title: Bartolomei_ATAC_Blood_BPA_10ug_5month_Female_biorep6

description: UUID:5c636095adb967a76ead393b,QC_score:-1,QC_stats:Fail


title: Aylor_ATAC_Liver_Ctrl_5month_Male_biorep6

status: Public on May 20 2020

type: SRA

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

country: USA

institute: Washington University in St. Louis

description: UUID:5d39fbfa79452c11b1795232,QC_score:10,QC_stats:Pass

library_source: genomic

data_processing:
RNA-seq and ATAC-seq were sequenced by data production centers and processed by the TaRGET II DCC with standardized data processing pipelines. Library QC was assayed based on key QC parameters. Please refer to the TaRGET II data portal for detailed pipeline description and QC standard (https://data.targetepigenomics.org).
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak output for ATAC-seq and gene count table for RNA-seq

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
Sample collection was performed by David Aylor lab at North Carolina State University. 5 month mice were CO2 euthanized. Liver and blood cells from individual mouse were isolated for subsequent DNA and RNA extractions according to the standard operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.
ATAC-seq and mRNA-seq experiments were performed by David Aylor lab at North Carolina State University. mRNA and nuclei from 5 month mice liver and blood were isolated for subsequent ATAC-seq and mRNA-seq library preparations according to the operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.

tag: strain

tag: age

value: 5 month

tag: gender

value: Male

tag: tissue

value: Liver

tag: treatment

value: Control Oral Gavage 10 microliter per kilogram


title: WT_selection_sRNA

city: Cambridge

first: David

middle: P.

last: Bartel

state: MA

address: 455 Main St.

institute: Whitehead Institute

library_source: transcriptomic

data_processing:
Illumina 1.5; Conventional base calls
The N. castellii genome used for analysis of small-RNA and RNA sequencing from wild-type (WT_non-selection), AGO1 slicing-impaired (ago1_mut_non-selection), and Δxrn1 (xrn1_KO_non-selection) strains was downloaded from NCBI (ASM23734v1), and the sequences of the Y′-consensus ORF (Drinnenberg et al., 2009) as well as the chloramphenicol and firefly luciferase internal-standard mRNA sequences were added to the FASTA file (Ncastellii_non-selection_genome.fsa).  The N. castellii genome used for analysis of RNA sequencing from wild-type (WT_selection) and Δxrn1 (xrn1_KO_selection) genetic-selection strains was downloaded from NCBI (ASM23734v1) and supplemented with the Y′-consensus ORF as well as the chloramphenicol and luciferase internal-standard mRNA sequences.  Sequences of the integrating plasmids containing GFP, URA3 and HIS3-PEST along with their silencing constructs, as well as the integrating plasmids containing extra copies of AGO1 and DCR1 were inserted into the FASTA file (Ncastellii_selection_genome.fsa).  STAR (v.2.4) was used to generate indexed genomes.  The coordinates of annotated small-RNA clusters (Drinnenberg et al., 2009) were converted from scaffolds of the unfinished N. castellii genome to the genomic coordinates of the finished N. castellii genome using the liftOver command line tool from UCSC (https://genome.ucsc.edu/).  The sequence of one annotated small-RNA cluster did not match the finished genome, and thus this cluster was omitted.  For some small-RNA clusters, the former scaffold coordinates overlapped in the finished genome; these were combined to generate larger clusters in the updated set of small-RNA clusters.  In instances in which a region of a previously annotated small-RNA cluster was partially deleted in the new genome, the remainder was retained as a smaller cluster.  In cases in which the scaffold sequence of a small-RNA cluster mapped to multiple sequences in the finished genome, only one set of coordinates for the cluster was retained.  Several new clusters were also identified as genomic regions for which 22–23-nt reads mapped but were not previously annotated as small-RNA clusters and did not overlap known rRNA or tRNA loci.  GTFs of the genomic coordinates of the small-RNA clusters is provided (Ncastellii_sRNA_cluster_non-selection strain, Ncastellii_sRNA_cluster_non-selection strain).
For the small RNA sequencing libraries, the first four nucleotides of each sequencing read were removed using fastx_trimmer from the FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html).  The 3′ adapter was then trimmed using cutadapt (v1.8) (Martin 2011) with parameters ‘-a NNNNTCGTATGCCGTCTTCTGCTTG -m 9’.  High-quality reads were then selected using fastq_quality_filter from the FASTX-toolkit with parameters ‘-v -q 30 -p 100 -Q 64 -z’.  9–26-nt, and 10–12-nt or 22–23-nt high-quality reads were selected using cutadapt (displayed in custom read counts tables).  Reads were aligned to their appropriate N. castellii genomes using STAR (v.2.4) allowing no mismatches or gaps with the parameters ‘--runThreadN 30 --alignIntronMax 1 --alignIntronMin 2 --scoreDelOpen -10000 --scoreInsOpen -10000 --outFilterMismatchNmax 0 --seedSplitMin 9 --outFilterType BySJout --outFilterMultimapNmax 1000 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignEndsType EndToEnd’.  To remove rRNA and tRNA reads, featureCounts (Liao et al., 2014) was used to fractionally count the number of times each read mapped to annotated rRNA loci and their intergenic regions (Ncas_Chr3: 572204–588441) and to annotated tRNA loci in the N. castellii genome (Ncastellii_rrna_w_intergenic_trna_no_intergenic.gtf) using the parameters ‘-s 1 -f -O -M --fraction --donotsort’.  Additionally, featureCounts was used to produce a SAM file of these rRNA and tRNA reads which were then removed from the original files of 9–26-nt, 10–12-nt or 22–23-nt high quality reads using custom Python scripts.  The high-quality reads that were depleted of rRNA and tRNA reads were then aligned to the appropriate N. castellii genomes using STAR (v.2.4) with the same parameters as before.  To fractionally count the number of times each read mapped to specific features in the N. castellii genome, featureCounts was utilized using the parameters ‘-s 1 -f -O -M --fraction --donotsort’.  For the small-RNA sequencing analysis with wild-type (WT_non-selection), AGO1 slicing-impaired (ago1_mut_non-selection), and Δxrn1 (xrn1_KO_non-selection) strains, this fractional counting was performed using a GTF file of the previously annotated small-RNA clusters, which included the Y′-consensus ORF (Ncastellii_sRNA_cluster_non-selection_strain.gtf).  For the small-RNA sequencing analysis with wild-type (WT_selection) and Δxrn1 (xrn1_KO_selection) genetic-selection strains, this fractional counting was performed using a GTF file of the previously annotated small-RNA clusters, including the Y′-consensus ORF as well as the synthetic hairpins used in the genetic selection (Ncastellii_sRNA_cluster_selection_strain.gtf).
For the RNA sequencing libraries, RNA-seq reads were aligned to the genome using STAR (v.2.4) with the parameters ‘--outFilterType BySJout --outFilterMultimapNmax 1000 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMax 1100 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outFilterIntronMotifs RemoveNoncanonicalUnannotated’.  As with the small-RNA sequencing, featureCounts were used to fractionally count the number of times each read mapped to the genome using the parameters ‘-s 2 -f -O -M --fraction --donotsort’.  This fractional counting was performed using GTF files of the previously annotated small-RNA clusters (Ncastellii_sRNA_cluster_non-selection_strain.gtf and .  The fractional counts were converted to transcripts per million and normalized in the same manner as the small-RNA sequencing libraries (Ncastellii_sRNA_cluster_selection_strain.gtf).
Genome_build: ASM23734v1 - N. castellii CBS4309; Additional sequences were added to this genome build as described above and the FASTA files are included.
Supplementary_files_format_and_content: FASTA files of the genome sequences of the N. castellii non-selection and genome-selection strains, as well as the GTF files annotating the small RNA (sRNA) clusters in each genome. A GTF file of the annotated rRNA and tRNA loci that were used to perform the removal of rRNA and tRNA reads as described above. Custom gene expression tables are tab-delimited text files that include fractional read counts for each sRNA cluster for each sample. Custom read counts tables are tab-delimited text files that include 9–26-nt, 10–12-nt or 22–23-nt read counts.

molecule: total RNA

organism: Naumovozyma castellii

source_name: N. castellii CBS4310

growth_protocol: Each N. castellii strain was grown at 30C until mid-log phase (OD 600 nm: ~0.8) in synthetic complete (+ 2% galactose) media.

