title: PDX1_Lungs_3

city: Basel

first: Mohamed

last: Bentires-Alj

address: Hebelstrasse 20

department: DBM

country: Switzerland

institute: University Hospital Basel

data_processing:
Standard Illumina software was used for base calling
Reads were aligned on the hg19 human genome using the R/Bioconductor package QuasR (with the unspliced option, using the TxDb.Hsapiens.UCSC.hg19.knownGene package for raw gene counts).
Genome_build: hg19
Supplementary_files_format_and_content: raw gene counts

source_name: breast cancer primary-derived xenograft

growth_protocol: MDA-MB 231 cells (10,000 cells) were resuspended in 40 µl Matrigel:PBS (1:1) and injected into the pre-cleared mammary fat-pads of 4- to 8-week-old female NSG mice. PDX models were transplanted into the pre-cleared 4th mammary fat-pads of NSG mice. Tumors were resected and processed when the largest diameter reached 10 mm. Mice were monitored regularly for signs of metastatic outgrowth and distress. Organs were collected after animal sacrifice and

extract_protocol:
Total RNA was extracted using the Arctutus PicoPure RNA Isolation Kit (cat. no. 12204-01). Ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit (Epicentre, MRZ11124C)
Ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit (Epicentre, MRZ11124C) before library preparation using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre)

tag: breast cancer model

value: PDX1 primary-derived xenograft

tag: mouse strain

value: NOD-scid IL2rγnull (NSG)


title: PDX1_Tumor_1

status: Public on Mar 14 2019

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens


title: PDX1_Lungs_4


title: 9.endo.1

city: Rochester

first: Purna

last: Kashyap

state: MN

address: 200 1st St SW

country: USA

institute: Mayo Clinic

data_processing:
MAPRSeq 2.1.1, aligner tophat 2.1.0 and expression counts collated with HTSeq
Genome_build: Homo_sapiens.GRCh38.78.mod.gtf

source_name: baseline

extract_protocol:
Biopsy samples were thawed on ice, homogenized and centrifuged at 13000 RPM and the supernatant was transferred to a new tube.  RNA was prepared using the RNeasy Mini Kit (QIAGEN, Hilden, Germany), using protocol instructions
Samples were stored at -20 and submitted to the Medical Genome Facility at Mayo Clinic, Rochester, MN for library preparation and sequencing on the Illumina HiSeq 2500 Rapid Run

treatment_protocol: This was a pilot prospective single-center dietary intervention study in healthy volunteers consuming a high fiber diet at baseline. The study was registered with clinicaltrials.gov NCT03266536.

tag: subject status

tag: age

tag: gender

value: F

tag: time point

value: baseline

tag: tissue

value: duodenum


title: genomic DNA from sample 61

type: genomic

city: Munich

first: Janine

last: Arloth

address: Kraepelinstr. 2-10

country: Germany

institute: Max Planck Institute of Psychiatry

description: whole blood case sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

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

data_processing:
Microarray methylation analysis was performed in R. Quality control, including intensity read outs, filtering as well as beta value calculation was done using the minfi Bioconductor package. Functional normalization onto control probes was then used to normalized the raw intensity values across all the arrays and to remove part of the variance attributable to technical batches. We excluded any CpG containing SNPs or cross-hybridizing probes and CpGs with a detection p-value > 0.01 in at least 50% of the samples.
Processed data in Series matrix table: Funnorm normalized

label: Cy5 and Cy3

molecule: genomic DNA

source_name: whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using the Allprep mini kit (QIAGEN GmbH, Hilden, Germany) following the manufacturer’s instructions

tag: diagnosis

value: case

tag: education level

tag: history of myocardial infarction

tag: Sex

tag: snp based principle component 1

tag: snp based principle component 2

tag: cellcount-nk

tag: cellcount-bcell

tag: cellcount-mono

tag: cellcount-gran

value: whole blood


title: PDX1_Lungs_2

tag: breast cancer model


title: PDX1_Tumor_4

tag: mouse strain


title: genomic DNA from sample 370

description: whole blood case sample

value: M


title: PDX1_Tumor_3


title: HYH_B3Rep2

city: Urbana

first: Matthew

middle: D.

last: Brooks

state: Illinois

address: 1201 W Gregory Drive

department: GCPRU

institute: USDA

data_processing:
Raw reads were trimmed to remove low quality bases (q<10) and adapter contamination.
Gene expression levels were determined by aligning reads to the Arabidopsis thaliana genome (TAIR10) using the TopHat (v2) package and estimating read counts by the GenomicFeatures/Alignments package.
Genes responding significantly (FDR adjusted p-val <0.05) to each of the "N-early response" TFs  relative to the empty vector control were identified using DESeq2 with a ~TF+Batch model.
Genome_build: TAIR10
Supplementary_files_format_and_content: Read counts output from GenomicFeatures/Alignments package

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: root protoplasts

growth_protocol: Arabidopsis seedlings grown on vertical plates containing MS basal media w/o C or N, 1% sucrose and 1mM KNO3

extract_protocol:
Approximately 10,000-20,000 cells were FACS sorted into RLT buffer and frozen. Total RNA was extracted using the RNeasy Micro Kit (Qiagen) with on-column DNase treatment. mRNA was purified using Dynabeads Oligo (dT).
Libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina. Final quantity was determined using the DNA TapeStation and KAPA Library Quant qPCR.

treatment_protocol: Protoplasts were isolated from root tissue and transfected with expression vector. The following morning protoplasts were treated with 60 mM nitrogen (20 mM KNO3 + 20 mM NH4NO3), 35 uM cycloheximide and 10uM dexamethasone

tag: organ

value: root

tag: ecotype

tag: treatments

value: Nitrogen, Cycloheximide, Dexamethasone

value: 10 days

tag: transfection

value: HYH


title: PMA_Bisulfite-seq

city: La Jolla

last: Denholtz

state: California

address: 9500 Gilman Drive, NSB 5108

institute: UCSD

description: Bisulfite-seq

library_source: genomic

data_processing:
BSseeker2 and HOMER were used for Bisulfite-seq data processing (Guo et al., BMC Genomics, 2013 & Heinz et al. Mol. Cell, 2010)
A bisulfite-seq reference genome was built using the bs_seeker2-build.py command
Alignment was performed using the bs_seeker2-align.py command with the following options: -m 6 -I 0 -X 800
Methylation levels were determined using bs_seeker2-call_methylation.py with default settings.
HOMER-formatted tag directories were built using HOMER’s makeTagDirectories command with the following options: -format allC -minCounts 0 -genome hg38.
awk was used to create tag directories containing only C's covered in both conditions
Genome_build: hg38
Supplementary_files_format_and_content: allC

source_name: Peripheral blood neutrophils

growth_protocol: Human blood collected into heperinized syringes via venupuncture , granulocytes were purified from whole blood via density centrifugation with PolymorphPrep reagent (Accurate Chemical Scientific Corp., cat# AN1114683), purified granulocytes were cultured in HBSS +Ca +Mg -Phenol red (Life Technologies, cat# 14025092) + 0.5% endotoxin free BSA (Akron Biotech cat# Ak8917-0100) at 37degC, 5% CO2

extract_protocol:
DNA was extracted from neutrophils using a Qiagen Blood and Tissue kit
DNA was bisulfite converted using a MethyCode Bisulfite conversion kit (Invitrogen cat# MECOV-50) and prepared for high throughput sequencing using TruSeq DNA Sample Preparation kit v2 for WGBS (Illumina cat# FC-121-2001)

treatment_protocol: Human neutrophils were stimulated for three hours with either 25nM PMA (Promega, cat# V1171) or via co-culture with E. coli strain K1 at an MOI of 5 in culture conditions mirroring those in the growth protocol above

tag: sample type

value: Bisulfite converted genomic DNA


title: genomic DNA from sample 176

description: whole blood control sample

tag: diagnosis

value: control

tag: age

tag: tissue


title: genomic DNA from sample 165

description: whole blood control sample

tag: education level

tag: history of myocardial infarction

tag: Sex


title: BEE2_B3Rep2


title: PDX1_Tumor_2


title: US_Bisulfite-seq

description: Bisulfite-seq


title: TGA4_B3Rep2


title: BEE2_B3Rep3


title: PDX2_Lungs_3

value: PDX2 primary-derived xenograft


title: genomic DNA from sample 107

description: whole blood case sample

tag: snp based principle component 1

tag: snp based principle component 2

tag: cellcount-nk


title: genomic DNA from sample 97

description: whole blood case sample

tag: cellcount-bcell

tag: cellcount-mono

tag: cellcount-gran


title: genomic DNA from sample 59

description: whole blood case sample


title: PDX2_Lungs_4

tag: breast cancer model

tag: mouse strain


title: CRF4_B3Rep2

tag: organ

tag: ecotype

tag: treatments


title: EV_B3Rep2

tag: transfection

value: empty vector


title: PDX2_Lungs_2


title: EV_B3Rep3

tag: age


title: genomic DNA from sample 48

description: whole blood case sample

tag: diagnosis

tag: tissue


title: HYH_B3Rep1


title: TGA4_B3Rep1


title: genomic DNA from sample 46

description: whole blood case sample

tag: education level

tag: history of myocardial infarction


title: genomic DNA from sample 194

description: whole blood control sample

tag: Sex

tag: snp based principle component 1


title: PDX2_Tumor_3


title: BEE2_B3Rep1


title: PDX2_Lungs_1


title: PDX2_Tumor_2


title: genomic DNA from sample 149

description: whole blood control sample

tag: snp based principle component 2

tag: cellcount-nk


title: genomic DNA from sample 294

description: whole blood case sample

tag: cellcount-bcell

tag: cellcount-mono


title: CRF4_B3Rep1


title: EV_B3Rep1


title: PDX2_Tumor_1

tag: breast cancer model


title: genomic DNA from sample 537

description: whole blood case sample

tag: cellcount-gran


title: HHO3_B3Rep3

tag: organ


title: genomic DNA from sample 280

description: whole blood control sample


title: GATA17L_B3Rep3

tag: ecotype


title: MDAMB231_CTC_3

source_name: breast cancer cell line

value: MDAMB231 cell line

tag: mouse strain


title: MDAMB231_Liver_3


title: MDAMB231_Lungs_3


title: COL5_B3Rep3

tag: treatments

tag: transfection


title: HHO3_B3Rep2

tag: age


title: GATA17L_B3Rep2


title: genomic DNA from sample 201

description: whole blood control sample

tag: diagnosis

tag: tissue


title: HHO3_B3Rep1


title: genomic DNA from sample 88

description: whole blood case sample

tag: education level

tag: history of myocardial infarction


title: genomic DNA from sample 27

description: whole blood case sample

tag: Sex

tag: snp based principle component 1


title: MDAMB231_Lungs_2


title: MDAMB231_Spleen_2


title: genomic DNA from sample 135

description: whole blood case sample

tag: snp based principle component 2

tag: cellcount-nk


title: COL5_B3Rep2


title: MDAMB231_CTC_2


title: PDX2_Tumor_4


title: COL5_B3Rep1


title: MDAMB231_Lungs_1


title: genomic DNA from sample 105

description: whole blood case sample

tag: cellcount-bcell

tag: cellcount-mono


title: genomic DNA from sample 16

description: whole blood case sample

tag: cellcount-gran


title: TGA1_B2Rep3

tag: organ


title: MDAMB231_Tumor_3

tag: breast cancer model


title: genomic DNA from sample 491

description: whole blood control sample


title: MDAMB231_Spleen_3

tag: mouse strain


title: genomic DNA from sample 329

description: whole blood control sample


title: genomic DNA from sample 64

description: whole blood case sample


title: E07B-3102772-12C44-TimePoint07-WholeBlood-20

city: Atlanta

first: Mary

last: Galinski

state: GA

address: 954 Gatewood Road

department: Vaccine Center at Yerkes

institute: Emory University

description:
Please note that the RNASeq data for this experiment was produced across three specimen types (venous whole blood (WB), bone marrow (BM), and spleen tissue (SP)) using RNAlater and PAXgene sample collection and storage technologies.  Please carefully review the two README files provided as supplementary files with this dataset for the details on the methods used for sequence generation and abundance measures.  README file names are as follows:  E07M99YSMfKnXXZZ_06062018-Readme_MULTIPL_GEO.txt  E07M99FGMfKnXXZZ_06292018-Readme_MULTIPL_GEO.txt  Please note that even though all file names indicate that the host is Macaca fascicularis, some (from NHP RAw8)  are derived from M. mulatta.
E07M99FGMfKnXXWB_Fascicularis-Genes-RawCounts-Results_MULTIPL_GEO.xlsx, E07M99FGMfKnXXWB_Knowlesi-Genes-RawCounts-Results_MULTIPL_GEO.xlsx

