title: Peritoneal_Mesothelioma_14


title: Peritoneal_Mesothelioma_11

status: Public on May 04 2010

type: RNA

city: Glasgow

first: W.

middle: Nicol

last: Keith

state: Lanarkshire

address: Center for Oncology and Applied Pharmacology, University of Glasgow, CRUK Beatson Laboratories, Garscube Estate, Switchback Road

country: United Kingdom

institute: The University of Glasgow

hyb_protocol: 100 μl of purified labelled total RNA was hybridised to Agilent 4x44K whole human genome arrays for 17 hours at 65 °C rotating at 10 rpm and washed as as per manufacturor's instructions for one colour arrays (Agilent Technologies).

scan_protocol: Slides were scanned using DNA microarray scanner model G2539A (Agilent Technologies) and Agilent Scan Control Software. Spot intensity and identity information was extracted using Agilent Feature Extraction Software.

data_processing: Normalised to the 75th percentile with intensities below 0.01 being set to 0.01.

molecule: total RNA

organism: Homo sapiens

source_name: Peritoneal Mesothelioma, Fresh Frozen

label_protocol: 800 ng of total RNA was labelled with Cy3 using the Low RNA Input Linear Amplification Kit (Agilent technologies) as per manufacturor's instructions.

extract_protocol: Frozen tumour tissue was disrupted using a Hybaid Ribolyser at a setting of 5.5 for 5 x 10 second pulses with 30 second pauses in between and RNA was extracted using the RNeasy Lipid kit (Qiagen Inc, Hilden, Germany) as per manufacturers’ instructions.

tag: sex

value: M

tag: age

tag: grade

value: unknown

tag: histology

value: Epithelial

tag: chemo/radio therapy given

value: cytoreductive surgery + hyperthermic i.p. chemotherapy (doxorubicin + cisplatin)

tag: survival (months)

tag: survival status


title: Peritoneal_Mesothelioma_12


title: Peritoneal_Mesothelioma_19

value: F

value: Epithelial tubulopapillary


title: Peritoneal_Mesothelioma_8

value: LTF


title: Peritoneal_Mesothelioma_6

value: Epithelial solid


title: HTCC1062_Control_1day_rep2

status: Public on May 05 2010

city: Corvallis

first: Daniel

middle: Patrick

last: Smith

state: OR

address: 220 Nash Hall

department: Microbiology Department

country: USA

institute: Oregon State University

hyb_protocol: 5.5 µg of labeled aRNA was hybridized to chips at 45˚C, rotating at 60 rpm for 16 hours.

scan_protocol: The samples were scanned with an Affymetrix GeneChip Scanner 3000 7G with autoloader using AGCC software.

data_processing: RMA normalization conducted with Affymetrix ExpressionConsole software package.

label: biotin

organism: Candidatus Pelagibacter ubique HTCC1062

source_name: Control culture, 1 Day

label_protocol: RNA was labeled with biotin labeled nucleotides (perkin-elmer) during the in-vitro transcription reaction.

growth_protocol: Natural seawater media amended with 50 µM pyruvate, 50 µM glucose, 10 µM nitrogen, 1 µM methionine, 1 µM glycine, 1 µM phosphate, and vitamins. Cells were grown at 16°C with intermittent light and sparging with air.

extract_protocol: Total RNA was extracted using RNeasy Kit (Qiagen) and amplified using MessageAmp-II-Bacteria RNA Amplification Kit (Ambion).

treatment_protocol: 40 ml of culture from each biological replicate were harvested via centrifugation (1 hour at 43 000 g, 10°C), then re-suspended in 1 ml of Bacteria Protect (Qiagen) for 15 min. Following RNA stabilization, cells were collected by centrifugation (30 min at 40 000 g, 10°C), the supernatant was removed, and cells were then stored frozen at -80°C prior to extraction.

tag: growth phase

value: Late Exponential


title: HTCC1062_Iron-Limited_1day_rep1

source_name: Iron-Limited Culture, 1 Day

value: Early Stationary


title: Peritoneal_Mesothelioma_10

value: Biphasic


title: Peritoneal_Mesothelioma_4


title: Peritoneal_Mesothelioma_3


title: H1299-vector-3

city: Beijing

first: Kaitai

last: Zhang

address: Pan jia yuan nan li #17

country: China

institute: Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences

description: RNA from H1299-DENND2D and H1299-vector cells was labeled by three times. cRNA used in replication 1 and 2 was from the same label reaction.

hyb_protocol: Using Agilent hybridizatio chambers and oven following manufacture's protocol (65C 10rpm for 17 hours).

scan_protocol: Scanned on an Agilent C2565BA scanner.

data_processing: Processed signal intensities are imported into GeneSpring GX 7.3 and were set measurements less than 0.01 to 0.01 and normalized to 50th percentile of per chip intensity. Intensities of replicate probes were represented as single value of average.

source_name: NCI-H1299 cell line transfected with vector

label_protocol: 500ng total RNA is amplified and labeled using Agilent's Low RNA Input Linear Amplification Kit PLUS following manufacture's protocol.

extract_protocol: RNA was purified from the H1299-DENND2D and H1299-vector cells using RNeasy kit (Qiagen, Germantown, MD) according to the user's guide.

tag: cell line

tag: vector

value: pcDNA3.1/V5-His TOPO TA


title: Peritoneal_Mesothelioma_5


title: H1299-vector-1


title: Peritoneal_Mesothelioma_1


title: H1299-vector-2


title: H1299-DENND2D-4

source_name: NCI-H1299 cell line transfected with Human DENND2D

tag: transfected gene


title: H1299-DENND2D-3


title: H1299-vector-4


title: H1299-DENND2D-2


title: H1299-DENND2D-1


title: Peritoneal_Mesothelioma_7


title: Peritoneal_Mesothelioma_2


title: SynovCTRL_022HACIZ_150.txt

status: Public on May 03 2010

city: Cincinnati

first: Bruce

middle: J

last: Aronow

state: OH

institute: Cincinnati Children's Hospital Medical Center

description:
Synovium; normal
Keywords = mouse gene expression database

organism: Mus musculus

source_name: Universal mouse reference RNA


title: Pancr_022HAFD3_060w.txt

description:
Pancreas
Keywords = mouse gene expression database

source_name: Pancreas


title: Pancr_022AAFD2_060w.txt


title: N2adults plate#1

city: Chapel Hill

first: Christina

middle: M

last: Whittle

state: NC

address: 406 Fordham Hall, CB#3280

department: Biology

institute: University of North Carolina-Chapel Hill

description: Gene expression data from N2 young adult hermaphrodites grown on NGM agar plates and fed on OP50.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. http://www.nimblegen.com/products/lit/index.html

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol.http://www.nimblegen.com/products/lit/index.html

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 the NimbleScan software package, version 2.4 (Roche NimbleGen, Inc.).

organism: Caenorhabditis elegans

source_name: plate-cultured N2 C. elegans

label_protocol: Cy3 Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. http://www.nimblegen.com/products/lit/index.html

growth_protocol: Embryos were obtained from bleached N2 gravid hermaphrodites. Embryos were cultured on NGM agar plates fed on OP50 until young adulthood.

extract_protocol: Worms were suspended in Trizol and freeze-cracked rapidly by thawing to 37C and refreezing on liquid nitrogen. RNA was then purified by phenol-chloroform extraction followed by ethanol precipitation.

tag: strain

tag: developmental stage

value: young adult

tag: culture conditions

value: plate


title: StomMucos_0229AFBC_064.txt

description:
Stom Mucos
Keywords = mouse gene expression database

source_name: Stom


title: N2adults-liquid#1

description: Gene expression data from N2 young adult hermaphrodites grown under standard liquid culture conditions.

source_name: liquid-cultured N2 C. elegans

growth_protocol: Embryos were obtained from bleached N2 gravid hermaphrodites. Embryos were cultured in standard s-basal liquid culture fed on HB101 until young adulthood.

