title: ATAC-seq_LPS_6h_Donor3


title: ATAC-seq_LPSGolgiPlug_6h_Donor1

status: Public on Jun 20 2022

type: SRA

city: Cambridge

first: Vinay

last: Kartha

state: MA

address: 7 Divinity Ave

country: USA

institute: Harvard University

library_source: genomic

data_processing:
Per-read bead barcodes were parsed and trimmed using UMI-TOOLs (https://github.com/CGATOxford/UMI-tools). Constitutive elements of the bead barcodes were assigned to the closest known sequence allowing for up to 1 mismatch per 6-mer or 7-mer (mean >99% parsing efficiency across experiments).
Paired-end reads were aligned to hg19 using BWA (http://bio-bwa.sourceforge.net/) on the Illumina BaseSpace online application.
We used bead-based ATAC-seq processing (BAP) (https://github.com/caleblareau/bap), to identify systematic biases (i.e. reads aligning to an inordinately large number of barcodes), barcode-aware deduplicate reads, and perform merging of multiple bead barcode instances associated with the same cell. Barcode merging is necessary due to the nature of the BioRad SureCell scATAC-seq procedure used in this study, which enables multiple beads per droplet. BAP uses as input an alignment (.bam) file for a given experiment with a bead barcode identifier indicated by a SAM tag.
Genome-wide chromatin accessibility peaks were called using MACS v2 (MACS2) (Zhang et al., 2008) on the merged aligned scATAC-seq reads per treatment condition, generating a list of peak summit calls per condition. As previously described, summits were then ranked per condition based on their FDR score (from MACS2), and the summit scores rank-normalized such that the normalized summit scores rendered are comparable across conditions (Satpathy et al., 2019). Peak summits were then padded by 400 bases on either end (generating 801 bp windows), and overlapping peak windows filtered iteratively such that windows with higher scores were retained at each step. This resulted in a filtered list of disjoint peaks (n=219,136), which were finally resized to 301 bp (i.e. + 150 bp from each peak summit) and used for all downstream analyses.
A matrix of reads in peaks counts for single cells was obtained by counting the number of uniquely aligned fragments (with coordinates offset +4/-5 bp for the +/- strand to adjust for Tn5 integration) overlapping the determined peak window genomic ranges, grouped by cell barcode ID, done using custom R code
Genome_build: hg19
Supplementary_files_format_and_content: Peak file (BED) contains chromsome, start and end coordinates for determined chromatin accessibility peak window ranges. cellMeta file contains single cell barcode information for the final set of filtered scATAC stimulation cells used in the analysis. Fragments.tsv.gz files contain all Tn5-corrected coordinates for aligned fragments generated using BAP, which can be used to overlap with peaks to get counts of Tn5 insertions falling within peaks for each cell barcode.

molecule: genomic DNA

organism: Homo sapiens

source_name: Human PBMCs

growth_protocol: Cryopreserved human peripheral blood mononuclear cells (PBMCs) were purchased from Allcells. Cells were quickly thawed in a 37°C water bath, rinsed with culture medium (RPMI 1640 medium supplemented with 15% FBS and 1% Pen/Strep) and then treated with 0.2 U/μL DNase I in 10mL of culture medium at 37°C for 30 min. After DNase I treatment, cells were washed with medium once, filtered with a 35 μm cell strainer and cell viability and concentration were measured with trypan blue on the TC20 Automated Cell Counter. Cell viability was greater than 90% for all samples.

extract_protocol:
After stimulation, cells were harvested and washed twice with ice cold 1x PBS + 0.1% BSA and cell viability and concentration were measured with trypan blue on the TC20 Automated Cell Counter. For a detailed description of tagmentation protocols and buffer formulations refer to the SureCell ATAC-Seq Library Prep Kit User Guide (17004620, Bio-Rad). Harvested cells and tagmentation related buffers were chilled on ice. Lysis was performed simultaneously with tagmentation. Washed and pelleted cells were resuspended in Whole Cell Tagmentation Mix containing 0.1% Tween-20, 0.01% Digitonin, 1x PBS supplemented with 0.1% BSA, ATAC Tagmentation Buffer and ATAC Tagmentation Enzyme (ATAC Tagmentation Buffer and Enzyme are both included in the SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad)). Cells were mixed and agitated on a ThermoMixer for 30 min at 37°C. Tagmented cells were kept on ice prior to encapsulation.
Tagmented cells were loaded onto a ddSEQ Single-Cell Isolator. Single-cell ATAC-seq libraries were prepared using the SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad) and SureCell ddSEQ Index Kit (12009360, Bio-Rad). Bead barcoding and sample indexing were performed in a C1000 Touch™ Thermal cycler with a 96-Deep Well Reaction Module: 37°C for 30 min, 85°C for 10 min, 72°C for 5 min, 98°C for 30 sec, 8 cycles of 98°C for 10 sec, 55°C for 30 sec, and 72°C for 60 sec, and a single 72°C extension for 5 min to finish. Emulsions were broken and products cleaned up using Ampure XP beads. Barcoded amplicons were further amplified using a C1000 Touch™ Thermal cycler with a 96-Deep Well Reaction Module: 98°C for 30 sec, 6-9 cycles (cycle number depending on the cell input, Section 4 Table 3 of the User Guide) of 98°C for 10 sec, 55°C for 30 sec, and 72°C for 60 sec, and a single 72°C extension for 5 min to finish. PCR products were purified using Ampure XP beads and quantified on an Agilent Bioanalyzer using the High-Sensitivity DNA kit. Libraries were loaded at 1.5 pM on a NextSeq 550 using the NextSeq High Output Kit and sequencing was performed using the following read protocol: Read 1 118 cycles, i7 index read 8 cycles, and Read 2 40 cycles. A custom sequencing primer is required for Read 1 (16005986, Bio-Rad; included in the kit).

treatment_protocol: Cells were plated at a concentration of 1 x 10^6 cell/mL, rested at 37°C and 5% CO2 for 1 h and then treated with the specified concentrations of the following stimulants (or DMSO as a control) for either 1 h or 6 h: 1) 20 ng/mL Lipopolysaccharide (LPS), 2) 50 ng/mL Phorbol 12-myristate 13-acetate (PMA) + 250 ng/mL Ionomycin calcium salt, 3) 20 ng/mL Interferon gamma (IFN-Ɣ). For the Golgi inhibitor experiments, cells were incubated for 6 h with GolgiPlug at a 1:1000 dilution plus stimulants at the concentrations indicated above (or GolgiPlug only as a control).

tag: cell type

value: PBMC

tag: stimulation

value: LPS + Golgi inhibitor

tag: donor

value: Donor 1

tag: time

value: 6 h


title: ATAC-seq_LPSGolgiPlug_6h_Donor2

value: Donor 2


title: ATAC-seq_LPS_1h_Donor4

value: LPS

value: Donor 4

value: 1 h


title: ATAC-seq_LPS_1h_Donor1


title: ATAC-seq_LPS_1h_Donor2


title: ATAC-seq_IFNGolgiPlug_6h_Donor3

value: Interferon gamma + Golgi inhibitor

value: Donor 3


title: ATAC-seq_IFNGolgiPlug_6h_Donor2


title: ATAC-seq_IFNGolgiPlug_6h_Donor1


title: ATAC-seq_IFN_6h_Donor2

value: Interferon gamma


title: ATAC-seq_IFN_6h_Donor3


title: ATAC-seq_ControlGolgiPlug_6h_Donor2

value: Control + Golgi inhibitor


title: ATAC-seq_IFN_6h_Donor1


title: ATAC-seq_ControlGolgiPlug_6h_Donor1


title: ATAC-seq_IFN_1h_Donor3


title: ATAC-seq_IFN_1h_Donor2


title: ATAC-seq_IFN_1h_Donor1


title: ATAC-seq_ControlGolgiPlug_6h_Donor3


title: ATAC-seq_Control_6h_Donor3

value: Control


title: ATAC-seq_Control_6h_Donor2


title: ATAC-seq_Control_6h_Donor4


title: ATAC-seq_Control_1h_Donor3


title: ATAC-seq_Control_1h_Donor4


title: ATAC-seq_Control_1h_Donor2


title: ATAC-seq_Control_1h_Donor1


title: ATAC-seq_LPS_1h_Donor3


title: 4C_Hoxd1_E125_FB_rep2

city: Geneva

first: Aurelie

last: Hintermann

address: 30 quai Ernest-Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

data_processing:
Library strategy: 4C-seq
All scripts are available on https://gitlab.unige.ch/Aurelie.Hintermann/hintermannetal2022
4C-seq reads were demultiplexed, mapped on GRCm38/mm10 mouse assembly and on GRCg6a/galGal6 chicken assembly, and analyzed using a local version of the 4C-seq pipeline of the Bioinformatics and Biostatistics Core Facility (BBCF) HTSstation (http://htsstation.epfl.ch) (David et al., 2014) using the facilities of the Scientific IT and Application Support Center of EPFL.
Profiles were normalized to a 5Mb region surrounding the HoxD cluster and smoothened using a window size of 11 fragments
Data was mapped on simplified genome assemblies comprising chromosomes only.
Genome_build: mm10
Genome_build: galGal6
Supplementary_files_format_and_content: Smoothed/normalized data (bedgraph), when multiple biological replicates were done, the average was done.
Supplementary_files_format_and_content: HoxD_minusNextVP (bedgraph) is the score of the viewpoint minus the score of the next viewpoint (i.e.Hoxd1 minus Hoxd4 and Hoxd4 minus Hoxd9)

organism: Mus musculus

source_name: forebrain

extract_protocol:
Circular chromosome conformation capture (4C-seq) was performed as described in (Noordermeer et al., 2011). Briefly, tissues were isolated in PBS supplemented with 10% Fetal Calf Serum and dissociated to single cell by collagenase treatment. Samples were fixed in 2% formaldehyde, lysed, and stored at −80°C. Samples were primarily digested with NlaIII (NEB, R0125L) followed by ligation under diluted conditions. After decrosslinking and DNA purification DpnII (NEB, R0543M) was used for the second restriction. All ligation steps were performed using highly concentrated T4 DNA ligase (Promega, M1794). For each viewpoint approximately 1μg of DNA was amplified by using 12 individual PCR reactions.
Libraries were constructed with inverse primers for different viewpoints (see Table 5) containing Illumina Solexa adapter sequences and sequenced on an Illumina HiSeq 2500 sequencer, as single-end reads (read length 100 base pairs or 80 base pairs). In some samples 4-bp barcodes were added between the adapter and each specific viewpoint to allow sample multiplexing.

treatment_protocol: Four telencephalons from E12.5 embryos were micro-dissected.

tag: developmental stage

tag: strains

tag: genotype

value: WT


title: 4C_Hoxd9_E125_FB_rep1


title: 4C_Hoxd9_E95_PT_rep2

data_processing:
Library strategy: 4C-seq
All scripts are available on https://gitlab.unige.ch/Aurelie.Hintermann/hintermannetal2022
4C-seq reads were demultiplexed, mapped on GRCm38/mm10 mouse assembly and on GRCg6a/galGal6 chicken assembly, and analyzed using a local version of the 4C-seq pipeline of the Bioinformatics and Biostatistics Core Facility (BBCF) HTSstation (http://htsstation.epfl.ch) (David et al., 2014) using the facilities of the Scientific IT and Application Support Center of EPFL.
Profiles were normalized to a 5Mb region surrounding the HoxD cluster and smoothened using a window size of 11 fragments
Data was mapped on simplified genome assemblies comprising chromosomes only.
Genome_build: mm10
Genome_build: galGal6
Supplementary_files_format_and_content: Smoothed/normalized data (bedgraph), when multiple biological replicates were done, the average was done.
Supplementary_files_format_and_content: HoxD_minusNextVP (bedgraph) is the score of the viewpoint minus the score of the next viewpoint (i.e.Hoxd1 minus Hoxd4 and Hoxd4 minus Hoxd9)
All scripts are available on https://gitlab.unige.ch/Aurelie.Hintermann/hintermannetal2022
4C-seq reads were demultiplexed, mapped on GRCm38/mm10 mouse assembly and on GRCg6a/galGal6 chicken assembly, and analyzed using a local version of the 4C-seq pipeline of the Bioinformatics and Biostatistics Core Facility (BBCF) HTSstation (http://htsstation.epfl.ch) (David et al., 2014) using the facilities of the Scientific IT and Application Support Center of EPFL.
First, scores were normalized to million mapped reads
Then, profiles were normalized to a 5Mb region surrounding the HoxD cluster and smoothened using a window size of 11 fragments
Data was mapped on simplified genome assemblies comprising chromosomes only.
processed data files format and content: bw: 4C coverage normalized by the number of reads mapped.

