title: UTHT5_ROW18_1


title: IAP CRTL 5µm_3

status: Public on Mar 09 2022

type: SRA

city: Leicester

first: Shaun

middle: Michael

last: Cowley

address: Henry Welcome Building, Leicester LE1 7RH

department: Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

library_source: transcriptomic

data_processing:
Hisat2 v2.2.1 alignment to GRCh38
Samtools v1.9 for sorting, bam coversion and indexing
LiBiNorm v2.5 run in (-z) htseq compatible mode for counting reads
DESeq2 was used for downstream processing
Genome_build: GRCh38 downloaded from HISAT2
https://genome-idx.s3.amazonaws.com/hisat/grch38_tran.tar.gz
Supplementary_files_format_and_content: counts

molecule: total RNA

organism: Homo sapiens

source_name: HCT116 from ATCC® CCL-247™

growth_protocol: The human colorectal carcinoma cell line HCT116 was obtained from ATCC (ATCC; CCL-247™). Cells were maintained in Dulbecco's Modified Eagle Medium (DMEM) (Gibco; 41963039), supplemented with 50 µL/mL (10% (v/v) foetal bovine serum (FBS) (Sigma; F9665) and 1.1 U/mL (1.1% v/v) Penicillin-Streptomycin-Glutamine (Gibco; 10378016); collectively termed M10 media. As an adherent cell line, HCT116 cells were seeded at a density of ~2.2 x 106 on 10 cm tissue culture treated plates for cell maintenance.

extract_protocol:
RNA was extracted from snap frozen pellets using Direct-Zol RNA MiniPrep kit (Zymo research #R2052)
Library preparation and sequencing was performed by Novogene (mRNA library preparation (poly A enrichment))

treatment_protocol: HCT116 cells were seeded at a density of 4x105 cells on 6-well plates for 24 hours prior to JPS0 treatment. Dilutions of JPS0S targeting class I HDACS were made from 50mM stock solutions synthesised and prepared in house by Joshua Smalley. HCT116 cells were then treated with JPS0 concentrations stated and harvested 24 hours later.

tag: cell line

tag: tumour type

value: colorectal carcinoma

tag: developmental stage

value: Adult

tag: gender

value: male

tag: agent

value: IAP CTRL 5microm


title: JPS027 5µm_3

value: JPS027 5microm


title: JPS026 5µm_3

value: JPS026 5microm


title: UTHT5_ROW13_16

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

country: Switzerland

institute: University of Geneva

description:
singlecell_countmatrix.tsv.gz
singlecell_metadata.tsv

data_processing:
Single cell only: The 4bp UMI sequence (initially sequenced in read1), are appended at the end of the headers of the reads (here the reads we provide are resulting from this operation)
Reads are mapped with STAR on the mouse genome GRCm38 considering Ensembl 85 as genome annoatations
Single cell only: bam files are processed with umi_tools to deduplicate reads with identical UMI sequence
gene expression are quantifyied using summarizeOverlaps() method of the R package GenomicsAlignments(). Only exonic reads are considered in the quantification (this includes 5' and 3' UTRs), and only reads with a mapping quality >=255 (to exclude those ambiguously mapping at multiple positions).
Genome_build: GRCm38
Supplementary_files_format_and_content: singlecell_countmatrix.tsv.gz: is a count matrix in tab-separated format. It contains the result of the single cell quantification for all genes. The integers values represent the number of exonic reads mapping into each gene after UMI correction. The first columns contains the gene name that is quantified.    bulk_countmatrix.tsv.gz: count matrix for the bulk experiments in tab-separated format.    singlecell_metadata.tsv: is a table containing metadata information for each cell in tab-separated. The content of the columns are: MT=proportion of mithocondrial reads; ngenes=number of expressed gene; epor_age=age at which the mous as been electroporated; collection_age=age at which cells were collected; cond=condition Control/miR-137/miR-122; cell_type, cell_type_pred1, cell_type_pred2: predicted cell types for the cell; tSNE1, tSNE2= coordinate of the cell in the t-SNE space

molecule: polyA RNA

organism: Mus musculus

source_name: cortex

extract_protocol:
Single-cell RNA sequencing    Embryonic cortex: Tissue collection was performed as in Telley et al., Science 2019. Briefly, pregnant females were sacrificed, and embryos were extracted in ice-cold HBSS either at E15.5 and E17.5 after E14.5 in utero electroporation. Three hundred micrometer- acute coronal brain sections were performed after embedding in 4% low melt- agar using a vibratome (Leica, #VT1000S) under RNase-free conditions. The putative primary somatosensory cortex (S1) was microdissected using a Leica Dissecting Microscope (Leica, #M165FC) and incubated in 0.05% trypsin at 37°C for 5 minutes. Following tissue digestion, cells were incubated in fetal bovine serum and cells were manually dissociated via gentle pipetting. Cells were then centrifuged for 5 minutes at 500 rpm, resuspended in 1 mL FACS buffer (2 mg/mL glucose, 0.1% bovine serum albumin, 1/50 citrate phosphate dextrose, 10 units/mL DNaseI, 1 uM MgCl2, in L15 medium) and filtered using a 70 mm- cell strainer (ClearLine, #141379C), before 10 minute- incubation with Hoechst (0.1 mg/mL) at 37°C .    Postnatal cortex: Tissue collection was performed as in Klingler et al., Curr Biol 2019. Briefly, 600 um acute coronal brain sections were cut on a vibratome and S1 was microdissected as described above in ice-cold oxygenated artificial cerebrospinal fluid (ACSF) under RNase-free conditions. Cells were next dissociated by incubating microdissected samples in 0.5 mg/mL pronase (Sigma, #P5147) at 37°C for 10 minutes, followed by a 3 minute- inactivation in 5% bovine serum albumin, washes in ACSF and manual trituration using pulled glass pipettes of decreasing diameters. Cells were then centrifuged for 10 minutes at 500 rpm, resuspended and filtered using a 70 um- cell strainer (ClearLine, #141379C), incubated for 10 minutes with Hoechst (0.1 mg/mL) at 37°C.    Singlet GFP+/Hoechst+ embryonic and postnatal cells were sorted using a Beckman Coulter Moflo Astrios FAC-sorter according to their Forward and Slide scattering properties, and their negativity for Draq7TM (Viability dye, far red DNA intercalating agent, Beckman Coulter, #B25595). Three microliters of C1 Suspension Reagent (Fluidigm) was added to 10 ul of FACsorted cells, which were captured into 800 well- AutoPrep integrated fluidic circuit (IFC) designed for 10 to 17 um diameter-cells (Fluidigm HT800, #100-57-80), and imaged using the ImageXpress Micro Widefield High Content Screening System (Molecular Devices®).        Bulk RNA sequencing    Brains were collected from E14.5 in utero electroporated miR-122 pups at P7. The primary somatosensory cortex was microdissected following the same procedure as described above with further separation of superficial (SL) and deep (DL) layers. SL and DL cells were dissociated and FACsorted as for single-cell RNA sequencing.
Single-cell RNA sequencing  cDNA synthesis and preamplification was processed following the manufacturer’s instructions (C1 system, Fluidigm). cDNA libraries were prepared using Nextera XT DNA library prep kit (Illumina), quality control was done using 2001 Bioanalyzer from Agilent, and sequenced using HiSeq 2500 sequencer for E14.5 electroporated pups, and HiSeq 5000 sequencer for E14 and E15.5 electroporated pups with an expected sequencing depth of 1M reads per single cell, and a final mapping read length of 70bp.    Bulk RNA sequencing  RNA from each sample was extracted and quality control was done using 2001 Bioanalyzer from Agilent. cDNA libraries were obtained using SMARTseq v4 kit (Clontech, # 634888) and sequenced using HiSeq 2500 sequencer.

tag: tissue

value: cortex


title: UTHT5_ROW16_14


title: JPS036 10µm_3

value: JPS036 10microm


title: UTHT5_ROW21_14


title: JPS035 10µm_3

value: JPS035 10microm


title: JPS039 10µm_3

value: JPS039 10microm


title: UTHT5_ROW28_5


title: UTHT5_ROW36_20


title: JPS004 10µm_3

value: JPS004 10microm


title: UTHT5_ROW27_16


title: DMSO_2

value: DMSO


title: UTHT5_ROW25_12


title: UTHT5_ROW16_6


title: DMSO_3


title: CI-994 10µm_3

value: CI-994 10microm


title: UTHT5_ROW27_11


title: UTHT5_ROW13_9


title: JPS014 10µm_3

value: JPS014 10microm


title: IAP CRTL 5µm_1


title: WT_3


title: UTHT5_ROW07_18


title: JPS027 5µm_1


title: JPS026 5µm_1


title: JPS036 10µm_1


title: JPS035 10µm_1


title: UTHT5_ROW24_20


title: UTHT5_ROW36_18


title: JPS016 10µm_1

value: JPS016 10microm


title: JPS039 10µm_1


title: UTHT5_ROW06_13


title: UTHT5_ROW02_19


title: JPS014 10µm_1


title: UTHT5_ROW21_17


title: JPS004 10µm_1


title: JPS016 10µm_3


title: UTHT5_ROW36_2


title: UTHT5_ROW03_19


title: UTHT5_ROW16_15


title: UTHT5_ROW26_18


title: UTHT5_ROW06_18


title: DMSO_1


title: UTHT5_ROW22_16


title: RESCUE_2

city: Madrid

first: Eduardo

last: Pérez-Gómez

state: Madrid

address: José Antonio Novais 12

department: Biochemistry and Molecular Biologý

country: Spain

institute: Universidad Complutense de Madrid)

data_processing:
Generation of sequencing libraries and sequencing were performed by Novogene Co Ltd (Cambridge, UK).
Sequencing libraries were constructed using amplified cDNAs with the TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina) and sequenced using the Illumina Novaseq6000 system in 150-bp paired-end mode. Bioinformatic analysis was performed by DREAMGENICS S.L. (Oviedo, Spain). First, sequenced reads were quality-checked with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The RNA reads were then aligned to the reference sequences of the Ensemble’s 2019 version of the human genome (GRCh38) using the Salmon algorithm, and relative gene expression was quantified as transcript per million (TPM).
For the analysis of differences in gene expression between conditions, the DESeq2 algorithm was used.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: sf

source_name: T47-D_epithelial cell

growth_protocol: Human Breast Cancer cell line T-47D were obtained from the American Type Culture Collection (ATCC). T-47D cells were cultured in RPMI medium (Sigma-Aldrich) with 10 % fetal bovine serum (FBS, Gibco), 10 µg/mL insulin (Sigma-Aldrich) and 1 % penicillin/streptomycin (Lonza). T-47D cells were maintained at 37 °C in a humidified atmosphere of 5 % CO2.  and routinely tested for Mycoplasma spp. contamination.

extract_protocol:
RNA was isolated with Nucleozol™ (Macherey-Nagel) following the extraction protocol suggested by the manufacturer. RNA was isolated as described above and resuspended in ultrapure water. Concentration and RNA integrity number > 7 were determined and 1 µg per sample was utilized for RNA-seq.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A T-47D FAAH KO cell line was generated by knocking out FAAH expression with a CRISPR/Cas9 kit from Origene. Briefly, the Amaxa™ HT Nucleofector™ (Lonza) was used to co-transfect 1 x 106 cells with 1 µg of guide RNA targeting FAAH (CCG CCA CGA AGC AGG CC) or a scrambled (SCR) vector together with 1 µg of donor DNA (which provided antibiotic resistance). Cells were passaged for an additional two weeks and then seeded at a low density in puromycin (0.5 µg/mL)-containing medium. After antibiotic selection, puromycin-resistant colonies were isolated, expanded and analyzed by genomic PCR. The T-47D FAAH KO cell line was subsequently used to obtain the T-47D rescue cell line by lentiviral delivery of human FAAH as described below.

tag: cell type

value: Breast cancer cell line

value: Breast; Mammary gland

tag: disease

value: Carcinoma; Ductal


title: WT_1

value: colorectal carcinoma

value: Adult


title: RESCUE_1


title: UTHT5_ROW30_15


title: UTHT5_ROW37_15


title: FAAH_KO_1


title: UTHT5_ROW06_14


title: UTHT5_ROW36_13


title: FAAH_KO_2


title: SCR_2


title: UTHT5_ROW03_7


title: SCR_1


title: GISTT1

city: New York

first: Prabhjot

middle: Singh

last: Mundi

state: NY

address: 1130 St. Nicholas Avenue

country: USA

institute: Columbia University Irving Medical Center

data_processing:
Alignment with STARv2.5.3 to GRCh38 or with bowtie2 to Hg19 and mm10 for PDX samples, as indicated below
Gene-level raw counts summarization with STARv2.5.3 quant-mode. In the case of PDX samples, xenomapper tool was to generate counts from reads selectively mapping to human transcriptome and not mouse.
Variance stabilization (normalization) with DESeq2 (R bioconductor package)
Gene expression signature and viper analysis as described in manuscript.
Genome_build: GRCh38.v90 or as indicated below.
Supplementary_files_format_and_content: Tab delimited text output of raw counts from STAR alignment and gene count quantification. Tab delimited text output for VIPER analysis of differential protein activity for perturbation or pharmacodynamic samples.

