title: CIT426

value: N

value: pMMR


title: CIT425

status: Public on May 22 2013

type: genomic

city: Paris

first: Nabila

last: Elarouci

address: 14 rue Corvisart

department: Recherche

country: France

institute: Ligue Nationale contre le Cancer

description: Array Version: CIT-CGH Homo sapiens 5.9K V7

hyb_protocol: After ethanol-coprecipitation with 140 µg of Human Cot-1 DNA (Roche, Basel, Switzerland), resuspension in 72.5 µl of hybridization buffer, denaturation at 100°C for 10 minutes and prehybridization at 37°C for 90 minutes, probes were hybridized on treated microarray slides in a humidity chamber at 37°C for 24 hours.

scan_protocol: After washing, slides were scanned with a GenePix 4000B scanner (Axon Instruments Inc., Union City, CA, USA) and analyzed with GenePix Pro 5.1 image analysis software, which defined the spots and determined the median intensities for the Cy3 and Cy5 signals of each BAC clone.

data_processing: Raw log2-ratio feature values were filtered from further analyses using a signal-to-noise threshold of 2.0 for the reference channel. The remaining values were normalized using the lowess within-print tip group method {Yang, 2002 #39}. For BACs in which more than 1 feature value remained after filtering and that yielded an inter-feature standard deviation of less than 0.25, an average normalized log2-ratio value was calculated. The iterative, data-adaptive smoothing technique Adaptive Weights Smoothing (AWS,Polzehl and Spokoiny) was applied to the normalized log2-ratio values [as adapted in the R GLAD package v1.8 {Hupe, 2004 #40}]. This yields smoothed log2-ratios values in homogeneous segments along the chromosome. We then determined the level of normal genomic ratios (copy number of 2) for each sample. This value corresponds to the first mode of the distribution of the normalized log2-ratio values across all chromosomes. The standard deviations of the smoothed log2-ratio segments are used as a threshold of determining breakpoints. All segments that are above or below this threshold are then classed as gains or losses, respectively. Outliers are classed manually and correspond to individual BACs that yielded log2-ratios three times the standard deviation threshold. This method allows for the partitioning of the smoothed CGH data into 3 different groups: gain (value=1), no change (value=0) or loss (value=-1).

molecule: genomic DNA

organism: Homo sapiens

source_name: Frozen tissue of primary colorectal Adenocarcinoma

label_protocol: Tumor DNAs were labeled by the random priming method (Bioprime DNA labelling system; Invitrogen, Cergy-Pontoise, France) with cyanine-5 (CyDye dCTP Multipack, Amersham GE Healthcare, Buckinghamshire, UK). Using the same procedure, we labeled control DNA with cyanine-3.

growth_protocol: Samples stored at -80 C

extract_protocol: E2: Manual-Phenol/Chloroform

tag: dataset

value: discovery

tag: Sex

value: M

value: distal

value: Y

tag: cit-coloncancermolecularsubtype

source_name: common reference

tag: reference

value: sex-matched gDNA pool human variation panel caucasian


title: Non-tumor adjacent tissue 128N

city: San Diego

first: Kai

last: Wang

state: CA

address: 10646 Science Center Dr

department: Oncology Research

country: USA

institute: Pfizer

description: Genomic DNA was genotyped using Illumina HumanOmni1-Quad BeadChip.

hyb_protocol: Samples were processed according to the manufacturers’ instructions (Illumina).

data_processing: Genomic DNA was genotyped using Infinium HD HumanOmni1-Quad Genotyping BeadChips (Illumina). Genotype: AA, AB, BB, or NC (no call)

label: C-Bio and A-DNP

extract_protocol: Extraction of genomic DNA was performed the QIAamp DNA mini kit.

tag: gender

value: Male

tag: tissue

value: Liver

tag: disease state

value: Non-tumor adjacent tissue


title: Hepatocellular carcinoma 127T

scan_protocol: Samples were processed according to the manufacturers’ instructions (Illumina).

value: Hepatocellular carcinoma


title: Hepatocellular carcinoma 123T

label_protocol: Samples were processed according to the manufacturers’ instructions (Illumina).


title: Hepatocellular carcinoma 124T


title: CIT423

value: F


title: Non-tumor adjacent tissue 127N


title: CIT424

value: proximal


title: CIT419

extract_protocol: E1: Manual-QIAamp DNA Mini (Qiagen)


title: Non-tumor adjacent tissue 124N


title: Non-tumor adjacent tissue 123N


title: CIT415


title: CIT420


title: Hepatocellular carcinoma 122T


title: CIT421


title: CIT412


title: CIT422


title: CIT413


title: CIT418


title: CIT414


title: CIT411

description: Array Version: CIT-CGH Homo sapiens 4.7K V6

value: pool of 20 sex-matched patients


title: CIT417


title: CIT416


title: Non-tumor adjacent tissue 122N


title: CIT408


title: CIT409


title: CIT410


title: Hepatocellular carcinoma 121T


title: CIT405


title: CIT404


title: Non-tumor adjacent tissue 121N


title: CIT406


title: CIT407


title: CIT402


title: Non-tumor adjacent tissue 120N

value: Female


title: Hepatocellular carcinoma 119T


title: Non-tumor adjacent tissue 119N


title: Hepatocellular carcinoma 120T


title: Hepatocellular carcinoma 118T


title: Hepatocellular carcinoma 117T


title: CIT401


title: CIT400


title: CIT395


title: CIT399


title: CIT394


title: CIT393


title: CIT391


title: Non-tumor adjacent tissue 117N


title: CIT396


title: CIT390

value: dMMR


title: CIT387


title: CIT388


title: Hepatocellular carcinoma 116T


title: CIT389


title: CIT386


title: Non-tumor adjacent tissue 118N


title: CIT385


title: Non-tumor adjacent tissue 116N


title: CIT383


title: CIT384


title: CIT403


title: CIT397


title: CIT379


title: Hepatocellular carcinoma 115T


title: CIT381


title: CIT382


title: Non-tumor adjacent tissue 115N


title: CIT398


title: CIT377


title: Hepatocellular carcinoma 114T


title: CIT376


title: Non-tumor adjacent tissue 114N


title: CIT374


title: Hepatocellular carcinoma 113T


title: CIT375


title: CIT371


title: Hepatocellular carcinoma 112T


title: CIT373


title: Non-tumor adjacent tissue 113N


title: CIT367


title: CIT378


title: CIT368


title: CIT380


title: Non-tumor adjacent tissue 112N


title: CIT370


title: Hepatocellular carcinoma 111T


title: CIT364


title: Non-tumor adjacent tissue 111N


title: CIT366


title: CIT365


title: CIT363


title: CIT359


title: Hepatocellular carcinoma 110T


title: CIT362


title: Non-tumor adjacent tissue 110N


title: CIT358


title: CIT355


title: CIT356


title: CIT357


title: CIT360


title: CIT361


title: Non-tumor adjacent tissue 109N


title: CIT353


title: CIT354


title: Non-tumor adjacent tissue 108N


title: CIT352


title: Hepatocellular carcinoma 108T


title: CIT350


title: CIT351

value: pool XX (20 healthy women)


title: CIT347

value: N


title: CIT348

value: pMMR


title: CIT346

value: discovery


title: CIT345

value: M


title: CIT349


title: Hepatocellular carcinoma 101T


title: CIT372

value: distal


title: CIT343

description: Array Version: CIT-CGH Homo sapiens 5.2K V6Plus

value: Y


title: CIT342


title: Hepatocellular carcinoma 107T


title: CIT337

value: DELA (bone marrow XY)


title: Non-tumor adjacent tissue 101N


title: Hepatocellular carcinoma 099T

value: Male


title: CIT341


title: CIT336


title: CIT340


title: CIT334


title: CIT338


title: CIT344


title: CIT339


title: Hepatocellular carcinoma 109T

value: Liver


title: Hepatocellular carcinoma 106T


title: Non-tumor adjacent tissue 106N

value: Non-tumor adjacent tissue


title: Non-tumor adjacent tissue 099N


title: Hepatocellular carcinoma 098T

value: Hepatocellular carcinoma


title: CIT332


title: CIT331


title: CIT329


title: Non-tumor adjacent tissue 098N


title: CIT335


title: Non-tumor adjacent tissue 107N


title: CIT328

value: F


title: CIT326


title: CIT327

value: proximal


title: CIT333


title: Hepatocellular carcinoma 097T


title: Non-tumor adjacent tissue 097N


title: CIT324


title: Hepatocellular carcinoma 096T


title: Non-tumor adjacent tissue 096N


title: CIT322


title: Hepatocellular carcinoma 095T


title: Non-tumor adjacent tissue 095N


title: CIT330


title: CIT313


title: CIT319


title: CIT317


title: CIT314


title: CIT318


title: CIT310


title: CIT311


title: Non-tumor adjacent tissue 094N


title: Hepatocellular carcinoma 093T


title: Non-tumor adjacent tissue 093N


title: Hepatocellular carcinoma 094T


title: CIT320


title: CIT308


title: CIT309


title: CIT307


title: CIT306


title: CIT315


title: CIT323


title: CIT312


title: CIT325


title: CIT303


title: CIT301


title: CIT305


title: CIT300


title: CIT304


title: CIT299


title: CIT298


title: CIT297


title: CIT294


title: CIT292


title: CIT302


title: CIT293


title: CIT295


title: CIT296


title: CIT289


title: CIT291


title: CIT290


title: CIT285


title: CIT284


title: CIT283


title: CIT281


title: CIT282


title: CIT286


title: CIT287


title: CIT279


title: CIT280


title: CIT277


title: CIT276


title: CIT278


title: CIT273


title: CIT275


title: CIT274


title: CIT269


title: CIT272


title: CIT271


title: CIT270


title: CIT268


title: CIT266


title: CIT316


title: CIT267


title: CIT265


title: CIT264


title: CIT254

value: pool of 20 sex-matched patients


title: CIT258


title: CIT255


title: CIT251


title: CIT249


title: CIT246


title: CIT252


title: CIT247


title: CIT244


title: CIT250


title: CIT242


title: CIT243


title: CIT245


title: Hepatocellular carcinoma cell line SNU-449

data_processing: Genomic DNA was genotyped using Infinium HD HumanOmni1-Quad Genotyping BeadChips (Illumina).

tag: cell line


title: CIT239


title: CIT241


title: Hepatocellular carcinoma cell line SNU-398


title: CIT237


title: Hepatocellular carcinoma cell line QGY-7703


title: CIT235


title: CIT236


title: Hepatocellular carcinoma cell line SNU-387


title: Hepatocellular carcinoma cell line SK-HEP-1


title: CIT233


title: Hepatocellular carcinoma cell line SMMC7721


title: Hepatocellular carcinoma cell line SNU-182


title: Hepatocellular carcinoma cell line PLC-PRF-5


title: Hepatocellular carcinoma cell line SNU-423


title: Hepatocellular carcinoma cell line MHCC97H


title: Hepatocellular carcinoma cell line LO2

source_name: Hepatocellular carcinoma cell line LO2


title: Hepatocellular carcinoma cell line QGY-7701


title: CIT226


title: CIT232


title: CIT222


title: Hepatocellular carcinoma cell line Jhh-7


title: Hepatocellular carcinoma cell line Jhh-2


title: CIT220


title: ctrl_H4-depletion_360min [nucleosome profile]