extract_protocol:
Total RNA was isolated from the cultures using the hot-phenol method.
For small-RNA sequencing, 0.5 nM of four small RNA oligonucleotides (xtr miR-427, 5′-GAAAGUGCUUUCUGUUUUGGGCG;   dme miR-14, 5′-GGGAGCGAGACGGGGACTCACT; Synthetic_siRNA_1_Guide, 5′-UAGUGCAGGUAGGUAUUUUUGUU; Synthetic_siRNA_1_Passenger, 5′-CAAAAAUACCUACCUGCACUAUA) were added to 10 ug of total RNA for use as internal standards.  Small-RNA cDNA libraries were prepared as described (Fang and Bartel, 2015), except 9–26-nt RNAs were isolated and sequenced, using 9-nt and 26-nt RNA radiolabeled standards (5′-AAACCAGUC and 5′ -AGCGUGUACUCCGAAGAGGAUCCAAA) to follow ligations and purifications. For RNA-seq, 0.5 ng of two mRNAs (chloramphenicol and firefly luciferase) were added to 5 ug of total RNA for use as internal standards.  Ribosomal RNA was depleted from the samples using Ribo-Zero Gold rRNA Removal Kit (Yeast) (Illumina, MRZY1324).  RNA cDNA libraries were prepared using NEXTflex rapid directional mRNA-seq kit (Bioo Scientific, NOVA-5138-10).

tag: genotype

value: WT (wild-type)

tag: strain background

value: Selection


title: Bartolomei_ATAC_Blood_BPA_10ug_5month_Female_biorep3

description: UUID:5c634691adb967f7cead37f7,QC_score:3,QC_stats:Fail

extract_protocol:
Sample collection was performed by Marisa Bartolomei lab at University of Pennsylvania. 5 month mice were CO2 euthanized. Liver and blood cells from individual mouse were isolated for subsequent DNA and RNA extractions according to the standard operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.
ATAC-seq and mRNA-seq experiments were performed by Marisa Bartolomei lab at University of Pennsylvania. mRNA and nuclei from 5 month mice liver and blood were isolated for subsequent ATAC-seq and mRNA-seq library preparations according to the operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.

value: Female

value: Blood

value: BPA (Bisphenol A) 10 UG/KGBW/DAY


title: Aylor_ATAC_Liver_Ctrl_5month_Male_biorep1

description: UUID:5d39fbbec310a97a40f3444b,QC_score:10,QC_stats:Pass


title: Bartolomei_ATAC_Blood_BPA_10ug_5month_Female_biorep2

description: UUID:5c634475306a394652749380,QC_score:0,QC_stats:Fail


title: Skeletal Muscle, M-M-06

city: New York

first: Yongchao

last: Ge

state: NY

address: One Gustave L Levy Place #1137

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The RNA-seq fastq files were aligned with STAR v2.5.1b with the human GENCODE annotation.
featureCounts v1.5.0-p1 is used to summarize the reads for all genes and samples.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited file including the counts of reads for all genes and for all samples

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
Skeletal muscle samples were homogenized in a Bead Ruptor Elite bead mill homogenizer cooled by liquid nitrogen to 10°C for 2 x 20 seconds at 4.2 m/s. Muscle homogenates were processed using the Agencourt RNAdvance Tissue Kit on a BioMek FXP Laboratory Automation Workstation
cDNA libraries were constructed from 250 ng of total RNA using the Universal Plus mRNA-Seq kit from NuGEN

tag: disease state

value: control

value: Skeletal Muscle (vastus lateralis muscle)

tag: Sex


title: Skeletal Muscle, M-M-07


title: ago1_mut_non-selection_sRNA

value: ago1 mutant (mut) - ago1-D1247R

value: Non-selection


title: Skeletal Muscle, M-M-11


title: Skeletal Muscle, M-M-05

value: Parkinson's Disease

value: 16-wk high intensity resistance training


title: Bartolomei_ATAC_Blood_BPA_10ug_5month_Female_biorep1

description: UUID:5c634385e905db02f4a4e085,QC_score:6,QC_stats:Pass


title: xrn1_KO_non-selection_sRNA

value: xrn1 knockout (KO)


title: Bartolomei_ATAC_Blood_BPA_10mg_5month_Male_biorep8

description: UUID:5de967dca0134f4f0fd8fec3,QC_score:6,QC_stats:Pass

value: BPA (Bisphenol A) 10 MG/KGBW/DAY


title: Aylor_ATAC_Blood_TCDD_5month_Male_biorep5

description: UUID:5dcdac3183b2bb6e43bc65d1,QC_score:0,QC_stats:Fail

value: 5 month

value: TCDD (2,3,7,8-tetrachlorodibenzo-p-dixoin) 1 microgram per kilogram


title: Aylor_ATAC_Blood_TCDD_5month_Male_biorep6

description: UUID:5dcdac3483b2bb9964bc65db,QC_score:0,QC_stats:Fail

value: Male


title: Bartolomei_ATAC_Blood_BPA_10ug_5month_Female_biorep7

description: UUID:5c63632aadb967c916ad395c,QC_score:6,QC_stats:Pass


title: Aylor_ATAC_Blood_TCDD_5month_Male_biorep4

description: UUID:5dcdac2e83b2bb3c2ebc65c6,QC_score:2,QC_stats:Fail


title: WT_non-selection_RNAseq


title: WT_non-selection_sRNA


title: Skeletal Muscle, M-M-04


title: Aylor_ATAC_Blood_TCDD_5month_Male_biorep3

description: UUID:5dcdac2d83b2bb6b58bc65c4,QC_score:7,QC_stats:Pass


title: Bartolomei_ATAC_Blood_BPA_10mg_5month_Male_biorep7

description: UUID:5c635f695ffef28524536810,QC_score:6,QC_stats:Pass


title: Skeletal Muscle, M-M-03


title: Bartolomei_ATAC_Blood_BPA_10mg_5month_Male_biorep6

description: UUID:5c635e015ffef231895367fd,QC_score:9,QC_stats:Pass


title: WTHF3

city: Suita

first: Hajime

last: Watanabe

address: Yamadaoka 2-1

country: Japan

institute: Osaka University

data_processing:
Processing of raw reads was done by Novogene as part of the service. According to their QC, all samples had quality score Q30 >90%. Delivered data were clean reads of 150 bp in lengh (trimmed of adapters), roughly 30,000,000 paired reads (15,000,000 pairs) per sample.
Mapping, expression profile comparison, all performed using the CLC Genomics Workbench software.
Genome_build: For mapping, we used the 2010 D. magna genome assembly v2.4 (GenBank accession LRGB00000000) together with the 2014 D. magna evg7f9b gene set as reference (http://arthropods.eugenes.org/EvidentialGene/daphnia/daphnia_magna/Genes/earlyaccess/). This gene set contains 29121 gene loci together with 17228 “culled” transcripts which may as well contain some valid loci. Among these genes, some are split-mapped, meaning that they consist of two fragments that mapped to distant positions in the genome assembly. Because these split-mapped genes disturb the visualization of gene distribution on the genome by the CLC Genomics Workbench software, we edited the gene set and treated the split fragments as two different genes. As a result, there are total 47,109 genes in the full set of our analysis. Also, although the original ID of each gene is in the format [Dapma7bEVm][6 digits], we added 7 characters indicating the scaffold/contig the gene is mapped to and 7 characters indicating its split attribute to make new unique IDs as can be seen in the processed data files.
Supplementary_files_format_and_content: D. magna_WT_12 days_HF.xlsx is a microsoft excel spreadsheet containing various information of all 47,109 genes. This sheet includes: 1) expression values (raw count), normalized expression values (RPM,TPM,CPM) of each gene across all 3 samples, 2) annotation (gene name, GO terms), and 3) other data such as gene location, exon length...

organism: Daphnia magna

source_name: Whole body

growth_protocol: 40 daphniid cultured in 2.5 L ADaM medium, fed with 1.5x10^9/mL cells per day. 5 daphniid of 3rd clutch is cultured in 50 ml tube, fed with 5.12x10^7 cells per day and cultured till day 12 with medium change every day. 5 daphniids (eggs are flushed out already) were collected for total RNA isolation.

extract_protocol:
each sample contained 5 daphniids (12 days old). Before storing at -80oC, eggs in the brood chamber were flushed out. Total RNA extraction was performed using Sepasol-RNAI solution (Nacalai Tesque, Kyoto, Japan), followed by phenol-chloroform purification. All 3 total RNA samples were submitted for mRNA sequencing service by Novogene. According to QC report, all samples passed agarose gel electrophoresis test and Agilent 2100 analysis test.
All libraries were constructed following Novogene's protocol (jp.novogene.com). According to their service description, mRNA was first enriched using oligo(dT) beads, fragmented, followed by cDNA synthesis using random hexamers. After terminal repair, A overhang and sequencing adaptor were added. Finally, cDNA library were completed through size selection and PCR enrichment and then sequenced by Illumina sequencer.

