title: BC00051

value: White

tag: pathological stage_t

value: neg

value: Basal

value: referene pool


title: human ileum, sample 34

status: Public on Dec 01 2012

type: RNA

city: Toronto

first: Boyko

last: Kabakchiev

state: Ontario

address: 60 Murray Street, Room L3-004

department: Samuel Lunenfeld Research Institute

country: Canada

institute: Mount Sinai Hospital

description:
sample_id: 117
Ileal tissue biopsies from human, post IPAA subjects

hyb_protocol: GeneChip Hybridization, Wash, and Stain Kit (Affymetrix)

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing:
Summarized probe cell intensity data were generated with an Affymetrix GeneChip Command Console. Probe-level summarization files were produced and the data were background-adjusted, normalized and log-transformed with a robust multiarray average (RMA) algorithm in Affymetrix Expression Console. The empirical Bayes (EB) method described by Johnson, W.E. et al. (2007) was applied to the normalized data to correct for batch effects which may have resulted from a non-linear sample extraction and microarray processing schedule. Lastly, duplicate and ambiguous Affymetrix probesets (Release 32) as well as those which no longer mapped to a gene in the current human genome build (GRCh37.p5) were removed from further analysis.
probe_group_file: HuGene-1_0-st-v1.r4.pgf
meta-probeset_file: HuGene-1_0-st-v1.r4.mps

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: ileum

label_protocol: GeneChip WT Terminal Labeling and Controls Kit (Affymetrix)

extract_protocol: miRNeasy Mini Kit (QIAGEN)

tag: batch

tag: gender

value: M

value: yes

tag: diagnosis

value: UC


title: human ileum, sample 37

description:
sample_id: 369
Ileal tissue biopsies from human, post IPAA subjects

value: F


title: human ileum, sample 35

description:
sample_id: 12
Ileal tissue biopsies from human, post IPAA subjects


title: BC00048 N

city: Chicago

first: Ravand

last: Samaeekia

state: IL

department: Ben May Department of Cancer Research

country: USA

institute: University of Chicago

description: Total RNA was submitted to exiqon for 757 miRNA expression detection and normalized based on pooled samples.

hyb_protocol: Using Tecan hybridization stations the hybridization and washing steps were fully automated for higher reproducibility.

scan_protocol: Arrays were scanned with highly sensitive equipment in ozone free environment to reduce day-to-day variation to a minimum. Image Analysis was then performed to quantify the signals on the arrays.

data_processing: First, a technical quality assessment was performed based on results from spike in controls, flagging of spots, background intensity levels and signal intensity distribution.The data obtained was normalized using methods applicable to the performed experiment. Customized data analysis can also be provided (including heat map/Unsupervised Hierarchical Clustering, PCA-plots etc based on TTests or ANOVA).

source_name: Normal

label_protocol: Exiqon commercial miRCURY™ LNA Array Power labeling kit for labeling. This method allowed highly efficient and uniform labeling of microRNAs with minimal sequence bias.

extract_protocol: The Qiagen miRNA easy kit with total RNA extraction.

tag: tissue

value: Normal

source_name: Common Reference Pool

tag: sample type


title: human ileum, sample 29

description:
sample_id: 161
Ileal tissue biopsies from human, post IPAA subjects

value: FAP


title: human ileum, sample 32

description:
sample_id: 619
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 33

description:
sample_id: 460
Ileal tissue biopsies from human, post IPAA subjects


title: BC00049

source_name: Breast Tumor

value: Breast Tumor

tag: OS time

tag: race

tag: grade

tag: tumor size

tag: tnm

tag: er

tag: pr

value: U

tag: tumor subtype ihc


title: BC00048 T


title: BC00053

value: Black

value: pos

value: Unclassified


title: PREC 2

type: genomic

city: Atlanta

first: Khanjan

last: Gandhi

state: Georgia

address: 1365-B Clifton Rd NE, Room 4107

institute: Winship Cancer Institute, Emory University.

description: SAMPLE 13

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: BeadChips were scanned using the Illumina BeadArray Scanner.

data_processing: Average beta values were calculated using Genome Studio Software v2010.3.

label: Biotin

molecule: genomic DNA

source_name: PREC normal prostate cells, untreated

label_protocol: PCR product was prepared with the standard Illumina protocol for arrays.

growth_protocol: ARCaP-E and ARCaP-M cells were purchased from Novicure Biotechnology and propagated in MCaP-Medium (Novicure Biotechnology, Inc, Birmingham, AL), supplemented with 5% FBS, 200mM L-glutamine, and pen-strep. Additionally, PREC cells (Lonza, Basel, Switzerland) were used as a normal human prostate cell line control.  Total DNA was submitted to the Emory Winship Cancer Institute Cancer Genomics Shared Resource for analysis with Illumina 27K CpG Methylation Arrays that interrogate 27,578 CpG loci > 14,000 genes using the Illumina Beadstation 500 instrument.

extract_protocol: DNA was isolated from the cells.

treatment_protocol: ARCaP-E and ARCaP-M cells were treated with DMSO control, 20 µM genistein, or 1 µM 5-aza for six days, and PrEC cells were untreated. Fresh drugs and media were changed every other day.

tag: cell line

value: PREC

tag: cell type

value: normal prostate cells

tag: treatment


title: ARCaP-E DMSO 2D

description: SAMPLE 14

source_name: ARCaP-E prostate cancer cells, DMSO

value: ARCaP-E

value: prostate cancer cells

value: DMSO


title: ARCaP-M 5-aza 1D

description: SAMPLE 11

source_name: ARCaP-M prostate cancer cells, 5-aza-deoxycytidine

value: ARCaP-M


title: human ileum, sample 30

description:
sample_id: 646
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 62

description:
sample_id: 225
Ileal tissue biopsies from human, post IPAA subjects


title: PREC 1

description: SAMPLE 12


title: ARCaP-E 5-aza 3D

description: SAMPLE 10

source_name: ARCaP-E prostate cancer cells, 5-aza-deoxycytidine


title: human ileum, sample 31

description:
sample_id: 122
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 28

description:
sample_id: 417
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 27

description:
sample_id: 300
Ileal tissue biopsies from human, post IPAA subjects

value: IC


title: ARCaP-M DMSO 2D

description: SAMPLE 7

source_name: ARCaP-M prostate cancer cells, DMSO


title: ARCaP-M GEN 3D

description: SAMPLE 9

source_name: ARCaP-M prostate cancer cells, genistein

value: genistein


title: BC00043

value: White

tag: pathological stage_t

value: neg

value: M

value: Basal

value: referene pool


title: BC00042

value: Breast Tumor

value: U

value: LumA


title: human ileum, sample 26

description:
sample_id: 392
Ileal tissue biopsies from human, post IPAA subjects

tag: batch

value: F

value: no

value: FAP


title: ARCaP-M DMSO 1D

description: SAMPLE 6


title: human ileum, sample 25

description:
sample_id: 378
Ileal tissue biopsies from human, post IPAA subjects

tag: gender

value: yes

value: UC


title: ARCaP-M GEN 2D

description: SAMPLE 8

value: prostate cancer cells


title: BC00040

value: unknown


title: BC00033

value: Black

value: pos

value: LumB


title: BC00036

value: neg


title: BC00030 N

value: Normal


title: BC00016 N

source_name: Normal Breast Tissue

value: Normal Breast Tissue


title: BC00017

value: White

value: referene pool


title: BC00016 T

value: Breast Tumor

value: U

value: unclassified


title: BC00030 T


title: human ileum, sample 24

description:
sample_id: 475
Ileal tissue biopsies from human, post IPAA subjects

value: M

tag: diagnosis


title: ARCaP-E DMSO 1D

description: SAMPLE 3

value: ARCaP-E

value: DMSO


title: 07C64722 genomic DNA from LCL

city: Los Angeles

first: Kimberly

middle: A

last: Aldinger

address: 1501 San Pablo St.

department: Zilkha Neurogenetic Institute

institute: University of Southern California

description: LCL sample

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: Signal intensities were extracted from BeadStudio and processed as per PMID:20399149. Average Beta VALUES are provided in the data table below and Unmethylated and methylated signal intensities are provided as a supplementary file on the Series record.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was purchased from Coriell or Rutgers repositories

value: Female

value: LCL

tag: disease state

value: Control


title: ARCaP-E GEN 1D

description: SAMPLE 5

source_name: ARCaP-E prostate cancer cells, genistein

value: prostate cancer cells

value: genistein


title: human ileum, sample 22

description:
sample_id: 546
Ileal tissue biopsies from human, post IPAA subjects

value: yes

value: FAP


title: BC00010

tag: tissue

value: neg

value: pos

tag: sample type


title: human ileum, sample 21

description:
sample_id: 351
Ileal tissue biopsies from human, post IPAA subjects

value: UC


title: human ileum, sample 23

description:
sample_id: 51
Ileal tissue biopsies from human, post IPAA subjects


title: ARCaP-E DMSO 3D

description: SAMPLE 4


title: human ileum, sample 18

description:
sample_id: 605
Ileal tissue biopsies from human, post IPAA subjects

value: F


title: 05C40435 genomic DNA from LCL

description: LCL sample


title: 04C36913 genomic DNA from LCL

description: LCL sample


title: human ileum, sample 17

description:
sample_id: 227
Ileal tissue biopsies from human, post IPAA subjects


title: 07C64541 genomic DNA from LCL

description: LCL sample


title: 04C31982 genomic DNA from LCL

description: LCL sample


title: human ileum, sample 20

description:
sample_id: 406
Ileal tissue biopsies from human, post IPAA subjects


title: 01C06493 genomic DNA from LCL

description: LCL sample


title: 01C06497 genomic DNA from LCL

description: LCL sample

value: Autism


title: human ileum, sample 16

description:
sample_id: 128
Ileal tissue biopsies from human, post IPAA subjects

value: no


title: 03C15943 genomic DNA from LCL

description: LCL sample


title: human ileum, sample 19

description:
sample_id: 617
Ileal tissue biopsies from human, post IPAA subjects


title: 63447

description: Total RNA was submitted to exiqon for 757 miRNA expression detection and normalized based on pooled samples.

