title: Liver_Control_Clamp_rep7

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description:
V_CL_32
Gene expression data from liver tissue derived from C57BL/6NTac control mice undergoing a hyperinsulinemic-euglycemic clamp.

hyb_protocol: According to the Affymetrix expression protocol (HWS kit).

scan_protocol: According to the Affymetrix expression protocol, Scanner 3000 7G.

data_processing: RMA probeset summary with standard settings of the Affymetrix Expression Console software (v.1.3.0.187) including median polish and Sketch-Quantile normalisation.

source_name: Liver tissue derived from C57BL/6NTac control mice undergoing a hyperinsulinemic-euglycemic clamp

label_protocol: Ovation PicoSL WTA System V2 and Encore Biotin Module (Nugen).

growth_protocol: Animals housed under spf conditions.

extract_protocol: miRNeasy Mini (Qiagen) including DNase treatment.

treatment_protocol:
As described in the paper. Briefly, mice were fasted for 10 h and were given 2 g/kg BM of PO (Landkrone, Germany) or water (VCL) per gavage. Lateral tail vein blood samples were obtained prior to treatment and 2 hours after. 6 hours after treatment, mice were euthanized with isoflurane and a vena cava-blood sample was collected, centrifuged at 4 °C, and plasma aliquots were immediately frozen in liquid nitrogen. Liver was dissected and immediately snap frozen in liquid nitrogen. For mice undergoing an hyperinsulinemic-euglycemic clamp, a permanent jugular vein catheter was placed in male C57BL/6NTac mice, while under ketamine/xylazine-anesthesia. 6-7 days later, mice were fasted for 10 hours, then received 2g/ kg BM PO or VCL via gavage. 6 hours later, unrestrained, conscious mice underwent euglycemic hyperinsulinemic clamp.
After 110 minutes of primed-continuous [3-3H]glucose infusion (1.85 kBq/min), a blood sample was collected to determine plasma insulin, glucose and [3-3H] glucose concentrations for calculating basal EGP. A [3-3H]glucose infusion (3.7 kBq/min) containing insulin (15 pmol/kg·min-1; HumulinR, Lilly, USA) was started. Blood glucose concentrations were measured every 10 minutes and target glycemia established by adjusting the GIR. At minute 120, 2-deoxy-D-[1-14C]glucose (370 kBq) was injected IV, to assess rates of tissue specific glucose uptake (Rg). Mice were euthanized by means of an IV ketamine/ xylazine injection. Liver was collected, immediately snap-frozen in liquid nitrogen, and stored at -80°C.

tag: strain/background

tag: genotype/variation

value: WT

value: 14 weeks

value: male

value: liver

tag: treatment

value: water

tag: hyperinsulinemic-euglycemic clamp

value: yes


title: RCH_ACV_U1

status: Public on Feb 02 2017

type: RNA

city: Iowa City

first: Miles

middle: A

last: Pufall

state: IA

address: 51 Newton Rd., BSB Rm 4-430

department: Biochemistry

country: USA

institute: University of Iowa

description: control

hyb_protocol: According to UCLA Neuroscience Genomics Core (UNGC) protocol

data_processing: Bioconductor lumi/limma

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: DSMZ cell line

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

growth_protocol: All cells were geown in RPMI plus 10% FBS with no antibiotics

extract_protocol: Qiagen miRNAeasy

treatment_protocol: Cells were treated with 1µM dexamethasone for 4 hours or 0.1% ethanol as a vehicle control

tag: cell line

value: B cell ALL cell line

tag: dex treatment

value: control

tag: treatment response

value: dexamethasone resistant

tag: diagnostic or relapse


title: C1 Synchronous Paraganglioma two

type: genomic

city: Melbourne

first: Aidan

middle: John

last: Flynn

state: Victoria

address: 305 Grattan St

department: Research

country: Australia

institute: Peter MacCallum Cancer Center

description:
Fresh Frozen DNA, CytoscanHD
C1-PGL2

hyb_protocol: Affymetrix CytoscanHD/OncoScan standard protocol

data_processing: Chromosome Analysis Suite (ChAS) with internal reference

molecule: genomic DNA

extract_protocol: DNA was extracted from fresh frozen tissue samples with the Qiagen Dneasy blood and tissue kit, or from formalin-fixed parrafin-embedded tissue using the Qiagen QIAamp FFPE DNA kit

tag: tissue

tag: Sex

value: Male

tag: Stage

value: benign


title: RCH_ACV_I1

description: treated

scan_protocol: According to UCLA Neuroscience Genomics Core (UNGC) protocol

value: dexamethasone


title: RS_4_11_I2

description: treated

value: dexamethasone sensitive


title: Nalm6_I2

description: treated


title: Liver_Control_Clamp_rep6

country: Germany

description:
V_CL_30
Gene expression data from liver tissue derived from C57BL/6NTac control mice undergoing a hyperinsulinemic-euglycemic clamp.

organism: Mus musculus

tag: age

tag: gender


title: Nalm6_U1

description: control


title: Nalm6_U3

description: control


title: Nalm6_U2

description: control


title: RS_4_11_I1

description: treated


title: RS_4_11_I3

description: treated


title: Nalm6_I1

description: treated


title: Nalm6_I3

description: treated


title: KOPN_8_I3

description: treated


title: RCH_ACV_I2

description: treated


title: Liver_Control_Clamp_rep3

description:
V_CL_23
Gene expression data from liver tissue derived from C57BL/6NTac control mice undergoing a hyperinsulinemic-euglycemic clamp.


title: Liver_Control_Clamp_rep5

description:
V_CL_29
Gene expression data from liver tissue derived from C57BL/6NTac control mice undergoing a hyperinsulinemic-euglycemic clamp.


title: KOPN_8_I1

description: treated


title: KOPN_8_I2

description: treated


title: KOPN_8_U3

description: control


title: Liver_Control_Clamp_rep4

description:
V_CL_26
Gene expression data from liver tissue derived from C57BL/6NTac control mice undergoing a hyperinsulinemic-euglycemic clamp.


title: Liver_Control_basal_rep6

description:
V_B _50
Gene expression data from liver tissue derived from C57BL/6NTac control mice.

source_name: Liver tissue derived from C57BL/6NTac control mice

value: no


title: Liver_Control_basal_rep1

description:
V_B _36
Gene expression data from liver tissue derived from C57BL/6NTac control mice.


title: Liver_Control_basal_rep7

description:
V_B _52
Gene expression data from liver tissue derived from C57BL/6NTac control mice.


title: Liver_Control_basal_rep2

description:
V_B _38
Gene expression data from liver tissue derived from C57BL/6NTac control mice.


title: Liver_Control_basal_rep3

description:
V_B _40
Gene expression data from liver tissue derived from C57BL/6NTac control mice.


title: Liver_Control_Clamp_rep1

description:
V_CL_16
Gene expression data from liver tissue derived from C57BL/6NTac control mice undergoing a hyperinsulinemic-euglycemic clamp.


title: LNA-control-treated MDA-MB-231 cells (rep1)

city: Gosselies

first: Martin

last: Bizet

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

description:
9978099040_B
Replicate 1

hyb_protocol: Total RNA (200ng) was amplified with the Illumina TotalPrep RNA Amplification Kit (Ambion) and hybridized with the Illumina HumanHT-12 v4 array according to the instructions of the Whole-Genome Gene Expression Direct Hybridization Assay (Illumina).

scan_protocol: Chips were scanned with the HiScan Reader (Illumina).

data_processing: Raw data were quantile normalized using the normalization method from the lumi package and batch effect corrected using Combat. Control probes have been filtered out (replaced by null). Log2-transformed data are provided.

source_name: MDA-MB-231 cell line, LNA_Ctrl

label_protocol: Standard Illumina protocol.

growth_protocol: MDA-MB-231 cells were grown in DMEM (Gibco) supplemented with 10% FBS (Gibco). They were maintained at 37°C in 5% CO2.

extract_protocol: RNA purification was performed with the RNeasy kit (Qiagen) according to the manufacturer's instructions. DNase treatment was performed with a DNA-free DNase kit (Ambion) according to the manufacturer's protocol.

treatment_protocol: Cells were treated with LNA gapmeRs (Exiqon) according to the manufacturer's instructions. Briefly, 300,000 cells were transfected in 6-well plates with 30 nM LNA gapmeRs and 5 μl Lipofectamine 2000 in 2 ml total volume and incubated for 24 h.

tag: cell type

value: breast cancer cell line

tag: lna type

value: Control

tag: batch


title: Liver_Control_basal_rep4

description:
V_B _44
Gene expression data from liver tissue derived from C57BL/6NTac control mice.


title: Liver_Control_Clamp_rep2

description:
V_CL_18
Gene expression data from liver tissue derived from C57BL/6NTac control mice undergoing a hyperinsulinemic-euglycemic clamp.


title: CYTOR-silenced MDA-MB-231 cells (rep6)

description:
9978099040_K
Replicate 6

source_name: MDA-MB-231 cell line, LNA_CYTOR

value: CYTOR (LINC00152)


title: LNA-control-treated MDA-MB-231 cells (rep6)

description:
9978099040_L
Replicate 6


title: CYTOR-silenced MDA-MB-231 cells (rep5)

description:
9978099040_I
Replicate 5


title: Liver_Control_basal_rep5

description:
V_B _46
Gene expression data from liver tissue derived from C57BL/6NTac control mice.

value: WT


title: LNA-control-treated MDA-MB-231 cells (rep3)

description:
9978099040_F
Replicate 3


title: CYTOR-silenced MDA-MB-231 cells (rep3)

description:
9978099040_E
Replicate 3


title: CYTOR-silenced MDA-MB-231 cells (rep1)

description:
9978099040_A
Replicate 1


title: Liver_PO_Clamp_rep9

description:
PO_CL_31
Gene expression data from liver tissue derived from C57BL/6NTac mice treated with palm oil and undergoing a hyperinsulinemic-euglycemic clamp.

source_name: Liver tissue derived from C57BL/6NTac mice treated with palm oil and undergoing a hyperinsulinemic-euglycemic clamp

value: 14 weeks

value: palm oil


title: CYTOR-silenced MDA-MB-231 cells (rep4)

description:
9978099040_G
Replicate 4


title: LNA-control-treated MDA-MB-231 cells (rep4)

description:
9978099040_H
Replicate 4


title: LNA-control-treated MDA-MB-231 cells (rep2)

description:
9978099040_D
Replicate 2


title: Liver_PO_Clamp_rep8

description:
PO_CL_28
Gene expression data from liver tissue derived from C57BL/6NTac mice treated with palm oil and undergoing a hyperinsulinemic-euglycemic clamp.

value: male

value: liver


title: LNA-control-treated MDA-MB-231 cells (rep5)

description:
9978099040_J
Replicate 5


title: CYTOR-silenced MDA-MB-231 cells (rep2)

description:
9978099040_C
Replicate 2


title: KOPN_8_U2

description: control


title: KOPN_8_U1

description: control


title: Liver_PO_Clamp_rep5

description:
PO_CL_24
Gene expression data from liver tissue derived from C57BL/6NTac mice treated with palm oil and undergoing a hyperinsulinemic-euglycemic clamp.

value: yes


title: Liver_PO_Clamp_rep6

description:
PO_CL_25
Gene expression data from liver tissue derived from C57BL/6NTac mice treated with palm oil and undergoing a hyperinsulinemic-euglycemic clamp.