value: liquid


title: SkinE16_0222ACI9_036.txt

description:
Skin; Fetal Skin Day 16
Keywords = mouse gene expression database


title: SkinE16_022PACIV_036.txt


title: N2adults-plate#2


title: StomMucos_0225AF6W_064.txt


title: N2adults-liquid#3


title: Thyroid_022LAFBO_045.txt

description:
Thyroid; Thyroid
Keywords = mouse gene expression database


title: PBMC_022WAFD0_096.txt

description:
Immune_Peripheral Blood Mononuclear Cells (ficoll)_1
Keywords = mouse gene expression database


title: PBMC_0223AFD1_096.txt

description:
Immune_Peripheral Blood Mononuclear Cells (ficoll)_2
Keywords = mouse gene expression database


title: N2adults-plate#3


title: Thyroid_022SAFBP_045.txt


title: SkinP2_022MACIA_037.txt

description:
Skin;  Skin postnatal Day 2-3
Keywords = mouse gene expression database


title: SkinP2_022WACIW_037.txt


title: DRG_022SAFCJ_newDG.txt

description:
Nervous Sysem; Peripheral, Sensory-dorsal root ganglion
Keywords = mouse gene expression database

source_name: Nervous System_DRG


title: T_active_022WAFCZ_093.txt

description:
Immune_CD4+_column purified_T-cells_antiCD3, antiCD28-activated
Keywords = mouse gene expression database


title: Striat_022MAC35_004.txt

description:
Nervous System; Striatum
Keywords = mouse gene expression database

source_name: Nervous System_Striat


title: Islets0228AC33_060.txt

description:
Pancreas; Islets
Keywords = mouse gene expression database


title: SynovCTRL_0227ACID_150.txt


title: SpinalCo_022ZAFCK_newSC.txt

description:
Nervous System; Spinal Cord
Keywords = mouse gene expression database

source_name: Nervous System_SpinalCo


title: NucAcumbs_022FAC34_005.txt

description:
Nervous System; Nucleus Accumbens
Keywords = mouse gene expression database

source_name: Nervous System_NucAccumbs


title: DRG_0225AFCQ_new018.txt


title: SpinalCo_0226AFCL_new008.txt


title: BrE18_5wt022EAFBN.txt

description:
Nervous System; Fetal day 18.5 brain
Keywords = mouse gene expression database

source_name: Nervous System_BrE18


title: Hypothal_225AFB3_0126.txt

description:
Nervous System; Hypothalamus
Keywords = mouse gene expression database

source_name: Nervous System_Hypothal


title: Hippocamp0227AC38_003.txt

description:
Nervous System; Hippocampus
Keywords = mouse gene expression database

source_name: Nervous System_Hippocamp


title: OlfacCortx_22YAFB2_002.txt

description:
Nervous System; Olfactory Cortex
Keywords = mouse gene expression database

source_name: Nervous System_OlfacCortx


title: BrE18_5wt0227AFBM.txt


title: Hippocamp22KAFAZ_003.txt


title: BrnD2_0220ACHI.txt

description:
Nervous System; Day 2 postnatal whole brain
Keywords = mouse gene expression database

source_name: Nervous System_BrnD2


title: N2adults-liquid#2

description: Gene expression data from N2 young adult hermaphrodites grown under standard liquid culture conditions.


title: OlfacCortx_0220AC37_002.txt


title: BrnD2_0227ACHJ.txt


title: NucAccumbs_0226AFBR_005.txt


title: Cerebel_0224ACIS_007.txt

description:
Nervous System; Cerebellum
Keywords = mouse gene expression database

source_name: Nervous System_Cerebel


title: Striat_022ZAFBQ_004.txt


title: Cerebel_2022HACI6_007.txt


title: Hypothal_022TAC36_0126.txt


title: NasalRespMuc_0222ACJ3_31.txt

description:
Nasal; Upper Repiratory Mucosa
Keywords = mouse gene expression database


title: NasalRespMuc_022ZACIH_31.txt


title: BladdD1_022YAC3A_043.txt

description:
Muscle; Smooth - Bladder- day 1 postnatal male
Keywords = mouse gene expression database


title: BladdAd_022EAC39_087.txt

description:
Muscle; Smooth-Bladder_adult
Keywords = mouse gene expression database


title: MucOlfEpith_022SACIG_030.txt

description:
Nasal; Olfactory Epithelium
Keywords = mouse gene expression database


title: MucOlfEpith_022VACJ2_030.txt


title: Peritoneal_Mesothelioma_15

source_name: Peritoneal Mesothelioma, Fresh Frozen


title: SkelMusc_022XAFC1_086.txt

description:
Muscle; Skeletal
Keywords = mouse gene expression database


title: BladdAd_22DAFAY_087.txt


title: MammInvol_022YACIM_054.txt

description:
Mammary; Involution
Keywords = mouse gene expression database


title: MammLac_022RACIL_053.txt

description:
Mammary; Lactating
Keywords = mouse gene expression database


title: SkelMusc_0224AFC2_086.txt


title: MammLac_022JACHV_053.txt


title: BladdD1_0226AFAX_043.txt


title: EpiHd_022PACI2_114a.txt

description:
Male; Epididymis-head
Keywords = mouse gene expression database


title: EpiTl_022WACI3_114b.txt

description:
Male; Epididymis-tail
Keywords = mouse gene expression database


title: EpiTl_022JACIP_114b.txt


title: MammInvol_022QACHW_054.txt


title: LungE185_22GAFBD_079.txt

description:
Lung; Fetal Day 18.5
Keywords = mouse gene expression database


title: LungP5_221AFBG_077b.txt

description:
Lung; Day 5 postnatal
Keywords = mouse gene expression database


title: Testes_0225ACIN_113.txt

description:
Male; Testes
Keywords = mouse gene expression database


title: LungE165_022JAF6Y_078.txt

description:
Lung; Fetal Day 16.5
Keywords = mouse gene expression database


title: LungE165_022NAFBE_078.txt


title: LungE185_022CAF6X_079.txt


title: LungE135_022WAF76_076.txt

description:
Lung; Fetal Day 13.5
Keywords = mouse gene expression database


title: LungE135_022KACGW_076.txt


title: LungP5_022QAF70_077b.txt


title: LungP24_022HAF79_077d.txt

description:
Lung; Day 24 postnatal
Keywords = mouse gene expression database


title: LungP12_022BAF73_077c.txt

description:
Lung; Day 12 postnatal
Keywords = mouse gene expression database


title: LungP12_022AAF78_077c.txt


title: Testes_022XACHX_113.txt


title: LungP1_022QAF6Z_077a.txt

description:
Lung; Day 1 postnatal
Keywords = mouse gene expression database


title: LungP1_22UAFBF_077a.txt


title: LiverAdult_022TACHH.txt

description:
Liver; Adult Fed
Keywords = mouse gene expression database


title: LungAd_022PAF75.txt

description:
Lung; Adult
Keywords = mouse gene expression database


title: LiverP14_022AACI5_062.txt

description:
Liver; day 14 postnatal_liver
Keywords = mouse gene expression database


title: LiverP14_022XACIR_062.txt


title: LiverAdult_022MACHG.txt


title: SpleenC57_022RAF6U_091.txt

description:
Immune; Spleen(C57)
Keywords = mouse gene expression database


title: KidE185_0225AFIQ_109.txt

description:
Kidney; Fetal Day 18.5
Keywords = mouse gene expression database


title: LungAd_022DACGV.txt


title: KidP2_022UAFAL_107.txt

description:
Kidney; Day 2 postnatal
Keywords = mouse gene expression database


title: KidAd_022NACJ6_105.txt

description:
Kidney; Adult
Keywords = mouse gene expression database


title: KidP2_0228ACJ9_107.txt


title: SpleenC57_222AFBB_091.txt


title: KidE185_0221ACJ8_109.txt


title: KidAd_022RAFIO_105.txt


title: Thymus_022LACHL_t1b.txt

description:
Immune; normal adult(2X+)
Keywords = mouse gene expression database


title: LymphNodUn_022VAFD5_0951.txt

description:
Immune; Lymph Node_unstimulated
Keywords = mouse gene expression database


title: Thymus_022EACHK_t1b.txt


title: LymphNodUn_022OAFD4_0951.txt


title: HeartE145_227AFIG_td1.txt

description:
Heart; embryonic_d14.5 wt heart
Keywords = mouse gene expression database


title: HeartVentr22MAFID_081.txt

description:
Heart; Ventricle
Keywords = mouse gene expression database


title: LymphNodeImm_022ZAFAW_094.txt

description:
Immune; Lymph Node_Comprlete Freunds Adjuvant stimulated
Keywords = mouse gene expression database


title: LymphNodeImm_0225AC3B_094.txt


title: HeartE145_220AFIF_td1.txt


title: UterViEs_0226ACII_112b.txt

description:
Female; Uterus-virgin estrus
Keywords = mouse gene expression database


title: HairCat_0220ACIC_039.txt

description:
Hair; Awn Hair (back) catagen
Keywords = mouse gene expression database


title: HeartAtrium22HAFI9_080.txt

description:
Heart; Atrium
Keywords = mouse gene expression database


title: HeartVentr22TAFIE_081.txt


title: UterViEs_022YACHS_112b.txt


title: UterViDi_0225ACHT_112a.txt

description:
Female; Uterus - virgin-diestrus
Keywords = mouse gene expression database


title: LiverE14_0223ACI4_099.txt

description:
Blood; Fetal Day 14 Liver Hematopoietic
Keywords = mouse gene expression database


