title: germ-free mice in experiment_1

status: Public on Apr 28 2011

city: Odawara

first: Yukio

last: Asami

address: 540 Naruda

department: Functional Evaluation

institute: Meiji Corporation, Food Science Institute

description: Gene expression data from stomach of germ free mouse, equal amount of RNA from three mice were pooled, and each experiment was performed independently.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

source_name: Mouse stomach, germ free mouse in experiment_1, pooled RNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug pooled total RNA from three mice in each group(GeneChip Expression Analysis Technical Manual, 2005-2009, Affymetrix).

growth_protocol: For inoculation bacteria into germ free mice, Lactobacillus gasseri OLL2716 (LG21) strain was grown in DifcoTM MRS broth for 37℃ for 1 day, and the Helicobacter pylori WT strain, had CagA, CagE and CagG, was incubated in DifcoTM Brucella broth containing 5% FBS at 37℃ for 3 days. Male BALB/c germ free mice were maintained in Trexler type flexible film plastic isolators with sterile food and water.

extract_protocol: Total RNA was prepared individually from the stomachs using a QIAGEN RNeasy Mini Kit according to the manufacturer's instructions. The quality and quantity of RNA in the samples were examined by measuring the optical density at 260 nm and 280 nm and by observing the gel electrophoresis pattern by Agilent 2100 Bioanalyzer.

treatment_protocol: To colonize the mice with lactobacilli, 109 colony-forming unit (CFU) of live lactobacilli suspended in 0.5 ml of PBS were orally inoculated once into 8-week-old germfree mice using a stomach tube. For infection with H. pylori, 8-week-old mice were orally inoculated using a stomach tube on three consecutive days with 109 CFU of H. pylori that were freshly prepared and re-suspended in 0.5 ml PBS. Ten days after the last inoculation, the stomach was excised for microarray analysis.

tag: mouse strain

value: BALB/c

tag: colonised bacteria

value: germ free


title: germ-free mice in experiment_2

type: RNA

state: Kanagawa

country: Japan

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Mouse stomach, germ free mouse in experiment_2, pooled RNA


title: lactobacilli associated gnotobiotic mice in experiment_2

description: Gene expression data from stomach of lactobacilli associated gnotobiotic mouse, equal amount of RNA from three mice were pooled, and each experiment was performed independently.

source_name: Mouse stomach, lactobacilli associated gnotobiotic mouse in experiment_2, pooled RNA

value: Lactobacillus gasseri OLL2716 strain


title: Patient 1, acute wound sample

status: Public on Apr 29 2011

city: Helsinki

first: Kristo

middle: Juhana

last: Nuutila

address: Haartmaninkatu 8, Biomedicum 1

department: Institute of Biomedicine

country: Finland

institute: University of Helsinki

description: Skin from split thickness skin grafting

hyb_protocol: According to Affymetrix GeneChip Hybridization, Wash and Stain Kit

scan_protocol: Chip scanning was performed with a GeneChip Scanner 3000 7G (Affymetrix)

data_processing: Data analysis was performed with GeneSpring GX software, version 11.0.1 (Agilent Technologies), normalized to the median, filtered by expression, and presented as gene expression-fold changes.The results are expressed as means ± SEM. Statistical analysis was performed, using GeneSpring GX software, version 11.0.1 (Agilent Technologies).  Differences between the groups were compared using one-way analysis of variance (ANOVA) with Benjamini-Hochberg posttesting.

organism: Homo sapiens

source_name: acute wound sample

label_protocol: According to Affymetrix GeneChip 3' IVT Express Kit

growth_protocol: No treatment, clinical patient samples from normal wound healing process.

extract_protocol: The skin samples were homogenized using the Precellys 24 tissue homogenizer with a Cryolys temperature controller unit (Bertin Technologies SA, Montigny-le-Bretonneux, France).Total RNA was extracted from the homogenized tissue samples with an RNeasy® mini kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: The skin biopsies were immediately immersed in RNAlater® (Qiagen) buffer, were incubated at +4°C for one day, and stored thereafter at -80°C until RNA isolation.

tag: tissue

value: skin


title: old-B6-B1a-PEC-1

city: Denver

first: Anatoly

middle: V

last: Rubtsov

address: 1400 Jackson St

country: USA

institute: National Jewish Health

description: Gene expression profile of different B cell populations in old mice

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were background corrected with the RMA algorithm using R and the Bioconductor's affy package.  All parameters were set at its default settings

source_name: mouse peritoneal cavity

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

growth_protocol: Cells were sorted directly from mouse organs (no culture was performed)

extract_protocol: total RNA was isolated using picoPure RNA isolation kit (Arcturus)

treatment_protocol: Cells were sorted from cell suspension using flow cytometry technique

tag: strain

tag: gender

value: female

tag: age

value: older than 15 months

tag: tissue source

value: peritoneal cavity

tag: cell type

value: B1 cells


title: germ-free mice in experiment_3

source_name: Mouse stomach, germ free mouse in experiment_3, pooled RNA


title: old-B6-FO-spl-2

source_name: mouse spleen

value: spleen

value: Follicular B cells


title: H. pylori associated gnotobiotic mice in experiment_3

description: Gene expression data from stomach of Helicobacter pylori associated gnotobiotic mouse, equal amount of RNA from three mice were pooled, and each experiment was performed independently.

source_name: Mouse stomach, H. pylori associated gnotobiotic mouse in experiment_3, pooled RNA

value: Helicobacter pylori


title: old-B6-ABC-spl-3

value: Age associated B cells


title: old-B6-B1a-PEC-3


title: young-B6-B1a-PEC-3

value: 8 weeks


title: young-B6-B1a-PEC-2


title: old-B6-ABC-spl-2


title: lactobacilli associated gnotobiotic mice in experiment_1

source_name: Mouse stomach, lactobacilli associated gnotobiotic mouse in experiment_1, pooled RNA


title: old-B6-ABC-spl-1


title: old-B6-B1a-PEC-2


title: young-B6-B1a-PEC-1


title: old-B6-FO-spl-3


title: old-B6-FO-spl-1


title: Dendritic, control (non-stimulated), replicate 2

city: La Jolla

first: Steven

last: Head

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the v3 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were analyzed with RMA Express using the default settings (Background Adjust - Yes, Normalization - Quantile, Summarization Method - Median Polish, Store Residuals - unchecked).

source_name: Dendritic, control (non-stimulated)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA using MessageAmp™ II aRNA Kit from Ambion

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

value: dendritic

tag: disease state

value: healthy


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN644

type: genomic

city: Uppsala

first: Anders

last: Isaksson

address: Akademiska sjukhuset ing61 3tr

country: Sweden

institute: Uppsala University

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
Quality control (QC), genotype calling and probe level normalization were performed in the Affymetrix GeneChip® Genotyping Analysis Software (GTYPE) 4.1. The Dynamic Model (DM) algorithm was used to perform single sample QC and genotype calls were made using BRLMM (34). Copy number normalization was performed in order to produce log2ratios using the Copy Number Analysis Tool (CNAT) 4.0.1. Eighty-two normal samples analyzed at the Uppsala Array Platform were used as reference set.
Standard Affymetrix CNCHP files with Log2 probe intenisities relative to reference

label: Biotin

molecule: genomic DNA

source_name: CLL cells from periferal blood sample

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of obtained from peripheral blood at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