source_name: posterior trunk

treatment_protocol: A portion of tissue corresponding to the tailbud, presomitic mesoderm, and 2-3 somite pairs, was micro-dissected from approximately fifteen E9.5 embryos.


title: 4C_Hoxd1_E125_FB_rep1


title: 4C_Hoxd4_E95_PT_rep1


title: 4C_Hoxd4_E125_FB_rep1


title: ATAC-seq_Control_6h_Donor1


title: 4C_Hoxd9_E95_PT_rep1


title: 4C_Hoxd4_E95_PT_rep2


title: 4C_Hoxd9_E125_FB_rep2


title: ChIP_H3K27ac_E125_FB_rep1

description: ChIP

data_processing:
All scripts are available on https://gitlab.unige.ch/Aurelie.Hintermann/hintermannetal2022
TruSeq adapters were removed from single-reads fastqs with cutadapt version 1.16 (Martin 2011 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -q 30 -m 15).
Filtered reads were mapped to the mouse genome mm10 with bowtie2 version 2.3.5 (Langmead et al. 2012 with default options). Only alignments with a mapping quality above 30 were kept (samtools version 1.9 Danecek et al. 2021).
Normalization was done by subsampling filtered reads with samtools view to the lowest number of reads among samples of one species, which is 42317564 for mouse and 22886295 for chicken.
Peak calling was run with a fixed fragment size of 200bp with macs2 callpeak version 2.1.1.20160309 (--call-summits --nomodel --extsize 200 -B).
Genome_build: mm10
Genome_build: galGal6
Supplementary_files_format_and_content: bigwig: normalized coverage track, when multiple biological replicates were done, the average was done
Supplementary_files_format_and_content: narrowPeak: narrowPeak from macs2
All scripts are available on https://gitlab.unige.ch/Aurelie.Hintermann/hintermannetal2022
TruSeq adapters were removed from single-reads fastqs with cutadapt version 1.16 (Martin 2011 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -q 30 -m 15).
Filtered reads were mapped to the mouse genome mm10 with bowtie2 version 2.3.5 (Langmead et al. 2012 with default options). Only alignments with a mapping quality above 30 were kept (samtools version 1.9 Danecek et al. 2021).
Normalization was done by subsampling filtered reads with samtools view to the lowest number of reads among samples of one species, which is 42317564 for mouse and 22886295 for chicken.
Peak calling was run with a fixed fragment size of 200bp with macs2 callpeak version 2.1.1.20160309 (--call-summits --nomodel --extsize 200 -B).
Open H3K27ac peaks were obtained by the intersection of H3K27ac peaks with ATAC peak regions in matching tissues, using betdtools intersect.
Conserved non-coding open H3K27ac peaks were obtained by the intersection of open H3K27ac peaks with conserved non-coding elements using betdtools intersect.
processed data files format and content: "OL_ATAC" narrowPeak: open H3K27ac peaks
processed data files format and content: "OL_ATAC_OL_CNEs" narrowPeak: conserved, non-coding and open H3K27ac peaks

extract_protocol:
ChIP-seq experiments were performed as described in (Rodríguez-Carballo et al 2017).
ChIP-seq libraries were prepared as described in (Rodríguez-Carballo et al 2017).

treatment_protocol: dissection: Six telencephalons from E12.5 embryos were micro-dissected.

tag: strain

tag: chip antibody

value: H3K27ac Diagenode #C15410196


title: RNAseq_whole_ear_skin_Sepi_aCTLA4_rep4

city: Bethesda

first: Verena

last: Link

address: 4 Memorial Drive

department: NIAID

institute: NIH

description: RNAseq_whole_ear_skin_Sepi_aCTLA4_rep4 TPM

library_source: transcriptomic

data_processing:
RNA-seq samples were mapped to the mm10 mouse genome with STAR. Samples which cluster together by treatment using Spearman correlation were kept, resulting in 5 replicates for S. epi treatment and 4 replicates for S. epi + anti-CTLA-4 treatment. Gene counts were calculated with HOMER’s analyzeRepeats with parameters -condenseGenes. Differential gene expression was calculated using DESeq2 (with HOMER’s getDiffExpression.pl) and genes with a fold change greater than 2 and FDR smaller than 0.05 were considered differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each RNA-seq sample

molecule: total RNA

source_name: whole tissue RNA-seq from mouse ear skin associated with S. epi for 8 days every other day and treated with anti-CTLA-4 immune checkpoint inhibitor

extract_protocol:
Mice were sacrificed 8 days after the first topical association of S. epi. Single-cell suspension from the ear pinnae were isolated as previously described were digested in RPMI 1640 containing 2 mM L-glutamine, 1 mM sodium pyruvate and nonessential amino acids, 20 mM HEPES, 100 U/ml penicillin, 100 mg/ml streptomycin, 50 mM β-mercaptoethanol, and 0.25 mg/ml Liberase purified enzyme blend (Roche Diagnostic Corp.) and incubated for 1 hour 45 minutes at 37°C in 5% CO2. Digested skin sheets were homogenized using the Medicon/Medimachine tissue homogenizer system (Becton Dickinson).
A ~1-mm skin region was micro-dissected at Day 8, submerged in RNAlater (Sigma Aldrich) and stored at −20°C. Total tissue RNA was isolated from skin tissue using the RNeasy Fibrous Tissue Mini kit (Qiagen), as per manufacturer’s instructions. Total mRNA library was prepared using 500 ng of input RNA with the Universal Plus# RNA-seq with NuQuant Library Prep Kit (Tecan) as per manufacturer’s instructions. Libraries were quantified using an Agilent Tapestation (High Sensitivity D1000 ScreenTape) and Qubit (Thermo Fisher Scientific). Libraries were pooled at equimolar concentrations and sequenced on an Illumina Nextseq 550 using the High Output v2 kit (75 cycles). Data was demultiplexed with blc2fastq.

treatment_protocol: S. epidermidis strain LM087 was cultured in tryptic soy broth at 37 C for 18 h. For topical association, mice were associated with S. epidermidis by applying bacterial suspension (109 CFU/ml) using a sterile cotton swab. Application of bacterial suspension was repeated every other day for 8 days.

tag: treatment

value: S. epi + anti-CTLA-4

tag: tissue

value: whole ear tissue


title: ChIP_H3K27ac_E125_WP_rep1

description: ChIP

source_name: whisker pad

treatment_protocol: dissection: Approximately twenty pairs of whisker pads were micro-dissected from E12.5 embryos.


title: EESREHAB->EES::cortex rep3

city: Vancouver

first: Jordan

middle: W

last: Squair

state: BC

address: 818 West 10th Avenue

country: Canada

institute: University of British Columbia

description:
10x v2
L-O8

data_processing:
Reads were aligned using Cellranger v.2.2.0
Exon and intron counts were tabulated using Velocyto
Data were analyzed using Seurat v3
Genome_build: mm10-1.2.0 (GRCm38.93)
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each cell with tab delimeters

source_name: Lumbar spinal cord

extract_protocol:
We performed single-nucleus dissociation of the mouse spinal cord according to our previously described procedures. Following euthanasia by isoflurane inhalation and cervical dislocation, the lumbar spinal cord site was immediately dissected and frozen on dry ice. We denounced spinal cords in 500 µl sucrose buffer (0.32 M sucrose, 10 mM HEPES [pH 8.0], 5 mM CaCl2, 3 mM Mg acetate, 0.1 mM EDTA, 1 mM DTT) and 0.1% Triton X-100 with the Kontes Dounce Tissue Grinder. 2 mL of sucrose buffer was then added and filtered through a µm cell strainer. The lysate was centrifuged at 3200 g for 10 min at 4°C. The supernatant was decanted, and 3 mL of sucrose buffer added to the pellet and incubated for 1 min. The pellet was homogenized using an Ultra-Turrax and 12.5 mL of density buffer (1 M sucrose, 10 mM HEPES [pH 8.0], 3 mM Mg acetate, 1 mM DTT) was added below the nuclei layer. The tube was centrifuged at 3200 g at 4°C and supernatant poured off. Nuclei on the bottom half of the tube wall were collected with 100 µl PBS with 0.04% BSA and 0.2 U/µl RNase inhibitor. Resuspended nuclei were filtered through a 30 µm strainer, and adjusted to 1000 nuclei/µl.
We carried out snRNA-seq library preparation using the 10x Genomics Chromium Single Cell Kit Version 2. The nuclei suspension was added to the Chromium RT mix to achieve loading numbers of 5,000. For downstream cDNA synthesis (13 PCR cycles), library preparation and sequencing, the manufacturer’s instructions were followed.

value: spinal cord

tag: condition

value: wild type

tag: molecule subtype

value: nuclear RNA


title: ChIP_H3K27ac_E125_DFL_rep1

description: ChIP

data_processing:
All scripts are available on https://gitlab.unige.ch/Aurelie.Hintermann/hintermannetal2022
TruSeq adapters were removed from single-reads fastqs with cutadapt version 1.16 (Martin 2011 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -q 30 -m 15).
Filtered reads were mapped to the mouse genome mm10 with bowtie2 version 2.3.5 (Langmead et al. 2012 with default options). Only alignments with a mapping quality above 30 were kept (samtools version 1.9 Danecek et al. 2021).
Normalization was done by subsampling filtered reads with samtools view to the lowest number of reads among samples of one species, which is 42317564 for mouse and 22886295 for chicken.
Peak calling was run with a fixed fragment size of 200bp with macs2 callpeak version 2.1.1.20160309 (--call-summits --nomodel --extsize 200 -B).
Genome_build: mm10
Genome_build: galGal6
Supplementary_files_format_and_content: bigwig: normalized coverage track, when multiple biological replicates were done, the average was done
Supplementary_files_format_and_content: narrowPeak: narrowPeak from macs2

source_name: distal forelimb

treatment_protocol: dissection: see (Rodríguez-Carballo et al., 2017)


title: ChIP_H3K27ac_E85_PT_rep2

description: ChIP

treatment_protocol: dissection: A portion of tissue corresponding to the tailbud, presomitic mesoderm, and 2-3 somite pairs, excluding as much as possible the region of the evaginating hindlimb buds, was micro-dissected from approximately sixty E8.5 embryos.


title: ChIP_H3K27ac_E85_PT_rep1

description: ChIP


title: 4C_Hoxd4_E125_FB_rep2


title: EESREHAB->EES::cortex rep2

description:
10x v2
L-O4


title: 4C_Hoxd1_E95_PT_rep1


title: ChIP_H3K27ac_E125_PFL_rep1

description: ChIP

source_name: proximal forelimb


title: EESREHAB->EES::cortex::walking rep3

description:
10x v2
K-O9


title: EESREHAB->EES::cortex rep1

description:
10x v2
L-O13


title: EESREHAB->EES::cortex::walking rep1

description:
10x v2
K-O3


title: RNAseq_whole_ear_skin_Sepi_aCTLA4_rep3

description: RNAseq_whole_ear_skin_Sepi_aCTLA4_rep3 TPM


title: EESREHAB->EES::cortex::walking rep2

description:
10x v2
K-O5


title: RNAseq_whole_ear_skin_Sepi_aCTLA4_rep2

description: RNAseq_whole_ear_skin_Sepi_aCTLA4_rep2 TPM


title: RNAseq_whole_ear_skin_Sepi_rep5

description: RNAseq_whole_ear_skin_Sepi_rep5 TPM

source_name: whole tissue RNA-seq from mouse ear skin associated with S. epi for 8 days every other day

value: S. epi


title: RNAseq_whole_ear_skin_Sepi_aCTLA4_rep1

description: RNAseq_whole_ear_skin_Sepi_aCTLA4_rep1 TPM


title: RNAseq_whole_ear_skin_Sepi_rep3

description: RNAseq_whole_ear_skin_Sepi_rep3 TPM


title: SCI->EES::walking rep3

description:
10x v2
J-O12


title: RNAseq_whole_ear_skin_Sepi_rep2

description: RNAseq_whole_ear_skin_Sepi_rep2 TPM


title: EESREHAB->EES rep2

description:
10x v2
I-34

value: EESREHAB->EES


title: EESREHAB->EES rep1

description:
10x v2
I-23


title: RNAseq_whole_ear_skin_Sepi_rep4

description: RNAseq_whole_ear_skin_Sepi_rep4 TPM


title: SCI->EES::walking rep2

description:
10x v2
J-36


title: EESREHAB->EES::walking rep3

description:
10x v2
H-8


title: EESREHAB->EES rep3

description:
10x v2
I-9


title: EESREHAB->EES::walking rep2

description:
10x v2
H-18


title: SCI->EES::walking rep1

description:
10x v2
J-32


title: AsPAC2

city: Frederiksberg C

first: Andrew

last: Williams

state: --- Select One ---

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

data_processing:
Adaptor sequences and low quality reads removed
Mapped to Sus Scrofa (ss11.1) using HISAT
DEG assessed using DeSeq2
Assembly: ss11.1
Supplementary files format and content: excel file with count data for each sample.