value: NIES

value: female

value: post natal day 12, releasing 2nd clutch

value: wild type


title: Skeletal Muscle, M-M-09

value: Female


title: WTHF1


title: Skeletal Muscle, M-M-01


title: Aylor_ATAC_Blood_TCDD_5month_Female_biorep5

description: UUID:5dcdac3772735269078a2314,QC_score:3,QC_stats:Fail

value: Blood


title: Bartolomei_ATAC_Blood_BPA_10mg_5month_Male_biorep4

description: UUID:5c6355cdadb9677e9bad387a,QC_score:-3,QC_stats:Fail


title: Aylor_ATAC_Blood_TCDD_5month_Male_biorep2

description: UUID:5dcdac2c83b2bbe276bc65c2,QC_score:7,QC_stats:Pass


title: Aylor_ATAC_Blood_TCDD_5month_Female_biorep4

description: UUID:5dcdac3283b2bb5645bc65d5,QC_score:2,QC_stats:Fail


title: Bartolomei_ATAC_Blood_BPA_10mg_5month_Male_biorep3

description: UUID:5c634a8dadb9673940ad3818,QC_score:6,QC_stats:Pass


title: NIES male A

data_processing:
Processing of raw reads was done by Novogene as part of the service. According to their QC, all samples had quality score Q30 >90%. Delivered data were clean reads of 150 bp in lengh (trimmed of adapters), roughly 20,000,000 paired reads (10,000,000 pairs) per sample.
Mapping, expression profile comparison, clustering and functional test were all performed using the CLC Genomics Workbench software.
Genome_build: For mapping, we used the 2010 D. magna genome assembly v2.4 (GenBank accession LRGB00000000) together with the 2014 D. magna evg7f9b gene set as reference (http://arthropods.eugenes.org/EvidentialGene/daphnia/daphnia_magna/Genes/earlyaccess/). This gene set contains 29121 gene loci together with 17228 “culled” transcripts which may as well contain some valid loci. Among these genes, some are split-mapped, meaning that they consist of two fragments that mapped to distant positions in the genome assembly. Because these split-mapped genes disturb the visualization of gene distribution on the genome by the CLC Genomics Workbench software, we edited the gene set and treated the split fragments as two different genes. As a result, there are total 47,109 genes in the full set of our analysis. Also, although the original ID of each gene is in the format [Dapma7bEVm][6 digits], we added 7 characters indicating the scaffold/contig the gene is mapped to and 7 characters indicating its split attribute to make new unique IDs as can be seen in the processed data files.
Supplementary_files_format_and_content: Expression_data.xlsx is a microsoft excel spreadsheet containing various information of all 47,109 genes. This sheet includes: 1) expression values (raw count), normalized expression values (reads per million) and transformed expression values (log2 of normalized expression values) of each gene across all 12 samples, 2) pair-wise EDGE-test results (p-value, q-value, foldchange, etc.), 3) annotation (gene name, GO terms), and 4) other data such as gene location, exon length...
Supplementary_files_format_and_content: K-medoids_clustering.xlsx is a microsoft excel spreadsheet containing the result of our k-medoids clustering analysis. The clustering was performed on 1354 differentially expressed genes between wildtype female and wildtype male (p-value < 0.05, absolute fold change > 1.2). Normalized expression values of each genes were first zero-centered by subtracting the mean expression, then all 1354 genes were divided into 24 clusters based on similarity in expression pattern across four groups using k-medoids method. We further combined the clusters into five categories: 'female-biased binary,' 'female-biased non-binary,' 'male-biased binary,' 'male-biased non-binary,' and 'others' ('binary' means expression level in Line A male and Line B male was similar to wildtype male, 'non-binary' means expression level in Line A male and Line B male was between wildtype female and wildtype male, 'others' are clusters which did not show correlation to sexual phenotypes). This file contains 5 sheets, one for each category with the name and zero-centered expression values of each gene.

growth_protocol: To maintain the Daphnia population in asexual cycle, 40 females were kept in 2.5 L ADaM (artificial daphnia medium), fed daily with 8×10^8 Chlorella vulgaris cells and juveniles are removed every one or two days. Culturing room was set at 22–24°C and under 16:8 h light-dark cycle.

extract_protocol:
Each sample contained 40 h embryos pooled from three mothers. Immediately after collecting, all samples were transferred to liquid nitrogen for flash-freezing. Total RNA extraction was performed shortly after using Sepasol-RNAI solution (Nacalai Tesque, Kyoto, Japan), followed by phenol-chloroform purification and DNase treatment to remove genomic DNA contaminant. All 12 total RNA samples were submitted for mRNA sequencing service by Novogene. According to QC report, all samples passed agarose gel electrophoresis test and Agilent 2100 analysis test.
All libraries were constructed following Novogene's protocol (jp.novogene.com). According to their service description, mRNA was first enriched using oligo(dT) beads, fragmented, followed by cDNA synthesis using random hexamers. After terminal repair, A overhang and sequencing adaptor were added. Finally, cDNA library were completed through size selection and PCR enrichment and then sequenced by Illumina sequencer.

treatment_protocol: Female daphniids were obtained from normal culture as D. magna population is all-female in optimal living condition. Male daphniid were obtained from hormone treatment. Briefly, mature females 18 h before oviposition were selected, moved to medium containing 1 μg/L fenoxycarb (a juvenile hormone analog) and cultured for 16 h. Embryos obtained after treatment would become males with 100% efficiency.

value: NIES (wildtype)

tag: sex type

value: 40 hour post oviposition


title: WTHF2


title: Line B male C

value: Line B

value: Slightly feminized male


title: NIES male C


title: Skeletal Muscle, M-M-02

value: control

value: Skeletal Muscle (vastus lateralis muscle)


title: Aylor_ATAC_Blood_TCDD_5month_Female_biorep1

description: UUID:5dcdac2b83b2bba067bc65bf,QC_score:2,QC_stats:Fail


title: Aylor_ATAC_Blood_TCDD_5month_Female_biorep3

description: UUID:5dcdac3083b2bbf15ebc65cf,QC_score:7,QC_stats:Pass


title: Bartolomei_ATAC_Blood_BPA_10mg_5month_Male_biorep1

description: UUID:5bd8d5ca06a95072a7a53c2c,QC_score:9,QC_stats:Pass


title: Bartolomei_ATAC_Blood_BPA_10mg_5month_Male_biorep2

description: UUID:5c6347faadb9678a6ead3801,QC_score:-1,QC_stats:Fail


title: Aylor_ATAC_Blood_TCDD_5month_Female_biorep2

description: UUID:5dcdac2f83b2bb2abfbc65cb,QC_score:5,QC_stats:Pass


title: Bartolomei_ATAC_Blood_BPA_10mg_5month_Female_biorep9

description: UUID:5de967e2a0134fd43ad8fecc,QC_score:9,QC_stats:Pass


title: Aylor_ATAC_Blood_TCDD_5month_Male_biorep1

description: UUID:5dcdac2b83b2bbdb0fbc65be,QC_score:3,QC_stats:Fail


title: Bartolomei_ATAC_Blood_BPA_10mg_5month_Female_biorep8

description: UUID:5de967e1a0134f0288d8fec9,QC_score:5,QC_stats:Pass


title: Aylor_ATAC_Blood_Ctrl_5month_Male_biorep6

description: UUID:5dcdac3483b2bb46e9bc65dc,QC_score:-2,QC_stats:Fail

value: Control Oral Gavage 10 microliter per kilogram


title: Line A male C

value: Line A

value: Severely feminized male


title: NIES male B


title: Line B male A


title: Bartolomei_ATAC_Blood_BPA_10mg_5month_Female_biorep7

description: UUID:5de967e0a0134fe841d8fec8,QC_score:3,QC_stats:Fail

value: 5 month

value: BPA (Bisphenol A) 10 MG/KGBW/DAY


title: Aylor_ATAC_Blood_Ctrl_5month_Male_biorep5

description: UUID:5dcdac3283b2bb5a66bc65d4,QC_score:0,QC_stats:Fail

value: Male


title: M6

type: RNA

city: Barcelona

first: Inmaculada

last: Fuertes

state: Barcelona

address: Calle Jordi Girona, 18-26

department: Department of Environmental Chemistry

country: Spain

institute: CSIC

description: Gene expression

hyb_protocol: according to manufacturer protocols Low input Quick Amp lebelling

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol GE1-v1_91 and Grid:066414_D_F_20140506)to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Daphnia M

growth_protocol: daphnias were cultured and grown according to Barata and Baird, 200

extract_protocol: Total RNA was extracted using Trizol according to Soetaert et al. 2007

treatment_protocol: Experiments follow previous procedures (Jordão et al., 2015; Jordão et al., 2016b) with 1 µg/L of carbamazepine,  0.1 µg/L of diazepan,  0.1 µg/L of propranolol and a 1/3 mixture of them, with ratio proportional to LOEC.

