04


title: 5%EFFHa_45_03


title: CTRLb_9b_03


title: 5%EFFHb_34b_04


title: 5%EFFHb_29b_02


title: 5%EFFHa_54_07

description:
Replicate 7
Gene expression after 14 days of exposure to Primary and Secondary Treated Effluents in male liver of Fathead Minnow (FHM).


title: 5%EFFHa_43_01


title: E2b_43b_05


title: 5%EFFHa_56_08

description:
Replicate 8
Gene expression after 14 days of exposure to Primary and Secondary Treated Effluents in male liver of Fathead Minnow (FHM).


title: 0.5%EFFLa_37_03

source_name: Liver, 14 d, 0.5%EFFLa

value: 0.5% primary treated effluent


title: 0.55EFFLa_34_02


title: 5%EFFHa_47_04


title: 5%EFFHb_26b_01


title: E2a_21_03

source_name: Liver, 14 d, E2a


title: 0.5%EFFLa_28_01


title: CTRLa_16_05

source_name: Liver, 14 d, CTRLa


title: CTRLa_15_04


title: E2a_22_04


title: E2a_19_02


title: E2a_18_01


title: CTRLa_12_03


title: CTRLa_8_02


title: CTRLa_4_01


title: Post-menopausal + Tamoxifen 8

status: Public on Aug 10 2009

city: Los Angeles

first: Steve

last: Cole

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

description: To compare eukocyte gene expression differs in individuals with varying levels of estrogen signaling.

hyb_protocol: Standard Affymetrix hybridization protocol for gene 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 mononuclear cells from post-menopausal patient receiving tamoxifen

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: Stage

value: Post-menopausal


title: Post-menopausal + Tamoxifen 5


title: Post-menopausal + Tamoxifen 6


title: Post-menopausal + Tamoxifen 2


title: Post-menopausal + Tamoxifen 9


title: Post-menopausal + Tamoxifen 3


title: Post-menopausal + Tamoxifen 12


title: Post-menopausal + Tamoxifen 7


title: Post-menopausal + Aromatase Inhibitor 9

source_name: Peripheral blood mononuclear cells from post-menopausal patient receiving aromatase inhibitors


title: Post-menopausal + Tamoxifen 10


title: GBM_differentiation_4 days_2

status: Public on Mar 01 2011

city: Pamplona

first: Victor

last: Segura

state: Navarra

address: Avda. Pío XII, 55

department: Unit of Proteomics, Genomics and Bioinformatics

country: Spain

institute: FIMA

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133A 2.0 chip according to the protocols provided by the manufacturer.

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

data_processing: Data analysis performed using R (2.8.1) and Bioconductor packages. The function rma of package affy (1.20.2) was used for normalization.

source_name: glioblastoma stem cells, differentiation, 4 days

label_protocol: The cDNA was prepared from 5 microg total RNA using the One –Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthezising the cRNA using the IVT labeling kit (Affimetrix). The synthezised cRNA was purified with the GeneChip Sample Cleanup Module (Affimetrix).

growth_protocol: Tumor cells were then resuspended in serum-free DMEM/F12 medium (Invitrogen, Carlsbad, CA) containing human recombinant EGF (20 ng/ml; Sigma, St. Louis, MO), bFGF (20 ng/ml; Sigma), B-27 (20 ml per ml of medium; Invitrogen) and heparin (2 mg/ml), and plated at a density of 3x106 live cells/60-mm plate

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: glioblastoma stem cells were differentiated in the presence of FCS for 4 days

