title: Sample 239_genomic DNA from 101279430031_R01C02

tag: age

tag: Sex

tag: race

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell


title: Sample 240_genomic DNA from 101279430031_R02C01

status: Public on Jul 23 2019

type: genomic

city: New Haven

first: Ke

last: Xu

state: CT

country: USA

institute: Yale University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol

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

data_processing:
GenomeStudio V2011.1
MatrixProcessed.txt: Quantile normalized Average Beta
MethylatedSignal.txt: Unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: DNAs were extracted from whole blood using the standard protocol.

value: Male

value: White

tag: mono

tag: tissue

value: whole blood


title: Sample 238_genomic DNA from 101279430031_R01C01


title: NT066_W18D2T30_Control

type: RNA

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Samples were hybridized to Affymetrix GeneChip Human Gene 1.1 ST array plates (Santa Clara, CA) according to manufacturer's instructions.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.30.0).

label: biotin

molecule: total RNA

source_name: Peripheral blood mononuclear cells isolated from subject 066, W18 = after intervention, Day 2 = OGTT, T30 = 30 minutes

label_protocol: One hundred nanogram of total RNA was used for whole transcript cDNA synthesis with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Included in this study were 72 healthy, overweight, Caucasian men and women, aged 50-65, with a BMI 25-35kg/m2, that were recruited from London (UK) and surroundings. Exclusion criteria included: weight change of ≥ 3kg in the preceding 3 months, current smokers, substance abuse, excess alcohol intake, pregnancy, diabetes, cardiovascular disease, cancer, gastrointestinal disease e.g. inflammatory bowel disease or irritable bowel syndrome, kidney disease, liver disease, pancreatitis, use of medications likely to interfere with energy metabolism, appetite regulation and hormonal balance (including: anti-inflammatory drugs or steroids, antibiotics, androgens, phenytoin, erythromycin or thyroid hormones), having any metallic or magnetic implants such as pacemakers, and claustrophobia. Before participating in the study, exach subject provided written informed consent. The study was approved by the Brent Ethics Committee (REC ref: 12/LO/0139) and was registered at clinicaltrials.gov as NCT01684917.

extract_protocol: RNA was isolated (RNeasy Micro kit, Qiagen, Venlo, the Netherlands), quantified (Nanodrop ND 1000, Nanodrop technologies, Wilmington, Delaware USA) and integrity was checked by an Agilent 2100 Bioanalyser with RNA 6000 microchips (Agilent Technologies, South Queensferry, UK). Samples were included for microarray analysis if the RNA integrity number (RIN) was > 7.

treatment_protocol: Intervention diets: Subjects were randomly assigned to either a 20% energy restriction (ER) diet  (n=40), or to a control diet (n=32) for 12 weeks. The ER diet consisted of 50% calories from carbohydrates, 35% from fat and 15% from protein, >18g of fibre, and at least five portions of fruit and vegetables a day. The control diet consisted of 40% calories from carbohydrates, 45% from fat and 15% from protein, and at least three portions of fruit and vegetables a day. Both groups completed a seven-day food diary the first and last week of the study. Diets were based on dietary advice. Compliance was assessed via a weekly telephone interview. Exercise was kept at the habitual level. Nutritional challenge tests: Before and after the intervention, all subjects were subjected to an oral glucose tolerance test (OGTT) and the next day to a mixed meal test (MMT). Peripheral blood mononuclear cells (PBMCs) were sampled at fasting, and postprandially during the OGTT at 30, 60, and 120 min and during MMT at 60, 120, 240, and 360 min. PBMCs were isolated from whole blood using BD Vacutainer Cell Preparation Tubes according to the manufacturer’s instructions.

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: OGTT

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

value: after intervention

tag: intervention group assignment (er/control)

value: control

tag: age (yrs)

tag: gender

value: Female

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: glucosamine sulphate

tag: microarray plate batch

value: VIII


title: NT045_W18D2T30_CR

source_name: Peripheral blood mononuclear cells isolated from subject 045, W18 = after intervention, Day 2 = OGTT, T30 = 30 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: ER

value: VI


title: NT077_W18D2T30_Control

source_name: Peripheral blood mononuclear cells isolated from subject 077, W18 = after intervention, Day 2 = OGTT, T30 = 30 minutes

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: IX


title: NT001_W18D2T30_CR

source_name: Peripheral blood mononuclear cells isolated from subject 001, W18 = after intervention, Day 2 = OGTT, T30 = 30 minutes

tag: age (yrs)

tag: gender

tag: body weight (kg)

value: Amlodipine stable

value: I


title: Sample 236_genomic DNA from 101279430027_R06C01

tag: age

tag: Sex

tag: race

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell

tag: mono

tag: tissue


title: Sample 237_genomic DNA from 101279430027_R06C02


title: NT034_W18D2T30_Control

source_name: Peripheral blood mononuclear cells isolated from subject 034, W18 = after intervention, Day 2 = OGTT, T30 = 30 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

tag: microarray plate batch

value: V


title: NT025_W18D2T30_CR

source_name: Peripheral blood mononuclear cells isolated from subject 025, W18 = after intervention, Day 2 = OGTT, T30 = 30 minutes

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

value: Ibuprofen, Paracitamol

value: IV


title: NT010_W18D2T30_Control

source_name: Peripheral blood mononuclear cells isolated from subject 010, W18 = after intervention, Day 2 = OGTT, T30 = 30 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: Nasal spray

value: II


title: NT150_W18D2T0_CR

source_name: Peripheral blood mononuclear cells isolated from subject 150, W18 = after intervention, Day 2 = OGTT, T0 = Fasting sample

tag: sampling time challenge test (h)

tag: body height (m)

tag: bmi (kg/m2)

value: Vitamin D spray, Vegeterian, gluten free diet

value: XIV


title: Sample 233_genomic DNA from 101279430027_R04C02

tag: age

tag: Sex

value: Male

tag: race

value: White

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell

tag: mono

tag: tissue

value: whole blood


title: Sample 235_genomic DNA from 101279430027_R05C02


title: Sample 234_genomic DNA from 101279430027_R05C01


title: NT114_W18D2T0_CR

source_name: Peripheral blood mononuclear cells isolated from subject 114, W18 = after intervention, Day 2 = OGTT, T0 = Fasting sample

tag: subject

value: OGTT

tag: moment of sampling / challenge test (before/after intervention)

value: after intervention

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

value: Female

tag: body weight (kg)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

tag: microarray plate batch

value: XI


title: NT143_W18D2T0_CR

source_name: Peripheral blood mononuclear cells isolated from subject 143, W18 = after intervention, Day 2 = OGTT, T0 = Fasting sample

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

value: ER

tag: body height (m)

tag: bmi (kg/m2)

value: Glucoasmine

value: XIII


title: Sample 232_genomic DNA from 101279430027_R04C01

tag: age

tag: Sex

tag: race

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell

tag: mono

tag: tissue


title: Sample 230_genomic DNA from 101279430027_R03C01


title: NT090_W18D2T0_CR

source_name: Peripheral blood mononuclear cells isolated from subject 090, W18 = after intervention, Day 2 = OGTT, T0 = Fasting sample

tag: subject

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

tag: microarray plate batch

value: X


title: Sample 229_genomic DNA from 101279430027_R02C02

tag: age

tag: Sex

tag: race

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell


title: NT056_W18D2T60_Control

source_name: Peripheral blood mononuclear cells isolated from subject 056, W18 = after intervention, Day 2 = OGTT, T60 = 60 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: control

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

value: VII


title: Sample 227_genomic DNA from 101279430027_R01C02

tag: age

tag: Sex

tag: race

tag: hiv

tag: smoking

tag: mono

tag: tissue


title: Sample 226_genomic DNA from 101279430027_R01C01

tag: artadherence

tag: gran

tag: nk

tag: bcell


title: Sample 225_genomic DNA from 101279430009_R06C02


title: Sample 224_genomic DNA from 101279430009_R06C01


title: Sample 223_genomic DNA from 101279430009_R05C02


title: Sample 222_genomic DNA from 101279430009_R05C01


title: Sample 221_genomic DNA from 101279430009_R04C02


title: Sample 231_genomic DNA from 101279430027_R03C02


title: NT066_W18D2T0_Control

source_name: Peripheral blood mononuclear cells isolated from subject 066, W18 = after intervention, Day 2 = OGTT, T0 = Fasting sample

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: glucosamine sulphate

tag: microarray plate batch

value: VIII


title: NT077_W18D2T0_Control

source_name: Peripheral blood mononuclear cells isolated from subject 077, W18 = after intervention, Day 2 = OGTT, T0 = Fasting sample

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

value: IX


title: NT034_W18D2T0_Control

source_name: Peripheral blood mononuclear cells isolated from subject 034, W18 = after intervention, Day 2 = OGTT, T0 = Fasting sample

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: V


title: NT056_W18D2T0_Control

source_name: Peripheral blood mononuclear cells isolated from subject 056, W18 = after intervention, Day 2 = OGTT, T0 = Fasting sample

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: Male


title: Sample 220_genomic DNA from 101279430009_R04C01

tag: age

tag: Sex

tag: race

value: White

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell

tag: mono

tag: tissue


title: Sample 228_genomic DNA from 101279430027_R02C01

value: whole blood


title: NT045_W18D2T0_CR

source_name: Peripheral blood mononuclear cells isolated from subject 045, W18 = after intervention, Day 2 = OGTT, T0 = Fasting sample

tag: subject

value: OGTT

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

tag: microarray plate batch

value: VI


title: NT010_W18D2T0_Control

source_name: Peripheral blood mononuclear cells isolated from subject 010, W18 = after intervention, Day 2 = OGTT, T0 = Fasting sample