data_processing:
Bases were called with Illumina RTA (Real-Time Analysis, v2.7.7) with default parameters. Illumina bcl2fastq v2.17.1.14 was used for demultiplexing. FASTQC (v0.10.1) was used to assess data quality, but the data were not filtered at this stage.
Reads were mapped to a composite reference assembly consisting of host, parasite, and ERCC control references with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Genome_build: RNA-Seq reads were mapped to both host and parasite genomes.  Host (Mf): The version of the Macaca fascicularis used was obtained from ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/364/345/GCF_000364345.1_Macaca_fascicularis_5.0 .  For more information see https://www.ncbi.nlm.nih.gov/assembly/GCF_000364345.1/ .  Parasite: Plasmodium knowlesi PK1 (A+) Malayan H strain  genome assembly and annotation was used. The assembly has been deposited in GenBank under the BioProject accession PRJNA377737  Note that M. mulatta samples were also mapped to the M. fascicularis reference genome.
Supplementary_files_format_and_content: Excel files contain raw counts at the gene level, for each individual. Raw counts are further classified by experimental Time Point and Specimen Type.    Note that in addition to raw counts, normalized data are available as supplementary files as described in the supplementary file E06M99FGMmKnXXZZ_06292018-Readme_MULTIPL_GEO.txt.
Supplementary_files_format_and_content: Host and Parasite Raw Read Counts Column headers are defined as follows:    'Gene ID':  Identifiers of all Genes in the annotation.     'Gene Symbol': Symbols of all Genes in the annotation.    'Sample Identifier / Raw file list / Abundances': The raw file names and sample identifers both contain information regarding Specimen Type, NHP ID, and Time Point.  Abundances measures are from the raw files listed.     Example Notes:  There are 12 columns representing 2 animals for Time Points T01-T05 and Necropsy.    There is a read count entry per sample for every gene that appears in the annotation. For genes where there was no detection of expression by reads that mapped to their loci, the raw count is 0.

organism:
Plasmodium knowlesi
Macaca fascicularis

source_name: Whole blood

growth_protocol: Animals approved for use were moved into experimental housing 10 days prior to the start of the experiment.

extract_protocol:
Please note that the RNASeq data for this experiment was produced across three specimen types (venous whole blood (WB), bone marrow (BM), and spleen tissue (SP)) using RNAlater and PAXgene sample collection and storage technologies.  Please carefully review the two README files provided as supplementary files with this dataset for the details on the methods used for sequence generation and abundance measures.  README file names are as follows:  E07M99YSMfKnXXZZ_06062018-Readme_MULTIPL_GEO.txt  E07M99FGMfKnXXZZ_06292018-Readme_MULTIPL_GEO.txt
Approximately 1 μg of total RNA per sample was converted to double-stranded cDNA using poly-A beads to enrich for mRNA, and Illumina TruSeq Stranded mRNA Sample Prep kits to generate strand-specific libraries.   As a quality control, 92 spike-in RNAs of known concentration and GC proportions (ERCC Spike-In Control, Life Technologies) were added to constitute approximately 1% of the total RNA for each library.  Adapters were ligated to facilitate multiplexed sequencing on an Illumina HiSeq3000 at the Yerkes Genomics Core, aiming for 50 million paired-end 100 base pair (bp) reads per library.
RNA was extracted using Tempus-Spin RNA isolation kits. The quality of all RNA samples was confirmed using a Bioanalyzer, with an RNA Integrity Number (RIN) greater than 8 recorded for all samples."

treatment_protocol: The E07 cohort was inoculated with freshly dissected P. knowlesi sporozoites on 11/01/16. However, for unexplained reasons blood-stage parasitemias did not occur. Consequently, the E07 cohort was reinoculated with cryopreserved P. knowlesi sporozoites. This inoculation was performed on 1/20/17.  Hence 'E07A' refers to samples and results from the failed inoculation from 11/01/16 and 'E07B' refers to samples and results from the successful inoculation on 1/20/17).  Telemetry devices (DSI, model L11) with blood pressure sensors and electrocardiogram (ECG) leads were surgically implanted in seven malaria-naive male long-tailed macaques (Macaca fascicularis), approximately five years of age.  After a resting period of three weeks, the telemetry implants were turned on and physiological data that include activity, temperature, ECG, and blood pressure were continuously collected.  After the E07A failed infection using a fresh preparation of salivary gland sporozoites, the implants were deactivated to preserve battery life. Between E07A and E07B, a single rhesus macaque (M. mulatta) was added to the cohort as an infection control with no telemetry implant.  At the start of E07B, telemetry implants were reactivated.  Ten days after reactivation all animals were inoculated intravenously with cryopreserved P. knowlesi Malayan strain salivary gland sporozoites, obtained from Anopheles dirus infected with parasites from the Pk1A+ clone and previously tested in E30 for their infectivity of macaques. The sporozoite stocks used were produced, isolated and cryopreserved at the Centers for Disease Control and Prevention, and then stored at Yerkes.  After inoculation, the macaques were profiled for clinical, hematological, parasitological, immunological, functional genomic, proteomic, and metabolomic measurements.  The experiment was designed with pathology studies and thus terminal necropsies, which were scheduled at the log phase of the infection, at the peak of parasitemias, at the middle of the chronic phase, or at the end of the follow-up period of 45 days after the inoculation of the sporozoites.  Capillary blood samples were collected daily for the measurement of complete blood counts (CBCs), reticulocytes, and parasitemias.  Capillary blood samples were collected every other day to obtain plasma for metabolomic analysis.  Venous blood and bone marrow samples were collected at six time points for functional genomic, targeted proteomic, targeted metabolomics, and immunological analyses.  Physiological data noted above were continuously captured via telemetry. Within the MaHPIC, this project is known as ‘Experiment 07 (E07A and 07B)’.  This dataset was produced by Dr. Steven E. Bosinger, Nirav Patel, and Gregory K Tharp at the Emory University Yerkes Genomics Core. To access other publicly available results from ‘E07' and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp .  This page will be updated as datasets are released to the public.  The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC) and the MRMC Office of Research Protection Animal Care and Use Review Office (ACURO).  This dataset contains results from both E07A and E07B.    During the experiment subjects experienced chronic infection.     Samples were collected either daily for select specimen types or on clinically determiend time point days. Time points were planned based on the expected progression of infection.  Sample collection at time points was planned to coincide with this expected clinical progression.  However, because of individual variations in the clinical progression of infection for each NHP the clinically defined stage of infection may differ between NHPs at the same time point.  For this reason it is imortant for anyone consuming these data to be aware of any differences between the 'Idealized' and 'Actual' disease progression for each NHP and the corresponding clinical stage of each NHP at each time point when samples were collected.  For this reason the supplementary file E07M99MEMfKnXXZZ_Supporting-Clinical-Information_MULTIPL.pdf is provided to clarify both the 'Idealized' or planned collection of time point samples and the clinically-defined 'Actual' disease progression for each NHP.  Anyone consuming these data should use this information to ensure they are aware of the clinical state of each NHP at each time point and be aware of differences between NHPs.  [E07A] Time point 1 = Pre-telemetry surgery implants baseline - NHPs were not yet infected with P. knowlesi. This time point is prior to failed inoculation with fresh sporozoites.  [E07A] Time point 2 = Post-telemetry surgery baseline - NHPs were not yet infected with P. knowlesi. This time point is prior to failed inoculation with fresh sporozoites.  [E07A] Time point 3 = Post-failed E07A inoculation - Post failed inoculation with fresh sporozoites, three days after failed inoculation.  Intended to take place during liver stage infection.  [E07B] Time point 2 =  Baseline 2 post-telemetry reactivation - Post-telemetry implantation baseline control: TP2 occurred after telemetry implant reactivation following E07A. NHPs were not yet infected with P. knowlesi.    [E07B] Time point 3 = Pre-Patent / Early Infection  - Post-inoculation with cryopreserved sporozoites: TP3 took place three days after inoculation and is representative of the liver stage infection.    [E07B] Time point 4 = Log Phase  - Log phase / pre-peak phase: This time point was intended to examine responses prior to the peak of parasitemia. Activation at cellular and immune levels, as well as differential telemetry results compared to baseline readings, was expected. Parasitemia of ~100-10,000/ul was expected.   [E07B] Time point 5 = Peak/Post-Peak of Infection  - Peak/post-peak infection: This time point examined the response of the immune system and metabolism of the host during the peak of infection whenever the animal infected with P. knowlesi is experiencing clinical signs of disease. Post-peak was observed for 12C53 and 11C131.   [E07B] Time point 6 = Chronic Phase 1 - Chronic phase of infection: M. fascicularis infected with P. knowlesi can self-control hyper-parasitemias, and they were expected to reach a chronic phase 20-25 days after experimental infection whenever the animal is experiencing clinical signs of disease. This time point examined the response of the immune system and metabolism of the host in early stages of the chronic infection.    [E07B] Time point 7 = Chronic Phase 2 - Chronic phase of infection: M. fascicularis infected with P. knowlesi can self-control hyper-parasitemias, and they were expected to reach a chronic phase 20-25 days after experimental infection whenever the animal is experiencing clinical signs of disease. This time point examined the response of the immune system and metabolism of the host in late stages of the chronic infection.   E07B] Necropsy = Necropsy - Terminal endpoint:  Staggered necropsy dates were carried out for all NHPs (days 10, 14, 27 or 45). The final necropsy occurred 45 days after experimental infection.

tag: collection time point (#) or necropsy

tag: gender

value: Male

tag: non human primate individual id

value: Whole blood


title: E07B-3100782-12C53-Necropsy-WholeBlood-20

value: Necropsy


title: E07B-3084213-H12C59-Necropsy-WholeBlood-20


title: E07B-3078648-H12c8-Necropsy-WholeBlood-20


title: E07B-3101118-11C166-Necropsy-WholeBlood-20


title: E07B-3111003-12C44-Necropsy-WholeBlood-20


title: E07B-3083877-12C136-Necropsy-WholeBlood-20


title: GATA17L_B3Rep1

tag: ecotype

tag: treatments

tag: age

tag: transfection


title: E07B-3078312-11C131-Necropsy-WholeBlood-20

tag: tissue


title: MDAMB231_Liver_2

value: NOD-scid IL2rγnull (NSG)


