title: esa1-L254P S MMS Treatment Replicate 2

description: esa1 S MMS-rep2


title: esa1-L254P WT S No Treatment Replicate 1

status: Public on Feb 21 2015

type: RNA

city: Calgary

first: Jennifer

last: Cobb

state: Alberta

address: 2A18 HRIC 3330 Hospital Dr NW

department: Biochemistry and Molecular Biology

country: Canada

institute: University of Calgary

description: esa1 WT S-rep1

hyb_protocol: Hybridization was performed according to the manufactruer's instruction (Agilent Technology). Microarray was washed in 6X SSPE/0.005% sodium N-lauroylsarcosine at room temperature for 5 min followed by a second wash in pre-heated 42°C 0.6X SSPE for 2 min.

scan_protocol: Microarrays were scanned on an GenePix 4200A instrument with GenePix 3.0 software

data_processing: The raw data was lowess normalized and the average log2 ratios with the corresponding t-test p values from the dye-swap experiments were obtained using the R version 3.1.1 Bioconductor Limma package version 3.0.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: esa1-L254P S

label_protocol: 2 ug of mRNA were converted into cDNA using 140 nmol of Oligo-dT(25) anchored primer (Sigma), 20 nmol of aminoallyl dUTP dNTP (Sigma) mixture, and 200 units of SuperScript II reverse transcriptase (Invitrogen). 1 ug of cDNA each from overexpression or deletion strain and empty vector control strain was labeled with Cy3 or Cy5 (GE Healthcare) and were combined for QIAquick purification (QIAGEN).

growth_protocol: Cells were synchronized in G1 with α-factor for two hours, washed in YPAD media, and released into media with or without 0.05% MMS for 1 hour.

extract_protocol: Total RNA was extracted using hot phenol-chloroform method, followed by mRNA isolation using gravity-flow Oligo-dT cellulose beads.

tag: strain background

tag: genotype/variation

tag: cell cycle phase

value: synchronized in G1 with α-factor for 2hrs and released into media

tag: treated with

value: none (untreated control)

source_name: Wild Type S

value: wild type


title: esa1-L254P WT S No Treatment Replicate 2

description: esa1 WT S-rep2


title: 662L185

type: genomic

city: Guelph

first: Tamas

last: Revay

state: ON

address: 50 Stone Rd E

department: Biomedical Sci

institute: University of Guelph

hyb_protocol: The protocol followed the manufacturers recommendations by the service provider DNA Landmarks, Quebec, Canada

data_processing: This work analysed DNA copy number variations only. The starting points were the GenomeStudio project files (.bsc) provided by DNAL Landmarks. The LogR data was  exported from GenomeStudio using the GoldenHelix SVS exporter. Copy number analysis was done in SNP and Variation Suite ver. 7.7.8. (SVS, GoldenHelix Inc.)

label: biotin

molecule: genomic DNA

organism: Sus scrofa

source_name: gDNA from ear notch

extract_protocol: Genomic DNA was extracted using a standard Proteinase K and phenol/chlorophorm method.

tag: tissue

value: ear notch

tag: breed

value: Landrace

tag: Sex

value: male

tag: fertility

value: low


title: 969L197

scan_protocol: The protocol followed the manufacturers recommendations by the service provider DNA Landmarks, Quebec, Canada


title: 981D197

label_protocol: The protocol followed the manufacturers recommendations by the service provider DNA Landmarks, Quebec, Canada

value: Duroc


title: 997Y197

value: Yorkshire


title: esa1-L254P WT G1 MMS Treatment Replicate 2

description: esa1 WT G1 MMS-rep2

source_name: Wild Type G1 MMS

growth_protocol: Cells were synchronized in G1 with α-factor for one hour and then treated with and without 0.05% MMS for 1 hour.

value: synchronized in G1 with α-factor for 1hr

value: 0.05% MMS for 1 hr

source_name: esa1-L254P G1 MMS


title: udmurd5

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

description: Genomic DNA extracted from blood was genotyped using Human610-Quad v1.0 BeadChip (Illumina).

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

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

data_processing:
Image data was analyzed using Genomestudio v2011.1 with GT module 1.9.4 (Illumina).
Genotype: AA,AB,BB,or NC (no call)

label: Cy3, Cy5

organism: Homo sapiens

source_name: blood

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

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

tag: gender

value: Male

tag: population

value: Udmurts

tag: region

value: Europe


title: udmurd7


title: udmurd8


title: WT S MMS Treatment Replicate 1

description: WT S MMS-rep1

source_name: Wild Type S MMS


title: WT S MMS Treatment Replicate 2

description: WT S MMS-rep2


title: esa1-L254P G1 MMS Treatment Replicate 1

description: esa1 G1 MMS-rep1

source_name: esa1-L254P G1


title: udmurd3


title: udmurd4


title: udmurd6


title: udmurd16


title: esa1-L254P WT G1 MMS Treatment Replicate 1

description: esa1 WT G1 MMS-rep1

source_name: esa1_L254P G1 MMS


title: udmurd9


title: esa1-L254P WT G1 No Treatment Replicate 2

description: esa1 WT G1-rep2

source_name: Wild Type G1


title: esa1-L254P WT G1 No Treatment Replicate 1

description: esa1 WT G1-rep1


title: WT G1 MMS Treatment Replicate 1

description: WT G1 MMS-rep1


title: udmurd15


title: udmurd2


title: WT G1 MMS Treatment Replicate 2

description: WT G1 MMS-rep2


title: udmurd12


title: udmurd13


title: udmurd11


title: udmurd10


title: udmurd1


title: tatars8

value: Tatars


title: tatars7


title: tatars9


title: tatars2


title: tatars3


title: esa1-L254P G1 MMS Treatment Replicate 2

description: esa1 G1 MMS-rep2


title: udmurd14


title: tatars4


title: yakut8_1m

description: Genomic DNA extracted from blood was genotyped using Illumina HumanOmni1-Quad BeadChip (Illumina).

value: Yakuts

value: Siberia


title: tatars5


title: tatars16


title: yakut1_1m

value: Female


title: UZB180_turkmen

value: Turkmens

value: Central Asia


title: yakut4_1m


title: tatars14


title: MCF10A cells (2)

city: Columbus

first: Lianbo

last: Yu

state: OH

address: 1800 Cannon Drive

department: Center for Biostatistics

country: USA

institute: The Ohio State University

hyb_protocol: See manufacturer's website (http://www.nanostring.com).

data_processing:
Normalized, background-adjusted counts were converted to miRNA copy # using a standard curve generated from the dilution series of the 6 positive controls in each sample.
miRNA copy # (basis = 10ng total RNA) were converted to miRNA copy #/cell using the total RNA extracted in each sample and the total number of cells in each sample.
miRNA counts were normalized for hybridization efficiency using the 6 positive controls in each sample, then quantile normalization was used to biologically normalize across samples.

molecule: total RNA

source_name: MCF10A cells

label_protocol: nCounter Human miRNA Assay Kit

growth_protocol: Cells grown in media containing FBS were allowed to reach 70-80% confluence and then incubated in serum-free media for 72 hrs.

extract_protocol:
Total RNA was extracted from cells and EVs using TRIzol reagent, and then further purified by ethanol precipitation.
RNA quantity/quality protocol: Total RNA was quantified using a NanoDrop 2000 spectrophotometer, and RNA was determined using an Agilent 2100 Bioanalyzer
assumed efficiencies: 75% (10%) for TRIzol extraction of cellular (EV) RNA; 100% (19%) for ethanol purification of extracted cellular (EV) RNA; 15% for EV isolations.

treatment_protocol: EVs were isolated from the serum-free media at 72 hrs of serum deprivation.

tag: cell type

value: normal cells


title: MCF7 cells (3)

scan_protocol: See manufacturer's website (http://www.nanostring.com).

source_name: MCF7 cells


title: MCF7 cells (2)


title: MCF7 cells (4)


title: MCF7 EVs (2)

source_name: MCF7 EVs

value: extracellular vesicles


title: MCF7 cells


title: MCF7 EVs


title: MCF10A cells (3)


title: MCF10A cells


title: UZB152_turkmen


title: MCF10A EVs

source_name: MCF10A EVs


title: tatars13


title: tatars6


title: UZB150_turkmen


title: UZB178_turkmen


title: tatars10


title: UZB102_turkmen


title: tatars15


title: tatars1


title: UZB105_turkmen


title: tatars11


title: nenets9

value: Nenets (Forest)


title: tunNenets_Sam749_1m

value: Nenets (Tundra)


title: nenets4


title: nenets2


title: tuva5_1m

value: Tuvans


title: nenets13


title: UZB101_turkmen


title: nenets11


title: TJ961_ishkashim

value: Tajiks (Pamir)


title: nenets15


title: tunNenets_Sam163_1m


title: TJ862_ishkasim


title: nenets10


title: tunNenets_Sam065_1m


title: nenets5


title: nenets14


title: TJ855_kirghizPamir

value: Kyrgyz


title: TJ762_rushanvanch


title: UZB111_turkmen


title: tatars12


title: TJ651_rushanvanch


title: nenets1


title: komi9

value: Komis


title: komi8


title: uighur4_1m

value: Uygurs


title: TJ364_tadjik_pl

value: Male

value: Tajiks


title: komi6

value: Europe


title: TJ354_tadjik_pl


title: komi7


title: TJ250_shugnan


title: komi4


title: komi5


title: TJ1101_tadjik_yag

value: Yaghnobi people


title: TJ1110_tadjik_yag


title: TJ1176_tadjik_yag


title: komi3


title: TJ1102_yagnobi


title: TJ096_tadjik_pl


title: komi16


title: komi15


title: TJ086_tadjik_pl


title: komi14


title: TJ1095_tadjik_yag


title: komi12


title: komi13


title: komi11


title: komi2


title: tdj938_ishkashim


title: tdj868_rushan


title: komi10


title: komi1


title: karelia9

value: Karelians


title: tdj54_rushan


title: tdj529_rushan


title: tdj521_rushan


title: karelia8


title: tdj979_shugnan


title: karelia6


title: tdj508_rushan


title: tdj447_ishkashim


title: karelia5


title: tdj430_shugnan


title: tdj412_shugnan


title: karelia3


title: TJ0197_tadjik_yag


title: karelia2


title: tdj409_shugnan


title: tdj305_shugnan


title: karelia14

value: Female


title: karelia15


title: tdj277_rushan


title: tdj291_ishkashim


title: karelia13


title: karelia11


title: tdj275_shugnan


title: tdj269_ishkashim


title: karelia10


title: tdj262_shugnan


title: tdj255_ishkashim


title: karelia1


title: tdj261_rushan


title: tdj252_ishkashim


title: tdj258_ishkashim


title: bashkir8

value: Bashkirs


title: karelia4


title: bashkir9


title: bashkir5


title: tdj0802_kirghiz_alitshor

value: Central Asia


title: tdj126_shugnan


title: tdj775_ishkashim


title: bashkir4


title: bashkir20


title: bashkir6


title: tdj0011_kirghiz_murgab


title: tdj12_rushan


title: karelia12


title: bashkir19


title: karelia7


title: bashkir2


title: tatar2_1m

value: Tatars


title: tatarmishar12_1m


title: tatar3_1m


title: bashkir18


title: bashkir17


title: bashkir16


title: nganassanVo32_1m

value: Nganasans

value: Siberia


title: MON414_mongol_Halha

value: Mongols (Mongolia)


title: bashkir15


title: bashkir7


title: MON085_mongol_Halha


title: tdj0635_kirghiz_murgab


title: LPGH119kazakh_cw

value: Kazakhs


title: bashkir3


title: bashkir14


title: kumyk14_1m

value: Kumyks

value: Caucasus


title: kumyk13_1m


title: kumyk11_1m


title: kryashen5_1m


title: bashkir11


title: kryashen8_1m


title: koryak42_1m

value: Koryaks


title: bashkir12


title: bashkir10


title: koryak33_1m


title: tatar0_1m


title: intervention_Ornish [cv000300 1 year]

city: Windber

first: Darrell

last: Ellsworth

state: PA

address: 620 Seventh St.

institute: Windber Research Institute

description: Gene expression data on human blood 1 year after CVD lifestyle intervention.

