title: MSC cultured in human MSC media, MSC-21

status: Public on Sep 25 2014

type: genomic

city: Oviedo

first: Agustin

last: Fernandez

email: affernandez@hca.es, agusff@gmail.com

state: Asturias

address: Avenida de Roma s/n

department: IUOPA

institute: Oviedo University-HUCA

description: healthy sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: R-bioconductor/minfi

label: Cy3, Cy5

source_name: human mesenchymal stem cell, 28-year-old female

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

value: mesenchymal stem cells (MSCs)

value: 28 years

tag: gender

value: male

tag: disease state

value: healthy


title: MSC cultured in human MSC media, MSC-22

middle: F

country: Spain

description: healthy sample

molecule: genomic DNA

organism: Homo sapiens

source_name: human mesenchymal stem cell, 29-year-old female

tag: cell type

tag: age

value: 29 years


title: MSC cultured in human MSC media, MSC-26

description: healthy sample

source_name: human mesenchymal stem cell, 63-year-old female

value: 63 years


title: MSC cultured in human MSC media, MSC-28

description: healthy sample

source_name: human mesenchymal stem cell, 80-year-old female

value: 80 years


title: MSC cultured in human MSC media, MSC-29

description: healthy sample

source_name: human mesenchymal stem cell, 10-year-old female

value: 10 years


title: MSC cultured in human MSC media, MSC-23

description: healthy sample

source_name: human mesenchymal stem cell, 22-year-old female

value: 22 years


title: Replication timing of 10-822 leukemic patient sample, replicate 3

status: Public on May 16 2012

city: Tallahassee

first: Tyrone

last: Ryba

state: FL

address: 319 Stadium Dr.

department: Biological Science

country: USA

institute: Florida State University

description: submitted as of 5/12/12

hyb_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, Cy3 and Cy5 labeled DNA samples (34 ug each) were co-hybridized to Nimblegen CGH arrays containing one oligonucleotide probe every 2.5 kb across the human genome.

scan_protocol: NimbleGen MS200 microarray scanner (Roche NimbleGen, Inc.) and MS200 data collection software were used per NimbleGen's standard protocol (www.nimblegen.com/products/lit/index.html).

data_processing: NimbleScan software was used to obtain .pair raw data per manufacturer's instructions. Raw early/late data (i.e. from .pair files) from two independent biological replicates in which early and late replicating DNA were differentially labeled were loess-normalized to remove signal intensity-dependent bias, then scaled to a reference data set to have the same median absolute deviation (limma package, R/Bioconductor).The early/late ratios were used to generate a smoothed profile (i.e. processed data) using local polynomial smoothing (loess, 300-kb span) for each chromosome using the loess function in the statistical language R. Processed data sets can be graphically displayed (and are also downloadable) on our web site (http://www.replicationdomain.org). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].

source_name: Early-replicating DNA of 10-822 leukemic patient sample

label_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, randomly-amplified BrdU-immunoprecipitated DNA samples (1 ug each) were Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.

extract_protocol: Replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays, as described in Hiratani et al [PLoS Biology (2008) 6: e245]. Briefly, replication intermediates are prepared from cells that are first pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].

tag: diagnosis

value: ALL (B), Pediatric

tag: age (yrs)

