title: XH1


title: B2B-RV16-T16-1-7 (repeat)

status: Public on Apr 01 2014

type: RNA

city: Singapore

first: Ahmad Nazri

last: Mohamed Naim

address: 60 Biopolis Street, Genome, #02-01

department: Infectious disease

country: Singapore

institute: Genome institute of Singapore

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were analysed in Genespring GX11.5 software. Measurements less than 0.01 was set to 0.01. Data was then normalised at the 80th percentile.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: whole blood

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep -96 RNA Amplification Kit for Illumina arrays

extract_protocol: Total RNA was extracted from whole blood drawn in pax-gene vacutainer tubes by PAX-gene RNA kit (Qiagen). Quality control was performed with NanoDrop 1000 instrument

tag: cell line

tag: sample type

value: Infected

tag: collection time

value: 16 hr


title: Whole Hipp Aged Impaired (5842733060_L)

city: Hershey

first: Penn State

last: COM

state: PA

address: 500 University Drive

department: Genome Sciences Facility

country: USA

institute: Penn State College of Medicine

description:
replicate 9
Whole Hipp Aged Impaired

data_processing: The data were normalized using average normalization

organism: Rattus norvegicus

source_name: Hippocampus

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep 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.

tag: strain

value: Fischer 344 x Brown Norway F1-hybrid (F344BN)

tag: age group

value: Aged Impaired (24M)

tag: tissue group

value: whole hippocampus


title: Gastric tumour GC0116

city: East Melbourne

first: Rita

middle: Ann

last: Busuttil

state: VIC

address: St Andrews Pl

department: Research

country: Australia

institute: Peter MacCallum Cancer Centre

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were washed using Affymetrix fluidics stations and scanned using the Gene Chip Scanner 3000.

data_processing: CEL files were produced using the Affymetrix ® GeneChip ® Command console ® Software (AGCC).

source_name: Primary gastric tumour

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 to 5 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

extract_protocol: Total RNA was extracted from primary tumors using Trizol extraction and RNeasy midi spin columns (Qiagen) according to the instructions of the manufacturer.

tag: tissue

value: Primary gastric tumour


title: Whole Hipp Aged Impaired (5842733060_K)

description:
replicate 8
Whole Hipp Aged Impaired


title: CA1 Adult (5842733059_I)

description:
replicate 1
CA1 Adult

value: Adult (12M)


title: B2B-RV16-T36-1-7 (repeat)

value: 36 hr


title: B2B-RV16-T72-UV-1-7

value: Mock Infected

value: 72 hr


title: Gastric tumour GC0113


title: B2B-RV16-T24-UV-1-7 (repeat)

value: 24 hr


title: Gastric tumour GC0114


title: Gastric tumour GC0115


title: DG Aged Impaired (5842733067_D)

description:
replicate 4
DG Aged Impaired

value: DG


title: Gastric tumour GC0105


title: Gastric tumour GC0111


title: B2B-RV16-T1 -1-7 (repeat)

value: 1 hr


title: Whole Hipp Aged Impaired (5842733040_L)

description:
replicate 4
Whole Hipp Aged Impaired


title: Whole Hipp Aged Impaired (5842733060_C)

description:
replicate 6
Whole Hipp Aged Impaired


title: Gastric tumour GC0099


title: Whole Hipp Aged Impaired (5842733060_A)

description:
replicate 5
Whole Hipp Aged Impaired


title: Whole Hipp Aged Impaired (5842733040_G)

description:
replicate 2
Whole Hipp Aged Impaired


title: Whole Hipp Aged Impaired (5842733040_I)

description:
replicate 3
Whole Hipp Aged Impaired


title: Gastric tumour GC0101


title: B2B-RV16-T60-UV-1-7

value: 60 hr


title: B2B-RV16-T72-2-7


title: Whole Hipp Aged Impaired (5842733060_D)

description:
replicate 7
Whole Hipp Aged Impaired


title: Gastric tumour GC0109


title: Gastric tumour GC0096


title: B2B-RV16-T48-UV-1-7

value: 48 hr


title: Gastric tumour GC0103


title: Whole Hipp Aged Impaired (5842733040_E)

description:
replicate 1
Whole Hipp Aged Impaired


title: B2B-RV16-T60-1-7+2-7


title: B2B-RV16-T72-3-7


title: Gastric tumour GC0095


title: B2B-RV16-T48-2-7


title: Whole Hipp Aged Intact (5842733060_F)

description:
replicate 7
Whole Hipp Aged Intact

value: Aged Intact (24M)


title: Whole Hipp Aged Intact (5842733060_H)

description:
replicate 8
Whole Hipp Aged Intact


title: Whole Hipp Aged Intact (5842733060_J)

description:
replicate 9
Whole Hipp Aged Intact


title: B2B-RV16-T72-1-7


title: Gastric tumour GC0097


title: B2B-RV16-T60-3-7


title: Gastric tumour GC0093


title: B2B-RV16-T48-3-7


title: B2B-RV16-T36-3-7


title: Gastric tumour GC0086


title: Gastric tumour GC0091


title: Gastric tumour GC0087


title: Whole Hipp Aged Intact (5842733040_D)

description:
replicate 3
Whole Hipp Aged Intact


title: Whole Hipp Aged Intact (5842733040_H)

description:
replicate 4
Whole Hipp Aged Intact


title: B2B-RV16-T48-1-7


title: B2B-RV16-T36-2-7


title: B2B-RV16-T36-1-7


title: Whole Hipp Aged Intact (5842733040_K)

description:
replicate 5
Whole Hipp Aged Intact


title: B2B-RV16-T36-UV-1-7


title: Whole Hipp Aged Intact (5842733040_A)

description:
replicate 1
Whole Hipp Aged Intact


title: Whole Hipp Adult (5842733060_I)

description:
replicate 6
Whole Hipp Adult


title: Whole Hipp Aged Intact (5842733060_B)

description:
replicate 6
Whole Hipp Aged Intact


title: Whole Hipp Aged Intact (5842733040_C)

description:
replicate 2
Whole Hipp Aged Intact


title: Whole Hipp Adult (5842733060_G)

description:
replicate 5
Whole Hipp Adult


title: B2B-RV16-T16-UV-1-7


title: B2B-RV16-T24-1-7


title: B2B-RV16-T24-UV-1-7


title: Gastric tumour GC0082


title: Gastric tumour GC0080


title: Gastric tumour GC0083


title: Gastric tumour GC0089


title: Whole Hipp Adult (5842733040_J)

description:
replicate 3
Whole Hipp Adult


title: Gastric tumour GC0073


title: Whole Hipp Adult (5842733060_E)

description:
replicate 4
Whole Hipp Adult


title: B2B-RV16-T24-3-7


title: B2B-RV16-T24-2-7


title: Gastric tumour GC0079


title: Gastric tumour GC0072


title: P19_white blood cells after exercise

city: Melbourne

first: Francine

last: Marques

address: Level 3, 75 Commercial Rd

institute: Baker IDI Heart and Diabetes

hyb_protocol: After fragmentation, samples were hybridized for 20 hr at 55°C to Agilent Human miRNA Microarrays (V3, release 16.0). Chips were washed and stained in the Agilent Microarray Hybridization Chamber SureHyb. The Agilent’s miRNA Complete Labeling and Hyb Kit was used according to Agilent's manual.

scan_protocol: The chips were scanned on an Agilent G2565BA scanner.

data_processing: The samples were between array normalized so that expression intensities were similar across all arrays using the quantile method, in the Partek Genomics Suite (v.6.6) application. Differentially expressed miRNAs were identified using a paired t-test.

source_name: white blood cells after exercise

label_protocol: 100ng of total RNA was prepared for hybridisation according to the standard Agilent protocol (microRNA Labeling & Hybridization Kit Manual, Agilent, Version 1.7, October 2009).

extract_protocol: miRNeasy kit (Qiagen) was used for extraction of total RNA and microRNA according to the manufacturer's instructions.

treatment_protocol: Whole blood was collected through venupuncture of the antecubital vein. White blood cells were isolated via red blood cell lysis and centrifugation. The cells were then stored in liquid nitrogen until RNA extraction.  Extracted RNA was stored at -80°C.

tag: participant id

tag: gender

value: male

tag: age

value: adults (19-39 years old)

tag: sample group

value: after exercise

value: white blood cells


title: P19_white blood cells before exercise

source_name: white blood cells before exercise

value: before exercise


title: P18_white blood cells after exercise


title: P18_white blood cells before exercise


title: P17_white blood cells before exercise


title: CA3 Aged Impaired (5842733015_D)

description:
replicate 4
CA3 Aged Impaired

value: Fischer 344 x Brown Norway F1-hybrid (F344BN)

value: Aged Impaired (24M)


title: B2B-RV16-T16-2-7

value: Infected

value: 16 hr


title: B2B-RV16-T16-3-7


title: Gastric tumour GC0065

value: Primary gastric tumour


title: Gastric tumour GC0068


title: Gastric tumour GC0062


title: B2B-RV16-T16-1-7


title: Gastric tumour GC0070


title: Whole Hipp Adult (5842733040_F)

description:
replicate 2
Whole Hipp Adult

value: Adult (12M)

value: whole hippocampus


title: Whole Hipp Adult (5842733040_B)

description:
replicate 1
Whole Hipp Adult


title: Gastric tumour GC0063


title: B2B-RV16-T12-2-7

value: 12 hr


title: CA3 Aged Impaired (5842733015_B)

description:
replicate 2
CA3 Aged Impaired


title: P17_white blood cells after exercise


title: B2B-RV16-T8-UV-1-7

value: Mock Infected

value: 8 hr


title: CA3 Aged Intact (5842733015_H)

description:
replicate 4
CA3 Aged Intact


title: CA3 Aged Impaired (5842733015_C)

description:
replicate 3
CA3 Aged Impaired


title: Gastric tumour GC0057


title: Gastric tumour GC0060


title: CA3 Aged Intact (5842733015_G)

description:
replicate 3
CA3 Aged Intact


title: P16_white blood cells after exercise


title: Gastric tumour GC0058


title: CA3 Aged Impaired (5842733015_A)

description:
replicate 1
CA3 Aged Impaired


title: B2B-RV16-T12-3-7


title: B2B-RV16-T12-UV-1-7


title: B2B-RV16-T12-1-7


title: CA3 Aged Intact (5842733015_F)

description:
replicate 2
CA3 Aged Intact


title: B2B-RV16-T8-2-7


title: B2B-RV16-T8-3-7


title: P16_white blood cells before exercise


title: P14_white blood cells after exercise


title: P14_white blood cells before exercise


title: P12_white blood cells before exercise


title: P12_white blood cells after exercise


title: CA3 Adult (5842733015_L)

description:
replicate 4
CA3 Adult


title: Gastric tumour GC0053


title: CA3 Aged Intact (5842733015_E)

description:
replicate 1
CA3 Aged Intact


title: CA3 Adult (5842733015_K)

description:
replicate 3
CA3 Adult


title: P8_white blood cells after exercise


title: Gastric tumour GC0050


title: P8_white blood cells before exercise


title: Gastric tumour GC0051


title: Gastric tumour GC0052


title: CA3 Adult (5842733015_J)

description:
replicate 2
CA3 Adult


title: B2B-RV16-T8-1-7


title: B2B-RV16-T6-3-7

value: 6 hr


title: Gastric tumour GC0055


title: P5_white blood cells after exercise


title: P5_white blood cells before exercise


title: B2B-RV16-T6-UV-1-7


title: B2B-RV16-T6-2-7


title: CA3 Adult (5842733015_I)

description:
replicate 1
CA3 Adult


title: Gastric tumour GC0047


title: B2B-RV16-T6-1-7


title: P3_white blood cells after exercise


title: Gastric tumour GC0046


title: Gastric tumour GC0049


title: Female_hs-KO 10

city: Houston

first: deqiang

last: sun

state: TX

address: 2121 W Holcombe Blvd

institute: Texas A&M University

data_processing: The data were normalised using quantile normalisation using corresponding functions in the R package lumi.

