title: Mix1_0-1_R1_P1_E_pool1

extract_protocol:
Cells were lysed and RNA was extracted according to BioSpyder's protocol
Total RNA input of 100 ng was used to build whole transcriptome Templated Oligo-Sequencing libraries using the TempO-Seq Human Whole Transcriptome 2.1 kit (BioSpyder, Carlsbad, CA); RNA was diluted to 50 ng/ul in 1 x TempO-Seq lysis buffer and 2 ul of this mixture was used as input. Briefly, detector oligos (DO) targeting whole transcriptome were annealed to mRNA. Each transcript is targeted by a pair of DOs. Bound DOs were ligated to form one contiguous sequence, while unbound DOs were eliminated by nuclease digestion. The ligated DOs were indexed and amplified by PCR, after which 96 [?] individual libraries were pooled to create a single pool for sequencing on the [instrument] (Illumina).
A 96-sample Human Whole Transcriptome Template Oligo-Sequencing (TempO-Seq) kit, which contains 50 nt detector oligos that target mRNA transcripts, was used to generate sequencing libraries.


title: PJS1-2_1

status: Public on Jun 30 2025

type: SRA

city: Chicago

first: Tahir

last: Khan

address: 255 E Chicago Street

country: USA

institute: Lurie Childrens Hospital

library_source: transcriptomic

data_processing:
The lllumina HiSeq 4000 sequencer was used to sequence the libraries with the production of single-end, 50 bp reads at the depth of 40-50 M reads per sample. The quality of reads, in FASTQ format, was evaluated using FastQC.Reads were trimmed to remove Illumina adapters from the 3’ ends using cutadapt.  Trimmed reads were aligned to the human genome (hg38) using STAR.
Assembly: hg38
Supplementary files format and content: Read counts for each gene were calculated using htseq-count in conjunction with a gene annotation file for hg38 obtained from Ensembl (http://useast.ensembl.org/index.html).Normalization and differential expression were calculated using DESeq2 that employs the Wald test

molecule: total RNA

organism: Homo sapiens

source_name: Skin

extract_protocol:
RNeasy Mini Kit
The Illumina Stranded mRNA Prep Kit was used to prepare sequencing libraries from 100 ng of high-quality RNA samples (all samples had RIN>8). The kit procedure was performed without modifications. This procedure includes mRNA purification and fragmentation, cDNA synthesis, 3’ end adenylation, Illumina adapter ligation, library PCR amplification and validation.

tag: tissue

value: Skin

tag: cell line

value: Fibroblast

tag: genotype

value: STK11 del


title: Control 1_3

value: WT


title: Control_3

city: Taipei

first: Hsi

last: Chang

state: Xinyi

address: No. 250, Wuxing Street

department: Pediatrics

country: Taiwan

institute: School of Medicine, College of Medicine, Taipei Medical University

data_processing:
Initial data analysis included quality control (FastQC), read trimming (Trimmomatic), alignment (HISAT2), quantification (featureCounts), and differential expression analysis using DESeq2 with  Relative Log Expression (RLE) normalization were conducted by Biotools (Tursi Biotechnology Co., New Taipei, Taiwan)
Assembly: NCBI-NR database using DIAMOND
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Mus musculus

extract_protocol:
RNA from C2C12 myoblasts was isolated using the EasyPrep Cell & Bacteria RNAprep Kit (Biotools Co., Taiwan). Reverse transcription was performed using the TOOLSquant II Fast RT Kit (Biotools Co.) to synthesize cDNA, which served as the template for PCR analyses.
Library preparation were conducted by Biotools (Tursi Biotechnology Co., New Taipei, Taiwan)

tag: cell type

value: skeletal muscle

tag: treatment

value: Control


title: Input DR_3

city: Wu'xi

first: Yu

last: Xin

state: Jiangsu

address: 1800 Lihu Road

country: China

institute: Jiangnan University

description:
DR_3
diabetic retinopathy

data_processing:
The sequencing platform is novaseq 6000. After the data is off the machine, RTA (real time analysis) is used to convert it into the original BCL file, and the version is v3.4.4; It is split by bcl2fastq (btq) software and converted into FQ, version v2.19. Fastp software is used for quality control, version 0.19.7, involving the parameter fastp-G-Q5-U50-N 15-L150.
Assembly: hg38
Supplementary files format and content: Fastq
Supplementary files format and content: tab-delimited text file includes raw counts and peaks of each sample

source_name: vitreous bodies

extract_protocol:
Vitreous body samples were obtained during pars plana vitrectomy of 90 diabetic retinopathy patients (DR group) and  90 non-diabetic retinopathy patients (NC group, including rhegmatogenous retinal detachment, macular hole, epimacular membrane). 30 samples of each group were combined and entitled as DR_1-3 and NC_1-3, respectively.  These samples were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries. The m6A RNA was concentrated via immunoprecipitation with anti-m6A antibody before sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: vitreous bodies


title: Input NC_1

description:
NC_1
non-diabetic retinopathy


title: Mix1_10_R1_P1_E_pool1

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

library_source: other

data_processing:
The BCL files were converted to FASTQ files and the reads were demultiplexed using bcl2fastq v. 2.20.0.422. The FASTQ files were were processed using the R-ODAF pipeline (https://github.com/R-ODAF/R-ODAF_Health_Canada). Briefly:
Reads were trimmed and filtered with fastp (--cut_front_window_size 1, --cut_front_mean_quality 3, --cut_tail_window_size 1, --cut_tail_mean_quality 3, --cut_right_window_size 4, --cut_right_mean_quality 15, --length_required 50). Passing reads were aligned with STAR against reference fasta and gtf files generated from Biospyder's manifest file (--alignEndsType EndToEnd,--scoreDelOpen  -1000000, --scoreInsOpen  -1000000, --outFilterMultimapNmax  1,--outFilterMismatchNmax 2). Quantification was performed in R using the qAlign function from the QuasR package.
Passing reads were aligned with STAR against reference fasta and gtf files generated from Biospyder's manifest file (--alignEndsType EndToEnd,--scoreDelOpen  -1000000, --scoreInsOpen  -1000000, --outFilterMultimapNmax  1,--outFilterMismatchNmax 2).
Quantification was performed in R using the qAlign function from the QuasR package.
Assembly: GTF file generated from probe sequences in Biospyder manifest file
Supplementary files format and content: Comma-delimited table containing read counts per TempO-Seq probe

molecule: other

growth_protocol: MCF-7 cells were maintained in complete media (phenol red DMEM + 10% FBS + 1% P/S) in 10 cm culture dishes at 37°C in a humidified atmosphere (5% CO2). Cells were depleted of estrogen for 96h in phenol red-free DMEM supplemented with CS 5% FBS + 1% P/S. 48h into the estrogen depletion cells were plated in 96-well plates prior to chemical exposure.

treatment_protocol: After estrogen depletion, cells were exposed to chemicals (dissolved in DMSO, final DMSO concentration 0.1%) under serum free conditions (phenol red-free DMEM + 2% BSA + 1%) for 48h.

tag: plate

tag: chemical

value: Mix 1

tag: dose


title: Control 1_1


title: CollagenI_1

value: Collagen I


title: Control 1_2


title: Mix1_0-01_R1_P1_E_pool1


title: CW44 bacteria, meropenem + tobramycin, 191hr, rep3

city: Parkville

first: Cornelia

last: Landersdorfer

state: Vic

address: 399 Royal Parade

department: Monash Institute of Pharmaceutical Sciences

country: Australia

institute: Monash University

description:
Hyp05_1_and_191hrPAO1.csv
Hyp02_F_191hr

data_processing:
Libraries were sequenced on an Illumina NextSeq500 instrument (Micromon, Monash University) generating single end 75bp reads.
Raw fastq files were trimmed using trimmomatic (v 0.36)
aligned to the P. aeruginosa strain PAO1 NCBI reference NC_002516.2  using Rsubread (v 1.30.1)
Reads were quantified using featureCounts producing the raw genes count matrix and various quality control metrics
Raw counts were then analyzed with Degust (a web tool which performs normalization using trimmed mean of M values (TMM)) and differential expression analysis using limma/voom with quality weights.
Assembly: P. aeruginosa strain PAO1 NCBI reference NC_002516.2
Supplementary files format and content: raw gene counts, text file, tab separated
Library strategy: Tru-seq

organism: Pseudomonas aeruginosa

source_name: Gram-negative bacteria

growth_protocol: The HFIM setup utilized cellulosic cartridges (C3008-1; FiberCell Systems Inc., Frederick, MD, USA) in a 36°C humidified incubator. Frozen isolates (stored at -80°C) were streaked onto cation adjusted mueller hinton agar and incubated for 48h at 36°C. Bacterial colonies were grown in CAMHB  overnight at 36°C to prepare the bacterial stock solution for each solate. The optical density of the stock solution was measured spectrophotometrically and diluted to a targeted initial inoculum of ~10^*(7.6)CFU/mL. Each HFIM cartridge was injected with 17mL of the bacterial suspension.

extract_protocol:
bacterial cells harvested by centrifugation (9,000×g, 4°C, 10min) and resuspended in 1mL  of RNAlater RNA stabilization reagent (Qiagen). After incubation for 5 min on ice, cells were centrifuged (5,000×g, room temperature, 10min) and supernatant was completely removed. Pellets were immediately stored at -80°C.  The cell pellet was resuspended in 200μL of lysis solution (40μg/μL proteinase K, 2mg/mL lysozyme, 40U/μL protector RNase inhibitor [Roche]) and incubated at room temperature for 10min with intermittent shaking. Total RNA was purified by using the RNeasy minikit (Qiagen) with DNase treatment according to the manufacturer's instructions.  RNA samples were quantified and analyzed for DNA contamination using the Qubit kit (Invitrogen) and visualized by gel electrophoresis. The rRNA was removed using the Ribo-Zero magnetic kit (Illumina) according to the manufacturer's instructions.
The TruSeq RNA sample preparation kit (Illumina) was used to construct cDNA libraries, with library validation, normalization, and pooling performed by Micromon (Monash University).

treatment_protocol: meropenem 1 2g every 8 h via 3-h infusion, and tobramycin 10mg/kg every 24 h via 0.5-h infusion. The simulated half-lives for meropenem and tobramycin in the HFIM were 0.8h and 3.5h, respectively. 1mL samples for transcriptomics were taken at 1h and 191h and stored on ice.

