title: induced clone of WBSCR1, biological replicate1

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description:
WBSCR1_t24_1.CEL
Gene expression data from mouse inducible ES stable clone

hyb_protocol: Biotinylated cRNAs were generated using the GeneChip IVT labelling kit (Affymetrix). 20µg of Biotinylated cRNA was fragmented and 10µg hybridised to the Affymetrix GeneChip Mouse Genome 430_2 array for 16hrs at 45°C using an Affymetrix GeneChip Fluidics Station 450 according to the manufacturer’ standard protocols.

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

data_processing: The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.

source_name: inducible ES stable cell line grown in medium deprived of Tetracycline

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

growth_protocol: The growth of each inducible clone was performed in medium deprived of Tetracycline for 17 or 24 hours, while the control clones were grown in medium containing Tetracycline and the total RNA was extracted. Total RNA was extracted from parental cell line EBRTcH3 (EB3) grown in medium containing Tetracycline.

extract_protocol: Total RNAs from all inducible ES clones and from EB3 were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.

treatment_protocol: The growth of each inducible clone was performed in medium deprived of Tetracycline for 17 or 24 hours, while the control clones and of parental cell line EB3 were grown in medium containing Tetracycline and the total RNA was extracted

value: Embryonic Stem (ES)  cells


title: LeafBlade_100DAT_20:00

status: Public on Dec 03 2012

type: RNA

city: Tsukuba

first: Yutaka

last: Sato

state: Ibaraki

address: 2-1-2 Kannondai

country: Japan

institute: National Institute of Agrobiological Sciences

description: Gene expression of leaf blade at 100 days after transplanting, 20:00

hyb_protocol: For hybridization, 1650 ng of cyanine 3-labeled cRNA is fragmented and hybridized on the slide of rice 4x44K microarray RAP-DB (G2519F#15241) at 65°C for 17 hours using the Agilent Gene Expression Hybridization Kit.

scan_protocol: Slides were scanned on an Agilent G2505B DNA microarray scanner using one-color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 5um,  Dye channel is set to Green PMT: XDR Hi 100%; XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities. The processed signal intensities were used for 75 percentile normalization and log2 transformation with GenespringGX11(Agilent).

molecule: total RNA

organism: Oryza sativa Japonica Group

source_name: Leaf blade, 100 days after transplanting, 20:00

label_protocol: 400 ng of total RNA was added with one-color spike-mix and labeling was performed using Quick Amp Labeling Kit, One-Color (Agilent) in the presence of cyanine-3-CTP accoring to the manufacturer's protocol. The cyanine-3-labeled cRNA was purified by RNeasy Mini Kit (QIAGEN), and quantified using NanoDrop ND-1000 UV-VIS spectrophotometer.

growth_protocol: All plants were grown in paddy field in Tsukuba, Japan (~36o N latitude) during a normal rice growing season in 2008.

extract_protocol: Total RNA was extracted using RNeasy Plant Mini Kit (QIAGEN) according to the manufacturer's protocol, quantitied using NanoDrop ND-1000 UV-VIS spectrophotometer (NanoDrop) and quality-checked using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

tag: cultivar

value: Nipponbare

tag: organ/tissue

value: Leaf Blade

tag: growth/development stage

value: 100 days after transplanting

tag: sampling time


title: induced clone of WBSCR1, biological replicate3

description:
WBSCR1_t24_3.CEL
Gene expression data from mouse inducible ES stable clone

label: biotin

organism: Mus musculus

tag: cell type


title: inducible clone of WBSCR1, biological replicate3

description:
WBSCR1_t0_3.CEL
Gene expression data from mouse inducible ES stable clone

source_name: inducible ES stable cell line grown in medium containing Tetracycline


title: induced clone of WBSCR1, biological replicate2

description:
WBSCR1_t24_2.CEL
Gene expression data from mouse inducible ES stable clone


title: LeafBlade_87DAT_06:00

description: Gene expression of leaf blade at 87 days after transplanting, 06:00

source_name: Leaf blade, 87 days after transplanting, 06:00

value: 87 days after transplanting


title: inducible clone of WBSCR1, biological replicate1

description:
WBSCR1_t0_1.CEL
Gene expression data from mouse inducible ES stable clone


title: LeafBlade_92DAT_16:00

description: Gene expression of leaf blade at 92 days after transplanting, 16:00

source_name: Leaf blade, 92 days after transplanting, 16:00

value: 92 days after transplanting


title: LeafBlade_92DAT_10:00

description: Gene expression of leaf blade at 92 days after transplanting, 10:00

source_name: Leaf blade, 92 days after transplanting, 10:00


title: LeafBlade_87DAT_10:00

description: Gene expression of leaf blade at 87 days after transplanting, 10:00

source_name: Leaf blade, 87 days after transplanting, 10:00


title: LeafBlade_92DAT_18:00

description: Gene expression of leaf blade at 92 days after transplanting, 18:00

source_name: Leaf blade, 92 days after transplanting, 18:00


title: LeafBlade_87DAT_08:00

description: Gene expression of leaf blade at 87 days after transplanting, 08:00

source_name: Leaf blade, 87 days after transplanting, 08:00


title: inducible clone of SUMF1, biological replicate3

description:
SUMF1_t0_3.CEL
Gene expression data from mouse inducible ES stable clone


title: LeafBlade_87DAT_02:00

description: Gene expression of leaf blade at 87 days after transplanting, 02:00

source_name: Leaf blade, 87 days after transplanting, 02:00


title: LeafBlade_86DAT_20:00

description: Gene expression of leaf blade at 86 days after transplanting, 20:00

source_name: Leaf blade, 86 days after transplanting, 20:00

value: 86 days after transplanting


title: LeafBlade_93DAT_02:00

description: Gene expression of leaf blade at 93 days after transplanting, 02:00

source_name: Leaf blade, 93 days after transplanting, 02:00

value: 93 days after transplanting


title: LeafBlade_86DAT_24:00

description: Gene expression of leaf blade at 86 days after transplanting, 24:00

source_name: Leaf blade, 86 days after transplanting, 24:00


title: LeafBlade_87DAT_04:00

description: Gene expression of leaf blade at 87 days after transplanting, 04:00

source_name: Leaf blade, 87 days after transplanting, 04:00


title: LeafBlade_86DAT_22:00

description: Gene expression of leaf blade at 86 days after transplanting, 22:00

source_name: Leaf blade, 86 days after transplanting, 22:00


title: induced clone of SUMF1, biological replicate1

description:
SUMF1_t24_1.CEL
Gene expression data from mouse inducible ES stable clone


title: inducible clone of WBSCR1, biological replicate2

description:
WBSCR1_t0_2.CEL
Gene expression data from mouse inducible ES stable clone


title: induced clone of SUMF1, biological replicate2

description:
SUMF1_t24_2.CEL
Gene expression data from mouse inducible ES stable clone


title: LeafBlade_86DAT_18:00

description: Gene expression of leaf blade at 86 days after transplanting, 18:00

source_name: Leaf blade, 86 days after transplanting, 18:00


title: induced clone of SUMF1, biological replicate3

description:
SUMF1_t24_3.CEL
Gene expression data from mouse inducible ES stable clone


title: inducible clone of SUMF1, biological replicate2

description:
SUMF1_t0_2.CEL
Gene expression data from mouse inducible ES stable clone


title: LeafBlade_86DAT_16:00

description: Gene expression of leaf blade at 86 days after transplanting, 16:00

source_name: Leaf blade, 86 days after transplanting, 16:00


title: LeafBlade_86DAT_12:00

description: Gene expression of leaf blade at 86 days after transplanting, 12:00

source_name: Leaf blade, 86 days after transplanting, 12:00


title: inducible clone of SUMF1, biological replicate1

description:
SUMF1_t0_1.CEL
Gene expression data from mouse inducible ES stable clone


title: induced clone of MYC, biological replicate3

description:
MYC_t17_3.CEL
Gene expression data from mouse inducible ES stable clone

source_name: inducible ES stable cell line grown in medium deprived of Tetracycline


title: LeafBlade_86DAT_06:00

description: Gene expression of leaf blade at 86 days after transplanting, 06:00

source_name: Leaf blade, 86 days after transplanting, 06:00


title: LeafBlade_86DAT_10:00

description: Gene expression of leaf blade at 86 days after transplanting, 10:00

source_name: Leaf blade, 86 days after transplanting, 10:00


title: LeafBlade_86DAT_04:00

description: Gene expression of leaf blade at 86 days after transplanting, 04:00

source_name: Leaf blade, 86 days after transplanting, 04:00


title: Large White 145 kg Replicate 8

city: saint-gilles

first: marie

last: damon

address: domaine de la prise

country: France

institute: INRA

description: Large white 145 kg sample Replicate 8 of 10

hyb_protocol: Microarray hybridizations were carried out in Agilent’s SureHyb hybridization chambers containing 300 ng of Cy3-labeled cRNA sample and 300 ng of Cy5-labeled reference pool per hybridization. Hybridization reactions were performed at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit.

scan_protocol: After washing, the microarrays were scanned at 5 µm/pixel resolution using the Agilent DNA Microarray Scanner G2505B. Images were analyzed with Agilent Feature Extraction Software (Version 10.5.1.1, protocol GE2_105_Dec08)

data_processing: All analyses were performed using the R software version 2.10.0 (R Development Core Team, 2008a). Raw spots intensities (gProcessed signal and rProcessed signal) were first submitted to quality filtration based on 4 criteria: intensity, uniformity, saturation and outliers detection. Intensities of filtered spots were transformed into log2(Cy3/Cy5), and data were normalized within chips by subtraction of the sample median value across all probes from all raw values and between chips using the “Rquantile” method of the Limma R package  (Smyth, G. K. et al. 2003) to obtain experimentally consolidated gene expression values. The “Rquantile” method was used since the red channel is a common reference throughout the experiment.

organism: Sus scrofa

source_name: Subcutaneous adipose tissue of 145 kg LW pig

label_protocol: Total RNA (350 ng) from each animal was labeled individually with Cy3 by using the Quick-Amp Labeling Kit  following the manufacturer’s instructions.

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

tag: tissue

value: subcutaneous adipose tissue

tag: breed

value: Large White

tag: pig live weight

tag: ChIP

source_name: reference pool composed of an equal amount of total RNA isolated from all 30 samples

tag: sample type


title: Large White 145 kg Replicate 9

description: Large white 145 kg sample Replicate 9 of 10

value: reference pool composed of an equal amount of total RNA isolated from all 30 samples


title: Large White 145 kg Replicate 7

description: Large white 145 kg sample Replicate 7 of 10


title: Large White 145 kg Replicate 10

description: Large white 145 kg sample Replicate 10 of 10


title: Large White 145 kg Replicate 6

description: Large white 145 kg sample Replicate 6 of 10


title: induced clone of MYC, biological replicate2

description:
MYC_t17_2.CEL
Gene expression data from mouse inducible ES stable clone


title: LeafBlade_86DAT_08:00

description: Gene expression of leaf blade at 86 days after transplanting, 08:00

source_name: Leaf blade, 86 days after transplanting, 08:00


title: induced clone of MYC, biological replicate1

description:
MYC_t17_1.CEL
Gene expression data from mouse inducible ES stable clone


title: inducible clone of MYC, biological replicate3

description:
MYC_t0_3.CEL
Gene expression data from mouse inducible ES stable clone

source_name: inducible ES stable cell line grown in medium containing Tetracycline


title: inducible clone of MYC, biological replicate2

description:
MYC_t0_2.CEL
Gene expression data from mouse inducible ES stable clone


title: LeafBlade_86DAT_02:00

description: Gene expression of leaf blade at 86 days after transplanting, 02:00

source_name: Leaf blade, 86 days after transplanting, 02:00


title: Large White 145 kg Replicate 5

description: Large white 145 kg sample Replicate 15 of 10


title: LeafBlade_85DAT_20:00

description: Gene expression of leaf blade at 85 days after transplanting, 20:00

source_name: Leaf blade, 85 days after transplanting, 20:00

value: 85 days after transplanting


title: LeafBlade_85DAT_22:00

description: Gene expression of leaf blade at 85 days after transplanting, 22:00

source_name: Leaf blade, 85 days after transplanting, 22:00


title: LeafBlade_85DAT_24:00

description: Gene expression of leaf blade at 85 days after transplanting, 24:00

source_name: Leaf blade, 85 days after transplanting, 24:00


title: Large White 145 kg Replicate 4

description: Large white 145 kg sample Replicate 4 of 10


title: LeafBlade_85DAT_16:00

description: Gene expression of leaf blade at 85 days after transplanting, 16:00

source_name: Leaf blade, 85 days after transplanting, 16:00


title: Large White 145 kg Replicate 3

description: Large white 145 kg sample Replicate 3 of 10


title: LeafBlade_85DAT_14:00

description: Gene expression of leaf blade at 85 days after transplanting, 14:00

source_name: Leaf blade, 85 days after transplanting, 14:00


title: inducible clone of MYC, biological replicate1

description:
MYC_t0_1.CEL
Gene expression data from mouse inducible ES stable clone


