title: Treated with Aphidicolin for 96h in differentiation medium rep3 [9479628135_I_Grn.idat]

description: replicate 3

value: Aphidicolin


title: Treated with Aphidicolin and AZD7762 for 96h in differentiation medium rep2 [9479628135_K_Grn.idat]

status: Public on Jul 28 2015

type: RNA

city: Singapore

first: Kevin Andrew

last: Gonzales

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were rank invariant normalized using BeadStudio

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: H1 hESCs

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

extract_protocol: RNA was extracted with Trizol reagent, followed by Dnase I treatment and clean-up with PureLink RNA Mini kit in accordance with the prescribed protocol provided with the kit.

tag: passage number

tag: treatment type

value: Aphidicolin and AZD7762

tag: treatment length

value: 96 hours

tag: incubation medium

value: mTeSR1 without select factors


title: Treated with Aphidicolin and AZD7762 for 48h in differentiation medium rep2 [9479628135_B_Grn.idat]

description: replicate 2

value: 48 hours


title: Treated with Aphidicolin for 96h in differentiation medium rep2 [9479628135_H_Grn.idat]

description: replicate 2


title: Treated with DMSO for 96h in differentiation medium rep2 [9479628135_E_Grn.idat]

description: replicate 2

value: DMSO


title: Treated with Aphidicolin for 96h in differentiation medium rep1 [9479628135_G_Grn.idat]

description: replicate 1


title: Treated with Aphidicolin and AZD7762 for 48h in differentiation medium rep1 [9479628135_A_Grn.idat]

description: replicate 1


title: 9374342135_R05C01 Normal 9

status: Public on Jul 29 2015

type: genomic

city: Toronto

first: Daniel

last: De Carvalho

state: ON

address: 101 College St

country: Canada

institute: Princess Margaret Cancer Centre

description: normal oral cavity

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

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

data_processing: GenomeStudio Software 2011.1

label: Cy5 and Cy3

molecule: genomic DNA

source_name: oral cavity

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from oral samples using Qiagen DNeasy Kit according to standard instructions

tag: sample type

value: genomic

tag: disease state

value: Normal


title: 9374342135_R04C01 Normal 7

description: normal oral cavity


title: Treated with DMSO for 96h in differentiation medium rep3 [9479628135_F_Grn.idat]

description: replicate 3


title: Treated with Aphidicolin for 48h in differentiation medium rep2 [9479628134_K_Grn.idat]

description: replicate 2


title: Treated with DMSO for 48h in differentiation medium rep3 [9479628134_I_Grn.idat]

description: replicate 3


title: 9374342135_R02C02 Normal 4

description: normal oral cavity


title: Treated with Aphidicolin for 48h in differentiation medium rep3 [9479628134_L_Grn.idat]

description: replicate 3


title: 9374342135_R03C01 Normal 5

description: normal oral cavity


title: Treated with Aphidicolin and AZD7762 for 48h in differentiation medium rep3 [9479628135_C_Grn.idat]

description: replicate 3


title: Pre-treated with Aphidicolin for 0h rep1 [9479628134_D_Grn.idat]

description: replicate 1

value: 0 hours


title: Treated with DMSO for 96h in differentiation medium rep1 [9479628135_D_Grn.idat]

description: replicate 1


title: Treated with DMSO for 48h in differentiation medium rep2 [9479628134_H_Grn.idat]

description: replicate 2


title: Treated with Aphidicolin and AZD7762 for 96h in pluripotency medium rep1 [7680504078_J_Grn.idat]

description: replicate 1


title: Pre-treated with Aphidicolin for 0h rep3 [9479628134_F_Grn.idat]

description: replicate 3


title: Pre-treated with DMSO for 0h rep1 [9479628134_A_Grn.idat]

description: replicate 1


title: D0_CLL315

city: Brisbane

first: Nicholas

last: Saunders

address: 37 Kent Street

country: Australia

institute: University of Queensland Diamantina Institute

description: Monocytes Sensitive CLL

hyb_protocol: Standard Illumina hybridisation protocol

data_processing: Data have been background corrected and quantile normalized using control probe with the neqc function of the limma R package (v3.24.4)

label: Biotin

source_name: sensitive CLL patient_CD14 monocytes_Day 0

label_protocol: Biotinylated cRNA was prepared with the Illumina TotalPrep RNA Amplification Kit (Applied Biosystems) for Illumina Arrays

growth_protocol: CLL PBMCs were isolated from patient blood. CD14 positive monocytes were selected from PBMCs on day 0 using MACS microbeads. CLL PBMCs were maintained in RPMI 10% FCS for seven days and MDCs isolated after removal on non-adherent cells

extract_protocol: RNA was extracted with Bioline Isolate II RNA Micro kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser

treatment_protocol: Untreated

tag: subject status

value: Chronic lymphocytic leukemia patient

tag: antibody response

value: Sensitive

tag: cell type

value: CD14 monocytes


title: Pre-treated with DMSO for 0h rep3 [9479628134_C_Grn.idat]

description: replicate 3


title: Treated with DMSO for 48h in differentiation medium rep1 [9479628134_G_Grn.idat]

description: replicate 1


title: Treated with Aphidicolin for 96h in pluripotency medium rep2 [7680504078_H_Grn.idat]

description: replicate 2


title: Treated with Aphidicolin and AZD7762 for 96h in pluripotency medium rep2 [7680504078_K_Grn.idat]

description: replicate 2


title: Treated with Aphidicolin for 96h in pluripotency medium rep1 [7680504078_G_Grn.idat]

description: replicate 1


title: Treated with DMSO for 96h in pluripotency medium rep2 [7680504078_E_Grn.idat]

description: replicate 2


title: 9374342135_R01C02 Normal 2

description: normal oral cavity


title: Treated with Aphidicolin and AZD7762 for 96h in pluripotency medium rep3 [7680504078_L_Grn.idat]

description: replicate 3


title: 9374342135_R02C01 Normal 3

description: normal oral cavity


title: Pre-treated with Aphidicolin for 0h rep2 [9479628134_E_Grn.idat]

description: replicate 2


title: Treated with DMSO for 96h in pluripotency medium rep3 [7680504078_F_Grn.idat]

description: replicate 3


title: Treated with DMSO for 96h in pluripotency medium rep1 [7680504078_D_Grn.idat]

description: replicate 1


title: Treated with Aphidicolin and AZD7762 for 48h in pluripotency medium rep3 [7680504078_C_Grn.idat]

description: replicate 3


title: Treated with Aphidicolin for 96h in pluripotency medium rep3 [7680504078_I_Grn.idat]

description: replicate 3


title: Treated with Aphidicolin and AZD7762 for 48h in pluripotency medium rep1 [7680504078_A_Grn.idat]

description: replicate 1


title: Pre-treated with DMSO for 0h rep2 [9479628134_B_Grn.idat]

description: replicate 2


title: Pre-treated with DMSO for 0h rep3 [7680504076_C_Grn.idat]

description: replicate 3


title: 9374342135_R01C01 Normal 1

description: normal oral cavity


title: Treated with Aphidicolin for 48h in pluripotency medium rep2 [7680504076_K_Grn.idat]

description: replicate 2


title: Treated with DMSO for 48h in pluripotency medium rep2 [7680504076_H_Grn.idat]

description: replicate 2


title: Treated with DMSO for 48h in pluripotency medium rep3 [7680504076_I_Grn.idat]

description: replicate 3


title: Pre-treated with DMSO for 0h rep1 [7680504076_A_Grn.idat]

description: replicate 1


title: MIV-Luc shIL13RA2 - IL13 sample 1

city: Nicosia

first: Panagiotis

last: Papageorgis

address: 75, Kallipoleos avenue

department: Biological Sciences

country: Cyprus

institute: University of Cyprus

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Hybridization solution was prepared using the Affymetrix HWS Kit according to NuGEN´ Applause WT Amp Plus System User Guide. The final concentration of cDNA is between 18 and 23 ng/μl.Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the ATLAS Biolabs GmbH (Berlin, Germany) microarray core facility

scan_protocol: Scanning was performed with the GeneChip Scanner 3000 7G (Affymetrix), which is controlled by Affymetrix´ GeneChip Command Console Software (AGCC)

data_processing: Raw data analysis was performed with Affymetrix´ software Expression Console v1 using the RMA algorithm.

source_name: MCF10CA1a cell line

label_protocol: cDNA synthesis was done with NuGEN´s Applause WT Amp System according to the manufacturers’ instructions, starting with 100 ng of total RNA. NuGEN’s Encore Biotin Module was used to fragment 2.5 μg cDNA  followed by Biotin-labeling according to the manufacturers’ instructions.

growth_protocol: MCF10CA1a cells were maintained in DMEM F/12 medium containing 5% heat inactivated horse serum, 10 μg/ml insulin, 20 ng/ml EGF, 0.1 ng/ml cholera enterotoxin, 0.5 μg/ml hydrocortisone and 1% penicillin/streptomycin.

extract_protocol: Total RNA was isolated from 1 million cells using the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

tag: cell line

value: breast cancer

tag: construct

tag: treatment

value: Mock


title: 13-029M

first: Matthew

last: Gazzellone

address: 686 Bay Street

institute: The Centre for Applied Genomics

hyb_protocol: RA1 resuspended DNA was loaded onto LCG BeadChip arrays. After overnight incubation at 48C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining LCG BeadChip arrays were coated with XC4/ethanol, dried for 10-15 minutes in a flow hood and scanned on an iScan Reader (Illumina).

data_processing: Genomic DNA extracted from saliva was genotyped using the Illumina HumanOmni2.5M-8v1-1_B. The processed data file "matrix_processed.txt" (available on the series record) contains the GC score, theta, R, B allele frequency, and log R ratios.

label: Cy3 and Cy5

source_name: Saliva

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37C using amplification master mix (LCG-MSM) and primer/neutralization mix (LCG-RPM). After incubation the amplified DNA was fragmented with fragmentation mix (LCG-FMS), precipitated with isopropanol and precipitation mix (LCG-PM1) and resuspended in hybridization buffer (RA1).

extract_protocol: Oragene saliva kits were heated o/n (5pm - 9am) at 50C in an air oven.  OG500 saliva kits collected from adults were extracted using Puregene chemistry on an AutopureLS automated DNA extractor. Saliva lysates were RNase a treated prior to extracting using either a 5.0ml or 2.5ml lysate protocol depending on collected saliva volume. OG575 saliva kits collected from children were extracted manually using same Puregene chemistry and RNase A treatment.  Pelleted DNA was rehydrated in TE overnight and quantitated next day using Hoescht dye and FLX800 Flurometer.

