title: KO_LP

city: St. Louis

first: Marco

last: Colonna

state: Missouri

address: 425 S. Euclid

department: Pathology and Immunology

institute: Washington University in St. Louis

description: Hobit KO, lamina propria ILC1 and NK cells

data_processing:
Cell ranger was used to align samples to the reference mm10 genome and generate gene-cell expression matrices.
Genome_build: mm10
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes, and file with expressed genes. Files are ready to be imported to Seurat package.

source_name: lamina propria lymphocytes

growth_protocol: Mice were housed under specific-pathogen-free conditions with free access to autoclaved food and water and were maintained on a 12h light/dark cycle.

extract_protocol:
Mice were perfused with 1x PBS by cardiac puncture prior to harvesting tissues. Single-cell suspension of spleen and liver were obtained by pushing tissues through 70mm filters. Salivary glands were first finely minced, then digested with collagenase D for 15 minutes at 37C with shaking. Digested contents were filtered through 70mm filters and subjected to density gradient using 40% and 70% Percoll. Small intestines were flushed and Peyer’s patches were removed. Then, small intestine were sliced and agitated in HBSS, HEPES, EDTA and BCS followed by collagenase IV digestion. Digested contents were filtered through 70mm filters and subjected to density gradient using 40% and 70% Percoll.
cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps.  Purified cDNA was amplified for 11-13 cycles before being cleaned up using SPRIselect beads.  Samples were then run on a Bioanalyzer to determine the cDNA concentration.  GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits User Guide (v3.1 Chemistry Dual Index) with appropriate modifications to the PCR cycles based on the calculated cDNA concentration.  For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell 3’ Kit v3.1, 16 rxns (PN-1000268), Chromium Next GEM Chip G Single Cell  Kit, 48 rxns (PN-1000120), and Dual Index Kit TT Set A, 96 rxns (PN-1000215) were used.  The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.  Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 28x10x10x150 sequencing recipe according to manufacturer protocol.  A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression Library.

value: zfp683 flox/flox; Ncr1-Cre

value: 8 weeks old

value: lamina propria lymphocytes


title: LG73_154_F_WT

status: Public on Dec 06 2021

type: SRA

city: San Francisco

first: Lay

last: Kodama

state: CA

address: 1650 Owens St.

department: Gladstone Institute of Neurological Disease

country: USA

institute: University of California San Francisco

description:
mRNA expression in hippocampal tissue
counts hippocampus.xlsx

library_source: transcriptomic

data_processing:
Reads were mapped with the Bluebee Genomics Platform and using the GENCODE  mouse genome GRCm38
Counts  were normalized with the trimmed mean normalization method
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw read counts in xlsx format

molecule: total RNA

organism: Mus musculus

source_name: hippocampal tissue

extract_protocol:
RNeasy mini kit (Qiagen, 74104) was used for RNA isolation and Oligo(dT) beads were used to enrich for mRNA
cDNA library generation was done using Novogene

tag: tissue

value: hippocampal tissue

tag: Sex

value: Female

tag: genotype


title: HEC108_ki47_postIP

city: Suita

first: Atsushi

last: Kumanogoh

state: Osaka

address: 2-2 Yamadaoka

country: Japan

institute: Osaka University

data_processing:
The adapter sequence was trimmed by trim_galore. Remaining trimmed reads were aligned to the human genome hg19 by tophat (v.2.1.1). The m6A-enriched peaks were detected by the MetPeak R package (v1.0.0) with default parameters as previously described (DOI: 10.1093/bioinformatics/btw281).
Genome_build: hg19
Supplementary_files_format_and_content: Bed files were created by MetPeak.

organism: Homo sapiens

source_name: endometrial cancer cell

growth_protocol: The cells were cultured in Dulbecco's modified Eagle medium containing 10% fetal bovine serum (Gibco) and 1% penicillin/streptomycin (Gibco). The cells were maintained at 37°C under a humidified atmosphere containing 5% CO2.

extract_protocol:
MeRIP-Seq was conducted as described previously (DOI: 10.1038/s41593-018-0173-6; 10.1016/j.cell.2012.05.003.) with some modifications. Briefly, total RNA was extracted with QIAZol Lysis Reagent (79306; QIAGEN) and purified using GenElute™ mRNA Miniprep Kits (MRN70, Sigma) twice. The recovered poly(A) RNA was fragmented with NEBNext Magnesium RNA Fragmentation Module (E6150S, NEB) with an incubation time of 11 min. Twenty micrograms of the fragmented RNA was incubated with 10 μg of anti-m6A antibody (202203, Synaptic Systems).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

tag: rip antibody

value: 202203, Synaptic Systems


title: A1-p1-NTG_232_mouse_Trem2_WT

description:
Sample3
mRNA expression in microglia

data_processing:
Prinseq (version 0.20.4) was first used to filter sequencing reads shorter than 30 bp (-min_len 30), trim the first 10 bp at the 5’-end (-trim_left 10) of the reads, trim reads with low quality from the 3’-end (-trim_qual_right 25) and remove low complexity reads (-lc_method entropy, -lc_threshold 65).
Trim Galore (version 0.4.3) was applied to trimmed the Nextera adapters (--stringency 1).
The remaining reads were aligned to the mm10 genome by calling STAR (version 2.5.3a) with the following options: --outFilterType BySJout, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.04, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outSAMstrandField intronMotif.
Picard was then used to remove the duplicate reads (VALIDATION_STRINGENCY=LENIENT, REMOVE_DUPLICATES=true).
The aligned reads were converted to counts for each gene by using HTSeq (-m intersection-nonempty, -s no)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited file (tsv) containing 1480 samples and mapped raw gene counts.

source_name: FACS isolated adult microglia

extract_protocol:
In online methods
Smart-Seq2 protocol (in online methods)

tag: trem2 species

value: mouse

tag: p301s status

value: no

tag: brain region

value: hippocampus

value: female

tag: gate

tag: cell type

value: microglia


title: HEC108_ki47_preIP


title: R4 Continuous CAR- T1 [RNA-seq]

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

description:
CD8.CS.CAR-.R4.1
TPMs_-_Presence.txt

data_processing:
Alignment: paired-end data were aligned to human genome assembly GRCh37/hg19 using STAR v2.5.2a with command-line parameters --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000
Post-processing: SAM files were converted to BAM format using samtools v1.1 (samtools view -bS)
Sorting: BAM files were sorted by position using samtools sort
Pooling of resequenced libraries: for replicate R2, several resequenced libraries were pooled after alignment to enhance coverage. This was accomplished using samtools merge as below:    R2 Control Day 0 CAR+ T1 - 4-Day0-CD8-CARpos_S7 with 16-Day0-CD8-CARpos_S5    R2 Control Day 0 CAR- T1 - 3-Day0-CD8-CARneg_S2 with 15-Day0-CD8-CARneg_S6    R2 Other CAR+ T1 - 21-IS-CD8-CARpos-10-24-2018_S11 with 12-IS-CD8-CARpos_S12 and 24-IS-CD8-CARpos_S10    R2 Continuous CAR+ T1 - 8-CS-CD8-CARpos_S9 with 20-CS-CD8-CARpos_S12    R2 Continuous CAR- T1 - 7-CS-CD8-CARneg_S6 with 19-CS-CD8-CARneg_S3
Tag counts per gene model: HTSeq v0.6.0 was used to count aligned tags over gene features with command-line python -m HTSeq.scripts.count -f bam -r pos -s no -t exon -i gene_id BAM_FILE GTF. The gene model GTF was constructed from RefSeq transcripts and UCSC Genome Browser's annotation of RefSeq transcript IDs to gene symbols.
Library size adjustment and significance testing: for the antigen exposure and time series analysis, DESeq2 was used to adjust library size and estimate significant differences at an FDR of 0.05.    Antigen exposure analysis: the Wald test was used to assess differences between control day 0 samples and continuous exposure samples. For this analysis we considered only CAR+ samples including control day 0, "other," and continuous exposure, with no day 16 time points. "Other" samples were included to adjust dispersions and library sizes but were not used for the contrast.    Time series analysis: the LRT was used to assess differences along the time course from day 0 to day 16 to day 28, with a full model of ~Replicate+Time and a reduced model of ~Replicate. For this analysis we considered only CAR+ samples including control day 0 and continuous exposure, with no "other" exposure.
Additional filtering: for the antigen exposure analysis, we removed genes which register as significantly different but which we expect to be artifacts due to SMART-seq's library construction; such genes fall along the extreme ends of a parabola in a volcano plot of the data. To remove these, we interpolated a line on the plot between IL22 and WDR63 (negative side) and another between ALK and INBHE (positive side). Any gene with a perpendicular < 1 to the lines was removed.
TPM calculation: to contrast CAR+ and CAR- samples, we calculated TPMs for each gene using the bioinfokit.analys module in python. Gene lengths were calculated from the GTF used to run HTSeq, taking the max of all summed exon lengths across multiple isoforms to be the length of each gene.
Genome_build: hg19
Supplementary_files_format_and_content: We include three tables of adjusted count data and two companion tables with DESeq2 significance testing results. For the antigen exposure analysis, we include the DESeq2 adjusted counts and DESeq2 significance results after processing to flag genes we deemed to be artifacts ("Additional filtering" above). For the time series analysis, we include the DESeq2 adjusted counts and DESeq2 significance results. For the CAR+ / CAR- analysis, we include a table of TPMs for all genes.

source_name: M5CAR T cells (PBMCs)

growth_protocol: Primary human CD4+ T and CD8+ T cells from normal donors were provided by University of Pennsylvania Human Immunology Core. CAR T cells were generated as previously described (Carpenito et al., 2009). Briefly, CD4+ and CD8+ T at 1:1 ratio at 1 x 10e6 cells/ml were activated with Dynabeads CD3/CD28 CTSTM (Gibco, Life Technologies) at a 3:1 bead-to-cell ratio. Approximately after 24 hours, T cells were transduced at a multiplicity of infection (MOI) of 5. At day 5 beads were removed from cultures. T cell cultures were maintained at 8 x 10e5 cells/ml. Cell number and volume were monitored daily using Multisizer 4 Coulter Counter (Beckmanwaslter). Transduced T cells were cryopreserved when reached the resting state, as determined by cell size.

extract_protocol:
For flow cytometry and sorting assays of CAE, M5 CAR T cells were stained in fluorescence-activated cell sorting (FACS) buffer consisting of PBS (Gibco), 0.5% bovine serum albumin (BSA) (GEMINI), 2 mM EDTA (Invitrogen), and 100ug/ml DNase (Roche). CountBrightTM Absolute Counting Beads, (ThermoFisher) were used as an internal standard according to the manufacturer's instructions to calculate absolute cell counts in cell suspensions.  Antibodies specific for human CD45 (ref 304032, clone HI30), CD3 (317322, OKT3), CD4 (357412, A161A1 / 317440), CD56 (304608, MEM-188), EpCAM (324226/324238, 9C4), CD94 (305520, DX22), KLRB1 (339918, HP-3G10), TIGIT (372716, A15153G), TCR Va24-Ja18 (342922, 6B11), PD-1 (329928, EH12.2H7) were purchased from BioLegend. Antibodies specific for human CD8 (560179, SK1) was purchased from BD Pharmingen. Antibodies specific for human NKG2A (FAB1059P, 131411) and Methothelin (FAB32652P, 420411) were purchased from R&D Systems. Antibodies specific for human CTLA-4 (12-1529-42, 14D3) was purchased from eBioscience. Antibody specific for human NKG2C (130-103-636, REA205) was purchased from Miltenyi.  M5 CAR expression was assessed using biotinylated goat anti-human IgG F(ab’)2 (Jackson ImmunoResearch, 109-066-006) followed by streptavidin (FITC or APC) (BioLegend) or using an anti-idiotype antibody provided by Novartis Pharmaceuticals. Live/dead staining was performed using a Live/Dead Fixable Aqua Dead Cell Stain Kit (Life Technologies following manufacturer’s protocol followed by cell surface staining for 20 minutes at room temperature in the dark. Intracellular staining was performed with the Foxp3/Transcription Factor Staining Buffer set (Thermo Fisher) according to the manufacturer’s instructions. Samples were acquired on an LSRII Fortessa Cytometer (BD Bioscience) and analyzed with FlowJo v10 software (FlowJo, LLC). Sorting assays were performed using a FACS Aria Cytometer (BD Bioscience).    Total RNA was extracted using Qiazol (Qiagen) from 300 cells for day 0, day 16 or day 28 for CD8+ T cells continuously stimulated with antigen (two sorted populations including surface CAR-positive and surface CAR-negative cells). Cells were recovered by RNA Clean and Concentrator spin columns (Zymo), followed by incubation with oligo-dT. The transcription reaction was carried out on 100pg of cDNA for 1min at 55°C.
RNA-seq libraries were made following the previously established SMARTseq2 protocol (Picelli et al., 2014). Libraries were uniquely barcoded (Buenrostro et al., 2013) and amplified for 14 cycles. Fragment size distribution was verified and paired-end sequencing (2 x 75 bp reads) was carried out on an Illumina NextSeq 500.