tag: hiearchical model of known recurrent aberrations

value: No


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN648


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN642


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN643


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN634


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN641


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN635


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN631


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN639


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN611


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN615


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN612


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN619


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN633


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN604


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN617


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN620


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN632


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN607


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN640


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN608


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN618


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN621


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN624


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN613


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN630


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN626


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN602


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN622


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN616


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN598


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN600


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN596


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN597


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN599


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN595


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN593


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN575


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN589


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN582


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN592


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN571


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN568


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN567


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN591


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN583


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN584


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN574


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN569


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN609


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN566


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN577


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN580


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN560


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN565


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN559


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN563


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN587


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN581


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN570


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN573


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN564


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN554


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN556


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN553


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN548


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN547


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN558


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN542


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN531


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN541


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN544


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN514


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN528


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN540


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN532


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN539


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN546


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN521


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN530


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN520


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN538


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN545


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN523


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN517


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN511


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN527


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN506


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN513


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN516


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN518


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN501


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN510


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN503


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN515


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN410


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN406


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN500


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN411


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN392


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN404


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN403


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN402


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN395


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN394


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN398


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN390


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN384


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN389


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN385


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN393


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN401


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN405


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN396


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN386


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN407


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN381


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN508


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN382


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN507


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN383


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN526


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN380


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN408


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN505


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN375


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN374


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN372


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN358


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN352


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN360


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN368


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN361


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN344


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN379


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN350


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN365


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN355


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN346


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN371


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN356


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN353


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN362


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN343


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN347


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN373


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN348


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN339


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN354


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN337


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN340


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN342


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN345


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN377


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN328


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN334


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN327


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN331


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN324


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN341


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN325


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN321


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN312


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN323


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN314


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN313


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN320


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN316


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN317


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN310


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN301


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN315


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN304


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN303


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN330


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN308


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN299


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN298


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN311


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN309


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN292


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN305


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN297


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN295


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN291


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN288


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN296


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN286


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN273


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN306


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN278


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN272


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN258


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN294


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN284


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN274


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN265


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN263


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN256


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN259


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN254


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN262


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN279


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN289


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN260


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN290


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN247


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN252


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN267


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN251


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN255


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN268


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN233


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN239


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN333


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN229


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN235


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN238


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN243


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN287


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN236


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN214


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN224


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN232


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN228


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN196


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN211


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN222


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN212


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN225


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN217


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN193


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN204


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN191


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN194


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN220


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN201


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN206


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN192


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN200


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN188


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN189


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN181


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN185


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN172


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN186


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN184


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN180


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN173


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN182


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN170


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN178


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN175


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN168


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN176


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN165


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN161


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN166


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN160


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN162


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN187


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN152


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN169


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN151


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN174


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN156


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN153


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN171


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN140


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN143


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN142


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN157


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN139


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN146


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN150


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN223


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN135


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN147


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN149


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN125


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN124


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN154


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN123


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN132


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN120


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN133


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN126


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN115


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN117


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN119


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN144


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN158


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN113


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN106


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN108


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN104


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN110


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN109


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN107


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN96


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN97


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN78


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN83


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN79


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN93


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN112


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN94


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN90


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN102


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN77


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN89


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN75


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN95


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN81


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN69


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN70


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN72


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN74


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN63


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN68


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN76


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN61


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN80


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN66


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN55


title: sample 42, brca1 mutation positive, follicular phase fallopian tube

city: Toronto

first: carl

last: virtanen

state: Ontario

address: 101 College St

department: Princess Margaret Genomics Centre

country: Canada

institute: University Health Network

description: Gene expression data from histologically normal fallopian tube epithelium.

hyb_protocol: 3.75ug of ssDNA was fragmented and labeled using the FL-Ovation kit (Nugen), and 200uL was hybridized for 17 hr at 45C on the Human U133plus2 GeneChip array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 7G using the standard protocol.

data_processing: The data were analyzed with Genespring Version 11.0.1 and summarized using the RMA quantile algorithm followed by a per-probe median-centered normalization.

source_name: histological normal fallopian tubes, brca1 mutation positive, follicular phase

label_protocol: Biotinylated ssDNA were prepared according to the Nugen Ovation V2 kit starting from 20ng of total RNA.

growth_protocol: Fallopian tube epithelia samples from BRCA1 positive and negative mutation patients in both the luteal and follicular phase were selected after ethical approval from the University Health Network Biobank.

extract_protocol: Total RNA was isolated using the Stratagene Absolutely RNA MicroPrep kit (Agilent Technologies Inc) according to the manufacturer's instructions.

treatment_protocol: Fallopian tube epithelia from BRCA1 mutation positive and negative groups were collected using laser capture microdissection and stored at -80 before RNA extraction.

value: fallopian tube epithelium

tag: histology

value: normal

tag: brca1 mutation

value: yes

tag: ovarian cycle status

value: follicular

tag: sample identifier


title: sample 44, brca1 mutation positive, luteal phase fallopian tube

source_name: histological normal fallopian tubes, brca1 mutation positive, luteal phase

value: luteal


title: sample 43, brca1 mutation negative, luteal phase fallopian tube

source_name: histological normal fallopian tubes, brca1 mutation negative, luteal phase

value: no


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN60


title: sample 41, brca1 mutation negative, follicular phase fallopian tube

source_name: histological normal fallopian tubes, brca1 mutation negative, follicular phase


title: sample 36, brca1 mutation positive, luteal phase fallopian tube


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN67


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN64


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN52


title: sample 35, brca1 mutation negative, luteal phase fallopian tube


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN45


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN46


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN141


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN47


title: sample 33, brca1 mutation negative, follicular phase fallopian tube


title: sample 34, brca1 mutation positive, follicular phase fallopian tube


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN39


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN44


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN48


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN34


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN118


title: sample 27, brca1 mutation negative, luteal phase fallopian tube


title: sample 26, brca1 mutation positive, follicular phase fallopian tube


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN32


title: sample 25, brca1 mutation negative, follicular phase fallopian tube


title: sample 18, brca1 mutation positive, follicular phase fallopian tube


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN51


title: sample 20, brca1 mutation positive, luteal phase fallopian tube


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN54


title: sample 17, brca1 mutation negative, luteal phase fallopian tube


title: sample 12, brca1 mutation positive, luteal phase fallopian tube


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN29


title: sample 11, brca1 mutation negative, luteal phase fallopian tube


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN36


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN35


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN30


title: sample 10, brca1 mutation positive, follicular phase fallopian tube


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN24


title: sample 19, brca1 mutation negative, luteal phase fallopian tube


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN22


title: sample 9, brca1 mutation negative, follicular phase fallopian tube


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN31


title: sample 4, brca1 mutation positive, luteal phase fallopian tube


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN23


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN62


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN28


title: sample 2, brca1 mutation positive, follicular phase fallopian tube


title: sample 1, brca1 mutation negative, follicular phase fallopian tube


title: sample 3, brca1 mutation negative, luteal phase fallopian tube


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN59


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN21


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN18


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN17


title: sample 28, brca1 mutation positive, luteal phase fallopian tube


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN19


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN15


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN16


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN14


title: csh2 4-OHT rep2

city: Beijing

first: Jun

last: Wu

address: No.7 Beitucheng West Road

country: China

institute: Beijing Institue of Genomics, Chinese Academy of Science

description: csh2 cell line under 4-OHT condition, MLL fusion inducible

hyb_protocol: Hybridized according to the Affymetrix’s specifications

scan_protocol: Scanned according to the Affymetrix’s specifications

data_processing: We used GeneBASE to estimate gene expression from the Affymetrix exon arrays (Kapur et al. 2007; Kapur et al. 2008). Specifically, probes were scalar normalized and then corrected for background using the MAT method (Johnson et al. 2006). For probes with high correlation with matching off-target transcripts, expression patterns were excluded. Among the remaining set of probes, we selected for probes with highly correlated intensities across different samples to be included in the gene-level estimates.

source_name: csh2 cell line, MLL fusion inducible

label_protocol: Labeled according to the Affymetrix’s specifications

growth_protocol: MLL-ENL inducible cell line (csh2) was obtained from Dr. Robert Slany (University Erlangen, Germany). Cells grow in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), with 5ng/ml IL-3, IL-6, GM-CSF 50ng/ml SCF, and 100nM 4-Hydroxy-tamoxifen (4-OHT)

extract_protocol: For each sample under the two experimental conditions, 4-OHT and No 4-OHT, each with one replicate, 20 ng of high-quality total RNAs were amplified.

tag: mll fusion

value: MLL fusion inducible

tag: cell line


title: csh2 No 4-OHT rep2

description: csh2 cell line 4-OHT withdrawal, MLL wild type

source_name: csh2 cell line, MLL wild type

value: MLL wild type


title: csh2 No 4-OHT rep1


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN11


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN7


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN8


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN12


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN6


title: csh2 4-OHT rep1


title: U937 H3K79me2 rep2

description: ChIP-chip U937 cell line, non-MLL-rearranged leukemia cell line, H3K79me2, rep2

hyb_protocol: Nimblegen's standard protocol

scan_protocol: Arrays were scanned using Nimblegen's standard protocol.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction. VALUE is scaled, log2 (ChIP/Input) ratio.

source_name: H3K79me2 ChIP DNA from U937 cell line, rep2

label_protocol: Nimblegen's standard protocol

growth_protocol: U937 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS).

extract_protocol: The ChIP was performed as follows. Briefly, crosslinked chromatin was sonicated, diluted, and immunoprecipitated with specific antibodies at 4°C overnight. Antibodies used were as follows: MLL (Bethyl A300-086A, A300-374A), the MLL anti-sera as described, H3K79me2(Abcam ab3594), and rabbit IgG (Santa Cruz, sc2027). Antibody precipitated DNA fragments are purified. Eluted DNA fragments were used directly for qPCR or array analysis.

