title: 601

city: fuzhou

first: mingrui

last: lin

address: 1 qiuyang

institute: fujian university of traditional chinese medicine

description: WT mice with 3-day LPS (10mg/kg) treatment and XJDHT (50mg/kg/d)

data_processing:
Data were filtered using the following specifications fastq software，The filtering standards from raw data to clean reads are:：  Check the sample for contamination and, if there is pollution, remove it  If the reads contains a joint sequence, the joint sequence is cut off first  a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window;  Remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed;  if the truncated read length is less than 50 bp, the entire read is removed  Remove unmatched reads  Q30，Q20 explanation：  Q30 indicates that the sequencing error rate of the base is 0.1%.  Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Assembly: GCRmm38/mm10(UCSC)
Supplementary files format and content: tab_delimited text files include FPKM values for each Sample

source_name: heart

extract_protocol:
A total amount of 1 μg RNA per sample was used. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer’s instructions.
mirVana miRNA Isolation Kit (Cat. AM1560, Ambion, Austin, USA)

treatment_protocol: The heart were dissected and  stored in liquid nitrogen and stored in low temperature.Total RNA was extracted with mirVana miRNA Isolation Kit (Cat. AM1560, Ambion, Austin, USA). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by Qubit RNA Assay Kit in a Qubit Fluorometer (Invitrogen, CA, USA).

value: heart

value: WT

tag: treatment 1

value: LPS

tag: treatment 2

value: XJDHT

tag: group

value: LPS+XJDHT


title: 602

status: Public on Oct 24 2022

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue

tag: genotype


title: KO cbx3 colon rep3

city: Paris

first: Laurence

last: Arbibe

address: 156 rue de Vaugirard

department: Immunology, microbiology and hematology

country: France

institute: INEM

description: jonctions_only_de_novo_present_only_in_KO_HP1_and_not_in_the_wt_Colon_RNA-seq.bed

data_processing:
Illumina HiSeq 2500 platform.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
250~300 bp insert strand specific library with rRNA removal
30 G raw data-100M raw reads/sample

source_name: intestine

extract_protocol:
Intestinal fragments were incubated 30 min at 4ºC in 10mM EDTA after which they were transferred to BSA 0,1% in PBS and vortexed between 30 s and 1 min. The supernatants containing the epithelial cells were filtered with a 70mm cell strainer. At this step, crypts went through the cell strainer and villi were retained on it. Crypt and villi fractions were then centrifuged separately and the pellets were frozen in liquid nitrogen until processed.
Total RNA library preparation and sequencing were performed by Novogene Co., Ltd, as a lncRNA sequencing service, including lncRNA directional library preparation with rRNA depletion (Ribo-Zero Magnetic Kit), quantitation, pooling and PE 150 sequencing (30G raw data) on Illumina HiSeq 2500 platform. Filtering and trimming of the RNA seq data left around 230-300 million reads pairs /sample for mapping to the mouse reference genome, with a Pearson correlation coefficient (R2) between biological replicates samples around 0.9, ensuring a reliable expression.

value: KO cbx3

tag: cell type

value: colon epithelial cells

value: intestine


title: KO cbx3 colon rep2


title: KO cbx3 colon rep1


title: 615

description: WT mice with 3-day LPS (10mg/kg) treatment

value: Saline


title: HeLa_polyA_WT_IVT_rep2

city: Chicago

first: Shun

last: Liu

state: IL

address: 929 E. 57th. Street

department: Chemistry

country: USA

institute: University of Chicago

data_processing:
Adapters of all raw eTAM-seq data sets were removed by Cutadapt v1.18. The six-nt-long random barcodes in the 5’ end of R2 reads were extracted by the subcommand extract from UMI-tools v1.1.1. R2 reads longer than 39 nt were used for further analysis. For HeLa cells, reads were first mapped to the human rRNA sequences using HISAT-3N v2.2.1. Then unmapped reads were mapped to the human genome (hg38) and the GENCODE v27 gene annotation. For mESCs, reads were first mapped to the mouse rRNA sequences using HISAT-3N. Then unmapped reads were mapped to the mouse genome (mm10) and the GENCODE vM25 gene annotation. Only uniquely mapped reads were remained and then subjected to deduplication by the subcommand dedup from UMI-tools. Reads with > 50% unconverted A were eliminated. Finally, custom scripts were used to count converted and unconverted As for each genomic positions.Site-specific quantification was estimated by the model developed in this study.
Assembly: hg38, mm10
Supplementary files format and content: m6A sites with accessibility and methylation levels in the plain txt format

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: Human HeLa cell line and wild-type (WT) mouse embryonic stem cells (mESC) were purchased from ATCC. HeLa cell line was grown in DMEM (Gibco, 11965092) media supplemented with 10% FBS (Gibco) and 1% 100× Pen/Strep (Gibco). mESCs were maintained in DMEM (Invitrogen) supplemented with 15% FBS (Gibco), 1% nucleosides (100×) (Millipore), 1 mM L-glutamine (Gibco), 1% nonessential amino acids (Gibco), 0.1 mM 2-mercaptoethanol (Sigma), 1,000 U/ml LIF (Millipore), 3 μM CHIR99021 (Stemcell), and 1 μM PD0325901 (Stemcell). All cells were cultured at 37°C under 5.0% CO2. Mettl3 cKO mES cell lines were generated following previously reported methods (PMID: 31949099). Briefly, mESCs derived from Mettl3flox/flox mouse blastocyst were transfected with 200 ng PB-CAG-Puromycin-P2A-CreERT2 and 100 ng PBase by electroporation. After 24 h, electroporated cells were treated with 1 μg/ml Puromycin to generate stable Mettl3flox/flox; CreERT2 mES clones. To induce deletion, Mettl3flox/flox; CreERT2 ESC cells were treated with 1 μg/ml 4-hydroxytamoxifen (Sigma). These Mettl3 KO cells were cultured for 48 h before harvesting. Untreated Mettl3flox/flox; CreERT2 ESC cells were used as ctrl mESCs.

extract_protocol:
Cells were cultured to 70-80% confluency, rinsed with 1× PBS (Gibco), and lysed by the direct addition of TRIzol reagent (Invitrogen). Total RNA was then collected following the manufacturer’s protocol. Poly A+ RNA was extracted from purified total RNA using Dynabeads mRNA DIRECT Purification Kits (Invitrogen). Modification-free control RNAs were prepared from HeLa or mESC total RNA according to a previously published protocol (PMID: 34594034, 32518404).
RNA was annealed to 2 pmol of RT primer (AGACGTGTGCTCTTCCGATCT) at 70ºC for 2 min, then reverse transcribed in 1× RT buffer (Thermo Scientific, EP0753, containing 50 mM Tris-HCl, pH 8.3; 75 mM KCl, 3 mM MgCl2, 10 mM DTT) with 5 mM of RNaseOUT (Invitrogen, 10777019) and 200 U of Maxima H- Reverse Transcriptase (Thermo Scientific, EP0753) at 50ºC for 1h. The cDNA was released by boiling the beads in 0.5% (v/v) SDS for 10 min. The eluate was purified by DNA Clean & Concentrator (Zymo) kits. Purified cDNA was ligated to cDNA Adapter (/5Phos/NNNNNN AGATCGGAAGAGCACACGTCTG/3SpC3/) using 30 U of T4 RNA ligase (NEB) at 25ºC overnight, following a previously published protocol (PMID: 35288668). The reaction was purified again by DNA Clean & Concentrator (Zymo) kits and then PCR amplified with NEBNext Ultra II Q5 Master Mix (NEB, M0544X) and NEBNext Unique Dual Index Primer for Illumina (NEB, E6440S) following the manufacturer’s directions. Typically, 10-11 cycles of PCR were carried out to generate enough DNA. The resulting library was purified by AMPure XP beads (Beckman Coulter, A63882) following the manufacturer’s directions and submitted for next-generation sequencing.

treatment_protocol: FTO-, FTO+ and IVT RNA samples were deaminated on beads with 200 pmol of TadA8.20 in the deamination buffer (50 mM Tris, 25 mM KCl, 2.5 mM MgCl2, 2 mM dithiothreitol, and 10 % (v/v) glycerol; pH 7.5) supplemented with 10% (v/v) of SUPERase•In RNase Inhibitor (Invitrogen, AM2696) at 53ºC for 1 h. This reaction was repeated twice at 44ºC, 1h each by draining the supernatant on a magnetic rack and resuspending the beads in fresh reaction mixtures, lasting 3 h in total. The beads were washed sequentially by resuspension in 0.1% PBST (v/v), 1× Binding/Wash buffer, and twice in 10 mM Tris HCl (pH 7.5).

value: HeLa

tag: treatment

value: wild type

tag: library type

value: in vitro transcribed RNA


title: 605


title: WAT ZT5 RNA 1 [CLH_RNA_22]

first: Nathan

last: Waldeck

address: 303 E Superior St, Lurie 7-220

institute: Northwestern University

description: processed data file: All_RNA_Counts.txt

data_processing:
ATAC-sequencing reads were trimmed and aligned to the mouse reference genome (mm10) using the ENCODE ATAC-sequencing pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline).
HOMER was used to identify and annotate peaks and motifs in ATAC-Seq data
RNA-seq reads aligned to mm10 using STAR 2.7.5
RSEM 1.3.0 was used to assign transcript counts to gene features (Ensembl 98)
Differential Gene epression (DESeq2), data visulaization (pheatmap, gplots, ggplot2), KEGG pathway analysis (limma), rhythmic analyses (JTK-Cycle) were performed in R (4.1.0)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Table with rhythmic genomic features obtained from JTK_Cycle

source_name: WAT ZT5 RNA

extract_protocol:
NuTRAP nuclei and ribosomal RNA were isolated according to established methods (PMID 28122230). Brown adipose and inguinal white adipose depots were snap frozen in liquid nitrogen, minced, dounce homogenized, spun down and FACS sorted to isolate for ATAC-Seq. Tissues were minced, homogenized, ribosomal RNA was affinity purified using anti-GFP antibodies and protein G Dynabeads and extracted using the Qiagen Micro RNeasy kit.
ATAC-seq libraries were constructed according to the Omni-ATAC protocol (PMID 28846090). RNA-Seq libraries were constructed from 250 ng of RNA using the NEBNext RNA Ultra Directional library prep kit

tag: time point

value: white adipocytes

tag: molecule subtype

value: ribosomal mRNA


title: 690


title: Spring Norstar [S001CC6]

city: Ottawa

first: Ziying

state: ON

address: 1200 Montreal Road

country: Canada

institute: National Research Council, Canada

description:
S001CC6
Wheat
RawCountData.xlsx

data_processing:
Read mapping and de novo assembly - We trimmed adaptor sequence, discarded low-quality reads (Phred Score <=20 (http://www.phrap.com/phred)) and eliminated short reads (length <= 20 bps) using a software package from Stanford (De Wit et al., 2012). STAR (v2.4.2a, Dobin et al., 2013) was used for mapping reads, and generating raw count/gene/sample.
The unmapped reads from the above mapping against IWGSC reference genome were submitted to Trinity (v2.1.1, Haas et al, 2013) for de novo assembly. The de novo assembled reference was annotated using BlastX against Arabidopsis thaliana (TAIR10) protein database. The de novo assembled reference was used for collecting read-counts for additional 58,180 genes.
DESeq2 (Love et al., 2014) was applied for data normalization across all 24 samples and subsequent DEG identification for each treatment-control pair and winter cultivars as compared with their spring counterparts. After calling for DEGs, the normalized data along with fold changes, p-values and other statistics are saved for downstream analysis.
Genome_build: IWGSC Version 2.2 survey genome assembly was used as reference [IWGSC reference genome 2.2 (2014). ftp://ftpmips.helmholtz-muenchen.de/plants/wheat/IWGSC/genome_assembly/genome_arm_assemblies_CLEANED_REPMASKED/].
Supplementary_files_format_and_content: RawCountData.xlsx: In Excel file format, including raw read counts data against wheat genome and de novo assembly.

organism: Triticum aestivum

growth_protocol: Plants for LT50 were grown hydroponically as described in detail previously (Limin and Fowler, 2002). The procedure outlined by Fowler (2008) was used to determine the LT50 of each genotype at the end of each cold acclimation period. Field wheat lines were seeded on August 29th in 2013 and 2014 in two replicates for each year. First leaf samples were collected on 30th of September in 2013 and 2014. Leaf samples were further collected after four weeks at 29th of October in 2013 and five weeks at 7th of November in 2014. The 2014 samples were left for five weeks of cold treatments due to high temperatures existing during the cold acclimation period. All leaf samples were frozen with liquid N2 immediately after harvesting and store at -80°C.

