title: serum Smear + Culture+ TB SD3002


title: serum Non-TB SD2080

status: Public on Jul 06 2012

type: protein

city: Bronx

first: Shajo

last: Kunnath-Velayudhan

state: NY

address: 1300 Morris Park Ave

department: Microbiology and Immunology

country: USA

institute: Albert Einstein College of Medicine

hyb_protocol: Sera were pre-absorbed with E. coli-lysate for 30 minutes.  Prior to incubating with serum, slides were blocked for 30 minutes with Blocking Solution (Candor Bioscience, Germany).  Slides were incubated with sera diluted with LowCross Buffer (Candor Bioscience, Germany) at 4 degree C overnight with gentle shaking.  After washing the slides, the arrays were incubated with biotinylated secondary antibody (Jackson Immunoresearch, USA) for one hour.  After washing, the arrays were incubated with streptavidin SureLightP-3 (Columbia Biosciences, USA) for one hour.  The slides were washed and dried by centrifugation before scanning.

scan_protocol: The slides were scanned with a Genepix 4200AL microarray scanner (Molecular Devices, USA). The scanner’s laser power and PMT gain were calibrated for each array in such a way that the saturated pixels constitute 0.2% of the total pixels in that array.  Fluorescence intensities were quantified by using Genepix Pro 6.0 (Molecular Devices, USA).

data_processing: log transformed raw data were used for analysis without normalization.

label: biotin-streptavidin

molecule: protein

organism: Homo sapiens

extract_protocol: fresh serum

tag: final diagnosis

value: NonTB

tag: age in years

tag: country of serum collection

value: Mexico

tag: m. tuberculosis culture

value: NEG

tag: acid fast bacilli (afb) smear microscopy

tag: previous history of active tb

value: NO

tag: bcg scar or history

tag: tuberculin skin test

tag: sample type

value: serum

tag: disease state

value: Non-tuberculosis


title: serum Non-TB SD2067

label_protocol: arrays were incubated with biotinylated secondary antibody (Jackson Immunoresearch, USA) for one hour.  After washing, the arrays were incubated with streptavidin SureLightP-3 (Columbia Biosciences, USA) for one hour.

value: YES

value: UNK


title: serum Smear + Culture+ TB SD2078

source_name: serum_Smear+ Culture+ TB

value: Smear+ Culture+ TB

value: POS

value: tuberculosis


title: serum Smear + Culture+ TB SD2069


title: serum Smear- Culture+ TB SD2065

source_name: serum_Smear- Culture+ TB

value: Smear- Culture+ TB


title: serum Non-TB SD2066


title: serum Smear + Culture+ TB SD2110


title: serum Smear + Culture+ TB SD2063


title: serum Non-TB SD2060


title: serum Smear + Culture+ TB SD2061


title: serum Non-TB SD2055


title: serum Non-TB SD2058


title: serum Non-TB SD2059


title: serum Non-TB SD2056


title: serum Smear + Culture+ TB SD2054


title: serum Non-TB SD2057


title: serum Smear- Culture+ TB SD2047


title: serum Smear + Culture+ TB SD2044


title: serum Smear + Culture+ TB SD2052


title: serum Non-TB SD2062


title: serum Smear + Culture+ TB SD2050


title: serum Smear- Culture+ TB SD2043


title: serum Smear- Culture+ TB SD2036


title: serum Smear + Culture+ TB SD2039


title: serum Smear + Culture+ TB SD2037


title: serum Non-TB SD2028


title: serum Smear- Culture+ TB SD2031


title: serum Smear + Culture+ TB SD2013


title: serum Smear + Culture+ TB SD2032


title: serum Smear + Culture+ TB SD2029


title: serum Smear + Culture+ TB SD2017


title: serum Non-TB SD2024


title: serum Smear + Culture+ TB SD2034


title: serum Non-TB SD2012


title: serum Smear + Culture+ TB SD1379

value: England


title: serum Non-TB SD2048


title: serum Non-TB SD1368


title: serum Non-TB SD1365


title: serum Smear- Culture+ TB SD1378


title: serum Non-TB SD1372


title: serum Smear + Culture+ TB SD1370


title: serum Non-TB SD1357


title: serum Non-TB SD1361


title: serum Non-TB SD1360


title: serum Non-TB SD1356


title: serum Smear + Culture+ TB SD2008


title: serum Non-TB SD1353


title: serum Smear- Culture+ TB SD1359


title: serum Smear- Culture+ TB SD1350


title: serum Non-TB SD1352


title: serum Non-TB SD2004


title: serum Smear + Culture+ TB SD1338


title: serum Non-TB SD1345


title: serum Non-TB SD1344


title: serum Non-TB SD1341


title: serum Non-TB SD1340


title: serum Smear + Culture+ TB SD1326


title: serum Non-TB SD1328


title: serum Non-TB SD1320


title: serum Non-TB SD1316


title: serum Non-TB SD1307


title: serum Non-TB SD1306


title: serum Non-TB SD1305


title: serum Non-TB SD1304


title: serum Non-TB SD1376


title: serum Non-TB SD1346


title: serum Non-TB SD1295


title: serum Smear + Culture+ TB SD1298


title: serum Smear + Culture+ TB SD1297


title: serum Smear + Culture+ TB SD1311


title: serum Non-TB SD1288


title: serum Non-TB SD1280


title: serum Non-TB SD1286


title: serum Non-TB SD1287


title: serum Non-TB SD1293


title: serum Non-TB SD1275


title: serum Non-TB SD1270


title: serum Non-TB SD1267


title: serum Non-TB SD1259


title: serum Non-TB SD1260


title: serum Non-TB SD1249


title: serum Smear- Culture+ TB SD1266


title: serum Smear + Culture+ TB SD1265


title: serum Non-TB SD1251


title: serum Smear- Culture+ TB SD1246


title: serum Non-TB SD1247


title: serum Non-TB SD1245


title: serum Smear + Culture+ TB SD1244


title: serum Smear- Culture+ TB SD1284


title: serum Non-TB SD1279


title: serum Non-TB SD1227


title: serum Non-TB SD1223


title: serum Non-TB SD1233


title: serum Non-TB SD1230


title: serum Non-TB SD1231


title: serum Non-TB SD1214


title: serum Smear + Culture+ TB SD1212


title: serum Non-TB SD1181


title: serum Non-TB SD1218


title: serum Non-TB SD1209


title: serum Smear + Culture+ TB SD1222


title: serum Non-TB SD1207


title: serum Non-TB SD1203


title: serum Non-TB SD1208


title: serum Non-TB SD1215


title: serum Non-TB SD1176


title: serum Smear- Culture+ TB SD1172


title: serum Non-TB SD1140


title: serum Smear + Culture+ TB SD1200


title: serum Smear + Culture+ TB SD1184


title: serum Non-TB SD1133


title: serum Non-TB SD1173


title: serum Non-TB SD1236


title: serum Non-TB SD1235


title: serum Non-TB SD1134


title: serum Non-TB SD1126


title: serum Non-TB SD1116


title: serum Non-TB SD1124


title: serum Non-TB SD1110


title: serum Non-TB SD1112


title: serum Smear + Culture+ TB SD1104


title: serum Non-TB SD1108


title: serum Non-TB SD1105


title: serum Non-TB SD1106


title: serum Non-TB SD1082


title: serum Non-TB SD1064


title: serum Smear + Culture+ TB SD1081


title: serum Smear + Culture+ TB SD1078


title: serum Non-TB SD1090


title: serum Non-TB SD1091


title: serum Non-TB SD1086


title: serum Non-TB SD1066


title: serum Non-TB SD1183


title: serum Smear- Culture+ TB SD1057


title: serum Non-TB SD1119


title: serum Non-TB SD1047


title: serum Non-TB SD1018


title: serum Smear + Culture+ TB SD1034


title: serum Non-TB SD1020


title: serum Smear + Culture+ TB SD1085


title: serum Smear + Culture+ TB SD1039


title: serum Non-TB SD1046


title: serum Non-TB SD1016


title: serum Latent Mky116 Day405

organism: Macaca fascicularis

value: Latent

tag: monkey id

tag: days after infection

value: Latent tuberculosis


title: serum Non-TB SD1004


title: serum Non-TB SD1007


title: serum Non-TB SD1001


title: serum Non-TB SD1015


title: serum Latent Mky116 Day373


title: serum Non-TB SD1103


title: serum Non-TB SD2026


title: serum Latent Mky116 Day231


title: serum Latent Mky116 Day301


title: serum Latent Mky116 Day267


title: serum Latent Mky116 Day344


title: serum Latent Mky116 Day56


title: serum Latent Mky116 Day120


title: serum Latent Mky116 Day181


title: serum Latent Mky116 Day91


title: serum Latent Mky109 Day0


title: serum Latent Mky116 Day28


title: serum Non-TB SD1017


title: serum Latent Mky116 Day0


title: serum Reactivation Mky115 Day455

value: Reactivation

value: Reactivated tuberculosis


title: serum Reactivation Mky115 Day636


title: serum Reactivation Mky115 Day252


title: serum Reactivation Mky115 Day328


title: serum Reactivation Mky115 Day232


title: serum Reactivation Mky115 Day371


title: serum Reactivation Mky115 Day412


title: serum Reactivation Mky115 Day181


title: serum Smear + Culture+ TB SD2027


title: serum Active Mky72 Day288

value: Active

value: Active tuberculosis


title: serum Reactivation Mky115 Day56


title: serum Reactivation Mky115 Day148


title: serum Reactivation Mky114 Day371


title: serum Reactivation Mky114 Day434


title: serum Reactivation Mky115 Day91


title: serum Reactivation Mky114 Day91


title: serum Reactivation Mky115 Day0


title: serum Reactivation Mky114 Day181


title: serum Reactivation Mky114 Day343


title: serum Reactivation Mky114 Day232


title: serum Active Mky72 Day245


title: serum Reactivation Mky114 Day309


title: serum Reactivation Mky114 Day56


title: serum Reactivation Mky114 Day252


title: serum Reactivation Mky114 Day29


title: serum Reactivation Mky114 Day0


title: serum Reactivation Mky115 Day29


title: serum Active Mky113 Day181


title: serum Reactivation Mky114 Day455


title: serum Active Mky113 Day134


title: serum Active Mky113 Day91


title: serum Reactivation Mky114 Day412


title: serum Non-TB SD1072

value: NonTB

value: NEG


title: serum Active Mky113 Day56

value: serum


title: serum Active Mky113 Day29


title: serum Active Mky72 Day181


title: serum Reactivation Mky114 Day149


title: serum Active Mky72 Day124


title: serum Active Mky113 Day0


title: serum Reactivation Mky112 Day232


title: serum Reactivation Mky112 Day262


title: serum Reactivation Mky112 Day56


title: serum Reactivation Mky111 Day461


title: serum Reactivation Mky111 Day827


title: serum Reactivation Mky112 Day181


title: serum Reactivation Mky112 Day0


title: serum Reactivation Mky111 Day344


title: serum Reactivation Mky111 Day405


title: serum Reactivation Mky112 Day29


title: serum Reactivation Mky111 Day771


title: serum Reactivation Mky111 Day301


title: serum Active Mky113 Day233


title: serum Reactivation Mky111 Day645


title: serum Reactivation Mky111 Day121


title: serum Latent Mky110 Day461


title: serum Reactivation Mky111 Day0


title: serum Latent Mky110 Day415


title: serum Latent Mky110 Day224


title: serum Active Mky72 Day54


title: serum Active Mky72 Day68


title: serum Reactivation Mky111 Day181


title: serum Reactivation Mky111 Day28


title: serum Reactivation Mky111 Day55


title: serum Reactivation Mky111 Day91


title: serum Latent Mky110 Day301


title: serum Reactivation Mky111 Day224


title: serum Latent Mky110 Day344


title: serum Latent Mky110 Day181


title: serum Latent Mky110 Day0


title: serum Latent Mky110 Day120


title: serum Latent Mky110 Day91


title: WT2_2

type: RNA

city: Atlanta

first: Gurudatta

last: Baraka Vishwanathan

state: GA

address: 1510 clifton road ne

department: Biology Department

institute: Emory University

hyb_protocol: Hybridization was performed by the FSU-NimbleGen Microarray Facility, following the NimbleGen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by the FSU-NimbleGen Microarray Facility, following the NimbleGen standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA using Partek software. only 16.6k probesets with unique transcript id (indicated in the EXEMPLAR_FOR column of the platform table)  were included the analysis. The partek software pakage was also used to normalise the data with biological replicates considering statstical cutoff 1.5 fold level as significantely changing  in transcription in the mutant ('BEAF-32_microarray_1.5fold.txt' available as a Series supplementary file).