title: Liver_PO_Clamp_rep1

description:
PO_CL_15
Gene expression data from liver tissue derived from C57BL/6NTac mice treated with palm oil and undergoing a hyperinsulinemic-euglycemic clamp.


title: Liver_PO_Clamp_rep4

description:
PO_CL_21
Gene expression data from liver tissue derived from C57BL/6NTac mice treated with palm oil and undergoing a hyperinsulinemic-euglycemic clamp.


title: soy estradiol rep 2

city: Little Rock

first: Horacio

last: Gomez-Acevedo

state: Arkansas

address: 4301 W. Markham St

department: Biomedical Informatics

institute: University of Arkansas for Medical Sciences

hyb_protocol: Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N = 3/treatment) for 16 h at 45ºC in the hybridization oven set at 60 rpm.

scan_protocol: The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.

data_processing: Cel files were generated using GCOS and utilized for analysis using R/Bioconductor 3.4

organism: Rattus norvegicus

source_name: postnatal day 34 rat testes

label_protocol: First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA  reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions

growth_protocol: Pups of Sprague-Dawley were feed casein AIN-93G diets thorugh lactation.  On postnatal day (PND) 21, pups were assigned to one of four diet groups: casein AIN-93G; casein AIN-93G and infused s.c 17beta estradiol at 10 ug/kg/d through mini-osmotic pumps; AIN-93G made with SPI in place of casein; AIN-93G made with SPI and infused s.c. 17beta estradiol. At sacrifice (PND 34) testes were collected and fresh frozen in liquid nitrogen.

extract_protocol: Total RNA was isolated from the rats testes using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion

treatment_protocol: Testes were collected and fresh frozen in liquid nitrogen

value: testes

tag: developmental stage

value: postnatal day 34

tag: diet

value: 17-b estradiol and SPI

tag: strain

value: Sprague-Dawley


title: soy rep 3

value: Soy protein isolate


title: Liver_PO_Clamp_rep7

description:
PO_CL_27
Gene expression data from liver tissue derived from C57BL/6NTac mice treated with palm oil and undergoing a hyperinsulinemic-euglycemic clamp.

tag: strain/background

tag: genotype/variation

tag: treatment


title: caseine estradiol rep 2

value: 17-b estradiol


title: Liver_PO_Clamp_rep2

description:
PO_CL_17
Gene expression data from liver tissue derived from C57BL/6NTac mice treated with palm oil and undergoing a hyperinsulinemic-euglycemic clamp.

tag: hyperinsulinemic-euglycemic clamp


title: soy estradiol rep 3


title: Liver_PO_basal_rep8

description:
PO_B _49
Gene expression data from liver tissue derived from C57BL/6NTac mice treated with palm oil.

source_name: Liver tissue derived from C57BL/6NTac mice treated with palm oil


title: soy rep 1


title: Liver_PO_basal_rep5

description:
PO_B _42
Gene expression data from liver tissue derived from C57BL/6NTac mice treated with palm oil.


title: soy estradiol rep 1


title: soy rep 2


title: caseine rep 1

value: Caseine


title: Liver_PO_basal_rep7

description:
PO_B _45
Gene expression data from liver tissue derived from C57BL/6NTac mice treated with palm oil.

value: no


title: caseine estradiol rep 1


title: Liver_PO_basal_rep9

description:
PO_B _51
Gene expression data from liver tissue derived from C57BL/6NTac mice treated with palm oil.


title: Liver_PO_basal_rep6

description:
PO_B _43
Gene expression data from liver tissue derived from C57BL/6NTac mice treated with palm oil.


title: Liver_PO_Clamp_rep3

description:
PO_CL_19
Gene expression data from liver tissue derived from C57BL/6NTac mice treated with palm oil and undergoing a hyperinsulinemic-euglycemic clamp.


title: caseine estradiol rep 3


title: Liver_PO_basal_rep3

description:
PO_B _37
Gene expression data from liver tissue derived from C57BL/6NTac mice treated with palm oil.


title: Liver_PO_basal_rep4

description:
PO_B _39
Gene expression data from liver tissue derived from C57BL/6NTac mice treated with palm oil.


title: caseine rep 2


title: Liver from MAT1A WT mice 665K placebo treated_Gene expression array

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

country: Spain

institute: CIC bioGUNE

description:
WTP
S_665K

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

label: Biotin

source_name: placebo-treated

label_protocol: TargetAmp™ Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System (Epicentre)

growth_protocol: Mice were breed and housed at the Animal Facility of CIC bioGUNE under controled conditions according to the animal care international gidelines.

extract_protocol: RNA was extracted from the livers using AllPrep DNA/RNA Mini Kit

tag: genotype

value: MAT1A WT

value: 10 month


title: C5 primary three

description:
FFPE DNA, Oncoscan
C5-T3

scan_protocol: Affymetrix CytoscanHD/OncoScan standard protocol

source_name: Medullary thyroid carcinoma, third primary tumour

value: Female


title: caseine rep 3


title: C5 primary two (low Ki67)

description:
FFPE DNA, Oncoscan
C5-T2LowKi67

source_name: Medullary thyroid carcinoma, second primary tumour with low Ki67

label_protocol: Affymetrix CytoscanHD/OncoScan standard protocol


title: C5 Primary one (High Ki67 region)

description:
FFPE DNA, Oncoscan
C5-T1HiKi67

source_name: Medullary thyroid carcinoma, first primary tumour, High Ki67 region


title: Liver from MAT1A WT mice 666K placebo treated_Gene expression array

description:
WTP
S_666K


title: Liver from MAT1A WT mice 660K placebo treated_Gene expression array

description:
WTP
S_660K


title: Liver from MAT1A WT mice 664K placebo treated_Gene expression array

description:
WTP
S_664K


title: Liver from MAT1A WT mice 663K placebo treated_Gene expression array

description:
WTP
S_663K


title: Liver from MAT1A KO mice 408G placebo treated_Gene expression array

description:
MKP
S_408G

value: MAT1A KO


title: Liver from MAT1A KO mice 324K SAMe treated_Gene expression array

description:
MKSAM
S_324K

source_name: SAMe-treated


title: Liver from MAT1A WT mice 658K placebo treated_Gene expression array

description:
WTP
S_658K


title: Liver_PO_basal_rep2

description:
PO_B _35
Gene expression data from liver tissue derived from C57BL/6NTac mice treated with palm oil.

value: WT

value: 14 weeks


title: Liver from MAT1A KO mice 990I SAMe treated_Gene expression array

description:
MKSAM
S_990I


title: Liver from MAT1A KO mice 409G placebo treated_Gene expression array

description:
MKP
S_409G


title: Liver from MAT1A KO mice 021J placebo treated_Gene expression array

description:
MKP
S_021J


title: Liver from MAT1A WT mice 661K placebo treated_Gene expression array

description:
WTP
S_661K


title: Liver from MAT1A KO mice 030J placebo treated_Gene expression array

description:
MKP
S_030J


title: Liver_PO_basal_rep1

description:
PO_B _33
Gene expression data from liver tissue derived from C57BL/6NTac mice treated with palm oil.

value: male

value: palm oil


title: Liver from MAT1A KO mice 986I SAMe treated_Gene expression array

description:
MKSAM
S_986I

value: liver


title: Liver from MAT1A KO mice 322K SAMe treated_Gene expression array

description:
MKSAM
S_322K


title: Liver from MAT1A WT mice 659K placebo treated_Gene expression array

description:
WTP
S_659K


title: Liver from MAT1A KO mice 849G SAMe treated_Gene expression array

description:
MKSAM
S_849G


title: Liver from MAT1A KO mice 024J placebo treated_Gene expression array

description:
MKP
S_024J


title: Liver from MAT1A KO mice 028J placebo treated_Gene expression array

description:
MKP
S_028J


title: DUCT-2

city: Glasgow

first: Torsten

last: Stein

address: College of MVLS

department: School of Medicine

country: United Kingdom

institute: University of Glasgow

hyb_protocol: Standard Manufacturer's (Affymetrix) protocol for mouse whole-genome exon arrays (GeneChip-Mouse-Exon-1.0-ST-Array, Affymetrix UK Ltd., High Wycombe, UK) using a GeneChip Fluidics Station 450/250.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G

data_processing:
CEL-files were analysed and normalised by RMA using the open-source ‘Altanalyze’ software (Emig et al., 2010), using default setting.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoGene-1_0-st-v1.na28.mm9.transcript.csv

source_name: Mouse mammary gland from 5-6 week old female pubertal mice_Ducts

growth_protocol: Mice were kept in the Biological Services Facility on a 12 hour night/day cycle with water and food available ad libidum

extract_protocol: RNA was isolated using TRI reagent, followed by further purification with a QIAGEN RNA Mini isolation kit and on-column DNase treatment. Biotinylated cRNA was prepared using 1.5 microg of total RNA. rRNA was removed using a RiboMinus Human/MouseTranscriptome Isolation kit and RiboMinus magnetic beads.

treatment_protocol: Mice were humanely killed at 6-7 weeks of age (16-18g) and the inguinal mammary glands were dissected and collected

value: female

value: 5-6 week old;  pubertal

value: 4th (inguinal) mammary gland

tag: tissue type

value: Ducts


title: TEB-1

source_name: Mouse mammary gland from 5-6 week old female pubertal mice_Terminal End Buds

label_protocol: Standard Manufacturer's (Affymetrix) protocol

tag: tissue

value: Terminal End Buds


title: TEB-2


title: Neutrophils, Patient, JIA, ID, Biological replicate 17 [miRNA]

status: Public on Feb 01 2017

city: Buffalo

first: kaiyu

last: Jiang

state: NY

address: 875 Ellicott Street

department: Pediatrics

institute: University at Buffalo

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr on Affymetrix human EXON 1.0 ST array or GeneChip™ miRNA 1.0 array following manufacturer's directions. GeneChips were washed and stained in an Affymetrix 450 Fluidics Station.

scan_protocol: GeneChips were scanned using an Affymetrix 3000 7G scanner.

data_processing: Expression summary values from Affymetrix Exon and miRNA arrays were generated using RMA software in the Affy package of Bioconductor in the R statistical computing environment.

source_name: neutrophil RNA, JIA, ID

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

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was further purified using RNeasy MiniElute Cleanup kit including a DNase digest according to the manufacturer's instructions (QIAGEN, Valencia, CA).

