title: ERMS tumor 22

city: Dallas

first: Vera

middle: Ashley

last: Paulson

address: 5323 Harry Hines Blvd

department: Pediatric Hematology-Oncology

institute: UT Southwestern

description: Case ID 22

hyb_protocol: Per NimbleGen CGH protocol

scan_protocol: Per NimbleGen CGH protocol

data_processing: Per NimbleGen CGH protocol (NimbleScan Software using the segMNT algorithm)

source_name: ERMS tumor 22

label_protocol: Per NimbleGen CGH protocol

extract_protocol: We isolated genomic DNA from five milligrams of frozen primary tumors as previously described (Sambrook and Russell, 2006). We assessed genomic DNA concentration and quality using a Nanodrop-1000 spectrophotometer (Nanodrop); all samples met strict cutoffs of 260/280 ≥ 1.8 and a 260/230 ≥ 1.9.  Electrophoresis of 250 nanograms of genomic DNA on a 0.8 percent agarose gel confirmed the presence of a single band > 10 kilobases in size.

value: M

tag: age (years)

value: embryonal rhabdomyosarcoma (ERMS)

tag: location

value: Retroperitoneum

tag: stage (years)

tag: group

tag: risk

value: Int

tag: status

value: Alive

source_name: Nimblegen pooled male reference

tag: reference

value: NimbleGen pooled male reference


title: PFC, 2 bottle choice, rep5

status: Public on Mar 01 2011

type: RNA

city: Richmond

first: Jonathan

last: Warner

state: Virginia

address: 1220 E. Broad St.

department: Pharmacology and Toxicology

country: USA

institute: Virginia Commonwealth University

hyb_protocol: Labeled cRNA from individual animals (n=19) was hybridized to a single microarray for each brain region (n=58 total microarrays).  Array hybridization and scanning were performed exactly according to manufacturer’s protocols.  Arrays were washed, stained with streptavidin-phycoerythrin (Molecular Probes, Eugene, OR) and scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: Microarray data were processed using the GeneChip Operating Software v4.1 (GCOS, Affymetrix) and normalized to a mean total hybridization intensity of 190.  Array quality was assessed by accepting arrays with scaling factor < 3, 3’-5’-actin ratio <2, and by examining linearity and inter-chip correlations of intensity values.  Arrays determined to be acceptable (57/58) were further analyzed using the Robust Multichip Average (RMA) low-level analysis algorithm to summarize probeset expression data (Irizarry et al. 2003).  Probesets with RMA expression values < 4.5 consistently across all microarrays were filtered to reduce variance from low expressing genes. To identify genes with expression values correlated with ethanol drinking behavior across individual mice, RMA values for each brain region were correlated (Pavlidis and Noble 2001) to a drinking scale calculated from each mouse’s ethanol intake averaged over the last 8 drinking days using the template matching tool in T-Mev (TIGR Multiple expression viewer (Saeed AI 2003)).  P-values from the template matching analysis were then used in estimating the false discovery rate (FDR) using the q value method (Storey and Tibshirani 2003) in the R programming environment (Team 2009). Probesets were considered significant using a FDR of 1%. Significant probesets were then used in subsequent bioinformatics analyses to identify genes with the most robust changes. All analyses were performed in each brain region separately.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Prefrontal cortex, 6 days following final ethanol drinking session

label_protocol: Biotin-labeled cRNA was synthesized from cDNA, purified and fragmented according to manufacturer's instructions.

extract_protocol: Total RNA was extracted from PFC, NAc and VTA from individual mice in STAT 60 reagent (Tel-Test, Friendswood, TX) according to the manufacturer’s protocol.  RNA concentration and quality was assessed by Experion-automated electrophoresis (BioRad, Hercules, CA).  Total RNA (2 ug) was reversed transcribed into double-stranded cDNA using the One-cycle Targeting and Control Reagent kit (Affymetrix, Santa Clara, CA).

treatment_protocol: Voluntary two-bottle choice drinking was performed as described previously (Khisti et al. 2006).  Briefly, two bottles containing 10%(w/v) ethanol (Aaper Alcohol and Chemical Co. Shelbyville, KY) or tap water were placed into the home cage at the beginning of the dark cycle.  Tube position was varied every two days (L, L, R, R).  Drinking sessions lasted 18 hours/day followed by 6 hours access to water only.  Mice had four consecutive drinking sessions followed by four days of abstinence repeated four times to give 16 total drinking sessions.  Three brain regions were harvested 6 days after the last drinking session: prefrontal cortex (PFC), nucleus accumbens (NAc) and ventral tegmental area (VTA) as previously described (Kerns et al. 2005).  Labeled cRNA from individual animals (n=19) was hybridized to a single microarray for each brain region (n=58 total microarrays).

tag: gender

value: male

tag: strain

tag: region

value: Prefrontal cortex


title: multiple sclerosis_4

city: Nashville

first: Fanglin

last: Zhang

state: TN

address: 2201 Childrens' way

institute: Vanderbilt University

hyb_protocol: The biotinylated cDNA (5 µg) was fragmented and hybridized to an Affymetrix GeneChip Human Gene 1.0 ST Array

scan_protocol: GeneChips were then scanned using GeneChip Scanner 3000 7G Plus 2 and Command Console Software (AGCC) version 1.0

data_processing: Raw gene expression data in the generated CEL files  were then normalized using the GC Robust MultiChip Averaging (GC-RMA) algorithm as implemented in Bioconductor. To identify groups of functionally related genes that were differentially expressed, we conducted gene set analysis using the mixed effects models approach.

organism: Homo sapiens

source_name: multiple sclerosis_4

label_protocol: A total of 100ng of total RNA was reverse transcribed to cDNA which was then used as template in an in-vitro transcription reaction followed by fragmentation of the single stranded cDNA and labeling through a terminal deoxy-transferase reaction.  The biotinylated cDNA (5 µg) was fragmented

extract_protocol: Total RNA was extracted from PBMC by RNeasy mini kit and treated with RNase-free DNase set, following manufacturer’s recommendation.

treatment_protocol: Peripheral blood mononuclear cells (PBMC) were isolated by density gradient centrifugation with Ficoll-Hypaque from freshly heparinized blood. The cells were washed in PBS and re-suspended at 1´106 cells/ml in complete medium RPMI-1640 for 48h before harvested for RNA extraction.

tag: cell type

value: peripheral blood mononuclear cells

tag: disease state

value: multiple sclerosis


title: CS28550:CS28459

city: Chicago

first: Justin

last: Borevitz

state: IL

department: Ecology and Evolution

institute: University of Chicago

description: total RNA followed by poly A-RNA purification and double-stranded cDNA synthesis, labelled products were hybridized to the array in a total amount of 20ug

hyb_protocol: Standard hybridization protocol for tiling array from Affymetrix

scan_protocol: Affymetrix Scanner 7G, GeneChip Operating Software Version 1.4 (GCOS)

data_processing: Bioconductor package Affy

organism: Arabidopsis thaliana

source_name: total RNA

label_protocol: Invitrogen Bioprime random labeling

extract_protocol: Qiagen RNeasy Plant Mini kit

tag: tissue

value: leaf

tag: genotype

value: F1 hybrid between accession CS28550 and CS28459

tag: age

value: 5th or 6th true leaf

tag: growth condition

value: Seeds were cold stratified in water for 5 days, sown in 96 cell flats in Promix 1:1 Metro:C2 soil. Plants were grown at 21 degrees C with 18 hours of fluorescent light.


title: ERMS tumor 23

type: genomic

state: TX

description: Case ID 23

molecule: genomic DNA

source_name: ERMS tumor 23

value: Nasopharynx


title: PFC, 2 bottle choice, rep4

scan_protocol: Arrays were washed, stained with streptavidin-phycoerythrin (Molecular Probes, Eugene, OR) and scanned using the GeneChip Scanner 3000 (Affymetrix).


title: ROSE199Red_ROSEA25Green

city: Berlin

first: Oleg

last: Tchernitsa

address: Chariteplatz 1

department: Institute of Pathology

country: Germany

institute: Charite

description:
The ROSE 199 cell line is a rat ovarian epithelial cell line first described by  Anne T. Adams and Nelly Auersperg, Expl Cell Biol 1985;53:181-188 (PMID 4029476).
The ROSEA 25 cell line is a KRAS V12-transformed derivate of ROSE 199 cells, described by Tchernitsa et al. Oncogene. 2004 Jun 3;23(26):4536-55 (PMID 15064704).

hyb_protocol: The second round of hybridization was performed in a reaction mix containing equal of 3DNA capture Reagent Cy3 and 3DNA Capture Reagent Cy5. The composition of the reaction mix, hybridization and washing conditions were as described in the Genisphere instruction manual. For each target RNA, we performed 2 independent hybridizations by inverting the Cy3 and Cy5 fluorescent dyes in the labeling reactions (dye swap).

scan_protocol: Microarray images were obtained on an Agilent G2565AA scanner at 10 μm resolution. Image analysis was performed using ImaGene software (BioDiscovery, USA).

data_processing: Global scaling normalization was performed using the median to set the average to 1 for all arrays. Imagene software (Biodiscovery, USA) was used for feature extraction.

organism: Rattus norvegicus

source_name: ROSE A25 cell line

label_protocol: We applied dendrimer technology for cDNA labeling and array hybridization using the 3DNA Array 900 MPX Kit for Microarray (Genisphere, USA). The two samples of cDNA were synthesized from each RNA probe (4 μg) by reverse transcription with random primers. The primers contained capture sequences that are complementary to Cy3- or Cy5-fluorescent dyes carrying capture reagents. The concentration of cDNA, hybridization and washing were carried out according to the kit manual.

extract_protocol: Total RNA from cells was prepared from cells 48 h after the last transfection with the TRIZOL reagent (Invitrogen, Karlsruhe, Germany) according to the manufacturer’s instructions.

tag: cell line

value: ROSE A25

value: rat ovary surface epithelium cells

source_name: ROSE 199 cell line

value: ROSE 199


title: PFC, 2 bottle choice, rep3


title: CS2249:FR2ALL1-3

value: F1 hybrid between accession CS2249 and FR2ALL1-3


title: ROSE199Green_ROSEA25Red


title: PFC, 2 bottle choice, rep2


title: ScrGreen_siOtx1N2Red

source_name: ROSE A25 cell line transfected with scrambled siRNA

tag: sirna

value: scrambled

source_name: ROSE A25 cell line transfected with Otx1 siRNA N2

tag: sirna #


title: ScrGreen_siOtx1N1Red

source_name: ROSE A25 cell line transfected with Otx1 siRNA N1


title: multiple sclerosis_2

source_name: multiple sclerosis_2


title: ERMS tumor 19

description: Case ID 19

source_name: ERMS tumor 19

value: F

tag: age (years)

value: embryonal rhabdomyosarcoma (ERMS)

tag: location

value: Pelvic, ind

tag: stage (years)

value: Int

value: Progression


title: multiple sclerosis_1

source_name: multiple sclerosis_1

value: peripheral blood mononuclear cells


title: ERMS tumor 20

description: Case ID 20

source_name: ERMS tumor 20

value: M

value: Cheek w/ PM extension

tag: group

tag: risk

tag: status

value: NimbleGen pooled male reference


title: ERMS tumor 24

description: Case ID 24

source_name: ERMS tumor 24

tag: gender

value: Peripharyngeal, head/neck/face

value: High

value: Alive

tag: reference


title: ERMS tumor 26

description: Case ID 26

source_name: ERMS tumor 26

value: 6(8) - 6 at first diagnosis, recurrence at 8

value: Omentum, Bladder

value: 4, recurrent

value: Dead


title: ScrGreen_siKlf6N2Red

value: ROSE A25

tag: cell type

value: rat ovary surface epithelium cells

value: scrambled

source_name: ROSE A25 cell line transfected with Klf6 siRNA N2


title: healthy control_4

source_name: health control_4

tag: disease state

value: healthy control


title: multiple sclerosis_3

source_name: multiple sclerosis_3

value: multiple sclerosis


title: ScrRed_siKlf6N1Green

source_name: ROSE A25 cell line transfected with Klf6 siRNA N1


title: ScrGreen_siKlf6N1Red


title: NAC, 2 bottle choice, rep19

source_name: Nucleus accumbens, 6 days following final ethanol drinking session

value: male

tag: strain

tag: region

value: Nucleus accumbens


title: healthy control_3

source_name: health control_3

value: peripheral blood mononuclear cells


title: NAC, 2 bottle choice, rep20


title: NAC, 2 bottle choice, rep18


title: ScrRed_siKlf6N2Green


title: ERMS tumor 21

description: Case ID 21

source_name: ERMS tumor 21

value: M

value: embryonal rhabdomyosarcoma (ERMS)

value: Middle ear & Nasopharynx

value: Int

source_name: Nimblegen pooled male reference


title: PFC, 2 bottle choice, rep1

source_name: Prefrontal cortex, 6 days following final ethanol drinking session

value: Prefrontal cortex


title: healthy control_1

source_name: health control_1


title: ScrRed_siJunbN2Green

source_name: ROSE A25 cell line transfected with Junb siRNA N2

value: Junb

source_name: ROSE A25 cell line transfected with scrambled siRNA


title: ScrGreen_siJunbN2Red


title: ERMS tumor 25

description: Case ID 25

source_name: ERMS tumor 25

value: F

value: Pelvic Mass

value: High

value: Alive

value: NimbleGen pooled male reference


title: MT19C treated tumor day 30, biological replicate 1

city: PROVIDENCE

first: Alexander

last: Brodsky

state: RI

address: 593 Eddy St.