value: 4 days

value: female

value: all body

value: equitoxic mixture of CBZ, DZP and PR (M)


title: M4

description: Gene expression

scan_protocol: according to manufacturer protocols Low input Quick Amp lebelling


title: PR2

description: Gene expression

source_name: Daphnia PR

label_protocol: according to manufacturer protocols Low input Quick Amp lebelling

value: 0.1 µg/L of propranolol


title: Aylor_ATAC_Blood_Ctrl_5month_Male_biorep4

description: UUID:5dcdac3283b2bb4c86bc65d6,QC_score:0,QC_stats:Fail

value: Blood


title: Line B male B

value: 40 hour post oviposition


title: Bartolomei_ATAC_Blood_BPA_10mg_5month_Female_biorep6

description: UUID:5c6360d1adb9677eaaad3943,QC_score:-3,QC_stats:Fail

value: Female


title: PR4

description: Gene expression


title: Bartolomei_ATAC_Blood_BPA_10mg_5month_Female_biorep4

description: UUID:5c635a06adb967b267ad38c2,QC_score:-2,QC_stats:Fail


title: Aylor_ATAC_Blood_Ctrl_5month_Male_biorep3

description: UUID:5dcdac3183b2bbd172bc65d0,QC_score:7,QC_stats:Pass


title: Bartolomei_ATAC_Blood_BPA_10mg_5month_Female_biorep5

description: UUID:5c63601eadb96710cbad3931,QC_score:-2,QC_stats:Fail


title: Aylor_ATAC_Blood_Ctrl_5month_Male_biorep2

description: UUID:5dcdac3183b2bb12bbbc65d2,QC_score:-2,QC_stats:Fail


title: Bartolomei_ATAC_Blood_BPA_10mg_5month_Female_biorep3

description: UUID:5c6359caadb96762f6ad38bc,QC_score:5,QC_stats:Pass


title: Aylor_ATAC_Blood_Ctrl_5month_Male_biorep1

description: UUID:5dcdac2f83b2bb6361bc65cc,QC_score:7,QC_stats:Pass


title: NIES female B

value: NIES (wildtype)


title: Bartolomei_ATAC_Blood_BPA_10mg_5month_Male_biorep5

description: UUID:5c635a7dadb96738e4ad38c8,QC_score:5,QC_stats:Pass


title: Aylor_ATAC_Blood_Ctrl_5month_Female_biorep5

description: UUID:5dcdac38727352366c8a2317,QC_score:0,QC_stats:Fail


title: Bartolomei_ATAC_Blood_BPA_10mg_5month_Female_biorep2

description: UUID:5c635952adb9674b68ad38b4,QC_score:7,QC_stats:Pass


title: DZP4

description: Gene expression

source_name: Daphnia DZP

value: 0.1 µg/L of diazepan


title: NIES female A


title: Aylor_ATAC_Blood_Ctrl_5month_Female_biorep4

description: UUID:5dcdac3383b2bb3f46bc65d9,QC_score:0,QC_stats:Fail


title: DZP1

description: Gene expression


title: Line A male A


title: DZP2

description: Gene expression


title: Aylor_ATAC_Blood_Ctrl_5month_Female_biorep2

description: UUID:5dcdac2e83b2bb935ebc65c9,QC_score:-2,QC_stats:Fail


title: NIES female C


title: Shox2-KO

city: New Orleans

first: YiPing

last: Chen

address: 6400 Freret Street

institute: Tulane University

description: single-cell RNA-seq

data_processing:
cells were loaded for capture onto 10x genomics Chromium single cell 3' library & gel bead kit v2
construct an Illumina sequencing library and sequenced on NextSeq 500 with 150 cycle sequencing
Illumina basecall files (*.bcl) were converted to FASTQs using CellRanger/3.0.1
FASTQ files were then aligned to mm10 mouse reference genome and transcriptome using the CellRanger/3.0.1 software pipeline with default parameters
Genome_build: mm10 with GFP made by customer reference
Supplementary_files_format_and_content: H5 file filtered-gene-barcode-matrix can be deconvoluted to tsv and mtx files

source_name: SAN cells including atrial cells

extract_protocol:
RNA was extracted from SAN (including atrium) single cell suspension using the 10X Genomics Chromium™ Single Cell A Chip Kit V2
Library construction was performed according to 10X v2 kit protocol.

tag: Stage

value: SAN cells including atrial cells


title: C. albicans cells 4-AN treated-rep2

city: Poznan

first: Aleksandra

middle: Maria

last: Swiercz

address: Piotrowo 2

department: Institute of Computing Science

country: Poland

institute: Poznan University of Technology

data_processing:
Raw paired-end reads were filtered according to the quality with the Trimmomatic tool  with parameters SLIDINGWINDOW:6:20 MINLEN:35
The remaining paired-end reads were mapped to the genome of Candida albicans SC531 (assembly ASM18296v3) with STAR using default parameters
The expression of all 6263 genes was calculated with the htseq-count tool. The genes with very low expression across the examined samples were discarded from further analysis. Thus, we obtained  5775 genes having on average at least 2 mapped reads.
The differential expression analysis of the control and 4-AN treated sample was performed with the negative binomial (Gamma-Poisson) distribution implemented in the DESeq2 R package.
Genome_build: Candida albicans SC531 (assembly ASM18296v3)
Supplementary_files_format_and_content: Matrix table tab delimited with raw gene counts for every gene and every sample

organism: Candida albicans

source_name: fungal cells

growth_protocol: Candida albicans (ATCC 10231) was cultured in duplicate in 100 ml flasks at 30°C with vigorous shaking in the presence of 4-AN at the concentration of MIC/4 (1 µg/ml) or 0.1% DMSO (control cells in duplicate). The cultures were terminated by centrifugation when OD600 reached a value of 1. Cells were frozen at -70°C or used immediately.

extract_protocol:
Total RNA was isolated from four cell samples using a YeaStarTM RNA kit (Zymo Research, USA) according to the manufacturer`s protocol.
The quality and integrity of total RNA was assessed with an Agilent 2100 Bioanalyzer using an RNA 6000 Nano Kit (Agilent Technologies, Ltd.). Strand-specific polyA enriched RNA libraries were prepared using the KAPA Stranded mRNA Sample Preparation Kit according to the manufacturer’s protocol (Kapa Biosystems, MA, USA). Briefly, mRNA molecules were enriched with 500ng of total RNA using poly-T oligo-attached magnetic beads (Kapa Biosystems, MA, USA). The mRNA was fragmented and the first-strand cDNA was synthesized using reverse transcriptase. Second cDNA synthesis was performed to generate double-stranded cDNA (dsDNA). Adenosines were added to the 3′ ends of dsDNA and adapters were ligated (adapters from NEB, Ipswich, MA, USA). Following the adapter ligation, uracil in a loop structure of the adapter was digested by USER enzyme from NEB (Ipswich, MA, USA). Adapters containing DNA fragments were amplified by PCR using NEB starters (Ipswich MA, USA). Library evaluation was done with an Agilent 2100 Bioanalyzer using the Agilent DNA High Sensitivity chip (Agilent Technologies, Ltd.) The mean library size was 300bp. The libraries were quantified using a Quantus fluorometer and QuantiFluor double stranded DNA System (Promega, Madison, Wisconsin, USA). The libraries were run in the rapid run flow cell and were paired-end sequenced (2x76bp) on HiSeq 1500 (Illumina, San Diego, CA 92122 USA).

tag: cells

value: Log phase cells


title: C. albicans cells 4-AN treated-rep1

treatment_protocol: Candida albicans (ATCC 10231) was cultured in duplicate in 100 ml flasks at 30°C with vigorous shaking in the presence of 4-AN at the concentration of MIC/4 (1 µg/ml) or 0.1% DMSO (control cells in duplicate). The cultures were terminated by centrifugation when OD600 reached a value of 1. Cells were frozen at -70°C or used immediately.