tag: tissue

value: Saliva

tag: gender

value: Female

tag: patient relationship

value: parent


title: Pre-treated with Aphidicolin for 0h rep1 [7680504076_D_Grn.idat]

description: replicate 1


title: Pre-treated with Aphidicolin for 0h rep2 [7680504076_E_Grn.idat]

description: replicate 2


title: MIV-Luc shIL13RA2 + IL13 sample 1


title: 13-032M


title: MIV-Luc shIL13RA2 + IL13 sample 2


title: Treated with Aphidicolin for 48h in pluripotency medium rep1 [7680504076_J_Grn.idat]

description: replicate 1

value: Aphidicolin


title: MIV-Luc shSCR + IL13 sample 1

value: pLKO-shSCR


title: MIV-Luc shIL13RA2 - IL13 sample 2


title: MIV-Luc shSCR + IL13 sample 2


title: Treated with Aphidicolin and AZD7762 for 48h in pluripotency medium rep2 [7680504078_B_Grn.idat]

description: replicate 2

value: Aphidicolin and AZD7762


title: Pre-treated with DMSO for 0h rep2 [7680504076_B_Grn.idat]

description: replicate 2


title: Treated with Aphidicolin for 48h in pluripotency medium rep3 [7680504076_L_Grn.idat]

description: replicate 3


title: Treated with DMSO for 48h in pluripotency medium rep1 [7680504076_G_Grn.idat]

description: replicate 1


title: Treated with Aphidicolin for 48h in differentiation medium rep1 [9479628134_J_Grn.idat]

description: replicate 1

value: mTeSR1 without select factors


title: 13-032f

value: Male


title: 13-029F


title: Pre-treated with Aphidicolin for 0h rep3 [7680504076_F_Grn.idat]

description: replicate 3


title: 12-0002F


title: 12-0002C

value: proband

value: Cerebral Palsy


title: 7-02C


title: 12-0008M


title: 12-0006M


title: 12-0007C


title: 12-0006F


title: 12-0006C


title: 13-029C


title: MIV-Luc shSCR - IL13 sample 2


title: 10-034M


title: MIV-Luc shSCR - IL13 sample 1


title: 10-034F


title: 13-042C


title: 13-043C


title: 10-038M


title: 10-036M


title: 10-034C


title: 10-036F


title: 10-036C


title: 13-042M


title: 13-043F


title: 13-042F


title: 10-039F


title: 10-038F


title: 10-039M


title: 10-038C


title: 13-032C


title: 12-0008C


title: 10-037C


title: 10-037M


title: 13-028M


title: 13-014M


title: 13-028C


title: 10-037F


title: 10-035M


title: 13-014C


title: 13-014F


title: 10-039C


title: 1-013M


title: 10-035C


title: 1-013C


title: 1-013F


title: 13-043M


title: 1-009M


title: 1-011M


title: 1-011F


title: 1-009C


title: 1-011C


title: 4-30M


title: 7-02M


title: 7-02F


title: 4-30F


title: 4-30C


title: 4-15C


title: 13-044M


title: 1-009F


title: 4-15M


title: 13-044F


title: 4-21M


title: 13-044C


title: 4-20M


title: 4-20C


title: 4-22F


title: 4-22M


title: 4-17F


title: 4-22C


title: 4-24C


title: 4-17M


title: 4-21C


title: 4-23M


title: 4-25M


title: 4-27C


title: 4-27M


title: 4-31F


title: 4-31C


title: 4-31M


title: 4-17C


title: 4-26F


title: 4-26M


title: 4-23F


title: 4-37F


title: 4-23C


title: 6-06F


title: 6-02M


title: 6-06C


title: 6-06M


title: 4-24M


title: 7-01M


title: 6-02F


title: 4-35F


title: 4-35M


title: 4-34M


title: 4-35C


title: 4-25C


title: 4-36F


title: 4-37C


title: 4-36C


title: 4-33M


title: 4-33C


title: 4-13C


title: 4-26C


title: 8-03F


title: 6-07F


title: 6-07M


title: 8-03C


title: 6-05F


title: 6-05M


title: 8-02M


title: 4-34F


title: 6-05C


title: 8-02F


title: 8-02C


title: 4-34C


title: 8-01M


title: 6-03C


title: 8-03M


title: 7-01C


title: 6-01M


title: 8-01F


title: 7-01F


title: 4-36M


title: 8-01C


title: 6-01F


title: 4-13F


title: 6-04C


title: 6-07C


title: 6-04M


title: 4-14F


title: 6-03F


title: 4-14C


title: 6-03M


title: 4-19C


title: 4-14M


title: 4-10M


title: 4-19M


title: 4-12C


title: 4-11C


title: 4-11F


title: 4-16C


title: 4-12M


title: 4-12F


title: 4-16F


title: 4-16M


title: 4-18F


title: 4-18M


title: 4-11M


title: 3-06C


title: 3-07C


title: 3-03M


title: 3-02C


title: 3-03F


title: 12-0001C


title: 13-016C


title: 3-09C


title: 12-0022M


title: 13-036M


title: 13-036C


title: 13-037F


title: 13-036F


title: 13-037M


title: 3-12M


title: 12-0002M


title: 3-15M


title: 3-12F


title: 3-15F


title: 3-05C


title: 13-037C


title: 3-14M


title: 3-15C


title: 3-01F


title: 3-14F


title: 3-13M


title: 3-13F


title: 3-04M


title: 3-13C


title: 3-12C


title: 3-11M


title: 3-11F


title: 3-08C


title: 3-08M


title: 3-08F


title: 3-11C


title: 3-05M


title: 3-14C


title: 3-04F


title: 3-10F


title: 3-09M


title: 3-10M


title: 3-06F


title: 3-07F


title: 3-09F


title: 3-07M


title: 3-03C


title: 3-04C


title: 13-020F


title: 13-020M


title: 13-041C


title: 13-041M


title: 13-006C


title: 13-006M


title: 13-017C


title: 10-031C


title: 13-040C


title: 13-017M


title: 13-038F


title: 3-02F


title: 3-06M


title: 3-01M


title: 13-038M


title: 10-018F


title: 10-018C


title: 10-018M


title: 10-025F


title: 10-029C


title: 10-029M


title: 13-041F


title: 12-0004F


title: 12-0003C


title: 12-0004M


title: 12-0004C


title: 12-0010M


title: 12-0010C


title: 13-038C


title: 12-0003M


title: 13-040M


title: 13-040F


title: 10-032F


title: 10-032M


title: 10-029F


title: 3-02M


title: 10-021M


title: 10-031M


title: 12-0005F


title: 12-0010F


title: 10-032C


title: 10-031F


title: 10-021C


title: 10-021F


title: 13-016M


title: 13-016F


title: 12-0005M


title: 13-023C


title: 13-023M


title: 13-023F


title: 13-026F


title: 4-10C


title: 4-10F


title: 13-026C


title: 4-09C


title: 10-026M


title: 10-026C


title: 10-022C


title: 10-019F


title: 10-022F


title: 10-026F


title: 12-0005C


title: 10-020M


title: 10-019M


title: 10-028C


title: 10-025M


title: 10-025C


title: 10-023M


title: 10-020F


title: 4-09M


title: 10-024M


title: 10-024F


title: 10-028M


title: 10-023C


title: 10-027C


title: 10-017M


title: 13-026M


title: 10-017C


title: 10-027F


title: 10-017F


title: 13-022M


title: 13-013F


title: 1-010M


title: 1-008C


title: 13-022F


title: 1-008M


title: 1-007F


title: 1-008F


title: 1-001M


title: 1-007C


title: 13-018C


title: 13-018M


title: 13-008M


title: 13-007C


title: 13-008C


title: 10-020C_A


title: 13-008F


title: 1-007M


title: 13-018F


title: 10-027M


title: 4-07M


title: 13-013M


title: 1-006F


title: 1-006M


title: 1-005C


title: 1-004C


title: 1-005F


title: 4-06C


title: 1-004F


title: 1-004M


title: 1-005M


title: 4-06F


title: 4-06M


title: 4-0008C


title: 10-013C


title: 10-014F


title: 10-013M


title: 4-0008M


title: 1-006C


title: 4-02MO


title: 4-02C


title: 1-003C


title: 4-02FA


title: 1-003F


title: 1-002C


title: 4-04C


title: 1-001C


title: 10-013F


title: 10-016C


title: 10-011F


title: 10-014M


title: 1-002M


title: 10-016M


title: 4-04F


title: 1-003M


title: 1-002F


title: 10-014C


title: 10-016F


title: 4-05C


title: 4-04M


title: 4-05F


title: 4-01MO


title: 4-01C


title: 4-01FA


title: 10-009F


title: 10-008C


title: 10-008F


title: 10-007F


title: 10-006C


title: 10-007M


title: 10-011C


title: 13-004F


title: 13-004M


title: 10-011M


title: 13-004C


title: 13-003F


title: 13-003C


title: 13-002F


title: 4-05M


title: 13-007F


title: 10-015M


title: 10-012C


title: 10-015C


title: 13-007M


title: 10-012F


title: 13-022C


title: 10-015F


title: 13-019M


title: 10-012M


title: 10-008M


title: 13-019C


title: 13-009M


title: 13-009F


title: 10-006M


title: 10-007C


title: 1-010C


title: 10-005C


title: 13-009C


title: 10-005M


title: 13-005F


title: 10-006F


title: 13-005M


title: 13-002M


title: 13-002C


title: 10-005F


title: 10-002-C


title: 10-002-M


title: 13-001F


title: 10-002-F


title: 13-005C


title: 10-001-C


title: 4-03C


title: 10-010C


title: 4-03FA


title: 13-001C


title: 10-010M


title: 10-009M


title: 10-001-M


title: 10-001-F


title: 10-004-C


title: 10-004-M


title: 10-004-F


title: 13-001M


title: 10-003-F


title: 10-010F


title: 10-003-M


title: 4-03MO


title: 10-003-C


title: ST WT biol1 over ST rpoN_compl biol1

city: Ede

first: Jos

last: Boekhorst

address: Kernhemseweg 2

country: Netherlands

institute: NIZO food research

description: Expression profiles of the rpoN deletion mutant (ΔrpoN) and the complemented strain (ΔrpoN-comp) were compared to the parental strain (WT) at static growth

hyb_protocol: Hybridization was performed as described in Mols et al., 2013.

scan_protocol: Slides were scanned with Agilent G2505C scanner

data_processing: Data were normalized using Lowess normalisation as available in MicroPrep and corrected for inter-slide differences. Median intensity of the different probes per gene and biological replicate was selected as the gene expression intensity.

organism: Bacillus cereus ATCC 14579

source_name: WT cells grown statically until OD(600nm)=0.2

label_protocol: Cy3 and Cy5 labeling of the cDNA was performed with CyScribe Post-Labeling kit (GE Healthcare)

growth_protocol: Liquid cultures of B. cereus ATCC14579 WT, ΔrpoN and ΔrpoN-comp strains were grown in BHI with aeration (200rpm) and statically in Erlenmeyer flasks at 30°C.

extract_protocol: Cultures were spinned down, resuspended in 1 ml TRI reagent (Ambion) and snap frozen in liquid nitrogen. RNA was extracted according to the RNAwiz (Ambion) protocol using Chloroform/isopropanol extraction. Residual DNA was enzymatically removed using the TURBO DNA-free (Ambion) kit following the instructions of the manufacturer.

treatment_protocol: Cells were harvested at above mentioned timepoints (see overall design) without any additional treatment.

tag: strain derivative

value: WT

source_name: rpoN-comp complemented mutant cells grown statically until OD(600nm)=0.2

value: ΔrpoN-comp


title: ST rpoN biol2 over ST WT biol2

source_name: rpoN deletion mutant cells grown statically until OD(600nm)=0.2

value: ΔrpoN


title: SH t2 rpoN biol1 over SH t2 rpoN biol2

description: Expression profiles of the rpoN deletion mutant (ΔrpoN) and the complemented strain (ΔrpoN-comp) were compared to the parental strain (WT) at aerated growth t2

source_name: rpoN deletion mutant cells grown with shaking until OD(600nm)=1.0


title: ST WT biol2 over ST rpoN_compl biol2


title: SH t2 WT biol1 over SH t2 rpoN_compl biol1

source_name: WT cells grown with shaking until OD(600nm)=1.0

source_name: rpoN-comp complemented mutant cells grown with shaking until OD(600nm)=1.0


title: SH t1 rpoN biol2 over SH t1 WT biol2

description: Expression profiles of the rpoN deletion mutant (ΔrpoN) and the complemented strain (ΔrpoN-comp) were compared to the parental strain (WT) at aerated growth t1

source_name: rpoN deletion mutant cells grown with shaking until OD(600nm)=0.2

source_name: WT cells grown with shaking until OD(600nm)=0.2


title: ST rpoN biol1 over ST rpoN_compl biol2


title: SH t1 rpoN_compl biol1 over SH t1 rpoN biol2

source_name: rpoN-comp complemented mutant cells grown with shaking until OD(600nm)=0.2


title: ST rpoN_compl biol1 over ST rpoN_compl biol2


title: SH t1 WT biol2 over SH t1 rpoN_compl biol2


title: SH t2 rpoN biol1 over SH t2 WT biol1


title: SH t1 rpoN_compl biol1 over SH t1 rpoN_compl biol2


title: SH t2 rpoN biol1 over SH t2 rpoN_compl biol2


title: ST rpoN_compl biol1 over ST rpoN biol2


title: piro__C

city: Glasgow

first: William

last: Weir

address: Room 220, Henry Wellcome Building, Garscube Campus, Bearsden Road

department: Institute of Infection, Immunity and Inflammation

country: United Kingdom

institute: University of Glasgow

description: This sample is of T. annulata piroplasms (3 of 4)