value: M

tag: disease stage

value: Relapse

tag: karyotype

source_name: Late replicating DNA of 10-822 leukemic patient sample


title: Replication timing of 11-221 leukemic patient sample, replicate 1

description: submitted as of 5/12/12

source_name: Early-replicating DNA of 11-221 leukemic patient sample

value: New Diagnosis

source_name: Late replicating DNA of 11-221 leukemic patient sample


title: Replication timing of 11-064 leukemic patient sample, replicate 1

description: submitted as of 5/12/12

source_name: Early-replicating DNA of 11-064 leukemic patient sample

value: F

source_name: Late replicating DNA of 11-064 leukemic patient sample


title: Replication timing of 11-118 leukemic patient sample, replicate 2

description: submitted as of 5/12/12

source_name: Early-replicating DNA of 11-118 leukemic patient sample

source_name: Late replicating DNA of 11-118 leukemic patient sample


title: Replication timing of 10-799 leukemic patient sample, replicate 1

description: submitted as of 5/12/12

source_name: Early-replicating DNA of 10-799 leukemic patient sample

value: ALL (T), Pediatric

source_name: Late replicating DNA of 10-799 leukemic patient sample


title: Replication timing of 10-771 leukemic patient sample, replicate 2

description: submitted as of 5/12/12

source_name: Early-replicating DNA of 10-771 leukemic patient sample

source_name: Late replicating DNA of 10-771 leukemic patient sample


title: Replication timing of 10-771 leukemic patient sample, replicate 1

description: submitted as of 5/12/12


title: Replication timing of 11-118 leukemic patient sample, replicate 1

description: submitted as of 5/12/12


title: Replication timing of 10-668 leukemic patient sample, replicate 1

description: submitted as of 5/12/12

source_name: Early-replicating DNA of 10-668 leukemic patient sample

source_name: Late replicating DNA of 10-668 leukemic patient  sample


title: MPB_CD34_R1

status: Public on May 28 2015

first: David

middle: M

last: Gilbert

address: 319 Stadium Drive

department: Biology

description: Human genomic data

hyb_protocol: Standard NimbleGen protocol. Briefly, Cy3 and Cy5 labeled DNA samples (31 ug each) were co-hybridized to Nimblegen CGH arrays containing oligonucleotide probes across the entire human genome.

scan_protocol: GenePix 4000B scanner (Molecular Devices) and GenePix software were used per NimbleGen's standard protocol (www.nimblegen.com/products/lit/index.html).

data_processing: DEVA (Nimblegen) software was used to obtain .pair raw data per manufacturer's instructions. Raw early/late data (i.e. from .pair files) from independent biological replicates in which early and late replicating DNA were labeled reciprocally were loess-normalized to remove signal intensity-dependent bias (limma package, R/Bioconductor) and early/late ratios were used to generate a smoothed profile (i.e. processed data) using local polynomial smoothing (loess, 300-kb span) for each chromosome using basic functions in the statistical language R. Processed data sets can be graphically displayed (and are also downloadable) on our web site (http://www.replicationdomain.org). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].

source_name: Early-replicating DNA

growth_protocol: Human CD34+ peripheral blood stem were harvested from G-CSF-treated normal adults undergoing apheresis as stem cell transplant donors and obtained from the Yale Center for Excellence in Molecular Hematology (Dr. Diane Krause, director) as de-identified samples. The CD34+ cells were selected using the ISOLEX 300i Magnetic Cell Selection System (Baxter) and cultured in StemSpan Expansion Medium (Stem Cell Technologies) with 1X Stem Span CC100 recombinant human cytokine cocktail containing 100 ng/mL Flt3 ligand, 100 ng/mL stem cell factor, 20 ng/mL IL-3, and 20 ng/mL IL-6. After seven days of expansion in culture, the cell number increased over 40 fold.

extract_protocol: Replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays, as previously described (Ryba, T. et al., 2011. Nat Protoc 6: 870–895). Briefly, replication intermediates were prepared from cells pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245] and Ryba, T. et al [Nat Protoc (2011) 6: 870–895].

