title: plate pool 15_long arm of chromosome 5A

description:
raw data file: 254552110007_660.txt (block 3)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Hippocampus, control rat-rep2

status: Public on Aug 13 2015

type: RNA

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

country: Switzerland

institute: ETH Zurich

description:
Gene expression data of hippocampi dissected out from 16 month-old male Wistar control rats.
Rat-control-2

hyb_protocol: For hybridization, 15 μg of fragmented, biotin-labeled cRNA were incubated with the gene chip (Affymetrix GeneChip Rat Genome 230. 2.0 Array) in 200 μl of the hybridization solution in a hybridization Oven 640 (Affymetrix) for 16 h at 45 °C. GeneChips were then washed and stained using the Affymetrix Fluidics Station 450 according to the GeneChip Expression Analysis Technical Manual.

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

data_processing: The signals were processed using Affymetrix GeneChip Operating Software (GCOS; v. 1.4; Affymetrix). To compare samples and experiments, the trimmed mean signal of each array was scaled to a target intensity of 300.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Hippocampi from 16 month-old male Wistar control rats

label_protocol: Biotin-labeled cRNA was prepared according to the protocol of the manufacturer (Affymetrix; GeneChip Expression Analysis Technical Manual).

growth_protocol: The study was performed with 16 month-old male Wistar rats, which had been subjected to the chronic unpredictable mild stress battery for four weeks. The age-matched control group was housed under standard conditions and had free access to food and water. At an age of 16 months, hippocampi were dissected out on ice and processed for whole genome microarray gene expression profiling.

extract_protocol: Total hippocampal RNA was isolated with the RNeasy Mini kit according to the protocol of the manufacturer (Qiagen).

treatment_protocol: The study was performed with hippocampi dissected out from two groups of male Wistar rats, i.e. (i) 16 month-old rats, which had been subjected to the chronic unpredictable mild stress battery for four weeks, and (ii) 16 month-old rats, which were housed under standard conditions and had free access to food and water.

tag: strain

value: Wistar

tag: gender

value: male

tag: stress

value: control

tag: age

value: 16 months old

tag: tissue

value: hippocampus


title: plate pool 14_long arm of chromosome 5A

type: genomic

city: Fiorenzuola d'Arda

first: Delfina

last: Barabaschi

address: Via San Protaso 302

country: Italy

institute: CRA-Genomics Research Centre

description:
raw data file: 254552110008_620.txt (block 8)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.

hyb_protocol: After a cooling step on ice of 3 min, non-reacted ULS-Cy3 were removed through KREApureTM columns (Kreatech Biotechnology) and the yield and degree of labeling was evaluated by the Nanodrop ND-1000. Hybridizations and washing were performed as recommended (Agilent Oligonucleotide Array-Based cgh for Genomic DNA Analysis v3.4).

scan_protocol: Scanning was performed on a Axon GenePix 4000A scanner.

data_processing: Data extraction was carried out using the GenePix Pro 7 software.

molecule: genomic DNA

organism: Triticum aestivum

source_name: 3D-pool of BAC clones of chromosome 5A

label_protocol: Briefly, 450 ng of DNA polymerase amplified DNA of each pool was fragmented for 10 min at 95°C and then labeled with Cy3 using the Genomic DNA ULS Labeling Kit according to manufacturer instructions (Agilent Technologies).

growth_protocol: BAC clones colonies (5,412 for 5AS and 8,709 for 5AL) were individually growth in 2YT media supplemented with 12.5 μg/mL chloramphenicol. The plate pools (PPs), column pools (CPs) and row pools (RPs) (15, 24, 16 for 5AS and 23, 24,16 for 5AL respectively) were obtained by mixing 10 μl of each bacterial culture, then adding 1 mL of fresh medium and growing for 16 h at 37°C.

extract_protocol: DNA from each pool was obtained employing the phi29 DNA polymerase rolling circle amplification (GenomiPhi V2 DNA Polymerase Kit, GE Healthcare, Dean et al, 2001). Briefly, 1 μl of each BAC pool was denatured in 9 μl sample buffer at 95°C for 5 min and then cooled on ice for 5 min. The denatured samples were mixed with 1 μl GenomiPhi phi29 DNA polymerase and 9 μl reaction buffer, and then incubated at 30°C for 2 hours; reaction was terminated at 65°C for 10 min.

tag: cultivar

value: Chinese spring

tag: chromosome arm

value: long arm


title: Multiple myeloma, TT2, relapse, 44

city: Little Rock

first: Joshua

last: Epstein

department: Myeloma Institute for Research and Therapy

country: USA

institute: University of Arkansas for Medical Sciances

description: Gene expression data from multiple myeloma plasma cells at relapse.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on an HG-U133-Plus-2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data 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.

organism: Homo sapiens

source_name: Multiple myeloma plasma cells, TT2, relapse

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

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

tag: cell type

value: multiple myeloma plasma cells

tag: treatment

tag: time of testing

value: relapse


title: Hippocampus, stressed rat-rep1

description:
Gene expression data of hippocampi dissected out from 16 month-old male Wistar rats after four weeks of chronic unpredictable mild stress.
Rat-stressed-1

source_name: Hippocampi from 16 month-old male Wistar rats after 4 weeks of chronic unpredictable mild stress

value: 4 weeks of chronic unpredictable mild stress.


title: Multiple myeloma, TT2, relapse, 42


title: plate pool 12_long arm of chromosome 5A

description:
raw data file: 254552110007_660.txt (block 5)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 41


title: Multiple myeloma, TT2, relapse, 47


title: plate pool 11_long arm of chromosome 5A

description:
raw data file: 254552110007_660.txt (block 6)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: plate pool 10_long arm of chromosome 5A

description:
raw data file: 254552110008_620.txt (block 3)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 40


title: Multiple myeloma, TT2, relapse, 43


title: Multiple myeloma, TT2, relapse, 38


title: plate pool 9_long arm of chromosome 5A

description:
raw data file: 254552110008_620.txt (block 2)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 37


title: Multiple myeloma, TT2, relapse, 35


title: Multiple myeloma, TT2, relapse, 36


title: plate pool 7_long arm of chromosome 5A

description:
raw data file: chip14_680.txt (block 1)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: plate pool 13_long arm of chromosome 5A

description:
raw data file: chip6_640.txt (block 4)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 39


title: plate pool 8_long arm of chromosome 5A

description:
raw data file: 254552110008_620.txt (block 7)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: plate pool 6_long arm of chromosome 5A

description:
raw data file: 254552110007_660.txt (block 8)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: YAP-overexpression 2

type: SRA

city: La Jolla

first: Hyun Woo

last: Park

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pharmacology

institute: UCSD

library_source: transcriptomic

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to hg19 human whole genome using bowtie v0.12.7
Count the mapped reads for each genes for each samples
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes raw counts for each genes for each samples

growth_protocol: MCF10A cell were cultured in DMEM/F12 supplemented with 5% horse serum, 20 ng/ml EGF, 0.5 ug/ml hydrocortisone, 100 ng/ml cholera toxin, and 10 ug/ml insulin.

extract_protocol:
RNA was extracted from control or YAP-overexpressing MCF10A cells (both serum-starved for 16 hr) using protocol from RNeasy kit (Qiagen).
Briefly, 1ug of total RNA was first converted to cDNA by superscript III first strand synthesis kit with primer Biotin-P7-dT(20). The cDNA was purified by NucleoSpin Gel and PCR Clean-Up Kit column (Clontech) to remove free primers and enzyme. Then terminal transferase (NEB) was applied to block the terminal of a cDNA 3’end.  Streptavidin-coaged magnetic beads (Life Technology) were further applied to purify cDNAs.  After RNA degradation by sodium hydroxide, second strand cDNA was synthesized by random priming with primer Adaptor-N8. The second strand cDNA was eluted from beads by heating.  The cDNA was then used as template to construct libraries by amplifying with barcode primers and primer P7. The sequencing was done on Hiseq 2000 system (Genomics. 2011;98(4):266-71).

treatment_protocol: Before harvest, cells were serum-starved for 16 hrs.

value: mammary gland epithelial cells

tag: cell line


title: Multiple myeloma, TT2, relapse, 34


title: Multiple myeloma, TT2, relapse, 33


title: Multiple myeloma, TT2, relapse, 32


title: YAP-overexpression 1


title: plate pool 5_long arm of chromosome 5A

description:
raw data file: 254552110008_620.txt (block 1)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 31


title: YAP-overexpression 3


title: plate pool 4_long arm of chromosome 5A

description:
raw data file: chip6_640.txt (block 3)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 30


title: Multiple myeloma, TT2, relapse, 29


title: 3832T

city: Newark

first: Saleena

last: Ghanny

address: 185 South Orange Ave

institute: Rutgers University

description:
GBM3832T
Infected with HCMV TR strain

hyb_protocol: The Affymetrix Genechip WT Terminal Labeling and Hybridization protocol was used

scan_protocol: Chips were scanned using the Affymetrix 7G Plus scanner and Command Console Software

data_processing: Data was processed by importing CEL files into Partek Software and RMA normalization was performed

label: Biotin

source_name: Primary GSC Infected TR treated control siRNA

label_protocol: The Ambion WT Expression Kit with accompanying protocol was used to label the samples

growth_protocol: Primary GBM lines were grown as neurospheres in Neural Basal Media + 20ng/ml FGF and EGF.

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

treatment_protocol: 40 nM final conc of control siRNA or IE siRNA (2 duplexes targeting IE1 and IE2 were added to triplicate wells. RNA harvested 72h following treatment

value: Brain Tumor

value: glioblastoma


title: vector control 2


title: vector control 3


title: plate pool 3_long arm of chromosome 5A

description:
raw data file: chip13_650.txt (block 5)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: vector control 1


title: 3832TSI

description:
GBM3832TSI
Infected with HCMV TR strain

source_name: Primary GSC infected TR treated IE siRNA


title: row pool 16_short arm of chromosome 5A

description:
raw data file: chip16_660.txt (block 8)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.

value: short arm


title: 0609TSI

description:
GBM0609TSI
Infected with HCMV TR strain

source_name: Primary GSC infected TR treated with IE siRNA


title: 0609T

description:
GBM0609T
Infected with HCMV TR strain


title: Multiple myeloma, TT2, relapse, 28


title: Multiple myeloma, TT2, relapse, 27


title: Multiple myeloma, TT2, relapse, 25


title: Multiple myeloma, TT2, relapse, 26


title: row pool 15_short arm of chromosome 5A

description:
raw data file: chip20_600.txt (block 7)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: plate pool 1_long arm of chromosome 5A

description:
raw data file: chip6_640.txt (block 1)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: plate pool 2_long arm of chromosome 5A

description:
raw data file: chip6_640.txt (block 2)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: row pool 13_short arm of chromosome 5A

description:
raw data file: chip16_660.txt (block 4)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: row pool 14_short arm of chromosome 5A

description:
raw data file: chip16_660.txt (block 6)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: row pool 11_short arm of chromosome 5A

description:
raw data file: chip20_600.txt (block 6)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: VMM1 - poly-ICLC Treated - mAdbID:119177

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: mAdb experiment ID: 119177

hyb_protocol: Affymetrix Hybrization Protocol Other: Terminally labeled cDNA were hybridized to the Human GeneChip 1.0 ST array and stained on a Genechip Fluidics Station 450 (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

scan_protocol: Affymetrix Scanning Protocol Other: Arrays were then scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Affymetrix RMA Data Processing
Calculation Method: Partek Genomics Suite 6.6 (St. Louis, MO) was used for data analysis. After Robust Multichip Average (RMA) normalization, differentially expressed genes were identified by paired t-tests with a significance cut off p<0.05.

