title: T8.D32.Liv2 [ATAC-seq]

data_processing:
The Encode ATAC-seq Pipeline v1.3.0 was used for read trimming, alignment, and peak identification. The parameters used were multimapping : 4, auto_detect_adapter : true, smooth_win :73, and idr_thresh : 0.05.
Supplementary_files_format_and_content: bigWig files were generated by the Encode ATAC-seq Pipeline v1.3.0 and and show fold enrichment of signal over expected background.
Supplementary_files_format_and_content: optimal_peak.narrowPeak files were generated by the Encode ATAC-seq Pipeline v1.3.0 and contain the set of reproducible peaks with and IDR value below 0.05 for the indicated tissue

extract_protocol:
To identify CD8+ T cells in the vasculature of non-lymphoid tissues (small intestine, kidney, salivary gland, fat, and liver), 3 µg of CD8α (53-6.7) conjugated to APC eFluor780 was injected by i.v. into mice three minutes prior to sacrifice, as has been previously described. Cells labeled with low to no CD8α antibody were considered to be outside of the vasculature. Single-cell suspensions of splenocytes were prepared by mechanical disaggregation followed by treatment with ACK lysis buffer. Blood samples were treated with ACK lysis buffer. Small intestine intraepithelial lymphocytes were prepared through the removal of Peyer’s patches and the luminal contents. The small intestine was then cut longitudinally and into 1 cm pieces, then incubated at 37°C for 30 min in HBSS with 2.1 mg/mL sodium bicarbonate, 2.4 mg/mL HEPES, 8% bovine growth serum, and 0.154 mg/mL of dithioetheritol (EMD Millipore). The kidneys, salivary glands, fat, and liver were minced into small pieces and then incubated in RPMI with 1.2 mg/mL HEPES, 292 µ/mL L-glutamine, 1 mM MgCl2, 1 mM CaCl2, 5% fetal bovine serum, and 100 U/mL collagenase (Worthington) at 37°C for 30 min. Lymphocytes from the small intestine, kidney, salivary gland, and liver were separated on a 44%/67% Percoll density gradient. For each replicate, cells from 10-15 mice were pooled and then sorted for bulk RNA-seq. 32 days after initial infection with LCMV, 5e3 P14 cells were sorted from the spleen and blood and 5e3 IV- P14 cells were sorted from the IEL, kidney, salivary gland, fat, and liver into PBS + 5% BSA. To further improve sample purity, 1e3 cells from each sample were resorted into 1x TCL lysis buffer + 1% 2-mercaptoethanol.
For each replicate, cells from 10-15 mice were pooled and then 2e4 cells were sorted into PBS + 5% BSA and spun down at 500 x g for 20 min at 4°C. The cell pellet was then resuspended in 25 µL lysis buffer and then spun down at 600 x g for 30 min at 4°C. The nuclei pellet was resuspended in 25 µL transposition reaction mixture containing Tn5 transposase from Nextera DNA Sample Perp Kit (Illumina) and incubated at 37°C for 30 min. The transposase-associated DNA was then purified using the Zymo DNA clean-up kit. To amplify the library, the DNA was first amplified for 5 cycles using indexing primers from the Nextera kit and NEBNext High-Fidelity 2X PCR master mix. To reduce the PCR amplification bias, after the first 5 cycles, 5 uL of amplified DNA was used to do qPCR to determine the number of cycles for the second round of PCR. The total amplified DNA was then size selected to fragments less than 800 bp using gel purification. The size of the pooled library was examined by tapestation.

value: CD8+ T cells


title: T8.D32.SG2 [scRNA-seq]

status: Public on Apr 18 2022

type: SRA

city: La Jolla

first: John

middle: Tyler

last: Crowl

state: California

address: 5107 Natural Sciences Building 0377, 9500 Gilman Drive

department: Molecular Biology

country: USA

institute: University of California - San Diego

library_source: transcriptomic

data_processing:
Cellranger count v4.0.0 was used to align reads to the mm10 genome.
The resulting counts matrices was processed using Seuratv3.1.1. Cells with < 500 or > 2500 detected genes or a mitochondrial read % greater than 10 were discarded. All samples were combined using the merge function, and data was then normalized (normalization.method = "LogNormalize", scale.factor = 10000). The top 2000 features were identified (selection.method = "vst") and the data was scaled. Dimensional reductions were calculated for PCA (npcs = 30) and UMAP (reduction = “pca”, dims = 1:20). Nearest neighbors were calculated (reduction = “pca”, dims = 1:20) and clusters were identified (resolution = 0.35)
Genome_build: mm10
Supplementary_files_format_and_content: seurat_object.rds contains the resulting Seurat object, including the counts matrix, dimensional reductions, and clustering, as described above.

molecule: polyA RNA

organism: Mus musculus

source_name: CD8+ T cells

extract_protocol:
To identify CD8+ T cells in the vasculature of non-lymphoid tissues (small intestine, kidney, salivary gland, fat, and liver), 3 µg of CD8α (53-6.7) conjugated to APC eFluor780 was injected by i.v. into mice three minutes prior to sacrifice, as has been previously described. Cells labeled with low to no CD8α antibody were considered to be outside of the vasculature. Single-cell suspensions of splenocytes were prepared by mechanical disaggregation followed by treatment with ACK lysis buffer. Blood samples were treated with ACK lysis buffer. Small intestine intraepithelial lymphocytes were prepared through the removal of Peyer’s patches and the luminal contents. The small intestine was then cut longitudinally and into 1 cm pieces, then incubated at 37°C for 30 min in HBSS with 2.1 mg/mL sodium bicarbonate, 2.4 mg/mL HEPES, 8% bovine growth serum, and 0.154 mg/mL of dithioetheritol (EMD Millipore). The kidneys, salivary glands, fat, and liver were minced into small pieces and then incubated in RPMI with 1.2 mg/mL HEPES, 292 µ/mL L-glutamine, 1 mM MgCl2, 1 mM CaCl2, 5% fetal bovine serum, and 100 U/mL collagenase (Worthington) at 37°C for 30 min. Lymphocytes from the small intestine, kidney, salivary gland, and liver were separated on a 44%/67% Percoll density gradient. For each replicate, cells from 10-15 mice were pooled and then sorted for bulk RNA-seq. 32 days after initial infection with LCMV, 1e4 P14 cells were sorted from the spleen and blood and 1e4 IV- P14 cells were sorted from the IEL, kidney, salivary gland, fat, and liver into T cell media. Cells were then spun down and media removed prior to starting library preparation.
Libraries were prepared using the Chromium Single Cell 3' kit with v3 chemistry according to manufacturer's instructions.

tag: tissue

value: Salivary Gland

tag: iv label

value: IV-

tag: days post infection with lcmv-arm


title: SP548

city: Beijing

first: Yiming

last: Zhang

address: No.9 Dongdan Santiao

country: China

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
Clean read data with adapters removed and low-quality reads filtered out were aligned to the hg19 reference sequence by Tophat2.
Gene annotation and quantification were performed by featureCounts (version 2.0.1)
Batch effect was romved by Combat-seq function in sva packages on R platform.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files were generated by featureCounts.

molecule: total RNA

organism: Homo sapiens

source_name: White blood cell

extract_protocol:
Whole blood was centrifuged at 2,000 rpm for 5 ~ 10 min at 25℃.  The lower blood cells were mixed with 10ml Red Blood Cell Lysis Buffer (R1010, Solarbio) for 5min on ice, and the mixture was centrifuged at 2,000~3,000 rpm for 5min at 4℃. Then adding 5ml Red Blood Cell Lysis Buffer to the precipitate and centrifuging it at 2,000 ~ 3,000rpm for 5min at 4℃, and discarding the supernatant. Finally, 1.5ml RNA later (76544, Qiagen) was added to the total RNA precipitate for RNA library preparation.
NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)

tag: disease state

value: Severe Community Acquired Pneumonia (SCAP)

tag: batch

tag: cell type

value: White blood cell


title: 20210106_HJZ086_RNA_3AA3_shDDIT3_techrep2_S8_R1_001

city: Boston

first: Cigall

last: Kadoch

state: MA

address: 44 Binney St

institute: Dana-Farber Cancer Institute

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
RNAseq reads were aligned to the hg19 genome with STAR v2.5.2b, which output gene count tables to the hg19 refFlat annotation, and ChIPseq reads were aligned with Bowtie2 v2.29 in the -k 1 reporting mode.
For the ATACseq data, quality read trimming was performed by Trimmmomatic v0.36, followed by alignment, duplicate read removal, and read quality filtering, using Bowtie2 v2.29, Picard v2.8.0, and SAMtools v0.1.19, respectively.
For the ChIPseq and ATACseq data, output BAM files were converted into BigWig track files using MACS2 and UCSC utilities in order to display coverage throughout the genome (in RPM).
For Cut & Run libraries, the CutRunTools pipeline was used to perform read trimming, quality filtering, alignment, peak calling, and track building using default parameters
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files give the normalized coverage of DNA fragments across the genome in reads per million and gene count tables give raw read counts mapped to exons of given genes. Spike-in normalization of bigWig files can be incoporated by scaling the bigWig files by the ratio of fly to human reads in the control sample divided by the ratio of fly to human reads in each sample, i.e. (fly / human)_control / (fly / human)_sample. The total number of mapped fly and human reads can be estimated by aligning the fastq files to the hg19 and dm3 genome and then summing the third column (mapped reads) from the samtools idxstats output.

source_name: cancer cell line

growth_protocol: MLPS-1765-92 and MLPS-402-91 cells were cultured in RPMI medium (Gibco) supplemented with 10% fetal bovine serum, 1% Glutamax (Gibco), 1% Sodium Pyruvate (Gibco), and 1% Penicillin-Streptomycin (Gibco). MLPS-DL221 cells were cultured in DMEM medium (Gibco) supplemented with 10% fetal bovine serum, 1% Glutamax (Gibco), 1% Sodium Pyruvate (Gibco), and 1% Penicillin-Streptomycin (Gibco). hTERT-MSC and AD-MSC lines were cultured in Mesenchymal Stem Cell Basal Medium (ATCC No. PCS-500-030) supplemented with the Mesenchymal Stem Cell Growth Kit for Adipose and Umbilical-derived MSCs - Low Serum (ATCC No. PCS-500-040) and 0.1% Penicillin-Streptomycin (Gibco). HEK293T LentiX cells were cultured in DMEM medium (Gibco) supplemented with 10% fetal bovine serum, 1% Glutamax (Gibco), 1% Sodium Pyruvate (Gibco), 1% HEPES (Gibco), 1% MEM NEAA (Gibco), and 1% Penicillin-Streptomycin (Gibco). All cells were maintained in a humidified incubator at 37°C with 5% CO2.     Deidentified myxoid liposarcoma (n=10 for RNA-seq), Ewing sarcoma (n=10 for RNA-seq), cases were identified, with pathology and diagnosis confirmed by two independent pathologists at MD Anderson Cancer Center (MDACC).