title: AdipBrn022QAFC0_048.txt

description:
Brown Adipose Tissue
Keywords = mouse gene expression database


title: UterViDi_2022DACIJ_112a.txt


title: HeartAtrium22FAFIC_080.txt


title: AdipBrn022QAFBZ_048.txt


title: HairAnag_0223ACIX_038.txt

description:
Hair; Awn Hair (back) anagen
Keywords = mouse gene expression database


title: ColonProx_0227AFAS_070.txt

description:
Large Intestine; Proximal Colon
Keywords = mouse gene expression database

source_name: GI, P.Col


title: ColonProx_022XAC3F_070.txt

source_name: Universal mouse reference RNA


title: HairAnag_022TACIB_038.txt


title: HairCat_022AACIY_039.txt


title: JejunProx022ZAF6Q_174.txt

description:
Small Intestine; proximal jejunum
Keywords = mouse gene expression database

source_name: GI, P.Jej


title: JejunProx0224AFB8_174.txt


title: LiverE14_022QACIQ_099.txt


title: IleumSBR_22QAFB6_177.txt

description:
Small Intestine; ileum short bowel resection
Keywords = mouse gene expression database

source_name: GI, ILSBR


title: IleumSBR_022LAF6O_177.txt


title: Ileum_022CAFB4_067.txt

description:
Small Intestine; Ileum
Keywords = mouse gene expression database

source_name: GI, IL


title: Duoden22VAFBA_066.txt

description:
Small Intestine; Duodenum
Keywords = mouse gene expression database

source_name: GI, Duo


title: Ileum_0221AC32_067.txt


title: Duoden022KAF6T_066.txt


title: SmIntP1_0226AF6R_172.txt

description:
Small Intestine; d1 small intestine
Keywords = mouse gene expression database

source_name: GI_dev, P1


title: SmIntP145_022JAFB5_173.txt

description:
Small Intestine; d14 small intestine
Keywords = mouse gene expression database

source_name: GI_dev, P145


title: SmIntP145_0223AF77_173.txt


title: RNA MIX Control 8_Chip2

status: Public on Feb 11 2010

city: Yokohama

first: Hiroyuki

last: Oshima

address: 10-1 Daikoku-cho, Tsurumi-ku

country: Japan

institute: Mitsubishi Rayon Co.,LTD

hyb_protocol: 5 μg of biotinylated aRNA, which was fragmented using Fragmentation Reagents (AppliedBiosystems), was suspended in a hybridization buffer containing 0.12 M Tris-HCl (pH 7.5), 0.12 M NaCl, and 0.05% Tween 20. The hybridization mixture was heated to 94°C for 2 min, then cooled to 37°C and injected into a hybridization chamber (Mitsubishi Rayon). Hybridization was carried out at 65°C for 16 hr. Microarrays were washed by soaking 48times in 0.12 M Tris-HCl (pH 7.5), 0.12 M NaCl, 0.05% and Tween 20 at 65°C for 4 min, then 16times in 0.12 M Tris-HCl (pH 7.5), 0.12 M NaCl at 65°C for 4 min. Microarrays were stained with 2 μg/ml Streptavidin-Cy5 (GE Healthcare) in a solution (0.12 M Tris-HCl (pH 7.5), and 0.12 M NaCl, and 0.05% Tween 20) at room temperature for 30 min, then washed 4 times by soaking in a wash solution (0.12 M Tris-HCl (pH 7.5), 0.12 M NaCl) at room temperature each for 5 min.

scan_protocol: Microarray was scanned at multiple exposure times ranging from 0 to 40s by DNA microarray reader (Yokogawa Electric Corporation). The intensity values with the best exposure condition for each spot were selected. Fluorescent intensity of images was quantified automatically with the software supplied with the microarray reader.

data_processing: All data were subtracted by background signal intensity of each array and normalized between arrays by constants calculated from signal raitio of 9 internal control probes(ACTB, ATP5F1, GAPDH, GTF2B, PLA2G5, RPS5, TUBA1B, GUSB, RPLP0).

source_name: RNA MIX Control

label_protocol: aRNA were amplified and biotinylated by MessageAmpTM II-Biotin Enhanced kit (AppliedBiosystems) according to the manufacturer’s protocol.

extract_protocol: Total RNA was extracted by using mirVana(TM) miRNA Isolation kit (AppliedBiosystems)

tag: disease type

value: none, RNA mix control


title: SmaliE165_022EAFCH_170.txt

description:
GI_dev, small bowel fetal day 16.5
Keywords = mouse gene expression database

source_name: GI_dev, E165


title: EpiHd_022CACIO_114a.txt

description:
Male; Epididymis-head
Keywords = mouse gene expression database


title: SmIntP1_022BAFB9_172.txt


title: Cecum022EAFAT_160.txt

description:
Large Intestine; Cecum
Keywords = mouse gene expression database

source_name: GI, Cec


title: ColonDistal0220AFAR_071.txt

description:
Large Intestine; Distal Colon
Keywords = mouse gene expression database

source_name: GI, D.Col


title: RNA MIX Control 6_Chip2


title: RNA MIX Control 7_Chip2


title: II-18_Snail_rep2

city: Fukuoka

first: Yuta

last: Shirogane

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Faculty of Medicine

institute: Kyushu University

description: A human lung adenocarcinoma cell line, II-18, was infected by retrovirus vectors expressing Snail. After 5 days postinfection, total RNA was extracted.

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using average normalization with Illumina BeadStudio (version 3.4).

source_name: II-18, Snail

label_protocol: Biotinylated cRNA was prepared with Illumina TotalPrep RNA Amplification Kit (Ambion).

extract_protocol: RNA was extracted with QIAGEN RNeasy Plus mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Experion automated electrophoresis system (Bio-Rad).

treatment_protocol: Cells were infected by retrovirus vectors expressing Snail or control vectors. After 5 days postinfection, cells were used for total RNA extraction.

tag: infection

value: Snail-expressing retrovirus vector


title: RNA MIX Control 5_Chip2


title: II-18_Snail_rep1

value: human lung adenocarcinoma cell line, II-18


title: RNA MIX Control 4_Chip2


title: RNA MIX Control 3_Chip2


title: II-18_control_rep3

description: A human lung adenocarcinoma cell line, II-18, was infected by control retrovirus vectors. After 5 days postinfection, total RNA was extracted.

source_name: II-18, control

value: control


title: SmaIntE165_022LAFCI_170.txt


title: II-18_control_rep2


title: II-18_Snail_rep3


title: RNA MIX Control 2_Chip2


title: RNA MIX Control 1_Chip2


title: II-18_control_rep1


title: OCH243_Chip2

description: Sustained virological responder

source_name: liver

value: Chronic hepatitis C patient

tag: therapy response

value: Sustained virological responder


title: OCH241_Chip2

description: Sustained virological responder


title: Cecum022QAC3E_160.txt


title: OCH228_Chip2

description: Sustained virological responder


title: OCH231_Chip2

description: Sustained virological responder


title: OCH236_Chip2

description: Sustained virological responder


title: OCH237_Chip2

description: Sustained virological responder


title: OCH233_Chip2

description: Sustained virological responder


title: OCH232_Chip2

description: Sustained virological responder


title: ColonDistal0224AC3G_071.txt


title: OCH234_Chip2

description: Sustained virological responder


title: LungP24_022IAF74_077d.txt

description:
Lung; Day 24 postnatal
Keywords = mouse gene expression database


title: OCH229_Chip2

description: Sustained virological responder


title: OCH230_Chip2

description: Sustained virological responder


title: OCH195_Chip2

description: Sustained virological responder


title: OCH194_Chip2

description: Sustained virological responder


title: OCH222_Chip2

description: Sustained virological responder


title: OCH190_Chip2

description: Sustained virological responder


title: OCH238_Chip2

description: Sustained virological responder


title: OCH191_Chip2

description: Sustained virological responder


title: OCH154_Chip2

description: Sustained virological responder


title: OCH143_Chip2

description: Sustained virological responder


title: OCH156_Chip2

description: Sustained virological responder


title: OCH240_Chip2

description: Sustained virological responder


title: OCH139_Chip2

description: Sustained virological responder


title: OCH138_Chip2

description: Sustained virological responder


title: OCH131_Chip2

description: Sustained virological responder


title: OCH186_Chip2

description: Sustained virological responder


title: OCH130_Chip2

description: Sustained virological responder


title: si DOT1L + 9hr Wnt

status: Public on Apr 20 2010

city: London

first: Vivian

last: Li

address: 1 Midland Road

institute: The Francis Crick Institute

description: 293T cells transfected with si-DOT1L, induced with Wnt3A medium for 9 hours.