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were separated from neutrophils and red blood cells by density-gradient centrifugation. Red cells were removed from neutrophils by hypotonic lysis. Neutrophils were then immediately placed in TRIzol® reagent (Invitrogen, Carlsbad, CA) and stored at -80C.

tag: disease state

value: juvenile idiopathic arthritis (JIA)

tag: group

value: inactive disease, on therapy (ID)

value: neutrophils


title: Neutrophils, Patient, JIA, ID, Biological replicate 16 [miRNA]


title: Neutrophils, Patient, JIA, ID, Biological replicate 12 [miRNA]


title: Neutrophils, Patient, JIA, ID, Biological replicate 15 [miRNA]


title: Neutrophils, Patient, JIA, ID, Biological replicate 11 [miRNA]


title: Neutrophils, Patient, JIA, ID, Biological replicate 14 [miRNA]


title: Neutrophils, Patient, JIA, ID, Biological replicate 13 [miRNA]


title: Neutrophils, Patient, JIA, ID, Biological replicate 9 [miRNA]


title: DUCT-1

tag: age


title: Neutrophils, Patient, JIA, ID, Biological replicate 7 [miRNA]


title: Neutrophils, Patient, JIA, ID, Biological replicate 8 [miRNA]


title: Neutrophils, Patient, JIA, ID, Biological replicate 10 [miRNA]


title: Neutrophils, Patient, JIA, ID, Biological replicate 6 [miRNA]


title: Neutrophils, Patient, JIA, ID, Biological replicate 5 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 30 [miRNA]

source_name: neutrophil RNA, JIA, CRM

value: clinical remission, on medication (CRM)


title: Neutrophils, Patient, JIA, ID, Biological replicate 1 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 31 [miRNA]


title: Neutrophils, Patient, JIA, ID, Biological replicate 2 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 32 [miRNA]


title: Neutrophils, Patient, JIA, ID, Biological replicate 4 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 25 [miRNA]


title: Neutrophils, Patient, JIA, ID, Biological replicate 3 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 24 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 26 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 29 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 23 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 20 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 22 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 21 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 19 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 28 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 13 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 12 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 16 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 27 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 11 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 14 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 15 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 10 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 17 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 7 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 6 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 9 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 3 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 18 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 5 [miRNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 25 [miRNA]

source_name: neutrophil RNA, JIA, ADM

value: active disease, on therapy (ADM)


title: Neutrophils, Patient, JIA, ADM, Biological replicate 27 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 4 [miRNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 23 [miRNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 21 [miRNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 20 [miRNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 26 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 8 [miRNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 19 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 2 [miRNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 22 [miRNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 24 [miRNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 16 [miRNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 13 [miRNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 12 [miRNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 14 [miRNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 18 [miRNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 1 [miRNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 5 [miRNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 15 [miRNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 10 [miRNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 17 [miRNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 7 [miRNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 9 [miRNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 11 [miRNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 4 [miRNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 2 [miRNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 3 [miRNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 8 [miRNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 1 [miRNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 6 [miRNA]


title: DP20_190

city: Hoesholm

first: Anker

last: Hansen

address: Venlighedsvej 1

country: Denmark

institute: Medical Prognosis Institute A/S

description: FFPE

hyb_protocol: Affymetrix standardized protocol for U133p2 array

data_processing: R, affypackage, justRMA

source_name: Ovarian cancer

label_protocol: Affymetrix FlashTag™ Biotin HSR RNA Labeling protocol

extract_protocol: RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE

tag: Stage

value: I-IV


title: DP20_198

description: FFPE

scan_protocol: Affymetrix standardized protocol for U133p2 array


title: DP20_194

description: FFPE


title: DP20_195

description: FFPE


title: DP20_192

description: FFPE


title: DP20_193

description: FFPE


title: DP20_191

description: FFPE


title: DP20_196

description: FFPE


title: DP20_197

description: FFPE


title: DP20_189

description: FFPE


title: DP20_188

description: FFPE


title: DP20_187

description: FFPE


title: DP20_183

description: FFPE


title: DP20_182

description: FFPE


title: DP20_180

description: FFPE


title: DP20_186

description: FFPE


title: DP20_181

description: FFPE


title: DP20_184

description: FFPE


title: DP20_185

description: FFPE


title: DP20_178

description: FFPE


title: DP20_176

description: FFPE


title: DP20_177

description: FFPE


title: DP20_173

description: FFPE


title: DP20_179

description: FFPE


title: DP20_172

description: FFPE


title: DP20_174

description: FFPE


title: DP20_175

description: FFPE


title: DP20_171

description: FFPE


title: DP20_170

description: FFPE


title: DP20_169

description: FFPE


title: DP20_168

description: FFPE


title: DP20_166

description: FFPE


title: DP20_164

description: FFPE


title: DP20_167

description: FFPE


title: DP20_159

description: FFPE


title: DP20_160

description: FFPE


title: DP20_165

description: FFPE


title: DP20_162

description: FFPE


title: DP20_163

description: FFPE


title: DP20_161

description: FFPE


title: DP20_152

description: FFPE


title: DP20_151

description: FFPE


title: DP20_153

description: FFPE


title: DP20_154

description: FFPE


title: DP20_142

description: FFPE


title: DP20_158

description: FFPE


title: DP20_141

description: FFPE


title: DP20_144

description: FFPE


title: DP20_146

description: FFPE


title: DP20_145

description: FFPE


title: DP20_149

description: FFPE


title: DP20_157

description: FFPE


title: DP20_155

description: FFPE


title: DP20_143

description: FFPE


title: DP20_156

description: FFPE


title: DP20_150

description: FFPE


title: DP20_148

description: FFPE


title: DP20_147

description: FFPE


title: DP20_134

description: FFPE


title: DP20_132

description: FFPE


title: DP20_140

description: FFPE


title: DP20_133

description: FFPE


title: DP20_136

description: FFPE


title: DP20_120

description: FFPE


title: DP20_137

description: FFPE


title: DP20_126

description: FFPE


title: DP20_138

description: FFPE


title: DP20_119

description: FFPE


title: DP20_118

description: FFPE


title: DP20_130

description: FFPE


title: DP20_122

description: FFPE


title: DP20_139

description: FFPE


title: DP20_117

description: FFPE


title: DP20_123

description: FFPE


title: DP20_131

description: FFPE


title: DP20_124

description: FFPE


title: DP20_121

description: FFPE


title: DP20_129

description: FFPE


title: DP20_125

description: FFPE


title: DP20_116

description: FFPE


title: DP20_127

description: FFPE


title: DP20_114

description: FFPE


title: DP20_113

description: FFPE


title: DP20_112

description: FFPE


title: DP20_128

description: FFPE


title: DP20_111

description: FFPE


title: DP20_115

description: FFPE


title: Neutrophils, Patient, JIA, ADM, Biological replicate 28 [miRNA]

tag: cell type


title: DP20_108

description: FFPE


title: DP20_109

description: FFPE


title: DP20_104

description: FFPE


title: DP20_098

description: FFPE


title: DP20_110

description: FFPE


title: DP20_103

description: FFPE


title: DP20_096

description: FFPE


title: DP20_099

description: FFPE


title: DP20_100

description: FFPE


title: DP20_101

description: FFPE


title: DP20_105

description: FFPE


title: DP20_090

description: FFPE


title: DP20_084

description: FFPE


title: DP20_085

description: FFPE


title: DP20_102

description: FFPE


title: DP20_092

description: FFPE


title: DP20_088

description: FFPE


title: DP20_086

description: FFPE


title: DP20_087

description: FFPE


title: DP20_106

description: FFPE


title: DP20_093

description: FFPE


title: DP20_107

description: FFPE


title: DP20_091

description: FFPE


title: DP20_094

description: FFPE


title: DP20_079

description: FFPE


title: DP20_083

description: FFPE


title: DP20_089

description: FFPE


title: DP20_095

description: FFPE


title: DP20_081

description: FFPE


title: DP20_080

description: FFPE


title: DP20_082

description: FFPE


title: DP20_097

description: FFPE


title: DP20_075

description: FFPE


title: DP20_069

description: FFPE


title: DP20_070

description: FFPE


title: DP20_077

description: FFPE


title: DP20_068

description: FFPE


title: DP20_076

description: FFPE


title: DP20_063

description: FFPE


title: DP20_071

description: FFPE


title: DP20_066

description: FFPE


title: DP20_065

description: FFPE


title: DP20_078

description: FFPE


title: DP20_067

description: FFPE


title: DP20_072

description: FFPE


title: DP20_073

description: FFPE


title: DP20_060

description: FFPE


title: DP20_062

description: FFPE


title: DP20_074

description: FFPE


title: DP20_058

description: FFPE


title: DP20_059

description: FFPE


title: DP20_061

description: FFPE


title: DP20_057

description: FFPE


title: DP20_054

description: FFPE


title: DP20_056

description: FFPE


title: DP20_055

description: FFPE


title: DP20_064

description: FFPE


title: DP20_051

description: FFPE


title: DP20_050

description: FFPE


title: DP20_049

description: FFPE


title: DP20_053

description: FFPE


title: DP20_048

description: FFPE


title: DP20_044

description: FFPE


title: DP20_052

description: FFPE


title: DP20_045

description: FFPE


title: DP20_047

description: FFPE


title: DP20_036

description: FFPE


title: DP20_041

description: FFPE


title: DP20_039

description: FFPE


title: DP20_037

description: FFPE


title: DP20_040

description: FFPE


title: DP20_042

description: FFPE


title: DP20_034

description: FFPE


title: DP20_043

description: FFPE


title: DP20_032

description: FFPE


title: DP20_035

description: FFPE


title: DP20_031

description: FFPE


title: DP20_033

description: FFPE


title: DP20_046

description: FFPE


title: DP20_028

description: FFPE


title: DP20_027

description: FFPE


title: DP20_038

description: FFPE


title: DP20_026

description: FFPE


title: DP20_025

description: FFPE


title: DP20_024

description: FFPE


title: DP20_135

description: FFPE


title: DP20_023

description: FFPE


title: DP20_029

description: FFPE


title: DP20_020

description: FFPE


title: DP20_022

description: FFPE


title: DP20_021

description: FFPE


title: DP20_017

description: FFPE


title: DP20_016

description: FFPE


title: DP20_030

description: FFPE


title: DP20_019

description: FFPE


title: DP20_015

description: FFPE


title: DP20_014

description: FFPE


title: DP20_011

description: FFPE


title: DP20_018

description: FFPE


title: DP20_012

description: FFPE


title: DP20_013

description: FFPE


title: DP20_010

description: FFPE


title: DP20_002

description: FFPE


title: DP20_009

description: FFPE


title: DP20_004

description: FFPE


title: DP20_007

description: FFPE


title: DP20_008

description: FFPE


title: DP20_001

description: FFPE


title: DP20_006

description: FFPE


title: DP20_005

description: FFPE


title: DP20_003

description: FFPE


title: CB_D4 rep 3

city: London

first: Jingwen

last: Lin

address: The Ridgeway

institute: The Francis Crick Institute

description:
replicate 3
8762536056_B

data_processing: The data were normalised using quantile normalisation with GeneSpring GX13.1

source_name: Mouse Blood

extract_protocol: RNA was isolated using PerfectPure RNA Blood Kit (5 PRIME) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Caliper LabChip GX (Caliper Life Sciences)

treatment_protocol: Globin mRNA removal using the mouse GLOBINclear kit (Ambion) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: gender

