title: COLON_2267_SALMON_baseline

description: history of polyps


title: COLON_468_SALMON_6months_after_intervention

status: Public on Feb 01 2025

type: RNA

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description: no history of polyps

hyb_protocol: Hybridisation of 10ug cRNA on  NuGO_Hs1a52018 arrays was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described n the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated using GCRMA, applying the Emperical Bayes estimate for background correction.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: colon biopsy

label_protocol: The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 350ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.

growth_protocol: Volounteers were recruited for the study through gastroenterology clinics across The Netherlands and the UK. Biopsies of 28 participants (15 female and 13 male) were used for array analyses. These subjects had a mean age of 56±11 years and a BMI of 26.5 kg m-2. All were disease free although 19 had previously had polyps removed. This study was approved by the Medical Ethical Committee of Nijmegen University Medical Centre St. Radboud, Netherlands (reference 2004/111), and the King’s Lynn Local Research Ethics Committee (reference 04/Q0105/8). All subjects gave written informed consent after the study was explained to them both in writing and verbally. The trial was registered at www.clinicaltrials.gov under identifier NCT00145015.

extract_protocol: Biopsies were put immediately into RNAlater (Qiagen), and total RNA was isolated from the samples using the RNeasy Plus Mini kit (Qiagen).

treatment_protocol: Subjects were randomised into one of three dietary interventions: salmon (300g/week), cod (300g/week) or no additional fish in a diet for six months. Dietary advice was offered to all three groups. Biopsies were taken from the sigmoid colon, and were collected at baseline and after 6 months dietary intervention.

tag: protocol

value: extra salmon

tag: time

value: after six months of intervention

tag: individual

value: subject 468

tag: gender

value: Male

tag: age


title: COLON_7815_COD_6months_after_intervention

description: history of polyps

value: extra cod

value: subject 7815


title: F_FEB_ADG

type: SRA

city: Nagoya

first: Junfeng

last: Chen

state: 23 - 愛知県

address: Nagoya University

country: Japan

institute: Nagoya University

library_source: transcriptomic

data_processing:
Mapping and quantification were performed by bowtie (v1.2.3) and RSEM (v1.3.3).
Assembly: Mmul_10
Supplementary files format and content: Excel files include FPM values for each tissue.

organism: Macaca mulatta

source_name: adrenal gland

growth_protocol: Adult rhesus macaques were kept in an open enclosure  with natural light and temperature at the Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Japan. Two meals were provided per day at the estimated ad libitum levels and water was always available ad libitum.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Universal Mini Kit (Qiagen).
3'RNA-Seq library was prepared by the Lasy-Seq v1.1 protocol (https://sites.google.com/view/lasy-seq/)

treatment_protocol: Macaques were immobilized with  10 mg/kg BW ketamine hydrochloride (intramuscularly), and anaesthesized with 80 mg/kg BW pentobarbital (intravenously), and perfused with ice-cold Ames' medium.

tag: sampling point

value: February, 2020

tag: tissue

value: adrenal gland

tag: Sex

value: F


title: F_DEC_WAT

source_name: white adipose tissue

value: December, 2019

value: white adipose tissue


title: COLON_3423_COD_6months_after_intervention

description: history of polyps

value: subject 3423

value: Female


title: F_FEB_CA3

source_name: hippocampus CA3

value: hippocampus CA3


title: COLON_9004_SALMON_6months_after_intervention

description: history of polyps

value: subject 9004


title: COLON_7413_COD_6months_after_intervention

description: no history of polyps

value: subject 7413


title: F_FEB_AMYL

source_name: amygdala lateral nucleus

value: amygdala lateral nucleus


title: COLON_211_COD_baseline

description: history of polyps

value: baseline

value: subject 211


title: COLON_211_COD_6months_after_intervention

description: history of polyps

value: after six months of intervention


title: F_FEB_AMYC

source_name: amygdala central nucleus

value: amygdala central nucleus


title: F_DEC_VTA

source_name: ventral tegmental area

value: ventral tegmental area


title: F_FEB_ANU

source_name: anus

value: anus


title: F_FEB_BOM

source_name: bone marrow

value: February, 2020

value: bone marrow


title: COLON_3423_COD_baseline

description: history of polyps

value: extra cod


title: F_DEC_VMH

source_name: ventromedial  hypothalamic nucleus

value: December, 2019

value: ventromedial  hypothalamic nucleus

value: F


title: als_embryo_rep3

city: SAINT PAUL

first: Gary

last: Muehlbauer

state: MN

address: 1991 Upper Buford Circle 411 Borlaug Hall

department: Agronomy and Plant Genetics

country: USA

institute: University of Minnesota

description: Gene expression data from embryo tissue

hyb_protocol: Labeled RNA (15 μg) was chemically fragmented using the Affymetrix GeneChip sample cleanup module (Affymetrix) and used for hybridization. The Affymetrix Barley1 GeneChip hybridizations, washes were conducted following standard  Affymetrix procedures.

scan_protocol: Chip reading was conducted using standard Affymetrix procedures using an Affymetrix gene chip scanner.

data_processing: GeneChip data were inspected for quality using the Expressionist Pro Refiner, v. 1.0 (Genedata, San Francisco, CA, USA). Normalization and summarization was performed with Microarray Suite version 5.0 (MAS 5.0)

organism: Hordeum vulgare

source_name: Embryo tissue was sampled 16-20 days after pollination.

label_protocol: Biotinylated cRNA was produced by transcribing the cDNA was transcribed in vitro using the Enzo BioArray HighYield RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY, U.S.A.) in the presence of biotinylated UTP and CTP. The biotin-labeled cRNA was purified with the Affymetrix Gene-Chip Sample Cleanup Module (Affymetrix).

growth_protocol: Seeds for each genotype were surface sterilized with bleach. For seedling samples seeds were germinated in sterile plastic petri dishes containing three layers of filter paper saturated with distilled H2O. The petri dishes were covered  with foil and transferred to a growth chamber set at 17 °C for 16 h and 12 °C for 8 h. For crown tissue plants were grown on vermiculite and for inflorescence and embryo tissue in potting mix in a growth chamber set at 17 °C for 16 h in light (200±20 μEm−1s−1) followed by 12 °C for 8 h in the dark.

extract_protocol: Tissue was pooled and ground to a fine powder in liquid nitrogen. Total RNA was extracted using the Trizol (Invitrogen, Carlsbad, CA, U.S.A.) protocol. Genomic DNA was digested using RNasefree DNase and the RNA was purified on RNeasy columns (Promega Corp., Madison, WI, U.S.A.). RNA quality was examined using an Agilent 2100 bioanalyzer. For cDNA synthesis an T7-Oligo(dT) primer (Proligo, Boulder, CO, U.S.A.) and the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) was used and cDNA was purified with the Affymetrix Gene-Chip sample cleanup module (Affymetrix, Santa Clara, CA,U.S.A.).

tag: tissue type

value: embryo

tag: genotype

value: absent lower laterals (als)


title: F_DEC_VIC

source_name: visual cortex

value: visual cortex


title: COLON_8458_SALMON_baseline

description: no history of polyps

value: extra salmon

value: subject 8458

value: Female


title: F_DEC_UTE

source_name: uterus

value: uterus


title: F_DEC_THA

source_name: thalamus

value: thalamus


title: als_crown_rep1

description: Gene expression data from crown tissue

source_name: Crown tissue was sampled from 10 - 14 day old plants.