treatment_protocol: U937 cell line is an established cell line

tag: genotype

value: WT/WT

tag: chip antibody

source_name: input DNA from U937 cell line, rep2

value: none, input DNA


title: ML-2 H3K79me2 rep2

description: ChIP-chip ML-2 cell line, MLL-rearranged leukemia cell line, H3K79me2, rep2

source_name: H3K79me2 ChIP DNA from ML-2 cell line, rep2

growth_protocol: ML-2 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS).

treatment_protocol: ML-2 cell line is an established cell line

value: fusion/fusion

source_name: input DNA from ML-2 cell line, rep2


title: MV4;11 MLL rep2

description: ChIP-chip MV4;11 cell line, MLL-rearranged leukemia cell line, MLL, rep2

source_name: MLL ChIP DNA from MV4;11 cell line, rep2

growth_protocol: MV4;11 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS).

treatment_protocol: MV4;11 cell line is an established cell line

value: fusion/WT

value: MLL

source_name: input DNA from MV4;11 cell line, rep2


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN3


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN5


title: THP-1 MLL rep1

description: ChIP-chip THP-1 cell line, MLL-rearranged leukemia cell line, MLL, rep1

source_name: MLL ChIP DNA from THP-1 cell line, rep1

growth_protocol: THP-1 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS).

treatment_protocol: THP-1 cell line is an established cell line

source_name: input DNA from THP-1 cell line, rep1


title: THP-1 MLL rep2

description: ChIP-chip THP-1 cell line, MLL-rearranged leukemia cell line, MLL, rep2

source_name: MLL ChIP DNA from THP-1 cell line, rep2

source_name: input DNA from THP-1 cell line, rep2


title: HL60 MLL rep2

description: ChIP-chip HL60 cell line, non-MLL-rearranged leukemia cell line, MLL, rep2

source_name: MLL ChIP DNA from HL60 cell line, rep2

growth_protocol: HL60 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS).

treatment_protocol: HL60 cell line is an established cell line

source_name: input DNA from HL60 cell line, rep2


title: THP-1 H3K79me2 rep2

description: ChIP-chip THP-1 cell line, MLL-rearranged leukemia cell line, H3K79me2, rep2

source_name: H3K79me2 ChIP DNA from THP-1 cell line, rep2


title: HL60 H3K79me2 rep2

description: ChIP-chip HL60 cell line, non-MLL-rearranged leukemia cell line, H3K79me2, rep2

source_name: H3K79me2 ChIP DNA from HL60 cell line, rep2


title: ML-2 H3K79me2 rep1

description: ChIP-chip ML-2 cell line, MLL-rearranged leukemia cell line, H3K79me2, rep1

source_name: H3K79me2 ChIP DNA from ML-2 cell line, rep1

source_name: input DNA from ML-2 cell line, rep1


title: HL60 MLL rep1

description: ChIP-chip HL60 cell line, non-MLL-rearranged leukemia cell line, MLL, rep1

source_name: MLL ChIP DNA from HL60 cell line, rep1

source_name: input DNA from HL60 cell line, rep1


title: MV4;11 H3K79me2 rep2

description: ChIP-chip MV4;11 cell line, MLL-rearranged leukemia cell line, H3K79me2, rep2

source_name: H3K79me2 ChIP DNA from MV4;11 cell line, rep2


title: ML-2 MLL rep1

description: ChIP-chip ML-2 cell line, MLL-rearranged leukemia cell line, MLL, rep1

source_name: MLL ChIP DNA from ML-2 cell line, rep1


title: THP-1 H3K79me2 rep1

description: ChIP-chip THP-1 cell line, MLL-rearranged leukemia cell line, H3K79me2, rep1

source_name: H3K79me2 ChIP DNA from THP-1 cell line, rep1


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN2

source_name: CLL cells from periferal blood sample


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN33


title: THP1_Microarray_rep1

city: Yokohama

first: Hideya

last: Kawaji

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Omics Science Center

institute: RIKEN

description: THP-1 total RNA

hyb_protocol: According to Illumina protocol

scan_protocol: According to Illumina protocol

data_processing: Chips scans were processed using Illumina BeadScan and BeadStudio software packages, and summarized data was generated in BeadStudio (version 3.4).

source_name: THP-1 cell line

label_protocol: According to Illumina protocol

growth_protocol: THP-1 cells were cultured in RPMI1640 (Invitrogen) supplemented with 10% FBS, Penicillin/Streptomycin (Invitrogen), 10 mM HEPES (Invitrogen), 1 mM sodium pyruvate and 50 µM 2-mercaptoethanol.   HeLa cells were cultured in Eagle’s MEM (Invitrogen) supplemented with 10% FBS, 1% NEAA (Invitrogen) and Penicillin/Streptomycin.

extract_protocol: Total cell lysates were harvested in TRIzol reagent (Invitrogen), total RNA was purified from TRIzol lysates according to manufacturer’s instructions and we used RNase free glycogen (Invitrogen) as carrier to the aqueous phase prior to precipitating the RNA with isopropyl alcohol. The quality of the extracted RNA was confirmed with Agilent 2100 Bioanalyzer.

tag: starting total rna


title: CD34+ cells treated with Dexamethasone and Lenalidomide, rep3

city: Cambridge

first: Fatima

last: Al-Shahrour

state: MA

address: 7 Cambridge Center

department: Cancer program

institute: Broad Institute of MIT and Harvard

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Signal normalization was performed by the RMA method.

source_name: Cryopreserved human bone marrow CD34+ cells, dexamethasone and lenalidomide

label_protocol: NuGen Ovation Biotin labeling system.

growth_protocol: Human CD34+ cells were cultured for 48 hours in the erythroid differentiation media described above with the addition of 40 ng/mL of FMS-like tyrosine kinase 3 (flt-3; Miltenyi Biotech) and 15 ng/mL of Granulocyte colony-stimulating factor (G-CSF; Amgen).

extract_protocol: RNA was purified using Trizol (Invitrogen). The RNA was amplified using a linear amplification protocol (Nugen Ovation V2 amplification system).

treatment_protocol: Cells were cultured in the presence of dexamethasone and lenalidomide, individually and in combination, for 24 hours.

value: bone marrow CD34+ cells

tag: treatment

value: dexamethasone and lenalidomide


title: HeLa_Microarray_rep3

description: HeLa total RNA

source_name: HeLa cell line

value: HeLa


title: Untreated CD34+ cells, rep2

source_name: Cryopreserved human bone marrow CD34+ cells, untreated


title: Untreated CD34+ cells, rep1


title: HL60 H3K79me2 rep1

description: ChIP-chip HL60 cell line, non-MLL-rearranged leukemia cell line, H3K79me2, rep1

source_name: H3K79me2 ChIP DNA from HL60 cell line, rep1


title: HeLa_Microarray_rep2

description: HeLa total RNA


title: MV4;11 MLL rep1

description: ChIP-chip MV4;11 cell line, MLL-rearranged leukemia cell line, MLL, rep1

source_name: MLL ChIP DNA from MV4;11 cell line, rep1

source_name: input DNA from MV4;11 cell line, rep1


title: CD34+ cells treated with Dexamethasone and Lenalidomide, rep2


title: ML-2 MLL rep2

description: ChIP-chip ML-2 cell line, MLL-rearranged leukemia cell line, MLL, rep2

source_name: MLL ChIP DNA from ML-2 cell line, rep2

source_name: input DNA from ML-2 cell line, rep2


title: CD34+ cells treated with Dexamethasone and Lenalidomide, rep1


title: U937 MLL rep1

description: ChIP-chip U937 cell line, non-MLL-rearranged leukemia cell line, MLL, rep1

source_name: MLL ChIP DNA from U937 cell line, rep1

source_name: input DNA from U937 cell line, rep1


title: NSC miR-128 2

first: Rachid

last: Karam

department: Reproductive Medicine

institute: UCSD

hyb_protocol: GeneChip® Hybridization, Wash and Stain Kit  was used to prepare samples for hybridization to the Gene 1.0 ST Array. More information about this protocol can be found on the Affymetrix website.

scan_protocol: Image analysis was performed using the standard Affymetrix protocols (GeneChip® Expression Wash, Stain and Scan User Manual (P/N 702731)). Scanning was performed using the GeneChip® Scanner 3000 and Affymetrix® GeneChip® Command Console® (AGCC).

data_processing: The raw CEL files were imported into R using the 'affy' package. Arrays were processed using RMA background correction, quantile normalization, and median polish summarization using only the perfect match (PM) probes.

