title: HUG1N shRNA Rep2

city: Boston

first: Ramesh

last: Shivdasani

state: Massachusetts

address: Dana Bldg, Room 720, 450 Brookline Ave

department: Department of Medical Oncology

institute: Dana-Farber Cancer Institute

description: Gene expression data from HuG-1 cells treated with GATA6 shRNA.

hyb_protocol: Hybridization was performed following the Affymetrix GeneChip 3’ IVT Express Kit instructions; washing and staining was done with the Affymetrix Fluidics Station 450.

scan_protocol: Scanning was performed according to manufacturer's instructions using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The .CEL files were GCRMA normalized using R/Bioconductor.

source_name: HUG1N shRNA treated cells

label_protocol: Labeling was performed following the Affymetrix GeneChip 3’ IVT Express Kit instructions.

growth_protocol: ATCC recommended media conditions at 37 degrees.

treatment_protocol: Cells were infected with GATA6 shRNA, selected with puromycin and harvested.


title: Coxiella treated with acidified citrate cysteine media 1 replicate 3

status: Public on Dec 02 2013

type: RNA

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

country: USA

institute: NIH

description: Gene expression data from_Coxiella treated with acidified citrate cysteine media1replicate 3

hyb_protocol: All cRNAs were hybridized to a custom Affymetrix GeneChip

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Ft genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

molecule: total RNA

organism: Coxiella burnetii

label_protocol: Biotin-labeled cRNA was then in vitro transcribed using cDNA as a template. Ten mg of labeled cRNA was fragmented using Ambion 10X fragmentation buffer (Invitrogen) and incubation at 75°C for 15 min.

growth_protocol: Host cell propagation of bacteria was conducted using African green monkey kidney (Vero) fibroblasts (CCL-81; American Type Culture Collection) grown in RPMI medium (Invitrogen) supplemented with 2% (v/v) fetal bovine serum (FBS).

extract_protocol: A MicrobEnrich kit (Applied Biosystems) was used to increase the relative level of C. burnetii RNA. Enriched RNA (~1 μg) was amplified using a MessageAmp II Bacteria kit (Applied Biosystems).

treatment_protocol: For axenic cultivation, C. burnetii was grown in ACCM-1 and ACCM-2

tag: growth medium


title: Coxiella treated with acidified citrate cysteine media 1 replicate 2

description: Gene expression data from_Coxiella treated with acidified citrate cysteine media1replicate 2


title: Coxiella treated with acidified citrate cysteine media 1 replicate 1

description: Gene expression data from_Coxiella treated with acidified citrate cysteine media1replicate 1


title: STROMA D12 MORN 3

city: Birmingham

last: Turan

address: University of Birmingham, Edgbaston

country: United Kingdom

institute: University of Birmingham

hyb_protocol: RNA was hybridised to Agilent Chicken (V1) microarrays and Human GE v2 microarrays (Agilent Technologies, CA). Due to the proximity of tumour cells to the surrounding chicken cells no attempt was made to separate them, instead pooled RNA from both types of cell were hybridised to chicken and human arrays. CAM cells distant from the tumour were hybridised to chicken arrays.

scan_protocol: Scanning and spot analysis were done according to the manufacturer’s instructions.

data_processing: Controls were removed from the data after scanning. The arrays were log2 transformed and normalised using between arrays quantile normalisation in the R software package preprocessCore from BioConductor

organism: Gallus gallus

source_name: STROMA D12 MORN

label_protocol: RNA was reverse transcribed (cDNA Synthesis System Kit, Roche Diagnostics), purified and transcribed in the presence of Cy3 and Cy5 labels (Megascript D7 Kit, Ambion, Austin, TX).

growth_protocol: U87 human glioma cells were cultured in DMEM with 10% FBS, antibiotics and L-glutamine. Fertilised chicken eggs were kept and prepared as described in (Hagedorn, M et al. 2002. PMID: 12460903)

extract_protocol: RNA was extracted using Qiagen (Valencia, CA) RNeasy columns

tag: tissue

value: CAM, at site of implantation


title: STROMA D12 EVE 2

source_name: STROMA D12 EVE


title: STROMA D12 MORN 2


title: Caco2 shRNA Rep2

description: Gene expression data from Caco-2 cells treated with GATA6 shRNA.

organism: Homo sapiens

source_name: Caco2 shRNA treated cells

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

tag: cell line


title: Caco2 shRNA Rep1


title: STROMA D12 EVE 1


title: STROMA D11 EVE 3

source_name: STROMA D11 EVE


title: Activated_Tcells_PsoriasisControl6

city: Barcelona

first: Antonio

last: Julià

state: Barcelona

address: c/ Baldiri Reixac nº15

department: Rheumatology Research Group

country: Spain

institute: Vall d'Hebron Hospital Research Institute

description: Control6 sample

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: log2 transformation and quantile normalization

source_name: PBMCs

label_protocol: Standard Illumina labeling protocol

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood of patients and controls by centrifugation on a Ficoll-Paque PLUS (GE Healthcare Biosciences AB, Uppsala, Sweden) density gradient. PBMCs were then seeded in complete RPMI 1640 medium supplemented with 100 U/ml penicillin, 100 U/ml streptomycin, 10% fetal bovine serum, 2 mM L-glutamine and 50 μM mercaptoethanol, and activated with 1μg/ml of anti-CD3 and anti-CD28 antibodies (eBioscience, San Diego, CA, USA). After 72 hours of stimulation, activated T cells were harvested by centrifugation and processed for flow cytometry study or frozen at -20ºC for subsequent RNA isolation.

extract_protocol: Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany).

treatment_protocol: anti-CD3 and anti-CD28 in vitro stimulation for 72 hours

tag: group

value: Healthy Control


title: STROMA D11 EVE 2


title: Activated_Tcells_PsoriasisControl7

description: Control7 sample


title: HUG1N Control Rep2

description: Gene expression data from HuG-1 control cells.

source_name: HUG1N control cells


title: Caco2 Control Rep1

description: Gene expression data from Caco-2 control cells.

source_name: Caco2 control cells


title: HUG1N shRNA Rep1


title: HUG1N Control Rep1


title: STROMA D12 MORN 1


title: Activated_Tcells_PsoriasisControl5

description: Control5 sample


title: STROMA D11 EVE 1


title: Activated_Tcells_PsoriasisControl3

description: Control3 sample


title: STROMA D11 MORN 3

source_name: STROMA D11 MORN


title: Caco2 Control Rep2


title: Activated_Tcells_PsoriasisPatient17

description: Patient 17 sample

value: Psoriasis Patient


title: STROMA D11 MORN 2


title: Activated_Tcells_PsoriasisControl4

description: Control4 sample


title: Activated_Tcells_PsoriasisPatient15

description: Patient 15 sample


title: Activated_Tcells_PsoriasisPatient16

description: Patient 16 sample


title: Activated_Tcells_PsoriasisPatient14

description: Patient 14 sample


title: Activated_Tcells_PsoriasisControl2

description: Control2 sample


title: Activated_Tcells_PsoriasisControl1

description: Control1 sample


title: STROMA D11 MORN 1


title: Activated_Tcells_PsoriasisPatient11

description: Patient 11 sample


title: Activated_Tcells_PsoriasisPatient13

description: Patient 13 sample


title: CAM D16 MORN 1

source_name: CAM D16 MORN

value: CAM, distant to implantation


title: CAM D15 EVE 1

source_name: CAM D15 EVE


title: Activated_Tcells_PsoriasisPatient7

description: Patient 7 sample


title: Activated_Tcells_PsoriasisPatient5

description: Patient 5 sample


title: CAM D15 EVE 2


title: Activated_Tcells_PsoriasisPatient9

description: Patient 9 sample


title: Activated_Tcells_PsoriasisPatient12

description: Patient 12 sample


title: CAM D15 MORN 3

source_name: CAM D15 MORN


title: CAM D15 EVE 3


title: Activated_Tcells_PsoriasisPatient6

description: Patient 6 sample


title: Activated_Tcells_PsoriasisPatient10

description: Patient 10 sample


title: Activated_Tcells_PsoriasisPatient3

description: Patient 3 sample


title: Activated_Tcells_PsoriasisPatient1

description: Patient 1 sample


title: Activated_Tcells_PsoriasisPatient8

description: Patient 8 sample


title: Activated_Tcells_PsoriasisPatient4

description: Patient 4 sample


title: Activated_Tcells_PsoriasisPatient2

description: Patient 2 sample


title: CAM D15 MORN 1


title: miR-199a-5p input rep 2

city: Herston

first: Nicole

last: Cloonan

state: Queensland

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer Medical Research Institute

description: replicate 2

data_processing: The data were preprocessed by Bioconductor lumi package (version 2.2.1). It was background adjusted, vst transformed and rsn normalized. Probes that did not have a detection p-value < 0.01 in all of the mock-transfected replicates were excluded from further analysis.

source_name: HEK293T cells

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

growth_protocol: HEK293T cells were grown in DMEM according to ATCC recommendations.

extract_protocol: Cells were harvested  24 hours post transfection, and the miRNAs and their bound targets were isolated using streptavidin myOne C1 Dynabeads. Beads were washed before RNA extraction using an RNeasy Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: 200pmols of synthetic biotin-labeled miRNA duplexes were transfected into HEK293T cells using HiPerFect Transfection Reagent (Qiagen).

tag: transfection molecule

tag: pull-down


title: miR-199a-5p rep 2

description: replicate 2

value: pull-down


title: miR-199a-5p input rep 3

description: replicate 3


title: miR-199a-5p input rep 1

description: replicate 1


title: miR-424-3p input rep 2

description: replicate 2


title: CAM D15 MORN 2


title: CAM D13 EVE 2

source_name: CAM D13 EVE


title: RN2_TRMPV_Rluc_dox_96h_1

city: Cold Spring Harbor

first: Christopher

middle: R

last: Vakoc

state: NY

address: 1 Bungtown Rd

institute: Cold Spring Harbor Lab

hyb_protocol: according to the manufacturer's instructions on Mouse Gene ST 1.0 GeneChips

data_processing: Data was processed by RMA in R software

label: Biotin

organism: Mus musculus

source_name: MLL-AF9/NrasG12D TtTMPV murine cell line

label_protocol: The cDNA was then fragmented and terminally labeled with biotin, using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix, Santa Clara, CA)

growth_protocol: Murine AML cell lines (RN2) transduced with indicated constructs were cultured in RPMI1640 supplement with 10% FBS and penicillin/streptomycin

extract_protocol: total RNA was isolated by using RNeasy Mini Kit (QIAGEN, #74104)

treatment_protocol: Before RNA preparation, murine AML cell lines (RN2) transduced with indicated constructs were treated with 1ug/ml doxycycline to induce shRNA expression for 96h. TRMPV_Rluc is negative control shRNA targeting Renilla luciferase.

tag: cell line background

value: MLL-AF9/NrasG12D TtTMPV

tag: cell type

value: Acute myeloid leukemia cells (AML)

tag: transfected with

value: TRMPV_Rluc (negative control shRNA)

tag: treated with

value: 1ug/ml doxycycline for 96h


title: miR-424-3p rep 2

description: replicate 2


title: RN2_TRMPV_Brg1sh_4935_dox_96h_2

scan_protocol: according to the manufacturer's instructions on Mouse Gene ST 1.0 GeneChips

source_name: MLL-AF9/NrasG12D murine cell line

value: TRMPV_Brg1sh (shRNA targeting Brg1)


title: CAM D14 MORN 1

source_name: CAM D14 MORN


title: RN2_TRMPV_Rluc_dox_96h_2


title: CAM D14 EVE 2

source_name: CAM D14 EVE


title: miR-424-3p rep 1

description: replicate 1


title: miR-199a-5p rep 3

description: replicate 3


title: RN2_TRMPV_Brg1sh_3364_dox_96h_1


title: RN2_TRMPV_Brg1sh_4935_dox_96h_1


title: RN2_TRMPV_Brg1sh_3364_dox_96h_2


title: CAM D14 EVE 1


title: RN2_TRMPV_Rluc_dox_96h_3


title: CAM D13 EVE 1


title: miR-424-3p input rep 1

description: replicate 1


title: miR-424-3p rep 3

description: replicate 3


title: CAM D14 MORN 2


title: RN2_TRMPV_Brg1sh_3232_dox_96h_2


title: miR-424-3p input rep 3

description: replicate 3


title: CAM D13 MORN 2

source_name: CAM D13 MORN


title: miR-199a-5p rep 1

description: replicate 1


title: CAM D13 MORN 1


title: RN2_TRMPV_Brg1sh_3232_dox_96h_1


title: CAM D13 EVE 3


title: D458 cell line, treated by JQ1 (form inactive)

first: Rameen

last: Beroukhim

state: MA

address: 450 Brookline Av

department: Cancer Biology

institute: DANA-FARBER CANCER INSTITUTE

description: Gene expression data from patient-derived medulloblastoma cell line D458, treated by JQ1R

hyb_protocol: Following fragmentation, 1.4ug ug of cDNA were hybridized for 16 hr at 45C on Human Gene 1.0 st Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed using GenePattern (The Broad Institute) using Affymetrix default analysis settings and RMA as normalization method.

source_name: patient-derived cell line D458

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: MB002 and MB004 cells were maintained in culture media with 1:1 Dulbecco modified Eagle medium (Gibco) and neural stem cell media (Gibco) supplemented with B27 (Gibco) EGF (02653, Stem Cell), FGF (GF003, Millipore), Heparin (07980, Stem Cell) and LIF (LIF1010, Millipore). D283, D458, D556 were maintained in Dulbecco modified Eagle medium (Gibco) supplemented with 10% FBS (100106, Benchmark) and 1% penicillin–streptomycin with 1% glutamine (Gibco).