value: crown


title: COLON_9004_SALMON_baseline

description: history of polyps

value: baseline

value: subject 9004


title: F_DEC_THR

source_name: thyroid

value: thyroid


title: F_DEC_TON

source_name: tongue

value: tongue


title: F_DEC_SPL

source_name: spleen

value: spleen


title: F_DEC_STM

source_name: stomach

value: December, 2019

value: stomach


title: F_DEC_SKNH

source_name: skin in the hindquarter

value: skin in the hindquarter

value: F


title: COLON_8458_SALMON_6months_after_intervention

description: no history of polyps

source_name: colon biopsy

value: after six months of intervention


title: COLON_5053_SALMON_baseline

description: history of polyps

value: subject 5053


title: F_DEC_SON

source_name: supraoptic nucleus

value: supraoptic nucleus


title: COLON_5053_SALMON_6months_after_intervention

description: history of polyps

value: extra salmon


title: COLON_2721_SALMON_6months_after_intervention

description: history of polyps

value: subject 2721

value: Male


title: COLON_2721_SALMON_baseline

description: history of polyps


title: COLON_2612_SALMON_6months_after_intervention

description: history of polyps

value: subject 2612

value: Female


title: F_DEC_SKNB

source_name: skin on the back

value: skin on the back


title: F_DEC_SN

source_name: substantia nigra

value: substantia nigra


title: F_DEC_SG

source_name: salivary gland

value: salivary gland


title: F_DEC_SCN

source_name: suprachiasmatic nucleus

value: suprachiasmatic nucleus


title: F_DEC_RPE

source_name: pigmental epithelial cells

value: pigmental epithelial cells


title: COLON_2410_SALMON_6months_after_intervention

description: history of polyps

value: subject 2410


title: COLON_1389_SALMON_baseline

description: history of polyps

value: baseline

value: subject 1389


title: COLON_2410_SALMON_baseline

description: history of polyps


title: COLON_1389_SALMON_6months_after_intervention

description: history of polyps


title: COLON_1618_SALMON_6months_after_intervention

description: history of polyps

value: subject 1618


title: COLON_1618_SALMON_baseline

description: history of polyps


title: F_DEC_PVN

source_name: paraventricular nucleus

value: December, 2019

value: paraventricular nucleus

value: F


title: F_DEC_PUT

source_name: putamen

value: putamen


title: F_DEC_RET

source_name: retina

value: retina


title: F_DEC_PIN

source_name: pineal gland

value: pineal gland


title: COLON_7641_COD_6months_after_intervention

description: history of polyps

value: extra cod

value: after six months of intervention

value: subject 7641

value: Male


title: F_DEC_REC

source_name: rectum

value: rectum


title: F_DEC_PAN

source_name: pancreas

value: pancreas


title: COLON_2612_SALMON_baseline

description: history of polyps

value: extra salmon

value: subject 2612

value: Female


title: COLON_7641_COD_baseline

description: history of polyps

value: baseline


title: COLON_6699_COD_baseline

description: history of polyps

value: subject 6699


title: COLON_8263_COD_6months_after_intervention

description: history of polyps


title: COLON_8263_COD_baseline

description: history of polyps

value: subject 8263


title: COLON_4726_COD_baseline

description: history of polyps

value: subject 4726


title: COLON_2168_COD_baseline

description: history of polyps

value: subject 2168


title: COLON_2760_COD_6months_after_intervention

description: history of polyps

value: subject 2760


title: F_DEC_NM

source_name: nasal mucosa

value: December, 2019

value: nasal mucosa

value: F


title: F_DEC_MUG

source_name: gastrocnemial muscle

value: gastrocnemial muscle


title: F_DEC_PT

source_name: pars tuberalis of the pituitary

value: pars tuberalis of the pituitary


title: F_DEC_PD

source_name: pars distalis of the pituitary

value: pars distalis of the pituitary


title: COLON_6699_COD_6months_after_intervention

description: history of polyps

source_name: colon biopsy

value: extra cod

value: after six months of intervention

value: Male


title: F_DEC_mPFC

source_name: medial prefrontal cortex

value: medial prefrontal cortex


title: COLON_4726_COD_6months_after_intervention

description: history of polyps

value: Female


title: COLON_1212_COD_6months_after_intervention

description: history of polyps

value: subject 1212


title: F_DEC_OVI

source_name: oviduct

value: oviduct


title: COLON_7991_SALMON_baseline

description: no history of polyps

value: extrasalmon

value: baseline

value: subject 7991


title: COLON_1212_COD_baseline

description: history of polyps


title: COLON_8353_SALMON_6months_after_intervention

description: no history of polyps

value: extra salmon

value: subject 8353


title: F_DEC_MMB

source_name: mammilary nuclei

value: December, 2019

value: mammilary nuclei


title: F_DEC_OVA

source_name: ovary

value: ovary

value: F


title: F_DEC_OLB

source_name: olfactory bulb

value: olfactory bulb


title: COLON_2760_COD_baseline

description: history of polyps

value: extra cod

value: subject 2760


title: F_DEC_NAc

source_name: nucleus accumbens

value: nucleus accumbens


title: F_DEC_OES

source_name: oesophagus

value: oesophagus


title: F_DEC_MUA

source_name: abdominal muscle

value: abdominal muscle


title: F_DEC_mPOA

source_name: medial preoptic area

value: medial preoptic area


title: COLON_8353_SALMON_baseline

description: no history of polyps

value: Female


title: COLON_4008_SALMON_baseline

description: no history of polyps

value: subject 4008


title: COLON_4008_SALMON_6months_after_intervention

description: no history of polyps

value: after six months of intervention


title: COLON_8901_COD_baseline

description: no history of polyps

value: baseline

value: subject 8901


title: COLON_7991_SALMON_6months_after_intervention

description: no history of polyps

value: extra salmon

value: subject 7991

value: Male


title: COLON_2168_COD_6months_after_intervention

description: history of polyps

value: subject 2168


title: F_DEC_LUN

source_name: lung

value: December, 2019

value: lung

value: F


title: F_DEC_LIV

source_name: liver

value: liver


title: F_DEC_LC

source_name: locus coeruleus

value: locus coeruleus


title: F_DEC_MEL

source_name: mesenteric lymph node

value: mesenteric lymph node


title: F_DEC_LHA

source_name: lateral hypothalamic nucleus

value: lateral hypothalamic nucleus


title: F_DEC_KIM

source_name: kidney medulla

value: kidney medulla


title: F_DEC_KIC

source_name: kidney cortex

value: kidney cortex


title: F_DEC_HEA

source_name: heart

value: heart


title: F_DEC_IRI

source_name: iris

value: iris


title: F_DEC_JEJ

source_name: jejunum

value: jejunum


title: F_DEC_GPi

source_name: globus pallidus internal segment

value: globus pallidus internal segment


title: COLON_2400_COD_baseline

description: no history of polyps

source_name: colon biopsy

value: extra cod

value: baseline

value: subject 2400


title: COLON_345_COD_baseline

description: no history of polyps

value: subject 345

value: Female


title: COLON_345_COD_6months_after_intervention

description: no history of polyps

value: after six months of intervention


title: F_DEC_HAB

source_name: habenula

value: December, 2019

value: habenula

value: F


title: COLON_2400_COD_6months_after_intervention

description: no history of polyps

value: Male


title: F_DEC_GPe

source_name: globus pallidus external segment

value: globus pallidus external segment


title: F_DEC_GUM

source_name: gum

value: gum


title: F_DEC_DUO

source_name: duodenum

value: duodenum


title: F_DEC_FOV

source_name: fovea centralis

value: fovea centralis


title: F_DEC_GAL

source_name: gallbladder

value: gallbladder


title: F_DEC_ILE

source_name: ileum

value: ileum


title: F_DEC_DRN

source_name: dorsal raphe

value: dorsal raphe


title: HWAT_38B_FIBRATE

hyb_protocol: Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

data_processing: Expression estimates were calculated using RMA in Bioconductor

source_name: white adipose tissue

label_protocol: Total RNA (300 ng/sample) was labelled with the 1-cycle cDNA labelling kit (MessageAmp II-Biotin Enhanced Kit, Ambion, Austin, TX, USA; P/N AM1791), as per the manufacturer's instructions.

growth_protocol: Subjects with a BMI of at least 27 kg/m2 were recruited via posters in the university and hospital buildings and via advertisements in local newspapers. Subjects came to the university for a screening visit. On this visit, fasting blood was sampled for analyses of serum lipids and lipoproteins. In addition, height and body weight were determined. Furthermore, subjects had to complete a medical and general questionnaire. Exclusion criteria were BMI below 27 kg/m2, impairment of kidney and liver function, serum total cholesterol above 8 mmol/L, serum triglycerides above 4 mmol/L, taking medication that could influence the study outcome or could interfere with fenofibrate treatment, use of fish oil supplements, consumption of plant sterol or stanol-enriched food products, having donated blood within 1 month prior to the start of the study, having a diagnosis of any long-term medical condition (e.g. diabetes, cardiovascular diseases, epilepsy) or experiencing strong symptoms of allergy. After screening, twenty-six subjects met all our inclusion criteria and started this study. Subjects received oral and written information about the nature and risk of the experimental procedures before their written informed consent before the start of the study. The study was approved by the Medical Ethical Committee of Maastricht University.

extract_protocol: A subcutaneous abdominal adipose tissue biopsy from the periumbillical region was taken. Under local anaesthesia (Lidocaine HCL 1%, B.Braun, Melsungen, Germany), a biopsy was taken with a needle (Braun Medical Sterican needle 2.1*80mm, B.Braun) connected to a vacuum syringe (Hepafix Luerlock, B.Braun). The adipose tissue biopsy was washed with a sterile physiological saline solution to wash off blood and connective tissue. Adipose tissue biopsies were homogenised in trizol using an ultrathurrax (IKA, Labortechnik, Staufen, Germany). Subsequently, RNA was isolated from trizol according to a standardized protocol as described by the manufacturer (Invitrogen Life Technologies). Next, RNA was purified and treated with DNAse on RNeasy micro columns (Qiagen Benelux B.V., Venlo, the Netherlands), followed by dissolving the RNA in RNAse and DNAse free water (Invitrogen Life Technologies, Breda, the Netherlands). RNA yield was quantified using the NanoDrop 1000 (NanoDrop Technologies, Wilmington, DE, USA). RNA integrity was evaluated using the Agilent 2100 BioAnalyzer (Agilent, Palo Alto, CA, USA) with RNA 6000 nano chips (Agilent Technologies, South Queensferry, UK). Samples with a RIN score > 8.0 were considered to be acceptable for further processing.

treatment_protocol: The study had a randomized, double-blind, placebo-controlled, crossover design. Each subject enrolled in random order in a fish oil, a fenofibrate and a placebo period for 6 weeks with a wash-out period of at least 2 weeks between the intervention periods. . During the fish oil intervention, subjects had to consume 8 fish oil capsules (Marinol C-38, Lipid Nutrition, Wormerveer, the Netherlands), providing approximately 3.7 g/d n-3 LCPUFA (1.7 g/d EPA and 1.2 g/d DHA, corresponding to 160-240 g fatty fish/d), together with 2 capsules placebo-matching fenofibrate (200 mg/d cellulose). During the fenofibrate period, subjects consumed 2 capsules providing 200 mg/d micronized fenofibrate (Lipanthyl®, Fournier Laboratories, Dijon, France), together with 8 placebo-matching fish oil capsules (containing 80% High Oleic Sunflower Oil (HOSO)). During the placebo period, subjects received 8 HOSO capsules together with 2 cellulose capsules. Subjects were instructed to ingest half of the capsules before breakfast and the other half before dinner with a glass of water. Subjects were restricted in their fish consumption to a maximum of one portion a week.

tag: ethnicity

value: Caucasian

value: male

value: 47 years

value: white adipose tissue

tag: agent

value: FIBRATE


title: HWAT_26C_PLACEBO

value: female

value: 48 years

value: PLACEBO


title: HWAT_20A_FIBRATE

value: 63 years


title: HWAT_20C_FISHOIL

value: FISHOIL


title: HWAT_26A_FIBRATE


title: HWAT_26B_FISHOIL


title: HWAT_36C_PLACEBO


title: F_DEC_CRB

source_name: cerebellum

value: December, 2019

value: cerebellum

value: F


title: HWAT_17B_PLACEBO

value: 45 years


title: F_DEC_COR

source_name: cornea

value: cornea


title: HWAT_38C_FISHOIL


title: HWAT_20B_PLACEBO


title: HWAT_38A_PLACEBO


title: HWAT_36A_FIBRATE


title: HWAT_17C_FIBRATE


title: F_DEC_CEC

source_name: cecum

value: cecum


title: F_DEC_DMH

source_name: dorsomedial hypothalamic nucleus

value: dorsomedial hypothalamic nucleus


title: HWAT_36B_FISHOIL

value: Caucasian


title: F_DEC_CAU

source_name: caudate nucleus

value: caudate nucleus


title: F_DEC_CA3

source_name: hippocampus CA3

value: hippocampus CA3


title: F_DEC_COL

source_name: colon

value: colon


title: F_DEC_CA1

source_name: hippocampus CA1

value: hippocampus CA1


title: HWAT_15B_FIBRATE

value: male

value: 41 years

value: white adipose tissue

value: FIBRATE


title: HWAT_13B_FISHOIL

value: 44 years

value: FISHOIL


title: F_DEC_BON

source_name: bone

value: December, 2019

value: bone


title: HWAT_17A_FISHOIL

value: female

value: 45 years


title: HWAT_13A_PLACEBO

value: PLACEBO


title: F_DEC_BOM

source_name: bone marrow

value: bone marrow

value: F


title: HWAT_13C_FIBRATE

value: Caucasian


title: F_DEC_BAT

source_name: brown adipose tissue

value: brown adipose tissue


title: F_DEC_CAT

source_name: cartilage

value: cartilage


title: F_DEC_BNST

source_name: bed nucleus of the stria terminalis

value: bed nucleus of the stria terminalis


title: F_DEC_AXL

source_name: axillary lymph node

value: axillary lymph node


title: F_DEC_AOR

source_name: aorta

value: aorta


title: F_DEC_ARC

source_name: arcuate nucleus

value: arcuate nucleus


title: HWAT_15A_PLACEBO

source_name: white adipose tissue

value: male

value: 41 years

value: white adipose tissue


title: HWAT_15C_FISHOIL

value: FISHOIL


title: F_DEC_ANU

source_name: anus

value: December, 2019

value: anus


title: COLON_8901_COD_6months_after_intervention

description: no history of polyps

source_name: colon biopsy

value: extra cod

value: after six months of intervention

value: subject 8901

value: Female


title: F_DEC_BRO

source_name: bronchus

value: bronchus

value: F


title: F_DEC_BLA

source_name: urinary bladder

value: urinary bladder


title: HWAT_09A_FISHOIL

value: Caucasian

value: 66 years


title: F_DEC_AMYC

source_name: amygdala central nucleus

value: amygdala central nucleus


title: HWAT_04A_FISHOIL

value: female

value: 69 years


title: HWAT_02C_PLACEBO

value: 24 years

value: PLACEBO


title: F_AUG_WAT

value: August, 2020

value: white adipose tissue


title: F_DEC_ADG

source_name: adrenal gland

value: December, 2019

value: adrenal gland


title: HWAT_09C_FIBRATE

value: male

value: FIBRATE


title: HWAT_12B_FISHOIL

value: 60 years

value: FISHOIL


title: F_AUG_VMH

source_name: ventromedial  hypothalamic nucleus

value: ventromedial  hypothalamic nucleus

value: F


title: HWAT_09B_PLACEBO

value: Caucasian


title: HWAT_12A_FIBRATE


title: F_AUG_VTA

source_name: ventral tegmental area

value: ventral tegmental area


title: HWAT_02B_FISHOIL


title: HWAT_04B_PLACEBO


title: F_AUG_VIC

source_name: visual cortex

value: visual cortex


title: F_DEC_AMYL

source_name: amygdala lateral nucleus

value: amygdala lateral nucleus


title: F_AUG_UTE

source_name: uterus

value: uterus


title: HWAT_12C_PLACEBO


title: F_AUG_TON

source_name: tongue

value: tongue


title: F_AUG_THR

source_name: thyroid

value: thyroid


title: F_AUG_THA

source_name: thalamus

value: August, 2020

value: thalamus


title: HPBMC_38B_FIBRATE

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

source_name: PBMC

extract_protocol: After sampling, PBMCs were directly isolated from an EDTA anti-coagulated peripheral fasted blood sample at the end (week 6) of each intervention period, through gradient centrifugation using lymphoprep (Nycomed, Oslo, Norway) according to the instructions from the manufacturer. The PBMCs were immediately lysed and homogenised in 1.5 mL Trizol (Invitrogen Life Technologies, Breda, the Netherlands) for RNA stabilisation, immediately frozen in liquid nitrogen, and stored in sterile polypropylene tubes at -80C until further processing.  Subsequently, RNA was isolated from trizol according to a standardized protocol as described by the manufacturer (Invitrogen Life Technologies). Next, RNA was purified and treated with DNAse on RNeasy micro columns (Qiagen Benelux B.V., Venlo, the Netherlands), followed by dissolving the RNA in RNAse and DNAse free water (Invitrogen Life Technologies, Breda, the Netherlands). RNA yield was quantified using the NanoDrop 1000 (NanoDrop Technologies, Wilmington, DE, USA). RNA integrity was evaluated using the Agilent 2100 BioAnalyzer (Agilent, Palo Alto, CA, USA) with RNA 6000 nano chips (Agilent Technologies, South Queensferry, UK). Samples with a RIN score > 8.0 were considered to be acceptable for further processing.

