title: embryo 21-24h H3 ChIP-chip

description:
H3 ChIP embryo 21-24h Biological Rep 1-3
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: embryo 21-24h H3 ChIP DNA

value: embryo 21-24h


title: Hypodip-SNP-#09

status: Public on Dec 12 2011

type: RNA

city: Memphis

first: Charles

middle: G

last: Mullighan

state: TN

address: 262 Danny Thomas Place

department: Pathology

country: USA

institute: St Jude Children's Research Hospital

hyb_protocol: Detailed protocols are as described at http://www.stjuderesearch.org/data/ALL3/

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: B-precursor ALL with miscellaneous karyotype

growth_protocol: RNA was extracted from cryopreserved mononuclear cell preparations of diagnostic bone marrow or peripheral blood from T-ALL cases at diagnosis.

extract_protocol: Total RNA extraction (Trizol)

tag: tissue

value: leukemic cells obtained from bone marrow or blood at diagnosis

tag: cell type


title: Hypodip-SNP-#03

scan_protocol: Detailed protocols are as described at http://www.stjuderesearch.org/data/ALL3/

value: B-precursor ALL with miscellaneous karyotype


title: embryo 2-12h H3 ChIP-chip

type: genomic

city: Rotterdam

first: Yuri

last: Moshkin

address: Dr. Molewaterplein 50

country: Netherlands

institute: Erasmus University Medical Center

description:
H3 ChIP embryo 2-12h Biological Rep 1-3
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

hyb_protocol: according to the manufacturer protocols

scan_protocol: according to the manufacturer protocols

data_processing:
Raw ChIP-chip and FAIRE-chip hybridization intensities were analyzed using R and R/Bioconductor packages. In brief, genome-wide ChIP-chip enrichment was estimated as following: 1) log2-scaled hybridization intensities from the input genomic DNA (5 replicas) were normalized by quantile normalization using Bioconductor package preprocessCore and averaged. 2) log2 – scaled ratios of ChIP hybridization intensities to averaged input were taken and quantile normalized independently for each antibodies giving log2(ChIP/Input) values. 3) The same was done for the Mock ChIP hybridization intensities giving log2(Mock/Input) values. 4) Averaged log2(ChIP/Input) and log2(Mock/Input) ratios were scaled by the median and the log2(Mock/Input)average ratio was subtracted from the log2(ChIP/Input)average ratio giving ChIP-chip enrichment score. For FAIRE-chip, enrichment score was calculated as averaged log2(FAIRE/Input) ratio, as this assay does not rely on antibodies. For histone H3 and H2B ChIP-chip and FAIRE-chip, the resulting enrichment scores were smoothened by running mean on the window of 250 bp. For FAIRE-chip, the results were centered by the mean. Binding sites of ATP-dependent chromatin remodelers were selected based on false discovery rate (FDR) estimation using modified procedure described by (Simonis et al., 2006) as following: 1) ChIP-chip enrichment scores were randomly permutated and a running mean with a window of 500 bp was applied. This provides a "null" distribution for FDR estimation 2) FDR was set at < 0.05 by taking the value from the "null" distribution above 95% this distribution. 3) Finally, a running mean with a window of 500 bp was applied to original data and signals (peaks) above the FDR threshold were taken. In addition, we discarded the peaks represented by less than 5 probes. For each remodeler two different antibodies were used and only sites which met the threshold for both antibodies were considered as positive remodeler-bound regions. The INO80 binding sites were selected at FDR <0.01.  Remodeler binding sites were derived by intersecting the sets of significant ChIP-chip peaks for each antibody (see  the additional results files: (P)BAP_sites.bed, NURD_sites.bed, INO80_sites.bed, ISWI_sites.bed files, which are linked as supplementary files on the Series record)
Results file descriptions:
1) raw.bar files contain ChIP.score calculated for each antibody.
2) raw.sgr files contain chromosome, position and ChIP.score.
3) bed files contain binding sites selected at false discovery rate (FDR) of < 0.05 per individual antibody against remodelers subunits. The INO80 sites were selected at FDR < 0.01.
4) Files (P)BAP_sites.bed, NURD_sites.bed, ISWI_sites.bed contain remodeler binding sites, which were derived by intersecting the sets of significant ChIP-chip peaks for each antibody. INO80_sites.bed contains INO80 sites filtered at FDR < 0.01. These bed files are linked as supplementary files on the Series record.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: embryo 2-12h H3 ChIP DNA

label_protocol: according to the manufacturer protocols

growth_protocol: Drosophila S2 cells were cultured in Schneider's media (Invitrogen 21720-024) supplied with 10% FBS and Penicillin/Streptomycin mixture at 25°C

extract_protocol: The following antibodies were used: anti-H3 (ab1791, Abcam), anti-H2B (raised against purified Drosophila core histones), anti-BAP111 and anti-BRM (Chalkley et al., 2008), anti-ISWI Ab14 (584-598aa), anti-ISWI Ab18 (1012-1027aa), anti-MI2 anti-MEP1 (Reddy et al., 2010) and anti-INO8016-310 (Klymenko et al., 2006). Log-phase S2 cells were fixed for 10 min with 1% formaldehyde. Fixation was stopped by 125 mM glycine, cells were washed with PBS and resuspended in ice-cold L buffer (1% sodium dodecyl sulfate, 10 mM EDTA, 50 mM Tris-HCl pH 8.1, 0.5 mM phenylmethylsulfonyl fluoride - PMSF, and 100 ng/ml of leupeptin and aprotinin). Cross-linked chromatin was sonicated to an apparent length of ~300-500 bp (corresponding to ~200-300 bp of free DNA). For Drosophila chromatin, 2 g of embryos, or larvae, were homogenized and fixed for 15’ in H buffer (30 mM KCl, 15 mM NaCl, 2 mM MgCl2, 7.5 mM HEPES pH 7.6, 0.5% Triton X-100 and 0.5 mM DTT) containing 2% formaldehyde. After blocking with 0.125 M glycine, the lysate was filtered through miracloth. Nuclei were purified by centrifugation through buffer H, containing 0.15 M sucrose and resuspended in ice-cold buffer L and sonicated as described above. 100 mkg of cross-linked chromatin was diluted with 9 volumes of buffer D (150 mM NaCl, 20 mM Tris-HCl pH8.1, 2 mM EDTA pH8.0, 1% Triton-X100, 0.5 mM PMSF, and 100 ng/ml of leupeptin and aprotinin), pre-cleared with 10 mkl (bed volume) protein A agarose blocked with salmon sperm DNA (16-157, Upstate), incubated ON at 4°C with ~10 mkl of appropriate antibodies, followed by 1 hr incubation with 20 mkl of pre-blocked protein A agarose. For Mock ChIP, chromatin was incubated with either 10 mkl of preimmune serum (4 replicas) or directly with 20 mkl of pre-blocked protein A agarose (6 replicas). Beads were washed 5x with buffer W (20 mM Tris-HCl pH 8.1, 2 mM EDTA pH 8.0, 0.1% SDS, 1% Triton X-100, 0.5 mM PMSF, and 100 ng/ml of leupeptin and aprotinin) containing 150 mM NaCl, and 1 x with buffer W/500 mM NaCl. DNA was eluted with 250 mkl buffer E (1% SDS, 0.1 M NaHCO3, 500 mkg/ml Proteinase K) for 2 hrs at 37°C and overnight at 65°C. DNA was then extracted with QIAquick PCR purification kit (Qiagen Cat. 28106). For FAIRE, 100 mkg of cross-linked chromatin was diluted 9x with buffer D, phenol-chloroform extracted followed by RNase A treatment (1 mkg/ml) for 2 hours at 37°C. Isolated DNA was amplified with REPLI-g (Qiagen Cat. 150025), digested with DNase, labeled and hybridized on Affymetrix Drosophila tiling 2.0R arrays.

treatment_protocol: Drosophila S2 cells were treated with double-stranded RNA (dsRNA) for 4 days as described (Worby, C. A., N. Simonson-Leff, and J. E. Dixon. 2001. RNA interference of gene expression (RNAi) in cultured Drosophila cells. Sci. STKE 2001:PL1). Double-stranded RNA was synthesized using an Ambion Megascript T7 kit according to the manufacturer's protocol.