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Theileria annulata

source_name: Piroplasm

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

growth_protocol: BL20, an uninfected bovine lymphosarcoma cell line (Olobo and Black, 1989. Vet. Immunol. Immunopathol. 20, 165-172) and TBL20, a T. annulata (Ankara strain) infected BL20 cell line (Shiels et al., 1986. Vet. Parasitol. 21, 1-10.) were cultured in standard complete medium (Swan et al., 1999. Mol. Biochem. Parasitol. 101, 117-129) except that heat-inactivated foetal bovine serum (FBS; Sigma) was used. Cultures were seeded with 200,000 cells/ml and maintained by feeding with fresh medium every two to three days (Schmuckli-Maurer et al., 2010. Cell Microbiol. 12, 158-173).

extract_protocol: Total RNA was extracted using Triazol (ref) and this was cleaned up using an RNeasy Mini kit (Qiagen Inc., CA, USA) . RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer (ref)

treatment_protocol: Stimulation of cells was carried out for up to 48 hours in six well plates with 5,000,000 cells/well in a total of 5 ml medium, set up immediately prior to addition of 1 μg/ml LPS (Sigma: L2630).

tag: differentiation time-point

tag: parasite strain


title: SH t1 rpoN biol1 over SH t1 rpoN biol2


title: SH t2 WT biol2 over SH t2 rpoN_compl biol2


title: piro__B

description: This sample is of T. annulata piroplasms (2 of 4)


title: macrophage infected with HIV-1 at Day3

city: Honjo, Chuo-ku, Kumamoto City

first: Shinya

last: Suzu

state: kumamoto

department: center for aids research

country: Japan

institute: kumamoto university

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degrees on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Single Array Analysis were calculated by  Microarray Suite version 5.0 (MAS5.0) with Affymetrix default setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: human myeloid cell

label_protocol: Biotinylated cRNA were synthesized by GeneChip 3'IVT Express Kit（Affymetrix) from 250 ng total RNA according to the manufacturer's instructions. Biotinylated cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA isolated using ISOGEN II.

value: macrophage

tag: infection

tag: time


title: SH t1 WT biol1 over SH t1 rpoN_compl biol1


title: ST rpoN biol1 over ST WT biol1


title: piroA_D

description: This sample is of T. annulata piroplasms (4 of 4)


title: fibrocyte infected with HIV-1 at Day12

value: fibrocyte


title: macrophage


title: SH t2 rpoN_compl biol1 over SH t2 rpoN biol2


title: SH t2 rpoN_compl biol1 over SH t2 rpoN_compl biol2


title: SH t2 rpoN biol2 over SH t2 WT biol2


title: SH t1 rpoN biol1 over SH t1 rpoN_compl biol2


title: SH t1 rpoN biol1 over SH t1 WT biol1


title: fibrocyte


title: D7_9__B

description: This sample is of a differentiating T. annulata infected cell line after 9 days at 41oC (2 of 3)

source_name: Merozoite

tag: infected host cell line

value: Bos taurus (bovine) lymphosarcoma cell line

value: Day 9


title: D7_7__C

description: This sample is of a differentiating T. annulata infected cell line after 7 days at 41oC (3 of 3)

source_name: Differentiating macroschizont

value: Day 7


title: D7_7__A

description: This sample is of a differentiating T. annulata infected cell line after 7 days at 41oC (1 of 3)


title: D7_7__B

description: This sample is of a differentiating T. annulata infected cell line after 7 days at 41oC (2 of 3)


title: piro__A

description: This sample is of T. annulata piroplasms (1 of 4)


title: D7_9__C

description: This sample is of a differentiating T. annulata infected cell line after 9 days at 41oC (3 of 3)


title: D7_4__C

description: This sample is of a differentiating T. annulata infected cell line after 4 days at 41oC (3 of 3)

value: Day 4


title: D7_4__B

description: This sample is of a differentiating T. annulata infected cell line after 4 days at 41oC (2 of 3)


title: D7_9__A

description: This sample is of a differentiating T. annulata infected cell line after 9 days at 41oC (1 of 3)


title: hES-derived neurons

city: Shanghai

first: Wenxiang

last: Hu

address: Yueyang Road 320

country: China

institute: Shanghai institutes for Biological Sciences, CAS

description: Gene expression data from H9.

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 640 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Affymetrix GeneChip Command Console (version 4.0, Affymetrix) was used to analyze array images to get raw data. Raw data were normalized with the RMA algorithm by Gene Spring Software 12.5 (Agilent technologies, Santa Clara, CA, US).

source_name: Neurons differentiated from H9.

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: HAFs were culture in DMEM/10%FBS/NEAA/Glutamax medium, pre-hciNs and hciNs were induced by the chemical cocktail treatment for different days (D3, D7, D14), and hES-Neurons were differentiated from H9.

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions

treatment_protocol: HAFs were induced by chemical cocktail of VPA, Repsox, Chir99021, Forskolin, Sp600125, Go6983, Y-27632 in DMEM/Neurobasal/N2/B27+bFGF+cAMP medium for different days.

tag: parental cell type

value: human embryonic cells

tag: derived cell type

value: hES-derived neurons


title: D7_4__A

description: This sample is of a differentiating T. annulata infected cell line after 4 days at 41oC (1 of 3)


title: D7_0__C

description: This sample is of a T. annulata infected cell line maintained at 37oC (3 of 3)

source_name: Macroschizont

value: Day 0


title: hciN, D14, biological rep2

description: Gene expression data from hciNs D14

source_name: HAFs on day 14 after chemical induction

value: human foreskin fibroblasts

value: chemical-induced neuron


title: hciN, D14, biological rep1

description: Gene expression data from hciNs D14


title: HAFs

description: Gene expression data from HAFs

source_name: Human adult fibroblasts


title: D7_0__B

description: This sample is of a T. annulata infected cell line maintained at 37oC (2 of 3)


title: Pre-hciN, D7

description: Gene expression data from pre-hicNs D7

source_name: HAFs on day 7 after chemical induction

value: Pre-chemical-induced neuron


title: Pre-hciN, D3

description: Gene expression data from pre-hciNs D3

source_name: HAFs on day 3 after chemical induction


title: D7_0__A

description: This sample is of a T. annulata infected cell line maintained at 37oC (1 of 3)


title: Infected with the CCNB1 overexpression lentiviral vector for 96h rep2

description: replicate 2

source_name: H1 hESCs

tag: passage number

tag: treatment type

value: CCNB1 overexpression

tag: treatment length

value: 96 hours

tag: incubation medium

value: mTeSR1 without select factors


title: Infected with the CCNB1 overexpression lentiviral vector for 96h rep3

description: replicate 3

tag: cell line


title: Infected with the CCNB1 overexpression lentiviral vector for 48h rep3

description: replicate 3

value: 48 hours


title: sporo_D

description: This sample is of T. annulata sporozoites prepared from ground-up tick stabilate (GUTS) (4 of 4)

source_name: Sporozoite

tag: infected host

value: Hyalomma (tick)

value: Ankara


title: Infected with the CCNB1 overexpression lentiviral vector for 48h rep2

description: replicate 2


title: mTEC_rep3

city: San Francisco

first: Imran

last: Khan

state: CA

address: 513 Parnassus Ave, HSW 1102

department: Diabetes Center

country: USA

institute: University of California, San Francisco

hyb_protocol: Labeled RNA was hybridized to Agilent custom UCSF miRNA v3.6 multi-species 8x15K Ink-jet arrays (Agilent). Hybridizations were performed for 16 hrs, according to the manufacturers protocol (Agilent).

scan_protocol: Arrays were scanned using the Agilent microarray scanner (Agilent) and raw signal intensities were extracted with Feature Extraction v10.1 software (Agilent).

data_processing: This dataset was normalized using the quantile normalization method that is proposed by Bolstad et al (2003).  No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization. A one-way ANOVA linear model was fit to the comparison to estimate the mean M values and calculated moderated t-statistic, B statistic, false discovery rate and p-value for each miRNA for the comparison of interest. Adjusted p-values were produced by the method proposed by Holm (1979). All procedures were carried out using functions in the R package limma in Bioconductor [Smyth (2004), Gentleman (2004)].

organism: Mus musculus

source_name: FACS-sorted mTECs, biological replicate 3

label_protocol: RNA was labeled with Cy3-CTP using the miRCURY LNA microRNA power labeling kit (Exiqon, Inc, Woburn, MA), according to manufacturers protocol.

extract_protocol: Total RNA was extracted from FACS-sorted samples using TRIzol (Invitrogen) according to the manufacturer’s instructions. Total RNA quality was assessed using a Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Cells were purified by flow cytometric sorting and collected in TRIzol (Invitrogen).

tag: strain

value: NOD wildtype

value: female

tag: age

tag: cell population

value: FACS-sorted mTECs


title: mTEC_rep2

source_name: FACS-sorted mTECs, biological replicate 2

tag: gender


title: mTEC_rep1

source_name: FACS-sorted mTECs, biological replicate 1


title: sporo_B

description: This sample is of T. annulata sporozoites prepared from ground-up tick stabilate (GUTS) (2 of 4)

tag: differentiation time-point


title: sporo_C

description: This sample is of T. annulata sporozoites prepared from ground-up tick stabilate (GUTS) (3 of 4)

tag: parasite strain


title: Infected with the CCNB1 overexpression lentiviral vector for 96h rep1

description: replicate 1


title: sporo_A

description: This sample is of T. annulata sporozoites prepared from ground-up tick stabilate (GUTS) (1 of 4)


title: Infected with the CCNB1 overexpression lentiviral vector for 48h rep1

description: replicate 1


title: Infected with the empty lentiviral vector for 48h rep1

description: replicate 1

value: empty vector


title: Infected with the empty lentiviral vector for 96h rep3

description: replicate 3


title: cTEC_rep2

source_name: FACS-sorted cTECs, biological replicate 2

value: FACS-sorted cTECs


title: Infected with the empty lentiviral vector for 48h rep3

description: replicate 3


title: Infected with the empty lentiviral vector for 96h rep1

description: replicate 1


title: SK-BR-3/ATCC

city: Genova

first: Patrizio

last: Castagnola

state: GE

address: Largo Rosanna Benzi 10

country: Italy

institute: IRCCS AOU San Martino - IST

description: Cell line culture, untreated, acquired, seeded, and harvested after no more than four passages

hyb_protocol: Cy5-labeled cell lines DNA was mixed with an equivalent amount of Cy3-labeled reference DNA. Repetitive sequences were blocked with human Cot-1 DNA (InvitrogenTM, Thermo Scientific, Inc.) and samples were hybridized with Oligo aCGH/ChIP-on-chip Hybridization Kit onto the microarrays slides, according to the Manufacturer’s instructions. Following hybridization at 65°C for 24h in a rotating oven (Agilent Technologies, Palo Alto, CA, USA) at 20rpm, slides were washed according to the Manufacturer’s instructions

scan_protocol: Scanned using a Agilent Microarray Scanner (G2505C).