source_name: VMM1 - poly-ICLC Treated

label_protocol:
Sample Labeling Protocol
Other: Total RNA was amplified using the Ambion WT expression kit (Life Technologies, Carlsbad, CA). Fragmented single-stranded sense DNA were terminally labeled.

extract_protocol:
Sample Extraction Protocol
Other: Cells were lysed directly in QIAzol Lysis Reagent (Qiagen, Hilden, Germany) and RNA was extracted according to the manufacturer's protocol.

treatment_protocol:
Agent: poly-ICLC
Treatment dose: 20 ug/mL
Treatment time: overnight
Treatment temperature: 37C
In-vitro treatment: Melanoma cell lines were seeded into 6-well plates at 1-3x10(5) cells per well in 3mL RPMI and individually stimulated overnight at 37C with TLR agonist, poly-ICLC (20 ug/mL) (Oncovir Inc, Washington, DC).

value: Melanoma

tag: disease state

tag: agent

value: poly-ICLC


title: VMM39 - Untreated - mAdbID:119180

description: mAdb experiment ID: 119180

source_name: VMM39 - Untreated

value: Untreated


title: Multiple myeloma, TT2, relapse, 22

description: Gene expression data from multiple myeloma plasma cells at relapse.


title: VMM1 - Untreated - repeat 1 - mAdbID:119176

description: mAdb experiment ID: 119176

source_name: VMM1 - Untreated


title: Multiple myeloma, TT2, relapse, 24


title: Multiple myeloma, TT2, relapse, 21


title: row pool 9_short arm of chromosome 5A

description:
raw data file: chip16_660.txt (block 5)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: VMM1 - Imiquimod Treated - mAdbID:119174

description: mAdb experiment ID: 119174

source_name: VMM1 - Imiquimod Treated

treatment_protocol:
Agent: Imiquimod
Treatment dose: 25 ug/mL
Treatment time: overnight
Treatment temperature: 37C
In-vitro treatment: Melanoma cell lines were seeded into 6-well plates at 1-3x10(5) cells per well in 3mL RPMI and individually stimulated overnight at 37C with TLR agonist, Imiquimod (25 ug/mL) (Imgenex).

value: Imiquimod


title: VMM1 - LPS Treated - mAdbID:119175

description: mAdb experiment ID: 119175

source_name: VMM1 - LPS Treated

treatment_protocol:
Agent: LPS
Treatment dose: 10 ug/mL
Treatment time: overnight
Treatment temperature: 37C
In-vitro treatment: Melanoma cell lines were seeded into 6-well plates at 1-3x10(5) cells per well in 3mL RPMI and individually stimulated overnight at 37C with TLR agonist, LPS (10 ug/mL).

value: LPS


title: VMM39 - Imiquimod Treated - mAdbID:119179

description: mAdb experiment ID: 119179

source_name: VMM39 - Imiquimod Treated


title: VMM1 - Resiquimod Treated - mAdbID:119178

description: mAdb experiment ID: 119178

source_name: VMM1 - Resiquimod Treated

treatment_protocol:
Agent: Resiquimod
Treatment dose: 5 ug/mL
Treatment time: overnight
Treatment temperature: 37C
In-vitro treatment: Melanoma cell lines were seeded into 6-well plates at 1-3x10(5) cells per well in 3mL RPMI and individually stimulated overnight at 37C with TLR agonist, Resiquimod (5 ug/mL).

value: Resiquimod


title: HEK293 - Resiquimod Treated - mAdbID:119172

description: mAdb experiment ID: 119172

source_name: HEK293 - Resiquimod Treated


title: HEK293 - poly-ICLC Treated - mAdbID:119171

description: mAdb experiment ID: 119171

source_name: HEK293 - poly-ICLC Treated


title: row pool 12_short arm of chromosome 5A

description:
raw data file: chip16_660.txt (block 2)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 19


title: Multiple myeloma, TT2, relapse, 20


title: VMM1 - CpG ODN Treated - mAdbID:119173

description: mAdb experiment ID: 119173

source_name: VMM1 - CpG ODN Treated

treatment_protocol:
Agent: CpG ODN
Treatment dose: 5 ug/mL
Treatment time: overnight
Treatment temperature: 37C
In-vitro treatment: Melanoma cell lines were seeded into 6-well plates at 1-3x10(5) cells per well in 3mL RPMI and individually stimulated overnight at 37C with TLR agonist, CpG ODN (5 ug/mL).

value: CpG ODN


title: Multiple myeloma, TT2, relapse, 23


title: Multiple myeloma, TT2, relapse, 45


title: Multiple myeloma, TT2, relapse, 17


title: row pool 10_short arm of chromosome 5A

description:
raw data file: chip16_660.txt (block 7)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: row pool 8_short arm of chromosome 5A

description:
raw data file: chip16_660.txt (block 3)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 16


title: row pool 7_short arm of chromosome 5A

description:
raw data file: chip16_660.txt (block 1)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 18


title: row pool 6_short arm of chromosome 5A

description:
raw data file: chip17_660.txt (block 8)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 14


title: row pool 5_short arm of chromosome 5A

description:
raw data file: chip17_660.txt (block 6)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: row pool 4_short arm of chromosome 5A

description:
raw data file: chip17_660.txt (block 4)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: HEK293 - Untreated - mAdbID:119170

description: mAdb experiment ID: 119170

source_name: HEK293 - Untreated


title: row pool 3_short arm of chromosome 5A

description:
raw data file: chip17_660.txt (block 2)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.

source_name: 3D-pool of BAC clones of chromosome 5A


title: HEK293 - Imiquimod Treated - mAdbID:119169

description: mAdb experiment ID: 119169

source_name: HEK293 - Imiquimod Treated


title: row pool 2_short arm of chromosome 5A

description:
raw data file: chip14_680.txt (block 3)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: row pool 1_short arm of chromosome 5A

description:
raw data file: chip17_660.txt (block 7)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 13

source_name: Multiple myeloma plasma cells, TT2, relapse


title: Multiple myeloma, TT2, relapse, 51


title: column pool 24_short arm of chromosome 5A

description:
raw data file: chip20_600.txt (block 5)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: HEK293 - CpG ODN Treated - mAdbID:119168

description: mAdb experiment ID: 119168

source_name: HEK293 - CpG ODN Treated


title: HEK293 - LPS Treated - mAdbID:119167

description: mAdb experiment ID: 119167

source_name: HEK293 - LPS Treated


title: Multiple myeloma, TT2, relapse, 48


title: Multiple myeloma, TT2, relapse, 15


title: Multiple myeloma, TT2, relapse, 12


title: TLR7 HEK293 - LPS Treated - mAdbID:119163

description: mAdb experiment ID: 119163

source_name: TLR7 HEK293 - LPS Treated

value: TLR7 HEK293


title: column pool 23_short arm of chromosome 5A

description:
raw data file: chip20_540.txt (block 4)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.

value: Chinese spring


title: Multiple myeloma, TT2, relapse, 10


title: TLR7 HEK293 - Untreated - mAdbID:119160

description: mAdb experiment ID: 119160

source_name: TLR7 HEK293 - Untreated


title: TLR7 HEK293 - poly-ICLC Treated - mAdbID:119161

description: mAdb experiment ID: 119161

source_name: TLR7 HEK293 - poly-ICLC Treated


title: TLR7 HEK293 - CpG ODN Treated - mAdbID:119159

description: mAdb experiment ID: 119159

source_name: TLR7 HEK293 - CpG ODN Treated


title: TLR7 HEK293 - Imiquimod Treated - mAdbID:119162

description: mAdb experiment ID: 119162

source_name: TLR7 HEK293 - Imiquimod Treated


title: Multiple myeloma, TT2, relapse, 11


title: TLR7 HEK293 - Resiquimod Treated - mAdbID:119158

description: mAdb experiment ID: 119158

source_name: TLR7 HEK293 - Resiquimod Treated


title: column pool 21_short arm of chromosome 5A

description:
raw data file: chip20_540.txt (block 2)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 8


title: Multiple myeloma, TT2, relapse, 7


title: column pool 22_short arm of chromosome 5A

description:
raw data file: chip20_540.txt (block 3)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Ramos - Resiquimod Treated - mAdbID:119157

description: mAdb experiment ID: 119157

source_name: Ramos - Resiquimod Treated

value: Ramos


title: Multiple myeloma, TT2, relapse, 6

value: multiple myeloma plasma cells


title: Multiple myeloma, TT2, relapse, 4

value: relapse


title: Multiple myeloma, TT2, relapse, 5


title: column pool 20_short arm of chromosome 5A

description:
raw data file: chip19_600.txt (block 8)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 9

description: Gene expression data from multiple myeloma plasma cells at relapse.


title: column pool 19_short arm of chromosome 5A

description:
raw data file: chip20_540.txt (block 1)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: column pool 18_short arm of chromosome 5A

description:
raw data file: chip19_600.txt (block 7)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: column pool 16_short arm of chromosome 5A

description:
raw data file: chip19_600.txt (block 5)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: column pool 17_short arm of chromosome 5A

description:
raw data file: chip19_600.txt (block 6)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Ramos - Untreated - mAdbID:119155

description: mAdb experiment ID: 119155

source_name: Ramos - Untreated


title: column pool 15_short arm of chromosome 5A

description:
raw data file: chip19_600.txt (block 4)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Ramos - poly-ICLC Treated - mAdbID:119156

description: mAdb experiment ID: 119156

source_name: Ramos - poly-ICLC Treated


title: Ramos - LPS Treated - mAdbID:119154

description: mAdb experiment ID: 119154

source_name: Ramos - LPS Treated


title: column pool 14_short arm of chromosome 5A

description:
raw data file: chip19_600.txt (block 3)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Multiple myeloma, TT2, relapse, 3


title: Multiple myeloma, TT2, relapse, 2


title: column pool 13_short arm of chromosome 5A

description:
raw data file: chip19_600.txt (block 2)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: Ramos - CpG ODN Treated - mAdbID:119152

description: mAdb experiment ID: 119152

source_name: Ramos - CpG ODN Treated


title: column pool 12_short arm of chromosome 5A

description:
raw data file: chip19_600.txt (block 1)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: column pool 11_short arm of chromosome 5A

description:
raw data file: chip18_640.txt (block 8)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: HUVEC - Untreated - mAdbID:119149

description: mAdb experiment ID: 119149

source_name: HUVEC - Untreated

value: umbilical vein

value: Human Umbilical Vein Endothelial Cells (HUVEC)

value: endothelial cells


title: Multiple myeloma, TT2, relapse, 1


title: HUVEC - Resiquimod Treated - mAdbID:119151

description: mAdb experiment ID: 119151

source_name: HUVEC - Resiquimod Treated


title: Ramos - Imiquimod Treated - mAdbID:119153

description: mAdb experiment ID: 119153

source_name: Ramos - Imiquimod Treated


title: column pool 10_short arm of chromosome 5A

description:
raw data file: chip18_760.txt (block 7)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.

source_name: 3D-pool of BAC clones of chromosome 5A


title: MMPC+MSC AFTER CO-CULTURE, 11

description: Gene expression data from multiple myeloma plasma cells and mesenchymal stem cells after co-culture.

source_name: Multiple myeloma plasma cells and mesenchymal stem cells, 18 hours

growth_protocol: MMPCs and MSCs were co-cultured for 18 hours.