department: MCB

institute: Rhode Island Hospital/Brown University

description: Gene expression data from MT19C treated SKOV-3 xenograft after 30 days

hyb_protocol: Following fragmentation,  of about 2.3 ug cRNA were hybridized for 17 hr at 45C on each GeneST 1.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using fluidics script FS450_007

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G scanner equipped with an autoloader.

data_processing: The data were analyzed with plier-gcbg from Affymetrix Power Tools using  HuGene-1_0-st-v1.r3.bgp, HuGene-1_0-st-v1.r3.pgf, and HuGene-1_0-st-v1.r3.clf f iles from Affymetrix.

source_name: SKOV-3 xenograft tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual, Affymetrix).

growth_protocol: SKOV-3 cells were suspended in matrigel and inoculated subcutaneously into nude mice for two weeks before treatments were initiated.

extract_protocol: Qiazol and Qiagen RNAsy was performed following the manufacturer's instructions.

treatment_protocol: Tumors were removed from mice and quickly frozen in liquid nitrogen.

tag: tissue

value: xenograft tumor

tag: treatment


title: ScrRed_siJunbN1Green

source_name: ROSE A25 cell line transfected with Junb siRNA N1

tag: cell line

value: ROSE A25

value: rat ovary surface epithelium cells

value: scrambled


title: NAC, 2 bottle choice, rep16

value: male

value: Nucleus accumbens


title: NAC, 2 bottle choice, rep15


title: MT19C treated tumor day 30, biological replicate 2


title: healthy control_2

source_name: health control_2

value: peripheral blood mononuclear cells

value: healthy control


title: Pneumo-CSP2-2min

city: Bronx

first: Masahide

last: Yano

state: NY

address: 1300 Morris Park Ave

department: Microbiology and Immunology

institute: Albert Einstein College of Medicine

hyb_protocol: Samples were hybridized using a Mix from nimblegen. See NimbleGen's NG_Expression_Guide_v5p1.pdf

scan_protocol: The arrays were scanned with the  MS200 microarray schanner. See NimbleGen's NG_Expression_Guide_v5p1.pdf

data_processing: Data were analyzed using Robust Multichip Average. See NimbleGen's NG_Expression_Guide_v5p1.pdf

organism: Streptococcus pneumoniae

source_name: CSP2-2 min

label_protocol: One color (Cy3) labeling. see NimbleGen's NG_Expression_Guide_v5p1.pdf

growth_protocol: Up to early log phase in bacterial growth medium at 30 degree

extract_protocol: mRNA was extracted with MICROBE express

treatment_protocol: RNAprotect was used to avoid degredation of RNA.   mRNA was amplified with mRNA enrichment kit

value: CSP2 (Streptococcus pneumoniae serotype 3 capsule specific monoclonal Ab)

tag: time

value: 2 min


title: ERMS tumor 15

description: Case ID 15

source_name: ERMS tumor 15

value: embryonal rhabdomyosarcoma (ERMS)

value: Retroperitoneum

value: Int


title: NAC, 2 bottle choice, rep17


title: ERMS tumor 18

description: Case ID 18

source_name: ERMS tumor 18

value: M

value: Nasopharynx

value: Dead


title: ERMS tumor 13

description: Case ID 13

source_name: ERMS tumor 13

value: Bladder

value: Alive

value: NimbleGen pooled male reference


title: Ull2-3:2CS6041

source_name: total RNA

value: leaf

tag: genotype

value: F1 hybrid between accession Ull2-3 and 2CS6041

tag: age

value: 5th or 6th true leaf

tag: growth condition

value: Seeds were cold stratified in water for 5 days, sown in 96 cell flats in Promix 1:1 Metro:C2 soil. Plants were grown at 21 degrees C with 18 hours of fluorescent light.


title: ERMS tumor 14

description: Case ID 14

source_name: ERMS tumor 14

value: F

tag: age (years)

tag: location

value: Larynx w/ PM extension

tag: stage (years)


title: ScrRed_siHmga2N2Green

source_name: ROSE A25 cell line transfected with Hmga2 siRNA N2

value: ROSE A25

value: rat ovary surface epithelium cells

tag: sirna

tag: sirna #

value: scrambled


title: NAC, 2 bottle choice, rep14

source_name: Nucleus accumbens, 6 days following final ethanol drinking session

tag: gender

value: male

value: Nucleus accumbens


title: Pneumo-1E2+CPS2-2min

source_name: 1E2 + CSP2 - 2 min

value: 1E2 (Streptococcus pneumoniae serotype 3 capsule specific monoclonal Ab) + CSP2 (Streptococcus pneumoniae serotype 3 capsule specific monoclonal Ab)

value: 2 min


title: MT19C treated tumor day 16, biological replicate 3

description: Gene expression data from MT19C treated SKOV-3 xenograft after 16 days

value: xenograft tumor


title: NAC, 2 bottle choice, rep13


title: ERMS tumor 16

description: Case ID 16

source_name: ERMS tumor 16

value: M

value: embryonal rhabdomyosarcoma (ERMS)

value: Bladder

tag: group

tag: risk

value: Int

tag: status

source_name: Nimblegen pooled male reference

tag: reference


title: MT19C treated tumor day 16, biological replicate 2

tag: tissue


title: Pneumo-1E2 1

tag: treatment

value: 1E2 (Streptococcus pneumoniae serotype 3 capsule specific monoclonal Ab)


title: ScrGreen_siHmga2N2Red

tag: cell line

tag: cell type


title: ERMS tumor 10

description: Case ID 10

source_name: ERMS tumor 10

tag: disease state

value: Retropertioneum

value: Dead

value: NimbleGen pooled male reference


title: NAC, 2 bottle choice, rep12

tag: strain

tag: region


title: MT19C treated tumor day 8, biological replicate 3

description: Gene expression data from MT19C treated SKOV-3 xenograft after 8 days


title: NAC, 2 bottle choice, rep11


title: Pneumo-31B12

value: 31B12 (Streptococcus pneumoniae serotype 8 capsule specific monoclonal Ab - control)


title: MT19C treated tumor day 16, biological replicate 1


title: ScrGreen_siHmga2N1Red

source_name: ROSE A25 cell line transfected with scrambled siRNA

value: ROSE A25

source_name: ROSE A25 cell line transfected with Hmga2 siRNA N1


title: ERMS tumor 12

description: Case ID 12

source_name: ERMS tumor 12

value: F

tag: age (years)

value: Middle Ear


title: Pneumo-untreated

source_name: untreated

value: untreated


title: ERMS tumor 17

description: Case ID 17

source_name: ERMS tumor 17

tag: location

value: Nasopharynx


title: MT19C treated tumor day 8, biological replicate 2

source_name: SKOV-3 xenograft tumor


title: ERMS tumor 11

description: Case ID 11

source_name: ERMS tumor 11

value: Prostate

tag: stage (years)

value: Alive


title: ScrRed_siGfi1N2Green

source_name: ROSE A25 cell line transfected with Gfi1 siRNA N2

value: rat ovary surface epithelium cells

tag: sirna

value: scrambled


title: MT19C treated tumor day 8, biological replicate 1

value: xenograft tumor


title: ERMS tumor 9

description: Case ID 9

source_name: ERMS tumor 9

value: embryonal rhabdomyosarcoma (ERMS)

value: Retroperitoneum


title: ScrGreen_siGfi1N2Red

tag: sirna #


title: ScrGreen_siJunbN1Red

source_name: ROSE A25 cell line transfected with Junb siRNA N1

value: Junb


title: NAC, 2 bottle choice, rep8

tag: gender

value: male

value: Nucleus accumbens


title: Naïve tumor day 30, biological replicate 1

description: Gene expression data from vehicle treated SKOV-3 xenograft after 30 days

value: vehicle


title: SrcRed_siGfi1N1Green

source_name: ROSE A25 cell line transfected with Gfi1 siRNA N1


title: ERMS tumor 8

description: Case ID 8

source_name: ERMS tumor 8

value: M

value: Bladder, pelvic mass

tag: group

value: Int

value: Progression

value: NimbleGen pooled male reference


title: Naïve tumor day 16, biological replicate 3

description: Gene expression data from vehicle treated SKOV-3 xenograft after 16 days


title: ERMS tumor 7

description: Case ID 7

source_name: ERMS tumor 7

tag: risk


title: SrcGreen_siGfi1N1Red

value: ROSE A25


title: SrcRed_Fosl1N2Green

source_name: ROSE A25 cell line transfected with Fosl1 siRNA N2


title: NAC, 2 bottle choice, rep5

source_name: Nucleus accumbens, 6 days following final ethanol drinking session


title: NAC, 2 bottle choice, rep6


title: SrcGreen_Fosl1N2Red


title: Naïve tumor day 16, biological replicate 1


title: Naïve tumor day 8, biological replicate 3

description: Gene expression data from vehicle treated SKOV-3 xenograft after 8 days


title: Pneumo-1E2+CPS2-8min

source_name: 1E2 + CSP2 - 8 min

value: 1E2 (Streptococcus pneumoniae serotype 3 capsule specific monoclonal Ab) + CSP2 (Streptococcus pneumoniae serotype 3 capsule specific monoclonal Ab)

tag: time

value: 8 min


title: NAC, 2 bottle choice, rep3


title: NAC, 2 bottle choice, rep7


title: NAC, 2 bottle choice, rep4


title: Naïve tumor day 16, biological replicate 2


title: NAC, 2 bottle choice, rep2


title: Naïve tumor day 8, biological replicate 2


title: siN1Fosl1Green_scrRed

source_name: ROSE A25 cell line transfected with Fosl1 siRNA N1

value: rat ovary surface epithelium cells


title: Seedlings, mutant, rep1

status: Public on Feb 28 2011

city: Oxford

first: Quinn

last: Li

state: OH

address: 316, Person Hall, High Str.

department: Botany

institute: Miami University

description: Gene expression data from 15-day old seedlings of pcfs4-1.

hyb_protocol: The labeled targets were hybridized to the Arabidopsis Tiling 1.0R array (Affymetrix, PN900594) using GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix, PN 900720). Hybridization was carried out on Affymetrix GeneChip Hybridization Oven 640, washed and post-hybridization stained on Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Hybridization signals were collected using an Affymetrix GCS 3000 7G scanner and processed with GeneChip Operating Software

data_processing:
The data were normalized with VSN of Bioconductor and further analyzed with a newly developed protocol, RADPRE, from our lab. In RADPRE, ratios of normalized probe intensities between control and treatment were first generated. With the probe ratios as inputs, a hierarchy of statistical tests was carried out to identify differentially processed genes (DPG) and differentially expressed genes (DEG). The false discovery rate (FDR) of this analysis was estimated by using the balanced random combinations of Control/treatment and treatment/Control ratios as inputs. The Arabidopsis*.txt files represent the data 'normalized with VSN of Bioconductor'.
The mapping information between 'bpmap' vs. 'NomralizedData' and the ratio data files:
pmindex (in the NormalizedData or Ratio) ＝ [PMX (in bpmap) ＋PMY(in bpmap)*2560+1] or [MMX (in bpmap)+MMY(in bpmap)*2560+1]

source_name: Above ground apart of 15-day old seedlings of pcfs4-1

label_protocol: The fragmented, double-stranded cDNA were prepared using the Affymetrix GeneChip WT Double-Stranded Target Assay kit (Affymetrix, PN900813) and further end-labeled with the biotin-labeled DLR (dual luciferase reporter) using Terminal Deoxynucleotidyl Transferase (Affymetrix, PN900812)

growth_protocol: The imbibed seeds were first stratified at 4°C in the dark for two days and then grown in growth chamber at 22°C, under 16h/8h light/dark cycles. The above ground tissue of 15-day old seedlings was collected 8 hours after dawn

extract_protocol: Total RNAs were extracted using Concert Plant RNA reagent (Invitrogen) and further treated with Turbo DNA-free (Ambion) following the manufacture’s instructions.

treatment_protocol: Wild type Col and mutant pcfs4-1 were grown in a randomized block design.

value: Seedlings

tag: genotype

tag: age

value: 15-day old


title: SrcGreen_siN1Fosl1Red

description:
The ROSE 199 cell line is a rat ovarian epithelial cell line first described by  Anne T. Adams and Nelly Auersperg, Expl Cell Biol 1985;53:181-188 (PMID 4029476).
The ROSEA 25 cell line is a KRAS V12-transformed derivate of ROSE 199 cells, described by Tchernitsa et al. Oncogene. 2004 Jun 3;23(26):4536-55 (PMID 15064704).
The ROSE 199 cell line is a rat ovarian epithelial cell line first described by  Anne T. Adams and Nelly Auersperg, Expl Cell Biol 1985;53:181-188 (PMID 4029476).
The ROSEA 25 cell line is a KRAS V12-transformed derivate of ROSE 199 cells, described by Tchernitsa et al. Oncogene. 2004 Jun 3;23(26):4536-55 (PMID 15064704).

source_name: ROSE A25 cell line transfected with scrambled siRNA

value: scrambled


title: Seedlings, mutant, rep3

tag: tissue


title: Seedlings, wild type, rep1

description: Gene expression data from 15-day old seedlings of Col.