hyb_protocol: The synthezied cRNA was then purified with RNeasy mini kit (Qiagen). 825ng of the corresponding Cy3 and Cy5 cRNA was fragmentated at 60°C for 30 min in the presence of blocking agent and fragmentation buffer (Agilent), then combined with 55ul 2X hybridization buffer (Agilent) and applied to 4X44k human expression microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially

scan_protocol: Scanned on an Agilent G2505 DNA microarray scanner.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: HEK293T human embryonic kidney cells

label_protocol: 2µg of total RNA were primed with 1.2 µl of T7 promoter primer at 65°C for 10 min together with control spike A/B, then reversed transcribed at 40°C for 2hrs in the presence of MMLV RTase (Agilent), and dNTP mix. It was then followed by the cRNA transcription at 40°C for 2hrs in the presence of T7 RNA polymerase, inorganic pyrophosphatase, NTP mix, DTT, PEG and Cy3/Cy5-labeled-CTP.

growth_protocol: Ls174T or HEK293T cells were seeded on 6-well plates and transfected with control/human b-catenin/MLLT10/DOT1L/BRG1/P300 15nM siRNA for 72 hours

extract_protocol: Total RNA extracted using RNeasy mini kit (Qiagen) following manufacturer's instructions

treatment_protocol: Control or Wnt3A conditioned medium was added to the HEK293T cells and incubate for 9 hours before RNA extraction