value: Female

value: 6-8 weeks

value: Blood

tag: experiment

tag: infection

value: P. c. chabaudi CB

tag: day

value: day 4

tag: mouse selection

value: random


title: CB_D8 rep 1

description:
replicate 1
8762536049_D

tag: strain

value: day 8


title: CB_D10 rep 4

description:
replicate 4
8762536079_D

value: day 10


title: CB_D9 rep 2

description:
replicate 2
8762536097_D

value: day 9

value: reached human end point


title: CB_D10 rep 1

description:
replicate 1
8762536049_C


title: CB_D4 rep 4

description:
replicate 4
8762536078_A


title: CB_D4 rep 2

description:
replicate 2
8762536054_D


title: CB_D6 rep 2

description:
replicate 2
8762536056_F

value: day 6


title: CB_D8 rep 3

description:
replicate 3
8762536078_D


title: CB_D6 rep 3

description:
replicate 3
8762536079_A


title: CB_D12 rep 3

description:
replicate 3
8762536079_B

value: day 12


title: CB_D8 rep 2

description:
replicate 2
8762536054_E


title: CB_D4 rep 1

description:
replicate 1
8762536049_F


title: CB_D6 rep 4

description:
replicate 4
8762536097_B


title: CB_D12 rep 1

description:
replicate 1
8762536049_E


title: CB_D9 rep 4

description:
replicate 4
8762536054_A


title: CB_D9 rep 1

description:
replicate 1
8762536055_B


title: CB_D10 rep 3

description:
replicate 3
8762536078_B


title: CB_D10 rep 2

description:
replicate 2
8762536056_C


title: CB_D2 rep 3

description:
replicate 3
8762536055_F

value: day 2


title: CB_D6 rep 1

description:
replicate 1
8762536055_A


title: CB_D12 rep 2

description:
replicate 2
8762536078_C


title: CB_D2 rep 1

description:
replicate 1
8762536049_B


title: CB_D8 rep 4

description:
replicate 4
8762536097_F


title: CB_D9 rep 3

description:
replicate 3
8762536078_F


title: CB_D2 rep 2

description:
replicate 2
8762536054_C


title: CB_D2 rep 4

description:
replicate 4
8762536079_C


title: CB_naive_D12 rep 1

description:
replicate 1
8762536054_F

value: naïve


title: AS_D12 rep 3

description:
replicate 3
8784170061_C

value: P. c. chabaudi AS


title: AS_D2 rep 4

description:
replicate 4
8784170059_C


title: AS_D4 rep 2

description:
replicate 2
8762536084_F


title: CB_naive_D12 rep 3

description:
replicate 3
8762536056_A


title: AS_D6 rep 3

description:
replicate 3
8784170059_B


title: AS_D8 rep 3

description:
replicate 3
8784170059_E


title: AS_D10 rep 2

description:
replicate 2
8762536135_D


title: CB_naive_D0 rep 1

description:
replicate 1
8762536055_D

value: day 0


title: AS_D12 rep 2

description:
replicate 2
8762536084_E


title: AS_D12 rep 1

description:
replicate 1
8762536072_C


title: CB_naive_D0 rep 3

description:
replicate 3
8762536079_E


title: AS_D2 rep 1

description:
replicate 1
8762536072_F


title: AS_D6 rep 2

description:
replicate 2
8762536135_A


title: AS_D10 rep 1

description:
replicate 1
8762536052_C


title: AS_D4 rep 3

description:
replicate 3
8784170061_A


title: AS_naive_D12 rep 3

description:
replicate 3
8784170059_F


title: AS_D2 rep 3

description:
replicate 3
8762536135_C


title: AS_D6 rep 1

description:
replicate 1
8762536052_E


title: CB_naive_D12 rep 2

description:
replicate 2
8762536055_E


title: AS_D8 rep 2

description:
replicate 2
8762536135_F


title: AS_D8 rep 1

description:
replicate 1
8762536084_D


title: AS_D10 rep 3

description:
replicate 3
8784170061_B


title: AS_naive_D12 rep 1

description:
replicate 1
8762536072_E


title: AS_naive_D12 rep 2

description:
replicate 2
8784170061_E


title: AS_naive_D0 rep 3

description:
replicate 3
8762536052_F


title: AS_D2 rep 2

description:
replicate 2
8762536084_B


title: AS_D4 rep 1

description:
replicate 1
8762536052_B


title: AS_naive_D0 rep 2

description:
replicate 2
8762536084_A


title: Lgr5+ Basal, replicate 3

city: Parkville

first: Matthew

last: Ritchie

address: 1G Royal Parade

department: Epigenetics and Development Division

institute: The Walter and Eliza Hall Institute of Medical Research

hyb_protocol: Hybridized to Illumina MouseWG-6 v2.0 expression BeadChip following the standard Illumina hybridization protocol.

scan_protocol: Illumina iScan following the standard Illumina scanning protocol.

data_processing: The scanner operating software, GenomeStudio, converts the signal on the array into a TXT file for analysis. The data were then calibrated and quantile normalized using the neqc method of Shi et al. (2010) [PMID: 20929874]. This analysis was carried out in R using the limma package.

source_name: FACS-sorted Lgr5+ basal cells from mouse mammary gland

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

extract_protocol: RNA was extracted using QIAGEN RNeasy micro kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: strain/background

tag: genotype/variation

value: 10-week-old virgin

value: mammary gland

tag: cell population

value: Lgr5+ basal

tag: lgr5 expression

tag: sample type

value: FACS-sorted cells

tag: pool

tag: beadchip position


title: Luminal, replicate 3

source_name: FACS-sorted luminal cells from mouse mammary gland

tag: tissue

value: luminal

value: wild-type


title: Luminal, replicate 1

tag: age


title: myoblasts_PAX7-FOXO1A_3

last: Arno

state: LONDON

address: 150 Stamford Street

department: Genomics Centre

institute: King's College London

description: Gene expression data with PAX7-FOXO1A encoding retrovirus - Mouse 3

hyb_protocol: Biotinylated fragmented cDNA was hybridised to Mouse Gene 1.0- ST arrays (Affymetrix) according to manufacturer's protocols.

scan_protocol: Arrays were processed and scanned according to Affymetrix standard procedures.

data_processing: CEL files were normalised, background corrected and summarised using the RMA sketch algorithm in Expression Console software (Affymetrix).

label_protocol: RNA (215ng) was labelled using the WT Expression kit from Ambion.

growth_protocol: Primary murine satellite cell-derived myoblasts were derived from 3 mice and then expanded for 6 days.

extract_protocol: RNA was extracted using Trizol according to manufacturer's instructiuons.

treatment_protocol: Myoblasts were then divided into sister cultures per mouse and each sister culture infected with a different construct and cultured for a further 48 hours.

tag: Sex

value: Male

value: 6-8 weeks old

value: Satellite cell-derived myoblasts from hindlimb skeletal muscle

tag: retroviral construct

value: myoblast


title: Lgr5+ Basal, replicate 2


title: myoblasts_dominant-negative-Pax7-ERD_2

description: Gene expression data with Dominant-negative PAX7-ERD-encoding retrovirus - Mouse 2

tag: cell type


title: myoblasts_dominant-negative-Pax7-ERD_3

description: Gene expression data with Dominant-negative PAX7-ERD-encoding retrovirus - Mouse 3


title: myoblasts_PAX7-FOXO1A_2

description: Gene expression data with PAX7-FOXO1A encoding retrovirus - Mouse 2


title: myoblasts_control-RV_3

description: Gene expression data with control retrovirus - Mouse 3

value: control virus


title: Lgr5+ Basal, replicate 1


title: myoblasts_Pax7_3

description: Gene expression data with Pax7-encoding retrovirus Mouse 3


title: Lgr5- Basal, replicate 2

source_name: FACS-sorted Lgr5- basal cells from mouse mammary gland

value: Lgr5- basal


title: myoblasts_dominant-negative-Pax7-ERD_1

description: Gene expression data with Dominant-negative PAX7-ERD-encoding retrovirus - Mouse 1


title: myoblasts_Pax7_2

description: Gene expression data with Pax7-encoding retrovirus - Mouse 2


title: myoblasts_control-RV_2

description: Gene expression data with control retrovirus - Mouse 2


title: myoblasts_PAX7-FOXO1A_1

description: Gene expression data with PAX7-FOXO1A encoding retrovirus - Mouse 1


title: myoblasts_control-RV_1

description: Gene expression data with control retrovirus - Mouse 1


title: myoblasts_Pax7_1

description: Gene expression data with Pax7-encoding retrovirus - Mouse 1


title: Lgr5- Basal, replicate 1


title: APP-PBS treatment, biological rep2

city: Boston

first: Erming

last: Wang

state: MA

address: 72 E Concord street

department: Pharmacology

institute: Boston University

description: Gene expression data from brain tissues of 5 x FAD mouse treated with PBS buffer

hyb_protocol: The labeled, fragmented cRNA was hybridized to the GeneChip Mouse 1.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce probeset-level expression values using the implementation of the Robust Multiarray Average (RMA) in the oligo Bioconductor R package.

source_name: The Jackson Laboratory (Bar Harbor, ME, USA).

label_protocol: Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).

growth_protocol: For this study, all mice were maintained in microisolator cages in the Animal Facilities of Boston University School of Medicine, Boston, MA, USA. All animal procedures were in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals and were approved by the Boston University Animal Care and Use Committee.

extract_protocol: Total RNAs from brain tissues were extracted using  QIAzol lysis reagents according to the manufacturer's instructions.

treatment_protocol: 5XFAD mice were treated by i.p. injection of human peptide amylin from AnaSpec (Fremont, CA, USA) or 1x phosphate-buffered saline (PBS) solution , while WT mice were treated i.p. with 1x PBS solution, on daily basis for 10 weeks.

value: brain tissues

tag: genotype

value: 5x FAD

value: about 5 months


title: WT, biological rep2

description: Gene expression data from brain tissues of wildtype mouse treated with PBS buffer

value: B6SJLF1/J wild type


title: WT, biological rep3


title: APP-amylin treatment, biological rep1

description: Gene expression data from brain tissues of 5 x FAD mouse treated with amylin


title: AS_naive_D0 rep 1

description:
replicate 1
8762536135_E

tag: gender

value: Female

value: 6-8 weeks

value: Blood

tag: experiment

tag: infection

value: naïve

value: day 0

value: random


title: WT, biological rep1


title: APP-amylin treatment, biological rep3


title: APP-amylin treatment, biological rep2


title: APP-PBS treatment, biological rep1


title: ifnar-/- MEFs LPS 8hr

city: Cambridge

first: Christine

middle: S

last: Cheng

address: 7 Cambridge Center

institute: Broad Institute of MIT and Harvard

description: MEF expression in response to LPS, TNF, PDGFb, IFNb

data_processing: Quantile normalized using Illumina Inc. BeadStudio

source_name: Primary mouse embryonic fibroblasts (MEFs)

