title: J558 allograft, TAK-931-2, Day 6

data_processing:
Sequence read was mapped to mouse genome using STAR (v2.6.1c).
acquire only unique reads (map255)
Assembly: mm10
Supplementary files format and content: tab-delimited text file including expression level for each sample (featureCounts)

source_name: allograft tumor

growth_protocol: J558 cells were maintained in DMEM supplemented with 10% Horse Serum and penicillin/Streptomycin in humidified atmosphere with 5% CO2 at 37C. The female BALB/c mice were inoculated subcutaneously with 5 × 10e5 J558 cells each (in 0.1 mL, no Matrigel) in the right flank.

treatment_protocol: The J558-allografted BALB/c female mice were orally administered 0.5% methylcellulose as vehicle or TAK-931 at 60 mg/kg, QD for 6 days.

value: allograft tumor

value: B lymphocyte

tag: time

value: Day 6


title: EAT, Sedentary, Non-occluded; N2_Landrace

status: Public on Nov 05 2023

type: SRA

city: College Station

first: James

last: Cai

state: TX

address: 4458 TAMU

department: Veterinary Intergrative Biosciences

country: USA

institute: Texas A&M University

library_source: transcriptomic single cell

data_processing:
Bulk RNA-seq: QC Reports completed with: FastQC v0.11.9. Mapping performed using Bowtie2 version 2.3.5.1 64-bit with default settings. Counting performed using htseq-count version 2.0.2. Data was normalized using upperquartile method. DE analysis preformed in R using edgeR version 3.34.1 and limma 3.48.3.
scRNA-seq: Sample demultiplexing, STAR alignment to the Landrace_pig_v1 transcriptome, filtering, and UMI counting were achieved using Cell Ranger 3.0.1 (10X Genomics)44.
Assembly: Sscrofa11.1
Supplementary files format and content: HDF5 files include filtered counts for scRNA-seq samples
Supplementary files format and content: comma-delimited text files include raw counts for Bulk RNA-seq samples

molecule: total RNA

organism: Sus scrofa

source_name: EAT, Sedentary, Non-occluded

extract_protocol:
Total RNA was extracted using TRIzol® (Thermofisher Scientific, Waltham, MA) for Bulk RNA-seq and
cDNA libraries for Bulk RNA-seq were prepared, and sequencing was performed at the Molecular Genomics Core, Texas A&M University. Single nuclei 3` sequencing libraries were generated following the 10x Genomics dual index manual preparation v3.1 reagent kit with a target nuclei recovery of approximately 5,000 – 10,000 nuclei for each reaction.

treatment_protocol: Animals were divided into two exercise (sedentary vs exercised) and two coronary artery (non-occluded and occluded) treatment groups. Surgeries were performed to place an ameroid constrictor (2.5-3.5 mm) around the proximal left circumflex artery.

tag: tissue

value: Epicardial Adipose Tissue

tag: treatment

value: Sedentary, Non-occluded


title: ARAC-gradual-TR1-PCR2-011119

city: Melbourne

first: Dane

middle: Aaron McKay

last: Vassiliadis

address: Parkville VIC 3000

country: Australia

institute: Peter MacCallum Cancer Centre

description: DNA barcode amplicon sequencing of MLL-AF9 cells cultured in vitro

library_source: genomic

data_processing:
Raw sequence data from population-based dose-escalation were processed using BARtab v1.3 with the following parameters: --mode “single-bulk”, --upconstant “CGATTGACTA”, --downconstant “TGCTAATGCG”, --alnmismatches 1, --minqual 20, --pctqual 80, --constants “up”, --constantmismatches 0.1, --barcode_length 60. Count files were imported into R v4.2 and further analysed with bartools v0.2.5.
Assembly: SPLINTR BFP V1 reference barcode list (Addgene #179776)
Supplementary files format and content: tab delimited text file contains raw counts per barcode for each sample

molecule: genomic DNA

organism: Mus musculus

source_name: in vitro

growth_protocol: Mouse MLL-AF9 leukaemia cells were generated from the bone marrow of female C56BL6/J mice as previously described (Fennell & Vassiliadis, Nature, 2022) and cultured in RPMI-1640 medium supplemented with mouse IL-3 (10 ng ml−1), human IL-6 (10 ng ml−1), mouse SCF (50 ng ml−1) 20% fetal bovine serum, streptomycin (100 µg ml−1), penicillin (100 U ml−1) and 2 mM GlutaMAX (Thermo Fisher Scientific) in 5% CO2 at 37 °C

extract_protocol:
5x10^5 cells were lysed in 40 µl Viagen lysis buffer containing 0.5 mg ml−1 proteinase K (Invitrogen) and split into technical replicates.
Barcode libraries were constructed using a two step PCR strategy using Q5 polymerase (NEB).
dual indexed PCR amplicon

treatment_protocol: Dose escalation cultures were supplemented with either 0.1% v/v DMSO, 400nM IBET or 300nM AraC. For the high dose arms, liquid cultures were supplemented with 800nM IBET or 700nM AraC. Drugs were replenished every three days by replating in fresh medium with drug. For the dose escalation, every 7 days, 5×10^5 cells were replated into fresh medium supplemented with an increased concentration of IBET (TP1 - 400nM, TP-2 - 600nM, TP-3 – 800nM and TP-4 - 1000nM), AraC (TP1 - 300nM, TP-2 - 300nM, TP-3 – 300nM and TP-4 - 500nM) or maintained in 0.1% v/v DMSO.

value: in vitro

tag: cell line

tag: cell type

value: mouse leukaemia MLL-AF9

tag: genotype

value: C57BL6/J background

value: Cytarabine


title: PRJ190281_BARtab_MLL-AF9_scRNA

description: 10X Genomics 3' scRNA v3 of SPLINTR barcoded MLL-AF9 cells cultured in vitro

data_processing:
Count matrices were generated from demultiplexed scRNA-seq fastq files using the 10x Genomics Cell Ranger (v.3.1.0) count pipeline against the mm10/GRCm38 reference genome. Quality control was performed using Seurat v4 in R v4.2 48. Low-quality cells were removed by filtering out cells that had fewer than 500 genes or 1,000 unique molecular identifiers (UMIs). Cells with greater than 15% mitochondrial RNA content were also removed. For lineage barcode identification and annotation to cells, unmapped reads in BAM file format were extracted from the dataset using Samtools (v1.9) and used as input for BARtab v1.3 running in “single-cell” mode with parameters as follows: --mode “single-cell” --pipeline “cellranger”.
Assembly: GRCm38
Supplementary files format and content: tab delimited text files of cell ids, gene features, BARtab barcode - cell id annotations and counts matrix

extract_protocol:
One million cells were harvested and processed for scRNAseq as per the manufactureres recommendations
scRNAseq library was generated using the 10X Genomics 3' scRNA-seq V3 protocol following the manufacturers recommendations.
10X Genomics 3' scRNA-seq V3

treatment_protocol: untreated


title: J558 allograft, Vehicle-2, Day 6

city: Kashiwa

first: Akihiro

last: Ohashi

state: Chiba

address: 6-5-1 Kashiwanoha

department: Exploratory Oncology Research and Clinical Center

country: Japan

institute: National Cancer Center Japan

library_source: transcriptomic

extract_protocol:
RNA was harvested using Rneasy Mini kit (QIAGEN).
RNA-seq was performed by Filgen, Inc.

value: 0.5% methylcellulose


title: ARAC-gradual-TR1-PCR1-221119


title: mRNA_20

city: Clayton

first: Nicholas

middle: C

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

institute: Monash University

data_processing:
Read alignment using STAR v2.5.2b
featureCounts from subread v1.5.1 for gene quantification
Differential Gene Expression analysis using Degust (DOI: 10.5281/zenodo.3258932)
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Gene counts table

molecule: polyA RNA

organism: Homo sapiens

source_name: Primary Lung Fibroblasts, Apex

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS and antibiotics (growth media) in 5% CO2 at 37°C in a humidified atmosphere. Cells at passages 3-4 were used in all experiments. In experiments, growth media is substituted with DMEM and antibiotics without serum (0% FBS).

extract_protocol:
After 24 hours, cells were lysed in RNA lysis buffer (Qiagen, Aus) and stored at -80°C until further extraction for transcriptomic analyses. RNA was extracted using the Quick-RNA MiniPrep Kit (Zymo, Australia) according to manufacturer’s instructions. RNA was extracted in groups of two patient samples per group per round to reduce batch effects. RNA was eluted into 30 μL RNase-free water and 24 μL was sent for sequencing
NEBNext® Ultra Directional RNA Library Prep Kit for Illumina®

treatment_protocol: Cells were plated at 100,000 cells per mL in growth media and incubated overnight. Following quiescing in 0% FBS media for 24 hours, cells were stimulated with growth media in the presence/absence of the drug ACT001.

tag: participant id

tag: age

tag: gender

value: F

tag: smoking history

value: Never, Ex-smoker

tag: fvc%

tag: dlco%

tag: disease state

value: Idiopathic Pulmonary Fibrosis (IPF)

tag: drug treatment

tag: drug concentration


title: EAT, Exercise, Non-occluded; N1_Landrace

source_name: EAT, Exercise, Non-occluded

value: Exercise, Non-occluded


title: J558 allograft, TAK-931-1, Day 6


title: F.MouseEmbryo.1sect.RBFOX2.rep1

city: Chicago

first: Yanming

last: Chen

address: 929 E 57th Street

institute: The University of Chicago

data_processing:
The adaptor sequences were trimmed with Cutadapt (v4.2) using the parameter cutadapt --nextseq-trim=20 -a AGATCGGAAGAGCACACGTCTGAACTCCAG; the 8-nt UMI sequences were moved and add to the read name for the further deduplication. Especially for libraries in Groups D-G with 8-nt inline barcodes at the 5'-end of the 3'-end adaptors, extra 8 nts should be trimmed after adapter sequence removal. For all libraries, extra 4 nts at the reads’ 3-end were removed from the adapter-free sequence to minimize mapping mismatch caused by the imperfect paired sequence in the random primer.
The reads were first mapped to the corresponding rRNA sequences using Bowtie2 (v2.4.4) with parameters: --seedlen=15, and the mapped reads were discarded to avoid rRNA contamination.
The remaining unmapped reads were mapped to the corresponding genome using STAR (v2.7.9a) with parameters: --readFilesCommand zcat --alignEndsType EndToEnd --genomeLoad NoSharedMemory --quantMode TranscriptomeSAM --alignMatesGapMax 15000 --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outSAMprimaryFlag AllBestScore --outSAMattributes All --outSAMtype BAM SortedByCoordinate --outFilterType BySJout --outReadsUnmapped Fastx --outFilterScoreMin 10 --outFilterMatchNmin 24.
Uniquely mapped reads were deduplicated to get the usable reads using UMI-tools with the parameter, --method unique (v1.1.2).
Assembly: GRCh38.p13, GRCm39
Supplementary files format and content: bigWig files for  ARTR-seq libraries were generated by bamCoverage with the parameters-normalizeUsing BPM --binSize 1. The tab-delimited text files include read counts for sodium arsenite-treated samples counted by featureCounts.
Library strategy: ARTR-seq (an Assay of Reverse Transcription-based RBP binding sites Sequencing)

source_name: embryo (E11)

growth_protocol: HeLa or HepG2 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics. K562 cells were cultured in RPMI 1640 medium supplementec with 10% FBS, 2mM L-glutamine and antibiotics. All cells were placed in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cells were fixed with 1.5 % formaldehyde for 10 minutes, quenched with 125 mM glycine at room temperature for 5 min, and permeabilized with 0.5% Triton X-100 on ice for 10min. Samples were blocked with 1 mg/ml BSA, followed by staining with primary antibody, secondary antibody and protein A/G-reverse transcriptase. Then, the in-situ reverse transcription was preformed at 37C for 30min. RT-primer Cells were digested with proteinase K at 37C for 2h, and total nucleic acids were extracted with phenol-chloroform extraction and concentrated by ethanol precipitation.
Biotinylated cDNA were enriched by strepavidin beads. 3' cDNA adapter (5′Phos-NNNNNNNNAGATCGGAAGAGCGTCGTGT-3′SpC3) was ligated by T4 RNA ligase 1 by incubating at 25 °C for 16 h. cDNA was recovered from beads. Then, the library can be obtained by PCR amplification with NGS sequencing primer and gel purification of size between 180bp and 400bp.