title: induced clone of GTF2IRD2, biological replicate3

description:
GTF2IRD2_t24_3.CEL
Gene expression data from mouse inducible ES stable clone


title: LeafBlade_85DAT_12:00

description: Gene expression of leaf blade at 85 days after transplanting, 12:00

source_name: Leaf blade, 85 days after transplanting, 12:00


title: Large White 145 kg Replicate 2

description: Large white 145 kg sample Replicate 2 of 10


title: Basque 145 kg Replicate 10

description: Basque 145 kg sample Replicate 10 of 10

source_name: Subcutaneous adipose tissue of 145 kg B pig

value: Basque


title: LeafBlade_85DAT_18:00

description: Gene expression of leaf blade at 85 days after transplanting, 18:00

source_name: Leaf blade, 85 days after transplanting, 18:00


title: Large White 145 kg Replicate 1

description: Large white 145 kg sample Replicate 1 of 10


title: LeafBlade_80DAT_06:00

description: Gene expression of leaf blade at 80 days after transplanting, 06:00

source_name: Leaf blade, 80 days after transplanting, 06:00

value: 80 days after transplanting


title: LeafBlade_80DAT_04:00

description: Gene expression of leaf blade at 80 days after transplanting, 04:00

source_name: Leaf blade, 80 days after transplanting, 04:00


title: inducible clone of GTF2IRD2, biological replicate3

description:
GTF2IRD2_t0_3.CEL
Gene expression data from mouse inducible ES stable clone


title: Basque 145 kg Replicate 9

description: Basque 145 kg sample Replicate 9 of 10


title: Basque 145 kg Replicate 8

description: Basque 145 kg sample Replicate 8 of 10


title: LeafBlade_79DAT_22:00

description: Gene expression of leaf blade at 79 days after transplanting, 22:00

source_name: Leaf blade, 79 days after transplanting, 22:00

value: 79 days after transplanting


title: LeafBlade_80DAT_02:00

description: Gene expression of leaf blade at 80 days after transplanting, 02:00

source_name: Leaf blade, 80 days after transplanting, 02:00


title: induced clone of GTF2IRD2, biological replicate2

description:
GTF2IRD2_t24_2.CEL
Gene expression data from mouse inducible ES stable clone

source_name: inducible ES stable cell line grown in medium deprived of Tetracycline


title: LeafBlade_79DAT_24:00

description: Gene expression of leaf blade at 79 days after transplanting, 24:00

source_name: Leaf blade, 79 days after transplanting, 24:00


title: LeafBlade_79DAT_16:00

description: Gene expression of leaf blade at 79 days after transplanting, 16:00

source_name: Leaf blade, 79 days after transplanting, 16:00


title: LeafBlade_85DAT_10:00

description: Gene expression of leaf blade at 85 days after transplanting, 10:00

source_name: Leaf blade, 85 days after transplanting, 10:00


title: LeafBlade_80DAT_10:00

description: Gene expression of leaf blade at 80 days after transplanting, 10:00

source_name: Leaf blade, 80 days after transplanting, 10:00


title: LeafBlade_79DAT_20:00

description: Gene expression of leaf blade at 79 days after transplanting, 20:00

source_name: Leaf blade, 79 days after transplanting, 20:00


title: LeafBlade_80DAT_08:00

description: Gene expression of leaf blade at 80 days after transplanting, 08:00

source_name: Leaf blade, 80 days after transplanting, 08:00


title: induced clone of GTF2IRD2, biological replicate1

description:
GTF2IRD2_t24_1.CEL
Gene expression data from mouse inducible ES stable clone


title: LeafBlade_79DAT_14:00

description: Gene expression of leaf blade at 79 days after transplanting, 14:00

source_name: Leaf blade, 79 days after transplanting, 14:00


title: LeafBlade_79DAT_12:00

description: Gene expression of leaf blade at 79 days after transplanting, 12:00

source_name: Leaf blade, 79 days after transplanting, 12:00


title: inducible clone of GTF2IRD2, biological replicate2

description:
GTF2IRD2_t0_2.CEL
Gene expression data from mouse inducible ES stable clone

source_name: inducible ES stable cell line grown in medium containing Tetracycline


title: inducible clone of GTF2IRD2, biological replicate1

description:
GTF2IRD2_t0_1.CEL
Gene expression data from mouse inducible ES stable clone


title: Basque 145 kg Replicate 7

description: Basque 145 kg sample Replicate 7 of 10

source_name: reference pool composed of an equal amount of total RNA isolated from all 30 samples


title: induced clone of GTF2IRD1, biological replicate3

description:
GTF2IRD1_t24_3.CEL
Gene expression data from mouse inducible ES stable clone


title: Basque 145 kg Replicate 6

description: Basque 145 kg sample Replicate 6 of 10

source_name: Subcutaneous adipose tissue of 145 kg B pig


title: LeafBlade_79DAT_08:00

description: Gene expression of leaf blade at 79 days after transplanting, 08:00

source_name: Leaf blade, 79 days after transplanting, 08:00


title: induced clone of GTF2IRD1, biological replicate2

description:
GTF2IRD1_t24_2.CEL
Gene expression data from mouse inducible ES stable clone


title: Basque 145 kg Replicate 2

description: Basque 145 kg sample Replicate 2 of 10


title: LeafBlade_79DAT_04:00

description: Gene expression of leaf blade at 79 days after transplanting, 04:00

source_name: Leaf blade, 79 days after transplanting, 04:00


title: Basque 145 kg Replicate 3

description: Basque 145 kg sample Replicate 3 of 10


title: LeafBlade_79DAT_06:00

description: Gene expression of leaf blade at 79 days after transplanting, 06:00

source_name: Leaf blade, 79 days after transplanting, 06:00


title: induced clone of GTF2IRD1, biological replicate1

description:
GTF2IRD1_t24_1.CEL
Gene expression data from mouse inducible ES stable clone


title: inducible clone of GTF2IRD1, biological replicate3

description:
GTF2IRD1_t0_3.CEL
Gene expression data from mouse inducible ES stable clone


title: inducible clone of GTF2IRD1, biological replicate2

description:
GTF2IRD1_t0_2.CEL
Gene expression data from mouse inducible ES stable clone


title: LeafBlade_78DAT_24:00

description: Gene expression of leaf blade at 78 days after transplanting, 24:00

source_name: Leaf blade, 78 days after transplanting, 24:00

value: 78 days after transplanting


title: LeafBlade_78DAT_20:00

description: Gene expression of leaf blade at 78 days after transplanting, 20:00

source_name: Leaf blade, 78 days after transplanting, 20:00


title: Basque 145 kg Replicate 4

description: Basque 145 kg sample Replicate 4 of 10


title: LeafBlade_78DAT_22:00

description: Gene expression of leaf blade at 78 days after transplanting, 22:00

source_name: Leaf blade, 78 days after transplanting, 22:00


title: LeafBlade_78DAT_16:00

description: Gene expression of leaf blade at 78 days after transplanting, 16:00

source_name: Leaf blade, 78 days after transplanting, 16:00


title: Basque 145 kg Replicate 5

description: Basque 145 kg sample Replicate 15 of 10


title: inducible clone of GTF2IRD1, biological replicate1

description:
GTF2IRD1_t0_1.CEL
Gene expression data from mouse inducible ES stable clone


title: Large White 35 kg Replicate 5

description: Large white 35 kg sample Replicate 5 of 5

source_name: Subcutaneous adipose tissue of 35 kg LW pig

value: 35 kg


title: Basque 145 kg Replicate 1

description: Basque 145 kg sample Replicate 1 of 10


title: LeafBlade_79DAT_18:00

description: Gene expression of leaf blade at 79 days after transplanting, 18:00

source_name: Leaf blade, 79 days after transplanting, 18:00


title: LeafBlade_59DAT_10:00

description: Gene expression of leaf blade at 59 days after transplanting, 10:00

source_name: Leaf blade, 59 days after transplanting, 10:00

value: 59 days after transplanting


title: LeafBlade_79DAT_10:00

description: Gene expression of leaf blade at 79 days after transplanting, 10:00

source_name: Leaf blade, 79 days after transplanting, 10:00

value: Nipponbare


title: induced clone of GTF2I, biological replicate2

description:
GTF2I_t24_2.CEL
Gene expression data from mouse inducible ES stable clone

source_name: inducible ES stable cell line grown in medium deprived of Tetracycline

value: Embryonic Stem (ES)  cells


title: LeafBlade_78DAT_12:00

description: Gene expression of leaf blade at 78 days after transplanting, 12:00

source_name: Leaf blade, 78 days after transplanting, 12:00

value: Leaf Blade


title: LeafBlade_79DAT_02:00

description: Gene expression of leaf blade at 79 days after transplanting, 02:00

source_name: Leaf blade, 79 days after transplanting, 02:00


title: induced clone of GTF2I, biological replicate3

description:
GTF2I_t24_3.CEL
Gene expression data from mouse inducible ES stable clone


title: induced clone of GTF2I, biological replicate1

description:
GTF2I_t24_1.CEL
Gene expression data from mouse inducible ES stable clone


title: LeafBlade_78DAT_14:00

description: Gene expression of leaf blade at 78 days after transplanting, 14:00

source_name: Leaf blade, 78 days after transplanting, 14:00


title: LeafBlade_59DAT_02:00

description: Gene expression of leaf blade at 59 days after transplanting, 02:00

source_name: Leaf blade, 59 days after transplanting, 02:00


title: LeafBlade_78DAT_18:00

description: Gene expression of leaf blade at 78 days after transplanting, 18:00

source_name: Leaf blade, 78 days after transplanting, 18:00


title: LeafBlade_78DAT_10:00

description: Gene expression of leaf blade at 78 days after transplanting, 10:00

source_name: Leaf blade, 78 days after transplanting, 10:00


title: Large White 35 kg Replicate 3

description: Large white 35 kg sample Replicate 3 of 5

source_name: reference pool composed of an equal amount of total RNA isolated from all 30 samples


title: LeafBlade_59DAT_06:00

description: Gene expression of leaf blade at 59 days after transplanting, 06:00

source_name: Leaf blade, 59 days after transplanting, 06:00


title: LeafBlade_59DAT_08:00

description: Gene expression of leaf blade at 59 days after transplanting, 08:00

source_name: Leaf blade, 59 days after transplanting, 08:00


title: LeafBlade_59DAT_04:00

description: Gene expression of leaf blade at 59 days after transplanting, 04:00

source_name: Leaf blade, 59 days after transplanting, 04:00


title: Large White 35 kg Replicate 4

description: Large white 35 kg sample Replicate 4 of 5


title: inducible clone of GTF2I, biological replicate3

description:
GTF2I_t0_3.CEL
Gene expression data from mouse inducible ES stable clone

source_name: inducible ES stable cell line grown in medium containing Tetracycline


title: Large White 35 kg Replicate 2

description: Large white 35 kg sample Replicate 2 of 5


title: LeafBlade_58DAT_24:00

description: Gene expression of leaf blade at 58 days after transplanting, 24:00

source_name: Leaf blade, 58 days after transplanting, 24:00

value: 58 days after transplanting


title: Large White 35 kg Replicate 1

description: Large white 35 kg sample Replicate 1 of 5

source_name: Subcutaneous adipose tissue of 35 kg LW pig


title: LeafBlade_58DAT_20:00

description: Gene expression of leaf blade at 58 days after transplanting, 20:00

source_name: Leaf blade, 58 days after transplanting, 20:00


title: inducible clone of GTF2I, biological replicate2

description:
GTF2I_t0_2.CEL
Gene expression data from mouse inducible ES stable clone