molecule: total RNA

organism: Drosophila melanogaster

source_name: WT_wing imaginal tissue

label_protocol: Labeling was performed by the FSU-NimbleGen Microarray Facility, following the NimbleGen standard operating protocol. See www.nimblegen.com.

growth_protocol: Third instar larve from OR and Mutant BEAF-32 (homozygous)  were disected in PBS and RNA was prepared from RNAeasy kit from Qiagen.

extract_protocol: RNA was purified from wing imaginal disc tissue with the RNeasy kit (Qiagen) RNA was digested with DNAseI and followed by purification using RNeasy kit. cDNA synthesis was performed with the Megascript reverse transcription kit (Sigma)with OligodT test. cDNA was digested with RNase A for 30 min at 37°C and cleaned through a PCR purification column (Qiagen). Sample

treatment_protocol: Wing imaginal tissue from the Wildtype (OR) and age matched BEAF-32 mutant imaginal tissue.

tag: strain

value: Orgon R

tag: genotype/variation

value: Wildtype OR

tag: developmental stage

value: Third instar larvae (L3)

tag: tissue

value: wing imaginal disc tissue


title: serum Latent Mky109 Day356


title: serum Latent Mky109 Day385


title: serum Active Mky72 Day28


title: serum Latent Mky109 Day332


title: serum Latent Mky109 Day301


title: serum Latent Mky110 Day55


title: serum Latent Mky109 Day461


title: serum Active Mky152 Day426


title: serum Active Mky152 Day390


title: WT2_1


title: MT2_2

source_name: mut_wing imaginal tissue

value: BEAF-32 homozygous mutant


title: serum Latent Mky109 Day420


title: serum Latent Mky109 Day267


title: MT2_1


title: serum Active Mky152 Day300


title: serum Active Mky152 Day201


title: WT1_2


title: MT1_2


title: MT1_1


title: WT1_1


title: CIRM-BIA9_4°C_3 days_rep3

city: Fermoy

first: Marion

last: Dalmasso

address: Moorepark

department: Food Safety

country: Ireland

institute: Teagasc

description: strain CIRM-BIA9, 4°C, 3 days, repetition 3

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of  25µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer instructions. On completion of the fragmentation reaction,  25µl of  2x Hi-RPM hybridization buffer (Agilent) was added to the fragmentation mixture and hybridized to Agilent  specific  8x15K microarray for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and for 1 minute with 37°C GE Wash buffer 2 (Agilent),  and terminal 1 min at room temperature with Acetonetril.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner  (G2565CA) using one color scan setting for  8x15K array slides (Scan Area 61x21.6 mm, Scan resolution 5µM, Dye channel  is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters ( GE1_105_Dec08 and Grid: array specific) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Propionibacterium freudenreichii subsp. shermanii

source_name: strain CIRM-BIA9, 4°C, 3 days

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from (50-100 ng) RNA using the  Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Bacteria were grown in YEL broth under air atmosphere without agitation. Cultures were incubated at 30°C until they reached an OD650nm of about 2. Then, cultures were incubated for a further 3 days at 4°C. Lactate was added after 24 h of incubation at 4°C in order to prevent carbon starvation.

extract_protocol: Cells were harvested (8000 × g, 10 min, ambient temperature or 4°C regarding the sampling time). Cell pellets were suspended in 100 µl of TE buffer 1x (Qiagen, Courtaboeuf, France) containing lysozyme (20 mg/ml), and incubated for 15 min at 24 °C before RLT buffer (from the Qiagen RNeasy minikit) addition at a ratio of 35/10 (vol/vol). 50 mg of zirconium beads and 100 µl of sodium dodecyl sulfate (SDS, 20%) were then added and cells were disrupted for 2 × 90 seconds at 30 Hz by using a Retsch MM301 high-speed mixer mill (Grosseron, France). RNA was extracted according to the instructions of the RNeasy kit. Then DNase treatments of the RNA samples were performed using a DNA-free kit (Ambion, Texas, USA) according to the manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).


title: serum Active Mky152 Day144


title: CIRM-BIA9_4°C_3 days_rep1

description: strain CIRM-BIA9, 4°C, 3 days, repetition 1


title: CIRM-BIA9_4°C_3 days_rep2

description: strain CIRM-BIA9, 4°C, 3 days, repetition 2


title: CIRM-BIA482_4°C_3 days_rep3

description: strain CIRM-BIA482, 4°C, 3 days, repetition 3

source_name: strain CIRM-BIA482, 4°C, 3 days


title: CIRM-BIA482_4°C_3 days_rep2

description: strain CIRM-BIA482, 4°C, 3 days, repetition 2


title: CIRM-BIA482_4°C_3 days_rep1

description: strain CIRM-BIA482, 4°C, 3 days, repetition 1


title: serum Latent Mky110 Day28


title: CIRM-BIA472_4°C_3 days_rep3

description: strain CIRM-BIA472, 4°C, 3 days, repetition 3

source_name: strain CIRM-BIA472, 4°C, 3 days


title: serum Active Mky152 Day110


title: serum Active Mky152 Day60


title: serum Latent Mky109 Day224


title: serum Active Mky152 Day46


title: serum Active Mky152 Day0


title: serum Active Mky151 Day116


title: serum Active Mky152 Day88


title: serum Active Mky152 Day74


title: CIRM-BIA472_4°C_3 days_rep1

description: strain CIRM-BIA472, 4°C, 3 days, repetition 1


title: serum Active Mky151 Day91


title: CIRM-BIA472_4°C_3 days_rep2

description: strain CIRM-BIA472, 4°C, 3 days, repetition 2


title: serum Active Mky151 Day54


title: CIRM-BIA472_4°C_3 days_rep3ii

description: strain CIRM-BIA472, 4°C, 3 days, repetition 3 (technical)


title: CIRM-BIA123_4°C_3 days_rep1ii

description: strain CIRM-BIA123, 4°C, 3 days, repetition 1 (technical)

source_name: strain CIRM-BIA123, 4°C, 3 days


title: CIRM-BIA123_4°C_3 days_rep1

description: strain CIRM-BIA123, 4°C, 3 days, repetition 1


title: CIRM-BIA123_4°C_3 days_rep2

description: strain CIRM-BIA123, 4°C, 3 days, repetition 2


title: CIRM-BIA122_4°C_3 days_rep3

description: strain CIRM-BIA122, 4°C, 3 days, repetition 3

source_name: strain CIRM-BIA122, 4°C, 3 days


title: serum Active Mky151 Day0


title: serum Active Mky151 Day40


title: serum Latent Mky109 Day163


title: serum Latent Mky146 Day119


title: serum Latent Mky146 Day91


title: serum Latent Mky146 Day54


title: CIRM-BIA122_4°C_3 days_rep2

description: strain CIRM-BIA122, 4°C, 3 days, repetition 2


title: serum Latent Mky146 Day40


title: CIRM-BIA122_4°C_3 days_rep1

description: strain CIRM-BIA122, 4°C, 3 days, repetition 1


title: CIRM-BIA9_30°C_20h_rep3

description: strain CIRM-BIA9, 30°C, 20h, repetition 3

source_name: strain CIRM-BIA9, 30°C, 20h


title: CIRM-BIA118_4°C_3 days_rep2

description: strain CIRM-BIA118, 4°C, 3 days, repetition 2

source_name: strain CIRM-BIA118, 4°C, 3 days


title: CIRM-BIA118_4°C_3 days_rep1

description: strain CIRM-BIA118, 4°C, 3 days, repetition 1


title: CIRM-BIA9_30°C_20h_rep2

description: strain CIRM-BIA9, 30°C, 20h, repetition 2


title: serum Latent Mky146 Day0


title: serum Latent Mky145 Day550


title: serum Latent Mky145 Day600


title: CIRM-BIA9_30°C_20h_rep1ii

description: strain CIRM-BIA9, 30°C, 20h, repetition 1 (technical)


title: serum Latent Mky145 Day509


title: CIRM-BIA9_30°C_20h_rep1

description: strain CIRM-BIA9, 30°C, 20h, repetition 1


title: CIRM-BIA482_30°C_20h_rep2

description: strain CIRM-BIA482, 30°C, 20h, repetition 2

source_name: strain CIRM-BIA482, 30°C, 20h


title: serum Latent Mky145 Day481


title: CIRM-BIA482_30°C_20h_rep3

description: strain CIRM-BIA482, 30°C, 20h, repetition 3


title: CIRM-BIA482_30°C_20h_rep3ii

description: strain CIRM-BIA482, 30°C, 20h, repetition 3 (technical)


title: serum Latent Mky145 Day447


title: serum Latent Mky145 Day361


title: serum Latent Mky145 Day280


title: serum Latent Mky109 Day120


title: CIRM-BIA482_30°C_20h_rep1

description: strain CIRM-BIA482, 30°C, 20h, repetition 1


title: CIRM-BIA472_30°C_20h_rep2

description: strain CIRM-BIA472, 30°C, 20h, repetition 2

source_name: strain CIRM-BIA472, 30°C, 20h


title: CIRM-BIA472_30°C_20h_rep3

description: strain CIRM-BIA472, 30°C, 20h, repetition 3


title: serum Latent Mky145 Day200


title: serum Latent Mky145 Day124


title: serum Latent Mky145 Day181


title: BJ-4F-1_iPSCs

city: San Francisco

first: Kiichiro

last: Tomoda

state: CA

address: 1650 Owens Street

institute: The Gladstone Institutes, UCSF

description: Gene expression in pluripotent stem cells

hyb_protocol: Agilent standard protocol

scan_protocol: Agilent standard protocol

data_processing: Data was extracted using Agilent Feature Extraction Software.

source_name: Male hiPSC

label_protocol: Agilent standard protocol

growth_protocol: Cultured on SNL feeder cells in KDMEM medium containing 20% KSR and bFGF.

extract_protocol: Total RNA was isolated with Trizol.