value: Gram-negative bacteria

tag: strain

value: meropenem and tobramycin

tag: time point


title: Mix1_0-001_R1_P1_E_pool1


title: MV-4-11 cells, treated by cytarabine (5 µM), and then treated with FL-Fc-DM1 (1 nM) 3

city: Shenzhen

first: Dengyang

last: Zhang

state: Guangdong

address: Zhenmei road, guangming district

institute: Seventh affiliated hospital, Sun Yat-sen University

description: Library name: Sample 15

data_processing:
Reads obtained from the sequencing machines, including raw reads were further filtered by fastp (version 0.18.0). Reads containing adapters, containing more than 10% of unknown nucleotides, and low-quality reads containing more than 50% of low-quality bases were removed.
rRNA-mapped reads were also removed. The paired-end clean reads were mapped to the human reference genome using HISAT2.2.4. The mapped reads of each sample were assembled using StringTie v1.3.1 in a reference-based approach. The FPKM method was used to eliminate the influence of different gene lengths and sequencing data amount on the calculation of gene expression. RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples).  The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥2 were considered differentially expressed genes/transcripts.
Assembly: rRNA-mapped reads were also removed. The paired-end clean reads were mapped to the human reference genome using HISAT2.2.4. The mapped reads of each sample were assembled using StringTie v1.3.1 in a reference-based approach. The FPKM method was used to eliminate the influence of different gene lengths and sequencing data amount on the calculation of gene expression. RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples).  The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥2 were considered differentially expressed genes/transcripts.
Supplementary files format and content: Microsoft excel format

molecule: polyA RNA

source_name: Blood

growth_protocol: MV-4-11 cells were cultured in RPMI 1640 medium supplemented with 10% FBS, in a 5% CO2, 37 °C incubator.

extract_protocol:
Cells from each group were extracted by using the Trizol method. RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA) and checked using RNase-free agarose gel electrophoresis.
Total mRNA was enriched by Oligo(dT) beads. Then, the enriched mRNA was fragmented and reverse-transcripted into cDNA with random primers. Second-strand cDNA was synthesized by DNA polymerase I. The cDNA fragments were purified with the QiaQuick PCR extraction kit (Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size-selected by agarose gel electrophoresis, PCR amplified and sequenced using Illumina HiSeq2500 by Gene Denovo Biotechnology Co. (China).

treatment_protocol: In the control group, MV-4-11 cells were cultured for 4 days. In the cytarabine group, MV-4-11 cells were treated with 2/5 µM cytarabine for 4 days. In the FL-Fc-DM1 treatment group, MV-4-11 cells were treated by cytarabine (2/5 µM) for 3 days and then treated with FL-Fc-DM1 (1 nM) for another 24 hours in the absence of cytarabine.

value: Blood

value: MV-4-11 cell line

value: The MV4-11 cell line was established by Rovera and associates from the blast cells of a 10-year-old male with biphenotypic B-myelomonocytic leukemia.

value: wild type

value: treated by cytarabine (5 µM) for 3 days, and then treated with FL-Fc-DM1 (1 nM) for 1 day in the absence of cytarabine


title: Control_2


title: Control_1


title: Input DR_1

description:
DR_1
diabetic retinopathy


title: MV-4-11 cells, treated by cytarabine (5 µM), and then treated with FL-Fc-DM1 (1 nM) 2

description: Library name: Sample 14


title: RMC44_Post, replicate1, BulkRNAseq

city: Houston

first: Pavlos

last: Msaouel

state: Texas

address: 1155 Pressler Street, Unit 1374

department: Genitourinary Medical Oncology

institute: The University of Texas MD Anderson Cancer Center

data_processing:
ScRNA - Sequence data was put through the 10X genomic cell ranger 6.0.1 pipeline. QC and Fastq files were obtained and checked for data quality, and Fastq files were used to do further analysis.
BulkRNA - Raw RNA Sequence data was processed by an in-house RNA Seq data analysis pipeline, which, among other tools uses the STAR aligner (Dobin, Davis et al. 2013) to align raw reads to hg19 version of Human reference genome, featureCounts (Liao, Smyth et al. 2014) to quantify aligned reads with to produce raw counts, Oncofuse (Shugay, Ortiz de Mendibil et al. 2013) to filter and prioritize fusion candidate generated by the STAR aligner, and FastQC and QualiMap (Okonechnikov, Conesa et al. 2016) to evaluate quality of raw reads and feature counts. We used a bioconductor package DESeq2 (Love, Huber et al. 2014) (with adjusted p-value < 0.05) to identify differentially expressed genes between TP53 mutated (4) and normal (4) samples. We used hierarchical clustering and k-means unsupervised clustering algorithms to cluster samples according to their RNASeq expression profiles. We used VirusFinder (Wang, Jia et al. 2013)(version 2.0) to align reads that do not map to the human reference genome to a viral database that contains viruses of 32,102 known classes (Bhaduri, Qu et al. 2012), and in particular all different variations of the Human Papilloma Virus and Polyoma Virus.
Assembly: GRCh38(ScRNA)/hg19(BulkRNA)
Supplementary files format and content: Tab-separated values and matrix files

source_name: Retroperitoneal lymph node

extract_protocol:
ScRNA - Tumor biopsy samples were thoroughly minced to size < 1mm and transferred to 2.0ml Eppendorf tube containing 0.1 mg/ml Liberase TM and 0.2 mg/ml DNase I (MillieporeSigma) in RPMI1640/0.1% BSA. Tubes were then incubated at 37 degrees Celsius for 15 minutes with gentle rotation. Samples were filtered through 70 µm filters, spun down, and red blood cell lysis was performed with ACK lysis buffer (ThermoFisher, catalog #A1049201). Cell viability will be determined with Trypan blue exclusion assay.
BulkRNA - RNA was extracted by NORGEN Total RNA Purification Kit (Cat. 37500) (NORGEN BIOTEK CORP). The extracted RNA was treated with DNase I to get rid of nay genomic DNA residues. The treated RNA then was cleaned-up using the AMPure XP beads (Beckman Coulter Life Sciences) and eluted into 1x TE buffer. The purified RNA was quantified using Quant-iT™ RiboGreen™ RNA Assay Kit (ThermoFisher SCIENTIFIC) and the RNA quality was accessed using Agilent RNA 6000 Nano Kit and the 2100 Bioanalyzer Instrument (Agilent Technologies). The cDNA was prepared from the extracted total RNA using Ovation® RNA-Seq System V2 (NuGEN). Amplification is initiated at the 3’ end as well as randomly throughout the transcriptome in the sample. The prepared cDNA was quantified using Quant-iT™ PicoGreen™ dsDNA Assay Kit (ThermoFisher SCIENTIFIC) and quality was accessed using Genomic DNA ScreenTape and Reagents on the Tapestation 4200 (Agilent Technologies)
ScRNA - Samples with >60% viability were further processed on Chromium iX (10x Genomics) to generate 5' v2 gel beads-in-emulsions (GEMs). The barcoded cDNA was purified and amplified for the final generation of 10x single cell RNA sequencing (scRNAseq) libraries. After quantification with a high sensitivity DNA chip run on a Bioanalyzer 2100 system (Agilent), the libraries were sequenced as recommended by the manufacturer (approximately 50,000 reads per cell) on a NovaSeq 6000 system.
BulkRNA - Up to 200 ng of each cDNA sample based on the PicoGreen quantification was sheared (mechanically fragmented) using the E220 Focused-ultrasonicator Covaris (Covaris). The sonication was performed under the following conditions: Peak Incident Power 200, Duty Cycle 25%, Cycles per Burst 50, and duration 10 seconds for 120 iterations. To ensure the proper fragment size, samples were examined on TapeStation 4200 using the DNA High Sensitivity kit (Agilent Technologies). The sheared cDNA was proceeded to library preparation using SureSelect XT Low Input Reagent Kit with indexes 1-96 (Agilent Technologies) as automated method on the Sciclone G3 NGSx Workstation (PerkinElmer, Inc.). This protocol consists of 3 enzymatic reactions for end repair, A-tailing and Adaptor ligation, followed by barcode insertion by PCR using Herculase II Fusion DNA Polymerase (8 to 14 cycles, based on input DNA quality and quantity). PCR primers were removed by using 1x volume of Agencourt AMPure PCR Purification kit (Agencourt Bioscience Corporation). The quality and quantity of the prepared libraries were evaluated using TapeStation 4200 and the DNA High Sensitivity kit (Agilent Technologies) to verify correct fragment size and to ensure complete removal of primer dimers.

value: Retroperitoneal lymph node

value: Post-NI


title: CW44 bacteria, tobramycin, 191hr, rep3

description:
Hyp05_1_and_191hrPAO1.csv
Hyp02_D_191hr

value: tobramycin


title: CollagenI_2


title: CW44 bacteria, meropenem + tobramycin, 191hr, rep1

description:
Hyp05_1_and_191hrPAO1.csv
Hyp05_G_191hr


title: MV-4-11 cells, treated by cytarabine (5 µM), and then treated with FL-Fc-DM1 (1 nM) 1

description: Library name: Sample 13


title: CW44 bacteria, tobramycin, 191hr, rep2

description:
Hyp05_1_and_191hrPAO1.csv
Hyp05_F_191hr


title: RMC25_Post, replicate1, BulkRNAseq

source_name: Lung

value: Lung


title: CW44 bacteria, tobramycin, 191hr, rep1

description:
Hyp05_1_and_191hrPAO1.csv
Hyp05_E_191hr


title: Input DR_2

description:
DR_2
diabetic retinopathy


title: Mut_RNA_1

city: 成都

first: ping

last: he

address: 17 Renmin South Road, Wuhou District, Chengdu

institute: sichuan university

data_processing:
Raw FASTQ files were first quality controlled using FastQC (v0.12.1), followed by adaptor trimming with fastp (0.23.4). The cleaned reads were then aligned to the mouse reference genome (mm10) using STAR (v2.7.1a). Data normalization and differential expression analysis were performed with DESeq2 (v1.38.3).
Assembly: mm10
Supplementary files format and content: tab-delimited text files including genes normalized data.

source_name: Brain

extract_protocol:
Primary mouse neurospheres were lysed with TRIzol (Thermo Fisher Scientific) and snap-frozen in liquid nitrogen after repeated blowing with pipettes until no clumps of cells could be seen.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L). The library fragments were purified with AMPure XP system (Beverly, USA). PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent 5400 system (Agilent, USA).