title: LeafBlade_58DAT_18:00

description: Gene expression of leaf blade at 58 days after transplanting, 18:00

source_name: Leaf blade, 58 days after transplanting, 18:00


title: Basque 35 kg Replicate 5

description: Basque 35 kg sample Replicate 5 of 5

source_name: Subcutaneous adipose tissue of 35 kg B pig


title: inducible clone of GTF2I, biological replicate1

description:
GTF2I_t0_1.CEL
Gene expression data from mouse inducible ES stable clone


title: LeafBlade_58DAT_16:00

description: Gene expression of leaf blade at 58 days after transplanting, 16:00

source_name: Leaf blade, 58 days after transplanting, 16:00


title: LeafBlade_58DAT_22:00

description: Gene expression of leaf blade at 58 days after transplanting, 22:00

source_name: Leaf blade, 58 days after transplanting, 22:00


title: Basque 35 kg Replicate 4

description: Basque 35 kg sample Replicate 4 of 5


title: Basque 35 kg Replicate 3

description: Basque 35 kg sample Replicate 3 of 5


title: induced clone of BRWD1, biological replicate3

description:
BRWD1_t24_3.CEL
Gene expression data from mouse inducible ES stable clone

source_name: inducible ES stable cell line grown in medium deprived of Tetracycline


title: LeafBlade_58DAT_12:00

description: Gene expression of leaf blade at 58 days after transplanting, 12:00

source_name: Leaf blade, 58 days after transplanting, 12:00


title: Basque 35 kg Replicate 2

description: Basque 35 kg sample Replicate 2 of 5


title: LeafBlade_86DAT_14:00

description: Gene expression of leaf blade at 86 days after transplanting, 14:00

source_name: Leaf blade, 86 days after transplanting, 14:00


title: LeafBlade_58DAT_08:00

description: Gene expression of leaf blade at 58 days after transplanting, 08:00

source_name: Leaf blade, 58 days after transplanting, 08:00


title: induced clone of BRWD1, biological replicate2

description:
BRWD1_t24_2.CEL
Gene expression data from mouse inducible ES stable clone


title: Basque 35 kg Replicate 1

description: Basque 35 kg sample Replicate 1 of 5


title: LeafBlade_58DAT_10:00

description: Gene expression of leaf blade at 58 days after transplanting, 10:00

source_name: Leaf blade, 58 days after transplanting, 10:00


title: inducible clone of BRWD1, biological replicate3

description:
BRWD1_t0_3.CEL
Gene expression data from mouse inducible ES stable clone


title: LeafBlade_58DAT_06:00

description: Gene expression of leaf blade at 58 days after transplanting, 06:00

source_name: Leaf blade, 58 days after transplanting, 06:00


title: induced clone of BRWD1, biological replicate1

description:
BRWD1_t24_1.CEL
Gene expression data from mouse inducible ES stable clone


title: LeafBlade_58DAT_14:00

description: Gene expression of leaf blade at 58 days after transplanting, 14:00

source_name: Leaf blade, 58 days after transplanting, 14:00


title: LeafBlade_57DAT_24:00

description: Gene expression of leaf blade at 57 days after transplanting, 24:00

source_name: Leaf blade, 57 days after transplanting, 24:00

value: 57 days after transplanting


title: LeafBlade_57DAT_18:00

description: Gene expression of leaf blade at 57 days after transplanting, 18:00

source_name: Leaf blade, 57 days after transplanting, 18:00


title: LeafBlade_58DAT_04:00

description: Gene expression of leaf blade at 58 days after transplanting, 04:00

source_name: Leaf blade, 58 days after transplanting, 04:00


title: LeafBlade_57DAT_20:00

description: Gene expression of leaf blade at 57 days after transplanting, 20:00

source_name: Leaf blade, 57 days after transplanting, 20:00


title: LeafBlade_57DAT_22:00

description: Gene expression of leaf blade at 57 days after transplanting, 22:00

source_name: Leaf blade, 57 days after transplanting, 22:00


title: LeafBlade_57DAT_16:00

description: Gene expression of leaf blade at 57 days after transplanting, 16:00

source_name: Leaf blade, 57 days after transplanting, 16:00


title: inducible clone of BRWD1, biological replicate1

description:
BRWD1_t0_1.CEL
Gene expression data from mouse inducible ES stable clone

source_name: inducible ES stable cell line grown in medium containing Tetracycline


title: LeafBlade_58DAT_02:00

description: Gene expression of leaf blade at 58 days after transplanting, 02:00

source_name: Leaf blade, 58 days after transplanting, 02:00


title: induced clone of AIRE deleted isoform, biological replicate3

description:
AIREdel_t24_3.CEL
Gene expression data from mouse inducible ES stable clone


title: Human Umbilical Vein Endothelial Cells

city: beijing

first: jun

last: li

address: heqinglu haidianqu

country: China

institute: tsinghua university

description: Gene expression data from cells

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse 430 2.0 Genome Array in the Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the affymetrix scanner 3000 7G.The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of AGCC.

data_processing: The data were analyzed with Expression Console Software using RMA algorithm.

label: Biotin

organism: Homo sapiens

source_name: Primary cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Cells were cultured at 37℃, 5%CO2

extract_protocol: Extraction of total RNA was performed using Qiagen RNeasy kit according to the manufacturer's instructions.

treatment_protocol: No special treatment

value: Human Umbilical Vein Endothelial Cells


title: LeafBlade_57DAT_14:00

description: Gene expression of leaf blade at 57 days after transplanting, 14:00

source_name: Leaf blade, 57 days after transplanting, 14:00


title: Fibroblast

description: Gene expression data from cells

value: Fibroblast


title: inducible clone of BRWD1, biological replicate2

description:
BRWD1_t0_2.CEL
Gene expression data from mouse inducible ES stable clone


title: induced clone of AIRE deleted isoform, biological replicate2

description:
AIREdel_t24_2.CEL
Gene expression data from mouse inducible ES stable clone

source_name: inducible ES stable cell line grown in medium deprived of Tetracycline


title: Induced endothelial cells from BJ

description: Gene expression data from cells

source_name: Purified cells

value: Induced endothelial cells

tag: cell line

value: BJ


title: LeafBlade_45DAT_10:00

description: Gene expression of leaf blade at 45 days after transplanting, 10:00

source_name: Leaf blade, 45 days after transplanting, 10:00

value: 45 days after transplanting


title: LeafBlade_57DAT_10:00

description: Gene expression of leaf blade at 57 days after transplanting, 10:00

source_name: Leaf blade, 57 days after transplanting, 10:00


title: inducible clone of AIRE deleted isoform, biological replicate2

description:
AIREdel_t0_2.CEL
Gene expression data from mouse inducible ES stable clone


title: LeafBlade_45DAT_04:00

description: Gene expression of leaf blade at 45 days after transplanting, 04:00

source_name: Leaf blade, 45 days after transplanting, 04:00


title: inducible clone of AIRE deleted isoform, biological replicate3

description:
AIREdel_t0_3.CEL
Gene expression data from mouse inducible ES stable clone


title: Induced endothelial cells from CRL-2097

description: Gene expression data from cells


title: LeafBlade_45DAT_02:00

description: Gene expression of leaf blade at 45 days after transplanting, 02:00

source_name: Leaf blade, 45 days after transplanting, 02:00


title: LeafBlade_45DAT_08:00

description: Gene expression of leaf blade at 45 days after transplanting, 08:00

source_name: Leaf blade, 45 days after transplanting, 08:00


title: LeafBlade_57DAT_12:00

description: Gene expression of leaf blade at 57 days after transplanting, 12:00

source_name: Leaf blade, 57 days after transplanting, 12:00


title: CL1-5 cell line expressing AK4 shRNA vector

city: Taipei

first: Michael

last: Hsiao

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

description: Gene expression data from CL1-5 cells expressing AK4 shRNA vector

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 PLUS 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

source_name: Lung  adenocarcinoma

growth_protocol: Cells were cultured in 5% CO2 incubator at 37℃.

extract_protocol: Qiagene RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cell were selected with puromycin for two weeks.  Stably transduced cells were use for this experiment.

value: CL1-5 lung cancer cell line

value: Type II alveolar cell

tag: genotype/variation

value: expressing AK4 shRNA vector


title: LeafBlade_44DAT_20:00

description: Gene expression of leaf blade at 44 days after transplanting, 20:00

source_name: Leaf blade, 44 days after transplanting, 20:00

value: 44 days after transplanting


title: LeafBlade_44DAT_22:00

description: Gene expression of leaf blade at 44 days after transplanting, 22:00

source_name: Leaf blade, 44 days after transplanting, 22:00


title: LeafBlade_44DAT_18:00

description: Gene expression of leaf blade at 44 days after transplanting, 18:00

source_name: Leaf blade, 44 days after transplanting, 18:00


title: Sixty-four hour sample control (cIg), rep 4

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

country: USA

institute: NIH

description: Gene expression data from sixty-four hour sample control (cIg), rep 4 of 4.

hyb_protocol: Hybridization and fluidics were performed according to standard Affymetrix protocols (http://www.affymetrix.com).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus according to standard Affymetrix protocols.

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis. The trimmed mean target intensity of each array was arbitrarily set to 1250.

source_name: sixty-four hour sample control (cIg)

label_protocol: cDNA was synthesized and labeled according to manufacturer instructions for Affymetrix.

growth_protocol: Primary, resting NK cells from 4 donors.

extract_protocol: Total RNA was isolated with an RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. RNase-free DNaseI (Amersham) was used to remove remaining DNA.

treatment_protocol: NK cells were stimulated with either cIg or anti-CD158d mAb for 4 h, 16 h or 64 h.

value: primary natural killer (NK) cells

tag: treatment

value: control

tag: time

value: 64 hr


title: CTRL, biological replicate 3

description:
EB3_3.CEL
Gene expression data from mouse inducible ES stable control clone

source_name: parental cell line EBRTcH3 (EB3)


title: CL1-5 cell line expressing Non-silencing shRNA vector

description: Gene expression data from CL1-5 cells expressing non-silencing shRNA vector

value: expressing non-silencing shRNA vector


title: LeafBlade_44DAT_10:00

description: Gene expression of leaf blade at 44 days after transplanting, 10:00

source_name: Leaf blade, 44 days after transplanting, 10:00

value: Nipponbare


title: LeafBlade_45DAT_06:00

description: Gene expression of leaf blade at 45 days after transplanting, 06:00

source_name: Leaf blade, 45 days after transplanting, 06:00

value: Leaf Blade


title: LeafBlade_44DAT_12:00

description: Gene expression of leaf blade at 44 days after transplanting, 12:00

source_name: Leaf blade, 44 days after transplanting, 12:00


title: induced clone of AIRE deleted isoform, biological replicate1

description:
AIREdel_t24_1.CEL
Gene expression data from mouse inducible ES stable clone

source_name: inducible ES stable cell line grown in medium deprived of Tetracycline

value: Embryonic Stem (ES)  cells


title: LeafBlade_44DAT_14:00

description: Gene expression of leaf blade at 44 days after transplanting, 14:00

source_name: Leaf blade, 44 days after transplanting, 14:00


title: inducible clone of AIRE deleted isoform, biological replicate1

description:
AIREdel_t0_1.CEL
Gene expression data from mouse inducible ES stable clone

source_name: inducible ES stable cell line grown in medium containing Tetracycline


title: CTRL, biological replicate 1

description:
EB3_1.CEL
Gene expression data from mouse inducible ES stable control clone


title: CTRL, biological replicate 2

description:
EB3_2.CEL
Gene expression data from mouse inducible ES stable control clone


title: LeafBlade_44DAT_16:00

description: Gene expression of leaf blade at 44 days after transplanting, 16:00

source_name: Leaf blade, 44 days after transplanting, 16:00


title: LeafBlade_44DAT_24:00

description: Gene expression of leaf blade at 44 days after transplanting, 24:00

source_name: Leaf blade, 44 days after transplanting, 24:00


title: CL1-0 cell line expressing AK4

description: Gene expression data from CL1-0 cells expressing AK4 vector

value: CL1-0 lung cancer cell line

value: expressing AK4 vector


title: CL1-0 cell line expressing control vector

description: Gene expression data from CL1-0 cells expressing control vector

value: expressing control vector


title: Sixty-four hour sample control (cIg), rep 3

description: Gene expression data from sixty-four hour sample control (cIg), rep 3 of 4.


title: Sixty-four hour sample control (cIg), rep 2

description: Gene expression data from sixty-four hour sample control (cIg), rep 2 of 4.