tag: gender

value: male

tag: cell type

value: induced pluripotent stem cell (hiPSC)

tag: feeders

value: on SNLs


title: H14_ESCs

source_name: Male hESC

value: embryonic stem cell (hESC)


title: BJ-Mix_iPSCs


title: serum Latent Mky145 Day57

tag: final diagnosis

value: Latent

value: Latent tuberculosis


title: CIRM-BIA122_30°C_20h_rep2

description: strain CIRM-BIA122, 30°C, 20h, repetition 2

source_name: strain CIRM-BIA122, 30°C, 20h


title: CIRM-BIA123_30°C_20h_rep1

description: strain CIRM-BIA123, 30°C, 20h, repetition 1

source_name: strain CIRM-BIA123, 30°C, 20h


title: serum Latent Mky145 Day90


title: CIRM-BIA122_30°C_20h_rep3

description: strain CIRM-BIA122, 30°C, 20h, repetition 3


title: H9r-3F-2_iPSCs

source_name: Female hiPSC

value: female


title: H1_ESCs


title: serum Latent Mky145 Day28


title: K-3F-2_p5_iPSCs

tag: passsage number


title: H13B_ESCs


title: CIRM-BIA118_4°C_3 days_rep3

description: strain CIRM-BIA118, 4°C, 3 days, repetition 3


title: CIRM-BIA123_30°C_20h_rep3

description: strain CIRM-BIA123, 30°C, 20h, repetition 3


title: CIRM-BIA472_30°C_20h_rep1

description: strain CIRM-BIA472, 30°C, 20h, repetition 1


title: H9r-4F-2_iPSCs


title: CIRM-BIA118_30°C_20h_rep3

description: strain CIRM-BIA118, 30°C, 20h, repetition 3

source_name: strain CIRM-BIA118, 30°C, 20h


title: CIRM-BIA122_4°C_3 days_rep2ii

description: strain CIRM-BIA122, 4°C, 3 days, repetition 2 (technical)


title: serum Latent Mky145 Day0


title: CIRM-BIA123_30°C_20h_rep2

description: strain CIRM-BIA123, 30°C, 20h, repetition 2


title: CIRM-BIA118_30°C_20h_rep2

description: strain CIRM-BIA118, 30°C, 20h, repetition 2


title: H9r-4F-1_iPSCs


title: K-3F-1_p5_iPSCs


title: serum Reactivation Mky144 Day1021

value: Reactivation

value: Reactivated tuberculosis


title: 3S-5F-4_p15_iPSCs


title: serum Reactivation Mky144 Day928


title: serum Reactivation Mky144 Day874


title: serum Reactivation Mky144 Day845


title: serum Latent Mky109 Day91


title: serum Reactivation Mky144 Day818


title: serum Reactivation Mky144 Day636


title: serum Reactivation Mky144 Day791


title: serum Reactivation Mky144 Day656


title: ESI03_ESCs

source_name: Female hESC


title: H9-reporter_ESCs


title: H7_ESCs


title: H9_ESCs


title: CIRM-BIA118_30°C_20h_rep1

description: strain CIRM-BIA118, 30°C, 20h, repetition 1


title: serum Reactivation Mky144 Day530


title: serum Reactivation Mky144 Day564


title: serum Reactivation Mky144 Day593


title: serum Reactivation Mky144 Day488


title: shSLX1shSLY spermatid 1

city: Canterbury

first: Peter

middle: James

last: Ellis

state: Kent

address: Stacey Building

department: School of Biosciences

country: United Kingdom

institute: University of Kent

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were normalised using Illumina Genome Studio (V.2011.1), quantile normalisation. Manifest version 3 was used for annotation.

label: biotin

organism: Mus musculus

source_name: Separated round spermatids from shSLX1shSLY testis

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

growth_protocol: Cells were separated from whole testis tissue followed by centrifugal elutriation or sedimentation under unit gravity.

extract_protocol: RNA was extracted using TRI reagent followed by cleanup and DNAse I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: background strain

tag: transgene(s) carried

value: shSLY and shSLX1

value: deficient for both Sly and Slx/Slxl1

value: young adult

tag: age

value: ~8 weeks

tag: tissue origin

value: testis

value: round spermatid


title: S6

city: Bethesda

first: Jennifer

last: Barb

state: MD

address: 12 South Drive Bldg 12A Room 2001

department: DCB

institute: NIH

description: total RNA from sickle cell patient's whole  blood sample

hyb_protocol: Labeled and Fragmented ST cDNA was hybridized to Human Exon 1.0St arrays for 16 hours at 45C in an hybridization oven. Hybridized probes were detected by Streptavidin-Phycoerythrin stain

scan_protocol: Stained chips were scanned in Affymetrix GCS 3000G scanner

data_processing: Affymetrix Expression Console RMA normalization, core probesets only

source_name: PAXgene whole blood

label_protocol: Target labeling of RNA for Human exon arrays was done using the Affymetrix/Ambion WT cDNA synthsis and labeling protocol

growth_protocol: whole blood samples were collected from study participants in paxgene tube

extract_protocol: RNA extraction was performed using the PAXgene RNA extraction kit following qiagen's protocol

treatment_protocol: Samples were lyxed and stabilized in paxgene tubes and stored in the freezer until RNA extraction

value: whole blood RNA

tag: disease status

value: sickle cell patient


title: S5


title: S4


title: shSLX1 spermatid 2

description: replicate 2

source_name: Separated round spermatids from shSLX1 testis

value: male

value: deficient for Slx/Slxl1


title: serum Reactivation Mky144 Day280

tag: sample type

value: serum

tag: disease state


title: serum Latent Mky109 Day55

tag: monkey id

tag: days after infection


title: shSLX1shSLY spermatid 2

description: replicate 2

tag: genotype/variation


title: shSLX1 spermatid 1

description: replicate 1

tag: developmental stage


title: shSLX1 spermatid 3

description: replicate 3


title: shSLX1shSLY spermatid 3

description: replicate 3


title: S3

tag: tissue


title: WT spermatid 4

description: replicate 4

source_name: Separated round spermatids from WT testis

tag: gender

value: wild type


title: serum Reactivation Mky144 Day447


title: C2

description: total RNA from Healthy control volunteer's whole  blood sample

value: healthy control


title: shSLY spermatid 2

description: replicate 2

source_name: Separated round spermatids from shSLY testis

value: shSLY

value: deficient for Sly

tag: cell type


title: shSLY spermatid 1

description: replicate 1


title: WT spermatid 2

description: replicate 2


title: shSLY spermatid 3

description: replicate 3


title: C5


title: WT spermatid 1

description: replicate 1


title: S2


title: C3


title: C4


title: S1


title: serum Reactivation Mky144 Day124

value: Reactivation


title: serum Active Mky72 Day0

value: Active

value: Active tuberculosis


title: serum Reactivation Mky144 Day91

value: Reactivated tuberculosis


title: serum Reactivation Mky144 Day181


title: serum Latent Mky109 Day28

value: Latent

value: Latent tuberculosis


title: serum Reactivation Mky144 Day68


title: serum Reactivation Mky144 Day0


title: BCR-ABL-Blk expressing LSC, Biological rep1

city: Worcester

first: shaoguang

last: li

state: MA

address: 364 Plantation street

department: medicine

institute: Umass medical school

hyb_protocol: Approximately 2.0µg of fragmented and biotin-labeled cDNA is then hybridized onto a Mouse Gene ST 1.0 Array (Affymetrix, Santa Clara, CA.) for 16 hours at 45°C. Post-hybridization staining and washing are performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).

scan_protocol: The arrays are scanned with a GeneChip Scanner 3000. Images are acquired and cel files generated which are then used for analysis.

data_processing:
DNA microarray analysis was carried out to compare gene expression between BCR-ABL-expressing  LSCs and BCR-ABL-Blk-expressing LSCs and Vector-expressing Lin-c-Kit+Sca-1+ cells.
Average signal intensities for each probe set within arrays were calculated by and exported from Affymetrix’s Expression Console (Version 1.1) software using the RMA method which incorporates convolution background correction and a summarization based on a multi-array model fit robustly using the median polish algorithm. These values were read into R/maanova and quantile-normalized. For this experiment, three pairwise comparisons will be used to statistically resolve gene expression differences between strain groups using the R/maanova analysis package (Wu et al. 2003). Specifically, differentially expressed genes will be detected by using Fs, a modified F-statistic incorporating shrinkage estimates of variance components from within the R/maanova package (Cui et al. 2005, Wu et.al 2003). Statistical significance levels of the pairwise comparison will be calculated by permutation analysis (1000 permutations) and adjusted for multiple testing using the false discovery rate (FDR), q-value, method (Storey, 2002). Differentially expressed genes are declared at an FDR q-value threshold of 0.05.

source_name: BCR-ABL-Blk expressing LSC

label_protocol: The fragmented cDNA is then labeled by terminal transferase attaching a biotin molecule using Affymetrix proprietary DNA labeling Reagent.

growth_protocol: We used the bone marrow transplantation mouse model of CML as an assay system, in which bone marrow cells from donor mice pre-treated with 5-fluorouracil (5-FU) and transduced with BCR-ABL result in development of CML in recipient mice. We transduced bone marrow cells from C57BL/6 (B6) mice with retrovirus containing BCR-ABL-GFP, BCR-ABL-Blk-GFP, or GFP alone under conditions for induction of CML, followed by transplantation of the transduced cells into B6 recipient mice. 14 days after BMT, bone marrow cells were isolated and subsequently sorted by FACS for LSCs (GFP+Lin-c-Kit+Sca-1+) .

extract_protocol: Total RNA is isolated by following the protocol for the RNeasy Micro Kit, and quality is assessed using a 2100 Bioanalyzer instrument and RNA 6000 Pico LabChip assay (Agilent Technologies, Palo Alto, CA). Utilizing the GeneChip Whole Transcript Sense Target Labeling Assay kit (Affymetrix, Santa Clara, CA.) between 100-300ng of total RNA undergoes reverse transcription with random hexamers tagged with T7 sequence. The double stranded cDNA that is generated is then amplified by T7 RNA polymerase to produce cRNA. Second cycle first strand cDNA synthesis then takes place incorporating dUTP which is later used as sites where fragmentation occurs by utilizing an uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1 enzyme mix.

tag: transgene

value: BCR-ABL-Blk

tag: strain

value: LSCs

value: WT

value: 8 weeks


title: WT spermatid 3

description: replicate 3

value: male

value: young adult

value: ~8 weeks

value: testis

value: round spermatid


title: serum Reactivation Mky144 Day54

tag: final diagnosis

value: serum


title: BCR-ABL-Blk expressing LSC, Biological rep2


title: serum Reactivation Mky144 Day40


title: BCR-ABL expressing LSC, Biological rep2

source_name: BCR-ABL expressing LSC

value: BCR-ABL


title: serum Reactivation Mky144 Day354

value: Reactivation


title: sh-scr_OHT_rep3

city: Durham

first: Igor

last: Shats

state: NC

address: 101 Science Drive

institute: Duke University

description: Gene expression data from U2OS ER-E2F1 cell line

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

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

data_processing: The data were analyzed with MAS5.0 using Bioconductor

source_name: Cultured cell line

label_protocol: Biotinylated cRNA were prepared using Ambion MessageAmp Premier labeling kit.

growth_protocol: Serum-starved U2OS ER-E2F1 cells

extract_protocol: RNeasy mini kit (Qiagen)

treatment_protocol: Lentiviral FOXO knocdown and six hours 20 nM OHT

value: osteosarcoma cell line

tag: cell line

value: U2OS ER-E2F1

tag: transfection

tag: treatment

value: six hours 20 nM OHT


title: Vector expressing HSC, Biological rep2

source_name: Vector expressing HSC

value: Vector control

value: HSCs

tag: age


title: shFOXO707_OHT_rep1


title: shFOXO33_OHT_rep2


title: shFOXO33_OHT_rep1


title: sh-scr_OHT_rep4


title: shFOXO707_OHT_rep2


title: sh-scr_con_rep4

value: con


title: sh-scr_OHT_rep2


title: DTCs (bone marrow aspirates) from Patient 11 (4424556027_C)

city: Toronto

first: Dong-Yu

last: Wang

address: 610 University Ave

country: Canada

institute: UHN-PMH-OCI

hyb_protocol: Illumina's protocol

scan_protocol: Illumina's protocol

data_processing: Image data were processed by BeadStudio software using background subtraction and Quantile normalization. The methods to adjust the normalized intensity values see MAQC Consortium’s description [PMID: 16964229]. Log2 expression ratio of an intensity value to the average signal in all samples for each transcript was calculated.

label_protocol: Illumina's protocol

extract_protocol: Total RNA was isolated using Qiagen (Germantown, MD) AllPrep DNA/RNA/Protein extraction kits

value: disseminated tumour cells

tag: disease

value: breast cancer


title: sh-scr_con_rep3


title: shFOXO707_con


title: sh-scr_con_rep2


title: MTCs (Computed Tomography) from Patient 11 (4424556027_E)

value: metastatic tumour cells


title: sh-scr_OHT_rep1


title: MTCs (Computed Tomography) from Patient 13 (4424556027_G)


title: BCR-ABL expressing LSC, Biological rep1

value: LSCs

value: WT

value: 8 weeks


title: MTCs (Computed Tomography) from Patient 12 (4424556027_F)


title: Vector expressing HSC, Biological rep1


title: DTCs (bone marrow aspirates) from Patient 13 (4424556027_D)


title: DTCs (bone marrow aspirates) from Patient 7 (4424556027_A)


title: shFOXO33_con


title: DTCs (bone marrow aspirates) from Patient 8 (4424556027_B)


title: PF_gametocyte D12_delta PfPuf2_Rep2

city: Tampa

first: JUN

last: MIAO

state: Florida

address: 3720 Spectrum Boulevard, MDC84

department: Internal Medicine

institute: University of South Florida

description: This sample is of Plasmodium falciparum 3D7 with deletion of PfPuf2 at gametocyte stage V. It is the second of three mutant strain biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by Genomics Core Facility of Pennsylvania State University. Incubate at 95C for 5 minutes, followed by 42C for 5 minutes. Attach appropriate mixer to the array and add hybridizations solution according to the manufacturer’s instructions (Roche NimbleGen). Hybridize with mixing in a MAUI hybridization instrument overnight at 42C.

