title: WTAP-Input

city: Harbin

first: Zheng

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11, Chen et al., 2018)  software. In 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 of  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 BWA (v 0.7.12) and clean reads were aligned to the  reference genome using BWA mem (v 0.7.12).
For a specific ChIP-seq binding site, individual reads mapping to the plus or minus strand and present  significant enrich. MACS2 scan all the genome with a specific window size and calculate the reads enrichment level. A particular number of windows were used as samples to  build enrichment model and to predict fragment size. The following peak calling analysis was based on  this predicted fragment size.
After mapping reads to the reference genome, we used the MACS2 (version 2.1.0) peak calling  software to identify regions of IP enrichment over background. A q-value threshold of 0.05 was used for all  data sets. After peak calling, the distribution of chromosome distribution, peak width, fold enrichment,  significant level and peak summit number per peak were all displayed.
Homer (Heinz et al., 2010) was used to detect the  denovo sequence motif and the matched known motifs.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: peaks

source_name: primary hepatocytes

growth_protocol: Primary hepatocytes were isolated from C57BL/6 mice by liver-perfusion with type II collagenase (Worthington Biochem, Lakewood, NJ) and cultured at 37°C and 5% CO2 in RPMI 1640 medium supplemented with 5% FBS

extract_protocol:
The nuclei were isolated from hepatocytes and subjected to sonication (M220 Focused-ultrasonicator; Covaris) to break genomic DNA into 500- to 1000-bp fragments using a chromatin shearing kit (520127 truChIP Chromatin Shearing Kit, Covaris). The samples were immunoprecipitated with Anti-FLAG M2 Magnetic Beads (M8823, Millipore). DNA was extracted and used for ChIP-seqencing analysis.
The purified DNA was used for ChIP-seq library preparation. The library was constructed by Novogene  Corporation (Beijing, China). Library quality was assessed on the Agilent Bioanalyzer 2100 system.
Pair-end sequencing of sample was performed on Illumina novoseq 6000 platform (Illumina, CA, USA).

treatment_protocol: primary hepatocytes were isolated and infected with Ad-Flag-WTAP adenovirus overnight.

value: primary hepatocytes

value: Ad-Flag-WTAP adenovirus


title: BMDM cells, LPS treatment, replicate 3

status: Public on Jun 02 2022

type: SRA

city: Solna

first: Heshuang

last: Qu

address: L8:03, visionsgatan 18

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic

data_processing:
The yield and quality of the amplified libraries was analyzed using Qubit by Thermo Fisher and quality was checked by using Agilent Tapestation
The indexed cDNA libraries were normalized and combined and the pools were sequenced on the Illumina Nextseq 2000 for a P2 100 cycle sequencing run, generating paired end reads.
Base calling and demultiplexing was performed using CASAVA software with default settings generating FASTQ files for further downstream mapping and analysis.
Reads were mapped to the GRCm38 reference genome using STAR
Data normalization and analysis of differential gene expression was done using the DESeq2 R-package using a negative binomial test.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw data count for each sample/library

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow

growth_protocol: Bone marrow cells from mouse hind limbs were pooled and matured into macrophages in DMEM supplemented with 10% fetal bovine serum (FBS; F7524, Sigma, St. Louis, MO, USA), 2 mM L-glutamine (Sigma), 1 mM sodium pyruvate (Sigma), 22 μM β-mercaptoethanol (Gibco, Paisley, United-Kingdom), 10,000 I.U./mL Penicillin–Streptomycin (PenStrep; Sigma), and 10 ng/mL macrophage colony-stimulating factor (M-CSF; R&D Systems, Minneapolis, MN, USA) for 10 days at 37 °C with 5% CO2.

extract_protocol:
Total RNA was isolated using RNeasy Plus Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer´s instructions.
To construct libraries suitable for Illumina sequencing, the Illumina stranded mRNA prep ligation sample preparation protocol was used with 200 ng total RNA as starting concentration. The protocol includes mRNA isolation, cDNA synthesis, ligation of adapters and amplification of indexed libraries.

treatment_protocol: BMDMs were detached from the flask using Trypsin (Sigma). Cells were washed and re-seeded in 24-well culturing plates (Sarstedt, Nümbrecht, Germany) at a density 0.5 million cells/well in DMEM containing 1% FBS and 10,000 I.U./mL PenStrep and rested overnight. To generate cells with an M1 phenotype, 100 ng/mL LPS-EK (InvivoGen, Toulouse, France) and 20 ng/mL IFN-γ (R&D Systems) were added. FrHMGB1 (in-house production) and dsHMGB1 (a kind gift from Prof. Kevin Tracey’s laboratory, Feinstein Institute, Mannhasset, NY, USA), produced and stored in buffers without DTT, was used in 5 µg/mL concentration. LPS-EK was used in 1 µg/mL concentration. PBS was included in all experiments as an unstimulated control. BMDMs were stimulated 24 hours at 37 °C with 5% CO2 before RNA isolation.

tag: tissue

value: Bone marrow

tag: cell type

value: Bone marrow derived macrophage

tag: genotype

value: WT

tag: treatment

value: 1ug/mL LPS-EK


title: BMDM cells, LPS treatment, replicate 1


title: Mock infected aSyn KO 3

city: Aurora

first: J.

middle: David

last: Beckham

state: Colorado

address: 12800 East 19th Avenue, RC1N\P18-8404A

department: Microbiology

country: USA

institute: University of Colorado Anschutz Medical Campus

data_processing:
Performed by Novogene
Overall gene expression was analyzed using principal component analysis and DESeq2 R package
ClusterProfiler software was used for enrichment
Supplementary files format and content: Xcel file including FPKM reads

source_name: Whole Brain

extract_protocol:
RNA was extracted using the E.Z.N.A. Total RNA kit II (Omega Bio-Tek).
RNA libraries were prepared for RNA-seq using the Agilent2100 system according to manufacturer protocol

treatment_protocol: Mice were infected via footpad injection with 1000 PFU of West Nile Virus NY99 strain. Brains were harvested 8 days post-infection.

value: Whole Brain

value: SNCA KO

value: Mock Infected


title: BMDM cells, dsHMGB1 treatment, replicate 2

value: 5ug/mL dsHMGB1


title: BMDM cells, dsHMGB1 treatment, replicate 3


title: patient 14_002 aortic wall  GCH_14_0023

type: RNA

city: Heidelberg

first: Philipp

last: Erhart

address: Im Neuenheimer Feld 420

department: Vascular and Endovascular Surgery

country: Germany

institute: Heidelberg University Hospital

description: biopsy from region with low wall stress

hyb_protocol: 750 ng of cRNA were hybridized for 17 hr at 58°C on Illumina Human HT-12-Microarray according to the Whole-Genome Gene Expression  Direct Hybridization Assay Guide.

scan_protocol: Gene Expression Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol  (Whole-Genome Gene Expression  Direct Hybridization Assay Guide)

data_processing: The data were normalised using quantile normalisation with R using function normalize.quantiles from Bioconductor package preprocessCore

label: Biotin, Cy3-Streptavidin

organism: Homo sapiens

source_name: abdominal aortic wall

label_protocol: The Illumina TotalPrep RNA Amplification Kit (life technologies) was used to generate single-stranded cRNA from input amounts of 200ng total RNA.

growth_protocol: no cell cuture used - RNA was extracted directly from aortic wall biopsies, immediately after tissue sampling during open surgical aortic replacement.

extract_protocol: Total RNA was extracted from fresh frozen biopsy material using RNeasy Fibrous Tissue Mini Kit (Qiagen, Hilden, Germany). A two-step quality and quantity control in terms of spectrophotometric analysis using the NanoDrop 2000c (Thermo Fisher Scientific, Waltham MA, USA was performed

treatment_protocol: no treatment applied

tag: Sex

value: male

tag: age

value: 70 years

tag: aaa diameter

tag: disease

value: abdominal aortic aneurysm


title: WtapHKO_3

last: Chen

country: China

library_source: genomic

data_processing:
Nextera adaptor sequences were firstly trimmed from the reads using skewer (0.2.2). These reads were aligned to a reference genome using BWA, with standard parameters. These reads were then filtered for high quality (MAPQ≥13), non mitochondrial chromosome, and properly paired reads (longer than 18 nt).
All peak calling was performed with macs2 using ‘macs2 callpeak --nomodel --keepdup all --call-summits’. For simulations of peaks called per input read, aligned and de-duplicated BAM files were used without any additional filtering.
Peaks were merged with ‘bedtoolsmerge’ for differential peak analysis. Differential peak calling was performed using our own R script. Only peaks with foldchange more than 0.5 were considered as differential peaks. Using the same method, genes associated with different peaks were identified and also do GO and KEGG enrichment analysis.
Genome_build: Ensemble_GRCm38.p6
Supplementary_files_format_and_content: HKO_vs_FF_peak_compare_table.xlsx

molecule: genomic DNA

source_name: Liver

extract_protocol:
Nuclei was extracted from liver samples, and the nuclei pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min.
Equimolar Adapter1 and Adatper 2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufactuer’s instructions. After cluster generation, the library preparations were  sequenced on an Illumina NovaSeq 6000 platform and 150 bp paired-end reads were generated.

treatment_protocol: Wtapflox/flox and WtapHKO mice were fed with normal chow diet for 8 weeks old

tag: strain

value: Liver

value: 8 weeks old

value: Wtap HKO (Wtapflox/flox Alb-Cre+/-)


title: BMDM cells, dsHMGB1 treatment, replicate 1


title: WtapFF_3

value: Wtapflox/flox


title: BMDM cells, frHMGB1 treatment, replicate 3

value: 5ug/mL frHMGB1


title: patient 14_003 aortic wall  GCH_14_0032

description: biopsy from region with high wall stress

value: 62 years


title: BMDM cells, LPS treatment, replicate 2

value: Bone marrow


title: WTFER1

city: Zwijnaarde

first: Bartosz

last: Wiernicki

address: Technologiepark 71

country: Belgium

institute: Ugent

description:
HWI-ST1276
WT DC with ferr cargo rep 1

data_processing:
Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced readsby CASAVA base recognition (Base Calling).
QC control: error rate (Phred score), GC content distribution, removing reads with adaptor contamination and with MAPQ<10  and with >5nt/100nt mismatches
Alignment to mm10 reference genome using HISAT2
BAM files were counted using the featureCounts function in the R package Rsubread.
Counting was performed using both mouse and human genomes for comparison although downstream analyses were only performed on mouse data.
DEG analysis was  performed using DESeq2 considering all genes with FDR ≤ 0.05 and 0.58 ≤ Log2FC ≤ -0.58.
Assembly: mm10 using HISAT2
Supplementary files format and content: The file consists of the raw counts for all analyzed genes in all processed samples.

source_name: dendritic cells (bone marrow derived using GM-CSF from immunocompetent C57/bl6 mice)

growth_protocol: Bone marrow derived dendritic cells were obtained from mouse bone marrow progenitors cultured in the presence of GM-CSF for 10 days.

extract_protocol:
Cells were collected, washed and lysed in TriZol buffer. After adding chloroform and seperating the phases, the aqueus phase was used for the Rneasy Mini Plus Kit. Minimum of 940ng was used for the analysis.
The mRNA was enriched in the sample using oligo(dT) beads whch was followed by random fragmentation of the mRNA and cDNA synthesis which was further sequenced.

value: dendritic cells

value: Co-culture with ferroptotic cells


title: WTFER2

description:
HWI-ST1276
WT DC with ferr cargo rep 2

value: dendritic cells (bone marrow derived using GM-CSF from immunocompetent C57/bl6 mice)

value: WT


title: WTFER3

description:
HWI-ST1276
WT DC with ferr cargo rep 3


title: patient 14_003 aortic wall  GCH_14_0033

description: biopsy from region with low wall stress


title: WTAP-IP

value: primary hepatocytes

value: Ad-Flag-WTAP adenovirus

tag: chip antibody

value: Anti-FLAG M2 Magnetic Beads (M8823, Millipore)


title: C. albicans culture, Control 2

city: Debrecen

first: Agnes

last: Jakab

address: Nagyerdei krt 98.

