title: IAV_PR8deltaNS1_7h-REP2

description:
MH-S cell line-Infected with influenza A virus (PR8 delta NS1), collected at 7h p.i.-REP2
MH-S cell line macrophage (alveolar) infected with influenza A virus (PR8 delta NS1), collected at 7h p.i.

value: MH-S cell line macrophage (alveolar)


title: lamina propria, T1L reovirus 6h, replicate 2

status: Public on Mar 01 2017

type: RNA

city: Cambridge

first: Mukund

last: Varma

state: MA

address: 415 Main Street

country: USA

institute: Broad Institute

description:
replicate 2
RB32

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were background corrected (Illumina BeadStudio), normalised using quantile normalization and then Log2 transformed.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Mouse lamina propria

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

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

tag: mouse strain

tag: mouse age

value: 6-8 weeks

tag: tissue

value: lamina propria

tag: stimulation

value: T1L reovirus

tag: virus titre

tag: time(hr)


title: lamina propria, Sham 6h, replicate 1

description:
replicate 1
RB28

value: Sham


title: IAV_NI-REP2

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description:
MH-S cell line-Not infected-REP2
MH-S cell line macrophage (alveolar). Not Infected.

hyb_protocol: Aliquots (1.2 µg) of antisense, labeled RNA were appropriately hybridized to Agilent oligomicroarrays. Each sample was directly hybridized on a single microarray.

scan_protocol: After washing, microarray slides were scanned using a Gene Pix 4100A scanner (Molecular Devices, Inc).

data_processing: Extraction of numerical data from scanned microarray images (one channel per slide) was carried out using the GenePix Pro software (Molecular Devices, Inc). Median intensity values for each spot were used in subsequent analysis. Background signal was removed by the normexp method (Silver et al., 2009) with an offset of 50. Background-removed intensities were normalized by quantile adjustment of all replicates involved in each comparison. Both background removal and data normalization steps were performed with limma package (Ritchie et al., 2015) (functions normexp and normalizeQuantiles, respectively).

source_name: MH-S cell line macrophage (alveolar)

label_protocol: One microgram of total RNA from each sample was amino-allyl labeled and amplified using the Amino Allyl MessageAmp II aRNA Amplification Kit (Applied Biosystems, Foster City, CA). Aliquots of antisense amplified RNA were fluorescently labeled using Cy3, according to manufacturer’s instructions.

growth_protocol: MH-S cells (ATCC® CRL-2019™) were originally obtained from bronchoalveolar lavage of BALB/cj mice and were in vitro transformed with SV40 (Mbawuike & Herscowitz, 1989). They lack contact inhibition of growth and are trypsin-sensitive but they maintain typical macrophage morphology, and express cell surface Ia and Mac-1 antigens. MH-S cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 4 mM L-glutamine, 100 U/ml penicillin and 100 U/ml streptomycin. All cells were incubated at 37ºC in a 5% CO2 atmosphere.

extract_protocol: For human RSV, MH-S subconfluent monolayers were either mock-infected or infected with RSV at a multiplicity of infection (MOI) of 3 plaque forming units (pfu) per cell. Cells were incubated with the viral inoculum in RPMI with 2% FBS (RPMI2) for 90 min at 37ºC. After that time, the inoculum was removed and fresh RPMI2 was added. At 1 h and 18 h post-infection, culture supernatants were removed, cells were trypsinized, washed with PBS and RNA was extracted. Infection of MH-S with influenza virus was done similarly at a MOI of 3 pfu/cell in RPMI2 and harvested 7 h after infection.

treatment_protocol: For S. aureus, S. pneumoniae,  and K. pneumoniae infections, MH-S cells were incubated with bacteria at a ratio of 1:50 for 30 min. Subsequently, cells were washed with PBS; then, fresh medium with gentamycin (100 µg/ml) and penicillin (100 U/ml) was added. At 1h, 4h, or 8h post-infection (Table I), cells were harvested, and total RNA extracted and stored at -80ºC until analysis. In addition, MH-S subconfluent monolayers were also incubated in quadruplicate with 1µg/ml of smooth lipopolysaccharide (LPS) from Escherichia coli O55B5 (Sigma-Aldrich, St. Louis, MO, U.S.A.) or buffer for 1h. Then culture supernatants were removed and cells were scraped and washed with PBS before RNA extraction.

tag: strain

value: BALB/c

tag: infectant

value: Not Infected

tag: time post infection


title: RSV_Long_1h-REP4

description:
MH-S cell line-Infected with respiratory syncytial virus Long (RSV Long), collected at 1h p.i.-REP4
MH-S cell line macrophage (alveolar) infected with respiratory syncytial virus Long (RSV Long), collected at 1h p.i.


title: lamina propria, T3D-RV reovirus 6h, replicate 1

description:
replicate 1
RB30

value: T3D-RV reovirus


title: mesenteric lymph node, Sham 6h, replicate 3

description:
replicate 3
RB25

source_name: Mouse mesenteric lymph node

value: mesenteric lymph node


title: mesenteric lymph node, T3D-RV reovirus 6h, replicate 2

description:
replicate 2
RB24


title: RSV_Long_1h-REP3

description:
MH-S cell line-Infected with respiratory syncytial virus Long (RSV Long), collected at 1h p.i.-REP3
MH-S cell line macrophage (alveolar) infected with respiratory syncytial virus Long (RSV Long), collected at 1h p.i.


title: lamina propria, T1L reovirus 6h, replicate 3

description:
replicate 3
RB35


title: IAV_NI-REP1

description:
MH-S cell line-Not infected-REP1
MH-S cell line macrophage (alveolar). Not Infected.


title: IAV_PR8deltaNS1_7h-REP3

description:
MH-S cell line-Infected with influenza A virus (PR8 delta NS1), collected at 7h p.i.-REP3
MH-S cell line macrophage (alveolar) infected with influenza A virus (PR8 delta NS1), collected at 7h p.i.

value: influenza A virus (PR8 delta NS1)


title: RSV_Long_1h-REP2

description:
MH-S cell line-Infected with respiratory syncytial virus Long (RSV Long), collected at 1h p.i.-REP2
MH-S cell line macrophage (alveolar) infected with respiratory syncytial virus Long (RSV Long), collected at 1h p.i.


title: RSV_Long_18h-REP4

description:
MH-S cell line-Infected with respiratory syncytial virus Long (RSV Long), collected at 18h p.i.-REP4
MH-S cell line macrophage (alveolar) infected with respiratory syncytial virus Long (RSV Long), collected at 18h p.i.


title: IAV_NI-REP3

description:
MH-S cell line-Not infected-REP3
MH-S cell line macrophage (alveolar). Not Infected.


title: RSV_Long_18h-REP1

description:
MH-S cell line-Infected with respiratory syncytial virus Long (RSV Long), collected at 18h p.i.-REP1
MH-S cell line macrophage (alveolar) infected with respiratory syncytial virus Long (RSV Long), collected at 18h p.i.


title: mesenteric lymph node, T1L reovirus 6h, replicate 3

description:
replicate 3
RB26


title: mesenteric lymph node, T3D-RV reovirus 6h, replicate 1

description:
replicate 1
RB23


title: lamina propria, Sham 6h, replicate 2

description:
replicate 2
RB31


title: lamina propria, T3D-RV reovirus 6h, replicate 2

description:
replicate 2
RB33


title: mesenteric lymph node, T1L reovirus 6h, replicate 1

description:
replicate 1
RB21


title: RSV-NI-REP1


title: mesenteric lymph node, T1L reovirus 6h, replicate 2

description:
replicate 2
RB22


title: RSV_A2_1h-REP3

description:
MH-S cell line-Infected with respiratory syncytial virus A2 (RSV A2), collected at 1h p.i.-REP3
MH-S cell line macrophage (alveolar) infected with respiratory syncytial virus A2 (RSV A2), collected at 1h p.i.

value: respiratory syncytial virus A2 (RSV A2)


title: lamina propria, T3D-RV reovirus 48h, replicate 3

description:
replicate 3
RB17


title: mesenteric lymph node, Sham 6h, replicate 1

description:
replicate 1
RB19


title: lamina propria, Sham 48h, replicate 2

description:
replicate 2
RB13


title: RSV_A2_18h-REP1

description:
MH-S cell line-Infected with respiratory syncytial virus A2 (RSV A2), collected at 18h p.i.-REP1
MH-S cell line macrophage (alveolar) infected with respiratory syncytial virus A2 (RSV A2), collected at 18h p.i.


title: RSV_A2_18h-REP3

description:
MH-S cell line-Infected with respiratory syncytial virus A2 (RSV A2), collected at 18h p.i.-REP3
MH-S cell line macrophage (alveolar) infected with respiratory syncytial virus A2 (RSV A2), collected at 18h p.i.


title: RSV_A2_1h-REP4

description:
MH-S cell line-Infected with respiratory syncytial virus A2 (RSV A2), collected at 1h p.i.-REP4
MH-S cell line macrophage (alveolar) infected with respiratory syncytial virus A2 (RSV A2), collected at 1h p.i.


title: RSV_A2_1h-REP2

description:
MH-S cell line-Infected with respiratory syncytial virus A2 (RSV A2), collected at 1h p.i.-REP2
MH-S cell line macrophage (alveolar) infected with respiratory syncytial virus A2 (RSV A2), collected at 1h p.i.


title: SPNEUMONIAE-D39_4h-REP4

description:
MH-S cell line-Infected with Streptococcus pneumoniae D39 , collected at 4h p.i.-REP4
MH-S cell line macrophage (alveolar) infected with Streptococcus pneumoniae D39 , collected at 4h p.i.

value: Streptococcus pneumoniae D39


title: lamina propria, T3D-RV reovirus 48h, replicate 2

description:
replicate 2
RB16


title: mesenteric lymph node, Sham 6h, replicate 2

description:
replicate 2
RB20


title: SPNEUMONIAE-D39_4h-REP3

description:
MH-S cell line-Infected with Streptococcus pneumoniae D39 , collected at 4h p.i.-REP3
MH-S cell line macrophage (alveolar) infected with Streptococcus pneumoniae D39 , collected at 4h p.i.


title: lamina propria, T3D-RV reovirus 48h, replicate 1

description:
replicate 1
RB12


title: lamina propria, Sham 48h, replicate 1

description:
replicate 1
RB10


title: RSV-NI-REP3


title: RSV-NI-REP2


title: lamina propria, Sham 48h, replicate 3

description:
replicate 3
RB18


title: lamina propria, T1L reovirus 48h, replicate 3

description:
replicate 3
RB15


title: lamina propria, T1L reovirus 48h, replicate 2

description:
replicate 2
RB14


title: RSV_A2_1h-REP1

description:
MH-S cell line-Infected with respiratory syncytial virus A2 (RSV A2), collected at 1h p.i.-REP1
MH-S cell line macrophage (alveolar) infected with respiratory syncytial virus A2 (RSV A2), collected at 1h p.i.


title: SPNEUMONIAE-D39_4h-REP1

description:
MH-S cell line-Infected with Streptococcus pneumoniae D39 , collected at 4h p.i.-REP1
MH-S cell line macrophage (alveolar) infected with Streptococcus pneumoniae D39 , collected at 4h p.i.


title: mesenteric lymph node, T1L reovirus 48h, replicate 3

description:
replicate 3
RB8


title: lamina propria, T1L reovirus 48h, replicate 1

description:
replicate 1
RB11


title: mesenteric lymph node, T3D-RV reovirus 48h, replicate 3

description:
replicate 3
RB9


title: RSV-NI-REP4

description:
MH-S cell line-Not infected-REP4
MH-S cell line macrophage (alveolar). Not Infected.


title: RSV_A2_18h-REP2

description:
MH-S cell line-Infected with respiratory syncytial virus A2 (RSV A2), collected at 18h p.i.-REP2
MH-S cell line macrophage (alveolar) infected with respiratory syncytial virus A2 (RSV A2), collected at 18h p.i.


title: SPNEUMONIAE-D39_1h-REP3

description:
MH-S cell line-Infected with Streptococcus pneumoniae D39 , collected at 1h p.i.-REP3
MH-S cell line macrophage (alveolar) infected with Streptococcus pneumoniae D39 , collected at 1h p.i.


title: SPNEUMONIAE-D39_1h-REP4

description:
MH-S cell line-Infected with Streptococcus pneumoniae D39 , collected at 1h p.i.-REP4
MH-S cell line macrophage (alveolar) infected with Streptococcus pneumoniae D39 , collected at 1h p.i.


title: mesenteric lymph node, T3D-RV reovirus 48h, replicate 1

description:
replicate 1
RB5


title: SPNEUMONIAE-D39_4h-REP2

description:
MH-S cell line-Infected with Streptococcus pneumoniae D39 , collected at 4h p.i.-REP2
MH-S cell line macrophage (alveolar) infected with Streptococcus pneumoniae D39 , collected at 4h p.i.


title: mesenteric lymph node, T1L reovirus 48h, replicate 2

description:
replicate 2
RB4


title: SPNEUMONIAE-NI-REP4


title: SPNEUMONIAE-D39_1h-REP1

description:
MH-S cell line-Infected with Streptococcus pneumoniae D39 , collected at 1h p.i.-REP1
MH-S cell line macrophage (alveolar) infected with Streptococcus pneumoniae D39 , collected at 1h p.i.