scan_protocol: Scanning was performed by Genomics Core Facility of Pennsylvania State University by using Axon GenePix 4000B.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in DNASTAR software-ArrayStar 4 (dnastar.com).

organism: Plasmodium falciparum 3D7

source_name: Plasmodium falciparum dalta PfPuf2, gametocyte stage V

label_protocol: Labeling was done by Genomics Core Facility of Pennsylvania State Univerity. Amplify 1ug of each sample using the Ambion (Life Technologies) Amino Allyl MessageAmp II aRNA Amplification Kit. Dye couple 15 ug of aRNA with Cy3 or Cy5 (GE Health Care #RPN5661), as appropriate, and subsequently purify according to the Ambion Kit instructions.(AM1753).

growth_protocol:
P. falciparum clone 3D7 and dalta PfPuf2 mutant were maintained as described previously (Trager and Jensen, 1976)
Induction of gametocytogenesis was performed as described (Fivelman et al., 2007).  Ganetocytes were harvested at Day 8 (stage III) and Day 12 (stage V)

extract_protocol: Total RNA was extracted using the Trizol reagent ((invirtogen.com)

value: delta-PfPuf2 mutant

value: Gametocyte Stage V

tag: phenotype

value: higher ratio of male/female gametocyte


title: sh-scr_con_rep1


title: PF_gametocyte D12_wildtype_Rep2

description: This sample is of wild-type Plasmodium falciparum 3D7 at gametocyte stage V. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Plasmodium falciparum 3D7 wildtype, gametocyte stage V

value: wild type

value: normal


title: MTCs (Computed Tomography) from Patient 10 (4424556026_G)


title: PF_gametocyte D12_delta PfPuf2_Rep3

description: This sample is of Plasmodium falciparum 3D7 with deletion of PfPuf2 at gametocyte stage V. It is the third of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: MTCs (Computed Tomography) from Patient 8 (4424556026_F)


title: PF_gametocyte D12_wildtype_Rep3

description: This sample is of wild-type Plasmodium falciparum 3D7 at gametocyte stage V. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: PF_gametocyte D12_delta PfPuf2_Rep1

description: This sample is of Plasmodium falciparum 3D7 with deletion of PfPuf2 at gametocyte stage V. It is the first of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: PF_gametocyte D12_wildtype_Rep1

description: This sample is of wild-type Plasmodium falciparum 3D7 at gametocyte stage V. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: MTCs (Computed Tomography) from Patient 3 (4424556026_E)


title: DTCs (bone marrow aspirates) from Patient 6 (4424556026_D)


title: PF_gametocyte D8_delta PfPuf2_Rep3

description: This sample is of Plasmodium falciparum 3D7 with deletion of PfPuf2 at gametocyte stage III. It is the third of three mutant strain biological replicates used in this experiment, each from separate cultures.

source_name: Plasmodium falciparum dalta PfPuf2, gametocyte stage III

value: Gametocyte Stage III


title: DTCs (bone marrow aspirates) from Patient 2 (4424556026_B)


title: DTCs (bone marrow aspirates) from Patient 1 (4424556026_A)


title: ZHBTc4 stem cell with dox and streptozotocin treatment, rep1

city: Youngun dong, jongro gu,Seoul

first: Taewan

last: Kim

address: biomedical science building 202ho

department: biomedical science

country: South Korea

institute: Seoul National University of medicine

description: Sample name: E

data_processing: Array data were filtered by detection p-value < 0.05 (similar to signal to noise) in at least 50% samples (we applied a filtering criterion for data analysis; higher signal value was required to obtain a detection p-value < 0.05). Selected gene signal value was transformed by logarithm and normalized by quantile method with IlluminaGUI in R.

source_name: E14 stem cell

label_protocol: Biotinylated cRNA were prepared for Illumina arrays per standard Illumina protocol

extract_protocol: RNA was extracted with Trizol reagent

value: ZHBTc4 stem cell

value: dox and streptozotocin


title: DTCs (bone marrow aspirates) from Patient 4 (4424556026_C)


title: ZHBTc4 stem cell with dox treatment, rep1

description: Sample name: D

value: dox


title: PF_gametocyte D8_delta PfPuf2_Rep1

description: This sample is of Plasmodium falciparum 3D7 with deletion of PfPuf2 at gametocyte stage III. It is the first of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: PF_gametocyte D8_delta PfPuf2_Rep2

description: This sample is of Plasmodium falciparum 3D7 with deletion of PfPuf2 at gametocyte stage III. It is the second of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: EB2, embryonic body formation for 2 days, rep 1

description: Sample name: B1

value: EB2, embryonic body


title: EB2, embryonic body formation for 2 days with streptozotocin, rep 1

description: Sample name: C1

value: streptozotocin


title: PF_gametocyte D8_wildtype_Rep3

description: This sample is of wild-type Plasmodium falciparum 3D7 at gametocyte stage III. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Plasmodium falciparum 3D7 wildtype, gametocyte stage III


title: E14 stem cell, undiffrentiated state, rep 2

description: Sample name: A2

value: E14 stem cell


title: emb24h_MeDIP Repl1

type: genomic

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

hyb_protocol: Hybridization done by Nimblegen as per normal service protocol

scan_protocol: Scanning done by Nimblegen as per normal service protocol

data_processing: log2 (MeDIP/Input) with biweight mean of values subtracted

molecule: genomic DNA

organism: Danio rerio

source_name: emb24h MeDIP ChIP DNA

label_protocol: Labeling done by Nimblegen as per normal service protocol

growth_protocol: Fish and embryos grown as per AAALAC certification

extract_protocol: Embryos and sperm were lysed in lysis buffer, proteinase K treated and sonicated with a Bioruptor (Diagenode). DNA was purified by PCI and ethanol precipitation, and treated with RNase. DNA was re-sonicated to 300-1000 bp fragments. MeDIPs were performed using 4 µg DNA and 5 µl (10 ng/µl) 5-methylcytosine antibody. Samples were washed, deproteinized and DNA purified. Input DNA was fragmented and treated as above without any immunoprecipitation. MeDIP and input DNA was amplified (Sigma-Aldrich, WGA2), cleaned up, eluted and processed for array hybridization (Roche-Nimblegen).

value: Embryonic cells

value: AB

value: 24 hpf embryo, pharyngula stage

tag: medip antibody

value: Anti-5-methylcytosine antibody (10 ng/µl)

tag: medip antibody catalog#

tag: medip antibody vendor

value: Diagenode

tag: sample preparation protocol

value: Chorions were removed with 1 mg/ml pronase and embryos washed in egg water. Yolk proteins were removed in a de-yolking buffer, embryos were sedimented and flash-frozen.

source_name: emb24h MeDIP Input DNA

tag: antibody

value: none, input


title: E14 stem cell, undiffrentiated state, rep 1

description: Sample name: A1


title: Sirt1 siRNA KD1 1

status: Public on Jul 05 2012

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

institute: Newcastle University

hyb_protocol: 750ng of biotinylated cRNA was hybridised to Illumina HT-12 v4 arrays using methods adapted from the Whole-Genome Gene Expression Direct Hybridization Assay Illumina protocol by ServiceXS

scan_protocol: Samples scanned using Illumina iScan array scanner to Illumina protocols

data_processing: Raw data is the output from Illumina Genomestudio v 2010.1

label_protocol: Illumina TotalPrep-96 RNA amplification kit was used to generate Biotin labeled cRNA according to manufacturers instructions

growth_protocol: Caco-2 cells were maintained  in DMEM medium, 10% Fetal Calf Serum at 37oC, 5% non-essential amino acids

extract_protocol: Total RNA was extracted using Trizol followed by Invitrogen PureLink RNA mini kit

treatment_protocol: Caco-2 cells were transfected with either the Sirt1 overexpression construct (pCMV-ENTRY Sirt1) or negative control (pCMV-Neo).  For knockdowns cells were transfected with one of two non-overlapping siRNAs and control samples with a low-GC scrambled siRNA control and cells lysed after 72 hours

value: Sirt1 siRNA Knockdown 1


title: Sirt1 siRNA KD2 2

value: Sirt1 siRNA Knockdown 2


title: Sirt1 siRNA KD1 2


title: ACD gDNA 96.3

city: Rotterdam

first: Erwin

last: Brosens

state: - If in U.S, Select a State -

address: Dr molewaterplein 50

department: Clinical genetics

country: Netherlands

institute: ErasmusMC

description: ACD patient

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505C scanner, Images were quantified using Agilent Feature Extraction Software (version A.8.1.3).

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Promega Male 25707201

label_protocol: Enzo labeling Wash Procedure A (without Stabilization and Drying Solution)   according to Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Enzymatic Labeling for Blood, Cells or Tissues (with a High Throughput option) Protocol Version 6.3 October 2010

growth_protocol: Cell cultures were performed in 75 cm2 culture flasks. (BD Biosciences Falcon™, San Jose, CA, USA) Incubation was performed at 37 º C,  5% CO2 in HAMF10 medium,12.5% Fetal Bovine Serum (Biowhittaker, CA, USA) and 1% Penicillin-streptomycin. The medium was changed every 2-3 days and the day before harvesting the cells. When harvesting the cells, the medium was removed and the cells were rinsed with DPBS (GIBCO®/ Invitrogen, Carlsbad, CA, USA) and trypsinised with TrypLE™ Express (Invitrogen, Carlsbad, CA, USA)  for exactly 5 minutes at 37 º C 5% CO2. The trypsinisation reaction was stopped with culture medium and the cells centrifuged for 5 min at 200g.

extract_protocol: DNA was extracted using the Qiagen DNA blood midikit (blood sample) and Qiagen DNA minikit (fibroblast cell culture)

treatment_protocol: peripheral blood was stored at +4°C prior to DNA extraction

value: Male

value: normal reference

source_name: Fibroblast culture derived Genomic DNA of ACD/MPV patient 96.3

value: ACD/MPV


title: Sirt1 siRNA KD2 3


title: sperm_MeDIP Repl2

source_name: sperm MeDIP ChIP DNA

growth_protocol: Fish and embryos grown as per AAALAC certification, sperm collected as described in Draper, B.W., Moens, C.B. A High-Throughput Method For Zebrafish Sperm Cryopreservation and In Vitro Fertilization. J. Vis. Exp. (29), e1395, DOI : 10.3791/1395 (2009).

value: Sperm

tag: developmental stage

value: Sperm [from adult males]

value: Zebrafish males were starved for 24 hrs and anesthetized in fish water with 0.016% tricaine (Sigma, Cat. No A-5040) immediately before sperm collection. Sperm was obtained with a capillary tube under gentle suction and flash frozen in liq. N2. Prior to DNA isolation, sperm was washed three times in T10N150E10 buffer (10 mM Tris-HCl pH 7.8, 150 mM NaCl,10 mM EDTA pH 8.0)

source_name: sperm MeDIP Input DNA


title: Sirt1 siRNA control 1

value: Sirt1 siRNA Knockdown Control


title: OE Sirt1 2

value: Sirt1 Overexpression


title: Sirt1 siRNA control 2


title: OE Sirt1 3


title: emb24h_MeDIP Repl2

value: Embryonic cells


title: ZF4_MeDIP_Repl1

source_name: MeDIP ChIP DNA

growth_protocol: Cell grown under standard condition as per Driever and Rangini, 1993 In vitro Cell Dev Biol.Anim 294, 749

tag: biomaterial provider

value: American Type Culture Collection

value: Embryo

tag: antibody catalog#

tag: antibody vendor

value: Cells were harvesdted by trypsination and flash frozen in liq. N2 as dry pellets

source_name: MeDIP Input DNA from ZF4 cells


title: Slide 176569

city: Jena

first: Akos

middle: T

last: Kovacs

address: Neugasse 23

department: Institute of Microbiology

country: Germany

institute: Friedrich Schiller University of Jena

description:
Net{A} is the raw signal of channel A minus the local corner background signal of channel A
Net{B}is the raw signal of channel B minus the local corner background signal of channel B

hyb_protocol: The protocol was performed as described in Lulko, et. al. J. Mol. Microbiol. Biotechnol. 12:82-95 PMID: 17183215