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

treatment_protocol: Cell lines were treated with JQ1R or JQ1S, 1μM for 24 hours

tag: tissue origin

value: pediatric medulloblastoma

tag: treatment

value: JQR 1 uM for 24 hours


title: CAM D14 EVE 3


title: CAM D12 EVE 1

source_name: CAM D12 EVE


title: D458 cell line, treated by JQ1 (form active)

description: Gene expression data from patient-derived medulloblastoma cell line D458, treated by JQ1S

value: JQS 1 uM for 24 hours


title: CAM D14 MORN 3


title: CAM D12 MORN 1

source_name: CAM D12 MORN


title: MB004 cell line, treated by JQ1 (form inactive)

description: Gene expression data from patient-derived medulloblastoma cell line MB004, treated by JQ1R

source_name: patient-derived cell line MB005


title: CAM D13 MORN 3


title: CAM D11 EVE 2

source_name: CAM D11 EVE


title: CAM D11 EVE 3


title: D556 cell line, treated by JQ1 (form active)

description: Gene expression data from patient-derived medulloblastoma cell line D556, treated by JQ1S

source_name: patient-derived cell line D556


title: CAM D12 MORN 2


title: MB002 cell line, treated by JQ1 (form inactive)

description: Gene expression data from patient-derived medulloblastoma cell line MB002, treated by JQ1R

source_name: patient-derived cell line MB003


title: CAM D12 EVE 2


title: MB002 cell line, treated by JQ1 (form active)

description: Gene expression data from patient-derived medulloblastoma cell line MB002, treated by JQ1S

source_name: patient-derived cell line MB002


title: CAM D12 EVE 3


title: CAM D11 EVE 1


title: D283 cell line, treated by JQ1 (form active)

description: Gene expression data from patient-derived medulloblastoma cell line D283, treated by JQ1S

source_name: patient-derived cell line D283


title: MB004 cell line, treated by JQ1 (form active)

description: Gene expression data from patient-derived medulloblastoma cell line MB004, treated by JQ1S

source_name: patient-derived cell line MB004


title: D556 cell line, treated by JQ1 (form inactive)

description: Gene expression data from patient-derived medulloblastoma cell line D556, treated by JQ1R


title: CAM D11 MORN 2

source_name: CAM D11 MORN


title: CAM D11 MORN 1


title: CAM D10 2

source_name: CAM D10

value: CAM, pre tumour implantation


title: D283 cell line, treated by JQ1 (form inactive)

description: Gene expression data from patient-derived medulloblastoma cell line D283, treated by JQ1R


title: CAM D10 1


title: CAM D10 3


title: 09RDR424

status: Public on Dec 01 2013

type: genomic

city: Amsterdam

first: Rinske

last: Drost

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

description: aCGH data of KB1P mouse mammary tumor

hyb_protocol: Samples were hybridized and washed according to manufacturer's protocol (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf).

scan_protocol: Arrays were scanned with the MS 200 Microarray Scanner and the MS 200 Data Collection Software according to manufacturer's protocol (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf).

data_processing: Background correction and normalization was performed in the NimbleScan program according to manufacturer's protocol (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf).    Background correction and normalization was performed in the NimbleScan program according to manufacturer's protocol (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf).

molecule: genomic DNA

source_name: DNA derived from KB1P mouse mammary tumor

label_protocol: Tumor and spleen samples were labeled with Nimblegen dual-color DNA labeling kit according to manufacturer's protocol (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf).

extract_protocol: Genomic DNA of tumor and spleen samples was extracted by proteinase K lysis and organic extraction with phenol-chloroform.

value: Mammary tumor

tag: genotype

source_name: DNA derived from KB1P mouse spleen

value: Spleen


title: CAM D11 MORN 3


title: 09RDR303

description: aCGH data of KB1P mouse mammary tumor


title: 09RDR340

description: aCGH data of KB1P mouse mammary tumor


title: 09RDR186

description: aCGH data of KB1P mouse mammary tumor


title: 10RDR055

description: aCGH data of KB1P mouse mammary tumor


title: 09RDR266

description: aCGH data of KB1P mouse mammary tumor


title: 10RDR360

description: aCGH data of KB1P mouse mammary tumor


title: 09RDR131

description: aCGH data of KB1P mouse mammary tumor


title: 10RDR439

description: aCGH data of KB1P mouse mammary tumor


title: 09RDR328

description: aCGH data of KB1P mouse mammary tumor


title: 09RDR373

description: aCGH data of KB1P mouse mammary tumor


title: 10RDR373

description: aCGH data of KB1P mouse mammary tumor


title: 09RDR223

description: aCGH data of KB1P mouse mammary tumor


title: 09RDR202

description: aCGH data of KB1P mouse mammary tumor


title: 09RDR157

description: aCGH data of KB1P mouse mammary tumor


title: 09RDR255

description: aCGH data of KB1P mouse mammary tumor


title: 09RDR258

description: aCGH data of KB1P mouse mammary tumor


title: 09RDR163

description: aCGH data of KB1P mouse mammary tumor


title: 09RDR116

description: aCGH data of KB1P mouse mammary tumor


title: LMN-1 DamID rep1

city: Seville

first: Peter

last: Askjaer

address: UPO Carretera de Utrera km 1

institute: Centro Andaluz de Biología del Desarrollo

description:
LMN1
Methylated DNA

hyb_protocol: Amplified Dam methylated DNA was hybridized by the Roche Nimblegen Service Laboratory.

scan_protocol: Amplified Dam methylated DNA was scanned by the Roche Nimblegen Service Laboratory.

data_processing: Raw data were analyzed using MA2C software that normalized the log2 ratio (log2 [Dam::fusion/GFP::Dam control]) of each probe based on the probe behavior estimated by its GC content, and then smoothed the value by assigning the median across sliding windows of 300 bp. The resultant values are MA2C scores.

organism: Caenorhabditis elegans

source_name: GFP::Dam_1 (control)

label_protocol: Amplified Dam methylated DNA was labeled by the Roche Nimblegen Service Laboratory.

extract_protocol: DamID strains were synchronized from eggs prepared by hypochlorite treatment of gravid adults fed with OP50 E. coli and left to hatch overnight at 20ºC in S-medium. Then, from each strain, approximately 35000 L1 larvae were grown in 50mL S-medium containing GM119 E. coli. Cultures were grown with continuous agitation (180rpm) at 20ºC for 53 h. Worms were frozen at -80ºC until further processing. Methylated genomic DNA was purified and amplified from 30 mg worms. Briefly, 2.5μg of gDNA isolated with DNAeasy kit (Qiagen), was digested with 10 units DpnI (New England Biolabs) overnight in 10μL to cut at GAmTC sites. DpnI was inactivated (80ºC, 20 min) and then, gDNA was ligated to double-stranded adaptors with 5 units T4 DNA ligase (5U/μL, Roche) in a volume of 20μL. After inactivation of the ligase (65ºC, 10 min), DNA fragments were digested with 5 units DpnII (New England Biolabs) in a final volume of 80µl to cut unmethylated GATC sites thereby preventing PCR amplification of unmethylated gDNA. Methylated DNA was amplified using adaptor-specific primers. PCR reactions were performed using 1 µl PCR Advantage enzyme mix (50x) (Clontech), 10μL of DpnII digestion and the following program: (1) 68ºC 10 min, (2) 94ºC 1 min, (3) 65ºC 5 min, (4) 68ºC 15 min, (5) 94ºC 1 min, (6) 65ºC 1 min, (7) 68ºC 10 min, (8) Go to step 5 3x, (9) 94ºC 1 min, (10) 65ºC 1 min, (11) 68ºC 2 min, (12) go to step 9 20x. To achieve sufficient material, 2 PCR reactions from the same DpnII digestion were pooled and purified with Qiaquick PCR purification kit (Qiagen).

tag: developmetal stage

value: young adult

value: wild type

tag: strain

source_name: Dam::LMN-1_1 (experiment)

tag: developmental stage


title: 09RDR151

description: aCGH data of KB1P mouse mammary tumor


title: 09RDR146

description: aCGH data of KB1P mouse mammary tumor


title: LMN-1 DamID in lem-2 (tm1582) rep.2

description:
LMNlem2
Methylated DNA

source_name: GFP::Dam lem-2(tm1582)_2 (control)

source_name: Dam::LMN-1 lem-2(tm1582)_2 (experiment)


title: LMN-1 DamID in lem-2 (tm1582) rep.3

description:
LMNlem3
Methylated DNA

source_name: Dam::LMN-1 lem-2(tm1582_3) (experiment)

source_name: GFP::Dam lem-2(tm1582)_3 (control)


title: 09RDR145

description: aCGH data of KB1P mouse mammary tumor


title: mouse 1 hMeSeal brain 5hmC profile

city: Edinburgh

first: John

middle: Paterson

last: Thomson

address: Crewe Road

department: MRC Human Genetics Unit

institute: University of Edinburgh

hyb_protocol: Labelled samples were applied to NimbleGen Mouse DNA Methylation 2.1M Economy Whole-Genome Tiling Arrays (2/4) : GPL17802

scan_protocol: Arrays were scanned in house on Nimblegen scanner

data_processing: Normalised data after normalised within arrays (loess) and between arrays (sclae normalisation) resulting in log2(IP/input) scores for each probe

source_name: normal whole brain

label_protocol: Amplification of DNA samples was carried out commercially by NimbleGen, Iceland  (Cy5- (IP) or Cy3- (Input) labelled)

extract_protocol: Genomic DNA (1 µg), sonicated to yield a fragment distribution of approximately 200-500 bp, enriched by one of three techniques described in summary

tag: gender

value: M

tag: antibody

value: active motif hydroxymethlycollector kit

value: none (Input)


title: CAM D12 MORN 3

source_name: CAM D12 MORN

tag: tissue

value: CAM, distant to implantation


title: 10RDR570

description: aCGH data of KB1(5382stop)P mouse mammary tumor

source_name: DNA derived from KB1(5382stop)P mouse mammary tumor

source_name: DNA derived from KB1(5382stop)P mouse spleen


title: 10RDR618


title: LMN-1 DamID in emr-1 (gk119) rep.3

description:
LMNemr3
Methylated DNA

source_name: GFP::LMN-1 emr-1(gk119)_3 (control)

source_name: Dam::LMN-1 emr-1(gk119)_3 (experiment)


title: LMN-1 DamID in lem-2 (tm1582) rep.1

description:
LMNlem1
Methylated DNA

source_name: GFP::Dam lem-2(tm1582)_1 (control)

source_name: Dam::LMN-1 lem-2(tm1582)_1 (experiment)


title: LMN-1 DamID rep3

description:
LMN3
Methylated DNA

source_name: GFP:Dam_3 (control)


title: EMR-1 DamID rep2

description:
EMR2
Methylated DNA

source_name: Dam::EMR-1_2 (experiment)

source_name: GFP:Dam_5 (control)


title: EMR-1 DamID rep1

description:
EMR1
Methylated DNA

source_name: GFP::Dam_4 (control)

source_name: Dam::EMR-1_1 (experiment)


title: mouse 1 HmeDIP brain 5hmC profile

value: active motif 5hmC antibody (cat#39769)