extract_protocol:
Total RNA was extracted from leaf tissues using the Plant Mini kit (Qiagen) according to manufacturer's instructions and its quantity and quality were measured with the NanoDrop 2000. One μg of total RNA was used for cDNA synthesis using the QuantiTect Reverse Transcription kit (Qiagen).
RNA-seq libraries were prepared according to Illumina's instructions, using the TruSeq RNA Sample Preparation Kit v2 (Illumina) and pair-end sequencing (126 cycles) was conducted on Illumina HiSeq 2500 following the manufacturer's protocols (https://www.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf).

treatment_protocol: For cold treatment, the selected wheat varieties grow in chambers with 16-h-light (~120 μmol m-2s-1) and 8-h-dark at 23°C up to the stage of 4 leaves (3-4 weeks) and then transferred at 4°C for cold treatment for six weeks. The 3rd fully opened leaf from not treated and cold treated plants was collected and immediately frozen in liquid N2. Samples were store at -80°C until lipid analysis.

tag: cultivar

value: Spring Norstar

value: Leaf tissues

value: Control


title: BAT ZT21 RNA 1 [CLH_RNA_16]

description: processed data file: All_RNA_Counts.txt

source_name: BAT ZT21 RNA

value: brown adipocytes


title: HeLa_polyA_WT_FTO-_rep3

value: in vivo transcribed RNA


title: ctrl colon rep3

description: jonctions_only_de_novo_present_only_in_the_wt_and_not_in_the_KO_HP1_Colon_RNA-seq.bed

value: control


title: MDMs HP 8 h biol rep 2

city: Marburg

first: Ho Ryun

last: Chung

address: Hans-Meerwein-Straße 6

department: Institute for Medical Bioinformatics and Biostatistics

country: Germany

institute: Philipps University of Marburg

data_processing:
Reads were mapped using salmon 1.3.0 in the quant mode with the options i ,l, SF, validateMappings and noLengthCorrection. A custom index was used to discriminate between human, Drosophila, and ERCC reads.
BAM files were sorted and indices were generated with samtools.
Differential gene expression was determined in R with the tximeta, SummarizedExperiment, and DESeq2 packages. The R script is available for download in this dataset.
Assembly: hg38, BDGP6.28
Supplementary files format and content: SF: salmon quantification file
Supplementary files format and content: TSV: tab-separated file

source_name: blood

extract_protocol:
3-5*10^5 MDMs were washed once with PBS. Trifast reagent (Peqlab) was added to the cells together with an amount of 10% of Drosophila Schneider S2 cells relative to MDMs; total TRIfast volume was 500 µl. The pellet was fully resuspended and incubated for 5 min at RT in an 1.5 ml Eppendorf tube. 100 µl of chloroform were added, and the tube was shaken by hand for 15 s. After 3 min of incubation at RT, the tube was centrifuged at 12.000g at 4 degrees centigrade. The upper phase was transferred to a fresh tube, and 2 µl of Glycoblue (Thermo Fisher Scientific) were added followed by 250 µl of isopropanol. After mixing by shaking, the sample was incubated for 10 min at RT followed by centrifugation at 12.000g at 4 degrees centigrade. The supernatant was discarded, and the pellet was washed with 500 µl of 70% (v/v) ethanol. The supernatant was discarded, the pellet was air-dried and subsequently dissolved in 40 µl of water supplemented with 20 U of SUPERase-In RNase inhibitor (Thermo Fisher Scientific). A synthetic ERCC RNA spike-in mix (Thermo Fisher Scientific) was added to the sample according to the manufactur
The QuantSeq FWD Kit (Lexogen) was used according to the manufacturer’s instructions.

value: blood

value: monocyte-derived macrophages (MDMs)

value: diploid female

value: HP 8 h


title: ctrl colon rep2

value: colon epithelial cells

value: intestine


title: BAT ZT17 RNA 1 [CLH_RNA_13]

description: processed data file: All_RNA_Counts.txt

source_name: BAT ZT17 RNA


title: BAT ZT17 RNA 2 [CLH_RNA_14]

description: processed data file: All_RNA_Counts.txt


title: HeLa_polyA_WT_FTO-_rep2

value: HeLa


title: 609

value: heart

value: WT

value: LPS

value: Saline


title: HeLa_polyA_WT_FTO-_rep1

value: wild type


title: BAT ZT21 RNA 3 [CLH_RNA_18]

description: processed data file: All_RNA_Counts.txt

value: ribosomal mRNA


title: ctrl colon rep1


title: BAT ZT13 RNA 3 [CLH_RNA_12]

description: processed data file: All_RNA_Counts.txt

source_name: BAT ZT13 RNA


title: 617


title: HeLa_polyA_WT_FTO+_rep1

value: TadA8.20 + FTO


title: Human Thyroid Organoid, day 58

city: Bruxelles

first: Sabine

last: Costagliola

address: 808 route de lennik

department: IRIBHM

country: Belgium

institute: Université Libre de Bruxelles

description: Raw Data Files split due to size issues.

library_source: transcriptomic single cell

data_processing:
The raw sequencing data were then processed with the ‘count’ command of the Cell Ranger software (v.6.0.1) provided by 10x Genomics with the option ‘–expect-cells’ set to 10,000 (all other options were used as per default).
Assembly: GRCh38
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: hESC-derived differentiated cells

extract_protocol:
Trypsin based dissociation followed by FACS sorting of 60% NKX2-1/GFP+ and 40% NKX2-1/GFP- alive cells
10x Chromium NextGEM SingleCell 5' Kit v2

tag: cell line

tag: time

value: thyroid differentiation protocol, at day 58


title: KO cbx3 rep3

description: jonctions_only_de_novo_present_only_in_KO_HP1_and_not_in_the_wt_Villi_RNA-seq.bed

value: KO cbx3

value: villi epithelial cells


title: in vivo remodelled ossicles

city: Lund

first: Paul

last: Bourgine

state: Skane

address: Sölvegatan 17

country: Sweden

institute: Lund University

description: 10x Genomics

data_processing:
Demultiplexing and mapping to the Hg38 genome
Demultiplexing and mapping to a combined Hg38_mm10 genome
Assembly: Hg38/Hg38_mm10
Supplementary files format and content: .h5ad Containing featureXcellId counts

source_name: MSODB

extract_protocol:
As described in: G. S. Gulatiet al., Isolation and functional assessment of mouse skeletal stem cell lineage. Nature protocols13, 1294-1309 (2018)
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Dual Index Kit TT Set A, 96 rxns (PN-1000215, 10X Genomics). Chromium™ Single Cell Controller & Accessory Kit (PN-120263, 10X Genomics), PCR: C1000 Touch™ Thermal Cycler with 96–Deep Well Reaction Module (#1851197, Bio Rad)

value: MSODB

value: Chondrogenic differentiation


title: BAT ZT13 RNA 2 [CLH_RNA_11]

description: processed data file: All_RNA_Counts.txt

value: brown adipocytes


title: 680

description: WT mice with 3-day Saline treatment

value: Control


title: KO cbx3 rep2


title: 684

description: WT mice with 3-day Saline treatment


title: 679

description: WT mice with 3-day Saline treatment


title: BAT ZT13 RNA 1 [CLH_RNA_10]

description: processed data file: All_RNA_Counts.txt


title: BAT ZT9 RNA 3 [CLH_RNA_9]

description: processed data file: All_RNA_Counts.txt

source_name: BAT ZT9 RNA


title: KO cbx3 rep1


title: BAT ZT21 RNA 2 [CLH_RNA_17]

description: processed data file: All_RNA_Counts.txt


title: ctrl villi rep3

description: jonctions_only_de_novo_present_only_in_the_wt_and_not_in_the_KO_HP1_Villi_RNA-seq.bed

value: control


title: 612


title: MAIT cells patients

city: Duarte

first: Anastasia

middle: I

last: Kousa

state: CA

address: 1500 E Duarte Rd

department: Hematology / HCT

institute: City of Hope

data_processing:
The cell-gene count matrix was constructed using the Sequence Quality Control (SEQC) package. Viable cells were identified on the basis of library size and complexity, whereas cells with >20% of transcripts derived from mitochondria were excluded from further analysis.
Genome_build: GRCm38.p5 (mm10)
Supplementary_files_format_and_content: *_HTO.h5ad =  An h5ad file with hashtag annotation per cell index
Supplementary_files_format_and_content: *_fastqc.html = A quality control report which can spot problems that originate either in the sequencer or in the starting library material.
Supplementary_files_format_and_content: *_HTO_final-classification.tsv.gz = A hashtag classification file that tells you which cell is classified as which hashtag (tab-separated, gzipped)
Supplementary_files_format_and_content: *_HTO_final-matrix.tsv.gz = A gene expression matrix + hashtag classification file. A cell x gene matrix from scRNA-seq + one additional column that tells you which hashtag a given cell is classified as. (tab-separated, gzipped)
Supplementary_files_format_and_content: *_HTO_reads_barcodes.tsv.gz = A file containing the feature names, in this context our tags.
Supplementary_files_format_and_content: *_HTO_reads_features.tsv.gz = A file containing the cell barcodes.
Supplementary_files_format_and_content: *_HTO_reads_matrix.mtx.gz = A file containing the actual read count values
Supplementary_files_format_and_content: *_HTO_run_report.yaml = contains the parameters used for the run as well as some statistics
Supplementary_files_format_and_content: *_HTO_tag-list.csv = A comma-separated file with the hashtag list
Supplementary_files_format_and_content: *_HTO_umis_barcodes.tsv.gz =  A file containing the feature names, in this context our tags.
Supplementary_files_format_and_content: *_HTO_umis_features.tsv.gz = A file containing the cell barcodes.
Supplementary_files_format_and_content: *_HTO_umis_matrix.mtx.gz = A file containing the collapsed umi counts
Supplementary_files_format_and_content: *.h5 = A ReadArray object containing cell barcode, UMI, gene ID, genomic locus, and its status (e.g. uniquely mapped, barcode error, ...) for each read
Supplementary_files_format_and_content: *_Aligned.out.bam = A file containing reads aligned to genome
Supplementary_files_format_and_content: *_alignment_summary.txt = A text file containing alignment summary statistics
Supplementary_files_format_and_content: *_cb-correction.csv.gz = Cell-barcode correction file. This file is only needed for Velopipe (RNA Velocity pipeline for SEQC)
Supplementary_files_format_and_content: *_cell_filters.png = Visualization of cell filtering applied
Supplementary_files_format_and_content: *_de_gene_list.txt = List of differentially expressed genes in each cluster compared to rest (using MAST)
Supplementary_files_format_and_content: *_dense.csv = Filtered count matrix. Rows are cells and collumns are genes.
Supplementary_files_format_and_content: *_mini_summary.json = Key metrics in JSON format: Number of recovered cells, Number of reads, Percentage of reads uniquely mapped to genome, Sequencing saturation rate and etc.
Supplementary_files_format_and_content: *_mini_summary.pdf = SEQC alignment summary as a pdf
Supplementary_files_format_and_content: *_seqc_log.txt = A log file generated during a SEQC run
Supplementary_files_format_and_content: *_sparse_counts_barcodes.csv = Cell barcodes in numeric format.
Supplementary_files_format_and_content: *_sparse_counts_genes.csv = Gene names in the data
Supplementary_files_format_and_content: *_sparse_molecule_counts.mtx = Unfiltered molecule (UMI) count matrix in sparse matrix data format.
Supplementary_files_format_and_content: *_sparse_read_counts.mtx = Unfiltered read count matrix in sparse matrix data format
Supplementary_files_format_and_content: *_summary.tar.gz = Detailed information about alignments, filtering, etc. in gzipped tarball format
Supplementary_files_format_and_content: *_umi-correction.csv.gz = Cell-barcode correction file. This file is only needed for Velopipe (RNA Velocity pipeline for SEQC)
Supplementary_files_format_and_content: *_clean.h5ad = H5AD file with raw and normalized read counts and cell annotation (after bad quality cell filtering)

source_name: Allo-HCT patients

extract_protocol:
PBMCs were collected into Becton Dickinson Vacutainer® CPTTM Cell Preparation Tubes with Sodium Citrate. Cells were frozen in liquid nitrogen in a freezing medium containing RPMI, 10% DMSO and 12.5% HSA. Between 0.3 and 10 x 106 PBMCs were stained in PBS with LIVE/DEAD Zombie UV Fixable dye (Biolegend) for 20 min at room temperature. Human Fc block (Miltenyi Biotec) was then added for 10 minutes at 4ºC, followed by a staining with MR1‐5‐OP‐RU APC and CD1d-PBS-57 BV421 or MR1‐Ac‐6‐FP and CD1d unloaded tetramer (acquired from NIH tetramer core facility) for 40 minutes at room temperature. The tetramer staining was followed by surface antibody staining for 15 minutes at room temperature. In each batch of samples (n per batch ranged from 23 to 30) we included one or more healthy control samples stained with loaded and unloaded tetramer and in most of the batches we included a pooled patient sample stained with the unloaded tetramer. PBMCs from healthy samples were isolated using density centrifugation with Ficoll Paque®. PBMC samples were stained for flow cytometry and purified populations of MAIT and Vd2 cells from 5 patients and 5 healthy controls were collected using FACS sorting.
The single-cell RNA-Seq of FACS-purifed cell suspensions was performed on Chromium instrument (10X genomics) following the user guide manual for 3′ v3.1. In brief, purified cells were washed once with PBS containing 1% bovine serum albumin (BSA) and resuspended in PBS containing 1% BSA to a final concentration of 700–1,300 cells per μl. The viability of cells was above 80%, as confirmed with 0.2% (w/v) Trypan Blue staining (Countess II). Cells were captured in droplets. Following reverse transcription and cell barcoding in droplets, emulsions were broken and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification per manual instruction. Between 6,000 to 30,000 cells were targeted for each sample. Samples were multiplexed together on one lane of 10X Chromium following cell hashing protocol. Final libraries were sequenced on Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles).
single cell RNA-seq

