title: 24 h post 5 cGy + 2 Gy radiation, biological rep1 (Agilent)

description:
microRNA expression data from AG 1522 human fibroblasts 24 h after 5 cGy + 2 Gy X-ray radiation (12 h interval).
AG_5p2Gy_24h_1


title: Blood03

status: Public on Jul 31 2014

type: genomic

city: daejeon

first: Jonglyul

last: Park

address: 52, Eoeun-dong, Yuseong-gu

department: Medical genomics

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description:
Blood
Sample3

hyb_protocol: Amplified DNA was hybridized on the Infinium HumanMethylation 450 BeadChip (Illumina), following the Illumina Infinium HD Methylation protocol.

scan_protocol: The arrays were imaged using the Illumina HiScan SQ scanner, and image processing and extraction of intensity data were performed according to Illumina’s instructions.

data_processing: Each methylation signal was used to compute the β value, which is a quantitative measure of DNA methylation ranging from 0 (for completely unmethylated cytosines) to 1 (for completely methylated cytosines) (Bibikova et al., 2006).

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood

label_protocol: standard Illumina protocol

extract_protocol: Genomic DNA (1 µg) from each sample was bisulfite converted using the EZ DNA methylation kit (Zymo Research), and 200 ng of the converted DNA was used for amplification.

tag: sample type

value: Blood

tag: tissue


title: Nestin GFP Postive, biological rep 1

status: Public on Jul 30 2014

type: RNA

city: New Brunswick

first: John

last: Langenfeld

state: NJ

address: One Robert Wood Johnson Place

department: Surgery

country: USA

institute: Rutgers-RWJMS

description: Gene expression data from H1299 cells Postive for Nestin promoter/GFP

hyb_protocol: The labelled a RNA was hybridized at 50 degree C for 16 hrs

scan_protocol: DNA microarrays (human onearray version 4.2) were scanned using GenePix 4000B Scanner.

data_processing: The normalized (dChip)  signal inentsity values were compared for differential expression.

molecule: total RNA

source_name: H1299 cells transfected with stable Nestin promoter/GFP reporter vectors

label_protocol: Cy3 labelled a RNA was prepared according to the standard microarray labelling protocol from 1 ug total RNA.

growth_protocol: H1229 lung cancer cell lines were cultured in DMEM (Sigma Aldrich) with 5% fetal bovine serum for 24 hrs.

extract_protocol: Total RNA was extarcted using RNeasy mini kit (QIAgen) according to the manufacturer's instructions.

treatment_protocol: H1299 cells were stably transfected with the Oct4 promoter/GFP or Nestin promoter/GFP reporter vectors.

tag: cell line


title: LK2_siSOX2

city: Miaoli County

first: Shih Sheng

last: Jiang

address: No. 35 Keyan Road, Zhunan County

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: We used GeneSpringGX 11 for quantile normalization. The base of log transformation applied to the quamtile normalization was 2.

label: biotin

source_name: Human lung squamous cell carcinoma cell line LK2, pooled siRNA sequences of SOX2.

label_protocol: Biotinylated cRNA were prepared with the TargetAmp Nano-G Bioti- aRNA Labeling kit (Epicentre) for Illumina arrays.

extract_protocol: Total RNA was extracted with QIAGEN RNeasy mini kit according to  protocol provided in the kit by the  manufacturer. Quality control was performed with Agilent Bioanalyser.

tag: treatment

value: SOX2 siRNA


title: 12 h post 5 cGy radiation, biological rep3 (Agilent)

city: Hefei

first: Wei

last: Han

state: Anhui

address: #155 Shushanghu Road

country: China

institute: Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences

description:
microRNA expression data from AG 1522 human fibroblasts 12 h after 5 cGy X-ray radiation.
AG_5cGy_12h_3

hyb_protocol: 100 ng Cy3-labeled RNA using the miRNA Complete Labeling and Hyb Kit (Agilent technologies, Santa Clara, CA, US) in the Hybridization Oven (Agilent technologies, Santa Clara, CA, US) at 55℃，20 rpm for 20 h according to the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent technologies, Santa Clara, CA, US) using the Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing: The raw data were normalized with quantile normalization to ensure comparability across samples.

source_name: Human skin fibroblast AG 1522 cells, 12 h after 5 cGy X-ray radiation

growth_protocol: Human skin fibroblast AG 1522 cells were cultured in modified α-MEM (Hyclone, Logan, US) supplemented with 20% fetal bovine serum (FBS) (Hyclone, Logan, US), 1% penicillin/streptomycin, 1% glutamine and 1% non-essential amino acids mix (Sigma-Aldrich, St. Louis, US). All cultures were grown in a humidified 5% CO2 atmosphere at 37℃. Prior to treatment, the confluence of cells obatined to 100%.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Then small molecular RNA was extracted using the mirVana miRNA Isolation Kit (Ambion, Austin, TX, US) following the manufacturer’s instructions.

treatment_protocol: The miRNA profiles for the 5 cGy5 cGy irradiation at 12 h after irradiation were examined.For the 2 Gy irradiation at 24 h after irradiation were examined.For the (5 cGy + 2 Gy) groups exposed to 5 cGy (priming dose) and then followed by 2 Gy (challenge dose), 24 h after application of the challenging dose were examined.

tag: cell type

value: skin fibroblast

value: 5 cGy X-ray radiation

tag: time


title: Nestin GFP Negative, biological rep 1

description: Gene expression data from H1299 cells negative for Nestin promoter/GFP

source_name: H1299 cells negative for Nestin promoter/GFP reporter vectors


title: 12 h post 5 cGy radiation, biological rep1 (Agilent)

description:
microRNA expression data from AG 1522 human fibroblasts 12 h after 5 cGy X-ray radiation.
AG_5cGy_12h_1

label_protocol: 100 ng Cy3-labeled RNA using the miRNA Complete Labeling and Hyb Kit (Agilent technologies, Santa Clara, CA, US) in the Hybridization Oven (Agilent technologies, Santa Clara, CA, US) at 55℃，20 rpm for 20 h according to the manufacturer’s instructions.


title: 24 h post 2 Gy radiation, biological rep3 (Agilent)

description:
microRNA expression data from AG 1522 human fibroblasts 24 h after 2 Gy X-ray radiation.
AG_2Gy_24h_3

source_name: Human skin fibroblast AG 1522 cells, 24 h after 2 Gy X-ray radiation

value: 2 Gy X-ray radiation


title: H520_siSOX2

source_name: Human lung squamous cell carcinoma cell line H520, pooled siRNA sequences of SOX2.


title: radiation sham, biological rep3 (Agilent)

description:
microRNA expression data from AG 1522 human fibroblasts after 0 Gy sham X-ray radiation.
AG_0Gy_0h_4

source_name: Human skin fibroblast AG 1522 cells, 0 Gy X-ray radiation

value: 0 Gy X-ray radiation

value: control


title: 12 h post 5 cGy radiation, biological rep2 (Agilent)

description:
microRNA expression data from AG 1522 human fibroblasts 12 h after 5 cGy X-ray radiation.
AG_5cGy_12h_2


title: radiation sham, biological rep2 (Agilent)

description:
microRNA expression data from AG 1522 human fibroblasts after 0 Gy sham X-ray radiation.
AG_0Gy_0h_3


title: Blood04

description:
Blood
Sample4


title: Vaginal secretion04

description:
Vaginal secretion
Sample14

source_name: Vaginal secretion

value: Vaginal secretion


title: Blood02

description:
Blood
Sample2


title: Blood01

description:
Blood
Sample1


title: 24 h post 2 Gy radiation, biological rep1 (Agilent)

description:
microRNA expression data from AG 1522 human fibroblasts 24 h after 2 Gy X-ray radiation.
AG_2Gy_24h_1


title: 24 h post 2 Gy radiation, biological rep2 (Agilent)

description:
microRNA expression data from AG 1522 human fibroblasts 24 h after 2 Gy X-ray radiation.
AG_2Gy_24h_2


title: radiation sham, biological rep1 (Agilent)

description:
microRNA expression data from AG 1522 human fibroblasts after 0 Gy sham X-ray radiation.
AG_0Gy_0h_1


title: CD19-enriched CLL patient sample, patient #9211

city: South San Francisco

first: Ru-Fang

last: Yeh

state: CA

address: 1 DNA Way

institute: Genentech

description:
CD19-enriched CLL clinical sample
A0020413

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials per manufacturers recommendation. Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 (fluidics protocol FS450_0001).

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000 7G and Gene-Chip Operating Software v.1.3.0 to produce .CEL intensity files.

data_processing:
.CEL files were background adjusted, quantile normalized and summarized at the transcript level using only core probesets that mapped to RefSeq transcripts, by apt (Affymetrix Power Tool version 1.12.0) software that used the RMA algorithm.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.na29.hg18.probeset.csv

source_name: CLL clinical sample, CD19-enriched

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Pretreatment specimens from relapsed chronic lymphocytic leukemia patients

extract_protocol: CLL samples were positively enriched by magnetic cell sorting using CD19 microbeads and MACS columns (Miltenyi Biotec Ltd, Surrey, UK). Total RNA was isolated using Trizol (Invitrogen) and RNeasy kit (QIAGEN).

