title: LSC0018_Bl_CD34pCD38m


title: hEST_N_11_18_hEST_N_11.Thalidomide.6

status: Public on May 03 2022

type: SRA

city: Basel

first: Jitao David

last: Zhang

address: Grenzacherstrasse 124

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

country: Switzerland

institute: F. Hoffmann-La Roche

library_source: transcriptomic

data_processing:
Base-calling was performed with Illumina NovaSeq 6000 Sequencing System.
Alignment was performed with Bowtie2 (2.3.5)
Quantification of amplicon-mapping reads was performed with BEDtools (2.29.2)
QC and filtering was performed with BioQC (1.20.0), ribiosExpression (1.1.9), and ribiosNGS (1.1.30), as well as custom software.
Factor analysis was performed with R (4.0.1) and the psych package (2.1.6)
Differential gene expression was performed with edgeR (3.34.0)
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements are tab-delimited files, containing genes and number of reads mapped to the pre-defined amplicons; raw counts are in the GCT (version 1.2) file, a tab-delimited format of aggregated gene counts.

molecule: total RNA

organism: Homo sapiens

source_name: Human induced pluripotent-stem-cell derived embryoid body

growth_protocol: The cells were passaged twice a week with a defined cell number of 2.4 × 104 cells/cm2 (three-day culture) or 1.2 × 104 cells/cm2 (four-day culture) to achieve a maximum confluence of 80%. The medium was removed and the cells were detached with StemPro Accutase™ Cell Dissociation Reagent (Thermo Fisher Scientific) for five minutes at 37°C/ 5% CO2. Cell detachment was stopped by adding StemFlex™ Medium (Thermo Fisher Scientific) to the detached cells, followed by centrifugation for five minutes at 240 × g. Afterwards, the cell pellet was gently suspended in culture medium and the cells were seeded into Geltrex™ coated culture flasks with complete StemFlex™ (containing 10% StemFlex™ Supplement and 1% RevitaCell™). StemFlex™ w/o RevitaCell™ replaced the medium completely the day after cell propagation. The cells were cultured throughout in a humidified incubator (Binder, Germany) at 37°C and 5% CO2.

extract_protocol:
Differentiated EBs were lysed after 7 days of differentiation in 350 μl MagNA Pure LC RNA Buffer (Roche Diagnostics) and purified by using the automated MagNA Pure 96 system (Roche Diagnostics).
The total RNA was quantified using the Qubit RNA Assay Kit (Thermo Fisher) on the Fluorometer Glomax (Promega). Total RNA with a maximum of 10 ng from each biological replicate was reverse transcribed to cDNA using Superscript IV Vilo (Thermo Fisher). Libraries were generated with the AmpliSeq Library Plus Kit (Illumina) according to the reference guide. Pipetting steps for target amplification, primer digestion, and adapter ligation were done with the mosquito automatic pipettor (SPT Labtech) in miniaturization. For the purifications before and after final library amplification, solid phase reversible immobilization magnetic bead purification (Clean NGS, LABGENE Scientific SA) was performed on the multidrop automated pipetting station (Thermo Fisher). We measured both amplicon sizes and cDNA concentrations using an Agilent High Sensitivity DNA Kit (Agilent Technologies) according to the manufacturer’s recommendation. Prior to sequencing, cDNA contents of the samples were normalized and pooled to 2 nM final concentration on Biomek FXP workstation.
RNA-Seq (Amplicon-based molecular phenotyping)

treatment_protocol: To start, human induced pluripotent stem cells (hiPSC) are seeded at a density of 120000 cells per well in 96-well microwell plates. They form homogenous embryoid bodies (EBs) which are spontaneously differentiated over 7 days. Compounds are added as six-point concentration range on day 0, day 3 and day 5. Single wells containing about 70 differentiated EBs are lysed to generate one sample for the viability assay and gene expression profiling.

tag: cell type

tag: run

tag: plate

value: Thalidomide

tag: usedforfactoranalysis

value: TRUE

tag: usedformodelbuilding

value: FALSE

tag: contrast

tag: concentration

tag: conclabel

tag: concstr

tag: teratogenicity


title: hEST_N_11_11_hEST_N_11.DMSO

value: Human induced pluripotent-stem-cell derived embryoid body

value: DMSO


title: LSC0023_Bl_CD34mCD38m

city: Toronto

first: Andy

last: Zeng

state: Ontario

address: 101 College Street

country: Canada

institute: University Health Network

data_processing:
Raw Data (BAM Files): Paired-end sequence data were analyzed with BWA/v0.6 alignment software with option (-s) to disable Smith-Waterman alignment. Reads were mapped onto GRCh37-lite reference genome and exon-exon junction reference whose coordinates were defined based on transcript annotations in Ensembl/v59. Reads with mapping quality < 10 were discarded and duplicate reads were tagged using the Picard's MarkDuplicates program. JAGuaR 2.1 was used to incorporate reads spanning multiple exons into the alignment by introducing large alignment gaps.
Processed Data (Raw Counts): Paired-end sequence data was aligned against GRCh38 and transcript sequences downloaded from Ensembl build 90 using STAR 2.5.2a. Default parameters were used except for the following: “–chimSegmentMin 12 –chimJunctionOverhangMin 12 –alignSJDBoverhangMin 10 –alignMatesGapMax 100000 –alignIntronMax 100000 –chimSegmentReadGapMax parameter 3 –alignSJstitchMismatchNmax 5 -1 5 5.” Raw counts were obtained using HTSeq v0.9.1.
Supplementary Files (Normalized Expression): For TPM normalization, raw counts for each gene were divided by the median length in kilobases of all GRCh38 annotated transcripts corresponding to a given gene. Sample-based normalization was subsequently performed such that the sum of all estimated transcript abundances for each sample equals 1,000,000. For VST normalized expression, variance-stabilizing transformation was performed on the raw counts using the vst function in DESeq2 v1.32.0.
Assembly: Raw BAM Files: GRCh37; Processed Data: GRCh38
Supplementary files format and content: Tab-delimited text files depict raw counts for each sample. Supplementary files contain processed data for all samples, including raw counts (ideal for differential expression), TPM-normalized expression (ideal for deconvolution), and VST-normalized expression (ideal for clustering, visualization, and precise quantification of specific genes) for each sample. Metadata for all samples is included as a separate tab-delimited text file.

source_name: Human acute myeloid leukemia cells

extract_protocol:
RNA was extracted from bulk peripheral blood mononuclear cells using an RNeasy Micro Kit (Qiagen).
Libraries were constructed using SMART-Seq (Clonetec)

treatment_protocol: T-cell depleted mononuclear cells from primary acute myeloid leukemia patients were thawed and flow-sorted according to expression of CD34 and CD38.

tag: patient

tag: fraction

tag: lsc activity

value: LSC-

value: Human acute myeloid leukemia cells


title: hEST_N_11_10_hEST_N_11.DMSO


title: LSC0016_Bl_CD34pCD38m

value: LSC+


title: LSC0019_Bl_CD34pCD38p


title: hEST_N_11_9_hEST_N_11.DMSO


title: LSC0017_Bl_CD34pCD38p


title: hEST_N_11_12_hEST_N_11.DMSO


title: hEST_N_11_8_hEST_N_11.DMSO


title: LSC0016_Bl_CD34mCD38p


title: hEST_N_11_6_hEST_N_11.DMSO


title: LSC0014_Bl_CD34pCD38m


title: LSC0016_Bl_CD34mCD38m


title: hEST_N_11_7_hEST_N_11.DMSO


title: LSC0018_Bl_CD34mCD38p


title: hEST_N_11_5_hEST_N_11.DMSO


title: hEST_N_11_3_hEST_N_11.DMSO


title: LSC0014_Bl_CD34mCD38p


title: LSC0013_Bl_CD34mCD38m


title: hEST_N_11_4_hEST_N_11.DMSO


title: hEST_N_11_2_hEST_N_11.DMSO


title: hEST_N_11_1_hEST_N_11.DMSO


title: LSC0013_Bl_CD34pCD38p


title: LSC0012_Bl_CD34pCD38m


title: LSC0012_Bl_CD34mCD38p


title: LSC0012_Bl_CD34mCD38m


title: LSC0007_Bl_CD34pCD38m


title: hEST_N_06_95_hEST_N_06.DMSO


title: LSC0008_Bl_CD34pCD38p


title: hEST_N_06_94_hEST_N_06.DMSO


title: LSC0009_Bl_CD34mCD38p


title: LSC0008_Bl_CD34pCD38m


title: hEST_N_06_93_hEST_N_06.DMSO


title: hEST_N_06_92_hEST_N_06.DMSO


title: LSC0007_Bl_CD34pCD38p


title: LSC0009_Bl_CD34pCD38p


title: LSC0005_Bl_CD34mCD38p


title: LSC0006_Bl_CD34pCD38m


title: LSC0006_Bl_CD34pCD38p


title: LSC0006_Bl_CD34mCD38p


title: LSC0005_Bl_CD34mCD38m


title: LSC0007_Bl_CD34mCD38p


title: LSC0004_Bl_CD34pCD38p


title: hEST_N_06_96_hEST_N_06.DMSO


title: hEST_N_06_90_hEST_N_06.DMSO


title: hEST_N_06_91_hEST_N_06.DMSO


title: hEST_N_11_55_hEST_N_11.S.Thalidomide.3

value: S-Thalidomide


title: hEST_N_06_12_hEST_N_06.DMSO


title: hEST_N_06_11_hEST_N_06.DMSO


title: hEST_N_06_86_hEST_N_06.DMSO


title: hEST_N_06_10_hEST_N_06.DMSO


title: hEST_N_06_8_hEST_N_06.DMSO


title: LSC0004_Bl_CD34pCD38m


title: hEST_N_06_9_hEST_N_06.DMSO


title: hEST_N_06_88_hEST_N_06.DMSO


title: hEST_N_06_89_hEST_N_06.DMSO


title: LSC0003_Bl_CD34mCD38m


title: hEST_N_06_85_hEST_N_06.DMSO


title: hEST_N_06_87_hEST_N_06.DMSO


title: LSC0002_Bl_CD34pCD38p


title: hEST_N_06_7_hEST_N_06.DMSO


title: LSC0002_Bl_CD34pCD38m


title: hEST_N_06_4_hEST_N_06.DMSO


title: hEST_N_06_5_hEST_N_06.DMSO


title: LSC0001_Bl_CD34pCD38p


title: hEST_N_06_2_hEST_N_06.DMSO


title: LSC0001_Bl_CD34pCD38m


title: hEST_N_06_3_hEST_N_06.DMSO


title: hEST_N_06_1_hEST_N_06.DMSO


title: LSC0003_Bl_CD34pCD38p


title: LSC0001_Bl_CD34mCD38m


title: LSC0004_Bl_CD34mCD38p


title: hEST_N_06_6_hEST_N_06.DMSO


title: hEST_N_07_190_hEST_N_07.DMSO


title: hEST_N_07_192_hEST_N_07.DMSO


title: hEST_N_07_188_hEST_N_07.DMSO


title: hEST_N_07_189_hEST_N_07.DMSO


title: LDXRX0015_Bl_Dx

tag: dxrel

value: Diagnosis

tag: relapse origin (shlush 2017)

value: ROc


title: hEST_N_07_191_hEST_N_07.DMSO


title: LDXRX0014_Bl_Rel

value: Relapse


title: LDXRX0014_Bl_Dx


title: LDXRX0012_Bl_Rel


title: LDXRX0012_Bl_Dx


title: hEST_N_07_185_hEST_N_07.DMSO


title: LSC0002_Bl_CD34mCD38p


title: LDXRX0011_Bl_Rel


title: LDXRX0011_Bl_Dx


title: hEST_N_07_186_hEST_N_07.DMSO


title: hEST_N_07_184_hEST_N_07.DMSO


title: LDXRX0010_Bl_Dx


title: LDXRX0010_Bl_Rel


title: hEST_N_07_181_hEST_N_07.DMSO


title: LDXRX0009_Bl_Rel

value: ROp


title: LDXRX0009_Bl_Dx


title: LDXRX0015_Bl_Rel


title: hEST_N_07_187_hEST_N_07.DMSO


title: LDXRX0008_Bl_Rel


title: hEST_N_07_108_hEST_N_07.DMSO


title: LDXRX0008_Bl_Dx


title: hEST_N_07_105_hEST_N_07.DMSO


title: LDXRX0006_Bl_Rel


title: hEST_N_07_106_hEST_N_07.DMSO


title: LDXRX0004_Bl_Dx


title: hEST_N_07_183_hEST_N_07.DMSO


title: hEST_N_07_104_hEST_N_07.DMSO


title: hEST_N_07_102_hEST_N_07.DMSO


title: hEST_N_07_103_hEST_N_07.DMSO


title: LDXRX0002_Bl_Dx


title: LDXRX0006_Bl_Dx


title: hEST_N_07_107_hEST_N_07.DMSO


title: LDXRX0003_Bl_Dx


title: hEST_N_07_97_hEST_N_07.DMSO


title: hEST_N_07_98_hEST_N_07.DMSO


title: hEST_N_07_182_hEST_N_07.DMSO


title: hEST_N_07_101_hEST_N_07.DMSO


title: LDXRX0002_Bl_Rel


title: hEST_N_07_100_hEST_N_07.DMSO


title: LDXRX0003_Bl_Rel


title: Mesothelioma tumor, ADU-S100 50µM

city: Boston

first: Michael

last: Tolstorukov

state: MA

address: 360 Longwood Avenue

department: Informatics

country: USA

institute: Dana Farber Cancer Institute

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Mesothelium

extract_protocol:
After 24 hours of treatment in a ULA dish, tumor spheroids were digested with trypsin in a 37°C incubator for 5 minutes to obtain single-cell suspensions. Cells were loaded onto a 10x chromium instrument (10x Genomics) per manufacturer’s instructions
ScRNA libraries were generated using the single cell 3′ reagent kit (10x Genomics) per the user guide