value: Brain

value: Mouse primary embryonic NSCs


title: RMC47_Baseline, replicate1, BulkRNAseq

source_name: Abdominal mass

value: Abdominal mass

value: Baseline


title: CW44 bacteria, meropenem + tobramycin, 191hr, rep2

description:
Hyp05_1_and_191hrPAO1.csv
Hyp05_H_191hr


title: MV-4-11 cells, treated by cytarabine (2 µM), and then treated with FL-Fc-DM1 (1 nM) 2

description: Library name: Sample 11

value: treated by cytarabine (2 µM) for 3 days, and then treated with FL-Fc-DM1 (1 nM) for 1 day in the absence of cytarabine


title: MV-4-11 cells, treated by cytarabine (2 µM), and then treated with FL-Fc-DM1 (1 nM) 1

description: Library name: Sample 10


title: CW44 bacteria, meropenem, 191hr, rep3

description:
Hyp05_1_and_191hrPAO1.csv
Hyp02_B_191hr

value: meropenem


title: RMC35_Baseline, replicate1, BulkRNAseq


title: WT_RNA_3

value: WT


title: CW44 bacteria, meropenem, 191hr, rep2

description:
Hyp05_1_and_191hrPAO1.csv
Hyp05_D_191hr

value: Gram-negative bacteria


title: Mut_RNA_4


title: CW44 bacteria, meropenem, 191hr, rep1

description:
Hyp05_1_and_191hrPAO1.csv
Hyp05_C_191hr


title: MV-4-11 cells, treated by cytarabine (5 µM) 2

description: Library name: Sample 8

value: Blood

value: cytarabine (5 µM) for 4 days


title: Mut_RNA_3


title: RMC61, replicate1, scRNAseq

description:
10x Genomics
ScRNA_count_matrix.tsv

library_source: transcriptomic single cell

source_name: Liver

value: Liver


title: RMC35_Post, replicate1, BulkRNAseq

source_name: Pleura

value: Pleura


title: CW44 bacteria, untreated, 191hr, rep3

description:
Hyp05_1_and_191hrPAO1.csv
Hyp02_A_191hr

value: untreated


title: WT_RNA_1


title: RMC57, replicate1, scRNAseq

description:
10x Genomics
ScRNA_count_matrix.tsv


title: Mut_RNA_2


title: MV-4-11 cells, treated by cytarabine (5 µM) 1

description: Library name: Sample 7

value: MV-4-11 cell line

value: The MV4-11 cell line was established by Rovera and associates from the blast cells of a 10-year-old male with biphenotypic B-myelomonocytic leukemia.

value: wild type


title: Mut_CUT&Tag_IgG

library_source: genomic

data_processing:
Reads were aligned to the mouse mm10 reference genome using Bowtie2 (v1.2.2) with the parameters: --local, --very-sensitive, --no-mixed, --no-discordant, --phred33, -I 10, and -X 700. PCR duplicates were removed using the MarkDuplicates from GATK (v4.1.3) using the option -REMOVE_DUPLICATES = true. H3K27ac peaks were called using SEACR (v1.3), and peak annotation was performed with R package ChIPseeker (v1.32.1). Normalized bigwig files were generated with bamCoverage from deepTools (v3.5.3) with bins per million (BPM) normalization.
Assembly: mm10
Supplementary files format and content: bed files including peak region for each CUT&Tag target. bigwig files  for each CUT&Tag target. tab-delimited text files including peak region and peak counts .
Library strategy: CUT&Tag

molecule: genomic DNA

extract_protocol:
The Phf23+/+ and  Phf23-/- neurospheres were dissociated enzymatically into single cells,
Use NovoNGS CUT&Tag3.0 High Sensitivity Kit. The single cells were treated with ConA beads, incubated with H3K27ac antibody (1:50, rabbit, abcam, ab4729) overnight at 4°C, incubated with secondary antibody for 1 hour at room temperature, and incubated with pAG-Tn5 for 1 hour. Fragment DNA at 37°C for 1 hour and stop with 10% SDS at 55°C for 10 min. Extract DNA fragments and amplify libraries. The libraries were quality-checked on the Agilent5400.

tag: antibody

value: IgG


title: WT_RNA_4

value: Brain


title: RMC71, replicate1, scRNAseq

description:
10x Genomics
ScRNA_count_matrix.tsv

source_name: Kidney

value: Kidney


title: CW44 bacteria, meropenem + tobramycin, 1hr, rep3

description:
Hyp05_1_and_191hrPAO1.csv
Hyp02_F_1hr

value: meropenem and tobramycin


title: MV-4-11 cells, treated by cytarabine (2 µM) 2

description: Library name: Sample 5

value: cytarabine (2 µM) for 4 days


title: CW44 bacteria, untreated, 191hr, rep1

description:
Hyp05_1_and_191hrPAO1.csv
Hyp05_A_191hr


title: RMC25_Baseline, replicate1, BulkRNAseq

value: Lung

value: Baseline


title: RMC53, replicate1, scRNAseq

description:
10x Genomics
ScRNA_count_matrix.tsv


title: Mut_CUT&Tag_3

value: Mouse primary embryonic NSCs


title: WT_RNA_2

value: WT


title: MV-4-11 cells, treated by cytarabine (5 µM) 3

description: Library name: Sample 9

value: Blood


title: RMC60, replicate1, scRNAseq

description:
10x Genomics
ScRNA_count_matrix.tsv


title: CW44 bacteria, meropenem + tobramycin, 1hr, rep2

description:
Hyp05_1_and_191hrPAO1.csv
Hyp05_H_1hr

value: Gram-negative bacteria


title: MV-4-11 cells, treated by cytarabine (2 µM) 1

description: Library name: Sample 4


title: Mut_CUT&Tag_1


title: MV-4-11 cells, control, cultured for 4 days 3

description: Library name: Sample 3


title: Mut_CUT&Tag_2


title: CW44 bacteria, meropenem + tobramycin, 1hr, rep1

description:
Hyp05_1_and_191hrPAO1.csv
Hyp05_G_1hr


title: WT_CUT&Tag_IgG


title: CW44 bacteria, untreated, 191hr, rep2

description:
Hyp05_1_and_191hrPAO1.csv
Hyp05_B_191hr


title: MV-4-11 cells, control, cultured for 4 days 2

description: Library name: Sample 2


title: WT_CUT&Tag_3


title: RMC56, replicate1, scRNAseq

description:
10x Genomics
ScRNA_count_matrix.tsv

value: Liver


title: RMC49, replicate1, scRNAseq

description:
10x Genomics
ScRNA_count_matrix.tsv

source_name: Lymph node

value: Lymph node


title: MV-4-11 cells, control, cultured for 4 days 1

description: Library name: Sample 1

value: untreated


title: CW44 bacteria, tobramycin, 1hr, rep2

description:
Hyp05_1_and_191hrPAO1.csv
Hyp05_F_1hr

value: tobramycin


title: MV-4-11 cells, treated by cytarabine (2 µM) 3

description: Library name: Sample 6

value: MV-4-11 cell line

value: The MV4-11 cell line was established by Rovera and associates from the blast cells of a 10-year-old male with biphenotypic B-myelomonocytic leukemia.


title: RMC46, replicate1, scRNAseq

description:
10x Genomics
ScRNA_count_matrix.tsv


title: Molm-13 cells, treated by cytarabine (1 µM), and then treated with FL-Fc-DM1 (1 nM) 3

description: Library name: Sample 15

growth_protocol: Molm-13 cells were cultured in RPMI 1640 medium supplemented with 10% FBS, in a 5% CO2, 37 °C incubator.

treatment_protocol: In the control group, Molm-13 cells were cultured for 4 days. In the cytarabine group, Molm-13 cells were treated with 0.5/1 µM cytarabine for 4 days. In the FL-Fc-DM1 treatment group, THP-1 cells were treated by cytarabine (0.5/1 µM) for 3 days and then treated with FL-Fc-DM1 (1 nM) for another 24 hours in the absence of cytarabine.

value: Molm-13 cell line

value: Established from the peripheral blood of a 20-year-old man with acute myeloid leukemia AML FAB M5a at relapse in 1995 after initial myelodysplastic syndrome (MDS, refractory anemia with excess of blasts, RAEB); described to carry internal tandem duplication of FLT3.

value: wild type

value: treated by cytarabine (1 µM) for 3 days, and then treated with FL-Fc-DM1 (1 nM) for 1 day in the absence of cytarabine


title: WT_CUT&Tag_2

value: Brain


title: RNA-seq_S10D_Post-mit_7h_Repeat_2

city: Bengaluru

first: Dimple

last: Notani

state: Karnataka

address: GKVK

country: India

institute: National Centre for Biological Sciences

data_processing:
For ChIP-seq analysis; fastq files were aligned to hg19 using Bowtie2 and read depth and input normalised using SAM tools, followed by processing the BAM files with MACS2 (default with broad mode) and bigwig conversion. The regions were called a using a method involving stitching of sliding window bins in genome based on H3S10p coverage.
For ATAC-seq analysis; fastq files were trimmed for adapter sequence and aligned to hg19 using Bowtie2 with read depth normalisation using SAM tools, followed by processing the BAM files with MACS2 and bigwig conversion.
For RNA-seq analysis; fastq files were subjected to Trimmomatic and FASTQC was done to check read quality. The reads were then aligned to hg19 using HISAT2. BAM files obtained were read depth normalised and FeatureCounts was used with default settings to get coverage at all GeneIDs. The fold changes between different lines were calculated using DeSeq2.
Assembly: hg19
Supplementary files format and content: bigwig: coverage file
Supplementary files format and content: bed, tabular: coordinate/ text file

source_name: Cervix; Uterus

growth_protocol: HeLa and MCF7 cell lines were cultured in DMEM with 10% FBS and 1% Pen-Strep at 37℃ and 5% CO2 in a humidified incubator. The cells were passaged every 3-4 days.

extract_protocol:
For ChIP-seq, genomic DNA was isolated as per standard ChIP-seq protocol. For ATAC-seq, genomic DNA was isolated as per standard ATA-seq protocol, following viable nuclei isolation. For RNA-seq, total RNA was isolated using trizol as per the reagent manual.
ChIP-seq and ATAC-seq library was prepared using the NEBNext® Ultra™II DNA Library Prep kit with Sample Purification Beads (Catalogue-E7103L) following the manufacturer's protocol. For total RNA-seq, rRNA depletion was done using NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) with RNA Sample Purification Beads(Catalog no-E7405L) and library was prepared using NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads(Catalog no-E7765L).