value: MAIT cells


title: BAT ZT9 RNA 1 [CLH_RNA_7]

description: processed data file: All_RNA_Counts.txt


title: BAT ZT9 RNA 2 [CLH_RNA_8]

description: processed data file: All_RNA_Counts.txt


title: 677

description: WT mice with 3-day Saline treatment


title: ctrl villi rep2

value: intestine


title: ctrl villi rep1


title: MAIT cells healthy

source_name: Healthy control subjects


title: BAT ZT5 RNA 3 [CLH_RNA_6]

description: processed data file: All_RNA_Counts.txt

source_name: BAT ZT5 RNA


title: KO cbx3 crypt rep3

description: jonctions_only_de_novo_present_only_in_KO_HP1_and_not_in_the_wt_Crypts_RNA-seq.bed

value: crypt epithelial cells


title: Ear skin, K14Ddx5f/f 2 (psoriatic mice)

city: Shanghai

first: Yuping

last: Lai

address: No.500 Minhang Dongchuan Road

institute: East China Normal University

description: K14Ddx5f/f  mice (DDX5f/f mice were crossed with the K14Cre transgenic mice)

data_processing:
RNA sequencing was performed using an Illumina systems following Illumina-provided protocols for 2x150 paired-end sequencing in WuXi NextCODE at Shanghai, China.
FastQC (version 0.11.9) was used for assessing the overall quality of raw reads and Trimmomatic (version 0.39) was applied for raw reads quality control to cut adapters and remove low-quality reads.
Samtools (version: 1.7) was used to convert SAM format files to BAM format files and sorted the BAM files.
Gene expression levels were quantified by FeatureCounts (version 1.6.3)Differential expression analysis was performed by R package DESeq2 (Version 1.34.0)and FDR<0.05 was considered to be significantly differentially expressed. Gene ontology (GO) and KEGG pathway enrichment analyses were performed in ClusterProfiler (version 4.2.0)
Differential alternative splicing events were detected by rMATS (version 3.1.0), and events with p value<0.05 were identified as significantly differentially expressed alternative splicing events.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each samples

source_name: Ear skin

extract_protocol:
Total RNAs were isolated with TRIzol (Takara) following the manufacturer's instructions .
The mRNA-focused sequencing libraries from total RNA were prepared using Truseq stranded mRNA（illumina)

treatment_protocol: A daily topical dose of 25 mg IMQ cream (5%) (Shichuan MedShine Pharmaceuticals Co.) per ear  for seven consecutive days. At day 8, ears were collected for RNA isolation.

value: Ear skin

tag: age

tag: Sex

value: male

value: IMQ

tag: condition

value: IMQ-induced psoriasis


title: Ear skin, K14Ddx5f/f 3 (psoriatic mice)


title: Ear skin, K14Ddx5f/f 1 (psoriatic mice)


title: BAT ZT5 RNA 2 [CLH_RNA_5]

description: processed data file: All_RNA_Counts.txt

value: ribosomal mRNA


title: N34

city: St. Louis

first: Tim

last: Kong

state: MO

address: CSRB 8838

institute: Washington University School of Medicine

description: 10x Genomics

data_processing:
Cellranger (10x Genomics, version 3.0.1) was used for transcript alignment, counting, and inter-library normalization of single cell samples. Seurat(version 4.0.0) was used for cluster analysis.
Supplementary files format and content: GRCh38

source_name: Bone marrow

extract_protocol:
Cryopreserved BMMCs/PBMCs
Non-lymphoid CD34 cells were identified by the following immunostaining panel: CD34, CD38, CD3, CD7, CD19, and 7AAD. 7AAD- CD3-CD7- CD19- CD34+ cells were sorted and subsequently labeled with a panel of oligonucleotide conjugated antibodies according to TotalSeqA protocol from 10X Genomics (Pleasanton, CA). Oligonucleotide labeled cells were subjected to droplet bead capture, followed by cell lysis, reverse transcription, and amplification following protocol.

value: Bone marrow

tag: disease state

value: healthy


title: BAT ZT5 RNA 1 [CLH_RNA_4]

description: processed data file: All_RNA_Counts.txt


title: Ear skin, Ddx5f/f 3 (psoriatic mice)


title: Vd2 cells patients

value: Vd2 cells


title: HEL FedP rep 1

description:
processed data file:
HEL_persistent_raw_counts
hel_fedp-1.AAGAGAGAAG-GCGACTCGTA.H7VW5DSXY_AAGAGAGAAG-GCGACTCGTA_L002

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.
TMM normalization size factors in EdgeR were calculated to adjust for samples for differences in library size.
Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.
Genome_build: GrCh38
Supplementary_files_format_and_content: Tab-separated values of raw counts.

source_name: HEL FedP

growth_protocol: HEL cells were cultured in RMPI with 10% fetal bovine serum and 1% penicillin/streptomycin. HEL JAK2 inhibitor persistent cells were generated through prolonged culturing in the presence of JAK2 inhibitors

extract_protocol:
Total RNA from cell lines was extracted with RNeasy Mini Kit (Qiagen, Hilden, Germany) with DNAse treatment following the manufacturer's protocol.
Samples were then indexed, pooled, and sequenced by Illumina NovaSeq 6000 following standard Illumina protocol.

treatment_protocol: HEL cells were treated in duplicate with DMSO, 1 µM BCI, 10 µM BI-D1870, or 1 µM BCI + 10 µM BI-D1870 for the indicated duration.

value: HEL

value: JAK2 V617F mutant cell line

value: Fedratinib-persistent


title: HEL RuxP rep 2

description:
processed data file:
HEL_persistent_raw_counts
hel_ruxp-2.CCACGACTTC-TAACTTGGTC.H7VW5DSXY_CCACGACTTC-TAACTTGGTC_L002

source_name: HEL RuxP

value: Ruxolitinib-persistent


title: Ear skin, Ddx5f/f 2 (psoriatic mice)


title: KO cbx3 crypt rep2

value: KO cbx3


title: KO cbx3 crypt rep1


title: HEL parental rep 2

description:
processed data file:
HEL_persistent_raw_counts
hel_parental-2.CCTCCAGAAG-ACATAACCAG.H7VW5DSXY_CCTCCAGAAG-ACATAACCAG_L002

source_name: HEL parental

value: parental


title: BAT ZT1 RNA 2 [CLH_RNA_2]

description: processed data file: All_RNA_Counts.txt

source_name: BAT ZT1 RNA

value: brown adipocytes


title: BAT ZT1 RNA 3 [CLH_RNA_3]

description: processed data file: All_RNA_Counts.txt


title: ctrl crypt rep2

description: jonctions_only_de_novo_present_only_in_the_wt_and_not_in_the_KO_HP1_Crypts_RNA-seq.bed

source_name: intestine

value: control

value: intestine


title: HEL RuxP rep 1

description:
processed data file:
HEL_persistent_raw_counts
hel_ruxp-1.CACAGACGTA-TTAAGAGGCG.H7VW5DSXY_CACAGACGTA-TTAAGAGGCG_L002


title: BAT ZT1 RNA 1 [CLH_RNA_1]

description: processed data file: All_RNA_Counts.txt


title: HEL parental rep 1

description:
processed data file:
HEL_persistent_raw_counts
hel_parental-1.AGATAGGCGA-GAAGCCTAGC.H7VW5DSXY_AGATAGGCGA-GAAGCCTAGC_L002


title: Ear skin, Ddx5f/f 1 (psoriatic mice)

value: Ear skin


title: HEL FedP rep 2

description:
processed data file:
HEL_persistent_raw_counts
hel_fedp-2.CACAGCATGA-TACAGCCTTG.H7VW5DSXY_CACAGCATGA-TACAGCCTTG_L002


title: ctrl crypt rep3

value: crypt epithelial cells


title: Ear skin, K14Ddx5f/f 4 (AD mice)

treatment_protocol: 1nmol MC903(Sigma) dissolved in 10 μL ethanol was painted on each ear of 8-week-old Ddx5f/f and K14Ddx5f/f  mice for 15 consecutive days. At day 16, ears were collected for RNA isolation.

value: 8 week old

value: female

value: MC903-induced atopic dermatitis


title: ctrl crypt rep1


title: WAT ZT21 ATAC 3 [CLH_ATAC_36]

description: processed data file: WAT_ATAC_peaks.txt

library_source: genomic

molecule: genomic DNA

source_name: WAT ZT21 ATAC

value: white adipocytes

value: nuclear DNA


title: HEL 24h BI-D1870 + BCI rep 2

description:
processed data file:
HEL_BID1870treatment_raw_counts
24h_bi-d1870-bci-2.AGGTCAGCGA-TACACGAAGA.HVCMMDSXY_AGGTCAGCGA-TACACGAAGA_L001

source_name: HEL 24h BI-D1870 + BCI

value: 10 µM BI-D1870 + 1 µM BCI

tag: treatment duration

value: 24 hours


title: Ear skin, K14Ddx5f/f 2 (AD mice)


title: WAT ZT21 ATAC 2 [CLH_ATAC_35]

description: processed data file: WAT_ATAC_peaks.txt


title: aTregBMPR_2

city: Columbus

first: Maciej

last: Pietrzak

state: OH

address: 1800 Cannon Drive, 340C Lincoln Tower

department: Department of Biomedical Informatics College of Medicine

institute: Ohio State University

data_processing:
Alignment to mouse GRCm38 reference genome using TopHat2.
Transcript assembly with Cufflinks.
Identification of differentially expressed genes with Cuffdiff.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: comma-separated values, FPKM values

source_name: adaptive Treg cells from mixed lymph node and spleen cell populations isolated from BMPR/CD4cre mice expressing Foxp3GFP reporter transgene

extract_protocol:
total RNA was extracted using Qiagen kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For aTreg cells total lymph node and spleen cells were isolated and activated in vitro with ConA (2 ug/ml) in the presence of TGF-beta (3 ng/ml) and IL-2 (10 ng/ml) for 3 days and flow cytometry sorted as CD4+Foxp3GFP+

value: CD4+ T cells

value: 8-12 weeks

tag: genotype/variation

value: BMPR-deficient aTreg cells


title: Ear skin, K14Ddx5f/f 1 (AD mice)


title: HEL 24h BI-D1870 + BCI rep 1

description:
processed data file:
HEL_BID1870treatment_raw_counts
24h_bi-d1870-bci-1.CGATCAGAAG-AGTAATCGAC.HVCMMDSXY_CGATCAGAAG-AGTAATCGAC_L001

value: HEL

value: JAK2 V617F mutant cell line


title: aTregBMPR_3

tag: strain


title: WAT ZT21 ATAC 1 [CLH_ATAC_34]

description: processed data file: WAT_ATAC_peaks.txt


title: aTregBMPR_1


title: WAT ZT17 ATAC 3 [CLH_ATAC_33]

description: processed data file: WAT_ATAC_peaks.txt

source_name: WAT ZT17 ATAC


title: Ear skin, Ddx5f/f 3 (AD mice)

tag: tissue

value: male


title: aTregWT_3

source_name: adaptive Treg cells from mixed lymph node and spleen cell populations isolated from normal B6 mice expressing Foxp3GFP reporter transgene

value: wild type


title: WAT ZT17 ATAC 1 [CLH_ATAC_31]

description: processed data file: WAT_ATAC_peaks.txt


title: WAT ZT17 ATAC 2 [CLH_ATAC_32]

description: processed data file: WAT_ATAC_peaks.txt


title: aTregWT_2


title: Ear skin, Ddx5f/f 2 (AD mice)

tag: genotype


title: HEL 24h DMSO rep 1

description:
processed data file:
HEL_BID1870treatment_raw_counts
24h_dmso-1.CCATCTGTCG-CTCTCATGCG.HVCMMDSXY_CCATCTGTCG-CTCTCATGCG_L001

source_name: HEL 24h DMSO

tag: cell type

value: DMSO


title: HEL 24h DMSO rep 2

description:
processed data file:
HEL_BID1870treatment_raw_counts
24h_dmso-2.CCTAAGCTGA-ACCAGATTCA.HVCMMDSXY_CCTAAGCTGA-ACCAGATTCA_L001

tag: treatment


title: Ear skin, Ddx5f/f 1 (AD mice)

value: Ear skin


title: HEL 48h BCI rep 2

description:
processed data file:
HEL_BCItreatment_raw_counts
48h_bci-2.CCGGATCCAA-ATGCGAATAG.HNJHFDSXY_CCGGATCCAA-ATGCGAATAG_L002

source_name: HEL 48h BCI

value: 1 µM BCI

value: 48 hours


title: RNA-Seq D4_WT_rep2

city: guangzhou

first: gongcheng

last: Hu

state: guangdong

address: 190 Kai Yuan Avenue, Science Park, Guangzhou, China

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

data_processing:
Adaptors in raw reads were trimmed using Trim Galore, then were quasi-mapped and quantified to mouse mm10 genome with salmon.
Transcript level counts were collapsed to gene level counts using tximport, and analyzed with DEseq2.
Genome_build: mm10
Supplementary_files_format_and_content: tsv files were generated from normalized RNAseq data.