value: embryo 2-12h

tag: antibody

value: H3 rabbit polyclonal (ab1791, Abcam)

source_name: Input/Mock-ChIP DNA

value: S2 cells

value: Mock ChIPs were performed with preimmune serum (preimmune) or protein A beads (protA)


title: Pseudodip-SNP-#02

label_protocol: Detailed protocols are as described at http://www.stjuderesearch.org/data/ALL3/


title: Other-SNP-#04


title: Other-SNP-#23


title: Pseudodip-SNP-#21


title: Hypodip-SNP-#05


title: Other-SNP-#18


title: Other-SNP-#12


title: embryo 21-24h FAIRE-chip

description:
FAIRE embryo 21-24h Biological Rep 1-3
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL

source_name: embryo 21-24h FAIRE DNA

value: None - FAIRE assay

source_name: Input DNA


title: S2 SMC3 RNAi FAIRE-chip

description:
FAIRE  SMC3 RNAi S2 cells Biological Rep 1-2
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL

source_name: S2 SMC3 RNAi FAIRE DNA


title: embryo 0-1h H3 ChIP-chip

description:
H3 ChIP embryo 0-1h Biological Rep 1-3
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: embryo 0-1h H3 ChIP DNA

value: embryo 0-1h


title: S2 SA RNAi FAIRE-chip

description:
FAIRE  SA RNAi S2 cells Biological Rep 1-2
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL

source_name: S2 SA RNAi FAIRE DNA


title: S2 ISWI RNAi FAIRE-chip

description:
FAIRE  ISWI RNAi S2 cells Biological Rep 1-3
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL

source_name: S2 ISWI RNAi FAIRE DNA


title: Other-SNP-#03


title: Other-SNP-#09


title: S2 INO80 RNAi FAIRE-chip

description:
FAIRE  INO80 RNAi S2 cells Biological Rep 1-8
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL

source_name: S2 INO80 RNAi FAIRE DNA


title: S2 MI2 RNAi FAIRE-chip

description:
FAIRE  MI2 RNAi S2 cells Biological Rep 1-3
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL

source_name: S2 MI2 RNAi FAIRE DNA


title: S2 BRM RNAi FAIRE-chip

description:
FAIRE  BRM RNAi S2 cells Biological Rep 1-5
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL

source_name: S2 BRM RNAi FAIRE DNA


title: S2 Mock RNAi FAIRE-chip

description:
FAIRE  Mock RNAi S2 cells Biological Rep 1-3
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL

source_name: S2 Mock RNAi FAIRE DNA


title: S2 FAIRE FAIRE-chip

description:
FAIRE  S2 cells Biological Rep 1-5
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL

source_name: S2 FAIRE DNA


title: S2 INO80 RNAi H2B ChIP-chip

description:
H2B ChIP INO80 RNAi S2 cells Biological Rep 1-4
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 INO80 RNAi H2B ChIP DNA

value: H2B rabbit polyclonal


title: S2 ISWI RNAi H2B ChIP-chip

description:
H2B ChIP ISWI RNAi S2 cells Biological Rep 1-3
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 ISWI RNAi H2B ChIP DNA


title: Hypodip-SNP-#04


title: S2 SAYP/OSA RNAi H2B ChIP-chip

description:
H2B ChIP SAYP/OSA double RNAi S2 cells Biological Rep 1-2
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 SAYP/OSA RNAi H2B ChIP DNA


title: S2 BRM RNAi H2B ChIP-chip

description:
H2B ChIP BRM RNAi S2 cells Biological Rep 1-3
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 BRM RNAi H2B ChIP DNA


title: Hypodip-SNP-#01

source_name: B-precursor ALL with miscellaneous karyotype


title: S2 H2B ChIP-chip

description:
H2B ChIP S2 cells Biological Rep 1-4
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 H2B ChIP DNA

source_name: Input/Mock-ChIP DNA


title: Hyperdip47-50-SNP-#24


title: S2 MI2 RNAi H2B ChIP-chip

description:
H2B ChIP MI2 RNAi S2 cells Biological Rep 1-3
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 MI2 RNAi H2B ChIP DNA


title: S2 SMC3 RNAi H3 ChIP-chip

description:
H3 ChIP SMC3 RNAi S2 cells Biological Rep 1-2
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 SMC3 RNAi H3 ChIP DNA


title: S2 SA RNAi H3 ChIP-chip

description:
H3 ChIP SA RNAi S2 cells Biological Rep 1-2
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 SA RNAi H3 ChIP DNA


title: Hyperdip47-50-SNP-#09


title: Hypodip-SNP-#02


title: Hyperdip47-50-SNP-#03


title: Hyperdip>50-SNP-#40

source_name: High hyperdiploid B-precursor ALL

value: High hyperdiploid B-precursor ALL


title: Hyperdip47-50-SNP-#13


title: Hyperdip47-50-SNP-#04


title: Hyperdip>50-SNP-#29


title: Hyperdip>50-SNP-#30


title: Hyperdip47-50-SNP-#11


title: Hyperdip47-50-SNP-#08


title: Hyperdip47-50-SNP-#01


title: Hyperdip>50-SNP-#23


title: Hyperdip47-50-SNP-#06


title: Hyperdip47-50-SNP-#05


title: S2 ISWI RNAi H3 ChIP-chip

description:
H3 ChIP ISWI RNAi S2 cells Biological Rep 1-3
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 ISWI RNAi H3 ChIP DNA


title: S2 SAYP/OSA RNAi H3 ChIP-chip

description:
H3 ChIP SAYP/OSA double RNAi S2 cells Biological Rep 1-2
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 SAYP/OSA RNAi H3 ChIP DNA


title: S2 BRM RNAi H3 ChIP-chip

description:
H3 ChIP BRM RNAi S2 cells Biological Rep 1-3
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 BRM RNAi H3 ChIP DNA


title: S2 INO80 RNAi H3 ChIP-chip

description:
H3 ChIP INO80 RNAi S2 cells Biological Rep 1-4
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 INO80 RNAi H3 ChIP DNA


title: S2 Mock RNAi H3 ChIP-chip

description:
H3 ChIP Mock RNAi S2 cells Biological Rep 1-3
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 Mock RNAi H3 ChIP DNA


title: S2 MI2 RNAi H3 ChIP-chip

description:
H3 ChIP MI2 RNAi S2 cells Biological Rep 1-3
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 MI2 RNAi H3 ChIP DNA


title: S2 H3 ChIP-chip

description:
H3 ChIP S2 cells Biological Rep 1-3
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 H3 ChIP DNA


title: S2 ISWI RNAi ISWI Ab18 ChIP-chip

description:
ISWI RNAi ISWI Ab18 ChIP-chip S2 cells Biological Rep 1-2
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 ISWI RNAi ISWI Ab18 ChIP DNA

value: ISWI rabbit polyclonal against KSEVVATSSNSKKKKK peptide 1012-1027 aa


title: Hyperdip>50-SNP-#22


title: Hyperdip>50-SNP-#24


title: S2 INO80 RNAi INO80 Ab1 ChIP-chip

description:
INO80 RNAi INO80 Ab1 ChIP-chip S2 cells Biological Rep 1-2
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 INO80 RNAi INO80 Ab1 ChIP DNA

value: INO80 rabbit polyclonal against 16-310 aa (Klymenko, T., Papp, B., Fischle, W., Kocher, T., Schelder, M., Fritsch, C., Wild, B., Wilm, M., and Muller, J. (2006). A Polycomb group protein complex with sequence-specific DNA-binding and selective methyl-lysine-binding activities. Genes & development 20, 1110-1122)


title: Hyperdip>50-SNP-#21


title: Hyperdip>50-SNP-#20


title: Hyperdip>50-SNP-#17


title: Hyperdip>50-SNP-#15


title: Hyperdip>50-SNP-#19


title: S2 OSA RNAi BAP111 ChIP-chip

description:
OSA RNAi BAP111 ChIP-chip S2 cells Biological Rep 1-2
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 OSA RNAi BAP111 ChIP DNA

value: BAP111 rabbit polyclonal (Chalkley, G.E., Moshkin, Y.M., Langenberg, K., Bezstarosti, K., Blastyak, A., Gyurkovics, H., Demmers, J.A., and Verrijzer, C.P. (2008). The transcriptional coactivator SAYP is a trithorax group signature subunit of the PBAP chromatin remodeling complex. Molecular and cellular biology 28, 2920-2929)


title: S2 ISWI RNAi ISWI Ab14 ChIP-chip

description:
ISWI RNAi ISWI Ab14 ChIP-chip S2 cells Biological Rep 1-2
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 ISWI RNAi ISWI Ab14 ChIP DNA

value: ISWI rabbit polyclonal against RLVDNRSNQLNKDEM peptide 584-598 aa


title: S2 SAYP/OSA RNAi BAP111 ChIP-chip

description:
SAYP/OSA double RNAi BAP111 ChIP-chip S2 cells Biological Rep 1-2
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 SAYP/OSA RNAi BAP111 ChIP DNA


title: S2 SAYP RNAi BAP111 ChIP-chip

description:
SAYP RNAi BAP111 ChIP-chip S2 cells Biological Rep 1-2
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 SAYP RNAi BAP111 ChIP DNA

source_name: Input/Mock-ChIP DNA


title: S2 BRM RNAi BRM ChIP-chip

description:
BRM RNAi BRM ChIP-chip S2 cells Biological Rep 1-2
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 BRM RNAi BRM ChIP DNA

value: BRM rabbit polyclonal (Chalkley, G.E., Moshkin, Y.M., Langenberg, K., Bezstarosti, K., Blastyak, A., Gyurkovics, H., Demmers, J.A., and Verrijzer, C.P. (2008). The transcriptional coactivator SAYP is a trithorax group signature subunit of the PBAP chromatin remodeling complex. Molecular and cellular biology 28, 2920-2929)


title: Hyperdip>50-SNP-#16


title: S2 BRM RNAi BAP111 ChIP-chip

description:
BRM RNAi BAP111 ChIP-chip S2 cells Biological Rep 1-2
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 BRM RNAi BAP111 ChIP DNA


title: Hyperdip>50-SNP-#12

source_name: High hyperdiploid B-precursor ALL


title: Hyperdip>50-SNP-#14


title: S2 MI2 RNAi MI2 ChIP-chip

description:
MI2 RNAi MI2 ChIP S2 cells Biological Rep 1-2
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 MI2 RNAi MI2 ChIP DNA

value: MI2 rabbit polyclonal (Reddy, B.A., Bajpe, P.K., Bassett, A., Moshkin, Y.M., Kozhevnikova, E., Bezstarosti, K., Demmers, J.A., Travers, A.A., and Verrijzer, C.P. (2010). Drosophila Transcription Factor Tramtrack69 Binds MEP1 to Recruit the Chromatin Remodeler NuRD. Molecular and cellular biology)