title: mouse 2 hMeSeal brain 5hmC profile


title: EMR-1 DamID rep3

description:
EMR3
Methylated DNA

source_name: GFP::Dam_6 (control)

source_name: Dam::EMR-_3 (experiment)


title: 11RDR012


title: 10RDR657


title: 10RDR665


title: mouse 2 HmeDIP liver 5hmC profile

source_name: normal whole liver


title: LMN-1 DamID in emr-1 (gk119) rep.2

description:
LMNemr2
Methylated DNA

source_name: Dam::LMN-1 emr-1(gk119)_2 (experiment)

source_name: GFP::Dam emr-1(gk119)_2 (control)


title: 10RDR223


title: 11RDR001


title: mouse 1 hMeSeal liver 5hmC profile


title: mouse 2 HmeDIP brain 5hmC profile

source_name: normal whole brain


title: LMN-1 DamID rep2

description:
LMN2
Methylated DNA

source_name: Dam::LMN-1_2 (experiment)

source_name: GFP::Dam_2 (control)


title: 10RDR200

source_name: DNA derived from KB1(5382stop)P mouse mammary tumor

source_name: DNA derived from KB1(5382stop)P mouse spleen


title: 10RDR157


title: 10RDR088


title: 10RDR099


title: 10RDR069


title: 09RDR213


title: 10RDR567


title: 09RDR310


title: 10RDR042


title: 09RDR296


title: mouse 1 HmeDIP liver 5hmC profile


title: 09RDR263


title: 09RDR250


title: mouse 2 hMeSeal liver 5hmC profile


title: 10RDR501

description: aCGH data of KB1(185stop)P mouse mammary tumor

source_name: DNA derived from KB1(185stop)P mouse mammary tumor

source_name: DNA derived from KB1(185stop)P mouse spleen


title: 10RDR536


title: 10RDR670


title: 10RDR686


title: 10RDR660


title: mouse 1 JBP brain 5hmC profile

value: Zymo research Quest 5hmC Enrichment Kit


title: 10RDR687


title: 10RDR691


title: 10RDR091


title: 10RDR154


title: 10RDR041


title: P-ID2 replicate 1

last: van Galen

address: 4 Blackfan Circle

department: Hematology

institute: Brigham and Women's Hospital / Broad Institute of MIT and Harvard

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Scanned on a BeadArray™ Reader using BeadScan software (v3.2).

data_processing: The data were normalized using quantile normalization in R (v2.12.1).

source_name: CB derived HSPC

label_protocol: standard Illumina protocol.

growth_protocol: Lineage depleted CB cells were transduced and expanded for 10 days in liquid TSGF6 culture conditions and injected into immune-deficient NSG mice.

extract_protocol: RNA was extracted from 2,000-10,000 sorted HSPCs using Trizol (Life Technologies).

treatment_protocol: Lineage depleted CB cells were transduced with P-CTRL or P-ID2 lentivirus and injected into immune-deficient NSG mice. After 8.5 weeks, HSPCs were isolated.

value: P-ID2 transduced

value: CB derived HSPC

tag: sample type

value: isolated from xenografted mouse BM


title: 09RDR321


title: P-ID2 replicate 3


title: 10RDR155


title: P-ID2 replicate 2


title: 10RDR011


title: 10RDR649


title: 10RDR002


title: 09RDR409


title: 10RDR175


title: 09RDR108


title: P-CTRL replicate 3

value: P-CTRL transduced


title: 10RDR683


title: 09RDR275


title: 10RDR013


title: P-CTRL replicate 2


title: 13871799

city: Lund

first: Rolf

last: Søkilde

address: Scheelevägen 2

department: Department of Oncology

country: Sweden

institute: Lund University, Sweden

hyb_protocol: The Hy3 and Hy5 labeled RNA samples were mixed, and co-hybridized to miRCURY™ LNA Arrays v.Dx10 and v.11 (Exiqon, Vedbæk, Denmark), which contain Tm normalized capture probes targeting miRNAs from human, mouse and rat , as registered in miRBase v.19.0 at the Sanger Institute (22) . Hybridization was carried out overnight for 16 hours at 65 °C in a Tecan HS4800 hybridization station (Tecan, Männedorf, Switzerland).

scan_protocol: After washing and drying, the microarray slides were scanned under ozone free conditions (ozone level < 2.0 ppb to minimize bleaching of the fluorescent dyes) in a G2565BA Microarray Scanner System, (Agilent, Santa Clara, CA). The resulting images were quantified using Imagene v. 8.0 (BioDiscovery, El Segundo, CA), and both automatic quality control (flagging of poor spots by the software) as well as manual, visual inspection was performed to ensure the highest possible data quality.

data_processing: All low-level analyses were carried out in the R environment, including importing and pre-processing of the data using the LIMMA package (http://bioconductor.org). Mean pixel intensities were used to calculate signal (foreground) spot intensities, and median pixel intensities were applied to estimate background intensity. After excluding flagged spots from the analysis, the “normexp” background correction method, with offset=10 was applied (23). For intra-slide normalization, the global Lowess (LOcally Weighted Scatterplot Smoothing) regression algorithm was applied, and log2 ratios of four intra-slide replicates were averaged. All expression data were deposited in the Rosetta Resolver (Rosetta Biosoftware, UK) data management and analysis system.

source_name: Pancreas

label_protocol: For microarray analysis, we applied a common reference design, where the reference sample contains a mixture of total RNA representing all tissue types in the study. This allows for both one- and two-channel data analysis, as described in detail by Søkilde et al. (21).  In the current study, we applied the two-channel ratio analysis, as this permits comparison across different array versions. 1 µg of total RNA from each sample was labeled using the miRCURY™ LNA microRNA Power labeling Kit (Exiqon, Vedbæk, Denmark) following a two-step protocol: First, Calf Intestinal Alkaline Phosphatase (CIAP) was applied to remove terminal 5’phosphates, and next, fluorescent labels were attached enzymatically to the 3’-end of the microRNAs. Sample specific RNA was labeled with Hy3 (green) fluorophore, while the common reference RNA pool was labeled with the Hy5 (red).

extract_protocol: Total RNA was extracted from 20µm FFPE sections with the High Pure miRNA Isolation Kit (Roche Applied Science, Mannheim, Germany) according to the manufacturer’s instructions. After elution in 40µl RNase free water, the RNA concentration (A260 nm) and purity (A260/280 and A260/230 ratios) were assessed with a Nanodrop ND-1000 spectrophotometer (Thermo Scientific, Wilmington DE). The RNA was stored at -80 C until further analysis.

value: Pancreas

source_name: Reference

value: mix of all tissues


title: 13871764

source_name: Colorectal

value: Colorectal


title: 13871798


title: 13865707


title: 13871751


title: 13871746


title: 13871761


title: iPSC-derived NPC-Affected-samp6-rep3

city: San Diego

first: Eric

last: Scott

state: California

address: 9500 Gilman Dr.

department: School of Medicine

institute: UC San Diego

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

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

data_processing:
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
The naming convention for pair files changed in between a few of the samples resulting in minor change in file names. The files were generated and processed in the same way.

source_name: NPC-Affected-samp6-rep3, Adenosine 10 uM + AICAr 500 uM

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

growth_protocol: NPCs are grwon in DMEM/F12 + 0.5XN2 + 0.5XB27 + 20ng/ul bFGF

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

treatment_protocol: For samples treated with adenosine: 10 uM adenosine was added for 7h and then substituted with normal growing medum for 7h more. For adenosine+AICAr treamtent: 10 uM adenosine was added for 7h and then substituted with 500 uM AICAr containing medium for 7h more

tag: individual

value: patient with pontocerebellar hypoplasia

value: iPSC derived Neural progenitor cells (NPC)

tag: sample

tag: replicate

value: Male

tag: disease state (phenotype)

value: Affected

value: Adenosine 10 uM + AICAr 500 uM


title: 13897391


title: 13897390


title: 13871742


title: 13871775


title: 13871738


title: 13865713


title: 13871838


title: 13871776

source_name: Ovary

value: Ovary


title: 13871855

source_name: Prostate

value: Prostate


title: 13871851


title: 13871842


title: 13865712


title: 13865691


title: 13865695

source_name: GIST

value: GIST


title: iPSC-derived NPC-Affected-samp5-rep3

source_name: NPC-Affected-samp5-rep3, Adenosine 10 uM

tag: cell type

value: Adenosine 10 uM


title: LMN-1 DamID in emr-1 (gk119) rep.1

description:
LMNemr1
Methylated DNA

source_name: GFP:Dam emr-1(gk119)_1 (control)

value: young adult

source_name: Dam::LMN-1 emr-1(gk119)_1 (experiment)


title: iPSC-derived NPC-Affected-samp6-rep2

source_name: NPC-Affected-samp6-rep2, Adenosine 10 uM + AICAr 500 uM


title: iPSC-derived NPC-Affected-samp5-rep2

source_name: NPC-Affected-samp5-rep2, Adenosine 10 uM


title: 13871768

source_name: Germ cell tumor

value: Germ cell tumor


title: iPSC-derived NPC-Wildtype-samp1-rep3

source_name: NPC-Wildtype-samp1-rep3, non-treated

value: unaffected parent

value: Female

value: Wildtype

value: non-treated


title: iPSC-derived NPC-Affected-samp4-rep1

source_name: NPC-Affected-samp4-rep1, non-treated


title: iPSC-derived NPC-Affected-samp4-rep3

source_name: NPC-Affected-samp4-rep3, non-treated


title: iPSC-derived NPC-Wildtype-samp2-rep3

source_name: NPC-Wildtype-samp2-rep3, Adenosine 10 uM


title: iPSC-derived NPC-Affected-samp5-rep1

source_name: NPC-Affected-samp5-rep1, Adenosine 10 uM


title: iPSC-derived NPC-Affected-samp4-rep2

source_name: NPC-Affected-samp4-rep2, non-treated


title: iPSC-derived NPC-Wildtype-samp3-rep2

source_name: NPC-Wildtype-samp3-rep2, Adenosine 10 uM + AICAr 500 uM


title: 13871780

source_name: Reference

value: mix of all tissues


title: iPSC-derived NPC-Wildtype-samp3-rep3

source_name: NPC-Wildtype-samp3-rep3, Adenosine 10 uM + AICAr 500 uM


title: iPSC-derived NPC-Wildtype-samp3-rep1

source_name: NPC-Wildtype-samp3-rep1, Adenosine 10 uM + AICAr 500 uM


title: iPSC-derived NPC-Wildtype-samp1-rep2

source_name: NPC-Wildtype-samp1-rep2, non-treated


title: iPSC-derived NPC-Wildtype-samp1-rep1

source_name: NPC-Wildtype-samp1-rep1, non-treated


title: iPSC-derived NPC-Wildtype-samp2-rep2

source_name: NPC-Wildtype-samp2-rep2, Adenosine 10 uM


title: iPSC-derived NPC-Wildtype-samp2-rep1

source_name: NPC-Wildtype-samp2-rep1, Adenosine 10 uM


title: P-CTRL replicate 1

source_name: CB derived HSPC

value: P-CTRL transduced

value: CB derived HSPC

value: isolated from xenografted mouse BM


title: iPSC-derived NPC-Affected-samp6-rep1

source_name: NPC-Affected-samp6-rep1, Adenosine 10 uM + AICAr 500 uM

value: patient with pontocerebellar hypoplasia

value: iPSC derived Neural progenitor cells (NPC)

value: Male


title: 13871737

source_name: Urothelial carcinoma

value: Urothelial carcinoma


title: 13897411


title: 13871741


title: 13871767


title: 13871774


title: 13897392

source_name: Pancreas

value: Pancreas


title: 13871791


title: 13865666


title: 13871801


title: 77_patient_DNA_during_season

city: Linkoping

first: Colm

middle: Eamonn

last: Nestor

address: KEF, Hälsuniversitetet

institute: Linkoping University

description:
CS_77P_DNA_DS
during pollen season

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

data_processing: BeadStudio software v3.2 and R programming language

label: Cy5 and Cy3

source_name: CD4+ T-cells

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using an Allprep DNA/RNA Mini Kit (Qiagen), and DNA quantity assessed by picogreen fluorometry. Subsequently, DNA was bisulfite converted, amplified, fragmented and hybridized to an Illumina HumanMethylation450 BeadChip and scanned according to the manufacturer’s instructions. Patient and control samples were randomized across microarray slides.