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner

data_processing: Dual-channel array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP as previously described (den Hengst et al J. Biol. Chem. 280:34332-34342; PMID: 16040604). Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets. Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of mutant strain over the wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.

organism: Bacillus cereus ATCC 14579

source_name: B. cereus codY deletion

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences)

growth_protocol: Cultures grown in BHI medium

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Lulko, et. al. J. Mol. Microbiol. Biotechnol. 12:82-95 PMID: 17183215). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

treatment_protocol: Samples were harvested at the exponential-growth phase (OD600=0,75)

tag: strain

value: codY

tag: genotype/variation

value: codY deletion

source_name: B. cereus wild type

value: wild type


title: Slide 176568


title: Slide 176570


title: PF_gametocyte D8_wildtype_Rep2

description: This sample is of wild-type Plasmodium falciparum 3D7 at gametocyte stage III. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.

value: Gametocyte Stage III

value: normal


title: OE Sirt1 1

tag: cell line


title: Slide 176567


title: EB2, embryonic body formation for 2 days with streptozotocin, rep 2

description: Sample name: C2

tag: cell type

value: EB2, embryonic body

value: streptozotocin


title: OE control 2

tag: treatment

value: Overexpression Control


title: postMBT_MeDIP Repl2

source_name: postMBT MeDIP ChIP DNA

value: AB

value: postMBT, 5.3 hpf, 50% epiboly

value: Anti-5-methylcytosine antibody (10 ng/µl)

value: Diagenode

value: Chorions were removed with 1 mg/ml pronase and embryos washed in egg water. Yolk proteins were removed in a de-yolking buffer, embryos were sedimented and flash-frozen.

source_name: postMBT MeDIP Input DNA

value: none, input


title: OE control 3


title: OE control 1


title: Gastric non-malignant 4348_Norm_Stom_U133A

city: Singapore

first: Wu

last: Yonghui

state: Choose your state

address: 8 College Road

country: Singapore

institute: NCCS

description: gene expression data from gastric non-malignant 4348_Norm_Stom_U133A

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16-18 hr at 45C on GeneChip Human Genome U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner GCS3000 7G.

data_processing: The data were RMA normalized with BRB-ArrayTools.

label: Biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2-5 ug total RNA

extract_protocol: Total RNA was extracted from gastric tissues using RNeasy mini spin columns (Qiagen) according to the instructions of the manufacturer.

tag: tissue

value: Gastric non-malignant


title: Gastric tumor 4351_Stom_Tum_U133A

description: gene expression data from gastric tumor 4351_Stom_Tum_U133A

source_name: Gastric tumor 4351_Stom_Tum_U133A

value: Gastric tumor

tag: intra-tumoral stroma


title: Gastric tumor 4350_Stom_Tum_U133A

description: gene expression data from gastric tumor 4350_Stom_Tum_U133A

source_name: Gastric tumor 4350_Stom_Tum_U133A


title: ACD gDNA 95.3

description: ACD patient

tag: gender

value: Male

tag: disease

value: normal reference

source_name: Blood derived Genomic DNA of ACD/MPV patient 95.3

value: Female

value: ACD/MPV


title: Gastric non-malignant 4347_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 4347_Norm_Stom_U133A


title: Gastric tumor 4349_Stom_Tum_U133A

description: gene expression data from gastric tumor 4349_Stom_Tum_U133A

source_name: Gastric tumor 4349_Stom_Tum_U133A


title: sperm_MeDIP Repl1

value: Sperm

value: Sperm [from adult males]

tag: medip antibody

tag: medip antibody catalog#

value: Zebrafish males were starved for 24 hrs and anesthetized in fish water with 0.016% tricaine (Sigma, Cat. No A-5040) immediately before sperm collection. Sperm was obtained with a capillary tube under gentle suction and flash frozen in liq. N2. Prior to DNA isolation, sperm was washed three times in T10N150E10 buffer (10 mM Tris-HCl pH 7.8, 150 mM NaCl,10 mM EDTA pH 8.0)


title: MBT_MeDIP Repl1

source_name: MBT MeDIP ChIP DNA

value: Embryonic cells

value: MBT, 3.5 hpf, 1000+-cell stage

tag: sample preparation protocol

source_name: MBT MeDIP Input DNA


title: ZF4_MeDIP_Repl2

value: American Type Culture Collection

value: Embryo

tag: antibody

value: Cells were harvesdted by trypsination and flash frozen in liq. N2 as dry pellets


title: Gastric tumor 4352_Stom_Tum_U133A

description: gene expression data from gastric tumor 4352_Stom_Tum_U133A

source_name: Gastric tumor 4352_Stom_Tum_U133A


title: Gastric non-malignant 3866_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 3866_Norm_Stom_U133A


title: Gastric tumor 3863_Stom_Tum_U133A

description: gene expression data from gastric tumor 3863_Stom_Tum_U133A

source_name: Gastric tumor 3863_Stom_Tum_U133A


title: Gastric non-malignant 4346_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 4346_Norm_Stom_U133A


title: Gastric tumor 3860_Stom_Tum_U133A

description: gene expression data from gastric tumor 3860_Stom_Tum_U133A

source_name: Gastric tumor 3860_Stom_Tum_U133A


title: Gastric tumor 3865_Stom_Tum_U133A

description: gene expression data from gastric tumor 3865_Stom_Tum_U133A

source_name: Gastric tumor 3865_Stom_Tum_U133A


title: Gastric non-malignant 4345_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 4345_Norm_Stom_U133A


title: Gastric tumor 3859_Stom_Tum_U133A

description: gene expression data from gastric tumor 3859_Stom_Tum_U133A

source_name: Gastric tumor 3859_Stom_Tum_U133A


title: Gastric tumor 3862_Stom_Tum_U133A

description: gene expression data from gastric tumor 3862_Stom_Tum_U133A

source_name: Gastric tumor 3862_Stom_Tum_U133A


title: Gastric tumor 3864_Stom_Tum_U133A

description: gene expression data from gastric tumor 3864_Stom_Tum_U133A

source_name: Gastric tumor 3864_Stom_Tum_U133A


title: Gastric tumor 3857_Stom_Tum_U133A

description: gene expression data from gastric tumor 3857_Stom_Tum_U133A

source_name: Gastric tumor 3857_Stom_Tum_U133A


title: Gastric non-malignant 3855_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 3855_Norm_Stom_U133A


title: Gastric non-malignant 3856_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 3856_Norm_Stom_U133A


title: Gastric tumor 3861_Stom_Tum_U133A

description: gene expression data from gastric tumor 3861_Stom_Tum_U133A

source_name: Gastric tumor 3861_Stom_Tum_U133A


title: Gastric tumor 3858_Stom_Tum_U133A

description: gene expression data from gastric tumor 3858_Stom_Tum_U133A

source_name: Gastric tumor 3858_Stom_Tum_U133A


title: PF_gametocyte D8_wildtype_Rep1

description: This sample is of wild-type Plasmodium falciparum 3D7 at gametocyte stage III. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Plasmodium falciparum 3D7 wildtype, gametocyte stage III

value: wild type

tag: developmental stage

value: Gametocyte Stage III

tag: phenotype

value: normal


title: Gastric non-malignant 4344_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 4344_Norm_Stom_U133A

value: Gastric non-malignant


title: Gastric non-malignant 3851_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 3851_Norm_Stom_U133A


title: Gastric non-malignant 3854_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 3854_Norm_Stom_U133A


title: Gastric non-malignant 3852_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 3852_Norm_Stom_U133A


title: Gastric non-malignant 3850_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 3850_Norm_Stom_U133A


title: Gastric non-malignant 3849_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 3849_Norm_Stom_U133A


title: Gastric non-malignant 3853_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 3853_Norm_Stom_U133A


title: preMBT_MeDIP Repl1

source_name: preMBT MeDIP ChIP DNA

value: AB

value: preMBT, 2.5 hpf, 256-cell stage

value: Anti-5-methylcytosine antibody (10 ng/µl)

tag: antibody catalog#

value: Diagenode

value: Chorions were removed with 1 mg/ml pronase and embryos washed in egg water. Yolk proteins were removed in a de-yolking buffer, embryos were sedimented and flash-frozen.

source_name: preMBT MeDIP Input DNA

value: none, input


title: Gastric non-malignant 3847_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 3847_Norm_Stom_U133A


title: EB2, embryonic body formation for 2 days, rep 2

description: Sample name: B2

source_name: E14 stem cell

value: EB2, embryonic body


title: Gastric non-malignant 3846_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 3846_Norm_Stom_U133A


title: Gastric non-malignant 3843_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 3843_Norm_Stom_U133A


title: Gastric tumor 3819_Stom_Tum_U133A

description: gene expression data from gastric tumor 3819_Stom_Tum_U133A

source_name: Gastric tumor 3819_Stom_Tum_U133A

value: Gastric tumor


title: Gastric non-malignant 3821_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 3821_Norm_Stom_U133A


title: Gastric tumor 3820_Stom_Tum_U133A

description: gene expression data from gastric tumor 3820_Stom_Tum_U133A

source_name: Gastric tumor 3820_Stom_Tum_U133A


title: Gastric tumor 3818_Stom_Tum_U133A

description: gene expression data from gastric tumor 3818_Stom_Tum_U133A

source_name: Gastric tumor 3818_Stom_Tum_U133A


title: Gastric non-malignant 3842_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 3842_Norm_Stom_U133A


title: Gastric non-malignant 3844_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 3844_Norm_Stom_U133A


title: Gastric non-malignant 3823_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 3823_Norm_Stom_U133A


title: Gastric tumor 3817_Stom_Tum_U133A

description: gene expression data from gastric tumor 3817_Stom_Tum_U133A

source_name: Gastric tumor 3817_Stom_Tum_U133A


title: Gastric non-malignant 3841_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 3841_Norm_Stom_U133A


title: Gastric non-malignant 3822_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 3822_Norm_Stom_U133A


title: Gastric non-malignant 3845_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 3845_Norm_Stom_U133A


title: Gastric tumor 3813_Stom_Tum_U133A

description: gene expression data from gastric tumor 3813_Stom_Tum_U133A

source_name: Gastric tumor 3813_Stom_Tum_U133A


title: Gastric tumor 3812_Stom_Tum_U133A

description: gene expression data from gastric tumor 3812_Stom_Tum_U133A

source_name: Gastric tumor 3812_Stom_Tum_U133A


title: Gastric tumor 3811_Stom_Tum_U133A

description: gene expression data from gastric tumor 3811_Stom_Tum_U133A

source_name: Gastric tumor 3811_Stom_Tum_U133A


title: Gastric tumor 3816_Stom_Tum_U133A

description: gene expression data from gastric tumor 3816_Stom_Tum_U133A

source_name: Gastric tumor 3816_Stom_Tum_U133A


title: Gastric non-malignant 3848_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 3848_Norm_Stom_U133A


title: Gastric tumor 3810_Stom_Tum_U133A

description: gene expression data from gastric tumor 3810_Stom_Tum_U133A

source_name: Gastric tumor 3810_Stom_Tum_U133A


title: postMBT_MeDIP Repl1

source_name: postMBT MeDIP ChIP DNA

value: Embryonic cells

value: postMBT, 5.3 hpf, 50% epiboly

tag: antibody vendor

source_name: postMBT MeDIP Input DNA


title: Chx10Cre; Rb lox/lox; p107 -/-; Dicer1 lox/lox 3

city: Gent

first: Pieter

last: mestdagh

address: De Pintelaan 185

country: Belgium

institute: Center for Medical Genetics

description:
DKO; DicKO-3_fig1
fig1 in paper

data_processing: Raw miRNA expression data were normalized using the global mean miRNA expression value (Mestdagh et al.,Genome Biology, 2009)