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome  U133A 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
The data were analyzed using Expression Console or GCOS using the MAS5 algorithm with Affymetrix default analysis settings .
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console
program-id = 1.1.2800.19935

label_protocol: Biotinylated aRNA were prepared according to the Message Amp II aRNA Amplificatin kit (Life Technologies) using the standard single round protocol.

extract_protocol: Blood samples were thawed at room temperature overnight.  Total RNA was extracted using the Qiagen Paxgene Blood RNA kit using the standard protocol.

treatment_protocol: Blood was collected in Paxgene (Qiagen) RNA tubes, inverted, set at room temperature for 4-24 hours then frozen at -80°C.

value: female

tag: age

tag: cad disease status

value: Yes

tag: 1 year weight loss (%)

tag: diabetes status

value: yes

value: blood


title: KKA076_karakalpak

value: Male

value: Karakalpaks


title: LHPG120_kazakhTienShan


title: bashkir1

value: Europe


title: KKA080_karakalpak


title: KKA073_karakalpak


title: bashkir13

value: Bashkirs


title: vepsa64

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

value: Vepsas


title: KKA066_karakalpak

value: Central Asia


title: KKA055_karakalpak


title: vepsa61


title: KKA052_karakalpak


title: vepsa59


title: KKA051_karakalpak


title: KKA048_karakalpak


title: kryashen4_1m

value: Tatars


title: KKA044_karakalpak


title: vepsa55


title: kirghiz3_1m

value: Female

value: Kyrgyz


title: KKA001_karakalpak


title: vepsa46


title: control_Ornish [cv000951 3months]

description: Gene expression data on human blood after 3 months of non-intervention.

value: male

value: no


title: control_Ornish [cv000951 baseline]

description: Gene expression data on human blood at baseline with no intervention.


title: intervention_Ornish [cv000300 3 months]

description: Gene expression data on human blood 3 months after CVD lifestyle intervention.


title: intervention_Ornish [cv000300 Baseline]

description: Gene expression data on human blood before CVD lifestyle intervention.


title: KGZ069_kirghiz


title: control_Ornish [cv000951 1year]

description: Gene expression data on human blood after 1 year of non-intervention.


title: vepsa34


title: vepsa28


title: keto019_1m

value: Kets

value: Siberia


title: intervention_Ornish [cv000933 3months]

source_name: human blood 3 months after CVD lifestyle intervention.

value: No


title: intervention_Ornish [cv000933 baseline]

source_name: human blood before CVD lifestyle intervention.


title: keto018_1m


title: Control mesenchymal stromal cells

city: Gifu

first: Tamotsu

last: Takeuchi

address: Yanagido

department: Pathology and Translational Research

country: Japan

institute: Gifu University School of Medcine

description: Breast cancer cell (MCF-7) and mesenchymal stroma cell (UE6E7T-2) co-culture system.

hyb_protocol: Hybridized to Agilent-039494 arrays at 65 degrees for 17 hours.

scan_protocol: 3 micrometer resolution using Agilent Technologies Microarray Scanner.

data_processing: Data was imported to GeneSpring GX. Per Chip: Normalized to 75 percentile.

source_name: UE6E7T-2 and MCF-7 co-culture, control UE6E7T-2 cells

label_protocol: cRNA was labeled using Low Input Quick Amp labeling kit (Agilent Technologies). Labeled cRNA was purified with RNeasy mini spin columns, Qiagen.

extract_protocol: After 48 h, total RNA was extracted from the co-cultured cells using RNeasy spin columns kit (Qiagen).

treatment_protocol: Beclin-1 siRNA-treated or control UE6E7T-2 cells (1 x 10^4) and MCF-7 cells (1 x 10^4) were co-cultured in 24-well plates.

tag: cell line

tag: treatment of ue6e7t-2

value: control


title: siRNA-mediated downregulation of beclin-1 in mesenchymal stromal cells

source_name: UE6E7T-2 and MCF-7 co-culture, beclin-1 siRNA-treated UE6E7T-2 cells

value: beclin-1 siRNA


title: intervention_Ornish [cv000919 baseline]

value: Yes

value: yes

value: blood


title: vepsa25

value: Male

value: Europe


title: intervention_Ornish [cv000933 1year]

source_name: human blood 1 year after CVD lifestyle intervention.


title: kabardin4_1m

value: Kabardins

value: Caucasus


title: kirghiz1_1m

value: Central Asia


title: kabardin1_1m

value: Female


title: KGZ067_kirgiz_TienShan

value: Kyrgyz


title: vepsa10

value: Vepsas


title: forNenets_tin029_1m

value: Nenets (Forest)


title: intervention_Ornish [cv000919 3months]

value: male


title: intervention_Ornish [cv000919 1year]


title: forNenets_tin028_1m

value: Siberia


title: vepsa19


title: forNenets_tin027_1m


title: KGZ003_kirghizTienShan


title: vepsa1


title: evenkAA7806_1m

value: Evenkis


title: control_Ornish [cv000913 baseline]

source_name: human blood at baseline with no intervention.

value: No

value: no


title: evenkAA7798_1m


title: tuva89

value: Tuvans


title: evenkAA7792_1m


title: evenAA7432_1m

value: Evens


title: tuva57


title: control_Ornish [cv000913 1year]

source_name: human blood after 1 year of non-intervention.

value: blood


title: evenAA7404_1m

value: Male


title: intervention_Ornish [cv000885 baseline]

value: Yes

value: yes


title: kabardin2_1m

value: Kabardins

value: Caucasus


title: control_Ornish [cv000913 3months]

source_name: human blood after 3 months of non-intervention.


title: even23_1m

source_name: blood


title: RussianVoron107

value: Russians (Central)

value: Europe


title: nganassanDu90_1m

value: Female

value: Nganasans


title: chuvash3_1m

value: Chuvashes


title: chuvash1_1m


title: RussianVoron105


title: buriat6_1m

value: Buryats

value: Siberia


title: chukchi2_1m

value: Chukchis


title: RussianVoron103


title: russianVoron101


title: buriat11_1m


title: buriat2_1m


title: intervention_Ornish [cv000885 1year]

value: male


title: bashkir4_1m

value: Bashkirs


title: russianOrjol89


title: bashkir2_1m


title: russianOrjol78


title: balkar4_1m

value: Balkars


title: balkar1_1m


title: intervention_Ornish [cv000883 3months]

value: no

value: blood


title: intervention_Ornish [cv000880 baseline]

value: No


title: balkar2_1m

value: Male


title: chukchi8_1m


title: AZR827_azer_Dagestan

value: Azeris (Dagestan)


title: RussianOrjol45


title: AZR535_azer_Dagestan

value: Caucasus


title: AZR8_azer_Dagestan


title: russianOrjol100

value: Russians (Central)


title: RussianOrjol34

value: Europe


title: AZR4_azer_Dagestan


title: bashkir3_1m


title: intervention_Ornish [cv000885 3months]

value: Yes

value: yes


title: intervention_Ornish [cv000880 3months]


title: azerbaijani13_1m

value: Azeris (Northwestern Iran)


title: russianOrjol1


title: intervention_Ornish [cv000880 1year]


title: altai3_1m

value: Altaians


title: intervention_Ornish [cv000815 baseline]


title: intervention_Ornish [cv000883 1year]


title: intervention_Ornish [cv000883  baseline]


title: intervention_Ornish [cv000812 baseline]


title: intervention_Ornish [cv000815 3months]


title: intervention_Ornish [cv000815 1year]


title: russianOrjol56


title: RussianKursk9


title: altai1_1m

value: Female

value: Siberia


title: russianKursk6


title: RussianKursk18


title: intervention_Ornish [cv000812 1year]

value: male


title: intervention_Ornish [cv000773 baseline]

value: female


title: azerbaijani14_1m


title: Russia_Smol349


title: Russia_Tver472


title: Russia_Tver415


title: RussianKursk15


title: Russia_Tver442


title: control_Ornish [cv000766 3months]


title: intervention_Ornish [cv000749 baseline]


title: intervention_Ornish [cv000749 3months]


title: intervention_Ornish [cv000773 1year]


title: intervention_Ornish [cv000773 3months]


title: AZR2_azer_Dagestan


title: control_Ornish [cv000766 baseline]


title: Russia_Smol304


title: Russia_Smol350


title: Russia_Smol303


title: intervention_Ornish [cv000812 3months]


title: Russia_Smol345


title: control_Ornish [cv000766 1year]


title: Russia_Kostr151


title: Russia_Smol339


title: Russia_Kostr149


title: Russia_Smol312


title: kalmyk9

value: Kalmyks


title: intervention_Ornish [cv000749 1year]


title: kalmyk67


title: control_Ornish [cv000741 3months]

value: no


title: control_Ornish [cv000741 1year]

value: blood


title: control_Ornish [cv000703 3months]


title: control_Ornish [cv000741 baseline]


title: intervention_Ornish [cv000667 baseline]


title: intervention_Ornish [cv000667 1year]


title: control_Ornish [cv000710 baseline]

value: No


title: control_Ornish [cv000703 1year]


title: kalmyk46

value: Male


title: Russia_Kostr170


title: control_Ornish [cv000710 3months]


title: intervention_Ornish [cv000579 3 months]


title: control_Ornish [cv000710 1year]


title: kalmyk44


title: Russia_Kostr128


title: RusArch305

value: Russians (North)


title: Russia_Kostr120


title: Russia_Kostr138


title: control_Ornish [cv000703 baseline]


title: kalmyk39

value: Caucasus


title: kalmyk40


title: kalmyk22


title: kalmyk69


title: kalmyk55


title: kalmyk13


title: kalmyk32


title: intervention_Ornish [cv000667 3months]


title: kalmyk14


title: intervention_Ornish [cv000579 1 year]


title: intervention_Ornish [cv000579 Baseline]


title: intervention_Ornish [cv000538 3 months]


title: kalmyk11


title: intervention_Ornish [cv000538 1 year]


title: intervention_Ornish [cv000536 Baseline]


title: German9

value: Germans


title: intervention_Ornish [cv000666 1year]


title: intervention_Ornish [cv000536 3 months]


title: intervention_Ornish [cv000666 baseline]


title: intervention_Ornish [cv000538 Baseline]


title: German3

value: Europe


title: Russia_Tver418

value: Russians (Central)


title: German2


title: German6


title: German5


title: German19


title: intervention_Ornish [cv000435 3months]

value: Yes


title: intervention_Ornish [cv000435 baseline]


title: intervention_Ornish [cv000536 1 year]


title: German17


title: intervention_Ornish [cv000429 1year]

value: yes


title: intervention_Ornish [cv000429 baseline]


title: German16


title: German15


title: intervention_Ornish [cv000429 3months]


title: intervention_Ornish [cv000427 baseline]


title: German14


title: intervention_Ornish [cv000427 3months]


title: intervention_Ornish [cv000435 1year]


title: German13


title: German1


title: German10


title: intervention_Ornish [cv000427 1year]


title: intervention_Ornish [cv000666 3months]


title: gagauz7

value: Gagauzes


title: gagauz8

value: Female


title: kalmyk70


title: gagauz5


title: Gagauz4


title: gagauz25


title: gagauz24


title: Gagauz22


title: gagauz23


title: intervention_Ornish [cv000414 1year]


title: intervention_Ornish [cv000414 3months]


title: Gagauz18


title: control_Ornish [cv000379 3months]


title: intervention_Ornish [cv000414 baseline]


title: control_Ornish [cv000373 Baseline]


title: azerF4

value: Azeris (Northwestern Iran)


title: gagauz3


title: control_Ornish [cv000379 1year]

value: male


title: azerF111


title: control_Ornish [cv000373 1 year]


title: intervention_Ornish [cv000357 3months]


title: control_Ornish [cv000379 baseline]


title: intervention_Ornish [cv000357 baseline]


title: azerE92


title: gagauz20


title: intervention_Ornish [cv000355 3months]

value: female


title: intervention_Ornish [cv000350 1year]


title: intervention_Ornish [cv000350 baseline]


title: intervention_Ornish [cv000355 baseline]


title: intervention_Ornish [cv000355 1year]


title: control_Ornish [cv000373 3 months]


title: azerE85


title: intervention_Ornish [cv000350 3months]


title: intervention_Ornish [cv000357 1year]


title: azerE82


title: azerE70


title: azerE6


title: azerE89


title: intervention_Ornish [cv000344 Baseline]


title: intervention_Ornish [cv000343 3months]


title: azerE3


title: gagauz14


title: azerE1


title: intervention_Ornish [cv000343 baseline]


title: azerB8


title: intervention_Ornish [cv000344 1 year]


title: azerb72


title: azerB64


title: intervention_Ornish [cv000343 1year]


title: intervention_Ornish [cv000293 baseline]


title: intervention_Ornish [cv000287 baseline]


title: intervention_Ornish [cv000293 3months]


title: intervention_Ornish [cv000293 1year]


title: intervention_Ornish [cv000287 3months]


title: azerB38


title: WT_treated_7d_female

city: Charleston

first: James

last: Cray

state: South Carolina

address: 173 Ashley Avenue, BSB230B

department: Oral Health Sciences

institute: Medical University of South Carolina

hyb_protocol: GeneChips were hybridized overnight at 45oC per recommendations for the Affymetrix format 100 array and then washed in an Affymetrix Fludics Station 450 using reagents from the Affymetrix Hybridization, Wash and Stain Kit

scan_protocol: Microarrays were scanned using an Affymetrix 7G Scanner

data_processing: CEL files were imported into Affymetrix Expression Console software and data were normalized using gene level RMA to obtain transcript expression values.

organism: Mus musculus

source_name: Wild Type_7 day treated_female

label_protocol: Total RNA (100ng) was converted into labeled material using the Affymetrix GeneChip WT PLUS Kit

growth_protocol: Coronal suture derived cells were isolate from 2 litters comprising mixed wild type C57BL6 and Twist 1 +/- animals. Males and females were seperated and seperation was conducted by genotype allowing for 8 independent samples and two time points.Cells were grown in a T-75 flask until transfer into T-175 flas. Cells were cultured in Dulbecco's Modified Eagle Medium supplemented with penicillin/strepromycin and amphoterecin and 10% FBS.

extract_protocol: Total RNA was extracted using an Qiagen RNeasy Mini Kit following manufacturer's instructions

treatment_protocol: The experiment was set up in 6 well plates with 3 wells as control untreated cells, and 3 wells of thyroxine treated cells for each of the 8 samples for 3 and 7 day time points (16 samples total). Seeding density was 65,000 cells per well. Treatments were set up as follows 1) proliferation medium: control cells fed with dmem or 2) thyroxine 10^-6 mol/liter suspended in DMEM.