organism: Sus scrofa

source_name: Liver tissue

growth_protocol: Pigs (aged 10 weeks) were infected with 5000 A. summ eggs or left as controls, and killed 14 days post-infection. Dietary treatments were for 28 days, 14 days pre- and 14 days post-infection

extract_protocol:
Tissue was collected at euthanasia. Total RNA was extracted using miRNAeasy kits (Qiagen).
Standard Illumina

tag: breed

value: Danish Landrace x yorkshire

tag: agent

value: A. suum

tag: diet

value: control diet supplemented with 1 percent PAC derived from grape seed


title: EESREHAB rep3

description:
10x v2
G-6

value: EESREHAB


title: EESREHAB rep2

description:
10x v2
G-2


title: As5

value: control diet


title: Uninjured rep3

description:
10x v2
A-48

value: Uninjured


title: As6


title: RNAseq_whole_ear_skin_Sepi_rep1

description: RNAseq_whole_ear_skin_Sepi_rep1 TPM


title: Uninjured rep1

description:
10x v2
A-45


title: As3


title: As2


title: AsPAC5


title: SCI rep3

description:
10x v2
F-14

value: SCI


title: AsPAC4


title: As1


title: SCI rep1

description:
10x v2
F-12


title: PAC4

value: Control


title: PAC5


title: EESREHAB->EES::walking rep1

description:
10x v2
H-16


title: AsPAC1


title: PB_3

city: Tianjin

first: Jian

middle: ming

last: Yang

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

country: China

institute: Tianjin Medical University

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle with default  parameters.
Then clean reads were separately aligned to reference genome with orientation mode  using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method.
RSEM was used to quantify gene abundances.
Genome_build: R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R, http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html) was utilized for differential expression analysis.
Supplementary_files_format_and_content: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

source_name: Bone marrow-derived macrophages

growth_protocol: Bone marrow derived macrophages (BMDMs) were isolated from female C57BL/6J mice, and cultured in Dulbecco’s modified Eagle’s medium/F12 containing 10% heat inactivated fetal bovine serum, penicillin (100 U/ml), streptomycin (100µg/ml), and 10 ng/ml of murine M-CSF (315-02-50, Peprotech, St. Louis, MO, USA). Cells were differentiated for 6 days in the presence of M-CSF. The culture medium was refreshed every 3 days.

extract_protocol:
BMDMs treated with CNF1 or dialysis buffer were lysis in Trizol reagent and harvested. Illumina TruSeq RNA Sample Prep Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Recombinant CNF1 or dialysis buffer were used to treat bone marrow-derived macrophages (BMDMs]) for 6 h.

value: Bone marrow-derived macrophages

value: treated with dialysis buffer


title: Uninjured rep2

description:
10x v2
A-46


title: EESREHAB rep1

description:
10x v2
G-17


title: Control, uninfected 6


title: Control, uninfected 5


title: PAC6


title: Control, uninfected 2


title: SCI rep2

description:
10x v2
F-13


title: 24HPI Rep 2

city: Athens

first: Oshri

last: Avraham

state: GA

address: 120 Cedar St

department: Cellular Biology

institute: University of Georgia

description: Spots were injured with a blade twenty-four hours prior to collection on DIV7

data_processing:
Adapter ends were trimmed using FastQC
Reads were aligned to mm10 using STAR-align with default settings
Reads aligned to genes were counted using Htseq-counts with default settings
Differential expression was calculated using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Text files include gene counts
Supplementary_files_format_and_content: XLSX File includes differential expression analysis from DESeq2

source_name: Embryonic Dorsal Root Ganglia

extract_protocol:
Invitrogen PureLink RNA Minikit with on-column Dnase treatment
Ribo-Zero Gold rRNA depletion then Clontech SMARTer cDNA Synthesis kit

treatment_protocol: Control cells were collected at DIV7. All other conditions were injured with a blade and collected at 1, 3, 8, 16, or 24 hours post axotomy.


title: Control, uninfected 3


title: AsPAC3


title: 16HPI Rep 2

description: Spots were injured with a blade sixteen hours prior to collection on DIV7


title: CHiC E9.5 posterior trunks

description: Capture Hi-C

data_processing:
All scripts are available on https://gitlab.unige.ch/Aurelie.Hintermann/hintermannetal2022
Raw reads were preprocessed with cutadapt version 1.16 (Martin 2011 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT --minimum-length=15 --pair-filter=any --quality-cutoff=30).
Then hicup version 0.6.1 (Dryden et al. 2014) with bowtie2 version 2.2.6 (Langmead et al. 2012) and samtools 1.2 (Danecek et al. 2021) were used with default parameters.
The pairs  with both mates MAPQ30 and in the capture region (chr2:72402000-77000000 (mm10) and chr7:15000000–17000000 (galGal6)) were then loaded to a 5kb (mouse) and 2.5kb (chicken) resolution matrices with cooler version 0.7.4 (Abdennur and Mirny 2020).
The matrices obtained were corrected with hicCorrectMatrix tool version 3.5.3  (Ramirez et al. 2018, Wolff et al. 2018 and Wolff et al. 2020) and cooler balance.
Genome_build: mm10
Genome_build: galGal6
Supplementary_files_format_and_content: validPairs_filtered.csort.gz: valid pairs in juicebox format: Each line is a pair: <readname> <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2> str = strand (0 for forward, anything else for reverse). Only pairs with both mates MAPQ30 and in the capture region (chr2:72402000-77000000 (mm10) and chr7:15000000–17000000 (galGal6)).
Supplementary_files_format_and_content: raw.cool: raw matrices
Supplementary_files_format_and_content: iced.cool: matrices ICEd normalized
Supplementary_files_format_and_content: domains.bed: TAD calling on Captured region

extract_protocol:
Micro-dissected E9.5 posterior trunks and HH18 posterior trunks were isolated in PBS supplemented with 10% Fetal Calf Serum and dissociated into single cell by collagenase treatment (10 µl of collagenase 50mg/ml (Sigma C9697) at 37º for approximately 15 mn). Samples were cross-linked with 2% formaldehyde (ThermoFisher 28908) for 10 minutes at room temperature and washed three times with PBS containing proteinase inhibitor. After discarding the supernatant cells were stored at -80º. Further processing was performed as described in (Yakushiji-Kaminatsui et al., 2018)
Following the Hi-C protocol, ligated DNA fragments were processed through the Agilent SureSelectXT protocol to enrich for fragments coming from the probe regions chr2:72240000-76840000 (mm9) and chr7:14946000–17870000 (galGal5).

value: WT


title: PAC1


title: CN_3

value: treated with CNF1


title: PAC3


title: CN_2


title: CN_1


title: 8HPI Rep 3

description: Spots were injured with a blade eight hours prior to collection on DIV7


title: PAC2


title: 8HPI Rep 2


title: Slide4_2_B2

description: courtine_lumbar-EES-rehab-spatial_UMI.mtx

data_processing:
Library strategy: Spatial transcriptomics
Reads were aligned using Cellranger v.2.2.0
Exon and intron counts were tabulated using Velocyto
Data were analyzed using Seurat v3
Genome_build: mm10-1.2.0 (GRCm38.101)
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each cell with tab delimeters

extract_protocol:
Mouse spinal cords were embedded in OCT and cryosections were generated at 10 µm at −20 °C. Sections were immediately placed on chilled Visium Tissue Optimization Slides (catalog no. 1000193, 10x Genomics) or Visium Spatial Gene Expression Slides (catalog no. 1000184, 10x Genomics). Tissue sections were then fixed in chilled methanol and stained according to the Visium Spatial Gene Expression User Guide (catalog no. CG000239 Rev A, 10x Genomics) or Visium Spatial Tissue Optimization User Guide (catalog no. CG000238 Rev A, 10x Genomics). For gene expression samples, tissue was permeabilized for 12 min , which was selected as the optimal time based on tissue optimization time-course experiments. Brightfield histology images were taken using a 10× objective on a slide scanner (Olympus VS-120 Slide scanner). For tissue optimization experiments, fluorescent images were taken with a TRITC filter using a 10× objective and 400-ms exposure time.
Spatial transcriptomics libraries were prepared according to the Visium Spatial Gene Expression User Guide. They were then clustered at 270 pM on a paired-end HiSeq4000 flow cell and sequenced on a HiSeq4000 System (Illumina) at a sequencing depth of approximately 140–180 Mio read per sample. Sequencing was performed using the following read protocol: read 1: 28 cycles; i7 index read: 8 cycles; i5 index read: 8 cycles; and read 2: 98 cycles.

value: spinal cord


title: PB_2


title: As4


title: PB_1


title: 3HPI Rep 3

description: Spots were injured with a blade three hours prior to collection on DIV7


title: Slide4_1_B2

value: wild type


title: 3HPI Rep 2


title: Slide3_4_B2


title: Slide3_3_B1


title: 24HPI Rep 3


title: 24HPI Rep 1


title: Control, uninfected 4


title: Slide3_2_B3


title: 1HPI Rep 3

description: Spots were injured with a blade one hour prior to collection on DIV7


title: 16HPI Rep 3


title: Slide2_4_B2


title: 1HPI Rep 1


title: 16HPI Rep 1


title: Slide4_4_B1


title: Control, uninfected 1


title: Slide4_3_B1


title: Slide2_1_B2


title: 8HPI Rep 1


title: Slide3_1_B3


title: Indeterminate, clone 6.4, 24 hpi - Replicate 2

city: São Paulo

first: Theo

last: Oliveira

state: State/Province Not Applicable

address: Av Dr Eneas de Carvalho 44

department: Heart Institute

country: Brazil

institute: University of São Paulo

data_processing:
Sequence QC was performed with FASTQC.
The raw reads were aligned by STAR to human genome (hg38)
Assembly: hg38
Supplementary files format and content: TXT file contains raw counts for each sample

source_name: Cardiac

growth_protocol: hiPSC-derived cardiomyocytes were maintained in RPMI supplemented with B27 , 1% PS, in a incubator at 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Trizol protocol according to the manufacturer's instructions.
Library preparation was conducted using the Nextera library preparation method.
RNA-seq library samples were pooled and run on four lanes (one flow cell) using the Illumina NextSeq500 platform.

treatment_protocol: Infected replicates were incubated with T. cruzi trypomastigotes in a ratio of 1:5 for 24 hours in RPMI supplemented with B27

value: Cardiac

tag: cell line

value: Cardiomyocytes

tag: disease state

value: Indeterminate

tag: infection

value: T. cruzi Y strain


title: Indeterminate, clone 6.4, 0 hpi - Replicate 1

tag: cell type

value: Non-infected


title: 3HPI Rep 1


title: Slide2_2_B1


title: Slide1_4_B1


title: LU5; rep2

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

description:
LU5_2
processed data file: count.txt

data_processing:
Basecalls performed using RTA 2.7.3.
Bad quality reads were filtered out using Trimmomatic (v 0.36) with the following parameters: HEADCROP:3 TRAILING:10 MINLEN:25
Paired-end reads were aligned to the mm10 genome assembly using STAR (v2.5.2b), and read count per gene was subsequently estimated with the following parameters: --outFilterType BySJout --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --outFilterMismatchNmax 2 --quantMode GeneCounts --runThreadN ${NBCPU} --outSAMtype BAM SortedByCoordinate
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: count.txt: Tab-delimited text file includes raw counts of sequencing reads per gene for each sample.