extract_protocol:
ChIP-seq protocol Cells were harvested following 72-hr exposure to specified lentivirus and 4 day selection with 2 μg/ml of puromycin. ChIP experiments were performed per standard protocols (Millipore, Billerica, MA) with minor modifications. Briefly, cells were cross-linked for 10 min with 1% formaldehyde at 37 °C. This reaction was subsequently quenched with 125 mM glycine for 5 min and 10 million fixed cells were used per ChIP experiment. Chromatin from fixed cells was fragmented by sonication with a Covaris E220 and the solubilized chromatin was incubated with the indicated antibody listed overnight at 4°C. Antibody-chromatin complexes were pulled down by incubation with Protein G-Dynabeads (Thermo Scientific) for 2 hours at 4°C, washed, and eluted. The samples then underwent crosslink reversal, RNase A (Roche) treatment, and proteinase K (Thermo Scientific) treatment before the captured DNA was extracted with AMPure XP beads (Beckman Coulter). ChIP-seq libraries were prepared with Illumina’s NEBNext Ultra II DNA library Prep Kit using standard protocols. ChIP-seq was sequenced on Illumina Next-seq 500 using 75 bp single-end sequencing parameters.
ATAC-seq protocol Cells were harvested following 72-hr exposure to lentivirus and 4 days of selection with 2 μg/ml of puromycin. ATAC-seq experiments were performed as previously described. Samples for ATAC-seq prepared using the Nextera DNA sample Prep Kit (Illumina). Briefly, 50K cells were incubated in hypotonic buffer and lysis buffer, then were resuspended in transposase reaction mixture for 30 min at 37°C with gentle shaking followed by DNA purification and 12 cycles of amplification. ATAC-seq samples were sequenced on Next-seq 500 (Illumina) using 37 bp pair-end sequencing parameters.
RNA-seq protocol Cells were harvested following 72-hr exposure to the specified lentivirus and either 4 day (day 7 post-transduction) or 11 day (day 14 post-transduction) selection with 2 μg/ml of puromycin for RNA-seq experiments. All RNA was collected using the RNeasy Mini Kit (Qiagen). RNA-seq libraries were prepared using the Nebnext Poly(A) mRNA Magnetic Isolation Module and the Nebnext Ultra II Directional RNA Library Prep Kit for Illumina using standard protocols. RNA was sequenced on Illumina Next-seq 500 (Illumina) using 75 bp single-end sequencing parameters.    Snap-frozen tumor tissue samples were obtained from the MD Anderson Institutional Tissue Bank (ITB) using an IRB-approved protocol. Frozen samples were embedded in O.C.T. (Tissue-Tek), sectioned in a Cryostat (Leica CM1680 UV) and underwent hematoxylin and eosin staining for pathologist review to confirm the presence of viable tumor tissue. Tissues were then excised from O.C.T. using scalpel and forceps and 30 mg samples were placed in RNAlater-ICE (Invitrogen) pre-chilled to -80°C. Samples were thawed overnight at -20°C, then disrupted using a TissueLyser LT (Qiagen) for 5 minutes at 50 Hz. RNA was isolated using the RNeasy Mini Kit (Qiagen), following the manufacturer protocol with on-column DNase I (Qiagen) digestion.
Cut & Run protocol Cells were harvested following 24-hr exposure to DMSO or 10uM of CMP12 (generous gift of Jun Qi) followed by 24-hr exposure to DMSO plus base media or StemPro Adipogenesis media (ThermoFisher) or 10uM CMP12 plus base media or StemPro Adipogenesis media. CUT&RUN experiments were performed according to established protocols with minor modifications. Briefly, 500K cells per sample were incubated with Concanavalin A-coated beads (Polysciences) for 10 min and then permeabilized with Triton X-100. Cell-bead complexes were then incubated with the indicated antibody for 2 hr at 4°C. Cell-bead complexes were washed and then incubated with pA-MNase for 1 hr at 4°C. Cell-bead complexes were washed and then cooled to ~0°C. pA-MNase was activated by the addition of calcium chloride and incubated for 30 min at ~0°C. The cleavage reaction was quenched with a solution containing spike-in DNA and RNAase A. Cleaved DNA fragments released into solution were then collected and treated with sodium dodecyl sulfate (SDS) and proteinase K (Thermo Scientific). DNA was then isolated using phenol-chloroform. CUT&RUN libraries were prepared with Illumina’s NEBNext Ultra II DNA library Prep Kit with modifications that aim to preserve short fragments.
ChIP-seq libraries were prepared with Illumina’s NEBNext Ultra II DNA library Prep Kit using standard protocols. ChIP-seq was sequenced on Illumina Next-seq 500 using 75 bp single-end sequencing parameters.    CUT&RUN libraries were prepared with Illumina’s NEBNext Ultra II DNA library Prep Kit with modifications that aim to preserve short fragments.    ATAC-seq samples were sequenced on Next-seq 500 (Illumina) using 37 bp pair-end sequencing parameters.    RNA-seq libraries were prepared using the Nebnext Poly(A) mRNA Magnetic Isolation Module and the Nebnext Ultra II Directional RNA Library Prep Kit for Illumina using standard protocols. RNA was sequenced on Illumina Next-seq 500 (Illumina) using 75 bp single-end sequencing parameters.

treatment_protocol: Constitutive expression of short-hairpin RNA (shRNA) constructs targeting either the C-terminal end of the FUS-DDIT3 fusion (shDDIT3: 5’-CGGCTCAAGCAGGAAATCG-3’), SMARCA4/BRG1 (shBRG1: 5’-AGCCTCAACGACCTAGAGA-3’), or a scrambled, non-silencing sequence (shSCR: 5’-TCTCGCTTGGGCGAGAGTAAG-3’) was achieved using lentiviral infection of the GIPZ vector selected with puromycin (2 μg/ml).    Lentivirus was produced by PEI (Polysciences) transfection of HEK293T LentiX cells (Clontech) with gene delivery vector co-transfected with packaging vectors pspax2 and pMD2.G. Viral supernatants were harvested 72 hr post-transfection and concentrated by ultracentrifugation at 20,000 rpm for 2.5 hr at 4°C. Virus containing pellets were resuspended in PBS and added dropwise to cells in the presence of 10 μg/mL polybrene. Selection of lentivirally-infected cells was achieved with puromycin used at 2 μg/ml. Knockdown efficiency and overexpression was measured by western blot analysis.    The SMARCB1 locus was targeted by the Ini1 (h) CRISPR/Cas9 KO Plasmid (Santa Cruz Biotechnology sc-423027) in MLPS-1765-92 cells following the manufacturer’s protocol with the Lipofectamine 3000 transfection reagent (Invitrogen). Cells were expanded for 72-96 hours and GFP+ cells expressing the KO plasmids were single-cell sorted using FACS (fluorescence-activated cell sorting). Single-cell clones were expanded and screened using immunoblot detection for identification of successful knockouts.

tag: cell line

tag: experimental condition

tag: chip antibody


title: 0210322_HJZ087_RNA_hTERT_MSC_DMSO_base_techrep1_S1_R1_001

source_name: stem cell line

value: MSCs-hTERT

tag: treatment

value: DMSO


title: SP569


title: 20210106_HJZ085_RNA_3AA3_shDDIT3_techrep1_S7_R1_001


title: EPS-shCtrl-F4H-D6-RNA-seq-rep1

city: guangzhou

first: xiaotao

last: dong

address: 190 Kai Yuan Avenue, Science Park

institute: Guangzhou Institutes of Biomedicine and Health Chinese Academy of Sciences

data_processing:
Illumina Casava software used for basecalling.
Reads were aligned to the mm10 genome using bowtie2 version 2.3.2.
Read coverage normalized by RPKM
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: bigwig; counts

source_name: EPS cells

growth_protocol: Mouse extended pluripotent stem cells were maintained in serum-free LCDM medium in 5% CO2 conditions on mitomycin C-inactivated MEF feeder cells or Matrigel-coated plates. Mouse embryonic stem cells were maintained in serum-free 2i medium in 5% CO2 conditions on mitomycin C-inactivated MEF feeder cells or Matrigel-coated plates.

extract_protocol:
For RNA-seq, Total RNAs were extracted with TRIzol. For quantitative PCR, cDNAs were synthesized with ReverTra Ace (Toyobo) and oligo dT (Takara), and then analyzed by qPCR with SYBR green mixture (Genstar) and performed on a CFX Real-Time System (Bio-Rad). For 10 × Genomics single cell RNaseq, the cells cultured in F4H medium for 6 days were dissociated with 0.25% TrypLE Express Enzyme at 37°C for 10 min. Single cell populations were resuspended in PBS with 0.04% BSA. Single cell libraries were created using Chromium Single Cell 30 Reagent Kits and sequenced on a Novaseq 6000 sequencer. Approximately 10000 cells were captured for each time point.CUT&Tag experiments were performed as previously described65. In brief, 100,000 cells were harvested washed twice with 200 µL Wash Buffer. 10 µL Concanavalin A beads (Bangs Laboratories) were added per sample and incubated at room time for 15 min. Add 100 µL Dig-wash Buffer containing 2 mM EDTA and 1µg primary antibody. Primary antibody incubation was performed on a rotating platform overnight at 4 °C. Add 200 µL Dig-Wash buffer to remove unbound antibodies. Then incubated with pAG-Tn5 (home-made) at 4 °C for 2 h. Add 200 µL Dig-med Buffer to remove unbound pAG-Tn5 protein. Next, cells were resuspended in 100 µL tagmentation buffer and incubated at 37 °C for 1 h. To stop tagmentation, 2.25 µL of 0.5 M EDTA, 2.75 µL of 10% SDS and 0.5 µL of 20 mg/mL Proteinase K was added to 50 µL of sample, which was incubated at 55 °C for 30 min, and then at 70 °C for 30 min to inactivate Proteinase K. Then extract the DNA. Antibodies included: H3K27ac (Active Motif, 39133).
RNA sequencing libraries were constructed using the VAHTS mRNA-seq V3 Library Prep Kit for Illumina (Vazyme).

tag: strain

value: EPS cells

tag: genotype/variation

value: control


title: 20210106_HJZ084_RNA_3AA3_shSCR_techrep2_S6_R1_001


title: SP537


title: SP536


title: 20210106_HJZ083_RNA_3AA3_shSCR_techrep1_S5_R1_001


title: SP535


title: EPS-shCtrl-F4H-D6-RNA-seq-rep2


title: EPS-shYy1-F4H-D6-RNA-seq-rep1


title: T8.D32.Fat1 [ATAC-seq]

library_source: genomic

molecule: genomic DNA

value: Gonadal Adipose Tissue


title: SP527


title: T8.D32.Liv1 [ATAC-seq]

value: Liver


title: SP423


title: T8.D32.SG1 [ATAC-seq]


title: T8.D32.Kid2 [ATAC-seq]

value: Kidney


title: T8.D32.SG2 [ATAC-seq]


title: ES-histone-ChIPseq-input

source_name: ES-histone-ChIPseq-input

extract_protocol:
For RNA-seq, Total RNAs were extracted with TRIzol. For quantitative PCR, cDNAs were synthesized with ReverTra Ace (Toyobo) and oligo dT (Takara), and then analyzed by qPCR with SYBR green mixture (Genstar) and performed on a CFX Real-Time System (Bio-Rad). For ATAC-seq, a total of 50,000 cells were washed once with cold PBS and resuspended in 50 μl lysis buffer. The suspension of nuclei was then centrifuged for 10 min at 500 g at 4°C, followed by the addition of 50 μl transposition reaction mix (10 μl TD buffer, 5 μl Tn5 transposase and 35 μl nuclease-free H2O). DNA was purified using a MinElute Kit (QIAGEN). The BL-Hi-C libraries were performed as previous described. Briefly, the cells were treated with 1% formaldehyde for 10 min at RT and the crosslink was quenched by adding 2.5 M glycine. Then, the cells were treated with 0.1% SDS FA lysis buffer and then with 1% SDS FA lysis buffer. After that, the genome was digested with restriction enzyme HaeIII into fragments with blunt-ends, which were treated with adenine and ligated with bridge linker containing biotin at 16°C for 4 hr. The unligated DNA fragments were digested with DNA exonuclease. Next, the cells were treated with SDS and proteinase K to digest proteins, and the DNA was purified using phenol-chloroform extraction with ethanol precipitation. Then, the DNA was fragmented into 300 bp on average by sonication and the biotin-labeled DNA fragments were pulled down with streptavidin coated M280 beads. ChIP experiments were performed as previously described. Briefly, 1 × 107 cells were crosslinked with 1% formaldehyde at room temperature for 10 min. Then the reaction was stopped by adding glycine (final concentration, 0.125 M). Crosslinked cells were lysed in ChIP SDS lysis buffer（1% SDS, 10mM EDTA, 50mM Tris-HCl (pH 8.0)) containing 1 ×  protease inhibitor cocktail and PMSF, then sonicated to achieve a chromatin sized of 200-400 bp. After sonication, the supernatant was diluted with IP buffer and then co-incubated with antibodies–dynabeads protein A/G (1:1 mixed) at 4°C overnight with rotation. Immune complexes were washed with the following buffers: low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.0), 150 mM NaCl), high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.0), 500 mM NaCl), LiCl wash buffer (0.25 M LiCl, 1% IGEPAL-CA630, 1% deoxycholic acid (sodium salt), 1 mM EDTA, 10 mM Tris-HCl (pH 8.0)) and TE buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA). Antibody-bound chromatin was reverse-crosslinked, and the ChIPed DNA samples were purified for ChIP-Seq library generation. For WGBS-seq, DNA was isolated using standard phenol/chloroform extraction and ethanol precipitation. C-T transformation of 1 μg genomic DNA and bisufile treatment were performed by using EZ DNA Methylation Gold™ Kit. Then modified DNA was treated as below: DNA fragment, end repair, A-tailing, ligate methylated adapter. And the target DNA samples were selected and treated with bisufile.
RNA sequencing libraries were constructed using the VAHTS mRNA-seq V3 Library Prep Kit for Illumina (Vazyme). ATAC libraries were constructed using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme). BL-Hi-C libraries were constructed into standard illumina libraries. ChIP-seq libraries were constructed using the VAHTSTM Universal DNA Library Prep Kit for Illumina® V2. WGBS libraries were constructed into standard illumina libraries.