value: 47 years

value: PBMC


title: HPBMC_26B_FISHOIL

value: female

value: 48 years


title: F_AUG_SPL

source_name: spleen

value: spleen


title: HPBMC_36C_PLACEBO

value: male

value: 63 years

value: PLACEBO


title: F_AUG_SON

source_name: supraoptic nucleus

value: supraoptic nucleus

value: F


title: F_AUG_SKNH

source_name: skin in the hindquarter

value: skin in the hindquarter


title: HPBMC_36A_FIBRATE

value: Caucasian

value: FIBRATE


title: F_AUG_SKNB

source_name: skin on the back

value: skin on the back


title: HPBMC_26C_PLACEBO


title: F_AUG_SG

source_name: salivary gland

value: salivary gland


title: F_AUG_SCN

source_name: suprachiasmatic nucleus

value: August, 2020

value: suprachiasmatic nucleus


title: HPBMC_38A_PLACEBO

value: 47 years


title: F_AUG_STM

source_name: stomach

value: stomach


title: HPBMC_26A_FIBRATE

value: female

value: PBMC


title: F_AUG_RPE

source_name: pigmental epithelial cells

value: pigmental epithelial cells


title: HPBMC_20B_PLACEBO


title: F_AUG_RET

source_name: retina

value: retina


title: HPBMC_36B_FISHOIL

value: male

value: 63 years

value: FISHOIL


title: HPBMC_15B_FIBRATE

value: 41 years


title: F_AUG_REC

source_name: rectum

value: rectum

value: F


title: HPBMC_20A_FIBRATE

value: Caucasian

value: FIBRATE


title: HPBMC_13C_FIBRATE

value: 44 years


title: F_AUG_PVN

source_name: paraventricular nucleus

value: August, 2020

value: paraventricular nucleus


title: HPBMC_20C_FISHOIL


title: HWAT_02A_FIBRATE

source_name: white adipose tissue

value: 24 years

value: white adipose tissue


title: HPBMC_17A_FISHOIL

value: female

value: 45 years


title: HPBMC_15A_PLACEBO

value: PBMC

value: PLACEBO


title: HPBMC_17C_FIBRATE


title: HWAT_04C_FIBRATE

value: 69 years


title: HPBMC_13A_PLACEBO

value: male


title: HPBMC_38C_FISHOIL

value: 47 years

value: FISHOIL


title: HPBMC_17B_PLACEBO


title: HPBMC_13B_FISHOIL


title: HPBMC_12A_FIBRATE

value: 60 years


title: HPBMC_09C_FIBRATE

value: 66 years


title: F_AUG_SN

source_name: substantia nigra

value: substantia nigra

value: F


title: F_AUG_PAN

source_name: pancreas

value: pancreas


title: HPBMC_15C_FISHOIL

value: Caucasian

value: 41 years


title: F_AUG_PT

source_name: pars tuberalis of the pituitary

value: August, 2020

value: pars tuberalis of the pituitary


title: F_AUG_PIN

source_name: pineal gland

value: pineal gland


title: F_AUG_OVA

source_name: ovary

value: ovary


title: F_AUG_PD

source_name: pars distalis of the pituitary

value: pars distalis of the pituitary


title: F_AUG_OES

source_name: oesophagus

value: oesophagus


title: F_AUG_OVI

source_name: oviduct

value: oviduct


title: F_AUG_MUG

source_name: gastrocnemial muscle

value: gastrocnemial muscle


title: HPBMC_12B_FISHOIL

source_name: PBMC

value: male

value: PBMC


title: HPBMC_12C_PLACEBO

value: 60 years

value: PLACEBO


title: F_AUG_PUT

source_name: putamen

value: putamen


title: F_AUG_MUA

source_name: abdominal muscle

value: abdominal muscle

value: F


title: F_AUG_OLB

source_name: olfactory bulb

value: olfactory bulb


title: F_AUG_mPFC

source_name: medial prefrontal cortex

value: medial prefrontal cortex


title: HPBMC_09B_PLACEBO

value: Caucasian

value: 66 years


title: F_AUG_NM

source_name: nasal mucosa

value: August, 2020

value: nasal mucosa


title: HPBMC_09A_FISHOIL

value: FISHOIL


title: HPBMC_02B_FISHOIL

value: female

value: 24 years


title: HPBMC_02A_FIBRATE

value: FIBRATE


title: HPBMC_04B_PLACEBO

value: 69 years


title: HMUSCLE_38B_FIBRATE

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning) (P/N 701028, revision 5).

source_name: muscle

label_protocol: Total RNA (300 ng/sample) was labelled with the 1-cycle cDNA labelling kit (MessageAmp II-Biotin Enhanced Kit, Ambion, Austin, TX, USA; P/N AM1791), as per the manufacturer's instructions.  Total RNA (300 ng/sample) was labelled with the 1-cycle cDNA labelling kit (MessageAmp II-Biotin Enhanced Kit, Ambion, Austin, TX, USA; P/N AM1791), as per the manufacturer's instructions.  Total RNA (300 ng/sample) was labelled with the 1-cycle cDNA labelling kit (MessageAmp II-Biotin Enhanced Kit, Ambion, Austin, TX, USA; P/N AM1791), as per the manufacturer's instructions.

extract_protocol: After local anaesthesia (Lidocaine HCL 1%, B.Braun, Melsungen, Germany), a muscle biopsy from the vastus lateralis was taken by passing a 5-mm diameter side-cutting needle through a 7 mm skin incision according to the technique from Bergstrom et al. Muscle  biopsies were homogenised in trizol using an ultrathurrax (IKA, Labortechnik, Staufen, Germany). Subsequently, RNA was isolated from trizol according to a standardized protocol as described by the manufacturer (Invitrogen Life Technologies). Next, RNA was purified and treated with DNAse on RNeasy micro columns (Qiagen Benelux B.V., Venlo, the Netherlands), followed by dissolving the RNA in RNAse and DNAse free water (Invitrogen Life Technologies, Breda, the Netherlands). RNA yield was quantified using the NanoDrop 1000 (NanoDrop Technologies, Wilmington, DE, USA). RNA integrity was evaluated using the Agilent 2100 BioAnalyzer (Agilent, Palo Alto, CA, USA) with RNA 6000 nano chips (Agilent Technologies, South Queensferry, UK). Samples with a RIN score > 8.0 were considered to be acceptable for further processing.

value: male

value: 47 years

value: muscle


title: HPBMC_02C_PLACEBO

value: PBMC

value: PLACEBO


title: HMUSCLE_38C_FISHOIL


title: HMUSCLE_36C_PLACEBO

value: 63 years


title: HPBMC_04A_FISHOIL


title: HPBMC_04C_FIBRATE


title: F_AUG_NAc

source_name: nucleus accumbens

value: nucleus accumbens

value: F


title: F_AUG_LHA

source_name: lateral hypothalamic nucleus

value: lateral hypothalamic nucleus


title: 544 cells, with shLEF1_3, biological rep-1

city: Tokyo

first: Takehiro

last: Yasukawa

address: 2-1-1 Hongo, Bunkyo-ku

institute: Juntendo University

description: Library name: Sample 7

data_processing:
For each sample, there are two Read1 files (*_Read1.fq.gz and *_Read1_2.fq.gz) and two  Read1 files (*_Read2.fq.gz and *_Read2_2.fq.gz).
The two Read 1 files were assembled into one file and the two Read 2 files into one file, and then the following steps were performed.
Adaptor sequences were removed using TrimGalore (version used must be 0.6.6).
Low-quality reads (Q < 20) were trimmed and resulting reads shorter than 20 bases were removed using FastqPuri (version used must be ver. 1.0).
Reads were aligned against GRCh38.109 human genome using HISAT2 (ver. 2.2.1) by RSEM (version used must be ver. 1.3.1).
Assembly: GRCh38.109
Supplementary files format and content: Tab-delimited text file (1.txt) contains results of raw counts.

source_name: mammary fibroblasts

extract_protocol:
RNA was prepared using NucleoSpin RNA (TaKaRa).
Libraries for RNA-seq were prepared using an MGIEasy RNA Directional Library Prep Set.

tag: cell type

value: mammary fibroblasts


title: 544 cells, with shLEF1_3, biological rep-3

description: Library name: Sample 9


title: F_AUG_mPOA

source_name: medial preoptic area

value: August, 2020

value: medial preoptic area


title: F_AUG_MMB

source_name: mammilary nuclei

value: mammilary nuclei


title: F_AUG_LC

source_name: locus coeruleus

value: locus coeruleus


title: 544 cells, with shLEF1_1, biological rep-3

description: Library name: Sample 6


title: HMUSCLE_26A_FIBRATE

value: Caucasian

value: female

value: 48 years


title: 544 cells, with shLEF1_9, biological rep-3

description: Library name: Sample 12


title: F_AUG_MEL

source_name: mesenteric lymph node

value: mesenteric lymph node


title: HMUSCLE_38A_PLACEBO

value: male

value: 47 years


title: F_AUG_LUN

source_name: lung

value: lung


title: HMUSCLE_36A_FIBRATE

value: muscle

value: FIBRATE


title: 544 cells, with shLEF1_9, biological rep-2

description: Library name: Sample 11


title: HMUSCLE_36B_FISHOIL

value: 63 years

value: FISHOIL


title: 544 cells, with shLEF1_9, biological rep-1

description: Library name: Sample 10


title: HMUSCLE_26C_PLACEBO

value: PLACEBO


title: F_AUG_LIV

source_name: liver

value: liver

value: F


title: 544 cells, with shLEF1_3, biological rep-2

description: Library name: Sample 8

value: mammary fibroblasts


title: HMUSCLE_20A_FIBRATE


title: HMUSCLE_26B_FISHOIL


title: F_AUG_IRI

source_name: iris

value: August, 2020

value: iris


title: 544 cells, with shCtrl, biological rep-2

description: Library name: Sample 2


title: F_AUG_ILE

source_name: ileum

value: ileum


title: F_AUG_KIM

source_name: kidney medulla

value: kidney medulla


title: F_AUG_KIC

source_name: kidney cortex

value: kidney cortex


title: 544 cells, with shCtrl, biological rep-1

description: Library name: Sample 1


title: 544 cells, with shCtrl, biological rep-3

description: Library name: Sample 3


title: F_AUG_JEJ

source_name: jejunum

value: jejunum


title: F_AUG_HAB

source_name: habenula

value: habenula


title: 544 cells, with shLEF1_1, biological rep-2

description: Library name: Sample 5


title: 544 cells, with shLEF1_1, biological rep-1

description: Library name: Sample 4


title: F_AUG_HEA

source_name: heart

value: heart


title: F_AUG_GPe

source_name: globus pallidus external segment

value: globus pallidus external segment


title: HMUSCLE_20B_PLACEBO

source_name: muscle

value: Caucasian

value: female

value: muscle


title: HMUSCLE_20C_FISHOIL

value: 63 years

value: FISHOIL


title: HMUSCLE_17B_PLACEBO

value: 45 years

value: PLACEBO


title: HMUSCLE_17C_FIBRATE

value: FIBRATE


title: F_AUG_GUM

source_name: gum

value: August, 2020

value: gum

value: F


title: HMUSCLE_17A_FISHOIL


title: HMUSCLE_15C_FISHOIL

value: male

value: 41 years


title: HMUSCLE_13C_FIBRATE

value: 44 years


title: HMUSCLE_15B_FIBRATE


title: F_AUG_GPi

source_name: globus pallidus internal segment

value: globus pallidus internal segment


title: HMUSCLE_15A_PLACEBO


title: HMUSCLE_13A_PLACEBO


title: F_AUG_DUO

source_name: duodenum

value: duodenum


title: F_AUG_GAL

source_name: gallbladder

value: gallbladder


title: F_AUG_FOV

source_name: fovea centralis

value: fovea centralis


title: HMUSCLE_13B_FISHOIL

value: Caucasian


title: PBMC-Normal-77N

type: genomic

city: Rochester

first: Tao

last: Ma

address: 200 1st ST SW

institute: Mayo Clinic

description: normal blood sample

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC array using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan System and iScan Control Software

data_processing: Raw signals from the IDAT files were processed to obtain beta values and detection P values utilizing the minfi R package (v1.48.0). Subsequently, the beta values underwent quantile normalization, and batch effects were mitigated utilizing the ComBat function within the SVA R package (v3.50.0).

label: Cy3, Cy5

molecule: genomic DNA

source_name: Peripheral blood mononuclear cells

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated and checked for quality by standard protocols. 1 µg genomic DNA then underwent bisulfite treatment using the TrueMethyl oxBS Module (Tecan Genomics, Männedorf, Switzerland) according to the manufacturer’s specifications. Briefly, DNA was purified using magnetic beads, denatured, and underwent bisulfite conversion followed by desulfonation and purification. The TrueMethyl converted DNA samples were then eluted in 10 µL and then processed through the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA) protocol. In brief, 7 µl of converted DNA was denatured with 1 µL of 0.4N sodium hydroxide prior to whole genome amplification on the MSA4 plate. All other steps were followed as per manufacturer’s guidelines.

value: female


title: pad4 Rep 4

city: Ithaca

first: Zhixue

last: Wang

address: 236 Tower Rd

institute: Cornell University

data_processing:
The files have been generated by the Illumina pipeline software v2.18; The raw reads obtained from the sequencing facility were analyzed
raw reads were aligned to TAIR 10 transcriptome using STAR
Differentially expressed genes were identified in R with edgeR pakage
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file include raw read values for each sample was generated

organism: Arabidopsis thaliana

source_name: two-week-old shoot

growth_protocol: two-week-old plants growing under 22C, 100 µmol m-2 s-1 constant light and 50% humidity.