value: Breast Tumor

tag: OS time

tag: race

value: Black

value: Basal

value: referene pool


title: human ileum, sample 15

description:
sample_id: 324
Ileal tissue biopsies from human, post IPAA subjects

value: M


title: 63239

tag: grade

tag: tumor size

value: u

value: unclassified


title: human ileum, sample 14

description:
sample_id: 212
Ileal tissue biopsies from human, post IPAA subjects


title: 01C08060 genomic DNA from LCL

description: LCL sample

value: Female

value: LCL

value: Control


title: 62566

tag: tnm

tag: er

value: U


title: 62414

value: neg

tag: pr

tag: tumor subtype ihc


title: 62389

value: pos

value: Lum A


title: 60216


title: 50382


title: 50377

value: LumA


title: human ileum, sample 13

description:
sample_id: 298
Ileal tissue biopsies from human, post IPAA subjects

value: F

value: yes

value: UC


title: 01C08028_2 genomic DNA from LCL

description: LCL sample


title: human ileum, sample 12

description:
sample_id: 603
Ileal tissue biopsies from human, post IPAA subjects

value: FAP


title: 03C16562 genomic DNA from LCL

description: LCL sample

value: Autism


title: 04C35584 genomic DNA from LCL

description: LCL sample


title: 01C06061 genomic DNA from LCL

description: LCL sample


title: human ileum, sample 10

description:
sample_id: 511
Ileal tissue biopsies from human, post IPAA subjects


title: 01C06052 genomic DNA from LCL

description: LCL sample


title: human ileum, sample 7

description:
sample_id: 670
Ileal tissue biopsies from human, post IPAA subjects


title: 01C05898 genomic DNA from LCL

description: LCL sample


title: 01C05915_2 genomic DNA from LCL

description: LCL sample


title: 01C07488 genomic DNA from LCL

description: LCL sample


title: Colon_HAW_8

city: North Ryde

first: Robert

last: Dunne

state: New South Wales

address: Locked Bag 17

country: Australia

institute: CSIRO

hyb_protocol: using the 225 GeneChip Hybridization, Wash and Stain Kit, the cRNA target was hybridized onto 226 the arrays in an Affymetrix Hybridization Oven.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using bioconductor and R. Data were normalized using RMA.

organism: Rattus norvegicus

label_protocol: taking 100ng of total RNA from the aforementioned extractions, poly-A RNA controls 214 were added, double-stranded cDNA was synthesised with random hexamers tagged 215 with a T7 promoter sequence using Affymetrix cDNA synthesis and amplification kit 216 and the product cleaned using the Affymetrix Sample Cleanup module

growth_protocol: Distal colon tissues sampled from 11 week old rats

extract_protocol: RNA extrac ed from distal colon tissue

treatment_protocol: rats fed different diets as described in  Conlon et al

value: colon

tag: diet

value: HAW


title: human ileum, sample 9

description:
sample_id: 386
Ileal tissue biopsies from human, post IPAA subjects


title: 04C32112_2 genomic DNA from LCL

description: LCL sample


title: Spinal cord_ 15Day after injury_ replicate 2

city: Singapore

first: Justin

middle: Jeyakani

last: Joseph Gnanakkan

state: Singapore

address: 60, Biopolis street

department: Computational and Systems Biology

country: Singapore

institute: Genome Institute of Singapore

description:
15Day-2
Gene expression in 15 day post injured spinal cord

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following manufacturer instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent G2514F-024129 Agilent Custom Microarray GE 4x44K (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 021643_D_F_20081005) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Danio rerio

source_name: Spinal cord, 15Day after injury

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug RNA using the Quick-Amp Labeling Kit, one-color kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from the uninjured and injured spinal cords of the experimental fishes using Trizol (Invitrogen,15596018) and quality  of RNA was checked  on Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Assay). RNA was prepared from a minimum of 3 biological replicates. For each biological replicate, spinal cord from about 50-60 fishes were pooled in the control and also in the regenerating samples.

value: Spinal cord

tag: age

value: 6 months adult


title: human ileum, sample 11

description:
sample_id: 480
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 8

description:
sample_id: 465
Ileal tissue biopsies from human, post IPAA subjects

value: M


title: Spinal cord_ 15Day after injury_ replicate 3

description:
15Day-3
Gene expression in 15 day post injured spinal cord


title: human ileum, sample 6

description:
sample_id: 631
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 5

description:
sample_id: 304
Ileal tissue biopsies from human, post IPAA subjects


title: Spinal cord_ 15Day after injury_ replicate 1

description:
15Day-1
Gene expression in 15 day post injured spinal cord


title: human ileum, sample 4

description:
sample_id: 488
Ileal tissue biopsies from human, post IPAA subjects


title: Colon_HAW_7


title: Colon_HAW_6


title: Colon_HAW_5


title: Spinal cord_ 10Day after injury_ replicate 3

description:
10Day-3
Gene expression in 10 day post injured spinal cord

source_name: Spinal cord, 10Day after injury


title: 04C36042 genomic DNA from LCL

description: LCL sample

value: Female

value: LCL


title: 05C42143 genomic DNA from LCL

description: LCL sample


title: Colon_HAW_4


title: Spinal cord_ 10Day after injury_ replicate 2

description:
10Day-2
Gene expression in 10 day post injured spinal cord


title: 05C47170 genomic DNA from LCL

description: LCL sample


title: human ileum, sample 2

description:
sample_id: 215
Ileal tissue biopsies from human, post IPAA subjects


title: human ileum, sample 3

description:
sample_id: 402
Ileal tissue biopsies from human, post IPAA subjects


title: Spinal cord_ 10Day after injury_ replicate 1

description:
10Day-1
Gene expression in 10 day post injured spinal cord


title: Colon_LAW_6

value: LAW


title: 00C04563 genomic DNA from LCL

description: LCL sample


title: 07C68500 genomic DNA from LCL

description: LCL sample

value: Control


title: Spinal cord_ 7Day after injury_ replicate 3

description:
7Day-3
Gene expression in 7 day post injured spinal cord

source_name: Spinal cord, 7Day after injury


title: 03C16444 genomic DNA from LCL

description: LCL sample


title: Colon_HAW_1


title: Spinal cord_ 7Day after injury_ replicate 2

description:
7Day-2
Gene expression in 7 day post injured spinal cord


title: human ileum, sample 1

description:
sample_id: 109
Ileal tissue biopsies from human, post IPAA subjects


title: Colon_LAW_4


title: Colon_HAW_2


title: Untreated 2

city: Boston

first: Vanessa

last: Beynon

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital

description:
gene expression from memory T-cells cocultured with monocytes
HW2010052517.CEL

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized overnight at 45C on Human Gene 1.0 ST Array by Affymetrix GeneChip Hybridization Oven 460

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed using Nexus Expression by Biodiscovery

source_name: Resorted memory T-cells from coculture with monocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from a minimum of 1 ug total RNA

extract_protocol: total RNA was extracted by QIAGEN Rneasy according to manufacturer's instructions

treatment_protocol:
Isolation_protocol: memory T-cells and monocytes were isolated by magnetic bead isolation from PBMCs after Ficoll-centrifugation of whole blood
memory T-cells and monocytes were cocultured for 16 h with or without interferon-beta and memory T-cells were resorted with a FACS Diva sorted after labelling with CD4 and CD14-specific antibodies

tag: cells

value: memory T-cells

tag: agent

value: untreated


title: Spinal cord_ 3Day after injury_ replicate 1

description:
3Day-1
Gene expression in 3 day post injured spinal cord

source_name: Spinal cord, 3Day after injury


title: 01C05712 genomic DNA from LCL

description: LCL sample

tag: gender


title: 03C17196 genomic DNA from LCL

description: LCL sample


title: Colon_HAW_3


title: Colon_LAW_3


title: Treated 1

description:
gene expression from memory T-cells cocultured with monocytes in the presence of interferon-beta
HW2010052516.CEL

source_name: Resorted memory T-cells from coculture with monocytes and interferon-beta

value: interferon-beta


title: Colon_LAW_5


title: HL60 WT replicate 2

city: St. John's

first: Touati

last: Benoukraf

state: NL

address: Craig L. Dobbin Genetics Research Centre,

department: Faculty of Medicine, Division of BioMedical Sciences

institute: Memorial University of Newfoundland

description: Gene expression data from WT myeloid cell lines HL-60

hyb_protocol: A total of 2.5µg of labelled cDNA, along with GeneChip Hybridization Control reagents (Affymetrix), was injected into an Affymetrix GeneChip Human Gene 1.0 ST Array. The chips were incubated for 18 hours at 45oC and rotated at 60rpm to allow hybridization. The chips were then washed and stained using GeneChip Hybridization Wash and Stain Kit (Affymetrix) using the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affimetrix GeneChip Scanner GCS 3000 with the GeneChip Operating software version 1.4.0.036

data_processing: CEL files were RMA normalized using R/bioconductor

source_name: myeloid cell lines HL-60

label_protocol: Gene expression array analysis was performed using Affymetrix GeneChip Human Gene 1.0ST Array system (Affymetrix, Santa Clara, CA) according to manufacturer’s instructions. Briefly, for each sample, 200ng of total RNA in a volume of 5µl was amplified using the Applause WT Amp ST, RNA Amplification System (NuGen, San Carlos, CA) and labelled with Encore Biotin Module, Post–Amplification System (NuGen).

growth_protocol: HL-60 were grown in DMEM supplemented with 10%FBS, at 37 °C in a humidified atmosphere with 5% CO2

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

tag: cell line


title: Spinal cord_ 1Day after injury_ replicate 3

description:
1Day-3
Gene expression in 1 day post injured spinal cord

source_name: Spinal cord, 1Day after injury


title: 03C15793 genomic DNA from LCL

description: LCL sample

tag: disease state


title: Untreated 1

description:
gene expression from memory T-cells cocultured with monocytes
HW2010052515.CEL


title: Treated 2

description:
gene expression from memory T-cells cocultured with monocytes in the presence of interferon-beta
HW2010052518.CEL


title: Spinal cord_ 7Day after injury_ replicate 1

description:
7Day-1
Gene expression in 7 day post injured spinal cord

tag: tissue


title: Colon_LAW_2


title: 04C24298 genomic DNA from LCL

description: LCL sample

tag: sample type


title: Colon_LAW_1


title: Spinal cord_ 3Day after injury_ replicate 2

description:
3Day-2
Gene expression in 3 day post injured spinal cord


title: Spinal cord_ 1Day after injury_ replicate 1

description:
1Day-1
Gene expression in 1 day post injured spinal cord


title: Spinal cord_ 3Day after injury_ replicate 3

description:
3Day-3
Gene expression in 3 day post injured spinal cord


title: Spinal cord_ 1Day after injury_ replicate 2

description:
1Day-2
Gene expression in 1 day post injured spinal cord


title: 01C06480 genomic DNA from LCL

description: LCL sample


title: Colon_HAMSB_9

value: HAMSB


title: GM16497_2 genomic DNA from LCL

description: LCL sample

value: Rett syndrome


title: HL60 WT replicate 1


title: Colon_HAMSB_8


title: EGFP replicate 3

first: jinmiao

last: chen

address: Biopolis

institute: Singapore Immunology Network

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw expression data was extracted using GenomeStudio and processed with loess normalization

organism: Mus musculus

source_name: bone marrow from 5-FU treated mice

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

growth_protocol: cells were grown in IMDM medium with 2% serum and supplemented with stem cell factor and IL-6