treatment_protocol: For stress treatment, HeLa cells were changed into fresh pre-warmed medium supplemented with 5mM sodium arsenite and incubated at 37C, 5% CO2.

value: embryo (E11)

value: embryo

value: WT

value: Rich Medium

tag: cell number

value: 1 section of mouse embryo

tag: antibody

value: RBFOX2(Proteintech, #12498-1-AP)


title: mRNA_145

value: M

value: Normal


title: mRNA_61


title: ARAC-gradual-TR1-PCR1-081119

value: in vitro


title: ARAC-gradual-TR1-PCR1-151119

value: mouse leukaemia MLL-AF9


title: J558 allograft, Vehicle-1, Day 6

value: allograft tumor

value: B lymphocyte

tag: time

value: Day 6


title: F.MouseEmbryo.1sect.Input.rep3

tag: tissue


title: F.MouseEmbryo.1sect.Input.rep2

tag: treatment


title: J558 allograft, TAK-931, Day 6

data_processing:
cellranger-6.0.0
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix file

extract_protocol:
The J558 allografted tumor samples were sliced into small pieces (2–4 mm3) and then isolated into single cells using Tumor Dissociation kit (Miltenyi Biotec). The cells were filtlated with 70 mm and 30 mm niron mesh. After centrifugation, the supernatant was discarded, suspended in 1xRBC lysis Solution (Invitrogen), centrifuged with 10% FBS/DMEM, and suspended in 10% FBS/PBS.
Library was performed according to the manufacter's instructions (Single Cell 3’ GEM v3.1, 10x Genomics).

tag: cell line


title: F.MouseEmbryo.1sect.Input.rep1

tag: cell type


title: mRNA_160

value: F


title: ARAC-gradual-TR1-PCR1-041119

tag: genotype

value: C57BL6/J background

value: Cytarabine


title: ARAC-gradual-TR1-PCR1-011119


title: mRNA_33

tag: participant id


title: F.MouseEmbryo.1sect.RBFOX2.rep2


title: J558 allograft, Vehicle, Day 6

value: 0.5% methylcellulose


title: mRNA_201

tag: age


title: mRNA_48

tag: gender

value: Never

value: Idiopathic Pulmonary Fibrosis (IPF)


title: KGN cells, SiSNHG5, rep3

city: Shanghai

first: Zuwei

last: Yang

address: No. 419, Fangxie Road

country: China

institute: Obstetrics and Gynecology Hospital, Fudan University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic software
Trimmed sequence reads were mapped to GRch38
Read count extraction and normalization were performed
Assembly: GRCh38
Supplementary files format and content: Text file includes reads counts for each sample
Supplementary files format and content: Text file includes FPKM for each sample

source_name: KGN

growth_protocol: KGN were cultured in DMEM/F12 containing 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin and incubated at 37 ℃ with 5% CO2.

extract_protocol:
Fourty-eight hours after transfection of either siRNA targeting SNHG5 or the control, KGN cells were harvested and RNA was extracted.1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were constructed using SMARTER mRNA-seq Library Prep Kit according to the manufacturer's protocols.

treatment_protocol: KGN cells were transfected with either siRNA targeting SNHG5 or the negative control siRNA.

value: KGN

value: human granulosa-like tumor cell line

value: SNHG5 knockdown

value: Transfected with siRNA targeting SNHG5


title: mRNA_229

tag: smoking history


title: gdTcells, gamma-delta TCR RNA-derived library, VDJ5PGD_TCR

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

country: Germany

institute: University Medical Center Freiburg

description:
VDJ library: read1 file contains cell barcode and UMI; read2 file contains transcript
gamma delta TCR RNA

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, chromatin accessibility, ADT and HTO barcode counts) and TCR clonotypes was performed using the 10x genomics Cell Ranger pipeline.
Further processing was done with Seurat and Signac (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis based on gene expression as well as chromatin accessibility). TCR analysis was performed using scRepertoire.
Assembly: Alignments were performed using pre-build Cell Ranger and Cell Ranger ARC mouse mm10 references.
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz, filtered_contig_annotations.csv

source_name: Liver, Lung, Small Intestine, Lymph nodes, and Spleen

extract_protocol:
Living TCRgd+ single gd T cells from different organs were baroded using hashtag oligos and were FACS sorted in BSA-coated tubes containing 50 µl of PBS. Using pulse geometry gates (FSC‐W × FSC‐H and SSC‐W × SSC‐H), doublets/multiplets will be excluded. After the completion of sorting, the cells will be processed through the different 10x Genomics workflows.
Single-cell RNA sequencing was performed using 10x Genomics with feature barcoding technology to multiplex cell samples from different organs so that they can be loaded on one well to reduce costs and minimize technical variability. Hashtag oligos were obtained as purified and already oligo-conjugated in TotalSeq-B (3’ chemistry) and TotalSeq-C (5’ chemistry) formats from BioLegend. Cells were stained with barcoded antibodies together with the staining solution prior to FACS sorting. Sorted cells were processed through 10x Genomics single-cell 3’ or V(D)J workflow according to the manufacturer’s instructions. Libraries were pooled to desired quantities to obtain appropriate sequencing depths as recommended by 10x Genomics and sequenced on a NovaSeq 6000 flow cell.
To profile gd T cells using antibodies for the quantification of cell surface proteins on a single-cell level, following antibodies were obtained as purified, oligo-conjugated TotalSeq-B reagents from BioLegend - CCR6, NKp46, CD117, KLRG1, CCR7, CD8a, CD5, CD122 (IL-2Rβ), CD127 (IL-7Rα), CD278 (ICOS), Ly-6A/E (Sca-1), CD69, CD44, CD27, CD24, CD62L, CD25, NK-1.1, CD4, CCR2, TCR Vg2, TCRb, CD11c, CD19, GR-1 and CSF1R. Cells were stained with barcoded antibodies together with the staining solution prior to FACS sorting as described above. Antibody concentrations were again 1 µg per million cells, as recommended by the manufacturer (BioLegend) for flow cytometry applications. Sorted gd T cells were processed through 10x Genomics 3’ workflow according to the manufacturer’s instructions. Libraries were pooled in desired ratio together with the gene expression libraries to obtain appropriate sequencing depths as recommended by 10x Genomics and sequenced on a NovaSeq 6000 flow cell.
To perform simultaneous measurement of chromatin accessibility and gene expression, we could not barcode different organs with hashtag oligos and hence, after sorting gd T cells from different tissues, we pooled them to obtain enough cells to perform the nuclei extraction according to 10x Genomics protocol. Thereafter, single nuclei were processed through Chromium Single Cell Multiome ATAC + Gene Expression workflow and processed according to the manufacturer’s instructions. Gene expression and chromatin accessibility libraries were sequenced to obtain appropriate sequencing depths as recommended by 10x Genomics using Illumina NovaSeq 6000 system.
Simultaneous single-cell RNA and TCR sequencing was performed using 10x Genomics V(D)J workflow with feature barcoding technology to multiplex cell samples from different organs. Hashtag oligos were obtained as purified and already oligo-conjugated in TotalSeq-C (5’ chemistry) format from BioLegend. Cells were stained with barcoded antibodies together with the staining solution prior to FACS sorting as described above. The antibody concentrations used were 1 µg per million cells, as recommended by the manufacturer (BioLegend) for flow cytometry applications. After staining, cells were washed three times in PBS containing 2% BSA and 0.01% Tween 20, followed by centrifugation (300 x g 5 min at 4 °C) and supernatant exchange. After the final wash, the cells were resuspended in PBS, filtered through 40 µm cell strainers and processed for sorting. Single-cell TCR libraries were generated using the following primers. 1st PCR: 2 μM of forward primer (5′- GATCTACACTCTTTCCCTACACGACGC-3′) and 0.5 μM of each reverse primer (5′-TCGAATCTCCATACTGACCAAGCTTGAC-3′, 5′-GTCTTCAGCGTATCCCCTTCCTGG-3′, 5′-CTTTCAGGCACAGTAAGCCAGC-3′ and 5′-TCTTCAGTCACCGTCAGCCAACTAA-3′). 2nd PCR: 1 μM of forward primer (5′- GATCTACACTCTTTCCCTACACGACGC-3′) and 1 μM of each reverse primer (5′- CCACAATCTTCTTGGATGATCTGAGACT-3′ and 5′- GTCCCAGTCTTATGGAGATTTGTTTCAGC-3′). Libraries were pooled to desired quantities to obtain appropriate sequencing depths as recommended by 10x Genomics and sequenced on a NovaSeq 6000 flow cell.

value: gamma delta T cells

tag: library type

value: gamma delta TCR RNA

tag: antibodies/tags


title: gdTcells, HTO-derived library, VDJ5PGD_HASH

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

library_source: other

molecule: protein

value: Liver, Lung, Small Intestine, Lymph nodes, and Spleen

value: HTO

value: TotalSeq™-C0301 anti-mouse Hashtag 1 Antibody for Spleen, TotalSeq™-C0302 anti-mouse Hashtag 2 Antibody for Lymph nodes, TotalSeq™-C0303 anti-mouse Hashtag 3 Antibody for Liver, TotalSeq™-C0304 anti-mouse Hashtag 4 Antibody for Lung and TotalSeq™-C0305 anti-mouse Hashtag 5 Antibody for Small Intestine


title: KGN cells, SiSNHG5, rep2


title: gdTcells, mRNA-derived library, VDJ5PGD_GEX

description:
mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

value: mRNA


title: KGN cells, SiSNHG5, rep1


title: mRNA_117

tag: fvc%

tag: dlco%

tag: disease state

value: Normal


title: L4-Bsh-Dam, rep2

city: Eugene

first: Chris

last: Doe

address: 1440 Franklin Blvd

institute: University of Oregon

data_processing:
each fastq file was assessed for quality using FastQC (v0.11.9)
The damidseq pipeline was run to generate Log2 ratio bedgraph files
The Log2 ratio bedgraph files were used for calling Bsh peaks in L4 neurons using find_peaks (FDR<0.01; 1126 min_quant=0.9)
Supplementary files format and content: bedgraph: it contains Log2 ratio (Bsh-Dam/Dam-only)
Supplementary files format and content: peak.gff: a gff file containing the mean binding intensity of the peak and FDR score
Supplementary files format and content: peaks.genes.in.peak.csv: a tab-delimited text file where 1st column is gene name and the 2nd column is score

organism: Drosophila melanogaster

source_name: Lamina neuron 4

extract_protocol:
DNA was extracted using a QIAamp DNA Micro Kit (Qiagen), digested with DpnI (NEB) overnight, and cleaned up using Qiagen PCR purification columns. DamID adaptors were ligated using T4 DNA ligase (NEB) followed by DpnII (NEB) digestion for 2 h and PCR amplification using MyTaq HS DNA polymerase (Bioline).
DamID-adaptors removed by AlwI-digestion, end-repaired, A-tailed, followed by ligation of Sequencing-adaptors and PCR-amplification (Marshall, O et al., 2016, Nat Protoc)

value: Lamina neuron 4


title: L4-Bsh-Dam, rep1


title: L4-Bsh-Dam, rep3


title: KGN cells, SiNC, rep3

value: WT

value: Transfected with negative control siRNA


title: gdTcells, mRNA-derived library MULTIOME_Paris_GEX_Lib_1

description:
gdTcells, mRNA-derived library
antibodies/tags:  none
mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, chromatin accessibility, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT and HTO sequences were concatenated.
Further processing was done with Seurat and Signac (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis based on gene expression as well as chromatin accessibility).
Assembly: Alignments were performed using pre-build Cell Ranger and Cell Ranger ARC mouse mm10 references.
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz

source_name: Lung, Liver, Spleen, Skin, Lymph nodes, Small and Large Intestine

extract_protocol:
Living TCRgd+ single gd T cells from different organs were baroded using hashtag oligos and were FACS sorted in BSA-coated tubes containing 50 µl of PBS. Using pulse geometry gates (FSC‐W × FSC‐H and SSC‐W × SSC‐H), doublets/multiplets will be excluded. After the completion of sorting, the cells will be processed through the different 10x Genomics workflows.
Single-cell RNA sequencing was performed using 10x Genomics with feature barcoding technology to multiplex cell samples from different organs so that they can be loaded on one well to reduce costs and minimize technical variability. Hashtag oligos were obtained as purified and already oligo-conjugated in TotalSeq-B (3’ chemistry) and TotalSeq-C (5’ chemistry) formats from BioLegend. Cells were stained with barcoded antibodies together with the staining solution prior to FACS sorting. Sorted cells were processed through 10x Genomics single-cell 3’ or V(D)J workflow according to the manufacturer’s instructions. Libraries were pooled to desired quantities to obtain appropriate sequencing depths as recommended by 10x Genomics and sequenced on a NovaSeq 6000 flow cell.
To profile gd T cells using antibodies for the quantification of cell surface proteins on a single-cell level, following antibodies were obtained as purified, oligo-conjugated TotalSeq-B reagents from BioLegend - CCR6, NKp46, CD117, KLRG1, CCR7, CD8a, CD5, CD122 (IL-2Rβ), CD127 (IL-7Rα), CD278 (ICOS), Ly-6A/E (Sca-1), CD69, CD44, CD27, CD24, CD62L, CD25, NK-1.1, CD4, CCR2, TCR Vg2, TCRb, CD11c, CD19, GR-1 and CSF1R. Cells were stained with barcoded antibodies together with the staining solution prior to FACS sorting as described above. Antibody concentrations were again 1 µg per million cells, as recommended by the manufacturer (BioLegend) for flow cytometry applications. Sorted gd T cells were processed through 10x Genomics 3’ workflow according to the manufacturer’s instructions. Libraries were pooled in desired ratio together with the gene expression libraries to obtain appropriate sequencing depths as recommended by 10x Genomics and sequenced on a NovaSeq 6000 flow cell.
To perform simultaneous measurement of chromatin accessibility and gene expression, we could not barcode different organs with hashtag oligos and hence, after sorting gd T cells from different tissues, we pooled them to obtain enough cells to perform the nuclei extraction according to 10x Genomics protocol. Thereafter, single nuclei were processed through Chromium Single Cell Multiome ATAC + Gene Expression workflow and processed according to the manufacturer’s instructions. Gene expression and chromatin accessibility libraries were sequenced to obtain appropriate sequencing depths as recommended by 10x Genomics using Illumina NovaSeq 6000 system.


title: KGN cells, SiNC, rep2


title: mRNA_89

tag: drug treatment

tag: drug concentration


title: HPV-CTL clone

city: Stanford

first: Kyomi

middle: J

last: Igarashi

state: CA

address: 265 Campus Drive

department: Genetics

institute: Stanford University

description: 10x Genomics

data_processing:
Fastq files were processed with cellranger (version 7.0.0) using the 10X human reference (2020-A; GRCh38 Ensembl 98) with default parameters.
Supplementary files format and content: GRCh38
Supplementary files format and content: CellRanger outputs: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: T cell

extract_protocol:
Approximately 2.0 x 106 cells, viability >85%, were suspended in 50 ml of chilled phosphate-buffered saline + 0.04% bovine serum albumin
Extracted cells were processed to yield scRNA-seq libraries using 10X Chromium Next Gem Single Cell 3’ Reagent Kits v 3.1

value: T cell


title: gdTcells, Open chromatin-derived library MULTIOME_Paris_ATAC_Lib2

description:
gdTcells, Open chromatin-derived library
antibodies/tags:  none
ATAC library: read1 file contains cell barcode and open chromatin; read2 file contains open chromatin
Open chromatin

value: Lung, Liver, Spleen, Skin, Lymph nodes, Small and Large Intestine

value: Open chromatin


title: mRNA_215

value: M

value: Idiopathic Pulmonary Fibrosis (IPF)


title: KGN cells, SiNC, rep1

value: KGN

value: human granulosa-like tumor cell line


title: mRNA_103

value: Never


title: Mouse_04_spleen_stereoseq

description: BGI Stereoseq of C57BL6 spleen containing SPLINTR barcoded MLL-AF9 cells

data_processing:
Section image data was quality controlled with ImageStudio v2.0.1 (BGI). Count matrices were generated from Stereo-seq fastq files using SAW v6.1.0. Reads were aligned to the mm10/GRCm38 reference genome. The Stereo-seq data was manually segmented using the lasso function of StereoMap v2.1.0 (BGI). Stereopy v0.11.0 (BGI) was used to aggregate the count matrix to bin50. Bins with less than 600 UMIs were removed, counts were log transformed and highly variable genes were identified using default parameters in Scanpy v1.9.3. Unaligned reads resulting from the SAW pipeline were processed with BARtab v1.3 using following parameters: upconstant: "TGACCATGTACGATTGACTA", downconstant: "TGCTAATGCGTACTGACTAG", alnmismatches: 2, constantmismatches: 0.2, barcode_length: 60, mode: "single-cell", input_type: "fastq", pipeline: "saw". Barcode counts were aggregated to bin size = 50 and merged with the spatial dataset count matrix based on coordinate ID.
Assembly: GRCm38
Supplementary files format and content: tab delimited text files of coordinate ID - Gene counts at bin 1 resolution, processed image file in bin 1 resolution

source_name: C57BL6/J spleen

growth_protocol: One million SPLINTR barcoded MLL-AF9 cells were transplanted into syngeneic host C57BL6 recipients via tail vein injection. Once fulminant leukaemia had developed, spleen samples containing SPLINTR barcoded MLL-AF9 leukaemia cells were harvested and flash frozen in liquid nitrogen prior to sectioning.

extract_protocol:
mouse spleen was flash frozen in liquid nitrogen prior to cryosectioning
BGI stereoseq assay was performed using v1.0 of the BGI Stereo-seq platform
BGI Stereo-seq V1.0 assay

value: C57BL6/J spleen

value: mouse leukaemia MLL-AF9

value: C57BL6/J background


title: gdTcells, Open chromatin-derived library MULTIOME_Paris_ATAC_Lib1

value: gamma delta T cells


title: gelADSC 2

city: Suita

first: Hiroki

last: Imamura

state: Osaka

address: 2-2 Yamada-oka

institute: Osaka University

data_processing:
Sequencing was conducted on a DNBSEQ-G400 sequencer from MGI, utilizing the 100-base single-read mode. After removing adapter sequences with Trimmomatic version 0.38, the reads were aligned to the human reference genome sequences (hg19) using TopHat2 version 2.1.1.
Assembly: hg19
Supplementary files format and content: To determine expression levels, the fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated by using Cufflinks version 2.2.1.

source_name: Liver

extract_protocol:
Total RNA was extracted from liver tissues and cultured cells, using the RNeasy Mini Kit (Qiagen, Hilden, Germany).
Library preparation was carried out using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

value: Liver

value: gelADSC


title: gelADSC 1


title: gdTcells, Open chromatin-derived library MULTIOME_MPI_ATAC_Lib1


title: mRNA_173

value: Normal


title: mRNA_187


title: mRNA_75

value: F


title: Control 2

value: control


title: gdTcells, HTO-derived library parabiosis_resident_p2_2_2_HTO

description:
gdTcells, HTO-derived library
antibodies/tags: TotalSeq™-B0301 anti-mouse Hashtag 1 Antibody and TotalSeq™-B0310 anti-mouse Hashtag 10 Antibody for Spleen, TotalSeq™-B0302 anti-mouse Hashtag 2 Antibody for Lymph Nodes, TotalSeq™-B0303 anti-mouse Hashtag 3 Antibody for Liver, TotalSeq™-B0304 anti-mouse Hashtag 4 Antibody for Lung, TotalSeq™-B0305 anti-mouse Hashtag 5 Antibody for Skin and TotalSeq™-B0307 anti-mouse Hashtag 7 Antibody for Large Intestine.
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

source_name: Lung, Liver, Spleen, Skin, Lymph nodes and Large Intestine

value: HTO


title: HLA-edited rejT

description: 10x Genomics

value: T cell


title: gdTcells, mRNA-derived library MULTIOME_Paris_GEX_Lib_2

value: Lung, Liver, Spleen, Skin, Lymph nodes, Small and Large Intestine

value: mRNA


title: mRNA_131

value: M

value: Idiopathic Pulmonary Fibrosis (IPF)


title: Control 1


title: mRNA_19

value: Never, Ex-smoker


title: mRNA_159


title: gdTcells, HTO-derived library parabiosis_resident_p1_1_1_HTO

value: Lung, Liver, Spleen, Skin, Lymph nodes and Large Intestine


title: gdTcells, mRNA-derived library parabiosis_resident_p2_2_2_GEX


title: gdTcells, mRNA-derived library MULTIOME_MPI_GEX_Library


title: mRNA_47

value: Never


title: gdTcells, mRNA-derived library parabiosis_resident_p1_1_1_GEX


title: mRNA_143

value: Control


title: E9_3

type: RNA

city: Pamplona

first: Aintzane

last: Zabaleta

state: Navarra

address: Avda. Pío XII 55

country: Spain

institute: FOUNDATION FOR APPLIED MEDICAL RESEARCH

description: Gene expression data from CD36- SLAN+ monocytes

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix HuGene-2_0-st chip according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing: Data was normalized using Bioconductor software and RMA algorithm.

label: Biotin

source_name: Healthy Donor 3

label_protocol: The sense cDNA was prepared from 300 ng of total RNA using the Ambion® WT Expression Kit. The sense strand cDNA was then fragmented and biotinylated with the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671).

growth_protocol: Cells were directly purified from fresh peripheral blood from healthy donors

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: PBMCs were isolated by Ficoll-Paque gradient as described elsewhere. Purified PBMCs were stained with the 7-color mAb combination - HLADR-PacB, CD45-OC515, CD36-FITC, SLAN-PE, CD16-PECy7, CD300e-APC, CD14APCH7 - with FSCintSSCintCD14lo/-CD36+/-CD45++CD300e+HLADR+ intermediate and non-classical monocytes being FACSorted into SLAN- and SLAN+ cells.

tag: individual

value: donor 3

value: healthy

value: Peripheral blood from healthy donor

value: CD36- SLAN+ monocytes


title: E8_3

description: Gene expression data from CD36- SLAN- monocytes

tag: tissue

value: CD36- SLAN- monocytes


title: E7_2

description: Gene expression data from CD36+ SLAN- monocytes

source_name: Healthy Donor 2

value: donor 2

value: CD36+ SLAN- monocytes


title: mRNA_59

value: F

value: Normal


title: mPFC, Control + Vehicle treatment, rep4

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

country: Switzerland

institute: F. Hoffmann - La Roche AG

data_processing:
Basecalls and sample de-multiplexing performed by bcl2fastq conversion with default parameters
Sequenced reads were quality check with fastqc default parameters and then mapped with STAR using default algorithm parameters against rn6
The resulting BAM files were processed with SAMtools to yield count data for RefSeq transcript annotations
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. In short, the number of reads mapping to transcripts were counted and normalized by the size of the longest transcript of a gene and by the size of the library.
RefSeq annotations from ref_Rnor_6.0_top_level.gff3.gz
Assembly: rn6
Supplementary files format and content: counts.gct contains raw read counts per RefSeq gene in gct format
Supplementary files format and content: rpkms.gct contains normalized read counts per RefSeq gene in gct format

organism: Rattus norvegicus

source_name: Brain

growth_protocol: N/A (rat brain tissue)

extract_protocol:
RNA was extracted using Qiagen RNeasy mini kit (Qiagen, Hilden, GER). RNA quality was checked using Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, US), RNA concentration was measured with Nanodrop (Thermo Fisher Scientific, Waltham, US).
500 ng of RNA was used as input for library preparation using the Illumina TruSeq Stranded mRNA library prep kit (Illumina, San Diego, US) according to the manufacturer's instructions. Libraries were quality checked on a Fragment Analyzer (Agilent Technologies) and concentration was measured with Qubit dsDNA HS Assay kit (Thermo Fisher Scientific). Libraries were pooled and sequenced on a HiSeq4000 (Illumina).

treatment_protocol: The mPFC was dissected out from the sections after electrophysiology, and the tissue was flash frozen in liquid nitrogen and stored at -80 °C until further use.