extract_protocol:
Total RNA was extracted by TRIzol reagent (Invitrogen, 15596026) and purified by RNA clean and concentrator-5 (ZYMO RESEARCH, R1014). Then RNA libraries were prepared for sequencing using standard Illumina protocols.
Total RNA was extracted by TRIzol reagent (Invitrogen, 15596026) and purified by RNA clean and concentrator-5 (ZYMO RESEARCH, R1014). Then RNA libraries were prepared for sequencing using standard Illumina protocols.
3' RNA-seq

value: pad4 mutant

value: two-week-old

value: whole shoot


title: HMUSCLE_12B_FISHOIL

value: 60 years

value: muscle

value: FISHOIL


title: aig2abc pad4 rep3

value: aig2abc pad4 mutant


title: HMUSCLE_12A_FIBRATE

value: FIBRATE


title: HMUSCLE_12C_PLACEBO

value: male

value: PLACEBO


title: aig2abc pad4 rep1


title: aig2abc pad4 rep2


title: PBMC-Normal-74N

description: normal blood sample


title: F_AUG_DRN

source_name: dorsal raphe

value: August, 2020

value: dorsal raphe

value: F


title: pad4 Rep 1


title: HMUSCLE_09C_FIBRATE

value: 66 years


title: F_AUG_DMH

source_name: dorsomedial hypothalamic nucleus

value: dorsomedial hypothalamic nucleus


title: aig2abc rep2

value: aig2abc mutant


title: pad4 Rep 2


title: F_AUG_COR

source_name: cornea

value: cornea


title: PBMC-Normal-73N

description: normal blood sample

value: female


title: aig2abc rep3

value: two-week-old


title: PBMC-Normal-64N

description: normal blood sample


title: PBMC-Normal-76N

description: normal blood sample


title: F_AUG_COL

source_name: colon

value: colon


title: PBMC-Normal-36N

description: normal blood sample


title: PBMC-Normal-60N

description: normal blood sample


title: HMUSCLE_09A_FISHOIL

value: Caucasian


title: PBMC-Normal-72N

description: normal blood sample


title: F_AUG_CRB

source_name: cerebellum

value: cerebellum


title: WT Col-0 Rep 3

value: wild type Col-0

value: whole shoot


title: PBMC-Normal-71N

description: normal blood sample


title: PBMC-Normal-75N

description: normal blood sample


title: aig2abc rep1


title: PBMC-Normal-69N

description: normal blood sample


title: PBMC-Normal-58N

description: normal blood sample


title: WT Col-0 Rep 2


title: HMUSCLE_04C_FIBRATE

value: 69 years

value: muscle

value: FIBRATE


title: Hep3B cells, Lenvatinib-treated, biol rep 3

city: Hamilton

first: Russta

last: Fayyazi

state: ON

address: 1280 Main St W

department: Medicine

country: Canada

institute: McMaster University

description: Library name: Hep3B Lenvatinib 3

data_processing:
Raw sequencing files imported into Galaxy (usegalaxy.org) for quality control and processing steps
FastQC tool used to check read quality
Cutadapt tool used to trim adaptor sequences and low quality reads
Remaining reads were mapped reference genome with HISAT2 tool. Cell data was mapped to the hg38 reference human genome. Mouse data was mapped to the mm10 reference mouse genome.
Counts were quantified with the featureCounts tool and imported into R for gene expression analyses
Counts data were VST-normalized in R using the DESeq2 package
Assembly: hg38, mm10
Supplementary files format and content: tab-delimited text file includes VST-normalized counts for each sample (in vitro cell data)
Supplementary files format and content: tab-delimited text file includes VST-normalized counts for each sample (in vivo mouse data)

source_name: HCC immortalized cells

extract_protocol:
RNA was isolated from cells or liver tissue using TRIzolTM (Life Technologies, Grand Island, USA) and purified using RNeasy kit (QIAGEN, Germantown, USA Cat#74106) according manufacturers instruction.
For both cells and liver tissue, RNA-Sequencing RNA sample quality was first assessed using Agilent 2100 Bioanalyzer G2938C with the Aligent RNA6000 Nano Kit (Agilent; Santa Clara, CA, USA). Next, the NEBNext Poly(A) mRNA Isolation Module (NEB, Ipswich, MA, USA) was used for mRNA enrichment, followed by NEBNext® Ultra™ II Directional RNA library kit (NEB, Ipswich, MA, USA) library preparation. Cell libraries were sequenced on an Illumia HiSeq 1500 machine (HiSeq Rapid v2 flow cell, 50bp reads yielding 400M clusters). Mouse libraries were sequenced on an Illumina NextSeq 2000 machine (P2, 2x50 bp).

value: HCC immortalized cells

tag: cell/mouse line

tag: condition

value: Lenvatinib-mesylate-treated

tag: treatment dose

value: Lenvatinib-mesylate 100nM

tag: age at_sacrifice_(mice)

tag: ccl4 model_diet_(mice)

tag: ccl4 model_dosage_(mice)


title: PBMC-Normal-63N

description: normal blood sample

value: male


title: WT Col-0 Rep 1


title: F_AUG_CAT

source_name: cartilage

value: August, 2020

value: cartilage

value: F


title: Hep3B cells, Salsalate-treated, biol rep 2

description: Library name: Hep3B Salsalate 2

value: Salicylic acid-treated

value: Salicylic acid 1mM


title: Hep3B cells, Salsalate-treated, biol rep 3

description: Library name: Hep3B Salsalate 3


title: PBMC-Normal-55N

description: normal blood sample


title: Hep3B cells, Combination-treated, biol rep 3

description: Library name: Hep3B Combination 3

value: Combination-treated

value: Salicylic acid 1mM + Lenvatinib-mesylate 100nM


title: PBMC-Normal-62N

description: normal blood sample

value: female


title: PBMC-Normal-68N

description: normal blood sample


title: F_AUG_CAU

source_name: caudate nucleus

value: caudate nucleus


title: Hep3B cells, Combination-treated, biol rep 2

description: Library name: Hep3B Combination 2


title: Hep3B cells, Combination-treated, biol rep 1

description: Library name: Hep3B Combination 1


title: HMUSCLE_02C_PLACEBO

value: Caucasian

value: 24 years

value: PLACEBO


title: HMUSCLE_04A_FISHOIL

value: 69 years

value: muscle

value: FISHOIL


title: PBMC-Normal-16N

description: normal blood sample


title: F_AUG_CA3

source_name: hippocampus CA3

value: hippocampus CA3


title: Hep3B cells, Salsalate-treated, biol rep 1

description: Library name: Hep3B Salsalate 1

value: HCC immortalized cells


title: PBMC-Normal-45N

description: normal blood sample

value: male


title: Hep3B cells, Lenvatinib-treated, biol rep 1

description: Library name: Hep3B Lenvatinib 1

value: Lenvatinib-mesylate-treated

value: Lenvatinib-mesylate 100nM


title: PBMC-Normal-46N

description: normal blood sample


title: HMUSCLE_04B_PLACEBO

source_name: muscle


title: F_AUG_CA1

source_name: hippocampus CA1

value: August, 2020

value: hippocampus CA1

value: F


title: PBMC-Normal-70N

description: normal blood sample


title: Hep3B cells, DMSO control, biol rep 2

description: Library name: Hep3B Vehicle 2

value: DMSO control


title: F_AUG_BRO

source_name: bronchus

value: bronchus


title: Hep3B cells, Lenvatinib-treated, biol rep 2

description: Library name: Hep3B Lenvatinib 2


title: F_AUG_BON

source_name: bone

value: bone


title: HMUSCLE_02B_FISHOIL

value: Caucasian

value: female


title: F_AUG_BOM

source_name: bone marrow

value: bone marrow


title: F_AUG_BNST

source_name: bed nucleus of the stria terminalis

value: bed nucleus of the stria terminalis


title: F_AUG_CEC

source_name: cecum

value: cecum


title: Hep3B cells, DMSO control, biol rep 1

description: Library name: Hep3B Vehicle 1


title: F_AUG_BAT

source_name: brown adipose tissue

value: brown adipose tissue


title: F_AUG_BLA

source_name: urinary bladder

value: urinary bladder


title: F_AUG_AXL

source_name: axillary lymph node

value: axillary lymph node


title: Lymph node tissue_Multicentric Lymphoma9

city: Gwangju

first: Ha-Jung

last: Kim

address: 77, Yongbong-ro, Buk-gu

country: South Korea

institute: Chonnam National University

description: Multicentric lymphoma (TNM : 4b, Phenotype : B) lymph node tissue from a 5-year-old spayed female Bichon Frise

hyb_protocol: 1650ng of each labeled cRNA was fragmented by adding 11 μl 10 x blocking agent and 2.2 μl of 25 x fragmentation buffer, and then heated at 60°C for 30 min. Finally 55 μl 2 x GE hybridization buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent Unrestricted AMADID Release GE 4x44K (Canine V2). The slides were incubated for 17 h at 65°C in an Agilent hybridization oven. then washed at room temperature by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010).

scan_protocol: The hybridized array was immediately scanned with an Agilent Microarray Scanner D (Agilent Technologies, Inc.)

data_processing: Microarray results were extracted using Agilent Feature Extraction software v11.0 (Agilent Technologies)

molecule: polyA RNA

organism: Canis lupus familiaris

source_name: lymph node, Multicentric Lymphoma9, 4b, B

label_protocol: RNA labeling and hybridization were performed by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010). Briefly, 100ng of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-2000(NanoDrop, Wilmington, USA).

extract_protocol: Total RNA was isolated using Transzol (TransGen Biotech, Cat#.ET101)-based RNA extraction protocol. Add 1ml Transzol and 3mm Tungsten Carbide Bead (Qiagen, Cat#.69997) into the tissue sample tube. Homogenize the tissue using TissueLyser Ⅱ(Qiagen) at 25Hz for 3min, add 200ul Chloroform. Separate the aqueous phase through centrifuge 13000g for 15min at 4℃. Add equal volume of iso-propanol for precipitation pellet through centrifuge 13000g for 10min at 4℃. And then proceed EtOH purification. Total RNA concentration and purity was measured using ND-2000 Spectrophotometer (NanoDrop, Wilmington, USA). Integrity was assessed using Agilent RNA 6000 Nano Kit on a 2100 Bioanalyzer instrument (Agilent Technologies, Palo Alto, USA). The RNA integrity number (RIN) score and the rRNA ratio were calculated.

tag: breed

value: Bichon Frise

value: Spayed Female

tag: tnm stage

tag: immuno phenotyping

value: B


title: Lymph node tissue_Multicentric Lymphoma6

description: Multicentric lymphoma (TNM : 3b, Phenotype : T) lymph node tissue from a 8-year-old castrated male Maltese

source_name: lymph node, Multicentric Lymphoma6, 3b, T

value: Maltese

tag: gender

value: Castrated Male

tag: age

value: T


title: PVN_N_Uninf_16hpi_C

city: ITHACA

first: Hector

last: Aguilar-Carreno

state: New York

address: T8016A Veterinary Research Tower

department: Microbiology and Immunology

description: Gene expression no infection control for 16h

hyb_protocol: Hybridization was performed using Agilent Microarray Hybridization Chamber at 65°C for 17 hours.

scan_protocol: Scanning was performed using Agilent Scanner G2505C.

data_processing: Background correction was carried out on microarray samples using the maximum likelihood estimation for the normal-exponential convolution model, with an offset of 50, as implemented in Bioconductor's limma package. Samples were then normalized using quantile normalization and outliers were detected using intensity distribution and a boxplot graph followed by hierarchical clustering and PCA analysis of expression profiles using the MVA package.

label_protocol: Cy3 labeling was performed using T7 promoter primer and T7 RNA polymerase.

growth_protocol: HEK293T cells were maintained in complete MDEM media with 10% Fetal Bovine Serum, 1% penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted using Trizol and quantified using the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. mRNAs were converted to cDNAs using AffinityScript reverse transcriptase and oligo-dT promoter primer. The second strand cDNA synthesiswas performed with AffinityScript reverse transcriptase. Cy3 labeled cRNA was synthesized with T7 RNA polymerase mix. cRNAs were purified using RNeasy mini kit. cRNA quantitiy was determined using NanoDrop ND-1000 UV-VIS spectrophotometer and cRNAs were hybridized onto Agilent 4 x 44K human genome microarray slides.

treatment_protocol: For each time-point ten 6-well plates were used, five of them were infected with NiV malaysia strain at moi1 for 4h, 8h, 12h, and 16h time point. Remaining five 6-well plates were used as uninfected controls.