source_name: Cancer Cell line, CUIMC sequenced, RNASeq

growth_protocol: The cells were grown in logarithomic phase till treatment

extract_protocol:
RNAs were extracted using polyA selection kits, TruSeq
For PLATEseq multiplexed platform protocol details, see reference PMID: 28740083.
RNA Sequencing was performed on an Illumina NextSeq 500 or NovaSeq 6000 sequencer, as indicated below for each file.

treatment_protocol: Drug perturbations profiles in cell lines were done at 6 and/or 24 hours after introducing drug, as indicated by appropriate column names in the sample plate maps and processed data files

tag: sample type

value: cell line


title: UTHT5_ROW39_16


title: UTHT5_ROW27_15


title: CI-994 10µm_1

value: male


title: UTHT5_ROW25_13


title: ASPC1


title: BT20


title: UTHT5_ROW22_6


title: UTHT5_ROW14_13


title: GIST430


title: UTHT5_ROW19_18


title: CUAC1903_human (BC.50291)

source_name: PDX tumor sample, RNASeq

value: PDX of breast cancer

tag: ID


title: UTHT5_ROW09_17

value: cortex


title: UTHT5_ROW29_19


title: CUAC1883_human (BC.50291)

source_name: Patient tumor sample, RNASeq

value: breast cancer

tag: condition

value: breast recurrence


title: CUAC1599_human (PAC.05647)

value: pancreatic cancer

value: liver metastasis


title: UTHT5_ROW20_20


title: UTHT5_ROW05_12


title: UTHT5_ROW33_13


title: UTHT5_ROW15_14


title: UTHT5_ROW07_4


title: UTHT5_ROW06_15


title: Human retina scRNA rep5 [scRNA_LGS2OD]

city: Stanford

first: Sean

middle: K

last: Wang

state: CA

address: 1291 Welch Rd

institute: Stanford University

description:
processed data file
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

data_processing:
Demultiplexed scRNA- and scATAC-seq fastq files were inputted into the Cell Ranger ARC pipeline (version 2.0.0) from 10x Genomics to generate barcoded count matrices of gene expression and ATAC data. For each sample, count matrices were loaded in ArchR and selected for barcodes that appeared in both the scRNA-seq and scATAC-seq datasets. Samples in ArchR were quality control filtered for nuclei with 200-50,000 RNA transcripts, <1% mitochondrial reads, <5% ribosomal reads, TSS enrichment >6, and >2,500 ATAC fragments. Quality control filtered nuclei subsequently underwent automated removal of doublets using the filterDoublets function in ArchR, which identifies and removes the nearest neighbors of simulated doublets.
scRNA-seq data from nuclei remaining after quality control filtering and automated removal of doublets were analyzed using Seurat (version 3.1.5). After merging all preprocessed samples into a single Seurat object, gene expression counts were normalized using the NormalizeData function, scaled using the ScaleData function, and batch corrected using Harmony. Graph-based clustering was then performed on the Harmony-corrected data using the top 20 principal components at a resolution of 0.5. Cluster identities were manually annotated based on the expression of genes from published scRNA-seq studies of the human retina. Clusters expressing canonical marker genes from different cell types were designated as putative doublets and excluded, after which re-clustering was performed using the same parameters. Clusters with no detected marker genes were also excluded, after which the dataset was also re-clustered.
scATAC-seq data were analyzed using ArchR (version 1.0.1) based on barcoded cell type identities from scRNA-seq. For each cell type, pseudo-bulk ATAC replicates were created using the addGroupCoverages function with default parameters, which generated between two to five replicates depending on how many cells of that type were present in each sample. Chromatin accessibility peaks on chromosomes 1-22 and X and outside of blacklist regions were then called using the addReproduciblePeakSet function and MACS2, with reproducible scATAC peaks for each cell type defined as those present in at least two pseudo-bulk ATAC replicates.
HiChIP sequencing files were initially processed using the HiC-Pro pipeline (version 2.11.0) to remove duplicate reads, assign reads to MboI restriction fragments, filter for valid interactions, and generate binned interaction matrices. Filtered read pairs from HiC-Pro were subsequently converted into .hic files and inputted into HiCCUPS from the Juicer pipeline to call loops.
Genome_build: hg38
Supplementary_files_format_and_content: hic files represent all valid interaction pairs detected by HiC-Pro following H3K27ac HiChIP of retina tissue from the specified donor. bedpe files represent H3K27ac HiChIP loops detected by HiCCUPS. tsv and mtx files represent raw gene counts for each barcode in the file scRNA-seq dataset. fragments files represent aggregated scATAC-seq fragments organized by cell type.

molecule: nuclear RNA

source_name: adult human retina

extract_protocol:
Joint scRNA- and scATAC-seq libraries were prepared using the 10x Genomics Single Cell Multiome ATAC + Gene Expression kit according to manufacturer’s instructions.
Nuclei were isolated from frozen retinas using the Omni-ATAC protocol (doi.org/10.17504/protocols.io.6t8herw)

value: Retina


title: Human retina scRNA rep2 [scRNA_LVG1OS]


title: Human retina scRNA rep7 [scRNA_LGS3OD]


title: UTHT5_ROW18_20


title: UTHT5_ROW38_14


title: UTHT5_ROW07_13


title: Human retina scRNA rep6 [scRNA_LGS2OS]


title: UTHT5_ROW22_4


title: UTHT5_ROW38_10


title: Human retina scRNA rep3 [scRNA_LGS1OD]


title: Human retina scATAC rep7 [scATAC_LGS3OD]

description:
processed data file
AIIamacrine_frags.tsv
Astrocyte_frags.tsv
Cone_frags.tsv
GABAamacrine_frags.tsv
Glyamacrine_frags.tsv
Horizontal_frags.tsv
Microglia_frags.tsv
Mullerglia_frags.tsv
OFFconebipolar_frags.tsv
ONconebipolar_frags.tsv
Retinalganglioncell_frags.tsv
Rodbipolar_frags.tsv
Rod_frags.tsv

library_source: genomic

molecule: genomic DNA


title: Human retina scATAC rep1 [scATAC_LVG1OD]


title: UTHT5_ROW28_16


title: Human retina scATAC rep5 [scATAC_LGS2OD]


title: Human retina scRNA rep8 [scRNA_LGS3OS]


title: Human retina scATAC rep8 [scATAC_LGS3OS]


title: UTHT5_ROW28_18


title: Human retina scRNA rep1 [scRNA_LVG1OD]


title: UTHT5_ROW03_12


title: UTHT5_ROW01_15


title: Human retina scATAC rep6 [scATAC_LGS2OS]


title: Human retina scATAC rep2 [scATAC_LVG1OS]


title: UTHT5_ROW23_2


title: Human retina scATAC rep4 [scATAC_LGS1OS]


title: UTHT5_ROW39_20


title: Human retina scRNA rep4 [scRNA_LGS1OS]


title: TARDBP K263E iPSC-derived neuron, rep3

first: Kent

last: Imaizumi

address: 318 Campus Drive

data_processing:
Sequences were produced using a NovaSeq6000 (Illumina)
Raw FASTQ files were trimmed for adapters by Cutadapt
We used Salmon to generate the TPM counts by using the transcript index from GRCh38 (Gencode v33)
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each Sample

source_name: TARDBP K263E iPSC-derived neuron

extract_protocol:
Total RNA was isolated by RNeasy mini kit (QIAGEN)
The indexed cDNA libraries were prepared using the TruSeq stranded mRNA Library Preparation kit (Illumina)

value: iPSC-derived Neuron

tag: replicate

tag: day in culture

tag: genotype

value: TARDBP K263E iPSC


title: UTHT5_ROW02_12


title: TARDBP K263E iPSC-derived neuron, rep2


title: Human retina scATAC rep3 [scATAC_LGS1OD]


title: TARDBP K263E iPSC-derived neuron, rep1


title: UTHT5_ROW38_16


title: UTHT5_ROW17_4


title: UTHT5_ROW26_14


title: UTHT5_ROW10_11


title: UTHT5_ROW01_16


title: Wild-type iPSC-derived neuron, rep3

source_name: Wild-type iPSC-derived neuron

value: Wild-type iPSC (201B7)


title: Wild-type iPSC-derived neuron, rep2


title: UTHT5_ROW33_19


title: UTHT5_ROW02_17


title: TARDBP K263E iPSC-derived NPC, rep3

source_name: TARDBP K263E iPSC-derived NPC

value: iPSC-derived Neuronal progenitor cell


title: Wild-type iPSC-derived neuron, rep1


title: TARDBP K263E iPSC-derived NPC, rep2


title: Wild-type iPSC-derived NPC, rep2

source_name: Wild-type iPSC-derived NPC


title: UTHT5_ROW12_3


title: TARDBP K263E iPSC, rep3

source_name: TARDBP K263E iPSC

value: iPSC


title: UTHT5_ROW29_18


title: TARDBP K263E iPSC-derived NPC, rep1


title: UTHT5_ROW21_19


title: UTHT5_ROW22_5


title: UTHT5_ROW29_9


title: Wild-type iPSC-derived NPC, rep1


title: Wild-type iPSC-derived NPC, rep3


title: TARDBP K263E iPSC, rep2


title: TARDBP K263E iPSC, rep1


title: UTHT5_ROW27_18


title: UTHT5_ROW23_20


title: UTHT5_ROW04_18


title: Feeder-free PSC

description: bisulfited DNA

data_processing:
Sequences were produced using a NovaSeq6000 (Illumina)
The obtained sequences were mapped to GRCh38, deduplicated, and methylation calls were extracted using Bismark. Methylation sites with at least 5X read coverage were retained.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files of methylation call generated by Bismark

source_name: ESC

extract_protocol:
Genomic DNA was isolated from ESCs with the DNeasy Blood & Tissue kit (Qiagen), fragmented into 200-400 bp by sonication (Covaris), and was processed for bisulfite modification using EZ DNA methylation Gold Kit (Zymo).
The libraries were prepared using Scale Methyl-DNA Lib Prep Kit for Illumina (ABclonal).

value: Feeder-free PSC

tag: treatment in ipsc stage

value: untreated


title: UTHT5_ROW24_12


title: 6-day differentiating cell from feeder-free iPSC, treated with PD173074, rep3

source_name: 6-day differentiating cell from iPSC


title: UTHT5_ROW29_13


title: 6-day differentiating cell from feeder-free iPSC, rep3


title: 6-day differentiating cell from feeder-free iPSC, treated with PD173074, rep1


title: UTHT5_ROW05_20


title: UTHT5_ROW28_2


title: 6-day differentiating cell from feeder-free iPSC, treated with PD173074, rep2


title: 6-day differentiating cell from on-feeder iPSC, rep3


title: UTHT5_ROW07_16


title: UTHT5_ROW12_18


title: 6-day differentiating cell from feeder-free iPSC, rep2


title: UTHT5_ROW02_5


title: 6-day differentiating cell from feeder-free iPSC, rep1


title: UTHT5_ROW05_18


title: UTHT5_ROW24_6


title: 6-day differentiating cell from on-feeder iPSC, rep2


title: UTHT5_ROW30_20


title: Feeder-free iPSC, treated with PD173074, rep2

source_name: iPSC

value: Feeder-free iPSC


title: 6-day differentiating cell from on-feeder iPSC, rep1


title: Feeder-free iPSC, rep2


title: UTHT5_ROW08_15


title: Feeder-free iPSC, treated with PD173074, rep3


title: UTHT5_ROW18_16


title: UTHT5_ROW31_12


title: Feeder-free PSC, treated with PD173074

description: bisulfited DNA


title: UTHT5_ROW15_18


title: Feeder-free iPSC, rep3


title: Feeder-free iPSC, rep1


title: UTHT5_ROW24_9


title: UTHT5_ROW10_14


title: UTHT5_ROW31_18


title: UTHT5_ROW35_20


title: On-feeder iPSC, rep1

value: On-feeder iPSC


title: Macrophages, NC410 plus Bintrafuap alfa (NcB_75)