country: Hungary

institute: University of Debrecen

data_processing:
Quality control of sequencing data was performed using FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc)
STAR RNA-Seq aligner was used to map the sequenced reads to the reference genome and generate BAM files
DESeq algorithm was used to obtain normalized gene expression values (StrandNGS software)
Gene expression differences between treated and control groups were compared by moderated T-test; Benjamini-Hochberg False Discovery Rate was used for multiple testing correction.
Raw reads were aligned to the reference genome (https://www.ncbi.nlm.nih.gov/genome/?term=Candida+albicans+SC5314) aligned reads varied between 92-95 % in each sample.
Genome_build: ASM18296v3
Supplementary files format and content: Excel file includes p corrected p values, fold change values and raw data.

organism: Candida albicans

source_name: fungal cells

growth_protocol: The strain was maintained on YPDA (1% yeast extract, 2% mycological peptone, 2% glucose, 2% agar, pH 5.6). The pre-cultures were grown in YPD medium at 37ºC  for 18 hours then diluted to OD640 0.1 value in 20 mL of YPD and incubated at 37ºC with 2.3 Hz shaking frequency.

extract_protocol:
Freeze- lyophilized cells were processed using TRISOL reagent (Invitrogen, Austria) reagent and glass beads. RNA concentration and purity were determined using NanoDrop (ThermoFisher Scientific, Waltham, MA USA) and capillary electrophoresis.
RNA-Seq libraries were prepared from total RNA using Ultra II RNA Sample Prep kit (New England BioLabs) according to the manufacturer’s protocol. Briefly, poly-A RNAs were captured by oligo-dT conjugated magnetic beads then the eluted mRNAs were fragmented at 94°C. First strand cDNA was generated by random priming reverse transcription; double stranded cDNA was generated in a second strand synthesis step. After repairing ends, A-tailing and adapter ligation steps, adapter-ligated fragments were amplified in enrichment PCR and finally sequencing libraries were generated. Sequencing libraries were normalized to the same molar concentration and pooled together. Library pool was sequenced on NextSeq500 instrument (Illumina, San Diego, CA, USA) generating single read 75bp-long sequencing reads. Fastq files were generated automatically after the sequencing run by Illumina BaseSpace.

treatment_protocol: Following 4 hours incubation time YPD medium was supplemented with a final concentration of 128 mg/L surfactin and fungal cells were collected 1 hour following surfactin exposure by centrifugation (5 min, RCF=4000g, 4°C). The cells were washed three times with phosphate-buffered saline and stored at -70°C until use.

value: wild type

value: Control


title: BMDM cells, PBS treatment, replicate 2

value: Bone marrow derived macrophage

value: 1X PBS


title: Liver, HKO2, Input

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp (version  0.19.11). In 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 BWA v0.7.12 and clean  reads were aligned to the reference genome using BWA mem v 0.7.12.
After mapping reads to the reference genome, exomePeak R package (version 2.16.0)  was used for the m6A peak identification in each anti-m6A immunoprecipitation group  with the corresponding input samples serving as a control, and q-value threshold of  enrichment of 0.01 was used for all data sets. The m6A-enriched motifs of each group  were identified by HOMER (version 4.9.1).
In the peak calling result, each peak was corresponding on gene, in which the peak was  located in its exon. These genes were supposed as peak related genes, and then Gene  Ontology (GO) enrichment analysis was performed to identify the function enrichment  results. GO enrichment analysis was implemented by the GOseq R package, in which  gene length bias was corrected. GO terms with corrected P-value less than 0.05 were  considered significantly enriched by peak related genes. KEGG is a database resource  for understanding high-level functions and utilities of the biological system, such as the  cell, the organism and the ecosystem, from molecular-level information, especially  large-scale molecular datasets generated by genome sequencing and other high-through  put experimental technologies (http://www.genome.jp/kegg/). We used KOBAS  software (version 3.0) to test the statistical enrichment of peak related genes in KEGG  pathways.  Besides, the distribution of peak on different function regions, such as 5’ UTR, CDS,  3’UTR was performed.
Differential peak calling was performed using exomePeak R package (version 2.16.0)  with parameters of P-value less than 0.01 and fold change more than 1. Using the same  method, genes associated with different peaks were identified and also do GO and  KEGG enrichment analysis.
Genome_build: Ensemble_GRCm38.92
Supplementary_files_format_and_content: m6A peak files with quantitative data for WtapFF and Wtap-HKO mice
Supplementary_files_format_and_content: fold_enrichment file

extract_protocol:
Total RNAs were extracted using TriPure Isolation Reagent (Roche, Mannheim, Germany) from livers of Wtapflox/flox and Wtap-HKO mice .
Poly(A)+ RNA was purified using Dynabeads™ mRNA Purification Kit (Invitrogen) following the manufacturer’s instructions. Fragmented poly(A)+ RNA was incubated with m6A antibody (Synaptic System, 202003) for immunoprecipitation. Then, immunoprecipitated mRNAs  or Input was used for library construction with NEBNext ultra RNA library prepare kit  for Illumina (New England Biolabs). The library preparations were sequenced on an Illumina Novaseq 6000 platform with a paired-end read length of 150 bp according to the standard protocols..
MeRIP-seq

treatment_protocol: Wtapflox/flox and Wtap-HKO mice were fed with normal chow diet for 8 weeks old

value: HKO (Wtap flox/flox Alb-Cre)

value: Liver

tag: rip antibody


title: BMDM cells, PBS treatment, replicate 1


title: BMDM cells, PBS treatment, replicate 3


title: WTFER4

description:
HWI-ST1276
WT DC with ferr cargo rep 4


title: C. albicans culture, Control 1


title: patient 14_002 aortic wall  GCH_14_0024

value: male

value: 70 years

value: abdominal aortic aneurysm


title: WT4

description:
HWI-ST1276
WT DC rep 4


title: Whole Blood Neutrophils, LOY BMT, bulkRNAseq [15KO]

city: Nagoya

first: Hayato

last: Ogawa

state: Aichi

address: Tsurumai-cho 65

department: Department of Cardiology

country: Japan

institute: Nagoya University Graduate School of Medicine

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software
In the initial analysis, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Assembly: mm10
Supplementary files format and content: Comma-Separated Values matrices contain normalized Transcripts Per Million reads (TPM) values

source_name: Blood

extract_protocol:
For bulk RNA-Seq analysis of the peripheral blood neutrophils, whole blood was collected and incubated with RBC lysis buffer. After staining with fluorescent-labeled monoclonal antibodies, a total of 10,000 blood neutrophils (Ly6G+CD115-RFP+) were sorted directly into 350 ul of buffer RLT (Qiagen, Cat. #79216) containing 1% b-mercaptoethanol using Influx Cell Sorter platform with 100 mm nozzle and flow pressure set to 20 psi (BD Biosciences). For cardiac macrophages and neutrophils, hearts were flushed with 15 ml of cold PBS from apex and excised. Right ventricles were removed, and left ventricles were minced and digested in collagenase I (450 U/ml), collagenase XI (125 U/ml), hyaluronidase (450 U/ml), and DNase I (60 U/ml) (Sigma-Aldrich, Cat. #C0130, C7657, H3506, and D4513, respectively) at 900 rpm at 37°C for 30 minutes using ThermoMixer® C (Eppendorf). Hearts were subsequently homogenized through a FisherbrandTM Cell Strainers. After dead cell staining with Live/Dead Fixable Aqua Dead Cell Stain Kit (Invitrogen, Cat. #L34957), single cell suspension of heart tissue was incubated with fluorochrome-conjugated antibodies for 20 minutes at room temperature. A total of 6,000 macrophages (CD45.2+Ly6G-CD64+RFP+) or 800 cardiac neutrophils (CD45.2+Ly6G+CD64-RFP+) were sorted in the same setting as blood neutrophils.
RNA extraction, RNA library preparations, sequencing reactions, and initial bioinformatics analysis were conducted at Genewiz, LLC. Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen). RNA was quantified using Qubit Fluorometer (Life Technologies) and RNA integrity was checked with TapeStation (Agilent Technologies). SMART-Seq v4 Ultra Low Input Kit for Sequencing was used for full-length cDNA synthesis and amplification (Clontech), and Illumina Nextera XT library was used for sequencing library preparation. Briefly, cDNA was fragmented, and adaptor was added using Transposase, followed by limited-cycle PCR to enrich and add index to the cDNA fragments. The final library was assessed with Agilent TapeStation. The sequencing libraries were multiplexed and clustered on one lane of a flowcell.

value: Blood

value: Neutrophils

value: LOY


title: WT3

description:
HWI-ST1276
WT DC rep 3

value: dendritic cells (bone marrow derived using GM-CSF from immunocompetent C57/bl6 mice)

value: dendritic cells


title: BMDM cells, frHMGB1 treatment, replicate 1

value: Bone marrow

value: WT

value: 5ug/mL frHMGB1


title: Liver, FF2, Input

value: Wtap flox/flox


title: Liver, HKO1, Input


title: Liver, FF1, Input


title: C. albicans culture, Control 3

value: wild type

value: Control


title: Whole Blood Neutrophils, LOY BMT, bulkRNAseq [19KO]


title: Whole Blood Neutrophils, LOY BMT, bulkRNAseq [9KO]


title: Whole Blood Neutrophils, LOY BMT, bulkRNAseq [5KO]


title: WT2

description:
HWI-ST1276
WT DC rep 2


title: Whole Blood Neutrophils, LOY BMT, bulkRNAseq [10KO]


title: patient 14_004 aortic wall  GCH_14_0045


title: Whole Blood Neutrophils, LOY BMT, bulkRNAseq [4KO]


title: Liver, HKO2, IP

value: m6A antibody (Synaptic System, 202003)


title: WT1

description:
HWI-ST1276
WT DC rep 1


title: Whole Blood Neutrophils, Control BMT, bulkRNAseq [18C]


title: Whole Blood Neutrophils, Control BMT, bulkRNAseq [17C]


title: Whole Blood Neutrophils, Control BMT, bulkRNAseq [12C]


title: Memory B cells from Lung

city: Marseille

first: Lionel

last: Spinelli

address: Avenue de Luminy

country: France

institute: CIML

description: Single-cell suspensions from lungs of three previously infected Aid-EYFP mice were prepared as described above with enzymatic digestion, and stained with a panel of antibodies for identifying subsets of antigen-specific memory B cells (GL7-PerCP-Cy5.5, HA-PE, Ccr6-PE-Dazzle594, CD38-PE-Cy7, NP-APC, CD19-APC-Cy7, Cxcr3-BV421, Live/Dead Aqua stain). FB5P-seq protocol was performed as previously described (Attaf et al., 2020). Briefly, single memory B cells were FACS sorted on a BD Influx into 96-well PCR plates containing 2µl lysis mix per well. The index-sorting mode was activated to record the different fluorescence intensities of each sorted cell. Immediately after cell sorting, plates containing single cells in lysis mix were frozen on dry ice and stored at -80°C until further processing.