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

value: after intervention

tag: intervention group assignment (er/control)

value: Female

value: Nasal spray

value: II


title: Sample 219_genomic DNA from 101279430009_R03C02

tag: age

tag: Sex

tag: race

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell

tag: mono

tag: tissue


title: NT129_W18D2T0_CR

source_name: Peripheral blood mononuclear cells isolated from subject 129, W18 = after intervention, Day 2 = OGTT, T0 = Fasting sample

tag: subject

value: ER

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: Boots A-Z, 50+

tag: microarray plate batch

value: XII


title: NT150_W5D2T120_CR

source_name: Peripheral blood mononuclear cells isolated from subject 150, W5 = before intervention, Day 2 = OGTT, T120 = 120 minutes

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

value: before intervention

tag: intervention group assignment (er/control)

value: Vitamin D spray, Vegeterian, gluten free diet

value: XIV


title: NT025_W18D2T0_CR

source_name: Peripheral blood mononuclear cells isolated from subject 025, W18 = after intervention, Day 2 = OGTT, T0 = Fasting sample

tag: subject

tag: age (yrs)

tag: gender

value: Ibuprofen, Paracitamol

value: IV


title: NT018_W18D2T0_CR

source_name: Peripheral blood mononuclear cells isolated from subject 018, W18 = after intervention, Day 2 = OGTT, T0 = Fasting sample

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

value: Simvastatin

value: III


title: NT143_W5D2T120_CR

source_name: Peripheral blood mononuclear cells isolated from subject 143, W5 = before intervention, Day 2 = OGTT, T120 = 120 minutes

value: Male

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

value: Glucoasmine

value: XIII


title: NT001_W18D2T0_CR

source_name: Peripheral blood mononuclear cells isolated from subject 001, W18 = after intervention, Day 2 = OGTT, T0 = Fasting sample

value: OGTT

value: after intervention

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

value: Amlodipine stable

value: I


title: NT129_W5D2T120_CR

source_name: Peripheral blood mononuclear cells isolated from subject 129, W5 = before intervention, Day 2 = OGTT, T120 = 120 minutes

tag: % body fat

value: ER

tag: medication/supplement/diet use

tag: microarray plate batch


title: Sample 218_genomic DNA from 101279430009_R03C01

tag: age

tag: Sex

tag: race

value: White

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell

tag: mono

tag: tissue

value: whole blood


title: Sample 217_genomic DNA from 101279430009_R02C02


title: Sample 216_genomic DNA from 101279430009_R02C01


title: NT090_W5D2T120_CR

source_name: Peripheral blood mononuclear cells isolated from subject 090, W5 = before intervention, Day 2 = OGTT, T120 = 120 minutes

tag: subject

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

value: before intervention

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

value: Female

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

value: X


title: Sample 215_genomic DNA from 101279430009_R01C02

tag: age

tag: Sex

tag: race

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell


title: Sample 214_genomic DNA from 101279430009_R01C01

tag: mono

tag: tissue


title: Sample 213_genomic DNA from 101274800047_R06C02


title: Sample 212_genomic DNA from 101274800047_R06C01


title: Sample 211_genomic DNA from 101274800047_R05C02


title: GGE versus SEMP 3

city: Vancouver

first: Hirofumi

last: Hara

state: BC

address: 2350 Health Science Mall

department: Microbilogy and Immunology

country: Canada

institute: University of British Columbia

hyb_protocol: DNA microarrays were incubated with SlideHyb Hybridization Buffer no. 1 (Ambion) in an automated hybridization machine, GeneTac HybStation (Genomic Solutions) at 42 degree C for 18 h.

scan_protocol: Scanned using a GenePix 4000B scanner (Axon Instruments)

data_processing: The spot intensities were quantified using Imagene 6.1 (BioDiscovery). LOWESS Normalization (VSN), background subtracted data obtained from log2 of processed Red signal/processed Green signal.

organism: Sphingobium sp. SYK-6

source_name: SYK-6 treated with GGE

label_protocol: Total RNA (6 ug) was labeled using an indirect method in which aminoallyl-dUTPs were incorporated by reverse transcription using a mixture of two kinds of random hexamers, normal-GC-content (Invitrogen) and high-GC-content (70%) (Sigma), 5-(3-aminoallyl)-dUTP (Ambion), and PrimeScript II reverse transcriptase (Takara Bio Inc.).

growth_protocol: Cells of SYK-6 were grown in Wx-SEMP until OD600 of the culture reached 0.5.

extract_protocol: Total RNA was isolated using ISOGEN II reagent (Nippon Gene) according to the manufacture's instructions.

treatment_protocol: Cultures were further incubated with 10 mM of each substrates for 6 hours.

tag: substrate

value: guaiacylglycerol guaiacyl ether for 6 hours

source_name: SYK-6 treated with SEMP for 6 hours

value: SEMP for 6 hours


title: SA versus SEMP 3

source_name: SYK-6 treated with SA

value: syringate for 6 hours


title: GGE versus SEMP 2


title: GGE versus SEMP 1


title: Sample 208_genomic DNA from 101274800047_R04C01


title: Sample 209_genomic DNA from 101274800047_R04C02


title: Sample 207_genomic DNA from 101274800047_R03C02


title: SA versus SEMP 2


title: Sample 210_genomic DNA from 101274800047_R05C01


title: SA versus SEMP 1


title: Sample 205_genomic DNA from 101274800047_R02C02


title: Sample 204_genomic DNA from 101274800047_R02C01


title: Sample 206_genomic DNA from 101274800047_R03C01


title: B1 versus SEMP 3

source_name: SYK-6 treated with B1

value: 1,2 bis(4 hydroxy 3 methoxyphehyl) 1,3 propanediol for 6 hours


title: B1 versus SEMP 2


title: Sample 203_genomic DNA from 101274800047_R01C02

value: Male


title: NT077_W5D2T120_Control

source_name: Peripheral blood mononuclear cells isolated from subject 077, W5 = before intervention, Day 2 = OGTT, T120 = 120 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: control

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

tag: microarray plate batch

value: IX


title: B1 versus SEMP 1


title: DDVA versus SEMP 3

source_name: SYK-6 treated with DDVA

value: 5,5'- dehydrodivanillate for 6 hours


title: NT114_W5D2T120_CR

source_name: Peripheral blood mononuclear cells isolated from subject 114, W5 = before intervention, Day 2 = OGTT, T120 = 120 minutes

value: OGTT

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

value: XI


title: Sample 202_genomic DNA from 101274800047_R01C01

tag: age

tag: Sex

tag: race

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell

tag: mono

tag: tissue


title: NT066_W5D2T120_Control

source_name: Peripheral blood mononuclear cells isolated from subject 066, W5 = before intervention, Day 2 = OGTT, T120 = 120 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: glucosamine sulphate

value: VIII


title: NT056_W5D2T120_Control

source_name: Peripheral blood mononuclear cells isolated from subject 056, W5 = before intervention, Day 2 = OGTT, T120 = 120 minutes

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: microarray plate batch

value: VII


title: NT025_W5D2T120_CR

source_name: Peripheral blood mononuclear cells isolated from subject 025, W5 = before intervention, Day 2 = OGTT, T120 = 120 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: ER

value: Ibuprofen, Paracitamol

value: IV


title: Sample 201_genomic DNA from 101274800046_R06C02

tag: age

tag: Sex

tag: race

value: White

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell

tag: mono

tag: tissue

value: whole blood


title: Sample 200_genomic DNA from 101274800046_R06C01


title: NT018_W5D2T120_CR

source_name: Peripheral blood mononuclear cells isolated from subject 018, W5 = before intervention, Day 2 = OGTT, T120 = 120 minutes

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

value: before intervention

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

value: Female

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: Simvastatin

value: III


title: Sample 197_genomic DNA from 101274800046_R04C02

tag: age

tag: Sex

value: Male

tag: race

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell


title: DDVA versus SEMP 2

tag: substrate

value: SEMP for 6 hours


title: NT045_W5D2T120_CR

source_name: Peripheral blood mononuclear cells isolated from subject 045, W5 = before intervention, Day 2 = OGTT, T120 = 120 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: diastolic blood pressure (mm hg)

tag: microarray plate batch

value: VI


title: NT034_W5D2T120_Control

source_name: Peripheral blood mononuclear cells isolated from subject 034, W5 = before intervention, Day 2 = OGTT, T120 = 120 minutes

value: OGTT

value: control

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: V


title: Sample 198_genomic DNA from 101274800046_R05C01

tag: age

tag: Sex

tag: race

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell

tag: mono

tag: tissue


title: Sample 199_genomic DNA from 101274800046_R05C02


title: NT010_W5D2T120_Control

source_name: Peripheral blood mononuclear cells isolated from subject 010, W5 = before intervention, Day 2 = OGTT, T120 = 120 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: diastolic blood pressure (mm hg)

value: Nasal spray

tag: microarray plate batch

value: II


title: Sample 196_genomic DNA from 101274800046_R04C01

tag: age

tag: Sex

tag: race

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell


title: Sample 195_genomic DNA from 101274800046_R03C02

tag: mono

tag: tissue


title: Sample 193_genomic DNA from 101274800046_R02C02


title: DDVA versus SEMP 1

tag: substrate

value: 5,5'- dehydrodivanillate for 6 hours


title: Sample 194_genomic DNA from 101274800046_R03C01


title: Sample 192_genomic DNA from 101274800046_R02C01


title: Sample 191_genomic DNA from 101274800046_R01C02


title: Sample 190_genomic DNA from 101274800046_R01C01


title: NT001_W5D2T120_CR

source_name: Peripheral blood mononuclear cells isolated from subject 001, W5 = before intervention, Day 2 = OGTT, T120 = 120 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: ER