tag: strain background

tag: genotype/variation

value: wild type

value: coronal suture cells

tag: culture condition

value: DMEM+Thyroxine

tag: time point

value: 7 days in culture


title: WT_control_7d_female

source_name: Wild Type_7 day control_female

value: DMEM


title: WT_treated_3d_male

source_name: Wild Type_3 day treated_male

value: 3 days in culture


title: Twist_control_7d_female

source_name: Mutant_7 day control_female

value: Twist 1+/-


title: intervention_Ornish [cv000344 3 months]

value: no

tag: tissue

value: blood


title: azerB59

value: Male

value: Caucasus


title: WT_treated_7d_male

source_name: Wild Type_7 day treated_male


title: WT_control_7d_male

source_name: Wild Type_7 day control_male


title: azerB61


title: Twist_control_7d_male

source_name: Mutant_7 day control_male


title: intervention_Ornish [cv000287 1year]

value: Yes

value: yes


title: WT_treated_3d_female

source_name: Wild Type_3 day treated_female


title: Twist_treated_7d_female

source_name: Mutant_7 day treated_female


title: Twist_treated_7d_male

source_name: Mutant_7 day treated_male


title: WT_control_3d_male

source_name: Wild Type_3 day control_male


title: Twist_control_3d_female

source_name: Mutant_3 day control_female


title: WT_control_3d_female

source_name: Wild Type_3 day control_female


title: Twist_treated_3d_male

source_name: Mutant_3 day treated_male


title: Twist_treated_3d_female

source_name: Mutant_3 day treated_female


title: Twist_control_3d_male

source_name: Mutant_3 day control_male


title: emptyvector_untreated_replicate2

status: Public on Feb 20 2015

city: Lund

first: Jillian

last: Howlin

address: Scheelevägen 2

department: Division of Oncology & Pathology

country: Sweden

institute: Lund University Cancer Center/ Medicon Village

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw data was quantile normalized and Illumina control probes were removed from subsequent analysis using BASE (Vallon-Christersson et al., 2009). The data were exported to MeV, log2 transformed and gene and sample centred (Saeed et al., 2003).

source_name: A2058 mmelanoma cell line

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays; Modified Illumina TotalPrep-96 RNA Amplification Kit (Cat #4393543)

extract_protocol: RNA was extracted  QIAGEN RNeasy plus mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were transfected with empty vector plasmid DNA using the recommended protocol for Lipofectamine2000 (Life Technologies), and treated with TGFbeta1 or vechicle control

tag: transfection

value: empty vector

tag: treatment

value: control vehicle


title: siCITED1#3 replicate2

source_name: HT144 melanoma cell line

growth_protocol: Cells were maintained in normal growth medium for 48 h post transfection

treatment_protocol: Cells were transfected with siRNA using the recommended protocol for Lipofectamine2000 (Life Technologies)

value: siRNA targeting CITED1


title: emptyvector_untreated_replicate4


title: emptyvector_untreated_replicate3


title: siCITED1#3 replicate3


title: siCITED1#1 replicate1


title: emptyvector_untreated_replicate1


title: emptyvector_TGFbetatreated_replicate4


title: siCITED1#1 replicate4


title: emptyvector_TGFbetatreated_replicate2


title: siCITED1#1 replicate2


title: emptyvector_TGFbetatreated_replicate1


title: siCITED1#3 replicate4


title: human prostate stem cells spheroid cells_patient 2_replicate 1

city: Heidelberg

first: Eisen

last: Christian

state: (Click to Select US State)

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center

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

source_name: Human prostate tissue

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

extract_protocol: RNA was extracted with the QIAGEN miRNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: individual

value: patient 2

value: prostate stem cells spheroid cells

tag: gender

value: male


title: siCITED1#3 replicate1


title: human prostate stem cells spheroid cells_patient 2_replicate 2


title: siCITED1#1 replicate3


title: siNEG replicate 3

value: negative control non-targeting siRNA


title: siNEG replicate 2


title: siNEG replicate 1


title: human prostate stem cells spheroid cells_patient 1_replicate 1

value: patient 1


title: human prostate stem cells spheroid cells_patient 2_replicate 3


title: emptyvector_TGFbetatreated_replicate3


title: human prostate stem cells spheroid cells_patient 1_replicate 3


title: siNEG replicate 4


title: human prostate stem cells adherent monolayer cells_patient 2_replicate 2


title: human prostate stem cells adherent monolayer cells_patient 2_replicate 3


title: human prostate stem cells spheroid cells_patient 1_replicate 2


title: human prostate stem cells adherent monolayer cells_patient 2_replicate 1


title: human prostate stem cells adherent monolayer cells_patient 1_replicate 3


title: human prostate stem cells adherent monolayer cells_patient 1_replicate 1


title: Microglia_Veh_WT_4

city: Stanford

first: Katrin

last: Andreasson

state: CA

address: 1201 Welch Road, MSLS P210

department: Neurology and Neurological Sciences

institute: Stanford University

hyb_protocol: Performed by the Stanford University PAN facility using the GeneChip Hybridization protocol from Affymetrix (P/N 702731)

scan_protocol: Performed by the Stanford University PAN facility using a GCS 3000 Scanner and Gene Chip Command Console software

data_processing: The data were analyzed using Partek Genomics Suite version 6.6, using RMA default settings.

source_name: Primary microglia from 8 month-old mice

label_protocol: Performed by the Stanford University PAN facility using the GeneChip Whole Transcript Sense Target Labeling Assay from Affymetrix (P/N 701880)

growth_protocol: Primary microglia were isolated directly from adult mouse brain and processed immediately for RNA extraction.

extract_protocol: Total RNA was isolated using Trizol followed by Qiagen RNeasy kit extraction according to the manufacturer's instructions

treatment_protocol: Primary microglia were from mice that 48h before had received I.C.V. injections of Aβ or vehicle.

value: I.C.V. Vehicle 48h prior to cell isolation

tag: genotype

value: CD11b-Cre ; EP2+/+

tag: strain

value: 8 month-old


title: Microglia_Veh_WT_2

tag: age


title: Microglia_Veh_WT_3


title: Microglia_Ab_WT_5

value: I.C.V. Aβ42 fibrillar 48h prior to cell isolation


title: Microglia_Veh_EP2_3

value: CD11b-Cre ; EP2lox/lox


title: Microglia_Veh_EP2_2


title: Microglia_Ab_WT_4


title: human prostate stem cells adherent monolayer cells_patient 1_replicate 2

tag: cell type


title: Microglia_Ab_WT_7


title: Microglia_Ab_WT_2


title: Microglia_Ab_EP2_1


title: thyroid K-3.a1.lbe1

city: Göteborg

first: Nils

last: Rudqvist

state: VG

address: Gula stråket 2b

institute: Gothenburg university

data_processing: The data were normalized using quantile normalization with BASE

source_name: Mouse thyroid, 0 kBq, 24 h

label_protocol: Standard Illumina labeling protocol

extract_protocol: Total RNA was extracted with RNeasy Lipid Tissue Mini Kit according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyzer.

value: Balb/c

value: thyroid

tag: injected activity

value: 0 kBq

tag: time of killing after administrations


title: thyroid D-3.a1.lbe1

source_name: Mouse thyroid, 100 kBq, 1 h

value: 100 kBq

value: 1 h


title: thyroid B-3.a1.lbe1


title: thyroid E-3.a1.lbe1

source_name: Mouse thyroid, 1.7 kBq, 6 h

value: 1.7 kBq

value: 6 h


title: thyroid C-3.a1.lbe1

source_name: Mouse thyroid, 1.7 kBq, 1 h


title: thyroid K-2.a1.lbe1

source_name: Mouse thyroid, 7.5 kBq, 6 h

value: 7.5 kBq


title: thyroid A-3.a1.lbe1

source_name: Mouse thyroid, 1.7 kBq, 168 h


title: Microglia_Ab_WT_6


title: Microglia_Ab_EP2_2


title: Microglia_Veh_WT_1


title: Microglia_Veh_EP2_1


title: Microglia_Ab_WT_1


title: thyroid F-3.a1.lbe1


title: Microglia_Ab_EP2_3


title: thyroid E-2.a1.lbe1


title: thyroid G-3.a1.lbe1


title: thyroid G-2.a1.lbe1


title: thyroid C-2.a1.lbe1


title: thyroid A-2.a1.lbe1


title: thyroid E-1.a1.lbe1


title: thyroid K-1.a1.lbe1


title: thyroid G-1.a1.lbe1


title: thyroid A-1.a1.lbe1


title: PB-Cre Ptenlox/lox p53lox/lox 6mo (pp_222)

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description: Gene expression data from established prostate cancer

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX mouse ref8 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using Illumina iScanner

data_processing: The data were analyzed with GenomeStudio using Illumina default analysis settings. No normalization and background correction are performed first, then quantile normalization and background correction are done.

source_name: PB-Cre Ptenlox/lox p53lox/lox (129/Bl6)

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

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

treatment_protocol: no treatment

value: prostate cancer

tag: gem model of prostate cancer

tag: time


title: PB-Cre Ptenlox/lox p53lox/lox 6mo (pp_333)


title: thyroid C-1.a1.lbe1


title: PB-Cre Ptenlox/lox p53lox/lox 6mo (pp_459)


title: thyroid D-1.a1.lbe1


title: PB-Cre Ptenlox/lox p53lox/lox 6mo (pp_460)


title: PB-Cre Ptenlox/lox p53lox/lox 6mo (pp_439)


title: PB-Cre Ptenlox/lox p53lox/lox 6mo (p_B357)


title: PB-Cre Ptenlox/lox p53lox/lox 6mo (pp_275)


title: thyroid B-2.a1.lbe1


title: thyroid F-1.a1.lbe1


title: thyroid B-1.a1.lbe1


title: PB-Cre Ptenlox/lox p53lox/lox 6mo (pp_258)


title: PB-Cre Ptenlox/lox 12 mo (p_23)

source_name: PB-Cre Ptenlox/lox (129/Bl6)

value: Pten-/-


title: PB-Cre Ptenlox/lox p53lox/lox 6mo (pp_336)


title: PB-Cre Ptenlox/lox p53lox/lox 6mo (p_B306)


title: PB-Cre Ptenlox/lox p53lox/lox 6mo (pp_463)


title: PB-Cre Ptenlox/lox p53lox/lox 6mo (pp_152)


title: PB-Cre Ptenlox/lox 12 mo (p_192)


title: thyroid D-2.a1.lbe1


title: PB-MYC prostate 18 mo (M_1055)

source_name: PB-MYC (FVB)

value: FVB

value: PB-MYC


title: PB-Cre Ptenlox/lox 12 mo (p_22)


title: PB-Cre Ptenlox/lox 12 mo (p_21)


title: PB-Cre Ptenlox/lox p53lox/lox 6mo (p_B339)


title: PB-MYC prostate 18 mo (M1049)


title: PB-MYC prostate 18 mo (M_1049D)


title: PB-MYC prostate 18 mo (M_25)


title: PB-MYC prostate 18 mo (M_1053)


title: PB-Cre Ptenlox/lox 12 mo (p_24)


title: PB-Cre Ptenlox/lox p53lox/lox 6mo (p_B383)


title: Penile Cancer E25 Barretos Hospital

city: Sao Paulo

first: Fabio

middle: Albuquerque

last: Marchi

address: Av Dr Arnaldo

department: CTO

country: Brazil

institute: ICESP

description: Tumor sample Cy3-labeled mixed with reference sample Cy5-labeled

hyb_protocol: The labeling efficiency of the samples was obtained based on the ratio pmol/uL concentration of dye in mg/uL. The reference and test samples with similar efficiencies were combined. Human Cot DNA, 2X and 10X Blocking Agent Hi-RPM Hybridization Solution were added to each reaction, it was denatured at 95°C for 3 min and incubated at 37°C for 30min. The samples were applied onto the 4x44 k (Agilent) slides and kept at 65°C at 20rpm for 24 hours.

scan_protocol: The array images were acquired with a DNA microarray scanner using SureScan High-Resolution Technology and the Scan Control (version 8.1) software program (Agilent Technologies, CA, USA). Images were quantified using Agilent Feature Extraction Software (version v.10.1.1.1).

data_processing: The data were analyzed using the Nexus Copy Number (version 6.0, Biodiscovery Inc., CA, USA) software program.

source_name: penile squamous cell carcinoma sample

label_protocol: Tumor and reference samples (500ng) were differentially labeled using the Genomic DNA Enzymatic Labeling Kit (Agilent Technologies, Santa Clara, CA, USA). Tumor were labeled using Cy3 and references were labeled by Cy5.

extract_protocol: Genomic DNA from 38 PC samples was isolated by the standard phenol/chloroform-based method.

tag: hospital

value: Barretos

value: carcinoma

value: male

source_name: reference commercial genomic DNA (Promega)

tag: sample type

value: reference


title: Penile Cancer E26 Barretos Hospital


title: Penile Cancer E24 Barretos Hospital


title: Microglia_Ab_WT_3

value: I.C.V. Aβ42 fibrillar 48h prior to cell isolation

value: CD11b-Cre ; EP2+/+

value: 8 month-old


title: Penile Cancer E23 Barretos Hospital


title: NF1_T_261

city: St Louis

first: Joshua

last: Rubin

state: MO

address: 660 S. Euclid Ave.

department: Pediatrics

institute: Washington University School of Medicine

description: some of the control samples are duplicated

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: Standard Affymetrix procedures using high-resolution microarray scanner

data_processing: The Birdseed-v2 was used to make initial genotype calls. Samples with a genotyping call rate <95% and contrast QC<0.4 according to the Affymetrix genotyping console analysis were removed and genotypes were regenerated using the remaining samples.  PLINK was used for SNP QC to exclude those failing Hardy-Weinberg test (P≤1e-06) or missingness test (P<0.1) or with a MAF <0.05.

source_name: NF1 patients

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was extracted from blood using Qiagen DNA Blood mini-kit (Valencia, CA) and from saliva using DNA Genotek Oragene DNA kits (Kanata, ON, CA) according to the manufacturers’ instructions.