title: CBZ1

description: Gene expression

source_name: Daphnia CBZ

value: 1 µg/L of carbamazepine


title: WT

description: single-cell RNA-seq


title: C. albicans cells untreated-rep1

value: DMSO


title: C. albicans cells untreated-rep2


title: CT1

description: Gene expression

source_name: Daphnia control

value: control-solvent


title: pMIG-BCR-ABL_minus_2A

status: Public on May 19 2020

city: Ulm

first: Marc

last: Young

state: Baden-Württemberg

address: Albert-Einstein-Allee 11

department: Institute für Immunologie

country: Germany

institute: Universitätsklinikum Ulm

data_processing:
The quality of the raw paired-end reads from the RNA-Seq data set was assessed using the program FastQC (v. 0.11.5).
Adapter clipping, read length quality trimming and length filtering was performed using the program Trimmomatic (v. 0.36) with the following settings: -validatePairs\ ILLUMINACLIP: TruSeq3-PE.fa:2:30:10:8:true \ LEADING:24 \  TRAILING:24 \  SLIDINGWINDOW:4:24 \  MINLEN:100
High quality paired-end reads were mapped to the Ensembl mouse reference genome (GRCm38.dna.chr) using the splice-aware mapper TopHat (v. 2.1.1) with the aligner Bowtie2 (v. 2.3.2). Read mapping was performed in a paired-end aware, strand-specific (--library-type fr-firststrand) manner with an expected (mean) inner distance between mate pairs of 70bp (-r 70).
FeatureCounts(v1.5.3)  was used to to count uniquely mapped read-pairs in a strand-specific manner using the Ensembl mouse gene annotation (GRCm38.89.chr.gtf) to create a raw read count table. The parameters for mapping were set as follows: both reads must align (-B); paired-end reads (-p); check fragment length when assigning fragments to meta-features or features (-P); minimum fragment/template length (-d) set to 100bp; maximum fragment/template length (-D) set to 500000; read counting performed in strand-specific manner (-s2 /reversely stranded).
The raw read count table was loaded into the R statistical computing environment (v.3.6.1) and the edgeR Bioconductor package (v. 3.18.1) was used to generate a DGEList data object. Using the org.Mm.eg.db annotation package only Ensembl gene accessions with corresponding Entrez Gene identifiers were retained in the DGEList. Subsequently genes with low expression (>2 counts per million) in 6 or more samples were filtered out and TMM normalization was applied to adjust for library sizes.  The design matrix was defined as additive linear model with mouse as a blocking factor in order to compare gene expression between empty vector and BCR-ABL1 transduced cells using the glmTreat function (FDR<0.05; fold change > 1.5).
Genome_build: Ensembl Mus musculus GRCm38
Supplementary_files_format_and_content: comma separated text file with raw gene counts for every gene and every sample

source_name: bone marrow-derived cells

growth_protocol: BM cells were isolated from 2 mice and kept in culture with IL7 for 7 days. The medium is composed of Iscove’s medium (Biochrom AG) containing 10% heat-inactivated FCS (Sigma-Aldrich), 2 mM l-glutamine, 100 U/ml penicillin (Gibco), 100 U/ml streptomycin (Gibco), and 50 µM 2-mercaptoethanol. The medium was supplemented in excess with the supernatant of J558L plasmacytoma cells stably transfected with a vector encoding murine IL7. Afterwards, pre-B cells from each mouse were transduced in with either an empty vector (EV) or with BCR-ABL retroviral vectors, generating a total of 12 transduced cell lines which were kept in culture for 48 hours in +IL7 medium. Biological triplicates were prepared in three independent experiments.  Then, IL7 was removed from cells transduced with BCR-ABL1 for 1 week until cells were completely transformed. Pre-B cells transduced with EV were kept in culture with IL7 for similar culturing timepoints as transformed cells, then sorted for GFP. Total RNA of pre-B cells transduced with either EV or with BCR-ABL1 was prepared using ReliaPrep™ RNA Miniprep Kit (Promega).

extract_protocol:
ReliaPrep™ RNA Miniprep Kit (Promega)
Libraries were prepared according to Illumina's instructions using the Illumina TruSeq® stranded total RNA (Gold) kit

treatment_protocol: No treatment was applied before treatment

tag: cell type

value: Pro-/pre B cells

tag: cell line

value: Mouse 2 derived cell line 1

tag: genotype/variation

value: transduced with BCR-ABL


title: Bartolomei_ATAC_Blood_BPA_10mg_5month_Female_biorep1

description: UUID:5c63520e5ffef2e0c8536783,QC_score:-2,QC_stats:Fail

value: 5 month

value: BPA (Bisphenol A) 10 MG/KGBW/DAY


title: pMIG-BCR-ABL_minus_2C

value: Mouse 2 derived cell line 3


title: Aylor_ATAC_Blood_Ctrl_5month_Female_biorep1

description: UUID:5dcdac2b83b2bb25a7bc65bd,QC_score:0,QC_stats:Fail

value: Control Oral Gavage 10 microliter per kilogram


title: pMIG-BCR-ABL_minus_2B

value: Mouse 2 derived cell line 2


title: M5

description: Gene expression

value: 4 days

value: female

value: all body

value: equitoxic mixture of CBZ, DZP and PR (M)


title: Aylor_ATAC_Liver_Ctrl_5month_Female_biorep1

description: UUID:5d39fbbcc310a93279f34445,QC_score:10,QC_stats:Pass

value: Female

value: Liver


title: pMIG_plus_1C

value: Mouse 1 derived cell line 3

value: transduced with empty vector


title: pMIG_plus_1B

value: Mouse 1 derived cell line 2


title: pMIG_plus_2C

value: Pro-/pre B cells


title: pMIG-BCR-ABL_minus_1C


title: CBZ2

description: Gene expression

value: 1 µg/L of carbamazepine


title: pMIG-BCR-ABL_minus_1B

value: transduced with BCR-ABL


title: PR5

description: Gene expression

value: 0.1 µg/L of propranolol


title: Aylor_ATAC_Blood_Ctrl_5month_Female_biorep3

description: UUID:5dcdac3083b2bb0b21bc65cd,QC_score:5,QC_stats:Pass

value: 5 month

value: Blood


title: pMIG_plus_2A

value: Mouse 2 derived cell line 1


title: pMIG-BCR-ABL_minus_1A

value: Mouse 1 derived cell line 1


title: pMIG_plus_2B

value: Mouse 2 derived cell line 2


title: CT2

description: Gene expression

value: 4 days

value: female

value: control-solvent


title: Double-KO

description: single-cell RNA-seq

value: SAN cells including atrial cells


title: pMIG_plus_1A


title: YF00104_36_D14

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

department: Medicine

institute: Northwestern University

description: post-vaccination blood transcriptional profilling

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized toHumanRefSeq8 V2 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol.

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).

data_processing: Analysis of the quantified output data was conducted using various software packages from R and Bioconductor. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

label: Biotin

source_name: Whole blood

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

extract_protocol: Cells were washed twice with cold PBS and lysed with 100 µl of cold RLT buffer (QIAGEN, Germany) supplemented with 1% beta-mercaptoethanol (BM) (Sigma, St. Louis, MO USA), and transferred to 1.7 ml tubes with 250 µl of cold RLT/BM buffer and quickly stored at -80oC. The samples underwent nucleic acid isolation in a designated Pre-PCR room using Qiagen’s RNeasy Micro Kit and underwent DNase I treatment. Total RNA concentrations were quantified using a NanoDrop 2000c spectrophotometer and quality was assessed using BioRad’s Experion automated electrophoresis system. With each batch of samples a 500 ng HeLa RNA control and two water non-template negative controls were included.