source_name: Above ground apart of 15-day old seedlings of Col

value: Col


title: ERMS tumor 5

description: Case ID 5

source_name: ERMS tumor 5

value: embryonal rhabdomyosarcoma (ERMS)

value: Middle Ear

tag: status

value: Alive

source_name: Nimblegen pooled male reference

tag: reference


title: ERMS tumor 4

description: Case ID 4

source_name: ERMS tumor 4

tag: disease state

value: Nasopharynx


title: NAC, 2 bottle choice, rep9

value: male

tag: strain

value: Nucleus accumbens


title: Seedlings, wild type, rep2


title: ERMS tumor 6

description: Case ID 6

source_name: ERMS tumor 6

value: M

value: Int

value: Dead


title: NAC, 2 bottle choice, rep1

tag: region


title: ERMS tumor 2

description: Case ID 2

source_name: ERMS tumor 2

value: F

tag: age (years)

value: Posterior nasal septum

value: Low

value: NimbleGen pooled male reference


title: ScrRed_siHmga2N1Green

source_name: ROSE A25 cell line transfected with Hmga2 siRNA N1

tag: cell line

value: ROSE A25

tag: cell type

value: rat ovary surface epithelium cells


title: Corresponding_Normal_Kidney_microRNA_3

first: Kimryn

last: Rathmell

address: 2220 Pierce Ave

department: Medicine

institute: Vanderbilt

description: MicroRNA data from Human Corresponding Normal Kidney sample

hyb_protocol: Hybridized on Agilent Whole Human Genome 4x44k arrays by UNC Lineberger Comprehensive Cancer Center Genomics Core

scan_protocol: Agilent gene chips were scanned on an Agilent scanner by UNC Lineberger Comprehensive Cancer Center Genomics Core

data_processing: UNC Microarry Database software was used to retrieve Log total gene signal, Blast geneID collapsed, filter for 70% good data (include only if spot has gene detected=1). Missing data was imputed with KNN (k=10) in SAM.

source_name: Corresponding Normal Kidney

label_protocol: According to Agilent protocol, ie, end-labelled by UNC Lineberger Comprehensive Cancer Center Genomics Core.

extract_protocol:
Frozen RCCs were obtained through University of North Carolina - Chapel Hill's Tissue Procurement Facility.  H&E was performed on tumor tissue samples to confirm clear cell or normal histopathology.
Total RNA was extracting with Qiagen miRNeasy kit.
RNA quality was determined using an Agilent LabChip Bioanalyzer.

tag: identifier

value: kidney

tag: histology

value: Normal

tag: biosourcetype

value: Frozen Sample


title: Renal_Cell_Carcinoma_microRNA_C5

description: MicroRNA data from Human RCC sample

source_name: Renal Clear Cell Carcinoma

value: Clear Cell

value: Clear Cell Carcinoma


title: Renal_Cell_Carcinoma_microRNA_A5

description: MicroRNA data from Human RCC sample


title: Renal_Cell_Carcinoma_microRNA_A4

description: MicroRNA data from Human RCC sample


title: Renal_Cell_Carcinoma_microRNA_A31

description: MicroRNA data from Human RCC sample


title: Renal_Cell_Carcinoma_microRNA_A27

description: MicroRNA data from Human RCC sample


title: Seedlings, mutant, rep2

value: Seedlings

value: 15-day old


title: Renal_Cell_Carcinoma_microRNA_C1

description: MicroRNA data from Human RCC sample


title: Renal_Cell_Carcinoma_microRNA_A30

description: MicroRNA data from Human RCC sample


title: Renal_Cell_Carcinoma_microRNA_A18

description: MicroRNA data from Human RCC sample


title: Renal_Cell_Carcinoma_microRNA_A13

description: MicroRNA data from Human RCC sample


title: ERMS tumor 3

description: Case ID 3

source_name: ERMS tumor 3

tag: gender

value: embryonal rhabdomyosarcoma (ERMS)

tag: location

value: Nasal cavity & sinus

tag: stage (years)

tag: group

value: Alive


title: Renal_Cell_Carcinoma_microRNA_25

description: MicroRNA data from Human RCC sample


title: Renal_Cell_Carcinoma_microRNA_21

description: MicroRNA data from Human RCC sample


title: Renal_Cell_Carcinoma_microRNA_27

description: MicroRNA data from Human RCC sample


title: Renal_Cell_Carcinoma_microRNA_A11

description: MicroRNA data from Human RCC sample


title: Renal_Cell_Carcinoma_microRNA_3

description: MicroRNA data from Human RCC sample


title: Renal_Cell_Carcinoma_microRNA_6

description: MicroRNA data from Human RCC sample


title: ERMS tumor 1

description: Case ID 1

source_name: ERMS tumor 1

value: Orbit

tag: risk


title: Corresponding_Normal_Kidney_microRNA_C13

tag: tissue


title: Renal_Cell_Carcinoma_microRNA_A16

description: MicroRNA data from Human RCC sample


title: Corresponding_Normal_Kidney_microRNA_C5


title: Seedlings, wild type, rep3

tag: genotype

value: Col

tag: age


title: Corresponding_Normal_Kidney_microRNA_A5

tag: disease state


title: Corresponding_Normal_Kidney_microRNA_A4


title: Corresponding_Normal_Kidney_microRNA_A31


title: Corresponding_Normal_Kidney_microRNA_A18


title: Corresponding_Normal_Kidney_microRNA_A27


title: Corresponding_Normal_Kidney_microRNA_A16


title: Corresponding_Normal_Kidney_microRNA_C1


title: Corresponding_Normal_Kidney_microRNA_A13


title: Corresponding_Normal_Kidney_microRNA_27


title: Corresponding_Normal_Kidney_microRNA_A30


title: Corresponding_Normal_Kidney_microRNA_6


title: Renal_Cell_Carcinoma_microRNA_C13

description: MicroRNA data from Human RCC sample


title: Corresponding_Normal_Kidney_microRNA_25


title: Corresponding_Normal_Kidney_microRNA_A11


title: Corresponding_Normal_Kidney_microRNA_21


title: Corresponding_Normal_Kidney_C5

description: Gene expression data from Human Corresponding Normal Kidney sample_C5

hyb_protocol: Tumor sample RNA and reference RNA were hybridized on Agilent Whole Human Genome 4x44k arrays by UNC Lineberger Comprehensive Cancer Center Genomics Core

data_processing: LOWESS normalized, log2 of processed Red/Green signal (median), filter for 70% good data (Exclude if spot is not found in either channel, spot or spot background is a non-uniform outlier, spot or spot background is a non-uniform outlier for the population, spot is not a positive and significant signal in either channel, or Ch1 and 2 lowess normalized net (median) <10). UNC Microarry Database software was used. Missing data was imputed with KNN (k=10) in SAM.

label_protocol: Tumor sample RNA and reference RNA was labelled by UNC Lineberger Comprehensive Cancer Center Genomics Core

extract_protocol:
Frozen RCCs were obtained through University of North Carolina - Chapel Hill's Tissue Procurement Facility.  H&E was performed on tumor tissue samples to confirm clear cell or normal histopathology.
RNA was extracted with Qiagen RNeasy kit.
RNA quality was determined using an Agilent LabChip Bioanalyzer.

source_name: Perou lab reference RNA

value: Cancer cell lines

value: various cancer cell lines (reference)


title: OAT_iPS_5.15

city: Rochester

first: Jeff

last: Nie

state: MN

address: 200 First St. SW

institute: Mayo Clinic

description:
R3
iPS cell line-derived OAT iPS 5 resulting from the random integration of the gene-targeting vector.

hyb_protocol: The sample/hybridization solution is added to the Roche NimbleGen (www.nimblegen.com) array/hybridization chamber (Roche Nimblegen, Madison, WI) assembly and incubated with active mixing on the Roche NimbleGen Hybridization System (Roche Nimblegen, Madison, WI) for 40–72 h at 48 °C . This station facilitates the hybridization of aCGH samples to microarrays by using air bladders to push the labeled sample back and forth over the array.

scan_protocol: InnoScan I-900AL scanner (Innopsys, Carbonne, France).

data_processing:
Data was analyzed using SignalMap software (Roche NimbleGen).
The signals were normalized and spatially corrected as described at NimbleGen (Guide_to_Your_CGH_Data_v4p0.pdf). Spatial correction was applied to the raw signal intensities to reduce variation that occurs along the length, and to a lesser extent, across the width of the array. Specifically, locally weighted polynomial regression (loess) was used to adjust the signal intensity of each feature based on the X and Y coordinate position of the probe on the array. The spatially corrected data are reported in two columns, EXP_SPATIAL andREF_SPATIAL, in the arrayID_segMNT.txt files. After combining the signal intensity information with the genomic coordinate information, and applying spatial correction, the Cy3 and Cy5 signal intensities were normalized to one another using qspline normalization (Workman C, et al., 2002). The normalized data are reported in two columns, EXP_NORM and REF_NORM, in the arrayID_segMNT.txt files. The VALUEs in the Sample data tables are the normalized and spatially corrected log2 ratios of the experimental and reference signals (e.g., iPS/fibroblasts or iPS/H1).

label_protocol: For W1, W2, W3, W4 and R3, the test sample was labeled with Cy-3 and the reference sample was labeled with Cy-5 fluorescent dyes. For R1 and R2, the test sample was labeled with Cy-5 and the reference sample was labeled with Cy-3 fluorescent dyes.

growth_protocol: TesR + matrigel.

extract_protocol: Patient fibroblasts were obtained and cultured in DMEM (Invitrogen) supplemented with 10% FBS (Hyclone) at 37°C, 5% CO2, 5%O2. Following isolation, iPS cells were maintained and expanded in TeSR and passaged routinely with EDTA.

value: gyrate atrophy

value: iPS cell

value: female

source_name: Fibroblast

growth_protocol: DMEM + 10% FBS.

value: normal health

value: foreskin fibroblasts

value: male

tag: sample type

value: reference


title: OAT_iPS_V

description:
R2
iPS cell line obtained following lentiviral reprogramming of OAT fibroblasts.


title: Corresponding_Normal_Kidney_A4

description: Gene expression data from Human Corresponding Normal Kidney sample_A4

value: kidney

value: Normal

value: Frozen Sample


title: Corresponding_Normal_Kidney_C13

description: Gene expression data from Human Corresponding Normal Kidney sample_C13


title: Corresponding_Normal_Kidney_A13

description: Gene expression data from Human Corresponding Normal Kidney sample_A13


title: Corresponding_Normal_Kidney_A16

description: Gene expression data from Human Corresponding Normal Kidney sample_A16


title: Corresponding_Normal_Kidney_21

description: Gene expression data from Human Corresponding Normal Kidney sample_21


title: Corresponding_Normal_Kidney_25

description: Gene expression data from Human Corresponding Normal Kidney sample_25


title: Corresponding_Normal_Kidney_A31

description: Gene expression data from Human Corresponding Normal Kidney sample_A31


title: Corresponding_Normal_Kidney_A30

description: Gene expression data from Human Corresponding Normal Kidney sample_A30


title: Corresponding_Normal_Kidney_C1

description: Gene expression data from Human Corresponding Normal Kidney sample_C1


title: Corresponding_Normal_Kidney_3

description: Gene expression data from Human Corresponding Normal Kidney sample_3


title: Corresponding_Normal_Kidney_A27

description: Gene expression data from Human Corresponding Normal Kidney sample_A27


title: OAT_iPS_12

description:
W3
iPS cell line obtained following episomal reprogramming of OAT fibroblasts (from a patient with gyrate atrophy).

source_name: HES H1

value: H1 human ES cells


title: OAT_iPS_12.4.2

description:
W4
Gene-corrected iPS cell line that has had the selection cassette removed with Cre-recombinase (derived from OAT iPS line 12.4).


title: Corresponding_Normal_Kidney_A18

description: Gene expression data from Human Corresponding Normal Kidney sample_A18


title: Corresponding_Normal_Kidney_A11

description: Gene expression data from Human Corresponding Normal Kidney sample_A11


title: Corresponding_Normal_Kidney_A5

description: Gene expression data from Human Corresponding Normal Kidney sample_A5


title: MIN6 HMGN3a OE rep 1

city: Rostock

first: Leila

last: Taher

address: Ernst-Heydemann-Str. 8

institute: University of Rostock

description: expression data from MIN6 cells

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Human (Mouse) Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affimetrix GeneChip Scanner 3000 controlled by Affymetrix Microarray AGCC 2.0.

data_processing: Gene expression data was processed using Robust Multi-Chip Average (RMA), as implemented in the R statistical package provided by Bioconductor.  RMA data processing includes background correction, quantile normalization, and expression summarization.  Genes were filtered in order to eliminate those with cross-sample variation, using a variation filter estimated on 14 HeLa cell lines and 5 Strategene samples.

source_name: MIN6 cells

label_protocol: Hybridization of biotin-labeled cRNA fragment to Mouse Genome 430 2.0 array, washing, staining with streptavidin–phycoerythrin (Molecular Probes), and signal amplification were performed according to the manufacturer’s instructions at the Laboratory of Molecular Technology (LMT, Frederic, NCI).

growth_protocol: DMEM 10%FCS.

extract_protocol: Trizol reagent followed by clean up on Rneasy kit with DnaseI treatment on the columns (Qiagen).

treatment_protocol: Retroviral infection with appropriate construct in the presence of polybrene at the concentration of 5 µg/ml and subsequent selection with puromycin at the concentration of 1 µg/ml for 7 days. Cells were grown 24hr without selection prior to RNA collection.

value: MIN6 cells

tag: genotype/variation

value: HMGN3a OE


title: MIN6 HMGN3a OE rep 2

description: expression data from MIN6 cells


title: Corresponding_Normal_Kidney_27

description: Gene expression data from Human Corresponding Normal Kidney sample_27


title: OAT_iPS_5

description:
R1
iPS cell line obtained following episomal reprogramming of OAT fibroblasts.