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
12 mRNA-Seq samples were pooled and sequenced on a NovaSeq 6000 SP using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.
Basecalling was performed by RTA (version 1.18.64).
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.17) allowing 1 mismatch.
Reads were filtered with a base call quality >94% of bases with Q30 and and above.
Trimming of adapters and low-quality bases was performed using Trimmomatic (version 0.33).
First pass alignment of reads to the hg38 reference genome was performed using STAR (version 2.5.2b) with parameters: STAR --genomeDir /path/to/genomeDir --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1  --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --clip3pAdapterSeq - --readFilesIn /path/to/read1.fastq.gz /path/to/read2.fastq.gz --readFilesCommand zcat --runThreadN 32 --outFileNamePrefix <prefix> --outSAMtype BAM Unsorted
Second pass alignment of reads to the hg38 reference genome was performed using STAR (version 2.5.2b) with parameters: STAR --genomeDir /path/to/genomeDir --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1  --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --clip3pAdapterSeq - --readFilesIn /path/to/read1.fastq.gz /path/to/read2.fastq.gz --readFilesCommand zcat --runThreadN 32 --outFileNamePrefix <prefix> --outSAMunmapped Within --outWigType None --outWigStrand Stranded --sjdbFileChrStartEnd /path/to/sjdbFile.txt --sjdbGTFfile /path/to/annotations.gtf --limitSjdbInsertNsj 4000000 --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate
Gene-level expression quantificiation and library size normalization in counts-per-million was performed using RSEM (version 1.3.0) and the hg38 v28 gene annotation.
Quantile-normalization and differential expression was performed using limma-voom (version 3.34.5).
Genome_build: hg38
Supplementary_files_format_and_content: .csv file containing raw counts produced by RSEM

source_name: Macrophages

growth_protocol: De-identified PBMC samples were obtained from healthy volunteers who provided written informed consent at the National Institute of Health Clinical Center Blood Bank (protocol NCT00001846). PBMC were plated in DMEM in 12-well tissue culture plates for 2 hr at 37°C. Non-adherent cells were removed and attached cells were cultured for 5 days in RPMI-1640 medium containing macrophage differentiation media: 10% FBS, 1x glutamine, and 50ng/ml human M-CSF (PeproTech). Media and cytokines were replaced every other day.

extract_protocol:
Total RNA from in vitro polarized macrophages was prepared using the RNeasy Mini Kit (Qiagen). RNA integrity was analyzed on an Agilent TapeStation (Agilent Technologies). Samples with a RIN value > 8.0 were sequenced by Novogene UC Davis Sequencing Center (Novogene Corporation, Ltd.)
Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: On day 5, macrophage differentiation media was added with M2 polarizing cytokines: 20ng/ml IL-4 (PeproTech), 20ng/ml IL-13 (PeproTech), and 20µg/ml native mouse collagen I/III (BioRad). No treatment, NC410 (100µg/ml), bintrafusp alfa (200 ng/ml) or the combination was added. Forty-eight hr after polarization, the attached cells were washed, scraped, and collected for analysis.

tag: disease state

value: Healthy Donor

tag: cell source

value: PBMC

value: M2 polarized macrophages

tag: treatment

value: NC410 plus Bintrafuap alfa


title: Macrophages, NC410 plus Bintrafuap alfa (NcB_68)


title: Feeder-free iPSC, treated with PD173074, rep1

tag: cell line


title: UTHT5_ROW10_8

value: cortex


title: UTHT5_ROW02_18


title: Macrophages, Bintrafusp alfa (Bin_55)

value: Bintrafusp alfa


title: UTHT5_ROW11_17


title: Macrophages, Bintrafusp alfa (Bin_75)


title: UTHT5_ROW22_2


title: Macrophages, Bintrafusp alfa (Bin_68)


title: Macrophages, NC410 (NC_55)


title: UTHT5_ROW16_20


title: Macrophages, NC410 (NC_68)


title: UTHT5_ROW08_16


title: UTHT5_ROW18_19


title: UTHT5_ROW36_5


title: Macrophages, Control (M2_75)

value: Control


title: UTHT5_ROW08_18


title: On-feeder iPSC, rep3


title: On-feeder iPSC, rep2


title: UTHT5_ROW09_12


title: UTHT5_ROW07_15


title: UTHT5_ROW20_14


title: UTHT5_ROW36_4


title: UTHT5_ROW05_14


title: UTHT5_ROW05_17


title: UTHT5_ROW34_20


title: UTHT5_ROW37_14


title: UTHT5_ROW34_18


title: UTHT5_ROW13_12


title: UTHT5_ROW18_4


title: UTHT5_ROW11_16


title: UTHT5_ROW26_10


title: Macrophages, NC410 plus Bintrafuap alfa (NcB_55)


title: UTHT5_ROW31_6


title: UTHT5_ROW18_3


title: UTHT5_ROW30_19


title: UTHT5_ROW35_18


title: UTHT5_ROW15_1


title: UTHT5_ROW12_15


title: UTHT5_ROW22_12


title: Macrophages, Control (M2_68)


title: UTHT5_ROW34_11


title: Macrophages, NC410 (NC_75)


title: UTHT5_ROW27_9


title: UTHT5_ROW22_20


title: UTHT5_ROW29_10


title: Macrophages, Control (M2_55)


title: UTHT5_ROW12_17


title: UTHT5_ROW26_20


title: UTHT5_ROW23_12


title: UTHT5_ROW25_14


title: UTHT5_ROW19_14


title: UTHT5_ROW27_5


title: UTHT5_ROW15_12


title: UTHT5_ROW14_17


title: P.Intermedia_Hinp1I_Miseq_plate_2

city: Tainan City

first: Shu-Yun

last: Chen

address: No. 1 University Road

country: Taiwan

institute: NCKU

data_processing:
Library strategy: GBS
Illumina sequence read processing, mapping, and SNP calling involved using the TASSEL-GBS pipeline (Bradbury et al., 2007)
Genome_build: Pha_eq_chr19.fa
Supplementary_files_format_and_content: tab-delimited text files include SNP for each Sample

organism: Phalaenopsis x intermedia

source_name: Phalaenopsis leaf

extract_protocol:
DNA extraction in volved using the Qiagen DNeasy 96 Plant kit
For the two-enzyme GBS approach, HinpI 1 and ApeK1 were paired with HaeIII for library preparation following a previous protocol (Elshire et al., 2011) with minor modifications. Single-end sequencing of multiplex GBS libraries involved using Mi-seq (for HinpI 1 library) and Illumina HiSeq2500 (for ApeK I library) platforms.

value: Leaf

tag: enzyme


title: UTHT5_ROW33_2


title: UTHT5_ROW10_3


title: Veros-APO-moi-0p1

city: La Jolla

first: Gene

last: Yeo

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

institute: UCSD

description: Vero E6 infected with SARS-CoV-2 at MOI 0.1 for 48 hours

data_processing:
Raw reads were trimmed using cutadapt (v1.14) using the following parameters -O 5 -f  fastq --match-read-wildcards --times 2 -e 0.0 --quality-cutoff 6 -m 18 -o data.fastqTr.fq -b TCGTATGCCGTCTTCTGCTTG -b ATCTCGTATGCCGTCTTCTGCTTG -b CGACAGGTTCAGAGTTCTACAGTCCGACGATC -b GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -b AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -b TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT data.fastq.gz
Trimmed reads were mapped to and filtered of repeat elements (RepBase 18.05) with STAR (2.5.2) using the following parameters: --alignEndsType  EndToEnd  --genomeDir  repbase  --genomeLoad  NoSharedMemory  --outBAMcompression  10  --outFileNamePrefix  data  --outFilterMultimapNmax  10  --outFilterMultimapScoreRange  1  --outFilterScoreMin  10  --outFilterType  BySJout  --outReadsUnmapped  Fastx  --outSAMattrRGline  ID:foo  --outSAMattributes  All  --outSAMmode  Full  --outSAMtype  BAM  Unsorted  --outSAMunmapped  Within  --outStd  Log  --readFilesIn data.fastqTr.fq  --runMode  alignReads  --runThreadN  8
Reads unmapped to repeat elements were mapped to the human genome with STAR using the same parameters as the previous step, using an hg19/ChlSab2 index in place of the repeat element index
Subread featureCounts (-a gencode.v19.annotation.gtf -s 2 -p -o counts.txt data.bam) was used to count features using human annotations (Gencode v19)
Genome_build: ChlSab2
Genome_build: hg19
Supplementary_files_format_and_content: BigWig

organism: Chlorocebus sabaeus

source_name: Vero E6 cells overexpressing APOBEC1

growth_protocol:
Vero E6 and A549-ACE2 cells were cultured in DMEM supplemented with 10% FBS.
BEAS-2B cells were cultured on Matrigel (Corning) coated plates and maintained in the PneumaCult-Ex Plus Medium (Stem Cell Technologies), supplemented with 33 µg/ml hydrocortisone (Stem Cell Technologies). Growth media was replaced every two days, and the cells were passaged every four days. Vero E6 cells were cultured in DMEM (ThermoFisher) supplemented with 10% FBS (ThermoFisher) and passaged every three days. All cell cultures were incubated at 37ºC and 5% CO2.

extract_protocol:
Trizol extraction (Fisher) and Direct-zol miniprep (Zymo Research) column purification in accordance with manufacturer protocol
Illumina Stranded mRNA Prep kit

treatment_protocol:
Vero E6 and A549-ACE2 cells were treated with 1µg/ml doxycyline and infected with SARS-CoV-2 at MOI 0.1 and MOI 3, respectively, for 48 hours before treating with Trizol.
BEAS-2B cells were treated with Trizol when 70-90% confluent.

value: Vero E6


title: UTHT5_ROW38_20

source_name: cortex


title: UTHT5_ROW32_20


title: P.Intermedia_Hinp1I_Miseq_plate_1


title: UTHT5_ROW04_11


title: UTHT5_ROW30_4


title: UTHT5_ROW33_9


title: UTHT5_ROW35_14


title: BT605_The SNP of whole genome

type: genomic

city: Hangzhou

first: Liu-Bin

address: 9 South Meiling road

department: Tea Research Institute

country: China

institute: Chinese Academy of Agricultural Sciences

description: Tea SNP 96-Array Plate detected the SNP of whole genome of tea

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the GeneTitan MC.

data_processing:
The array image was acquired using Affymetrix AxiomTM Tea SNP 96 -Array Plate detected the SNP of whole genome of tea plant
SNP call:G/G,T/G,T/T,C/C,etc.

label: biotin

organism: Camellia sinensis

source_name: BT605 SNP of whole genome

label_protocol: As per manufacturer (Affymetrix).

growth_protocol: Tea plant  were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from young leafs of tea using the TianGen DNA Kit. DNA quality and quantity was assessed using a Nanodrop.