title: genomic DNA from sample 80

description: whole blood case sample

tag: diagnosis

tag: education level

tag: history of myocardial infarction

tag: Sex

tag: snp based principle component 1


title: genomic DNA from sample 84

description: whole blood case sample

tag: snp based principle component 2

tag: cellcount-nk

tag: cellcount-bcell

tag: cellcount-mono

tag: cellcount-gran


title: TGA1_B2Rep2

tag: organ


title: TGA1_B2Rep1


title: MDAMB231_Spleen_1

tag: breast cancer model

tag: mouse strain


title: E07B-3092087-11C166-TimePoint06-WholeBlood-20

tag: collection time point (#) or necropsy

tag: gender

tag: non human primate individual id


title: genomic DNA from sample 283

description: whole blood case sample

tag: age

tag: tissue


title: genomic DNA from sample 372

description: whole blood control sample

tag: diagnosis

tag: education level

value: F


title: genomic DNA from sample 302

description: whole blood case sample

value: case

tag: history of myocardial infarction

tag: Sex


title: EV_B2Rep1

tag: ecotype

tag: treatments

tag: transfection


title: GATA17_B1Rep3


title: E07B-3091988-12C44-TimePoint06-WholeBlood-20


title: E07B-3091889-12C53-TimePoint06-WholeBlood-20


title: MDAMB231_CTC_1


title: genomic DNA from sample 361

description: whole blood case sample

tag: snp based principle component 1

tag: snp based principle component 2

tag: cellcount-nk

tag: cellcount-bcell

tag: cellcount-mono

value: whole blood


title: genomic DNA from sample 21

description: whole blood case sample

value: M

tag: cellcount-gran


title: genomic DNA from sample 427

description: whole blood control sample


title: ERF056_B1Rep3

tag: organ

value: root


title: E07B-3079380-11C166-TimePoint05-WholeBlood-24

tag: collection time point (#) or necropsy

tag: gender

tag: non human primate individual id


title: E07B-3079479-H12C59-TimePoint05-WholeBlood-24

tag: tissue


title: MDAMB231_Tumor_2

tag: breast cancer model

tag: mouse strain


title: MDAMB231_Tumor_1


title: PDX3_Liver_1

value: PDX3 primary-derived xenograft


title: MDAMB231_Liver_1


title: PDX3_Tumor_3


title: PDX3_Liver_4


title: genomic DNA from sample 244

description: whole blood control sample

tag: diagnosis

tag: education level

tag: history of myocardial infarction

tag: age

tag: Sex


title: PDX3_Lungs_4


title: EV_B2Rep3

tag: ecotype

tag: treatments

value: Nitrogen, Cycloheximide, Dexamethasone

value: 10 days

tag: transfection


title: EV_B1Rep3


title: EV_B2Rep2


title: genomic DNA from sample 509

description: whole blood control sample

tag: snp based principle component 1

tag: snp based principle component 2

tag: cellcount-nk

tag: cellcount-bcell

tag: cellcount-mono


title: E07B-3079083-12C136-TimePoint05-WholeBlood-24

tag: collection time point (#) or necropsy

tag: gender

tag: non human primate individual id


title: E07B-3079182-12C53-TimePoint05-WholeBlood-24

tag: tissue


title: E07B-3079281-12C44-TimePoint05-WholeBlood-24


title: E07B-3078062-H12C59-TimePoint04-WholeBlood-24


title: GATA17_B1Rep2

tag: organ


title: HSFB2A_B1Rep3


title: PDX3_Tumor_4

tag: breast cancer model

tag: mouse strain


title: E07B-3077963-H12c8-TimePoint04-WholeBlood-24


title: HSFB2A_B1Rep2

tag: age


title: genomic DNA from sample 534

description: whole blood case sample

tag: diagnosis

tag: education level

tag: history of myocardial infarction

tag: Sex

tag: cellcount-gran


title: E07B-3077864-11C166-TimePoint04-WholeBlood-24


title: genomic DNA from sample 429

description: whole blood case sample

tag: snp based principle component 1

tag: snp based principle component 2


title: genomic DNA from sample 143

description: whole blood control sample

tag: cellcount-nk

tag: cellcount-bcell


title: GATA17_B1Rep1

tag: ecotype

tag: treatments

tag: transfection


title: E07B-3077666-12C53-TimePoint04-WholeBlood-24

tag: collection time point (#) or necropsy

tag: gender

tag: non human primate individual id

tag: tissue


title: HSFB2A_B1Rep1

tag: organ

tag: age


title: E07B-3077765-12C44-TimePoint04-WholeBlood-24


title: E07B-3077567-12C136-TimePoint04-WholeBlood-24


title: PDX3_Lungs_3

tag: breast cancer model

tag: mouse strain


title: genomic DNA from sample 162

description: whole blood control sample

tag: diagnosis

tag: education level

tag: history of myocardial infarction

tag: Sex

tag: cellcount-mono


title: PDX3_Liver_3


title: PDX3_Lungs_5


title: PDX3_Lungs_1


title: ERF056_B1Rep1


title: PDX3_Tumor_1


title: PDX3_Tumor_5


title: genomic DNA from sample 421

description: whole blood case sample

tag: snp based principle component 1

tag: snp based principle component 2

tag: cellcount-nk

tag: cellcount-bcell

tag: cellcount-gran


title: E07B-3069392-H12C59-TimePoint03-WholeBlood-20

tag: collection time point (#) or necropsy

tag: gender


title: E07B-3077468-11C131-TimePoint04-WholeBlood-24

tag: non human primate individual id

tag: tissue


title: EV_B1Rep1

tag: organ

tag: ecotype

tag: treatments

tag: age

tag: transfection


title: genomic DNA from sample 412

description: whole blood case sample

tag: diagnosis

tag: education level

tag: history of myocardial infarction


title: genomic DNA from sample 490

description: whole blood control sample

tag: Sex

tag: snp based principle component 1

tag: cellcount-mono


title: ERF056_B1Rep2


title: 997: Adult Liver

city: Indianapolis

first: Yunlong

last: Liu

address: 410 west 10th street

institute: Indiana University

data_processing:
Sequence reads were aligned with BFAST (v.0.7.0a) towards reference genome and junction library. Details refers to Breese and Liu, Bioinformatics, 2013, PMID: 23314324
Aligned reads were fitered with NGSUtils (Breese and Liu, Bioinformatics 2013), only unique mapped reads with no more than 2 mismatchs were kept.
Read counts were calculated with NGSUtils.
Differential expression analysis was performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including raw read counts for each Sample

source_name: Human liver tissue

extract_protocol:
Qiagen miRNAeasy Mini Kit. Briefly, 2μg of total RNA per sample of 30 human liver samples (fetal, pediatric, and adult; n=10) were used for library preparation. The rRNA was depleted using RiboMinus Eukaryote Kit for RNA-Seq.
SOLiD Total RNA-seq Kit

value: Liver

value: Adult


title: EV_B1Rep2


title: genomic DNA from sample 293

description: whole blood case sample

tag: snp based principle component 2

tag: cellcount-nk

tag: cellcount-bcell


title: E07B-3069194-11C166-TimePoint03-WholeBlood-20

tag: collection time point (#) or necropsy

tag: gender


title: E07B-3069293-H12c8-TimePoint03-WholeBlood-20

tag: non human primate individual id

tag: tissue


title: 9609: Pediatric Liver

value: Pediatric


title: E07B-3069095-12C44-TimePoint03-WholeBlood-20


title: genomic DNA from sample 13

description: whole blood case sample

tag: cellcount-gran


title: 939: Adult Liver


title: PVV3.5: Ishikawa control 3

city: Barcelona

first: Adria

last: Caballe

address: C/ Baldiri Reixac 10

department: biostatistics

country: Spain

institute: IRB

description:
barcode: GATCAG
results file: Ishikawa_GFPneg_vs_Ishikawa_control.csv

data_processing:
FastQ files were aligned against the hg19 version of the human genome with the STAR software v2.3.0e and default parameters
Aligned BAM files were sorted and indexed using Sambamba v0.5.9
Per-gene counts (hg19 genome, Biomart v2.34.2 annotation) were generated with featureCounts function from the Rsubread v1.28.1 R package
Differential expression was performed with DESeq2 with processing batch as covariate.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files include DESeq2 output results with Ensembl gene ID, baseMean, log2FoldChange, lfcSE, stat, pvalue and BH adjusted pvalue for all comparisons
Supplementary_files_format_and_content: HEC1A_control_vs_Ishikawa_control.csv: DESeq2 results for HEC1A vs Ishikawa in control samples
Supplementary_files_format_and_content: HEC1A_GFPneg_vs_HEC1A_control.csv: DESeq2 results for GFPneg vs control in HEC1A samples
Supplementary_files_format_and_content: HEC1A_GFPpos_vs_Ishikawa_GFPpos.csv: DESeq2 results for HEC1A vs Ishikawa in GFPpos samples
Supplementary_files_format_and_content: HEC1A_GFPpos_vs_JEG3_control.csv: DESeq2 results for HEC1A GFPos vs JEG3 controls
Supplementary_files_format_and_content: Ishikawa_GFPneg_vs_Ishikawa_control.csv: DESeq2 results for GFPpos vs control in Ishikawa samples
Supplementary_files_format_and_content: Ishikawa_GFPpos_vs_JEG3_control.csv: DESeq2 results for Ishikawa GFPpos vs JEG3 controls
Supplementary_files_format_and_content: HEC1ADiffvsIshiDiff.csv: DESeq2 results HEC1A_GFPneg-HEC1A_control differences vs Ishikawa_GFPneg-Ishikawa_control differences

source_name: Endometrial adenocarcinoma

growth_protocol: Ishikawa cells were maintained in MEM (MEM α, nucleosides, no phenol red) supplemented with 5% fetal bovine serum, 10 mM of non-essential amino acids (MEM Non-Essential Amino Acids Solution) and 100 mg/ml streptomycin and 100 IU/ml penicillin (PenStrep). HEC-1-A were maintained in McCoy´s 5A (McCoy's 5A (Modified) Medium, GlutaMAX™ Supplement) supplemented with 10% fetal bovine serum and 100 mg/ml streptomycin and 100 IU/ml penicillin (PenStrep). JEG-3 cells were cultured in DMEM (DMEM, high glucose, GlutaMAX™ supplement) containing 10% fetal bovine serum, 1 mM sodium pyruvate and 100 mg/ml streptomycin and 100 IU/ml penicillin (PenStrep).

extract_protocol:
RNA from each sample was isolated using RNeasy Mini Kit (Qiagen N. V., Netherlands) following manufacturer´s recommendations and eluted in 30 µl nuclease free water. RNA was purified using RNase-Free DNase Set (Qiagen N. V., Netherlands).
RNA libraries were prepared for sequencing using the kits NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat# E7490) and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (Cat#E7770), following manufacturer´s instructions and 8-11 cycles of amplification.

treatment_protocol: Recombinant lentiviral particles (third generation self-inactivating vector system) expressing GFP from a PGK promoter were produced as described (Tiscornia et al., 2006) and used to transduce the JEG-3 trophoblast cells. Cell suspensions of GFP positive JEG-3 cells were diluted to a final concentration of 3x104 cells/ml. 100 μl of the cell suspension were seeded in U-bottom ultra-low attachment 96-well plates (Corning, NY, USA). Plates were centrifuged at room temperature during 10 min at 250 x g and cultured for 48 hours at 37ºC and 5% CO2 generating fluorescent spheroids of 250-300 µM.