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for wild-type strain compared to genomic DNA control

hyb_protocol: 6 μg of biotinylated cDNA was hybridized at 45C for 16 hours, and then washed and stained according to Affymetrix protocol EukGE-WS2v4_450 in an Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned in an Affymetrix 7G scanner.

data_processing: Raw data files were normalized with Affymetrix Tiling Analysis Software (TAS) v1.1. Treatment and control samples were quantile normalized in pairs using only perfect match probes with a bandwidth of 20.

label: Biotin

organism: Saccharomyces cerevisiae

source_name: Control for 6 hours of H4 depletion

label_protocol: Mono-nucleosomal DNA was fragmented by nuclease digestion in a solution containing 1X One-Phor-All buffer (GE Healthcare) and DNase I (GE Healthcare) at 37C until the average fragment size was approximately 70 bp. The fragmentation reaction was stopped by incubating at 95C for 10 min. Fragmented samples were biotinylated with Biotin-N6-ddATP (Enzo Life Sciences) using terminal deoxynucleotidyl transferase at 37C for 2 hours.

growth_protocol: For the histone depletion time course, the UKY403 strain harboring a deletion of both Histone H4 genes (HHF1, HHF2), a plasmid with the GAL1 promoter driving expression of Histone H4 (HHF2) and a plasmid with the GAL1 promoter driving expression of Histone H4 (HHF2), was grown in YP with 2% galactose until mid log phase. Cells were then collected by centrifugation and transferred to YPD for 0, 1⁄4,1, 3, 5, and 6 hrs. After each time point, samples were taken for nucleosome and expression analysis.

extract_protocol: Cells were crosslinked by direct addition of methanol-free formaldehyde (Polysciences) to a final concentration of 2% for 30 min while shaking at 30 °C. The reaction was quenched by adding glycine to a final concentration of 125 mM for 5 min. Cells were pelleted, washed with 20 mL phosphate buffered saline solution once, and resuspended in 6 mL of [1 M sorbitol, 50 mM Tris 7.4] with freshly added 10 mM β-mercaptoethanol in a 15 mL conical tube. Zymolyase (20T, TakaRa Biotechnology Co., Ltd, Japan) was added to a final concentration of 0.25 mg/mL and cells were spheroplasted at 30 °C while gently rolling for 30 min. After zymolyase treatment, cells were pelleted and resuspended in 4 mL of [1 M sorbitol, 50 mM NaCl, 10 mM Tris 7.4, 5 mM MgCl2, 1 mM CaCl2, 0.075% NP-40] with freshly added 1 mM β-mercaptoethanol and 500 μM spermidine. Spheroplasts were divided into 6 aliquots of 300 μL each and transferred into 1.5 mL Eppendorf tubes. Micrococcal nuclease (MNase; Worthington) dissolved in water at 0.1 U/μL stock was added to the tubes at concentrations of 0, 25, 50, 75, 100, and 150 U per sample. The digestion reactions were incubated at 37 °C for 45 min and reactions were stopped by adding 75 μL of [5% SDS, 50 mM EDTA]. Remaining proteins were digested by adding 3 uL of 20 mg/mL proteinase K solution (Qiagen) was added to each tube for an overnight incubation at 65 °C. DNA from each MNase aliquot was isolated by phenol/chloroform extraction, concentrated via ethanol precipitation and treated with RNaseA (Fermentas) at a final concentration of 1mg/ml for 1 hour. Samples were then separated on a 2% agarose gel and bands corresponding to ~147bp (mono-nucleosomal fragments) were gel-extracted using the QIAquick kit (Qiagen) for each of the digestions.

tag: strain

value: UKY403, MATa ade2-101 his3-A200 leu2-3, 112 lys-801 trpl-A901 ura3-52 GAL+ thr tyr arg4-1 Ah4-J[HIS3+] Ah4-2[LEU2+ ]/pUK421 (CEN TRPI+ GAL-H4-2 +)

tag: genotype/variation

value: Control for 6 hours of H4 depletion

tag: molecule subtype

value: Nucleosomal DNA from the indicated test strain

source_name: MNase-treated total genomic DNA from WT (BY4741) strain

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0


title: Hepatocellular carcinoma cell line Jhh-5


title: ctrl_H4-depletion_180min [nucleosome profile]

source_name: Control for 3 hours of H4 depletion

value: Control for 3 hours of H4 depletion


title: ctrl_H4-depletion_015min [nucleosome profile]

source_name: Control for 15 mins of H4 depletion

value: Control for 15 mins of H4 depletion


title: geo_1647 lymphnode benign reactive 24

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

hyb_protocol: DNA was hybridized to the Illumina GoldenGate Cancer Panel I array using the standard Illumina protocol DNA was hybridized to the Illumina GoldenGate Cancer Panel I array using the standard Illumina protocol

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

data_processing:
Cy3, Cy5, Average Beta, and detection p-values were extracted using BeadStudio software
Cy3, Cy5, Average Beta, and detection p-values were extracted using BeadStudio software

label: Cy5, Cy3

source_name: lymph node benign reactive

label_protocol:
DNA was bisulfite converted, amplified, and labeled
DNA was bisulfite converted, amplified, and labeled

extract_protocol:
Genomic DNA was extracted using standard techniques
Genomic DNA was extracted using standard techniques

value: lymph node benign reactive

value: lymph node


title: geo_1642 lymphnode benign reactive 23


title: Hepatocellular carcinoma cell line Jhh-4


title: CIT218

value: discovery

value: M

value: distal

value: Y

value: pMMR


title: CIT216

value: N


title: geo_1639 lymphnode benign reactive 22


title: Hepatocellular carcinoma cell line Huh-6

value: Liver

value: Hepatocellular carcinoma


title: Hepatocellular carcinoma cell line Huh-7


title: Hepatocellular carcinoma cell line SNU-475


title: geo_1641 lymphnode benign reactive 21


title: geo_1640 lymphnode benign reactive 20


title: ctrl_WT-wTBF1_ts [nucleosome profile]

source_name: Wild-type control for TBF1_ts strain

growth_protocol: Controls for temperature-sensitive strains were grown at 22°C (permissive temperature) until mid-log phase. An equal volume of hot medium was then added to equilibrate the culture to 37°C (restrictive temperature), followed by a further 3 to 7 hours incubation at this temperature until a difference in OD between the mutant strain and its corresponding wild-type control became apparent.

value: Wild-type control for TBF1_ts strain


title: CIT186

value: F

value: proximal

value: pool of 20 sex-matched patients


title: CIT203


title: CIT188


title: CIT211


title: ctrl_H4-depletion_060min [nucleosome profile]

source_name: Control for 1 hour of H4 depletion

value: UKY403, MATa ade2-101 his3-A200 leu2-3, 112 lys-801 trpl-A901 ura3-52 GAL+ thr tyr arg4-1 Ah4-J[HIS3+] Ah4-2[LEU2+ ]/pUK421 (CEN TRPI+ GAL-H4-2 +)

value: Control for 1 hour of H4 depletion

value: Nucleosomal DNA from the indicated test strain

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0


title: CIT176

value: pool XX (20 healthy women)


title: CIT234

value: discovery


title: Hepatocellular carcinoma cell line Huh-1


title: Hepatocellular carcinoma cell line HepG2


title: Hepatocellular carcinoma cell line Jhh-1


title: CIT175


title: geo_1648 lymphnode benign reactive 19

value: lymph node benign reactive

value: lymph node


title: Hepatocellular carcinoma cell line MHCC97L


title: CIT174

value: M

value: distal

value: pool XY (20 healthy men)


title: Hepatocellular carcinoma cell line Jhh-6

value: Liver


title: geo_1638 lymphnode benign reactive 18


title: ctrl_H4-depletion_000min [nucleosome profile]

source_name: Control for 0 mins of H4 depletion

value: Control for 0 mins of H4 depletion


title: ctrl_WT-wRPO21_ts [nucleosome profile]

source_name: Wild-type control for RPO21_ts strain

value: Wild-type control for RPO21_ts strain


title: CIT173

value: N

value: pMMR


title: ctrl_WT-wRRN3_tet [nucleosome profile]

source_name: Wild-type control for RRN3_tet strain

growth_protocol: For controls of Tet promoter-shutoff strains, doxycyline was added at 10μg/ml for 24 h in order to obtain down-regulation for the gene of interest. Cells were then diluted to an OD600 of 0.2 and grown in the presence of doxycycline (10μg/ml) until mid-log phase.

value: Wild-type control for RRN3_tet strain


title: ctrl_WT-wREB1_ts_rep2 [nucleosome profile]

source_name: Wild-type control for REB1_ts strain

value: Wild-type control for REB1_ts strain


title: CIT172

value: Y


title: CIT191

value: pool of 20 sex-matched patients


title: ctrl_WT-wREB1_ts_rep1 [nucleosome profile]

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0

value: Nucleosomal DNA from the indicated test strain


title: CIT171

value: discovery

value: F

value: pool XX (20 healthy women)


title: ctrl_WT-wRAP1-RPB2-RPA190_tet [nucleosome profile]

source_name: Wild-type control for RAP1, RPB2, and RPA190 Tet strains


title: CIT169


title: CIT168


title: geo_1644 lymphnode benign reactive 15

value: lymph node benign reactive

value: lymph node


title: CIT165

value: M

value: distal

value: pool XY (20 healthy men)


title: geo_1643 lymphnode benign reactive 14


title: geo_1646 lymphnode benign reactive 16


title: ctrl_WT-wRAP1_ts [nucleosome profile]

source_name: Wild-type control for RAP1_ts strain

value: Wild-type control for RAP1_ts strain


title: CIT219

value: N


title: CIT162

value: pMMR


title: CIT160


title: CIT159


title: ctrl_WT-wMCM1_ts [nucleosome profile]

source_name: Wild-type control for MCM1_ts strain

value: Wild-type control for MCM1_ts strain


title: geo_2015 gist sdh positive 46

source_name: gist sdh positive

value: gist sdh positive


title: geo_2014 gist sdh positive 45


title: CIT158

source_name: Frozen tissue of primary colorectal Adenocarcinoma

value: proximal

value: Y

source_name: common reference


title: ctrl_WT-wHSF1_ts [nucleosome profile]

source_name: Wild-type control for HSF1_ts strain

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0

value: Wild-type control for HSF1_ts strain


title: CIT153

value: discovery


title: ctrl_WT-wRSC3_ts [nucleosome profile]

source_name: Wild-type control for RSC3_ts strain

value: Wild-type control for RSC3_ts strain

value: Nucleosomal DNA from the indicated test strain

source_name: MNase-treated total genomic DNA from WT (BY4741) strain


title: geo_2013 gist sdh positive 44


title: ctrl_WT-wBDP1_tet [nucleosome profile]

source_name: Wild-type control for BDP1_tet strain

value: Wild-type control for BDP1_tet strain


title: ctrl_WT-wGCR1_tet [nucleosome profile]

source_name: Wild-type control for GCR1_tet strain

value: Wild-type control for GCR1_tet strain


title: ctrl_WT-wABF1_ts [nucleosome profile]

source_name: Wild-type control for ABF1_ts strain

value: Wild-type control for ABF1_ts strain


title: Hepatocellular carcinoma cell line Bel-7404

value: Liver

value: Hepatocellular carcinoma


title: geo_2012 gist sdh positive 43


title: geo_2011 gist sdh positive 42


title: Hepatocellular carcinoma cell line HCCC-9810


title: CIT141

value: M

value: pool XY (20 healthy men)


title: CIT139

value: distal

value: N

value: pMMR


title: geo_2010 gist sdh positive 41

value: gist sdh positive


title: CIT149

value: Y


title: CIT140

value: F

value: pool XX (20 healthy women)


title: CIT142

value: discovery


title: CIT147


title: ctrl_WT-LS20-wINO80_rep1 [nucleosome profile]

source_name: Wild-type control for INO80 strain

growth_protocol: 5 mL cultures were grown overnight at 30 °C in YPD. Cells were diluted to OD600 0.2/mL in 400 mL of YPD media the next morning, and grown to mid-log phase (OD600 0.8-1.0/ml) in 1L flasks at 30 °C while shaking, at which point RNA and nucleosomal DNA were isolated.