treatment_protocol: AsPC-1 cells were routinely seeded in 6-well plates at 1 x 10e6 cells/well the day preceding T cell seeding. M5 CAR T cells (30 - 50% of transduction efficiency) were thawed and rested at 1 x 10e6 cells/ml in T75 flasks with R10 media. After 24 hours, the T cell number (CD45+EpCAM-) was calculated and 2.5 x 10e5 T cells/well were transferred to the AsPC-1 plates. After 3 - 4 days, the cocultures were thoroughly suspended by frequent pipetting and 300 - 400µl of the cell suspension was used for T cell counting assessment and flow cytometry staining. The remaining cell suspension was spun down and the supernatant (conditioned media) was collected and filtered with a 0.45µm filter (Corning). The cells were resuspended in media containing equal amounts of conditioned and fresh R10. The resulting T cell suspension was transferred into AsPC-1-coated plates cells (2.5 x 10e5 T cells/well) for continuous co-culture. This process was repeated for 20-35 days.

tag: replicate

tag: car presence

value: Absent

tag: antigen exposure

value: Continuous

tag: time

value: Day 28


title: HEC108_ki91_preIP


title: HEC108_ki778_postIP


title: A1-p1-K1_243_human_TREM2_R47H_het

description:
Sample2
mRNA expression in microglia

value: human


title: R5 Control Day 0 CAR+ T1 [RNA-seq]

description:
CD8.D0.CAR+.R5.1
Adjusted_Counts_-_Exposure.txt
TPMs_-_Presence.txt
Adjusted_Counts_-_Time_Series.txt
DESeq2_Results_-_Exposure.txt
DESeq2_Results_-_Time_Series.txt

value: Present

value: Control

value: Day 0


title: R4 Day 16 CAR+ T1 [RNA-seq]

description:
CD8.D16.CAR+.R4.1
Adjusted_Counts_-_Time_Series.txt
DESeq2_Results_-_Time_Series.txt

value: Day 16


title: R4 Continuous CAR+ T2 [RNA-seq]

description:
CD8.CS.CAR+.R4.2
Adjusted_Counts_-_Exposure.txt
TPMs_-_Presence.txt
Adjusted_Counts_-_Time_Series.txt
DESeq2_Results_-_Exposure.txt
DESeq2_Results_-_Time_Series.txt


title: WT_LP

description: wild type, lamina propria ILC1 and NK cells

tag: strain

value: wild type

tag: age

value: 8 weeks old

value: lamina propria lymphocytes


title: KO_SG

description: Hobit KO, salivary gland ILC1 and NK cells

source_name: salivary gland lymphocytes

value: zfp683 flox/flox; Ncr1-Cre

value: salivary gland lymphocytes


title: R4 Continuous CAR+ T1 [RNA-seq]

description:
CD8.CS.CAR+.R4.1
Adjusted_Counts_-_Exposure.txt
TPMs_-_Presence.txt
Adjusted_Counts_-_Time_Series.txt
DESeq2_Results_-_Exposure.txt
DESeq2_Results_-_Time_Series.txt


title: LG73_145_F_WT

value: hippocampal tissue

value: Female


title: Arrb2KO-envA5d-1

city: Boston

first: David

last: Brann

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

description:
10x genomics, v3.1
Arrb2KO_umi_counts.csv.gz
Arrb2KO_metadata.csv.gz

data_processing:
Demultiplexed fastq files were generated by mkfastq function in Cell Ranger software. Demultiplexed fastq files were aligned to the mouse reference genome mm10 (Ensembl 93) and converted into bam files using the 10x Genomics Cell Ranger software (version 2.2.0 (v2 and v3 samples) or 4.0.0 (v3.1 samples))
multimapped reads were filtered out by removing any read in the possorted_genome_bam.bam file with a MM:i:1 tag. UMIs in which separate reads were uniquely mapped to different genes were removed. The gene expression matrix was then recomputed by counting the number of distinct UMIs for each cell barcode for each gene.
mature olfactory sensory neurons (OSNs) were identified via iterative subclustering in Scanpy, and any mature OSN expressing a single OR (detected in at least 2-3 UMIs) were kept
Genome_build: Ensembl Rel 93 (GRCm38.p6)
Supplementary_files_format_and_content: <EXPT>_umi_counts.csv.gz: UMI counts for each gene for each mOSN used (cells x genes)  <EXPT>_metadata.csv.gz: Metadata for each cell, including which OR was expressed  Dataset_raw_file_names.csv.gz: Description of each replicate, and name of raw bam file, as well as the corresponding counts and metadata files.  Table_S1_datasets.csv.gz: Summary of single cell RNA-seq datasets for mature olfactory sensory neurons used in this study.  Table_S2_nmf_loadings.csv.gz: Loadings of 1,350 highly variable genes for 16 gene expression programs identified by consensus non-negative matrix factorization of the home cage dataset.  Table_S3_ES_neuronal_genes.csv.gz: 117 environmental state genes that have putative neuronal functions, including 73 genes with putative functions that affect sensory responses.  Table_S4_delta_ES_neuronal_gene_expression.csv.gz: Changes in z-scored expression of 117 environmental state genes for each OSN subtype across conditions.  Table_S5_activation_genes.csv.gz: 472 acute odor response-dependent genes used to calculate activation score. 8 values that characterize 472 genes that were used to calculate activation score are shown. Columns are as follows: “activation_score_loading”: gene loading for calculating activation score. “ess_correlation”: Spearman's rho between normalized expression and environmental state score in the home cage dataset on OR-by-OR basis. “p_adj_ACE2h”: FDR corrected p-values for the differential expression (via Wilcoxon signed-rank test) between control and acetophenone 2h samples for acetophenone responsive ORs on OR-by-OR basis. “ctl_expr_ACE2h”: Normalized mean expression for OSNs expressing-acetophenone responsive ORs in the control data. “expression_ACE2h”: Normalized mean expression for OSNs expressing acetophenone responsive ORs in the acetophenone 2h data. “p_adj_OCT2h”, “ctl_expr_OCT2h”, “expression_OCT2h”: same as the previous 3 columns for acetophenone responsive ORs, but for OSNs expressing octanal-responsive ORs.

source_name: whole olfactory mucosa

extract_protocol:
The main olfactory epithelium was dissected and cleaned up in the Earle’s Balanced Salt Solution (EBSS, pre-treated with carbogen for at least 5 minutes before each use, Worthington), then transferred to a round-bottomed glass dish containing 750 µL of papain solution (one vial of Papain, (Worthington) dissolved in 5 mL of EBSS and then equilibrated 10 minutes at 37 °C) and 100 µL of DNase solution (one vial of DNase-I (Worthington) dissolved in 500 µL of EBSS). Bone was removed from the epithelium under a dissecting microscope and the resultant tissue was placed in a 5 mL tube (Becton Dickinson) with an additional 1.75 mL of Papain solution and 200 µL of DNase-I solution and rocked gently for ~60 minutes at 37 °C. The tissue was then gently triturated with a 5 mL pipette 10-15 times, passed through a 40 µm cell strainer (Becton Dickinson), and washed with 1 mL of Hibernate-A medium containing 10 % Fetal Bovine Serum (FBS, GIBCO). Filtered cells were transferred to a new 5 mL tube and centrifuged 5 minutes at 300 x g. The supernatant was decanted, the cells were washed once with 4 mL Hibernate-A containing 10 % FBS and resuspended in 1 mL Hibernate-A containing 0.2 % FBS. Each of the solutions above contained transcriptional inhibitors (5 µg/mL of Actinomycin D, 10 µg/mL of Anisomycin and 10 µM of Triptolide, all obtained from Sigma) for all experiments, except where noted (Table S1). Dissociated cells were stained with propidium iodide (final concentration 1.65 µg/mL), and subject to FACS to remove dead cells and obvious doublets. For GFP-expressing mouse lines (OMP-IRES-GFP, P2(P2 locus), M72(S50 locus) and S50(M72 locus)), GFP positive and negative cells were sorted separately using a FITC filter. Cells were sorted into Hibernate-A containing 5 % FBS (also include 0.1x of transcriptional inhibitors), centrifuged for 5 minutes at 300 g, and resuspended with PBS.
Prepared single cell suspensions were used to prepare single cell RNA-seq library with the chromium single cell gene expression system (chromium single cell 3’ reagents and GEM v2, v3 or v3.1 dual index, 10x genomics), using the default protocols provided by 10x genomics. Each of the replicates other than GFP-positive ones was aimed to have 10,000 cells. The expected multiplet rate is ~8.0 %.
single cell 3' end RNA-seq

value: whole olfactory mucosa

value: 6-12 weeks


title: HEC108_ki747_postIP

value: 202203, Synaptic Systems


title: LG73_144_F_WT


title: A1-p1-K1_241_human_TREM2_R47H_het

description:
Sample1
mRNA expression in microglia

value: no

value: hippocampus

value: female

value: microglia


title: HEC108_ki778_preIP


title: WT_SG

description: wild type, salivary gland ILC1 and NK Cells


title: HEC108_ki747_preIP


title: R4 Other CAR+ T1 [RNA-seq]

description:
CD8.IS.CAR+.R4.1
Adjusted_Counts_-_Exposure.txt
DESeq2_Results_-_Exposure.txt

value: Present

value: Other

value: Day 28


title: R4 Other CAR+ T2 [RNA-seq]

description:
CD8.IS.CAR+.R4.2
Adjusted_Counts_-_Exposure.txt
DESeq2_Results_-_Exposure.txt


title: LG73_132_F_WT


title: KO_liver

description: Hobit KO, liver ILC1 and NK cells

source_name: liver lymphocytes

value: liver lymphocytes


title: HEC108_ki732_postIP


title: R4 Control Day 0 CAR- T2 [RNA-seq]

description:
CD8.D0.CAR-.R4.2
TPMs_-_Presence.txt

value: Absent

value: Control

value: Day 0


title: HEC108_ki732_preIP


title: LG73_106_F_WT


title: WT_liver

description: wild type, liver ILC1 and NK cells

value: wild type

value: 8 weeks old


title: LG73_98_F_Trem2

value: hippocampal tissue

value: Female


title: HEC108_ki071_postIP


title: R4 Control Day 0 CAR+ T2 [RNA-seq]

description:
CD8.D0.CAR+.R4.2
Adjusted_Counts_-_Exposure.txt
TPMs_-_Presence.txt
Adjusted_Counts_-_Time_Series.txt
DESeq2_Results_-_Exposure.txt
DESeq2_Results_-_Time_Series.txt


title: R4 Control Day 0 CAR- T1 [RNA-seq]

description:
CD8.D0.CAR-.R4.1
TPMs_-_Presence.txt


title: LG73_96_F_Trem2


title: Vagus nerve, single nuclei RNA-seq vagus2

city: St Louis

first: Jeffrey

last: Milbrandt

address: 660 S Euclid Ave #5101

department: Genetics

institute: Washington University School of Medicine

description:
peripheral-nerves_single-nuclei-atlas-22Jan2021.RDS
peripheral-nerves-Schwann-cell-specific_single-nuclei-atlas-8Feb2021.RDS

data_processing:
Demultiplexed by bcl2fastq
The reads were then aligned to mouse genome mm10 using Cell Ranger v3.0.2 from 10X Genomics. As nuclei contain mostly pre-mRNA with intron retention, over 40% of the mapped reads were at introns. We therefore incorporated both intronic and exonic reads during the analysis and then determined the UMI counts for each gene. The first QC step involved the removal of nuclei with less than 500 genes and genes seen in 10 or fewer nuclei, the second QC step involved the removal of nuclei with high mitochondrial content (>5%). The expression matrix of individual library was then normalized and scaled based on the UMI counts and mitochondria percentage. Highly variable genes were identified by using FindVariableGenes function in Seurat and subjected to downstream analysis. For sciatic nerve atlas generated from Sun1-GFP/+;ActB-Cre/+ mice as well as peripheral nerve atlas that combined three nerve types, the batch effect was corrected by using DeepImpute and Seurat multi-CCA. For Mpz-nuclei atlas generated from Sun1-GFP/+;Mpz-Cre/+ mice and vagus nerve atlas generated from Sun1-GFP/+;ActB-Cre/+ mice, the batch effect was corrected by CCA. For peroneal nerve atlas generated from Sun1-GFP/+;ActB-Cre/+ mice, only one library was generated and hence principal component analysis (PCA) was performed and PCA dimensions were used for downstream analysis. As the third QC step, we calculated the ratio of variance explained by CCA and removed nuclei with inconsistent lower dimensional CCA information, which were likely to be caused by doublets or nuclei rupture during the nuclei capture step in creating the single nucleus libraries. Clustering analysis was then performed by using shared nearest neighbor (SNN) modularity optimization approach with at least 100 random starts and 100 iterations. Data visualization was performed using t-SNE. For cell trajectory analysis, the normalized matrix was imported to Monocle and cell trajectory analysis was performed. The analyses were done by using customized R code, Seurat (v3.2.3), DeepImpute (Apr2020), Monocle (v2.9.0) and Python3.6.
Users are highly recommended to extract the reads from BAM files and redo the alignment using the latest reference and tools
Genome_build: mm10
Supplementary_files_format_and_content: RDS