value: Uterus

tag: biological replicate

tag: total yield (ng)

tag: cell type

value: Ishikawa control


title: PVV3.4: HEC1A co-culture_GFP- 3

description:
barcode: CAGATC
results file: HEC1A_GFPpos_vs_JEG3_control.csv

value: HEC-1-A substrates co-cultured with JEG-3 spheroids


title: genomic DNA from sample 37

description: whole blood case sample

tag: diagnosis

tag: age


title: genomic DNA from sample 390

description: whole blood control sample

value: control

tag: education level

tag: history of myocardial infarction


title: E07B-3068996-12C53-TimePoint03-WholeBlood-20

value: Male

value: Whole blood


title: genomic DNA from sample 426

description: whole blood case sample

tag: Sex

tag: snp based principle component 1


title: PVV3.3: HEC1A co-culture_GFP+ 3

description:
barcode: ACAGTG
results file: HEC1A_GFPpos_vs_Ishikawa_GFPpos.csv

source_name: Choriocarcinoma

value: Placenta

value: JEG-3 spheroids co-cultured with HEC-1-A substrates


title: 9006: Pediatric Liver


title: 9011: Pediatric Liver


title: PVV3.1: Ishikawa co-culture_GFP+ 3

description:
barcode: ATCACG
results file: HEC1A_control_vs_Ishikawa_control.csv

value: JEG-3 spheroids co-cultured with Ishikawa substrates


title: PVV3.6: HEC1A control 3

description:
barcode: TAGCTT
results file: Ishikawa_GFPpos_vs_JEG3_control.csv

value: HEC1A control


title: PVV3.7: JEG-3 control 3

description:
barcode: GGCTAC
results file: HEC1ADiffvsIshiDiff.csv

value: JEG-3 control


title: E07B-3068798-11C131-TimePoint03-WholeBlood-20


title: PVV3.2: Ishikawa co-culture_GFP- 3

description:
barcode: TTAGGC
results file: HEC1A_GFPneg_vs_HEC1A_control.csv

value: Ishikawa substrates co-cultured with JEG-3 spheroids


title: E07B-3059524-H12C59-TimePoint02-WholeBlood-20


title: E07B-3068897-12C136-TimePoint03-WholeBlood-20


title: genomic DNA from sample 212

description: whole blood control sample

value: F

tag: snp based principle component 2

tag: cellcount-mono

value: whole blood


title: genomic DNA from sample 93

description: whole blood case sample

value: case

value: M

tag: cellcount-nk

tag: cellcount-bcell


title: 9003: Pediatric Liver

value: Liver

value: Pediatric


title: 8926: Pediatric Liver


title: genomic DNA from sample 356

description: whole blood case sample


title: E07B-3059425-H12c8-TimePoint02-WholeBlood-20

tag: collection time point (#) or necropsy

tag: gender


title: PVV2.7: JEG-3 control 2

tag: tissue


title: genomic DNA from sample 419

description: whole blood case sample

tag: cellcount-gran


title: E07B-3059326-11C166-TimePoint02-WholeBlood-20

tag: non human primate individual id


title: PVV2.6: HEC1A control 2

value: Uterus

tag: biological replicate

tag: total yield (ng)


title: 917: Adult Liver

value: Adult


title: E07B-3059227-12C44-TimePoint02-WholeBlood-20


title: PVV2.5: Ishikawa control 2

tag: cell type

value: Ishikawa control


title: genomic DNA from sample 524

description: whole blood case sample

tag: diagnosis

tag: age


title: genomic DNA from sample 386

description: whole blood case sample

tag: education level

tag: history of myocardial infarction


title: 8917: Pediatric Liver


title: E07B-3059128-12C53-TimePoint02-WholeBlood-20

value: Male


title: 8910: Pediatric Liver


title: PVV2.3: HEC1A co-culture_GFP+ 2


title: 863: Adult Liver


title: genomic DNA from sample 354

description: whole blood case sample

tag: Sex

tag: snp based principle component 1


title: genomic DNA from sample 189

description: whole blood control sample

value: control

tag: snp based principle component 2

tag: cellcount-mono


title: PVV2.1: Ishikawa co-culture_GFP+ 2

value: Placenta


title: PVV2.2: Ishikawa co-culture_GFP- 2


title: E07B-3059029-12C136-TimePoint02-WholeBlood-20

value: Whole blood


title: E07B-3058930-11C131-TimePoint02-WholeBlood-20


title: genomic DNA from sample 296

description: whole blood case sample

tag: cellcount-nk

tag: cellcount-bcell


title: E07A-3026575-H12C59-TimePoint02-WholeBlood-20

tag: collection time point (#) or necropsy

tag: gender


title: 21526: Fetal Liver

tag: tissue

value: Fetal


title: genomic DNA from sample 155

description: whole blood control sample

tag: cellcount-gran


title: PVV1.7: JEG-3 control 1

tag: biological replicate


title: 20908: Fetal Liver


title: PVV1.6: HEC1A control 1

tag: total yield (ng)

value: HEC1A control


title: 8924: Pediatric Liver


title: E07A-3026379-11C166-TimePoint02-WholeBlood-20

tag: non human primate individual id


title: genomic DNA from sample 508

description: whole blood control sample

tag: diagnosis


title: E07A-3026477-H12c8-TimePoint02-WholeBlood-20


title: 20906: Fetal Liver

tag: age


title: PVV2.4: HEC1A co-culture_GFP- 2

tag: cell type

value: HEC-1-A substrates co-cultured with JEG-3 spheroids


title: E07A-3026281-12C44-TimePoint02-WholeBlood-20


title: genomic DNA from sample 494

description: whole blood control sample

tag: education level

tag: history of myocardial infarction


title: 20900: Fetal Liver


title: genomic DNA from sample 180

description: whole blood control sample

tag: Sex

tag: snp based principle component 1


title: 71209: Adult Liver


title: E07A-3026066-12C53-TimePoint02-WholeBlood-20


title: 20718: Fetal Liver


title: PVV1.4: HEC1A co-culture_GFP- 1


title: PVV1.2: Ishikawa co-culture_GFP- 1

value: Ishikawa substrates co-cultured with JEG-3 spheroids


title: genomic DNA from sample 49

description: whole blood case sample

tag: snp based principle component 2

tag: cellcount-mono


title: 20523: Fetal Liver


title: 20636: Fetal Liver


title: genomic DNA from sample 437

description: whole blood control sample

tag: cellcount-nk

tag: cellcount-bcell


title: E07A-3025870-11C131-TimePoint02-WholeBlood-20

tag: collection time point (#) or necropsy

tag: gender


title: E07A-3025968-12C136-TimePoint02-WholeBlood-20

tag: tissue


title: genomic DNA from sample 366

description: whole blood case sample

tag: cellcount-gran


title: 20196: Fetal Liver


title: E07A-3022711-H12c8-TimePoint01-WholeBlood-20


title: PVV1.5: Ishikawa control 1

tag: biological replicate

tag: total yield (ng)


title: genomic DNA from sample 78

description: whole blood case sample

tag: diagnosis

value: F


title: 19999: Fetal Liver

tag: age


title: E07A-3022614-11C166-TimePoint01-WholeBlood-20

tag: non human primate individual id


title: genomic DNA from sample 492

description: whole blood control sample

tag: education level

value: whole blood


title: lung adenocarcinoma [LC6]

city: Beijing

first: Hua

last: Fang

address: Xicheng district Fu Xing Men Wai Da Jie No.20

department: Department of Oncology

country: China

institute: Fu Xing Hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500 platform and 50bp single-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw datas were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference.
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2(Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures.
Supplementary_files_format_and_content: read counts, TPM

source_name: exosome

extract_protocol:
Exosomes were obtained from plamsa samples by ultracentrifuge and totoal RNAs were extracted using Trizol Reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols
A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.)

tag: disease

value: lung adenocarcinoma


title: 19023: Fetal Liver


title: E07A-3022517-12C44-TimePoint01-WholeBlood-20


title: PVV1.3: HEC1A co-culture_GFP+ 1

tag: cell type

value: JEG-3 spheroids co-cultured with HEC-1-A substrates


title: 1307: Pediatric Liver

value: Liver


title: genomic DNA from sample 260

description: whole blood control sample

tag: history of myocardial infarction

tag: Sex

value: M

tag: snp based principle component 1


title: 1223: Adult Liver


title: E07A-3017386-12C53-TimePoint01-WholeBlood-20


title: lung adenocarcinoma [LC5]


title: lung adenocarcinoma [LC4]


title: lung adenocarcinoma [LC3]


title: E07A-3017289-12C136-TimePoint01-WholeBlood-20


title: PVV1.1: Ishikawa co-culture_GFP+ 1

value: JEG-3 spheroids co-cultured with Ishikawa substrates


title: 1201: Adult Liver

value: Adult


title: E07A-3022808-H12C59-TimePoint01-WholeBlood-20


title: genomic DNA from sample 34

description: whole blood case sample

value: case

tag: snp based principle component 2

tag: cellcount-nk

tag: cellcount-mono


title: lung adenocarcinoma [LC11]


title: E07A-3017192-11C131-TimePoint01-WholeBlood-20

tag: collection time point (#) or necropsy

tag: gender

value: Male


title: genomic DNA from sample 466

description: whole blood case sample

tag: cellcount-bcell

tag: cellcount-gran

tag: tissue


title: E07B-3111158-12C44-Necropsy-Spleen-20

description:
Please note that the RNASeq data for this experiment was produced across three specimen types (venous whole blood (WB), bone marrow (BM), and spleen tissue (SP)) using RNAlater and PAXgene sample collection and storage technologies.  Please carefully review the two README files provided as supplementary files with this dataset for the details on the methods used for sequence generation and abundance measures.  README file names are as follows:  E07M99YSMfKnXXZZ_06062018-Readme_MULTIPL_GEO.txt  E07M99FGMfKnXXZZ_06292018-Readme_MULTIPL_GEO.txt  Please note that even though all file names indicate that the host is Macaca fascicularis, some (from NHP RAw8)  are derived from M. mulatta.
E07M99FGMfKnXXSP_Fascicularis-Genes-RawCounts-Results_MULTIPL_GEO.xlsx, E07M99FGMfKnXXSP_Knowlesi-Genes-RawCounts-Results_MULTIPL_GEO.xlsx

source_name: Spleen

value: Necropsy

value: Spleen


title: 1062: Adult Liver


title: E07B-3101273-11C166-Necropsy-Spleen-20


title: healthy control [NC4]

value: healthy


title: 1046: Adult Liver


title: E07B-3100937-12C53-Necropsy-Spleen-20


title: genomic DNA from sample 137

description: whole blood control sample

tag: diagnosis

value: control


title: genomic DNA from sample 5

description: whole blood case sample

tag: age


title: healthy control [NC2]


title: genomic DNA from sample 295

description: whole blood case sample


title: genomic DNA from sample 275

description: whole blood control sample


title: 1034: Adult Liver


title: healthy control [NC1]


title: 1002: Pediatric Liver

value: Pediatric


title: healthy control [NC5]


title: genomic DNA from sample 309

description: whole blood case sample


title: genomic DNA from sample 340

description: whole blood case sample


title: E07B-3084368-H12C59-Necropsy-Spleen-20

tag: non human primate individual id


title: E07B-3084032-12C136-Necropsy-Spleen-20


title: genomic DNA from sample 163

description: whole blood control sample

tag: education level


title: E07B-3078803-H12c8-Necropsy-Spleen-20


title: genomic DNA from sample 174

description: whole blood case sample


title: E07B-3078467-11C131-Necropsy-Spleen-20


title: ler_T2h_1

city: Gif-sur-Yvette

first: Thomas

last: Blein

address: Avenue des Sciences

country: France

institute: CNRS

data_processing:
Genome_build: genome of Arabidopsis thaliana TAIR10
Mapping and counts of reads by locus gene (tophat2/bowtie2). If PE reads, count only consistent PE reads
Supplementary_files_format_and_content: type:count file (txt); content:gene ID,length of Gene,nb single reads,nb PE reads

growth_protocol: Media = MS/10 +P (KH2PO4 500µM) hygrometry = 33% humidity Temperature = 24°C day/ 21°c night Light = 16 hours day / 8 hours night

extract_protocol:
ler_T2h_1(10ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

treatment_protocol: Name:MS/10-P media 2h - time course study - compound addition,phosphate:time 2hour . Plants were sowed in line on nylon mesh (100µ) (about 150-200 seeds/line). The nylon mesh were put on a MS/10+P media. Seeds were synchronized 24h at 4°C obscurity then plates were transfered into phytotron (16hd/8hn, 24°C/21°C, 33%humidity). Plants were grown for 7 days. Then the nylon mesh with plants were transfered to a new MS/10+P media (for T0 time) or MS/10-P media (for T1h or T2h). Root apices (about 0.5cm) were harvested and frozen into liquide nitrogen. Plants were sowed in line on nylon mesh (100µ) (about 150-200 seeds/line). The nylon mesh were put on a MS/10+P media. Seeds were synchronized 24h at 4°C obscurity then plates were transfered into phytotron (16hd/8hn, 24°C/21°C, 33%humidity). Plants were grown for 7 days. Then the nylon mesh with plants were transfered to a new MS/10+P media (for T0 time) or MS/10-P media (for T1h or T2h). Root apices (about 0.5cm) were harvested and frozen into liquide nitrogen.