source_name: Differentiated embryoid bodies at day 4

growth_protocol: mESC lines E14Tg2A were cultured on mitomycin C-inactivated mouse embryo fibroblasts in DMEM media containing 15% fetal bovine serum (FBS; Gibco), 1 mM sodium pyruvate (Gibco), 1 mM non-essential amino acids (Gibco), 1× GlutaMAX (Gibco), 0.1 mM 2-mercaptoethanol (Gibco), 1000 U/ml leukemia inhibitory factor, and the 2i inhibitors (3 μM CHIR99021, and 1 μM PD0325901).

extract_protocol:
RNA was isolated with Trizol reagents.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: In mESCs, CTCF lysine 20 was mutated to arginine by CRISPR/Cas9 technology. mESCs were differentiated into EBs using the hanging-drop method (with 1,000 cells/drop) in DMEM media with 15% serum without LIF.

value: EBs at day 4


title: HEL 48h DMSO rep 2

description:
processed data file:
HEL_BCItreatment_raw_counts
48h_dmso-2.GCTCTGTGTC-ACCGCGCTAA.HNJHFDSXY_GCTCTGTGTC-ACCGCGCTAA_L002

source_name: HEL 48h DMSO


title: WAT ZT13 ATAC 2 [CLH_ATAC_29]

description: processed data file: WAT_ATAC_peaks.txt

source_name: WAT ZT13 ATAC


title: RNA-Seq D4_K20R_rep2


title: Ear skin, K14Ddx5f/f 3 (AD mice)

source_name: Ear skin

value: 8 week old

value: female

value: MC903-induced atopic dermatitis


title: WAT ZT13 ATAC 3 [CLH_ATAC_30]

description: processed data file: WAT_ATAC_peaks.txt

value: white adipocytes

value: nuclear DNA


title: WAT ZT13 ATAC 1 [CLH_ATAC_28]

description: processed data file: WAT_ATAC_peaks.txt


title: HEL 48h BCI rep 1

description:
processed data file:
HEL_BCItreatment_raw_counts
48h_bci-1.TCGTGACGAC-GATGAGCGGT.HNJHFDSXY_TCGTGACGAC-GATGAGCGGT_L002


title: aTregWT_1

value: CD4+ T cells


title: RNA-Seq D0_K20R_rep2

source_name: mouse ES cells

value: mESCs


title: Zmynd8-cKO female cardiomyocyte, rep1

city: Honolulu

first: Andrew

middle: Kekūpaʻa

last: Knutson

state: HI

address: 651 Ilalo St.

department: Center for Cardiovascular Research

institute: John A. Burns School of Medicine - University of Hawaiʻi

data_processing:
Raw sequences were mapped to mm10 using HISAT2. Duplicate reads were excluded from analyses.
Differential gene expression was calculated using DESeq2 with default parameters.
Normalized read counts per transcript (RPKM) values were calculated using CuffDiff2.
Assembly: mm10
Supplementary files format and content: Ensembl Gene ID, and Differential expression comparison data (Mean expression, log2(Fold Change), BH adjusted p-value), and Read counts for individual replicates.

source_name: Heart

growth_protocol: cell isolation protocol: Rod cardiomyocytes were isolated from 4-week old mouse hearts using a langendorff-free method using collagenases 2 and 4 followed by plating on laminin coated dishes.

extract_protocol:
Total RNA was extracted in Trizol and RNA quality was assessed on a Bioanalyzer. Only RNA with an RNA integrity number of >7 was used in library construction.
Approximately 250 ng of RNA was used to construct each library. Ribosomal RNA was depleted using NEBNext rRNA Depletion Kit original or vs (Human/Mouse/Rat) (E6310 or E7400) and libraries were built using the NEBNext Ultra II RNA Library Prep Kit for Illumina (E7770).

value: Heart

value: 4 week

value: Cardiomyocyte

value: Myh6-CreTg/0;  Zmynd8fl/fl

tag: background


title: Zmynd8-cKO female cardiomyocyte, rep2


title: HEL 24h BI-D1870 rep 1

description:
processed data file:
HEL_BID1870treatment_raw_counts
24h_bi-d1870-1.AGGTGAGAGC-CTGCACACTG.HVCMMDSXY_AGGTGAGAGC-CTGCACACTG_L001

source_name: HEL 24h BI-D1870

value: HEL

value: JAK2 V617F mutant cell line

value: 24 hours


title: WAT ZT9 ATAC 3 [CLH_ATAC_27]

description: processed data file: WAT_ATAC_peaks.txt

source_name: WAT ZT9 ATAC

tag: time point


title: HEL 4h BCI rep 2

description:
processed data file:
HEL_BCItreatment_raw_counts
4h_bci-2.AATCCGAGTA-TTAGAATCGG.HNJHFDSXY_AATCCGAGTA-TTAGAATCGG_L002

source_name: HEL 4h BCI

value: 1 µM BCI

value: 4 hours


title: RNA-Seq D4_WT_rep1

value: wild type

value: EBs at day 4


title: WAT ZT9 ATAC 2 [CLH_ATAC_26]

description: processed data file: WAT_ATAC_peaks.txt

tag: molecule subtype


title: Zmynd8-cKO male cardiomyocyte, rep1

value: male


title: Zmynd8-cKO male cardiomyocyte, rep2


title: RNA-Seq D4_K20R_rep1


title: HEL 24h BI-D1870 rep 2

description:
processed data file:
HEL_BID1870treatment_raw_counts
24h_bi-d1870-2.GTCCGAGGAA-CTTCAGGTAA.HVCMMDSXY_GTCCGAGGAA-CTTCAGGTAA_L001


title: RNA-Seq D0_K20R_rep1


title: RNA-Seq D0_WT_rep2


title: HEL 4h DMSO rep 2

description:
processed data file:
HEL_BCItreatment_raw_counts
4h_dmso-2.CAGTTCATGG-CTTGGACCTG.HNJHFDSXY_CAGTTCATGG-CTTGGACCTG_L002

source_name: HEL 4h DMSO

value: DMSO


title: D4_K20R_input

data_processing:
Raw reads were trimmed with Trim_Galore and aligned to mouse mm10 genome using bowtie2 with parameter “--very-sensitive --end-to-end --no-unal”.
Reads with mapping quality lower than 30 were discarded. Duplicated reads were removed with sambamba. Reads overlapped with mouse mm10 blacklist regions were excluded.
10 million reads were randomly subsampled. Peaks were called using MACS2 with default parameters, and bigwig files were generated from deeptools.
Genome_build: mm10
Supplementary_files_format_and_content: Peak files were generated from MACS2.  Bigwig files were generated from deeptools.

extract_protocol:
cells were crosslinked with 1% formaldehyde at room temperature for 10 min. Then the reaction was stopped by adding glycine (final concentration, 0.125 M). The cells were sonicated in SDS lysis buffer containing 1 x protease inhibitor cocktails and 1 mM PMSF to achieve a chromatin sized of 100-300 bp. The sonicated chromatin was incubated with indicated antibodies coupled with dynabeads protein A and G (1:1 mixed) at 4℃ overnight with rotation. Immune complexes were washed with the following buffers: low salt wash buffer (0.1% SDS, 1%Triton X-100, 2mMEDTA, 20mM Tris-HCl (pH 8.0), 150 mMNaCl), high salt wash buffer (0.1% SDS, 1% Triton X-100, 2mMEDTA, 20mM Tris-HCl (pH 8.0), 500 mM NaCl), LiCl wash buffer (0.25 MLiCl, 1% IGEPAL-CA630, 1% deoxycholic acid (sodium salt), 1 mM EDTA, 10 mM Tris-HCl (pH 8.0)) and TE buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA). Antibody-bound chromatin was reverse-crosslinked, and the ChIPed DNA samples were purified for sequencing.
ChIP DNA libraries were constructed following the Illumina ChIP-Seq library generation protocol.

tag: chip antibody


title: Control female cardimyocyte, rep1

value: female


title: Control female cardimyocyte, rep2


title: HEL 48h DMSO rep 1

description:
processed data file:
HEL_BCItreatment_raw_counts
48h_dmso-1.CACAGCCAAC-TAACACCGGC.HNJHFDSXY_CACAGCCAAC-TAACACCGGC_L002

tag: cell line

value: 48 hours


title: WAT ZT5 ATAC 1 [CLH_ATAC_22]

description: processed data file: WAT_ATAC_peaks.txt

source_name: WAT ZT5 ATAC

value: white adipocytes

value: nuclear DNA


title: HEL 4h BCI rep 1

description:
processed data file:
HEL_BCItreatment_raw_counts
4h_bci-1.CCGTGAACTG-TATGCAACTC.HNJHFDSXY_CCGTGAACTG-TATGCAACTC_L002


title: WAT ZT1 ATAC 3 [CLH_ATAC_21]

description: processed data file: WAT_ATAC_peaks.txt

source_name: WAT ZT1 ATAC


title: WAT ZT9 ATAC 1 [CLH_ATAC_25]

description: processed data file: WAT_ATAC_peaks.txt


title: WT1 5aza treated ATAC hair matrix P4.5

city: BOSTON

first: Guodong

last: Chen

state: MA

address: 609 Albany Street, ROOM 414

department: Dermatology

institute: Boston University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Reads were trimmed by using trim-galore with default paramaters.
Trimmed eads were aligned to the GRCm38 genome using Bowtie. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using bamCoverage in deeptools. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig

source_name: Primary keratinocytes

extract_protocol:
Native cells were isolated from mice skin with FACS. Only living cells were used for ATAC following the manual of Active Motif ATAC-seq kit.
DNA is amplified with NEBNext® High-Fidelity 2x PCR Master Mix (NEB, #M0541) as well as unique i5 and i7 index primers for 10 cycles to prepare DNA library.

tag: developmental stage

value: WT

value: Primary keratinocytes

value: Hair matrix keratinocytes


title: WAT ZT5 ATAC 3 [CLH_ATAC_24]

description: processed data file: WAT_ATAC_peaks.txt


title: D0_K20R_input

value: mESCs


title: WAT ZT5 ATAC 2 [CLH_ATAC_23]

description: processed data file: WAT_ATAC_peaks.txt


title: WT2 5aza treated ATAC hair matrix P4.5


title: HEL 4h DMSO rep 1

description:
processed data file:
HEL_BCItreatment_raw_counts
4h_dmso-1.GTATGGCTAA-GCCAGCTATC.HNJHFDSXY_GTATGGCTAA-GCCAGCTATC_L002

value: HEL


title: GSC2-Sample1: without Chi3l1 incubation (control)

city: Bronx

first: Jorge

middle: Eduardo

last: Fajardo

state: NY

address: 1300 Morris Park Avenue

department: Systems and Computational Biology

institute: Albert Einstein College of Medicine

data_processing:
fastq files as well as CellRanger count output were provided by Dana Farber Cancer Institute(DFCI) Genomics core (MBCF)
Jaccard analysis was performed to determine the clusturization
Seurat, velocity and scVelo were used for downstream analysis with the use of R packages

source_name: Patient derived glioma stem cells

growth_protocol: The IRB of Rhode Island Hospital has approved the collection of patient-derived glioblastoma multiforme (GBM) tissue. All collections were performed with patient consent and in completely de-identified manner. Primary hGSC spheres were cultured from human glioma samples as previously described (Galli et al., 2004) All hGCs used in this study were authenticated by ATCC using short tandem repeat (STR) analysis. All human primary cells used were between passages 5 and 30. GSCs were cultured either as spheres or as attached on fibronectin-coated plates (10ug/ml, Millipore Sigma) in a medium of 1X Neurobasal Medium (Fisher Scientific), B27 serum-free supplement, minus Vitamin A (Fisher Scientific), 100X Glutamax (Fisher Scientific), 1mg/ml Heparin (STEMCELL Technologies), 20 ng/ml epidermal growth factor (Peprotech), 20ng/ml basic-fibroblast growth factor (Peprotech), and 1% Antibiotic-Antimycotic (Fisher Scientific).