title: S2 ISWI_Ab18 ChIP-chip

description:
ISWI_Ab18 ChIP S2 cells Biological Rep 1-2
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 ISWI_Ab18 ChIP DNA


title: Hyperdip>50-SNP-#10


title: S2 ISWI_Ab14 ChIP-chip

description:
ISWI_Ab14 ChIP S2 cells Biological Rep 1-2
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 ISWI_Ab14 ChIP DNA


title: S2 BAP111 RNAi BAP111 ChIP-chip

description:
BAP111 RNAi BAP111 ChIP-chip S2 cells Biological Rep 1-2
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 BAP111 RNAi BAP111 ChIP DNA


title: S2 Ino80 ChIP-chip

description:
Ino80 Ab1 ChIP S2 cells Biological Rep 1-3
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 Ino80 ChIP DNA


title: S2 MEP1 RNAi MEP1 ChIP-chip

description:
MEP1 RNAi MEP1 ChIP-chip S2 cells Biological Rep 1-2
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 MEP1 RNAi MEP1 ChIP DNA

value: MEP1 rabbit polyclonal (Reddy, B.A., Bajpe, P.K., Bassett, A., Moshkin, Y.M., Kozhevnikova, E., Bezstarosti, K., Demmers, J.A., Travers, A.A., and Verrijzer, C.P. (2010). Drosophila Transcription Factor Tramtrack69 Binds MEP1 to Recruit the Chromatin Remodeler NuRD. Molecular and cellular biology)


title: Hyperdip>50-SNP-#08

value: leukemic cells obtained from bone marrow or blood at diagnosis


title: Hyperdip>50-SNP-#09


title: S2 MI2 ChIP-chip

description:
MI2 ChIP S2 cells Biological Rep 1-2
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 MI2 ChIP DNA


title: Hyperdip>50-SNP-#07


title: S2 MEP1 ChIP-chip

description:
MEP1 ChIP S2 cells Biological Rep 1-2
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 MEP1 ChIP DNA


title: Hyperdip>50-SNP-#27


title: Hyperdip>50-SNP-#04


title: E2A-PBX1-SNP-#17

source_name: TCF3-PBX1 B-precursor ALL

value: TCF3-PBX1 B-precursor ALL


title: Hyperdip>50-SNP-#05


title: Hyperdip>50-SNP-#13


title: Hyperdip>50-SNP-#01


title: Hyperdip>50-SNP-#06


title: Hyperdip>50-SNP-#11


title: 061K5_CTRL

city: Cincinnati

first: Michael

last: Barnes

state: OH

address: 3333 Burnet Ave

department: Rheumatology

institute: Cincinnati Childrens Hospital Medical Center

description: Control

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard scanning

data_processing: Data were imported into GeneSpring 7.3 with RMA preprocessing and normalized to median of all samples.  Normalized data were exported and subjected to Distance Weighted Discrimination (DWD) to account for any batch effects then reimported into Gene Spring and analyzed.

label: Biotin

source_name: Control

label_protocol: NuGEN Ovation labeling

extract_protocol: Peripheral blood was drawn and PBMC were isollated over Ficoll.  Samples were stored in Trizol at -80oC until extracted according to manufacturers directions.

value: Peripheral Blood Mononuclear Cells (PBMC)


title: E2A-PBX1-SNP-#13


title: E2A-PBX1-SNP-#12


title: E2A-PBX1-SNP-#15


title: E2A-PBX1-SNP-#16


title: S2 BRM ChIP-chip

description:
BRM ChIP S2 cells Biological Rep 1-2
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 BRM ChIP DNA


title: Hyperdip>50-SNP-#03


title: E2A-PBX1-SNP-#10


title: Hyperdip47-50-SNP-#10

source_name: B-precursor ALL with miscellaneous karyotype


title: S2 BAP111 ChIP-chip

description:
BAP111 ChIP S2 cells Biological Rep 1-2
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: S2 BAP111 ChIP DNA


title: 061K3_CTRL

description: Control


title: Hyperdip>50-SNP-#02


title: E2A-PBX1-SNP-#07


title: E2A-PBX1-SNP-#11


title: E2A-PBX1-SNP-#14


title: E2A-PBX1-SNP-#06


title: 061K0_CTRL

description: Control


title: 061J5_CTRL

description: Control


title: E2A-PBX1-SNP-#05


title: 061J3_CTRL

description: Control


title: 061J0_CTRL

description: Control


title: E2A-PBX1-SNP-#02


title: E2A-PBX1-SNP-#04


title: 061J4_CTRL

description: Control


title: 061HZ_CTRL

description: Control


title: BCR-ABL-SNP-#19

source_name: BCR-ABL1 B-precursor ALL

value: BCR-ABL1 B-precursor ALL


title: E2A-PBX1-SNP-#01


title: 01N70_CTRL

description: Control


title: Other-SNP-#02

value: B-precursor ALL with miscellaneous karyotype


title: 01N71_CTRL

description: Control


title: 01N72_CTRL

description: Control


title: BCR-ABL-SNP-#15


title: 01LQK_CTRL

description: Control


title: 01LQD_CTRL

description: Control


title: 01LQH_CTRL

description: Control


title: 01N6Z_CTRL

description: Control


title: 01LQJ_CTRL

description: Control


title: 01LNK_CTRL

description: Control


title: 01LNH_CTRL

description: Control


title: 01LQE_CTRL

description: Control


title: T-ALL-SNP-#28

source_name: RNA extracted from T-lineage ALL

value: T-lineage ALL


title: T-ALL-SNP-#19


title: T-ALL-SNP-#15


title: T-ALL-SNP-#22


title: 01LNM_CTRL

description: Control


title: 01LNJ_CTRL

description: Control


title: T-ALL-SNP-#04

source_name: RNA extracted from T-lineage ALL and early thymic progenitor immunophenotype


title: T-ALL-SNP-#27


title: 01LLB_CTRL

description: Control


title: 01LLX_CTRL

description: Control


title: 01LLJ_CTRL

description: Control


title: Pseudodip-SNP-#12

source_name: RNA extracted from B-precursor ALL with pseudodiploid karyotype


title: 01LKV_CTRL

description: Control


title: T-ALL-SNP-#8

source_name: RNA extracted from T-lineage ALL with MLL rearrangement

value: T-lineage ALL with MLL rearrangement


title: 01LKT_CTRL

description: Control


title: Pseudodip-SNP-#07

value: B-precursor ALL with pseudodiploid karyotype


title: 01L4M_CTRL

description: Control


title: Hypodip-SNP-#06

source_name: RNA extracted from B-precursor ALL with hypodiploid karyotype


title: Hyperdip47-50-SNP-#07

source_name: RNA extracted from tumor with alteration of ERG

value: tumor with alteration of ERG


title: 01L4N_CTRL

description: Control


title: 01LLR_CTRL

description: Control


title: 01LKM_CTRL

description: Control


title: 01L4J_CTRL

description: Control


title: Hyperdip47-50-SNP-#02

source_name: RNA extracted from tumor cells obtained at diagnosis in childhood ALL with CRLF2 rearrangement

value: childhood ALL with CRLF2 rearrangement


title: T-ALL-SNP-#10

value: T-lineage ALL and early thymic progenitor immunophenotype


title: Other-SNP-#07

source_name: RNA extracted from B-precursor ALL with miscellaneous karyotype


title: Hyperdip47-50-SNP-#12


title: P96_WT

description: WT

source_name: Untreated familial hemophagocytic lymphohistiocytosis (FHL)


title: Pseudodip-SNP-#04


title: BCR-ABL-SNP-#18

source_name: RNA extracted from tumor cells obtained at diagnosis in childhood ALL with BCR-ABL1 rearrangement


title: 01LNL_CTRL

description: Control


title: BCR-ABL-SNP-#21

value: childhood ALL with BCR-ABL1 rearrangement


title: P98WT

description: WT


title: 01L4G_CTRL

description: Control


title: P92_WT

description: WT


title: P66_WT

description: WT


title: P76_WT

description: WT


title: BCR-ABL-SNP-#17


title: BCR-ABL-SNP-#20


title: P101_WT

description: WT


title: BCR-ABL-SNP-#10


title: P1002_WT

description: WT


title: BCR-ABL-SNP-#11


title: P59_PRF


title: BCR-ABL-SNP-#12


title: P35_PRF


title: BCR-ABL-SNP-#14


title: BCR-ABL-SNP-#05


title: Rec_6_2

city: Saint Herblain

first: Wilfried

last: Gouraud

address: bd Jacques Monod

department: Integrated Center of Oncology René Gauducheau

country: France

institute: ICO (Integrated Center of Oncology Nantes)

hyb_protocol: Double-stranded complementary DNA (cDNA) and labeled complementary RNA (cRNA) were synthesized from the total RNA and hybridized to the Affymetrix Human U133 Plus 2 gene chips (Affymetrix, Santa Clara, CA).

scan_protocol: The chips were further processed and scanned according to the manufacturer’s protocol using the GeneChip Scanner 3000 7G.

data_processing: The arrays were normalized using the MAS 5.0 Affymetrix software (Expression Console - Affymetrix).