value: Brain

tag: treatment

value: Control + Vehicle treatment


title: gdTcells, HTO-derived library parabiosis_circulating_p2_1_1_HTO

value: gamma delta T cells

value: HTO


title: mPFC, Control + Vehicle treatment, rep3


title: mPFC, Control + Vehicle treatment, rep2


title: mPFC, Control + Vehicle treatment, rep1


title: E9_2


title: gdTcells, mRNA-derived library parabiosis_circulating_p2_1_1_GEX

value: mRNA


title: mRNA_31


title: mPFC, chronic PFC activation model + RO6958375, rep4


title: gdTcells, HTO-derived library parabiosis_circulating_p1_2_2_HTO

value: Lung, Liver, Spleen, Skin, Lymph nodes and Large Intestine


title: mRNA_227


title: gdTcells, mRNA-derived library parabiosis_circulating_p1_2_2_GEX


title: mRNA_199


title: mPFC, chronic PFC activation model + RO6958375, rep3


title: E7_3


title: gdTcells, HTO and ADT-derived library OCT_GD_HTO_ADT

description:
gdTcells, HTO and ADT-derived library
antibodies/tags: TotalSeq™-B0303 anti-mouse Hashtag 3 Antibody for Liver, TotalSeq™-B0304 anti-mouse Hashtag 4 Antibody for Lung, TotalSeq™-B0305 anti-mouse Hashtag 5 Antibody for Small Intestine and TotalSeq™-B0306 anti-mouse Hashtag 6 Antibody for Large Intestine. All cells were stained with TotalSeq™-B0225 anti-mouse CD196 (CCR6)  TotalSeq™-B0184 anti-mouse CD335 (NKp46)  TotalSeq™-B0012 anti-mouse CD117 (c-Kit)  TotalSeq™-B0250 anti-mouse/human KLRG1 (MAFA)  TotalSeq™-B0377 anti-mouse CD197 (CCR7)  TotalSeq™-B0002 anti-mouse CD8a  TotalSeq™-B0111 anti-mouse CD5  TotalSeq™-B0227 anti-mouse CD122 (IL-2Rβ)  TotalSeq™-B0093 anti-mouse CD19  TotalSeq™-B0198 anti-mouse CD127 (IL-7Rα)  TotalSeq™-B0105 anti-mouse CD115 (CSF-1R)  TotalSeq™-B0171 anti-human/mouse/rat CD278 (ICOS)  TotalSeq™-B0130 anti-mouse Ly-6A/E (Sca-1)  TotalSeq™-B0197 anti-mouse CD69  TotalSeq™-B0120 anti-mouse TCR β chain  TotalSeq™-B0073 anti-mouse/human CD44  TotalSeq™-B0191 anti-mouse/rat/human CD27  TotalSeq™-B0212 anti-mouse CD24  TotalSeq™-B0112 anti-mouse CD62L  TotalSeq™-B0106 anti-mouse CD11c  TotalSeq™-B0097 anti-mouse CD25  TotalSeq™-B0118 anti-mouse NK-1.1  TotalSeq™-B0116 anti-mouse Ly-6G/Ly-6C (Gr-1)  TotalSeq™-B0001 anti-mouse CD4  TotalSeq™-B0426 anti-mouse CD192 (CCR2)  TotalSeq™-B0211 anti-mouse TCR Vγ2
Cell Hashing and Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived and Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO) and Antibody-derived oligonucleotide (ADT)

source_name: Lung, Liver, Small and Large Intestine

value: Lung, Liver, Small and Large Intestine

value: HTO and ADT


title: mPFC, chronic PFC activation model + RO6958375, rep2


title: mRNA_171

value: Control


title: E9_1

source_name: Healthy Donor 1

value: donor 1

value: healthy


title: gdTcells, mRNA-derived library OCT_GD_GEX


title: E8_1

value: Peripheral blood from healthy donor


title: mPFC, chronic PFC activation model + RO6958375, rep1


title: mRNA_87


title: gdTcells, mRNA-derived library DEC_GD_GEX

source_name: Lung, Liver, Spleen, Small and Large Intestine


title: mPFC, chronic PFC activation model + Vehicle treatment, rep4


title: E8_2

value: CD36- SLAN- monocytes


title: gdTcells, HTO-derived library DEC_GD_HTO

description:
gdTcells, HTO-derived library
antibodies/tags: TotalSeq™-C0304 anti-mouse Hashtag 4 Antibody for Lung, TotalSeq™-C0305 anti-mouse Hashtag 5 Antibody for Liver, TotalSeq™-C0306 anti-mouse Hashtag 6 Antibody for Small Intestine, TotalSeq™-C0307 anti-mouse Hashtag 7 Antibody for Large Intestine and TotalSeq™-C0308 anti-mouse Hashtag 8 Antibody for spleen
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

value: Lung, Liver, Spleen, Small and Large Intestine


title: mPFC, chronic PFC activation model + Vehicle treatment, rep3


title: mPFC, chronic PFC activation model + Vehicle treatment, rep2


title: E7_1

value: CD36+ SLAN- monocytes


title: MDMpSTR_3

description: Gene expression data from MDM cells from donor 3 co-cultured in the presence of MM-BMSC

source_name: MDM from donor 3 co-cultured in the presence of MM-BMSC

growth_protocol: MACS sorted CD14+ monocytes were differentiated into M2-like macrophages in RPMI supplemented with 10% FBS and M-CSF (10 ng/ml) for 7 days at 37ºC 5% CO2. Differentiated MDM were co-cultured for 24 hours in the presence of MM cells (1:5 ratio), in the presnece of confluet monolayer of MM-BMSC or both.

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: After 24 hours cells were harvested by pipetting and stained with the 7-color mAb combination - HLADR-PacB, CD45-OC515, CD36-FITC, SLAN-PE, CD16-PECy7, CD300e-APC, CD14-APCH7 for FACSorting.

value: donor 3

value: MDM from healthy donor

tag: protocol

value: co-cultured in the presence of MM-BMSC


title: mRNA_129

source_name: Primary Lung Fibroblasts, Apex

value: M

value: Idiopathic Pulmonary Fibrosis (IPF)


title: mRNA_101

value: Never


title: MDMpMM1SpSTR_3

description: Gene expression data from MDM cells from donor 3 co-cultured in the presence of MM and MM-BMSC

source_name: MDM from donor 3 co-cultured in the presence of MM and MM-BMSC

tag: cell type


title: mPFC, chronic PFC activation model + Vehicle treatment, rep1

value: Brain


title: RNA_seq-R1_C5_r1

first: Gufa

last: Lin

address: 1239 Siping road Tongji university

department: Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University

institute: Tongji University

data_processing:
The raw paired end reads were trimmed and quality controlled by Trimmomatic with parameters (SLIDINGWINDOW:4:15 MINLEN:75) (version 0.36)
clean reads were separately aligned to reference genome with orientation mode using bowtie2
MACS2  for peak calling : The candidate peak region was extended to be long enough for modeling. Dynamic Possion Distribution was used to calculated p-value of the specific region based on the unique mapped reads. The region would be defined as a peak when p-value < le-03.
For RNA-seq, clean reads were separately aligned to reference genome with orientation mode using hisat2.The quality assessment of these data were taken by qualimap_v2.2.1.Use htseq to count each gene reads.
Genome_build: mm10 for R1 cell line
Genome_build: hg38 for H9 cell line
Supplementary_files_format_and_content: bdg and bw files were used for represent RIP-seq data
Supplementary_files_format_and_content: xlsx file with raw gene counts for every gene and every sample

source_name: mouse embryo stem cell

growth_protocol: H9 hESCs were cultured using mTeSR medium (Stemcell technologies, Cambridge, USA). Cells were cultured on Matrigel (Fisher Scientific) -coated culture dishes, with daily medium change. H9 hESCs were passaged as small cluster using Versene solution (Thermo Fisher Scientific, USA). R1 mESCs were cultured on mouse embryonic fibroblast feeder cells inactivated with mitomycin-C (Sigma-Aldrich), using mouse ESC (mESC) medium (knockout DMEM, Life Technologies, Carlsbad, CA, USA) supplemented with 15% knockout serum replacer (Life Technologies, Carlsbad, CA, USA), 1×GlutaMAX (Life Technologies, Carlsbad, CA, USA), 1×Anti-Anti (Life Technologies, Carlsbad, CA, USA), 1% MEM non-essential amino acids (Life Technologies, Carlsbad, CA, USA), 0.1 mM 2-Mercaptoethanol (Sigma-Aldrich, St. Louis, MO, USA) and 1000 Units/ml ESGRO-mLIF (Millipore, Burlington, MA, USA), at 37˚C in 5% CO2. R1 mESCs were passaged as single cell using 0.05%-trypsin-EDTA (Life Technologies, Carlsbad, CA, USA).   H9 cells were induced to the naïve state using the 5i method (Theunissen et al., 2014). Briefly, H9 cells maintained on Matrigel were seeded onto feeder cells for two generations for acclimation with mTeSR medium, and were dissociated into single cells using Accutase (Thermo Fisher, USA). Dissociated H9 cells (2 × 105, for one well of a 12-well plate) were cultured with mTeSR supplemented with 10 μM Y27632 (Stemcell technologies, Cambridge, USA) for one day before switching to the 5i medium (DMEM/F12 : Neural basal = 1:1 mix, 1×N, 1× B27, 1×GlutaMAX, 1% NEAA, 0.1 mM BME, 1 μM PD0325901, 3 μM Chir99021, 0.5 μM SB590885, 1 μM  WH-4-023, 10 μM Y27632, 20 ng/mL hLIF, 20 ng/mL Activin  A, 8 ng/mL FGF2). Induced naïve state colonies with translucent edges were visible after 10 days of culture, and passaged using Accutase (Thermo Fisher, USA).

extract_protocol:
For RNA-seq, total RNA was extracted from the cells using TRIzol® Reagent (Invitrogen) and genomic DNA was removed using DNase I (TaKara). For RIP-sequencing, RNA was extracted from RNA precipitation preparations. Then RNA quality was determined using 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). High-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) is used to construct sequencing library.  For RIP-seq,RNA immunoprecipitation was performed with reversible cross-linking of the cells, as previously described (Niranjanakumari et al., 2002). In brief, 1×107 cells were washed three times with pre-chilled PBS and resuspended in 10 mL of PBS, cells were fixed with 1% formaldehyde (diluted from 37% HCHO/10% methanol stock solution, Sigma-Aldrich) at room temperature for 10 minutes with slow mixing. Crosslinking reactions was quenched by the addition of glycine (pH 7.0) to a final concentration of 0.25 M, followed by incubation at room temperature for 5 minutes. The cells were harvested by centrifugation and washed twice with ice-chilled PBS. Fixed cells were resuspended in 2 mL of RIPA buffer containing protease inhibitors (Roche) and RNAase inhibitors (Ambion), and sonication was used to solubilize RNPs. Insoluble material was removed by centrifugation at 16,000g for 10 minutes at 4 °C. The supernatant was mixed with the antibody and incubated overnight at 4˚C with rotation, followed by incubation with protein A/G beads. The beads were collected by centrifugation at 6000 rpm for 30s and washed five times with wash buffer (50 mM Tris–Cl, pH 7.5, 1% NP-40, 1% sodium deoxycholate, 0.1% sodium dodecyl sulfate (SDS), 1 mM EDTA, 1 M NaCl and 0.2 mM PMSF). The beads containing the immunoprecipitated samples are collected and resuspended in resuspended buffer (50 mM Tris–Cl, pH 7.0, 5 mM EDTA, 10 mM DTT and 1% SDS). Samples (resuspended beads) are incubated at 70°C for 45 minutes to reverse the crosslinks. The RNA was extracted from these samples using Trizol reagent (Invitrogen) and used for RIP-Seq.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: culture medium

value: MES+LIF

tag: genotype

value: MSI1 Knockout

tag: rip antibody


title: RNA_seq-R1_C5_r2


title: MDMpSTR_1

description: Gene expression data from MDM cells from donor 1 co-cultured in the presence of MM-BMSC

source_name: MDM from donor 1 co-cultured in the presence of MM-BMSC


title: MDMpMM1SpSTR_2

description: Gene expression data from MDM cells from donor 2 co-cultured in the presence of MM and MM-BMSC

source_name: MDM from donor 2 co-cultured in the presence of MM and MM-BMSC

value: donor 2


title: MDMpMM1SpSTR_1

description: Gene expression data from MDM cells from donor 1 co-cultured in the presence of MM and MM-BMSC

source_name: MDM from donor 1 co-cultured in the presence of MM and MM-BMSC


title: mRNA_213

tag: participant id

tag: age

tag: gender

tag: smoking history

value: Control


title: MDMpMM1S_3

description: Gene expression data from MDM cells from donor 3 co-cultured in the presence of MM

source_name: MDM from donor 3 co-cultured in the presence of MM

value: co-cultured in the presence of MM


title: RNA_seq-R1_WT_r1

value: wild type


title: mRNA_115

tag: fvc%

tag: dlco%

value: Normal


title: mRNA_73

value: F

tag: disease state

tag: drug treatment


title: RNA_seq-R1_WT_r2


title: MDMpMM1S_2

description: Gene expression data from MDM cells from donor 2 co-cultured in the presence of MM

source_name: MDM from donor 2 co-cultured in the presence of MM

tag: individual

value: healthy


title: mRNA_185

tag: drug concentration


title: CLFT071_Rep2

city: Riverside

first: Jason

last: Stajich

state: California

address: 900 Univeristy Avenue

department: Microbiology and Plant Pathology

institute: University of California, Riverside

data_processing:
Reads were aligned to reference genome annotation GCA_000149865.1 using kallisto
Read count normalization and Differential Expression Analysis conducted using the R package DESEQ2
Assembly: GCA_000149865.1
Supplementary files format and content: comma separated (csv) file includes basemean, log2fold change, bonferonni adjusted p-value, raw counts, and Transcripts per million (TPM) for all genes and samples

organism: Batrachochytrium dendrobatidis

source_name: cultures

growth_protocol: RNA was extracted from 7 day old cultures of CLFT044, CLFT067 and CLFT071 grown on 1% Tryptone Agar at 18*C using TRIzol following manufacturer’s instructions and incorporating a 12 hour isopropanol precipitation to increase yields.