value: ES cells

value: histone


title: 20210106_HJZ082_RNA_1BD5_shDDIT3_techrep2_S4_R1_001


title: ES-oeCtrl-F4H-D6-RNA-seq-rep1

source_name: ES cells


title: 20210106_HJZ081_RNA_1BD5_shDDIT3_techrep1_S3_R1_001


title: ES-oeCtrl-F4H-D6-RNA-seq-rep2


title: 20210106_HJZ080_RNA_1BD5_shSCR_techrep2_S2_R1_001


title: T8.D32.Kid1 [ATAC-seq]


title: SP420


title: T8.D32.Fat2 [ATAC-seq]


title: EPS-H3K4me1-ChIPseq


title: SP330


title: ES-H3K4me1-ChIPseq


title: 20210318_HJZ033_ATAC_AD_MSC_CMP12_StemProAdipogenesis_24hr

value: MSCs-AD


title: EPS-histone-ChIPseq-input

source_name: EPS-histone-ChIPseq-input


title: T8.D32.IEL2 [ATAC-seq]

value: IEL


title: EPS-shYy1-F4H-D6-RNA-seq-rep2


title: T8.D32.IEL1 [ATAC-seq]


title: SP285


title: T8.D32.IEL3 [ATAC-seq]


title: EPS-H3K27ac-ChIPseq


title: SP284


title: SP349


title: 20210318_HJZ032_ATAC_AD_MSC_CMP12_base


title: 20210318_HJZ031_ATAC_AD_MSC_DMSO_StemProAdipogenesis_24hr


title: SP291


title: SP258


title: 20210318_HJZ030_ATAC_AD_MSC_DMSO_base


title: 20210106_HJZ079_RNA_1BD5_shSCR_techrep1_S1_R1_001


title: EPS-shYy1-histone-ChIPseq-input


title: ES-H3K27ac-ChIPseq


title: T8.D32.Spl3 [ATAC-seq]

value: Spleen


title: EPS-shCtrl-histone-ChIPseq-input

source_name: EPS-shCtrl-histone-ChIPseq-input

value: Ctrl shRNA


title: T8.D32.Spl2 [ATAC-seq]

value: CD8+ T cells


title: 20210317_HJZ028_ATAC_hTERT_MSC_CMP12_StemProAdipogenesis_24hr


title: 20210317_HJZ025_ATAC_hTERT_MSC_DMSO_base


title: 20210317_HJZ026_ATAC_hTERT_MSC_DMSO_StemProAdipogenesis_24hr


title: SP253


title: EPS-shYy1-CTCF-ChIPseq-input


title: T8.D32.Spl1 [ATAC-seq]


title: SP257


title: T8.D32.Spl4 [ATAC-seq]


title: SP229


title: EPS-shCtrl-H3K4me3-ChIPseq


title: 20210317_HJZ027_ATAC_hTERT_MSC_CMP12_base


title: SP252


title: 20181015_HJZ016_ATAC_MLS1765_shDDIT3_0720

value: genotype:FUS-DDIT3 fusion shDDIT3


title: EPS-shYy1-H3K4me3-ChIPseq


title: SP236

value: Severe Community Acquired Pneumonia (SCAP)


title: EPS-shCtrl-CTCF-ChIPseq-input

source_name: EPS-shCtrl-CTCF-ChIPseq-input


title: 20181015_HJZ015_ATAC_MLS1765_shSCR_0720

value: genotype:FUS-DDIT3 fusion shSCR


title: SP227

value: White blood cell


title: EPS-shYy1-CTCF-ChIPseq


title: EPS-shCtrl-CTCF-ChIPseq

source_name: EPS-shCtrl-CTCF-ChIPseq


title: 20181015_HJZ013_ATAC_MLS1765_shDDIT3_0706


title: SP219


title: EPS-shYy1-BL-HiCseq-rep2


title: 20181015_HJZ012_ATAC_MLS1765_shSCR_0706


title: SP216


title: EPS-shYy1-BL-HiCseq-rep1


title: SP212


title: 20210209_HJZ023_ATAC_3AA3_shDDIT3


title: 20210209_HJZ022_ATAC_3AA3_shSCR


title: EPS-shCtrl-BL-HiCseq-rep1

source_name: EPS-shCtrl-BL-HiCseq


title: EPS-shCtrl-BL-HiCseq-rep2


title: WASP_OE_Input

city: Thuwal

first: Gerardo

last: Ramos-Mandujano

department: Biological and Environmental Science and Engineering Division

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

data_processing:
Basecalling software: bcl2fastq/2.17.1.14
ChIP-Seq reads were mapped to hg38 by DNASTAR SeqMan NGen v2.5.1 with default parameters
Genome_build: hg38
Supplementary_files_format_and_content: BED files exported by DNASTAR SeqMan NGen v2.5.1 with default parameters

source_name: Lymphoblastoid cell line ID00003/WASP-c-EOS

growth_protocol: GM11518 and ID00003/WASP-c-mEOS were cultured (37°C, 5% CO2) in RPMI 1640 with L-Glutamine plus heat inactivated Fetal Bovine Serum (15%) and PEN/STREP (1x).

extract_protocol:
Cell samples were processed using the Magna ChIP TM HiSens (17-10604) by homogenization  and sonication steps, and WASP-DNA complexes were immunoprecipitated with the WASP antibody D1 (Santa Cruz Biothecnology), and DNA was purified (ChIP DNA Clean & Concentrator Kit Zymo Research D5205) after crosslink-reversed.
Libraries were prepared according to MicroPlex Library Preparation Kit v2; Cat. No. C05010012, diagenode.

tag: cell line specifications

value: ID00003 cell line [Coriell Institute:WAS gene (431G>A)] rescued with wild-type WASP (WASP overexpressed)

value: lymphoblastoid cells

tag: genotype

value: WASP overexpressed


title: SP193


title: WASP_GM_Input

source_name: Lymphoblastoid cell line GM11518

value: Wild-type B cells  (Coriell Institute)

value: wild-type


title: EP3-/- brown preadipocyte (IP)

type: RNA

city: Tianjin

first: Yujun

last: Shen

address: 22 Qixiangtai Road, Heping District

institute: Tianjin Medical University

description: E.txt

hyb_protocol: Cy3 and Cy5 labeled cRNAs were combined together and hybridized to Arraystar Human mRNA&lncRNA Epitranscriptomic Arrays (8x60K, Arraystar) at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with Agilent Scanner G2505C.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 4 out of 8 samples were retained as “All Targets Value” in the Excel sheet for further “m6A methylation level” and “m6A quantity” and “expression level” analyses. “m6A methylation level” was calculated for the percentage of modification based on the IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities. “expression level” was calculated based on the total of IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities.
Differentially m6A-methylated RNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds.

source_name: IP

label_protocol: The total RNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”. The “IP” and “Sup” RNAs were labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar Super RNA Labeling Kit.

growth_protocol: Lin−CD29+CD34+Sca1+ brown preadipocytes were obtained by flow cytometric cell sorting

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

tag: gender

value: male

tag: age

value: EP3 cKO

value: brown preadipocyte

tag: antibody

value: anti-N6-methyadenosine (m6A) antibody


title: WASP_GM_ChIP

value: αWASP D-1 (SC-5300 Santa Cruz Biotechnology)


title: EP3-/- brown preadipocyte (Sup)

description: E.txt

source_name: supernant

value: supernant

value: none (supernatant)


title: WASP_OE_ChIP


title: 20210209_HJZ021_ATAC_1BD5_shDDIT3


title: EPS-shYy1-WGBSseq-rep2

value: EPS cells


title: Control brown preadipocyte (IP)

description: C.txt

value: CON


title: Control brown preadipocyte (Sup)

description: C.txt


title: SP160

value: Severe Community Acquired Pneumonia (SCAP)


title: 20210209_HJZ020_ATAC_1BD5_shSCR


title: EPS-shYy1-WGBSseq-rep1


title: 20200729_HJZ061_402_shSCR_D14_CEBPB_S11_R1_001

value: genotype:FUS-DDIT3 fusion shSCR

value: CEBPB


title: anac017, GR24, biol-rep2

city: Klosterneuburg

first: Michelle

last: Gallei

address: Am Campus 1

country: Austria

institute: IST Austria

data_processing:
Reads from RNAseq were analyzed using DESeq2
The RNAseq data processing was performed by the Next Generation Sequencing Facility at Vienna BioCenter Core Facilities (VBCF), member of the Vienna BioCenter (VBC), Austria.
Assembly: TAIR10
Supplementary files format and content: .xlsx files corresponding to multiple samples, column names in the file are referring to library names stated here

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Arabidopsis thaliana seedlings were grown for 7 days under long-day growth conditions

extract_protocol:
Total RNA was harvested using the Rneasy mini kit (Qiagen)
RNA libraries for RNA-seq were prepared using Lexogen QuantSeq V2 adaptors

treatment_protocol: whole seedlings were treated in either 25uM GR24 or Acetone in 2ml of 1/2 MS liquid medium in an embryo dish for 6 hours

value: whole seedlings

value: 25uM GR24

tag: time


title: anac017, GR24, biol-rep1


title: anac017, GR24, biol-rep3


title: 20200729_HJZ062_402_shDDIT3_D14_CEBPB_S12_R1_001

value: genotype:FUS-DDIT3 fusion shDDIT3


title: SP158

value: White blood cell


title: anac017, Acetone, biol-rep3

value: Acetone


title: anac017, Acetone, biol-rep2


title: SP152


title: SP186


title: EPS-shCtrl-WGBSseq-rep1

source_name: EPS-shCtrl-WGBSseq

value: Ctrl shRNA


title: 20200728_HJZ050_402_shDDIT3_D14_ChIP_155_S12_R1_001


title: SP140

source_name: White blood cell


title: Col-0, GR24, biol-rep2, rep2

value: Col-0 (WT)


title: ES-oeYy1-RNAseq-rep2

value: ES cells


title: SP100


title: 20200728_HJZ049_402_shDDIT3_D14_INPUT_S11_R1_001

source_name: cancer cell line

value: Input


title: Col-0, GR24, biol-rep3, rep2


title: ES-oeCtrl-RNAseq-rep2

source_name: ES-oeCtrl-RNAseq

value: oeCtrl


title: 20200728_HJZ047_402_shSCR_D14_INPUT_S9_R1_001


title: SP099


title: 20200728_HJZ048_402_shSCR_D14_ChIP_155_S10_R1_001


title: Col-0, GR24, biol-rep1, rep2


title: EPS-shCtrl-WGBSseq-rep2


title: ES-oeCtrl-RNAseq-rep1


title: SP085


title: Col-0, Acetone, biol-rep3, rep2


title: EPS-shYy1-RNAseq-rep1


title: SP098


title: 20190311_HJZ022_ChIPCEBPB_MLS1765_shDDIT3_0208_S11_R1_001


title: 20190311_HJZ021_ChIP155_MLS1765_shDDIT3_0208_S10_R1_001


title: Col-0, Acetone, biol-rep2, rep2


title: EPS-shYy1-RNAseq-rep2


title: Col-0, Acetone, biol-rep1, rep2


title: anac017, Acetone, biol-rep1


title: SP075


title: EPS-shCtrl-RNAseq-rep2

source_name: EPS-shCtrl-RNAseq


title: Col-0, GR24, biol-rep3, rep1


title: SP124


title: ES-oeYy1-RNAseq-rep1


title: EPS-shCtrl-RNAseq-rep1


title: 20190311_HJZ020_ChIPH3K27ac_MLS1765_shDDIT3_0706_S9_R1_001


title: SP061


title: EPS-RNAseq-rep2

source_name: EPS-RNAseq


title: 20190311_HJZ023_ChIPH3K27ac_MLS1765_shDDIT3_0208_S12_R1_001


title: EPS-RNAseq-rep3


title: Col-0, GR24, biol-rep2, rep1


title: 20190311_HJZ019_ChIPCEBPB_MLS1765_shDDIT3_0706_S8_R1_001


title: Col-0, GR24, biol-rep1, rep1


title: SP058


title: 20190311_HJZ017_ChIPH3K27ac_MLS1765_shSCR_0208_S6_R1_001


title: 20190311_HJZ016_ChIPCEBPB_MLS1765_shSCR_0208_S5_R1_001


title: SP057


title: 20190311_HJZ018_ChIP155_MLS1765_shDDIT3_0706_S7_R1_001


title: SP083


title: pig1, GR24, biol-rep3


title: ES-RNAseq-rep3

source_name: ES-RNAseq


title: pig1, GR24, biol-rep2


title: 20190311_HJZ015_ChIP155_MLS1765_shSCR_0208_S4_R1_001


title: SP043


title: SP039


title: pig1, GR24, biol-rep1


title: 20190311_HJZ014_ChIPH3K27ac_MLS1765_shSCR_0706_S3_R1_001


title: SP032


title: PIN1-GFP, GR24, biol-rep3

value: PIN1::PIN1-GFP in Col-0


title: 20190311_HJZ013_ChIPCEBPB_MLS1765_shSCR_0706_S2_R1_001


title: SP026


title: ES-RNAseq-rep1


title: PIN1-GFP, GR24, biol-rep2


title: EPS-ATACseq-rep3

source_name: EPS-ATACseq


title: 20190311_HJZ012_ChIP155_MLS1765_shSCR_0706_S1_R1_001


title: PIN1-GFP, GR24, biol-rep1


title: pig1, Acetone, biol-rep3


title: EPS-RNAseq-rep1


title: 20180926_HJZ008_ChIP_DDIT3_MLS1765_shSCR_0706_S3_R1_001


title: EPS-ATACseq-rep2


title: SP010


title: pig1, Acetone, biol-rep2


title: 20180926_HJZ006_INPUT_MLS1765_shDDIT3_0706_S1_R1_001


title: 20180926_HJZ007_ChIP_DDIT3_MLS1765_shDDIT3_0706_S2_R1_001


title: EPS-ATACseq-rep1


title: ES-ATACseq-rep2

source_name: ES-ATACseq


title: ES-ATACseq-rep3


title: pig1, Acetone, biol-rep1


title: 20180801_HJZ005_ChIP_MLS1765_shDDIT3_0720_S11_R1_001


title: ES-RNAseq-rep2


title: 20180801_HJZ004_ChIP_MLS1765_shSCR_0720_S10_R1_001


title: NC8

value: Healthy


title: Col-0, Acetone, biol-rep3, rep1


title: ES-ATACseq-rep1


title: Col-0, Acetone, biol-rep2, rep1


title: NC7


title: Cell_NECA2

first: Jie

last: Zhou

address: No22.Qixiangtai Rd.,Heping Dist,Tianjin P.R. China

description: PMN-MDSC RNA

data_processing:
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of million paired-end reads of bp length. This yielded gigabases (Gb) of sequence. Prior to assembly, the low quality reads (1, reads containing sequencing adaptors; 2, reads containing sequencing primer; 3, nucleotide with q quality score lower than 20) were removed.
RNA-seq reads mapping were using HISAT package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT allows multiple alignments per read (up to 20 by default) and a maximum of two mismatches when mapping the reads to the reference.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the ﬁnal transcriptome was generated, StringTie and edgeR were used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Tab-delimited text files include counts and FPKMs.