data_processing:
Fastq files were obtained (i) for datasets 10x_190712_m_moFluMemB And 10x_191105_m_moFluMemB from the sequencing facility (running Illumina NextSeq550 with HighOutput75cycles) after demultiplexing with bcl2fastq (ii) for dataset custom_201216_m_moFluMemB from the sequencing facility (running Illumina NextSeq2000 with HighOutput150cycles) after demultiplexing with bcl2fastq
For datasets 10x_190712_m_moFluMemB And 10x_191105_m_moFluMemB, raw fastq files from gene expression libraries were processed using Cell Ranger software, with alignment on the mm10 reference genome. For each experiment, cells with less than 200 genes detected and genes detected in less than 3 cells were removed. We further excluded bad quality cells expressing less than 2,000 UMI, more than 40% mitochondrial genes or less than 10% ribosomal genes. HTO barcodes for sample demultiplexing after hashing were counted using CITE-seq-count and were normalized for each cell using a centered log ratio (CLR) transformation across cells implemented in the Seurat function NormalizeData. Cells were demultiplexed using Seurat MULTIseqDemux function and barcodes assigned as doublets or negative were excluded from further analysis. The resulting filtered UMI count matrices were log-normalized with Seurat NormalizeData with a scale factor of 10,000.
For datasets 10x_190712_m_moFluMemB And 10x_191105_m_moFluMemB, BCR-seq raw fastq files were processed with the FB5P-seq pipeline (Attaf et al., 2020) as described above for FB5P-seq datasets, omitting the part of the pipeline related to gene expression analysis, and using the list of cell-associated 10x barcodes from CellRanger analysis as inputs for splitting bam files upstream Trinity assembly of BCR contigs. BCR metadata from the MigMap and Blastn annotations were appended to the gene expression metadata for each cell. Heavy and light chain variable sequences, trimmed to retain only sequences from FR1 to the first 36 nucleotides of FR4 regions, were exported as fasta files for further analysis of clonotypes and BCR phylogenies.
For dataset custom_201216_m_moFluMemB, we used a custom bioinformatics pipeline to process fastq files and generate single-cell gene expression matrices and BCR sequence files as previously described (Attaf et al., 2020). Detailed instructions for running the FB5P-seq bioinformatics pipeline can be found at https://github.com/MilpiedLab/FB5P-seq. Quality control was performed to remove poor quality cells.  Cells with less than 500 genes detected and genes detected in at least 3 cells were removed. We further excluded bad quality cells expressing more than 3% of mitochondrial genes or less than 10% of ribosomal genes.  For each cell, gene expression UMI count values were log-normalized with Seurat NormalizeData with a scale factor of 10,000 (Stuart et al., 2019). Index-sorting FCS files were visualized in FlowJo software and compensated parameters values were exported in CSV tables for further processing. For visualization on linear scales in the R programming software, we applied the hyperbolic arcsine transformation on fluorescence parameters (Finak et al., 2010).
For dataset custom_201216_m_moFluMemB, for BCR sequence reconstruction, the FB5P-seq pipeline used Trinity for de novo transcriptome assembly for each cell based on Read1 sequences, then MigMap for filtering the resulting contigs for productive BCR sequences and identifying germline V, D and J genes and CDR3 sequence for each contig. Filtered contigs were aligned to reference constant region sequences using Blastn. The FB5P-seq pipeline also ran the pseudoaligner Kallisto to map each cell’s FB5P-seq Read1 sequences on its reconstructed contigs and quantify contig expression. The outputs of the FB5P-seq pipeline were further processed and filtered with custom R scripts. For each cell, reconstructed contigs corresponding to the same V(D)J rearrangement were merged, keeping the largest sequence for further analysis. We discarded contigs with no constant region identified in-frame with the V(D)J rearrangement. In cases where several contigs corresponding to the same BCR chain had passed the above filters, we retained the contig with the highest expression level. BCR metadata from the MigMap and Blastn annotations were appended to the gene expression and index sorting metadata for each cell. Finally, heavy and light chain contig sequences were trimmed to retain only sequences from FR1 to the first 36 nucleotides of FR4 regions, and were exported as fasta files for further analysis of clonotypes and BCR phylogenies.
Genome_build: mm10
Supplementary_files_format_and_content: tsv and mtx files containing cell barcodes, features and count matrix for mRNA and HTO libraries, csv files containing gene UMI counts for BCR analysis, csv files containing additional cell-specific metadata (QC values, index sorting parameters, BCR parameters) for each filtered cell identified by a UniqueCellID.

molecule: polyA RNA

source_name: Lung

extract_protocol: 10x 5’ scRNA-seq libraries were prepared according to the manufacturer’s instructions with modifications for generating the BCR-seq libraries. Following cDNA amplification, SPRI select beads were used to separate the large cDNA fraction derived from cellular mRNAs (retained on beads) from the HTO-containing fraction (in supernatant). For the cDNA fraction derived from mRNAs, 50ng were used to generate transcriptome library and around 5ng were used for BCR library construction. Gene expression libraries were prepared according to manufacturer’s instructions. For BCR libraries, heavy and light chain cDNA were amplified by two rounds of PCR (6 cycles + 8 cycles) using external primers recommended by 10x Genomics, and 800 pg of purified amplified cDNA was tagmented using Nextera XT DNA sample Preparation kit (Illumina) and amplified for 12 cycles using the SI-PCR forward primer (10x Genomics) and a Nextera i7 reverse primer (Illumina). For the HTO-containing fraction, 5ng were used to generate the HTO library. The resulting libraries were pooled and sequenced together on an Illumina NextSeq550 platform, using High Output 75-cycle flow cells, targeting 5×104 reads per cell for gene expression, 5x103 reads per cell for BCR, 2x103 reads per cell for hashtag, in paired-end single-index mode (Read 1: 26 cycles, Read i7: 8 cycles, Read 2: 57 cycles).  FB5P-seq: For each plate, library preparation consisted in RT with template switching for incorporating well-specific barcodes and UMIs, cDNA amplification with 22 cycles of PCR, pooling of 96 wells into one tube, and 5’-end RNA-seq library preparation using tagmentation-based modified Nextera XT DNA sample Preparation kit (Illumina). Libraries were tagged with a plate-specific i7 index and were pooled for sequencing on an Illumina NextSeq2000 platform, with P2 flow cells, targeting 2.5×105 reads per cell in paired-end single-index mode (Read 1: 103 cycles, Read i7: 8 cycles, Read 2: 16 cycles).

tag: cell types

value: Memory (Mem) B cells


title: Liver, FF1, IP

value: Liver


title: Whole Blood Neutrophils, Control BMT, bulkRNAseq [1C]


title: Whole Blood Neutrophils, Control BMT, bulkRNAseq [2C]


title: Heart Neutrophils, Control BMT, bulkRNAseq [5KO]

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software
In the initial analysis, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Assembly: mm10
Supplementary files format and content: normalized Transcripts Per Million reads (TPM) values

source_name: Heart

value: Heart


title: Heart Neutrophils, Control BMT, bulkRNAseq [14KO]


title: Heart Neutrophils, Control BMT, bulkRNAseq [15KO]


title: Heart Neutrophils, Control BMT, bulkRNAseq [10KO]


title: Heart Neutrophils, Control BMT, bulkRNAseq [12C]


title: Whole Blood Neutrophils, Control BMT, bulkRNAseq [6C]


title: Heart Neutrophils, Control BMT, bulkRNAseq [3KO]


title: WtapFF_1

data_processing:
Nextera adaptor sequences were firstly trimmed from the reads using skewer (0.2.2). These reads were aligned to a reference genome using BWA, with standard parameters. These reads were then filtered for high quality (MAPQ≥13), non mitochondrial chromosome, and properly paired reads (longer than 18 nt).
All peak calling was performed with macs2 using ‘macs2 callpeak --nomodel --keepdup all --call-summits’. For simulations of peaks called per input read, aligned and de-duplicated BAM files were used without any additional filtering.
Genome_build: Ensemble_GRCm38.p6
Supplementary_files_format_and_content: HKO_vs_FF_peak_compare_table.xlsx

value: 8 weeks old

value: Wtapflox/flox


title: Heart Neutrophils, Control BMT, bulkRNAseq [6C]


title: BMDM cells, frHMGB1 treatment, replicate 2

value: Bone marrow derived macrophage


title: Liver, HKO1, IP

value: HKO (Wtap flox/flox Alb-Cre)


title: WtapFF_2


title: Heart Neutrophils, Control BMT, bulkRNAseq [2C]

value: Neutrophils


title: HKO1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ensemble_GRCm38.p6 whole genome using tophat2  with parameters  -p 8 -N 2 --read-edit-dist 2
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then   F  PKM   of each gene was calculated based on the length of the gene and reads count mapped   to this   gene.  F  PKM,   expected  number  of  Fragment  s  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 (  Tr  apnell, Cole, et al., 2010  )
Genome_build: Ensemble_GRCm38.p6

extract_protocol:
Livers were removed, flash frozen on liqid nitrogen, and total RNA was harvested using TriPure reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Wtapflox/flox and Wtap-HKO mice were fed with a normal chow diet for 8 weeks

value: 8 weeks

value: Wtap-HKO (Wtapflox/flox Alb-Cre+/-)


title: Liver, FF2, IP


title: HKO2


title: FF3


title: Heart Neutrophils, Control BMT, bulkRNAseq [7C]


title: Heart Neutrophils, Control BMT, bulkRNAseq [11C]


title: Heart Neutrophils, Control BMT, bulkRNAseq [4KO]

value: LOY


title: WtapHKO_2

value: Wtap HKO (Wtapflox/flox Alb-Cre+/-)


title: Heart Macrophages, LOY BMT, bulkRNAseq [41x1]

value: Macrophages


title: HKO3


title: Heart Neutrophils, Control BMT, bulkRNAseq [8C]


title: FF2


title: Heart Macrophages, Control BMT, bulkRNAseq [control4]


title: Heart Macrophages, LOY BMT, bulkRNAseq [41x3]


title: Heart Macrophages, LOY BMT, bulkRNAseq [41x4]


title: PMNs, fl- Cre+-, GM-CSF+LPS (Sample 11)

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

institute: University Medical Center Mainz

data_processing:
Sequence reads were trimmed for adapter sequences and further processed using the software CLC Genomics workbench (v20.0 with CLC's default settings for RNA-Seq analysis). Reads were aligned to GRCm38 genome.
Genome_build: GRCm38
Supplementary_files_format_and_content: txt files report gene-level abundance measurements (Expression value, TPM, RPKM)

growth_protocol: We isolated PMN from bone marrow of CD18fl/fl and CD18DLy6G mice (n=3). Each 10^6 PMN were either lysed directly after isolation or cultured overnight with GM-CSF (10ng/ml) plus LPS (1µg/ml). Subsequently RNA was purified and quantified with a Qubit fluorometer in order to compare genotype-dependent expression levels both for untreated and treated conditions.

extract_protocol:
Cells enriched by flow cytometry were directly collected in RNA extraction buffer. RNA was isolated using the Rneasy plus micro kit (Qiagen).
Quantity of total RNA was assessed with the Qubit 2.0 and quality was checked using a RNA 6000 Pico chip on Agilent's bioanalyzer. Barcoded mRNA seq libraries were prepared from 10 ng total RNA using a NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® according to the manual. All quality controls were done using Invitrogen’s Qubit HS assay and fragment size was determined on Agilent’s 2100 Bioanalyzer HS DNA assay.

treatment_protocol: 5 replicates were treated overnight with GM-CSF (100ng/ml) plus LPS (1µg/ml)

value: Bone marrow

value: polymorphonuclear granulocytes (PMN)

value: GM-CSF+LPS


title: PMNs, fl- Cre--, GM-CSF+LPS (Sample 12)


title: PMNs, fl- Cre+-, GM-CSF+LPS (Sample 9)


title: Heart Macrophages, Control BMT, bulkRNAseq [control1]

value: Control


title: Heart Macrophages, Control BMT, bulkRNAseq [control2]


title: FF1


title: PMNs, fl- Cre+-, untreated (Sample 5)

value: untreated


title: PMNs, fl- Cre--, GM-CSF+LPS (Sample 8)


title: PMNs, fl- Cre--, untreated (Sample 6)


title: Heart Macrophages, Control BMT, bulkRNAseq [control3]


title: NK-92 cells, lenti-NHE1, rep 3

city: Philadelphia

first: Yao-Yu

last: Gong

state: Pennsylvania

address: University of Pennsylvania

institute: University of Pennsylvania

data_processing:
Reads files of technical replicates of the same sample were combined by concatenation prior to analysis.
The quality of the sequencing reads was checked using FastQC. Read mapping was performed using Kallisto (parameters: --single -l 100 -s 30).
All downstream analyses were performed using R (version 4.1.2) with indicated packages.
Raw counts were extracted using tximport (parameters: type = "kallisto", countsFromAbundance = "lengthScaledTPM").
Normalized, log2-transformed counts per million bases (CPM) values were calculated using edgeR by first converting counts to CPM using the function cpm and then normalizing using the functions calcNormFactors (parameter: method = "TMM") and cpm (parameter: log = TRUE).
Assembly: Genome Reference Consortium Human Build 38, release 106
Supplementary files format and content: Tab-delimited text files including raw counts for each sample
Supplementary files format and content: Tab-delimited text files including normalized, log2-transformed counts per million bases (CPM) values for each sample

growth_protocol: NK-92 cells were maintained in RPMI 1640 with 25 mM HEPES (Corning) supplemented with 10% fetal bovine serum (FBS) (GeminiBio), 1 mM sodium pyruvate, 2 mM L-glutamine, 1x MEM Non-Essential Amino Acids (Gibco), 2x 2-mercaptoethanol (Gibco), and 300 IU/ml recombinant human IL-2 (STEMCELL Technologies).

