title: 54556502

description: Shoots from Olea europaea taken at 24 months of growth

source_name: 24-months a

value: 24 months


title: 54557602

status: Public on Nov 09 2013

type: RNA

city: Vairao

first: Antonio

last: Muñoz

state: Porto

address: Rua Padre Armando Quintas, 7 (Campus Agrario)

country: Portugal

institute: CIBIO-InBIO (University of Porto)

description: Shoots from Olea europaea taken at 27 months of growth

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

molecule: polyA RNA

organism: Olea europaea

source_name: 27-months c

label_protocol: PolyA RNA was obtained and labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com

growth_protocol: 21 seedlings originating from open pollination of olive cultivar ‘Arbequina’ were grown in a greenhouse in Centro IFAPA “Churriana” Málaga, Spain. At the sixth month the apical shoot was removed and kept for genomic analysis. Any lateral shoot was removed to force the growth along just one axis.

extract_protocol: 1 cm long apical-shoot tips of olive seedlings were taken every three months, starting at the sixth month and frozen in liquid nitrogen. Tissues were homogenized with a mixer mill MM 400 (Retsch). Total RNA was extracted and purified from samples by TRIzol® Reagent (Invitrogen Corporation, Carlsbad, CA, USA) and treated with DNase I RNase free (Roche, Basel, Switzerland). Finally, total RNA was purified with the RNeasy Mini Kit® (Quiagen) and quantified by spectrophotometry with a Take3 Synergy HT spectrophotometer (Bio-Tek) and stored at -80°C until used.

treatment_protocol: Every three months a new (1 cm long) apical-shoot tip was taken, which included the meristem down to two very small young leaves. When the apical-shoot tip is removed the two lateral buds immediately below are activated, one of them is removed, and the other one becomes the new apical-shoot tip. Seedlings reaching 50 nodes or 1 m high were allowed to form a top canopy. From then, the samples were taken from apical shoots of higher branches.

tag: cultivar

value: Arbequina

tag: tissue

value: apical shoot

tag: collection time

value: 27 months


title: 54555902

description: Shoots from Olea europaea taken at 12 months of growth

value: 12 months


title: 3TG-C-CxF1

status: Public on Sep 16 2013

type: genomic

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: R packages: lumi, genefilter, mpm

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6 Brain Frontal Cortex 356-C-CxF1

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from brain samples using phenol-extraction standard protocol.

tag: strain

value: Brain Frontal Cortex


title: 54555802

description: Shoots from Olea europaea taken at 9 months of growth

value: 9 months


title: 54555402

description: Shoots from Olea europaea taken at 21 months of growth

source_name: 21-months b

value: 21 months


title: 54555702

source_name: 24-months b


title: 54555002

source_name: 24-months c


title: Unbound fraction Sleep dep animal, biological rep 11

status: Public on Aug 20 2013

city: Madison

first: Michele

last: Bellesi

state: WI

address: 6001 Research Park Blvd

country: USA

institute: University Wisconsin-Madison

description: Expression data from the unbound fraction of sleep deprived mice

hyb_protocol: Samples were hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 arrays (n=36, one chip per mouse) following Affymetrix standard protocol

scan_protocol: Samples were scanned using the GC3000 7G scanner (Affymetrix)

data_processing: For both IP and UB replicates, GeneChip Cel files were imported into Bioconductor, data were converted to log2 scale, and transcripts called “absent” in all chips were not used for analysis. Data were normalized within each behavioral state group using Robust Multi-array Average (RMA, (Irizarry et al., 2003)).

label: biotin

molecule: total RNA

source_name: Unbound fraction Sleep deprived animal

label_protocol: Five µg of amplified material was then fragmented, biotin labeled with the Encore Biotin Module (Nugen, #4200)

extract_protocol: RNA, which represents the mRNA immunoprecipitated from the targeted cell type (B fraction), was purified following the Nanoprep protocol including on column DNase digestion. The RNA from the supernatant (unbound fraction; UB) was isolated using the RNeasy Mini kit (Qiagen).

treatment_protocol:
sleeping mice were killed during the light phase (at ~3-5 pm), at the end of a long period of sleep (> 45 min, interrupted by periods of wake of < 4 min), and after spending at least 75% of the previous 6–7 h asleep.
awake mice were killed during the dark period (at ~3-5 am) at the end of a long period of wake (> 1 h, interrupted by periods of sleep of < 5 min), and after spending at least 70% of the previous 6–7 h awake.
sleep deprived mice were spontaneously awake during most of the dark phase and then maintained awake during the light period for 4h by exposure to novel objects.

value: brain

tag: genotype/variation

value: Cnp – eGFP-L10a


title: Unbound fraction Sleep dep animal, biological rep 10


title: 54555602

description: Shoots from Olea europaea taken at 15 months of growth

value: 15 months


title: 54556402

description: Shoots from Olea europaea taken at 18 months of growth

source_name: 18-months a

value: 18 months


title: 54555502

source_name: 27-months b


title: 54555302

source_name: 18-months c


title: 54557802

description: Shoots from Olea europaea taken at 33 months of growth

source_name: 33-months a

value: 33 months


title: Unbound fraction Sleep dep animal, biological rep 9


title: Unbound fraction Sleep dep animal, biological rep 8


title: Unbound fraction Sleep dep animal, biological rep 7


title: Unbound fraction Waking animal, biological rep 6

description: Expression data from the unbound fraction of waking mice

source_name: Unbound fraction Waking animal


title: Unbound fraction Waking animal, biological rep 5


title: F2_H3K27me3_rep2

status: Public on Jun 01 2014

city: Paris

first: Celine

last: Morey

address: 35 rue Hélène Brion

department: University Paris 7

country: France

institute: UMR7216-Epigenetics and stem cell

description: Sample 2

hyb_protocol: Hybridisation was performed by NimbleGen (http://www.nimblegen.com/products/chip/)

scan_protocol: Scanning was performed by NimbleGen (http://www.nimblegen.com/products/chip/)

data_processing: Reproducibility and quality control of the data were assessed using the “R” software combined with an algorithm especially developed for ChIP-on-Chip data analysis of histone modifications (http://www.epigenome-noe.net/WWW/researchtools/protocol.php?protid=43). Briefly, the global hybridisation patterns across each array were controlled by MA-plotting of all the probe signals on the array and by calculating the Pearson correlation coefficients between pairs of replicates (all the coefficients were > 0.8). The two replicates showing the highest Pearson correlation coefficient were used for further analysis. We applied a Lowess normalisation to each dataset and the 'SAM' algorithms to determined statistically enriched probe (Tusher et al., PNAS, 2001). A VSN (variance stabilization) normalisation of each array was also performed independently, then a SAM algorithm and a lfdr > 0,2 (local false discovery rate probability test) to determine the significance of enrichment of each probel were applied (data not included in this submission but available upon request).

label_protocol: Labelling was performed by NimbleGen using 4 ug of ChIP DNA and 4 ug of Input DNA (http://www.nimblegen.com/products/chip/tutorial.html)

extract_protocol: Chromatin was fixed in 1% formaldehyde for 10 min, sheared to 200-700 bp using a Bioruptor (Diagenode). It was immunoprecipitated using the indicated antibody. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input by phenol extraction and ethanol precipitation. The ChIP material was amplified using whole genome amplification (WGA-2, SIGMA). For detailed protocol see (Navarro et al., Genes Dev, 2005).