organism: Mus musculus

source_name: Mouse liver tissue

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

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

value: female

tag: genotype

value: liver

value: 2 months


title: Female_hs-KO 8


title: P3_white blood cells before exercise

value: male

value: adults (19-39 years old)


title: P2_white blood cells after exercise

value: after exercise

value: white blood cells


title: B2B-RV16-T4-UV-1-7

value: 4 hr


title: Gastric tumour GC0045


title: Female_hs-KO 9


title: B2B-RV16-T4-2-7

value: Infected


title: Gastric tumour GC0043


title: P2_white blood cells before exercise

value: before exercise


title: B2B-RV16-T4-3-7


title: Female_hs-KO 7


title: Gastric tumour GC0041

value: Primary gastric tumour


title: Gastric tumour GC0039


title: B2B-RV16-T4-1-7


title: Female_hs-KO 6


title: B2B-RV16-T3-1-7

value: 3 hr


title: Gastric tumour GC0037


title: Gastric tumour GC0036


title: B2B-RV16-T3-3-7


title: B2B-RV16-T3-UV-1-7


title: Male_hs-KO 4


title: B2B-RV16-T2-UV-1-7

value: 2 hr


title: Male_hs-KO 5


title: Male_hs-KO 6


title: B2B-RV16-T3-2-7


title: Female_WT 5

value: Wild-type


title: larval_ trachea_rep2

city: Cologne

first: Julia

last: Hoffmann

address: Joseph-Stelzmann-Str. 9b

department: Partridge

country: Germany

institute: MPI for Biology of Ageing

hyb_protocol: 200 pmol of the labelled samples (corresponding to approx. 2-3 µg cRNA) in hybridization buffer containing salmon testes DNA and yeast tRNA were hybridized to the array at 42°C overnight. After hybridization, slides were washed twice with 1 × SSC at RT for 1 h; 1 × SSC, 0.1% Triton-X- 100 at 60°C for 30 minutes and with 0.1 × SSC, 0.1% Tri- ton-X-100 at 37°C for 30 min. Subsequently, they were washed with 0.1 × SSC for 30 seconds at RT and rinsed with water before dried.

scan_protocol: The slides were scanned with the GenePixTM4000B scanner (Axon Instruments, Molecular Devices, Munich, Germany). For spot finding and generating preliminary result files the raw scanned image files were analyzed using GenePixPro version 6.0 (Axon Instruments) whereas data normalization and further data filtering were performed with Acuity 4.1 (Axon Instruments).

data_processing: Ratio-based normalization using default settings in Acuity. Criteria for inclusion of data in further analysis: Signal-to noise-ratio for at least one of the wavelengths > 3; -10 > log2 ratio ch2/ch1> 10; feature is not flagged bad or absent in previous GenePix analysis.

label: Alexa Fluor 555

organism: Drosophila melanogaster

source_name: larval trachea, primary branches

label_protocol: In brief, cDNA synthesis from RNA isolated from fat bodies was performed with Prime Script RT (Takara) using the following primers: OdT T7 I (5’-GAG AGA GGA TCC AAG TAC TAA TAC GAC TCA CTA TAG GGA GAT TTT TTT TTT TTT TTT TTT TTT T G/A/C-3’) and CapFinder Sp6rG (5’-CAG CGG CCG CAG ATT TAG GTG ACA CTA TAG A rGrGrG-3’). cDNA was amplified with OdT T7 II (5’-GAG AGA GGA TCC AAG TAC TAA TAC GAC TCA CTA TAG G-3’) and Adaptor Sp6rG (5’-GAC GCC TGC AGG CGA TGA ATT TAG G-3’) and LA Taq polymerase. cDNA was transcribed with MEGAscript® T7 (Ambion) including aminoallyl-UTP (Ambion) and subsequently labeled with Alexa Fluor 555 or 647 (Invitrogen) for control or experimental sample, respectively.

growth_protocol: Fly stocks were raised on standard cornmeal-agar medium at 25 °C under a 12 h/12 h light/dark cycle.

extract_protocol: Isolation of total RNA with Trizol (RNAmagic, Biobudget)

tag: fly line

tag: larval stage

value: 3rd instar larvae

value: trachea, primary branches

label: Alexa Fluor 647

source_name: larval trachea, secondary + tertiary branches

value: trachea, secondary + tertiary branches


title: larval_ trachea_rep3


title: larval_ trachea_rep1


title: Female_WT 4

value: female


title: B2B-RV16-T2-2-7


title: Gastric tumour GC0034


title: Gastric tumour GC0033


title: B2B-RV16-T2-3-7


title: Female_WT 3

value: liver


title: Female_WT 2

value: 2 months


title: Repl_LB_Delta PePNA

city: Bangalore

first: Dipankar

last: Nandi

address: CV Raman Avenue

department: Biochemistry

country: India

institute: Indian Institute of Science

description: referred as ΔpepN colony A LBHT

hyb_protocol: The labeled cRNA samples were hybridized on to an Agilent Custom S.typhimurium Custom Array 8x15k designed by Genotypic Technology Pvt. Ltd. 600 ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: scanned using the Agilent Microarray Scanner G Model G2565BA at 5 micron resolution.

data_processing: Data extraction from Images was done using Agilent Feature Extraction software v 10.5.1.1  and 75th percentile shift Normalization of the data was done in GeneSpring GX V 11.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: ΔpepN bacterial cell pellet, 6h, grown in LB at 42°C, colony A

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

growth_protocol: Overnight grown cultures of S. typhimurium WT and ΔpepN were transferred to either complete medium (LB) or minimal medium (MM). Cultures were grown initially at 37° for 3.5 hours and subsequently tranferred to 42°C, after 6 hour growth cultures were pelleted at 2000g and RNA was isolated for microarray analysis.

extract_protocol: RNA isolation was done by using Qiagen Rneasy Minikit as per the manufacturer’s instructions RNA integrity was assessed using RNA 6000 Nano Lab Chip on the 2100 Bioanalyzer (Agilent, Palo Alto, CA) following the manufacturer’s protocol. Total RNA purity was assessed by the NanoDrop® ND-1000 UV-Vis Spectrophotometer (Nanodrop technologies, Rockland, USA). We considered RNA to be good quality based on the rRNA 28S/18S ratios and RNA integrity number (RIN)

treatment_protocol: Analysis was performed in two ways i) S. typhimurium grown in LBHT Vs NDHT and ii) WT Vs ΔpepN grown in either LBHT or NDHT

tag: genotype/variation

value: ΔpepN

tag: growth medium

value: LB


title: Repl_Delta PePNB

description: referred as ΔpepN colony B NDHT

source_name: ΔpepN bacterial cell pellet, 6h, grown in MM at 42°C, colony B

value: MM


title: Gastric tumour GC0032


title: Gastric tumour GC0028


title: Female_WT 1


title: B2B-RV16-T2-1-7


title: B2B-RV16-T1 -UV-1-7

value: Mock Infected

value: 1 hr


title: Repl_MMWTA

description: referred as WT colony A NDHT

source_name: WT bacterial cell pellet, 6h, grown in MM at 42°C, colony A

value: wild-type


title: Gastric tumour GC0029


title: Male_WT 3

value: male


title: Gastric tumour GC0031

value: Primary gastric tumour


title: LB_Pep_NB

description: referred as ΔpepN colony B LBHT

source_name: ΔpepN bacterial cell pellet, 6h, grown in LB at 42°C, colony B


title: Repl_MMWTB

description: referred as WT colony B NDHT

source_name: WT bacterial cell pellet, 6h, grown in MM at 42°C, colony B


title: Male_WT 1


title: Repl_Delta PePNA

description: referred as ΔpepN colony A NDHT

source_name: ΔpepN bacterial cell pellet, 6h, grown in MM at 42°C, colony A


title: Gastric tumour GC0026


title: Gastric tumour GC0024


title: Male_WT 2


title: B2B-RV16-T0 -UV-1-7

value: 0 hr


title: LB_WT_A

description: referred as WT colony A LBHT

source_name: WT bacterial cell pellet, 6h, grown in LB at 42°C, colony A


title: B2B-RV16-T0 -3-7

value: Infected


title: B2B-RV16-T1 -2-7


title: koTG rep2

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

description: replicate 2

data_processing: The data were normalized using quantile normalization approach with Illumina GenomeStudio.

source_name: Siah1a/Siah2 KO MEF cell treated with TG for 6 h

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

tag: genotype/variations

value: Siah1a-/-::Siah2-/- (KO) mice

tag: cell type

value: MEFs

tag: treatment

value: treated with TG for 6 h


title: LB_WT_B

description: referred as WT colony B LBHT

source_name: WT bacterial cell pellet, 6h, grown in LB at 42°C, colony B


title: B2B-RV16-T1 -3-7

source_name: whole blood

tag: cell line

tag: sample type

tag: collection time


title: Gastric tumour GC0023


title: B2B-RV16-T1 -1-7


title: wtTG rep2

description: replicate 2

source_name: MEF cell treated with TG for 6 h

value: wild-type mice


title: Gastric tumour GC0021

source_name: Primary gastric tumour


title: Gastric tumour GC0020


title: B2B-RV16-T0 -2-7


title: koTM rep2

description: replicate 2

source_name: Siah1a/Siah2 KO MEF cell treated with TM for 6 h

value: treated with TM for 6 h


title: koOGD rep2

description: replicate 2

source_name: Siah1a/Siah2 KO MEF cell treated for 12 h under a combination of oxygen and glucose deprivation


title: B2B-RV16-T0 -1-7


title: Gastric tumour GC0018


title: wtOGD rep2

description: replicate 2

source_name: MEF cell treated for 12 h under a combination of oxygen and glucose deprivation


title: wtTM rep2

description: replicate 2

source_name: MEF cell treated with TM for 6 h


title: Gastric tumour GC0015


title: Gastric tumour GC0019


title: B2B-RV16-T0 UNINFECT-UV-1-7

value: Mock Uninfected


title: Gastric tumour GC0012


title: B2B-RV16-T0 UNINFECT-2-7

value: Uninfected


title: B2B-RV16-T0 UNINFECT-3-7


title: Gastric tumour GC0014


title: Control Islets 2

city: Toronto

first: Michael

middle: B

last: Wheeler

state: Ontario

address: 1 King's College Circle

department: Physiology

country: Canada

institute: University of Toronto

description: Control-treated male CD1 islets.