treatment_protocol: not applicable

tag: subject status

value: relapsed chronic lymphocytic leukemia (CLL) patient

tag: patient id

value: patient #9211

tag: binet stage

value: B

value: CD19-enriched CLL patient sample


title: CD19-enriched CLL patient sample, patient #9001

description:
CD19-enriched CLL clinical sample
A0020411

value: patient #9001


title: CD19-enriched CLL patient sample, patient #5304

description:
CD19-enriched CLL clinical sample
A0020408

value: patient #5304


title: CD19-enriched CLL patient sample, patient #7002

description:
CD19-enriched CLL clinical sample
A0020409

value: patient #7002

value: C


title: CD19-enriched CLL patient sample, patient #3904

description:
CD19-enriched CLL clinical sample
A0020406

value: patient #3904


title: CD19-enriched CLL patient sample, patient #3103

description:
CD19-enriched CLL clinical sample
A0020403

value: patient #3103


title: CD19-enriched CLL patient sample, patient #308

description:
CD19-enriched CLL clinical sample
A0020402

value: patient #308


title: CD19-enriched CLL patient sample, patient #9511

description:
CD19-enriched CLL clinical sample
A0020414

value: patient #9511


title: CD19-enriched CLL patient sample, patient #302

description:
CD19-enriched CLL clinical sample
A0020401

value: patient #302


title: CD19-enriched CLL patient sample, patient #8103

description:
CD19-enriched CLL clinical sample
A0020410

value: patient #8103


title: CD19-enriched CLL patient sample, patient #6606

description:
CD19-enriched CLL clinical sample
A0018820

value: patient #6606


title: CD19-enriched CLL patient sample, patient #3107

description:
CD19-enriched CLL clinical sample
A0020404

value: patient #3107


title: CD19-enriched CLL patient sample, patient #5301

description:
CD19-enriched CLL clinical sample
A0020407

value: patient #5301


title: CD19-enriched CLL patient sample, patient #9811

description:
CD19-enriched CLL clinical sample
A0020416

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #9811


title: CD19-enriched CLL patient sample, patient #3513

description:
CD19-enriched CLL clinical sample
A0018810

value: patient #3513

value: B


title: CD19-enriched CLL patient sample, patient #9023

description:
CD19-enriched CLL clinical sample
A0018809

value: patient #9023

value: CD19-enriched CLL patient sample


title: CD19-enriched CLL patient sample, patient #3806

description:
CD19-enriched CLL clinical sample
A0020405

value: patient #3806


title: CD19-enriched CLL patient sample, patient #3801

description:
CD19-enriched CLL clinical sample
A0018811

value: patient #3801

value: C


title: CD19-enriched CLL patient sample, patient #3808

description:
CD19-enriched CLL clinical sample
A0018814

value: patient #3808


title: CD19-enriched CLL patient sample, patient #4213

description:
CD19-enriched CLL clinical sample
A0018813

value: patient #4213

value: A


title: CD19-enriched CLL patient sample, patient #6305

description:
CD19-enriched CLL clinical sample
A0018805

value: patient #6305


title: CD19-enriched CLL patient sample, patient #3003

description:
CD19-enriched CLL clinical sample
A0018806

value: patient #3003


title: CD19-enriched CLL patient sample, patient #9522

description:
CD19-enriched CLL clinical sample
A0018807

value: patient #9522


title: CD19-enriched CLL patient sample, patient #7006

description:
CD19-enriched CLL clinical sample
A0018817

value: patient #7006


title: CD19-enriched CLL patient sample, patient #6904

description:
CD19-enriched CLL clinical sample
A0018803

value: patient #6904


title: CD19-enriched CLL patient sample, patient #8104

description:
CD19-enriched CLL clinical sample
A0018815

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #8104


title: CD19-enriched CLL patient sample, patient #2201

description:
CD19-enriched CLL clinical sample
A0018808

value: patient #2201


title: CD19-enriched CLL patient sample, patient #9513

description:
CD19-enriched CLL clinical sample
A0018798

value: patient #9513

value: B


title: CD19-enriched CLL patient sample, patient #2904

description:
CD19-enriched CLL clinical sample
A0018799

value: patient #2904

value: CD19-enriched CLL patient sample


title: CD19-enriched CLL patient sample, patient #6402

description:
CD19-enriched CLL clinical sample
A0018795

value: patient #6402


title: CD19-enriched CLL patient sample, patient #4604

description:
CD19-enriched CLL clinical sample
A0018801

value: patient #4604


title: CD19-enriched CLL patient sample, patient #9716

description:
CD19-enriched CLL clinical sample
A0018785

value: patient #9716


title: CD19-enriched CLL patient sample, patient #8007

description:
CD19-enriched CLL clinical sample
A0018787

value: patient #8007


title: CD19-enriched CLL patient sample, patient #3505

description:
CD19-enriched CLL clinical sample
A0018790

value: patient #3505


title: CD19-enriched CLL patient sample, patient #1402

description:
CD19-enriched CLL clinical sample
A0018792

value: patient #1402


title: CD19-enriched CLL patient sample, patient #6309

description:
CD19-enriched CLL clinical sample
A0018786

value: patient #6309

value: C


title: CD19-enriched CLL patient sample, patient #6202

description:
CD19-enriched CLL clinical sample
A0018794

value: patient #6202


title: CD19-enriched CLL patient sample, patient #2412

description:
CD19-enriched CLL clinical sample
A0018802

value: patient #2412


title: CD19-enriched CLL patient sample, patient #3812

description:
CD19-enriched CLL clinical sample
A0018783

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #3812


title: CD19-enriched CLL patient sample, patient #4709

description:
CD19-enriched CLL clinical sample
A0018782

value: patient #4709


title: CD19-enriched CLL patient sample, patient #6101

description:
CD19-enriched CLL clinical sample
A0018776

value: patient #6101


title: CD19-enriched CLL patient sample, patient #1903

description:
CD19-enriched CLL clinical sample
A0018777

value: patient #1903

value: B


title: CD19-enriched CLL patient sample, patient #9019

description:
CD19-enriched CLL clinical sample
A0018767

value: patient #9019

value: CD19-enriched CLL patient sample


title: CD19-enriched CLL patient sample, patient #9910

description:
CD19-enriched CLL clinical sample
A0018800

value: patient #9910


title: CD19-enriched CLL patient sample, patient #604

description:
CD19-enriched CLL clinical sample
A0018781

value: patient #604


title: CD19-enriched CLL patient sample, patient #9714

description:
CD19-enriched CLL clinical sample
A0018773

value: patient #9714


title: CD19-enriched CLL patient sample, patient #9210

description:
CD19-enriched CLL clinical sample
A0018766

value: patient #9210


title: CD19-enriched CLL patient sample, patient #2202

description:
CD19-enriched CLL clinical sample
A0018774

value: patient #2202


title: CD19-enriched CLL patient sample, patient #2809

description:
CD19-enriched CLL clinical sample
A0018765

value: patient #2809


title: CD19-enriched CLL patient sample, patient #9017

description:
CD19-enriched CLL clinical sample
A0018763

value: patient #9017


title: CD19-enriched CLL patient sample, patient #4009

description:
CD19-enriched CLL clinical sample
A0018769

value: patient #4009


title: CD19-enriched CLL patient sample, patient #4211

description:
CD19-enriched CLL clinical sample
A0018764

value: patient #4211

value: C


title: CD19-enriched CLL patient sample, patient #9713

description:
CD19-enriched CLL clinical sample
A0018770

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #9713


title: CD19-enriched CLL patient sample, patient #6806

description:
CD19-enriched CLL clinical sample
A0018771

value: patient #6806


title: CD19-enriched CLL patient sample, patient #106

description:
CD19-enriched CLL clinical sample
A0018762

value: patient #106


title: CD19-enriched CLL patient sample, patient #4102

description:
CD19-enriched CLL clinical sample
A0018759

value: patient #4102


title: CD19-enriched CLL patient sample, patient #9209

description:
CD19-enriched CLL clinical sample
A0018768

value: patient #9209


title: CD19-enriched CLL patient sample, patient #3310

description:
CD19-enriched CLL clinical sample
A0018772

value: patient #3310

value: B

value: CD19-enriched CLL patient sample


title: CD19-enriched CLL patient sample, patient #6903

description:
CD19-enriched CLL clinical sample
A0018757

value: patient #6903

value: A


title: CD19-enriched CLL patient sample, patient #3512

description:
CD19-enriched CLL clinical sample
A0018756

value: patient #3512


title: CD19-enriched CLL patient sample, patient #8706

description:
CD19-enriched CLL clinical sample
A0018740

value: patient #8706


title: CD19-enriched CLL patient sample, patient #9517

description:
CD19-enriched CLL clinical sample
A0018758

value: patient #9517


title: CD19-enriched CLL patient sample, patient #6603

description:
CD19-enriched CLL clinical sample
A0018746

value: patient #6603


title: CD19-enriched CLL patient sample, patient #9902

description:
CD19-enriched CLL clinical sample
A0018742

value: patient #9902


title: CD19-enriched CLL patient sample, patient #9502

description:
CD19-enriched CLL clinical sample
A0018730

value: patient #9502

value: C


title: CD19-enriched CLL patient sample, patient #803

description:
CD19-enriched CLL clinical sample
A0018739

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #803


title: CD19-enriched CLL patient sample, patient #7102

description:
CD19-enriched CLL clinical sample
A0018744

value: patient #7102


title: CD19-enriched CLL patient sample, patient #6006

description:
CD19-enriched CLL clinical sample
A0018728

value: patient #6006


title: CD19-enriched CLL patient sample, patient #6103

description:
CD19-enriched CLL clinical sample
A0018721

value: patient #6103


title: CD19-enriched CLL patient sample, patient #1905

description:
CD19-enriched CLL clinical sample
A0018722

value: patient #1905


title: CD19-enriched CLL patient sample, patient #3303

description:
CD19-enriched CLL clinical sample
A0018735

value: patient #3303

value: B


title: CD19-enriched CLL patient sample, patient #6604

description:
CD19-enriched CLL clinical sample
A0018747

value: patient #6604

value: CD19-enriched CLL patient sample


title: CD19-enriched CLL patient sample, patient #2404

description:
CD19-enriched CLL clinical sample
A0018731

value: patient #2404

value: A


title: CD19-enriched CLL patient sample, patient #4704

description:
CD19-enriched CLL clinical sample
A0018738

value: patient #4704


title: CD19-enriched CLL patient sample, patient #201

description:
CD19-enriched CLL clinical sample
A0018732

value: patient #201


title: CD19-enriched CLL patient sample, patient #203

description:
CD19-enriched CLL clinical sample
A0018752

value: patient #203


title: CD19-enriched CLL patient sample, patient #6303

description:
CD19-enriched CLL clinical sample
A0018734

value: patient #6303


title: CD19-enriched CLL patient sample, patient #1401

description:
CD19-enriched CLL clinical sample
A0018733

value: patient #1401

value: C


title: CD19-enriched CLL patient sample, patient #2909

description:
CD19-enriched CLL clinical sample
A0018720

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #2909


title: CD19-enriched CLL patient sample, patient #6104

description:
CD19-enriched CLL clinical sample
A0018723

value: patient #6104


title: CD19-enriched CLL patient sample, patient #9524

description:
CD19-enriched CLL clinical sample
A0018718

value: patient #9524


title: CD19-enriched CLL patient sample, patient #602

description:
CD19-enriched CLL clinical sample
A0018715

value: patient #602


title: CD19-enriched CLL patient sample, patient #603

description:
CD19-enriched CLL clinical sample
A0018717

value: patient #603


title: CD19-enriched CLL patient sample, patient #5102

description:
CD19-enriched CLL clinical sample
A0018713

value: patient #5102


title: CD19-enriched CLL patient sample, patient #4708

description:
CD19-enriched CLL clinical sample
A0018710

value: patient #4708


title: CD19-enriched CLL patient sample, patient #5103

description:
CD19-enriched CLL clinical sample
A0018716

value: patient #5103

value: B

value: CD19-enriched CLL patient sample


title: CD19-enriched CLL patient sample, patient #601

description:
CD19-enriched CLL clinical sample
A0018714

value: patient #601


title: CD19-enriched CLL patient sample, patient #204

description:
CD19-enriched CLL clinical sample
A0020400

value: patient #204


title: CD19-enriched CLL patient sample, patient #9005

description:
CD19-enriched CLL clinical sample
A0020412

value: patient #9005


title: CD19-enriched CLL patient sample, patient #9521

description:
CD19-enriched CLL clinical sample
A0018705

value: patient #9521


title: CD19-enriched CLL patient sample, patient #9812

description:
CD19-enriched CLL clinical sample
A0018708

value: patient #9812


title: Before MOF supplementation_Subject10

city: Saint Genes Champanelle

first: Celine

last: BOBY

address: Centre INRA Auvergne-Rhône-Alpes

country: France

institute: INRA

description: EDTA-blood sample

hyb_protocol: Bisulphite converted DNA from the subjects was hybridized to the Illumina HumanMethylation450 BeadChip arrays. Briefly, 4 μg of bisulfite-converted DNA was isothermally amplified overnight (20–24 h) and fragmented enzymatically. Precipitated DNA was resuspended in hybridization buffer and dispensed onto the Infinium HumanMethylation450 BeadChips (12 samples/chip) using a Freedom EVO robot (Tecan). The hybridization procedure was performed at 48°C overnight (16–20 h) using an Illumina Hybridization oven. After hybridization, free DNA was washed away and the BeadChips were processed through a single nucleotide extension followed by immunohistochemistry staining using a Freedom EVO robot (Tecan).

scan_protocol: The BeadChips were imaged using an Illumina iScan.

data_processing: Detection p-values were calculated to identify failed probes as per Illumina's recommendations. Probes on sex chromosomes or containing SNPs (dbSNP v132) in the probe sequence were excluded. Raw data were normalized using Illumina's control probe scaling procedure and converted to methylation values on the 0–1 scale (M/(M + U + 100), where M and U represent the methylated and unmethylated signal intensities, respectively).

label_protocol: See hyb protocol

extract_protocol: gDNA from EDTA-treated blood was extracted by a DNeasy blood & tissue kit (Qiagen, Courtaboeuf, France)

tag: gender

value: Male

tag: age

tag: cig/dag

tag: years of smoking

tag: pack years

tag: bmi

tag: tchol (mmol/l)