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: cells isolated from 5-FU treated mice were transfected with NUP98-CDX1, NUP98-CDX4 or EGFP

tag: strain

value: 6-8 weeks

value: bone marrow

tag: genotype/variation

value: transfected with EGFP


title: ND09027 genomic DNA from LCL

description: LCL sample

value: Epilepsy


title: EGFP replicate 1

description: replicate 1


title: ND21676 genomic DNA from LCL

description: LCL sample


title: Colon_HAMSB_7

value: colon


title: Spinal cord_ Uninjured_replicate 3

description:
NSC-3
Gene expression in uninjured spinal cord

source_name: Spinal cord, Uninjured

value: Spinal cord


title: EGFP replicate 2

description: replicate 2


title: ND08877 genomic DNA from LCL

description: LCL sample


title: Colon_HAMSB_5


title: GM16271_2 genomic DNA from LCL

description: LCL sample


title: Spinal cord_ Uninjured_replicate 2

description:
NSC-2
Gene expression in uninjured spinal cord

value: 6 months adult


title: NUP98-CDX4 replicate 2

description: replicate 2

value: transfected with NUP98-CDX4


title: Spinal cord_ Uninjured_replicate 1

description:
NSC-1
Gene expression in uninjured spinal cord


title: ND06755 genomic DNA from LCL

description: LCL sample

value: Female


title: Colon_HAMSB_6


title: Colon_HAMSB_4


title: NUP98-CDX4 replicate 1

description: replicate 1


title: Colon_HAMSB_3


title: Giardia lamblia WB: 5'5npac control vs pPPax2

city: Taipei

first: Chin-Hung

last: Sun

address: Department of Parasitology, College of Medicine, National Taiwan University

department: Department of Parasitology

country: Taiwan

hyb_protocol: Correspondingly fragmented labeled cRNA was then pooled and hybridized to a G. lamblia oligonucleotide microarray (Agilent Technologies, USA) at 60°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays were scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3 and 625 nm for Cy5.

data_processing: Scanned images were analyzed by Feature Extraction version 9.1 software (Agilent Technologies, USA), and image analysis and normalization software was used to quantify signal and background intensity for each feature; data were substantially normalized by the rank consistency filtering LOWESS method.

organism: Giardia duodenalis

source_name: Giardia lamblia WB

label_protocol: 0.5 mg of total RNA was amplified by a Low RNA Input Fluor Linear Amp kit (Agilent Technologies) and labeled with Cy3 or Cy5 (CyDye, PerkinElmer Life Sciences) during the in vitro transcription process. 0.825 mg of Cy-labeled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60oC for 30 minutes.

growth_protocol: PCR amplification and standard cloning techniques were used to insert Pax2 gene from genomic DNA and then cloned into the pPop2NHA vector, resulting in plasmid pPPax2.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Giardia cells were transfected with the pPPax2 or 5'5npac plasmid containing the pac gene were selected and maintained with 54 ug/ml puromycin.

tag: vector

value: 5'pac5n control


title: NUP98-CDX4 replicate 3

description: replicate 3


title: GM17583 genomic DNA from LCL

description: LCL sample

value: LCL


title: ND04353 genomic DNA from LCL

description: LCL sample


title: Striped oocytes of individual F29, stage 3, female, from Argenton

city: Caen

first: Nolwenn

middle: Marie

last: Dheilly

address: Esplanade de la Paix

department: Biological sciences

country: France

institute: Universite de caen

hyb_protocol: Hybridization was performed using the Agilent’s Gene expression hybridization kit as described by the purchaser with 1.65μg of aRNA samples labeled with Cy3. Subsequently, slides were washed with Gene expression wash buffer kit (Agilent Technologies), dried and stabilized in Stabilization and Drying solution (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565AA) using one color scan setting for 4x44k array slides (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 6.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. A matrix of gene expression levels was generated, where each row corresponds to a different gene and each column to one sample. The expression level of each gene was then logarithmically transformed, centered, and reduced, so that relative variations rather than absolute values were used for interpretation.

organism: Magallana gigas

source_name: Striped oocytes, stage 3, female, Argenton

label_protocol: 200 ng of total RNA was indirectly labeled with Cy3 using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions. Qiagen's RNeasy mini spin columns were used for purifying amplified RNA (aRNA) samples. After purification, aRNA amplification and dye incorporation rates were controlled using a ND-1000 spectrophotometer (Nanodrop Technologies) and were comprised respectively between 200 and 500 ng/μL (concentration) and between 20 and 50 pmol/μg aRNA (dye incorporation).

extract_protocol: Total RNA was extracted from the tissues with Tri-Reagent kit (Sigma) and subsequently cleaned with nucleospin RNA Clean-up (Macherev Nagel) isolation columns. After homogenization of the N2 grinding powder in Tri-reagent and the first centrifugation, the aqueous phase was extracted to directly isolate the total RNA on the column as described by the provider. RNA concentrations were measured using an ND-1000 spectrophotometer (Nanodrop Technologies), and RNA integrity was controlled on the Agilent Bioanalyzer using the RNA 6000 nano kit (Agilent Technologies).

treatment_protocol: Oysters were sampled in the field and tissues were immediately dissected, snap-frozen in liquid nitrogen, and stored at -80 degrees Celsius for total RNA extraction.

tag: individual/pool

value: individual

value: female

value: gonad

tag: Stage

tag: location

value: Argenton


title: Striped oocytes of individual F3, stage 3, female, from Argenton


title: Colon_HAMSB_2

value: HAMSB


title: NUP98-CDX1 replicate 2

description: replicate 2

value: transfected with NUP98-CDX1


title: Striped oocytes of individual F26, stage 3, female, from Argenton


title: ND02110 genomic DNA from LCL

description: LCL sample


title: NUP98-CDX1 replicate 3

description: replicate 3

value: 6-8 weeks


title: NUP98-CDX1 replicate 1

description: replicate 1

value: bone marrow


title: GM16560 genomic DNA from LCL

description: LCL sample

value: Rett syndrome


title: Colon_HAMSB_1


title: Striped oocytes of individual F28, stage 3, female, from Argenton


title: GM16405 genomic DNA from LCL

description: LCL sample


title: Treated with RNAi against STAC3 at day 1, 24h after switching to differentiation media, 48h after treatment, R1-1_r

city: St Lucia

first: Neil

last: Bower

state: Qld

address: Carmody Road

department: Institute for Molecular Bioscience

institute: University of Queensland

hyb_protocol: Samples were processed commercially at Cambridge Bioscience, UK.

data_processing: The data were filtered to remove any probes with a detection p-value above 0.01 for all the samples in the set. This removes any probes not detected at all in the set. It was done before transformation via variance stabilization and normalization in order to reduce the noise of the set before normalization. As the normalization algorithm is quantile normalization, it uses the data to fit a distribution on to it and having no expressed probe in the set would have an impact on the quality of the data. Quantile normalization was performed using the program R and the Bioconductor package Lumi (PMID 18467348).

source_name: myogenic cell line, STAC3 RNAi, day 1

growth_protocol: Cells at day 0 were grown in growth media, 20% FBS + DMEM. Cells at day 1 were grown in differentiation media, 2% FBS in DMEM.

extract_protocol: RNA was extracted using an RNeasy Plus RNA extraction kit (Qiagen).

treatment_protocol: RNAi-treated cells were transfected with an RNAi directed against STAC3 (Invitrogen). Control cells were transfected with a high-GC content control RNAi (Invitrogen).

tag: cell type

value: myogenic cells

tag: treatment

value: STAC3 RNAi

tag: time point

value: day 1 (24 h after switching to differentiation media, 48 h after treatment)


title: Treated with RNAi against STAC3 at day 1, 24h after switching to differentiation media, 48h after treatment, R1-3

scan_protocol: Samples were processed commercially at Cambridge Bioscience, UK.


title: GM16382 genomic DNA from LCL

description: LCL sample


title: Colon_HAM_7

value: colon

tag: diet

value: HAM


title: Treated with RNAi against STAC3 at day 1, 24h after switching to differentiation media, 48h after treatment, R1-4

label_protocol: Samples were processed commercially at Cambridge Bioscience, UK.


title: Colon_HAM_8


title: GM11313 genomic DNA from LCL

description: LCL sample

value: Female


title: Colon_HAM_5


title: GM16547 genomic DNA from LCL

description: LCL sample


title: Striped oocytes of individual F18, stage 3, female, from Argenton


title: Striped oocytes of individual F15, stage 3, female, from Argenton


title: Gonad of individual F23, stage 3, male, from Locmariaquer

description: St3M F23

source_name: Gonad, stage 3, male, Locmariaquer

value: male

value: Locmariaquer


title: Treated with RNAi against STAC3 at day 1, 24h after switching to differentiation media, 48h after treatment, R1-1


title: Colon_HAM_4


title: Gonad of individual F4, stage 3, male, from Locmariaquer

description: St3M F4

value: individual


title: GM11301 genomic DNA from LCL

description: LCL sample

value: LCL


title: Control at day 1, 24h after switching to differentiation media, 48h after treatment, C1-4

source_name: myogenic cell line, control RNAi, day 1

value: control RNAi


title: GM07983 genomic DNA from LCL

description: LCL sample


title: Colon_HAM_6


title: Gonad of individual E47, stage 3, male, from Locmariaquer

description: St3M E47

value: gonad


title: Treated with RNAi against STAC3 at day 1, 24h after switching to differentiation media, 48h after treatment, R1-2


title: Gonad of individual E31, stage 3, male, from Locmariaquer

description: St3M E31


title: 01C08028_1 genomic DNA from LCL

description: LCL sample

value: Control


title: Colon_HAM_3


title: Colon_HAM_1


title: Colon_HAM_2


title: 01C05915_1 genomic DNA from LCL

description: LCL sample


title: Control at day 1, 24h after switching to differentiation media, 48h after treatment, C1-2


title: Control at day 1, 24h after switching to differentiation media, 48h after treatment, C1-3


title: 01C07372 genomic DNA from LCL

description: LCL sample


title: 01C08448 genomic DNA from LCL

description: LCL sample


title: Control at day 1, 24h after switching to differentiation media, 48h after treatment, C1-1


title: Treated with RNAi against STAC3 at day 0 in growth media, 24h after treatment, R0-4

source_name: myogenic cell line, STAC3 RNAi, day 0

value: day 0 (in growth media, 24 h after treatment)


title: Striped oocytes of individual F21, stage 3, female, from Argenton

value: female

value: Argenton


title: Gonad of individual F14, stage 3, female, from Locmariaquer

description: St3F F14

source_name: Gonad, stage 3, female, Locmariaquer


title: Gonad of individual D34, stage 2, male, from Locmariaquer

description: St2M D34

source_name: Gonad, stage 2, male, Locmariaquer


title: Gonad of individual F32, stage 3, female, from Locmariaquer

description: St3F F32


title: Colon_LAM_4

value: LAMS


title: 04C35560 genomic DNA from LCL

description: LCL sample

value: Autism


title: 04C36352 genomic DNA from LCL

description: LCL sample


title: Gonad of individual F9, stage 3, female, from Locmariaquer

description: St3F F9


title: Gonad of individual F15, stage 3, female, from Locmariaquer

description: St3F F15


title: 04C32112_1 genomic DNA from LCL

description: LCL sample


title: Colon_LAM_6


title: Colon_LAM_5


title: Treated with RNAi against STAC3 at day 0 in growth media, 24h after treatment, R0-3