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse 430_2 GeneChip. EukGE-WSv4_450 was used to stain and wash the arrays.

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

data_processing: The data were analyzed with Affymetrix Expression Console (Version 1.1) using Affymetrix default analysis settings and RMA as normalization method.

label: Biotin

source_name: CD1 mouse islets, control

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Islets were isolated from 8-week-old male CD1 mice and incubated overnight in standard RPMI media at 37C.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Plus Mini Kit according to manufacturer instructions.

treatment_protocol: Islets were treated with either vehicle (0.1% ethanol) or 200uM CMPF for 24hrs.

tag: strain/background

value: 8 weeks

value: isolated pancreatic islets

value: vehicle control for 24hrs


title: ko rep2

description: replicate 2

source_name: Siah1a/Siah2 KO MEF cell


title: B2B-RV16-T0 UNINFECT-1-7


title: Gastric tumour GC0016

tag: tissue


title: koOD rep2

description: replicate 2

source_name: Siah1a/Siah2 KO MEF cell treated for 12 h under oxygen deprivation


title: Control Islets 3

description: Control-treated male CD1 islets.


title: infected embryo: biological replicate 3

city: Auckland

first: Cris

last: Print

address: Grafton Campus, Park Rd

country: New Zealand

institute: Auckland University

description: biotin

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were normalised with the RMA algorithym using default settings which included background correction.

organism: Danio rerio

source_name: 4 dpf dissected larval zebrafish trunks injected at 2 dpf with live Salmonella enterica serovar Typhimurium bacteria

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

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

value: dissected larval zebrafish trunks (approx 50)


title: infected embryo: biological replicate 2

description: biotin

value: injected at 2 dpf with live Salmonella enterica serovar Typhimurium bacteria


title: control embryo: biological replicate 3

description: biotin

source_name: 4 dpf dissected larval zebrafish trunks injected at 2 dpf with PBS

value: injected at 2 dpf with PBS


title: CMPF Islets 2

description: CMPF-treated male CD1 islets.

source_name: CD1 mouse islets, CMPF

value: male

value: CMPF for 24hrs


title: koGD rep2

description: replicate 2

source_name: Siah1a/Siah2 KO MEF cell treated for 12 h under glucose deprivation


title: CMPF Islets 3

description: CMPF-treated male CD1 islets.


title: Gastric tumour GC0010

value: Primary gastric tumour


title: wtOD rep2

description: replicate 2

source_name: MEF cell treated for 12 h under oxygen deprivation


title: CMPF Islets 1

description: CMPF-treated male CD1 islets.


title: Gastric tumour GC0008


title: infected embryo: biological replicate 1

description: biotin


title: wtGD rep2

description: replicate 2

source_name: MEF cell treated for 12 h under glucose deprivation


title: Gastric tumour GC0006


title: wt rep2

description: replicate 2

source_name: MEF cell


title: Gastric tumour GC0002


title: Gastric tumour GC0001


title: koTG rep1

description: replicate 1

source_name: Siah1a/Siah2 KO MEF cell treated with TG for 6 h


title: control embryo: biological replicate 1

description: biotin


title: Embryo irradiated, high dose, replicate 1

city: Augusta

first: Robert

last: Podolsky

state: GA

institute: Georgia Regents University

description: livers of 16 week old adults, irradiated as embryos

hyb_protocol: Total RNA extraction, cDNA synthesis, and synthesis and labeling of antisense RNA was performed as recommended by Affymetrix using Life Technologies kits.

scan_protocol: standard Affymetrix protocol

data_processing: The data were analyzed using Bioconductor, using quantile normalization and RMA for background subtraction.

growth_protocol: Embryos in all groups were allowed to grow and develop at 28 ºC using standard maintenance protocols

treatment_protocol: zebrafish embryos were collected from three wild type breeding pairs, pooled, and allowed to develop for 24 hours. One group of ~50 embryos was withdrawn to serve as the non-irradiated control (Group A). To investigate the long-term response, two other groups of ~50 embryos each were withdrawn and irradiated with 0.1 Gy (Group B) or 1.0 Gy (Group C) of 137Cs γ-rays (Model 68A irradiator, J. L. Shepherd & Associates, San Fernando, CA).  At 16 weeks post-fertilization, six males from each group were randomly selected, anesthetized with MS-222 (ethyl 3-aminobenzoate methanesulfonate salt; Sigma–Aldrich, St. Louis, MO), sacrificed, sex verified, and dissected. Livers were removed and rapidly frozen in TRIzol Reagent (Life Technologies, Grand Island, NY). In addition, 12 males from Group A were randomly selected and used to establish the acute response groups.  These were subjected to whole body irradiation at 0.1 Gy (Group D) or 1.0 Gy (Group E) and sacrificed for analysis at 4 hours post-irradiation

tag: radiation timing

value: embryo

value: liver

value: 16 wk

tag: deveopmental stage

value: adult

tag: genetic background

value: AB


title: Mut veh 3

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: mouse uteri (SRC-2 wild-type), vehicle-treated, pooled rep 3

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized on Mouse430_2 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-WS2v5 (for FS400) or FS450_0001 (for FS450).

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner (Agilent).

data_processing: The data were analyzed with dChip version2006 using Affymetrix default analysis settings, PM-MM model, and quantile normalization method.

source_name: mouse uteri (SRC-2 mutant), vehicle-treated

growth_protocol: Microarray analysis was performed using eighteen SRC-2flox/flox (SRC-2f/f) and eighteen PRCre/+ SRC-2flox/flox (SRC-2d/d) mice. Mice were maintained in the designated animal care facility at the Baylor College of Medicine and mice were handled in accordance with Institutional Guideline for the Care and handling of laboratory animals.

extract_protocol: After six hours uteri from each mouse were collected and total RNA was isolated using QIAGEN RNeasy total RNA isolation kit. RNA from three mice per genotype per treatment were pooled and assigned as one sample (three samples per genotype per treatment). Quality of all RNA samples were analyzed with a Bioanalyzer 2100 (AgilentTechnologies, Palo Alto, CA) before microarray hybridization.

treatment_protocol: Mice were ovariectomized at 6 weeks and after 2 weeks mice were either treated with sesame oil (vehicle) or 1 mg of P4.

value: SRC-2 mutant

value: uteri


title: control embryo: biological replicate 2

description: biotin


title: Embryo irradiated, low dose, replicate 3

source_name: livers of 16 week old adults, irradiated as embryos

label_protocol: Total RNA extraction, cDNA synthesis, and synthesis and labeling of antisense RNA was performed as recommended by Affymetrix using Life Technologies kits.

tag: age


title: Mut veh 2

description: mouse uteri (SRC-2 wild-type), vehicle-treated, pooled rep 2


title: Mut P4 2

source_name: mouse uteri (SRC-2 mutant), progesterone (P4)-treated


title: Mut veh 1

description: mouse uteri (SRC-2 wild-type), vehicle-treated, pooled rep 1


title: Mut P4 3


title: Mut P4 1


title: con-56_C

city: Detroit

middle: J

last: Bannon

state: MI

address: 540 E Canfield

department: Pharmacology

institute: Wayne State University School of Medicine

data_processing: The data were normalized using quantile normalization with Illumina BeadStudio. They were also batch normalized.

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 Bioanalyzer.

tag: disease state

value: control

tag: organ

value: Brain

value: Ventral midbrain

value: Postmortem

tag: Cause of death

value: multiple gunshot wounds


title: wtTM rep1

description: replicate 1

value: wild-type mice

value: MEFs

value: treated with TM for 6 h


title: Embryo irradiated, high dose, replicate 3

extract_protocol: Total RNA extraction, cDNA synthesis, and synthesis and labeling of antisense RNA was performed as recommended by Affymetrix using Life Technologies kits.


title: coc-57_B

value: cocaine addiction

value: cocaine related


title: Embryo irradiated, high dose, replicate 2

value: embryo


title: koOGD rep1

description: replicate 1

source_name: Siah1a/Siah2 KO MEF cell treated for 12 h under a combination of oxygen and glucose deprivation

value: Siah1a-/-::Siah2-/- (KO) mice


title: coc-57_C


title: wtTG rep1

description: replicate 1

source_name: MEF cell treated with TG for 6 h

value: treated with TG for 6 h


title: coc-57_A


title: koOD rep1

description: replicate 1

value: treated for 12 h under oxygen deprivation


title: Embryo irradiated, low dose, replicate 2

value: liver

value: 16 wk

value: adult

value: AB


title: Control Islets 1

description: Control-treated male CD1 islets.

tag: gender

value: male

value: 8 weeks

value: isolated pancreatic islets

value: vehicle control for 24hrs


title: con-56_B

value: control

value: Brain

value: Ventral midbrain

value: Postmortem

value: multiple gunshot wounds


title: wtOD rep1

description: replicate 1

value: wild-type mice

value: MEFs


title: WT P4 3

source_name: mouse uteri (SRC-2 wild-type), progesterone (P4)-treated

tag: genotype/variation

value: SRC-2 wild-type

value: uteri


title: WT P4 2


title: Embryo irradiated, low dose, replicate 1

value: embryo

value: liver


title: ko rep1

description: replicate 1

tag: genotype/variations

value: Siah1a-/-::Siah2-/- (KO) mice


title: WT P4 1


title: wtOGD rep1

description: replicate 1

source_name: MEF cell treated for 12 h under a combination of oxygen and glucose deprivation

tag: cell type


title: koGD rep1

description: replicate 1

tag: treatment

value: treated for 12 h under glucose deprivation


title: coc-53_C

value: cocaine addiction

value: cocaine related


title: wtGD rep1

description: replicate 1


title: Non-irradiate control, biological replicate 3

description: livers of 16 week old adults, irradiated as adults

value: 0 Gy

value: 16 wk

value: adult

value: AB


title: WT veh 3

source_name: mouse uteri (SRC-2 wild-type), vehicle-treated


title: con-56_A

value: control

value: Brain

value: Ventral midbrain


title: Adult irradiated, high dose, replicate 2

source_name: livers of 16 week old adults, irradiated as adults


title: coc-53_B

value: Postmortem


title: WT veh 1


title: coc-53_A


title: wt rep1

description: replicate 1

value: wild-type mice

value: MEFs


title: con-52_B

value: hypertensive cardiomyopathy


title: Gene expression of WT and Ring1B KO liver at E13.5

city: Yokohama City

first: Yasuharu

last: Ueno

state: Kanagawa

address: 3-9  Fuku-ura, Kanazawa-ku

department: Graduate School of Medicine

country: Japan

institute: Yokohama City University

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: Liver cells from E13.5 CreERT2-/-Ring1BF/F  mice

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: RNA was prepared using the TRIzol Reagent (invitrogen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: For conditional knockout of Ring1B, the Ring1B f/f mice were crossed with Rosa26::CreER(T2) mice. Mice were intraperitoneally injected with 100 μl of tamoxifen (10 mg / ml, dissolved in corn oil) daily from E8.5 to E10.5 to induce Cre-ERT activity. Embryonic hepatic progenitors (CD45- Ter119-) were collected at E13.5 as described above from Rosa26::CreER(T2)+/-:Ring1Bf/f and Rosa26::CreER(T2)-/-:Ring1Bf/f littermates.