title: MIN6 HMGN1 OE rep 2

description: expression data from MIN6 cells

value: HMGN1 OE


title: MIN6 HMGN1 OE rep 3

description: expression data from MIN6 cells


title: Corresponding_Normal_Kidney_6

description: Gene expression data from Human Corresponding Normal Kidney sample_6


title: Naïve tumor day 8, biological replicate 1

description: Gene expression data from vehicle treated SKOV-3 xenograft after 8 days

source_name: SKOV-3 xenograft tumor

value: xenograft tumor

tag: treatment

value: vehicle


title: MIN6 empty vector OE rep 1

description: expression data from MIN6 cells

value: empty vector OE


title: MEFs HMGN1_N2swap rep 2

description: expression data from SV40  transformed MEFs

source_name: SV40 transformed MEFs

value: SV40 transformed MEFs

tag: source

value: ATCC (CRL-2214)


title: MIN6 HMGN3a OE rep 3

description: expression data from MIN6 cells

tag: cell type


title: MEFs HMGN1_N3swap rep 1


title: MEFs HMGN1_N2swap rep 1


title: OAT_fibroblast

value: gyrate atrophy

value: fibroblast

value: female


title: MEFs HMGN5SE OE rep 3

value: HMGN5SE OE


title: MEFs HMGN5SE OE rep 1


title: MEFs HMGN1_N3swap rep 3


title: MEFs HMGN5 OE rep 3

value: HMGN5 OE


title: MEFs HMGN1_N3swap rep 2


title: MIN6 empty vector OE rep 2

description: expression data from MIN6 cells


title: MEFs HMGN5 OE rep 2


title: MIN6 empty vector OE rep 3

description: expression data from MIN6 cells


title: MIN6 HMGN1 OE rep 1

description: expression data from MIN6 cells


title: MEFs HMGN5SE OE rep 2


title: MEFs HMGN5 OE rep 1


title: MEFs HMGN3a OE rep 3


title: MEFs HMGN1_N2swap rep 3


title: MEFs HMGN3a OE rep 2


title: MEFs HMGN3a OE rep 1


title: MEFs HMGN2 OE rep 2

value: HMGN2 OE


title: MEFs HMGN1 OE rep 3


title: MEFs HMGN5 WT  rep 3

description: expression data from primary WT MEFs

source_name: primary MEFs

value: primary MEFs

tag: strain

value: HMGN5 WT


title: MEFs HMGN2 OE rep 1


title: MEFs HMGN1 OE rep 1


title: MEFs HMGN1 OE rep 2


title: MEFs empty vector OE rep 3


title: MEFs HMGN5 WT  rep 2

description: expression data from primary WT MEFs


title: MEFs empty vector OE rep 2


title: MEFs empty vector OE rep 1


title: MEFs HMGN2 OE rep 3


title: MEFs HMGN3 knock out rep 1

description: expression data from primary KO MEFs

value: HMGN3 knock out


title: MEFs HMGN5 knock out rep 3

description: expression data from primary KO MEFs

value: HMGN5 knock out


title: MEFs HMGN3 WT  rep 2

description: expression data from primary WT MEFs

value: HMGN3 WT


title: MEFs HMGN1 WT  rep 1

description: expression data from primary WT MEFs

value: HMGN1 WT


title: MEFs HMGN5 knock out rep 1

description: expression data from primary KO MEFs


title: E12-16_CBP_1_3 extraction3_array1

status: Public on Dec 10 2010

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: channel ch1 is negative control for ChIP; Antibody information listed below: official name: No Antibody Control;target name: Not Applicable;host: None-Control;antigen: NONE;clonal: None-Control;purified: None-Control;company: None-Control;catalog: Not Applicable;reference: Not Applicable;short description: Specific Antibodies were omitted from this immunoprecipitation reaction (as a negative control).;

hyb_protocol: This protocol is used for hybridization of ChIP samples on 244K Agilent arrays.  The hybridization solution is composed of 5 ug each of Cy3- and Cy5-labeled DNA, 50 ug of salmon sperm DNA, Agilent Blocking Agent and Agilent Hyb Buffer. The mixture is heated to 95*C for 3 min and then 37*C for 30 minutes immediately prior to hybridization. Samples are hybridized for 40 hours at 65*C. After hybridization the slides are washed in Agilent Wash Buffer 1 for 5 minutes at room temperature and then in Agilent Wash Buffer 2 for 5 minutes at 31*C.

scan_protocol: Arrays are scanned on Agilent's DNA Microarray Scanner G2505B at a resolution of 5 microns. Data is extracted from the images using Agilent's Feature Extraction Software 9.5.3.1.

data_processing: Agilent ChIP data processing:KW:1 protocol. We preprocessed microarray data to normalize it and reduce experimental noise as described in Qi et al. (Qi et al., Nature biotechnology 2006). In short, the raw intensities from each channel was divided by the median intensity from that channel before computing a ratio to arrive at a median adjusted ratio. We further subtracted average value of negative control probes on the array and then added one as a regularization parameter. For factors that mark regions (e.g. H3K27me3), the data was quantile normalized, replicates were merged and HMM based segmentation was carried out.

organism: Drosophila melanogaster

label_protocol: Attached as supplementary file

extract_protocol:
Collection of Drosophila embryos at time-point 12-16h of development for further ChIP experiments  or RNA extraction.
Formaldehyde Cross-linking of Chromatin from any Drosophila tissue (Embryos, Larvae, Pupae, Adult flies).1. Homogenize the material (about 150-200 mg of embryos, pupae, adµlts, larvae, sufficient for four-five independent immuno-precipitations) in 5 ml of buffer A1 + 1.8% formaldehyde (290 µl of 37% solution) at room temperature using first a Potter homogenizer and then a Douncer with type A pestle (3 strokes). Wait 15? (total time starting from beginning of homogenization). Add glycin solution to 225 mM (540 µl of 2.5 M solution for 6 ml of cross-linked mixture), mix and incubate 5?. Put on ice. Keep on ice unless specified.2. Transfer the homogenate to a 15 ml tube. Centrifuge 5 min, at 4000 g at 4°C. Discard supernatant. Add 3 ml of buffer A1, resuspend pellet and spin down the same way. Repeat washing step 3 times.3. Wash once in 3 ml of lysis buffer without SDS. Spin down, 5 min at 4000g.4. Resuspend cross-linked material in 0.5 ml of lysis buffer and add SDS to 0.1% (2.5 µl) and N-lauroylsarcosine to 0.5% (12.5 µl). Incubate 10 min at 4°C in a rotating wheel.5. Sonicate in Polypropylene 15ml Falcon tubes according to .Diagenode instructions. The settings are: High power, 15 minutes, 30 seconds off, 30 seconds on. The water bath shoµld be kept cold either in a cold room or by a cold water pump.6. Rotate 10'. Transfer to eppendorf tubes and centrifuge 5', room temperature at maximum speed. Transfer supernatant to the new tube. Add another 0.5 ml of lysis buffer to the pellet, rotate for 10 min. Repeat centrifugation and combine supernatants. Centrifuge the combined supernatant 2x10 min at max speed. The supernatant from this stage will be referred as chromatin extract. Chromatin can be stored at ?80°C for several months at this stage. Add sodium azide to 0.02% for storage.7. [Optional : Purification of chromatin. Put chromatin extract in Centricon YM-100 column (4212), centrifuge 3x40' (or more) at 1000 g while adding lysis buffer. At least 3 vol. of lysis buffer should pass through column. Bring the final volume of chromatin extract to 1 ml by lysis buffer + protease inhibitors.][edit]
Solutions and MaterialsLysis buffer: (see above)5mg/ml RNaseA (DNase free)PAS suspension: 100 mg of CL-4B (Amersham, 17-0780-01) PAS shoµld be resuspended in 1 ml of lysis buffer + protease inhibitors + 0.1 mg/ml BSA for 50 %v suspension. Wash in lysis buffer 2-3 times, overall equilibration time 1h. Store up to one week at 4 C.TE: 10 mM Tris-HCl pH 8.0, 1 mM EDTAElution buffer1: 10 mM EDTA, 1% SDS, 50 mM Tris-Cl pH 8.Elution buffer2: TE+0.67% SDS.LiCL 4M? Protocol 1. To an amount of chromatin corresponding to 150 mg of biological material, suspended in a final volume of chromatin extract of 1 ml (in lysis buffer + protease inhibitors), add 100 µl of PAS suspension for preincubation. Incubate several hours or overnight at 4°C, then remove PAS. Crosslinked chromatin at this stage can be stored several days at 4°C or frozen at ?70°C.2. [Optional : Check for amount of DNA. From the 1 ml solution above, take a 100 µl aliquot, Add proteinase K up to 100 ug/ml and SDS to 1%, incubate 6h at 60°C, then 20 min at 70°C, add RNAse to 50 ug/ml and incubate additional 2h at 37°C. Phenol-chlorophorm extract, ethanol precipitate. Run on an agarose gel to check amount and size of DNA.]3. Separate chromatin sample into 4x250 µl aliquots (one aliquot is enough for one IP but the amount may be decreased further). Immunoprecipitate chromatin by adding the antibody (Ab) of interest (amount of Ab shoµld be determined empirically, usually the same concentration than for a successfµl IF experiement). Keep a control sample without Ab IP, named "Mock".4. Incubate 4 h at 4°C on a head to head rotating wheel, then add 50 µl of PAS suspension and incubate 4 h or overnight. Spin down PAS and proceed to washes.5. Wash PAS 4x with lysis buffer, followed by 2x with TE (without protease inhibitors). Each wash is for 5 min at 4°C, using 1 ml of solution.6. Elution of precipitated material. Spin down PAS. Add 100 µl of elution buffer, mix and incubate 10 min at 65°C. Spin down PAS and transfer supernatant to new tube. Add 150 µl of elution buffer 2 to PAS, mix, centrifuge at fµll speed and transfer eluate to a tube together with the eluate from the first centrifugation. The combined material is the "chromatin precipitate" (approx. 250 µl).7. Incubate precipitate 6 h (or overnight) at 65 C to reverse cross-links. Add 250 µl of Proteinase K solution, incubate at 50°C 2-3 h.8. Add 55 µl of 4M LiCl and 500 µl of phenol-chlorophorm. Mix and microfuge at fµll speed at RT. Transfer aqueous phase to a new tube and precipitate with 1 ml of 100% ethanol. Wash with 750 µl of 70% ethanol. Spin down and dry precipitate.9. Dissolve in 25 µl of water. This is the chromatin immunoprecipitate or ?Native ChIP? sample.
LM-PCR amplification of the native ChIP sample to obtain a sufficient quantity for further hybridization on microarrays.