tag: transfection

tag: induction

value: +Wnt3A, 9 hours

source_name: Human reference RNA

tag: reference

value: Human reference RNA


title: OCH136_Chip2

description: Sustained virological responder


title: OCH124_Chip2

description: Sustained virological responder


title: OCH121_Chip2

description: Sustained virological responder


title: OCH116_Chip2

description: Sustained virological responder


title: OCH158_Chip2

description: Sustained virological responder


title: OCH221_Chip2

description: Relapse

value: Relapse


title: OCH239_Chip2

description: Relapse


title: OCH110_Chip2

description: Sustained virological responder


title: OCH104_Chip2

description: Sustained virological responder


title: OCH103_Chip2

description: Sustained virological responder


title: OCH108_Chip2

description: Sustained virological responder


title: OCH219_Chip2

description: Relapse


title: OCH217_Chip2

description: Relapse


title: OCH214_Chip2

description: Relapse


title: OCH215_Chip2

description: Relapse


title: OCH216_Chip2

description: Relapse


title: OCH218_Chip2

description: Relapse


title: OCH213_Chip2

description: Relapse


title: OCH152_Chip2

description: Relapse


title: OCH141_Chip2

description: Relapse


title: OCH134_Chip2

description: Relapse


title: OCH135_Chip2

description: Relapse


title: OCH128_Chip2

description: Relapse


title: OCH129_Chip2

description: Relapse


title: OCH220_Chip2

description: Relapse


title: OCH112_Chip2

description: Sustained virological responder


title: OCH115_Chip2

description: Relapse


title: OCH113_Chip2

description: Relapse


title: OCH106_Chip2

description: Relapse


title: OCH117_Chip2

description: Relapse


title: OCH223_Chip2

description: Non-virological responder of IFN and ribavirin therapy


title: OCH242_Chip2

value: Non-virological responder of IFN and ribavirin therapy


title: OCH211_Chip2


title: OCH125_Chip2

description: Relapse


title: OCH209_Chip2


title: OCH208_Chip2


title: OCH150_Chip2


title: OCH204_Chip2


title: OCH207_Chip2


title: OCH192_Chip2


title: OCH205_Chip2


title: OCH142_Chip2


title: OCH145_Chip2


title: OCH101_Chip2

description: Relapse


title: OCH140_Chip2


title: OCH132_Chip2


title: OCH126_Chip2


title: OCH127_Chip2


title: OCH137_Chip2


title: OCH206_Chip2


title: OCH123_Chip2


title: NS040_Chip2

description: Receive no therapy for HCV

value: fatty liver patient without HCV infection

value: Receive no therapy for HCV


title: NS039_Chip2

description: Receive no therapy for HCV


title: NS038_Chip2

description: Receive no therapy for HCV


title: OCH105_Chip2


title: OCH119_Chip2


title: OCH111_Chip2


title: OCH118_Chip2


title: OCH122_Chip2


title: NS037_Chip2

description: Receive no therapy for HCV


title: NS036_Chip2

description: Receive no therapy for HCV


title: NS034_Chip2

description: Receive no therapy for HCV


title: NS033_Chip2

description: Receive no therapy for HCV


title: NS031_Chip2

description: Receive no therapy for HCV


title: RNA MIX Control 6_Chip1


title: NS035_Chip2

description: Receive no therapy for HCV


title: RNA MIX Control 7_Chip1


title: OCH133_Chip2

description: Relapse


title: RNA MIX Control 8_Chip1


title: RNA MIX Control 2_Chip1


title: RNA MIX Control 4_Chip1


title: RNA MIX Control 3_Chip1


title: RNA MIX Control 5_Chip1


title: RNA MIX Control 1_Chip1


title: OCH243_Chip1

description: Sustained virological responder


title: OCH240_Chip1

description: Sustained virological responder


title: OCH231_Chip1

description: Sustained virological responder


title: OCH237_Chip1

description: Sustained virological responder


title: OCH241_Chip1

description: Sustained virological responder


title: OCH238_Chip1

description: Sustained virological responder


title: OCH236_Chip1

description: Sustained virological responder


title: OCH114_Chip2

description: Sustained virological responder


title: NS032_Chip2

description: Receive no therapy for HCV


title: OCH232_Chip1

description: Sustained virological responder


title: OCH233_Chip1

description: Sustained virological responder


title: OCH234_Chip1

description: Sustained virological responder


title: OCH230_Chip1

description: Sustained virological responder


title: OCH229_Chip1

description: Sustained virological responder


title: OCH222_Chip1

description: Sustained virological responder


title: OCH228_Chip1

description: Sustained virological responder


title: OCH190_Chip1

description: Sustained virological responder


title: OCH158_Chip1

description: Sustained virological responder


title: OCH191_Chip1

description: Sustained virological responder


title: OCH194_Chip1

description: Sustained virological responder


title: OCH195_Chip1

description: Sustained virological responder


title: OCH156_Chip1

description: Sustained virological responder


title: OCH154_Chip1

description: Sustained virological responder


title: OCH139_Chip1

description: Sustained virological responder


title: OCH138_Chip1

description: Sustained virological responder


title: OCH143_Chip1

description: Sustained virological responder


title: OCH136_Chip1

description: Sustained virological responder


title: OCH131_Chip1

description: Sustained virological responder


title: OCH108_Chip1

description: Sustained virological responder


title: OCH121_Chip1

description: Sustained virological responder


title: OCH124_Chip1

description: Sustained virological responder


title: OCH114_Chip1

description: Sustained virological responder


title: OCH110_Chip1

description: Sustained virological responder


title: OCH112_Chip1

description: Sustained virological responder


title: OCH107_Chip1

description: Sustained virological responder


title: OCH130_Chip1

description: Sustained virological responder


title: OCH239_Chip1

description: Relapse


title: OCH186_Chip1

description: Sustained virological responder


title: OCH220_Chip1

description: Relapse


title: OCH219_Chip1

description: Relapse


title: OCH221_Chip1

description: Relapse


title: OCH109_Chip1

description: Sustained virological responder


title: OCH116_Chip1

description: Sustained virological responder


title: OCH217_Chip1

description: Relapse


title: OCH214_Chip1

description: Relapse


title: OCH141_Chip1

description: Relapse


title: OCH103_Chip1

description: Sustained virological responder


title: OCH104_Chip1

description: Sustained virological responder


title: OCH152_Chip1

description: Relapse


title: OCH213_Chip1

description: Relapse


title: OCH215_Chip1

description: Relapse


title: OCH216_Chip1

description: Relapse


title: OCH134_Chip1

description: Relapse


title: OCH109_Chip2

description: Sustained virological responder


title: OCH218_Chip1

description: Relapse


title: OCH107_Chip2

description: Sustained virological responder


title: OCH129_Chip1

description: Relapse


title: OCH133_Chip1

description: Relapse


title: OCH115_Chip1

description: Relapse


title: OCH128_Chip1

description: Relapse


title: OCH113_Chip1

description: Relapse


title: OCH117_Chip1

description: Relapse


title: OCH120_Chip1

description: Relapse


title: OCH125_Chip1

description: Relapse


title: OCH106_Chip1

description: Relapse


title: OCH101_Chip1

description: Relapse


title: OCH102_Chip1

description: Relapse


title: OCH135_Chip1

description: Relapse


title: OCH211_Chip1


title: OCH242_Chip1


title: OCH223_Chip1


title: OCH120_Chip2

description: Relapse


title: OCH150_Chip1


title: OCH145_Chip1


title: OCH205_Chip1


title: OCH206_Chip1


title: OCH209_Chip1


title: OCH132_Chip1


title: OCH208_Chip1


title: OCH140_Chip1


title: OCH207_Chip1


title: OCH127_Chip1


title: OCH126_Chip1


title: OCH137_Chip1


title: OCH118_Chip1


title: OCH105_Chip1


title: OCH111_Chip1


title: NS040_Chip1

description: Receive no therapy for HCV


title: OCH119_Chip1


title: OCH122_Chip1


title: OCH123_Chip1


title: OCH102_Chip2

description: Relapse


title: NS039_Chip1

description: Receive no therapy for HCV


title: OCH192_Chip1


title: OCH204_Chip1


title: NS038_Chip1

description: Receive no therapy for HCV


title: NS035_Chip1

description: Receive no therapy for HCV


title: OCH142_Chip1


title: NS033_Chip1

description: Receive no therapy for HCV


title: NS037_Chip1

description: Receive no therapy for HCV


title: NS036_Chip1

description: Receive no therapy for HCV


title: NS034_Chip1

description: Receive no therapy for HCV


title: NS031_Chip1

description: Receive no therapy for HCV


title: NS032_Chip1

description: Receive no therapy for HCV


title: Schistosoma mansoni exposed 32d 3

status: Public on Jan 01 2010

city: Albuquerque

first: Patrick

middle: C

last: Hanington

state: NM

address: 1 University of New Mexico

department: Department of Biology, University of New Mexico

institute: Center for Evolutionary and Theoretical Immunology

description: no additional information

hyb_protocol: Purified Cy3 and Cy5 labeled products were then pooled, ethanol precipitated, resuspended in 100 µL hybridization buffer (40 % formamide, 5x Denhardt’s, 5x SSC, 1 mM sodium pyrophosphate, 50 mM Tris (pH 7.4) and 0.1 % SDS) and incubated at 95°C for 5 min followed by 50°C for 5 min. Arrays were pre-hybridized for 3.0 h at 42°C in hybridization buffer prior to hybridization with labeled probes. Labeled cDNA was hybridized overnight at 42°C.

scan_protocol: Microarray slides were scanned with a GenePix® 4000B scanner (Axon Instruments) with GenePix® Pro 6.0 (Axon Instruments) software using a modified protocol as described by Aragon and colleagues.

data_processing: A preloaded grid was used to align and identify array spots. Alignment diameter minimum and maximums were set at 50% and 200%, respectively. Nearest negative control spots were selected for background subtraction. Acuity version 4.0 (Axon Instruments) software was used in array analyses and arrays were normalized using a ratio of medians to Alien control spots. SAM was used to determine significiantly differentially regulated genes with a cut of of 2-fold and a false positive rate of less then 10%

organism: Biomphalaria glabrata

source_name: 4-8 mm Biomphalaria glabrata, Schistosoma mansoni-infected

label_protocol: Complementary DNA was synthesized, amplified, labeled and hybridized using the modified SMART (Clontech) cDNA labeling protocol described by Petalidis and colleagues. Briefly, 300 ng total RNA were mixed with 3 µL of 10 μM 3′ SMART CDS primer IIA (5′-AAGCAGTGGTATCAACGCAGAGTACT30VN-3′) and 3 µL 10 μM template switching primer (5′-d(AAGCAGTGGTATCAACGCAGAGTACGC)r(GGG)-3′) and brought to a final volume of 15 µL with RNase free dH2O. The template switching primer is a DNA:RNA hybrid where the last 3 bases are RNA. The reaction was then incubated at 72°C for 2 min and then placed on ice. Six microliters of 5x first-strand buffer (Clontech), 3 µL DTT (20 mM), 3 µL dNTPs (10 mM), and 3 µL and PowerScriptTM reverse transcriptase (Clontech) were then added to the reaction and the mixture incubated at 42°C for 1.0 h to generate first strand cDNA. Second-strand cDNA was then amplified by mixing 15 µL of the first-strand cDNA reaction with 57 µL dH2O, 10 µL 10x PCR buffer II (Applied Biosystems), 10 µL 25 mM MgCl2, 2 µL 10 mM dNTPs, 4 µL 10 μM 5’ PCR primer (5′-AAGCAGTGGTATCAACGCAGAGT-3′) and 2 µl AmpliTaq® (40 U/µL). Amplification conditions were 95°C for 1 min for one cycle followed by 95°C for 5 s, 65°C for 5 s, and 68°C for 6 min for 15 cycles. Second strand cDNA was then purified using a QIAquick® PCR Purification Kit (Qiagen), quantified using a NanoDrop® ND-1000 spectrophotometer and labeled with Cy3/Cy5 d-CTPs (GE Healthcare-Amersham) using BioPrime® DNA Labeling System (Invitrogen). For labeling, 200 ng of second-strand cDNA suspended in 21 µL dH2O was mixed with 20 μL of 2.5x random primer reaction buffer (Invitrogen) and incubated at 95°C for 5 min, then placed on ice. While on ice, 2 µL dH2O, 5 μL low-C dNTP mix (5 mM dATP, 5 mM dGTP, 5 mM dTTP, 2 mM dCTP), 1 µL Cy3 or Cy5 dCTP and 1 μL Klenow enzyme (40 U/µL; Invitrogen) were mixed and incubated at 37°C for 2.0 h. The labeling reaction was stopped by adding 5 μL stop buffer (Invitrogen). For all experiments, reference samples were labeled with Cy3 and experimental samples with Cy5. Cy3 and Cy5 labeled probes were purified separately using an AutoSeqTM G-50 Dye Terminator Removal Kit (GE Healthcare) and labeling efficiency quantified using a NanoDrop® ND-1000 spectrophotometer.

growth_protocol: Snails and trematodes used in this study were maintained at the University of New Mexico

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

treatment_protocol: The trematode infected experimental groups and one control group examined this study were non-infected M line (control) , Echinostoma paraensei infected and Schistosoma mansoni infected B. glabrata. For each treatment three pools of 5 snails were used as the biological replicates to reduce individual variability. Individual juvenile snails (shell diameter 4-8mm) B. glabrata were exposed to 15-20 S. mansoni or E. paraensei miracidia in artificial spring water (ASW), (Loker and Hertel, 1987) and kept alive before RNA extraction which was performed on days 0.5, 1, 2, 4, 8, 16 and 32 post infection. Control snails were placed into 24-well plates with ASW for 12 hours to mimic the conditions of infection protocol, afterwards RNA was extraction at the same time points as in the experimental groups.

value: M-line

value: Schistosoma mansoni

tag: time

source_name: Reference

tag: control

value: Reference sample RNA consisted of a mixture of RNA from snails


title: Schistosoma mansoni exposed 32d 2

description: no additional information


title: Schistosoma mansoni exposed 32d 1

description: no additional information


title: Schistosoma mansoni exposed 16d 1

description: no additional information


title: Schistosoma mansoni exposed 16d 2

description: no additional information


title: Schistosoma mansoni exposed 16d 3

description: no additional information


title: Schistosoma mansoni exposed 8d 3

description: no additional information


title: Schistosoma mansoni exposed 4d 3

description: no additional information


title: Schistosoma mansoni exposed 8d 2

description: no additional information


title: Schistosoma mansoni exposed 8d 1

description: no additional information


title: Schistosoma mansoni exposed 2d 1

description: no additional information


title: Schistosoma mansoni exposed 2d 2

description: no additional information


title: Schistosoma mansoni exposed 1d 3

description: no additional information


title: Schistosoma mansoni exposed 4d 2

description: no additional information


title: Schistosoma mansoni exposed 2d 3

description: no additional information


title: Schistosoma mansoni exposed 4d 1

description: no additional information


title: Schistosoma mansoni exposed 1d 2

description: no additional information


title: Schistosoma mansoni exposed 0.5d 3

description: no additional information


title: Schistosoma mansoni exposed1d 1

description: no additional information


title: Schistosoma mansoni exposed 0.5d 2

description: no additional information


title: Uninfected control 7 for Sm

description: no additional information

source_name: 4-8 mm Biomphalaria glabrata, uninfected

value: Uninfected (control for Sm)