source_name: KRAS(G12v)-expressing sarcoma cells

growth_protocol: shASNS, shLuc and wild-type mouse sarcoma cells were grown in DMEM containing 0 mg/L asparagine, 5 mg/L asparagine, or 100mg/L asparagine. shLuc mouse sarcoma cells were grown in DMEM containing 5 mg/L asparagine.

extract_protocol:
Cells were harvested, and total RNA was isolated using TRIzol Reagent (Ambion, 15596018).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Standard DMEM was supplemented with 0 mg/l, 5mg/l or 100mg/l asparagine.

value: sarcoma cells

tag: shRNA

value: shLuc

tag: asparagine supplementation

value: 5 mg/L asparagine


title: Indeterminate, clone 4.5, 0 hpi - Replicate 2


title: Indeterminate, clone 4.5, 24 hpi - Replicate 1


title: AS100; rep1

description:
AS100_1
processed data file: count.txt

value: shAsns

value: 100 mg/L asparagine


title: Indeterminate, clone 4.5, 0 hpi - Replicate 1


title: Chagas Cardiomyopathy, clone 6.6, 0 hpi - Replicate 2

value: Chagas Cardiomyopathy


title: Slide2_3_B3


title: AS0; rep2

description:
AS0_2
processed data file: count.txt

value: 0 mg/L asparagine


title: AS0; rep1

description:
AS0_1
processed data file: count.txt


title: Chagas Cardiomyopathy, clone 5.1, 24 hpi - Replicate 2


title: Chagas Cardiomyopathy, clone 6.6, 0 hpi - Replicate 1


title: Control Rep 2

description: Spots were collected at DIV 7

tag: developmental stage


title: Control Rep 1

description: Spots were collected at DIV 7


title: Control Rep 3

description: Spots were collected at DIV 7


title: Slide1_3_B2

tag: genotype


title: Torin2_H3K27me3_rep1

city: Boston

first: Jen

last: Sheen

address: 185 Cambridge st. CPZN7620

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
The quality of each sequencing library was assessed by examining fastq files with FastQC (version 0.11.5). Then, sequencing adaptors were removed using Trimmomatic (version 0.36). The Sickle program was used to eliminate bases with low quality scores (< 20) and short reads (length < 20).
The ChIP-seq reads were mapped to Arabidopsis (TAIR10) and human (hg19) combined genome, using BWA-MEM (version 0.7.15-r1142-dirty). Moreover, the view function of samtools (version 1.6) was used to remove reads with quality (Q) < 20 [Q = -10log10(p), where p is an estimate of the probability that the alignment does not correspond to the read’s true point of origin]. The rmdup function of samtools (version 1.6) was used to remove duplicated reads mapped to exactly the same position because they were considered to be artifacts caused by PCR during the library construction step. The number of reads mapped to human genome was used to calculate reference derived normalization factor as previously described. MACS2 utility callpeak was used to identify read-enriched regions (peaks) and utility pileup was used to generate bedgraph files with default settings. The number of reads in the bedgraphs were then scaled by the reference derived normalization factor to generate reference-adjusted reads per million (RRPM). The bedGraphToBigWig (version 4) of UCSC was used to transfer bedgraph files to bigwig files, and then the bigwig files were loaded onto JBrowse (version 1.12.1) for data visualization.
The RNA-seq reads were mapped to the Arabidopsis (TAIR10) genome with HISAT2 program (version 2.1.0). The featureCount program of Subread package (version 1.5.3) was used to quantify the RNA-seq expression levels of the TAIR10 annotated gene models.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig; peak files

organism: Arabidopsis thaliana

source_name: Seven-day-old seedlings

growth_protocol: Col-0 and tor-es grown in the ½ MS (with 0.5% Sucrose, PH 5.7) liqid medium were collected at the seventh day. Transgenic Arabidopsis expressing FIE artificial miRNA was generated with PLB21 vector. The heterozygote fie mutant plants were complemented with wild-type and phosphorylation site mutant form of GFP-FIE. Western blot was used to confirm the protein expression. Homozygote plants were isolated with genotyping. Plants were grown on ½ MS (with 0.5% Sucrose, PH 5.7) solid medium.  Then, the aerial part of plants was collected after two weeks.

extract_protocol:
For ChIP-seq, 1 g of seedlings were collected after removing all the liquid with Kimwipes. Plant materials were ground into powder and suspended in 25 mL of nuclear isolation buffer. The crude extracts were incubated with 1% formaldehyde at room temperature for 20 minutes and stopped by adding 3.4 mL1M glycine.   Histone-DNA complexes were isolated from  sonicated nuclei with antibody.  For-RNA-seq, whole seedlings from liquid medium or the aerial parts of plants from the agar plate were harvested and frozen in liquid nitrogen.  Total RNA was isolated from liquid nitrogen ground samples with the Trizol reagent (Invitrogen), DNase I treated (RQ1 RNase-free DNase I, Promega). The resulting RNA (0.5 μg) was used for preparing the library
For ChIP-seq, NEBNext Ultra II DNA Library Prep Kit was used to make the library with 10 ng DNA. For enrich DNA fragments step, all the template and amplify 7 cycles. For-RNA-seq, NEBNext® Ultra II™ RNA Library Prep Kit for Illumina® using 500 ng of total RNA per library.  For enrich DNA fragments step, the templates were amplified for 8 cycles.

treatment_protocol: For TOR inhibator treaments, DMSO or 10 um Torin2 or AZD8055 were added to the midium on the fourth day, and treated for three more days.

value: H3K27me3 (Millipore, 07-449)


title: Chagas Cardiomyopathy, clone 5.1, 0 hpi - Replicate 2


title: Torin2_H3K27me3_rep2


title: AZD8055_H3K27me3_rep3


title: Indeterminate, clone 6.4, 0 hpi - Replicate 2


title: Slide1_2_B3

tag: strain


title: Chagas Cardiomyopathy, clone 5.1, 0 hpi - Replicate 1


title: Indeterminate, clone 4.5, 24 hpi - Replicate 2


title: Indeterminate, clone 6.4, 24 hpi - Replicate 1


title: DMSO_H3K27me3_rep3

tag: chip antibody

value: DMSO


title: Chagas Cardiomyopathy, clone 4.3, 24 hpi - Replicate 1


title: Slide1_1_B1


title: 1HPI Rep 2


title: AS5; rep2

description:
AS5_2
processed data file: count.txt


title: Col-0_H3K9me2_rep1

data_processing:
The quality of each sequencing library was assessed by examining fastq files with FastQC (version 0.11.5). Then, sequencing adaptors were removed using Trimmomatic (version 0.36). The Sickle program was used to eliminate bases with low quality scores (< 20) and short reads (length < 20).
The ChIP-seq reads were mapped to Arabidopsis (TAIR10) and human (hg19) combined genome, using BWA-MEM (version 0.7.15-r1142-dirty). Moreover, the view function of samtools (version 1.6) was used to remove reads with quality (Q) < 20 [Q = -10log10(p), where p is an estimate of the probability that the alignment does not correspond to the read’s true point of origin]. The rmdup function of samtools (version 1.6) was used to remove duplicated reads mapped to exactly the same position because they were considered to be artifacts caused by PCR during the library construction step. The number of reads mapped to human genome was used to calculate reference derived normalization factor as previously described. MACS2 utility callpeak was used to identify read-enriched regions (peaks) and utility pileup was used to generate bedgraph files with default settings. The number of reads in the bedgraphs were then scaled by the reference derived normalization factor to generate reference-adjusted reads per million (RRPM). The bedGraphToBigWig (version 4) of UCSC was used to transfer bedgraph files to bigwig files, and then the bigwig files were loaded onto JBrowse (version 1.12.1) for data visualization.

growth_protocol: Col-0 and tor-es grown in the ½ MS (with 0.5% Sucrose, PH 5.7) liqid medium  were collected at the seventh day. Transgenic Arabidopsis expressing FIE artificial miRNA was generated with PLB21 vector. The heterozygote fie mutant plants were complemented with wild-type and phosphorylation site mutant form of GFP-FIE. Western blot was used to confirm the protein expression. Homozygote plants were isolated with genotyping. Plants were grown on ½ MS (with 0.5% Sucrose, PH 5.7) solid medium.  Then, the aerial part of plants was collected after two weeks.

treatment_protocol: For es-tor mutant, 10 mM Oestradiol was added into the medium at the third day to induce TOR depletion. For fie-amiR-es mutant, 10 mM Oestradiol was added into the medium at the beginning to induce FIE depletion.

value: H3K9me2 (Millipore, 17-643)


title: tor-es_H3K9me2_rep2

value: tor-es


title: Col-0_H3K9me2_rep2


title: Chagas Cardiomyopathy, clone 6.6, 24 hpi - Replicate 2


title: tor-es_H3K9me2_rep3


title: AS100; rep2

description:
AS100_2
processed data file: count.txt


title: tor-es_H3K27me3_rep3


title: Chagas Cardiomyopathy, clone 6.6, 24 hpi - Replicate 1


title: AS5; rep1

description:
AS5_1
processed data file: count.txt


title: Torin2_H3K27me3_rep3

tag: treatment


title: AZD8055_H3K27me3_rep1


title: Chagas Cardiomyopathy, clone 4.3, 0 hpi - Replicate 2

tag: tissue


title: Chagas Cardiomyopathy, clone 5.1, 24 hpi - Replicate 1


title: AZD8055_H3K27me3_rep2


title: LU5; rep1

description:
LU5_1
processed data file: count.txt


title: DMSO_H3K27me3_rep2


title: Col-0_H3K27me3_rep1


title: SSTS/AAAA_H3K27me3_rep2

source_name: the aerial part of two-week-old seedlings

value: SSTS/AAAA/fie


title: DMSO_H3K27me3_rep1


title: tor-es_H3K27me3_rep2


title: GFP-FIE_H3K27me3_rep3

value: GFP-FIE/ fie


title: amiR-fie-es_H3K27me3_rep3

value: amiR-fie-es


title: Ctrl_H3K27me3_rep3


title: tor-es_H3K27me3_rep1


title: amiR-fie-es_H3K27me3_rep1


title: Chagas Cardiomyopathy, clone 4.3, 24 hpi - Replicate 2

value: Cardiac

value: Cardiomyocytes


title: Col-0_H3K9me2_rep3


title: Chagas Cardiomyopathy, clone 4.3, 0 hpi - Replicate 1

value: Non-infected


title: Col-0_H3K27me3_rep3


title: Col-0_H3K27me3_rep2


title: SSTS/AAAA_H3K27me3_rep3


title: GFP-FIE_rep3

data_processing:
The quality of each sequencing library was assessed by examining fastq files with FastQC (version 0.11.5). Then, sequencing adaptors were removed using Trimmomatic (version 0.36). The Sickle program was used to eliminate bases with low quality scores (< 20) and short reads (length < 20).
The RNA-seq reads were mapped to the Arabidopsis (TAIR10) genome with HISAT2 program (version 2.1.0). The featureCount program of Subread package (version 1.5.3) was used to quantify the RNA-seq expression levels of the TAIR10 annotated gene models.


title: GFP-FIE_rep1


title: GFP-FIE_rep2


title: tor-es_H3K9me2_rep1


title: GFP-FIE_H3K27me3_rep1


title: Ctrl_H3K27me3_rep1


title: Ctrl_H3K27me3_rep2


title: amiR-fie-es_H3K27me3_rep2


title: SSTS/AAAA_H3K27me3_rep1


title: Ctrl_rep3


title: 4C_HOXD9_HH35_FB_rep1

organism: Gallus gallus

treatment_protocol: A portion of forbrain was micro-dissected from approximately twenty HH18 embryos.

tag: strains

value: White Leghorn

value: WT


title: SSTS/AAAA_rep3


title: SSTS/AAAA_rep2


title: ChIP_H3K27ac_HH28_PFL_rep1

description: ChIP

treatment_protocol: dissection: see (Yakushiji-Kaminatsui et al., 2018)

value: H3K27ac Abcam #ab4729


title: amiR-fie-es_rep3


title: 210203874

type: RNA

city: Nanjing

first: Xiangyi

last: Kong

address: Hanzhong road

institute: The First Affiliated Hospital of Nanjing Medical University

description: Gene expression was measured using the nCounter platform (NanoString Technologies, Seattle, WA) and transcriptome analysis was based on the 289-immuno-gene panel. This panel allows simultaneous analysis of 289 genes involved in the immune response in cancer. Samples qualified for quality control were included in subsequent analysis.