title: SAUREUS-Newman_4h-REP2

description:
MH-S cell line-Infected with Staphylococcus aureus (Newman strain), collected at 4h p.i.-REP2
MH-S cell line macrophage (alveolar) infected with Staphylococcus aureus (Newman strain), collected at 4h p.i.

value: Staphylococcus aureus (Newman strain)


title: mesenteric lymph node, Sham 48h, replicate 1

description:
replicate 1
RB1


title: mesenteric lymph node, Sham 48h, replicate 3

description:
replicate 3
RB7


title: mesenteric lymph node, T3D-RV reovirus 48h, replicate 2

description:
replicate 2
RB6


title: SPNEUMONIAE-D39_1h-REP2

description:
MH-S cell line-Infected with Streptococcus pneumoniae D39 , collected at 1h p.i.-REP2
MH-S cell line macrophage (alveolar) infected with Streptococcus pneumoniae D39 , collected at 1h p.i.


title: SPNEUMONIAE-NI-REP3

description:
MH-S cell line-Not infected-REP3
MH-S cell line macrophage (alveolar). Not Infected.


title: mesenteric lymph node, Sham 48h, replicate 2

description:
replicate 2
RB2


title: SAUREUS-Newman_4h-REP3

description:
MH-S cell line-Infected with Staphylococcus aureus (Newman strain), collected at 4h p.i.-REP3
MH-S cell line macrophage (alveolar) infected with Staphylococcus aureus (Newman strain), collected at 4h p.i.


title: SPNEUMONIAE-NI-REP1

description:
MH-S cell line-Not infected-REP1
MH-S cell line macrophage (alveolar). Not Infected.


title: SAUREUS-Newman_4h-REP4

description:
MH-S cell line-Infected with Staphylococcus aureus (Newman strain), collected at 4h p.i.-REP4
MH-S cell line macrophage (alveolar) infected with Staphylococcus aureus (Newman strain), collected at 4h p.i.


title: SPNEUMONIAE-NI-REP2

description:
MH-S cell line-Not infected-REP2
MH-S cell line macrophage (alveolar). Not Infected.


title: mesenteric lymph node, T1L reovirus 48h, replicate 1

description:
replicate 1
RB3


title: SAUREUS-Newman_4h-REP1

description:
MH-S cell line-Infected with Staphylococcus aureus (Newman strain), collected at 4h p.i.-REP1
MH-S cell line macrophage (alveolar) infected with Staphylococcus aureus (Newman strain), collected at 4h p.i.


title: SAUREUS-NI-REP4


title: SAUREUS-Newman_1h-REP1

description:
MH-S cell line-Infected with Staphylococcus aureus (Newman strain), collected at 1h p.i.-REP1
MH-S cell line macrophage (alveolar) infected with Staphylococcus aureus (Newman strain), collected at 1h p.i.


title: SAUREUS-Newman_1h-REP4

description:
MH-S cell line-Infected with Staphylococcus aureus (Newman strain), collected at 1h p.i.-REP4
MH-S cell line macrophage (alveolar) infected with Staphylococcus aureus (Newman strain), collected at 1h p.i.


title: SAUREUS-Newman_1h-REP2

description:
MH-S cell line-Infected with Staphylococcus aureus (Newman strain), collected at 1h p.i.-REP2
MH-S cell line macrophage (alveolar) infected with Staphylococcus aureus (Newman strain), collected at 1h p.i.


title: SAUREUS-NI-REP2


title: SAUREUS-Newman_1h-REP3

description:
MH-S cell line-Infected with Staphylococcus aureus (Newman strain), collected at 1h p.i.-REP3
MH-S cell line macrophage (alveolar) infected with Staphylococcus aureus (Newman strain), collected at 1h p.i.


title: SAUREUS-NI-REP1


title: SAUREUS-NI-REP3


title: KPNEUMONIAE-52145_8h-REP2

description:
MH-S cell line-Infected with Klebsiella pneumoniae (52145 strain), collected at 8h p.i.-REP2
MH-S cell line macrophage (alveolar) infected with Klebsiella pneumoniae (52145 strain), collected at 8h p.i.

value: Klebsiella pneumoniae (52145 strain)


title: KPNEUMONIAE-52145_8h-REP3

description:
MH-S cell line-Infected with Klebsiella pneumoniae (52145 strain), collected at 8h p.i.-REP3
MH-S cell line macrophage (alveolar) infected with Klebsiella pneumoniae (52145 strain), collected at 8h p.i.


title: KPNEUMONIAE-52145_8h-REP4

description:
MH-S cell line-Infected with Klebsiella pneumoniae (52145 strain), collected at 8h p.i.-REP4
MH-S cell line macrophage (alveolar) infected with Klebsiella pneumoniae (52145 strain), collected at 8h p.i.


title: KPNEUMONIAE-52145_8h-REP1

description:
MH-S cell line-Infected with Klebsiella pneumoniae (52145 strain), collected at 8h p.i.-REP1
MH-S cell line macrophage (alveolar) infected with Klebsiella pneumoniae (52145 strain), collected at 8h p.i.


title: KPNEUMONIAE-52145_4h-REP2

description:
MH-S cell line-Infected with Klebsiella pneumoniae (52145 strain), collected at 4h p.i.-REP2
MH-S cell line macrophage (alveolar) infected with Klebsiella pneumoniae (52145 strain), collected at 4h p.i.


title: KPNEUMONIAE-52145_4h-REP4

description:
MH-S cell line-Infected with Klebsiella pneumoniae (52145 strain), collected at 4h p.i.-REP4
MH-S cell line macrophage (alveolar) infected with Klebsiella pneumoniae (52145 strain), collected at 4h p.i.


title: KPNEUMONIAE-52145_1h-REP1

description:
MH-S cell line-Infected with Klebsiella pneumoniae (52145 strain), collected at 1h p.i.-REP1
MH-S cell line macrophage (alveolar) infected with Klebsiella pneumoniae (52145 strain), collected at 1h p.i.


title: KPNEUMONIAE-43816_8h-REP2

description:
MH-S cell line-Infected with Klebsiella pneumoniae (43186 strain), collected at 8h p.i.-REP2
MH-S cell line macrophage (alveolar) infected with Klebsiella pneumoniae (43186 strain), collected at 8h p.i.

value: Klebsiella pneumoniae (43186 strain)


title: KPNEUMONIAE-52145_1h-REP4

description:
MH-S cell line-Infected with Klebsiella pneumoniae (52145 strain), collected at 1h p.i.-REP4
MH-S cell line macrophage (alveolar) infected with Klebsiella pneumoniae (52145 strain), collected at 1h p.i.


title: KPNEUMONIAE-43816_1h-REP1

description:
MH-S cell line-Infected with Klebsiella pneumoniae (43186 strain), collected at 1h p.i.-REP1
MH-S cell line macrophage (alveolar) infected with Klebsiella pneumoniae (43186 strain), collected at 1h p.i.


title: KPNEUMONIAE-43816_4h-REP1

description:
MH-S cell line-Infected with Klebsiella pneumoniae (43186 strain), collected at 4h p.i.-REP1
MH-S cell line macrophage (alveolar) infected with Klebsiella pneumoniae (43186 strain), collected at 4h p.i.


title: KPNEUMONIAE-52145_1h-REP3

description:
MH-S cell line-Infected with Klebsiella pneumoniae (52145 strain), collected at 1h p.i.-REP3
MH-S cell line macrophage (alveolar) infected with Klebsiella pneumoniae (52145 strain), collected at 1h p.i.


title: KPNEUMONIAE-43816_4h-REP2

description:
MH-S cell line-Infected with Klebsiella pneumoniae (43186 strain), collected at 4h p.i.-REP2
MH-S cell line macrophage (alveolar) infected with Klebsiella pneumoniae (43186 strain), collected at 4h p.i.


title: KPNEUMONIAE-43816_1h-REP3

description:
MH-S cell line-Infected with Klebsiella pneumoniae (43186 strain), collected at 1h p.i.-REP3
MH-S cell line macrophage (alveolar) infected with Klebsiella pneumoniae (43186 strain), collected at 1h p.i.


title: KPNEUMONIAE-43816_1h-REP2

description:
MH-S cell line-Infected with Klebsiella pneumoniae (43186 strain), collected at 1h p.i.-REP2
MH-S cell line macrophage (alveolar) infected with Klebsiella pneumoniae (43186 strain), collected at 1h p.i.


title: KPNEUMONIAE-43816_8h-REP4

description:
MH-S cell line-Infected with Klebsiella pneumoniae (43186 strain), collected at 8h p.i.-REP4
MH-S cell line macrophage (alveolar) infected with Klebsiella pneumoniae (43186 strain), collected at 8h p.i.


title: KPNEUMONIAE-43816_4h-REP3

description:
MH-S cell line-Infected with Klebsiella pneumoniae (43186 strain), collected at 4h p.i.-REP3
MH-S cell line macrophage (alveolar) infected with Klebsiella pneumoniae (43186 strain), collected at 4h p.i.


title: KPNEUMONIAE-43816_8h-REP3

description:
MH-S cell line-Infected with Klebsiella pneumoniae (43186 strain), collected at 8h p.i.-REP3
MH-S cell line macrophage (alveolar) infected with Klebsiella pneumoniae (43186 strain), collected at 8h p.i.


title: KPNEUMONIAE-43816_1h-REP4

description:
MH-S cell line-Infected with Klebsiella pneumoniae (43186 strain), collected at 1h p.i.-REP4
MH-S cell line macrophage (alveolar) infected with Klebsiella pneumoniae (43186 strain), collected at 1h p.i.


title: KPNEUMONIAE-43816_8h-REP1

description:
MH-S cell line-Infected with Klebsiella pneumoniae (43186 strain), collected at 8h p.i.-REP1
MH-S cell line macrophage (alveolar) infected with Klebsiella pneumoniae (43186 strain), collected at 8h p.i.


title: KPNEUMONIAE-NI-REP6

description:
MH-S cell line-Not infected-REP6
MH-S cell line macrophage (alveolar). Not Infected.


title: KPNEUMONIAE-43816_4h-REP4

description:
MH-S cell line-Infected with Klebsiella pneumoniae (43186 strain), collected at 4h p.i.-REP4
MH-S cell line macrophage (alveolar) infected with Klebsiella pneumoniae (43186 strain), collected at 4h p.i.


title: KPNEUMONIAE-52145_4h-REP3

description:
MH-S cell line-Infected with Klebsiella pneumoniae (52145 strain), collected at 4h p.i.-REP3
MH-S cell line macrophage (alveolar) infected with Klebsiella pneumoniae (52145 strain), collected at 4h p.i.


title: KPNEUMONIAE-52145_1h-REP2

description:
MH-S cell line-Infected with Klebsiella pneumoniae (52145 strain), collected at 1h p.i.-REP2
MH-S cell line macrophage (alveolar) infected with Klebsiella pneumoniae (52145 strain), collected at 1h p.i.


title: KPNEUMONIAE-NI-REP2

description:
MH-S cell line-Not infected-REP2
MH-S cell line macrophage (alveolar). Not Infected.


title: KPNEUMONIAE-NI-REP1

description:
MH-S cell line-Not infected-REP1
MH-S cell line macrophage (alveolar). Not Infected.


title: KPNEUMONIAE-NI-REP4

description:
MH-S cell line-Not infected-REP4
MH-S cell line macrophage (alveolar). Not Infected.


title: KPNEUMONIAE-NI-REP3

description:
MH-S cell line-Not infected-REP3
MH-S cell line macrophage (alveolar). Not Infected.


title: KPNEUMONIAE-NI-REP5

description:
MH-S cell line-Not infected-REP5
MH-S cell line macrophage (alveolar). Not Infected.


title: LSK cultured 18h without EV rep5

city: Barcelona

first: Gregoire

last: Stik

state: select a state

address: 88 Dr Aiguader

institute: CRG

description: Gene expression data from LSK cells

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C and 60rpm on Gene Mouse2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: LSK cultured 18h without EV

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500pg total RNA (Mouse Gene 2.0, picoWT, Affymetrix).

growth_protocol: LSK cells recovered after cell corting or mainatin 18h in Myelocult Medium M5300

extract_protocol: Total RNA were extracted using Nucleospin miRNAeasy kit  (macherey Nagel)

treatment_protocol: Cultured LSK cells were treated or not with Evs derived from AFT cells

tag: cell type

value: HSPC

tag: growth condition

value: 18h without EV


title: LSK cultured 18h without EV rep1

description: Gene expression data from LSK cells


title: LSK non cultured rep3

description: Gene expression data from LSK cells

source_name: LSK non cultured

value: non-cultured


title: LSK non cultured rep2

description: Gene expression data from LSK cells


title: LSK cultured 18h with EV rep4

description: Gene expression data from LSK cells

source_name: LSK cultured 18h with EV

value: cultured 18h with EV


title: LSK cultured 18h without EV rep4

description: Gene expression data from LSK cells


title: LSK cultured 18h without EV rep2

description: Gene expression data from LSK cells


title: LSK cultured 18h without EV rep3

description: Gene expression data from LSK cells


title: LSK cultured 18h with EV rep5

description: Gene expression data from LSK cells


title: Maf1 mice, ZT18, REP 3

city: Lausanne

first: Francois

last: Mange

state: VAUD

address: Genopode building

department: Center for Integrative Genomic

country: Switzerland

institute: University of Lausanne

hyb_protocol: Affymetrix mouse gene 2.0ST arrays (Affymetrix, Santa Clara , CA, USA) were hybridized with 3.7mg of fragmented target, at 45°C for 16 hours washed and stained according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0002).