tag: cultivar


title: BT604_The SNP of whole genome

source_name: BT604 SNP of whole genome


title: BT603_The SNP of whole genome

source_name: BT603 SNP of whole genome


title: UTHT5_ROW39_9


title: BT602_The SNP of whole genome

source_name: BT602 SNP of whole genome


title: UTHT5_ROW28_4


title: UTHT5_ROW12_14


title: UTHT5_ROW06_12


title: UTHT5_ROW17_18


title: UTHT5_ROW24_18


title: UTHT5_ROW04_16


title: UTHT5_ROW35_19


title: UTHT5_ROW04_14


title: BT476_The SNP of whole genome

source_name: BT476 SNP of whole genome


title: UTHT5_ROW25_20


title: BT475_The SNP of whole genome

source_name: BT475 SNP of whole genome


title: UTHT5_ROW27_10


title: UTHT5_ROW01_14


title: UTHT5_ROW17_3


title: UTHT5_ROW19_2


title: UTHT5_ROW33_12


title: BT606_The SNP of whole genome

source_name: BT606 SNP of whole genome


title: UTHT5_ROW10_18


title: UTHT5_ROW40_2


title: BT472_The SNP of whole genome

source_name: BT472 SNP of whole genome


title: BT473_The SNP of whole genome

source_name: BT473 SNP of whole genome


title: BT469_The SNP of whole genome

source_name: BT469 SNP of whole genome


title: BT474_The SNP of whole genome

source_name: BT474 SNP of whole genome


title: UTHT5_ROW09_5


title: BT463_The SNP of whole genome

source_name: BT463 SNP of whole genome


title: UTHT5_ROW20_9


title: UTHT5_ROW20_8


title: UTHT5_ROW37_9


title: BT601_The SNP of whole genome

source_name: BT601 SNP of whole genome


title: BT467_The SNP of whole genome

source_name: BT467 SNP of whole genome


title: UTHT5_ROW36_9


title: UTHT5_ROW25_9


title: UTHT5_ROW11_18


title: UTHT5_ROW33_1


title: UTHT5_ROW29_12


title: BT327_The SNP of whole genome

source_name: BT327 SNP of whole genome


title: BT326_The SNP of whole genome

source_name: BT326 SNP of whole genome


title: UTHT5_ROW09_11

source_name: cortex


title: UTHT5_ROW20_12


title: UTHT5_ROW25_15


title: BT323_The SNP of whole genome

source_name: BT323 SNP of whole genome


title: UTHT4_ROW28_16


title: UTHT5_ROW01_12


title: BT380_The SNP of whole genome

source_name: BT380 SNP of whole genome


title: UTHT4_ROW20_17


title: UTHT5_ROW09_18


title: UTHT5_ROW17_14


title: UTHT5_ROW05_16


title: BT378_The SNP of whole genome

source_name: BT378 SNP of whole genome


title: BT325_The SNP of whole genome

source_name: BT325 SNP of whole genome


title: UTHT5_ROW23_19


title: BT377_The SNP of whole genome

source_name: BT377 SNP of whole genome


title: BT375_The SNP of whole genome

source_name: BT375 SNP of whole genome


title: BT376_The SNP of whole genome

source_name: BT376 SNP of whole genome


title: UTHT4_ROW10_14


title: UTHT4_ROW02_15


title: UTHT4_ROW32_19


title: UTHT5_ROW17_20


title: UTHT4_ROW28_19


title: UTHT4_ROW09_19


title: UTHT4_ROW12_18


title: UTHT4_ROW40_16


title: UTHT4_ROW27_13


title: UTHT4_ROW01_17


title: BT373_The SNP of whole genome

source_name: BT373 SNP of whole genome


title: BT374_The SNP of whole genome

source_name: BT374 SNP of whole genome


title: BT379_The SNP of whole genome

source_name: BT379 SNP of whole genome


title: BT372_The SNP of whole genome

source_name: BT372 SNP of whole genome


title: UTHT5_ROW31_15


title: UTHT4_ROW29_20


title: BT371_The SNP of whole genome

source_name: BT371 SNP of whole genome


title: UTHT4_ROW19_17


title: UTHT4_ROW28_13


title: UTHT4_ROW15_16


title: BT369_The SNP of whole genome

source_name: BT369 SNP of whole genome


title: UTHT4_ROW38_16


title: UTHT4_ROW27_18


title: BT370_The SNP of whole genome

source_name: BT370 SNP of whole genome


title: UTHT4_ROW32_14


title: UTHT4_ROW31_18


title: UTHT4_ROW03_18


title: UTHT4_ROW34_11


title: UTHT4_ROW10_16


title: UTHT4_ROW28_11


title: UTHT4_ROW05_16


title: BT367_The SNP of whole genome

source_name: BT367 SNP of whole genome


title: UTHT4_ROW17_13


title: UTHT5_ROW39_8


title: BT366_The SNP of whole genome

source_name: BT366 SNP of whole genome


title: BT365_The SNP of whole genome

source_name: BT365 SNP of whole genome


title: UTHT4_ROW09_17

source_name: cortex


title: UTHT4_ROW13_16


title: UTHT4_ROW26_12


title: UTHT4_ROW14_20


title: UTHT4_ROW02_13


title: UTHT4_ROW14_18


title: BT364_The SNP of whole genome

source_name: BT364 SNP of whole genome


title: BT368_The SNP of whole genome

source_name: BT368 SNP of whole genome


title: UTHT4_ROW01_18


title: UTHT4_ROW17_19


title: BT362_The SNP of whole genome

source_name: BT362 SNP of whole genome


title: UTHT4_ROW40_13


title: UTHT4_ROW14_17


title: UTHT4_ROW34_15


title: UTHT4_ROW08_12


title: UTHT4_ROW34_12


title: UTHT4_ROW08_17


title: BT358_The SNP of whole genome

source_name: BT358 SNP of whole genome


title: BT360_The SNP of whole genome

source_name: BT360 SNP of whole genome


title: UTHT4_ROW23_14


title: UTHT4_ROW31_4


title: UTHT4_ROW06_11


title: UTHT4_ROW19_11


title: BT357_The SNP of whole genome

source_name: BT357 SNP of whole genome


title: UTHT4_ROW01_13


title: UTHT4_ROW25_1


title: BT356_The SNP of whole genome

source_name: BT356 SNP of whole genome


title: BT355_The SNP of whole genome

source_name: BT355 SNP of whole genome


title: UTHT4_ROW16_14


title: UTHT4_ROW34_1


title: BT363_The SNP of whole genome

source_name: BT363 SNP of whole genome


title: UTHT4_ROW36_18


title: UTHT4_ROW37_20


title: BT354_The SNP of whole genome

source_name: BT354 SNP of whole genome


title: UTHT4_ROW15_5


title: UTHT4_ROW05_9


title: BT361_The SNP of whole genome

source_name: BT361 SNP of whole genome


title: UTHT4_ROW23_19


title: BT359_The SNP of whole genome

source_name: BT359 SNP of whole genome


title: UTHT4_ROW33_15


title: UTHT4_ROW20_15


title: BT352_The SNP of whole genome

source_name: BT352 SNP of whole genome


title: BT351_The SNP of whole genome

source_name: BT351 SNP of whole genome


title: UTHT4_ROW29_10


title: UTHT4_ROW19_18


title: UTHT4_ROW34_18


title: UTHT4_ROW26_5


title: BT349_The SNP of whole genome

source_name: BT349 SNP of whole genome


title: UTHT4_ROW31_3


title: BT348_The SNP of whole genome

source_name: BT348 SNP of whole genome


title: UTHT5_ROW14_2

source_name: cortex


title: UTHT4_ROW04_9


title: UTHT4_ROW12_14


title: BT353_The SNP of whole genome

source_name: BT353 SNP of whole genome


title: BT350_The SNP of whole genome

source_name: BT350 SNP of whole genome


title: BT347_The SNP of whole genome

source_name: BT347 SNP of whole genome


title: BT346_The SNP of whole genome

source_name: BT346 SNP of whole genome


title: UTHT4_ROW09_5


title: UTHT4_ROW33_13


title: UTHT4_ROW17_12


title: BT343_The SNP of whole genome

source_name: BT343 SNP of whole genome


title: BT342_The SNP of whole genome

source_name: BT342 SNP of whole genome


title: BT345_The SNP of whole genome

source_name: BT345 SNP of whole genome


title: UTHT4_ROW18_11


title: BT344_The SNP of whole genome

source_name: BT344 SNP of whole genome


title: UTHT4_ROW39_9


title: UTHT4_ROW37_5


title: UTHT4_ROW21_10


title: UTHT4_ROW40_10


title: UTHT4_ROW39_2


title: UTHT4_ROW12_9


title: UTHT4_ROW18_2


title: BT339_The SNP of whole genome

source_name: BT339 SNP of whole genome


title: BT340_The SNP of whole genome

source_name: BT340 SNP of whole genome


title: UTHT4_ROW12_16


title: UTHT4_ROW24_17


title: UTHT4_ROW03_17


title: UTHT4_ROW22_15


title: BT338_The SNP of whole genome

source_name: BT338 SNP of whole genome


title: BT337_The SNP of whole genome

source_name: BT337 SNP of whole genome


title: UTHT4_ROW08_3


title: UTHT4_ROW38_5


title: BT341_The SNP of whole genome

source_name: BT341 SNP of whole genome


title: UTHT4_ROW11_3


title: UTHT4_ROW31_15


title: UTHT4_ROW02_1


title: UTHT4_ROW32_5


title: BT335_The SNP of whole genome

source_name: BT335 SNP of whole genome


title: UTHT4_ROW16_4


title: UTHT4_ROW12_19


title: UTHT4_ROW33_9


title: UTHT4_ROW30_4


title: UTHT4_ROW18_12


title: UTHT4_ROW07_3


title: BT332_The SNP of whole genome

source_name: BT332 SNP of whole genome


title: UTHT4_ROW27_15


title: UTHT4_ROW01_1


title: UTHT4_ROW25_11


title: UTHT4_ROW27_1


title: UTHT4_ROW17_14


title: BT330_The SNP of whole genome

source_name: BT330 SNP of whole genome


title: BT334_The SNP of whole genome

source_name: BT334 SNP of whole genome


title: UTHT4_ROW10_20

source_name: cortex


title: UTHT4_ROW07_9


title: BT329_The SNP of whole genome

source_name: BT329 SNP of whole genome


title: UTHT4_ROW18_20


title: UTHT4_ROW38_4


title: UTHT4_ROW13_20


title: BT336_The SNP of whole genome

source_name: BT336 SNP of whole genome


title: BT322_The SNP of whole genome

source_name: BT322 SNP of whole genome


title: UTHT4_ROW38_15


title: BT333_The SNP of whole genome

source_name: BT333 SNP of whole genome


title: UTHT4_ROW32_18


title: UTHT4_ROW11_5


title: UTHT4_ROW16_6


title: BT331_The SNP of whole genome

source_name: BT331 SNP of whole genome


title: UTHT4_ROW21_13


title: UTHT4_ROW11_9


title: BT318_The SNP of whole genome

source_name: BT318 SNP of whole genome


title: BT328_The SNP of whole genome

source_name: BT328 SNP of whole genome


title: UTHT4_ROW25_18


title: UTHT4_ROW30_20


title: BT316_The SNP of whole genome

source_name: BT316 SNP of whole genome


title: UTHT4_ROW39_5


title: UTHT4_ROW15_19


title: UTHT4_ROW30_15


title: UTHT4_ROW23_16


title: UTHT4_ROW19_13


title: UTHT4_ROW07_13


title: UTHT4_ROW21_20


title: UTHT4_ROW11_14


title: BT317_The SNP of whole genome

source_name: BT317 SNP of whole genome


title: BT321_The SNP of whole genome

source_name: BT321 SNP of whole genome


title: BT319_The SNP of whole genome

source_name: BT319 SNP of whole genome


title: BT320_The SNP of whole genome

source_name: BT320 SNP of whole genome


title: UTHT4_ROW14_6


title: UTHT4_ROW34_6


title: UTHT4_ROW28_9


title: UTHT4_ROW33_11


title: UTHT4_ROW28_20


title: UTHT4_ROW33_17


title: UTHT4_ROW08_20


title: UTHT4_ROW09_7


title: BT313_The SNP of whole genome

source_name: BT313 SNP of whole genome


title: UTHT4_ROW32_17


title: UTHT4_ROW23_7


title: BT311_The SNP of whole genome

source_name: BT311 SNP of whole genome


title: UTHT4_ROW15_4


title: UTHT4_ROW02_4


title: BT315_The SNP of whole genome

source_name: BT315 SNP of whole genome


title: UTHT4_ROW09_20


title: UTHT4_ROW12_11


title: BT314_The SNP of whole genome

source_name: BT314 SNP of whole genome


title: BT309_The SNP of whole genome

source_name: BT309 SNP of whole genome


title: UTHT4_ROW20_20

source_name: cortex


title: BT308_The SNP of whole genome

source_name: BT308 SNP of whole genome


title: UTHT4_ROW17_10


title: UTHT4_ROW06_16


title: UTHT4_ROW21_4


title: UTHT4_ROW24_4


title: UTHT4_ROW34_19


title: UTHT4_ROW32_15


title: UTHT4_ROW30_12


title: UTHT4_ROW28_15


title: BT307_The SNP of whole genome

source_name: BT307 SNP of whole genome


title: BT306_The SNP of whole genome

source_name: BT306 SNP of whole genome


title: BT305_The SNP of whole genome

source_name: BT305 SNP of whole genome


title: BT312_The SNP of whole genome

source_name: BT312 SNP of whole genome


title: BT304_The SNP of whole genome

source_name: BT304 SNP of whole genome


title: UTHT4_ROW05_7


title: UTHT4_ROW22_11


title: UTHT4_ROW18_7


title: UTHT4_ROW20_9


title: BT303_The SNP of whole genome

source_name: BT303 SNP of whole genome


title: BT302_The SNP of whole genome

source_name: BT302 SNP of whole genome


title: UTHT4_ROW22_6


title: BT310_The SNP of whole genome

source_name: BT310 SNP of whole genome


title: UTHT4_ROW22_20


title: UTHT4_ROW31_10


title: UTHT4_ROW27_5


title: BT300_The SNP of whole genome

source_name: BT300 SNP of whole genome


title: UTHT4_ROW18_14


title: UTHT4_ROW09_12


title: UTHT4_ROW15_20


title: UTHT4_ROW13_12


title: UTHT4_ROW02_5


title: UTHT4_ROW38_11


title: UTHT4_ROW22_14


title: BT461_The SNP of whole genome

source_name: BT461 SNP of whole genome


title: BT295_The SNP of whole genome

source_name: BT295 SNP of whole genome


title: UTHT4_ROW35_17


title: BT460_The SNP of whole genome

source_name: BT460 SNP of whole genome


title: UTHT4_ROW26_16


title: BT462_The SNP of whole genome

source_name: BT462 SNP of whole genome


title: UTHT4_ROW11_16


title: UTHT4_ROW08_2


title: UTHT4_ROW13_14


title: UTHT4_ROW21_15


title: BT299_The SNP of whole genome

source_name: BT299 SNP of whole genome


title: UTHT4_ROW03_10


title: BT459_The SNP of whole genome

source_name: BT459 SNP of whole genome