source_name: mNSC nucleofected with miR-128l, replicate

label_protocol: One μg of total RNA was labeled following the GeneChip® Whole Transcript (WT) Sence Target Labeling Protocol (P/N 701880)

growth_protocol: mouse NSCs were grown as neurospheres and in proliferation conditions.

extract_protocol: Trizol followed by Rneasy Column purification

treatment_protocol: mouse NSCs were nucleofected either with miR-128 mimic or miR-Control

value: Neuronal Stem Cells

tag: developmental stage

tag: strain

value: CD-1 albino


title: Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN4


title: Untreated CD34+ cells, rep3


title: CD34+ cells treated with Lenalidomide, rep3

source_name: Cryopreserved human bone marrow CD34+ cells, lenalidomide

value: lenalidomide


title: U937 MLL rep2

description: ChIP-chip U937 cell line, non-MLL-rearranged leukemia cell line, MLL, rep2

source_name: MLL ChIP DNA from U937 cell line, rep2

source_name: input DNA from U937 cell line, rep2


title: CD34+ cells treated with Lenalidomide, rep2


title: NSC miR-128 3


title: HeLa_Microarray_rep1

description: HeLa total RNA


title: H3K79me2 No 4-OHT rep2

description: ChIP-chipcsh2 cell line H3K79me2, no 4-OHT rep2, MLL wild type

source_name: H3K79me2 ChIP DNA from csh2 cell line, no 4-OHT rep2

growth_protocol: Cells grow in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), with 5ng/ml IL-3, IL-6, GM-CSF 50ng/ml SCF, and 100nM 4-Hydroxy-tamoxifen (4-OHT).

treatment_protocol: MLL-ENL inducible cell line (csh2) was obtained from Dr. Robert Slany (University Erlangen, Germany).

value: csh2 cell line

value: No 4-OHT, MLL wild type

source_name: Input DNA from csh2 cell line, no 4-OHT rep2


title: HUES9 duplicate2

first: Li

last: Wenlin

address: 10550 North Torrey Pines Road

hyb_protocol: BeadChip Hyb Wheel

scan_protocol: Illumina BeadArray Reader

data_processing: Illumina BeadStudio Software using the rank invariant option

source_name: hESCs

label_protocol: Biotin

growth_protocol: Primitive neural stem cells were cultured in neural induction media containing Advanced DMEM/F12:Neurobasal (1:1), 1xN2, 1xB27, 1% Glutmax, 5 μg/ml BSA, 10 ng/ml hLIF, 3 μM CHIR99021 and 2 μM SB431542.

extract_protocol: RNeasy Plus Mini Kit

treatment_protocol: No treatment

value: hESCs


title: Passage 27 pNSCs duplicate2

source_name: primitive neural stem cells

value: primitive neural stem cells

tag: cell passage


title: THP1_Microarray_rep2

description: THP-1 total RNA

source_name: THP-1 cell line


title: HUES9 duplicate1


title: NSC miR-128 1


title: CD34+ cells treated with Dexamethasone, rep2

source_name: Cryopreserved human bone marrow CD34+ cells, dexamethasone

value: dexamethasone


title: N2_mixed_replica2 [ChIP01]

status: Public on Apr 27 2011

city: Worcester

first: Kirsten

last: Hagstrom

address: 377 Plantation street

department: Molecular Medicine

institute: University of Massachusetts, Medical School

description: LIN-54 ChIP-chip on wild type worms (biological replica 2)

hyb_protocol: Samples were then hybridized on the Nimblegen C. elegans ChIP-chip 385K Whole-Genome Tiling - 3 Array Set (GPL7482, GPL7483, GPL7484) using standard Nimblegen protocols.

scan_protocol: Arrays were scanned on Nimblegen's 2-μm, high-resolution MS 200 Microarray Scanner. Data was extracted from the images at Roche NimbleGen, according to the protocol described NimbleScan v2.5 Software User's Guide, Version 2.5, October 2008.

data_processing: Raw ChIP-chip data were retrieved from Nimblegen and analyzed using MA2C (Song et al., Genome Biol, 2007). MA2C analysis was performed with the following settings: # MA2C Score Method (median), Band Width (300), p-value cut off (-6), and other parameters were set as default. WS180 was used to annotate gene names. MA2C-defined LIN-54 ChIP peaks are listed in the file 'GSE28852_MA2C_processed_LIN-54_ChIP_peaks.txt'.

organism: Caenorhabditis elegans

source_name: LIN-54 ChIP DNA

label_protocol: For each experiment, a control sample as well as an experimental sample were prepared with a concentration of ~250 ng/ul. At least 4 ug of each of these samples was then sent to Nimblegen where the samples were labeled with respectively Cy-3 and Cy-5 dyes using standard Nimblegen protocols.

extract_protocol: ChIP was performed as described (Mukhopadhyay et al., Nat. Protocol., 2008). Briefly, mixed stage wild-type worms were cultured in S-basal at 20oC. Lysates were cross-linked in 1% formaldehyde, sonicated, and immunoprecipitated with anti-LIN-54 antibody or pre-bleed antibody control. ChIP samples including the input were subjected to two rounds of linear amplification, using the genomePlex complete whole genome amplification kit (Sigma), and minimum difference between original precipitates and amplified precipitate confirmed by qPCR.

value: N2 (Bristol)

tag: antibody

value: LIN-54 antibody; non-commercial antibody raised in guinea pig, see Harrison et al. PNAS 2006

value: mixed staged worm culture

source_name: input DNA from pre-bleed antibody control.

treatment_protocol: Lysates were cross-linked in 1% formaldehyde, sonicated, and immunoprecipitated with  pre-bleed antibody control.


title: CD34+ cells treated with Lenalidomide, rep1

tag: cell type


title: N2_mixed_replica1 [ChIP01]

description: LIN-54 ChIP-chip on wild type worms (biological replica 1)

growth_protocol: mixed stage wild-type worms were cultured in S-basal at 20oC.

treatment_protocol: Lysates were cross-linked in 1% formaldehyde, sonicated, and immunoprecipitated with anti-LIN-54 antibody.


title: Passage 27 pNSCs duplicate1


title: NSC miR-Control 3

source_name: mNSC nucleofected with miR-Control, replicate


title: U937 H3K79me2 rep1

description: ChIP-chip U937 cell line, non-MLL-rearranged leukemia cell line, H3K79me2, rep1

source_name: H3K79me2 ChIP DNA from U937 cell line, rep1

value: WT/WT

value: none, input DNA


title: MLL No 4-OHT rep1

description: ChIP-chip csh2 cell line MLL, no 4-OHT rep1, MLL wild type

source_name: MLL ChIP DNA from csh2 cell line, no 4-OHT rep1

value: MLL

source_name: Input DNA from csh2 cell line, no 4-OHT rep1


title: Passage 6 pNSCs duplicate2


title: THP1_Microarray_rep3

description: THP-1 total RNA


title: CD34+ cells treated with Dexamethasone, rep3

value: bone marrow CD34+ cells


title: 184

city: Edmonton

first: Kathryn

last: Graham

state: Alberta

address: 11560 University Ave

department: Oncology

institute: University of Alberta

description: gene expression in normal breast tissue

hyb_protocol: 1.5 ug 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 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) 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 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, 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 (protocol GE1-v5_95_Feb07 and Grid: 014850_D_F_20090416) to obtain background subtracted and spatially detrended Processed Signal intensities.  The data was them imported into GeneSpring 7.3.1 and default normalization procedures were used.

source_name: normal breast tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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.

extract_protocol: A polytron was used to disrupt tissue in the pressence of Trizol (SigmaAldrich). The sample was then phenol/chloroform extracted, the aquaous layer was adjusted to 30% ethanol and applied to an RNeasy column (Qiagen) 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).

tag: disease state

value: normal breast tissue


title: MLL 4-OHT rep1

description: ChIP-chip csh2 cell line MLL, 4-OHT rep1, MLL fusion inducible

source_name: MLL ChIP DNA from csh2 cell line, 4-OHT rep1

value: 4-OHT, MLL fusion inducible

source_name: Input DNA from csh2 cell line, 4-OHT rep1


title: MV4;11 H3K79me2 rep1

description: ChIP-chip MV4;11 cell line, MLL-rearranged leukemia cell line, H3K79me2, rep1

source_name: H3K79me2 ChIP DNA from MV4;11 cell line, rep1

value: fusion/WT

source_name: input DNA from MV4;11 cell line, rep1


title: H3K79me2 No 4-OHT rep1

description: ChIP-chip csh2 cell line H3K79me2, no 4-OHT rep1, MLL wild type

source_name: H3K79me2 ChIP DNA from csh2 cell line, no 4-OHT rep1


title: NSC miR-Control 1

value: Neuronal Stem Cells

value: CD-1 albino


title: Cyclophosphamide-treated spleen 5 days - Biological Replicate 5 - Technical Replicate 1

city: Roma

first: Federica

last: Moschella

address: Viale Regina Elena 299

department: Cell Biology and Neurosciences

country: Italy

institute: Istituto Superiore di Sanità

description: Biological replicate 5 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day5

hyb_protocol: Labeled samples, diluted in Hybridization buffer (5X SSC; 50% Formamide; salmon sperm-DNA 100 ng/ul; 0.1% SDS), were applied to microarrays enclosed in Corning hybridization chambers - 42°C over night.