tag: time

tag: ecotype

value: Landsberg erecta

tag: genotype

value: wild type

tag: developmental stage

value: roots


title: ler_T2h_3

extract_protocol:
ler_T2h_3(10ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

treatment_protocol: Name:MS/10-P media 2h - time course study - compound addition,phosphate:time 2hour . Plants were sowed in line on nylon mesh (100µ) (about 150-200 seeds/line). The nylon mesh were put on a MS/10+P media. Seeds were synchronized 24h at 4°C obscurity then plates were transfered into phytotron (16hd/8hn, 24°C/21°C, 33%humidity). Plants were grown for 7 days. Then the nylon mesh with plants were transfered to a new MS/10+P media (for T0 time) or MS/10-P media (for T1h or T2h). Root apices (about 0.5cm) were harvested and frozen into liquide nitrogen. Plants were sowed in line on nylon mesh (100µ) (about 150-200 seeds/line). The nylon mesh were put on a MS/10+P media. Seeds were synchronized 24h at 4°C obscurity then plates were transfered into phytotron (16hd/8hn, 24°C/21°C, 33%humidity). Plants were grown for 7 days. Then the nylon mesh with plants were transfered to a new MS/10+P media (for T0 time) or MS/10-P media (T1h or T2h). Root apices (about 0.5cm) were harvested and frozen into liquide nitrogen.


title: healthy control [NC3]

tag: disease


title: ler_T2h_2

extract_protocol:
ler_T2h_2(10ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: genomic DNA from sample 425

description: whole blood case sample

tag: history of myocardial infarction

tag: Sex

value: F

tag: snp based principle component 1

tag: snp based principle component 2

value: whole blood


title: E07B-3101151-11C166-Necropsy-BoneMarrow-16

description:
Please note that the RNASeq data for this experiment was produced across three specimen types (venous whole blood (WB), bone marrow (BM), and spleen tissue (SP)) using RNAlater and PAXgene sample collection and storage technologies.  Please carefully review the two README files provided as supplementary files with this dataset for the details on the methods used for sequence generation and abundance measures.  README file names are as follows:  E07M99YSMfKnXXZZ_06062018-Readme_MULTIPL_GEO.txt  E07M99FGMfKnXXZZ_06292018-Readme_MULTIPL_GEO.txt  Please note that even though all file names indicate that the host is Macaca fascicularis, some (from NHP RAw8)  are derived from M. mulatta.
E07M99FGMfKnXXBM_Fascicularis-Genes-RawCounts-Results_MULTIPL_GEO.xlsx, E07M99FGMfKnXXBM_Knowlesi-Genes-RawCounts-Results_MULTIPL_GEO.xlsx

source_name: Bone Marrow

tag: collection time point (#) or necropsy

tag: gender

value: Bone Marrow


title: E07B-3111036-12C44-Necropsy-BoneMarrow-16


title: ler_T1h_2

extract_protocol:
ler_T1h_2(10ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

treatment_protocol: Name:MS/10-P media 1h - time course study - compound addition,phosphate:time 1hour . Plants were sowed in line on nylon mesh (100µ) (about 150-200 seeds/line). The nylon mesh were put on a MS/10+P media. Seeds were synchronized 24h at 4°C obscurity then plates were transfered into phytotron (16hd/8hn, 24°C/21°C, 33%humidity). Plants were grown for 7 days. Then the nylon mesh with plants were transfered to a new MS/10+P media (for T0 time) or MS/10-P media (for T1h or T2h). Root apices (about 0.5cm) were harvested and frozen into liquide nitrogen. Plants were sowed in line on nylon mesh (100µ) (about 150-200 seeds/line). The nylon mesh were put on a MS/10+P media. Seeds were synchronized 24h at 4°C obscurity then plates were transfered into phytotron (16hd/8hn, 24°C/21°C, 33%humidity). Plants were grown for 7 days. Then the nylon mesh with plants were transfered to a new MS/10+P media (for T0 time) or MS/10-P media (for T1h or T2h). Root apices (about 0.5cm) were harvested and frozen into liquide nitrogen.


title: E07B-3100815-12C53-Necropsy-BoneMarrow-16


title: genomic DNA from sample 457

description: whole blood control sample

tag: cellcount-nk

tag: cellcount-bcell

tag: cellcount-mono

tag: cellcount-gran


title: ler_T1h_3

extract_protocol:
ler_T1h_3(10ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

tag: tissue


title: E07B-3084246-H12C59-Necropsy-BoneMarrow-16

tag: non human primate individual id


title: genomic DNA from sample 259

description: whole blood control sample

tag: diagnosis

tag: education level

tag: age


title: ler_T1h_1

extract_protocol:
ler_T1h_1(10ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

tag: time

tag: ecotype

tag: genotype

tag: developmental stage


title: genomic DNA from sample 73

description: whole blood case sample

tag: history of myocardial infarction

tag: Sex

tag: snp based principle component 1


title: ler_T0_3

extract_protocol:
ler_T0_3(10ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

treatment_protocol: no treatment


title: E07B-3083910-12C136-Necropsy-BoneMarrow-16

tag: collection time point (#) or necropsy

tag: gender


title: ler_T0_2

extract_protocol:
ler_T0_2(10ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: Naïve fish

type: RNA

city: Incheon

first: Yunkyoung

last: Lee

address: Inha-ro 100

country: South Korea

institute: Inha University

description: Gene expression data from brain of zebrafish (L/D)

hyb_protocol: Approximately 5.5 µg/g of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45˚C for 16 hr.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC).

label: biotin

organism: Danio rerio

source_name: Adult zebrafish brain-L/D

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT using the GeneChip WT Terminal labeling kit.

growth_protocol: 6 months old adult zebrafish maintained at 28˚C. Water in the containers was aerated continuously and maintained at a pH between 6.5 and 7.5. The zebrafish were fed twice a day with flake food.

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

treatment_protocol: Naïve fish were maintained under a 14:10 light-dark cycle (light off at 22:00, light on at 8:00). For generating the SD model, zebrafish were exposed to extended light (24:0) for 3 days. We performed inhibitory avoidance learning for fear conditioning.

tag: stress

value: Control

value: Brain


title: Sleep-deprived fish

description: Gene expression data from brain of zebrafish (LD)-SD

source_name: Adult zebrafish brain-L/D-SD

value: Sleep deprivation


title: Learning-trained fish

description: Gene expression data from brain of zebrafish (L/D)-L

source_name: Adult zebrafish brain-L/D-L

value: Fear condition


title: genomic DNA from sample 440

description: whole blood control sample

value: M

tag: snp based principle component 2

tag: cellcount-nk

tag: cellcount-bcell

tag: cellcount-mono


title: genomic DNA from sample 185

description: whole blood case sample

tag: diagnosis

value: case

tag: cellcount-gran

tag: tissue


title: col_T2h_3

extract_protocol:
col_T2h_3(10ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

tag: time

value: Columbia


title: ler_T0_1

extract_protocol:
ler_T0_1(10ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

tag: ecotype


title: genomic DNA from sample 71

description: whole blood case sample

extract_protocol: genomic DNA was extracted using the Allprep mini kit (QIAGEN GmbH, Hilden, Germany) following the manufacturer’s instructions

tag: education level

tag: age


title: E07B-3078345-11C131-Necropsy-BoneMarrow-16

value: Necropsy

value: Male

tag: non human primate individual id


title: col_T2h_2

extract_protocol:
col_T2h_2(10ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

tag: genotype

tag: developmental stage


title: E07B-3102786-12C44-TimePoint07-BoneMarrow-16

extract_protocol:
Please note that the RNASeq data for this experiment was produced across three specimen types (venous whole blood (WB), bone marrow (BM), and spleen tissue (SP)) using RNAlater and PAXgene sample collection and storage technologies.  Please carefully review the two README files provided as supplementary files with this dataset for the details on the methods used for sequence generation and abundance measures.  README file names are as follows:  E07M99YSMfKnXXZZ_06062018-Readme_MULTIPL_GEO.txt  E07M99FGMfKnXXZZ_06292018-Readme_MULTIPL_GEO.txt
Approximately 1 μg of total RNA per sample was converted to double-stranded cDNA using poly-A beads to enrich for mRNA, and Illumina TruSeq Stranded mRNA Sample Prep kits to generate strand-specific libraries.   As a quality control, 92 spike-in RNAs of known concentration and GC proportions (ERCC Spike-In Control, Life Technologies) were added to constitute approximately 1% of the total RNA for each library.  Adapters were ligated to facilitate multiplexed sequencing on an Illumina HiSeq3000 at the Yerkes Genomics Core, aiming for 50 million paired-end 100 base pair (bp) reads per library.
RNA was extracted using Tempus-Spin RNA isolation kits. The quality of all RNA samples was confirmed using a Bioanalyzer, with an RNA Integrity Number (RIN) greater than 8 recorded for all samples."

tag: collection time point (#) or necropsy


title: genomic DNA from sample 219

description: whole blood control sample

value: control

tag: history of myocardial infarction

tag: Sex

tag: snp based principle component 1


title: E07B-3092101-11C166-TimePoint06-BoneMarrow-16

tag: gender


title: col_T2h_1

extract_protocol:
col_T2h_1(10ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: genomic DNA from sample 493

description: whole blood control sample

tag: snp based principle component 2

tag: cellcount-nk

tag: cellcount-bcell


title: E07B-3092002-12C44-TimePoint06-BoneMarrow-16


title: genomic DNA from sample 335

description: whole blood case sample

tag: diagnosis

tag: cellcount-mono

tag: cellcount-gran


title: E07B-3078681-H12c8-Necropsy-BoneMarrow-16

tag: tissue


title: E07B-3091903-12C53-TimePoint06-BoneMarrow-16


title: col_T1h_2

extract_protocol:
col_T1h_2(10ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

tag: time

tag: ecotype


title: E07B-3079493-H12C59-TimePoint05-BoneMarrow-20

tag: non human primate individual id


title: col_T1h_3

extract_protocol:
col_T1h_3(10ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

tag: genotype


title: INF + BZ + SIMV 4

city: Santiago

first: Christian

last: Castillo

state: Metropolitana

address: Independencia 1027

department: Faculty of medicine

country: Chile

institute: Universidad de Chile

description: Gene expression after 16 hrs seeding in M200 media, 24hrs incubation with Benznidazole/Simvastatin combination and 16 hrs infection in cell:parasite MOI 1:16

hyb_protocol: . Hybridization with SurePrint G3 Human GE 8x60K chips (Agilent Technologies) were performed for 17° at 60° C in an Agilent hybridization oven at 10 rpm. Agilent’s Low Input Quick Amp Labeling Kit instructions were followed for washing, stabilization and drying of microarray chips.

scan_protocol: Chips were scanned in an Agilent microarray scanner G256BA and data was collected with Agilent Feature Extraction (version 9.5.1) that was also used for quality control, data filtering and normalization.

data_processing: Data generated with microarray experiments were analyzed with GeneSpring GX 13 software.  Fold changes equal or superior to 2 and p≤0.05 were considered differentially expressed, ANOVA followed by Benjamini-Hochberg false discovery rate correction for multiple testing were used for statistical analysis.

source_name: HUVEC cells preincubated with benznidazole/simvastatin and T cruzi infected

label_protocol: From 200 ng of total RNA we generated cDNA by reverse-transcription, transcribed back to cRNA and generated cRNA labeled with Cy3 fluorescent probe according to Low Input Quick Amp-One Color Labeling Kit (Agilent Technologies). Total yield of Cy3-labeled cRNA was purified with Illustra RNAspin Mini Isolation kit (GE Healthcare) and Qubit RNA HS kit (ThermoFisher Scientific) was used for quantification

growth_protocol: Human umbilical vein endothelial cells (HUVEC) were maintained in cell culture media 200 supplemented with LSGS and FBS (2% v/v) (ThermoFisher Scientific).