treatment_protocol: 24-hour treatment of S1 fraction from PDOTS (see methods) ex vivo

tag: disease state

value: mesothelioma

value: Cancer (mesothelioma)

tag: tissue

value: Mesothelium

tag: treatment

value: ADU-S100 50µM

tag: age


title: hEST_N_01_94_hEST_N_01.DMSO

tag: cell type

tag: run

tag: plate


title: RBC3

city: Yangzhou

first: Zhe

last: Yang

state: Jiangsu province

address: No.88, South University Road, Yangzhou

department: medical college

country: China

institute: Yangzhou university

data_processing:
RNA concentration of library was measured using Qubit® RNA Assay Kit in Qubit® 3.0 to preliminary quantify
Insert size was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA), and qualified insert size was accurate quantification using StepOnePlus™ Real-Time PCR System (Library valid concentration＞10 nM).
The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer's instructions. After cluster generation, the libraries were sequenced on an Illumina platform and 150 bp paired-end reads were generated.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Mus musculus

source_name: embryonic liver

extract_protocol:
TER cells were sorted from 1 week old neonatal mice spleen with CD19+TER119+CD71+CD45+, BLs (B lymphocytes) were sorted from adult C57BL6 mice spleen with CD19+TER119-CD45+, RBCs (embryo liver erythrocytes) were from the 14.5 days C57BL6 mice embryonic liver with CD19-TER119+CD71+CD45-.
RNA purity was checked using the kaiaoK5500®Spectrophotometer (Kaiao, Beijing, China). RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair,A-tailing and adapter added were implemented. The aimed products were retrieved and PCR was performed, then the library was completed.

value: embryonic liver

value: EL RBCs

tag: genotype

value: sorted from the 14.5 days C57BL6 mice embryonic liver


title: Mesothelioma tumor, ADU-S100 10µM

description: 10x Genomics

value: ADU-S100 10µM


title: hEST_N_01_95_hEST_N_01.DMSO

value: Human induced pluripotent-stem-cell derived embryoid body

value: DMSO

tag: usedforfactoranalysis

value: TRUE

tag: usedformodelbuilding

tag: contrast

tag: concentration


title: Mesothelioma tumor, Control (dH20)

description: 10x Genomics

value: control


title: LDXRX0004_Bl_Rel

tag: patient

value: Human acute myeloid leukemia cells


title: hEST_N_07_99_hEST_N_07.DMSO

tag: conclabel

tag: concstr

tag: teratogenicity


title: hEST_N_01_93_hEST_N_01.DMSO


title: TER2

source_name: spleen

value: spleen

value: TER cells

value: sorted from 1 week  old neonatal mice spleen


title: hEST_N_01_92_hEST_N_01.DMSO


title: TER3


title: RBC2


title: hEST_N_01_90_hEST_N_01.DMSO


title: RBC1


title: TER1


title: BL3

value: B lymphocytes

value: sorted from adult C57BL6 mice spleen


title: hEST_N_01_89_hEST_N_01.DMSO


title: hEST_N_01_96_hEST_N_01.DMSO


title: BL2


title: PMA_Iono-_LysoPS+

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 or NovaSeq 6000 platforms in 75 or 101-base single-end mode, respectively.
The sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: mm10

extract_protocol:
Total RNA was purified using the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: Murine naive CD4+ T cells were isolated from splenocytes with FACSAria, and cultured in the Th1 condition with LysoPS or vehicle control. Cells were harvested and library preparation was performed.

value: naive CD4+ T cells isolated from splenocytes and cultured in the Th1 condition with LysoPS cells


title: hEST_N_01_87_hEST_N_01.DMSO


title: hEST_N_01_85_hEST_N_01.DMSO


title: hEST_N_01_86_hEST_N_01.DMSO


title: hEST_N_01_88_hEST_N_01.DMSO


title: PMA_Iono+_LysoPS+

treatment_protocol: Murine naive CD4+ T cells were isolated from splenocytes with FACSAria, and cultured in the Th1 condition with LysoPS or vehicle control. Then cells were stimulated by PMA and ionomycin for 1 hr. Cells were harvested and library preparation was performed.

value: naive CD4+ T cells isolated from splenocytes, cultured in the Th1 condition with LysoPS and stimulated by PMA and ionomycin for 1 hr cells


title: PMA_Iono-_LysoPS-

value: naive CD4+ T cells isolated from splenocytes and cultured in the Th1 condition without LysoPS cells


title: hEST_N_01_10_hEST_N_01.DMSO


title: hEST_N_01_11_hEST_N_01.DMSO


title: naive_T_cells

growth_protocol: naïve CD4+ T cells were isolated from spleen using FACSAria.

treatment_protocol: Murine naive CD4+ T cells were isolated from splenocytes with FACSAria. Cells were collected and library preparation was performed.


title: hEST_N_01_6_hEST_N_01.DMSO


title: BL1


title: hEST_N_01_9_hEST_N_01.DMSO


title: hEST_N_01_7_hEST_N_01.DMSO


title: hEST_N_01_91_hEST_N_01.DMSO


title: hEST_N_01_12_hEST_N_01.DMSO


title: hEST_N_01_5_hEST_N_01.DMSO


title: hEST_N_01_4_hEST_N_01.DMSO


title: hEST_N_01_2_hEST_N_01.DMSO


title: hEST_N_01_8_hEST_N_01.DMSO


title: PMA_Iono+_LysoPS-

value: naive CD4+ T cells isolated from splenocytes, cultured in the Th1 condition without LysoPS and stimulated by PMA and ionomycin for 1 hr cells


title: hEST_N_01_1_hEST_N_01.DMSO


title: M8_77_IWP.2_DoseF

value: Positive


title: M8_78_Valproic.Acid_DoseF

value: Valproic acid


title: Serum, healthy control H47

city: Padova

first: Giulio

last: Ceolotto

address: Via Orus 2B

department: Medicine

country: Italy

institute: University of Padova

data_processing:
Data analysis was performed using CLC Genomics Workbench software 21.0.3 (Quiagen)
Reads from FASTq files was filtered for quality and aligned to the Ensembl-v99-hg38 version of the reference human genome and miRbase v.22.1  as annotation model
Normalization of the data was performed using TMM method (trimmed Mean of M-values)
Differential Expression analysis was performed using Generalized Linear Model (GLM) and Trimmed mean of M-values (TMM) normalized counts (CPM) were used as input data, considering significant Benjamini-Hochberg adjusted p-values ≤ 0.05
Assembly: Ensembl-v99-hg38
Supplementary files format and content: File includes raw data and cpm values (TMM-adjusted) for each Sample

source_name: serum (blood)

growth_protocol: Peripheral blood samples were collected at the time of hospital admission, and before starting medications. Sera were separated from whole blood by centrifugation for 15 min at 3,000 rpm at 4 °C and stored at -80 °C until processing. Serum samples from 45 healthy volunteers collected before September 2019 and stored at -80 °C were used as negative control group.

extract_protocol:
Total RNA was isolated from serum by RNeasy Mini kit (Qiagen).
Small RNA libraries from serum samples were obtained using QIAseq® miRNA Library kit (Qiagen, Hilden, Germany), according to the manufacturer protocol. NGS Library Quality Control (QC) analysis and quantification were performed before sequencing

value: serum (blood)

value: healthy control


title: LC31-High-fat diet-16W

type: RNA

city: Weifang

first: Fengqi

last: Liu

address: Baotong Street

institute: Weifang Medical University

hyb_protocol: 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven

scan_protocol: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 4 out of 8 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering.

source_name: Mouse liver tissue, 16W

label_protocol: The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA.

growth_protocol: Male C57BL/6J mice (n=32) were maintained under a controlled temperature condition of 20±2 ◦C, with a 12 h light-dark cycle environment and free access to standard mice chow and water. After 1 week of acclimation, mice were randomly distributed into two groups: NC and HFD group.

extract_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, each RNA sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar).

treatment_protocol: The liver tissues of mice were collected for microarray analysis after 16 weeks of feeding.

tag: gender

value: Male

value: liver


title: M8_76_Dorsomorphin_DoseF

value: Human induced pluripotent-stem-cell derived embryoid body

value: Dorsomorphin

value: TRUE


title: Serum, healthy control H45

tag: disease state


title: M8_66_Valproic.Acid_DoseE


title: Serum, healthy control H44

tag: tissue


title: Serum, healthy control H46


title: Serum, healthy control H41


title: LC21-Normal contral-16W


title: LC39-High-fat diet-16W


title: LC26-High-fat diet-16W


title: LC19-Normal contral-16W


title: M8_75_DAPT_DoseF

value: DAPT


title: Serum, healthy control H43


title: LC27-High-fat diet-16W


title: hEST_N_01_3_hEST_N_01.DMSO

value: DMSO


title: LC25-Normal contral-16W


title: LC22-Normal contral-16W


title: M8_73_Cyclopamine_DoseF

value: Cyclopamine


title: Serum, healthy control H40


title: M8_64_Dorsomorphin_DoseE


title: Serum, healthy control H38


title: M8_65_IWP.2_DoseE


title: Serum, healthy control H37


title: M8_74_Dabrafenib_DoseF

value: Dabrafenib


title: Serum, healthy control H39


title: Serum, healthy control H36


title: Serum, healthy control H35


title: M8_63_DAPT_DoseE


title: M8_54_Valproic.Acid_DoseD


title: M8_61_Cyclopamine_DoseE


title: Serum, healthy control H30


title: Serum, healthy control H32


title: Serum, healthy control H31


title: Serum, healthy control H33


title: M8_51_DAPT_DoseD


title: M8_49_Cyclopamine_DoseD


title: M8_42_Valproic.Acid_DoseC


title: M8_41_IWP.2_DoseC


title: M8_50_Dabrafenib_DoseD


title: Serum, healthy control H26


title: M8_53_IWP.2_DoseD


title: M8_40_Dorsomorphin_DoseC


title: Serum, healthy control H34


title: Serum, healthy control H27


title: Serum, healthy control H28


title: Serum, healthy control H24


title: Serum, healthy control H29


title: Serum, healthy control H23


title: M8_37_Cyclopamine_DoseC


title: M8_39_DAPT_DoseC


title: Serum, healthy control H22


title: Serum, healthy control H20


title: M8_62_Dabrafenib_DoseE


title: M8_29_IWP.2_DoseB


title: M8_52_Dorsomorphin_DoseD


title: M8_27_DAPT_DoseB


title: Serum, healthy control H25


title: Serum, healthy control H21


title: M8_30_Valproic.Acid_DoseB


title: Serum, healthy control H19


title: Serum, healthy control H15


title: Serum, healthy control H18


title: M8_28_Dorsomorphin_DoseB


title: Serum, healthy control H14


title: Serum, healthy control H12


title: M8_13_Cyclopamine_DoseA


title: M8_38_Dabrafenib_DoseC


title: M8_26_Dabrafenib_DoseB


title: Serum, healthy control H17


title: Serum, healthy control H16


title: M8_18_Valproic.Acid_DoseA


title: M8_16_Dorsomorphin_DoseA


title: Serum, healthy control H13


title: Serum, healthy control H8


title: M8_17_IWP.2_DoseA


title: M8_14_Dabrafenib_DoseA


title: M8_15_DAPT_DoseA


title: Serum, healthy control H4


title: M8_9_DMSO_ctrl


title: Serum, healthy control H11


title: Serum, healthy control H9


title: M8_12_DMSO_ctrl


title: Serum, healthy control H2


title: M8_25_Cyclopamine_DoseB


title: Serum, patient with mild covid C26

value: mild covid


title: Serum, healthy control H7


title: M8_10_DMSO_ctrl


title: M8_11_DMSO_ctrl


title: Serum, healthy control H6


title: M8_8_DMSO_ctrl


title: Serum, healthy control H5


title: Serum, healthy control H3


title: Serum, patient with mild covid C1_24


title: M7_78_Valproic.Acid_DoseF


title: M8_2_DMSO_ctrl


title: M8_7_DMSO_ctrl


title: M8_1_DMSO_ctrl


title: M8_4_DMSO_ctrl


title: Serum, patient with mild covid C22


title: M7_76_Dorsomorphin_DoseF


title: M8_5_DMSO_ctrl


title: M8_6_DMSO_ctrl


title: Serum, patient with mild covid C23


title: Serum, patient with mild covid C19


title: M7_77_IWP.2_DoseF


title: M7_73_Cyclopamine_DoseF


title: Serum, patient with mild covid C21


title: Serum, patient with mild covid C15


title: Serum, patient with mild covid C1_13


title: Serum, patient with mild covid C20


title: M7_63_DAPT_DoseE


title: M7_75_DAPT_DoseF


title: Serum, patient with mild covid C9


title: Dox_Os-3

city: Shanghai

first: Moyang

address: dongchuan road 800

department: School of Agriculture and Biology

institute: Shanghai Jiao Tong University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Assembly: TAIR10;IRGSP-1.0; SL3.0
Supplementary files format and content: tab-delimited text files include count for each Sample