scan_protocol: Slides were scanned on GenePix® 4200A instrument (Axon Instruments) Images were quantified using GenePix Pro 6.0

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

source_name: splenocytes

label_protocol: aRNA were obtained using the Ambion Amino Allyl MessageAmp™ II aRNA Amplification Kit, according to the manufacturer's instructions. 12 µg of aRNA were labeled with Amersham Cy5 (RNA samples) or Cy3 (Reference RNA)

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

treatment_protocol: Mice were injected i.p. with 83 mg/Kg cyclophosphamide. Splenocytes were harvested 5 days after treatment

tag: fresh tissue

value: splenocytes

source_name: bone marrow cells

treatment_protocol: Mice were treated with 83 mg/Kg cyclophosphamide

value: pool of untreated bone marrow cells

tag: sample type

value: reference


title: NSC miR-Control 2


title: 186

description: gene expression in normal breast tissue


title: 185

description: gene expression in normal breast tissue


title: Cyclophosphamide-treated spleen 5 days - Biological Replicate 2 - Technical Replicate 1

description: Biological replicate 2 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day 5


title: 183

description: gene expression in normal breast tissue


title: Passage 6 pNSCs duplicate1

source_name: primitive neural stem cells

value: primitive neural stem cells


title: H3K79me2 4-OHT rep2

description: ChIP-chip csh2 cell line H3K79me2, 4-OHT rep2, MLL fusion inducible

source_name: H3K79me2 ChIP DNA from csh2 cell line, 4-OHT rep2

value: csh2 cell line

source_name: Input DNA from csh2 cell line, 4-OHT rep2


title: Cyclophosphamide-treated spleen 5 days - Biological Replicate 3 - Technical Replicate 1

description: Biological replicate 3 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day 5


title: CD34+ cells treated with Dexamethasone, rep1

source_name: Cryopreserved human bone marrow CD34+ cells, dexamethasone

value: dexamethasone


title: 178

description: gene expression in normal breast tissue


title: Cyclophosphamide-treated spleen 5 days - Biological Replicate 5 - Technical Replicate 2

description: Biological replicate 5 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated splenocytes, day5


title: 179

description: gene expression in normal breast tissue


title: 182

description: gene expression in normal breast tissue


title: Cyclophosphamide-treated spleen 5 days - Biological Replicate 2 - Technical Replicate 2

description: Biological replicate 2 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated splenocytes, day 5


title: 180

description: gene expression in normal breast tissue


title: Cyclophosphamide-treated spleen 2 days - Biological Replicate 5 - Technical Replicate 2

description: Biological replicate 5 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated splenocytes, day 2

treatment_protocol: Mice were injected i.p. with 83 mg/Kg cyclophosphamide. Splenocytes were harvested 2 days after treatment


title: Cyclophosphamide-treated spleen 2 days - Biological Replicate 5 - Technical Replicate 1

description: Biological replicate 5 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day 2


title: MLL 4-OHT rep2

description: ChIP-chip csh2 cell line MLL, 4-OHT rep2, MLL fusion inducible

source_name: MLL ChIP DNA from csh2 cell line, 4-OHT rep2


title: Cyclophosphamide-treated spleen 2 days - Biological Replicate 4 - Technical Replicate 2

description: Biological replicate 4 of 5. Technical Replicate 2 of 2.Cyclophosphamide-treated splenocytes, day 2


title: 177

description: gene expression in normal breast tissue


title: Cyclophosphamide-treated spleen 5 days - Biological Replicate 4 - Technical Replicate 2

description: Biological replicate 4 of 5. Technical Replicate 2 of 2.Cyclophosphamide-treated splenocytes, day 5


title: Cyclophosphamide-treated spleen 2 days - Biological Replicate 4 - Technical Replicate 1

description: Biological replicate 4 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day 2


title: Cyclophosphamide-treated spleen 5 days - Biological Replicate 4 - Technical Replicate 1

description: Biological replicate 4 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day 5


title: 181

description: gene expression in normal breast tissue


title: Cyclophosphamide-treated spleen 5 days - Biological Replicate 3 - Technical Replicate 2

description: Biological replicate 3 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated splenocytes, day 5


title: Cyclophosphamide-treated spleen 5 days - Biological Replicate 1 - Technical Replicate 2

description: Biological replicate 1 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated splenocytes, day 5


title: Cyclophosphamide-treated spleen 2 days - Biological Replicate 3 - Technical Replicate 1

description: Biological replicate 3 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day 2


title: Cyclophosphamide-treated spleen 2 days - Biological Replicate 2 - Technical Replicate 2

description: Biological replicate 2 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated splenocytes, day 2


title: MLL No 4-OHT rep2

description: ChIP-chip csh2 cell line MLL, no 4-OHT rep2, MLL wild type

source_name: MLL ChIP DNA from csh2 cell line, no 4-OHT rep2

value: No 4-OHT, MLL wild type

source_name: Input DNA from csh2 cell line, no 4-OHT rep2


title: Cyclophosphamide-treated spleen 2 days - Biological Replicate 2 - Technical Replicate 1

description: Biological replicate 2 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day 2


title: Control spleen - Biological Replicate 5 - Technical Replicate 2

description: Biological replicate 5 of 5. Technical Replicate 2 of 2. Control splenocytes, untreated

treatment_protocol: Untreated mice


title: Control spleen - Biological Replicate 5 - Technical Replicate 1

description: Biological replicate 5 of 5. Technical Replicate 1 of 2. Control splenocytes, untreated


title: Cyclophosphamide-treated spleen 2 days - Biological Replicate 1 - Technical Replicate 2

description: Biological replicate 1 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated splenocytes, day 2


title: Cyclophosphamide-treated spleen 5 days - Biological Replicate 1 - Technical Replicate 1

description: Biological replicate 1 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day 5


title: Cyclophosphamide-treated spleen 1 day - Biological Replicate 3 - Technical Replicate 2

description: Biological replicate 3 of 4. Technical Replicate 2 of 2. Cyclophosphamide-treated splenocytes, day1

treatment_protocol: Mice were injected i.p. with 83 mg/Kg cyclophosphamide. Splenocytes were harvested 1 day after treatment


title: Control spleen - Biological Replicate 3 - Technical Replicate 2

description: Biological replicate 3 of 5. Technical Replicate 2 of 2. Control splenocytes, untreated


title: Control spleen - Biological Replicate 3 - Technical Replicate 1

description: Biological replicate 3 of 5. Technical Replicate 1 of 2. Control splenocytes, untreated


title: Control spleen - Biological Replicate 1 - Technical Replicate 2

description: Biological replicate 1 of 5. Technical Replicate 2 of 2. Control splenocytes, untreated


title: Control spleen - Biological Replicate 4 - Technical Replicate 2

description: Biological replicate 4 of 5. Technical Replicate 2 of 2. Control splenocytes, untreated


title: Control spleen - Biological Replicate 1 - Technical Replicate 1

description: Biological replicate 1 of 5. Technical Replicate 1 of 2. Control splenocytes, untreated


title: Cyclophosphamide-treated peripheral blood leukocytes 5 days - Biological Replicate 3 - Technical Replicate 2

description: Biological replicate 3 of 3. Technical Replicate 2 of 2. Peripheral blood leukocytes,  CTX-treated day 5

source_name: peripheral blood leukocytes, Cyclophosphamide-treated 5 days

treatment_protocol: Mice were injected i.p. with 83 mg/Kg cyclophosphamide. Blood was drawn  5 days after treatment

value: Peripheral blood leukocytes

source_name: Bone marrow cells


title: H3K79me2 4-OHT rep1

description: ChIP-chip csh2 cell line H3K79me2, 4-OHT rep1, MLL fusion inducible

source_name: H3K79me2 ChIP DNA from csh2 cell line, 4-OHT rep1


title: Control spleen - Biological Replicate 2 - Technical Replicate 1

description: Biological replicate 2 of 5. Technical Replicate 1 of 2. Control splenocytes, untreated