label: FAM

label_protocol: megaplex RT using 522 stem-loop miRNA primers followed by 14-cycle pre-amplification

growth_protocol: none, fresh primary cells

extract_protocol: microRNeasy, Qiagen

value: retina

tag: background strain

value: mixed

value: DKO; DicKO


title: Dicer1 lox/lox 3

description:
DicKO-3_fig1
fig1 in paper

source_name: Dicer1 lox/lox

tag: genotype/variation

value: DicKO


title: Chx10Cre; Rb lox/lox; p107 -/-; Dicer1 lox/lox 2

description:
DKO; DicKO-2_fig1
fig1 in paper


title: Chx10Cre; Rb lox/lox; p107 -/-; Dicer1 lox/lox 4

description:
DKO; DicKO-4_fig1
fig1 in paper


title: Chx10Cre; Rb lox/lox; p107 -/-; Dicer1 lox/lox 1

description:
DKO; DicKO-1_fig1
fig1 in paper


title: MBT_MeDIP Repl2

source_name: MBT MeDIP ChIP DNA

tag: strain

value: MBT, 3.5 hpf, 1000+-cell stage

source_name: MBT MeDIP Input DNA


title: Gastric tumor 3815_Stom_Tum_U133A

description: gene expression data from gastric tumor 3815_Stom_Tum_U133A

source_name: Gastric tumor 3815_Stom_Tum_U133A


title: Gastric tumor 3803_Stom_Tum_U133A

description: gene expression data from gastric tumor 3803_Stom_Tum_U133A

source_name: Gastric tumor 3803_Stom_Tum_U133A


title: Gastric tumor 3793_Stom_Tum_U133A

description: gene expression data from gastric tumor 3793_Stom_Tum_U133A

source_name: Gastric tumor 3793_Stom_Tum_U133A


title: Gastric non-malignant 3800_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 3800_Norm_Stom_U133A


title: Dicer1 lox/lox 2

description:
DicKO-2_fig1
fig1 in paper


title: Gastric non-malignant 3807_Norm_Stom_Mus_U133A

description: gene expression data from gastric non-malignant 3807_Norm_Stom_Mus_U133A


title: Gastric non-malignant 3797_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 3797_Norm_Stom_U133A


title: Gastric non-malignant 3804_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 3804_Norm_Stom_U133A


title: Gastric non-malignant 3802_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 3802_Norm_Stom_U133A


title: Gastric non-malignant 3805_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 3805_Norm_Stom_U133A


title: Gastric tumor 3796_Stom_Tum_U133A

description: gene expression data from gastric tumor 3796_Stom_Tum_U133A

source_name: Gastric tumor 3796_Stom_Tum_U133A


title: Gastric tumor 3794_Stom_Tum_U133A

description: gene expression data from gastric tumor 3794_Stom_Tum_U133A

source_name: Gastric tumor 3794_Stom_Tum_U133A


title: Gastric non-malignant 3808_Norm_Stom_Mus_U133A

description: gene expression data from gastric non-malignant 3808_Norm_Stom_Mus_U133A


title: Gastric non-malignant 3801_Norm_Stom_Mus_U133A

description: gene expression data from gastric non-malignant 3801_Norm_Stom_Mus_U133A


title: Gastric non-malignant 3806_Norm_Stom_Mus_U133A

description: gene expression data from gastric non-malignant 3806_Norm_Stom_Mus_U133A


title: Gastric non-malignant 3791_Norm_Stom_Mus_U133A

description: gene expression data from gastric non-malignant 3791_Norm_Stom_Mus_U133A


title: preMBT_MeDIP Repl2

source_name: preMBT MeDIP ChIP DNA

tag: cell type

source_name: preMBT MeDIP Input DNA


title: Gastric non-malignant 3799_Norm_Stom_U133A

description: gene expression data from gastric non-malignant 3799_Norm_Stom_U133A


title: gastric non-malignant sample NS3

description: gene expression data from gastric non-malignant sample NS3

source_name: gastric non-malignant NS3

value: gastric non-malignant sample


title: Gastric tumor 3792_Stom_Tum_U133A

description: gene expression data from gastric tumor 3792_Stom_Tum_U133A

source_name: Gastric tumor 3792_Stom_Tum_U133A


title: gastric non-malignant sample NS1

description: gene expression data from gastric non-malignant sample NS1

source_name: gastric non-malignant NS1


title: gastric non-malignant sample NS2

description: gene expression data from gastric non-malignant sample NS2

source_name: gastric non-malignant NS2


title: gastric tumor 990515T-U133A

description: gene expression data from gastric tumor 990515T-U133A

source_name: gastric tumor 990515T-U133A

value: gastric tumor


title: Gastric tumor 3798_Stom_Tum_U133A

description: gene expression data from gastric tumor 3798_Stom_Tum_U133A

source_name: Gastric tumor 3798_Stom_Tum_U133A


title: Chx10Cre; Rb lox/lox; p107 -/- 3

description:
DKO-3_fig1
fig1 in paper

source_name: Chx10Cre; Rb lox/lox; p107 -/-

value: DKO


title: Chx10Cre; Rb lox/lox; p107 -/- 2

description:
DKO-2_fig1
fig1 in paper


title: gastric tumor 990428T-U133A

description: gene expression data from gastric tumor 990428T-U133A

source_name: gastric tumor 990428T-U133A


title: gastric tumor 990424-GC

description: gene expression data from gastric tumor 990424-GC

source_name: gastric tumor 990424-GC


title: Chx10Cre; Rb lox/lox; p107 -/- 1

description:
DKO-1_fig1
fig1 in paper


title: gastric tumor 990436T-U133A

description: gene expression data from gastric tumor 990436T-U133A

source_name: gastric tumor 990436T-U133A


title: WT-3_fig1

description:
WT-3_fig1
fig1 in paper

value: WT


title: WT-2_fig1

description:
WT-2_fig1
fig1 in paper


title: gastric tumor 990360T-U133A

description: gene expression data from gastric tumor 990360T-U133A

source_name: gastric tumor 990360T-U133A


title: gastric tumor 990296T-U133A

description: gene expression data from gastric tumor 990296T-U133A

source_name: gastric tumor 990296T-U133A


title: gastric tumor 990384T-U133A

description: gene expression data from gastric tumor 990384T-U133A

source_name: gastric tumor 990384T-U133A


title: murine retina-DKO_P53KO-3

description:
DKO_P53KO-3
fig5 in paper

source_name: murine retina-DKO_P53KO-3


title: murine retina-DKO_P53KO-4

description:
DKO_P53KO-4
fig5 in paper

source_name: murine retina-DKO_P53KO-4


title: murine retina-DKO_P53KO-2

description:
DKO_P53KO-2
fig5 in paper

source_name: murine retina-DKO_P53KO-2


title: murine retina-DKO_P53KO-1

description:
DKO_P53KO-1
fig5 in paper

source_name: murine retina-DKO_P53KO-1


title: WT-1_fig1

description:
WT-1_fig1
fig1 in paper


title: murine retina-DKO-3

description:
DKO-3
fig5 in paper

source_name: murine retina-DKO-3


title: gastric tumor 990203T-U133A

description: gene expression data from gastric tumor 990203T-U133A

source_name: gastric tumor 990203T-U133A


title: murine retina-WT-3_fig5

description:
WT-3_fig5
fig5 in paper

source_name: murine retina-WT-3_fig5


title: gastric tumor 990231T-U133A

description: gene expression data from gastric tumor 990231T-U133A

source_name: gastric tumor 990231T-U133A


title: gastric tumor 990275T-U133A

description: gene expression data from gastric tumor 990275T-U133A

source_name: gastric tumor 990275T-U133A


title: murine retina-DKO-2

description:
DKO-2
fig5 in paper

source_name: murine retina-DKO-2


title: gastric tumor 990108T-U133A

description: gene expression data from gastric tumor 990108T-U133A

source_name: gastric tumor 990108T-U133A


title: murine retina-WT-2_fig5

description:
WT-2_fig5
fig5 in paper

source_name: murine retina-WT-2_fig5


title: murine retina-DKO-1

description:
DKO-1
fig5 in paper

source_name: murine retina-DKO-1


title: gastric tumor 990172T-U133A

description: gene expression data from gastric tumor 990172T-U133A

source_name: gastric tumor 990172T-U133A


title: murine retina-WT-1

description:
WT-1_fig5
fig5 in paper

source_name: murine retina-WT-1


title: human retina sample - 3

source_name: normal

label_protocol: megaplex RT using 448 stem-loop miRNA primers followed by 14-cycle pre-amplification