treatment_protocol: HeLa and MCF-7 cells were treated with DMSO or Nocodazole(100ng/ml) for 24h for mitotic arrest and H3S10p ChIP-seq. HeLa stable lines: H3S10, H3S10A and H3S10D were treated with Thymidine(2mM) for 24h, followed by wash and Doxycycline(1ug/ml) for 8h and finally washed and treated with Nocodazole(100ng/ml) for mitotic arrest with induction and HA, H3, H3S10p ChIP-seq. For RNA-seq and ATAC-seq, the stables lines were subjected to mitotic arrest with induction as mentioned, and followed by a mitotic release into fresh media for 7h.

value: Cervix; Uterus

value: HeLa

value: epithelial cell

value: Thymidine 24h, wash and Doxycycline 8h, wash and Nocodazole 12h, wash and release 7h

tag: chip antibody


title: WT_CUT&Tag_1

value: Mouse primary embryonic NSCs

value: WT


title: Molm-13 cells, treated by cytarabine (1 µM), and then treated with FL-Fc-DM1 (1 nM) 2

description: Library name: Sample 14

value: Blood


title: CW44 bacteria, tobramycin, 1hr, rep1

description:
Hyp05_1_and_191hrPAO1.csv
Hyp05_E_1hr

value: Gram-negative bacteria


title: CW44 bacteria, meropenem, 1hr, rep3

description:
Hyp05_1_and_191hrPAO1.csv
Hyp02_B_1hr

value: meropenem


title: RMC66, replicate1, scRNAseq

description:
10x Genomics
ScRNA_count_matrix.tsv

value: Liver

value: Baseline


title: Med13L KO_cortex_E13.5, scRNA

city: SHanghai

first: Yulan

last: Zhao

address: North Zhongshan Rd 3663#

institute: East China Normal University

description: 10X Genomics

data_processing:
For bulk RNA-seq, quality control of the RNA-seq data was performed using FastQC (version 0.11.9). Paired-end reads were trimmed to remove adapters and low-quality reads using skewer (version 0.2.2). Clean reads were aligned to UCSC mm10 mouse genome using STAR (version 25.2b) with default parameters. The number of mapped reads was counted using stringtie (version 2.2.1). For scRNA-seq, CellRanger 6.6.1 was applied for preliminary data analysis. Raw data from single-cell RNA-seq libraries were first trimmed to remove the template switch oligo (TSO) sequence and poly(A) tail sequence. Reads with adaptor contaminants and low-quality bases were removed. Clean reads were aligned to the reference genome. Gene expression levels were quantified as transcripts per million (TPM). Valid barcodes and Unique Molecular Identifiers (UMIs) were used to generate the gene-barcode matrix for single cells. Seurat was used for quality control and data analysis in R.
Assembly: mm10
Supplementary files format and content: Tab includes raw counts for each sample
Supplementary files format and content: Tab-seperated value files and matrix files

source_name: embryonic brain cortex

growth_protocol: Med13L Het mice were inbred and E13.5 embryonic cortex were isolated after genotyping.

extract_protocol:
For bulk RNA sequencing, total mRNA from mouse cortical tissues was isolated using the RNAiso Plus kit (Takara, #9109) on ice. For scRNA sequencing, cortex from 5 embryos of the same genotype from 3 litters were pooled into 5 ml tissue storage solution (Miltenyi Biotec, Inc, MD, USA) on ice and carefully cut into small pieces of 1-3 mm. Tissue samples were subjected to enzymatic digestion with 0.25% Trypsin-EDTA (Thermo Fisher Scientific) at 37°C in an atmosphere of 5% CO2 for up to 30 min. Cell suspensions were centrifuged at 300 × g for 5 min at 4℃. The pellets were further digested in basal media supplemented with 0.2% type II collagenase (Sigma-Aldrich) at 37°C for up to 4 h. Isolated cells were filtered through 70 mm nylon filters (BD), washed twice with sterile PBS. Samples with a cell density of 700-1200 cells/ml and a viability higher than 85% were proceeded for scRNA-seq.
For bulk RNA sequencing, RNA-seq libraries were constructed using the VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version, NR616). For scRNA sequencing, Droplet-based scRNA-seq was performed using the 10x Genomics Chromium Single Cell 3′ Reagents Kit (v3.1). The single cell samples were passed through a 40 μm cell strainer and counted using a hemocytometer with trypan blue. Subsequently, the single cell suspension, Gel Beads and oils were added to the 10x Genomics single-cell A chip. After droplet generation, samples were transferred into PCR tubes and reverse transcription was performed using a T100 Thermal Cycler (Bio-Rad). After reverse transcription, cDNA was recovered using a recovery agent, provided by 10x Genomics, followed by silane DynaBead clean-up as outlined in the user guide. Before clean-up using SPRIselect beads, cDNA was amplified for 10 cycles. Libraries were submitted to 150 bp paired-end sequencing on an Illumina Novaseq 6000 platform, yielding 150 G of sequencing data per sample.

value: embryonic brain cortex

value: Med13L KO


title: Med13L Het_cortex_E13.5, scRNA

description: 10X Genomics

value: Med13L Het


title: Molm-13 cells, treated by cytarabine (0.5 µM), and then treated with FL-Fc-DM1 (1 nM) 3

description: Library name: Sample 12

value: Molm-13 cell line

value: Established from the peripheral blood of a 20-year-old man with acute myeloid leukemia AML FAB M5a at relapse in 1995 after initial myelodysplastic syndrome (MDS, refractory anemia with excess of blasts, RAEB); described to carry internal tandem duplication of FLT3.

value: wild type

value: treated by cytarabine (0.5 µM) for 3 days, and then treated with FL-Fc-DM1 (1 nM) for 1 day in the absence of cytarabine


title: CW44 bacteria, tobramycin, 1hr, rep3

description:
Hyp05_1_and_191hrPAO1.csv
Hyp02_D_1hr

value: tobramycin


title: CW44 bacteria, meropenem, 1hr, rep2

description:
Hyp05_1_and_191hrPAO1.csv
Hyp05_D_1hr


title: Molm-13 cells, treated by cytarabine (1 µM), and then treated with FL-Fc-DM1 (1 nM) 1

description: Library name: Sample 13

value: treated by cytarabine (1 µM) for 3 days, and then treated with FL-Fc-DM1 (1 nM) for 1 day in the absence of cytarabine


title: Molm-13 cells, treated by cytarabine (0.5 µM), and then treated with FL-Fc-DM1 (1 nM) 2

description: Library name: Sample 11


title: CW44 bacteria, meropenem, 1hr, rep1

description:
Hyp05_1_and_191hrPAO1.csv
Hyp05_C_1hr


title: RNA-seq_S10A_Post-mit_7h_Repeat_2

value: Cervix; Uterus

value: HeLa

value: epithelial cell

value: Thymidine 24h, wash and Doxycycline 8h, wash and Nocodazole 12h, wash and release 7h


title: RNA-seq_S10D_Post-mit_7h_Repeat_1


title: RNA-seq_S10A_Post-mit_7h_Repeat_1


title: Med13L WT_cortex_E13.5, scRNA

description: 10X Genomics

value: Med13L WT


title: Molm-13 cells, treated by cytarabine (0.5 µM), and then treated with FL-Fc-DM1 (1 nM) 1

description: Library name: Sample 10

value: Blood


title: CW44 bacteria, untreated, 1hr, rep2

description:
Hyp05_1_and_191hrPAO1.csv
Hyp05_B_1hr

value: Gram-negative bacteria

value: untreated


title: Mm, fmi, 15.5dpc, 164396

city: New Haven

first: Gunter

middle: P

last: Wagner

state: CT

address: 165 Prospect Street

department: Ecology & Evolutionary Biology

institute: Yale University

description: 10x Genomics

data_processing:
CellRanger v7.0.0-v8.0.0
Assembly: GRCm39 (M. musculus); cavPor3 (C. porcellus); ASM229v1 (M. domestica); Draft Genome (T. ecaudatus)
Supplementary files format and content: CellRanger tab-separated features and cell barcodes and matrix expression files.
Supplementary files format and content: Raw counts in annotated h5 format with hierarchical cell type annotations, and gene annotations according to ENSEMBL and BLAST to human.

source_name: uterus + placenta

extract_protocol:
All tissue was processed as follows, with small species-specific modifications as noted. Tissue was minced with a scalpel into ~1 mm3 cubes in 2 mL of digestive solution containing 0.2 mg/mL Liberase TL (05401020001, Sigma). Tissue suspensions were heated at 37°C for 15 minutes and then passed 10 times through a 16-gauge needle attached to a 3-mL syringe. This incubation and needle passage process was repeated two more times, with the substitution of an 18-gauge needle. Finally, 2 mL of charcoal-stripped fetal bovine serum (100-199, Gemini) was added and the suspension was immediately passed through a 70-μm cell strainer then a 40-μm cell strainer. The flowthrough was pelleted by centrifugation at 500 g for 5 minutes and cells were resuspended in 1x ACK red blood cell lysis buffer (A1049201, Thermo-Fisher), incubated at room temperature for 5 minutes, centrifuged again and resuspended in PBS containing 0.04% bovine serum albumen (A9647, Sigma). At this point, cells were examined on a hemocytometer to gauge concentration and check for debris and cell death using trypan blue stain (15250061, ThermoFisher). Mouse tissue was processed as above with the addition of Accumax (Stem Cell Technologies) to the final 0.04% bovine serum albumen solution. Guinea pig tissue was processed as with the mouse with the following modifications: a wide-bore 1 mL pipette tip was substituted for the 16-gauge needle, and 0.2 mg/mL collagenase I (17018029, Thermo-Fisher) was added to the digestion solution. As tenrec and guinea pig tissue showed higher cell death, a fractionated protocol was adopted to reduce exposure of cells to digestive enzymes. For these species, cells which had dislodged following each passage step were separated from intact tissue and immediately passed through a 70-μm cell strainer into 2 mL of charcoal-stripped fetal bovine serum (100-199, Gemini), while remaining intact tissue was allowed to continue with further digestion. Each fraction was centrifuged at 300 rpm for 5 minutes and resuspended in 500 μL ACK red blood cell lysis buffer (A1049201, Thermo-Fisher) for 5 minutes, then centrifuged at 500 rpm for 2 minutes and resuspended in 0.04% bovine serum albumen (A9647, Sigma) and kept on ice until dissociation was complete. Cells were counted on a hemocytometer and recombined in a proportional manner before sequencing. Cells were captured using the 10X Chromium platform (3’ chemistry, version 3)
Libraries were generated according to manufacturer protocols (CG000315: 10x Genomics 3’ chemistry, version 3).