value: myogenic cells

value: STAC3 RNAi


title: Gonad of individual D14, stage 2, male, from Locmariaquer

description: St2M D14


title: 01C05476 genomic DNA from LCL

description: LCL sample


title: Control at day 0 in growth media, 24h after treatment, C0-4

source_name: myogenic cell line, control RNAi, day 0


title: Control at day 0 in growth media, 24h after treatment, C0-4_r


title: Gonad of individual D7, stage 2, male, from Locmariaquer

description: St2M D7


title: Colon_control_5

value: colon

value: control


title: Gonad of individual E54, stage 2, female, from Locmariaquer

description: St2F E54

source_name: Gonad, stage 2, female, Locmariaquer


title: Gonad of individual D21, stage 2, male, from Locmariaquer

description: St2M D21


title: Colon_LAM_3


title: Control at day 0 in growth media, 24h after treatment, C0-3


title: Control at day 1, 24h after switching to differentiation media, 48h after treatment, C1-3_r

value: day 1 (24 h after switching to differentiation media, 48 h after treatment)


title: Colon_LAM_2


title: Colon_LAM_7


title: 05C40546 genomic DNA from LCL

description: LCL sample

value: Female


title: Treated with RNAi against STAC3 at day 0 in growth media, 24h after treatment, R0-2


title: 01C07313 genomic DNA from LCL

description: LCL sample


title: Control at day 0 in growth media, 24h after treatment, C0-2


title: Colon_LAM_1


title: Colon_control_4


title: Colon_control_3


title: Colon_control_2


title: Gonad of individual E44, stage 2, female, from Locmariaquer

description: St2F E44

value: Locmariaquer


title: GM16497_1 genomic DNA from LCL

description: LCL sample

value: Rett syndrome


title: Colon_control_1


title: Gonad of individual E28, stage 2, female, from Locmariaquer

description: St2F E28

value: individual


title: Gonad of individual C22, stage 1, male, from Locmariaquer

description: St1M C22

source_name: Gonad, stage 1, male, Locmariaquer

value: male


title: GM16480 genomic DNA from LCL

description: LCL sample

value: LCL


title: GM16546 genomic DNA from LCL

description: LCL sample


title: GM17540 genomic DNA from LCL

description: LCL sample


title: Gonad of individual C7, stage 1, male, from Locmariaquer

description: St1M C7

value: gonad


title: GM16368 genomic DNA from LCL

description: LCL sample


title: GUJ_RNA_CNTRL

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression analysis of biodegradation and 16S rRNA genes using BiodegPhyloChip in soil from a site with no known history of any type of chemical contamination (biological control).

hyb_protocol: 600 ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours.

scan_protocol: The hybridized slides were washed using Agilent aCGH wash buffers (Part No: 5188-5221/22) and  Agilent Gene Expression wash buffers (Part No: 5188-5327) and scanned using the Agilent Microarray Scanner  5 micron resolution.

data_processing: Images were quantified using Agilent Feature Extraction Software and obtained background subtracted and spatially detrended Processed Signal intensities. 50th Percentile Shift Normalization.

organism: soil metagenome

source_name: Total RNA isolated from soil sample collected from a site with no known history of any type of chemical contamination (biological control)

label_protocol: Poly (A)-tails were added to the 3’-end of RNA by using A-plus Poly (A) polymerase tailing kit (Epicentre Biotechnologies). Then  the samples  were labeled using Agilent Quick Amp Kit PLUS (Part number: 5190-0442).  Five hundred nanograms each of the samples were incubated with reverse trancription mix at 42°C and converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

extract_protocol: Samples (soil and sludge) were collected at five highly polluted areas in the state of Gujarat in Western India. At each sampling location, multiple samples were collected from close (100 m) and far (500 m) from the industry, along the effluent channel and at the place where effluent channel from the industrial area falls into the river. The samples were collected in air tight vessels, transported on ice (4○C) to the laboratory and processed immediately for DNA and RNA isolation. The total DNA to be used as target for microarray hybridization was isolated from soil/ sludge samples using the Mo Bio Power soil DNA kit (Mo Bio Inc., CA, USA) as per manufacturer's instructions. Before processing for DNA isolation, the soil /sludge were mixed thoroughly using a mortar-pestle. One gm of soil/sediment was taken for DNA isolation, and during processing with the kit, lysozyme was added to facilitate the lysis of bacteria. The total soil RNA was extracted from one gm of soil /sludge using the Mo Bio Power soil RNA isolation kit (Mo Bio Inc., USA). The concentration of DNA and RNA was analyzed by Nanodrop Spectrophotometer (Nanodrop Technologies Inc, Rockland, USA), and quality was determined by analysis on DNA 12000 kit and RNA 6000 nano kit (Caliper Sciences, USA), respectively using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

tag: environmental sample

value: Soil


title: GUJ_RNA_2

description: Gene expression analysis of biodegradation and 16S rRNA genes using BiodegPhyloChip in secondary sludge from CETP reactor at Vatwa GIDC,  Ahmadabad.

source_name: Total RNA of secondary sludge from CETP reactor at Vatwa GIDC,  Ahmadabad

value: Secondary sludge


title: GUJ_RNA_3

description: Gene expression analysis of biodegradation and 16S rRNA genes using BiodegPhyloChip in sludge/sediment from Damanganga river, Vapi, Valsad.

source_name: Total RNA of sludge/sediments from Damanganga river, Vapi, Valsad

value: Sludge/sediment


title: Gonad of individual C36, stage 1, female, from Locmariaquer

description: St1F C36

source_name: Gonad, stage 1, female, Locmariaquer

value: female


title: GUJ_RNA_5

description: Gene expression analysis of biodegradation and 16S rRNA genes using BiodegPhyloChip in sediments from Mini River, Nandesari GIDC, Vadodara.

source_name: Total RNA of sediments from Mini River, Nandesari GIDC, Vadodara

value: Sediment


title: Gonad of individual C1, stage 1, male, from Locmariaquer

description: St1M C1


title: Gonad of individual C19, stage 1, male, from Locmariaquer

description: St1M C19


title: Gonad of individual C35, stage 1, female, from Locmariaquer

description: St1F C35


title: GM11304 genomic DNA from LCL

description: LCL sample


title: GM11310 genomic DNA from LCL

description: LCL sample


title: GUJ_DNA_CNTRL

description: Comparative genomic hybridization using BiodegPhyloChip  for profiling of biodegradation and bacterial 16S rRNA genes in soil from a site with no known history of any type of chemical contamination (biological control).

hyb_protocol: 1.25 micrograms of cy3 labeled samples were hybridized.  Hybridizations were done using the aCGH Hybridization kit of Agilent (Part Number: 5190-0404). Hybridization was carried out in Agilent's Surehyb Chambers at 65º C for 24 hours.

source_name: Total DNA isolated from soil sample collected from a site with no known history of any type of chemical contamination (biological control)

label_protocol: The samples for Comparative Genomic DNA Hybridization were labeled using Agilent Genomic DNA labeling Kit (Part Number: 5190-0453). DNA of each sample was digested using Alu1 and Rsa1. This restricted DNA was then labeled with Cy3  dUTP using random primer labeling method. The labeled DNA was then concentrated and quality assessed for yields.


title: GM11300 genomic DNA from LCL

description: LCL sample


title: GM16270 genomic DNA from LCL

description: LCL sample


title: GUJ_RNA_4

description: Gene expression analysis of biodegradation and 16S rRNA genes using BiodegPhyloChip in sludge/sediment from effluent stream of Vapi CETP, Valsad.

source_name: Total RNA of sludge/sediments from effluent stream of Vapi CETP, Valsad


title: GM16271_1 genomic DNA from LCL

description: LCL sample


title: Gonad of individual C32, stage 1, female, from Locmariaquer

description: St1F C32


title: Gonad of individual E2, stage 2, female, from Locmariaquer

description: St2F E2


title: GUJ_DNA_5

description: Comparative genomic hybridization using BiodegPhyloChip for profiling of biodegradation and 16S rRNA genes in sediments from Mini River, Nandesari GIDC, Vadodara.

source_name: Total DNA of sediments from Mini River, Nandesari GIDC, Vadodara


title: GUJ_RNA_1

description: Gene expression analysis of biodegradation and 16S rRNA genes using BiodegPhyloChip in soil/sludge from Khariked Canal, Vatwa GIDC,  Ahmadabad.

source_name: Total RNA of soil/sludge from Khariked Canal, Vatwa GIDC,  Ahmadabad

value: Soil/sludge


title: GUJ_DNA_2

description: Comparative genomic hybridization using BiodegPhyloChip for profiling of biodegradation and 16S rRNA genes in secondary sludge from CETP reactor at Vatwa GIDC,  Ahmadabad.

source_name: Total DNA of secondary sludge from CETP reactor at Vatwa GIDC,  Ahmadabad


title: Gonad of individual C23, stage 1, female, from Locmariaquer

description: St1F C23


title: SW48_control

city: Dallas

first: Masanobu

last: Takahashi

address: 3500 Gaston Avenue, suite H-250

institute: Baylor University Medical Center

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

data_processing: BeadStudio software v3.2

source_name: SW48, non-treated

growth_protocol: The SW48 cells were cultured in Iscove's Modified Dulbecco's Medium with 10% fetal bovine serum.

extract_protocol: DNA was extracted with QIAmp DNA Mini Kit (Qiagen).

treatment_protocol: The cells were treated with 0.1% DMSO (vehicle controls) or AKBA (Sigma Chemical Co.), at a 20 μM for 6 days. As a positive control, the cells were treated with 2.5 μM of DAC.

value: colorectal cancer


title: SW48_DAC

source_name: SW48, DAC treated, 6 d


title: Gonad of individual B16, stage 0, sex undetermined, from Locmariaquer

description: St0 B16

source_name: Gonad, stage 0, undetermined, Locmariaquer

value: undetermined (NI)


title: Gonad of individual A12, stage 0, sex undetermined, from Locmariaquer

description: St0 A12


title: GUJ_DNA_3

description: Comparative genomic hybridization using BiodegPhyloChip for profiling of biodegradation and 16S rRNA genes in sludge/sediments from Damanganga river, Vapi, Valsad.

source_name: Total DNA of sludge/sediments from Damanganga river, Vapi, Valsad


title: GUJ_DNA_4

description: Comparative genomic hybridization using BiodegPhyloChip for profiling of biodegradation and 16S rRNA genes in sludge/sediments from effluent stream of Vapi CETP, Valsad.