value: brain

value: glioblastoma

tag: cell type

value: stem cells G52


title: GBM_stem_4 days_3

source_name: glioblastoma stem cells, stem, 4 days

tag: tissue

value: stem cells G63


title: GBM_stem_4 days_1

value: stem cells G48


title: GBM_differentiation_4 days_1


title: Post-menopausal + Tamoxifen 1


title: Post-menopausal + Aromatase Inhibitor 5


title: GBM_differentiation_4 days_3


title: Post-menopausal + Aromatase Inhibitor 10


title: Post-menopausal + Aromatase Inhibitor 3


title: Post-menopausal + Aromatase Inhibitor 2


title: Post-menopausal + Aromatase Inhibitor 4


title: Post-menopausal + Aromatase Inhibitor 7


title: Post-menopausal + Aromatase Inhibitor 6


title: Post-menopausal + Aromatase Inhibitor 1


title: Post-menopausal 11

source_name: Peripheral blood mononuclear cells from post-menopausal


title: Post-menopausal 10


title: Post-menopausal 9


title: Post-menopausal + Aromatase Inhibitor 8


title: Post-menopausal 8


title: Post-menopausal 7


title: Post-menopausal 3


title: Post-menopausal 6


title: Post-menopausal 1


title: Post-menopausal 12


title: Post-menopausal 4


title: Post-menopausal 2


title: Post-menopausal 5


title: Pre-menopausal 11

source_name: Peripheral blood mononuclear cells from pre-menopausal

value: Pre-menopausal


title: Pre-menopausal 10


title: Pre-menopausal 9


title: Pre-menopausal 5


title: Pre-menopausal 3


title: Pre-menopausal 2


title: Pre-menopausal 8


title: Pre-menopausal 1


title: Pre-menopausal 6


title: GBM_stem_4 days_2


title: accumbens rattus_norvegicus_strain iNP animal_number 8

status: Public on Jul 28 2007

city: Westfield

first: Mark

middle: William

last: Kimpel

state: IN

address: 15032 Hunter Court

department: Psychiatry

institute: Indiana University

description: Gene expression data from brain of adult rats

hyb_protocol: Fifteen µg of fragmented, biotinylated cRNA was mixed into 300 µl of hybridization cocktail, of which 200 µl was used for each hybridization. Hybridization was for 17 hr at 42°C. Washing, staining and scanning were carried out according to the standard protocol.

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

data_processing: The data were analyzed with BioConductor package 'affy', function mas5 using using default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

organism: Rattus norvegicus

label_protocol: RNA from each individual rat was labeled and analyzed separately. Starting with 10 µg of total RNA, first and second-strand cDNA synthesis was carried out according to the standard protocol. Biotinylated cRNA was synthesized in vitro from the double-stranded cDNA using the ENZO BioArray High Yield RNA Transcript Labeling Kit according to the Affymetrix protocol.

growth_protocol: Animals were received in our facilities 3 weeks prior to the experiment. Rats were double housed on a 12:12 light dark cycle with lights on at 0700 hours. Rats had water and rat chow ad libitum. Animals were habituated (by the same experimenter) to handling and to the guillotine daily between 0900 - 1000 hr for 10 days prior to sacrifice.

treatment_protocol: Animal was sacrificed by decapitation between 0900 and 1000 hr. The head was immediately placed in a cold box maintained at -15ºC, where the brain was rapidly removed and placed on a glass plate for dissection. All equipment used to obtain tissue was treated with RNAse Zap.

tag: Genotype

value: Strain iNP

tag: _Age_90-100 days old


title: accumbens rattus_norvegicus_strain iP animal_number 5

value: Strain iP


title: accumbens rattus_norvegicus_strain iNP animal_number 12


title: MOLT3 CompE 24h rep1

status: Public on Aug 20 2008

first: Adolfo

last: Ferrando

address: 1130 St Nicholas Ave Irving Cancer Research Center 5-505A

department: Institute for Cancer Genetics

institute: Columbia University

description: Standard Affymetrix procedure

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: Affymetrix Microarray Suite Version 5 followed by  Dchip data normalization for adjustment of interarray intensity differences and calculation of  model based expression (VALUE).

source_name: MOLT3 Human T-cell lymphoblastic cell line gamma-secretase inhibitor (CompE 500nM) treatment 24h

label_protocol: Approx. 10micrograms of total RNA was processed to produce biotinylated cRNA targets

growth_protocol: Cells were cultured in RPMI1640 media supplemented with 10% fetal bovine serum plus antibiotics (pen/strep) in a humidified incubator with 5% CO2 atmosphere at 37C

extract_protocol: RNA was extracted with RNAqueous minikit (Ambion) following the manufacturer’s instructions

treatment_protocol: Compound E (CompE) [ (2S)-2-{[ (3,5-Difluorophenyl)acetyl]amino}-N-[(3S)-1-methyl-2-oxo-5-phenyl-2,3-dihydro-1H-1,4-benzodiazepin-3-yl] propanamide] (Alexis Biochemicals) a cell permeable, potent, selective, non-transition state and non-competitive inhibitor of gamma-secretase treatment at 500nM in DMSO for 24h.