title: LeafBlade_44DAT_06:00

description: Gene expression of leaf blade at 44 days after transplanting, 06:00

source_name: Leaf blade, 44 days after transplanting, 06:00


title: LeafBlade_44DAT_08:00

description: Gene expression of leaf blade at 44 days after transplanting, 08:00

source_name: Leaf blade, 44 days after transplanting, 08:00


title: TG, Rep2

city: Columbus

first: Sukhinder

last: Sandhu

state: OH

address: 460 W 12th Ave

institute: The Ohio State University

description: Gene expression data from TG FVB mouse B-cells

hyb_protocol: 15ug of labeled and fragmented cRNA was hybridized at 45C for 16 hours at 60rpm to Mouse Genome 430_2 chips. GeneChips were then washed and stained on the Affymetrix Fluidics Station 450 according to the manufacturer’s protocol

scan_protocol: GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 7G.  Raw data files were generated and processed with Affymetrix AGCC software.

data_processing: The data was used using Bioconductor and GCRMA normalization.

source_name: Eu-miR-155 Transgenic mouse spleen B-cells

label_protocol: 1ug RNA was used to generate cRNA according to the manufacturer’s protocol in the Affymetrix GeneChip® Expression Analysis Technical Manual.

extract_protocol: B-cells were isolated from mice spleens using B-cell isolation kit (MACs, Miltenyi). Total RNA was extracted using Trizol

tag: genotype

value: Transgenic


title: LeafBlade_44DAT_02:00

description: Gene expression of leaf blade at 44 days after transplanting, 02:00

source_name: Leaf blade, 44 days after transplanting, 02:00


title: LeafBlade_43DAT_22:00

description: Gene expression of leaf blade at 43 days after transplanting, 22:00

source_name: Leaf blade, 43 days after transplanting, 22:00

value: 43 days after transplanting


title: Sixty-four hour sample with agonist anti-CD158d mAb, rep 4

description: Gene expression data from sixty-four hour sample with agonist anti-CD158d mAb, rep 4 of 4.

value: anti-CD158d mAb


title: Sixty-four hour sample with agonist anti-CD158d mAb, rep 3

description: Gene expression data from sixty-four hour sample with agonist anti-CD158d mAb, rep 3 of 4.


title: LeafBlade_44DAT_04:00

description: Gene expression of leaf blade at 44 days after transplanting, 04:00

source_name: Leaf blade, 44 days after transplanting, 04:00


title: LeafBlade_43DAT_18:00

description: Gene expression of leaf blade at 43 days after transplanting, 18:00

source_name: Leaf blade, 43 days after transplanting, 18:00


title: Sixty-four hour sample control (cIg), rep 1

description: Gene expression data from sixty-four hour sample control (cIg), rep 1 of 4.

source_name: sixty-four hour sample control (cIg)


title: LeafBlade_43DAT_14:00

description: Gene expression of leaf blade at 43 days after transplanting, 14:00

source_name: Leaf blade, 43 days after transplanting, 14:00


title: LeafBlade_43DAT_12:00

description: Gene expression of leaf blade at 43 days after transplanting, 12:00

source_name: Leaf blade, 43 days after transplanting, 12:00


title: LeafBlade_43DAT_16:00

description: Gene expression of leaf blade at 43 days after transplanting, 16:00

source_name: Leaf blade, 43 days after transplanting, 16:00


title: Sixty-four hour sample with agonist anti-CD158d mAb, rep 2

description: Gene expression data from sixty-four hour sample with agonist anti-CD158d mAb, rep 2 of 4.


title: TG, Rep1


title: WT, Rep4

description: Gene expression data from WT FVB mouse B-cells

source_name: Wild Type mouse spleen B-cells

value: Wild Type


title: LeafBlade_43DAT_24:00

description: Gene expression of leaf blade at 43 days after transplanting, 24:00

source_name: Leaf blade, 43 days after transplanting, 24:00


title: Sixty-four hour sample with agonist anti-CD158d mAb, rep 1

description: Gene expression data from sixty-four hour sample with agonist anti-CD158d mAb, rep 1 of 4.


title: TG, Rep3


title: WT, Rep3


title: Sixteen hour sample control (cIg), rep 3

description: Gene expression data from sixteen hour sample control (cIg), rep 3 of 4.

source_name: sixteen hour sample control (cIg)

value: 16 hr


title: LeafBlade_43DAT_10:00

description: Gene expression of leaf blade at 43 days after transplanting, 10:00

source_name: Leaf blade, 43 days after transplanting, 10:00


title: LeafBlade_31DAT_10:00

description: Gene expression of leaf blade at 31 days after transplanting, 10:00

source_name: Leaf blade, 31 days after transplanting, 10:00

value: 31 days after transplanting


title: LeafBlade_31DAT_08:00

description: Gene expression of leaf blade at 31 days after transplanting, 08:00

source_name: Leaf blade, 31 days after transplanting, 08:00


title: Sixteen hour sample control (cIg), rep 4

description: Gene expression data from sixteen hour sample control (cIg), rep 4 of 4.


title: WT, Rep2


title: LeafBlade_31DAT_06:00

description: Gene expression of leaf blade at 31 days after transplanting, 06:00

source_name: Leaf blade, 31 days after transplanting, 06:00


title: WT, Rep1


title: LeafBlade_31DAT_02:00

description: Gene expression of leaf blade at 31 days after transplanting, 02:00

source_name: Leaf blade, 31 days after transplanting, 02:00


title: LeafBlade_31DAT_04:00

description: Gene expression of leaf blade at 31 days after transplanting, 04:00

source_name: Leaf blade, 31 days after transplanting, 04:00


title: Serum_restimulation_48hours

city: Princeton

first: Eric

middle: Jungwoo

last: Suh

state: NJ

address: 14 Washington Rd

department: Molecular Biology

institute: Princeton University

hyb_protocol: Labeled cRNA were hybridized to arrays according to Agilent's manufacturer's protocol

scan_protocol: Scanned using Agilent G2505B array scanner according to manufacturer's protocol.

data_processing: Probes were filtered to eliminate those with either a final processed signal intensity below 350 or flagged by Feature Extractor for saturation or no signal above background in any array. Replicated signals from identical sequence-probes were averaged. For each array, the ratio of Cy5 to Cy3 (red to green) was log2 transformed and zero-centered.

source_name: 96 hours serum starved, 48 hours serum restimulated fibroblasts

label_protocol: Total RNA extracts were cRNA labeled using the Agilent Low RNA Input Fluorescent Labeling Kit according to the manufacturer's protocol

extract_protocol: Total RNA isolated from fibroblasts using mirVana total RNA isolation kit and procedure.

treatment_protocol: Fibroblasts were maintained in asynchronously proliferating culture in DMEM + 10% FBS, serum starved at 0.1% FBS for 4 days, and then restimulated in DMEM + 10% FBS for 2 days. Samples were collected periodically during this timecourse.

tag: gender

value: Male

value: Fibroblast

source_name: 96 hours serum starved fibroblasts


title: LeafBlade_43DAT_20:00

description: Gene expression of leaf blade at 43 days after transplanting, 20:00

source_name: Leaf blade, 43 days after transplanting, 20:00


title: Serum_restimulation_1hour

source_name: 96 hours serum starved, 1 hour serum restimulated fibroblasts


title: Serum_restimulation_24hours

source_name: 96 hours serum starved, 24 hours serum restimulated fibroblasts


title: Sixteen hour sample control (cIg), rep 1

description: Gene expression data from sixteen hour sample control (cIg), rep 1 of 4.

value: primary natural killer (NK) cells

value: control


title: Serum_restimulation_2hours

source_name: 96 hours serum starved, 2 hours serum restimulated fibroblasts


title: Sixteen hour sample control (cIg), rep 2

description: Gene expression data from sixteen hour sample control (cIg), rep 2 of 4.


title: LeafBlade_30DAT_18:00

description: Gene expression of leaf blade at 30 days after transplanting, 18:00

source_name: Leaf blade, 30 days after transplanting, 18:00

value: 30 days after transplanting


title: LeafBlade_30DAT_22:00

description: Gene expression of leaf blade at 30 days after transplanting, 22:00

source_name: Leaf blade, 30 days after transplanting, 22:00

value: Nipponbare


title: LeafBlade_30DAT_14:00

description: Gene expression of leaf blade at 30 days after transplanting, 14:00

source_name: Leaf blade, 30 days after transplanting, 14:00

value: Leaf Blade


title: LeafBlade_30DAT_12:00

description: Gene expression of leaf blade at 30 days after transplanting, 12:00

source_name: Leaf blade, 30 days after transplanting, 12:00


title: Serum_restimulation_4hours

source_name: 96 hours serum starved, 4 hours serum restimulated fibroblasts


title: LeafBlade_30DAT_24:00

description: Gene expression of leaf blade at 30 days after transplanting, 24:00

source_name: Leaf blade, 30 days after transplanting, 24:00


title: Sixteen hour sample with agonist anti-CD158d mAb, rep 3

description: Gene expression data from sixteen hour sample with agonist anti-CD158d mAb, rep 3 of 4.


title: LeafBlade_30DAT_20:00

description: Gene expression of leaf blade at 30 days after transplanting, 20:00

source_name: Leaf blade, 30 days after transplanting, 20:00


title: LeafBlade_30DAT_16:00

description: Gene expression of leaf blade at 30 days after transplanting, 16:00

source_name: Leaf blade, 30 days after transplanting, 16:00


title: Sixteen hour sample with agonist anti-CD158d mAb, rep 1

description: Gene expression data from sixteen hour sample with agonist anti-CD158d mAb, rep 1 of 4.


title: Four hour sample control (cIg), rep 4

description: Gene expression data from four hour sample control (cIg), rep 4 of 4.

source_name: four hour sample control (cIg)

value: 4 hr


title: Sixteen hour sample with agonist anti-CD158d mAb, rep 4

description: Gene expression data from sixteen hour sample with agonist anti-CD158d mAb, rep 4 of 4.


title: Sixteen hour sample with agonist anti-CD158d mAb, rep 2

description: Gene expression data from sixteen hour sample with agonist anti-CD158d mAb, rep 2 of 4.


title: Serum_withdrawal_8hours

source_name: 8 hours serum starved fibroblasts


title: LeafBlade_30DAT_02:00

description: Gene expression of leaf blade at 30 days after transplanting, 02:00

source_name: Leaf blade, 30 days after transplanting, 02:00


title: Serum_withdrawal_24hours

source_name: 24 hours serum starved fibroblasts


title: Four hour sample control (cIg), rep 2

description: Gene expression data from four hour sample control (cIg), rep 2 of 4.


title: Serum_withdrawal_96hours

source_name: 96 hours serum starved fibroblasts


title: LeafBlade_30DAT_04:00

description: Gene expression of leaf blade at 30 days after transplanting, 04:00

source_name: Leaf blade, 30 days after transplanting, 04:00


title: Serum_withdrawal_2hours

source_name: 2 hours serum starved fibroblasts


title: LeafBlade_30DAT_06:00

description: Gene expression of leaf blade at 30 days after transplanting, 06:00

source_name: Leaf blade, 30 days after transplanting, 06:00


title: Four hour sample control (cIg), rep 1

description: Gene expression data from four hour sample control (cIg), rep 1 of 4.


title: LeafBlade_30DAT_10:00

description: Gene expression of leaf blade at 30 days after transplanting, 10:00

source_name: Leaf blade, 30 days after transplanting, 10:00


title: Serum_withdrawal_4hours

source_name: 4 hours serum starved fibroblasts


title: LeafBlade_29DAT_24:00

description: Gene expression of leaf blade at 29 days after transplanting, 24:00

source_name: Leaf blade, 29 days after transplanting, 24:00

value: 29 days after transplanting


title: Four hour sample with agonist anti-CD158d mAb, rep 4

description: Gene expression data from four hour sample with agonist anti-CD158d mAb, rep 4 of 4.


title: Four hour sample control (cIg), rep 3

description: Gene expression data from four hour sample control (cIg), rep 3 of 4.


title: Four hour sample with agonist anti-CD158d mAb, rep 1

description: Gene expression data from four hour sample with agonist anti-CD158d mAb, rep 1 of 4.