title: gastric tumor 990069T-U133A

description: gene expression data from gastric tumor 990069T-U133A

source_name: gastric tumor 990069T-U133A


title: gastric tumor 990098T-U133A

description: gene expression data from gastric tumor 990098T-U133A

source_name: gastric tumor 990098T-U133A


title: human retina sample - 4


title: human retina sample - 5


title: gastric tumor 990286T-U133A

description: gene expression data from gastric tumor 990286T-U133A

source_name: gastric tumor 990286T-U133A


title: human retina sample - 6


title: human retina sample - 2


title: human retina sample - 1


title: human retinoblastoma tumour sample - 30

source_name: tumour

value: retinoblastoma


title: gastric tumor 990071T-U133A

description: gene expression data from gastric tumor 990071T-U133A

source_name: gastric tumor 990071T-U133A


title: gastric tumor 990046T-U133A

description: gene expression data from gastric tumor 990046T-U133A

source_name: gastric tumor 990046T-U133A


title: human retinoblastoma tumour sample - 28


title: human retinoblastoma tumour sample - 29


title: gastric tumor 990020T-U133A

description: gene expression data from gastric tumor 990020T-U133A

source_name: gastric tumor 990020T-U133A


title: gastric tumor 990170T-U133A

description: gene expression data from gastric tumor 990170T-U133A

source_name: gastric tumor 990170T-U133A


title: gastric tumor 980447T-U133A

description: gene expression data from gastric tumor 980447T-U133A

source_name: gastric tumor 980447T-U133A


title: gastric tumor 980417T-U133A

description: gene expression data from gastric tumor 980417T-U133A

source_name: gastric tumor 980417T-U133A


title: gastric tumor 980364-GC

description: gene expression data from gastric tumor 980364-GC

source_name: gastric tumor 980364-GC


title: gastric tumor 980390T-U133A

description: gene expression data from gastric tumor 980390T-U133A

source_name: gastric tumor 980390T-U133A


title: gastric tumor 990129T-U133A

description: gene expression data from gastric tumor 990129T-U133A

source_name: gastric tumor 990129T-U133A


title: gastric tumor 980308-GC

description: gene expression data from gastric tumor 980308-GC

source_name: gastric tumor 980308-GC


title: human retinoblastoma tumour sample - 26


title: human retinoblastoma tumour sample - 27


title: gastric tumor 980344T-U133A

description: gene expression data from gastric tumor 980344T-U133A

source_name: gastric tumor 980344T-U133A


title: human retinoblastoma tumour sample - 25


title: gastric tumor 980444-GC

description: gene expression data from gastric tumor 980444-GC

source_name: gastric tumor 980444-GC


title: gastric tumor 980269T-U133A

description: gene expression data from gastric tumor 980269T-U133A

source_name: gastric tumor 980269T-U133A


title: gastric tumor 980239T-U133A

description: gene expression data from gastric tumor 980239T-U133A

source_name: gastric tumor 980239T-U133A


title: human retinoblastoma tumour sample - 22


title: human retinoblastoma tumour sample - 23


title: human retinoblastoma tumour sample - 24


title: gastric tumor 980151T-U133A

description: gene expression data from gastric tumor 980151T-U133A

source_name: gastric tumor 980151T-U133A


title: gastric tumor 980204T-U133A

description: gene expression data from gastric tumor 980204T-U133A

source_name: gastric tumor 980204T-U133A


title: human retinoblastoma tumour sample - 21

source_name: tumour


title: gastric tumor 980138T-U133A

description: gene expression data from gastric tumor 980138T-U133A

source_name: gastric tumor 980138T-U133A


title: gastric tumor 980148T-U133A

description: gene expression data from gastric tumor 980148T-U133A

source_name: gastric tumor 980148T-U133A


title: human retinoblastoma tumour sample - 17


title: human retinoblastoma tumour sample - 18


title: human retinoblastoma tumour sample - 16


title: human retinoblastoma tumour sample - 19


title: gastric tumor 980125T-U133A

description: gene expression data from gastric tumor 980125T-U133A

source_name: gastric tumor 980125T-U133A


title: human retinoblastoma tumour sample - 15


title: gastric tumor 980048T-U133A

description: gene expression data from gastric tumor 980048T-U133A

source_name: gastric tumor 980048T-U133A


title: gastric tumor 980024T-U133A

description: gene expression data from gastric tumor 980024T-U133A

source_name: gastric tumor 980024T-U133A


title: gastric tumor 980026T-U133A

description: gene expression data from gastric tumor 980026T-U133A

source_name: gastric tumor 980026T-U133A


title: human retinoblastoma tumour sample - 14


title: gastric tumor 980063-GC

description: gene expression data from gastric tumor 980063-GC

source_name: gastric tumor 980063-GC


title: gastric tumor 980009T-U133A

description: gene expression data from gastric tumor 980009T-U133A

source_name: gastric tumor 980009T-U133A


title: human retinoblastoma tumour sample - 13


title: human retinoblastoma tumour sample - 12


title: human retinoblastoma tumour sample - 20


title: gastric tumor 980021T-U133A

description: gene expression data from gastric tumor 980021T-U133A

source_name: gastric tumor 980021T-U133A


title: human retinoblastoma tumour sample - 11


title: human retinoblastoma tumour sample - 9


title: gastric tumor 96GC-u133a

description: gene expression data from gastric tumor 96GC-u133a

source_name: gastric tumor 96GC-u133a


title: gastric tumor 95GC-u133a

description: gene expression data from gastric tumor 95GC-u133a

source_name: gastric tumor 95GC-u133a


title: gastric tumor 980019T-U133A

description: gene expression data from gastric tumor 980019T-U133A

source_name: gastric tumor 980019T-U133A


title: gastric tumor 88GC-u133a

description: gene expression data from gastric tumor 88GC-u133a

source_name: gastric tumor 88GC-u133a


title: gastric tumor 91GC-u133a

description: gene expression data from gastric tumor 91GC-u133a

source_name: gastric tumor 91GC-u133a


title: gastric tumor 90GC-u133a

description: gene expression data from gastric tumor 90GC-u133a

source_name: gastric tumor 90GC-u133a


title: gastric tumor 87GC-u133a

description: gene expression data from gastric tumor 87GC-u133a

source_name: gastric tumor 87GC-u133a


title: human retinoblastoma tumour sample - 2

source_name: tumour


title: human retinoblastoma tumour sample - 3


title: human retinoblastoma tumour sample - 1


title: human retinoblastoma tumour sample - 6


title: human retinoblastoma tumour sample - 5


title: gastric tumor 83GC-u133a

description: gene expression data from gastric tumor 83GC-u133a

source_name: gastric tumor 83GC-u133a


title: gastric tumor 86GC-u133a

description: gene expression data from gastric tumor 86GC-u133a

source_name: gastric tumor 86GC-u133a


title: gastric tumor 79GC-u133a

description: gene expression data from gastric tumor 79GC-u133a

source_name: gastric tumor 79GC-u133a


title: gastric tumor 80GC-u133a

description: gene expression data from gastric tumor 80GC-u133a

source_name: gastric tumor 80GC-u133a


title: human retinoblastoma tumour sample - 8


title: human retinoblastoma tumour sample - 4


title: gastric tumor 63GC-u133a

description: gene expression data from gastric tumor 63GC-u133a

source_name: gastric tumor 63GC-u133a


title: gastric tumor 20021048-GC

description: gene expression data from gastric tumor 20021048-GC

source_name: gastric tumor 20021048-GC


title: gastric tumor 85GC-u133a

description: gene expression data from gastric tumor 85GC-u133a

source_name: gastric tumor 85GC-u133a


title: gastric tumor 61GC-u133a

description: gene expression data from gastric tumor 61GC-u133a

source_name: gastric tumor 61GC-u133a


title: human retinoblastoma tumour sample - 7


title: gastric tumor 92GC-u133a

description: gene expression data from gastric tumor 92GC-u133a

source_name: gastric tumor 92GC-u133a


title: gastric tumor 20021013-GC

description: gene expression data from gastric tumor 20021013-GC

source_name: gastric tumor 20021013-GC


title: gastric tumor 20020953-GC

description: gene expression data from gastric tumor 20020953-GC

source_name: gastric tumor 20020953-GC


title: gastric tumor 20021031-GC

description: gene expression data from gastric tumor 20021031-GC

source_name: gastric tumor 20021031-GC


title: gastric tumor 20020945-GC

description: gene expression data from gastric tumor 20020945-GC

source_name: gastric tumor 20020945-GC


title: gastric tumor 20020859-GC

description: gene expression data from gastric tumor 20020859-GC

source_name: gastric tumor 20020859-GC


title: gastric tumor 20021007-GC

description: gene expression data from gastric tumor 20021007-GC

source_name: gastric tumor 20021007-GC


title: gastric tumor 81GC-u133a

description: gene expression data from gastric tumor 81GC-u133a

source_name: gastric tumor 81GC-u133a


title: gastric tumor 20021047-GC

description: gene expression data from gastric tumor 20021047-GC

source_name: gastric tumor 20021047-GC


title: gastric tumor 20020876-GC

description: gene expression data from gastric tumor 20020876-GC

source_name: gastric tumor 20020876-GC


title: gastric tumor 2000137-GC

description: gene expression data from gastric tumor 2000137-GC

source_name: gastric tumor 2000137-GC


title: gastric tumor 2000040T-U133A

description: gene expression data from gastric tumor 2000040T-U133A

source_name: gastric tumor 2000040T-U133A


title: gastric tumor 127GC-u133a

description: gene expression data from gastric tumor 127GC-u133a

source_name: gastric tumor 127GC-u133a


title: gastric tumor 125GC-u133a

description: gene expression data from gastric tumor 125GC-u133a

source_name: gastric tumor 125GC-u133a


title: gastric tumor 122GC-u133a

description: gene expression data from gastric tumor 122GC-u133a

source_name: gastric tumor 122GC-u133a


title: gastric tumor 2000068T-U133A

description: gene expression data from gastric tumor 2000068T-U133A

source_name: gastric tumor 2000068T-U133A


title: Dicer1 lox/lox 1

description:
DicKO-1_fig1
fig1 in paper

source_name: Dicer1 lox/lox


title: gastric tumor 2000038T-U133A

description: gene expression data from gastric tumor 2000038T-U133A

source_name: gastric tumor 2000038T-U133A


title: gastric tumor 114GC-u133a

description: gene expression data from gastric tumor 114GC-u133a

source_name: gastric tumor 114GC-u133a


title: gastric tumor #37

description: gene expression data from gastric tumor #37

hyb_protocol: The labeled target was dissolved in 127-μL hybridization mixture containing 46% formamide (Invitrogen), 9.5% dextran sulfate (U.S. Biochemical Corp., Cleveland, OH), 2× SSC, and 0.2% SDS. The labeled target was heated to 70°C for 10 minutes and annealed at 37°C for 1 hour. Slides were prehybridized in hybridization mix with 30 μg salmon sperm DNA (Invitrogen) for 1 hour at 37°C followed by 14 hours at 37°C overnight (HybArray 12, Perkin-Elmer, Zaventem, Belgium). After hybridization, the slides were washed in the HybArray 12, with 50% formamide (FLUKA, Sigma-Aldrich Chemie), 2× SSC (pH 7) at 35°C for 15 minutes followed by PI buffer [0.1 mol/L sodium phosphate, 0.1% Igepal Ca630 (pH 8)] at room temperature and three washes of 0.2× SSC, 0.1× SSC, and 0.01× SSC at room temperature followed by centrifugation

scan_protocol: Arrays were scanned using a laser scanner (ScanArray Express, Perkin-Elmer)

data_processing: Imagene version 5.6 (Westburg). The data were median center normalized for each chip.

source_name: Stratagene,universal human reference RNA, Catalog #74033

label_protocol: Labeling was done according to the aminoallyl-labeling protocol developed by DeRisi. Briefly, cDNA was incubated at room temperature for 1 hour with fluorolink monofunctional Cy5 or Cy3 dye (Amersham, Roosendaal, The Netherlands) followed by 15 minutes of 4 mol/L hydroxylamine treatment. Uncoupled dyes were removed using Qiaquick PCR purification columns (Qiagen, Westburg B.V., Leusden, The Netherlands) and mixed with 12 μg poly(dA) (Amersham), 60 μg yeast tRNA (Sigma-Aldrich Chemie), and 24 μg Cot-1 DNA (Invitrogen).

extract_protocol: Total RNA isolation were done using the TriZol (Invitrogen, Leek, The Netherlands) method according to the manufacturer's protocol. Total RNA concentration was measured by A260 and RNA integrity judged on a 1.2% agarose gel. Samples were dissolved in 100% DMPC-treated H2O and stored at −80°C before use in either the microarray hybridizations or real-time PCR confirmation of the microarray results.

tag: reference

source_name: gastric tumor #37

tag: mortality

value: other death

tag: follow up (years)


title: gastric tumor 113GC-u133a

description: gene expression data from gastric tumor 113GC-u133a

source_name: gastric tumor 113GC-u133a

tag: tissue


title: gastric tumor 124GC-u133a

description: gene expression data from gastric tumor 124GC-u133a

source_name: gastric tumor 124GC-u133a


title: gastric tumor 108GC-u133a

description: gene expression data from gastric tumor 108GC-u133a

source_name: gastric tumor 108GC-u133a


title: gastric tumor 106GC-u133a

description: gene expression data from gastric tumor 106GC-u133a

source_name: gastric tumor 106GC-u133a


title: gastric tumor #38

description: gene expression data from gastric tumor #38

source_name: Stratagene,universal human reference RNA, Catalog #74032

source_name: gastric tumor #38

value: alive


title: gastric tumor #42B

description: gene expression data from gastric tumor #42B

source_name: Stratagene,universal human reference RNA, Catalog #74029

source_name: gastric tumor #42B

value: death due to cancer


title: gastric tumor #43C

description: gene expression data from gastric tumor #43C

source_name: Stratagene,universal human reference RNA, Catalog #74028

source_name: gastric tumor #43C


title: gastric tumor #40

description: gene expression data from gastric tumor #40

source_name: Stratagene,universal human reference RNA, Catalog #74031

source_name: gastric tumor #40

value: operative mortality


title: gastric tumor 120GC-u133a

description: gene expression data from gastric tumor 120GC-u133a

source_name: gastric tumor 120GC-u133a


title: gastric tumor 104GC-u133a

description: gene expression data from gastric tumor 104GC-u133a

source_name: gastric tumor 104GC-u133a


title: gastric tumor 20020858-GC

description: gene expression data from gastric tumor 20020858-GC

source_name: gastric tumor 20020858-GC


title: gastric tumor 101GC-u133a

description: gene expression data from gastric tumor 101GC-u133a

source_name: gastric tumor 101GC-u133a


title: E. coli O157:H7 EDL933 in LB at 37oC for 7 hrs incubation with indole-3-acetaldehyde

city: Gyeongsan-Si

first: Jintae

last: Lee

state: Gyeongsangbuk-Do

address: 214-1 Daedong

department: Chemical engineering

institute: Yeungnam University

description: RNA extracted from E. coli EDL933 cells grown on glass wool for 7 hrs in LB at 37ºC

hyb_protocol: Following affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

scan_protocol: Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Escherichia coli

source_name: RNA extracted from e. coli o157: H7 EDL933 cells grown (7 hrs incubation) in LB at 37ºC with 0.1 mg/ml of IAAld

label_protocol:
Following affymetrix protocol.
cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

extract_protocol: E. coli O157:H7 EDL933 was inoculated in 100 ml of LB in 250 ml shake flasks with overnight cultures that were diluted 1:100. Cells were shaken with 4 g of glass wool at 250 rpm and 37°C for 7 hrs.  Cells were immediately chilled with dry ice and 95% ethanol (to prevent RNA degradation) for 30 sec before centrifugation in 50 ml centrifuge tubes at 13,000 g for 2 min; cell pellets were frozen immediately with dry ice and stored -80°C.  RNA was isolated using Qiagen RNeasy mini Kit (Cat# 74104) with Qiagen RNase-free DNase I (Cat# 79254).