value: CD45- Ter119- liver cells

source_name: Liver cells from E13.5 CreERT2+/-Ring1BF/F  mice


title: Adult irradiated, high dose, replicate 3

value: liver


title: Non-irradiate control, biological replicate 2


title: Adult irradiated, high dose, replicate 1


title: con-52_C


title: WT veh 2

value: SRC-2 wild-type

value: uteri


title: con-52_A


title: AGS_Vehicle-2, Biological Replicate 2

city: Madurai

first: Kumaresan

last: Ganesan

state: Tamil Nadu

address: School of Biological Sciences,

department: Genetics

institute: Madurai Kamaraj University

description:
Gene expression data of AGS gastric cancer cell line as ethanol control
AGS_Vehicle-2

hyb_protocol: The fragmented and labelled cDNA were hybridized for 16 hr at 45°C with Affymetrix Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000.

data_processing: Gene level normalized expression signals were calculated from Affymetrix CEL files by RMA,in Affymetrix Expression Console version 1.1.

source_name: AGS_Vehicle control

label_protocol: 500 ng of total RNA was used to generate fragmented and biotin labelled sense cDNA using Ambion WT Expression kit (Affymetrix).

growth_protocol: AGS gastric cancer cells were seeded in 6 well culture plate and maintained in DMEM-F12 media with 10% FBS in a humidified incubator at 37˚C and 5% CO2.

extract_protocol: After the treatment, the total RNA was isolated from the cells using Trizol (Invitrogen).

treatment_protocol: When the cells reach 80% confluency, the cells were treated with 0.01% ornithogalum or with ethanol as vehicle control for 36 hours.

tag: cell line

value: AGS

tag: tissue origin

value: stomach

value: human gastric carcinoma cells

tag: treated with

value: ethanol (vehicle control) for 36 hrs


title: Adult irradiated, low dose, replicate 2

description: livers of 16 week old adults

source_name: livers of 16 week old adults

value: adult

value: 16 wk


title: Adult irradiated, low dose, replicate 3

value: AB


title: AGS_Ornith-2, Biological Replicate 2

description:
Gene expression data of AGS gastric cancer cell line treated with Ornithogalum
AGS_Ornith-2

source_name: AGS_Ornithogalum treated

value: 0.01% ornithogalum for 36hrs


title: Adult irradiated, low dose, replicate 1

description: livers of 16 week old adults


title: AGS_Vehicle-1, Biological Replicate 1

description:
Gene expression data of AGS gastric cancer cell line as ethanol control
AGS_Vehicle-1


title: coc-51_B

value: cocaine addiction

value: Brain

value: Ventral midbrain

tag: sample type

value: cocaine related


title: coc-51_C

tag: tissue

value: Postmortem


title: koTM rep1

description: replicate 1

source_name: Siah1a/Siah2 KO MEF cell treated with TM for 6 h

value: Siah1a-/-::Siah2-/- (KO) mice

value: MEFs

value: treated with TM for 6 h


title: AGS_Ornith-1, Biological Replicate 1

description:
Gene expression data of AGS gastric cancer cell line treated with Ornithogalum
AGS_Ornith-1


title: coc-51_A


title: spine, immunized, biological replicate 2

city: Chicago

first: Tibor

middle: T

last: Glant

state: IL

address: 1735 West Harrison

department: Orthopedic Surgery

institute: Rush University Medical Center

hyb_protocol: Following fragmentation, 1.5 ug of labeled cRNA were hybridized according to standard Affymetrix protocols on Affymetrix GeneChip ‘Mouse Genome 430 2.0’ arrays using ‘GeneChip Fluidics Station 450’.

scan_protocol: Affymetrix GeneChip arrays were scanned according to standard Affymetrix protocols on an ‘Affymetrix GeneChip Scanner 3000 7G’.  Each array was analyzed for the following quality metrics:  3’/5’ signal ratio of house-keeping genes, signal intensity of species-specific house-keeping genes, signal intensities of Poly-A controls, signal intensities of hybridization controls, relative logarithmic probe cell intensity- and relative logarithmic expression signal values.

data_processing: Data was analyzed in GeneSpring GX 10.0 (Agilent Technologies, Santa Clara, CA).  Robust Multi-array Average (RMA) (Irizarry, 2003) summarization algorithm (with Quantile Normalization and Median Polish probe summarization procedure) and baseline transformation (baseline to median of all 8 samples) was run on data using logarithmic scale. All 8 samples passed quality control based on hybridization controls, 3'/5' ratios for internal controls, Pearson correlation and Principal Component Analysis (PCA). Probe sets were filtered by expression values based on percentiles. To identify statistically significant (p-value cutoff 0.05), differentially expressed transcripts between naive and immunized mice with spondylitis, unpaired T-test was done. Asymptotic p-value computation was applied. Statistical test p-values were corrected for False Discovery Rate (FDR) by Benjamini-Hochberg (BH) procedure. Differentially expressed transcripts were annotated with GeneSpring GX 10.0.

source_name: intervertebral disc

label_protocol: Biotinylated cRNA were prepared according to standard Affymetrix recommended protocols from 2 to 5 ug total RNA (Affymetrix Expression Analysis Technical Manual, P/N 702232 Rev.2).

growth_protocol: Five BALB/c mice were immunized with an emulsion of cartilage PG (100 µg protein) and 2 mg dimethyldioctadecyl-ammonium bromide (DDA) adjuvant on days 0, 21 and 42 (Glant,T.T. and Mikecz,K., Proteoglycan aggrecan-induced arthritis.  A murine autoimmune model of rheumatoid arthritis. Methods Mol.Med. 2004. 102: 313-338.). Three age matched, naive BALB/c mice were used as controls.

extract_protocol: Total RNA was isolated with TriReagent (Sigma) according to the manufacturers instructions.

treatment_protocol: RNA was isolated from lumbar L1-L6 IVDs of naïve and immunized BALB/c mice. RNA samples of 6 pooled IVDs were prepared and the quality and quantity was determined by Agilent 2100 Bioanalyzer.

tag: Strain

value: BALB/c

tag: Gender

value: female

tag: PG-immunized

tag: Inflamed


title: spine, immunized, biological replicate 3


title: spine, immunized, biological replicate 4


title: spine, immunized, biological replicate 5


title: con-50_C

tag: disease state

value: control

value: arteriosclerotic cardiovascular disease


title: AGS cells - Celecoxib treated biological rep 2

description: Celecoxib 2

hyb_protocol: Following fragmentation, single stranded DNA obtained from 10 mg of cRNA were hybridized for 16 hr at 45°C inAffymetrix “HuGene-1_0-st” (Human Gene 1.0 ST ) array GeneChip with Hybridization Oven 640. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000.

data_processing: The raw data was normalized in Affymetrix Expression Console (v.1.1), using RMA algorithm

source_name: AGS_Celecoxib treated

label_protocol: Biotin labelled fragmented single stranded DNA was prepared from 250 ng of total RNA. The steps were followed as per the instructions in the user manuals of Ambion® WT Expression Kit, GeneChip® WT Terminal Labeling and Hybridization kit (Affymetrix).

growth_protocol: AGS cells purchased from NCCS Pune were grown in DMEM/F12 media supplemented with 10% FBS, 2mM Glutamine, 100U/ml penicillin, 100μg/ml streptomycin antibiotics and incubated in 5% CO2 incubator at 37⁰C. At 90% confluency, cells were trypsinized, counted and 3x10⁵ cells were seeded in 6 well plates and further incubated for 48 hours

extract_protocol: After 24 hours incubation, cells were rinsed once with 1X PBS. For each well, 1ml of Trizol (Invitrogen)was added for the extraction of total RNA as per manufacturer's instructions. RNA integrity was evaluated using MultiNA nucleic acid analyzer then control and celecoxib treated samples were pooled.

treatment_protocol: Celecoxib (Sigma) was dissolved in DMSO and 10mM stock was prepared. AGS cells were treated with 20μM celecoxib in separate wells and incubated for 24 hours.

value: AGS

value: stomach

value: human gastric carcinoma cells

value: 20μM celecoxib for 24hrs


title: spine, naïve, biological replicate 3

tag: Naïve

tag: Normal


title: spine, immunized, biological replicate 1


title: con-50_A

tag: organ

tag: Cause of death


title: AGS control biological rep 3

description: Control 3

value: none (control)


title: coc-42_B

value: cocaine addiction


title: AGS cells - Celecoxib treated biological rep 3

description: Celecoxib 3


title: AGS control biological rep 2

description: Control 2


title: tdf embryo

city: Taian

first: Qing-Xin

last: Liu

state: Shandong

address: No. 61 Daizong Street

country: China

institute: Shandong Agricultural University

description: Gene expression data from tdf embryos

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Following Affymetrix GeneChip Expression Analysis 2000 manual.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Drosophila tdf embryos

label_protocol: Biotinylated cRNA probes were prepared from total RNA of each sample following the Affymetrix IVT labeling protocol.

growth_protocol: Incubate embryos for 16 hours after egg laying on an apple juice plate at 25°C.

extract_protocol: Total RNA was extracted separately for each of the yw and homozygous tdf mutant embryos using the QIAGEN RNeasy isolation kit.

treatment_protocol: tdf mutant embryos were identified using CyOact-GFP balancer chromosome.

tag: developmental stage

value: embryo

tag: genotype/variation

value: tdf


title: AGS control biological rep 1

description: Control 1

tag: cell type


title: con-41_C

value: Brain

value: Ventral midbrain

value: gun shot wound


title: AGS cells - Celecoxib treated biological rep 1

description: Celecoxib 1

tag: cell line


title: yw embryo

description: Gene expression data from yw embryos

source_name: Drosophila yw embryos

value: yw


title: coc-42_A

value: Postmortem

value: cocaine related


title: B-cell_K15_EBV_rep4

city: Neuherberg

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

institute: Helmholtz Zentrum München

hyb_protocol: Affymetrix GeneChip® WT Terminal and Hybridization Kit

data_processing: Microarray datasets were normalized using Bioconductor 'RMA' algorithm. Probe sets were filtered using the 'nsFilter' (available with the R 'genefilter' package)

source_name: Human unsorted B cells from donor 4 infected with K15 EBV

label_protocol: Affymetrix GeneChip® WT Terminal Labeling kit

growth_protocol: Gene expression profiling experiments were performed with adenoid B cells purified after sheep erythrocyte rosetting and Ficoll density centrifugation

extract_protocol: RNeasy MiniKit (Qiagen)

treatment_protocol: Two different MOIs (MOI 0.05 and 0.1) were used in order to equilibrate the fraction of EBV transformed B cells during infection as the EBV stocks differed in their transformation efficiencies. One day p.i., the cells were kept under reduced oxygene levels (5%) for seven days. On day eight p.i., cells with characteristics of lymphoblastoid cells were identified by forward and sideward scatter criteria and physically sorted on a FACS Aria III instrument (Becton Dickinson).