tag: co-culture time

value: 18 hrs


title: MMPC+MSC AFTER CO-CULTURE, 12

value: multiple myeloma plasma cells and mesenchymal stem cells


title: HMVECad - Resiquimod Treated - mAdbID:119144

description: mAdb experiment ID: 119144

source_name: HMVECad - Resiquimod Treated

value: dermis

value: Human Microvascular Endothelial Cells, adult dermis (HMVECad)


title: MMPC+MSC BEFORE CO-CULTURE, 11

description: Gene expression data from multiple myeloma plasma cells and mesenchymal stem cells before co-culture.

source_name: Multiple myeloma plasma cells and mesenchymal stem cells, time zero

value: 0 hrs


title: HUVEC - LPS Treated - mAdbID:119148

description: mAdb experiment ID: 119148

source_name: HUVEC - LPS Treated


title: MMPC+MSC AFTER CO-CULTURE, 10


title: column pool 9_short arm of chromosome 5A

description:
raw data file: chip18_640.txt (block 6)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.

value: short arm


title: HUVEC - Imiquimod Treated - mAdbID:119146

description: mAdb experiment ID: 119146

source_name: HUVEC - Imiquimod Treated

value: Imiquimod


title: MMPC+MSC BEFORE CO-CULTURE, 12


title: MMPC+MSC BEFORE CO-CULTURE, 13


title: HMVECad - poly-ICLC Treated - mAdbID:119143

description: mAdb experiment ID: 119143

source_name: HMVECad - poly-ICLC Treated

value: poly-ICLC


title: HUVEC - poly-ICLC Treated - mAdbID:119150

description: mAdb experiment ID: 119150

source_name: HUVEC - poly-ICLC Treated


title: column pool 8_short arm of chromosome 5A

description:
raw data file: chip18_640.txt (block 5)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: MMPC+MSC AFTER CO-CULTURE, 9


title: column pool 7_short arm of chromosome 5A

description:
raw data file: chip18_640.txt (block 4)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: MMPC+MSC BEFORE CO-CULTURE, 10


title: MMPC+MSC AFTER CO-CULTURE, 13


title: column pool 6_short arm of chromosome 5A

description:
raw data file: chip18_640.txt (block 2)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: MMPC+MSC BEFORE CO-CULTURE, 9


title: HUVEC - CpG ODN Treated - mAdbID:119145

description: mAdb experiment ID: 119145

source_name: HUVEC - CpG ODN Treated

value: CpG ODN


title: column pool 4_short arm of chromosome 5A

description:
raw data file: chip17_660.txt (block 5)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: HMVECad - LPS Treated - mAdbID:119141

description: mAdb experiment ID: 119141

source_name: HMVECad - LPS Treated

value: LPS


title: column pool 3_short arm of chromosome 5A

description:
raw data file: chip18_640.txt (block 1)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.

value: Chinese spring


title: column pool 2_short arm of chromosome 5A

description:
raw data file: chip17_660.txt (block 3)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: HMVECad - Imiquimod Treated - mAdbID:119140

description: mAdb experiment ID: 119140

source_name: HMVECad - Imiquimod Treated


title: plate pool 15_short arm of chromosome 5A

description:
raw data file: chip22_560.txt (block 6)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: MMPC+MSC AFTER CO-CULTURE, 8


title: column pool 1_short arm of chromosome 5A

description:
raw data file: chip17_660.txt (block 1)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: MMPC+MSC AFTER CO-CULTURE, 7


title: plate pool 14_short arm of chromosome 5A

description:
raw data file: chip22_560.txt (block 5)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: column pool 5_short arm of chromosome 5A

description:
raw data file: chip18_640.txt (block 3)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: plate pool 13_short arm of chromosome 5A

description:
raw data file: chip22_600.txt (block 4)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: HMVECad - CpG ODN Treated - mAdbID:119139

description: mAdb experiment ID: 119139

source_name: HMVECad - CpG ODN Treated


title: MMPC+MSC BEFORE CO-CULTURE, 7


title: HMVECad - Untreated - mAdbID:119142

description: mAdb experiment ID: 119142

source_name: HMVECad - Untreated

value: Untreated


title: DM122 - Untreated - mAdbID:119135

description: mAdb experiment ID: 119135

source_name: DM122 - Untreated

value: Melanoma


title: DM122 - Resiquimod Treated - mAdbID:119138

description: mAdb experiment ID: 119138

source_name: DM122 - Resiquimod Treated

value: Resiquimod


title: MMPC+MSC BEFORE CO-CULTURE, 6


title: plate pool 12_short arm of chromosome 5A

description:
raw data file: chip22_600.txt (block 3)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: DM122 - CpG ODN Treated - mAdbID:119137

description: mAdb experiment ID: 119137

source_name: DM122 - CpG ODN Treated


title: DM122 - LPS Treated - mAdbID:119134

description: mAdb experiment ID: 119134

source_name: DM122 - LPS Treated


title: plate pool 11_short arm of chromosome 5A

description:
raw data file: chip22_600.txt (block 2)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.

source_name: 3D-pool of BAC clones of chromosome 5A


title: MMPC+MSC AFTER CO-CULTURE, 4

source_name: Multiple myeloma plasma cells and mesenchymal stem cells, 18 hours


title: DM122 - Imiquimod Treated - mAdbID:119133

description: mAdb experiment ID: 119133

source_name: DM122 - Imiquimod Treated


title: MMPC+MSC AFTER CO-CULTURE, 5


title: plate pool 10_short arm of chromosome 5A

description:
raw data file: chip22_600.txt (block 1)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: MMPC+MSC BEFORE CO-CULTURE, 4

source_name: Multiple myeloma plasma cells and mesenchymal stem cells, time zero


title: MMPC+MSC BEFORE CO-CULTURE, 5


title: DM93 - Resiquimod Treated - mAdbID:119132

description: mAdb experiment ID: 119132

source_name: DM93 - Resiquimod Treated


title: MMPC+MSC BEFORE CO-CULTURE, 3


title: DM122 - poly-ICLC Treated - mAdbID:119136

description: mAdb experiment ID: 119136

source_name: DM122 - poly-ICLC Treated


title: DM93 - poly-ICLC Treated - mAdbID:119131

description: mAdb experiment ID: 119131

source_name: DM93 - poly-ICLC Treated


title: DM93 - Untreated - mAdbID:119130

description: mAdb experiment ID: 119130

source_name: DM93 - Untreated


title: MMPC+MSC AFTER CO-CULTURE, 6

description: Gene expression data from multiple myeloma plasma cells and mesenchymal stem cells after co-culture.


title: MMPC+MSC AFTER CO-CULTURE, 3


title: plate pool 9_short arm of chromosome 5A

description:
raw data file: chip21_580.txt (block 8)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: plate pool 8_short arm of chromosome 5A

description:
raw data file: chip21_580.txt (block 7)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: MMPC+MSC AFTER CO-CULTURE, 2


title: plate pool 7_short arm of chromosome 5A

description:
raw data file: chip21_580.txt (block 6)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: plate pool 6_short arm of chromosome 5A

description:
raw data file: chip21_580.txt (block 5)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: MMPC+MSC AFTER CO-CULTURE, 1


title: MMPC+MSC BEFORE CO-CULTURE, 2

description: Gene expression data from multiple myeloma plasma cells and mesenchymal stem cells before co-culture.


title: plate pool 4_short arm of chromosome 5A

description:
raw data file: chip21_580.txt (block 3)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: plate pool 5_short arm of chromosome 5A

description:
raw data file: chip21_580.txt (block 4)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: plate pool 3_short arm of chromosome 5A

description:
raw data file: chip21_580.txt (block 2)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: plate pool 2_short arm of chromosome 5A

description:
raw data file: chip21_580.txt (block 1)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: plate pool 1_short arm of chromosome 5A

description:
raw data file: chip20_600.txt (block 8)
The DNAs derive from BAC clones of the Minimal Tiling Paths produced by physical assemly of BAC fingerprints.


title: DM13 - poly-ICLC Treated - mAdbID:119126

description: mAdb experiment ID: 119126

source_name: DM13 - poly-ICLC Treated


title: DM13 - Untreated - mAdbID:119124

description: mAdb experiment ID: 119124

source_name: DM13 - Untreated


title: DM93 - LPS Treated - mAdbID:119129

description: mAdb experiment ID: 119129

source_name: DM93 - LPS Treated


title: DM13 - Resiquimod Treated - mAdbID:119127

description: mAdb experiment ID: 119127

source_name: DM13 - Resiquimod Treated


title: OC8 BEFORE co-culture MMPC

description:
OC8B
Gene expression data from osteoclasts.

source_name: Osteoclasts, alone

growth_protocol: Osteoclasts were cultured with or without MMPCs for 96 hours.

value: osteoclasts

tag: co-culture

tag: patient identifier


title: MMPC+MSC BEFORE CO-CULTURE, 1


title: VMM1 - Untreated - repeat 2 - mAdbID:119125

description: mAdb experiment ID: 119125

source_name: VMM1 - Untreated


title: MMPC+MSC BEFORE CO-CULTURE, 8


title: DM13 - CpG ODN Treated - mAdbID:119121

description: mAdb experiment ID: 119121

source_name: DM13 - CpG ODN Treated


title: DM13 - Imiquimod Treated - mAdbID:119122

description: mAdb experiment ID: 119122

source_name: DM13 - Imiquimod Treated


title: OC5 AFTER co-culture MMPC

description:
OC5A
Gene expression data from osteoclasts after co-culture with multiple myeloma plasma cells.

source_name: Osteoclasts, 96 hours with multiple myeloma plasma cells

value: multiple myeloma plasma cells


title: OC5 BEFORE co-culture MMPC

description:
OC5B
Gene expression data from osteoclasts.


title: OC7 AFTER co-culture MMPC

description:
OC7A
Gene expression data from osteoclasts after co-culture with multiple myeloma plasma cells.


title: BM Dnmt2

city: Mannheim

first: Francesca

last: Tuorto

address: Ludolf-Krehl-Str. 13-17

department: Division of Biochemistry  Mannheim Institute for Innate Immunoscience (MI3)

country: Germany

institute: Deutsches Krebsforschungszentrum

description: replicate 1

hyb_protocol: Hybridization is performed at 58°C, in GEX-HCB buffer (Illumina Inc.) at a concentration of 100 ng cRNA/µl, unsealed in a wet chamber for 20h. Spike-in controls for low, medium and highly abundant RNAs were added, as well as mismatch control and biotinylation control oligonucleotides. Microarrays were washed once in High Temp Wash buffer (Illumina Inc.) at 55°C and then twice in E1BC buffer (Illumina Inc.) at room temperature for 5 minutes (in between washed with ethanol at room temperature). After blocking for 5 min in 4 ml of 1% (wt/vol) Blocker Casein in phosphate buffered saline Hammarsten grade (Pierce Biotechnology, Inc., Rockford, IL), array signals are developed by a 10-min incubation in 2 ml of 1 µg/ml Cy3-streptavidin (Amersham Biosciences, Buckinghamshire, UK) solution and 1% blocking solution. After a final wash in E1BC, the arrays are dried and scanned.

scan_protocol: Microarray scanning was done using an iScan array scanner.