molecule: nuclear RNA

source_name: Nuclei isolated from vagus nerves

extract_protocol:
For sciatic nerve snRNA-seq libraries, 2 male and 2 female mice were pooled for each experiment. For vagus nerve snRNA-seq libraries, were prepared from a pool of 9 male and 9 female mice. For peroneal and sural nerve snRNA-seq libraries, 5 male and 5 female mice were pooled for each experiment. Upon dissection, the nerves were immediately transferred to digestion media containing 0.3% collagenase IV (Sigma Aldrich C5138), 0.04% hyaluronidase (Sigma Aldrich H3506) and 0.04% DNase I (Sigma Aldrich DN25)  for 10-15 min at 37C. The cells were filtered through 70 um cell strainers and washed twice with cold 5% PBS containing 0.1% BSA, RNaseIn and SuperaseIn. Cells were mechanically dissociated using a Dounce homognizer on ice; media for mechanical dissociation was prepared according to Krishnaswami’s protocol87. The nuclei and cellular debris were filtered through 40 um cell strainers and washed with cold 5% PBS containing 0.1% BSA, RNaseIn (Ambion AM2682) and SuperaseIn (Invitrogen AM2694) and the debris was removed from the nuclei by immediate FACS sorting. The purified nuclei were used to prepare single nuclei RNA-seq libraries following manufacturer’s instructions (10X Genomics). A total of 11 single nuclei libraries were prepared: 5 libraries from sciatic nerves from Sun1-GFP/+:ActB-Cre/+ mice; 2 libraries from sciatic nerves from Sun1-GFP/+:Mpz-Cre/+ mice; 2 libraries from vagus nerves from Sun1-GFP/+:ActB-Cre/+ mice; 1 library from peroneal nerves dissected from Sun1-GFP/+:ActB-Cre/+ mice; 1 library from sural nerves dissected from Sun1-GFP/+:ActB-Cre/+ mice.
10X genomics single-cell and single-nuclei RNA-seq libraries
single-cell and single-nuclei RNA-seq
bam files contain reads generated by both instruments HiSeq2500 / NovaSeq6000

tag: treatment

value: vagus nerves

tag: sample type

value: single nuclei RNA


title: Vagus nerve, single nuclei RNA-seq vagus1

tag: tissue


title: LG73_136_F_WT

tag: Sex

tag: genotype


title: HEC108_ki071_preIP

tag: cell line

tag: rip antibody

value: 202203, Synaptic Systems


title: R3 Continuous CAR- T2 [RNA-seq]

description:
CD8.CS.CAR-.R3.2
TPMs_-_Presence.txt

value: Continuous


title: HEC108_ki045_preIP


title: Sciatic nerve, single nuclei RNA-seq SNC2

description:
peripheral-nerves-Schwann-cell-specific_single-nuclei-atlas-8Feb2021.RDS
peripheral-nerves_single-nuclei-atlas-22Jan2021.RDS
schwann_cell_single-nuclei-atlas-12Jan2021.RDS
sciatic-nerve_single-nuclei-atlas-16Dec2020.RDS

source_name: Nuclei isolated from sciatic nerves

value: sciatic nerves


title: HEC108_ki045_postIP


title: R4 Control Day 0 CAR+ T1 [RNA-seq]

description:
CD8.D0.CAR+.R4.1
Adjusted_Counts_-_Exposure.txt
TPMs_-_Presence.txt
Adjusted_Counts_-_Time_Series.txt
DESeq2_Results_-_Exposure.txt
DESeq2_Results_-_Time_Series.txt


title: LG72_94_M_R47H

value: Male


title: HEC108_ki042_postIP


title: Sural nerve, single nuclei RNA-seq sural

source_name: Nuclei isolated from sural nerves

value: sural nerves


title: Sciatic nerve, single nuclei RNA-seq SNC1


title: LG73_94_F_Trem2


title: R3 Continuous CAR+ T2 [RNA-seq]

description:
CD8.CS.CAR+.R3.2
Adjusted_Counts_-_Exposure.txt
TPMs_-_Presence.txt
Adjusted_Counts_-_Time_Series.txt
DESeq2_Results_-_Time_Series.txt

value: Present


title: R3 Continuous CAR- T1 [RNA-seq]

description:
CD8.CS.CAR-.R3.1
TPMs_-_Presence.txt

value: Day 28


title: R3 Continuous CAR+ T1 [RNA-seq]

description:
CD8.CS.CAR+.R3.1
Adjusted_Counts_-_Exposure.txt
TPMs_-_Presence.txt
Adjusted_Counts_-_Time_Series.txt
DESeq2_Results_-_Time_Series.txt


title: LG72_72_M_R47H

description:
mRNA expression in hippocampal tissue
counts hippocampus.xlsx


title: LG72_124_M_R47H


title: 2466-2 _CD4_ BCG

city: San Diego

first: Paige

last: Dubelko

address: 9420 Athena Circle

institute: La Jolla Institure for Immunology

description:
all_counts.tsv
Mtb14_107

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were mapped against the human GRCh38 reference using Tophat v1.4.1 (--library-type fr-firststrand)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Genome_build: GRCh38
Supplementary_files_format_and_content: count matrix with rows as genes and columns as samples

extract_protocol:
Total RNA was purified using an miRNeasy Micro Kit (QIAGEN) and quantified by quantitative PCR. Purified total RNA (1-5 ng) was amplified following the Smart-Seq2 protocol.
mRNA was captured using poly-dT oligonucleotides and directly reverse transcribed into full-length cDNA (amplified by PCR for 16 cycles). cDNA was purified using AMPure XP beads (Beckman Coulter). From this step, 1 ng of cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina). Whole-transcriptome amplification and sequencing library preparations were performed in a 96-well format to reduce assay-to-assay variability. Barcoded Illumina sequencing libraries (Nextera, Illumina) were generated using the automated platform (Biomek FXp). Libraries were sequenced on a HiSeq 2500 Illumina platform to obtain 50-bp single-end reads (TruSeq Rapid kit; Illumina).

treatment_protocol: PBMCs were stimulated with a Mtb-derived epitope pool (MTB300), BCG bacteria, or left unstimulated for 24 hours before sorting.

tag: stimulation

value: BCG

tag: bcg state

value: post


title: Sciatic nerve, single nuclei RNA-seq SN3


title: Sciatic nerve, single nuclei RNA-seq SN2


title: R3 Other CAR+ T2 [RNA-seq]

description:
CD8.IS.CAR+.R3.2
Adjusted_Counts_-_Exposure.txt

value: Other


title: LG72_63_M_R47H


title: 2466-2 _CD4_ MTB300

description:
all_counts.tsv
Mtb14_106


title: R3 Other CAR+ T1 [RNA-seq]

description:
CD8.IS.CAR+.R3.1
Adjusted_Counts_-_Exposure.txt


title: LG72_88_M_Trem2


title: Peroneal nerve, single nuclei RNA-seq peroneal

source_name: Nuclei isolated from peroneal nerves

value: peroneal nerves


title: HEC108_ki042_preIP


title: Sciatic nerve, single nuclei RNA-seq SN1


title: 2466-2 _CD4_ unstim

description:
all_counts.tsv
Mtb14_105

value: Unstim


title: LG72_49_M_R47H


title: Sciatic nerve, Mpz-Sun1 single nuclei RNA-seq S2

description:
schwann_cell_single-nuclei-atlas-12Jan2021.RDS
peripheral-nerves-Schwann-cell-specific_single-nuclei-atlas-8Feb2021.RDS

source_name: Mpz-Cre:Sun1-GFP + cells from sciatic nerve

value: Mpz-Cre:Sun1-GFP + cells


title: R3 Control Day 0 CAR- T2 [RNA-seq]

description:
CD8.D0.CAR-.R3.2
TPMs_-_Presence.txt

value: Absent

value: Control

value: Day 0


title: Sciatic nerve, Mpz-Sun1 single nuclei RNA-seq S1r

value: single nuclei RNA


title: 2466-2_PMBC_MTB300

description:
all_counts.tsv
Mtb14_102

source_name: PBMC

value: PBMC


title: LG72_70_M_Trem2

value: hippocampal tissue


title: 2466-2_PMBC_BCG

description:
all_counts.tsv
Mtb14_103


title: R3 Control Day 0 CAR+ T2 [RNA-seq]

description:
CD8.D0.CAR+.R3.2
Adjusted_Counts_-_Exposure.txt
TPMs_-_Presence.txt
Adjusted_Counts_-_Time_Series.txt
DESeq2_Results_-_Time_Series.txt


title: LG72_126_F_Trem2

value: Female


title: Sciatic nerve, CD45+ single cell RNA-seq

description: immune-cell_single-cell-atlas-15Jan2021.RDS

source_name: Immune cells from sciatic nerves

value: sciatic nerves

value: immune cells

value: single cell RNA


title: baseline-ON-2

description:
10x genomics, v3.1
envA_timecourse_umi_counts.csv.gz
envA_timecourse_metadata.csv.gz

extract_protocol:
The main olfactory epithelium was dissected and cleaned up in the Earle’s Balanced Salt Solution (EBSS, pre-treated with carbogen for at least 5 minutes before each use, Worthington), then transferred to a round-bottomed glass dish containing 750 µL of papain solution (one vial of Papain, (Worthington) dissolved in 5 mL of EBSS and then equilibrated 10 minutes at 37 °C) and 100 µL of DNase solution (one vial of DNase-I (Worthington) dissolved in 500 µL of EBSS). Bone was removed from the epithelium under a dissecting microscope and the resultant tissue was placed in a 5 mL tube (Becton Dickinson) with an additional 1.75 mL of Papain solution and 200 µL of DNase-I solution and rocked gently for ~60 minutes at 37 °C. The tissue was then gently triturated with a 5 mL pipette 10-15 times, passed through a 40 µm cell strainer (Becton Dickinson), and washed with 1 mL of Hibernate-A medium containing 10 % Fetal Bovine Serum (FBS, GIBCO). Filtered cells were transferred to a new 5 mL tube and centrifuged 5 minutes at 300 x g. The supernatant was decanted, the cells were washed once with 4 mL Hibernate-A containing 10 % FBS and resuspended in 1 mL Hibernate-A containing 0.2 % FBS. Each of the solutions above contained transcriptional inhibitors (5 µg/mL of Actinomycin D, 10 µg/mL of Anisomycin and 10 µM of Triptolide, all obtained from Sigma) for all experiments, except where noted (Table S1). Dissociated cells were stained with propidium iodide (final concentration 1.65 µg/mL), and subject to FACS to remove dead cells and obvious doublets. For GFP-expressing mouse lines (OMP-IRES-GFP, P2(P2 locus), M72(S50 locus) and S50(M72 locus)), GFP positive and negative cells were sorted separately using a FITC filter. Cells were sorted into Hibernate-A containing 5 % FBS (also include 0.1x of transcriptional inhibitors), centrifuged for 5 minutes at 300 g, and resuspended with PBS.
Prepared single cell suspensions were used to prepare single cell RNA-seq library with the chromium single cell gene expression system (chromium single cell 3’ reagents and GEM v2, v3 or v3.1 dual index, 10x genomics), using the default protocols provided by 10x genomics. Each of the replicates other than GFP-positive ones was aimed to have 10,000 cells. The expected multiplet rate is ~8.0 %.