tag: ebv strain

tag: donor

value: unsorted B cells


title: B-cell_K15_EBV_rep3

source_name: Human unsorted B cells from donor 3 infected with K15 EBV


title: Cigarette smoke-exposed 5

city: Hamilton

first: Mathieu

middle: C

last: Morissette

address: 1280 Main St W

department: Pathology and Molecular Biology

institute: McMaster University

description: Exposed to cigarette smoke for 8 weeks

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (GPL7202) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Exposed to cigarette smoke for 8 weeks

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Lungs were homogenized and RNA was extracted using the Qiagen Rneasy kit. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: strain

value: BALB/c

value: lung

tag: gender

value: female


title: Non-irradiate control, biological replicate 1

description: livers of 16 week old adults

tag: treatment

value: 0 Gy

tag: radiation timing

tag: tissue

value: liver

tag: age

value: 16 wk

tag: deveopmental stage

value: adult

tag: genetic background

value: AB


title: Cigarette smoke-exposed 4

description: Exposed to cigarette smoke for 8 weeks

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (GPL7202) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.


title: con-41_B

hyb_protocol: Standard Illumina hybridization protocol

tag: disease state

value: control

tag: sample type


title: con-50_B

tag: organ

tag: Cause of death

value: arteriosclerotic cardiovascular disease


title: spine, naïve, biological replicate 1

tag: Strain

tag: Gender

tag: Naïve

tag: Normal


title: spine, naïve, biological replicate 2


title: Cigarette smoke-exposed 3

description: Exposed to cigarette smoke for 8 weeks


title: coc-42_C

value: cocaine addiction

value: Brain


title: B-cell_K15_EBV_rep2

source_name: Human unsorted B cells from donor 2 infected with K15 EBV

tag: ebv strain

tag: donor

tag: cell type


title: B-cell_K15_EBV_rep1

source_name: Human unsorted B cells from donor 1 infected with K15 EBV


title: con-41_A

value: Ventral midbrain

value: gun shot wound


title: Cigarette smoke-exposed 2

description: Exposed to cigarette smoke for 8 weeks

tag: strain

tag: gender


title: coc-38_C

tag: tissue

value: Postmortem


title: B-cell_K1_EBV_rep4

source_name: Human unsorted B cells from donor 4 infected with K1 EBV


title: B-cell_K1_EBV_rep3

source_name: Human unsorted B cells from donor 3 infected with K1 EBV


title: Room air-exposed 5

description: Exposed to room air for 8 weeks

source_name: Exposed to room air for 8 weeks


title: Cigarette smoke-exposed 1

description: Exposed to cigarette smoke for 8 weeks


title: coc-38_A

value: cocaine related


title: B-cell_K1_EBV_rep2

source_name: Human unsorted B cells from donor 2 infected with K1 EBV

value: unsorted B cells


title: Room air-exposed 3

description: Exposed to room air for 8 weeks

value: BALB/c


title: Room air-exposed 4

description: Exposed to room air for 8 weeks

value: lung


title: B-cell_K1_EBV_rep1

source_name: Human unsorted B cells from donor 1 infected with K1 EBV


title: con-37_B


title: B-cell_LMP2A_EBV_rep4

source_name: Human unsorted B cells from donor 4 infected with ΔLMP2A EBV

value: Delta LMP2A


title: con-37_A


title: con-37_C


title: B-cell_LMP2A_EBV_rep3

source_name: Human unsorted B cells from donor 3 infected with ΔLMP2A EBV


title: Room air-exposed 1

description: Exposed to room air for 8 weeks

value: female


title: CDC1551 kasB T334A T336A Transcriptome Replicate 3

city: Saranac Lake

first: Brian

last: Weinrick

state: NY

address: 154 Algonquin Avenue

institute: Trudeau Institute

description: effect of kasB T334A T336A

hyb_protocol: Slide was hybridized for 16 hours at 42 in water bath with volume of 60 uL in solution of standard gene expression hybridization solution, and blocked in standard prehybridization solution. After hybridization, the slide was washed with standard wash protocol. refer to PFGRC protocol SOP#M008

scan_protocol: scanned with PMT voltage adjusted for maximum dynamic range

data_processing: In MIDAS, lowess normalization, standard deviation regularization, in-slide replicate analysis, one bad channel policy set to generous, all flags on

organism: Mycobacterium tuberculosis

source_name: whole_organism from Mycobacterium tuberculosis CDC1551 labeled with Cy3.

label_protocol: 2 ug total RNA was used as template for reverse transcription with random hexamer primers and aminoallyl-dUTP in a 2:3 ratio to dTTP in the nucleotide mix.  After overnight incubation at 42°C, the reaction was stopped, RNA was hydrolyzed, and unincorporated nucleotides and free amines were removed with the Qiagen MinElute kit as per protocol, with amine-free phosphate wash and elution buffers.  cDNA concentration and purity were measured by Nanodrop.  Cy3 and Cy5 dyes were coupled to the aminoallyl-cDNA, which was then purified using a MinElute kit.  Probe concentration, purity, and dye incorporation were measured by Nanodrop.

extract_protocol: Cells are collected by centrifugation and resuspended in 1mL buffer RLT from a Qiagen RNeasy kit.  The suspension is transferred to Fast-Prep Blue Cap tubes and processed for 45 seconds at speed 6.5 in a Fast-Prep apparatus.  After a brief incubation on ice the debris is spun down and the supernatant (~750uL) is removed to a fresh microcentrifuge tube.  525uL absolute ethanol is added and the samples are applied to RNeasy columns in two applications.  At this point the RNA is purified as recommended by the Qiagen protocol.

treatment_protocol: nucleic_acid_extraction: total RNA prep

tag: media

value: liquid

tag: genotype

value: parental wildtype

source_name: whole_organism from Mycobacterium tuberculosis CDC1551 labeled with Cy5.

value: kasB T334A T336A


title: Escherichia coli OP50-fed Caenorhabditis elegans

city: Seoul

first: Junhyeok

last: Go

address: Sinchon-dong, Seodaemun-gu

country: South Korea

institute: Yonsei university

description: Gene expression during Escherichia coli OP50 feeding

hyb_protocol: Microarray samples were hybridized using Agilent’s Gene Expression Hybridization Kit according to the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner.

data_processing: After image analysis with Feature Extraction Software (Agilent), The scanned images were analyzed with Agilent's GeneSpring Software to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Caenorhabditis elegans

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Agilent’s Low RNA Input Linear Amplification kit PLUS according to the manufacturer's instructions.

extract_protocol: RNA was prepared using the QIAGEN Rneasy Mini Kit following the manufacturer's recommendations.  RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: After hatching, each group of C. elegans was fed with E. coli OP50 and soil-isolated L. sphaericus until the warms were into young adult phase at 20 ºC.

value: whole body

tag: Stage

value: young adult


title: Room air-exposed 2

description: Exposed to room air for 8 weeks


city: Tampa

first: jianguo

last: tao

state: FL

address: 12902 Magnolia Dr

institute: H Lee Moffitt Cancer Center

description:
S4+HK
B lymphocyte + FDC-like cell line.
Enriched small RNA.

hyb_protocol: The melting temperature of detection probes was balanced by incorporating varying numbers of modified nucleotides with increased binding affinities. For quality control, we hybridized a group of control oligos to evaluate array quality and mixed a fixed amount of 20-mer RNA oligos to samples as external controls.

scan_protocol: Axon GenePix 4000B Microarray Scanner.

data_processing: Data were processed by subtracting background and normalizing the signals using a LOWESS filter (locally weighted regression) method to remove system-related variations.A detectable transcript was defined by fulfilling the following criteria: 1) signal intensity >3× background standard deviation; 2) spot CV (standard deviation/signal intensity) <0.5; and 3) signals from at least 50% of the repeating probes above detection level.

source_name: SUDHL-4 lymphoma cells co-cultured with HK cells, 24hrs

label_protocol: RNA samples for comparison were labeled with tag-specific dendrimer Cy3 and Cy5 fluorescent dyes.

growth_protocol: SU-4 cells in suspension and after 24 and 48 h of co-culture with HK cells were sorted out by CD19 magnet beads, and isolated total RNA was then applied for miRNA array assay.

extract_protocol: RNA samples for miRNA microarray or miRNA quantification, total RNA enriched with small RNAs was isolated by using mirVana miRNA isolation kit (Ambion) according to the manufacturer's protocol.

tag: cell line

value: B lymphocyte

tag: growth type

value: co-culture with HK cells

tag: time

source_name: SUDHL-4 lymphoma cells co-cultured with HK cells, 48hrs

value: B lymphocytes


title: CDC1551 kasB KO Transcriptome Replicate 3

description: effect of kasB KO

value: kasB KO


title: Lysinibacillus sphaericus-fed Caenorhabditis elegans

description: Gene expression during Lysinibacillus sphaericus feeding


title: IMPC_MP09_tumoral sample

type: genomic

city: Paris

first: Jaydutt

middle: D

last: Bhalshankar

address: 26 rue d'Ulm

department: INSERM UNIT 830

country: France

institute: Institut CURIE

description: Hybridized to SNP6.57

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 to generate .CEL files for downstream analysis.

data_processing: CEL files and TXT files (generated by Affymetrix Genotyping Console 3.0.1) were processed by GAP (Popova T et al, Genome Biol, 2009) and Partek® GS software version 6.5 build 6.10.1020

molecule: genomic DNA

source_name: IMPC tumoral sample

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from tumor fragments using a standard phenol/chloroform procedure. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: breast cancer

tag: tissue subtype

value: Invasive Micropapillary Carcinoma (IMPC)

tag: tumor grade


title: coc-16_B

scan_protocol: Standard Illumina scanning protocol

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

tag: disease state

value: cocaine addiction

tag: organ

value: Brain

value: Ventral midbrain

tag: sample type

value: Postmortem

tag: Cause of death

value: cocaine related


title: coc-16_C


title: B-cell_LMP2A_EBV_rep2

source_name: Human unsorted B cells from donor 2 infected with ΔLMP2A EBV

tag: ebv strain

value: Delta LMP2A

tag: donor

value: unsorted B cells


title: B-cell_LMP2A_EBV_rep1

source_name: Human unsorted B cells from donor 1 infected with ΔLMP2A EBV

tag: cell type


title: coc-16_A


title: con-15_C

value: control

value: hypertensive cardiomyopathy


title: B-cell_wt_EBV_rep4

source_name: Human unsorted B cells from donor 4 infected with wt EBV

value: wt


title: coc-38_B


title: ChIPseq_PolII_iSLK219

type: SRA

city: EMERYVILLE

first: ALEXANDRE

last: MERCIER

state: CA

address: 5300 CHIRON WAY

department: INFECTIOUS DISEASES

institute: NOVARTIS INSTITUTES FOR BIOMEDICAL RESEARCH

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8
ChIPseq: reads were aligned to the hg19 genome assembly using Bowtie2 (v2.1.0, default parameters)
ChIPseq: peaks were called using MACS 1.4.2 using the default parameters except when otherwise specified (see Samples section)
RNAseq: reads were aligned to the hg19 genome assembly using TopHat2 (v2.0.8b, default parameters)
RNAseq: gene expression analysis was performed with the Cufflinks/Cuffdiff package v2.1.1 using default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: ChIPseq: peak calling output files from the MACS program (tab-delimited text format). Contain peak genomic location, tag abundance and peak score (p-value, FDR)
Supplementary_files_format_and_content: RNAseq: output files from Cufflinks and Cuffdiff (tab-delimited format) that include FPKM values, gene expression ratios (LEC219 vs LEC) and statistical analysis (scores) for all hg19-annotated genes

