title: 4-month old BEN-NULL biological replicate 4

status: Public on Dec 31 2014

type: RNA

city: Baltimore

first: Don

last: Zack

state: Maryland

address: 400 N Broadway

country: USA

institute: Johns Hopkins University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 2 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute. • Hybridize 17 hours at 45° at 60rpm. • Fluidics washing is FS450_0001.

scan_protocol: AGCC 4.1

data_processing:
We used Partek Genomic Suite software to normalize expression data of all extended level probe sets using the following options: GC pre-background adjustment, RMA background correction and quantile normalization. The overall expression level for a given gene is defined as the average expression level of all exons for the gene.
probe group file: MoEx-1_0-st_v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm8.mps

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: 4-month BEN-NULL

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

growth_protocol: Mouse retinas dissected from 2-week or 2-months old mouse eyes

extract_protocol: Total RNA was individually extracted from four Gtf2ird1 null mouse retinas and four age-matched WT retinas at 2 weeks and 4 months using Trizol (Invitrogen). Those RNA samples were further purified using the RNeasy Mini kit (Qiagen) labeled and hybridzed to the Affymetrix Mouse Exon 1.0 array at the Johns Hopkins Deep Sequencing and Microarray Core Facility.

treatment_protocol: not applicable

tag: age

tag: tissue

value: retina


title: 4-month old BEN-NULL biological replicate 3


title: 4-month old WT biological replicate 2

source_name: 4-month WT


title: 2-week old WT biological replicate 2

source_name: 2-week WT


title: 2-week old WT biological replicate 3


title: 2-week old WT biological replicate 1


title: 4-month old BEN-NULL biological replicate 2


title: 4-month old BEN-NULL biological replicate 1


title: 4-month old WT biological replicate 4


title: 2-week old BEN-NULL biological replicate 4

source_name: 2-week BEN-NULL


title: 2-week old BEN-NULL biological replicate 2


title: 2-week old BEN-NULL biological replicate 3


title: 2-week old WT biological replicate 4


title: 4-month old WT biological replicate 3


title: 2-week old BEN-NULL biological replicate 1


title: 4-month old WT biological replicate 1


title: 13-302

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

hyb_protocol: Whole Genome Gene Expression Direct Hybridization

scan_protocol: Illumina HiScan

data_processing:
The data were normalised using quantile method
Signal calculated by GenomeStudio Data Analysis Software’s Gene Expression Module (GSGX) Version 1.5.4 (Illumina, Inc.)

source_name: TCL1_anti-PtC BCR

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays

growth_protocol: in vivo

extract_protocol: RNA extraction was performed using a commercially available kit (RNeasy, Qiagen, Frederick,MD) according to the manufactures’ recommendations. RNA quality was confirmed based on a RNA integrity number >8 by use of an electrophoresis bioanalyzer (2100 Agilent Bioanalyser).

treatment_protocol: treatment with 4-hydroxytamoxifen

value: TCL1 leukemias

tag: bcr type

value: anti-PtC BCR (type 1 BCR)


title: 13-304


title: CLV4

city: Grafton

first: Brya

last: Matthews

state: Auckland

address: 85 Park Rd

department: Molecular Medicine and Pathology

country: New Zealand

institute: University of Auckland

description: OC-GFP+ Calvarial osteoblasts rep 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were processed with the Bioconductor lumi package using a variance-stabilizing transformation (VST) algorithm for data normalization.

source_name: Calvaria

label_protocol: RNA was amplified and biotinylated using the Ambion MessageAmp Premier RNA Amplification Kit

growth_protocol: Mice were housed in standard conditions

extract_protocol:
Dissected tissue was digested in PBS containing 0.25% trypsin, 0.2% collagenase A at 37°C with agitation, after 20 mins the supernatent was discarded, then the remaning tissue digested for 1h prior to cell sorting.
RNA was extracted with Trizol reagent according to the manufacturer's instructions

tag: gender

value: Mixed

tag: strain

value: 6-7 weeks

tag: genotype

value: OC-GFP

tag: n animals


title: 28TOOTH

description: OC-GFP+ cementoblasts rep 2

source_name: Periodontium

extract_protocol:
Dissected tissue was digested in PBS containing 0.25% trypsin, 0.2% collagenase A at 37°C with agitation for 1h prior to cell sorting.
RNA was extracted with Trizol reagent according to the manufacturer's instructions

value: 5-6 weeks


title: 13-292


title: 13-305

source_name: TCL1_anti-Sm BCR

value: anti-Sm BCR (Type 2 BCR)


title: 13-306


title: 27TOOTH

description: OC-GFP+ cementoblasts rep 1


title: 28CLV

description: OC-GFP+ Calvarial osteoblasts rep 2


title: 22CLV

description: OC-GFP+ Calvarial osteoblasts rep 1

value: 6 weeks


title: 13-300


title: TOOTH4

description: OC-GFP+ cementoblasts rep 3


title: 13-299


title: 13-298


title: 13-294


title: 13-296


title: 13-295


title: 13-308


title: 13-311


title: 13-309


title: 13-310


title: 8615501094_C

city: La Jolla

first: Gen-Sheng

last: Feng

state: CA

address: 9500 Gilman Dr.

department: Pathology

institute: University of California San Diego

description: 2 month old not-fasted

hyb_protocol: The labeled cRNA (750 ng) was hybridized overnight at 58°C to the Sentrix Mouse -8 Expression BeadChip (>23,000 gene transcripts; Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

scan_protocol: BeadChips were scanned with an Illumina BeadArray Reader

data_processing: quatile normalized background substracted signal intensity

source_name: Shp2hep-/- #1

label_protocol: Labeled cRNA was prepared from 500 ng RNA using the Illumina® RNA Amplification Kit from Ambion (Austin, TX, USA).

extract_protocol: RNA were prepared with Rneasy Mini Kit

value: 2 month old


title: 13-307


title: 8615501094_D

description: 2 month old not-fasted

source_name: Shp2hep-/- #2


title: 8615501094_B

description: 2 month old not-fasted

source_name: WT Shp2Floxed/Floxed


title: thymocyte_FoxP3neg_KO_rep1

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

description:
E2Af/fHEBf/f/ER-Cre/Foxp3KI mice
_9253995055_G

scan_protocol: Standard Illumina scanning protocol with Illumina HiScan-SQ

data_processing: Signal data was extracted from the image files with the Gene Expression module (v. 1.9.0) of the GenomeStudio software (v. 2011.1) from Illumina, Inc. Signal intensities were converted to log 2 scale. Probes that didn't show detection p-value < 0.1 in at least 2 arrays were removed from the dataset.  After filtering probes, quantile normalization was applied across all arrays. ANOVA was performed on the normalized log2 expression estimates to test for mRNA expression differences by strain (wild type [WT] or knockout [KO] of E-proteins) and sort fraction (FoxP3+ or FoxP3-). A p-value of 0.05 was used for the statistical significance cutoff, after adjusting for the familywize error rate (FWER) using Benjamini–Hochberg method to account for multiple testing. Statistical analysis was performed using JMP/Genomics software version 6.0.

source_name: thymus T-cells

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion)

growth_protocol: WT or floxed mice were orally administered tamoxifen dissolved in corn oil 4 times every other day (3mg/mice) over a period of 10 days to induce deletion of E-protein in vivo

extract_protocol: RNA was purified by Qiagen RNAeasy kit

treatment_protocol: thymocytes sorted for either CD4+Foxp3+ and CD4SPFoxp3-

value: E2A HEB Knockout

value: T-cell

tag: organ

value: thymus


title: 8615501094_A

description: 2 month old not-fasted


title: thymocyte_Foxp3pos_KO_rep2

description:
E2Af/fHEBf/f/ER-Cre/Foxp3KI mice
_9253995055_F


title: thymocyte_FoxP3neg_KO_rep2

description:
E2Af/fHEBf/f/ER-Cre/Foxp3KI mice
_9253995055_H


title: thymocyte_FoxP3neg_WT_rep2

description:
WT Foxp3KI mice
_9253995055_D

value: Wild type


title: thymocyte_Foxp3pos_WT_rep1

description:
WT Foxp3KI mice
_9253995055_A


title: thymocyte_FoxP3neg_WT_rep1

description:
WT Foxp3KI mice
_9253995055_C


title: thymocyte_Foxp3pos_KO_rep1

description:
E2Af/fHEBf/f/ER-Cre/Foxp3KI mice
_9253995055_E


title: Pten cKO rep1

first: Hyung Jin

last: Kim

address: 187 Osongsaengmyeong 2-ro

department: Division of Intractable Diseases, Center for Biomedical Sciences

country: South Korea

institute: Korea National Institute of Health

description: replicate 1

data_processing: Data processing and analysis were performed using Illumina GenomeStudio v1.5.4  (Gene Expression Module v2009.2)

source_name: Mouse inner ear

label_protocol: Biotinylated cRNA were prepared with Illumina TotalPrep RNA Amplification Kit (Ambion).

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

tag: developmental stage


title: Pten cKO rep3

description: replicate 3


title: Pten cKO rep2

description: replicate 2


title: thymocyte_Foxp3pos_WT_rep2

description:
WT Foxp3KI mice
_9253995055_B


title: Wild-type rep3

description: replicate 3

value: PtenloxP/+ and PtenloxP/loxP


title: Wild-type rep2

description: replicate 2


title: Wild-type rep1

description: replicate 1


title: control #5

city: Heidelberg

first: Hagen

last: Wende

address: Im Neuenheimer Feld 366

department: Institute of Pharmacology

country: Germany

institute: Heidelberg University

description:
4936640006_B
Replicate 5 of 6.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization with Illumina Genome Studio.

source_name: mouse dorsal root ganglion, control

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplif Kit.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

value: C57/BL6;129Ola mixed

value: wildtype

value: 15 days

value: dorsal root ganglion


title: control #4

description:
4936640006_G
Replicate 4 of 6.


title: control #3

description:
4936640004_H
Replicate 3 of 6.


title: control #2

description:
4936640004_E
Replicate 2 of 6.


title: c-Maf mutant #2

description:
4936640004_D
Replicate 2 of 6.

source_name: mouse dorsal root ganglion, c-Maf mutant

value: c-Maf mutant


title: c-Maf mutant #6

description:
4936640006_F
Replicate 6 of 6.


title: c-Maf mutant #4

description:
4936640006_A
Replicate 4 of 6.


title: control #1

description:
4936640004_B
Replicate 1 of 6.


title: c-Maf mutant #1

description:
4936640004_A
Replicate 1 of 6.


title: c-Maf mutant #5

description:
4936640006_C
Replicate 5 of 6.


title: control #6

description:
4936640006_E
Replicate 6 of 6.


title: c-Maf mutant #3

description:
4936640004_G
Replicate 3 of 6.


title: CD70Tg_CD34Pos_1

city: Leiden

first: Peter

last: 't Hoen

address: PO Box 9600

department: Center for Human and Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

description: FACS pools of CD34 positive cells obtained from two mice

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing:
Beadarray v1.3 probe summarization; vsn normalization
Matrix non-normalized: Two columns per sample. First column contains intensity values; second column contains detection p-value, is low when intensity value is above background threshold. Matrix normalized: Two columns per sample. First column contains vsn normalized intensity values; second column contains same detection p-values as non-normalized data

label_protocol: RNA was amplified with Ambion MessageAmp kit for Illumina arrays and biotinylated during a second round of amplification with the same kit

extract_protocol: Rneasy Plus micro kit (Qiagen)

treatment_protocol: For analysis of hematopoietic progenitors by flow cytometry, bone marrow cells were stained with antibodies against lineage markers, CD34, Flt3, Sca-1, c-Kit, Cd16/32 (93), IL-7Rα (A7R34), CD48 (HM-48-1), CD150 (TCF15-12F12.2, Biolegend) and CD27 (LG.7F9) and identified as: LT-HSC (Lin-c-Kit+Sca-1+CD34-Flt3-), ST-HSC (Lin-c-Kit+Sca-1+CD34-Flt3-)

tag: cell type

tag: genotype/variation

value: CD70TG (IFNgamma-/-xCD70TG)


title: CD70Tg_CD34Pos_4


title: CD70Tg_CD34Neg_2

description: FACS pools of CD34 negative cells obtained from two mice


title: control_CD34Pos_4

value: control (IFNgamma-/-)


title: CD70Tg_CD34Pos_2


title: control_CD34Pos_1


title: control_CD34Pos_3


title: CD70Tg_CD34Pos_3


title: control_CD34Pos_2


title: CD70Tg_CD34Neg_3


title: control_CD34Neg_2


title: control_CD34Neg_3


title: CD70Tg_CD34Neg_4


title: CD70Tg_CD34Neg_1


title: control_CD34Neg_1


city: Oslo

first: Leonardo

middle: A.