title: Schistosoma mansoni exposed 0.5d 1

description: no additional information


title: Echinostoma paraensei 32d exposed 1

description: no additional information

source_name: 4-8 mm Biomphalaria glabrata, Echinostoma paraensei-infected

value: Echinostoma paraensei


title: Echinostoma paraensei 32d exposed 2

description: no additional information


title: Echinostoma paraensei 32d exposed 3

description: no additional information


title: Uninfected control 5 for Sm

description: no additional information


title: Uninfected control 4 for Sm

description: no additional information


title: Uninfected control 6 for Sm

description: no additional information


title: Echinostoma paraensei 16d exposed 2

description: no additional information


title: Echinostoma paraensei 16d exposed 1

description: no additional information


title: Echinostoma paraensei 8d exposed 3

description: no additional information


title: Echinostoma paraensei 8d exposed 1

description: no additional information


title: Echinostoma paraensei 8d exposed 2

description: no additional information


title: Echinostoma paraensei 4d exposed 1

description: no additional information


title: Echinostoma paraensei 4d exposed 2

description: no additional information


title: Echinostoma paraensei 16d exposed 3

description: no additional information


title: Echinostoma paraensei 4d exposed 3

description: no additional information


title: Echinostoma paraensei 1d exposed 3

description: no additional information


title: Echinostoma paraensei 2d exposed 3

description: no additional information


title: Echinostoma paraensei 2d exposed 2

description: no additional information


title: Echinostoma paraensei 2d exposed 1

description: no additional information


title: Echinostoma paraensei 0.5d exposed 1

description: no additional information


title: Uninfected control 3 for Ep

description: no additional information

value: Uninfected (control for Ep)


title: Echinostoma paraensei 0.5d exposed 3

description: no additional information


title: Echinostoma paraensei 0.5d exposed 2

description: no additional information


title: Echinostoma paraensei 1d exposed 1

description: no additional information


title: Echinostoma paraensei 1d exposed 2

description: no additional information


title: Uninfected control 2 for Ep

description: no additional information


title: Uninfected control 1 for Ep

description: no additional information


title: T3-9

type: genomic

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description:
stage 3-9
Sample 28

hyb_protocol: According to NimbleGen Kit

scan_protocol: Follow NimbleScan's default using Agilent Scanner

data_processing: The log2 ratio of the input signals for the enriched and input samples that were co-hybridized to the array is computed and scaled to center the ratio data around zero. Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. VALUE is the P value derived from Kolmogorov-Smirnov test using 750bp window size of the Cy5/Cy3 log2 ratio using NimbleScan.

molecule: genomic DNA

source_name: input, astrocytoma T3-9

label_protocol: According to NimbleGen Kit

extract_protocol: Standard phenol/chloroform method was used for DNA extraction. The MIRA procedure was as described in Rauch et al., 2006. Cancer Research 66:7939–7947.

tag: fraction

value: input

tag: stage

value: stage 3

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T3-9

value: methylated DNA-enriched


title: T4-5

description:
stage 4-5
Sample 23

source_name: input, astrocytoma T4-5

value: stage 4

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T4-5


title: T3-4

description:
stage 3-4
Sample 16

source_name: input, astrocytoma T3-4

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T3-4


title: T3-3

description:
stage 3-3
Sample 15

source_name: input, astrocytoma T3-3

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T3-3


title: T4-8

description:
stage 4-8
Sample 30

source_name: input, astrocytoma T4-8

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T4-8


title: T4-7

description:
stage 4-7
Sample 29

source_name: input, astrocytoma T4-7

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T4-7


title: T3-5

description:
stage 3-5
Sample 17

source_name: input, astrocytoma T3-5

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T3-5


title: T3-2

description:
stage 3-2
Sample 14

source_name: input, astrocytoma T3-2

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T3-2


title: T4-4

description:
stage 4-4
Sample 22

source_name: input, astrocytoma T4-4

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T4-4


title: T4-2

description:
stage 4-2
Sample 20

source_name: input, astrocytoma T4-2

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T4-2


title: T3-6

description:
stage 3-6
Sample 18

source_name: input, astrocytoma T3-6

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T3-6


title: T3-7

description:
stage 3-7
Sample 26

source_name: input, astrocytoma T3-7

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T3-7


title: T4-3

description:
stage 4-3
Sample 21

source_name: input, astrocytoma T4-3

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T4-3


title: T3-1

description:
stage 3-1
Sample 13

source_name: input, astrocytoma T3-1

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T3-1


title: T2-4

description:
stage 2-4
Sample 10

source_name: input, astrocytoma T2-4

value: stage 2

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T2-4


title: T4-6

description:
stage 4-6
Sample 24

source_name: input, astrocytoma T4-6

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T4-6


title: T4-1

description:
stage 4-1
Sample 19

source_name: input, astrocytoma T4-1

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T4-1


title: T2-3

description:
stage 2-3
Sample 9

source_name: input, astrocytoma T2-3

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T2-3


title: T2-6

description:
stage 2-6
Sample 12

source_name: input, astrocytoma T2-6

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T2-6


title: T1-3

description:
Stage 1-3
Sample 3

source_name: input, astrocytoma T1-3

value: stage 1

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T1-3


title: T2-2

description:
stage 2-2
Sample 8

source_name: input, astrocytoma T2-2

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T2-2


title: T1-6

description:
Stage 1-6
Sample 6

source_name: input, astrocytoma T1-6

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T1-6


title: T1-4

description:
Stage 1-4
Sample 4

source_name: input, astrocytoma T1-4

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T1-4


title: T1-5

description:
Stage 1-5
Sample 5

source_name: input, astrocytoma T1-5

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T1-5


title: T2-1

description:
stage 2-1
Sample 7

source_name: input, astrocytoma T2-1

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T2-1


title: T3-8

description:
stage 3-8
Sample 27

source_name: input, astrocytoma T3-8

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T3-8


title: N6

description:
normal 6
Sample 32

source_name: input, normal N6

value: normal

source_name: methylated CpG-island recovery assay (MIRA) enriched, normal N6


title: T1-2

description:
Stage 1-2
Sample 2

source_name: input, astrocytoma T1-2

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T1-2


title: Human Cavernosal Endothelial Cell Phenotype HCA 285

status: Public on Sep 28 2009

city: Seattle

first: Hunter

last: Wessells

state: WA

address: 300 Ninth Avenue

department: Urology

institute: University of Washington

hyb_protocol: Each target was hybridized to an Affymetrix Human U133A GeneChip

scan_protocol: GeneChips were washed and scanned at the University of Washington’s Center for Expression Arrays according to procedures developed by the manufacturer

data_processing: MAS 5

source_name: HCAEC

label_protocol: Biotin labeled target cRNA was prepared according to the Affymetrix eukaryotic target labeling protocol starting with 5ug total RNA for each sample.

growth_protocol: Endothelial cells were grown on 2% gelatin type B (Sigma)/15% fetal bovine serum (Gibco) coated tissue culture dishes in Medium 199 (Gibco) supplemented with 20% FBS, EGM-2MV (Clonetics), L-glutamine and 10,000u/ml Penicillin, 10,000u/ml Streptomycin, and 25mg/ml Fungizone. All cells were grown in a humidified incubator at 37 oC and 5% CO2 with media changed every 2-3 days.

extract_protocol:
Total RNA isolation for the arrays was performed using Qiagen RNeasy mini
columns according to manufacturers instructions (RNeasy Mini Handbook). Briefly, cells grown in T-75 culture flasks were trypsinized with 0.25% trypsin/1 mM EDTA (Gibco) between the third and seventh passages and centrifuged to pellet the cells. Next, cells were disrupted and homogenized in RNeasy lysis buffer using a 1ml syringe with 21-gauge needle. Ethanol was added to allow binding of RNA to the silica-gel-based membrane of the mini column. Several washes as well as on-column DNase treatment were used to ensure that contaminants and DNA were effectively removed from the column. Finally, RNA was eluted in approximately 30ul of RNase free water.

tag: gender

value: male

tag: cell type

value: cultured human coronary artery endothelial cells (HCAEC) from donor without erectile dysfunction (ED)


title: Human Cavernosal Endothelial Cell Phenotype HCA 1175


title: T1-1

description:
Stage 1-1
Sample 1

source_name: input, astrocytoma T1-1

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T1-1


title: Human Cavernosal Endothelial Cell Phenotype HCA 1348


title: Human Cavernosal Endothelial Cell Phenotype HUV 121

source_name: HUVEC

value: cultured human umbilical vein endothelial cells (HUVEC) from donor without erectile dysfunction (ED)


title: N3

description:
normal 3
Sample 35

source_name: input, normal N3

source_name: methylated CpG-island recovery assay (MIRA) enriched, normal N3


title: N1

description:
normal 1
Sample 33

source_name: input, normal N1

source_name: methylated CpG-island recovery assay (MIRA) enriched, normal N1


title: Human Cavernosal Endothelial Cell Phenotype HCA 239


title: N5

description:
normal 5
Sample 31

source_name: input, normal N5

source_name: methylated CpG-island recovery assay (MIRA) enriched, normal N5


title: N2

description:
normal 2
Sample 34

source_name: input, normal N2

source_name: methylated CpG-island recovery assay (MIRA) enriched, normal N2


title: Human Cavernosal Endothelial Cell Phenotype HUV 64


title: Human Cavernosal Endothelial Cell Phenotype HUV 5171


title: T2-5

description:
stage 2-5
Sample 11

source_name: input, astrocytoma T2-5

source_name: methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T2-5


title: N4

description:
normal 4
Sample 36

source_name: input, normal N4

source_name: methylated CpG-island recovery assay (MIRA) enriched, normal N4


title: Human Cavernosal Endothelial Cell Phenotype HCC 27

source_name: HCCEC

value: cultured human corpus cavernosum endothelial cells (HCCEC) from donor with erectile dysfunction (ED)


title: 01UNM_PolyRF+

status: Public on Jun 30 2009

first: Michael

last: Barnes

address: 3333 Burnet Ave

department: Rheumatology

institute: Cincinnati Childrens Hospital Medical Center

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard scanning

data_processing: Data were imported into GeneSpring 7.3 with RMA preprocessing and normalized to median of all samples.  Normalized data were exported and subjected to Distance Weighted Discrimination (DWD) to account for any batch effects then reimported into Gene Spring and analyzed.