extract_protocol:
Samples preparation were prepared following 10x Genomics user guide : Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index)
Libraries were prepared according to 10x Genomics user guide : Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index)

treatment_protocol: GSCs were treated for 7 days with/without Chi3l1. Media was replaced every 2-3 days.

value: brain

value: Untreated

value: glioma stem cells


title: Tet2/3 DKO2 5aza treated ATAC hair matrix P4.5

value: Tet2/3 DKO


title: Tet2/3 DKO1 5aza treated ATAC hair matrix P4.5


title: GSC1-Sample2: with Chi3l1 incubation

value: Treated with 500 ng recCHI3L1


title: GSC2-Sample2: with Chi3l1 incubation


title: WT2 ATAC hair matrix P4.5


title: D0_WT_input

value: wild type


title: WAT ZT1 ATAC 1 [CLH_ATAC_19]

description: processed data file: WAT_ATAC_peaks.txt


title: GSC1-Sample1: without Chi3l1 incubation (control)


title: RNA-Seq D0_WT_rep1


title: WT1 ATAC hair matrix P4.5


title: BAT ZT21 ATAC 3 [CLH_ATAC_18]

description: processed data file: BAT_ATAC_peaks.txt

source_name: BAT ZT21 ATAC

value: brown adipocytes


title: D4_H3K27ac_K20R

value: EBs at day 4

value: H3K27ac(Active motif, 39133)


title: Tet2/3 DKO2 ATAC hair matrix P4.5


title: WAT ZT1 ATAC 2 [CLH_ATAC_20]

description: processed data file: WAT_ATAC_peaks.txt


title: BAT ZT21 ATAC 1 [CLH_ATAC_16]

description: processed data file: BAT_ATAC_peaks.txt


title: D4_CTCF_K20R_rep2

value: CTCF(Active motif, 61311)


title: D4_H3K27ac_WT


title: mirna sequences

city: shanghai

first: zhu

last: caibin

state: china

address: chenqiao road 2358#

institute: Cheermore Cosmetic Dermatology Laboratory

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Mapping to Phellinus igniarius genomes using miRDeep2's mapper.pl
Genome_build: Phellinus igniarius
Supplementary_files_format_and_content: read counts

organism: Phellinus igniarius

source_name: fungus

extract_protocol:
Total RNA was extracted using TRIzol reagents (Thermo Fisher Scientific). RNA concentrations were measured by Qubit fluorometer (Thermo Fisher Scientific) and RNA quality were evaluated by 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Only samples with RIN higher than 7.0 were chosen for library preparation.
Library preparation was performed using the NEBNext Multiplex Small RNA Library Prep kit (NEB, Ipswich, MA) with 1 μg of total RNA as input, following the manufacturer’s instructions. In brief, the RNA 3' adaptor was specifically ligated to miRNA with the excess adaptor removed by hybridization. The 5’ ends of miRNA were then ligated to the 5’ adaptor, followed by reverse transcription to convert the ligated small RNA into cDNA, which was then uniquely indexed by PCR to generate the sequencing library. Libraries of 147bp were recovery in a 6% polyacrylamide gel electrophoresis, and quantified with Kapa Library Quantification kit (Kapa Biosystems, Wilmington, MA) using an ABI 9700HT Fast Real-Time PCR system (Thermo Fisher Scientific). Sequencing was performed on NovaSeq 6000 platform (Illumina)

tag: molecule type

value: microRNA


title: D4_WT_input


title: iWAT_input

data_processing:
ATAC-sequencing reads were trimmed and aligned to the mouse reference genome (mm10) using the ENCODE ATAC-sequencing pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline).
HOMER was used to identify and annotate peaks and motifs in ATAC-Seq data
RNA-seq reads aligned to mm10 using STAR 2.7.5
RSEM 1.3.0 was used to assign transcript counts to gene features (Ensembl 98)
Differential Gene epression (DESeq2), data visulaization (pheatmap, gplots, ggplot2), KEGG pathway analysis (limma), rhythmic analyses (JTK-Cycle) were performed in R (4.1.0)
ChIP-seq reads were aligned ChIP were aligned using Bowtie2 (v2.4.1).
Tag directorie creation, peak identification and bigwig file production for ChIP-seq samples using HOMER
Genome_build: mm10
Supplementary_files_format_and_content: mm10.chrom.sizes” for visualization on the UCSC genome browser.
Supplementary_files_format_and_content: Table with rhythmic genomic features obtained from JTK_Cycle

source_name: white adipocytes

extract_protocol:
NuTRAP nuclei and ribosomal RNA were isolated according to established methods (PMID 28122230). Brown adipose and inguinal white adipose depots were snap frozen in liquid nitrogen, minced, dounce homogenized, spun down and FACS sorted to isolate for ATAC-Seq. Tissues were minced, homogenized, ribosomal RNA was affinity purified using anti-GFP antibodies and protein G Dynabeads and extracted using the Qiagen Micro RNeasy kit. For ChIP-seq experiments, minced inguinal WAT was fixed in disuccinimidyl glutarate (2mM in PBS + 1% DMSO, 30 min) and  formaldehyde (1% in PBS, 10 min). Nuclei were isolated in buffer (150 mM NaCl, 5 mM EDTA pH8, 50  mM Tris-HCl pH8, 0.35% NP-40) in the presence of protease inhibitors by dounce homogenization, then  sheared in 1% SDS buffer by sonication using a Covaris E220 (5% duty factor, 140 W power, 200 cycles  per burst, 4 minute total shearing time, 4°C). An aliquot for input samples was taken after shearing.  Chromatin was diluted 1:10 in dilution buffer (0.01% SDS, 1.1% Triton X-100, 167 mM NaCl, 1.2 mM  EDTA pH 8, 1.67 mM Tris-HCl pH 7.4). Immunoprecipitation was performed using 15 μg of BMAL1  antibody (Millipore ABE2599) at 4°C with rotation. Protein A paramagnetic beads (ThermoFisher) were  used to pull down protein/DNA complexes. Chromatin was de-crosslinked and purified by QIAGEN  MinElute column prior to library prep with NEBNext Ultra II DNA library prep kit. Inputs were  quantified by Qubit Fluorometer (Invitrogen), pooled, and 2 ng were processed into libraries. Libraries  were size-selected to 200-600 bp on the Sage Pippin Prep, amplified and barcoded using 13 cycles of  PCR, and sequenced using single-end 75 bp sequencing on a NextSeq 500 to an average depth of ~30M  reads.
ATAC-seq libraries were constructed according to the Omni-ATAC protocol (PMID 28846090). RNA-Seq libraries were constructed from 250 ng of RNA using the NEBNext RNA Ultra Directional library prep kit. ChIP-seq samples were de-crosslinked and purified by QIAGEN  MinElute column prior to library prep with NEBNext Ultra II DNA library prep kit. Inputs were  quantified by Qubit Fluorometer (Invitrogen), pooled, and 2 ng were processed into libraries. Libraries  were size-selected to 200-600 bp on the Sage Pippin Prep, amplified and barcoded using 13 cycles of  PCR.

value: white adipocytes

value: nuclear DNA

value: none (input)


title: D4_CTCF_K20R_rep1

source_name: Differentiated embryoid bodies at day 4


title: Human Thyroid Organoid

description: Raw Data Files split into 12 due to size issues.

data_processing:
The raw sequencing data were then processed with the ‘count’ command of the Cell Ranger software (v.6.0.1) provided by 10x Genomics with the option ‘–expect-cells’ set to 10,000 (all other options were used as per default).
Genome_build: GRCh38
Supplementary_files_format_and_content: barcodes.tsv.gz: Tab Seperated File containing Cell barcodes. Cell barcodes correspond to columns of the matrix.
Supplementary_files_format_and_content: features.tsv.gz: Tab Seperated File containing gene names. Gene names correspond to rows of the matrix.
Supplementary_files_format_and_content: matrix.mtx.gz: Sparse martix containing counts obtained from Cell Ranger output.

source_name: hESC-derived differentiated cells


title: iWAT_BMAL1-1

value: anti-BMAL1 (Millipore ABE2599)


title: BAT ZT21 ATAC 2 [CLH_ATAC_17]

description: processed data file: BAT_ATAC_peaks.txt

data_processing:
ATAC-sequencing reads were trimmed and aligned to the mouse reference genome (mm10) using the ENCODE ATAC-sequencing pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline).
HOMER was used to identify and annotate peaks and motifs in ATAC-Seq data
RNA-seq reads aligned to mm10 using STAR 2.7.5
RSEM 1.3.0 was used to assign transcript counts to gene features (Ensembl 98)
Differential Gene epression (DESeq2), data visulaization (pheatmap, gplots, ggplot2), KEGG pathway analysis (limma), rhythmic analyses (JTK-Cycle) were performed in R (4.1.0)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Table with rhythmic genomic features obtained from JTK_Cycle

extract_protocol:
NuTRAP nuclei and ribosomal RNA were isolated according to established methods (PMID 28122230). Brown adipose and inguinal white adipose depots were snap frozen in liquid nitrogen, minced, dounce homogenized, spun down and FACS sorted to isolate for ATAC-Seq. Tissues were minced, homogenized, ribosomal RNA was affinity purified using anti-GFP antibodies and protein G Dynabeads and extracted using the Qiagen Micro RNeasy kit.
ATAC-seq libraries were constructed according to the Omni-ATAC protocol (PMID 28846090). RNA-Seq libraries were constructed from 250 ng of RNA using the NEBNext RNA Ultra Directional library prep kit


title: Tet2/3 DKO1 ATAC hair matrix P4.5

value: Primary keratinocytes

value: Hair matrix keratinocytes


title: D4_CTCF_WT_rep2


title: BAT ZT17 ATAC 2 [CLH_ATAC_14]

description: processed data file: BAT_ATAC_peaks.txt

source_name: BAT ZT17 ATAC


title: BAT ZT17 ATAC 3 [CLH_ATAC_15]

description: processed data file: BAT_ATAC_peaks.txt


title: iWAT_BMAL1-2


title: BAT ZT17 ATAC 1 [CLH_ATAC_13]

description: processed data file: BAT_ATAC_peaks.txt


title: BAT ZT13 ATAC 3 [CLH_ATAC_12]

description: processed data file: BAT_ATAC_peaks.txt

source_name: BAT ZT13 ATAC


title: G2M_EMseq_rep3

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: CPR

data_processing:
Library strategy: EM-seq
Fastq files were generated using bcl2fastq v2.19.1.
FastQC v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) was used for QC metrics, and multiqc v1.7 for reporting.
Reads were trimmed with trim_galore 0.6.4 (https://github.com/FelixKrueger/TrimGalore).
Trimmed reads were mapped to the GRCm38/mm10 mouse reference genome and control genomes with bowtie2 using Bismark v0.22.1 (bismark -N 1 -L 20 -X 1000).
Mapped reads were deduplicated with deduplicate_bismark.
Reads with MAPQ < 20 and PCR duplicates were discarded, as were reads found in outlier regions with a raw read count >10 above the median when the genome was partitioned into 25-kilobase windows. Remaining reads were used in downstream analyses.
Genome_build: mm10
Supplementary_files_format_and_content: The processed data file contains the coordinates of 100-CpG windows that contained a minimum of 1 in 5 observed CpGs in all datasets. Average CpG methylation across these windows is quantitated in all replicates.

source_name: Embryonic stem cells

growth_protocol: Mouse embryonic stem cells (ESCs) were grown on gelatinized plates in 15% fetal bovine serum with penicillin/ streptomycin, GlutaMAX, non-essential amino acids, beta-mercaptoethanol, and homemade LIF.