organism: Oryza sativa Japonica Group

source_name: leaf

extract_protocol:
10 μg/mg doxycycline treated and  control check leaves were sampled, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the Vonstruction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: leaf

value: WT

tag: treatment

value: 10 μg/mg doxycycline


title: M7_74_Dabrafenib_DoseF

value: Positive


title: Serum, patient with mild covid C25


title: M7_51_DAPT_DoseD


title: Serum, patient with mild covid C17


title: Serum, patient with mild covid C16


title: M7_65_IWP.2_DoseE


title: Serum, patient with mild covid C14


title: M7_66_Valproic.Acid_DoseE

value: Valproic acid


title: M7_50_Dabrafenib_DoseD


title: M7_64_Dorsomorphin_DoseE


title: M7_62_Dabrafenib_DoseE


title: Serum, patient with mild covid C12

value: serum (blood)


title: M7_54_Valproic.Acid_DoseD


title: M7_61_Cyclopamine_DoseE


title: Serum, patient with mild covid C11


title: M7_49_Cyclopamine_DoseD


title: M7_53_IWP.2_DoseD


title: M7_42_Valproic.Acid_DoseC


title: Serum, patient with mild covid C1_10


title: Serum, patient with mild covid C6


title: M7_52_Dorsomorphin_DoseD


title: M7_40_Dorsomorphin_DoseC


title: Dox_Os-2


title: CK_Os-3

value: CK


title: M7_39_DAPT_DoseC


title: M8_3_DMSO_ctrl


title: Dox_Os-1


title: Serum, patient with mild covid C1-5


title: CK_Os-2


title: M7_37_Cyclopamine_DoseC


title: M7_41_IWP.2_DoseC


title: CK_Os-1


title: M7_38_Dabrafenib_DoseC


title: M7_27_DAPT_DoseB


title: M7_29_IWP.2_DoseB


title: Serum, patient with mild covid C3


title: Serum, patient with mild covid C8


title: RH_G08_rep9

city: San Diego

first: Jill

middle: P

last: Mesirov

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

description:
none
5500024030700072107993.G08

hyb_protocol: Gene expression data was generated by hybridizing labeled RNAs to Affymetrix HT HG-U133A arrays (Affymetrix, Santa Clara, CA).

scan_protocol: standard Affymetrix protocol

data_processing: Samples meeting a minimum of 37% p-calls were used in this analysis. A number of samples with borderline 3′/5′ GAPDH and ACTIN ratios were identified but did not contribute to any batch effects in our non-negative matrix factorization (NMF) analysis; these remained in our subsequent analyses. Gene expression data from Kool et al3 and Fattet et al7 were obtained from the Gene Expression Omnibus (GSE10327 and GSE12992, respectively). Gene expression data from Thomson et al4 was downloaded from http://www.stjuderesearch.org/data/medulloblastoma/. All data sets were preprocessed with the Robust Multichip Average (RMA) algorithm to generate the .gct files used in subsequent analyses (Irizarry RA, et al: Biostatistics 4:249-264, 2003).

label: biotin

source_name: Brain

label_protocol: standard Affymetrix protocol

growth_protocol: Snap-frozen tumors were obtained from Children's Oncology Group (ACNS02B3; n = 89) and from Children's Hospital Boston (n = 55), University of Washington Medical Center (n = 27), Texas Children's Hospital (n = 24), and Johns Hopkins Medical Center (n = 10). Normal cerebellum (n = 11) was obtained from University of Washington Medical Center and NICHD Brain and Tissue Bank for Developmental Disorders, University of Maryland, Baltimore, MD. All samples were collected with approval from respective institutional review boards, and proper informed consent and/or assent was obtained from all patients or their parents.    Tumors were processed at Children's Hospital Boston except for samples from Texas Children's, where similar protocols were used.

extract_protocol: DNA was prepared by using the Puregene DNA Extraction Kit (Gentra Systems, Minneapolis, MN), and total RNA was extracted by using Trizol (Invitrogen, Carlsbad, CA), both per manufacturers' instructions.

value: other

tag: subtype

value: ATRT (L CPA)

tag: clinical outcomes


title: M7_26_Dabrafenib_DoseB

tag: cell type

value: Human induced pluripotent-stem-cell derived embryoid body

tag: run


title: Serum, patient with mild covid C1


title: RH_G07_rep8

description:
none
5500024030700072107993.G07

value: ATRT (L parietal)


title: Serum, healthy control H1

value: healthy control


title: M7_17_IWP.2_DoseA

tag: plate

value: TRUE


title: Serum, patient with mild covid C4


title: M7_16_Dorsomorphin_DoseA

value: Dorsomorphin

tag: usedforfactoranalysis


title: M7_30_Valproic.Acid_DoseB

tag: usedformodelbuilding


title: Serum, patient with moderate covid B28

value: moderate covid


title: M7_15_DAPT_DoseA

value: DAPT

tag: contrast


title: Serum, patient with mild covid C7

value: mild covid


title: M7_14_Dabrafenib_DoseA

value: Dabrafenib

tag: concentration


title: RH_F08_rep5

description:
none
5500024024214122006605.F08

value: medullo-ATRT hybrid

value: A


title: Serum, patient with moderate covid B26


title: M7_28_Dorsomorphin_DoseB

value: Positive


title: Serum, patient with mild covid C2


title: M7_9_DMSO_ctrl

value: DMSO


title: M7_25_Cyclopamine_DoseB

value: Cyclopamine


title: M7_11_DMSO_ctrl


title: Serum, patient with moderate covid B27

value: serum (blood)


title: M7_18_Valproic.Acid_DoseA

value: Valproic acid


title: RH_G06_rep7.1

description:
none
5500024030700072107993.G06

value: other

value: ATRT (R temporal)


title: Serum, patient with moderate covid B29


title: RH_B07_rep6

description:
none
5500024024214122006605.B07

value: D


title: M7_6_DMSO_ctrl

value: Human induced pluripotent-stem-cell derived embryoid body


title: M7_5_DMSO_ctrl

value: TRUE


title: Serum, patient with moderate covid B23


title: M7_13_Cyclopamine_DoseA


title: M7_12_DMSO_ctrl


title: RH_H08_rep2

description:
none
5500024030700072107993.H08

value: ATRT (p fossa)


title: RH_G09_rep10

description:
none
5500024030700072107993.G09

value: undifferentiated infratentorial tumor


title: RH_F08_rep12

description:
none
5500024030700072107993.F08


title: M7_1_DMSO_ctrl


title: M7_10_DMSO_ctrl


title: Serum, patient with moderate covid B20

value: moderate covid


title: NC_E01_rep6

description:
none
5500024024214122006610.E01

value: normal cerebellum


title: Serum, patient with moderate covid B25


title: M7_8_DMSO_ctrl


title: M7_7_DMSO_ctrl


title: Serum, patient with moderate covid B24


title: RH_H07_rep1

description:
none
5500024030700072107993.H07


title: NC_F01_rep9

description:
none
5500024024214122006605.F01


title: M6_79_Penicillin.G_DoseF

value: Penicillin G

value: Negative


title: M7_3_DMSO_ctrl


title: Serum, patient with moderate covid B22


title: M7_2_DMSO_ctrl


title: M6_78_Misoprostol_DoseF

value: Misoprostol

value: FALSE


title: Serum, patient with moderate covid B17


title: M6_77_Methotrexate_DoseF

value: Methotrexate

value: Positive


title: M6_75_Isotretinoin_DoseF

value: Isotretinoin


title: NC_D01_rep7

description:
none
5500024024214122006605.D01


title: Serum, patient with moderate covid B21

value: serum (blood)


title: M6_73_Ibuprofen_DoseF

value: Ibuprofen


title: M6_84_SB431542_DoseF


title: NC_E01_rep5

description:
none
5500024024214122006605.E01


title: M6_81_Progesteron_DoseF

value: Progesterone


title: Serum, patient with moderate covid B19


title: M7_4_DMSO_ctrl

value: DMSO


title: Serum, patient with mild covid C1_18

value: mild covid


title: NC_F01_rep12

description:
none
5500024024214122006610.F01


title: M6_70_Retinoic.Acid_DoseE

value: Human induced pluripotent-stem-cell derived embryoid body

value: Retinoic acid

value: TRUE


title: NC_B01_rep11

description:
none
5500024024214122006605.B01


title: M6_80_Phenytoin_DoseF

value: Phenytoin


title: Serum, patient with moderate covid B14

value: moderate covid


title: NC_A01_rep1

description:
none
5500024024214122006605.A01

value: normal cerebellum


title: NC_A01_rep2

description:
none
5500024024214122006610.A01


title: Serum, patient with moderate covid B18


title: Serum, patient with moderate covid B13


title: M6_83_Thalidomide_DoseF

value: Thalidomide


title: Serum, patient with moderate covid B12


title: M6_76_Metformin_DoseF

value: Metformin

value: Negative


title: M6_82_Retinoic.Acid_DoseF


title: NC_G01_rep14

description:
none
5500024024214122006610.G01


title: MD_F06_rep99.1

description:
none
5500024024214122006610.F06

value: primary medulloblastoma

value: classic

value: D


title: Serum, patient with moderate covid B16

value: serum (blood)


title: M6_74_Imatinib_DoseF

value: Imatinib

value: Positive


title: Serum, patient with moderate covid B11


title: NC_G01_rep13

description:
none
5500024024214122006605.G01


title: NC_C01_rep3

description:
none
5500024024214122006605.C01


title: Serum, patient with moderate covid B15


title: M6_71_Thalidomide_DoseE


title: M6_62_Imatinib_DoseE


title: M6_68_Phenytoin_DoseE

value: FALSE


title: M6_66_Misoprostol_DoseE

value: Misoprostol


title: M6_72_SB431542_DoseE

value: Human induced pluripotent-stem-cell derived embryoid body


title: M6_67_Penicillin.G_DoseE

value: Penicillin G


title: M6_65_Methotrexate_DoseE

value: Methotrexate

value: TRUE


title: MD_D12_rep92

description:
none
5500024024214122006605.D12

value: NOS


title: M6_60_SB431542_DoseD


title: MD_E11_rep85

description:
none
5500024024214122006610.E11


title: M6_64_Metformin_DoseE


title: MD_B08_rep97

description:
none
5500024024214122006605.B08

value: nodular/desmoplastic

value: A


title: M6_59_Thalidomide_DoseD

value: Thalidomide


title: MD_F10_rep8.1

description:
none
5500024030700072107993.F10


title: M6_63_Isotretinoin_DoseE

value: Isotretinoin


title: Serum, patient with moderate covid B10

value: moderate covid


title: M6_69_Progesteron_DoseE

value: Progesterone

value: Negative


title: M6_61_Ibuprofen_DoseE

value: Ibuprofen


title: M6_55_Penicillin.G_DoseD


title: Serum, patient with moderate covid B9

value: serum (blood)


title: Serum, patient with moderate covid B7


title: M6_57_Progesteron_DoseD


title: Serum, patient with moderate covid B6


title: M6_56_Phenytoin_DoseD

value: Phenytoin


title: MD_C03_rep81

description:
none
5500024030700072107993.C03

value: primary medulloblastoma

value: classic


title: M6_54_Misoprostol_DoseD

value: Human induced pluripotent-stem-cell derived embryoid body

value: Misoprostol

value: FALSE


title: Serum, patient with moderate covid B8


title: Serum, patient with moderate covid B4


title: MD_G05_rep76

description:
none
5500024030700072107993.G05


title: MD_E06_rep78

description:
none
5500024030403071907254.E06


title: M6_53_Methotrexate_DoseD

value: Methotrexate

value: TRUE

value: Positive


title: M6_58_Retinoic.Acid_DoseD

value: Retinoic acid


title: M6_48_SB431542_DoseC


title: M6_50_Imatinib_DoseD

value: Imatinib


title: M6_49_Ibuprofen_DoseD


title: Serum, patient with moderate covid B3


title: MD_G04_rep72

description:
none
5500024030700072107993.G04


title: M6_45_Progesteron_DoseC


title: MD_F10_rep7.1

description:
none
5500024030403071907254.F10


title: MD_D12_rep74

description:
none
5500024028849050407170.D12

value: large cell/anaplastic


title: M6_46_Retinoic.Acid_DoseC


title: M6_44_Phenytoin_DoseC


title: M6_42_Misoprostol_DoseC


title: Serum, patient with severe covid A33

value: severe covid


title: MD_G12_rep71

description:
none
5500024028849050407170.G12


title: M6_41_Methotrexate_DoseC


title: M6_52_Metformin_DoseD

value: Metformin


title: Serum, patient with moderate covid B2

value: moderate covid


title: Serum, patient with moderate covid B5


title: M6_37_Ibuprofen_DoseC

value: Ibuprofen

value: Negative


title: MD_B03_rep63

description:
none
5500024030700072107993.B03


title: M6_51_Isotretinoin_DoseD

value: Isotretinoin


title: M6_43_Penicillin.G_DoseC

value: Penicillin G


title: M6_35_Thalidomide_DoseB

value: Thalidomide


title: M6_34_Retinoic.Acid_DoseB

value: Human induced pluripotent-stem-cell derived embryoid body


title: M6_33_Progesteron_DoseB

value: Progesterone


title: Serum, patient with severe covid A29

value: serum (blood)