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: Amlodipine stable

value: I


title: NT150_W5D2T60_CR

source_name: Peripheral blood mononuclear cells isolated from subject 150, W5 = before intervention, Day 2 = OGTT, T60 = 60 minutes

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: diastolic blood pressure (mm hg)

value: Vitamin D spray, Vegeterian, gluten free diet

tag: microarray plate batch

value: XIV


title: Sample 188_genomic DNA from 101274800023_R06C01

tag: age

tag: Sex

tag: race

value: White

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell

tag: mono

tag: tissue

value: whole blood


title: Sample 186_genomic DNA from 101274800023_R05C01


title: Sample 187_genomic DNA from 101274800023_R05C02


title: Sample 185_genomic DNA from 101274800023_R04C02


title: FA versus SEMP 2

source_name: SYK-6 treated with FA

tag: substrate

value: fellulate for 6 hours


title: NT129_W5D2T60_CR

source_name: Peripheral blood mononuclear cells isolated from subject 129, W5 = before intervention, Day 2 = OGTT, T60 = 60 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

value: before intervention

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

value: Male

tag: body weight (kg)

tag: body height (m)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: Boots A-Z, 50+

value: XII


title: FA versus SEMP 1

source_name: SYK-6 treated with SEMP for 6 hours

value: SEMP for 6 hours


title: PCA versus SEMP 3

source_name: SYK-6 treated with PCA

value: protocatechuate for 6 hours


title: FA versus SEMP 3


title: Sample 184_genomic DNA from 101274800023_R04C01

tag: age

tag: Sex

tag: race

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell

tag: mono

tag: tissue


title: PCA versus SEMP 2

tag: substrate


title: Sample 182_genomic DNA from 101274800023_R03C01


title: NT143_W5D2T60_CR

source_name: Peripheral blood mononuclear cells isolated from subject 143, W5 = before intervention, Day 2 = OGTT, T60 = 60 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: OGTT

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: diastolic blood pressure (mm hg)

value: Glucoasmine

tag: microarray plate batch

value: XIII


title: Sample 189_genomic DNA from 101274800023_R06C02

tag: age

tag: Sex

tag: race

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell

tag: mono

tag: tissue


title: Sample 180_genomic DNA from 101274800023_R02C01


title: PCA versus SEMP 1

tag: substrate


title: Sample 177_genomic DNA from 101231030075_R06C02


title: Sample 178_genomic DNA from 101274800023_R01C01


title: Sample 179_genomic DNA from 101274800023_R01C02


title: VN versus SEMP 3

source_name: SYK-6 treated with VN

value: vanillin  for 6 hours


title: VN versus SEMP 2


title: Sample 183_genomic DNA from 101274800023_R03C02


title: NT090_W5D2T60_CR

source_name: Peripheral blood mononuclear cells isolated from subject 090, W5 = before intervention, Day 2 = OGTT, T60 = 60 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: ER

tag: age (yrs)

tag: gender

value: Female

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: waist hip ratio (ratio)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: X


title: Sample 176_genomic DNA from 101231030075_R06C01

tag: age

tag: Sex

tag: race

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell

tag: mono

tag: tissue


title: Sample 181_genomic DNA from 101274800023_R02C02


title: VA versus SEMP 2

source_name: SYK-6 treated with VA

tag: substrate

value: vanillate for 6 hours


title: Sample 174_genomic DNA from 101231030075_R05C01

value: White


title: VA versus SEMP 1


title: Sample 175_genomic DNA from 101231030075_R05C02

value: whole blood


title: NT066_W5D2T60_Control

source_name: Peripheral blood mononuclear cells isolated from subject 066, W5 = before intervention, Day 2 = OGTT, T60 = 60 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: control

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: diastolic blood pressure (mm hg)

value: glucosamine sulphate

tag: microarray plate batch

value: VIII


title: NT056_W5D2T60_Control

source_name: Peripheral blood mononuclear cells isolated from subject 056, W5 = before intervention, Day 2 = OGTT, T60 = 60 minutes

value: before intervention

value: Male

tag: waist hip ratio (ratio)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: VII


title: VA versus SEMP 3

tag: substrate

value: SEMP for 6 hours


title: VN versus SEMP 1


title: NT045_W5D2T60_CR

source_name: Peripheral blood mononuclear cells isolated from subject 045, W5 = before intervention, Day 2 = OGTT, T60 = 60 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: OGTT

tag: sampling time challenge test (h)

value: VI


title: NT114_W5D2T60_CR

source_name: Peripheral blood mononuclear cells isolated from subject 114, W5 = before intervention, Day 2 = OGTT, T60 = 60 minutes

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

value: XI


title: PC versus SEMP 3

source_name: SYK-6 treated with PC

value: phenylcoumarane for 6 hours


title: NT034_W5D2T60_Control

source_name: Peripheral blood mononuclear cells isolated from subject 034, W5 = before intervention, Day 2 = OGTT, T60 = 60 minutes

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

value: V


title: NT077_W5D2T60_Control

source_name: Peripheral blood mononuclear cells isolated from subject 077, W5 = before intervention, Day 2 = OGTT, T60 = 60 minutes

value: Female

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: microarray plate batch

value: IX


title: NT025_W5D2T60_CR

source_name: Peripheral blood mononuclear cells isolated from subject 025, W5 = before intervention, Day 2 = OGTT, T60 = 60 minutes

value: ER

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: Ibuprofen, Paracitamol

value: IV


title: NT018_W5D2T60_CR

source_name: Peripheral blood mononuclear cells isolated from subject 018, W5 = before intervention, Day 2 = OGTT, T60 = 60 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: Simvastatin

value: III


title: NT010_W5D2T60_Control

source_name: Peripheral blood mononuclear cells isolated from subject 010, W5 = before intervention, Day 2 = OGTT, T60 = 60 minutes

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: control

value: Nasal spray

value: II


title: Sample 172_genomic DNA from 101231030075_R04C01

tag: age

tag: Sex

value: Male

tag: race

value: White

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell

tag: mono

tag: tissue

value: whole blood


title: NT001_W5D2T60_CR

source_name: Peripheral blood mononuclear cells isolated from subject 001, W5 = before intervention, Day 2 = OGTT, T60 = 60 minutes

tag: subject

value: OGTT

value: before intervention

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: Amlodipine stable

tag: microarray plate batch

value: I


title: Sample 169_genomic DNA from 101231030075_R02C02

tag: age

tag: Sex

tag: race

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell


title: Sample 168_genomic DNA from 101231030075_R02C01

tag: mono

tag: tissue


title: Sample 170_genomic DNA from 101231030075_R03C01


title: Sample 167_genomic DNA from 101231030075_R01C02


title: Sample 173_genomic DNA from 101231030075_R04C02


title: Sample 166_genomic DNA from 101231030075_R01C01


title: PC versus SEMP 1

tag: substrate

value: phenylcoumarane for 6 hours

source_name: SYK-6 treated with SEMP for 6 hours

value: SEMP for 6 hours


title: AV versus SEMP 3

source_name: SYK-6 treated with AV

value: acetovanillone for 6 hours


title: Sample 164_genomic DNA from 101231030073_R05C02


title: Sample 165_genomic DNA from 101231030073_R06C01


title: Sample 160_genomic DNA from 101231030073_R03C02


title: Sample 161_genomic DNA from 101231030073_R04C01


title: Sample 163_genomic DNA from 101231030073_R05C01


title: Sample 159_genomic DNA from 101231030073_R03C01


title: PC versus SEMP 2


title: Sample 162_genomic DNA from 101231030073_R04C02


title: Sample 171_genomic DNA from 101231030075_R03C02


title: Sample 158_genomic DNA from 101231030073_R02C02


title: Sample 157_genomic DNA from 101231030073_R02C01


title: AV versus SEMP 1


title: PR versus SEMP 3

source_name: SYK-6 treated with PR

value: pinoresinol for 6 hours


title: PR versus SEMP 2


title: AV versus SEMP 2


title: NT150_W5D2T30_CR

source_name: Peripheral blood mononuclear cells isolated from subject 150, W5 = before intervention, Day 2 = OGTT, T30 = 30 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: ER

tag: age (yrs)

tag: gender

value: Female

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

value: Vitamin D spray, Vegeterian, gluten free diet

value: XIV


title: PR versus SEMP 1


title: NT143_W5D2T30_CR

source_name: Peripheral blood mononuclear cells isolated from subject 143, W5 = before intervention, Day 2 = OGTT, T30 = 30 minutes