last: Meza-Zepeda

address: Ullernchausseen 70

department: Department of Tumor Biology

country: Norway

institute: Oslo University Hospital

data_processing: The data was quantile normalisation in GeneSpring GX10 (Agilent)

label: Biotin

organism: Homo sapiens

source_name: Immortalized human bone marrow-derived mesenchymal stromal cell line IMSC#3, 7 days adipocyte differentiation, replicate 3

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

growth_protocol: Cells were seeded in 48- and 6-well plates (Nunc) at 25,000 and 100,000 cells per well, respectively. Next day, the medium was replaced with adipocyte induction medium containing 1 µM Dexamethasone (Decadron), 0.5 mM iso-butyl-methyl-xanthine and 50 µM Indomethacine (both from Sigma-Aldrich). The differentiation medium was replaced twice a week for 21 days.

extract_protocol: RNA was isolated using the standard TRIzol procedure (Invitrogen), and further purified with an RNeasy mini column (Qiagen GmbH, Hilden, Germany), according to the manufacturers’ instructions.

tag: cell line

tag: sample origin

value: Human bone marrow-derived mesenchymal stromal cell

value: Male


source_name: Immortalized human bone marrow-derived mesenchymal stromal cell line IMSC#3, 21 days adipocyte differentiation, replicate 3


source_name: Immortalized human bone marrow-derived mesenchymal stromal cell line IMSC#3, 72 hrs adipocyte differentiation, replicate 3


source_name: Immortalized human bone marrow-derived mesenchymal stromal cell line IMSC#3, 7 days adipocyte differentiation, replicate 2


source_name: Immortalized human bone marrow-derived mesenchymal stromal cell line IMSC#3, 72 hrs adipocyte differentiation, replicate 2


source_name: Immortalized human bone marrow-derived mesenchymal stromal cell line IMSC#3, 24 hrs adipocyte differentiation, replicate 3


source_name: Immortalized human bone marrow-derived mesenchymal stromal cell line IMSC#3, 0 hrs adipocyte differentiation, replicate 2


source_name: Immortalized human bone marrow-derived mesenchymal stromal cell line IMSC#3, 14 days adipocyte differentiation, replicate 2


source_name: Immortalized human bone marrow-derived mesenchymal stromal cell line IMSC#3, 21 days adipocyte differentiation, replicate 2


source_name: Immortalized human bone marrow-derived mesenchymal stromal cell line IMSC#3, 14 days adipocyte differentiation, replicate 3


source_name: Immortalized human bone marrow-derived mesenchymal stromal cell line IMSC#3, 24 hrs adipocyte differentiation, replicate 2


title: Immortalized human bone marrow-derived mesenchymal stromal cell line iMSC#3, Affymetrix SNP 6

type: genomic

hyb_protocol: Standard Affymetrix hyb protocol

scan_protocol: Standard Affymetrix scan protocol

data_processing:
Quality control was performed using the Genotyping Console v3.0.1 software (Affymetrix), applying the contrast quality control (CQC) algorithm with a minimal call rate of > 86 %. DNA copy number analysis was performed using the Nexus software (BioDiscovery, California, USA), with the SNPRank segmentation algorithm using default settings (threshold of 0.6 for high copy gain, 0.2 for gain, -0.2 for loss and -1.0 for homozygous loss).
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
Copy number probes and segments, as well as SNP calls and segments obtained from NEXUS copy number. Used Hg19

molecule: genomic DNA

label_protocol: Standard Affymetrix label protocol

growth_protocol: iMSC#3 was cultured in minimum essential medium (MEM) Alpha medium (cat. no. 22561) supplemented with 10% FBS (PAA Laboratories), GlutaMAX, penicillin (100U/mL), and streptomycin (100 mg/mL) (all from Life Technologies) at 37C and 5% CO2. Non-adherent cells were removed after approximately 24 h by replacement of the medium. Subsequently, the adherent cells were allowed to expand until 70% confluence (5–6 days) before they were harvested and further expanded.

extract_protocol: DNA was isolated using the Wizard Genomic DNA Purification Kit (Promega, Madison, USA).


source_name: Immortalized human bone marrow-derived mesenchymal stromal cell line IMSC#3, 0 hrs adipocyte differentiation, replicate 3


title: MCF-7-TF_1

city: Seattle

first: Xin

last: Cai

state: WA

address: 1100 Fairview Ave N

department: Clinical Research Division

institute: FHCRC

description:
replicate 1
breast cancer cell line stably overexpressing NKG2D

data_processing: Signal intensities were quantile normalized using the Bioconductor package lumi.

label: biotin label

label_protocol: Illumina TotalPrep RNA Amplification Kit

growth_protocol: MCF-7 mock and MCF-7-TF cells were maintained in RPMI160 /10% fetal bovine serum (FBS)/ antibiotics.

extract_protocol: RNA samples of MCF-7-mock and MCF-7-TF cells were extracted using RNeasy Plus Mini Kit (Qiagen), and their integrity was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies).

value: breast cancer

tag: nkg2d expression status

value: over-expression


title: MCF-7-TF_2

description:
replicate 2
breast cancer cell line stably overexpressing NKG2D


title: MCF-7-mock_2

description:
replicate 2
breast cancer cell line

source_name: breast cancer cell line mock-transfected


title: MCF-7-mock_1

description:
replicate 1
breast cancer cell line


title: MCF-7-TF_3

description:
replicate 3
breast cancer cell line stably overexpressing NKG2D


title: MCF-7-TF_4

description:
replicate 4
breast cancer cell line stably overexpressing NKG2D


title: MCF-7-mock_3

description:
replicate 3
breast cancer cell line


title: MCF-7-mock_4

description:
replicate 4
breast cancer cell line


title: control_CD34Neg_4


title: HCT 72h rep2

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

description: replicate 2

hyb_protocol: Hybridization is performed at 58°C, in GEX-HCB buffer (Illumina Inc.) at a concentration of 100 ng cRNA/µl, unsealed in a wet chamber for 20h. Spike-in controls for low, medium and highly abundant RNAs were added, as well as mismatch control and biotinylation control oligonucleotides. Microarrays were washed twice in E1BC buffer (Illumina Inc.) at room temperature for 5 minutes. After blocking for 5 min in 4 ml of 1% (wt/vol) Blocker Casein in phosphate buffered saline Hammarsten grade (Pierce Biotechnology, Inc., Rockford, IL), array signals are developed by a 10-min incubation in 2 ml of 1 µg/ml Cy3-streptavidin (Amersham Biosciences, Buckinghamshire, UK) solution and 1% blocking solution. After a final wash in E1BC, the arrays are dried and scanned.

data_processing: All array data processing and analysis was performed using R statistical language v. 2.9. The data were normalised using quantile normalisation with IlluminaGUI in R 2.5

source_name: BE(2)C neuroblastoma cells

label_protocol: Biotin-labeled cRNA samples were prepared according to Illumina's recommended sample labeling procedure based on the modified Eberwine protocol (Eberwine et al., 1992). In brief, 250 ng total RNA was used for complementary DNA (cDNA) synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA according to the MessageAmp II aRNA Amplification kit (Ambion, Inc., Austin, TX). Biotin-16-UTP was purchased from Roche Applied Science, Penzberg, Germany. The cRNA was column purified according to TotalPrep RNA Amplification Kit, and eluted in 60 µl of water. Quality of cRNA was controlled using the RNA Nano Chip Assay on an Agilent 2100 Bioanalyzer and spectrophotometrically quantified (NanoDrop).

growth_protocol: cells were grown under adherent subconfluent culture condition in RPMI medium supplemented with 10% FCS and 5% C02

extract_protocol: Total RNA was isolated from cell cultures using Qiagen’s RNeasy MiniKit according to the manufacturer's instructions.

treatment_protocol: Cells were transiently transfected using HiPerFect (Qiagen) with 25 nM siRNA or treated with MeoH or treated with pan-HDAC inhibitor HC-Toxin.

value: BE(2)C neuroblastoma cells

tag: time

tag: treatment

value: pan-HDAC inhibitor HC-Toxin


title: MeOH 72h rep3

description: replicate 3

value: MeoH (solvent)


title: HCT 72h rep3

description: replicate 3


title: HCT 72h rep1

description: replicate 1


title: MeOH 72h rep2

description: replicate 2


title: siHDAC11_b 96h rep2

description: replicate 2

tag: sirna


title: MeOH 72h rep1

description: replicate 1


title: siHDAC11_b 96h rep3

description: replicate 3


title: siHDAC11_b 96h rep1

description: replicate 1


title: siHDAC11_b_negctrl 96h rep3

description: replicate 3

value: scrambled (neg control)


title: siHDAC11_b_negctrl 96h rep1

description: replicate 1


title: siHDAC11_a 48h rep 2

description: replicate 2


title: siHDAC11_b_negctrl 96h rep2

description: replicate 2


title: siHDAC11_a 48h rep 1

description: replicate 1


title: siHDAC11_a_negctrl 48h rep1

description: replicate 1


title: siHDAC11_a 48h rep 3

description: replicate 3


title: siHDAC11_a_negctrl 48h rep3

description: replicate 3


title: siHDAC11_a_negctrl 48h rep2

description: replicate 2


title: CR-l-B

city: Los Angeles

first: William

middle: Alexander

last: Freije

address: 650 Charles Young Drive, South CHS B8-127

department: Obstetrics and Gynecology

institute: UCLA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Affymetrix Rat Gene 1.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: Standard Affymetrix scanning

data_processing: Microarrays were normalized using RMA in the Affymetrix software Expression Console

organism: Rattus norvegicus

source_name: Hypothalamic sample from day 21 female rat offspring from mothers fed a calorie restricted diet and who received leptin treatment, replicate B

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Female offspring from timed mated and pregnant Sprague-Dawley rats were used for these experiments.

extract_protocol: RNA extraction through Trizol followed by Rneasy Cleanup

treatment_protocol: Control (Con) offspring born to mothers who were fed normally throughout gestation and lactation; calorie restricted offspring (CR) born to mothers who had 50% restriction of calories from GD11 to GD21 and post-natally. Saline or leptin replenishment was admisnistered during the early postnatal period (PN2-PN8).

value: Sprague-Dawley

value: hypothalamus

tag: age

value: female


title: Con-l-A

source_name: Hypothalamic sample from day 21 female rat offspring from mothers fed a control diet and who received leptin treatment, replicate A

tag: tissue


title: Parp inhibitor treated mouse embryonic stem cell line (J1)

city: Tokyo

first: Hiroaki

last: Fujimori

address: Tsukiji 5-1-1

country: Japan

institute: National Cancer Center Research Institute

hyb_protocol: Labelled DNA mixed with Cot-1 DNA and Agilent blocking solution was hybridized to arrays for 40 hours at 67C and 10rpm. Arrays were washed as per Agilent protocol.

scan_protocol: Arrays were washed and scanned immediately with Agilent microarray scanner G2565BA. Images were quantified using Agilent Feature Extraction 9.1 Software.

data_processing: Arrays were processed using Agilent Feature Extraction 9.1 software and normalized (background subtraction and interarray median normalization) using Agilent Chip Analytics 1.3 software.