hyb_protocol: Reporter and Capture probes against genes of interest were prepared as previously described by Geiss et al. (2008; PMID: 18278033). Data were collected and analyzed using the nCounter Digital Analyzer.

scan_protocol: according to the manufacturer's instructions (NanoStrings Technologies, Seattle, WA)

data_processing: The nSolver Analysis Software (NanoString Technologies) was used for the extraction of raw miRNA data and for checking the quality of the data. Using the positive control data, a generalized linear model was fitted with 8 negative and 6 positive controls, where the counts for each positive control follow a Poisson's distribution with the mean modeled as a linear function of concentration. Each sample was then normalized to the median slope and intercept of all samples and Iog2 transformed. Using the transformed data of all genes, a Bland-Altman plot was generated for each sample to compare the sample to the average of all samples. A loess curve was fitted for each Bland-Altman plot to globally normalize the transformed data as described in our recent publication. A two sample t-statistical was performed on each miRNA, and the miRNA was filtered based on the following three criteria: (a) p-value < 0.08; (b) the Iog2 fold change between PD and control is greater than 0.263 in absolute value, equivalent to 20% change; and (c) the mean of the Iog2 transformed gene expression for one of the two groups is at least 5.

label: biotin

source_name: primary liver cancer

label_protocol: Using 225 ng total RNA, 134 gene transcripts levels were assayed using Nanostring nCounter assay kits by direct digital detection following the manufacturer's guidelines (NanoString Technologies, Seattle, WA).

extract_protocol: Human Hepatocellular carcinoma tissues were collected from Hepatobiliary/Liver Transplantation Center, the First Affiliated Hospital of Nanjing Medical University and stored at -80℃ until RNA isolation.Total RNA was extracted using the miRvana RNA isolation kit,following the manufacturer's instructions(Ambion).

value: primary liver cancer

tag: histology

value: Hepatocellular carcinoma

tag: age

value: 86 years

tag: Sex

value: Female

tag: Stage

value: IIIA


title: amiR-fie-es_rep2


title: SSTS/AAAA_rep1


title: 4C_HOXD4_HH18_PT_rep1

treatment_protocol: A portion of tissue corresponding to the tailbud, presomitic mesoderm, and 2-3 somite pairs, was micro-dissected from approximately twenty HH18 embryos.


title: amiR-fie-es_rep1


title: Ctrl_rep2


title: 210203882

value: 74 years

value: Male


title: 4C_HOXD4_HH35_FB_rep1

data_processing:
Library strategy: 4C-seq
All scripts are available on https://gitlab.unige.ch/Aurelie.Hintermann/hintermannetal2022
4C-seq reads were demultiplexed, mapped on GRCm38/mm10 mouse assembly and on GRCg6a/galGal6 chicken assembly, and analyzed using a local version of the 4C-seq pipeline of the Bioinformatics and Biostatistics Core Facility (BBCF) HTSstation (http://htsstation.epfl.ch) (David et al., 2014) using the facilities of the Scientific IT and Application Support Center of EPFL.
Profiles were normalized to a 5Mb region surrounding the HoxD cluster and smoothened using a window size of 11 fragments
Data was mapped on simplified genome assemblies comprising chromosomes only.
Genome_build: mm10
Genome_build: galGal6
Supplementary_files_format_and_content: Smoothed/normalized data (bedgraph), when multiple biological replicates were done, the average was done.
Supplementary_files_format_and_content: HoxD_minusNextVP (bedgraph) is the score of the viewpoint minus the score of the next viewpoint (i.e.Hoxd1 minus Hoxd4 and Hoxd4 minus Hoxd9)


title: 4C_HOXD1_HH35_FB_rep1


title: GFP-FIE_H3K27me3_rep2

value: H3K27me3 (Millipore, 07-449)


title: Ctrl_rep1


title: 4C_HOXD1_HH18_PT_rep1

data_processing:
Library strategy: 4C-seq
All scripts are available on https://gitlab.unige.ch/Aurelie.Hintermann/hintermannetal2022
4C-seq reads were demultiplexed, mapped on GRCm38/mm10 mouse assembly and on GRCg6a/galGal6 chicken assembly, and analyzed using a local version of the 4C-seq pipeline of the Bioinformatics and Biostatistics Core Facility (BBCF) HTSstation (http://htsstation.epfl.ch) (David et al., 2014) using the facilities of the Scientific IT and Application Support Center of EPFL.
Profiles were normalized to a 5Mb region surrounding the HoxD cluster and smoothened using a window size of 11 fragments
Data was mapped on simplified genome assemblies comprising chromosomes only.
Genome_build: mm10
Genome_build: galGal6
Supplementary_files_format_and_content: Smoothed/normalized data (bedgraph), when multiple biological replicates were done, the average was done.
Supplementary_files_format_and_content: HoxD_minusNextVP (bedgraph) is the score of the viewpoint minus the score of the next viewpoint (i.e.Hoxd1 minus Hoxd4 and Hoxd4 minus Hoxd9)
All scripts are available on https://gitlab.unige.ch/Aurelie.Hintermann/hintermannetal2022
4C-seq reads were demultiplexed, mapped on GRCm38/mm10 mouse assembly and on GRCg6a/galGal6 chicken assembly, and analyzed using a local version of the 4C-seq pipeline of the Bioinformatics and Biostatistics Core Facility (BBCF) HTSstation (http://htsstation.epfl.ch) (David et al., 2014) using the facilities of the Scientific IT and Application Support Center of EPFL.
First, scores were normalized to million mapped reads
Then, profiles were normalized to a 5Mb region surrounding the HoxD cluster and smoothened using a window size of 11 fragments
Data was mapped on simplified genome assemblies comprising chromosomes only.
processed data files format and content: bw: 4C coverage normalized by the number of reads mapped.


title: 201204297

value: 88 years

value: IIIB


title: 4C_HOXD9_HH18_PT_rep1


title: ChIP_H3K27ac_HH28_DFL_rep1

description: ChIP


title: 201204301

value: 66 years


title: T3 1nM 3

city: Botucatu

first: Célia

middle: Regina

last: Nogueira

address: Av. Prof. Mário Rubens Guimarães Montenegro, s.n.

institute: Faculdade de Medicina de Botucatu - Unesp

data_processing:
Steps for adapter removal and low quality read filtering were performed using Cutadapt and Trimmomatic software.
The reads were aligned and quantified in Kallisto (version 0.43.0) using the Gh38 human genome index (GRCh38.p12 release-92) as a reference.
The abundance data (Counts) generated were imported using the Bioconductor Tximport package from R  and used for the analysis of differential gene expression with the Deseq2 package. Multifactor design analysis was used to control the effect of biological variation between samples from the same condition.
Assembly: GRCh38.p12 release-92
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Adipose tissue mesenchymal stem cells

growth_protocol: Primary cultures were derived from subcutaneous adipose tissue samples subjected to enzymatic digestion. Isolated adipose tissue-derived mesenchymal stem cells were plated at a density of 2 × 10^5 cells in 25cm^2 flasks and grown in Dulbecco's modified Eagle medium (DMEM), containing 10% fetal bovine serum (FBS) with 1% penicillin-streptomycin and 0.1% gentamicin (10 mg/mL; Invitrogen). Upon reaching 70% confluency, cells were trypsinized and transferred to a T75 flask for cell expansion. All cell cultures were maintained at 37°C in a humidified atmosphere with 5% CO2. For hASC differentiation into osteoblasts, cells were kept in complete DMEM supplemented with 0.1 μM dexamethasone (Sigma-Aldrich), 50 μM ascorbic acid (Sigma-Aldrich), and 10 mM β-glycerophosphate (Sigma-Aldrich) for 16 days.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA). RNA samples were quantified in Qubit and the integrity of the RNA was analyzed using a  Bioanalyzer 2100® (Agilent, Santa Clara, CA, USA). Three RNA samples from each group were used to build each of the libraries.
The libraries were constructed using the TruSeq1 RNA Sample Prep kit v2 (Illumina, San Diego, CA, USA) following the protocol suggested by the manufacturer. Runs were performed on the Illumina HiSeq2500 platform with 100 bp paired end reads.

treatment_protocol: After 16d of growth in differentiation medium, osteoblast-like cells were treated with either 1nM or 10nM T3 for 72h. Osteoblast-like cells grown in the absence of T3 were used as controls.

value: Osteoblast-like cell

value: treated with T3 1nM


title: 201204285

value: 42 years


title: T3 10nM 2

value: treated with T3 10nM


title: 210203912

value: 53 years


title: 210203877

value: 65 years

value: II


title: 201204290

value: primary liver cancer

value: Hepatocellular carcinoma

value: 60 years


title: 201204241

value: 64 years

value: Female


title: 201204292

value: 59 years

value: Male


title: T3 10nM 3


title: 201204299

value: 77 years


title: 201204286

value: 71 years


title: 210206563

value: IIIA


title: T3 10nM 1

value: Osteoblast-like cell


title: 200807569

value: 48 years


title: CTRL 3

value: untreated


title: 210201425

value: 47 years

value: IIIB


title: 210303763

value: 83 years


title: T3 1nM 2

value: treated with T3 1nM


title: 201204309

value: primary liver cancer

value: 85 years


title: 201204230

value: Hepatocellular carcinoma

value: 72 years


title: T3 1nM 1


title: CTRL 1


title: 200807576

value: 75 years


title: 200807550

value: 61 years

value: Female


title: 210409607

value: 66 years

value: Male


title: CTRL 2


title: BSL, wtBCG cultured at stationary phase in lipids

city: Mexico city

first: Lazaro

last: Garcia-Morales

state: Mexico

address: Av. Intituto Politecnico Nacional

department: MOLECULAR BIOMEDICIN

country: Mexico

institute: Center for Research and Advanced Studies of the National Polytechnic Institute

data_processing:
RNA-seq data were obtained via HiSeq 2500 System using HCS v2.2 software and obtained reads were processed to remove poly(A) and spacer sequences, and only those with quality scores of Q30 and a minimal length of 50 bases were used for analysis.
Assessment of read quality was carried out using the FASTX toolkit v. 0.0.13
Reads were cleaned in silico from rRNA sequences in order to increment the efficiency of the assembly process using the SortMeRNA software as described previously by Kopylova et al., (2002).
rRNA free mRNA were mapped against the M. bovis BCG Pasteur reference genome (accession no. NC_008769.1) with Bowtie v.1.1.2  and visualized with the Artemis sequence visualization and annotation tool v 16.0. Reads that mapped to more than one site were excluded.
The coverage estimation of the transcriptome of M. bovis BCG was determined by saturation curves from the “counts” values (number of reads that have been assigned to a gene) determined using the FeatureCounts software v 1. 5. 0.
Genome_build: Bowtie v.1.1.2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mycobacterium tuberculosis variant bovis BCG

source_name: cells

growth_protocol: M. bovis BCG Pasteur 1173P2 (wtBCG) and M. bovis BCG 2177c_Tngfp (mtBCG), a mutant strain obtained by transposition of the Tngfp in the BCG2177c gen (TetR repressor, Otal et al., 2017), were grown with agitation at 37 °C in Middlebrook 7H9 broth containing 0.2% dextrose (control medium) or a lipid mixture (oleic acid, palmitic acid, stearic acid, at a final concentration of 0.001% each, plus 0.01% cholesterol), as previously reported (Soto-Ramirez et al., 2017).