source_name: Total DNA of sludge/sediments from effluent stream of Vapi CETP, Valsad


title: Gonad of individual A17, stage 0, sex undetermined, from Locmariaquer

description: St0 A17


title: Gonad of individual A11, stage 0, sex undetermined, from Locmariaquer

description: St0 A11


title: SW48_AKBA

source_name: SW48, AKBA treated, 6 d


title: Gonad of individual B14, stage 0, sex undetermined, from Locmariaquer

description: St0 B14


title: Adult fibroblasts_rep2

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description: replicate 2

data_processing: The data were normalised using quantile normalisation in R

source_name: primary adult mouse fibroblasts

growth_protocol: αPIG-ES and αPIG-iPS cells were cultured on Mitomycin C-inactivated neomycin resistant murine embryonic fibroblasts in the presence of LIF. αPIG-ES and αPIG-iPS cells were differentiated in a standardized spinner flask system to allow spontaneous differentiation. Briefly, one million undifferentiated ES or iPS cells were suspended in 14 ml of differentiation medium (Iscove’s Modified Dulbecco’s Medium supplemented with 20% FBS, 10 μM 2 mercaptoethanol and 1x non-essential amino acids) and cultured for 2 days in non-adherent plates on a shaker under continuous agitation to allow formation of embryoid bodies (referred to as ES-EB and iPS-EB hereafter). At day 2 of differentiation, the formed EB were counted and diluted into fresh 200 ml medium contained within a sterile spinner flask (Cell spin 250) to a density of 28000 EB per one spinner flask. The differentiation process continued for 6-7 days (without medium change) until the first appearance of green fluorescence in spontaneously beating EBs. On day 9 of differentiation, fresh medium supplemented with puromycin (8 μg/ml) was added to select for pure CM. After 2-3 days of selection, the surviving cardiac clusters were pooled together by removing from spinner. These were then resuspended in fresh medium with puromycin and then incubated in non-adherent culture dishes and cultured for another 5-6 days on the shaker. Fresh medium containing puromycin was replaced every 2 days until pure beating cardiac clusters were obtained. On day 16 of differentiation after 6-8 days of puromycin treatment cardiac clusters were used for RNA isolation using Trizol reagent. RNA was also isolated from the same batch of untreated whole EBs at day 16 of differentiation. Primary murine adult tail tip fibroblasts were established in cultured and used for RNA preparation.

extract_protocol: Total RNA from all cell samples was isolated using TRIzol Reagent (Invitrogen).

tag: developmental stage

value: 8 weeks old mice

tag: passage number

value: passage 3

value: primary fibroblasts in culture

tag: origin of a cell line

value: F1 mice of 129Sv x c57BL6


title: GUJ_DNA_1

description: Comparative genomic hybridization using BiodegPhyloChip for profiling of biodegradation and 16S rRNA genes in sludge sample of Khariked Canal, Vatwa GIDC, Ahmadabad.

source_name: Total DNA of soil/sludge from Khariked Canal, Vatwa GIDC,  Ahmadabad


title: Adult fibroblasts_rep3

description: replicate 3

value: passage 4

tag: cell line


title: H69_TGX221_2

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

hyb_protocol: 10 μg of cRNA/sample were hybridized for 16 h at 45°C. Washing and staining with streptavidin-conjugated phycoerythrin were done using a GeneChip Fluidics Station 400 (Affymetrix).

scan_protocol: Scanning was done with the GeneChip® Scanner 3000 7G (Affymetrix) using the Affymetrix Command Console as instrument control software.

data_processing: Quality control and microarray data analysis was done using R/Bioconductor [Gentleman RC et al., 2004; R Development Core Team, 2011; http://www.bioconductor.org/]. Expression values were computed RMA (robust multi array average) [Irizarry et al., 2003a, b] as processing algorithm.

source_name: SCLC cells

label_protocol: Biotinylated cRNA were prepared from 2 ug total RNA using Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents according to the manufacturer’s protocol.

growth_protocol: The human SCLC cell line H69 was cultured in RPMI medium containing 10% heat-inactivated FCS, 1% L-Glutamine and 1% penicillin/streptomycin at 37°C/5% CO2 (humidified atmosphere).

extract_protocol: Total cellular RNA was extracted using the RNeasy Mini  Kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: H69 cells were treated with DMSO (control),  PIK75 (100 nM) or TGX221 (1 mM) for 24 hrs at 37 °C in complete RPMI medium.


title: Treated with RNAi against STAC3 at day 0 in growth media, 24h after treatment, R0-1

source_name: myogenic cell line, STAC3 RNAi, day 0

value: myogenic cells

value: STAC3 RNAi

value: day 0 (in growth media, 24 h after treatment)


title: H69_TGX221_3


title: Gonad of individual A5, stage 0, sex undetermined, from Locmariaquer

description: St0 A5

value: individual

tag: gender

tag: tissue

value: gonad

value: Locmariaquer


title: Adult fibroblasts_rep1

description: replicate 1

value: passage 2


title: iPS_d16 CM_rep3

description: replicate 3

source_name: iPS cell-derived cardiomyocytes

value: day 16 of in vitro differentiation

value: passage 8

value: aPIG TiB7.4 iPS cells

value: Reference:Meissner A. et al., Nat. Biotechnol. 25(10):1177-1181, 2007.


title: Gonad of individual A3, stage 0, sex undetermined, from Locmariaquer

description: St0 A3

value: undetermined (NI)


title: H69_TGX221_5


title: iPS_d16 CM_rep2

description: replicate 2

value: passage 7


title: H69_PIK75_5


title: Gonad of individual A1, stage 0, sex undetermined, from Locmariaquer

description: St0 A1


title: H69_PIK75_3


title: iPS_d16 CM_rep1

description: replicate 1

value: passage  5


title: Pool d of gonads stage 3 females from Locmariaquer

description: Gl3 Fd

source_name: Gonad pool, stage 3, females, Locmariaquer

value: pool

value: female

value: Baie des Veys


title: Pool b of gonads stage 3 females from Locmariaquer

description: Gl3 Fb


title: iPS_d16 EB_rep3

description: replicate 3

source_name: iPS cell-derived whole EBs


title: H69_Ctr_3


title: H69_Ctr_5


title: H69_PIK75_1


title: Pool a of gonads stage 3 females from Locmariaquer

description: Gl3 Fa


title: iPS_d16 EB_rep2

description: replicate 2


title: H69_Ctr_1


title: iPS_d16 EB_rep1

description: replicate 1


title: iPS_undifferentiated_3

description: replicate 3

source_name: undifferentiated murine iPS cells

value: undifferentiated murine iPS cells


title: Pool b of gonads stage 3 females from Baie des Veys

description: Gc3 Fb

source_name: Gonad pool, stage 3, females, BaiedesVeys


title: iPS_undifferentiated_2

description: replicate 2


title: HBV-associated acute liver failure liver from patient 241-3

city: Bethesda

first: Patrizia

last: Farci

state: MD

address: 50 South Drive

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

description: Gene expression data from liver

hyb_protocol: Following fragmentation, 10 to 18 µg (mean 12.8) of cRNA hybridized for 16 hr at 45°C on Affymetrics Human U133 Plus 2 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using GeneArray Scanner 3000_7Gplus

data_processing: Affymetrics probeset summaries were computed using RMA algorithm.  Data were then imported to BRB-ArrayTools and subsequent data filtering, median normalization and statistical analyses were performed using this software.

source_name: specimen obtained from explanted liver Patient 241

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 50 ng total RNA (GeneChip Expression Analysis Technical Manual, 2005-2006, Affymetrix).

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

tag: disease state

value: HBV-associated acute liver failure

tag: subject

value: Patient 241

value: liver explant


title: HBV-associated acute liver failure liver from patient 241-1

description: Gene expression data from liver


title: iPS_undifferentiated_1

description: replicate 1


title: HBV-associated acute liver failure liver from patient 219-5

description: Gene expression data from liver

source_name: specimen obtained from explanted liver Patient 219

value: Patient 219


title: HBV-associated acute liver failure liver from patient 241-2

description: Gene expression data from liver


title: HBV-associated acute liver failure liver from patient 241-4

description: Gene expression data from liver


title: Pool c of gonads stage 3 females from Baie des Veys

description: Gc3 Fc

value: gonad

value: Locmariaquer


title: ES_day16 CM_rep2

description: replicate 2

source_name: ES cell-derived cardiomyocytes

value: day 16 of in vitro differentiation

value: passage 9

value: aPIG D3 ES cells

value: Reference:Kolossov E. et al., J Exp Med 203(10):2315-2327, 2006.


title: ES_day16 CM_rep3

description: replicate 3

value: passage 10


title: ES_day16 CM_rep1

description: replicate 1

value: passage 7


title: HBV-associated acute liver failure liver from patient 219-4

description: Gene expression data from liver


title: Pool a of gonads stage 3 females from Baie des Veys

description: Gc3 Fa


title: ES_day16 EB_rep3

description: replicate 3

source_name: ES cell-derived whole EBs


title: HBV-associated acute liver failure liver from patient 219-2

description: Gene expression data from liver


title: ES_day16 EB_rep1

description: replicate 1


title: HBV-associated acute liver failure liver from patient 219-3

description: Gene expression data from liver


title: ES_undifferentiated_rep3

description: replicate 3

source_name: undifferentiated murine ES cells

value: undifferentiated murine ES cells


title: ES_day16 EB_rep2

description: replicate 2


title: HBV-associated acute liver failure liver from patient 219-1

description: Gene expression data from liver


title: HBV-associated acute liver failure liver from patient 32-4

description: Gene expression data from liver

source_name: specimen obtained from explanted liver Patient 32

value: Patient 32


title: HBV-associated acute liver failure liver from patient 32-3

description: Gene expression data from liver


title: ES_undifferentiated_rep2

description: replicate 2


title: HBV-associated acute liver failure liver from patient 32-2

description: Gene expression data from liver


title: ES_undifferentiated_rep1

description: replicate 1


title: Adipose tissue_ad lib_rep 6

city: Umeå

first: Stefan

middle: K

last: Nilsson

address: Building 6M 3tr

country: Sweden

institute: Umeå University

hyb_protocol: Performed according to Illumina protocol

scan_protocol: Illumina Beadstation 500GX according to Illumina protocol

data_processing: Illumina Genome Studio 3 was used. Cubic spline normalization, subtracted background.

source_name: Epididymal adipose tissue, ad lib

label_protocol: Illumina TotalPrep RNA Amplification Kit was used

extract_protocol: Pieces of adipose tissue was put in RNAlater

tag: strain

value: Sprague-Dawley

value: Male

tag: age

value: 40 days


title: HBV-associated acute liver failure liver from patient 31-4

description: Gene expression data from liver

source_name: specimen obtained from explanted liver Patient 31

value: HBV-associated acute liver failure

value: Patient 31


title: HBV-associated acute liver failure liver from patient 31-3

description: Gene expression data from liver

value: liver explant


title: Core area at 3d of pMCAo ARR24

city: Madrid

first: Jaime

middle: Ramos

last: Cejudo

address: Paseo de la Castellana, 261

department: Neuroscience

country: Spain

institute: La Paz University Hospital

description: I_Core 3d

hyb_protocol: 1.65 micrograms of Cy3-labeled aRNA were hybridized for 17 hours at 65ºC in an Agilent hybridization oven (G2545A, Agilent Technologies) set at 10 rpm in a final concentration of 1x GEx Hybridization Buffer HI-RPM (Agilent Technologies). Arrays were washed and dried out using a centrifuge according to the manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies)

scan_protocol: Arrays were scanned at 5mm resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for 4x44k format one-color arrays.

data_processing:
Images provided by the scanner were analyzed using Feature Extraction software v10.7.3.1 (Agilent Technologies).
Notes : Entity List : Filtered on Flags [Detected, Compromised]
Interpretation : All Samples
Entities where atleast 1 out of 1  conditions have CV >= 2.5 percent

source_name: Core area at 3d of pMCAo

label_protocol: miRNA Labeling Kit (Agilent Technologies) was used to label RNA. Basically, 100 ng of total RNA were dephosphorylated and Cyanine 3-pCp molecule was ligated to the 3´ end of each RNA molecule by using T4 RNA ligase.