title: LeafBlade_30DAT_08:00

description: Gene expression of leaf blade at 30 days after transplanting, 08:00

source_name: Leaf blade, 30 days after transplanting, 08:00


title: Serum_restimulation_8hours

source_name: 96 hours serum starved, 8 hours serum restimulated fibroblasts


title: Serum_withdrawal_1hour

source_name: 1 hour serum starved fibroblasts


title: LeafBlade_29DAT_20:00

description: Gene expression of leaf blade at 29 days after transplanting, 20:00

source_name: Leaf blade, 29 days after transplanting, 20:00


title: 28_87_years_old_f

city: Leiden

first: Marius

last: Gheorghe

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: LUMC

description: SAMPLE 28

hyb_protocol: According to Illumina protocols

scan_protocol: According to Illumina protocols

data_processing: Microarray measurements were normalized using the quantile method. The quality of the data was assessed by principal component analysis (PCA). Human subjects were grouped into controls, pre-symptomatic, and symptomatic subjects. P-value cut-off of 0.05 were used due to high inter-individual variation. Probe annotation was done using the illuminaHumanv3BeadID package in R.

source_name: vastus laterlalis

extract_protocol:
Human quadriceps muscle samples were collected with the needle or by an open surgical procedure from anonymous healthy individuals that gave informed consent. Only age and gender are noted for those.
Total RNA was extracted from skeletal muscles using RNA Bee (Amsbio) according to the manufacturer's instructions. RNA integration number (RIN) was determined with RNA 6000 Nano (Agilent Technologies). RNA with RIN >7 were used for subsequent steps. RNA labeling was performed with the Illumina® TotalPrep RNA Amplification kit (Ambion) according to the manufacturer's protocol, and subsequently was hybridized to Illumina Human v3 Bead arrays.

value: female

value: muscles

tag: age

value: 87 years old


title: 29_89_years_old_f

description: SAMPLE 29

label_protocol: RNA labeling was performed with the Illumina® TotalPrep RNA Amplification kit (Ambion) according to the manufacturer's protocol, and subsequently was hybridized to Illumina Human v3 Bead arrays.

value: 89 years old


title: LeafBlade_29DAT_22:00

description: Gene expression of leaf blade at 29 days after transplanting, 22:00

source_name: Leaf blade, 29 days after transplanting, 22:00

tag: cultivar


title: 27_85_years_old_f

description: SAMPLE 27

value: 85 years old


title: Four hour sample with agonist anti-CD158d mAb, rep 2

description: Gene expression data from four hour sample with agonist anti-CD158d mAb, rep 2 of 4.

value: anti-CD158d mAb


title: Four hour sample with agonist anti-CD158d mAb, rep 3

description: Gene expression data from four hour sample with agonist anti-CD158d mAb, rep 3 of 4.


title: 26_77_years_old_m

description: SAMPLE 26

value: male

value: 77 years old


title: LeafBlade_29DAT_18:00

description: Gene expression of leaf blade at 29 days after transplanting, 18:00

source_name: Leaf blade, 29 days after transplanting, 18:00

tag: organ/tissue


title: 25_73_years_old_m

description: SAMPLE 25

value: 73 years old


title: LeafBlade_29DAT_16:00

description: Gene expression of leaf blade at 29 days after transplanting, 16:00

source_name: Leaf blade, 29 days after transplanting, 16:00

tag: growth/development stage


title: LeafBlade_29DAT_14:00

description: Gene expression of leaf blade at 29 days after transplanting, 14:00

source_name: Leaf blade, 29 days after transplanting, 14:00

tag: sampling time


title: LeafBlade_17DAT_08:00

description: Gene expression of leaf blade at 17 days after transplanting, 08:00

source_name: Leaf blade, 17 days after transplanting, 08:00

value: 17 days after transplanting


title: LeafBlade_17DAT_10:00

description: Gene expression of leaf blade at 17 days after transplanting, 10:00

source_name: Leaf blade, 17 days after transplanting, 10:00


title: 21_60_years_old_m

description: SAMPLE 21

value: 60 years old


title: LeafBlade_17DAT_06:00

description: Gene expression of leaf blade at 17 days after transplanting, 06:00

source_name: Leaf blade, 17 days after transplanting, 06:00


title: 24_68_years_old_m

description: SAMPLE 24

value: 68 years old


title: Il4 4C S6KO rep2

type: genomic

city: Bethesda

first: Myong-Hee

last: Sung

state: MD

address: 41 Library Dr

department: NCI

hyb_protocol: 25-30 µg of the Cy5 labeled 4C DNA was mixed equal emount of Cy3 labeled genomic DNA and precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol. DNA was recovered and hybridized in 39ul hybridization buffer following chromatin immunoprecipitation (ChIP)-chip protocols (Nimblegen Systems). (chapter 4 in http://www.nimblegen.com/products/lit/NG_ChIP-chip_Guide_v6p2.pdf).   Arrays were sealed with Maui mixer SL and hybridized in Maui hybridization stations for 16 h at 42C. Arrays were washed at room temperature in 6X SSPE/5x10E-3 % Sodium N-lauroylsarcosinate for 5 minutes and two 5 minutes washes with 0.06% SSPE.

scan_protocol: Arrays were scanned on an Agilent G2939A scanner per manufacturer's protocol.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2 ChIP data extraction.  Logratios of PAIR file values were taken; then quantile normalization was applied to generate .ratio files (log2 ratios included in VALUE column).

molecule: genomic DNA

source_name: Il4 4C / Stat6 KO Th2 cells

label_protocol: 1 µg purified 4C DNA was labeled with Cy5. Genomic DNA from the corresponding cell cut with HindIII and Csp6I was similarly labeled with Cy3 as control for hybridization efficiency. Labeling was done according to standard chromatin immunoprecipitation (ChIP)-chip protocols (Nimblegen Systems). (chapter 3 in http://www.nimblegen.com/products/lit/NG_ChIP-chip_Guide_v6p2.pdf)

extract_protocol: 2x10E7 adherent cells were fixed with 2% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS, scraped and collected in a 50ml tube. Nuclei were isolates in 10 ml of lysis buffer (0.2% NP-40, 10 mM NaCl, 10 mM Tris pH8.0) for 1hr on ice. Following centrifugation the nuclei were suspended in 1ml 1.2X HindIII buffer (New England Biolabs buffer 2).  The nuclei were incubated in 0.3% SDS for 1hr at 37ºC (60 µl 20% SDS) and then SDS was quenched by incubation in 2% Triton X-100 for 1hr at 37ºC (200 µl 10% Triton X-100. Digestion was done with 800 U of HindIII (New England Biolabs) overnight at 37ºC while shaking gently. Before ligation, the HindIII was inactivated at 65C for 20 minutes, and the chromatin was ligated in 14 ml with 200 U T4 DNA ligase (Roche) for 4hr at 16ºC. To reverse the crosslinks, the sample was incubated overnight at 16ºC with 600 µg Proteinase K following by RNA elimination by incubation with 600µg RNAse for 45 minutes at 37ºC. The 3C DNA was purified by phenol-chloroform extraction and ethanol precipitation. This 3C DNA sample was further cut with 150 U Csp6I (Fermantas) overnight at 37ºC. The restriction enzyme was inactivated at 65C for 20 minutes and removed by phenol-chloroform extraction. Ligation was performed as in the previous step to favor circulization of the DNA molecules in 14 ml with 200 U T4 DNA ligase (Roche) for 4hr at 16ºC. Ligation products were phenol-chloroform extracted and ethanol precipitated. Digested products were purified using a QIAquick PCR purification kit (Qiagen). The bait (Lcn2, Arrdc2, or Anxa5) contact loci were amplified by inverse PCR using bait-specific primers using the Expand Long Template PCR system (Roche).  For each experiment (repeat) PCR was performed in 16 PCR reactions of 50µl using 200ng 4C DNA as template in each reaction. PCR conditions were as follows: 94 °C for 2 min, 30 cycles of 94°C for 15 s, 60°C for 1 min and 68°C for 3 min; followed by a final step of 68 °C for 7 min. Primer sequences that were used to PCR amplify 4C DNA: Lcn2_4CF 5’GGGAGGTTAGTCACAGGGA3’, Lcn2_4CR 5’AGGGAGGATGACTTAAGGAG3’,  Arrdc2_4CF 5’CAAATGCCAAAAGGAAGGAA3’,  Arrdc2_4CR 5’TCAGTCAACATGCATCTCAGAA3’,  Anxa5_4CF 5’CACCAGTTAACTAGCTTGCTTGC 3’ and Anxa5_4CR 5’TGAACAGGTCAGTCACATTGG3’. All 16 PCR reactions were pooled and purified this 4C template using QIAquick PCR purification kit (Qiagen).

tag: cell type

value: primary CD4+ T cells

source_name: Input control


title: LeafBlade_29DAT_12:00

description: Gene expression of leaf blade at 29 days after transplanting, 12:00

source_name: Leaf blade, 29 days after transplanting, 12:00

value: Nipponbare


title: LeafBlade_29DAT_10:00

description: Gene expression of leaf blade at 29 days after transplanting, 10:00

source_name: Leaf blade, 29 days after transplanting, 10:00

value: Leaf Blade


title: Il4 4C S6KO rep1


title: 23_66_years_old_m

description: SAMPLE 23

tag: tissue

value: 66 years old


title: 22_60_years_old_f

description: SAMPLE 22


title: Il4 4C Th2 rep1

source_name: Il4 4C / Th2 cells


title: 20_60_years_old_f

description: SAMPLE 20


title: LeafBlade_17DAT_04:00

description: Gene expression of leaf blade at 17 days after transplanting, 04:00

source_name: Leaf blade, 17 days after transplanting, 04:00


title: Ifng 4C S4KO rep2

source_name: Ifng 4C / Stat4 KO Th1 cells


title: 19_58_years_old_f

description: SAMPLE 19

value: 58 years old


title: Il4 4C Th2 rep2


title: Il4 4C naïve rep1

source_name: Il4 4C / naïve CD4 T cells


title: Il4 4C naïve rep2


title: Ifng 4C 3T3 rep1

source_name: Ifng 4C / 3T3-L1 cell line


title: LeafBlade_16DAT_22:00

description: Gene expression of leaf blade at 16 days after transplanting, 22:00

source_name: Leaf blade, 16 days after transplanting, 22:00

value: 16 days after transplanting


title: 18_58_years_old_f

description: SAMPLE 18

source_name: vastus laterlalis

value: female

value: muscles


title: Il4 4C Th1 rep2

source_name: Il4 4C / Th1 cells


title: LeafBlade_16DAT_20:00

description: Gene expression of leaf blade at 16 days after transplanting, 20:00

source_name: Leaf blade, 16 days after transplanting, 20:00


title: 151K_2 ug/ml

type: protein

city: Durham

first: Guang

last: Yang

state: NC

address: DUMC 3010

institute: Duke University

description: Protein-Ab interactions were detected by AF647-labelled antibody against human IgG.

hyb_protocol: The arrays were blocked, washed, and detected according to the manufacturer's instructions. Briefly, ProtoArray 5 were blocked and blotted with 2 µg/mL 2F5, 4E10, or human myeloma 151K for 90 min. Protein-Ab interactions were detected using 1 µg/mL anti-human IgG conjugated with Alexa Fluor 647 [Vendor, Invitrogen; Cat#, A21445; Lot#, 857219].

scan_protocol: The arrays were scanned at 635 nm with 10 μm resolution using 100% power and 600 gain (GenePix 4000B scanner, Molecular Devices).

data_processing:
Fluorescence intensities were quantified using GenePix Pro 5.0 (Molecular Devices). Lot-specific protein spot definitions were provided by the microarray manufacturer and aligned to the image data.
Mean of fluorescent signal, as determined by GenePix Pro 5.0, used to draw study conclusions.

label: Alexa Fluor 647

molecule: protein

source_name: commercial human myeloma protein

label_protocol: There was no labelling of the antibodies.

extract_protocol: The monoclonal antibodies were commercially purchased.