source_name: polymorphonuclear myeloid-derived suppressor cells

extract_protocol:
Three hundred thousand PMN-MDSCs from each condition were lysed in 5 mL 10 ´ lysis buffer. SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells.
Amplify sscDNA by LD PCR and get enough dscDNA for library construction. cDNA was fragmented by dsDNA Fragmentase (NEB, M0348S) by incubate at 37°C for 30min. Library construction begins with fragmented cDNA.
Paired-end sequencing on an Illumina Novaseq™ 6000.

treatment_protocol: Purified spleen PMN-MDSC treated with or without NECA for 5 days.

tag: tissue

value: spleen

value: PMN-MDSC

value: newborn

value: NECA


title: SP023

value: Severe Community Acquired Pneumonia (SCAP)


title: 20180801_HJZ003_ChIP_MLS1765_shDDIT3_0706_S9_R1_001


title: NC6


title: NC9


title: SP004


title: NC5


title: Cell_NECA1

description: PMN-MDSC RNA


title: PIN1-GFP, Acetone, biol-rep3

value: whole seedlings


title: Cell_DMSO2

description: PMN-MDSC RNA

value: DMSO


title: 20180801_HJZ001_ChIP_MLS1765_INPUT_S7_R1_001

value: genotype:FUS-DDIT3 fusion shSCR


title: PIN1-GFP, Acetone, biol-rep2


title: 20201217_HJZ082_1BD5_shDDIT3_ChIP_H3K27ac_S17_R1_001


title: NC3

value: White blood cell


title: Cell_DMSO1

description: PMN-MDSC RNA


title: Tissue_NECA3

description: intestine tissue total-RNA

source_name: intestine

extract_protocol:
Intestine tissue from each condition were lysed in 5 mL 10 ´ lysis buffer. SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells.
Amplify sscDNA by LD PCR and get enough dscDNA for library construction. cDNA was fragmented by dsDNA Fragmentase (NEB, M0348S) by incubate at 37°C for 30min. Library construction begins with fragmented cDNA.
Paired-end sequencing on an Illumina Novaseq™ 6000.

treatment_protocol: Intestine tissue treated with or without NECA for 5 days.

value: intestine


title: grp7_2

city: Davis

first: Patricia

last: Baldrich Gonzalez

state: CA

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

data_processing:
Read quality control using FastQC
Adaptor trimming and chopping using Cutadapt
Genome alignment unig Bowtie2 and HISAT2 with TAIR10 Arabidopsis genome
sequences were then converted to fasta format
Genome_build: TAIR10 Arabidopsis genome
Supplementary_files_format_and_content: individual mapping gtf files with counts

source_name: Whole plant

growth_protocol: Arabidopsis plants were grown in growth rooms under fluorescent light bulbs (~150 µE/m2/sec), at 9h/16h light/dark photoperiod and 24C/22C light/dark temperatures

extract_protocol:
RNA was isolated from 100 µL of P100 pellet using a PicoPure RNA isolation kit (ThermoFisher). The RNA (1-3 µg) was then treated with 5 units of RNase R (Lucigen. RNR07250) for one hour at 37°C.
RNA-seq libraries were generated using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (catalog number E7765; New England Biolabs) using 500 ng of total RNA as starting material.
RNA-seq libraries were sequenced using paired-end 300-bp reads.  Sequencing was performed at the Center for Genomics and Bioinformatics at Indiana University, Bloomington (IN, USA).

treatment_protocol: P100 pellets were isolated from  apoplastic wash fluids of Arabidopsis wild-type Col-0 rosette leaves using the protocol  described in Rutter et al (2017) .  Pellets were treated with mock solution, RNAse, or trypsin and RNase before RNA extraction

tag: ecotype

value: Whole plant

value: grp7 mutant


title: 20201217_HJZ081_1BD5_shDDIT3_ChIP_CEBPB_S16_R1_001

value: CEBPB


title: 20201217_HJZ080_1BD5_shDDIT3_ChIP_DDIT3_S15_R1_001


title: Col-0, Acetone, biol-rep1, rep1

value: Col-0 (WT)

value: Acetone


title: NC4

tag: disease state


title: Tissue_NECA2

description: intestine tissue total-RNA


title: 20201217_HJZ079_1BD5_shDDIT3_ChIP_155_S14_R1_001


title: ago2_2

value: ago2 mutant


title: NC20

value: Healthy

tag: batch


title: Tissue_NECA1

description: intestine tissue total-RNA


title: 20180801_HJZ002_ChIP_MLS1765_shSCR_0706_S8_R1_001


title: Tissue_DMSO3

description: intestine tissue total-RNA


title: NC21

tag: cell type


title: NC19


title: grp7_1


title: Tissue_DMSO2

description: intestine tissue total-RNA


title: PIN1-GFP, Acetone, biol-rep1

value: PIN1::PIN1-GFP in Col-0


title: ago2_1


title: NC18


title: 20201217_HJZ078_1BD5_shDDIT3_INPUT_S13_R1_001

tag: cell line

value: Input


title: Tissue_DMSO1

description: intestine tissue total-RNA

value: newborn


title: 20201217_HJZ076_1BD5_shSCR_ChIP_CEBPB_S11_R1_001

tag: experimental condition


title: 20201217_HJZ077_1BD5_shSCR_ChIP_H3K27ac_S12_R1_001

tag: chip antibody


title: NC2


title: NC17


title: sorted cells from LNs, CD, Hom samples, scRNAseq

city: Munich

first: Christian

last: Weber

address: Pettenkoferstreet 8a and 9

country: Germany

institute: Institute for Cardiovascular Prevention, Ludwig-Maximilians-University Munich

description: 10x Gemonics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Further processing was done with Seurat v3.2.3 (cell and gene filtering, clustering, differential gene expression analysis).
Assembly: customized reference based on mm10 (GFP was incoperated into the gene CCL17)
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: metadata files: comma-separated values files

source_name: lymph nodes

extract_protocol:
For the scRNA-seq experiment of pooled lymph nodes (including mesenteric, paraaortic, inguinal, axillary, brachial and mandibular LNs), eight male Apoe-/-Ccl17wt/e and six Apoe-/-Ccl17e/e mice were fed on normal chow diet. Perfusion was performed with 5 mL PBS. Pooled lymph nodes from either  Apoe-/-Ccl17wt/e or Apoe-/-Ccl17e/e mice were mechanically crushed and passed through a 30 μm cell strainer using Hank’s Medium (HBSS + 0.04% BSA) to obtain single cell suspensions, followed by B cell depletion using CD19 MicroBead. B cell-depleted fractions were stained with Viability Dye, anti-CD45, anti-CD3, anti-CD19 and anti-CD11c at 4°C for 20 minutes. Cells were washed and resuspended in Hank’s Medium and then isolated by fluorescence-activated cell sorting, by gating for Live CD45+CD11c+CD3-CD19- cells. The cell suspension with viability > 80% was ready for subsequent single cell capture and library preparation. For the scRNA-seq experiment of para-aortic LNs, seven male Apoe-/-Ccl17wt/e and ten Apoe-/-Ccl17e/e mice were fed on 6-week HFD. Paraaortic LNs of same genotype were pooled and strained as aforementioned. Cells were resuspended in Hank’s Medium, stained, and isolated by fluorescence-activated cell sorting, by gating for Live CD45+CD19-MHCII+ cells. The cell suspension with viability > 80% was ready for subsequent single cell capture and library preparation.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, FACS-sorted cells  were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: lymph nodes

value: FACS-sorted CD45+CD11c+CD3-CD19- cells

tag: diet

value: chew diet


title: Control1

value: Control


title: 20201217_HJZ075_1BD5_shSCR_ChIP_DDIT3_S10_R1_001


title: sorted cells from LNs, CD, Het samples, scRNAseq

description: 10x Gemonics

tag: strain


title: 20201217_HJZ073_1BD5_shSCR_INPUT_S8_R1_001


title: 20201217_HJZ074_1BD5_shSCR_ChIP_155_S9_R1_001


title: NC15


title: PNI day35-CD11c-Positive 4

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

data_processing:
Only insert read (read2) were used for the analysis.
Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore.
Reads were aligned to the GRCm38 reference using HISAT2.
Read counts for each gene were obtained by using featureCounts.
Assembly: GRCm38
Supplementary files format and content: comma-separated text file includes raw count values for each Sample

source_name: brain

extract_protocol:
Microglia cells were FACS-sorted into 1.5-ml tube containing lysis buffer (TaKaRa 635013) with RNase inhibitor (TaKaRa 2313A). After samples were mixed briefly by vortexing and spinning down, the lysates were used for library preparation
Libraries were prepared using CEL-Seq2 protocol and primers (Hashimshony T et al.) except that MaximaH minus reverse transcriptase (Thermo Scientific, #EP0751) was used for single-stranded synthesis and Second Strand Synthesis Module (NEB, #E6111) for double-stranded cDNA synthesis

treatment_protocol: Peripheral nerve injury (PNI): Under isoflurane (2%) anesthesia, a small incision at L3–S1 was made. The paraspinal muscle and fat were removed from the L5 traverse process, which exposed the parallel-lying L3 and L4 spinal nerves. The L4 nerve was then carefully isolated and cut. The wound and the surrounding skin were sutured with 5-0 silk.

value: brain

value: microglia

value: wild type

tag: treatment

value: PNI post-day35


title: NC14

value: White blood cell


title: NC13


title: 20201216_HJZ072_3AA3_shDDIT3_ChIP_H3K27ac_S16_R1_001


title: Control2

value: Whole plant


title: 20201216_HJZ071_3AA3_shDDIT3_ChIP_CEBPB_S15_R1_001

value: CEBPB


title: PNI day35-CD11c-Positive 2


title: NC12


title: PNI day35-CD11c-Positive 1


title: 20201216_HJZ070_3AA3_shDDIT3_ChIP_DDIT3_S14_R1_001


title: RNAse1_RNA

data_processing:
Read quality control using FastQC
Adaptor trimming and chopping using Cutadapt
Genome alignment unig Bowtie2 and HISAT2 with TAIR10 Arabidopsis genome
sequences were then converted to fasta format
Genome_build: TAIR10 Arabidopsis genome
Supplementary_files_format_and_content: For sRNAseq, final trimmed and cropped output file in count format. For RNAseq, we provide individual mapping gtf files with counts

extract_protocol:
Following trypsin and RNase treatments,  RNA was extracted using a Trizol/chloroform protocol.
sRNA libraries were constructed as described using the RealSeq-AC kit (no. 500-00048; RealSeq Biosciences), following the manufacturers’ recommendations.  In order to capture all types of small RNAs, we used 1ug of RNA as starting material. RNAseq libraries were generated using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB #E7765; New England Biolabs), using 500 ng of total RNA as starting material. All ibraries were sequenced on a NextSeq 550 instrument with single- end 75-bp reads at the Delaware Biotechnology Institure (DE, USA).
small RNA and RNA-seq libraries were sequenced on an Illumina NextSeq 550 instrument with single- end 75-bp reads at the Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN USA.