tag: cell line

tag: treatment

value: No infection control

tag: time


title: PVN_N_Uninf_16hpi_E


title: PVN_N_Uninf_16hpi_A


title: Hep3B cells, DMSO control, biol rep 3

description: Library name: Hep3B Vehicle 3

tag: tissue

value: HCC immortalized cells

value: DMSO control


title: Lymph node tissue_Multicentric Lymphoma8

description: Multicentric lymphoma (TNM : 5a, Phenotype : B) lymph node tissue from a 8-year-old female Maltese

source_name: lymph node, Multicentric Lymphoma8, 5a, B

value: Female


title: PVN_N_Uninf_16hpi_B


title: F_AUG_AOR

source_name: aorta

tag: sampling point

value: August, 2020

value: aorta

tag: Sex

value: F


title: Lymph node tissue_Multicentric Lymphoma4

description: Multicentric lymphoma (TNM : 4b, Phenotype : T) lymph node tissue from a 6-year-old male Mixed breed

source_name: lymph node, Multicentric Lymphoma4, 4b, T

value: Mixed

value: Male


title: HMUSCLE_02A_FIBRATE

tag: ethnicity

value: Caucasian

value: female

value: 24 years

value: muscle

tag: agent

value: FIBRATE


title: Lymph node tissue_Multicentric Lymphoma3

description: Multicentric lymphoma (TNM : 4b, Phenotype : B) lymph node tissue from a 9-year-old castrated male Poodle

source_name: lymph node, Multicentric Lymphoma3, 4b, B

value: Poodle

value: B


title: F_AUG_ARC

source_name: arcuate nucleus

value: arcuate nucleus


title: Lymph node tissue_Multicentric Lymphoma1

description: Multicentric lymphoma (TNM : 4b, Phenotype : B) lymph node tissue from a 17-year-old male Maltese

source_name: lymph node, Multicentric Lymphoma1, 4b, B

value: Maltese


title: PVN_N_Uninf_16hpi_D

value: No infection control


title: Lymph node tissue_Multicentric Lymphoma5

description: Multicentric lymphoma (TNM : 4b, Phenotype : T) lymph node tissue from a 7-year-old castrated male Chihuahua

source_name: lymph node, Multicentric Lymphoma5, 4b, T

value: Chihuahua

value: Castrated Male

value: T


title: HMUSCLE_09B_PLACEBO

source_name: muscle

value: male

value: 66 years

value: PLACEBO


title: Lymph node tissue_Multicentric Lymphoma2

description: Multicentric lymphoma (TNM : 4b, Phenotype : T) lymph node tissue from an 14-year-old female Mixed breed

source_name: lymph node, Multicentric Lymphoma2, 4b, T

value: Mixed

value: Female


title: Lymph node tissue_Multicentric Lymphoma10

description: Multicentric lymphoma (TNM : 4a, Phenotype : T) lymph node tissue from a 4-year-old castrated male Poodle

source_name: lymph node, Multicentric Lymphoma10, 4a, T


title: PVN_N_Uninf_12hpi_E

description: Gene expression no infection control for 12h


title: Lymph node tissue_Healthy7

description: Healthy lymph node tissue from a 1.5-year-old female Beagle

source_name: lymph node tissue, Healthy7

value: Beagle


title: F_AUG_ANU

source_name: anus

value: August, 2020

value: anus

value: F


title: Pat 7 Visit 1 SF right Treg

city: Utrecht

first: Aridaman

last: Pandit

address: Heidelberglaan 100

institute: University Medical Center Utrecht

description: TCR-beta sequences

data_processing:
Raw paired-end reads were assembled using Paired-End reAd mergeR (PEAR)
TCR sequencing analysis was performed using RTCR as previously described(Gerritsen et al., 2016).
Genome_build: GRCh38
Supplementary_files_format_and_content: Comma-seperated values (csv) file containing TCRβ sequences and counts after error correction and post-processing using the RTCR pipeline

source_name: Regulatory T cells

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen) for cell fractions ≥0.2 million cells and the RNeasy Micro Kit (Qiagen) for fractions ≤0.2 million cells, following the manufacturer’s instructions.
cDNA was synthesized using the SMARTer RACE cDNA Amplification kit (Clontech). Amplification of the TCRβ VDJ region was performed using previously described primers and amplification protocols(Zhou et al., 2006). PCR product fragment size was analyzed using the QIAxcel Advanced System (Qiagen). End repair and barcode adapter ligation were performed with the NGSgo®-LibrX and NGSgo®-IndX (GenDx) according to the manufacturer’s instructions. Cleanup of the samples was performed after each step using HighPrep PCR beads and following the manufacturer’s instructions (GC Biotech).

value: Synovial fluid right knee

tag: celltype

value: CD3+CD4+CD25highCD127low Treg

tag: subject

value: JIA patient 7

tag: visit

value: Visit 1 february 2016


title: PVN_N_Uninf_12hpi_C

value: No infection control


title: Pat 7 Visit 1 SF right non-Treg

description: TCR-beta sequences

source_name: Non-Regulatory T cells


title: Lymph node tissue_Healthy6

source_name: lymph node tissue, Healthy6


title: Lymph node tissue_Healthy5

source_name: lymph node tissue, Healthy5


title: F_AUG_AMYL

source_name: amygdala lateral nucleus

value: amygdala lateral nucleus


title: Pat 7 Visit 1 SF left non-Treg

description: TCR-beta sequences

value: Synovial fluid left knee


title: Pat 7 Visit 1 PB non-Treg

description: TCR-beta sequences

value: Peripheral blood


title: Pat 7 Visit 1 PB Treg

description: TCR-beta sequences


title: PVN_N_Uninf_12hpi_D


title: Pat 6 Visit 1 SF right non-Treg

description: TCR-beta sequences

value: JIA patient 6


title: Pat 7 Visit 1 SF left Treg

description: TCR-beta sequences


title: Pat 6 Visit 1 SF right Treg

description: TCR-beta sequences


title: F_AUG_AMYC

source_name: amygdala central nucleus

value: amygdala central nucleus


title: F_APR_WAT

source_name: white adipose tissue

value: April, 2020

value: white adipose tissue


title: Lymph node tissue_Healthy3

source_name: lymph node tissue, Healthy3

value: Female


title: Lymph node tissue_Healthy4

source_name: lymph node tissue, Healthy4

value: Beagle


title: PVN_N_Uninf_12hpi_B


title: Lymph node tissue_Healthy1

description: Healthy lymph node tissue from a 1.5-year-old male Beagle

source_name: lymph node tissue, Healthy1

value: Male


title: Lymph node tissue_Multicentric Lymphoma7

description: Multicentric lymphoma (TNM : 5a, Phenotype : T) lymph node tissue from a 11-year-old castrated Maltese

source_name: lymph node, Multicentric Lymphoma7, 5a, T

value: Maltese

value: Castrated Male

value: T


title: F_AUG_ADG

source_name: adrenal gland

value: August, 2020

value: adrenal gland

value: F


title: PVN_N_Uninf_8hpi_B

description: Gene expression no infection control for 8h

value: No infection control


title: PVN_N_Uninf_12hpi_A


title: PVN_N_Uninf_8hpi_E


title: Pat 6 Visit 1 SF left non-Treg

description: TCR-beta sequences

value: Visit 1 february 2016


title: Lymph node tissue_Healthy2

source_name: lymph node tissue, Healthy2


title: PVN_N_Uninf_8hpi_D


title: Pat 6 Visit 1 SF left Treg

description: TCR-beta sequences

value: Synovial fluid left knee

value: CD3+CD4+CD25highCD127low Treg


title: F_APR_VTA

source_name: ventral tegmental area

value: ventral tegmental area


title: F_APR_VMH

source_name: ventromedial  hypothalamic nucleus

value: ventromedial  hypothalamic nucleus


title: Pat 5 Visit 2 PB non-Treg

description: TCR-beta sequences

value: Peripheral blood

value: JIA patient 5

value: Visit 2 december 2015


title: F_APR_VIC

source_name: visual cortex

value: April, 2020

value: visual cortex


title: Pat 6 Visit 1 PB Treg

description: TCR-beta sequences

value: JIA patient 6


title: Pat 5 Visit 2 SF left Treg

description: TCR-beta sequences


title: F_APR_UTE

source_name: uterus

value: uterus


title: Pat 5 Visit 1 SF left Treg

description: TCR-beta sequences

source_name: Regulatory T cells

value: Visit 1 june 2015


title: F_APR_TON

source_name: tongue

value: tongue


title: Pat 5 Visit 2 PB Treg

description: TCR-beta sequences


title: Pat 5 Visit 1 SF left non-Treg

description: TCR-beta sequences

source_name: Non-Regulatory T cells


title: PVN_N_Uninf_8hpi_C


title: Pat 6 Visit 1 PB non-Treg

description: TCR-beta sequences


title: PVN_N_Uninf_4hpi_E

description: Gene expression no infection control for 4h


title: PVN_N_Uninf_4hpi_C


title: PVN_N_Uninf_8hpi_A


title: F_APR_THR

source_name: thyroid

value: thyroid


title: F_APR_THA

source_name: thalamus

value: thalamus

value: F


title: Pat 4 Visit 2 SF left Treg

description: TCR-beta sequences

value: JIA patient 4

value: Visit 2 october 2015


title: Pat 5 Visit 1 SF right non-Treg

description: TCR-beta sequences

value: Synovial fluid right knee


title: Pat 4 Visit 2 SF left non-Treg

description: TCR-beta sequences

value: Synovial fluid left knee


title: Pat 4 Visit 1 SF left Treg

description: TCR-beta sequences

value: CD3+CD4+CD25highCD127low Treg

value: Visit 1 april 2015


title: Pat 5 Visit 2 SF left non-Treg

description: TCR-beta sequences

value: JIA patient 5


title: Pat 4 Visit 1 SF left non-Treg

description: TCR-beta sequences


title: F_APR_SPL

source_name: spleen

value: spleen


title: Pat 3 Visit 3 SF right non-Treg

description: TCR-beta sequences

value: JIA patient 3

value: Visit 3 january 2016


title: Pat 3 Visit 3 SF right Treg

description: TCR-beta sequences


title: Pat 3 Visit 2 SF right Treg

description: TCR-beta sequences

value: Visit 2 july 2015


title: Pat 5 Visit 1 SF right Treg

description: TCR-beta sequences


title: PVN_N_Uninf_4hpi_D

value: No infection control


title: Pat 3 Visit 1 SF right non-Treg

description: TCR-beta sequences

value: Visit 1 june 2014


title: F_APR_SON

source_name: supraoptic nucleus

value: April, 2020

value: supraoptic nucleus


title: Pat 3 Visit 1 SF right Treg

description: TCR-beta sequences


title: PVN_N_Uninf_4hpi_B


title: Pat 3 Visit 2 SF right non-Treg

description: TCR-beta sequences


title: Pat 2 Visit 2 SF left non-Treg

description: TCR-beta sequences

value: JIA patient 2

value: Visit 2 february 2015


title: F_APR_SN

source_name: substantia nigra

value: substantia nigra

value: F


title: PVN_N_Moi1_16hpi_B

description: Gene expression for moi 1 after 16h

value: infected with NiV Malaysia strain


title: PVN_N_Moi1_16hpi_E

description: Gene expression for moi 1 after 16h


title: Pat 2 Visit 1 SF left non-Treg

description: TCR-beta sequences

value: Synovial fluid left knee

value: Visit 1 may 2014


title: F_APR_SKNB

source_name: skin on the back

value: skin on the back


title: Pat 2 Visit 2 SF left Treg

description: TCR-beta sequences

value: CD3+CD4+CD25highCD127low Treg


title: PVN_N_Moi1_16hpi_C

description: Gene expression for moi 1 after 16h


title: Pat 2 Visit 1 SF left Treg

description: TCR-beta sequences


title: F_APR_STM

source_name: stomach

value: stomach


title: F_APR_SKNH

source_name: skin in the hindquarter

value: skin in the hindquarter


title: Pat 2 Visit 1 PB non-Treg

description: TCR-beta sequences

value: Peripheral blood


title: Pat 2 Visit 1 PB Treg

description: TCR-beta sequences


title: PVN_N_Uninf_4hpi_A


title: PVN_N_Moi1_16hpi_D

description: Gene expression for moi 1 after 16h


title: F_APR_SG

source_name: salivary gland

value: salivary gland


title: Pat 1 Visit 4 SF right Treg

description: TCR-beta sequences

value: JIA patient 1

value: Visit 4 august 2015


title: PVN_N_Moi1_12hpi_E

description: Gene expression for moi 1 after 12h


title: F_APR_RPE

source_name: pigmental epithelial cells

value: April, 2020

value: pigmental epithelial cells


title: F_APR_SCN

source_name: suprachiasmatic nucleus

value: suprachiasmatic nucleus


title: PVN_N_Moi1_12hpi_D

description: Gene expression for moi 1 after 12h


title: PVN_N_Moi1_16hpi_A

description: Gene expression for moi 1 after 16h


title: Pat 1 Visit 2 SF right non-Treg

description: TCR-beta sequences

value: Synovial fluid right knee

value: Visit 2 january 2015


title: Pat 1 Visit 2 SF right Treg

description: TCR-beta sequences


title: Pat 1 Visit 2 PB non-Treg

description: TCR-beta sequences


title: F_APR_RET

source_name: retina

value: retina

value: F


title: F_APR_PVN

source_name: paraventricular nucleus

value: paraventricular nucleus


title: PVN_N_Moi1_12hpi_C

description: Gene expression for moi 1 after 12h

value: infected with NiV Malaysia strain


title: Pat 1 Visit 1 SF right non-Treg

description: TCR-beta sequences

value: Visit 1 july 2014


title: F_APR_REC

source_name: rectum

value: rectum


title: Pat 1 Visit 1 PB non-Treg

description: TCR-beta sequences


title: PVN_N_Moi1_12hpi_B

description: Gene expression for moi 1 after 12h


title: Pat 1 Visit 4 SF right non-Treg

description: TCR-beta sequences

value: Synovial fluid left knee


title: Pat 1 Visit 2 PB Treg

description: TCR-beta sequences

source_name: Regulatory T cells

value: CD3+CD4+CD25highCD127low Treg


title: F_APR_PUT

source_name: putamen

value: putamen


title: ADAR,hPGCLC,day4,rep2

city: Haining

first: zhaoyu

last: Gu

state: Zhejiang

address: 718 East Haizhou Road

department: ZJE

country: China

institute: Zhejiang University

description: Library name: CGS622

data_processing:
Step 1: Data preprocessing using Cutadapt. - Software: Cutadapt - Version: 4.1 - Parameters: -j 20 -u 20 -U 20
Step 2: Quality control and trimming using Trim Galore. - Software: Trim Galore - Version: 0.6.7 - Parameters: -q 25 --phred33 -e 0.1 --stringency 4 --gzip --trim-n
Step 3: Read alignment using STAR. - Software: STAR - Version: 2.7.10a - Parameters: --runThreadN 15 --runMode alignReads --readFilesCommand zcat --twopassMode Basic --outSAMtype BAM SortedByCoordinate --genomeDir /home/data/genome/STAR_RNA_UCSCfa_GENCODEgtf_hg38_index --readFilesIn ${i}/02_trimmed/${i}_1_cut_val_1.fq.gz ${i}/02_trimmed/${i}_2_cut_val_2.fq.gz --outFileNamePrefix ${i}/03_mapped/
Step 4: Sorting using Samtools. - Software: Samtools - Version: 1.6 - Parameters: sort -@ 20
Step 5: Counting using FeatureCounts. - Software: FeatureCounts - Version: 2.0.1 - Parameters: -T 10 -a /home/data/genome/GENCODE/gencode_v41_gtf/gencode.v41.annotation.gtf -p -C -t exon -g gene_name
Assembly: hg38
Supplementary files format and content: The "Geneid" column contains the gene identifiers, while the "Chr", "Start", "End", "Strand", and "Length" columns provide genomic information about each gene.  The remaining columns contain the read counts for each sample, indicating the number of reads mapped to each gene in the specified sample.