value: LS20, matΔ, his3Δ, ade2Δ, can1Δ, trp1Δ, ura3Δ, leu2Δ, lys5Δ, cyh2r, ade3::GalHO

value: Wild-type control for INO80 strain

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0


title: ctrl_WT-LS20-wINO80_rep2 [nucleosome profile]

value: Nucleosomal DNA from the indicated test strain


title: geo_2009 gist sdh positive 40


title: geo_1650 lymphnode benign reactive 17

source_name: lymph node benign reactive

value: lymph node benign reactive

value: lymph node


title: CIT151


title: geo_2036 gist sdh positive 39


title: CIT135


title: ctrl_WT-FY85-wSPT6_ts [nucleosome profile]

source_name: Wild-type control for SPT6_ts strain

value: FY85, MATa his4-912δ lys2-128δ leu2Δ1 ura3-52

value: Wild-type control for SPT6_ts strain


title: ctrl_WT-FY85-wSPT16_ts [nucleosome profile]

source_name: Wild-type control for SPT16_ts strain

value: Wild-type control for SPT16_ts strain


title: CIT134

value: distal


title: CIT133

value: proximal

value: N


title: geo_2035 gist sdh positive 38

value: gist sdh positive


title: CIT136

value: pMMR


title: CIT161

value: F

value: Y


title: CIT148

value: discovery

value: pool XX (20 healthy women)


title: ctrl_WT_del_rep13 [nucleosome profile]

source_name: Wild-type control for deletion strains

growth_protocol: For deletion strain controls, 5 mL cultures were grown overnight at 30 °C in YPD. Cells were diluted to OD600 0.2/mL in 400 mL of YPD media the next morning, and grown to mid-log phase (OD600 0.8-1.0/ml) in 1L flasks at 30 °C while shaking, at which point RNA and nucleosomal DNA were isolated.

value: Wild-type control for deletion strains


title: ctrl_WT_del_rep12 [nucleosome profile]

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0


title: Hepatocellular carcinoma cell line Bel-7402

value: Liver

value: Hepatocellular carcinoma


title: ctrl_WT_del_rep11 [nucleosome profile]

value: Nucleosomal DNA from the indicated test strain


title: CIT137


title: Hepatocellular carcinoma cell line Hep3B


title: CIT131


title: Hepatocellular carcinoma cell line HLE

source_name: Hepatocellular carcinoma cell line HLE

value: HLE


title: CIT132


title: CIT130

value: M

value: pool XY (20 healthy men)


title: CIT129


title: geo_2034 gist sdh positive 37


title: geo_2033 gist sdh positive 36


title: Hepatocellular carcinoma cell line HLF

source_name: Hepatocellular carcinoma cell line HLF

value: HLF


title: geo_2032 gist sdh positive 35


title: CIT127

value: distal


title: ctrl_WT_del_rep09 [nucleosome profile]


title: ctrl_WT_del_rep10 [nucleosome profile]


title: CIT128

value: N


title: CIT126


title: CIT122


title: geo_2031 gist sdh positive 34

value: gist sdh positive


title: CIT124


title: ctrl_WT_del_rep08 [nucleosome profile]


title: CIT125


title: CIT123


title: CIT121


title: CIT119


title: CIT120

value: proximal


title: ctrl_WT_del_rep07 [nucleosome profile]


title: CIT117

value: F


title: geo_2028 gist sdh positive 31


title: geo_2029 gist sdh positive 32


title: geo_2030 gist sdh positive 33


title: CIT111


title: ctrl_WT_del_rep04 [nucleosome profile]


title: geo_2027 gist sdh positive 30


title: geo_2026 gist sdh positive 29


title: ctrl_WT_del_rep05 [nucleosome profile]


title: CIT114

value: Y


title: ctrl_WT_del_rep06 [nucleosome profile]


title: CIT116

value: discovery


title: geo_2025 gist sdh positive 28


title: CIT115

value: pool XX (20 healthy women)


title: ctrl_WT_del_rep03 [nucleosome profile]

value: Wild-type control for deletion strains


title: CIT113


title: geo_2024 gist sdh positive 27


title: geo_2023 gist sdh positive 26


title: ctrl_WT_del_rep02 [nucleosome profile]

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0


title: ctrl_WT_del_rep01 [nucleosome profile]


title: CIT109


title: CIT110


title: CIT106

value: pMMR


title: CIT107


title: CIT104


title: CIT105


title: CIT112


title: CIT108


title: TUP1_del_rep2 [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for TUP1 deletion strain compared to genomic DNA control

source_name: TUP1 deletion strain

growth_protocol: For deletion strains, 5 mL cultures were grown overnight at 30 °C in YPD. Cells were diluted to OD600 0.2/mL in 400 mL of YPD media the next morning, and grown to mid-log phase (OD600 0.8-1.0/ml) in 1L flasks at 30 °C while shaking, at which point RNA and nucleosomal DNA were isolated.

value: TUP1 deletion strain


title: VPS75_del [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for VPS75 deletion strain compared to genomic DNA control

source_name: VPS75 deletion strain

value: VPS75 deletion strain

value: Nucleosomal DNA from the indicated test strain


title: TUP1_del_rep1 [nucleosome profile]


title: geo_2020 gist sdh positive 23

source_name: gist sdh positive


title: geo_2018 gist sdh positive 21


title: geo_2017 gist sdh positive 20


title: CIT097

source_name: Frozen tissue of primary colorectal Adenocarcinoma

value: M

source_name: common reference


title: CIT098

value: pool XY (20 healthy men)


title: CIT100


title: CIT101


title: CIT102


title: geo_2022 gist sdh positive 25


title: CIT103


title: geo_2021 gist sdh positive 24


title: CIT095


title: CIT094


title: CIT096


title: SWR1_del [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for SWR1 deletion strain compared to genomic DNA control

source_name: SWR1 deletion strain

value: SWR1 deletion strain


title: TBF1_ts [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for TBF1 temperature-sensive strain grown at restrictive temperature compared to genomic DNA control

growth_protocol: Temperature-sensitive strains were grown at 22°C (permissive temperature) until mid-log phase. An equal volume of hot medium was then added to equilibrate the culture to 37°C (restrictive temperature), followed by a further 3 to 7 hours incubation at this temperature until a difference in OD between the mutant strain and its corresponding wild-type control became apparent.

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 KanMX::tbf1-URA3

value: TBF1 temperature-sensive strain

source_name: MNase-treated total genomic DNA from WT (BY4741) strain


title: geo_2016 gist sdh positive 19

value: gist sdh positive


title: CIT099

value: distal

value: N


title: geo_2019 gist sdh positive 22


title: CIT093

value: proximal


title: SWI4_del [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for SWI4 deletion strain compared to genomic DNA control

source_name: SWI4 deletion strain

value: SWI4 deletion strain


title: CIT092

value: discovery

value: F

value: Y

value: pool XX (20 healthy women)


title: geo_2008 gist sdh positive 18


title: STB2_del [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for STB2 deletion strain compared to genomic DNA control

source_name: STB2 deletion strain

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0

value: STB2 deletion strain


title: geo_2007 gist sdh positive 17


title: CIT089

value: pMMR


title: SPT6_ts [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for SPT6 temperature-sensive strain grown at restrictive temperature compared to genomic DNA control

value: SPT6 temperature-sensive strain

value: Nucleosomal DNA from the indicated test strain


title: SPT21_del [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for SPT21 deletion strain compared to genomic DNA control

source_name: SPT21 deletion strain

value: SPT21 deletion strain


title: CIT087

value: M

value: pool XY (20 healthy men)


title: geo_2002 gist sdh positive 16

value: gist sdh positive


title: geo_2006 gist sdh negative 34

source_name: gist sdh negative

value: gist sdh negative


title: SPT15_ts [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for SPT15 temperature-sensive strain grown at restrictive temperature compared to genomic DNA control

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 spt15-I143N::KanMX

value: SPT15 temperature-sensive strain


title: CIT085

value: distal

value: N


title: CIT086

value: discovery

value: proximal


title: CIT091

value: F

value: pool XX (20 healthy women)


title: CIT081


title: geo_2003 muscularis 7

source_name: muscularis

value: muscularis normal

value: muscularis


title: geo_1999 gist sdh negative 33


title: CIT084

value: pMMR


title: CIT083

value: Y


title: CIT082


title: CIT088


title: SPT10_del [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for SPT10 deletion strain compared to genomic DNA control

source_name: SPT10 deletion strain

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0

value: SPT10 deletion strain

value: Nucleosomal DNA from the indicated test strain


title: geo_1998 stomach 9

source_name: stomach

value: stomach normal

value: stomach


title: geo_1997 gist sdh positive 15

value: gist sdh positive


title: SPT16_ts [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for SPT16 temperature-sensive strain grown at restrictive temperature compared to genomic DNA control

value: SPT16 temperature-sensive strain


title: SNF2_del [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for SNF2 deletion strain compared to genomic DNA control

source_name: SNF2 deletion strain

value: SNF2 deletion strain


title: CIT074

description: Array Version: CIT-CGH Homo sapiens 5.9K V7


title: SNF1_del [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for SNF1 deletion strain compared to genomic DNA control

source_name: SNF1 deletion strain

value: SNF1 deletion strain


title: geo_1994 gist sdh positive 14


title: CIT071

value: discovery


title: CIT070

value: M

value: distal

value: pool XY (20 healthy men)


title: SIR2_del [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for SIR2 deletion strain compared to genomic DNA control

source_name: SIR2 deletion strain

value: SIR2 deletion strain


title: CIT069


title: SET2_del_rep2 [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for SET2 deletion strain compared to genomic DNA control

source_name: SET2 deletion strain

value: SET2 deletion strain


title: CIT073

value: pMMR


title: CIT068

value: Y


title: geo_1991 gist sdh negative 32

value: gist sdh negative


title: SET2_del_rep1 [nucleosome profile]

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0


title: geo_1993 gist sdh positive 13


title: CIT072

value: F

value: proximal

value: pool XX (20 healthy women)


title: CIT065


title: geo_1990 gist sdh negative 31


title: geo_1989 muscularis 6

value: muscularis normal

value: muscularis


title: SET1_del [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for SET1 deletion strain compared to genomic DNA control

source_name: SET1 deletion strain

value: SET1 deletion strain

value: Nucleosomal DNA from the indicated test strain


title: CIT064

value: discovery


title: CIT063

value: M


title: geo_1987 gist sdh negative 30


title: CIT066


title: CIT138

value: N


title: geo_1986 gist sdh negative 29


title: CIT067

value: distal


title: CIT651

value: Pool XX (20 patients)


title: CIT061


title: CIT062


title: RSC30_del [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for RSC30 deletion strain compared to genomic DNA control

source_name: RSC30 deletion strain

value: RSC30 deletion strain


title: RRN3_tet [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for RRN3 Tet promotor-shutoff strain compared to genomic DNA control

source_name: RRN3 Tet promotor-shutoff strain

growth_protocol: For Tet promoter-shutoff strains, doxycyline was added at 10μg/ml for 24 h in order to obtain down-regulation for the gene of interest. Cells were then diluted to an OD600 of 0.2 and grown in the presence of doxycycline (10μg/ml) until mid-log phase.