treatment_protocol: No treatment

value: XHprt-/Y

tag: gender

value: male

tag: cell type

value: Trophoblast Stem cells isolated from E3.5 blastocysts

tag: chip antibody

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #

source_name: input DNA from wildtype male TS cells H3K27me3 ChIP DNA

value: none, input DNA


title: F3_H3K27me3_rep1

description: Sample 3

value: XHprt-/XWT

value: female

source_name: input DNA from wildtype female TS cells H3K27me3 ChIP DNA


title: Unbound fraction Sleep animal, biological rep 3

description: Expression data from the unbound fraction of sleeping mice

source_name: Unbound fraction Sleep animal


title: Unbound fraction Sleep dep animal, biological rep 6


title: Unbound fraction Sleep animal, biological rep 6


title: Unbound fraction Sleep animal, biological rep 4


title: Unbound fraction Waking animal, biological rep 1


title: Unbound fraction Sleep animal, biological rep 1


title: Unbound fraction Sleep animal, biological rep 5


title: Unbound fraction Waking animal, biological rep 3


title: Myocardium_Pulmonary banding 60 min_Pig V_Control

status: Public on Jun 11 2013

city: Uppsala

first: Per

last: Vikholm

address: Akademiska sjukhuset

department: Cardiothoracic Surgery

country: Sweden

institute: Uppsala University

hyb_protocol: AffymetrixGeneChip® expression arrays (GeneChip® Porcine Genome Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm.

scan_protocol: Arrays were washed and stained with the Fluidics Station 450 and scanned with the GeneChip® Scanner 3000 7G.

data_processing: Analysis of the gene expression data was in the statistical language R (http://www.r-project.org) with packages available from the Bioconductor project (www.bioconductor.org). The raw data were normalized with the robust multi-array average (RMA) method.

label: Biotin

organism: Sus scrofa

source_name: Myocardium, Pulmonary banding 60 minutes

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

extract_protocol: Biopsies was homogenized, then total RNA was extracted using TRIZOL reagent. RNA was purified using Rneasy.

tag: pig id

value: Pig V_control group

value: myocardium; right ventricular free wall

tag: treatment

value: Pulmonary banding 60 minutes (after RVF was established)


title: F1 64_UD:0000039 38E-L

status: Public on Aug 13 2014

city: S. Michele a/Adige

first: Giulia

last: Malacarne

state: Trento

address: Via Edmund Mach,1

department: Genomics and Biology of Fruit Crops Department

country: Italy

institute: Edmund Mach Foundation

description: Gene expression data from berry skin at stage UD:0000039 38E-L of a low flavonoid producer

hyb_protocol: Following fragmentation, 10 mg of cRNAs were hybridized on GeneChip® GrapeGena520510F Arrays for 16 hr at 45°C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Robust Multi-array Analysis (RMA) algorithm was used for background correction, normalization and expression levels summarization (Irizarry et al., 2003). Probesets with significant differential expression (DEPs) between LFPs and HFPs were selected in two steps and under the assumption that the four individuals of the LFPs and HFPs groups can be treated as biological replicates (pseudoreplicates). Step 1: within each group (LFPs and HFPs), the data were analyzed through pairwise comparisons of developmental stages (PV vs. VER, PV vs. MAT and VER vs. MAT). Differential expression analysis was performed with the Bayes t-statistics from LIMMA (Linear Models for Microarray Data), and p-values were corrected for multiple testing using the Benjamini-Hochberg method (Benjamini and Hochberg, 1995). Three lists of DEPs for each group were thus obtained (with a False Discovery Rate (FDR) < 5% and a cut-off of 2-fold change (FC) between each pair of stages). Step 2: the lists of DEPs were then compared between LFPs and HFPs to provide a final list of probesets either exclusively modulated in LFPs or in HFPs, or modulated in both groups but with low correlation (-0.5 > (logFCLFPs - logFCHFPs) pairwise comparison > 0.5).

organism: Vitis vinifera

source_name: F1 64_exocarp_UD:0000039 38E-L_low flavonoid producer

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 4 mg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The population derived from 'Syrah' x 'Pinot Noir' was obtained at Edmund Mach Foundation (FEM, San Michele all'Adige, Italy, 46°18' N, 11°13' E). All the plants were grown at the experimental field "Giaroni" of FEM, grafted on the rootstock Kober 5BB and trained according to the Guyot system. One representative sample for each genotype at each developmental stage was collected in the early morning. To be more representative of the canopy, berries were collected both from a cluster on the shady side and from a cluster on the sunny side. From the second stage (35E-L), the collected berries were dissected into skin, flesh and seeds and then skins were frozen in nitrogen liquid and stored at -80°C till transcriptome analysis.

extract_protocol: Total RNA was extracted from frozen berries using the Spectrum Plant Total RNA Kit  (Sigma Aldrich)

tag: genotype

value: F1 64 (Syrah x Pinot Noir cross)

tag: organism part

tag: developmental stage

tag: metabolic profile

value: low flavonoid producer

tag: growth media

value: field soil


title: Unbound fraction Waking animal, biological rep 2

value: brain

value: Cnp – eGFP-L10a


title: Myocardium_Pulmonary banding 120 min_Pig III_Control

source_name: Myocardium, Pulmonary banding 120 minutes

value: Pig III_control group

value: Pulmonary banding 120 minutes (to induce RVF)


title: Myocardium_Baseline_Pig IV_Control

source_name: Myocardium, Baseline

value: Pig IV_control group

value: Baseline


title: Myocardium_Pulmonary banding 120 min_Pig IV_Control


title: Myocardium_Pulmonary banding 60 min_Pig IV_Control


title: Unbound fraction Waking animal, biological rep 4


title: Unbound fraction Sleep animal, biological rep 2


title: Myocardium_Pulmonary banding 120 min_Pig II_Control

value: Pig II_control group


title: Myocardium_Pulmonary banding 60 min_Pig III_Control


title: Myocardium_Baseline_Pig V_Control


title: Myocardium_Baseline_Pig III_Control


title: F2_H3K27me3_rep1

description: Sample 1

source_name: wildtype male TS cells H3K27me3 ChIP DNA

value: XHprt-/Y

value: male

value: Trophoblast Stem cells isolated from E3.5 blastocysts

value: Millipore


title: Myocardium_Pulmonary banding 60 min_Pig II_Control


title: Myocardium_Pulmonary banding 120 min_Pig V_Control

value: Pig V_control group


title: F3_H3K27me3_rep2

description: Sample 4

source_name: wildtype female TS cells H3K27me3 ChIP DNA

value: XHprt-/XWT

value: female

value: none, input DNA


title: Myocardium_Pulmonary banding 120 min_Pig I_Control

value: Pig I_control group

value: myocardium; right ventricular free wall


title: Myocardium_Pulmonary banding 60 min_Pig I_Control

value: Pulmonary banding 60 minutes (after RVF was established)


title: Myocardium_Baseline_Pig II_Control


title: Myocardium_Pulmonary banding 120 min_Pig III_Shunt

value: Pig III_shunt group


title: Myocardium_Pulmonary banding 120 min_Pig I_Shunt

value: Pig I_shunt group


title: Myocardium_Baseline_Pig IV_Shunt

value: Pig IV_shunt group


title: Myocardium_Pulmonary banding 60 min + Shunt_Pig VI_Shunt

source_name: Myocardium, Pulmonary banding 60 minutes + treatment with Glenn-shunt

value: Pig VI_shunt group

value: Pulmonary banding 60 minutes + treatment with Glenn-shunt (after RVF was established)


title: Myocardium_Pulmonary banding 120 min_Pig II_Shunt

value: Pig II_shunt group

value: Pulmonary banding 120 minutes (to induce RVF)