scan_protocol: The arrays were scanned with the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: Normalized expression signals were calculated from Affymetrix CEL files by the Robust Multi-array Average algorithm (RMA), using the Affymetrix Expression Console Software (version 1.3.1.187). Hybridization quality was assessed using Expression Console Software as well.

label_protocol: 5.5mg of the cDNA was fragmented and labeled with GeneChip® WT Terminal Labeling kit (901525, Affymetrix).

extract_protocol: 50-100 mg pieces of perfused livers were added to 1 ml of TRIzol (Life technologies) and mechanically homogenized. RNA was then extracted according to the manufacturer’s  instructions. Three samples for the control and the Arntl KO mice and 5-6 samples for the constantly fed mice were processed.    All RNA quantities were assessed by NanoDrop®ND-1000 spectrophotometer and the RNA quality was assessed using the Fragment Analyzer (Advanced Analytical Technologies, Ankeny, USA). For each sample, 100ng of total RNA were amplified using the Ambion® WT Expression Kit (4411973, life technologies) kit.

value: Liver

tag: genotype

value: Maf1 KO

tag: circadian clock

tag: age

value: 12-14 weeks


title: Maf1 mice, ZT22, REP 1


title: LSK non cultured rep1

description: Gene expression data from LSK cells


title: LSK cultured 18h with EV rep3

description: Gene expression data from LSK cells


title: Maf1 mice, ZT18, REP 1


title: PIKfyve KO AM

city: Ikoma

first: Takumi

last: Kawasaki

state: Nara

address: 8916-5 Takayama

department: Bioscience

country: Japan

institute: Nara Institute of Science and Technology

description: gene expression in PIKfyve f_f_lysm_cre

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

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

data_processing: RMA normalization

source_name: alveolar macrophage in lung

label_protocol: Biotinylated DNA were prepared by encore biotn module kit from NuGEN using cDNA expanded by Ovation RNA amplification system from 10 ng total RNA

growth_protocol: Mice were maintained in SPF condition. WT and KO littermate mice were selected for analysis.

extract_protocol: Total RNA were isolated by RNA isolation kit from zymo research according to the manufacturer's instructions.

treatment_protocol: Lungs were isolated and singlnized the cells by collagenase treatmet. Lung cells were stained by DAPI, anti-Siglec-F and anti CD11c and sorted DAPI-Siglec-F+CD11c+ cells as alveolar macrophage

value: PIKfyve KO

value: adult

value: lung

value: alveolar macrophage


title: LSK non cultured rep5

description: Gene expression data from LSK cells


title: LSK cultured 18h with EV rep1

description: Gene expression data from LSK cells


title: Maf1 mice, ZT18, REP 2


title: LSK non cultured rep4

description: Gene expression data from LSK cells


title: Maf1 mice, ZT14, REP 2


title: wild type AM

description: gene expression in PIKfyve f_f

value: wild type


title: Maf1 mice, ZT14, REP 3


title: LSK cultured 18h with EV rep2

description: Gene expression data from LSK cells


title: Maf1 mice, ZT22, REP 2


title: Maf1 mice, ZT14, REP 1


title: Maf1 mice, ZT22, REP 3


title: Maf1 mice, ZT10, REP 1


title: Maf1 mice, ZT10, REP 3


title: KPNEUMONIAE-52145_4h-REP1

description:
MH-S cell line-Infected with Klebsiella pneumoniae (52145 strain), collected at 4h p.i.-REP1
MH-S cell line macrophage (alveolar) infected with Klebsiella pneumoniae (52145 strain), collected at 4h p.i.

value: BALB/c

value: MH-S cell line macrophage (alveolar)


title: Maf1 mice, ZT10, REP 2


title: Maf1 mice, ZT06, REP 3


title: Maf1 mice, ZT06, REP 1


title: Maf1 mice, ZT02, REP 3


title: Arntl mice, ZT22, REP 2

value: Arntl KO


title: Arntl mice, ZT18, REP 1


title: Arntl mice, ZT18, REP 2


title: Arntl mice, ZT02, REP 2


title: Arntl mice, ZT14, REP 3


title: Maf1 mice, ZT06, REP 2


title: Arntl mice, ZT14, REP 1


title: Arntl mice, ZT10, REP 2


title: Arntl mice, ZT06, REP 3


title: Maf1 mice, ZT02, REP 2


title: Arntl mice, ZT02, REP 1


title: Arntl mice, ZT06, REP 2


title: Arntl mice, ZT22, REP 1


title: Arntl mice, ZT06, REP 1


title: Arntl mice, ZT14, REP 2


title: Maf1 mice, ZT02, REP 1


title: Constantly fed mice, ZT22, REP 6

value: Wild type


title: Arntl mice, ZT10, REP 3


title: Arntl mice, ZT18, REP 3


title: Arntl mice, ZT10, REP 1


title: Arntl mice, ZT02, REP 3


title: Constantly fed mice, ZT22, REP 4


title: Constantly fed mice, ZT22, REP 5


title: Constantly fed mice, ZT22, REP 3


title: Constantly fed mice, ZT18, REP 5


title: Arntl mice, ZT22, REP 3


title: Constantly fed mice, ZT22, REP 1


title: Constantly fed mice, ZT22, REP 2


title: Constantly fed mice, ZT18, REP 3


title: Constantly fed mice, ZT18, REP 2


title: Constantly fed mice, ZT14, REP 4


title: Constantly fed mice, ZT18, REP 1


title: Constantly fed mice, ZT10, REP 5


title: Constantly fed mice, ZT14, REP 3


title: Constantly fed mice, ZT18, REP 4


title: Constantly fed mice, ZT14, REP 1


title: Constantly fed mice, ZT06, REP 5


title: JAK2 WT 231-BM cells

city: Houston

first: chunru

last: lin

state: TX

address: 1515 Holcombe Blvd

department: Molecular & Cellular Oncology

institute: MD Anderson Cancer Center

description: single pair

hyb_protocol: 0.825 ug of cyanine3 and cyanine5 labeled targets and Agilent  Hybridization buffer and block reagent were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Agilent Technologies Scanner G2505C US23502373

data_processing: Agilent Feature Extraction protocol GE2_1100_Jul11 (Read Only)

organism: Homo sapiens

source_name: breast cancer brain metastasis cell line

label_protocol: 1 µg of total RNA was primed with 1.8 µl of T7 primer at 65°C for 10 min, then on ice for 5 min followed by reversed transcribed at 40°C for 2 h,  and  70°C for 15 min. cRNA was generated by in vitro transcription incorporated Cyanine 3-CTP or cyanine 5-CTP.

growth_protocol: 231-BM cells cultured in DMEM medium. The media were supplemented with 10% fetal bovine serum (FBS). Cultures were incubated at 37°C in a humidified chamber with 5% CO2.

extract_protocol: Total RNA extracted using RNeasy Plus Mini Kit with QIAshredder columns (Qiagen) following manufacturer's instructions

treatment_protocol: The cells were plated at a density of 5×105 cells/well in 6-well plates in medium containing 10% FBS. When the cells were 80% confluent, they were treated with OSM for 4 hours.

tag: cell line

value: 231-BM cells

tag: treatment

value: treated without OSM

value: treated with OSM


title: Constantly fed mice, ZT06, REP 3


title: Constantly fed mice, ZT06, REP 2


title: Constantly fed mice, ZT14, REP 2


title: Constantly fed mice, ZT06, REP 6


title: 231-BM cells harboring Lnc-BM shRNA2

description: single pair


title: Constantly fed mice, ZT10, REP 4


title: 231-BM cells harboring Lnc-BM shRNA1

description: single pair


title: Constantly fed mice, ZT10, REP 6


title: Constantly fed mice, ZT10, REP 2


title: JAK2 KO 231-BM cells

description: single pair


title: Constantly fed mice, ZT26, REP 4


title: Constantly fed mice, ZT06, REP 1


title: Constantly fed mice, ZT10, REP 3


title: Constantly fed mice, ZT14, REP 5


title: Constantly fed mice, ZT06, REP 4


title: Constantly fed mice, ZT26, REP 2


title: Constantly fed mice, ZT26, REP 1


title: Constantly fed mice, ZT26, REP 3


title: Control mice, ZT18, REP 3


title: 4769_Ad3 lacrimal gland

city: Miami

first: Dmitry

last: Ivanov

state: FL

address: 1638 NW 10th Avenue

department: Ophthalmology

institute: University of Miami Miller School of Medicine

description: RNA samples were extracted from adult (3-month-old) lacrimal glands using the Absolutely RNA Microprep kit

hyb_protocol: Biotinylated complementary RNA samples were fragmented, diluted in a formamide-containing hybridization buffer, and loaded on to the Mouse Exonic Evidence Based Oligonucleotide (MEEBO) microarray slides enclosed in custom hybridization chambers (for more information on the MEEBO oligonucleotide set please refer to http://alizadehlab.stanford.edu/). The slides were hybridized for 16-18 hours in a Model 400 hybridization oven (Scigene, Sunnyvale, CA).

scan_protocol: After hybridization, the microarray slides were washed under stringent conditions, stained with Streptavidin-Alexa-647 (Invitrogen, Carlsbad, CA), and scanned using an Axon GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA).

data_processing: Spot intensities for each probe were calculated by subtracting median local background from median local foreground for each spot. The spot intensities were then normalized. After removing data for low quality spots, the mouse probes’ intensities were filtered to identify all probes with intensity above a normalized threshold. For statistical analysis, microarray data were examined for differences by One-way ANOVA or Student's t-test. Values of P < 0.05 were designated as statistically significant.

source_name: lacrimal gland

label_protocol: Biotin-labeled complementary RNA was made from total RNA according to Van Gelder’s protocol (Van Gelder RN, von Zastrow ME, Yool A, Dement WC, Barchas JD, et al. (1990) Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc Natl Acad Sci U S A 87: 1663-1667.)

extract_protocol: RNA samples were extracted from adult (3-month-old) and embryonic (E16.5) lacrimal glands using the Absolutely RNA Microprep and Nanoprep kits, respectively (Agilent Technologies, Santa Clara, CA).

value: lacrimal gland

tag: developmental stage

value: adult (3-month-old)


title: 4768_Ad2 lacrimal gland


title: 231-BM cells harboring control shRNA

description: single pair


title: Control mice, ZT22, REP 1

value: Liver


title: Control mice, ZT22, REP 3


title: Constantly fed mice, ZT10, REP 1


title: 4767_Ad1 lacrimal gland


title: Control mice, ZT18, REP 1


title: Control mice, ZT14, REP 3


title: 4763_Em2 lacrimal gland

description: RNA samples were extracted from embryonic (E16.5) lacrimal glands using the Absolutely RNA Nanoprep kit

value: embryonic day 16.5 (E16.5)


title: 4764_Em3 lacrimal gland


title: Control mice, ZT18, REP 2

value: 12-14 weeks


title: 4762_Em1 lacrimal gland


title: patient 125 control

city: Naples

first: Angela

last: Nebbioso

state: Italy

address: Vico Luigi De Crecchio 7

department: Biophysics, Biochemestry and General Patology

country: Italy

institute: Seconda Università degli Studi di Napoli

description: replicate 3

data_processing: Data were pre-processed using the Bioconductor package lumi, normalized using quantile method and signals were log2-transformed

source_name: blasts of AML patient

growth_protocol: The AML cell lines U937, NB4 and K562 were cultured in RPMI with 10% foetal bovine serum (FBS)(SIGMA), 2 mM L-glutamine (Euroclone) and antibiotics (100 U/mL penicillin, 100 µg/mL streptomycin and 250 ng/mL amphotericin-B). The blasts were cultured in RPMI with 20% FBS (Sigma), 2 mM L-glutamine (Euroclone) and antibiotics (100 U/mL penicillin, 100 µg/mL streptomycin and 250 ng/mL amphotericin-B).