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

organism: Mus musculus

source_name: BM Dnmt2-/-

label_protocol: cRNA samples were prepared according to Illumina's recommended sample labeling procedure based on the modified Eberwine protocol (Eberwine et al., 1992). In brief, 200 ng total RNA was used for complementary DNA (cDNA) synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA according to the Illumina® Total Prep™ RNA Amplification Kit (Life Technologies). Biotin-16-UTP was purchased from Roche Applied Science, Penzberg, Germany. The cRNA was column purified according to TotalPrep RNA Amplification Kit, and eluted in 70 µl of water. Quality of cRNA was controlled using the RNA Nano Chip Assay on an Agilent 2100 Bioanalyzer and spectrophotometrically quantified (NanoDrop).

extract_protocol: RNA was extracted with Trizol reagent, Quality control was performed with Agilent Bioanalyser.

tag: genotype

value: 8 days

tag: tissue type

value: bone marrow


title: DM13 - LPS Treated - mAdbID:119123

description: mAdb experiment ID: 119123

source_name: DM13 - LPS Treated


title: OC6 BEFORE co-culture MMPC

description:
OC6B
Gene expression data from osteoclasts.


title: OC4 AFTER co-culture MMPC

description:
OC4A
Gene expression data from osteoclasts after co-culture with multiple myeloma plasma cells.


title: BM wt

description: replicate 1

source_name: BM wildtype

value: Wildtype


title: OC7 BEFORE co-culture MMPC

description:
OC7B
Gene expression data from osteoclasts.


title: OC6 AFTER co-culture MMPC

description:
OC6A
Gene expression data from osteoclasts after co-culture with multiple myeloma plasma cells.


title: OC4 BEFORE co-culture MMPC

description:
OC4B
Gene expression data from osteoclasts.


title: mouse glioma [12-05-11-5(30.1)]

description: Gene expression data from mouse brain

source_name: brain

growth_protocol: Mice injected at birth with DNA plasmids as described above developed spontaneous gliomas, which were harvested at day 50-60 post injection

extract_protocol: RNA was extracted usign RNEasy Qiagen kit according to manufacturer's instructions

treatment_protocol: Initial DNA plasmid injection was the only treatment administered to mice

tag: strain

value: Balb/c

value: glioma


title: Aged matched control [12-05-11-7(B6 Control)]

description: Gene expression data from mouse brain

value: control


title: Aged matched control [12-05-11-6(BalbC Control)]

description: Gene expression data from mouse brain


title: DM93 - Imiquimod Treated - mAdbID:119128

description: mAdb experiment ID: 119128

source_name: DM93 - Imiquimod Treated


title: CD4 T HDM-treated, biological replicate 3

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

description: CD4T from hdm-treated lung

hyb_protocol: Standard Affymetrix protocol. cDNA was hybrised on Affymetrix GeneChip Mouse Gene 2.0 ST Arrays.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using Bioconductor. Normalisation was done by RMA.

label_protocol: Affymetrix WT Terminal Labeling Kit

growth_protocol: Lung was minced and digested with Liberase TM (0.02mg/ml; Roche) and Dnase I recombinant (0.01 U/µl; Roche) for 30 min at 37°C in HBSS followed by lysis of red blood cells. Whole lung cells were stained for CD45, CD4, CD11b, F4/80 and purified using a FACSAriaIII. CD4+CD45+CD11b-F4/80- cells were gated on and collected in 100% FCS. Cells were spun down into centrifuge tubes.

extract_protocol: Standard Trizol extraction was performed.

treatment_protocol: Not applicable

value: Lung

value: WT

value: house dust mites


title: OC3 BEFORE co-culture MMPC

description:
OC3B
Gene expression data from osteoclasts.


title: mouse glioma [12-05-11-4(30.2)]

description: Gene expression data from mouse brain


title: CD4 T HDM-treated, biological replicate 2

description: CD4T from hdm-treated lung


title: OC8 AFTER co-culture MMPC

description:
OC8A
Gene expression data from osteoclasts after co-culture with multiple myeloma plasma cells.


title: mouse glioma [12-05-11-8(B6 Tumor)]

description: Gene expression data from mouse brain


title: mouse glioma [12-05-11-3(29.9)]

description: Gene expression data from mouse brain


title: CD4 T control, biological replicate 3

description: CD4T from pbs-treated lung

value: PBS


title: CD4 T HDM-treated, biological replicate 1

description: CD4T from hdm-treated lung


title: mouse glioma [12-05-11-2(29.5)]

description: Gene expression data from mouse brain


title: OC1 AFTER co-culture MMPC

description:
OC1A
Gene expression data from osteoclasts after co-culture with multiple myeloma plasma cells.


title: CD4 T control, biological replicate 1

description: CD4T from pbs-treated lung


title: K8 PIK3CA H1047R Lum Sca1 neg GFP pos rep3

status: Public on Aug 12 2015

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

institute: FMI

description: Luminal CD24high Sca1 negative H1047R-expressing subset from K8-creERT2/PIK3CA H1047R mice

hyb_protocol: Affymetrix Gene Chip Mouse gene 1.0 ST microarrays were hybridized according to the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16 hours.

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control Software v. 3.0.0.1214 on a GeneChip Scanner 3000 7 G with autoloader.

data_processing: Arrays were normalized and probeset-level expression values were calculated with R/Bioconductor's (v3.0.1) 'affy' package using the rma() function.

source_name: K8-creERT2/PIK3CA H1047R

label_protocol: Total RNA from 2000 sorted cells was used as the input for synthesis of amplified cDNA with the NuGen Ovation Pico WTA System (NuGen Inc.) The resulting double-stranded cDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix).

growth_protocol: primary cells from mixed background FVB/CD-1 mice

extract_protocol: Arcturus PicoPure RNA isolation kit (Life technologies)

treatment_protocol: Mammary subsets were sorted using CD45, CD24 and Sca1 (CD45 negative, CD24low Sca1 negative= basal subset; CD45 negative CD24high Sca1 negative/positive=luminal subsets). Subsets were gated on GFP-negative cells in K8-creERT2 control mice and GFP-positive (=PIK3CA H1047R expressing) and GFP-negative (=non-PIK3CA H1047R expressing) epithelium in K8-creERT2/PIK3CA H1047R mutants (indicated in sample name). Sorting was performed into the extraction buffer of the Arcturus PicoPure RNA Isolation kit.

value: mixed background FVB/CD-1

tag: genotype/variation (animal)

value: K8-creERT2/PIK3CA H1047R

value: activation of PIK3CA H1047R transgene expression by Tamoxifen injection

tag: time

value: 4 wks post-Tamoxifen

tag: cell type (mammary cell subpopulation)

value: luminal CD24high Sca1 negative H1047R-expressing subset


title: mouse glioma [12-05-11-1(29.1)]

description: Gene expression data from mouse brain


title: K8 PIK3CA H1047R Lum Sca1 pos GFP pos rep1

description: Luminal CD24high Sca1 positive H1047R-expressing subset from K8-creERT2/PIK3CA H1047R mice

value: luminal CD24high Sca1 positive H1047R-expressing subset


title: OC2 BEFORE co-culture MMPC

description:
OC2B
Gene expression data from osteoclasts.

value: osteoclasts


title: OC3 AFTER co-culture MMPC

description:
OC3A
Gene expression data from osteoclasts after co-culture with multiple myeloma plasma cells.

value: multiple myeloma plasma cells


title: OC1 BEFORE co-culture MMPC

description:
OC1B
Gene expression data from osteoclasts.


title: OC2 AFTER co-culture MMPC

description:
OC2A
Gene expression data from osteoclasts after co-culture with multiple myeloma plasma cells.


title: CD4 T control, biological replicate 2

description: CD4T from pbs-treated lung

tag: tissue


title: K8 PIK3CA H1047R Lum Sca1 neg GFP pos rep1


title: K8 PIK3CA H1047R Lum Sca1 pos GFP pos rep3


title: K8 PIK3CA H1047R basal GFP pos rep3

description: basal H1047R-expressing subset from K8-creERT2/PIK3CA H1047R animals

value: basal H1047R-expressing subset


title: K8 PIK3CA H1047R basal GFP neg rep3

description: basal subset without PIK3CA H1047R-expressing cells from K8-creERT2/PIK3CA H1047R animals


title: K8 PIK3CA H1047R basal GFP pos rep1


title: K8 PIK3CA H1047R Lum Sca1 neg GFP pos rep2


title: K8 PIK3CA H1047R basal GFP pos rep2


title: K8 PIK3CA H1047R basal GFP neg rep1

value: basal subset without PIK3CA H1047R-expressing cells


title: K8 ctrl Lum Sca1 pos GFP neg rep2

description: control Luminal CD24high Sca1 positive subset

source_name: K8-creERT2 control

value: K8-creERT2 control

value: luminal CD24high Sca1 positive subset, control


title: K8 ctrl Lum Sca1neg GFP neg rep3

description: control Luminal CD24high Sca1 negative subset

value: luminal CD24high Sca1 negative subset, control


title: K8 PIK3CA H1047R basal GFP neg rep2


title: K8 ctrl Lum Sca1 pos GFP neg rep1


title: Lgr5-creERT2 ctrl mammary glands rep3

description:
reference mammary glands from Lgr5-creERT2 control mice
270E23_gbentire

source_name: mammary gland

label_protocol: Total RNA from 100 ng tumor tissue was used as the input for synthesis of amplified cDNA with the NuGen Ovation Pico WTA System (NuGen Inc.) The resulting double-stranded cDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix).

growth_protocol: tumor cells from Lgr5-creERT2/PIK3CA H1047R (mixed background FVB/C57/BL6) and K8-creERT2/PIK3CA H1047R (mixed background FVB/CD1) animals

extract_protocol: Trizol method

treatment_protocol: Adult (7-8 week old) mice were injected with Tamoxifen to induce PIK3CA H1047R expression. After tumor development, tumors were collected and cryo-homogenized.

value: mixed background FVB/C57/BL6

tag: genotype/variation

value: Lgr5-creERT2 ctrl

value: mammary gland


title: K8-creERT2 ctrl mammary glands rep2

description:
reference mammary glands from K8-creERT2 control mice
270E25_gbentire

value: mixed background FVB/CD1

value: K8-creERT2 ctrl


title: Lgr5-creERT2/PIK3CA H1047R tumor 1

description:
mammary tumor evoked by expression of PIK3CA H1047R in Lgr5-positive mammary cells
270E19_gbentire

source_name: mammary tumor

value: Lgr5-creERT2/PIK3CA H1047R

value: mammary tumor


title: K8 ctrl basal GFP neg rep1

description: control basal CD24low Sca1 negative subset

value: mixed background FVB/CD-1

value: activation of PIK3CA H1047R transgene expression by Tamoxifen injection

value: 4 wks post-Tamoxifen

value: basal CD24low Sca1 negative subset, control


title: K8-creERT2 ctrl mammary glands rep1

description:
reference mammary glands from K8-creERT2 control mice
270E24_gbentire


title: Lgr5-creERT2/PIK3CA H1047R tumor 8

description:
mammary tumor evoked by expression of PIK3CA H1047R in Lgr5-positive mammary cells
270E15_gbentire


title: K8 ctrl Lum Sca1neg GFP neg rep2


title: pSK 12h, biological rep3

city: Nanjing

first: libin

last: wen

address: zhongling street 50

country: China

institute: Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences

description: Gene expression data from PK15 cells transfected with pSK vetor.

hyb_protocol: Total mRNA was hybridized on  Affymetrix Porcine Gene 1.1 ST array strips.  Affymetrix hybridization, wash, and stain Kit for WT Array Strips were used.

scan_protocol: Quantification of transcript expression on a GeneAtlas imaging station (Affymetrix).

data_processing: Performance quality tests of the arrays including the labelling, hybridization, scanning and background signals by a Robust Multichip Analysis were performed on the CEL files using Affymetrix Expression ConsoleTM

organism: Sus scrofa

source_name: PK15 cell,pSK, 12h

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

growth_protocol: PK15 cells were grown in RPMI 1640 medium at 37℃ in an atmosphere of 5% CO2.

treatment_protocol: PK15  cells were harvested at 12h post-transfection for RNA extraction.