tag: developmental stage

tag: Sex

value: Unknown


title: MEFs HMGN1 WT  rep 2

description: expression data from primary WT MEFs


title: MEFs HMGN5 knock out rep 2

description: expression data from primary KO MEFs


title: E12-16_CBP_1_1 extraction1_array1


title: E12-16_CBP_1_2 extraction2_array1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: CBP antibody;target name: nejire;host: Rabbit;antigen: MMADHLDEPPQKRVKMDPTDISYFLEENLPDELVSSNSGWSDQLTGGAGG GNGGGGASGVTTNPTSGPNPGGGPNKPAAQGPGSGTGGVGVGVNVGVGGV VGVGVVPSQMNGAGGGNGSGTGGDDGSGNGSGAGNRISQMQHQQLQHLLQ QQQQGQKGAMVVPGMQQLGSKSPNLQSPNQGGMQQVVGTQMGMVNSMPMS ISNNGNNGMNAIPGMNTIAQGNLGNMVLTNSVGGGMGGMVNHLKQQPGGG GGGMINSVSVPGGPGAGAGGVGAGGGGAVAANQGMHMQNGPMMGRMVGQQ HMLRGPHLMGASGGAGGPGNGPGGGGPRMQNPNMQMTQLNSLPYGVGQYG GPGGGNNPQQQQQQQQQQLLAQQMAQRGGVVPGMPQGNRPVGTVVPMSTL GGDGSGPAGQLVSGNPQQQQMLAQQQTGAMGPRPPQPNQLLGHPGQQQQQ QQQPGTSQQQQQQQGVGIGGAGVVANAGTVAGVPAVAGGGAGGAVQSSGP GGANRDVPDDRKRQIQQQLMLLLHAHKCNRRENLNPNREVCNVNYCKAMK SVLAHMGTCKQSKDCTMQHCASSRQILLHYKTCQNSGCVICYPFRQNHSV FQNANVPPGGGPAGIGGAPPGGGGAGGGAAGAGGNLQQQQQQQQQQQQNQ QPNLTGLVVDGKQGQQVAPGGGQNTAIVLPQQQGAGGAPGAPKTPADMVQ QLTQQQQQQQQQVHQQQVQQQELRRFDGMSQQVVAGGMQQQQQQGLPPVI RIQGAQPAVRVLGPGGPGGPSGPNVLPNDVNSLHQQQQQMLQQQQQQGQN RRRGGLATMVEQQQQHQQQQQQPNPAQLGGNIPAPLSVNVGGFGNTNFGG AAAGGAVGANDKQQLKVAQVHPQSHGVGAGGASAGAGASGGQVAAGSSVL MPADTTGSGNAGNPNQNAGGVAGGAGGGNGGNTGPPGDNEKDWRESVTAD LRNHLVHKLVQAIFPTSDPTTMQDKRMHNLVSYAEKVEKDMYEMAKSRSE YYHLLAEKIYKIQKELEEKRLKRKEQHQQMLMQQQGVANPVAGGAAGGAG SAAGVAGGVVLPQQQQQQQQQQQQQGQQPLQSCIHPSISPMGGVMPPQQL RPQGPPGILGQQTAAGLGVGVGVTNNMVTMRSHSPGGNMLALQQQQRMQF PQQQQQQPPGSGAGKMLVGPPGPSPGGMVVNPALSPYQTTNVLTSPVPGQ QQQQQFINANGGTGANPQLSEIMKQRHIHQQQQQQQQQQQQGMLLPQSPF SNSTPLQQQQQQQQQQQQQQQATSNSFSSPMQQQQQGQQQQQQKPGSVLN NMPPTPTSLEALNAGAGAPGTGGSASNVTVSAPSPSPGFLSNGPSIGTPS NNNNNSSANNNPPSVSSLMQQPLSNRPGTPPYIPASPVPATSASGLAASS TPASAAATCASSGSGSNSSSGATAAGASSTSSSSSAGSGTPLSSVSTPTS ATMATSSGGGGGGGGNAGGGSSTTPASNPLLLMSGGTAGGGTGATTTTST SSSSRMMSSSSSLSSQMAALEAAARDNDDETPSPSGENTNGSGGSGNAGG MASKGKLDSIKQDDDIKKEFMDDSCGGNNDSSQMDCSTGGGKGKNVNNDG TSMIKMEIKTEDGLDGEVKIKTEAMDVDEAGGSTAGEHHGEGGGGSGVGG GKDNINGAHDGGATGGAVDIKPKTETKPLVPEPLAPNAGDKKKKCQFNPE ELRTALLPTLEKLYRQEPESVPFRYPVDPQALGIPDYFEIVKKPMDLGTI RTNIQNGKYSDPWEYVDDVWLMFDNAWLYNRKTSRVYRYCTKLSEVFEAE IDPVMQALGYCCGRKYTFNPQVLCCYGKQLCTIPRDAKYYSYQNSLKEYG VASNRYTYCQKCFNDIQGDTVTLGDDPLQSQTQIKKDQFKEMKNDHLELE PFVNCQECGRKQHQICVLWLDSIWPGGFVCDNCLKKKNSKRKENKFNAKR LPTTKLGVYIETRVNNFLKKKEAGAGEVHIRVVSSSDKCVEVKPGMRRRF VEQGEMMNEFPYRAKALFAFEEVDGIDVCFFGMHVQEYGSECPAPNTRRV YIAYLDSVHFFRPRQYRTAVYHEILLGYMDYVKQLGYTMAHIWACPPSEG DDYIFHCHPTDQKIPKPKRLQEWYKKMLDKGMIERIIQDYKDILKQAMED KLGSAAELPYFEGDFWPNVLEESIKELDQEEEEKRKQAEAAEAAAAANLF SIEENEVSGDGKKKGQKKAKKSNKSKAAQRKNSKKSNEHQSGNDLSTKIY ATMEKHKEVFFVIRLHSAQSAASLAPIQDPDPLLTCDLMDGRDAFLTLAR DKHFEFSSLRRAQFSTLSMLYELHNQGQDKFVYTCNHCKTAVETRYHCTV CDDFDLCIVCKEKVGHQHKMEKLGFDIDDGSALADHKQANPQEARKQSIQ RCIQSLAHACQCRDANCRLPSCQKMKLVVQHTKNCKRKPNGGCPICKQLI ALCCYHAKNCEEQKCPVPFCPNIKHKLKQQQSQQKFQQQQLLRRRVALMS RTAAPAALQGPAAVSGPTVVSGGVPVVGMSGVAVSQQVIPGQAGILPPGA GGMSPSTVAVPSPVSGGAGAGGMGGMTSPHPHQPGIGMKPGGGHSPSPNV LQVVKQVQEEAARQQVSHGGGFGKGVPMAPPVMNRPMGGAGPNQNVVNQL GGMGVGVGGVGGVGVGGVGGVGVNQLNSGGGNTPGAPISGPGMNVNHLMS MDQWGGGGAGGGGANPGGGNPQARYANNTGGMRQPTHVMQTNLIPPQQQQ QMMGGLGGPNQLGGGQMPVGGQHGGMGMGMGAPPMAGTVGGVRPSPGAGG GGGSATGGGLNTQQLALIMQKIKNNPTNESNQHILAILKQNPQIMAAIIK QRQQSQNNAAAGGGAPGPGGALQQQQAGNGPQNPQQQQQQQQQQQVMQQQ QMQHMMNQQQGGGGPQQMNPNQQQQQQQVNLMQQQQQGGPGGPGSGLPTR MPNMPNALGMLQSLPPNMSPGVSTQGGMVPNQNWNKMRYMQMSQYPPPYP QRQRGPHMGGAGPGPGQQQFPGGGGGAGNFNAGGAGGAGGVVGVGGVPGG AGTVPGGDQYSMANAAAASNMLQQQQGQVGVGVGVGVKPGPGQQQQQMGV GMPPGMQQQQQQQQPLQQQQMMQVAMPNANAQNPSAVVGGPNAQVMGPPT PHSLQQQLMQSARSSPPIRSPQPTPSPRSAPSPRAAPSASPRAQPSPHHV MSSHSPAPQGPPHDGMHNHGMHHQSPLPGVPQDVGVGVGVGVGVGVNVNV GNVGVGNAGGALPDASDQLTKFVERL;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Mattias Mannervik's Lab;short description: Rabbit affinity purified antisera raised against the CBP protein. This is a gift from Mattias Mannervik's Lab.;


title: MEFs HMGN3 knock out rep 2

description: expression data from primary KO MEFs


title: MEFs HMGN5 WT  rep 1

description: expression data from primary WT MEFs


title: MEFs HMGN1 knock out rep 1

description: expression data from primary KO MEFs

value: HMGN1 knock out


title: MEFs HMGN1 WT  rep 3

description: expression data from primary WT MEFs


title: MEFs HMGN3 knock out rep 3

description: expression data from primary KO MEFs


title: MEFs HMGN3 WT  rep 1

description: expression data from primary WT MEFs


title: MEFs HMGN1 knock out rep 3

description: expression data from primary KO MEFs


title: MEFs HMGN3 WT  rep 3

description: expression data from primary WT MEFs


title: ChIP_STAT3_DU145_DMSO

status: Public on Dec 09 2010

city: Washington

first: Olga

middle: A

last: Timofeeva

state: DC

address: 3900 Reservoir Rd NW

department: Oncology

institute: Georgetown University Medical Center

description: STAT3 binding in DU145 cells biological replicas 1 and 2

hyb_protocol: 7.5μg of DNA was hybridzed per array using the Affymetrix hybridization kit  for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing:
Data was quantile normalized and analyzed with Partek Genomic Suite using MAT-based statistic algoriphm.
Bed files contain information about chromosome start and end position of STAT3-bound picks, numer of probes and lenth of region, p-value and MAT-score and Affy probe ID for corresponding transcript

source_name: STAT3 ChIP DNA from DU145 cells treated with DMSO

label_protocol: Samples were enzymatically fragmented and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments

growth_protocol: DU145 prostate cancer cell line was obtained from American Type Culture Collection. Cells were maintained in RPMI 1640 supplemented with 10% heat-inactivated FBS. Cell cultures were maintained at 37°C under a humidified atmosphere of 5% CO2 in an incubator.

extract_protocol: Chromatin has been prepared according the protocol for Enzymatic Magnetic ChIP assay from Cell Signaling Technology (http://www.cellsignal.com/support/protocols/chip_magnetic.html).

treatment_protocol: Cells were treated with ST3-Hel2A-2 or DMSO for 3 hr

tag: cell line

value: DU145 prostate cancer cell line

tag: agent

value: DMSO

tag: chip antibody

value: STAT3 antibody

tag: chip antibody vendor

value: Cell Signaling Technology

tag: chip antibody lot#

tag: chip antibody catalog#

source_name: IgG ChIP DNA from DU145 cells treated with DMSO

value: IgG antibody (control)


title: ChIP_STAT3_DU145_ST3

description: STAT3 binding in DU145 cells treated with ST3-Hel2A-2 biological replicas 1 and 2

source_name: STAT3 ChIP DNA from DU145 cells treated with ST3-Hel2A-2 inhibitor

source_name: IgG ChIP DNA from DU145 cells treated with ST3-Hel2A-2 inhibitor


title: PDL  stimulated by mechanical stress loading for 48h

status: Public on Dec 20 2010

city: Fukuoka

first: Hiroshi

last: Kajiya

address: 2-15-1 Tamura, Sawara-ku

department: Physiological Science and Molecular Biology

country: Japan

institute: Fukuoka Dental College

description: Gene expression data from human periodontal ligament cells, i.e. after stimulate by intermittent mechanical stress for 48h

hyb_protocol: GeneChips were washed, stained with streptavidin-phycoerythrin

scan_protocol: GeneChips were scanned using the affymetrix GeneChip Scanner.

data_processing: The data were analyzed with Affymetrix GeneChip Command Console and  Affymetrix Expression Console softwares using Affymetrix default analysis settings and global scaling as normalization.

source_name: human periodontal ligament cells

label_protocol: Biotinylated cRNA were prepared according to manufacturer's instructions from 15 ug total RNA using an Rneasy mini kit (QIAGEN K.K, Tokyo, Japan).

growth_protocol: Human periodontal ligament cells were obtained from third molars extracted from healthy donors. PDL cells were scraped off with a surgiical knife from the mid-third of each root.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Invitrogen, Carlsbad, CA, USA).

treatment_protocol: PDL cells were cultured in α-minimal essential medium containg 10% fetal bovine serum. after 4-8 passages, PDL were cultured in silicon rubber chmbers. Stimulated by intermittent mechanical stretch (Conditions:60 s/returns;resting time:29 s; stretch length: 1.6 mm; stretch ratio: 105%)

tag: tissue

value: human periodontal ligament cells

value: 20 years old


title: MEFs HMGN1 knock out rep 2

description: expression data from primary KO MEFs


title: OAT_iPS_12.4

description:
W2
Gene-targeted iPS cell line obtained following  transfection of gene-targeting vector in OAT iPS  cell line 12.

value: gyrate atrophy

value: iPS cell

tag: gender

value: female

value: normal health

value: H1 human ES cells

value: male

value: reference


title: DvH continuous culture at 24 hr retention timemin. DvH Mm co-culture lactate only FC36 FC38 FC44 Co-culture set1587

status: Public on Sep 16 2010

city: Berkeley

first: Adam

middle: P.

last: Arkin

state: CA

address: 1 Cyclotron Road

department: Physical Biosciences Division

institute: Virtual Institute for Microbial Stress and Survival

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Co-culture. This sample was treated with DvH + Mm co-culture + lactate only FC36, FC38, FC44  Co-culture.  Treatment time point = continuous culture at 24 hr retention time min.

hyb_protocol: He, Z., Wu, L., Li, X., Fields, M., and Zhou, J. 2005.  Empirical Establishment of Oligonucleotide Probe Design Criteria. Appl. Environ. Microbiol. 71:3753-3760.

scan_protocol: ImaGene software

data_processing: See Methods in: S. R. Chhabra, Q. He, K. H. Huang, S. P. Gaucher, E. J. Alm, Z. He, M. Z. Hadi, T. C. Hazen, J. D. Wall, J. Zhou, A. . Arkin, and A. K. Singh, Global Analysis of Heat Shock Response in Desulfovibrio vulgaris Hildenborough, J Bacteriol. 2006 March; 188(5): 1817-1828. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16484192.  The expression level for each spot was calculated from the ratio of mRNA over genomic DNA.  To estimate the differential gene expression between the control and treatment conditions, normalized log ratios were calculated. Each log ratio was calculated as log2(treatment) - log2(control). This log ratio was normalized using LOWESS (locally weighted scatterplot smoothing) on the difference versus the sum of the log expression level.

label: Cy5, Cy3

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, continuous culture at 24 hr retention timemin. DvH + Mm co-culture + lactate only FC36, FC38, FC44  Co-culture

growth_protocol: Three replicates of D. vulgaris cocultured with a hydrogenotrophic methanogen were grown in a minimal salts media containing 30 mM lactate (CCM).  These biological replicates represented the treatment condition.  Similarly, three continuously grown D. vulgaris monocultures grown on CCM, but amended with 10 mM sulfate, were generated as control cultures.  All cultures were grown in a bioreactor under continuous culture conditions with a 90% N2:10% CO2 headspace.  Biomass (2 L cultures) for each sample of three replicates was harvested during continuous culture after 3 retention periods of approximately 24 hours each (ca. 0.27 OD600).  Cells were harvested using an ice-chilled sterile stainless steel tube connected to the chemostat medium exhaust line.  Culture fluid was transferred to Falcon tubes (50 ml) that had been stored in an anoxic chamber and pre-chilled on ice.  The tubes were centrifuged for 15 min at 3,220 g at 4 C.  After centrifugation, the supernatant was poured off and tubes immediately frozen at -80 C.

treatment_protocol: continuous culture at 24 hr retention timemin. DvH + Mm co-culture + lactate only FC36, FC38, FC44  Co-culture.