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: SAHA (Merck) and MS27-275 (Bayer-Schering AG) were dissolved in DMSO (Sigma) and used at 5x10-6 M for 6 hours.

value: AML blasts

value: control


title: patient 117 saha

description: replicate 2

value: SAHA (Merck)


title: patient 125 saha

description: replicate 3


title: Control mice, ZT22, REP 2


title: patient 117 control

description: replicate 2


title: U937 MS 6h rep2

description: replicate 2

source_name: AML cell lines

value: MS27-275 (Bayer-Schering AG)


title: Control mice, ZT06, REP 3


title: Control mice, ZT14, REP 1


title: U937 Control 6h rep2

description: replicate 2


title: patient 75 saha

description: replicate 1


title: NB4 SAHA 6h rep2

description: replicate 2


title: patient 75 control

description: replicate 1


title: Control mice, ZT14, REP 2


title: Control mice, ZT10, REP 3


title: K562 MS 6h rep2

description: replicate 2


title: Control mice, ZT10, REP 2


title: K562 SAHA 6h rep2

description: replicate 2


title: Control mice, ZT06, REP 2


title: Control mice, ZT10, REP 1


title: NB4 MS 6h rep2

description: replicate 2


title: Control mice, ZT06, REP 1


title: Control mice, ZT02, REP 3


title: Control mice, ZT02, REP 1


title: K562 Control 6h rep2

description: replicate 2


title: Control mice, ZT02, REP 2


title: NB4 Control 6h rep2

description: replicate 2


title: U937 SAHA 6h rep2

description: replicate 2


title: U937 MS 6h rep1

description: replicate 1

growth_protocol: The AML cell lines U937, NB4 and K562 were cultured in RPMI with 10% foetal bovine serum (FBS)(SIGMA), 2 mM L-glutamine (Euroclone) and antibiotics (100 U/mL penicillin, 100 µg/mL streptomycin and 250 ng/mL amphotericin-B).

treatment_protocol: SAHA (Merck), MS27-275  (Bayer-Schering AG)  were dissolved in DMSO (Sigma) and used at 5x10-6 M for 6 hours.


title: MC38_sh Ctrl

city: Munich

first: Georgios

middle: T

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

country: Germany

institute: Helmholz Zentrum Munich

description: MC38 wild type, mouse colon adenocarcinoma

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
The data were processed and analyzed using GeneSpring 12.5 GX (Agilent) software.
RMA-16 normalized expression values by Genespring 12.5 GX (Agilent) software.

source_name: MC38 sh Ctrl

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

growth_protocol: Cancer cells were cultured using Dulbecco's Modified Eagle's Medium (DMEM) from Sigma Lot D6429. To make the complete growth medium, we added fetal bovine serum to a final concentration of 10%. Cells incubated at 37°C with 5% CO2.

extract_protocol: Trizol followed by RNAeasy spin columns

treatment_protocol: Not applicable

value: MC38 colon adenocarcinoma

tag: genotype/variation

value: wild type


title: U937 SAHA 6h rep1

description: replicate 1


title: U937 Control 6h rep1

description: replicate 1


title: AE17_sh Spp1

description: AE17 sh Spp1, mouse malignant mesothelioma

source_name: AE17 sh Spp1

value: AE17 malignant mesothelioma

value: Spp1 depletion


title: AE17_sh Ctrl

description: AE17 wild type, mouse malignant mesothelioma

source_name: AE17 sh Ctrl


title: MC38_sh Spp1

description: MC38 sh Spp1, mouse colon adenocarcinoma

source_name: MC38 sh Spp1


title: K562 SAHA 6h rep1

description: replicate 1


title: LLC_sh Ctrl

description: LLC wild type, Lewis lung carcinoma wild type, mouse lung cancer

source_name: LLC sh Ctrl

value: LLC Lewis lung carcinoma


title: LLC_sh Spp1

description: LLC sh Spp1, Lewis lung carcinoma wild type, mouse lung cancer

source_name: LLC sh Spp1


title: genomic DNA of mouse brain, GZH018

type: genomic

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description: tissue from mouse brain with Medulloblastoma

hyb_protocol: Prior to hybridization, the test and reference probes were combined with 100 ug mouse fluorimetric Cot-1 (Invitrogen) and ethanol precipitated. Following centrifugation, the probes were resuspended in 110ul SlideHyb Buffer #3 (Ambion) containing 5ul of 100µg/ul Yeast tRNA (Invitrogen), heated to 95ºC for 5 minutes and incubated for 30 minutes at 37ºC to block repetitive elements on the probe. Hybridization was performed for 16 hours at 55ºC using a GeneMachine hybridization station (Genomic Solutions, Inc.) as described (Cowell, J. K. and N. J. Nowak. 2003. High-resolution analysis of genetic events in cancer cells using bacterial artificial chromosome arrays and comparative genome hybridization. Adv Cancer Res 90:91-125). After hybridization, the slides were automatically washed in the GeneMachines station with reducing concentrations of SSC and SDS. The final wash was 30 seconds in 0.1X SSC, followed by a two second 100 % ethanol dip. The slides were spun dry and scanned immediately at 5µm resolution using a GenePix 4000B laser scanner (Axon Inc.)

scan_protocol: Slides were scanned on a GenePix 4000B laser Scanner (Axon Inc.) using GenePix Pro V6.0/1. Both lasers were set to 100% and the PMT was set to 500 for cy3 and 450 for cy5

data_processing: Images were analyzed using Imagene 6.0 (BioDiscovery Inc.). The output of Image analysis was further processed by in-house developed programs. The log2 ratios of the test/control (values are not background subtracted) were normalized using a subgrid loess, with all flagged spots and clones on the sex chromosome are given a weight of zero. The mean of the replicate measures was taken and the final normalized log2 ratio was plotted against its genomic location.

molecule: genomic DNA

source_name: Mouse brain

label_protocol: Genomic DNA Labeling Kit (Enzo Life Sciences, Farmingdale, NY) was used as per manufacturer's protocol.

extract_protocol: Pulverized tissue was lysed in 200mM NaCl, 5mM EDTA, 0.2% SDS, 100mM Tris pH8.5, 100ug/ml proteinase K overnight at 55C, then extracted with phenol/chloroform.

tag: background strain

tag: gender

value: F

tag: genotype/varation

value: Pten;p53 double knockout

value: Medulloblastoma

source_name: normal genomic DNA with opposite sex to ch1

value: normal brain


title: genomic DNA of mouse brain, GZH004

tag: tissue


title: NB4 MS 6h rep1

description: replicate 1


title: genomic DNA of mouse brain, GZH007


title: genomic DNA of mouse brain, GZH019


title: normal colonic mucosa, AOM-DSS treatment, mutant, biological rep1

city: Montreal

first: Rima

last: Rozen

state: Qc

address: 1001 Decarie Blvd

department: Human genetics

country: Canada

institute: McGill University

description:
Gene expression data from normal colonic mucosa, adjacent to tumor
Mouse Mthfd1S+/-_Mut_A11

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: The data were analyzed with Expression Console (Affymetrix default analysis settings, CGRMA algorithm, One-way ANOVA analysis, FDR corrections)

source_name: Murine normal colonic mucosa after AOM-DSS treatment, Mthfd1+/- mouse

label_protocol: Standard Affymetrix procedures

growth_protocol: The mice in this study were ≥10 generations backcrossed onto the BALB/cAnN background (Harlan), and can be considered congenic with this strain. Experiments were performed according to the guidelines of the Canadian Council on Animal Care and approved by the Animal Care Committees of McGill University and the Research Institute of the McGill University Health Centre. Mice were housed under specific pathogen-free conditions in a controlled environment (12 h light/dark cycle, 18–24oC) with ad libitum access to food (standard chow) and water. During the experiment, mice were weighed weekly, and body condition monitored. Mice were euthanized if they showed signs of undue discomfort.

extract_protocol: Total RNA was extracted from frozen normal colon samples using the RNeasy Mini kit with on-column DNase I treatment (Qiagen).

treatment_protocol: Three-month-old male and female Mthfd1S+/+ and Mthfd1S+/- MTHFD1-synthetase deficient mice were injected with 6 mg/kg AOM, intraperitoneally, followed by two 4-day cycles of 3% DSS treatment at 1 and 4 weeks post AOM injection. Mice were monitored daily during, and for 5 days following, DSS treatment. The mice were sacrificed 13 weeks after the AOM injection.

value: BALB/c

value: male

value: AOM-DSS

value: seven months old


title: K562 MS 6h rep1

description: replicate 1


title: NB4 SAHA 6h rep1

description: replicate 1


title: normal colonic mucosa, AOM-DSS treatment, WT, biological rep3

description:
Gene expression data from normal colonic mucosa, adjacent to tumor
Mouse Mthfd1S+/+_Ctrl_B10

source_name: Murine normal colonic mucosa after AOM-DSS treatment, WT mouse


title: genomic DNA of mouse brain, GZH016


title: genomic DNA of mouse brain, GZH013


title: genomic DNA of mouse brain, GZH008


title: normal colonic mucosa, AOM-DSS treatment, mutant, biological rep2

description:
Gene expression data from normal colonic mucosa, adjacent to tumor
Mouse Mthfd1S+/-_Mut_B8


title: K562 Control 6h rep1

description: replicate 1


title: normal colonic mucosa, AOM-DSS treatment, WT, biological rep1

description:
Gene expression data from normal colonic mucosa, adjacent to tumor
Mouse Mthfd1S+/+_Ctrl_A8


title: normal colonic mucosa, AOM-DSS treatment, WT, biological rep2

description:
Gene expression data from normal colonic mucosa, adjacent to tumor
Mouse Mthfd1S+/+_Ctrl_B1


title: genomic DNA of mouse brain, GZH006

value: M


title: genomic DNA of mouse brain, GZH012


title: genomic DNA of mouse brain, GZH014


title: genomic DNA of mouse brain, GZH005


title: genomic DNA of mouse brain, GZH015


title: normal colonic mucosa, AOM-DSS treatment, WT, biological rep4

description:
Gene expression data from normal colonic mucosa, adjacent to tumor
Mouse Mthfd1S+/+_Ctrl_B13


title: genomic DNA of mouse brain, GZH009


title: genomic DNA of mouse brain, GZH023


title: genomic DNA of mouse brain, GZH021


title: NB4 Control 6h rep1

description: replicate 1


title: AE17 sh Ctrl

data_processing: The data were processed and analyzed using GeneSpring 12.5 GX (Agilent) software.

value: malignant mesothelioma


title: A-135_ARR_D77

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

hyb_protocol: Samples were hybridized on  HG-133 plus 2.0  chips

scan_protocol: Plates were scanned on GeneTitan multichannel instrument (Affymetrix)

data_processing: Probe level processing was done by RMA with log2 transform and probe summary by median polish using JMP Genomics v. 6.0 (SAS Institute, Cary NC USA)

label: Biotin

label_protocol: Fragemented cRNA was lebeled with biotin

extract_protocol: RNA was isolated from whole blood Paxgene tubes using RNAeasy kit (Quagen)

tag: subject id

tag: subject status

value: healthy malaria-naïve volunteer

tag: vaccine

value: ARR

tag: time

tag: positive blood smear (1=yes, 0=no)

value: PBMC


title: genomic DNA of mouse brain, GZH022


title: AE17 sh Nras

description: AE17 sh Nras, mouse malignant mesothelioma

source_name: AE17 sh Nras

tag: cell type


title: R-23_RRR_D28

value: RRR


title: A-47_ARR_D34


title: A-153_ARR_D78


title: LLC sh Ctrl

value: LLC

value: Lewis lung carcinoma


title: R-68_RRR_D2


title: A-83_ARR_D1


title: A-33_ARR_D34


title: A-168_ARR_D28


title: A-157_ARR_D78


title: LLC sh Nras

description: LLC sh Nras, Lewis lung carcinoma wild type, mouse lung cancer

source_name: LLC sh Nras


title: A-35_ARR_D2


title: genomic DNA of mouse brain, GZH011


title: genomic DNA of mouse brain, GZH020


title: R-165_RRR_D29


title: A-83_ARR_D57


title: R-68_RRR_D28


title: R-136_RRR_D2


title: R-136_RRR_D14


title: A-153_ARR_D2


title: R-128_RRR_D77


title: FaDu cells expressing GLUT4

city: Taipei

first: Michael

last: Hsiao

address: Academia Road, Section 2, Nankang, Taipei, 115, Ta

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

description:
Pharynx cells
Gene expression data from FaDu cells expressing GLUT4 vector.