tag: cohort

tag: biospecimen

value: saliva

tag: sample source

value: WU

tag: tumor

value: T


title: thyroid F-2.a1.lbe1

value: Balb/c

tag: tissue

value: thyroid

value: 100 kBq

value: 1 h


title: NF1_T_258


title: Penile Cancer E21 Barretos Hospital


title: NF1_T_254


title: NF1_T_256


title: NF1_T_255


title: NF1_T_260


title: NF1_T_253


title: NF1_T_249


title: NF1_NT_263

value: NT


title: NF1_NT_262


title: NF1_NT_264


title: Penile Cancer E22 Barretos Hospital


title: Penile Cancer E18 Barretos Hospital


title: NF1_T_245


title: Penile Cancer E17 Barretos Hospital


title: Penile Cancer E19 Barretos Hospital


title: NF1_NT_252


title: NF1_T_259


title: NF1_T_248


title: NF1_T_251


title: NF1_T_246


title: Penile Cancer E15 Barretos Hospital


title: NF1_T_250


title: NF1_T_247


title: NF1_T_257


title: Penile Cancer E12 Barretos Hospital


title: Penile Cancer E9 Barretos Hospital


title: NF1_T_243


title: NF1_T_242


title: NF1_T_244


title: Penile Cancer E8 Barretos Hospital


title: Penile Cancer E11 Barretos Hospital


title: Penile Cancer E4 Barretos Hospital


title: NF1_NT_265


title: Penile Cancer E1 Barretos Hospital


title: Penile Cancer E2 Barretos Hospital


title: Penile Cancer E16 Barretos Hospital


title: Penile Cancer E6 Barretos Hospital


title: NF1_T_240


title: NF1_NT_241


title: Penile Cancer L2_AC Camargo Hospital

value: Carmargo


title: Penile Cancer E10 Barretos Hospital


title: Penile Cancer L3_AC Camargo Hospital


title: Penile Cancer L1_AC Camargo Hospital


title: Penile Cancer 1411_AC Camargo Hospital


title: Penile Cancer 1388_AC Camargo Hospital


title: Penile Cancer A29_AC Camargo Hospital


title: NF1_T_239


title: NF1_T_235


title: Penile Cancer 1389_AC Camargo Hospital


title: Penile Cancer A19_AC Camargo Hospital


title: Penile Cancer 1410_AC Camargo Hospital


title: NF1_T_234


title: Penile Cancer A26_AC Camargo Hospital


title: NF1_T_236


title: NF1_T_232


title: Penile Cancer A13_AC Camargo Hospital


title: NF1_T_233


title: NF1_T_237


title: Penile Cancer A17_AC Camargo Hospital


title: NF1_NT_231


title: NF1_T_238


title: NF1_NT_226


title: NF1_T_227


title: Penile Cancer A12_AC Camargo Hospital


title: NF1_T_230


title: Penile Cancer A10_AC Camargo Hospital


title: Penile Cancer A9_AC Camargo Hospital


title: NF1_T_225


title: NF1_T_229


title: CHOP DLBCL 142

city: Hørsholm

first: Thomas

last: Jensen

address: Venlighedsvej 1

department: lab

country: Denmark

institute: MPI

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA normalised

source_name: Biopsy FFPE

label_protocol: Flashtaq HSR biotin

extract_protocol: Ambion Recoverall

treatment_protocol: no treatment prior to extraction

tag: disease state

value: DLBCL

value: F

tag: age (y)

tag: ldh increased

value: ja

tag: ipi

tag: treatment

value: CHOP

tag: kaplan meier days

tag: dead (1=yes)

tag: relapse (1=yes)

value: lymph node biopsy


title: Penile Cancer A7_AC Camargo Hospital

value: carcinoma

tag: gender

value: male

value: reference


title: Penile Cancer A6_AC Camargo Hospital


title: Penile Cancer A5_AC Camargo Hospital


title: NF1_NT_222

value: saliva


title: CHOP DLBCL 141

value: M

value: nej


title: NF1_T_219

value: WU

value: T


title: NF1_NT_220


title: CHOP DLBCL 140


title: NF1_NT_223


title: NF1_T_228


title: NF1_NT_221


title: NF1_NT_224


title: CHOP DLBCL 138


title: NF1_NT_217


title: CHOP DLBCL 137


title: CHOP DLBCL 136


title: CHOP DLBCL 135


title: CHOEP DLBCL 133

value: CHOEP


title: NF1_NT_214


title: CHOEP DLBCL 134


title: DRYNMC_rep_4

city: Sutton Bonington

first: Simon

middle: Peter

last: Pearce

state: Leicestershire

address: Sutton Bonington Campus

department: Plant and Crop Sciences

country: United Kingdom

institute: University of Nottingham

hyb_protocol: Fragmented cRNA at a final concentration of 0.0375ng/μl was used for hybridization. The GeneChip (#900720) HWS Kit was used for hybridization, washing and staining.

scan_protocol: The scanning was performed using the Affymetrix 3000G scanner

data_processing: The data was analysed using RMA in the affy Bioconductor package in R, using the v14.0.0 Arabidopsis CustomCDF from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF along with a novel cross-species masking technique involving taking an ANOVA for each probe to determine whether it is registering signal or noise. See paper for details.

organism: Lepidium sativum

source_name: Dry cotyledon and non micropylar endosperm

label_protocol: The Affymetrix 3' IVT-Express Labeling Kit was used to synthesize Biotin-labeled cRNA. For each sample 100 ng was used as input.

growth_protocol: Seeds of Lepidium sativum FR14 (Quedlinburger Saatgut GmbH) were sown on filter disks with 6ml of sterile, pure water and incubated at 24°C with continuous light

extract_protocol: Lepidium seed tissues (100 radicles or 100 micropylar endosperms,  100 non-micropylar endosperms,  50 cotyledons) were homogenized twice in liquid nitrogen with the precellys homogenisator at 6100 rpm (peqlab, Erlangen), thawed in 1 ml CTAB-buffer (2% [w/v] hexadecyl trimethyl-ammonium bromide (CTAB); 2% [w/v] polyvinylpyrrolidone PVP (MW=40000/K30); 100 mM Tris-HCl, pH 8.0; 25 mM EDTA, pH 8.0; 2 M NaCl; 2% [v/v] ß-mercaptoethanol) homogenized again and then incubated at 65°C for 15 min. After two extraction steps with 1 ml chloroform:isoamylalcohol (24:1 [v/v]) the volume of the hydrophilic phase was determined and ¼ of that volume 10 M LiCl was added. The RNA was precipitated at 4°C overnight. After centrifugation at 13.000 rpm and 4°C, the pellet was resuspended in 600 μl SSTE-buffer (1 M NaCl; 0.5% [w/v]sodium dodecyl sulfate (SDS); 10 mM Tris-HCl, pH 8.0; 1 mM EDTA) and two more chloroform extractions were performed in PhaseLock vials (5prime, Hamburg). The RNA in the hydrophilic phase was precipitated with Na-Acetate/Ethanol at -20°C, the pellet washed with Ethanol, air-dried and resuspended in RNAse-free water. An RNeasy column clean-up was performed according to the manufacturer’s instructions to remove remaining impurities (Qiagen, Hilden). The optional DNAse treatment was performed on the column according to manufacturer’s instructions.

treatment_protocol: At ten stages seeds were disected using a scalpel and a dissecting needle into the above specified compartments

value: Seed


title: NF1_NT_213

value: NT


title: CHOP DLBCL 132


title: NF1_NT_216


title: NF1_NT_215


title: CHOP DLBCL 131


title: NF1_NT_218


title: DRYNMC_rep_3


title: NF1_NT_212


title: NF1_NT_210


title: DRYNMC_rep_1


title: French_progeny_male (IDR97M)

city: Nantes

first: Rossana

last: Sussarellu

address: Rue de l'Ile d'Yeu

department: Ressources Biologiques et Environnement

country: France

institute: Ifremer

hyb_protocol: Hybridization was performed using the Agilent Gene expression hybridization kit (5188-5242), with 1.65 μg of labeled RNA, randomly onto 48 different slides for 16 h at 65 °C

scan_protocol: Slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system at 5 μm resolution, using default parameters

data_processing: Features were extracted using the Agilent Feature Extraction software 6.1. Quantile normalization was performed on background-corrected features with the limma package. Filtering step was performed according to Agilent Feature Extraction software results on spot quality and spot intensity reliability. Missing values were imputed with Impute package.

organism: Magallana gigas

source_name: Gonads_French_progeny_male (IDR97M)

label_protocol: 200 ng of total RNA were indirectly labeled with Cy3 using the Low Input Quick Amp Labeling kit One-Color

growth_protocol: Standard hatchery conditions to induce gametogenesis

extract_protocol: For each progeny 100 oysters were randomly collected, and gonads were immediately dissected from each oyster and frozen in liquid nitrogen. Gonad tissues were crushed to a fine powder at -196°C with an oscillating mill mixer and stored in liquid nitrogen until RNA extraction and biochemical analyses. In 180 samples (60 per progeny) total RNA was isolated using 1.5 mL of Extract-all Reagent per 50 mg of gonad powder.

treatment_protocol: Gonadal maturation

tag: population

value: French

value: Gonads

tag: age


title: DRYRC_rep_4

source_name: Dry radicle and cap


title: CHOEP DLBCL 130

value: DLBCL

value: F


title: CHOP DLBCL 129

value: CHOP


title: DRYRC_rep_3


title: NF1_NT_209


title: CHOP DLBCL 127

value: lymph node biopsy


title: NF1_NT_211


title: French_progeny_male (IDR84M)

source_name: Gonads_French_progeny_male (IDR84M)


title: DRYRC_rep_2


title: CHOP DLBCL 128


title: NF1_T_206

value: blood

value: TOR


title: French_progeny_male (IDR88M)

source_name: Gonads_French_progeny_male (IDR88M)

value: male


title: DRYRC_rep_1


title: CHOP DLBCL 126


title: NF1_NT_202


title: NF1_NT_205


title: NF1_T_204


title: NF1_NT_208

value: saliva


title: NF1_T_203


title: NF1_T_207


title: NF1_T_201


title: NF1_NT_199


title: CHOP DLBCL 124

value: ja


title: DRY_rep_2

source_name: Whole dry seeds


title: NF1_NT_200


title: DRY_rep_3


title: French_progeny_male (IDR87M)

source_name: Gonads_French_progeny_male (IDR87M)


title: French_progeny_male (IDR83M)

source_name: Gonads_French_progeny_male (IDR83M)


title: CHOP DLBCL 125

value: nej


title: French_progeny_male (IDR78M)

source_name: Gonads_French_progeny_male (IDR78M)


title: NF1_T_198


title: CHOP DLBCL 123

value: M


title: LIF+ e4C 1

city: Maebashi showa-machi

first: Kenji

last: Ito

department: Graduate school pf medicine

institute: Gunma university

description: DNA regions associate with Gfap promoter region

hyb_protocol: The labeled DNA was precipitated with 1 volume isopropanol. Hybridization mix including 15ug labeled DNA was prepared using Nimblegen hybridization kit (cat.#05583683001). Arrays were hybridized in Nimblegen hybridization system 4 station for 16-18 h at 42ºC, and then washed in 1XWash solution I, II and III (cat.#5584507001).Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/downloads/support/06584098001_NG_Epigenetics_UGuide_v1p0.pdf)

scan_protocol: Arrays were scanned on a Nimblegen MS200 scanner per manufacturer's protocol (http://www.nimblegen.com/downloads/support/scanner_ms200_manual_v1p0.pdf).

data_processing: Data were extracted and processed using Nimblescan software (http://www.nimblegen.com/downloads/support/NimbleScan_v2p6_UsersGuide.pdf).

source_name: LIF+ replicate 1

label_protocol: 1 µg ChIP and input DNA was directly labeled by Klenow random priming with Cy5 and Cy3 nonamers with Nimblegen Dual-color DNA labeling kit (cat.# 06370250001) following manufacturer's user's guide Chip-chip arrays v6.1.

growth_protocol: NPCs isolated from E14.5 mouse telencephalon were cultured and replated on day 4.

extract_protocol: Cells were exposed to 2% formaldehyde for 10 min. After being quenched with 125 mM glycine, cells were collected. After being homogenized, the cells were lysed in 2 ml lysis buffer (10 mM Tris-HCl, ph 7.5, 10 mM NaCl, 0.2% NP-40, 1x protease inhibitor cocktail [Nacalai Tesque]) for 1.5 h at 4°C and centrifuged to remove the supernatant. Extracted nuclei were treated with 0.1 N HCl for 10 min and neutralized with 0.1 N NaOH, and then incubated with 850 U BglⅡ (New England Biolabs) overnight at 37°C. After being inactivated in 1.6% SDS at 65°C for 20 min, samples were diluted in 4.8 ml of ligation buffer (66 mM Tris-HCl, ph 7.5, 6.6 mM MgCl2, 10 mM DTT, 0.1 mM ATP) and 2400 U T4 ligase (New England Biolabs) and incubated at 16°C for 4 hr. Ligated chromatin was digested by proteinase K (100 ng/mL; Merck).Genomic DNA was isolated  by phenol extraction and ethanol precipitation.

treatment_protocol: LIF+ were collected after an additional 4 days of culture with LIF.