title: UTHT4_ROW35_11

source_name: cortex


title: UTHT4_ROW31_6


title: UTHT4_ROW34_5


title: BT296_The SNP of whole genome

source_name: BT296 SNP of whole genome


title: UTHT4_ROW20_10


title: BT458_The SNP of whole genome

source_name: BT458 SNP of whole genome


title: UTHT4_ROW07_10


title: BT456_The SNP of whole genome

source_name: BT456 SNP of whole genome


title: BT455_The SNP of whole genome

source_name: BT455 SNP of whole genome


title: UTHT4_ROW19_5


title: UTHT4_ROW30_14


title: UTHT4_ROW01_5


title: UTHT4_ROW10_1


title: UTHT4_ROW22_19


title: BT454_The SNP of whole genome

source_name: BT454 SNP of whole genome


title: UTHT4_ROW13_18


title: UTHT4_ROW11_4


title: UTHT4_ROW12_4


title: UTHT4_ROW11_7


title: BT452_The SNP of whole genome

source_name: BT452 SNP of whole genome


title: BT451_The SNP of whole genome

source_name: BT451 SNP of whole genome


title: UTHT4_ROW28_2


title: BT453_The SNP of whole genome

source_name: BT453 SNP of whole genome


title: UTHT4_ROW15_9


title: UTHT4_ROW29_2


title: UTHT4_ROW32_4


title: UTHT4_ROW35_9


title: UTHT4_ROW09_3


title: UTHT4_ROW40_20


title: BT457_The SNP of whole genome

source_name: BT457 SNP of whole genome


title: UTHT4_ROW06_10


title: BT450_The SNP of whole genome

source_name: BT450 SNP of whole genome


title: UTHT4_ROW21_16


title: BT449_The SNP of whole genome

source_name: BT449 SNP of whole genome


title: BT446_The SNP of whole genome

source_name: BT446 SNP of whole genome


title: UTHT4_ROW23_9


title: UTHT4_ROW21_9


title: BT445_The SNP of whole genome

source_name: BT445 SNP of whole genome


title: UTHT4_ROW25_3


title: BT444_The SNP of whole genome

source_name: BT444 SNP of whole genome


title: BT448_The SNP of whole genome

source_name: BT448 SNP of whole genome


title: UTHT4_ROW27_9


title: UTHT4_ROW36_20


title: UTHT4_ROW28_3


title: BT447_The SNP of whole genome

source_name: BT447 SNP of whole genome


title: UTHT4_ROW17_4

source_name: cortex


title: UTHT4_ROW24_3


title: BT442_The SNP of whole genome

source_name: BT442 SNP of whole genome


title: BT443_The SNP of whole genome

source_name: BT443 SNP of whole genome


title: UTHT4_ROW07_1


title: BT440_The SNP of whole genome

source_name: BT440 SNP of whole genome


title: UTHT4_ROW37_16


title: UTHT4_ROW31_12


title: BT301_The SNP of whole genome

source_name: BT301 SNP of whole genome


title: BT439_The SNP of whole genome

source_name: BT439 SNP of whole genome


title: BT441_The SNP of whole genome

source_name: BT441 SNP of whole genome


title: UTHT4_ROW38_20


title: UTHT4_ROW38_17


title: UTHT4_ROW05_14


title: UTHT4_ROW29_9


title: UTHT4_ROW40_12


title: UTHT4_ROW29_15


title: UTHT4_ROW39_10


title: UTHT4_ROW30_16


title: BT435_The SNP of whole genome

source_name: BT435 SNP of whole genome


title: UTHT4_ROW38_14


title: BT298_The SNP of whole genome

source_name: BT298 SNP of whole genome


title: BT297_The SNP of whole genome

source_name: BT297 SNP of whole genome


title: BT438_The SNP of whole genome

source_name: BT438 SNP of whole genome


title: UTHT4_ROW38_13


title: BT437_The SNP of whole genome

source_name: BT437 SNP of whole genome


title: UTHT4_ROW02_7


title: UTHT4_ROW38_10


title: UTHT4_ROW03_13


title: BT433_The SNP of whole genome

source_name: BT433 SNP of whole genome


title: UTHT4_ROW21_14


title: UTHT4_ROW24_19


title: UTHT4_ROW26_4


title: UTHT4_ROW15_13


title: UTHT4_ROW32_2


title: BT434_The SNP of whole genome

source_name: BT434 SNP of whole genome


title: UTHT4_ROW34_16


title: UTHT4_ROW14_10


title: BT431_The SNP of whole genome

source_name: BT431 SNP of whole genome


title: UTHT4_ROW05_12


title: UTHT4_ROW18_18


title: UTHT4_ROW16_7


title: UTHT4_ROW10_5


title: UTHT4_ROW29_5


title: BT429_The SNP of whole genome

source_name: BT429 SNP of whole genome


title: BT430_The SNP of whole genome

source_name: BT430 SNP of whole genome


title: UTHT4_ROW33_1

source_name: cortex


title: UTHT4_ROW19_7


title: UTHT4_ROW34_4


title: UTHT4_ROW32_6


title: UTHT4_ROW06_3


title: BT428_The SNP of whole genome

source_name: BT428 SNP of whole genome


title: BT427_The SNP of whole genome

source_name: BT427 SNP of whole genome


title: UTHT4_ROW04_18


title: UTHT4_ROW34_9


title: UTHT4_ROW12_10


title: BT425_The SNP of whole genome

source_name: BT425 SNP of whole genome


title: BT426_The SNP of whole genome

source_name: BT426 SNP of whole genome


title: UTHT4_ROW25_14


title: UTHT4_ROW36_11


title: UTHT4_ROW38_6


title: BT424_The SNP of whole genome

source_name: BT424 SNP of whole genome


title: UTHT4_ROW32_3


title: BT423_The SNP of whole genome

source_name: BT423 SNP of whole genome


title: UTHT4_ROW01_6


title: UTHT4_ROW35_16


title: BT422_The SNP of whole genome

source_name: BT422 SNP of whole genome


title: BT421_The SNP of whole genome

source_name: BT421 SNP of whole genome


title: UTHT4_ROW08_19


title: UTHT4_ROW36_19


title: BT420_The SNP of whole genome

source_name: BT420 SNP of whole genome


title: UTHT4_ROW19_9


title: Arabidopsis thaliana Col-0 seedlings White light (W2)

city: riverside

first: Peter

middle: H

last: Quail

address: 7774 Kingdom Dr

department: PMB

institute: UC Berkeley

data_processing:
The 5′-end 36-nt trimmed reads were aligned to the TAIR9 representative transcriptome using Bowtie with zero mismatches allowed. Only reads mapping uniquely to the 3′-end 500-bp region of the coding strand were counted for gene expression
Differentially expressed genes were identified using the edgeR package.
Genome_build: TAIR9
Supplementary_files_format_and_content: WT-RNAseq_pseudocounts.xlsx
Supplementary_files_format_and_content: Pseudocounts of every gene in Arabidopsis TAIR9 genome

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: Plants were germinated in true-dark conditions as described in (Leivar et al., 2008). Briefly, seeds were sterilized, plated in MS medium without sucrose, irradiated for 3h with white light to induce germination, followed by a saturating far-red light pulse during 5 min before being stratified for 4 days at 4ºC in darkness. They were grown in the dark at 21ºC for 2 days before being collected (D samples) or grown in the dark for 47 hours and treated with 10 μE⋅m−2⋅s−1 red light for 1 hour (R1 samples). White-light grown samples (WLc) were grown under continuous white-light (100 μE⋅m−2⋅s−1 PAR) after stratification for 2 days.

extract_protocol:
RNA was extracted using RNeasy Plant Mini Kit (Qiagen cat. 74904) using RNase-Free DNase (Qiagen cat. 79254) following manufacturer instructions
The sequencing library construction was adapted from 3′-end RNA-seq protocol. The mRNA was fractionated from 20 µg of total RNA using Dynabeads Oligo (dT)25 (Invitrogen), and fragmented using Fragmentation Reagents (Ambion) at 70°C for 2.5 min in 20 µl of reaction. The polyA-tailed 3′-end fragments were captured by another run of mRNA purification as described above, and then treated by Antarctic Phosphatase (NEB) and T4 Polynucleotide Kinase (NEB) at 37°C for 1 h and 2 h, respectively. The sample was purified using RNeasy MinElute Cleanup Kit (Qiagen) according to Illumina's protocol. The eluted mRNA fragments were ligated with 2.5 µM of Illumina's SRA 5′ adaptor by T4 RNA Ligase 1 (NEB) at 20°C for 4 h. The 3′ cDNA adapter derived from Illumina's v1.5 sRNA 3′ adapter was conjugated with the anchored oligo (dT)20 primer, and introduced through reverse transcription using the SuperScript III First-Strand Synthesis System (Invitrogen). The first-strand cDNA was purified using the Agencourt AMPure XP system, and then amplified by PCR reaction using Phusion High-Fidelity DNA Polymerase with Illumina's sRNA PCR primer set. The size of purified library DNA was validated by Bioanalyzer 2000.

tag: ecotype

value: wild type

value: White light (W2)

value: Seedling


title: BT418_The SNP of whole genome

source_name: BT418 SNP of whole genome

tag: tissue


title: Obese, diabetic and steatosis=3 rep 2

type: RNA

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

country: Italy

institute: European Brain Research Institute

description: gene expression data from

hyb_protocol: Labeled cRNA were hybridized was on Human Genome U133 Plus 2.0 Array (Affymetrix). FS450_0001 protocol is used for staining and washing the GeneChips.

scan_protocol: Hybridized chips were read on a model M10 Affymetrix scanner.

data_processing: Data were analyzed using Expression Console and normalized by the RMA algorithm.

source_name: liver

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

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

value: liver

tag: gender

value: Male

tag: glucose tolerance

value: diabetic


title: Obese, non-diabetic and non-steatosis rep 1

description: gene expression data from

value: non-diabetic

value: non-steatosis


title: Obese, non-diabetic and non-steatosis rep 2

description: gene expression data from

value: Female


title: BT417_The SNP of whole genome

source_name: BT417 SNP of whole genome


title: Obese, diabetic and steatosis=3 rep 1

description: gene expression data from


title: Arabidopsis thaliana Col-0 seedlings Darkness + 1h Red light (R3)

treatment_protocol: Plants were germinated in true-dark conditions as described in (Leivar et al., 2008). Briefly, seeds were sterilized, plated in MS medium without sucrose, irradiated for 3h with white light to induce germination, followed by a saturating far-red light pulse during 5 min before being stratified for 4 days at 4ºC in darkness. They were grown in the dark at 21ºC for 2 days before being collected (D samples) or grown in the dark for 47 hours and treated with 10 μE⋅m−2⋅s−1 red light for 1 hour (R1 samples). White-light grown samples (WLc) were grown under continuous white-light (100 μE⋅m−2⋅s−1 PAR) after stratification for 2 days.

value: Darkness + 1h Red light (R3)


title: UTHT4_ROW17_7


title: BT415_The SNP of whole genome

source_name: BT415 SNP of whole genome


title: UTHT4_ROW20_6


title: Arabidopsis thaliana Col-0 seedlings White light (W3)

value: White light (W3)


title: Arabidopsis thaliana Col-0 seedlings Darkness + 1h Red light (R1)

value: Darkness + 1h Red light (R1)


title: Obese, diabetic and steatosis=3 rep 3

description: gene expression data from


title: BT414_The SNP of whole genome

source_name: BT414 SNP of whole genome


title: UTHT4_ROW13_13

value: cortex


title: Arabidopsis thaliana Col-0 seedlings Darkness + 1h Red light (R2)

value: Darkness + 1h Red light (R2)


title: UTHT4_ROW37_14


title: Arabidopsis thaliana Col-0 seedlings Darkness (D3)

value: Darkness (D3)


title: UTHT4_ROW16_12


title: Arabidopsis thaliana Col-0 seedlings White light (W1)

value: White light (W1)


title: UTHT4_ROW01_2


title: UTHT4_ROW28_5


title: BT413_The SNP of whole genome

source_name: BT413 SNP of whole genome

value: Leaf


title: UTHT4_ROW30_5

source_name: cortex


title: Arabidopsis thaliana Col-0 seedlings Darkness (D2)

value: wild type

value: Darkness (D2)


title: BT416_The SNP of whole genome

source_name: BT416 SNP of whole genome


title: BT411_The SNP of whole genome

source_name: BT411 SNP of whole genome


title: BT412_The SNP of whole genome

source_name: BT412 SNP of whole genome


title: BT419_The SNP of whole genome

source_name: BT419 SNP of whole genome


title: Arabidopsis thaliana Col-0 seedlings Darkness (D1)

value: Darkness (D1)

value: Seedling


title: UTHT4_ROW30_18


title: BT410_The SNP of whole genome

source_name: BT410 SNP of whole genome


title: UTHT4_ROW38_18


title: UTHT4_ROW17_16


title: UTHT4_ROW18_4


title: BT409_The SNP of whole genome

source_name: BT409 SNP of whole genome


title: BT408_The SNP of whole genome

source_name: BT408 SNP of whole genome


title: UTHT4_ROW06_2


title: 1uM RA replicate 3

first: Ziyan

last: Lin

department: Applied Bioinformatics Laboratories

institute: NYU Grossman School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality bases, then mapped to XENLA_9.2 whole genome using STAR aligner (v2.7.3) following sns rna-star (https://igordot.github.io/sns/routes/rna-star.html) pipeline
Genome_build: XENLA_9.2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Xenopus laevis

source_name: NF stage 15 embryo

growth_protocol: WT Xenopus embryos from 3 different femles were cultured in 0.1X NAM. Membranes were removed and anterior halves were dissected at NF stage 12.5.