title: Cyclophosphamide-treated spleen 2 days - Biological Replicate 3 - Technical Replicate 2

description: Biological replicate 3 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated splenocytes, day 2


title: Cyclophosphamide-treated spleen 2 days - Biological Replicate 1 - Technical Replicate 1

description: Biological replicate 1 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day 2


title: Cyclophosphamide-treated peripheral blood leukocytes 5 days - Biological Replicate 1 - Technical Replicate 2

description: Biological replicate 1 of 3. Technical Replicate 2 of 2. Peripheral blood leukocytes,  CTX-treated day 5


title: Cyclophosphamide-treated spleen 1 day - Biological Replicate 4 - Technical Replicate 2

description: Biological replicate 4 of 4. Technical Replicate 2 of 2.Cyclophosphamide-treated splenocytes, day1


title: Cyclophosphamide-treated spleen 1 day - Biological Replicate 4 - Technical Replicate 1

description: Biological replicate 4 of 4. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day1


title: Cyclophosphamide-treated peripheral blood leukocytes 2 days - Biological Replicate 4 - Technical Replicate 2

description: Biological replicate 4 of 4. Technical Replicate 2 of 2. Peripheral blood leukocytes,  CTX-treated day 2

source_name: peripheral blood leukocytes, Cyclophosphamide-treated 2 days

treatment_protocol: Mice were injected i.p. with 83 mg/Kg cyclophosphamide. Blood was drawn 2 days after treatment


title: Cyclophosphamide-treated peripheral blood leukocytes 5 days - Biological Replicate 1 - Technical Replicate 1

description: Biological replicate 1 of 3. Technical Replicate 1 of 2. Peripheral blood leukocytes, CTX-treated day 5

treatment_protocol: Mice were injected i.p. with 83 mg/Kg cyclophosphamide. Blood was drawn 5 days after treatment


title: Cyclophosphamide-treated spleen 1 day - Biological Replicate 3 - Technical Replicate 1

description: Biological replicate 3 of 4. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day1


title: Cyclophosphamide-treated peripheral blood leukocytes 2 days - Biological Replicate 2 - Technical Replicate 1

description: Biological replicate 2 of 4. Technical Replicate 1 of 2. Peripheral blood leukocytes,  CTX-treated day 2


title: Cyclophosphamide-treated peripheral blood leukocytes 2 days - Biological Replicate 2 - Technical Replicate 2

description: Biological replicate 2 of 4. Technical Replicate 2 of 2. Peripheral blood leukocytes,  CTX-treated day 2


title: Cyclophosphamide-treated spleen 1 day - Biological Replicate 2 - Technical Replicate 2

description: Biological replicate 2 of 4. Technical Replicate 2 of 2. Cyclophosphamide-treated splenocytes, day1


title: Cyclophosphamide-treated spleen 1 day - Biological Replicate 1 - Technical Replicate 2

description: Biological replicate 1 of 4. Technical Replicate 2 of 2. Cyclophosphamide-treated splenocytes, day1


title: Cyclophosphamide-treated spleen 1 day - Biological Replicate 2 - Technical Replicate 1

description: Biological replicate 2 of 4. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day1


title: Cyclophosphamide-treated peripheral blood leukocytes 5 days - Biological Replicate 2 - Technical Replicate 2

description: Biological replicate 2 of 3. Technical Replicate 2 of 2. Peripheral blood leukocytes,  CTX-treated day 5


title: Cyclophosphamide-treated spleen 1 day - Biological Replicate 1 - Technical Replicate 1

description: Biological replicate 1 of 4. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day1


title: M34

city: Lund

first: Katarina

last: Bartuma

address: Barn garan 2b

institute: department of Oncology

hyb_protocol: Hybridizations were conducted using the MAUI® Hybridization System (BioMicro systems Inc, Salt Lake City, UT, USA).

scan_protocol: The slides were scanned in an Agilent Microarray Scanner (Agilent Technologies).

data_processing: TIFF images were analysed using the GenePixTM Pro. 4.1 software (Axon Instruments Inc., Foster City, CA, USA) and quantified data matrices were uploaded in the web based BioArray Software Environment software (BASE) (Saal et al., 2002). Positive and nonsaturated spots were background corrected using the median background intensities for each channel and log2 ratios were calculated from the background corrected intensities. Data were filtered for flagged features and spots below signal to noise ratio 3 for both channels were eliminated. Data was normalized using an implementation of a population based LOWESS algorithm (Staaf et al., 2007).

source_name: Ovarian cancer_formalin fixed, paraffin embedded

label_protocol: 2-8 μg tumor DNA and 2 µg reference DNA (Promega Corporation, Madison, WI, USA) were labeled with Cy3-dCTP and Cy5-dCTP, using BioPrime Array CGH Genomic Labeling System (Invitrogen Life Technologies, Carlsbad, CA, USA).

extract_protocol: DNA was extracted from formalin fixed, paraffin embedded tumor tissue according to protocols from the UCSF Waldman Laboratory, San Francisco, CA, USA (http://cc.ucsf.edu/people/waldman/Protocols/paraffin.html), with an additional purification step using Phase Lock Gel tubes (Eppendorf AG, Hamburg, Germany).

treatment_protocol: Formalin fixed, paraffin embedded

tag: histology

value: serous

tag: mutation

tag: differentiation

tag: figo stage

value: III

tag: age

source_name: Pooled male reference

tag: gender

value: Male


title: M29


title: Control spleen - Biological Replicate 4 - Technical Replicate 1

description: Biological replicate 4 of 5. Technical Replicate 1 of 2. Control splenocytes, untreated


title: Control spleen - Biological Replicate 2 - Technical Replicate 2

description: Biological replicate 2 of 5. Technical Replicate 2 of 2. Control splenocytes, untreated


title: Cyclophosphamide-treated peripheral blood leukocytes 1 day - Biological Replicate 4 - Technical Replicate 1

description: Biological replicate 4 of 4. Technical Replicate 1 of 2. Peripheral blood leukocytes,  CTX-treated day 1

source_name: peripheral blood leukocytes, Cyclophosphamide-treated 1 day

treatment_protocol: Mice were injected i.p. with 83 mg/Kg cyclophosphamide. Blood was drawn 1 day after treatment


title: Cyclophosphamide-treated peripheral blood leukocytes 2 days - Biological Replicate 1 - Technical Replicate 1

description: Biological replicate 1 of 4. Technical Replicate 1 of 2. Peripheral blood leukocytes, CTX-treated day 2


title: Cyclophosphamide-treated peripheral blood leukocytes 5 days - Biological Replicate 3 - Technical Replicate 1

description: Biological replicate 3 of 3. Technical Replicate 1 of 2. Peripheral blood leukocytes,  CTX-treated day 5


title: M20

value: IV


title: M21

value: endometrioid


title: Cyclophosphamide-treated peripheral blood leukocytes 1 day - Biological Replicate 2 - Technical Replicate 2

description: Biological replicate 2 of 4. Technical Replicate 2 of 2. Peripheral blood leukocytes,  CTX-treated day 1


title: Cyclophosphamide-treated peripheral blood leukocytes 5 days - Biological Replicate 2 - Technical Replicate 1

description: Biological replicate 2 of 3. Technical Replicate 1 of 2. Peripheral blood leukocytes,  CTX-treated day 5


title: Cyclophosphamide-treated peripheral blood leukocytes 2 days - Biological Replicate 4 - Technical Replicate 1

description: Biological replicate 4 of 4. Technical Replicate 1 of 2. Peripheral blood leukocytes,  CTX-treated day 2


title: Cyclophosphamide-treated peripheral blood leukocytes 1 day - Biological Replicate 1 - Technical Replicate 1

description: Biological replicate 1 of 4. Technical Replicate 1 of 2. Peripheral blood leukocytes, CTX-treated day 1


title: Cyclophosphamide-treated peripheral blood leukocytes 2 days - Biological Replicate 3 - Technical Replicate 1

description: Biological replicate 3 of 4. Technical Replicate 1 of 2. Peripheral blood leukocytes,  CTX-treated day 2


title: Cyclophosphamide-treated peripheral blood leukocytes 2 days - Biological Replicate 3 - Technical Replicate 2

description: Biological replicate 3 of 4. Technical Replicate 2 of 2. Peripheral blood leukocytes,  CTX-treated day 2


title: M11


title: K8

value: Sporadic


title: Control peripheral blood leukocytes - Biological Replicate 4 - Technical Replicate 2

description: Biological replicate 4 of 4. Technical Replicate 2 of 2. Control Peripheral blood leukocytes, untreated