tag: e4c restriction enzyme (6base)

value: BglⅡ

tag: e4c restriction enzyme (4base)

value: NlaⅢ

tag: e4c bait

value: Gfap promoter

tag: strain

value: ICR

growth_protocol: Genomic DNA derived from ICR mice tail

treatment_protocol: genomic DNA was treated with BglⅡ and NlaⅢ

tag: sample type

value: input


title: CHOP DLBCL 121

tag: tissue


title: DRY_rep_4

value: Seed


title: French_progeny_male (IDR80M)

source_name: Gonads_French_progeny_male (IDR80M)

value: French

value: Gonads


title: CHOP DLBCL 119

tag: disease state

value: DLBCL

value: CHOP


title: French_progeny_male (IDR6M)

source_name: Gonads_French_progeny_male (IDR6M)


title: NME_13h_rep_4

source_name: Excised Non-micropylar endosperm, 13h after sowing

value: Endosperm


title: NF1_NT_195

tag: cohort

tag: biospecimen

tag: sample source

value: NYU

tag: tumor

value: NT


title: French_progeny_male (IDR7M)

source_name: Gonads_French_progeny_male (IDR7M)

value: male


title: LIF- e4C 1

source_name: LIF- replicate 1

treatment_protocol: LIF- were collected after an additional 4 days of culture without LIF.


title: NF1_T_197

source_name: NF1 patients

value: saliva

value: T


title: CHOP DLBCL 118

source_name: Biopsy FFPE

value: F

tag: age (y)

tag: ldh increased

value: ja

tag: ipi

tag: treatment

tag: kaplan meier days

value: lymph node biopsy


title: NME_13h_rep_2


title: LIF- e4C 2

source_name: LIF- replicate 2

value: BglⅡ

value: NlaⅢ

value: Gfap promoter


title: NF1_NT_196


title: NF1_T_194


title: NME_13h_rep_3


title: French_progeny_male (IDR68M)

source_name: Gonads_French_progeny_male (IDR68M)

tag: population

tag: gender

tag: age


title: CHOP DLBCL 116

value: nej

tag: dead (1=yes)

tag: relapse (1=yes)


title: DRY_rep_1

value: Seed


title: LIF+ e4C 2

source_name: LIF+ replicate 2

tag: e4c restriction enzyme (6base)

tag: e4c restriction enzyme (4base)

tag: e4c bait

tag: strain

value: ICR

tag: sample type

value: input


title: NME_13h_rep_1

tag: tissue


title: CHOP DLBCL 111

tag: disease state

value: DLBCL

value: M

value: CHOP


title: French_progeny_male (IDR66M)

source_name: Gonads_French_progeny_male (IDR66M)

value: French

value: Gonads


title: NF1_T_193

tag: cohort

tag: biospecimen

value: saliva

tag: sample source

value: NYU

tag: tumor


title: RAD_16h_rup_rep_4

source_name: Excised Radicle and lower hypocoytl, 16h after sowing, endosperm ruptured seeds

value: Embryo


title: RAD_16h_rup_rep_3


title: French_progeny_male (IDR57M)

source_name: Gonads_French_progeny_male (IDR57M)

value: male


title: CHOEP DLBCL 110

tag: age (y)

tag: ldh increased

value: ja

tag: ipi

tag: treatment

value: CHOEP

tag: kaplan meier days

value: lymph node biopsy


title: French_progeny_male (IDR61M)

source_name: Gonads_French_progeny_male (IDR61M)

tag: population

tag: gender

tag: age


title: NPCs e4C 2

source_name: NPCs replicate 2

treatment_protocol: NPCs were cultured after an additional 1 day of culture without LIF.

tag: e4c restriction enzyme (6base)

value: BglⅡ

tag: e4c restriction enzyme (4base)

value: NlaⅢ

tag: e4c bait

value: Gfap promoter


title: CHOP DLBCL 108

value: F

tag: dead (1=yes)

tag: relapse (1=yes)

tag: tissue


title: CHOEP DLBCL 107

tag: disease state


title: NPCs e4C 1

source_name: NPCs replicate 1

tag: strain

value: ICR

tag: sample type

value: input


title: French_progeny_male (IDR69M)

source_name: Gonads_French_progeny_male (IDR69M)


title: NF1_NT_191

tag: cohort

tag: biospecimen

tag: sample source

tag: tumor

value: NT


title: CHOP DLBCL 106

value: DLBCL

value: M

tag: age (y)

tag: ldh increased

value: nej

tag: ipi

tag: treatment

value: CHOP

tag: kaplan meier days


title: RAD_16h_rup_rep_1


title: RAD_16h_rup_rep_2


title: CHOP DLBCL 105

tag: gender


title: CAP_16h_rup_rep_4

source_name: Excised Micropylar Endosperms, 16h after sowing, endosperm ruptured seeds

value: Endosperm


title: NF1_NT_192

value: saliva

value: NYU


title: CHOP DLBCL 103

value: ja


title: NF1_NT_190


title: CAP_16h_rup_rep_2


title: CAP_16h_rup_rep_3


title: French_progeny_male (IDR44M)

source_name: Gonads_French_progeny_male (IDR44M)

tag: population

value: French

value: Gonads

value: male

tag: age


title: French_progeny_male (IDR39M)

source_name: Gonads_French_progeny_male (IDR39M)


title: French_progeny_male (IDR46M)

source_name: Gonads_French_progeny_male (IDR46M)


title: French_progeny_male (IDR41M)

source_name: Gonads_French_progeny_male (IDR41M)


title: CHOP DLBCL 101

tag: dead (1=yes)

tag: relapse (1=yes)

value: lymph node biopsy


title: CAP_16h_rup_rep_1

tag: tissue


title: NF1_T_188

source_name: NF1 patients

value: T


title: French_progeny_male (IDR36M)

source_name: Gonads_French_progeny_male (IDR36M)


title: CHOEP DLBCL 100

source_name: Biopsy FFPE

tag: disease state

value: CHOEP


title: RAD_16h_nonrup_rep_4

source_name: Excised Radicle and lower hypocoytl, 16h after sowing, non endosperm ruptured seeds

value: Embryo


title: French_progeny_male (IDR31M)

source_name: Gonads_French_progeny_male (IDR31M)


title: NF1_T_189


title: NF1_NT_186


title: French_progeny_male (IDR35M)

source_name: Gonads_French_progeny_male (IDR35M)


title: NF1_T_185


title: CHOEP DLBCL 98


title: CHOP DLBCL 99


title: CHOEP DLBCL 102

value: F


title: RAD_16h_nonrup_rep_2


title: RAD_16h_nonrup_rep_3


title: CHOP DLBCL 97


title: RAD_16h_nonrup_rep_1


title: French_progeny_male (IDR24M)

source_name: Gonads_French_progeny_male (IDR24M)


title: French_progeny_male (IDR28M)

source_name: Gonads_French_progeny_male (IDR28M)


title: NF1_NT_187

value: NT


title: French_progeny_male (IDR52M)

source_name: Gonads_French_progeny_male (IDR52M)


title: French_progeny_male (IDR20M)

source_name: Gonads_French_progeny_male (IDR20M)


title: NF1_T_183

value: blood

value: UT


title: CHOEP DLBCL 95

value: DLBCL

value: M

value: nej


title: CHOEP DLBCL 94


title: CHOP DLBCL 93

value: CHOP


title: NF1_T_181


title: CAP_16h_nonrup_rep_2

source_name: Excised Micropylar Endosperms, 16h after sowing, non endosperm ruptured seeds

value: Endosperm


title: NF1_T_182


title: NF1_T_184


title: CHOP DLBCL 90

value: ja


title: CAP_16h_nonrup_rep_3


title: French_progeny_male (IDR1M)

source_name: Gonads_French_progeny_male (IDR1M)

value: French


title: CHOP DLBCL 89


title: COT_13h_rep_4

source_name: Excised Cotyledons, 13h after sowing


title: CAP_16h_nonrup_rep_1


title: French_progeny_male (IDR13M)

source_name: Gonads_French_progeny_male (IDR13M)

value: Gonads


title: NF1_T_177


title: French_progeny_male (IDR47M)

source_name: Gonads_French_progeny_male (IDR47M)

value: male


title: French_progeny_male (IDR18M)

source_name: Gonads_French_progeny_male (IDR18M)


title: French_progeny_male (IDR14M)

source_name: Gonads_French_progeny_male (IDR14M)


title: COT_13h_rep_2


title: CHOP DLBCL 87

value: lymph node biopsy


title: NF1_NT_179

source_name: NF1 patients


title: CHOP DLBCL 88


title: NF1_NT_180


title: COT_13h_rep_3


title: NF1_T_178

value: T


title: NF1_NT_176


title: COT_13h_rep_1


title: NF1_NT_175


title: French_progeny_female (IDR94F)

source_name: Gonads_French_progeny_female (IDR94F)

value: female


title: French_progeny_female (IDR98F)

source_name: Gonads_French_progeny_female (IDR98F)


title: CHOP DLBCL 82

source_name: Biopsy FFPE


title: French_progeny_female (IDR99F)

source_name: Gonads_French_progeny_female (IDR99F)


title: RAD_13h_rep_4

source_name: Excised Radicle and lower hypocoytl, 13h after sowing

value: Embryo


title: NF1_NT_173


title: NF1_NT_174


title: RAD_13h_rep_3


title: CAP_16h_nonrup_rep_4


title: French_progeny_female (IDR91F)

source_name: Gonads_French_progeny_female (IDR91F)


title: CHOP DLBCL 81


title: CHOP DLBCL 78


title: CHOP DLBCL 76

value: F


title: French_progeny_female (IDR8F)

source_name: Gonads_French_progeny_female (IDR8F)


title: CHOP DLBCL 75


title: RAD_13h_rep_2


title: RAD_13h_rep_1


title: CAP_13h_rep_4

source_name: Excised Micropylar Endosperms, 13h after sowing


title: French_progeny_female (IDR85F)

source_name: Gonads_French_progeny_female (IDR85F)


title: CAP_13h_rep_3


title: NF1_T_170


title: CHOP DLBCL 74


title: French_progeny_female (IDR82F)

source_name: Gonads_French_progeny_female (IDR82F)


title: NF1_NT_169

value: NT


title: NF1_NT_168

value: blood


title: CHOP DLBCL 73


title: NF1_T_171

value: UT


title: CAP_13h_rep_2


title: French_progeny_female (IDR81F)

source_name: Gonads_French_progeny_female (IDR81F)


title: French_progeny_female (IDR76F)

source_name: Gonads_French_progeny_female (IDR76F)


title: CHOP DLBCL 83

value: DLBCL


title: CHOP DLBCL 72


title: CAP_13h_rep_1


title: RAD_10h_rep_4

source_name: Excised Radicle and lower hypocoytl, 10h after sowing


title: CHOP DLBCL 71


title: French_progeny_female (IDR70F)

source_name: Gonads_French_progeny_female (IDR70F)


title: French_progeny_female (IDR75F)

source_name: Gonads_French_progeny_female (IDR75F)


title: NF1_T_167


title: French_progeny_female (IDR72F)

source_name: Gonads_French_progeny_female (IDR72F)


title: NF1_NT_172

source_name: NF1 patients


title: CHOP DLBCL 69

value: M


title: CHOP DLBCL 68


title: CHOP DLBCL 66


title: RAD_10h_rep_2


title: RAD_10h_rep_1


title: NF1_NT_166


title: CAP_10h_rep_4

source_name: Excised Micropylar Endosperms, 10h after sowing


title: French_progeny_female (IDR64F)

source_name: Gonads_French_progeny_female (IDR64F)


title: French_progeny_female (IDR65F)

source_name: Gonads_French_progeny_female (IDR65F)


title: RAD_10h_rep_3


title: CHOP DLBCL 65

source_name: Biopsy FFPE


title: NF1_NT_164


title: CHOP DLBCL 64


title: NF1_NT_165


title: NF1_T_163


title: French_progeny_female (IDR62F)

source_name: Gonads_French_progeny_female (IDR62F)


title: CAP_10h_rep_3


title: CAP_10h_rep_1


title: NF1_NT_159


title: NF1_NT_161


title: NF1_T_162


title: CHOP DLBCL 60

value: nej


title: RAD_7h_rup_rep_4

source_name: Excised Radicle and lower hypocoytl, 7h after sowing, testa ruptured seeds


title: CHOP DLBCL 61

value: CHOP


title: CAP_10h_rep_2

value: Endosperm


title: French_progeny_female (IDR63F)

source_name: Gonads_French_progeny_female (IDR63F)


title: CHOP DLBCL 57

value: ja


title: French_progeny_female (IDR43F)

source_name: Gonads_French_progeny_female (IDR43F)

value: French


title: CHOP DLBCL 59


title: NF1_T_160


title: French_progeny_female (IDR4F)

source_name: Gonads_French_progeny_female (IDR4F)

value: Gonads


title: RAD_7h_rup_rep_3


title: French_progeny_female (IDR32F)

source_name: Gonads_French_progeny_female (IDR32F)


title: RAD_7h_rup_rep_2


title: French_progeny_female (IDR37F)

source_name: Gonads_French_progeny_female (IDR37F)


title: CHOP DLBCL 55


title: CHOP DLBCL 54


title: NF1_T_155


title: CHOP DLBCL 56


title: NF1_NT_158


title: RAD_7h_rup_rep_1


title: NF1_NT_156


title: French_progeny_female (IDR26F)

source_name: Gonads_French_progeny_female (IDR26F)


title: French_progeny_female (IDR30F)

source_name: Gonads_French_progeny_female (IDR30F)


title: NF1_T_153


title: CAP_7h_rup_rep_4

source_name: Excised Micropylar Endosperms, 7h after sowing, testa ruptured seeds


title: CHOP DLBCL 53


title: French_progeny_female (IDR27F)

source_name: Gonads_French_progeny_female (IDR27F)


title: NF1_T_157


title: CAP_7h_rup_rep_2


title: NF1_NT_154


title: CHOP DLBCL 50


title: French_progeny_female (IDR23F)