value: uterus + placenta

tag: Sex

value: Female

tag: developmental stage

value: 15.5 days post copulation


title: RNA-seq_S10_Post-mit_7h_Repeat_2


title: CW44 bacteria, untreated, 1hr, rep3

description:
Hyp05_1_and_191hrPAO1.csv
Hyp02_A_1hr


title: Mm, fmi, 15.5dpc, 164397

description: 10x Genomics


title: RNA-seq_S10_Post-mit_7h_Repeat_1


title: Molm-13 cells, treated by cytarabine (1 µM) 3

description: Library name: Sample 9

value: Molm-13 cell line

value: cytarabine (1 µM) for 4 days


title: CW44 bacteria, untreated, 1hr, rep1

description:
Hyp05_1_and_191hrPAO1.csv
Hyp05_A_1hr


title: P53-cHyper_Multiome_ATAC

first: Noah

last: Gamble

state: IL

department: Pathology

institute: University of Chicago

data_processing:
Following sequencing, BCL files were converted to FASTQ using cellranger-arc (v2.0.2) mkfastq. FASTQ files were aligned to the mm10 or hg38 genome assembly using cellranger-arc count. ATAC fragment files were used as inputs to the ArchR (v1.0.2) analysis pipeline in R (v4.3.2). Transcript count matrices were used as inputs to the Seurat gene expression analysis pipeline.
Assembly: mm10 or hg38
Supplementary files format and content: BAM
Supplementary files format and content: Zip file of multiome processed results
Library strategy: scMultiome

source_name: Thymus

extract_protocol:
Mouse: Thymic epithelial cells were isolated using a previously published protocol (Kim & Serwold, Methods in Molecular Biology, 2019) with minor modifications. Briefly, thymi from 4-5 week-old mice were harvested and connective tissue was removed. Stromal tissue was perforated using scissors and incubated with rotation in DMEM-F12 (Sigma D6421) at room temperature for for 10min to liberate thymocytes. Remaining stromal tissue was enzymatically digested (0.5mg/mL Collagenase D (Sigma 11088858001), 0.2mg/mL DNaseI (Sigma 10104159001), 0.5mg/mL Papain (Worthington Biochemical LS003126)). Cells were stained with anti-EpCAM antibodies conjugated to APC-Cy7 and EpCAM+ cells were enriched via positive selection using magnetic anti-Cy7 beads (Miltenyi 130-091-652). Enriched fraction was stained with fluorescently conjugated antibodies for FACS or analysis.  Human: Excised thymic tissue from one patient (3-month-old male) was obtained during the course of corrective cardiac surgery at the Advocate Children’s Hospital, Chicago, IL, USA. Patient was de-identified upon receipt with written informed consent for release of genomic sequence data in accordance with IRB approved protocols by the Advocate Children’s Hospital, University of Chicago, and the National Institute of Health. Connective tissue was removed, and stromal tissue was minced using scissors. Tissue was incubated with rotation in DMEM-F12 (Sigma) at 4C for 20min to liberate thymocytes. Further thymocyte liberation was achieved via enzymatic digestion using 0.5mg/mL Collagenase D (Millipore 11088858001) and 0.2mg/mL DNase I (Sigma 10104159001) at 37C for 20min. Remaining fragments were incubated with rotation in 0.5mg/mL Papain (Worthington), 0.25mg/mL Collagenase D and 0.1mg/mL DNase I at 37C for 20min. Digestion was quenched by addition of FACS buffer. Cells were stained with anti-EpCAM antibodies conjugated to APC-Cy7 (BioLegend 324245 clone 9C4 1:100) and EpCAM+ cells were enriched via positive selection with magnetic anti-Cy7 beads (Miltenyi). Enriched fraction was stained with DAPI (Invitrogen), CD45 (BioLegend 368508 clone 2D1 1:100), LY51/CD249 (Fisher Scientific BDB564533 clone 2D3/APA 1:100) and HLA-DRA (BioLegend 307622 clone L243 1:100) and sorted on a Symphony S6 (BD Biosciences).
For all multiome experiments, we used the ATAC+GEX single-cell kit and protocol (10X Genomics 1000236 with protocol CG000338 RevE) with minor modifications to sample preparation. Briefly, 40,000 mTECs were FACS-sorted into 1X PBS supplemented with 2% BSA and centrifuged at 300rcf for 5 min. Cells were gently washed in 50uL Lysis Buffer (10mM Tris, 10mM NaCl, 3mM MgCl2 in nuclease-free water) and centrifuged at 300rcf for 5 min. Cells were resuspended in  50uL permeabilization buffer (10mM Tris, 10mM NaCl, 3mM MgCl2, 0.1% Tween20, 0.01% digitonin, and RNase inhibitor (Millipore) in nuclease-free water) and incubated for 5 minutes on ice. Nuclei were gently washed with wash buffer (10mM Tris, 10mM NaCl, 3mM MgCl2, 0.1% Tween20, and RNase inhibitor in nuclease-free water) and centrifuged at 500rcf for 5 min. Finally, nuclei wee resuspended in 5uL chilled diluted nuclei buffer (10X Genomics) and added to transposition mix. Paired-end, dual-index sequencing was performed on the Illumina NextSeq 500 or NovaSeq 6000 platform.

value: Thymus

value: mTEC


title: Molm-13 cells, treated by cytarabine (1 µM) 2

description: Library name: Sample 8

value: Established from the peripheral blood of a 20-year-old man with acute myeloid leukemia AML FAB M5a at relapse in 1995 after initial myelodysplastic syndrome (MDS, refractory anemia with excess of blasts, RAEB); described to carry internal tandem duplication of FLT3.

value: wild type


title: ATAC-seq_S10D_Post-mit_7h

value: Cervix; Uterus


title: CW8 bacteria, meropenem + tobramycin, 191hr, rep3

description:
Hyp04_1_and_191_hr_PAO1.csv
Hyp01_F_191hr

value: meropenem and tobramycin


title: P53-WT_Multiome_ATAC


title: ATAC-seq_S10A_Post-mit_7h

value: HeLa

value: epithelial cell


title: Molm-13 cells, treated by cytarabine (1 µM) 1

description: Library name: Sample 7


title: CW8 bacteria, meropenem + tobramycin, 191hr, rep2

description:
Hyp04_1_and_191_hr_PAO1.csv
Hyp04_H_191hr


title: Molm-13 cells, treated by cytarabine (0.5 µM) 3

description: Library name: Sample 6

value: cytarabine (0.5 µM) for 4 days


title: ATAC-seq_S10_Post-mit_7h

value: Thymidine 24h, wash and Doxycycline 8h, wash and Nocodazole 12h, wash and release 7h


title: P53-cHyper_mTEChi_Rep3

data_processing:
RNA-seq reads were mapped to the mm10 mouse genome assembly using TopHat (v2.1.1) with setting --microexon-search. Unmapped, unpaired and low quality reads (MAPQ < 5) were removed using samtools (v1.9) view with settings -q 5 -f 2. Paired reads were counted for each gene using featureCounts from Subread (v2.0.1). Transcripts-per-million (TPM) values were calculated for each gene to quantify the relative abundance of transcripts for clustering analysis.
Assembly: mm10
Supplementary files format and content: Count matrix text file

extract_protocol:
Thymic epithelial cells were isolated using a previously published protocol (Kim & Serwold, Methods in Molecular Biology, 2019) with minor modifications. Briefly, thymi from 4-5 week-old mice were harvested and connective tissue was removed. Stromal tissue was perforated using scissors and incubated with rotation in DMEM-F12 (Sigma D6421) at room temperature for for 10min to liberate thymocytes. Remaining stromal tissue was enzymatically digested (0.5mg/mL Collagenase D (Sigma 11088858001), 0.2mg/mL DNaseI (Sigma 10104159001), 0.5mg/mL Papain (Worthington Biochemical LS003126)). Cells were stained with anti-EpCAM antibodies conjugated to APC-Cy7 and EpCAM+ cells were enriched via positive selection using magnetic anti-Cy7 beads (Miltenyi 130-091-652). Enriched fraction was stained with fluorescently conjugated antibodies for FACS or analysis. 75,000 primary mTECs were FACS-sorted directly into RULT lysis buffer (Qiagen RNEasy Kit) and total RNA was extracted using manufacturer’s instructions.
mRNA was enriched and RNA-seq libraries were constructed using the Illumina TruSeq Stranded mRNA Kit. Paired-end, dual-index sequencing was performed on the Illumina NovaSeq 6000 platform.

value: mTEChi


title: Molm-13 cells, treated by cytarabine (0.5 µM) 2

description: Library name: Sample 5

value: Blood


title: CW8 bacteria, tobramycin, 191hr, rep3

description:
Hyp04_1_and_191_hr_PAO1.csv
Hyp01_D_191hr

value: Gram-negative bacteria

value: tobramycin


title: ChIP-seq_MCF-7_H3S10p_Asyn

source_name: Breast, mammary gland

value: Breast, mammary gland

value: DMSO 24h

value: anti-H3S10p (Abcam ab5176)


title: CW8 bacteria, tobramycin, 191hr, rep2

description:
Hyp04_1_and_191_hr_PAO1.csv
Hyp04_F_191hr


title: P53-WT_Multiome_GEX

molecule: nuclear RNA

value: Thymus


title: ChIP-seq_MCF-7_H3S10p_Mit

value: Nocodazole 24h


title: CW8 bacteria, meropenem + tobramycin, 191hr, rep1

description:
Hyp04_1_and_191_hr_PAO1.csv
Hyp04_G_191hr


title: P53-cHyper_mTEClo_Rep3

value: mTEClo


title: Non_7

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

description: mRNA expression in human superior frontal gyrus

data_processing:
Gene counts were obtained by aligning reads to human genome (hg38) mouse genome (mm10) with Cell Ranger software (v.3.1.0) (10× Genomics).
To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than three cells, cells with a unique gene count over 9000 or less than 300, cells with UMI over 50000 and cells with a high fraction of mitochondrial reads (>5%).
Potential doublet cells were predicted and removed using DoubletFinder for each sample.
Seurat v3.0.182 R package used for analysis
Assembly: hg38 and mm10 genome
Supplementary files format and content: barcodes.tsv.gz: cellular barcodes present in datase
Supplementary files format and content: features.tsv.gz: IDs of quantified genes
Supplementary files format and content: matrix.mtx.gz: a matrix of count values, where rows are associated with the gene IDs above and columns correspond to the cellular barcodes.