source_name: Rectal tumor biopsy

label_protocol: According to manufacturer protocol

extract_protocol: Total RNA was prepared using the RNeasy® Mini kit (Qiagen, Valencia, CA). The integrity of the RNA was assessed for each sample using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: rectum tumor biopsy

value: one hour after a dose of 7.2 Gy (4th fraction) during RT


title: Rec_4_2


title: BCR-ABL-SNP-#04


title: BCR-ABL-SNP-#09


title: Rec_4_1

value: before RT


title: BCR-ABL-SNP-#08


title: BCR-ABL-SNP-#02


title: BCR-ABL-SNP-#13


title: P33_PRF


title: BCR-ABL-SNP-#03


title: Rec_3_2


title: Rec_5_1


title: P94_WT

description: WT


title: Rec_6_1


title: Rec_5_2


title: MLL-SNP-#23

source_name: RNA extracted from tumor cells obtained at diagnosis in childhood ALL with MLL rearrangement

value: childhood ALL with MLL rearrangement


title: BCR-ABL-SNP-#01


title: Rec_3_1


title: MLL-SNP-#18


title: Rec_2_2


title: Rec_1_1

description: Rectum tumor biopsy: before RT


title: MLL-SNP-#10


title: MLL-SNP-#09


title: MLL-SNP-#08


title: 160_BM_1Y

city: Duarte

first: Ravi

last: Bhatia

state: CA

address: 1500 E Duarte Road

department: Hematopoietic Stem Cell and Leukemia Research

institute: City of Hope Beckman Research Institute

description: Gene expression data at the time of development t-MDS/AML timepoint for cases and coresponding timepoint for controls

hyb_protocol: 15 µg biotin-labeled cRNA from each sample was hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays.

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

data_processing: Microarray data were analyzed using R (version 2.9) with genomic analysis packages from Bioconductor (version 2.4). Data for PBSC and BM samples were normalized separately using robust multiarray averages with consideration of GC content (GCRMA). Probesets with low expression or variability were filtered. Expression of genes represented by multiple probesets was set as the median of the probesets. Using conditional logistic model (CLM) to retain matching between cases and controls, we analyzed the magnitude of association [expressed as odds ratio (OR)] between t-MDS/AML and i) gene expression levels in PBSC at the pre-aHCT time point; ii) gene expression levels in BM at time of t-MDS/AML; and iii) change of expression of individual genes from PBSC to time of t-MDS/AML. False discovery rate (FDR) was applied to adjust for multiple testing.

source_name: CD34+ cells

label_protocol: Total RNA from 1000 cells was amplified and labeled with Biotin using GeneChip Two-Cycle Target Labeling and Control Reagents (Affymetrix, Santa Clara, CA).

growth_protocol: PBSC samples and mononuclear cells (MNC) isolated from BM samples using Ficoll-Hypaque density gradient separation were cryopreserved in LN2. Frozen cells were thawed and incubated in IMDM supplemented with 20% FBS and DNAse I (Sigma) for 3 hour incubation at 37°C.

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen).

treatment_protocol: Cells were labeled with anti-CD34 APC and anti-CD45 FITC (BD biosciences) and CD34+CD45dim cells were sorted using a MoFlo cytometer (Beckman-Coulter, Miami, FL).

tag: patient id

tag: sample type

value: BM

tag: sample set for prediction study

tag: patient status

value: Control

tag: matching group


title: MLL-SNP-#17

value: leukemic cells obtained from bone marrow or blood at diagnosis


title: MLL-SNP-#04


title: 144_BM_2Y


title: MLL-SNP-#06


title: 152_BM_3Y


title: MLL-SNP-#11


title: Rec_1_2


title: 168_BM_3y

value: Case


title: 149_BM_2Y


title: 228_BM_D100


title: 155_BM_1y


title: 243_BM_1Y


title: MLL-SNP-#07


title: 120_BM_3y


title: 137_BM_6m


title: MLL-SNP-#02


title: MLL-SNP-#01


title: 111_BM_1Y


title: Rec_2_1


title: TEL-AML1-SNP-#34

source_name: RNA extracted from tumor cells obtained at diagnosis in childhood ALL with ETV6-RUNX1 rearrangement


title: TEL-AML1-SNP-#36

value: childhood ALL with ETV6-RUNX1 rearrangement


title: TEL-AML1-SNP-#19


title: TEL-AML1-SNP-#18


title: 109_BM_2Y


title: 125_BM_4Y


title: TEL-AML1-SNP-#13


title: TEL-AML1-SNP-#20


title: TEL-AML1-SNP-#17


title: TEL-AML1-SNP-#14


title: 114_BM_3Y


title: TEL-AML1-SNP-#06


title: 66_BM_6M


title: 93_BM_4Y


title: 91_BM_3y


title: 51_BM_1y


title: 61_BM_5Y


title: 68_BM_5Y


title: TEL-AML1-SNP-#02


title: 55_BM_3Y


title: 53_BM_3yr


title: 50_BM_1yr


title: 96_BM_2Y


title: E2A-PBX1-SNP-#09

source_name: RNA extracted from tumor cells obtained at diagnosis in childhood ALL with TCF3-PBX1 rearrangement


title: TEL-AML1-SNP-#03


title: E2A-PBX1-SNP-#03

value: childhood ALL with TCF3-PBX1 rearrangement


title: 24_BM_5y


title: 39_BM_1Y


title: 56_BM_4Y


title: 13_BM_5Y


title: 25_BM_2yr


title: 11_BM_1y


title: 62_BM_5Y


title: 8_BM_3yr


title: 61_PBSC

description: Gene expression data at pre-transplant timepoint

value: PBSC

value: Training


title: 62_PBSC


title: 95_BM_5Y


title: 76_PBSC


title: 95_PBSC


title: 25_PBSC


title: 93_PBSC


title: 187_PBSC


title: 5005_PBSC


title: TEL-AML1-SNP-#11


title: TEL-AML1-SNP-#05


title: 141_PBSC


title: 91_PBSC


title: 144_PBSC


title: 109_PBSC


title: 11_PBSC


title: 160_PBSC


title: 53_PBSC


title: 45_PBSC


title: 8_PBSC


title: Kshatriya Uttar Pradesh India 209e

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

description: Genomic DNA extracted from blood was genotyped using HumanHap650Yv3_A   Genotyping BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Genomestudio v2009.2 with GT module 1.5.16 (Illumina).

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

tag: gender

value: Male

tag: population

value: Kshatriya

tag: region

value: Uttar Pradesh India

value: blood


title: Kshatriya Uttar Pradesh India 208e


title: Kshatriya Uttar Pradesh India 204e


title: 114_PBSC


title: Kurmi Uttar Pradesh India evo_10

value: Kurmi


title: Mawasi CHATTISGARH India Mawasi1

value: Mawasi

value: CHATTISGARH India


title: Kshatriya Uttar Pradesh India 201


title: 55_PBSC


title: Lambadi Andhra Pradesh India A311

value: Lambadi

value: Andhra Pradesh India


title: Kshatriya Uttar Pradesh India 199e


title: 168_PBSC


title: Kol Uttar Pradesh India 335e

value: Kol


title: Kol Uttar Pradesh India 323


title: Kol Uttar Pradesh India 332


title: Kshatriya Uttar Pradesh India 198


title: Kshatriya Uttar Pradesh India 195


title: Kol Uttar Pradesh India 330e


title: Kol Uttar Pradesh India 298


title: 56_PBSC

value: Control


title: 51_PBSC


title: Kol Uttar Pradesh India 321e


title: 125_PBSC


title: Kol Uttar Pradesh India 306


title: Kol Uttar Pradesh India 328e


title: Velmas Andhra Pradesh India VELZ265

description: Genomic DNA extracted from blood was genotyped using Human610-Quad v1.0  Genotyping BeadChips (Illumina).