extract_protocol:
RNA was extracted using TRIzol following manufacturer's protocols and incorporating a 12 hour isopropanol precipitation to increase yields.
mRNA library preparation (poly A enrichment) at Novogene

tag: tissue

value: cultures

tag: treatment

value: Viral -


title: MDM_2

description: Gene expression data from MDM cells from donor 2

source_name: MDM from donor 2

tag: cell type

value: MDM from healthy donor

tag: protocol

value: control


title: CLFT071_Rep1


title: mRNA_157


title: CLFT067_Rep3

value: Viral +


title: RIP_seq-R1_WT_r1

tag: cell line

tag: culture medium

value: Anti-MSI1(abcam, ab52865)


title: RIP_seq-R1_WT_r2

tag: genotype

tag: rip antibody


title: mRNA_17

tag: participant id

tag: age

value: Never, Ex-smoker

value: Idiopathic Pulmonary Fibrosis (IPF)


title: CLFT067_Rep2


title: MDMpMM1S_1

description: Gene expression data from MDM cells from donor 1 co-cultured in the presence of MM

source_name: MDM from donor 1 co-cultured in the presence of MM

value: donor 1


title: P42_new_IHCs_10x

city: Beijing

first: Zhiyong

last: Liu

address: 7 Science Park Road ZGC Life Science Park

institute: National Institute of Biological Sciences, Beijing

data_processing:
FastQC (v0.11.9) and Trimmomatic (v0.39) were used for quality control. Reads were mapped to the mouse reference genome (mm10) with high quality, using Hisat2 (v2.1.0) with default parameters.
Transcript Per Million (TPM) were calculated by StringTie  (v1.3.5) with default parameters.
Raw counts were calculated by HTSeq (v0.10.0) software.
Cell Ranger (v3.0.2) was used for analysis of 10x libraries.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for smartseq. Feature-barcode-matrix output from Cell Ranger for 10x data.

source_name: Mixture of many cochlear cell types in the compound models with pre-damage of IHCs

extract_protocol:
Cell dissociation protocal was described in our previous studies (PMID: 29706463, and PMID: 26472907)
Smart-Seq HT kit (Cat# 634437, Takara) was used to generate full-length cDNA. The cDNAs (1 ng each) were tagmented using a TruePrep DNA Library Prep Kit V2 for Illumina (Cat# TD503-02, Vazyme) and a TruePrep Index Kit V2 for Illumina (Cat# TD202, Vazyme).
Single cell full length cDNA RNA-Seq

treatment_protocol: WT-Cochlear IHCs-P30 (#1-#26) were obtained from vGlut3-P2A-iCreER/+; Ai9/+ mice that were administered tamoxifen at P10 and P11, and sacrificed at P30. P42_IBCs/IPhs_10x cells were obtained from Plp1-CreER+; Ai9/+ mice that were administered tamoxifen at P0 and P1, and sacrificed at P42. P42_new IHCs_10x cells were obtained from Plp1-TAT-DTR mice that were adminstered tamoxifen at P0 and P1, DT at P2, TMP at P3 and P4, and were finally sacrificed at P42.

tag: strain

value: Cochlea

value: postnatal day 42


title: KO-H-P

first: Haibo

last: Zhang

address: Dongchuan road 800

institute: Shanghai Jiaotong University

data_processing:
Advanced volcano plots and KEGG enrichment scatter plots were generated using the OmicStudio tools at https://www.omicstudio.cn/tool, and were analyzed with OmicStudioClassic (1.22.0), OmicStudioKits (2.12.0), and ggplot2 (3.3.3) using R version 4.1.3. According to function classification,
KEGG is usually divided into three levels, level 1, level 2, and level 3. Level 1 contains six categories: metabolism, genetic information processing, environmental information processing, cellular processes, organismal systems, and human diseases (specific species comments may have been cut); level 2 contains approximately 44 categories, including cell growth and death, transcription, and development. Level 3 is for conventional enrichment using hundreds of pathways, namely from level 1 to level 3, that function more specifically.

source_name: aveolar macrophage

extract_protocol:
six- to eight-week-old mice were randomly divided into control and model groups. All mice were anesthetized with 150 μl 5% (m/v) chloral hydrate via intraperitoneal injection and sensitized intranasally from one nostril using 250 µg/kg HDM in 20 µl PBS on day 0. On days 7–11, mice were challenged daily with 250 µg/kg HDM in 20 µl PBS intranasally. On day 13, mice were intranasally administered PR8 (1×106 PFU/kg)
Total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, California). RNA-seq detection and data processing were performed by the Shanghai Applied Protein Technology Corporation (Shanghai, China). For data quality control, genes were pre-filtered by counts >20 and reads per kilobase million (RPKM) >1 in at least one sample. Differentially expressed genes were identified using DESeq2 with a fold change >2 and an adjusted P value (FDR) <0.01, and the P value was calculated using the Z test (Pearson’s chi-square test) in the Agilent GeneSpring GX suite.

value: aveolar macrophage

value: BALF


title: CLFT071_Rep3


title: WT-H-P


title: CLFT067_Rep1


title: P42_IBCs_IPhs_10x

source_name: Mixture of many wild type cochlear cell types

value: Plp1-CreER+; Ai9/+


title: MDM_1

description: Gene expression data from MDM cells from donor 1

source_name: MDM from donor 1


title: ChIP-Input-Jurkat-gSMARCA4_A2_biol_rep_2

status: Public on Nov 04 2023

city: Kyoto

first: Kosuke

last: Yusa

state: Kyoto

address: 53 Shogoin Kawaharacho, Sakyo-ku

department: Institue for Life and Medical Sciences

institute: Kyoto University

data_processing:
Sequencing reads were processed using fastp for adaptor trimming and quality filtering.
The reads were mapped to reference human genome hg38 using Bowtie2 (with the parameter --very-sensitive).
Output files were converted to sorted bam files, proper-paired reads were extracted, and PCR duplicates were removed using SAMtools.
Bam files from replicates were merged, and coverage tracks were generated using deepTools bamCoverage.
Peaks were called using MACS2 (with the parameter -q 1e-10)
Assembly: hg38
Supplementary files format and content: bigwig

source_name: Jurkat

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Pico instrument (Diagenode).
Sequencing libraries were constructed using ThruPLEX DNA-seq kit (Takara, R400674) according to the manufacturer’s protocol

value: Jurkat

value: T-ALL

tag: chip antibody

value: gSMARCA4_A2 transduction

tag: time

value: 7 days


title: ChIP-Input-Jurkat-gARID1A_1B_biol_rep_2

value: gARID1A_1B transduction


title: ChIP-Input-Jurkat-gARID1A_1B_biol_rep_1


title: ChIP-Input-Jurkat-gAAVS1_biol_rep_2

value: gAAVS1 transduction


title: WT-C


title: ChIP-Input-Jurkat-gSMARCA4_A2_biol_rep_1


title: ChIP-Input-Jurkat-gAAVS1_biol_rep_1


title: B16 cas9 cells, DMSO

first: Mark

last: Dawson

address: 305 Grattan Street

department: Cancer Research

data_processing:
fastq files generated using bcl2fastq (v2.20.0.422)
Trim fastq files with cutadapt (v2.1)
Alignment with bowtie2 (v2.3.3)
Assembly: mm10
Supplementary files format and content: Counts of each sgRNA in tab delimited format

growth_protocol: 4.7 × 10^8 cells were infected with a whole-genome pooled lentiviral sgRNA Brie library (Addgene 73633) at a multiplicity of infection of 0.3 and subsequently selected with 1 μg/mL of puromycin for 72 hours commencing 48 hours after transduction.

extract_protocol:
Genomics DNA was extracted using NucleoSpin BloodXL (Machery-Nagel)
sgRNA sequences were amplified using a single round of PCR with adapters added for Illumina sequencing.
Samples were sequenced with single-end 75-bp reads on an Illumina NextSeq.

treatment_protocol: Cells were then treated with DMSO or STM2457 at 5 and 20 μmol/L for 48 hours before being cocultured with OT-I cells for ∼12 hours (prepared as per cocultures above) at effector:target ratios of 1:1, 1:5, and 1:20. T cells were washed off, and cells were rested for 24 hours before being exposed to drug and coculture for a second round.

value: melanoma

value: DMSO


title: B16 cas9 cells, early time point


title: ChIP-RUNX1-Jurkat-gARID1A_1B_biol_rep_2

value: RUNX1/AML1 (abcam, ab23980)


title: B16 cas9 cells, 5 μmol/L Mettl3i

value: 5 μmol/L Mettl3i


title: B16 cas9 cells, 20 μmol/L Mettl3i

value: 20 μmol/L Mettl3i


title: ChIP-RUNX1-Jurkat-gSMARCA4_A2_biol_rep_2


title: B16 cas9 cells, co-cultured with OT-I cells 1:5 (E:T), DMSO


title: WT-H


title: ChIP-RUNX1-Jurkat-gAAVS1_biol_rep_2


title: ChIP-RUNX1-Jurkat-gARID1A_1B_biol_rep_1


title: B16 cas9 cells, co-cultured with OT-I cells 1:5 (E:T), 5 μmol/L Mettl3i


title: mRNA_45

data_processing:
Read alignment using STAR v2.5.2b
featureCounts from subread v1.5.1 for gene quantification
Differential Gene Expression analysis using Degust (DOI: 10.5281/zenodo.3258932)
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Gene counts table

extract_protocol:
After 24 hours, cells were lysed in RNA lysis buffer (Qiagen, Aus) and stored at -80°C until further extraction for transcriptomic analyses. RNA was extracted using the Quick-RNA MiniPrep Kit (Zymo, Australia) according to manufacturer’s instructions. RNA was extracted in groups of two patient samples per group per round to reduce batch effects. RNA was eluted into 30 μL RNase-free water and 24 μL was sent for sequencing
NEBNext® Ultra Directional RNA Library Prep Kit for Illumina®

tag: gender

value: F

tag: smoking history

value: Never

tag: fvc%

tag: dlco%

tag: disease state

value: Idiopathic Pulmonary Fibrosis (IPF)

value: Control


title: ChIP-RUNX1-Jurkat-gSMARCA4_A2_biol_rep_1

tag: treatment


title: B16 cas9 cells, co-cultured with OT-I cells 1:20 (E:T), DMSO

tag: cell type


title: ChIP-RUNX1-Jurkat-gAAVS1_biol_rep_1


title: B16 cas9 cells, co-cultured with OT-I cells 1:5 (E:T), 20 μmol/L Mettl3i


title: B16 cas9 cells, co-cultured with OT-I cells 1:1 (E:T), DMSO


title: RNA-Jurkat-DMSO_8d_biol_rep_1

description:
Aoki_RNA_Sample 43
Jurkat_TPM_v2.txt

data_processing:
Sequencing reads were mapped to reference human genome hg38 using HISAT2 (v2.2.1)
The reads assigned to genes were counted using featureCounts (v2.0.3)
Differentially expressed genes were analysed using DESeq2 (v1.38.2) with filtering out genes with low expression (average read counts in all conditions are less than 10)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

extract_protocol:
For Jurkat cells, RNA was extracted using Maxwell® simplyRNA Tissue Kit and Maxwell® RSC Instrument (Promega). For CCRF-CEM, KOPT-K1 and TALL-1 cells, RNA was extracted using RNeasy Mini Kit (QIAGEN)
RNA-seq libraries were prepared using the NEBNext Ultra II RNA Library Prep kit for Illumina (New England BioLabs) for Jurkat cells, or NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs) for other T-ALL cells.