data_processing: Elaborated and quality-checked using the Feature Extraction software v11.01.1, Log10 ratios from Agilent feature extraction .txt files were imported in R using the data.table package, averaged over probe replicates using the limma BioConductor package, and log2 transformed. Probe to be mapped to the NCBI37/hg19 build of the human genome using the UCSC liftOver utility (https://genome.ucsc.edu/cgi-bin/hgLiftOver)

label_protocol: 0.8 µg of amplified test and reference (female normal genomic DNA: Promega, Madison,WI) were labeled using Sure Tag DNA labeling kit (Agilent Technologies, Palo Alto, CA, USA) with Cy5-dUTP and Cy3-dUTP respectively according to CGH Enzymatic Labeling Kit Protocol v.7.2 (Agilent Technologies, Palo Alto, CA, USA). Unincorporated nucleotides were then removed using centrifugal filters (Amicon Ultra 0.5ml, Merck Millipore, Merck KGaA, Darmstadt, Germany) according to the Manufacturer’s protocol. Quality analysis and quantization of labeled DNA were performed by NanoDrop® ND-1000 (Thermo Scientific, Inc.) spectrophotometry measuring A260 (for DNA), A550 (for Cy5) and A649 (for Cy3) to evaluate yield, degree of labeling, or specific activity.

growth_protocol: MCF-7, T-47D, MDA-MB-468 and MDA-MB-231 cell lines were maintained in RPMI1640 medium supplemented with 10% FBS, penicillin (50 units/ml), and streptomycin (50 μg/ml) (LifeTechnologies, Italy). Hs 578T cell line was maintained in DMEM medium supplemented with 10% FBS, insulin (0.01 mg/ml), penicillin (50 units/ml), and streptomycin (50 μg/ml) (LifeTechnologies, Italy). SK-BR-3 cell line was maintained in McCoy's 5a medium supplemented with 10% FBS, penicillin (50 units/ml), and streptomycin (50 μg/ml) (LifeTechnologies, Italy).

extract_protocol: DNA from cell lines was extracted and amplified using DNeasy Blood & Tissue Kit (Qiagen GmbH, D-40724 Hilden). DNA samples were diluted in 200 μL Nuclease-Free water according to the Manufacturer’s instructions.

tag: tissue

value: breast cancer

source_name: female normal genomic DNA

tag: control type

value: normal reference DNA


title: Infected with the empty lentiviral vector for 48h rep2

description: replicate 2


title: T-47D/NCI60


title: Infected with the empty lentiviral vector for 96h rep2

description: replicate 2


title: Hs 578T/ATCC

source_name: Hs 578T/ATCC

value: Hs 578T


title: Infected with the empty lentiviral vector for 24h rep3

description: replicate 3

value: 0 hours


title: Infected with the empty lentiviral vector for 24h rep2

description: replicate 2


title: AC16-HYPOTHERMIA-6HOUR-REP2

city: shenyang

first: huishan

last: wang

state: liaoning

address: No.83, Wenhua Road

department: Department of Cardiovascular Surgery

institute: General Hospital of Shenyang Military Area Command

description: Gene expression data from AC16 treated with 28 °C

hyb_protocol: Following fragmentation, 10 ug of 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: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with robustmultiarray average (RMA) 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: AC16 human adult ventricular cardiomyocyte cells cultured at 28 °C with 5% CO2 for 6 hours

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

growth_protocol: AC16 human adult ventricular cardiomyocyte cells(Davidson et al. 2005) were purchased from the American Type Cell Culture (ATCC). The cells were maintained in DMEM/F-12 supplemented with 10% fetal bovine serum, 100 units/ml penicillin, and 100μg/ml streptomycin. Cells were cultured at 37 °C or 28 °C with 5% CO2.

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


title: MDA-MB-468/NCI60


title: AC16-HYPOTHERMIA-6HOUR-REP3

treatment_protocol: Cells were cultured at 37 °C or 28 °C with 5% CO2.

value: AC16 human adult ventricular cardiomyocyte cells


title: cTEC_rep1

source_name: FACS-sorted cTECs, biological replicate 1


title: MCF-7/ATCC


title: MDA-MB-231/ATCC


title: CD45_rep3

source_name: FACS-sorted CD45+ cells, biological replicate 3

value: FACS-sorted CD45+ cells


title: CD45_rep2

source_name: FACS-sorted CD45+ cells, biological replicate 2


title: CD45_rep1

source_name: FACS-sorted CD45+ cells, biological replicate 1


title: AC16-CONTROL-6HOUR-REP3

description: Gene expression data from AC16 treated with 37 °C

source_name: AC16 human adult ventricular cardiomyocyte cells cultured at 37 °C with 5% CO2 for 6 hours


title: ST rpoN biol1 over ST rpoN biol2

description: Expression profiles of the rpoN deletion mutant (ΔrpoN) and the complemented strain (ΔrpoN-comp) were compared to the parental strain (WT) at static growth

source_name: rpoN deletion mutant cells grown statically until OD(600nm)=0.2

tag: strain derivative

value: ΔrpoN


title: Infected with the empty lentiviral vector for 24h rep1

description: replicate 1


title: AC16-HYPOTHERMIA-6HOUR-REP1


title: AC16-CONTROL-6HOUR-REP1


title: AC16-CONTROL-6HOUR-REP2


title: Jejunum mucosa-HS treated/Control-6d-rep2

city: Changsha

first: Lili

last: Liu

state: Hunan

address: SchooI of AnimaI Science and Technologe, Hunan AgricuIturaI University, Changsha, Hunan Province,China.

institute: Hunan AgricuIturaI University

description: The full-sib as genetic relationship between NT and HT treated individuals each repeat; the half-sib as all individuals with a shared male parent among three repeats.

hyb_protocol: Each Slide was hybridized with 0.825μg Cy3-labeled cRNA and 0.825μg Cy-5 labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US)in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), Stabilization and Drying Solution (Cat#5185-5979, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Red&Green, Scan resolution=5μm, PMT 100%, 10% , 16bit. and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)

data_processing: Raw data were normalized by Lowess(locally weighted scatter plot smoothing) algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Gallus gallus

source_name: Jejunum mucosa

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, Two-Color (Cat#5190-2306, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Female 28-day shared paternal family Xuefeng black-bone chicken. After a 2-week adaptation period, the 18 black-boned chickens were divided into two groups according to full-sib individuals (6 chickens/each full-sib), and made the half-sib as the test repeated (n=3). In group one, 9 black-boned chickens were maintained at 24 ± 2°C for 24 h/d (normal temperature, NT). The other group which included 9 chickens were housed in temperature-controlled rooms at 37 ± 2°C for 8 h/d (high temperature, HT; 0930–1730 h) followed by housing at 24 ± 2°C for the remaining 16 h/d. HT treatment lasted for 6d.According to the above experimental design, the candidate chickens were prepared for 3 groups. The experimental birds were slaughtered at 48-day of age. The jejunum mucosa were sampled, frozen in liquid nitrogen, and stored at −80°C.

tag: Sex

tag: treatment

value: normal temperature

value: 6-day high temperature


title: Wildtype Wt1 Pax8-Cre positive Replicate 2

status: Public on Jul 27 2015

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description:
SAMPLE 23
Whole kidney obtained from a Wildtype Wt1, Pax8-Cre positive embryonic mouse at E18.5.

hyb_protocol: Illumina Ref8 v2.0 beadchips

scan_protocol: Illumina iScan with Illumina Genome Studio

data_processing:
Data processing and analysis was performed in GeneSpring v7
Data were normalized based on the median intensity value of control samples for each condition.

source_name: Whole kidney

label_protocol: Illumina Total Prep RNA Amplification Kit (Life technologies)

growth_protocol: Whole kidneys were derived from embryos were taken at E18.5

extract_protocol: RNAeasy microcolumns and on-column Dnase treatment (Qiagen)

tag: genotype/variation

value: Wildtype Wt1

tag: cre status

value: Pax8-Cre positive


title: Jejunum mucosa-HS treated/Control-6d-rep1


title: Jejunum mucosa-HS treated/Control-6d-rep3


title: Homozygous Wt1 wildtype None Replicate 3

description:
SAMPLE 9
Whole kidney obtained from a Homozygous Wt1 wildtype, None embryonic mouse at E18.5.

value: Homozygous Wt1 wildtype


title: Wildtype Wt1 Wnt4-CreGFP positive Replicate 3

description:
SAMPLE 15
Whole kidney obtained from a Wildtype Wt1, Wnt4-CreGFP positive embryonic mouse at E18.5.

value: Wnt4-CreGFP positive


title: Wildtype Wt1 Pax8-Cre positive Replicate 1

description:
SAMPLE 22
Whole kidney obtained from a Wildtype Wt1, Pax8-Cre positive embryonic mouse at E18.5.


title: Homozygous Wt1 conditional Wnt4-CreGFP positive Replicate 1

description:
SAMPLE 16
Whole kidney obtained from a Homozygous Wt1 conditional, Wnt4-CreGFP positive embryonic mouse at E18.5.

value: Homozygous Wt1 conditional


title: Homozygous Wt1 wildtype None Replicate 2

description:
SAMPLE 8
Whole kidney obtained from a Homozygous Wt1 wildtype, None embryonic mouse at E18.5.


title: Wildtype Wt1 Nes-Cre positive Replicate 2

description:
SAMPLE 11
Whole kidney obtained from a Wildtype Wt1, Nes-Cre positive embryonic mouse at E18.5.

value: Nes-Cre positive


title: Homozygous Wt1 conditional Wnt4-CreGFP positive Replicate 3

description:
SAMPLE 18
Whole kidney obtained from a Homozygous Wt1 conditional, Wnt4-CreGFP positive embryonic mouse at E18.5.


title: Wildtype Wt1 Wnt4-CreGFP positive Replicate 2

description:
SAMPLE 14
Whole kidney obtained from a Wildtype Wt1, Wnt4-CreGFP positive embryonic mouse at E18.5.


title: Homozygous Wt1 wildtype None Replicate 1

description:
SAMPLE 7
Whole kidney obtained from a Homozygous Wt1 wildtype, None embryonic mouse at E18.5.


title: Homozygous Wt1 conditional Pax8-Cre positive Replicate 1

description:
SAMPLE 19
Whole kidney obtained from a Homozygous Wt1 conditional, Pax8-Cre positive embryonic mouse at E18.5.


title: Homozygous Wt1 conditional Pax8-Cre positive Replicate 3

description:
SAMPLE 21
Whole kidney obtained from a Homozygous Wt1 conditional, Pax8-Cre positive embryonic mouse at E18.5.


title: Wildtype Wt1 Nes-Cre positive Replicate 3

description:
SAMPLE 12
Whole kidney obtained from a Wildtype Wt1, Nes-Cre positive embryonic mouse at E18.5.


title: Wildtype Wt1 Pax8-Cre positive Replicate 3

description:
SAMPLE 24
Whole kidney obtained from a Wildtype Wt1, Pax8-Cre positive embryonic mouse at E18.5.


title: Homozygous Wt1 conditional Wnt4-CreGFP positive Replicate 2

description:
SAMPLE 17
Whole kidney obtained from a Homozygous Wt1 conditional, Wnt4-CreGFP positive embryonic mouse at E18.5.


title: Homozygous Wt1 conditional Cre negative Replicate 1

description:
SAMPLE 1
Whole kidney obtained from a Homozygous Wt1 conditional, Cre negative embryonic mouse at E18.5.

value: Cre negative


title: Homozygous Wt1 conditional Nes-Cre positive Replicate 1

description:
SAMPLE 4
Whole kidney obtained from a Homozygous Wt1 conditional, Nes-Cre positive embryonic mouse at E18.5.