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

growth_protocol: MEF cells were maintained in DMEM supplemented with 10% bovine calf serum (BCS) to passages 5 to 6

extract_protocol: Total RNA was extracted from MEFs with RNeasy columns (Qiagen)

treatment_protocol: MEFs were stimulated with LPS, TNF, PDGFb, IFNb

value: ifnar-/-

tag: agent

value: LPS

tag: time point

tag: strain


title: crel-/-p65-/- MEFs LPS 3hr

tag: genotype/variation


title: ifnar-/- MEFs LPS 1hr


title: ifnar-/- MEFs LPS 0hr


title: crel-/-p65-/-irf3-/- MEFs LPS 3hr


title: crel-/-p65-/- MEFs LPS 8hr


title: crel-/-p65-/-relb-/- MEFs IFNb 8hr

value: IFNb


title: crel-/-p65-/-relb-/- MEFs TNF 0hr

value: TNF


title: ifnar-/- MEFs LPS 3hr


title: crel-/-p65-/- MEFs PDGFb 0hr

value: PDGFb


title: crel-/-p65-/-irf3-/- MEFs LPS 0hr


title: crel-/-p65-/-irf3-/- MEFs LPS 1hr


title: crel-/-p65-/- MEFs LPS 1hr


title: CB_naive_D0 rep 2

description:
replicate 2
8762536056_E

tag: day

tag: mouse selection


title: crel-/-p65-/- MEFs PDGFb 8hr


title: WT MEFs LPS (3hr) + actD 3hr

value: WT

tag: agent (time point)

value: LPS (3hr) + actD (3hr)


title: crel-/-p65-/-irf3-/- MEFs LPS 8hr


title: crel-/-p65-/-relb-/- MEFs IFNb 0hr


title: APP-PBS treatment, biological rep3

value: brain tissues


title: crel-/-p65-/- MEFs LPS 0hr


title: WT MEFs IFNb (2hr) + TNF 8hr

description:
MEF expression in response to LPS, TNF, PDGFb, IFNb
GSM870107: 0hr time point

value: IFNb (2hr) + TNF (8hr)


title: WT MEFs IFNb (2hr) + TNF 3hr

value: IFNb (2hr) + TNF (3hr)


title: WT MEFs IFNb 3hr


title: WT MEFs LPS (3hr) + actD 1hr

value: LPS (3hr) + actD (1hr)


title: WT MEFs IFNb 1hr


title: WT MEFs IFNb 8hr


title: WT MEFs TNF 8hr


title: WT MEFs PDGFb 0hr


title: WT MEFs TNF 3hr


title: crel-/-p65-/- MEFs PDGFb 1hr


title: WT MEFs PDGFb 1hr


title: WT MEFs TNF 0hr


title: WT MEFs LPS 1hr


title: crel-/-p65-/-relb-/- MEFs TNF 1hr


title: WT MEFs LPS 3hr


title: P21.U

city: Leuven

first: Tim

last: Dierckx

state: Vlaams Brabant

address: Herestraat 49 - 1040

department: Microbiology and Immunology

institute: KU Leuven

description:
unique sample, no replicates
hyb10095

hyb_protocol: Affymetrix GeneChip Human Gene 1.0 ST arrays were hybridized with biotin-labeled cDNA, washed, stained, and scanned according to the protocol described in WT Sense Target Labeling Assay Manual (Version 4; FS450_0007).

scan_protocol: Affymetrix GeneChip Human Gene 1.0 ST arrays were scanned according to the protocol described in WT Sense Target Labeling Assay Manual (Version 4; FS450_0007).

data_processing: Data were analysed using the limma R package (version 3.28.17) based on the Robust Multichip Average (RMA) expression values as obtained with the oligo R package (version 1.36.1).

source_name: PBMCs ex vivo_untreated

label_protocol: Whole Human Genome microarray analysis was performed by the VIB MicroArray Facility (Leuven, Belgium). Labeling of RNA (100ng each) with Ambion kit was performed using manufacturer's instructions.

growth_protocol: PBMCs (1-2M cells/ml) from 8 unique ATL patients were cultured short term (48h) at 37°C and 5% CO2 in RPMI + 10% FCS at 1ml/well in 24 well plates

extract_protocol: Following Trizol extraction, total RNA was further purified using RNeasy kit, according to the manufacturer’s protocol (QIAGEN, Venlo, the Netherlands).

treatment_protocol: Parallel 48h cultures were left untreated or treated with 1000 IU ofeither IFN-a or IFN-b

tag: patient id

tag: patient status

value: Adult T-cell leukemia (ATL)

value: peripheral blood mononuclear cells (PBMCs)

tag: treatment condition

value: untreated


title: P21.B

description:
unique sample, no replicates
hyb10097

source_name: PBMCs ex vivo_IFN-b

value: IFN-b


title: P17.U

description:
unique sample, no replicates
hyb10098


title: WT MEFs TNF 1hr


title: WT MEFs IFNb 0hr


title: WT MEFs PDGFb 8hr


title: P19.A

description:
unique sample, no replicates
hyb10093

source_name: PBMCs ex vivo_IFN-a

value: IFN-a


title: P19.B

description:
unique sample, no replicates
hyb10094


title: WT MEFs PDGFb 3hr


title: P20.A

description:
unique sample, no replicates
hyb10090


title: P19.U

description:
unique sample, no replicates
hyb10092


title: P20.U

description:
unique sample, no replicates
hyb10089


title: WT MEFs LPS 0hr


title: P21.A

description:
unique sample, no replicates
hyb10096


title: P20.B

description:
unique sample, no replicates
hyb10091


title: P15.A

description:
unique sample, no replicates
hyb10087


title: P15.U

description:
unique sample, no replicates
hyb10086


title: P16.B

description:
unique sample, no replicates
hyb10085


title: lung adenocarcinoma_control_rep6

city: Changsha

first: Zhen

middle: zi

last: Peng

state: Hunan

address: Xiangya Road 87th

country: China

institute: Xiangya hospital

description:
7B
lncRNAs and mRNAs expression.

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to OE Human lncRNA Microarray V4.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with GeneSpring 13.0 (Agilent). Probes that had at least 1 out of 2 samples flagged as Detected were maintained.

source_name: adjacent normal lung tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Pathological diagnosis of patients.

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

treatment_protocol: Tumor tissues and adjacent non-tumor tissues of lung adenocarcinoma patients were cut off and immediately frozen on dry ice and stored at -80°C until further analysis.

tag: disease state

value: lung adenocarcinoma (ADC)

tag: tissue

value: adjacent normal lung

value: female

tag: age

tag: sample type

value: control


title: P15.B

description:
unique sample, no replicates
hyb10088

tag: cell type


title: lung adenocarcinoma_control_rep4

description:
4B
lncRNAs and mRNAs expression.

tag: gender


title: P16.A

description:
unique sample, no replicates
hyb10084


title: lung adenocarcinoma_case_rep3

description:
3C
lncRNAs and mRNAs expression.

source_name: tumor tissue

value: lung adenocarcinoma

value: case


title: lung adenocarcinoma_case_rep6

description:
7C
lncRNAs and mRNAs expression.


title: Lgr5- Basal, replicate 3

tag: strain/background

value: 10-week-old virgin

value: mammary gland

tag: cell population

value: Lgr5- basal

tag: lgr5 expression

value: FACS-sorted cells

tag: pool

tag: beadchip position


title: lung adenocarcinoma_case_rep5

description:
5C
lncRNAs and mRNAs expression.


title: P18.U

description:
unique sample, no replicates
hyb10080


title: lung adenocarcinoma_control_rep5

description:
5B
lncRNAs and mRNAs expression.


title: lung adenocarcinoma_case_rep2

description:
2C
lncRNAs and mRNAs expression.


title: P18.A

description:
unique sample, no replicates
hyb10081


title: P18.B

description:
unique sample, no replicates
hyb10082


title: lung adenocarcinoma_case_rep4

description:
4C
lncRNAs and mRNAs expression.


title: P1.U

description:
unique sample, no replicates
hyb10078


title: lung adenocarcinoma_control_rep2

description:
2B
lncRNAs and mRNAs expression.


title: Luminal, replicate 2

tag: genotype/variation

value: luminal

value: wild-type


title: 11789

description: unique sample, no replicates

data_processing: Data were analysed using the Affymetrix GeneChip software based on the Robust Multichip Average (RMA) expression values as obtained with the xps package version 1.8.0.

source_name: PBMC in vitro_aFas Agonist

growth_protocol: PBMCs from LCL patients and healthy controls were processed in parallel and immediately frozen in Trizol lysis buffer to preserve RNA integrity.

treatment_protocol: Untreated ex vivo PBMCs OR in vitro treatment with mock, agonist and antagonist anti-FAS antibodies.

tag: subject status

value: HTLV-1 Associated Myelopathy/Tropical Spastic Paraparesis (HAM/TSP) patient

value: Peripheral blood mononuclear cells (PBMCs)

tag: treatment

value: aFas Agonist


title: WT MEFs LPS (3hr) + actD 0hr

value: WT

tag: agent (time point)

value: LPS (3hr) + actD (0hr)

tag: strain


title: 11788

description: unique sample, no replicates

source_name: PBMC in vitro_aFas Antagonist

value: aFas Antagonist


title: lung adenocarcinoma_control_rep1

description:
1B
lncRNAs and mRNAs expression.

value: lung adenocarcinoma (ADC)

value: adjacent normal lung


title: KS8 grown in response to glucose, 1st replicate

city: Durham

first: Amy

middle: K

last: Schmid

state: NC

address: 125 Science Dr.

department: Biology

institute: Duke University

description: This sample is of the ∆glpR mutant strain, KS8, derived from H26 ∆pyrF of Haloferax volcanii, grown in the presence of glucose It is the first of three biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Labeled cDNA samples were hybridized to 144k feature single-color custom microarrays (Roche) containing 98% of the annotated genes in the Hfx. volcanii genome (Hartman et al., 2010) at FSU-NimbleGen certified facility (The Florida State University, Tallahassee, FL) according to NimbleGen Array User's Guide: Gene Expression Arrays version 5.0.

scan_protocol: Array scanning was conducted according to NimbleGen Array User's Guide: Gene Expression Arrays version 5.0.

data_processing: Raw spot intensities were first normalized within arrays using RMA, then normalized to quantiles of the distribution across arrays using the ANAIS online server (http://anais.versailles.inra.fr/normalization.html; Simon and Biot, 2010, Bioinformatics, 26(19):2468-9). The 32 replicate probes corresponding to the same gene were averaged following normalization using ddply() in the R package plyr.

organism: Haloferax volcanii

source_name: Haloferax volcanii KS8, glucose

label_protocol: One µg of cDNA from each biological replicate was labeled with Cy3 dye according to NimbleGen Array User's Guide: Gene Expression Arrays version 5.0.

growth_protocol: Hfx. volcanii strains were grown to mid-logarithmic phase at 42 °C in minimal medium (MM) supplemented with 10 ug/mL uracil to complement the ∆pyrF parental deletion. MM formula was according to The Halohandbook (http://www.haloarchaea.com/resources/halohandbook/)

extract_protocol: Total RNA was extracted from three biological replicate cultures under each condition using TRI-Reagent (Sigma-Aldrich) according to manufacturer’s instructions. RNA quality was ensured using an Agilent Bioanalyzer 2100. Double-stranded cDNA libraries were created from the extracted RNA using Superscript cDNA synthesis kit according to manufacturer instructions (Invitrogen).

treatment_protocol: Parent (H26) and mutant (KS8) strain cultures were grown in MM supplemented with 20 mM glycerol or glucose as indicated above (see characteristics: sugar additive).

tag: genotype

value: ∆pyrF∆glpR

tag: sugar additive

value: glucose


title: lung adenocarcinoma_control_rep3

description:
3B
lncRNAs and mRNAs expression.

tag: disease state

tag: tissue

value: female

value: control


title: H26 grown in response to glucose, 3rd replicate

description: This sample is of the parent strain, H26, ∆pyrF of Haloferax volcanii (derived from DS2), grown in the presence of glucose. It is the third of three parent strain biological replicates used in this experiment, each from separate cultures.

source_name: Haloferax volcanii H26, glucose

value: DS2 wild type, H26 ∆pyrF


title: KS8 grown in response to glucose, 2nd replicate

description: This sample is of the ∆glpR mutant strain, KS8, derived from H26 ∆pyrF of Haloferax volcanii, grown in the presence of glucose It is the second of three biological replicates used in this experiment, each from separate cultures.