value: 8 days


title: RNA-Jurkat-DMSO_8d_biol_rep_3

description:
Aoki_RNA_Sample 45
Jurkat_TPM_v2.txt


title: B16 cas9 cells, co-cultured with OT-I cells 1:1 (E:T), 20 μmol/L Mettl3i

value: 20 μmol/L Mettl3i,


title: RNA-Jurkat-DMSO_8d_biol_rep_2

description:
Aoki_RNA_Sample 44
Jurkat_TPM_v2.txt

value: Jurkat


title: B16 cas9 cells, co-cultured with OT-I cells 1:20 (E:T), 20 μmol/L Mettl3i


title: RNA-Jurkat-BRM014_8d_biol_rep_3

description:
Aoki_RNA_Sample 42
Jurkat_TPM_v2.txt

value: T-ALL

value: 1 uM BRM014


title: Mix3T3-293T

city: Hangzhou

first: Haide

address: 866 Yuhangtang road

institute: Zhejiang University

data_processing:
For each sequencing library, the poly-A tail was trimmed from each raw sequencing read using Cutadapt. Subsequently, real cells were identified based on the number of reads per cell, utilizing a manually defined minimal read cutoff determined by the results of the UMI-tools whitelist function. Reads were then aligned to the GRCh38 reference genome using the STAR 2-pass mode, and only uniquely mapped reads were retained. Each read was assigned to its corresponding gene using the 'gene' tag within the GRCh38 GTF by employing featureCount. The digital gene expression matrix (DGE) was generated using the UMI-tools count function. Batches were defined as each sequencing library for each patient. For each batch, quality control (QC) was performed using Scanpy. Low-quality cells or potential doublets were removed by applying a manually defined cutoff for the number of UFIs and genes per cell, and genes expressed in less than 0.25% of the cells were also removed
the 7 samples are paired-end. They have different cell barcode numbers.
Read 1 only has cell barcode1 and UFI.
Read 2 has cell barcode 2 in Index_frozen_59, Index_frozen_60, and Index_fresh_65;
Read 2 has no cell barcode 2 in No_index_frozen_57, No_index_frozen_58, No_index_fresh_61, No_index_fresh_63.
To reduce confusion, cell barcode and UFI were extracted from read1 (30bp cell barcode1, 8bp UFI)/read2(10bp or 0 bp barcode 2) and then added onto the read name of read2 using UMItools extract. For each sample, only read2 from different experimental batch were reserved.
Read Name Example:
@E100051605L1C001R00100002278_ATATGTGTGATACTTAAGGCGGCGGAAACGGAGTGGCATG_ATCTCGGT
@E100051605L1C001R00100002278: Read Name from Sequencing Platform
ATATGTGTGATACTTAAGGCGGCGGAAACGGAGTGGCATG: 40bp Cell Barcode (First 30bp: Cell Barcode from read1 & Last 10bp: cell barcode 2 from read2)
ATCTCGGT: UFI
Assembly: GRCm38/mm10 reference genome
Supplementary files format and content: Tab-separated values files and matrix files

organism:
Homo sapiens
Mus musculus

source_name: cell line

growth_protocol: 293T and 3T3  were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Mouse tissues were ground in liquid nitrogen using a tamping tank. Cold tissue powder was rapidly transferred into a 1.5-ml centrifuge tube. Cell line was washed using PBS. Cell pellet (cell line or tissue powder) was lysed in 1 ml ice-cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% Murine RNase inhibitor (Vazyme Biotech), 0.1% IGEPAL CA-630, 1 mM DTT) and incubated on ice for 2 minutes (tissue), 5 minutes (cell line). Then, 5 ml ice-cold RSBT buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) was added to quench the lysis reaction. The medium was then filtered using a 40μm strainer. The nuclei were centrifuged at 500 g for 5 min at 4 ℃ and washed with 1 ml cold RSBT buffer.
Library preparations were performed with the HH-seq protocol

treatment_protocol: The 7 mouse brain samples were analyzed in four conditions of HH-seq: different reverse transcription primer (No_index, RT primer without cell barcode 2; Index, RT primer with cell barcode 2), different sample storage (frozen, nuclei isolated from frozen sample; fresh, nuclei isolated from fresh sample).

tag: tissue

value: cell line

value: reverse transcription using RT primer with cell barcode 2


title: LHa5-2: GMP_Control2

city: Boston

first: I-Hsiu

last: Lee

state: Massachusetts

address: 185 Cambridge Street

department: Center for Systems Biology

institute: Mass General Hospital/Harvard University

data_processing:
Base-calling was carried out with Illumina proprietary software
Sequencing reads were aligned to the mouse reference genome GRCm38.p6 with STAR 2.7.3a.
Read count per gene was obtained from STAR’s “quantMode” with the “GeneCounts” option using the mouse genome annotations from Ensembl database release 98
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text file includes gene-level raw counts for each sample

source_name: bone marrow

extract_protocol:
Bone marrow was flushed from femurs. Lineage depletion was performed with PE-coupled antibodies (anti-mouse CD4, CD8, CD19, B220, NK1.1, Ter119, CD11b, CD11c, Ly6G, Il7Ralpha), anti-PE microbeads (130-097-054, Miltenyi Biotec) and magnetic separation,  (130-042-901, LD columns, Miltenyi Biotec, Bergisch Gladbach, Germany). RNA was extracted from flow sorted cells using the NucleoSpin RNA XS Kit (740902.50, Takara Bio, Kusatsu, Japan). Then Lin(neg)Sca1(pos)ckit(pos)CD34(pos)CD16/32(pos) was sorted for downstream process
NGS library construction was performed using Clontech SMARTer Ultra Low Input RNA kit for Illumina (634936, TaKaRa Bio USA, Mountain View/CA, USA).

value: 14 weeks


title: RNA-Jurkat-BRM014_8d_biol_rep_1

description:
Aoki_RNA_Sample 40
Jurkat_TPM_v2.txt

tag: cell line


title: RNA-Jurkat-BRM014_8d_biol_rep_2

description:
Aoki_RNA_Sample 41
Jurkat_TPM_v2.txt


title: LHa5-1: GMP_Control1


title: LHa4-6: GMP_Inflammation3


title: LHa4-5: GMP_Inflammation2


title: LHa5-3: GMP_Control3


title: RNA-Jurkat-DMSO_6h_biol_rep_3

description:
Aoki_RNA_Sample 21
Jurkat_TPM_v2.txt

source_name: Jurakt

value: 6 hours


title: RNA-Jurkat-DMSO_6h_biol_rep_1

description:
Aoki_RNA_Sample 19
Jurkat_TPM_v2.txt


title: RNA-Jurkat-BRM014_6h_biol_rep_3

description:
Aoki_RNA_Sample 18
Jurkat_TPM_v2.txt


title: RNA-Jurkat-DMSO_6h_biol_rep_2

description:
Aoki_RNA_Sample 20
Jurkat_TPM_v2.txt


title: healthy volunteers 5

city: Zhengzhou

first: Yuna

last: Chai

state: Henan

address: Jianshe East Road

department: Department of Pharmacy

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
Raw data files in FASTQ format were generated from the Illumina sequencer.  After Illumina quality control, the sequencing reads were 5‘, 3’-adaptor trimmed, and discarded reads (length < 14nt or length > 40nt) with cutadapt , and were recorded in FASTA format.
Trimmed reads in FASTA format are aligned allowing for 1 mismatch only to the mature tRNA sequences,then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software.The remaining reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2.
tRF & tiRNA ID will be divided into four parts by the horizontal line, eg: 'tRF-Gly-TCC-001'. The following is a brief description of these fields:(1) tRF or tiRNA, The type of tRF & tiRNA, eg: tRF; (2) amino acid, Type of amino acid, eg: Gly; (3) anticodon, Type of anticodon, eg: TCC; (4) Serial, The serial number of tRF & tiRNA derived from the tRNA of the same anticodon, eg: 001
The differentially expressed tRFs & tiRNAs and miRNAs are screened based on the count value with R package edgeR. Principal Component Analysis(PCA), Correlation Analysis, Pie plots, Venn plots, Hierarchical clustering, Scatter plots and Volcano plots are performed in R or perl environment for statistical computing and graphics of the expressed tRF & tiRNA.
Genome_build: GtRNAdb, tRFdb
Supplementary_files_format_and_content: text file with abundance

source_name: intestinal biopsies_control

extract_protocol:
Total RNAs that were extracted from plasma were pretreated with rtStar tRF & tiRNA Pretreatment Kits to remove RNA modifications that interfere with the construction of small RNA-seq libraries.
The cDNA was then synthesized and amplified using Illumina’s proprietary RT primers and amplification primers. Subsequently, 134–160-bp PCR-amplified fragments (corresponding to small RNAs that were each 14–40 nt in length) were extracted and purified from an agarose gel.

tag: subject status

value: healthy volunteers

value: intestinal mucosa

tag: group

value: Control group


title: healthy volunteers 4


title: LHa4-4: GMP_Inflammation1


title: RNA-Jurkat-BRM014_6h_biol_rep_2

description:
Aoki_RNA_Sample 17
Jurkat_TPM_v2.txt


title: healthy volunteers 3


title: RNA-Jurkat-BRM014_6h_biol_rep_1

description:
Aoki_RNA_Sample 16
Jurkat_TPM_v2.txt


title: RNA-Jurkat-gSMARCA4_biol_rep_3

description:
Aoki_RNA_Sample 15
Jurkat_TPM_v2.txt

value: gSMARCA4 transduction

value: 10 days


title: healthy volunteers 2


title: healthy volunteers 1


title: RNA-Jurkat-gSMARCA4_biol_rep_1

description:
Aoki_RNA_Sample 13
Jurkat_TPM_v2.txt


title: RNA-Jurkat-gSMARCA4_biol_rep_2

description:
Aoki_RNA_Sample 14
Jurkat_TPM_v2.txt


title: RNA-Jurkat-gSMARCA4_A2_biol_rep_3

description:
Aoki_RNA_Sample 12
Jurkat_TPM_v2.txt

value: gSMARCA4_A2 transduction


title: IBS-D patient 5

source_name: intestinal biopsies_IBS-D

value: IBS-D patient

value: Disease group


title: RNA-Jurkat-gSMARCA4_A2_biol_rep_1

description:
Aoki_RNA_Sample 10
Jurkat_TPM_v2.txt


title: IBS-D patient 4


title: RNA-Jurkat-gSMARCA4_A2_biol_rep_2

description:
Aoki_RNA_Sample 11
Jurkat_TPM_v2.txt


title: RNA-Jurkat-gARID1A_biol_rep_2

description:
Aoki_RNA_Sample 8
Jurkat_TPM_v2.txt

value: gARID1A transduction


title: IBS-D patient 2


title: RNA-Jurkat-gARID1A_biol_rep_1

description:
Aoki_RNA_Sample 7
Jurkat_TPM_v2.txt


title: IBS-D patient 1


title: JK19

city: Chuo-ku

first: Yusuke

last: Yamamoto

state: Tokyo

address: 5-1-1, Tsukiji, Chuo-ku

institute: National cancer center research institute

data_processing:
Raw sequencing data were processed with the CellRanger pipeline (version 3.0.2, 10X Genomics) and mapped to the human genome (GRCh38) to generate matrices of gene counts by cell barcodes.
Assembly: GRCh38
Supplementary files format and content: COPD_meta_new.xlsx

source_name: Human Lung

extract_protocol:
Single cells were isolated from patient-derived lungs using Lung Dissociation Kit protocol (Miltenyi Biotec, 130-095-927).  Single cells  were processed using the Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1 and Chromium Next GEM Chip G Single Cell Kit according to the manufacturer’s instructions in the Chromium Next GEM Single Cell 3′ Reagents Kits V3.1 User Guide(10X Genomics). Briefly, 6,000 cells were loaded into each chip channel and partitioned into Gel Beads-in-emulsion (GEMs) on the Chromium Controller, followed by cell lysis and barcoded RNA reverse transcription.
Library preparation was performed after breaking of single-cell emulsions, and included cDNA amplification, fragmentation, hearing and 5′ adaptor and sample index attachment. Sequencing was performed on a HiSeq X (Illumina, Inc., San Diego, CA)