extract_protocol:
Cultured ES cells were EdU labelled, harvested, and fixed in 70% ethanol. Cells were treated with Click-iT to label EdU+ cells and PI for DNA content and sorted via fluorescence-activated cell sorting to obtain pure G1 and G2/M populations. Genomic DNA was isolated from sorted cells using the Zymo Duet MiniPrep kit (D7001).
Libraries were generated using the EM-seq method (NEB, E7120S). 125 ng DNA per sample was mixed with 1 pg pUC19 DNA and 20 pg lambda DNA and sonicated to 200 bp using a Covaris E220. Drosophila DNA was sonicated in parallel, 7.5 pg was added to sonicates, and PCR-grade water was added to a final volume of 50 μL. 7 μL NEBNext Ultra II End Prep Reaction Buffer and 3 μL NEBNext Ultra II End Prep Enzyme Mix was added to each sample, mixed, and incubated at 20 °C for 30 minutes followed by 65 °C for 30 minutes in a thermocycler with a lid heated to 65 °C. On ice, 2.5 μL NEBNext EM-seq Adaptor, 1 μL NEBNext Ligation Enhancer, and 30 μL NEBNext Ultra II Ligation Master Mix was added to each sample, mixed, and incubated at 20 °C for 60 minutes in a thermocycler with an opened lid. Samples were purified using NEBNext Sample Purification Beads, 1.18:1 bead:sample ratio, and eluted in 28 μL Elution Buffer. 10 μL freshly prepared TET2 Reaction Buffer, 1 μL Oxidation Supplement, 1 μL DTT, 1 μL Oxidation Enhancer, and 4 μL TET2 enzyme were added to each sample and mixed. 5 μL freshly diluted 400 μM Fe(II) Solution was added to each sample, mixed, and incubated at 37 °C for 60 minutes in a thermocycler with a lid heated to 45 °C. On ice, 1 μL Stop Reagent was added to each sample, mixed, and incubated at 37 °C for 30 minutes in a thermocycler with a lid heated to 45 °C. Samples were purified using NEBNext Sample Purification Beads, 1.8:1 bead:sample ratio, and eluted in 16 μL Elution Buffer. Samples were denatured by adding 4 μL freshly prepared, mixing, and incubating at 50 °C for 10 minutes in a thermocycler with a lid heated to 60 °C. On ice, 68 μL PCR-grade water, 10 μL APOBEC Reaction Buffer, 1 μL BSA, and 1 μL APOBEC enzyme were added to each sample, mixed, and incubated at 37 °C for 3 hours in a thermocycler with a lid heated to 45 °C. Samples were purified using NEBNext Sample Purification Beads, 1:1 bead:sample ratio, and eluted in 20 μL Elution Buffer. Libraries were amplified by adding 5 μL EM-seq Index Primer and 25 μL NEBNext Q5U Master Mix to each sample, mixing, and cycling with the following conditions: 98 °C, 30 seconds; 5 cycles of: 98 °C, 10 seconds; 62 °C, 30 seconds; 65 °C, 60 seconds; followed by a 65 °C, 5 minutes final extension. Libraries were purified in two rounds using NEBNext Sample Purification Beads, first round 0.9:1 bead:sample ratio; second round 1:1 bead:sample ratio, and eluted in 10 μL Elution Buffer. Libraries were checked for quality control by BioAnalyzer and Qubit quantification before sequencing.

tag: passages

tag: cell cycle phase


title: D0_CTCF_K20R_rep2

source_name: mouse ES cells

value: mESCs


title: G2M_EMseq_rep2


title: R2-WT-infected

type: RNA

city: Izmir

first: Mayda

last: Gursel

address: Dokuz Eylül Üniversitesi İnciraltı Yerleşkesi

department: Basic and Translational Research Program

country: Turkey

institute: Izmir Biomedicine and Genome Center

hyb_protocol: Hybridization protocol was conducted according to the instructions of manufacturer of nCounter PanCancer Immune Profiling CS Kit (no MK).

scan_protocol: Scan protocol was conducted according to the instructions of manufacturer of nCounter PanCancer Immune Profiling CS Kit (no MK).

data_processing: by nSolver Analysis software (v4.) and nCounter® Advanced Analysis Software (v2.)

label: Nanostring reporter probe

source_name: WT KO THP1-Dual Cell Line

label_protocol: Labeling protocol was conducted according to the instructions of manufacturer of nCounter PanCancer Immune Profiling CS Kit (no MK).

growth_protocol: THP1 cell lines were cultured in 10% (v/v) FBS supplemented RPMI 1640 medium containing 100 μg/ml zeocin and 10 μg/ml blasticidin at 37°C with 5% CO2 and humidity. Leishmania major were cultured in 20% (v/v) FBS supplemented RPMI 1640 medium in plug sealed flasks at 26°C.

extract_protocol: Cellular material was collected with RiboExTM followed by instructions of RNA Clean & Concentrator™-25 (Zymo Research, U.S.A.) kit.

treatment_protocol: Infection was performed in 2% (v/v) FBS supplemented RPMI1640 medium for 6 hours, followed by DPBS wash thrice, and replacement of media with 10% (v/v) FBS supplemented RPMI 1640 medium.

value: WT

value: Leishmania major infected


title: R3-WT-infected


title: D0_CTCF_K20R_rep1


title: BAT ZT13 ATAC 2 [CLH_ATAC_11]

description: processed data file: BAT_ATAC_peaks.txt


title: R1-WT-infected


title: D4_CTCF_WT_rep1


title: G2M_EMseq_rep1


title: D0_CTCF_WT_rep2


title: G1_EMseq_rep2


title: BAT ZT9 ATAC 3 [CLH_ATAC_9]

description: processed data file: BAT_ATAC_peaks.txt

source_name: BAT ZT9 ATAC


title: G1_EMseq_rep3


title: BAT ZT9 ATAC 2 [CLH_ATAC_8]

description: processed data file: BAT_ATAC_peaks.txt


title: HaCaT cells, KO3

data_processing:
RNA sequencing was performed using an Illumina systems following Illumina-provided protocols for 2x150 paired-end sequencing in WuXi NextCODE at Shanghai, China.
FastQC (version 0.11.9) was used for assessing the overall quality of raw reads and Trimmomatic (version 0.39) was applied for raw reads quality control to cut adapters and remove low-quality reads.
Samtools (version: 1.7) was used to convert SAM format files to BAM format files and sorted the BAM files.
Gene expression levels were quantified by FeatureCounts (version 1.6.3)Differential expression analysis was performed by R package DESeq2 (Version 1.34.0)and FDR<0.05 was considered to be significantly differentially expressed. Gene ontology (GO) and KEGG pathway enrichment analyses were performed in ClusterProfiler (version 4.2.0)
Differential alternative splicing events were detected by rMATS (version 3.1.0), and events with p value<0.05 were identified as significantly differentially expressed alternative splicing events.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include count values for each samples

source_name: HaCaT cell

growth_protocol: WT and DDX5-/- immortalized human keratinocyte cell line HaCaT was cultured in RPMI1640 (GIBCO) medium containing 10% FBS (GIBICO), 50 U/mL penicillin and 50μg/mL streptomycin (Shanghai Yuan Pei) under standard culture conditions

extract_protocol:
Total RNAs were isolated with TRIzol (Takara).  1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Gold library following manufacturer's protocols.

treatment_protocol: WT and DDX5-/-HaCaT were treated with 100ng/mL IL-36γ (Novoprotein) for 4 hours.

value: HaCaT cell

value: Keratinocytes

value: Stimulated by 100ng/mL IL-36γ for 4 hours


title: D0_CTCF_WT_rep1

value: wild type


title: D4_K20R_rep2

data_processing:
Raw reads were trimmed with Trim_Galore and aligned to mouse mm10 genome using bowtie2 with parameter “--very-sensitive --end-to-end --no-unal”.
Reads with mapping quality lower than 30 were discarded. Duplicated reads were removed with sambamba. Reads overlapped with mouse mm10 blacklist regions were excluded.
MACS2 was used to call peaks, and bigwig files were generated from deeptools.
Genome_build: mm10
Supplementary_files_format_and_content: Peak files were generated from MACS2.  Bigwig files were generated from deeptools.

extract_protocol:
Cells were resuspended in 50 μL lysis buffers (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.2% (v/v) IGEPAL CA-630). Then the suspension of nuclei was centrifuged 500 × g at 4°C for 10 min. The pellet was resuspended with 50 μL transposition reaction mix (10 μL TD buffer, 5 μL Tn5 transposase and 35 μL nuclease-free H2O), and incubated at 37°C for 30 min. Finally, DNA was isolated using MinElute PCR Purification Kit (QIAGEN).
ATAC libraries were prepared for sequencing using standard Illumina protocols.

value: Day 4 of wild CTCF-K20R

value: EBs


title: R1-TBK1-infected

source_name: TBK1 KO THP1-Dual Cell Line

value: TBK1 KO


title: R2-TBK1-infected


title: BAT ZT13 ATAC 1 [CLH_ATAC_10]

description: processed data file: BAT_ATAC_peaks.txt

value: brown adipocytes


title: BAT ZT9 ATAC 1 [CLH_ATAC_7]

description: processed data file: BAT_ATAC_peaks.txt


title: R3-cGAS-infected

source_name: cGAS KO THP1-Dual Cell Line

value: cGAS KO


title: D4_K20R_rep1


title: R2-cGAS-infected


title: G1_EMseq_rep1


title: BAT ZT5 ATAC 3 [CLH_ATAC_6]

description: processed data file: BAT_ATAC_peaks.txt

source_name: BAT ZT5 ATAC

value: nuclear DNA


title: R1-cGAS-infected


title: R3-TBK1-infected


title: D4_WT_rep2

value: Day 4 of wild type


title: HaCaT cells, KO2


title: Tail region spinal cord - ATAC-seq rep-2

city: Seoul

first: DongAhn

last: Yoo

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

description:
Spinal_Pooled_ATAC.bw
Spinal_peaks.xls_peaks.bed

data_processing:
The quality of the raw sequence data was investigated with FastQC (v. 0.11.9) followed by trimming of sequences with low quality and NexteraPE adapter sequences using trimmomatic-0.39 with following options: “ILLUMINACLIP:[AdapterFile]:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:30”. The clean reads were aligned to the newly assembled little skate genome with BWA (v. 0.7.17).
Peak calling was performed for each tissue after pooling the replicates of respective tissue (pectoral/pelvic fin MN and tail region spinal cord) using following options: “--keep-dup all --nomodel, -q 0.05 --shift -100 --extsize 200 -B”. Consensus ACRs were defined by merging the peaks from the two tissues using bedtools merge (v. 2.29.2).
bigWig file was generated with the pooled bam file of each tissue via bamCoverage of deeptools 3.4.3 using the following options: "--binSize 10 --smoothLength 200 --effectiveGenomeSize 1974810099 --normalizeUsing CPM".
Genome_build: The newly assembled genome described in manuscript
Supplementary_files_format_and_content: deeptools bigWig files
Supplementary_files_format_and_content: MACS2 peak files

organism: Leucoraja erinaceus

source_name: Tail region spinal cord

extract_protocol:
In stage 30 little skates, pectoral and pelvic motor neurons were labeled by injecting rhodamine-dextran (3K, Invitrogen). After 1-2 day incubation at RT, cell dissociation was performed. Spinal cords were isolated and digested with pronase for 30min at RT and dissociated motor neurons from several labeled spinal cords were collected manually.
150-426 labeled motor neurons were collected in 25µl cold ATAC-seq RSB (10mM Tris-HCl pH7.4, 10mM NaCl, and 3mM MgCl2 in Nuclease free water) and centrifuged at 500rcf for 10min in a pre-chilled fixed-angle centrifuge. The supernatant was removed and 10µl of transposition mix (3.3µl PBS, 1.15 µl Nuclease free water, 5 µl 2X TD buffer, 0.25 µl (Tn5, 1/10 diluted: 5µl 2X TD buffer, 4µl nuclease free water, 1µl Tn5), 0.1 µl 1% digitonin) was added and resuspended by pipetting six times. The samples were incubated with shaking at 1000rpm for 30min at 37℃. Tagmented DNA was purified with Qiagen minelute reaction cleanup kit (Qiagen, 28206). PCR mixtures (10µl Nuclease free water, 2.5µl 25µM primer (Ad1), 2.5µl 25µM primer (Ad2.X), 25µl 2X NEB master mix, Transposed sample 20µl) were prepared and primary PCR was performed in the following condition: 72℃ 5min, 1cycle; 98℃ 30sec, 1cycle; 98℃ 10sec, 63℃ 30sec, 72℃ 1min 5cycles; hold at 4℃. PCR mixture (3.76µl nuclease free water, 0.5µl 25µM primers (Ad1.1), 0.5µl 25µM primers (Ad2.X), 0.24µl 25X SybrGold in DMSO, 5µl 2X NEB master mix, 5µl pre-Amplified sample) were prepared and quantitative PCR was performed as follows: 98℃ 30sec, 1cycle; 98℃ 10sec, 63℃ 30sec, 72℃ 1min 20cycles; hold at 4℃. 1/4 max cycles were determined (N) and the primary PCR reaction products underwent N more PCR cycles. For the tail region spinal cord, 240-1000 cells from two embryos were used for ATAC sequencing library preparation.   The primes used in the ATAC library preparation were as follows:  AD1.1:AATGATACGGCGACCACCGAGATCTACACTAGATCGCTCGTCGGCAGCGTCAGATGTG; AD2.1:TAAGGCGACAAGCAGAAGACGGCATACGAGATTCGCCTTAGTCTCGTGGGCTCGGAGATGT; AD2.2:CGTACTAGCAAGCAGAAGACGGCATACGAGATCTAGTACGGTCTCGTGGGCTCGGAGATGT; AD2.3:AGGCAGAACAAGCAGAAGACGGCATACGAGATTTCTGCCTGTCTCGTGGGCTCGGAGATGT; AD2.4:TCCTGAGCCAAGCAGAAGACGGCATACGAGATGCTCAGGAGTCTCGTGGGCTCGGAGATGT; AD2.5:GGACTCCTCAAGCAGAAGACGGCATACGAGATAGGAGTCCGTCTCGTGGGCTCGGAGATGT

value: Tail region spinal cord

value: stage 30


title: Tail region spinal cord - ATAC-seq rep-3


title: BAT ZT5 ATAC 2 [CLH_ATAC_5]

city: Chicago

first: Nathan

address: 303 E Superior St, Lurie 7-220

institute: Northwestern University

description: processed data file: BAT_ATAC_peaks.txt


title: D4_WT_rep1


title: HiC_D4_K20R_rep2

data_processing:
Library strategy: BL-Hi-C
Raw reads were first submmited to Trim_Galore to remove adaptors, then linkers were trimmed with parameters “-m 1 -k 2 -e 1 -l 15 -A ACGCGATATCTTATC -B AGTCAGATAAGATAT” using ChIA-PET2.
The trimmed reads were handled using HiC-Pro.
Hi-C data were normalized using hiccompare. Normalized matrix was transformed to hic format using Juicer tools.
Genome_build: mm10
Supplementary_files_format_and_content: hic

extract_protocol:
The BL-Hi-C libraries were performed as previous described (Liang et al., 2017).
The libraries were constructed using Q5 Hot Star DNA Polymerase (NEB) for PCR amplification. PCR products between 300-700 bp were purified as BL-Hi-C library using Ampure XP beads (Beckman Coulter).