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 URA3::CMV-tTA

value: RRN3 Tet promotor-shutoff strain


title: RSC3_ts [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for RSC3 temperature-sensive strain grown at restrictive temperature compared to genomic DNA control

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 rsc3-1::KanMX

value: RSC3 temperature-sensive strain


title: RPO21_ts [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for RPO21_rep1 temperature-sensive strain grown at restrictive temperature compared to genomic DNA control

source_name: RPO21 temperature-sensive strain grown at restrictive temperature

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 rpo21-1::KanMX

value: RPO21 temperature-sensive strain


title: RPO21_tet [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for RPO21 Tet promotor-shutoff strain compared to genomic DNA control

source_name: RPO21 Tet promotor-shutoff strain

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0

value: RPO21 Tet promotor-shutoff strain


title: CIT645

source_name: Frozen tissue of primary colorectal Adenocarcinoma

source_name: common reference

value: Pool XY (20 patients)


title: geo_1985 liver 5

source_name: liver

value: liver normal

value: liver


title: CIT646

value: discovery


title: CIT647


title: geo_1984 gist sdh negative 28

value: gist sdh negative


title: CIT650


title: CIT643


title: geo_1983 liver 4


title: geo_1982 gist sdh positive 12

source_name: gist sdh positive

value: gist sdh positive


title: CIT648


title: CIT649


title: RPD3_del [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for RPD3 deletion strain compared to genomic DNA control

source_name: RPD3 deletion strain

value: RPD3 deletion strain

value: Nucleosomal DNA from the indicated test strain

source_name: MNase-treated total genomic DNA from WT (BY4741) strain


title: CIT642

value: Pool XX (20 patients)


title: geo_1981 gist sdh positive 11


title: RPB2_tet [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for RPB2 Tet promotor-shutoff strain compared to genomic DNA control

source_name: RPB2 Tet promotor-shutoff strain

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 URA3::CMV-tTA

value: RPB2 Tet promotor-shutoff strain


title: CIT641


title: CIT640


title: RPA190_tet [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for RPA190 Tet promotor-shutoff strain compared to genomic DNA control

source_name: RPA190 Tet promotor-shutoff strain

value: RPA190 Tet promotor-shutoff strain


title: RLF2_del_rep2 [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for RLF2 deletion strain compared to genomic DNA control

source_name: RLF2 deletion strain

value: RLF2 deletion strain


title: RLF2_del_rep1 [nucleosome profile]


title: CIT644


title: geo_1980 gist sdh negative 27

source_name: gist sdh negative


title: geo_1977 liver 3


title: Inflammatory leiomyosarcoma case 2

city: Lund

first: Karolin

middle: H

last: Nord

address: BMC C13

department: Dept of Clinical Genetics

country: Sweden

institute: Lund University

description: Genomic DNA extracted from tumor biopsy was analyzed using Illumina Human CNV370-Quad v3.0 BeadChip (Illumina).

hyb_protocol: Hybridization was done according to the manufacturer's instructions (Illumina).

scan_protocol: Scanning was done according to the manufacturer's instructions (Illumina).

data_processing: Data analysis was performed using the GenomeStudio software (Illumina), detecting imbalances by visual inspection.

source_name: Inflammatory leiomyosarcoma

label_protocol: standard Illumina protocol

extract_protocol: DNA was extracted from fresh frozen tumour biopsies using the DNeasy Tissue Kit including the optional RNaseH treatment, according to the manufacturer's instructions (Qiagen, Valencia, CA, USA).

value: Male

value: Tumor tissue

value: sarcoma


title: geo_1979 stomach 8

source_name: stomach

value: stomach normal

value: stomach


title: geo_1976 gist sdh negative 25


title: REB1_ts_rep2 [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for REB1 temperature-sensive strain grown at restrictive temperature compared to genomic DNA control

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 KanMX::reb1-212-URA3

value: REB1 temperature-sensive strain


title: CIT635

value: discovery

value: Pool XY (20 patients)


title: CIT634


title: CIT630


title: CIT637


title: CIT090

value: M

value: distal

value: N

value: pMMR

value: pool XY (20 healthy men)


title: REB1_ts_rep1 [nucleosome profile]

source_name: REB1 temperature-sensive strain grown at restrictive temperature

value: Nucleosomal DNA from the indicated test strain

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0


title: CIT639


title: CIT631

value: Pool XX (20 patients)


title: geo_1978 gist sdh negative 26

value: gist sdh negative


title: CIT636


title: geo_1975 stomach 7


title: CIT629


title: CIT633


title: CIT627


title: CIT638


title: CIT632


title: RAP1_ts [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for RAP1 temperature-sensive strain grown at restrictive temperature compared to genomic DNA control

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 rap1-1::KanMX

value: RAP1 temperature-sensive strain


title: RAP1_tet [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for RAP1 Tet promotor-shutoff strain compared to genomic DNA control

source_name: RAP1 Tet promotor-shutoff strain

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 URA3::CMV-tTA

value: RAP1 Tet promotor-shutoff strain


title: geo_1974 gist sdh negative 24


title: geo_1973 muscularis 5

source_name: muscularis

value: muscularis normal

value: muscularis


title: PAF1_del [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for PAF1 deletion strain compared to genomic DNA control

source_name: PAF1 deletion strain

value: PAF1 deletion strain


title: geo_1972 gist sdh negative 23


title: MSI1_del_rep2 [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for MSI1 deletion strain compared to genomic DNA control

source_name: MSI1 deletion strain

value: MSI1 deletion strain


title: MSI1_del_rep1 [nucleosome profile]


title: CIT624

description: Array Version: CIT-CGH Homo sapiens 5.9K V7

source_name: Frozen tissue of primary colorectal Adenocarcinoma

value: discovery

value: Pool XY (20 patients)


title: CIT625

source_name: common reference


title: CIT626


title: geo_1970 gist sdh negative 22


title: CIT619


title: MCM1_ts [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for MCM1 temperature-sensive strain grown at restrictive temperature compared to genomic DNA control

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 KanMX::mcm1-URA3

value: MCM1 temperature-sensive strain


title: geo_1967 gist sdh positive 9

value: gist sdh positive


title: geo_1969 gist sdh positive 10


title: geo_1968 gist sdh negative 21


title: CIT618


title: CIT620


title: CIT615


title: CIT614


title: CIT079

value: F

value: proximal

value: N

value: pMMR

value: pool XX (20 healthy women)


title: CIT617

value: Pool XX (20 patients)


title: ISW2_del_rep2 [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for ISW2 deletion strain compared to genomic DNA control

source_name: ISW2 deletion strain

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0

value: ISW2 deletion strain

value: Nucleosomal DNA from the indicated test strain


title: geo_1964 gist sdh negative 20

value: gist sdh negative


title: ISW2_del_rep1 [nucleosome profile]


title: CIT613


title: CIT076


title: CIT616


title: CIT612


title: CIT611


title: geo_1963 gist sdh negative 19


title: CIT610


title: ISW1_del_rep2 [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for ISW1 deletion strain compared to genomic DNA control

source_name: ISW1 deletion strain

value: ISW1 deletion strain


title: ISW1_del_rep1 [nucleosome profile]


title: geo_1962 gist sdh negative 18


title: geo_1961 gist sdh negative 17


title: Inflammatory leiomyosarcoma case 3

value: Male

value: Tumor tissue

value: sarcoma


title: geo_1960 gist sdh negative 16


title: CIT609

value: discovery


title: CIT605


title: CIT628

value: Pool XY (20 patients)


title: CIT608


title: HTZ1_del_rep2 [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for HTZ1 deletion strain compared to genomic DNA control

source_name: HTZ1 deletion strain

value: HTZ1 deletion strain


title: CIT607


title: CIT602


title: geo_1958 gist sdh negative 15


title: CIT606


title: NAP1_del [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for NAP1 deletion strain compared to genomic DNA control

source_name: NAP1 deletion strain

value: NAP1 deletion strain

source_name: MNase-treated total genomic DNA from WT (BY4741) strain


title: geo_1959 gist sdh positive 8

source_name: gist sdh positive

value: gist sdh positive


title: INO80_del_rep1 [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for INO80 deletion strain compared to genomic DNA control

source_name: INO80 deletion strain

value: LS20, matΔ, his3Δ, ade2Δ, can1Δ, trp1Δ, ura3Δ, leu2Δ, lys5Δ, cyh2r, ade3::GalHO

value: INO80 deletion strain


title: CIT603


title: INO80_del_rep2 [nucleosome profile]


title: HTZ1_del_rep1 [nucleosome profile]


title: CIT604


title: geo_1957 gist sdh positive 7


title: geo_1956 gist sdh negative 14

source_name: gist sdh negative


title: HSF1_ts [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for HSF1 temperature-sensive strain grown at restrictive temperature compared to genomic DNA control

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 hsf1-848::KanMX

value: HSF1 temperature-sensive strain


title: CIT623

value: Pool XX (20 patients)


title: CIT600


title: CIT601


title: geo_1955 gist sdh negative 13


title: Strain HR, biological rep3

type: RNA

city: Madison

first: Oleg

last: Moskvin

state: WI

address: 1220 Capitol Court

institute: University of Wisconsin-Madison

description: gene expression data from strain HR

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: generation of CEL files with Affymetrix MAS5.0, expression computation using RMA

label: biotin

molecule: total RNA

organism: Cereibacter sphaeroides

source_name: photoheterotrophically grown R.sphaeroides cells

label_protocol: standard Affymetrix protocol with ddNTP labeling kit

growth_protocol: R.sphaeroides cells were grown photoheterotrophically at 30 oC in Ormerod's medium containing malate as a carbon source, under incadescent illumination.

extract_protocol: RNeasy Midi Kit (Qiagen, Valencia, CA).