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: Glucoasmine

tag: microarray plate batch

value: XIII


title: NT114_W5D2T30_CR

source_name: Peripheral blood mononuclear cells isolated from subject 114, W5 = before intervention, Day 2 = OGTT, T30 = 30 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: XI


title: Sample 156_genomic DNA from 101231030073_R01C02

tag: age

tag: Sex

value: Male

tag: race

value: White

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell

tag: mono

tag: tissue


title: Sample 155_genomic DNA from 101231030073_R01C01

value: whole blood


title: Sample 153_genomic DNA from 101231030014_R06C01


title: NT129_W5D2T30_CR

source_name: Peripheral blood mononuclear cells isolated from subject 129, W5 = before intervention, Day 2 = OGTT, T30 = 30 minutes

value: OGTT

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

value: before intervention

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

value: Boots A-Z, 50+

value: XII


title: Sample 152_genomic DNA from 101231030014_R05C02

tag: age

tag: Sex

tag: race

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell


title: Sample 151_genomic DNA from 101231030014_R05C01

tag: mono

tag: tissue


title: Sample 149_genomic DNA from 101231030014_R04C01


title: Sample 147_genomic DNA from 101231030014_R03C01


title: Sample 148_genomic DNA from 101231030014_R03C02


title: Sample 154_genomic DNA from 101231030014_R06C02


title: Sample 146_genomic DNA from 101231030014_R02C02


title: Sample 150_genomic DNA from 101231030014_R04C02


title: Sample 144_genomic DNA from 101231030014_R01C02


title: Sample 143_genomic DNA from 101231030014_R01C01


title: NT045_W5D2T30_CR

source_name: Peripheral blood mononuclear cells isolated from subject 045, W5 = before intervention, Day 2 = OGTT, T30 = 30 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: medication/supplement/diet use

tag: microarray plate batch

value: VI


title: NT077_W5D2T30_Control

source_name: Peripheral blood mononuclear cells isolated from subject 077, W5 = before intervention, Day 2 = OGTT, T30 = 30 minutes

value: control

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

value: IX


title: MCF7linc00052-3

city: México

first: Vilma

middle: Araceli

last: Maldonado

state: Distrito Federal

address: Periferico  4809

department: Investigacion

country: Mexico

institute: INMEGEN

description: MCF-7 stably transfected with shRN- linc00052

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Transcriptome Analysis Console (TAC 4.0) software from Affimetrix and Limma eBayes protocol

source_name: MCF-7 cell line

label_protocol: standard Affymetrix protocol

growth_protocol: MCF-7 were transfected with shRNAs and selected with 0.6/ml puromycin for 14 days.

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

treatment_protocol: Transfected with shRNALuciferase or shRNAlinc00052

tag: transfection


title: Estradiol rep1

type: SRA

city: Houston

first: MURUGESAN

last: PALANIAPPAN

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

library_source: transcriptomic

data_processing:
The reads were mapped to the mouse Ensembl reference set of 82,508 transcripts (annotated to 31034 genes) using TopHat.
Relative transcript abundance was identified using the RSEM algorithm.
The edgeR  package was used to identify differential regulated gene expression.
Genome_build: mm9

organism: Mus musculus

source_name: Estradiol_mammary glands

growth_protocol: At 6 weeks of age, mice were ovariectomized and rested for 10 days and then mice were injected with vehicle (seasame oil) or 17β-estradiol (100ng) for 2 hours.

extract_protocol:
RNA extraction using the Qiagen RNeasy Lipid Tissue Midi Kit according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All mice were treated with vehicle (seasame oil) or 17β-estradiol (100ng) for2 h

tag: strain

value: BALB/c

tag: age

value: 6 weeks

tag: genotype/variation

value: wild type

tag: treatment

value: 17β-Estradiol for 2 hours

tag: tissue

value: Mammary gland (#4)


title: NT090_W5D2T30_CR

source_name: Peripheral blood mononuclear cells isolated from subject 090, W5 = before intervention, Day 2 = OGTT, T30 = 30 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: ER

tag: age (yrs)

tag: gender

value: Female

tag: body weight (kg)

value: X


title: Sample 145_genomic DNA from 101231030014_R02C01

tag: Sex

value: Male

tag: race

value: White

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell

tag: mono


title: NT025_W5D2T30_CR

source_name: Peripheral blood mononuclear cells isolated from subject 025, W5 = before intervention, Day 2 = OGTT, T30 = 30 minutes

tag: subject

tag: % body fat

value: OGTT

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: Ibuprofen, Paracitamol

tag: microarray plate batch

value: IV


title: MCF7linc00052-2

tag: transfection


title: NT056_W5D2T30_Control

source_name: Peripheral blood mononuclear cells isolated from subject 056, W5 = before intervention, Day 2 = OGTT, T30 = 30 minutes

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

value: before intervention

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

value: VII


title: Sample 142_genomic DNA from 101231030013_R06C02

tag: age

tag: Sex

tag: race

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell

tag: mono

tag: tissue

value: whole blood


title: NT066_W5D2T30_Control

source_name: Peripheral blood mononuclear cells isolated from subject 066, W5 = before intervention, Day 2 = OGTT, T30 = 30 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

value: control

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: glucosamine sulphate

tag: microarray plate batch

value: VIII


title: NT010_W5D2T30_Control

source_name: Peripheral blood mononuclear cells isolated from subject 010, W5 = before intervention, Day 2 = OGTT, T30 = 30 minutes

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

value: Nasal spray

value: II


title: MCF7linc00052-1

tag: transfection


title: NT034_W5D2T30_Control

source_name: Peripheral blood mononuclear cells isolated from subject 034, W5 = before intervention, Day 2 = OGTT, T30 = 30 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

value: V


title: Estradiol rep2

tag: strain

value: BALB/c

tag: age

value: 6 weeks

tag: genotype/variation

value: wild type

tag: treatment

value: 17β-Estradiol for 2 hours

tag: tissue

value: Mammary gland (#4)


title: Sample 141_genomic DNA from 101231030013_R06C01

tag: Sex

value: Male

tag: race

value: White

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell

tag: mono


title: Control rep1

source_name: control_mammary glands


title: Sample 140_genomic DNA from 101231030013_R05C02


title: MCFLUC2

description: MCF-7 stably transfected with shRN- luc

tag: transfection

value: shluc


title: MCF7LUC-1

description: MCF-7 stably transfected with shRN- luc


title: NT018_W5D2T30_CR

source_name: Peripheral blood mononuclear cells isolated from subject 018, W5 = before intervention, Day 2 = OGTT, T30 = 30 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: OGTT

tag: moment of sampling / challenge test (before/after intervention)

value: before intervention

tag: intervention group assignment (er/control)

value: ER

tag: age (yrs)

tag: gender

value: Female

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: Simvastatin

tag: microarray plate batch

value: III


title: MCFLUC3

description: MCF-7 stably transfected with shRN- luc

tag: transfection


title: NT001_W5D2T30_CR

source_name: Peripheral blood mononuclear cells isolated from subject 001, W5 = before intervention, Day 2 = OGTT, T30 = 30 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

value: Amlodipine stable

value: I


title: Sample 138_genomic DNA from 101231030013_R04C02

tag: age

tag: Sex

tag: race

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell

tag: mono

tag: tissue

value: whole blood


title: NT150_W5D2T0_CR

source_name: Peripheral blood mononuclear cells isolated from subject 150, W5 = before intervention, Day 2 = OGTT, T0 = Fasting sample

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: Vitamin D spray, Vegeterian, gluten free diet

tag: microarray plate batch

value: XIV


title: Sample 136_genomic DNA from 101231030013_R03C02

tag: age

tag: Sex

tag: race

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell

tag: mono


title: Sample 137_genomic DNA from 101231030013_R04C01

tag: tissue


title: Control rep2

tag: strain

value: BALB/c

value: 6 weeks

tag: genotype/variation

value: wild type


title: Input

library_source: genomic

data_processing:
DNA libraries were sequenced on a Illumina HiSeq 2500.
Sequences (50-nt reads) were aligned to the mouse genome (mm9) using the BWA algorithm with default settings.
Peak locations were determined using the Model-based Analysis of ChIP-seq Algorithm with a cutoff of p-value 1e-8.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files

source_name: WT mammary glands treated with E2h

growth_protocol: At 6 weeks of age, mice were ovariectomized and rested for 10 days and then mice were injected with 17β-estradiol (100ng) for 2 hours.

extract_protocol:
Mammary glands were treated with a TissueTearer followed by dounce-homogenization in lysis buffer.  Lysates were sonicated and ERα-DNA complexes were isolated using a ERα antibody.
ChIP and input DNA were amplified using the Illumina ChIP-Seq DNA Sample Prep Kit.

treatment_protocol: All mice were treatedwith 17β-estradiol (100ng) for2 h

value: Mammary gland

tag: genotype

value: WT


title: ERα ChIP-seq replicate 2

tag: chip antibody

value: ERα (Santa Cruz, sc-542)


title: NT143_W5D2T0_CR

source_name: Peripheral blood mononuclear cells isolated from subject 143, W5 = before intervention, Day 2 = OGTT, T0 = Fasting sample

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: OGTT

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

value: Male

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: Glucoasmine

value: XIII


title: Sample 134_genomic DNA from 101231030013_R02C02

tag: age

tag: Sex

tag: race

value: White

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell

tag: mono

tag: tissue


title: Sample 135_genomic DNA from 101231030013_R03C01


title: Sample 133_genomic DNA from 101231030013_R02C01


title: Sample 132_genomic DNA from 101231030013_R01C02


title: ERα ChIP-seq replicate 1

tag: strain

tag: genotype

tag: chip antibody


title: Sample 129_genomic DNA from 101231000143_R06C01


title: Sample 130_genomic DNA from 101231000143_R06C02


title: Sample 139_genomic DNA from 101231030013_R05C01


title: Sample 128_genomic DNA from 101231000143_R05C02


title: NT114_W5D2T0_CR

source_name: Peripheral blood mononuclear cells isolated from subject 114, W5 = before intervention, Day 2 = OGTT, T0 = Fasting sample