label_protocol: Sonicated DNA was labelled using Agilent Genomic DNA Labeling Kit PLUS (5188-5309).

extract_protocol: Genomic DNA was extracted by the phenol/chloroform method.

value: Parp inhibitor treated

value: mouse embryonic stem cell line

tag: dna treatment

value: Sonicated

source_name: Parp inhibitor (PJ34) treated mouse embryonic stem cell line (J1)

label_protocol: Sonicated/IP DNA was labelled using Agilent Genomic DNA Labeling Kit PLUS (5188-5309).

value: Sonicated and immunoprecipitated with anti-5-methyl cytidine antibody (Diagenode, Liége, Belgium)


title: Parp-1 deficient embryonic stem cell line (226-47) derived from J1

value: Parp-1 deficient

value: mouse embryonic stem cell line (226-47)


title: mouse embryonic stem cell line (J1)

source_name: mouse embryonic stem cell line (J1)

tag: cell


title: Con-l-B

source_name: Hypothalamic sample from day 21 female rat offspring from mothers fed a control diet and who received leptin treatment, replicate B

tag: strain

tag: gender


title: CR-s-A

source_name: Hypothalamic sample from day 21 female rat offspring from mothers fed a calorie restricted diet and who received saline treatment, replicate A


title: Con-s-B

source_name: Hypothalamic sample from day 21 female rat offspring from mothers fed a control diet and who received saline treatment, replicate B


title: CR-s-B

source_name: Hypothalamic sample from day 21 female rat offspring from mothers fed a calorie restricted diet and who received saline treatment, replicate B


title: Parp-1 deficient embryonic stem cell line (210-58) derived from J1

value: mouse embryonic stem cell line (210-58)


title: Con-s-A

source_name: Hypothalamic sample from day 21 female rat offspring from mothers fed a control diet and who received saline treatment, replicate A


title: CR-l-A

source_name: Hypothalamic sample from day 21 female rat offspring from mothers fed a calorie restricted diet and who received leptin treatment, replicate A


title: N2 Rifampicin, Biological rep1

city: New Delhi

first: Arnab

last: Mukhopadhyay

address: Aruna Asaf Ali Marg

country: India

institute: National Institute of Immunology

description: Gene expression of Rifampicin treated N2 worms

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip C.elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The primary data was analyzed with Affymetirx Expression Console. Futher differential  gene expression and cluster analysis was  done using Genespring GX 11.1 . In Genespring GX, Affymetrix default analysis settings and RMA as normalization method used. The probes of intensities less than the 20.0 percentile in the raw data were excluded before differential  gene expression analysis.

organism: Caenorhabditis elegans

source_name: Rifampicin treated N2 worms

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

growth_protocol: Worms were grown on Nematode Growth Media (NGM) media seeded with E. coli OP50-AMP plates.  E. coli OP50-AMP bacteria were grown overnight at 37°C in LB media, the plates were seeded and dried and stored at 4°C till use.

extract_protocol: RNA was isolated using Trizol (Invitrogen, USA).  Briefly, worms grown in liquid media were harvested from  DMSO or  RIF-treated plates and washed with M9 buffer. Then, 0.3 ml of Trizol reagent was added and the worms lysed by vigorous vortexing. RNA was purified by phenol:chloroform:isoamylalcohol extraction and followed by ethanol precipitation. The concentration and the purity of the RNA were determined using Bioanalyzer (Agilent, USA). Alternatively, the quality of the ribosomal 28 S and 18 S on an agarose gel was used as a measure of integrity and the absorbance at 260/280 nm was used to determine quantity.

treatment_protocol: Worms were grown on E. coli OP50 till young adult stage. The young adult worms were harvested using M9 Buffer and washed 4 times to remove all the bactrial feed.  E. coli OP50 transformed with L4440  vector (OP50-AMP) was grown overnight at 37°C with 100 mg/ml ampicillin. The culture was pelleted  and S-Complete Buffer was added to make a 100 mg/ml stock. This stock was heated in boling water bath for  45 min and and killing of bacteria confirmed by streaking on LB Amp plates. This feed was used for further experimentations  Worms were transfered to liquid medium with 100 mg/ml  heat killed E. coli OP50-AMP along with 50 mg/ml carbenicillin, 250 µg/ml Amphoterecin B  and 0.6 mM Fudr to prevent egg laying. The worms were fed again on 5th day of adult hood with 100 mg/ml heat killed E. coli OP50-AMPr. The worms were harvested on 8th day adulthood and washed throughly with M9 buffer to remove all traces of feed.

value: whole organism total RNA isolated, idr-1 RNAi treated, replicate-1

value: 8th day of adulthood


title: N2 DMSO, Biological rep2

description: Gene expression of DMSO treated N2 worms

source_name: DMSO treated N2 worms

value: whole organism total RNA isolated, Control RNAi treated, replicate-2


title: ws_24h4c_Rep2_q8ws

city: Raleigh

first: Colleen

middle: J

last: Doherty

state: NC

address: 128 Polk Hall CB7622

department: Biochemistry

institute: North Carolina State University

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol (GeneChip¬ Expression Analysis Technical Manual) processed at the processed at the PRL DOE Genomics facility

scan_protocol: Affymetrix GeneChip Scanner 3000 with GCOS software according to manufactuer's protocol (GeneChip¬ Expression Analysis Technical Manual) processed at the processed at the PRL DOE Genomics facility

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy.

organism: Arabidopsis thaliana

source_name: seedlings, 10 days old, WS ecotype

label_protocol: Affymetrix GeneChip¬ IVT Labeling Kit, according to manufactuer's protocol (GeneChip¬ Expression Analysis Technical Manual) processed at the PRL DOE Genomics  facility

extract_protocol: Plant RNA prep using RNeasy (Qiagen) using the manufacturers protocols with RLT buffer

tag: ecotype

tag: genotype

value: WT

value: whole seedlings

tag: media

value: grown on Gamborgs media no sucrose

tag: environment

value: Grown in Constant Light ~60-80 microE at 22C

value: cold-treated moved to a 4C chamber for 24h


title: ws_24h4c_Rep1_q6ws


title: col_24h4c_Rep2

source_name: seedlings, 10 days old, Col-0 ecotype


title: col_24h4c_Rep1


title: N2 DMSO, Biological rep1

value: whole organism total RNA isolated, Control RNAi treated, replicate-1


title: col_0h4c_Rep2

value: Mock-treated moved to a new 22C chamber NO cold treatment


title: col_24h4c_set4_Rep1


title: col_24h4c_set4_Rep2


title: col_24h4c_Rep3


title: col_0h4c_Rep1

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol (GeneChip¬ Expression Analysis Technical Manual) processed at the processed at the PRL DOE Genomics facility.


title: Differentiation 36h repe

city: Kobe

first: Yuki

last: Kondo

address: 1-1 Rokkodai-cho, Nada-ku

department: Graduate School of Science

institute: Kobe University

description: Leaf disk 36h

hyb_protocol: Hybridization, washing, staining procedures were conducted with Fluidics Station 450 as described in the GeneChip Expression Analysis Techinical Manual (Affymetrix).

scan_protocol: Scanning procedure ws conducted with GeneChip Scanner 3000 7G as described in the GeneChip Expression Analysis Techinical Manual (Affymetrix).

source_name: Col-0, 25-day-old seedlings, leaf disks in 1mm diameter

label_protocol: Biotinylated cRNA was prepared from total RNA with GeneChip One-Cycle Target Labeling and Control Reagents (Affymetrix).

growth_protocol: Arabidopsis seeds were sterilized with sodium hypochlorite for 5 min, and then washed with sterile water. These seeds were grown on MS medium at 22ºC under the continuous light conditions for 25 days.

extract_protocol: Total RNA was extracted with TRIzol (Invitrogen) and purified with Rneasy Micro Kit (QIAGEN).

treatment_protocol: Leaf disks in 1 mm diameter were made from rosette leaves and then were cultured with the induction medium containing 2,4-D (1.25 mg/L), kinetin (0.25 mg/L), and bikinin (10 μM). Samples were collected at every 12 hours from 0 to 48 hours.

value: leaves

value: induction after 36h


title: Differentiation 24h rep3

description: Leaf disk 24h

value: induction after 24h


title: Differentiation 36h rep2

description: Leaf disk 36h


title: Differentiation 48h rep1

description: Leaf disk 48h

value: induction after 48h


title: Differentiation 12h rep3

description: Leaf disk 12h

value: induction after 12h


title: Differentiation 24h rep2

description: Leaf disk 24h


title: Differentiation 48h rep2

description: Leaf disk 48h


title: Differentiation 0h rep3

description: Leaf disk 0h

value: induction after 0h


title: Differentiation 0h rep2

description: Leaf disk 0h


title: Differentiation 48h rep3

description: Leaf disk 48h


title: Differentiation 12h rep2

description: Leaf disk 12h


title: JF_kidney_day7_mix4

first: Hidehiro

address: 4-5-7 Konan, Minato

institute: Tokyo University of Marine Science and Technology

description: Total RNA was extracted from fish kidneys using the RNeasy Mini Kit. RNA was reverse-transcribed into cDNA with a T7-(dT) oligomer to prime the double-strand synthesis.  double-strand cDNA was converted and labeled into cRNA with Cy3. Cy3-labeld cRNA was purified using the RNeasy mini kit. Following cleanup, fragmentation of the cRNA for target preparation was done according to the Agilent QuickAmp Labeling kit one-color protocol. After hybridization cocktails preparation, the Agilent 8x15k custom oligo DNA microarray was hybridized with the fragmented labelled cRNA for 15 h at 65 °C as described in the Agilent QuickAmp Labeling kit one-color protocol. Oligo DNA microarray, bound to Cy3-labeled cRNA, were processed using the Genepix pro v6.0 and scanned with a Axon Genepix4000B scanner

hyb_protocol: After hybridization cocktails preparation, the Agilent 8x15k oligo DNA microarray was hybridized with the fragmented labelled cRNA for 15 h at 65℃ as described in the Agilent's manuals.

scan_protocol: Oligo DNA microarray, bound to Cy3-labeled cRNA, were processed using the Genepix pro v6.0. and scanned with a Genepix4000B (Axon, USA). Scanner setting was a 5μm resolution using a PMT setting of 600 and a laser power of 100 percents.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent, USA) using default parameters (protocol GE1-v5_95 and Grid: 025875_D_F_20091023) to obtain background subtracted and spatially detrended Processed Signal intensities (raw values). GeneSpring GX v11.0 calculated normalized values that the log summarized values from the baseline transformed by control samples after corrected the average of a 75th percentile values of the arrays in the experiments.

organism: Paralichthys olivaceus

source_name: Kidney of Paralichthys olivaceus after 7 days from a vaccination using formalin killed typical type Edwardsiella tarda strain UH6

label_protocol: Conversion of double stranded cDNA into Cy3-labeled cRNA was accomplished using the QuickAmp Labeling kit one-color (Agilent, USA) according to the manufacturer’s instructions

growth_protocol: Fishes were fed a one percent of body weight per two day.

extract_protocol:
Kidney was sampled after 7 days from a vaccination.
Total RNA was extracted from fish kidney using RNeasy mini kit according to the manufacturer’s instructions (Qiagen, Germany).

treatment_protocol:
The fishes were kept in an artificial seawater 50 liter tank with a recirculating system at 24℃.
The fishes were vaccinated with an intramuscular injection using a 1.0 x 10^8 cell of an equal (1:1) mixture of formalin-killed E. tarda strain UH6 and UT1

tag: FISH body weight

value: kidney

source_name: average of control group


title: Differentiation 0h rep1

description: Leaf disk 0h


title: JF_kidney_day7_mix2

source_name: Kidney of Paralichthys olivaceus after 7 days from a vaccination using a mixture of formalin killed Edwardsiella tarda strain UH6 and UT1

extract_protocol: Total RNA was extracted from fish kidney using RNeasy mini kit according to the manufacturer’s instructions (Qiagen, Germany).