value: strain HR


title: Strain PHC, biological rep3

description: gene expression data from strain PHC

value: strain PHC


title: Strain PHC, biological rep2

description: gene expression data from strain PHC


title: Strain PHC, biological rep1

description: gene expression data from strain PHC


title: CIT622


title: HIR1_del [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for HIR1 deletion strain compared to genomic DNA control

source_name: HIR1 deletion strain

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0

value: HIR1 deletion strain

value: Nucleosomal DNA from the indicated test strain


title: HHT2_del [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for HHT2 deletion strain compared to genomic DNA control

source_name: HHT2 deletion strain

value: HHT2 deletion strain


title: Strain HR, biological rep2

description: gene expression data from strain HR


title: Strain HR, biological rep1

description: gene expression data from strain HR


title: geo_1954 gist sdh positive 6


title: geo_1953 gist sdh negative 12

value: gist sdh negative


title: HHO1_del [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for HHO1 deletion strain compared to genomic DNA control

source_name: HHO1 deletion strain

value: HHO1 deletion strain


title: H4-depletion_360min [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile after 6 hours of histone H4 depletion compared to genomic DNA control

source_name: UKY403 after 6 hours of histone H4 depletion

value: UKY403, MATa ade2-101 his3-A200 leu2-3, 112 lys-801 trpl-A901 ura3-52 GAL+ thr tyr arg4-1 Ah4-J[HIS3+] Ah4-2[LEU2+ ]/pUK421 (CEN TRPI+ GAL-H4-2 +)


title: Strain 16, biological rep3

description: gene expression data from strain 16

value: strain 16


title: H4-depletion_180min [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile after 3 hours of histone H4 depletion compared to genomic DNA control

source_name: UKY403 after 3 hours of histone H4 depletion


title: geo_1951 gist sdh negative 11


title: H4-depletion_060min [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile after 1 hour of histone H4 depletion compared to genomic DNA control

source_name: UKY403 after 1 hour of histone H4 depletion


title: gDNA F17

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description:
gDNA V10_L2_F17
Ramdom priming gDNA hybridization macrochip V10_L2_F17

hyb_protocol: Hybridization Solution was 0.5M Na-Phosphate buffer, 1mM EDTA and 7% SDS, pH 7.2. The hybridization protocol used was as follows: Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 1-5X10exp6 dpm/mL of radioactive sample and hybridized for 48h. Washing conditions were 20 min at 65ºC in 1X SSC, 0.5% SDS, and twice at 65ºC for 10 min in 0.5X SSC, 0.1% SDS. After quantification, filters were stripped by washing them once with 50 mM NaOH at 45ºC, once with 50 mM Tris-HCl, pH 7.5, 0.1x SSC, 0.1% SDS and once pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were checked with a Geiger counter.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times.

data_processing: Raw image quantification background was subtracted. For the processed data, we normalized by gDNA and by using ArrayStat software (Median Absolute Deviation).

source_name: Wild type cells grown in YPD to exponential phase

label_protocol: In vivo labeling by run-on (GRO) was done using 33P-UTP. Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, they were permeabilized with 20 mL of 0.5% sarkosyl and cells were recovered by low-speed centrifugation and the supernatant was removed. In vivo transcription was performed by resuspending cells in 115 µl of RNA water and adding 162 µL of Run On Mix (120 µl of 2.5x transcription buffer [50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2], 20 µl of AGC mix [10 mM each of CTP, ATP and GTP], 6 µl of DTT [0.1 M] and 13 µl of [α-33P]UTP [3000 Ci/mmol, 10 Ci/µL]). The mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix.

growth_protocol: Exponential growth in YPD at 28ºC.

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. (1986), but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York.

tag: strain/background

value: wild type

tag: macrochip


title: H4-depletion_015min [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile after 15 min of histone H4 depletion compared to genomic DNA control

source_name: UKY403 after 15 mins of histone H4 depletion


title: gDNA F16

description:
gDNA V10_L2_F16
Ramdom priming gDNA hybridization macrochip V10_L2_F16


title: Strain 16, biological rep1

description: gene expression data from strain 16


title: Strain 16, biological rep2

description: gene expression data from strain 16


title: geo_1950 gist sdh negative 10


title: geo_1952 gist sdh positive 5

value: gist sdh positive


title: geo_1948 muscularis 4

source_name: muscularis

value: muscularis normal

value: muscularis


title: gDNA F18

description:
gDNA V10_L2_F18
Ramdom priming gDNA hybridization macrochip V10_L2_F18


title: H4-depletion_000min [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile after 0 min of histone H4 depletion compared to genomic DNA control

source_name: UKY403 after 0 hours of histone H4 depletion


title: cDNA Δxrn1

description:
cDNA (1) YMC511 F18
cDNA (2) YMC511 F18
cDNA (3) YMC511 F18
First replica: cDNA labelling from xrn1 strain YMC511. Hybridization on macrochip F18.
Second replica: cDNA labelling from xrn1 strain YMC511. Hybridization on macrochip F18.
Third replica: cDNA labelling from xrn1 strain YMC511. Hybridization on macrochip F18.

source_name: Δxrn1cells grown in YPD to exponential phase

value: Δxrn1 deletory mutation

tag: sample type

value: mRNA amount (RA)


title: CIT621

description: Array Version: CIT-CGH Homo sapiens 5.9K V7

source_name: Frozen tissue of primary colorectal Adenocarcinoma

value: discovery

source_name: common reference

value: Pool XY (20 patients)


title: LMS_18b Leiomyosarcoma

description: Global gene expression data

hyb_protocol: Biotinylated cDNA was hybridized to GeneChip Gene 1_0 st arrays. Arrays were washed and stained on an Affymetrix Fluidics Station 450.

scan_protocol: Scanning was carried out with the GeneChip Scanner 3000 (Affymetrix).

data_processing: Image analysis was perfomed using the GeneChip Operating Software (GCOS, Affymetrix). Background correction, normalization and probe summarization was done with the robust multichip average (RMA) algorithm implemented in the Expression Console software (Affymetrix). Control probes and probes for non-coding RNAs have been removed from the data tables. We analyzed the results for known ref seq genes.

source_name: soft tissue

label_protocol: cDNA was labelled with TdT using the WT Terminal Labeling kit (Affymetrix).

extract_protocol: RNA was extracted using the TRIzol reagent (Invitrogen) and purified with Qiagen´s RNeasy kit according to the manufacturers´ instructions.

value: conventional leiomyosarcoma

value: tumor biopsy


title: LMS_21 Leiomyosarcoma

description: Leiomyosarcoma


title: FPR4_del [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for FPR4 deletion strain compared to genomic DNA control

source_name: FPR4 deletion strain

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0

value: FPR4 deletion strain

source_name: MNase-treated total genomic DNA from WT (BY4741) strain


title: geo_1946 gist sdh negative 9

source_name: gist sdh negative


title: geo_1943 liver 2

source_name: liver

value: liver normal

value: liver


title: LMS_22 Leiomyosarcoma

description: Leiomyosarcoma


title: ESA1_ts [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for ESA1 temperature-sensive strain grown at restrictive temperature compared to genomic DNA control

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 esa1-Δ414::KanMX

value: ESA1 temperature-sensive strain

value: Nucleosomal DNA from the indicated test strain


title: LMS_20 Leiomyosarcoma

description: Leiomyosarcoma


title: DST1_del [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for DST1 deletion strain compared to genomic DNA control

source_name: DST1 deletion strain

value: DST1 deletion strain


title: geo_1942 stomach 5

source_name: stomach

value: stomach normal

value: stomach


title: LMS_18a Leiomyosarcoma

description: Leiomyosarcoma


title: GCR1_tet [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for GCR1 Tet promotor-shutoff strain compared to genomic DNA control

source_name: GCR1 Tet promotor-shutoff strain

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 URA3::CMV-tTA

value: GCR1 Tet promotor-shutoff strain


title: cDNA wt

description:
cDNA (1) YMC458 F16
cDNA (2) YMC458 F16
cDNA (3) YMC458 F16
First replica: cDNA labelling from wt strain YMC458. Hybridization on macrochip F16.
Second replica: cDNA labelling from wt strain YMC458. Hybridization on macrochip F16.
Third replica: cDNA labelling from wt strain YMC458. Hybridization on macrochip F16.

value: wild type

value: mRNA amount (RA)


title: geo_1944 stomach 6


title: drug_SB-IC50 [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for yeast strain BY4741 grown in the presence of 20 mM Sodium Butyrate for 2 hours (IC50) compared to genomic DNA control

growth_protocol: The haploid yeast strain BY4741 (parental strain of the haploid yeast deletion collection) was used for drug treatments. Cells were grown overnight and then diluted to an OD600 of 0.4. The drugs Nicotinamide (82 mM, IC50), Sodium Butyrate (20 mM, IC50), 1,10-Phenanthroline (100 μM, IC90) or 6-Azauracil (6 mM, IC90), all obtained from Sigma-Aldrich, were added to the media for 2 hours. Drug concentrations were predetermined to inhibit growth by 50% or 90%.


title: cDNA xrn1-D208A

description:
cDNA (1) YMC461 F17
cDNA (2) YMC461 F17
cDNA (3) YMC461 F17
First replica: cDNA labelling from xrn1-D208A strain YMC461. Hybridization on macrochip F17.
Second replica: cDNA labelling from xrn1-D208A strain YMC461. Hybridization on macrochip F17.
Third replica: cDNA labelling from xrn1-D208A strain YMC461. Hybridization on macrochip F17.

source_name: xrn1-D208A cells grown in YPD to exponential phase

value: xrn1-D208 point mutation


title: geo_1939 muscularis 3

value: muscularis normal

value: muscularis


title: geo_1940 stomach 4


title: primary abdominal NB tumor TTT013

city: Memphis

first: Yong-Dong

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description: Biological replicate 7 of 7, deficient caspase-8, with metastasis

hyb_protocol: Microarray hybridization was performed at 55°C for 20 hours in Agilent's microarray hybridization chambers, followed by wash procedures according to the manufacturer’s recommended protocols

scan_protocol: Microarray was scanned in an Agilent scanner at 5μm resolution, and the array data was extracted with Agilent feature extraction software using the miRNA_105_Jan09 protocol

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) was used, followed by a log transformation, percentile normalization across probes, and scaling through the samples, prior to actual analysis.

organism: Mus musculus

source_name: primary abdominal NB tumor

label_protocol: 100ng of total RNA were labeled with Cy3 according to Agilent's labeling protocol

extract_protocol: Total RNA was extracted from mouse tumors using Trizol reagent (Invitrogen) with two washes with 75% ethanol. RNA quality was confirmed by analysis on the Agilient 2100 Bioanalyzer.

value: primary abdominal NB tumor

value: deficient caspase-8, with metastasis to the bone marrow


title: GRO Δxrn1

description:
GRO (1) YMC511 F18
GRO (2) YMC511 F18
GRO (3) YMC511 F18
First replica: Run-on labelling from xrn1 strain YMC511. Hybridization on macrochip F18.
Second replica: Run-on labelling from xrn1 strain YMC511. Hybridization on macrochip F18.
Third replica: Run-on labelling from xrn1 strain YMC511. Hybridization on macrochip F18.