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

value: before intervention

tag: intervention group assignment (er/control)

value: ER

tag: age (yrs)

tag: gender

value: Female

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: microarray plate batch

value: XI


title: NT129_W5D2T0_CR

source_name: Peripheral blood mononuclear cells isolated from subject 129, W5 = before intervention, Day 2 = OGTT, T0 = Fasting sample

tag: subject

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: Boots A-Z, 50+

value: XII


title: Sample 124_genomic DNA from 101231000143_R03C02

tag: age

tag: Sex

tag: race

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell

tag: mono

tag: tissue

value: whole blood


title: Sample 125_genomic DNA from 101231000143_R04C01


title: Sample 126_genomic DNA from 101231000143_R04C02


title: NT090_W5D2T0_CR

source_name: Peripheral blood mononuclear cells isolated from subject 090, W5 = before intervention, Day 2 = OGTT, T0 = Fasting sample

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

value: X


title: NT066_W5D2T0_Control

source_name: Peripheral blood mononuclear cells isolated from subject 066, W5 = before intervention, Day 2 = OGTT, T0 = Fasting sample

tag: subject

value: control

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: glucosamine sulphate

tag: microarray plate batch

value: VIII


title: Sample 123_genomic DNA from 101231000143_R03C01

tag: age

tag: Sex

tag: race

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell

tag: mono

tag: tissue


title: Sample 120_genomic DNA from 101231000143_R01C02


title: Sample 119_genomic DNA from 101231000143_R01C01


title: Sample 122_genomic DNA from 101231000143_R02C02


title: Sample 117_genomic DNA from 101231000133_R06C01


title: Sample 118_genomic DNA from 101231000133_R06C02


title: Sample 115_genomic DNA from 101231000133_R05C01


title: Sample 116_genomic DNA from 101231000133_R05C02


title: Sample 131_genomic DNA from 101231030013_R01C01


title: NT056_W5D2T0_Control

source_name: Peripheral blood mononuclear cells isolated from subject 056, W5 = before intervention, Day 2 = OGTT, T0 = Fasting sample

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

value: VII


title: Sample 113_genomic DNA from 101231000133_R04C01

tag: age

tag: Sex

tag: race

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell


title: Sample 127_genomic DNA from 101231000143_R05C01

tag: mono

tag: tissue


title: Sample 111_genomic DNA from 101231000133_R03C01


title: Sample 112_genomic DNA from 101231000133_R03C02


title: shKIAA1429-rep2-MeRIP

city: Chengdu

first: Tian

last: Lan

state: Sichuan

address: No. 37 of Guoxue Lane

department: Department of Liver Surgery & Liver Transplantation

country: China

institute: West China Hospital

data_processing:
Off-Line Base Caller software (Solexa pipeline v1.8) software was used for basecalling.
FastQC (v0.11.7) was used for quality control.
Sequenced reads were filtered by Trimmomatic (V0.32).
Filtere high-quality data were mapped to Ensembl genome using HISAT2 v2.1.0
m6A peaks were determined bu using exomePeak (v2.13.2) and were annotated according to Ensembl dataset. Sequence motifs were identified using MEME-ChIP analysis.
Genome_build: Ensembl genes (see contents of processed data for version)
Supplementary_files_format_and_content: The fold enrichment within the peak in the IP sample compared with the input sample

source_name: HCC cells

extract_protocol:
120 ug of purified total RNA was determined with NanoDrop ND-1000. Intact mRNA was isolated from total RNA samples using Arraystar Seq-StarTM poly (A) mRNA Isolation Kit (Arrarystar, MD, USA) following the manufacturer’s instructions, and was chemically fragmented into 100-nucleotide-long fragments by incubation in fragmentation buffer. Fragmented mRNA was immunoprecipitated with anti-N6-methyladenosine (m6A) antibody (Synaptic Systems, Goettingen, Germany), and also 1/10 of the fragmented mRNA was kept as input.
RNA-seq libraries were prepared using KAPA Stranded mRNA-seq Kit (Illumina, CA, USA). The completed libraries, qualified by Agilent 2100 Bioanalyzer, were denatured and diluted to loading volume of a loading concentration. Clustered libraries were loaded onto reagent cartridge and forwarded to sequencing run on Illumina Hiseq 4000 system by Aksomics (Shanghai, China).
MeRIP-seq

tag: cell type

value: HCCLM3 cells

tag: methods

value: methylated RNA immunoprecipitation

tag: intervention


title: NT034_W5D2T0_Control

source_name: Peripheral blood mononuclear cells isolated from subject 034, W5 = before intervention, Day 2 = OGTT, T0 = Fasting sample

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: OGTT

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

value: Male

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

tag: microarray plate batch

value: V


title: NT025_W5D2T0_CR

source_name: Peripheral blood mononuclear cells isolated from subject 025, W5 = before intervention, Day 2 = OGTT, T0 = Fasting sample

tag: subject

value: before intervention

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

value: Ibuprofen, Paracitamol

value: IV


title: NT077_W5D2T0_Control

source_name: Peripheral blood mononuclear cells isolated from subject 077, W5 = before intervention, Day 2 = OGTT, T0 = Fasting sample

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

value: Female

value: IX


title: NT045_W5D2T0_CR

source_name: Peripheral blood mononuclear cells isolated from subject 045, W5 = before intervention, Day 2 = OGTT, T0 = Fasting sample

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: ER

tag: age (yrs)

value: VI


title: shKIAA1429-rep1-MeRIP

tag: cell type

tag: methods

tag: intervention


title: NT018_W5D2T0_CR

source_name: Peripheral blood mononuclear cells isolated from subject 018, W5 = before intervention, Day 2 = OGTT, T0 = Fasting sample

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

value: Simvastatin

value: III


title: Sample 110_genomic DNA from 101231000133_R02C02

tag: age

tag: Sex

tag: race

value: White

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell

tag: mono

tag: tissue

value: whole blood


title: Sample 121_genomic DNA from 101231000143_R02C01


title: Sample 109_genomic DNA from 101231000133_R02C01


title: shKIAA1429-Input

tag: cell type

tag: methods

tag: intervention


title: NT010_W5D2T0_Control

source_name: Peripheral blood mononuclear cells isolated from subject 010, W5 = before intervention, Day 2 = OGTT, T0 = Fasting sample

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: control

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: Nasal spray

tag: microarray plate batch

value: II


title: Sample 108_genomic DNA from 101231000133_R01C02

tag: age

tag: Sex

tag: race

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell

tag: mono

tag: tissue


title: Sample 107_genomic DNA from 101231000133_R01C01


title: shCtrl-rep2-MeRIP

tag: cell type

value: HCCLM3 cells

tag: methods

value: methylated RNA immunoprecipitation

tag: intervention

value: shCtrl


title: NT001_W5D2T0_CR

source_name: Peripheral blood mononuclear cells isolated from subject 001, W5 = before intervention, Day 2 = OGTT, T0 = Fasting sample

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: OGTT

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

value: before intervention

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

value: Male

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

value: Amlodipine stable

value: I


title: NPK_shNsd2_3

city: Hospitalet de Llobregat

first: Alvaro

last: Aytes

state: Catalonia

address: Granvia 199

department: ProCURE

country: Spain

institute: IDIBELL

data_processing:
RNA-seq pipeline description:
We use RTA (Illumina) for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming. We map the reads to a reference genome (Mouse: UCSC/mm9) using Tophat [1] (version 2.1.0) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10). To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.  We estimate the relative abundance (aka expression level) of genes and splice isoforms using cufflinks [2] (version 2.0.2) with default settings. We test for differentially expressed genes under various conditions using DEseq [3]. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Raw RNAseq counts were normalized (variance stabilization) using DESeq2 package in R-studio Version 0.99.484
Genome_build: Mouse: UCSC/mm9
Supplementary_files_format_and_content: Text file include DESeq normalized values for each Sample

source_name: shRNA induced slencing of Nsd4

extract_protocol:
RNA was extracted using the MagMAX-96 RNA isolation kit (Ambion). Quality control was performed with Agilent Bioanalyser 2100
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit. Libraries are then sequenced using Illumina HiSeq2500 at CNAG (Spanish National Genomics Centre). We multiplex samples in each lane, which yields targeted number of single-end/paired-end 75bp reads for each sample, as a fraction of 180 million reads for the whole lane.   Samples were sequenced twice to achieve desired sequencing depth. There are two SRR for each sample.

tag: cell line

value: NPK

tag: cell type

value: Prostate cancer cells


title: Sample 105_genomic DNA from 101231000121_R06C01

tag: age

tag: Sex

tag: race

tag: hiv

tag: smoking

tag: artadherence

tag: gran

tag: nk

tag: bcell

tag: mono

tag: tissue


title: NPK_shNsd2_2

source_name: shRNA induced slencing of Nsd3


title: Sample 104_genomic DNA from 101231000121_R05C02


title: shCtrl-Input

tag: methods

tag: intervention


title: shCtrl-rep1-MeRIP


title: Sample 114_genomic DNA from 101231000133_R04C02


title: Sample 103_genomic DNA from 101231000121_R05C01


title: NPK_shNsd2_1

source_name: shRNA induced slencing of Nsd2


title: Sample 102_genomic DNA from 101231000121_R04C02


title: Transformed_EZH2i_rep3

city: London

first: Paola

last: Scaffidi

state: Choose a state

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description: Transformed.txt

data_processing:
Adapter trimming was undertaken using cutadapt (version 1.9.1) with parameters “--minimum-length=25 --qualitycutoff= 20 -a AGATCGGAAGAGC -A AGATCGGAAGAGC”.
The RSEM package (version 1.2.29) in conjunction with the STAR alignment algorithm (version 2.5.1b) was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to hg19 RefSeq genes downloaded from the UCSC Table Browser.
Differential expression analysis was performed for DMSO vs EPZ-6438 (EZH2 pharmacological inhibitor) treated cells with the DESeq2 package (version 1.10.1).
Genome_build: Hg19
Supplementary_files_format_and_content: Tab-delimited text files including gene expression TPM, Log2 fold change (EZH2i vs DMSO) and FDR values

source_name: Dermal fibroblasts

growth_protocol: All cell lines were cultured at 37⁰C in 5% CO2 in Modified Eagle Media (Gibco) + 15% tetracycline free fetal bovine serum (Gibco) + 100mM L-glutamine + Penicillin/streptomycin.