extract_protocol:
RNA was extracted using RNeasy Plus Mini Kit (Qiagen) following manufacturer's instructions. 100 ng of Dnase I-treated total RNA was used for the construction of sequencing libraries.
Libraries were generated using QuantSeq 3' mRNA-Seq Library Prep Kit FWD (Lexogen), according to the manufacturer's directions

treatment_protocol: Cells were cultured in the medium for 24 hours before being harvested.

tag: cell line

value: natural killer cell line

value: NHE1 overexpression


title: PMNs, fl- Cre--, untreated (Sample 2)


title: PMNs, fl- Cre--, untreated (Sample 4)


title: PMNs, fl- Cre+-, untreated (Sample 1)


title: NK-92 cells, lenti-NHE1, rep 2


title: PMNs, fl- Cre--, GM-CSF+LPS (Sample 10)


title: PMNs, fl- Cre+-, untreated (Sample 3)


title: WtapHKO_1

value: Liver

value: 8 weeks old


title: NK-92 cells, lenti-NHE1, rep 1


title: Heart Macrophages, LOY BMT, bulkRNAseq [41x2]

value: Heart


title: NK-92 cells, lenti-EV, rep 3

value: empty vector control


title: NK-92 cells, lenti-EV, rep 2


title: NK-92 cells, lenti-EV, rep 1


title: SARS-CoV-2 M protein-specific CD4+ T cell lines

city: Bethesda

first: Eric

last: Dang

state: Maryland

address: 9000 Rockville Pike

department: NIAID

institute: NIH

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: PBMCs

extract_protocol:
Approximately a thousand cells per donor for each cell line were loaded in three lanes of the Chromium Next GEM Chip G (10x Genomics) respectively, one for MP-S, another for MP-M and another for CMV-specific-CD4+ TCLs, resulting in three 10x Genomics Single Cell Chromium 3' mRNA libraries, made in accordance with Chromium Single Cell 3' Reagent Kits User Guide (v3.1).
Three 10x Genomics Single Cell Chromium 3' mRNA libraries were made in accordance with Chromium Single Cell 3' Reagent Kits User Guide (v3.1) and sequenced as part of one Illumina NextSeq run.

tag: donor diagnosis

value: Healthy

value: PBMCs

value: CD4+ T cell lines

tag: reactivity

value: SARS-CoV-2 M protein


title: SARS-CoV-2 S protein-specific CD4+ T cell lines

description: 10x Genomics

value: SARS-CoV-2 S protein


title: HeLa_MUT_2

city: Dallas

first: Weibo

last: Luo

state: Texas

address: 5323 Harry Hines Blvd.

department: Pathology

institute: UT Southwestern Medical Center

data_processing:
Basecalls performed using bcl2fastq (v2.17)
mRNA-seq Fastq files were subjected to quality check using fastqc (version 0.11.2, http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and fastq_screen (version 0.4.4, http://www.bioinformatics.babraham.ac.uk/projects/ fastq_screen), and trimmed using fastq-mcf (ea-utils/version 1.1.2-806, https://github.com/ExpressionAnalysis/ea-utils). Trimmed fastq files were mapped to hg19 (UCSC version from igenomes) using Tophat. Duplicates were marked using picard-tools (version 1.127, https://broadinstitute.github.io/picard/). Read counts were generated using featureCounts and the differential expression analysis was performed using edgeR with FDR<0.05.
Genome_build: hg19
Supplementary_files_format_and_content: TXT

source_name: HeLa cells

growth_protocol: Cells were cultured with DMEM+10% FBS.

extract_protocol:
Total RNA was isolated using a RNeasy Mini kit and treated with DNase (Qiagen).
mRNA-seq libraries were prepared with a KAPA mRNA HyperPrep kit (Roche).

value: HeLa

tag: knockout

value: KDM6B mutant rescue


title: ZMYND8 knockout spheres

data_processing:
ChIP-seq Fastq files were subjected to quality check using fastqc (version 0.11.2, http://www.bioinformatics.babraham.ac.uk/projects/fastqc), fastq_screen (version 0.4.4, http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen), and mapped to human genome (hg19) using bowtie2 (version 2.2.3), filtering out alignments with mapping quality less than 10. Duplicate alignments were removed using picard-tools (version 1.127, https://broadinstitute.github.io/picard/). The ChIP-seq peaks were called using MACS2 (version 2.0.10), with a q-value threshold of 0.05 and using the random background of ChIP samples as controls.
Assembly: hg19
Supplementary files format and content: bed

source_name: ZMYND8 knockout spheres

growth_protocol: Mammospheres were cultured with MammoCult medium.

extract_protocol:
Chromatin was isolated using a SimpleChIP Enzymatic Chromatin IP kit (Cell Signaling Technology), sonicated to 200-300 bp in length, and subjected to immunoprecipitation overnight with respective antibodies. The ChIP DNA was eluted, decrosslinked, and purified.
ChIP-seq libraries were prepared with a KAPA Hyper Library Preparation kit.

value: ZMYND8 (Bethyl Laboratories, Cat.#A302-089A)

value: ZMYND8 knockout


title: MDA-MB-231 spheres

source_name: MDA-MB-231 spheres

value: wildtype


title: Human_BrainTumorR02

type: genomic

city: Kyoto

first: Yasuhide

last: Takeuchi

state: Kyoto

address: 54 Shogoin Kawahara-cho, Sakyo-ku, Department of Diagnostic Pathology, Kyoto University Hospital

department: Department of Diagnostic Pathology

institute: Kyoto University Hospital

hyb_protocol: Infinium® MethylationEPIC BeadChip system

label: cy3, cy5

source_name: Tumor in left parietal lobe

extract_protocol: AllPrep DNA/RNA Mini kit

tag: gender

value: Male

value: Tumor in left parietal lobe


title: rat_epididymal cells_day 60_rep3

city: Laval

first: Daniel

middle: G

last: Cyr

state: QC

address: 531 boul. des Prairies

country: Canada

institute: INRS-Centre Armand-Frappier Santé Biotechnologie

description: gene expression data from epididymal total cells in 60 days-old rat

hyb_protocol: Hybridization and staining with a streptavidin-phycoerythrin conjugate was done according to GeneChip WT Plus Reagent kit's protocol.

scan_protocol: GeneChips were scanned using the GeneChipScanner 3000 7G.

data_processing: Raw data were corrected for background, quantile normalized and summarized using the RMA algorithm of the Transcriptome Analysis Console (TAC) Software 4.0.1 from Thermo Fisher Scientific.

label: biotin

organism: Rattus norvegicus

source_name: total epididymal cells 60 days

label_protocol: The GeneChip WT Plus Reagent kit from Thermo Fisher Scientific was used to reverse transcribe the RNA samples into cDNA, amplify them by in vitro transcription and convert them into biotin-labeled cDNA.

growth_protocol: Rats were acclimated for one week under constant photoperiod (12h light: 12h dark), prepubertal rats (days 0-7; days 12-18) day were held with lactating mothers while day 28 and day 60 rats received food and water ad libitum.

extract_protocol: Extraction of total RNA was performed using Nucleospin RNA Plus Kit from Macherey-Nagel, DNase-treated with Qiagen's RNase-Free DNase set and purified using the RNeasy Mini Kit from Qiagen.

treatment_protocol: Epididymides dissected from rats were frozen in liquid nitrogen and stored at -86ºC.

value: Sprague-Dawley

tag: tissue

value: epididymis

value: 60 days


title: HeLa_WT_2

tag: cell type

value: KDM6B WT rescue


title: rat_epididymal cells_day 28_rep3

description: gene expression data from epididymal total cells in 28 days-old rat

source_name: total epididymal cells 28 days

value: 28 days


title: HeLa_WT_1


title: rat_epididymal cells_day 60_rep1


title: HeLa_KO_2

value: KDM6B KO


title: HeLa_MUT_1


title: HeLa_KO_1


title: rat_epididymal cells_day 28_rep4


title: CMV-specific CD4+ T cell lines

description: 10x Genomics

value: Healthy

value: PBMCs

value: CMV


title: HeLa_SC_2

value: Scrambled Control


title: rat_epididymal cells_day 28_rep2


title: HeLa_SC_1

value: HeLa


title: rat_epididymal cells_day 60_rep2


title: sRES_2

data_processing:
Basecalls performed using bcl2fastq (v2.17)
mRNA-seq Fastq files were subjected to quality check using fastqc (version 0.11.2, http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and fastq_screen (version 0.4.4, http://www.bioinformatics.babraham.ac.uk/projects/ fastq_screen), and trimmed using fastq-mcf (ea-utils/version 1.1.2-806, https://github.com/ExpressionAnalysis/ea-utils). Trimmed fastq files were mapped to hg19 (UCSC version from igenomes) using Tophat. Duplicates were marked using picard-tools (version 1.127, https://broadinstitute.github.io/picard/). Read counts were generated using featureCounts and the differential expression analysis was performed using edgeR with FDR<0.05.
ChIP-seq Fastq files were subjected to quality check using fastqc (version 0.11.2, http://www.bioinformatics.babraham.ac.uk/projects/fastqc), fastq_screen (version 0.4.4, http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen), and mapped to human genome (hg19) using bowtie2 (version 2.2.3), filtering out alignments with mapping quality less than 10. Duplicate alignments were removed using picard-tools (version 1.127, https://broadinstitute.github.io/picard/). The ChIP-seq peaks were called using MACS2 (version 2.0.10), with a q-value threshold of 0.05 and using the random background of ChIP samples as controls.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig

source_name: MDA-MB-231 cells

growth_protocol: Monolayer cells were cultured with DMEM+10% FBS. Mammospheres were cultured with MammoCult medium.

extract_protocol:
Total RNA was isolated using a RNeasy Mini kit and treated with DNase (Qiagen). Chromatin was isolated using a SimpleChIP Enzymatic Chromatin IP kit (Cell Signaling Technology), sonicated to 200-300 bp in length, and subjected to immunoprecipitation overnight with respective antibodies. The ChIP DNA was eluted, decrosslinked, and purified.
mRNA-seq libraries were prepared with a KAPA mRNA HyperPrep kit (Roche). ChIP-seq libraries were prepared with a KAPA Hyper Library Preparation kit.

value: mommosphere culture

value: ZMYND8 rescue


title: genomic DNA from skull base chordomas 40

city: Beijing

first: Xulei

last: Huo

address: Beijing

institute: Beijing tiantan hospital

description: tumor sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

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

label: Cy5 and Cy3

source_name: skull base chordomas 40

label_protocol: Standard Illumina Protocol

growth_protocol: Not applicable

extract_protocol: genomic DNA was extracted and purified from chordoma samples according to standard instructions

treatment_protocol: Not applicable

value: female

value: chordoma

tag: disease state

value: tumor


title: genomic DNA from skull base chordomas 44

description: tumor sample

source_name: skull base chordomas 44


title: sKO_2

tag: treatment

value: ZMYND8 KO


title: sRES_1


title: genomic DNA from skull base chordomas 2

description: tumor sample

source_name: skull base chordomas 2

tag: Sex


title: rat_epididymal cells_day 28_rep1

value: Sprague-Dawley

tag: age


title: sKO_1


title: rat_epididymal cells_day 18_rep3

description: gene expression data from epididymal total cells in 18 days-old rat

source_name: total epididymal cells 18 days

value: epididymis

value: 18 days


title: BMDM+Apoptotic thymocyte 24hr_3

city: Taipei

first: Chia-Lin

last: Hsu

address: R309, Biomedical Building, NYCU, No. 155, Sec. 2, Linong St., Beitou Dist.