value: Human lung from COPD patients


title: JK27


title: JK26

value: Human lung from Non-COPD smokers


title: JK24


title: RNA-Jurkat-gARID1A_1B_biol_rep_3

description:
Aoki_RNA_Sample 6
Jurkat_TPM_v2.txt

value: Jurkat

value: T-ALL

value: gARID1A_1B transduction


title: RNA-Jurkat-gARID1A_1B_biol_rep_1

description:
Aoki_RNA_Sample 4
Jurkat_TPM_v2.txt


title: RNA-Jurkat-gARID1A_1B_biol_rep_2

description:
Aoki_RNA_Sample 5
Jurkat_TPM_v2.txt


title: JK21


title: RNA-Jurkat-gAAVS1_biol_rep_3

description:
Aoki_RNA_Sample 3
Jurkat_TPM_v2.txt

value: gAAVS1 transduction


title: IBS-D patient 3


title: RNA-Jurkat-gAAVS1_biol_rep_1

description:
Aoki_RNA_Sample 1
Jurkat_TPM_v2.txt


title: RNA-Jurkat-gARID1A_biol_rep_3

description:
Aoki_RNA_Sample 9
Jurkat_TPM_v2.txt


title: IPF_18

city: Suita-shi

first: Kazuyo

last: Moro

address: 2-2 Yamadaoka

department: Department of Microbiology and Immunology

institute: Osaka University Graduate School of Medicine

data_processing:
Basecalls were converted to fastq files by using blc2fastq2 package of illumina software.
Quality control was performed using fastp (v0.21.0). Gene counts were obtained by aligning reads to the hg38 genome using HISAT2(v2.2.1) followed by processing with samtools (v1.12) and the Rsubread package (v2.4.3) of R software.
Genome_build: hg38
Supplementary_files_format_and_content: Table with raw gene counts for every gene

source_name: Freshly sorted blood ILC2s from IPF patients

extract_protocol:
PBMC were isolated from whole blood. Lineage (CD3, CD4, CD14, CD16, CD19, and FceR1a)-CD45+CD161+CRTH2+CD127+ cells were identified as ILC2s and were sorted using a FACSAria IIIu flow cytometer (BD Bioscience).
Library construction were performed using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (New England Biolabs Japan), according to the manufacturer’s instructions.

value: Peripheral blood

value: IPF


title: IPF_19


title: IPF_16


title: IPF_17


title: IPF_14


title: JK29


title: IPF_12


title: RNA-Jurkat-gAAVS1_biol_rep_2

description:
Aoki_RNA_Sample 2
Jurkat_TPM_v2.txt


title: IPF_11


title: IPF_10


title: IPF_9


title: IPF_8


title: IPF_7


title: IPF_15


title: IPF_6


title: IPF_4


title: IPF_13


title: IPF_5


title: IPF_2


title: bioreactor culture, day4, replicate 3

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix CHO Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.40.2).

label: biotin

organism: Cricetulus griseus

source_name: CHO-k1 IgG-secreting cell line BC®, cultured for 4 days in a bioreactor

label_protocol: Purified total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: The CHO-k1 IgG-secreting cell line BC® was provided by Bioceros Holding BV, The Netherlands. All the cultures used chemically defined CD FortiCHO™ Medium (Gibco®, Life Technologies), supplemented with 4 mM L-glutamine and 0.5% (v/v) anti-clumping agent (both from Gibco®, Life Technologies). Pre-cultures were maintained in a 125 mL un-baffled shake flask (VWR, USA) with 20 ml working volume supplemented with selection reagents (200 µg/mL ZeocinTM and 5 µg/mL Blasticidin, both from Life technologies) for five passages prior to the experiments.

extract_protocol: Total RNA was isolated using RNeasy micro kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Bioreactor batch culture conditions were kept at 37 oC with a working volume of 600 ml in a 1 litre DasGip parallel bioreactor systems (DasGip, an Eppendorf Company, Germany). pH was kept constant at 7.2 using CO2 sparging combined with 0.5 M NaOH. Agitation was kept at 100 rpm. Sparging with a mixture of oxygen and nitrogen was used to maintain the DO at 50 % air saturation. Total of 10 ppm concentration of Antifoam (Antifoam C Emulsion, Sigma-Aldrich®) was added to the bioreactors. Addition was done when needed. For the cultivation in a batch shake flask, the working volume was 60 ml in 250 ml total volume (VWR, USA) in an incubator (Multitron CO2 incubator; Infors HT) operated with 90% humidity, 8% CO2, and 37 oC at 100 rpm rotational speed and 50 mm orbital shaking diameter. Inocula for the batch shake flasks and the bioreactors were prepared from one pool of cells (shake flask). The starting cell density in both systems was 0.3 x106 cells ml−1. At the indicated time points, samples (3 ml) were taken from both the bioreactors and the shake flasks, centrifuged at 300 g for 10 minutes, after which the cell pellet was snap-frozen in liquid nitrogen and stored at -80 oC for later analysis.

value: CHO-k1 IgG-secreting cell line BC

tag: culture system

value: bioreactor

tag: sampling time

value: day 4

tag: culture system id


title: bioreactor culture, day5, replicate 2

source_name: CHO-k1 IgG-secreting cell line BC®, cultured for 5 days in a bioreactor

value: day 5


title: flask culture, day5, replicate 1

source_name: CHO-k1 IgG-secreting cell line BC®, cultured for 5 days in a shake flask

value: shake flask


title: flask culture, day4, replicate 2

source_name: CHO-k1 IgG-secreting cell line BC®, cultured for 4 days in a shake flask


title: flask culture, day4, replicate 3


title: flask culture, day5, replicate 2


title: bioreactor culture, day4, replicate 2


title: flask culture, day5, replicate 3


title: bioreactor culture, day5, replicate 1


title: bioreactor culture, day5, replicate 3


title: bioreactor culture, day2, replicate 1

source_name: CHO-k1 IgG-secreting cell line BC®, cultured for 2 days in a bioreactor

value: day 2


title: bioreactor culture, day2, replicate 3


title: IPF_1


title: flask culture, day4, replicate 1


title: HC_12

source_name: Freshly sorted blood ILC2s from healthy subjects

value: Healthy


title: HC_11


title: flask culture, day2, replicate 3

source_name: CHO-k1 IgG-secreting cell line BC®, cultured for 2 days in a shake flask


title: flask culture, day2, replicate 2


title: HGC-27 shACAT2-3

city: Tianjin

first: Mengmeng

address: Huanhuxi Street

department: Department of Gastric Surgery, Tianjin Medical University Cancer Institute & Hospital

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In 1 this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routinesfor determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value<0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: stomach

growth_protocol: HGC-27 cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) (HyClone, South Logan, UT, USA), penicillin (100 U/ml), and streptomycin (100 U/ml) at 37℃ in a humidified 5% CO2 incubator.

extract_protocol:
Cells were washed twice with pre-chilled PBS, and then total RNAs were harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: HGC-27 cells were transfected with pSIH-H1-Puro-shACAT2 or pSIH-H1-Puro-shNC respectively for 24 hours,then added puro screening for 7days

value: stomach

value: gastric cancer cells

tag: genotype

value: ACAT2 knockdown

value: transfected with pSIH-H1-Puro-shACAT2


title: HC_10


title: IPF_3


title: HGC-27 shACAT2-1

institute: Tianjin Medical University Cancer Institute & Hospital


title: HGC-27 shNC-3

value: WT

value: transfected with pSIH-H1-Puro-shNC


title: HC_9


title: HGC-27 shNC-2


title: HC_6


title: HC_4


title: HGC-27 shACAT2-2


title: HC_5


title: HC_8


title: HC_2


title: HC_1


title: T21/GATA1s/DYRK1A-/-/- Day 7 progenitors, clone 1 biol rep 3 [S31]

city: Philadelphia

first: Eric

last: Wafula

state: PA

address: 2714-2720 South Street

department: DBHi

institute: Children's Hospital of Philadelphia

data_processing:
The RNA-seq data in .fastq files were aligned to the Homo sapiens reference genome GRCh38 and transcriptome using theSTAR(Spliced Transcripts Alignment to a Reference) program. STAR was run in the 2-pass mode to align reads to the reference genome and transcriptome, as well as novel splice junction sites detected by multiple experimental samples. Aligned reads in .bam files were loaded into R and mapped to the sense strand of known exons and genes. A gene-level read count matrix based on uniquely mapped and properly paired reads was used for analysis of differential expression after reads of technical replicates were pooled together. The pooled read counts were converted to FPKM (fragment per kilobase per million reads) to represent gene expression levels.
The R/Bioconductor DESeq2 package was used to test differential gene expression between DYRK1A wild-type and knockout samples. The top differentially expressed genes (DEGs) were selected using a log2 fold change of >2.0, a standard false discovery rate (FDR) of 0.25, and a p-value of <0.01. Gene set enrichment analysis (GSEA) was run on the identified DEGs using gene set collections obtained from BioSystems, KEGG, and MSigDb.V7.4. All genes with detectable expression in the RNA-seq samples were used as background to test enrichment of predefined gene sets.
Samples S18 was determined to be an outlier following exploratory data analysis and was not included in statistical analyses, including differential expression analysis.
Assembly: GRCh38
Supplementary files format and content: One tab-delimited text file of read count matrix by genes (rows) and samples (columns)

source_name: iPSC

growth_protocol: iPSC culture and hematopoietic differentiation by embryoid body (EB) formation were performed as previously described (PMID 25621499, 23045704).

extract_protocol:
Total RNA was extracted from sorted cells using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions.
Library preparation were perform according to the manufacturer’s instructions (Truseq Stranded Total RNA with Illumina Ribo-Zero Plus rRNA Depletion, Illumina).

treatment_protocol: Day 7 HPCs and day 4 iPSC-derived megakaryocytes were sorted for CD41+235+ and CD41+CD42b+, respectively.

value: iPSC

value: TMD8 clone 9

value: iPSC-derived CD43+41+235+ progenitors

value: DYRK1A knockout

value: Hematopoietic EB differentiation


title: T21/GATA1s/DYRK1A+/+/+ Day 4 megakaryocytes, biol rep 4 [S30]

value: iPSC-derived CD41+CD42b+ megakaryocytes

value: DYRK1A untargeted


title: T21/GATA1s/DYRK1A-/-/- Day 4 megakaryocytes, clone 2 biol rep 3 [S29]


title: T21/GATA1s/DYRK1A+/+/+ Day 7 progenitors, biol rep 3 [S27]


title: HC_7

value: Peripheral blood


title: T21/GATA1s/DYRK1A-/-/- Day 4 megakaryocytes, clone 1 biol rep 3 [S28]


title: TR18102799

first: Yi

last: Hu

address: No. 28 Fuxing Rd， Haidian district，Beijing

institute: Chinese PLA General Hospital

data_processing:
Illumina Hiseq platform used for basecalling.
Sequence alignment to the hg19 reference genome was performed using TopHat v2.1.0 with the default parameters.
Gene expression levels were normalized to the FPKM values using Cufflinks v2.2.0.
Genome_build: hg19
Supplementary_files_format_and_content: fpkm

source_name: bronchial epithelium

growth_protocol: The cells were cultured in serum-free LHC-8 medium (Gibco,   USA) at 37°C in an atmosphere containing 95% air and 5% CO2. The culture medium was   changed every 3 days. When cells reached 90% confluency, they were detached by using   trypsin (Sigma-Aldrich, USA) for 5 min, and the suspension  was  separated by   centrifugation to collect the cells. The cells were then subjected to subculturing.

extract_protocol:
RNA was extracted using a RNAiso Reagent.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer’s recommendations and index codes were added to attribute sequences to sample. Finally, the library preparations were sequenced on an Illumina Hiseq platform and 150 bp paired-end reads were generated.

treatment_protocol: The malignant transformed cell lines BERP35T1 and BERP35T4 were derived from BEP2D cells irradiated with 1.5 Gy of α-particles emitted from a 238Pu source and were described in detail in a previous paper (Sun, J.F.  et al.  International Journal of Radiation Biology, 2002.).