extract_protocol:
Total RNA was extracted using RNeasy Micro kit (Qiagen, Cat# 74004) as per manufacturer’s instructions, including on-column DNase I digestion 15 mins at room temp to eliminate genomic DNA.
Extracted Total RNA from anterior halves of NF stage 15 embryos was verified on the Agilent Bioanalyzer system using a nanochip to verify the RNA integrity number (RIN). High quality total RNA (500ng) was input into the Illumina Truseq v2 stranded mRNA library prep kit (cat#20020595) according to the manufacturer’s protocol. Generated cDNA was amplified with 12 pcr cycles. Final generated libraries were verified on the Agilent Tapestation 2200 system using high sensitivity DNA Screentape.  Generated cDNA was amplified with 12 pcr cycles. Final generated libraries were verified on the Agilent Tapestation 2200 system using high sensitivity DNA Screentape. Sample concentration was checked on the Invitrogen qubit system using the high sensitivity DNA reagent. Each sample was normalized to a specific nanomolar concentration and pooled equally into a final combined pool. The pool was run on 1 lane of Novaseq SP100 flow cell (run length was 50 paired end bases) on the Illumina Novaseq 6000 sequencing system.

treatment_protocol: 10uM DMSO, 1uM RA or 10uM 4-oxo-RA dilutions were made in 0.1X NAM and anterior halves of Xenopus embryos were treated from NF stage 12.5 to NF stage 15, when they were collected for RNA extraction.

tag: tissue/age

value: Anterior half of NF stage 15 embryo

value: 1uM RA treated


title: UTHT4_ROW10_3


title: 1uM RA replicate 2


title: UTHT4_ROW27_7


title: 1uM RA replicate 1


title: BT405_The SNP of whole genome

source_name: BT405 SNP of whole genome


title: BT404_The SNP of whole genome

source_name: BT404 SNP of whole genome


title: Huh7_siHINT1/siControl_rep2

city: KUNMING City

first: Cheng

last: Zhang

state: Yunnan Province

address: No. 374 Kunrui Road

department: Department of hepatobiliary surgery

institute: The Second Affiliated Hospital of Kunming Medical University

description: differentially expressed lncRNAs and mRNAs of siHINT1 VS. siControl in Huh9cells

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by lowess normalization.

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

growth_protocol: Huh7 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS, Life Technologies, Gaithersburg, MD, USA) at 37 °C under a humidified atmosphere of 5% CO2.

extract_protocol: Total RNA was extracted from siHINT1 and shControl Huh7 cells using TRIzol reagent following the manufacturer's recommendation. RNA was quantified using a NanoDrop-2000 spectrophotometer and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

treatment_protocol: Huh7 cells were transfected with the control (sc-37007, Santa Cruz biotechnology, CA, USA), Hint1-specific siRNA (sc-92005, Santa Cruz biotechnology, CA, USA) using Lipofectamine RNAiMax and Opti-MEM medium (Invitrogen). After 48 h culture, the efficacy of specific gene silencing was determined by Western blot.After selection, siHINT1 and shControl Huh7 cells were used to performed gene expression profile analysis.

tag: cell type

value: Hepatocellular carcinoma cell line

tag: genotype/variation

value: siControl


title: UTHT4_ROW22_5


title: Huh7_siHINT1/siControl_rep1


title: UTHT4_ROW10_19


title: BT403_The SNP of whole genome

source_name: BT403 SNP of whole genome


title: BT402_The SNP of whole genome

source_name: BT402 SNP of whole genome


title: UTHT4_ROW36_15


title: UTHT4_ROW24_18


title: 10uM DMSO replicate 1

value: 10uM DMSO treated


title: BT407_The SNP of whole genome

source_name: BT407 SNP of whole genome


title: BT406_The SNP of whole genome

source_name: BT406 SNP of whole genome


title: BT400_The SNP of whole genome

source_name: BT400 SNP of whole genome


title: UTHT4_ROW11_18


title: Huh7_siHINT1/siControl_rep3


title: 10uM DMSO replicate 3


title: BT399_The SNP of whole genome

source_name: BT399 SNP of whole genome


title: UTHT4_ROW03_16

source_name: cortex


title: 10uM DMSO replicate 2


title: BT398_The SNP of whole genome

source_name: BT398 SNP of whole genome


title: UTHT4_ROW11_11


title: 8226_REIIBP - Input

city: Singapore

first: Phyllis

last: Chong

address: 14 Medical Drive #12-01

country: Singapore

institute: Cancer Science Institute of Singapore

data_processing:
The library was constructed by Novogene Corporation (Beijing, China)
Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA)
Library quality was assessed on the Agilent Bioanalyzer 2100 system.
Clean reads were aligned to the reference genome using BWA mem (v 0.7.12).
After mapping reads to the reference genome, we used the MACS2 (version 2.1.0) peak calling software to identify regions of IP enrichment over background. A q-value threshold of 0.05 was used for all data sets.
Genome_build: The reference genome ID used was ensembl_homo_sapiens_grch38_p12_gca_000001405_27
Supplementary_files_format_and_content: bigwig

source_name: Multiple Myeloma

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.

tag: chip antibody

value: REIIBP overexpression


title: UTHT4_ROW03_14


title: 8226_Vcon - Input

value: Control


title: 8226_REIIBP - H3K4me3


title: BT396_The SNP of whole genome

source_name: BT396 SNP of whole genome


title: UTHT4_ROW04_12


title: UTHT4_ROW33_10


title: 10uM 4oxoRA replicate 3

value: 10uM 4-oxo-RA treated


title: 10uM 4oxoRA replicate 1


title: BT395_The SNP of whole genome

source_name: BT395 SNP of whole genome


title: 8226_Vcon - H3K4me3


title: BT436_The SNP of whole genome

source_name: BT436 SNP of whole genome


title: 10uM 4oxoRA replicate 2


title: UTHT4_ROW13_11

value: cortex


title: 8226_REIIBP - H3K27me3


title: Obese, non-diabetic and non-steatosis rep 3

description: gene expression data from

source_name: liver

value: liver

value: Female

value: non-diabetic

value: non-steatosis


title: BT393_The SNP of whole genome

source_name: BT393 SNP of whole genome

value: Leaf


title: BT397_The SNP of whole genome

source_name: BT397 SNP of whole genome


title: 8226_Vcon - H3K27me3


title: BT432_The SNP of whole genome

source_name: BT432 SNP of whole genome


title: BT392_The SNP of whole genome

source_name: BT392 SNP of whole genome


title: 1299_Input

city: Zhengzhou

first: li

last: yixin

state: China

address: No. 50, Jianshe East Road, Erqi District

institute: First Affiliated Hospital of Zhengzhou University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.   The clean reads were used for protein binding site analysis. They were mapped to the reference genome of human using STAR software (version 2.5.3a) with default parameters. The RSeQC（version 2.6）was used for reads distribution analysis.The MACS2 software（Version 2.1.1）was used for peak calling. The bedtools（Version 2.25.0）was used for peaks annotation and peak distribution analysis. The differentially binding peaks were identified by a python script，using fisher test. The Homer（version 4.10）was used for motifs analysis. Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for annotated genes were both implemented by KOBAS software (version: 2.1.1) with a corrected P-value cutoff of 0.05 to judge statistically significant enrichment.
Genome_build: GRCh38
Supplementary_files_format_and_content: peak

source_name: lung adenocarcinoma

extract_protocol:
Lysates were clarified from sonicated nuclei and nuclear protein/DNA complex was isolated with antibody.
The ChIP procedure was performed as illustrated in the ChIP kit (#9002S, CST, Danvers, MA). Briefly, the tested cell lines were fixed with formaldehyde, and cross-linking was performed by adding glycine. The samples were placed on ice and sonicated to separate the DNA into 100 to 1000-bp fragments. Then, they were incubated with antibodies at a dilution of 1:50 overnight, followed by incubation with protein G agarose beads at 4 °C overnight. Next, the bound DNA-protein mixtures were eluted, and cross-linking was reversed after several washes. The precipitated chromatin DNA was then collected and analyzed by ChIP-seq aligned to human genome (Seqhealth Co., Wuhan, China).

tag: strain

value: lung adenocarcinoma

value: untreated


title: 1299_IP

value: HNRNPK (Proteintech, #11426-1-AP)


title: UTHT4_ROW33_3


title: UTHT4_ROW07_5


title: BT391_The SNP of whole genome

source_name: BT391 SNP of whole genome


title: UTHT4_ROW37_6


title: UTHT4_ROW01_12


title: BT390_The SNP of whole genome

source_name: BT390 SNP of whole genome


title: T95.3

city: Pullman

first: Michael

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: test.results.csv.gz

data_processing:
Basic read quality was verified using summaries produced by FastQC. Trimmomatic was used to remove low quality reads and bases
The reads for each sample were mapped to the human (GRCh38) genome using Bowtie2
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 1000 bp windows. The edgeR Pvalue was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR P value less than an arbitrarily chosen threshold were considered DMR. The DMR edges were extended until no genomic window with an edgeR P value less than 0.1 remained within 1000 bp of the DMR.
The selected DMR were then summarized and annotated.
In addition to the main analysis, two sets of test samples were collected. A first internal test set was composed of technical replicates of samples from the main analysis. These samples were used to identify potential batch effects. A second external test set was composed of additional samples not included in the main analysis. These samples were used to determine whether the preterm birth status could be predicted from the DMRs identified in the main analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window and other summary values.

source_name: buccal

growth_protocol: St. Franciscan Hospital and Indiana University School of Medicine. IU Health Hospitals (Riley Hospital for Children, IUH Methodist, IUH North) and Franciscan Health, Indianapolis, Indiana, USA provided samples for the study. Informed consent and HIPAA authorization was obtained from all participants prior to the clinical sample collection. The study protocol was approved by the Indiana University Institutional Review Board (IRB) #1901985132 and the Franciscan Institutional Review Board (IRB), #1489434-5. All research was performed in accordance with relevant guidelines/regulations. Informed consent and HIPAA authorization was obtained from all participants prior to sample collection. For sample collection involving human participants that are minors, informed consent from a parent and/or legal guardian for study participation was obtained prior to sample collection.