value: Velmas


title: Kol Uttar Pradesh India 290


title: Kol Uttar Pradesh India 314


title: Kol Uttar Pradesh India 308e


title: Kol Uttar Pradesh India 296e


title: 112_PBSC


title: 54_PBSC


title: Kol Uttar Pradesh India 310e


title: Kol Uttar Pradesh India 319


title: Velmas Andhra Pradesh India VELZ274


title: Kol Uttar Pradesh India 288


title: 231_PBSC

value: Case


title: Velmas Andhra Pradesh India VELZ271


title: Kol Uttar Pradesh India 309e


title: 96_PBSC


title: Kanjars Uttar Pradesh India evo_35

value: Kanjars


title: 155_PBSC


title: Velmas Andhra Pradesh India VELZ264


title: Velmas Andhra Pradesh India VELZ277


title: Kanjars Uttar Pradesh India evo_38


title: Kanjars Uttar Pradesh India evo_37


title: 85_PBSC


title: 49_PBSC


title: Kanjars Uttar Pradesh India evo_34


title: Velmas Andhra Pradesh India VELZ281


title: Velmas Andhra Pradesh India VELZ272


title: 86_PBSC


title: 5036_PBSC


title: Kanjars Uttar Pradesh India evo_36


title: Velmas Andhra Pradesh India VELZ260


title: Velmas Andhra Pradesh India VELZ267


title: 43_PBSC


title: Pulliyar Tamil Nadu India PULD160

value: Pulliyar

value: Tamil Nadu India


title: 5042_PBSC

value: PBSC

value: Training


title: Velmas Andhra Pradesh India VELZ275

value: Male


title: Dusadh Uttar Pradesh India D494

value: Dusadh

value: Uttar Pradesh India


title: 126_PBSC


title: Pulliyar Tamil Nadu India PULD162

value: blood


title: 17_PBSC


title: Gond MADHYA PRADESH India G53

value: Gond

value: MADHYA PRADESH India


title: 132_PBSC


title: Kanjars Uttar Pradesh India evo_33


title: Pulliyar Tamil Nadu India PULD171


title: Piramalai Kallars Tamil Nadu India PK6422

value: Female

value: Piramalai Kallars


title: Pulliyar Tamil Nadu India PULD151


title: Dusadh Uttar Pradesh India A397


title: Dusadh Uttar Pradesh India A394


title: Pulliyar Tamil Nadu India PULD172


title: 87_PBSC


title: 228_PBSC


title: Piramalai Kallars Tamil Nadu India PK6442


title: 5040_PBSC


title: 66_PBSC


title: Dusadh Uttar Pradesh India A392


title: Dusadh Uttar Pradesh India A393


title: Kanjars Uttar Pradesh India A143


title: 137_PBSC


title: 152_PBSC


title: 69_PBSC


title: Piramalai Kallars Tamil Nadu India PK6490


title: Piramalai Kallars Tamil Nadu India PK6459


title: Dusadh Uttar Pradesh India A396


title: Dusadh Uttar Pradesh India A387


title: Piramalai Kallars Tamil Nadu India PK6458


title: Piramalai Kallars Tamil Nadu India PK6491


title: Dusadh Uttar Pradesh India A388


title: Piramalai Kallars Tamil Nadu India PK6468


title: TN Low Caste TAMIL NADU India TN26

value: TN Low Caste

value: TAMIL NADU India


title: Piramalai Kallars Tamil Nadu India PK6415


title: 50_PBSC

value: Control


title: 243_PBSC


title: Dharkars Uttar Pradesh India HA042

value: Dharkars


title: Dusadh Uttar Pradesh India A386


title: Kanjars Uttar Pradesh India A141

value: Kanjars


title: 120_PBSC

value: Case


title: 111_PBSC


title: Dharkars Uttar Pradesh India HA048


title: Dhurwa ORISSA India ORI23

value: Dhurwa

value: ORISSA India


title: 165_PBSC

value: PBSC

value: Training


title: TN Low Caste TAMIL NADU India TN18


title: Dusadh Uttar Pradesh India A395

value: Dusadh


title: Nihali MAHARASHTRA India NIH1

value: Male

value: Nihali

value: MAHARASHTRA India


title: 40_PBSC


title: 101_PBSC


title: Naga NAGALAND India NAG134

value: Naga

value: NAGALAND India

value: blood


title: Dharkars Uttar Pradesh India HA039

value: Uttar Pradesh India


title: Dharkars Uttar Pradesh India HA041


title: Dharkars Uttar Pradesh India HA038


title: Dharkars Uttar Pradesh India HA030


title: 149_PBSC


title: Dharkars Uttar Pradesh India HA037


title: 68_PBSC


title: Naga NAGALAND India NAG133


title: 24_PBSC


title: Dharkars Uttar Pradesh India HA040


title: Dharkars Uttar Pradesh India HA029


title: Naga NAGALAND India NAG129


title: Naga NAGALAND India NAG131


title: 5069_PBSC

value: Test


title: 39_PBSC

value: Control


title: 59_PBSC


title: Kurumba TAMIL NADU India KUR4

value: Kurumba

value: TAMIL NADU India


title: 474_PBSC


title: Kurumba TAMIL NADU India KUR1


title: Kurumba TAMIL NADU India KUR2


title: Dharkars Uttar Pradesh India HA023

value: Dharkars


title: Nihali MAHARASHTRA India NIH2


title: 650_PBSC

value: Case


title: 745_PBSC


title: Kurumba TAMIL NADU India KUR3


title: Halakipikki KARNATAKA India HLKP252

value: Halakipikki

value: KARNATAKA India


title: Dharkars Uttar Pradesh India DH001


title: 719_PBSC

value: PBSC


title: Halakipikki KARNATAKA India HLKP245


title: Chamar Uttar Pradesh India evo_43

value: Chamar


title: Chamar Uttar Pradesh India evo_42

value: Female


title: 211_PBSC


title: Halakipikki KARNATAKA India HLKP243

value: Male


title: Chamar Uttar Pradesh India evo_41


title: 904_PBSC


title: Chamar Uttar Pradesh India evo_40


title: Halakipikki KARNATAKA India HLKP241


title: Gond CHATTISGARH India GONC8

value: Gond

value: CHATTISGARH India


title: 15011_PBSC


title: Chamar Uttar Pradesh India A266


title: Dharkars Uttar Pradesh India HA045


title: 265_PBSC


title: 15009_PBSC


title: Gond CHATTISGARH India GONC1


title: Chamar Uttar Pradesh India A260


title: Gond CHATTISGARH India GONC5


title: 80_PBSC


title: Chenchus Andhra Pradesh India CHEND95

value: Chenchus

value: Andhra Pradesh India


title: 81_PBSC


title: MCK-PPARb, biological rep1

city: Orlando

first: Zhenji

last: Gan

state: FL

address: 6400 Sanger Rd

institute: SBMRI

description: Muscle RNA from muscle-specific PPARbeta overexpressing transgenic mouse

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: MAS 5.0 in GCOS

organism: Mus musculus

source_name: Gastrocnemius muscle from PPARbeta overexpressing mouse

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

extract_protocol: RNAzol B -followed manufacturer's protocol

value: gastrocnemius muscle

tag: genotype/variation

value: PPARbeta overexpressing

tag: age

value: 6 weeks of age


title: 15008_PBSC

value: Test


title: Chamar Uttar Pradesh India A261

value: Uttar Pradesh India

value: blood


title: Chamar Uttar Pradesh India A253


title: Chamar Uttar Pradesh India A268


title: Chenchus Andhra Pradesh India CHEND85


title: MCK-PPARb, biological rep2


title: Brahmins Uttaranchal UTTARANCHAL India H1

value: Brahmins Uttaranchal

value: UTTARANCHAL India


title: 15007_PBSC

value: Case


title: Chamar Uttar Pradesh India A259


title: Non-transgenic mouse, biological rep2

description: Muscle RNA from littermate control mice for muscle-specific PPARbeta overexpressing transgenic mice

source_name: Gastrocnemius muscle from wild-type mouse

value: wild-type


title: Non-transgenic mouse, biological rep1


title: Chenchus Andhra Pradesh India CHEND90


title: 340_PBSC

value: PBSC

value: Control


title: Brahmins TN TAMIL NADU India SB001

value: Male

value: Brahmins TN

value: TAMIL NADU India


title: 15006_PBSC


title: Chenchus Andhra Pradesh India CHEND96

value: Chenchus


title: 230_PBSC


title: BBN + nicotinamide-treated bladder BBN+nicotinamide.3

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

description: To export to gene expression data based on unique probe id, we use Illumina BeadStudio software.

hyb_protocol: Labeled, amplified material (1,500 ng per array) was hybridized to a ver. 1.0 of the Illumina Mouse-6 BeadChips (46K) according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA). Array signals were developed by Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the BeadChip manual.

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions.

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin.

source_name: BBN+nicotinamide-treated non-tumorigenic mouse bladder

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina’s recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina® TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using RiboGreen were measured (Quant-iTTM RiboGreen® RNA assay kit; Invitrogen-Molecular Probes, ON, Canada) by the Victor3 spectrophotometer (PerkinElmer, CT) and cRNA quality was checked on a 1% agarose gel.

extract_protocol: Total RNA was isolated from tissues with TRIzol (Life Technologies, NY) reagent according to the manufacturer’s protocol. RNA quality and integrity were confirmed by electrophoresis on agarose gel stained with ethidium bromide and examined under ultraviolet light.

tag: biological source

value: non-tumorigenic mouse bladder

tag: treatment

value: BBN+nicotinamide


title: 696_PBSC


title: BBN + nicotinamide-treated bladder BBN+nicotinamide.2


title: BBN + nicotinamide-treated bladder BBN+nicotinamide.4


title: BBN + nicotinamide-treated bladder BBN+nicotinamide.5


title: BBN + nicotinamide-treated bladder BBN+nicotinamide.1


title: Brahmins Uttar Pradesh Uttar Pradesh India DEL007

value: Brahmins Uttar Pradesh


title: Brahmins TN TAMIL NADU India SB003


title: 146_PBSC


title: Brahmins Uttar Pradesh Uttar Pradesh India BRG001


title: 15_PBSC


title: Brahmins Uttar Pradesh Uttar Pradesh India BR084


title: 15005_PBSC


title: Brahmins Uttar Pradesh Uttar Pradesh India BR052


title: Brahmins Uttar Pradesh Uttar Pradesh India BR008


title: Nicotinamide-treated bladder nicotinamide.2

source_name: Nicotinamide-treated normal mouse bladder

value: normal mouse bladder

value: nicotinamide


title: Nicotinamide-treated bladder nicotinamide.4


title: Bhunjia CHATTISGARH India D201

value: Female

value: Bhunjia

value: CHATTISGARH India


title: Brahmins Uttar Pradesh Uttar Pradesh India 177e

value: Uttar Pradesh India

value: blood


title: Nicotinamide-treated bladder nicotinamide.3


title: Bengali JHARKHAND India Bengali1

value: Bengali

value: JHARKHAND India


title: heterozygous, prenatal stress, biological rep3

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

country: Germany

institute: University of Wuerzburg

description: Gene expression data from left hippocampus of mice offspring of 5HTT+/- parents at P100, several behavioural tests

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on a Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station_450