value: Hildenborough

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, sulfur-limited DvH mono-culture: FC40, FC41, FC47


title: Escherichia coli O157:H7 EDL933 Inside Acanthamoeba vs. Control Slide 1

status: Public on Dec 01 2010

city: Ames

first: Chris

last: Minion

state: IA

address: 1130 Vet Med

department: VMPM

institute: Iowa State University

description: To better understand the impact of intracellular carriage of E. coli O157:H7 within a ruminant protozoa, global transcript levels of strain EDL933 cells grown under within Acanthamoeba were compared to cells grown in ATCC PYG712 using microarrays.

hyb_protocol: From each paired sample, 1.5 μg of labeled cDNA was combined, dried-down, resuspended in 60 μl Pronto! cDNA/long oligonucleotide hybridization solution (Corning), incubated at 95°C for 5 min and centrifuged at 13,000 × g for 2 min at room temperature. This solution was then pipetted on a freshly pre-hybridized microarray slide, covered with a 22 x 60 mm HybriSlip (Grace Bio Labs, Bend, OR), placed in a Corning hybridization chamber, and incubated in a 42°C water bath for 12 to 16 h. Array pre-hybridization was conducted using sodium borohydride as previously described (Raghavachari, et al., 2003). Slides were washed according to Corning’s UltraGAPS protocol and dried by centrifugation.

scan_protocol: Scanning, image segmentation, and normalization were conducted as previously described (Madsen, et al., 2006).

data_processing: Mixed model analysis was conducted as previously described (Madsen, et al., 2006) excluding slide region and slide-by-region interaction effects. The value column was not used for analysis or in publication. The normalized values for duplicate spots were averaged within each array to produce one normalized measure of expression for each of the probe sequences and each of the RNA samples. [mean log transformed median centered lowess normalized signal intensity]

organism: Escherichia coli

label_protocol: Targets were generated from 10 µg of DNase treated total RNA as follows. Ten µg of total RNA was combined with 1 μl of 10 µg/μl random hexamers (Integrated DNA Technologies) and ddH20 was added to bring the total reaction volume to 15.5 μl. Samples were incubated at 70°C for 10 min followed by 10 min incubation on ice. After incubation, 14.5 μl of a reaction mix (6 μl of 5x First Strand Buffer, 1.2 μl of 25x aa-dUTP/dNTP mix (Fermentas, Glen Burnie, MD), 3 μl 0.1M DTT, 2 μl Superscript III 200U/ μl (Invitrogen Corp., Carlsbad, CA), 2.4 μl RNase-free water) was added and reactions were incubated at 42°C for at least 2 hrs. After incubation, RNA was immediately hydrolyzed by incubation with 3 μl 0.1 M ETDA and 3.5 μl 0.1 M NaOH at 65°C for 10 min. The pH was neutralized with the addition of 36.5 μl of 500 mM HEPES (pH 7.0). Reactions were purified using the Mo Bio UltraClean PCR Clean-Up Kit (MO BIO Laboratories, Inc., Carlsbad, CA), quantified using the ND-1000 spectrophotometer, dried-down, and resuspended in 10 μl RNase-free water and 1.5 μl sodium bicarbonate (pH 8.7). After 10 min, 6 μl of Cy 3 (catalog number PA25001) or Cy 5 (catalog number PA23001) (GE Healthcare, Piscataway, NJ) were added according the microarray experimental design, and samples were incubated at room temperature for 3 h. Dyes were prepared by resuspending a single tube of dye in 72 μl of DMSO and storing in 6 μl aliquots at -70°C until use. Dye coupled reactions were purified in the same manner as cDNA synthesis reactions. Frequency of dye incorporation and yield was determined using the ND-1000 spectrophotometer.

extract_protocol: RNA was isolated from samples using the RNeasy Mini Kit (Qiagen). Prior to lysis all samples were incubated for 30 min on ice in RNA stop solution (0.1% SDS, 1% Acidic phenol, 19% ethanol, ice cold). The lysis and digestion protocol was followed with two 50 μl ddH20 elutions. Each sample was treated with 2 μl of DNase (Ambion, Austin, TX) at 37°C for 30 min. Samples were purified and concentrated using Microcon YM-30 columns (Millipore, Billerica, MA), and the quantity and purity were determined using an ND-1000 spectrophotometer (Nanodrop, Wilmington, DE). Samples were determined to be free of contaminating genomic DNA by absence of a band on a DNA electrophoresis gel after 30 rounds of PCR.

tag: growth condition

value: Inside Acanthamoeba

source_name: Escherichia coli O157:H7 EDL933 Outside Control

value: Outside Control


title: OsMKK4DD DEX 12h 2

status: Public on Jul 30 2010

city: Tsukuba

first: Hirohiko

last: Hirochika

state: Ibaraki

address: 2-1-2 Kannondai

department: Division of Genome and Biodiversity Research

institute: National Institute of Agrobiological Sciences

description: 400 ng RNAs were labeled and 825ng of Cy3- and Cy5-labeled cRNAs were used.

hyb_protocol: Cy3-labelled cRNA and Cy5-labelled cRNA (825ng each) were mixed, fragmented and hybridized with the rice 4x44K microarray RAP-DB (G2519F#15241) for 17 hours at 65°C using the Agilent Gene Expression Hybridization kit.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities.

organism: Oryza sativa

source_name: OsMKK4DD DEX 12h 2

label_protocol: Labeled cRNA was prepared from 400 ng RNA using the Low RNA Input Linear Amplification/Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Calli of O. sativa L. cv. Nipponbare were generated from seed scutellum and suspension-cultured at 25˚C in N6D liquid medium and subcultured in fresh medium every 7 days. For DEX treatment, suspension cell cultures were subcultured for 3 days in a fresh medium.

extract_protocol: RNA was prepared using the Isogen (Nippongene) and RNeasy Plant Mini kit (Qiagen) following the manufacturer's recommendations. The protocol includes an on-column DNase digestion. RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Suspension cells were treated with Dexamethasone (DEX) (10 micro molar) and harvested at indicated times.

tag: protocol

value: suspension cell culture

value: Dex

tag: time

value: 12 hr

tag: cultivar

value: Nipponbare

value: callus of the DEX inducible OsMKK4DD line

source_name: Vector control DEX 12h 2

value: callus of the vector control line


title: OsMKK4DD DEX 2h 3

source_name: OsMKK4DD DEX 2h 3

tag: treatment

value: 2 hr

source_name: Vector control DEX 2h 3


title: OsMKK4WT DEX 2h 2

source_name: OsMKK4WT DEX 2h 2

value: callus of the DEX inducible OsMKK4WT line

source_name: Vector control DEX 2h 2


title: OsMKK4DD DEX 12h 1 color swap

source_name: Vector control DEX 12h 1

source_name: OsMKK4DD DEX 12h 1


title: OsMKK4DD DEX 6h 3

source_name: OsMKK4DD DEX 6h 3

value: 6 hr

source_name: Vector control DEX 6h 3


title: OsMKK4DD DEX 12h 3

source_name: OsMKK4DD DEX 12h 3

source_name: Vector control DEX 12h 3


title: OsMKK4WT DEX 12h 3

source_name: OsMKK4WT DEX 12h 3


title: OsMKK4WT DEX 0h 2

source_name: OsMKK4WT DEX 0h 2

value: control

value: 0 hr

source_name: Vector control DEX 0h 2


title: OsMKK4WT DEX 2h 3

source_name: OsMKK4WT DEX 2h 3


title: OsMKK4WT DEX 6h 1

source_name: OsMKK4WT DEX 6h 1

source_name: Vector control DEX 6h 1


title: OsMKK4DD DEX 0h 3

source_name: OsMKK4DD DEX 0h 3

source_name: Vector control DEX 0h 3


title: OsMKK4WT DEX 6h 3

source_name: OsMKK4WT DEX 6h 3


title: OsMKK4DD DEX 12h 1

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities.


title: OsMKK4DD DEX 2h 1

source_name: OsMKK4DD DEX 2h 1

source_name: Vector control DEX 2h 1


title: OsMKK4WT DEX 0h 3

source_name: OsMKK4WT DEX 0h 3


title: OsMKK4DD DEX 6h 2

source_name: OsMKK4DD DEX 6h 2

source_name: Vector control DEX 6h 2


title: OsMKK4WT DEX 12h 2

source_name: OsMKK4WT DEX 12h 2

source_name: Vector control DEX 12h 2


title: OsMKK4WT DEX 12h 1

source_name: OsMKK4WT DEX 12h 1

source_name: Vector control DEX 12h 1


title: OsMKK4DD DEX 0h 2

source_name: OsMKK4DD DEX 0h 2


title: OsMKK4WT DEX 6h 2

source_name: OsMKK4WT DEX 6h 2


title: OsMKK4DD DEX 6h 1

source_name: OsMKK4DD DEX 6h 1


title: H3K79me2 ChIP replicate 2 [ChIP]

status: Public on Oct 01 2010

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description: H3K79me2 ChIP untreated Kc167 cells

hyb_protocol: 13 µg labeled DNA per, 2.4 µl alignment oligo and 24 µl NimbleGen hybridiziation component A and 1x hybridization buffer in a total volume of 120 µl were heated to 98°C for 5 min and hybridized in a TECAN hybridization station for 16 hrs. at 42°C. Slides were washed sequentially with NimbleGen wash buffers I, II and III with 0.1 mM DTT at 42°C, 25°C, and 23°C, respectively.

scan_protocol: Microarrays were scanned in a DNA Microarray Scanner (Model G2505B, Serial number US22502518) from Agilent Technologies, which uses Scan Control software (Version A.6.11). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were scanned at multiple PMT (100/70/30/10%) for each channel at 5 um resolution using a suitable scan area.

data_processing: Scans were processed with NimbleScan 2.3 using standard settings. Values of all reporters except NimbleGen control reporters were extracted from pair files and represented as log2-ratios, normalized using the the loess() function in R with parameter control=loess.control(trace.hat='approximate') and then median centered. All four scan intensities were processed in that way, and the highest intensity not suffering from overt saturation in either replicate was retained and used for further analyses.

source_name: Embryonic Drosophila cells, Kc167 cells, ChIP fraction

label_protocol: 1 µg purified methyl-PCR or ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy dye-coupled nonamers (Trilink Biotech) according to NimbleGen Sample Labeling protocol in NimbleGen Array User's Guide, v4.1 (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C.

extract_protocol: For DamID samples, sample extraction was performed as described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003). All ChIP experiments and the subsequent linear amplification reactions were performed as described in Kind, J. et al., Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila. Cell 133, 813-828, 2008.

value: anti-H3K79me2 (Schuebeler D. et al., Genes Dev 18, 1263-1271, 2004)

source_name: Embryonic Drosophila cells, Kc167 cells, input

value: none (input chromatin)


title: OsMKK4DD DEX 2h 2

source_name: OsMKK4DD DEX 2h 2

source_name: Vector control DEX 2h 2


title: OsMKK4DD DEX 0h 1

source_name: OsMKK4DD DEX 0h 1

source_name: Vector control DEX 0h 1


title: OsMKK4DD DEX 0h 1 color swap


title: OsMKK4WT DEX 2h 1

scan_protocol: Agilent scanner model G2505B, software G2565BA

source_name: OsMKK4WT DEX2h 1

source_name: Vector control DEX 2h 1


title: OsMKK4WT DEX0h 1

source_name: OsMKK4WT DEX0h 1

source_name: Vector control DEX0h 1


title: Run5.aUa.010110d.SkmDbt2447D.CEL-DB basal

status: Public on Jun 16 2010

city: Birmingham

first: Jelai

last: Wang

state: AL

address: 1665 University Blvd, Ryals 327

department: Biostatistics

institute: University of Alabama at Birmingham

hyb_protocol: The labeled cRNA were hybridized for 16 h at 45C on Affymetrix Hu95A chip. Affymetrix chips were washed and then stained with a streptavidin-phycoerythrin conjugate.

scan_protocol: The arrays were scanned at a resolution of 3mm, using a specifically design confocal scanner (Affymetrix).

data_processing: The data were normalized  by using quantile normalization and then obtained the probe set intensity using RMA or MAS5 as implemented in the affy package in Bioconductor. The present/absent calls for each probe set were generated based on Wilcoxon signed rank test using the mass5call function in the affy package.

source_name: human skeletal muscle from diabetic individuals before insulin therapy

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

growth_protocol: human skeletal muscle collected from 20 insulin sensitive, 20 insulin resistant, and 15 diabetic individuals

extract_protocol: Total RNA was extracted by Ultraspec RNA isolation Kit from Biotecx Laboratories, Inc according to the manufacturer's instructions.

