title: SGK1-IL23 rep2

treatment_protocol: For Th17 differentiation: 2ng/mL rhTGF-β1 (Miltenyi Biotec), 25ng/mL rmIl-6 (Miltenyi Biotec), 20ng/ml rmIl-23 (Miltenyi Biotec), and 20ng/ml rmIL-β1 (Miltenyi Biotec). After differentiation, the cells were then rested for 72 h and restimulated with IL-23


title: WT-IL23 rep1

status: Public on Mar 07 2013

type: RNA

city: Berkeley

first: Nir

last: Yosef

state: CA

address: Berkeley

department: EECS

country: USA

institute: UC Berkeley

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse 430 2.0 microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Expression data was preprocessed using the RMA algorithm followed by quantile normalization, with the parameters in the ExpressionFileCreator module of the GenePattern suite set to default

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Th17 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (3' IVT Express Kit, Affymetrix).

growth_protocol: Cd4+ T cells were purified from spleen and lymph nodes using anti-CD4 microbeads (Miltenyi Biotech) then stained in PBS with 1% FCS for 20 min at room temperature with anti-Cd4-PerCP, anti-Cd62l-APC, and anti-Cd44-PE antibodies (all Biolegend, CA). Naïve Cd4+ Cd62lhigh Cd44low T cells were sorted using the BD FACSAria cell sorter.  Sorted cells were activated with plate bound anti-Cd3 (2μg/ml) and anti-Cd28 (2μg/ml) in the presence of cytokines.

extract_protocol: Extraction of total RNA was performed according to the RNeasy Mini Kit (Qiagen) manufacturer's instructions.

tag: genotype

value: WT

tag: cell type


title: WT_TgfbpIL6_wt72

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix microarray HT_MG-430A. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

treatment_protocol: For Th17 differentiation: 2ng/mL rhTGF-β1 (Miltenyi Biotec), 25ng/mL rmIl-6 (Miltenyi Biotec), 20ng/ml rmIl-23 (Miltenyi Biotec), and 20ng/ml rmIL-β1 (Miltenyi Biotec). Cells were cultured for 48 hours.

tag: time (hr)

tag: treatment


title: KO_TgfbpIL6_ko54

value: IL23R knockout


title: 24_(-) 24hi

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: RMA normalisation using GeneSpring GX11.5

label: Biotin

source_name: thymus_Treg Foxp3-GFP-  CD24hi

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix 3´ IVT Labeling  protocol from 50ng of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNA was extracted using Qiagen RNAeasy according to manufacturer's manual.

tag: strain background

value: Balb/c

tag: tissue

value: thymus

value: T-Lymphocytes

tag: cell subtype

value: Treg Foxp3-GFP-  CD24hi


title: KO_TgfbpIL6_ko65


title: KO_TgfbpIL6_ko72


title: KO_TgfbpIL6pIL23_KO54IL23


title: 18_(-) 24lo

source_name: thymus_Treg Foxp3-GFP-  CD24low

value: Treg Foxp3-GFP-  CD24low


title: KO_TgfbpIL6_ko49


title: 12_(+) 24lo

source_name: thymus_Treg Foxp3+GFP+  CD24low

value: Treg Foxp3+GFP+  CD24low


title: KO_TgfbpIL6_ko24


title: WT_TgfbpIL6pIL23_WT72IL23


title: 21_(-) 24int

source_name: thymus_Treg Foxp3-GFP-  CD24intermediate

value: Treg Foxp3-GFP-  CD24intermediate


title: WT_TgfbpIL6pIL23_wt49IL23


title: WT_TgfbpIL6_wt54


title: WT_TgfbpIL6pIL23_WT65IL23


title: SGK1-IL23 rep1


title: WT_TgfbpIL6_wt65


title: WT-IL23 rep2


title: KO_TgfbpIL6pIL23_KO72IL23


title: KO_TgfbpIL6pIL23_KO65IL23


title: WT_TgfbpIL6_wt48


title: WT_TgfbpIL6_wt49


title: repeat Tgfb+Il6_52hrwIL23_HJ


title: 09_(+) 24int

source_name: thymus_Treg Foxp3+GFP+  CD24int

value: Treg Foxp3+GFP+  CD24int


title: WT_TgfbpIL6_wt24


title: repeat Tgfb+Il6_60hrwIL23_HJ


title: repeat Tgfb+Il6_60hr_HJ


title: repeat Tgfb+Il6_10hr_HJ


title: repeat Tgfb+Il6_52hr_HJ


title: 27_PN

source_name: Lymphnode_peri naive Tcell

value: Lymphnode

value: peri naive Tcell


title: repeat Tgfb+Il6_42hr_HJ


title: repeat Tgfb+Il6_20hr_HJ


title: 03_Prec

source_name: thymus_Treg precursor cell

value: Treg precursor cell


title: repeat Tgfb+Il6_30hr_HJ


title: repeat Th0_52hr_HJ


title: 17_(-) 24lo


title: 15_PTr

source_name: Lymphnode_peri Treg

value: peri Treg


title: 06_(+) 24hi

source_name: thymus_Treg Foxp3+GFP+  CD24hi

value: Treg Foxp3+GFP+  CD24hi


title: repeat Tgfb+Il6_1hr_HJ


title: 20_(-) 24int


title: repeat Th0_30hr_HJ


title: repeat Th0_42hr_HJ


title: repeat Th0_4hr_HJ


title: repeat Th0_60hr_HJ


title: repeat Th0_1hr_HJ


title: repeat Th0_10hr_HJ


title: repeat Th0_20hr_HJ


title: 08_(+) 24int


title: 11_(+) 24lo


title: repeat Tgfb+Il6_4hr_HJ


title: Tgfb+Il6_72hrwIL23_HJ


title: 23_(-) 24hi


title: Tgfb+Il6_52hrwIL23_HJ


title: Tgfb+Il6_60hrwIL23_HJ


title: Tgfb+Il6_72hr_HJ


title: 26_PN


title: 05_(+) 24hi


title: 02_Prec


title: Tgfb+Il6_42hr_HJ


title: Tgfb+Il6_60hr_HJ


title: 19_(-) 24int


title: Tgfb+Il6_52hr_HJ


title: 14_PTr


title: Tgfb+Il6_50hr_HJ


title: 16_(-) 24lo


title: Tgfb+Il6_48hr_HJ


title: Tgfb+Il6_30hr_HJ


title: 22_(-) 24hi


title: 07_(+) 24int


title: Tgfb+Il6_16hr_HJ


title: 01_Prec


title: Tgfb+Il6_20hr_HJ


title: 10_(+) 24lo


title: 04_(+) 24hi


title: 25_PN


title: 13_PTr


title: Tgfb+Il6_10hr_HJ


title: BRAF(V600E)+MITF engineered melanomas replicate 3

city: Boston

first: Hans

middle: R

last: WIDLUND

state: MA

address: 77 Avenue Louis Pasteur

department: Dermatology

institute: Brigham and Women's Hospital

description: Gene expression data from cells log growth cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133AV2 arrrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the GeneArray Scanner M10

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings to generate the CEL files. dCHIP was used to normalize, model, and extract the probe set values

organism: Homo sapiens

source_name: Isogenic melanomas driven by BRAF(V600E) and MITF overexpression

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

growth_protocol: Engineered human melanoma cells were grown in Ham's F12 media supplemented with 10% FBS, glutamine, and antibiotics

extract_protocol: Total RNA was extracted using Qiagen RNeasy plus mini kit using standard protcol

treatment_protocol: Logarithmic cultures of enginneered cells were logarithmic growth at time of RNA extraction

value: engineered mammary epithelial cells


title: BRAF(V600E)+MITF engineered melanomas replicate 2


title: Tgfb+Il6_12hr_HJ


title: Tgfb+Il6_24hr_HJ


title: BRAF(V600E)+MITF engineered melanomas replicate 1


title: BRAF(V600E) engineered melanomas replicate 2

source_name: Isogenic melanomas driven by BRAF(V600E)


title: Tgfb+Il6_6hr_HJ


title: BRAF(V600E) engineered melanomas replicate 3


title: BimKOKLRG1lo - rep2

city: San Diego

first: John

middle: Adam

last: Best

state: California

address: 9500 Gilman Dr

institute: UCSD

hyb_protocol: cRNA was hybridized to GeneChip Mouse Gene 1.0 ST arrays

scan_protocol: Affymetrix GeneChip Scanner

data_processing:
RMA, Genepattern, The Sample data table contains raw expression data post RMA, excluding unlabeled probes or duplicate probes (that showed identical value).
probe group file: MoGene-1_0-st-v1.na32.mm9.probeset.csv

source_name: BimKO OTI KLRG1lo cells - day 6 of listeria infection

label_protocol: RNA was labeled with biotin with the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics) and purified with an Rneasy Mini Kit (Qiagen).

growth_protocol: 1x104 cells from fetal liver chimeras were transferred into congenically matched recipient mice. Mice were infected with listera-ova the next day. On day 6 of infection cells were purified by flow cytometry.

extract_protocol: RNA was extracted with TRIzol reagent (Invitrogen) and was amplified twice with MessageAmp RNA Amplification kit (Ambion)

value: effector CD8+ cells

tag: strain

value: BimKO


title: Tgfb+Il6_8hr_HJ


title: BRAF(V600E) engineered melanomas replicate 1


title: WTKLRG1lo-rep5

source_name: WT OTI KLRG1lo cells - day 6 of listeria infection

value: Wild type


title: Tgfb+Il6_2hr_HJ


title: Tgfb+Il6_4hr_HJ


title: Id2KOBimKOKLRG1lo-rep2

source_name: Id2KOBImKO KLRG1lo cells - day 6 of listeria infection


title: Tgfb+Il6_1hr_HJ


title: Th0_72hr_HJ


title: Tgfb+Il6_0.5hr_HJ


title: WTKLRG1lo-rep3


title: Th0_52hr_HJ


title: WTKLRG1lo-rep4


title: Th0_50hr_HJ


title: Th0_60hr_HJ


title: BimKOKLRG1lo - rep1


title: Id2KOKLRG1lo-rep2

source_name: Id2KO OTI KLRG1lo cells - day 6 of Listeria infection


title: Tgfb+Il6_50hrwIL23_HJ


title: Th0_42hr_HJ


title: WTKLRG1lo-rep2


title: Id2KOBimKOKLRG1lo-rep1


title: Th0_30hr_HJ


title: WTKLRG1hi-rep3

source_name: WT OTI KLRG1h icells - day 6 of listeria infection


title: Th0_24hr_HJ

source_name: Th17 cells


title: Id2KOKLRG1lo-rep1


title: WTKLRG1lo-rep1


title: Th0_20hr_HJ


title: Th0_16hr_HJ


title: WTKLRG1hi-rep2


title: Th0_12hr_HJ


title: Th0_8hr_HJ


title: WTKLRG1hi-rep1


title: Th0_10hr_HJ


title: C2 mDAN

city: Münster

first: Peter

last: Reinhardt

address: Von-Esmarch-Straße 54

institute: Max Planck Institute for Molecular Biomedicine

hyb_protocol: According to manufacturer's instructions. Hybridization time: 18h

scan_protocol: Illumina iScan system using default settings

data_processing: Cubic Spline normalization with background subtraction in Illumina GenomeStudio. Signal intensities below 40 were arbitrarily trimmed to the value of 40.

source_name: human iPS cell line C2 (age- and sex-matched healthy control person for L2) differentiated for 30 days

label_protocol: Ambion TotalPrep RNA Amplification Kit. RNA in put: 400ng, IVT: 12h

growth_protocol: completely confluent human pluripotent stem cells were differentiated as a monolayer on matrigel using double-SMAD inhibition by SB-431542, Dorsomorphin and Purmorphamine and matured for 30 days with spliting when too confluent.