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000

data_processing: The data were analyzed with Bioconductor packages (under R) and vsn as normalization method using perfect match only

source_name: left hippocampus of 5HTT +/- prenatal stressed mice

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

growth_protocol: heterozygous (+/-) 5-HTT knockout mice ([B6.129(Cg)-Slc6a4tm1Kpl/J] (Bengel, Murphy et al. 1998) were used for breeding. The hippocampi of the offspring were examined.

extract_protocol: The tissue was homogenized using 500µl PegGOLD RNAPure (Peglab) and metal beads (3 min., 20Hz in a Tissue Lyser (Qiagen)). After that 100µl chloroform was added and centrifuged (5 min., 4°C, 12.000 x g). The water phase was then mixed with 250µl ethanol and from that point on the the protocol of the RNeasy Mini Kit (Qiagen) was followed

treatment_protocol: Prenatal maternal stress daily during E13–E17, restraining the dams in transparent 250 ml glass cylinders filled up to a height of 5 mm with water, bright light exposure, 3 times daily, for 45 min. per session. Control pregnant females were left undisturbed in their home cages.

tag: genetic background

value: female

value: left hippocampus

tag: genotype

value: prenatal stress


title: Nicotinamide-treated bladder nicotinamide.5


title: heterozygous, prenatal stress, biological rep2

tag: tissue


title: Brahmins Uttar Pradesh Uttar Pradesh India evo_9

value: Male


title: 15003_PBSC

value: PBSC

value: Test

value: Case


title: 445_PBSC

value: Control


title: BBN-induced bladder cancer BBN.5

source_name: BBN-induced mouse bladder cancer

value: mouse bladder cancer

value: BBN


title: Nicotinamide-treated bladder nicotinamide.1

value: normal mouse bladder

value: nicotinamide


title: 15004_PBSC


title: heterozygous, prenatal stress, biological rep1


title: 15002_PBSC


title: 217_PBSC


title: UP Low Caste Uttar Pradesh India Z225

value: UP Low Caste


title: heterozygous, control, biological rep3

source_name: left hippocampus of 5HTT +/- control mice

value: control


title: BBN-induced bladder cancer BBN.3


title: Skov3_shEZH2.2_2

city: Philadelphia

last: Slifker

state: PA

address: 333 Cottman Ave.

institute: Fox Chase Cancer Center

description:
S1545-2
Gene expression in short-hairpin EZH2 knockdown, number 2

hyb_protocol: 1.65 mg of Cy-3 labeled cRNA targets is hybridized onto Agilent 4 x 44k whole genome arrays for 17 hours at 65C and washed according to Agilent procedure.

scan_protocol: The hybridized slides are scanned at 5 μm resolution on Agilent scanner (Agilent) and fluorescent intensities of hybridization signals are extracted using Agilent Feature Extraction software.

data_processing: Agilent FE 9.5 gMeanSignal values were background corrected (BG measure=gBGUsed) using normexp method (offset=25). After removing control probes, arrays were quantile-normalized (as part of a larger dataset).

label_protocol: 500 ng total RNA was amplified and labeled using Agilent QuickAmp labeling kit following the manufacturer protocol.

growth_protocol: SKOV3 human EOC cell line was cultured according to the American Type Culture Collection standards.

extract_protocol: RNA from cultured human SKOV3 EOC cells was isolated using Trizol (Invitrogen) according to manufacturer’s instruction. For qRT-PCR, Trizol-isolated RNA was further purified using an RNeasy kit (Qiagen) following manufacture's instruction.

treatment_protocol: SKOV3 cells at 40-50% confluence were infected with lentivirus expressing shRNA to EZH2 or vector control. The infected cells were drug-selected with 3 μg/ml of puromycin to eliminate non-infected cells

tag: cell line

value: SKOV3 human EOC cell line


title: 898_PBSC


title: BBN-induced bladder cancer BBN.4


title: Skov3_shEZH2.2_3

description:
S1545-3
Gene expression in short-hairpin EZH2 knockdown, number 2

value: infected with lentivirus expressing shRNA to EZH2


title: UP Low Caste Uttar Pradesh India Z220

value: Uttar Pradesh India

value: blood


title: Skov3_shEZH2.2_1

description:
S1545-1
Gene expression in short-hairpin EZH2 knockdown, number 2


title: BBN-induced bladder cancer BBN.2


title: wild type, prenatal stress, biological rep3

source_name: left hippocampus of prenatal stressed mice

value: female

value: left hippocampus

value: wild type


title: 15001_PBSC

value: PBSC


title: BBN-induced bladder cancer BBN.1


title: heterozygous, control, biological rep1


title: 493_PBSC

value: Test


title: UP Low Caste Uttar Pradesh India Z217

value: Male


title: Tharus Uttar Pradesh India D260

value: Tharus


title: Normal bladder Normal.5

source_name: Normal mouse bladder


title: 75_PBSC

value: Control


title: wild type, prenatal stress, biological rep1

value: prenatal stress


title: Normal bladder Normal.3

value: normal mouse bladder


title: Skov3_shEZH2.1_2

description:
S1543-2
Gene expression in short-hairpin EZH2 knockdown, number 1


title: wild type, prenatal stress, biological rep2


title: Normal bladder Normal.4


title: 5099_PBSC

value: Case


title: UP Low Caste Uttar Pradesh India Z224

value: UP Low Caste


title: UP Low Caste Uttar Pradesh India Z218


title: wild type, control, biological rep3

source_name: left hippocampus of control mice

value: control


title: 138_PBSC


title: wild type, control, biological rep2


title: Normal bladder Normal.2


title: 5035_PBSC


title: Skov3_shEZH2.1_3

description:
S1543-3
Gene expression in short-hairpin EZH2 knockdown, number 1

value: SKOV3 human EOC cell line


title: 104_PBSC


title: Skov3_ctrl_2

description:
S1222-2
Gene expression in control cells

value: infected with lentivirus expressing vector control


title: Skov3_ctrl_1

description:
S1222-1
Gene expression in control cells


title: Skov3_shEZH2.1_1

description:
S1543-1
Gene expression in short-hairpin EZH2 knockdown, number 1

value: infected with lentivirus expressing shRNA to EZH2


title: Tharus Uttar Pradesh India D254

value: Uttar Pradesh India

value: blood


title: Muslim Uttar Pradesh India MV015

value: Muslim


title: Muslim Uttar Pradesh India MV013


title: Skov3_ctrl_3

description:
S1222-3
Gene expression in control cells


title: Normal bladder Normal.1


title: 166c

status: Public on Dec 11 2011

city: Subiaco

first: Anthony

last: Bosco

state: WA

address: 100 Roberts Road

country: Australia

institute: Telethon Kids Institute

description: Nasal lavage cells obtained 7-14 days post virus-induced exacerbation from asthmatic child 166

hyb_protocol: The samples were hybridized to HuGene ST1.0 microarrays according to standardized protocols and reagents from Affymetrix.

scan_protocol: The samples were scanned on a GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed in Expression Console software (Affymetrix) employing the probe logarithmic intensity error algorithm (parameters - PM-GCBG background subtraction, quantile normalization, iterPLIER summarization).

source_name: Nasal lavage cells obtained 7-14 days after acute exacerbation

label_protocol: The samples were labelled according to standardized protocols and reagents from Affymetrix.

growth_protocol: Asthmatic children were instructed to visit the study center within 24 h of experiencing symptoms of an exacerbation.

extract_protocol: Total RNA was extracted from nasal lavage cells employing TRIzol followed by RNeasy.

treatment_protocol: Nasal lavage cells were collected in sterile 3 % saline, processed by vigorous pipetting, and stablized in RNALater.

tag: phenotype

value: Asthmatic child with Picornavirus-induced exacerbation

tag: cell type

value: nasal lavage


title: 161x

description: Nasal lavage cells obtained during virus-exacerbation from asthmatic child 161

source_name: Nasal lavage cells obtained during acute virus-induced exacerbation


title: 166x

description: Nasal lavage cells obtained during virus-exacerbation from asthmatic child 166


title: 161c

description: Nasal lavage cells obtained 7-14 days post virus-induced exacerbation from asthmatic child 161


title: Meena RAJASTHAN India A105

description: Genomic DNA extracted from blood was genotyped using HumanHap650Yv3_A   Genotyping BeadChips (Illumina).

value: Meena

value: RAJASTHAN India


title: 163c

description: Nasal lavage cells obtained 7-14 days post virus-induced exacerbation from asthmatic child 163


title: 165x

description: Nasal lavage cells obtained during virus-exacerbation from asthmatic child 165


title: 165c

description: Nasal lavage cells obtained 7-14 days post virus-induced exacerbation from asthmatic child 165


title: 167x

description: Nasal lavage cells obtained during virus-exacerbation from asthmatic child 167


title: 160c

description: Nasal lavage cells obtained 7-14 days post virus-induced exacerbation from asthmatic child 160


title: heterozygous, control, biological rep2

description: Gene expression data from left hippocampus of mice offspring of 5HTT+/- parents at P100, several behavioural tests

value: female

value: left hippocampus


title: 156x

description: Nasal lavage cells obtained during virus-exacerbation from asthmatic child 156


title: 158x

description: Nasal lavage cells obtained during virus-exacerbation from asthmatic child 158


title: 163x

description: Nasal lavage cells obtained during virus-exacerbation from asthmatic child 163


title: 151x

description: Nasal lavage cells obtained during virus-exacerbation from asthmatic child 151


title: 5008_PBSC

description: Gene expression data at pre-transplant timepoint

tag: patient id

tag: sample type

value: PBSC

value: Test


title: 158c

description: Nasal lavage cells obtained 7-14 days post virus-induced exacerbation from asthmatic child 158


title: wild type, control, biological rep1

value: wild type


title: Muslim Uttar Pradesh India MV003

value: Male


title: ALS10

city: Charlotte

first: Jean-Luc

middle: C

last: Mougeot

state: NC

address: 1542 Garden Terrace

department: Internal Medicine

institute: Carolinas Medical Center

description:
Pooled RNA from HC1 to HC11 for cohybridization with Cy5 labelled RNA
patient samples: Lymphocytes were isolated from whole blood drawn by venipuncture into BD ACD tubes using the method described by Repnik et al. (2003) [PMID:12957415].