title: Myocardium_Baseline_Pig VI_Shunt

value: Baseline


title: Myocardium_Pulmonary banding 60 min + Shunt_Pig I_Shunt


title: Myocardium_Pulmonary banding 60 min + Shunt_Pig II_Shunt


title: Myocardium_Pulmonary banding 60 min + Shunt_Pig III_Shunt


title: Myocardium_Pulmonary banding 60 min + Shunt_Pig IV_Shunt


title: Myocardium_Pulmonary banding 60 min + Shunt_Pig V_Shunt

value: Pig V_shunt group


title: Myocardium_Pulmonary banding 120 min_Pig IV_Shunt


title: Myocardium_Baseline_Pig III_Shunt


title: Myocardium_Pulmonary banding 120 min_Pig VI_Shunt


title: Myocardium_Baseline_Pig I_Shunt


title: Myocardium_Pulmonary banding 120 min_Pig V_Shunt


title: Myocardium_Baseline_Pig II_Shunt


title: N39 non-OSCC

status: Public on May 02 2013

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

country: Taiwan

institute: Taiwan National Health Research Institute

description: OSCC

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data analysis was performed with GeneSpring GX software (Agilent Technologies). Arrays with less than 50% detected probes were excluded. Array data from 28 tumor and non-tumor pair-wise sample were then subjected to further analysis. Quantile normalisation was performed.

organism: Homo sapiens

source_name: adjacent non-tumor epithelia

label_protocol: 500ng total RNA was converted into cDNA using biotinylated random nonamers, oligodeoxythymidine 18 primers and Illumina-supplied reagents, according to Illumina manufacturer's instructions.

extract_protocol: OSCC and non-OSCC pair-wise samples were prepared after cutting into 5μm-thick sections on a microtome with a disposable blade.Total RNA was isolated using an RNeasy mini kit (Qiagen) according to the manufacturer's instruction.

value: oral epithelia


title: N40 non-OSCC

description: OSCC


title: N38 non-OSCC

description: OSCC


title: N36 non-OSCC

description: OSCC


title: N35 non-OSCC

description: OSCC


title: N37 non-OSCC

description: OSCC


title: N33 non-OSCC

description: OSCC


title: Myocardium_Baseline_Pig I_Control


title: N29 non-OSCC

description: OSCC


title: N31 non-OSCC

description: OSCC


title: N22 non-OSCC

description: OSCC


title: N34 non-OSCC

description: OSCC


title: N26 non-OSCC

description: OSCC


title: N24 non-OSCC

description: OSCC


title: N17 non-OSCC

description: OSCC


title: N20 non-OSCC

description: OSCC


title: N25 non-OSCC

description: OSCC


title: N27 non-OSCC

description: OSCC


title: Myocardium_Baseline_Pig V_Shunt


title: N19 non-OSCC

description: OSCC


title: N18 non-OSCC

description: OSCC


title: N28 non-OSCC

description: OSCC


title: N21 non-OSCC

description: OSCC


title: N11 non-OSCC

description: OSCC


title: N30 non-OSCC

description: OSCC


title: N32 non-OSCC

description: OSCC


title: N12 non-OSCC

description: OSCC


title: N23 non-OSCC

description: OSCC


title: N16 non-OSCC

description: OSCC


title: N13 non-OSCC

description: OSCC


title: N8 non-OSCC

description: OSCC


title: N14 non-OSCC

description: OSCC


title: N15 non-OSCC

description: OSCC


title: N5 non-OSCC

description: OSCC


title: N10 non-OSCC

description: OSCC


title: N1 non-OSCC

description: OSCC


title: T36 OSCC

description: non-OSCC

source_name: oral squamous cell carcinoma

value: oral squamous cell carcinoma


title: T40 OSCC

description: non-OSCC


title: N6 non-OSCC

description: OSCC


title: N9 non-OSCC

description: OSCC


title: N2 non-OSCC

description: OSCC


title: T26 OSCC

description: non-OSCC


title: T33 OSCC

description: non-OSCC


title: T23 OSCC

description: non-OSCC


title: N3 non-OSCC

description: OSCC


title: T35 OSCC

description: non-OSCC


title: T34 OSCC

description: non-OSCC


title: T38 OSCC

description: non-OSCC


title: T39 OSCC

description: non-OSCC


title: T27 OSCC

description: non-OSCC


title: T22 OSCC

description: non-OSCC


title: T37 OSCC

description: non-OSCC


title: N4 non-OSCC

description: OSCC


title: T28 OSCC

description: non-OSCC


title: T25 OSCC

description: non-OSCC


title: T21 OSCC

description: non-OSCC


title: T29 OSCC

description: non-OSCC


title: T24 OSCC

description: non-OSCC


title: T32 OSCC

description: non-OSCC


title: T30 OSCC

description: non-OSCC


title: T19 OSCC

description: non-OSCC


title: T18 OSCC

description: non-OSCC


title: T16 OSCC

description: non-OSCC


title: T17 OSCC

description: non-OSCC


title: T15 OSCC

description: non-OSCC


title: T20 OSCC

description: non-OSCC


title: T12 OSCC

description: non-OSCC


title: T11 OSCC

description: non-OSCC


title: T2 OSCC

description: non-OSCC


title: T13 OSCC

description: non-OSCC


title: Rv0043c OE by ATc 100 ng Atc 18 Hours TFOE_9257_0043c

status: Public on Feb 19 2013

city: Seattle

first: Tige

last: Rustad

state: WA

address: 307 Westlake Avenue N, Suite 500

department: Pathobiology

institute: Seattle Biomedical Research Institute

description:
TFOE_9257_0043c
Rv0043c OE by ATc
18
Hours
100
ng

hyb_protocol: Hybridization was performed following the standard operating protocol recommended by NimbleGen Systems Inc., Madison, WI, USA . See www.nimblegen.com.

scan_protocol: Scanning was performed using a GenePix 4000B using a single intensity for all 12 arrays on each slide.

data_processing: Data was normalized using RMA normalization with the 'affy' package for R.

organism: Mycobacterium tuberculosis H37Rv

label_protocol: Labeling was performed using indirect labelling of amino-allyl dUTP using protocol from PFGRC (www.pfgrc.org).

growth_protocol: H37Rv was grown to log phase (0.1-0.5 OD600) in Middlebrook 7H9 media supplemented with ADC (Difco) at 37C.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

treatment_protocol: TFOE experiments done at indicated concentration of anhydrotetracycline.  Hypoxic experiments conducted as described previously (Rustad et al., 2008)

tag: experiment

tag: replicate

value: A

tag: time

value: 18 Hours

tag: dose

value: 100 ng Atc

value: Rv0043c OE by ATc


title: T7 OSCC

description: non-OSCC

tag: tissue


title: T4 OSCC

description: non-OSCC


title: T9 OSCC

description: non-OSCC


title: Rv0232 OE by ATc 100 ng Atc 18 Hours TFOE_7879_0232

description:
TFOE_7879_0232
Rv0232 OE by ATc
18
Hours
100
ng

value: Rv0232 OE by ATc


title: N7 non-OSCC

description: OSCC


title: Rv0081-Atc dilution OE by ATc 100 ng Atc 18 Hours TFOE_4428_0081_100ng

description:
TFOE_4428_0081_100ng
Rv0081-Atc dilution OE by ATc
18
Hours
100
ng

value: Rv0081-Atc dilution OE by ATc


title: T3 OSCC

description: non-OSCC


title: Rv0081 OE by ATc 100 ng Atc 18 Hours TFOE_8710_0081

description:
TFOE_8710_0081
Rv0081 OE by ATc
18
Hours
100
ng

value: B

value: Rv0081 OE by ATc


title: Rv0081 OE by ATc 100 ng Atc 18 Hours TFOE_7211_0081_2B

description:
TFOE_7211_0081_2B
Rv0081 OE by ATc
18
Hours
100
ng

value: C


title: T10 OSCC

description: non-OSCC


title: T8 OSCC

description: non-OSCC


title: T5 OSCC

description: non-OSCC


title: T14 OSCC

description: non-OSCC


title: T1 OSCC

description: non-OSCC


title: T6 OSCC

description: non-OSCC


title: Differentiated myotubes (reference) vs G0 synchronized Myoblasts (test) rep2