tag: donor

tag: baseline nab titer

tag: day84 nab titer

value: F


title: CT3

description: Gene expression

tag: age

value: all body


title: CBZ4

description: Gene expression


title: YF00104_30_D84

tag: gender


title: YF00104_30_D14


title: YF00104_31_D3


title: YF00104_30_D7


title: YF00104_31_D7


title: YF00104_31_D84


title: YF00104_25_D7


title: YF00104_36_D3


title: YF00104_36_D7


title: YF00104_36_D84


title: YF00104_31_D14


title: YF00104_24_D14


title: YF00104_25_D84


title: YF00104_25_D14


title: YF00104_24_D7


title: YF00104_30_D3


title: YF00104_24_D3


title: YF00104_21_D7


title: YF00104_21_D14


title: YF00104_22_D7


title: YF00104_24_D84


title: YF00104_22_D84


title: YF00104_21_D84


title: YF00104_23_D3


title: YF00104_21_D3


title: YF00104_22_D14


title: Line A male B

tag: strain

value: Line A

value: Severely feminized male

value: 40 hour post oviposition


title: YF00104_22_D3


title: YF00104_23_D14


title: YF00104_23_D7


title: YF00104_25_D3


title: YF00104_33_D7


title: YF00104_8_D7


title: YF00104_13_D3


title: YF00104_13_D7


title: YF00104_23_D84


title: YF00104_13_D14


title: YF00104_8_D84


title: YF00104_33_D3


title: YF00104_33_D14


title: YF00104_13_D84


title: YF00104_32_D14

value: M


title: YF00104_29_D14


title: YF00104_8_D3


title: YF00104_32_D7


title: YF00104_29_D7


title: YF00104_32_D84


title: YF00104_8_D14


title: YF00104_29_D84


title: YF00104_32_D3


title: YF00104_17_D3


title: YF00104_33_D84


title: YF00104_17_D7


title: YF00104_29_D3


title: YF00104_17_D14


title: YF00104_17_D84


title: YF00104_19_D14


title: YF00104_19_D84


title: YF00104_19_D7


title: YF00104_15_D3


title: YF00104_16_D84


title: YF00104_16_D7


title: YF00104_16_D3


title: YF00104_15_D7


title: YF00104_16_D14


title: YF00104_15_D84


title: YF00104_9_D3


title: YF00104_5_D14


title: YF00104_27_D7


title: YF00104_5_D7


title: YF00104_20_D84


title: YF00104_9_D84


title: YF00104_5_D84


title: YF00104_15_D14


title: YF00104_27_D3


title: YF00104_27_D14


title: YF00104_27_D84


title: YF00104_9_D7


title: YF00104_20_D7


title: YF00104_6_D3


title: YF00104_9_D14


title: YF00104_20_D14


title: YF00104_20_D3


title: YF00104_6_D14


title: YF00104_5_D3


title: YF00104_12_D14


title: YF00104_6_D84


title: YF00104_12_D3


title: YF00104_28_D84


title: YF00104_6_D7


title: YF00104_12_D84


title: YF00104_12_D7


title: YF00104_28_D7


title: YF00104_35_D84


title: YF00104_28_D14


title: YF00104_19_D3


title: YF00104_35_D3


title: YF00104_18_D84


title: YF00104_18_D3


title: YF00104_18_D7


title: YF00104_3_D3


title: YF00104_3_D7


title: YF00104_34_D84


title: YF00104_18_D14


title: YF00104_11_D84


title: YF00104_35_D7


title: YF00104_3_D14


title: YF00104_11_D14


title: YF00104_3_D84


title: YF00104_11_D7


title: YF00104_34_D14


title: YF00104_34_D3


title: YF00104_34_D7


title: YF00104_26_D84


title: YF00104_28_D3


title: YF00104_14_D84


title: YF00104_14_D14


title: YF00104_26_D3


title: YF00104_11_D3


title: YF00104_26_D14


title: YF00104_35_D14


title: YF00104_10_D3


title: YF00104_4_D14


title: YF00104_4_D7


title: YF00104_26_D7


title: YF00104_10_D84


title: YF00104_2_D84


title: YF00104_1_D7


title: YF00104_4_D84


title: YF00104_2_D3


title: YF00104_4_D3


title: YF00104_14_D3


title: YF00104_2_D7


title: YF00104_14_D7


title: YF00104_10_D7


title: YF00104_1_D84


title: YF00104_2_D14


title: YF00104_7_D3


title: YF00104_7_D7


title: YF00104_7_D14


title: YF00104_10_D14


title: LLC3 [miRNA]

city: Botucatu

first: Geysson Javier

middle: Fernandez

last: Garcia

state: Sao Paulo

address: Departamento morfologia IBB UNESPRubiao Junior

country: Brazil

institute: UNESP

data_processing:
Sequenced reads were performed quality assessment using FastQC.
Adapters were removed using trimomatic in the default options
Single-end reads for miRNA were mapped to miRBase version 21  using Bowtie, with this option -n 0 -l 8 -a --best --strata --phred33-quals
Counts for RefSeq genes were obtained using HTSeq with the default settings
DESeq2 was used to normalize expression counts.
Genome_build: miRBase version 21
Supplementary_files_format_and_content: tab-delimited text files include Counts for miRNA genes for each Sample

source_name: Tibialis anterior skeletal muscle

growth_protocol: LLC cells with up to 10 pasagges were cultured in DMEM medium supplied with 10% of fetal bovine serum and 1% penicillin/streptomycin and maintained in a 5% CO2, 37°C humidified incubator.

extract_protocol:
RNA extraction was performed using TRIZOL reagent (Thermo Scientific, USA), according the manufacturer's instructions. The RNA was quantitated by spectrophotometry using the equipment NanoVue (GE Healthcare Life Sciences, USA). RNA Integrity was ensured by obtaining RNA Integrity Number - RIN > 8 with Agilent 2100 Bioanalyzer (Agilent Technologies, Germany). RNA samples were treated with DNA Free Kit (Thermo Scientific, USA) to remove genomic DNA contamination.
RNA sequencing libraries were constructed with TruSeq Small RNA Sample Preparation kit  (Illumina, USA) using 1000 ng total RNA. Samples were indexed with adaptors and submitted for single-end  50-bp sequencing using an Illumina HiSeq 2000 instrument.

treatment_protocol: Isogenic C57BL/6J mice were randomly assigned to a non-tumor control group (n=4) or LCC-tumor-bearing group (n=5). For tumor development, 7.5 x 10E5 LLC cells in 100 μl PBS were subcutaneously injected in each lower flanks of 10 weeks age C57BL/6J mice. non-tumor control group mice were injected with 100 μl PBS in each flank. After 22 days of cell injection LLC tumor bearing mice exhibited 14.4% of body weight loss and an average tumors weight of 4 grams. Tibialis anterior were collected and total RNA was extracted.

tag: tissue

value: Tibialis anterior skeletal muscle

tag: tumor development

value: 22 days


title: LLC5 [miRNA]


title: LLC6 [miRNA]


title: LLC2 [miRNA]


title: 1_S1_Medulloblastoma_scRNA-seq

city: Philadelphia

first: Zeng-jie

last: Yang

state: Pennsylvania

address: 333  Cottman Avenue

department: Cancer Biology Program

institute: Fox Chase Cancer Center

data_processing:
The Cell Ranger Single Cell Software Suite v.2.0.1 (http://support.10xgenomics.com/) by 10x Genomics was used to perform sample de-multiplexing, barcode processing and single-cell 3′ gene counting. In brief, base call files were fastq format were aligned to the mm10 reference genome that used an aligner called STAR with default settings, and aligned reads were filtered for valid cell barcodes and UMI to generate filtered gene-barcode matrices. The pre-processed 10X and DGE matrices were then imported using the Seurat package for the R programming language (version 3.5.4), and the data were filtered to include genes detected in >5 cells, and cells with 500~6000 detected genes and UMI with 1000~30000 and <15% mitochondrial genes. For single-dataset analyses, Log-normalized expression values were obtained by the NormalizeData function, and variable genes were identified using the FindVariableGenes Seurat function, TPM values were obtained from raw UMI counts by normalizing with total UMI counts per cell.
Genome_build: mm9

source_name: Medulloblastoma cells from Patched 1 deficient mice

extract_protocol:
tumor cells were dissociated enzymatically by papain for 30 mins and then harvested by centrifugation.
Single cells were partitioned into Gel Beads in Emulsion (GEMs) in the Chromium Controller instrument with cell lysis and barcoded reverse transcription of RNA, followed by cDNA amplification, shearing, library construction and indexing by PCR amplification. Subsequently, libraries were sequenced by Illumina 2x150 bp sequencing.

value: Medulloblastoma

value: Patched 1 deficient


title: YF00104_1_D3


title: YF00104_7_D84


title: YF00104_1_D14


title: LLC1 [miRNA]


title: Control 2 [miRNA]

value: 0 days


title: Control 3 [miRNA]


title: Control 1 [miRNA]


title: LLC5

data_processing:
Sequenced reads were performed quality assessment using FastQC.
Adapters were removed using trimomatic in the default options
Paired-end reads for mRNA were mapped to the mm10 genome using TopHat, with this option --mate-inner-dist 200 --mate-std-dev 100 --no-novel-juncs --min-intron-length 40
Counts for RefSeq genes were obtained using HTSeq with the default settings
DESeq2 was used to normalize expression counts.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Counts for RefSeq genes for each Sample

extract_protocol:
RNA extraction was performed using TRIZOL reagent (Thermo Scientific, USA), according the manufacturer's instructions. The RNA was quantitated by spectrophotometry using the equipment NanoVue (GE Healthcare Life Sciences, USA). RNA Integrity was ensured by obtaining RNA Integrity Number - RIN > 8 with Agilent 2100 Bioanalyzer (Agilent Technologies, Germany). RNA samples were treated with DNA Free Kit (Thermo Scientific, USA) to remove genomic DNA contamination.
RNA sequencing libraries were constructed with TruSeq Strandes Total RNA Sample Prep Kits (Illumina, USA) using 1000 ng total RNA. Samples were indexed with adaptors and submitted for paired-end 2 × 100-bp sequencing using an Illumina HiSeq 2000 instrument.

treatment_protocol: Isogenic C57BL/6J mice were randomly assigned to a non-tumor control group (n=4) or LCC-tumor-bearing group (n=6). For tumor development, 7.5 x 10E5 LLC cells in 100 μl PBS were subcutaneously injected in each lower flanks of 10 weeks age C57BL/6J mice. non-tumor control group mice were injected with 100 μl PBS in each flank. After 23 days of cell injection LLC tumor bearing mice exhibited 14.4% of body weight loss and an average tumors weight of 4 grams. Tibialis anterior were collected and total RNA was extracted.

tag: model

value: LLC tumor

value: 23 days


title: LLC6


title: LLC3


title: LLC4


title: LLC1


title: Control 4

value: control


title: LLC2


title: Control 3


title: Control 1


title: Control 2


title: 201870620025_R07C01

type: genomic

city: London

first: Oliver

last: Robinson

state: London

address: St Mary's Campus, Norfolk Place

department: School of Public Health

country: United Kingdom

institute: IMPERIAL COLLEGE LONDON

description: normal blood sample

hyb_protocol: Then, bisulfite-converted DNA was used for hybridization on the Infinium HumanMethylation EPIC BeadChip, following the Illumina Infinium HD Methylation protocol. Briefly, a whole genome amplification step was followed by enzymatic end-point fragmentation and hybridization to HumanMethylation EPIC BeadChips at 48°C for 17 h, followed by single nucleotide extension. The incorporated nucleotides were labelled with biotin (ddCTP and ddGTP) and 2,4-dinitrophenol (DNP) (ddATP and ddTTP).