department: Institute of Microbiology and Immunology

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
The sequencing was done by using a NextSeq 550 platform. The RNA concentration was measured by using a Qubit fluorometer with a Quant-iT RNA BR assay kit, and the RNA quality was examined on the Agilent Technologies 2100 Bioanalyzer with RNA nanochip. The library was prepared by using Illumina TruSeq Stranded mRNA Sample Prep Kit and sequenced by Illumina NextSeq High Output Kit v2.5-75 cycles on the sequencing platform. The raw data were aligned and analyzed following the CLC Genomics Workbench 20.0.4 pipeline. The sequence was annotated according to Mus musculus GRCm38 mm10 and calculated as RPKM.
The parameters in Trim sequences were set to Quality limit=0.01; Ambiguous limit=2; Remove 5' terminal nucleotides=12; Remove 3' terminal nucleotides=No; Maximum length=150.
CLC Genomics Workbench 20.0.4; Genome annotated with genes and transcripts
The parameters in RNA-seq analysis were set to Mismatch cos=2; Insertion cost=3; Deletion cost=3; Length fraction=0.8; Similarity fraction=0.8; Maximum number of hits for a read=10.
Assembly: GRCm38; mm10
Supplementary files format and content: Comma-separated values files. The file includes gene identifier, gene name, and chromosome region. Gene expression is shown in RPKM format.

source_name: Bone-marrow-derived macrophage

extract_protocol: Bone-marrow-derived macrophages generated from C57BL mice were treated with or without dexamethasone-induce apoptotic thymocytes at the ratio of 1:40. After 24 hr, the apoptotic cells were removed and the macrophages were harvested for RNA extraction. The RNA concentration was measured by using a Qubit fluorometer with a Quant-iT RNA BR assay kit, and the RNA quality was examined on the Agilent Technologies 2100 Bioanalyzer with RNA nanochip. The library was prepared by using Illumina TruSeq Stranded mRNA Sample Prep Kit and sequenced by Illumina NextSeq High Output Kit v2.5-75 cycles on the NextSeq 550 platform.

value: Bone-marrow-derived macrophage

tag: genotype

value: wild type

value: apoptotic cell treatment for 24hr


title: genomic DNA from skull base chordomas 1

description: tumor sample

source_name: skull base chordomas 1

tag: disease


title: genomic DNA from skull base chordomas 37

description: tumor sample

source_name: skull base chordomas 37


title: rat_epididymal cells_day 18_rep2

tag: strain


title: sSC_2

value: SC


title: BMDM+Apoptotic thymocyte 24hr_2


title: sSC_1


title: cRES_2

value: Monolayer culture


title: BMDM+Apoptotic thymocyte 24hr_1


title: rat_epididymal cells_day 18_rep4


title: BMDM_untreated_3

value: untreated


title: genomic DNA from skull base chordomas 24

description: tumor sample

source_name: skull base chordomas 24


title: genomic DNA from skull base chordomas 29

description: tumor sample

source_name: skull base chordomas 29


title: BMDM_untreated_2


title: genomic DNA from skull base chordomas 33

description: tumor sample

source_name: skull base chordomas 33


title: ChREBPbeta 11 mM c

city: New York

first: Donald

middle: K

last: Scott

state: New York

address: 1428 Madison Avenue

department: Diabetes Obesity and Metabolism Institute

institute: MSSM

data_processing:
Raw counts were processed for DGE analysis using the edgeR R package, using a minimum fold change of 1.2.
DGEs were conducted to reflect comparisons of the 4 groups.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: GFP_vs_Beta.txt: Tab-delimited text file includes FPKM values for each Sample.

source_name: INS-1 832/13 cells

extract_protocol:
Total RNA from ~1 x 10^6 INS-1 cells was isolated using the RNeasy mini kit (Qiagen) according to the manufacturer’s protocol.
Samples were submitted to the Genewiz and RNA was amplified via the NuGEN Ovation RNA-Seq System V2 prior to RNA sequencing.

value: insulin secreting insulinoma

tag: adenovirus expression

value: ChREBPbeta

value: 11 mM glucose


title: genomic DNA from skull base chordomas 30

description: tumor sample

source_name: skull base chordomas 30


title: cKO_2


title: BMDM_untreated_1


title: rat_epididymal cells_day 7_rep2

description: gene expression data from epididymal total cells in 7 days-old rat

source_name: total epididymal cells 7 days

value: 7 days


title: genomic DNA from skull base chordomas 25

description: tumor sample

source_name: skull base chordomas 25

value: female


title: rat_epididymal cells_day 7_rep3


title: cRES_1

value: ZMYND8 rescue


title: ChREBPbeta 11 mM b


title: genomic DNA from skull base chordomas 22

description: tumor sample

source_name: skull base chordomas 22

value: chordoma

value: tumor


title: genomic DNA from skull base chordomas 28

description: tumor sample

source_name: skull base chordomas 28


title: cKO_1

source_name: MDA-MB-231 cells

value: ZMYND8 KO


title: genomic DNA from skull base chordomas 26

description: tumor sample

source_name: skull base chordomas 26


title: genomic DNA from skull base chordomas 15

description: tumor sample

source_name: skull base chordomas 15


title: rat_epididymal cells_day 7_rep1

value: Sprague-Dawley

value: epididymis


title: cSC_1


title: cSC_2


title: ChREBPbeta 11 mM a


title: genomic DNA from skull base chordomas 14

description: tumor sample

source_name: skull base chordomas 14


title: genomic DNA from skull base chordomas 9

description: tumor sample

source_name: skull base chordomas 9


title: ChREBPbeta 2 mM c

value: 2 mM glucose


title: H3K14ac_ChIPseq 2

tag: chip antibody

value: H3K14ac (Abcam, Cat.#ab52946)


title: HTO for Memory B cells from Lung, Spleen and Lymph Node with mechanic dissociation

description: Single cell suspensions of mediastinal lymph nodes and spleens were obtained by pressing organs through a 70μm nylon mesh cell strainer with a plastic plunge in PBS 2%FCS 2mM EDTA. Because enzymatic digestion of tissues at 37°C induced the expression of dissociation-induced genes in some lung memory B cells, we performed that experiment using only mechanical dissociation of lung tissue at 4°C. For spleen and lungs, cell suspensions were further incubated with red blood cell lysis buffer for 5 minutes. We used cell hashing with hashtag oligonucleotides (HTO) to multiplex 3 organ samples from 3 individual mice as previously described (Mimitou et al., 2019). After cell surface staining with the mix of antibodies used for gating memory B cells, single-cell suspensions from each organ of each individual mice were independently stained with a distinct barcoded anti-mouse CD45 antibody (in-house conjugated) in PBS 2%FCS 2mM EDTA for 30 min on ice, then washed and resuspended in PBS.

source_name: Lung, Spleen, Lymph node

tag: cell types

value: Memory (Mem) B cells


title: ChREBPbeta 2 mM a

tag: cell line


title: HTO for Memory B cells from Lung, Spleen and Lymph Node with enzymatic dissociation

description: Single cell suspensions of mediastinal lymph nodes and spleens were obtained by pressing organs through a 70μm nylon mesh cell strainer with a plastic plunge in PBS 2%FCS 2mM EDTA. For lungs, single cell suspensions were obtained with the mouse lung dissociation kit (Miltenyi) according to manufacturer instructions. For spleen and lungs, cell suspensions were further incubated with red blood cell lysis buffer for 5 minutes.  We used cell hashing with hashtag oligonucleotides (HTO) to multiplex 3 organ samples from 3 individual mice as previously described (Mimitou et al., 2019). After cell surface staining with the mix of antibodies used for gating memory B cells, single-cell suspensions from each organ of each individual mice were independently stained with a distinct barcoded anti-mouse CD45 antibody (in-house conjugated) in PBS 2%FCS 2mM EDTA for 30 min on ice, then washed and resuspended in PBS.


title: Memory B cells from Lung, Spleen and Lymph Node with mechanic dissociation

description: Single cell suspensions of mediastinal lymph nodes and spleens were obtained by pressing organs through a 70μm nylon mesh cell strainer with a plastic plunge in PBS 2%FCS 2mM EDTA. Because enzymatic digestion of tissues at 37°C induced the expression of dissociation-induced genes in some lung memory B cells, we performed that experiment using only mechanical dissociation of lung tissue at 4°C. For spleen and lungs, cell suspensions were further incubated with red blood cell lysis buffer for 5 minutes. For each sample, live memory B cells (DAPI-CD19+eYFP+CD38+GL7-) were bulk-sorted with BD FACS Aria II. Sorted cell samples (1,319 lung cells, 1,436 lymph node cells, 1,500 spleen cells) were pooled and loaded in a single capture well for subsequent 10x Genomics Single Cell 5’ v1 workflow.


title: H3K14ac_ChIPseq 1


title: ChREBPbeta 2 mM b


title: Memory B cells from Lung, Spleen and Lymph Node with enzymatic dissociation

description: Single cell suspensions of mediastinal lymph nodes and spleens were obtained by pressing organs through a 70μm nylon mesh cell strainer with a plastic plunge in PBS 2%FCS 2mM EDTA. For lungs, single cell suspensions were obtained with the mouse lung dissociation kit (Miltenyi) according to manufacturer instructions. For spleen and lungs, cell suspensions were further incubated with red blood cell lysis buffer for 5 minutes. For each sample, live memory B cells (DAPI-CD19+eYFP+CD38+GL7-) were bulk-sorted with BD FACS Aria II. Sorted cell samples (13,126 lung cells, 3,414 lymph node cells, 12,838 spleen cells) were pooled and loaded in a single capture well for subsequent 10x Genomics Single Cell 5’ v1 workflow.


title: genomic DNA from skull base chordomas 12

description: tumor sample

source_name: skull base chordomas 12


title: ZMYND8_ChIPseq 2

value: ZMYND8 (Bethyl Laboratories, Cat.#A302-089A)


title: GFP 11 mM c

value: GFP


title: bru1M3 IFM 1d adult rep2

city: Martinsried-Planegg

first: Maria

middle: Lynn

last: Spletter

state: Bayern

address: Grosshaderner Str. 9

department: Physiological Chemistry

institute: Ludwig-Maximilians-University Munich

data_processing:
basecalling and demultiplexing by LC Sciences using Illumina software
Sequenced reads were mapped to the Ensembl BDGP6.22 whole genome using STAR v2.7.3a
mapped reads were sorted and indexed using samtools v1.1
bam files were converted into bigwig for visualisation using ucsc-wigtobigwig v377, or visualized directly as .bam files in IGV
Counting the mapped reads on the gene and exon level using featureCounts in subread v.2.0.0
differential gene expression analysis using the R package DESeq2 v1.32.0
differential exon usage with the R package DEXSeq v1.38.0
Assembly: BDGP6.22 from ENSEMBL
Supplementary files format and content: tab delimited text files including normalized counts from DESeq2 analysis
Supplementary files format and content: tab delimited text files including differential expression results from DESeq2 analysis
Supplementary files format and content: tab delimited text files including differential expression results from DEXSeq analysis

organism: Drosophila melanogaster

source_name: bru1 mutant sample, dissected IFM

growth_protocol: flies were grown at 27C on standard medium using standard fly husbandry

extract_protocol:
total RNA isolated in Trizol (phenol-choloform), mRNA selection by LC Sciences
RNA libraries were prepared for sequencing by LC Sciences (Houston, TX, USA) using standard Illumina protocols

treatment_protocol: tissues were dissected for up to 30 min. in PBS, spun-down at 2000xg for 5 min. to remove buffer and stored in Tri-Pure (Roche) reagent at -80C until extraction (see Kao et al., JoVE, 2019 for details)

value: indirect flight muscle

tag: developmental stage

value: 1d adult

tag: muscle type

value: fibrillar

tag: growth protocol

value: grown at 27C, collected after eclosion


title: bru1M3 IFM 1d adult rep1


title: ZMYND8_ChIPseq 1


title: GFP 11 mM b

value: insulin secreting insulinoma

value: 11 mM glucose


title: GFP 11 mM a


title: GFP 2 mM c


title: WT IFM 1d adult rep2

source_name: wildtype sample, dissected IFM


title: U2OS_TSA-seq_Input_THZ1_hg19

city: CHARLESTOWN

first: Takaaki

last: Yasuhara

state: MA

department: Cancer Center

institute: Massachusetts General Hospital

data_processing:
Library strategy: TSA-seq
ChIP-seq reads were aligned to GRCh37 using bwa. TSA-seq reads were aligned to the hg19 genome assembly using bowtie2 with the default configuration
Data were filtered to exclude PCR duplicates using RmDup. The fragments were extended to 150 bp to approximate fragment sizes for ChIP-seq
For ChIP-seq, bigwig files were generated by counting the number of fragments overlapping each position using IGV tools and normalized to 10 million reads. For generation of bigwig files of TSA-seq, aligned reads were averaged in a 1-Mb window for each 100-bp bin.
For spike-in normalization, the total number of sequences which uniquely mapping to the D. melanogaster genome (mm6) is counted for each paired sample and used to calculate correction factors. Correction factors were then used for the scaling of human sequences
Assembly: hg19, human rDNA complete repeating unit (GenBank: U13369.1)
Supplementary files format and content: bigwig

growth_protocol: U2OS (ATCC) was cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS), 4 mM L-glutamine, and 1% penicillin/streptomycin. U2OS was cultured in a 37 °C incubator at 5% CO2.