source_name: Gonads_French_progeny_female (IDR23F)


title: NF1_NT_151

source_name: NF1 patients


title: NF1_NT_150


title: CAP_7h_rup_rep_1


title: CHOP DLBCL 52


title: French_progeny_female (IDR21F)

source_name: Gonads_French_progeny_female (IDR21F)


title: NF1_NT_148


title: NF1_NT_149


title: NF1_NT_152


title: French_progeny_female (IDR17F)

source_name: Gonads_French_progeny_female (IDR17F)


title: French_progeny_female (IDR12F)

source_name: Gonads_French_progeny_female (IDR12F)


title: NME_7h_nonrup_rep_4

source_name: Excised Non-micropylar endosperm, 7h after sowing


title: CHOEP DLBCL 48

source_name: Biopsy FFPE

value: CHOEP


title: NME_7h_nonrup_rep_3


title: CHOEP DLBCL 49

value: lymph node biopsy


title: French_progeny_female (IDR3F)

source_name: Gonads_French_progeny_female (IDR3F)


title: NME_7h_nonrup_rep_2


title: French_progeny_female (IDR15F)

source_name: Gonads_French_progeny_female (IDR15F)


title: CHOEP DLBCL 46


title: CAP_7h_rup_rep_3


title: CHOEP DLBCL 47


title: CHOEP DLBCL 45


title: CHOP DLBCL 44


title: CHOP DLBCL 43


title: NME_7h_nonrup_rep_1


title: COT_7h_nonrup_rep_4

source_name: Excised Cotyledons, 7h after sowing, non testa ruptured seeds


title: NF1_NT_145


title: COT_7h_nonrup_rep_3


title: Hybrid_progeny_male (HYB89M)

source_name: Gonads_Hybrid_progeny_male (HYB89M)

value: Hybrid

value: male


title: NF1_NT_147


title: Hybrid_progeny_male (HYB92M)

source_name: Gonads_Hybrid_progeny_male (HYB92M)


title: NF1_NT_144


title: RAD_7h_nonrup_rep_4

source_name: Excised Radicle and lower hypocoytl, 7h after sowing, non testa ruptured seeds

value: Embryo


title: CHOP DLBCL 42

value: F


title: COT_7h_nonrup_rep_1


title: Hybrid_progeny_male (HYB8M)

source_name: Gonads_Hybrid_progeny_male (HYB8M)


title: RAD_7h_nonrup_rep_3


title: COT_7h_nonrup_rep_2


title: CHOP DLBCL 41


title: Hybrid_progeny_male (HYB7M)

source_name: Gonads_Hybrid_progeny_male (HYB7M)


title: CHOP DLBCL 40


title: Hybrid_progeny_male (HYB80M)

source_name: Gonads_Hybrid_progeny_male (HYB80M)


title: NF1_T_143

value: T


title: RAD_7h_nonrup_rep_2


title: Hybrid_progeny_male (HYB77M)

source_name: Gonads_Hybrid_progeny_male (HYB77M)


title: Hybrid_progeny_male (HYB78M)

source_name: Gonads_Hybrid_progeny_male (HYB78M)


title: NF1_NT_141

source_name: NF1 patients

value: blood

value: NT


title: CHOP DLBCL 39

value: DLBCL


title: NF1_T_142

value: UT


title: RAD_7h_nonrup_rep_1


title: CAP_7h_nonrup_rep_4

source_name: Excised Micropylar Endosperms, 7h after sowing, non testa ruptured seeds


title: Hybrid_progeny_male (HYB76M)

source_name: Gonads_Hybrid_progeny_male (HYB76M)


title: Hybrid_progeny_male (HYB75M)

source_name: Gonads_Hybrid_progeny_male (HYB75M)


title: CHOP DLBCL 38


title: CHOP DLBCL 37

value: M


title: NF1_NT_140


title: CHOP DLBCL 35

value: nej

value: CHOP


title: NF1_NT_146


title: CAP_7h_nonrup_rep_2

value: Endosperm


title: Hybrid_progeny_male (HYB61M)

source_name: Gonads_Hybrid_progeny_male (HYB61M)


title: CHOP DLBCL 34

source_name: Biopsy FFPE

value: ja


title: Hybrid_progeny_male (HYB60M)

source_name: Gonads_Hybrid_progeny_male (HYB60M)

value: Gonads


title: NF1_T_139


title: Hybrid_progeny_male (HYB57M)

source_name: Gonads_Hybrid_progeny_male (HYB57M)


title: NF1_NT_137


title: RAD_5h_rep_4

source_name: Excised Radicle and lower hypocoytl, 5h after sowing


title: Hybrid_progeny_male (HYB54M)

source_name: Gonads_Hybrid_progeny_male (HYB54M)


title: Hybrid_progeny_male (HYB81M)

source_name: Gonads_Hybrid_progeny_male (HYB81M)


title: NF1_T_136


title: CAP_7h_nonrup_rep_3


title: NF1_NT_135


title: CHOP DLBCL 33


title: NF1_NT_134


title: RAD_5h_rep_3


title: NF1_NT_133


title: CHOP DLBCL 36


title: Hybrid_progeny_male (HYB51M)

source_name: Gonads_Hybrid_progeny_male (HYB51M)


title: CAP_7h_nonrup_rep_1


title: CHOEP DLBCL 31

value: CHOEP


title: CHOEP DLBCL 32

value: lymph node biopsy


title: NF1_T_132


title: Hybrid_progeny_male (HYB4M)

source_name: Gonads_Hybrid_progeny_male (HYB4M)

value: Hybrid


title: RAD_5h_rep_2


title: CHOEP DLBCL 30


title: Hybrid_progeny_male (HYB44M)

source_name: Gonads_Hybrid_progeny_male (HYB44M)

value: male


title: CHOP DLBCL 28


title: RAD_5h_rep_1

value: Embryo


title: CAP_5h_rep_4

source_name: Excised Micropylar Endosperms, 5h after sowing


title: NF1_T_128


title: CAP_5h_rep_3


title: CAP_5h_rep_2


title: CHOEP DLBCL 29

value: F


title: Hybrid_progeny_male (HYB43M)

source_name: Gonads_Hybrid_progeny_male (HYB43M)


title: NF1_NT_131


title: Hybrid_progeny_male (HYB49M)

source_name: Gonads_Hybrid_progeny_male (HYB49M)


title: NF1_NT_126

source_name: NF1 patients


title: Hybrid_progeny_male (HYB39M)

source_name: Gonads_Hybrid_progeny_male (HYB39M)


title: CHOP DLBCL 27


title: NF1_NT_138


title: CHOP DLBCL 26


title: NME_3h_rep_4

source_name: Excised Non-micropylar endosperm, 3h after sowing


title: CHOP DLBCL 25


title: Hybrid_progeny_male (HYB35M)

source_name: Gonads_Hybrid_progeny_male (HYB35M)


title: NF1_NT_129


title: NME_3h_rep_2


title: Hybrid_progeny_male (HYB34M)

source_name: Gonads_Hybrid_progeny_male (HYB34M)


title: NF1_NT_130


title: CAP_5h_rep_1


title: NME_3h_rep_3


title: CHOP DLBCL 24

source_name: Biopsy FFPE


title: NF1_T_127

value: T


title: CHOP DLBCL 22


title: NF1_NT_125

value: blood


title: Hybrid_progeny_male (HYB31M)

source_name: Gonads_Hybrid_progeny_male (HYB31M)


title: Hybrid_progeny_male (HYB21M)

source_name: Gonads_Hybrid_progeny_male (HYB21M)


title: Hybrid_progeny_male (HYB23M)

source_name: Gonads_Hybrid_progeny_male (HYB23M)


title: CHOP DLBCL 20


title: NF1_T_122


title: NF1_NT_123

value: NT


title: CHOP DLBCL 19

value: DLBCL


title: Hybrid_progeny_male (HYB20M)

source_name: Gonads_Hybrid_progeny_male (HYB20M)


title: COT_3h_rep_3

source_name: Excised Cotyledons, 3h after sowing


title: COT_3h_rep_2


title: COT_3h_rep_4


title: NF1_T_124

value: UT


title: NF1_NT_119


title: CHOP DLBCL 18

value: M


title: CHOP DLBCL 17

value: nej


title: Hybrid_progeny_male (HYB18M)

source_name: Gonads_Hybrid_progeny_male (HYB18M)


title: Hybrid_progeny_male (HYB13M)

source_name: Gonads_Hybrid_progeny_male (HYB13M)


title: Hybrid_progeny_male (HYB100M)

source_name: Gonads_Hybrid_progeny_male (HYB100M)


title: Hybrid_progeny_male (HYB11M)

source_name: Gonads_Hybrid_progeny_male (HYB11M)


title: COT_3h_rep_1


title: NF1_T_120


title: RAD_3h_rep_4

source_name: Excised Radicle and lower hypocoytl, 3h after sowing


title: NF1_T_121


title: Hybrid_progeny_female (HYB9F)

source_name: Gonads_Hybrid_progeny_female (HYB9F)

value: female


title: CHOP DLBCL 16

value: CHOP


title: CHOP DLBCL 15


title: NF1_CTRL_116

source_name: Control

value: CTRL


title: RAD_3h_rep_3


title: RAD_3h_rep_2


title: NF1_CTRL_118


title: RAD_3h_rep_1


title: CHOP DLBCL 14

value: ja


title: NF1_CTRL_117


title: CHOP DLBCL 13


title: CAP_3h_rep_4

source_name: Excised Micropylar Endosperms, 3h after sowing

value: Endosperm


title: CHOP DLBCL 21

value: lymph node biopsy


title: NF1_CTRL_115


title: Hybrid_progeny_female (HYB87F)

source_name: Gonads_Hybrid_progeny_female (HYB87F)

value: Hybrid

value: Gonads


title: Hybrid_progeny_female (HYB98F)

source_name: Gonads_Hybrid_progeny_female (HYB98F)


title: NME_3h_rep_1

source_name: Excised Non-micropylar endosperm, 3h after sowing


title: Hybrid_progeny_female (HYB96F)

source_name: Gonads_Hybrid_progeny_female (HYB96F)


title: CHOEP DLBCL 12

source_name: Biopsy FFPE

value: CHOEP


title: NF1_CTRL_114


title: CHOP DLBCL 9

value: F


title: CHOEP DLBCL 10


title: NF1_CTRL_113


title: CAP_3h_rep_1


title: Hybrid_progeny_female (HYB85F)

source_name: Gonads_Hybrid_progeny_female (HYB85F)


title: CAP_3h_rep_2


title: Hybrid_progeny_female (HYB74F)

source_name: Gonads_Hybrid_progeny_female (HYB74F)


title: CAP_3h_rep_3


title: Hybrid_progeny_female (HYB86F)

source_name: Gonads_Hybrid_progeny_female (HYB86F)


title: NF1_CTRL_110


title: NF1_CTRL_112


title: CHOP DLBCL 11


title: CHOP DLBCL 8


title: NF1_CTRL_111


title: CHOP DLBCL 7


title: RAD_1h_rep_4

source_name: Excised Radicle and lower hypocoytl, 1h after sowing

value: Embryo


title: RAD_1h_rep_3


title: Hybrid_progeny_female (HYB6F)

source_name: Gonads_Hybrid_progeny_female (HYB6F)


title: NF1_CTRL_108


title: Hybrid_progeny_female (HYB69F)

source_name: Gonads_Hybrid_progeny_female (HYB69F)


title: NF1_CTRL_109


title: Hybrid_progeny_female (HYB71F)

source_name: Gonads_Hybrid_progeny_female (HYB71F)


title: CHOP DLBCL 6


title: RAD_1h_rep_2


title: CHOP DLBCL 5


title: CHOP DLBCL 4


title: Hybrid_progeny_female (HYB67F)

source_name: Gonads_Hybrid_progeny_female (HYB67F)


title: CAP_1h_rep_4

source_name: Excised Micropylar Endosperms, 1h after sowing


title: NF1_CTRL_107


title: NF1_CTRL_105


title: CHOP DLBCL 3


title: NF1_CTRL_106


title: Hybrid_progeny_female (HYB66F)

source_name: Gonads_Hybrid_progeny_female (HYB66F)


title: RAD_1h_rep_1


title: Hybrid_progeny_female (HYB65F)

source_name: Gonads_Hybrid_progeny_female (HYB65F)


title: CHOP DLBCL 2


title: CHOP DLBCL 1


title: Hybrid_progeny_female (HYB64F)

source_name: Gonads_Hybrid_progeny_female (HYB64F)


title: CAP_1h_rep_3


title: NF1_CTRL_102

source_name: Control

value: blood


title: CAP_1h_rep_1


title: Hybrid_progeny_female (HYB63F)

source_name: Gonads_Hybrid_progeny_female (HYB63F)


title: Hybrid_progeny_female (HYB5F)

source_name: Gonads_Hybrid_progeny_female (HYB5F)


title: NF1_CTRL_101


title: NF1_CTRL_104


title: CAP_1h_rep_2


title: NF1_CTRL_100


title: ST486 EV IP Cy5

city: Groningen

first: Anke

last: van den Berg

address: Hanzeplein 1

department: Department of Pathology and Medical Biology

country: Netherlands

institute: University of Groningen, University Medical Center Groningen

description: Ago2-IP RNA

hyb_protocol: Equal amounts of Cy3 and Cy5-labeled cRNA were combined and hybridized following the Agilent's protocol

scan_protocol: Slides were scanned immediately after washing on the G25052C DNA microarray scanner (Agilent) following the manufacturer's protocol.