title: JF_kidney_day7_atypical1

source_name: Kidney of Paralichthys olivaceus after 7 days from a vaccination using formalin killed atypical type Edwardsiella tarda strain UT1

extract_protocol:
Kidney was sampled after 7 days from a vaccination.
Total RNA was extracted from fish kidney using RNeasy mini kit according to the manufacturer’s instructions (Qiagen, Germany). Furthermore, total RNA was pooled from two fishes.

treatment_protocol:
The fishes were kept in an artificial seawater 50 liter tank with a recirculating system at 24℃.
The fishes were vaccinated with an intramuscular injection using a 1.0 x 10^8 cell of a formalin-killed atypical type E. tarda strain UT1 isolated from Paralichthys olivaceus in Ehime prefecture in 06' Japan


title: Differentiation 36h rep1

description: Leaf disk 36h


title: JF_kidney_day7_mix3


title: JF_kidney_day7_atypical3


title: JF_kidney_day7_typical3

treatment_protocol:
The fishes were kept in an artificial seawater 50 liter tank with a recirculating system at 24℃.
The fishes were vaccinated with an intramuscular injection using a 1.0 x 10^8 cell of a formalin-killed typical type E. tarda strain UH6 isolated from Paralichthys olivaceus in Ehime prefecture in 06' Japan


title: JF_kidney_day7_atypical2

extract_protocol: Total RNA was extracted from fish kidney using RNeasy mini kit according to the manufacturer’s instructions (Qiagen, Germany). Furthermore, total RNA was pooled from two fishes.


title: JF_kidney_day3_mix2

source_name: Kidney of Paralichthys olivaceus after 3 days from a vaccination using a mixture of formalin killed Edwardsiella tarda strain UH6 and UT1

extract_protocol:
Kidney was sampled after 3 days from a vaccination.
Total RNA was extracted from fish kidney using RNeasy mini kit according to the manufacturer’s instructions (Qiagen, Germany). Furthermore, total RNA was pooled from two fishes


title: JF_kidney_day7_mix1


title: Differentiation 24h rep1

description: Leaf disk 24h


title: JF_kidney_day3_mix3

extract_protocol:
Kidney was sampled after 3 days from a vaccination.
Total RNA was extracted from fish kidney using RNeasy mini kit according to the manufacturer’s instructions (Qiagen, Germany).


title: JF_kidney_day3_atypical3

source_name: Kidney of Paralichthys olivaceus after 3 days from a vaccination using formalin killed atypical type Edwardsiella tarda strain UT1


title: Differentiation 12h rep1

description: Leaf disk 12h


title: JF_kidney_day7_typical2

extract_protocol:
Kidney was sampled after 7 days from a vaccination.
Total RNA was extracted from fish kidney using RNeasy mini kit according to the manufacturer’s instructions (Qiagen, Germany). Furthermore, total RNA was pooled from two fishes


title: JF_kidney_day7_typical1

extract_protocol: Total RNA was extracted from fish kidney using RNeasy mini kit according to the manufacturer’s instructions (Qiagen, Germany). Furthermore, total RNA was pooled from two fishes


title: JF_kidney_day3_mix1


title: JF_kidney_day3_typical3

source_name: Kidney of Paralichthys olivaceus after 3 days from a vaccination using formalin killed typical type Edwardsiella tarda strain UH6


title: JF_kidney_control3

source_name: Kidney of Japanese flounder, non-vaccinated as a control

treatment_protocol: Fishes were kept in an artificial seawater 50 liter tank with a recirculating system at 24℃.


title: JF_kidney_day3_atypical1

extract_protocol:
Kidney was sampled after 3 days from a vaccination.
Total RNA was extracted from fish kidney using RNeasy mini kit according to the manufacturer’s instructions (Qiagen, Germany). Furthermore, total RNA was pooled from two fishes.


title: JF_kidney_day3_atypical2


title: JF_kidney_day3_typical2


title: JF_kidney_day3_typical1


title: JF_kidney_control1


title: Amastigote extract Replicate 3

city: Quebec City

first: Frederic

last: Raymond

state: Quebec

address: 2440 Bd Hochelaga Suite 1710

department: École de nutrition

country: Canada

institute: Université Laval

description: Amastigote biological replicate 3 of 3.

hyb_protocol: After pre-hybridization of the array, probes were hybridized overnight at 42°C (2.5X modified Denhardt, 30% deionized formamide, 6X SSPE, 0.5% SDS, 0.1 mg ml-1 ssDNA and 0.75 mg ml-1 yeast tRNA).

scan_protocol: The fluorescence signal intensities were measured using the Perkin Elmer ScanArray Express scanner.

data_processing: Statistical analysis was performed in R 2.2.1 using Limma 3.12.0. Background correction used the Edwards method, within array normalization was done using the Loess method and inter-array normalization was done using quantiles of A. Significant genes were determined the false discovery rate (FDR) method with a threshold p value of 0.05 and minimum log2-ratio of 0.6.

label: Alexa Fluor 555

organism: Leishmania infantum

source_name: wild type

label_protocol: cDNA was obtained starting with 5 µg of total RNA using random primer hexamer and aminoallyl-dUTP mix following the protocol for Superscript III and purified using MinElute PCR purification columns. cDNA was coupled with Alexa 555 or Alexa 647 dyes and purified with MinElute PCR purification columns.

growth_protocol: Promastigotes were cultured at 25°C in SDM-79 medium pH 7 with 5 mg ml-1 hemin and 10 % heat-inactivated FCS. Axenic Amastigotes were cultured at 37°C, 5% CO2 in MAA/20 medium pH 5.8 20 % FCS. Parasites were harvested in exponential growth phase.

extract_protocol: Total RNA extracted using RNeasy Plus (Qiagen) following manufacturer's instructions

label: Alexa Fluor 647


title: JF_kidney_control2


title: skin-bodyside-rep1

city: Qingdao

first: Hegang

last: Li

state: Shandong

address: 149 Xiazhuang Road, Licang District

department: Animal Reproduction and Breeding

country: China

institute: Qingdao Institute of Animal Science and Veterinary Medicine

description: Gene expression at 16 month body side skin

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505B).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2505B, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

data_processing: Agilent Feature Extraction software (version 10.5.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.0 software package (Agilent Technologies). After Quantile normalization of the raw data, genes that at least 1 out of 6 samples have flags in Present (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.0).

organism: Ovis aries

source_name: skin,16 month body side

label_protocol: 1 μg of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: These three sheep were reared normally in pens.

extract_protocol: All samples were immediately put into collection tubes and stored in liquid nitrogen for RNA extraction. TRIzol (Invitrogen) was used for total RNA extractions according to the manufacturer’s protocol. RNA quantity and quality were measured by NanoDrop ND-1000. Its OD260/OD280 ratio was confirmed to be higher than 1.8. RNA integrity was assessed by standard denaturing agarose gel electrophoresis. The RNA samples were sent to Kangchen Biotechnology Limited Company (Shanghai, China) for hybridization to the Agilent Sheep Gene Expression Microarray (Santa Clara, CA, USA).

treatment_protocol: All animals were treated in accordance with the animal protocols deﬁned by national and local animal welfare bodies, and all animal work was approved by the Shandong Province Biological Studies Animal Care and Use Committee.One ram and two ewes of 16-month-old Aohan fine wool sheep were used in the microarray study. These animals were half sibs (sharing the same father). In December 2010, two areas of full-thickness skin were sampled from the same animal under local anaesthesia: body side skin (wool bearing) and groin skin (non-wool bearing) for microarray and proteomic experiments. The area of each sample was about 1 cm2.

tag: breed

value: Aohan

tag: body part

value: body side

value: skin


title: skin-groin-rep2

description: Gene expression at 16 month groin skin

source_name: skin,16 month groin

value: groin


title: Amastigote extract Replicate 1

description: Amastigote biological replicate 1 of 3.


title: skin-bodyside-rep3


title: Promastigote extract Replicate 1

description: Promastigote biological replicate 1 of 3.


title: Amastigote extract Replicate 2

description: Amastigote biological replicate 2 of 3.


title: Promastigote extract Replicate 3

description: Promastigote biological replicate 3 of 3.


title: skin-groin-rep3

description: Gene expression at 16 month groin skin


title: Promastigote extract Replicate 2

description: Promastigote biological replicate 2 of 3.


title: skin-groin-rep1

description: Gene expression at 16 month groin skin


title: skin-bodyside-rep2


title: sample747

city: Homburg

first: Andreas

last: Keller

address: Building 60

institute: Saarland University

hyb_protocol: according to manufacturers instruction (febit biomed)

scan_protocol: Wizard software on standard Microsoft Windows Workstation PC

data_processing: Summarizing of technical replica by median and quantile normalization. Following BG correction, negative values were corrected to 1. R Version 3.0.2

source_name: RNA from blood

label_protocol: MPEA, microfluidic primer extension assay Biotin labeling

extract_protocol: Blood of controls and patients was extracted in PAXgene Blood RNA tubes (BD, Franklin Lakes, New Jersey USA). The content of blood sampling tubes of each patient and healthy donor was used for RNAe extraction. The total RNA including the miRNA was isolated using the miRNeasy kit (Qiagen GmbH, Hilden) according to manufacturers instructions..

treatment_protocol: stored at -20 degree

tag: disease

value: chronic obstructive pulmonary disease (COPD)


title: sample750


title: sample748


title: sample754

value: colon cancer


title: sample752

value: lung cancer


title: sample753


title: sample755


title: sample757

value: Wilms Tumor


title: sample756


title: sample746


title: sample751


title: sample749


title: N2 Rifampicin, Biological rep2

source_name: Rifampicin treated N2 worms

value: whole organism total RNA isolated, idr-1 RNAi treated, replicate-2

value: 8th day of adulthood


title: sample745


title: sample743


title: sample741


title: sample742


title: sample740


title: sample739


title: sample736

value: others


title: sample737


title: sample738


title: sample735


title: sample734


title: sample744


title: sample733

value: non-ischaemic systolic heart failure


title: sample730


title: sample729


title: sample728


title: sample718


title: sample722


title: sample717


title: sample725


title: sample721


title: sample723

value: normal


title: sample724


title: sample726


title: sample732


title: sample731


title: sample713


title: sample720


title: sample727


title: sample719


title: sample716


title: sample709


title: sample707


title: sample705


title: sample715


title: sample714


title: sample700


title: sample698


title: sample694


title: sample692


title: sample712


title: sample702


title: sample711


title: sample710


title: sample706


title: sample704


title: sample708


title: sample691


title: sample703


title: sample689


title: sample686


title: sample687


title: sample688


title: sample695


title: sample701


title: sample696


title: sample697


title: sample699


title: sample682


title: sample684


title: sample683


title: sample693


title: sample690


title: sample681


title: sample680


title: sample679


title: sample676


title: sample677


title: sample685


title: sample671


title: sample669


title: sample675


title: sample673


title: sample674


title: sample672


title: sample668


title: sample670


title: sample667


title: sample665


title: sample666


title: sample664


title: sample658


title: sample656


title: sample659


title: sample662


title: sample660


title: sample661


title: sample663


title: sample678


title: sample655


title: sample654


title: sample653

value: glioma


title: sample652


title: sample649


title: sample650


title: sample646


title: sample643


title: sample647


title: sample644


title: sample645


title: sample642


title: sample641


title: sample640


title: sample639


title: sample638


title: sample648


title: sample651


title: sample657


title: sample637


title: sample633


title: sample632


title: sample631


title: sample634


title: sample636


title: sample635


title: sample630


title: sample629


title: sample628


title: sample627


title: sample623

value: ovarian cancer


title: sample626


title: sample624


title: sample625


title: sample622


title: sample621


title: sample620


title: sample616

value: psoriasis


title: sample619


title: sample618


title: sample614


title: sample615


title: sample612


title: sample613


title: sample611


title: sample609


title: sample610


title: sample608


title: sample607


title: sample617


title: sample606


title: sample603


title: sample605


title: sample602


title: sample604


title: non-tumor tissue from patient 2

city: Calgary

first: Wei

last: Wu

address: 3330 Hospital Dr. NW

institute: 1.Zhengzhou Central Hospital, Affiliated to Zhengzhou University, China; 2. University of Calgary

hyb_protocol: the Cy3-labelled test DNA and Cy5-labelled reference DNA were mixed and combined with 2 × hybridization buffer, 10 × blocking agent (Agilent), and human Cot-1 DNA. The hybridization mixture was carefully dispensed to microarray chip (Agilent 1M) and assembled with Agilent SureHyb chamber. Then, the slide chamber was placed in the rotator rack in a hybridization oven set to 65 °C for 40 h with suitable rotation.