value: Δxrn1 deletory mutation

value: transcription rate (TR)


title: GRO xrn1-D208A

description:
GRO (1) YMC461 F17
GRO (2) YMC461 F17
GRO (3) YMC461 F17
First replica: Run-on labelling from xrn1-D208A strain YMC461. Hybridization on macrochip F17.
Second replica: Run-on labelling from xrn1-D208A strain YMC461. Hybridization on macrochip F17.


title: GRO wt

description:
GRO (1) YMC458 F16
GRO (2) YMC458 F16
GRO (3) YMC458 F16
First replica: Run-on labelling from wt strain YMC458. Hybridization on macrochip F16.
Second replica: Run-on labelling from wt strain YMC458. Hybridization on macrochip F16.
Third replica: Run-on labelling from wt strain YMC458. Hybridization on macrochip F16.

source_name: Wild type cells grown in YPD to exponential phase


title: drug_Nic-IC50 [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for yeast strain BY4741 grown in the presence of 82 mM Nicotinamide for 2 hours (IC50) compared to genomic DNA control

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0


title: LMS_17 Leiomyosarcoma

description: Leiomyosarcoma

value: conventional leiomyosarcoma

value: tumor biopsy


title: LMS_15 Leiomyosarcoma

description: Leiomyosarcoma


title: drug_6-Az_ic90 [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for yeast strain BY4741 grown in the presence of 6 mM 6-azauracil for 2 hours (IC90) compared to genomic DNA control

value: Nucleosomal DNA from the indicated test strain


title: geo_1938 gist sdh positive 4

source_name: gist sdh positive

value: gist sdh positive


title: LMS_19 Leiomyosarcoma

description: Leiomyosarcoma


title: geo_1935 gist sdh positive 3


title: primary abdominal NB tumor TTT010

description: Biological replicate 4 of 7, deficient caspase-8, with metastasis


title: DAT1_del [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for DAT1 deletion strain compared to genomic DNA control

source_name: DAT1 deletion strain

value: DAT1 deletion strain


title: primary abdominal NB tumor TTT012

description: Biological replicate 6 of 7, deficient caspase-8, with metastasis


title: primary abdominal NB tumor TTT009

description: Biological replicate 3 of 7, deficient caspase-8, with metastasis


title: DOT1_del [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for DOT1 deletion strain compared to genomic DNA control

source_name: DOT1 deletion strain

value: DOT1 deletion strain


title: geo_1937 gist sdh negative 8

value: gist sdh negative


title: CYC8_del_rep2 [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for CYC8 deletion strain compared to genomic DNA control

source_name: CYC8 deletion strain

value: CYC8 deletion strain


title: LMS_13 Leiomyosarcoma

description: Leiomyosarcoma


title: primary abdominal NB tumor TTT011

description: Biological replicate 5 of 7, deficient caspase-8, with metastasis


title: LMS_16 Leiomyosarcoma

description: Leiomyosarcoma


title: LMS_12 Leiomyosarcoma

description: Leiomyosarcoma


title: geo_1931 gist sdh negative 6


title: LMS_11 Leiomyosarcoma

description: Leiomyosarcoma


title: geo_1934 gist sdh negative 7


title: drug_1-10-PHE_ic90 [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for yeast strain BY4741 grown in the presence of 100μM 1,10-Phenanthroline for 2 hours (IC90) compared to genomic DNA control


title: primary abdominal NB tumor TTT008

description: Biological replicate 2 of 7, deficient caspase-8, with metastasis


title: geo_1930 muscularis 2

source_name: muscularis


title: CYC8_del_rep1 [nucleosome profile]


title: primary abdominal NB tumor TTT007

description: Biological replicate 1 of 7, deficient caspase-8, with metastasis


title: LMS_10 Leiomyosarcoma

description: Leiomyosarcoma


title: LMS_8 Leiomyosarcoma

description: Leiomyosarcoma


title: geo_1929 gist sdh negative 5


title: CHD1_del [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for CHD1 deletion strain compared to genomic DNA control

source_name: CHD1 deletion strain

value: CHD1 deletion strain


title: primary abdominal NB tumor TTT006

description: Biological replicate 6 of 6, wild type caspase-8, no metastasis

value: wild type caspase-8, no metastasis to the bone marrow


title: CAC2_del [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for CAC2 deletion strain compared to genomic DNA control

source_name: CAC2 deletion strain

value: CAC2 deletion strain


title: primary abdominal NB tumor TTT005

description: Biological replicate 5 of 6, wild type caspase-8, no metastasis


title: geo_1927 stomach 3

value: stomach normal

value: stomach


title: geo_1923 muscularis 1

value: muscularis normal

value: muscularis


title: BRE1_del [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for BRE1 deletion strain compared to genomic DNA control

source_name: BRE1 deletion strain

value: BRE1 deletion strain


title: BDP1_tet [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for BDP1 Tet promotor-shutoff strain compared to genomic DNA control

source_name: BDP1 Tet promotor-shutoff strain

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 URA3::CMV-tTA

value: BDP1 Tet promotor-shutoff strain

source_name: MNase-treated total genomic DNA from WT (BY4741) strain

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0


title: geo_1922 gist sdh negative 4

source_name: gist sdh negative


title: primary abdominal NB tumor TTT003

description: Biological replicate 3 of 6, wild type caspase-8, no metastasis

value: primary abdominal NB tumor


title: geo_1924 stomach 2


title: ILMS_3 Inflammatory leiomyosarcoma

description: Inflammatory leiomyosarcoma

source_name: soft tissue

value: inflammatory leiomyosarcoma

value: tumor biopsy


title: primary abdominal NB tumor TTT002

description: Biological replicate 2 of 6, wild type caspase-8, no metastasis


title: primary abdominal NB tumor TTT001

description: Biological replicate 1 of 6, wild type caspase-8, no metastasis


title: ILMS_2 Inflammatory leiomyosarcoma

description: Inflammatory leiomyosarcoma


title: LMS_9 Leiomyosarcoma

description: Leiomyosarcoma

value: conventional leiomyosarcoma


title: ASF1_del [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for ASF1 deletion strain compared to genomic DNA control

source_name: ASF1 deletion strain

value: ASF1 deletion strain

value: Nucleosomal DNA from the indicated test strain


title: geo_1921 stomach 1

source_name: stomach


title: ABF1_ts [nucleosome profile]

description:
ctrl CEL files:
gDNA-control_rep1.CEL; gDNA-control_rep2.CEL;
gDNA-control_rep3.CEL; gDNA-control_rep4.CEL
Monococcal nuclease treated chromatin profile for ABF1 temperature-sensive strain grown at restrictive temperature compared to genomic DNA control

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 abf1-101::KanMX

value: ABF1 temperature-sensive strain


title: ILMS_1 Inflammatory leiomyosarcoma

description: Inflammatory leiomyosarcoma


title: geo_1919 gist sdh positive 2

value: gist sdh positive


title: LMS_14 Leiomyosarcoma

description: Leiomyosarcoma


title: primary abdominal NB tumor TTT004

description: Biological replicate 4 of 6, wild type caspase-8, no metastasis

value: wild type caspase-8, no metastasis to the bone marrow


title: drug_SB-IC50 [transcript profile]

description:
ctrl CEL file; b20_YPD_cDNA.CEL
drug_SB-IC50
Expression profile for yeast strain BY4741 grown in the presence of 20 mM Sodium Butyrate for 2 hours (IC50) compared to wild-type control

data_processing: Raw data files were normalized with Affymetrix Tiling Analysis Software (TAS) v1.1. Treatment and control samples were quantile normalized in pairs using only perfect match probes with a bandwidth of 20. The files ending in 'forward.bar' and 'reverse.bar' correspond to normalized signals from the forward and reverse strand, respectively.

label_protocol: cDNA was fragmented by nuclease digestion in a solution containing 1X One-Phor-All buffer (GE Healthcare) and DNase I (GE Healthcare) at 37ｰC until the average fragment size was approximately 70 bp. The fragmentation reaction was stopped by incubating at 95C for 10 min. Fragmented samples were biotinylated with Biotin-N6-ddATP (Enzo Life Sciences) using terminal deoxynucleotidyl transferase at 37C for 2 hours.

extract_protocol: Total RNA was extracted from yeast cells by vortexing with glass beads in the presence of hot acid phenol and cleaned by phenol:chlorophorm extraction followed by ethanol precipitation. After DNaseI (GE Healthcare) treatment to remove residual genomic DNA, 25 ug of total RNA was incubated with random hexamers at 70C for 10 min, incubated at 15C for 30 min and reverse transcribed to single-stranded cDNA for 2 hours at 42C with Superscript II (Invitrogen) in the presence of 6 μg/ml Actinomycin D to prevent antisense artifacts. RNA was subsequently removed by hydrolysis and cDNA was cleaned up and concentrated on MinElute PCR purification columns (Qiagen).

tag: strain background

value: wild type

source_name: total RNA from matched wild type control


title: eel sampled in Wijmeers pond [BE29_WI]

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

description: liver RNA of Anguilla anguilla

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5 and normalized by quantile normalization of gProcessed signal using R2.6.1 statistical software.

label: Cyanine 3

organism: Anguilla anguilla

source_name: Liver of European eel collected during October 2009 in the Wijmeers pond

label_protocol: Amplified and labeled according to Agilent Low input One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Extracted according to QiAgen RNeasy MiniKit protocol for tissue samples

tag: location

value: sampled in the Wijmeers pond


title: drug_6-Az_ic90 [transcript profile]

description:
ctrl CEL file; b20_YPD_cDNA.CEL
drug_6-Az_ic90
Expression profile for yeast strain BY4741 grown in the presence of 6 mM 6-azauracil for 2 hours (IC90) compared to wild-type control


title: drug_Nic-IC50 [transcript profile]

description:
ctrl CEL file; b20_YPD_cDNA.CEL
drug_Nic-IC50
Expression profile for yeast strain BY4741 grown in the presence of 82 mM Nicotinamide for 2 hours (IC50) compared to wild-type control


title: eel sampled in Wijmeers pond [BE30_WI]

description: liver RNA of Anguilla anguilla


title: geo_1920 gist sdh negative 3

value: gist sdh negative


title: geo_1918 gist sdh negative 2


title: 1827-DB-6 parietal mesothelium, biological replicate 2

city: Nashville

first: David

last: Bader

address: Pierce

institute: Vanderbilt

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix mouse Gene 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Affymetrix high resolution GenePix 4000B scanner

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

source_name: parietal mesothelium

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

growth_protocol: Primary tissues were obtained from Wt1-cre;Rosa26ReYFP mice

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

treatment_protocol: No treatment

tag: age

value: adult

value: parietal mesothelium


title: 1827-DB-3 visceral mesothelium (omentum), biological replicate 2

source_name: visceral mesothelium (omentum)

value: visceral mesothelium


title: geo_1915 gist sdh positive 1

source_name: gist sdh positive


title: eel sampled in Wijmeers pond [BE28_WI]

description: liver RNA of Anguilla anguilla


title: eel sampled in Wijmeers pond [BE27_WI]

description: liver RNA of Anguilla anguilla


title: drug_1-10-PHE_ic90 [transcript profile]

description:
ctrl CEL file; b20_YPD_cDNA.CEL
drug_1-10-PHE_ic90
Expression profile for yeast strain BY4741 grown in the presence of 100μM 1,10-Phenanthroline for 2 hours (IC90) compared to wild-type control