growth_protocol: Adult Sprague-Dawley rats were subjected to permanent Middle Cerebral Artery occlusion (pMCAo) for 24hours or 3 days. Reproducible infarcts were obtained with core, periinfarct well delimited.

extract_protocol: Total RNA was extracted with TRIzol reagent (Invitrogen) and the miRNeasy® mini kit (Quiagen),Integrity and quantity were checked with the Agilent Bio-Analyzer QC

treatment_protocol: Animals were anesthetized before surgery by ketamine (25 mg/kg), diazepam (2 mg/kg), and atropine (0.1 mg/kg) at a dose of 2.5 ml/kg by intraperitoneal injection. Analgesia was provided with subcutaneus meloxicam 2 mg/kg. A small craniotomy was made above the rhinal fissure over the branch of the right middle cerebral artery (MCA), which was permanently ligated just before its bifurcation between the frontal and parietal branches. Complete interruption of blood flow was confirmed. An identical protocol was applied to Sham-operated rats, which were subjected to exactly the same surgery protocol but without infarct. All rats were fed ad libitum in their home cages until sacrifice at 24h or 3days

tag: brain region

value: Core area

value: brain cortex

tag: time

value: infarct

tag: rat


title: HBV-associated acute liver failure liver from patient 32-1

description: Gene expression data from liver


title: Adipose tissue_ad lib_rep 5


title: Core area at 3d of pMCAo ARR30

description: I_Core 3d

tag: treatment


title: HBV-associated acute liver failure liver from patient 31-2

description: Gene expression data from liver


title: Adipose tissue_ad lib_rep 3


title: Whole blood 167

city: Toronto

first: Boyko

last: Kabakchiev

address: 60 Murray Street, Room L3-004

institute: Mount Sinai Hospital

description: sample id: 2770

hyb_protocol: Standard Illumina protocol for HumanOmniExpress and HumanOmni2.5-Quad Beadchips

data_processing: Genomic DNA extracted from whole blood was genotyped using Illumina HumanOmniExpress_12v1 and HumanOmni2.5-Quad_4v1 Beadchips

label: Biotin-NTP

source_name: Whole blood

extract_protocol: Extraction of genomic DNA from whole blood with Gentra Puregene Blood Kit (QIAGEN)

value: M

value: Whole blood


title: Periinfarct area at 24h of pMCAo ARR11

description: I_Peri 24h

source_name: Periinfarct area at 24h of pMCAo

value: Periinfarct area


title: Whole blood 169

description: sample id: 3615

scan_protocol: Standard Illumina protocol for HumanOmniExpress and HumanOmni2.5-Quad Beadchips


title: Adipose tissue_ad lib_rep 4


title: HBV-associated acute liver failure liver from patient 31-1

description: Gene expression data from liver


title: Whole blood 168

description: sample id: 2950

label_protocol: Standard Illumina protocol for HumanOmniExpress and HumanOmni2.5-Quad Beadchips


title: Whole blood 165

description: sample id: 295


title: Periinfarct area at 24h of pMCAo ARR8

description: I_peri 24h


title: Adipose tissue_ad lib_rep 1


title: normal liver from patient 112

description: Gene expression data from liver

source_name: specimen obtained from explanted liver Patient 112

value: normal

value: Patient 112


title: Core area at 3d of pMCAo ARR21

description: I_Core 3d


title: Adipose tissue_ad lib_rep 2


title: Whole blood 163

description: sample id: 639

value: F


title: Contralateral cortex at 24h of pMCAo  ARR9

description: I_Clat 24h

source_name: Contralateral cortex at 24h of pMCAo

value: Contralateral area


title: Whole blood 164

description: sample id: 2504


title: normal liver from patient 101

description: Gene expression data from liver

source_name: specimen obtained from explanted liver Patient 101

value: Patient 101


title: Whole blood 166

description: sample id: 1374


title: Contralateral cortex at 24h of pMCAo  ARR6

description: I_Clat 24h

value: Sprague-Dawley


title: Adipose tissue_food removed_rep 5

source_name: Epididymal adipose tissue, food removed, 6h

value: Male


title: normal liver from patient 62

description: Gene expression data from liver

source_name: specimen obtained from explanted liver Patient 62

value: Patient 62


title: Periinfarct area at 24h of pMCAo ARR5

description: I_peri 24h


title: normal liver from patient 60

description: Gene expression data from liver

source_name: specimen obtained from explanted liver Patient 60

value: Patient 60


title: Adipose tissue_food removed_rep 6

value: 40 days


title: Adipose tissue_food removed_rep 4


title: Whole blood 158

description: sample id: 2665


title: Whole blood 159

description: sample id: 417


title: normal liver from patient 37

description: Gene expression data from liver

source_name: specimen obtained from explanted liver Patient 37

value: Patient 37

value: liver explant


title: Whole blood 154

description: sample id: 689


title: Whole blood 162

description: sample id: 142


title: Whole blood 153

description: sample id: 2992


title: Whole blood 155

description: sample id: 2645


title: Adipose tissue_food removed_rep 2


title: Adipose tissue_food removed_rep 3


title: Whole blood 157

description: sample id: 2490


title: normal liver from patient 29

description: Gene expression data from liver

source_name: specimen obtained from explanted liver Patient 29

value: Patient 29


title: Whole blood 161

description: sample id: 2503


title: Whole blood 150

description: sample id: 3154


title: normal liver from patient 20

description: Gene expression data from liver

source_name: specimen obtained from explanted liver Patient 20

value: Patient 20


title: Ipsilateral area of Healthy at baseline ARR44

description: H_ipsi 0h

source_name: Ipsilateral area of Healthy at baseline

value: Ipsilateral area

value: brain cortex

value: healthy


title: Whole blood 156

description: sample id: 2664

value: Whole blood


title: Core area at 24h of pMCAo  ARR7

description: I_core 24h

source_name: Core area at 24h of pMCAo

value: Core area

value: infarct


title: P5_DP_Sox2_cKO_biological replicate 2

city: New York

first: Michael

last: Rendl

state: NY

address: 1428 Madison Avenue

institute: Mount Sinai School of Medicine

description: Gene expression data from Sox2 cKO

hyb_protocol: Affymetrix Gene ST 1.0 arrays were hybridized according to manufacturer’s descriptions

scan_protocol: Affymetrix 7G GeneArray scanner

data_processing: The probe-level analysis of the CEL files was performed by the RMA algorithm using Agilent Genespring GX11 program.

source_name: Mouse P5 DP cKO

label_protocol: WT-Ovation Amp followed by Encore Biotin Module kits (Nugen)

extract_protocol: Absolutely RNA microprep kit (Stratagene)

value: Dermal Papilla


title: Whole blood 160

description: sample id: 2679

value: F


title: normal liver from patient 18

description: Gene expression data from liver

source_name: specimen obtained from explanted liver Patient 18

value: normal

value: Patient 18


title: Adipose tissue, food removed, rep 1

value: Sprague-Dawley

value: Male


title: Ipsilateral area of Healthy at baseline ARR41

description: H_ipsi 0h


title: Ipsilateral area of Healthy at baseline ARR42

description: H_ipsi 0h


title: Whole blood 151

description: sample id: 3063

value: M


title: Contralateral cortex of sham-operated at 3d ARR40

description: S_clat 3d

value: Contralateral area

value: sham


title: Core area at 24h of pMCAo  ARR4

description: I_core 24h


title: P5_DP_Sox2_cKO_biological replicate 1

description: Gene expression data from Sox2 cKO


title: Ipsilateral area of Healthy at baseline ARR43

description: H_ipsi 0h


title: pretreatment CLL sample [100_AL-LU]

city: Rome

first: Sabina

last: Chiaretti

address: Via Benevento, 6

department: Cellular Technologies and Hematology

country: Italy

institute: Division of Hematology

description:
100_AL-LU_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0

scan_protocol: GeneChips were scanned using the 7G Scanner

data_processing: The data were analyzed with dChip software. For normalization, model based expressions were computed for each array and probe set, using the PM-only model

source_name: Leukemic peripheral blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA.

growth_protocol: Peripheral blood was obtained from elderly patients with a diagnosis of CLL prior to any treatment.

extract_protocol: Total RNA was extracted using Trizol.

treatment_protocol: Ficoll-Hypaque

value: Leukemic peripheral blood

tag: sample status

value: pretreatment CLL sample

tag: status of disease

value: Progressive

tag: response to therapy

value: Non Responder


title: P5_DP_Sox2_Het_biological replicate 1

description: Gene expression data from Sox2 Het

source_name: Mouse P5 DP Het


title: P5_DP_Sox2_Het_biological replicate 2

description: Gene expression data from Sox2 Het


title: Ipsilateral area of sham-operated at 3d ARR39

description: S_ipsi 3d

source_name: Ipsilateral area of sham-operated at 3d

value: Ipsilateral area

value: brain cortex


title: normal liver from patient 16

description: Gene expression data from liver

source_name: specimen obtained from explanted liver Patient 16

value: Patient 16

value: liver explant


title: normal liver from patient 8

description: Gene expression data from liver

source_name: specimen obtained from explanted liver Patient 8

value: Patient 8


title: HCC AFP-NICD 5

city: Barcelona

first: Clara

last: Alsinet

state: Catalonia

address: Rosselló 153

institute: IDIBAPS - Hospital Clínic

hyb_protocol: Samples were hybridized with GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix) and scanned at the MSSM Life Sciences Technology Laboratory.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix).

data_processing: R-based GenePattern modules and custom-generated R code  (version 2.13.1, http://www.r-project.org/) were used for RMA preprocessing and data analysis.

source_name: Hepatocellular carcinoma

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Mice were maintained in a pathogen-free environment. All studies were performed in accordance with policies for the humane use of animals established by the University of Pennsylvania and the NIH.

extract_protocol: RNA was extracted from tumor and control tissues using Qiagen RNeasy Minikit and eluted in water .

treatment_protocol: Mice harboring the AFP-promoter driving the expression of Cre were crossed to animals with the Rosa26-lsl-NICD allele. Litters were genotyped and maintained as normal for the study along with age-matched controls.