extract_protocol:
RNA from cell pellets was extracted using an RNeasy Plus Mini Kit (Qiagen) in accordance with the manufacturer’s instructions.
Sequencing libraries were prepared using a KAPA Stranded RNA-Seq Kit with RiboErase (Roche) according to the manufacturer’s instructions. To reduce sequencing lane biases, the library of each sample was split across two lanes, generating two fastq files for each sample. The pair of fastq files were subsequently merged for the next analysis steps.

treatment_protocol: Cell lines were treated with either a pharmacological EZH2 inhibitor  (EPZ-6438, Selleckchem), dissolved in DMSO, or DMSO alone for 12 days. To sustain EZH2 inhibition, drug and media was changed every three days.

tag: treatment

value: 3uM EPZ-6438 (EZH2 inhibitor)

tag: treatment time

value: 12 days

tag: replicate number


title: Sample 100_genomic DNA from 101231000121_R03C02

value: White


title: Sample 101_genomic DNA from 101231000121_R04C01

value: whole blood


title: NPK_MCTP40_2

source_name: Treated with MCTP40

tag: cell line

tag: cell type


title: NPK_MCTP41_3

source_name: Treated with MCTP41


title: Transformed_EZH2i_rep2

description: Transformed.txt


title: Sample 98_genomic DNA from 101231000121_R02C02

tag: age

tag: Sex


title: Transformed_EZH2i_rep1

description: Transformed.txt


title: NPK_MCTP39_1

source_name: Treated with MCTP39


title: Sample 99_genomic DNA from 101231000121_R03C01

tag: race

tag: hiv


title: Sample 96_genomic DNA from 101231000121_R01C02

tag: smoking

tag: artadherence


title: Transformed_DMSO_rep3

description: Transformed.txt

value: DMSO


title: NPK_3

source_name: Control cells


title: Sample 95_genomic DNA from 101231000121_R01C01

tag: gran

tag: nk


title: Sample 94_genomic DNA from 101231000120_R06C02

tag: bcell

tag: mono


title: Sample 106_genomic DNA from 101231000121_R06C02

tag: tissue


title: Sample 91_genomic DNA from 101231000120_R05C01


title: NPK_2


title: Transformed_DMSO_rep1

description: Transformed.txt


title: Sample 90_genomic DNA from 101231000120_R04C02


title: Sample 92_genomic DNA from 101231000120_R05C02


title: Sample 88_genomic DNA from 101231000120_R03C02


title: NPK_1


title: H-29: Keratinocytes from healthy skin

city: Stockholm

first: Ankit

last: Srivastava

state: - Select a State -

address: CMM L8:02

department: Department of Medicine

country: Sweden

institute: Karolinska Institutet

data_processing:
Solexa standard protocol was used for base-calling
Adapters and the low quality tags were removed from the sequencing data. Clean reads were mapped and aligned to known miRNAs sequences (miRBase 21).
Data were normalized (transcripts per million, TPM) and analysed using Bioconductor-EdgeR.
Group comparisons (P vs. H, P vs. N and N vs. H) were performed.
miRNAs with <10% FDR, fold change >1.4 (1 TPM at least in one of the groups and expressed in half of the samples in any group) were considered statistically significant.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts and normalized TPM values for each samples

source_name: Keratinocytes from healthy skin

extract_protocol:
Keratinocytes were sorted (MACS) from the epidermis compartment of healthy and psoriasis (lesional and non-lesional) skin. Total RNA containing small RNA fraction was isolated from these cells and small RNA libraries were constructed.
Small RNA libraries were prepared for sequencing using standard protocols (Solexa/Illumina)

value: healthy skin

value: Keratinocytes

tag: ethnicity

value: Caucasian


title: Sample 89_genomic DNA from 101231000120_R04C01


title: Preneoplastic_EZH2i_rep3

description: Preneoplastic.txt

tag: treatment


title: Preneoplastic_EZH2i_rep2

description: Preneoplastic.txt

tag: treatment time


title: Sample 87_genomic DNA from 101231000120_R03C01


title: H-28: Keratinocytes from healthy skin


title: Sample 86_genomic DNA from 101231000120_R02C02


title: Sample 85_genomic DNA from 101231000120_R02C01


title: Sample 97_genomic DNA from 101231000121_R02C01


title: Preneoplastic_EZH2i_rep1

description: Preneoplastic.txt

tag: replicate number


title: Sample 84_genomic DNA from 101231000120_R01C02


title: Preneoplastic_DMSO_rep3

description: Preneoplastic.txt


title: Sample 83_genomic DNA from 101231000120_R01C01


title: H-26: Keratinocytes from healthy skin


title: Sample 93_genomic DNA from 101231000120_R06C01


title: Sample 80_genomic DNA from 101231000119_R05C02


title: Sample 81_genomic DNA from 101231000119_R06C01


title: Transformed_DMSO_rep2

description: Transformed.txt


title: Preneoplastic_DMSO_rep1

description: Preneoplastic.txt


title: Sample 82_genomic DNA from 101231000119_R06C02


title: Sample 79_genomic DNA from 101231000119_R04C02


title: Untransformed_EZH2i_rep3

description: Untransformed.txt


title: H-23: Keratinocytes from healthy skin


title: Sample 78_genomic DNA from 101231000119_R04C01


title: Sample 77_genomic DNA from 101231000119_R03C02


title: H-24: Keratinocytes from healthy skin


title: Untransformed_EZH2i_rep2

description: Untransformed.txt


title: Sample 76_genomic DNA from 101231000119_R03C01


title: Sample 75_genomic DNA from 101231000119_R02C02


title: H-22: Keratinocytes from healthy skin


title: H-27: Keratinocytes from healthy skin


title: Untransformed_EZH2i_rep1

description: Untransformed.txt


title: Sample 73_genomic DNA from 101231000119_R01C02


title: Sample 74_genomic DNA from 101231000119_R02C01


title: H-21: Keratinocytes from healthy skin


title: Preneoplastic_DMSO_rep2

description: Preneoplastic.txt


title: Untransformed_DMSO_rep3

description: Untransformed.txt


title: H-25: Keratinocytes from healthy skin


title: Sample 70_genomic DNA from 101231000099_R06C01


title: N-19: Keratinocytes from psoriasis non-lesional skin

value: psoriasis non-lesional skin


title: Sample 72_genomic DNA from 101231000119_R01C01


title: Untransformed_DMSO_rep2

description: Untransformed.txt


title: N-18: Keratinocytes from psoriasis non-lesional skin


title: Sample 69_genomic DNA from 101231000099_R05C02


title: N-17: Keratinocytes from psoriasis non-lesional skin


title: Untransformed_DMSO_rep1

description: Untransformed.txt


title: Sample 67_genomic DNA from 101231000099_R04C02


title: Sample 66_genomic DNA from 101231000099_R04C01


title: HNRNPKi_RNAPol2_CHIPseq_rep_2

city: San Diego

first: George

last: Sen

state: CA

address: 9500 Gilman Drive

institute: UCSD

description:
ChIP-seq protocol
DIFF.RNAPOL2.CHIPseq.txt

data_processing:
Raw ChIP-seq reads were aligned using Bowtie v2.2.5.
MACS2 (version 2.0.10) was used for call peaks in individual replicates using Input ChIP-seq as the control sample.
Peaks overlapped among all replicates were obtained using bedtools.
Differential peaks between samples were obtained by DiffReps 1.55.4 (4) using negative binomial test with a scanning window size of 1000 bp, step size of 100 bp, and a cutoff p-value of 0.0001.
Genome_build: hg19
Supplementary_files_format_and_content: output from diffReps

source_name: Human epidermal keratinocyte

growth_protocol: Primary keratinocytes were grown on culture dishes and maintained in keratinocyte SFM medium (Life technologies).