title: Bs_B4_M19

city: Mölndal

first: Ramy

last: Elgendy

state: Göteborg

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca

description:
Tissue aliquot from the biceps brachii aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
Bt_560_03

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing:
Data processed with FeatureExtraction v9.5 and normalized using R2.15.0 statistical software
Normalized with quantile method; 'blank' (no value) corresponds to probes not considered for the normalization step; null corresponds to missing and/or genes didn't pass the filtering step.

organism: Bos taurus

label_protocol: Amplified and labeled according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: RNA from Biceps brachii muscle aliquots was extracted using Trizol reagent according to manufacturer's instruction and purified according to Qiagen RNeasy Mini Kit protocol for tissue samples

value: male

value: 18-20 months

tag: treated with

value: dexamethasone+clenbuterol

value: Biceps brachii muscle


title: Bs_B4_M24

description:
Tissue aliquot from the biceps brachii aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
Bt_581_02


title: Wildtype Wt1 Nes-Cre positive Replicate 1

description:
SAMPLE 10
Whole kidney obtained from a Wildtype Wt1, Nes-Cre positive embryonic mouse at E18.5.


title: Homozygous Wt1 conditional Cre negative Replicate 2

description:
SAMPLE 2
Whole kidney obtained from a Homozygous Wt1 conditional, Cre negative embryonic mouse at E18.5.


title: Homozygous Wt1 conditional Pax8-Cre positive Replicate 2

description:
SAMPLE 20
Whole kidney obtained from a Homozygous Wt1 conditional, Pax8-Cre positive embryonic mouse at E18.5.


title: Wildtype Wt1 Wnt4-CreGFP positive Replicate 1

description:
SAMPLE 13
Whole kidney obtained from a Wildtype Wt1, Wnt4-CreGFP positive embryonic mouse at E18.5.


title: Homozygous Wt1 conditional Cre negative Replicate 3

description:
SAMPLE 3
Whole kidney obtained from a Homozygous Wt1 conditional, Cre negative embryonic mouse at E18.5.


title: Homozygous Wt1 conditional Nes-Cre positive Replicate 2

description:
SAMPLE 5
Whole kidney obtained from a Homozygous Wt1 conditional, Nes-Cre positive embryonic mouse at E18.5.


title: Bs_B4_M17

description:
Tissue aliquot from the biceps brachii aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
Bt_560_02


title: Bs_B4_M21

description:
Tissue aliquot from the biceps brachii aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
Bt_560_04


title: Homozygous Wt1 conditional Nes-Cre positive Replicate 3

description:
SAMPLE 6
Whole kidney obtained from a Homozygous Wt1 conditional, Nes-Cre positive embryonic mouse at E18.5.


title: Bs_B4_M12

description:
Tissue aliquot from the biceps brachii aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
Bt_559_4

value: dexamethasone


title: Bs_B4_M7

description:
Tissue aliquot from the biceps brachii aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
Bt_558_03

source_name: Bull_untreated control

value: none (untreated control)


title: Bs_B4_M11

description:
Tissue aliquot from the biceps brachii aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
Bt_559_3


title: Bs_B4_M8

description:
Tissue aliquot from the biceps brachii aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
Bt_559_1


title: esophageal squamous cell carcinoma_responder_biological rep11

city: Guangzhou

first: Jing

last: Wen

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

description: miRNA expression data from cancer tissues of esophageal squamous cell carcinoma patients with pathologic complete response after preoperative chemoradiotherapy

hyb_protocol: 100 ng of Cy3-labelled RNA was hybridized using Agilent’s miRNA Complete Labeling and Hyb Kit (Agilent). Prepare hybridization samples by resuspending the dried Cy3-labelled samples in nuclease-free water, and adding proper amount of 10×GE Blocking Agent and 2× Hi-RPM Hybridization Buffer. Then the sample was hybridized to Agilent human miRNA microarrays based on miRBase (release 18.0) GeneChip for 20 hours at 55°C in a rotating hybridization oven set. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent Technologies Scanner (G2505C) using one color scan setting for 8x15K array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel was set to Green and Green PMT was set as XDR Hi 100% and XDR Lo 5%).

data_processing: The microarray image information was converted in to spot intensity values using Feature Extraction Software version 10.7.3 (Agilent).

source_name: esophageal squamous cell carcinoma from patient responsing to preoperative chemoradiotherapy

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from100 ng RNA using Agilent’s miRNA Complete Labeling and Hyb Kit (Agilent) according to the manufacturer's instructions. The labeled miRNA was purified using the Micro Bio-spin 6 colums and completely dried.

growth_protocol: Patients were eligible in the study if they fulfill all of the following criteria: with Stage IIB-III squamous cell carcinoma of the thoracic esophagus according to the 6th AJCC Cancer Staging which were potentially resectable; no previous anticancer-treatment; an age range from 18 to 70 years; a Karnofsky performance status (KPS) of 90 or more; and medical fitness for surgery; and approval for tissue collection during the diagnostic endoscopic procedure.

extract_protocol: Total RNA were isolated using mirVana miRNA Isolation Kit (Ambion) according to the manufacture's instruction.

treatment_protocol: For the 28 patients who received preoperative chemoradiotherapy composed of vinorelbine and cisplatin and subsequent surgical resection, tumor tissues were collected during preoperative endoscopy. All the tissue specimens were snap frozen in liquid nitrogen and stored at -80℃ until use.

value: pretreatment cancer biopsy

value: Male

tag: tumor stage

tag: pathological response to preoperative chemoradiotherapy

value: pathological complete response


title: Bs_B4_M16

description:
Tissue aliquot from the biceps brachii aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
Bt_560_01


title: Bs_B4_M9

description:
Tissue aliquot from the biceps brachii aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
Bt_559_2


title: esophageal squamous cell carcinoma_responder_biological rep8


title: Bs_B4_M4

description:
Tissue aliquot from the biceps brachii aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
Bt_558_02


title: esophageal squamous cell carcinoma_responder_biological rep6


title: esophageal squamous cell carcinoma_responder_biological rep9


title: Bs_B4_M2

description:
Tissue aliquot from the biceps brachii aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
Bt_558_01


title: esophageal squamous cell carcinoma_responder_biological rep3

value: Female


title: esophageal squamous cell carcinoma_responder_biological rep5


title: esophageal squamous cell carcinoma_responder_biological rep4


title: Spontaneous PCT, Sample.99

city: Iowa City

first: Ramakrishna

last: Sompallae

state: IA

address: 285 Newton Road, 5292 CBRB

department: Iowa Institute of Human Genetics

institute: University of Iowa

description:
Sample name: Sample.99
Replicate 9

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation with Partek Genomics Suite.

source_name: Whole tumor, spontaneous PCT

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

growth_protocol: All studies were performed on the BALB/c background and approved under the University of Iowa IACUC Protocol 0006A56361.

extract_protocol: Frozen mouse tissue (1-3mm x 1–3 mm) was submerged in liquid nitrogen in a ceramic mortar, ground to powder, and immediately processed for mRNA isolation using Trizol reagent (Invitrogen, Carlsbad, CA) for total mouse RNA.

tag: background

value: BALB/c

tag: age (days)

value: lymph node

tag: pct type

value: spontaneous


title: esophageal squamous cell carcinoma_responder_biological rep10

tag: age


title: Spontaneous PCT, Sample.100

description:
Sample name: Sample.100
Replicate 10

tag: strain


title: esophageal squamous cell carcinoma_responder_biological rep2

tag: gender


title: Spontaneous PCT, Sample.101

description:
Sample name: Sample.101
Replicate 11


title: Spontaneous PCT, Sample.97

description:
Sample name: Sample.97
Replicate 7


title: esophageal squamous cell carcinoma_non_responder_biological rep16

description: miRNA expression data from cancer tissues of esophageal squamous cell carcinoma patients without pathologic complete response after preoperative chemoradiotherapy

source_name: esophageal squamous cell carcinoma from patient not responsing to preoperative chemoradiotherapy

value: not pathological complete response


title: Spontaneous PCT, Sample.95

description:
Sample name: Sample.95
Replicate 5


title: esophageal squamous cell carcinoma_non_responder_biological rep17


title: esophageal squamous cell carcinoma_responder_biological rep7


title: esophageal squamous cell carcinoma_responder_biological rep1


title: Spontaneous PCT, Sample.96

description:
Sample name: Sample.96
Replicate 6


title: esophageal squamous cell carcinoma_non_responder_biological rep15


title: Spontaneous PCT, Sample.98

description:
Sample name: Sample.98
Replicate 8


title: esophageal squamous cell carcinoma_non_responder_biological rep12


title: Spontaneous PCT, Sample.94

description:
Sample name: Sample.94
Replicate 4


title: Adoptive-transfer PCT, Sample.53

description:
Sample name: Sample.53
Replicate 12

source_name: Whole tumor, adoptive-transfer PCT

value: oil granuloma

value: adoptive-transfer


title: Adoptive-transfer PCT, Sample.52

description:
Sample name: Sample.52
Replicate 11


title: Adoptive-transfer PCT, Sample.54

description:
Sample name: Sample.54
Replicate 13


title: Spontaneous PCT, Sample.92

description:
Sample name: Sample.92
Replicate 2


title: Spontaneous PCT, Sample.91

description:
Sample name: Sample.91
Replicate 1


title: Spontaneous PCT, Sample.93

description:
Sample name: Sample.93
Replicate 3


title: esophageal squamous cell carcinoma_non_responder_biological rep14


title: Adoptive-transfer PCT, Sample.56

description:
Sample name: Sample.56
Replicate 14


title: esophageal squamous cell carcinoma_non_responder_biological rep6


title: esophageal squamous cell carcinoma_non_responder_biological rep8


title: Adoptive-transfer PCT, Sample.51

description:
Sample name: Sample.51
Replicate 10


title: esophageal squamous cell carcinoma_non_responder_biological rep7


title: esophageal squamous cell carcinoma_non_responder_biological rep10


title: Adoptive-transfer PCT, Sample.45

description:
Sample name: Sample.45
Replicate 9


title: esophageal squamous cell carcinoma_non_responder_biological rep5


title: esophageal squamous cell carcinoma_non_responder_biological rep11


title: esophageal squamous cell carcinoma_non_responder_biological rep13


title: Adoptive-transfer PCT, Sample.44

description:
Sample name: Sample.44
Replicate 8


title: Adoptive-transfer PCT, Sample.42

description:
Sample name: Sample.42
Replicate 7


title: esophageal squamous cell carcinoma_non_responder_biological rep9


title: esophageal squamous cell carcinoma_non_responder_biological rep4


title: Adoptive-transfer PCT, Sample.39

description:
Sample name: Sample.39
Replicate 5


title: Adoptive-transfer PCT, Sample.41

description:
Sample name: Sample.41
Replicate 6


title: esophageal squamous cell carcinoma_non_responder_biological rep3


title: Adoptive-transfer PCT, Sample.33

description:
Sample name: Sample.33
Replicate 2


title: Adoptive-transfer PCT, Sample.32

description:
Sample name: Sample.32
Replicate 1


title: esophageal squamous cell carcinoma_non_responder_biological rep2


title: esophageal squamous cell carcinoma_non_responder_biological rep1


title: #404-2 0 hour

city: Baltimore

first: Dmitry

middle: N

last: Grigoryev

state: MD

address: 620 W. Lexington St.

department: Alumni

institute: UMB

description:
SAMPLE 15 1519120009_G
replicate 2

scan_protocol: The hybridized biotinylated cRNA was detected with streptavidin-Cy3 and quantified with Illumina’s BeadStation 500GX Genetic Analysis Systems scanners. Preliminary analysis of the scanned data was performed using Illumina BeadStudio software.