value: Hepatocellular carcinoma

tag: genotype

tag: genetic background

value: hybrid 129 x C57BL/6


title: Contralateral cortex of sham-operated at 3d ARR38

description: S_clat 3d


title: HCC AFP-NICD 4


title: pretreatment CLL sample [99_A-S]

description:
99_A-S_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL

value: Partial Responder


title: Whole blood 149

description: sample id: 3251

source_name: Whole blood

value: Whole blood


title: Whole blood 146

description: sample id: 3603

value: F


title: Whole blood 152

description: sample id: 3572


title: pretreatment CLL sample [97_DE-AN]

description:
97_DE-AN_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL

value: Complete Responder


title: pretreatment CLL sample [96_B-P]

description:
96_B-P_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL

value: M


title: Contralateral cortex of sham-operated at 3d ARR36

description: S_clat 3d

value: Contralateral area

value: Sprague-Dawley

value: sham


title: pretreatment CLL sample [98_MI-GI]

description:
98_MI-GI_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL

value: Leukemic peripheral blood

value: pretreatment CLL sample

value: Progressive


title: HCC AFP-NICD 2


title: Ipsilateral area of sham-operated at 3d ARR37

description: S_ipsi 3d

value: Ipsilateral area

value: brain cortex


title: pretreatment CLL sample [94_BR-CA]

description:
94_BR-CA_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: Whole blood 147

description: sample id: 3138


title: Ipsilateral area of sham-operated at 3d ARR35

description: S_ipsi 3d


title: Liver Rosa26-lsl-NICD 4

source_name: Healthy liver

value: healthy liver

value: control monotransgenic Rosa26-lsl-NICD


title: Whole blood 144

description: sample id: 3018


title: HCC AFP-NICD 3

value: Hepatocellular carcinoma


title: pretreatment CLL sample [93_BU-RO]

description:
93_BU-RO_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: Whole blood 145

description: sample id: 2974


title: Ipsilateral area of sham-operated at 3d ARR33

description: S_ipsi 3d


title: Whole blood 148

description: sample id: 3250


title: Contralateral cortex at 3d of pMCAo ARR32

description: I_Clat 3d

source_name: Contralateral cortex at 3d of pMCAo

value: infarct


title: pretreatment CLL sample [92_AN-CO]

description:
92_AN-CO_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL

value: Partial Responder


title: Liver Rosa26-lsl-NICD 3

value: hybrid 129 x C57BL/6


title: Liver Rosa26-lsl-NICD 2


title: Periinfarct area at 3d of pMCAo ARR31

description: I_peri 3d

source_name: Periinfarct area at 3d of pMCAo

value: Periinfarct area


title: Liver Rosa26-lsl-NICD 1


title: HCC AFP-NICD 1


title: Periinfarct area at 3d of pMCAo ARR28

description: I_peri 3d


title: Contralateral cortex at 24h of pMCAo  ARR3

description: I_Clat 24h

source_name: Contralateral cortex at 24h of pMCAo


title: pretreatment CLL sample [88_LU-SA]

description:
88_LU-SA_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL

value: F


title: Contralateral area at 3d of pMCAo ARR29

description: I_Clat 3d

source_name: Contralateral area at 3d of pMCAo


title: pretreatment CLL sample [90_GI-GI]

description:
90_GI-GI_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL

value: Complete Responder


title: pretreatment CLL sample [89_G-V]

description:
89_G-V_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: pretreatment CLL sample [91_F-N]

description:
91_F-N_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL

value: M


title: Whole blood 142

description: sample id: 3583

value: Whole blood


title: pretreatment CLL sample [86_MI-GI]

description:
86_MI-GI_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: Whole blood 138

description: sample id: 864


title: Contralateral cortex at 3d of pMCAo ARR26

description: I_Clat 3d

value: Contralateral area

value: Sprague-Dawley


title: Whole blood 140

description: sample id: 5004


title: Whole blood 143

description: sample id: 2973


title: Contralateral cortex of sham-operated at 3d ARR34

description: S_Clat 3d

value: sham


title: Whole blood 141

description: sample id: 3095


title: Periinfarct area at 3d of pMCAo ARR25

description: I_peri 3d


title: pretreatment CLL sample [83_GI-RE]

description:
83_GI-RE_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL

value: Leukemic peripheral blood

value: pretreatment CLL sample

value: Progressive


title: Core area at 3d of pMCAo ARR27

description: I_core 3d

source_name: Core area at 3d of pMCAo

value: Core area

value: brain cortex


title: Periinfarct area at 3d of pMCAo ARR22

description: I_peri 3d


title: Contralateral cortex of sham-operated at 24h ARR20

description: S_Clat 24h


title: pretreatment CLL sample [79_C-O]

description:
79_C-O_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: Whole blood 139

description: sample id: 4926


title: pretreatment CLL sample [82_F-G]

description:
82_F-G_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: pretreatment CLL sample [77_C-C]

description:
77_C-C_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: pretreatment CLL sample [84_NE-GI]

description:
84_NE-GI_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: Whole blood 137

description: sample id: 2239


title: Whole blood 136

description: sample id: 5031


title: Whole blood 134

description: sample id: 2015


title: Periinfarct area at 24h of pMCAo ARR2

description: I_peri 24h

source_name: Periinfarct area at 24h of pMCAo


title: Whole blood 133

description: sample id: 4895


title: pretreatment CLL sample [85_CA-MA]

description:
85_CA-MA_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: pretreatment CLL sample [76_AN-CA]

description:
76_AN-CA_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: Whole blood 130

description: sample id: 3986


title: Whole blood 135

description: sample id: 4900


title: pretreatment CLL sample [74_LE-MA]

description:
74_LE-MA_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: Whole blood 128

description: sample id: 4183


title: Contralateral cortex of sham-operated at 24h ARR18

description: S_Clat 24h


title: Ipsilateral area of sham-operated at 24h ARR17

description: S_ipsi 24h

value: Ipsilateral area


title: Whole blood 131

description: sample id: 1762


title: pretreatment CLL sample [73_BS]

description:
73_BS_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: Contralateral cortex of sham-operated at 24h ARR16

description: S_Clat 24h


title: pretreatment CLL sample [72_TE-RU]

description:
72_TE-RU_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: Whole blood 126

description: sample id: 4457


title: Whole blood 127

description: sample id: 3911


title: Contralateral cortex at 3d of pMCAo ARR23

description: I_Clat 3d

value: infarct


title: Whole blood 132

description: sample id: 5020


title: Whole blood 124

description: sample id: 4160


title: Ipsilateral area of sham-operated at 24h ARR19

description: S_Ipsi 24h


title: pretreatment CLL sample [75_M-M]

description:
75_M-M_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: Whole blood 122

description: sample id: 4156


title: Ipsilateral area of sham-operated at 24h ARR15

description: S_Ipsi 24h


title: pretreatment CLL sample [70_BA-GI]

description:
70_BA-GI_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: Whole blood 125

description: sample id: 3909


title: Contralateral cortex of sham-operated at 24h ARR14

description: S_Clat 24h


title: Whole blood 123

description: sample id: 3879


title: Whole blood 118

description: sample id: 4702


title: Ipsilateral area of sham-operated at 24h ARR13

description: S_Ipsi 24h


title: pretreatment CLL sample [68_LU-DE]

description:
68_LU-DE_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL

value: Partial Responder


title: Contralateral cortex at 24h of pMCAo  ARR12

description: I_Clat 24h


title: pretreatment CLL sample [67_AS]

description:
67_AS_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: Whole blood 119

description: sample id: 4844


title: Whole blood 121

description: sample id: 4768


title: 3342

city: Rochester

first: Alexey

middle: Aleksandrovich

last: Leontovich

state: MN

address: 200 First street

department: Health Science Research

institute: Mayo Clinic

description: Total RNA extracted from whole blood of a progressive supranuclear palsy patient

hyb_protocol: Standard methods following recommendations of the manufacturer were used to hybridize the samples to the SpliceArrays. The arrays were washed and stained using the FS450-0001 Fluidics protocol.

scan_protocol: The scanning was done using the Affymetrix GeneChipÂ® Scanner 3000 7G.

data_processing: The probe level normalization with RMA algorithm and further summarization was done using Partek Genomics Suite v 6.09.0129

source_name: progressive supranuclear palsy, whole blood

label_protocol: Sample amplification and labeling was performed using the WT-Ovation Pico RNA  Amplification System and the FL-Ovation cDNA Biotin Module v2 (NuGen, Inc., San Carlos, CA ) according to manufacturer's instructions.

extract_protocol: RNA was extracted using the PAXgene blood RNA kit according to the manufacturer’s protocol followed by DNase I digestion.

treatment_protocol: Whole blood was collected in PAXgene tubes and incubated at room temperature for 24h before RNA extraction

value: Progressive Supranuclear Palsy


title: pretreatment CLL sample [64_FI-VI]

description:
64_FI-VI_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: Core area at 24h of pMCAo  ARR1

description: I_Core 24h

source_name: Core area at 24h of pMCAo


title: Core area at 24h of pMCAo  ARR10

description: I_Core 24h


title: Whole blood 129

description: sample id: 4864


title: pretreatment CLL sample [63_MR]

description:
63_MR_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: pretreatment CLL sample [69_AL-MA]

description:
69_AL-MA_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: pretreatment CLL sample [61_CO-TO]

description:
61_CO-TO_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: Thrombopoietin protects against heart damage induced by MI_MI+TPO_rep2

city: Hong Kong

first: Kathy

middle: YY

last: Chan

address: Rm84041, 6/F, Clinical Science Building, Prince of Wales Hospital, Shatin, N.T.

department: Paediatrics

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Gene expression of the rat heart tissue after MI + TPO treatment (Left ventricle)

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
GeneSpring data process settings: Threshold: 1   Logbase: 2   Technology: Agilent.SingleColor.14879  Normalization: Shift to 75.0 percentile   Baseline Transformation: Median of all samples   FlagSettings:  Feature is not Uniform:A  Feature is a population outlier:A  Feature is Saturated:A  Feature is not positive and significant:A  Feature is not above background:A

source_name: TPO treated MI heart_week 4, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).

growth_protocol: Animals weighing 250-300 g were subjected to left coronary artery ligation or sham surgery under anesthesia (ketamine 75 mg/Kg + xylazine 10 mg/Kg).

extract_protocol: RNA was prepared using the Trizol Reagent (Invitrogen, Carlsbad, CA) and Rneasy Mini kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. The RNA quality and integrity were analyzed with Nanodrop ND 1000 spectrophotometer (Rockland, DE) and Bioanalyzer (Agilent, Cheshire, UK).

treatment_protocol: Thrombopoietin (TPO) at 10 µg/Kg i.p. was administered immediately after induction of MI, and 3 doses weekly for 2 weeks. The sham-operated and the MI groups were given saline under the same schedule.

tag: group

value: MI+TPO

tag: replicate

value: Whole Heart


title: Thrombopoietin protects against heart damage induced by MI_MI+TPO_rep1

source_name: TPO treated MI heart_week 4, replicate 1


title: 1159


title: Whole blood 117

description: sample id: 4060

tag: gender

value: F


title: Whole blood 116

description: sample id: 4754

value: M

tag: tissue


title: pretreatment CLL sample [57_GI-TO]

description:
57_GI-TO_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL

source_name: Leukemic peripheral blood


title: Whole blood 113

description: sample id: 3025

value: Whole blood


title: pretreatment CLL sample [59_AU-ME]

description:
59_AU-ME_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: Whole blood 114

description: sample id: 4485


title: 1890

description: Total RNA extracted from whole blood of a Parkinson's desease patient

source_name: Parkinson’s disease, whole blood

tag: disease state

value: Parkinson's disease


title: 1905


title: Thrombopoietin protects against heart damage induced by MI_MI_rep1

description: Gene expression of the rat heart tissue after MI (Left ventricle)

source_name: MI damaged heart_week 4, replicate 1

value: MI


title: Whole blood 115

description: sample id: 4748


title: 3103


title: 2049


title: 1643


title: 1722


title: pretreatment CLL sample [56_AL-PO]

description:
56_AL-PO_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL

value: Complete Responder


title: Whole blood 111

description: sample id: 2934


title: Whole blood 112

description: sample id: 2873


title: Thrombopoietin protects against heart damage induced by MI_sham_rep2

description: Gene expression of the rat heart tissue (Left ventricle)

source_name: Control heart_week 4, replicate 2

value: sham


title: Whole blood 110

description: sample id: 2776


title: Strain 2221ΔrivRX, experimental replicate B

city: Reno

first: Paul

last: Sumby

state: NV

address: 1554 N. Virginia St.