extract_protocol: Total RNA was isolated with Total RNA Isolation mini-kit (Agilent Technologies) according to manufacturer instructions. RNA concentration and purity were quantified by spectrophotometry (NanoDrop 2000/2000c spectrophotometer), obtaining A260/A280 ratio purity values between 1.9 and 2.0. To assess RNA integrity, we performed microchip capillary electrophoresis (Bioanalyzer 2100, Agilent Technologies) in order to obtain RNA Integrity Number (RIN), where a RIN of 1 means a totally degraded RNA and a RIN of 10 a perfectly conserved RNA. RIN values for all samples where above 9.

treatment_protocol: 5x106 HUVEC cells were seeded in 75 cm2 multiwell plates for 24 hrs, then incubated for 24 hrs with Benznidazole (Bz) 20 µM, simvastatin (Simv) 5 µM, Aspirin (Asa) 125 uM, or Bz 10µM/Simv 1µM and Bz 10 µM / ASA 40 µM combinations.  After the incubation, media was removed, and cells were washed with sterile PBS in order to remove dead cell debris, after that, cells were infected with T. cruzi trypomastigotes (DM28 strain) at cell:parasite ratio on 1:10 for 16 hrs. Cells without parasites or pharmacological treatment were used as uninfected control

tag: cell type

value: Human umbilical vein endothelial cells


title: genomic DNA from sample 422

description: whole blood case sample

tag: education level

tag: age


title: E07B-3079394-11C166-TimePoint05-BoneMarrow-20

tag: collection time point (#) or necropsy


title: INF + BZ + SIMV 2

description: Gene expression after 16 hrs seeding in M200 media, 24hrs incubation with Benznidazole/Simvastatin combination and 16 hrs infection in cell:parasite MOI 1:14


title: genomic DNA from sample 403

description: whole blood control sample

tag: history of myocardial infarction

tag: Sex

tag: snp based principle component 1


title: genomic DNA from sample 420

description: whole blood case sample

tag: snp based principle component 2

tag: cellcount-nk


title: E07B-3079295-12C44-TimePoint05-BoneMarrow-20

tag: gender


title: INF + BZ + SIMV 3

description: Gene expression after 16 hrs seeding in M200 media, 24hrs incubation with Benznidazole/Simvastatin combination and 16 hrs infection in cell:parasite MOI 1:15


title: INF + BZ + SIMV 1

description: Gene expression after 16 hrs seeding in M200 media, 24hrs incubation with Benznidazole/Simvastatin combination and 16 hrs infection in cell:parasite MOI 1:13


title: col_T0_3

extract_protocol:
col_T0_3(10ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

tag: developmental stage


title: genomic DNA from sample 124

description: whole blood case sample

tag: diagnosis

tag: cellcount-bcell

tag: cellcount-mono

tag: cellcount-gran


title: col_T1h_1

extract_protocol:
col_T1h_1(10ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

tag: time

tag: ecotype

tag: tissue


title: INF + ASA + SIMV 3

description: Gene expression after 16 hrs seeding in M200 media, 24hrs incubation with Aspirin/Simvastatin combination and 16 hrs infection in cell:parasite MOI 1:12

source_name: HUVEC cells preincubated with aspirin/simvastatin and T cruzi infected

tag: cell type


title: INF + ASA + SIMV 1

description: Gene expression after 16 hrs seeding in M200 media, 24hrs incubation with Aspirin/Simvastatin combination and 16 hrs infection in cell:parasite MOI 1:10


title: INF + ASA + SIMV 2

description: Gene expression after 16 hrs seeding in M200 media, 24hrs incubation with Aspirin/Simvastatin combination and 16 hrs infection in cell:parasite MOI 1:11


title: col_T0_2

extract_protocol:
col_T0_2(10ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf

tag: genotype


title: col_T0_1

extract_protocol:
col_T0_1(10ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf


title: E07B-3079196-12C53-TimePoint05-BoneMarrow-20

tag: collection time point (#) or necropsy

tag: non human primate individual id


title: INF + ASA 2

description: Gene expression after 16 hrs seeding in M200 media, 24hrs incubation with Aspirin and 16 hrs infection in cell:parasite MOI 1:2

source_name: HUVEC cells preincubated with aspirin and T cruzi infected


title: INF + ASA 3

description: Gene expression after 16 hrs seeding in M200 media, 24hrs incubation with Aspirin and 16 hrs infection in cell:parasite MOI 1:3


title: genomic DNA from sample 349

description: whole blood control sample

source_name: whole blood

tag: education level

tag: history of myocardial infarction

tag: age

tag: Sex


title: genomic DNA from sample 359

description: whole blood case sample

tag: snp based principle component 1

tag: snp based principle component 2

tag: cellcount-nk


title: INF + ASA 1

description: Gene expression after 16 hrs seeding in M200 media, 24hrs incubation with Aspirin and 16 hrs infection in cell:parasite MOI 1:1


title: E07B-3078076-H12C59-TimePoint04-BoneMarrow-20

tag: gender


title: INF + SIMV 4

description: Gene expression after 16 hrs seeding in M200 media, 24hrs incubation with Simvastatin and 16 hrs infection in cell:parasite MOI 1:10

source_name: HUVEC cells preincubated with simvastatin and T cruzi infected


title: E07B-3079097-12C136-TimePoint05-BoneMarrow-20


title: genomic DNA from sample 262

description: whole blood control sample

tag: diagnosis

tag: cellcount-bcell

tag: cellcount-mono


title: INF + SIMV 3


title: INF + SIMV 1


title: genomic DNA from sample 74

description: whole blood case sample

tag: cellcount-gran


title: genomic DNA from sample 279

description: whole blood case sample

tag: tissue


title: INF + SIMV 2

tag: cell type


title: INF + BZ 4

description: Gene expression after 16 hrs seeding in M200 media, 24hrs incubation with Benznidazole and 16 hrs infection in cell:parasite MOI 1:10

source_name: HUVEC cells preincubated with benznidazole and T cruzi infected


title: E07B-3077878-11C166-TimePoint04-BoneMarrow-20


title: genomic DNA from sample 396

description: whole blood control sample


title: E07B-3077680-12C53-TimePoint04-BoneMarrow-20


title: E07B-3077779-12C44-TimePoint04-BoneMarrow-20


title: genomic DNA from sample 35

description: whole blood case sample


title: E07B-3077581-12C136-TimePoint04-BoneMarrow-20


title: E07B-3077977-H12c8-TimePoint04-BoneMarrow-20


title: genomic DNA from sample 153

description: whole blood control sample


title: INF + BZ 3


title: BJ/hTERT LT/ST HRAS cells, rep1

city: udine

first: raffaella

last: picco

address: piazzale kolbe 4

department: department of medical and biological sciences

country: Italy

institute: university of Udine

hyb_protocol: Labeled cRNA was hybridized on Affymetrix Clariom S Human array

scan_protocol: Scanning was performed using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data processing was performed with BioConductor packages (http://www.bioconductor.org/). Robust Multi-Array Average (RMA) normalization was applied. Normalized intensity values for all probes on the Affymetrix chip are presented in the Matrix table. Data analysis was performed using the moderated t-test as implemented in the limma package. P values were adjusted for multiple testing using the False Discovery Rate method.

source_name: BJ/hTERT LT/ST HRAS

label_protocol: RNA samples were labeled according to the standard one-cycle amplification and labeling protocol (Affymetrix, Santa Clara, CA).

growth_protocol: BJ/TERT cells were cultured in Earle’s salts minimal essential medium (EMEM) (Euroclone) completed with nonessential amino acids (HyClone).  Media was supplemented with 10% fetal bovine serum (FBS), L-glutamine (2mM), penicillin (100U/ml), and streptomycin (100µg/ml) (Lonza)

extract_protocol: Total RNA was isolated using Direct-zol RNA mini prep (Zymo Research). RNA samples concentration and purity (assessed as 260/280 nm and 260/230 nm ratios) were evaluated by NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies; Wilmington, DE), while RNA integrity was assessed by using the Agilent 2100 Bioanalyzer (Agilent Technologies; Waldbrunn, Germany).

value: human fibroblasts


title: BJ/hTERT LT/ST HRAS cells, rep2


title: INF + BZ 1


title: INF 2

description: Gene expression after 16 hrs seeding in M200 media and 16 hrs infection in cell:parasite MOI 1:10

source_name: HUVEC Infected cells with T cruzi


title: INF + BZ 2


title: genomic DNA from sample 469

description: whole blood case sample


title: E07B-3077482-11C131-TimePoint04-BoneMarrow-20

description:
Please note that the RNASeq data for this experiment was produced across three specimen types (venous whole blood (WB), bone marrow (BM), and spleen tissue (SP)) using RNAlater and PAXgene sample collection and storage technologies.  Please carefully review the two README files provided as supplementary files with this dataset for the details on the methods used for sequence generation and abundance measures.  README file names are as follows:  E07M99YSMfKnXXZZ_06062018-Readme_MULTIPL_GEO.txt  E07M99FGMfKnXXZZ_06292018-Readme_MULTIPL_GEO.txt  Please note that even though all file names indicate that the host is Macaca fascicularis, some (from NHP RAw8)  are derived from M. mulatta.
E07M99FGMfKnXXBM_Fascicularis-Genes-RawCounts-Results_MULTIPL_GEO.xlsx, E07M99FGMfKnXXBM_Knowlesi-Genes-RawCounts-Results_MULTIPL_GEO.xlsx


title: CTRL 3

description: Gene expression after 16 hrs seeding in M200 media

source_name: HUVEC uninfected cells


title: CTRL 2


title: BJ/hTERT LT/ST HDAC4 TM cells, rep2

source_name: BJ/hTERT LT/ST HDAC4 TM


title: BJ/hTERT LT/ST HDAC4 TM cells, rep1


title: genomic DNA from sample 99

description: whole blood case sample


title: E07B-3069406-H12C59-TimePoint03-BoneMarrow-16


title: E07B-3069307-H12c8-TimePoint03-BoneMarrow-16


title: S19_up_mem_1

city: Novosibirsk

first: Marsel

last: Kabilov

address: Lavrentyev av. 8

country: Russia

institute: ICBFM SB RAS

description: cross-linked RNA

data_processing:
bcl2fastq v2.20.0.422
demultiplexing by CEL-Seq script (Hashimshony T, 2016. doi: 10.1186/s13059-016-0938-8)
Adapter and low-quality sequences were removed using TrimGalore v.0.5.0
Read mapping was performed against the Ensembl annotated human genome (GRCh38.93) with STAR v.2.6.1
BAM deduplication by unique molecular indexes was carried out with “dedup” script from UMI-tools (Smith T, 2017, doi: 10.1101/gr.209601.116).
Transitions (T/C for plus DNA stands and A/G for minus DNA strands) were found by Basic Variant Detection in CLC GW v.12.0 software (Qiagen) with parameters: minimum coverage, 5; minimum count, 1; minimum frequency, 1%.
Genomic coordinates of T/C (A/G) transitions were annotated using R custom script and Homo_sapiens.GRCh38.93.gtf as an annotation source (www.ensembl.org/info/data/ftp). Only CDS related T/C-transition coordinates were remained for downstream analysis. For each CDS contatning T/C-transitions the coverage (nucleotide resolution) were calculated utilizing R Bioconductor CoverageView package (v 1.20.0) and bam file as well as Homo_sapiens.GRCh38.93.gtf  as an input. Peaks were found using R Bioconductor chipseq package (v 1.32.0) and coverage vector for each CDS generated by CoverageView as an input. Resulting peaks coordinates were matched with T/C-transition coordinates using R custom script. Data on T/C-transition containing peaks was recorded to bed file.
Human CDS and proteins sequences were uploaded from www.ensembl.org/info/data/ftp and were used for extracted peak subsequences falling between -19 to +19 triplets from the main (with the highest parameter of transition freq*position coverage)T/C-transition . These subsequences were used for LOGO creation utilizing Weblogo tool (https://weblogo.berkeley.edu/)
The amino acid sequences were scanned for the presence of any of the (E/K)12 motifs using the R Bioconductor Biostrings package (v2.50.1) with the vcount-Pattern function with the max.mismatch parameter equal to 4 and other parameters default.
Genome_build: Ensembl annotated human genome (GRCh38.93)
Supplementary_files_format_and_content: BED file with coordinates of peaks
Supplementary_files_format_and_content: VCF file with T/C and A/G transitions

source_name: Cell culture

growth_protocol: Adherent pAG-1(FLAG-uS19)-derivatized HEK293 cells in 15-cm Petri dishes were cultured in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% FBS and 100 U/ml of Penicillin-Streptomycin  in CO2-incubator (5% CO2) at 37°C

extract_protocol:
The cell lysate was clarified by centrifugation, treated by RNase I, cross-linked RNA-uS19 complexes were isolated by anti-FLAG-M2 antibodies with subsequent purification by PAGE-SDS electrophoresis followed by transfer onto nitrocellulose membrane. RNA fragments were recovered by proteinase K treatment followed by phenol-chloroform extraction.
DNA libraries were prepared according to (Kargapolova Y, 2017, doi: 10.1093/nar/gkx152)

treatment_protocol: At 60-70 % confluency, the production of FLAG-uS19 in cells was induced with DOX (2 μg/ml) and after 44 h, s4U was added to 250 μM. After 6 h, cycloheximide was added to a concentration of 100 μg/ml and the cells were kept on ice for 10 min, followed by washing with ice-cold PBS. Cross-linking was performed by irradiation of the cells with UV light at 365 nm (0.5 J/cm2) in Bio-Link (Vilber Lourmat) on ice.