title: CD19-enriched CLL patient sample, patient #8205

description:
CD19-enriched CLL clinical sample
A0018706

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #8205

value: C


title: CD19-enriched CLL patient sample, patient #4011

description:
CD19-enriched CLL clinical sample
A0018707

value: patient #4011


title: CD19-enriched CLL patient sample, patient #7004

description:
CD19-enriched CLL clinical sample
A0018704

value: patient #7004


title: CD19-enriched CLL patient sample, patient #2304

description:
CD19-enriched CLL clinical sample
A0018702

value: patient #2304

value: A


title: After 8wk MOF supplementation_Subject9

description: EDTA-blood sample


title: After 8wk MOF supplementation_Subject8

description: EDTA-blood sample


title: Before MOF supplementation_Subject9

description: EDTA-blood sample


title: CD19-enriched CLL patient sample, patient #4907

description:
CD19-enriched CLL clinical sample
A0018700

value: patient #4907


title: Before MOF supplementation_Subject8

description: EDTA-blood sample


title: After 8wk MOF supplementation_Subject7

description: EDTA-blood sample


title: CD19-enriched CLL patient sample, patient #2906

description:
CD19-enriched CLL clinical sample
A0018701

value: patient #2906


title: Before MOF supplementation_Subject7

description: EDTA-blood sample


title: CD19-enriched CLL patient sample, patient #3314

description:
CD19-enriched CLL clinical sample
A0018784

value: patient #3314


title: CD19-enriched CLL patient sample, patient #3811

description:
CD19-enriched CLL clinical sample
A0018719

value: patient #3811

value: B

value: CD19-enriched CLL patient sample


title: CD19-enriched CLL patient sample, patient #3202

description:
CD19-enriched CLL clinical sample
A0018695

value: patient #3202


title: CD19-enriched CLL patient sample, patient #1901

description:
CD19-enriched CLL clinical sample
A0018689

value: patient #1901


title: CD19-enriched CLL patient sample, patient #9006

description:
CD19-enriched CLL clinical sample
A0018685

value: patient #9006


title: CD19-enriched CLL patient sample, patient #5007

description:
CD19-enriched CLL clinical sample
A0018691

value: patient #5007


title: CD19-enriched CLL patient sample, patient #8402

description:
CD19-enriched CLL clinical sample
A0018678

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #8402


title: Before MOF supplementation_Subject6

description: EDTA-blood sample

value: Male


title: CD19-enriched CLL patient sample, patient #4602

description:
CD19-enriched CLL clinical sample
A0018679

value: patient #4602

value: C


title: CD19-enriched CLL patient sample, patient #3307

description:
CD19-enriched CLL clinical sample
A0018697

value: patient #3307


title: CD19-enriched CLL patient sample, patient #9014

description:
CD19-enriched CLL clinical sample
A0018694

value: patient #9014


title: CD19-enriched CLL patient sample, patient #7001

description:
CD19-enriched CLL clinical sample
A0018677

value: patient #7001


title: CD19-enriched CLL patient sample, patient #9018

description:
CD19-enriched CLL clinical sample
A0018698

value: patient #9018


title: CD19-enriched CLL patient sample, patient #2409

description:
CD19-enriched CLL clinical sample
A0018680

value: patient #2409


title: CD19-enriched CLL patient sample, patient #9803

description:
CD19-enriched CLL clinical sample
A0018682

value: patient #9803


title: CD19-enriched CLL patient sample, patient #9807

description:
CD19-enriched CLL clinical sample
A0018692

value: patient #9807

value: B


title: CD19-enriched CLL patient sample, patient #3511

description:
CD19-enriched CLL clinical sample
A0018684

value: patient #3511

value: CD19-enriched CLL patient sample


title: CD19-enriched CLL patient sample, patient #7202

description:
CD19-enriched CLL clinical sample
A0018699

value: patient #7202

value: A


title: After 8wk MOF supplementation_Subject6

description: EDTA-blood sample


title: Before MOF supplementation_Subject4

description: EDTA-blood sample


title: After 8wk MOF supplementation_Subject3

description: EDTA-blood sample


title: After 8wk MOF supplementation_Subject10

description: EDTA-blood sample


title: CD19-enriched CLL patient sample, patient #6902

description:
CD19-enriched CLL clinical sample
A0018671

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #6902


title: CD19-enriched CLL patient sample, patient #8401

description:
CD19-enriched CLL clinical sample
A0018674

value: patient #8401


title: CD19-enriched CLL patient sample, patient #3301

description:
CD19-enriched CLL clinical sample
A0018668

value: patient #3301


title: After 8wk MOF supplementation_Subject4

description: EDTA-blood sample

value: Male


title: CD19-enriched CLL patient sample, patient #8004

description:
CD19-enriched CLL clinical sample
A0018673

value: patient #8004


title: CD19-enriched CLL patient sample, patient #9814

description:
CD19-enriched CLL clinical sample
A0018649

value: patient #9814

value: C


title: CD19-enriched CLL patient sample, patient #1702

description:
CD19-enriched CLL clinical sample
A0018669

value: patient #1702


title: CD19-enriched CLL patient sample, patient #5105

description:
CD19-enriched CLL clinical sample
A0018659

value: patient #5105


title: CD19-enriched CLL patient sample, patient #8505

description:
CD19-enriched CLL clinical sample
A0018656

value: patient #8505


title: CD19-enriched CLL patient sample, patient #6911

description:
CD19-enriched CLL clinical sample
A0018658

value: patient #6911


title: CD19-enriched CLL patient sample, patient #4903

description:
CD19-enriched CLL clinical sample
A0018666

value: patient #4903

value: B


title: CD19-enriched CLL patient sample, patient #2303

description:
CD19-enriched CLL clinical sample
A0018670

value: patient #2303

value: CD19-enriched CLL patient sample


title: CD19-enriched CLL patient sample, patient #6605

description:
CD19-enriched CLL clinical sample
A0018651

value: patient #6605


title: CD19-enriched CLL patient sample, patient #6408

description:
CD19-enriched CLL clinical sample
A0018655

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #6408


title: CD19-enriched CLL patient sample, patient #7204

description:
CD19-enriched CLL clinical sample
A0018657

value: patient #7204


title: After 8wk MOF supplementation_Subject2

description: EDTA-blood sample


title: Before MOF supplementation_Subject5

description: EDTA-blood sample


title: CD19-enriched CLL patient sample, patient #2601

description:
CD19-enriched CLL clinical sample
A0018663

value: patient #2601


title: Before MOF supplementation_Subject2

description: EDTA-blood sample

value: Male


title: After 8wk MOF supplementation_Subject5

description: EDTA-blood sample


title: CD19-enriched CLL patient sample, patient #3504

description:
CD19-enriched CLL clinical sample
A0018664

value: patient #3504

value: A


title: After 8wk MOF supplementation_Subject1

description: EDTA-blood sample


title: CD19-enriched CLL patient sample, patient #5013

description:
CD19-enriched CLL clinical sample
A0018652

value: patient #5013

value: C


title: CD19-enriched CLL patient sample, patient #3802

description:
CD19-enriched CLL clinical sample
A0018648

value: patient #3802


title: CD19-enriched CLL patient sample, patient #6810

description:
CD19-enriched CLL clinical sample
A0018647

value: patient #6810


title: Before MOF supplementation_Subject1

description: EDTA-blood sample


title: Before MOF supplementation_Subject3

description: EDTA-blood sample


title: CD19-enriched CLL patient sample, patient #6306

description:
CD19-enriched CLL clinical sample
A0018642

value: patient #6306


title: CD19-enriched CLL patient sample, patient #310

description:
CD19-enriched CLL clinical sample
A0018640

value: patient #310


title: CD19-enriched CLL patient sample, patient #3309

description:
CD19-enriched CLL clinical sample
A0018641

value: patient #3309

value: B


title: CD19-enriched CLL patient sample, patient #3308

description:
CD19-enriched CLL clinical sample
A0018639

value: patient #3308

value: CD19-enriched CLL patient sample


title: CD19-enriched CLL patient sample, patient #6809

description:
CD19-enriched CLL clinical sample
A0018644

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #6809


title: CD19-enriched CLL patient sample, patient #3004

description:
CD19-enriched CLL clinical sample
A0018643

value: patient #3004


title: PBL_Ctrl_2

city: Singapore

first: Manikandan

last: Jayapal

address: 2 Medical Drive

country: Singapore

institute: National University of Singapore

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized each chip to the 50th Percentile of the measurements taken from that chip using GeneSpring GX 7.3 software

label_protocol: Biotinylated cRNA were prepared with Enzo Diagnostics, USAbiotin labelled cRNA synthesis, in vitro transcription reaction was performed in the presence of T7 RNA polymerase and biotinylated ribonucleotides (Enzo Diagnostics, USA).

extract_protocol: Cells were subjected to appropriate treatment and the total RNA was extracted (RNeasy Kit, Qiagen). Double stranded cDNA was synthesised from 5 μg of total RNA using Superscript system (Invitrogen, USA) primed with T7- (dT)-24 primer.

value: Control

tag: replicate

value: PBL


title: PBL_Rad_2

value: Radiation


title: H1F_Ctrl_2


title: CD19-enriched CLL patient sample, patient #3105

description:
CD19-enriched CLL clinical sample
A0018646

value: patient #3105


title: CD19-enriched CLL patient sample, patient #9020

description:
CD19-enriched CLL clinical sample
A0018638

value: patient #9020


title: hESCs_Rad_1

value: hESCs


title: hESCs_Rad_2


title: H1F_Ctrl_1


title: hESCs_Ctrl_2


title: CD19-enriched CLL patient sample, patient #6803

description:
CD19-enriched CLL clinical sample
A0018637

value: patient #6803


title: PBL_Ctrl_1


title: H1F_Rad_2


title: CD19-enriched CLL patient sample, patient #3205

description:
CD19-enriched CLL clinical sample
A0018696

value: patient #3205

value: C


title: PBL_Rad_1


title: H1F_Rad_1


title: CD19-enriched CLL patient sample, patient #4008

description:
CD19-enriched CLL clinical sample
A0018636

value: patient #4008


title: HEPM_Ctrl_1

value: HEPM


title: hESCs_Ctrl_1


title: HEPM_Ctrl_2


title: HEPM_Rad_1


title: HEPM_Rad_2


title: CD19-enriched CLL patient sample, patient #9520

description:
CD19-enriched CLL clinical sample
A0018634

value: patient #9520


title: CD19-enriched CLL patient sample, patient #7203

description:
CD19-enriched CLL clinical sample
A0018633

value: patient #7203

value: B


title: CD19-enriched CLL patient sample, patient #6406

description:
CD19-enriched CLL clinical sample
A0018630

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #6406

value: A

value: CD19-enriched CLL patient sample


title: Jmjd3-deleted differentiating SVZ cells-#2

city: SAN FRANCISCO

last: Liu

state: California

address: 35 Medical Center Way

institute: UCSF

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

organism: Mus musculus

source_name: Subventricular zone cells

label_protocol: Biotinylated cRNA was generated from total RNA using an Ambion Illumina RNA amplification kit (Ambion)

growth_protocol: SVZ NSCs were passaged 5 times in proliferation medium(DMEM/F12/N2 – Invitrogen, 5% FCS - Hyclone, 20 ng ml-1 EGF, 20 ng ml-1 bFGF, 35 ?g ml-1 bovine pituitary extract – Peprotech) before switching to differentiation media (same as proliferation media exc

extract_protocol: Total RNA was isolated by Trizol (Life Technologies), purified using the RNeasy Plus Mini Kit (Qiagen) and quantified using the NanoDrop spectrophotometer. Samples were checked for quality using an Agilent TapeStation

tag: growth media

value: Differentiation media for 30 hr

value: post natal day 9

tag: genotype/variation


title: WT differentiating SVZ cells-#3


title: Jmjd3-deleted differentiating SVZ cells-#3


title: WT proliferating SVZ cells-#1

value: Self-renewal media


title: CD19-enriched CLL patient sample, patient #9708

description:
CD19-enriched CLL clinical sample
A0018632

value: patient #9708

tag: tissue


title: CD19-enriched CLL patient sample, patient #7305

description:
CD19-enriched CLL clinical sample
A0018626

value: patient #7305


title: CD19-enriched CLL patient sample, patient #6304

description:
CD19-enriched CLL clinical sample
A0018631

value: patient #6304


title: CD19-enriched CLL patient sample, patient #6012

description:
CD19-enriched CLL clinical sample
A0018629

value: patient #6012


title: CD19-enriched CLL patient sample, patient #1504

description:
CD19-enriched CLL clinical sample
A0018628

value: patient #1504


title: Jmjd3-deleted differentiating SVZ cells-#1


title: WT proliferating SVZ cells-#3


title: WT differentiating SVZ cells-#1


title: WT proliferating SVZ cells-#2


title: WT differentiating SVZ cells-#2


title: Old Day 4 #1

city: Boston

first: Michio

last: Painter

state: MA

address: 3 Blackfan Circle

department: Neurobiology

institute: Children's Hospital Boston

description:
replicate 1
M16_inj_o_4d

data_processing: The data were normalised using standard RMA.