growth_protocol: The H1 hESCs (46, XY) were cultured in the Nuwacell® ncTarget hPSC medium (Nuwacell, RP01020) supplemented with 50ng/ml Primocin (InvivoGen, ant-pm-2) on Matrigel (Corning, 354234)-coated plates. The cells were maintained at 37℃ with 5% CO2. The medium was changed every other day. The cells were passaged with Dispase (STEMCELL, 07923) when they were approximately 80% confluent. For the induction of iMeLC and hPGCLCs, hESCs were cultured on irradiated mouse embryonic fibroblasts (MEFs) in basic DMEM/F-12 (1:1) medium (GIBCO, C11330500BT) supplemented with 20% KnockOut Serum (GIBCO, 10828028), 1% non-essential amino acids (GIBCO, 11140-050), 0.1 nM β-mercaptoethanol (GIBCO, 21985023), 1× Penicillin-Streptomycin-Glutamine (Invitrogen, 10378016) and 10 ng/ml FGF2 (Peprotech, 100-18B). The cells were maintained at 37℃ with 5% CO2. The medium was changed every other day. The cells were passaged with Dispase (STEMCELL, 07923) when they were approximately 80% confluent.

extract_protocol:
The cells were pelleted down and snap frozen until use. RNA samples were extracted with RNeasy kit following manufacturer's protocol.
For hPGCLCs, to enrich mRNA from extracted total RNA, VAHTS mRNA Capture Beads (Vazyme, N401) was applied. After enrichment, VAHTS universal V8 RNA-seq library Prep Kit for Illumina (Vazyme, NR605) was utilized to prepare libraries for sequencing, which briefly contains fragmentation, cDNA synthesis, adapter ligation, PCR amplification and purification. For hESCs and three different germ lyers,after the RNA sample passes the test, magnetic beads with Oligo(dT) are used to enrich eukaryotic mRNA. Then fragmentation buffer is added to break the mRNA into short fragments. Using the mRNA as a template, six-base random primers (random hexamers) are used to synthesize one-strand cDNA. Then buffer, dNTPs, and DNA polymerase I and RNase H are added to synthesize two-strand cDNA. Double-stranded cDNA was then purified using AMPure XP beads. The purified double-stranded cDNA is first subjected to end repair, A-tailing and ligation of sequencing adapters, and then AMPure XP beads are used for fragment size selection. Finally, PCR amplification was performed, and the PCR product was purified with AMPure XP beads to obtain the final sequencing library.

tag: cell type

value: hESCs

tag: genotype

value: ADAR


title: Pat 1 Visit 3 SF right non-Treg

description: TCR-beta sequences

source_name: Non-Regulatory T cells

value: JIA patient 1

value: Visit 3 june 2015


title: PVN_N_Moi1_8hpi_E

description: Gene expression for moi 1 after 8h


title: F_APR_PT

source_name: pars tuberalis of the pituitary

value: April, 2020

value: pars tuberalis of the pituitary


title: Pat 1 Visit 3 SF right Treg

description: TCR-beta sequences

value: Synovial fluid right knee


title: PVN_N_Moi1_8hpi_B

description: Gene expression for moi 1 after 8h


title: ADAR,hPGCLC,day4,rep1

description: Library name: CGS621

treatment_protocol: For the induction of iMeLC and hPGCLCs, hESCs were cultured on irradiated mouse embryonic fibroblasts (MEFs) in basic DMEM/F-12 (1:1) medium (GIBCO, C11330500BT) supplemented with 20% KnockOut Serum (GIBCO, 10828028), 1% non-essential amino acids (GIBCO, 11140-050), 0.1 nM β-mercaptoethanol (GIBCO, 21985023), 1× Penicillin-Streptomycin-Glutamine (Invitrogen, 10378016) and 10 ng/ml FGF2 (Peprotech, 100-18B). The cells were maintained at 37℃ with 5% CO2. The medium was changed every other day. The cells were passaged with Dispase (STEMCELL, 07923) when they were approximately 80% confluent.


title: rAPOBEC1,hESC,rep2

description: Library name: CGS614


title: Pat 1 Visit 1 PB Treg

description: TCR-beta sequences

value: Peripheral blood


title: rAPOBEC1,hESC,rep1

description: Library name: CGS613


title: ADAR,hESC,rep2

description: Library name: CGS612


title: PVN_N_Moi1_8hpi_A

description: Gene expression for moi 1 after 8h


title: Pat 1 Visit 1 SF right Treg

description: TCR-beta sequences


title: F_APR_PD

source_name: pars distalis of the pituitary

value: pars distalis of the pituitary


title: Lateral Cartilage 8

city: shenyang

first: juntan

last: Li

address: huaxiang street

institute: Shengjing hospital of China Medical University

description: Library name: LC8

data_processing:
• Quality Control: Raw FASTQ files were evaluated using FastQC.  • Trimming: Low-quality reads and adapter sequences were trimmed using Trimmomatic.  • Alignment: Reads were aligned to the reference genome using HISAT2.  • Quantification: Gene expression was quantified using featureCounts or StringTie.
Assembly: • Reference Genome: Homo sapiens (GRCh38/hg38).  • Annotation File: GENCODE v38 or Ensembl annotation.
Supplementary files format and content: Gene expression counts: TXT  files with sample-specific gene counts.
Supplementary files format and content: gene_count

source_name: Cartilage

extract_protocol:
RNA sequencing： Total RNA was extracted from human knee cartilage or primary-culture chondrocytes using TRIzol reagent, with RNA quality and quantity assessed using the RNA Nano 6000 Assay Kit and the Bioanalyzer 2100 system. mRNA was isolated from total RNA using poly-T oligo-attached magnetic beads and fragmented with divalent cations in an elevated temperature. cDNA synthesis involved using random hexamer primers and M-MuLV Reverse Transcriptase, followed by RNA degradation with RNaseH and second-strand cDNA synthesis using DNA Polymerase I and dNTP. Blunt ends were formed from overhangs, and adaptors with hairpin loop structures were attached. The library fragments, sized 370~420 bp, were purified using the AMPure XP system, PCR-amplified, and purified again. Library quality was verified using Qubit2.0 Fluorometer and Agilent 2100 bioanalyzer, ensuring an effective concentration above 2nM. Qualified libraries were pooled and sequenced on the Illumina NovaSeq 6000, producing 150bp paired-end reads. Sequencing involved fluorescence-labeled dNTPs and real-time synthesis and detection. Image data were converted into sequence data (reads) using CASAVA. Raw data were processed to remove adapters and low-quality reads, generating clean data for downstream analysis. The reference genome was indexed using Hisat2, and clean reads were aligned to the reference genome using the same tool, benefiting from its ability to generate a splice junction database from the gene model annotation file for enhanced mapping results.
• Library Preparation Kit: Illumina TruSeq RNA Sample Preparation Kit was used.  • Steps:  • mRNA was isolated using poly-A selection.  • Fragmentation was performed using divalent cations.  • First- and second-strand cDNA synthesis was conducted using random primers.  • cDNA was end-repaired, A-tailed, and ligated with indexed adapters.  • PCR amplification was conducted for library enrichment.  • Quality Control: Libraries were quantified using a Qubit Fluorometer and validated on an Agilent Bioanalyzer.

value: Cartilage


title: Lateral Cartilage 7

description: Library name: LC7


title: Lateral Cartilage 6

description: Library name: LC6


title: PVN_N_Moi1_8hpi_C

description: Gene expression for moi 1 after 8h


title: Lateral Cartilage 5

description: Library name: LC5


title: F_APR_OVI

source_name: oviduct

value: oviduct

value: F


title: PVN_N_Moi1_4hpi_E

description: Gene expression for moi 1 after 4h

value: infected with NiV Malaysia strain


title: F_APR_PAN

source_name: pancreas

value: pancreas


title: Lateral Cartilage 4

description: Library name: LC4


title: Lateral Cartilage 3

description: Library name: LC3


title: PVN_N_Moi1_4hpi_C

description: Gene expression for moi 1 after 4h


title: F_APR_OVA

source_name: ovary

value: ovary


title: Medical Cartilage 8

description: Library name: MC8


title: PVN_N_Moi1_4hpi_B

description: Gene expression for moi 1 after 4h


title: Medical Cartilage 7

description: Library name: MC7


title: Lateral Cartilage 1

description: Library name: LC1


title: PVN_N_Moi1_4hpi_A

description: Gene expression for moi 1 after 4h


title: ADAR,hESC,rep1

description: Library name: CGS611


title: F_APR_OES

source_name: oesophagus

value: oesophagus


title: Medical Cartilage 6

description: Library name: MC6


title: Medical Cartilage 5

description: Library name: MC5


title: F_APR_PIN

source_name: pineal gland

value: pineal gland


title: F_APR_NM

source_name: nasal mucosa

value: nasal mucosa


title: PVN_K_MFG_44hr_29

description:
MFG_transfection_rep4
MFG transfection gene expression rep4

treatment_protocol: For each time-point ten 6-well plates were used, five of them were transfected with NiV genes F, G, M and combinations for 44h. Remaining five 6-well plates were used as uninfected controls.

value: MFG transfection


title: Medical Cartilage 4

description: Library name: MC4


title: PVN_K_MFG_44hr_30

description:
MFG_transfection_rep5
MFG transfection gene expression rep5


title: PVN_N_Moi1_4hpi_D

description: Gene expression for moi 1 after 4h


title: F_APR_NAc

source_name: nucleus accumbens

value: nucleus accumbens


title: Medical Cartilage 3

description: Library name: MC3


title: Medical Cartilage 2

description: Library name: MC2


title: Lateral Cartilage 2

description: Library name: LC2


title: F_APR_MUG

source_name: gastrocnemial muscle

value: gastrocnemial muscle


title: Medical Cartilage 1

description: Library name: MC1


title: PVN_N_Moi1_12hpi_A

description: Gene expression for moi 1 after 12h


title: si-TL1A2

description: Library name: si-TL1A2

data_processing:
• Quality Control: Raw FASTQ files were evaluated using FastQC.  • Trimming: Low-quality reads and adapter sequences were trimmed using Trimmomatic.  • Alignment: Reads were aligned to the reference genome using HISAT2.  • Quantification: Gene expression was quantified using featureCounts or StringTie.
Assembly: • Reference Genome: Homo sapiens (GRCh38/hg38).  • Annotation File: GENCODE v38 or Ensembl annotation.
Supplementary files format and content: Gene expression counts: csv  files with sample-specific gene counts.
Supplementary files format and content: count_matrix.csv

source_name: cartilage

value: cartilage


title: si-TL1A3

description: Library name: si-TL1A3


title: PVN_K_MFG_44hr_27

description:
MFG_transfection_rep2
MFG transfection gene expression rep2


title: PVN_K_MFG_44hr_26

description:
MFG_transfection_rep1
MFG transfection gene expression rep1


title: si-TL1A1

description: Library name: si-TL1A1


title: PVN_K_MFG_44hr_28

description:
MFG_transfection_rep3
MFG transfection gene expression rep3


title: PVN_N_Moi1_8hpi_D

description: Gene expression for moi 1 after 8h


title: F_APR_MUA

source_name: abdominal muscle

value: April, 2020

value: abdominal muscle


title: F_APR_mPOA

source_name: medial preoptic area

value: medial preoptic area


title: NC3

description: Library name: NC3


title: F_APR_OLB

source_name: olfactory bulb

value: olfactory bulb


title: NC2

description: Library name: NC2


title: NC1

description: Library name: NC1


title: MCPH1_ICRF193_R3

city: Darmstadt

first: Maria

middle: C

last: Arroyo Lopez

state: Hessen

address: Schnittspahnstr.