title: Serum, patient with moderate covid B1


title: M6_38_Imatinib_DoseC


title: M6_47_Thalidomide_DoseC


title: Serum, patient with severe covid A32


title: Serum, patient with severe covid A28


title: MD_A10_rep67

description:
none
5500024030700072107993.A10

value: primary medulloblastoma

value: classic


title: Serum, patient with severe covid A30


title: MD_B08_rep64

description:
none
5500024030700072107993.B08


title: Serum, patient with severe covid A31


title: MD_B11_rep61

description:
none
5500024030700072107993.B11


title: MD_D01_rep69

description:
none
5500024030700072107993.D01


title: MD_C06_rep59

description:
none
5500024030700072107993.C06


title: M6_39_Isotretinoin_DoseC

value: TRUE

value: Positive


title: MD_C05_rep57

description:
none
5500024030700072107993.C05

value: nodular/desmoplastic


title: Serum, patient with severe covid A34


title: M6_40_Metformin_DoseC


title: Serum, patient with severe covid A26


title: M6_31_Penicillin.G_DoseB


title: M6_32_Phenytoin_DoseB

value: Phenytoin

value: FALSE


title: M6_28_Metformin_DoseB

value: Metformin


title: MD_C09_rep58

description:
none
5500024030700072107993.C09


title: M6_30_Misoprostol_DoseB

value: Misoprostol


title: Serum, patient with severe covid A27

value: severe covid


title: M6_25_Ibuprofen_DoseB

value: Ibuprofen

value: Negative


title: M6_36_SB431542_DoseB


title: M6_24_SB431542_DoseA


title: MD_B10_rep55

description:
none
5500024030402071707278.B10


title: M6_26_Imatinib_DoseB

value: Imatinib


title: Serum, patient with severe covid A24


title: M6_29_Methotrexate_DoseB

value: Methotrexate


title: M6_23_Thalidomide_DoseA

value: Human induced pluripotent-stem-cell derived embryoid body

value: Thalidomide


title: M6_22_Retinoic.Acid_DoseA

value: Retinoic acid


title: MD_B05_rep51

description:
none
5500024030700072107993.B05

value: primary medulloblastoma


title: Serum, patient with severe covid A25

value: serum (blood)


title: Serum, patient with severe covid A23


title: MD_B10_rep50

description:
none
5500024030700072107993.B10


title: M6_19_Penicillin.G_DoseA

value: Penicillin G

value: TRUE


title: M6_20_Phenytoin_DoseA


title: MD_A06_rep49

description:
none
5500024030700072107993.A06

value: large cell/anaplastic


title: M6_18_Misoprostol_DoseA


title: M6_27_Isotretinoin_DoseB

value: Isotretinoin

value: Positive


title: M6_21_Progesteron_DoseA

value: Progesterone


title: Serum, patient with severe covid A21


title: Serum, patient with severe covid A20


title: M6_16_Metformin_DoseA

value: Metformin


title: Serum, patient with severe covid A22

value: severe covid


title: MD_A04_rep48

description:
none
5500024030700072107993.A04


title: M6_17_Methotrexate_DoseA


title: M6_15_Isotretinoin_DoseA


title: M6_14_Imatinib_DoseA


title: Serum, patient with severe covid A19


title: MD_E06_rep54

description:
none
5500024035736031208619.E06

value: classic

value: A


title: M6_12_DMSO_ctrl

value: DMSO


title: MD_D08_rep46

description:
none
5500024035736031208619.D08


title: M6_11_DMSO_ctrl


title: M6_10_DMSO_ctrl


title: Serum, patient with severe covid A18


title: M6_9_DMSO_ctrl


title: MD_B03_rep44

description:
none
5500024024214122006605.B03


title: Serum, patient with severe covid A17


title: M6_8_DMSO_ctrl


title: M6_7_DMSO_ctrl


title: MD_C07_rep47

description:
none
5500024030700072107993.C07

value: nodular/desmoplastic


title: Serum, patient with severe covid A16


title: MD_C10_rep38

description:
none
5500024024214122006610.C10


title: M6_13_Ibuprofen_DoseA

value: Human induced pluripotent-stem-cell derived embryoid body

value: Ibuprofen

value: Negative


title: MD_A12_rep35

description:
none
5500024030700072107993.A12

value: primary medulloblastoma


title: M6_4_DMSO_ctrl


title: Serum, patient with severe covid A13

value: serum (blood)


title: MD_B08_rep37

description:
none
5500024030402071707278.B08


title: M6_6_DMSO_ctrl


title: MD_H12_rep4

description:
none
5500024024214122006610.H12


title: Serum, patient with severe covid A15


title: M6_2_DMSO_ctrl


title: M6_1_DMSO_ctrl


title: Serum, patient with severe covid A12


title: MD_H11_rep33

description:
none
5500024024214122006610.H11


title: M5_84_SB431542_DoseF


title: M5_83_Thalidomide_DoseF

value: Thalidomide


title: M6_3_DMSO_ctrl

value: TRUE


title: M5_78_Misoprostol_DoseF

value: Misoprostol

value: FALSE


title: M5_82_Retinoic.Acid_DoseF

value: Retinoic acid

value: Positive


title: MD_H12_rep34

description:
none
5500024024214122006605.H12

value: large cell/anaplastic


title: M5_80_Phenytoin_DoseF

value: Phenytoin


title: M5_79_Penicillin.G_DoseF

value: Penicillin G


title: M6_5_DMSO_ctrl


title: M5_77_Methotrexate_DoseF

value: Methotrexate


title: MD_D05_rep3

description:
none
5500024024214122006605.D05

value: classic


title: Serum, patient with severe covid A8

value: severe covid


title: MD_E12_rep273

description:
none
5500024030700072107993.E12


title: Serum, patient with severe covid A7


title: MD_E02_rep29

description:
none
5500024035736031208619.E02


title: Serum, patient with severe covid A10


title: M5_72_SB431542_DoseE

value: Human induced pluripotent-stem-cell derived embryoid body


title: M5_81_Progesteron_DoseF

value: Progesterone


title: M5_75_Isotretinoin_DoseF

value: Isotretinoin


title: Serum, patient with severe covid A6


title: Serum, patient with severe covid A11


title: MD_C12_rep269

description:
none
5500024024214122006605.C12

value: primary medulloblastoma

value: NOS


title: M5_74_Imatinib_DoseF

value: Imatinib


title: Serum, patient with severe covid A9

value: serum (blood)


title: M5_68_Phenytoin_DoseE

value: TRUE


title: M5_71_Thalidomide_DoseE

value: Thalidomide


title: MD_D07_rep268

description:
none
5500024035736031208619.D07


title: M5_70_Retinoic.Acid_DoseE

value: Retinoic acid


title: MD_G08_rep257

description:
none
5500024035736031208619.G08

value: A


title: Serum, patient with severe covid A5


title: M5_69_Progesteron_DoseE

value: Negative


title: MD_G11_rep260

description:
none
5500024035736031208619.G11


title: Serum, patient with severe covid A3


title: M5_67_Penicillin.G_DoseE


title: Serum, patient with severe covid A4


title: M5_73_Ibuprofen_DoseF

value: Ibuprofen


title: M5_62_Imatinib_DoseE

value: Positive


title: M5_76_Metformin_DoseF

value: Metformin


title: M5_61_Ibuprofen_DoseE


title: M5_64_Metformin_DoseE


title: M5_66_Misoprostol_DoseE

value: Misoprostol

value: FALSE


title: MD_B07_rep25

description:
none
5500024030402071707278.B07

value: classic


title: M5_65_Methotrexate_DoseE

value: Human induced pluripotent-stem-cell derived embryoid body

value: Methotrexate


title: MD_C11_rep254

description:
none
5500024024214122006605.C11

value: primary medulloblastoma


title: M5_59_Thalidomide_DoseD


title: Serum, patient with severe covid A2

value: severe covid


title: M5_63_Isotretinoin_DoseE

value: Isotretinoin


title: Genome_in_a_Bottle_F_WaveCONTROL

city: Glasgow

first: Neil

middle: A

last: Robertson

state: Scotland

address: Switchback Road

department: Beatson Institute for Cancer Research

country: United Kingdom

institute: University of Glasgow

description:
DNA (Targeted Myeloid Panel)
LBC_ARCHER.1PCT_VAF.Feb22.non-synonymous.tsv
LBC_ARCHER.1PCT_VAF.Feb22.synonymous.tsv
LBC_ARCHER.2PCT_VAF.Feb22.non-synonymous.tsv
LBC_ARCHER.2PCT_VAF.Feb22.synonymous.tsv

library_source: genomic

data_processing:
Reads were filtered for phred ≥30 and adapters removed using Trimmomatic (Bolger et al., 2014) before undergoing guided alignment to human genome assembly hg19 using bwa-mem and bowtie2.
Unique molecular barcodes (ligated prior to PCR amplification) were utilised for read deduplication to support quantitative multiplexed analysis and confident mutation detection. Within targeted regions, variants were called using three tools (Lofreq (Wilm et al., 2012), Freebayes (Garrison and Marth, 2012) and Vision (ArcherDX, unpublished) – building a consensus from the output of all callers
All filtered variants at 0.02 VAF met the following criteria: 1) the number of reads supporting the alternative allele surpasses the coverage criteria while exhibiting no directional biases (AO ≥ 5, UAO ≥ 3); 2) variants are significantly underrepresented within the Genome Aggregation Database (gnomAD; p ≤ 0.05); 3) variants are not obviously germline variants (stable VAF across all waves ~0.5 or ~1) that may have been underrepresented in the gnomAD database due to the narrow geographical origin of the Lothian Birth Cohort participants; 4) contain events that are overrepresented across the dataset - generally frameshift duplications and deletions - whose reads share some sequence homology to target regions yet are likely misaligned artefact from the capture method. In addition, we manually curated this list checking for variants that were previously reported, as per Jaiswal et al. (Jaiswal et al., 2014b), in the COSMIC (Catalogue of Somatic Mutations in Cancer) database or within the published literature (Table 4).
For any variant that surpassed the above criteria at, or above, 0.02 VAF across the measured time period, we endeavored to include all other participant matched data points regardless of VAF level
Genome_build: hg19
Supplementary_files_format_and_content: Extended MAF Format (Mutation Annotation Format)

molecule: genomic DNA

source_name: Human Blood (PBMCs)

growth_protocol: DNA was extracted from EDTA whole blood using the Nucleon BACC3 kit, following the manufacturer’s instructions. Libraries were prepared from 200ng of each DNA sample using the Archer VariantPlex 75 Myeloid gene panel and VariantPlex Somatic Protocol for Illumina Sequencing (Invitae, Table 2), including modifications for detecting low allele frequencies.

extract_protocol: Sequencing of each pool was performed using the NextSeq 500/550 High-Output v2.5 (300 cycle) kit on the NextSeq 550 platform. To inform reproducibility, background model for error and batch correction, we sequenced “genome in a bottle” DNA in each batch of samples (DNA NA12878 Coriell Institute).

tag: wave

value: CONTROL

tag: cohort

tag: sequencing batch

value: Blood

value: PBMCs


title: M5_57_Progesteron_DoseD

value: Progesterone

value: TRUE

tag: conclabel

tag: concstr

tag: teratogenicity


title: M5_56_Phenytoin_DoseD

value: Phenytoin


title: MD_G07_rep253

description:
none
5500024035736031208619.G07

tag: tissue

value: A


title: Serum, patient with severe covid A1

value: serum (blood)

tag: disease state


title: M5_60_SB431542_DoseD

value: Positive


title: M5_54_Misoprostol_DoseD

value: Misoprostol


title: M5_53_Methotrexate_DoseD


title: M5_58_Retinoic.Acid_DoseD

value: Retinoic acid


title: MD_G05_rep248

description:
none
5500024035736031208619.G05

tag: subtype

value: large cell/anaplastic


title: Genome-in-a-Bottle-B_WaveCONTROL


title: M5_50_Imatinib_DoseD

value: Human induced pluripotent-stem-cell derived embryoid body

value: Imatinib


title: MD_G01_rep243

description:
none
5500024035736031208619.G01

value: primary medulloblastoma

value: NOS

tag: clinical outcomes


title: Genome_in_a_Bottle_E_WaveCONTROL

tag: cell type


title: M5_52_Metformin_DoseD

tag: run

value: Metformin

value: Negative


title: MD_F12_rep242

description:
none
5500024035736031208619.F12

value: classic


title: MD_G04_rep247

description:
none
5500024035736031208619.G04


title: M5_55_Penicillin.G_DoseD

tag: plate

value: Penicillin G


title: MD_G02_rep244

description:
none
5500024035736031208619.G02


title: MD_D04_rep263

description:
none
5500024035736031208619.D04


title: M5_51_Isotretinoin_DoseD

value: Isotretinoin

tag: usedforfactoranalysis


title: GenomeInABottle_C_WaveCONTROL

value: CONTROL

value: Blood

value: PBMCs


title: M5_49_Ibuprofen_DoseD

value: Ibuprofen

value: TRUE

tag: usedformodelbuilding


title: Genome-in-a-Bottle-A_WaveCONTROL


title: M5_47_Thalidomide_DoseC

value: Thalidomide

tag: contrast

value: Positive


title: MD_F10_rep240

description:
none
5500024035736031208619.F10

value: A


title: MD_F11_rep241

description:
none
5500024035736031208619.F11


title: M5_48_SB431542_DoseC

value: Human induced pluripotent-stem-cell derived embryoid body

tag: concentration


title: GenomeInABottle8_WaveCONTROL

tag: wave


title: M5_44_Phenytoin_DoseC

value: Phenytoin

value: FALSE


title: M5_46_Retinoic.Acid_DoseC

value: Retinoic acid


title: GenomeInABottle6_WaveCONTROL

tag: cohort


title: GenomeInABottle_D_WaveCONTROL

tag: sequencing batch


title: MD_F08_rep236

description:
none
5500024035736031208619.F08

value: primary medulloblastoma

value: NOS


title: M5_45_Progesteron_DoseC

value: Progesterone

tag: conclabel

value: Negative


title: GenomeInABottle7_WaveCONTROL


title: M5_43_Penicillin.G_DoseC

value: Penicillin G

tag: concstr


title: Serum, patient with severe covid A14

value: serum (blood)