extract_protocol: Qiagen RNeasy kit with on-column DNA digestion

tag: cell line

value: midbrain dopaminergic neurons


title: Th0_6hr_HJ


title: HB-2

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

description: gene expression upon knockdown with Hlxb9 siRNA

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: RMA by software Partek

source_name: MIN6 cell line

growth_protocol: MIN6 cells were cultured in DMEM low glucose medium supplemented with 15% FBS and, antibiotic and antimycotic, at 37˚C and 5% CO2.

extract_protocol: Total RNA was isolated using the RNAeasy kit according to the manufacturer's instructions (Qiagen).

treatment_protocol: MIN6 cells were transfected with negative control siRNA (control) or Hlxb9 siRNA (HB9) using the nucleofection method with  Solution -T (Amaxa/Lonza), and  RNAiMax (Invitrogen). Total RNA was isolated 72 hours post-transfection.

tag: sample type

value: sorted cell subpopulations

tag: transfection

value: Hlxb9 siRNA


title: Th0_48hr_HJ


title: Th0_2hr_HJ


title: HB-3


title: Th0_1hr_HJ


title: HB-1


title: Th0_0.5hr_HJ


title: C1-1 mDAN

source_name: human iPS cell line C1-1 (age- and sex-matched healthy control person for L1) differentiated for 30 days


title: L2-2Mut mDAN

description: midbrain dopaminergic neurons derived from human iPS cells

source_name: human iPS cell line L2-2Mut carrying the LRRK2 G2019S mutation differentiated for 30 days


title: Control-1

description: gene expression upon knockdown with negative control siRNA

value: negative control siRNA


title: Control-2


title: L1-1GC2 mDAN

source_name: human iPS cell line L1-1GC2 (isogenic to L1-1Mut) carrying the LRRK2 WT allele differentiated for 30 days


title: L2-3Mut mDAN

source_name: human iPS cell line L2-3Mut carrying the LRRK2 G2019S mutation differentiated for 30 days


title: Th0_4hr_HJ


title: AS1-ChIP expt2

status: Public on Mar 06 2013

type: genomic

city: Kanazawa

first: Hiro

last: Takahashi

state: Ishikawa

address: Kakuma-machi

country: Japan

institute: Kanazawa University

hyb_protocol: Hybridization, staining, and washing were performed with GeneChip Arabidopsis Tiling 1.0R arrays (Affymetrix).

scan_protocol: Scanning was performed at 0.7-μm resolution with a GeneChip Scanner 3000 7G system.

data_processing:
Arabidopsis Tiling 1.0R arrays, the AS1 antibody data set (AS1 antibody versus mock), and the T7 antibody data set (T7 antibody versus mock) were analyzed by the Affimetrix GeneChip Command Console.
Raw CEL data files obtained from tiling array experiments were analyzed with Tiling Analysis Software (TAS Version 1.1.02, Affymetrix). Signal intensities were calculated only from perfect match probes for probe analysis. Array data from each chip were scaled to a target intensity of 1000 and quantile normalized with TAS. For both data sets, each parameter of analysis on TAS was a bandwidth (distance in base pairs for which data were grouped for statistical evaluation) of 100, a maximum gap (maximum tolerated gap between signals in an interval) of 196, and a minimum run (minimum size in base pairs of a detected interval) of 125. Genomic regions of 9,864 for the AS1 antibody data set, and of 16,365, for the T7 antibody data set, were detected by interval analysis with a cutoff of -fold change, of grater than 2.0 and of grater than 1.6, respectively.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: T7-ChIP DNA from pAS:T7:AS1/as1-1

label_protocol: Fragmentation and labeling of amplified samples were performed with the GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Plants were grown on MS medium under long day condition (16 hours light and 8 hours dark) for 14 days.

extract_protocol: Chromatin was prepared from as1-1 seedlings containing pAS1:T7:AS1, and fragmented chromatin was immunoprecipitated with T7-specific and AS1-specific antibodies. The fragmented chromatin was also precipitated without serum, and the resultant precipitates were used as mock controls.

tag: ecotype

value: Columbia

value: seedlings

tag: antibody

source_name: mock

value: mock


title: AS1-ChIP expt1

source_name: AS1-ChIP DNA from pAS:T7:AS1/as1-1


title: Control-3


title: L2-2GC mDAN

source_name: human iPS cell line L2-2GC (isogenic to L2-2Mut) carrying the LRRK2 WT allele differentiated for 30 days


title: L1-1Mut mDAN

source_name: human iPS cell line L1-1Mut carrying the LRRK2 G2019S mutation differentiated for 30 days


title: Wild Type CFA

city: 89 Beaumont ave

first: Dimitry

last: Krementsov

state: VT

address: 312C Rowell bldg, 106 Carrigan drive

department: BHSC

institute: University of Vermont

description: Total RNA from lymph node of wild type animals treated with complete freund's adjuvant

hyb_protocol: hyb protocol: The biotinylated cRNAs were fragmented into 50- to 200-base fragments and then hybridized to GeneChip Mouse Genome 430A 2.0 Arrays for 16h at 45°C in a rotating Affymetrix GeneChip Hybridization Oven 320.  After hybridization, arrays were washed and stained with streptavidin-phycoerythrin on an automated Affymetrix GeneChip Fluidic Station F450.

scan_protocol: The arrays were scanned with an Affymetrix GeneChip Scanner 2700 and the images quantified using Affymetrix GeneChip Operating Software.

data_processing: The signal intensity for each probe on each chip was calculated from scanned images using GeneChip Operating Software (Affymetrix), and signal intensities were analyzed using BioConductor (http://www.bioconductor.org).  Probe intensities were background corrected, normalized, and summarized using the Robust Multichip Average method described by Speed and coworkers (Bolstad et al., 2003; Irizarry et al., 2003).  An alternative normalization method based on housekeeping genes did not significantly change the results.  Probe sets were considered differentially expressed when the signed fold change was ≥ 2, and the P-value was < 0.05.

source_name: Wild Type CFA

label_protocol: RNA amplification and microarray analysis for both experiments was performed at the University of Vermont microarray core facility using previously described protocols (Affymetrix, 2005-2006).  Briefly, 2 ug of total RNA from each pooled sample were reverse transcribed to the single stranded cDNA using a T7-oligo(dT) primer.  T4 DNA polymerase was used to synthesize double-stranded cDNA, which served as a template for in vitro transcription using T7 RNA polymerase to produce biotinylated cRNA.

extract_protocol: LN  was removed from C57Bl/6 WT and H3RKO mice at 8 weeks, snap frozen in liquid N2. Isolation and purification of RNA was completed using the RNeasy RNA extraction kit (Qiagen).

tag: genotype/variation

value: wild-type

value: lymph node


title: Wild Type Control 2

description: Total RNA from lymph node of control wild type animals; replicate 2

source_name: Wild Type Control


title: Wild Type Control 1

description: Total RNA from lymph node of control wild type animals; replicate 1


title: Wild Type PTX

description: Total RNA from lymph node of wild type animals treated with complete freund's adjuvant and pertussis toxin

source_name: Wild Type PTX


title: H3RKO CFA

description: Total RNA from lymph node of H3RKO animals treated with complete freund's adjuvant

source_name: H3RKO CFA


title: H3RKO Control 2

description: Total RNA from lymph node of control H3RKO animals; replicate 2

source_name: H3RKO Control


title: H3RKO PTX

description: Total RNA from lymph node of H3RKO animals treated with complete freund's adjuvant and pertussis toxin

source_name: H3RKO PTX


title: H3RKO Control 1

description: Total RNA from lymph node of control H3RKO animals; replicate 1


title: W303doxy 0h vs 10h - Exp 1

city: Lleida

first: Jordi

last: Tamarit

address: Av Rovira Roure 80

department: Ciències Mèdiques Bàsiques

country: Spain

institute: Universitat de Lleida

hyb_protocol: Prehybridizations of the DNA microarrays were carried out at 42 oC for 1 h in a solution containing 5x SSC, 0.1% SDS, 1% bovine serum albumin. For hybridization, dried Cy3-and Cy5-labelled probes were resuspended in 35 ul of hybridization solution (50% fo

scan_protocol: The scanner ScanArray 4000 (Packard) was used to obtain the Cy3 and Cy5 images with a resolution of 10 um.  The fluorescent intensity of the spots was measured and processed using the GenePix Pro 6.0 software (Molecular Devices)

data_processing: The GEPAS server (http://gepas3.bioinfo.cipf.es) was used to preprocess the data: merge replicates and remove inconsistent replicates (Maximum distance to median of replicates=0.5)

organism: Saccharomyces cerevisiae

source_name: yeast cells grown exponentially in YPG and treated with doxycycline for 10 h

label_protocol: Fluorescent labeled cDNA was prepared from 8 ug of purified total RNA by the indirect dUTP-labeling method, using the CyScribe post-labeling kit (Amersham Biosciences)

growth_protocol: Grown at 30ºC in YPG rich medium until A600=0.5. 30 ml of yeast culture was harvested by centrifugation and washed with cold water. Dried cell pellet was kept at -80 oC until RNA purification

extract_protocol: Total RNA purification using the Ambion RiboPure-Yeast Total RNA Isolation Kit

treatment_protocol: Where indicated, 2ug/ml doxycycline

tag: strain/genotype

value: treated with doxycycline for 10 h

source_name: yeast cells grown exponentially  in YPG


title: W303doxy 0h vs 10h - Exp 2

source_name: yeast cells grown exponentially in YPG

source_name: yeast cells grown exponentially  in YPG and treated with doxycycline for 10 h


title: HP1 wa191 Nuclear L2 HP1c D.melanogaster ChIP Rep2

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

hyb_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.

scan_protocol: Standard Affymetrix Array Scanning Protocol was used

data_processing: M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

organism: Drosophila melanogaster

source_name: HP1 wa191 Nuc. L2 HP1c ChIP expt.1212 channel_1

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Growth conditions and collection protocol to harvest third instar larvae from bottles.
Drosophila tissues were homogenized, and treated with formaldehyde.  Nuclei were lysed with SDS and sonication in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

value: HP1c mutant

tag: developmental stage

value: 3rd Instar Larvae

tag: transgene

value: PBac insertion


title: tetYFH1doxy 0h vs 10h - B Exp 2

value: BQS201:W303-1A  tetO7-YFH1::kanMX4


title: tetYFH1doxy 0h vs 10h -A  Exp 2


title: tetYFH1doxy 0h vs 10h - A Exp 1


title: tetYFH1doxy 0h vs 10h - B Exp 1


title: HP1 wa191 Nuclear L2 HP1c D.melanogaster ChIP Rep1

source_name: HP1 wa191 Nuc. L2 HP1c ChIP expt.1211 channel_1

label_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.