scan_protocol: After washing, all microarray slides were scanned on an Agilent Microarray Scanner G2565C with 2 μm resolution. Data were extracted from scanned images by the Feature Extraction software, version 11 (Agilent) and DNAcopy were used to segmentation analysis.

data_processing: The Agilent feature extracted files were imported into Partek Genomics Suite 6.6 for copy number analsysis, followed by R program analysis.

source_name: Normal

label_protocol: DNA was labelled with fluorescent dyes Cy3 (test samples) or Cy5 (reference DNA), using the SureTag Complete DNA Labelling kit (Agilent), the individually labelled test and reference samples were then purified using Microcon YM-30 filters (Millipore).

extract_protocol: The different regional samples were obtained immediately from the surgical specimens, transported with liquid nitrogen tank, stored in -80 till use.   The DNAs were then extracted using Qiagen kits.

value: Male

tag: type of cancer

value: esophageal squamous cell carcinoma

source_name: reference

tag: reference type

value: human male genomicDNA


title: Tumor tissue regional 4 from patient 2

source_name: Tumor


title: Tumor tissue regional 3 from patient 2


title: Tumor tissue regional 2 from patient 2


title: Tumor tissue regional 4 from patient 1


title: sample601


title: Tumor tissue regional 1 from patient 2


title: sample600


title: Tumor tissue regional 3 from patient 1


title: MCF10A_PCR_SC_R5

city: Manchester

first: Ged

last: Brady

address: Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Rd

department: Clinical and Experimental Pharmacology

country: United Kingdom

institute: Caner Research UK Manchester Institute

description: Amplified cDNA from single cell

data_processing: As an initial processing stage, 35-Cq was calculated for each probe to facilitate simple, intuitive analysis (it was a 35 cycle qPCR). A subset of informative probes were selected based on consistent expression above a background threshold of 10 in either cell line (mean (35-Cq)>10 and stdev<1.5 in either MCF7 or MCF10A cDNA generated from 1ng amplified RNA), excluding repetitive probes. A single probe per gene was then selected from this informative set based on visual inspection of the data for MCF7 and MCF10A unamplified cDNA and cDNA generated from 1ng amplified RNA.

label: sybr green

source_name: MCF10A single cell

label_protocol: Gene expression was assessed using the SmartChip Real-Time PCR System (WaferGen BioSystems, Fremont, USA). Sample and assay mixes were prepared with SensiFASTTM SYBR Hi-ROX (Bioline) in 384-well source plates using a Freedom Evo 150 robot (Tecan). Assay and sample mixes were then automatically loaded into the nanowells of a MyDesign SmartChip with WaferGen’s MultiSample NanoDispenser using a ‘384 assays x 12 samples’ dispensing layout. In total 8 chips were prepared and analyzed, corresponding to a total of 96 samples for 384 unique targets. The final reaction volume per nanowell was 100 nl, with an equivalent of 100 pg unamplified cDNA (total RNA equivalents) loaded per reaction. SmartChips were run in the SmartChip Cycler, and the cycling conditions were comprised of 3 minutes activation at 95°C, and 40 cycles of 30 seconds at 95°C and 60s at 60°C, followed by a dissociation curve analysis from 60°C to 95°C. Cq values, generated by the software from the SmartChip Cycler were used for down-stream data-analysis.

growth_protocol: The human epithelial cell lines MCF7 and MCF10A were grown in DMEM (Gibco, Paisley, Scotland) supplemented with 10% heat-inactivated FCS, 2.5% HEPES buffer (pH 7.2), 0.1% β-mercaptoethanol and 2mM L-glutamine (all from Sigma, UK). Both cell lines were maintained in a 5% CO2 humidified incubator at 37°C and were routinely tested for the presence of mycoplasma.

extract_protocol: RNA (1ng-25pg) or cell lysates in CLS were adjusted to 6.75ml volume and RNA-amplified using the EpiStem RNA-Amp Kit according to the manufacturers protocols (EpiStem, Manchester, UK). Briefly the samples underwent oligo-dT priming and 5’ capping prior to x35 cycles of PCR amplification using the conditions 90ºC 30 sec, 42ºC 2 min and 72ºC 6 min. Following amplification all samples were purified using a MoBio UltraClean® PCR Clean-Up Kit (Carlsbad, CA, USA) and quantified on a NanoDrop spectrophotometer.

tag: cell line


title: sample598

value: prostate cancer


title: sample599


title: Set3-TAP complex-1

city: MIAOLI COUNTY

first: GUNN-GUANG

last: LIOU

state: TAIWAN

address: 35 KEYAN ROAD, JHUNAN TOWN

department: INSTITUTE OF MOLECULAR AND GENOMIC MEDICINE

country: Taiwan

institute: NATIONAL HEALTH RESEARCH INSTITUTES

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., following their standard operating protocol.(NG_Chip-chip_Guide_v6p2)

scan_protocol: The protocol for scanning one-color NimbleGen arrays with a GenePix 4000B Scanner and associated software Genepix6.0. (NimbleGen_ChIP_Users_Guide_v3p1)

data_processing: Images were aligned and quantified using NimbleScan software  (V2.4) (Roche NimbleGen) which produced .pair reports of raw data and converted to ratio of Cy5 vs cy3

organism: Saccharomyces cerevisiae

source_name: cell lysate

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol.(NG_Chip-chip_Guide_v6p2)

extract_protocol: IgG coupled resin was incubated with cell lysate at 4°C overnight. Beads were then washed once with cell lysis buffer (50 mM Hepes-KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 0.5% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, and protease inhibitors), twice with 50 mM Hepes-KOH pH 7.5, 250 mM NaCl, 1 mM EDTA, 0.25% Triton X-100, 0.1% sodium deoxycholate, 0.05% SDS, and protease inhibitors, twice with 10 mM Tris-HCl pH 8.0, 0.25 M LiCl, 0.5% NP40, 0.5% sodium deoxycholate, and 1 mM EDTA, twice with 10 mM Tris-HCl pH 8.0, 0.25 M LiCl and 1 mM EDTA, and once with TE (10 mM Tris-HCl pH 8.0 and 1 mM EDTA pH 8.0) at room temperature. Beads were eluted by incubating with 100 ul of 50 mM Tris-HCl pH 8.0, 10 mM EDTA, and 1% SDS at 65°C for 15 minutes. Elute was transferred to a fresh tube and pooled with a final bead wash of 150 ul TE with 0.67% SDS. For input DNA, 200 ul TE with 1% SDS was added to 50 ul cell lysate extract. To reverse the cross-links, all samples were incubated at 65°C overnight, combined with 250 ul TE, 5 ug glycogen, and 100 mg proteinase K, and incubated at 37°C for 2 h. After adding 55 ul of 4 M LiCl, samples were extracted once with phenol/chloroform and once with chloroform. The remaining associated DNA was precipitated by the addition of 400 mM LiCl, and 2 volumes of ethanol, washed with 75% ethanol, air dried, and resuspended in 50 ul TE with RNase A (20 mg/ml for input DNA and 2 mg/ml for affinity-precipitated DNA) and incubated at 37°C for 1 hour

tag: antibody

tag: sample type

value: input DNA


title: MCF10A_PCR_SC_R4

description: Amplified cDNA from single cell


title: Tumor tissue regional 2 from patient1


title: non-tumor tissue from patient 1


title: MCF10A_PCR_SC_R2

description: Amplified cDNA from single cell


title: metastatic tissue (lymph node) from patient 2

source_name: Metastasis


title: sample595


title: MCF10A_PCR_SC_R3

description: Amplified cDNA from single cell


title: sample597

value: benign prostate hyperplasia


title: sample596


title: MCF10A_PCR_SC_R1

description: Amplified cDNA from single cell


title: MCF7_PCR_SC_R5

description: Amplified cDNA from single cell

source_name: MCF7 single cell


title: Tumor tissue regional 1 from patient 1


title: sample592


title: sample593


title: MCF7_PCR_SC_R3

description: Amplified cDNA from single cell


title: sample594


title: sample591


title: MCF7_PCR_SC_R2

description: Amplified cDNA from single cell


title: MCF10A_PCR_1ng_R3

description: Amplified cDNA from 1ng RNA

source_name: MCF10A cells


title: sample589


title: Set3-TAP complex-2


title: Snt1-TAP complex-2


title: MCF7_PCR_SC_R1

description: Amplified cDNA from single cell


title: sample587


title: sample588


title: sample590


title: sample586


title: MCF10A_PCR_1ng_R1

description: Amplified cDNA from 1ng RNA


title: sample585


title: MCF7_PCR_1ng_R2

description: Amplified cDNA from 1ng RNA

source_name: MCF7 cells


title: sample583


title: MCF7_PCR_1ng_R3

description: Amplified cDNA from 1ng RNA


title: MCF10A_PCR_1ng_R2

description: Amplified cDNA from 1ng RNA


title: Snt1-TAP complex-1


title: sample582


title: MCF10A_PCR_1μg_R3

description: Unamplified cDNA from 1 μg RNA


title: sample581


title: MCF7_PCR_1ng_R1

description: Amplified cDNA from 1ng RNA


title: sample579


title: sample580


title: MCF10A_PCR_1μg_R1

description: Unamplified cDNA from 1 μg RNA


title: MCF7_PCR_1μg_R1

description: Unamplified cDNA from 1 μg RNA


title: sample578


title: MCF7_PCR_1μg_R3

description: Unamplified cDNA from 1 μg RNA


title: sample577


title: sample576


title: MCF7_PCR_SC_R4

description: Amplified cDNA from single cell


title: sample574


title: sample573


title: sample575


title: sample571


title: sample570


title: CB ZSFC-115C

city: Shanghai

first: Ruo-Ying

last: Tan

address: 2nd Floor, 1st Building, 2140 Xietu Road,

institute: Biovue Technology (China) Ltd

description: ovarian cancer boundary tissue

data_processing: Data analysis was performed using R and Bioconductor packages. For data normalization, Quantile-Median method was used to process the raw Ct measurements. Samples that showed significant difference in profiles (mean absolute difference, Bioconductor package “arrayQualityMetrics”) were considered as outliers and were removed from downstream analysis.

label: SYBR green

source_name: ovarian tissue sample

label_protocol: PCR assays were performed using Biovue's Sharpvue Primer miRNA Array Panels (A-E) following the Manufacturer’s instructions. The purified total RNA (including small RNA) was diluted to 125ng/ml with 0.1x RNA storage buffer (Ambion, USA) with 0.1% Tween-20 (Sigma). Poly(A) tails were added on 3’ end of miRNAs and were used in the reverse transcript reaction by the SharpvueTM miRNA First Strand Kit (Biovue, Shanghai, China) to generate the first-strand cDNA per the instructions in the kit. miRNAs expression levels were quantified using ABI 7900HT Fast Real-Time PCR System (Applied Biosystems, USA). The reactions were incubated in a 384-well optical plate at 95°C for 2 min, followed by 3 cycles of 96°C for 5 s and 60°C for 1 min, 37 cycles of 96°C for 5 s and 60°C for 30 s, and running melting curve at the end. SYBR green dye and Rox dye were used as reporter and reference, respectively.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit , The quality of the isolated RNA was detected by agarose gel electrophoresis, and the quantity was analyzed by a ultraviolet spectrophotometric method using Biomate3 .