tag: serotype


title: MYCN 5

city: Sutton

first: Teeara

last: Berry

state: Surrey

address: 15 Cotswold Road

department: Paediatric Oncology

institute: The Institute of Cancer Research

description: Biological replicate 5 of 5. Untreated tumour from MYCN-expressing mice.

hyb_protocol: standard Agilent protocol

scan_protocol: Slides were scanned on an Agilent C Scanner at 3um using the 20bit setting.

data_processing: Resulting data were feature extracted using Agilent Feature extraction v10.7.3. Raw data were first normalized by Agilent GeneSpring 11.5.1 software using the default normalization setting and relative expression value compared to the reference control calculated for each probe (threshold raw signals to 1, percentile shift to 75, baseline to the median of all samples). The genes with flags present in at least 100% of the values in any one out of the two groups (ALK^F1174L/MYCN and MYCN) were filtered.

source_name: MYCN+/- tumor cells

label_protocol: Samples were labeled and processed using the Agilent Low Input Quick Amp two colour Cy3 (sample) and Cy5 (mouse reference) RNA labeling kit (Stratagene) according to the manufacturer's instructions.

extract_protocol: RNA was extracted from tumours using the miRNeasy Mini kit (Qiagen) according to the manufacturer's instructions.

value: neuroblastoma tumor

tag: genotype

value: MYCN+/- transgenic

tag: genetic background

source_name: Universal Mouse Reference RNA

tag: sample type

value: Stratagene Universal Mouse Reference (RNA from 11 murine cell lines)


title: E. coli O157:H7 EDL933 in LB at 37oC for 7 hrs incubation with DMSO

source_name: RNA extracted from e. coli o157: H7 EDL933 cells grown (7 hrs incubation) in LB at 37ºC with DMSO


title: gastric tumor #41

description: gene expression data from gastric tumor #41

source_name: Stratagene,universal human reference RNA, Catalog #74030

source_name: gastric tumor #41


title: gastric tumor #50A

description: gene expression data from gastric tumor #50A

source_name: Stratagene,universal human reference RNA, Catalog #74025

source_name: gastric tumor #50A


title: gastric tumor #56

description: gene expression data from gastric tumor #56

source_name: Stratagene,universal human reference RNA, Catalog #74022

source_name: gastric tumor #56


title: gastric tumor #55

description: gene expression data from gastric tumor #55

source_name: Stratagene,universal human reference RNA, Catalog #74023

source_name: gastric tumor #55


title: gastric tumor #67

description: gene expression data from gastric tumor #67

source_name: Stratagene,universal human reference RNA, Catalog #74017

source_name: gastric tumor #67


title: gastric tumor #69

description: gene expression data from gastric tumor #69

source_name: Stratagene,universal human reference RNA, Catalog #74016

source_name: gastric tumor #69


title: gastric tumor #59

description: gene expression data from gastric tumor #59

source_name: Stratagene,universal human reference RNA, Catalog #74021

source_name: gastric tumor #59


title: gastric tumor #64

description: gene expression data from gastric tumor #64

source_name: Stratagene,universal human reference RNA, Catalog #74019

source_name: gastric tumor #64


title: gastric tumor #70

description: gene expression data from gastric tumor #70

source_name: Stratagene,universal human reference RNA, Catalog #74015

source_name: gastric tumor #70


title: ALK/MYCN 2

description: Biological replicate 2 of 5. Untreated tumour from ALK^F1174L + MYCN-expressing mice.

source_name: ALK+/-, MYCN+/- tumor cells

value: ALK+/-, MYCN+/- transgenic

source_name: Universal Mouse Reference RNA


title: gastric tumor #73

description: gene expression data from gastric tumor #73

source_name: Stratagene,universal human reference RNA, Catalog #74014

source_name: gastric tumor #73


title: gastric tumor #75

description: gene expression data from gastric tumor #75

source_name: Stratagene,universal human reference RNA, Catalog #74013

source_name: gastric tumor #75


title: ALK/MYCN 3

description: Biological replicate 3 of 5. Untreated tumour from ALK^F1174L + MYCN-expressing mice.


title: gastric tumor 62GC-u133a

description: gene expression data from gastric tumor 62GC-u133a

source_name: gastric tumor 62GC-u133a


title: gastric tumor #48

description: gene expression data from gastric tumor #48

source_name: Stratagene,universal human reference RNA, Catalog #74026

source_name: gastric tumor #48


title: ALK/MYCN 5

description: Biological replicate 5 of 5. Untreated tumour from ALK^F1174L + MYCN-expressing mice.


title: gastric tumor #61A

description: gene expression data from gastric tumor #61A

source_name: Stratagene,universal human reference RNA, Catalog #74020

source_name: gastric tumor #61A


title: gastric tumor #47

description: gene expression data from gastric tumor #47

source_name: Stratagene,universal human reference RNA, Catalog #74027

source_name: gastric tumor #47


title: MYCN 4

description: Biological replicate 4 of 5. Untreated tumour from MYCN-expressing mice.

source_name: MYCN+/- tumor cells


title: gastric tumor #53A

description: gene expression data from gastric tumor #53A

source_name: Stratagene,universal human reference RNA, Catalog #74024

source_name: gastric tumor #53A


title: gastric tumor #76

description: gene expression data from gastric tumor #76

source_name: Stratagene,universal human reference RNA, Catalog #74012

source_name: gastric tumor #76


title: MYCN 1

description: Biological replicate 1 of 5. Untreated tumour from MYCN-expressing mice.

source_name: Universal Mouse Reference RNA


title: MYCN 2

description: Biological replicate 2 of 5. Untreated tumour from MYCN-expressing mice.


title: MYCN 3

description: Biological replicate 3 of 5. Untreated tumour from MYCN-expressing mice.


title: ALK/MYCN 1

description: Biological replicate 1 of 5. Untreated tumour from ALK^F1174L + MYCN-expressing mice.

source_name: ALK+/-, MYCN+/- tumor cells


title: gastric tumor #85

description: gene expression data from gastric tumor #85

source_name: Stratagene,universal human reference RNA, Catalog #74010

source_name: gastric tumor #85


title: gastric tumor #6

description: gene expression data from gastric tumor #6

source_name: Stratagene,universal human reference RNA, Catalog #74006

source_name: gastric tumor #6


title: gastric tumor #87

description: gene expression data from gastric tumor #87

source_name: Stratagene,universal human reference RNA, Catalog #74009

source_name: gastric tumor #87


title: gastric tumor #92

description: gene expression data from gastric tumor #92

source_name: Stratagene,universal human reference RNA, Catalog #74008

source_name: gastric tumor #92


title: gastric tumor #23A

description: gene expression data from gastric tumor #23A

source_name: Stratagene,universal human reference RNA, Catalog #74003

source_name: gastric tumor #23A


title: gastric tumor #66

description: gene expression data from gastric tumor #66

source_name: Stratagene,universal human reference RNA, Catalog #74018

source_name: gastric tumor #66


title: liver-HCV-Non Tumor-rep7 [miRNA]

city: StLouis

first: Nobish

last: Varghese

state: MO

address: 4444 Forest Park Ave.

institute: Washington University in St.Louis

hyb_protocol: Samples were hybridized onto beadchips according to microRNA expression profiling protocol from Illumina.

scan_protocol: Arrays were scanned on an Illumina BeadArray Reader.  Laser power and PMT voltage were kept constant for Cy3 scans.  Images were quantitated by Illumina Beadscan, v3.  Quantitated data was imported into Beadstudio software.  On-slide spot replicates were averaged by Beadstudio and individual spot data was reported

data_processing: The data were normalized using quantile normalization implemented in Illumina Genome studio version 1.7.0.

source_name: liver-HCV-Non Tumor

label_protocol: Samples were labeled according to microRNA expression profiling protocol from Illumina.

growth_protocol: The study was approved by the Institutional Review Board at Washington University in St. Louis and all patients were enrolled after informed consent.

extract_protocol: Liver biopsy that were snap frozen obtained from HCV or control normal liver, were used to isolate RNA using Trizol reagent (Invitrogen, Carlsbad, CA) as per manufacturer’s protocol.

value: liver

tag: tissue subtype

value: Non Tumor


title: ALK/MYCN 4

description: Biological replicate 4 of 5. Untreated tumour from ALK^F1174L + MYCN-expressing mice.


title: gastric tumor #118

description: gene expression data from gastric tumor #118

source_name: Stratagene,universal human reference RNA, Catalog #74007

source_name: gastric tumor #118


title: gastric tumor #79

description: gene expression data from gastric tumor #79

source_name: Stratagene,universal human reference RNA, Catalog #74011

source_name: gastric tumor #79


title: liver-HCV-Non Tumor-rep8 [miRNA]


title: gastric tumor #33B

description: gene expression data from gastric tumor #33B

source_name: Stratagene,universal human reference RNA, Catalog #74000

source_name: gastric tumor #33B


title: liver-HCV-Non Tumor-rep6 [miRNA]


title: liver-HCV-Non Tumor-rep5 [miRNA]


title: gastric tumor #12

description: gene expression data from gastric tumor #12

source_name: Stratagene,universal human reference RNA, Catalog #74005

source_name: gastric tumor #12


title: gastric tumor #30A

description: gene expression data from gastric tumor #30A

source_name: Stratagene,universal human reference RNA, Catalog #74001

source_name: gastric tumor #30A


title: liver-Tumor-rep5 [miRNA]

source_name: liver-Tumor

value: Tumor


title: gastric tumor #21

description: gene expression data from gastric tumor #21

source_name: Stratagene,universal human reference RNA, Catalog #74004

source_name: gastric tumor #21


title: liver-Tumor-rep4 [miRNA]


title: liver-Tumor-rep6 [miRNA]


title: human retinoblastoma tumour sample - 10

source_name: tumour


title: gastric tumor #29

description: gene expression data from gastric tumor #29

source_name: Stratagene,universal human reference RNA, Catalog #74002

source_name: gastric tumor #29


title: gastric tumor Gastric0117

first: Zhengdeng

last: Lei

institute: Duke-NUS graduate medical school

description: gene expression data from gastric tumor Gastric0117

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were RMA normalized with R package affy.

source_name: gastric tumor Gastric0117

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 to 5 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

growth_protocol: gastric tumor tissue.

extract_protocol: Total RNA was extracted from primary tumors using RNeasy mini spin columns (Qiagen) according to the instructions of the manufacturer.

treatment_protocol: gastric tumor tissue.

value: gastric adenocarcinoma

tag: subtype

value: Proliferative


title: Gastric tumor 4352_Stom_Tum_U133B

description: gene expression data from gastric tumor 4352_Stom_Tum_U133B

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16-18 hr at 45C on GeneChip Human Genome U133B Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

source_name: Gastric tumor 4352_Stom_Tum_U133B

value: Gastric tumor

tag: intra-tumoral stroma


title: gastric tumor Gastric0115

description: gene expression data from gastric tumor Gastric0115

source_name: gastric tumor Gastric0115


title: gastric tumor Gastric0114

description: gene expression data from gastric tumor Gastric0114

source_name: gastric tumor Gastric0114


title: gastric tumor Gastric0111

description: gene expression data from gastric tumor Gastric0111

source_name: gastric tumor Gastric0111

value: Invasive


title: gastric tumor Gastric0116

description: gene expression data from gastric tumor Gastric0116

source_name: gastric tumor Gastric0116