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0


title: TBF1_ts [transcript profile]

description:
ctrl CEL file: b21_WT_cDNA_ts.CEL
TBF1_ts
Expression profile for TBF1 temperature-sensive strain grown at restrictive temperature compared to wild-type control

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 KanMX::tbf1-URA3

value: TBF1 temperature-sensive strain


title: geo_1462 liver 1

source_name: liver

value: liver normal

value: liver


title: 1827-DB-2 visceral mesothelium (omentum), biological replicate 1


title: SPT6_ts [transcript profile]

description:
ctrl CEL file: b06_WT_cDNA_ts.CEL
SPT6_ts
Expression profile for SPT6 temperature-sensive strain grown at restrictive temperature compared to wild-type control

value: SPT6 temperature-sensive strain

value: FY85, MATa his4-912δ lys2-128δ leu2Δ1 ura3-52


title: eel sampled in Wijmeers pond [BE26_WI]

description: liver RNA of Anguilla anguilla


title: geo_1916 gist sdh negative 1


title: eel sampled in Wijmeers pond [BE25_WI]

description: liver RNA of Anguilla anguilla


title: geo_1113 brain neuronal 14

source_name: brain neuronal

value: brain neuronal normal

tag: cell type

value: brain neuron


title: Sca1-HGAL 2

city: Houston

first: Michael

middle: R

last: Green

state: TX

address: 1515 Holcombe Blvd, Unit 903

department: Lymphoma/Myeloma

institute: MD Anderson Cancer Center

hyb_protocol: Following fragmentation, cRNA was hybridized overnight according to the Affymetrix protocol.

scan_protocol: Chips scanned using an Affymetrix GeneChip 3000 scanner.

data_processing: Raw data was normalized using RMA preprocessed with quantile normalization and median scaling. We used the "ExpressionFileCreator" module of GenePattern for RMA normalization.

source_name: Gene expression data from CD22+B220+ FACS-purified splenocytes of adult Sca1-HGAL knock-in CBAxC57BL/6J mice

extract_protocol: Total RNA was isolated in two steps using TRIzol (Life Technologies, Inc., Grand Island, NY) followed by Rneasy Mini-Kit (Qiagen Inc., Valencia, CA) purification following the manufacturer’s RNA Clean-up protocol with the optional On-column DNase treatment.

tag: genotype

value: Sca1-HGAL knock-in

value: Spleen

value: CD22+B220+ B-cells


title: geo_1103 brain neuronal 13


title: Sca1-HGAL 4

label_protocol: Following fragmentation, cRNA was hybridized overnight according to the Affymetrix protocol.


title: 1827-DB-5 parietal mesothelium, biological replicate 1


title: SPT15_ts [transcript profile]

description:
ctrl CEL file; b08_WT_cDNA_ts.CEL
SPT15_ts
Expression profile for SPT15 temperature-sensive strain grown at restrictive temperature compared to wild-type control

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 spt15-I143N::KanMX

value: SPT15 temperature-sensive strain

value: wild type


title: SPT16_ts [transcript profile]

description:
ctrl CEL file: b04_WT_cDNA_ts.CEL
SPT16_ts
Expression profile for SPT16 temperature-sensive strain grown at restrictive temperature compared to wild-type control

value: SPT16 temperature-sensive strain


title: geo_1102 brain neuronal 12


title: Sca1-HGAL 3


title: RSC3_ts [transcript profile]

description:
ctrl CEL file: b01_WT_cDNA_ts.CEL
RSC3_ts
Expression profile for RSC3 temperature-sensive strain grown at restrictive temperature compared to wild-type control

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 rsc3-1::KanMX

value: RSC3 temperature-sensive strain


title: Control 4

source_name: Gene expression data from CD22+B220+ FACS-purified splenocytes of adult CBAxC57BL/6J mice

value: Wild-Type


title: geo_1088 brain neuronal 11


title: RPO21_ts_rep2 [transcript profile]

description:
ctrl CEL file: b91_WT_cDNA_ts.CEL
RPO21_ts_rep2
Expression profile for RPO21_rep2 temperature-sensive strain grown at restrictive temperature compared to wild-type control

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 rpo21-1::KanMX

value: RPO21_rep2 temperature-sensive strain


title: geo_1087 brain neuronal 10


title: eel sampled in Wijmeers pond [BE24_WI]

description: liver RNA of Anguilla anguilla

value: sampled in the Wijmeers pond


title: Sca1-HGAL 1


title: Inflammatory leiomyosarcoma case 1

description: Genomic DNA extracted from tumor biopsy was analyzed using Illumina Human CNV370-Quad v3.0 BeadChip (Illumina).

source_name: Inflammatory leiomyosarcoma

value: Male

value: Tumor tissue

value: sarcoma


title: RPO21_ts_rep1 [transcript profile]

description:
ctrl CEL file; b08_WT_cDNA_ts.CEL
RPO21_ts_rep1
Expression profile for RPO21_rep1 temperature-sensive strain grown at restrictive temperature compared to wild-type control

value: RPO21_rep1 temperature-sensive strain

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0


title: Control 3

value: Spleen


title: geo_1080 brain neuronal 9

value: brain neuronal normal

value: brain neuron


title: eel sampled in Dessel-Schotel canal [BE22_SC]

description: liver RNA of Anguilla anguilla

source_name: Liver of European eel collected during October 2009 in the Dessel-Schotel canal

value: sampled in the Dessel-Schotel canal


title: REB1_ts [transcript profile]

description:
ctrl CEL file: b18_WT_cDNA_ts.CEL
REB1_ts
Expression profile for REB1 temperature-sensive strain grown at restrictive temperature compared to wild-type control

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 KanMX::reb1-212-URA3

value: REB1 temperature-sensive strain

value: wild type


title: geo_1079 brain neuronal 8


title: eel sampled in Dessel-Schotel canal [BE21_SC]

description: liver RNA of Anguilla anguilla


title: eel sampled in Dessel-Schotel canal [BE20_SC]

description: liver RNA of Anguilla anguilla


title: RAP1_ts [transcript profile]

description:
ctrl CEL file; b05_WT_cDNA_ts.CEL
RAP1_ts
Expression profile for RAP1 temperature-sensive strain grown at restrictive temperature compared to wild-type control

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 rap1-1::KanMX

value: RAP1 temperature-sensive strain


title: MCM1_ts [transcript profile]

description:
ctrl CEL file: b26_WT_cDNA_ts.CEL
MCM1_ts
Expression profile for MCM1 temperature-sensive strain grown at restrictive temperature compared to wild-type control

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 KanMX::mcm1-URA3

value: MCM1 temperature-sensive strain


title: Control 1

value: Wild-Type

value: CD22+B220+ B-cells


title: eel sampled in Dessel-Schotel canal [BE23_SC]

description: liver RNA of Anguilla anguilla


title: Control 2


title: geo_1078 brain neuronal 7


title: ESA1_ts [transcript profile]

description:
ctrl CEL file; b05_WT_cDNA_ts.CEL
ESA1_ts
Expression profile for ESA1 temperature-sensive strain grown at restrictive temperature compared to wild-type control

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 esa1-Δ414::KanMX

value: ESA1 temperature-sensive strain


title: eel sampled in Dessel-Schotel canal [BE18_SC]

description: liver RNA of Anguilla anguilla


title: eel sampled in Dessel-Schotel canal [BE17_SC]

description: liver RNA of Anguilla anguilla


title: geo_1069 brain neuronal 6


title: geo_1068 brain neuronal 5


title: 1562 q3

city: Covington

first: Smriti

last: Mehra

state: LA

address: 18703 Three Rivers Road, 2-209

institute: TNPRC

hyb_protocol: As described in previous publications including Mehra et al 2010 PMCID: PMCID: PMC2930844;  Dutta et al 2012 PMCID: PMC3250399; Mehra et al 2012 PMCID:PMCID: PMC3308902; Mehra et al 2013 PMID: 23255564

data_processing: Data analysis procedures have been described in detail in the above referenced previous publications from our group. Briefly, data was extracted from 16 BIT TIFF files scanned using GenePix 4000B scanner (5um res) using GenePix pro 7.0 and then uploaded to Spotfire DecisionSite for Microarray Analysis. Array data was then filtered for abberant SNR, flags etc and normalized using the S+ ArrayAnalyzer LOWESS normalization script resident within Spotfire. Statistical significance was determined using Spotfire. Analyzed data were then exported to Excel.

organism: Macaca mulatta

source_name: Macaca mulatta (rhesus macaque) bone marrow derived macrophages

growth_protocol: Rh-BMDMs were cultured as previously described (Mehra et al 2010 PMCID: PMC3052882  and Dutta et al 2012 PMCID: PMC3250399

extract_protocol: As described in previous publications including Mehra et al 2010 PMCID: PMCID: PMC2930844 and Dutta et al 2012 PMCID: PMC3250399

treatment_protocol: treatment was i) Mtb grown in Middlebrook 7H9 supplemented media as described earlier (Mehra et al 2009 PMCID: PMC2698404) and ii) Mtb grown in the identical media but in reduced oxygen as described earlier (Saini et al PMID: 15073296 ).

value: BMDMs

tag: treatment

value: uninfected

value: infected with Mtb grown in hypoxia


title: eel sampled in Dessel-Schotel canal [BE19_SC]

description: liver RNA of Anguilla anguilla


title: 1562 q4

scan_protocol: As described in previous publications including Mehra et al 2010 PMCID: PMCID: PMC2930844;  Dutta et al 2012 PMCID: PMC3250399; Mehra et al 2012 PMCID:PMCID: PMC3308902; Mehra et al 2013 PMID: 23255564


title: eel sampled in Dessel-Schotel canal [BE16_SC]

description: liver RNA of Anguilla anguilla


title: geo_1061 brain neuronal 4

value: brain neuronal normal


title: eel sampled in Dessel-Schotel canal [BE15_SC]

description: liver RNA of Anguilla anguilla


title: 1562 q1

label_protocol: As described in previous publications including Mehra et al 2010 PMCID: PMCID: PMC2930844;  Dutta et al 2012 PMCID: PMC3250399; Mehra et al 2012 PMCID:PMCID: PMC3308902; Mehra et al 2013 PMID: 23255564

value: infected with Mtb grown in normal oxygen


title: 1562 q2


title: eel sampled in Dessel-Schotel canal [BE14_SC]

description: liver RNA of Anguilla anguilla

value: sampled in the Dessel-Schotel canal


title: H4-depletion_360min [transcript profile]

description:
ctrl CEL file: MHY6.CEL
H4-depletion_360min
Expression profile after 6 hours of histone H4 depletion compared to wild-type control

source_name: UKY403 after 6 hours of histone H4 depletion

value: UKY403, MATa ade2-101 his3-A200 leu2-3, 112 lys-801 trpl-A901 ura3-52 GAL+ thr tyr arg4-1 Ah4-J[HIS3+] Ah4-2[LEU2+ ]/pUK421 (CEN TRPI+ GAL-H4-2 +)


title: eel sampled in Dessel-Schotel canal [BE13_SC]

description: liver RNA of Anguilla anguilla


title: eel sampled in Dessel-Schotel canal [BE12_SC]

description: liver RNA of Anguilla anguilla


title: H4-depletion_300min [transcript profile]

description:
ctrl CEL file: MHY5.CEL
H4-depletion_300min
Expression profile after 5 hours of histone H4 depletion compared to wild-type control

source_name: UKY403 after 5 hours of histone H4 depletion


title: geo_1048 brain neuronal 2

value: brain neuron


title: geo_1060 brain neuronal 3


title: HSF1_ts [transcript profile]

description:
ctrl CEL file: b09_WT_cDNA_ts.CEL
HSF1_ts
Expression profile for HSF1 temperature-sensive strain grown at restrictive temperature compared to wild-type control