value: RNAse treatment


title: NC16


title: NC11


title: RNAse2_RNA


title: 20201216_HJZ069_3AA3_shDDIT3_ChIP_155_S13_R1_001


title: TrypsinRNAse3_RNA

value: Trypsin and RNAse treatment


title: NC10

value: Healthy


title: NC1


title: 20201216_HJZ068_3AA3_shDDIT3_INPUT_S12_R1_001


title: PNI day35-CD11c-Positive 3


title: 20201216_HJZ067_3AA3_shSCR_ChIP_H3K27ac_S11_R1_001


title: RNAse3_RNA


title: WASP_KO_Clone3

city: Jeddah

first: Baolei

last: Yuan

state: Makkah

address: Thuwal

data_processing:
Basecalls performed using CASAVA version 1.4
The analysis was done on the AIR online platform (www.transcriptomics.com). Low quality bases and adapters were removed with trimmomatic v0.39 setting a minimum base quality of 30 and minimum read length of 35 bp
The trimmed reads were mapped against the reference genome using STAR v2.7.6a with default parameters
Gene Expression quantification was performed with featureCounts v2.0.0 setting a minimum mapping quality of 30. TMM normalization was applied in R and the differential expression analysis was performed using edgeR.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: macrophages

extract_protocol:
Total RNA was extracted from TRIzol reagent,  rRNA was removed using Ribo-Zero kit and the mRNA was subjected to Eukaryotic strand-specific Transcriptome library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: iPSC-derived macrophages

value: WAS-/-


title: PNI day14-CD11c-Positive 3

value: PNI post-day14


title: Control2_RNA

value: No treatment


title: PNI day14-CD11c-Positive 2


title: TrypsinRNAse2_RNA


title: Control1_RNA


title: 20201216_HJZ066_3AA3_shSCR_ChIP_CEBPB_S10_R1_001


title: WASP_KO_Clone2


title: PNI day14-CD11c-Positive 5


title: 20201216_HJZ065_3AA3_shSCR_ChIP_DDIT3_S9_R1_001


title: TrypsinRNAse3_smallRNA


title: PNI day14-CD11c-Positive 1


title: WASP_KO_Clone1


title: PNI day14-CD11c-Positive 4


title: TrypsinRNAse2_smallRNA


title: Control3_RNA


title: 20201216_HJZ064_3AA3_shSCR_ChIP_155_S8_R1_001


title: WT_rep2


title: PNI day35-CD11c-Negative 5


title: TrypsinRNAse1_smallRNA


title: 20201216_HJZ063_3AA3_shSCR_INPUT_S7_R1_001

value: Input


title: PNI day35-CD11c-Negative 4


title: RNAse3_smallRNA


title: WT_rep1


title: PNI day35-CD11c-Negative 3


title: RNAse2_smallRNA


title: PNI day35-CD11c-Negative 2


title: TrypsinRNAse1_RNA


title: RNAse1_smallRNA


title: Control3_smallRNA


title: PNI day35-CD11c-Negative 1


title: PNI day14-CD11c-Negative 4


title: LPS, 1000 ng/ml 2

city: New Orleans

first: Heping

last: Cao

state: LA

address: 1100 Robert E. Lee Blvd

department: Southern Regional Research Center

institute: USDA-ARS

description: Test

hyb_protocol: SYBR Green qPCR reaction mixtures contained 5 ng of total RNA-derived cDNAs, forward primer, reverse primer and 1X iQ SYBR Green Supermix (Bio-Rad Laboratories, Hercules, CA). The thermal cycle conditions were as follows: 3 min at 95°C, followed by 40 cycles at 95°C for 10 s, 65°C for 30 s and 72°C for 30 s. The qPCR reactions were performed in 96-well clear plates sealed by adhesives with a CFX96 real-time system-C1000 Thermal Cycler (Bio-Rad Laboratories).

data_processing:
BCL2 mRNA was selected as the internal reference for qPCR analysis for this cell type (HKG).
1% DMSO treatment was used as sample control
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
Normalized to Bcl2 worksheet reports normalized signal (against housekeeping genes), where deltaCt = (Ct_Target − Ct_Bcl2)
Normalized to Bcl2 and DMSO worksheet reports normalized signal (against housekeeping genes and smaple control), where deltadeltaCt = delta(Ct_Target )− delta(Ct_DMSO)
Fold Change worksheet reports test/control (i.e., test/DMSO control) ratios. The 2-ΔΔCT method of relative quantification was used to determine the fold change in expression.

label: SYBR Green

source_name: COLO 225

label_protocol: The cDNAs were synthesized from total RNA using SuperScript II reverse transcriptase (Life Technologies). The cDNA synthesis mixture (20 μl) contained 2.5 μg total RNA, 2.4 μg oligo(dT)12-18 primer, 0.1 μg random primers, 500 μM dNTPs, 10 mM DTT, 40 units RNaseOUT and 200 units SuperScript II reverse transcriptase in 1X first-strand synthesis buffer (Life Technologies). The cDNA synthesis reactions were incubated at 42°C for 50 min. The cDNA samples were stored in -80°C freezer and diluted with water to 1 ng/µl before qPCR analyses.

extract_protocol: Total RNA was extracted from the human colon cancer cells with Trozol reagent followed by DNase I treatment.

value: epithelial cells isolated in 1975 from ascitic fluid derived from a 70-year-old, Caucasian man with colon cancer.

tag: activation agent

value: LPS, 1000 ng/ml

value: 8 h


title: LPS, 1000 ng/ml 1

description: Test


title: LPS, 100 ng/ml 3

description: Test

value: LPS, 100 ng/ml


title: Control2_smallRNA


title: LPS, 100 ng/ml 2

description: Test


title: LPS, 100 ng/ml 1

description: Test


title: Control1_smallRNA


title: LPS, 10 ng/ml 3

description: Test

value: LPS, 10 ng/ml


title: WT-Liver

city: Cincinnati

first: Yin Yeng

last: Lee

state: Ohio

address: 3333 Burnet Avenue

department: Department of Pediatrics

institute: Cincinnati Children's Hospital Medical Center

description: 4 libraries were prepared and sequenced from 4 individual hamsters. Reads were merged into one fastq file

data_processing:
Reads from liver tissues from the same genotype were merged into one fastq file.
Sequencing reads were aligned to the hamster reference genome using Kallisto.
Estimated counts for transcripts from the same genes were added up using the tx2gene function integrated in tximport.
Genome_build: MesAur2.0
Supplementary_files_format_and_content: Estimated read count and normalized count (TPM) is attached.

organism: Mesocricetus auratus

source_name: liver

growth_protocol: Animals were raised in a 14:10 LD cycle and allowed ad libitum access to food and water.

extract_protocol:
RNA was extracted using TRIzol (Invitrogen). For cortex and SCN, tissues from 4 samples of the same genotype were mixed before library construction. Liver tissues from each individual hamster were used for library construction. In total, 12 libraries were constructed for the experiment. 8 libraries were prepared (4 for wild type, 4 for duper). In total, 12 libraries were pooled and subjected to 2×100bp sequencing in two lanes on a HiSeq 2000 sequencer (Illumina).
TruSeq Stranded mRNA Sample Preparation Kit (Illumina)

treatment_protocol: Tissues were collected at CT15 for wild type and duper hamsters.

tag: genotype

value: wild type

value: liver


title: PNI day14-CD11c-Negative 2

value: brain

value: microglia


title: PNI day0-CD11c-Neg 5

value: without PNI


title: WT-SCN

description: Tissues from 4 hamsters were mixed before library construction

source_name: suprachiasmatic nucleus

value: SCN


title: PNI day14-CD11c-Negative 1


title: LPS, 10 ng/ml 2

description: Test


title: PNI day0-CD11c-Neg 4


title: WT-Cortex

source_name: cortex

value: cortex


title: LPS, 10 ng/ml 1

description: Test


title: PNI day14-CD11c-Negative 3


title: Duper-Liver

value: duper


title: DMSO, 1% 3

description: Control

value: DMSO, 1%


title: Huh7 cells-transfected with siRNA-rep2

city: Hangzhou

last: Li

address: 866 Yuhangtang Road, Hangzhou, Zhejiang Province, China

institute: Zhejiang University School of Medicine

description:
total RNA of Huh7 cells
Hu7RP2

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0 (Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: Huh7 cells-transfected with siRNA

label_protocol: standard Affymetrix protocol

growth_protocol: All cells were cultured in minimum essential medium (MEM) supplemented with 10% fetal bovine serum (FBS) and were cultured at 37°C in a 5% CO2 containing atmosphere.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: Total RNA was extracted from Huh7 and Hep3B cells transfected with siRNA or negative control after 48 hours.

value: HCC cells

value: transfected with siRNA


title: PNI day0-CD11c-Neg 3


title: Huh7 cells-transfected with siRNA-rep1

description:
total RNA of Huh7 cells
Hu7RP1


title: Huh7 cells-transfected with siRNA-rep3

description:
total RNA of Huh7 cells
Hu7RP3


title: LPS, 1000 ng/ml 3

description: Test


title: Huh7 cells-transfected with negtive control-rep2

description:
total RNA of Huh7 cells
Hu7NC2

value: transfected with negtive control


title: Duper-SCN


title: PNI day0-CD11c-Neg 2


title: Huh7 cells-transfected with negtive control-rep1

description:
total RNA of Hep3B cells
Hu7NC1


title: Hep3B cells-transfected with siRNA-rep3

description:
total RNA of Hep3B cells
3BRP3

source_name: Hep3B cells-transfected with siRNA


title: Hep3B cells-transfected with siRNA-rep2

description:
total RNA of Hep3B cells
3BRP2


title: DMSO, 1% 2

description: Control

value: epithelial cells isolated in 1975 from ascitic fluid derived from a 70-year-old, Caucasian man with colon cancer.


title: Huh7 cells-transfected with negtive control-rep3

description:
total RNA of Huh7 cells
Hu7NC3


title: Duper-Cortex


title: PNI day0-CD11c-Neg 1


title: DMSO, 1% 1

description: Control


title: control27

status: Public on Apr 17 2022

city: Cambridge

first: Sunwoo

address: Academic Laboratory of Medical Genetics, Lv 6 Addenbrooke's Treatment Centre, Cambridge Biomedical Campus

department: Medical Genetics

country: United Kingdom

institute: University of Cambridge

description: healthy control 27

data_processing:
filtering performed by Trim-galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) package
PCR duplicates were removed with the ‘deduplicate bismark’ option from bismark software v0.17.0
methylation value extracted by bismark methylation extractor
Assembly: hg19 (Genome Reference Consortium Human Build 37)
Supplementary files format and content: bismark coverage files

source_name: peripheral blood

extract_protocol:
Genomic DNA from a total of 20 samples from patients with a germline KMT2B or KMT2D variant was extracted from peripheral blood using Gentra Puregene Blood Kit (Qiagen) or other standard methods and quantified by Qubit™ dsDNA BR Assay Kit (Invitrogen, ThermoFisher).
All DNA Samples were sequenced on an Illumina HiSeq 4000 analyser (Illumina, San Diego, CA) using TruSeq® Methyl Capture EPIC kit. Bisulfite conversion, library preparation, target enrichment and sequencing were performed at the Cambridge University Department of Medical Genetics Stratified Medicine Core Laboratory (SMCL).

tag: gender

value: F

tag: mutation

tag: disease

value: healthy control


title: control26

description: healthy control 26

tag: age

value: M


title: control28

description: healthy control 28


title: control23

description: healthy control 23


title: control22

description: healthy control 22


title: control19

description: healthy control 19


title: control20

description: healthy control 20


title: control21

description: healthy control 21


title: control24

description: healthy control 24


title: control29

description: healthy control 29


title: Hep3B cells-transfected with negtive control-rep3

description:
total RNA of Hep3B cells
3BNC3


title: control16

description: healthy control 16


title: control18

description: healthy control 18


title: control17

description: healthy control 17


title: Hep3B cells-transfected with siRNA-rep1

description:
total RNA of Hep3B cells
3BRP1


title: control15

description: healthy control 15


title: Hep3B cells-transfected with negtive control-rep2

description:
total RNA of Hep3B cells
3BNC2


title: control14

description: healthy control 14


title: control12

description: healthy control 12


title: control25

description: healthy control 25


title: control11

description: healthy control 11


title: control9

description: healthy control 9


title: control8

description: healthy control 8


title: control7

description: healthy control 7


title: control6

description: healthy control 6


title: Hep3B cells-transfected with negtive control-rep1

description:
total RNA of Hep3B cells
3BNC1


title: control5

description: healthy control 5


title: control4

description: healthy control 4


title: control3

description: healthy control 3


title: KMT2D_10

description: Kabuki syndrom 10

value: Kabuki syndrome


title: control13

description: healthy control 13


title: control2

description: healthy control 2


title: control1

description: healthy control 1


title: KMT2D_8

description: Kabuki syndrom 8


title: KMT2D_7

description: Kabuki syndrom 7


title: KMT2D_6

description: Kabuki syndrom 6


title: KMT2D_9

description: Kabuki syndrom 9


title: KMT2D_3

description: Kabuki syndrom 3


title: KMT2D_5

description: Kabuki syndrom 5


title: KMT2D_4

description: Kabuki syndrom 4


title: KMT2B_10

description: childhood-onset dystonia 10

value: childhood-onset dystonia


title: KMT2D_1

description: Kabuki syndrom 1


title: KMT2D_2

description: Kabuki syndrom 2


title: KMT2B_9

description: childhood-onset dystonia 9


title: KMT2B_7

description: childhood-onset dystonia 7


title: KMT2B_8

description: childhood-onset dystonia 8


title: KMT2B_6

description: childhood-onset dystonia 6


title: KMT2B_1

description: childhood-onset dystonia 1


title: KMT2B_3

description: childhood-onset dystonia 3


title: KMT2B_5

description: childhood-onset dystonia 5


title: KMT2B_4

description: childhood-onset dystonia 4


title: KMT2B_2

description: childhood-onset dystonia 2


title: mouseliver_150dpi_Con_rep3

city: lanzhou

first: xiaofeng

last: nian

address: No.1 of xujiaping

institute: LVRI

description:
Gene expression at 150 days  control of liver replicate 3
SAMPLE 9-12