data_processing: Data were extracted using Feature Extraction software (v10.5.1.1, Agilent). Two-color microarrays were analyzed as one-color microarrays using GeneSpring GX, version 12.5 (Agilent). Data from TXT files were quantile normalized (threshold raw signal to 1.0) without baseline transformation. Probes detected in at least half of the samples (2 out of 4, Cy3 and Cy5 averaged), with consistent Cy3 and Cy5 signals in all samples were analyzed. Control probes were excluded.

source_name: ST486 cell line with empty MXW-PGK-IRES-GFP

label_protocol: ~ 100 ng of RNA was Cy3 or Cy5 labeled using two-color Quick Amp Labeling Kit  (Agilent) following the manufacturer's protocols. Dye incorporation and cRNA yield were checked with the NanoDrop 1000

growth_protocol: Cells were maintained in RPMI-1640 with 20%FCS, ultraglutamine (2mM), penicillin (100U/ml), streptomycin (0.1mg/ml) under standard culturing conditions.

extract_protocol: Immunoprecipitation was performed using Ago2 ab (Clone 2E12-1C9). RNA from IP fraction was extracted using the miRNeasy Mini Kit (Qiagen, Venlo, The Netherlands) following manufacturer's instructions.

tag: malignancy

value: Burkitt lymphoma

value: Cells were transduced with empty MXW-PGK-IRES-GFP vector and GFP+ cells were sorted


title: ST486 miR-155 IP Cy5

description: Ago2-IP RNA

source_name: ST486 cell line with ectopic miR-155

value: Cells were transduced with MXW-PGK-IRES-GFP vector containing miR-155 and GFP+ cells were sorted


title: ST486 miR-155 Total Cy5

description: Total RNA

extract_protocol: Total cellular RNA was extracted using the miRNeasy Mini Kit (Qiagen, Venlo, The Netherlands) following manufacturer's instructions.


title: Hybrid_progeny_female (HYB45F)

source_name: Gonads_Hybrid_progeny_female (HYB45F)


title: PBMC_NK_NKG2C-_enriched cNK2

city: East Lansing

first: Sungjin

last: Kim

state: MI

address: 567 Wilson Rd

department: Department of Microbiology and Molecular Genetics

institute: Michigan State University

description:
sorted NK cells, KIR negative population
732_NKG2C_negative

hyb_protocol: 3ug of Cy3-labelled cDNA (specific activity >10.0 pmol Cy3/ug cDNA) was incubated at 60°C for 5 minutes in a reaction volume of 55ul containing 2x Agilent blocking agent. 55ul of 2x Agilent hybridization buffer was then added and the mixture was hybridized to Agilent Human GE 4x44K V2 arrays (G4845A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash Buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Immediately after washing, slides were scanned on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel was set to Green and Green PMT was set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 026652_D_F_20140813) to obtain spatially detrended Processed Signal intensities. The values were normalized within each of the donor samples and used to calculate fold differences in expression.

source_name: human Natural Killer cells

label_protocol: Amplified cDNA was prepared from 5ng total RNA using the Ovation Pico SL WTA System V2 Kit (Nugen Technologies Inc., San Carlos, CA) according to the manufacturer's instructions. Cyanine-3 (Cy3) labeling was then carried out on 2ug amplified cDNA using the BioPrime Array Genomic Labeling System (Life Technologies). Dye incorporation and cDNA yield were verified with the BioDrop Spectrophotometer.

extract_protocol: RNA was purified using TRIzol Plus RNA Purification Kit (Life Technologies) and treated with Dnase (QIAGEN) as suggested by the manufacturers.

treatment_protocol: Peripheral blood from healthy volunteers was stained with fluorochrome conjugated anti-CD3, CD14, CD19, CD56, and additionally stained with specific NK cell surface markers as indicated. CD3-CD14-CD19-CD56+ cells were sorted into two groups, those expressing the specific marker and those not expressing the specific marker.

value: whole blood


title: PBMC_NK_NCR+_enriched cNK

description:
sorted NK cells, NCR positive population
724_NCR_positve


title: Hybrid_progeny_female (HYB33F)

source_name: Gonads_Hybrid_progeny_female (HYB33F)


title: Hybrid_progeny_female (HYB3F)

source_name: Gonads_Hybrid_progeny_female (HYB3F)


title: PBMC_NK_NCR-_enriched gNK

description:
sorted NK cells, NCR negative population
724_NCR_negative


title: PBMC_NK_NKG2C+_enriched gNK2

description:
sorted NK cells, KIR positive population
732_NKG2C_positive


title: NF1_CTRL_103

tag: cohort


title: ST486 EV Total Cy5

description: Total RNA


title: Hybrid_progeny_female (HYB36F)

source_name: Gonads_Hybrid_progeny_female (HYB36F)


title: NF1_CTRL_98

tag: biospecimen


title: NF1_CTRL_99

tag: sample source


title: PBMC_NK_KIR-_enriched cNK

description:
sorted NK cells, KIR negative population
221_KIR_negative


title: NF1_CTRL_95

tag: tumor


title: PBMC_NK_NKG2C-_enriched cNK

description:
sorted NK cells, KIR negative population
234_NKG2C_negative


title: ST486 miR-155 Total Cy3

description: Total RNA


title: Hybrid_progeny_female (HYB28F)

source_name: Gonads_Hybrid_progeny_female (HYB28F)


title: PBMC_NK_NKG2C+_enriched gNK

description:
sorted NK cells, KIR positive population
234_NKG2C_positive


title: ST486 miR-155 IP Cy3

description: Ago2-IP RNA


title: ST486 EV IP Cy3

description: Ago2-IP RNA

scan_protocol: Slides were scanned immediately after washing on the G25052C DNA microarray scanner (Agilent) following the manufacturer's protocol

source_name: ST486 cell line with empty MXW-PGK-IRES-GFP vector

growth_protocol: Cells were maintained in RPMI-1640 with 20%FCS, ultraglutamine (2mM), penicillin (100U/ml), streptomycin (0.1mg/ml) under standard culturing conditions

extract_protocol: Immunoprecipitation was performed using Ago2 ab (Clone 2E12-1C9). RNA from IP fraction was extracted using the miRNeasy Mini Kit (Qiagen, Venlo, The Netherlands), following manufacturer's instructions.


title: Hybrid_progeny_female (HYB29F)

source_name: Gonads_Hybrid_progeny_female (HYB29F)


title: PBMC_NK_KIR+_enriched gNK

description:
sorted NK cells, KIR positive population
221_KIR_positive


title: Hybrid_progeny_female (HYB2F)

source_name: Gonads_Hybrid_progeny_female (HYB2F)


title: Hybrid_progeny_female (HYB24F)

source_name: Gonads_Hybrid_progeny_female (HYB24F)


title: 10986 - E10.5 bmp4 ko ov1

city: Saint Louis

first: David

middle: Cy

last: Beebe

department: Ophthalmology and Visual Science

description: Sample name: 9255008057_F

hyb_protocol: Performed using standard Illumina protocol on Illumina Mouse6 v2.0 bead arrays by the Genome Technology Access Center (GTAC) at Washington University

scan_protocol: Standard Illumina protocol for bead arrays.

data_processing:
Background subtraction and cubic spline normalization and differential expression in the wild type and knockout prospective lens and retina were performed using Illumina Genome Studio software
Value is the mean hybridization intensity for all beads (~25-50 ) contining the indicated oligonucleotide probe.

source_name: Bmp4 KO distal optic vesicle 1

label_protocol: The resulting cDNA was biotin labeled using the Illumina biotinylation kit.

growth_protocol: Pregnant mice euthanized and embryos removed at E10.5

extract_protocol: Total RNA was extracted and purified from the prospective lens or retina tissue using a Qiagen RNeasy Microkit (Qiagen# 74004). 15 ng of total RNA was amplified to produce 3–5 μg of cDNA using Nugen WT-Ovation™ Pico RNA Amplification System (NuGEN Technologies Inc, #3300-12).

treatment_protocol: Embryos frozen in OCT and sectioned at 10 microns. Laser microdissection of the lens ectoderm and distal optic vesicle (prospective retina) on a Leica LMD-6000 system after slides were dipped in 70% ethanol at 4 °C for 1 min, washed in RNAase-free water twice for 30 s, rinsed in 95% ethanol, and stained in Eosin Y. Stained samples were washed in 95% ethanol and dehydrated in 100% ethanol and xylene..

tag: strain

value: mixed background (C57BL6, FVB)

value: distal optic vesicle

tag: genotype/variation

value: Bmp4 KO


title: NF1_CTRL_94

value: CTRL


title: NF1_CTRL_96


title: NF1_CTRL_92


title: Hybrid_progeny_female (HYB30F)

source_name: Gonads_Hybrid_progeny_female (HYB30F)

value: female


title: NF1_CTRL_93

source_name: Control


title: Hybrid_progeny_female (HYB19F)

source_name: Gonads_Hybrid_progeny_female (HYB19F)


title: NF1_CTRL_97


title: 10984 - E10.5 bmp4 ko se2

description: Sample name: 9255008057_E

source_name: Bmp4 KO surface ectoderm 2

value: surface ectoderm


title: NF1_CTRL_91


title: 20w_ST_HSC_3

city: Cambridge

first: Elisa

last: Laurenti

address: Jeffrey Cheah Biomedical Centre

department: Haematology

institute: University of Cambridge

description: 20w_ST_HSC_3  AVG_Signal

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Scanned on a BeadArray™ Reader using BeadScan software (v3.2).

data_processing: The data were normalized using quantile normalization in R (v2.12.1)

source_name: Bone marrow of xenografts 20 weeks post-transplantation of human cord blood progenitors

label_protocol: Biotin

extract_protocol: RNA was extracted from 2,000-5,000 sorted cells with Trizol reagent.

treatment_protocol: Lineage-depleted cord blood cells were thawed. An aliquoted was flow-sorted for LT-HSC, ST-HSC and MLP at time 0 and the others Lin- cells were injected intrafemorally into NSG mice (70000 Lin-/mouse). At 4, 12, 20 weeks post-transplantation, pools of 5-10 mice were sacrificed and human LT-HSC, ST-HSC and MLP were flow sorted.

value: ST-HSC:Lin- CD34+ CD38- CD45RA- CD90- CD49f-


title: 20w_MLP_1

description: 20w_MLP_1  AVG_Signal

value: MLP:Lin- CD34+ CD38- CD45RA+ CD10+


title: Hybrid_progeny_female (HYB12F)

source_name: Gonads_Hybrid_progeny_female (HYB12F)

value: Hybrid

value: Gonads


title: 10981 - E10.5 bmp4 wt ov2

description: Sample name: 9255008057_B

source_name: Bmp4 WT distal optic vesicle 2

value: Bmp4 WT


title: NF1_T_87

source_name: NF1 patients

value: WashU

value: saliva

value: WU

value: T


title: 10979 - E10.5 bmp4 wt se3

description: Sample name: 9255008057_C

source_name: Bmp4 WT surface ectoderm 3


title: Hybrid_progeny_female (HYB16F)

source_name: Gonads_Hybrid_progeny_female (HYB16F)


title: Hybrid_progeny_female (HYB17F)

source_name: Gonads_Hybrid_progeny_female (HYB17F)


title: 20w_LT_HSC_1

description: 20w_LT_HSC_1  AVG_Signal

value: LT-HSC:Lin- CD34+ CD38- CD45RA- CD90+ CD49f+


title: NF1_T_89


title: NF1_T_88


title: Danish_progeny_male (DAN9M)

source_name: Gonads_Danish_progeny_male (DAN9M)

value: Danish

value: male


title: NF1_T_84


title: 20w_MLP_3

description: 20w_MLP_3  AVG_Signal


title: NF1_T_86


title: NF1_CTRL_90

value: blood


title: 20w_ST_HSC_2

description: 20w_ST_HSC_2  AVG_Signal


title: 10978 - E10.5 bmp4 wt se2

description: Sample name: 9255008050_E

source_name: Bmp4 WT surface ectoderm 2

value: mixed background (C57BL6, FVB)


title: 10987 - E10.5 bmp4 ko ov2

description: Sample name: 9255008050_D

source_name: Bmp4 KO distal optic vesicle 2

value: distal optic vesicle

value: Bmp4 KO


title: 10977 - E10.5 bmp4 wt se1

description: Sample name: 9255008050_F

source_name: Bmp4 WT surface ectoderm 1

value: surface ectoderm


title: 10982 - E10.5 bmp4 wt ov3

description: Sample name: 9255008057_D

source_name: Bmp4 WT distal optic vesicle 3


title: Danish_progeny_male (DAN8M)

source_name: Gonads_Danish_progeny_male (DAN8M)


title: 10983 - E10.5 bmp4 ko se1

description: Sample name: 9255008050_C

source_name: Bmp4 KO surface ectoderm 1


title: Danish_progeny_male (DAN81M)

source_name: Gonads_Danish_progeny_male (DAN81M)


title: Hybrid_progeny_female (HYB27F)

source_name: Gonads_Hybrid_progeny_female (HYB27F)

value: female


title: NF1_T_85


title: NF1_T_81


title: NF1_T_83


title: 20w_LT_HSC_2

description: 20w_LT_HSC_2  AVG_Signal


title: 20w_LT_HSC_3

description: 20w_LT_HSC_3  AVG_Signal


title: Danish_progeny_male (DAN69M)

source_name: Gonads_Danish_progeny_male (DAN69M)


title: 10985 - E10.5 bmp4 ko se3

description: Sample name: 9255008050_A

source_name: Bmp4 KO surface ectoderm 3


title: Danish_progeny_male (DAN73M)

source_name: Gonads_Danish_progeny_male (DAN73M)