tag: genotype


title: HP1 wa191 Nuclear L2 HP1c D.melanogaster Input Rep2

description: Served as Input for: 1212.Mvalues.bedgraph

source_name: HP1 wa191 Nuc. L2 HP1c Input expt.1214 channel_1


title: genomic DNA from xenograft [AML-XG1 DAC]

city: Birmingham

first: sarah

last: leonard

address: Edgbaston

department: School of cancer sciences

country: United Kingdom

institute: University of Birmingham

description: AML xenograft sample

hyb_protocol: bisulphite converted DNA was fragmented and hybridised to Illumina Infinium 450Human Methylation arrays using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: normalized (Genome studio) Average Beta

label: Cy5 and Cy3

source_name: xenograft

label_protocol: Standard Illumina Protocol

growth_protocol: genomic DNA was extracted and purified from treated AML samples using Qiagen Allprep kit according to standard instructions

treatment_protocol: Standard Illumina Protocol

tag: disease

value: Paediatric AML

value: DAC


title: L2-3GC mDAN

source_name: human iPS cell line L2-3GC (isogenic to L2-3Mut) carrying the LRRK2 WT allele differentiated for 30 days


title: HP1 wa191 Nuclear L2 HP1c D.melanogaster Input Rep1

description: Served as Input for: 1211.Mvalues.bedgraph

source_name: HP1 wa191 Nuc. L2 HP1c Input expt.1213 channel_1


title: genomic DNA from xenograft [AML-XG1 PBS]

description: AML xenograft sample

extract_protocol: genomic DNA was extracted and purified from treated AML samples using Qiagen Allprep kit according to standard instructions

value: PBS


title: genomic DNA from xenograft [AML-XG1 Ara-C]

description: AML xenograft sample

value: Ara-C


title: genomic DNA from xenograft [AML-XG1 A/D]

description: AML xenograft sample

value: A/D


title: H3K9me3 (new lot) Nuclear L3 Sexed Male Jil D.melanogaster ChIP Rep2

source_name: H3K9me3 (new lot) Nuc. L3 SexedMJil ChIP expt.2057 channel_1

value: Sexed male Jil mutant

value: 3rd Instar Larvae Sexed Male

value: Jil-1 z2/Jil-1z2

tag: Sex

value: Male

value: deletion


title: genomic DNA from cell line KG1A [KG1A DAC treated]

description: cell line

source_name: cell line KG1A

tag: treatment


title: genomic DNA from xenograft [AML-XG1 D+A]

description: AML xenograft sample

value: D+A


title: H3K9me3 (new lot) Nuclear L3 Sexed Male Jil D.melanogaster Input Rep1

description: Served as Input for: 1991.Mvalues.bedgraph

source_name: H3K9me3 (new lot) Nuc. L3 SexedMJil Input expt.1994 channel_1


title: H3K9me3 (new lot) Nuclear L3 Sexed Male Jil D.melanogaster Input Rep2

description: Served as Input for: 2057.Mvalues.bedgraph

source_name: H3K9me3 (new lot) Nuc. L3 SexedMJil Input expt.2061 channel_1


title: genomic DNA from xenograft [AML-XG1 D/A]

description: AML xenograft sample

value: D/A


title: H3K9me3 (new lot) Nuclear L3 Sexed Male Jil D.melanogaster ChIP Rep1

source_name: H3K9me3 (new lot) Nuc. L3 SexedMJil ChIP expt.1991 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 Sexed Female Jil D.melanogaster ChIP Rep2

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 SexedFJil ChIP expt.1174 channel_1

value: Sexed Female Jil mutant

value: 3rd Instar Larvae Sexed Female

value: Jil-1 z2/ Jil-1 z2

value: Female


title: genomic DNA from cell line KG1A [KG1A PBS treated]

description: cell line


title: genomic DNA from AML patient 3 [AML-3 PBS treated]

description: Bone marrow sample grown in cultutre

source_name: AML patient 3


title: genomic DNA from cell line HL-60 [HL-60 PBS treated]

description: cell line

source_name: cell line HL-60


title: genomic DNA from AML patient 4 [AML-4 DAC treated]

description: Bone marrow sample grown in cultutre

source_name: AML patient 4


title: genomic DNA from AML patient 5 [AML-5 DAC treated]

description: Bone marrow sample grown in cultutre

source_name: AML patient 5


title: H3K9me2-Ab2 (new lot) Nuclear L3 Sexed Female Jil D.melanogaster Input Rep1

description: Served as Input for: 1172.Mvalues.bedgraph

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 SexedFJil Input expt.1181 channel_1


title: genomic DNA from AML patient 7 [AML-7 DAC treated]

description: Bone marrow sample grown in cultutre

source_name: AML patient 7


title: genomic DNA from AML patient 8 [AML-8 PBS treated]

description: Bone marrow sample grown in cultutre

source_name: AML patient 8


title: genomic DNA from AML patient 5 [AML-5 PBS treated]

description: Bone marrow sample grown in cultutre


title: genomic DNA from AML patient 8 [AML-8 DAC treated]

description: Bone marrow sample grown in cultutre


title: H3K36me3 abcam Nuclear L3 G9a D.melanogaster ChIP Rep2

source_name: H3K36me3 abcam Nuc. L3 G9a ChIP expt.2168 channel_1

value: G9a mutant

value: 3rd Instar Larvae


title: genomic DNA from AML patient 6 [AML-6 PBS treated]

description: Bone marrow sample grown in cultutre

source_name: AML patient 6

value: Paediatric AML


title: H3K9me2-Ab2 (new lot) Nuclear L3 Sexed Female Jil D.melanogaster ChIP Rep1

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 SexedFJil ChIP expt.1172 channel_1


title: genomic DNA from AML patient 6 [AML-6 DAC treated]

description: Bone marrow sample grown in cultutre

value: DAC


title: genomic DNA from AML patient 2 [AML-2 PBS treated]

description: Bone marrow sample grown in cultutre

source_name: AML patient 2

value: PBS


title: genomic DNA from AML patient 3 [AML-3 DAC treated]

description: Bone marrow sample grown in cultutre


title: genomic DNA from AML patient 7 [AML-7 PBS treated]

description: Bone marrow sample grown in cultutre


title: H3K36me3 abcam Nuclear L3 G9a D.melanogaster ChIP Rep1

source_name: H3K36me3 abcam Nuc. L3 G9a ChIP expt.2167 channel_1


title: genomic DNA from cell line HL-60 [HL-60 DAC treated]

description: cell line


title: genomic DNA from AML patient 4 [AML-4 PBS treated]

description: Bone marrow sample grown in cultutre


title: H3K36me3 abcam Nuclear L3 G9a D.melanogaster Input Rep1

description: Served as Input for: 2167.Mvalues.bedgraph

source_name: H3K36me3 abcam Nuc. L3 G9a Input expt.2159 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 HP1b D.melanogaster ChIP Rep2

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 HP1b ChIP expt.1853 channel_1

value: HP1b mutant


title: genomic DNA from AML patient 1 [AML-1 DAC treated]

description: Bone marrow sample grown in cultutre

source_name: AML patient 1


title: genomic DNA from AML patient 2 [AML-2 DAC treated]

description: Bone marrow sample grown in cultutre


title: H3K9me2-Ab2 (new lot) Nuclear L3 HP1b D.melanogaster Input Rep1

description: Served as Input for: 1852.Mvalues.bedgraph

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 HP1b Input expt.1844 channel_1


title: Buccal cell Birth twin 2, B3006

city: NEDLANDS

first: David

last: Martino

state: Western Australia

address: Perth Childrens Hospital, 15 Hospital Avenue

country: Australia

institute: Telethon Kids Institute

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to the Illumina Infinium Human Methylation27 BeadChip using the standard llumina protocol.

scan_protocol: Arrays were imaged using the BeadArray Reader using the standard recommended Illumina scanner setting.

data_processing: Data were preprocessed using the Bioconductor Minfi package in R by the 'illumina' method and normalized to control probes. Subset quantile normalization was performed on type 1 and type 2 probes. Probes failing P detection cutoff of <0.01 were removed. Probes on the X and Y chromosomes have been removed from the processed data. Outlier samples were removed. Between-array quantile normalization was performed to arrive at the final data set of 330168 probes and 53 samples.

source_name: Buccal cheek swab, DZ, birth

label_protocol: Bisulphite conversion was carried out using the Methyl Xceed bisulphite kit as per the manufacturer's instructions.

extract_protocol: gDNA was purified from buccal swabs using phenol chloroform extraction.

tag: gender

value: male

tag: age

value: birth

tag: cell type

value: normal buccal cells

tag: monozygotic

tag: dizygotic

tag: monochorionic

tag: sibship

tag: twin


title: Buccal cell 18m twin 1, B3006

source_name: Buccal cheek swab, DZ, 18 months

value: 18 months


title: Buccal cell 18m twin 2, B3006


title: H3K9me2-Ab2 (new lot) Nuclear L3 HP1b D.melanogaster ChIP Rep1

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 HP1b ChIP expt.1852 channel_1

tag: strain


title: Buccal cell Birth twin 1, B3006


title: H3K9me2-Ab2 (new lot) Nuclear L3 Sexed Male Jil D.melanogaster ChIP Rep2

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 SexedMJil ChIP expt.1173 channel_1

value: Sexed male Jil mutant

value: 3rd Instar Larvae Sexed Male

value: Jil-1 z2/Jil-1z2

value: Male

value: deletion


title: genomic DNA from AML patient 1 [AML-1 PBS treated]

description: Bone marrow sample grown in cultutre


title: H3K36me3 abcam Nuclear L3 G9a D.melanogaster Input Rep2

description: Served as Input for: 2168.Mvalues.bedgraph

source_name: H3K36me3 abcam Nuc. L3 G9a Input expt.2160 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 HP1b D.melanogaster Input Rep2

description: Served as Input for: 1853.Mvalues.bedgraph

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 HP1b Input expt.1845 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 Sexed Male Jil D.melanogaster Input Rep1

description: Served as Input for: 1171.Mvalues.bedgraph

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 SexedMJil Input expt.1180 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 Sexed Male Jil D.melanogaster Input Rep2

description: Served as Input for: 1173.Mvalues.bedgraph

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 SexedMJil Input expt.1182 channel_1


title: H3K9me2-Ab2 (new lot) Nuclear L3 Sexed Male Jil D.melanogaster ChIP Rep1

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 SexedMJil ChIP expt.1171 channel_1


title: Buccal cell 18m twin 2, B1126

source_name: Buccal cheek swab, MZ, 18 months

value: female


title: H3K9me2-Ab2 (new lot) Nuclear L3 Sexed Female Jil D.melanogaster Input Rep2

description: Served as Input for: 1174.Mvalues.bedgraph

source_name: H3K9me2-Ab2 (new lot) Nuc. L3 SexedFJil Input expt.1183 channel_1

value: Sexed Female Jil mutant

value: 3rd Instar Larvae Sexed Female

value: Jil-1 z2/ Jil-1 z2

value: Female


title: H3K9me3 (new lot) Nuclear L3 Sexed Female Jil D.melanogaster ChIP Rep2

source_name: H3K9me3 (new lot) Nuc. L3 SexedFJil ChIP expt.2058 channel_1


title: H3K9me3 (new lot) Nuclear L3 Sexed Female Jil D.melanogaster ChIP Rep1

source_name: H3K9me3 (new lot) Nuc. L3 SexedFJil ChIP expt.1992 channel_1


title: H3K9me3 (new lot) Nuclear L3 Sexed Female Jil D.melanogaster Input Rep2

description: Served as Input for: 2058.Mvalues.bedgraph

source_name: H3K9me3 (new lot) Nuc. L3 SexedFJil Input expt.2060 channel_1


title: Buccal cell Birth twin 2, B1126

source_name: Buccal cheek swab, MZ, birth


title: Buccal cell Birth twin 1, B1107


title: H3K9me3 (new lot) Nuclear L3 Sexed Female Jil Heterozygous D.melanogaster ChIP Rep2

source_name: H3K9me3 (new lot) Nuc. L3 SexedFJilHZ ChIP expt.2056 channel_1

value: Sexed Female Jil mutant-heterozygous

value: Jil-1 z2/TM3 Ser-GFP


title: H3K9me3 (new lot) Nuclear L3 Sexed Female Jil D.melanogaster Input Rep1

description: Served as Input for: 1992.Mvalues.bedgraph

source_name: H3K9me3 (new lot) Nuc. L3 SexedFJil Input expt.1995 channel_1


title: H3K9me3 (new lot) Nuclear L3 Sexed Female Jil Heterozygous D.melanogaster ChIP Rep1

source_name: H3K9me3 (new lot) Nuc. L3 SexedFJilHZ ChIP expt.1990 channel_1


title: H3K9me3 (new lot) Nuclear L3 Sexed Female Jil Heterozygous D.melanogaster Input Rep2