source_name: Mouse sciatic nerve

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

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

tag: strain

value: 24 months

value: sciatic nerve

tag: treatment

value: sciatic nerve crush injury


title: Old Day 1 #2

description:
replicate 2
M14_inj_o_1d

tag: time


title: CD19-enriched CLL patient sample, patient #9206

description:
CD19-enriched CLL clinical sample
A0018624

tag: subject status

value: patient #9206


title: Young Day 1 #3

description:
replicate 3
M9_inj_y_1d

value: 2 months


title: CD19-enriched CLL patient sample, patient #2411

description:
CD19-enriched CLL clinical sample
A0018625

value: relapsed chronic lymphocytic leukemia (CLL) patient

tag: patient id

value: patient #2411


title: Young Day 4 #2

description:
replicate 2
M11_inj_y_4d


title: Young Day 1 #2

description:
replicate 2
M8_inj_y_1d


title: Old Day 1 #3

description:
replicate 3
M15_inj_o_1d


title: Old Day 1 #1

description:
replicate 1
M13_inj_o_1d


title: Old Day 4 #3

description:
replicate 3
M18_inj_o_4d


title: Young Day 4 #1

description:
replicate 1
M10_inj_y_4d


title: Old Day 4 #2

description:
replicate 2
M17_inj_o_4d


title: Young Day 4 #3

description:
replicate 3
M12_inj_y_4d


title: Young Day 1 #1

description:
replicate 1
M7_inj_y_1d


title: CD19-enriched CLL patient sample, patient #7702

description:
CD19-enriched CLL clinical sample
A0018620

value: patient #7702

tag: binet stage

value: B


title: CD19-enriched CLL patient sample, patient #9002

description:
CD19-enriched CLL clinical sample
A0018613

value: patient #9002

value: CD19-enriched CLL patient sample


title: Old Day 0 #3

description:
replicate 3
M6_con_o_0d

value: control


title: CD19-enriched CLL patient sample, patient #9909

description:
CD19-enriched CLL clinical sample
A0018623

value: patient #9909

value: C


title: CD19-enriched CLL patient sample, patient #9515

description:
CD19-enriched CLL clinical sample
A0018622

value: patient #9515


title: Old Day 0 #2

description:
replicate 2
M5_con_o_0d


title: CD19-enriched CLL patient sample, patient #6010

description:
CD19-enriched CLL clinical sample
A0018612

value: patient #6010


title: Young Day 0 #1

description:
replicate 1
M1_con_y_0d


title: Old Day 0 #1

description:
replicate 1
M4_con_o_0d


title: CD19-enriched CLL patient sample, patient #9703

description:
CD19-enriched CLL clinical sample
A0018609

value: patient #9703


title: Young Day 0 #3

description:
replicate 3
M3_con_y_0d


title: Young Day 0 #2

description:
replicate 2
M2_con_y_0d


title: Young Pre-conditioned #3

description: replicate 3

source_name: Young Pre-conditioned #3

value: dorsal root ganglia


title: Old Pre-conditioned #3

description: replicate 3

source_name: Old Pre-conditioned #3

value: 24 months


title: Old Naïve #2

description: replicate 2

source_name: Old Naïve #2


title: Old Naïve #1

description: replicate 1

source_name: Old Naïve #1


title: CD19-enriched CLL patient sample, patient #4502

description:
CD19-enriched CLL clinical sample
A0018606

value: patient #4502


title: CD19-enriched CLL patient sample, patient #9202

description:
CD19-enriched CLL clinical sample
A0018604

value: patient #9202


title: Old Pre-conditioned #1

description: replicate 1

source_name: Old Pre-conditioned #1


title: CD19-enriched CLL patient sample, patient #2804

description:
CD19-enriched CLL clinical sample
A0018602

value: patient #2804


title: Old Pre-conditioned #2

description: replicate 2

source_name: Old Pre-conditioned #2


title: CD19-enriched CLL patient sample, patient #4002

description:
CD19-enriched CLL clinical sample
A0018600

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #4002


title: CD19-enriched CLL patient sample, patient #6201

description:
CD19-enriched CLL clinical sample
A0018601

value: patient #6201


title: Young Naïve #2

description: replicate 2

source_name: Young Naïve #2

value: 2 months


title: Young Pre-conditioned #1

description: replicate 1

source_name: Young Pre-conditioned #1


title: Young Pre-conditioned #2

description: replicate 2

source_name: Young Pre-conditioned #2


title: Young Naïve #3

description: replicate 3

source_name: Young Naïve #3


title: Young Naïve #1

description: replicate 1

source_name: Young Naïve #1


title: CD19-enriched CLL patient sample, patient #802

description:
CD19-enriched CLL clinical sample
A0018598

value: patient #802


title: CD19-enriched CLL patient sample, patient #2001

description:
CD19-enriched CLL clinical sample
A0018599

value: patient #2001

value: CD19-enriched CLL patient sample


title: BMM_RANKL 2day_rep2

city: Los Angeles

first: Kyunghwan

last: Kim

address: 1450 Biggy Street NRT6517

department: Biochemistry and Molecular Biology

institute: University of Southern California

description: replicate 2

data_processing: The data were processed and anlayzed by the Array Pipe software.

source_name: Bone marrow-derived macrophage cells

label_protocol: Biotinylated cRNA was prepared with the Ambion MessageAmp kit for Illumina array.

growth_protocol: Bone marrow (BM) cells were collected by flushing femurs and tibias from 6- to 8-week-old C57BL/6 mice. Cells were cultured in α-minimum essential medium (α-MEM) supplemented with 10% FBS and M-CSF (5 ng/ml) for 16 h.  Non-adherent cells were harvested and cultured with M-CSF (30 ng/ml) for 3 days. Floating cells were removed and adherent cells were used as bone marrow-derived macrophage (BMM) cells.

extract_protocol: Total RNA was isolated using the TRIzol reagent according to the manufacturer's instructinos.

treatment_protocol: To generate osteoclasts, BMMs were cultured in the presence of M-CSF (30 ng/ml) and RANKL (50 ng/ml).

tag: cell culture type

value: Primary cells

tag: cell type

value: Bone marrow-derived macrophage cells

value: 6-8 weeks


title: BMM_RANKL 1day_rep2

description: replicate 2

tag: age


title: BMM_RANKL 2day_rep1

description: replicate 1


title: CD19-enriched CLL patient sample, patient #605

description:
CD19-enriched CLL clinical sample
A0018594

value: patient #605

value: B


title: CD19-enriched CLL patient sample, patient #1904

description:
CD19-enriched CLL clinical sample
A0018595

value: patient #1904


title: BMM_RANKL 1day_rep1

description: replicate 1


title: CD19-enriched CLL patient sample, patient #3810

description:
CD19-enriched CLL clinical sample
A0018592

value: patient #3810


title: CD19-enriched CLL patient sample, patient #3804

description:
CD19-enriched CLL clinical sample
A0018588

value: patient #3804


title: CD19-enriched CLL patient sample, patient #5104

description:
CD19-enriched CLL clinical sample
A0018593

value: patient #5104


title: MT (clone 5)

data_processing: Quantile normalization using GeneSpring11.

source_name: Stable clone of NIH3T3 cell line, sW182* mutant, clone 5.

tag: cell line

value: Stable transfectant of plasmid encoding mutant PreS/S gene (sW182*) of HBV.


first: Kian Leong

last: LEE

state: Singapore

address: #07-21, 8 College Road

department: Duke-NUS Medical School

institute: National University of Singapore (NUS)

hyb_protocol: 750ng of each cRNA sample was hybridized to MouseRef-8 v2.0 Expression BeadChip microarrays (Illumina) as per manufacturer specifications.

scan_protocol: Microarrays were scanned on the BeadArray Reader (Illumina, USA) at scan factor 1 as per manufacturer specifications.

data_processing:
Raw intensity values were subjected to background subtraction on the BeadStudio Data Analysis Software (Illumina) and normalized using the cross-correlation method (Chua et al., 2006). Differential gene expression was identified based on a fold change cutoff of >1.5 compared to the average of the wild-type normoxic controls.
Normalized values represent linear relative data that have not been log transformed. They were obtained from the original microarray raw data after background subtraction on the Illumina Beadstudio platform followed by normalization using the cross-correlation method (Chua et al., 2006) performed on MATLAB.
references: Chua SW, Vijayakumar P, Nissom PM, Yam CY, Wong VV, Yang H: A novel normalization method for effective removal of systematic variation in microarray data. Nucleic acids research 2006, 34(5):e38.

source_name: TT2 Mouse ES cells G9a KO1 reconstituted Hypoxia 4h 2X10^5 cells/6cm plate

label_protocol: 500ng of total RNA from each sample was reverse transcribed into cDNA and in vitro transcribed into biotin-labelled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion).

growth_protocol: Mouse ES cells were maintained and expanded in DMEM supplemented with 10% fetal calf serum, LIF (500U/ml), 55uM 2-mercaptoethanol, 2mM GlutaMAX, 0.1mM non-essential amino acids, 100U/ml Penicillin and 100ug/ml Steptomycin (Invitrogen).

extract_protocol: Total RNA was extracted from wild-type, JMJD1a KO, G9a KO or reconstituted G9a KO ES cells subjected to 24 hours normoxia, 4 hours hypoxia or 24 hours hypoxia treatments using the RNeasy Mini kit (Qiagen) according to manufacturer instructions. RNA quality was assessed on the 2100 Bioanalyser (Agilent) using the RNA 6000 Nano Chip kit (Agilent) for intact 18S and 28S ribosomal peaks without significant degradation (RNA Integrity Number >8) for all samples.

treatment_protocol: Cells were cultured under hypoxic conditions (1% O2, 5% CO2 at 37°C) in an Invivo2 Hypoxia Workstation 400 hypoxic chamber (Ruskinn Technology) for 4 or 24 hours. Control cells were cultured in normoxic conditions (21% O2, 5% CO2 at 37°C) in a Forma Steri-Cycle CO2 incubator (Thermo Scientific)

tag: gender

value: Male

value: TT2 (c57BL/6xCBA)

value: ES cells

tag: genotype

value: G9a KO reconstituted with G9a transgene

value: Hypoxia

tag: cell density

value: 2X10^5 cells/6cm plate


title: Vector (clone 4)

source_name: Stable clone of NIH3T3 cell line, vector control, clone 4.

value: Stable transfectant of control vector plasmid


source_name: TT2 Mouse ES cells G9a KO1 reconstituted Hypoxia 24h 4X10^5 cells/6cm plate

value: 4X10^5 cells/6cm plate


source_name: TT2 Mouse ES cells G9a KO1 reconstituted Hypoxia 24h 6X10^5 cells/6cm plate

value: 6X10^5 cells/6cm plate


title: WT (clone 3)

source_name: Stable clone of NIH3T3 cell line, wild type PreS/S gene of HBV, clone 3.

value: Stable transfectant of plasmid encoding wild type PreS/S gene of HBV.


title: CD19-enriched CLL patient sample, patient #3313

description:
CD19-enriched CLL clinical sample
A0018590

source_name: CLL clinical sample, CD19-enriched

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #3313

value: C

value: CD19-enriched CLL patient sample


title: WT (clone 8)

source_name: Stable clone of NIH3T3 cell line, wild type PreS/S gene of HBV, clone 8.


source_name: TT2 Mouse ES cells G9a KO1 reconstituted Hypoxia 4h 6X10^5 cells/6cm plate


source_name: TT2 Mouse ES cells G9a KO1 reconstituted Hypoxia 4h 4X10^5 cells/6cm plate


source_name: TT2 Mouse ES cells G9a KO1 reconstituted Hypoxia 24h 2X10^5 cells/6cm plate


source_name: TT2 Mouse ES cells G9a KO1 reconstituted Normoxia 24h 6X10^5 cells/6cm plate

value: Normoxia


title: CD19-enriched CLL patient sample, patient #9216

description:
CD19-enriched CLL clinical sample
A0018587

value: patient #9216

value: B


source_name: TT2 Mouse ES cells G9a KO2 Hypoxia 24h 6X10^5 cells/6cm plate

value: Male

value: G9a KO


source_name: TT2 Mouse ES cells G9a KO1 reconstituted Normoxia 24h 4X10^5 cells/6cm plate

value: TT2 (c57BL/6xCBA)

value: ES cells


source_name: TT2 Mouse ES cells G9a KO1 reconstituted Normoxia 24h 2X10^5 cells/6cm plate

value: G9a KO reconstituted with G9a transgene


title: CD19-enriched CLL patient sample, patient #9213

description:
CD19-enriched CLL clinical sample
A0018586

value: patient #9213


source_name: TT2 Mouse ES cells G9a KO2 Hypoxia 24h 2X10^5 cells/6cm plate

value: Hypoxia

value: 2X10^5 cells/6cm plate


source_name: TT2 Mouse ES cells G9a KO2 Hypoxia 4h 6X10^5 cells/6cm plate

value: 6X10^5 cells/6cm plate


title: CD19-enriched CLL patient sample, patient #6805

description:
CD19-enriched CLL clinical sample
A0018585

value: patient #6805

value: A


title: CD19-enriched CLL patient sample, patient #9712

description:
CD19-enriched CLL clinical sample
A0018583

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #9712


title: MT (clone 6)

source_name: Stable clone of NIH3T3 cell line, sW182* mutant, clone 6.

value: Stable transfectant of plasmid encoding mutant PreS/S gene (sW182*) of HBV.