extract_protocol:
DNA was isolated with Thermo Scientific's GeneJET Gel Extraction kit
ChIP-seq libraries were prepared with TruSeq RNA Library Prep Kit (Illumina) then multiplexed

treatment_protocol: 10 million cells were crosslinked with 2mM DSG and 1% formaldehyde and used in the experiment. The ChIP experiment was done using the Lab ChIP-seq protocol

value: Neonatal foreskin

value: primary keratinocytes

tag: genotype

value: HNRNPK shRNA knockdown

tag: antibody

value: RNA POL II (Active Motif 39097)


title: N-16: Keratinocytes from psoriasis non-lesional skin

tag: cell type


title: Sample 64_genomic DNA from 101231000099_R03C01

tag: age

tag: Sex

value: Male


title: Sample 65_genomic DNA from 101231000099_R03C02

tag: race

tag: hiv


title: Sample 63_genomic DNA from 101231000099_R02C02

tag: smoking

tag: artadherence


title: Sample 62_genomic DNA from 101231000099_R02C01

tag: gran

tag: nk


title: N-15: Keratinocytes from psoriasis non-lesional skin


title: CTLi_RNAPol2_CHIPseq_rep_2

value: Control shRNA


title: N-14: Keratinocytes from psoriasis non-lesional skin


title: Sample 61_genomic DNA from 101231000099_R01C02

tag: bcell

tag: mono


title: Sample 60_genomic DNA from 101231000099_R01C01

tag: tissue


title: CTLi_RNAPol2_CHIPseq_rep_1


title: Sample 59_genomic DNA from 101178130043_R06C02


title: Sample 71_genomic DNA from 101231000099_R06C02


title: N-13: Keratinocytes from psoriasis non-lesional skin

tag: ethnicity


title: HNRNPKi_Input_Pol2CHIP

value: none (input)


title: Sample 57_genomic DNA from 101178130043_R05C02


title: N-12: Keratinocytes from psoriasis non-lesional skin


title: CTLi_Input_Pol2CHIP


title: Sample 58_genomic DNA from 101178130043_R06C01


title: Sample 56_genomic DNA from 101178130043_R05C01


title: Sample 68_genomic DNA from 101231000099_R05C01


title: Sample 55_genomic DNA from 101178130043_R04C02


title: Sample 54_genomic DNA from 101178130043_R04C01


title: N-11: Keratinocytes from psoriasis non-lesional skin


title: Input_ChIPseq_rep_1

description:
ChIP-seq protocol
HNRNPK.CHIPseq.peaks.bed

data_processing:
Raw ChIP-seq reads were aligned using Bowtie v2.2.5.
MACS2 (version 2.0.10) was used for call peaks in individual replicates using Input ChIP-seq as the control sample.
Peaks overlapped among all replicates were obtained using bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: BED file with called peaks

value: wildtype


title: P-09: Keratinocytes from psoriasis lesions

source_name: Keratinocytes from psoriasis lesions

value: psoriasis lesions


title: HNRNPK_ChIPseq_rep_3

value: HNRNPK (Bethyl Laboratories A300-674A)


title: Sample 52_genomic DNA from 101178130043_R03C01

value: White


title: HNRNPKi_RNAPol2_CHIPseq_rep_1


title: P-08: Keratinocytes from psoriasis lesions


title: Sample 51_genomic DNA from 101178130043_R02C02

value: whole blood


title: HNRNPK_ChIPseq_rep_2


title: Sample 49_genomic DNA from 101178130043_R01C02


title: P-07: Keratinocytes from psoriasis lesions


title: HNRNPK_ChIPseq_rep_1


title: Sample 48_genomic DNA from 101178130043_R01C01


title: P-06: Keratinocytes from psoriasis lesions


title: IGG_RIPseq_rep_2

description:
RNA IP-seq protocol
HNRNPK.RIPseq

data_processing:
Illumina Hiseq 4000 reads were trimmed and filtered using Partek Flow. High quality reads were aligned using TopHat v2.1.0 for alignment into BAM files.
BAM files were imported into the RNA-seq pipeline of Partek Genomic Suite, version 6.6 (Copyright 2009, Partek Inc., St. Louis, MO, USA), and RPKM counts were calculated (RefSeq Transcripts 85 2018-05-02). Exclusions include a mininum reads of 10 in one out of 4 samples. RPKM values were log2-transformed with an offset value of 0.000001.
Genome_build: hg19
Supplementary_files_format_and_content: text file with log2 RPKM with offset of 0.000001

extract_protocol:
HNRNPK RNA IP was performed using Magna RIP RNA IP kit(17-700) from Millipore.
RNA-seq libraries were prepared with TruSeq RNA Library Prep Kit (Illumina) then multiplexed

value: rabbit IGG (Millipore 12-370)


title: Sample 45_genomic DNA from 101032610108_R05C02


title: Sample 46_genomic DNA from 101032610108_R06C01


title: P-05: Keratinocytes from psoriasis lesions


title: IGG_RIPseq_rep_1

description:
RNA IP-seq protocol
HNRNPK.RIPseq


title: Sample 43_genomic DNA from 101032610108_R04C02


title: Sample 44_genomic DNA from 101032610108_R05C01


title: Sample 42_genomic DNA from 101032610108_R04C01


title: P-04: Keratinocytes from psoriasis lesions


title: HNRNPK_RIPseq_rep_2

description:
RNA IP-seq protocol
HNRNPK.RIPseq


title: P-03: Keratinocytes from psoriasis lesions


title: Sample 41_genomic DNA from 101032610108_R03C02


title: HNRNPK_RIPseq_rep_1

description:
RNA IP-seq protocol
HNRNPK.RIPseq


title: Sample 53_genomic DNA from 101178130043_R03C02


title: P-02: Keratinocytes from psoriasis lesions


title: HNRNPKi_RNAseq_rep_2

description:
RNA-seq protocol
HNRNPK.RNAseq

extract_protocol:
RNA was isolated using GeneJET RNA purification kit (Thermo Scientific).
RNA-seq libraries were prepared with TruSeq RNA Library Prep Kit (Illumina) then multiplexed

treatment_protocol: HNRNPK shRNA knockdown


title: Sample 50_genomic DNA from 101178130043_R02C01


title: Sample 38_genomic DNA from 101032610108_R02C01


title: Sample 39_genomic DNA from 101032610108_R02C02


title: Sample 40_genomic DNA from 101032610108_R03C01


title: P-01: Keratinocytes from psoriasis lesions


title: HNRNPKi_RNAseq_rep_1

description:
RNA-seq protocol
HNRNPK.RNAseq


title: Sample 36_genomic DNA from 101032610033_R06C02


title: Sample 47_genomic DNA from 101032610108_R06C02


title: CTLi_RNAseq_rep_2

description:
RNA-seq protocol
HNRNPK.RNAseq


title: Sample 35_genomic DNA from 101032610033_R06C01


title: CTLi_RNAseq_rep_1

description:
RNA-seq protocol
HNRNPK.RNAseq


title: Sample 31_genomic DNA from 101032610033_R04C01


title: Sample 30_genomic DNA from 101032610033_R03C02


title: Sample 29_genomic DNA from 101032610033_R03C01


title: Sample 32_genomic DNA from 101032610033_R04C02


title: Sample 28_genomic DNA from 101032610033_R02C02


title: Sample 33_genomic DNA from 101032610033_R05C01


title: meg-3(ax3055) meg-4(ax3052) JH3745 outcrossed young mother on HT115-L4440 bacteria replicate 2-sRNAseq

city: Baltimore

first: Geraldine

last: Seydoux

state: MD

address: 725 North Wolfe Street, PCTB 706

department: Molecular Biology and Genetics

institute: JHU School of Medicine

description:
meg34outcrossed_hrde1meg34_young_mother_HT115_L4440_smRNA_ID.txt
smRNA-Seq

data_processing:
Adapters were trimmed with Cutadapt.
Reads were aligned with Bowtie2
Read alignments were counted with HTseq-count
Normalized read counts were obtained with DEseq2
Genome browser views were obtained with IGV
Genome_build: ce10
Supplementary_files_format_and_content: Tab delimited .txt files with log2FCs, q-values, RPMs, etc.

organism: Caenorhabditis elegans

source_name: Whole worm, young mother

growth_protocol: Starvation synchronized. Grown on HT115 bacteria with L4440 vector until young mother stage at 20 C.

extract_protocol:
TRIzol and Zymo RNA purification kit. TRIzol and Zymo RNA Concentrator
TruSeq Small RNA Library Preparation Kit.

treatment_protocol: RNA was treated with 5’ polyphosphatase.

tag: strain/genotype

value: whole worm

tag: group

value: young mother


title: meg-3(ax3055) meg-4(ax3052) JH3745 outcrossed young mother on HT115-L4440 bacteria replicate 1-sRNAseq


title: Sample 27_genomic DNA from 101032610033_R02C01


title: Sample 26_genomic DNA from 101032610033_R01C02


title: Sample 37_genomic DNA from 101032610108_R01C01


title: hrde-1(tm1200); meg-3(ax3055) meg-4(ax3052) young mother on HT115-L4440 bacteria replicate 2-sRNAseq

description:
N2_hrde1meg34_young_mother_HT115_L4440_smRNA_ID.txt
smRNA-Seq


title: hrde-1(tm1200); meg-3(ax3055) meg-4(ax3052) young mother on HT115-L4440 bacteria replicate 1-sRNAseq


title: Sample 25_genomic DNA from 101032610033_R01C01


title: Sample 23_genomic DNA from 101032610010_R06C01


title: Sample 24_genomic DNA from 101032610010_R06C02


title: Sample 34_genomic DNA from 101032610033_R05C02


title: hrde-1(tm1200) young mother on HT115-L4440 bacteria replicate 2-sRNAseq

description:
N2_hrde1_young_mother_HT115_L4440_smRNA_ID.txt
smRNA-Seq


title: Sample 22_genomic DNA from 101032610010_R05C02


title: Sample 21_genomic DNA from 101032610010_R05C01


title: hrde-1(tm1200) young mother on HT115-L4440 bacteria replicate 1-sRNAseq


title: Sample 20_genomic DNA from 101032610010_R04C02


title: Sample 19_genomic DNA from 101032610010_R04C01


title: meg-3(ax3055) meg-4(ax4312) JH3674 mixed population on NA22 bacteria replicate 2-sRNAseq

description:
smRNA-Seq
N2_meg34_strain4_mixed_NA22_smRNA_ID.txt

data_processing:
Adapters were trimmed with Cutadapt for sRNAseq. This step was omitted for mRNAseq.
Reads were aligned with Bowtie2 for sRNAseq and HiSat2 for mRNAseq.
Read alignments were counted with HTSeq-count for both sRNAseq and mRNAseq.
Normalized read counts were obtained with DEseq2 for both sRNAseq and mRNAseq.
Genome browser views were obtained with IGV.
Genome_build: ce10
Supplementary_files_format_and_content: Tab delimited .txt files with log2FCs, q-values, RPMs, etc.