label: Biotin

source_name: Peripheral blood mononuclear cells, RF+ polyarthritis

label_protocol: NuGEN Ovation labeling

extract_protocol: Peripheral blood was drawn and PBMC were isolated over Ficoll.  Samples were stored in Trizol at -80oC until extracted according to manufacturer's directions.

tag: Race=Black or African American

tag: Sex=Female

tag: Group=A


title: 01UND_PolyRF+

tag: Race=Caucasian/White

tag: Group=B


title: Human Cavernosal Endothelial Cell Phenotype HCC 43

label_protocol: Label protocol Biotin labeled target cRNA was prepared according to the Affymetrix eukaryotic target labeling protocol starting with 5ug total RNA for each sample.

extract_protocol:
Extracted molecule total RNA
Extraction protocol Total RNA isolation for the arrays was performed using Qiagen RNeasy mini
columns according to manufacturers instructions (RNeasy Mini Handbook). Briefly, cells grown in T-75 culture flasks were trypsinized with 0.25% trypsin/1 mM EDTA (Gibco) between the third and seventh passages and centrifuged to pellet the cells. Next, cells were disrupted and homogenized in RNeasy lysis buffer using a 1ml syringe with 21-gauge needle. Ethanol was added to allow binding of RNA to the silica-gel-based membrane of the mini column. Several washes as well as on-column DNase treatment were used to ensure that contaminants and DNA were effectively removed from the column. Finally, RNA was eluted in approximately 30ul of RNase free water.

value: cultured human corpus cavernosum endothelial cells (HCCEC) from donor without erectile dysfunction (ED)


title: 01UNB_PolyRF-

source_name: Peripheral blood mononuclear cells, RF- polyarthritis

tag: Sex=Male

tag: Group=C


title: Human Cavernosal Endothelial Cell Phenotype HCC 33


title: 01UNZ_PolyRF+


title: 01MLR_PolyRF+


title: Human Cavernosal Endothelial Cell Phenotype HCC 45


title: Human Cavernosal Endothelial Cell Phenotype HCC 28


title: 01MLF_PolyRF+

tag: Group=Con


title: 01MH9_PolyRF+

tag: Race=Asian


title: 01N3L_PolyRF-

value: Peripheral blood mononuclear cells

tag: original diagnosis

value: RF- polyarticular JIA

tag: ttf

tag: race

value: Caucasian/White

tag: sex

value: Female

tag: group

value: B

tag: prototype

value: N


title: 01LNY_PolyRF+


title: 01N1N_PolyRF-

value: Con


title: 01MHR_PolyRF+


title: 01MJT_PolyRF+


title: 01LM4_PolyRF-

value: A

value: Y


title: 01LR0_PolyRF+


title: 01LLA_PolyRF+


title: 01LM1_PolyRF+


title: Human Breast Tumor 64

status: Public on May 06 2009

city: Genoa

first: Paolo

last: Uva

address: Via Gerolamo Gaslini, 5

country: Italy

institute: IRCCS Istituto Giannina Gaslini

description: Breast tumor

hyb_protocol: 5 μg of labelled-RNA from each sample were co-hybridized with 5 μg of a normal reference pool, consisting of an equal amount of cRNA extracted from mammary healthy samples. Labelled cRNAs were fragmented to an average size of 50-100 nucleotides by heating the samples to 60°C with 10mM of zinc chloride and then adding an hybridization buffer containing 1M NaCl, 0.5% sodium sarcosine, 50mM MES, pH6.5, and formamide to a final concentration  of 30%. The final volume was 3ml at 40°C.

scan_protocol: Slides were washed and scanned using a confocal laser scanner (Agilent Technologies). Images were quantified using Agilent Feature Extraction Software (version 9.1).

data_processing: Lowess normalized, background subtracted data obtained from log10 of processed Red signal/processed Green signal. Rosetta Resolver gene expression analysis software (version 3.2, Rosetta Biosoftware, Seattle, WA) was used.

source_name: Breast tumor

label_protocol: cRNA was generated by in vitro transcription using T7 RNA polymerase on 5 μg of total RNA and labelled with Cy5 or Cy3 (Cy Dye, Amersham Pharmacia Biotech).

extract_protocol: Total RNA was isolated with RNAzolB and finally dissolved in RNase-free water. Then 25μg of total RNA was treated with DNase using the Qiagen RNase-free DNase kit and RNeasy spin columns. Total RNA was dissolved in RNase-free water to a final concentration of 0.2 μg/μl.