tag: cells

tag: transfection virus

value: pSK


title: Lgr5-creERT2 ctrl mammary glands rep1

description:
reference mammary glands from Lgr5-creERT2 control mice
270E21_gbentire


title: Lgr5-creERT2/PIK3CA H1047R tumor 10

description:
mammary tumor evoked by expression of PIK3CA H1047R in Lgr5-positive mammary cells
270E20_gbentire


title: Lgr5-creERT2/PIK3CA H1047R tumor 9

description:
mammary tumor evoked by expression of PIK3CA H1047R in Lgr5-positive mammary cells
270E17_gbentire


title: Lgr5-creERT2/PIK3CA H1047R tumor 5

description:
mammary tumor evoked by expression of PIK3CA H1047R in Lgr5-positive mammary cells
270E13_gbentire


title: Lgr5-creERT2/PIK3CA H1047R tumor 4

description:
mammary tumor evoked by expression of PIK3CA H1047R in Lgr5-positive mammary cells
270E12_gbentire


title: K8 ctrl basal GFP neg rep2

tag: treatment


title: Lgr5-creERT2 ctrl mammary glands rep2

description:
reference mammary glands from Lgr5-creERT2 control mice
270E22_gbentire


title: K8 ctrl Lum Sca1neg GFP neg rep1


title: Lgr5-creERT2/PIK3CA H1047R tumor 2

description:
mammary tumor evoked by expression of PIK3CA H1047R in Lgr5-positive mammary cells
270E18_gbentire


title: pSK 12h, biological rep2


title: Lgr5-creERT2/PIK3CA H1047R tumor 7

description:
mammary tumor evoked by expression of PIK3CA H1047R in Lgr5-positive mammary cells
270E16_gbentire


title: Mock cell 12h, biological rep2

description: Gene expression data from PK15 cells.

source_name: PK15 cell, 12h

value: mock


title: Lgr5-creERT2/PIK3CA H1047R tumor 6

description:
mammary tumor evoked by expression of PIK3CA H1047R in Lgr5-positive mammary cells
270E14_gbentire


title: pSK 12h, biological rep1


title: Mock cell 12h, biological rep1

description: Gene expression data from PK15 cells .


title: HCT116 H2B-GFP chr 8/3 clone 3

city: Utrecht

first: Wigard

last: Kloosterman

address: Universiteitsweg 100

country: Netherlands

institute: University Medical Center Utrecht

description: Genomic DNA extracted from sample was genotyped using Illumina Infinium CytoSNP-850K beadchips

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

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

data_processing: Data processing was done using GenomeStudio (Illumina)

label: Biotin (C, G), DNP (A,T)

source_name: DNA from cultured cells

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (MSM) and primer/neutralization mix (MA1-MA2-0.1N NaOH). After incubation the amplified DNA was fragmented with fragmentation mix (FMS), precipitated with isopropanol and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction.

tag: cell line

tag: cell type

value: Human colon cancer cells

tag: transferred chromosome

tag: ploidy

value: diploid


title: VL264d 12h, biological rep2

description: Gene expression data from PK15 cells transfected with the cloned VL264d plasmid DNA

source_name: PK15 cell,VL264d, 12h


title: VL264s 12h, biological rep3

description: Gene expression data from PK15 cells transfected with the cloned VL264s plasmid DNA

source_name: PK15 cell,VL264s, 12h


title: VL264s 12h, biological rep2


title: K8-creERT2/PIK3CA H1047R tumor 6

description:
mammary tumor evoked by expression of PIK3CA H1047R in K8-positive mammary cells
270E9_gbentire

value: K8-creERT2/PIK3CA H1047R


title: K8-creERT2/PIK3CA H1047R tumor 3

description:
mammary tumor evoked by expression of PIK3CA H1047R in K8-positive mammary cells
270E8_gbentire


title: K8-creERT2/PIK3CA H1047R tumor 10

description:
mammary tumor evoked by expression of PIK3CA H1047R in K8-positive mammary cells
270E6_gbentire


title: Lgr5-creERT2/PIK3CA H1047R tumor 3

description:
mammary tumor evoked by expression of PIK3CA H1047R in Lgr5-positive mammary cells
270E11_gbentire


title: K8-creERT2/PIK3CA H1047R tumor 2

description:
mammary tumor evoked by expression of PIK3CA H1047R in K8-positive mammary cells
270E7_gbentire


title: K8-creERT2/PIK3CA H1047R tumor 7

description:
mammary tumor evoked by expression of PIK3CA H1047R in K8-positive mammary cells
270E1_gbentire


title: VL258d 12h, biological rep1

description: Gene expression data from PK15 cells transfected with the cloned VL258d plasmid DNA

source_name: PK15 cell,VL258d, 12h


title: VL258d 12h, biological rep2

source_name: PK15 cell,VL258d,12h


title: K8-creERT2/PIK3CA H1047R tumor 5

description:
mammary tumor evoked by expression of PIK3CA H1047R in K8-positive mammary cells
270E10_gbentire


title: VL258d 12h, biological rep3


title: VL264d 12h, biological rep3


title: K8-creERT2/PIK3CA H1047R tumor 4

description:
mammary tumor evoked by expression of PIK3CA H1047R in K8-positive mammary cells
270E5_gbentire


title: VL258s 12h, biological rep3

description: Gene expression data from PK15 cells transfected with the cloned VL258s plasmid DNA

source_name: PK15 cell,VL258s, 12h


title: Lgr5 PIK3CA H1047R Lum Sca1 pos GFP pos rep3

description:
Luminal CD24high Sca1 positive  H1047R-expressing subset from Lgr5 PIK3CA H1047R mice
mb20131101mg10_24

source_name: Lgr5-creERT2/PIK3CA H1047R

label_protocol: Total RNA from 250 sorted cells was used as the input for synthesis of amplified cDNA with the NuGen Ovation Pico WTA System (NuGen Inc.) The resulting double-stranded cDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix).

growth_protocol: primary cells from mixed background FVB/C57BL6 mice

treatment_protocol: Mammary subsets were sorted using CD45, CD24 and Sca1 (CD45 negative, CD24low Sca1 negative= basal subset; CD45 negative CD24high Sca1 negative/positive=luminal subsets). Subsets were gated on GFP-positive (=Lgr5- and/or PIK3CA H1047R expressing) and -negative epithelium. Sorting was performed into the extraction buffer of the Arcturus PicoPure RNA Isolation kit.

value: mixed background FVB/C57BL6

tag: animal

value: Lgr5-creERT2/PIK3CA H1047R mice

value: 4 wks post Tamoxifen

value: preneoplastic mammary gland

value: luminal subset CD24high Sca1 positive H1047R-expressing


title: VL264s 12h, biological rep1

description: Gene expression data from PK15 cells transfected with the cloned VL264s plasmid DNA.


title: K8-creERT2/PIK3CA H1047R tumor 1

description:
mammary tumor evoked by expression of PIK3CA H1047R in K8-positive mammary cells
270E4_gbentire

value: mixed background FVB/CD1


title: HCT116 H2B-GFP chr 8/3 clone 4


title: K8-creERT2/PIK3CA H1047R tumor 9

description:
mammary tumor evoked by expression of PIK3CA H1047R in K8-positive mammary cells
270E2_gbentire


title: VL258s 12h, biological rep2


title: VL264d 12h, biological rep1


title: HCT116 H2B-GFP chr 8/3 clone 1

description: Genomic DNA extracted from sample was genotyped using Illumina Infinium CytoSNP-850K beadchips


title: K8 ctrl basal GFP neg rep3

description: control basal CD24low Sca1 negative subset

value: K8-creERT2 control


title: VL258s 12h, biological rep1

description: Gene expression data from PK15 cells transfected with the cloned VL258s plasmid DNA.


title: K8-creERT2/PIK3CA H1047R tumor 8

description:
mammary tumor evoked by expression of PIK3CA H1047R in K8-positive mammary cells
270E3_gbentire

value: mammary tumor


title: Lgr5 PIK3CA H1047R Lum Sca1 pos GFP pos rep2

description:
Luminal CD24high Sca1 positive  H1047R-expressing subset from Lgr5 PIK3CA H1047R mice
mb20131101mg10_23


title: Lgr5 PIK3CA H1047R Lum Sca1 neg GFP pos rep3

description:
Luminal CD24high Sca1 negative  H1047R-expressing subset from Lgr5 PIK3CA H1047R mice
mb20131101mg10_21

value: luminal subset CD24high Sca1 negative H1047R-expressing


title: Lgr5 PIK3CA H1047R Lum Sca1 pos GFP pos rep1

description:
Luminal CD24high Sca1 positive  H1047R-expressing subset from Lgr5 PIK3CA H1047R mice
mb20131101mg10_22


title: PCV2 12h, biological rep3

description: Gene expression data from PK15 cells transfected with the cloned PCV2 plasmid DNA.

source_name: PK15 cell,PCV2, 12h


title: Mock cell 12h, biological rep3

description: Gene expression data from PK15 cells.


title: ZJ-R 12h, biological rep1

description: Gene expression data from PK15 cells transfected with the cloned ZJ-R plasmid DNA.

source_name: PK15 cell,ZJ-R ,12h

value: ZJ-R


title: P2 12h, biological rep3

description: Gene expression data from PK15 cells transfected with the cloned P2 plasmid DNA.

source_name: PK15 cell,P2, 12h


title: Lgr5 PIK3CA H1047R Lum Sca1 neg GFP pos rep2

description:
Luminal CD24high Sca1 negative  H1047R-expressing subset from Lgr5 PIK3CA H1047R mice
mb20131101mg10_20


title: ZJ-R 12h, biological rep3

source_name: PK15 cell,ZJ-R, 12h


title: P2 12h, biological rep2


title: HCT116 H2B-GFP chr 8/3 clone 2


title: P2 12h, biological rep1

source_name: PK15 cell, P2,12h


title: Lgr5 PIK3CA H1047R basal GFP pos rep3

description:
basal H1047R-expressing subset from Lgr5 PIK3CA H1047R animals
mb20131101mg10_18

value: basal subset H1047R-expressing


title: Lgr5 PIK3CA H1047R Lum Sca1 neg GFP pos rep1

description:
Luminal CD24high Sca1 negative  H1047R-expressing subset from Lgr5 PIK3CA H1047R mice
mb20131101mg10_19


title: ZJ-R 12h, biological rep2


title: PCV2 12h, biological rep1


title: Lgr5 PIK3CA H1047R basal GFP neg rep3

description:
basal subset without Lgr5 and H1047R-expression from Lgr5 PIK3CA H1047R animals
mb20131101mg10_15


title: PCV2 12h, biological rep2


title: Lgr5 PIK3CA H1047R basal GFP pos rep1

description:
basal H1047R-expressing subset from Lgr5 PIK3CA H1047R animals
mb20131101mg10_16


title: P1 12h, biological rep3

description: Gene expression data from PK15 cells transfected with the cloned P1 plasmid DNA.