hyb_protocol: Equal amounts of Cy3 and Cy5-labeled cRNA (825 ng) from two different samples (test and reference pool) were hybridized to Agilent Human Whole Genome 4x44k Microarrays.

scan_protocol: The hybridized arrays were washed and scanned using Agilent G2565BA scanner and data were extracted from the scanned image using Feature Extraction version 10.2 (Agilent Technologies).

data_processing: Conversion of raw data .txt files to .mev files, data normalization and filtering using the TM4 (MIDAS pipeline) were performed by the PI Jean-Luc Mougeot. Raw data .txt files in Agilent format were converted to .mev files using ExpressConverterTM v2.1 of the TM4 Microarray Suite (TIGR Genomics, Rockville, CA). Background-subtracted raw data were normalized using the MIDAS pipeline (TM4, TIGR Genomics, Rockville, MD) according to Sioson et al. (2006) [PMID: 16626497] with the following steps: total intensity normalization, LocFit (LOWESS), standard deviation regularization and low intensity trim. We generated two datasets for further analysis, DS3500 and DS7000 where both Cy3 and Cy5 integrated intensities (ISI) were above one (ISI=3500) or two (ISI=7000) standard deviation(s) of their respective background.

source_name: Lymphocytes definite sALS

label_protocol: Fifty nanograms of total RNA was converted into labeled cRNA with nucleotides coupled to a fluorescent dye (either Cy3 or Cy5) using the Quick Amp Kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s protocol.

extract_protocol:
RNA isolation, quality control evaluation and microarray experiments were performed at Cogenics Inc. (Morrisville, NC). Total RNA was extracted from the cell samples at Cogenics Inc. (Morrisville, NC) using standard procedures: TRIzol extraction following manufacturer's instructions (Invitrogen Life Technologies Carlsbad, CA) and RNA purification using Rneasy Mini-kit (Qiagen, Valencia, CA).
quality control: The quantity of each of the total RNA samples (A260/280 ratio and yield) was determined by spectrophotometry and the size distribution (RIN) was assessed using an Agilent Bioanalyzer 2100.

treatment_protocol: Presence of disease (amyotrophic lateral sclerosis) compared to absence of disease (healthy control subjects with no presence of cancer, autoimmune disease or neurological disease)

tag: de-identified research code

source_name: HC Reference pool HC1 to HC11

tag: reference

value: HC Reference pool


title: 156c

description: Nasal lavage cells obtained 7-14 days post virus-induced exacerbation from asthmatic child 156


title: ALS11

tag: gender

value: Female


title: 160x

description: Nasal lavage cells obtained during virus-exacerbation from asthmatic child 160


title: 167c

description: Nasal lavage cells obtained 7-14 days post virus-induced exacerbation from asthmatic child 167


title: 151c

description: Nasal lavage cells obtained 7-14 days post virus-induced exacerbation from asthmatic child 151


title: Muslim Uttar Pradesh India MV012

description: Genomic DNA extracted from blood was genotyped using HumanHap650Yv3_A   Genotyping BeadChips (Illumina).

tag: population


title: ALS9


title: 150x

description: Nasal lavage cells obtained during virus-exacerbation from asthmatic child 150


title: 150c

description: Nasal lavage cells obtained 7-14 days post virus-induced exacerbation from asthmatic child 150


title: ALS8


title: 149x

description: Nasal lavage cells obtained during virus-exacerbation from asthmatic child 149


title: ALS7


title: ALS4


title: Meghawal RAJASTHAN India D442

value: Meghawal

tag: region


title: ALS6


title: 132c

description: Nasal lavage cells obtained 7-14 days post virus-induced exacerbation from asthmatic child 132


title: ALS5


title: 149c

description: Nasal lavage cells obtained 7-14 days post virus-induced exacerbation from asthmatic child 149


title: 126c

description: Nasal lavage cells obtained 7-14 days post virus-induced exacerbation from asthmatic child 126


title: HC9

source_name: Lymphocytes Healthy Control Subject


title: 106x

description: Nasal lavage cells obtained during virus-exacerbation from asthmatic child 106


title: 131c

description: Nasal lavage cells obtained 7-14 days post virus-induced exacerbation from asthmatic child 131


title: Muslim Uttar Pradesh India MV009


title: ALS3


title: 131x

description: Nasal lavage cells obtained during virus-exacerbation from asthmatic child 131


title: HC6


title: HC11


title: 106c

description: Nasal lavage cells obtained 7-14 days post virus-induced exacerbation from asthmatic child 106


title: ALS2


title: HC8


title: 105x

description: Nasal lavage cells obtained during virus-exacerbation from asthmatic child 105


title: HC10

description:
Pooled RNA from HC1 to HC11 for cohybridization with Cy5 labelled RNA
patient samples: Lymphocytes were isolated from whole blood drawn by venipuncture into BD ACD tubes using the method described by Repnik et al. (2003) [PMID:12957415].


title: ALS1


title: 105c

description: Nasal lavage cells obtained 7-14 days post virus-induced exacerbation from asthmatic child 105


title: 126x

description: Nasal lavage cells obtained during virus-exacerbation from asthmatic child 126


title: HC7


title: HC4


title: HC3


title: HC5


title: HC2


title: Baseline (0 months) - Progressive CADI score (Project 2) [KT858_2_6_09]

status: Public on Dec 10 2011

city: Stanford

first: Maarten

last: Naesens

address: Pasteur Drive

institute: Stanford University

hyb_protocol: The cDNA fragments of all 120 biopsies were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays comprising more than 54,000 probe sets, covering more than 47,000 transcripts and variants, including 38,500 well-characterized human genes (Affymetrix Inc., Santa Clara, CA, USA).

scan_protocol: The microarrays were scanned using GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA, USA).

data_processing: For processing and normalization of the scanned images, dChip 2006 software was used, with perfect match [PM]/mismatch [MM] difference modeling and invariant set normalization

source_name: Kidney transplant biopsy

label_protocol: biotin labeling using the OvationTM Biotin System (NuGEN Technologies, San Carlos, CA, USA)

extract_protocol: each kidney allograft biopsy (n=120), a separate biopsy core was placed in RNAlater (Ambion Inc, Austin, TX, USA) and stored at –20°C until RNA extraction. Total RNA was extracted from each biopsy using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA).

treatment_protocol: Tacrolimus-Mycophenolate mofetil

value: Kidney transplant biopsy

tag: i-ifta grade

tag: total i score

tag: cadi score

tag: time point

value: 00 months


title: Baseline (0 months) - Progressive CADI score (Project 2) [KT949_2_16_09]


title: Validation set high CADI score (Project 1 + Project 4) and 24 months high CADI score (Project 2) [KT1065_2_18_09]

value: 24 months


title: 6 months - Progressive CADI score (Project 2 and Project 3) [KT1115_2_18_09]

value: 06 months


title: K562_rep02

city: Hangzhou

first: wu

last: hao

state: Zhejiang

address: 88, JieFang Road

department: Cancer Institute

country: China

institute: Zhejiang University

description: Gene expression data from normal K562 cell line

hyb_protocol: Following fragmentation,  cRNA were hybridized for 16 hr at 45C on Human U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data was analyzed with GC-RMA using Expression console software (Affymetrix) and default analysis setting

source_name: Normal K562

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol(Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: Cultured in RPMI-1640 medium with 10% FBS, incubated at 5% CO2 and 37C

extract_protocol: RNA was extracted with Rneasy mini Kit(Qiagen), according to manufacturer's protocol

treatment_protocol: K562 cell was treated by 4uM shikonin for 4hours, then allowed to die and grow back in fresh medium. Once recovered, cells were immidiatly subjected to another treatment.

value: Normal K562


title: Baseline (0 months) - Progressive CADI score (Project 2) [KT859_2_6_09]


title: Baseline (0 months) - Progressive CADI score (Project 2) [KT766_2_16_09]


title: Validation set high CADI score (Project 1 + Project 4) and 24 months high CADI score (Project 2) [KT1384_2_20_09]


title: K562_Shk_rep01

description: Gene expression data from shikonin resistant K562 cell line

source_name: Shikonin resistant K562

value: Shikonin resistant K562


title: K562_rep01


title: K562_rep03


title: 6 months - Progressive CADI score (Project 2 and Project 3) [KT1034_2_18_09]


title: Validation set high CADI score (Project 1 + Project 4) and 24 months high CADI score (Project 2) [KT1331_2_20_09]


title: Validation set high CADI score (Project 1 + Project 4) and 24 months high CADI score (Project 2) [KT1255_2_18_09]


title: HC1

tag: age


title: Validation set high CADI score (Project 1 + Project 4) and 24 months high CADI score (Project 2) [KT1325_2_20_09]


title: 6 months - Progressive CADI score (Project 2 and Project 3) [KT675_2_16_09]


title: K562_Shk_rep03


title: 6 months - Progressive CADI score (Project 2 and Project 3) [KT860_2_16_09]


title: K562_Shk_rep02


title: 6 months - Progressive CADI score (Project 2 and Project 3) [KT1040_2_18_09]


title: Baseline (0 months) - Progressive CADI score (Project 2) [KT609_2_16_09]


title: ElavC155-GAL4 2

city: Madison

first: Andrew

middle: Jay

last: Petersen

state: WI

address: 1300 University Avenue, 379MSC

department: Department of Cellular and Regenerative Biology

institute: University of Wisconsin-Madison

description: Biological replicate 2 of the ElavC155-GAL4 condition

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 ArrayStar 3.0.2 program (DNASTAR, Inc. Madison, WI, USA).