department: Biology

country: Germany

institute: Technical University of Darmstadt

description:
Library name: ABA30590
hTERT RPE-1 MCPH1 KO cells, +ICRF193, replicate 3

data_processing:
The libraries were sequenced on NovaSeq 6000 (Illumina) with a read length of 2x51bp, following the manufacturer’s protocol for dual indexing.
Image analysis, base calling, and quality scoring of the run were processed using the manufacturer’s software Real-Time Analysis (RTA 3.4.4).
RNA-seq reads were mapped against the Homo sapiens reference genome (GRCh38) with STAR/2.7.8a using ENCODE parameters.
Genes were quantified with RSEM/1.3.0 with default parameters and using the human gencode.v42 annotation.
Differential expression analysis was performed with the R package limma using Voom function. Functional enrichment analysis of the differentially expressed genes was performed with g:Profiler. IGV (v2.8.12) was used to visualize bam files of interest
Assembly: Homo sapiens reference genome (GRCh38)
Supplementary files format and content: xlsx file  file includes raw counts for each Sample
Supplementary files format and content: xlsx file include normalized counts, FPKM values for each Sample

source_name: Eye; Pigmented epithelium; Retina

growth_protocol: hTERT RPE-1 cells were cultured in Dubelccos Modified Eagles Medium (DMEM) F-12 (Invitrogen) supplemented with 1x penicillin/streptomycin and 10% Fetal Bovine Serum (FBS) at 37 ºC and 5% of CO2. As an MCPH1 mutated model, we made use of gene-edited cell clones obtained in the laboratory of Felipe Cortés-Ledesma (CNIO, Spain). Of note, our RPE1 cell model is p53 mutant (c.332delT p.L111Rfs*122), since it was not possible to obtain viable RPE1 cells with CrisprCas-mutated MCPH1 under p53 WT background.

extract_protocol:
Total RNA was extracted using the RNAeasy kit (Qiagen, Germantown, USA, Cat.No.: 74104) following the manufacturer’s instructions. RNA samples were quantified by Qubit RNA BR Assay kit (Thermo Fisher Scientific) and the RNA integrity was estimated with Agilent RNA 6000 Nano Bioanalyzer 2100 Assay (Agilent).
RNA-Seq libraries were prepared with KAPA Stranded mRNA-Seq Illumina Platforms Kit (Roche) following the manufacturer's recommendations. Briefly, 500 ng of total RNA underwent poly-A enrichment, fragmentation, and second-strand synthesis with dUTP. The resulting cDNA was adenylated, ligated with adaptors (Integrated DNA Technologies), and enriched with 15 PCR cycles.

treatment_protocol: Before drug treatments, cells were seeded into fresh medium in 100 mm plates at 70% confluence one day before starting with drug incubations. Cells were treated with ICRF-193 (10 uM, SIGMA) for 12 hours. Untreated cells were incubated with a similar volume of the solvent DMSO.

value: Eye; Pigmented epithelium; Retina

value: hTERT RPE-1 MCPH1 KO

value: immortalized retinal pigment epithelial cells

value: MCPH1 knockout

value: ICRF193 (TOP2A inhibition)


title: F_APR_mPFC

source_name: medial prefrontal cortex

value: medial prefrontal cortex

value: F


title: MCPH1_ICRF193_R1

description:
Library name: ABA30587
hTERT RPE-1 MCPH1 KO cells, +ICRF193, replicate 1


title: MCPH1_ICRF193_R2

description:
Library name: ABA30588
hTERT RPE-1 MCPH1 KO cells, +ICRF193, replicate 2


title: PVN_K_MG_44hr_25

description:
MG_transfection_rep5
MG transfection gene expression rep5

value: MG transfection


title: MCPH1_NT_R3

description:
Library name: ABA30586
hTERT RPE-1 MCPH1 KO cells, untreated, replicate 3

value: NT (untreated)


title: MCPH1_NT_R2

description:
Library name: ABA30585
hTERT RPE-1 MCPH1 KO cells, untreated, replicate 2


title: PVN_K_MG_44hr_23

description:
MG_transfection_rep3
MG transfection gene expression rep3


title: F_APR_MEL

source_name: mesenteric lymph node

value: mesenteric lymph node


title: F_APR_LUN

source_name: lung

value: lung


title: WT_ICRF193_R3

description:
Library name: ABA30583
hTERT RPE-1 WT cells, +ICRF193, replicate 3

value: hTERT RPE-1 WT

value: wild-type


title: WT_ICRF193_R2

description:
Library name: ABA30582
hTERT RPE-1 WT cells, +ICRF193, replicate 2


title: PVN_K_MG_44hr_22

description:
MG_transfection_rep2
MG transfection gene expression rep2


title: F_APR_LIV

source_name: liver

value: April, 2020

value: liver


title: PVN_K_MF_44hr_20

description:
MF_transfection_rep5
MF transfection gene expression rep5

value: MF transfection


title: WT_ICRF193_R1

description:
Library name: ABA30581
hTERT RPE-1 WT cells, +ICRF193, replicate 1


title: PVN_K_MG_44hr_21

description:
MG_transfection_rep1
MG transfection gene expression rep1


title: F_APR_LHA

source_name: lateral hypothalamic nucleus

value: lateral hypothalamic nucleus


title: WT_NT_R3

description:
Library name: ABA30580
hTERT RPE-1 WT cells, untreated, replicate 3

value: Eye; Pigmented epithelium; Retina


title: F_APR_LC

source_name: locus coeruleus

value: locus coeruleus


title: WT_NT_R1

description:
Library name: ABA30578
hTERT RPE-1 WT cells, untreated, replicate 1

value: immortalized retinal pigment epithelial cells


title: MUTZ3 - RNAseq - SHcontrol378 - 96HRS - REP3

city: Rotterdam

first: Ruud

last: Delwel

address: Dr. Molewaterplein 40

institute: Erasmus MC

description: Library name: MUTZ3_SHcontrol378_96HRS_REP3

data_processing:
Base calling was conducted with bcl2fastq v1.8.4 with the settings --no-eamss --mismatches 1
Transcript abundance was quantified using Salmon v0.3.1 for pseudoalignment against RefSeq gene transcripts of the hg38 human reference build
Assembly: hg38
Supplementary files format and content: quant.sf contain transcript abundance and transcripts per million (TPM) quantified by Salmon

source_name: Bone marrow

growth_protocol: MUTZ3 cells were cultured in Alpha mem medium supplemented with 20% supernatant of urinary bladder carcinoma cell line 5637, and 20% FCS. Medium used was supplemented with 50U/ml penicillin and 50 U/ml streptomycin.

extract_protocol:
Total RNA was isolated by phenol chloroform extraction followed by DNase digestion. The SuperScript II Reverse Transcriptase kit (Invitrogen) was used for synthesis of cDNA.
The cDNA was sheared with the Covaris device and further processed according to the TruSeq RNA Sample Preparation v2 Guide (Illumina)

treatment_protocol: MUTZ3 cells received one of the following treatments in order to interfere with MECOM function: 1) we targeted the MECOM RNA for degradation with short hairpin RNA (shRNA); 2) we prevented interaction of MECOM with its partner CTBP using a PLDLS peptide.

value: Bone marrow

value: acute myelomonocytic leukemia

value: shControl

tag: timepoint


title: F_APR_MMB

source_name: mammilary nuclei

value: mammilary nuclei

value: F


title: WT_NT_R2

description:
Library name: ABA30579
hTERT RPE-1 WT cells, untreated, replicate 2

value: NT (untreated)


title: MUTZ3 - RNAseq - SHcontrol378 - 96HRS - REP2

description: Library name: MUTZ3_SHcontrol378_96HRS_REP2


title: F_APR_KIM

source_name: kidney medulla

value: kidney medulla


title: PVN_K_MG_44hr_24

description:
MG_transfection_rep4
MG transfection gene expression rep4

value: MG transfection


title: MUTZ3 - RNAseq - SHcontrol378 - 96HRS - REP1

description: Library name: MUTZ3_SHcontrol378_96HRS_REP1


title: MUTZ3 - RNAseq - SHcontrol378 - 72HRS - REP3

description: Library name: MUTZ3_SHcontrol378_72HRS_REP3


title: F_APR_KIC

source_name: kidney cortex

value: kidney cortex


title: MCPH1_NT_R1

description:
Library name: ABA30584
hTERT RPE-1 MCPH1 KO cells, untreated, replicate 1