status: Public on Apr 16 2013

city: SAN ANTONIO

first: PRETHISH

last: SREENIVAS

state: TX

address: 8403 Floyd Curl Dr

department: GCCRI

institute: UTHSCSA

description:
C2C12 MT Vs S48  Rep 2
Expression profile of differentially expressed genes in quiescent myoblast
G0=S48=quiescence

hyb_protocol: Purified Cy3,Cy5 Labelled cDNA was incubated on the NIA15K5  chip at 42 degree celsius for 16hr.washed with 1XSSC+0.2%SDS for 5 min then second wash with 0.1XSSC+0.2%SDS for 5 min and third wash with 0.1XSSC for 5 min and dried the chip by spinning briefly.

scan_protocol: Scanned using  Molecular Dynamics scanner using excitation wavelengths of 543nm and 663nm.

data_processing: LOWESS normalized, TIGR MIDAS, background subtracted VALUE data obtained from log2 of processed Experimental signal/processed reference signal.

source_name: C2C12_differentiated myotubes (MT)

label_protocol: 20 micrograms of RNA is taken for labelling with Cy3/Cy5 dyes. Reverse transcription was performed to make cDNA (1hr 30 min at 42 degrees celsius using SuperScript II from Invitrogen). Unincorporated nucleotides were removed using Millipore Spin columns.

growth_protocol: Grown in Dulbecco's modified Eagle medium supplemented with 20% Fetal calf serum

extract_protocol: RNA was isolated using Trizol Invitrogen.

treatment_protocol: Synchronized cells in G0 and reactivated to enter cell cycle by replating and grown for 24hrs to get synchronized S phase cells

tag: cell line

value: C2C12 cells differentiated in low serum media

source_name: C2C12_G0 synchronized Myoblas (S48)

value: C2C12 cells differentiated in semi-solid media


title: Differentiated myotubes (reference) vs G0 synchronized Myoblasts (test) rep1

description:
C2C12 MT Vs S48  Rep 1
Expression profile of differentially expressed genes in quiescent myoblast
G0=S48=quiescence

tag: cell type

source_name: C2C12_G0 synchronized Myoblast (S48)

value: C2C12 cells suspended in semi-solid media


title: Rv0117 OE by ATc 100 ng Atc 18 Hours TFOE_1280_0117

description:
TFOE_1280_0117
Rv0117 OE by ATc
18
Hours
100
ng

value: Rv0117 OE by ATc


title: Rv0232 OE by ATc 100 ng Atc 18 Hours TFOE_3113_0232

description:
TFOE_3113_0232
Rv0232 OE by ATc
18
Hours
100
ng


title: Rv0078 OE by ATc 100 ng Atc 18 Hours TFOE_4225_0078

description:
TFOE_4225_0078
Rv0078 OE by ATc
18
Hours
100
ng

value: Rv0078 OE by ATc


title: Rv0054 OE by Atc 100 ng Atc 18 Hours TFOE_2431_0054

description:
TFOE_2431_0054
Rv0054 OE by Atc
18
Hours
100
ng

value: Rv0054 OE by Atc


title: Rv0195 OE by Atc 100 ng Atc 18 Hours TFOE_9056_0195

description:
TFOE_9056_0195
Rv0195 OE by Atc
18
Hours
100
ng

value: Rv0195 OE by Atc


title: Rv0081 OE by ATc 100 ng Atc 18 Hours TFOE_4177_0081_3B

description:
TFOE_4177_0081_3B
Rv0081 OE by ATc
18
Hours
100
ng

value: D


title: Liver_animal_2237_resection_0_weeks

status: Public on Jan 01 2013

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

department: Department of Genetics and Biotechnology

country: Denmark

institute: Aarhus University, Faculty of Agricultural Sciences

description: The differential expression of genes regulating the termination of liver regeneration was studied in resected pigs during a time frame of six weeks, and compared with the normal gene expression profiles in sham and control animals. Gene expression profiles were obtained from biopsies sampled in the liver remnant at time points 0 minutes, 3 and 6 weeks after resection and primary surgery in sham and control animals.

hyb_protocol: The labelled and purified reference samples were mixed and divided into aliquots before combining it with a labelled sample. Each of the 36 labelled samples were co-hybridized with an aliquot of the labelled reference sample and a hybridization blocker containing polydA (Invitrogen Corporation, CA, USA) and Yeast tRNA (Invitrogen Corporation, CA, USA) to 27k pig oligonucleotide microarrays (GEO accession: GPL5972) using a Discovery XT hybridisation station (Ventana Discovery Systems, Tucson, AZ, USA). Chip Prep-2 was transferred from 4 ºC to room temperature 1 hour before use. ChipSpread was prepared by mixing equal volumes of ChipSpread A (20 mg/mL BSA, 4x SSC, 0.5 mg/mL sodium azide) and B (formamide; 2 mg/mL SDS) followed by incubation at room temperature for 1 hour before use. Labels were printed, trimmed and placed on the slides. The Chip Map reagents (Chip Prep-1, -2 and - 3) were mixed by inversion; the caps were removed and the reagents were placed in the Discovery. The slides were placed in the machine and the run was initiated. The slides were covered with 2.5 mL ChipSpread when the message appeared and the machine used app. 1.5 hours for pre-hybridization of the slides. The Chiphybe80 was mixed and 200 µL were added to the sample (<20 µL) followed by careful mixing. The sample mixtures were heated at 90°C for 3 minutes in a PCR machine carefully mixed by pipetting. The "button" on the machine was pressed to prepare the slides for hybridization. When prompted to, the samples were applied to the slides which were hybridized at 48 ºC for 6 hours. Oil was wiped from the backside of the slides using a clean-room napkin and the slides were placed in the slide-holder from the High Throughput Wash Station (Telechem, cat.no. HTW) placed in a mTub filled with RiboWash. If processing more than 20 slides, an equal number of slides were placed in two slide-holders and continued in parallel. The slide-holder was transferred to a HTW filled with RiboWash and washed for 2 min with magnetic stirring at 700 rpm. The HTW was refilled with RiboWash and the wash was repeated. The slide-holder was dipped in 2x SSC filled in a mTub (200 mL 20x SSC, Elga H2O + 1800 mL water). The slide-holder was then transferred to a HTW filled with 2x SSC and washed for 2 min with magnetic stirring at 700 rpm followed by refill of the HTW with 2x SSC and repetition of the wash. The slide-holder was dipped 10 times in 0.1x SSC filled in a mTub (5 mL 20x SSC, Elga H2O + 995 mL water) and the holder was left submerged in 0.1x SSC. The slides were transferred to a mBox slide holder placed in a mTub filled with Elga H2O. Arrays were dried by centrifugation (at 300 x g for 4 min placed in a mBox).

scan_protocol: Scanner: ScanArray Express HT system (Perkin Elmer), 5 µm resolution, 100 % laser power and PMT adjusted individually for each channel. Image analysis software: GenePix Pro (version 6.1.0.4,, Molecular Devices) using FeatureType = Irregular Filled and LocalFeature as background measurement.