tag: antibody

value: 151K [Vendor, Southern Biotech; Cat#, 0151K-14; Lot#, H2408-VG09J]

tag: isotype


title: Il4 4C Th1 rep1


title: 17_57_years_old_m

description: SAMPLE 17

value: 57 years old


title: 16_57_years_old_f

description: SAMPLE 16


title: Ifng 4C 3T3 rep2


title: LeafBlade_16DAT_16:00

description: Gene expression of leaf blade at 16 days after transplanting, 16:00

source_name: Leaf blade, 16 days after transplanting, 16:00


title: 4E10_2 ug/ml

source_name: commercial mAb from hybridoma


title: LeafBlade_16DAT_24:00

description: Gene expression of leaf blade at 16 days after transplanting, 24:00

source_name: Leaf blade, 16 days after transplanting, 24:00


title: LeafBlade_16DAT_18:00

description: Gene expression of leaf blade at 16 days after transplanting, 18:00

source_name: Leaf blade, 16 days after transplanting, 18:00


title: LeafBlade_16DAT_12:00

description: Gene expression of leaf blade at 16 days after transplanting, 12:00

source_name: Leaf blade, 16 days after transplanting, 12:00


title: LeafBlade_16DAT_14:00

description: Gene expression of leaf blade at 16 days after transplanting, 14:00

source_name: Leaf blade, 16 days after transplanting, 14:00


title: Ifng 4C Th2 rep1

source_name: Ifng 4C / Th2 cells

source_name: Input control


title: LeafBlade_16DAT_10:00

description: Gene expression of leaf blade at 16 days after transplanting, 10:00

source_name: Leaf blade, 16 days after transplanting, 10:00


title: Ifng 4C S4KO rep1

source_name: Ifng 4C / Stat4 KO Th1 cells


title: Ifng 4C Th2 rep2


title: 2F5_2 ug/ml

value: 2F5 [Vendor, Polymun; Cat#, AB001; Lot#, T33/C2F5/0499-A]


title: LeafBlade_17DAT_02:00

description: Gene expression of leaf blade at 17 days after transplanting, 02:00

source_name: Leaf blade, 17 days after transplanting, 02:00


title: 15_56_ years_old_m

description: SAMPLE 15

value: male

value: 56 years old


title: Ifng 4C Th1 rep2

source_name: Ifng 4C / Th1 cells


title: Ifng 4C Th1 rep1


title: LeafBlade_16DAT_02:00

description: Gene expression of leaf blade at 16 days after transplanting, 02:00

source_name: Leaf blade, 16 days after transplanting, 02:00


title: Ifng 4C naïve rep2

source_name: Ifng 4C / naïve CD4 T cells


title: LeafBlade_16DAT_08:00

description: Gene expression of leaf blade at 16 days after transplanting, 08:00

source_name: Leaf blade, 16 days after transplanting, 08:00


title: LeafBlade_15DAT_24:00

description: Gene expression of leaf blade at 15 days after transplanting, 24:00

source_name: Leaf blade, 15 days after transplanting, 24:00

value: 15 days after transplanting


title: LeafBlade_16DAT_04:00

description: Gene expression of leaf blade at 16 days after transplanting, 04:00

source_name: Leaf blade, 16 days after transplanting, 04:00


title: LeafBlade_15DAT_22:00

description: Gene expression of leaf blade at 15 days after transplanting, 22:00

source_name: Leaf blade, 15 days after transplanting, 22:00


title: LeafBlade_16DAT_06:00

description: Gene expression of leaf blade at 16 days after transplanting, 06:00

source_name: Leaf blade, 16 days after transplanting, 06:00


title: Col4WT-salt-Rep1

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: Gene expression data of Col4WT plants grown on 1/2 MS plant medium supplemented with 50 mM NaCl

hyb_protocol: Fragmented biotinylated cDNA was hybridized on Affymetrix Arabidopsis Tiling 1.0R arrays , and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).

scan_protocol: To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).

data_processing: Raw data were processed with the RMA algorithm (Irizarry et al., 2003) using the Tiling 1.0R array CDF created by Naouar et al. (2009)

organism: Arabidopsis thaliana

label_protocol: Per sample, 7 µg of total RNA was converted to double-stranded cDNA in a cDNA reverse transcription reaction (without amplification) according to the manufacturer's protocol (Affymetrix - GeneChip® Whole Transcript (WT) Double-Stranded Target Assay). Subsequently, the sample was fragmented and labeled with biotin according to the manufacturer’s protocol (Affymetrix - WT Double-Stranded DNA Terminal Labeling Kit).

growth_protocol: Arabidopsis Col4WT and WRKY15OE seeds were sown in triplicate on half-strength MS plant medium supplemented with 0 or 50 mM NaCl and grown at 21°C and 65-80 μmol.m-2.s-1 radiation in a 16 h/8 h light/dark photoperiod. Seeds were sterilized by overnight incubation with chlorine gas (100 ml 12% NaOCl and 3 ml 37% HCl).

extract_protocol: Total RNA was isolated with TRIzol Reagent (Invitrogen, Carlsbad, CA). Concentration and quality were determined using a Nanodrop ND-1000 UV-Vis spectrophotometer (www.nanodrop.com) and the RNA 6000 Nano Assay (Agilent 2100 BioAnalyzer – www.agilent.com).

treatment_protocol: At the developmental stage of 1.05 (Boyes et al., 2001), shoot material of 20 plantlets was harvested.

tag: plant age

value: 14 days

tag: growth protocol


title: WRKY15OE-salt-Rep3

description: Gene expression data of WRKY15OE plants grown on 1/2 MS plant medium supplemented with 50 mM NaCl


title: LeafBlade_15DAT_20:00

description: Gene expression of leaf blade at 15 days after transplanting, 20:00

source_name: Leaf blade, 15 days after transplanting, 20:00


title: WRKY15OE-Rep3

description: Gene expression data of WRKY15OE plants grown on 1/2 MS plant medium

value: 1/2 MS plant medium with 0 mM NaCl


title: LeafBlade_15DAT_16:00

description: Gene expression of leaf blade at 15 days after transplanting, 16:00

source_name: Leaf blade, 15 days after transplanting, 16:00


title: WRKY15OE-Rep2

source_name: WRKY15OE plants grown on 1/2 MS plant medium


title: Col4WT-Rep3

description: Gene expression data of Col4WT plants grown on 1/2 MS plant medium


title: WRKY15OE-salt-Rep2

source_name: WRKY15OE plants grown on 1/2 MS plant medium supplemented with 50 mM NaCl


title: Ifng 4C naïve rep1


title: LeafBlade_15DAT_14:00

description: Gene expression of leaf blade at 15 days after transplanting, 14:00

source_name: Leaf blade, 15 days after transplanting, 14:00


title: Col4WT-salt-Rep2

source_name: Col4WT plants grown on 1/2 MS plant medium supplemented with 50 mM NaCl


title: LeafBlade_15DAT_18:00

description: Gene expression of leaf blade at 15 days after transplanting, 18:00

source_name: Leaf blade, 15 days after transplanting, 18:00


title: ZG-09

city: Los Angeles

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

description: Affymetrix Rhesus genome array

hyb_protocol: Standard Affymetrix hybridization protocol for gene expression profiling (carried out by Assuragen Inc.).

scan_protocol: Standard Affymetrix scan protocol for gene expression profiling (carried out Assuragen Inc.).

data_processing: RMA (RMAExpress) processing of Affymetrix .CEL files generated by Assuragen Inc.

organism: Macaca mulatta

source_name: PBMC

label_protocol: Standard Affymetrix probe synthesis for gene expression profiling (carried out Assuragen Inc.).

extract_protocol: Primary peripheral blood mononuclear cells were isolated and total RNA was extracted using Qiagen RNEasy.

tag: rearing condition

value: Surrogate-peer reared

value: 4 month old


title: WRKY15OE-salt-Rep1

tag: genotype/variation

value: 1/2 MS plant medium supplemented with 50 mM NaCl


title: LeafBlade_15DAT_10:00

description: Gene expression of leaf blade at 15 days after transplanting, 10:00

source_name: Leaf blade, 15 days after transplanting, 10:00

value: Nipponbare

value: Leaf Blade


title: Col4WT-salt-Rep3


title: ZG-13

description: Affymetrix Rhesus genome array


title: LeafBlade_15DAT_12:00

description: Gene expression of leaf blade at 15 days after transplanting, 12:00

source_name: Leaf blade, 15 days after transplanting, 12:00


title: Col4WT-Rep1

source_name: Col4WT plants grown on 1/2 MS plant medium


title: WRKY15OE-Rep1


title: ZG-32

description: Affymetrix Rhesus genome array


title: Col4WT-Rep2


title: ZG-41

description: Affymetrix Rhesus genome array

value: Maternally reared


title: ZG-47

description: Affymetrix Rhesus genome array

value: Peer reared


title: ZG-31

description: Affymetrix Rhesus genome array


title: ZG-44

description: Affymetrix Rhesus genome array


title: XP5%

city: Newcastle upon Tyne

first: Maya

last: Sieber-Blum

address: Centre for Life

department: Institute of Genetic Medicine

country: United Kingdom

institute: Newcastle University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Genome Studio

source_name: hair follicle bulge

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: De-identified pubic hairy skin biopsies were obtained with ethical approval (REC REF: 08/H0907/1) from consenting individuals undergoing repeat elective Caesarean sections. The cells were expanded ex vivo exactly as described by Clewes et al, 2011 (“XP” medium) for seven days in expansion medium (XP) in a humidified incubator at 5% 02 and 5% C02. Part of the cells were lysed in TRIzol and processed for Illumina profiling. The culture medium was the changed to NP1 medium and cultured for 6 days in NP1 medium. NP1 medium consisted of ITS+3, GlutaMAX, penicillin/streptomycin, Amphotericin B, rhFGF2 (10 ng/ml), rhEGF (20 ng/ml), rhSCF (5 ng/ml) and rhNT-3 (10 ng/ml) in NeuroCult NSA. After 6 days in NP1 medium the cells were lysed and processed for Illumina profiling. Illumina profiling was performed on a Human HT-12 v4 array.

extract_protocol: RNA was extracted with Trizol reagent, followed by DNAse I treatment (Inivtrogen Cat18068)  in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

value: female

value: hair follicle bulge

tag: culture medium

value: XP


title: ZG-43

description: Affymetrix Rhesus genome array


title: RR2_SL1344_hydrated_Cy5_ch1_dessic_Cy3_ch2_7DE_6566

city: Irvine

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description: biological replicate, Date of Scan 2009/12/07 10:34:17

hyb_protocol: Corning ULTRAGAPS slides were prehybridizated in 5x SSC, 0.1% SDS, 1% BSA for 45 min at 65°C.The dry probes were then resuspended in hybridization buffer (3x SSC, 0.17% SDS, 0.4 ug/uL yeast tRNA) and hybridized to the array at 65°C in a hybridization chamber (Corning) overnight.

scan_protocol: Slides were scanned using the GenePix4000B Scanner (Axon). Data was extracted from the resulting images using GenePix Pro 4.1 software (Axon).

data_processing: normalized based on total signal for each channel, background subtracted VALUE data obtained from log of normalized background subtracted ch1/ch2 signal.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: hydrated SL1344, replicate 3

label_protocol: cDNA was generated with N6 random primers (Invitrogen) from 2?g of total RNA at 42°C overnight.  cDNA synthesis was performed with aa-dUTP. Coupling to the Cy dye was performed in 0.1 M sodium carbonate buffer pH 8.6 for 1h at RT.

growth_protocol: overnight LB agar grown bacteria were resuspended in 13ml DDW at ~2x10^9 CFU/ml, and the suspensions were grown for 22h at 25°C in 50 ml polypropylene screw-capped tubes

extract_protocol: Bacteria were resuspended in 20% stop solution  (5% H2O-phenol and 95% ethanol) and incubated on ice for 30 min. Total RNA was then extracted using the Promega total RNA extraction kit, following manufacturer's instructions.

tag: strain

source_name: desiccated SL1344, replicate 3

growth_protocol: overnight LB agar grown bacteria were resuspended in 13ml DDW at ~2x10^9 CFU/ml, and the suspensions were air-dried for 22h at 25°C ~ 40% RH


title: ZG-37

description: Affymetrix Rhesus genome array


title: ZG-40

description: Affymetrix Rhesus genome array


title: ZG-25

description: Affymetrix Rhesus genome array


title: ZG-55

description: Affymetrix Rhesus genome array


title: NP5%

description: NP5% NEW

value: XP, NP1


title: RR2_SL1344_hydrated_Cy5_ch1_dessic_Cy3_ch2_7DE_6543

description: biological replicate, Date of Scan 2009/12/07 09:49:47

source_name: hydrated SL1344, replicate 2

source_name: desiccated SL1344, replicate 2


title: ZG-35

description: Affymetrix Rhesus genome array


title: RR2_SL1344_dessic_Cy5_ch1_hydrated_Cy3_ch2_7DE_6899

description: biological replicate, Date of Scan 2009/12/07 14:35:56

source_name: desiccated SL1344, replicate 4

source_name: hydrated SL1344, replicate 4


title: RR2_SL1344_dessic_Cy5_ch1_hydrated_Cy3_ch2_7DE_6542

description: biological replicate, Date of Scan 2009/12/07 11:58:04

source_name: desiccated SL1344, replicate 1

source_name: hydrated SL1344, replicate 1


title: Control wild type vs control ΔcalA strains time point 4 hours

status: Public on Dec 02 2012

city: Ribeirao Preto

first: Gustavo

middle: Henrique

last: Goldman

state: Sao Paulo

address: Avenida do Café, s/n

department: Departament of Pharmaceutical Sciences

country: Brazil

institute: Faculty of Pharmaceutical Sciences of Ribeirao Preto

description:
Af293 4h vs CalA 4h_13941913: Experimental replicate
CalA 4h vs Af293 4h_13941914: Experimental replicate (dye swap)

hyb_protocol: Hybridizations were performed as per JCVI PFGRC SOP m008 (http://pfgrc.jcvi.org/index.php/microarray/protocols.html) Briefly: Hybridizations were incubated for 18 h at 42C. Post hybridization washes included (twice each) 55C in 2x ssc, 0.1% SDS, RT in 0.1x SSC, 0.1% SDS and RT 0.1x SSC.