extract_protocol:
For ChIP, chromatin from formaldehyde-fixed cells was fragmented to a size range of 200–700 bp with a Branson 250 sonicator. Solubilized chromatin was immunoprecipitated with 2 μg antibodies against SFPQ, NONO, and TAF15 at 4 °C overnight. Antibody–chromatin complexes were pulled down with protein G Dynabeads, washed, and then eluted. After cross-link reversal and RNase A and proteinase K treatment, immunoprecipitated DNA was extracted with AMP Pure beads. For TSA-UBF labelling, cells were fixed with paraformaldehyde and permeabilized. For TSA-SFPQ labelling, cells were pre-extracted and fixed with paraformaldehyde. Cells were incubated with UBF antibody (1:100) for 2 hr at 37 °C or SFPQ antibody (1:1,000) overnight at 4 °C, followed by incubation with mouse/rabbit-HRP secondary antibody for 1 hr at 37 °C. After washing, cells were incubated with 25 μM Tyramide-Biotin, 0.0015% H2O2, 50% Sucrose for 30 min at room temperature. After sequential wash, cells were lysed and incubated at 65 °C overnight to reverse the crosslink. After genomic DNA extraction and sonication, gDNA was subjected to pull-down by Dynabeads M-280 Streptavidin for 2 hr. The pull-down DNA was eluted from beads for 3 min at 95 °C and purified using QIAquick PCR Purification Kit.
ChIP/TSA DNA samples were used to prepare sequencing libraries with Ultralow V2 DNA-Seq Library Preparation Kit

treatment_protocol: THZ1 (1 µM) 1 hour

value: Bone osteosarcoma cells

tag: genome build

tag: antibody


title: genomic DNA from skull base chordomas 46

description: tumor sample

source_name: skull base chordomas 46

value: male

value: chordoma


title: genomic DNA from skull base chordomas 5

description: tumor sample

source_name: skull base chordomas 5

value: female

value: tumor


title: U2OS_TSA-seq_Input_THZ1_rDNA repeats

description: Alignment to human rDNA complete repeating unit (GenBank: U13369.1)

tag: cell type


title: U2OS_TSA-seq_SFPQ_THZ1_hg19

value: SFPQ


title: GFP 2 mM b

source_name: INS-1 832/13 cells

value: 2 mM glucose


title: U2OS_TSA-seq_SFPQ_THZ1_rDNA repeats


title: IPS_Glu_H3K27ac_90_Rep2

first: Matthew

middle: A

last: Lalli

state: NY

address: 1 Gustave L. Levy Pl

department: Psychiatry

institute: Icahn School of Medicine at Mount Sinai

description: DNA released from nuclei

data_processing:
Library strategy: CUT&RUN
Illumina adapters were trimmed from reads using trimmomatic:  trimmomatic PE -threads 8 -phred33 R1_001.fastq.gz R2_001.fastq.gz ILLUMINACLIP:$adapterpath/TruSeqAdapters.fa:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25
Trimmed reads were mapped to the human genome (hg38) using bowtie2:  bowtie2 -p 8 --dovetail --phred33 --local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 700 -x $bt2idx/GRCh38_noalt_as
Aligned reads were sorted and indexed using samtools
Bigwig files were gneerated for visualizing sample using bamCoverage:  bamCoverage -b  aligned_sorted.bam -o aligned.bigwig -p 4 --normalizeUsing RPKM --extendReads 160
Broad peaks were called using MACS2:  macs2 callpeak -t sorted_sample.bam -c sorted_control.bam-f BAMPE -g hs --nomodel --keep-dup all --broad
Genome_build: hg38 (GRCh38_noalt_as)
Supplementary_files_format_and_content: Bigwig files (.bigwig) can be used to visualize each sample on a gennome browser
Supplementary_files_format_and_content: Peak files (.broadPeak) contain the called peaks from MACS2

source_name: NSB3188 (iPSC)

extract_protocol:
CUT&RUN was performed as previously described. Nuclei (50,000) were extracted from neurons using NE1 buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.5 805 mM Spermidine, 0.1% Triton X-100, 20% Glycerol and Roche Complete Protease Inhibitor EDTA-Free and used as the input source. Nuclei bound to Concanavalin-coated magnetic beads (Bangs Laboratories BP531) were incubated with the relevant antibody: H3K27ac (Abcam AB4729), FOS (Abcam AB208942), rabbit IgG (Abcam AB46540) or guinea pig IgG (Novus NBP1-2763). The next day, the beads were placed on a magnet to remove supernatant, washed, and incubated with Protein AG-MNase. To fragment the DNA, samples were first chilled to 0º C, the digestion was then activated by the addition of 2 mM of CaCl2. Reactions were stopped by 2×Stop buffer (340mM NaCl, 20mM EDTA, 4mM EGTA (Alfa Aesar J60767), 0.05% Digitonin, 100ug/mL RNAse A (Thermo Fisher Scientific EN0531), 50ug/mL Glycogen).
DNA fragments released from the nuclei were purified by extraction with phenol-chloroform and ethanol precipitated. DNA was quantified with a fluorescence-based method using Qubit 4 Fluorometer dsDNA HS assay. CUT&RUN DNA (10ng) was processed using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs 816 E7645) for library preparation according to manufacturer’s instructions. Briefly, purified DNA was repaired, ligated with 1.5μM NEBNext Adaptors and amplified for 14 cycles by PCR. DNA was enriched for fragments of size 150-350bp for transcription factor and 150-800 bp for histone markers using Ampure XP beads. Final libraries were quantified with Qubit dsDNA HS assay and the size distribution was determined by Agilent 4200 TapeStation. Libraries were mixed at an equal ratio to achieve a final concentration as recommended by the manufacturer and sequenced on an Illumina HiSeq 4000 system.

treatment_protocol: Prior to depolarization, medium was replaced with serum free Neurobasal A/B27/Glutamax for 3 days. The neuronal culture was then silenced using 1μM of Tetrodotoxin citrate (TTX) (Labome 1069/1) and 100μM of DL-2-amino-5-phosphopentnoic acid (DL-AP5) (Abcam ab120271) for 12-16h. The neurons were then depolarized by adding depolarization buffer (170 mM KCl, 2 mM CaCl2, 1 mM MgCl and 10 mM HEPES directly into the media to a final concentration of 30% of the total culture media. Neurons were collected at different time points after depolarization for experiments.

value: induced glutamatergic neurons

value: depolarization

tag: timepoint (minutes)


title: genomic DNA from skull base chordomas 45

description: tumor sample

source_name: skull base chordomas 45

tag: disease state


title: WT IFM 1d adult rep1

tag: tissue


title: GFP 2 mM a

tag: treatment


title: U2OS_TSA-seq_Input_DMSO_rDNA repeats

value: DMSO


title: IPS_Glu_H3K27ac_90_Rep3

description: DNA released from nuclei


title: rat_epididymal cells_day 18_rep1

source_name: total epididymal cells 18 days

value: Sprague-Dawley

value: epididymis

tag: age

value: 18 days


title: IPS_Glu_H3K27ac_90_Rep1

description: DNA released from nuclei


title: IPS_Glu_H3K27ac_30_Rep3

description: DNA released from nuclei


title: U2OS_TSA-seq_Input_DMSO_hg19


title: genomic DNA from skull base chordomas 43

description: tumor sample

source_name: skull base chordomas 43

tag: Sex

tag: disease


title: BPDCN Leukemia

city: Foshan

first: Ying

last: Zhao

address: Shiwan Street, Chancheng District, Foshan City

institute: Department of Hematology, First People’s Hospital of Foshan

description: Peripheral blood mononuclear cell samples with four protein tags in the data, namely 'CD141|THBD|AHS0083|pAbO', 'CD11c:S-HCL-3|ITGAX|AHS0183|pAbO',  'HLA-DR|CD74|AHS0035|pAbO',and 'CD123|IL3RA|AHS0020|pAbO', can be used to extract the protein data matrix.

data_processing:
Raw files obtained by sequencing with Illumina high-throughput sequencers
The original file is an image file, and after base calling and Bcl2Fastq transformation, the original sequenced sequence (sequenced reads) in FASTQ (fq for short) format can be obtained
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: BPDCN Leukemia

extract_protocol:
Cells were collected from peripheral blood, bone marrow and tissue samples of leukemia patients and single cell whole transcriptome sequencing libraries were constructed using the BD platform R hapsody reverse transcription kit and BD R hapsody whole transcriptome amplification kit
RNA libraries were prepared for sequencing using standard BD RhapsodyTM Single cell 3’ whole transcriptome amplification (WTA) with sample multiplexing kit (SMK) protocol

value: multiplexed sample:pbmc and bmnc and bone marrow tissue

tag: sample tag

value: SampleTag08, SampleTag09, SampleTag10


title: 45yAM1-M4b.FLT3(+) and 64yAM1-M5

description: Peripheral blood mononuclear cell samples or bone marrow mononuclear cell samples with three protein tags in the data, namely 'CD141|THBD|AHS0083|pAbO', 'CD11c:S-HCL-3|ITGAX|AHS0183|pAbO', and 'HLA-DR|CD74|AHS0035|pAbO', can be used to extract the protein data matrix.

source_name: 45yAM1-M4b.FLT3(+) CR after multiple courses and 64yAM1-M5 Specific type Primary treatment

value: multiplexed sample:pbmc and bmnc

value: SampleTag06, SampleTag07, SampleTag08


title: U2OS_TSA-seq_SFPQ_DMSO_rDNA repeats

value: Bone osteosarcoma cells


title: U2OS_TSA-seq_SFPQ_DMSO_hg19


title: IPS_Glu_H3K27ac_30_Rep1

description: DNA released from nuclei


title: U2OS_TSA-seq_UBF_THZ1-siTAF15_hg19

value: UBF


title: hESC-derived xEM cells by BMP4/FGF2 differentiation on soft substrates

first: Mijo

last: Simunovic

institute: Columbia University

description: 10x genomics

data_processing:
Data was aligned to hg19 using Cellranger and quality processed using the default settings to generate the counts file. Single cell data was further processed using Scanpy. Cells expressing >15,000 total genes or >20% mitochondrial genes were removed. Processed data here is generated using the write_csvs function in Scanpy, which split the dataframe into three files: the count matrix (.X), the annotation of features (.var) file, and the annotation of observations (.obs) file.
Assembly: hg19
Supplementary files format and content: comma separated values containing: count matrix (.X file), annotation of features (.var file) and annotations of observations (.obs file)

extract_protocol:
The samples were dissociated with Accutase for 15-30 min at 37 °C until they completely dissociated into single cells assessed by light microscopy. The dissociation solution was thoroughly washed, then samples were loaded for capture onthe 10x Chromium platform using the Single Cell 3′ v3 reagents. cDNA was synthesized and amplified according to the manufacturer's instructions (10X Genomics). The resulting libraries were sequenced on the Nova-seq platform.
10x genomics v3
10x genomics v3

treatment_protocol: 2 days of 50ng/mL BMP4, 20ng/mL FGF2 treatment in conditioned media on 1.5kPa substrate


title: IPS_Glu_H3K27ac_30_Rep2

description: DNA released from nuclei


title: IPS_Glu_H3K27ac_t15_Rep3

description: DNA released from nuclei


title: embryo model, 2.5 days after tissue assembly

description: 10x genomics

data_processing:
Data was aligned to hg19 using Cellranger and quality processed using the default settings to generate the counts file. Single cell data was further processed using Scanpy. Cells expressing >15,000 total genes or >20% mitochondrial genes were removed. This dataset was further quality controlled to remove an entire cluster with few transcripts. Processed data here is generated using the write_csvs function in Scanpy, which split the dataframe into three files: the count matrix (.X), the annotation of features (.var) file, and the annotation of observations (.obs) file.
Assembly: hg19
Supplementary files format and content: comma separated values containing: count matrix (.X file), annotation of features (.var file) and annotations of observations (.obs file)

treatment_protocol: 3D epiblast and dissociated RUES2-xEM cells are mixed overnight with LDN, next day selected assembloids transferred to attachment substrate, cultured for 1.5 more days. Attached embryoids with a prominent 3D feature scraped off and dissociated for sequencing.