department: Microbiology & Immunology

institute: University of Nevada

hyb_protocol: Labeled cDNA was hybridized to out custom array for 16h at 40 degrees C.  GeneChips were washed and stained using  the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using a GeneArray Scanner G2500A.

data_processing: The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method.

organism: Streptococcus pyogenes

source_name: Exponential phase sample B

label_protocol: RNA was converted to cDNA, the cDNA was fragmented, and the cDNA labeled with biotin

growth_protocol: GAS strains were grown in THY broth to O.D. 600 of 0.5.

extract_protocol: Total RNA was extracted via mechanical disruption and purified using the Qiagen Rneasy kit.

treatment_protocol: Two volumes of RNAprotect was added to each strain, incubated at RT for 5 mins, centrifuged, a bacterial cell pellet quick frozen in liquid nitrogen.

value: rivRX mutant


title: 1724


title: 1917


title: Thrombopoietin protects against heart damage induced by MI_MI_rep2

source_name: MI damaged heart_week 4, replicate 2


title: pretreatment CLL sample [55_SI-ZA]

description:
55_SI-ZA_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL

value: Leukemic peripheral blood

value: pretreatment CLL sample

value: Progressive


title: pretreatment CLL sample [54_GA-MO]

description:
54_GA-MO_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: 1503


title: 1550


title: Whole blood 120

description: sample id: 4718

source_name: Whole blood


title: pretreatment CLL sample [53_SA-MO]

description:
53_SA-MO_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: Strain 2221ΔrivRX, experimental replicate A

source_name: Exponential phase sample A


title: Whole blood 108

description: sample id: 2772


title: Strain MGAS2221, experimental replicate B

value: WT


title: Strain MGAS2221, experimental replicate A


title: Whole blood 109

description: sample id: 2815


title: pretreatment CLL sample [49_AN-VI]

description:
49_AN-VI_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: pretreatment CLL sample [50_MA-MA]

description:
50_MA-MA_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: pretreatment CLL sample [44_NI-ST]

description:
44_NI-ST_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: pretreatment CLL sample [52_M-C]

description:
52_MC_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: Whole blood 106

description: sample id: 2952


title: 1462


title: 3006

description: Total RNA extracted from whole blood of a progressive supranuclear palsy patient


title: Thrombopoietin protects against heart damage induced by MI_sham_rep1

source_name: Control heart_week 4, replicate 1


title: Whole blood 104

description: sample id: 2747


title: Whole blood 105

description: sample id: 2858


title: 1395


title: Whole blood 107

description: sample id: 2748


title: 1436


title: Blastocyst staged mouse whole embryos rep 4

city: East Lansing

first: Jason

last: Knott

address: 1230 H Anthony Hall

department: Animal Science

institute: Michigan State University

description: 1-cell zygote embryos were collected and in vitro cultured in KSOM medium

hyb_protocol: aRNA was hybridized for 16 hr on Affymetrix mouse 430 v2.0 microarrays. GeneChips were washed and stained using an Affymetrix Fluidics Station 450.

scan_protocol: Default Affymetrix GCOS settings for GeneChip 3000 7G scanner

data_processing: Microarray Analysis Suite 5.0 (MAS, Affymetrix) was used to quantify microarray signals with default analysis parameters and global scaling to target MEAN = 150

source_name: Embryo

label_protocol: Biotinylated cRNA were prepared using ENZO BioArray HighYied RNA transcript labeling Kit according to the manufacturer's instructions.

growth_protocol: All mouse embryos were collected and washed in M2 medium and incubated in modified KSOM under mineral oil in a humidfied atmosphere of 5% CO2, 5% O2, 90% N2 atmosphere at 37°C until use

extract_protocol: Total RNA was isolated uisng the PicoPure RNA isolation kit (Arcturus). Isolated RNA was subsequently amplified using GeneChip® Eukaryotic Small Sample Target Labeling Assay Version II

treatment_protocol: Not applicable

tag: developmental stage

value: Blastocyst

value: E4.5 (120 hours post hCG)

value: Whole embryo

value: wild-type


title: pretreatment CLL sample [39_PO-LU]

description:
39_PO-LU_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: pretreatment CLL sample [42_EL-EN]

description:
42_EL-EN_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL

value: Partial Responder


title: Whole blood 102

department: Samuel Lunenfeld Research Institute

description: sample id: 2918

value: F


title: Whole blood 103

description: sample id: 2856


title: 1154


title: pretreatment CLL sample [37_AN-MI]

description:
37_AN-MI_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL

value: M


title: 1155


title: pretreatment CLL sample [36_AN-CO]

description:
36_AN-CO_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: Whole blood 101

description: sample id: 2800

value: Whole blood


title: Blastocyst staged mouse whole embryos rep 3

tag: strain


title: Whole blood 99

description: sample id: 2841


title: pretreatment CLL sample [38_LA-GI]

description:
38_LA-GI_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL

tag: age


title: 1025

description: Total RNA extracted from whole blood of a Parkinson's desease patient

value: Parkinson's disease


title: Blastocyst staged mouse whole embryos rep 1


title: Whole blood 100

description: sample id: 2700


title: 1028


title: 3285

description: Total RNA extracted from whole blood of a multiple system atrophy patient

source_name: multiple system atrophy, whole blood

value: Multiple System Atrophy


title: 8-cell staged mouse whole embryos rep 4

value: E2.5 (66 hours post  hCG)


title: pretreatment CLL sample [34_BE-TR]

description:
34_BE-TR_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: 1084


title: Whole blood 97

description: sample id: 2696


title: pretreatment CLL sample [35_LU-SC]

description:
35_LU-SC_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL

value: Non Responder


title: Blastocyst staged mouse whole embryos rep 2


title: pretreatment CLL sample [32_AR-FE]

description:
32_AR-FE_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: 8-cell staged mouse whole embryos rep 3


title: 8-cell staged mouse whole embryos rep 2


title: 3007


title: Whole blood 95

description: sample id: 2840


title: 8-cell staged mouse whole embryos rep 1


title: Whole blood 96

description: sample id: 2890


title: Whole blood 98

description: sample id: 2740


title: Whole blood 94

description: sample id: 2789


title: pretreatment CLL sample [30_144146007]

description:
30_144146007_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: pretreatment CLL sample [28_144146002]

description:
28_144146002_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: Myoblast from HMGA2 KO mice, biological replicate 3

city: Cambrdige

first: Yunyu

last: Zhang

state: MA

address: 22 Windsor Ave

institute: Novartis Institute for Biomedical Research

description:
myoblast_KO_M_5
Gene expression data from myoblasts of C57BL/6 HMGA2 -/- mice.

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix Mouse Genome Array 430 v2 according to the standard Affymetrix protocols.

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

data_processing: Raw data were normalized and summarized using R and the Bioconductor package plier.

source_name: myoblasts from HMGA2 -/- mice, male, #5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 400 ug total RNA (Affymetrix 2010).

extract_protocol: Total RNA was extracted using Trizol and RNase.

treatment_protocol: None.

tag: strain/background

tag: genotype/variation

value: HMGA2 -/-

value: male

tag: cell type

value: myoblasts


title: Myoblast from HMGA2 KO mice, biological replicate 4

description:
myoblast_KO_F_6
Gene expression data from myoblasts of C57BL/6 HMGA2 -/- mice.

source_name: myoblasts from HMGA2 -/- mice, female, #6

value: female


title: pretreatment CLL sample [25_GI-CU]

description:
25_GI-CU_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL

value: Leukemic peripheral blood

value: pretreatment CLL sample

value: Progressive


title: 1176


title: 3405

description: Total RNA extracted from whole blood of healty individual

source_name: healthy control, whole blood

value: healthy


title: Myoblast from HMGA2 KO mice, biological replicate 2

description:
myoblast_KO_F_4
Gene expression data from myoblasts of C57BL/6 HMGA2 -/- mice.

source_name: myoblasts from HMGA2 -/- mice, female, #3


title: 3283


title: Whole blood 93

description: sample id: 2739


title: pretreatment CLL sample [20_DCG]

description:
20_DCG_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: pretreatment CLL sample [19_BA-VI]

description:
19_BA-VI_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: 3462


title: pretreatment CLL sample [18_G-P]

description:
18_G-P_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: Myoblast from wild type mice, biological replicate 3

description:
myoblast_WT_F_6
Gene expression data from myoblasts of C57BL/6 wild type mice.

source_name: myoblasts from wild type mice, female, #6

value: wild type


title: Myoblast from HMGA2 KO mice, biological replicate 1

description:
myoblast_KO_M_2
Gene expression data from myoblasts of C57BL/6 HMGA2 -/- mice.

source_name: myoblasts from HMGA2 -/- mice, male, #2


title: Patient 8 - Repeat Biopsy

first: Ilias

last: Alevizos

state: Maryland

address: 10 Center Dr., RM 1N110

institute: National Institute for Dental and Craniofacial Research (NIDCR)

hyb_protocol: Performed by Asuragen using Affymetrix GeneChip miRNA Array protocols.

data_processing: RMA Background correction with quantile normalization.

source_name: Renal needle biopsy

label_protocol: Asuragen has a proprietary labeling method.

extract_protocol: Total RNA was extracted from FFPE kidney specimens using RecoverAll Total RNA Isolation Kit (Ambion Inc, TX). RNA qualities were assessed with NanoDrop 2000 to determine the concentration and 260/280 ratio.

tag: progression

value: Repeat

tag: activity

value: high

tag: chronicity

tag: years to dialysis

value: Renal needle biopsy

value: Lupus Nephritis

tag: subject

value: Patient 8


title: Myoblast from wild type mice, biological replicate 2

description:
myoblast_WT_F_4
Gene expression data from myoblasts of C57BL/6 wild type mice.

source_name: myoblasts from wild type mice, female, #4


title: 3401


title: Whole blood 92

description: sample id: 2943

value: M

value: Whole blood


title: pretreatment CLL sample [21_FA-ET]

description:
21_FA-ET_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL

source_name: Leukemic peripheral blood

tag: sample status

tag: status of disease

tag: response to therapy

value: Partial Responder


title: 3362


title: 3307

description: Total RNA extracted from whole blood of a multiple system atrophy patient

value: Multiple System Atrophy


title: 1315

description: Total RNA extracted from whole blood of a Parkinson's desease patient

source_name: Parkinson’s disease, whole blood

value: Parkinson's disease


title: 3310


title: Patient 8 - Baseline

scan_protocol: Performed by Asuragen using Affymetrix GeneChip miRNA Array protocols.

value: Baseline

value: low