extract_protocol:
Frozen human buccal samples were thawed for analysis. Genomic DNA from buccal samples was prepared as follows: The buccal brush was suspended in 750 μl of cell lysis solution and 3.5 µl of Proteinase K (20 mg/ml). This suspension was incubated at 55ºC for 3 hours, then vortexed and centrifuged briefly. The lysis solution was then transferred to a new 1.5 µl microcentrifuge tube. The microcentrifuge tube with the buccal brush was centrifuged again to retain any remaining solution which was combined with the transferred lysis solution. The buccal brush was discarded and 300 µl of protein precipitation solution (Promega, A795A, Madison, WI) was added to the lysis solution. The sample was incubated on ice for 15 minutes, then centrifuged at 4C for 30 minutes. The supernatant was transferred to a fresh 2 mL microcentrifuge tube and 1,000 µl ice cold isopropanol was added along with 2 µL glycoblue. This suspension was mixed thoroughly and incubated at -20 ºC overnight. The suspension was then centrifuged at 4ºC for 20 minutes, the supernatant was discarded, and the pellet was washed with 75% ethanol, then air-dried and resuspended in 100 μl H2O. DNA concentration was measured using the Nanodrop (Thermo Fisher, Waltham, MA). Methylated DNA Immunoprecipitation (MeDIP) with genomic DNA was performed as follows: individual DNA samples (2-4 ug of total DNA) were diluted to 130 μl with 1x Tris-EDTA (TE, 10 mM Tris, 1 mM EDTA) and sonicated with the Covaris M220 using the 300 bp setting. Fragment size was verified on a 2% E-gel agarose gel. The sonicated DNA was transferred from the Covaris tube to a 1.7 ml microfuge tube, and the volume was measured. The sonicated DNA was then diluted with TE buffer (10mM Tris HCl, pH7.5; 1mM EDTA) to 400 μl, heat-denatured for 10 min at 95 C, then immediately cooled on ice for 10 min. Then 100 μl of 5X IP buffer and 5 μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added to the denatured sonicated DNA. The DNA-antibody mixture was incubated overnight on a rotator at 4 C. The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; 11201D) were pre-washed as follows: The beads were resuspended in the vial, then the appropriate volume (50 μl per sample) was transferred to a microfuge tube. The same volume of Washing Buffer (at least 1 mL 1XPBS with 0.1% BSA and 2mM EDTA) was added and the bead sample was resuspended. The tube was then placed into a magnetic rack for 1-2 min and the supernatant was discarded. The tube was removed from the magnetic rack and the beads were washed once. The washed beads were resuspended in the same volume of 1xIP buffer (50 mM sodium phosphate ph7.0, 700 mM NaCl, 0.25% TritonX-100) as the initial volume of beads. 50μl of beads were added to the 500μl of DNA-antibody mixture from the overnight incubation, then incubated for 2 hours on a rotator at 4 C. After the incubation, the bead-antibody-DNA complex was washed three times with 1X IP buffer as follows: The tube was placed into a magnetic rack for 1-2 min and the supernatant was discarded, then the magnetic bead antibody pellet was washed with 1xIP buffer 3 times. The washed bead antibody DNA pellet was then resuspended in 250 μl digestion buffer with 3.5 μl Proteinase K (20mg/ml). The sample was incubated for 2-3 hours on a rotator at 55 C, then 250 μl of buffered Phenol-Chloroform- Isoamylalcohol solution was added to the sample, and the tube was vortexed for 30 sec and then centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was carefully removed and transferred to a fresh microfuge tube. Then 250 μl chloroform were added to the supernatant from the previous step, vortexed for 30 sec and centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was removed and transferred to a fresh microfuge tube. To the supernatant 2μl of glycoblue (20mg/ml), 20μl of 5M NaCl and 500μl ethanol were added and mixed well, then precipitated in -20 C freezer for 1 hour to overnight. The precipitate was centrifuged at 14,000rpm for 20 min at 4 C and the supernatant was removed, while not disturbing the pellet. The pellet was washed with 500μl cold 70% ethanol in -20 C freezer for 15 min then centrifuged again at 14,000rpm for 5 min at 4 C and the supernatant was discarded. The tube was spun again briefly to collect residual ethanol to the bottom of the tube and as much liquid as possible was removed with gel loading tip. The pellet was air-dried at RT until it looked dry (about 5 min) then resuspended in 20μl H2O or TE. DNA concentration was measured in Qubit (Life Technologies) with ssDNA kit (Molecular Probes Q10212).
The MeDIP DNA samples (50 ng of each) were used to create libraries for next generation sequencing (NGS) using the NEBNext Ultra RNA Library Prep Kit for Illumina (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed. Each sample received a separate index primer. NGS was performed at WSU Spokane Genomics Core using the Illumina HiSeq 2500 with a PE50 application, with a read size of approximately 50bp and approximately 5-35 million reads per sample, and 6-7 sample libraries each were run in one lane.

treatment_protocol: Buccal samples were collected from the mother, father, and child in instances where pre-term birth occurred (case), or where term birth occurred (control). Buccal swabs were stored at -80 C until use.

tag: treatment group

value: test control

tag: family member

value: female child


title: BT389_The SNP of whole genome

source_name: BT389 SNP of whole genome


title: UTHT4_ROW18_9

data_processing:
Single cell only: The 4bp UMI sequence (initially sequenced in read1), are appended at the end of the headers of the reads (here the reads we provide are resulting from this operation)
Reads are mapped with STAR on the mouse genome GRCm38 considering Ensembl 85 as genome annoatations
Single cell only: bam files are processed with umi_tools to deduplicate reads with identical UMI sequence
gene expression are quantifyied using summarizeOverlaps() method of the R package GenomicsAlignments(). Only exonic reads are considered in the quantification (this includes 5' and 3' UTRs), and only reads with a mapping quality >=255 (to exclude those ambiguously mapping at multiple positions).
Genome_build: GRCm38
Supplementary_files_format_and_content: singlecell_countmatrix.tsv.gz: is a count matrix in tab-separated format. It contains the result of the single cell quantification for all genes. The integers values represent the number of exonic reads mapping into each gene after UMI correction. The first columns contains the gene name that is quantified.    bulk_countmatrix.tsv.gz: count matrix for the bulk experiments in tab-separated format.    singlecell_metadata.tsv: is a table containing metadata information for each cell in tab-separated. The content of the columns are: MT=proportion of mithocondrial reads; ngenes=number of expressed gene; epor_age=age at which the mous as been electroporated; collection_age=age at which cells were collected; cond=condition Control/miR-137/miR-122; cell_type, cell_type_pred1, cell_type_pred2: predicted cell types for the cell; tSNE1, tSNE2= coordinate of the cell in the t-SNE space

extract_protocol:
Single-cell RNA sequencing    Embryonic cortex: Tissue collection was performed as in Telley et al., Science 2019. Briefly, pregnant females were sacrificed, and embryos were extracted in ice-cold HBSS either at E15.5 and E17.5 after E14.5 in utero electroporation. Three hundred micrometer- acute coronal brain sections were performed after embedding in 4% low melt- agar using a vibratome (Leica, #VT1000S) under RNase-free conditions. The putative primary somatosensory cortex (S1) was microdissected using a Leica Dissecting Microscope (Leica, #M165FC) and incubated in 0.05% trypsin at 37°C for 5 minutes. Following tissue digestion, cells were incubated in fetal bovine serum and cells were manually dissociated via gentle pipetting. Cells were then centrifuged for 5 minutes at 500 rpm, resuspended in 1 mL FACS buffer (2 mg/mL glucose, 0.1% bovine serum albumin, 1/50 citrate phosphate dextrose, 10 units/mL DNaseI, 1 uM MgCl2, in L15 medium) and filtered using a 70 mm- cell strainer (ClearLine, #141379C), before 10 minute- incubation with Hoechst (0.1 mg/mL) at 37°C .    Postnatal cortex: Tissue collection was performed as in Klingler et al., Curr Biol 2019. Briefly, 600 um acute coronal brain sections were cut on a vibratome and S1 was microdissected as described above in ice-cold oxygenated artificial cerebrospinal fluid (ACSF) under RNase-free conditions. Cells were next dissociated by incubating microdissected samples in 0.5 mg/mL pronase (Sigma, #P5147) at 37°C for 10 minutes, followed by a 3 minute- inactivation in 5% bovine serum albumin, washes in ACSF and manual trituration using pulled glass pipettes of decreasing diameters. Cells were then centrifuged for 10 minutes at 500 rpm, resuspended and filtered using a 70 um- cell strainer (ClearLine, #141379C), incubated for 10 minutes with Hoechst (0.1 mg/mL) at 37°C.    Singlet GFP+/Hoechst+ embryonic and postnatal cells were sorted using a Beckman Coulter Moflo Astrios FAC-sorter according to their Forward and Slide scattering properties, and their negativity for Draq7TM (Viability dye, far red DNA intercalating agent, Beckman Coulter, #B25595). Three microliters of C1 Suspension Reagent (Fluidigm) was added to 10 ul of FACsorted cells, which were captured into 800 well- AutoPrep integrated fluidic circuit (IFC) designed for 10 to 17 um diameter-cells (Fluidigm HT800, #100-57-80), and imaged using the ImageXpress Micro Widefield High Content Screening System (Molecular Devices®).        Bulk RNA sequencing    Brains were collected from E14.5 in utero electroporated miR-122 pups at P7. The primary somatosensory cortex was microdissected following the same procedure as described above with further separation of superficial (SL) and deep (DL) layers. SL and DL cells were dissociated and FACsorted as for single-cell RNA sequencing.
Single-cell RNA sequencing  cDNA synthesis and preamplification was processed following the manufacturer’s instructions (C1 system, Fluidigm). cDNA libraries were prepared using Nextera XT DNA library prep kit (Illumina), quality control was done using 2001 Bioanalyzer from Agilent, and sequenced using HiSeq 2500 sequencer for E14.5 electroporated pups, and HiSeq 5000 sequencer for E14 and E15.5 electroporated pups with an expected sequencing depth of 1M reads per single cell, and a final mapping read length of 70bp.    Bulk RNA sequencing  RNA from each sample was extracted and quality control was done using 2001 Bioanalyzer from Agilent. cDNA libraries were obtained using SMARTseq v4 kit (Clontech, # 634888) and sequenced using HiSeq 2500 sequencer.