title: genomic DNA from skull base chordomas 41

description: tumor sample

source_name: skull base chordomas 41

value: male

value: chordoma


title: IPS_Glu_H3K27ac_t15_Rep2

description: DNA released from nuclei


title: E10 human embryo, in vitro attached

description: 10x genomics

source_name: human embryo

extract_protocol:
The samples were dissociated with TrypLE for 15-30 min at 37 °C until they completely dissociated into single cells assessed by light microscopy. The dissociation solution was thoroughly washed, then samples were loaded for capture onthe 10x Chromium platform using the Single Cell 3′ v3 reagents. cDNA was synthesized and amplified according to the manufacturer's instructions (10X Genomics). The resulting libraries were sequenced on the Nova-seq platform.
10x genomics v3
10x genomics v3

treatment_protocol: Cultured on plastic dish in IVC2 media.

value: human embryo


title: U2OS_TSA-seq_UBF_DMSO-siTAF15_hg19


title: genomic DNA from skull base chordomas 42

description: tumor sample

source_name: skull base chordomas 42

value: tumor


title: OVCAR-3, FC-A + IFNα (Combi), 6 hours, rep2 [S3341Nr23]

city: Eindhoven

first: Blaž

last: Andlovic

address: Den Dolech 2

country: Netherlands

institute: Eindhoven University of Technology

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.20).
Adapters were trimmed with Skewer (version 0.2.2). Quality trimming of the reads has not been performed.
Trimmed raw reads were aligned to hg19-cegat using STAR (version 2.7.3)
Pseudoautosomal regions (PAR) were masked on chromosome Y (chrY:10001-2649520, chrY:59034050-59363566). Reads originating from these regions can be found at the respective location on chromosome X.
The quality of the FASTQ files was analyzed with FastQC.
Differential expression analysis between groups was performed with DESeq2 (version 1.24.0)
Assembly: hg19
Supplementary files format and content: tab-delimited TSV files with normalized counts, differentially expressed genes

source_name: ovary

extract_protocol:
RNA was harvested using Rneasy Mini Kit  (Qiagen). 100 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA (Illumina)

value: ovary

value: epithelial cell

tag: genotype

value: wt

value: Adenocarcinoma

tag: time

value: 6 hours

value: FC-A + IFNα (Combi)


title: genomic DNA from skull base chordomas 35

description: tumor sample

source_name: skull base chordomas 35


title: IPS_Glu_IgG_Rep2

description: DNA released from nuclei

value: induced glutamatergic neurons

value: depolarization


title: IPS_Glu_H3K27ac_t15_Rep1

description: DNA released from nuclei


title: OVCAR-3, FC-A + IFNα (Combi), 6 hours, rep1 [S3341Nr22]

tag: cell line


title: U2OS_TSA-seq_UBF_DMSO-siControl_hg19

value: DMSO


title: OVCAR-3, IFNα, 6 hours, rep3 [S3341Nr21]

value: IFNα (interferon alpha)


title: U2OS_TSA-seq_UBF_THZ1_hg19


title: genomic DNA from skull base chordomas 27

description: tumor sample

source_name: skull base chordomas 27


title: genomic DNA from skull base chordomas 31

description: tumor sample

source_name: skull base chordomas 31


title: genomic DNA from skull base chordomas 39

description: tumor sample

source_name: skull base chordomas 39


title: genomic DNA from skull base chordomas 23

description: tumor sample

source_name: skull base chordomas 23


title: IPS_Glu_H3K27ac_t0_Rep3

description: DNA released from nuclei


title: OVCAR-3, IFNα, 6 hours, rep2 [S3341Nr20]


title: OVCAR-3, FC-A + IFNα (Combi), 6 hours, rep3 [S3341Nr24]


title: genomic DNA from skull base chordomas 34

description: tumor sample

source_name: skull base chordomas 34


title: U2OS_ChIP-seq_Rabbit IgG_THZ1 (Spike-in)_hg19

data_processing:
ChIP-seq reads were aligned to GRCh37 using bwa. TSA-seq reads were aligned to the hg19 genome assembly using bowtie2 with the default configuration
Data were filtered to exclude PCR duplicates using RmDup. The fragments were extended to 150 bp to approximate fragment sizes for ChIP-seq
For ChIP-seq, bigwig files were generated by counting the number of fragments overlapping each position using IGV tools and normalized to 10 million reads. For generation of bigwig files of TSA-seq, aligned reads were averaged in a 1-Mb window for each 100-bp bin.
For spike-in normalization, the total number of sequences which uniquely mapping to the D. melanogaster genome (mm6) is counted for each paired sample and used to calculate correction factors. Correction factors were then used for the scaling of human sequences
Assembly: hg19, human rDNA complete repeating unit (GenBank: U13369.1)
Supplementary files format and content: bigwig

value: rabbit IgG

tag: spike-in

value: D. melanogaster genomic DNA


title: U2OS_TSA-seq_UBF_DMSO_hg19

value: Bone osteosarcoma cells

value: UBF


title: IPS_Glu_H3K27ac_t0_Rep2

description: DNA released from nuclei


title: genomic DNA from skull base chordomas 32

description: tumor sample

source_name: skull base chordomas 32

value: male

value: chordoma


title: IPS_Glu_H3K27ac_t0_Rep1

description: DNA released from nuclei

source_name: NSB3188 (iPSC)


title: genomic DNA from skull base chordomas 21

description: tumor sample

source_name: skull base chordomas 21

value: tumor


title: genomic DNA from skull base chordomas 20

description: tumor sample

source_name: skull base chordomas 20


title: genomic DNA from skull base chordomas 36

description: tumor sample

source_name: skull base chordomas 36


title: genomic DNA from skull base chordomas 38

description: tumor sample

source_name: skull base chordomas 38


title: U2OS_ChIP-seq_Mouse IgG_THZ1 (Spike-in)_hg19

value: mouse IgG


title: OVCAR-3, IFNα, 6 hours, rep1 [S3341Nr19]

value: ovary

value: epithelial cell


title: input-3xFLAG-Ubx-haltere-1

first: Siqian

last: Feng

address: 612 West 130th St, floor 9 Room L9-005

data_processing:
mapping was done against dm6 with the bowtie2 tool on usegalaxy.eu
ChIP-seq peak calling was performed using the galaxy version of MACS2 (“MACS2 callpeak” on usegalaxy.eu), with the following setting: --nomodel –extsize 200, and all other parameters were default
Genome_build: dm6
Supplementary_files_format_and_content: bigwig

source_name: haltere imaginal discs, wandering larvae

growth_protocol: Drosophila larvae were grown on standard cornmeal or molasses food at 25°C.

extract_protocol:
Tissues were crosslinked with 1% formaldehyde for 10 minutes at RT, and were sonicated. DNA was purified from input and ChIP samples.
ChIP-seq libraries were constructed using NEBNext Ultra™ II DNA Library Prep Kit (NEB E7103)

tag: chip antibody


title: OVCAR-3, FC-A, 6 hours, rep1 [S3341Nr16]

value: wt

value: Adenocarcinoma

value: FC-A (Fusicoccin A)


title: IPS_GABA_H3K27ac_t90_Rep2

description: DNA released from nuclei

value: induced GABAergic neurons


title: IPS_GABA_H3K27ac_t90_Rep1

description: DNA released from nuclei

value: depolarization


title: ChIP-3xFLAG-Ubx-haltere-1

value: anti-FLAG monoclonal M2


title: input-ubi-Ubx-spyChIP-haltere-2


title: U2OS_ChIP-seq_Input_THZ1 (Spike-in)_hg19


title: U2OS_ChIP-seq_Mouse IgG_DMSO (Spike-in)_hg19

value: DMSO


title: OVCAR-3, DMSO control, 6 hours, rep3 [S3341Nr15]

value: 6 hours


title: U2OS_ChIP-seq_Rabbit IgG_DMSO (Spike-in)_hg19

value: rabbit IgG

value: D. melanogaster genomic DNA


title: IPS_GABA_H3K27ac_t30_Rep2

description: DNA released from nuclei


title: IPS_GABA_H3K27ac_t30_Rep3

description: DNA released from nuclei


title: OVCAR-3, DMSO control, 6 hours, rep1 [S3341Nr13]


title: U2OS_ChIP-seq_TAF15_THZ1 (Spike-in)_hg19

value: Bone osteosarcoma cells


title: IPS_GABA_H3K27ac_t90_Rep3

description: DNA released from nuclei


title: ChIP-ubi-Ubx-spyChIP-haltere-2


title: OVCAR-3, DMSO control, 6 hours, rep2 [S3341Nr14]


title: U2OS_ChIP-seq_Input_DMSO (Spike-in)_hg19


title: IPS_GABA_H3K27ac_t30_Rep1

description: DNA released from nuclei


title: IPS_Glu_IgG_Rep1

description: DNA released from nuclei

value: induced glutamatergic neurons


title: U2OS_TSA-seq_Input_THZ1 (Spike-in)_rDNA repeats

value: Biotinylated D. melanogaster genomic DNA


title: U2OS_TSA-seq_UBF_THZ1-siControl_hg19

value: UBF


title: U2OS_TSA-seq_Input_THZ1 (Spike-in)_hg19


title: IPS_GABA_H3K27ac_t15_Rep3

description: DNA released from nuclei


title: ChIP-ubi-Ubx-spyChIP-haltere-1


title: IPS_GABA_H3K27ac_t15_Rep2

description: DNA released from nuclei


title: U2OS_ChIP-seq_TAF15_THZ1_hg19


title: U2OS_ChIP-seq_TAF15_DMSO (Spike-in)_hg19


title: OVCAR-3, FC-A, 6 hours, rep3 [S3341Nr18]


title: IPS_GABA_H3K27ac_t15_Rep1

description: DNA released from nuclei


title: input-tsh-Ubx-spyChIP-haltere-2


title: U2OS_ChIP-seq_TAF15_DMSO_hg19


title: U2OS_TSA-seq_SFPQ_THZ1 (Spike-in)_rDNA repeats

value: SFPQ


title: U2OS_ChIP-seq_SFPQ_THZ1 (Spike-in)_rDNA repeats


title: input-ubi-Ubx-spyChIP-haltere-1


title: U2OS_TSA-seq_SFPQ_THZ1 (Spike-in)_hg19


title: ChIP-tsh-Ubx-spyChIP-haltere-2


title: IPS_GABA_IgG_Rep2

description: DNA released from nuclei


title: U2OS_ChIP-seq_SFPQ_THZ1 (Spike-in)_hg19


title: IPS_GABA_IgG_Rep1

description: DNA released from nuclei


title: U2OS_TSA-seq_Input_DMSO (Spike-in)_hg19


title: U2OS_ChIP-seq_SFPQ_THZ1_hg19


title: ChIP-tsh-Ubx-spyChIP-haltere-1


title: U2OS_TSA-seq_SFPQ_DMSO (Spike-in)_rDNA repeats


title: U2OS_TSA-seq_SFPQ_DMSO (Spike-in)_hg19


title: U2OS_ChIP-seq_SFPQ_DMSO (Spike-in)_rDNA repeats


title: input-nub-Ubx-spyChIP-haltere-3


title: U2OS_TSA-seq_Input_DMSO (Spike-in)_rDNA repeats


title: input-tsh-Ubx-spyChIP-haltere-1


title: U2OS_ChIP-seq_SFPQ_DMSO (Spike-in)_hg19


title: ChIP-nub-Ubx-spyChIP-haltere-3


title: IPS_GABA_H3K27ac_t0_Rep1

description: DNA released from nuclei


title: U2OS_ChIP-seq_SFPQ_DMSO_hg19


title: G555-45

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

data_processing:
Bcl converion and demultiplexing using Illumina bcl2fastq (released version 2.18.0.12) allowing no mismatches in the index read. Adapter masked fastq files were generated.
Quality filter by FASTQC 0.11.6
Read alignment using RNA STAR (Galaxy version 2.5.2b-0). BAM files were generated.
Reads were counted using HTSeq-Count set to union mode with a minimum alignment quality of 10 (Galaxy version 0.6.1galaxy3).
Genome_build: hg19
Supplementary_files_format_and_content: xlsx file of raw read counts