description: Served as Input for: 2056.Mvalues.bedgraph

source_name: H3K9me3 (new lot) Nuc. L3 SexedFJilHZ Input expt.1909 channel_1


title: Buccal cell Birth twin 2, B1107


title: H3K9me3 (new lot) Nuclear L3 Sexed Female Jil Heterozygous D.melanogaster Input Rep1

description: Served as Input for: 1990.Mvalues.bedgraph

source_name: H3K9me3 (new lot) Nuc. L3 SexedFJilHZ Input expt.1908 channel_1


title: HP1 wa191 Nuclear L3 HP1b D.melanogaster ChIP Rep2

source_name: HP1 wa191 Nuc. L3 HP1b ChIP expt.1941 channel_1

value: HP1b mutant

value: 3rd Instar Larvae


title: HP1 wa191 Nuclear L3 HP1b D.melanogaster ChIP Rep1

source_name: HP1 wa191 Nuc. L3 HP1b ChIP expt.1940 channel_1


title: HP1 wa191 Nuclear L3 HP1b D.melanogaster Input Rep1

description: Served as Input for: 1940.Mvalues.bedgraph

source_name: HP1 wa191 Nuc. L3 HP1b Input expt.1844 channel_1


title: HP1 wa191 Nuclear L3 HP1b D.melanogaster Input Rep2

description: Served as Input for: 1941.Mvalues.bedgraph

source_name: HP1 wa191 Nuc. L3 HP1b Input expt.1845 channel_1


title: Buccal cell 18m twin 2, B1107


title: Buccal cell Birth twin 2, B1058

value: male

value: birth


title: H3K36me3 abcam Nuclear L3 HP1b D.melanogaster ChIP Rep2

source_name: H3K36me3 abcam Nuc. L3 HP1b ChIP expt.1855 channel_1


title: Buccal cell Birth twin 1, B1072

source_name: Buccal cheek swab, DZ, birth

value: normal buccal cells


title: Buccal cell Birth twin 1, B1058


title: Buccal cell 18m twin 2, B1072

source_name: Buccal cheek swab, DZ, 18 months

value: 18 months


title: Buccal cell 18m twin 1, B1072


title: H3K36me3 abcam Nuclear L3 HP1b D.melanogaster ChIP Rep1

source_name: H3K36me3 abcam Nuc. L3 HP1b ChIP expt.1854 channel_1


title: Buccal cell 18m twin 1, B1046

source_name: Buccal cheek swab, MZ, 18 months


title: Buccal cell 18m twin 2, B1046


title: H3K36me3 abcam Nuclear L3 HP1b D.melanogaster Input Rep2

description: Served as Input for: 1855.Mvalues.bedgraph

source_name: H3K36me3 abcam Nuc. L3 HP1b Input expt.1845 channel_1


title: Buccal cell 18m twin 1, B1058


title: Buccal cell Birth twin 1, B1057

description: B1057.1 _B


title: Buccal cell 18m twin 2, B1058


title: Buccal cell Birth twin 2, B1057


title: Buccal cell Birth twin 1, B1046


title: Buccal cell Birth twin 2, B1046


title: Buccal cell 18m twin 2, B1057


title: Buccal cell Birth twin 2, B1042


title: H3K36me3 abcam Nuclear L3 HP1b D.melanogaster Input Rep1

description: Served as Input for: 1854.Mvalues.bedgraph

source_name: H3K36me3 abcam Nuc. L3 HP1b Input expt.1844 channel_1


title: Buccal cell Birth twin 2, B1032


title: Buccal cell Birth twin 1, B1042


title: HP1c (MO 462) Nuclear L3 HP1b D.melanogaster ChIP Rep2

source_name: HP1c (MO 462) Nuc. L3 HP1b ChIP expt.1849 channel_1


title: Buccal cell 18m twin 2, B1042


title: Buccal cell Birth twin 1, B1032


title: Buccal cell 18m twin 2, B1032


title: HP1c (MO 462) Nuclear L3 HP1b D.melanogaster ChIP Rep1

source_name: HP1c (MO 462) Nuc. L3 HP1b ChIP expt.1848 channel_1


title: Buccal cell Birth twin 1, B1024

source_name: Buccal cheek swab, MZ, birth


title: Buccal cell 18m twin 1, B1042


title: Buccal cell Birth twin 2, B1022


title: Buccal cell Birth twin 1, B1126


title: HP1c (MO 462) Nuclear L3 HP1b D.melanogaster Input Rep2

description: Served as Input for: 1849.Mvalues.bedgraph

source_name: HP1c (MO 462) Nuc. L3 HP1b Input expt.1845 channel_1


title: iPS cells of a young hematopoietic origin, biological replicate 2

city: Lund

first: Martin

last: Wahlestedt

address: Klinikgatan 26

department: Divison of Molecular Hematology

country: Sweden

institute: Lund University

description:
YoungBiPS2
Cells cultured on MEF feeders in standard ES cell culture conditions

hyb_protocol: RNA hybridized to MOE430_2. Chips according to manufacturer manual

scan_protocol: GeneChips were scanned using the GeneChipTM Scanner 3000

data_processing: Probe level expression values and normalization were calculated using RMAExpress and further analysis was done using dChip

source_name: YoungBiPS

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10.000 cells

extract_protocol: Total RNA extraction was performed with QIAGEN microRNeasy kit according to the manufacturer's instructions.

tag: background strain

tag: genotype/variation

value: wild type

value: Cultured cells (iPS cells of a young hematopoietic origin)


title: iPS cells of a aged hematopoietic origin, biological replicate 1

description:
AgedBiPS1
Cells cultured on MEF feeders in standard ES cell culture conditions

source_name: AgedBiPS

value: Cultured cells (iPS cells of a aged hematopoietic origin)


title: iPS cells of a young hematopoietic origin, biological replicate 1

description:
YoungBiPS1
Cells cultured on MEF feeders in standard ES cell culture conditions


title: Buccal cell 18m twin 2, B1024


title: Young steady-state male HSC, biological replicate 2

description: Young steadystate male #2

source_name: Steady-state HSC Young

tag: tissue

value: Murine bone marrow

value: 3-4 months


title: iPS cells of a aged hematopoietic origin, biological replicate 2

description:
AgedBiPS2
Cells cultured on MEF feeders in standard ES cell culture conditions


title: HP1c (MO 462) Nuclear L3 HP1b D.melanogaster Input Rep1

description: Served as Input for: 1848.Mvalues.bedgraph

source_name: HP1c (MO 462) Nuc. L3 HP1b Input expt.1844 channel_1

tag: developmental stage

tag: transgene


title: Buccal cell 18m twin 1, B1057


title: Young steady-state male HSC, biological replicate 3

description: Young steadystate male #3


title: Buccal cell 18m twin 1, B1024

value: female


title: Aged steady-state male HSC, biological replicate 3

description: Aged steadystate male #3

source_name: Steady-state HSC Aged

value: 21-24 months


title: H3K9me3 (new lot) Nuclear L3 Sexed Male Jil Heterozygous D.melanogaster ChIP Rep2

source_name: H3K9me3 (new lot) Nuc. L3 SexedMJilHZ ChIP expt.2055 channel_1

value: Sexed male Jil mutant-heterozygous

value: 3rd Instar Larvae Sexed Male

tag: genotype

value: Male

value: deletion


title: Buccal cell Birth twin 2, B1072


title: H3K9me3 (new lot) Nuclear L3 Sexed Male Jil Heterozygous D.melanogaster Input Rep2

description: Served as Input for: 2055.Mvalues.bedgraph

source_name: H3K9me3 (new lot) Nuc. L3 SexedMJilHZ Input expt.1907 channel_1

value: Jil-1 z2/TM3 Ser-GFP

tag: Sex


title: H3K9me3 (new lot) Nuclear L3 Sexed Male Jil Heterozygous D.melanogaster Input Rep1

description: Served as Input for: 1989.Mvalues.bedgraph

source_name: H3K9me3 (new lot) Nuc. L3 SexedMJilHZ Input expt.1906 channel_1


title: Aged steady-state male HSC, biological replicate 2

description: Aged steadystate male #2


title: ES cells from Primogenix

description:
ESC Primogenix
Cells cultured on MEF feeders in standard ES cell culture conditions

source_name: ESC Primogenix

value: Cultured cells (ESC)


title: Aged steady-state male HSC, biological replicate 1

description: Aged steadystate male #1


title: ES cells from Open Biosystems

description:
ESC Open Biosystems
Cells cultured on MEF feeders in standard ES cell culture conditions

source_name: ESC Open Biosystems


title: cortex_hypoxia_NBQX_1-Week_rep4

city: Cambridge

first: Joachim

last: Theilhaber

address: 270 Albany Street

department: Translational Medicine

institute: Sanofi

description:
cortex of P10 rat pup subjected to 15 min. hypoxia condition, followed by four IP administrations of NBQX over a 48h period, and killed at 168h post-hypoxia/normoxic control condition.
Response to hypoxic seizures in conjunction with post-hypoxia treatment with anti-epileptogenic compound NBQX, in cortical tissues.

hyb_protocol: Following fragmentation, cRNA were hybridized  on Affymetrix HT_Rat-Focus Array according to standard Affymetrix protocol. Chips were washed and stained in the  Affymetrix Fluidics Station 4500.

scan_protocol: Microarrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: Probe set intensity values were summarized using the MAS5 algorithm implemented as a stand-alone command-line application. Linear scaling of samples using 75th percentile of MAS5 present probe-set intensities was used to normalize the gene expression profiles to each other.

organism: Rattus norvegicus

source_name: cortex of P10 rat pup

label_protocol: Biotin-labeled cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Post-natal day 10 (P10) Long-Evans rat pups raised in their original litters were used.

extract_protocol: Total RNA was extracted from homogenized hippocampi and cortices using Qiagen Rneasy kit.

treatment_protocol: The animals were subjected to 15 minute mild hypoxia (5% O2) or normoxic control sham event, and subsequently treated with NBQX or vehicle control through 4 repeated IP injections over a 48 h period. At the end of a specified time interval in the set {1h, 6h, 12h, 48h or 168h}, each animal was sacrificed and hippocampi and cortices isolated for gene expression profiling.

tag: compound

value: NBQX

tag: flagbothtissues

tag: hypoxia

value: hypoxia

tag: post-hypoxia-temperature

tag: pre-hypoxia-temperature

tag: ratuniqueidentifier

tag: timetofirstszmin

value: cortex


title: Buccal cell Birth twin 1, B1016

tag: gender

value: male

tag: age

value: birth

tag: cell type

value: normal buccal cells

tag: monozygotic

tag: dizygotic

tag: monochorionic

tag: sibship


title: Buccal cell Birth twin 1, B1022

tag: twin


title: Buccal cell Birth twin 2, 2034


title: HP1 wa191 Nuclear L3 G9a D.melanogaster ChIP Rep1

source_name: HP1 wa191 Nuc. L3 G9a ChIP expt.2539 channel_1

tag: strain

value: G9a mutant

tag: developmental stage

value: 3rd Instar Larvae

tag: genotype

tag: transgene


title: Buccal cell Birth twin 1, 3014


title: HP1 wa191 Nuclear L3 G9a D.melanogaster Input Rep2

description: Served as Input for: 2540.Mvalues.bedgraph

source_name: HP1 wa191 Nuc. L3 G9a Input expt.2160 channel_1


title: cortex_hypoxia_NBQX_1-Week_rep2

tag: compound

tag: flagbothtissues

tag: hypoxia

tag: tissue


title: Buccal cell 18m twin 2, 3014

source_name: Buccal cheek swab, MZ, 18 months

value: 18 months


title: cortex_hypoxia_NBQX_48-Hour_rep5

description:
cortex of P10 rat pup subjected to 15 min. hypoxia condition, followed by four IP administrations of NBQX over a 48h period, and killed at 48h post-hypoxia/normoxic control condition.
Response to hypoxic seizures in conjunction with post-hypoxia treatment with anti-epileptogenic compound NBQX, in cortical tissues.