title: KS8 grown in response to glucose, 3rd replicate


title: H26 grown in response to glucose, 2nd replicate

description: This sample is of the parent strain, H26, ∆pyrF of Haloferax volcanii (derived from DS2), grown in the presence of glucose. It is the second of three parent strain biological replicates used in this experiment, each from separate cultures.


title: H26 grown in response to glucose, 1st replicate

description: This sample is of the parent strain, H26, ∆pyrF of Haloferax volcanii (derived from DS2), grown in the presence of glucose. It is the first of three parent strain biological replicates used in this experiment, each from separate cultures.


title: KS8 grown in response to glycerol, 3rd replicate

description: This sample is of the ∆glpR mutant strain, KS8, derived from H26 ∆pyrF of Haloferax volcanii, grown in the presence of glycerol. It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: Haloferax volcanii KS8, glycerol

value: glycerol


title: KS8 grown in response to glycerol, 2nd replicate

description: This sample is of the ∆glpR mutant strain, KS8, derived from H26 ∆pyrF of Haloferax volcanii, grown in the presence of glycerol. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: 11787

description: unique sample, no replicates

source_name: PBMC in vitro_control


title: 9314

description: unique sample, no replicates


title: lung adenocarcinoma_case_rep1

description:
1C
lncRNAs and mRNAs expression.

value: lung adenocarcinoma

tag: age

tag: sample type

value: case


title: 9315

description: unique sample, no replicates

tag: cell type


title: 9313

description: unique sample, no replicates


title: 9309

description: unique sample, no replicates


title: 9307

description: unique sample, no replicates


title: E11.5_placenta_miRNA_rep3

city: Tsukuba

first: Kimiko

last: Inoue

state: Ibaraki

address: 3-1-1 Koyadai

department: Bioresource Engineering Division

country: Japan

institute: BRC, RIKEN

description: embryonic day E11.5, mouse, placenta, in vitro fertilized embryo, microRNA, replicate3

hyb_protocol: For miRNA analysis, Cy3-labeled RNAs was hybridized with the miRNA Complete Labeling Reagent and Hyb Kit onto mouse miRNA Microarray rel.17.0 (Agilent Technologies) at 65°C for 17 hours according to manufacture's instructions. For mRNA analysis, 0.6ug Cy3-labelled RNAs were fragmented at 60°C for 30 minutes and hybridized onto SurePrint G3 Mouse GE microarray 8x60K (Agilent Technologies) at 65°C for 17 hours according to manufacture's instructions.

scan_protocol: Scanning of microarray slides was performed with a DNA microarray scanner at 3 um resolution (Agilent Technologies).

data_processing: Scanned image files were processed to give signal intensities using Feature Extraction software (Agilent Technologies). miRNA raw intensity signals were not normalized.

source_name: embryonic day 11.5, placenta, IVF derived, microRNA, replicate3

label_protocol: For miRNA analysis, total RNA from placentas was labeled with the miRNA Complete Labeling Reagent and Hyb Kit (Agilent Technologies). For mRNA analysis, total RNAs were labeled with a Low Input Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: In vitro-fertilized embryos derived from wild-type and miRNA-deleted mice were cultured in KSOM medium at 37°C for 16 hours. Cultured embryos were transferred into pseudopregnant ICR females and E11.5 embryos were retrieved from the uterus.

extract_protocol: Placentas with deciduas removed were lysed and the total and miRNA isolated using a mirVana miRNA isolation kit (Themo Fisher Scientific).

value: placenta

tag: embryonic day


title: E11.5_placenta_miRNA_rep4

description: embryonic day E11.5, mouse, placenta, in vitro fertilized embryo, microRNA, replicate4

source_name: embryonic day 11.5, placenta, IVF derived, microRNA, replicate4


title: E11.5_placenta_miRNA_rep2

description: embryonic day E11.5, mouse, placenta, in vitro fertilized embryo, microRNA, replicate2

source_name: embryonic day 11.5, placenta, IVF derived, microRNA, replicate2


title: E11.5_placenta_miRNA_rep1

description: embryonic day E11.5, mouse, placenta, in vitro fertilized embryo, microRNA, replicate1

source_name: embryonic day 11.5, placenta, IVF derived, microRNA, replicate1


title: H26 grown in response to glycerol, 2nd replicate

description: This sample is of the parent strain, H26, ∆pyrF of Haloferax volcanii (derived from DS2), grown in the presence of glycerol. It is the second of three parent strain biological replicates used in this experiment, each from separate cultures.

source_name: Haloferax volcanii H26, glycerol


title: H26 grown in response to glycerol, 3rd replicate

description: This sample is of the parent strain, H26, ∆pyrF of Haloferax volcanii (derived from DS2), grown in the presence of glycerol. It is the third of three parent strain biological replicates used in this experiment, each from separate cultures.


title: KS8 grown in response to glycerol, 1st replicate

description: This sample is of the ∆glpR mutant strain, KS8, derived from H26 ∆pyrF of Haloferax volcanii, grown in the presence of glycerol. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: H26 grown in response to glycerol, 1st replicate

description: This sample is of the parent strain, H26, ∆pyrF of Haloferax volcanii (derived from DS2), grown in the presence of glycerol. It is the first of three parent strain biological replicates used in this experiment, each from separate cultures.


title: 9326

description: unique sample, no replicates

source_name: PBMC ex vivo_uncultured

value: HTLV-1 Associated Myelopathy/Tropical Spastic Paraparesis (HAM/TSP) patient

value: uncultured


title: 9330

description: unique sample, no replicates

value: Peripheral blood mononuclear cells (PBMCs)


title: 9332

description: unique sample, no replicates


title: WT MEFs LPS 8hr

description: MEF expression in response to LPS, TNF, PDGFb, IFNb

source_name: Primary mouse embryonic fibroblasts (MEFs)

value: WT

tag: agent

value: LPS

tag: time point


title: HeLa_Si-NPM1_TNF-a +

city: Pheladelphia

first: Jianhuang

state: PA

address: 3601 Spruce St

institute: Wistar Institute

description: treatment: Si-NPM1; TNF-a +

hyb_protocol: The fragmented and labeled cDNA were injected to the Gene Arrays 1.0 ST and placed in 45C overn at 60 rpm, hybridized for 17 hr.The hybridized samples were washed and stained using Affymetrix fluidics station 450.

scan_protocol: GeneChips were scanned using scanned using Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: The raw date were analyzed with the function rma(robust multichip averaging) in R-Bioconductorpackage “affy” with default setting. The raw intensity values are background corrected, log2 transformed, quantile normalized and then calculated by the method medianpolish.

source_name: HeLa,Si-NPM1,TNF-a +

label_protocol: The sense-strand cDNA were parepared using Ambion WT Expression Kit (Affymetrix, Santa Clara, CA) according to the manufacturer's instructions from 200 ng total RNA. 5.5 ug of the cDNA were then fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions.

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum (FBS) at 37ºC with 5% CO2

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

treatment_protocol: HeLa cells were transfected with NPM1 specific or negative control siRNA, 72 h after transfection, cells were either untreated or treated with 20 ng/ml TNF-α for 2 h.

tag: cell line

value: HeLa


title: 9325

description: unique sample, no replicates


title: 9308

description: unique sample, no replicates

value: aFas Antagonist


title: HeLa_Si-control_TNF-a +

description: treatment: Si-control; TNF-a +

source_name: HeLa,Si-control,TNF-a +


title: SEM

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: Labeled cDNA from the four cell lines was analyzed using Affymetrix human gene ST 1.0 microarray, according to manufacturer instructions.

scan_protocol: Microarrays were scanned by GeneChip scanner 3000 7G

data_processing: Statistical analysis of data was performed using the Partek® Genomics Suite (Partek Inc., St. Louis, Missouri 63141) software. CEL files (containing raw expression measurements) were imported to Partek® Genomics SuiteTM and data was preprocessed and normalized using the RMA (Robust Multichip Average) algorithm with GC correction.

source_name: acute lymphoblastic leukemia (ALL) precursor B cell line carrying the chromosome translocation t(4;11)

label_protocol: Purified RNA was reverse-transcribed, amplified and labeled with Affymetrix GeneChip whole transcript sense target labeling kit

growth_protocol: Regular RPMI medium with 10% fetal bovine serum

extract_protocol: Total RNA and was isolated using TRI Reagent®, according to manufacturer instructions.

treatment_protocol: Grown to sub confluency

value: SEM

tag: cell attribute

value: Precursor ALL containing  the t(4;11) abnormality


title: adult_rep3

city: odense

first: mads

last: thomassen

address: soender boulevard 29

institute: odense university hospital

description: AxL M3

hyb_protocol: Hybridization to Affymetrix Mouse Genome 430 2.0 Array following the Affymetrix standard protocol.

scan_protocol: GeneChip Scanner 3000.

data_processing: Standard quality assessment procedures, including the quality test generated by affyQCReport package in R, were performed for all existing CEL-files. By using the variance stabilization and normalization (vsn) package in R, the microarray data were normalized at a probe set level, before the expression indexes were calculated using the Robust MultiArray Average (RMA) package in R.

source_name: hippocampus, AxL

growth_protocol: Eight- to ten-week-old female SJL/J mice were obtained from Harlan Laboratories, housed in groups of eight mice per cage, maintained in a temperature- and humidity-controlled environment with a 12-hour light-dark cycle, and provided with food and water ad libitum.

extract_protocol: Total RNA was isolated from fresh frozen whole hippocampi from five TPlp+AxL and five AxL mice with 2 days post lesion (dpl) survival.

tag: strain/background

value: SJL/J

tag: Sex

value: adult

value: hippocampus

value: axonal lesion (AxL)

value: 2 days post lesion


title: RS4;11


title: HeLa_Si-control_TNF-a -

description: treatment: Si-control; TNF-a -

source_name: HeLa,Si-control,TNF-a -


title: adult_Tcell_rep2

description:
TPlP+AxL M2
Adoptively transferred with proteolipid protein (Plp)-specific T cells.

source_name: hippocampus, TPlp+AxL

value: female

tag: treatment

value: adoptive transfer with TPlp cells, followed by axonal lesion (TPlp+AxL)


title: 9331

description: unique sample, no replicates

tag: subject status


title: REH

source_name: acute lymphoblastic leukemia (ALL) precursor B cell lines

value: REH

value: Precursor ALL lacking the t(4;11) abnormality


title: adult_Tcell_rep5

description:
TPlP+AxL M5
Adoptively transferred with proteolipid protein (Plp)-specific T cells.


title: 9329

description: unique sample, no replicates

value: HTLV-1 Associated Myelopathy/Tropical Spastic Paraparesis (HAM/TSP) patient

value: uncultured


title: adult_Tcell_rep3

description:
TPlP+AxL M3
Adoptively transferred with proteolipid protein (Plp)-specific T cells.


title: adult_Tcell_rep1

description:
TPlP+AxL M1
Adoptively transferred with proteolipid protein (Plp)-specific T cells.


title: adult_rep5

description: AxL M5


title: adult_Tcell_rep4

description:
TPlP+AxL M4
Adoptively transferred with proteolipid protein (Plp)-specific T cells.