value: severe covid


title: MD_F09_rep237

description:
none
5500024035736031208619.F09


title: M5_38_Imatinib_DoseC

value: Imatinib

tag: teratogenicity


title: MD_G12_rep21

description:
none
5500024030403071907254.G12

tag: tissue

value: classic


title: M5_42_Misoprostol_DoseC

value: Misoprostol

value: TRUE


title: GenomeInABottle3_WaveCONTROL

value: CONTROL

value: Blood

value: PBMCs


title: MD_H02_rep20.1

description:
none
5500024030700072107993.H02


title: M5_41_Methotrexate_DoseC

value: Human induced pluripotent-stem-cell derived embryoid body

value: Methotrexate

value: Positive


title: M5_35_Thalidomide_DoseB

value: Thalidomide


title: M5_34_Retinoic.Acid_DoseB

value: Retinoic acid


title: GenomeInABottle2_WaveCONTROL


title: MD_F09_rep2.1

description:
none
5500024030700072107993.F09

value: primary medulloblastoma


title: M5_40_Metformin_DoseC

value: Metformin

value: Negative


title: GenomeInABottle5_WaveCONTROL


title: MD_A12_rep216

description:
none
5500024024214122006605.A12


title: M5_32_Phenytoin_DoseB

value: Phenytoin

value: FALSE


title: M5_37_Ibuprofen_DoseC

value: Ibuprofen


title: M5_39_Isotretinoin_DoseC

value: Isotretinoin


title: M5_36_SB431542_DoseB


title: MD_G08_rep194

description:
none
5500024024214122006610.G08

value: classic

value: A


title: GenomeInABottle4_WaveCONTROL

value: CONTROL


title: M5_33_Progesteron_DoseB

value: Progesterone

value: TRUE


title: M5_29_Methotrexate_DoseB

value: Human induced pluripotent-stem-cell derived embryoid body


title: M5_28_Metformin_DoseB


title: GenomeInABottle1_WaveCONTROL

value: Blood

value: PBMCs


title: M5_27_Isotretinoin_DoseB

value: Positive


title: MD_G08_rep178

description:
none
5500024024214122006605.G08

value: nodular/desmoplastic

value: D(comp)


title: M5_31_Penicillin.G_DoseB

value: Penicillin G


title: CHIP_LBC36_001_Wave5


title: M5_25_Ibuprofen_DoseB

value: Negative


title: M5_21_Progesteron_DoseA


title: MD_A02_rep163

description:
none
5500024024214122006610.A02

value: primary medulloblastoma

value: D


title: M5_30_Misoprostol_DoseB

value: Misoprostol

value: FALSE


title: CHIP_LBC36_031_Wave5


title: MD_G09_rep179

description:
none
5500024024214122006605.G09


title: CHIP_LBC36_002_Wave5


title: M5_26_Imatinib_DoseB

value: Imatinib


title: M5_24_SB431542_DoseA


title: M5_19_Penicillin.G_DoseA


title: CHIP_LBC21_038_Wave5


title: MD_A11_rep168

description:
none
5500024024214122006605.A11

value: classic

value: A


title: MD_A06_rep176

description:
none
5500024024214122006610.A06


title: CHIP_LBC21_040_Wave5


title: CHIP_LBC21_035_Wave5


title: M5_22_Retinoic.Acid_DoseA

value: Retinoic acid


title: M5_15_Isotretinoin_DoseA

value: Isotretinoin

value: TRUE


title: CHIP_LBC21_034_Wave5

value: Blood


title: M5_20_Phenytoin_DoseA

value: Human induced pluripotent-stem-cell derived embryoid body

value: Phenytoin


title: MD_D03_rep16

description:
none
5500024024214122006605.D03

value: melanotic


title: MD_F02_rep150

description:
none
5500024024214122006610.F02


title: CHIP_LBC21_039_Wave5

value: PBMCs


title: M5_23_Thalidomide_DoseA

value: Thalidomide

value: Positive


title: CHIP_LBC21_033_Wave5


title: MD_F07_rep157

description:
none
5500024024214122006605.F07

value: primary medulloblastoma


title: M5_17_Methotrexate_DoseA

value: Methotrexate


title: MD_F03_rep152

description:
none
5500024024214122006610.F03

value: nodular/desmoplastic


title: M5_16_Metformin_DoseA

value: Metformin

value: Negative


title: CHIP_LBC21_045_Wave5


title: M5_14_Imatinib_DoseA

value: Imatinib


title: M5_18_Misoprostol_DoseA

value: Misoprostol

value: FALSE


title: M5_9_DMSO_ctrl

value: DMSO


title: MD_D06_rep14

description:
none
5500024024214122006605.D06

value: classic


title: MD_B12_rep143

description:
none
5500024030402071707278.B12

value: A


title: M5_13_Ibuprofen_DoseA

value: Human induced pluripotent-stem-cell derived embryoid body

value: Ibuprofen

value: TRUE


title: CHIP_LBC21_031_Wave5

value: Blood

value: PBMCs


title: M5_8_DMSO_ctrl


title: CHIP_LBC21_030_Wave5


title: M5_4_DMSO_ctrl


title: M5_12_DMSO_ctrl


title: MD_F12_rep130.1

description:
none
5500024024214122006610.F12


title: MD_E12_rep139

description:
none
5500024024214122006605.E12


title: M5_5_DMSO_ctrl


title: MD_F03_rep145

description:
none
5500024030700072107993.F03


title: CHIP_LBC21_027_Wave5


title: MD_G11_rep13.1

description:
none
5500024030403071907254.G11


title: M5_10_DMSO_ctrl


title: M5_2_DMSO_ctrl


title: M5_11_DMSO_ctrl


title: CHIP_LBC21_032_Wave5


title: MD_C02_rep127

description:
none
5500024024214122006610.C02


title: M5_7_DMSO_ctrl


title: M4_81_Dasatinib_DoseF

value: Dasatinib

value: Positive


title: M4_80_Cyproheptadine_DoseF

value: Cyproheptadine


title: CHIP_LBC21_023_Wave5


title: M5_6_DMSO_ctrl


title: CHIP_LBC21_021_Wave5


title: CHIP_LBC21_028_Wave5


title: M5_3_DMSO_ctrl


title: M4_79_Cetirizine_DoseF

value: Cetirizine


title: CHIP_LBC21_018_Wave5


title: M4_78_Carbamazepine_DoseF

value: Carbamazepine


title: M4_77_Busulfan_DoseF

value: Busulfan


title: CHIP_LBC21_026_Wave5


title: M5_1_DMSO_ctrl


title: MD_D07_rep124

description:
none
5500024030700072107993.D07

value: primary medulloblastoma


title: M4_82_Dexamethasone_DoseF

value: Dexamethasone

value: Negative


title: M4_84_Hydroxyurea_DoseF

value: Hydroxyurea


title: M4_83_Doxycycline_DoseF

value: Doxycycline


title: CHIP_LBC21_012_Wave5


title: MD_E11_rep123.2

description:
none
5500024030700072107993.E11

value: classic

value: D


title: CHIP_LBC21_011_Wave5


title: M4_70_Dexamethasone_DoseE

value: Human induced pluripotent-stem-cell derived embryoid body


title: M4_68CP_Cyproheptadine_DoseE

value: TRUE


title: M4_71_Doxycycline_DoseE


title: M4_69_Dasatinib_DoseE


title: MD_E08_rep109

description:
none
5500024024214122006610.E08

value: nodular/desmoplastic

value: A


title: M4_74_Artesunate_DoseF

value: Artesunate


title: MD_E09_rep106

description:
none
5500024024214122006605.E09


title: M4_75_Ascorbic.Acid_DoseF

value: Ascorbic acid


title: M4_65_Busulfan_DoseE

value: Positive


title: CHIP_LBC21_016_Wave5

value: Blood

value: PBMCs


title: M4_66_Carbamazepine_DoseE

value: Carbamazepine


title: MD_F08_rep108.1

description:
none
5500024024214122006610.F08

value: primary medulloblastoma


title: CHIP_LBC21_009_Wave5


title: M4_76_Bosentan_DoseF

value: Bosentan


title: CHIP_LBC21_017_Wave5


title: MD_E10_rep1

description:
none
5500024030403071907254.E10


title: MD_D04_rep10

description:
none
5500024024214122006605.D04


title: M4_67_Cetirizine_DoseE

value: Cetirizine

value: Negative


title: M4_73_Amoxicillin_DoseF

value: Amoxycillin


title: M4_72_Hydroxyurea_DoseE

value: Hydroxyurea


title: CHIP_LBC21_014_Wave5


title: M4_60_Hydroxyurea_DoseD


title: M4_63_Ascorbic.Acid_DoseE


title: CHIP_LBC21_006_Wave5


title: CHIP_LBC21_004_Wave5


title: CHIP_LBC21_002_Wave5


title: M4_64_Bosentan_DoseE


title: M4_59_Doxycycline_DoseD

value: Doxycycline


title: M4_57_Dasatinib_DoseD

value: Human induced pluripotent-stem-cell derived embryoid body

value: Dasatinib


title: M4_62_Artesunate_DoseE

value: TRUE


title: M4_58_Dexamethasone_DoseD

value: Dexamethasone


title: M4_54_Carbamazepine_DoseD


title: M4_55_Cetirizine_DoseD


title: M4_52_Bosentan_DoseD


title: PBMCs, Grapefruit juice, Volunteer 4

city: Kannapolis

first: Dragan

last: Milenkovic

state: NC

address: 600 Laureate Way

department: Department of Food Bioprocessing & Nutrition Sciences

institute: North Carolina State University

description: Biological replicate (subject) 4 of 9. PBMCs, harvested after the consumption of grapefruit juice for 6 months

hyb_protocol: Fragmentation mix and hybridization buffer (Agilent Low Input Quick Amp Labeling two color Kit) were added and 825 ng of labelled cRNA were hybridized onto G4845A Human GE 4x44K v2 microarray (Agilent, USA) using Agilent SureHyb microarray hybridisation chamber at 65°C for 17 hours. After hybridization, slides were washed in washing buffers.

scan_protocol: Scanned on an Agilent G2505 scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

data_processing: Agilent Feature Extraction Software (version 10.7.3.1) was used for background subtraction and Lowess normalization.  In the Agilent FE files: In the columns “ProcessedSignal” are signals post Lowess normalization and post surrogate processing, so normalized data.  In the columns “MeanSignal” are raw mean signal of the spot.