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: mouse liver, 150dpi, control, replicate 3

label_protocol: standard protocol

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: mice in the CA group were injected intraperitoneally with 100 μl of protoscolex suspension containing about 1,000 Em protoscolices, while mice in the Con group were given the same volume of sterile saline solution using the same surgical procedure. Each group was randomly divided into eight sub-groups (four mice per subgroup in separate cages) corresponding to eight autopsy time points (2, 4, 8, 15, 30, 60, 90 and 150 dpi).

value: female

tag: tissue

value: mouse liver

tag: time point

tag: sample group

value: control


title: mouseliver_150dpi_CA_rep4

description:
Gene expression at 150 days  post infection of liver replicate 4
SAMPLE 9-9

source_name: mouse liver, 150dpi, infection, replicate 4

value: infection


title: mouseliver_150dpi_Con_rep4

description:
Gene expression at 150 days  control of liver replicate 4
SAMPLE 9-13

source_name: mouse liver, 150dpi, control, replicate 4


title: mouseliver_90dpi_Con_rep3

description:
Gene expression at 90 days  control of liver replicate 3
SAMPLE 8-13

source_name: mouse liver, 90dpi, control, replicate 3


title: mouseliver_90dpi_CA_rep4

description:
Gene expression at 90 days  post infection of liver replicate 4
SAMPLE 8-10

source_name: mouse liver, 90dpi, infection, replicate 4


title: mouseliver_60dpi_Con_rep4

description:
Gene expression at 60 days  control of liver replicate 4
SAMPLE 7-14

source_name: mouse liver, 60dpi, control, replicate 4


title: mouseliver_90dpi_Con_rep4

description:
Gene expression at 90 days  control of liver replicate 4
SAMPLE 8-14

source_name: mouse liver, 90dpi, control, replicate 4


title: mouseliver_60dpi_CA_rep4

description:
Gene expression at 60 days  post infection of liver replicate 4
SAMPLE 7-9

source_name: mouse liver, 60dpi, infection, replicate 4


title: mouseliver_2dpi_Con_rep4

description:
Gene expression at 2 days  control of liver replicate 4
SAMPLE 2-14

source_name: mouse liver, 2dpi, control, replicate 4


title: mouseliver_15dpi_CA_rep4

description:
Gene expression at 15 days  post infection of liver replicate 4
SAMPLE 5-9

source_name: mouse liver, 15dpi, infection, replicate 4


title: mouseliver_30dpi_Con_rep3

description:
Gene expression at 30 days  control of liver replicate 3
SAMPLE 6-13

source_name: mouse liver, 30dpi, control, replicate 3


title: mouseliver_15dpi_Con_rep3

description:
Gene expression at 15 days  control of liver replicate 3
SAMPLE 5-13

source_name: mouse liver, 15dpi, control, replicate 3


title: mouseliver_15dpi_Con_rep4

description:
Gene expression at 15 days  control of liver replicate 4
SAMPLE 5-14

source_name: mouse liver, 15dpi, control, replicate 4


title: mouseliver_8dpi_Con_rep4

description:
Gene expression at 8 days  control of liver replicate 4
SAMPLE 4-14

source_name: mouse liver, 8dpi, control, replicate 4


title: mouseliver_4dpi_Con_rep4

description:
Gene expression at 4 days  control of liver replicate 4
SAMPLE 3-14

source_name: mouse liver, 4dpi, control, replicate 4


title: mouseliver_60dpi_Con_rep3

description:
Gene expression at 60 days  control of liver replicate 3
SAMPLE 7-13

source_name: mouse liver, 60dpi, control, replicate 3


title: mouseliver_150dpi_CA_rep3

description: Gene expression at 150 days  post infection of liver replicate 3

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: mouse liver, 150dpi, infection, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using the mirVana miRNA Isolation Kit (Ambion, AM1561) following the manufacturer's recommendations. RNA was quantified by NanoDrop ND-2000  spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: mice in the CA group were injected intraperitoneally with 100 μl of protoscolex suspension containing about 1,000 Em protoscolices, while mice in the Con group were given the same volume of sterile saline solution using the same surgical procedure. Each group was randomly divided into eight sub-groups (three mice per subgroup in separate cages) corresponding to eight autopsy time points (2, 4, 8, 15, 30, 60, 90 and 150 dpi).

value: liver

tag: agent

value: Echinococcus multilocularis


title: mouseliver_150dpi_Con_rep2

description: Gene expression at 150 days  control of liver replicate 2

source_name: mouse liver, 150dpi, control, replicate 2


title: mouseliver_8dpi_CA_rep4

description:
Gene expression at 8 days  post infection of liver replicate 4
SAMPLE 4-9

source_name: mouse liver, 8dpi, infection, replicate 4


title: mouseliver_2dpi_Con_rep3

description:
Gene expression at 2 days  control of liver replicate 3
SAMPLE 2-13

source_name: mouse liver, 2dpi, control, replicate 3


title: mouseliver_8dpi_Con_rep3

description:
Gene expression at 8 days  control of liver replicate 3
SAMPLE 4-13

source_name: mouse liver, 8dpi, control, replicate 3


title: mouseliver_2dpi_CA_rep4

description:
Gene expression at 2 days  post infection of liver replicate 4
SAMPLE 2-9

source_name: mouse liver, 2dpi, infection, replicate 4


title: mouseliver_150dpi_CA_rep2

description: Gene expression at 150 days  post infection of liver replicate 2

source_name: mouse liver, 150dpi, infection, replicate 2


title: mouseliver_30dpi_Con_rep4

description:
Gene expression at 30 days  control of liver replicate 4
SAMPLE 6-14

source_name: mouse liver, 30dpi, control, replicate 4


title: mouseliver_150dpi_Con_rep1

description: Gene expression at 150 days  control of liver replicate 1

source_name: mouse liver, 150dpi, control, replicate 1


title: mouseliver_4dpi_CA_rep4

description:
Gene expression at 4 days  post infection of liver replicate 4
SAMPLE 3-9

source_name: mouse liver, 4dpi, infection, replicate 4


title: mouseliver_150dpi_CA_rep1

description: Gene expression at 150 days  post infection of liver replicate 1

source_name: mouse liver, 150dpi, infection, replicate 1


title: mouseliver_4dpi_Con_rep3

description:
Gene expression at 4 days  control of liver replicate 3
SAMPLE 3-13

source_name: mouse liver, 4dpi, control, replicate 3


title: mouseliver_30dpi_CA_rep4

description:
Gene expression at 30 days  post infection of liver replicate 4
SAMPLE 6-9

source_name: mouse liver, 30dpi, infection, replicate 4


title: mouseliver_90dpi_CA_rep3

description: Gene expression at 90 days  post infection of liver replicate 3

source_name: mouse liver, 90dpi, infection, replicate 3


title: mouseliver_90dpi_Con_rep2

description: Gene expression at 90 days  control of liver replicate 2

source_name: mouse liver, 90dpi, control, replicate 2


title: mouseliver_90dpi_CA_rep2

description: Gene expression at 90 days  post infection of liver replicate 2

source_name: mouse liver, 90dpi, infection, replicate 2


title: mouseliver_90dpi_Con_rep1

description: Gene expression at 90 days  control of liver replicate 1

source_name: mouse liver, 90dpi, control, replicate 1


title: control10

description: healthy control 10

source_name: peripheral blood

tag: batch


title: mouseliver_60dpi_Con_rep2

description: Gene expression at 60 days  control of liver replicate 2

source_name: mouse liver, 60dpi, control, replicate 2


title: mouseliver_90dpi_CA_rep1

description: Gene expression at 90 days  post infection of liver replicate 1

source_name: mouse liver, 90dpi, infection, replicate 1


title: mouseliver_30dpi_CA_rep1

description: Gene expression at 30 days  post infection of liver replicate 1

source_name: mouse liver, 30dpi, infection, replicate 1


title: mouseliver_60dpi_Con_rep1

description: Gene expression at 60 days  control of liver replicate 1

source_name: mouse liver, 60dpi, control, replicate 1


title: mouseliver_60dpi_CA_rep3

description: Gene expression at 60 days  post infection of liver replicate 3

source_name: mouse liver, 60dpi, infection, replicate 3


title: mouseliver_30dpi_Con_rep2

description: Gene expression at 30 days  control of liver replicate 2

source_name: mouse liver, 30dpi, control, replicate 2


title: mouseliver_30dpi_CA_rep2

description: Gene expression at 30 days  post infection of liver replicate 2

source_name: mouse liver, 30dpi, infection, replicate 2


title: mouseliver_60dpi_CA_rep1

description: Gene expression at 60 days  post infection of liver replicate 1

source_name: mouse liver, 60dpi, infection, replicate 1


title: mouseliver_30dpi_Con_rep1

description: Gene expression at 30 days  control of liver replicate 1

source_name: mouse liver, 30dpi, control, replicate 1


title: mouseliver_15dpi_CA_rep1

description: Gene expression at 15 days  post infection of liver replicate 1

source_name: mouse liver, 15dpi, infection, replicate 1


title: mouseliver_15dpi_CA_rep3

description: Gene expression at 15 days  post infection of liver replicate 3

source_name: mouse liver, 15dpi, infection, replicate 3


title: mouseliver_8dpi_CA_rep2

description: Gene expression at 8 days  post infection of liver replicate 2

source_name: mouse liver, 8dpi, infection, replicate 2


title: mouseliver_4dpi_Con_rep2

description: Gene expression at 4 days  control of liver replicate 2

source_name: mouse liver, 4dpi, control, replicate 2


title: mouseliver_15dpi_Con_rep1

description: Gene expression at 15 days  control of liver replicate 1

source_name: mouse liver, 15dpi, control, replicate 1


title: mouseliver_15dpi_CA_rep2

description: Gene expression at 15 days  post infection of liver replicate 2

source_name: mouse liver, 15dpi, infection, replicate 2


title: mouseliver_8dpi_Con_rep2

description: Gene expression at 8 days  control of liver replicate 2

source_name: mouse liver, 8dpi, control, replicate 2


title: mouseliver_8dpi_Con_rep1

description: Gene expression at 8 days  control of liver replicate 1

source_name: mouse liver, 8dpi, control, replicate 1


title: mouseliver_8dpi_CA_rep1

description: Gene expression at 8 days  post infection of liver replicate 1

source_name: mouse liver, 8dpi, infection, replicate 1


title: BEAS-2B_Untrtd [TC00504137_O12]

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

data_processing:
Each FASTQ file was aligned to the probe sequences in the hWTv2 assay using HISAT2 v2.1.0 with spliced alignment disabled.
Aligned reads in SAM format were processed with SAMtools v1.9 to compute the number of uniquely aligned reads for each probe. Probe counts and associated meta-data for each well were stored for analysis using MongoDB v3.6.14.
Assembly: hWTv2
Supplementary files format and content: Processed data provided as a single table of counts for all probes x all samples

growth_protocol: The BEAS-2B cells used are a non-diseased, viral transformed human bronchial epithelial cell line acquired from ATCC (Manassas, VA, CRL-9609). Prior to cell culture, T75 flasks (Corning, One Riverfront Plaza, NY, 430641) and 6.5 mm Transwell® Inserts (Costar, Corning, NY, 3470) were coated with 100 µg/mL bovine collagen (PureCol Collagen [Advanced Biomatrix, San Diego, CA, 5005] diluted in Ultrapure Molecular (nuclease free) Water [Invitrogen, ThermoFisher Scientific, Rockford, IL, 10977023]) for 2 h at room temperature, followed by a water rinse. To prepare the cells for exposure at ALI, cells were thawed from pre-passaged frozen vials, grown on a T75 flask at 37 C 5% CO2 incubator conditions. The cells proliferated while submerged in Keratinocyte Growth Medium (KGM) (Keratinocyte Basal Medium (KBM) [Lonza, Walkersville, MD] plus KGM Gold Bullet Kit [Lonza, Walkersville, MD, 00192151]) with 25 mM HEPES Buffer (Sigma-Aldrich, St. Louis, MO) or Bronchial Epithelial Growth Medium (BEGM) (Bronchial Epithelial Basal Medium (BEBM) [Lonza, Walkersville, MD, CC-3171] plus BEGM Bullet Kit [Lonza, Walkersville, MD, CC-3170]. The utilized media type was switched to the latter (BEGM) for the experiments with dichloromethane, trichloroethylene, carbon tetrachloride, and 1-bromopropane due to vendor formulation changes and availability. BEAS2B Cells were grown for a minimum of two subsequent passages after thawing. Cells were passaged when approximately 75% confluent and new flasks seeded at 1 x 106 cells. The 6.5 mm inserts were seeded at 2-5 x 105 cells/insert and were maintained for 48-72 h before being used for exposure as a fully confluent monolayer. All apical media was removed at least 5 days before using BEAS-2B cells for exposure to the test agent. No FBS was used in the culture of BEAS-2B cells which were observed to have normal basal respiratory cell morphology at ALI. Primary human bronchial epithelial cells (pHBEC) were obtained via bronchial brushing from healthy, non-smoking donors aged 21–40 years. Donors gave their consent after being informed of procedures and associated risks. This study utilized cells from 12 healthy non-smoking donors, 10 male and 2 female donors between age 26-41. The consent and collection protocol were approved by the University of North Carolina School of Medicine Committee on the Protection of the Rights of Human Subjects and by the US Environmental Protection Agency. After collection, pHBECs were seeded at approximately 1 x 106 cells and cultured in BEGM (BEGM Bullet Kit, Lonza, Walkersville, MD CC-3170) on plastic T75 tissue culture flasks and expanded until the third passage. For all exposures, cells were lifted using trypsin-EDTA (Gibco 25300062) and plated on uncoated 6.5 mm diameter (24-well format) Transwell™ inserts (Costar, Corning, NY, 3470) at a density of 1 x 105 cells/insert depending on the donor. Each insert of cells was initially grown submerged with 1:1 DMEM-H (Gibco, 11995-065) and BEGM with complete bullet kit of growth supplements, 50 µg/mL of bovine pituitary extract (Lonza) and 1.5 µg/mL Bovine Serum Albumin (Sigma, A9418) on both the basolateral and apical compartments. The pHBECs were then expanded and grown for 2-4 days until they reached confluency. The cells were then placed at ALI by removing all apical medium and replacing the basolateral medium with the base media described above, supplemented with 100 nM retinol. The pHBECs continue to differentiate for at least 21 days before being used in an exposure. Previous research categorizing the pHBECs we use show a columnar pseudostratified cell layer with both cilia and mucin producing cells present after day 21 of ALI culture.