value: whole olfactory mucosa

value: 6-12 weeks


title: R3 Control Day 0 CAR+ T1 [RNA-seq]

description:
CD8.D0.CAR+.R3.1
Adjusted_Counts_-_Exposure.txt
TPMs_-_Presence.txt
Adjusted_Counts_-_Time_Series.txt
DESeq2_Results_-_Time_Series.txt

value: Present


title: LG72_55_F_Trem2


title: R2 Continuous CAR- T1 [RNA-seq]

description:
CD8.CS.CAR-.R2.1
TPMs_-_Presence.txt

value: Continuous

value: Day 28


title: R2 Continuous CAR+ T1 [RNA-seq]

description:
CD8.CS.CAR+.R2.1
Adjusted_Counts_-_Exposure.txt
TPMs_-_Presence.txt
Adjusted_Counts_-_Time_Series.txt
DESeq2_Results_-_Exposure.txt
DESeq2_Results_-_Time_Series.txt


title: 1502-2 _CD4_ unstim

description:
all_counts.tsv
Mtb14_89

value: Unstim

value: post


title: 1502-2 _CD4_ MTB300

description:
all_counts.tsv
Mtb14_90


title: 1502-2 _CD4_ BCG

description:
all_counts.tsv
Mtb14_91

value: BCG


title: LG72_77_F_R47H


title: LG72_127_F_R47H


title: envB-DPG30m-2

description:
10x genomics, v3.1
env_switch_umi_counts.csv.gz
env_switch_metadata.csv.gz


title: HEC108_ki64_postIP

value: 202203, Synaptic Systems


title: LG72_59_F_R47H


title: envB-DPG30m-1


title: 1502-2_PMBC_MTB300

description:
all_counts.tsv
Mtb14_86


title: R3 Control Day 0 CAR- T1 [RNA-seq]

description:
CD8.D0.CAR-.R3.1
TPMs_-_Presence.txt

value: Absent

value: Control

value: Day 0


title: baseline-ON-1


title: R2 Other CAR+ T2 [RNA-seq]

description:
CD8.IS.CAR+.R2.2
Adjusted_Counts_-_Exposure.txt
DESeq2_Results_-_Exposure.txt

value: Other


title: LG72_101_F_Trem2

value: hippocampal tissue

value: Female


title: R2 Continuous CAR+ T2 [RNA-seq]

description:
CD8.CS.CAR+.R2.2
Adjusted_Counts_-_Exposure.txt
TPMs_-_Presence.txt
Adjusted_Counts_-_Time_Series.txt
DESeq2_Results_-_Exposure.txt
DESeq2_Results_-_Time_Series.txt


title: 1502-2_PMBC_unstim

description:
all_counts.tsv
Mtb14_85

value: PBMC


title: R2 Other CAR+ T1 [RNA-seq]

description:
CD8.IS.CAR+.R2.1
Adjusted_Counts_-_Exposure.txt
DESeq2_Results_-_Exposure.txt


title: LG72_54_F_R47H


title: envB-DPG2h-1


title: envB-DPG2h-2


title: R2 Control Day 0 CAR- T1 [RNA-seq]

description:
CD8.D0.CAR-.R2.1
TPMs_-_Presence.txt


title: LG72_53_F_R47H


title: envB-ACE2h-2


title: 1500-2 _CD4_ BCG

description:
all_counts.tsv
Mtb14_75


title: R2 Control Day 0 CAR+ T2 [RNA-seq]

description:
CD8.D0.CAR+.R2.2
Adjusted_Counts_-_Exposure.txt
TPMs_-_Presence.txt
Adjusted_Counts_-_Time_Series.txt
DESeq2_Results_-_Exposure.txt
DESeq2_Results_-_Time_Series.txt


title: envA-DPG30m-2


title: envB-ACE2h-1


title: esgTS Rep 3

city: Bloomington

first: Nick

last: Sokol

state: IN

address: 1001 E 3rd Street, Biology Building

institute: Indiana University

data_processing:
Quality trimming was performed using Cutadapt version 2.9.
Ribosomal RNA (rRNA) reads were removed using Tagdust2 version 2.2.
Remaining reads were aligned to the BDGP assembly release 6.28 (Ensembl release 100) reference genome using STAR version 2.7.3a.
Alignment output files were coordinate sorted and duplicated reades were removed using SAMtools version 1.10.
The Subread version 2.0.0 function featureCounts was used to count the number of aligned reads to the nearest overlapping feature.
Genome_build: BDGP assembly release 6.28 (Ensembl release 100)
Supplementary_files_format_and_content: CSV file containing raw read counts
Supplementary_files_format_and_content: CSV file containing differential gene expression results obtained using DESeq2
Supplementary_files_format_and_content: Bigwig files for genome browser visualization

organism: Drosophila melanogaster

source_name: Dissected intestines

extract_protocol:
Gastrointestinal (GI) tracts of 100 adult female flies (per replicate, reared at 29oC for 6 days) were dissected in ice-cold 1xPBS. Then cells were dissociated by treating intestines with 1mg/ml elastase at 27oC for 1 hour with agitation. Subsequently, ~30,000-50,000 GFP+ intestinal progenitor cells were sorted using a BD FACSAriaTM II flow cytometer equipped with a 100µm nozzle at the IUB Flow Cytometry Core Facility. Total RNA was prepared using the TRIzol® LS reagent (Ambion). The rRNA-depleted libraries were prepared using the Ovation® SoLo RNA-seq system (Part No. 0502 including Parts 0407 and S02240) following manufacturer’s instructions. The quality and quantity of final libraries were assessed using Agilent 2200 TapeStation and KAPA Library Quantification Kit, respectively.
The rRNA-depleted RNA-seq libraries were prepared using the Ovation® SoLo RNA-seq system (Part No. 0502 including Parts 0407 and S02240) following manufacturer’s instructions.

value: Intestinal progenitor cells

tag: developmental stage

value: Adult

tag: genotype/variation

value: esgTS


title: 1500-2 _CD4_ unstim

description:
all_counts.tsv
Mtb14_73

tag: cell type


title: 1500-2 _CD4_ MTB300

description:
all_counts.tsv
Mtb14_74


title: Hallikar_ Infected_61

city: Bengaluru

first: Suresh

middle: H

last: Basagoudanavar

state: Karnataka

address: IVRI, Hebbal

department: FMD Research Laboratory

country: India

institute: Indian Veterinary Research Institute

data_processing:
Tophat-2.0.13
DESeq2
Genome_build: ARS UCD 1.2
Supplementary_files_format_and_content: Txt files with raw counts

molecule: polyA RNA

organism: Bos indicus

source_name: Ventral soft palate

growth_protocol: Cattle calves were experimentally infected with FMDV serotype ‘O’ by intradermolingual inoculation. Ventral soft palate tissue biopsy was collected at 48 hours post infection. Transcript profile from the tissue biopsies  were analysed for differential gene expression.

extract_protocol:
RNA was isolated from tissue samples using RNAeasy kit (Qiagen, USA). The total RNA was used to enrich mRNA using NEB Magnetic mRNA Isolation Kit.
The transcriptome library was prepared using NEB ultraII RNA library prep kit and sequenced using Illumina HiSeq (151 nt, paired-end), technology

treatment_protocol: Experimental infection of 6-9 month old cattle calves with Foot and mouth Disease Virus serotype ‘O’ by intradermolingual inoculation.

tag: breed

value: Hallikar

value: FMDV infected

value: Ventral soft palate

value: Epithelial


title: 1500-2_PMBC_BCG

description:
all_counts.tsv
Mtb14_71

value: post


title: R2 Control Day 0 CAR+ T1 [RNA-seq]

description:
CD8.D0.CAR+.R2.1
Adjusted_Counts_-_Exposure.txt
TPMs_-_Presence.txt
Adjusted_Counts_-_Time_Series.txt
DESeq2_Results_-_Exposure.txt
DESeq2_Results_-_Time_Series.txt

tag: replicate

tag: car presence

value: Present

tag: antigen exposure


title: envA-DPG30m-1

tag: strain

value: whole olfactory mucosa

tag: age

value: 6-12 weeks


title: 1500-2_PMBC_MTB300

description:
all_counts.tsv
Mtb14_70


title: Patr1 Rep3


title: R5 Control Day 0 CAR+ T1 [ATAC-seq]

description: Control.Common.NoBL.bed

data_processing:
Alignment: data were aligned to the GRCh37/hg19 assembly of the human genome using bowtie2 (v2.3.4.1), with parameters --local -X 1000.
Filtering: SAM files were converted to BAM using samtools view -bS (samtools v1.1) and filtered for match quality using -q 5.
Sorting: BAM files across four NextSeq lanes were merged using samtools merge -n to sort by read name. Because we are submitting one FASTQ for each sample, this step is no longer necessary, but the data can be sorted (necessary for the following PCR de-duplication step) using samtools sort -n.
PCR de-duplication: BAM files were de-duplicated using PICARD MarkDuplicates with parameters REMOVE_DUPLICATES=True ASSUME_SORT_ORDER=queryname
Post-processing: alignment data were converted to BED format using BEDtools bamToBed. Files were further processed to remove all alignments on chrM and to remove alignments with mate distance > 1kb. Alignments with a mate distance under 100 bp were kept as "sub-nucleosome fragment size" signal. For R2, re-sequenced libraries were pooled using UNIX cat (4-Day0-CD8-CARpos-R_S13 with 4-Day0-CD8-CARpos-10-24-2018_S6 and 8-CS-CD8-CARpos-R_S7 with 8-CS-CD8-CARpos-10-24-2018_S5). For R5, re-sequenced libraries were pooled using UNIX cat (2-Day0-CD8-CARpos-REP5-ATAC-re_S17 with 2-Day0-CD8-CARpos-REP5-ATAC_S17 and 4-CS-CD8-CARpos-REP5-ATAC-re_S15 with 4-CS-CD8-CARpos-REP5-ATAC_S18).
Peak calling: peaks were called on the subnucleosome fragment fraction of alignments using MACS2 callpeak with parameters -s 42 -q 0.01 and no explicit background control sample. Peaks were then filtered for adjusted p-value < 0.001.
Library size adjustment: peaks for either control or continuous exposure were combined across replicates, collapsing overlapping peak loci into a single locus. Combined peaks were then assessed for overlaps in all four replicates using BEDtools intersect, and peaks with overlaps in all four replicates were kept. These were then combined for control and continuous exposure, collapsing overlapping peak loci into a single locus, forming a pan peak set. Pan peaks were assessed for tag counts across all samples and the resulting table was input to DESeq2 to estimate  size factors.
Track generation: bigWig files were created by first transforming subnucleosome-sized fragment alignments into a coverage map using BEDtools genomeCoverageBed -bg. Resulting bedGraph files were adjusted for library size by dividing by the size factors reported by DESeq2. Files were then sorted using UCSC Genome Browser's bedSort and converted to bigWig using bedGraphToBigWig.
Genome_build: hg19
Supplementary_files_format_and_content: We include a track file (bigWig) for each sample, representing subnucleosome fragment size alignments, or chromatin openness. Additionally, a peak file derived from subnucleosome fragment size alignments is included for both conditions, containing replicate-merged peaks which have overlaps to peaks in all four replicates. Peaks intersecting ENCODE blacklisted regions have been removed from these sets.

extract_protocol:
For flow cytometry and sorting assays of CAE, M5 CAR T cells were stained in fluorescence-activated cell sorting (FACS) buffer consisting of PBS (Gibco), 0.5% bovine serum albumin (BSA) (GEMINI), 2 mM EDTA (Invitrogen), and 100ug/ml DNase (Roche). CountBrightTM Absolute Counting Beads, (ThermoFisher) were used as an internal standard according to the manufacturer's instructions to calculate absolute cell counts in cell suspensions.  Antibodies specific for human CD45 (ref 304032, clone HI30), CD3 (317322, OKT3), CD4 (357412, A161A1 / 317440), CD56 (304608, MEM-188), EpCAM (324226/324238, 9C4), CD94 (305520, DX22), KLRB1 (339918, HP-3G10), TIGIT (372716, A15153G), TCR Va24-Ja18 (342922, 6B11), PD-1 (329928, EH12.2H7) were purchased from BioLegend. Antibodies specific for human CD8 (560179, SK1) was purchased from BD Pharmingen. Antibodies specific for human NKG2A (FAB1059P, 131411) and Methothelin (FAB32652P, 420411) were purchased from R&D Systems. Antibodies specific for human CTLA-4 (12-1529-42, 14D3) was purchased from eBioscience. Antibody specific for human NKG2C (130-103-636, REA205) was purchased from Miltenyi.  M5 CAR expression was assessed using biotinylated goat anti-human IgG F(ab’)2 (Jackson ImmunoResearch, 109-066-006) followed by streptavidin (FITC or APC) (BioLegend) or using an anti-idiotype antibody provided by Novartis Pharmaceuticals. Live/dead staining was performed using a Live/Dead Fixable Aqua Dead Cell Stain Kit (Life Technologies following manufacturer’s protocol followed by cell surface staining for 20 minutes at room temperature in the dark. Intracellular staining was performed with the Foxp3/Transcription Factor Staining Buffer set (Thermo Fisher) according to the manufacturer’s instructions. Samples were acquired on an LSRII Fortessa Cytometer (BD Bioscience) and analyzed with FlowJo v10 software (FlowJo, LLC). Sorting assays were performed using a FACS Aria Cytometer (BD Bioscience).    Nuclei were isolated from 30,000 sorted CD8+ surface CAR+ T cells, followed by the transposition reaction using Tn5 transposase (Illumina) for 30 minutes at 37° C with 1000rpm mixing. Purification of transposed DNA was completed with DNA Clean and Concentrator (Zymo) and fragments were barcoded with ATAC-seq indices (Buenrostro et al., 2013).
Omni ATAC-seq libraries were made as previously described (Corces et al., 2017). Final libraries were double size selected using AMPure beads prior to sequencing. Paired-end sequencing (2 x 75 bp reads) was carried out on an Illumina NextSeq 500 platform.