source_name: superior frontal gyrus

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2019
Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics)

value: superior frontal gyrus

value: Female

tag: age

value: GRN+/+


title: Molm-13 cells, control 3

description: Library name: Sample 3

value: Molm-13 cell line

value: Established from the peripheral blood of a 20-year-old man with acute myeloid leukemia AML FAB M5a at relapse in 1995 after initial myelodysplastic syndrome (MDS, refractory anemia with excess of blasts, RAEB); described to carry internal tandem duplication of FLT3.

value: wild type

value: untreated, culture for 4 days


title: P53-WT_mTEChi_Rep3

value: mTEChi


title: Molm-13 cells, treated by cytarabine (0.5 µM) 1

description: Library name: Sample 4

value: Blood

value: cytarabine (0.5 µM) for 4 days


title: CW8 bacteria, tobramycin, 191hr, rep1

description:
Hyp04_1_and_191_hr_PAO1.csv
Hyp04_E_191hr

value: Gram-negative bacteria

value: tobramycin


title: Molm-13 cells, control 2

description: Library name: Sample 2


title: CW8 bacteria, meropenem, 191hr, rep3

description:
Hyp04_1_and_191_hr_PAO1.csv
Hyp01_B_191hr

value: meropenem


title: Non_8


title: Non_6

value: Male


title: P53-WT_mTEClo_Rep3

value: Thymus


title: P53-cHyper_mTEChi_Rep2_FC02


title: CW8 bacteria, meropenem, 191hr, rep2

description:
Hyp04_1_and_191_hr_PAO1.csv
Hyp04_D_191hr


title: P53-cHyper_Multiome_GEX

value: mTEC


title: Molm-13 cells, control 1

description: Library name: Sample 1


title: Non_5


title: CW8 bacteria, meropenem, 191hr, rep1

description:
Hyp04_1_and_191_hr_PAO1.csv
Hyp04_C_191hr


title: P53-cHyper_mTEChi_Rep2_FC01


title: THP-1 cells, treated by FL-Fc-DM1 (3 nM)

description: Library name: Sample 3

growth_protocol: THP-1 cells were cultured in RPMI 1640 medium supplemented with 10% FBS, in a 5% CO2, 37 °C incubator.

treatment_protocol: In the control group, THP-1 cells were cultured for 1 day. In the FL-Fc-DM1 treatment groups, THP-1 cells were treated with FL-Fc-DM1 (1 and 3 nM) for 1 day.

value: THP-1 cell line

value: THP-1 is a suspension cell line isolated from peripheral blood of an acute monocytic leukemia patient.

value: FL-Fc-DM1 (3 nM) for 1 day


title: P53-cHyper_mTEClo_Rep2_FC02

value: mTEClo


title: THP-1 cells, treated by FL-Fc-DM1 (1 nM)

description: Library name: Sample 2

value: FL-Fc-DM1 (1 nM) for 1 day


title: THP-1 cells, control, cultured for 1 days

description: Library name: Sample 1

value: untreated


title: Non_4

value: superior frontal gyrus

value: Female

value: GRN+/+


title: CW8 bacteria, untreated, 191hr, rep3

description:
Hyp04_1_and_191_hr_PAO1.csv
Hyp01_A_191hr


title: P53-cHyper_mTEClo_Rep2_FC01


title: CW8 bacteria, untreated, 191hr, rep2

description:
Hyp04_1_and_191_hr_PAO1.csv
Hyp04_B_191hr


title: Non_3


title: CW8 bacteria, untreated, 191hr, rep1

description:
Hyp04_1_and_191_hr_PAO1.csv
Hyp04_A_191hr


title: MV-4-11 cells, treated by FL-Fc-DM1 (1.5 nM)

description: Library name: Sample 3

data_processing:
Reads obtained from the sequencing machines, including raw reads were further filtered by fastp (version 0.18.0). Reads containing adapters, containing more than 10% of unknown nucleotides, and low-quality reads containing more than 50% of low-quality bases were removed.
rRNA-mapped reads were also removed. The paired-end clean reads were mapped to the human reference genome using HISAT2.2.4. The mapped reads of each sample were assembled using StringTie v1.3.1 in a reference-based approach. The FPKM method was used to eliminate the influence of different gene lengths and sequencing data amount on the calculation of gene expression. RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples).  The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥2 were considered differentially expressed genes/transcripts.
Assembly: rRNA-mapped reads were also removed. The paired-end clean reads were mapped to the human reference genome using HISAT2.2.4. The mapped reads of each sample were assembled using StringTie v1.3.1 in a reference-based approach. The FPKM method was used to eliminate the influence of different gene lengths and sequencing data amount on the calculation of gene expression. RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples).  The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥2 were considered differentially expressed genes/transcripts.
Supplementary files format and content: Micorsoft excel format

growth_protocol: MV-4-11 cells were cultured in IMDM medium supplemented with 10% FBS, in a 5% CO2, 37 °C incubator.

treatment_protocol: In the control group, MV-4-11 cells were cultured for 1 day. In the FL-Fc-DM1 treatment groups, MV-4-11 cells were treated with FL-Fc-DM1 (0.5 and 1.5 nM) for 1 day.

value: Blood

value: MV-4-11 cell line

value: The MV4-11 cell line was established by Rovera and associates from the blast cells of a 10-year-old male with biphenotypic B-myelomonocytic leukemia.

value: wild type

value: FL-Fc-DM1 (1.5 nM) for 1 day


title: P53-WT_mTEChi_Rep2_FC02

value: mTEChi


title: Non_1


title: CW8 bacteria, meropenem + tobramycin, 1hr, rep3

description:
Hyp04_1_and_191_hr_PAO1.csv
Hyp01_F_1hr

value: Gram-negative bacteria

value: meropenem and tobramycin


title: P53-WT_mTEChi_Rep2_FC01

value: Thymus


title: Non_2


title: MV-4-11 cells, control, cultured for 1 days

description: Library name: Sample 1


title: P53-WT_mTEClo_Rep2_FC02


title: MV-4-11 cells, treated by FL-Fc-DM1 (0.5 nM)

description: Library name: Sample 2

value: FL-Fc-DM1 (0.5 nM) for 1 day


title: FTD_6

value: GRN+/-


title: P53-WT_mTEClo_Rep2_FC01

value: mTEClo


title: Molm-13 cells, treated by FL-Fc-DM1 (1 nM)

description: Library name: Sample 2

treatment_protocol: In the control group, Molm-13 cells were cultured for 1 day. In the FL-Fc-DM1 treatment groups, Molm-13 cells were treated with FL-Fc-DM1 (1 and 3 nM) for 1 day.

value: Molm-13 cell line

value: Established from the peripheral blood of a 20-year-old man with acute myeloid leukemia AML FAB M5a at relapse in 1995 after initial myelodysplastic syndrome (MDS, refractory anemia with excess of blasts, RAEB); described to carry internal tandem duplication of FLT3.

value: FL-Fc-DM1 (1 nM) for 1 day


title: CW8 bacteria, meropenem + tobramycin, 1hr, rep2

description:
Hyp04_1_and_191_hr_PAO1.csv
Hyp04_H_1hr


title: Molm-13 cells, treated by FL-Fc-DM1 (3 nM)

description: Library name: Sample 3

value: FL-Fc-DM1 (3 nM) for 1 day


title: FTD_5

value: superior frontal gyrus

value: Female


title: CW8 bacteria, tobramycin, 1hr, rep3

description:
Hyp04_1_and_191_hr_PAO1.csv
Hyp01_D_1hr

value: tobramycin


title: P53-cHyper_mTEChi_Rep1_FC02


title: FTD_7


title: CW8 bacteria, tobramycin, 1hr, rep2

description:
Hyp04_1_and_191_hr_PAO1.csv
Hyp04_F_1hr


title: Molm-13 cells, control, cultured for 1 days

description: Library name: Sample 1

value: Blood

value: untreated


title: OE-SOX3_3

city: Hefei

first: Qiang

last: Hong

address: Hefei

institute: Anhui Medical University

description: Library name: Sample 6

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the human reference genome (hg38) utilizing the HISAT2 software, mapped to the reference coding genes through the HTSeq-count tool.
fragment per kilo bases per million fragment (FPKM) values were calculated for every gene using the RSEM tool
Assembly: hg38
Supplementary files format and content: The excel file includes the ID of genes and the FPKM values for each Sample.

source_name: KGN cell

extract_protocol:
Total RNAs were isolated from OE-NC and OE-SOX3 KGN cells by TRIzol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina HiSeq 2500 protocols.

value: KGN cell

value: human ovarian granulosa cells

value: overexpression of SOX3


title: FTD_4

value: Male


title: CW8 bacteria, meropenem + tobramycin, 1hr, rep1

description:
Hyp04_1_and_191_hr_PAO1.csv
Hyp04_G_1hr

source_name: Gram-negative bacteria

value: Gram-negative bacteria

value: meropenem and tobramycin


title: P53-cHyper_mTEChi_Rep1_FC01

value: Thymus

value: mTEChi


title: OE-SOX3_2

description: Library name: Sample 5


title: CW8 bacteria, tobramycin, 1hr, rep1

description:
Hyp04_1_and_191_hr_PAO1.csv
Hyp04_E_1hr


title: FTD_3

value: GRN+/-


title: P53-cHyper_mTEClo_Rep1_FC02

value: mTEClo


title: CW8 bacteria, meropenem, 1hr, rep3

description:
Hyp04_1_and_191_hr_PAO1.csv
Hyp01_B_1hr

value: meropenem


title: P53-cHyper_mTEClo_Rep1_FC01


title: OE-SOX3_1

description: Library name: Sample 4


title: FTD_2


title: CW8 bacteria, meropenem, 1hr, rep2

description:
Hyp04_1_and_191_hr_PAO1.csv
Hyp04_D_1hr


title: P53-WT_mTEChi_Rep1_FC02


title: OE-NC_3

description: Library name: Sample 3

value: WT


title: FTD_1

value: superior frontal gyrus


title: sublib8, 48samples

city: Iowa city

first: Alejandro

middle: Pezzulo

last: Colmenares

state: Iowa

address: 169 Newton Road

department: Internal medicine

institute: University of Iowa

data_processing:
Pair-ends reads obtained from Illumina NovaSeq were processed and mapped to the human-SARS-CoV-2 combined reference genome using STAR and Samtools package implemented via Split Bio data analysis pipeline; split-pipe v0.7.5p in Amazon Web Services platform according to the suggested data processing protocol by the manufacturer.
Output files (a matrix with cell-gene counts, cell metadata file, genes info file) from all 8 sub-libraries were imported and merged into a single Seurat object using Seurat v4.0.1 in R v4.0.5 for further analyses.
Low-quality and duplicated cells were filtered and only cells with 1) % of mitochondrial genes <0.5, 2) 2500<UMI counts per cells >40,000, 3) 1,000 < number of genes per cells >8,000 was selected for downstream analysis
Assembly: Human- SARS-CoV-2 combined reference genome was made using human reference genome-build GRCh38.p13(accession GCF_000001405.39) and SARS-CoV-2/human/USA/WA-CDC-WA1/2020 isolate (GenBank assembly accession: GCA_009937905.1).
Supplementary files format and content: scRNA_seurat_data.RData file : contains raw and processed seurat objects. raw_seurat_object: seurat object , contains raw output from splitseq for all 48 samples along with cell metadata. This was created by merging outputfile files from split-seq (cell_metadata.csv, DGE.mtx and genes.csv ) from all 8 sub-libraries. processed_seurat_object: a processed seurat object with cell barcode, gene counts and additional sample metadata(cell types, infection, conditions) for all 48 samples.