tag: differentiation stage

value: CD34+ peripheral blood stem and progenitor cells

tag: cell line

value: Primary cells

source_name: Late-replicating DNA


title: Replication timing of 10-820 leukemic patient sample, replicate 1

description: submitted as of 5/12/12

source_name: Early-replicating DNA of 10-820 leukemic patient sample

source_name: Late replicating DNA of 10-820 leukemic patient sample


title: Replication timing of 11-220 leukemic patient sample, replicate 1

description: submitted as of 5/12/12

source_name: Early-replicating DNA of 11-220 leukemic patient sample

source_name: Late replicating DNA of 11-220 leukemic patient sample


title: Replication timing of 10-822 leukemic patient sample, replicate 2

description: submitted as of 5/12/12

source_name: Early-replicating DNA of 10-822 leukemic patient sample

source_name: Late replicating DNA of 10-822 leukemic patient sample


title: Replication timing of 10-828 leukemic patient sample, replicate 1

description: submitted as of 5/12/12

source_name: Early-replicating DNA of 10-828 leukemic patient sample

value: Unknown

source_name: Late replicating DNA of 10-828 leukemic patient sample


title: Replication timing of MHH-CALL2 leukemic cell line, replicate 1

description: submitted as of 5/12/12

source_name: Early-replicating DNA of MHH-CALL2 leukemic cell line

source_name: Late replicating DNA of MHH-CALL2 leukemic cell line


title: Replication timing of 10-838 leukemic patient sample, replicate 1

description: submitted as of 5/12/12

source_name: Early-replicating DNA of 10-838 leukemic patient sample

source_name: Late replicating DNA of 10-838 leukemic patient sample


title: Replication timing of 10-356 leukemic patient sample, replicate 1

description: submitted as of 5/12/12

source_name: Early-replicating DNA of 10-356 leukemic patient sample

value: AML M2, Pediatric

source_name: Late replicating DNA of 10-356 leukemic patient sample


title: Replication timing of 11-253 leukemic patient sample, replicate 1

description: submitted as of 5/12/12

source_name: Early-replicating DNA of 11-253 leukemic patient sample

source_name: Late replicating DNA of 11-253 leukemic patient sample


title: MPB_MyeD5_R1

description: Human genomic data

source_name: Early-replicating DNA

growth_protocol: CD45RA+ cells (derived from human CD34+ peripheral blood stem cells) were used and expanded in medium supplemented as follows:  Days 0-4:  50 ng/ml stem cell factor, 100 ng/ml Flt3 ligand, 5 ng/ml IL-3, 5 ng/ml GM-CSF, 30 ng/ml G-CSF; then  with 5 ng/ml IL-3, 30 ng/ml G-CSF (Heike and Nakahata. 2002. Biochim Biophys Acta 1592: 313–321; Mayani et al. 1993, J Cell Physiol 157: 579–586; Manz et al. 2002, Proc Natl Acad Sci USA 99: 11872–11877).

value: Myeloid differentiation day 5 from CD34+ peripheral blood stem and progenitor cells

source_name: Late-replicating DNA


title: Replication timing of 10-770 leukemic patient sample, replicate 1

description: submitted as of 5/12/12

source_name: Early-replicating DNA of 10-770 leukemic patient sample

source_name: Late replicating DNA of 10-770 leukemic patient sample


title: Replication timing of 10-822 leukemic patient sample, replicate 1

description: submitted as of 5/12/12


title: MPB_EpoD5_R1

description: Human genomic data

growth_protocol: Erythroid differentiation was induced in the CD45RA- fraction of cells (from human CD34+ peripheral blood stem cells) by an erythroid “cocktail” supplementing the stem cell expansion medium with 10ng/ml SCF, 5ng/ml IL3, recombinant erythropoietin 1 unit/ml, dexamethasone with a final concentration of 2 micromolar, and Estradiol with a final concentration of 0.2 micromolar for 5 days (Migliaccio et al. 2009. Curr Opin Hematol 16: 259–268; Mahajan et al. 2009, Exp Hematol 37: 1143–1156.e3).

value: Erythroid differentiation day 5 from CD34+ peripheral blood stem and progenitor cells


title: IL-1B LCM BA 2

status: Public on Jan 31 2011

type: RNA

city: München

first: Michael

last: Quante

address: Ismaninger Str 22

department: II Medizinische Klinik

country: Germany

institute: Technische Universität München

description: biological replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Illumina’s GenomeStudio (v2010.1) gene expression module (v1.6.0) to report both un-normalized and quantile normalized, background corrected gene expression signal levels. Expression intensities were obtained from the illumina arrays using the standard illumina algorithm and software (Kuhn et al., 2004). Differential expression was obtained using Limma (Smyth, 2004) as implemented in oneChannelGUI (Sanges et al., 2007) operating as part of the Bioconductor Suite (Gentleman et al., 2004)  in the R statistical computing environment (Ihaka and Gentleman, 1996). A significance cutoff of the Benjamini-Hochberg False Discovery Rate <0.05 was used (Benjamini and Hochberg, 1995)

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: stomach

label_protocol: Ambion Illumina TotalPrep RNA Amplification Kit (Ambion, Inc.) as per manufacturer’s instructions

extract_protocol: Frozen sections (20µm) were cut onto ultraviolet- irradiated P.A.L.M. membrane slides (P.A.L.M. Microlaser Biotechnologies, Bernried, Germany). BE epithelium at the SCJ in 15 month-old L2-IL-1β mice or 9 months old BA-treated L2-IL-1β mice and squamous epithelum of WT control mice were cut carefully into sterile, ultra- violet-irradiated, 0.5ml P.A.L.M. tubes with adhesive caps using a P.A.L.M Laser Microdissection system and were stored on dry ice. After centrifugation (7000g for 10 minutes) the RNA was isolated using a specialized RNA isolation and purification kit for small amounts (Macherey Nagel, NucleoSpinXS). Low amounts of RNA were amplified using the Nugene Ovation  system (Ovation Amp V2).