scan_protocol: the BeadChip was scanned using the Illumina HiScan SQ scanner. The intensities of the images were extracted using in-house software written for the R statistical computing environment. The methylation score for each CpG was represented as a β-value according to the fluorescent intensity ratio representing any value between 0 (unmethylated) and 1 (completely methylated).

data_processing:
DNA methylation (DNAm) data were pre-processed and normalized using in-house software written for the R statistical computing environment, including background and color bias correction, quantile normalization, and Beta MIxture Quantile dilation (BMIQ) procedure to remove type I/type II probes bias, as described elsewhere (Fiorito et al., 2017). DNAm levels were expressed as the ratio of the intensities of methylated cytosines over the total intensities (β values). Cross-reactive and polymorphic probes - with minor allele frequency greater than 0.01 in Europeans (Y. A. Chen et al., 2013) - were excluded. Methylation measures were set to missing if the detection p-value was greater than 0.01. Samples with the bisulfite conversion control fluorescence intensity lower than 10,000 for both type I and type II probes and those with total call rate lower than 95% were excluded. Finally, samples were excluded if the predicted sex (based on chromosome X methylation) did not match that self-reported.
DNAm levels were expressed as the ratio of the intensities of methylated cytosines over the total intensities (β values).

source_name: blood samples

extract_protocol: bisulphite conversion of 500 ng of each DNA sample was performed using the EZ DNA Methylation-Lightning Kit according to the manufacturer’s protocol (Zymo Research, Orange, CA).

tag: person id

tag: disease state

value: normal


title: 201870620135_R08C01

description: normal blood sample

label: biotin (ddCTP and ddGTP) and 2,4-dinitrophenol (DNP) (ddATP and ddTTP)

label_protocol: Illumina Infinium HD Methylation protocol

tag: Sex


title: Control 4 [miRNA]


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description: normal blood sample


title: 201530470053_R05C01

description: normal blood sample


title: 201530470053_R01C01

description: normal blood sample


title: 201530470047_R08C01

description: normal blood sample


title: 201530470047_R07C01

description: normal blood sample


title: 201530470047_R05C01

description: normal blood sample


title: 201530470047_R06C01

description: normal blood sample


title: 201530480008_R05C01

description: normal blood sample


title: 201530470053_R02C01

description: normal blood sample


title: 201530480008_R03C01

description: normal blood sample


title: 201530470047_R03C01

description: normal blood sample


title: 201530470047_R04C01

description: normal blood sample


title: 201530470047_R02C01

description: normal blood sample


title: 201530470047_R01C01

description: normal blood sample


title: 201530470006_R08C01

description: normal blood sample


title: 201530470006_R07C01

description: normal blood sample


title: 201530470006_R03C01

description: normal blood sample


title: 201530470006_R02C01

description: normal blood sample


title: 201530470053_R04C01

description: normal blood sample


title: 201530470006_R05C01

description: normal blood sample


title: 201530470006_R04C01

description: normal blood sample


title: 201516350059_R08C01

description: normal blood sample


title: 201516350059_R07C01

description: normal blood sample


title: 201516350059_R06C01

description: normal blood sample


title: 201530470006_R01C01

description: normal blood sample


title: 201516350059_R05C01

description: normal blood sample


title: 201516350059_R03C01

description: normal blood sample


title: 201516350059_R04C01

description: normal blood sample


title: 201516350055_R08C01

description: normal blood sample


title: 201516350055_R07C01

description: normal blood sample


title: 201516350059_R01C01

description: normal blood sample


title: 201516350059_R02C01

description: normal blood sample


title: 201516350055_R06C01

description: normal blood sample


title: 201516350055_R05C01

description: normal blood sample


title: 201516350055_R03C01

description: normal blood sample


title: 201516350055_R01C01

description: normal blood sample


title: 201516350045_R08C01

description: normal blood sample


title: 201516350055_R04C01

description: normal blood sample


title: 201516350045_R07C01

description: normal blood sample


title: 201516350055_R02C01

description: normal blood sample


title: 201516350045_R05C01

description: normal blood sample


title: 201516350045_R06C01

description: normal blood sample


title: 201516350045_R04C01

description: normal blood sample


title: 201516350045_R02C01

description: normal blood sample


title: 201516350045_R03C01

description: normal blood sample


title: 201516350043_R08C01

description: normal blood sample


title: 201516350045_R01C01

description: normal blood sample


title: 201516350043_R06C01

description: normal blood sample


title: 201516350043_R07C01

description: normal blood sample


title: 201516350043_R05C01

description: normal blood sample


title: 201516350043_R04C01

description: normal blood sample


title: 201516350036_R08C01

description: normal blood sample


title: 201516350043_R02C01

description: normal blood sample


title: 201516350043_R03C01

description: normal blood sample


title: 201516350043_R01C01

description: normal blood sample


title: 201516350036_R07C01

description: normal blood sample


title: 201516350036_R06C01

description: normal blood sample


title: 201516350036_R04C01

description: normal blood sample


title: 201516350036_R03C01

description: normal blood sample


title: 201530470006_R06C01

description: normal blood sample


title: 201516350036_R05C01

description: normal blood sample


title: 201516350036_R02C01

description: normal blood sample


title: 201516350032_R06C01

description: normal blood sample


title: 201516350032_R08C01

description: normal blood sample


title: spleen DX2 TG, biological rep 1

city: Incheon

first: Doyeun

last: Kim

address: 85 Songdogwahak-ro, Yeonsu-gu

country: South Korea

institute: Yonsei University

description: Gene expression data from AIMP2-DX2 overexpressing mouse spleen

hyb_protocol: RNA was hybridized to Affymetrix GeneChip Mouse Gene 2.0 ST Arrays following manufacturers instructions, by the DNAlink, Inc, Korea

scan_protocol: GeneChips were scanned using the Affimetrix GeneChip Scanner 3000 7G following manufacturers instructions, by the DNAlink, Inc, Korea

data_processing: Microarray data were analyzed using Affymetrix GeneChip Comand Console Software (AGCC). Microarray CEL files were imported into AGCC and normalized using RMA.

label: biotin

source_name: spleen

label_protocol: RNA was labeled with biotin using the Affymetrix IVT express kit

growth_protocol: AIMP2 DX2 overepressing or control mice were fed with doxycycline contatining pellet since they were 8 weeks old

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

treatment_protocol: Mice were grown in the SPF facility and doxycycline (6.25 mg/kg) containing pellet were given ad libitum until 1 year old

value: spleen

value: 1 year

tag: genotype

value: CAG-rtTA; TRE DX2/+


title: 201516350032_R04C01

description: normal blood sample


title: spleen DX2 TG; biological rep 3


title: post-vaccination blood sample from donor 2106

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45oC with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: The data were analyzed with preprocessed in R using the RMA normalization method.

source_name: Blood sample from donor 2106

label_protocol: Nugen amplification protocol

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

value: Blood

tag: donor set

tag: vaccination time

value: post-vaccination

tag: visit number

tag: hepatitis b average concentration (unit)

value: mIU/mL

tag: hepatitis b average concentration (pre-vax)

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

value: IU/mL

tag: diphtheria average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (unit)

value: 1/dilution factor

tag: cholera normalized titer (pre-vax)

tag: cholera normalized titer (post-vax)


title: spleen DX2 TG, biological rep 2

tag: tissue

tag: age


title: post-vaccination blood sample from donor 2105

source_name: Blood sample from donor 2105

tag: donor

tag: donor set

tag: gender

value: M


title: 201516350036_R01C01

description: normal blood sample

tag: Sex

tag: person id

tag: disease state


title: 201516350032_R07C01

description: normal blood sample

value: F


title: 201516350032_R05C01

description: normal blood sample


title: post-vaccination blood sample from donor 2109

source_name: Blood sample from donor 2109

tag: vaccination time

tag: visit number

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (pre-vax)

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)


title: post-vaccination blood sample from donor 2107

source_name: Blood sample from donor 2107

tag: diphtheria average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (unit)


title: post-vaccination blood sample from donor 2108

source_name: Blood sample from donor 2108

tag: tissue

tag: donor

tag: donor set

tag: cholera normalized titer (pre-vax)

tag: cholera normalized titer (post-vax)

tag: age


title: 201516350032_R03C01

description: normal blood sample

tag: Sex

tag: person id

tag: disease state


title: 201516350032_R02C01

description: normal blood sample


title: spleen DX2 con, biological rep 2

description: Gene expression data from control littermate mouse spleen

tag: genotype

value: 0; TRE DX2 /+


title: spleen DX2 con, biological rep 1


title: post-vaccination blood sample from donor 2103

source_name: Blood sample from donor 2103

tag: vaccination time

tag: visit number

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (pre-vax)