value: Control

tag: time


title: envA-DPG2h-2

tag: tissue


title: 1500-2_PMBC_unstim

description:
all_counts.tsv
Mtb14_69

value: Unstim


title: Patr1 Rep1

tag: Sex


title: 1494-2 _CD4_ BCG

description:
all_counts.tsv
Mtb14_59

value: BCG


title: Patr1 Rep2


title: envA-ACE2h-2


title: R4 Control Day 0 CAR+ T1 [ATAC-seq]

description: Control.Common.NoBL.bed

value: Day 0


title: 1494-2 _CD4_ MTB300

description:
all_counts.tsv
Mtb14_58


title: opto12h-ctrl-PI

description:
10x genomics, v3.1
opto_umi_counts.csv.gz
opto_metadata.csv.gz


title: R3 Continuous CAR+ T1 [ATAC-seq]

description: Continuous.Common.NoBL.bed

value: Continuous

value: Day 28


title: R5 Continuous CAR+ T1 [ATAC-seq]

description: Continuous.Common.NoBL.bed


title: envA-ACE2h-1


title: esgTS Rep 1

value: Intestinal progenitor cells

value: Female


title: 1494-2 _CD4_ unstim

description:
all_counts.tsv
Mtb14_57


title: R2 Continuous CAR+ T1 [ATAC-seq]

description: Continuous.Common.NoBL.bed


title: homecage-DPG30m-1


title: R3 Control Day 0 CAR+ T1 [ATAC-seq]

description: Control.Common.NoBL.bed


title: homecage-DPG30m-2


title: 1494-2_PMBC_MTB300

description:
all_counts.tsv
Mtb14_54

value: PBMC


title: R4 Continuous CAR+ T1 [ATAC-seq]

description: Continuous.Common.NoBL.bed


title: R2 Control Day 0 CAR+ T1 [ATAC-seq]

description: Control.Common.NoBL.bed


title: 1494-2_PMBC_BCG

description:
all_counts.tsv
Mtb14_55


title: 2466-2_PMBC_unstim

description:
all_counts.tsv
Mtb14_101


title: homecage-DPG2h-2


title: 1494-2_PMBC_unstim

description:
all_counts.tsv
Mtb14_53


title: envA-DPG2h-1


title: homecage-DPG2h-1


title: homecage-ACE2h-2


title: esgTS Rep 2

value: Adult

value: esgTS


title: homecage-ACE2h-1


title: 1492-2 _CD4_ unstim

description:
all_counts.tsv
Mtb14_41


title: wPlug-3plugged

description:
10x genomics, v3
RevOccl_umi_counts.csv.gz
RevOccl_metadata.csv.gz


title: wPlug-3open


title: 1492-2_PMBC_MTB300

description:
all_counts.tsv
Mtb14_38


title: wPlug-2plugged


title: 1492-2_PMBC_BCG

description:
all_counts.tsv
Mtb14_39


title: 1492-2_PMBC_unstim

description:
all_counts.tsv
Mtb14_37


title: 1492-2 _CD4_ MTB300

description:
all_counts.tsv
Mtb14_42


title: ∆18672_RNASeq

city: Shanghai

first: Jun

last: Zhang

state: Shanghai

address: NO.130 meilong road

department: School of biological engineering

country: China

institute: East China University Of Science and Technology

data_processing:
Rockhopper version 2.0.3 software used for basecalling, alignment, filtering, peak-calling, generation of normalized abundance measurements, summarization the whole transcript based on genome Vibrio alginolyticus ATCC 17749
Genome_build: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/354/175/GCF_000354175.2_ASM35417v2/GCF_000354175.2_ASM35417v2_genomic.gbff.gz
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Vibrio alginolyticus

source_name: in vitro

extract_protocol:
The total RNA from strain was isolated using TRIzol (Thermo Fisher Science), rRNA was removed from sample using Ribo-Zero (Illumina, San Diego, CA, USA)
library construction refered to TruSeq RNA sample Prep kit (Illumina, San Diego, CA, USA). The final libraries were sequenced on a HiSeq X-Ten platform (GENEWIZ, Su Zhou, China).

value: EPGS

tag: genotype

value: 18672 deletion mutant


title: wPlug-2open


title: BC-2_shALDH1A1-#B

type: RNA

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

institute: Saitama Medical University

description: Gene expression data from bladder cancer patient-deived spheroids BC-2 transduced with shALDH1A1-#B

hyb_protocol: Following fragmentation, 4 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip (Clariom S Array). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed with Affymetrix Expression Console software (build.1.2.1.20) using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.

label: biotin

source_name: BC-2 PDCs treated with shALDH1A1-#B

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA.

growth_protocol: Patient-derived bladder cancer cells were cultured on ultra-low-attachment culture dishes in STEMPRO hESC SFM supplemented with 8 ng/mL basic fibroblast growth factor and 20 mmol/L ROCK inhibitor Y-27632.

extract_protocol: Total RNA was extracted using ISOGEN reagent (Nippon Gene, Japan).

treatment_protocol: Patient-derived bladder cancer cells were transduced with shControl or shALDH1A1.

value: Patient-derived bladder cancer cells

tag: shRNA

tag: gender

value: Male


title: Clone derived from H9 cells transduced with pHIV-EF1α-H2A.XT136S139AA-IRES-eGFP 1

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

country: Canada

institute: McMaster University

hyb_protocol: In accordance with manufacturer's protocols

scan_protocol: GeneChips were scanned using  Affymetrix® Scanner 3000 7G.

data_processing: Data was normalized using Robust Multichip Averaging (RMA) algorithm using Partek Genomics Suite 6.6 software.

source_name: Human Embryonic Stem Cell derived cell line (H9)

growth_protocol: Clones were grown on Mouse Embryonic Fibroblast (MEF) feeder layer in MEF-conditioned medium plus 8ng/ml bFGF

extract_protocol: Extraction of total RNA using total RNA purification kit (Norgen Biotek, Canada) was performed according to the manufacturer's instructions.

treatment_protocol: H9 cells were transduced with the different vectors, GFP/TRA 1-60 double positive cell sorted and plated as single cells on MEFs, single colonies expanded.

value: Clone derived from hESC line H9


title: Sample908.Greater spear-nosed bat.205483080041_R06C02

type: genomic

city: Los Angeles

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

description: genomic DNA methylation from wing punch

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

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

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

label: Cy3 and Cy5

molecule: genomic DNA

organism: Phyllostomus hastatus

source_name: Skin

label_protocol: Standard Illumina Protocol

growth_protocol: DNA extracted from tissues

extract_protocol: genomic DNA was extracted

treatment_protocol: Standard Illumina Protocol

tag: canbeusedforagingstudies

value: yes

tag: confidenceinageestimate


title: BC-2_shALDH1A1-#A

description: Gene expression data from bladder cancer patient-deived spheroids BC-2 transduced with shALDH1A1-#A

source_name: BC-2 PDCs treated with shALDH1A1-#A


title: 1492-2 _CD4_ BCG

description:
all_counts.tsv
Mtb14_43

tag: stimulation

tag: bcg state

value: post


title: BC-1_shALDH1A1-#B

description: Gene expression data from bladder cancer patient-deived spheroids BC-1 transduced with shALDH1A1-#B

source_name: BC-1 PDCs treated with shALDH1A1-#B

tag: cell type


title: BC-1_shControl

description: Gene expression data from bladder cancer patient-deived spheroids BC-1 transduced with shControl

source_name: BC-1 PDCs treated with shControl

value: shControl


title: BC-1_shALDH1A1-#A

description: Gene expression data from bladder cancer patient-deived spheroids BC-1 transduced with shALDH1A1-#A

source_name: BC-1 PDCs treated with shALDH1A1-#A


title: Sample907.Greater spear-nosed bat.205483080041_R05C02

description: genomic DNA methylation from wing punch


title: 1491-2 _CD4_ BCG

description:
all_counts.tsv
Mtb14_28

value: BCG


title: Sample904.Greater spear-nosed bat.205483080041_R02C02

description: genomic DNA methylation from wing punch


title: wt_RNASeq

value: wild type


title: wPlug-1plugged

source_name: whole olfactory mucosa

value: whole olfactory mucosa

value: 6-12 weeks


title: Clone derived from H9 cells transduced with pHIV-EF1α-H2A.XS139E-IRES-eGFP 2

label_protocol: In accordance with manufacturer's protocols


title: RNAseq4

city: Paris

first: Christophe

last: Rusniok

address: 25, 28 rue du Docteur Roux

department: Genomes et Genetique

country: France

institute: Institut Pasteur

description: total RNA extracted from the same culture of Sample 4

data_processing:
Basecalls performed using CASAVA version 1.5 for Sample 5 (RNAseq1) and version 1.9 for all the other samples.
Adapters removal with cutadapt software version 1.15
Trimming of the reads using Sickle, with a quality threshold of 20 (-q 20). Reads shorter than 21 nucleotides were removed (-l 21)
Reads corresponding to the rRNA sequences are first removed using Bowtie and sequences of ribosomal RNA (rRNA) operons of Legionella pneumophila strain Paris (NC_006368.1). Remaining reads were aligned to the L. pneumophila strain Paris chromosome sequence (NCBI Acc.-No: NC_006368.1) using Bowtie 2 (verson 2.3.4.3) with --local option. BAM files are build, sorted and indexed with the Samtools suite version 1.3.
Reads count with featureCounts programm (from the Subreads package). We used --primary option and stranded counts (option -s 1)
Differential analysis performed with Sartools version 1.3.0 (DESeq2 methods and "median" option to compute size factors).
Genome_build: NC_006368.1
Supplementary_files_format_and_content: columns of this TSV result file are tabular separated. This analysis file contains reads count and normalized reads count (norm. ...) for each sample (column 1 to 17). In column 18 to the end, there are different calculations like fold change, log2 fold change, P-value, adjusted p-value for the comparison between the two conditions (MVseq versus RNAseq).

organism: Legionella pneumophila

source_name: bacterial cells

growth_protocol: Legionella strains were grown in liquid BYE medium until post-exponential phase (OD 4.2).

extract_protocol:
RNA of bacteria cell pellet and purified Lp-MVs were extracted using the miRNeasy®Mini kit (Qiagen). Bacterial RNA was rRNA depleted using the RiboZero rRNA Removal Kit for Gram-negative bacteria (Illumina) and metal‐catalyzed heat‐fragmented to a size around 100–200 nt using the RNA fragmentation kit (Ambion).
TruSeq small RNA library

treatment_protocol: Bacterial cells were harvested by centrifugation at 5.000xg, 4°C for 15 min and pellet was frozen at -80°C for further used as total bacterial control The supernatant was twice passed through a 0.2µm PES membrane Stericup® Quick Release (Millipore) and re-centrifuged for 15min at 15.000xg, 4°C. The supernatant was treated with RNaseA/T1 (Thermo Scientific) at a final concentration of 2µg/ml RNaseA for 1h at 37°C followed by centrifugation at 150.000xg for 2h at 4°C to pellet the MVs. The MV-pellet was washed, re-centrifuged and resuspended in PBS.