source_name: Whole worm, mixed population on NA22

growth_protocol: Starvation synchronized or mixed population. Grown on either NA22 or HT115 bacteria with L4440 vector at 20 C.

extract_protocol:
TRIzol and Zymo RNA purification kit. TRIzol and Zymo RNA Concentrator
TruSeq Small RNA Library Preparation Kit/TruSeq RNA Library Preparation Kit.

treatment_protocol: RNA for sRNAseq libraries was treated with 5’ polyphosphatase. RNA for mRNAseq libraries was treated with the RiboZero Gold Epedemiology Kit and supplemented with the ERCC Spike-in.

tag: growth

value: on NA22

value: mixed population


title: Sample 17_genomic DNA from 101032610010_R03C01


title: Sample 18_genomic DNA from 101032610010_R03C02


title: Sample 16_genomic DNA from 101032610010_R02C02


title: meg-3(ax3055) meg-4(ax4312) JH3674 mixed population on NA22 bacteria replicate 1-sRNAseq


title: meg-3(ax3055) meg-4(ax4311) JH3673 mixed population on NA22 bacteria replicate 2-sRNAseq

description:
smRNA-Seq
N2_meg34_strain3_mixed_NA22_smRNA_ID.txt


title: Sample 14_genomic DNA from 101032610010_R01C02


title: Sample 15_genomic DNA from 101032610010_R02C01


title: Sample 13_genomic DNA from 101032610010_R01C01


title: meg-3(ax3055) meg-4(ax4311) JH3673 mixed population on NA22 bacteria replicate 1-sRNAseq


title: Sample 11_genomic DNA from 101032570226_R06C01


title: Mouse embryonic stem cells differentiation D2.5 Dox-

city: Kyoto

first: Tomohiro

last: Minakawa

address: Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Cira, Kyoto Univ.

description:
Gene expression data during differentiation
k08_25minus_avg100

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: Affymetrix GeneChip Operating Software (GCOS) Version 1.0. with target intensity=100.

source_name: Day2.5 Dox-

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

growth_protocol: ESCs were maintained in Glasgow Minimum Essential Medium (GMEM; 11710-035, Thermo Fisher Scientific) containing 10% KnockOut Serum Replacement (KSR; 10828-028, Thermo Fisher Scientific), 1% fetal bovine serum (FBS; SAFC Biosciences, USA), 2,000 units/mL leukemia inhibitory factor (LIF; Merck Millipore), 1 mM Sodium pyruvate (Sigma-Aldrich), 1% MEM Non-Essential Amino Acids (NEAA; 11140-050, Thermo Fisher Scientific), 50 U/ml penicillin (Meiji Seika Pharma, Japan), 50 µg/ml streptomycin (Meiji Seika Pharma, Japan), 0.1 mM 2-mercaptoethanol (2-ME; 21985-023, Thermo Fisher Scientific) and 1 µg/ml doxycycline (Dox; D9891, Sigma-Aldrich).Differentiation was induced in MEM alpha (11900-024, Thermo Fisher Scientific) containing 10% FBS (10437-028, Thermo Fisher Scientific), 2.2 µg/mL NaHCO3 (09655-25, Nacalai Tesque, Japan), 50 U/ml penicillin, 50 µg/ml streptomycin and 0.1 mM 2-ME.

extract_protocol: Total RNA was collected with TRI reagent according to manufacturer’s instructions.

treatment_protocol: Cells were incubated with or without 1μg/mL of doxycycline.

tag: cell

value: ES cells

tag: protocol

value: Differentiation

tag: time

tag: agent

value: Dox-


title: Sample 12_genomic DNA from 101032570226_R06C02

tag: age

tag: Sex

tag: race


title: Mouse embryonic stem cells differentiation D3.5 Dox-

description:
Gene expression data during differentiation
k09_35minus_avg100

source_name: Day3.5 Dox-


title: Sample 10_genomic DNA from 101032570226_R05C02

tag: hiv

tag: smoking

tag: artadherence


title: Mouse embryonic stem cells differentiation D1.5 Dox-

description:
Gene expression data during differentiation
k07_15minus_avg100

source_name: Day1.5 Dox-


title: Mouse embryonic stem cells differentiation D2.5 Dox+

description:
Gene expression data during differentiation
k04_25plus_avg100

source_name: Day2.5 Dox+

value: Dox+


title: Bx oocyte

city: Nagoya

first: Atsushi

last: Murai

address: Furo-cho, Chikusa-ku

department: Department of Animal Sciences

institute: Nagoya University

hyb_protocol: Following fragmentation, biotinylated cRNA were hybridized for 17 hr at 45C on GeneChip Chicken Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 System.

data_processing:
The data were analyzed with GeneChip Expression Analysis Data Analysis Fundamentals using GeneChip Operating Software ver 1.4 with MAS5 algorithm.
Algorithm: ExpressionStat 5.0

organism: Gallus gallus

source_name: oocyte of brusectomized laying hens

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Affymetrix Gene Chip 3' IVT PLUS Reagent Kit, Affymetrix).

growth_protocol: On the 17-18 d of incubation, surgical bursectomy was performed. After allowing 24 h for hatching, female chicks were housed until sexual maturity.

extract_protocol: Total RNA was isolated from the pooled F5-F7 germinal discs using an RNeasy Micro kit (Qiagen, Hilden, Germany). Total RNA from three birds per treatment was pooled for each chip.

treatment_protocol: The control and the Bx groups (n=3) were prepared. At 25 wk of age, germinal disc region including oocyte nucleus was collected from F5-F7 yellow ovarian follicles. The all collected samples (9 germinal discs of 3 birds) were preserved in RNAlater.

tag: surgical operation

value: Bx

value: F5-F7 oocytes


title: Mouse embryonic stem cells differentiation D0.5 Dox-

description:
Gene expression data during differentiation
k06_05minus_avg100

source_name: Day0.5 Dox-


title: Mouse embryonic stem cells differentiation D3.5 Dox+

description:
Gene expression data during differentiation
k05_35plus_avg100

source_name: Day3.5 Dox+


title: Control oocyte

source_name: oocyte of control laying hens

value: Control


title: Mouse embryonic stem cells differentiation D0.5 Dox+

description:
Gene expression data during differentiation
k02_05plus_avg100

source_name: Day0.5 Dox+


title: Mouse embryonic stem cells differentiation D1.5 Dox+

description:
Gene expression data during differentiation
k03_15plus_avg100

source_name: Day1.5 Dox+


title: Sample 9_genomic DNA from 101032570226_R05C01

data_processing:
GenomeStudio V2011.1
MatrixProcessed.txt: Quantile normalized Average Beta
MethylatedSignal.txt: Unmethylated and methylated signal intensities

extract_protocol: DNAs were extracted from whole blood using the standard protocol.

value: Male

tag: gran

tag: nk

tag: bcell

tag: mono


title: meg-3(ax3055) meg-4(ax4310) JH3672 mixed population on NA22 bacteria replicate 1-sRNAseq

description:
smRNA-Seq
N2_meg34_strain2_mixed_NA22_smRNA_ID.txt

tag: strain/genotype

tag: tissue

tag: group


title: Mouse embryonic stem cells undifferentiated

description:
Gene expression data of ES cells
k01_zero_avg100

source_name: ES cells

tag: cell

tag: protocol

value: Undifferentiated


title: Sample 8_genomic DNA from 101032570226_R04C02


title: Sample 7_genomic DNA from 101032570226_R04C01


title: meg-3(ax3055) meg-4(ax3052) JH3475 young mother on HT115-L4440 bacteria replicate 2-mRNAseq

description:
RNA-Seq
N2_meg34_strain1_young_mother_HT115_L4440_mRNA_ID.txt

source_name: Whole worm, young mother on HT115-L4440

tag: growth


title: Sample 5_genomic DNA from 101032570226_R03C01

tag: age


title: Sample 4_genomic DNA from 101032570226_R02C02

tag: Sex


title: Sample 6_genomic DNA from 101032570226_R03C02

tag: race


title: meg-3(ax3055) meg-4(ax4310) JH3672 mixed population on NA22 bacteria replicate 2-sRNAseq


title: meg-3(ax3055) meg-4(ax3052) JH3475 young mother on HT115-L4440 bacteria replicate 1-mRNAseq


title: Sample 2_genomic DNA from 101032570226_R01C02

tag: hiv


title: N2 young mother on HT115-L4440 bacteria replicate 2-mRNAseq


title: Sample 3_genomic DNA from 101032570226_R02C01

tag: smoking


title: Sample 1_genomic DNA from 101032570226_R01C01

tag: artadherence


title: meg-3(ax3055) meg-4(ax3052) mixed population on NA22 bacteria replicate 2-sRNAseq

description:
smRNA-Seq
N2_meg34_strain1_mixed_NA22_smRNA_ID.txt


title: N2 young mother on HT115-L4440 bacteria replicate 1-mRNAseq


title: meg-3(ax3055) meg-4(ax3052) mixed population on NA22 bacteria replicate 1-sRNAseq