tag: T-cell acute lymphoblastic leukemia cell line


title: accumbens rattus_norvegicus_strain iP animal_number 4


title: accumbens rattus_norvegicus_strain iP animal_number 2


title: accumbens rattus_norvegicus_strain iNP animal_number 7


title: accumbens rattus_norvegicus_strain iP animal_number 3


title: accumbens rattus_norvegicus_strain iNP animal_number 11


title: Post-menopausal + Tamoxifen 4


title: amygdala rattus_norvegicus_strain iNP animal_number 12


title: amygdala rattus_norvegicus_strain iNP animal_number 11


title: accumbens rattus_norvegicus_strain iP animal_number 6


title: amygdala rattus_norvegicus_strain iNP animal_number 8


title: amygdala rattus_norvegicus_strain iNP animal_number 9


title: amygdala rattus_norvegicus_strain iP animal_number 6


title: amygdala rattus_norvegicus_strain iNP animal_number 7


title: accumbens rattus_norvegicus_strain iNP animal_number 10


title: amygdala rattus_norvegicus_strain iNP animal_number 10


title: amygdala rattus_norvegicus_strain iP animal_number 5


title: amygdala rattus_norvegicus_strain iP animal_number 2


title: Post-menopausal + Tamoxifen 11


title: hippocampus rattus_norvegicus_strain iNP animal_number 11


title: amygdala rattus_norvegicus_strain iP animal_number 3


title: amygdala rattus_norvegicus_strain iP animal_number 4


title: hippocampus rattus_norvegicus_strain iNP animal_number 7


title: hippocampus rattus_norvegicus_strain iNP animal_number 10


title: amygdala rattus_norvegicus_strain iP animal_number 1


title: hippocampus rattus_norvegicus_strain iP animal_number 3


title: striatum rattus_norvegicus_strain iNP animal_number 12


title: hippocampus rattus_norvegicus_strain iNP animal_number 8


title: hippocampus rattus_norvegicus_strain iP animal_number 4


title: hippocampus rattus_norvegicus_strain iNP animal_number 9


title: striatum rattus_norvegicus_strain iNP animal_number 10


title: striatum rattus_norvegicus_strain iP animal_number 6


title: hippocampus rattus_norvegicus_strain iNP animal_number 12


title: hippocampus rattus_norvegicus_strain iP animal_number 5


title: striatum rattus_norvegicus_strain iNP animal_number 7


title: striatum rattus_norvegicus_strain iNP animal_number 9


title: striatum rattus_norvegicus_strain iP animal_number 4


title: striatum rattus_norvegicus_strain iNP animal_number 11


title: striatum rattus_norvegicus_strain iP animal_number 3


title: hippocampus rattus_norvegicus_strain iP animal_number 2


title: striatum rattus_norvegicus_strain iNP animal_number 8


title: hippocampus rattus_norvegicus_strain iP animal_number 6


title: striatum rattus_norvegicus_strain iP animal_number 5


title: striatum rattus_norvegicus_strain iP animal_number 2


title: hippocampus rattus_norvegicus_strain iP animal_number 1


title: accumbens rattus_norvegicus_strain iP animal_number 1


title: cortex rattus_norvegicus_strain iNP animal_number 11


title: cortex rattus_norvegicus_strain iP animal_number 3


title: cortex rattus_norvegicus_strain iP animal_number 5


title: cortex rattus_norvegicus_strain iP animal_number 4


title: cortex rattus_norvegicus_strain iNP animal_number 12


title: striatum rattus_norvegicus_strain iP animal_number 1


title: cortex rattus_norvegicus_strain iP animal_number 2


title: cortex rattus_norvegicus_strain iNP animal_number 8


title: cortex rattus_norvegicus_strain iNP animal_number 10


title: cortex rattus_norvegicus_strain iNP animal_number 7


title: accumbens rattus_norvegicus_strain iNP animal_number 9


title: cortex rattus_norvegicus_strain iNP animal_number 9


title: cortex rattus_norvegicus_strain iP animal_number 1


title: A NUH.BT097

status: Public on Jul 13 2006

city: Singapore

first: Lance

middle: David

last: Miller

address: 60 Bioplois Street, #02-01 Genome

department: Microarray and Expression Genomics

country: Singapore

institute: Genome Institute of Singapore

description: Series of 40 tumours

data_processing: Affymetrix Microarray Suite Version 5.0

source_name: Breast Tumor

label_protocol: Approximately 10ug of total RNA was processed to produce biotynylated cRNA targets

extract_protocol: Qiagen RNeasy Mini Kit

tag: NUH-sample ID

tag: grade

tag: Probability 1-like (by SWS classifier)

tag: Probability 3-like (by SWS classifier)

tag: Genetic grade signature status prediction (by SWS classifier)