data_processing: Statistical analysis was carried out in the R computing environment (version 2.6.1 for Windows) using the package Linear Models for Microarray Analysis (Limma, version 2.12.0) which is part of the Bioconductor project. Spots marked as "Not found" by GenePix and spots with more than 50 % of saturated pixels were weighted "0" before the log2-transformed ratios of Alexa-647 to Alexa-555 (not background corrected) were normalized within-slide using global-loess with default parameters as implemented in Limma. The set of normalized log-ratios were then analyzed in Limma to identify genes being significantly differentially expressed due to resection over time adjusting for effects by using the expression profiles obtained from the control animals and the sham operated animals. The false discovery rate was controlled using the method of Benjamini and Hochberg as implemented in Limma and a corrected P-value below 0.20 was considered significant. According to OMIM and Ace View, all genes were classified into 14 groups by molecular function and biological process, illustrated by top tables. This set of genes was further analysed by finding genes associated with another set of genes regulating cell cycle propagation and apoptosis and intracellular redox status that as previously found in an acute model of liver resection.

label_protocol: Total-RNA was extracted from each sample and DNase treated using RNeasy Maxi Kit (Qiagen) following the enclosed protocols. Quantities were measured using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, DE, USA) and qualities were examined by the 28S:18S rRNA ratio using the RNA 6000 Nano LabChip Kit on 2100 Bioanalyzer (Agilent Technologies, CA, USA). Alexa Flour-labeled cDNA was synthesized from 20 µg of total-RNA using Superscript Plus Direct cDNA Labeling System (Invitrogen) and purified using the NucleoSpin 96 Extract II PCR Clean-up kit (Macherey-Nagel, Düren, Germany) following the enclosed protocols. Spike-in RNA from the Lucidea Universal ScoreCard (Amersham Biosciences) was added to the cDNA reactions. "Green" spike-in RNA was added to the common reference samples and "red" spike-in RNA was added to the samples.

growth_protocol: The animals were acclimatized in the animal department for at least 48 hours prior to experiments. They were housed in a closed-system indoor facility with 55   10   relative humidity, 17-18 air changes per hour, temperature of 20   1  C and a 12-hour light/dark cycle. The pigs shared fenceline contact with another familiar pig and were singly housed in 1.5   1.5 m pens with ad libitum access to tap water from nipple waterers, liquid dietary supplement and digestive energy mixed with water, but were fasted overnight prior to the experiment with free access to water. All animals were premedicated with 20 mg Esomeprazol twice daily to prevent ventricular ulcers.

extract_protocol: RNeasy Maxi Kit with DNase treatment following the enclosed protocol (Qiagen).

treatment_protocol: Animals were premedicated with an intramuscular injection of ketamine (10 mg/kg) and atropin (0.05 mg/kg). All animals were intubated and ventilated on a Servo Ventilator 900 (Elema-Schønander, Sweden), and anaesthesia was maintained with Isofluran 1.5-2 % mixed with 50-60 % oxygen. Respiratory rate was adjusted to achieve an Et CO2 between 35 and 40 mmHg. I.v. access was obtained through a vein on the ear. Analgesia was induced and maintained with Fentanyl 0.01 mg/kg, i.v. All animals received a peroperative i.v. volume load consisting of 1000 ml Ringer solution. Volume infusion was continued thereafter with 20 ml/kg/hr 0.9 % NaCl and 10 % Glucose. Before surgery, all animals received a single injection of antibiotic prophylaxis with Enrofloxacin 2.5 mg/kg intramuscularly. The cardio-respiratory status was monitored with an electrocardiogram (ECG), with invasive arterial blood pressure via a cannula in the femoral artery and by hourly arterial blood gas analysis. Intravascular pressure monitoring was performed using calibrated transducers connected to an amplifier (Gould, 2800S, Ohio, USA). Portal venous pressure was monitored via a paediatric CVK (Arrow International) placed directly in the portal vein. Mean alveolar concentration of Isoflurane was monitored using a Capnomac (Nycomed Jean Mette). Body temperature was maintained at approximately 39 ºC with a heating blanket. All recordings were documented hourly until extubation. Operative procedures: A midline laparotomy was used for access to the hepatic hilus. A reference biopsy was sampled from segment IV before resection (t=0) and stored immediately in RNALater (Ambion). Blood extraction was performed via a Hickman catheter (BARD Access Systems) placed in the Jugular vein. This access was also used for blood sampling and postoperative administration of intravenous fluids and medication. A Freka Percutaneous Enteral Gastrostomy (PEG, Fresenius Kabi AG) was placed in the stomach to prevent ventricular retention, observed in pilot experiments. The hepatic artery supplying segments II and III together with these segments’ portal branch were ligated using an absorbable polyfilament suture on a large needle. Thereafter the lobe was strangulated with a 0.5 cm wide cotton ribbon and then removed and weighed. Segments IV, V and VIII were removed in a similar manner leaving segments VI, VII and I in place corresponding to an approximate 60 % PHx. In group two (sham), the pigs underwent exactly the same procedure performed in group one, except the liver resection. In group three (control), the pigs underwent a minimal laparotomy for biopsy sampling from segment IV. Blood was sampled from the jugular vein. No catheters were used. Postoperative pain management was maintained with a transdermal Fentanyl patch (Hexal A/S) delivering 50 µg/h, exchanged with a patch delivering 25 µg/h Fentanyl the following three days. All pigs received water ad libitum and 3 dl of liquid dietary supplements four times daily the first postoperative week, together with a standardized amount of solid pig-feed amounting to 2546 Kcal per day. I.v. fluids were administered daily via the Hickman catheter in the right Jugular vein for pigs in group one and two. The first week the pigs received 250 ml 5 % Glucose (Fresenius Kabi AB) mixed with 20 mg Esomeprazol (Astra Zeneca) in the morning, 500 ml Ringer’s solution (Baxter Medical AB) mixed with 50 mg Erytromycin (Abbott Scandinavia AB) at noon, and 250 ml 5 % Glucose mixed with 20 mg Esomeprazol in the afternoon. Extended i.v. Glucose infusion (500 ml 5 % glucose) was given when the animals in the resection group suffered of anorexia postoperatively. Oral medication was continued with 5 mg/kg Erytromycin daily and 20 mg Esomeprazol twice daily, until biopsy three weeks post PHx. After biopsy the third week, the pigs in group one and two again received i.v. fluids via a new Hickman catheter placed in the left jugular vein. The same amount of fluids and medication was given at the same time each day as after primary operation, but only for three days postoperatively. Oral medication was continued with 5 mg/kg Erytromycin daily and 20 mg Esomeprazol two times per day, until sacrificing the sixth week. Sampling time points were before primary surgery and at three and six weeks postoperatively. The second and third biopsies were sampled from segment IV in sham and control pigs, and segment VI in resected pigs and placed immediately in RNALater (Ambion®). All biopsies were stored overnight in 4 ºC and thereafter in – 70 ºC until further processing. The pigs were sacrificed with an intravenous overdose of 100 mg pentobarbital and 20mmol KCl intracardially on completion of the experiment.