source_name: PBMCs, postmenopausal women, Grapefruit juice 6 months

label_protocol: 50 ng of total RNA extracted were amplified and fluorescently labelled to produce Cy5 or Cy3 cRNA using the Low Input Quick Amp Labeling two color Kit (Agilent, Santa Clara, CA, USA) in the presence of spike-in two colour control as recommended by the manufacturer

extract_protocol: Total RNA extracted using RNeasy Micro Kit following manufacturer's instructions

treatment_protocol: grapefruit juice vs placebo drink

value: Peripheral Blood mononuclear cells

tag: gender

value: women

tag: treatment

value: Grapefruit juice


title: M4_53_Busulfan_DoseD

value: Busulfan

value: Positive


title: M4_51_Ascorbic.Acid_DoseD

value: Ascorbic acid


title: PBMCs, Grapefruit juice, Volunteer 5

description: Biological replicate (subject) 5 of 9. PBMCs, harvested after the consumption of grapefruit juice for 6 months


title: PBMCs, Grapefruit juice, Volunteer 3

description: Biological replicate (subject) 3 of 9. PBMCs, harvested after the consumption of grapefruit juice for 6 months


title: CHIP_LBC36_002_Wave4

value: Blood

value: PBMCs


title: CHIP_LBC36_001_Wave4


title: CHIP_LBC36_031_Wave4


title: PBMCs, Grapefruit juice, Volunteer 2

description: Biological replicate (subject) 2 of 9. PBMCs, harvested after the consumption of grapefruit juice for 6 months


title: PBMCs, Grapefruit juice, Volunteer 6

description: Biological replicate (subject) 6 of 9. PBMCs, harvested after the consumption of grapefruit juice for 6 months


title: M4_56_Cyproheptadine_DoseD

value: Cyproheptadine


title: CHIP_LBC21_045_Wave4


title: PBMCs, Grapefruit juice, Volunteer 1

description: Biological replicate (subject) 1 of 9. PBMCs, harvested after the consumption of grapefruit juice for 6 months


title: PBMCs, Grapefruit juice, Volunteer 7

description: Biological replicate (subject) 7 of 9. PBMCs, harvested after the consumption of grapefruit juice for 6 months


title: PBMCs, Grapefruit juice, Volunteer 9

description: Biological replicate (subject) 9 of 9. PBMCs, harvested after the consumption of grapefruit juice for 6 months


title: PBMCs, Grapefruit juice, Volunteer 8

description: Biological replicate (subject) 8 of 9. PBMCs, harvested after the consumption of grapefruit juice for 6 months


title: CHIP_LBC21_040_Wave4


title: M4_49_Amoxicillin_DoseD

value: Negative


title: M4_50_Artesunate_DoseD

value: Artesunate


title: M4_61_Amoxicillin_DoseE

value: Amoxycillin


title: PBMCs, Placebo, Volunteer 9

description: Biological replicate (subject) 9 of 9. PBMCs, harvested after the consumption of placebo drink for 6 months

source_name: PBMCs, postmenopausal women, Placebo drink 6 months

value: control


title: M4_48_Hydroxyurea_DoseC

value: Human induced pluripotent-stem-cell derived embryoid body

value: Hydroxyurea


title: CHIP_LBC21_039_Wave4


title: M4_45_Dasatinib_DoseC

value: Dasatinib

value: TRUE


title: M4_47_Doxycycline_DoseC

value: Doxycycline


title: PBMCs, Placebo, Volunteer 8

description: Biological replicate (subject) 8 of 9. PBMCs, harvested after the consumption of placebo drink for 6 months

value: Peripheral Blood mononuclear cells

value: women


title: PBMCs, Placebo, Volunteer 7

description: Biological replicate (subject) 7 of 9. PBMCs, harvested after the consumption of placebo drink for 6 months


title: M4_42_Carbamazepine_DoseC

value: Carbamazepine


title: M4_41_Busulfan_DoseC

value: Busulfan

value: Positive


title: PBMCs, Placebo, Volunteer 6

description: Biological replicate (subject) 6 of 9. PBMCs, harvested after the consumption of placebo drink for 6 months


title: M4_46_Dexamethasone_DoseC

value: Dexamethasone


title: CHIP_LBC21_034_Wave4

value: Blood

value: PBMCs


title: CHIP_LBC21_038_Wave4


title: CHIP_LBC21_035_Wave4


title: M4_40_Bosentan_DoseC

value: Bosentan


title: M4_43_Cetirizine_DoseC

value: Cetirizine

value: Negative


title: M4_37_Amoxicillin_DoseC

value: Amoxycillin


title: PBMCs, Placebo, Volunteer 5

description: Biological replicate (subject) 5 of 9. PBMCs, harvested after the consumption of placebo drink for 6 months

value: control


title: CHIP_LBC21_033_Wave4


title: M4_35_Doxycycline_DoseB

value: Human induced pluripotent-stem-cell derived embryoid body


title: M4_36_Hydroxyurea_DoseB

value: Hydroxyurea


title: CHIP_LBC21_031_Wave4


title: M4_39_Ascorbic.Acid_DoseC

value: Ascorbic acid

value: TRUE


title: CHIP_LBC21_032_Wave4


title: PBMCs, Placebo, Volunteer 3

description: Biological replicate (subject) 3 of 9. PBMCs, harvested after the consumption of placebo drink for 6 months

value: Peripheral Blood mononuclear cells


title: PBMCs, Placebo, Volunteer 4

description: Biological replicate (subject) 4 of 9. PBMCs, harvested after the consumption of placebo drink for 6 months

value: women


title: M4_44_Cyproheptadine_DoseC

value: Cyproheptadine


title: M4_34_Dexamethasone_DoseB


title: M4_33_Dasatinib_DoseB

value: Dasatinib


title: PBMCs, Placebo, Volunteer 1

description: Biological replicate (subject) 1 of 9. PBMCs, harvested after the consumption of placebo drink for 6 months


title: CHIP_LBC21_030_Wave4

description:
DNA (Targeted Myeloid Panel)
LBC_ARCHER.1PCT_VAF.Feb22.non-synonymous.tsv
LBC_ARCHER.1PCT_VAF.Feb22.synonymous.tsv
LBC_ARCHER.2PCT_VAF.Feb22.non-synonymous.tsv
LBC_ARCHER.2PCT_VAF.Feb22.synonymous.tsv


title: CAR T cells, CD58KO-2

city: beijing

first: Xin

last: Yan

address: 28 Fuxing Road

institute: Chinese PLA General Hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM, TPM, readcount values for each Sample

source_name: Blood

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: cell line

value: PBMC

value: Chimeric antigen receptor T cell

value: co-cultured with CD58KO Nalm6 cells


title: M4_31_Cetirizine_DoseB

tag: cell type


title: PBMCs, Placebo, Volunteer 2

description: Biological replicate (subject) 2 of 9. PBMCs, harvested after the consumption of placebo drink for 6 months


title: M4_32_Cyproheptadine_DoseB

tag: run


title: M4_28_Bosentan_DoseB

tag: plate

value: Positive


title: M4_29_Busulfan_DoseB

value: Busulfan

tag: usedforfactoranalysis


title: CHIP_LBC21_023_Wave4

value: Blood

value: PBMCs


title: M4_38_Artesunate_DoseC

value: Artesunate

tag: usedformodelbuilding


title: CAR T cells, WT-1

value: co-cultured with WT


title: LuCaP_208.4_s4_ET4426_PDX_Tumor

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

data_processing:
Sequencing reads were mapped to the hg38 human genome and mm10 mouse genomes using STAR.v2.7.3a. Sequences aligning to the mouse genome deriving from potential contamination with mouse tissue were removed from the analysis using XenofilteR (v1.6).
Gene level abundance was quantitated using the GenomicAlignments summarizeOverlaps function using mode=IntersectionStrict, restricting to primary aligned reads, and counting reads mapping to the exonic regions of genes.
Assembly: hg38
Supplementary files format and content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: LuCaP 208.4 PDX Tumor

growth_protocol: LuCaP xenograft lines were established from specimens acquired at either radical prostatectomy or at autopsy, implanted, and maintained by serial passage in intact immune compromised male mice (PMID: 28156002).

extract_protocol:
Total RNA was isolated from flash frozen LuCaP xenograft tissue with RNA STAT-60 (Tel-Test) followed by purification with RNeasy Mini Kit (Qiagen) utilizing the manufacturer’s recommended DNase digestion (Qiagen).
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.