value: Paris

tag: growth phase

value: post-exponential growth phase (OD4,2)

tag: sample type

value: bacterial culture


title: 1491-2 _CD4_ MTB300

description:
all_counts.tsv
Mtb14_27


title: 1491-2_PMBC_BCG

description:
all_counts.tsv
Mtb14_25

value: PBMC


title: Clone derived from H9 cells transduced with pHIV-EF1α-IRES-eGFP 2


title: Clone derived from H9 cells transduced with pHIV-EF1α-H2A.XT136S139AA-IRES-eGFP 2


title: Clone derived from H9 cells transduced with pHIV-EF1α-IRES-eGFP 1


title: Sample906.Big brown bat.205483080041_R04C02

description: genomic DNA methylation from wing punch

organism: Eptesicus fuscus


title: Sample905.Greater spear-nosed bat.205483080041_R03C02

description: genomic DNA methylation from wing punch


title: RNAseq3

description: total RNA extracted from the same culture of Sample 3


title: RNAseq2

description: total RNA extracted from the same culture of Sample 2


title: 1491-2_PMBC_MTB300

description:
all_counts.tsv
Mtb14_23


title: RevOccl-DPG-3open


title: RevOccl-DPG-2unplugged


title: MVseq4

description: RNA extracted from purified Legionella-vesicles

source_name: bacterial cells/extracellular vesicles

value: Extracellular vesicles (EVs)


title: Sample903.Greater spear-nosed bat.205483080041_R01C02

description: genomic DNA methylation from wing punch


title: 1491-2_PMBC_unstim

description:
all_counts.tsv
Mtb14_22

value: Unstim


title: 1489-2 _CD4_ BCG

description:
all_counts.tsv
Mtb14_14


title: wPlug-1open


title: 1489-2 _CD4_ unstim

description:
all_counts.tsv
Mtb14_11


title: RevOccl-DPG-2open


title: MVseq3


title: RevOccl-DPG-3unplugged


title: Sample902.Greater spear-nosed bat.205483080041_R06C01

description: genomic DNA methylation from wing punch

value: Female


title: 1489-2_PMBC_BCG

description:
all_counts.tsv
Mtb14_10


title: Sample901.Big brown bat.205483080041_R05C01

description: genomic DNA methylation from wing punch


title: RevOccl-DPG-1unplugged


title: MVseq1


title: 1489-2_PMBC_MTB300

description:
all_counts.tsv
Mtb14_8


title: RevOccl-DPG-1open


title: Sample899.Big brown bat.205483080041_R03C01

description: genomic DNA methylation from wing punch


title: Sample900.Big brown bat.205483080041_R04C01

description: genomic DNA methylation from wing punch


title: RevOccl-ACE-2unplugged


title: Sample898.Greater spear-nosed bat.205483080041_R02C01

description: genomic DNA methylation from wing punch


title: MVseq2


title: 1489-2_PMBC_unstim

description:
all_counts.tsv
Mtb14_7


title: RevOccl-ACE-2open


title: Sample 7_Endometrial Organoid

city: Melbourne

first: Caitlin

middle: E

last: Filby

state: Victoria

address: TRF L5, 27-31 Wright Street Clayton VIC 3168, Australia

department: The Ritchie Centre

country: Australia

institute: Hudson Institute of Medical Research

data_processing:
Read quality was checked using FastQC v0.11.7and MultiQC v1.6.
Low quality reads, were trimmed using Trimmomatic v0.39.
HISAT2 v2.2.1 was used to map trimmed reads to the Ensembl Homo sapiens GRCh38 release 84.
Assembly of known transcripts (Ensembl Homo sapiens CRCh38 release 91 reference assembly) and counting using StringTie v.2.1.6.
Raw gene counts were extracted using a Python script provided by StringTie.
Lowly expressed and mitochondrial genes removed, TMM normalisation performed using edgeR R package v.3.34.1 .
Genome_build: Ensembl Homo sapiens GRCh38
Supplementary_files_format_and_content: comma deliminated file (csv) with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: comma deliminated file (csv) with TTM normalised CPM values for each sample following gene filtering.

source_name: Endometrial epithelial cells

growth_protocol: Endometrial organoids were isolated from endometrial epithelial clusters of cells and seeded in matrigel, media changed every 2-3 days and organoids passaged every 7-10 days.

extract_protocol:
Passage 3 organoids grown to day 7 and snap frozen until RNA extraction (Qiagen microRNAeasy, 74004).
RNA samples with RIN scores >8.5 were selected for library generation (Trio RNA-Seq library preparation, Tecan)
RNAseq libraries were sequenced with Illumina next Seq550, 150bp PE.

tag: hormonal medication

tag: disease state

value: Menorrhagia, Cystic Hyperplasia

tag: menstrual stage

value: Proliferative

tag: sampling method

value: Biopsy


title: Sample897.Greater spear-nosed bat.205483080041_R01C01

description: genomic DNA methylation from wing punch

value: yes

tag: age


title: Sample 6_Endometrial Organoid

value: Menorrhagia

value: 67 days since LMP


title: 2466_1 _CD4_ BCG

description:
all_counts.tsv
Mtb14_99

value: BCG

value: pre


title: Sample 5_Hormone-treated Endometrial Organoid

source_name: Hormone-treated endometrial epithelial cells

value: OCP

value: Endometriosis

value: Menstrual


title: Sample896.Greater spear-nosed bat.205483080039_R06C02

description: genomic DNA methylation from wing punch

value: Male


title: RevOccl-ACE-1unplugged

tag: strain

tag: tissue

value: whole olfactory mucosa

value: 6-12 weeks


title: Sample895.Seba's short-tailed bat.205483080039_R05C02

description: genomic DNA methylation from wing punch

organism: Carollia perspicillata

tag: Sex


title: BC-2_shControl

description: Gene expression data from bladder cancer patient-deived spheroids BC-2 transduced with shControl

source_name: BC-2 PDCs treated with shControl

value: Patient-derived bladder cancer cells

tag: shRNA

value: shControl


title: Clone derived from H9 cells transduced with pHIV-EF1α-H2A.XS139E-IRES-eGFP 1

value: Clone derived from hESC line H9


title: Sample894.Greater spear-nosed bat.205483080039_R04C02

description: genomic DNA methylation from wing punch


title: 2466_1 _CD4_ MTB300

description:
all_counts.tsv
Mtb14_98


title: RevOccl-ACE-1open


title: 2466_1 _CD4_ unstim

description:
all_counts.tsv
Mtb14_97

value: Unstim


title: Sample 3_Hormone-treated Endometrial Organoid

value: OCP (193 days since LMP)


title: v3-OCT2h-2

description:
10x genomics, v3
ActSeq_umi_counts.csv.gz
ActSeq_metadata.csv.gz


title: 2466_1_PMBC_BCG

description:
all_counts.tsv
Mtb14_95

source_name: PBMC

value: PBMC


title: Sample 2_Menstrual Fluid Organoid

source_name: Menstrual fluid endometrial epithelial cells

value: Menstrual fluid


title: 2466_1_PMBC_MTB300

description:
all_counts.tsv
Mtb14_94


title: v3-OCT2h-1


title: Sample892.Greater spear-nosed bat.205483080039_R02C02

description: genomic DNA methylation from wing punch

value: yes


title: Sample 1_Menstrual Fluid Organoid

value: Population Control


title: v3-DPG30m-2


title: 1502_1 _CD4_ BCG

description:
all_counts.tsv
Mtb14_83

value: BCG


title: v3-DPG30m-1


title: v3-DPG2h-2


title: 2466_1_PMBC_unstim

description:
all_counts.tsv
Mtb14_93

value: pre


title: Sample 4_Hormone-treated Endometrial Organoid

value: Mirena

value: Mirena® (53 days since LMP)

value: Hysterectomy tissue


title: 1502_1 _CD4_ MTB300

description:
all_counts.tsv
Mtb14_82


title: Sample891.Greater spear-nosed bat.205483080039_R01C02

description: genomic DNA methylation from wing punch

value: Male


title: A375 shCCDC50-2 rep3

first: Tian

last: Tian

address: 3615 Civic Center Blvd

department: Center of Applied Genomics

institute: Children's Hospital of Philadelphia

data_processing:
Raw fastq files were trimmed by trim-galore to remove adapters and low-quality bases
Trimed reads were aligned to hg38 by Hisat2
Read counts were summaried by StringTie2
Supplementary_files_format_and_content: raw count

source_name: A375 cell

growth_protocol: DMEM medium containing with 10% FBS, 1% L-glutamine (200 mM) and 1% penicillin/streptomycin.

extract_protocol:
The cells were collected and and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: morphology

value: epithelial

tag: genotype

value: CCDC50 knock-down


title: A375 shCCDC50-2 rep1


title: A375 shCCDC50-1 rep3


title: A375 shCCDC50-2 rep2


title: Sample890.Greater spear-nosed bat.205483080039_R06C01

description: genomic DNA methylation from wing punch

tag: canbeusedforagingstudies

tag: confidenceinageestimate

value: Female


title: A375 shCCDC50-1 rep2


title: Sample889.Big brown bat.205483080039_R05C01

description: genomic DNA methylation from wing punch


title: v3-ACE2h-1

value: whole olfactory mucosa

value: 6-12 weeks


title: A375 shCCDC50-1 rep1


title: 1502_1_PMBC_MTB300

description:
all_counts.tsv
Mtb14_78

tag: cell type

tag: stimulation

tag: bcg state


title: 1502_1_PMBC_unstim

description:
all_counts.tsv
Mtb14_77

value: Unstim


title: ChronicOccl-3occluded

description:
10x genomics, v3.1
ChronicOccl_umi_counts.csv.gz
ChronicOccl_metadata.csv.gz

value: 5 weeks


title: v3-ACE2h-2


title: Sample885.Greater spear-nosed bat.205483080039_R01C01

description: genomic DNA methylation from wing punch


title: Sample888.Greater spear-nosed bat.205483080039_R04C01

description: genomic DNA methylation from wing punch


title: Sample887.Greater spear-nosed bat.205483080039_R03C01

description: genomic DNA methylation from wing punch


title: 1500_1 _CD4_ BCG

description:
all_counts.tsv
Mtb14_67


title: A375 shControl rep3

value: wild type


title: Sample886.Big brown bat.205483080039_R02C01

description: genomic DNA methylation from wing punch


title: Sample884.Greater spear-nosed bat.205483080002_R06C02

description: genomic DNA methylation from wing punch


title: ChronicOccl-3open


title: Sample883.Seba's short-tailed bat.205483080002_R05C02

description: genomic DNA methylation from wing punch


title: 1500_1 _CD4_ MTB300

description:
all_counts.tsv
Mtb14_66


title: v3-DPG2h-1


title: 1502_1 _CD4_ unstim

description:
all_counts.tsv
Mtb14_81


title: ChronicOccl-2occluded


title: A375 shControl rep2


title: Sample882.Big brown bat.205483080002_R04C02

description: genomic DNA methylation from wing punch


title: 1500_1 _CD4_ unstim

description:
all_counts.tsv
Mtb14_65


title: A375 shControl rep1


title: 1500_1_PMBC_BCG

description:
all_counts.tsv
Mtb14_63

value: PBMC


title: ChronicOccl-1occluded


title: liver, train_overfeed_6

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
TPM abundance estimates, generated with kallisto quant 0.4.6
Genome_build: GRCz11
Supplementary_files_format_and_content: TPM abundance estimates and raw counts generated with kallisto.

organism: Danio rerio

source_name: liver

growth_protocol: Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.

extract_protocol:
Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN (Hilden, Germany).
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

treatment_protocol:
Fish of the overfeeding groups (ctr_overfeed and train_overfeed) were fed with 9 mL of living shrimps per fish spread over the morning (3 times 3 mL) and 2 spoons of SDS 400 per tank in the afternoon.
Fish of the training groups (train_ctrl and train_overfeed) were trained every other day from Monday to Friday (alternating twice or thrice per week) for 8 weeks (20 training sessions in total).