value: bronchial epithelium


title: T21/GATA1s/DYRK1A-/-/- Day 7 progenitors, clone 2 biol rep 2 [S32]


title: bioreactor culture, day2, replicate 2

value: CHO-k1 IgG-secreting cell line BC

value: bioreactor

value: day 2


title: TR18102797


title: T21/GATA1s/DYRK1A-/-/- Day 7 progenitors, clone 1 biol rep 2 [S25]


title: TR18102787


title: T21/GATA1s/DYRK1A-/-/- Day 4 megakaryocytes, clone 2 biol rep 2 [S24]


title: TR18102785


title: bioreactor culture, day4, replicate 1

value: day 4


title: TR18102783


title: flask culture, day2, replicate 1

value: shake flask


title: T21/GATA1s/DYRK1A-/-/- Day 4 megakaryocytes, clone 1 biol rep 2 [S23]


title: T21/GATA1s/DYRK1A-/-/- Day 7 progenitors, clone 2 biol rep 3 [S33]


title: HC_3

value: Healthy


title: T21/GATA1s/DYRK1A+/+/+ Day 4 megakaryocytes, biol rep 3 [S22]


title: T21/GATA1s/DYRK1A-/-/- Day 4 megakaryocytes, clone 2 biol rep 1 [S21]


title: T21/GATA1s/DYRK1A-/-/- Day 4 megakaryocytes, clone 1 biol rep 1 [S20]


title: T21/GATA1s/DYRK1A+/+/+ Day 4 megakaryocytes, biol rep 2 [S19]


title: TR18102795


title: BERP35T4C [Hi-C]

data_processing:
Sequence alignment to the hg19 reference genome was performed using Bowtie2 v2.1.0.
The HOMER package (v4.10) was used to process aligned data. First, the “makeTagDirectory” command was used to remove all PCR duplicates and to create a HOMER tag directory with the parameter “-tbp 1” and default parameters otherwise.
The “AnalyzeHiC” command was used to generate normalized Hi-C contact matrices using the following parameter: “-res 20000 -window 20000 -balance”. Other parameters were set to the default.
The “runHiCpca.pl” script was used for PCA and the calculation of the first eigenvector (PC1) for A/B compartment assignment. We used the following parameters: “-res 200000 -window 200000” and default parameters otherwise.
The “findTADsAndLoops.pl” script was used to detect TADs and loops with the following parameters: “-res 20000 -window 20000” and default parameters otherwise.
Genome_build: hg19
Supplementary_files_format_and_content: bed

extract_protocol:
Nuclei were extracted and the chromatin was applied with 4 cutter restriction enzyme (400 units MboI).
The next steps included making the DNA ends with biotin-14-dCTP and performing blunt-end ligation of crosslinked fragments. Finally, after shearing to approximately 200-600 bp by sonication, the libraries were constructed through end-repair, A-tailing, adapter ligation and amplifying.


title: HGC-27 shNC-1

value: stomach

value: gastric cancer cells

value: WT


title: TR18102779


title: T21/GATA1s/DYRK1A-/-/- Day 7 progenitors, clone 1 biol rep 1 [S18]

value: iPSC

value: TMD8 clone 9


title: BERP35T4B [Hi-C]


title: BERP35T4A [Hi-C]


title: T21/GATA1s/DYRK1A+/+/+ Day 7 progenitors, biol rep 1 [S15]

value: iPSC-derived CD43+41+235+ progenitors


title: BERP35T1D [Hi-C]


title: BERP35T1B [Hi-C]


title: T21/GATA1s/DYRK1A-/-/- Day 7 progenitors, clone 2 biol rep 1 [S26]

value: DYRK1A knockout

value: Hematopoietic EB differentiation


title: TR18102777


title: T21/GATA1s/DYRK1A+/+/+ Day 7 progenitors, biol rep 2 [S17]

value: DYRK1A untargeted


title: T21/GATA1s/DYRK1A+/+/+ Day 4 megakaryocytes, biol rep 1 [S16]

value: iPSC-derived CD41+CD42b+ megakaryocytes


title: BERP35T1A [Hi-C]

value: bronchial epithelium


title: ATAC-Jurkat-gSMARCA4_biol_rep_3

description:
Aoki_ATAC_Sample 25
Jurkat_gSMARCA4.proper_pairs.rmdup_merged.BPM.bw

data_processing:
Sequencing reads were processed using fastp (v0.23.2) for adaptor trimming and quality filtering.
The reads were mapped to reference human genome hg38 using Bowtie2 (v2.5.0) (with the parameter --no-mixed --no-discordant --very-sensitive -X 2000).
Output files were converted to sorted bam files, and proper-paired reads were extracted using SAMtools (v1.16.1). Reads mapped to mitochondria genome or PCR duplicates were removed using SAMtools or Picard (v2.27.5) MarkDuplicates, respectively.
Bam files from replicates were merged, and coverage tracks were generated using deepTools (v3.5.1) bamCoverage for visualizing.
Peaks were called using MACS2 (v2.2.7.1) (with the parameter -f BAMPE  --keep-dup all)11, and all peaks from knockout experimental conditions were merged using BEDtools (v2.30.0)
Assembly: hg38

extract_protocol:
Freshly isolated 50,000 cells were subjected to transposition reactions at 37°C for 30 min. Transposed DNA was purified using QIAGEN MinElute Reaction Cleanup Kit.
Transposed fragments were PCR-amplified.

value: Jurakt

value: T-ALL

value: gSMARCA4 transduction

value: 10 days


title: ATAC-Jurkat-gSMARCA4_biol_rep_2

description:
Aoki_ATAC_Sample 24
Jurkat_gSMARCA4.proper_pairs.rmdup_merged.BPM.bw


title: BEP2DC [Hi-C]


title: ATAC-Jurkat-gSMARCA4_biol_rep_1

description:
Aoki_ATAC_Sample 23
Jurkat_gSMARCA4.proper_pairs.rmdup_merged.BPM.bw


title: BEP2DB [Hi-C]


title: BEP2DA [Hi-C]


title: ATAC-Jurkat-gSMARCA4_A2_biol_rep_1

description:
Aoki_ATAC_Sample 20
Jurkat_gSMARCA4_A2.proper_pairs.rmdup_merged.BPM.bw

value: gSMARCA4_A2 transduction


title: ATAC-Jurkat-gSMARCA4_A2_biol_rep_2

description:
Aoki_ATAC_Sample 21
Jurkat_gSMARCA4_A2.proper_pairs.rmdup_merged.BPM.bw


title: ATAC-Jurkat-gSMARCA4_A2_biol_rep_3

description:
Aoki_ATAC_Sample 22
Jurkat_gSMARCA4_A2.proper_pairs.rmdup_merged.BPM.bw


title: TR18102781


title: MIX2000

last: Chen

data_processing:
For each sequencing library, the poly-A tail was trimmed from each raw sequencing read using Cutadapt. Subsequently, real cells were identified based on the number of reads per cell, utilizing a manually defined minimal read cutoff determined by the results of the UMI-tools whitelist function. Reads were then aligned to the GRCh38 reference genome using the STAR 2-pass mode, and only uniquely mapped reads were retained. Each read was assigned to its corresponding gene using the 'gene' tag within the GRCh38 GTF by employing featureCount. The digital gene expression matrix (DGE) was generated using the UMI-tools count function. Batches were defined as each sequencing library for each patient. For each batch, quality control (QC) was performed using Scanpy. Low-quality cells or potential doublets were removed by applying a manually defined cutoff for the number of UFIs and genes per cell, and genes expressed in less than 0.25% of the cells were also removed
Assembly: GRCm38/mm10 reference genome
Supplementary files format and content: Tab-separated values files and matrix files

source_name: 2 cell lines

growth_protocol: 293T and 3T3 were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cell line was washed using PBS. Cell pellet (cell line or tissue powder) was lysed in 1 ml ice-cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% Murine RNase inhibitor (Vazyme Biotech), 0.1% IGEPAL CA-630, 1 mM DTT) and incubated on ice for 2 minutes (tissue), 5 minutes (cell line). Then, 5 ml ice-cold RSBT buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) was added to quench the lysis reaction. The medium was then filtered using a 40μm strainer. The nuclei were centrifuged at 500 g for 5 min at 4 ℃ and washed with 1 ml cold RSBT buffer.
Library preparations were performed with the HH-seq protocol
snRNA-seq

tag: cell loading concentration in microfluidic


title: melanoma cells IP BRG1, 2

city: New York

first: Pietro

last: Berico

state: NY

address: 550 1st Ave

department: Pathology

institute: NYU Langone Health

data_processing:
All quality controls presented in this section have been computed using FASTQC
FastQScreen was used to map a subset of reads (10,000,000) from each sample to selected DNA sequences in order to assess the presence of contamination within the samples.
Peaks detected were annotated using HOMER (http://biowhat.ucsd.edu/homer/ngs/annotation.html) as well as TSS protein enrichment comparison.
As reference coordinates, we used the MACS-determined peaks or the annotated TSS/TTS of human genes as defined by RefSeq database.
Sequence enrichment was performed using RSAT (http://rsat.sb-roscoff.fr) with MACS-determined peaks as reference.
Assembly: hg19
Library strategy: CUT&Tag

source_name: Human melanoma cells

extract_protocol:
Assays were performed following the manufacturer's instructions (Active motif CUT&Tag-IT™ Assay Kit, #53165, #53160). Briefly, 500 000 cells per condition were used. The cells were washed 2 time before the binding on Concanavalin A beads and then incubated overnight with BAHCC1, BRG1, H3K27ac, H3K27me3 or HA primary antibodies at the recommended dilution (1:50) or without antibody (negative control). The next day the corresponding secondary antibody, a guinea pig Anti-rabbit antibody was used following a 1:100 dilution in digitonin buffer and incubated at room temperature for 1 hour. The CUT&Tag-IT™ Assembled pA-Tn5 Transposomes were incubated for 1 hour at room temperature before tagmentation. Cells were resuspended in Tagmentation buffer and incubated at 37°C for 1 hour, then the tagmentation process was stopped by addition of EDTA and SDS. Protein digestion was performed by the addition of 80µg/mL of proteinase K and incubated at 55°C for 60 minutes. DNA was retrieved on DNA purification columns provided by the manufacturer.
Library preparation and PCR amplification were done using the Kit primers and purified by 2 successive washes with SPRI beads. Libraries were sequenced on an Illumina HiSeq 4000 sequencer as paired-end 100 base reads.

tag: antibody

value: Skin

value: GapmerR GR4


title: ATAC-Jurkat-gARID1A_1B_biol_rep_3

description:
Aoki_ATAC_Sample 16
Jurkat_gARID1A_1B.proper_pairs.rmdup_merged.BPM.bw

source_name: Jurakt

value: gARID1A_1B transduction

tag: time


title: melanoma cells IP BRG1, 1

value: GapmeR NEG


title: ATAC-Jurkat-gARID1A_1B_biol_rep_2

description:
Aoki_ATAC_Sample 15
Jurkat_gARID1A_1B.proper_pairs.rmdup_merged.BPM.bw


title: ATAC-Jurkat-gARID1A_1B_biol_rep_1

description:
Aoki_ATAC_Sample 14
Jurkat_gARID1A_1B.proper_pairs.rmdup_merged.BPM.bw


title: MIX1200


title: melanoma cells IP H3K27ac, 2


title: melanoma cells IP H3K27ac, 1


title: ATAC-Jurkat-gAAVS1_biol_rep_2

description:
Aoki_ATAC_Sample 12
Jurkat_gAAVS1.proper_pairs.rmdup_merged.BPM.bw

value: gAAVS1 transduction


title: melanoma cells IP H3K27me3, 2


title: MIX600


title: ATAC-Jurkat-DMSO_8d_biol_rep_3

description:
Aoki_ATAC_Sample 10
Jurkat_DMSO_8d.proper_pairs.rmdup_merged.BPM.bw

value: 8 days


title: melanoma cells IP H3K27me3, 1


title: ATAC-Jurkat-gAAVS1_biol_rep_1

description:
Aoki_ATAC_Sample 11
Jurkat_gAAVS1.proper_pairs.rmdup_merged.BPM.bw


title: ATAC-Jurkat-DMSO_8d_biol_rep_1

description:
Aoki_ATAC_Sample 9
Jurkat_DMSO_8d.proper_pairs.rmdup_merged.BPM.bw


title: RNA-TALL1-BRM014-6h_biol_rep_3

description:
Aoki_RNA_Sample 39
CEM_KK1_TALL1_TPM.txt

value: 1 uM BRM014

value: 6 hours


title: RNA-TALL1-BRM014-6h_biol_rep_2

description:
Aoki_RNA_Sample 38
CEM_KK1_TALL1_TPM.txt