value: hTERT RPE-1 MCPH1 KO

value: MCPH1 knockout


title: MUTZ3 - RNAseq - SHcontrol378 - 72HRS - REP1

description: Library name: MUTZ3_SHcontrol378_72HRS_REP1


title: PVN_K_MF_44hr_19

description:
MF_transfection_rep4
MF transfection gene expression rep4


title: PVN_K_MF_44hr_18

description:
MF_transfection_rep3
MF transfection gene expression rep3


title: PVN_K_MF_44hr_16

description:
MF_transfection_rep1
MF transfection gene expression rep1


title: F_APR_JEJ

source_name: jejunum

value: April, 2020

value: jejunum


title: PVN_K_MF_44hr_17

description:
MF_transfection_rep2
MF transfection gene expression rep2

value: MF transfection


title: PVN_K_F_44hr_15

description:
F_transfection_rep5
F transfection gene expression rep5

value: F transfection


title: MUTZ3 - RNAseq - SHcontrol378 - 48HRS - REP3

description: Library name: MUTZ3_SHcontrol378_48HRS_REP3


title: MUTZ3 - RNAseq - SHcontrol378 - 48HRS - REP2

description: Library name: MUTZ3_SHcontrol378_48HRS_REP2


title: MUTZ3 - RNAseq - SHcontrol378 - 48HRS - REP1

description: Library name: MUTZ3_SHcontrol378_48HRS_REP1


title: MUTZ3 - RNAseq - SHcontrol378 - 24HRS - REP3

description: Library name: MUTZ3_SHcontrol378_24HRS_REP3


title: F_APR_IRI

source_name: iris

value: iris


title: MUTZ3 - RNAseq - SHcontrol378 - 24HRS - REP2

description: Library name: MUTZ3_SHcontrol378_24HRS_REP2


title: PVN_K_F_44hr_14

description:
F_transfection_rep4
F transfection gene expression rep4


title: MUTZ3 - RNAseq - SHcontrol378 - 24HRS - REP1

description: Library name: MUTZ3_SHcontrol378_24HRS_REP1


title: F_APR_HEA

source_name: heart

value: heart


title: MUTZ3 - RNAseq - SHcontrol378 - 120HRS - REP2

description: Library name: MUTZ3_SHcontrol378_120HRS_REP2

value: Bone marrow


title: PVN_K_F_44hr_13

description:
F_transfection_rep3
F transfection gene expression rep3


title: F_APR_HAB

source_name: habenula

value: habenula


title: MUTZ3 - RNAseq - SHcontrol378 - 120HRS - REP3

description: Library name: MUTZ3_SHcontrol378_120HRS_REP3

value: acute myelomonocytic leukemia

value: shControl


title: PVN_K_F_44hr_12

description:
F_transfection_rep2
F transfection gene expression rep2


title: MUTZ3 - RNAseq - SHcontrol378 - 120HRS - REP1

description: Library name: MUTZ3_SHcontrol378_120HRS_REP1


title: MUTZ3 - RNAseq - SHcontrol378 - 72HRS - REP2

description: Library name: MUTZ3_SHcontrol378_72HRS_REP2


title: MUTZ3 - RNAseq - SH1150 - 96HRS - REP3

description: Library name: MUTZ3_SH1150_96HRS_REP3


title: MUTZ3 - RNAseq - SH1150 - 96HRS - REP2

description: Library name: MUTZ3_SH1150_96HRS_REP2


title: F_APR_GUM

source_name: gum

value: gum

value: F


title: F_APR_GPi

source_name: globus pallidus internal segment

value: globus pallidus internal segment


title: MUTZ3 - RNAseq - SH1150 - 96HRS - REP1

description: Library name: MUTZ3_SH1150_96HRS_REP1


title: PVN_K_F_44hr_11

description:
F_transfection_rep1
F transfection gene expression rep1


title: MUTZ3 - RNAseq - SH1150 - 72HRS - REP1

description: Library name: MUTZ3_SH1150_72HRS_REP1


title: F_APR_GPe

source_name: globus pallidus external segment

value: globus pallidus external segment


title: PVN_K_M_44hr_10

description:
M_transfection_rep5
M transfection gene expression rep5

value: M transfection


title: MUTZ3 - RNAseq - SH1150 - 72HRS - REP2

description: Library name: MUTZ3_SH1150_72HRS_REP2


title: MUTZ3 - RNAseq - SH1150 - 48HRS - REP3

description: Library name: MUTZ3_SH1150_48HRS_REP3


title: F_APR_ILE

source_name: ileum

value: ileum


title: MUTZ3 - RNAseq - SH1150 - 48HRS - REP2

description: Library name: MUTZ3_SH1150_48HRS_REP2


title: MUTZ3 - RNAseq - SH1150 - 48HRS - REP1

description: Library name: MUTZ3_SH1150_48HRS_REP1


title: F_APR_GAL

source_name: gallbladder

value: gallbladder


title: MUTZ3 - RNAseq - SH1150 - 24HRS - REP1

description: Library name: MUTZ3_SH1150_24HRS_REP1


title: PVN_K_M_44hr_8

description:
M_transfection_rep3
M transfection gene expression rep3


title: MUTZ3 - RNAseq - SH1150 - 24HRS - REP2

description: Library name: MUTZ3_SH1150_24HRS_REP2


title: PVN_K_M_44hr_9

description:
M_transfection_rep4
M transfection gene expression rep4


title: PVN_K_M_44hr_7

description:
M_transfection_rep2
M transfection gene expression rep2


title: F_APR_DUO

source_name: duodenum

value: April, 2020

value: duodenum


title: MUTZ3 - RNAseq - SH1150 - 120HRS - REP3

description: Library name: MUTZ3_SH1150_120HRS_REP3


title: MUTZ3 - RNAseq - SH1150 - 120HRS - REP2

description: Library name: MUTZ3_SH1150_120HRS_REP2


title: PVN_K_M_44hr_6

description:
M_transfection_rep1
M transfection gene expression rep1


title: MUTZ3 - RNAseq - SH1150 - 72HRS - REP3

description: Library name: MUTZ3_SH1150_72HRS_REP3


title: MUTZ3 - RNAseq - SH1150 - 24HRS - REP3

description: Library name: MUTZ3_SH1150_24HRS_REP3


title: F_APR_DRN

source_name: dorsal raphe

value: dorsal raphe


title: PVN_K_C_44hr_5

description:
no_transfection_control_rep5
No transfection gene expression rep5

value: control


title: MUTZ3 - RNAseq - SH1150 - 120HRS - REP1

description: Library name: MUTZ3_SH1150_120HRS_REP1


title: F_APR_DMH

source_name: dorsomedial hypothalamic nucleus

value: dorsomedial hypothalamic nucleus


title: MUTZ3 - RNAseq - SH1147 - 96HRS - REP2

description: Library name: MUTZ3_SH1147_96HRS_REP2


title: F_APR_COR

source_name: cornea

value: cornea


title: F_APR_FOV

source_name: fovea centralis

value: fovea centralis


title: PVN_K_C_44hr_3

description:
no_transfection_control_rep3
No transfection gene expression rep3


title: MUTZ3 - RNAseq - SH1147 - 72HRS - REP1

description: Library name: MUTZ3_SH1147_72HRS_REP1

source_name: Bone marrow

value: Bone marrow


title: MUTZ3 - RNAseq - SH1147 - 96HRS - REP1

description: Library name: MUTZ3_SH1147_96HRS_REP1

value: acute myelomonocytic leukemia


title: MUTZ3 - RNAseq - SH1147 - 72HRS - REP3

description: Library name: MUTZ3_SH1147_72HRS_REP3


title: PVN_K_C_44hr_1

description:
no_transfection_control_rep1
No transfection gene expression rep1


title: PVN_K_C_44hr_2

description:
no_transfection_control_rep2
No transfection gene expression rep2


title: F_APR_COL

source_name: colon

value: colon


title: MUTZ3 - RNAseq - SH1147 - 72HRS - REP2

description: Library name: MUTZ3_SH1147_72HRS_REP2


title: MUTZ3 - RNAseq - SH1147 - 48HRS - REP3

description: Library name: MUTZ3_SH1147_48HRS_REP3


title: MUTZ3 - RNAseq - SH1147 - 48HRS - REP1

description: Library name: MUTZ3_SH1147_48HRS_REP1


title: PVN_K_C_44hr_4

description:
no_transfection_control_rep4
No transfection gene expression rep4


title: PVHN_G_Hendra_19h_RNA_30

description:
HeV_FG_VLP_19h_rep5
Gene expression at 19h

treatment_protocol: For each time-point ten 6-well plates were used, five of them were incubated with NiV or HeV VLPs generated by related FG genes for 2h and 19h time point. Remaining five 6-well plates were used as uninfected controls.

value: incubated with HeV_FG_VLP


title: MUTZ3 - RNAseq - SH1147 - 24HRS - REP2

description: Library name: MUTZ3_SH1147_24HRS_REP2


title: MUTZ3 - RNAseq - SH1147 - 96HRS - REP3

description: Library name: MUTZ3_SH1147_96HRS_REP3


title: MUTZ3 - RNAseq - SH1147 - 48HRS - REP2

description: Library name: MUTZ3_SH1147_48HRS_REP2


title: MUTZ3 - RNAseq - SH1147 - 24HRS - REP1

description: Library name: MUTZ3_SH1147_24HRS_REP1


title: PVHN_G_Hendra_19h_RNA_29

description:
HeV_FG_VLP_19h_rep4
Gene expression at 19h


title: MUTZ3 - RNAseq - SH1147 - 120HRS - REP3

description: Library name: MUTZ3_SH1147_120HRS_REP3


title: F_APR_CAT

source_name: cartilage

value: cartilage

value: F


title: MUTZ3 - RNAseq - SH1147 - 24HRS - REP3

description: Library name: MUTZ3_SH1147_24HRS_REP3


title: F_APR_CRB

source_name: cerebellum

value: cerebellum


title: F_APR_CAU

source_name: caudate nucleus

value: caudate nucleus


title: MUTZ3 - RNAseq - SH1147 - 120HRS - REP2

description: Library name: MUTZ3_SH1147_120HRS_REP2


title: F_APR_CA3

source_name: hippocampus CA3

value: hippocampus CA3


title: MUTZ3 - RNAseq - SH1147 - 120HRS - REP1

description: Library name: MUTZ3_SH1147_120HRS_REP1


title: MUTZ3 - RNAseq - pCW_4xPLDLS_Clone8 - no_dox

description: Library name: WT_MUTZ3_1675_4xPLDLS_CL8


title: PVHN_G_Hendra_19h_RNA_27

description:
HeV_FG_VLP_19h_rep2
Gene expression at 19h


title: PVHN_G_Hendra_19h_RNA_28

description:
HeV_FG_VLP_19h_rep3
Gene expression at 19h


title: PVHN_G_Hendra_19h_RNA_26

description:
HeV_FG_VLP_19h_rep1
Gene expression at 19h


title: F_APR_CA1

source_name: hippocampus CA1

value: hippocampus CA1


title: F_APR_CEC

source_name: cecum

value: April, 2020

value: cecum


title: MUTZ3 - RNAseq - pCW_4xPLDLS_Clone6 - no_dox

description: Library name: WT_MUTZ3_1675_4xPLDLS_CL6


title: F_APR_BRO

source_name: bronchus

value: bronchus


title: MUTZ3 - RNAseq - pCW_4xPLDLS_Clone6 - dox

description: Library name: WT_MUTZ3_1675_4xPLDLS_CL6_DOX

value: dox


title: PVHN_G_Nipah_19h_RNA_24

description:
NiV_FG_VLP_19h_rep4
Gene expression at 19h

value: incubated with NiV_FG_VLP


title: MUTZ3 - RNAseq - pCW_4xPLDLS_Clone4 - no_dox

description: Library name: WT_MUTZ3_1675_4xPLDLS_CL4


title: F_APR_BON

source_name: bone

value: bone


title: MUTZ3 - RNAseq - pCW_4xPLDLS_Clone14 - no_dox

description: Library name: WT_MUTZ3_1675_4xPLDLS_CL14


title: F_APR_BOM

source_name: bone marrow

value: bone marrow


title: PVHN_G_Nipah_19h_RNA_23

description:
NiV_FG_VLP_19h_rep3
Gene expression at 19h


title: F_APR_BNST

source_name: bed nucleus of the stria terminalis

value: bed nucleus of the stria terminalis


title: MUTZ3 - RNAseq_SLAM - WT - NoAuxin_S4U

description: Library name: WT_MUTZ3_S4U

data_processing:
Base calling was conducted with bcl2fastq v1.8.4 with the settings --no-eamss --mismatches 1
Reads were processed with the SLAM-DUNK pipeline, adapted to take total RNA as input instead of 3’UTR only. Briefly,  a nucleotide conversion-aware read mapping algorithm was used to align reads with a high number of mismatches, followed by masking of single nucleotide reads. Finally, T>C conversions induced by S4U labeling was quantified on a gene level basis.
Assembly: hg19
Supplementary files format and content: tcount.tsv contains gene-level counts, including total reads, T>C converted reads and multimapping reads

extract_protocol:
After 1.5, hours nascent RNA was labeled for 3 hours using 300 µM/ml 4-Thiouridine. At 3 HRS of 4-Thiouridine labeling RNA was isolated using Qiagen rnease mini kit . Alkylation of thiol groups was performed according to manufacturer’s protocol.
500 ng total RNA was used to generate libraries using the KAPA RNA HyperPrep kit with RiboErase

treatment_protocol: MUTZ3 MECOM-V5-AID-T2A-GFP cells were treated with auxin in order to induce degradation of MECOM

value: Bone marrow

value: acute myelomonocytic leukemia

value: WT


title: MUTZ3 - RNAseq_SLAM - WT - Auxin_S4U

description: Library name: WT_MUTZ3_AUXIN_S4U


title: MUTZ3 - RNAseq_SLAM - MECOM_V5_AID_Tir1_Clone9 - NoAuxin_S4U

description: Library name: MUTZ3_V5_AID_GFP_TIR1_CL9_S4U


title: MUTZ3 - RNAseq - pCW_4xPLDLS_Clone14 - dox

description: Library name: WT_MUTZ3_1675_4xPLDLS_CL14_DOX


title: MUTZ3 - RNAseq - pCW_4xPLDLS_Clone8 - dox

description: Library name: WT_MUTZ3_1675_4xPLDLS_CL8_DOX


title: MUTZ3 - RNAseq_SLAM - MECOM_V5_AID_Tir1_Clone9 - Auxin_S4U

description: Library name: MUTZ3_V5_AID_GFP_TIR1_CL9_AUXIN_S4U


title: F_APR_BAT

source_name: brown adipose tissue

extract_protocol:
Total RNA was extracted using the RNeasy Plus Universal Mini Kit (Qiagen).
3'RNA-Seq library was prepared by the Lasy-Seq v1.1 protocol (https://sites.google.com/view/lasy-seq/)

value: brown adipose tissue


title: PVHN_G_Nipah_19h_RNA_25

description:
NiV_FG_VLP_19h_rep5
Gene expression at 19h


title: MUTZ3 - RNAseq_SLAM - MECOM_V5_AID_Tir1_Clone8 - Auxin_S4U

description: Library name: MUTZ3_V5_AID_GFP_TIR1_CL8_AUXIN_S4U


title: dD2EB

city: New York city

first: Feifei

last: Yuan

state: NY

institute: Columbia University

description:
Library name: WF02
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software 8.0.1
The scRNA-seq filtered raw counts matrices were analyzed in Seurat (v5.0.1) using R (v4.3.2).
Assembly: mm10
Supplementary files format and content: cell barcodes (barcodes.tsv), genes (genes.tsv),  and count matrix (matrix.mtx)

organism: Mus musculus

source_name: embryonic stem cell

extract_protocol:
EBs were dissociated with 0.05% Trypsin-EDTA (Gibco, 25200054) and washed with DMEM containing 10% FBS. Samples were filtered with a 40-μm cell strainer, and filtered cells were used for single-cell sequencing in the genomic core facility of Columbia University.
scRNA-seq libraries were prepared using a Chromium Single Cell 3’ Reagent kit (10x Genomics) according to the manufacturer’s instructions.

treatment_protocol: EBs treated with DMSO or dTAG13 for two days (D2EBs vs. dD2EBs) were collected.

value: embryonic stem cell

tag: strain

value: Male

value: dTAG13 treatment for two days


title: MUTZ3 - RNAseq_SLAM - MECOM_V5_AID_Tir1_Clone8 - NoAuxin_S4U

description: Library name: MUTZ3_V5_AID_GFP_TIR1_CL8_S4U


title: PVHN_G_Nipah_19h_RNA_21

description:
NiV_FG_VLP_19h_rep1
Gene expression at 19h


title: PVHN_G_Nipah_19h_RNA_22

description:
NiV_FG_VLP_19h_rep2
Gene expression at 19h


title: PVHN_G_Control_19h_RNA_20

description:
No_VLP_control_19h_rep5
Gene expression at 19h

value: control


title: PVHN_G_Control_19h_RNA_19

description:
No_VLP_control_19h_rep4
Gene expression at 19h


title: F_APR_AXL

data_processing:
Mapping and quantification were performed by bowtie (v1.2.3) and RSEM (v1.3.3).
Assembly: Mmul_10
Supplementary files format and content: Excel files include FPM values for each tissue.

source_name: axillary lymph node

value: axillary lymph node

value: F


title: F_APR_ARC

source_name: arcuate nucleus

value: April, 2020

value: arcuate nucleus


title: D2EB

description:
Library name: WF01
10x Genomics

value: DMSO treatment for two days


title: MUTZ3 - RNAseq_SLAM - MECOM_V5_AID_Tir1_Clone1 - NoAuxin_S4U

description: Library name: MUTZ3_V5_AID_GFP_TIR1_CL1_S4U


title: MUTZ3 - RNAseq - pCW_4xPLDLS_Clone4 - dox

description: Library name: WT_MUTZ3_1675_4xPLDLS_CL4_DOX

value: dox


title: F_APR_AOR

source_name: aorta

value: aorta


title: F_APR_ANU

source_name: anus

value: anus