tag: tissue

value: ovarian cancer boundary tissue

tag: age

value: F

tag: tumor histology

value: Mixed eptithelial

tag: figo stage

value: I

tag: tumor grade

tag: relapse flag

tag: relapse month

tag: overall survival flag

tag: t

tag: n

tag: m

tag: Stage


title: CB ZSFC-140C

description: ovarian cancer boundary tissue

tag: gender

value: Undifferentiated

value: Ic


title: CB ZSFC-175C

description: ovarian cancer boundary tissue

value: Serous


title: CB ZSFC-205C

description: ovarian cancer boundary tissue

value: ia


title: CB ZSFC-073C

description: ovarian cancer boundary tissue


title: sample569

tag: disease


title: MCF7_PCR_1μg_R2

description: Unamplified cDNA from 1 μg RNA

tag: cell line


title: N ZSFC-210N

description: normal tissue

value: normal tissue


title: CB ZSFC-043C

description: ovarian cancer boundary tissue


title: sample568


title: sample584

value: others


title: sample572

value: normal


title: sample567


title: N ZSFC-190N

description: normal tissue


title: sample566


title: sample565


title: N ZSFC-189N

description: normal tissue


title: sample564


title: N ZSFC-176N

description: normal tissue


title: sample563

value: glioma


title: N ZSFC-34N

description: normal tissue


title: sample562


title: N ZSFC-160N

description: normal tissue


title: MCF10A_PCR_1μg_R2

description: Unamplified cDNA from 1 μg RNA


title: sample561


title: N ZSFC-061N

description: normal tissue


title: N ZSFC-108N

description: normal tissue


title: N ZSFC-056N

description: normal tissue


title: sample559


title: sample560


title: sample556

value: psoriasis


title: sample558


title: sample557


title: N ZSFC-058N

description: normal tissue


title: N ZSFC-027N

description: normal tissue


title: N ZSFC-019N

description: normal tissue


title: sample554


title: N ZSFC-017N

description: normal tissue


title: CE ZSFC-238C

description: ovarian epithelial carcinoma

value: ovarian epithelial carcinoma

value: III

value: IIIC


title: N ZSFC-030N

description: normal tissue


title: sample553


title: sample555


title: CE ZSFC-237C

description: ovarian epithelial carcinoma

value: Endometroid

value: IC


title: sample551


title: CE ZSFC-231C

description: ovarian epithelial carcinoma

value: F

value: IIIB


title: CE ZSFC-232C

description: ovarian epithelial carcinoma


title: CE ZSFC-230C

description: ovarian epithelial carcinoma


title: sample552


title: CE ZSFC-228C

description: ovarian epithelial carcinoma


title: CE ZSFC-227C

description: ovarian epithelial carcinoma

value: ClearCell

value: I


title: sample550

value: prostate cancer


title: sample548


title: sample549

value: benign prostate hyperplasia


title: CE ZSFC-222C

description: ovarian epithelial carcinoma

value: Serous


title: sample547


title: CE ZSFC-209C

description: ovarian epithelial carcinoma

value: iiic


title: CE ZSFC-213C

description: ovarian epithelial carcinoma

value: II

value: iib


title: sample546


title: CE ZSFC-212C

description: ovarian epithelial carcinoma


title: sample545


title: sample543


title: CE ZSFC-221C

description: ovarian epithelial carcinoma

value: IA


title: sample544


title: CE ZSFC-194C

description: ovarian epithelial carcinoma


title: CE ZSFC-181C

description: ovarian epithelial carcinoma

value: IIB


title: CE ZSFC-178C

description: ovarian epithelial carcinoma

value: ovarian epithelial carcinoma


title: CE ZSFC-180C

description: ovarian epithelial carcinoma

value: III


title: sample540

value: others


title: sample541


title: sample542


title: sample539


title: CE ZSFC-162C

description: ovarian epithelial carcinoma

value: IIIc


title: CE ZSFC-155C

description: ovarian epithelial carcinoma

value: IIIc-IV


title: CE ZSFC-182C

description: ovarian epithelial carcinoma

value: F

value: IIIC


title: sample538


title: sample536


title: CE ZSFC-154C

description: ovarian epithelial carcinoma


title: CE ZSFC-153C

description: ovarian epithelial carcinoma

value: IIA


title: sample535

value: glioma


title: sample537


title: sample533


title: sample534


title: CE ZSFC-139C

description: ovarian epithelial carcinoma

value: ClearCell

value: I


title: sample529


title: sample530

value: normal


title: sample528


title: sample532


title: sample531


title: CE ZSFC-102C

description: ovarian epithelial carcinoma

value: Serous


title: CE ZSFC-101C

description: ovarian epithelial carcinoma


title: CE ZSFC-094C

description: ovarian epithelial carcinoma

value: AdenocarcinomaNOS


title: sample527


title: CE ZSFC-082C

description: ovarian epithelial carcinoma


title: CE ZSFC-084C

description: ovarian epithelial carcinoma


title: CE ZSFC-087C

description: ovarian epithelial carcinoma


title: sample525


title: sample523


title: CE ZSFC-079C

description: ovarian epithelial carcinoma


title: sample524


title: CE ZSFC-074C

description: ovarian epithelial carcinoma

value: II


title: sample521

value: benign prostate hyperplasia


title: CE ZSFC-041C

description: ovarian epithelial carcinoma


title: CE ZSFC-119C

description: ovarian epithelial carcinoma

value: IV


title: sample520


title: sample519


title: CE ZSFC-038C

description: ovarian epithelial carcinoma

value: ovarian epithelial carcinoma


title: sample526


title: sample518


title: CE ZSFC-036C

description: ovarian epithelial carcinoma

value: III


title: CE ZSFC-072C

description: ovarian epithelial carcinoma


title: sample522


title: CE ZSFC-029C

description: ovarian epithelial carcinoma

value: Endometroid


title: CE ZSFC-020C

description: ovarian epithelial carcinoma


title: sample513

value: Wilms Tumor


title: sample515

value: prostate cancer


title: sample512


title: sample516


title: sample514


title: CE ZSFC-103C

description: ovarian epithelial carcinoma

value: F

value: Undifferentiated


title: sample511


title: sample510


title: BCGevo 30.09.10_14

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: Cy3- labeled aRNA was hybridized to Agilent´s 8x15k Mycobacterium bovis BCG Pasteur microarrays for 16 h at 68 ºC and scanned using the Agilent DNA Microarray Scanner.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) according to manufacture´s recommendation

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_105_Dec08, GE1_107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Mycobacterium tuberculosis variant bovis BCG

label_protocol: 200 ng of total RNA were applied for Cy3-labelling reaction using the MessageAmp II-Bacteria Kit according to supplier´s recommendation (Ambion). As a result of IVT (in vitro transcription) reaction using aminoallyl-dUTP antisense aRNA were generated and subsequently coupled with fluorescent dye Cy3.

extract_protocol: We used 4M guanidinium thiocyanate (GTC)-based lysis solution to extract total RNA from bacteria recovered from inside RAW macrophages. Briefly, RAW cells seeded on 20 T-150 flask (Marienfeld GmbH & Co, Germany) were infected with ancestral or selected bacteria (OD600: 0.025) from the in vitro culture in full D-MEM medium during 24 h. The infected monolayer were resuspended in GCT solution (4 M guanidine thiocyanate, 0.5% sodium N-lauryl sarcosine, 25 mM tri-sodium citrate, 0.1 M 2-mercaptoethanol, 0.5% Tween-80, pH to 7.0 with 1 M HCl (All the reagents were from Sigma, Germany)). The bacteria in the GCT solution were centrifuged and the bacterial pellet was disrupted using FastRNA® Pro Blue kit from Q-BIOgene (MP Biomedicals, CA, USA) following the manufacture’s instructions. Mycobacterial RNA was extracted with the RNeasy mini kit (QIAGEN) and next resuspended in RNAse-free water.

treatment_protocol: Macrophages were infected with Mycobacterium bovis BCG-GFP at a Multiplicity Of Infection (MOI) of 10. The starting cultures of bacteria used for infection were preserved in frozen aliquots representing the “ancestral” bacteria (BCGanc). After infection, macrophages were re-plated when confluent during a period of at least two years (BCGevo).

tag: strain

value: BCGevo


title: BCGanc 30.09.10_11

value: BCGanc


title: BCGevo 30.09.10_13


title: CE ZSFC-048C

description: ovarian epithelial carcinoma

value: IIIC


title: sample517


title: sample506


title: BCGanc 05.08.10_9


title: BCGanc 30.09.10_12


title: BCGanc 10.07.10_8


title: BCGevo 30.08.10_6


title: sample507


title: BCGevo 30.08.10_5


title: sample505


title: sample509


title: BCGanc 05.08.10_4


title: sample502


title: BCGevo 30.08.10_10


title: BCGevo 09.09.10_11


title: BCGanc 10.07.10_2


title: Nodule 21d_NOA treated_rep2

city: MONTPELLIER CDX 5

first: Valérie

last: HOCHER

address: 911 av. Agropolis BP64501

department: DIADE

country: France

institute: IRD

description: Gene expression in nodules sampled 21 days after inoculation with the bacteria Frankia on plants cultivated without nitrogen and with 25 µM 1-NOA

hyb_protocol: The Agilent Hybridization Kit (catalog no. 5188-5242) was used . 600 ng of the labeled sample RNA was used for hybridization according to the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol. The hybridization was performed for 17 h at 65°C. Slides were them washed for 1 min at room temperature in Wash Solution 1 (catalog no. 5188-5325) and 1 min at room temperature in Wash Solution 2, prewarmed to 37°C (catalog no. 5188-5326).

scan_protocol: Scanning  was performed with the Agilent scanner (G2505B) using default parameters for 8 x 15 K formats and the one-color protocol. (scan area 61 X 21.6 mm; scan resolution 5µm; single pass; dye channel is set to green and green PMT is set to 100%).

data_processing: Data were extracted with Feature Extraction 9.1 software (Agilent Technologies) according to the 1-color Agilent protocol (GE1-v5_95_Feb protocol). This software reads and processes microarray image files to prepare them for analysis. Feature Extraction automatically assigns a grid template and a protocol, based on the barcode of the slide. It determines feature intensities, rejects outliers and calculates statistical confidence intervals. Genespring sofware was then used for data processing. Normalization was done as follows: data transformation (Set measurements less than 5.0 to 5.0), per chip : normalized to 50th percentile (probes with presence flags only), per gene : normalized to median. Data were then filtered using flag parameter (Flags (Absent, Marginal, Present) : All control -> Absent, Saturated spot -> Marginal, Spot not uniform -> Marginal, Spot not positive and not significant -> Absent, Spot not above background -> Absent, Population outlier -> Marginal) and each probe must be present for 2/3 of the tested conditions.

organism: Casuarina glauca

source_name: Nodule, inoculated, no N2, 1-NOA 25µM, 21d post inoculation

label_protocol: Five hundred nanograms of RNA and Agilent One-Color RNA Spike-In RNA were labeled with the Agilent Low RNA Input Linear Amplification Kit PLUS, One-Color according to the manufacturer's instructions as follows: 1.2 µl of T7 Promoter Primer was added to 500 ng of RNA and 5 µl of spike-in control (in a 11.5-µl volume) and denatured at 65°C. First-Strand Buffer (to 1x), DTT (to 10 mM), dNTP (to 0.5 mM), Moloney murine leukemia virus (MMLV) reverse transcriptase (1 µl of stock provided in the kit in a 20-µl reaction), and RNaseOut (0.5 µl of stock provided in the kit in a 20-µl reaction) were added. The cDNA was synthesized during the following incubation step (2 h at 40°C). After 10-min denaturation at 65°C and the addition of Cy3-labeled CTP (to 0.3 mM), Transcription Buffer (to 1x), DTT (to 10 mM), NTP (8 µl of stock provided in the kit in a 80-µl reaction), RNaseOUT (0.5 µl of stock provided in the kit in a 80-µl reaction), inorganic phosphatase (0.6 µl of stock provided in the kit in a 80-µl reaction), and T7 RNA polymerase (0.8 µl of stock provided in the kit in a 80-µl reaction), the synthesis of the fluorescent labeled cRNA was performed during the second incubation step (2 h at 40°C). The labeled cRNA was purified with the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol.