source_name: peripheral blood leukocytes, untreated


title: M8


title: M3


title: M35

value: clear cell


title: Control peripheral blood leukocytes - Biological Replicate 3 - Technical Replicate 2

description: Biological replicate 3 of 4. Technical Replicate 2 of 2. Control Peripheral blood leukocytes, untreated


title: Control peripheral blood leukocytes - Biological Replicate 3 - Technical Replicate 1

description: Biological replicate 3 of 4. Technical Replicate 1 of 2. Control Peripheral blood leukocytes, untreated


title: Cyclophosphamide-treated peripheral blood leukocytes 2 days - Biological Replicate 1 - Technical Replicate 2

description: Biological replicate 1 of 4. Technical Replicate 2 of 2. Peripheral blood leukocytes,  CTX-treated day 2


title: K79


title: M23

value: II


title: K74

value: mucinous

value: I


title: M24


title: Cyclophosphamide-treated peripheral blood leukocytes 1 day - Biological Replicate 4 - Technical Replicate 2

description: Biological replicate 4 of 4. Technical Replicate 2 of 2. Peripheral blood leukocytes,  CTX-treated day 1

value: pool of untreated bone marrow cells


title: K76


title: K71


title: Cyclophosphamide-treated peripheral blood leukocytes 1 day - Biological Replicate 3 - Technical Replicate 2

description: Biological replicate 3 of 4. Technical Replicate 2 of 2. Peripheral blood leukocytes,  CTX-treated day 1

value: reference


title: Control peripheral blood leukocytes - Biological Replicate 2 - Technical Replicate 1

description: Biological replicate 2 of 4. Technical Replicate 1 of 2. Control Peripheral blood leukocytes, untreated


title: K69


title: Cyclophosphamide-treated peripheral blood leukocytes 1 day - Biological Replicate 3 - Technical Replicate 1

description: Biological replicate 3 of 4. Technical Replicate 1 of 2. Peripheral blood leukocytes,  CTX-treated day 1


title: M2


title: M16


title: Cyclophosphamide-treated peripheral blood leukocytes 1 day - Biological Replicate 1 - Technical Replicate 2

description: Biological replicate 1 of 4. Technical Replicate 2 of 2. Peripheral blood leukocytes,  CTX-treated day 1


title: Cyclophosphamide-treated bone marrow 5 days - Biological Replicate 3 - Technical Replicate 2

description: Biological replicate 3 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated bone marrow cells, day 5

treatment_protocol: Mice were injected i.p. with 83 mg/Kg cyclophosphamide. Bone marrow was harvested 5 days after treatment

value: bone marrow cells


title: Cyclophosphamide-treated peripheral blood leukocytes 1 day - Biological Replicate 2 - Technical Replicate 1

description: Biological replicate 2 of 4. Technical Replicate 1 of 2. Peripheral blood leukocytes,  CTX-treated day 1


title: K84


title: K5


title: Cyclophosphamide-treated bone marrow 5 days - Biological Replicate 4 - Technical Replicate 2

description: Biological replicate 4 of 5. Technical Replicate 2 of 2.Cyclophosphamide-treated bone marrow cells, day 5


title: Cyclophosphamide-treated bone marrow 5 days - Biological Replicate 2 - Technical Replicate 2

description: Biological replicate 2 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated bone marrow cells, day 5


title: Cyclophosphamide-treated bone marrow 5 days - Biological Replicate 1 - Technical Replicate 2

description: Biological replicate 1 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated bone marrow cells, day 5


title: K22


title: K32


title: Cyclophosphamide-treated bone marrow 5 days - Biological Replicate 2 - Technical Replicate 1

description: Biological replicate 2 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day 5


title: Control peripheral blood leukocytes - Biological Replicate 4 - Technical Replicate 1

description: Biological replicate 4 of 4. Technical Replicate 1 of 2. Control Peripheral blood leukocytes, untreated


title: K75


title: Control peripheral blood leukocytes - Biological Replicate 2 - Technical Replicate 2

description: Biological replicate 2 of 4. Technical Replicate 2 of 2. Control Peripheral blood leukocytes, untreated


title: K18


title: K78


title: K12


title: K14


title: Cyclophosphamide-treated bone marrow 5 days - Biological Replicate 5 - Technical Replicate 2

description: Biological replicate 5 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated bone marrow cells, day 5


title: Cyclophosphamide-treated bone marrow 2 days - Biological Replicate 4 - Technical Replicate 2

description: Biological replicate 4 of 5. Technical Replicate 2 of 2.Cyclophosphamide-treated bone marrow cells, day 2

treatment_protocol: Mice were injected i.p. with 83 mg/Kg cyclophosphamide. Bone marrow was harvested 2 days after treatment


title: Control peripheral blood leukocytes - Biological Replicate 1 - Technical Replicate 2

description: Biological replicate 1 of 4. Technical Replicate 2 of 2. Control Peripheral blood leukocytes, untreated


title: Cyclophosphamide-treated bone marrow 2 days - Biological Replicate 4 - Technical Replicate 1

description: Biological replicate 4 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day 2


title: Control peripheral blood leukocytes - Biological Replicate 1 - Technical Replicate 1

description: Biological replicate 1 of 4. Technical Replicate 1 of 2. Control Peripheral blood leukocytes, untreated


title: K65


title: Cyclophosphamide-treated bone marrow 2 days - Biological Replicate 2 - Technical Replicate 1

description: Biological replicate 2 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day 2


title: K7


title: K61


title: Cyclophosphamide-treated bone marrow 2 days - Biological Replicate 2 - Technical Replicate 2

description: Biological replicate 2 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated bone marrow cells, day 2


title: Cyclophosphamide-treated bone marrow 2 days - Biological Replicate 3 - Technical Replicate 2

description: Biological replicate 3 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated bone marrow cells, day 2


title: Cyclophosphamide-treated bone marrow 5 days - Biological Replicate 4 - Technical Replicate 1

description: Biological replicate 4 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day 5


title: Cyclophosphamide-treated bone marrow 5 days - Biological Replicate 5 - Technical Replicate 1

description: Biological replicate 5 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day 5


title: K10


title: Cyclophosphamide-treated bone marrow 5 days - Biological Replicate 3 - Technical Replicate 1

description: Biological replicate 3 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day 5


title: Cyclophosphamide-treated bone marrow 2 days - Biological Replicate 1 - Technical Replicate 2

description: Biological replicate 1 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated bone marrow cells, day 2


title: L9891

value: Mismtach repair


title: Cyclophosphamide-treated bone marrow 1 day - Biological Replicate 5 - Technical Replicate 2

description: Biological replicate 5 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated bone marrow cells, day1

treatment_protocol: Mice were injected i.p. with 83 mg/Kg cyclophosphamide. Bone marrow was harvested 1 day after treatment


title: K41


title: K54


title: L5


title: Liver_APG hepatotoxicity_100mgR1

city: Lucknow

first: Prabhat

last: Singh

state: Uttar Pradesh

address: MG Marg

department: Toxicology

country: India

institute: Central Drug Research Institute

description: Mice (Mus musculus) were sacrificed and livers were snap frozen in liquid nitrogen, and subsequently stored at -80 degree C till further use. Liver samples were mechanically homogenized and total RNA was extracted with TRI reagent (Sigma). 25 µg of total RNA was converted into labeled cDNA using CyScribe first strand cDNA labeling kit (Amersham). Purified labelled cDNA was concentrated by evaporation under vacuum after estimating the percent incorporation of the dyes spectrophotometrically.

hyb_protocol: The Cy5 and Cy3 labelled cDNAs were resuspended in Cyscribe Hyb buffer(Amersham) containing 10ug/ml sheared Salmon sperm DNA, and 10ug/ml yeast tRNA.The samples were heated at 95 degree C for 3 minutes and immediately chilled to avoid secondary structures. The labeled samples were hybridized to the arrays and incubated for 16-18hrs at 42 degree C. The arrays were washed with 1xSSC + 0.2% SDS and 0.1xSSC + 0.2SDS at 42 degree C and 0.1xSSC at room temperature for 15 minutes each. The arrays were dried immediately at 1000rpm for 2 minutes.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with Molecular dynamics III scanner supported with ImageQuant v5.0 at default settings.

data_processing: Image intensity data were extracted and analyzed with ArrayVision v8.0 analysis software. Raw intensity data was analyzed with Avadis Express version 4.3 (Strand life Sciences) and the background corrected intensity data was LOWESS normalized (Cy5 against Cy3) to obtain log (base 2) ratios. Technical replicate data belonging to all the three doses were transformed to account for dye swap discrepancies. Two-sample t-test was applied between the control and the treatment groups on mean log transformed data belonging to all the three doses to find probes with statistically significant p values (uncorrected) and fold-changes.