scan_protocol: After washing, slides were scanned with a GenePix 4000b scanner using GenePix Pro 3.0 software. PMT gains were changed in order to generate images with red:green ratios of as close to 1:1 as possible. Images were saved as .TIF files and TIGR Spotfinder (Saeed et al, 2003) was used to quantitate fluorescent intensities. Poor quality spots were identified manually and flagged. After Spotfinder analysis, resulst were exported as TIGR software compatible MEV files following local background subtraction.

data_processing: MEV files were loaded into the JCVI MIDAS array normalization program where they were first normalized by block locally-weighted scatter plot smoothing (LOWESS). After LOWESS, the flip-dye pairs were combined a consistency check was applied to remove any spots that do not fall within a specified deviation of the array-wide average log2 ratio of the fluorescence values for spot on both slides. After the flip-dye consistency check the values underwent inter-slide standard deviation regularisation by averaging the values of the replicate spots for each gene.

label: Cy3, Cy5

organism: Aspergillus fumigatus

source_name: Infection of mouse with Af293 wild type strain

label_protocol: cDNA synthesis and labeling were performed as per JCVI PFGRC SOP m007 (http://pfgrc.jcvi.org/index.php/microarray/protocols.html) Briefly: cDNA were generated using Invitrogen Superscript II, incorporating aminoallyl-dUTP. cDNA Samples were labeled with Cy3 or Cy5 during a 2 hour room temperature incubation followed by purification with a Qiagen PCR purification column to remove unbound dye.

extract_protocol: Total RNA extraction was performed using the filamentous fungi protocol of the Rneasy mini Kit (Qiagen)

treatment_protocol:
Time point: Af293 wild type strain from BALF at 4 hours time point (experimental)
Inoculum: A. fumigatus spores for inoculation were grown on Aspergillus complete medium, containing 1% (v/v) glucose and 5 mM ammonium (+)-tartrate for 5 days prior to infection. Conidia were freshly harvested using sterile saline and filtered through Miracloth. Conidial suspensions were spun for 10 min at 3000 g, washed twice with sterile saline, counted using a hemocytometer and re-suspended at a concentration of 2.5e9 cfu/mL. Viable counts from administered inocula were determined following serial dilution by plating on Aspergillus complete medium containing 1% (v/v) glucose and 5 mM ammonium (+)-tartrate and growth at 37°C.
Immunosuppresion protocol: 10 weeks old outbred CD1 male mice were immunosuppressed intraperitonially with 150 mg/kg of cyclophosphamide at day -3 of the infection. At day -1, animals were boosted with 150 mg/kg of cyclophosphamide plus 112.5 mg/kg of hydrocortisone acetate. Cyclophosphamide boosts were done in each 3 days until the end of the experiment. During the immunosuppresion regimen, animals received 1 g/L tetracyclin and 64 mg/L ciprofloxacin in drinking water to avoid secondary infections.
Infection: immunosuppressed mice were anaesthetized by halothane inhalation and infected intranasal insttilation of 10e8 spores in 40 microlitersof saline. Mice were weighed every 24 h from day of infection and visual inspection made twice daily. In the majority of cases the end-point for survival experimentation was a 20% reduction in body weight measured from day of infection, at which point mice were sacrificed.

tag: infection

value: Af293 wild type strain

tag: time point

value: 4 hours

source_name: Infection of mouse with ΔcalA mutant strain

treatment_protocol:
Time point: ΔcalA  mutant strain from BALF at 4 hours time point (contol)
Inoculum: A. fumigatus spores for inoculation were grown on Aspergillus complete medium, containing 1% (v/v) glucose and 5 mM ammonium (+)-tartrate for 5 days prior to infection. Conidia were freshly harvested using sterile saline and filtered through Miracloth. Conidial suspensions were spun for 10 min at 3000 g, washed twice with sterile saline, counted using a hemocytometer and re-suspended at a concentration of 2.5e9 cfu/mL. Viable counts from administered inocula were determined following serial dilution by plating on Aspergillus complete medium containing 1% (v/v) glucose and 5 mM ammonium (+)-tartrate and growth at 37°C.
Immunosuppresion protocol: 10 weeks old outbred CD1 male mice were immunosuppressed intraperitonially with 150 mg/kg of cyclophosphamide at day -3 of the infection. At day -1, animals were boosted with 150 mg/kg of cyclophosphamide plus 112.5 mg/kg of hydrocortisone acetate. Cyclophosphamide boosts were done in each 3 days until the end of the experiment. During the immunosuppresion regimen, animals received 1 g/L tetracyclin and 64 mg/L ciprofloxacin in drinking water to avoid secondary infections.
Infection: immunosuppressed mice were anaesthetized by halothane inhalation and infected intranasal insttilation of 10e8 spores in 40 microlitersof saline. Mice were weighed every 24 h from day of infection and visual inspection made twice daily. In the majority of cases the end-point for survival experimentation was a 20% reduction in body weight measured from day of infection, at which point mice were sacrificed.

value: ΔcalA mutant strain


title: Control wild type vs control akuB(KU80) strains time point 12 hours

description:
Af293 12h vs Ku80 12h_13941902: Experimental replicate
Ku80 12h vs Af293 12h_13941903: Experimental replicate (dye swap)

treatment_protocol:
Time point: Af293 wild type strain from BALF at 12 hours time point (experimental)
Inoculum: A. fumigatus spores for inoculation were grown on Aspergillus complete medium, containing 1% (v/v) glucose and 5 mM ammonium (+)-tartrate for 5 days prior to infection. Conidia were freshly harvested using sterile saline and filtered through Miracloth. Conidial suspensions were spun for 10 min at 3000 g, washed twice with sterile saline, counted using a hemocytometer and re-suspended at a concentration of 2.5e9 cfu/mL. Viable counts from administered inocula were determined following serial dilution by plating on Aspergillus complete medium containing 1% (v/v) glucose and 5 mM ammonium (+)-tartrate and growth at 37°C.
Immunosuppresion protocol: 10 weeks old outbred CD1 male mice were immunosuppressed intraperitonially with 150 mg/kg of cyclophosphamide at day -3 of the infection. At day -1, animals were boosted with 150 mg/kg of cyclophosphamide plus 112.5 mg/kg of hydrocortisone acetate. Cyclophosphamide boosts were done in each 3 days until the end of the experiment. During the immunosuppresion regimen, animals received 1 g/L tetracyclin and 64 mg/L ciprofloxacin in drinking water to avoid secondary infections.
Infection: immunosuppressed mice were anaesthetized by halothane inhalation and infected intranasal insttilation of 10e8 spores in 40 microlitersof saline. Mice were weighed every 24 h from day of infection and visual inspection made twice daily. In the majority of cases the end-point for survival experimentation was a 20% reduction in body weight measured from day of infection, at which point mice were sacrificed.

value: 12 hours

source_name: Infection of mouse with akuB(KU80) mutant strain

treatment_protocol:
Time point: akuB(KU80)  mutant strain from BALF at 12 hours time point (contol)
Inoculum: A. fumigatus spores for inoculation were grown on Aspergillus complete medium, containing 1% (v/v) glucose and 5 mM ammonium (+)-tartrate for 5 days prior to infection. Conidia were freshly harvested using sterile saline and filtered through Miracloth. Conidial suspensions were spun for 10 min at 3000 g, washed twice with sterile saline, counted using a hemocytometer and re-suspended at a concentration of 2.5e9 cfu/mL. Viable counts from administered inocula were determined following serial dilution by plating on Aspergillus complete medium containing 1% (v/v) glucose and 5 mM ammonium (+)-tartrate and growth at 37°C.
Immunosuppresion protocol: 10 weeks old outbred CD1 male mice were immunosuppressed intraperitonially with 150 mg/kg of cyclophosphamide at day -3 of the infection. At day -1, animals were boosted with 150 mg/kg of cyclophosphamide plus 112.5 mg/kg of hydrocortisone acetate. Cyclophosphamide boosts were done in each 3 days until the end of the experiment. During the immunosuppresion regimen, animals received 1 g/L tetracyclin and 64 mg/L ciprofloxacin in drinking water to avoid secondary infections.
Infection: immunosuppressed mice were anaesthetized by halothane inhalation and infected intranasal insttilation of 10e8 spores in 40 microlitersof saline. Mice were weighed every 24 h from day of infection and visual inspection made twice daily. In the majority of cases the end-point for survival experimentation was a 20% reduction in body weight measured from day of infection, at which point mice were sacrificed.

value: akuB(KU80) mutant strain


title: Dermis Ad+MVA 24h, replicate 3

status: Public on Dec 01 2012

city: Oxford

first: Arturo

last: Reyes-Sandoval

state: Oxfordshire

address: ORCRB, Roosevelt Dr.

department: The Jenner Institute

institute: University of Oxford

description:
Ame 24h 3
Replicate 3 of 4.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: We used the quantile normalization method for all of the analyses reported here and implemented background correction within Illumina's proprietary BeadStudio software. The results of the experiment were analyzed using Bioconductor libraries limma and beadarray.

source_name: BALB/c mouse ear biopsy, Ad+MVA, 24h

label_protocol: Standard Illumina label protocol.

extract_protocol: Total RNA was isolated using the miRNeasy kit (QIAGEN, UK) within 2 h of sample collection.

treatment_protocol: Mice were vaccinated with adenovirus, MVA or Ad+MVA mixed co-administration.

value: BALB/c

tag: age

value: 6 weeks

value: ear biopsy

tag: treatment

value: Ad+MVA

tag: time


title: Control wild type vs control ΔcrzA strains time point 12 hours

description:
Af293 12h vs Crz 12_13941908: Experimental replicate
Crz 12h vs Af293 12_13941909: Experimental replicate (dye swap)

source_name: Infection of mouse with ΔcrzA mutant strain

treatment_protocol:
Time point: ΔcrzA  mutant strain from BALF at 12 hours time point (contol)
Inoculum: A. fumigatus spores for inoculation were grown on Aspergillus complete medium, containing 1% (v/v) glucose and 5 mM ammonium (+)-tartrate for 5 days prior to infection. Conidia were freshly harvested using sterile saline and filtered through Miracloth. Conidial suspensions were spun for 10 min at 3000 g, washed twice with sterile saline, counted using a hemocytometer and re-suspended at a concentration of 2.5e9 cfu/mL. Viable counts from administered inocula were determined following serial dilution by plating on Aspergillus complete medium containing 1% (v/v) glucose and 5 mM ammonium (+)-tartrate and growth at 37°C.
Immunosuppresion protocol: 10 weeks old outbred CD1 male mice were immunosuppressed intraperitonially with 150 mg/kg of cyclophosphamide at day -3 of the infection. At day -1, animals were boosted with 150 mg/kg of cyclophosphamide plus 112.5 mg/kg of hydrocortisone acetate. Cyclophosphamide boosts were done in each 3 days until the end of the experiment. During the immunosuppresion regimen, animals received 1 g/L tetracyclin and 64 mg/L ciprofloxacin in drinking water to avoid secondary infections.
Infection: immunosuppressed mice were anaesthetized by halothane inhalation and infected intranasal insttilation of 10e8 spores in 40 microlitersof saline. Mice were weighed every 24 h from day of infection and visual inspection made twice daily. In the majority of cases the end-point for survival experimentation was a 20% reduction in body weight measured from day of infection, at which point mice were sacrificed.