source_name: TT2 Mouse ES cells G9a KO2 Hypoxia 4h 2X10^5 cells/6cm plate


source_name: TT2 Mouse ES cells G9a KO2 Normoxia 24h 6X10^5 cells/6cm plate

value: Normoxia


source_name: TT2 Mouse ES cells G9a KO2 Hypoxia 24h 4X10^5 cells/6cm plate

value: 4X10^5 cells/6cm plate


source_name: TT2 Mouse ES cells G9a KO2 Hypoxia 4h 4X10^5 cells/6cm plate


source_name: TT2 Mouse ES cells G9a KO2 Normoxia 24h 4X10^5 cells/6cm plate


title: CD19-enriched CLL patient sample, patient #309

description:
CD19-enriched CLL clinical sample
A0018582

source_name: CLL clinical sample, CD19-enriched

value: patient #309

value: CD19-enriched CLL patient sample


title: CD19-enriched CLL patient sample, patient #8703

description:
CD19-enriched CLL clinical sample
A0018577

value: patient #8703

value: B


source_name: TT2 Mouse ES cells G9a KO2 Normoxia 24h 2X10^5 cells/6cm plate

value: Male

value: TT2 (c57BL/6xCBA)

value: ES cells

value: G9a KO


source_name: TT2 Mouse ES cells G9a KO1 Hypoxia 24h 4X10^5 cells/6cm plate

value: Hypoxia


title: CD19-enriched CLL patient sample, patient #9219

description:
CD19-enriched CLL clinical sample
A0018591

value: patient #9219


source_name: TT2 Mouse ES cells G9a KO1 Hypoxia 24h 6X10^5 cells/6cm plate

value: 6X10^5 cells/6cm plate


title: CD19-enriched CLL patient sample, patient #9021

description:
CD19-enriched CLL clinical sample
A0018580

value: patient #9021


source_name: TT2 Mouse ES cells G9a KO1 Hypoxia 4h 4X10^5 cells/6cm plate


source_name: TT2 Mouse ES cells G9a KO1 Hypoxia 4h 6X10^5 cells/6cm plate


source_name: TT2 Mouse ES cells G9a KO1 Hypoxia 4h 2X10^5 cells/6cm plate

value: 2X10^5 cells/6cm plate


source_name: TT2 Mouse ES cells G9a KO1 Hypoxia 24h 2X10^5 cells/6cm plate


title: CD19-enriched CLL patient sample, patient #9606

description:
CD19-enriched CLL clinical sample
A0018575

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #9606

value: C


source_name: TT2 Mouse ES cells G9a KO1 Normoxia 24h 6X10^5 cells/6cm plate

value: Normoxia


title: CD19-enriched CLL patient sample, patient #9207

description:
CD19-enriched CLL clinical sample
A0018572

value: patient #9207


title: CD19-enriched CLL patient sample, patient #9709

description:
CD19-enriched CLL clinical sample
A0018574

value: patient #9709

value: CD19-enriched CLL patient sample


source_name: TT2 Mouse ES cells G9a KO1 Normoxia 24h 2X10^5 cells/6cm plate


source_name: TT2 Mouse ES cells JMJD1a KO2 Hypoxia 24h 6X10^5 cells/6cm plate

value: JMJD1a KO


title: Control vs. Tellurite replicate1

city: Santiago

first: David

middle: Enrique

last: Loyola

state: Santiago

address: Avenida Libertador Bernardo O'Higgins 340

country: Chile

institute: OMICS Solutions, Centro Nacional de Genómica y Bioinformática

description: Biological replicate 1 of 2 (Dye swap)

hyb_protocol: Hybridization buffer (6X SSC buffer; 0.2 % SDS; 5 % Denhardt's solution; Salmon sperm DNA 13 µg/ml; 25 % deionized formamide; 23 µl of tagged cDNA) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially

scan_protocol: Slides were scanned on a ScanArray Gx scanner (PerkinElmer).

data_processing: LOESS normalized, Normexp background subtracted data obtained from log2 of processed target/reference signal. Limma package used implemented in Bioconductor

label: Alexa Fluor 555

organism: Escherichia coli K-12

source_name: Total RNA extracted from tellurite exposed cultures

label_protocol: 20 µg of total RNA were primed with 2 µl of 3 µg/µl Random primer at 80°C for 5 min, then reversed transcribed at 42°C for 2.5 h in the presence of 200 U SuperScript II Reverse transcriptase (Invitrogen), and 10 mM each dATP, dCTP, dGTP, with 4 mM dTTP, 1 mM Alexa fluor 555 aha dUTP (or 1mM Alexa fluor 647 aha dUTP)

growth_protocol: An overnight E. coli culture was inoculated (in a 1:1000 dilution) in fresh LB containing flasks and incubated with vigorous shaking to 37 °C. At an OD600 ~0.4

extract_protocol: Total RNA was extracted using Rneasy Mini Kit (Qiagen) following manufacturer's instructions

treatment_protocol: Cultures were exposed to tellurite (0.5 µg/ml) during 15 min and incubated to 37 °C with vigorous shaking

label: Alexa Fluor 647

source_name: Total RNA extracted from untreated cultures


source_name: TT2 Mouse ES cells JMJD1a KO2 Hypoxia 24h 4X10^5 cells/6cm plate

value: Male

value: 4X10^5 cells/6cm plate


source_name: TT2 Mouse ES cells G9a KO1 Normoxia 24h 4X10^5 cells/6cm plate

value: TT2 (c57BL/6xCBA)

value: ES cells


title: CD19-enriched CLL patient sample, patient #9809

description:
CD19-enriched CLL clinical sample
A0018571

value: patient #9809

value: B


title: Control vs. Tellurite replicate2

description: Biological replicate 2 of 2 (Dye swap)


source_name: TT2 Mouse ES cells JMJD1a KO2 Hypoxia 24h 2X10^5 cells/6cm plate

value: Hypoxia


title: CD19-enriched CLL patient sample, patient #8503

description:
CD19-enriched CLL clinical sample
A0018570

value: patient #8503


title: GSC microRNA rep2

city: beijing

first: Shuang

address: Navy General Hospital PLA

institute: Navy General Hospital

hyb_protocol: a pre-hybridization step prior to hybridization of the labeled target.Complete the Hybridization Using the Glass Cover Slide Method. Wash the Hybridized Microarray

scan_protocol: Molecular Devices Axon GenePix 4000B and 4200 series

data_processing: The data from all microarrays in each experimental set was then analyzed using Omicsoft Array Studio software; control and missing features were removed, and the remaining signals were quantile normalized. Testing was performed by combining technical replicates and performing statistical analyses using Rosetta Resolver’s proprietary modeling techniques.

source_name: brain glioma stem cells

label_protocol: Kreatech ULS miRNA labeling kit: ULS Labeling Procedure 1)  Mix all kit components thoroughly by vortexing and briefly spin down. 2)Use the same input amount of labeled small RNA and adjust the sample volume to final 15.5μl.  Small RNA (100-500 ng) 10 x labeling solution  Cy5 ULS  Total volume 15.5 μl  2 μl  2.5 μl  20μl 3)  Label sample by incubation for 15 minutes at 85 ℃. 4)  Add 10 μl of  Nuclease-free Water and spin the sample and place on ice till purification using the KREApure columns. Dye removal using KREApure columns :1)  Resuspend the column by vortex. 2)  Loosen the cap and snap off the bottom closure. 3)  Place the column into a 2ml collection tube and pre-spinning the column for 1 min at 13000rpm. Discard flow-through. 4)  Wash the column with 300 μl RNase-free water for spinning column for 1 minute at 13000 rpm. 5)  Discard collection tube and flow-through and put column in a new (RNase free) 1.5 ml tube. 6)  Add  ULS  labeled  sample  on  the  middle  of  the  column  bed without touching it and centrifuge for 1 min at 13000rpm and  10  Human miRNA OneArray ?  User Guide v4  Phalanx Biotech Group collect the flow-through. Keep the labeled samples on ice, in dark and proceed the hybridization. 7)  1.5 μl of labeled miRNA sample, proceed OD reading (260, 280, 550, 649 nm) and calculate labeled small RNA amount and  the  labeling  efficiency.(If    you  start  labeling  with  100-500 ng small RNA , you should get 80-400 ng labeled small RNA. Be sure to use the same input amount of small RNA for hybridization )

extract_protocol: Use Pall Nanosep 100K protocol：Add 50 ul of nuclease-free water to the membrane of the sample reservoir of Nanosep 100K. 2)  Spin at 14,000 x g for 10 min, and transfer the sample reservoir of Nanosep 100K to 1.5 ml collect tube 3)  Add the ULS labeling sample to sample reservoir of Nanosep 100K. Spin at 5,000 x g for 10 min; collect the flow-through sample. 4)  Proceed OD reading and calculate the small RNA amount.

value: brain glioma stem cells


title: GSC microRNA rep1


title: GSC microRNA rep3


source_name: TT2 Mouse ES cells JMJD1a KO2 Hypoxia 4h 4X10^5 cells/6cm plate


source_name: TT2 Mouse ES cells JMJD1a KO2 Hypoxia 4h 2X10^5 cells/6cm plate

value: 2X10^5 cells/6cm plate


title: CD19-enriched CLL patient sample, patient #6404

description:
CD19-enriched CLL clinical sample
A0018569

source_name: CLL clinical sample, CD19-enriched

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #6404


title: NSC microRNA rep2

source_name: normal neural stem cells

value: normal neural stem cells


title: CD19-enriched CLL patient sample, patient #9518

description:
CD19-enriched CLL clinical sample
A0018568

value: patient #9518

value: C


title: CD19-enriched CLL patient sample, patient #6013

description:
CD19-enriched CLL clinical sample
A0018573

value: patient #6013

value: CD19-enriched CLL patient sample


source_name: TT2 Mouse ES cells JMJD1a KO2 Normoxia 24h 6X10^5 cells/6cm plate

value: Male

value: JMJD1a KO

value: Normoxia

value: 6X10^5 cells/6cm plate


title: NSC microRNA rep3


source_name: TT2 Mouse ES cells JMJD1a KO2 Normoxia 24h 2X10^5 cells/6cm plate

value: TT2 (c57BL/6xCBA)

value: ES cells


title: GSC mRNA rep2

hyb_protocol: 2.5 µRNA was hybridized to Human OneArray glass slide containing 29,187 human genome probes and 1,082 experimental control probes according to the manufacturer's standard protocols (PhalanxBio, CA, USA). The Human OneArray slide was prehybridized for 2 h at 42C with OneArray Pre-hybridization buffer and then hybridized for 16 h at 42C with OneArray hybridization buffer. The slides were then washed according to the manufacturer’PhalanxBio Inc, CA, USA). 10 µRNA was hybridized to Human OneArray glass slide containing 30,968 human genome probes and 1,082 experimental control probes according to the manufacturer's standard protocols (PhalanxBio, CA, USA).

scan_protocol: The arrays were scanned at 5 μm resolution using a Molecular Dynamics Axon 4100A scanner. Raw intensity signals for each microarray were captured and computed using the GenePixPro™ Software. Raw data formats were stored in TIFF images and GPR data files.

label_protocol: 10 μg of total RNA was amplified with the Amino Allyl MessageAmp II aRNA Amplification Kit (Cat. No. 1753) (Applied Biosystems) according to the instructions. The aRNA product was subsequently conjugated with Cy5? NHS ester (GEH Lifesciences). RNA was purified and fragmented using Ambion’s RNA Fragmentation Reagents.