tag: post-hypoxia-temperature

tag: pre-hypoxia-temperature

tag: ratuniqueidentifier

tag: timetofirstszmin


title: HP1 wa191 Nuclear L3 G9a D.melanogaster ChIP Rep2

source_name: HP1 wa191 Nuc. L3 G9a ChIP expt.2540 channel_1


title: Buccal cell Birth twin 2, B1016

source_name: Buccal cheek swab, MZ, birth

tag: gender

tag: age

tag: cell type

tag: monozygotic


title: cortex_hypoxia_NBQX_1-Week_rep5


title: H3K9me3 (new lot) Nuclear L3 Sexed Male Jil Heterozygous D.melanogaster ChIP Rep1

source_name: H3K9me3 (new lot) Nuc. L3 SexedMJilHZ ChIP expt.1989 channel_1

tag: Sex


title: Buccal cell Birth twin 2, 3014

tag: dizygotic

tag: monochorionic

tag: sibship

tag: twin


title: cortex_hypoxia_NBQX_48-Hour_rep4

tag: compound


title: cortex_hypoxia_NBQX_1-Week_rep3

tag: flagbothtissues


title: Buccal cell 18m twin 1, 3014


title: cortex_hypoxia_NBQX_48-Hour_rep3

tag: hypoxia


title: Young transplanted HSC, biological replicate 2

description: Young transplanted 2

source_name: Transplanted HSC Young

tag: background strain

tag: genotype/variation

value: wild type

tag: tissue

value: Murine bone marrow


title: Buccal cell Birth twin 1, 1035

value: female


title: HP1 wa191 Nuclear L3 G9a D.melanogaster Input Rep1

description: Served as Input for: 2539.Mvalues.bedgraph

source_name: HP1 wa191 Nuc. L3 G9a Input expt.2159 channel_1

tag: strain

tag: developmental stage

tag: genotype

tag: transgene


title: Buccal cell 18m twin 1, 2034

tag: gender

tag: age

tag: cell type


title: cortex_hypoxia_NBQX_1-Week_rep1

tag: post-hypoxia-temperature

tag: pre-hypoxia-temperature

tag: ratuniqueidentifier

tag: timetofirstszmin


title: Buccal cell Birth twin 1, 2034

tag: monozygotic

tag: dizygotic

tag: monochorionic

tag: sibship

tag: twin


title: Aged transplanted HSC, biological replicate 2

description: Aged transplanted 2

source_name: Transplanted HSC Aged

tag: background strain

tag: genotype/variation

tag: tissue


title: HP1 wa191 Nuclear L3 piwi2 D.melanogaster ChIP Rep2

source_name: HP1 wa191 Nuc. L3 piwi2 ChIP expt.2087 channel_1

tag: strain

value: PIWI2 mutant

tag: developmental stage

tag: genotype


title: HP1 wa191 Nuclear L3 piwi2 D.melanogaster ChIP Rep1

source_name: HP1 wa191 Nuc. L3 piwi2 ChIP expt.2086 channel_1

tag: transgene


title: Buccal cell Birth twin 2, 1035

tag: gender

tag: age

tag: cell type


title: cortex_hypoxia_NBQX_48-Hour_rep2

tag: compound

tag: flagbothtissues

tag: hypoxia

tag: post-hypoxia-temperature

tag: pre-hypoxia-temperature

tag: ratuniqueidentifier


title: Buccal cell 18m twin 1, 1035

tag: monozygotic

tag: dizygotic

tag: monochorionic

tag: sibship

tag: twin


title: Buccal cell 18m twin 2, 2034


title: HP1 wa191 Nuclear L3 piwi2 D.melanogaster Input Rep1

description: Served as Input for: 2086.Mvalues.bedgraph

source_name: HP1 wa191 Nuc. L3 piwi2 Input expt.1979 channel_1

tag: strain

tag: developmental stage


title: HP1 wa191 Nuclear L3 piwi2 D.melanogaster Input Rep2

description: Served as Input for: 2087.Mvalues.bedgraph

source_name: HP1 wa191 Nuc. L3 piwi2 Input expt.1980 channel_1

tag: genotype

tag: transgene


title: cortex_hypoxia_NBQX_48-Hour_rep1

tag: timetofirstszmin

tag: tissue


title: Young transplanted HSC, biological replicate 1

description: Young transplanted 1

tag: background strain

tag: genotype/variation

tag: age


title: Aged transplanted HSC, biological replicate 1

description: Aged transplanted 1


title: cortex_hypoxia_NBQX_12-Hour_rep1

description:
cortex of P10 rat pup subjected to 15 min. hypoxia condition, followed by four IP administrations of NBQX over a 48h period, and killed at 12h post-hypoxia/normoxic control condition.
Response to hypoxic seizures in conjunction with post-hypoxia treatment with anti-epileptogenic compound NBQX, in cortical tissues.

tag: compound

tag: flagbothtissues

tag: hypoxia

tag: post-hypoxia-temperature


title: d14 GC V23_rep2

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

description: Gene expression data from d14 GC V23

hyb_protocol: Samples are hybridized to arrays for 16 hours at 45C. The standard array is then washed and stained using the fluidics station and then scanned.

scan_protocol: The images are analyzed using Affymetrix Command Console Viewer and metric analyses are carried out according to the instructions provided by Affymetrix using the Affymetrix Expression Console.

data_processing: Raw microarray data in CEL file format were read in and normalized with the R Bioconductor gcrma package.

source_name: d14 GC V23

label_protocol: A total of 15 μg of labeled cRNA was chemically fragmented at 94°C for 35 min in a 40 mM Tris-acetate (pH 8.1), 100 mM potassium acetate, 30 mM magnesium acetate buffer, and then hybridized to Affymetrix Mouse 430 2.0 oligonucleotide chips

growth_protocol: Cells were kept at 4°C in buffers containing 0.05% sodium azide to minimize alterations in gene expression.

extract_protocol: Total RNA was extracted from FACS-sorted B cells using the RNeasy Mini kit with on-column DNase digestion (Qiagen) and 1–4 μg were used to prepare biotinylated cRNA

treatment_protocol: For isolation of germinal center B cells, Balb/c background mice carrying IgH transgenic alleles and targeted deletions of the endogenous JH locus (VH186.2-Tg JH KO (B1-8) and V23-Tg JH KO (V23)) were immunized i.p. with  50 ug of NP25- chicken gamma globulin (NP-CGG) precipitated in alum. 14-day later, splenocytes were isolated and stained with fluorescently labeled peanut agglutinin (PNA, Vector Laboratories), anti- λ (goat polyclonal, SouthernBiotech) and anti-CD45R/B220 (RA3-6B2) to identify λ+ PNA+ B220+ cells. Naive B cell controls were isolate from spleens of unimmunized Balb/c mice and cells were purified on a FACSAria cell sorter (Becton Dickinson), as previously described. Live/dead discrimination was accomplished based on forward/side scatter (FSC/SSC) and propidium iodide exclusion.

tag: cell

value: B cell

value: Balb/c


title: cortex_hypoxia_NBQX_12-Hour_rep4

tag: pre-hypoxia-temperature

tag: ratuniqueidentifier


title: H4 2-4 hr OR embryo D.melanogaster ChIP Rep2

source_name: H4 2-4 hr OR Em. ChIP expt.1538 channel_1

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Embryos not older than 16h were collected, bleached in 2.5-3.0% Na-hypochlorite solution, washed two times in cold EWB. Incubated with freshly made 1.8% formaldehyde in X-linking buffer in the presence of of n-heptane.After incubation, embryos were re-suspended in Stop solution Washed at +40C in ChIP wash A solution and then at +40C in ChIP wash B. After sedimentation of the embryos ChIP wash B solution was removed and the embryos were used in an experiment or frozen in liquid N2.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

value: Oregon-R

value: Embryo 2-4hr OR


title: cortex_hypoxia_NBQX_12-Hour_rep2

value: NBQX


title: cortex_hypoxia_NBQX_12-Hour_rep5

value: hypoxia


title: Buccal cell 18m twin 1, B1016

tag: gender

tag: cell type

tag: monozygotic

tag: dizygotic

tag: monochorionic

tag: sibship

tag: twin


title: Buccal cell 18m twin 2, 1035


title: cortex_hypoxia_NBQX_6-Hour_rep4

description:
cortex of P10 rat pup subjected to 15 min. hypoxia condition, followed by four IP administrations of NBQX over a 48h period, and killed at 6h post-hypoxia/normoxic control condition.
Response to hypoxic seizures in conjunction with post-hypoxia treatment with anti-epileptogenic compound NBQX, in cortical tissues.

tag: timetofirstszmin

tag: tissue

value: cortex


title: H4 2-4 hr OR embryo D.melanogaster ChIP Rep1

source_name: H4 2-4 hr OR Em. ChIP expt.1537 channel_1

tag: strain

tag: developmental stage

tag: genotype


title: H4 2-4 hr OR embryo D.melanogaster Input Rep2

description: Served as Input for: 1537.Mvalues.bedgraph

source_name: H4 2-4 hr OR Em. Input expt.910 channel_1


title: Young steady-state male HSC, biological replicate 1

description: Young steadystate male #1

source_name: Steady-state HSC Young

tag: background strain

tag: genotype/variation

tag: age

value: 3-4 months


title: cortex_hypoxia_NBQX_6-Hour_rep5

source_name: cortex of P10 rat pup

tag: compound

tag: flagbothtissues

tag: hypoxia

tag: post-hypoxia-temperature

tag: pre-hypoxia-temperature


title: d14 GC V23_rep1

description: Gene expression data from d14 GC V23

tag: cell


title: H4 2-4 hr OR embryo D.melanogaster Input Rep1

description: Served as Input for: 1538.Mvalues.bedgraph

source_name: H4 2-4 hr OR Em. Input expt.909 channel_1


title: cortex_hypoxia_NBQX_6-Hour_rep3

tag: ratuniqueidentifier


title: cortex_hypoxia_NBQX_6-Hour_rep1


title: cortex_hypoxia_NBQX_1-Hour_rep3

description:
cortex of P10 rat pup subjected to 15 min. hypoxia condition, followed by four IP administrations of NBQX over a 48h period, and killed at 1h post-hypoxia/normoxic control condition.
Response to hypoxic seizures in conjunction with post-hypoxia treatment with anti-epileptogenic compound NBQX, in cortical tissues.


title: d14 GC B1-8_rep3

description: Gene expression data from d14 GC B1-8


title: d14 GC B1-8_rep1

description: Gene expression data from d14 GC B1-8


title: HP4 Q4072 Kc167 D.melanogaster ChIP Rep2

source_name: HP4 Q4072 Kc ChIP expt.1683 channel_1

extract_protocol:
1. Grow cell cultures in large T-flasks (175-225cm2) to a density of~5x106 cells/ml. Combine the content of 2-3 flasks in one. Immediately proceed with the following steps.   2. Add 37% formaldehyde (Sigma) to final concentration 1.8% directly to the culture incubate for 10min at 250C on a rotating or rocking platform.   3. Stop reaction by adding 1.25M glycine pH 7.0 to each culture to the final concentration of 125mM. Mix well, within next 5 min aliquot cell suspension into 50ml falcon tubes and accumulate them on ice.   4. Pellet fixed cells by spinning for 2? at 1500g, +40C. Use swinging bucket rotor.   5. Resuspend each pellet in 5ml of sterile 1xPBS, pool suspensions together.   6. Pellet the cells by spinning for 2? at 1500g, +40C.   7. Resuspend the cells in 10ml of ChIP wash A solution. Transfer suspension to a new 15ml Falcon tube. Wash fixed cells for 10min at +40C using rotating wheel. Pellet as above.   8. Thoroughly resuspend fixed cells in 10ml of  ChIP wash B solution, wash for 10min at +40C. Use rotating wheel.
After treatment with formaldehyde, Drosophila tissue culture cells were lysed with SDS and sonication (on ice) in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.  Ribonucleic acid was removed by RNAse A, and the DNA was purified using SDS, proteinase K, and organic extraction, followed by ethanol precipitation.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

tag: cell line

value: embryo-derived cell-line

value: late embryonic stage

value: se/e

tag: Sex

value: Female


title: cortex_hypoxia_NBQX_6-Hour_rep2

tag: timetofirstszmin


title: cortex_hypoxia_NBQX_1-Hour_rep2

tag: tissue


title: cortex_hypoxia_vehicleControl_1-Week_rep5

description:
cortex of P10 rat pup subjected to 15 min. hypoxia condition, followed by four IP administrations of vehicleControl over a 48h period, and killed at 168h post-hypoxia/normoxic control condition.
Response to hypoxic seizures in cortical tissues.