source_name: ileum tissue

extract_protocol:
Surgical specimens were transferred immediately from the operating room to the surgical pathology lab where a section of full-thickness ileum was obtained from a site of active inflammation and stored in RNAlater. RNA was extracted from tissue samples using trizol reagent followed by purification with the Qiagen RNeasy Mini Kit.
The cDNA libraries were prepared using the TruSeq® Stranded mRNA Library Prep Kit (Illumina) as per the manufacturer’s instructions. Briefly, polyA RNA was purified from 200 ng of total RNA using oligo (dT) beads. The extracted mRNA fraction was subjected to fragmentation, reverse transcription, end repair, 3’– end adenylation, and adaptor ligation, followed by PCR amplification and SPRI bead purification (Beckman Coulter). The unique dual index sequences (NEXTFLEX® Unique Dual Index Barcodes, BioO Scientific) were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using Bio Analyzer High Sensitivity DNA Kit (Agilent Technologies). The libraries were pooled and diluted to 3 nM using 10 mM Tris-HCl, pH 8.5 and then denatured using the Illumina protocol. The denatured libraries were loaded onto an S1 flow cell on an Illumina NovaSeq 6000 (Illumina) and run for 2X50 cycles according to the manufacturer's instructions.

value: CD

value: ileum

value: Male

tag: smoking history

value: Never Smoked

tag: age at diagnosis

tag: age at surgery

tag: bmi


title: input-nub-Ubx-spyChIP-haltere-2

tag: genome build


title: H1_Glu_H3K27ac_t90_Rep3

description: DNA released from nuclei

source_name: WA01 (H1 ES)

tag: cell type

tag: timepoint (minutes)


title: G555-44

tag: tissue


title: IPS_GABA_H3K27ac_t0_Rep3

description: DNA released from nuclei

tag: treatment


title: IPS_GABA_H3K27ac_t0_Rep2

description: DNA released from nuclei


title: ChIP-nub-Ubx-spyChIP-haltere-2


title: Spleen IGRP+ scTCR-seq Round 2

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

data_processing:
Reads were aligned to mouse reference genome mm10
Assembly: mm10
Supplementary files format and content: Matrix files were generated using Cell Ranger (10x Genomics).

source_name: Spleen

extract_protocol:
Pancreatic islets were isolated as previously described (Foda et al., 2020). Briefly, pancreatic islets were isolated by perfusing the pancreas via the common bile duct with collagenase P solution (0.5 units/mL). The inflated pancreata were incubated for 16 minutes at 37 ºC, agitated, and washed with Hank’s balanced salt solution (Sigma Aldrich) plus 2% fetal bovine serum. Islets were hand-picked from the pancreas digestion slurry and dissociated in non-enzymatic cell dissociation buffer. Islet cell suspensions were resuspended in RPMI and incubated at 37 ºC for 1 hour. Final islet single cell suspensions were washed and resuspended in RPMI. Spleens were harvested and mechanically processed with a 70 µm filter to obtain a single-cell suspension. Red blood cell lysis was performed using ACK lysing buffer (Lonza). Splenocytes were enriched for CD8 T cells using magnetic bead-based negative selection (CD8 mouse T cell isolation kit, Miltenyi Biotec). Final spleen single-cell suspensions were washed and resuspended in RPMI. Islets and spleens were each pooled from 10 mice for both scRNA-seq experiments. Spleen and islet single cell suspensions were incubated with 5 µg/mL of FC block (anti-mouse CD16/CD32 clone 2.4G2; Bio X Cell). Cells were simultaneously incubated for 15 minutes at room temperature with MHC class I (Kd) tetramers loaded with mimotope peptide NRP-V7 (Trudeau et al., 2003). Cells were then stained with antibodies against CD45.1 (A20), CD8 (53-6.7), CD44 (IM7), and lineage markers (Lin) CD4 (RM4-5), B220 (RA3-6B2), and CD11b (M1/70) for 30 minutes at 4 ºC and were then washed and passed through a 30 µm filter. Single CD45.1+ Lin–CD8+ NRP-V7 Tet+ cells were sorted from spleen and islet samples and single CD45.1+ Lin–CD8+ NRP-V7 Tet– cells were sorted from islet samples using a FACSAria II cell sorter (BD Biosciences).
Cells were loaded into the 10x Chromium Controller (10x Genomics) for barcoding. scRNA-seq and scTCR-seq libraries were prepared using the Chromium Single Cell 5’ v3 Reagent Kit according to the manufacturer’s protocol. Libraries were quantified using a KAPA library quantification kit (Roche Sequencing) and loaded onto an Illumina NextSeq 500 sequencer. A NextSeq 500/550 High Output Kit v2.5 (150 cycles) (20024907, Illumina) with 28 cycles for read 1, 91 cycles for read 2, and 8 cycles for i7 index reads was used for scRNA-seq libraries from the first experiment (Round 1). A NextSeq 500/550 High Output Kit v2.5 (300 cycles) (20024908, Illumina) with 28 cycles for read 1, 91 cycles for read 2, and 8 cycles for i7 index reads was used for scTCR-seq libraries from Round 1. A NextSeq 500/550 High Output Kit v2 (150 cycles) (FC-404-2002, Illumina) with 26 cycles for read 1, 98 cycles for read 2, and 8 cycles for i7 index reads was used for pooled scRNA-seq and scTCR-seq libraries from the second experiment (Round 2). Raw sequencing data were downloaded from Illumina BaseSpace and demultiplexed using the “mkfastq” and “count” functions in Cell Ranger (v 6.0) (10x Genomics). scRNA-seq FASTQ files were aligned to the mm10 reference transcriptome (10x Genomics) using the “count” function while scTCR-seq FASTQ files were aligned to the GRCm38 V(D)J reference transcriptome (10x Genomics).

treatment_protocol: NOD mice were euthanized at 10-15 weeks of age

tag: strain

value: NOD/ShiLtJ (NOD)

value: Spleen


title: input-nub-Ubx-spyChIP-haltere-1


title: G555-43

tag: disease

tag: Sex

value: Current Smoker


title: Islet IGRP+ scTCR-seq Round 2

source_name: Islets

value: Islets


title: H1_Glu_H3K27ac_t30_Rep3

description: DNA released from nuclei

value: depolarization


title: Islet IGRP– scTCR-seq Round 2


title: OVCAR-3, FC-A, 6 hours, rep2 [S3341Nr17]

source_name: ovary

value: ovary

value: epithelial cell

tag: genotype

value: wt

value: Adenocarcinoma

value: 6 hours

value: FC-A (Fusicoccin A)


title: H1_Glu_H3K27ac_t0_Rep3

description: DNA released from nuclei

value: induced glutamatergic neurons


title: G555-41

value: Female


title: H1_Glu_H3K27ac_t90_Rep2

description: DNA released from nuclei


title: ChIP-nub-Ubx-spyChIP-haltere-1

value: anti-FLAG monoclonal M2


title: Spleen IGRP+ scTCR-seq Round 1


title: G555-40

value: CD

value: ileum

value: Ex-smoker


title: Dax1-Dux-KD-replicate2

first: Zuo

last: Feifei

address: Zhongguancun Street, Haidian District

institute: Tsinghua University

data_processing:
For ChIP-seq analysis, the data were trimmed using TrimGalore and then aligned to mm10 using Bowtie2.We chose MACS2 to call the peaks using the ‘‘broad peaks’’ setting for GFP-Trim66, GFP-Dax1, H3K9me3 and H3K18ac. GFP-Dax1 ChIP-seq peaks that were significantly increased in the presence of Trim66 were then identified using the DiffBind package in R. We subsequently generated bigwig files from the bam files using the Coverage function in deepTools.
RNA-seq data were mapped to the mouse reference genome (mm10) using HISAT2 (version 2.1.0) and removed duplicates using PicardTools. The levels of gene expression were calculated by Cufflinks (version 2.2.1) based on mm10 annotations. Differential testing and log2 fold change calculations were performed using TEanalysis (version 4.6), with the implementation of two biological replicates. Volcano plots were generated by ggplot2 showing the log transformed p values in the y-axis and the log2 fold-change in the x-axis.
Genome_build: mm10
Supplementary_files_format_and_content: We subsequently generated bigwig files from the bam files using the Coverage function in deepTools. For visualization purposes, we normalized the data to 1X genome coverage (mm10), ignoring PCR duplicates. Representative track diagrams were generated using the Integrated Genomics Viewer software

source_name: mouse embryonic stem cell

growth_protocol: mESCs were cultured on gelatin coated plates with 15% serum ESC culture medium and then Cells were harvested for ChIP or RNA extraction.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with GFP-trapped beads or antibody. Total RNA was extracted by commerical RNA extraction Kit.
DNA and RNA libraries were prepared for sequencing using standard Illumina protocols

value: ESCs

value: Dax1 Dux double knockdown

value: untreated


title: H1_Glu_H3K27ac_t30_Rep2

description: DNA released from nuclei


title: CTR-Dax1-Dux-KD-replicate2

value: WT


title: Islet IGRP+ scTCR-seq Round 1

value: NOD/ShiLtJ (NOD)

value: Islets


title: G555-39

value: Never Smoked


title: Dax1-Dux-KD-replicate1


title: H1_Glu_H3K27ac_t0_Rep2

description: DNA released from nuclei

value: depolarization


title: G555-38


title: Islet IGRP– scTCR-seq Round 1


title: H1_Glu_IgG_Rep1

description: DNA released from nuclei


title: CTR-Dax1-Dux-KD-replicate1


title: G555-37

value: Male


title: H1_Glu_H3K27ac_t90_Rep1

description: DNA released from nuclei


title: G555-36

value: Current Smoker


title: Dax1-sh2-replicate2

value: Dax1 knockdown


title: Islet IGRP+ scRNA-seq Round 2


title: H1_Glu_H3K27ac_t30_Rep1

description: DNA released from nuclei

value: induced glutamatergic neurons


title: Islet IGRP– scRNA-seq Round 2


title: Dax1-sh1-replicate2


title: H1_Glu_H3K27ac_t0_Rep1

description: DNA released from nuclei


title: Spleen IGRP+ scRNA-seq Round 1

value: Spleen


title: G555-34


title: Spleen IGRP+ scRNA-seq Round 2


title: H1_GABA_H3K27ac_t90_Rep3

description: DNA released from nuclei

value: induced GABAergic neurons


title: G555-32

value: CD

value: Female


title: Islet IGRP+ scRNA-seq Round 1


title: Dax1-sh1-replicate1


title: H1_GABA_H3K27ac_t30_Rep3

description: DNA released from nuclei


title: G555-29

value: ileum


title: CTR-shDax1-replicate2

value: ESCs


title: Islet IGRP– scRNA-seq Round 1


title: G555-35


title: H1_GABA_H3K27ac_t0_Rep3

description: DNA released from nuclei


title: Dax1-sh2-replicate1


title: G555-28


title: CTR-shDax1-replicate1


title: G555-27


title: H1_GABA_IgG_Rep2

description: DNA released from nuclei


title: GFP-TRIM66-replicate2

value: TRIM66 overexpression


title: H1_GABA_H3K27ac_t90_Rep2

description: DNA released from nuclei