extract_protocol:
An optimized whole cell lysis procedure was used to preserve the RNA of both BEAS-2B and pHBEC samples. After a 4 h recovery post 2 h test agent exposure, the two technical replicate inserts from each exposure condition were placed on a new 24-well plate (Corning, NY). A single replicate insert of the incubator control cells was also preserved for whole cell lysis. Prior to adding the lysis buffer, the cells were thoroughly washed twice with DPBS to remove any remaining apical mucus or surfactant which may interfere with complete lysis. When transferring the BEAS-2B cells or pHBECs, the BioSpyder lysis buffer (Carlsbad, CA) was added to each of the samples and allowed to incubate for 15 minutes at room temperature. Each sample was mixed and pipetted into an individual well in the 384-well optical imaging plate (Corning, NY). After placing each of the samples into the 384-well plate, it was sealed with ThermalSeal RT 2mil Film (Sigma-Aldrich, MO) and stored in a -80°C freezer until shipment to BioSpyder for analysis.
384-well plates containing cell lysates were shipped to BioSpyder, Inc. frozen (on dry ice) using overnight priority shipping. BEAS-2B and pHBEC lysates were then analyzed by BioSpyder using the TempO-Seq human whole transcriptome version 2 (hWTv2) assay, which includes 22,537 probes covering 19,703 genes. Lysates were processed as described in. In brief, 2 µL of each lysate was hybridized with 2 µL of detector oligos from the hWTv2 assay using the following thermal cycler protocol: 10 min at 70°C, followed by gradual decrease to 45°C over 49 min, terminating with 45°C incubation for 16-24 h. Excess oligos were then removed via nuclease digestion (90 min at 37°C), and hybridized detector oligos were ligated (1 h at 37°C) following respective additions of 24 µL TempO-Seq nuclease and ligation mixes. RNA/DNA duplexes were then heat-denatured, and 10 µL of each ligation product were transferred to an amplification microplate containing 10 µL of PCR master mix per well. Ligation products were then uniquely labeled during product amplification with well coordinate-specific “barcoded” primer pairs containing universal adaptors for sequencing. Samples were pooled into sequencing libraries, distributed across multiple lanes of a HiSeq dual flow cell and analyzed on a HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina, San Diego, CA). The target depth for each test sample was 6 x 10^6 total sequenced reads.

treatment_protocol: Beginning 2 h prior to test agent exposure, designated cells were prepped for exposure by performing an apical wash with Dulbecco’s Phosphate-Buffered Saline (DPBS) and replacing the basolateral compartment with 0.5 mL of fresh media with 25 mM HEPES Buffer. Cells remained in the incubator (37oC, 5% CO2) to recover for 2 h before being placed in the Cell Culture Exposure System (CCES) to undergo test agent exposures. The CCES was developed at EPA’s Inhalation Toxicology Facility and is comprised of a base module that accommodates a 24-well tissue culture plate with 6.5 mm diameter Transwell® inserts. It supplies air under positive pressure and exhausts air under negative pressure to provide a known concentration of test article over a specific time.  Two CCES modules are used simultaneously. One CCES module receives the test agent at six different concentrations while the other CCES module received filtered humidified dilution air and evaluated as a sham exposure control. A uniform air flow distribution was maintained through each nozzle so the cells in each Transwell® insert was exposed to either humidified air or diluted test agent at a flow rate of 12.5 mL/min/well. Optimal exposure temperature (37oC), relative humidity (85%) and air flow rates were tested and validated for the CCES in previous studies designed to optimize low variability in delivered material to the replicate wells. Cells were exposed to the test agent at ALI for 2 h before being transported back to the incubator (37oC, 5% CO2) for 4 h prior to sample collection and analysis. All sample collection and assays were run 4 h post-exposure to complete a 6 h timepoint to reflect both standard in vivo inhalation exposure regimes of 4 to 6 h of exposure and high-throughput screening studies. A sham exposure control cell culture plate which received only humidified air and an incubator control plate were tested in parallel with the plate which received the test agent.

tag: cell line

value: NA NA NA

tag: chemical name

tag: chemical id

tag: chemical concentration

value: NA NA

tag: dose level

tag: assay plate

tag: assay plate well


title: mouseliver_2dpi_CA_rep2

description: Gene expression at 2 days  post infection of liver replicate 2

source_name: mouse liver, 2dpi, infection, replicate 2


title: mouseliver_2dpi_Con_rep1

description: Gene expression at 2 days  control of liver replicate 1

source_name: mouse liver, 2dpi, control, replicate 1


title: mouseliver_4dpi_CA_rep2

description: Gene expression at 4 days  post infection of liver replicate 2

source_name: mouse liver, 4dpi, infection, replicate 2


title: mouseliver_4dpi_CA_rep3

description: Gene expression at 4 days  post infection of liver replicate 3

source_name: mouse liver, 4dpi, infection, replicate 3


title: mouseliver_15dpi_Con_rep2

description: Gene expression at 15 days  control of liver replicate 2

source_name: mouse liver, 15dpi, control, replicate 2


title: mouseliver_30dpi_CA_rep3

description: Gene expression at 30 days  post infection of liver replicate 3

source_name: mouse liver, 30dpi, infection, replicate 3


title: BEAS-2B_Untrtd [TC00504137_O09]

tag: treatment


title: BEAS-2B_Untrtd [TC00504137_O10]


title: BEAS-2B_Untrtd [TC00504137_O11]


title: mouseliver_2dpi_CA_rep3

description: Gene expression at 2 days  post infection of liver replicate 3

source_name: mouse liver, 2dpi, infection, replicate 3

tag: gender


title: BEAS-2B_Untrtd [TC00504137_O07]


title: BEAS-2B_Untrtd [TC00504137_O13]


title: BEAS-2B_Untrtd [TC00504137_O06]


title: mouseliver_4dpi_Con_rep1

description: Gene expression at 4 days  control of liver replicate 1

source_name: mouse liver, 4dpi, control, replicate 1


title: mouseliver_4dpi_CA_rep1

description: Gene expression at 4 days  post infection of liver replicate 1

source_name: mouse liver, 4dpi, infection, replicate 1


title: mouseliver_8dpi_CA_rep3

description: Gene expression at 8 days  post infection of liver replicate 3

source_name: mouse liver, 8dpi, infection, replicate 3


title: mouseliver_2dpi_CA_rep1

description: Gene expression at 2 days  post infection of liver replicate 1

source_name: mouse liver, 2dpi, infection, replicate 1


title: BEAS-2B_Untrtd [TC00504137_O04]


title: BEAS-2B_Untrtd [TC00504137_O03]


title: BEAS-2B_Clean_Air [TC00504137_N13]

value: 0 ppm NA

value: 0 ppm


title: BEAS-2B_Clean_Air [TC00504137_N11]


title: BEAS-2B_Clean_Air [TC00504137_N09]


title: BEAS-2B_Clean_Air [TC00504137_N10]


title: BEAS-2B_Clean_Air [TC00504137_N08]


title: BEAS-2B_Clean_Air [TC00504137_N06]


title: BEAS-2B_Clean_Air [TC00504137_N05]


title: BEAS-2B_Clean_Air [TC00504137_N07]


title: BEAS-2B_Clean_Air [TC00504137_M13]


title: BEAS-2B_Clean_Air [TC00504137_N02]


title: BEAS-2B_Clean_Air [TC00504137_M11]


title: BEAS-2B_Clean_Air [TC00504137_N04]


title: BEAS-2B_Clean_Air [TC00504137_N03]


title: mouseliver_2dpi_Con_rep2

description: Gene expression at 2 days  control of liver replicate 2

source_name: mouse liver, 2dpi, control, replicate 2


title: BEAS-2B_Clean_Air [TC00504137_M12]


title: BEAS-2B_Clean_Air [TC00504137_N12]


title: BEAS-2B_Clean_Air [TC00504137_M10]


title: BEAS-2B_Clean_Air [TC00504137_M08]


title: BEAS-2B_Clean_Air [TC00504137_M09]


title: BEAS-2B_Clean_Air [TC00504137_M07]


title: BEAS-2B_Clean_Air [TC00504137_M06]


title: BEAS-2B_Clean_Air [TC00504137_M04]


title: BEAS-2B_Untrtd [TC00504137_O05]


title: BEAS-2B_Clean_Air [TC00504137_M05]


title: BEAS-2B_Untrtd [TC00504137_O08]


title: BEAS-2B_DTXSID0020868_1_1.59ppm [TC00504137_L13]

value: 1.59 ppm Dichloromethane

value: Dichloromethane


title: BEAS-2B_DTXSID0020868_1_1.59ppm [TC00504137_L12]


title: BEAS-2B_DTXSID6021874_1_0.031ppm [TC00504137_L09]

value: 0.031 ppm 1-Bromopropane


title: BEAS-2B_DTXSID0020868_1_1.59ppm [TC00504137_L11]


title: BEAS-2B_DTXSID0021383_1_0.32ppm [TC00504137_L07]

value: 0.32 ppm Trichloroethylene

value: Trichloroethylene


title: BEAS-2B_Clean_Air [TC00504137_M03]


title: BEAS-2B_DTXSID8020250_1_0.16ppm [TC00504137_L04]

value: 0.16 ppm Carbon Tetrachloride

value: Carbon Tetrachloride


title: BEAS-2B_DTXSID8020250_1_0.16ppm [TC00504137_L02]


title: BEAS-2B_DTXSID0020868_1_1.59ppm [TC00504137_K12]


title: BEAS-2B_DTXSID8020250_1_0.16ppm [TC00504137_L03]


title: BEAS-2B_DTXSID0021383_1_0.32ppm [TC00504137_L05]


title: BEAS-2B_DTXSID0021383_1_0.32ppm [TC00504137_K06]


title: mouseliver_60dpi_CA_rep2

description: Gene expression at 60 days  post infection of liver replicate 2

source_name: mouse liver, 60dpi, infection, replicate 2

value: female


title: BEAS-2B_DTXSID6021874_1_0.031ppm [TC00504137_K08]


title: BEAS-2B_DTXSID6021874_1_0.031ppm [TC00504137_K09]


title: BEAS-2B_DTXSID6021874_1_0.031ppm [TC00504137_K10]


title: BEAS-2B_DTXSID0020868_1_1.59ppm [TC00504137_K11]


title: BEAS-2B_DTXSID8020250_1_0.16ppm [TC00504137_K03]


title: BEAS-2B_DTXSID6021874_1_0.031ppm [TC00504137_L10]


title: BEAS-2B_DTXSID0021383_1_0.32ppm [TC00504137_K07]


title: BEAS-2B_DTXSID6021874_2_0.1ppm [TC00504137_J10]

value: 0.1 ppm 1-Bromopropane

value: 0.1 ppm


title: BEAS-2B_DTXSID0021383_1_0.32ppm [TC00504137_K05]


title: BEAS-2B_DTXSID0020868_2_5.01ppm [TC00504137_J11]

value: 5.01 ppm Dichloromethane


title: BEAS-2B_DTXSID8020250_1_0.16ppm [TC00504137_K04]


title: BEAS-2B_DTXSID0020868_2_5.01ppm [TC00504137_J13]


title: BEAS-2B_DTXSID8020250_1_0.16ppm [TC00504137_K02]