value: vehicleControl


title: cortex_hypoxia_NBQX_1-Hour_rep4


title: Navie_rep4

description: Gene expression data from navie sample

source_name: Navie


title: d14 GC V23_rep3

description: Gene expression data from d14 GC V23


title: HP4 Q4072 Kc167 D.melanogaster ChIP Rep1

source_name: HP4 Q4072 Kc ChIP expt.1682 channel_1


title: Navie_rep3

description: Gene expression data from navie sample


title: d14 GC B1-8_rep2

description: Gene expression data from d14 GC B1-8


title: cortex_hypoxia_NBQX_1-Hour_rep1


title: cortex_hypoxia_NBQX_12-Hour_rep3


title: HP4 Q4072 Kc167 D.melanogaster Input Rep2

description: Served as Input for: 1683.Mvalues.bedgraph

source_name: HP4 Q4072 Kc Input expt.815 channel_1


title: cortex_hypoxia_vehicleControl_1-Week_rep2


title: cortex_hypoxia_vehicleControl_1-Week_rep3


title: cortex_hypoxia_vehicleControl_1-Week_rep4


title: Navie_rep1

description: Gene expression data from navie sample


title: cortex_hypoxia_vehicleControl_1-Week_rep1


title: Navie_rep2

description: Gene expression data from navie sample


title: cortex_hypoxia_vehicleControl_48-Hour_rep5

description:
cortex of P10 rat pup subjected to 15 min. hypoxia condition, followed by four IP administrations of vehicleControl over a 48h period, and killed at 48h post-hypoxia/normoxic control condition.
Response to hypoxic seizures in cortical tissues.


title: cortex_hypoxia_vehicleControl_48-Hour_rep3


title: cortex_hypoxia_vehicleControl_48-Hour_rep4


title: HP4 Q4072 Kc167 D.melanogaster Input Rep1

description: Served as Input for: 1682.Mvalues.bedgraph

source_name: HP4 Q4072 Kc Input expt.814 channel_1


title: H3K23ac 2-4 hr OR embryo D.melanogaster ChIP Rep2

source_name: H3K23ac 2-4 hr OR Em. ChIP expt.895 channel_1

tag: strain

value: wild type


title: H3K23ac 2-4 hr OR embryo D.melanogaster ChIP Rep3

source_name: H3K23ac 2-4 hr OR Em. ChIP expt.1053 channel_1

tag: developmental stage


title: cortex_hypoxia_vehicleControl_48-Hour_rep2


title: H3K23ac 2-4 hr OR embryo D.melanogaster Input Rep2,3

description: Served as Input for: 895.Mvalues.bedgraph, 1053.Mvalues.bedgraph

source_name: H3K23ac 2-4 hr OR Em. Input expt.800 channel_1

tag: genotype


title: H3K23ac 2-4 hr OR embryo D.melanogaster ChIP Rep1

source_name: H3K23ac 2-4 hr OR Em. ChIP expt.894 channel_1


title: Testis_10.0ug/LEE2_Day7_repB

city: Durham

first: Hilary

last: Miller

state: NC

address: LSRC Science Drive Rm A305

institute: Duke University

description: Testicular gene expression of adult medaka of exposure day 7 (10.0 ug/L EE2)

hyb_protocol: Cy3-labeled cRNA (1.65 mg) from each sample was hybridized to an Agilent Custom Medaka Microarray, AMADID 022364. Control or experimental cRNA (0.75 μg) was hybridized to each array as a single channel hybridization. Hybridization was conducted on a custom 15K x 8 Agilent medaka array using the “In situ hybridization Kit-Plus” (Agilent) at 60 °C for 17 h. The arrays were washed according to Agilent's SSPE wash protocol using a solution of 6× SSPE, 0.005% N-lauroylsarcosine, followed by a solution of 0.06× SSPE, 0.005% N-lauroylsarcosine, and Agilent's Stabilization and Drying Solution.

scan_protocol: The arrays were scanned on an Agilent G2565BA Microarray Scanner.

data_processing: Data from the scans were compiled with Agilent Feature Extraction Software 8.1 Analysis of the microarray data was performed using JMP Genomics 4.1(SAS Institute Inc, Cary, North Carolina).  Data was log2 transformed during the import process and normalized using the standard normalization routine implemented in JMP Genomics 4.1. A distribution analysis was conducted for quality control purposes prior- and subsequent to normalization and alignment of the overlay plots was used as an indicator of high quality data. Data analysis was performed by conducting a Principal components analysis (PCA) by day and treatment using time-matched treatment-to-control differences calculated from standard least-square mean. An ANOVA was performed to test for statistical differences between treatment and control groups on a day by day basis. The False Discovery Rate (FDR) at alpha 0.05 was used to account for the multiple testing problem. Hierarchical clustering was performed using the significant gene sets derived from the ANOVA analysis data set.

organism: Oryzias latipes

source_name: Testis, Day 7, 10.0ug/L EE2, replicate 2

label_protocol: Two hundred nanograms of total RNA was converted into labeled cRNA with nucleotides coupled to fluorescent dye Cy3 using the Quick Amp Kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s protocol. The quality of the labeled cRNA was verified and concentration was measured spectrophotometrically.

extract_protocol: Each sample (comprised of 3 pooled testes) were homogenized with 1 ml RNA Bee (TelTest, Friendswood, Texas) using a Polytron homogenizer (Kinematica, Bohemia, New York) cleaned with RNaseZAP (Sigma, St. Louis, Missouri), diethylpyrocarbonate (DEPC) treated water, and sterile de-ionized water. Total RNA was purified from the homogenate using RNeasy Mini Kit (Qiagen, Valencia, California) followed by an on-column-digest with DNase to eliminate DNA contamination using RNase-free DNase Set according to manufacturer’s instructions (Qiagen, Valencia, California).  The sample was then eluted with 30 µl RNase-free water (52°C). Total RNA samples were stored at -80°C.The quantity of each of the total RNA samples associated with this project was determined by spectrophotometry and the size distribution was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, California).

treatment_protocol: Six month old male medaka were exposed to ethinyl estradiol (EE2; Control (DMSO), 1.0ug/L EE2 or 10.0ug/L EE2) for a 14 day time period. Fish were sampled for gene expression on days 1, 7 and 14 of exposure. Five male fish were placed in 2-liter beaker replicates for each treatment and sampling time point. ERM was spiked with the appropriate EE2 stock (0.0025% of total volume) and equally distributed between the 2-L beakers for a total of 2 L spiked ERM per beaker with a 50% renewal of spiked ERM every other day for 14 days. The fish were maintained under a 16:8 hour light:dark cycle and fed ad libitum the dry diet as above on alternate days. On each sampling day, the testis of three fish per replicate beaker (n=3) were removed, pooled and immediately frozen in liquid nitrogen for RNA isolation.

value: Testis

tag: gender

value: male

value: 6 months

tag: treatment

tag: treatment dose

tag: exposure day

value: Day 7

tag: replicate

value: rep B

tag: testicular histology

value: thickening of the interstitial tissue, increased apoptosis of spermatocytes and spermatids

tag: fertilization rate


title: Testis_10.0ug/LEE2_Day14_repC

description: Testicular gene expression of adult medaka of exposure day 14 (10.0 ug/L EE2)

source_name: Testis, Day 14, 10.0ug/L EE2, replicate 3

tag: age

value: Day 14

value: rep C

value: increased thickening of the interstitial tissue as well as altered spermatogenesis and a loss of germinal epithelium


title: cortex_hypoxia_vehicleControl_48-Hour_rep1

tag: compound

tag: flagbothtissues

tag: hypoxia

value: hypoxia

tag: post-hypoxia-temperature

tag: pre-hypoxia-temperature

value: cortex


title: cortex_hypoxia_vehicleControl_12-Hour_rep3

description:
cortex of P10 rat pup subjected to 15 min. hypoxia condition, followed by four IP administrations of vehicleControl over a 48h period, and killed at 12h post-hypoxia/normoxic control condition.
Response to hypoxic seizures in cortical tissues.

tag: ratuniqueidentifier

tag: timetofirstszmin

tag: tissue


title: Testis_10.0ug/LEE2_Day1_repC

description: Testicular gene expression of adult medaka of exposure day 1 (10.0 ug/L EE2)

source_name: Testis, Day 1, 10.0ug/L EE2, replicate 3

value: Day 1

value: not different from controls


title: cortex_hypoxia_vehicleControl_12-Hour_rep2


title: Testis_10.0ug/LEE2_Day7_repA

source_name: Testis, Day 7, 10.0ug/L EE2, replicate 1

value: rep A


title: Testis_10.0ug/LEE2_Day14_repA

source_name: Testis, Day 14, 10.0ug/L EE2, replicate 1


title: cortex_hypoxia_vehicleControl_6-Hour_rep2

description:
cortex of P10 rat pup subjected to 15 min. hypoxia condition, followed by four IP administrations of vehicleControl over a 48h period, and killed at 6h post-hypoxia/normoxic control condition.
Response to hypoxic seizures in cortical tissues.


title: cortex_hypoxia_vehicleControl_12-Hour_rep4


title: cortex_hypoxia_vehicleControl_12-Hour_rep1


title: POF (MO 459) 2-4 hr OR embryo D.melanogaster ChIP Rep2

source_name: POF (MO 459) 2-4 hr OR Em. ChIP expt.2007 channel_1

tag: strain

value: Oregon-R

tag: developmental stage

value: Embryo 2-4hr OR

tag: genotype


title: Testis_1.0ug/LEE2_Day14_repC

description: Testicular gene expression of adult medaka of exposure day 14 (1.0 ug/L EE2)

source_name: Testis, Day 14, 1.0ug/L EE2, replicate 3

tag: gender

tag: treatment

tag: treatment dose

value: thickening of interstitial tissue, increased apoptotic spermatocytes and spermatids, small percentage of animal with decrease in spermatozoa


title: Testis_10.0ug/LEE2_Day1_repB

source_name: Testis, Day 1, 10.0ug/L EE2, replicate 2

value: Testis

tag: exposure day

tag: replicate

tag: testicular histology


title: Testis_10.0ug/LEE2_Day7_repC

source_name: Testis, Day 7, 10.0ug/L EE2, replicate 3

value: male

tag: age

tag: fertilization rate


title: POF (MO 459) 2-4 hr OR embryo D.melanogaster ChIP Rep1

source_name: POF (MO 459) 2-4 hr OR Em. ChIP expt.2006 channel_1

value: wild type


title: Testis_10.0ug/LEE2_Day14_repB

source_name: Testis, Day 14, 10.0ug/L EE2, replicate 2

value: 6 months


title: cortex_hypoxia_vehicleControl_1-Hour_rep4

description:
cortex of P10 rat pup subjected to 15 min. hypoxia condition, followed by four IP administrations of vehicleControl over a 48h period, and killed at 1h post-hypoxia/normoxic control condition.
Response to hypoxic seizures in cortical tissues.