source_name: PK15 cell, P1, 12h


title: P1 12h, biological rep2


title: Lgr5 ctrl Lum Sca1 pos GFP neg rep3

description:
control Luminal CD24high Sca1 positive subset
mb20131101mg10_12

source_name: Lgr5-creERT2 control

value: Lgr5-creERT2 control mice

value: luminal subset CD24high Sca1 positive


title: P1 12h, biological rep1


title: Lgr5 PIK3CA H1047R basal GFP pos rep2

description:
basal H1047R-expressing subset from Lgr5 PIK3CA H1047R animals
mb20131101mg10_17


title: Lgr5 PIK3CA H1047R basal GFP neg rep2

description:
basal subset without Lgr5 and H1047R-expression from Lgr5 PIK3CA H1047R animals
mb20131101mg10_14


title: K8 ctrl Lum Sca1 pos GFP neg rep3

description: control Luminal CD24high Sca1 positive subset

source_name: K8-creERT2 control

value: mixed background FVB/CD-1

value: activation of PIK3CA H1047R transgene expression by Tamoxifen injection

value: 4 wks post-Tamoxifen

value: luminal CD24high Sca1 positive subset, control


title: Lgr5 ctrl Lum Sca1 pos GFP neg rep2

description:
control Luminal CD24high Sca1 positive subset
mb20131101mg10_11

value: mixed background FVB/C57BL6


title: P1 ORF5 12h, biological rep3

description: Gene expression data from PK15 cells transfected with P1 ORF5.

source_name: PK15 cell, P1 ORF5, 12h

value: P1 ORF5


title: P1 ORF5 12h, biological rep2


title: Lgr5 ctrl Lum Sca1neg GFP neg rep3

description:
control Luminal CD24high Sca1 negative subset
mb20131101mg10_09

value: 4 wks post Tamoxifen

value: luminal subset CD24high Sca1 negative


title: Lgr5 ctrl Lum Sca1 pos GFP neg rep1

description:
control Luminal CD24high Sca1 positive subset
mb20131101mg10_10

value: preneoplastic mammary gland


title: P1 ORF5 12h, biological rep1


title: P1 ORF3 12h, biological rep3

description: Gene expression data from PK15 cells transfected with P1 ORF3.

source_name: PK15 cell, P1 ORF3, 12h

value: P1 ORF3


title: Lgr5 PIK3CA H1047R basal GFP neg rep1

description:
basal subset without Lgr5 and H1047R-expression from Lgr5 PIK3CA H1047R animals
mb20131101mg10_13

value: Lgr5-creERT2/PIK3CA H1047R mice


title: Lgr5 ctrl Lum Sca1neg GFP neg rep1

description:
control Luminal CD24high Sca1 negative subset
mb20131101mg10_07


title: P1 ΔORF8 12h, biological rep2

description: Gene expression data from PK15 cells transfected with P1 ΔORF8.

source_name: PK15 cell, P1 ΔORF8, 12h

value: P1 ΔORF8


title: P1 ΔORF7 12h, biological rep3

description: Gene expression data from PK15 cells transfected with P1 ΔORF7.

source_name: PK15 cell, P1 ΔORF7, 12h

value: P1 ΔORF7


title: Lgr5 ctrl basal GFP neg rep3

description:
control basal subset without Lgr5-expressing cells
mb20131101mg10_03

value: basal subset without Lgr5-expression


title: Lgr5 ctrl basal GFP pos rep2

description:
control basal Lgr5-expressing subset
mb20131101mg10_05

value: basal subset Lgr5-expressing


title: Lgr5 ctrl basal GFP pos rep3

description:
control basal Lgr5-expressing subset
mb20131101mg10_06

value: Lgr5-creERT2 control mice


title: P1 ΔORF8 12h, biological rep3


title: P1 ΔORF6 12h, biological rep3

description: Gene expression data from PK15 cells transfected with P1 ΔORF6.

source_name: PK15 cell, P1 ΔORF6,12h

value: P1 ΔORF6


title: P1 ΔORF7 12h, biological rep1


title: P1 ORF3 12h, biological rep1


title: Lgr5 ctrl basal GFP neg rep2

description:
control basal subset without Lgr5-expressing cells
mb20131101mg10_02


title: P1 ORF3 12h, biological rep2


title: K_1/64_5d_shoot_rep3

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 rice shoot at 5 days after potassium deficiency treatment (1/64 concentration)

hyb_protocol: 1,650 ng Cy3-labeled cRNA was fragmented and hybridized on a slide of rice 4x44K microarray RAP-DB (Agilent; G2519F#15241) at 65℃ for 17 hours. Hybridization and washing of the hybridized slide were performed according to the manufacture’s instruction.

scan_protocol: Slides were scanned on an Agilent G2505C DNA microarray scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities. The processed signal intensities were used for 75th percentile normalization and log2 transformation with R

organism: Oryza sativa Japonica Group

label_protocol: One-color spike-mix was added to the total RNA prior to the labeling reaction and labeling was performed using a Quick Amp Labeling Kit, One-Color (Agilent Technologies) in the presence of cyanine-3 (Cy3)-CTP according to the modified manufacturer’s protocol. The cyanine-3-labeled cRNA was purified by RNeasy Mini Kit (Qiagen) and the cRNA yield was determined using the NanoDrop ND-1000 UV-VIS spectrophotomer (NanoDrop).

growth_protocol: Rice seeds were sterilized with 70% (v/v) ethanol solution and 1% (v/v) sodium hypochlorite solution, imbibed in distilled water in the dark at 28°C for 2 days, and transferred onto a nylon net floated in distilled water in a growth chamber (60% humidity; 14.5 h light period at 28°C and 9.5 h dark period at 23°C). After 3 days of germination, the seedlings were transferred in Yoshida nutrient solution (5-fold dilution, pH 5.5) and allowed to grow for another 4 days. The pH of the nutrient solution was adjusted using 1N NaOH and maintained using MES (buffer). The solution was renewed every 2 days.

extract_protocol: Total RNA was extracted from the each sample with a RNeasy Plant Mini kit (QIAGEN) according to the manufacturer’s protocol. The quantity and quality of the obtained RNAs were checked with Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: The 7-day old seedlings were exposed to N, P, and K deficiency treatments (1/4, 1/16 and 1/64 of normal concentration) and control conditions, respectively. Shoot samples were collected at 5 days after nutrient starvation. To exclude potential effects of osmotic pressure, NaCl and Na2SO4 were added into the low P and K treatment solutions, respectively, and the osmotic level was adjusted to the same level as the control.

tag: cultivar

value: Nipponbare

tag: organ

value: Shoot

tag: nutrient

value: Potassium

value: Deficiency (1/64)


title: Lgr5 ctrl basal GFP pos rep1

description:
control basal Lgr5-expressing subset
mb20131101mg10_04

tag: strain

value: mixed background FVB/C57BL6


title: Lgr5 ctrl Lum Sca1neg GFP neg rep2

description:
control Luminal CD24high Sca1 negative subset
mb20131101mg10_08


title: K_1/16_5d_shoot_rep2

description: Gene expression of rice shoot at 5 days after potassium deficiency treatment (1/16 concentration)

value: Deficiency (1/16)


title: P1 ΔORF7 12h, biological rep2


title: P1 ΔORF8 12h, biological rep1


title: K_1/16_5d_shoot_rep3


title: K_1/64_5d_shoot_rep2


title: K_1/16_5d_shoot_rep1


title: K_1/64_5d_shoot_rep1


title: P1 ΔORF5 12h, biological rep3

description: Gene expression data from PK15 cells transfected with P1 ΔORF5.

source_name: PK15 cell, P1 ΔORF5,12h

value: P1 ΔORF5


title: P1 ΔORF6 12h, biological rep2

source_name: PK15 cell, P1 ΔORF6, 12h


title: P1 ΔORF5 12h, biological rep2

source_name: PK15 cell, P1 ΔORF5, 12h


title: P1 ΔORF5 12h, biological rep1


title: K_1/4_5d_shoot_rep2

description: Gene expression of rice shoot at 5 days after potassium deficiency treatment (1/4 concentration)

value: Deficiency (1/4)


title: K_1/4_5d_shoot_rep1


title: P1 ΔORF6 12h, biological rep1


title: P1 ΔORF4 12h, biological rep3

description: Gene expression data from PK15 cells transfected with P1 ΔORF4.

source_name: PK15 cell, P1 ΔORF4, 12h

value: P1 ΔORF4


title: P1 ΔORF3 12h, biological rep3

description: Gene expression data from PK15 cells transfected with P1 ΔORF3.

source_name: PK15 cell, P1 ΔORF3, 12h

value: P1 ΔORF3


title: P1 ΔORF4 12h, biological rep1


title: P1 ΔORF3 12h, biological rep2


title: P_1/64_5d_shoot_rep1

description: Gene expression of rice shoot at 5 days after phosphorus deficiency treatment (1/64 concentration)

value: Phosphorus


title: WT BMDC LPS treated, biological rep 3

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

hyb_protocol: Biotinylated fragmented ssDNA was hybridized onto the GeneChip® Mouse Gene 2.0 ST Array (Affymetrix) according to the manufacturer's recommendation. The hybridization was performed for 16 h at 45°C in the GeneChip® Hybridization Oven 640 (Affymetrix). Washing and staining of the arrays were done on the Gene Chip® Fluidics Station 450 (Affymetrix) according to the manufacturer's recommendation

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix)

data_processing: Data were quantile normalized and log2 transformed using R and Bioconductor package limma.

source_name: Wildtype BMDC_LPS treated

label_protocol: For each experimental sample, RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100. 0.3 µg of total RNA was used as start Material. The labeling reaction was performed by using the GeneChip® WT PLUS Reagent Kit from Affymetrix (Cat N° 902281) following manufacturer´s instructions.

growth_protocol: We obtained bone marrow from 8 weeks old mice. Cells were homogenized through a 40 µm cell strainer (BD Biosciences) and incubated in red blood cell lysis buffer (0.15 M NH4Cl, 10 mM KHCO3, 0.1 mM Na2EDTA in ddH2O at pH 7.4) for 5 min. We cultured remaining cells in 100 ml cell culture flasks (Sarstedt) in mouse complete medium (10% FCS, 50 μM 2-mercaptoethanol, 100 U/ml penicillin/streptomycin in RPMI1640) containing 20 ng/ml GM-CSF (PeproTech). We changed medium every other day by carefully replacing the supernatant with fresh medium containing 20 ng/ml GM-CSF. We harvested semi adherent BMDCs on day seven.

extract_protocol: Cell samples were homogenized in Trizol buffer and mRNA was isolated in a single-step acid guanidinium thiocyanate-phenol-chloroform extraction following manufacturer´s instructions (http://tools.invitrogen.com/content/sfs/manuals/trizol_reagent.pdf). RNA-precipitation was done with Ethanol. RNA was diluted in nuclease-free water and concentrations were determined using a Nanodrop spectrophotometer.

treatment_protocol: We incubated 1.5 Mio. BMDCs from wildtype and Arc/Arg3.1–/– mice for 30 min with medium or LPS (100 ng/ml), washed three times with medium and incubated cells again in medium for 1 h before pelleting.

tag: strain background

tag: age

value: 8 weeks

tag: gender

value: male

value: Bone marrow-derived dendritic cells (BMDC)

tag: treated with

value: LPS


title: P_1/64_5d_shoot_rep3


title: P1 ΔORF3 12h, biological rep1


title: WT BMDC untreated, biological rep 2

source_name: Wildtype BMDC_untreated

tag: genotype/variation

value: none (untreated)


title: WT BMDC untreated, biological rep 3


title: KO BMDC LPS treated, biological rep 3

source_name: Arc/Arg3.1 knockout BMDC_LPS treated

value: Arc/Arg3.1 –/–


title: P1 ΔORF2 12h, biological rep3

description: Gene expression data from PK15 cells transfected with P1 ΔORF2.

source_name: PK15 cell, P1 ΔORF2, 12h

tag: cells

value: P1 ΔORF2


title: P_1/16_5d_shoot_rep3

description: Gene expression of rice shoot at 5 days after phosphorus deficiency treatment (1/16 concentration)

value: Nipponbare

value: Shoot


title: WT BMDC LPS treated, biological rep 2


title: WT BMDC untreated, biological rep 1


title: P1 ΔORF1 12h, biological rep3

description: Gene expression data from PK15 cells transfected with P1 ΔORF1.