treatment_protocol: regular insulin (Humulin, Eli Lily & Co., Indianapolis, IN) at a constant rate of 200 mU/m2/min

value: skeletal muscle

tag: status

value: diabetic

value: untreated


title: Run5.aUa.010110d.SkmDbt1961D.CEL-DB basal


title: Run5.aUa.010110d.SkmDbt2448D.CEL-DB stimulate

source_name: human skeletal muscle from diabetic individuals after insulin therapy

value: insulin


title: Run5.aUa.010110d.SkmDbt1962D.CEL-DB stimulate


title: Run5.aUa.010110d.SkMDbt1153D.CEL-DB stimulate


title: Run5.aUa.010110d.SkmDbt1960D.CEL-DB stimulate


title: Run4.aUa.010110d.SkMDbt1150D.CEL-DB basal


title: Run5.aUa.010110d.SkMDbt1152D.CEL-DB basal


title: Run5.aUa.010110d.SkMDbt1151D.CEL-DB stimulate


title: Run7.aUa.010110d.SkMDbt1155D.CEL-DB stimulate


title: Run5.aUa.010110d.SkmDbt1959D.CEL-DB basal


title: Run5.aUa.010110d.SkMDbt1154D.CEL-DB basal


title: Run4.aUa.010110d.SkMDbt1147D.CEL-DB stimulate


title: Run4.aUa.010110d.SkMDbt1148D.CEL-DB basal


title: Run4.aUa.010110d.SkMDbt1144D.CEL-DB basal


title: Run4.aUa.010110d.SkMDbt1146D.CEL-DB basal


title: Run4.aUa.010110d.SkMDbt1141D.CEL-DB stimulate


title: Run4.aUa.010110d.SkMDbt1149D.CEL-DB stimulate


title: Run3.aUa.010110d.SkMDbt1137D.CEL-DB stimulate


title: Run3.aUa.010110d.SkMDbt1139D.CEL-DB stimulate


title: Run3.aUa.010110d.SkMDbt1136D.CEL-DB basal


title: Run3.aUa.010110d.SkMDbt1138D.CEL-DB basal


title: Run4.aUa.010110d.SkMDbt1142D.CEL-DB basal


title: Run4.aUa.010110d.SkMDbt1145D.CEL-DB stimulate


title: Run4.aUa.010110d.SkMDbt1143D.CEL-DB stimulate


title: Run3.aUa.010110d.SkMDbt1140D.CEL-DB basal


title: Run3.aUa.010110d.SkMDbt1135D.CEL-DB stimulate


title: Run3.aUa.010110d.SkMDbt1134D.CEL-DB basal


title: H3K79me2 ChIP replicate 1 [ChIP]

description: H3K79me2 ChIP untreated Kc167 cells


title: Run3.aUa.010110d.SkMDbt1133D.CEL-DB stimulate


title: Run7.aUa.010110d.SkMInR1131D.CEL-IR stimulate

source_name: human skeletal muscle from insulin resistant individuals after insulin therapy

value: insulin resistant


title: Run7.aUa.010110d.SkMDbt1132D.CEL-DB basal


title: Run6.aUa.010110d.SkMInR1128D.CEL-IR basal

source_name: human skeletal muscle from insulin resistant individuals before insulin therapy

tag: meanrqa

tag: choa

tag: fata

tag: eea

tag: wtkg

tag: perfat

tag: lbm


title: Run6.aUa.010110d.SkMInR1127D.CEL-IR stimulate

tag: agent


title: Run6.aUa.010110d.SkMInR1126D.CEL-IR basal


title: Run6.aUa.010110d.SkMInR1125D.CEL-IR stimulate


title: Run6.aUa.010110d.SkMInR1123D.CEL-IR stimulate


title: Run5.aUa.010110d.SkMInR1120D.CEL-IR basal


title: Run6.aUa.010110d.SkMInR1121D.CEL-IR stimulate


title: Run6.aUa.010110d.SkMInR1129D.CEL-IR stimulate


title: Run6.aUa.010110d.SkMInR1122D.CEL-IR basal


title: Run5.aUa.010110d.SkMInR1118D.CEL-IR basal


title: Run6.aUa.010110d.SkMInR1130D.CEL-IR basal


title: Run5.aUa.010110d.SkMInR1117D.CEL-IR stimulate


title: Run5.aUa.010110d.SkMInR1115D.CEL-IR stimulate


title: Run5.aUa.010110d.SkMInR1113D.CEL-IR stimulate


title: Run2.aUa.001206d.SkMInR1106D.CEL-IR basal


title: Run2.aUa.001206d.SkMInR1105D.CEL-IR stimulate


title: Run7.aUa.001206d.SkMInR1107D.CEL-IR stimulate


title: Run6.aUa.010110d.SkMInR1124D.CEL-IR basal


title: Run5.aUa.010110d.SkMInR1109D.CEL-IR stimulate


title: Run5.aUa.010110d.SkMInR1114D.CEL-IR basal


title: Run2.aUa.001206d.SkMInR1104D.CEL-IR basal


title: Run5.aUa.010110d.SkMInR1111D.CEL-IR stimulate


title: Run7.aUa.010110d.SkMInR1108D.CEL-IR basal


title: Run2.aUa.001206d.SkMInR1103D.CEL-IR stimulate


title: Run5.aUa.010110d.SkMInR1119D.CEL-IR stimulate


title: Run5.aUa.010110d.SkMInR1116D.CEL-IR basal


title: Run5.aUa.010110d.SkMInR1112D.CEL-IR basal


title: Run7.aUa.010110d.SkMInR1102D.CEL-IR basal


title: Run2.aUa.001206d.SkMInR1094D.CEL-IR basal


title: Run2.aUa.001206d.SkMInR1097D.CEL-IR stimulate


title: Run2.aUa.001206d.SkMInR1096D.CEL-IR basal


title: Run2.aUa.001206d.SkMInR1095D.CEL-IR stimulate


title: Run2.aUa.001206d.SkMInR1098D.CEL-IR basal


title: Run2.aUa.001206d.SkMInR1099D.CEL-IR stimulate


title: Run2.aUa.001206d.SkMInR1093D.CEL-IR stimulate


title: Run7.aUa.001206d.SkMInS1091D.CEL-IS stimulate

source_name: human skeletal muscle from insulin sensitive individuals after insulin therapy

value: insulin sensitive


title: Run5.aUa.010110d.SkMInR1110D.CEL-IR basal


title: Run7.aUa.001206d.SkMInR1101D.CEL-IR stimulate


title: Run7.aUa.001206d.SkMInR1092D.CEL-IR basal


title: Run2.aUa.001206d.SkMInS1088D.CEL-IS basal

source_name: human skeletal muscle from insulin sensitive individuals before insulin therapy


title: Run2.aUa.001206d.SkMInR1100D.CEL-IR basal


title: Run2.aUa.001206d.SkMInS1089D.CEL-IS stimulate


title: Run7.aUa.001206d.SkMInS1083D.CEL-IS stimulate


title: Run8.aUa.010615d.SkMInS1084D.CEL-IS basal


title: Run2.aUa.001206d.SkMInS1087D.CEL-IS stimulate


title: Run7.aUa.001206d.SkMInS1085D.CEL-IS stimulate


title: Run7.aUa.001206d.SkMInS1081D.CEL-IS stimulate


title: Run8.aUa.010615d.SkMInS1078D.CEL-IS basal


title: Run2.aUa.001206d.SkMInS1090D.CEL-IS basal


title: Run7.aUa.001206d.SkMInS1079D.CEL-IS stimulate


title: Run7.aUa.001206d.SkMInS1077D.CEL-IS stimulate


title: Run8.aUa.010615d.SkMInS1082D.CEL-IS basal


title: Run8.aUa.010615d.SkMInS1080D.CEL-IS basal


title: Run7.aUa.001206d.SkMInS1073D.CEL-IS stimulate


title: Run7.aUa.001206d.SkMInS1075D.CEL-IS stimulate


title: Run8.aUa.010615d.SkMInS1074D.CEL-IS basal


title: Run8.aUa.010615d.SkMInS1086D.CEL-IS basal


title: Run8.aUa.010615d.SkMInS1076D.CEL-IS basal


title: Run7.aUa.001206d.SkMInS1072D.CEL-IS basal

tag: meanrqa:

tag: choa:

tag: fata:

tag: eea:


title: Run1.a10a.000609jd.2.SkMNor914.CEL-IS stimulate

tag: tissue


title: Run1.a10a.000609jd.2.SkMNor913.CEL-IS basal


title: Run1.a10a.000609jd.2.SkMNor909.CEL-IS basal


title: Run1.a10a.000608jd.2.SkMNor925.CEL-IS basal


title: Run1.a10a.000608jd.2.SkMNor926.CEL-IS stimulate


title: Run1.a10a.000608jd.2.SkMNor923.CEL-IS basal


title: Run1.a10a.000607jd.2.SkMNor920.CEL-IS stimulate


title: Run1.a10a.000607jd.2.SkMNor919.CEL-IS basal


title: Run1.a10a.000607jd.2.SkMNor921.CEL-IS basal


title: Run1.a10a.000607jd.2.SkMNor918.CEL-IS stimulate


title: Run1.a10a.000606jd.2.SkMNor912.CEL-IS stimulate


title: Run1.a10a.000607jd.2.SkMNor916.CEL-IS stimulate


title: Run1.a10a.000607jd.2.SkMNor915.CEL-IS basal


title: a10a.000606jd.2.SkMNor911.CEL-IS basal

tag: lbm:


title: Run1.a10a.000607jd.2.SkMNor917.CEL-IS basal


title: a10a.000606jd.2.SkMNor908.CEL-IS stimulate


title: a10a.000606jd.2.SkMNor907.CEL-IS basal


title: Run1.a10a.000608jd.2.SkMNor924.CEL-IS stimulate


title: Run1.a10a.000607jd.2.SkMNor922.CEL-IS stimulate


title: Primary medulloblastoma  MDT-MB-48 MB90

status: Public on Apr 02 2010

city: HEIDELBERG

first: Paul

middle: A.

last: Northcott

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center (DKFZ)

hyb_protocol: As directed by the manufacturer.

scan_protocol: As directed by the manufacturer.

data_processing:
Affymetrix CEL files were imported into Affymetrix Expression Console (Version 1.1) and gene-level analysis (FULL content) was performed.  Arrays were quantile normalized (sketch) and summarized using PLIER with PM-GCBG background correction.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.full.mps

source_name: Primary medulloblastoma

label_protocol: As directed by the manufacturer.

extract_protocol: Trizol method as directed by the manufacturer.

value: Primary medulloblastoma

tag: age

tag: gender

value: M

tag: histological subtype

value: Classic

tag: molecular subgroup

value: GroupC


title: Primary medulloblastoma  MDT-MB-49 MB90

value: GroupD


title: Primary medulloblastoma  MDT-MB-9 MB90


title: Primary medulloblastoma  MDT-MB-7 MB90

value: SHH


title: Primary medulloblastoma  MDT-MB-45 MB90


title: Primary medulloblastoma  MDT-MB-8 MB90

value: Large cell anaplastic


title: Comparison between ventral striati from food-restricted weight-matched animals and tumor-bearing rats

status: Public on Apr 10 2010

city: Bordeaux

first: Jan Pieter

last: Konsman

address: 146, rue Léo Saignat

country: France

institute: CNRS

description: Comparison between food-restricted weight-matched animals and tumor-bearing rats

hyb_protocol: Agilent oligo microarray hybridation protocol

scan_protocol: Dual-laser microarray scanner agilent technologies, 10µm resolution, 100% PMT

data_processing: Agilent Feature-extraction software version A.7.5.1. Spot analysis method using Cookie Cutter, pixel outlier rejection based on IQR, non-uniformity outlier flagging on, population outlier flagging on, no background subtraction, spatial detrend on, normalization feature selection by using rank consistency filter, normalization method linear and LOWESS, multiplicative errors of 0.15 for red and 0.25 for green, additive errors of 20 for both channels.

source_name: Tumor-bearing rats

label_protocol: Total RNA extracts from individual animals were purified (RNeasy MinElute Cleanup kit, Qiagen, Courtaboeuf, France) and treated with DNaseI (Ambion, Austin, TX, USA), after which 2.0 μg of purified RNA were retrotranscribed to double stranded cDNA. A pool of cDNA for each experimental group containing an equal amount of cDNA of each individual was used for in vitro transcription to yield multiple copies of amino-allyl-modified antisense RNA (aRNA) using amino-allyl-labeled UTP (Ambion, Austin, TX, USA). Subsequently, aimine groups of the fluorescent Cy3 or Cy5 dyes (Amersham Biosciences, GE Healthcare, Munich, Germany ) were coupled to the a RNA amino allyl groups following manufacturer’s instructions.

extract_protocol: RNA was extracted using 500 ul Trizol following manufacturer’s protocol (Invitrogen, Carlsblad, CA, USA)

treatment_protocol: Subcutaneous injection between scapulae with ten million Morris hepatoma 7777 cells. Tumor-bearing rats had ad libitum access to food.

tag: sample type

value: Ventral striatum of 160-230g Buffalo rats

value: ventral striatum

tag: strain

value: Buffalo

source_name: Food-restricted weight-matched animals

treatment_protocol: When the difference in body weight gain between ad libitum fed tumor-bearing rats and PBS-injected animals reached 10%, eight rats were subjected to a 33% food restriction until they reached the same body weight as the former.