title: HaCaT cells, KO1


title: BAT ZT5 ATAC 1 [CLH_ATAC_4]

description: processed data file: BAT_ATAC_peaks.txt


title: Pectoral and pelvic fin motor neurons - ATAC-seq rep-4

description:
PecPel_Pooled_ATAC.bw
PecPel_peaks.xls_peaks.bed

source_name: Pectoral and pelvic fin motor neurons

value: Pectoral and pelvic fin motor neurons


title: BAT ZT1 ATAC 2 [CLH_ATAC_2]

description: processed data file: BAT_ATAC_peaks.txt

source_name: BAT ZT1 ATAC


title: Pectoral and pelvic fin motor neurons - ATAC-seq rep-3


title: BAT ZT1 ATAC 3 [CLH_ATAC_3]

description: processed data file: BAT_ATAC_peaks.txt


title: HaCaT cells, WT3


title: HiC_D4_WT_rep2


title: HaCaT cells, WT2


title: HiC_D4_K20R_rep1


title: TRA_72h_3

status: Public on Oct 23 2022

city: Haikou

first: tian

last: jiang

address: 58 of Ren min Road

institute: Hainan University

data_processing:
The de novo assembly was performed on cleaned reads using Trinity (Grabherr et al., 2011). Before assembly, raw reads were trimmed by removing adaptor sequences and ambiguous nucleotides. Reads with quality scores less than 20 and length below 30 bp were all trimmed. The resulting high-quality sequences were used in subsequent assembly. Briefly, the raw reads were assembled into the unique sequences of transcripts in Inchworm via greedy K-mer extension (k-mer 25).
After mapping of reads to Inchworm contig bundles, Chrysalis incorporated reads into de Bruijn graphs. Butterfly then processed the individual graphs in parallel, reporting full-length transcripts and paralogous genes. After assembly, the open reading frame (ORF) of each unisequence was predicted by using Trinity software. Unisequences were used for BLAST search and annotation against the NR, NT, STRING (http://string-db.org/) (Franceschini et al., 2013), COG (http://www.ncbi.nlm.nih.gov/COG/), KEGG (http://www.genome.jp/kegg/) databases using an E-value cut-off of 10-5 (Camacho et al., 2009). Functional annotation by gene ontology (GO, http://www.geneontology.org) terms was analysed by using BLAST2GO software (NCBI) (Conesa et al., 2005).
Genome_build: not provided
Supplementary_files_format_and_content: Identified mRNAs in each library with count reads and normalized data

organism: Trachinotus blochii

source_name: mRNA derived from gill tissue of the T. blochii at 72h of the C. irritansinfection

growth_protocol: The experimental fish were reared in the sea water with theronts density of 600/L, the incident of infection involved 6000 theronts/fish which was a lethal concentration verified in the preliminary challenge result. The infection was performed in 200-L tank filled with 10 L of water for each fish. The experiment lasted three days. When the fish lost their balance and could not recover in 10 s, the death time were recorded. After the end of challenge test, the remaining alive individuals with no skin lesions and normal feeding state were considered as survival fish. Throughout the course of the entire experiment, the physicochemical conditions of the water were the same as those of the relaying period.

extract_protocol:
The total RNA was harvested using Trizol-LS reagent.
Total RNA was extracted from liver and brain using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s directions. RNA samples were digested using DNase I to remove potential genomic DNA and stored at -80℃. RNA was quantified and quality was assessed by NanoDrop Spectrophotometer 2000c (NanoDrop Technologies, Wilmington, DE, USA) and 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and all samples were standardised to 500 ng/μl. Three samples from per group at each time point were used for RNA library construction which OD ratios of 260/280 and 260/230 greater than 1.8 and RNA Integrity Number (RIN) greater than 8. RNA-seq library preparation and sequencing were carried out by Annoroad Gene Technology Co., Ltd (Beijing, China), forty five sequencing libraries were constructed using a TruSeq™ RNA Sample Preparation Kit (Illumina) according to the manufacturer’s directions. The next step was KAPA quantifcation and dilution, after which the library was sequenced on an Illumina HiSeq.2500 with 125-bp paired-end reads. After removing adaptor sequences, ambiguous N nucleotides (those an N ratio <5%) and low quality sequences (reads with <50% bases of quality value), the remaining clean reads were assembled using Trinity sofware

treatment_protocol: After C. irritans challenge for 0 h, 12 h, and 72 h, the gill of six fish (three T. blochii and three S. oramin, respectively) at each sampling time points were collected in the infection group, named TRA_0h, 12h, 72h and SIG_0h, 12h, 72h, respectively. First, the experimental fish was anesthetized with MS-222, the spine of the fish was severed and immediately dissected to collect gill tissues. All samples were collected in 2 mL cryotubes and rapidly frozen in liquid nitrogen and stored at -80 °C until total RNA was isolated.

value: gill

tag: treatment/time point

value: at 72h of the C. irritansinfection


title: HiC_D4_WT_rep1


title: BAT ZT1 ATAC 1 [CLH_ATAC_1]

last: Waldeck

description: processed data file: BAT_ATAC_peaks.txt


title: HaCaT cells, WT1

value: WT


title: TRA_12h_3

source_name: mRNA derived from gill tissue of the T. blochii at 12h of the C. irritansinfection

value: at 12h of the C. irritansinfection


title: TRA_72h_2


title: TRA_72h_1


title: Pectoral and pelvic fin motor neurons - ATAC-seq rep-2


title: TRA_12h_1


title: Pectoral and pelvic fin motor neurons - ATAC-seq rep-1


title: Tail region spinal cord - ATAC-seq rep-1


title: TRA_12h_2


title: TRA_0h_3

source_name: mRNA derived from gill tissue of the T. blochii at 0h of the C. irritansinfection

value: at 0h of the C. irritansinfection


title: TRA_0h_2


title: Endoderm_St13_rep1

city: Evanston

first: Carole

last: LaBonne

address: 2205 Tech Dr

department: Molecular Biosciences

data_processing:
Read quality evaluated with FastQC
Mapped to X. laevis v9.2 genome downloaded from xenbase using STAR2.6.0
Assembly: X. laevis v9.2
Supplementary files format and content: single csv file of read count for all genes in each sample

organism: Xenopus laevis

source_name: animal cap

growth_protocol: population of animal caps were dissected at stage 8.5 and collected at respective stages

extract_protocol:
Animal caps were flash frozen in trizol. RNA was harvested using Trizol reagent extraction from Xenopus animal caps. 1ug total RNA was used for construction of sequencing libraries
Illumina TruSeq mRNA-Seq Library Prep Kit- standard protocols

treatment_protocol: see characteristic:treatment in Samples section above

value: 160 ng/uL activin

tag: lineage

value: Endoderm


title: Endoderm_St13_rep2


title: Endoderm_St12_rep1


title: TRA_0h_1


title: Endoderm_St13_rep3


title: Endoderm_St11_rep2


title: Endoderm_St11_rep1


title: Endoderm_St11_rep3


title: Endoderm_St10.5_rep2


title: Endoderm_St10_rep3


title: Endoderm_St10_rep1


title: Endoderm_St9_rep1


title: Endoderm_St10.5_rep1


title: Endoderm_St10_rep2


title: Endoderm_St12_rep3


title: Neural_St13_rep3

value: 100 ng/uL noggin

value: Neural


title: Endoderm_St9_rep3


title: Neural_St12_rep2


title: Endoderm_St9_rep2


title: Neural_St12_rep3


title: Neural_St12_rep1


title: Neural_St13_rep1


title: Endoderm_St10.5_rep3


title: Neural_St11_rep3


title: Endoderm_St12_rep2


title: Neural_St11_rep2


title: Neural_St10.5_rep3


title: Neural_St10_rep2


title: Neural_St10.5_rep1


title: Neural_St13_rep2


title: Neural_St10.5_rep2


title: Neural_St9_rep3


title: Neural_St11_rep1


title: Neural_St10_rep3


title: Neural_St9_rep2


title: Neural_St9_rep1


title: Epidermal_St13_rep3

value: untreated

value: Epidermal


title: Epidermal_St13_rep2


title: Epidermal_St13_rep1


title: Epidermal_St12_rep3


title: Epidermal_St11_rep3


title: Epidermal_St11_rep2


title: Epidermal_St10.5_rep1


title: Epidermal_St11_rep1


title: Epidermal_St9_rep3


title: Epidermal_St10_rep3


title: Epidermal_St10_rep1


title: Epidermal_St10_rep2


title: Epidermal_St10.5_rep2


title: Epidermal_St10.5_rep3


title: Neural_St10_rep1


title: Epidermal_St9_rep2


title: M2_Day33_TCR

first: Weiguo

last: Cui

address: 303 E Chicago Ave

department: Pathology

data_processing:
Reads were aligned to mouse reference genome mm10
Assembly: mm10
Supplementary files format and content: Demultiplexing and alignment were performed with Cell Ranger (v3.0, 10x Genomics) and the mm10 reference transcriptome (10x Genomics).

source_name: Spleen

extract_protocol: 10x Genomics

value: Spleen

value: C57BL/6 mice

tag: timepoint

value: Day 33

tag: infection

value: LCMV Clone 13

tag: condition

value: ScTCR-seq


title: Epidermal_St9_rep1


title: M3_Day35_GEX

tag: tissue

tag: strain

value: Day 35

value: ScRNA-seq


title: M3_Day35_TCR


title: M2_Day33_GEX


title: M1_Day33_GEX


title: pSN p1 [S5]

city: Berlin

first: Niccolò

last: Zampieri

address: Robert-Rössle-Str. 10

department: Development and Function of Neural Circuits

institute: Max-Delbrück-Center for Molecular Medicine

description:
Single cell sequencing
mRNA

data_processing:
Data was processed using scrub using the default values. The barcode and demultiplex steps using scrub was defined as bcStart = 7, bcStop   = 12,  umiStart  = 1,  umiStop   = 6.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.tsv: Tab-delimited text files include raw counts.

source_name: dorsal root ganglia

extract_protocol:
Single proprioceptive sensory neurons were extracted from dorsal rot ganglia by enzymatic digestion. Afterwards single tdTomato positive neurons were isolated using fluorescence-activated cell sorting.
CEL-Seq2 protocol (Hashimshony et al., 2016).