growth_protocol: Seeds were grown for one month in a soil/vermiculite substrate (1:1, vol/vol) in a greenhouse. Plantlets were transferred to a Broughton and Dilworth's modified liquid medium (BD medium) with nitrogen in plastic pots and grown for 3 weeks under these hydroponic conditions. Then they were grown for one week without nitrogen. After this starvation step which is necessary for optimal induction of symbiosis,  plants were sub-divided according to the treatment.

extract_protocol: Total RNA was purified from sampled nodules by ultracentrifugation  (Chirgwin et al., 1979). Residual DNA was removed from RNA samples using the Turbo DNA free kit (Ambion, USA), quantified using a NanoDrop spectrophotometer (Thermo Fisher Scientific, Courtaboeuf, France) and qualitatively assessed using a Bioanalyser 2100 (Agilent p/n G2938A) according to the manufacturer’s instructions (Agilent, Santa Clara, CA, USA).

treatment_protocol: The starting point of the treatment was the day of inoculation of plant with the bacteria (0d). At 0d, a set of plants was inoculated  with the bacteria in the BD medium without nitrogen  (control condition) and one set of plants was inoculated  with the bacteria in the BD medium without nitrogen containing 25 µM of 1-naphtoxy acetic acid (1-NOA), which is an auxin influx inhibitor  (treated condition). Medium were replaced twice a week with freshly prepared medium (with or without 1-NOA according to treatment). 21 days after inoculation, nodules (specific organs that develop in symbiosis) were sampled of control and treated plants. All samples were frozen in liquid nitrogen and conserved at -80°C before RNA extraction

value: Root nodule

tag: culture condition

value: Cultivated without nitrogen, with 25 µM 1-NOA

tag: treatment

value: Inoculated with symbiotic Frankia bacteria in presence of 25µM 1-NOA

tag: developmental stage

value: Root nodule, 21 days regarding inoculation time


title: sample504


title: Nodule 21d_not treated_rep3

description: Gene expression in nodules sampled 21 days after inoculation with the bacteria Frankia on plants cultivated without nitrogen

source_name: Nodule, inoculated, no N2, 21d post inoculation

tag: tissue

value: Cultivated without nitrogen

value: Inoculated with symbiotic Frankia bacteria


title: sample500


title: sample508


title: sample503


title: BCGanc 05.08.10_3


title: sample498


title: Exp3 Control

city: Utrecht

first: Jurian

last: Schuijers

state: Utrecht

address: Uppsalalaan 8

institute: Hubrecht Insitute

description:
Ascl2loxp/loxp organoids
reference DNA labeled with both Cy5 and Cy3 for control

data_processing: Microarray signal and background information were retrieved and data was normalized using the feature extraction program (V.9.5.3, Agilent Technologies).

source_name: Small intestinal organoids

label_protocol: 500 ng of total RNA was labeled using Quick Amp Labeling Kit, two-color (Agilent Technologies, Pato Alto, CA, USA)

treatment_protocol: Koo et al, Nat Methods. 2011 Dec 4;9(1):81-3

tag: genotype/variation

value: Small intestinal organoids

value: 16h pulse of 4OH-tamoxifen


title: sample499


title: retina_CNTF_CNGB3-affected_2

city: Philadelphia

first: Sem

last: Genini

state: PA

address: 3900 Delancey Street

department: Clinical Studies

institute: University of Pennsylvania

description: genotype: CNGB3m/m

hyb_protocol: A total of 1.65 µg Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. After completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the canine Agilent Oligo Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed one minute at room temperature with GE Wash Buffer 1 (Agilent) and one minute with GE Wash Buffer 2 (Agilent) pre-heated at 37°C, and finally dried by brief centrifugation.

scan_protocol: Following the washing step, microarray slides were scanned immediately with a GenePix 4000B Microarray Scanner (Axon Instruments, Union City, CA).

data_processing:
The scanned images were analyzed with Feature Extraction Software (version 9.5.3.1, Agilent) using default parameters to obtain background subtracted and spatially detrended raw data (gProcessedSignal values). Feature non-uniform outliers flagged in Feature Extraction were excluded from further analyses.
The Partek Genomics Suite 6.4 software (Partek Incorporated, St. Louis, MO) was used for all statistical analyses; specifically it was used to extract the gProcessedSignal values from Agilent, log2 transform and quantile normalize them. A one-way ANOVA was then applied to compare gene expression of CNGB3-affected vs. normal retinas in either the PBS or the CNTF injected eye, while a 2-way ANOVA was used to compare CNTF vs. PBS injected eyes in either normals or CNGB3-affected dogs. Genes with Benjamini Hochberg (BH)-adjusted (stepup) p < 0.05 and fold change (FC) > +/-2 were considered statistically significant differentially expressed (DE).

organism: Canis lupus familiaris

source_name: CNGB3 retina, CNTF injected, 1 week

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using the Low Input Quick Amp WT Labeling Kit, One-Color, according to the manufacturer's instructions (Agilent), followed by RNAeasy mini column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yields were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Samples were obtained from dogs of a research colony with a common genetic background that were maintained at the Retinal Disease Studies Facility (RDSF) in Kennett Square, Pennsylvania. Both eyes were enucleated following intravenous anesthesia with sodium pentobarbital, and the dogs were euthanatized with an overdose of euthanasia solution (Euthasol; Virbac, Fort Worth, TX). Retina and choroid samples were immediately collected, flash frozen in liquid nitrogen, and stored in -80°C until use. The research was conducted in full compliance with the ARVO Resolution on the Use of Animals in Ophthalmic and Vision Research.

extract_protocol: Total RNA was extracted from dog retinas following standard procedures of the manufacturer (miRNeasy minikit; Qiagen Inc, Valencia, CA). RNA concentration was quantified with a NanoDrop-1000 Spectrophotometer (NanoDrop Technologies, Thermo Fisher Scientific, Wilmington, DE) and RNA quality was verified by microcapillary electrophoresis with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). RNA with RIN> 8 and A260/280 ratio> 1.9 was used in both microarray and the following qRT-PCR analyses.

treatment_protocol: Five CNGB3-mutant dogs (carrying the D262N missense mutation; CNGB3m/m) and 5 normal control (homozygous: CNGB3+/+; heterozygous CNGB3+/m) dogs were injected unilaterally with 12 µg of intravitreal CNTF (OD eyes) and the contralateral eyes (OS) served as controls and were injected with PBS. Retinas were collected at 1 week post injection.

value: female

tag: age

value: 11.5 weeks

value: retina

value: CNTF injected

tag: genotype


title: Exp2 TCF7L2null /Ascl2 OE

description: dsGFP transduced organoids and Tcf7l2null/Ascl2 over expressing organoids

value: dsGFP transduced

value: 16h pulse of 4OH-tamoxifen, inducing GFP expression

value: Tcf7l2null/Ascl2 over expressing

value: 16h pulse of 4OH-tamoxifen, deleting Tcf7l2 and inducing Ascl2 expression


title: sample497

value: Wilms Tumor


title: Exp2 Control

description:
dsGFP transduced organoids
reference DNA labeled with both Cy5 and Cy3 for control


title: Nodule 21d_NOA treated_rep3

value: Root nodule


title: Nodule 21d_not treated_rep2


title: GM12878 cells RNA polymerase ChIP Nsp array

city: Bethesda

first: Howard

last: Yang

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

description: ChIP DNA amplified using SIGMA WGA2 kit

hyb_protocol: Affymetrix hybridization oven at 49C, 60rpm for 16 hrs.  Wash and stain were performed on Affymetrix Fluidics Station 450

scan_protocol: Genechips were scanned using an Affymetrix GeneChip Scanner 3000 and data was collected using Affymetrix AGCC software.

data_processing:
Analyzing 250K Nsp and 250K Sty chip CEL files by Affymetrix Genotyping Console v4.1, we obtained the probe level intensity data for all match and mismatch probes. We applied quantile normalization to probe level ratios a=PMA/MMA and b=PMB/MMB. Then for each probeset or SNP, we computed the allelic intensities A=max(mean(log2(a)), 0) for allele A and B=max(mean(log2(b)), 0) for allele B based on the normalized ratios a and b. Finally, we obtained the total intensity A+B for each SNP on the 250K Nsp chips and the 250K Sty chips. The intensity data from two kind of chips were combined into one file.
The AplusB8GMs3types.ns.txt matrix file contains the total intensity data. It has 25 columns and 500568 rows. The Affymetrix SNP ids are in the first column. The rest  columns contain 3 assays for each of the 8 CEPH samples.

label_protocol: Affymetrix standard SNP array protocol

growth_protocol: Cells were grown in RPMI medium 1640 supplemented with 2mM L-glutamine and 15% FBS.

extract_protocol: ChIP DNA amplified using SIGMA WGA2 kit

treatment_protocol: Cells were grown to ~80% confluency and colleced after changing the media at -8hrs.

tag: sample type

value: RNA polymerase ChIP DNA


title: GM12878 cells RNA (cDNA) Nsp array

description: Qiagen RNeasy isolated RNA was amplified using Affymetrix amplified double stranded cDNA synthesis kit

source_name: GM12878 cells RNA (cDNA) Nsp array

value: amplified cDNA from total RNA


title: Exp2 TCF7L2null

description: dsGFP transduced organoids and Tcf7l2null organoids

value: 16h pulse of 4OH-tamoxifen, deleting Tcf7l2


title: BCGanc 10.07.10_1

value: BCGanc


title: GM12802 cells RNA (cDNA) Nsp array

source_name: GM12802 cells RNA (cDNA) Nsp array

extract_protocol: Qiagen RNeasy isolated RNA was amplified using Affymetrix amplified double stranded cDNA synthesis kit


title: retina_CNTF_CNGB3-affected_3

description: genotype: CNGB3m/m


title: Exp3 Ascl2null

description: VillinCreERT2 organoids and Ascl2null organoids

value: 16h pulse of 4OH-tamoxifen, deleting Ascl2


title: retina_CNTF_normal_5

description: genotype: CNGB3+/m

source_name: normal retina, CNTF injected, 1 week

value: male

value: 8.9 weeks

value: control


title: Exp1 Ascl2 OE rep1

description: Ascl2 over-expressing organoids and VillinCreERT2 organoids

value: Small intestinal organoids

value: 16h pulse of 4OH-tamoxifen

value: Ascl2 transduced

value: 16h pulse of 4OH-tamoxifen to induce CMV-driven Ascl2 expression, RNA extraction after 24h