source_name: Kidney epithelium

extract_protocol:
1 x 10^7 cells were fixed with 1% formaldehyde 5 minutes prior to harvest. Nuclei preparations were done using the truChIP High Cell Chromatin Shearing Kit with SDS from Covaris and chromatin was sheared with a Covaris E220 Ultrasonicator. The average size of chromatin fragments was ~200 bp. Antibodies for ChIP were coupled to Dynabeads (Invitrogen) and incubated with chromatin extracts for 4 hours at 4C in cold RIPA buffer (10 mM Tris pH 8.0, 1 mM EDTA, 150 mM NaCl, 5% glycerol, 0.1% Na deoxycholate, 0.1% SDS, 1% Triton X-100, protease inhibitors (Complete Mini, Roche)). Antibodies used for ChIP: rat α-LANA (Advanced Biotechnologies, 13-210-100), α-H3K4me3 (Abcam, ab8580), α-H3K27me3 (Millipore, 07-449), α-H3K36me3 (Abcam, ab9050), and α-Pol II (Santa Cruz Biotechnology, sc-899 X). The immunoprecipitated chromatin was sequentially washed in high salt RIPA buffer (500 mM NaCl) and LiCl wash buffer (50 mM Tris pH 8.0, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 0.5% Na deoxycholate). Chromatin crosslinks were reversed by incubating samples overnight at 65°C in the presence of proteinase K (200 µg/ml, Invitrogen). DNA was recovered using AMPure XP beads (Beckman Coulter, Inc).
Libraries were prepared according to Illumina's instructions (TruSeq ChIP Sample Prep Kit, part # 15034288)

treatment_protocol: When indicated, 1 µM doxycyclin (dox) and 500 µM phosphonoformic acid (PFA) were added to the culture medium for 72 hrs

value: Kidney epithelial cells

tag: infection

tag: chip antibody


title: IMPC_MP03_tumoral sample

description: Hybridized to SNP6.55

tag: tissue


title: B-cell_wt_EBV_rep2

source_name: Human unsorted B cells from donor 2 infected with wt EBV


title: IDC_D40_tumoral sample

description: Hybridized to SNP6.0

source_name: IDC tumoral sample

value: Invasive Ductal Carcinoma (IDC)


title: con-15_B


title: B-cell_wt_EBV_rep1

source_name: Human unsorted B cells from donor 1 infected with wt EBV


title: IMPC_MP07_tumoral sample

description: Hybridized to SNP6.56


title: con-15_A


title: coc-14_C


title: B-cell_wt_EBV_rep3

source_name: Human unsorted B cells from donor 3 infected with wt EBV


title: IDC_D39_tumoral sample

description: Hybridized to SNP6.0


title: Rag2 -/- H3K27me3 ChIP-Seq biorep 2 techrep 2

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

description: Sample 14

data_processing:
For the Genome Analyzer II System, basecalls were performed using manufacturer’s instructions. For the SOLiD 4 System, high-quality reads were matched to individual samples based on the barcode tag and using default parameters in SOLiD Experimental Tracking Software (SETS) v4.0.1. For SOLiD 5500xl, basecalls were performed using 5500 Series Genetic Analyzers Instrument Control Software v1.2. For the HiSeq 2000 System, basecalls were performed using manufacturer's instructions (CASAVA).
Alignment of reads to the mm9 genome was conducted using CASAVA Eland and BFast 0.7.0 for Illumina and SOLiD sequencing runs, respectively, according to manufacturer’s instructions. Only reads with a unique best scoring alignment were retained. Clonal artifacts were filtered out retaining the longer reads.
Aligned reads were processed using a previously described in-house ChIP-Seq analysis pipeline (Koch, Fenouil et al 2011).  Using a stepwise tag size extension in 10bp increments, fragment size was estimated in silico for DN and DP ChIPs.
Tags were then elongated to the estimated mean fragment size and converted to wig format using a binning window of 50bp. Replicate tracks were subsequently merged by addition. To account for differences in tag counts between DN and DP experiments, tag count normalization was performed by scaling DP datasets to DN tag counts. Visual inspection of invariant targets (e.g. Eβ for Ets1, β-actin for Pol II, H3K4me1/2, Mnase, the Hoxa locus for H3K27me3) allowed further fine tuning and scaling of DP tag-counts to reflect potential differences in signal to noise ratios between DN and DP experiments.
Peak detection was carried out with CoCAS using averaged into 50bp windows and converted to general feature format (GFF). Thresholds were 7.5 x SD + mean for the main window and 5 x SD + mean for the extension window. Artifacts were detected and removed by performing peak detection in CoCAS (using 2 X SD + mean and SD + mean as main and extension window thresholds, respectively) in reads originating from the Input treatment. Peaks were annotated to the nearest TSS, except in the case of intragenic peaks which were assigned to the surrounding gene. Peaks outside of [-5kb; +5kb] around known TSSs (refSeq, miRNA, rRNA, scRNA, snRNA, snoRNA and tRNA) were considered to be distal, while those falling within [-5kb; +5kb] around known TSSs were considered proximal. Distal peaks within a gene body were considered intragenic and those outside of gene bodies were considered intergenic.
Genome_build: mm9
Supplementary_files_format_and_content: Fragments were extended using an R pipeline described in Koch, Fenouil, Gut et al. 2011. Fixed-step 50bp wig files were generated using an R pipeline described in Koch, Fenouil, Gut et al. 2011. Peaks were called using CoCAS

source_name: primary Rag2 -/- thymocytes

growth_protocol: Thymuses were extracted from 5-6-week-old Rag2-/- knockout as well as C57BL/6 wild type mice and stored in RPMI medium. Cohorts of litter mates were used as biological replicates. To recover thymocytes, thymuses were subsequently passed twice through a 70µm Falcon cell strainer and stored in PBS. Cells were crosslinked 10 min in 10% formaldehyde followed by 5 min quenching in 250 mM glycine. DP cells were subsequently sorted via AutoMACS using, in turn, α-CD8-PE antibody conjugated to α-PE beads, and α-CD4 beads (Miltenyi). FACS profiles and cell purities were obtained for Rag2-/- and DP thymocytes via CD44-APC, CD25-FITC and CD8-PE, CD4-FITC staining, respectively

extract_protocol:
Phenol-chroloform
For ChIP-Seq, thymocytes were  aliquoted in crosslinked pellets of 5 107 cells and lysed by rotation for 10 min at 4°C in 2x 1.25ml LB1 (50mM Hepes pH 7.5, 140mM NaCl, 1mM EDTA, pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100). Following centrifugation at 1,350g for 5 minutes at 4°C, nuclei were subsequently treated with 2x1.25ml LB2 (200mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8) on a rotating wheel for 10 minutes at 4°C. Chromatin was resuspended in 1.5ml LB3 (1mM EDTA pH8, 0.5mM EGTA pH 8, 10mM Tris pH 8, 100mM, NaCl, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine) in 15ml polypropylene falcon tubes and then sonicated for 10 cycles (30 seconds on, 30 seconds off) at 40W using a VCX130 sonicator (VibraCell) down to an average size of about 250bp. 50µl aliquots were collected as Input controls. All buffers contained final concentrations of 1X protease inhibitors (Roche, France) as well as 0.2mM PMSF and 1μg /ml pepstatin. ChIPs were conducted using either α-rabbit (Ets1) or protein-G (all other ChIPs) DynaBeads (Invitrogen).Antibody and bead mixes were washed three times with 1ml BSA blocking buffer (0.5% BSA in 1x DPBS), incubated and rotated overnight at 4°C, and subsequently washed another three times  with 1ml BSA blocking buffer. Immunoprecipitation was carried out overnight in 750µl LB3 at 4°C on a rotating wheel. Samples were then washed 8 times in 1ml RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA pH 8, 1% NP-40, 0.7% Na-Deoxycholate) and once in 1ml TE buffer with 50mM NaCL. Two 15-min and 10-min subsequent elutions were carried out in a waterbath at 65°C, vortexing every other minute, for a final volume of 100µl. 100µl 1X elution buffer (50mM Tris pH 8, 10mM EDTA pH 8, 1% SDS) was added to eluates which were reverse-crosslinked overnight in a 65°C waterbath. Equal volumes of TE buffer (100µl) were added to samples as well as 0.2μg/ml RNAse A and placed at 37°C for 2 hours, followed by proteinase K treatment at 0.2μg/ml at 55°C. DNA purification was carried out via phenol-chloroform extraction followed by elution using QiaQuick PCR purification kits. (QiaGen) Samples were pooled per replicate then SpeedVac-ed down to 30µl. DNA quantification of eluates was obtained using Bioanalyzer High Sensitivity chips (Agilent). Library preparation was carried out as per manufacturer’s instructions (Illumina) using 10ng material. Samples were subsequently size-selected via gel migration and extraction, with average cut sizes at about 230 bp for DN and 250 bp for DP, including adapters.  Sequencing was performed using either Genome Analyzer II (Illumina) or SOLiD 5500xl sequencers (Applied Biosystems), whereby samples were sequenced at the CNAG, Barcelona, Spain and TAGC, Marseille, France, respectively. For SOLiD 5500xl sequencing, ChIP-seq libraries were been prepared according to the Life Technologies protocol, SOLiD ChIP-seq kit guide (A12066), using 15 PCR cycles. The quality of the libraries was checked with the BioAnalyzer DNA High sensitivity and by Q-PCR.

tag: strain

tag: age

value: 5-6 weeks

tag: genotype/variation

tag: cells used

tag: antibody

value: Abcam (ab6002)

tag: antibody quantity

value: 2 µg

tag: magnetic beads

value: Protein G dynabeads

tag: bead volume

tag: estimated fragment size


title: IDC_D24_tumoral sample

description: Hybridized to SNP6.0

value: breast cancer

tag: tissue subtype

tag: tumor grade


title: Rag2 -/- H3K27me3 ChIP-Seq biorep 2 techrep 1

description: Sample 13


title: coc-14_A

tag: disease state

value: cocaine addiction

tag: organ

tag: sample type

tag: Cause of death


title: Patient hiPSC-derived neural progenitor cells 4 a

city: New York

first: Kristen

last: Brennand

address: 1425 Madison Ave, 9-20B

department: Psychiatry

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: standard Affymetrix protocol

data_processing: Partek Genomics Suite

source_name: hiPSC-derived neural progenitor cells

label_protocol: GeneChip WT Sense Target Labeling and Control Reagents (900652) and GeneChip WT cDNA Synthesis and Amplification Kits (900672 and 900673)

growth_protocol: hiPSC forebrain NPCs were derived as described previously (Brennand et al., 2011). Forebrain NPCs were maintained at high density, grown on either Matrigel or PORN/Laminin-coated plates in NPC media (DMEM/F12, 1x N2, 1x B27-RA (Invitrogen), 1 μg/ml Laminin (Invitrogen) and 20 ng/ml FGF2 (Invitrogen) and split approximately 1:3-1:4 every week with Accutase (Millipore). Midbrain NPCs were maintained at high density, grown on either Matrigel or poly-ornithine/Laminin-coated plates in NPC media (DMEM/F12, 1x N2, 1x B27-RA (Invitrogen), 1 μg/ml Laminin (Invitrogen), 100 ng/ml FGF8 (Peprotech) and 200 ng/ml SHH (R&D) and split approximately 1:3-1:4 every week with Accutase (Millipore).  NPCs could be expanded up to 10 passages.