extract_protocol: Standard Agilent protocol for 2100  Bioanalyzer  from  Agilent Technologies


title: GSC mRNA rep3


title: GSC mRNA rep1


title: NSC microRNA rep1


source_name: TT2 Mouse ES cells JMJD1a KO2 Hypoxia 4h 6X10^5 cells/6cm plate

value: Hypoxia


source_name: TT2 Mouse ES cells JMJD1a KO2 Normoxia 24h 4X10^5 cells/6cm plate

value: 4X10^5 cells/6cm plate


title: CD19-enriched CLL patient sample, patient #9908

description:
CD19-enriched CLL clinical sample
A0018566

value: patient #9908


title: NSC mRNA rep3


title: CD19-enriched CLL patient sample, patient #9516

description:
CD19-enriched CLL clinical sample
A0018567

value: patient #9516


source_name: TT2 Mouse ES cells JMJD1a KO1 Hypoxia 24h 4X10^5 cells/6cm plate


source_name: TT2 Mouse ES cells JMJD1a KO1 Hypoxia 24h 6X10^5 cells/6cm plate


title: CD19-enriched CLL patient sample, patient #9907

description:
CD19-enriched CLL clinical sample
A0018565

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #9907


title: NSC mRNA rep2

value: normal neural stem cells


source_name: TT2 Mouse ES cells JMJD1a KO1 Hypoxia 24h 2X10^5 cells/6cm plate

value: 2X10^5 cells/6cm plate


title: NSC mRNA rep1


title: CD19-enriched CLL patient sample, patient #2903

description:
CD19-enriched CLL clinical sample
A0018564

value: patient #2903

value: B


source_name: TT2 Mouse ES cells JMJD1a KO1 Normoxia 24h 6X10^5 cells/6cm plate


title: CD19-enriched CLL patient sample, patient #304

description:
CD19-enriched CLL clinical sample
A0018558

value: patient #304

value: CD19-enriched CLL patient sample


title: CD19-enriched CLL patient sample, patient #5804

description:
CD19-enriched CLL clinical sample
A0018563

value: patient #5804


title: CD19-enriched CLL patient sample, patient #7108

description:
CD19-enriched CLL clinical sample
A0018562

value: patient #7108

value: C


title: CD19-enriched CLL patient sample, patient #9801

description:
CD19-enriched CLL clinical sample
A0018553

value: patient #9801


source_name: TT2 Mouse ES cells JMJD1a KO1 Normoxia 24h 4X10^5 cells/6cm plate

value: Male

value: TT2 (c57BL/6xCBA)

value: ES cells

value: JMJD1a KO

value: Normoxia


title: CD19-enriched CLL patient sample, patient #7103

description:
CD19-enriched CLL clinical sample
A0018555

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #7103

value: A


source_name: TT2 Mouse ES cells JMJD1a KO1 Hypoxia 4h 4X10^5 cells/6cm plate

value: Hypoxia

value: 4X10^5 cells/6cm plate


title: WT2 Hypoxia 24h 4X10^5 cells/6cm plate

source_name: TT2 Mouse ES cells WT2 Hypoxia 24h 4X10^5 cells/6cm plate

value: Wild-type


source_name: TT2 Mouse ES cells JMJD1a KO1 Hypoxia 4h 6X10^5 cells/6cm plate

value: 6X10^5 cells/6cm plate


title: CD19-enriched CLL patient sample, patient #4705

description:
CD19-enriched CLL clinical sample
A0018554

value: patient #4705

value: B

value: CD19-enriched CLL patient sample


source_name: TT2 Mouse ES cells JMJD1a KO1 Hypoxia 4h 2X10^5 cells/6cm plate

value: 2X10^5 cells/6cm plate


title: CD19-enriched CLL patient sample, patient #104

description:
CD19-enriched CLL clinical sample
A0018551

value: patient #104


title: WT2 Hypoxia 24h 6X10^5 cells/6cm plate

source_name: TT2 Mouse ES cells WT2 Hypoxia 24h 6X10^5 cells/6cm plate

value: Male


source_name: TT2 Mouse ES cells JMJD1a KO1 Normoxia 24h 2X10^5 cells/6cm plate

value: TT2 (c57BL/6xCBA)


title: CD19-enriched CLL patient sample, patient #9904

description:
CD19-enriched CLL clinical sample
A0018559

source_name: CLL clinical sample, CD19-enriched

value: patient #9904


title: CD19-enriched CLL patient sample, patient #2002

description:
CD19-enriched CLL clinical sample
A0018552

value: patient #2002

value: C


title: WT2 Hypoxia 4h 6X10^5 cells/6cm plate

source_name: TT2 Mouse ES cells WT2 Hypoxia 4h 6X10^5 cells/6cm plate

value: ES cells


title: CD19-enriched CLL patient sample, patient #2406

description:
CD19-enriched CLL clinical sample
A0018546

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #2406


title: CD19-enriched CLL patient sample, patient #8201

description:
CD19-enriched CLL clinical sample
A0018547

value: patient #8201


title: WT2 Hypoxia 4h 4X10^5 cells/6cm plate

source_name: TT2 Mouse ES cells WT2 Hypoxia 4h 4X10^5 cells/6cm plate

value: Hypoxia

value: 4X10^5 cells/6cm plate


title: WT2 Hypoxia 4h 2X10^5 cells/6cm plate

source_name: TT2 Mouse ES cells WT2 Hypoxia 4h 2X10^5 cells/6cm plate

value: Wild-type


title: WT2 Hypoxia 24h 2X10^5 cells/6cm plate

source_name: TT2 Mouse ES cells WT2 Hypoxia 24h 2X10^5 cells/6cm plate


title: CD19-enriched CLL patient sample, patient #4206

description:
CD19-enriched CLL clinical sample
A0018550

value: patient #4206


title: Sirt6_KO_retina_rep3

first: Kenneth

middle: N

last: Ross

address: 450 Brookline Ave., Rm M640

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description:
whole retina mRNA from Sirt6 knock-out mice replicate 6/7
Sirt6_KO_6_7

hyb_protocol: Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix MoGene-2_1-st arrays at 45°C for 16 hours.

scan_protocol: Scans were performed on Affymetrix scanners.

data_processing: Raw expression values were normalized using Robust Multiarray Averaging (RMA).

source_name: Mouse total retinal RNA from Sirt6 KO mouse

label_protocol: First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.

growth_protocol: Total retinal RNA from 15 day old Sirt6 wild-type (WT) and knock-out (KO) mice.

extract_protocol: RNA was extracted with chloroform and precipitated with isopropanol by centrifugation (12,000g) at 4°C. The RNA pellet was washed twice with 75% ethanol and resuspended in 30 μL of water treated with diethylpyrocarbonate. The concentration and quality of total RNA samples were assessed using a NANODROP 2000 spectrophotometer (Thermo Scientific Inc., Newark, DE). Only RNA samples with adequate purity ratios (A260/A280 ~ 1.9–2.1) were used for subsequent analyses. Total RNA was isolated using RNeasy Mini Kit (QIAGEN) and cDNA was generated using QuantiTect Reverse Transcription Kit (QIAGEN) according to manufacturer instructions.

treatment_protocol: Retinas were homogenized in phenol-guanidine isothiocyanate (Invitrogen Life Technologies).

value: 15 days old

value: Sirt6 KO

value: retina


title: Sirt6_KO_retina_rep1

description:
whole retina mRNA from Sirt6 knock-out mice replicate 5/31
Sirt6_KO_5_31


title: Sirt6_KO_retina_rep2

description:
whole retina mRNA from Sirt6 knock-out mice replicate 6/6
Sirt6_KO_6_6


title: CD19-enriched CLL patient sample, patient #8001

description:
CD19-enriched CLL clinical sample
A0018541

value: patient #8001

value: CD19-enriched CLL patient sample


title: WT2 Normoxia 24h 6X10^5 cells/6cm plate

source_name: TT2 Mouse ES cells WT2 Normoxia 24h 6X10^5 cells/6cm plate

value: Male

value: TT2 (c57BL/6xCBA)

value: Normoxia

value: 6X10^5 cells/6cm plate


title: CD19-enriched CLL patient sample, patient #9504

description:
CD19-enriched CLL clinical sample
A0018542

value: patient #9504

value: B


title: CD19-enriched CLL patient sample, patient #2705

description:
CD19-enriched CLL clinical sample
A0018543

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #2705


title: Sirt6_WT_retina_rep1

description:
whole retina mRNA from Sirt6 wild-type mice replicate 5/31
Sirt6_WT_5_31

source_name: Mouse total retinal RNA from Sirt6 WT mouse

value: Sirt6 WT


title: WT2 Normoxia 24h 4X10^5 cells/6cm plate

source_name: TT2 Mouse ES cells WT2 Normoxia 24h 4X10^5 cells/6cm plate

value: ES cells

value: 4X10^5 cells/6cm plate


title: Sirt6_WT_retina_rep3

description:
whole retina mRNA from Sirt6 wild-type mice replicate 6/7
Sirt6_WT_6_7


title: WT1 Hypoxia 24h 6X10^5 cells/6cm plate

source_name: TT2 Mouse ES cells WT1 Hypoxia 24h 6X10^5 cells/6cm plate

value: Wild-type

value: Hypoxia


title: Sirt6_WT_retina_rep2

description:
whole retina mRNA from Sirt6 wild-type mice replicate 6/6
Sirt6_WT_6_6

value: 15 days old


title: CD19-enriched CLL patient sample, patient #5003

description:
CD19-enriched CLL clinical sample
A0018539

value: patient #5003

value: C


title: WT1 Hypoxia 24h 4X10^5 cells/6cm plate

source_name: TT2 Mouse ES cells WT1 Hypoxia 24h 4X10^5 cells/6cm plate


title: WT2 Normoxia 24h 2X10^5 cells/6cm plate

source_name: TT2 Mouse ES cells WT2 Normoxia 24h 2X10^5 cells/6cm plate

value: 2X10^5 cells/6cm plate


title: WT1 Hypoxia 24h 2X10^5 cells/6cm plate

source_name: TT2 Mouse ES cells WT1 Hypoxia 24h 2X10^5 cells/6cm plate

value: Male


title: CD19-enriched CLL patient sample, patient #6302

description:
CD19-enriched CLL clinical sample
A0018537

value: patient #6302

value: CD19-enriched CLL patient sample


title: WT1 Hypoxia 4h 6X10^5 cells/6cm plate

source_name: TT2 Mouse ES cells WT1 Hypoxia 4h 6X10^5 cells/6cm plate

value: TT2 (c57BL/6xCBA)

value: 6X10^5 cells/6cm plate


title: c-Kit+NS-GFPmiddle

city: Kanazawa

first: Atsushi

last: Hirao

address: kakuma

department: Division of Molecular Genetics

country: Japan

institute: kanazawa university

description: c-Kit+NS-GFPmiddle cells

hyb_protocol: Mouse Genome 430 2.0 Array (Affymetrix Inc., Santa Clara, CA) was used for hybridization. The array was stained and washed with GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: Images were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: The scanned image of the microarray was converted to fluorescence intensities for 45,101 probe sets by using GeneChip Operating Software (GCOS ver. 1.2, Affymetrix). CEL files were processed using Data Mining Tools(Affymetrix) and Microarray Suite version 5.0 (MAS 5.0) for background correction and probe summarization.We extracted 17419 probes which detected as present in all 4 samples from 45101 probes. The data were normalized with R version 3.0.2.  In global normalization, the trimmed mean target intensity of each array was arbitrarily set to 500. The expression data was log2 transformed.

source_name: sorted AML cells mouse bone marrow

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

extract_protocol: Total RNA from 2 x 104 each fractionated leukemia cells based on NS-GFP level and c-Kit expression was isolated by using TRIzol (Invitrogen).

tag: strain background

value: bone marrow

value: sorted c-Kit+NS-GFP middle cells


title: CD19-enriched CLL patient sample, patient #502

description:
CD19-enriched CLL clinical sample
A0018536

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #502

value: B


title: CD19-enriched CLL patient sample, patient #2802

description:
CD19-enriched CLL clinical sample
A0018534

value: patient #2802


title: CD19-enriched CLL patient sample, patient #2910

description:
CD19-enriched CLL clinical sample
A0018531

value: patient #2910


title: CD19-enriched CLL patient sample, patient #6308

description:
CD19-enriched CLL clinical sample
A0018528

value: patient #6308

value: A


title: CD19-enriched CLL patient sample, patient #8405

description:
CD19-enriched CLL clinical sample
A0018530

value: patient #8405


title: c-Kit+NS-GFPhigh

description: c-Kit+NS-GFPhigh cells

value: sorted c-Kit+NS-GFP high cells


title: WT1 Normoxia 24h 6X10^5 cells/6cm plate

source_name: TT2 Mouse ES cells WT1 Normoxia 24h 6X10^5 cells/6cm plate

value: ES cells

value: Wild-type

value: Normoxia


title: WT1 Hypoxia 4h 2X10^5 cells/6cm plate

source_name: TT2 Mouse ES cells WT1 Hypoxia 4h 2X10^5 cells/6cm plate

value: Male

value: Hypoxia

value: 2X10^5 cells/6cm plate


title: WT1 Normoxia 24h 4X10^5 cells/6cm plate

source_name: TT2 Mouse ES cells WT1 Normoxia 24h 4X10^5 cells/6cm plate

value: TT2 (c57BL/6xCBA)

value: 4X10^5 cells/6cm plate


title: WT1 Normoxia 24h 2X10^5 cells/6cm plate

source_name: TT2 Mouse ES cells WT1 Normoxia 24h 2X10^5 cells/6cm plate


title: WT1 Hypoxia 4h 4X10^5 cells/6cm plate

source_name: TT2 Mouse ES cells WT1 Hypoxia 4h 4X10^5 cells/6cm plate


title: CD19-enriched CLL patient sample, patient #9815

description:
CD19-enriched CLL clinical sample
A0018526

source_name: CLL clinical sample, CD19-enriched

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #9815

value: CD19-enriched CLL patient sample


title: c-Kit-NS-GFPlow

description: c-Kit-NS-GFPlow cells

value: bone marrow

value: sorted c-Kit-NS-GFP low cells


title: HDAC4 KO, rep10

city: Lausanne

first: Tamara

last: Seredenin

address: AI2135 Station 15 EPFL

country: Switzerland

institute: EPFL

description: Gene expression data.

hyb_protocol: cRNA (15 ug) was hybridized to GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix) at 45°C for 17 hours, washed and stained according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007).