value: Human embryonic kidney

tag: cell line


title: S19_up_mem_3

description: cross-linked RNA


title: E07B-3069208-11C166-TimePoint03-BoneMarrow-16

tag: collection time point (#) or necropsy


title: INF 1


title: genomic DNA from sample 31

description: whole blood case sample


title: genomic DNA from sample 325

description: whole blood case sample


title: CTRL 1


title: S19_down_mem_3

description: cross-linked RNA


title: IPECJ2_Scenedesmus and Chlorella-ETEC_6 hours_replica 2

city: Lelystad

first: Marcel

last: Hulst

state: Flevoland

address: Edelhertweg 15

department: Livestock research

country: Netherlands

institute: Animal Sciences Group

description: Gene expression analysis after 6 hours of incubation in IPECJ2 cells

hyb_protocol: Hybridization was performed as described in the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labeling protocol from Agilent in the hybridization oven (G2545A hybridization Oven Agilent Technologies) The hybridization temperature was 65°C with rotation speed 10 rpm for 17 hours. After 17 hours the arrays were washed as described in the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling protocol from Agilent.

scan_protocol: Agilent microarray slides (G2519F Sus scrofa Agilent-035953, costumized in situ oligonucleotide array printed in 8 patches of 60K) harbouring 43,803 probes, were used and scanned using the DNA microarray scanner with Surescan high resolution Technology (Agilent Technologies). Agilent Scan Control with resolution of 5µ, 16 bits and PMT of 100%.

data_processing: Feature extraction was performed using protocol 10.7.3.1 (v10.7) for 1 colour gene expression. Background substracted signal intensity (gBGSubSigna) in the Metadata sheet are provided for all probes (ID-REF) on the array.

organism: Sus scrofa

source_name: IPECJ2_AM extract and ETEC challenge_6 hours incubation

label_protocol: Labelling was done as recommended by Agilent Technologies using the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labeling. 500 ng RNA of each sample was amplified and labelled with the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling kit and 600 ng of Cy3 labelled cRNA was used for hybridisation on each patch.

extract_protocol: Total RNA was isolated from IPECJ2 monolayers with TRIzol® reagent (Invitrogen) and treated with DNase. The RNA was further purified using QIAamp MinElute Virus Spin Kit columns (Qiagen, Venlo, the Netherlands) according to the manufacturers’ instructions.

value: IPECJ2 cultured cells

tag: protocol

value: AM extract and ETEC challenge

tag: time point

value: 6 hours


title: BJ/hTERT LT/ST HYGRO cells, rep2

source_name: BJ/hTERT LT/ST HYGRO


title: genomic DNA from sample 258

description: whole blood control sample

tag: education level

tag: history of myocardial infarction

value: whole blood


title: IPECJ2_Scenedesmus and Chlorella-ETEC_6 hours_replica 1


title: E07B-3069010-12C53-TimePoint03-BoneMarrow-16

source_name: Bone Marrow

tag: non human primate individual id

value: Bone Marrow


title: S19_down_mem_2

description: cross-linked RNA


title: E07B-3069109-12C44-TimePoint03-BoneMarrow-16


title: S19_down_mem_1

description: cross-linked RNA


title: E07B-3068911-12C136-TimePoint03-BoneMarrow-16


title: S19_up_mem_2

description: cross-linked RNA


title: IPECJ2_Scenedesmus and Chlorella_6 hours_replica 1

source_name: IPECJ2_AM extract challenge_6 hours incubation

value: AM extract challenge


title: BJ/hTERT LT/ST HYGRO cells, rep1


title: genomic DNA from sample 152

description: whole blood control sample

tag: age

tag: Sex

value: F

tag: snp based principle component 1


title: IPECJ2_Scenedesmus and Chlorella_6 hours_replica 2


title: IPECJ2_Spirulina-ETEC_6 hours_replica 2

source_name: IPECJ2_S extract and ETEC challenge_6 hours incubation

value: S extract and ETEC challenge


title: WT6

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

description: total RNA in muscle tissue containing  Schwann cells

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using STAR aligner with the default settings
Reads counts for each gene were generated and were further used to compute the rpkm values
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Mus musculus

source_name: Diaphragm muscle

growth_protocol: Timed pregnancie, sacrificed at specific time

extract_protocol:
For Wnt1-Cre, ribotag samples, polysome IP with anti-hemagluttinin antibodies
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Specific genotypes confirmed by PCR

value: embryo

tag: genotype/variation

value: erbB3 WT


title: E07B-3068812-11C131-TimePoint03-BoneMarrow-16

tag: gender


title: genomic DNA from sample 4

description: whole blood case sample

tag: diagnosis

value: case

tag: snp based principle component 2

tag: cellcount-nk

tag: cellcount-bcell


title: IPECJ2_Spirulina-ETEC_6 hours_replica 1


title: genomic DNA from sample 167

description: whole blood control sample

value: M

tag: cellcount-mono

tag: cellcount-gran

tag: tissue


title: WT5


title: genomic DNA from sample 344

description: whole blood case sample


title: TOM1

description:
Ribosome IP'd RNA
Schwann cell-specific RNA in muscle containing Schwann cells

value: Wnt1-Cre, Ribotag, erbB3 WT

tag: antibody

value: anti-hemagluttinin


title: E07B-3059538-H12C59-TimePoint02-BoneMarrow-16

tag: collection time point (#) or necropsy

value: Male


title: IPECJ2_Spirulina-ETEC_2 hours_replica 1

description: Gene expression analysis after 2 hours of incubation in IPECJ2 cells

source_name: IPECJ2_S extract and ETEC challenge_2 hours incubation

tag: cell line

tag: protocol

tag: time point

value: 2 hours


title: genomic DNA from sample 530

description: whole blood case sample

tag: education level

tag: history of myocardial infarction

tag: age


title: E07B-3059340-11C166-TimePoint02-BoneMarrow-16

tag: non human primate individual id


title: E07B-3059439-H12c8-TimePoint02-BoneMarrow-16

tag: gender


title: genomic DNA from sample 526

description: whole blood case sample

tag: diagnosis

tag: Sex

tag: snp based principle component 1


title: KO2

description: total RNA in muscle tissue lacking Schwann cells

tag: genotype/variation

value: erbB3 KO


title: KO1


title: IPECJ2_Spirulina-ETEC_2 hours_replica 2

value: IPECJ2 cultured cells


title: genomic DNA from sample 278

description: whole blood control sample

value: control

tag: snp based principle component 2

tag: cellcount-nk

tag: cellcount-bcell

tag: cellcount-mono


title: E07B-3059241-12C44-TimePoint02-BoneMarrow-16

tag: collection time point (#) or necropsy

tag: tissue


title: E07B-3059142-12C53-TimePoint02-BoneMarrow-16


title: IPECJ2_Spirulina_6 hours_replica 2

source_name: IPECJ2_S extract challenge_6 hours incubation

tag: cell line

tag: protocol

value: S extract challenge

value: 6 hours


title: IPECJ2_Spirulina_6 hours_replica 1

tag: time point


title: IPECJ2_Spirulina_2 hours_replica 1

source_name: IPECJ2_S extract challenge_2 hours incubation


title: E07B-3059043-12C136-TimePoint02-BoneMarrow-16

value: Bone Marrow


title: TOM2

tag: antibody


title: e_sgDnmt1_e4

city: New York

first: Craig

last: Thompson

state: NY

address: 411 East 67th Street RRL 469

institute: Memorial Sloan Kettering Cancer Center

data_processing:
FASTQ files were processed as follows: Adapter sequences (Illumina TruSeq, “AGATCGAAGAGAC”) were hard-clipped from raw paired-end FASTQ’s using Trim Galore v0.4.4 (https://github.com/FelixKrueger/TrimGalore). Resulting reads were then aligned with default parameters for bwa-meth (https://github.com/brentp/bwa-meth) to a reference genome comprised of concatenated mm10, pUC19, and Lambda sequences with the exception of inclusion of the “bwa mem -Y” flag and flagging of QC-failed reads (0x200 flag) when alignment length was less than 0.2 x read-length. Aligned BAM’s were split into separate mm10, pUC19, or BAM’s for downstream analysis. These split BAM’s are duplicate marked using Picard v2.8.0 (http://broadinstitute.github.io/picard). Methylation genotyping was performed on each using MethylDackel v0.1.13 (https://github.com/dpryan79/MethylDackel).
Genome_build: mm10

source_name: CD4+CD8- T cells

growth_protocol: Naïve CD8+ T cells were isolated from spleen and lymph nodes of C57BL/6J mice by cell sorting (CD8+CD4-CD62L+CD44-CD25-) and cultured in T cell media (RPMI, 10% FBS, 4mM glutamine, 50uM BME, 20mM HEPES, 100U/mL human IL-2) for 7 days

extract_protocol:
T cells were sorted based on CD8 and CD4 expression after 5 additional days of culture.
DNA was isolated from T cells using phenol-chloroform extraction. For each sample, 100ng input of DNA was sheared with a Covaris LE220 instrument aiming for 450bp fragments. Sheared DNA was prepared with an EM-Seq kit (NEB) following the manufacturer’s instructions. Briefly, the treatment includes a TET2-mediated oxidation of 5mCs to 5hmCs. This is followed by APOBEC cytosine deaminase treatment, resulting in conversion of unmethylated cytosines to uracil and their appearance as thymidines in the final sequencing data. Methylated and hydroxy methylated cytosines are indistinguishable from each other and are present as cytosines in the sequencing data. Unmethylated (Lambda) and fully CpG methylated (pUC19) DNA were spiked into each sample and used as internal control for conversion efficiencies. The final sequencing libraries were amplified with 4 Cycles of PCR and libraries were sequenced on Illumina HiSeqX targeting 30X coverage per sample.

treatment_protocol: Immediately after sorting, T cells were electroporated with indicated sgRNAs and then activated in T cell media containing anti-CD3 and anti-CD28 (see methods for more details).