extract_protocol:
Total RNA from each culture condition was isolated as previously reported (Soto-Ramirez et al., 2017) and purified using Trizol™ reagent (Invitrogen, USA). As two strains (wtBCG and mtBCG) were used and four conditions were tested (exponential, stationary, dextrose and lipids). All samples  passed the quality tests required for RNAseq analysis: 1) concentration was evaluated using Qubit™ RNA HS Assay Kit in the Qubit™ 2.0 fluorometer, 2) DNA absence was analyzed by qPCR and 3) RNA integrity was analyzed with a bioanalyzer (Agilent Technologies).
RNA-seq libraries were prepared in accordance with the protocols reported previously (Rodriguez et al., 2014; Waldbauer et al.,2012). Briefly, RNA samples were diluted at a concentration of 0.4 µg/µL for rRNA removal using the mRNA Enrichment, MICROBExpress™ kit (Invitrogen, USA). mRNA was precipitated and solubilized in 20 µL DEPC-treated water. Purified mRNA was fragmented by divalent-cation hydrolysis (Fragmentation Buffer; Ambion, Austin, TX) at 70°C for 12 min to yield fragment sizes between 60 and 200 nt. After purification by the RNA Clean and Concentrator™ kit (Zymo Research, USA), mRNA samples were subjected to poly(A) tailing and end repairing (NEB Reagents). RNA was treated with antarctic phosphatase (New England Biolabs) and then phosphorylated at the 5’ ends with T4 PNK (New England Biolabs). The transcribed strand was labeled by ligation of a 5’ hybrid DNA-RNA primer (5-hybrid-0) and after purification with RNA clean XP beads (Beckman Coulter Genomics), the first strand cDNA synthesis reaction was carried out with SuperScript II reverse transcriptase (Invitrogen, USA) and Illumina’s poly(T) primer (IGA-dT16-VN). Reaction components of cDNA synthesis were removed by treatment with Agencourt AMPure XP SPRI beads (Beckman, USA), and primary transcripts were enriched with a high-fidelity polymerase (Accuzyme™ kit, Bioline) and the Illumina spacers as primers. Illumina adaptors and bar codes were ligated by PCR in accordance with the manufacturer’s instructions. Libraries were purified with SPRI beads (Beckman) and evaluated by Qubit™ 2.0 and Bioanalyzer (Agilent Technologies).  Finally, we obtained cDNA libraries with size of 350 bp and concentrations from 12.5 ng/µL to 35.7 ng/µL

treatment_protocol: We analyzed four conditions for each strain (exponential and stationary phases in the presence of lipids or dextrose as carbon sources). In order to obtain cultures at exponential and stationary phases, mycobacterial growth was monitored by measuring OD at 600nm each 24 h for 30 days. Hence, cultures from exponential phases were collected at day five (in lipids), and at day eight (in dextrose); while all stationary phases cultures were collected at day 25 regardless of the main carbon source. Cells of each condition were harvested for RNA isolation. Each condition included two biological replicates.

value: wild-type

tag: phase of growth

value: stationary

tag: carbon source

value: lipid mixture (fatty acids/cholesterol)


title: 201204220

value: 78 years

value: II


title: BSD, wtBCG cultured at stationary phase in dextrose

value: dextrose


title: MSD, mtBCG cultured at stationary phase in dextrose

value: mutant strain obtained by transposition of the gene BCG_ BCG_2177c


title: 210303142

value: 70 years

value: IIIA


title: FDUSCC3M

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2
Gene were quantified using featureCounts
Assembly: hg38
Supplementary files format and content: FPKM

source_name: Ovary

extract_protocol:
RNAstormTM FFPE kit (CELLDATA) was used to isolate total RNA from formalin-fixed paraffin-embedded surgically resected samples.
SMARTer Stranded Total RNA-Seq Kit—Pico Input Mammalian Library preparation kit (Clontech) was used for the preparation of strand-specific RNA-seq library.

tag: tissue type

value: ovarian metastasis of gastric adenocarcinoma

tag: source tumor type

value: adenocarcinoma with low differentiation


title: FDUSCC2N

source_name: Stomach

value: normal gastric mucosa


title: FDUSCC2M


title: MSL, wtBCG cultured at stationary phase in lipids.


title: FDUSCC3N


title: 200807566

value: primary liver cancer

value: Hepatocellular carcinoma

value: 57 years


title: 200807565

value: 74 years

value: Female


title: 200807543

value: 67 years

value: Male


title: FDUSCC2P

value: gastric adenocarcinoma


title: FDUSCC1M


title: FDUSCC1N


title: MED, mtBCG cultured at exponential phase in dextrose

value: exponential


title: MEL, wtBCG cultured at exponential phase in lipids

value: lipid mixture (fatty acids/cholesterol)


title: FDUSCC1P


title: 200807549

value: 63 years

value: IIIB


title: D2-PD1-19bbz

first: Jiqin

last: Zhang

address: No.500 Dongchuan Road

institute: East China Normal University

data_processing:
Basecalls performed using CASAVA version 1.8
cellranger (v3.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20%  passed the cell quality filtering and mitochondria genes were removed in the expression table. Seurat package (version: 2.3.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data. PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Assembly: GRCh38Ensembl104
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: T-cell product

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3’ V3.1 Reagent Kits (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ V3.1 Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols

tag: cell type

value: Primary cells


title: FDUSCC3P


title: D2-Untreated

source_name: T-cell

value: Untreated


title: snATAC-seq male e-cigarette

city: Loma Linda

first: Charles

last: Wang

state: CA

address: 11021 Campus Street

department: Department of Basic Sciences

institute: Loma Linda University

description:
snATAC_MEcig
10X single-cell chromatin accessibility
Droplet single nucleus-ATAC-seq
Single nuclei isolation and capture

data_processing:
HiSeq 4000 onboard basecalling by RTA 2.7.7.
snRNA-seq fastq files were generated using 10X Genomics cellranger (v3.1.0) mkfastq. Reads alignment, filtering, barcode and UMI counting were performed by cellrange count.
snATAC-seq fastq files were generated using 10X Genomics cellranger-atac (v1.0.0) mkfastq. Single-cell chromatin accessibility counts were generated by cellrange-atac count.
Genome_build: NCBI Rnor_6.0
Supplementary_files_format_and_content: For snRNA-seq, cell barcodes and genes are in tsv format; gene expression is in mtx format.
Supplementary_files_format_and_content: For snATAC-seq, barcoded and aligned fragment files are in tsv format, called peak locations are in BED format, and filtered peak barcode is in hdf5 format.

organism: Rattus norvegicus

source_name: P7 rat brain

growth_protocol: Pregnant Sprague-Dawley rats were purchased from Charles River Laboratories (Portage, MI) and were housed under controlled temperature (22 ºC) and photoperiod (12-h light and 12-h dark cycle) with food and water ad libitum.

extract_protocol:
10X Genomics protocol CG000124 (Isolation of nuclei for single cell RNA sequencing) and protocol CG000122 (Nuclei isolation from mouse brain tissue for single cell ATAC sequencing).
Chromium Next GEM Single Cell 3ʹ v3.1 and Chromium Next GEM Single Cell ATAC v1.1.

treatment_protocol: E-cigarette aerosol was delivered with a puff duration of 4 sec, 3 puffs in an inter-puff interval of 30 sec per vaping episode, and one episode per 1 hour in the dark phase of 12 hrs each day, which generates similar nicotine blood pharmacokinetics in the pregnant rats to those observed in human e-cigarette users. The dams were exposed to e-cigarettes for a total of 17 days from gestational day 4 (E4) to E20.

value: Sprague-Dawley

value: dam exposed to e-cigarette vapor

value: cortex and hippocampus

value: male


title: snATAC-seq female e-cigarette

description:
snATAC_FEcig
10X single-cell chromatin accessibility
Droplet single nucleus-ATAC-seq
Single nuclei isolation and capture


title: D1-Untreated


title: Cisplatin-treated sorted CSC-like MDA-MB-231, exosome (Replicate 2)

city: Semenyih

first: May Zie

last: Koh

state: Selangor

address: Jalan Broga

department: Faculty of Sciences and Engineering

country: Malaysia

institute: University of Nottingham Malaysia

hyb_protocol: The mixture were hybridization, followed by removal of unligated material via enzymatic purification. The aligned and immobilized probe-bound miRNAs on a surface of nCounter Cartridge prior scanning

scan_protocol: Quantification was conducted by scanning the fluorescent color-coded bar tags on the reporter probes with max-density scan (555 fields of view per sample)

data_processing:
Quality of Nanostring data was assessed based on four default parameters, including imaging, binding density, positive control linearity and positive control limit of detection. Background correction was performed on detected miRNA from Nanostring nCounter by subtracting mean plus twice the standard deviation (SD) of the eight negative controls as a cut-off point. Normalisation was performed using geometric mean of top 100 expressed miRNAs as normalisation factor.
nSolver 4.0 computed normalized signal intensity

label: fluorescent color-coded bar

label_protocol: RNA input was mixed with pairs of capture and reporter probes tailored to each miRNA

growth_protocol: The parental and sorted CSC-like MDA-MB-231 were cultured with or without 56µM of cisplatin treatment for 48 hours. All cells were maintained in 5% CO2 humidified incubator in exosomes depleted serum.

extract_protocol: Total RNA with retention of small RNAs from the cells were extracted using ExoRNeasy.

treatment_protocol: Cells were treated with 56µM of cisplatin for 48 hours prior to exosomes for RNA extraction.

tag: cell line

value: cisplatin


title: Sorted CSC-like MDA-MB-231, exosome (Replicate 2)

source_name: Sorted CSC-like MDA-MB-231, exosome

value: parental


title: D2-LV-19bbz


title: D2-AAVS1-19bbz


title: BEL, wtBCG cultured at exponential phase in lipids

value: wild-type


title: BED, wtBCG cultured at exponential phase in dextrose

value: dextrose


title: snATAC-seq female control

description:
snATAC_FCtr
10X single-cell chromatin accessibility
Droplet single nucleus-ATAC-seq
Single nuclei isolation and capture

value: dam exposed to regular air


title: snRNA-seq male e-cigarette

description:
snRNA_MEcig
10X single-cell gene expression
Droplet single nucleus-RNA-seq
Single nuclei isolation and capture
Premature RNA

value: female


title: D1-PD1-19bbz

value: Male


title: D1-AAVS1-19bbz


title: D1-LV-19bbz


title: Cisplatin-treated sorted CSC-like MDA-MB-231, exosome (Replicate 1)


title: Sorted CSC-like MDA-MB-231, exosome (Replicate 3)


title: Participant_19_Protein_After

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

institute: Copenhagen University

data_processing:
Basecalls performed using bcl2fastq version 2.20.0
STAR v. 2.7.2b was used to align reads onto the ENSEMBL 98 hg38 human genome assembly, with the GENCODE 32 gene model, both retrieved on 07.10.2019
reads were summarized onto genes by featureCounts v. 1.6.4. Fragments were only counted where both ends of the fragment were aligned
Genome_build: hg38
Supplementary_files_format_and_content: csv file with raw gene counts

source_name: Adipose tissue

extract_protocol:
Biopsy of subcutaneous adipose tissue (40 mg) was taken after local anesthesia from 21 individuals by a trained surgeon from Ribeirao Preto Medical School-USP. Systematically, all first biopsies were collected from the right side of the abdomen (first day of each nutritional intervention) and the second biopsy from the left side of the abdomen (last day of each nutritional intervention). The adipose tissue was rapidly transported to the research laboratory. Tissue samples were rinsed in phosphate-buffered saline to remove adhering blood, then were snap-frozen in liquid nitrogen and stored at -80ºC until completion of the study.
Libraries were prepared for RNAseq as previously described (ref Dall&Hassing et al 2021, PMID: 34762911). Briefly, RNA was isolated using Trizol (Thermofisher) followed by purification with an RNeasy mini kit (Qiagen). Libraries were prepared using the Illumina TruSeq Stranded total RNA Gold protocol (Illumina). Total RNA was depleted of rRNA, fragmented and converted to cDNA. cDNA was subsequently adenylated to prime for adaptor ligation and cleaned using AMPure beads. DNA fragments were amplified using PCR and subject to a final cleanup. Libraries were quality controlled using a Bioanalyzer instrument (Agilent Technologies). Libraries were subjected to 51-bp paired-end sequencing on a NovaSeq 6000 system (Illumina).