value: liver

tag: training

value: trained

tag: feed

value: overfeed

tag: gender

value: male

value: ABTL


title: ChronicOccl-1open


title: Sample881.Big brown bat.205483080002_R03C02

description: genomic DNA methylation from wing punch

value: yes


title: 1494_1 _CD4_ BCG

description:
all_counts.tsv
Mtb14_51

value: BCG

value: pre


title: Sample880.Big brown bat.205483080002_R02C02

description: genomic DNA methylation from wing punch


title: Sample879.Greater spear-nosed bat.205483080002_R01C02

description: genomic DNA methylation from wing punch


title: homecage-6

description:
10x genomics, v3.1
home_cage_umi_counts.csv.gz
home_cage_metadata.csv.gz
home_cage_immature_metadata.csv.gz
home_cage_immature_umi_counts.csv.gz


title: 1500_1_PMBC_MTB300

description:
all_counts.tsv
Mtb14_62


title: liver, train_overfeed_4


title: Sample878.Big brown bat.205483080002_R06C01

description: genomic DNA methylation from wing punch


title: 1494_1 _CD4_ MTB300

description:
all_counts.tsv
Mtb14_50


title: liver, train_overfeed_2

value: female


title: ChronicOccl-2open


title: homecage-5


title: liver, train_overfeed_3


title: 1494_1 _CD4_ unstim

description:
all_counts.tsv
Mtb14_49


title: 1494_1_PMBC_BCG

description:
all_counts.tsv
Mtb14_47


title: homecage-4


title: homecage-2


title: Sample877.Greater spear-nosed bat.205483080002_R05C01

description: genomic DNA methylation from wing punch

value: Male


title: 1500_1_PMBC_unstim

description:
all_counts.tsv
Mtb14_61


title: 1494_1_PMBC_MTB300

description:
all_counts.tsv
Mtb14_46


title: liver, train_overfeed_5


title: liver, train_overfeed_1


title: liver, train_ctrl_5

value: ctrl


title: homecage-3

value: whole olfactory mucosa


title: ADX_Male_Cast

city: RTP

first: Xiaojiang

last: Xu

state: North Carolina

address: 111 T. W. Alexander Dr.,

institute: NIEHS

data_processing:
Demultiplexed FASTQ files (paired-end,Read 1: 30bp, Read 2:100bp) were generated using the CellRanger mkfastq command. The primary data analyses which included alignment, filtering, barcode counting and UMI quantification, quality control, clustering and statistical analysis were performed using CellRanger count command. Gene positions were annotated using Ensembl build 93 and filtered for biotype. Raw gene expression matrices were imported into R (version 3.6.1) and converted to a Seurat object using the Seurat R package (version 3.1.0). To remove dead cells and doublets, the total number of UMIs and genes and the percentage of UMIs derived from the mitochondrial genome for each cell were counted.  The upper and lower bounds were defined as the mean +/- two standard deviations for both the total UMIs and genes, respectively. Cells which had over 10% UMIs derived from mitochondrial genome were discarded. Finally, cells with total UMIs or genes outside of the upper and lower bounds were removed. For the remaining 5534 out of 6290 cells, gene expression matrices were normalized to the total cellular read count and to mitochondrial read count. Highly variably genes (HVG) were selected from the normalized data using Seurat SCTransform function. The top 3000 HVGs were used as features for dimensionality reduction and clustering. The Seurat RunPCA and JackStraw functions were performed to calculate and to select significant (P-value <0.05) principal components (PCs), respectively.  The RunUMAP function was then applied to plot the selected significant PCs. The FindNeighbors constructed a Shared Nearest Neighbor (SNN) Graph, and FindClusters function with “resolution = 0.1” parameter was carried out to cluster cells into different groups. Marker genes were defined based on the following criteria: 1) the average expression value in the cluster of interest was at least 1.2-fold higher than the average expression in the rest of clusters; 2) there are greater than 10% of cells in the cluster of interest which were detectable; and 3) marker genes should have the highest mean expression in the cluster of interest compared to the rest of clusters. Canonical marker genes were used to annotate cell clusters.
Genome_build: mm10
Supplementary_files_format_and_content: hd5 file, data matrix from cell ranger exprot

source_name: Stomach

extract_protocol:
The corpus from three mice tissue was combined in the same tube and washed 2x in Hanks Balanced Salt Solution without Ca2+ or Mg2+ containing 5 mM HEPES, 5 mM EDTA, and 5% FBS for 20 minutes at 37oC. Tissue was then washed in Hanks Balanced Salt Solution with Ca2+ and Mg2+ for 10 minutes at 37oC and then digested in 1 mg/ml type 1 collagenase (Worthington Biochemical) and 1.5 mg/ml DNase I (Worthington Biochemical, Lakewood, NJ) for 20 minutes at 37oC. After digestions the tissue fragments were pushed through a 100 µm strainer. Fc receptors were blocked with TruStain (Bioledgend, San Diego, CA) and then stained for with anti-CD45 (Cone 104) for 20 minuets at 4oC. Actinomycin D (ThermoFisher) was used to label dead cells. Viable CD45+ cells were sorted using a FACS Aria II (BD Bioscience, San Jose, CA) running FACS Diva software and resuspended at a concentration of 1.0 x 106 cells/ml in RPMI 1640 + 10% FBS.
Single cell libraries were prepared on a 10x Genomics Chromium controller (10x Genomics, Pleasanton, CA) using the version 3 reagent kit according to the manufacturer’s instructions. The reagent mixture was calculated for capturing 6000 cells. The libraries were sequenced on a NovaSeq (Illumina, San Diego, CA) by the NIEHS Epigenomics core laboratory. Raw read processing was carried out using the Cell Ranger Single-Cell Software Suite (version 3.0.1, 10X Genomics).

value: Stomach

tag: dignosis

value: ADX + Cast

tag: treatment


title: Sample875.Greater spear-nosed bat.205483080002_R03C01

description: genomic DNA methylation from wing punch

tag: age


title: Sample876.Greater spear-nosed bat.205483080002_R04C01

description: genomic DNA methylation from wing punch

value: Female


title: 1494_1_PMBC_unstim

description:
all_counts.tsv
Mtb14_45

value: Unstim


title: ADX_Female

tag: tissue

value: ADX


title: liver, train_ctrl_3

value: liver

tag: strain


title: 1492_1 _CD4_ BCG

description:
all_counts.tsv
Mtb14_35


title: liver, train_ctrl_2

value: trained


title: 1492_1_PMBC_BCG

description:
all_counts.tsv
Mtb14_31

value: PBMC


title: homecage-1

value: 6-12 weeks


title: Sample873.Greater spear-nosed bat.205483080002_R01C01

description: genomic DNA methylation from wing punch

tag: Sex


title: Sample874.Seba's short-tailed bat.205483080002_R02C01

description: genomic DNA methylation from wing punch


title: liver, ctrl_overfeed_6

value: overfeed

value: ABTL


title: Sample872.Big brown bat.205483080038_R06C02

description: genomic DNA methylation from wing punch

value: yes


title: Sample870.Greater spear-nosed bat.205483080038_R04C02

description: genomic DNA methylation from wing punch


title: Sham_FemaleR2

value: normal

value: Sham


title: liver, train_ctrl_6

value: male


title: Sample893.Big brown bat.205483080039_R03C02

description: genomic DNA methylation from wing punch

value: Male


title: 1492_1 _CD4_ unstim

description:
all_counts.tsv
Mtb14_33

value: pre


title: liver, train_ctrl_1

value: ctrl

value: female


title: 1492_1 _CD4_ MTB300

description:
all_counts.tsv
Mtb14_34


title: liver, train_ctrl_4


title: Sham_MaleR2

value: Stomach


title: 1492_1_PMBC_unstim

description:
all_counts.tsv
Mtb14_29

value: Unstim


title: liver, ctrl_overfeed_4


title: liver, ctrl_overfeed_2


title: liver, ctrl_overfeed_5


title: fat body, g1

city: Reading

first: Justin

last: DiAngelo

address: P.O. Box 7009, Tulpehocken Rd.

institute: Penn State Berks

data_processing:
Base calling using Illumina HiSeq software
Sequence reads were trimmed using Trimmomatic v.0.36
Trimmed reads were mapped to the Drosophila melanogaster BDGP6 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b (BAM files were generated as a result)
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2
Genome_build: BDGP6 Drosophila melanogaster reference genome
Supplementary_files_format_and_content: Unique reads that fell within exon regions of genes for each sample

source_name: Adult female cuticle with fat body attached

extract_protocol:
Total RNA was extracted using VWR Life Science RiboZol RNA Extraction Reagent
mRNA was enriched using polyA selection, mRNA was fragmented and first and second strand cDNA synthesis was performed, adaptors were ligated and samples PCR enriched before Illumina sequencing.

tag: developmental stage

value: 1 week old adult

value: fat body


title: 1492_1_PMBC_MTB300

description:
all_counts.tsv
Mtb14_30


title: fat body, w4


title: fat body, g4


title: liver, ctrl_overfeed_1

value: liver


title: 1491_1_PMBC_BCG

description:
all_counts.tsv
Mtb14_18

value: PBMC

value: BCG


title: Sample869.Greater spear-nosed bat.205483080038_R03C02

description: genomic DNA methylation from wing punch

source_name: Skin


title: fat body, w3


title: NOV0092.Sham-Male_20190522_103218

value: gastric corpus

value: CD45+ leukocytes


title: fat body, g3


title: 1491_1_CD4_ BCG

description:
all_counts.tsv
Mtb14_21


title: Veh-3 ON: 16 h Veh rep 3

city: La Jolla

first: R.

middle: Luke

last: Wiseman

address: 10550 N Torrey Pines Rd

department: Dept. of Molecular Medicine

institute: The Scripps Research Institute

data_processing:
DNAstar Lasergene SeqManPro used to align reads from fastq files
ArrayStar 12.2  QSeq package used to generate read counts per transcript
DESeq2 used for differential expression analysis
Genome_build: mm9
Supplementary_files_format_and_content: .csv contains read counts for DESeq2 output

source_name: HT22 cells

growth_protocol: Cells were grown in a 12 well tissue culture treated plate in DMEM supplemented with 10% FBS and 1% Penicillin-Streptomycin and 1% glutamine.

extract_protocol:
RNA was extracted using QuickRNA mini kit (Zymo).
non-stranded mRNA sequencing

treatment_protocol: Cells were treated with 10mM AA147 or DMSO for 16 h.

value: HT22 immortailized hippocampal neurons

value: veh


title: Sample868.Seba's short-tailed bat.205483080038_R02C02

description: genomic DNA methylation from wing punch

value: yes


title: Sample871.Big brown bat.205483080038_R05C02

description: genomic DNA methylation from wing punch


title: Sample867.Big brown bat.205483080038_R01C02

description: genomic DNA methylation from wing punch

value: Female


title: Sample865.Greater spear-nosed bat.205483080038_R05C01

description: genomic DNA methylation from wing punch

value: Male


title: Sample866.Greater spear-nosed bat.205483080038_R06C01

description: genomic DNA methylation from wing punch


title: 1491_1_PMBC_unstim

description:
all_counts.tsv
Mtb14_15

value: pre


title: fat body, g2


title: Sample863.Big brown bat.205483080038_R03C01

description: genomic DNA methylation from wing punch


title: 1491_1_CD4_ MTB300

description:
all_counts.tsv
Mtb14_20


title: Sample864.Big brown bat.205483080038_R04C01

description: genomic DNA methylation from wing punch


title: 1491_1_PMBC_MTB300

description:
all_counts.tsv
Mtb14_16


title: liver, ctrl_ctrl_6

value: ctrl

value: male

value: ABTL


title: fat body, w2

value: female


title: Veh-2 ON: 16 h Veh rep 2


title: fat body, w1

value: 1 week old adult


title: 1489_1_CD4_ BCG

description:
all_counts.tsv
Mtb14_6


title: 1489_1_CD4_ unstim

description:
all_counts.tsv
Mtb14_5

value: Unstim


title: liver, ctrl_ctrl_3

value: liver


title: liver, ctrl_overfeed_3

value: overfeed


title: Veh-1 ON: 16 h Veh rep 1


title: 147-3 ON: 16 h AA147 rep 3


title: 1489_1_PBMC_BCG

description:
all_counts.tsv
Mtb14_4

value: PBMC

value: BCG


title: 147-2 ON: 16 h AA147 rep 2


title: ChIP DNA - TH2A

city: Mumbai

first: Priyanka

last: Parte

state: Maharashtra

address: J.M.Street, Parel

department: Gamete Immunobiology

institute: ICMR-National Institute for Research in Reproductive and Child Health

description: Native ChIP

library_source: genomic

data_processing:
Alignment to mouse genome mm10 was performed using BWA MEM(Ver-0.7.12)
Using SAMtools unaligned reads were filtered out followed by the sorting of the alignment files, and their conversion to BAM file.
Peak calling was performed with Model-based Analysis of ChIP-Seq (MACS 2.1.3 version).Statistically significant peaks were filtered based on p-value cut off < 0.05
The peaks were annotated to the nearest gene or Transcription Start Site (TSS) using HOMER (annotatepeaks)
Genome_build: mm10
Supplementary_files_format_and_content: peak text files

source_name: Mature Caudal sperm

extract_protocol:
The protocol described by Hisano et al., 2013 was followed for ChIP in mice sperm with slight modifications (Hisano et al., 2013).
TH2A and TH2B library preparation was done and the quality assessment was performed on automated electrophoresis system using TapeStation Analysis Software A.02.02 (SR1) (Agilent). Sequencing was performed with Illumina Hiseq using 150 bp paired end sequencing. For Input and TH2B ChIP‐Seq libraries, ~ 30 million and for TH2A 34 million unique paired end reads were attained. The fastq file were checked using FastQC. Based on quality report of fastq, files were trimmed using Trimmomatic (Ver-0.36) and were processed further.