source_name: Mice Liver

label_protocol: CyScribe First Strand cDNA Labelling Kit Protocol

growth_protocol: The animals were housed in plastic cages and acclimated to controlled conditions of light and dark (12 h each), and temperature (23±2ºC) for next 24 hrs. after drug administration. Access to food and water was ‘ad libitum’ before and after drug treatment.

extract_protocol: TRI Reagent Protocol

treatment_protocol: Vehicle Treatment (DMSO)

tag: Organism

value: Mus musculus

tag: Strain

value: Swiss albino

tag: Gender

tag: Age

value: 8-10 weeks

tag: Tissue

value: Liver

label_protocol: CyScribe First Strand cDNA Labeling Kit Protocol

treatment_protocol: Mice were administered with 100mg/kg bw of apigenin


title: Cyclophosphamide-treated bone marrow 1 day - Biological Replicate 4 - Technical Replicate 1

description: Biological replicate 4 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day1

source_name: bone marrow cells

tag: strain


title: Liver_APG hepatotoxicity_100mgR2


title: L22809

value: III


title: Cyclophosphamide-treated bone marrow 2 days - Biological Replicate 1 - Technical Replicate 1

description: Biological replicate 1 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day 2


title: Liver_APG hepatotoxicity_100mgF2

value: Male


title: K21


title: Cyclophosphamide-treated bone marrow 5 days - Biological Replicate 1 - Technical Replicate 1

description: Biological replicate 1 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day 5


title: Cyclophosphamide-treated bone marrow 1 day - Biological Replicate 4 - Technical Replicate 2

description: Biological replicate 4 of 5. Technical Replicate 2 of 2.Cyclophosphamide-treated bone marrow cells, day1


title: Cyclophosphamide-treated bone marrow 1 day - Biological Replicate 3 - Technical Replicate 2

description: Biological replicate 3 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated bone marrow cells, day1


title: Liver_APG hepatotoxicity_100mgF1


title: Cyclophosphamide-treated bone marrow 2 days - Biological Replicate 5 - Technical Replicate 2

description: Biological replicate 5 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated bone marrow cells, day 2


title: Cyclophosphamide-treated bone marrow 2 days - Biological Replicate 5 - Technical Replicate 1

description: Biological replicate 5 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day 2


title: Cyclophosphamide-treated bone marrow 1 day - Biological Replicate 2 - Technical Replicate 2

description: Biological replicate 2 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated bone marrow cells, day1


title: K17

value: serous


title: Cyclophosphamide-treated bone marrow 1 day - Biological Replicate 1 - Technical Replicate 2

description: Biological replicate 1 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated bone marrow cells, day1


title: Cyclophosphamide-treated bone marrow 1 day - Biological Replicate 2 - Technical Replicate 1

description: Biological replicate 2 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day1


title: Cyclophosphamide-treated bone marrow 2 days - Biological Replicate 3 - Technical Replicate 1

description: Biological replicate 3 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day 2


title: K53


title: Control bone marrow - Biological Replicate 5 - Technical Replicate 2

description: Biological replicate 5 of 5. Technical Replicate 2 of 2. Control bone marrow cells, untreated


title: Liver_APG hepatotoxicity_50mgF1

treatment_protocol: Mice were administered with 50mg/kg bw of apigenin


title: Control bone marrow - Biological Replicate 5 - Technical Replicate 1

description: Biological replicate 5 of 5. Technical Replicate 1 of 2. Control bone marrow cells, untreated


title: Liver_APG hepatotoxicity_50mgF2


title: Liver_APG hepatotoxicity_50mgR1


title: L90


title: Cyclophosphamide-treated bone marrow 1 day - Biological Replicate 5 - Technical Replicate 1

description: Biological replicate 5 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day1


title: Liver_APG hepatotoxicity_25mgR1

treatment_protocol: Mice were administered with 25mg/kg bw of apigenin


title: L6


title: Control bone marrow - Biological Replicate 4 - Technical Replicate 2

description: Biological replicate 4 of 5. Technical Replicate 2 of 2. Control bone marrow cells, untreated


title: L4

value: IV


title: Liver_APG hepatotoxicity_25mgR2


title: Control bone marrow - Biological Replicate 4 - Technical Replicate 1

description: Biological replicate 4 of 5. Technical Replicate 1 of 2. Control bone marrow cells, untreated


title: L3

value: endometrioid


title: Liver_APG hepatotoxicity_25mgF1

description: Mice (Mus musculus) were sacrificed and livers were snap frozen in liquid nitrogen, and subsequently stored at -80 degree C till further use. Liver samples were mechanically homogenized and total RNA was extracted with TRI reagent (Sigma). 25 µg of total RNA was converted into labeled cDNA using CyScribe first strand cDNA labeling kit (Amersham). Purified labelled cDNA was concentrated by evaporation under vacuum after estimating the percent incorporation of the dyes spectrophotometrically.

value: 8-10 weeks old


title: WT Kidney_c

description: gene expression in knockout vs wild type mice

hyb_protocol: 1.5 ug 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 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4648A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014868_D_F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  The data was them imported into GeneSpring 10 and default normalization (75th percentile) procedures were used. The kidney samples were normalized as a group and the heart samples normalized seperately as another group.

source_name: kidney, wildtype (FVB/N)

tag: genotype

value: wildtype

tag: genetic background

value: FVB/N

tag: tissue

value: kidney


title: Control bone marrow - Biological Replicate 3 - Technical Replicate 2

description: Biological replicate 3 of 5. Technical Replicate 2 of 2. Control bone marrow cells, untreated

tag: cell type

value: pool of untreated bone marrow cells


title: mENT1-KO Kidney_c

source_name: kidney, mENT1 knockout

value: mENT1 knockout


title: L17761

value: II


title: Cyclophosphamide-treated bone marrow 1 day - Biological Replicate 1 - Technical Replicate 1

description: Biological replicate 1 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day1

value: bone marrow cells

tag: sample type

value: reference


title: mENT1-KO Kidney_b


title: Liver_APG hepatotoxicity_50mgR2

value: Mus musculus

value: Swiss albino


title: N2_mixed_replica2 [ChIP02]

description: LIN-54 ChIP-chip on wild type worms (biological replica 2)

source_name: LIN-54 ChIP DNA

treatment_protocol: Lysates were cross-linked in 1% formaldehyde, sonicated, and immunoprecipitated with anti-LIN-54 antibody

value: N2 (Bristol)

tag: antibody

value: LIN-54 antibody; non-commercial antibody raised in guinea pig, see Harrison et al. PNAS 2006

tag: developmental stage

value: mixed staged worm culture

source_name: input DNA from pre-bleed antibody control.

treatment_protocol: Lysates were cross-linked in 1% formaldehyde, sonicated, and immunoprecipitated with  pre-bleed antibody control.


title: N2_mixed_replica1 [ChIP02]

description: LIN-54 ChIP-chip on wild type worms (biological replica 1)

treatment_protocol: Lysates were cross-linked in 1% formaldehyde, sonicated, and immunoprecipitated with anti-LIN-54 antibody.


title: WT Kidney_a


title: Cyclophosphamide-treated bone marrow 1 day - Biological Replicate 3 - Technical Replicate 1

description: Biological replicate 3 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day1

treatment_protocol: Mice were treated with 83 mg/Kg cyclophosphamide


title: WT Kidney_b


title: Control bone marrow - Biological Replicate 3 - Technical Replicate 1

description: Biological replicate 3 of 5. Technical Replicate 1 of 2. Control bone marrow cells, untreated

treatment_protocol: Untreated mice


title: Control bone marrow - Biological Replicate 1 - Technical Replicate 1

description: Biological replicate 1 of 5. Technical Replicate 1 of 2. Control bone marrow cells, untreated


title: Liver_APG hepatotoxicity_25mgF2

value: Male

value: 8-10 weeks

value: Liver


title: WT Heart_c

source_name: heart, wildtype (FVB/N)

value: heart


title: Control bone marrow - Biological Replicate 2 - Technical Replicate 1

description: Biological replicate 2 of 5. Technical Replicate 1 of 2. Control bone marrow cells, untreated


title: mENT1-KO Kidney_a


title: Control bone marrow - Biological Replicate 1 - Technical Replicate 2

description: Biological replicate 1 of 5. Technical Replicate 2 of 2. Control bone marrow cells, untreated


title: mENT1-KO Heart_c

source_name: heart, mENT1 knockout


title: mENT1-KO Heart_a


title: WT Heart_a

value: wildtype


title: N2_mixed_replica2 [ChIP03]