tag: tissue

value: breast tumor

tag: disease state

value: infiltrating ductal mammary carcinoma

source_name: Adjacent non-involved breast tissue reference pool

tag: sample

value: Pool of normal samples


title: Human Breast Tumor 65

description: Breast tumor


title: Human Breast Tumor 66

description: Breast tumor


title: Human Breast Tumor 61

description: Breast tumor


title: Human Breast Tumor 59

description: Breast tumor


title: Human Breast Tumor 63

description: Breast tumor


title: Human Breast Tumor 60

description: Breast tumor


title: Human Breast Tumor 68

description: Breast tumor


title: Human Breast Tumor 67

description: Breast tumor


title: Human Breast Tumor 62

description: Breast tumor


title: Human Breast Tumor 56

description: Breast tumor


title: Human Breast Tumor 55

description: Breast tumor


title: Human Breast Tumor 58

description: Breast tumor


title: Human Breast Tumor 57

description: Breast tumor


title: Human Breast Tumor 54

description: Breast tumor


title: Human Breast Tumor 53

description: Breast tumor


title: Human Breast Tumor 44

description: Breast tumor


title: Human Breast Tumor 51

description: Breast tumor


title: Human Breast Tumor 49

description: Breast tumor


title: Human Breast Tumor 43

description: Breast tumor


title: Human Breast Tumor 52

description: Breast tumor


title: Human Breast Tumor 50

description: Breast tumor


title: Human Breast Tumor 45

description: Breast tumor


title: Human Breast Tumor 42

description: Breast tumor


title: Human Breast Tumor 47

description: Breast tumor


title: Human Breast Tumor 39

description: Breast tumor


title: Human Breast Tumor 46

description: Breast tumor


title: Human Breast Tumor 48

description: Breast tumor


title: Human Breast Tumor 40

description: Breast tumor


title: Human Breast Tumor 37

description: Breast tumor


title: Human Breast Tumor 38

description: Breast tumor


title: Human Breast Tumor 41

description: Breast tumor


title: Human Breast Tumor 35

description: Breast tumor


title: Human Breast Tumor 29

description: Breast tumor


title: Human Breast Tumor 33

description: Breast tumor


title: Human Breast Tumor 30

description: Breast tumor


title: Human Breast Tumor 28

description: Breast tumor


title: Human Breast Tumor 32

description: Breast tumor


title: Human Breast Tumor 31

description: Breast tumor


title: Human Breast Tumor 27

description: Breast tumor


title: Human Breast Tumor 26

description: Breast tumor


title: Human Breast Tumor 24

description: Breast tumor


title: Human Breast Tumor 34

description: Breast tumor


title: Human Breast Tumor 25

description: Breast tumor


title: Human Breast Tumor 36

description: Breast tumor


title: Human Breast Tumor 8

description: Breast tumor


title: Human Breast Tumor 23

description: Breast tumor


title: Human Breast Tumor 16

description: Breast tumor


title: Human Breast Tumor 12

description: Breast tumor


title: Human Breast Tumor 3

description: Breast tumor


title: Human Breast Tumor 6

description: Breast tumor


title: Human Breast Tumor 7

description: Breast tumor


title: Human Breast Tumor 20

description: Breast tumor


title: Human Breast Tumor 2

description: Breast tumor


title: Human Adjacent non-involved breast tissue 60

description: Adjacent non-involved breast tissue

source_name: Adjacent non-involved breast tissue

value: adjacent non-involved breast tissue

value: normal mammary sample


title: Human Breast Tumor 13

description: Breast tumor


title: Human Breast Tumor 17

description: Breast tumor


title: Human Adjacent non-involved breast tissue 61

description: Adjacent non-involved breast tissue


title: Human Breast Tumor 19

description: Breast tumor


title: Human Breast Tumor 14

description: Breast tumor


title: Human Adjacent non-involved breast tissue 57

description: Adjacent non-involved breast tissue


title: Human Breast Tumor 11

description: Breast tumor


title: Human Breast Tumor 4

description: Breast tumor


title: Human Adjacent non-involved breast tissue 59

description: Adjacent non-involved breast tissue


title: Human Breast Tumor 5

description: Breast tumor


title: Human Breast Tumor 15

description: Breast tumor


title: Human Breast Tumor 10

description: Breast tumor


title: Human Breast Tumor 1

description: Breast tumor


title: Human Adjacent non-involved breast tissue 56

description: Adjacent non-involved breast tissue


title: Human Breast Tumor 21

description: Breast tumor


title: Human Breast Tumor 9

description: Breast tumor


title: Human Breast Tumor 18

description: Breast tumor


title: Human Adjacent non-involved breast tissue 58

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 50

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 53

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 54

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 52

description: Adjacent non-involved breast tissue


title: Human Breast Tumor 22

description: Breast tumor


title: Human Adjacent non-involved breast tissue 47

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 49

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 48

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 42

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 51

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 37

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 40

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 35

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 38

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 43

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 34

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 45

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 46

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 39

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 33

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 31

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 41

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 32

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 28

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 30

description: Adjacent non-involved breast tissue


title: Dog Breast tumor 25

description: Breast tumor

organism: Canis lupus familiaris

value: malignant tumor

value: breast

source_name: Normal reference pool


title: Dog Breast tumor 26

description: Breast tumor


title: Human Adjacent non-involved breast tissue 27

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 55

description: Adjacent non-involved breast tissue


title: Dog Breast tumor 22

description: Breast tumor


title: Dog Breast tumor 24

description: Breast tumor


title: Human Adjacent non-involved breast tissue 29

description: Adjacent non-involved breast tissue


title: Dog Breast tumor 23

description: Breast tumor


title: Dog Breast tumor 19

description: Breast tumor


title: Human Adjacent non-involved breast tissue 25

description: Adjacent non-involved breast tissue


title: Dog Breast tumor 21

description: Breast tumor


title: Dog Breast tumor 18

description: Breast tumor


title: Dog Breast tumor 17

description: Breast tumor


title: Dog Breast tumor 20

description: Breast tumor


title: Human Adjacent non-involved breast tissue 24

description: Adjacent non-involved breast tissue


title: Dog Breast tumor 16

description: Breast tumor


title: Human Adjacent non-involved breast tissue 23

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 26

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 22

description: Adjacent non-involved breast tissue


title: Dog Breast tumor 14

description: Breast tumor


title: Dog Breast tumor 15

description: Breast tumor

value: benign tumor


title: Human Adjacent non-involved breast tissue 21

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 20

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 19

description: Adjacent non-involved breast tissue


title: Dog Breast tumor 13

description: Breast tumor


title: Human Adjacent non-involved breast tissue 17

description: Adjacent non-involved breast tissue


title: Dog Breast tumor 12

description: Breast tumor

value: hyperplasia/displasia


title: Human Adjacent non-involved breast tissue 14

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 18

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 36

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 10

description: Adjacent non-involved breast tissue


title: Dog Breast tumor 11

description: Breast tumor


title: Dog Breast tumor 8

description: Breast tumor


title: Dog Breast tumor 9

description: Breast tumor


title: Human Adjacent non-involved breast tissue 16

description: Adjacent non-involved breast tissue


title: Dog Breast tumor 6

description: Breast tumor


title: Human Adjacent non-involved breast tissue 13

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 11

description: Adjacent non-involved breast tissue


title: Dog Breast tumor 7

description: Breast tumor


title: Human Adjacent non-involved breast tissue 44

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 12

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 15

description: Adjacent non-involved breast tissue


title: Dog Breast tumor 10

description: Breast tumor


title: Dog Breast tumor 4

description: Breast tumor


title: Dog Breast tumor 5

description: Breast tumor


title: Human Adjacent non-involved breast tissue 6

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 7

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 9

description: Adjacent non-involved breast tissue


title: Dog Breast tumor 1

description: Breast tumor


title: Dog Normal mammary gland 7

description: Normal mammary gland

source_name: Normal mammary gland

value: normal tissue

value: mammary gland


title: Human Adjacent non-involved breast tissue 8

description: Adjacent non-involved breast tissue


title: Dog Normal mammary gland 6

description: Normal mammary gland


title: Human Adjacent non-involved breast tissue 5

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 4

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 3

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 2

description: Adjacent non-involved breast tissue


title: Human Adjacent non-involved breast tissue 1

description: Adjacent non-involved breast tissue


title: Dog Normal mammary gland 4

description: Normal mammary gland


title: Dog Normal mammary gland 3

description: Normal mammary gland


title: EZH2 RNAi, replicate 2

status: Public on Apr 28 2009

city: Ann Arbor

first: Christopher

last: Maher

state: MI

address: 1500 E. Medical Center Drive

institute: Michigan Center for Translational Pathology

description:
EZH2 RNAi vs. EZH2 control siRNA
Replicate 2 of 2

hyb_protocol: According to the manufacturer's protocol.

scan_protocol: Scanned on Agilent Technologies Scanner G2505B. Images were quantified using Agilent Feature Extraction Software.

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: SKBr3 cells, EZH2 RNAi

tag: cell line

source_name: SKBr3 cells, EZH2 control siRNA


title: NO_KIDNEY_10

status: Public on Jun 05 2008

city: Grand Rapids

first: Eric

last: Kort

address: 333 Bostwick NE

institute: Van Andel Research Institute

description: Clear cell, chromophobe, papillary (types 1 and 2), oncocytoma, and Wilms tumor were compared to normal kidney tissue.

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

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

data_processing: The data were analyzed with custom CDF environments created by the MBNI - The version 6 entrez gene ID CDF was used.  Data were then rma normalized using R and the bioconductor suite of analysis tools (eset <- rma(ab))

label: SAPE

source_name: Normal kidney

label_protocol: 10 ug of Qiagen-purified total RNA was labeled with 6ul of 1mg/ml R-Phycoerythrin Streptavidin (SAPE)

extract_protocol: Trizol extraction of total RNA was performed according to manufacturer's protocol

tag: Gender

value: M

tag: Stage

tag: Normal kidney


title: NO_KIDNEY_9


title: Dog Normal mammary gland 2

description: Normal mammary gland


title: NO_KIDNEY_11


title: NO_KIDNEY_8


title: Dog Normal mammary gland 1

description: Normal mammary gland


title: EZH2 RNAi, replicate 1

description:
EZH2 RNAi vs. EZH2 control siRNA
Replicate 1 of 2

label_protocol: According to the manufacturer's protocol.


title: NO_KIDNEY_4

value: F


title: NO_KIDNEY_7


title: NO_KIDNEY_6


title: Dog Normal mammary gland 5

description: Normal mammary gland


title: NO_KIDNEY_5


title: miR101 overexpression, replicate 1

description:
miR101 overexpression vs. miR101 control
Replicate 1 of 2

source_name: SKBr3 cells, miR101 overexpression

extract_protocol: According to the manufacturer's protocol.

source_name: SKBr3 cells, miR101 control


title: NO_KIDNEY_1


title: NO_KIDNEY_12

status: Public on Jun 12 2007

first: Karl

last: Dykema

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: Gene expression data from human normal kidney tissue and human kidney tumor tissues. Tumor subtypes include Papillary types 1, 1.2A, 2A, and 2B.

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

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

data_processing: The data were analyzed with custom CDF environments created by the MBNI - The version 6 entrez gene ID CDF was used.

label: R-Phycoerythrin Streptavidin (SAPE), from Molecular Probes, 1 mg/ml  ( we use 6 ul per reaction )

source_name: subtype: NO

label_protocol: 10 ug of Qiagen-purified total RNA

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

tag: subtype

value: NO


title: NO_KIDNEY_2


title: miR101 overexpression, replicate 2

description:
miR101 overexpression vs. miR101 control
Replicate 2 of 2


title: NO_KIDNEY_3


title: day9 slide1

status: Public on Dec 05 2005

city: Lelystad

first: Saskia

middle: van

last: Hemert

address: PO box 65

country: Netherlands

institute: Animal Sciences Group

description: comparison 2 chicken lines

data_processing: genepix pro

organism: Gallus gallus

source_name: jejunum fast control d9

value: jejunum

tag: infection

value: control

source_name: jejunum fast salmonella d9

value: salmonella


title: Dog Breast tumor 3

description: Breast tumor


title: Dog Breast tumor 2

description: Breast tumor