source_name: primary airway epithelia

growth_protocol: Primary epithelial cells were isolated from the human trachea and bronchi by enzymatic digestion and were grown at air-liquid interface using previously described method (73). Passage -0 primary differentiated human airway epithelia (HAE) from 3 human donors were obtained from the University of Iowa Cells and Tissue Core.

extract_protocol:
Cells were fixed, permeabilized and 8 cDNA sub-libraries were generated using the SPLiT-seq (77) protocol V3.0 from Parse Biosciences following the manufacturer’s instructions.
Concentration and fragment size of the pooled cDNA library was measured using Qubit HS and High Sensitivity DNA Assay. Fragment size for the library was ~430bp which falls within the recommended 150-850bp. Pair-end reads sequencing was performed on the pooled library using two lanes of Illumina NovaSeq 6000 S1 Flowcell instrument (approximately 800 million PE reads per lane) for 300 cycles to generate 150bp paired-end reads. The sequencing was configured for 66nt (transcript sequence) read1, 94nt (cell-specific barcodes and UMI) read2 and an additional 6nt read1 index for sub-library indices as described in the manufacturer’s protocol. Sequencing was performed by the University of Iowa Genomics Facility.

treatment_protocol: Cell cultures were treated with 20 ng/mL recombinant IL-13 or 20 ng/mL recombinant IL-17 combined with 10 ng/mL tumor necrosis factor alpha (TNFα) for 4 or 55 days. The cytokines were applied to both apical and basolateral side of HAE. The cells were then infected with SARS-CoV-2 (MOI 0.1), the strain isolated from the first US patient (2019-nCoV/USA-WA1/2020, GenBank:MN985325.1) for 6 or 72 hours.

value: primary airway epithelia

value: mixed sample (cytokine, viral)

tag: donor

value: mixed samples(3donors)


title: CW8 bacteria, meropenem, 1hr, rep1

description:
Hyp04_1_and_191_hr_PAO1.csv
Hyp04_C_1hr


title: P53-WT_mTEChi_Rep1_FC01


title: sublib7, 48samples


title: OE-NC_2

description: Library name: Sample 2


title: CW8 bacteria, untreated, 1hr, rep3

description:
Hyp04_1_and_191_hr_PAO1.csv
Hyp01_A_1hr

value: untreated


title: OE-NC_1

description: Library name: Sample 1

value: KGN cell


title: P53-WT_mTEClo_Rep1_FC02


title: sublib6, 48samples


title: P53-WT_mTEClo_Rep1_FC01


title: CW8 bacteria, untreated, 1hr, rep2

description:
Hyp04_1_and_191_hr_PAO1.csv
Hyp04_B_1hr


title: sublib5, 48samples


description: Library name: ChIP-seq_H3_S10A_Mit_Repeat_1_without-spike-in

data_processing:
For ChIP-seq analysis; fastq files were aligned to hg19 using Bowtie2 and read depth and input normalised using SAM tools, followed by processing the BAM files with MACS2 (default with broad mode) and bigwig conversion. The regions were called a using a method involving stitching of sliding window bins in genome based on H3S10p coverage. For ChIP-seq with S2 chromatin spike-in, in addition to the above, the fastq files were aligned to dm3 or dm6 using Bowtie2. This was followed by the above stated method for coverage file making along with spike-in normalisation in addition to depth normalisation.
For ATAC-seq analysis; fastq files were trimmed for adapter sequence and aligned to hg19 using Bowtie2 with read depth normalisation using SAM tools, followed by processing the BAM files with MACS2 and bigwig conversion.
For RNA-seq analysis; fastq files were subjected to Trimmomatic and FASTQC was done to check read quality. The reads were then aligned to hg19 using HISAT2. BAM files obtained were read depth normalised and FeatureCounts was used with default settings to get coverage at all GeneIDs. The fold changes between different lines were calculated using DeSeq2.
Assembly: hg19
Supplementary files format and content: bigwig
Supplementary files format and content: bed, tabular

value: Cervix; Uterus

value: HeLa

value: epithelial cell

value: Thymidine 24h, wash and Doxycycline 8h, wash and Nocodazole 12h


title: CW8 bacteria, untreated, 1hr, rep1

description:
Hyp04_1_and_191_hr_PAO1.csv
Hyp04_A_1hr

value: Gram-negative bacteria


title: HO [scRNA-seq]

first: Bon-chu

last: Chung

address: No. 128, Sec. 2 Academia Rd., Nangang Dist.

department: Institute of Molecular Biology

institute: Academia Sinica

data_processing:
The raw base call (BCL) files were transferred to FASTQ file by Cell Ranger (10x Genomics) pipeline, cellranger mkfastq.
The mapping to zebrafish genome, GRCz11, and the calculation of gene expression was performed by Cell Ranger (10x Genomics) pipeline, cellranger count
Genome_build: GRCz11
Supplementary_files_format_and_content: Tab-delimited raw count matrices
Supplementary_files_format_and_content: Tab-delimited normalized expression value matrices

organism: Danio rerio

source_name: gonad

extract_protocol:
Trunks of ziwi:egfp;foxl2l-/- or ziwi:foxl2l+/+ containing gonad were dissociated by 0.4% collagenase and 0.5% trypsin at 26 dpf. Germ cells were then sorted by fluorescence activated cell sorter. Around 3000 EGFP+ cell were collected in each genotype.
cDNA library was constructed by Chromium Next GEM Single Cell 3' Library Construction Kit v3.1 kit (10x Genomics) following the manufacturer's protocol

value: TL

value: germ cell

value: 26 days post fertilization


description: Library name: ChIP-seq_H3_S10_Mit_Repeat_1_without-spike-in


title: sublib3, 48samples


title: WT [scRNA-seq]


title: sublib4, 48samples


title: tumor-WT-CD45_melanoma

city: Philadelphia

first: Megan

middle: Lynn

last: Clark

state: PA

address: 421 Curie Blvd, Room 320

institute: University of Pennsylvania

description: S1 100cycle

data_processing:
Cellranger v(3.1.0) pipeline with default parameters
Single cell transcriptome sequencing data was aligned and processed using 10x Cell Ranger v3.1 with the mm10 reference genome. Filtered matrices from Cell Ranger output were further processed using Seurat 3.1.4 (https://satijalab.org/seurat/) (Stuart et al., 2019). Low quality cells with <300 genes or >0.15 mitochondrial gene fraction were filtered out. Cell cycle score and phase were determined for each cell using the CellCycleScoring function (https://satijalab.org/seurat/v3.1/cell_cycle_vignette.html). Scaling and normalization were performed on each object using SCTransform, while regressing cell cycle scores and mitochondrial fraction. The first 15 principal components were used to generate UMAPs. To identify likely doublets, doubletFinder_v3 was run on these objects using an expectation of 6% doublets, based on the 10x user guide, and with the following additional settings: pN = 0.25, pK = 0.09, PCs = 1:15, sct = T. Seurat objects were then merged into a master object, and detected doublets were removed.
The final Seurat object containing quality filtered singlets was converted into a cell_data_set object in Monocle3 (https://cole-trapnell-lab.github.io/monocle3), which was used for all further transcriptional analyses. Preprocess_cds was run using the top 20 PCA dimensions (determined by elbow plot of PCAs) and align_cds was run with the alignment_group sent as the sample, with regression of cycle scores and mito fraction. Cells were plotted in UMAP space and Leiden clusters found using cluster_cells. Top gene IDs per cluster were identified using the top_markers function, and only markers with a specificity of above 0.3 and a q-value below 0.01 were retained. Broad clusters were identified based on their marker genes using ImmGen and literature review. For further subsetting analyses of tumor only data or various cell type specific subpopulations, such as macrophages or T cells, the above steps starting from preprocess_cds were repeated in the same manner. Further transcriptional analyses and visualization were done primarily using Monocle 3 and in some cases Seurat or using custom R scripts where needed.
Assembly: GRCm38 - mm10
Supplementary files format and content: Output of CellRanger software : Features, Barcodes and Matrix

source_name: B16-F10 melanoma tumor

extract_protocol:
After gating live singlets, CD45+ CD11b+ myeloid cells were isolated from dissociated spleens, and CD45+ immune cells were isolated from dissociated tumors using a BD FACS Aria II using the purity setting. Equal numbers of cells were sorted per mouse from 3-4 mice into one pooled sample per genotype for spleens and for tumors. After sorting, samples were centrifuged at 500g for 5 min. Supernatant was removed to leave 25ul of solution to not disturb pellets. Remaining volume was measured and raised to 50ul total by adding a 1:1 mixture of cold FACS buffer and nuclease-free water. 16,000 cells were loaded per 10x lane (Chromium Single Cell 3’ Reagent Kit v3.1).
Single cell RNA-seq library and transcriptome library construction were prepared according to the 10x Chromium Single Cell 3’ v3.1 user guide (Rev A). Indexed and pooled single cell transcriptome libraries for each mouse were sequenced on the NovaSeq 6000 System with an S1 100-cycle kit.