title: BEAS-2B_DTXSID0021383_2_1ppm [TC00504137_J06]

value: 1 ppm Trichloroethylene

value: 1 ppm


title: BEAS-2B_DTXSID0020868_2_5.01ppm [TC00504137_J12]


title: BEAS-2B_DTXSID0021383_1_0.32ppm [TC00504137_L06]


title: BEAS-2B_DTXSID6021874_2_0.1ppm [TC00504137_J08]


title: BEAS-2B_DTXSID6021874_1_0.031ppm [TC00504137_L08]


title: BEAS-2B_DTXSID8020250_2_0.5ppm [TC00504137_J03]

value: 0.5 ppm Carbon Tetrachloride

value: 0.5 ppm


title: BEAS-2B_DTXSID0020868_1_1.59ppm [TC00504137_K13]


title: BEAS-2B_DTXSID0021383_2_1ppm [TC00504137_J07]


title: BEAS-2B_DTXSID0020868_2_5.01ppm [TC00504137_I12]


title: BEAS-2B_DTXSID0020868_2_5.01ppm [TC00504137_I11]


title: BEAS-2B_DTXSID0021383_2_1ppm [TC00504137_I06]


title: BEAS-2B_DTXSID8020250_2_0.5ppm [TC00504137_J02]


title: BEAS-2B_DTXSID6021874_2_0.1ppm [TC00504137_I08]


title: BEAS-2B_DTXSID6021874_2_0.1ppm [TC00504137_I09]


title: BEAS-2B_DTXSID6021874_2_0.1ppm [TC00504137_I10]


title: BEAS-2B_DTXSID6021874_2_0.1ppm [TC00504137_J09]


title: BEAS-2B_DTXSID0021383_2_1ppm [TC00504137_J05]


title: BEAS-2B_DTXSID0021383_3_3.16ppm [TC00504137_H05]

value: 3.16 ppm Trichloroethylene


title: BEAS-2B_DTXSID8020250_2_0.5ppm [TC00504137_J04]


title: BEAS-2B_DTXSID0020868_2_5.01ppm [TC00504137_I13]


title: BEAS-2B_DTXSID0021383_3_3.16ppm [TC00504137_H07]


title: BEAS-2B_DTXSID0021383_3_3.16ppm [TC00504137_H06]


title: BEAS-2B_DTXSID6021874_3_0.31ppm [TC00504137_H10]

value: 0.31 ppm 1-Bromopropane


title: BEAS-2B_DTXSID0021383_2_1ppm [TC00504137_I07]


title: BEAS-2B_DTXSID0020868_3_15.85ppm [TC00504137_H12]

value: 15.85 ppm Dichloromethane


title: BEAS-2B_DTXSID8020250_2_0.5ppm [TC00504137_I04]


title: BEAS-2B_DTXSID0021383_2_1ppm [TC00504137_I05]


title: BEAS-2B_DTXSID8020250_2_0.5ppm [TC00504137_I02]


title: BEAS-2B_DTXSID6021874_3_0.31ppm [TC00504137_H08]


title: BEAS-2B_DTXSID0020868_3_15.85ppm [TC00504137_H11]

value: Dichloromethane


title: BEAS-2B_DTXSID8020250_3_1.6ppm [TC00504137_H04]

value: 1.6 ppm Carbon Tetrachloride

value: 1.6 ppm


title: BEAS-2B_DTXSID0020868_3_15.85ppm [TC00504137_H13]


title: BEAS-2B_DTXSID8020250_3_1.6ppm [TC00504137_H03]


title: BEAS-2B_DTXSID0020868_3_15.85ppm [TC00504137_G12]


title: BEAS-2B_DTXSID8020250_2_0.5ppm [TC00504137_I03]


title: BEAS-2B_DTXSID6021874_3_0.31ppm [TC00504137_G08]


title: BEAS-2B_DTXSID6021874_3_0.31ppm [TC00504137_G10]


title: BEAS-2B_DTXSID0020868_3_15.85ppm [TC00504137_G11]


title: BEAS-2B_DTXSID6021874_3_0.31ppm [TC00504137_G09]


title: BEAS-2B_DTXSID0020868_3_15.85ppm [TC00504137_G13]


title: BEAS-2B_DTXSID8020250_3_1.6ppm [TC00504137_H02]


title: BEAS-2B_DTXSID0021383_3_3.16ppm [TC00504137_G06]

value: Trichloroethylene


title: BEAS-2B_DTXSID0021383_3_3.16ppm [TC00504137_G07]


title: BEAS-2B_DTXSID6021874_3_0.31ppm [TC00504137_H09]


title: BEAS-2B_DTXSID0021383_3_3.16ppm [TC00504137_G05]


title: BEAS-2B_DTXSID8020250_3_1.6ppm [TC00504137_G04]


title: BEAS-2B_DTXSID0020868_4_50.1ppm [TC00504137_F13]

value: 50.1 ppm Dichloromethane


title: BEAS-2B_DTXSID8020250_3_1.6ppm [TC00504137_G03]

value: Carbon Tetrachloride


title: BEAS-2B_DTXSID6021874_4_1ppm [TC00504137_F09]

value: 1 ppm 1-Bromopropane


title: BEAS-2B_DTXSID6021874_4_1ppm [TC00504137_F10]


title: BEAS-2B_DTXSID8020250_3_1.6ppm [TC00504137_G02]


title: BEAS-2B_DTXSID0020868_4_50.1ppm [TC00504137_F11]


title: BEAS-2B_DTXSID0021383_4_10ppm [TC00504137_F07]

value: 10 ppm Trichloroethylene

value: 10 ppm


title: BEAS-2B_DTXSID6021874_4_1ppm [TC00504137_F08]


title: BEAS-2B_DTXSID0020868_4_50.1ppm [TC00504137_E13]


title: BEAS-2B_DTXSID0021383_4_10ppm [TC00504137_F05]


title: BEAS-2B_DTXSID0020868_4_50.1ppm [TC00504137_E11]


title: BEAS-2B_DTXSID0020868_4_50.1ppm [TC00504137_E12]


title: BEAS-2B_DTXSID8020250_4_5ppm [TC00504137_F02]

value: 5 ppm Carbon Tetrachloride

value: 5 ppm


title: BEAS-2B_DTXSID8020250_4_5ppm [TC00504137_F04]


title: BEAS-2B_DTXSID0021383_4_10ppm [TC00504137_F06]


title: BEAS-2B_DTXSID8020250_4_5ppm [TC00504137_F03]


title: BEAS-2B_DTXSID0021383_4_10ppm [TC00504137_E07]


title: BEAS-2B_DTXSID6021874_4_1ppm [TC00504137_E08]

value: 1 ppm


title: BEAS-2B_DTXSID6021874_4_1ppm [TC00504137_E10]


title: BEAS-2B_DTXSID8020250_4_5ppm [TC00504137_E04]


title: BEAS-2B_DTXSID0021383_4_10ppm [TC00504137_E06]


title: BEAS-2B_DTXSID6021874_4_1ppm [TC00504137_E09]


title: BEAS-2B_DTXSID8020250_4_5ppm [TC00504137_E03]


title: BEAS-2B_DTXSID0020868_4_50.1ppm [TC00504137_F12]


title: BEAS-2B_DTXSID0020868_5_158.2ppm [TC00504137_D13]

value: 158.2 ppm Dichloromethane


title: BEAS-2B_DTXSID8020250_4_5ppm [TC00504137_E02]


title: BEAS-2B_DTXSID0020868_5_158.2ppm [TC00504137_D12]


title: BEAS-2B_DTXSID0020868_5_158.2ppm [TC00504137_D11]


title: BEAS-2B_DTXSID6021874_5_3.1ppm [TC00504137_D10]

value: 3.1 ppm 1-Bromopropane

value: 3.1 ppm


title: BEAS-2B_DTXSID6021874_5_3.1ppm [TC00504137_D09]


title: BEAS-2B_DTXSID0021383_5_31.6ppm [TC00504137_D07]

value: 31.6 ppm Trichloroethylene


title: BEAS-2B_DTXSID6021874_5_3.1ppm [TC00504137_D08]


title: BEAS-2B_DTXSID0021383_4_10ppm [TC00504137_E05]


title: BEAS-2B_DTXSID0021383_5_31.6ppm [TC00504137_D06]


title: BEAS-2B_DTXSID8020250_5_15.9ppm [TC00504137_D03]

value: 15.9 ppm Carbon Tetrachloride


title: BEAS-2B_DTXSID0021383_5_31.6ppm [TC00504137_D05]


title: BEAS-2B_DTXSID8020250_5_15.9ppm [TC00504137_D04]


title: BEAS-2B_DTXSID0021383_5_31.6ppm [TC00504137_C06]


title: BEAS-2B_DTXSID0020868_5_158.2ppm [TC00504137_C12]

value: Dichloromethane


title: BEAS-2B_DTXSID6021874_5_3.1ppm [TC00504137_C08]


title: BEAS-2B_DTXSID6021874_5_3.1ppm [TC00504137_C09]


title: BEAS-2B_DTXSID8020250_5_15.9ppm [TC00504137_C03]


title: BEAS-2B_DTXSID0020868_5_158.2ppm [TC00504137_C13]


title: BEAS-2B_DTXSID6021874_5_3.1ppm [TC00504137_C10]


title: BEAS-2B_DTXSID0020868_5_158.2ppm [TC00504137_C11]


title: BEAS-2B_DTXSID0021383_5_31.6ppm [TC00504137_C07]


title: BEAS-2B_Untrtd [TC00504137_O02]

value: NA NA NA

value: NA NA


title: BEAS-2B_DTXSID0021383_5_31.6ppm [TC00504137_C05]

value: Trichloroethylene


title: BEAS-2B_DTXSID8020250_5_15.9ppm [TC00504137_C04]


title: BEAS-2B_DTXSID8020250_5_15.9ppm [TC00504137_C02]


title: BEAS-2B_DTXSID0020868_6_500ppm [TC00504137_B12]

value: 500 ppm Dichloromethane

value: 500 ppm


title: BEAS-2B_Clean_Air [TC00504137_M02]

value: 0 ppm NA

value: 0 ppm


title: BEAS-2B_DTXSID0020868_6_500ppm [TC00504137_B11]


title: BEAS-2B_DTXSID0020868_6_500ppm [TC00504137_B13]


title: BEAS-2B_DTXSID6021874_6_10ppm [TC00504137_B10]

value: 10 ppm 1-Bromopropane

value: 10 ppm


title: BEAS-2B_DTXSID6021874_6_10ppm [TC00504137_B09]


title: BEAS-2B_DTXSID8020250_5_15.9ppm [TC00504137_D02]

value: Carbon Tetrachloride


title: BEAS-2B_DTXSID6021874_6_10ppm [TC00504137_B08]


title: BEAS-2B_DTXSID0021383_6_100ppm [TC00504137_B07]

value: 100 ppm Trichloroethylene

value: 100 ppm


title: BEAS-2B_DTXSID0021383_6_100ppm [TC00504137_B06]


title: BEAS-2B_DTXSID0021383_6_100ppm [TC00504137_B05]


title: BEAS-2B_DTXSID8020250_6_50ppm [TC00504137_B03]

value: 50 ppm Carbon Tetrachloride

value: 50 ppm


title: BEAS-2B_DTXSID8020250_6_50ppm [TC00504137_B04]


title: BEAS-2B_DTXSID0020868_6_500ppm [TC00504137_A12]


title: BEAS-2B_DTXSID6021874_6_10ppm [TC00504137_A09]


title: BEAS-2B_DTXSID8020250_6_50ppm [TC00504137_A03]


title: BEAS-2B_DTXSID0021383_6_100ppm [TC00504137_A05]


title: BEAS-2B_DTXSID0020868_6_500ppm [TC00504137_A11]


title: BEAS-2B_DTXSID8020250_6_50ppm [TC00504137_A02]


title: BEAS-2B_DTXSID0020868_6_500ppm [TC00504137_A13]


title: BEAS-2B_DTXSID0021383_6_100ppm [TC00504137_A06]


title: BEAS-2B_DTXSID6021874_6_10ppm [TC00504137_A08]


title: BEAS-2B_DTXSID6021874_6_10ppm [TC00504137_A10]


title: HBEC_Untrtd [TC00504136_O12]

source_name: HBEC

value: HBEC


title: HBEC_Untrtd [TC00504136_O13]


title: HBEC_Untrtd [TC00504136_O11]


title: HBEC_Untrtd [TC00504136_O10]


title: HBEC_Untrtd [TC00504136_O08]


title: HBEC_Untrtd [TC00504136_O09]


title: HBEC_Untrtd [TC00504136_O07]


title: HBEC_Untrtd [TC00504136_O06]


title: HBEC_Untrtd [TC00504136_O05]


title: HBEC_Untrtd [TC00504136_O04]


title: BEAS-2B_DTXSID8020250_6_50ppm [TC00504137_B02]


title: HBEC_Untrtd [TC00504136_O02]


title: BEAS-2B_DTXSID0021383_6_100ppm [TC00504137_A07]