value: ΔcrzA mutant strain


title: Dermis Ad 24h, replicate 4

description:
Ae 24h 4
Replicate 4 of 4.

source_name: BALB/c mouse ear biopsy, Ad, 24h

value: Ad


title: Dermis Ad 24h, replicate 2

description:
Ae 24h 2
Replicate 2 of 4.


title: Dermis Ad+MVA 24h, replicate 2

description:
Ame 24h 2
Replicate 2 of 4.


title: Dermis Ad+MVA 24h, replicate 1

description:
Ame 24h 1
Replicate 1 of 4.


title: Control wild type vs control ΔcalA strains time point 12 hours

description:
Af293 12h vs CalA 12h_13941905: Experimental replicate
CalA 12 vs Af293 12_13941907: Experimental replicate (dye swap)

treatment_protocol:
Time point: ΔcalA  mutant strain from BALF at 12 hours time point (contol)
Inoculum: A. fumigatus spores for inoculation were grown on Aspergillus complete medium, containing 1% (v/v) glucose and 5 mM ammonium (+)-tartrate for 5 days prior to infection. Conidia were freshly harvested using sterile saline and filtered through Miracloth. Conidial suspensions were spun for 10 min at 3000 g, washed twice with sterile saline, counted using a hemocytometer and re-suspended at a concentration of 2.5e9 cfu/mL. Viable counts from administered inocula were determined following serial dilution by plating on Aspergillus complete medium containing 1% (v/v) glucose and 5 mM ammonium (+)-tartrate and growth at 37°C.
Immunosuppresion protocol: 10 weeks old outbred CD1 male mice were immunosuppressed intraperitonially with 150 mg/kg of cyclophosphamide at day -3 of the infection. At day -1, animals were boosted with 150 mg/kg of cyclophosphamide plus 112.5 mg/kg of hydrocortisone acetate. Cyclophosphamide boosts were done in each 3 days until the end of the experiment. During the immunosuppresion regimen, animals received 1 g/L tetracyclin and 64 mg/L ciprofloxacin in drinking water to avoid secondary infections.
Infection: immunosuppressed mice were anaesthetized by halothane inhalation and infected intranasal insttilation of 10e8 spores in 40 microlitersof saline. Mice were weighed every 24 h from day of infection and visual inspection made twice daily. In the majority of cases the end-point for survival experimentation was a 20% reduction in body weight measured from day of infection, at which point mice were sacrificed.


title: Dermis MVA 24h, replicate 1

description:
Me 24h 1
Replicate 1 of 4.

source_name: BALB/c mouse ear biopsy, MVA, 24h

value: MVA


title: Dermis Ad 24h, replicate 1

description:
Ae 24h 1
Replicate 1 of 4.


title: Dermis MVA 24h, replicate 2

description:
Me 24h 2
Replicate 2 of 4.


title: Control wild type vs control ΔcrzA strains time point 4 hours

description:
Af293 4h vs Crz 4h_13941915: Experimental replicate
Crz 4h vs Af293 4h_13941916: Experimental replicate (dye swap)

treatment_protocol:
Time point: ΔcrzA  mutant strain from BALF at 4 hours time point (contol)
Inoculum: A. fumigatus spores for inoculation were grown on Aspergillus complete medium, containing 1% (v/v) glucose and 5 mM ammonium (+)-tartrate for 5 days prior to infection. Conidia were freshly harvested using sterile saline and filtered through Miracloth. Conidial suspensions were spun for 10 min at 3000 g, washed twice with sterile saline, counted using a hemocytometer and re-suspended at a concentration of 2.5e9 cfu/mL. Viable counts from administered inocula were determined following serial dilution by plating on Aspergillus complete medium containing 1% (v/v) glucose and 5 mM ammonium (+)-tartrate and growth at 37°C.
Immunosuppresion protocol: 10 weeks old outbred CD1 male mice were immunosuppressed intraperitonially with 150 mg/kg of cyclophosphamide at day -3 of the infection. At day -1, animals were boosted with 150 mg/kg of cyclophosphamide plus 112.5 mg/kg of hydrocortisone acetate. Cyclophosphamide boosts were done in each 3 days until the end of the experiment. During the immunosuppresion regimen, animals received 1 g/L tetracyclin and 64 mg/L ciprofloxacin in drinking water to avoid secondary infections.
Infection: immunosuppressed mice were anaesthetized by halothane inhalation and infected intranasal insttilation of 10e8 spores in 40 microlitersof saline. Mice were weighed every 24 h from day of infection and visual inspection made twice daily. In the majority of cases the end-point for survival experimentation was a 20% reduction in body weight measured from day of infection, at which point mice were sacrificed.


title: Control wild type vs control akuB(KU80) strains time point 4 hours

description:
Af293 4h vs Ku80 4h_13941910: Experimental replicate
Ku80 4h vs Af293 4h_13941911: Experimental replicate (dye swap)

treatment_protocol:
Time point: akuB(KU80)  mutant strain from BALF at 4 hours time point (contol)
Inoculum: A. fumigatus spores for inoculation were grown on Aspergillus complete medium, containing 1% (v/v) glucose and 5 mM ammonium (+)-tartrate for 5 days prior to infection. Conidia were freshly harvested using sterile saline and filtered through Miracloth. Conidial suspensions were spun for 10 min at 3000 g, washed twice with sterile saline, counted using a hemocytometer and re-suspended at a concentration of 2.5e9 cfu/mL. Viable counts from administered inocula were determined following serial dilution by plating on Aspergillus complete medium containing 1% (v/v) glucose and 5 mM ammonium (+)-tartrate and growth at 37°C.
Immunosuppresion protocol: 10 weeks old outbred CD1 male mice were immunosuppressed intraperitonially with 150 mg/kg of cyclophosphamide at day -3 of the infection. At day -1, animals were boosted with 150 mg/kg of cyclophosphamide plus 112.5 mg/kg of hydrocortisone acetate. Cyclophosphamide boosts were done in each 3 days until the end of the experiment. During the immunosuppresion regimen, animals received 1 g/L tetracyclin and 64 mg/L ciprofloxacin in drinking water to avoid secondary infections.
Infection: immunosuppressed mice were anaesthetized by halothane inhalation and infected intranasal insttilation of 10e8 spores in 40 microlitersof saline. Mice were weighed every 24 h from day of infection and visual inspection made twice daily. In the majority of cases the end-point for survival experimentation was a 20% reduction in body weight measured from day of infection, at which point mice were sacrificed.


title: Dermis Naive, replicate 4

description:
Ne 4
Replicate 4 of 4.

source_name: BALB/c mouse ear biopsy, naive


title: Dermis Ad 6h, replicate 4

description:
Ae 6h 4
Replicate 4 of 4.

source_name: BALB/c mouse ear biopsy, Ad, 6h


title: Dermis Ad+MVA 6h, replicate 3

description:
Ame 6h 3
Replicate 3 of 4.

source_name: BALB/c mouse ear biopsy, Ad+MVA, 6h


title: Dermis Naive, replicate 2

description:
Ne 2
Replicate 2 of 4.


title: Dermis MVA 24h, replicate 4

description:
Me 24h 4
Replicate 4 of 4.


title: Dermis Naive, replicate 3

description:
Ne 3
Replicate 3 of 4.


title: Dermis Naive, replicate 1

description:
Ne 1
Replicate 1 of 4.


title: Dermis Ad+MVA 6h, replicate 2

description:
Ame 6h 2
Replicate 2 of 4.


title: Dermis Ad+MVA 6h, replicate 4

description:
Ame 6h 4
Replicate 4 of 4.


title: Dermis Ad 6h, replicate 2

description:
Ae 6h 2
Replicate 2 of 4.


title: Lymph node naive, replicate 2

description:
N2
Replicate 2 of 3.

source_name: BALB/c mouse auricular draining lymph node, naive

value: lymph node


title: Dermis MVA 6h, replicate 1

description:
Me 6h 1
Replicate 1 of 4.

source_name: BALB/c mouse ear biopsy, MVA, 6h


title: Lymph node naive, replicate 3

description:
N3
Replicate 3 of 3.


title: Lymph node Ad+MVA 72h, replicate 4

description:
Mix 72h 4
Replicate 4 of 4.

source_name: BALB/c mouse auricular draining lymph node, Ad+MVA, 72h


title: Dermis Ad 6h, replicate 1

description:
Ae 6h 1
Replicate 1 of 4.


title: Dermis MVA 6h, replicate 3

description:
Me 6h 3
Replicate 3 of 4.


title: Lymph node naive, replicate 1

description:
N1
Replicate 1 of 3.


title: Lymph node MVA 72h, replicate 4

description:
M 72h 4
Replicate 4 of 4.

source_name: BALB/c mouse auricular draining lymph node, MVA, 72h


title: Dermis MVA 6h, replicate 4

description:
Me 6h 4
Replicate 4 of 4.


title: Lymph node Ad 72h, replicate 3

description:
A72h 3
Replicate 3 of 4.

source_name: BALB/c mouse auricular draining lymph node, Ad, 72h


title: Lymph node Ad 72h, replicate 4

description:
A72h 4
Replicate 4 of 4.


title: Lymph node Ad+MVA 72h, replicate 2

description:
Mix 72h 2
Replicate 2 of 4.


title: Lymph node Ad+MVA 72h, replicate 1

description:
Mix 72h 1
Replicate 1 of 4.


title: Lymph node MVA 72h, replicate 3

description:
M 72h 3
Replicate 3 of 4.


title: Lymph node MVA 72h, replicate 1

description:
M 72h 1
Replicate 1 of 4.


title: Lymph node Ad 72h, replicate 1

description:
A72h 1
Replicate 1 of 4.


title: Lymph node Ad+MVA 24h, replicate 4

description:
Mix 24h 4
Replicate 4 of 4.

source_name: BALB/c mouse auricular draining lymph node, Ad+MVA, 24h


title: Lymph node Ad 72h, replicate 2

description:
A72h 2
Replicate 2 of 4.


title: Dermis Ad 6h, replicate 3

description:
Ae 6h 3
Replicate 3 of 4.


title: Lymph node Ad+MVA 24h, replicate 2

description:
Mix 24h 2
Replicate 2 of 4.


title: Lymph node Ad+MVA 24h, replicate 1

description:
Mix 24h 1
Replicate 1 of 4.


title: Lymph node Ad+MVA 24h, replicate 3

description:
Mix 24h 3
Replicate 3 of 4.


title: Lymph node MVA 24h, replicate 4

description:
M24h 4
Replicate 4 of 4.

source_name: BALB/c mouse auricular draining lymph node, MVA, 24h


title: Lymph node MVA 72h, replicate 2

description:
M 72h 2
Replicate 2 of 4.


title: Lymph node Ad+MVA 72h, replicate 3

description:
Mix 72h 3
Replicate 3 of 4.


title: Lymph node MVA 24h, replicate 3

description:
M24h 3
Replicate 3 of 4.


title: Lymph node MVA 24h, replicate 2

description:
M24h 2
Replicate 2 of 4.


title: Lymph node MVA 24h, replicate 1

description:
M24h 1
Replicate 1 of 4.


title: Lymph node Ad 24h, replicate 4

description:
A24h 4
Replicate 4 of 4.

source_name: BALB/c mouse auricular draining lymph node, Ad, 24h


title: Lymph node Ad 24h, replicate 2

description:
A24h 2
Replicate 2 of 4.


title: Lymph node Ad+MVA 9h, replicate 4

description:
Mix 9h 4
Replicate 4 of 4.

source_name: BALB/c mouse auricular draining lymph node, Ad+MVA, 9h


title: Lymph node Ad 24h, replicate 3

description:
A24h 3
Replicate 3 of 4.


title: Lymph node Ad 24h, replicate 1

description:
A24h 1
Replicate 1 of 4.


title: Lymph node Ad+MVA 9h, replicate 3

description:
Mix 9h 3
Replicate 3 of 4.


title: Lymph node Ad+MVA 9h, replicate 2

description:
Mix 9h 2
Replicate 2 of 4.


title: Lymph node MVA 9h, replicate 4

description:
M9h 4
Replicate 4 of 4.

source_name: BALB/c mouse auricular draining lymph node, MVA, 9h


title: Lymph node Ad+MVA 9h, replicate 1

description:
Mix 9h 1
Replicate 1 of 4.


title: Lymph node MVA 9h, replicate 2

description:
M9h 2
Replicate 2 of 4.


title: Lymph node MVA 9h, replicate 1

description:
M9h 1
Replicate 1 of 4.