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: gender


title: spleen DX2 con; biological rep 3

tag: tissue


title: post-vaccination blood sample from donor 2104

source_name: Blood sample from donor 2104

tag: donor

tag: diphtheria average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (unit)


title: post-vaccination blood sample from donor 2098

source_name: Blood sample from donor 2098

tag: donor set

tag: cholera normalized titer (pre-vax)

tag: cholera normalized titer (post-vax)

tag: age


title: post-vaccination blood sample from donor 2100

source_name: Blood sample from donor 2100

tag: vaccination time

tag: visit number

tag: hepatitis b average concentration (unit)


title: post-vaccination blood sample from donor 2101

source_name: Blood sample from donor 2101

tag: hepatitis b average concentration (pre-vax)

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)


title: post-vaccination blood sample from donor 2102

source_name: Blood sample from donor 2102

tag: tissue

tag: donor

tag: gender


title: 201516350032_R01C01

description: normal blood sample

tag: Sex

tag: person id

tag: disease state


title: 201516350031_R07C01

description: normal blood sample


title: 201516350031_R08C01

description: normal blood sample


title: 201516350031_R06C01

description: normal blood sample


title: post-vaccination blood sample from donor 2097

source_name: Blood sample from donor 2097

tag: diphtheria average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (unit)


title: post-vaccination blood sample from donor 2095

source_name: Blood sample from donor 2095

tag: donor set

tag: vaccination time

tag: visit number

tag: cholera normalized titer (pre-vax)

tag: cholera normalized titer (post-vax)

tag: age


title: post-vaccination blood sample from donor 2096

source_name: Blood sample from donor 2096

tag: tissue

tag: donor

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (pre-vax)

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)


title: post-vaccination blood sample from donor 2099

source_name: Blood sample from donor 2099

tag: diphtheria average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: gender


title: 201530480019_R04C01

description: normal blood sample

source_name: blood samples

tag: Sex

tag: person id

tag: disease state


title: 201516350031_R04C01

description: normal blood sample


title: 201516350031_R03C01

description: normal blood sample


title: 201516350031_R05C01

description: normal blood sample


title: 201516350031_R02C01

description: normal blood sample


title: 201516350025_R06C01

description: normal blood sample


title: 201516350031_R01C01

description: normal blood sample


title: 201516350025_R05C01

description: normal blood sample


title: 201516350025_R04C01

description: normal blood sample


title: 201516350025_R02C01

description: normal blood sample


title: 201516350025_R01C01

description: normal blood sample


title: post-vaccination blood sample from donor 2094

source_name: Blood sample from donor 2094

tag: donor set

tag: vaccination time

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (unit)


title: post-vaccination blood sample from donor 2093

source_name: Blood sample from donor 2093

tag: tissue

tag: donor

tag: visit number

tag: cholera normalized titer (pre-vax)

tag: cholera normalized titer (post-vax)

tag: age


title: post-vaccination blood sample from donor 2091

source_name: Blood sample from donor 2091

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (pre-vax)

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)


title: post-vaccination blood sample from donor 2086

source_name: Blood sample from donor 2086

tag: donor set

tag: vaccination time

tag: gender


title: post-vaccination blood sample from donor 2088

source_name: Blood sample from donor 2088

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)


title: post-vaccination blood sample from donor 2092

source_name: Blood sample from donor 2092

tag: tissue

tag: donor

tag: cholera normalized titer (unit)


title: post-vaccination blood sample from donor 2087

source_name: Blood sample from donor 2087

tag: visit number

tag: cholera normalized titer (pre-vax)

tag: cholera normalized titer (post-vax)


title: post-vaccination blood sample from donor 2084

source_name: Blood sample from donor 2084

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (pre-vax)

tag: age


title: post-vaccination blood sample from donor 2089

source_name: Blood sample from donor 2089

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)


title: post-vaccination blood sample from donor 2082

source_name: Blood sample from donor 2082

tag: donor set

tag: vaccination time

tag: diphtheria average concentration (post-vax)


title: post-vaccination blood sample from donor 2090

source_name: Blood sample from donor 2090

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: gender


title: post-vaccination blood sample from donor 2085

source_name: Blood sample from donor 2085

tag: tissue

tag: donor

tag: tetanus average concentration (post-vax)


title: 201516350018_R05C01

description: normal blood sample

tag: Sex

tag: person id

tag: disease state


title: 201516350018_R04C01

description: normal blood sample


title: 201516350018_R07C01

description: normal blood sample


title: 201516350025_R03C01

description: normal blood sample


title: 201516350018_R02C01

description: normal blood sample


title: 201516350018_R08C01

description: normal blood sample


title: 201516350018_R01C01

description: normal blood sample


title: 201516350013_R08C01

description: normal blood sample


title: 201516350018_R06C01

description: normal blood sample


title: post-vaccination blood sample from donor 2078

source_name: Blood sample from donor 2078

tag: visit number

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (pre-vax)

tag: cholera normalized titer (unit)

tag: cholera normalized titer (pre-vax)

tag: cholera normalized titer (post-vax)


title: 201516350013_R06C01

description: normal blood sample

tag: age


title: 201516350013_R07C01

description: normal blood sample


title: 201516350013_R04C01

description: normal blood sample


title: 201516350013_R03C01

description: normal blood sample


title: post-vaccination blood sample from donor 2080

source_name: Blood sample from donor 2080

tag: donor set

tag: vaccination time

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)


title: post-vaccination blood sample from donor 2079

source_name: Blood sample from donor 2079

tag: tissue

tag: donor

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: gender


title: 201516350013_R05C01

description: normal blood sample

tag: Sex

tag: person id

tag: disease state


title: post-vaccination blood sample from donor 2073

source_name: Blood sample from donor 2073

tag: visit number

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (pre-vax)

tag: cholera normalized titer (unit)

tag: cholera normalized titer (pre-vax)

tag: cholera normalized titer (post-vax)


title: 201516350011_R08C01

description: normal blood sample

source_name: blood samples

tag: age


title: 201516350018_R03C01

description: normal blood sample


title: 201516350013_R02C01

description: normal blood sample


title: post-vaccination blood sample from donor 2068

source_name: Blood sample from donor 2068

tag: donor set

tag: vaccination time

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)


title: post-vaccination blood sample from donor 2069

source_name: Blood sample from donor 2069

tag: tissue

tag: donor

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: gender


title: 201516350013_R01C01

description: normal blood sample

tag: Sex

tag: person id

tag: disease state


title: post-vaccination blood sample from donor 2067

source_name: Blood sample from donor 2067

tag: visit number

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (pre-vax)

tag: cholera normalized titer (unit)

tag: cholera normalized titer (pre-vax)

tag: cholera normalized titer (post-vax)


title: post-vaccination blood sample from donor 2076

source_name: Blood sample from donor 2076

tag: donor set

tag: vaccination time

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)

tag: age


title: post-vaccination blood sample from donor 2066

source_name: Blood sample from donor 2066

tag: tissue

tag: donor

tag: diphtheria average concentration (post-vax)

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)


title: post-vaccination blood sample from donor 2077

source_name: Blood sample from donor 2077

tag: visit number

tag: hepatitis b average concentration (unit)

tag: gender


title: 201516350011_R07C01

description: normal blood sample

tag: Sex

tag: person id

tag: disease state


title: post-vaccination blood sample from donor 2071

source_name: Blood sample from donor 2071

tag: donor set

tag: vaccination time

tag: hepatitis b average concentration (pre-vax)

tag: cholera normalized titer (unit)

tag: cholera normalized titer (pre-vax)

tag: cholera normalized titer (post-vax)


title: 201516350011_R06C01

description: normal blood sample

tag: age


title: post-vaccination blood sample from donor 2074

source_name: Blood sample from donor 2074

tag: tissue

tag: donor

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)


title: 201516350011_R04C01

description: normal blood sample


title: 201516350011_R05C01

description: normal blood sample


title: post-vaccination blood sample from donor 2064

source_name: Blood sample from donor 2064

tag: visit number

tag: hepatitis b average concentration (unit)

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: gender


title: post-vaccination blood sample from donor 2075

source_name: Blood sample from donor 2075

tag: donor set

tag: vaccination time

tag: hepatitis b average concentration (pre-vax)


title: post-vaccination blood sample from donor 2072

source_name: Blood sample from donor 2072

tag: cholera normalized titer (unit)

tag: cholera normalized titer (pre-vax)

tag: cholera normalized titer (post-vax)


title: 201516350011_R03C01

description: normal blood sample

tag: age

tag: Sex

tag: person id

tag: disease state