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: Microarray quality control was performed using the software package provided on RACE (http://race.unil.ch). Chips with a median normalized unscaled standard error > 1.05 were excluded. Affymetrix annotations (version 30) were used for probeset-to-gene assignments. T-test was performed to assess the differences in gene expression between treated and untreated groups for each genotype.

label: Biotin

source_name: Brain, HDAC4 KO, P3

label_protocol: Biotinylated cRNAs were prepared from 200ng of total RNA using the GeneChip® 3' IVT Express Kit (Affymetrix) following the instructions of the manufacturer.

growth_protocol: Mouse housing conditions and genotyping were performed according to relevant national and international giudelines. The Hdac4 knock-out colony was maintained by backcrossing heterozygous males to B6CBAF1/OlaHsd females (Harlan Olac, Bicester, UK). Homozygotes were generated by intercrossing as required. All animals had unlimited access to water and breeding chow (Special Diet Services, Witham, UK). Mice were subject to a 12 hour light/dark cycle.

extract_protocol: Total RNA from whole postnatal brains at P3 was extracted with the mini-RNA kit according to manufacturer instructions (Qiagen). The reverse transcription reaction (RT) was performed using MMLV superscript reverse transcriptase (Invitrogen) and random hexamers (Operon).

treatment_protocol: No treatment.

tag: strain/background

value: HDAC4 KO

value: male

value: brain

value: postnatal day 3


title: HDAC4 KO, rep8

description: Gene expression data.

tag: genotype/variation


title: HDAC4 KO, rep9

description: Gene expression data.

value: female

tag: tissue


title: HDAC4 KO, rep7

description: Gene expression data.


title: CD19-enriched CLL patient sample, patient #3807

description:
CD19-enriched CLL clinical sample
A0018525

value: patient #3807

value: A


title: HDAC4 KO, rep6

description: Gene expression data.


title: Med23null2_Mock

city: Memphis

first: Suzanne

middle: J

last: Baker

state: TN

address: 262 Danny Thomas Place

department: Developmental Neurobiology

institute: St Jude Children's Research Hospital

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on an Affymetrix Murine Genome U74A Version 2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000.

data_processing: The data were analyzed with GeneChip Operating Software version 1.4 using the default MAS 5.0 algorithm settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Med23flox/flox;Lck-Cre thymocytes (mouse ID LK1840) rested 4 hours then 3hrs mock treatment

label_protocol: Biotinylated cRNA were prepared from 10 micrograms of total RNA according to the standard Affymetrix protocol (Expression Analysis Technical Manual 701025 rev1, 2001, Affymetrix)

growth_protocol: Mice were maintained under protocols in accordance with St Jude IACUC

extract_protocol: Following treatment, the cells were spun down and resuspended in 1ml of Trizol.  RNA was extracted following the manufacturers instructions.

treatment_protocol: Thymuses were harvested from mice sacrificed by CO2 inhalation and placed in DPBS+2%FBS on ice.  Single cell suspensions were made by pressing the thymus through a 70um mesh strainer using the rubber plunger end from a 3cc plastic syringe and 6ml warm RPMI+10%FBS/P/S/l-glu/BME.  Cells were counted and seeded at 3x10^7 per single well of a 6 well plate in 3ml final volume of same medium and allowed to rest in 37C incubator for four hours.  After rest period, the thymocytes and medium were transferred to a new well +/-plate bound anti-CD3 for three hours.

value: thymus

value: thymocytes

tag: strain

value: 6-7 weeks


title: Med23null1_Mock

source_name: Med23flox/flox;Lck-Cre thymocytes (mouse ID LK1836) rested 4 hours then 3hrs mock treatment


title: CD19-enriched CLL patient sample, patient #6908

description:
CD19-enriched CLL clinical sample
A0018524

value: patient #6908

value: B


title: CD19-enriched CLL patient sample, patient #5303

description:
CD19-enriched CLL clinical sample
A0018527

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #5303


title: Med23null2_CD3

source_name: Med23flox/flox;Lck-Cre thymocytes (mouse ID LK1840) rested 4 hours then 3hrs plate bound CD3


title: HDAC4 KO, rep5

description: Gene expression data.


title: Med23null1_CD3

source_name: Med23flox/flox;Lck-Cre thymocytes (mouse ID LK1836) rested 4 hours then 3hrs plate bound CD3


title: Med23flox2_Mock

source_name: Med23flox/flox thymocytes (mouse ID LK1844) rested 4 hours then 3hrs mock treatment


title: HDAC4 KO, rep4

description: Gene expression data.


title: CD19-enriched CLL patient sample, patient #3312

description:
CD19-enriched CLL clinical sample
A0018521

value: patient #3312

value: C

value: CD19-enriched CLL patient sample


title: Med23flox2_CD3

source_name: Med23flox/flox thymocytes (mouse ID LK1844) rested 4 hours then 3hrs plate bound CD3


title: Med23flox1_CD3

source_name: Med23flox/flox thymocytes (mouse ID LK1826) rested 4 hours then 3hrs plate bound CD3


title: CD19-enriched CLL patient sample, patient #3006

description:
CD19-enriched CLL clinical sample
A0018520

value: patient #3006


title: CD19-enriched CLL patient sample, patient #3311

description:
CD19-enriched CLL clinical sample
A0018519

value: patient #3311


title: CD19-enriched CLL patient sample, patient #3803

description:
CD19-enriched CLL clinical sample
A0018523

value: patient #3803


title: Lck2_CD3

source_name: Med23+/+;Lck-Cre thymocytes (mouse ID LK1862) rested 4 hours then 3hrs plate bound CD3


title: HDAC4 KO, rep1

description: Gene expression data.

value: HDAC4 KO

value: brain

value: postnatal day 3


title: HDAC4 KO, rep3

description: Gene expression data.

value: male


title: HDAC4 KO, rep2

description: Gene expression data.


title: Med23flox1_Mock

source_name: Med23flox/flox thymocytes (mouse ID LK1826) rested 4 hours then 3hrs mock treatment

value: thymus

value: female


title: Lck2_Mock

source_name: Med23+/+;Lck-Cre thymocytes (mouse ID LK1862) rested 4 hours then 3hrs mock treatment

value: thymocytes

value: 6-7 weeks


title: CD19-enriched CLL patient sample, patient #6907

description:
CD19-enriched CLL clinical sample
A0018518

value: patient #6907


title: CD19-enriched CLL patient sample, patient #9813

description:
CD19-enriched CLL clinical sample
A0018522

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #9813

value: B


title: WT, rep9

description: Gene expression data.

source_name: Brain, WT, P3

value: WT


title: CD19-enriched CLL patient sample, patient #9218

description:
CD19-enriched CLL clinical sample
A0018517

value: patient #9218

value: CD19-enriched CLL patient sample


title: WT, rep10

description: Gene expression data.


title: WT, rep8

description: Gene expression data.


title: WT, rep7

description: Gene expression data.


title: WT, rep6

description: Gene expression data.


title: Lck1_CD3

source_name: Med23+/+;Lck-Cre thymocytes (mouse ID LK1816) rested 4 hours then 3hrs plate bound CD3


title: CD19-enriched CLL patient sample, patient #9710

description:
CD19-enriched CLL clinical sample
A0018513

value: patient #9710


title: WT, rep5

description: Gene expression data.


title: WT, rep4

description: Gene expression data.


title: CD19-enriched CLL patient sample, patient #8005

description:
CD19-enriched CLL clinical sample
A0018514

value: patient #8005


title: CD19-enriched CLL patient sample, patient #1404

description:
CD19-enriched CLL clinical sample
A0018508

value: patient #1404


title: CD19-enriched CLL patient sample, patient #9810

description:
CD19-enriched CLL clinical sample
A0018512

value: patient #9810


title: CD19-enriched CLL patient sample, patient #6011

description:
CD19-enriched CLL clinical sample
A0018511

value: patient #6011


title: CD19-enriched CLL patient sample, patient #9707

description:
CD19-enriched CLL clinical sample
A0018509

value: patient #9707


title: Lck1_Mock

source_name: Med23+/+;Lck-Cre thymocytes (mouse ID LK1816) rested 4 hours then 3hrs mock treatment

value: thymus


title: WT, rep2

description: Gene expression data.

value: female

value: brain

value: postnatal day 3


title: CD19-enriched CLL patient sample, patient #4707

description:
CD19-enriched CLL clinical sample
A0018516

value: patient #4707


title: OE-HRA1 #1_2NS

city: Riverside

first: Seung Cho

last: Lee

address: 2150 Batchelor Hall

department: Botany & Plant Sciences

institute: University of California Riverside

hyb_protocol: Hybridization of 12 μg of biotin-labeled cRNA to each Arabidopsis ATH1 Genome Array (GeneChip System®, Affymetrix) chips were performed at 45 °C for 16 h, in the Affymetrix GeneChip Workstation (hybridization oven 640, Fluidics Station 450), using 10 µg of Biotin-labeled aRNA, according to the manufacturer's protocol.

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

data_processing: CEL files from the Affymetrix Chips were processed by use of the R program (http://cran.at.r-project.org/) and Bioconductor packages (http://www.bioconductor.org/). The Robust Multi-chip Average (RMA) normalization was performed using the default settings of the corresponding R function. Present, Marginal or Absent (P/M/A) calls were computed with the affy MAS5.0 package .

organism: Arabidopsis thaliana

source_name: 7-d-old seedlings_OE-HRA1#1_2NS

label_protocol: biotin

growth_protocol: Arabidopsis seeds were sterilized, stratified for 3 days at 4 °C and grown on solid MS media [0.43 % (w/v) Murashigi Skoog (MS) salts (Sigma)], 0.4 % (w/v) Phytagel (Sigma), 1 % (w/v) sucrose, pH 5.7) in a vertical orientation in a growth chamber (Model # CU36L5, Percival Scientific, Perry, IA) under a long day cycle (16 h light at ~80 μmol photons m-2 s-1 and 8 h darkness) at 23°C for 7 days before treatments.

extract_protocol: Total RNA was extracted from frozen pulverized plant tissues using QIAGEN RNeasy Plant Mini kit according to the manufacture's protocol. RNase-Free DNase treatment was conducted during the column purification process.

treatment_protocol: Plates with 7-d-old seedlings were transferred to Lucite chambers where they were deprived of air by displacement for argon gas (99.9%) for 2 hours. The hypoxic stress (2HS) treatment was applied under dim light (5 to 7 μmol photons m-2 s-1) at the end of light cycle. For non-stress (2NS) treatment, MS plates were placed for 2 hours in the Lucite chambers that were open to ambient air.

tag: ecotype

value: HRA1 overexpression

tag: treatment

value: 2 h non-stress (2NS)

value: 7-day-old seedlings


title: WT, rep1

description: Gene expression data.

value: WT

value: male


title: OE-HRA1 #2_2HS

source_name: 7-d-old seedlings_OE-HRA1#2_2HS

value: 2 h hypoxia stress (2HS)


title: CD19-enriched CLL patient sample, patient #1004

description:
CD19-enriched CLL clinical sample
A0018507

source_name: CLL clinical sample, CD19-enriched

tag: subject status

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #1004

value: C

value: CD19-enriched CLL patient sample


title: CD19-enriched CLL patient sample, patient #9015

description:
CD19-enriched CLL clinical sample
A0018506

tag: patient id

value: patient #9015

value: A


title: CD19-enriched CLL patient sample, patient #7201

description:
CD19-enriched CLL clinical sample
A0018504

value: patient #7201

tag: binet stage

value: B


title: Col-0_2HS_rep1

source_name: 7-d-old seedlings_Col-0_2NS

value: wild-type


title: Col-0_2HS_rep2


title: H460R2 vs WT TechRep2

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description: H460R (Sample2) (Cy5) vs H460 (Sample1) (Cy3)

hyb_protocol: Hybridization was made according to the Agilent kit: Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling)

scan_protocol: Scanned on an Agilent DNA Microarray Scanner G2505C

data_processing: Raw intensities were background-substracted by normexp with an offset of 50. Background-substracted values were log2 scaled, normalized by loess (intra-slide) and then by inter-slide quantile adjustment (of the loess-normalized intensities). All calculations were performed with the corresponding functions of Bioconductor packages limma and Affy.