value: Mature Caudal sperm

value: 8-12 weeks

tag: chip antibody

value: rabbit anti-mouse TH2A (from Dr. Toshie Shinagawa, RIKEN)


title: 1489_1_PBMC_unstim

description:
all_counts.tsv
Mtb14_1

extract_protocol:
Total RNA was purified using an miRNeasy Micro Kit (QIAGEN) and quantified by quantitative PCR. Purified total RNA (1-5 ng) was amplified following the Smart-Seq2 protocol.
mRNA was captured using poly-dT oligonucleotides and directly reverse transcribed into full-length cDNA (amplified by PCR for 16 cycles). cDNA was purified using AMPure XP beads (Beckman Coulter). From this step, 1 ng of cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina). Whole-transcriptome amplification and sequencing library preparations were performed in a 96-well format to reduce assay-to-assay variability. Barcoded Illumina sequencing libraries (Nextera, Illumina) were generated using the automated platform (Biomek FXp). Libraries were sequenced on a HiSeq 2500 Illumina platform to obtain 50-bp single-end reads (TruSeq Rapid kit; Illumina).


title: liver, ctrl_ctrl_1


title: 1489_1_PBMC_MTB300

description:
all_counts.tsv
Mtb14_2


title: ChIP DNA - TH2B

description: Native ChIP

value: rabbit anti mouse TH2B Antibody (Sigma-Aldrich #07-680)


title: 147-1 ON: 16 h AA147 rep 1

value: HT22 immortailized hippocampal neurons


title: Input DNA

description: Mononucleosomal DNA


title: Sample861.Greater spear-nosed bat.205483080038_R01C01

description: genomic DNA methylation from wing punch

value: yes

value: Male


title: Sample862.Greater spear-nosed bat.205483080038_R02C01

description: genomic DNA methylation from wing punch


title: liver, ctrl_ctrl_5

value: ctrl


title: liver, ctrl_ctrl_2


title: cell_He3B_rep1

status: Public on Dec 05 2021

first: Xiaojin

last: Yang

address: No. 128 Ruili Road

department: Department of infectious diseases

institute: Shanghai Fifth People's Hospital, Fudan University

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent Technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent Technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat.# 5188-5327, Agilent Technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent Technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent Technologies, Santa Clara, CA, US).

label_protocol: cRNAs was labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent Technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was isolated using RNeasy Total RNA Isolation Kit (Qiagen, GmBH, Germany)/ TRIzol reagent (Life Technologies, Carlsbad, CA, US) according to the manufacturer’s instructions, and purified by using a RNeasy Mini Kit (Qiagen, GmBH, Germany).

tag: cell line

value: HBV-positive liver cancer cells


title: cell_HepG2.2.15_rep1


title: T. cati cerebellum d70 rep 2

city: Hannover

first: Christina

last: Strube

address: Bünteweg 17

department: Institute for Parasitology

institute: University of Veterinary Medicine Hannover

description: Gene expression in the cerebellum 70 days post infection. Infection with 2000 embryonated T. cati eggs.

hyb_protocol: Cy3- labeled cRNA was hybridized to Agilent´s mouse 4x44k GE microarrays  for 16 h at 68 ºC and scanned using the Agilent DNA Microarray Scanner.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) according to manufacture´s recommendation

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_105_Dec08, GE1_107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: cerebellum, T. cati-infected

label_protocol: 100 ng of total RNA were applied for Cy3-labelling reaction using the MessageAmp II-Bacteria Kit according to supplier´s recommendation (Ambion). As a result of IVT (in vitro transcription) reaction using aminoallyl-dUTP antisense aRNA were generated and subsequently coupled with fluorescent dye Cy3.

extract_protocol: Total RNA was extracted with the RNeasy® Lipid Tissue Mini kit (Qiagen, Hilden, Germany) according to the manufacturers instructions. On-column Dnase digestion was included in the protocol as described in the manual. RNA was eluted twice with 40 Âµl each time, resulting in a total volume of 80 Âµl RNA/sample. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

treatment_protocol: Cerebra and cerebella were stored in RNAlater (Qiagen, Hilden, Germany) upon extraction.

value: cerebellum

value: Female

tag: infection

value: T. cati-infected

value: 16 weeks


title: HT29-exos-1

first: Senlin

last: Zhao

address: 270 Dong An Road

department: Colorectal Surgery

institute: Cancer Hospital, Fudan University

hyb_protocol: After purification the labeled RNAs were hybridized onto the microarray.

scan_protocol: After washing, the arrays were scanned with the Agilent Scanner G2505C (Agilent Technologies).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Next, GeneSpring software (version 14.8, Agilent Technologies) was employed to finish the basic analysis with the raw data. The raw data was normalized with the quantile algorithm.

source_name: exosomes from weakly metastatic CRC cells HT29-1

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were dephosphorylated, denatured and then labeled with Cyanine-3-CTP.

extract_protocol: Total RNA was extracted using the mirVana miRNA Isolation Kit (Cat. AM1561, Invitrogen, Thermo Fisher Scientific Inc., USA) following the manufacturer’s protocol. RNA purity and quantification were evaluated using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

value: exosomes


title: RKO-exos-2

source_name: exosomes from highly metastatic CRC cells RKO-2

value: RKO


title: T. cati cerebellum d70 rep 1


title: T. cati cerebellum d120 rep 3

description: Gene expression in the cerebellum 120 days post infection. Infection with 2000 embryonated T. cati eggs.

value: 23 weeks


title: T. cati cerebellum d98 rep 2

description: Gene expression in the cerebellum 98 days post infection. Infection with 2000 embryonated T. cati eggs.

value: 20 weeks


title: RKO-exos-3

source_name: exosomes from highly metastatic CRC cells RKO-3


title: SW620-exos-3

source_name: exosomes from highly metastatic CRC cells SW620-3


title: T. cati cerebellum d98 rep 1


title: T. cati cerebellum d120 rep 2


title: T. cati cerebellum d70 rep 3


title: T. cati cerebellum d120 rep 1


title: T. cati cerebellum d98 rep 3


title: SW480-exos-1

source_name: exosomes from weakly metastatic CRC cells SW480-1


title: SW620-exos-1

source_name: exosomes from highly metastatic CRC cells SW620-1


title: RKO-exos-1

source_name: exosomes from highly metastatic CRC cells RKO-1


title: T. cati cerebellum d28 rep 3

description: Gene expression in the cerebellum 28 days post infection. Infection with 2000 embryonated T. cati eggs.

value: 10 weeks


title: SW620-exos-2

source_name: exosomes from highly metastatic CRC cells SW620-2


title: HT29-exos-3

source_name: exosomes from weakly metastatic CRC cells HT29-3


title: cell_HepG2_rep1

value: HBV-negative liver cancer cells


title: HT29-exos-2

source_name: exosomes from weakly metastatic CRC cells HT29-2


title: T. cati cerebellum d28 rep 2


title: A549-ATOH8

city: Guangzhou

first: Ximeng

last: Liu

address: Zhongshan Road No.2 Yuexiu district

institute: SUN YAT-SEN UNIVERSITY

data_processing:
Illumina CASAVA software used for basecalling.
Original sequencing data were filtered out those containing Adapter, excessive N or a large number of low-quality bases to obtain high-quality sequencing data (clean reads).
Hisat2 used for alignment.
Cufflinks-2.2.1 used for calculating FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.FPKM.txt: Tab-delimited text files include FPKM values.
Supplementary_files_format_and_content: A549_vector_vs_A549_ATOH8.DiffExpGeneFilter.anno.txt: Tab-delimited text file includes differential expression analysis.

source_name: A549 cells with retroviral ATOH8 stably transduced

growth_protocol: The cells were grown in DMEM (Termo Fisher) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (penicillin 100 U ml–1 and streptomycin 10 μg ml–1).

extract_protocol:
The culture medium were removed, 1xPBS washed twice and RNA was harvested using Trizol reagent on ice. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Lung adenocarcinoma cell line

value: stable transduction with ATOH8


title: T. cati cerebellum d28 rep 1


title: SW480-exos-2

source_name: exosomes from weakly metastatic CRC cells SW480-2


title: SW480-exos-3

source_name: exosomes from weakly metastatic CRC cells SW480-3


title: A549-vector

source_name: A549 cells with retroviral vector stably transduced

value: stable transduction with vector


title: T. cati cerebellum d14 rep 3

description: Gene expression in the cerebellum 14 days post infection. Infection with 2000 embryonated T. cati eggs.

value: 8 weeks


title: T. cati cerebellum d14 rep 2

value: Male


title: T. cati cerebrum d120 rep 2

description: Gene expression in the cerebrum 120 days post infection. Infection with 2000 embryonated T. cati eggs.

source_name: cerebrum, T. cati-infected

value: cerebrum


title: T. cati cerebrum d120 rep 1


title: T. cati cerebrum d98 rep 1

description: Gene expression in the cerebrum 98 days post infection. Infection with 2000 embryonated T. cati eggs.


title: T. cati cerebrum d120 rep 3


title: T. cati cerebrum d98 rep 3


title: T. cati cerebrum d98 rep 2


title: T. cati cerebrum d70 rep 1

description: Gene expression in the cerebrum 70 days post infection. Infection with 2000 embryonated T. cati eggs.


title: T. cati cerebrum d70 rep 3


title: T. cati cerebrum d28 rep 2

description: Gene expression in the cerebrum 28 days post infection. Infection with 2000 embryonated T. cati eggs.


title: cell_Huh7_rep1


title: T. canis cerebellum d120 rep 1

description: Gene expression in the cerebellum 120 days post infection. Infection with 2000 embryonated T. canis eggs.

source_name: cerebellum, T. canis-infected

value: T. canis-infected


title: T. canis cerebellum d120 rep 2

value: cerebellum


title: T. cati cerebrum d28 rep 3

value: Female


title: T. cati cerebrum d14 rep 1

description: Gene expression in the cerebrum 14 days post infection. Infection with 2000 embryonated T. cati eggs.

value: T. cati-infected


title: T. cati cerebrum d14 rep 3


title: T. canis cerebellum d98 rep 2

description: Gene expression in the cerebellum 98 days post infection. Infection with 2000 embryonated T. canis eggs.


title: T. canis cerebellum d98 rep 3


title: T. cati cerebrum d28 rep 1


title: T. cati cerebrum d14 rep 2


title: T. canis cerebellum d70 rep 3

description: Gene expression in the cerebellum 70 days post infection. Infection with 2000 embryonated T. canis eggs.

value: 16 weeks


title: T. canis cerebellum d98 rep 1


title: T. canis cerebellum d70 rep 1


title: T. canis cerebellum d28 rep 3

description: Gene expression in the cerebellum 28 days post infection. Infection with 2000 embryonated T. canis eggs.


title: T. canis cerebellum d70 rep 2


title: T. canis cerebellum d28 rep 2


title: T. cati cerebellum d14 rep 1

source_name: cerebellum, T. cati-infected


title: liver, ctrl_ctrl_4

source_name: liver

value: liver

value: ctrl

value: male

value: ABTL


title: T. canis cerebellum d14 rep 3

description: Gene expression in the cerebellum 14 days post infection. Infection with 2000 embryonated T. canis eggs.


title: T. canis cerebellum d28 rep 1

value: 10 weeks


title: T. cati cerebrum d70 rep 2


title: T. canis cerebellum d14 rep 2


title: T. canis cerebrum d120 rep 3

description: Gene expression in the cerebrum 120 days post infection. Infection with 2000 embryonated T. canis eggs.

source_name: cerebrum, T. canis-infected

value: 23 weeks


title: T. canis cerebrum d120 rep 2


title: T. canis cerebrum d120 rep 1


title: T. canis cerebrum d98 rep 2

description: Gene expression in the cerebrum 98 days post infection. Infection with 2000 embryonated T. canis eggs.

value: 20 weeks


title: T. canis cerebrum d98 rep 1


title: T. canis cerebrum d70 rep 3

description: Gene expression in the cerebrum 70 days post infection. Infection with 2000 embryonated T. canis eggs.


title: T. canis cerebrum d98 rep 3


title: T. canis cerebrum d14 rep 3

description: Gene expression in the cerebrum 14 days post infection. Infection with 2000 embryonated T. canis eggs.


title: T. canis cerebrum d28 rep 3

description: Gene expression in the cerebrum 28 days post infection. Infection with 2000 embryonated T. canis eggs.


title: T. canis cerebrum d70 rep 2


title: T. canis cerebrum d14 rep 1


title: T. canis cerebrum d28 rep 2


title: T. canis cerebrum d14 rep 2