data_processing:
The expression data was stratified by experimental conditions (n=4) and hybridization of each transcript was evaluated. The transcripts that were detectable by BeadStudio (IR>0.95) and produced signal at least twice as high as that of background in at least 3 out of 4 hybridizations in any given experimental condition were considered truly expressed.
The signal intensity values of these transcripts from each chip were increased by corresponding to a given chip background value (background adjustment) and divided by a chip brightness coefficient (normalization).

source_name: PBMCs

label_protocol: cRNA was labeled by incorporating biotin-16-UTP. 0.85 ugs of biotin-labeled cRNA was hybridized (16 hours) to Illumina’s Sentrix HumanRef-8 Expression BeadChips (Illumina, San Diego, CA 92121-1975, cat.no. 11201828).

extract_protocol: Total RNA was isolated from PBMCs using the Trizol Reagent method (Invitrogen, Carlsbad, California 92008, cat. no. 15596-026) with subsequent RNEasy clean up (Qiagen, Valencia, CA 913555, cat. no. 74104).

treatment_protocol: IH was induced by inspiration of the hypoxic (95% N2 and 5% O2) gas until the oxyhemoglobin saturation dropped to 85% followed by reoxygenation to the baseline, resulting in ~25 hypoxic events/h. In control exposures hypoxic gas was substituted with air. Whole blood was collected before and after the exposures.

tag: individual

tag: exposure

value: before IH

tag: time

value: 0 hour

tag: cell type

value: PBMC


title: Adoptive-transfer PCT, Sample.34

description:
Sample name: Sample.34
Replicate 3

tag: tissue


title: #403-2 0 hour

description:
SAMPLE 11 1519120009_C
replicate 2

hyb_protocol: 0.85 ugs of biotin-labeled cRNA was hybridized (16 hours) to Illumina’s Sentrix HumanRef-8 Expression BeadChips (Illumina, San Diego, CA 92121-1975, cat.no. 11201828).


title: #403-2 5 hour

description:
SAMPLE 12 1519120009_D
replicate 2

value: after IH

value: 5 hour


title: Normal B cells, Sample.11

description:
Sample name: Sample.11
Replicate 2

source_name: Splenocytes, normal B cells

tag: strain/background

value: spleen

value: normal B cells


title: Normal B cells, Sample.13

description:
Sample name: Sample.13
Replicate 3


title: #404 5 hour

description:
SAMPLE 14 1519120009_F
replicate 1

value: after control


title: #403 5 hour

description:
SAMPLE 10 1519120009_B
replicate 1


title: #402 5 hour

description:
SAMPLE 6 1519120007_F
replicate 1


title: #402-2 0 hour

description:
SAMPLE 7 1519120007_G
replicate 2

value: before control


title: #401 0 hour

description:
SAMPLE 1 1519120007_A
replicate 1


title: #401 5 hour

description:
SAMPLE 2 1519120007_B
replicate 1


title: #401-2 5 hour

description:
SAMPLE 4 1519120007_D
replicate 1


title: #404-2 5 hour

description:
SAMPLE 16 1519120009_H
replicate 2


title: #401-2 0 hour

description:
SAMPLE 3 1519120007_C
replicate 1


title: #404 0 hour

description:
SAMPLE 13 1519120009_E
replicate 1


title: #403 0 hour

description:
SAMPLE 9 1519120009_A
replicate 1


title: #402-2 5 hour

description:
SAMPLE 8 1519120007_H
replicate 2


title: #402 0 hour

description:
SAMPLE 5 1519120007_E
replicate 1


title: health control group, biological rep1

city: beijing

first: ai

middle: aa

last: gao

address: NO10, Xi tou tiao, Youanmen,Fengtai District

institute: School of Public Health, Capital Medical University

description: LncRNA and mRNA expression data from health control 1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Gene 2.0 ST Chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G/4 Color Early Access.

data_processing: The data were analyzed with the affymetrix Expression Console software using Affymetrix default analysis settings and RMA as normalization method.We applied the RVM F-test to filter the differentially expressed genes. After the significance analysis and false discovery rate (FDR) analysis, we selected the differentially expressed genes according to the P value threshold. Both p-value <0.05 and FDR<0.01 were considered statistically significant.

source_name: health control 1

label_protocol: Biotinylated cRNA were prepared according to the protocol from the Ambion® WT Expression kit for Affymettrix® GeneChip®Whole Transcrpit (WT) Expression Arrays

growth_protocol: peripheral blood samples were

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s protocol.

treatment_protocol: All blood samples from each subject were centrifuged and subjected to RNA extraction.

value: Peripheral blood

tag: treatment

value: control


title: Normal B cells, Sample.9

description:
Sample name: Sample.9
Replicate 1

value: BALB/c


title: health control group, biological rep2

description: LncRNA and mRNA expression data from health control 2

source_name: health control 2


title: benzene-exposed group,biological rep2

description: LncRNA and mRNA expression data from benzene-exposed worker 2

source_name: benzene-exposed worker 2

value: benzene exposed


title: benzene-exposed group,biological rep1

description: LncRNA and mRNA expression data from benzene-exposed worker 1

source_name: benzene-exposed worker 1


title: benzene poisoning group,biological rep3

description: LncRNA and mRNA expression data from benzene poisoning patient 3

source_name: benzene poisoning patient 3

value: benzene poisoning


title: Expanded Islets- donor I51p6-ZEB1 inhibition

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

description:
gene expression data of expanded islet cells tranduced with ZEB1 shRNA
growth protocol differentiation: Human islets were received 2-4 days following isolation from individual donors. Islets were dissociated into single cells and cultured in CMRL 1066 medium containing 5.6 mM D-glucose and supplemented with 10% FCS (HyClone, Logan, UT), 100 U/ml penicillin, 100 μg/ml streptomycin, 100 μg/ml gentamycin, and 5 μg/ml amphotericine B (all tissue culture reagents were from Biological Industries, Israel) (growth medium) as described 5. Culture medium was changed every 3-4 days. Once confluency was reached (day 7-10 in each passage), cells were detached by trypsin (Bio-Lab Ltd., Jerusalem, Israel) and reseeded at a 1:2 ratio.
preparation of islet cells: as described in: Ouziel-Yahalom L, Zalzman M, Anker-Kitai L, Knoller S, Bar Y, Glandt M, Herold K, Efrat S (2006) Expansion and redifferentiation of adult human pancreatic islet cells. Biochem Biophys Res Commun 341:291-298.

hyb_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)

data_processing: Gene-level analyses was performed. RMA normalization and summarization by mean, all were done by Partek Genomics suite (version 6.6) Copyright ©

source_name: Pancreatic Islets from individual donors

extract_protocol: according to the manufacturer's protocol (Trizol, Sigma-Aldrich)

tag: date

value: islet cells with ZEB1 shRNA

value: islet cells


title: Expanded Islets- donor F32p6-Control

description:
gene expression data of expanded islet cells tranduced with control shRNA
growth protocol differentiation: Human islets were received 2-4 days following isolation from individual donors. Islets were dissociated into single cells and cultured in CMRL 1066 medium containing 5.6 mM D-glucose and supplemented with 10% FCS (HyClone, Logan, UT), 100 U/ml penicillin, 100 μg/ml streptomycin, 100 μg/ml gentamycin, and 5 μg/ml amphotericine B (all tissue culture reagents were from Biological Industries, Israel) (growth medium) as described 5. Culture medium was changed every 3-4 days. Once confluency was reached (day 7-10 in each passage), cells were detached by trypsin (Bio-Lab Ltd., Jerusalem, Israel) and reseeded at a 1:2 ratio.
preparation of islet cells: as described in: Ouziel-Yahalom L, Zalzman M, Anker-Kitai L, Knoller S, Bar Y, Glandt M, Herold K, Efrat S (2006) Expansion and redifferentiation of adult human pancreatic islet cells. Biochem Biophys Res Commun 341:291-298.

scan_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)

value: islet cells with control shRNA


title: Expanded Islets- donor F32p6-ZEB1 inhibition

label_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)


title: benzene poisoning group,biological rep2

description: LncRNA and mRNA expression data from benzene poisoning patient 2

source_name: benzene poisoning patient 2


title: health control group, biological rep3

description: LncRNA and mRNA expression data from health control 3

source_name: health control 3


title: Expanded Islets- donor S114p7-Control


title: normal vulvar tissue/cells (D239_MVN3)

status: Public on Jul 26 2015

city: New York

first: Prokopios Alexandros

last: Polyzos

address: 413 E 69th St

institute: Weill Cornell Medicine

description: Gene expression data from normal vulvar tissue/cells

data_processing: The data were analyzed with R/Bioconductor RMA algorithm. Data were log2 transformed

source_name: normal vulvar tissue/cells

value: vulvar

tag: disease state

value: normal


title: Expanded Islets- donor S106p6-ZEB1 inhibition


title: Expanded Islets- donor I51p6-Control


title: normal vulvar tissue/cells (A872_VN50)


title: normal vulvar tissue/cells (A112_VN27)


title: benzene poisoning group,biological rep1

description: LncRNA and mRNA expression data from benzene poisoning patient 1

source_name: benzene poisoning patient 1


title: normal vulvar tissue/cells (A106_VN26)


title: benzene poisoning group,biological rep4

description: LncRNA and mRNA expression data from benzene poisoning patient 4

source_name: benzene poisoning patient 4


title: vulvar cancer tissue/cells (D400_T70-MV17)

description: Gene expression data from vulvar carcinoma tissue/cells

source_name: vulvar cancer tissue/cells

value: carcinoma


title: normal vulvar tissue/cells (A871_VN29)


title: Expanded Islets- donor S114p7-ZEB1 inhibition


title: Expanded Islets- donor S106p6-Control


title: benzene-exposed group,biological rep3

description: LncRNA and mRNA expression data from benzene-exposed worker 3

source_name: benzene-exposed worker 3


title: normal vulvar tissue/cells (A128_V42)


title: vulvar cancer tissue/cells (A126_V26)


title: vulvar cancer tissue/cells (A139_V33)


title: vulvar cancer tissue/cells (A111_V34)


title: vulvar cancer tissue/cells (A105_V21)


title: normal endometrial tissue/cells (D249_MEN12)

description: Gene expression data from normal endometrial tissue/cells

source_name: normal endometrial tissue/cells

value: endometrium


title: vulvar cancer tissue/cells (A127_V32)


title: normal vulvar tissue/cells (A870_VN28)


title: endometrial cancer tissue/cells (T68_E1)

description: Gene expression data from endometrial carcinoma tissue/cells

source_name: endometrial cancer tissue/cells


title: normal endometrial tissue/cells (A110_EN11)


title: endometrial cancer tissue/cells (D246_ME19)


title: normal endometrial tissue/cells (A104_EN7)


title: normal endometrial tissue/cells (D248_MEN10)


title: endometrial cancer tissue/cells (D245_ME20)


title: normal endometrial tissue/cells (D247_MEN6)


title: endometrial cancer tissue/cells (A124_E12)


title: endometrial cancer tissue/cells (D244_ME16)


title: normal cervical tissue/cells (D241_MCN17)

description: Gene expression data from normal cervical tissue/cells

source_name: normal cervical tissue/cells

value: cervix


title: normal cervical tissue/cells (xD242_MCN_18)


title: normal cervical tissue/cells (A140_CeN12)


title: endometrial cancer tissue/cells (A109_ME27)


title: normal cervical tissue/cells (A102_CeN11)


title: cervical cancer tissue/cells (D399_T67-MC1)

description: Gene expression data from cervical carcinoma tissue/cells

source_name: cervical cancer tissue/cells


title: SK-N-MC_siEGR2_8

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

country: Germany

institute: German Cancer Research Center (DKFZ)

description: Gene expression data from human SK-N-MC Ewing sarcoma cells transfected with specific siRNA directed against EGR2

hyb_protocol: Following fragmentation, 5,5 µg of cDNA were hybridized for 17 h at 47°C on Human Gene 2.1 ST arrays.