title: A NUH.BT094

description: Series of 40 tumours


title: A NUH.BT095

description: Series of 40 tumours


title: Burn Sham Spleen 3 day rep 1

status: Public on Mar 31 2007

city: Boston

first: Wenzhong Xiao

address: 55 Fruit Street, GRV 1302

department: Department of Surgery

institute: Massachusetts General Hospital

description: trauma hemorrage injury model

hyb_protocol: Labeled targets were hybridized to Affymetrix (Santa Clara, CA) Mouse Genome 430 2.0 Array GeneChip™ microarrays for 16 hours at 45° C. The arrays were washed and scanned according to Affymetrix standard protocols

scan_protocol: Scanned according to Affymetrix standard protocols.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0/GCOS 1.4 ) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: mouse splenocytes

label_protocol: 1-2 μg of total RNA was used to make single-stranded antisense cDNA using the NuGEN Technologies (San Carlo, CA) Ovation™ Biotin System in accordance with the manufacturer’s directions.

extract_protocol: Total RNA was isolated using the manufacturer’s recommended protocol for RNeasy (Qiagen, Valencia, CA).

treatment_protocol: Leukocyte isolation from cardiac puncture followed by RBC lysis with proprietary buffer, followed by suspension in RLT buffer ;  Splenocytes in Dulbeco's PBS followed by the same RBC lysis RLT suspension process.

tag: Male C57BL/6J


title: A NUH.BT114

description: Series of 40 tumours


title: A NUH.BT108

description: Series of 40 tumours


title: Pre-menopausal 7


title: A NUH.BT104

description: Series of 40 tumours


title: A NUH.BT103

description: Series of 40 tumours


title: A NUH.BT119

description: Series of 40 tumours


title: A NUH.BT096

description: Series of 40 tumours


title: A NUH.BT093

description: Series of 40 tumours


title: A NUH.BT090

description: Series of 40 tumours


title: A NUH.BT113

description: Series of 40 tumours


title: A NUH.BT111

description: Series of 40 tumours


title: Trauma Hemorrhage Burn  7 day rep 1

description: trauma hemorrage injury model

source_name: mouse leukocytes


title: A NUH.BT087

description: Series of 40 tumours


title: A NUH.BT078

description: Series of 40 tumours


title: A NUH.BT067

description: Series of 40 tumours


title: A NUH.BT074

description: Series of 40 tumours


title: A NUH.BT055

description: Series of 40 tumours


title: A NUH.BT086

description: Series of 40 tumours


title: A NUH.BT088

description: Series of 40 tumours


title: A NUH.BT083

description: Series of 40 tumours


title: A NUH.BT049

description: Series of 40 tumours


title: A NUH.BT047

description: Series of 40 tumours


title: A NUH.BT061

description: Series of 40 tumours


title: A NUH.BT068

description: Series of 40 tumours


title: A NUH.BT046

description: Series of 40 tumours


title: A NUH.BT035

description: Series of 40 tumours


title: A NUH.BT054

description: Series of 40 tumours


title: A NUH.BT070

description: Series of 40 tumours


title: A NUH.BT019

description: Series of 40 tumours


title: A NUH.BT029

description: Series of 40 tumours


title: A NUH.BT031

description: Series of 40 tumours


title: A NUH.BT042

description: Series of 40 tumours


title: Pre-menopausal 4


title: A NUH.BT023

description: Series of 40 tumours


title: A NUH.BT009

description: Series of 40 tumours


title: A NUH.BT014

description: Series of 40 tumours


title: New El-Ashry 002.CEL

status: Public on Apr 06 2006

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: MCF-7 sham-transfected, adapted for long-term growth in absence of E2

hyb_protocol: Standard protocol

scan_protocol: Standard protocol

data_processing: RMAExpress version 0.3

label_protocol: Standard protocol

extract_protocol: Standard protocol

tag: cell line

value: MCF-7 breast cancer cells


title: A NUH.BT018

description: Series of 40 tumours


title: El-Ashry 002.CEL


title: New El-Ashry 001.CEL

description: MCF-7 sham-transfected, grown in FBS


title: E1_T7_R1, Control, monolayer, antibiotics

status: Public on Aug 01 2005

city: Blacksburg

middle: F.