source_name: ElavC155-GAL4 control fly, 4-6 days aged at 25°C

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

growth_protocol: ATM^8/+ and ATM^8/ATM^8  flies were cultured at 18°C prior to eclosion and  for 0-3 days post-eclosion.  All other genotypes were maintained at 25°C prior to eclosion and for 0-3 days post-eclosion.

extract_protocol: Total RNA was extracted from fly heads after liquid nitrogen-induced shearing using the TRI reagent (Sigma-Aldrich, St. Louis, MO, USA), DNA was removed by treatment with a TURBO DNA-free DNase kit (Ambion). RNA quality and concentration was determined at the NimbleGen Systems Inc., Madison, WI, USA facilities.

treatment_protocol: Flies were collected at 0-3 days post-eclosion and maintained at 25°C for 3 days prior to RNA collection.

tag: genotype

value: head

tag: genetic background


title: Elav-ATMi 3

description: Biological replicate 3 of the Elav-ATMi condition

source_name: Elav-GAL4, UAS-RNAiATM 4-6 days aged at 25°C

value: +/+; Elav-GAL4/+; UAS-RNAiATM/+

tag: tissue


title: ElavC155-ATMi 2

description: Biological replicate 2 of the ElavC155-ATMi condition

source_name: ElavC155-GAL4, UAS-RNAiATM 4-6 days aged at 25°C

value: ElavC155-GAL4/+; +/+; UAS-RNAiATM/+


title: Elav-ATMi 4

description: Biological replicate 4 of the Elav-ATMi condition


title: ElavC155-ATMi 1

description: Biological replicate 1 of the ElavC155-ATMi condition


title: 6 months - Progressive CADI score (Project 2 and Project 3) [KT1010_2_18_09]


title: ElavC155-GAL4 1

description: Biological replicate 1 of the ElavC155-GAL4 condition


title: Elav-GAL4 4

description: Biological replicate 4 of the Elav-GAL4 condition

source_name: Elav-GAL4 control fly, 4-6 days aged at 25°C


title: Validation set high CADI score (Project 1 + Project 4) and 24 months high CADI score (Project 2) [KT1316_2_20_09]


title: Elav-GAL4 3

description: Biological replicate 3 of the Elav-GAL4 condition


title: Elav-ATMi 1

description: Biological replicate 1 of the Elav-ATMi condition


title: Elav-ATMi 2

description: Biological replicate 2 of the Elav-ATMi condition


title: 6 months - Progressive CADI score (Project 2 and Project 3) [KT1183_2_18_09]


title: Elav-GAL4 2

description: Biological replicate 2 of the Elav-GAL4 condition


title: Repo-GAL4 1

description: Biological replicate 1 of the Repo-GAL4 condition

source_name: Repo-GAL4 control 4-6 days aged at 25°C


title: Validation set high CADI score (Project 1 + Project 4) and 24 months high CADI score (Project 2) [KT1328_2_20_09]


title: Baseline (0 months) - Progressive CADI score (Project 2) [KT849_1_2_6_09]


title: Repo-ATMi 2

description: Biological replicate 2 of the Repo-ATMi condition

source_name: Repo-GAL4, UAS-RNAiATM 4-6 days aged at 25°C

value: +/+; +/+; Repo-GAL4/UAS-RNAiATM


title: 132x

description: Nasal lavage cells obtained during virus-exacerbation from asthmatic child 132

tag: phenotype

value: Asthmatic child with Picornavirus-induced exacerbation

value: nasal lavage


title: Baseline (0 months) - Progressive CADI score (Project 2) [KT764_2_16_09]


title: Repo-GAL4 2

description: Biological replicate 2 of the Repo-GAL4 condition


title: Elav-GAL4 1

description: Biological replicate 1 of the Elav-GAL4 condition


title: Baseline (0 months) - Progressive CADI score (Project 2) [KT923_2_16_09]


title: Validation set high CADI score (Project 1 + Project 4) and 24 months high CADI score (Project 2) [KT1446_2_6_09]


title: Validation set high CADI score (Project 1 + Project 4) and 24 months high CADI score (Project 2) [KT1371_2_20_09]


title: ATM^8 1

description: Biological replicate 1 of the ATM^8/ATM^8 condition

source_name: ATM^8 homozygotes, 0-3 days at 18°C, 3 days at 25°C

value: p^p e^1


title: 6 months - Progressive CADI score (Project 2 and Project 3) [KT894_2_16_09]


title: ATM^8 2

description: Biological replicate 2 of the ATM^8/ATM^8 condition


title: ATM^8/+ 1

description: Biological replicate 1 of the ATM^8/+ condition

source_name: ATM^8/+ heterozygotes, 0-3 days at 18°C, 3 days at 25°C


title: Baseline (0 months) - Progressive CADI score (Project 2) [KT752_06_25_07]


title: 6 months - Progressive CADI score (Project 2 and Project 3) [KT855_2_6_09]


title: Validation set high CADI score (Project 1 + Project 4) and 24 months high CADI score (Project 2) [KT1232_2_18_09]


title: Validation set high CADI score (Project 1 + Project 4) and 24 months high CADI score (Project 2) [KT1287_2_18_09]


title: Baseline (0 months) - Progressive CADI score (Project 2) [KT754_2_16_09]


title: 6 months - Progressive CADI score (Project 2 and Project 3) [KT847_06_28_07]


title: Repo-ATMi 1

description: Biological replicate 1 of the Repo-ATMi condition


title: ATM^8/+ 2

description: Biological replicate 2 of the ATM^8/+ condition


title: Blood-AH

city: Berlin

first: Dido

last: Lenze

address: Hindenburgdamm 30

department: Pathologie, Campus Benjamin Franklin

institute: Charité-Universitätsmedizin Berlin

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on Canine Genome 2.0 Arrays (Affymetrix). GeneChips were washed and stained with standard protocols in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scanner G3000

data_processing: Affymetrix CEL files were imported into Partek Genomic Suite Software (Version 6.5, Partek Inc., St. Louis, USA) and processed by the implemented RMA workflow (median polish probe set summarization, RMA background correction, quantile normalization).

organism: Canis lupus familiaris

source_name: peripheral blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (One Cycle Target labeling protocol) from 2ug total RNA

extract_protocol: Peripheral blood samples were collected in EDTA containing tubes and diluted 1:6 in Erythrocyte lysis buffer (0.13 M NH4CL, 0.1 M KHC03 and 1.2x10-4 M EDTA ) in order to eliminate red blood cells. After incubation for 30 minutes at 4ºC samples were centrifuged at 1500 rpm for 15 minutes and the supernatant was discharged in order to obtain a pellet composed mainly by peripheral blood leukocytes (PBL). The procedure was repeated until a clear, white pellet was obtained. The two canine mammary carcinoma cell lines, CMM115 and CMM26, were cultivated in RPMI1640 medium supplemented with 10% bovine fetal serum. The cells were incubated in 75 cm3 tissue culture flasks, with air containing 5 % CO2 at 37oC. After the formation of a confluent monolayer, cells were harvested by washing once with PBS, pH 7,3 and incubation with in PBS containing 0,02 % EDTA  and 0,25 % trypsin for five minutes a 37°C. RNA isolation from the PBL pellets and cell lines was performed using a commercial kit (Nucleo Spin RNAII, Macherey-Nagel) according to the manufacturer’s instructions with subsequent DNAse treatment.

tag: disease state

value: normal


title: 6 months - Progressive CADI score (Project 2 and Project 3) [KT932_2_16_09]


title: Blood-H1


title: 6 months - Non-progressive CADI score (Project 2 and Project 3) [KT967_06_28_07]


title: CMM26

source_name: mammary carcinoma cell line

tag: cell line

value: tumor


title: Blood-H2


title: Validation set high CADI score (Project 1 + Project 4) and 24 months high CADI score (Project 2) [KT1284_2_18_09]


title: Baseline (0 months) - Non-progressive CADI score (Project 2) [KT818_05_25_07]


title: CMM115


title: 6 months - Non-progressive CADI score (Project 2 and Project 3) [KT961_06_28_07]


title: Baseline (0 months) - Progressive CADI score (Project 2) [KT783_1_2_16_09]


title: Validation set low CADI score (Project 1 and Project 4) and 24 months low CADI score (Project 2) [KT1300_2_6_09]


title: 6 months - Progressive CADI score (Project 2 and Project 3) [KT930_2_16_09]


title: Validation set low CADI score (Project 1 and Project 4) and 24 months low CADI score (Project 2) [KT1313_2_20_09]


title: Baseline (0 months) - Progressive CADI score (Project 2) [KT778_2_16_09]


title: Baseline (0 months) - Non-progressive CADI score (Project 2) [KT832_06_28_07]