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

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

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

source_name: FaDu cells expressing GLUT4

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

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

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

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

value: FaDu

value: head and neck squamous cancer cell line

tag: stable expression


title: A-168_ARR_D56


title: R-128_RRR_D6


title: A-25_ARR_D29


title: A-139_ARR_D6


title: A-153_ARR_D28


title: A-87_ARR_D56


title: A-168_ARR_D77


title: FaDu cells expressing vector control

description:
Pharynx cells
Gene expression data from FaDu cells expressing control vector.

source_name: FaDu cells expressing vector control

value: control vector


title: R-165_RRR_D2


title: A-25_ARR_D6


title: A-25_ARR_D62


title: R-40_RRR_D2


title: A-47_ARR_D6


title: A-25_ARR_D1


title: A-153_ARR_D1


title: A-67_ARR_D77


title: A-25_ARR_D34


title: A-47_ARR_D1


title: A-25_ARR_D78


title: A-25_ARR_D57


title: A-25_ARR_D28


title: A-25_ARR_D56


title: A-47_ARR_D2


title: R-68_RRR_D62


title: A-25_ARR_D77


title: A-25_ARR_D14


title: A-25_ARR_D2


title: R-68_RRR_D82


title: R-68_RRR_D1


title: A-47_ARR_D77


title: R-68_RRR_D29


title: A-71_ARR_D78


title: R-68_RRR_D34


title: A-47_ARR_D28


title: A-47_ARR_D78


title: R-68_RRR_D14


title: R-68_RRR_Pre

value: Pre


title: R-68_RRR_D56


title: A-47_ARR_D14


title: A-47_ARR_D56


title: A-71_ARR_D57


title: R-68_RRR_D6


title: A-47_ARR_D82


title: A-25_ARR_D82


title: R-68_RRR_D78


title: A-47_ARR_D57


title: R-140_RRR_D14


title: A-131_ARR_D56


title: A-131_ARR_D28


title: R-140_RRR_D56


title: A-47_ARR_D62


title: A-131_ARR_D57


title: A-131_ARR_Pre


title: R-68_RRR_D77


title: A-71_ARR_D77


title: A-131_ARR_D82


title: A-131_ARR_D29


title: R-140_RRR_D28


title: A-131_ARR_D34


title: A-131_ARR_D62


title: R-140_RRR_Pre


title: R-140_RRR_D57


title: R-140_RRR_D1


title: A-131_ARR_D1


title: A-71_ARR_D82


title: A-131_ARR_D2


title: A-71_ARR_D28


title: A-71_ARR_D2


title: R-140_RRR_D78


title: R-140_RRR_D2


title: R-140_RRR_D6


title: A-25_ARR_Pre


title: A-47_ARR_Pre


title: R-140_RRR_D34


title: R-140_RRR_D29


title: R-140_RRR_D82


title: A-131_ARR_D14


title: R-140_RRR_D77


title: A-71_ARR_D62


title: A-71_ARR_Pre


title: A-131_ARR_D78


title: A-71_ARR_D34


title: A-71_ARR_D14


title: A-131_ARR_D77


title: A-131_ARR_D6


title: R-23_RRR_D82


title: R-23_RRR_Pre


title: R-151_RRR_D78


title: R-23_RRR_D78


title: A-157_ARR_Pre


title: R-23_RRR_D14


title: R-23_RRR_D34


title: A-104_ARR_Pre


title: A-145_ARR_D62


title: A-145_ARR_D14


title: A-145_ARR_D78


title: A-104_ARR_D2


title: R-23_RRR_D77


title: A-145_ARR_Pre


title: A-104_ARR_D1


title: A-145_ARR_D29


title: A-157_ARR_D6


title: A-145_ARR_D6


title: A-104_ARR_D28


title: A-145_ARR_D57


title: A-104_ARR_D6


title: A-104_ARR_D77


title: R-151_RRR_D2


title: R-151_RRR_Pre


title: A-104_ARR_D78


title: A-104_ARR_D34


title: A-145_ARR_D34


title: A-157_ARR_D34


title: A-157_ARR_D14


title: A-145_ARR_D2


title: A-157_ARR_D1


title: A-157_ARR_D28


title: A-157_ARR_D77


title: A-145_ARR_D82


title: A-157_ARR_D57


title: A-157_ARR_D62


title: A-104_ARR_D56


title: A-104_ARR_D14


title: A-104_ARR_D29


title: R-151_RRR_D62


title: R-151_RRR_D77


title: R-151_RRR_D1


title: R-151_RRR_D29


title: R-151_RRR_D14


title: A-157_ARR_D29


title: A-157_ARR_D82


title: A-157_ARR_D2


title: A-145_ARR_D77


title: A-145_ARR_D56


title: A-157_ARR_D56


title: R-151_RRR_D6


title: A-139_ARR_D1


title: A-145_ARR_D1


title: A-139_ARR_D2


title: R-151_RRR_D34


title: A-135_ARR_D62


title: A-104_ARR_D62


title: R-151_RRR_D28


title: A-139_ARR_Pre


title: A-39_ARR_D82


title: R-40_RRR_D29


title: R-151_RRR_D56


title: A-39_ARR_D62


title: A-135_ARR_D56


title: R-136_RRR_D62


title: A-135_ARR_D14


title: R-40_RRR_D34


title: A-39_ARR_D28


title: A-39_ARR_D29


title: R-136_RRR_D6


title: A-139_ARR_D29


title: A-135_ARR_D34


title: A-145_ARR_D28


title: A-39_ARR_D14


title: R-151_RRR_D57


title: A-104_ARR_D82


title: A-135_ARR_D78


title: A-135_ARR_D2


title: R-136_RRR_Pre


title: A-39_ARR_D2


title: Patient 8 - Untreated Biopsy - Day 24 - mAdbID:125530

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: 125530

hyb_protocol: Affymetrix Hybridization Protocol Other: Fragmented single-stranded sense DNA were hybridized to the Human GeneChip 2.0 ST array and stained on a Genechip Fluidics Station 450 (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

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

data_processing:
Data Processing Protocol
Calculation Method: Data were analyzed using Expression Console and Transcriptome Analysis Console Software. After Robust Multichip Average normalization, differentially expressed genes were identified by paired ANOVA test with a significance cut off p <= 0.05 and fold change (linear) of < -2 or > 2 (Affymetrix).

source_name: Untreated Biopsy - Day 24

label_protocol:
Affymetrix Labeling Protocol
Other: RNA was amplified using the Ambion WT expression kit (Life Technologies, Carlsbad, CA). Fragmented single-stranded sense DNA were terminally labeled with biotin according to the manufacturer's protocol.

extract_protocol:
Sample Extraction Protocol
Other: Portions of each melanoma metastasis were quick-frozen in liquid nitrogen. These were lysed directly in QIAzol Lysis Reagent (Qiagen, Hilden, Germany) and RNA was extracted according to the manufacturer's protocol.

treatment_protocol:
Treatment time: day 24
In-vivo treatment: Biopsies (incisional, core or excisional biopsies) of cutaneous or subcutaneous metastatic melanoma were obtained. When possible, biopsies at day 24 included an uninjected tumor.

value: skin

tag: disease state

value: metastatic melanoma


title: A-135_ARR_D1


title: A-39_ARR_D1


title: Patient 8 - Biopsy with IFNgamma - Day 22 - mAdbID:125529

description: mAdb experiment ID: 125529

source_name: Biopsy with IFNgamma - Day 22

treatment_protocol:
Treatment type: small molecule
Agent: IFNgamma
Treatment time: day 22
In-vivo treatment: Biopsies (incisional, core or excisional biopsies) of cutaneous or subcutaneous metastatic melanoma were obtained on day 22 (1 week after the third vaccine).


title: Patient 8 - Biopsy with IFNgamma - Day 24 - mAdbID:125531

description: mAdb experiment ID: 125531

source_name: Biopsy with IFNgamma - Day 24

treatment_protocol:
Treatment type: small molecule
Agent: IFNgamma
Treatment time: day 24
In-vivo treatment: Biopsies (incisional, core or excisional biopsies) of cutaneous or subcutaneous metastatic melanoma were obtained on day 24 (48 hrs after intratumoral injection of IFNgamma).


title: Patient 7 - Biopsy with IFNgamma - Day 22 - mAdbID:125526

description: mAdb experiment ID: 125526


title: A-39_ARR_D56


title: A-139_ARR_D28


title: A-107_ARR_D82


title: A-39_ARR_D6


title: Patient 8 - Pre-treatment Biopsy - Day 1 - mAdbID:125528

description: mAdb experiment ID: 125528

source_name: Pre-treatment Biopsy - Day 1

treatment_protocol:
Treatment time: day 1
In-vivo treatment: Biopsies (incisional, core or excisional biopsies) of cutaneous or subcutaneous metastatic melanoma were obtained on day 1 (baseline, pre-treatment).


title: R-136_RRR_D82


title: Patient 5 - Biopsy with IFNgamma - Day 24 - mAdbID:125520

description: mAdb experiment ID: 125520


title: Patient 7 - Pre-treatment Biopsy - Day 1 - mAdbID:125525

description: mAdb experiment ID: 125525


title: Patient 6 - Biopsy with IFNgamma - Day 24 - mAdbID:125524

description: mAdb experiment ID: 125524


title: A-39_ARR_D57


title: R-40_RRR_D56


title: A-139_ARR_D14


title: R-136_RRR_D78


title: A-135_ARR_D6


title: Patient 6 - Untreated Biopsy - Day 24 - mAdbID:125523

description: mAdb experiment ID: 125523


title: Patient 6 - Biopsy with IFNgamma - Day 22 - mAdbID:125522

description: mAdb experiment ID: 125522


title: Patient 7 - Biopsy with IFNgamma - Day 24 - mAdbID:125527

description: mAdb experiment ID: 125527


title: Patient 6 - Pre-treatment Biopsy - Day 1 - mAdbID:125521

description: mAdb experiment ID: 125521


title: R-136_RRR_D28


title: A-39_ARR_D78


title: Patient 5 - Biopsy with IFNgamma - Day 22 - mAdbID:125519

description: mAdb experiment ID: 125519


title: Patient 5 - Pre-treatment Biopsy - Day 1 - mAdbID:125518

description: mAdb experiment ID: 125518


title: A-107_ARR_Pre


title: Patient 4 - Biopsy with IFNgamma - Day 24 - mAdbID:125516

description: mAdb experiment ID: 125516


title: Patient 4 - Untreated Biopsy - Day 24 - mAdbID:125517

description: mAdb experiment ID: 125517


title: A-39_ARR_Pre


title: R-136_RRR_D1


title: A-139_ARR_D34


title: R-136_RRR_D77


title: A-139_ARR_D78


title: Patient 1 - Biopsy with IFNgamma - Day 24 - mAdbID:125510

description: mAdb experiment ID: 125510


title: Patient 1 - Pre-treatment Biopsy - Day 1 - mAdbID:125508

description: mAdb experiment ID: 125508


title: Patient 4 - Pre-treatment Biopsy - Day 1 - mAdbID:125514

description: mAdb experiment ID: 125514


title: A-107_ARR_D56


title: A-39_ARR_D77


title: Patient 4 - Biopsy with IFNgamma - Day 22 - mAdbID:125515

description: mAdb experiment ID: 125515


title: R-136_RRR_D57


title: A-139_ARR_D57


title: Patient 3 - Pre-treatment Biopsy - Day 1 - mAdbID:125511

description: mAdb experiment ID: 125511


title: Patient 3 - Biopsy with IFNgamma - Day 24 - mAdbID:125513

description: mAdb experiment ID: 125513


title: MDA231shSiA_2

city: Philadelphia

first: Xiaowei

last: Chen

state: PA

address: 333 Cottman Avenue

institute: Fox Chase Cancer Center

description: Gene expression of shRNA2 knockdown, replicate 2

hyb_protocol: Samples are hybridized for 16 hours at 45º C and washed according to Affymetrix procedure.

scan_protocol: The hybridized slides are scanned on Affymetrix scanner 700G

data_processing: Scanned microarray images were analyzed using the Affymetrix Gene Expression Console with RMA (Robust Multi-array Average) normalization algorithm. Further statistical Analyses were performed using BRB-ArrayTools developed by Dr. Richard Simon and BRB-ArrayTools Development Team. Gene classification into ontology categories (OG) was performed using BLAST2GO® version 2.6.4 (Biobam Bioinformatics, Valencia, Spain).

source_name: shRNA2, replicate 2

label_protocol: 250 ng total RNA samples are labeled and hybridized to the Affymetrix  Human Gene 2.0 ST Array according to the manufacturer's instructions (Affymetrix, Santa Clara, CA). For each condition, XX biological replicate samples were used for microarray experiments.

growth_protocol: MDA231 cells were maintained according to ATCC recommended medium at 37 ºC in the presence of 5% CO2 and were harvested at about 70% confluence.

extract_protocol: Total RNA is isolated using TRIzol reagent (Invitrogen, Carlsbad, CA) and further purified by RNeasy kit (Qiagen, Valencia, CA) according to manufacturer’s instructions.  The quality of total RNA is assessed by the ratios OD260/OD280 and OD260/OD230 and using an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA).

value: breast tumor cells


title: R-40_RRR_D77


title: Patient 3 - Biopsy with IFNgamma - Day 22 - mAdbID:125512

description: mAdb experiment ID: 125512


title: A-139_ARR_D77


title: MDA231sh681_2

description: Gene expression of shRNA1 knockdown, replicate 2

source_name: shRNA1, replicate 2


title: A-135_ARR_D82


title: Patient 1 - Biopsy with IFNgamma - Day 22 - mAdbID:125509

description: mAdb experiment ID: 125509


title: MDA231shSiA_1

description: Gene expression of shRNA2 knockdown, replicate 1

source_name: shRNA2, replicate 1


title: R-136_RRR_D34


title: A-107_ARR_D34


title: A-39_ARR_D34


title: A-107_ARR_D14


title: MDA231sh681_1

description: Gene expression of shRNA1 knockdown, replicate 1

source_name: shRNA1, replicate 1


title: Vector2

description: Gene expression of Vector Control, replicate 2

source_name: Vector, replicate 2


title: A-107_ARR_D6


title: A-107_ARR_D28


title: Chinese Lung ADC sample_97

city: Shanghai

first: Hongbin

last: Ji

address: YueYang Rd

country: China

institute: SIBCB

description: Hybridized to SNP 6.0

hyb_protocol: Affymetrix standard procedures

scan_protocol: Affymetrix standard procedures

data_processing: Image scanning and preprocessing followed Affymetrix standard procedures. Birdsuite package was used to compute genomic segment copy numbers, which were then annotated to gene-level copy numbers.