tag: Sex

value: male

tag: status

value: patient

tag: season

value: during pollen season

value: CD4+ T-cells


title: 13897406


title: 13871793


title: 13871802


title: 13871740


title: 13897398


title: 13871835

source_name: Ovary

value: Ovary


title: 40_healthy_DNA_outside_season

description:
CS_40H_DNA_AS
outside pollen season

value: healthy

value: outside pollen season


title: 40_healthy_DNA_during_season

description:
CS_40H_DNA_DS
during pollen season


title: 13865694


title: 74_patient_DNA_during_season

description:
CS_74P_DNA_DS
during pollen season


title: 13871847


title: 13871759


title: 77_patient_DNA_outside_season

description:
CS_77P_DNA_AS
outside pollen season


title: 13865690


title: 13871854


title: 13871750

source_name: Melanoma

value: Melanoma


title: 13897405

value: mix of all tissues


title: 28_healthy_DNA_during_season

description:
CS_28H_DNA_DS
during pollen season

value: female


title: 13871850

source_name: Lymphoma

value: Lymphoma


title: 75_patient_DNA_during_season

description:
CS_75P_DNA_DS
during pollen season


title: 13871848


title: 13897408


title: 13871840


title: 13871846


title: 13871853

source_name: Lung - adenocarcinoma

value: Lung - adenocarcinoma


title: 28_healthy_DNA_outside_season

description:
CS_28H_DNA_AS
outside pollen season


title: 74_patient_DNA_outside_season

description:
CS_74P_DNA_AS
outside pollen season


title: 13871849


title: 13871789


title: 11_healthy_DNA_during_season

description:
CS_11H_DNA_DS
during pollen season


title: 24_healthy_DNA_outside_season

description:
CS_24H_DNA_AS
outside pollen season


title: 72_patient_DNA_during_season

description:
CS_72P_DNA_DS
during pollen season


title: 11_healthy_DNA_outside_season

description:
CS_11H_DNA_AS
outside pollen season


title: 57_patient_DNA_outside_season

description:
CS_57P_DNA_AS
outside pollen season


title: 73_patient_DNA_during_season

description:
CS_73P_DNA_DS
during pollen season


title: 57_patient_DNA_during_season

description:
CS_57P_DNA_DS
during pollen season


title: 24_healthy_DNA_during_season

description:
CS_24H_DNA_DS
during pollen season


title: 13871852

source_name: Kidney

value: Kidney


title: 75_patient_DNA_outside_season

description:
CS_75P_DNA_AS
outside pollen season


title: 32_healthy_DNA_during_season

description:
CS_32H_DNA_DS
during pollen season


title: 38_healthy_DNA_during_season

description:
CS_38H_DNA_DS
during pollen season


title: 13871836

source_name: Reference


title: 76_healthy_DNA_during_season

description:
CS_76H_DNA_DS
during pollen season


title: 32_healthy_DNA_outside_season

description:
CS_32H_DNA_AS
outside pollen season


title: 71_patient_DNA_during_season

description:
CS_71P_DNA_DS
during pollen season


title: 80_healthy_DNA_during_season

description:
CS_80H_DNA_DS
during pollen season


title: 38_healthy_DNA_outside_season

description:
CS_38H_DNA_AS
outside pollen season


title: 02_patient_DNA_during_season

description:
CS_02P_DNA_DS
during pollen season


title: 13871757


title: 13871753


title: 72_patient_DNA_outside_season

description:
CS_72P_DNA_AS
outside pollen season


title: 13871769


title: POL 4h 3

city: Columbus

first: Ramiro

last: Garzon

address: 460 12th street

institute: Ohio State University

hyb_protocol: Labeled targets from 5 μg of total RNA was used for hybridization on each OSU-CCC  miRNA microarray custom version 4, containing  393 mouse, 409 humans and  962 ultraconserved sequences in quadruplicate. All probes on these microarrays are 40-mer oligonucleotides spotted by contacting technologies and covalently attached to a polymeric matrix. The microarrays were hybridized in 6× SSPE (0.9 M sodium chloride/60 mM sodium phosphate/8 mM EDTA, pH 7.4)/30% formamide at 25°C for 18 h, washed in 0.75× TNT (Tris·HCl/sodium chloride/Tween 20) at 37°C for 40 min, and processed by using direct detection of the biotin-containing transcripts by Streptavidin-Alexa647 conjugate

scan_protocol: Processed slides were scanned by using a PerkinElmer ScanArray XL5K Scanner with the laser set to 635 nm, at power 80 and PMT 70 settings, and a scan resolution of 10 μm.

data_processing: miRNA microarray images were analyzed using GENEPIX PRO. Average values of the replicate spots of each miRNA were background subtracted; log2-transformed and normalized using quantiles.

source_name: Acute myelogenous leukemia cell line

label_protocol: Five micrograms of total RNA were separately added to reaction mix in a final volume of 12 μl, containing 1 μg of [3′-(N)8-(A)12-biotin-(A)12-biotin-5′] oligonucleotide primer. The mixture was incubated for 10 min at 70°C and chilled on ice. With the mixture remaining on ice, 4 μl of 5× first-strand buffer, 2 μl of 0.1 M DTT, 1 μl of 10 mM dNTP mix, and 1 μl of SuperScript II RNaseH- reverse transcriptase (200 units/μl) was added to a final volume of 20 μl, and the mixture was incubated for 90 min in a 37°C water bath. After incubation for first-strand cDNA synthesis, 3.5 μl of 0.5 M NaOH/50 mM EDTA was added into 20 μl of first-strand reaction mix and incubated at 65°C for 15 min to denature the RNA/DNA hybrids and degrade RNA templates. Then, 5 μl of 1 M Tris·HCI (pH 7.6, Sigma) was added to neutralize the reaction mix, and labeled targets were stored in 28.5 μl at -80°C until chip hybridization.     Five micrograms of total RNA were separately added to reaction mix in a final volume of 12 μl, containing 1 μg of [3′-(N)8-(A)12-biotin-(A)12-biotin-5′] oligonucleotide primer. The mixture was incubated for 10 min at 70°C and chilled on ice. With the mixture remaining on ice, 4 μl of 5× first-strand buffer, 2 μl of 0.1 M DTT, 1 μl of 10 mM dNTP mix, and 1 μl of SuperScript II RNaseH- reverse transcriptase (200 units/μl) was added to a final volume of 20 μl, and the mixture was incubated for 90 min in a 37°C water bath. After incubation for first-strand cDNA synthesis, 3.5 μl of 0.5 M NaOH/50 mM EDTA was added into 20 μl of first-strand reaction mix and incubated at 65°C for 15 min to denature the RNA/DNA hybrids and degrade RNA templates. Then, 5 μl of 1 M Tris·HCI (pH 7.6, Sigma) was added to neutralize the reaction mix, and labeled targets were stored in 28.5 μl at -80°C until chip hybridization.

growth_protocol: The human AML cell lines OCI-AML3 was cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum. Cell lines were harvested during the log-phase of growth and seeded at a density of 0.2×106 cells/mL.

extract_protocol: Total RNA was extracted with miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: OCI-AML3 cells were treated with 100 ng/mL SDF-1α or 250 nM POL6326 (a CXCR4 antagonist, Allschwil, Switzerland) up to 8hour. total RNA was extracted at specific time points (0,1,  2, 4, and 8 h), The 0 time point are untreated cells and are used as controls.

tag: cell line

tag: treatment

tag: time point

value: 4 hour


title: POL 4h 2


title: 13871752


title: 13871731


title: POL 8h 2

value: 8 hour


title: POL 8h 1


title: POL 8h 3


title: 71_patient_DNA_outside_season

description:
CS_71P_DNA_AS
outside pollen season


title: 13871756


title: 73_patient_DNA_outside_season

description:
CS_73P_DNA_AS
outside pollen season


title: 02_patient_DNA_outside_season

description:
CS_02P_DNA_AS
outside pollen season


title: 13871745


title: POL 2h 2

value: 2 hour


title: 13897395


title: 13897397


title: 80_healthy_DNA_outside_season

description:
CS_80H_DNA_AS
outside pollen season


title: POL 1h 3

value: 1 hour


title: 13865684


title: 13871730


title: 13897401


title: HepG2_Z0_2

city: Setagaya

first: Kazuhiko

last: Nakabayashi

state: Tokyo

department: Department of Maternal-Fetal Biology

country: Japan

institute: National Research Institute for Child Health and Development

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using iScan array scanner (illumina) using standard setting.

data_processing: GenomeStudio V2011.1 was used to determine the methylation level at each CpG site as beta value. Normalization to internal controls and background subtraction were applied to determine normalized average beta values.

label_protocol: Standard Illumina protocol

growth_protocol: HepG2 cells were maintained at 37oC under an atmosphere of 95% air and 5% CO2 in DMEM containing 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/ml streptomycin.

extract_protocol: Genomic DNA was extracted using  the AllPrep DNA/RNA mini kit (Qiagen).

treatment_protocol: HepG2 cells were cultured under the presence (1000 μM) or absence of zebularine for 72 h.

value: hepatocellular carcinoma cells

tag: batch


title: POL 2h 3


title: 13865683


title: POL 1h 1


title: 13871766


title: POL 2h 1


title: 13897399


title: SDF-1α 8h 3

value: SDF-1α 100 ng/ml

value: 8 hours


title: HepG2_Z0_3


title: 76_healthy_DNA_outside_season

description:
CS_76H_DNA_AS
outside pollen season

value: male

value: CD4+ T-cells


title: POL 1h 2


title: HepG2_Z0_1


title: 13897388


title: SDF-1α 8h 1


title: SDF-1α 8h 2


title: SDF-1α 4h 3

value: 4 hours


title: SDF-1α 4h 2


title: 13865718

source_name: EG - junction

value: EG - junction


title: 13865679


title: SDF-1α 2h 2

value: 2 hours


title: SDF-1α 2h 1


title: 13865682

value: mix of all tissues


title: SDF-1α 2h 3


title: HepG2_Z1000_2

source_name: HepG2_1000 μM zebularine for 72 h

tag: treated with

value: 1000 μM zebularine for 72 h


title: 13871778

source_name: Colorectal

value: Colorectal


title: SDF-1α 4h 1


title: 13871765


title: 13871763


title: HepG2_Z1000_1


title: SDF-1α 1h 2


title: SDF-1α 1h 3


title: 13871762


title: SDF-1α 1h 1


title: Control 3


title: Control 2


title: 13871758


title: POL 4h 1


title: Control 1


title: HepG2_Z1000_3


title: 13897404


title: 13865716


title: 13865700


title: 13865688


title: 13865723


title: 13871747


title: 13871734


title: 13865678


title: 13865687


title: Culture 2 - time 48 min

city: Hørsholm

first: Christian

middle: Bille

last: Jendresen

address: Kogle Allé 6

country: Denmark

institute: Technical University of Denmark

hyb_protocol: Hybridization according to Agilent protocol. Agilent 8x15k custom microarray G2509F

scan_protocol: Agilent Technologies Scanner G2505C. Agilent's Feature Extraction software.

data_processing: Quantile normalization (R Bioconductor package preprocessCore)

organism: Lactococcus cremoris subsp. cremoris MG1363

source_name: Bacterial whole RNA

label_protocol: Labelling according to Agilent protocol using random hexamer and Cy3

growth_protocol: Cells were grown in chemically defined SA medium containing 1% glucose and a limited amount of hypoxanthine.

extract_protocol: Culture was quickly chilled in glass on ice-water. Phenol extraction.