scan_protocol: GeneChips were scanned using an Affymetrix Genetitan scanner.

data_processing: Data were normalized using the PLIER algorithm and brainarray v16 ENTREZG CDF files in R.

source_name: human Ewing sarcoma cell line SK-N-MC

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol from 100 ng of total RNA.

growth_protocol: Cells were grown at 37°C in 5% CO2 in a humidified atmosphere in Roswell Park Memorial Institute (RPMI) 1640 GlutaMAX medium (Gibco, Cergy Pontoise, France) containing 10% foetal calf serum (FCS) (Eurobio, Courtaboeuf, France), 100 U/ml penicillin and 100 μg/ml streptomycin (Gibco).

extract_protocol: RNA extraction was performed with the Nucleospin II kit (Macherey-Nagel, Düren, Germany), which includes a 15 min on-column DNase treatment, according to the manufacturer's instructions.

treatment_protocol: For transfection with siRNA, cells were seeded at a density of 2x106/dish in a final volume of 12 ml RPMI 1640 medium supplemented with 10% FCS and standard antibiotics. Cells were transfected with siRNA (15 nM) using RNAiMAX (Invitrogen, Saint Aubin, France). Knockdown efficacy of specific siRNAs was assessed by qRT-PCR 48 h after transfection. The Qiagen AllStars Negative Control non-targeting siRNA was used as a control.

tag: cell line

value: SK-N-MC


title: Adoptive-transfer PCT, Sample.35

description:
Sample name: Sample.35
Replicate 4

source_name: Whole tumor, adoptive-transfer PCT

value: oil granuloma

value: adoptive-transfer


title: SK-N-MC_siEWSR1-FLI1

description: Gene expression data from human SK-N-MC Ewing sarcoma cells transfected with specific siRNA directed against EWSR1-FLI1


title: normal cervical tissue/cells (D240_MCN7)


title: A673_siEGR2_8

description: Gene expression data from human A673 Ewing sarcoma cells transfected with specific siRNA directed against EGR2

source_name: human Ewing sarcoma cell line A673


title: endometrial cancer tissue/cells (D243_ME15)


title: SK-N-MC_siEGR2_122

value: transfected with specific siRNA directed against EGR2


title: A673_siControl_rep2

description: Gene expression data from human A673 Ewing sarcoma cells transfected with non-targeting control siRNA


title: cervical cancer tissue/cells (D236_MC35)


title: cervical cancer tissue/cells (A107_Ce38)


title: cervical cancer tissue/cells (A101_Ce36)


title: MEDME control

status: Public on Jul 25 2015

city: Toronto

first: Eric

middle: J

last: Chater-Diehl

address: 686 Bay St.

institute: SickKids Research Institute

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with Cy3/5 labelled DNA in NimbleGen hybridization buffer/ hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA). For array hybridization, Roche NimbleGen's MM9 Meth 2.1M CpG plus

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Raw data was extracted as pair files by NimbleScan software. We performed Median-centering, quantile normalization, and linear smoothing by Bioconductor packages Ringo, limma, and MEDME. After normalization, a normalized log2-ratio data (*_ratio.gff file) was created for each sample. From the normalized log2-ratio data, a sliding-window peak-finding algorithm provided by NimbleScan v2.5 (Roche-NimbleGen) was applied to find the enriched peaks with specified parameters. The gff files contain the scaled, log2 (ChIP/Input) ratio.

source_name: pool of samples 1-6

label_protocol: 1 μg DNA of each sample was incubated for 10 min at 98°C with 1 OD of Cy5-9mer primer (IP sample) or Cy3-9mer primer (Input sample). Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled DNA was purified by isopropanol / ethanol precipitation

growth_protocol: pool of samples 1-6 enzymatically fully methylated at all CpG sites

extract_protocol: DNA and RNA were isolated with AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s protocol.

value: pooled

tag: Sex

value: male

value: post-natal day 70

tag: developmental stage

value: adult

value: hippocampus

tag: antibody


title: A673_siEGR2_122


title: Control 3

source_name: 5mC ChIP DNA from adult mouse hippocampus

growth_protocol: Mice housed and standard conditions prior to sacrifice

treatment_protocol: Mice injected with saline on PD 4 and 7

value: saline

source_name: input DNA from adult mouse hippocampus


title: A673_siEWSR1-FLI1

description: Gene expression data from human A673 Ewing sarcoma cells transfected with specific siRNA directed against EWSR1-FLI1


title: SK-N-MC_siControl_rep2

description: Gene expression data from human SK-N-MC Ewing sarcoma cells transfected with non-targeting control siRNA


title: wt_P2-suc-2

city: Hamilton

first: Turlough

middle: M

last: Finan

state: Ontario

address: 1280 Main Street West

institute: McMaster University

hyb_protocol: Standard NimbleGen protocol: hybridized to the microarrays for 16 hours at 42°C

scan_protocol: NimbleGen scanned at 5μm resolution using a GenePix 4000B microarray scanner (Molecular Devices, Sunnyvale, CA).

data_processing: The raw data (.pair file) was subjected to quantile normalization (Bolstad et al. Bioinformatics 19(2):185). Feature expression (value) was the uncorrected median of normalized probe intensity for each experiment. Background was estimated from the median of the normalized null probes for each experiment.

organism: Sinorhizobium meliloti

label_protocol: Standard NimbleGen protocol: RNA converted to cDNA, random prime lagelled with Cy3

growth_protocol: Growth medium: MOPS-buffered minimal salts = 40 mM MOPS, 20 mM KOH, 20 mM NH4Cl, 1.2 mM CaCl2, 100 mM NaCl, 2 mM MgSO4, 2 mM KH2PO4, 0.5 µg ml-1 biotin, and 1x trace element (trace element solution (1000x consisted of the following amounts of compounds per liter of H2O: 1 g H3BO3, 1 g  ZnSO4 · 7H2O, 0.5 g CuSO4 · 5H2O, 0.5 g MnCl2 · 4H2O, 1 g Na2MoO4 · 2H2O, 10 g Na2EDTA · 2H2O,  and 2 g NaFeEDTA); Growth temperature: 30C; exponential phase cells, aerated mid-log phase cultures (OD600 0.4 to 0.6)

extract_protocol: Following extraction, the RNA was further purified and DNA removed using RNeasy minikits (Qiagen).

treatment_protocol: RNA was isolated as previously described (MacLellan et al., 2006. Microbiol  152: 1751-1763.) from aerated mid-log phase cultures (OD600 0.4 to 0.6).

tag: carbon source

value: 15 mM succinate


title: Ethanol 3

treatment_protocol: Mice injected with 2.5g/kg ethanol on PD 4 and 7

value: ethanol

tag: age


title: A673_siControl_rep1

value: transfected with non-targeting control siRNA


title: tme_P2-glu-1

source_name: RmP2179 = RmP110 tme::ΩSpr

value: 15 mM glucose

tag: strain


title: dme_P2-suc-1

source_name: RmP2189 = RmP110 dme::ΩSpr


title: wt_P2-glu-1


title: wt_P2-glu-2


title: tme_P2-glu-2


title: Control 2


title: tme_P2-suc-2


title: wt_P2-suc-1


title: dme_P2-suc-2


title: cervical cancer tissue/cells (D237_MC4)

value: carcinoma


title: tme_P2-suc-1


title: dme_P2-glu-2


title: dme_P2-glu-1


title: Ethanol 1


title: Arabidopsis_L4h_rep1 [array]

city: Taipei

first: Chiung-Swey

middle: Joanne

last: Chang

address: 128 Sec. 2, Academia Rd, Nankang,

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

description:
Biosample: SAMN02251447
Sample name: ASarray_DL4h_1

hyb_protocol: Following fragmentation (~65nt), 825 ng of cRNA were hybridized for 17 hr at 65℃on the Agilent custom gene expression microarray. GeneChips were washed before scaned.

scan_protocol: GeneChips were scanned using the Agilent microarray scanner, G2565CA.

data_processing:
The data were analyzed with GeneSpring GX 10.0.2 (Agilent Technologies) and were normalized with ‘LOWESS Normalization’ and ‘PerChip: normalized to 50th percentile’.
The reciprocal normalized log2 ratio (Cy5/Cy3 = D/L4h) was used to represent light responsiveness as described in manuscript  (log2 L4h/D).

organism: Arabidopsis thaliana

source_name: dark-grown

label_protocol: Cy5- and Cy3- labeled cRNA were prepared according to standard Agilent protocol from 8 ng poly A+ RNA (Two-color Microarray-based Gene Expression Analysis protocol, v. 5.7, Agilent Technologies).

growth_protocol: Seeds were surface sterilized and plated on 1/2 MS plates and grown 4 days at 22 under the dark.

extract_protocol: Pine Tree Method as described in Chang et al, Plant J 54, 205 (2008) (PMID 18182030).  mRNA was purified by Oligotex mRNA isolation kit (Qiagen, Valenica, CA).

treatment_protocol: 4-day-old etiolated seedlings

value: seedling

value: 4 days

tag: growth protocol

value: dark-grown

treatment_protocol: 4-day-old etiolated seedlings were illuminated with white light (100 mole m-2 s-1) at 22℃ for 4 h (L4 h).


title: Control 1


title: Foxp3EGFPCre#5

city: Boston

first: Talal

last: Chatila

state: MA

address: 1 Blackfan Circle Karp Family Building, RB10-214

department: Division of Immunology

institute: Harvard Medical School Division of Immunology The Boston Children's Hospital

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

source_name: Spleen

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

value: spleen

value: regulatory T cells

value: 6 Weeks Old

tag: exclusion markers

value: CD8, B220, CD11b, CD11c, Gr1, DAPI

tag: genetic background

value: Foxp3EGFPcre (Bluestone)

tag: phenotype markers

value: CD3, TCRbeta, CD4 and GFP (Foxp3)

tag: separation method

value: MoFlo Sorter

value: Male


title: Arabidopsis_L4h_rep3 [array]

description:
Biosample: SAMN02251449
Sample name: ASarray_DL4h_3


title: SK-N-MC_siControl_rep1

value: SK-N-MC


title: Ethanol 2

value: male

value: post-natal day 70

value: adult

tag: tissue

value: hippocampus


title: Foxp3EGFPCre#4

tag: cell type


title: Foxp3EGFPCre#3


title: Arabidopsis_L4h_rep2 [array]

description:
Biosample: SAMN02251448
Sample name: ASarray_DL4h_2


title: Foxp3EGFPCreRBPJ∆/∆#2

value: RBPJfl/fl (Pr Tasuku Honjo) x Foxp3EGFPcre (Bluestone)


title: WT7_vs_WT0_rep1

city: Lille

first: Mathias

last: Chamaillard

address: 1, rue Prof A. Calmette

department: Center for Infection and Immunity of Lille

country: France

institute: Inserm

description:
C rodentium infected Wild-type mouse at day 7 (test) versus non-infected Wild-type mice replicate 1  (reference)
Biological replicate 1 of 2

hyb_protocol: 850 ng of each linearly amplified cRNA per cyanine were cohybridized on microarrays ( Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F) using  Agilent Gene Expression Hybridization Kit , and enclosed in Agilent SureHyb-enabled hybridization chambers during 17 hours at 65°C rotated at 10 rpm . After hybridization, slides were washed sequential

scan_protocol: Scanned on an Innoscan 700 scanner ( Innopsys ) Images were quantified using Mapix Software (version 3.2.1).

data_processing: A specific script on R was used ( limma library ) for LOWESS normalization within slide and between slides.