source_name: tumor sample

label_protocol: Affymetrix standard procedures

extract_protocol: Genomic DNA was extracted from tumor samples following recommended protocols.

value: lung adenocarcinomas


title: Chinese Lung ADC sample_513

description: Hybridized to SNP 6.0


title: A-107_ARR_D78


title: A-139_ARR_D56


title: A-139_ARR_D82


title: A-180_ARR_D62


title: Vector1

description: Gene expression of Vector Control, replicate 1

source_name: Vector, replicate 1


title: R-40_RRR_D78


title: R-40_RRR_D14


title: A-107_ARR_D62


title: A-117_ARR_D2


title: R-40_RRR_D82


title: A-107_ARR_D77


title: A-107_ARR_D2


title: R-40_RRR_D6


title: Chinese Lung ADC sample_511

description: Hybridized to SNP 6.0


title: R-165_RRR_D6


title: A-117_ARR_Pre


title: A-180_ARR_D34


title: Chinese Lung ADC sample_512

description: Hybridized to SNP 6.0


title: R-165_RRR_D78


title: R-28_RRR_D1


title: A-107_ARR_D1


title: A-180_ARR_D77


title: Chinese Lung ADC sample_491

description: Hybridized to SNP 6.0


title: A-117_ARR_D1


title: R-40_RRR_D28


title: A-87_ARR_D1


title: A-87_ARR_Pre


title: A-87_ARR_D82


title: Chinese Lung ADC sample_439

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_456

description: Hybridized to SNP 6.0


title: A-87_ARR_D14


title: Chinese Lung ADC sample_426

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_481

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_485

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_423

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_448

description: Hybridized to SNP 6.0


title: A-117_ARR_D77


title: A-117_ARR_D56


title: Chinese Lung ADC sample_435

description: Hybridized to SNP 6.0


title: A-87_ARR_D28


title: Chinese Lung ADC sample_421

description: Hybridized to SNP 6.0


title: A-87_ARR_D78


title: Chinese Lung ADC sample_412

description: Hybridized to SNP 6.0


title: A-117_ARR_D28


title: A-117_ARR_D14


title: Chinese Lung ADC sample_393

description: Hybridized to SNP 6.0


title: A-87_ARR_D57


title: Chinese Lung ADC sample_385

description: Hybridized to SNP 6.0


title: A-87_ARR_D29


title: Chinese Lung ADC sample_411

description: Hybridized to SNP 6.0


title: A-117_ARR_D62


title: A-87_ARR_D6


title: Chinese Lung ADC sample_399

description: Hybridized to SNP 6.0


title: A-117_ARR_D78


title: Chinese Lung ADC sample_397

description: Hybridized to SNP 6.0


title: A-87_ARR_D77


title: A-87_ARR_D34


title: R-28_RRR_D82


title: Chinese Lung ADC sample_380

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_382

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_374

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_355

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_345

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_338

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_363

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_347

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_368

description: Hybridized to SNP 6.0


title: A-117_ARR_D82


title: R-28_RRR_D57


title: Chinese Lung ADC sample_339

description: Hybridized to SNP 6.0


title: R-165_RRR_D57


title: Chinese Lung ADC sample_325

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_329

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_373

description: Hybridized to SNP 6.0


title: R-111_RRR_D62


title: A-180_ARR_D56


title: Chinese Lung ADC sample_327

description: Hybridized to SNP 6.0


title: A-87_ARR_D2


title: R-28_RRR_D2


title: A-117_ARR_D34


title: A-117_ARR_D29


title: A-180_ARR_D6


title: Chinese Lung ADC sample_336

description: Hybridized to SNP 6.0


title: R-28_RRR_D56


title: R-111_RRR_D78


title: R-28_RRR_D34


title: A-117_ARR_D6


title: R-165_RRR_D14


title: Chinese Lung ADC sample_309

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_318

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_324

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_280

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_316

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_305

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_277

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_291

description: Hybridized to SNP 6.0


title: A-180_ARR_D57


title: R-165_RRR_D1


title: A-180_ARR_D78


title: R-28_RRR_D14


title: R-28_RRR_D62


title: Chinese Lung ADC sample_300

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_276

description: Hybridized to SNP 6.0


title: R-111_RRR_D57


title: R-28_RRR_D77


title: Chinese Lung ADC sample_275

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_272

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_269

description: Hybridized to SNP 6.0


title: R-165_RRR_D77


title: A-180_ARR_D2


title: Chinese Lung ADC sample_267

description: Hybridized to SNP 6.0


title: R-165_RRR_D56


title: R-165_RRR_Pre


title: R-28_RRR_D78


title: A-180_ARR_D14


title: R-28_RRR_D6


title: BreastTumor_COCA-425-U-T1 [miRNA]

city: Oslo

first: Miriam

middle: Ragle

last: Aure

address: Ullernchauséen 70

department: Dept. of Cancer Genetics

country: Norway

institute: Oslo University Hospital Radiumhospitalet

hyb_protocol: Agilent miRNA Labeling Reagent and Hybridization Kit, Protocol v.2.3.

scan_protocol: Scanning on Agilent scanner G2565A and Feature Extraction (FE) v10.7.3.1 was used to extract signals

data_processing: Signals were extracted using Feature Extraction v10.7.3.1 and the subsequent data processing was performed using the GeneSpring software v11.0 (Agilent Technologies). In brief, the miRNA signal intensities were log2-transformed and normalized to the 90th percentile, and miRNAs that were detected in less than 10% of the samples were excluded. This resulted in 421 unique mature miRNAs.

source_name: Breast primary tumor

growth_protocol: Human primary tumors

extract_protocol: TRIzol, following manufactors protocol

treatment_protocol: Fresh frozen in liquid nitrogen

tag: tissue type

value: Breast tumor tissue

tag: hospital id

tag: estrogen receptor (er) status

value: pos

tag: human epidermal growth factor receptor 2 (her2) status

value: neg

tag: histological grade

tag: pam50 subtype


title: R-28_RRR_Pre

value: healthy malaria-naïve volunteer


title: BreastTumor_COCA-424-U-T1 [miRNA]

label_protocol: Agilent miRNA Labeling Reagent and Hybridization Kit, Protocol v.2.3.

value: Normal


title: BreastTumor_COCA-417-U-T1 [miRNA]

value: Basal


title: BreastTumor_COCA-420-U-T1 [miRNA]

value: LumA


title: BreastTumor_COCA-415-U-T1 [miRNA]


title: BreastTumor_COCA-405-U-T1 [miRNA]

value: LumB


title: BreastTumor_COCA-409-U-T1 [miRNA]


title: BreastTumor_COCA-398-U-T1 [miRNA]


title: BreastTumor_COCA-395-U-T1 [miRNA]


title: Chinese Lung ADC sample_259

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_262

description: Hybridized to SNP 6.0


title: BreastTumor_COCA-389-U-T1 [miRNA]


title: BreastTumor_COCA-394-U-T1 [miRNA]


title: BreastTumor_COCA-396-U-T1 [miRNA]


title: Chinese Lung ADC sample_245

description: Hybridized to SNP 6.0


title: BreastTumor_COCA-387-U-T1 [miRNA]


title: BreastTumor_COCA-388-U-T1 [miRNA]


title: Chinese Lung ADC sample_244

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_249

description: Hybridized to SNP 6.0


title: R-111_RRR_D6

value: RRR

value: PBMC


title: R-111_RRR_D82


title: BreastTumor_COCA-385-U-T1 [miRNA]


title: R-111_RRR_D14


title: R-111_RRR_Pre


title: R-111_RRR_D1


title: R-28_RRR_D28


title: Chinese Lung ADC sample_243

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_240

description: Hybridized to SNP 6.0


title: BreastTumor_COCA-384-U-T1 [miRNA]


title: BreastTumor_COCA-360-U-T1 [miRNA]


title: Chinese Lung ADC sample_231

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_230

description: Hybridized to SNP 6.0


title: BreastTumor_COCA-370-U-T1 [miRNA]


title: BreastTumor_COCA-341-U-T1 [miRNA]


title: BreastTumor_COCA-342-U-T5 [miRNA]


title: Chinese Lung ADC sample_224

description: Hybridized to SNP 6.0


title: R-165_RRR_D28


title: Chinese Lung ADC sample_212

description: Hybridized to SNP 6.0


title: BreastTumor_COCA-336-U-T1 [miRNA]


title: R-165_RRR_D34


title: A-180_ARR_D82

value: ARR


title: BreastTumor_COCA-331-U-T1 [miRNA]


title: BreastTumor_COCA-364-U-T1 [miRNA]


title: A-180_ARR_D1


title: BreastTumor_COCA-350-U-T1 [miRNA]


title: BreastTumor_COCA-315-U-T1 [miRNA]


title: A-180_ARR_Pre


title: BreastTumor_COCA-309-U-T1 [miRNA]


title: Chinese Lung ADC sample_203

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_202

description: Hybridized to SNP 6.0


title: R-111_RRR_D77


title: R-165_RRR_D82


title: BreastTumor_COCA-335-U-T1 [miRNA]


title: BreastTumor_COCA-339-U-T1 [miRNA]


title: R-111_RRR_D56


title: BreastTumor_COCA-296-U-T1 [miRNA]


title: BreastTumor_COCA-292-U-T1 [miRNA]


title: BreastTumor_COCA-282-U-T1 [miRNA]


title: BreastTumor_COCA-284-U-T1 [miRNA]


title: Chinese Lung ADC sample_218

description: Hybridized to SNP 6.0


title: BreastTumor_COCA-267-U-T1 [miRNA]


title: BreastTumor_COCA-257-U-T6 [miRNA]


title: BreastTumor_COCA-249-U-T1 [miRNA]


title: BreastTumor_COCA-246-U-T1 [miRNA]


title: Chinese Lung ADC sample_198

description: Hybridized to SNP 6.0


title: BreastTumor_COCA-214-U-T1 [miRNA]


title: BreastTumor_COCA-241-U-T4 [miRNA]


title: Chinese Lung ADC sample_197

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_194

description: Hybridized to SNP 6.0


title: R-111_RRR_D2


title: BreastTumor_COCA-210-U-T1 [miRNA]


title: Chinese Lung ADC sample_181

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_182

description: Hybridized to SNP 6.0


title: R-111_RRR_D34


title: R-111_RRR_D28


title: BreastTumor_COCA-209-U-T1 [miRNA]


title: A-67_ARR_D28


title: BreastTumor_COCA-206-U-T5 [miRNA]


title: A-67_ARR_D56


title: Chinese Lung ADC sample_178

description: Hybridized to SNP 6.0


title: BreastTumor_COCA-205-U-T6 [miRNA]


title: BreastTumor_COCA-189-U-T1 [miRNA]


title: BreastTumor_COCA-184-U-T1 [miRNA]


title: A-67_ARR_D82


title: BreastTumor_COCA-177-U-T1 [miRNA]


title: Chinese Lung ADC sample_168

description: Hybridized to SNP 6.0


title: BreastTumor_COCA-169-U-T1 [miRNA]


title: Chinese Lung ADC sample_163

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_180

description: Hybridized to SNP 6.0


title: A-67_ARR_D29


title: BreastTumor_COCA-168-U-T1 [miRNA]


title: A-67_ARR_D6


title: BreastTumor_COCA-153-U-T1 [miRNA]


title: BreastTumor_COCA-148-U-T1 [miRNA]


title: BreastTumor_COCA-146-U-T1 [miRNA]


title: Chinese Lung ADC sample_136

description: Hybridized to SNP 6.0


title: Chinese Lung ADC sample_129

description: Hybridized to SNP 6.0


title: BreastTumor_COCA-145-U-T1 [miRNA]


title: Chinese Lung ADC sample_128

description: Hybridized to SNP 6.0


title: BreastTumor_COCA-142-U-T1 [miRNA]


title: A-67_ARR_D62


title: BreastTumor_COCA-83-R-T1 [miRNA]


title: BreastTumor_COCA-119-U-T1 [miRNA]


title: BreastTumor_COCA-91-R-T4 [miRNA]


title: BreastTumor_COCA-120-U-T1 [miRNA]


title: BreastTumor_COCA-110-U-T4 [miRNA]


title: BreastTumor_COCA-95-U-T1 [miRNA]


title: BreastTumor_COCA-122-U-T1 [miRNA]


title: BreastTumor_COCA-121-U-T1 [miRNA]


title: BreastTumor_COCA-113-U-T1 [miRNA]


title: Chinese Lung ADC sample_123

description: Hybridized to SNP 6.0


title: BreastTumor_COCA-81-R-T2 [miRNA]


title: BreastTumor_COCA-79-R-T1 [miRNA]


title: BreastTumor_COCA-80-R-T1 [miRNA]


title: BreastTumor_COCA-90-R-T3 [miRNA]


title: A-67_ARR_D2


title: A-153_ARR_D82


title: Chinese Lung ADC sample_105

description: Hybridized to SNP 6.0


title: A-153_ARR_D34


title: A-67_ARR_D57


title: 2A Replicate 3

city: Stuttgart

first: Hiltrud

last: Brauch

address: Auerbachstr. 112

institute: Dr. Margarete Fischer-Bosch - Institute of Clinical Pharmacology

description: miRNA expression data from untreated MCF-7:2A cells

hyb_protocol: Hybridisation, washing  and staining of GeneChip miRNA 2.0 arrays on Fluidics station 450 (fluidics script FS450_0003) was done as described in the specifications from Affymetrix.