title: HeLa_Si-NPM1_TNF-a -

description: treatment: Si-NPM1; TNF-a -

source_name: HeLa,Si-NPM1,TNF-a -


title: adult_rep4

description: AxL M4


title: adult_rep1

description: AxL M1


title: adult_rep2

description: AxL M2


title: aNPC_control_48h

city: Warsaw

first: Pawel

last: Niewiadomski

address: Banacha 2c

department: Centre of New Technologies

country: Poland

institute: University of Warsaw

description: Gene expression data from aNPCs cultured for 48h in the absence of PACAP

hyb_protocol: Standard protocol used by the UCLA DNA Microarray Facility

data_processing: CEL files were processed in Affymetrix Expression Console software (build 1.4.1.46) using the RMA algorithm and standard settings (quantile normalization, RMA background correction)

source_name: cultured adult neural progenitor cells

growth_protocol: aNPCs were isolated from the SVZs of 7-8-week old male C57Bl/6 mice as described [33]. Briefly, the mice were sacrificed by pentobarbital injection, and their skulls were opened to expose the brain. The brain was cooled in ice-cold DMEM/F12 supplemented with HEPES. The rostral part of the brain was sectioned coronally on a mouse brain slicer, and the periventricular region was isolated using fine scissors from 2-3 1mm-thick sections, starting from the ventral-most section in which the ventricle was apparent. The periventricular tissue was cut into small pieces using fine scissors and transferred to a conical tube containing ice-cold DMEM/F12 with HEPES. The tissue was transferred to a biological safety cabinet and washed 3x with sterile Hank’s Buffered Salt Solution. This solution was replaced with DMEM/F12 supplemented with B-27 (Life Technologies) and gently triturated with a 1mL pipette tip. Trypsin (Trypsin-EDTA solution, Life Technologies) was added to a final concentration of 1mg/mL and DNAse I (Worthington) was added to a final concentration of 0.1mg/mL to dissociate the cells. The tissue was allowed to incubate at 37˚C for 30 min with manual agitation after every 10 min interval. The trypsin was inactivated by adding FBS to a final concentration of 10%. The tissue was then triturated using two sterile diminishing-bore fire-polished glass Pasteur pipettes and passed through a 40μm cell strainer (Corning Falcon). The cells were centrifuged at 200xg for 2 min and resuspended at 104 cells/mL in neurosphere media, containing Neurobasal, L-glutamine (0.5mM), penicillin/streptomycin (1x), B-27 supplement (1x), EGF (10ng/mL), bFGF (10ng/mL), and heparin (2μg/mL). All neurosphere media components were purchased from Life Technologies, except heparin and EGF, which were from Sigma, and bFGF, which was from Peprotech. The cells were placed in non-tissue culture-treated 25cm2 flasks at 7x104 cells per flask (Nunc) for 7 days, and EGF and bFGF were re-added at 5ng/mL each on day 3 and 5 of culture. The first neurospheres started appearing after 3-5 days and were fully grown by day 7. For replating, the spheres were centrifuged at 200xg for 5 min, and the media was replaced with 500μL Accutase (Life Technologies). The spheres were incubated for 5 min at 37˚C, triturated with a 200μL pipette tip, incubated for 10 more min at 37˚C and triturated with a small-bore fire-polished pipette until very few visible spheres remained. The suspension was centrifuged at 200xg for 5 min, and the cell pellet was resuspended in neurosphere media. The remaining spheres were removed from the suspension by passing it through a 40μm cell strainer, the cells were counted and replated at 104 cells/mL in non-tissue culture-treated flasks (7x104 cells per flask). Experiments were performed on cells from passage 3 to 6.

extract_protocol: RNA was isolated using TRIzol from all cells (both floating and attached) treated for 24h or 96h with either vehicle (control) or PACAP (10nM). RNA from 5-6 independent samples per group was pooled and cleaned using RNeasy spin columns (Qiagen), yielding ~10μg RNA per treatment.

treatment_protocol: aNPCs were treated with vehicle (PBS) or 10nM PACAP for 24, 48, or 96 hours. For the 96h treatment protocol, additional 5nM PACAP was added after 48h.

value: cultured adult neural progenitor cells

tag: strain

value: control

tag: time


title: Blood_post_XB0030_rep2

first: Thalia

last: Eley

address: DeCrespigny Park, Denmark Hill

department: SGDP Centre, Institute of Psychiatry, Psychology & Neuroscience

description: Network outlier - removed

data_processing: Stringent quality control processing of the data was conducted using standardised procedures from internal pipelines (available at https://github.com/snewhouse/BRC_MH_Bioinformatics). Expression data was background corrected using Module-based Background Correction for Beadarray (Ding et al., 2008). Probes were then filtered by selecting probes with expression levels >2SD greater than the mean intensity of the negative control (background) beads. Reported gender was compared to XIST gene expression (female specific) and Y chromosome gene expression (male specific). Each probe was then transformed and normalised using log2 transformation and Robust-Spline Normalisation (Schmid et al., 2010, Du et al., 2008). Sample relationships within the co-expression network were assessed and outliers were removed (Oldham et al., 2012).

source_name: Human, Whole Blood, post-therapy

label_protocol: Biotinylated, amplified cRNA was generated using the Illumina® TotalPrep™-96 RNA Amplification Kit for Illumina Sentrix Arrays.

extract_protocol: Blood RNA was isolated and purified using the PAXgene Blood miRNA Kit according to the manufacturer’s protocol using the Qiagen Qiacube. RNA quality and integrity were measured using both the Nanodrop 1000 spectrophotometer.

tag: gender

value: FEMALE

value: Blood

tag: timepoint

value: post


title: Blood_pre_XD0001_rep1

description: Network outlier - removed

source_name: Human, Whole Blood, pre-therapy

value: MALE

tag: tissue

value: pre


title: Blood_pre_XB0066_rep1

description: Network outlier - removed


title: aNPC_control_96h

description: Gene expression data from aNPCs cultured for 96h in the absence of PACAP

scan_protocol: Standard protocol used by the UCLA DNA Microarray Facility


title: Blood_pre_XD0094_rep1

description: Network outlier - removed


title: Blood_fu_XB0037_rep1

description: Network outlier - removed

source_name: Human, Whole Blood, follow-up-therapy

value: follow-up


title: Blood_fu_XB0109_rep1

description: Network outlier - removed


title: aNPC_PACAP_24h

description: Gene expression data from aNPCs cultured for 24h with 10nM PACAP

label_protocol: Standard protocol used by the UCLA DNA Microarray Facility

value: PACAP 10nM


title: aNPC_control_24h

description: Gene expression data from aNPCs cultured for 24h in the absence of PACAP


title: aNPC_PACAP_96h

description: Gene expression data from aNPCs cultured for 96h with 10nM PACAP


title: Blood_pre_XB0063_rep1

description: Network outlier - removed


title: NALM6


title: Blood_fu_XB0048_rep1

description: Network outlier - removed


title: P16.U

description:
unique sample, no replicates
hyb10083

source_name: PBMCs ex vivo_untreated

tag: patient id

tag: patient status

value: Adult T-cell leukemia (ATL)

value: peripheral blood mononuclear cells (PBMCs)

tag: treatment condition

value: untreated


title: Blood_post_XB0007_rep1

description: Network outlier - removed


title: Blood_pre_XD0044_rep1

description: Network outlier - removed


title: Blood_post_XD0079_rep1

description: Network outlier - removed


title: Blood_pre_XB0007_rep1

description: Network outlier - removed


title: Blood_fu_XB0026_rep1

description: Network outlier - removed


title: Blood_fu_XB0011_rep1

description: Network outlier - removed


title: Blood_pre_XB0010_rep1

description: Network outlier - removed


title: Blood_pre_XB0030_rep1

description: QC ok


title: aNPC_PACAP_48h

description: Gene expression data from aNPCs cultured for 48h with 10nM PACAP

tag: cell type


title: Blood_fu_XB0030_rep1

description: QC ok


title: Huh 7.5M cells Translatome 2

city: HYDERABAD

first: KRISHNAN

middle: HARINIVAS

last: HARSHAN

address: HABSIGUDA

country: India

institute: CENTRE FOR CELLULAR AND MOLECULAR BIOLOGY

description:
Huh 7.5M cells_80% confluent_ polysome fraction
polysomal mRNA

hyb_protocol: 600ng of labeled cRNA were hybridized on the array using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: Scannedusing  Agilent Technologies G2505C scanner

data_processing: Images were quantified using Feature Extraction Software (Version-10.7, Agilent). Feature extracted raw data was analyzed using GeneSpring GX Version 12.0 software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift

source_name: Human hepatoma celline 7.5

label_protocol: The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using Qiagen RNeasy columns(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop. Samples that pass the QC for specific activity were taken for hybridization.

growth_protocol: Huh7.5 and Huh7.5M cells were cultured in complete DMEM supplemented with 10% FBS, 1X Non essential Amino acids, 1X Penicillin Streptomycin solution at 37°C with 5% CO2

extract_protocol: For total RNA preparartion, MN RNA extraction Kit was used and total RNA was extracted and quantified. For Polysomal RNA preparation to study translatome, cells were lysed and normalized volumes containing 175 ug of corresponding RNA were separated on Sucrose gradient (10%-50%), samples were then  fractionated into mRNP, monosomal and polysomal fractions. Polysomal fractions were pooled based on their profilies and RNA was prepared by initial ethanol precipitation followed by lithium chloride extraction and subsequent purification by MN RNA kit spin columns. Enriched polysomal RNA was used for microarray analysis.

treatment_protocol: 70-80% confluent Huh7.5 and Huh7.5M cells were trypsinised with 0.05% Trypsin EDTA. Cells were then washed with 1X PBS containing Cycloheximide (100µg/ml). For total RNA preparartion, MN  RNA extraction Kit was used and total RNA was extracted and quantified. For Polysomal RNA preparation, Cells were lysed with Lysis buffer containing 20mM Tris pH-8.0, 140mM KCl, 1.5mM MgCl2, 1% Triton-X-100, 0.5mM DTT, 100 µg/ml Cycloheximide, 1X Protease Inhibitor cocktail, 1mg/ml Heparin and 100U of Ribolock and 175 ug of corresponding RNA from crude lysate was loaded onto Sucrose gradient (10%-50%). Samples were then centrifuged at 35000 rpm for 4 hrs at 4°C using Beckmann SW41 rotor. Resolved sucrose gradient samples were fractionated using Density gradient fractionator. Polysomal fractions were pooled based on their profilies and RNA was prepared by initial ethanol precipitation followed by Lithium chloride extraction. Enriched polysomal RNA was used for microarray analysis.

value: Geneticin resistant Huh 7.5M cells


title: Neutrophils, Patient, JIA, ID, Biological replicate 9 [RNA]

data_processing: Expression summary values from Affymetrix Exon and miRNA arrays were generated using RMA software in the Affy package of Bioconductor in the R statistical computing environment.

source_name: neutrophil RNA, JIA, ID

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was further purified using RNeasy MiniElute Cleanup kit including a DNase digest according to the manufacturer's instructions (QIAGEN, Valencia, CA).