value: male

value: prostate cancer

tag: molecular phenotype


title: M4_22_Dexamethasone_DoseA

value: Human induced pluripotent-stem-cell derived embryoid body

value: Dexamethasone

tag: contrast

tag: concentration

value: Negative


title: CHIP_LBC21_017_Wave4

tag: wave

tag: cohort


title: M4_21_Dasatinib_DoseA

value: TRUE

tag: conclabel


title: CHIP_LBC21_027_Wave4

tag: sequencing batch


title: CAR T cells, CD58KO-1


title: CHIP_LBC21_026_Wave4


title: M4_30_Carbamazepine_DoseB

value: Carbamazepine

tag: concstr

tag: teratogenicity


title: CAR T cells, WT-2

tag: tissue


title: M4_27_Ascorbic.Acid_DoseB

value: Ascorbic acid


title: M4_26CP_Artesunate_DoseB


title: M4_19_Cetirizine_DoseA

value: Cetirizine


title: CHIP_LBC21_018_Wave4


title: CHIP_LBC21_016_Wave4


title: CHIP_LBC21_021_Wave4


title: LuCaP_208.4_s1_ET3748_PDX_Tumor

tag: gender


title: M4_25_Amoxicillin_DoseB

value: Amoxycillin


title: M4_18_Carbamazepine_DoseA


title: CHIP_LBC21_028_Wave4


title: LuCaP_208.2_s1_ET3778_PDX_Tumor

source_name: LuCaP 208.2 PDX Tumor


title: CHIP_LBC21_014_Wave4


title: M4_23_Doxycycline_DoseA

value: Doxycycline


title: CHIP_LBC21_012_Wave4


title: LuCaP_208.1_s1_ET3823_PDX_Tumor

source_name: LuCaP 208.1 PDX Tumor


title: M4_14_Artesunate_DoseA

value: Positive


title: M4_17_Busulfan_DoseA

value: Busulfan


title: M4_15_Ascorbic.Acid_DoseA


title: LuCaP_208.2_s3_ET4494_PDX_Tumor


title: CHIP_LBC21_011_Wave4

value: Blood


title: M4_24_Hydroxyurea_DoseA

value: Hydroxyurea


title: M4_20_Cyproheptadine_DoseA

value: Cyproheptadine


title: M4_11_DMSO_ctrl

value: DMSO


title: M4_16_Bosentan_DoseA

value: Bosentan


title: LuCaP_208.1_s4_ET4589_PDX_Tumor

value: male

value: prostate cancer


title: M4_12_DMSO_ctrl

value: Human induced pluripotent-stem-cell derived embryoid body


title: M4_9_DMSO_ctrl


title: M4_7_DMSO_ctrl


title: M4_10_DMSO_ctrl


title: M4_4_DMSO_ctrl


title: M4_8_DMSO_ctrl


title: M4_3_DMSO_ctrl


title: M4_5_DMSO_ctrl


title: CHIP_LBC21_006_Wave4

value: PBMCs


title: M4_13_Amoxicillin_DoseA

value: TRUE

value: Negative


title: CHIP_LBC21_004_Wave4


title: CHIP_LBC36_042_Wave4


title: M4_1_DMSO_ctrl


title: M4_2_DMSO_ctrl


title: CHIP_LBC21_002_Wave4


title: M3_82_Dexamethasone_DoseF

value: Dexamethasone


title: M3_80_Cyproheptadine_DoseF


title: M4_6_DMSO_ctrl


title: CHIP_LBC36_036_Wave4


title: M3_81_Dasatinib_DoseF

value: Dasatinib


title: CHIP_LBC36_041_Wave4


title: M3_79_Cetirizine_DoseF

value: Cetirizine


title: CHIP_LBC21_009_Wave4


title: CHIP_LBC36_034_Wave4


title: CHIP_LBC36_038_Wave4


title: M3_74_Artesunate_DoseF

value: Artesunate


title: M3_76_Bosentan_DoseF

value: Positive


title: CHIP_LBC36_035_Wave4


title: M3_84_Hydroxyurea_DoseF


title: CHIP_LBC36_037_Wave4


title: CHIP_LBC36_029_Wave4


title: M3_78_Carbamazepine_DoseF

value: Carbamazepine


title: M3_62_Artesunate_DoseE


title: M3_77_Busulfan_DoseF

value: Busulfan


title: M3_83_Doxycycline_DoseF

value: Doxycycline


title: CHIP_LBC36_033_Wave4

value: Blood


title: CHIP_LBC36_026_Wave4


title: M3_67_Cetirizine_DoseE


title: M3_68_Cyproheptadine_DoseE

value: Cyproheptadine


title: M3_64_Bosentan_DoseE

value: Bosentan


title: M3_66_Carbamazepine_DoseE


title: M3_65_Busulfan_DoseE


title: M3_72_Hydroxyurea_DoseE

value: Hydroxyurea


title: M3_70_Dexamethasone_DoseE


title: CHIP_LBC36_032_Wave4


title: M3_59_Doxycycline_DoseD


title: M3_60_Hydroxyurea_DoseD


title: M3_71_Doxycycline_DoseE


title: M3_58_Dexamethasone_DoseD


title: CHIP_LBC36_027_Wave4


title: M3_75_Ascorbic.Acid_DoseF

value: Ascorbic acid


title: LuCaP_173.2A_s11_ET2699_PDX_Tumor

source_name: LuCaP 173.2A PDX Tumor

value: male

value: prostate cancer


title: CHIP_LBC36_021_Wave4

value: PBMCs


title: M3_73_Amoxicillin_DoseF

source_name: Human induced pluripotent-stem-cell derived embryoid body

value: Amoxycillin

value: TRUE

value: Negative


title: M3_69_Dasatinib_DoseE

value: Human induced pluripotent-stem-cell derived embryoid body

value: Dasatinib


title: CHIP_LBC36_024_Wave4


title: M3_63_Ascorbic.Acid_DoseE


title: M3_57_Dasatinib_DoseD

value: Positive


title: CHIP_LBC36_020_Wave4


title: CHIP_LBC36_030_Wave4


title: M3_61_Amoxicillin_DoseE


title: CHIP_LBC36_018_Wave4


title: CHIP_LBC36_014_Wave4


title: CHIP_LBC36_010_Wave4


title: M3_50_Artesunate_DoseD

value: Artesunate


title: M3_51_Ascorbic.Acid_DoseD


title: M3_54_Carbamazepine_DoseD

value: Carbamazepine


title: M3_44_Cyproheptadine_DoseC


title: CHIP_LBC36_017_Wave4


title: M3_49_Amoxicillin_DoseD


title: CHIP_LBC36_009_Wave4


title: M3_52_Bosentan_DoseD


title: M3_46_Dexamethasone_DoseC

value: Dexamethasone


title: M3_45_Dasatinib_DoseC


title: CHIP_LBC36_007_Wave4

value: Blood


title: M3_55_Cetirizine_DoseD

value: Cetirizine


title: M3_41_Busulfan_DoseC

value: Busulfan


title: M3_48_Hydroxyurea_DoseC

value: Hydroxyurea


title: CHIP_LBC36_008_Wave4


title: M3_47_Doxycycline_DoseC

value: Doxycycline


title: M3_42_Carbamazepine_DoseC


title: M3_43_Cetirizine_DoseC


title: M3_53_Busulfan_DoseD


title: M3_39_Ascorbic.Acid_DoseC

value: Ascorbic acid


title: CHIP_LBC36_006_Wave4


title: M3_56_Cyproheptadine_DoseD

value: Cyproheptadine


title: M3_40_Bosentan_DoseC

value: Bosentan


title: CHIP_LBC36_005_Wave4

value: PBMCs


title: M3_35_Doxycycline_DoseB

value: TRUE


title: CHIP_LBC36_003_Wave4


title: M3_37_Amoxicillin_DoseC

value: Amoxycillin

value: Negative


title: M3_33_Dasatinib_DoseB

value: Human induced pluripotent-stem-cell derived embryoid body

value: Dasatinib


title: M3_34_Dexamethasone_DoseB


title: CHIP_LBC21_046_Wave4


title: M3_26_Artesunate_DoseB

value: Artesunate

value: Positive


title: M3_31CP_Cetirizine_DoseB


title: M3_29_Busulfan_DoseB


title: CHIP_LBC21_024_Wave4


title: CHIP_LBC21_036_Wave4


title: CHIP_LBC21_037_Wave4


title: M3_28_Bosentan_DoseB


title: M3_36_Hydroxyurea_DoseB


title: M3_38_Artesunate_DoseC


title: M3_32_Cyproheptadine_DoseB


title: M3_23_Doxycycline_DoseA


title: M3_21_Dasatinib_DoseA


title: CHIP_LBC21_001_Wave4


title: CHIP_LBC36_002_Wave3


title: CHIP_LBC21_019_Wave4


title: CHIP_LBC21_010_Wave4


title: M3_25_Amoxicillin_DoseB


title: M3_27_Ascorbic.Acid_DoseB


title: M3_20_Cyproheptadine_DoseA


title: M3_22_Dexamethasone_DoseA

value: Dexamethasone


title: M3_24_Hydroxyurea_DoseA


title: M3_18_Carbamazepine_DoseA

value: Carbamazepine


title: CHIP_LBC21_015_Wave4

value: Blood


title: M3_30_Carbamazepine_DoseB


title: M3_19_Cetirizine_DoseA

value: Cetirizine


title: M3_16_Bosentan_DoseA


title: M3_15_Ascorbic.Acid_DoseA


title: M3_14_Artesunate_DoseA


title: M3_17_Busulfan_DoseA

value: Busulfan


title: CHIP_LBC21_040_Wave3


title: CHIP_LBC21_039_Wave3


title: CHIP_LBC36_001_Wave3


title: M3_8_DMSO_ctrl

value: DMSO


title: M3_11_DMSO_ctrl


title: M3_5_DMSO_ctrl


title: M3_9_DMSO_ctrl


title: M3_12_DMSO_ctrl


title: CHIP_LBC21_045_Wave3


title: M3_13_Amoxicillin_DoseA


title: M3_10_DMSO_ctrl


title: CHIP_LBC21_032_Wave3


title: M2_84_RO-12_DoseF


title: M2_82_RO-10_DoseF


title: M3_7_DMSO_ctrl


title: M3_6_DMSO_ctrl


title: CHIP_LBC21_031_Wave3


title: M3_1_DMSO_ctrl


title: CHIP_LBC21_035_Wave3


title: M3_4_DMSO_ctrl


title: CHIP_LBC21_038_Wave3


title: CHIP_LBC21_034_Wave3


title: M2_81_RO-9_DoseF


title: M3_2_DMSO_ctrl


title: CHIP_LBC21_033_Wave3


title: M2_79_RO-7_DoseF


title: CHIP_LBC21_030_Wave3


title: M2_77_RO-5_DoseF


title: M3_3_DMSO_ctrl


title: CHIP_LBC21_026_Wave3


title: M2_75_RO-3_DoseF


title: M2_76_RO-4_DoseF


title: M2_74_RO-2_DoseF


title: M2_73_RO-1_DoseF


title: M2_83_RO-11_DoseF


title: CHIP_LBC21_021_Wave3


title: M2_80_RO-8_DoseF


title: CHIP_LBC21_028_Wave3


title: CHIP_LBC21_018_Wave3


title: M2_78_RO-6_DoseF


title: M2_70_RO-10_DoseE


title: CHIP_LBC21_017_Wave3


title: CHIP_LBC21_016_Wave3


title: M2_66_RO-6_DoseE


title: CHIP_LBC21_012_Wave3


title: M2_64_RO-4_DoseE


title: M2_60_RO-12_DoseD


title: M2_62_RO-2_DoseE


title: CHIP_LBC21_023_Wave3


title: M2_72_RO-12_DoseE


title: CHIP_LBC21_027_Wave3


title: M2_71_RO-11_DoseE


title: M2_68_RO-8_DoseE


title: M2_53_RO-5_DoseD


title: M2_50_RO-2_DoseD


title: CHIP_LBC21_002_Wave3


title: CHIP_LBC36_042_Wave3


title: M2_67_RO-7_DoseE


title: CHIP_LBC21_014_Wave3


title: M2_48_RO-12_DoseC


title: M2_65_RO-5_DoseE


title: M2_61_RO-1_DoseE


title: M2_69_RO-9_DoseE


title: M2_45_RO-9_DoseC


title: CHIP_LBC21_006_Wave3


title: M2_63_RO-3_DoseE


title: M2_52_RO-4_DoseD


title: M2_58_RO-10_DoseD


title: M2_44_RO-8_DoseC


title: CHIP_LBC21_004_Wave3


title: M2_43_RO-7_DoseC


title: M2_55_RO-7_DoseD


title: CHIP_LBC36_038_Wave3


title: M2_56_RO-8_DoseD


title: M2_42_RO-6_DoseC


title: M2_54_RO-6_DoseD


title: CHIP_LBC21_011_Wave3


title: CHIP_LBC36_041_Wave3


title: M2_51_RO-3_DoseD


title: M2_57_RO-9_DoseD


title: CHIP_LBC36_037_Wave3


title: M2_59_RO-11_DoseD


title: M2_47_RO-11_DoseC


title: CHIP_LBC21_009_Wave3


title: M2_49_RO-1_DoseD


title: CHIP_LBC36_040_Wave3


title: CHIP_LBC36_035_Wave3


title: M2_40_RO-4_DoseC


title: WGBS_ES_RF_necropsy_#1_Muscle

city: Columbia

first: Rocío

middle: Melissa

last: Rivera

state: MO

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: University of Missouri, Columbia

data_processing:
Duplicated reads generated during PCR and sequencing were removed from raw sequencing reads using the clumpify function of BBMap (version 38.90). The remaining raw reads were trimmed for adapter sequences and low quality bases using trimmomatic (version 0.39) with parameters ‘ILLUMINACLIP:adapter_seq:2:30:10:1:true LEADING:20 TRAILING:20 AVGQUAL:20 MAXINFO:0:0.5’. Trimmed reads were aligned to the bovine genome using bismark (version 0.23.0) with parameters ‘-X 900 --unmapped --ambiguous --non_bs_mm’. Trimmed reads were also aligned to lambda phage genome to determine bisulfite conversion rates. Samtools (version 1.13) was used to convert, sort, filter, and index bam files. MarkDuplicates function of picard (version 2.25.5) was used to further remove duplicated reads after alignment. Read groups were added for each samples using AddOrReplaceReadGroups function of picard. The dataset of known variants in bovine, namely ARS1.2PlusY_BQSR_v3.vcf.gz, was acquired from the 1000 bull genome project and served as reference to identify genomic variants in WGBS data. Indel realignment was performed using RealignerTargetCreator and IndelRealigner functions of BisSNP (version 1.0.1). Base quality recalibration was carried out using BisulfiteCountCovariates and BisulfiteTableRecalibration functions of BisSNP (version 0.82.2) since these functions are missing in version 1.0.0 and 1.0.1. Parameters used for BisulfiteCountCovariates were ‘-cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -baqGOP 30’. Genomic variants were identified using BisSNP (version 1.0.1) with default setting expect that ‘-bsRate’ was changed to bisulfite conversion rate observed from lambda phage genome alignment for each sample. BisSNP identified variants were filtered by its VCFpostprocess function with parameter ‘-windSizeForSNPfilter 0’. Additionally, genomic variants were identified using BS-SNPer (version 1.0) with parameters ‘-minhetfreq 0.1 --minhomfreq 0.85 --minquali 15 --mincover 5 --maxcover 1000 --minread2 2 --errorate 0.02 --mapvalue 20’. M-bias plots were generated using bismark and the first 3 bases of R1 reads and the first 4 bases of R2 reads showed biased CpG methylation level, thus these bases were excluded from downstream analyses. CpG methylation information were extracted from the bam files using bismark_methylation_extractor function of bismark with parameters ‘-p --ignore 3 --ignore_r2 4 --comprehensive --no_header –gzip --bedGraph --buffer_size 50% --cytosine_report’. Statistical analyses were conducted using R package hummingbird (version 1.2.0) with parameter ‘minCpGs = 10, minLength = 100, maxGap = 300’ to identify differentially methylated regions (DMRs) in various comparisons. DMRs with at least 15% difference in methylation level (both gain and loss of methylation) and at least 4 mean read coverage at CpG sites were reported. The sex chromosomes were not analyzed to circumvent confounding created by X chromosome inactivation associated DNA methylation.
Assembly: ARS-UCD1.2
Supplementary files format and content: Read coverage and DNA methylation percentage for CpG sites in BEDGRAPH format.

organism: Bos taurus

source_name: Muscle

growth_protocol: US_Control animals were purchased from the University of Missouri Foremost Dairy Research Center and used as tissue donors. Tissue samples of stillborn US_SLOS animals were collected by their owners, veterinarians, or our collaborators and shipped to us. Animals from Spain were generated as described previously (PMID: 32781545) and used as tissue donors.

extract_protocol:
Blood cells and tissues were lysed in lysis buffer (0.05 M Tris-HCl (pH 8.0), 0.1 M EDTA, and 0.5% (w/v) SDS) with proteinase K (Fisher BioReagents, BP1700) at 55°C for four hours (for blood cells) or overnight (for tissues). Genomic DNA was extracted with Phenol:Chloroform:Isoamyl Alcohol (SIGMA, P3803) following the manufacturer’s instructions. The concentration of DNA was measured by using a NanoDrop® ND-1000 Spectrophotometer (Thermo Fisher Scientific) and DNA integrity was confirmed by electrophoresis on a 0.7% agarose gel. Genomic DNA samples were stored at -20°C.
This WGBS was conducted by CD Genomics (Shirley, NY, USA). Information on library preparation and sequencing obtained from the company is as follows: For WGBS library preparation, 1 ug of genomic DNA was fragmented by sonication to a mean size of approximately 200-400 bp. Fragmented DNA was end-repaired, 5'-phosphorylated, 3'-dA-tailed and then ligated to methylated adapters. The methylated adapter-ligated DNAs were purified using 0.8× Agencourt AMPure XP magnetic beads and subjected to bisulfite conversion by ZYMO EZ DNA Methylation-Gold Kit (zymo). The converted DNAs were then amplified using 25 μl KAPA HiFi HotStart Uracil+ ReadyMix (2X) and 8-bp index primers with a final concentration of 1 μM each. The constructed WGBS libraries were then analyzed by Agilent 2100 Bioanalyzer and quantified by a Qubit fluorometer with Quant-iT dsDNA HS Assay Kit (Invitrogen), and finally sequenced on Illumina Hiseq X ten sequencer. 0.1-1% lambda DNA were added during the library preparation to monitor bisulfite conversion rate.

treatment_protocol: For Spain animals, the control group (ES_Control) were conceived by artificial insemination using frozen-thawed semen from one bull among synchronized cows on the day of presumptive estrus. In vitro produced animals were generated using slaughterhouse oocytes and semen from the same bull as controls. Following fertilization, embryos were separated in two different groups: one culture group (ES_ART) composed of synthetic oviductal fluid (SOF) media supplemented with bovine serum albumin during the 7-8 days of culture and another group (ES_RF) composed of SOF media supplemented with bovine oviductal fluid (NaturARTs-BOF-EL, Embryocloud, Spain) for the first 4 days and bovine uterine fluid (NaturARTs-BUF-ML, Embryocloud) for the following days. Embryos (blastocysts and expanded blastocysts) were vitrified on day 7 or 8 of culture and stored until use. Recipients were synchronized and on day 6 to 8 after presumptive estrus, each cow received one thawed embryo.