scan_protocol: GeneChip scanning was performed on the Affymetrix GCS3000 Scanner with autoloader, default AGCC scan parametres have been used.

data_processing:
Affymetrix software miRNA QC Tool (version 1.1.1.0, Affymetrix, 2010) was used for quality control of microarrays. Pre-processing of expression data was performed by robust multichip average (RMA) over 12 samples.
Resulting data were on log2 -scale and pre-processed data of the 9 samples (triplicates for WS8, 2A and 5C) were extracted for this study.

source_name: 2A Replicate 3

label_protocol: 1 µg of total RNA were labeled with biotin according to the standard Affymetrix protocol (FlashTag Biotin HSR Labeling procedure).

growth_protocol: Estrogen-dependent WS8 cells were maintained in fully-estrogenized media [phenol red-containing RPMI-1640 and 10% whole fetal bovine serum (FBS), supplemented with 6 ng/ml insulin, 2 mM glutamine, 100 μM non-essential amino acids, and 100 U of penicillin and streptomycin per ml], while 5C and 2A cells were maintained in estrogen-free medium (phenol red-free RPMI-1640 plus 10% dextran-coated charcoal-stripped FBS and the same supplements as for fully-estrogenized medium). Estrogen-dependent WS8 cells were switched to estrogen-free media for 3 days before all experiments.

extract_protocol: Total RNA was isolated using the mirVanaTM miRNA Isolation Kit (Applied Biosystems, AM1560) according to the manufacturer’s specifications. RNA samples were controlled for purity and integrity using a Nanodrop 1000 spectrophotometer and an Agilent 2100 Bioanalyzer by requiring each sample to exhibit an RNA Integrity Number (RIN) of 9.8-10.0.

treatment_protocol: MCF-7:WS8 cells were parsed into 2 groups of 3 replicate plates, and then treated with either 0.1% ethanol (vehicle control) or 10-9 M E2 for 72h. At 48 h, media on the remaining cells was replenished.

tag: cell line

tag: treatment


title: R-64_RRR_D78

tag: tissue


title: R-64_RRR_D77

tag: subject id


title: 2A Replicate 1

source_name: 2A Replicate 1


title: BreastTumor_COCA-76-R-T1 [miRNA]


title: BreastTumor_COCA-386-U-T4 [miRNA]


title: BreastTumor_COCA-78-R-T3 [miRNA]


title: 5C Replicate 3

description: miRNA expression data from untreated MCF-7:5C cells

source_name: 5C Replicate 3


title: BreastTumor_COCA-70-A-T [miRNA]


title: A-67_ARR_D78

tag: subject status


title: BreastTumor_COCA-73-R-T1 [miRNA]


title: A-153_ARR_D77

tag: vaccine


title: A-67_ARR_D34

tag: time


title: BreastTumor_COCA-69-A-T [miRNA]


title: 2A Replicate 2

source_name: 2A Replicate 2


title: 5C Replicate 2

source_name: 5C Replicate 2


title: BreastTumor_COCA-68-A-T [miRNA]


title: BreastTumor_COCA-67-A-T [miRNA]


title: BreastTumor_COCA-75-R-T1 [miRNA]


title: R-64_RRR_D29

tag: positive blood smear (1=yes, 0=no)


title: BreastTumor_COCA-66-A-T [miRNA]


title: 5C Replicate 1

source_name: 5C Replicate 1


title: WS8 E2 72 hr Replicate 3

description: miRNA expression data from 72h E2-treated MCF-7:WS8 cells

source_name: E2-treated WS8 72hr Replicate 3

value: 17beta-estradiol (E2)


title: R-64_RRR_D56


title: BreastTumor_COCA-65-A-T [miRNA]


title: WS8 E2 72 hr Replicate 1

source_name: E2-treated WS8 72hr Replicate 1


title: BreastTumor_COCA-59-A-T [miRNA]


title: BreastTumor_COCA-63-A-T [miRNA]


title: BreastTumor_COCA-61-A-T [miRNA]


title: BreastTumor_COCA-62-A-T [miRNA]


title: BreastTumor_COCA-60-A-T [miRNA]


title: R-64_RRR_D57


title: WS8 E2 72 hr Replicate 2

source_name: E2-treated WS8 72hr Replicate 2


title: R-64_RRR_D28


title: R-64_RRR_Pre

value: Pre


title: BreastTumor_COCA-57-A-T [miRNA]


title: BreastTumor_COCA-58-A-T [miRNA]


title: BreastTumor_COCA-56-A-T [miRNA]


title: R-64_RRR_D82


title: WS8 72hr Replicate 3

description: miRNA expression data from untreated MCF-7:WS8 cells

source_name: Control-treated WS8 72hr Replicate 3

value: vehicle


title: WS8 72hr Replicate 1

source_name: Control-treated WS8 72hr Replicate 1


title: BreastTumor_COCA-54-A-T [miRNA]


title: WS8 72hr Replicate 2

source_name: Control-treated WS8 72hr Replicate 2


title: A-35_ARR_D34


title: BreastTumor_COCA-55-A-T [miRNA]


title: BreastTumor_COCA-53-A-T [miRNA]


title: BreastTumor_COCA-52-A-T [miRNA]


title: BreastTumor_COCA-50-A-T [miRNA]


title: R-64_RRR_D62


title: A-67_ARR_Pre


title: A-67_ARR_D14


title: R-64_RRR_D1


title: A-35_ARR_D82


title: BreastTumor_COCA-47-A-T [miRNA]


title: BreastTumor_COCA-49-A-T [miRNA]


title: BreastTumor_COCA-51-A-T [miRNA]


title: BreastTumor_COCA-46-A-T [miRNA]


title: BreastTumor_COCA-44-A-T [miRNA]


title: BreastTumor_COCA-43-A-T [miRNA]


title: BreastTumor_COCA-41-A-T [miRNA]


title: BreastTumor_COCA-42-A-T [miRNA]


title: BreastTumor_COCA-40-A-T [miRNA]


title: BreastTumor_COCA-48-A-T [miRNA]


title: A-67_ARR_D1


title: BreastTumor_COCA-429-A-T [miRNA]


title: BreastTumor_COCA-39-A-T [miRNA]


title: BreastTumor_COCA-38-A-T [miRNA]


title: BreastTumor_COCA-45-A-T [miRNA]


title: BreastTumor_COCA-37-A-T [miRNA]


title: BreastTumor_COCA-36-A-T [miRNA]


title: BreastTumor_COCA-35-A-T [miRNA]


title: BreastTumor_COCA-34-A-T [miRNA]


title: BreastTumor_COCA-33-A-T [miRNA]


title: R-64_RRR_D34


title: A-35_ARR_D77


title: A-35_ARR_D29


title: A-35_ARR_D56


title: R-64_RRR_D14


title: R-64_RRR_D6


title: R-64_RRR_D2


title: BreastTumor_COCA-32-A-T [miRNA]


title: BreastTumor_COCA-30-A-T [miRNA]


title: BreastTumor_COCA-29-A-T [miRNA]


title: BreastTumor_COCA-27-A-T [miRNA]


title: A-35_ARR_D28


title: BreastTumor_COCA-26-A-T [miRNA]


title: BreastTumor_COCA-24-A-T [miRNA]


title: BreastTumor_COCA-23-A-T [miRNA]


title: BreastTumor_COCA-25-A-T [miRNA]


title: BreastTumor_COCA-428-A-T [miRNA]


title: BreastTumor_COCA-31-A-T [miRNA]


title: BreastTumor_COCA-28-A-T [miRNA]


title: BreastTumor_COCA-22-A-T [miRNA]


title: BreastTumor_COCA-20-A-T [miRNA]


title: BreastTumor_COCA-21-A-T [miRNA]


title: BreastTumor_COCA-19-A-T [miRNA]


title: A-153_ARR_D56


title: A-35_ARR_D62


title: BreastTumor_COCA-17-A-T [miRNA]


title: BreastTumor_COCA-16-A-T [miRNA]


title: BreastTumor_COCA-18-A-T [miRNA]


title: A-153_ARR_D14


title: BreastTumor_COCA-15-A-T [miRNA]


title: A-35_ARR_D78


title: A-168_ARR_D34


title: BreastTumor_COCA-14-A-T [miRNA]


title: A-168_ARR_D29


title: A-168_ARR_D78


title: A-168_ARR_D14


title: A-153_ARR_D29


title: BreastTumor_COCA-12-A-T [miRNA]


title: BreastTumor_COCA-10-A-T [miRNA]


title: BreastTumor_COCA-9-A-T [miRNA]


title: BreastTumor_COCA-11-A-T [miRNA]


title: BreastTumor_COCA-13-A-T [miRNA]


title: BreastTumor_COCA-7-A-T [miRNA]


title: BreastTumor_COCA-8-A-T [miRNA]


title: BreastTumor_COCA-6-A-T [miRNA]


title: A-35_ARR_D6


title: A-168_ARR_D6


title: A-153_ARR_D6


title: BreastTumor_COCA-64-A-T [miRNA]


title: BreastTumor_COCA-5-A-T [miRNA]


title: BreastTumor_COCA-3-A-T [miRNA]


title: BreastTumor_COCA-2-A-T [miRNA]


title: BreastTumor_COCA-1-A-T [miRNA]


title: A-35_ARR_D14


title: A-153_ARR_D62


title: BreastTumor_COCA-4-A-T [miRNA]


title: A-35_ARR_Pre


title: A-168_ARR_D2


title: Salubrinal_24h_rep3

city: Oxford

first: Colin

last: Goding

address: ORCRB

country: United Kingdom

institute: LICR, University of Oxford

description: SAMPLE 13

hyb_protocol: Standard Illumina hybridisation protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Average probe intensities were neqc and log2-transformed using limma.

label_protocol: Biotinylated cRNA was synthesised using standard Ambion protocol.

growth_protocol: 501mel cells were grown in DMEM supplemented with 10% FBS.

extract_protocol: Total RNA was extracted with the RNeasy kit (QIAGEN).

treatment_protocol: Cells were left untreated or treated with Salubrinal (20 mM) for 12, 24, 48 or 72 hours.

tag: cell type

value: melanoma

tag: time point

tag: agent

value: Salubrinal (20 mM)


title: A-35_ARR_D1


title: A-168_ARR_D1


title: Salubrinal_72h_rep3

description: SAMPLE 15


title: Salubrinal_72h_rep2

description: SAMPLE 11


title: A-168_ARR_D82


title: Salubrinal_48h_rep2

description: SAMPLE 10


title: R-37_RRR_D29


title: Salubrinal_24h_rep2

description: SAMPLE 9


title: A-168_ARR_D62


title: Salubrinal_12h_rep2

description: SAMPLE 8


title: Salubrinal_12h_rep3

description: SAMPLE 12


title: Salubrinal_72h_rep1

description: SAMPLE 7


title: Salubrinal_48h_rep1

description: SAMPLE 6


title: Salubrinal_48h_rep3

description: SAMPLE 14


title: Salubrinal_24h_rep1

description: SAMPLE 5


title: R-176_RRR_D62


title: Ctrl_rep3

description: SAMPLE 3

value: untreated Control sample


title: R-128_RRR_D14


title: Salubrinal_12h_rep1

description: SAMPLE 4


title: R-37_RRR_Pre


title: Ctrl_rep1

description: SAMPLE 1


title: T98G ctrl Radio replicate 3

city: Heidelberg

first: Maximilian

middle: Georg

last: Schliesser

address: INF 280

institute: DKFZ

description: 23.7 T98G ctrl Radio_9371242051_K

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Microarray scanning was done using an iScan array scanner

data_processing: Data extraction was done for all beads individually, and outliers were removed when the absolute difference to the median was greater than 2.5 times MAD(2.5 Hampel’s method). All remaining bead level data points were than quantile normalized (Bolstad 2001). Benjamini-Hochberg correction (Benjamini and Hochberg 1995) was applied to the set of preprocessed ProbeIDs

source_name: T98G cell line

label_protocol: according to Illumina's recommended sample labeling procedure based on the modified Eberwine protocol (Eberwine et al. 1992).

growth_protocol: cells were cultured in 200 µg/ml Hygromycin (Invitrogen) containing DMEM (Sigma-Aldrich, St. Louis, MO, USA) with 10% FBS (Sigma-Aldrich) and 1% PenStrep (Sigma-Aldrich).