source_name: caecum

label_protocol: 500 ng of total RNA were labeled using Quick-amp labeling kit 2 colors, following manufacturer's informations

growth_protocol: RNA was isolated from the caecum of Nlrp12-deficient and wild type mice at day 0 and 7 post C. rodentium infection

extract_protocol: Total RNA extracted using Rneasy Mini kit- Qiagen following manufacturer's instructions

treatment_protocol: Nlrp12-deficient and wild type C57BL6/J mice were infected or not with 1x10^9 colony-forming units of C. rodentium

value: caecum

tag: genotype

value: non-infected wild-type

tag: treatment

value: day 0

value: infected wild-type

value: day 7


title: Foxp3EGFPCreRBPJ∆/∆#1

value: spleen

value: regulatory T cells

value: 6 Weeks Old


title: Foxp3EGFPCreR26N1c/N1c#4

value: CD8, B220, CD11b, CD11c, Gr1, DAPI

value: R26N1c/N1c  (Douglas A Melton) x Foxp3EGFPcre (Bluestone)

value: CD3, TCRbeta, CD4 and GFP (Foxp3)


title: Foxp3EGFPCre#2

value: Foxp3EGFPcre (Bluestone)

value: MoFlo Sorter

value: Male


title: Foxp3EGFPCreR26N1c/N1c#2


title: WT7_vs_WT0_rep1_dye_swap

description:
C rodentium infected Wild-type mouse at day 7 (test) versus non-infected Wild-type mice replicate 1 by dye swap color (reference)
Biological replicate 1 of 2
In the sample table, the dye-swap sample values have been inversed, so that all table values display test over reference.


title: Foxp3EGFPCreR26N1c/N1c#5


title: M7_vs_WT7_rep2_dye_swap

description:
C rodentium infected Nlrp12-deficient C57BL6J mouse at day 7 (test) versus C rodentium infected Wild-type mouse at day 7 replicate 2 by dye swap color (reference)
Biological replicate 2 of 3
In the sample table, the dye-swap sample values have been inversed, so that all table values display test over reference.

value: infected Nlrp12-/-


title: WT7_vs_WT0_rep2

description:
C rodentium infected Wild-type mouse at day 7 (test) versus non-infected Wild-type mice replicate 2 (reference)
Biological replicate 2 of 2


title: Foxp3EGFPCreR26N1c/N1c#1


title: Foxp3EGFPCreRBPJ∆/∆#4


title: M7_vs_WT7_rep2

description:
C rodentium infected Nlrp12-deficient C57BL6J mouse at day 7 (test) versus C rodentium infected Wild-type mouse at day 7 replicate 2 (reference)
Biological replicate 2 of 3


title: M7_vs_WT7_rep3_dye_swap

description:
C rodentium infected Nlrp12-deficient C57BL6J mouse at day 7 (test) versus C rodentium infected Wild-type mouse at day 7 replicate 3 by dye swap color (reference)
Biological replicate 3 of 3
In the sample table, the dye-swap sample values have been inversed, so that all table values display test over reference.


title: WT7_vs_WT0_rep2_dye_swap

description:
C rodentium infected Wild-type mouse at day 7 (test) versus non-infected Wild-type mice replicate 2 by dye swap color (reference)
Biological replicate 2 of 2
In the sample table, the dye-swap sample values have been inversed, so that all table values display test over reference.


title: M7_vs_WT7_rep1

description:
C rodentium infected Nlrp12-deficient C57BL6J mouse at day 7 (test) versus C rodentium infected Wild-type mouse at day 7 replicate 1  (reference)
Biological replicate 1 of 3


title: Colon_RPS_rep4

city: Nanjing

first: Yong

last: Su

address: Weigang 1#

institute: Nanjing Agricultural University

description: Gene expression in the colonic mucosa of pigs fed RPS diet

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using a Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, CA, USA) in a hybridization oven.

scan_protocol: After 17 h of hybridization, the slides were washed with a Gene Expression Wash Buffer Kit (Agilent technologies, Santa Clara, CA, USA), according to the manufacturer’s instructions. The slides were then scanned on an Agilent Microarray Scanner (Agilent Technologies, Santa Clara, CA, USA).

data_processing: data was extracted using Feature Extraction Software 10.7 (Agilent Technologies, Santa Clara, CA, USA). The raw data was normalized using a quantile algorithm, Gene Spring Software 11.0 (Agilent Technologies, Santa Clara, CA, USA).

organism: Sus scrofa

source_name: Colon, RPS group, replicate 4

label_protocol: The total RNA was amplified and labeled using a Low Input Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA), following the manufacturer’s instructions.

growth_protocol: Pigs in the control group were offered a corn/soybean-based diet, while 230 g/kg purified corn starch (CS) was replaced with purified RPS in the RPS diet group. Diets were formulated according to the nutrient requirements of the National Research Council (1998). When animals reached the age of 120 days, diets were adapted to the nutrient requirements of the animals (finishing diet) and the amount of purified starch increased to 280 g of CS or RPS per kilogram of feed. Pigs had unlimited access to feed and water throughout the experimental period, which consisted of two 50-day trials in which the pigs consumed the growing diet (days 0-50) and finishing diet (days 51-100), respectively.

extract_protocol: The total RNA was extracted using the TRIzol reagent (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions and then checked for RNA integrity and purity using an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). The total qualified RNA was further purified using an RNeasy mini kit (QIAGEN, GmBH, Germany) and an RNase-Free DNase Set (QIAGEN, GmBH, Germany). Only those samples that had an OD260/OD280 ratio of approximately 2.0 and showed no degradation (RNA integrity number ≥ 7.0) were used to generate labeled targets.

treatment_protocol: The liver and colonic mucosa tissues were collected and preserved in liquid nitrogen.

tag: breed

value: Duroc × Landrace × Large White

value: colonic mucosa

tag: gender

value: male


title: Foxp3EGFPCreR26N1c/N1cRBPJ∆/∆#1

value: RBPJfl/fl (Pr Tasuku Honjo) xR26N1c/N1c  (Douglas A Melton)x Foxp3EGFPcre (Bluestone)

value: FACSAria

tag: Sex


title: M7_vs_WT7_rep3

description:
C rodentium infected Nlrp12-deficient C57BL6J mouse at day 7 (test) versus C rodentium infected Wild-type mouse at day 7 replicate 3 (reference)
Biological replicate 3 of 3

value: caecum

value: infected wild-type


title: Foxp3EGFPCreRBPJ∆/∆#3

value: spleen

value: RBPJfl/fl (Pr Tasuku Honjo) x Foxp3EGFPcre (Bluestone)


title: Colon_RPS_rep1

source_name: Colon, RPS group, replicate 1


title: Foxp3EGFPCreR26N1c/N1cRBPJ∆/∆#2

value: regulatory T cells

value: 6 Weeks Old


title: M7_vs_M0_rep2_dye_swap

description:
C rodentium infected Nlrp12-deficient C57BL6J mouse at day 7 (test) versus non-infected Nlrp12-deficient mice replicate 2 by dye swap color (reference)
Biological replicate 2 of 2
In the sample table, the dye-swap sample values have been inversed, so that all table values display test over reference.

value: day 7

value: non-infected Nlrp12-/-

value: day 0


title: M7_vs_WT7_rep1_dye_swap

description:
C rodentium infected Nlrp12-deficient C57BL6J mouse at day 7 (test) versus C rodentium infected Wild-type mouse at day 7 replicate 1 by dye swap color (reference)
Biological replicate 1 of 3
In the sample table, the dye-swap sample values have been inversed, so that all table values display test over reference.


title: Colon_RPS_rep3

source_name: Colon, RPS group, replicate 3


title: M7_vs_M0_rep1

description:
C rodentium infected Nlrp12-deficient C57BL6J mouse at day 7 (test) versus non-infected Nlrp12-deficient mice replicate 1  (reference)
Biological replicate 1 of 2


title: Colon_CS_rep2

description: Gene expression in the colonic mucosa of pigs fed CS diet

source_name: Colon, CS group, replicate 2


title: Colon_CS_rep4

source_name: Colon, CS group, replicate 4


title: Colon_CS_rep3

source_name: Colon, CS group, replicate 3


title: M0_vs_WT0_rep3

description:
Nlrp12-deficient C57BL6J mouse at day 0 (test) versus Wild-type mouse at day 0 both infected by Citrobacter rodentium replicate 3 (reference)
Biological replicate 3 of 3


title: CTR LC 4

first: Jeremy

last: Price

state: NY

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: According to ImmGen SOP

scan_protocol: According to ImmGen SOP

data_processing: RMA normalization according to ImmGen SOP

source_name: Mouse LC isolated from naïve mice

label_protocol: According to ImmGen SOP

growth_protocol: Adult wild type C57:Bl6 mice were ordered from NCI Frederick.

extract_protocol: Cells were isolated by flow cytometry directly into Trizol. Samples were then packaged and sent to the Immgen Consortium for processing (Immgen.org)

value: Langerhans cells

value: wildtype


title: LC + IR 3

source_name: Mouse LC isolated from mice pretreated with 12 Gy ionizing radiation


title: M0_vs_WT0_rep3_dye_swap

description:
Nlrp12-deficient C57BL6J mouse at day 0 (test) versus Wild-type mouse at day 0 both infected by Citrobacter rodentium replicate 3 by dye swap color (reference)
Biological replicate 3 of 3
In the sample table, the dye-swap sample values have been inversed, so that all table values display test over reference.

value: infected Nlrp12-/-


title: M7_vs_M0_rep1_dye_swap

description:
C rodentium infected Nlrp12-deficient C57BL6J mouse at day 7 (test) versus non-infected Nlrp12-deficient mice replicate 1 by dye swap color (reference)
Biological replicate 1 of 2
In the sample table, the dye-swap sample values have been inversed, so that all table values display test over reference.


title: Colon_RPS_rep2

source_name: Colon, RPS group, replicate 2

value: Duroc × Landrace × Large White


title: Liver_RPS_rep4

description: Gene expression in the liver of pigs fed RPS diet

source_name: Liver, RPS group, replicate 4

value: liver


title: CTR LC 3


title: LC + IR 1


title: Liver_RPS_rep3

source_name: Liver, RPS group, replicate 3

value: male


title: Liver_RPS_rep1

source_name: Liver, RPS group, replicate 1


title: Colon_CS_rep1

source_name: Colon, CS group, replicate 1

value: colonic mucosa


title: Liver_RPS_rep2

source_name: Liver, RPS group, replicate 2


title: M0_vs_WT0_rep1_dye_swap

description:
Nlrp12-deficient C57BL6J mouse at day 0 (test) versus Wild-type mouse at day 0 both infected by Citrobacter rodentium replicate 1 by dye swap color (reference)
Biological replicate 1 of 3
In the sample table, the dye-swap sample values have been inversed, so that all table values display test over reference.


title: CTR LC 1


title: Liver_CS_rep3

description: Gene expression in the liver of pigs fed CS diet

source_name: Liver, CS group, replicate 3


title: CTR LC 2


title: LC + IR 2


title: Liver_CS_rep4

source_name: Liver, CS group, replicate 4


title: M0_vs_WT0_rep2

description:
Nlrp12-deficient C57BL6J mouse at day 0 (test) versus Wild-type mouse at day 0 both infected by Citrobacter rodentium replicate 2 (reference)
Biological replicate 2 of 3

source_name: caecum


title: M0_vs_WT0_rep1

description:
Nlrp12-deficient C57BL6J mouse at day 0 (test) versus Wild-type mouse at day 0 both infected by Citrobacter rodentium replicate 1 (reference)
Biological replicate 1 of 3


title: Foxp3EGFPCreR26N1c/N1cRBPJ∆/∆#3

source_name: Spleen

value: CD8, B220, CD11b, CD11c, Gr1, DAPI

value: RBPJfl/fl (Pr Tasuku Honjo) xR26N1c/N1c  (Douglas A Melton)x Foxp3EGFPcre (Bluestone)

value: CD3, TCRbeta, CD4 and GFP (Foxp3)

value: FACSAria

value: Male