tag: cell type

tag: strain

value: CD8+ T cells

tag: phenotype


title: e_sgOlfr2_e2


title: IPECJ2_Haematococcus-ETEC_6 hours_replica 1

source_name: IPECJ2_H extract and ETEC challenge_6 hours incubation

value: H extract and ETEC challenge


title: E07A-3026589-H12C59-TimePoint02-BoneMarrow-16

tag: gender

tag: non human primate individual id


title: E07A-3026393-11C166-TimePoint02-BoneMarrow-16


title: TFAM overexpression, ATF4 RNAi rep 4

city: London

first: Joseph

middle: Matthew

last: Bateman

address: Cutcombe Road

department: Basic & Clinical Neuroscience

country: United Kingdom

institute: King's College London

data_processing:
Illumina NextSeq 500 RTA v2 used for base calling.
Adaptors were automatically trimmed from the reads by the NextSeq 500, but a check for residual untrimmed adaptors was performed by FastQC (Galaxy Version 0.52), accessed via the user interface software Galaxy (UseGalaxy.org). RNA reads were then aligned to the dm6 genome using Bowtie2 (Galaxy Version 2.3.4.2) with default settings.
Raw fragment counts were compiled by FeatureCounts (Galaxy Version 1.6.3+galaxy2), accessed via the user interface software Galaxy (UseGalaxy.org), with default settings.
Differential gene expression was assessed via DESeq2 (Galaxy Version 2.11.40.6), accessed via UseGalaxy.org, with default settings.
Genome_build: dm6
Supplementary_files_format_and_content: Excel spreadsheets containing base means, log2(fold change), fold changes, standard errors, Wald statistics, p-values and adjusted p-values for each pair of samples.

organism: Drosophila melanogaster

source_name: Central nervous system

growth_protocol: Larvae were grown on standard fly food at 25 degrees celsius.

extract_protocol:
For each replicate, the complete CNS from 20 wandering third instar larvae were dissected in PBS and then transferred into 100ul of lysis buffer (with β-mercaptoethanol) from the Absolutely RNA Microprep kit (Stratagene) and vortexed for 5 seconds. Total RNA was then prepared using this kit. For each genotype RNA samples were prepared in quadruplicate and stored at -80 degrees celsius.
RNA samples were couriered on dry ice to the Glasgow Polyomics facility (University of Glasgow), where polyA cDNA libraries were constructed using the TruSeq Stranded mRNA Kit (Illumina).

treatment_protocol: One control and two experimental genotypes were used: Control (nsybGal4/+), Experimental group 1: TFAM3M (nsybGal4>UAS-TFAM3M), Experimental group 2: TFAM3M, ATF4 RNAi (nsybGal4>UAS-TFAM3M, UAS-ATF4 RNAi).

value: Central nervous system

tag: developmental stage

value: Late third instar larvae

value: TFAM overexpression, ATF4 RNAi


title: TFAM overexpression, ATF4 RNAi rep 3

tag: genotype/variation


title: e_sgDnmt3a_e19

source_name: CD8+CD4+ T cells


title: E07A-3026491-H12c8-TimePoint02-BoneMarrow-16


title: TFAM overexpression rep 4

value: TFAM overexpression


title: TFAM overexpression, ATF4 RNAi rep 2


title: TFAM overexpression, ATF4 RNAi rep 1


title: E07A-3026080-12C53-TimePoint02-BoneMarrow-16


title: E07A-3025982-12C136-TimePoint02-BoneMarrow-16


title: E07B-3058944-11C131-TimePoint02-BoneMarrow-16


title: TFAM overexpression rep 3


title: TFAM overexpression rep 2


title: IPECJ2_Haematococcus-ETEC_2 hours_replica 1

source_name: IPECJ2_H extract and ETEC challenge_2 hours incubation


title: IPECJ2_Haematococcus_2 hours_replica 2

source_name: IPECJ2_H extract challenge_2 hours incubation

value: H extract challenge


title: IPECJ2_Haematococcus-ETEC_6 hours_replica 2


title: IPECJ2_Haematococcus-ETEC_2 hours_replica 2


title: IPECJ2_Haematococcus_6 hours_replica 2

source_name: IPECJ2_H extract challenge_6 hours incubation


title: E07A-3022821-H12C59-TimePoint01-BoneMarrow-16


title: E07A-3025884-11C131-TimePoint02-BoneMarrow-16


title: IPECJ2_Chlorella-ETEC_6 hours_replica 2

source_name: IPECJ2_C extract and ETEC challenge_6 hours incubation

value: C extract and ETEC challenge


title: TFAM overexpression rep 1


title: IPECJ2_Chlorella-ETEC_6 hours_replica 1


title: E07A-3026295-12C44-TimePoint02-BoneMarrow-16


title: IPECJ2_Chlorella-ETEC_2 hours_replica 2

source_name: IPECJ2_C extract and ETEC challenge_2 hours incubation


title: Control rep 4

value: Control


title: IPECJ2_Haematococcus_6 hours_replica 1


title: Control rep 3


title: Control rep 2


title: IPECJ2_Haematococcus_2 hours_replica 1


title: IPECJ2_Chlorella-ETEC_2 hours_replica 1


title: E07A-3022627-11C166-TimePoint01-BoneMarrow-16

value: Male


title: IPECJ2_Chlorella_6 hours_replica 2

source_name: IPECJ2_C extract challenge_6 hours incubation

value: C extract challenge


title: Control rep 1


title: E07A-3017399-12C53-TimePoint01-BoneMarrow-16

source_name: Bone Marrow


title: E07A-3022724-H12c8-TimePoint01-BoneMarrow-16


title: IPECJ2_Chlorella_6 hours_replica 1


title: E07A-3017302-12C136-TimePoint01-BoneMarrow-16


title: E07A-3017205-11C131-TimePoint01-BoneMarrow-16


title: E07B-3077369-RAw8-TimePoint04-WholeBlood-24

description:
Please note that the RNASeq data for this experiment was produced across three specimen types (venous whole blood (WB), bone marrow (BM), and spleen tissue (SP)) using RNAlater and PAXgene sample collection and storage technologies.  Please carefully review the two README files provided as supplementary files with this dataset for the details on the methods used for sequence generation and abundance measures.  README file names are as follows:  E07M99YSMfKnXXZZ_06062018-Readme_MULTIPL_GEO.txt  E07M99FGMfKnXXZZ_06292018-Readme_MULTIPL_GEO.txt  Please note that even though all file names indicate that the host is Macaca fascicularis, some (from NHP RAw8)  are derived from M. mulatta.
E07M99FGMfKnXXWB_Fascicularis-Genes-RawCounts-Results_MULTIPL_GEO.xlsx, E07M99FGMfKnXXWB_Knowlesi-Genes-RawCounts-Results_MULTIPL_GEO.xlsx

organism:
Plasmodium knowlesi
Macaca mulatta

source_name: Whole blood

value: Whole blood


title: E07B-3068699-RAw8-TimePoint03-WholeBlood-20


title: IPECJ2_Chlorella_2 hours_replica 2

source_name: IPECJ2_C extract challenge_2 hours incubation

value: IPECJ2 cultured cells

value: 2 hours


title: E07A-3022530-12C44-TimePoint01-BoneMarrow-16


title: IPECJ2_Chlorella_2 hours_replica 1


title: E07B-3058831-RAw8-TimePoint02-WholeBlood-20


title: IPECJ2_ETEC_6 hours_replica 2

source_name: IPECJ2_ETEC challenge_6 hours incubation

value: ETEC challenge


title: E07B-3077383-RAw8-TimePoint04-BoneMarrow-20


title: E07B-3068713-RAw8-TimePoint03-BoneMarrow-16


title: IPECJ2_ETEC_2 hours_replica 2

source_name: IPECJ2_ETEC challenge_2 hours incubation


title: E07B-3058845-RAw8-TimePoint02-BoneMarrow-16


title: AF_RA_31

status: Public on Mar 13 2019

first: Alison

last: Thomas

state: London

address: WHRI, Charterhouse Square

institute: Dr

data_processing:
Sequencing read quality was accessed using FastQC (version 0.11.2). Followed by trimming for adaptor sequences and poor quality reads using Trim Galore (version 0.3.7).
Trimmed sequences were aligned to the human reference genome (GRCh37) using TopHat2 (version 2.0.13) and bowtie2 (version 2.2.3) as backend.
Transcript abundance was then calculated using HTSeq-counts software (version 0.6.0).
Differential expression analysis was investigated using edgeR (version_3.8.6).
Genome_build: GRCh37
Supplementary_files_format_and_content: tab delimited text files of HTSeq-counts showing raw counts per sample

source_name: right atrial appendage

extract_protocol:
RNA was extracted from each sample using QIAGEN Rneasy Mini kit with DnaseI treatment.
Libraries were generated using TruSeq Stranded Total RNA library prep with RiboZero (Illumina, Cat No:RS-122-2203).

treatment_protocol: During surgery a section of atrial appendage was removed and immediately immersed in RNAlater.

value: atrial appendage

tag: Sex


title: AF_LA_31

source_name: left atrial appendage


title: AF_RA_28


title: IPECJ2_ETEC_2 hours_replica 1


title: AF_LA_25


title: AF_LA_28


title: AF_RA_25


title: IPECJ2_ETEC_6 hours_replica 1

value: 6 hours


title: Sep10_1_1_3dpf_gpr124MUTvsWT_(1)

city: Gosselies

first: Raoul

last: Germano

address: 12, rue des Profs. Jeener et Brachet

department: Institute of Molecular Biology and Medicine

country: Belgium

institute: Free University of Brussels

description: Biological replicate 1 of 2, 3dpf total ECs CNS vascular mutant versus total ECs WT

hyb_protocol: Scanned on an Agilent G2565AA scanner

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1 & 10.10.1.1 for arrays Sep09 and Sep10 respectively).

data_processing: Agilent Feature Extraction Software ((version 10.7.3.1 & 10.10.1.1 for arrays of Sep09 and Sep10 respectively) was used for background subtraction and linear Lowess normalization.

source_name: zebrafish larvae

label_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

growth_protocol: Zebrafish were maintained and handled at standard conditions (Westerfield 2007), 3dpf corresponds to larvae at 72 hours post fertilization grown at 28dgr, transgenic line used is Tg(kdrl:GFP), mutant strain is gpr124s984 (Vanhollebeke et al_elife_2015)

extract_protocol: 50ng of total RNA was amplified and labeled using Agilent Low Input Quick Amp Labeling Kit

treatment_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: strain/genotype

value: AB;Tg(kdrl:GFP), gpr124s984-/-

value: ECs, gpr124 mutants

value: AB;Tg(kdrl:GFP), gpr124s984+/+

value: ECs, wt


title: AF_RA_14


title: AF_LA_5


title: IPECJ2_Spirulina_2 hours_replica 2

source_name: IPECJ2_S extract challenge_2 hours incubation

value: S extract challenge


title: Sep09_1_3_adultBrainvsLiver_(1)

description: Biological replicate 1 of 2, adult brain ECs versus liver ECs

source_name: zebrafish adult

value: 6 mpf

value: Brain ECs

value: liver ECs


title: Sep10_1_3_3dpf_ECvsP_(2)

description: Biological replicate 2 of 2, 3dpf total Ecs versus total ECs WT

value: total ECs

value: non-ECs (periphery)


title: Sep10_1_4_3dpf_gpr124mutvsWT_(2)

description: Biological replicate 2 of 2, 3dpf total ECs CNS vascular mutant versus total ECs WT


title: IPECJ2_control medium_2 hours_replica 1

source_name: IPECJ2_no challenge_2 hours incubation

value: no challenge


title: Sep10_1_2_3dpf_ECvsP_(1)

description: Biological replicate 1 of 2, 3dpf total Ecs versus total ECs WT


title: IPECJ2_control medium_2 hours_replica 2


title: AF_LA_14

value: Male


title: Sep09_1_4_AdultBrainvsLiver_(2)

description: Biological replicate 2 of 2, adult brain ECs versus liver negative ECs


title: SR_RA_27


title: AF_RA_5


title: IPECJ2_control medium_6 hours_replica 2

source_name: IPECJ2_no challenge_6 hours incubation

value: IPECJ2 cultured cells


title: SR_LA_30


title: Sep09_1_2_DAPIposvsneg_(2)

description: Biological replicate 2 of 2, 3dpf  DAPI positive ECs versus DAPI negative ECs

value: DAPI positive ECs

value: DAPI negative ECs


title: IPECJ2_control medium_6 hours_replica 1


title: SR_LA_20

value: atrial appendage


title: SR_RA_20


title: SR_RA_30


title: SR_RA_12b


title: SR_LA_7


title: SR_LA_12b


title: SR_RA_7