extract_protocol: Qiagen RNeasy Kit, standard protocol

treatment_protocol: TMZ: 72h 300µM; Radio: 4Gy

tag: status

value: control

value: Radio


title: T98G ctrl noRadio replicate 3

description: 23.5 T98G ctrl noRadio_9371242051_I

value: noRadio


title: T98G 155OE Radio replicate 3

description: 23.8 T98G 155OE Radio_9371242051_L

value: miR-155 overexpression


title: T98G 155OE noRadio replicate 3

description: 23.6 T98G 155OE noRadio_9371242051_J


title: T98G ctrl TMZ replicate 3

description: 23.3 T98G ctrl TMZ_9371242051_G

value: TMZ


title: Ctrl_rep2

description: SAMPLE 2


title: T98G 155OE TMZ replicate 3

description: 23.4 T98G 155OE TMZ_9371242051_H


title: A-153_ARR_Pre

value: healthy malaria-naïve volunteer


title: R-37_RRR_D56


title: R-37_RRR_D1


title: R-128_RRR_D28


title: R-37_RRR_D14


title: R-37_RRR_D57


title: T98G ctrl Radio replicate 2

description: 22.7 T98G ctrl Radio_9371242051_C


title: T98G 155OE DMSO replicate 3

description: 23.2 T98G 155OE DMSO_9371242051_F

value: DMSO


title: T98G 155OE noRadio replicate 2

description: 22.6 T98G 155OE noRadio_9371242051_B


title: T98G ctrl DMSO replicate 3

description: 23.1 T98G ctrl DMSO_9371242051_E


title: T98G 155OE TMZ replicate 2

description: 22.4 T98G 155OE TMZ_9371242050_L


title: T98G ctrl noRadio replicate 2

description: 22.5 T98G ctrl noRadio_9371242051_A


title: R-37_RRR_D77


title: R-128_RRR_D29


title: T98G ctrl TMZ replicate 2

description: 22.3 T98G ctrl TMZ_9371242050_K


title: R-176_RRR_D82


title: R-128_RRR_D62


title: T98G ctrl DMSO replicate 2

description: 22.1 T98G ctrl DMSO_9371242050_I


title: T98G 155OE DMSO replicate 2

description: 22.2 T98G 155OE DMSO_9371242050_J


title: R-128_RRR_D56


title: T98G ctrl noRadio replicate 1

description: 21.5 T98G ctrl noRadio_9371242050_E


title: T98G 155OE noRadio replicate 1

description: 21.6 T98G 155OE noRadio_9371242050_F


title: T98G 155OE Radio replicate 1

description: 21.8 T98G 155OE Radio_9371242050_H


title: R-37_RRR_D34


title: T98G 155OE TMZ replicate 1

description: 21.4 T98G 155OE TMZ_9371242050_D


title: T98G 155OE Radio replicate 2

description: 22.8 T98G 155OE Radio_9371242051_D


title: T98G 155OE DMSO replicate 1

description: 21.2 T98G 155OE DMSO_9371242050_B


title: T98G ctrl Radio replicate 1

description: 21.7 T98G ctrl Radio_9371242050_G


title: ev_DOX_3

first: Leonie

last: Ratz

address: Im Neuenheimer Feld 460

department: Cancer Genome Research

description:
replicate 3
SAMPLE 10

scan_protocol: Microarray scanning was done using an iScan array scanner. Data extraction was done for all beads individually, and outliers are removed when the absolute difference to the median is greater than 2.5 times MAD(2.5 Hampel’s method). All remaining bead level data points are than quantile normalized.

data_processing: The raw-data are quantil-normalized with R and the Bioconductor package preprocessCore. As test for significance the student’s t-test is used on the bead expression values of the two groups of interest. In the case of significance of expression against background we tested for greater than all negative beads for this sample and in the case of comparing separate groups we tested for inequality of the means of the groups. In both cases Benjamini-Hochberg correction was applied to the complete set of p-values of all 48107 ProbeIDs on the chip. The average expression value is calculated as mean of the measured expressions of beads together with the standard deviation of the beads.

source_name: LNCaP_empty vector_dox

label_protocol: Biotin-labeled cRNA

growth_protocol: Stably transfected LNCaP cells were cultured in RPMI1640 (Invitrogen) + 10% tet-system approved FBS (Clontech), supplemented with 80µg/mL Hygromycin B (Invitrogen).

extract_protocol: Qiagen miRNeasy and on-column DNase I digest. Procedure was performed in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Induction of transgene expression was achieved by supplementing the growth medium RPMI160 + 10% tet-FBS with 50ng/mL Doxycycline (Sigma) for 72h.

value: LNCaP

tag: transfcted withg

value: empty vector

tag: induced with

value: 50ng/mL Doxycycline for 72h


title: R-37_RRR_D6

value: RRR

value: PBMC


title: R-176_RRR_D57


title: R-176_RRR_D78


title: R-37_RRR_D2


title: R-37_RRR_D28


title: T98G ctrl DMSO replicate 1

description: 21.1 T98G ctrl DMSO_9371242050_A


title: ev_3

description:
replicate 3
SAMPLE 9

source_name: LNCaP_empty vector


title: T/E_III_3

description:
replicate 3
SAMPLE 11

source_name: LNCaP_TMPRSS2:ERG fusion variant III_dox

value: TMPRSS2:ERG fusion variant III


title: R-128_RRR_D57


title: T98G ctrl TMZ replicate 1

description: 21.3 T98G ctrl TMZ_9371242050_C


title: T/E_VI_1

description:
replicate 1
SAMPLE 4

source_name: LNCaP_TMPRSS2:ERG fusion variant IV_dox

value: TMPRSS2:ERG fusion variant VI


title: T/E_VI_3

description:
replicate 3
SAMPLE 12


title: ev_2

description:
replicate 2
SAMPLE 5


title: T/E_III_2

description:
replicate 2
SAMPLE 7


title: ev_DOX_2

description:
replicate 2
SAMPLE 6


title: R-176_RRR_D77


title: R-176_RRR_D56


title: R-128_RRR_D78


title: R-176_RRR_D34


title: MEM_24h_rep1

description: SAMPLE 7

hyb_protocol: Standard Illumina hybridization protocol.

growth_protocol: IGR37 cells were grown in DMEM supplemented with 10% FBS (BioSera).

treatment_protocol: Cells were transferred or not to MEM supplemented with dialyzed FBS (Invitrogen).

value: melanoma

tag: growth media

value: transferred from DMEM to MEM

tag: time (in mem)


title: MEM_72h_rep2

description: SAMPLE 11


title: MEM_6h_rep2

description: SAMPLE 5


title: R-176_RRR_D28


title: MEM_72h_rep3

description: SAMPLE 12


title: ev_1

description:
replicate 1
SAMPLE 1


title: ev_DOX_1

description:
replicate 1
SAMPLE 2


title: R-128_RRR_D2


title: DMEM_rep3

description: SAMPLE 3

value: DMEM


title: A-61_ARR_D6

value: ARR


title: DMEM_rep1

description: SAMPLE 1


title: T/E_III_1

description:
replicate 1
SAMPLE 3


title: MEM_72h_rep1

description: SAMPLE 10


title: R-48_RRR_D57


title: PDX + control (rep2)

city: Grand Rapids

first: Bin

state: MI

address: 15 Michigan St. NE

institute: Michigan State University

description: replicate 2

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0). Array probes transformed by logarithm and normalized by quantile method.

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)

growth_protocol: HepG2 cells were seeded at 20% confluency, and grown 72h in Eagle’s MEM containing 10% FBS, penicillin and streptomycin at 37ºC and 5% CO2. To build PDX models, HCC tissues were collected from HCC patients who had undergone liver resection as part of their treatment.  Single tumor cells labeled with luciferase gene were suspended in BEME medium containing 50% Matrix Matrigel, and then subcutaneously injected into 4–8 week old male NSG mice (20-25 g body weight). Tumor development was monitored daily. Once the subcutaneous xenograft reached 1 cm in diameter, it was removed and cut into 2 mm pieces and surgically implanted into the left lobe of the liver of another group of 6 weeks old NSG mice. Tumor growth was monitored once a week using the Xenogen IVIS in vivo imaging system (Caliper Life Sciences, Hopkinton, CA).

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

treatment_protocol: Before harvesting, HepG2 cells were incubated 6h with 10μM of NEN, 10μM of niclosamide, DMSO control. Treatment was initiated within one week after transplantation of the Patient Derived Xenograft (PDX). For each PDX model, tumor-bearing mice with similar initial bioluminescence signals were allocated into three groups (n=5 each), to be given daily: 1) NEN (200 mg/kg) mixed in autoclaved food, or 2) regular food, for six weeks. Tumor cells were harvested for the microarray experiment.

tag: pdx

value: HCC patient derived xenografts

value: regular food


title: MEM_24h_rep3

description: SAMPLE 9

tag: cell line


title: MEM_24h_rep2

description: SAMPLE 8


title: PDX + NEN (rep3)

description: replicate 3

tag: treatment

value: NEN (200 mg/kg) mixed in autoclaved food


title: MEM_6h_rep3

description: SAMPLE 6


title: PDX + control (rep3)

description: replicate 3


title: PDX + control (rep1)

description: replicate 1


title: A-61_ARR_D28

tag: tissue


title: DMEM_rep2

description: SAMPLE 2


title: MEM_6h_rep1

description: SAMPLE 4


title: T/E_VI_2

description:
replicate 2
SAMPLE 8


title: PDX + NEN (rep2)

description: replicate 2


title: R-48_RRR_D56

tag: subject id


title: HepG2 + NEN

description: treated with NEN

value: 10μM of NEN


title: PDX + NEN (rep1)

description: replicate 1


title: HepG2 + Niclosamide

description: treated with niclosamide

value: 10μM of niclosamide


title: R-48_RRR_D1

tag: subject status

value: healthy malaria-naïve volunteer


title: Mat-DC_rep4

city: Newcastle

first: John

last: Casement

address: Framlington Place

department: Bioinformatics Support Unit

institute: Newcastle University

scan_protocol: Standard Illumina scanning protocol

data_processing: Data processing was carried out with the BioConductor lumi package. Raw data was variance stabilised with the lumiT function and normalised with the lumiN function. Quality assessment was carried out with the lumiQ function and with the BioConductor arrayQualityMetrics package.

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

growth_protocol: Mature and immature DCs (mat-DC and imm-DC) were generated from magnetically isolated CD14+ monocytes cultured with IL-4 and GM-CSF (50ng/ml, Immunotools) for 7days.

extract_protocol: RNA was extracted using QIAGEN RNeasy micro kit in accordance with the manufacturer's protocol. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: LPS (100ng/ml; Sigma) was added to Treg-MATDC and Mat-DC on day 6. Regulatory T cells were added to the DCs on Day 3 at a 3:1 ratio.

value: mature dendritic cell


title: HepG2

description: treated with control

value: DMSO control


title: Treg-MatDC_rep4

value: Treg-conditioned dendritic cells


title: R-48_RRR_D2

tag: vaccine

value: RRR


title: R-48_RRR_D28

tag: time

value: PBMC


title: R-48_RRR_D82

tag: positive blood smear (1=yes, 0=no)


title: R-48_RRR_Pre

value: Pre


title: Im-DC_rep3

tag: cell type

value: immature dendritic cell


title: Im-DC_rep4


title: R-48_RRR_D78


title: Im-DC_rep1


title: A-61_ARR_D14


title: Mat-DC_rep3


title: Im-DC_rep2


title: R-48_RRR_D62


title: Mat-DC_rep1


title: A-61_ARR_Pre


title: Treg-MatDC_rep3


title: Mat-DC_rep2


title: R-48_RRR_D77


title: A-61_ARR_D1


title: A-61_ARR_D2


title: R-48_RRR_D14


title: R-48_RRR_D6


title: R-48_RRR_D29


title: A-61_ARR_D78


title: A-83_ARR_D29


title: R-176_RRR_D6


title: A-61_ARR_D57


title: A-83_ARR_D82


title: A-61_ARR_D82


title: R-176_RRR_D14


title: R-176_RRR_D2


title: A-83_ARR_D78


title: A-61_ARR_D62


title: A-83_ARR_D2


title: R-37_RRR_D82


title: R-37_RRR_D78


title: A-83_ARR_D28


title: R-128_RRR_D82


title: A-83_ARR_D56


title: R-128_RRR_D1


title: R-128_RRR_Pre


title: A-61_ARR_D77


title: A-83_ARR_D14


title: A-61_ARR_D34


title: A-83_ARR_Pre


title: A-61_ARR_D29


title: A-83_ARR_D77


title: R-37_RRR_D62


title: A-61_ARR_D56


title: R-128_RRR_D34


title: R-72_RRR_D28


title: R-176_RRR_Pre


title: R-81_RRR_D28


title: R-81_RRR_D34


title: A-103_ARR_D78


title: R-81_RRR_D14


title: R-72_RRR_D1


title: R-72_RRR_D2


title: R-81_RRR_D29


title: R-72_RRR_D29


title: R-72_RRR_Pre


title: R-72_RRR_D14


title: A-149_ARR_D2


title: R-81_RRR_D82


title: A-103_ARR_D82


title: R-72_RRR_D34


title: A-149_ARR_Pre


title: A-103_ARR_D34


title: R-72_RRR_D6


title: A-103_ARR_D77


title: A-103_ARR_D1


title: A-103_ARR_D56


title: R-81_RRR_D78


title: R-48_RRR_D34


title: A-149_ARR_D77