title: T95.2

description: test.results.csv.gz

value: father


title: T95.1

description: test.results.csv.gz

value: mother


title: UTHT4_ROW28_18


title: T79.3

description: test.results.csv.gz

value: technical replicate control

value: male child


title: BT387_The SNP of whole genome

source_name: BT387 SNP of whole genome


title: UTHT4_ROW29_16

source_name: cortex


title: BT394_The SNP of whole genome

source_name: BT394 SNP of whole genome


title: BT386_The SNP of whole genome

source_name: BT386 SNP of whole genome


title: BT385_The SNP of whole genome

source_name: BT385 SNP of whole genome


title: T79.1

description: test.results.csv.gz


title: UTHT4_ROW25_7


title: UTHT4_ROW22_17


title: T73.3

description: test.results.csv.gz


title: BT382_The SNP of whole genome

source_name: BT382 SNP of whole genome


title: UTHT4_ROW39_13


title: UTHT4_ROW28_10


title: UTHT4_ROW13_2


title: BT383_The SNP of whole genome

source_name: BT383 SNP of whole genome


title: T62.3

description: test.results.csv.gz


title: T73.2

description: test.results.csv.gz


title: BT384_The SNP of whole genome

source_name: BT384 SNP of whole genome


title: UTHT4_ROW05_19


title: BT261_The SNP of whole genome

source_name: BT261 SNP of whole genome


title: UTHT4_ROW05_4


title: BT388_The SNP of whole genome

source_name: BT388 SNP of whole genome


title: BT258_The SNP of whole genome

source_name: BT258 SNP of whole genome


title: BT381_The SNP of whole genome

source_name: BT381 SNP of whole genome


title: UTHT4_ROW21_11


title: UTHT4_ROW16_20


title: UTHT4_ROW04_16


title: T62.1

description: test.results.csv.gz


title: T79.2

description: test.results.csv.gz


title: BT211_The SNP of whole genome

source_name: BT211 SNP of whole genome


title: T62.2

description: test.results.csv.gz


title: T58.3

description: test.results.csv.gz

value: test preterm birth


title: UTHT4_ROW29_3


title: UTHT4_ROW05_5


title: T58.1

description: test.results.csv.gz


title: BT094_The SNP of whole genome

source_name: BT094 SNP of whole genome


title: T58.2

description: test.results.csv.gz


title: UTHT4_ROW36_12


title: T56.3

description: test.results.csv.gz

value: technical replicate preterm birth


title: T73.1

description: test.results.csv.gz


title: UTHT4_ROW12_7

value: cortex


title: UTHT4_ROW37_10


title: T56.2

description: test.results.csv.gz


title: BT056_The SNP of whole genome

source_name: BT056 SNP of whole genome


title: BT018_The SNP of whole genome

source_name: BT018 SNP of whole genome


title: BT292_The SNP of whole genome

source_name: BT292 SNP of whole genome


title: BT012_The SNP of whole genome

source_name: BT012 SNP of whole genome


title: UTHT4_ROW21_5

source_name: cortex


title: UTHT4_ROW24_9


title: UTHT4_ROW06_18


title: BT291_The SNP of whole genome

source_name: BT291 SNP of whole genome


title: T51.1

description: test.results.csv.gz

source_name: buccal


title: T51.2

description: test.results.csv.gz


title: BT294_The SNP of whole genome

source_name: BT294 SNP of whole genome


title: T56.1

description: test.results.csv.gz


title: BT293_The SNP of whole genome

source_name: BT293 SNP of whole genome


title: T51.3

description: test.results.csv.gz


title: UTHT4_ROW32_10


title: UTHT4_ROW25_16


title: T47.2

description: test.results.csv.gz


title: UTHT4_ROW25_5


title: T47.3

description: test.results.csv.gz


title: BT290_The SNP of whole genome

source_name: BT290 SNP of whole genome


title: UTHT4_ROW23_15


title: BT287_The SNP of whole genome

source_name: BT287 SNP of whole genome


title: BT289_The SNP of whole genome

source_name: BT289 SNP of whole genome


title: BT286_The SNP of whole genome

source_name: BT286 SNP of whole genome


title: BT285_The SNP of whole genome

source_name: BT285 SNP of whole genome


title: UTHT4_ROW26_15


title: BT288_The SNP of whole genome

source_name: BT288 SNP of whole genome


title: BT284_The SNP of whole genome

source_name: BT284 SNP of whole genome


title: UTHT4_ROW40_5


title: BT283_The SNP of whole genome

source_name: BT283 SNP of whole genome


title: UTHT4_ROW26_20


title: T47.1

description: test.results.csv.gz


title: T44.2

description: test.results.csv.gz


title: UTHT4_ROW25_15


title: UTHT4_ROW31_11


title: UTHT4_ROW32_20


title: UTHT4_ROW31_1


title: UTHT4_ROW02_12


title: BT280_The SNP of whole genome

source_name: BT280 SNP of whole genome


title: BT279_The SNP of whole genome

source_name: BT279 SNP of whole genome


title: T44.3

description: test.results.csv.gz


title: T41.3

description: test.results.csv.gz


title: T44.1

description: test.results.csv.gz


title: T41.1

description: test.results.csv.gz


title: UTHT4_ROW37_12


title: T35.3

description: test.results.csv.gz


title: UTHT4_ROW02_14


title: BT278_The SNP of whole genome

source_name: BT278 SNP of whole genome


title: BT276_The SNP of whole genome

source_name: BT276 SNP of whole genome


title: UTHT4_ROW29_13

source_name: cortex


title: BT282_The SNP of whole genome

source_name: BT282 SNP of whole genome


title: T38.2

description: test.results.csv.gz

source_name: buccal


title: T34.2

description: test.results.csv.gz


title: T41.2

description: test.results.csv.gz


title: T38.3

description: test.results.csv.gz


title: UTHT4_ROW36_13


title: BT401_The SNP of whole genome

source_name: BT401 SNP of whole genome


title: BT277_The SNP of whole genome

source_name: BT277 SNP of whole genome


title: T35.1

description: test.results.csv.gz


title: BT272_The SNP of whole genome

source_name: BT272 SNP of whole genome


title: T34.1

description: test.results.csv.gz


title: T32.3

description: test.results.csv.gz


title: UTHT4_ROW39_20


title: UTHT4_ROW19_19


title: BT271_The SNP of whole genome

source_name: BT271 SNP of whole genome


title: UTHT4_ROW27_16


title: T38.1

description: test.results.csv.gz


title: BT275_The SNP of whole genome

source_name: BT275 SNP of whole genome


title: BT274_The SNP of whole genome

source_name: BT274 SNP of whole genome


title: UTHT4_ROW35_14


title: BT273_The SNP of whole genome

source_name: BT273 SNP of whole genome


title: BT281_The SNP of whole genome

source_name: BT281 SNP of whole genome


title: UTHT4_ROW22_2


title: UTHT4_ROW36_7


title: T32.2

description: test.results.csv.gz


title: T35.2

description: test.results.csv.gz


title: T32.1

description: test.results.csv.gz


title: UTHT4_ROW07_16


title: BT266_The SNP of whole genome

source_name: BT266 SNP of whole genome


title: BT265_The SNP of whole genome

source_name: BT265 SNP of whole genome


title: UTHT4_ROW19_16


title: UTHT4_ROW39_12


title: BT269_The SNP of whole genome

source_name: BT269 SNP of whole genome


title: UTHT4_ROW20_18


title: BT270_The SNP of whole genome

source_name: BT270 SNP of whole genome


title: T34.3

description: test.results.csv.gz


title: T19.3

description: test.results.csv.gz


title: T19.1

description: test.results.csv.gz


title: T22.2

description: test.results.csv.gz


title: BT267_The SNP of whole genome

source_name: BT267 SNP of whole genome


title: UTHT4_ROW06_13


title: BT268_The SNP of whole genome

source_name: BT268 SNP of whole genome


title: T22.1

description: test.results.csv.gz


title: BT264_The SNP of whole genome

source_name: BT264 SNP of whole genome


title: BT263_The SNP of whole genome

source_name: BT263 SNP of whole genome


title: T11.3

description: test.results.csv.gz

source_name: buccal


title: T22.3

description: test.results.csv.gz


title: UTHT4_ROW36_6

source_name: cortex


title: T19.2

description: test.results.csv.gz


title: UTHT4_ROW24_1


title: T11.2

description: test.results.csv.gz


title: UTHT4_ROW37_9


title: BT262_The SNP of whole genome

source_name: BT262 SNP of whole genome


title: T11.1

description: test.results.csv.gz


title: UTHT4_ROW23_17


title: BT260_The SNP of whole genome

source_name: BT260 SNP of whole genome


title: UTHT4_ROW33_14


title: UTHT4_ROW24_6


title: UTHT4_ROW32_7


title: BT259_The SNP of whole genome

source_name: BT259 SNP of whole genome


title: T8.2

description: test.results.csv.gz


title: T8.1

description: test.results.csv.gz


title: BT257_The SNP of whole genome

source_name: BT257 SNP of whole genome


title: UTHT4_ROW16_19


title: BT256_The SNP of whole genome

source_name: BT256 SNP of whole genome


title: T6.2

description: test.results.csv.gz


title: T6.3

description: test.results.csv.gz


title: UTHT4_ROW40_18


title: UTHT4_ROW21_2


title: BT253_The SNP of whole genome

source_name: BT253 SNP of whole genome


title: T6.1

description: test.results.csv.gz


title: T4.3

description: test.results.csv.gz


title: UTHT4_ROW21_12


title: UTHT4_ROW39_19


title: BT255_The SNP of whole genome

source_name: BT255 SNP of whole genome


title: T4.2

description: test.results.csv.gz


title: BT252_The SNP of whole genome

source_name: BT252 SNP of whole genome


title: BT254_The SNP of whole genome

source_name: BT254 SNP of whole genome


title: BT251_The SNP of whole genome

source_name: BT251 SNP of whole genome


title: UTHT4_ROW17_20


title: UTHT4_ROW13_7


title: T4.1

description: test.results.csv.gz


title: BT250_The SNP of whole genome

source_name: BT250 SNP of whole genome


title: T8.3

description: test.results.csv.gz


title: BT249_The SNP of whole genome

source_name: BT249 SNP of whole genome


title: UTHT4_ROW40_3


title: UTHT4_ROW36_17


title: PT443M

description: mother.results.csv.gz

value: control


title: PT443F

description: father.results.csv.gz


title: UTHT4_ROW29_6


title: BT246_The SNP of whole genome

source_name: BT246 SNP of whole genome


title: PT443C

description: male.child.results.csv.gz


title: BT247_The SNP of whole genome

source_name: BT247 SNP of whole genome


title: UTHT4_ROW12_12


title: PT442M

description: mother.results.csv.gz


title: PT442F

description: father.results.csv.gz


title: UTHT4_ROW07_17


title: UTHT4_ROW39_11


title: BT245_The SNP of whole genome

source_name: BT245 SNP of whole genome


title: PT441M

description: mother.results.csv.gz

source_name: buccal


title: PT442C

description: male.child.results.csv.gz


title: BT244_The SNP of whole genome

source_name: BT244 SNP of whole genome


title: UTHT4_ROW22_18

source_name: cortex


title: UTHT4_ROW29_18


title: PT441F

description: father.results.csv.gz


title: BT243_The SNP of whole genome

source_name: BT243 SNP of whole genome


title: BT242_The SNP of whole genome

source_name: BT242 SNP of whole genome


title: BT241_The SNP of whole genome

source_name: BT241 SNP of whole genome


title: UTHT4_ROW34_20


title: BT239_The SNP of whole genome

source_name: BT239 SNP of whole genome


title: UTHT4_ROW15_6


title: BT248_The SNP of whole genome

source_name: BT248 SNP of whole genome


title: UTHT4_ROW37_3


title: PT440C

description: female.child.results.csv.gz


title: PT440M

description: mother.results.csv.gz


title: BT240_The SNP of whole genome

source_name: BT240 SNP of whole genome


title: PT439M

description: mother.results.csv.gz


title: BT237_The SNP of whole genome

source_name: BT237 SNP of whole genome


title: PT439F

description: father.results.csv.gz


title: PT441C

description: female.child.results.csv.gz


title: UTHT4_ROW06_20


title: BT236_The SNP of whole genome

source_name: BT236 SNP of whole genome


title: PT439C

description: male.child.results.csv.gz


title: BT234_The SNP of whole genome

source_name: BT234 SNP of whole genome


title: PT438M

description: mother.results.csv.gz


title: UTHT4_ROW04_7


title: PT438F

description: father.results.csv.gz


title: UTHT4_ROW15_14


title: UTHT4_ROW23_12


title: PT440F

description: father.results.csv.gz


title: UTHT4_ROW24_5


title: BT233_The SNP of whole genome

source_name: BT233 SNP of whole genome


title: BT231_The SNP of whole genome

source_name: BT231 SNP of whole genome


title: BT232_The SNP of whole genome

source_name: BT232 SNP of whole genome


title: PT438C

description: female.child.results.csv.gz


title: UTHT4_ROW02_18


title: BT235_The SNP of whole genome

source_name: BT235 SNP of whole genome


title: UTHT4_ROW25_20


title: PT437C

description: female.child.results.csv.gz


title: PT437M

description: mother.results.csv.gz


title: UTHT4_ROW35_20


title: BT238_The SNP of whole genome

source_name: BT238 SNP of whole genome


title: BT229_The SNP of whole genome

source_name: BT229 SNP of whole genome


title: UTHT4_ROW23_5


title: BT230_The SNP of whole genome

source_name: BT230 SNP of whole genome


title: UTHT4_ROW29_11

source_name: cortex


title: PT437F

description: father.results.csv.gz

source_name: buccal


title: UTHT4_ROW33_19


title: BT228_The SNP of whole genome

source_name: BT228 SNP of whole genome


title: UTHT4_ROW07_12


title: UTHT4_ROW33_6


title: PT436M

description: mother.results.csv.gz


title: BT226_The SNP of whole genome

source_name: BT226 SNP of whole genome


title: PT436C

description: female.child.results.csv.gz


title: BT225_The SNP of whole genome

source_name: BT225 SNP of whole genome


title: PT433M

description: mother.results.csv.gz


title: BT224_The SNP of whole genome

source_name: BT224 SNP of whole genome


title: PT436F

description: father.results.csv.gz


title: UTHT4_ROW36_5


title: PT433F

description: father.results.csv.gz


title: UTHT4_ROW05_6


title: BT223_The SNP of whole genome

source_name: BT223 SNP of whole genome


title: PT433C

description: female.child.results.csv.gz


title: UTHT4_ROW39_3


title: PT432M

description: mother.results.csv.gz


title: UTHT4_ROW14_1


title: BT222_The SNP of whole genome

source_name: BT222 SNP of whole genome


title: BT221_The SNP of whole genome

source_name: BT221 SNP of whole genome


title: PT432F

description: father.results.csv.gz


title: UTHT4_ROW07_14


title: PT431F

description: father.results.csv.gz


title: PT432C

description: female.child.results.csv.gz


title: BT218_The SNP of whole genome

source_name: BT218 SNP of whole genome


title: BT220_The SNP of whole genome

source_name: BT220 SNP of whole genome


title: PT431C

description: male.child.results.csv.gz


title: BT227_The SNP of whole genome

source_name: BT227 SNP of whole genome


title: PT430F

description: father.results.csv.gz


title: PT431M

description: mother.results.csv.gz


title: BT217_The SNP of whole genome

source_name: BT217 SNP of whole genome


title: UTHT4_ROW26_10


title: UTHT4_ROW17_5


title: PT430C

description: male.child.results.csv.gz


title: BT216_The SNP of whole genome

source_name: BT216 SNP of whole genome


title: UTHT4_ROW01_7


title: PT429M

description: mother.results.csv.gz


title: BT215_The SNP of whole genome

source_name: BT215 SNP of whole genome


title: UTHT4_ROW26_9


title: BT213_The SNP of whole genome

source_name: BT213 SNP of whole genome


title: UTHT4_ROW36_16


title: BT219_The SNP of whole genome

source_name: BT219 SNP of whole genome


title: BT214_The SNP of whole genome

source_name: BT214 SNP of whole genome


title: PT429F

description: father.results.csv.gz

source_name: buccal


title: UTHT4_ROW30_10

source_name: cortex


title: BT212_The SNP of whole genome

source_name: BT212 SNP of whole genome


title: PT429C

description: female.child.results.csv.gz


title: UTHT4_ROW04_6


title: UTHT4_ROW36_4


title: BT210_The SNP of whole genome

source_name: BT210 SNP of whole genome


title: PT428M

description: mother.results.csv.gz


title: PT430M

description: mother.results.csv.gz


title: UTHT4_ROW07_6


title: PT428F

description: father.results.csv.gz


title: UTHT4_ROW03_5


title: UTHT4_ROW31_16


title: PT427M

description: mother.results.csv.gz


title: BT208_The SNP of whole genome

source_name: BT208 SNP of whole genome


title: UTHT4_ROW40_11


title: UTHT4_ROW22_3


title: PT427C

description: female.child.results.csv.gz


title: UTHT4_ROW20_13


title: PT428C

description: male.child.results.csv.gz


title: BT204_The SNP of whole genome

source_name: BT204 SNP of whole genome


title: PT427F

description: father.results.csv.gz


title: PT426M

description: mother.results.csv.gz


title: UTHT4_ROW08_18


title: BT202_The SNP of whole genome

source_name: BT202 SNP of whole genome


title: UTHT4_ROW33_7


title: UTHT4_ROW23_10


title: BT201_The SNP of whole genome

source_name: BT201 SNP of whole genome


title: UTHT4_ROW29_19


title: PT425F

description: father.results.csv.gz


title: UTHT4_ROW05_3