tag: culture

value: 48 min


title: Culture 2 - time 55 min

value: 55 min


title: 13897402

source_name: Cholangiocarcinoma

value: Cholangiocarcinoma


title: 13865669


title: Culture 2 - time 79 min

value: 79 min


title: 13865675


title: Culture 2 - time 35 min

value: 35 min


title: Culture 2 - time 63 min

value: 63 min


title: Culture 2 - time 94 min

value: 94 min


title: 13865720


title: Culture 2 - time 0 min

value: 0 min


title: Culture 1 - time 101 min

value: 101 min


title: Culture 1 - time 91 min

value: 91 min


title: Culture 1 - time 81 min

value: 81 min


title: 14115105

hyb_protocol: The Hy3 and Hy5 labeled RNA samples were mixed, and co-hybridized to miRCURY™ LNA Arrays v.Dx10 and v.11 (Exiqon, Vedbæk, Denmark), which contain Tm normalized capture probes targeting miRNAs from human, mouse and rat , as registered in miRBase v.19.0 at

scan_protocol: After washing and drying, the microarray slides were scanned under ozone free conditions (ozone level < 2.0 ppb to minimize bleaching of the fluorescent dyes) in a G2565BA Microarray Scanner System, (Agilent, Santa Clara, CA). The resulting images were qu

data_processing: All low-level analyses were carried out in the R environment, including importing and pre-processing of the data using the LIMMA package (http://bioconductor.org). Mean pixel intensities were used to calculate signal (foreground) spot intensities, and med

label_protocol: For microarray analysis, we applied a common reference design, where the reference sample contains a mixture of total RNA representing all tissue types in the study. This allows for both one- and two-channel data analysis, as described in detail by Søkild

extract_protocol: Total RNA was extracted from 20µm FFPE sections with the High Pure miRNA Isolation Kit (Roche Applied Science, Mannheim, Germany) according to the manufacturer’s instructions. After elution in 40µl RNase free water, the RNA concentration (A260 nm) and pur


title: 14115104


title: 13871744


title: 14115103


title: pG-106a~363-2

city: Aurora

first: Layne

last: Dylla

state: CO

department: Pathology

institute: University of Colorado Anschutz Medical Campus

description: Sk-ES-1 pG-106a-2

hyb_protocol: Samples were hybridized using the Gene Atlas Microarray System (Affymetrix) hybridization chamber; 20 hours at 48 C

scan_protocol: Samples were scanned and imaged using the Gene Atlas Microarray System Fludics and Imaging equipment (Affymetrix)

data_processing: CEL files were processed in Partek Genomic Suite using RMA Quantile normalization; intensity values were scaled by log2 transformation

source_name: Sk-ES-1 stable pG-106a~363 cell lines

label_protocol: Fragmented ssDNA was labeled with the Affymetrix WT Terminal Labeling and Hybridization kit according to the instructions, using Affymetrix proprietary biotinylated labeling reagent.

growth_protocol: Sk-ES-1 cells were grown in DMEM 10% FBS media under standard tissue culture practices. Cells were stably transduced with the designated miRNA sponge and maintained under 0.5ug/ml puromycin selection for 5-7 days prior to harvesting for RNA

extract_protocol: Total RNA was harvested using the RNEasy mini kit (Qiagen). 100ng total RNA per sample was used for array analysis

treatment_protocol: Sk-ES-1 cells were stably transduced with either the control CXCR4 miRNA sponge or the miR-106a~363 blocking miRNA sponge

value: Ewing Sarcoma cell lines

value: Sk-ES-1 stable pG-106a~363 cell lines


title: Culture 1 - time 64 min

value: 64 min


title: pG-106a~363-3

description: Sk-ES-1 pG-106a-3


title: Culture 1 - time 25 min

value: 25 min


title: S. pimpinellifolium, population 1592, drought treatment, rep 4

city: Memphis

first: Takuya

last: Nakazato

state: Tennessee

address: 3774 Walker Avenue

department: Biological Sciences

institute: The University of Memphis

hyb_protocol: The purified and labeled aRNA was fragmented and hybridized to the Affymetrix Tomato Genome Arrays overnight in Affymetrix 450 hybridization oven. The chips were washed, stained on Affymetrix Fluidics Station 450 in the following day.

scan_protocol: Chips were scanned with Affymetrix Genechip scanner 3000.

data_processing: Arrays were normalized using the dChip software with the default setting using P1597D2 as a baseline array, which had the median probe intensity.

organism: Solanum pimpinellifolium

source_name: lateral root tissue, drought treatment

label_protocol: 100 ng of total RNA was biotin-labeled using the Affymetrix Genechip IVT Express kit (Affymetrix) following the manufacturer’s instructions.

growth_protocol: Plants were grown in commercial garden soil  with natural lighting at a temperature range of 22-30oC until they started to form flower buds.

extract_protocol: Total RNA was extracted from tomato root tissue by grinding to a powder in liquid nitrogen using a modified protocol of Griffiths et al. (1999, J Exp Bot 50:793).

treatment_protocol: Control plants were watered to keep the soil moist at all times. Drought plants were watered until the soil is fully hydrated and left unwatered until all leaves showed sign of wilting. This cycle was repeated three times.

tag: organism

value: S. pimpinellifolium

value: lateral root tissue

tag: population

value: population 1592

value: drought treatment


title: 14115102

tag: tissue

value: mix of all tissues


title: pG-CXCR4-3

description: Sk-ES-1 pG-CXCR4-3

source_name: Sk-ES-1 stable pG-CXCR4 cell lines

value: Sk-ES-1 stable pG-CXCR4 cell lines


title: pG-106a~363-1

description: Sk-ES-1 pG-106a-1


title: S. pimpinellifolium, population 1630, drought treatment, rep 4

value: population 1630


title: 14115099


title: 14115101


title: S. pimpinellifolium, population 1630, control treatment, rep 4

source_name: lateral root tissue, control treatment

value: control treatment


title: 14115097


title: 14115100


title: Culture 1 - time 48 min

value: 48 min


title: S. lycopersicum, population 2789, drought treatment, rep 4

organism: Solanum lycopersicum

value: S. lycopersicum

value: population 2789


title: Culture 1 - time 37 min

value: 37 min


title: 14115094


title: 13871772

value: Colorectal


title: pG-CXCR4-2

description: Sk-ES-1 pG-CXCR4-2

value: Ewing Sarcoma cell lines


title: 14115091


title: S. lycopersicum, population 2789, control treatment, rep 4


title: 14115098


title: S. pimpinellifolium, population 1597, drought treatment, rep 4

value: population 1597


title: pG-CXCR4-1

description: Sk-ES-1 pG-CXCR4-1


title: S. pimpinellifolium, population 1592, control treatment, rep 2


title: 14115095


title: S. lycopersicum, population 1421, control treatment, rep 4

value: population 1421


title: 14115096


title: 14115093


title: S. lycopersicum, population 2618, control treatment, rep 4

value: population 2618


title: 14115087


title: S. pimpinellifolium, population 1592, drought treatment, rep 2

value: S. pimpinellifolium


title: S. pimpinellifolium, population 1592, control treatment, rep 3

value: lateral root tissue


title: S. pimpinellifolium, population 1592, drought treatment, rep 3

value: population 1592


title: 14115090


title: 14059841

source_name: Pancreas

value: Pancreas


title: S. pimpinellifolium, population 1592, drought treatment, rep 1

value: drought treatment


title: 14034242

value: Lung - adenocarcinoma

value: mix of all tissues


title: 14115089


title: 14059685

source_name: Urothelial carcinoma

value: Urothelial carcinoma


title: 14034243


title: 14035238


title: S. pimpinellifolium, population 1592, control treatment, rep 1

value: control treatment


title: 14059689

value: EG - junction


title: 14059873


title: 14059870


title: S. pimpinellifolium, population 1630, drought treatment, rep 3

value: population 1630


title: S. lycopersicum, population 1421, drought treatment, rep 4

value: S. lycopersicum


title: S. pimpinellifolium, population 1630, control treatment, rep 2


title: S. pimpinellifolium, population 1630, control treatment, rep 1


title: S. pimpinellifolium, population 1597, control treatment, rep 3


title: 14059787

value: Kidney


title: S. pimpinellifolium, population 1597, control treatment, rep 1


title: S. pimpinellifolium, population 1630, control treatment, rep 3


title: 14091246


title: Culture 2 - time 19 min

value: 19 min


title: S. pimpinellifolium, population 1597, control treatment, rep 2

value: population 1597


title: 14091245


title: 14115075

source_name: Ovary

value: Ovary


title: 14115074


title: S. lycopersicum, population 2618, drought treatment, rep 4

value: population 2618


title: S. pimpinellifolium, population 1630, drought treatment, rep 1

value: S. pimpinellifolium


title: S. pimpinellifolium, population 1630, drought treatment, rep 2

value: lateral root tissue


title: 14115073


title: 14115071


title: S. pimpinellifolium, population 1597, drought treatment, rep 1


title: 14115068


title: S. lycopersicum, population 2789, control treatment, rep 3

value: population 2789


title: 14115070

value: Colorectal


title: S. pimpinellifolium, population 1597, drought treatment, rep 2

value: drought treatment


title: S. lycopersicum, population 2789, control treatment, rep 2


title: S. lycopersicum, population 2789, drought treatment, rep 3


title: S. lycopersicum, population 2789, control treatment, rep 1


title: 14115063


title: 14115064


title: 14115067


title: S. lycopersicum, population 1421, control treatment, rep 3

value: population 1421


title: 14115061

value: mix of all tissues


title: S. pimpinellifolium, population 1597, drought treatment, rep 3


title: 14115060


title: S. lycopersicum, population 1421, control treatment, rep 2


title: S. lycopersicum, population 1421, control treatment, rep 1


title: S. lycopersicum, population 2789, drought treatment, rep 1


title: 14115058


title: 14115052


title: S. lycopersicum, population 1421, drought treatment, rep 2


title: S. lycopersicum, population 1421, drought treatment, rep 1


title: 14115081


title: 14115083

value: Pancreas


title: 14115084


title: S. lycopersicum, population 2618, control treatment, rep 3

value: control treatment


title: S. lycopersicum, population 2618, drought treatment, rep 2


title: S. lycopersicum, population 2618, drought treatment, rep 3


title: 14115059


title: S. lycopersicum, population 1421, drought treatment, rep 3


title: 14115082

source_name: Prostate

value: Prostate


title: 14115079

source_name: Adrenal cortical neoplasm

value: Adrenal cortical neoplasm


title: S. lycopersicum, population 2618, control treatment, rep 1

value: S. lycopersicum


title: 14115086


title: 14059849


title: S. lycopersicum, population 2789, drought treatment, rep 2


title: 14034071


title: S. lycopersicum, population 2618, control treatment, rep 2


title: 14115077

value: Cholangiocarcinoma


title: S. lycopersicum, population 2618, drought treatment, rep 1


title: Lame 42

city: Nouzilly

first: Joel

last: Gautron

address: UR83 Recherches avicoles

country: France

institute: INRA

description: Twenty micrograms of total RNA from various regions of oviduct were used to produce fluorescently labelled cDNA with the Superscript Indirect cDNA Labelling System (Invitrogen, USA). After synthesis and purification, the cDNA was assessed with a Nanodrop ND 1000 (Nanodrop, Nyxor biotech, France). cDNA was used to perform fluorescent dye coupling reaction. The dye incorporation rate was assessed with a Nanodrop ND 1000. Only cDNA-probes with frequency of incorporation (Dye molecules/1000 bases) > 11.4 were used for hybridization.

hyb_protocol: All microarrays slides were prehybridized using 100 µL of DIG easy buffer (Roche) in humidified chambers for 1 hr at 42°C. Slides were then washed with distilled water for 10 min with mild agitation. The hybridization solution contained 80 µl of DIG easy buffer, 2.5 µl of yeast tRNA, 2.5 µl DNA salmon sperm (10µg/ µl) and 2 µl PolyA RNA (1µg/µl). An equal amount of Alexa 555- and Alexa 647-labelled cDNA probes from two samples was added to the mixture, which was denatured at 100°C for 2 min. The mixture of Alexa® 555 and Alexa 647® labeled samples was pipetted onto the slides, which were covered with a Lifter cover slips in hybridization chambers and the microarray hybridized for 16 hr at 42°C. The slides were washed in 0.2X saline sodium citrate (SSC) buffer and 0.1% sodium dodecyl sulfate (SDS) for 15 min at 42°C. The slides were washed a second time with 0.2x SSC for 15 min at room temperature. Finally, the slides were rinsed with distilled water and dried by centrifugation.

scan_protocol: Microarray slides were scanned at 532 nm for Alexa® 555 and 635 nm for Alexa® 647 using a GenePix 4000B microarray scanner. The GenePix Pro 6.0 software was used to acquire the fluorescent images, align the spots, quantify their intensity and finally export GenePix report (GPR) files containing spot intensity raw data. The GPR files were stored in the BioArray Software Environment (BASE) of SIGENAE (SystÃ¨me d'Information du projet d'Analyse des Genomes des Animaux d'Elevage) for further processing and analysis.

data_processing: The identification of differentially expressed genes was performed using anapuce package. Spot intensities were calculated using the median value that was logarithm transformed (log2). A normalization consisting of global locally-weighted regression (LOWESS) was applied on the overall intensity log ratio to remove the bias due to fluorescence incorporation. A block effect was also corrected by subtracting the median value of the block. Differential analysis was performed on data where at least four repeated expressions by gene were available. The gene variance was a mixture model by using the varmixt method. On both dataset, unilateral statistical t-test was performed according to varmixt method. Taking into account that all tests were simultaneous, P-values were adjusted by a Benjamini-Hochberg (BH) multiple testing procedures, to control False Discovery Rate to less than 0.05.