source_name: PK15 cell, P1 ΔORF1, 12h

tag: transfection virus

value: P1 ΔORF1


title: P_1/64_5d_shoot_rep2

tag: treatment

value: Deficiency (1/64)


title: KO BMDC untreated, biological rep 3

source_name: Arc/Arg3.1 knockout BMDC_untreated


title: KO BMDC untreated, biological rep 2


title: P1 ΔORF4 12h, biological rep2


title: P1 ΔORF1 12h, biological rep2


title: P_1/4_5d_shoot_rep3

description: Gene expression of rice shoot at 5 days after phosphorus deficiency treatment (1/4 concentration)


title: WT BMDC LPS treated, biological rep 1


title: P_1/16_5d_shoot_rep2

value: Deficiency (1/16)


title: KO BMDC LPS treated, biological rep 1


title: P1 ΔORF2 12h, biological rep2


title: P_1/16_5d_shoot_rep1


title: KO BMDC LPS treated, biological rep 2


title: P_1/4_5d_shoot_rep2


title: P_1/4_5d_shoot_rep1


title: N_1/4_5d_shoot_rep3

description: Gene expression of rice shoot at 5 days after nitrogen deficiency treatment (1/4 concentration)

value: Nitrogen


title: N_1/16_5d_shoot_rep3

description: Gene expression of rice shoot at 5 days after nitrogen deficiency treatment (1/16 concentration)


title: N_1/64_5d_shoot_rep1

description: Gene expression of rice shoot at 5 days after nitrogen deficiency treatment (1/64 concentration)


title: N_1/64_5d_shoot_rep3


title: P1 ΔORF2 12h, biological rep1


title: N_1/64_5d_shoot_rep2


title: N_1/4_5d_shoot_rep2

value: Deficiency (1/4)


title: N_1/16_5d_shoot_rep1


title: Lgr5 ctrl basal GFP neg rep1

description:
control basal subset without Lgr5-expressing cells
mb20131101mg10_01

source_name: Lgr5-creERT2 control

value: mixed background FVB/C57BL6

value: Lgr5-creERT2 control mice

value: 4 wks post Tamoxifen

tag: tissue

value: preneoplastic mammary gland

tag: cell type (mammary cell subpopulation)

value: basal subset without Lgr5-expression


title: K_1/4_5d_shoot_rep3

value: Potassium


title: N_1/4_5d_shoot_rep1


title: KO BMDC untreated, biological rep 1

value: 8 weeks

value: male

tag: cell type

value: Bone marrow-derived dendritic cells (BMDC)


title: P1 ΔORF1 12h, biological rep1


title: N_1/16_5d_shoot_rep2


title: mouse fibroblasts

city: Kyoto

first: Kenta

last: Yamamoto

address: Kajicho 465

department: Immunology

institute: Kyoto Prefectural University of Medicine

description: cultivation cell

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 100μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0007

data_processing:
Data were processed using Expression Console software. Gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: MoGene-1_0-st-v1.r3.pgf
meta-probeset file:MoGene-1_0-st-v1.r3.pgf

source_name: cultivation cell

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Each cells were cultured at 37℃ in a humid atmosphere with 5% CO2.

extract_protocol: Total RNA were extracted using ISOGENII

treatment_protocol: not applicable

value: mouse fibroblasts


title: dBA3

description: cultivation cell

data_processing:
Data were processed using Expression Console software. Gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: HuGene-1_0-st-v1.r3.pgf
meta-probeset file: HuGene-1_0-st-v1.r3.mps


title: BA

description: cultivation cell

source_name: brown adipose tissue

value: brown adipose tissue


title: Acquired gefitinib-resistant lung cancer cell line,biological rep2

city: Taipei

first: Jin-Yuan

last: Shih

address: #7, Chung-Shan South Road,

department: Internal Medicine

country: Taiwan

institute: National Taiwan University Hospital

description: Gene expression data from the acquired gefitinib-resistant lung cancer cells

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45°C on Affymetrix Human Genome U133 plus 2.0 GeneChip on Affymetrix Hybridization Oven 645, 60 RPM, then washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: standard Affymetrix protocol

data_processing: The expression data were analyzed by the SAS JMP Genomics software (Version 4.0; SAS Institute Inc., Cary, NC). Affymetrix CEL files were transformed by RMA algorithm, imported at the probe level and log2 transformed, and each probe set was summarized using the median of the corresponding probes. Each array was normalized by Quantile Normalization.

source_name: lung cancer cells, long term gefitinib treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)(Santa Clara, CA, USA, http://www.affymetrix.com).

growth_protocol: Cells were cultured in RPMI-1640 medium  with 10% fetal bovine serum (FBS), 100 u/ml penicillin and 100 mg/ml streptomycin at 37 °C in a humidified atmosphere of 5% CO2.

treatment_protocol: PC9/gef cells were selected from parental PC9 cells that had been continuously exposed to increasing concentrations of gefitinib.

tag: cell line

tag: tumor type

value: lung adenocacinoma


title: Acquired gefitinib-resistant lung cancer cell line,biological rep3


title: Acquired gefitinib-resistant lung cancer cell line,biological rep1


title: DiBA

description: cultivation cell

value: DiBA


title: dBA1

description: cultivation cell


title: Gefitinib-sensitive lung cancer cell line,biological rep1

description: Gene expression data from the gefitinib-sensitive lung cancer cells

source_name: lung cancer cells


title: iBA2

description: cultivation cell


title: dBA2

description: cultivation cell


title: Gefitinib-sensitive lung cancer cell line,biological rep2


title: iBA1

description: cultivation cell


title: Bodi_H1_Start_Yeast

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

department: School of Life Sciences

country: United Kingdom

institute: University of Nottingham

description: input RNA samples not fractionated on sucrose gradient

hyb_protocol: hybridization was carried out as per the manufacturer's instructions as described in Affymetrix GeneChip Expression analysis technical manual (Affymetrix, www.affymetrix.com)

scan_protocol: GeneChip arrays were scanned with an Affymetrix G2500A GeneArray scanner, as described in the Affymetrix GeneChip Expression Analysis Technical Manual.

data_processing: The raw chip data were analyzed using Partek GS 6.0 software. After initial probe-level RMA normalization the signals were further normalized by standardizing the signal value of each probe-set to the median of that probe-set across all hybridizations.

organism: Saccharomyces cerevisiae SK1

label_protocol: Total RNA samples were processed and labelled using the GeneChip 3? IVT Expression Kit, (Affymetrix, cat#901228), as described by the Affymetrix GeneChip Expression Analysis Technical Manual (http://www.affymetrix.com).

growth_protocol: All analysis was carried out using the SK1 (can1), diploid strain (ATCC).  Cultures were routinely grown in YPD (1% Bacto-yeast extract, 2% Bacto-peptone, 2% glucose) to the required cell density. For sporulation experiments, one single colony was inoculated in YPD and grown to 2x107cell/ml. After centrifugation and washing with sterile water, the pellet was resuspended to a 5x106cell/ml density in PSP2 medium (31). The culture was grown for five generations at 28-30oC with vigorous shaking, and then harvested and washed with water, followed by resuspending in SPM (0.3% potassium acetate, 0.02% raffinose) (31) to a 107cell/ml density to induce sporulation. Following 3 hours vigorous shaking at 28-30oC, the culture was spun down and the pellet was used for RNA extraction, or polysome profiling.

extract_protocol: For total RNA extraction we used a hot phenol extraction method ,and the quality of the mRNA was checked on an RNA 6000 LabChip, with Agilent Bioanalyzer (Ambion).

treatment_protocol: Polysome profiles The ribosomal complexes in the yeast cultures were stabilized by adding cycloheximide to a 100µg/ml final concentration prior to harvest. The cell were spun down immediately, and frozen in liquid N2. They were either stored at -70oC or processed immediately by grinding in pestle and mortar, under liquid N2 to fine powder. The cells were lysed in 0.5ml lysis buffer (0.3M NaCl, 15mM MgCl2, 15mM Tris-HCl pH7.5, cycloheximide 100ug/ml, Heparin (sodium salt) 1mg/ml, 1% Triton X-100). The lysates were loaded on a sucrose gradient column and spun for two hours at 38 000 rpm at 4oC. After the gradient centrifugation 12x 1ml fractions were collected and precipitated in equal volume isopropanol. After several washes with 80% ethanol the samples were resuspended in water and processed.

tag: line

tag: developmental stage

value: 3 hours sporulating

tag: fraction

value: input RNA (non-fractionated)


title: Bodi_H1_9-10_Yeast

description: RNA samples from polysome fractions 9-10

value: polysome fractions 9-10


title: MDA-MB-361_shDCD_clone_2

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

hyb_protocol: Standard Affymetrix protocol

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner M10

data_processing: The data were normalized by dCHIP.

source_name: MDA-MB-361 human breast cancer cell line expressing DCD-targeting shRNA, clone 2, in pLKO vector

label_protocol: Standard Affymetrix protocol

growth_protocol: MDA-MB-361 cell lines and transfectants were grown in ATCC recommended culture medium

treatment_protocol: we designed shRNA against different regions of DCD transcript and subcloned into pLKO-puro lentivival construct and generated three different clones of DCD-targeting cell lines using MDA-MB-361


title: Gefitinib-sensitive lung cancer cell line,biological rep3


title: Bodi_H1_7-8_Yeast

description: RNA samples from polysome fractions 7-8

source_name: RNA samples from polysome fractions 7-8

value: polysome fractions 7-8


title: MDA-MB-361_pLKO

source_name: MDA-MB-361 human breast cancer cell line expressing pLKO control vector


title: MDA-MB-361_shDCD_clone_1

source_name: MDA-MB-361 human breast cancer cell line expressing DCD-targeting shRNA, clone 1, in pLKO vector


title: MDA-MB-361_shDCD_clone_3

source_name: MDA-MB-361 human breast cancer cell line expressing DCD-targeting shRNA, clone 3, in pLKO vector


title: Bodi_H1_4-6_Yeast

description: RNA samples from polysome fractions 4-6

source_name: RNA samples from polysome fractions 4-6

value: polysome fractions 4-6


title: L8 rHSC

city: Brussels

first: Adil

last: El Taghdouini

address: Laarbeeklaan, 103

department: Cell Biology

institute: Vrije Universiteit Brussel

description: L8 rHSC_IIARRAY HUMA PICO_E09

hyb_protocol: Hybridized overnight to the Affymetrix Human Genome U219 array (Standard Affymetrix protocol)

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: Data processing cel files were normalized with 'rma' function of the Bioconductor package (v2.4) in R.3.0.1

source_name: Hepatic stellate cell population in vitro activated and reverted to quiescence by RM

label_protocol: Biotin-labeling (Standard Affymetrix protocol)

extract_protocol: Total RNA was purified from qHSCs, aHSCs and hepatocyte samples using RNeasy MICROKit (QIAGEN GmbH, Hilden, Germany) following a deviation of the standard protocol as recommended by the manufacturer and using 1.5 volumes of 100% ethanol before applying the sample into the column. Total RNA concentration and quality control was assessed using the RNA 6000 pico kit (Agilent, Santa Clara, CA).

treatment_protocol: Transcriptomic profiling of primary human quiescent HSCs were purified from healthy livers (qHSCs). In vitro activated HSCs (aHSCs) were generated by seeding qHSCs on plastic culture dishes and were expanded for up to 4 passages. The activated phenotype of HSCs was reverted by exposing the cells for 6 days to a combination of EGF (20ng/mL), FGF2 (10ng/mL), oleic acid (100µM), palmitic acid (100µM) and retinol (5µM) (Reverting Medium;RM).