tag: breed

value: Norwegian landrace

tag: gender

value: female

tag: weight

value: app. 30 Kg

value: liver

tag: animal id

tag: treatment group

value: resection

tag: time point

value: 0 weeks

tag: Reference sample consisting of equal amounts of total-RNA from all samples


title: Liver_animal_2273_control_3_weeks

value: control

value: 3 weeks


title: Liver_animal_2345_resection_0_weeks


title: Liver_animal_2344_resection_6_weeks

value: 6 weeks


title: Liver_animal_2387_sham_6_weeks

value: sham


title: Liver_animal_2385_sham_6_weeks


title: Liver_animal_2273_control_6_weeks


title: Liver_animal_2285_sham_0_weeks


title: Liver_animal_2346_sham_6_weeks


title: Liver_animal_2386_control_6_weeks


title: Liver_animal_2237_resection_6_weeks


title: Liver_animal_2286_control_6_weeks


title: Liver_animal_2286_control_0_weeks


title: Liver_animal_2234_control_0_weeks


title: Liver_animal_2329_resection_6_weeks


title: Liver_animal_2344_resection_3_weeks


title: Liver_animal_2385_sham_3_weeks


title: Liver_animal_2329_resection_3_weeks


title: Liver_animal_2386_control_3_weeks


title: Liver_animal_2234_control_6_weeks


title: Liver_animal_2285_sham_6_weeks


title: Liver_animal_2344_resection_0_weeks


title: Liver_animal_2345_resection_3_weeks


title: Liver_animal_2273_control_0_weeks


title: Liver_animal_2234_control_3_weeks


title: Liver_animal_2286_control_3_weeks


title: Liver_animal_2329_resection_0_weeks


title: high-Myc - Replicate 2

status: Public on Oct 25 2012

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized at 45C for 16 hr at 60RPM on GeneChip Arrays (PrimeView). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manurfacturer's instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Expression Console. A CDF containing the ERCC probes was provided by Affymetrix.

data_processing:
A CDF provided by Affymetrix, which contained the ERCC probes (PrimeView_withERCC_binary.cdf) was used instead of the standard PrimeView cdf.
The data were analyzed with Bioconductor using the MAS5 normalization method. Then, these data were renormalized to the external spike-ins. See manuscript for additional details.

source_name: P493-6 cells expressing a high level of c-Myc

label_protocol: Biotinylated aRNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3' IVT Express Kit User Manual, 2009, Affymetrix).

growth_protocol: RPMI 1640 + FBS. Tetracycline repressed c-Myc transgene expression. c-Myc expression released for 24 hours.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
External spike-in RNAs (ERCC ExFold RNA Spike-In kit, Ambion, 4456739) were added based on cell number. See manuscript for details.

treatment_protocol: c-Myc expression released for 24 hours.

value: B-cell lymphoma


title: Liver_animal_2285_sham_3_weeks


title: Liver_animal_2387_sham_0_weeks


title: Liver_animal_2387_sham_3_weeks


title: low-Myc - Replicate 2

source_name: P493-6 cells expressing a low level of c-Myc

growth_protocol: RPMI 1640 + FBS. Tetracycline repressed c-Myc transgene expression. c-Myc expression released for 0 hours.

treatment_protocol: c-Myc expression released for 0 hours.


title: Liver_animal_2386_control_0_weeks


title: Liver_animal_2346_sham_3_weeks


title: high-Myc - Replicate 1


title: T31 OSCC

description: non-OSCC

value: oral squamous cell carcinoma


title: low-Myc - Replicate 1


title: ada2Δ H3K9ac IP replicate 2

status: Public on Dec 10 2011

type: SRA

city: St. Louis

first: Brian

middle: Clifton

last: Haynes

state: MO

address: 4444 Forest Park Ave

department: Computer Science

institute: Washington University

description: Chromatin IP against H3K9ac

library_source: genomic

data_processing:
sam: To produce sam alignments, sequenced reads were aligned to the C. neoformans H99 reference sequence (v2) using Bowtie (v0.12.7).  Reads that mapped to multiple loci were discarded.
bed: SAM alignments were converted to bed files using sam2bed provided by MACS (v1.4.0)
bed (peaks): Peak calling was performed with MACS (v1.4.0) on each biological replicate, using the IP reads as the treatment sample and the input reads as the control sample.  A cutoff p-value for peak detection was selected empirically based on the degree of overlap between biological replicates.

organism: Cryptococcus neoformans

source_name: cultured cells

growth_protocol: Wildtype and ada2Δ cell were cultured in triplicate overnight in YPD, and grown in capsule-inducing conditions (DMEM, 37 ºC, 5% CO2) for 90 minutes.

extract_protocol: Cells were then fixed for 5 min in 1% (v/v) formaldehyde, and the reaction quenched with a final concentration of 125 mM glycine. Fixed cells were collected by centrifugation, washed with PBS, and resuspended in Buffer A (50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% v/v Triton X-100, 0.1% w/v sodium deoxycholate) supplemented with protease inhibitors and 20 mM sodium butyrate (a histone deacetylase inhibitor). The cell suspension was subjected to mechanical bead-beating with 0.5-mm zirconium silicate beads for 2 min at 4ºC, followed by a 2-min rest, for a total of 10 cycles. Chromatin was then sheared by sonicating the lysate for 30 sec at 40% power output, followed by a 1-min rest on ice, for a total of 40 cycles, and the lysate clarified by centrifugation.  A fraction of the sheared chromatin was reserved as an input sample and the remainder was used for immunoprecipitation. Acetylated histone H3 was immunoprecipitated overnight with anti-acetyl-H3 (K9) antibody (from Millipore) tethered to protein-A sepharose (10 ml in a total volume of 700 ml). The beads were next washed sequentially in Buffer A, Buffer B (50 mM HEPES pH 7.5, 500 mM NaCl, 1 mM EDTA, 1% (v/v) Triton X-100, 0.1% (w/v) sodium deoxycholate), Buffer C (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% (v/v) NP-40, 0.5% w/v sodium deoxycholate), and Buffer D (10 mM Tris, 1 mM EDTA), and immunoprecipitated protein was eluted with Buffer E (50 mM Tris pH 8.0, 10 mM EDTA, 1% (w/v) SDS). Crosslinked DNA  from input and IP samples was released by incubating the eluate at 65ºC overnight, and extracted with a solution of phenol/chloroform/isoamyl alcohol (25:24:1) prior to ethanol precipitation and resuspension in water. Mock IP reactions with no antibody yielded no measurable product and were not quantified further. ChIP-DNA for input and IP samples was end-repaired with Klenow DNA Polymerase and the DNA was purified with AMPure XP System beads (Beckman Coulter Genomics) and modified with A-tails using Klenow exo- before ligation to adapters to incorporate 7-base index sequences using T4 DNA ligase (Enzymatics).  Adapter addition was confirmed on an Agilent 2100 bioanalyzer, and the DNA was PCR-amplified and then gel purified to remove adapter dimers and select sizes optimal for high-throughput sequencing (150 to 300 bp).  Libraries were 12-way multiplexed on an individual lane of an Illumina Hi-Seq 2000 flow cell.

tag: strain

tag: genotype/variation

tag: fraction

value: Chromatin IP

tag: antibody

tag: antibody vendor

value: Millipore

tag: antibody cat#

tag: antibody lot#


title: ada2Δ H3K9ac IP replicate 3

description: Chromatin IP against H3K9ac


title: ada2Δ input replicate 3

description: input DNA

value: input DNA


title: ada2Δ input replicate 2

description: input DNA


title: Liver_animal_2385_sham_0_weeks

tag: tissue


title: ada2Δ input replicate 1

description: input DNA


title: Liver_animal_2237_resection_3_weeks


title: Liver_animal_2346_sham_0_weeks


title: knock-out heart, biological rep3

status: Public on Feb 01 2012

city: Nashville

first: David

last: Bader

address: Pierce

institute: Vanderbilt

description:
Gene expression data from knock-out mouse hearts
2029DB0003-20111221-MoGene.rma-gene-default.chp
2029DB0003-20111221-MoGene.CEL

hyb_protocol: Following labeling, 5 ug of cRNA were hybridized for 16 hr at 45C on Mouse Gene 1.1 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Affymetrix high resolution GenePix 4000B scanner in Vanderbilt Functional Shared Resources (http://www.thefgsr.com/).