title: Primary medulloblastoma  MDT-MB-199 MB90


title: Primary medulloblastoma  MDT-MB-5 MB90

value: F


title: Primary medulloblastoma  MDT-MB-203 MB90


title: Primary medulloblastoma  MDT-MB-29 MB90


title: Primary medulloblastoma  MDT-MB-193 MB90

value: Desmoplastic


title: Primary medulloblastoma  MDT-MB-198 MB90


title: Primary medulloblastoma  MDT-MB-3 MB90


title: Primary medulloblastoma  MDT-MB-188 MB90


title: Primary medulloblastoma  MDT-MB-6 MB90


title: Primary medulloblastoma  MDT-MB-195 MB90


title: Primary medulloblastoma  MDT-MB-211 MB90


title: Primary medulloblastoma  MDT-MB-194 MB90


title: Primary medulloblastoma  MDT-MB-189 MB90


title: Primary medulloblastoma  MDT-MB-26 MB90


title: Primary medulloblastoma  MDT-MB-207 MB90


title: Primary medulloblastoma  MDT-MB-196 MB90


title: Primary medulloblastoma  MDT-MB-205 MB90

value: MBEN


title: Primary medulloblastoma  MDT-MB-184 MB90


title: Primary medulloblastoma  MDT-MB-18 MB90

value: WNT


title: Primary medulloblastoma  MDT-MB-4 MB90


title: Primary medulloblastoma  MDT-MB-44 MB90


title: Run1.a10a.000609jd.2.SkMNor910.CEL-IS stimulate

value: skeletal muscle

tag: status

value: insulin


title: Primary medulloblastoma  MDT-MB-179 MB90


title: Primary medulloblastoma  MDT-MB-180 MB90


title: Primary medulloblastoma  MDT-MB-174 MB90


title: Primary medulloblastoma  MDT-MB-178 MB90


title: Primary medulloblastoma  MDT-MB-177 MB90


title: Primary medulloblastoma  MDT-MB-176 MB90


title: Primary medulloblastoma  MDT-MB-164 MB90


title: Primary medulloblastoma  MDT-MB-17 MB90


title: Primary medulloblastoma  MDT-MB-173 MB90


title: Primary medulloblastoma  MDT-MB-162 MB90


title: Primary medulloblastoma  MDT-MB-182 MB90


title: Primary medulloblastoma  MDT-MB-166 MB90


title: Primary medulloblastoma  MDT-MB-158 MB90


title: Primary medulloblastoma  MDT-MB-160 MB90


title: Primary medulloblastoma  MDT-MB-163 MB90


title: Primary medulloblastoma  MDT-MB-165 MB90


title: Primary medulloblastoma  MDT-MB-168 MB90


title: Primary medulloblastoma  MDT-MB-161 MB90


title: Primary medulloblastoma  MDT-MB-154 MB90


title: Primary medulloblastoma  MDT-MB-153 MB90


title: Primary medulloblastoma  MDT-MB-16 MB90


title: Primary medulloblastoma  MDT-MB-156 MB90


title: Primary medulloblastoma  MDT-MB-157 MB90


title: Primary medulloblastoma  MDT-MB-172 MB90


title: Primary medulloblastoma  MDT-MB-155 MB90


title: Primary medulloblastoma  MDT-MB-152 MB90


title: Primary medulloblastoma  MDT-MB-150 MB90


title: Primary medulloblastoma  MDT-MB-181 MB90


title: Primary medulloblastoma  MDT-MB-151 MB90


title: Primary medulloblastoma  MDT-MB-167 MB90


title: Primary medulloblastoma  MDT-MB-147 MB90


title: Primary medulloblastoma  MDT-MB-15 MB90


title: Primary medulloblastoma  MDT-MB-14 MB90


title: Primary medulloblastoma  MDT-MB-141 MB90


title: Primary medulloblastoma  MDT-MB-135 MB90


title: Primary medulloblastoma  MDT-MB-145 MB90


title: Primary medulloblastoma  MDT-MB-134 MB90


title: Primary medulloblastoma  MDT-MB-139 MB90


title: Primary medulloblastoma  MDT-MB-146 MB90


title: Primary medulloblastoma  MDT-MB-133 MB90


title: Primary medulloblastoma  MDT-MB-129 MB90


title: Primary medulloblastoma  MDT-MB-130 MB90


title: Primary medulloblastoma  MDT-MB-128 MB90


title: Primary medulloblastoma  MDT-MB-125 MB90


title: Primary medulloblastoma  MDT-MB-103 MB90


title: Primary medulloblastoma  MDT-MB-122 MB90


title: Primary medulloblastoma  MDT-MB-106 MB90


title: Pool16

status: Public on Mar 01 2010

city: Ann Arbor

first: Jun

state: MI

address: 5789A Medical Science II, Box 5618

institute: University of Michigan

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in R

source_name: hypothalamus

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocols.

tag: genotype

tag: fasting

value: No

tag: pool

tag: sample id

value: HD


title: Pool13

description: replicate 1

value: wild-type

value: GW


title: Pool15

description: replicate 1

value: HW


title: Pool14

description: replicate 1

value: GD


title: Primary medulloblastoma  MDT-MB-108 MB90

value: Primary medulloblastoma

value: SHH


title: Primary medulloblastoma  MDT-MB-11 MB90

value: Classic


title: Primary medulloblastoma  MDT-MB-101 MB90

value: M

value: GroupC


title: Primary medulloblastoma  MDT-MB-119 MB90

value: F

value: GroupD


title: Pool12

description: replicate 1

value: FD


title: Primary medulloblastoma  MDT-MB-123 MB90


title: Primary medulloblastoma  MDT-MB-127 MB90


title: Primary medulloblastoma  MDT-MB-13 MB90

value: Desmoplastic


title: Primary medulloblastoma  MDT-MB-132 MB90


title: Pool11

description: replicate 1

value: FW


title: Primary medulloblastoma  MDT-MB-121 MB90


title: Primary medulloblastoma  MDT-MB-138 MB90


title: Pool10

description: replicate 1

value: ED


title: Primary medulloblastoma  MDT-MB-124 MB90


title: Primary medulloblastoma  MDT-MB-107 MB90


title: Pool8

description: replicate 1

value: Yes

value: DD


title: MP-apc blocking apc

status: Public on Feb 28 2010

city: Liverpool

first: Margarita

last: Perez-Casal

state: Merseyside

address: Daulby Street

department: Haematology

country: United Kingdom

institute: Royal Liverpool University Hospital

description: Comparing gene profile of cells on baseline gene expression and different treatments with APC and APC-generated MPs.

hyb_protocol: As per manufacturer's instructions.

scan_protocol: Digital imager Fuji.

data_processing: Data was normalised with the median value of each array and the background was removed on a local basis.

label: Biotin

source_name: huvec

label_protocol: Ampolabeling-kit from Superarray using 0.5ug RNA.

growth_protocol: Cells were cultured in Iscove's modified medium with 20% FCS, supplemented with Glutamine, Pen-Strep and EGF. Grown at 37C, 5% CO2 and media changed every 3 days.

extract_protocol: RNEasy Mini Kit from QIAGEN.

treatment_protocol: Cells were serum-straved overnight and then treated with serum-free medium for 4h prior to cell lysis and RNA extraction.

tag: passage 3 confluent


title: Pool7

description: replicate 1

value: wild-type

value: DW


title: Primary medulloblastoma  MDT-MB-1 MB90


title: APC-mp par1 blocking


title: apc-MP

tag: huvec passage 3, confluent


title: apc blocking

tag: passage 3, confluent cells


title: Pool6

description: replicate 1

value: No

value: CD


title: Pool2

description: replicate 1

value: AD


title: par1 blocking

tag: huvec passage 3 confluent


title: Pool1

description: replicate 1

value: AW


title: apc-treated cells

tag: passage 3 confluent cells


title: Pool3

description: replicate 1

value: BW


title: Pool4

description: replicate 1

value: BD


title: Pool5

description: replicate 1

value: CW


title: Primary medulloblastoma  MDT-MB-136 MB90

tag: tissue

value: Primary medulloblastoma

value: F

value: SHH


title: Primary medulloblastoma  MDT-MB-105 MB90

tag: age

value: Desmoplastic


title: In vitro APC-MP array results

source_name: HUVEC

tag: HUVEC on passage 3, 90-100% confluent.


title: Primary medulloblastoma  MDT-MB-118 MB90

tag: gender

value: M

tag: histological subtype

value: Large cell anaplastic


title: Pool9

description: replicate 1

value: EW


title: N_M43_?_04

status: Public on Jan 28 2010

city: Houston

first: Mario

last: Sirito

address: 1515 Holcombe blvd

department: Cancer Genetics

institute: M. D. Anderson Cancer Center

description: Normal Adult patient, age 43, gender Male

scan_protocol: Scanning was performed using the Affymetrix Fluidic Station 450, protocol EuKGE-WS2v5

data_processing: from the CEL files, we normalyzed and analyzed the data using the DChip 2006 (DNA-Chip Analyzer) software (MBEI analysis, PM only model). Build date: Feb 16 2006. Normalization was carried against a normal control sample (N_M43_?_03)

source_name: Skeletal Muscle

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix GeneChip Expression Analysis Technical Manual, Rev5, using 5 ug total RNA

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

tag: Normal Adult patient

tag: biopsy site

value: unknown


title: N_M43_?_03

hyb_protocol: standard Affymetrix GeneChip Expression Analysis Technical Manual, Rev5


title: DM2_F58_?_18

description: DM2 patient, age 58, gender Female

tag: DM2 patient


title: DM2_F42_?_15

description: DM2 patient, age 42, gender Female


title: DM2_M51_?_19

description: DM2 patient, age 51, gender Male


title: DM2_F55_?_20

description: DM2 patient, age 55, gender Female


title: DM2_F65_?_14

description: DM2 patient, age 65, gender Female


title: N_M85_?_02

description: Normal Adult patient, age 85, gender Male


title: N_F61_?_01

description: Normal Adult patient, age 61, gender Female


title: DM2_F51_?_17

description: DM2 patient, age 51, gender Female


title: DM2_F50_?_16

description: DM2 patient, age 50, gender Female


title: N_M26_?_05

description: Normal Adult patient, age 26, gender Male


title: N_MF43-46_?_06

description: Normal Adult patients pool, age 43-46, gender Male/Female


title: DM2_M54_VL_12

description: DM2 patient, age 54, gender Male

value: Vastus Lateralis


title: DM2_F47_D_07

description: DM2 patient, age 47, gender Female

value: Deltoid


title: DM2_M39_BB_02

description: DM2 patient, age 39, gender Male

value: Biceps Brachii


title: DM2_M69_Q_03

description: DM2 patient, age 69, gender Male

value: Quadriceps


title: DM1_M21_?_10

description: DM1 patient, age 21, gender Male

tag: DM1 patient


title: DM2_F37_VL_10

description: DM2 patient, age 37, gender Female


title: DM2_F43_VL_09

description: DM2 patient, age 43, gender Female


title: DM2_M68_D_05

description: DM2 patient, age 68, gender Male


title: DM2_F57_VL_08

description: DM2 patient, age 57, gender Female


title: DM2_F71_BB_01

description: DM2 patient, age 71, gender Female


title: DM2_F43_?_13

description: DM2 patient, age 43, gender Female


title: DM2_M47_VL_11

description: DM2 patient, age 47, gender Male


title: DM2_M?_BB_04

description: DM2 patient, age unknown, gender Male


title: DM1_M25_?_07

description: DM1 patient, age 25, gender Male


title: DM1_F54_?_06

description: DM1 patient, age 54, gender Female


title: DM1_??_?_09

description: DM1 patient, age unknown, gender Unknown


title: 3 hour old early-schistosomula treated with human TNF alpha during 1h and their respective control rep 3 cy3

status: Public on Dec 15 2009

city: São Paulo

first: Katia

middle: Cristina Pereira

last: Oliveira

state: O

address: Av Prof lineu prestes 748

department: Centro de Parasitologia e Micologia

country: Brazil

institute: Instituto Adolfo Lutz

description: No additional information

hyb_protocol: The hybridization solution and procedure were prepared according to manufacturer´s instructions.

scan_protocol: Slides were air dried and scanned using a microarray dual channel laser scanner (GenePix 4000B, Molecular Devices, USA) 100 % laser power and PMT levels were adjusted in order to obtain similar average intensities of red and green signal.

data_processing: Data was extracted from images using the Feature Extraction software (Agilent Technologies). Spots with low intensities were filtered out according to criteria established by Feature Extraction software (IsPosAndSig collun). Normalization was perfomed using the Quantiles algorithm.

organism: Schistosoma mansoni

source_name: 3 hour old-early-schistosomula

label_protocol: Three hundred nanograms of total RNA from each sample were amplified using the Linear RNA amplification and labeling kit (Agilent Technologies) according to manufacturer´s instructions. Eight hundred and twenty five nanograms Cy3 labeled cRNA was used to hibridization.

extract_protocol: Total RNA was obtained using Trizol reagent (Invitrogen) according to the manufacturer's instructions. The RNA was quantified using the Nanodrop ND-1000 UV/Vis spectrophotometer and RNA integrity was checked by electrophoresis with an Agilent 2100 Bioanalyzer. Total RNA was treated with DNAse I (QIAGEN) and subsequently purified using RNA easy mini kit

tag: stage

value: cercariae-to-schistosomula


title: 3 hour old early-schistosomula treated with human TNF alpha during 1h and their respective control rep 3 2 cy3

description: No additional information

source_name: 3 hour old early-schistosomula


title: DM2_M32_D_06

description: DM2 patient, age 32, gender Male


title: Adult worms treated Tris 10nM pH 8,8 (vehicle) during 24hs rep 3 (Control sample 3) cy3

description: No additional information

source_name: Adult worms

value: adult worms recovered forty-two days after infection of hamster


title: 3 hour old early-schistosomula treated with human TNF-alpha during 1h rep 3 2 cy5

description: No additional information


title: DM1_F?_BB_01

description: DM1 patient, age unknown, gender Female


title: DM1_F55_D_04

description: DM1 patient, age 55, gender Female


title: DM1_??_?_05


title: Adult worms treated with human TNF-alpha during 24hs rep 3 cy5

description: No additional information


title: DM1_F29_BB_08

description: DM1 patient, age 29, gender Female


title: Adult worms treated Tris 10nM pH 8,8 (vehicle) during 24hs rep 3 (Control sample 3) cy5

description: No additional information


title: DM1_F?_BB_02

description: DM1 patient, age unknown, gender Female