title: 20w_MLP_2

description: 20w_MLP_2  AVG_Signal

source_name: Bone marrow of xenografts 20 weeks post-transplantation of human cord blood progenitors

value: MLP:Lin- CD34+ CD38- CD45RA+ CD10+


title: Danish_progeny_male (DAN78M)

source_name: Gonads_Danish_progeny_male (DAN78M)


title: 10980 - E10.5 bmp4 wt ov1

description: Sample name: 9255008050_B

source_name: Bmp4 WT distal optic vesicle 1


title: 12w_MLP_2

description: 12w_MLP_2  AVG_Signal

source_name: Bone marrow of xenografts 12 weeks post-transplantation of human cord blood progenitors


title: 20w_ST_HSC_1

description: 20w_ST_HSC_1  AVG_Signal

value: ST-HSC:Lin- CD34+ CD38- CD45RA- CD90- CD49f-


title: NF1_T_79

source_name: NF1 patients


title: murine prostate stem cells spheroid cells_mouse 1_replicate 3

source_name: murine prostate tissue

tag: cell type

value: prostate stem cells spheroid cells


title: 12w_LT_HSC_1

description: 12w_LT_HSC_1  AVG_Signal


title: murine prostate stem cells spheroid cells_mouse 1_pool of replicates 1-3


title: 12w_ST_HSC_1

description: 12w_ST_HSC_1  AVG_Signal


title: Danish_progeny_male (DAN68M)

source_name: Gonads_Danish_progeny_male (DAN68M)

value: Gonads


title: NF1_NT_76

value: WashU

value: NT


title: NF1_NT_78

value: saliva

value: WU


title: Danish_progeny_male (DAN62M)

source_name: Gonads_Danish_progeny_male (DAN62M)


title: Danish_progeny_male (DAN63M)

source_name: Gonads_Danish_progeny_male (DAN63M)


title: 10988 - E10.5 bmp4 ko ov3

description: Sample name: 9255008057_A

source_name: Bmp4 KO distal optic vesicle 3


title: murine prostate stem cells spheroid cells_mouse 1_replicate 1


title: 12w_MLP_1

description: 12w_MLP_1  AVG_Signal


title: 12w_ST_HSC_2

description: 12w_ST_HSC_2  AVG_Signal


title: murine prostate stem cells spheroid cells_mouse 1_replicate 2


title: NF1_NT_77


title: murine prostate stem cells adherent monolayer cells_mouse 2_pool of replicates 1-3


title: NF1_T_82

value: T


title: NF1_NT_75


title: NF1_T_80


title: Danish_progeny_male (DAN64M)

source_name: Gonads_Danish_progeny_male (DAN64M)

value: Danish


title: murine prostate stem cells adherent monolayer cells_mouse 2_replicate 3


title: Danish_progeny_male (DAN60M)

source_name: Gonads_Danish_progeny_male (DAN60M)

value: male


title: Danish_progeny_male (DAN61M)

source_name: Gonads_Danish_progeny_male (DAN61M)


title: NF1_NT_74


title: Danish_progeny_male (DAN59M)

source_name: Gonads_Danish_progeny_male (DAN59M)


title: 12w_LT_HSC_2

description: 12w_LT_HSC_2  AVG_Signal

value: LT-HSC:Lin- CD34+ CD38- CD45RA- CD90+ CD49f+


title: 12w_LT_HSC_3

description: 12w_LT_HSC_3  AVG_Signal


title: murine prostate stem cells adherent monolayer cells_mouse 2_replicate 2


title: Danish_progeny_male (DAN57M)

source_name: Gonads_Danish_progeny_male (DAN57M)


title: 12w_MLP_3

description: 12w_MLP_3  AVG_Signal


title: 12w_ST_HSC_3

description: 12w_ST_HSC_3  AVG_Signal


title: murine prostate stem cells adherent monolayer cells_mouse 1_pool of replicates 1-3


title: murine prostate stem cells adherent monolayer cells_mouse 2_replicate 1


title: Danish_progeny_male (DAN55M)

source_name: Gonads_Danish_progeny_male (DAN55M)


title: 4w_ST_HSC_1

description: 4w_ST_HSC_1  AVG_Signal

source_name: Bone marrow of xenografts 4 weeks post-transplantation of human cord blood progenitors


title: murine prostate stem cells adherent monolayer cells_mouse 1_replicate 3


title: Danish_progeny_male (DAN98M)

source_name: Gonads_Danish_progeny_male (DAN98M)


title: NF1_NT_73


title: NF1_NT_71


title: Danish_progeny_male (DAN54M)

source_name: Gonads_Danish_progeny_male (DAN54M)


title: NF1_NT_72


title: 4w_LT_HSC_3

description: 4w_LT_HSC_3  AVG_Signal


title: Danish_progeny_male (DAN50M)

source_name: Gonads_Danish_progeny_male (DAN50M)


title: murine prostate stem cells adherent monolayer cells_mouse 1_replicate 1


title: 4w_MLP_2

description: 4w_MLP_2  AVG_Signal


title: murine prostate stem cells adherent monolayer cells_mouse 1_replicate 2


title: 4w_MLP_3

description: 4w_MLP_3  AVG_Signal


title: 4w_LT_HSC_2

description: 4w_LT_HSC_2  AVG_Signal


title: IFNgamma, TNFalpha and Vemurafenib Treated - repeat 1 - mAdbID:127785

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: 127785

hyb_protocol: Hybridization Protocol Other: Biotinylated cDNA was then hybridized to Mouse Gene 1.0 ST arrays (Affymetrix) overnight at 45 C and stained on a Genechip Fluidics Station 450 (Affymetrix), according to the respective manufacturers' instructions.

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

data_processing:
Data Processing Protocol
Calculation Method: Global gene expression profiles rank ordered by relative fold-change values were analysed by using Gene set enrichment analysis software (Broad Institute, MIT). P values were calculated using Student's t-test using Partek Genomic Suite after RMA (Robust Multiarray Average) normalization.

label_protocol:
Encore Biotin Module
Other: Samples were fragmentated and biotinylated using the Encore Biotin Module (NuGEN) according to the manufacturer's instructions.

extract_protocol:
Ovation Pico WTA System V2
Other: 100 ng of total RNA was extracted using Ovation Pico WTA System V2 (NuGEN) according to the manufacturer's instructions.

treatment_protocol:
Treatment type: compound
Agent: IFNgamma; TNFalpha; Vemurafenib
Treatment dose: IFNgamma (2.4 ng/ml); TNFalpha (0.24 ng/mL); Vemurafenib (1 uM)
Treatment time: 96 hours
In-vitro treatment: The SB-3123p cell line was derived from spontaneously arising melanoma in a female Tyr::CreER; BRAF(CA/CA); PTEN(lox4-5/lox4-5); CTNNB1(loxex3/loxex3) transgenic mouse. The tumor was initially divided into small pieces and then implanted onto C57BL/6 female mice. Growing tumors were serially implanted onto C57BL/6 mice and after the second in vivo passage were minced and seeded under tissue culture conditions to derive the SB-3123p cell line. Cells were treated with mouse IFNgamma (2.4 ng/ml), mouse TNFalpha (0.24 ng/mL), and Vemurafenib (1 uM) (PeproTech) and incubated for 96 hours.

tag: cell line

value: melanoma


title: IFNgamma, TNFalpha and Vemurafenib Treated - repeat 2 - mAdbID:127786

description: mAdb experiment ID: 127786


title: NF1_T_69


title: Danish_progeny_male (DAN44M)

source_name: Gonads_Danish_progeny_male (DAN44M)


title: IFNgamma, TNFalpha and Vemurafenib Treated - repeat 3 - mAdbID:127787

description: mAdb experiment ID: 127787


title: 4w_ST_HSC_3

description: 4w_ST_HSC_3  AVG_Signal


title: Danish_progeny_male (DAN26M)

source_name: Gonads_Danish_progeny_male (DAN26M)


title: Danish_progeny_male (DAN21M)

source_name: Gonads_Danish_progeny_male (DAN21M)


title: Vemurafenib Treated - repeat 3 - mAdbID:127784

description: mAdb experiment ID: 127784

source_name: Vemurafenib Treated

treatment_protocol:
Treatment type: compound
Agent: Vemurafenib
Treatment dose: 1 uM
Treatment time: 96 hours
In-vitro treatment: The SB-3123p cell line was derived from spontaneously arising melanoma in a female Tyr::CreER; BRAF(CA/CA); PTEN(lox4-5/lox4-5); CTNNB1(loxex3/loxex3) transgenic mouse. The tumor was initially divided into small pieces and then implanted onto C57BL/6 female mice. Growing tumors were serially implanted onto C57BL/6 mice and after the second in vivo passage were minced and seeded under tissue culture conditions to derive the SB-3123p cell line. Cells were treated with Vemurafenib (1 uM) (PeproTech) and incubated for 96 hours.


title: Danish_progeny_male (DAN45M)

source_name: Gonads_Danish_progeny_male (DAN45M)


title: 4w_ST_HSC_2

description: 4w_ST_HSC_2  AVG_Signal


title: NF1_T_67

source_name: NF1 patients


title: Danish_progeny_male (DAN25M)

source_name: Gonads_Danish_progeny_male (DAN25M)


title: NF1_T_68


title: NF1_NT_70


title: NF1_NT_65


title: NF1_NT_66


title: IFNgamma and TNFalpha Treated - repeat 3 - mAdbID:127781

description: mAdb experiment ID: 127781

source_name: IFNgamma and TNFalpha Treated

treatment_protocol:
Treatment type: compound
Agent: IFNgamma; TNFalpha
Treatment dose: IFNgamma (2.4 ng/ml); TNFalpha (0.24 ng/mL)
Treatment time: 96 hours
In-vitro treatment: The SB-3123p cell line was derived from spontaneously arising melanoma in a female Tyr::CreER; BRAF(CA/CA); PTEN(lox4-5/lox4-5); CTNNB1(loxex3/loxex3) transgenic mouse. The tumor was initially divided into small pieces and then implanted onto C57BL/6 female mice. Growing tumors were serially implanted onto C57BL/6 mice and after the second in vivo passage were minced and seeded under tissue culture conditions to derive the SB-3123p cell line. Cells were treated with mouse IFNgamma (2.4 ng/ml) and mouse TNFalpha (0.24 ng/mL) (PeproTech) and incubated for 96 hours.


title: CB_MLP_2

description: CB_MLP_2  AVG_Signal

source_name: human cord blood progenitor cells


title: Danish_progeny_male (DAN15M)

source_name: Gonads_Danish_progeny_male (DAN15M)


title: NF1_T_63

value: blood

value: TOR


title: 4w_LT_HSC_1

description: 4w_LT_HSC_1  AVG_Signal


title: Danish_progeny_male (DAN13M)

source_name: Gonads_Danish_progeny_male (DAN13M)


title: Danish_progeny_male (DAN14M)

source_name: Gonads_Danish_progeny_male (DAN14M)


title: CB_ST_HSC_2

description: CB_ST_HSC_2 AVG_Signal


title: NF1_NT_64


title: NF1_T_62


title: Danish_progeny_male (DAN11M)

source_name: Gonads_Danish_progeny_male (DAN11M)


title: NF1_T_59


title: NF1_T_58


title: CB_LT_HSC_1

description: CB_LT_HSC_1 AVG_Signal


title: IFNgamma and TNFalpha Treated - repeat 1 - mAdbID:127779

description: mAdb experiment ID: 127779


title: Danish_progeny_female (DAN95F)

source_name: Gonads_Danish_progeny_female (DAN95F)


title: Untreated Control - repeat 3 - mAdbID:127778

description: mAdb experiment ID: 127778

source_name: Untreated Control

treatment_protocol:
Treatment type: compound
Agent: DMSO
Treatment time: 96 hours
In-vitro treatment: The SB-3123p cell line was derived from spontaneously arising melanoma in a female Tyr::CreER; BRAF(CA/CA); PTEN(lox4-5/lox4-5); CTNNB1(loxex3/loxex3) transgenic mouse. The tumor was initially divided into small pieces and then implanted onto C57BL/6 female mice. Growing tumors were serially implanted onto C57BL/6 mice and after the second in vivo passage were minced and seeded under tissue culture conditions to derive the SB-3123p cell line. Cells were incubated in DMSO for 96 hours.


title: IFNgamma and TNFalpha Treated - repeat 2 - mAdbID:127780

description: mAdb experiment ID: 127780


title: NF1_T_60


title: NF1_T_61


title: Untreated Control - repeat 2 - mAdbID:127777

description: mAdb experiment ID: 127777


title: CB_MLP_1

description: CB_MLP_1  AVG_Signal


title: Untreated Control - repeat 1 - mAdbID:127776

description: mAdb experiment ID: 127776


title: Danish_progeny_female (DAN87F)

source_name: Gonads_Danish_progeny_female (DAN87F)


title: NF1_T_56


title: CB_LT_HSC_2

description: CB_LT_HSC_2  AVG_Signal


title: Danish_progeny_female (DAN82F)

source_name: Gonads_Danish_progeny_female (DAN82F)


title: Danish_progeny_female (DAN7F)

source_name: Gonads_Danish_progeny_female (DAN7F)


title: NF1_NT_55


title: Vemurafenib Treated - repeat 1 - mAdbID:127782

description: mAdb experiment ID: 127782


title: Vemurafenib Treated - repeat 2 - mAdbID:127783

description: mAdb experiment ID: 127783


title: NF1_NT_57


title: 4w_MLP_1

description: 4w_MLP_1  AVG_Signal

source_name: Bone marrow of xenografts 4 weeks post-transplantation of human cord blood progenitors


title: CB_MLP_3

description: CB_MLP_3  AVG_Signal


title: NF1_T_54