data_processing: The data were analyzed with Partek Genomics Suite 6.6 using Affymetrix default analysis settings and Robust Multi-chip Average (RMA)  as normalization method.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 50 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: mice were grown to 12 months old

extract_protocol: RNA was extracted with Trizol and further purified with Rneasy kit

treatment_protocol: no treatment

value: heart

value: cenpf knock-out

tag: age

value: 12 months


title: wild-type heart, biological rep1

description:
Gene expression data from wild-type mouse hearts
2029DB0004-20111221-MoGene.rma-gene-default.chp
2029DB0004-20111221-MoGene.CEL

value: wild-type


title: wild-type heart, biological rep2

description:
Gene expression data from wild-type mouse hearts
2029DB0005-20111221-MoGene.rma-gene-default.chp
2029DB0005-20111221-MoGene.CEL


title: wild-type heart, biological rep3

description:
Gene expression data from wild-type mouse hearts
2029DB0006-20111221-MoGene.rma-gene-default.chp
2029DB0006-20111221-MoGene.CEL


title: wildtype input replicate 3

description: input DNA

value: wildtype


title: ada2Δ H3K9ac IP replicate 1

description: Chromatin IP against H3K9ac


title: wildtype H3K9ac IP replicate 3

description: Chromatin IP against H3K9ac


title: knock-out heart, biological rep2

description:
Gene expression data from knock-out mouse hearts
2029DB0002-20111221-MoGene.rma-gene-default.chp
2029DB0002-20111221-MoGene.CEL


title: wildtype H3K9ac IP replicate 2

description: Chromatin IP against H3K9ac


title: wildtype input replicate 2

description: input DNA


title: wildtype input replicate 1

description: input DNA


title: wildtype H3K9ac IP replicate 1

description: Chromatin IP against H3K9ac


title: knock-out heart, biological rep1

description:
Gene expression data from knock-out mouse hearts
2029DB0001-20111221-MoGene.rma-gene-default.chp
2029DB0001-20111221-MoGene.CEL


title: DMEM + CO2 replicate 2

description: DMEM + CO2 biological replicate 2 of 3

hyb_protocol: For hybridization, each sample pair (~5 µl) was mixed with 26 µl formamide-based hybridization buffer (vial 7; Genisphere), 2 µl Array 50dT blocker (Genisphere), and 19 µl RNase/DNase-free water. The  primary hybridization was performed by incubating 48 µl of sample on the microarray under a supported glass coverslip (Erie Scientific, Portsmouth, NH) for 16 to 20 h at 43°C at high humidity. The slides were then gently submerged for three sequential 11-min incubations in 2X SSC with 0.2% sodium dodecyl sulfate (SDS) at 43°C, 2X SSC at RT, and 0.2X SSC at RT and dried by centrifugation. Secondary hybridization was carried out using the complementary capture reagents provided in the 3DNA Array 350 kit (Genisphere). For each reaction mixture, 2.5 µl 3DNA capture reagent with Cy3, 2.5 µl 3DNA capture reagent with Cy5, 26 µl SDS-based hybridization buffer (vial 6; Genisphere), and 21 µl RNase/DNase-free water were used. These reagents were mixed and incubated in the dark for 10 min at 80°C, followed by 15 min at 50°C. Each slide was incubated in the dark with 48 µl of this solution under a supported glass coverslip for 3 h at 65°C at high humidity. The slides were then submerged for three sequential 11-min incubations in 2X SSC with 0.2% SDS at 65°C, 2X SSC at RT, and 0.2X SSC at RT and dried by centrifugation. To prevent fluorophore degradation, the arrays were treated with Dyesaver (Genisphere) according to the manufacturer’s instructions.

scan_protocol: Slides were scanned on a Perkin-Elmer ScanArray Express HT scanner

data_processing: Normalization of the raw spot intensities was performed with LIMMA, using normexp followed by loess and quantile normalization. Values for replicate probes averaged.

label_protocol: First-strand cDNA was generated by oligo(dT)-primed reverse transcription (Superscript II; Invitrogen) using the 3DNA Array 350 kit (Genisphere, Hatfield, PA) and modified oligo(dT) primers in which a fluorophore/dendrimer-specific sequence occurs at the 5’ end of the dT primer. For cDNA synthesis, 1 µl fluorophore-specific oligo(dT) primer was added to 8 µg total RNA, and the solution was incubated at 80°C for 10 min and then cooled on ice for 2 min. Each sample was then combined with 1 µl RNase inhibitor (Superase-In; Ambion, Foster City, CA), 4 µl 5X first-strand buffer, 1 µl deoxynucleoside triphosphate mix (10 mM each dATP, dCTP, dGTP, and dTTP), 2 µl 0.1 M dithiothreitol, and 1 µl Superscript II RNase H reverse transcriptase (Invitrogen). Reverse transcription was allowed to proceed for 2 h at 42°C. The reaction was terminated by the addition of 3.5 µl 0.5 M NaOH–50 mM EDTA, incubated for 15 min at 65°C, and neutralized with 5 µl 1 M Tris-HCl (pH 7).

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

tag: growth condition

value: Dulbecco's Modified Eagle's Medium (DMEM)

source_name: Total RNA pooled from all samples


title: DMEM + CO2 replicate 3

description: DMEM + CO2 biological replicate 3 of 3


title: Littman's Low Thiamine replicate 1

description: Littman's Low Thiamine biological replicate 1 of 3

value: Littman's media + 0.01 ug/ml thiamine


title: Littman's Low Thiamine replicate 2

description: Littman's Low Thiamine biological replicate 2 of 3


title: PBS + FBS replicate 3

description: PBS + FBS biological replicate 3 of 3

value: PBS + 10% v/v fetal bovine serum


title: LIM + EDTA/BPDS replicate 2

description: LIM + EDTA/BPDS biological replicate 2 of 3

value: Low iron media + 500 mM ethylenediaminetetraacetic acid (EDTA) and 10 mM bathophenanthroline disulfonate (BPDS)


title: PBS + FBS replicate 2

description: PBS + FBS biological replicate 2 of 3


title: LIM replicate 3

description: LIM biological replicate 3 of 3

value: Low iron media


title: LIM + EDTA/BPDS replicate 1

description: LIM + EDTA/BPDS biological replicate 1 of 3


title: LIM replicate 1

description: LIM biological replicate 1 of 3


title: LIM + EDTA/BPDS replicate 3

description: LIM + EDTA/BPDS biological replicate 3 of 3


title: DMEM replicate 1

description: DMEM biological replicate 1 of 1

value: Dulbecco's Modified Eagle's Medium (DMEM) + 5% CO2


title: DMEM + CO2 replicate 1

description: DMEM + CO2 biological replicate 1 of 3


title: LIM replicate 2

description: LIM biological replicate 2 of 3


title: genomic DNA of normal sample N6

status: Public on Dec 15 2011

city: Bruxelles

first: Matthieu

last: Defrance

address: CP614 route de Lennik 808

country: Belgium

institute: Université Libre de Bruxelles

description:
Normal fresh frozen breast tissue sample
Sample_12.AVG_Beta

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 Beadchip using standard Infinium HD  Methylation Assay protocol.