extract_protocol: Cells were lysed in RNA BEE (Tel-test, Inc). RNA was chloroform extracted, pelleted with isopropanol, washed with 70% ethanol and resuspended in water. RNA was treated with RQ1 RNAse-free DNAse (Promega) for 30 minutes at 37C and then the reaction was inactivated by incubation with EGTA Stop buffer at 65C for 10 minutes.

value: Schizophrenic

tag: gender

value: Male

tag: cell type

value: hiPSC-derived neural progenitor cells


title: Patient hiPSC-derived neural progenitor cells 4 c


title: SUDHL-4 cells cultured in suspension

description:
S4
B lymphocyte.
Enriched small RNA.

source_name: SUDHL-4 lymphoma cells, 24hrs

tag: cell line

value: B lymphocyte

tag: growth type

value: suspension

tag: time

source_name: SUDHL-4 lymphoma cells, 48hrs

value: B lymphocytes


title: IDC_D20_tumoral sample

description: Hybridized to SNP6.54

tag: tissue


title: Rag2 -/- H3K27me3 ChIP-Seq biorep 1 techrep 2

description: Sample 12

tag: strain

tag: age

tag: genotype/variation

tag: cells used

tag: antibody


title: con-13_C

first: Michael

value: control

value: Brain

value: Ventral midbrain

value: Postmortem

value: gun shot wound


title: Patient hiPSC-derived neural progenitor cells 1 c


title: con-13_B


title: Patient hiPSC-derived neural progenitor cells 4 b


title: coc-14_B

value: cocaine related


title: Patient hiPSC-derived neural progenitor cells 1 b


title: Rag2 -/- H3K4me3 ChIP-Seq biorep 2

description: Sample 10

value: 5-6 weeks

value: Diagenode (pAb-003-050)

tag: antibody quantity

tag: magnetic beads

tag: bead volume

tag: estimated fragment size


title: Rag2 -/- H3K27me3 ChIP-Seq biorep 1 techrep 1

description: Sample 11

value: Abcam (ab6002)

value: 2 µg

value: Protein G dynabeads


title: IDC_D30_tumoral sample

description: Hybridized to SNP6.0

value: breast cancer

tag: tissue subtype

value: Invasive Ductal Carcinoma (IDC)

tag: tumor grade


title: IDC_D19_tumoral sample

description: Hybridized to SNP6.0


title: con-13_A

tag: disease state

tag: organ

tag: sample type

tag: Cause of death


title: IDC_D18_tumoral sample

description: Hybridized to SNP6.0


title: Patient hiPSC-derived neural progenitor cells 1 a

value: Schizophrenic

tag: gender

value: Male

tag: cell type

value: hiPSC-derived neural progenitor cells


title: coc-12_C

value: cocaine addiction

tag: tissue


title: Patient hiPSC-derived neural progenitor cells 3 c

value: Female


title: Rag2 -/- H3K4me2 ChIP-Seq biorep 2

description: Sample 8

tag: strain

tag: age

value: Abcam (ab32356)


title: Patient hiPSC-derived neural progenitor cells 3 b


title: coc-12_B

value: Brain

value: Ventral midbrain


title: Rag2 -/- H3K4me2 ChIP-Seq biorep 1

description: Sample 7

tag: genotype/variation

tag: cells used


title: coc-12_A

value: Postmortem


title: Patient hiPSC-derived neural progenitor cells 3 a


title: Rag2 -/- H3K4me3 ChIP-Seq biorep 1

description: Sample 9

tag: antibody

tag: antibody quantity


title: con-11_C

value: control

value: arteriosclerotic cardiovascular disease


title: Patient hiPSC-derived neural progenitor cells 2 b


title: Patient hiPSC-derived neural progenitor cells 2 c


title: IDC_D02_tumoral sample

description: Hybridized to SNP6.0


title: IDC_D17_tumoral sample

description: Hybridized to SNP6.0


title: IDC_D01_tumoral sample

description: Hybridized to SNP6.0


title: Patient hiPSC-derived neural progenitor cells 2 a


title: Rag2 -/- RNA Pol II (N20) ChIP-Seq biorep 2

description: Sample 4

value: 5-6 weeks

value: Santa Cruz (sc-899x)

value: 5 µg

tag: magnetic beads

tag: bead volume


title: con-11_A


title: con-11_B


title: Control hiPSC-derived neural progenitor cells 4 c

value: Control


title: Rag2 -/- RNA Pol II (N20) ChIP-Seq biorep 1

description: Sample 3

value: Protein G dynabeads

tag: estimated fragment size


title: IDC_C23_tumoral sample

description: Hybridized to SNP6.0

value: breast cancer

tag: tissue subtype

value: Invasive Ductal Carcinoma (IDC)

tag: tumor grade


title: IDC_C21_tumoral sample

description: Hybridized to SNP6.0


title: coc-10_B

tag: disease state

tag: organ

value: cocaine related


title: Control hiPSC-derived neural progenitor cells 4 b

value: hiPSC-derived neural progenitor cells


title: coc-10_C

value: cocaine addiction

tag: sample type

tag: Cause of death


title: IDC_C51_tumoral sample

description: Hybridized to SNP6.0


title: IDC_C10_tumoral sample

description: Hybridized to SNP6.0


title: con-9_C

value: multiple gunshot wounds


title: Control hiPSC-derived neural progenitor cells 3 c

tag: gender

value: Female

tag: cell type


title: coc-10_A

value: Brain

tag: tissue


title: IDC_C34_tumoral sample

description: Hybridized to SNP6.0


title: Control hiPSC-derived neural progenitor cells 3 b


title: con-9_B

value: Ventral midbrain


title: IMPC_MP41_tumoral sample

description: Hybridized to SNP6.0

value: Invasive Micropapillary Carcinoma (IMPC)


title: Control hiPSC-derived neural progenitor cells 3 a


title: coc-8_C

value: Postmortem


title: con-9_A

value: control


title: Control hiPSC-derived neural progenitor cells 4 a


title: Control hiPSC-derived neural progenitor cells 2 c


title: Control hiPSC-derived neural progenitor cells 2 b


title: coc-8_B


title: Control hiPSC-derived neural progenitor cells 2 a


title: IMPC_MP44_tumoral sample

description: Hybridized to SNP6.0


title: con-7_C

value: arteriosclerotic cardiovascular disease


title: Control hiPSC-derived neural progenitor cells 1 b

value: Male


title: coc-8_A


title: IMPC_MP43_tumoral sample

description: Hybridized to SNP6.0


title: IMPC_MP49_tumoral sample

description: Hybridized to SNP6.0


title: con-7_B


title: IDC_C02_tumoral sample

description: Hybridized to SNP6.0


title: spleen-GA infected -tumor

city: Harbin

first: Zhijie

last: Li

address: No. 427 Maduan St.

institute: Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences

hyb_protocol: Hybridization was performed overnight on a μParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://www.mirbase.org/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 L 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics)

data_processing: Data were analyzed by first subtracting the background, then the signals were normalized using a Lowess (locally weighted regression) filter. The raw microarray data set was filtered according to a standard procedure to exclude spots with minimum intensity. It was arbitrarily set to an intensity parameter of P100 for the miRNA microarray data. Spots with diameters less than 10 μm and flagged spots were also excluded from the analyses.

organism: Gallus gallus

source_name: GA-infected splenic tumor

label_protocol: Labeling of total RNA was performed according to the protocol from LC Science for a single-color experiment with no modification.

extract_protocol: Total RNA from each tissue sample was extracted using TRK-1001 kit (LC Sciences) according to the manufacturer’s instructions.

value: MDV infected splenic tumor


title: con-7_A

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 Bioanalyzer.


title: IMPC_MP38_tumoral sample

description: Hybridized to SNP6.0


title: IMPC_MP33_tumoral sample

description: Hybridized to SNP6.0


title: Control hiPSC-derived neural progenitor cells 1 a

value: Control


title: spleen-GA infected

source_name: GA-infected non-tumorous spleen

value: MDV infected spleen


title: IMPC_MP50_tumoral sample

description: Hybridized to SNP6.0

value: breast cancer


title: spleen-control

source_name: control spleen

value: normal spleen


title: IMPC_MP57_tumoral sample

description: Hybridized to SNP6.0


title: Control hiPSC-derived neural progenitor cells 1 c


title: IMPC_MP36_tumoral sample

description: Hybridized to SNP6.0


title: IMPC_MP32_tumoral sample

description: Hybridized to SNP6.0


title: IDC_C14_tumoral sample

description: Hybridized to SNP6.0

value: Invasive Ductal Carcinoma (IDC)


title: IMPC_MP59_tumoral sample

description: Hybridized to SNP6.0


title: IMPC_MP29_tumoral sample

description: Hybridized to SNP6.0


title: IMPC_MP55_tumoral sample

description: Hybridized to SNP6.0


title: IMPC_MP42_tumoral sample

description: Hybridized to SNP6.0


title: IMPC_MP27_tumoral sample

description: Hybridized to SNP6.0


title: IMPC_MP45_tumoral sample

description: Hybridized to SNP6.0


title: IMPC_MP26_tumoral sample

description: Hybridized to SNP6.0


title: IMPC_MP31_tumoral sample

description: Hybridized to SNP6.0


title: IMPC_MP21_tumoral sample

description: Hybridized to SNP6.0


title: IMPC_MP20_tumoral sample

description: Hybridized to SNP6.0


title: DG_Flx-4wks

city: Tokyo

first: Eri

last: Segi-Nishida

state: Tokyo

address: Niijuku 6-3-1

institute: Tokyo University of Science

description: Gene expression data from chronic fluoxetine-treated mouse DG

hyb_protocol: Following fragmentation, 5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip® Mouse Genome 430A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned by GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: mouse dentate gyrus of hippocampus, fluoxetine (22mg/kg), 28days

label_protocol: The total RNA samples of the same groups were put together. From each group, 100 ng of total RNA was amplified with 3’IVT Express kit (Affymetrix, Inc., Santa Clara, CA, USA).

extract_protocol: Total RNA was extracted from the dentate gyrus dissected by using an RNeasy micro kit (Qiagen) .