source_name: cortex of P10 rat pup

tag: compound

value: vehicleControl

tag: flagbothtissues

tag: hypoxia


title: cortex_hypoxia_vehicleControl_6-Hour_rep4

tag: post-hypoxia-temperature

tag: pre-hypoxia-temperature

tag: ratuniqueidentifier


title: cortex_hypoxia_vehicleControl_1-Hour_rep2

tag: timetofirstszmin

tag: tissue


title: cortex_hypoxia_vehicleControl_1-Hour_rep3


title: cortex_hypoxia_vehicleControl_1-Hour_rep5


title: POF (MO 459) 2-4 hr OR embryo D.melanogaster Input Rep2

description: Served as Input for: 2007.Mvalues.bedgraph

source_name: POF (MO 459) 2-4 hr OR Em. Input expt.1997 channel_1

tag: strain

tag: developmental stage

tag: genotype


title: cortex_hypoxia_vehicleControl_6-Hour_rep3


title: cortex_hypoxia_vehicleControl_1-Hour_rep1


title: POF (MO 459) 2-4 hr OR embryo D.melanogaster Input Rep1

description: Served as Input for: 2006.Mvalues.bedgraph

source_name: POF (MO 459) 2-4 hr OR Em. Input expt.1996 channel_1


title: Testis_1.0ug/LEE2_Day14_repB

source_name: Testis, Day 14, 1.0ug/L EE2, replicate 2

tag: gender

tag: treatment

tag: treatment dose

value: rep B


title: cortex_hypoxia_vehicleControl_6-Hour_rep1


title: cortex_normoxicControl_vehicleControl_1-Week_rep5

description:
cortex of P10 rat pup subjected to 15 min. normoxicControl condition, followed by four IP administrations of vehicleControl over a 48h period, and killed at 168h post-hypoxia/normoxic control condition.
Developmental baseline for cortical tissues.

value: normoxicControl


title: H3K23ac 2-4 hr OR embryo D.melanogaster Input Rep1

description: Served as Input for: 894.Mvalues.bedgraph

source_name: H3K23ac 2-4 hr OR Em. Input expt.690 channel_1


title: cortex_normoxicControl_vehicleControl_1-Week_rep3


title: cortex_normoxicControl_vehicleControl_1-Week_rep2


title: Testis_1.0ug/LEE2_Day1_repC

description: Testicular gene expression of adult medaka of exposure day 1 (1.0 ug/L EE2)

source_name: Testis, Day 1, 1.0ug/L EE2, replicate 3

tag: exposure day

tag: replicate

value: rep C

tag: testicular histology


title: cortex_normoxicControl_vehicleControl_1-Week_rep4

tag: compound


title: cortex_normoxicControl_vehicleControl_48-Hour_rep4

description:
cortex of P10 rat pup subjected to 15 min. normoxicControl condition, followed by four IP administrations of vehicleControl over a 48h period, and killed at 48h post-hypoxia/normoxic control condition.
Developmental baseline for cortical tissues.

tag: flagbothtissues


title: cortex_normoxicControl_vehicleControl_12-Hour_rep5

description:
cortex of P10 rat pup subjected to 15 min. normoxicControl condition, followed by four IP administrations of vehicleControl over a 48h period, and killed at 12h post-hypoxia/normoxic control condition.
Developmental baseline for cortical tissues.

tag: hypoxia


title: cortex_normoxicControl_vehicleControl_48-Hour_rep5

tag: post-hypoxia-temperature


title: cortex_normoxicControl_vehicleControl_12-Hour_rep4

tag: pre-hypoxia-temperature


title: cortex_normoxicControl_vehicleControl_1-Week_rep1

tag: ratuniqueidentifier


title: C-D5

city: Fukuoka

first: Satoshi

last: Matsuo

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

department: Department of Neurosurgery

institute: Graduate School of Medical Sciences, Kyushu University

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (Rabbit Custom Gene Expression Microarray, 4x44K ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

organism: Oryctolagus cuniculus

source_name: basilar artery, day5, replicate3

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

value: basilar artery

tag: condition

value: SAH (day5)


title: cortex_normoxicControl_vehicleControl_48-Hour_rep2

tag: timetofirstszmin

tag: tissue

value: cortex


title: cortex_normoxicControl_vehicleControl_12-Hour_rep3


title: Testis_1.0ug/LEE2_Day7_repB

description: Testicular gene expression of adult medaka of exposure day 7 (1.0 ug/L EE2)

source_name: Testis, Day 7, 1.0ug/L EE2, replicate 2

tag: age

value: Day 7

value: small percent of animals with thickening of the interstitial tissue and decreased spermatozoa

tag: fertilization rate


title: C-D7

source_name: basilar artery, day7, replicate3

value: SAH (day7)


title: cortex_normoxicControl_vehicleControl_48-Hour_rep3


title: Testis_1.0ug/LEE2_Day14_repA

source_name: Testis, Day 14, 1.0ug/L EE2, replicate 1

tag: gender

value: Day 14

value: rep A


title: cortex_normoxicControl_vehicleControl_12-Hour_rep2


title: Testis_1.0ug/LEE2_Day7_repC

source_name: Testis, Day 7, 1.0ug/L EE2, replicate 3

tag: treatment


title: C-ctrl

source_name: basilar artery, control, replicate3

value: normal


title: Testis_1.0ug/LEE2_Day7_repA

source_name: Testis, Day 7, 1.0ug/L EE2, replicate 1

value: Testis

tag: treatment dose


title: C-D3

source_name: basilar artery, day3, replicate3

value: SAH (day3)


title: cortex_normoxicControl_vehicleControl_48-Hour_rep1


title: cortex_normoxicControl_vehicleControl_12-Hour_rep1


title: B-D7

source_name: basilar artery, day7, replicate2


title: Testis_Control_Day14_repC

description: Testicular gene expression of adult medaka of exposure day 14 (control)

source_name: Testis, Day 14, Control (DMSO) replicate 3

value: male

value: Control (DMSO)

tag: exposure day

value: Normal histology with the presence of active spermatigenesis


title: Testis_1.0ug/LEE2_Day1_repB

source_name: Testis, Day 1, 1.0ug/L EE2, replicate 2

value: 6 months

value: Day 1

tag: replicate

value: rep B

value: not different from controls


title: cortex_normoxicControl_vehicleControl_6-Hour_rep5

description:
cortex of P10 rat pup subjected to 15 min. normoxicControl condition, followed by four IP administrations of vehicleControl over a 48h period, and killed at 6h post-hypoxia/normoxic control condition.
Developmental baseline for cortical tissues.

source_name: cortex of P10 rat pup

value: vehicleControl

value: normoxicControl


title: Testis_1.0ug/LEE2_Day1_repA

source_name: Testis, Day 1, 1.0ug/L EE2, replicate 1

tag: testicular histology


title: Testis_Control_Day14_repB

source_name: Testis, Day 14, Control (DMSO) replicate 2


title: B-D5

source_name: basilar artery, day5, replicate2

value: basilar artery

value: SAH (day5)


title: cortex_normoxicControl_vehicleControl_6-Hour_rep4

tag: compound

value: cortex


title: cortex_normoxicControl_vehicleControl_6-Hour_rep1

tag: flagbothtissues


title: B-D3

source_name: basilar artery, day3, replicate2


title: cortex_normoxicControl_vehicleControl_6-Hour_rep6

tag: hypoxia


title: Testis_Control_Day7_repC

description: Testicular gene expression of adult medaka of exposure day 7 (control)

source_name: Testis, Day 7, Control (DMSO) replicate 3

value: Day 7

value: rep C


title: cortex_normoxicControl_vehicleControl_6-Hour_rep2

tag: post-hypoxia-temperature


title: cortex_normoxicControl_vehicleControl_1-Hour_rep4

description:
cortex of P10 rat pup subjected to 15 min. normoxicControl condition, followed by four IP administrations of vehicleControl over a 48h period, and killed at 1h post-hypoxia/normoxic control condition.
Developmental baseline for cortical tissues.

tag: pre-hypoxia-temperature


title: A-D7

source_name: basilar artery, day7, replicate1

value: SAH (day7)


title: hippocampus_hypoxia_NBQX_1-Week_rep3

description:
hippocampus of P10 rat pup subjected to 15 min. hypoxia condition, followed by four IP administrations of NBQX over a 48h period, and killed at 168h post-hypoxia/normoxic control condition.
Response to hypoxic seizures in conjunction with post-hypoxia treatment with anti-epileptogenic compound NBQX, in hippocampal tissues.

source_name: hippocampus of P10 rat pup

value: NBQX

value: hypoxia

tag: ratuniqueidentifier

value: hippocampus


title: Testis_Control_Day14_repA

source_name: Testis, Day 14, Control (DMSO) replicate 1

value: Testis

value: male

value: Control (DMSO)

value: Day 14

value: rep A


title: cortex_normoxicControl_vehicleControl_1-Hour_rep3


title: Testis_Control_Day1_repC

description: Testicular gene expression of adult medaka of exposure day 1 (control)

source_name: Testis, Day 1, Control (DMSO) replicate 3

value: 6 months

value: Day 1

value: Normal histology with the presence of active spermatigenesis


title: Testis_Control_Day7_repA

source_name: Testis, Day 7, Control (DMSO) replicate 1


title: hippocampus_hypoxia_NBQX_1-Week_rep4


title: Testis_Control_Day1_repB

source_name: Testis, Day 1, Control (DMSO) replicate 2

value: rep B


title: Testis_Control_Day7_repB

source_name: Testis, Day 7, Control (DMSO) replicate 2


title: cortex_normoxicControl_vehicleControl_1-Hour_rep2

value: vehicleControl

value: normoxicControl


title: A-D3

source_name: basilar artery, day3, replicate1

value: basilar artery

tag: condition

value: SAH (day3)


title: hippocampus_hypoxia_NBQX_1-Week_rep2

tag: timetofirstszmin


title: cortex_normoxicControl_vehicleControl_1-Hour_rep1

tag: tissue

value: cortex


title: hippocampus_hypoxia_NBQX_48-Hour_rep3

description:
hippocampus of P10 rat pup subjected to 15 min. hypoxia condition, followed by four IP administrations of NBQX over a 48h period, and killed at 48h post-hypoxia/normoxic control condition.
Response to hypoxic seizures in conjunction with post-hypoxia treatment with anti-epileptogenic compound NBQX, in hippocampal tissues.

value: NBQX


title: hippocampus_hypoxia_NBQX_48-Hour_rep5

value: hypoxia


title: hippocampus_hypoxia_NBQX_1-Week_rep1

value: hippocampus


title: cortex_normoxicControl_vehicleControl_6-Hour_rep3


title: B-ctrl

source_name: basilar artery, control, replicate2

value: normal


title: hippocampus_hypoxia_NBQX_48-Hour_rep4


title: hippocampus_hypoxia_NBQX_12-Hour_rep4

description:
hippocampus of P10 rat pup subjected to 15 min. hypoxia condition, followed by four IP administrations of NBQX over a 48h period, and killed at 12h post-hypoxia/normoxic control condition.
Response to hypoxic seizures in conjunction with post-hypoxia treatment with anti-epileptogenic compound NBQX, in hippocampal tissues.


title: hippocampus_hypoxia_NBQX_48-Hour_rep1


title: A-ctrl

source_name: basilar artery, control, replicate1


title: hippocampus_hypoxia_NBQX_48-Hour_rep2


title: hippocampus_hypoxia_NBQX_12-Hour_rep2


title: hippocampus_hypoxia_NBQX_12-Hour_rep3


title: 23-A375-sh1999-3hrs-ctrl-HSP990 Repeat 1

first: Yaoyu

state: MASSACHUSETTS

address: 250 Massachusetts Ave

institute: Novartis institution of biomedical research

description: Gene expression data from W741C/T877A overexpressing cells treated with 10uM MDV

hyb_protocol: Affymetrix GeneChip eukaryotic hybridization protocol (Affymetrix Inc.)