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

data_processing: GenomeStudio software v2010.3, Methylation module v1.8.5

label: Cy5 and Cy3

source_name: Breast

label_protocol: Standard Infinium HD Methylation Assay protocol

extract_protocol: Genomic DNA was extracted and purified using Qiagen QiaAMP Kit according to standard instructions. The recommended RNase treatment was performed.

tag: sample type

value: Fresh frozen breast tissue sample

value: normal breast


title: PBS + FBS replicate 1

description: PBS + FBS biological replicate 1 of 3


title: genomic DNA of tumor sample BC8

description:
Breast tumor fresh frozen sample
Sample_22.AVG_Beta

value: breast cancer tumor


title: Littman's High Thiamine replicate 3

description: Littman's High Thiamine biological replicate 3 of 3

value: Littman's media + 1 ug/ml thiamine


title: genomic DNA of tumor sample BC7

description:
Breast tumor fresh frozen sample
Sample_21.AVG_Beta


title: PBS replicate 3

description: PBS biological replicate 3 of 3

value: PBS


title: Littman's High Thiamine replicate 1

description: Littman's High Thiamine biological replicate 1 of 3


title: PBS replicate 2

description: PBS biological replicate 2 of 3


title: genomic DNA of tumor sample BC1

description:
Breast tumor fresh frozen sample
Sample_15.AVG_Beta


title: genomic DNA of normal sample N8

description:
Normal fresh frozen breast tissue sample
Sample_14.AVG_Beta


title: Littman's High Thiamine replicate 2

description: Littman's High Thiamine biological replicate 2 of 3


title: genomic DNA of tumor sample BC5

description:
Breast tumor fresh frozen sample
Sample_19.AVG_Beta


title: genomic DNA of tumor sample BC2

description:
Breast tumor fresh frozen sample
Sample_16.AVG_Beta


title: genomic DNA of normal sample N1

description:
Normal fresh frozen breast tissue sample
Sample_7.AVG_Beta


title: genomic DNA of tumor sample BC3

description:
Breast tumor fresh frozen sample
Sample_17.AVG_Beta


title: genomic DNA of normal sample N7

description:
Normal fresh frozen breast tissue sample
Sample_13.AVG_Beta


title: genomic DNA of normal sample N2

description:
Normal fresh frozen breast tissue sample
Sample_8.AVG_Beta


title: NCSC rep3

status: Public on Jun 15 2010

city: Ann Arbor

first: Elizabeth

middle: R

last: Lawlor

state: MI

address: 1600 Huron Parkway, NCRC Bldg 520

institute: University of Michigan

description: hESC-derived NCSC

hyb_protocol: hybridization to HuEx1.0 microarrays was carried out following the manufacturer’s instructions

data_processing:
Signal intensities from core probesets were quantile normalized by robust multichip averaging and transcript expression levels median summarized using Partek Genomics Suite software (Partek, St. Louis, MO).
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: hNCSC

label_protocol: Samples were prepared in the CHLA genome core using the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix, Santa Clara)

extract_protocol: Qiagen miRNA easy

tag: cell type

value: NCSC


title: genomic DNA of tumor sample BC6

description:
Breast tumor fresh frozen sample
Sample_20.AVG_Beta


title: BM-MSC rep2

description: adult bone-marrow MSC

scan_protocol: hybridization to HuEx1.0 microarrays was carried out following the manufacturer’s instructions

source_name: BM-MSC

value: Bone marrow-MSC


title: BM-MSC rep1

description: adult bone-marrow MSC


title: Littman's Low Thiamine replicate 3

description: Littman's Low Thiamine biological replicate 3 of 3


title: ssDNA in dmc1 cells replicate 2

status: Public on Aug 15 2011

city: New York

first: Andreas

last: Hochwagen

state: NY

address: 1009 Silver Center 100 Washington Square East

institute: New York University

description: biological replicate 2 of 2 of ssDNA in dmc1 cells

hyb_protocol: Samples were co-hybridized to custom Agilent arrays in 1X Agilent hybridization buffer at 65 degrees for 16 hours. Samples were washed according to manufacturer's instructions.

scan_protocol: Agilent scanner using the AgilentHD_CGH protocol (5μM resolution, 100% PMT for each laser). Images were quantified using Agilent Feature Extraction Software (version 10.1.1.1).

data_processing:
Cy3 and Cy5 levels and background were calculated using Agilent Feature Extractor software. Background normalization, log2 ratios for each experiment and scale normalizations across each set of duplicated experiments were calculated using the sma package in R (Yang, et al., 2001), a computer language and environment for statistical computing (v2.1.0, http://www.r-project.org).
Replicate datesets are the normalized log2 ratio (experimental ssDNA signal (5 hours timepoint) / control ssDNA (0 hour timepoint)). The final values are average of the individual replicate log2 ratios.

organism: Saccharomyces cerevisiae

source_name: meiotic budding yeast cells, 0 or 5 hours in SPO-medium

label_protocol: 1.5 μg of ssDNA was labeled with Cy3-dUTP or Cy5-dUTP (GE Healthcare) by random priming without denaturation using 4 µg random nonamer oligo (Integrated DNA Technologies) and 10 units of Klenow (New England Biolabs). Unincorporated dye was removed using microcon columns (30-kDa MW cutoff, Millipore).

growth_protocol: Cells were pre-grown in presporulation medium (BYTA) and transferred into sporulation medium (SPO) at 0 hours. Samples were isolated at the indicated timepoints.

extract_protocol: To isolate ssDNA, ~10^9 cells were fixed in 70% ethanol at –20°C. Cells were spheroplasted in sorbitol buffer (1M sorbitol, 1% beta-mercaptoethanol, 0.2 mg/ml zymolyase 100T, 0.1M EDTA, pH 7.4), lysed in NDS (0.6% SDS, 300mM EDTA, 10mM Tris.HCl, pH 9.5). DNA was deproteinated with proteinase K (0.25mg/ml; Roche) at 50°C, twice phenol extracted, treated with RNase A, and stored in TE (1mM EDTA, 10mM Tris.HCl, pH 7.5) at 4°C. 25 μg DNA were digested to completion with EcoRI (New England Biolabs). ssDNA was enriched by batch absorption to BND cellulose (Sigma). Briefly, a 50% slurry of BND-cellulose was equilibrated in NET (1M NaCl, 10mM Tris, pH 7.6, 1mM EDTA). Digested DNA was adjusted to 1M NaCl and ssDNA was incubated with a 500 μl bed volume of BND-cellulose for 5 minutes. Resin was washed with five bed volumes of NET. ssDNA was eluted five times with 600 μl NET + 1.8% caffeine. DNA was precipitated and concentrated for microarray analysis.

tag: time in spo (hours)


title: genomic DNA of normal sample N3

description:
Normal fresh frozen breast tissue sample
Sample_9.AVG_Beta


title: genomic DNA of normal sample N4

description:
Normal fresh frozen breast tissue sample
Sample_10.AVG_Beta


title: genomic DNA of normal sample N5

description:
Normal fresh frozen breast tissue sample
Sample_11.AVG_Beta


title: BM-MSC rep3

description: adult bone-marrow MSC


title: PBS replicate 1

description: PBS biological replicate 1 of 3


title: NC-MSC control rep1

description: hESC-derived neural crest-MSC isolated 5 days after lentiviral transduction with control vector

source_name: hNC-MSC control

value: NC-MSC


title: NCSC rep2

description: hESC-derived NCSC


title: NC-MSC control rep2


title: ssDNA in dmc1 cells replicate 1

description: biological replicate 1 of 2 of ssDNA in dmc1 cells


title: NC-MSC control rep3


title: genomic DNA of tumor sample BC4

description:
Breast tumor fresh frozen sample
Sample_18.AVG_Beta


title: NCSC rep1

description: hESC-derived NCSC