label: Alexa Fluor 647

source_name: Poule IsaBrown 19 stade 17h59

label_protocol: The methods for generating fluorescently labelled cDNA were performed according to the procedure recommended by the manufacturer (Invitrogen, USA). Twenty micrograms of total RNA from various regions of oviduct were used to produce fluorescently labelled cDNA with the Superscript Indirect cDNA Labelling System (Invitrogen, USA). After synthesis and purification, the cDNA was assessed with a Nanodrop ND 1000 (Nanodrop, Nyxor biotech, France). cDNA was used to perform fluorescent dye coupling reaction. The experimental design used a dye switch procedure in which half of samples were labelled with Alexa 555 fluorescent probe and the other half using Alexa 647 (Fisher Scientific BioBLock, France). The dye incorporation rate was assessed with a Nanodrop ND 1000. Only cDNA-probes with frequency of incorporation (Dye molecules/1000 bases) > 11.4 were used for hybridization.

extract_protocol: Total RNA was extracted from frozen tissue samples using a commercial kit (RNeasy mini kit, Qiagen, France) and simultaneously treated with DNase (RNase-free DNase set, Qiagen, France) according to the manufacture procedure. RNA concentrations were measured by absorption at 260 nm. The integrity of RNA was electrophoretically evaluated on a 1% agarose gel and using an agilent 2100 bio analyzer (Agilent technology, USA). Only RNA samples with a 28S/18S ratio > 1.3 were considered as good enough quality and used for hybridization experiments.

value: white isthmus

label: Alexa Fluor 555

value: magnum


title: 14059845

source_name: Reference


title: 14059840


title: Lame 22

source_name: Poule IsaBrown 29 stade 18h03


title: 14059867


title: 14059837


title: Lame 44

source_name: Poule IsaBrown 51 stade 17h44


title: 14034069


title: 14059809


title: 14059863


title: Lame 25

source_name: Poule Isabrown 56 stade 17h50


title: Lame 28

source_name: Poule IsaBrown 23 stade 17h51


title: 14034282


title: 14034286


title: 32D-CEBPalpha-ER-MUT_T4h_rep1

city: Rotterdam

first: Erdogan

last: Taskesen

address: dr. molewaterplein 50

institute: Erasmus University Medical Center (EMC)

description: cellline", "species", "construct", "32D", "mus musculus", "CEBPalpha-ER-MUTANT

hyb_protocol: Labeling, hybridization to Affymetrix Mouse Promoter 1.0R arrays, staining, washing and scanning were performed according to the manufacturer’s recommendations.

data_processing: The probe-intensity values are normalized according model-based analysis of tiling-arrays for chip-chip (MAT) using default parameters

label: GeneChip® WT Double-Stranded DNA Terminal Labeling Kit

source_name: 32D cell line, CEBPalpha-ER-mutant, estradiol induced

extract_protocol: Chromatin immunoprecipitation (ChIP) was carried out according to a protocol from Affymetrix (Santa Clara, CA, USA), modified as follows. Fifty to 100 million cells were cultured in the presence of 1 μM 17β-estradiol (E2) (Sigma-Aldrich, St. Louis, MO, USA) for 4 hours. Protein and DNA were cross-linked by incubation with formaldehyde (Sigma-Aldrich; final concentration 1%) for 10 minutes, followed by quenching with glycine (Sigma-Aldrich; final concentration 0.125 M) for 5 minutes. Cells were pelleted, washed twice with ice cold phosphate buffered saline (PBS) and three times with lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.5% IGEPAL (Sigma-Aldrich), 1 mM PMSF), and then resuspended in pre-IP dilution buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 1 mM CaCl2, 4% IGEPAL, 1 mM phenylmethanesulfonyl fluoride solution (PMSF; Sigma-Aldrich)). Material was sonicated in a total volume of 1 ml using a Soniprep 150 device (Machine Shop Equipment (MSE), London, UK) for 6 cycles of 20 seconds pulse/90 seconds rest at an amplitude of 6 microns. An aliquot was de-crosslinked, purified and subjected to ethidium bromide agarose gel electrophoresis to ensure the predominant presence of fragments of 100-1000 nucleotides. Cellular debris was removed by pelleting. Ten % of the supernatant was kept aside as input control, and the remainder was used for immunoprecipitation (IP) after addition of 5 volumes of IP dilution buffer (20 mM Tris-Hcl, 2 mM EDTA, 1% Triton X-100 (Roche, Basel, Switzerland), 150 mM NaCl and fresh protease inhibitor (Roche)). Chromatin was pre-cleared by incubation for 30 minutes at 4°C with pre-equilibrated protein G-coupled magnetic beads (Dynabeads; Invitrogen, Carlsbad, CA, USA). Immunoprecipitation was carried out overnight at 4°C using 20 μg rabbit polyclonal IgG anti-ERα (Santa Cruz sc543X). Samples were incubated for 2.5 hours at room temperature in the presence of two hundred μl of pre-equilibrated magnetic beads. The beads were washed twice with ChIP wash 1 (20 mM Tris-HCl, 2 mM EDTA, 1% Triton X-100, 150 mM NaCl and 1 mM PMSF), once with ChIP wash 2 (20 mM Tris-HCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS, 500 mM NaCl and 1 mM PMSF), once with ChIP wash 3 (10 mM Tris-HCl, 1 mM EDTA, 0.25 M LiCl, 0.5% IGEPAL and 0.5% deoxycholate), and twice with TE. Protein/DNA complexes were eluted into 400 μl elution buffer (25 mM Tris-HCl, 10 mM EDTA, 0.5% SDS) by heating at 65°C for 30 minutes. Cross-links were reversed overnight at 65°C in the presence of 20 μl proteinase K (20 mg/ml; New England Biolabs, Ipswich, MA, USA). The non-immunoprecipitated 10% input control sample was processed similarly. De-crosslinked material was purified using a Qiagen (Valencia, CA, USA) PCR Purification Kit and eluted into 20 μl buffer EB.

treatment_protocol: estradiol incubation

tag: genotype/variation

value: CEBPalpha-ER-mutant

value: 32D myeloid progenitor

tag: antibody

value: anti-ER


title: 32D-CEBPalpha-ER-MUT_T4h_rep2

scan_protocol: Labeling, hybridization to Affymetrix Mouse Promoter 1.0R arrays, staining, washing and scanning were performed according to the manufacturer’s recommendations.


title: Lame 17

source_name: Poule IsaBrown 24 stade 17h57


title: 32D-ER_T4h_rep1

description:
cellline", "species", "construct", "32D", "mus musculus", "ER
In this experiment we have performed chromatin IP in 32D cells containing a CEBPalpha-ER construct, as a control 32D cells with only an ER contruct was used. With an anti-ER antibody the genomic regions bound by either CEBPalpha-ER or ER were immunoprecipitated. All regions also bound by the ER construct itself are considered not to be CEBPalpha targets. Only regions bound by CEBPalpha-ER and not by ER are considered to be potential CEBPalpha targets.
10% input samples were taken for all 5 experments, however, we did not put these input samples on chip, since the comparison between CEBPalpha-ER and ER will not be much influenced by their input samples.

source_name: 32D cell line, ER, estradiol induced

label_protocol: Labeling, hybridization to Affymetrix Mouse Promoter 1.0R arrays, staining, washing and scanning were performed according to the manufacturer’s recommendations.

value: ER


title: 32D-ER_T4h_rep2


title: 14059799


title: 14059803


title: 14034280


title: Lame 13

source_name: Poule IsaBrown 38 stade 17h57


title: 14034065


title: 6474981015_L

city: Los Angeles

first: Kate

last: Lawrenson

state: CA

address: 1450 Biggy Street

department: Preventive Medicine

institute: University of Southern California

description: NOF+EOC

hyb_protocol: Samples were profiled using Illumina HumanHT-12 v3 Expression BeadChip microarrays at the USC Epigenome Core facility.

scan_protocol: USC Epigenome Core facility

data_processing: The data were background corrected with RMA and normalized with variance stabilizing normalization in R using the readIllumina function of the Bioconductor beadarray package. Normalized data are log2 vsn-normalized.

source_name: NOFs co-cultured with epithelial ovarian cancer cells

label_protocol: USC Epigenome Core facility

extract_protocol: QIAgen RNA extraction kit (RNeasy)

treatment_protocol: Stromal cells were cultured alone, or were co-cultured with normal epithelial cells or with epithelial ovarian cancer cells

value: Normal ovarian fibroblasts co-cultured with epithelial ovarian cancer cells


title: Lame 15

source_name: Poule IsaBrown 8 stade 18h01


title: 32D-CEBPalpha-ER_T4h_rep1

description:
cellline", "species", "construct", "32D", "mus musculus", "CEBPalpha-ER
In this experiment we have performed chromatin IP in 32D cells containing a CEBPalpha-ER construct, as a control 32D cells with only an ER contruct was used. With an anti-ER antibody the genomic regions bound by either CEBPalpha-ER or ER were immunoprecipitated. All regions also bound by the ER construct itself are considered not to be CEBPalpha targets. Only regions bound by CEBPalpha-ER and not by ER are considered to be potential CEBPalpha targets.
10% input samples were taken for all 5 experments, however, we did not put these input samples on chip, since the comparison between CEBPalpha-ER and ER will not be much influenced by their input samples.

source_name: 32D cell line, CEBPalpha-ER, estradiol induced

value: CEBPalpha-ER


title: 32D-CEBPalpha-ER_T4h_rep3


title: 32D-CEBPalpha-ER_T4h_rep2


title: 6474981015_K

description: NOF+IOSE

source_name: NOFs co-cultured with normal ovarian epithelial cells

value: Normal ovarian fibroblasts co-cultured with normal ovarian epithelial cells


title: 14034053

source_name: Pancreas


title: 6474981015_J

description: MSC+EOC

source_name: MSCs co-cultured with epithelial ovarian cancer cells

value: Mesenchymal stem cells co-cultured with epithelial ovarian cancer cells


title: 6474981015_H

source_name: Normal ovarian fibroblasts (NOFs) cultured alone (control)

value: Normal ovarian fibroblasts


title: 14059782

source_name: Ovary

value: Ovary

value: mix of all tissues


title: 14059783

value: Pancreas

source_name: Reference


title: 6474981015_I

description: MSC+IOSE

source_name: MSCs co-cultured with normal ovarian epithelial cells

value: Mesenchymal stem cells co-cultured with normal ovarian epithelial cells


title: Twin-N-iPSC

city: Geneva

first: Audrey

last: Letourneau

address: Rue Michel-Servet 1

department: Genetic Medicine and Development

country: Switzerland

institute: University of Geneva Medical School

description: Sample 1

hyb_protocol: Hybridization was done according the manufactor's procedure

scan_protocol: Fluorescence was scanned in a dual-laser scanner (Agilent DNA microarray scanner G2565CA)

data_processing: Images were extracted and analysed with Agilent Feature Extraction software (v9.5.3.1) and Workbench analysis software (v7.0) respectively

source_name: induced pluripotent stem cells

label_protocol: 1 µg of iPSC DNAs were processed according to the manufacturer’s protocol

extract_protocol: Total DNA was extracted using the QIAGEN Mini Blood according to the manufacturer’s protocol.

tag: disease

value: Normal

value: induced pluripotent stem cells

source_name: reference genomic DNA

tag: gender

value: female

tag: sample type

value: normal human genomic DNA

tag: reference dna vendor

value: Promega

tag: reference dna cat. #


title: 6474981015_G

source_name: Mesenchymal stem cells (MSCs) cultured alone (control)

tag: cell type

value: Mesenchymal stem cells


title: 6474981015_F

description: NOF+EOC


title: 14059722


title: 14059724


title: Twin-DS-iPSC

description: Sample 2

value: Trisomie 21


title: 6474981015_E

description: NOF+IOSE


title: 14034055


title: 6474981015_C

description: MSC+IOSE


title: P.alba_CONTROLvsUVB_T30h_rep4

city: Florence

first: Giovanni

last: Emiliani

address: via S. Bonaventura, 13

department: Dept. of Environmental and Forestry Technologies and Sciences

country: Italy

institute: University of Florence

description: Transcriptional profiling of UV-B response of Populus alba

hyb_protocol: Hybridisation was performed in an HS400 hybridisation station (Tecan, Reading, UK). The slides were washed for 1 min in pre-hybridisation buffer. The prepared probe was then added, and the slides hybridised for 16 hr at 42 °C with low agitation frequency. The slides were then washed 5 times for 1 min in each of WBI (1X SSC, 0.2% SDS), WBII (0.1X SSC, 0.1% SDS) and WBIII, and then for 1 min in H2O, and 1 min in 100% EtOH. The slides were dried with nitrogen gas

scan_protocol: The slides were scanned on a Genetix Aquire scanner (Genetix, Hampshire, UK) at 5 μm resolution. PMT settings were adjusted to equalise the channel intensities.