tag: disease state

value: juvenile idiopathic arthritis (JIA)

tag: group

value: inactive disease, on therapy (ID)

value: neutrophils


title: Blood_fu_XD0109_rep1

description: QC ok

scan_protocol: Standard Illumina scanning protocol


title: Neutrophils, Patient, JIA, ID, Biological replicate 12 [RNA]


title: Blood_post_XB0030_rep1

description: QC ok


title: Neutrophils, Patient, JIA, ID, Biological replicate 8 [RNA]


title: Blood_post_XD0109_rep1

description: QC ok


title: Huh 7.5M cells Transcriptome 2

description:
Huh 7.5M cells_80% confluent_Total RNA
total RNA

tag: cell line


title: Neutrophils, Patient, JIA, ID, Biological replicate 10 [RNA]


title: Neutrophils, Patient, JIA, ID, Biological replicate 3 [RNA]


title: Huh 7.5 cells Translatome 2

description:
Huh 7.5 cells_80% confluent_Polysome fraction
polysomal mRNA

value: Geneticin sensitive Huh7.5 cells


title: Neutrophils, Patient, JIA, ID, Biological replicate 5 [RNA]


title: Neutrophils, Patient, JIA, ID, Biological replicate 14 [RNA]


title: Neutrophils, Patient, JIA, ID, Biological replicate 2 [RNA]


title: Blood_pre_XD0109_rep1

description: QC ok


title: Neutrophils, Patient, JIA, ID, Biological replicate 4 [RNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 20 [RNA]

source_name: neutrophil RNA, JIA, CRM

value: clinical remission, on medication (CRM)


title: Neutrophils, Patient, JIA, ID, Biological replicate 7 [RNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 28 [RNA]


title: Huh 7.5 cells Transcriptome 2

description:
Huh 7.5 cells_80% confluent_Total RNA
total RNA


title: Neutrophils, Patient, JIA, CRM, Biological replicate 22 [RNA]


title: Blood_fu_XD0108_rep1

description: QC ok


title: Neutrophils, Patient, JIA, CRM, Biological replicate 18 [RNA]


title: Neutrophils, Patient, JIA, ID, Biological replicate 6 [RNA]


title: Neutrophils, Patient, JIA, ID, Biological replicate 1 [RNA]


title: Neutrophils, Patient, JIA, ID, Biological replicate 11 [RNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 27 [RNA]


title: Neutrophils, Patient, JIA, ID, Biological replicate 13 [RNA]


title: Blood_post_XD0108_rep1

description: QC ok


title: Neutrophils, Patient, JIA, CRM, Biological replicate 26 [RNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 25 [RNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 21 [RNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 24 [RNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 17 [RNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 23 [RNA]


title: Blood_fu_XD0105_rep1

description: QC ok


title: Neutrophils, Patient, JIA, CRM, Biological replicate 19 [RNA]


title: Huh 7.5M cells Transcriptome 1


title: MB_CD:UPRT, 5EC fed, rep. 2

city: Merced

first: Michael

last: Cleary

state: CA

address: 5200 N. Lake Rd.

department: School of Natural Sciences

institute: University of California, Merced

hyb_protocol: 1.65 micrograms of Cy3 labeled cRNA was combined with the recommended dilution of spike-in control and hybridized following manufacturer's instructions

scan_protocol: Slides were scanned immediately after washing on the GenePix 4000B scanner, with pixel size 10, scan power 100%, and 532nm PMTGain set between 500 and 700.

data_processing: Spot alignments and data measurements were made using GenePix Pro 5.1 software. Post-processing of GenePix Pro data was performed in R.

organism: Drosophila melanogaster

source_name: MB 5EC 2

label_protocol: Purified EU-RNA plus a spike-in control (One-Color RNA Spike-In Kit, Agilent) was used to generate Cy3 labeled cRNA (Low Input Quick Amp Labeling Kit, Agilent) and hybridized to Agilent 4x44K Drosophila gene expression microarrays.

growth_protocol: larvae were cultured on standard growth medium at 25C.

extract_protocol: Total RNA was extracted using Trizol.  RNA biotinylation and purification was performed using the Click IT Nascent RNA Capture Kit (ThermoFisher) (with modifications)

treatment_protocol: 5EUd and 5EC feeding was performed for 24 hours in standard media.

value: mushroom body

tag: genotype

value: MB247-Gal4 X UAS-CD:UPRT

tag: age

value: early L3


title: MB_CD:UPRT, 5EC fed, rep. 1

source_name: MB 5EC 1


title: Huh 7.5 cells Transcriptome 1


title: Blood_post_XD0105_rep1

description: QC ok

hyb_protocol: Standard Illumina hybridization protocol

value: FEMALE

value: Blood

value: post


title: Blood_pre_XD0105_rep1

description: QC ok

value: pre


title: Neutrophils, Patient, JIA, CRM, Biological replicate 16 [RNA]

first: kaiyu

last: Jiang

address: 875 Ellicott Street

institute: University at Buffalo


title: Blood_fu_XD0101_rep1

description: QC ok

value: follow-up


title: Huh 7.5 cells Translatome 1


title: 12B08_CD:UPRT, 5EC fed, rep. 1

value: neural, imaginal discs

value: GMR12B08-Gal4 X UAS-CD:UPRT


title: Blood_post_XD0101_rep1

description: QC ok


title: Neutrophils, Patient, JIA, CRM, Biological replicate 15 [RNA]


title: Huh 7.5M cells Translatome 1


title: reference, Eud fed, replicate 2

source_name: whole larvae Eud 2

value: whole larvae

value: wildtype


title: Blood_pre_XD0101_rep1

description: QC ok


title: Blood_pre_XD0108_rep1

description: QC ok


title: Blood_fu_XB0115_rep1

description: QC ok


title: reference, Eud fed, replicate 1

source_name: whole larvae Eud 1


title: 12B08_CD:UPRT, 5EC fed, rep. 2


title: Neutrophils, Patient, JIA, CRM, Biological replicate 12 [RNA]

value: juvenile idiopathic arthritis (JIA)


title: Neutrophils, Patient, JIA, CRM, Biological replicate 9 [RNA]


title: Blood_pre_XB0115_rep1

description: QC ok


title: Ink4a Null - 10

city: Bethesda

first: Prasun

middle: J.

last: Mishra

state: MD

address: 37 Convent Drive

department: United States Department of Health and Human Services

institute: National Cancer Institute, National Institutes of Health

hyb_protocol: Not provided

scan_protocol: According to the Affymetrix standard protocol {Affymetrix GeneChip Mouse Genome 430 2.0 Array [Mouse430_2]}

data_processing: Data was analysed using GeneSpringGX using following parameters: Filtered expression (20.0); Mann-Whitney unpaired p  cut-off > 0.05; Raw data is provided

source_name: Cutaneous melanoma tumor tissue

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

growth_protocol: Mice carrying an HGF/SF transgene whose expression is regulated by a metallothionein gene promoter and flanking regions were used to generate mice carrying specific inactivating mutations in ARF or INK4a. All melanomas arose from mice on a genetic background consisting of ≈90% FVB/N: 10% C57BL/6.

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

treatment_protocol: All melanomas were initiated by a single dose of UV radiation to new born mice at 3.5 days of age.

value: Cutaneous melanoma tumor

tag: genotype/variation

value: ARF Null


title: Neutrophils, Patient, JIA, CRM, Biological replicate 6 [RNA]

city: Buffalo

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr on Affymetrix human EXON 1.0 ST array or GeneChip™ miRNA 1.0 array following manufacturer's directions. GeneChips were washed and stained in an Affymetrix 450 Fluidics Station.

scan_protocol: GeneChips were scanned using an Affymetrix 3000 7G scanner.

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

value: neutrophils


title: Neutrophils, Patient, JIA, CRM, Biological replicate 5 [RNA]

value: clinical remission, on medication (CRM)


title: Neutrophils, Patient, JIA, CRM, Biological replicate 11 [RNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 13 [RNA]


title: Ink4a Heterozygous - 9

value: ARF Heterozygous


title: Neutrophils, Patient, JIA, CRM, Biological replicate 8 [RNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 14 [RNA]


title: Blood_post_XB0110_rep1

description: QC ok


title: Neutrophils, Patient, JIA, CRM, Biological replicate 10 [RNA]


title: Ink4a Heterozygous - 8


title: Neutrophils, Patient, JIA, CRM, Biological replicate 4 [RNA]


title: Neutrophils, Patient, JIA, CRM, Biological replicate 7 [RNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 24 [RNA]

source_name: neutrophil RNA, JIA, ADM

value: active disease, on therapy (ADM)


title: Neutrophils, Patient, JIA, ADM, Biological replicate 21 [RNA]


title: Blood_pre_XB0110_rep1

description: QC ok


title: Neutrophils, Patient, JIA, CRM, Biological replicate 2 [RNA]


title: Blood_post_XB0115_rep1

description: QC ok


title: Ink4a Heterozygous - 14


title: Neutrophils, Patient, JIA, CRM, Biological replicate 3 [RNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 20 [RNA]


title: Ink4a Heterozygous - 13


title: Blood_fu_XB0110_rep1

description: QC ok


title: Blood_fu_XB0103_rep1

description: QC ok


title: Ink4a Heterozygous - 12


title: Neutrophils, Patient, JIA, ADM, Biological replicate 19 [RNA]


title: Blood_pre_XB0103_rep1

description: QC ok


title: Blood_post_XB0103_rep1

description: QC ok


title: Neutrophils, Patient, JIA, ADM, Biological replicate 26 [RNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 22 [RNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 25 [RNA]


title: Ink4a Null - 7.2

value: Ink4a Null


title: Neutrophils, Patient, JIA, ADM, Biological replicate 16 [RNA]


title: Ink4a Null - 3


title: Blood_fu_XB0100_rep1

description: QC ok

value: MALE


title: Blood_pre_XB0100_rep1

description: QC ok

value: Blood


title: Neutrophils, Patient, JIA, ADM, Biological replicate 15 [RNA]


title: Ink4a Null - 1.2


title: Ink4a Null - 2.2


title: Neutrophils, Patient, JIA, ADM, Biological replicate 13 [RNA]


title: Blood_post_XB0099_rep1

description: QC ok

value: FEMALE

value: post


title: Neutrophils, Patient, JIA, CRM, Biological replicate 1 [RNA]


title: Neutron_0.25Gy_day3_rep 3

city: New York

first: Sally

last: Amundson

department: Center for Radiological Research

institute: Columbia University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k v.2 array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.2 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid: 026655_D_F_20140728) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers or not significantly above background were excluded.

source_name: blood

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

extract_protocol: RNA was purified following the PAXgene RNA kit recommendations with on-column DNase I treatment

treatment_protocol: Blood was collected by cardiac puncture at the time of euthanasia at days 1, 3, and 7 post-irradiation. Each sample  was added to a 15 ml centrifuge tube that contained of PAXgene Blood RNA stabilization and lysis solution and mixed thoroughly

tag: protocol

value: male


title: Neutrophils, Patient, JIA, ADM, Biological replicate 11 [RNA]


title: Neutron_0.25Gy_day3_rep 2


title: Ink4a Heterozygous - 6.2

value: Ink4a Heterozygous


title: Ink4a Heterozygous - 5.2


title: Neutron_0.25Gy_day3_rep 1


title: Neutrophils, Patient, JIA, ADM, Biological replicate 17 [RNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 12 [RNA]


title: Ink4a Heterozygous - 15


title: X-ray_4Gy_day7_rep 6


title: X-ray_4Gy_day7_rep 5


title: Blood_fu_XB0094_rep1

city: London

description: QC ok

value: follow-up


title: Neutrophils, Patient, JIA, ADM, Biological replicate 8 [RNA]


title: X-ray_4Gy_day7_rep 2


title: X-ray_4Gy_day7_rep 4


title: X-ray_4Gy_day7_rep 3


title: Blood_post_XB0100_rep1

description: QC ok