treatment_protocol: 0.2% Deoxycholate in the drinking water was administerd for 9-12 months

tag: strain

tag: genotype/variation

value: IL-1ß transgenic

tag: treatment

value: 12 months

tag: diagnose

value: bile acid induced intestinal metaplasia


title: MPB_MyeD3_R1

description: Human genomic data

growth_protocol: CD45RA+ cells (derived from human CD34+ peripheral blood stem cells) were used and expanded in medium supplemented as follows: 50 ng/ml stem cell factor, 100 ng/ml Flt3 ligand, 5 ng/ml IL-3, 5 ng/ml GM-CSF, 30 ng/ml G-CSF (Heike and Nakahata. 2002. Biochim Biophys Acta 1592: 313–321; Mayani et al. 1993, J Cell Physiol 157: 579–586; Manz et al. 2002, Proc Natl Acad Sci USA 99: 11872–11877).

value: Myeloid differentiation day 3 from CD34+ peripheral blood stem and progenitor cells


title: IL-1B LCM TU 2

description: biological replicate 2

value: bile acid in drinking water

value: 15 months

value: adenocarcinoma


title: IL-1B LCM BA 1

description: biological replicate 1


title: IL-1B LCM SQ 3

description: biological replicate 3

value: wild type

value: normal squamous epithelium


title: IL-1B LCM BE 2

description: biological replicate 2

value: intestinal metaplasia


title: IL-1B LCM SQ 2

description: biological replicate 2


title: IL-1B LCM BA 3

description: biological replicate 3


title: IL-1B LCM BE 3

description: biological replicate 3


title: IL-1B LCM BE 1

description: biological replicate 1


title: IL-1B LCM TU 1

description: biological replicate 1


title: IL-1B LCM TU 3

description: biological replicate 3


title: IL-1B LCM SQ 1

description: biological replicate 1


title: Replication timing of RCH-ACV leukemic cell line, replicate 3

description: submitted as of 5/12/12

source_name: Early-replicating DNA of RCH-ACV leukemic cell line

value: ALL (B), Pediatric

value: F

value: Relapse

source_name: Late replicating DNA of RCH-ACV leukemic cell line


title: Replication timing of RCH-ACV leukemic cell line, replicate 2

description: submitted as of 5/12/12


title: MPB_EpoD3_R1

description: Human genomic data

growth_protocol: Erythroid differentiation was induced in the CD45RA- fraction of cells (from human CD34+ peripheral blood stem cells) by an erythroid “cocktail” supplementing the stem cell expansion medium with 10ng/ml SCF, 5ng/ml IL3, recombinant erythropoietin 1 unit/ml, dexamethasone with a final concentration of 2 micromolar, and Estradiol with a final concentration of 0.2 micromolar for 3 days (Migliaccio et al. 2009. Curr Opin Hematol 16: 259–268; Mahajan et al. 2009, Exp Hematol 37: 1143–1156.e3).

value: Erythroid differentiation day 3 from CD34+ peripheral blood stem and progenitor cells

value: Primary cells


title: Replication timing of RCH-ACV leukemic cell line, replicate 1

description: submitted as of 5/12/12


title: Replication timing of REH leukemic cell line, replicate 1

description: submitted as of 5/12/12

source_name: Early-replicating DNA of REH leukemic cell line

source_name: Late replicating DNA of REH leukemic cell line


title: Replication timing of REH leukemic cell line, replicate 2

description: submitted as of 5/12/12


title: Replication timing of NC-NC lymphoblastoid cells, replicate 1

description: submitted as of 5/12/12

source_name: Early-replicating DNA of NC-NC lymphoblastoid cells

source_name: Late replicating DNA of NC-NC lymphoblastoid cells


title: Replication timing of GM06990 lymphoblastoid cells, replicate 1

description: submitted as of 5/12/12

source_name: Early-replicating DNA of GM06990 lymphoblastoid cells

source_name: Late replicating DNA of GM06990 lymphoblastoid cells


title: Replication timing of peripheral T-lymphoblast cells, replicate 1

description: submitted as of 5/12/12

source_name: Early-replicating DNA of peripheral T-lymphoblast cells

value: Unknown

value: M

source_name: Late replicating DNA of peripheral T-lymphoblast cells


title: Replication timing of GM06999 lymphoblastoid cells, replicate 1

description: submitted as of 5/12/12

source_name: Early-replicating DNA of GM06999 lymphoblastoid cells

source_name: Late replicating DNA of GM06999 lymphoblastoid cells


title: Replication timing of C0202 lymphoblastoid cells, replicate 2

description: submitted as of 5/12/12

source_name: Early-replicating DNA of C0202 lymphoblastoid cells

source_name: Late replicating DNA of C0202 lymphoblastoid cells


title: Replication timing of GM06990 lymphoblastoid cells, replicate 2

description: submitted as of 5/12/12


title: Replication timing of C0202 lymphoblastoid cells, replicate 1

description: submitted as of 5/12/12