source_name: H460R Rep2

label_protocol: Probes were labeled using the Agilent kit: Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) following the provided instructions.

growth_protocol: H460 and H460R cells were grown in RPMI media supplemented with 10% Foetal Bovine Serum. H460C (CSC) cells were grown in DMEM/F12 (1:1) media supplemented with 2mM glutamine, 5mM Hepes, 0.4% BSA, N2 supplement (Gibco) and 20ng/mm of EGF and FGF-b growth factors.

extract_protocol: Total RNA was extracted using Trizol according to the manufacturer's instructions

treatment_protocol: H460R cells were treated with 0.5 µg/ml of cisplatin for 72 hours and cultured in drug-free medium thereafter. H460C CSCs were obtained by culturing H460 cells in the above mentioned defined media (growth protocol) under non-adherent conditions.

value: cisplatin-resistant H460 cells (H460R)

source_name: H460 NSCLC cell line


title: Col-0_2NS_rep1


title: WT, rep3

description: Gene expression data.

value: female

value: brain

value: postnatal day 3


title: T2DM_15

type: protein

city: Pohang, Gyungbuk

first: Sehyun

last: Chae

address: San 31, Hyoja-Dong, Nam-Gu

department: Department of Interdisciplinary Bioscience and Bioengineering(I-BIO)

institute: POSTECH

description: Auto-antibodies from serum samples were profiled using a high-density, fluorescence-based protein microarray containing duplicate spots of 9,480 human proteins derived from the Ultimate ORF collection

hyb_protocol: Following the manufacturers’ instructions, serum diluted 1:500 in PBST buffer was incubated on the microarray slides for 90 minutes.

scan_protocol: The array slides were scanned with a GenePix® 4000B Fluorescent Scanner (Molecular Devices).

data_processing:
Signal intensities were acquired using ProtoArray™ Prospector, a software tool developed for ProtoArray data by Invitrogen.
Protein microarray used for this study contains 18,960 protein spots and >4,000 control spots. Raw data (gpr file) obtained from GenePix image quantification software contains all the information of intensities about protein and control spots. Analysing the gpr file containing 23,232 spot intensities (18,960 protein spots + >4,000 control spots), ProtoArray Prospector software provides 18,960 intensity values of signal from protein features. Please note that the output of ProtoArray Prospector v5.2 contains Database ID (e.g. NM_024548.2, BC011414.1 etc), Ultimate ORF ID (e.g. IOH27601, IOH9720 etc) which corresponds to Ultimate ORFs provided in a Gateway entry vector, and Array ID (e.g. B01R01C01). The sample data table is formatted using Database IDs.
The signal intensities were converted to log2-intensities and then normalized using the quantile normalization method

molecule: protein

label_protocol: standard Invitrogen protocol

extract_protocol: The serum was collected from 16 T1DM, 16 type 2 diabetes (T2DM) patients, and 27 healthy controls with normal glucose tolerance (NGT)

tag: disease state

value: type 2 diabetes mellitus (T2DM)

tag: age (yrs)

value: Serum


title: H460R1 vs WT TechRep1

description: H460R (Sample1) (Cy3) vs H460 (Sample1) (Cy5)

source_name: H460R Rep1


title: H460C2 vs WT TechRep2

description: H460C (Sample2) (Cy5) vs H460 (Sample1) (Cy3)

source_name: H460C Rep2

value: H460-derived cancer stem cells (H460C)


title: H460R2 vs WT TechRep1

description: H460R (Sample2) (Cy3) vs H460 (Sample1) (Cy5)


title: CD19-enriched CLL patient sample, patient #2902

description:
CD19-enriched CLL clinical sample
A0018497

data_processing:
.CEL files were background adjusted, quantile normalized and summarized at the transcript level using only core probesets that mapped to RefSeq transcripts, by apt (Affymetrix Power Tool version 1.12.0) software that used the RMA algorithm.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.na29.hg18.probeset.csv

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: CLL samples were positively enriched by magnetic cell sorting using CD19 microbeads and MACS columns (Miltenyi Biotec Ltd, Surrey, UK). Total RNA was isolated using Trizol (Invitrogen) and RNeasy kit (QIAGEN).

value: patient #2902


title: H460R1 vs WT TechRep2

description: H460R (Sample1) (Cy5) vs H460 (Sample1) (Cy3)


title: T2DM_16


title: T2DM_14


title: CD19-enriched CLL patient sample, patient #9204

description:
CD19-enriched CLL clinical sample
A0018493

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #9204


title: CD19-enriched CLL patient sample, patient #6601

description:
CD19-enriched CLL clinical sample
A0018489

value: patient #6601

value: C


title: T2DM_12


title: CD19-enriched CLL patient sample, patient #9507

description:
CD19-enriched CLL clinical sample
A0018491

value: patient #9507

value: CD19-enriched CLL patient sample


title: Col-0_2NS_rep2

value: 2 h non-stress (2NS)

value: 7-day-old seedlings


title: T2DM_13


title: CD19-enriched CLL patient sample, patient #9510

description:
CD19-enriched CLL clinical sample
A0018496

value: patient #9510


title: T2DM_10


title: H460C1 vs WT TechRep1

description: H460C (Sample1) (Cy3) vs H460 (Sample1) (Cy5)

source_name: H460C Rep1


title: H460_cells-24h-differentiation-REP1

hyb_protocol: For each hybridization 600 ng of Cy3 probes were mixed and added to 5 ul of 10x Blocking Agent, 1 ul of 25x Fragmentation Buffer and Nuclease free water in a 25 ul reaction, incubated at 60¼C for 30 minutes to fragment RNA and stopped with  25 ul of 2x Hybridization Buffer. The samples were placed on ice and quickly loaded onto arrays, hybridized at 65¼C for 17 hours in a Hybridization oven rotator and then washed in GE wash buffer 1 at room temperature (1 minute) and in GE Wash Buffer 2 at 37¼C (1 minute). Arrays were dried by centrifugation at 2000 rpm for 2 minutes.

scan_protocol: Raw GPR files were obtained by Axon's GenePix 4000B scanner and GenePixPro 5.1 software.

data_processing: Local background was corrected by normexp method of limma package with an offset of 50 (Smyth, 2004). Background corrected intensities were transformed to log scale (base 2). To have similar intensity distribution across all arrays, background-corrected-intensity values were normalized by adjusting their quantiles (Bolstad et al., 2003).

label_protocol: Total RNA (200 ng) was amplified using One Color Low Input Quick Amp Labeling Kit (Agilent Technologies) and purified with RNeasy Mini Kit (Qiagen).

growth_protocol: H460C (CSC) cells were grown in DMEM/F12 (1:1) media supplemented with 2mM glutamine, 5mM Hepes, 0.4% BSA, N2 supplement (Gibco) and 20ng/mm of EGF and FGF-b growth factors

treatment_protocol: H460C cells were differentiated by culture in RPMI media supplemented with 10% Foetal Bovine Serum under adherent conditions.

value: Lung cancer (NSCL) H460 cells

tag: time culture (hours)


title: CD19-enriched CLL patient sample, patient #8701

description:
CD19-enriched CLL clinical sample
A0018487

value: patient #8701

value: B


title: H460C2 vs WT TechRep1

description: H460C (Sample2) (Cy3) vs H460 (Sample1) (Cy5)

tag: cell line


title: c-Kit-NS-GFPmiddle

description: c-Kit-NS-GFPmiddle cells

source_name: sorted AML cells mouse bone marrow

value: bone marrow

tag: cell type

value: sorted c-Kit-NS-GFP middle cells


title: CD19-enriched CLL patient sample, patient #2408

description:
CD19-enriched CLL clinical sample
A0018486

value: patient #2408


title: T2DM_9

value: type 2 diabetes mellitus (T2DM)

value: Serum


title: T2DM_11


title: CD19-enriched CLL patient sample, patient #9201

description:
CD19-enriched CLL clinical sample
A0018485

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #9201


title: T2DM_8


title: T2DM_6


title: H460C1 vs WT TechRep2

description: H460C (Sample1) (Cy5) vs H460 (Sample1) (Cy3)

value: H460-derived cancer stem cells (H460C)


title: H460_cells-9h-differentiation-REP2


title: CD19-enriched CLL patient sample, patient #9602

description:
CD19-enriched CLL clinical sample
A0018481

value: patient #9602


title: H460_cells-3h-differentiation-REP2


title: T2DM_7

description: Auto-antibodies from serum samples were profiled using a high-density, fluorescence-based protein microarray containing duplicate spots of 9,480 human proteins derived from the Ultimate ORF collection


title: CD19-enriched CLL patient sample, patient #2302

description:
CD19-enriched CLL clinical sample
A0018482

value: patient #2302

value: C


title: H460_cells-9h-differentiation-REP1


title: T2DM_5


title: CD19-enriched CLL patient sample, patient #9601

description:
CD19-enriched CLL clinical sample
A0018480

value: patient #9601

value: CD19-enriched CLL patient sample


title: H460_cells-3h-differentiation-REP1


title: CD19-enriched CLL patient sample, patient #303

description:
CD19-enriched CLL clinical sample
A0018479

value: patient #303


title: T2DM_3


title: CD19-enriched CLL patient sample, patient #3901

description:
CD19-enriched CLL clinical sample
A0018477

value: patient #3901


title: CD19-enriched CLL patient sample, patient #7301

description:
CD19-enriched CLL clinical sample
A0018476

value: patient #7301


title: H460_cells-undifferentiated-REP2

value: Lung cancer (NSCL) H460 cells


title: T2DM_4


title: T2DM_2


title: CD19-enriched CLL patient sample, patient #6007

description:
CD19-enriched CLL clinical sample
A0018475

value: patient #6007

value: B


title: CD19-enriched CLL patient sample, patient #5701

description:
CD19-enriched CLL clinical sample
A0018474

value: patient #5701


title: T2DM_1

value: type 2 diabetes mellitus (T2DM)


title: T1DM_16

value: type 1 diabetes mellitus (T1DM)

value: Serum


title: CD19-enriched CLL patient sample, patient #4902

description:
CD19-enriched CLL clinical sample
A0018473

value: relapsed chronic lymphocytic leukemia (CLL) patient

value: patient #4902


title: T1DM_15


title: prostate cancer biopsy-3

last: Mizokami

state: Ishikawa

address: 13-1 Takara-machi

department: School of Medicine

institute: Kanazawa University

description: Gleason score (4+3=7), PSA 96.7

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505B Microarray Scanner at 5 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 014850_D_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: prostate biopsy sample

label_protocol: Agilent one-color Quick Amp Labeling Kit labeling protocol

extract_protocol: Total RNA extracted using Rneasy Mini Kit (QIAGEN) following manufacurer's instruction.

treatment_protocol: We performed prostate needle biopsy for diagnosis and they were not conducted by any treatments until biopsy.

tag: age

value: 82 years old

tag: case

value: Prostate cancer, Stage T3a,N0,M0

tag: gleason score

tag: psa


title: prostate cancer biopsy-2

description: Gleason score (4+4=8), PSA 227.8

value: 72 years old

value: Prostate cancer, Stage T4, N1,M0


title: H460_cells-undifferentiated-REP1


title: normal prostate biopsy-3

description: Benign prostate hypertrophy (50 g)

value: 70 years old

value: Benign prostate hypertrophy (50 g)


title: prostate cancer biopsy-1

description: Gleason score (4+4=8), PSA 55.0

value: 77 years old

value: Prostate cancer, Stgae T3a,N0,M0


title: T1DM_13


title: normal prostate biopsy-1

description: Benign prostate hypertrophy (33 g)

value: 59 years old

value: Benign prostate hypertrophy (33 g)


title: normal prostate biopsy-2

description: Benign prostate hypertrophy (67 g)

value: 74 years old

value: Benign prostate hypertrophy (67 g)


title: CD19-enriched CLL patient sample, patient #301

address: 1 DNA Way

institute: Genentech

description:
CD19-enriched CLL clinical sample
A0018472

value: patient #301

value: C

value: CD19-enriched CLL patient sample


title: T1DM_14

value: type 1 diabetes mellitus (T1DM)

value: Serum


title: T1DM_12