value: Adipose tissue

tag: timepoint

value: After

value: Protein restriction

tag: participant

value: Female

tag: library pool

value: A

tag: sequencing lane


title: Participant_20_Protein_After

description: Excluded from final analysis

tag: treatment

value: B


title: Participant_19_Protein_Before

tag: tissue

value: Before


title: Participant_18_Protein_Before

value: C


title: snRNA-seq female control

description:
snRNA_FCtr
10X single-cell gene expression
Droplet single nucleus-RNA-seq
Single nuclei isolation and capture
Premature RNA

tag: strain

value: Sprague-Dawley

value: cortex and hippocampus


title: MDA-MB-231 parental, exosome (Replicate 3)

source_name: MDA-MB-231 parental, exosome


title: snRNA-seq male control

description:
snRNA_MCtr
10X single-cell gene expression
Droplet single nucleus-RNA-seq
Single nuclei isolation and capture
Premature RNA


title: rdd_flg22_24h_WGBS_rep2

city: Wuhan

first: mengling

state: Hubei

address: shizisan

department: College of Plant Science and Technology

institute: Huazhong Agricultural Universityhuazong

description:
rdd-flg22-24h.CG.wig
rdd-flg22-24h.CHG.wig
rdd-flg22-24h.CHH.wig

data_processing:
Whole-Genome Bisulfite Sequencing were performed by BGI Genomics (Shenzhen, China). Sequencing was performed on an Illumina HiSeq 4000 instrument to generate paired-end reads.For data analysis, paired-end sequencing reads were first trimmed with Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) for removal of Illumina adapters and low-quality bases (Phred score < 20). The cleaned reads were then aligned to TAIR10 genome using bsmap with default settings. Only uniquely mapped reads were retained for further analysis. PCR duplicates were marked by Picard (https://broadinstitute.github.io/picard/). Further processing was accomplished via SAMtools , BAMtools  and bamUtil (https://github.com/statgen/bamUtil/). Methylation ratio was extracted with BatMeth2 .
Genome_build: TAIR 10
Supplementary_files_format_and_content: wig files were generated using script

growth_protocol: Plants were grown in soil (Metro Mix 366)  in a growth room at 21°C, 45% humidity, and 75 μE m-2 s-1 light with a 12-h-light/12-h-dark photoperiod.Seedlings were germinated on half-strength Murashige and Skoog (½MS) plates containing 1% sucrose and 0.8% agar, and grown under the same conditions as above.

extract_protocol:
Genomic DNA was extracted from ten-day-old seedlings by CTAB
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Seedlings were treated  with or without 100 nM flg22 for 6 h; 4-week-old plants were hand-inoculated with water or 100 nM flg22 for 24 h.

value: leaves

tag: genotype

value: rdd

value: hand-inoculated with 100 nm flg22 for 24 h


title: Cisplatin-treated sorted CSC-like MDA-MB-231, exosome (Replicate 3)

value: cisplatin


title: Sorted CSC-like MDA-MB-231, exosome (Replicate 1)

value: parental


title: Participant_17_Protein_Before


title: rdd_flg22_24h_WGBS_rep1

tag: age


title: Cisplatin-treated MDA-MB-231 parental, exosome (Replicate 3)


title: snRNA-seq female e-cigarette

description:
snRNA_FEcig
10X single-cell gene expression
Droplet single nucleus-RNA-seq
Single nuclei isolation and capture
Premature RNA

value: dam exposed to e-cigarette vapor

tag: Sex

value: female


title: Cisplatin-treated MDA-MB-231 parental, exosome (Replicate 2)


title: Cisplatin-treated MDA-MB-231 parental, exosome (Replicate 1)


title: rdd_6h_WGBS_rep3

description:
rdd-6h.CG.wig
rdd-6h.CHG.wig
rdd-6h.CHH.wig

value: seedlings

value: with 100 nm flg22 for 6 h


title: Participant_17_Protein_After

value: Adipose tissue

value: After

value: Protein restriction

value: Male


title: rdd_6h_WGBS_rep2


title: Participant_20_Protein_Before

description: Excluded from final analysis

value: Before

value: Female

value: B


title: MDA-MB-231 parental, exosome (Replicate 2)


title: Participant_16_Protein_After

value: C


title: rdd_H2O_24h_WGBS_rep2

description:
rdd-H2O-24h.CG.wig
rdd-H2O-24h.CHG.wig
rdd-H2O-24h.CHH.wig

value: leaves

value: hand-inoculated with H2O for 24 h


title: Participant_15_Protein_Before

value: A


title: Participant_14_Protein_After


title: J_3_3: F_hepatica_eggs_10_days_sample_t10_repl_3

city: Brno

first: Jiri

last: Vorel

address: Kotlarska 267/2

department: Department of Botany and Zoology

country: Czech Republic

institute: Masaryk University

data_processing:
Demultiplexing and conversion of base call files into FASTQ format: bcl2fastq v2.20.0.422
Quality check: FastQC v0.11.8
Trimming of adaptors: Trimmomatic v0.38 (HEADCROP:18)
Quantification of F. hepatica transcripts (PRJEB25283, deposited in WormBaseParasite database ): RSEM v1.3.3 (--bowtie2)
Non-normalized expected count values were analysed by DESeq2 v1.29.6 in R v4.0.1. Only transcripts with adjusted P-value < 0.05 and log2 fold change > 1 or <  -1 were considered as significantly differentially expressed.
Genome_build: GCA_900302435.1
Supplementary_files_format_and_content: Text files (tab-delimited) containing quantification of transcripts in each replicate.

molecule: polyA RNA

organism: Fasciola hepatica

source_name: Eggs

growth_protocol: Incubation of eggs for 5 and 10 days in sterilized water supplemented with penicillin (50 U/ml) and streptomycin (50 µg/ml).

extract_protocol:
Phenol-chloroform extraction with TRIzol Reagent (Invitrogen), according to manufacturer’s instructions.
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina, according to manufacturer’s instructions.

tag: developmental stage

value: Egg

value: 10 days

value: untreated


title: J_2_3: F_hepatica_eggs_5_days_sample_t5_repl_3

value: 5 days


title: rdd_6h_WGBS_rep1

value: seedlings

value: rdd


title: J_3_2: F_hepatica_eggs_10_days_sample_t10_repl_2


title: Participant_16_Protein_Before

value: Adipose tissue


title: J_3_1: F_hepatica_eggs_10_days_sample_t10_repl_1


title: Participant_13_Protein_After

value: After


title: WT_flg22_24h_WGBS_rep1

description:
WT-flg22-24h.CG.wig
WT-flg22-24h.CHG.wig
WT-flg22-24h.CHH.wig

value: wild type

value: hand-inoculated with 100 nm flg22 for 24 h


title: MDA-MB-231 parental, exosome (Replicate 1)

value: parental


title: Participant_13_Protein_Before

value: Before

value: Protein restriction

value: Female


title: J_2_2: F_hepatica_eggs_5_days_sample_t5_repl_2


title: WT_flg22_24h_WGBS_rep2

value: leaves


title: rdd_H2O_24h_WGBS_rep1

value: hand-inoculated with H2O for 24 h


title: Participant_15_Protein_After

value: Male

value: A


title: Participant_14_Protein_Before


title: WT_H2O_24h_WGBS_rep2

description:
WT-H2O-24h.CG.wig
WT-H2O-24h.CHG.wig
WT-H2O-24h.CHH.wig


title: Participant_12_Protein_After

value: C


title: WT_6h_WGBS_rep2

description:
WT-6h.CG.wig
WT-6h.CHG.wig
WT-6h.CHH.wig

value: with 100 nm flg22 for 6 h


title: J_2_1: F_hepatica_eggs_5_days_sample_t5_repl_1

value: Egg

value: 5 days

value: untreated


title: WT_H2O_24h_WGBS_rep1


title: J_1_1: F_hepatica_eggs_0_days_sample_t0_repl_1

value: 0 days


title: J_1_3: F_hepatica_eggs_0_days_sample_t0_repl_3


title: Participant_11_Protein_After

description: Excluded from final analysis

value: Adipose tissue

value: After

value: B


title: WT_6h_WGBS_rep3

value: seedlings

value: wild type


title: J_1_2: F_hepatica_eggs_0_days_sample_t0_repl_2


title: Participant_10_Calorie_After

value: Calorie restriction


title: rdd_12h_WGBS_rep2

description:
rdd-12h.CG.wig
rdd-12h.CHG.wig
rdd-12h.CHH.wig

data_processing:
RNA-seq library preparation and sequencing were performed on an Illunima HiSeq X-ten (Beijing, China). RNA-seq reads with low sequencing quality or reads with sequencing adaptors were filtered from the raw data. The resulting clean reads were then aligned to the Arabidopsis reference genome (TAIR10) using Hisat2  with default parameters. A GFF (general feature format) formatted gene model annotation file was provided for reads alignment. Following the alignments, transcriptome quantification based on gene level was performed by FeatureCounts  and then used DESeq2  to find the significant differential gene expression. Genes with expression fold change > 2 and Padj < 0.05 were considered as significantly different between samples with and without flg22 treatment.
Whole-Genome Bisulfite Sequencing were performed by BGI Genomics (Shenzhen, China). Sequencing was performed on an Illumina HiSeq 4000 instrument to generate paired-end reads.For data analysis, paired-end sequencing reads were first trimmed with Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) for removal of Illumina adapters and low-quality bases (Phred score < 20). The cleaned reads were then aligned to TAIR10 genome using bsmap with default settings. Only uniquely mapped reads were retained for further analysis. PCR duplicates were marked by Picard (https://broadinstitute.github.io/picard/). Further processing was accomplished via SAMtools , BAMtools  and bamUtil (https://github.com/statgen/bamUtil/). Methylation ratio was extracted with BatMeth2 .
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for every gene and every sample
Supplementary_files_format_and_content: wig files were generated using script

extract_protocol:
Total RNA was extracted from ten-day-old seedlings or leaves from 4-week-old soil-grown Arabidopsis plants by TRNzol reagent.                                                                                Genomic DNA was extracted from ten-day-old seedlings by CTAB
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Seedlings were treated  with or without 100 nM flg22 for 1 h, 3 h, 12 h; 4-week-old plants were hand-inoculated with water or 100 nM flg22 for 24 h; p1: Leaves from 4-week-old plants were hand-inoculated with or without 100 nM flg22, and 24 h later hand-inoculated with Pst DC3000 hrcC at 2*10e8 cfu/mL for 1 h.

value: rdd

value: with 100 nm flg22 for 12 h


title: Participant_10_Calorie_Before

value: Before

value: Female


title: Participant_9_Calorie_After

value: A


title: rdd_12h_WGBS_rep1


title: Participant_12_Protein_Before

value: Protein restriction

value: C


title: Participant_11_Protein_Before

description: Excluded from final analysis

value: Male


title: WT_6h_WGBS_rep1

value: with 100 nm flg22 for 6 h


title: rdd_12h_WGBS_rep3


title: Participant_9_Calorie_Before


title: ATAC_HH19_PT_rep1

city: Geneva

first: Aurelie

last: Hintermann

address: 30 quai Ernest-Ansermet

institute: University of Geneva

description:
ATAC HH19 posterior trunk
ATAC

data_processing:
All scripts are available on https://gitlab.unige.ch/Aurelie.Hintermann/hintermannetal2022
Sequenced DNA fragments were processed as previously reported in (Amândio et al., 2020) with a minor modification on a local Galaxy server: the BAM file was converted to BED prior to peak calling with bedtools version 2.30.0
Peak calling was done using MACS2 (v2.1.1.20160309) callpeak (--no-model --shift -100 --extsize 200 --call-summits --keep-dup all).
Peak regions for each condition were obtained from the union of the peak region of both replicates with bedtools merge (v2.30.0) and extended by 660 bp each side with bedtools slop.
Each replicate was normalized per million reads mapped in their own peaks, subsetted in the HoxD region (mm10,chr2:73000000-77000000 ; galGal6, chr7:13000000-17000000) and the neq2 coverage is the mean of normalized replicates
Assembly: mm10
Assembly: galGal6
Supplementary files format and content: bigwig: coverage from MACS2
Supplementary files format and content: narrowPeak: narrowPeak from MACS2
Supplementary files format and content: bedgraph: replicates were  normalized to the number of million reads falling in their own peaks, subsetted in the HoxD region (mm10,chr2:73000000-77000000 ; galGal6, chr7:13000000-17000000) and averaged.
Supplementary files format and content: bed: narrowPeaks of both replicates were pooled, extended by 660 bp each side and then merged to obtain non-overlapping intervals.

source_name: White Leghorn

extract_protocol:
ATAC-seq experiments were performed as described in (Bolt et al., 2022)
ATAC-seq librairies were prepared as described in (Bolt et al., 2022)

value: White Leghorn

value: WT

tag: dissection

value: A portion of tissue corresponding to the tailbud, presomitic mesoderm, and 2-3 somite pairs, was micro-dissected from one HH19 embryo.