value: Calf muscle

tag: breed

value: Asturian Valley x Limousin crossbred

tag: Sex

value: Male

tag: country

value: Spain (ES)

tag: conception method

value: Assisted reproductive technology supplemented reproductive fluids

tag: disease status

value: LOS

value: Muscle


title: WGBS_ES_RF_#2_Muscle

value: Healthy


title: CHIP_LBC36_034_Wave3

tag: cell type

value: PBMCs


title: WGBS_ES_RF_necropsy_#2_Muscle

value: Female


title: CHIP_LBC36_033_Wave3


title: M2_41_RO-5_DoseC

value: Human induced pluripotent-stem-cell derived embryoid body

tag: run

tag: plate

tag: usedforfactoranalysis

value: TRUE

tag: usedformodelbuilding

value: Negative


title: CHIP_LBC36_039_Wave3

tag: wave

tag: cohort

value: Blood


title: WGBS_ES_RF_#3_Muscle


title: WGBS_ES_ART_#1_Muscle

value: Assisted reproductive technology


title: WGBS_ES_Control_#3_Muscle

value: Asturian Valley x Holstein

value: Artificial insemination


title: CHIP_LBC36_028_Wave3

tag: sequencing batch


title: M2_46_RO-10_DoseC

tag: contrast

tag: concentration

tag: conclabel

tag: concstr

value: Positive


title: CHIP_LBC36_036_Wave3

tag: tissue


title: M2_33_RO-9_DoseB

tag: teratogenicity


title: LuCaP_77CR_s24n2_ET2383_PDX_Tumor

source_name: LuCaP 77CR PDX Tumor

tag: gender

value: male

value: prostate cancer

tag: molecular phenotype


title: CHIP_LBC36_027_Wave3


title: WGBS_US_SLOS_#8_Tongue

source_name: Tongue

value: Calf tongue

tag: breed

value: Shorthorn crossbred

tag: Sex

value: Male

tag: country

value: United States (US)

tag: conception method

value: Artificial insemination/natural mating

tag: disease status

value: SLOS

value: Tongue


title: LuCaP_77CR_s17n2_ET138_PDX_Tumor

tag: cell type


title: M2_39_RO-3_DoseC

value: Human induced pluripotent-stem-cell derived embryoid body

tag: run

tag: plate

tag: usedforfactoranalysis

tag: usedformodelbuilding


title: WGBS_ES_RF_#1_Muscle

value: Calf muscle

value: Asturian Valley x Limousin crossbred

value: Spain (ES)

value: Assisted reproductive technology supplemented reproductive fluids

value: Healthy

value: Muscle


title: WGBS_ES_Control_#1_Muscle

value: Asturian Valley x Holstein

value: Artificial insemination


title: WGBS_ES_ART_#4_Muscle

value: Assisted reproductive technology


title: CHIP_LBC36_030_Wave3

tag: wave

tag: cohort

tag: sequencing batch

value: Blood

value: PBMCs


title: M2_38_RO-2_DoseC

value: TRUE

tag: contrast

tag: concentration

tag: conclabel

tag: concstr

value: Negative


title: CHIP_LBC36_024_Wave3

tag: tissue


title: CHIP_LBC36_023_Wave3


title: M2_36_RO-12_DoseB

tag: teratogenicity


title: CHIP_LBC36_032_Wave3


title: M2_29_RO-5_DoseB


title: M2_35_RO-11_DoseB


title: CHIP_LBC36_029_Wave3


title: M2_34_RO-10_DoseB

value: Positive


title: M2_37_RO-1_DoseC


title: WGBS_ES_Control_#2_Muscle

tag: breed

tag: Sex

value: Male

tag: country


title: M2_28_RO-4_DoseB

tag: cell type


title: WGBS_US_SLOS_#5_Muscle

value: Angus

value: Female

value: United States (US)

tag: conception method

value: Artificial insemination/natural mating

tag: disease status

value: SLOS


title: WGBS_ES_ART_#3_Muscle

value: Calf muscle

value: Asturian Valley x Limousin crossbred

value: Spain (ES)


title: WGBS_US_SLOS_#7_Muscle

value: Shorthorn crossbred

value: Muscle


title: WGBS_US_SLOS_#8_Muscle


title: CHIP_LBC36_026_Wave3


title: WGBS_US_SLOS_#7_Tongue

value: Calf tongue

value: Tongue


title: M2_31_RO-7_DoseB

value: Human induced pluripotent-stem-cell derived embryoid body

tag: run

tag: plate

tag: usedforfactoranalysis


title: M2_25_RO-1_DoseB

value: TRUE

tag: usedformodelbuilding


title: CHIP_LBC36_018_Wave3

tag: wave

tag: cohort

tag: sequencing batch

value: Blood

value: PBMCs


title: M2_30_RO-6_DoseB

tag: contrast

tag: concentration

tag: conclabel

value: Negative


title: CHIP_LBC36_014_Wave3

tag: tissue


title: WGBS_US_SLOS_#4_Muscle

description: Female (predicted based on chromosome Y alignment)

tag: breed

value: Hereford


title: M2_26_RO-2_DoseB

tag: concstr

tag: teratogenicity


title: WGBS_US_SLOS_#3_Tongue

description: Male (predicted based on chromosome Y alignment)

value: Simmental

tag: Sex

value: Male

tag: country


title: M2_32_RO-8_DoseB

tag: cell type

value: Positive


title: CHIP_LBC36_022_Wave3


title: CHIP_LBC36_021_Wave3


title: WGBS_US_SLOS_#6_Muscle

value: Charolais

value: United States (US)

tag: conception method

value: Artificial insemination/natural mating

tag: disease status

value: SLOS


title: WGBS_US_SLOS_#6_Tongue


title: CHIP_LBC36_012_Wave3


title: LuCaP_49_p70s18n16_PDX_Tumor

source_name: LuCaP 49 PDX Tumor

tag: gender

value: male

value: prostate cancer

tag: molecular phenotype


title: CHIP_LBC36_020_Wave3

tag: wave


title: M2_21_RO-9_DoseA

tag: run

tag: plate

tag: usedforfactoranalysis

tag: usedformodelbuilding


title: CHIP_LBC36_011_Wave3

tag: cohort

tag: sequencing batch


title: M2_27_RO-3_DoseB

tag: contrast

tag: concentration

tag: conclabel


title: M2_24_RO-12_DoseA

tag: concstr

tag: teratogenicity


title: CHIP_LBC36_013_Wave3

tag: tissue

tag: cell type


title: M2_23_RO-11_DoseA


title: WGBS_US_SLOS_#1_Ear

source_name: Ear

value: Calf ear

tag: breed

value: Angus

tag: Sex

tag: country

tag: conception method

tag: disease status

value: Ear


title: WGBS_US_SLOS_#2_Muscle

value: Calf muscle

value: Muscle


title: CHIP_LBC36_017_Wave3

tag: wave

value: Blood

value: PBMCs


title: M2_22_RO-10_DoseA

value: Human induced pluripotent-stem-cell derived embryoid body

tag: run

tag: plate

tag: usedforfactoranalysis

value: TRUE


title: WGBS_US_Control_#3_Muscle

value: Holstein

value: Male

value: Artificial insemination

value: Healthy


title: M2_17_RO-5_DoseA

tag: usedformodelbuilding

value: Negative


title: CHIP_LBC36_008_Wave3

tag: cohort

tag: sequencing batch


title: WGBS_US_Control_#2_Muscle

value: United States (US)


title: M2_16_RO-4_DoseA

tag: contrast

tag: concentration

tag: conclabel


title: WGBS_ES_RF_#3_Blood

tag: tissue

value: Calf blood

value: Asturian Valley x Limousin crossbred

value: Spain (ES)

value: Assisted reproductive technology supplemented reproductive fluids


title: M2_20_RO-8_DoseA

tag: cell type

tag: concstr

tag: teratogenicity

value: Positive


title: M2_15_RO-3_DoseA


title: CHIP_LBC36_006_Wave3


title: WGBS_ES_ART_#2_Blood

tag: breed

tag: Sex

value: Female

tag: country

value: Assisted reproductive technology

value: LOS


title: M2_19_RO-7_DoseA


title: CHIP_LBC36_005_Wave3

tag: wave

value: Blood

value: PBMCs


title: CHIP_LBC36_010_Wave3


title: WGBS_ES_RF_#2_Blood

tag: conception method

tag: disease status


title: CHIP_LBC21_046_Wave3


title: WGBS_US_Control_#1_Muscle

value: Calf muscle

value: Muscle


title: WGBS_ES_Control_#1_Blood

value: Asturian Valley x Holstein

value: Male


title: CHIP_LBC36_007_Wave3


title: WGBS_ES_Control_#3_Blood

value: Artificial insemination

value: Healthy


title: M2_13_RO-1_DoseA

value: Human induced pluripotent-stem-cell derived embryoid body

tag: run

tag: plate

tag: usedforfactoranalysis

value: TRUE


title: Dox_At-1

organism: Arabidopsis thaliana

value: leaf

tag: genotype

value: WT

tag: treatment

value: 10 μg/mg doxycycline


title: WGBS_ES_RF_#1_Blood

value: Calf blood

value: Asturian Valley x Limousin crossbred

value: Spain (ES)

value: Assisted reproductive technology supplemented reproductive fluids


title: CHIP_LBC36_009_Wave3

tag: cohort

tag: sequencing batch

value: Blood


title: CHIP_LBC21_037_Wave3

tag: tissue

value: PBMCs


title: CK_At-3

value: CK


title: Dox_At-3


title: M2_14_RO-2_DoseA

tag: cell type

tag: usedformodelbuilding

tag: contrast

tag: concentration

tag: conclabel

value: Negative


title: WGBS_US_SLOS_#6_sibling_Blood

tag: breed

value: Charolais

tag: Sex

tag: country

value: United States (US)

value: Artificial insemination/natural mating


title: CHIP_LBC21_029_Wave3

tag: wave


title: M2_18_RO-6_DoseA

tag: run

tag: concstr

tag: teratogenicity


title: CK_At-1

tag: genotype


title: WGBS_ES_Control_#2_Blood

value: Asturian Valley x Holstein

value: Male

tag: conception method

value: Artificial insemination

tag: disease status

value: Healthy


title: CHIP_LBC21_025_Wave3

tag: cohort

tag: sequencing batch


title: WGBS_US_SLOS_#6_dam_Blood

tag: tissue

value: Female


title: Dox_At-2

value: leaf

value: WT

tag: treatment

value: 10 μg/mg doxycycline


title: WGBS_US_Control_#3_Blood

value: Calf blood

value: Holstein


title: M2_12_DMSO_ctrl

tag: cell type

value: Human induced pluripotent-stem-cell derived embryoid body

tag: plate

value: DMSO

tag: usedforfactoranalysis

value: TRUE

tag: usedformodelbuilding

tag: contrast


title: Arabidopsis root, suvh6, H.schachtii infected_RNA_rep 3

city: Knoxville

first: Morgan

last: Bennett

email: mmbennet@vols.utk.edu, thewezi@utk.edu

state: TN

address: 2505 E J Chapman Drive

department: Plant Sciences

institute: University of Tennessee

data_processing:
Quality assessment was performed on fastq raw data files using FastQC.
Paired-end RNA-seq reads were mapped to the Arabidopsis thaliana reference genome with STAR (v2.5) using default settings.
Uniquely mapped paired-end reads were counted using Htseq (v0.10.0).
The mapping output files of the three replicates for each genotype/ condition were merged. Then, read counts of uniquely mapped reads were analyzed for their differential expression between mutant versus wild-type plants and infected versus noninfected plants using DESeq in the R environment.
Genome_build: Arabidopsis thaliana TAIR10.28
Supplementary_files_format_and_content: Read count text files were generated using Htseq.

source_name: root tissue

growth_protocol: Mutant and wild-type seeds were germinated on modified Knop's medium in large petri plates and grown at 22°C under long day conditions.

extract_protocol:
Root tissues of 15-day-old (noninfected) or 5 dpi (H. schachtii infected) plants were collected and frozen immediately in liquid nitrogen. Total RNA was extracted using Trizol reagent (Invitrogen) using the Zymo Direct-zol RNA Miniprep Plus kit (R2071). RNA quality was assessed using an RNA nano bioanalyzer chip (Agilent 2100).
For the costrucion of a non-stranded, non-directional mRNA library, mature mRNAs were processed and captured using olido(dT) beads following the addition of a 3' poly(A) tail.

treatment_protocol: Replicates of each genotype were inoculated with 100 freshly-hatched J2 H. schachtii per plant at 10-days-old. Inoculated replicates were incubated in the dark at 26°C for 24 hours to facillitate nematode infection. Following incubation, inoculates replicates were grown in light conditions as previously described until 5 days post inoculation (dpi).

tag: developmental stage

value: 5 days post inoculation

value: inoculated with 100 J2 H. schachtii per plant at 10 days old


title: M2_11_DMSO_ctrl

tag: concentration

tag: conclabel


title: CHIP_LBC36_003_Wave3

tag: wave

value: Blood

value: PBMCs


title: CHIP_LBC21_022_Wave3


title: M2_7_DMSO_ctrl

tag: run

tag: concstr

tag: teratogenicity


title: CHIP_LBC21_036_Wave3


title: M2_6_DMSO_ctrl


title: Arabidopsis root, suvh6, H.schachtii infected_RNA_rep 1

tag: genotype


title: CHIP_LBC21_020_Wave3

tag: cohort


title: Arabidopsis root, suvh6, noninfected_RNA_rep 3

value: 15 days old

value: untreated


title: CHIP_LBC21_019_Wave3

tag: sequencing batch


title: M2_4_DMSO_ctrl


title: Arabidopsis root, suvh6, noninfected_RNA_rep 2


title: CHIP_LBC21_013_Wave3

tag: tissue