data_processing: The TIFF images were analysed using GenePixPro 5.1 (Axon Instruments, Union City, California). Spots were flagged as “bad” if the median signal intensity was equal to 65535 or if less than 150 µm in diameter. Images were also checked manually and miss-called spots were manually flagged as bad. A combination of custom functions and functions from within the LIMMA package were used to produce pre- and post-normalized quality control plots to ensure data quality. Background subtraction was achieved by removing the local median background intensity from the spot foreground median intensity. Background corrected data were then normalized using a print-tip LOWESS normalization, and spots with a ‘bad’ flag had a negative weighting factor of 0.1 applied to them. A cross-slide normalization was also applied to ensure consistency of scale. Normalized data were then filtered based on A value [(log2 R + log2 G)/2] to remove spots with low intensities in both channels (the threshold value for A was set to 8.0, equating to a raw intensity of 256)

organism: Populus alba

source_name: T30h bulked leaves of control replicate 4

label_protocol: Total RNA was primed with 2 µl of anchored oligo(dt)20 primer and reverse transcribed over night at 48 ºC with the Superscript™ reverse transcriptase system (Invitrogen, Paisley, UK) (aa-dUTP:dTTP, 4:1). cDNA was purified using a Qiagen PCR purification kit according to the manufacturers instructions. 35 µl 100 mM sodium acetate (pH 5.2) was then added to each purified and this then added to an aliquot of CyDye™ ester (Amersham, Buckinghamshire, UK). Cy3 and Cy5 were added to control and treatment respectively, and for nearly 50 % of the samples this orientation was reversed to account for any dye binding bias. The samples were gently agitated and then left in the dark at room temperature for 2 hours. Dye-coupled cDNA was purified using Qiagen PCR purification kit (Qiagen, Crawley, UK). The Cy3-labelled cDNA was purified according to the manufacturer’s protocol. The Cy5-labelled sample was treated the same and eluted into the same eppendorf tube as the corresponding Cy3-labelled sample, following randomised paring between control and treated samples. The total eluate containing 200 µl of Cy3-and-Cy5 coupled cDNA was concentrated down to 25 µl in a spin concentrator (Eppendorf Concentrator 5301, Eppendorf, Cambridge, UK). The dye-labelled cDNA target (25 µl) was denatured by the addition of 50 µl formamide, 25 µl of hybridisation buffer (Amersham, Buckinghamshire, UK) was added and the sample heated at 95 ºC for 1 minute and then chilled on ice.

growth_protocol: Plants were grown in a nursery for 1 year and then acclimated in the chambers for 2 week before the start of the UVB treatment; plants were randomized inside the chamber during the experiment to exclude position effect as well as swapped between the two chambers to avoid a chamber effect.

extract_protocol: Total RNA was extracted following Chang et al., 1993

treatment_protocol: Plants were treated for 12 hours with an UVBbe (UVB biologically effective radiation, Caldwell, 1971) supplementary dose of 6 kJ/m2/day (0.15 W/m2 at 100 cm from the lamps) and allowed to recover during the night. Growing conditions were as follow: temperature 25 °C during the day and 20 °C during the night, relative humidity 60%, CO2 concentration 350 ppm.

tag: Two years old micropropagated plants, rooted and grown in nursery for 1 year before the radiation treatment

source_name: T30h bulked leaves of UV-B treated replicate 4


title: 6474981015_D

description: MSC+EOC


title: 14059720


title: 14034051


title: 14059794


title: P.alba_CONTROLvsUVB_T30h_rep1

source_name: T30h bulked leaves of control replicate 1

source_name: T30h bulked leaves of UV-B treated replicate 1


title: 6474981015_A


title: 6474981015_B


title: 14034050


title: 14034046


title: 6303221029_K

description: NOF+IOSE


title: 14059780


title: 14034048


title: P.alba_CONTROLvsUVB_T30h_rep3

source_name: T30h bulked leaves of control replicate 3

source_name: T30h bulked leaves of UV-B treated replicate 3


title: 6303221029_I

description: MSC+IOSE


title: P.alba_CONTROLvsUVB_T30h_rep2

source_name: T30h bulked leaves of control replicate 2

source_name: T30h bulked leaves of UV-B treated replicate 2


title: 6303221029_H


title: 6303221029_J

description: MSC+EOC


title: 6303221029_G


title: 6303221029_L

description: NOF+EOC

source_name: NOFs co-cultured with epithelial ovarian cancer cells


title: 14034044


title: 14035240

source_name: Colorectal

value: Colorectal


title: 14059862

source_name: Pancreas


title: 14091263

source_name: Ovary


title: 14034049

source_name: Reference


title: 14034054


title: 14059738

source_name: Lung - adenocarcinoma

value: Lung - adenocarcinoma


title: 14059733


title: 14034045


title: 14059691


title: 14059701


title: 14034009


title: 14091113

source_name: Thyroid

value: Thyroid


title: 14091108


title: 14091111


title: 14091107


title: 14091109


title: 14091241

source_name: GIST

value: GIST


title: 14091101


title: 14034011


title: 14091240


title: 14059871


title: U937_Biological Replicate 2

city: Beijing

first: jing

last: wang

address: Tsinghu University

country: China

institute: Medical Systems Biology Research Center School of Medicine Tsinghua University

description:
Biological replicate 2,differentiation (treated ) vs normal(control)
U937_normal_cy3+differentiation_cy5(2).LSR

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: Intensity data was extracted from the TIFF images using LuxScanTM 3.0 software (CapitalBio Corp, Peking, China). The low-intensity spots were removed for which fewer than 30% of the signal pixels exceeded the median background plus two times its standard deviation.

source_name: U937 cells treated with TPA

label_protocol: 4μg of low-molecular-weight RNA was labeled with 500 ng 5'-phosphate-cytidyl-uridyl-cy3-3' (Dharmacon) with 2 units T4 RNA ligase (NEB). The labeling reaction was performed at 4℃ for 2 hours.

growth_protocol: All cells were cultured in a sterile incubator at 37˚C

extract_protocol: Total RNA samples were extracted from normal leukemia cells  and differentiated leukemia cells  using Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions. Low-molecuar-weight RNA derived from total RNA.

treatment_protocol: Before microarray analysis,differentiation of leukemia cells was induced by adding TPA (Sigma-Aldrich, St. Louis, USA) to a final concentration of 30 nM to the culture media and incubating the cells for 48 h.

tag: cell line

value: U937 leukemia cell line

tag: disease state

value: human monocyte lymphoma

tag: agent

value: TPA

source_name: U937 cells

value: untreated


title: U937_Biological Replicate 1(dye-swap)

description:
Dye-swap of Biological replicate 1,differentiation (treated ) vs normal(control)
U937_normal_cy5+differentiation_cy3(1).LSR


title: 14091239

value: mix of all tissues


title: U937_Biological Replicate 2(dye-swap)

description:
Dye-swap of Biological replicate 2,differentiation (treated ) vs normal(control)
U937_normal_cy5+differentiation_cy3(2).LSR


title: 14091031

source_name: Germ cell tumor

value: Germ cell tumor


title: KS patient 2

city: London

first: Charles

last: Mein

address: Charterhouse Square

department: Genome Centre

institute: Queen Mary University

hyb_protocol: Standard Illumina

scan_protocol: Standard Illumina

data_processing: Genome Studio, Data normalised with Quantile Normalisation

source_name: upper arm skin biopsies

label_protocol: Ambion Total Prep 96

extract_protocol: Total RNA was extracted using the RNeasy Fibrous Tissue Mini kit (Qiagen) and quantity and quality were measured on a Nanodrop spectrophotometer (Nanodrop, Wilmington, DE, U.S.A.).

value: woman

tag: age

value: 7 years

value: Kindler syndrome disease

value: homozygous nonsense mutation +/+ p.Glu616X

tag: origin

value: Indian


title: 14091030


title: U937_Biological Replicate 3

description:
Biological replicate 3,differentiation (treated ) vs normal(control)
U937_normal_cy3+differentiation_cy5(3).LSR


title: NHS 2


title: NHS 3

value: 19 years

value: Middle Eastern


title: K562_Biological Replicate 3(dye-swap)

description:
Dye-swap of Biological replicate 3,differentiation (treated ) vs normal(control)
K562_normal_cy5+differentiation_cy3(3).LSR

source_name: K562 cells

value: K562 leukemia cell line

value: chronic myeloid leukemia

source_name: K562 cells treated with TPA


title: KS patient 3

value: nonsense mutation +/+ p.Try616X

value: Omani


title: K562_Biological Replicate 2

description:
Biological replicate 2,differentiation (treated ) vs normal(control)
K562_normal_cy3+differentiation_cy5(2).LSR


title: NB4_Biological Replicate 1

description:
Biological replicate 1,differentiation (treated ) vs normal(control)
NB4_normal_cy3+differentiation_cy5(1).LSR

source_name: NB4 cells treated with TPA

value: NB4 leukemia cell line

value: acute promyelocytic leukemia

source_name: NB4 cells


title: NB4_Biological Replicate 1(dye-swap)

description:
Dye-swap of Biological replicate 1,differentiation (treated ) vs normal(control)
NB4_normal_cy5+differentiation_cy3(1).LSR

value: TPA


title: K562_Biological Replicate 2(dye-swap)

description:
Dye-swap of Biological replicate 2,differentiation (treated ) vs normal(control)
K562_normal_cy5+differentiation_cy3(2).LSR

value: untreated


title: 14035223

source_name: Adrenal cortical neoplasm

value: Adrenal cortical neoplasm

value: mix of all tissues


title: K562_Biological Replicate 3

description:
Biological replicate 3,differentiation (treated ) vs normal(control)
K562_normal_cy3+differentiation_cy5(3).LSR


title: HL-60_Biological Replicate 2

description:
Biological replicate 2,differentiation (treated ) vs normal(control)
HL-60_normal_cy3+differentiation_cy5(2).LSR

source_name: HL-60 cells treated with TPA

value: HL-60 leukemia cell line

value: acute myeloid leukemia

source_name: HL-60 cells


title: 14035221


title: 14035220


title: 14091027

value: Germ cell tumor


title: 14035226


title: 14091029


title: 14035225


title: 14035222


title: 14035224


title: 14035227


title: 14091028


title: NB4_Biological Replicate 3

description:
Biological replicate 3,differentiation (treated ) vs normal(control)
NB4_normal_cy3+differentiation_cy5(3).LSR


title: NB4_Biological Replicate 2(dye-swap)

description:
Dye-swap of Biological replicate 2,differentiation (treated ) vs normal(control)
NB4_normal_cy5+differentiation_cy3(2).LSR


title: NB4_Biological Replicate 2

description:
Biological replicate 2,differentiation (treated ) vs normal(control)
NB4_normal_cy3+differentiation_cy5(2).LSR


title: NB4_Biological Replicate 3(dye-swap)

description:
Dye-swap of Biological replicate 3,differentiation (treated ) vs normal(control)
NB4_normal_cy5+differentiation_cy3(3).LSR


title: NHS 1

value: woman

value: 22 years


title: U937_Biological Replicate 1

description:
Biological replicate 1,differentiation (treated ) vs normal(control)
U937_normal_cy3+differentiation_cy5(1).LSR

value: U937 leukemia cell line

value: human monocyte lymphoma


title: HL-60_Biological Replicate 3

description:
Biological replicate 3,differentiation (treated ) vs normal(control)
HL-60_normal_cy3+differentiation_cy5(3).LSR


title: HL-60_Biological Replicate 3(dye-swap)

description:
Dye-swap of Biological replicate 3,differentiation (treated ) vs normal(control)
HL-60_normal_cy5+differentiation_cy3(3).LSR


title: K562_Biological Replicate 1

description:
Biological replicate 1,differentiation (treated ) vs normal(control)
K562_normal_cy3+differentiation_cy5(1).LSR

value: K562 leukemia cell line


title: K562_Biological Replicate 1(dye-swap)

description:
Dye-swap of Biological replicate 1,differentiation (treated ) vs normal(control)
K562_normal_cy5+differentiation_cy3(1).LSR

value: chronic myeloid leukemia


title: HL-60_Biological Replicate 2(dye-swap)

description:
Dye-swap of Biological replicate 2,differentiation (treated ) vs normal(control)
HL-60_normal_cy5+differentiation_cy3(2).LSR


title: 14059684

source_name: Urothelial carcinoma

value: Urothelial carcinoma


title: 14059682


title: HL-60_Biological Replicate 1(dye-swap)

description:
Dye-swap of Biological replicate 1,differentiation (treated ) vs normal(control)
HL-60_normal_cy5+differentiation_cy3(1).LSR


title: 14033994


title: 14034001


title: 14059681


title: 14091253


title: 14034002


title: 14033992


title: 14033989


title: KS patient 1

value: Kindler syndrome disease

value: homozygous nonsense mutation +/+ p.Arg271X

value: Omani


title: 14034072

source_name: Pancreas

value: Pancreas


title: 14034070

source_name: Reference


title: 14059854


title: 14033988


title: HEK293 ALKBH7 induced replicate 3,  Illumina HumanMethylation27 BeadChip

city: Oslo

first: Leonardo

middle: A.