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 hsf1-848::KanMX

value: HSF1 temperature-sensive strain

value: wild type


title: H4-depletion_180min [transcript profile]

description:
ctrl CEL file: MHY3.CEL
H4-depletion_180min
Expression profile after 3 hours of histone H4 depletion compared to wild-type control

source_name: UKY403 after 3 hours of histone H4 depletion


title: SPT16_tet [transcript profile]

description:
ctrl CEL file; b23_WT2_cDNA.CEL
SPT16_tet
Expression profile for SPT16 Tet promotor-shutoff strain compared to wild-type control

source_name: SPT16 Tet promotor-shutoff strain

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 URA3::CMV-tTA

value: SPT16 Tet promotor-shutoff strain


title: geo_1054 brain neuronal 1


title: eel sampled in Dessel-Schotel canal [BE11_SC]

description: liver RNA of Anguilla anguilla


title: geo_852 small intestine normal 5

source_name: small intestine normal

value: small intestine normal

value: small intestine


title: geo_848 small intestine normal 4


title: eel sampled in Dessel-Schotel canal [BE10_SC]

description: liver RNA of Anguilla anguilla


title: RRN3_tet [transcript profile]

description:
ctrl CEL file; b23_WT2_cDNA.CEL
RRN3_tet
Expression profile for RRN3 Tet promotor-shutoff strain compared to wild-type control

source_name: RRN3 Tet promotor-shutoff strain

value: RRN3 Tet promotor-shutoff strain

source_name: total RNA from matched wild type control


title: ABF1_ts [transcript profile]

description:
ctrl CEL file: b07_WT_cDNA_ts.CEL
ABF1_ts
Expression profile for ABF1 temperature-sensive strain grown at restrictive temperature compared to wild-type control

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 abf1-101::KanMX

value: ABF1 temperature-sensive strain


title: RPO21_tet [transcript profile]

description:
ctrl CEL file; b22_WT1_cDNA.CEL
RPO21_tet
Expression profile for RPO21 Tet promotor-shutoff strain compared to wild-type control

source_name: RPO21 Tet promotor-shutoff strain

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0

value: RPO21 Tet promotor-shutoff strain


title: RPB2_tet [transcript profile]

description:
ctrl CEL file; b24_WT3_cDNA.CEL
RPB2_tet
Expression profile for RPB2 Tet promotor-shutoff strain compared to wild-type control

source_name: RPB2 Tet promotor-shutoff strain

value: RPB2 Tet promotor-shutoff strain


title: geo_1700 small intestine normal 1


title: geo_1651 lymphnode benign reactive 13

source_name: lymph node benign reactive

value: lymph node benign reactive


title: geo_1649 lymphnode benign reactive 12

value: lymph node


title: geo_1704 small intestine normal 2


title: eel sampled in Dessel-Schotel canal [BE9_SC]

description: liver RNA of Anguilla anguilla

value: sampled in the Dessel-Schotel canal


title: RAP1_tet [transcript profile]

description:
ctrl CEL file; b22_WT1_cDNA.CEL
RAP1_tet
Expression profile for RAP1 Tet promotor-shutoff strain compared to wild-type control

source_name: RAP1 Tet promotor-shutoff strain

value: RAP1 Tet promotor-shutoff strain


title: geo_847 small intestine normal 3


title: BDP1_tet [transcript profile]

description:
ctrl CEL file: b12_WT2_cDNA.CEL
BDP1_tet
Expression profile for BDP1 Tet promotor-shutoff strain compared to wild-type control

source_name: BDP1 Tet promotor-shutoff strain

value: BDP1 Tet promotor-shutoff strain


title: GCR1_tet [transcript profile]

description:
ctrl CEL file: b11_WT1_cDNA.CEL
GCR1_tet
Expression profile for GCR1 Tet promotor-shutoff strain compared to wild-type control

source_name: GCR1 Tet promotor-shutoff strain

value: GCR1 Tet promotor-shutoff strain


title: geo_1645 lymphnode benign reactive 11


title: eel sampled in Hazewinkel pond [BE8_HA]

description: liver RNA of Anguilla anguilla

source_name: Liver of European eel collected during October 2009 in the Hazewinkel pond

value: sampled in the Hazewinkel pond


title: eel sampled in Hazewinkel pond [BE5_HA]

description: liver RNA of Anguilla anguilla


title: geo_804 lymphnode benign reactive 10


title: eel sampled in Hazewinkel pond [BE7_HA]

description: liver RNA of Anguilla anguilla


title: geo_806 lymphnode benign reactive 9


title: RPA190_tet [transcript profile]

description:
ctrl CEL file; b24_WT3_cDNA.CEL
RPA190_tet
Expression profile for RPA190 Tet promotor-shutoff strain compared to wild-type control

source_name: RPA190 Tet promotor-shutoff strain

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 URA3::CMV-tTA

value: RPA190 Tet promotor-shutoff strain

value: wild type


title: eel sampled in Hazewinkel pond [BE6_HA]

description: liver RNA of Anguilla anguilla


title: VPS75_del [transcript profile]

description:
ctrl CEL file; b02_WT2_cDNA.CEL
VPS75_del
Expression profile for VPS75 deletion strain compared to wild-type control

source_name: VPS75 deletion strain

value: VPS75 deletion strain


title: geo_807 lymphnode benign reactive 8


title: eel sampled in Hazewinkel pond [BE3_HA]

description: liver RNA of Anguilla anguilla


title: eel sampled in Hazewinkel pond [BE2_HA]

description: liver RNA of Anguilla anguilla


title: TUP1_del [transcript profile]

description:
ctrl CEL file; b02_WT2_cDNA.CEL
TUP1_del
Expression profile for TUP1 deletion strain compared to wild-type control

source_name: TUP1 deletion strain

value: TUP1 deletion strain


title: SWR1_del [transcript profile]

description:
ctrl CEL file; b02_WT2_cDNA.CEL
SWR1_del
Expression profile for SWR1 deletion strain compared to wild-type control

source_name: SWR1 deletion strain

value: SWR1 deletion strain


title: eel sampled in Hazewinkel pond [BE4_HA]

description: liver RNA of Anguilla anguilla


title: SWI4_del [transcript profile]

description:
ctrl CEL file: b34_WT_cDNA.CEL
SWI4_del
Expression profile for SWI4 deletion strain compared to wild-type control

source_name: SWI4 deletion strain

value: SWI4 deletion strain


title: STB2_del [transcript profile]

description:
ctrl CEL file; b03_WT_cDNA.CEL
STB2_del
Expression profile for STB2 deletion strain compared to wild-type control

source_name: STB2 deletion strain

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0

value: STB2 deletion strain


title: geo_808 lymphnode benign reactive 6


title: geo_809 lymphnode benign reactive 7


title: geo_813 lymphnode benign reactive 3


title: geo_805 lymphnode benign reactive 4


title: eel sampled in Bolsena Lake [BL118]

description: liver RNA of Anguilla anguilla

source_name: Liver of European eel collected during October 2009 in the lake of Bolsena, Italy

value: sampled in the lake of Bolsena


title: geo_812 lymphnode benign reactive 5

value: lymph node benign reactive


title: eel sampled in Bolsena Lake [BL131]

description: liver RNA of Anguilla anguilla


title: Quiescent MCF10A cells infected with Adb-gal B1

city: Chicago

first: Ghata

last: Singhal

state: Illinois

address: 303 E Chicago Avenue

department: Microbiology-Immunology

institute: Northwestern University

description: Replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: cultured breast cells

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

growth_protocol: human MCF10A cells  were maintained in DMEM containing 10% fetal bovine serum

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: cells were infected with human adenovirus variants

tag: infection

value: Adb-gal


title: geo_810 lymphnode benign reactive 2

value: lymph node


title: Quiescent MCF10A cells infected with Adb-gal B2

description: Replicate 2


title: SNF1_del [transcript profile]

description:
ctrl CEL file; b13_WT1_cDNA.CEL
SNF1_del
Expression profile for SNF1 deletion strain compared to wild-type control

source_name: SNF1 deletion strain

value: SNF1 deletion strain


title: geo_811 lymphnode benign reactive 1


title: SNF2_del [transcript profile]

description:
ctrl CEL file; b28_WT_cDNA.CEL
SNF2_del
Expression profile for SNF2 deletion strain compared to wild-type control

source_name: SNF2 deletion strain

value: SNF2 deletion strain

source_name: total RNA from matched wild type control


title: Quiescent MCF10A cells infected with AdE1A virus E2

description: Replicate 2

value: AdE1A virus


title: eel sampled in Hazewinkel pond [BE1_HA]

description: liver RNA of Anguilla anguilla

value: sampled in the Hazewinkel pond


title: SPT21_del [transcript profile]

description:
ctrl CEL file; b02_WT2_cDNA.CEL
SPT21_del
Expression profile for SPT21 deletion strain compared to wild-type control

source_name: SPT21 deletion strain

value: SPT21 deletion strain


title: eel sampled in Bolsena Lake [BL130]

description: liver RNA of Anguilla anguilla


title: eel sampled in Bolsena Lake [BL129]

description: liver RNA of Anguilla anguilla


title: Quiescent MCF10A cells infected with AdE1A virus E1

description: Replicate 1


title: eel sampled in Bolsena Lake [BL114]

description: liver RNA of Anguilla anguilla


title: eel sampled in Bolsena Lake [BL126]

description: liver RNA of Anguilla anguilla


title: SIR2_del [transcript profile]

description:
ctrl CEL file; b13_WT1_cDNA.CEL
SIR2_del
Expression profile for SIR2 deletion strain compared to wild-type control

source_name: SIR2 deletion strain

value: SIR2 deletion strain


title: SPT10_del [transcript profile]

description:
ctrl CEL file: b16_WT_cDNA.CEL
SPT10_del
Expression profile for SPT10 deletion strain compared to wild-type control

source_name: SPT10 deletion strain

value: SPT10 deletion strain

value: wild type


title: eel sampled in Bolsena Lake [BL112]

description: liver RNA of Anguilla anguilla


title: eel sampled in Bolsena Lake [BL115]

description: liver RNA of Anguilla anguilla