scan_protocol: GeneChip Scanner 3000 (Affymetrix Inc.)

data_processing: Micorarray Analysis Suite version 5.0 (MAS 5.0) background correction, scaled to 150

label_protocol: Nugen Ovation RNA Amplification System+ WB + FL cDNA Biotin Module V2 (NuGen Lts)

growth_protocol: All lines were cultured in RPMI-1640 supplemented with 10% FCS and 100ng/ml Doxycycline for 3d prior to treatment with 0.1% DMSO or 100nM HSP990for 3h.

extract_protocol: RNeasy Plus kit (qiagen) following the manufacturers instructions

treatment_protocol: 300K cells were seeded in 6 wells for 3d with 100ng/ml doxyxycline prior to treatment for 3 h

tag: cell line

tag: hsf1 kd

value: no


title: 22-A375-NTC-3hrs-Dox-HSP990 Repeat 1

description: Gene expression data from F876L/T877A AR overexpressing cells treated with 10uM MDV


title: Testis_Control_Day1_repA

source_name: Testis, Day 1, Control (DMSO) replicate 1

value: Testis

tag: gender

value: male

tag: age

value: Control (DMSO)

tag: fertilization rate


title: 24-A375-sh1999-3hrs-Dox-HSP990 Repeat 1

value: Yes

tag: treatment


title: hippocampus_hypoxia_NBQX_6-Hour_rep6

description:
hippocampus of P10 rat pup subjected to 15 min. hypoxia condition, followed by four IP administrations of NBQX over a 48h period, and killed at 6h post-hypoxia/normoxic control condition.
Response to hypoxic seizures in conjunction with post-hypoxia treatment with anti-epileptogenic compound NBQX, in hippocampal tissues.


title: 21-A375-NTC-3hrs-ctrl-HSP990 Repeat 1


title: 20-A375-sh1999-3hrs-Dox-DMSO Repeat 1

description: Gene expression data from T877A AR overexpressing LNCaPs treated with 10uM MDV

value: DMSO


title: hippocampus_hypoxia_NBQX_12-Hour_rep1


title: 19-A375-sh1999-3hrs-ctrl-DMSO Repeat 1


title: hippocampus_hypoxia_NBQX_6-Hour_rep2


title: hippocampus_hypoxia_NBQX_1-Hour_rep4

description:
hippocampus of P10 rat pup subjected to 15 min. hypoxia condition, followed by four IP administrations of NBQX over a 48h period, and killed at 1h post-hypoxia/normoxic control condition.
Response to hypoxic seizures in conjunction with post-hypoxia treatment with anti-epileptogenic compound NBQX, in hippocampal tissues.


title: hippocampus_hypoxia_NBQX_6-Hour_rep3


title: 8-A375-sh1999-3hrs-Dox-HSP990

description: Gene expression data from W741C/T877A overexpressing cells treated with 0.1% DMSO


title: A-D5

source_name: basilar artery, day5, replicate1

value: SAH (day5)


title: hippocampus_hypoxia_NBQX_6-Hour_rep5


title: hippocampus_hypoxia_NBQX_6-Hour_rep1


title: hippocampus_hypoxia_NBQX_1-Hour_rep2


title: hippocampus_hypoxia_NBQX_1-Hour_rep3


title: 18-A375-NTC-3hrs-Dox-DMSO Repeat 1

description: Gene expression data from vec control cells treated with 10uM MDV


title: M/M vs V/V, replicate 5

city: New York

first: Pei-Ken

last: Hsu

state: NY

institute: Columbia University

description: Biological replicate 5 of 5

hyb_protocol: hybridized to dual-channel microarray μParaFlo microfluidics chips (LC Sciences)

scan_protocol: Images were collected using a GenePix 4000B laser scanner (Molecular Devices) and digitized them using Array-Pro image analysis software (Media Cybernetics).

data_processing: The microarray data were corrected by removing spots with intensity equal to or below median background and then normalized with the LOWESS (locally weighted regression) method implemented in ArrayAssist 5.5 software (Stratagene)

source_name: Total RNA from hippocampi of an adult (8 wk) Met/Met mouse

label_protocol: purified small RNAs were labeled with Cy5 (hBDNFVal/Val ) or Cy3 (hBDNFMet/Met) fluorescent dye

extract_protocol: Total RNA extracted using mirVana miRNA isolation kit (Ambion) following manufacturer's instructions

tag: strain

source_name: Total RNA from hippocampi of an adult (8 wk) Val/Val mouse


title: M/M vs V/V, replicate 4

description: Biological replicate 4 of 5


title: M/M vs V/V, replicate 2

description: Biological replicate 2 of 5


title: hippocampus_hypoxia_NBQX_1-Hour_rep1


title: M/M vs V/V, replicate 1

description: Biological replicate 1 of 5


title: 7-A375-sh1999-3hrs-ctrl-HSP990


title: hippocampus_hypoxia_vehicleControl_1-Week_rep1

description:
hippocampus of P10 rat pup subjected to 15 min. hypoxia condition, followed by four IP administrations of vehicleControl over a 48h period, and killed at 168h post-hypoxia/normoxic control condition.
Response to hypoxic seizures in hippocampal tissues.


title: hippocampus_hypoxia_vehicleControl_1-Week_rep2


title: hippocampus_hypoxia_NBQX_6-Hour_rep4


title: hippocampus_hypoxia_vehicleControl_1-Week_rep3


title: 17-A375-NTC-3hrs-ctrl-DMSO Repeat 1


title: M/M vs V/V, replicate 3

description: Biological replicate 3 of 5


title: hippocampus_hypoxia_vehicleControl_1-Week_rep4


title: hippocampus_hypoxia_vehicleControl_48-Hour_rep5

description:
hippocampus of P10 rat pup subjected to 15 min. hypoxia condition, followed by four IP administrations of vehicleControl over a 48h period, and killed at 48h post-hypoxia/normoxic control condition.
Response to hypoxic seizures in hippocampal tissues.


title: 5-A375-NTC-3hrs-ctrl-HSP990

description: Gene expression data from F876L/T877A AR overexpressing cells treated with 0.1% DMSO


title: hippocampus_hypoxia_vehicleControl_1-Week_rep5


title: 6-A375-NTC-3hrs-Dox-HSP990


title: hippocampus_hypoxia_vehicleControl_48-Hour_rep4


title: hippocampus_hypoxia_vehicleControl_48-Hour_rep3


title: hippocampus_hypoxia_vehicleControl_48-Hour_rep2


title: hippocampus_hypoxia_vehicleControl_12-Hour_rep3

description:
hippocampus of P10 rat pup subjected to 15 min. hypoxia condition, followed by four IP administrations of vehicleControl over a 48h period, and killed at 12h post-hypoxia/normoxic control condition.
Response to hypoxic seizures in hippocampal tissues.


title: hippocampus_hypoxia_vehicleControl_48-Hour_rep1


title: hippocampus_hypoxia_vehicleControl_6-Hour_rep3

description:
hippocampus of P10 rat pup subjected to 15 min. hypoxia condition, followed by four IP administrations of vehicleControl over a 48h period, and killed at 6h post-hypoxia/normoxic control condition.
Response to hypoxic seizures in hippocampal tissues.


title: 3-A375-sh1999-3hrs-ctrl-DMSO

description: Gene expression data from T877A AR overexpressing LNCaPs treated with 0.1% DMSO


title: 4-A375-sh1999-3hrs-Dox-DMSO


title: hippocampus_hypoxia_vehicleControl_12-Hour_rep1


title: hippocampus_hypoxia_vehicleControl_1-Hour_rep4

description:
hippocampus of P10 rat pup subjected to 15 min. hypoxia condition, followed by four IP administrations of vehicleControl over a 48h period, and killed at 1h post-hypoxia/normoxic control condition.
Response to hypoxic seizures in hippocampal tissues.


title: hippocampus_hypoxia_vehicleControl_1-Hour_rep3


title: FB3

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description:
FB_3-4.txt
Gene expression in hypothalamic ARC nuclei of prenatally betamethasone treated P14 female rat

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two pups were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) rat (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing: The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction 10.7.3.1 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.

source_name: Control (prenatally (G15) expossed to betamethasone) P14 female rat hypothalamic ARC nucleus Replicate 3

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: Time-pregnant Sprague-Dawley rats were purchased from approved source (Taconic Farms, Germantown, NY). The rats were housed individually during the remainder of their pregnancy in the animal facility with free access to standard rat chow and water on the regular 12 hour light-dark cycle with the lights on at 07:00 am.

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE) Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: On G15, some pregnant rats received 2 injections of betamethasone (Sigma-Aldrich, St. Louis, MO) at 0.4 mg/kg each at 08:30 and 18:30; controls received vehicle (normal saline) instead. Delivery was consistent on G23, considered as postnatal day (P) 0 for the offspring. On P1, the offspring were identified and marked, and litters were culled down to four males and four females.

tag: Sex

value: female

value: Sprague-Dawley

value: hypothalamic ARC nuclei

tag: developmental stage


title: FB1

description:
FB_1-2.txt
Gene expression in hypothalamic ARC nuclei of prenatally betamethasone treated P14 female rat

source_name: Control (prenatally (G15) expossed to betamethasone) P14 female rat hypothalamic ARC nucleus Replicate 1


title: hippocampus_hypoxia_vehicleControl_6-Hour_rep4

tag: compound

value: vehicleControl

tag: flagbothtissues


title: MB4

description:
MB_3-4.txt
Gene expression in hypothalamic ARC nuclei of prenatally betamethasone treated P14 male rat

source_name: Control (prenatally (G15) expossed to betamethasone) P14 male rat hypothalamic ARC nucleus Replicate 4


title: hippocampus_hypoxia_vehicleControl_12-Hour_rep4

tag: hypoxia

tag: post-hypoxia-temperature


title: MB3

source_name: Control (prenatally (G15) expossed to betamethasone) P14 male rat hypothalamic ARC nucleus Replicate 3


title: hippocampus_hypoxia_vehicleControl_6-Hour_rep2

source_name: hippocampus of P10 rat pup

tag: pre-hypoxia-temperature

tag: ratuniqueidentifier


title: DAC RL

description: RNA from xenograft bone marrow

hyb_protocol: Hybridization was performed by the Affymetrix service provider in the University of Birmingham

scan_protocol: Scanning was performed by the Affymetrix service provider in the University of Birmingham

data_processing: Data was quantile normalized. Differentially regulated genes were identified using Limma. Each drug treated sample was compared to the PBS control and the FC shown in an excel sheet.

source_name: AML xenograft bone marrow treated with DAC

label_protocol: Samples were fragmented and labeled using the WT Labeling Kit (Affymetrix)

extract_protocol: RNA was extracted from the xenograft bone marrow using the Qiagen all prep kit

value: bone marrow

tag: disease

value: paediatric AML


title: hippocampus_hypoxia_vehicleControl_6-Hour_rep1

tag: timetofirstszmin

tag: tissue


title: hippocampus_hypoxia_vehicleControl_1-Hour_rep2


title: hippocampus_hypoxia_vehicleControl_12-Hour_rep2


title: PBS RB

description: RNA from xenograft bone marrow

source_name: AML xenograft bone marrow treated with PBS (control)


title: PBS RL

description: RNA from xenograft bone marrow


title: PBS GB

description: RNA from xenograft bone marrow


title: hippocampus_hypoxia_vehicleControl_1-Hour_rep1


title: hippocampus_hypoxia_vehicleControl_1-Hour_rep5


title: 2-A375-NTC-3hrs-Dox-DMSO

description: Gene expression data from vec control cells treated with 0.1% DMSO

tag: cell line

tag: hsf1 kd


title: FB2

source_name: Control (prenatally (G15) expossed to betamethasone) P14 female rat hypothalamic ARC nucleus Replicate 2


title: 1-A375-NTC-3hrs-ctrl-DMSO