title: GM12802 cells RNA polymerase ChIP Nsp array

description: ChIP DNA amplified using SIGMA WGA2 kit


title: sample496

source_name: RNA from blood


title: GM12740 cells RNA (cDNA) Nsp array

source_name: GM12740 cells RNA (cDNA) Nsp array


title: sample495


title: GM12802 cells gDNA Nsp array

description: QIAGEN Blood and Cell Culture Midi kit isolated

source_name: GM12802 cells gDNA Nsp array

value: genomic DNA


title: sample494


title: GM12878 cells gDNA Nsp array

source_name: GM12878 cells gDNA Nsp array

extract_protocol: QIAGEN Blood and Cell Culture Midi kit isolated


title: GM12740 cells RNA polymerase ChIP Nsp array

description: ChIP DNA amplified using SIGMA WGA2 kit


title: GM12740 cells gDNA Nsp array

source_name: GM12740 cells gDNA Nsp array


title: sample493


title: retina_CNTF_CNGB3-affected_4

description: genotype: CNGB3m/m

value: 10.7 weeks

value: retina

value: CNTF injected


title: retina_CNTF_CNGB3-affected_1

description: genotype: CNGB3m/m

value: 11.4 weeks


title: GM10839 cells RNA (cDNA) Nsp array

source_name: GM10839 cells RNA (cDNA) Nsp array


title: GM10863 cells gDNA Nsp array

source_name: GM10863 cells gDNA Nsp array


title: retina_CNTF_normal_4

description: genotype: CNGB3+/m


title: GM10839 cells RNA polymerase ChIP Nsp array

description: ChIP DNA amplified using SIGMA WGA2 kit

value: RNA polymerase ChIP DNA


title: retina_CNTF_normal_2

description: genotype: CNGB3+/m


title: sample492

value: Wilms Tumor


title: sample491

value: benign prostate hyperplasia


title: retina_CNTF_normal_3

description: genotype: CNGB3+/+


title: retina_PBS_CNGB3-affected_5

description: genotype: CNGB3m/m

source_name: CNGB3 retina, PBS injected, 1 week

value: female

value: PBS injected


title: GM10839 cells gDNA Nsp array

source_name: GM10839 cells gDNA Nsp array


title: GM10831 cells RNA (cDNA) Nsp array

source_name: GM10831 cells RNA (cDNA) Nsp array

value: amplified cDNA from total RNA


title: Exp1 Ascl2 OE rep2


title: GM10831 cells RNA polymerase ChIP Nsp array

description: ChIP DNA amplified using SIGMA WGA2 kit


title: retina_CNTF_normal_1

description: genotype: CNGB3+/m

value: male

value: 8.9 weeks


title: retina_PBS_CNGB3-affected_2

description: genotype: CNGB3m/m

value: 11.5 weeks


title: retina_PBS_CNGB3-affected_4

description: genotype: CNGB3m/m


title: GM10863 cells RNA polymerase ChIP Nsp array

description: ChIP DNA amplified using SIGMA WGA2 kit


title: sample490


title: retina_PBS_CNGB3-affected_3

description: genotype: CNGB3m/m


title: GM07019 cells RNA (cDNA) Nsp array

source_name: GM07019 cells RNA (cDNA) Nsp array


title: GM10863 cells RNA (cDNA) Nsp array

source_name: GM10863 cells RNA (cDNA) Nsp array


title: sample489

value: others


title: retina_CNTF_CNGB3-affected_5

description: genotype: CNGB3m/m


title: GM07019 cells gDNA Nsp array

source_name: GM07019 cells gDNA Nsp array


title: GM07019 cells RNA polymerase ChIP Nsp array

description: ChIP DNA amplified using SIGMA WGA2 kit


title: GM06991 cells RNA polymerase ChIP Nsp array

description: ChIP DNA amplified using SIGMA WGA2 kit


title: GM06991 cells RNA (cDNA) Nsp array

source_name: GM06991 cells RNA (cDNA) Nsp array


title: sample488


title: sample487

value: prostate cancer


title: GM06991 cells gDNA Nsp array

source_name: GM06991 cells gDNA Nsp array


title: GM10831 cells gDNA Nsp array

source_name: GM10831 cells gDNA Nsp array


title: sample485


title: sample486


title: retina_PBS_CNGB3-affected_1

description: genotype: CNGB3m/m


title: sample484


title: retina_PBS_normal_5

description: genotype: CNGB3+/m

source_name: normal retina, PBS injected, 1 week

value: control


title: retina_PBS_normal_4

description: genotype: CNGB3+/m


title: sample483

source_name: RNA from blood


title: sample482


title: sample481


title: retina_PBS_normal_3

description: genotype: CNGB3+/+


title: retina_PBS_normal_2

description: genotype: CNGB3+/m


title: sample480


title: Mouse_70_controle_ZT20_T4

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

institute: University of Amsterdam

description: Quality Control: Approved

hyb_protocol: RNA was hybridized on Affymetrix HT Mouse Genome 430 PM Array plates (Affymetrix Inc., Santa Clara, CA, USA) at the Microarray Department of the University of Amsterdam, the Netherlands.

scan_protocol: The array images were acquired using a GeneChip HT Array Plate Scanner (Affymetrix)

data_processing: The array images analyzed with Affymetrix HT software suite including expression console software (Affymetrix).

label_protocol: biotins labeled cRNA samples were prepared as described in the Affymetrix GeneChip HT 3” IVT Express Technical Manual (Affymetrix) using 200 ng of purified total RNA as template for the reaction.

growth_protocol: Three-week-old male C57BL/6 mice were purchased from Charles River Laboratories International, Inc., France. Animals were synchronized to a 12-hr light: 12-hr dark cycle for 5 weeks. Food and water were provided ad libitum.

extract_protocol: RNA was extracted from liver stored in RNAlater using the miRNeasy Mini Kit (Qiagen Benelux, Venlo, The Netherlands ).

treatment_protocol: At 8 weeks of age mice received a single i.p. injection of either 300 mg/kg bodyweight Cyclophosphamide (CP, CAS 6055-19-2, Sigma-Aldrich) or the vehicle (PBS) at two different Zeitgeber times, ZT8 and ZT20 (ZT0 = lights on). Animals (n=4 per time point) were sacrificed by cervical dislocation at 0.5, 1, 2 and 4 hours after CP injection (T0.5, T1, T2 and T4), and at 0 and 4 hours after vehicle injection (C0 and C4).

tag: Sex

value: Male

value: controle

tag: regime

tag: time


title: Mouse_68_controle_ZT20_T4

description: Quality Control: Approved


title: D2 P9 rep1

city: Vancouver

first: Thomas

last: Ha

state: British Columbia

address: 950 West 28th Avenue

department: CMMT

institute: University of British Columbia

description:
P9  4370199023_F
biological replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: DBA/2J mouse whole cerebellum

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

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.

value: whole cerebellum


title: sample479


title: Mouse_69_controle_ZT20_T4

description: Quality Control: Approved


title: D2 P6 rep2

description:
P6  1855545021_D
biological replicate 2


title: Mouse_71_controle_ZT20_T4

description: Quality Control: Approved


title: Mouse_65_cyclophosphamide_ZT20_T4

description: Quality Control: Approved

value: cyclophosphamide


title: D2 P6 rep1

description:
P6  1735640153_F
biological replicate 1


title: retina_PBS_normal_1

description: genotype: CNGB3+/m

value: retina


title: D2 P3 rep2

description:
P3  1735640153_D
biological replicate 2


title: D2 P6 rep3

description:
P6  1855545021_E
biological replicate 3


title: D2 P3 rep1

description:
P3  1735640153_B
biological replicate 1


title: D2 P0 rep3

description:
P0  1863191035_A
biological replicate 3


title: D2 P3 rep3

description:
P3  1855545041_F
biological replicate 3


title: sample501


title: Exp2 Ascl2 OE

description: dsGFP transduced organoids and Ascl2 over expressing organoids

source_name: Small intestinal organoids

value: dsGFP transduced

value: Small intestinal organoids

value: 16h pulse of 4OH-tamoxifen, inducing GFP expression

value: Ascl2 over expressing

value: 16h pulse of 4OH-tamoxifen, inducing Ascl2 expression


title: D2 E18 rep3

description:
E18  1725572018_B
biological replicate 3


title: sample478

value: Wilms Tumor


title: sample477


title: sample475

value: chronic obstructive pulmonary disease (COPD)


title: sample474


title: sample476


title: D2 E17 rep3

description:
E17  4370199023_D
biological replicate 3


title: Mouse_63_cyclophosphamide_ZT20_T4

description: Quality Control: Approved


title: D2 P0 rep2

description:
P0  1855545021_A
biological replicate 2


title: Mouse_62_cyclophosphamide_ZT20_T4

description: Quality Control: Approved


title: Mouse_59_cyclophosphamide_ZT20_T2

description: Quality Control: Approved


title: Mouse_57_cyclophosphamide_ZT20_T2

description: Quality Control: Approved


title: D2 E18 rep2

description:
E18  1725572018_A
biological replicate 2


title: D2 P0 rep1

description:
P0  1855545021_B
biological replicate 1


title: Mouse_64_cyclophosphamide_ZT20_T4

description: Quality Control: Approved


title: D2 E17 rep2

description:
E17  1735640022_F
biological replicate 2


title: sample473


title: D2 E16 rep3

description:
E16  1735640151_A
biological replicate 3


title: D2 E17 rep1

description:
E17  1735640022_E
biological replicate 1


title: D2 E16 rep2

description:
E16  1735640022_B
biological replicate 2


title: Mouse_58_cyclophosphamide_ZT20_T2

description: Quality Control: Approved


title: D2 E15 rep3

description:
E15  4370199020_A
biological replicate 3


title: D2 E16 rep1

description:
E16  1735640022_A
biological replicate 1


title: Mouse_56_cyclophosphamide_ZT20_T2

description: Quality Control: Approved


title: Molt cells control (exon), replicate 1

city: Esch-sur-Alzette

first: Ines

last: Thiele

address: 7, avenue des Hauts-Fourneaux

department: Luxembourg Centre for Systems Biomedicine

country: Luxembourg

institute: University of Luxembourg

description: Molt-4 cells control

hyb_protocol: standard Affymetrix protocol by Aros (Aarhus, Denmark)

data_processing:
We generated DABG calls using ROOT (version 22) and XPS package for R (version 11.1). Calls for data mapping were assigned based on p<0.05 as cutoff probability distinguishing presence versus absence of genes. All 18 data sets were summarized for this analysis, using RMA.    Analysis for differential gene expression and alternative splicing were performed using AltAnalyse software (v2.02beta) using default options from raw data (CEL) files and Homo sapiens Ensemble release 65 database, probe set filtering was kept as DABG p-value < 0.05 and non-log expression < 70 for constitutive probe sets to determine gene expression levels. AltAnalyse relies on RMA for normalization.  For the comparison, CCRF-CEM was the experimental and Molt-4 the baseline group, and only CEL files of CCRF-CEM cells control replicate 1-3, and Mot-4 cells control replicate 1-3 were introduced into the analysis. The set of differentially expressed genes among cell lines was identified based on a p<0.05 FDR cutoff. Alternative splicing analysis was performed on core probe sets with a minimum alternative exon score of 2 and a maximum absolute gene expression change of 3.
AltAnalyze & XPS: HuEx-1_0-st-v2.r2.pgf
Bioconductor XPS package was used to generate Detection above background (DABG) calls after RMA normalisation for the entire data set of 18 CEL files (MixRMAMetacore and MixDABGMetacore_pval). Additionally, higher-level analysis of Differential gene expression (DATASET-CompareCelllines(geneLevel)) and Alternative splicing (Hs_Exon_C_vs_M.p5_average-splicing-index-exon-inclusion-GENE-results) were carried out for a subset of 6 CEL files (A834_01-A834_03 and A834_10-A834_12) using Altanalyse software after pre-processing of the  Affymetrix CEL files by AltAnalyze (using APT and RMA). Expression values for the RMA normalization for the subset of 6 CEL files (exp.CompareCellines(probesetLevel)).

source_name: Molt-4 cells

extract_protocol: Molt-4 and CCRF-CEM growing in RPMI advanced, 2 mM glutamax were resuspended in medium containing DMSO (0.67%) or 0.5 mM AICAR or 0.1 mM A-769662 at a cell concentration of 5 x 105 cells/ml. 2 ml cell suspensions were seeded in 12 well plates in triplicates. After 48 hrs of growth the cells were collected by centrifugation at 201 x g for 5 min. Cell pellets were snap frozen in liquid N2 and kept frozen until RNA extraction and analysis by Aros (Aarhus, Denmark).

value: Molt-4 cells


title: sample472


title: CCRF-CEM cells control (exon), replicate 2

description: CCRF-CEM cells control

scan_protocol: standard Affymetrix protocol by Aros (Aarhus, Denmark)

source_name: CCRF-CEM cells

value: CCRF-CEM cells