treatment_protocol: Bilateral ECS (current, 25 mA; shock duration, 1 sec; frequency, 100 pulse/sec; pulse width, 0.5 msec) was administered via moistened, spring-loaded ear-clip electrodes with a pulse generator (ECT Unit; Ugo Basile, Comeria, Italy) to mice that were anesthetized with isoflurane (1.5 to 2%) in order to avoid sudden unexpected death associated with seizures.ECS was administered 4 times a week for 3 weeks. The Sham-treated animals were handled in an identical manner to the ECS-treated animals, without the administration of shock. For chronic SSRI administration, fluoxetine hydrochloride was dissolved in drinking water and orally applied at a dose of 22 mg/kg/day for 4 weeks. The fluoxetine solutions were prepared everyday, and daily fluoxetine intake was determined for individual mice on the basis of the water consumption during the preceding 24 h and the body weight measured every other day. Saccharin (0.2%) was included in the fluoxetine solution to keep water intake comparable to the baseline.

tag: strain

value: dentate gyrus of hippocampus


title: IMPC_MP06_tumoral sample

description: Hybridized to SNP6.0

source_name: IMPC tumoral sample


title: DG_Veh-4wks

description: Gene expression data from vehicle-treated mouse DG

source_name: mouse dentate gyrus of hippocampus, water, 28days


title: IMPC_MP08_tumoral sample

description: Hybridized to SNP6.0


title: DG_ECS-11times

description: Gene expression data from chronic ECS-treated mouse DG

source_name: mouse dentate gyrus of hippocampus, ECS, 11 times, 6 h


title: IMPC_MP12_tumoral sample

description: Hybridized to SNP6.0


title: Class IV da Neuron-2

city: Fairfax

first: Daniel

middle: N

last: Cox

state: VA

address: 4400 University Drive, MSN 2A1

department: School of Systems Biology, Krasnow Institute

institute: George Mason University

description: Transcriptional Profile of Class IV da neurons

hyb_protocol: The Cy3- labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Drosophila Melanogaster Genome Oligo Microarrays 4 x 44K (table 3) using Agilent’s recommended hybridization chamber and oven.Finally, the microarrays were washed once with 6x SSPE buffer containing 0.005% Nlauroylsarcosine for 1 min at room temperature followed by a second wash with pre-heated 0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies)

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences.

source_name: PPK-1.9 GAL4, UAS-mCD8::GFP

label_protocol: 250 ng of each of the cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

growth_protocol: Drosophila stocks were raised on standard cornmeal-molasses-agar media at 25˚C.

extract_protocol: The isolation and purification of C-IV da neurons was performed as previously described (Iyer et al., 2009).  Briefly, 40-50 age-matched third instar larvae expressing mCD8::GFP under the control of the GAL4ppk.1.9 driver were collected and washed several times in ddH20. The larvae were then rinsed in RNAse away, ddH20 and finally dissected. The tissue was then dissociated using a combination of enzymatic and mechanical perturbations to yield single cell suspensions which were filtered using a 30µm membrane. The filtrate is then incubated with magnetic beads coupled with rat anti-CD8 antibody (Invitrogen) for 60 minutes. Finally the C-IV neurons attached to the magnetic beads were then separated using a powerful magnetic field. The cells were washed 3-4 times, before lysing them in SuperAmp™ (Miltenyi Biotec) RNA lysis buffer followed by storage of the RNA at -80˚C.

treatment_protocol: Age-matched third larvae were used without any treatment.

value: Multidendritic Class IV neurons

tag: developmental stage

value: third larvae


title: DG_sham-11times

description: Gene expression data from sham-treated mouse DG

source_name: mouse dentate gyrus of hippocampus, sham, 11 times, 6 h


title: non-SP fraction 4T1_rep1

city: Fukuoka

first: kenzaburo

last: tani

address: 3-1-1 Maidashi

department: Medical Institute of Bioregulation

institute: Kyushu University

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8×60K ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

source_name: non-SP fraction 4T1

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from tissues using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

tag: cell line


title: IMPC_MP13_tumoral sample

description: Hybridized to SNP6.0


title: IMPC_MP01_tumoral sample

description: Hybridized to SNP6.0


title: IMPC_MP18_tumoral sample

description: Hybridized to SNP6.0


title: SP fraction_ 4T1_rep1

source_name: SP fraction_ 4T1


title: IMPC_MP14_tumoral sample

description: Hybridized to SNP6.0


title: IMPC_MP02_tumoral sample

description: Hybridized to SNP6.0


title: IMPC_MP16_tumoral sample

description: Hybridized to SNP6.0


title: IDC_D22_tumoral sample

description: Hybridized to SNP6.0

source_name: IDC tumoral sample


title: ES-SCs 1

status: Public on Mar 28 2014

city: Sapporo

first: Ken-ichiro

last: Seino

state: Hokkaido

address: Kitaku, Kita 15 Nishi 7

institute: Hokkaido Univ.

description: Gene expression of ESdSC.

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture. 40 ul of the solution was hybridized to Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting (Scan resolution 3 um).

data_processing: The scanned images were analyzed with Feature Extraction Software10.7.3.1 (Agilent).

source_name: ESdSC, replicate 1

label_protocol: Labeled cRNA was prepared using the Low Input Quick Amp Labeling kit (Agilent) following the manufacturer's recommendations.

extract_protocol: RNA was prepared using the RNeasy Mini kit (QIAGEN) following the manufacturer's recommendations.  The protocol includes an on-column DNase digestion. RNA  quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: ES cells were induced into ESdSCs and ESdDCs by  adding of following cytokines; for ESdDCs, M-CSF (from day 5 to day 10), GM-CSF (from day 5 to day 17) and IL-4 (from day 10 to day 17), for EDdSCs, M-CSF (from day 5 to day 10), GM-CSF (from day 5 to day 20), IL-4 (from day 15 to day 26) and LPS (from day 24 to day 26).

value: ES

tag: genotype/variation

value: ESdSC


title: IMPC_MP04_tumoral sample

description: Hybridized to SNP6.0


title: IDC_C09_tumoral sample

description: Hybridized to SNP6.0


title: ES-DCs 1

description: Gene expression of ESdDC.

source_name: ESdDC, replicate 1

value: ESdDC


title: ES-DCs 2

description: Gene expression of ESdDC.

source_name: ESdDC, replicate 2


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at12:00_Per3_4\4genotype_Subject_BB0289_R_T12

status: Public on Jan 23 2014

city: Guildford

first: Emma

last: Laing

address: Stag Hill

country: United Kingdom

institute: University of Surrey

description: Blood take at 12:00 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0289)

hyb_protocol: Labelled cRNA (1.65 μg) was hybridized on a Whole Human Genome 4 x 44K custom oligonucleotide microarray (G2514F, AMADID 026817; Agilent Technologies). Standard manufacturer's instructions for one-colour gene expression hybridization and washing steps were followed. The microarrays were hybridized at 65°C for 17 h in an Agilent hybridization oven with rotisserie at 10 rpm. The microarrays were washed with Agilent Wash Buffer 1, pre-warmed Wash Buffer 2 (37C) and acetonitrile according to the manufacturer’s instructions. The last washing step was performed with Agilent Stabilization and Drying Solution for 30 sec.

scan_protocol: The processed microarrays were scanned using an Agilent Microarray Scanner with a resolution of 5 μm, exploiting the extended dynamic range feature. The two images derived from each slide scanned at 10% and 100% PMT were imported into Agilent Feature Extraction software (Version 10.7.1.1) for image analysis.

data_processing: Individual samples were filtered based on AgilentQC metrics of reproducibility statistics, minimum detection level estimates and feature flags. Samples with a median coefficient of variation of less than 10% in spike ins or non-control replicated probes (NCRPs) were retained and quantile-normalised using the R Bioconductor package limma. NCRPs along with their corresponding flags were averaged. Probes with more than 5 flagged samples within a subject in more than half of the total number of subjects were excluded. In addition, for time-series analyses, series with 2 consecutive or more than 2 missing time points were excluded.

label_protocol: cRNA was synthesized and fluorescently labelled with Cy3-CTP from 100 ng of total RNA using Agilent's Low Input Quick Amp Labeling Kit.

growth_protocol: Blood samples were collected via an indwelling venous cannula sited in the forearm for minimum discomfort and restriction of movement. Cannulae were kept patent by the use of sterile saline. Each sample tube was coded for subject and sample collection time (participant code/sample type/sequential number)

extract_protocol: Total RNA was isolated using a PAXgene Blood RNA Kit and a QiaCube robot (Qiagen, Hilden, Germany). The RNA was quantified and the A260/280 nm and A260/230 nm ratios were determined using a NanoDrop ND1000 spectrophotometer (Wilmington, DE). RNA quality was assessed using the Bioanalyzer 2100 (Agilent, Santa Clara, CA).

treatment_protocol: 2.5 ml of blood is drawn into the PAXGene tube at each sampling point. The tube is inverted 10 times to mix. The tube is then stored at room temperature for 4 hours in upright position. The tube is transferred to -50°C and placed lying down (never in upright position as this may cause the tube to crack) for storage at the university of Surrey Clinical Research Centre. The tube is transferred on ice to University of Surrey Faculty of Health and Medical Sciences for storage/processing

value: Blood

tag: sleep timing

value: Out of phase with respect to melatonin

tag: per3 genotype

tag: time sample taken

tag: day sample was taken in protocol

tag: time point

tag: subject


title: IDC_513036_tumoral sample

description: Hybridized to SNP6.0

tag: tissue subtype

tag: tumor grade

value: ND


title: ES-SCs 2

description: Gene expression of ESdSC.

source_name: ESdSC, replicate 2


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at04:05_Per3_4\4genotype_Subject_BB0289_R_T10

description: Blood take at 04:05 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0289)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at20:09_Per3_4\4genotype_Subject_BB0289_R_T14

description: Blood take at 20:09 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0289)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at08:08_Per3_4\4genotype_Subject_BB0289_R_T11

description: Blood take at 08:08 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0289)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at16:25_Per3_4\4genotype_Subject_BB0289_R_T13

description: Blood take at 16:25 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0289)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at00:05_Per3_4\4genotype_Subject_BB0289_R_T9

description: Blood take at 00:05 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0289)


title: IDC_522419_tumoral sample

description: Hybridized to SNP6.0


title: IMPC_MP10_tumoral sample

description: Hybridized to SNP6.0

value: Invasive Micropapillary Carcinoma (IMPC)


title: IMPC_MP17_tumoral sample

description: Hybridized to SNP6.0


title: Class IV da Neuron-1


title: IDC_497927_tumoral sample

description: Hybridized to SNP6.0


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at20:08_Per3_4\4genotype_Subject_BB0289_R_T8

description: Blood take at 20:08 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0289)


title: Blood_TakenInPhaseWithRespectToMelatonin_at20:07_Per3_4\4genotype_Subject_BB0289_R_T1

description: Blood take at 20:07 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0289)

value: In phase with respect to melatonin


title: Blood_TakenInPhaseWithRespectToMelatonin_at04:06_Per3_4\4genotype_Subject_BB0289_R_T3

description: Blood take at 04:06 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0289)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at09:57_Per3_4\4genotype_Subject_BB0272_R_T12

description: Blood take at 09:57 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0272)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at06:00_Per3_4\4genotype_Subject_BB0272_R_T11

description: Blood take at 06:00 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0272)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at22:00_Per3_4\4genotype_Subject_BB0272_R_T9

description: Blood take at 22:00 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0272)