last: Helm

state: VA

address: West Campus Drive

department: Biochemistry, Fralin Biotechnology Center

institute: Virginia Polytechnic Institute and State University

description:
1x10^7 Human embryonic kidney cell spheroids were grown for 7 days in suspension over agarose prepared with FBS supplemented DMEM containing 50mM HEPES, pH 7.2, and 1xGlutamax-1 (Invitrogen).
Following growth, media was removed and the spheroids were stored on the surface of the agarose in sealed flasks for 2,4, and 6 week intervals at room temperature in the dark.
The samples were compared against unstored controls of both spheroids and monolayer (at 30-40% confluence)samples. All samples were conducted in triplicate.
For each storage timepoint, a set of unrehydrated samples were analyzed, and an additional set of rehydrated samples were analyzed after allowing for growth in a treated tissue culture flask, to assess how well the samples returned to a normal, pre-storage state.
Rehydration was conducted with DMEM (Invitrogen) containing 20%FBS and antibiotics (100U penicillin, 100ug/mL streptomycin, and 0.25ug Fungizone), with HEPES and Glutamax as stated previously.

source_name: Kidney 293 HEK Cells

value: 2-D monolayer

tag: stress

value: no dry storage

tag: time

tag: antibiotics (yes or no?)

value: yes


title: E1_T1_R2, Control, monolayer

value: no


title: New El-Ashry 008.CEL


title: A NUH.BT022

description: Series of 40 tumours


title: New El-Ashry 007.CEL

description: MCF-7 sham-transfected, grown in FBS


title: MPI-149

status: Public on Jun 07 2006

first: Michael

last: Hummel

address: Hindenburgdamm 30

department: Institute of Pathology

institute: Universitätsmedizin Berlin, Campus Benjamin Franklin

description: Mature aggressive B-cell lymphoma

data_processing: Probe level normalization was done using the calibration and variance stabilization method by Huber et al. (Bioinformatics 2002, PMID: 12169536).  Probe-set summarization was performed using the median polish method on the normalized data (Irrizary et al. Nucleic Acids Research 2003, PMID: 12582260).

source_name: Frozen tissue

tag: Relapse

tag: Age

tag: Sex

value: male

value: DLBCL

value: present

value: absent

value: MYC-negative

value: IV

tag: Lesions

value: nodal

value: dead

tag: Radiotherapy

tag: RITUXIMAB

tag: Chemotherapy

value: CHOP-like

value: non-mBL

value: ABC

value: Training


title: T3.CEL

status: Public on Jan 15 2006

description: T47-D grown in the presence of Estrogen (24 hr)

value: T47-D breast cancer cells


title: B1.CEL

description: BT-474 grown in the absence of Estrogen

value: BT-474 breast cancer cells


title: E1_T1_R1, Control, monolayer

tag: cell type

value: 2-D monolayer

value: no dry storage


title: El-Ashry 001.CEL

description: MCF-7 sham-transfected, grown in FBS

value: MCF-7 breast cancer cells


title: T2.CEL

description: T47-D grown in the absence of Estrogen


title: UMI_3_U133.CEL

description: MCF-7 grown in the presence of Estrogen (24 hr)


title: T4.CEL


title: B2.CEL

description: BT-474 grown in the absence of Estrogen


title: E1_T1_R3, Control, monolayer

value: no


title: E1_T6_R3, six week storage/0hr recovery

value: 3-D spheroid

value: 6 wk dry storage

value: 0 h recovery


title: E1_T7_R2, Control, monolayer, antibiotics

value: yes


title: UMI_1B_U133.CEL

description: MCF-7 grown in the absence of Estrogen


title: B4.CEL

description: BT-474 grown in the presence of Estrogen (24 hr)


title: UMI_1A_U133.CEL

description: MCF-7 grown in the absence of Estrogen


title: B3.CEL


title: UMI_2_U133.CEL


title: T1.CEL

description: T47-D grown in the absence of Estrogen


title: E1_T7_R3, Control, monolayer, antibiotics


title: E1_T6_R1, six week storage/0hr recovery


title: E1_T6_R2, six week storage/0hr recovery


title: E1_T5_R3, four week storage/0hr recovery

value: 4 wk dry storage


title: E1_T5_R2, four week storage/0hr recovery


title: E1_T5_R1, four week storage/0hr recovery


title: E1_T4_R3, two week storage/full recovery

value: 2 wk dry storage

value: 72 hr recovery


title: E1_T4_R2, two week storage/full recovery


title: E1_T3_R2, two week storage/0hr recovery


title: E1_T4_R1, two week storage/full recovery


title: E1_T3_R3, two week storage/0hr recovery


title: E1_T2_R1, Spheroid, no storage


title: E1_T2_R3, Spheroid, no storage


title: E1_T2_R2, Spheroid, no storage


title: E1_T3_R1, two week storage/0hr recovery