last: Meza-Zepeda

address: Ullernchausseen 70

department: Dept. of Tumor Biology

country: Norway

institute: The Norwegian Radium Hospital

hyb_protocol: Standard Ilumina hyb protocol

scan_protocol: Standard Ilumina scan protocol

data_processing: Data extraction and initial quality control of the bead summary raw data were performed using BeadStudio v3.1.0.0 and the Methylation module v1.9, both provided by Illumina.

label: Biotin and dinitrophenyl

label_protocol: Standard Ilumina label protocol

growth_protocol: HEL293 were grown in Dulbecco’s modified Eagle’s medium (DMEM) (Lonza) supplemented with 10 % tetracycline-free fetal bovine serum (FBS) (Clontech), 100 U/ml penicillin (Lonza), 100 U/ml streptomycin (Lonza), 2 mM L-glutamine (Lonza), 15 μg/ml blasticidin-S (Invitrogen) and 200 μg/ml hygromycin B.), at 37°C with 5 % CO2. All cells were split when reaching 80 % confluency.

extract_protocol: DNA was isolated using the  QIAamp DNA mini kit  from Qiagen.

tag: expression

value: ALKBH7 induced

value: Human Embryonic Kidney

tag: provider

value: Life Technologies

tag: catalog number


title: HEK293 ALKBH7 induced replicate 2,  Illumina HumanMethylation27 BeadChip


title: HEK293 ALKBH4 induced replicate 3,  Illumina HumanMethylation27 BeadChip

value: ALKBH4 induced


title: HEK293 ALKBH7 uninduced replicate 2,  Illumina HumanMethylation27 BeadChip

value: ALKBH7 uninduced


title: HEK293 ALKBH4 induced replicate 1,  Illumina HumanMethylation27 BeadChip


title: HEK293 ALKBH7 induced replicate 1,  Illumina HumanMethylation27 BeadChip


title: 14034068

tag: tissue

value: mix of all tissues


title: 14059844


title: 14059866


title: HEK293 ALKBH4 induced replicate 2,  Illumina HumanMethylation27 BeadChip


title: 14059808


title: HEK293 ALKBH4 uninduced replicate 3,  Illumina HumanMethylation27 BeadChip

value: ALKBH4 uninduced


title: HEK293 ALKBH7 uninduced replicate 1, Illumina HumanMethylation27 BeadChip


title: 14059838


title: 14059869


title: 14034283


title: HEK293 ALKBH7 uninduced replicate 3,  Illumina HumanMethylation27 BeadChip


title: 14034281


title: HL-60_Biological Replicate 1

description:
Biological replicate 1,differentiation (treated ) vs normal(control)
HL-60_normal_cy3+differentiation_cy5(1).LSR

value: HL-60 leukemia cell line

value: acute myeloid leukemia

value: TPA

value: untreated


title: 14059801


title: HEK293 ALKBH4 uninduced replicate 1,  Illumina HumanMethylation27 BeadChip


title: 14059797


title: 14059800


title: HEK293 ALKBH4 uninduced replicate 2,  Illumina HumanMethylation27 BeadChip


title: 14059786


title: 14059790


title: 14034064


title: 13333.p1

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

description:
Autism: affected individual diagnosed as autistic
Autism-sib: non-affected sibling with an autistic brother
P1: label for probands (i.e. autistic individuals) as described by the Simons foundation. Please note these should all be classified as "autism"
S1: label for controls (i.e. unaffected individuals with autistic brothers), also as described by the Simons foundation. Please note these should all be classified as "autism-sib"
The sites (fl, gv, hv, kc, kr, lu, oi, ox, pb, sb, vn, xm, xx) are designators of the collection site for the Simons trial. We are currently blinded to the actual location, but we have analyzed the data with site as a covariate to adjust for any potential site-specific influences so I thought we should include it in our public data submission.
Group designates the shipment batch that we received the samples from the biobank at Rutgers where Simons houses their specimens. These groups of samples were run in multiple experiments denoted by the Experiment variable. Finally, distribution denotes the shipment from Simons to the biobank at Rutgers. All these variables are potential covariates in analysis to ensure we adjusting for batch effects.

scan_protocol: Followed the manufacturer's (Illumina) specifications on either a BeadStation 500 or an iScan

data_processing: Avg beta (β), detection value, and signal for Probe A (unmethylated) and Probe B were exported from GenomeStudio v2010.3 Methylation Module 1.8.5. The manufacturer measures methylation through the beta (β) value calculated as probe B signal / (probe A signal + probe B signal + 100). Based on better reproducibility of the controls we calculated the methylation using a metric denoted beta prime (β') which is calculated as probe B signal / (probe A signal + probe B signal).

label: biotin nucleotide or dinitrophenyl labeled

source_name: leukocyte

label_protocol: A single nucleotide extension was labeled either with biotin or dinitrophenyl according to the manufacturer's (Illumina) specifications

extract_protocol: DNA was extracted by the Rutgers University Cell and DNA Repository RUCDR

treatment_protocol: Extracted DNA was bisulfite treated with the Zymo bisulfite kit according the manufacturer's specifications

tag: sample id

value: Male

tag: sentrix id

tag: sentrix position

value: G

tag: experiment

tag: group

tag: family

tag: distribution

tag: site

value: xx

tag: cpea dx

tag: age at collection (months)

tag: ethnicity

value: white

value: leukocyte


title: 14059781

city: Lund

first: Rolf

last: Søkilde

institute: Lund University, Sweden

source_name: Ovary

value: Ovary


title: 13324.p1

hyb_protocol: Followed the manufacturer's (Illumina) specifications

tag: gender

value: H

tag: cell type


title: 13358.p1

value: L

value: hv


title: 13300.p1

value: D


title: 14091297


title: 14091298


title: 14034287


title: 14059721


title: 13317.s2

value: J

value: more-than-one-race


title: 13226.p1

value: kc

value: not-specified


title: 13319.p1

value: I


title: 13341.p1

value: asian


title: 13218.s1

value: vn


title: 13317.p1

value: Male

value: F


title: 14091261

value: mix of all tissues


title: 13340.p1

value: E

value: xx

value: white


title: 14091262

value: Ovary


title: 13381.p1

value: H

value: xm

value: leukocyte


title: 13306.p1

value: hv


title: 13290.p1

value: lu

value: african-amer


title: 13204.s1

value: L


title: 13218.p1

value: D


title: 14091260


title: 13254.p1


title: 14091259


title: 13301.p1

value: G


title: 14091257


title: 14091258


title: 14091256


title: 13196.p1


title: 13195.p1

value: J

value: sb

value: more-than-one-race


title: 14091255

value: mix of all tissues


title: 14091254


title: 13166.p1

value: Male


title: 13283.p1

value: E


title: 13187.p1

value: I

value: white


title: 13165.p1

value: vn


title: 13216.p1


title: 13166.s1

value: K


title: 13151.p1

value: oi

value: leukocyte


title: 13159.p1

value: ox


title: 13174.p1


title: 14115076

source_name: Melanoma

value: Melanoma


title: 13193.p1

value: C

value: hv


title: 13180.p1

value: F

value: asian


title: 13135.p1

value: H

value: lu


title: 14115072

value: mix of all tissues


title: 13204.p1

value: Male

value: xm


title: 13169.p1

value: G

value: kc


title: 14115069


title: 13163.s1

value: D

value: white


title: 14115053


title: 14115062


title: 14091243


title: 13144.p1

value: oi


title: 13153.p1

value: E

value: leukocyte


title: 13096.p1

value: other


title: 13107.p1

value: L

value: fl


title: 14091237

source_name: Lymphoma

value: Lymphoma


title: 14091236


title: 13077.p1

value: B


title: 13064.p1

value: sb


title: Untagged GFP

city: San Francisco

first: Jose

middle: Christian

last: Perez

department: Microbiology and Immunology

institute: University of California, San Francisco

description:
control GFP
Comparison of IP/input in tagged strains to untagged cells immunoprecipitated with the same antibody.

hyb_protocol: The labeled DNA was purified with Zymo columns (Zymo Research). Equal amounts of ChIP and input DNAs (~3 µg each) were mixed and hybridized in a final volume of 500 µl containing Agilent hybridization buffer (Agilent), Agilent blocking agent (Agilent), and 50 µg of human COT1 DNA (Invitrogen). Arrays were hybridized in a hybridization oven for 40 h at 65 degrees C, and then washed with Agilent Oligo aCGH/ChIP-on-chip wash buffers (Agilent) as described by the manufacturer's protocols.

scan_protocol: Arrays were scanned on a GenePix 4000B scanner following manufacturer's protocol.

data_processing: Data normalized using global lowess as implemented in R.

organism: Candida albicans

source_name: ChIP DNA from untagged cells

label_protocol: Aminoallyl-dUTP (Ambion) was incorporated into 1-2 µg of ChIP and input DNA using Klenow (New England Biolabs) and random DNA nonamers. Dye coupling was carried out by incubating 4-5 µg of aminoallyl-dUTP-labeled ChIP and input DNAs with Cy5 or Cy3, respectively.

growth_protocol: Cells were grown in liquid YPD to logarithmic phase at 30 degrees C.

extract_protocol: Formaldehyde (1% final concentration) was added to 200 ml of Candida albicans cultures at OD600 ~0.5. After crosslinking (15 min), glycine (125 mM final concentration) was added to quench the reaction. Cells were washed twice with 1X TBS and lysed by vortexing for ~2h at 4 degrees C in a suspension containing glass beads. Chromatin was sheared in a Diagenode Bioruptor and immunoprecipitated with the respective antibody.

treatment_protocol: No treatment.

tag: chip antibody

value: GFP (Living Colors Polyclonal antibody raised in rabbit, Clontech, cat no. 632460, lot# 1105002)

source_name: Input DNA from untagged cells


title: 13050.p1

value: J

value: hv


title: 13120.p1

value: Male

value: C

value: more-than-one-race


title: 13111.p1

value: I


title: 13041.p1

value: lu

value: white


title: 13069.s1

value: A


title: 13163.p1

value: oi

value: leukocyte


title: 13096.s1

value: F

value: other


title: GFP-LYS144

description:
LYS144
Comparison of IP/input in tagged strains to untagged cells immunoprecipitated with the same antibody.

source_name: LYS144 ChIP DNA from GFP-LYS144 cells

source_name: Input DNA from GFP-LYS144 cells


title: 14091177

value: Lymphoma

value: mix of all tissues


title: 14091235


title: 14091176


title: 13039.p1

value: K

value: kc

value: asian


title: 14091173


title: 14091172


title: 13064.s1

value: sb


title: 13039.s1

value: Male

value: H


title: 13038.p1

value: C


title: 14091171


title: 14091170


title: 12976.p1

value: E

value: hv

value: more-than-one-race


title: 13018.p1

value: fl

value: white


title: 12969.p1

value: xm

value: leukocyte


title: 14034241

source_name: Lung - adenocarcinoma

value: Lung - adenocarcinoma


title: 12984.p1

value: A


title: 13001.p1

value: G


title: 13069.p1

value: lu


title: 13034.p1

value: B