value: Trpv1Cre; PvFlp; Ai65 and PvCre; Ai14

value: proprioceptive sensory neurons

tag: age


title: pSN p1 [S6]

description:
Single cell sequencing
mRNA


title: pSN p1 [S4]

description:
Single cell sequencing
mRNA


title: pSN p1 [S3]

description:
Single cell sequencing
mRNA


title: Epidermal_St12_rep2

tag: treatment


title: Epidermal_St12_rep1


title: pSN p1 [S2]

description:
Single cell sequencing
mRNA


title: pSN p1 [S1]

description:
Single cell sequencing
mRNA


title: pSN e15.5 [S10]

description:
Single cell sequencing
mRNA

value: PvtdTom


title: IL33C

city: Nanjing

first: Lei

last: Xu

address: longmian avenue

institute: Nanjing Medical University

data_processing:
BGISEQ-500 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GCF_000001635.26_GRCm38.p6 whole genome using SOAPnuke v1.5.2 with parameters -l 15 -q 0.2 -n 0.05 .
Clean reads were mapped to GCF_000001635.26_GRCm38.p6 whole genome useing  Bowtie2 v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200 ,and the gene expression levels of each sample were calculated useing RSEM v1.2.8 with parameters -p 8 --forward-prob 0.5 --paired-end.
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: Matrix table includes FPKM values and TPM values for each Sample

source_name: thymic epithelial cells

extract_protocol:
Thymic epithelial cells were isolated by MACS from thymus, and RNA was harvested using Trizol reagent.
The cDNA library construction were conducted on a BGISEQ platform at Huada Gene Technology Co., Ltd. (Shenzhen, China)

value: thymus


title: pSN e15.5 [S8]

description:
Single cell sequencing
mRNA


title: pSN e15.5 [S7]

description:
Single cell sequencing
mRNA


title: pSN e15.5 [S5]

description:
Single cell sequencing
mRNA


title: IL33B


title: AP1-GR - H3K27me3 t5 rep2

city: Harbin

first: Ralf

last: Mueller-Xing

address: NO.26 Hexing Road

institute: Northeast Forestry University

description: H3K27me3 dexamethasone treated rep2

data_processing:
H3K27me3 ChIP-Seq data was mapped to the Arabidopsis thaliana TAIR10 reference using Bowtie2 with default parameters.
Multi-mapping reads were discarded together with unmapped reads, only leaving uniquely mapped reads for downstream analysis.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated.
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: TDF

organism: Arabidopsis thaliana

source_name: inflorescence

growth_protocol: Arabidopsis AP1-GR ap1-1 cal-1 were grown under long-day (16 h light/8 h dark) condition.

extract_protocol:
31 DAG, the untreated inflorescenes were sampled as t0 and the dexamethasone treated ones as t5. After tissue grinding and nuclei isolation, lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27me3 antibodies.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After bolting (26 DAG), half of the plants were treated with dexamethasone.

value: AP1-GR ap1-1 cal-1

value: dexamethasone treated


title: IL33A


title: M1_Day33_TCR


title: pSN e15.5 [S6]

description:
Single cell sequencing
mRNA


title: AP1-GR - H3K27me3 t5 rep1

description: H3K27me3 dexamethasone treated rep1


title: pSN e15.5 [S3]

description:
Single cell sequencing
mRNA


title: PBSB

value: PBS


title: AP1-GR - H3K27me3 t0 rep1

description: H3K27me3 untreated rep1


title: PBSC


title: pSN e15.5 [S1]

description:
Single cell sequencing
mRNA


title: pSN e15.5 [S4]

description:
Single cell sequencing
mRNA


title: pSN e15.5 [S9]

description:
Single cell sequencing
mRNA


title: lung, mouse, ntm+bcg, rep 2

city: Fort collins

first: Marcela

last: Henao-Tamayo

state: CO

address: 1682 Campus delivery, 200 W Lake street

department: Microbiology, Immunology, anad Pathology

institute: Colorado State University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Space Ranger software.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

organism: Mus

source_name: Lungs

extract_protocol:
10X Visium for FFPE tissues
spatial transcriptomics

value: Lungs

value: ntm+bcg


title: pSN e15.5 [S2]

description:
Single cell sequencing
mRNA


title: N2a PICD-3

city: Edison

first: Jiali

last: Li

state: middlesex

address: 65 James ST

department: Neuroscience Intitute

institute: HMH JFK Medical Center

data_processing:
FastQC (v0.119) and Fastx-Toolkit (v0.0.13) were used to clean the sequencing data
Tophat (v2.1.1) were used to align clean sequencing reads to exon of reference genome (Mus musculus (house mouse), GRCm38.p6)
Cufflinks (v2.1.1) use the alignment files from Tophat to assemble and reconstruct the transcriptome
The transcript abundances were estimates by Cuffnorm and differential expression of transcripts performed by Cuffdiff
Genome_build: Mus musculus (house mouse), GRCm38.p6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: N2a cell line

extract_protocol: For each group, total RNAs were prepared using PureLink micro-to-midi total RNA purification system (Invitrogen). Libraries were prepared from RNA of three 3 biologically independent experiments. Sequence-libraries of each sample were equimolarly pooled and sequenced at the core facility of Kunming Institute of Zoology.

tag: genotype/variation


title: N2a PICD-2


title: N2a Vector-2


title: PBSA


title: N2a Vector-3


title: lung, mouse, ntm+bcg, rep 1


title: INF2A

source_name: naïve CD4+ T cells

extract_protocol:
Naïve CD4+T cells were isolated by MACS from spleens, and RNA was harvested using Trizol reagent.
The cDNA library construction were conducted on a BGISEQ platform at Huada Gene Technology Co., Ltd. (Shenzhen, China)

value: spleen

tag: cell type

value: CD4+ T cells

value: schistosome-infected


title: AP1-GR - H3K27me3 t0 rep2

description: H3K27me3 untreated rep2

tag: chip antibody

value: untreated


title: N2a Vector-1

tag: cell line


title: lung, mouse, bcg, rep 2

value: bcg


title: INF1A


title: lung, mouse, bcg, rep 1


title: INF3A


title: N2a PICD-1


title: NC2A

value: uninfected


title: SL09_107_KO_S

city: Morgantown

first: Christina

middle: M

last: Umbright

state: WV

address: 1095 Willowdale Road

department: HELD

institute: DHHS/PHS/CDC/NIOSH

data_processing:
Basecalls were performed using bcl2fastq/2.19.
Sequence reads were trimmed for adaptor sequence low-quality using Trimmomatic/0.35 with the following parameters ILLUMINACLIP:adapters/TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MENLEN:60
Sequences were mapped  to mm10 whole genome using Hisat2/2.1.0 with the following parameters: -q --downstream-transcriptome-assembly --dta-cufflinks --fr --no-mixed --time --non-deterministic --met-file
Aligned sequences were identified, sorted, and counted using Samtools/1.8 and HTSeq/0.11.2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimted text file including raw counts in a matrix containing all samples

growth_protocol: This study was conducted in an AAALAC approved animal facility (NIOSH, Morgantown, WV) following a protocol approved by the Institutional Animal Care and Use Committee. Heterozygous 129S-Slc26a4tm1Erg/AjgJ mice (Stock no: 018424) were purchased from the Jackson Laboratory (Bar Harbor, ME) and bred in our animal facility (NIOSH, Morgantown, WV). Progeny were genotyped to identify homozygous wildtype (Pds+/+), homozygous knockout (Pds-/-), and heterozygous (Pds+/-) mice. Approximately 3 months old male Pds+/+ and Pds‑/- were used in the study. Throughout the period of the study, the mice were housed in groups of < 5 mice/cage and maintained on a 12-hour light-dark cycle in a temperature (68-72oF) and humidity (30-70%) controlled room with free access to 7913 NIH-31 diet (Envigo, Indianapolis, IN) and filtered tap water.

extract_protocol:
Total RNA, including miRNA and other small RNA molecules, was isolated from a piece of the lung tissue using the miRNeasy Mini Kit (Qiagen, Inc.; Valencia, CA) following the procedure provided by the manufacturer, including optional DNase treatment with RNase-Free DNase (Qiagen, Inc.; Valencia, CA).
One microgram total RNA/sample was used to create sequencing libraries using the Illumina TruSeq® Stranded Total RNA Library Prep  (Illumina, Inc., San Diego, CA) following the  manufacturer's protocol.  Briefly, following depletion of  ribosomal RNA (rRNA), the RNA samples were purified, fragmented (68°C for 5 minutes), and primed for cDNA synthesis.  The denatured and cleaved RNA fragments were purified using a bead cleanup and reverse transcribed into first strand cDNA using reverse transcriptase and random primers.  While synthesizing the double stranded cDNA, dUPT was incorporated in place of dTTP followed by the addition of a single ‘A’ nucleotide to the 3 prime ends to facilitate proper adapter ligation to each sample. Indexing adapters provided in the library preparation kit were ligated to the ends of the ds cDNA.  After adapter ligation, the samples were PCR amplified (12 cycles) to enrich the DNA fragments containing the adapter molecules and to enhance the amount of DNA in the library using a Veriti™ 96 Well Thermal Cycler (Applied Biosystems; Foster City, CA).

treatment_protocol: Exposures were performed in a whole-body inhalation chamber. There were 4 different exposure groups: wildtype mice exposed to air; wildtype mice exposed to silica (15mg/m3, 6hours/day, 4days Min-U-Sil5 silica); knockout mice exposed to air; knockout mice exposed to silica (15mg/m3, 6hours/day, 4days Min-U-Sil5 silica). There were 3 different post-exposure time points at which point the mice were euthanized and samples collected: 01 day, 03 months, and 09 months following exposure to air or silica.

tag: strain background

tag: slc26a4 genotype

value: homozygous knockout

value: silica

tag: post-exposure timepoint

value: 09 months

value: lung

value: total RNA including small RNAs


title: SL09_111_KO_S

tag: molecule type


title: lung, mouse, ntm, rep 2

value: ntm


title: NC1A


title: SL09_105_KO_S


title: SL09_094_KO_A

source_name: homozygous knockout_air_9 months_lung

value: air


title: lung, mouse, saline, rep 2

value: saline


title: lung, mouse, ntm, rep 1


title: Ivabradine_3

city: Guangzhou

first: Jing

last: Tan

address: No.74 Zhongshan Rd II

department: Department of Biochemistry, Zhongshan Medical School

institute: Sun Yat-sen University

data_processing:
We used internal software SOAPnuke to filter reads, followed as: 1) Remove reads with adaptors; 2) Remove reads in which unknown bases(N) are more than 10%; 3) Remove low quality reads (we define the low quality read as the percentage of base which quality is lesser than 15 is greater than 50% in a read). After filtering, the remaining reads are called "Clean Reads" and stored in FASTQ format (see FASTQ Format in help page FASTQ Format).
We used HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step. For HISAT which is much faster, sensitive and high accuracy analysis software.
We mapped clean reads to reference using Bowtie2, v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: AllSamples.GeneExpression.FPKM.txt: Tab-delimited text file includes FPKM values for each Sample.

source_name: heart apex

extract_protocol:
Hearts were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. We used Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC: RNA concentration, RIN value, 28S/18S and the fragment length distribution.
1) mRNA enrichment: Oligo dT Selection or rRNA depletion; 2) RNA fragment and reverse transcription: Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer; 3) End repair, add A tailing and adaptor ligation: The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments; 4) PCR amplification: The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer; 5) Denature and cyclization: Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase; 6) Sequencing on BGISEQ-500 platform.

treatment_protocol: 1-day-old neonatal mice that underwent apical resection were injected subcutaneously with anti-arrhythmic drugs (amiodarone, metoprolol, propranolol, lidocaine, ivabradine) or isoproterenol for seven consecutive days.

value: post natal day 7

value: ICR

value: apical resection and ivabradine treatment

value: heart apex


title: SL09_093_KO_A


title: SL09_090_KO_A


title: Ivabradine_2


title: lung, mouse, saline, rep 1

value: Lungs


title: SL09_089_KO_A


title: SL09_079_WT_S

value: homozygous wildtype


title: SL09_110_KO_S


title: SL09_078_WT_S


title: Ivabradine_1


title: SIG_72h_2

organism: Siganus canaliculatus

source_name: mRNA derived from gill tissue of the S. oramin at 72h of the C. irritansinfection

value: gill

tag: developmental stage

tag: treatment/time point

value: at 72h of the C. irritansinfection


title: NC3A

value: spleen

value: CD4+ T cells

value: uninfected


title: SL09_109_KO_S

value: homozygous knockout

value: silica

value: 09 months


title: SL09_106_KO_S

value: lung

value: total RNA including small RNAs


title: SL09_077_WT_S


title: SL09_095_KO_A

value: air


title: Lidocaline_3

value: post natal day 7

value: apical resection and lidocaine treatment


title: SL09_076_WT_S


title: SIG_72h_1


title: Lidocaline_2

value: ICR


title: SL09_092_KO_A


title: SL09_066_WT_A

source_name: homozygous wildtype_air_9 months_lung


title: Lidocaline_1

value: heart apex


title: SL09_065_WT_A


title: SIG_12h_3

source_name: mRNA derived from gill tissue of the S. oramin at 12h of the C. irritansinfection

value: at 12h of the C. irritansinfection


title: SIG_12h_2


title: SIG_0h_2

source_name: mRNA derived from gill tissue of the S. oramin at 0h of the C. irritansinfection

value: at 0h of the C. irritansinfection


title: propranol_3

value: apical resection and propranolol treatment


title: SL03_056_KO_S

value: 03 months


title: SIG_12h_1

value: gill


title: SL03_054_KO_S


title: SL09_075_WT_S

value: homozygous wildtype


title: SL03_053_KO_S


title: SL09_063_WT_A


title: propranol_2


title: SIG_0h_1


title: propranol_1


title: SL09_068_WT_A


title: SL09_067_WT_A