title: rdd_1h_WGBS_rep1

description:
rdd-1h.CG.wig
rdd-1h.CHG.wig
rdd-1h.CHH.wig

value: with 100 nm flg22 for 1 h


title: rdd_1h_WGBS_rep3


title: Participant_8_Calorie_After

value: Adipose tissue

value: After

value: B


title: Participant_8_Calorie_Before

value: Calorie restriction


title: ATAC_HH19_PT_rep2

description:
ATAC HH19 posterior trunk
ATAC


title: rdd_0h_WGBS_rep1

description:
rdd-0h.CG.wig
rdd-0h.CHG.wig
rdd-0h.CHH.wig

value: seedlings

value: rdd

value: with 100 nm flg22 for 0 h


title: rdd_1h_WGBS_rep2


title: rdd_0h_WGBS_rep3


title: WT_12h_WGBS_rep3

description:
WT-12h.CG.wig
WT-12h.CHG.wig
WT-12h.CHH.wig

value: wild type

value: with 100 nm flg22 for 12 h


title: snATAC-seq male control

description:
snATAC_MCtr
10X single-cell chromatin accessibility
Droplet single nucleus-ATAC-seq
Single nuclei isolation and capture

value: Sprague-Dawley

value: dam exposed to regular air

value: cortex and hippocampus

value: male


title: Participant_6_Calorie_Before

value: Before

value: Female

value: C


title: WT_12h_WGBS_rep2


title: Participant_7_Calorie_After

value: A


title: rdd_0h_WGBS_rep2


title: Participant_7_Calorie_Before

value: Adipose tissue


title: WT_12h_WGBS_rep1


title: Participant_6_Calorie_After

description: Excluded from final analysis

value: After


title: Participant_5_Calorie_After

value: Male


title: WT_1h_WGBS_rep2

description:
WT-1h.CG.wig
WT-1h.CHG.wig
WT-1h.CHH.wig

value: with 100 nm flg22 for 1 h


title: WT_1h_WGBS_rep1

value: seedlings


title: Participant_3_Calorie_After

value: Calorie restriction


title: Participant_5_Calorie_Before


title: WT_1h_WGBS_rep3


title: WT_0h_WGBS_rep2

description:
WT-0h.CG.wig
WT-0h.CHG.wig
WT-0h.CHH.wig

value: with 100 nm flg22 for 0 h


title: HCT116-SMCHD1-41-1

city: Tallahassee

first: Sunny

last: Das

state: FL

address: 319 Stadium Drive

department: Biological Science

institute: Florida State University

description: HCT116-SMCHD1 homozygous mutant

hyb_protocol: Hybridization was performed at a NimbleGen Systems certified core facility at FSU, FL, USA, following the NimbleGen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed at a NimbleGen Systems certified core facilty at FSU, FL, USA, following the NimbleGen standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: HCT116_SMCHD1 knockout_41

label_protocol: Labeling was performed at a NimbleGen Systems certified core facility at FSU, FL, USA, following the NimbleGen standard operating protocol. See www.nimblegen.com.

growth_protocol: Cells were grown in DMEM/High Glucose, supplemented with 10% FBS, Pen/Strep and 2mM L-Glutamine. Cells were maintained at 37C in 5% CO2, humidified.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Spin Kit. RNA was treated with DNaseI, before cleaning on an RNeasy spin column. Confirmation of DNA absence was performed by PCR to the repeat element DXZ4, and RNA quality was determined by agarose gel electrophoresis.

treatment_protocol: The SMCHD1 gene was knocked out by targeting both copies of exon-2 using Transcription Activator Like Effector Nucleases (40, 41 and 43 - all independent clones).

tag: gender

value: colorectal carcinoma epithilial cells

tag: genotype/variation

value: SMCHD1 knockout

tag: clone id


title: HCT116-SMCHD1-41-3

description: HCT116-SMCHD1 homozygous mutant

tag: cell type


title: HCT116-SMCHD1-43-1

description: HCT116-SMCHD1 homozygous mutant

source_name: HCT116_SMCHD1 knockout_43

tag: cell line


title: HCT116-SMCHD1-40-2

description: HCT116-SMCHD1 homozygous mutant

source_name: HCT116_SMCHD1 knockout_40


title: HCT116-SMCHD1-43-2

description: HCT116-SMCHD1 homozygous mutant


title: HCT116-SMCHD1-41-2

description: HCT116-SMCHD1 homozygous mutant


title: HCT116-SMCHD1-43-3

description: HCT116-SMCHD1 homozygous mutant


title: HCT116-SMCHD1-40-1

description: HCT116-SMCHD1 homozygous mutant


title: Participant_3_Calorie_Before

tag: timepoint


title: HCT116-SMCHD1-40-3

description: HCT116-SMCHD1 homozygous mutant


title: Participant_4_Calorie_After

tag: participant

value: B


title: Participant_1_Calorie_After

tag: library pool


title: WT_0h_WGBS_rep1

value: wild type


title: Participant_4_Calorie_Before

tag: sequencing lane


title: Sporulated Rep1

city: Zurich

first: Chandra

last: Ramakrishnan

address: Winterthurerstrasse 266a

department: Institute of Parasitology

institute: University of Zurich

data_processing:
Adaptor sequences and low quality stretches were removed with fastp.
Transcripts were quantified with Salmon (options –type quasi -k 31 for the index build step and options –validateMappings for the quantification step) using the cDNA and gene annotation available from ToxoDB (release 41).
Differential gene expression was analysed with a general linear model in DESeq2 according to a design with a single factor comprising all time points. All time points were compared to each other and the latest time point was compared to the average of the two earlier time points. Within each comparison, p-values were adjusted for multiple testing (Benjamini-Hochberg).
Supplementary files format and content: Normalized data: log2(x+1); x = normalized counts
Supplementary files format and content: LFCs: log2 fold changes with p-values and adjusted p-values

organism: Toxoplasma gondii

source_name: CZ clone H3

extract_protocol:
Total RNA was extracted using the Zymo Direct-zol RNA Miniprep kit.
Library preparation was performed using the Illumina TruSeq RNA Sample Prep Kit v2.

value: CZ clone H3

value: Oocysts

value: WT

tag: treatment

value: Sporulation


title: Sporulated Rep2


title: Participant_1_Calorie_Before

tag: tissue

value: Before

value: C


title: Sporulating Rep2


title: WT_0h_WGBS_rep3


title: Sporulating Rep1


title: HLCs, S37

city: Philadelphia

first: Christopher

last: Brown

state: PA

address: CRB, 415 Curie Bouevard

institute: University of Pennsylvania

data_processing:
Library strategy: Capture-C
wwwwwwwwwwwww
Supplementary_files_format_and_content: HEP.4frag.chicagoRes.ibed

source_name: Hepatocyte-like cells

extract_protocol: qqqqqqqqqqqq

value: hepatocyte-like cell

tag: disease state

value: undiseased


title: Participant_2_Calorie_After

description: Excluded from final analysis

value: Adipose tissue

value: After

value: Male


title: Cold-active-protease_lot3

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

data_processing:
Library strategy: BRB-seq
Extraction of sample barcodes and unique-molecular-identifiers (UMIs) was performed using UMI-tools (version 1.0.1) with the following commands: umi_tools extract -I r1.fastq --read2-in=r2.fastq --bc-pattern=NNNNNNCCCCCC --read2-stdout.
The reads were trimmed using Cutadapt (M. Martin, 2011)  (version 2.6) wapper, Trim Galore! (version 0.6.6), with the option:  -a GATCGTCGGACT. The reads were mapped by the aligning software HISAT2 (D. Kim et al., 2015, M. Pertea et al., 2016, D. Kim et al., 2019) (version 2.1.0) to the reference genome (GRCm38, pre-built HISAT2 index, genome_snp_tran).
Read counts per gene were obtained using featureCounts (Liao Y et al., 2014) (version 2.0.1).  UMIs were not used and mitochondrial genes are excluded in the following analysis.
Downstream analysis was conducted by DESeq2 software (M. I. Love et al., 2014) (1.28.1).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: *.csv file include comma-delimited RNA-seq read count matrix, normalized count matrix, and TPM matrix.

source_name: C2C12 cell line

growth_protocol: C2C12 cells were cultured in 6 well plates in Dulbecco’s modified Eagle’s medium (DMEM) (1g/L D-glucose) supplemented with 20% fetal bovine serum (FBS), 2 mM L-glutamine, and 1% penicillin-streptomycin.

extract_protocol:
All samples were collected by adding lysis buffer to the cell culture plates followed by scraping (Control) and re-suspending cells. Total RNAs were extracted from lysate using NucleoSpin RNA XS (Takara).
Sequencing was performed using HiSeq PE Rapid Cluster Kit v2 and HiSeq Rapid SBS Kit v2 (50 Cycles) on Illumina HiSeq 1500 sequencers, with 15 cycles for read 1 and 45 cycles for read 2.

treatment_protocol:
For time series analysis, cells were washed twice with PBS and treated with 200 µL of 0.25% trypsin for 30 sec, 3 min or 30 min at 37ºC.
For low trypsin level treatment, cells were washed twice with PBS, and treated with 200 µL of 0.25% trypsin. Trypsin was removed immediately and cells were incubated at 37 °C for 3 min.
For cold-active protease treatment, cells were washed twice with PBS followed by adding 200 µL of cold protease. Cells were incubated at 4 °C for 5 min with shaking.

value: myoblast


title: HLCs, S334


title: Participant_2_Calorie_Before

value: Calorie restriction


title: HLCs, S233


title: Low-trypsin-level_lot1


title: HCT116-Parental-3

description: Parental HCT116 cells

value: male

value: colorectal carcinoma epithilial cells

value: parental


title: Time-series-30min_lot2


title: Cold-active-protease_lot1


title: HCT116-Parental-1

description: Parental HCT116 cells


title: HCT116-Parental-2

description: Parental HCT116 cells


title: P2-PD1-19bbz

data_processing:
Basecalls performed using CASAVA version 1.8
cellranger (v3.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20%  passed the cell quality filtering and mitochondria genes were removed in the expression table.   Seurat package (version: 3.1.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.   PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

treatment_protocol: treatment naive

value: Primary cells

tag: agent


title: P2-AAVS1-19bbz

tag: age


title: Low-trypsin-level_lot2


title: rdd_H2O_priming_RNAseq_rep2

value: leaves

tag: genotype

value: rdd

value: hand-inoculated with H2O,and 24 h later hand-inoculated with Pst DC3000 hrcC at 2*108 cfu/mL for 1 h.


title: Unsporulated Rep1

value: CZ clone H3

value: Oocysts

value: WT


title: P2-LV-19bbz_PD1-KO

tag: Sex


title: Time-series-30min_lot3


title: Cold-active-protease_lot2


title: rdd_flg22_priming_RNAseq_rep2

value: hand-inoculated with 100 nm flg22,and 24 h later hand-inoculated with Pst DC3000 hrcC at 2*108 cfu/mL for 1 h.


title: Time-series-3min_lot2


title: Unsporulated Rep2


title: P2-Untreated

value: Untreated


title: rdd_flg22_24h_RNAseq_rep2

value: hand-inoculated with 100 nm flg22 for 24 h


title: P1-AAVS1-19bbz


title: rdd_flg22_priming_RNAseq_rep1


title: Time-series-30sec_lot2


title: Low-trypsin-level_lot3


title: P1-LV-19bbz_PD1-KO


title: rdd_H2O_24h_RNAseq_rep3

value: hand-inoculated with H2O for 24 h


title: rdd_H2O_priming_RNAseq_rep1


title: Time-series-3min_lot3


title: P2-LV-19bbz

value: Male


title: P1-LV-19bbz


title: Control_lot3

value: myoblast


title: Time-series-3min_lot1


title: rdd_H2O_24h_RNAseq_rep1


title: rdd_flg22_24h_RNAseq_rep3


title: Patient-3_D28

data_processing:
Basecalls performed using CASAVA version 1.8
cellranger (v3.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20% passed the cell quality filtering and mitochondria genes were removed in the expression table.   Seurat package (version: 2.3.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.   PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10 principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Genome_build: GRCh38Ensembl91
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

source_name: PBMC

tag: individual

value: Primary cells (PBMC)