tag: individual

value: donor L8

value: Male

value: 1 day

value: Reverted HSC


title: Bodi_H2_Start_Yeast

source_name: input RNA samples not fractionated on sucrose gradient


title: L12 aHSC

description: L12 aHSC _IIARRAY HUMA PICO_G09

source_name: Hepatic stellate cell population isolated from healthy liver culture-activated by seeding on regular tissue culture plates

value: donor L12

value: 12.5 years

value: Activated HSC


title: L4 rHSC

description: L4 rHSC_IIARRAY HUMA PICO_C09

value: donor L4

value: Female

value: 12 years


title: L8 aHSC

description: L8 aHSC_IIARRAY HUMA PICO_F09


title: White Adipocytes

description: cultivation cell

value: White Adipocytes


title: L12 rHSC

description: L12 rHSC_IIARRAY HUMA PICO_H09


title: L4 aHSC

description: L4 aHSC_IIARRAY HUMA PICO_D09


title: Bodi_2H_9-10_Yeast

source_name: RNA samples from polysome fractions 9-10


title: L10 QHSC

description: L10 QHSC _ 230712_E05

source_name: Hepatic stellate cell population isolated from healthy liver

value: donor L10

value: 7 months

value: Quiescent HSC


title: Bodi_2_Start_Yeast

value: 3 hours sporulating

value: input RNA (non-fractionated)


title: Bodi_2H_7-8_Yeast

description: RNA samples from polysome fractions 7-8

value: polysome fractions 7-8


title: Bodi_2_9-10_Yeast

value: polysome fractions 9-10


title: L8 QHSC

description: L8 QHSC _ 230712_C05

value: donor L8

value: Male


title: Bodi_2H_4-6_Yeast

description: RNA samples from polysome fractions 4-6

value: polysome fractions 4-6


title: L4 QHSC

description: L4 QHSC _ 230712_D09


title: Bodi_2_7-8_Yeast

description: RNA samples from polysome fractions 7-8


title: Group B2: B denotes embolic stroke and 2 denotes heart disease.

first: Pengfei

last: Li

state: Jiangsu

address: NO.155 Hanzhong Road, Baixia District

department: Clinical Laboratory

institute: Jiangsu Province Hospital of TCM

hyb_protocol: RNA samples were hybridized on the miRCURY™ LNA Array (v.18.0) according to manufacturer’s instructions.

scan_protocol: Following the washing steps the slides were scanned using the Axon GenePix 4000B microarray scanner.

data_processing:
Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.
Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs were identified through Fold Change filtering. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.

source_name: ischemic stroke serum

label_protocol: The RNAs were labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit according to manufacturer’s instructions.

extract_protocol: Total RNA was harvested using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions. The integrity of RNA was assessed by electrophoresis on a denaturing agarose gel. The Nanodrop instrument is used for accurate for measurement of concentrations (abs 260), protein contamination (ratio abs260/abs280) or contamination with organic compounds (ratio abs260/abs230).

tag: sample group

value: embolic stroke and heart disease

tag: tissue type

value: ischemic stroke serum


title: Group A1: A denotes thrombotic stroke and 1 denotes hepertension

value: thrombotic stroke and hepertension


title: Group A14: A denotes thrombotic stroke, 1 denotes hepertension and 4 denotes hyperlipidemia.

value: thrombotic stroke, hepertension and hyperlipidemia


title: Bodi_2_4-6_Yeast

description: RNA samples from polysome fractions 4-6


title: Group 0: healthy control group.

source_name: healthy control serum

value: healthy control

value: healthy control serum


title: Group B12: B denotes embolic stroke, 1 denotes hepertension and 2 denotes heart disease.

value: embolic stroke, hepertension and heart disease


title: Patient-50

status: Public on Aug 11 2015

city: Newcastle upon Tyne

first: Alem

middle: Selassie

last: Gabriel

address: Queen Victoria Rd

department: Northern Institute for Cancer Research

institute: Newcastle University

description:
SAMPLE 50
7970368152_R03C01

hyb_protocol: Illumina protocol

scan_protocol: Beadstation GX scanner

data_processing: R-environment (minifi package)

label: Cy5 and Cy3

source_name: Bone marrow

label_protocol: Illumina protocol

growth_protocol: Primary cells

extract_protocol: qiagen extraction kit

treatment_protocol: Bone marrow extraction

tag: all cytogenetic subtype

tag: outcome

value: in remission

tag: gender

value: Female


title: Patient-49

description:
SAMPLE 49
7878191115_R04C02


title: Patient-51

description:
SAMPLE 51
7970368152_R03C02


title: Patient-48

description:
SAMPLE 48
7878191155_R03C02


title: Patient-42

description:
SAMPLE 42
7970368152_R02C02

value: went on to relapse


title: Patient-39

description:
SAMPLE 39
7878191115_R02C02


title: Patient-38

description:
SAMPLE 38
7878191155_R06C02


title: Patient-47

description:
SAMPLE 47
7878191155_R02C02


title: Patient-44

description:
SAMPLE 44
7878191128_R03C02


title: Patient-46

description:
SAMPLE 46
7878191155_R03C01


title: Patient-41

description:
SAMPLE 41
7970368152_R01C02


title: Patient-26

description:
SAMPLE 26
7878191155_R04C02

value: HeH


title: Patient-43

description:
SAMPLE 43
7878191128_R04C01


title: Patient-30

description:
SAMPLE 30
7878191115_R01C02


title: Patient-34

description:
SAMPLE 34
7878191128_R05C01


title: Patient-33

description:
SAMPLE 33
7878191128_R02C01


title: Patient-45

description:
SAMPLE 45
7878191128_R05C02


title: Patient-23

description:
SAMPLE 23
7878191128_R03C01


title: Patient-37

description:
SAMPLE 37
7878191155_R06C01


title: Patient-52

description:
SAMPLE 52
7970368152_R04C02


title: Patient-36

description:
SAMPLE 36
7878191128_R04C02


title: Patient-31

description:
SAMPLE 31
7970368152_R01C01


title: Patient-40

description:
SAMPLE 40
7878191115_R06C02


title: Patient-27

description:
SAMPLE 27
7878191115_R01C01


title: Patient-25

description:
SAMPLE 25
7878191155_R01C02


title: Patient-35

description:
SAMPLE 35
7878191128_R02C02


title: Patient-28

description:
SAMPLE 28
7878191115_R03C01


title: Patient-24

description:
SAMPLE 24
7878191155_R02C01


title: Patient-32

description:
SAMPLE 32
7970368152_R05C02


title: Patient-29

description:
SAMPLE 29
7878191115_R04C01


title: Ex_W_tg_1

city: Zurich

first: Matthias

last: Schäfer

address: Otto-Stern-Weg 7

institute: ETH Zurich

hyb_protocol: 10 μg of cRNA/sample were hybridized for 16 h at 45°C. Washing and staining with streptavidin-conjugated phycoerythrin were done using a GeneChip Fluidics Station 400 (Affymetrix).

scan_protocol: Standard Affymetrix procedures using a Hewlett-Packard scanner

data_processing: Raw gene expression data generated by the GeneChip Operating Software (Affymetrix) were normalized for all probe sets on the array using the Robust Multichip Average (RMA) method.

source_name: K5cre/caNrf2_whole skin

label_protocol: Biotinylated cRNA were prepared from 2 ug total RNA using Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents according to the manufacturer’s protocol.

growth_protocol: 3 female K5cre-caNrf2 (tg/tg) and 3 female K5cre-wt (tg/wt) mice of one litter were sacrificed at P2.5

extract_protocol: back skin was cut out and snap frozen in N2, RNA was extracted using GSCN and phenol/chloroform

tag: strain background

value: FVB/N/C57BL/6 mixed

tag: age

tag: genotype/variation

value: K5cre-caNrf2 (tg/tg)

value: female

value: whole skin


title: myoblast treated with LncMyoD shRNA, biological rep3

city: Cambrdige

first: Yunyu

last: Zhang

address: 22 Windsor Ave

institute: Novartis Institute for Biomedical Research

description: Gene expression data from myoblast treated with LncMyoD shRNA

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix Mouse Genome Array 430 v2 according to the standard Affymetrix protocols.

scan_protocol: Arrays were scanned using GeneChip® Scanner 3000 7G

data_processing: Raw signals from CEL files were normalized and summarized into probe-set level intensities using the PLIER (Probe Logarithm Intensity ERror) method. Affymetrix MAS5 present/absent calls were calculated and probe-sets with “present” calls in less than 50% of samples within all treatment groups were removed for further statistical analyses.

source_name: Primary myoblast treated with LynMyoD shRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 400 ug total RNA. (Affymetrix 2010)

growth_protocol: Cells were cultured in F10 (GIBCO) +20% FBS (Fetal Bovine Serum, GIBCO) +2.5ng/ml bFGF (Invitrogen) + 1% penicillin/streptomycin. When induced for differentiation, myoblasts were switched to differentiation medium (DMEM supplemented with 5% horse serum).

extract_protocol: Total RNA was extracted using the TRIzol reagent (Invitrogen) and purified with Qiagen RNeasy separation columns (Qiagen).

treatment_protocol: shRNA sequences targeting LncMyoD were cloned into a Tet-pLKO-puro vector (addgene 21915) . Lentivirus was produced using a ViraPower Lentiviral Packaging Mix (life technologies) in 293T cells, filtered and used to infect myoblast cells.

value: 21 days old


title: myoblast treated with LncMyoD shRNA, biological rep2


title: Ex_W_wt_2

source_name: K5cre/wt_whole skin

value: tg/wtK5cre-wt (tg/wt=control)

tag: tissue


title: myoblast control, biological rep2

description: Gene expression data from myoblast

source_name: Primary myoblast


title: myoblast treated with LncMyoD shRNA, biological rep1


title: myoblast control, biological rep3

description: Gene expression data from myoblast


title: Patient-20

description:
SAMPLE 20
7970368152_R02C01


title: Ex_W_tg_3


title: Ex_W_wt_3


title: Ex_W_wt_1


title: Patient-21

description:
SAMPLE 21
7970368152_R04C01

value: Male


title: myoblast control, biological rep1

description: Gene expression data from myoblast


title: Ex_W_tg_2


title: Patient-18

description:
SAMPLE 18
7878191115_R06C01


title: TET_siTDP43_3 (gene-level)

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

data_processing:
Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
HJAY_r2.pgf
HJAY_r2.full.mps

growth_protocol: Cells were cultured under DMEM(10%FBS, 1% penicillin-streptomycine). Atmosphere: air, 95%; carbon dioxide (CO2), 5%. Temperature, 37.0°C

extract_protocol: Total RNA extracted using RNeasy Mini Kit (Qiagen) following manufacturer´s instructions

treatment_protocol: Flp-In HEK293 (Invitrogen) carrying  inducible siRNA resistant FLAG-tagged wild type TDP-43, F4L mutant, and TDP43-12XQ/N constructs were induced  (to obtain tagged TDP-43 expression) with 1μg/ml tetracycline (Sigma). Depletion of endogenous TDP-43 was performed by RNA interference using HiPerFect Transfection Reagent (Qiagen) and siRNA specific for TDP-43 (Dharmacon; target sequence 5’-aagcaaagccaagaugagccu-3’).

value: siTDP43-treated HEK-293 cells


title: TET_siTDP43_2 (gene-level)


title: TET_siTDP43_1 (gene-level)


title: Patient-16

description:
SAMPLE 16
7878191155_R04C01


title: Patient-12

description:
SAMPLE 12
6222421026_R01C01