value: B16-F10 melanoma tumor

value: CD45+ tumor-infiltrating immune cell

value: Wild-type


title: BC17009,TIL non response

city: Seoul

first: INWON

last: LEE

address: 25, Misagangbyeonjungang-ro 7beonan-gil, Hanam-si, Gyeonggi-do

country: South Korea

institute: NeogenTC

data_processing:
RNA-Seq read were preprocessed with trimmomaticv0.39 and aligned to hg38 reference genome with STAR v2.7.10a and expression calculated with RSEM v1.3.3.
Assembly: hg38
Supplementary files format and content: RNA-Seq read depths (in expected count)

source_name: Breast cancer

growth_protocol: Breast cancer tissue was placed in RPMI 1640 medium and brought to the laboratory within 2 h of surgery. After washing with phosphate-buffered saline (PBS) containing 1× ZellShield anticontaminant agent, the tumor tissues were minced into 1-mm-diameter pieces. The minced fragments were plated into a 24-well plate (four fragments/well) containing 2 mL of TIL culture medium (RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 1× ZellShield, 1× 2-mercaptoethanol, and 1,000 IU/mL IL-2). Plates were incubated at 37°C for 14 days to allow TILs to extravasate from the tissue fragment and expand. Half of the medium was changed every 2 days, and the cells were expanded into additional wells when the medium turned yellow. After 14 days, TILs were recovered by centrifugation at 1,500 rpm for 5 min after passing the mixture of tissue fragments and TIL through a 40-μm-pore nylon mesh strainer. TILs were then counted and cryopreserved. For further rapid expansion of TILs, 5 × 10^4 TILs were cultured at 37°C in a T25 flask containing 3 mL of 50% RPMI 1640 and 50% AIM-V media supplemented with 10% FBS, 1× ZellShield, and 1,000 IU/mL IL-2 as well as 30 ng/mL human anti-CD3 antibody and 1 × 10^7 irradiated (50 Gy) allogeneic peripheral blood mononuclear cell feeders. On day 4, 3 mL of the same media was added to the flask, and then 3 mL of media was added every 2 days. After 14 days, TILs (post-REP TILs) were collected, counted, and cryopreserved.

extract_protocol:
RNA was extracted using a Qiagen RNeasy Kits
CDNA was synthesized from mRNA fragments using Illumina TruSeq RNA Library Prep Kit

treatment_protocol: To assess the capability of IFNγ production by TILs, 1 × 10^5 post-REP TILs were stimulated with PMA (32.4 nM) and ION (1 μg/mL) in 96-well plates for 24 h. To examine the reactivity of the TILs against autologous cancer cells, the TILs were co-cultured for 24 h with 1 × 10^5 autologous breast cancer cells in 96-well plates at effector:target cell ratios of 1:1, 2:1, and 4:1. After stimulation of TILs with PMA/ION or co-culture, culture supernatants were collected after centrifuging the culture plate at 1,500 rpm for 5 min to exclude cells and debris. The IFNγ level was measured using a human IFN-γ ELISA kit according to the manufacturer’s guidelines.

value: Breast cancer

value: Tumor-infiltrating lymphocyte

value: Post-REP TILs

value: Non reactive to autologous breast cancer cells


title: sublib2, 48samples

value: primary airway epithelia

value: mixed sample (cytokine, viral)

value: mixed samples(3donors)


title: BC16223,TIL non response


title: spleen-Ndufa4KO-CD45_CD11b

description: S1 100cycle

source_name: Mouse spleen

value: Mouse spleen

value: CD45+ CD11b+ splenocyte


title: MV-4-11 cells, treated by cytarabine (2 µM), and then treated with FL-Fc-DM1 (1 nM) 3

description: Library name: Sample 12

data_processing:
Reads obtained from the sequencing machines, including raw reads were further filtered by fastp (version 0.18.0). Reads containing adapters, containing more than 10% of unknown nucleotides, and low-quality reads containing more than 50% of low-quality bases were removed.
rRNA-mapped reads were also removed. The paired-end clean reads were mapped to the human reference genome using HISAT2.2.4. The mapped reads of each sample were assembled using StringTie v1.3.1 in a reference-based approach. The FPKM method was used to eliminate the influence of different gene lengths and sequencing data amount on the calculation of gene expression. RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples).  The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥2 were considered differentially expressed genes/transcripts.
Assembly: rRNA-mapped reads were also removed. The paired-end clean reads were mapped to the human reference genome using HISAT2.2.4. The mapped reads of each sample were assembled using StringTie v1.3.1 in a reference-based approach. The FPKM method was used to eliminate the influence of different gene lengths and sequencing data amount on the calculation of gene expression. RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples).  The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥2 were considered differentially expressed genes/transcripts.
Supplementary files format and content: Microsoft excel format

source_name: Blood

value: Blood

value: MV-4-11 cell line

value: The MV4-11 cell line was established by Rovera and associates from the blast cells of a 10-year-old male with biphenotypic B-myelomonocytic leukemia.

value: wild type

value: treated by cytarabine (2 µM) for 3 days, and then treated with FL-Fc-DM1 (1 nM) for 1 day in the absence of cytarabine


description: Library name: ChIP-seq_H3_S10D_Mit_Repeat_1_without-spike-in

value: Cervix; Uterus

value: HeLa

value: epithelial cell

value: Thymidine 24h, wash and Doxycycline 8h, wash and Nocodazole 12h


title: sublib1, 48samples


title: spleen-WT-CD45_CD11b

description: S1 100cycle

value: Wild-type


title: Aortic smooth muscle,Pinch1,WT1,CUTtag

city: Shanghai

first: Chunxiao

last: Wang

address: Siping road

institute: Tongji university

data_processing:
Basecalls were performed using bel2fastq v2. 17 for Novaseq output.
CUT&Tag reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0 33, discarding reads left with < 20 bp.
CUT&Tag reads were aligned to the UCSC hg38 genome using Bowtie version 1.1 2. Only uniquely mapping reads with at most two mismatches were retained.
To create CUT&Tag coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2. 1.0 with the significance cut-off a-value <=0.01.
Assembly: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Supplementary files format and content: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: CUT&Tag

source_name: Aortic smooth muscle

extract_protocol:
Fresh embryo tissue sample was separated and liquid nitrogen quick freezing. Nucleus were extracted using nuclear extraction kit (Solarbio).
CUT&Tag libraries were prepared using the hyperactive universal CUT&Tag assay kit for illumina pro TD904 (Vazyme) following manufacturer’s protocols.

value: Aortic smooth muscle

tag: cuttag antibody

value: WT


title: BC16208,TIL non response

tag: tissue

value: Breast cancer

value: Tumor-infiltrating lymphocyte

value: Post-REP TILs

value: Non reactive to autologous breast cancer cells


title: T cells, DNR,  bio rep 3 [RNA-Seq]

first: Qinlan

address: Chongqingnan R.280

institute: Shanghai Jiaotong University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: from mouse spleen

growth_protocol: Primary CD8+ T cells were maintained in complete RPMI 1640 media [10% fetal bovine serum( FBS), 0.05 mM 2-mercaptoethanol, 1 mM NEAA] in humidified atmosphere with 5% CO2

extract_protocol:
Cells were fed with complete RPMI 1640 media.
RNA was harvested, 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: T cells were treated with DMSO or DNR for 2h.

value: from mouse spleen

tag: cell line

value: primary CD8+ T cells

value: T cells

value: wildtype

value: DNR


title: BC16204,TIL non response


title: RA9 shNAT10 ip

city: Guangzhou

first: Yu

last: Kuang

address: No.58 Zhongshan Er Road Guangzhou

institute: The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China)

data_processing:
Paired-end reads were harvested from Illumina Novaseq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Acetylated sites on RNAs (peaks) were identified by MACS software. Differentially acetylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts. GO and Pathway enrichment analysis were performed by the differentially acetylated protein coding genes.
Assembly: UCSC hg19
Supplementary files format and content: excel format for each processed data file

source_name: synovial tissues

extract_protocol:
Total RNA was rRNA depleted with Ribo-zero (Illumina) and then subjected to immunoprecipitation with the GenSeqTM ac4C-IP Kit (GenSeq Inc., China) by following the manufacturer’s instructions.
RNA was randomly fragmented to ~200 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the ac4C antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. The RNA/antibody complexes are then digested with Proteinase K and the eluted RNA is purified by phenol:chloroform extraction. RNA libraries for IP and input samples were then constructed with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA) by following the manufacturer’s instructions. Libraries were qualified using Agilent 2100 bioanalyzer and then sequenced in a HiSeq platform (Illumina)
ac4c RIP-seq

value: synovial tissues

value: primary cell

value: rheumatoid arthritis fibroblast synoviocytes

tag: genotype

value: NAT10 knockdown

value: shNAT10-lentivirus infection


title: circRNA profile of case [95T]

type: RNA

first: YUE NING

last: WANG

address: 651 Dongfeng Road East

institute: Sun Yat-Sen University Cancer Centre

description: The microarray was used to acquire circRNA expression profiles of 841 circRNAs.

hyb_protocol: The labeled cDNAs were hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 45°C for 12 to 16 hours.

scan_protocol: Scanned in a InnoScan 710 Microarray Scanner (Innopsys, France).

data_processing: Quantile normalization across multiple arrays,GPR normailization software, log 2 transformation of expression levels was used.

source_name: hepatocellular carcinoma

label_protocol: 2 μg of total RNA of hepatocellular carcinoma / adjacent noncancerous tissue was employed with 100 nmol/L of Cy5-dUTP (Enzo, New York USA) in reverse transcription.

extract_protocol: Total RNA was extracted using an acid phenol/chloroform extraction method followed by ethanol precipitation.

tag: group

value: tumor

tag: disease

value: hepatocellular carcinoma


title: tumor-Ndufa4KO-CD45_melanoma

description: S1 100cycle

value: B16-F10 melanoma tumor

tag: cell type

value: CD45+ tumor-infiltrating immune cell


title: circRNA profile of case [93T]


title: circRNA profile of case [94T]


title: circRNA profile of case [91T]


title: T cells, DNR,  bio rep 2 [RNA-Seq]

tag: treatment


title: RA9 control  ip

value: WT

value: control lentivirus infection


title: BC16166,TIL non response

value: Breast cancer

value: Tumor-infiltrating lymphocyte

value: Post-REP TILs

value: Non reactive to autologous breast cancer cells


title: BC16154,TIL reaction

value: Reactive to autologous breast cancer cells


title: RA9 control  input


title: T cells, DNR,  bio rep 1 [RNA-Seq]

value: from mouse spleen

value: primary CD8+ T cells

value: T cells

value: wildtype

value: DNR


title: RA7 shNAT10 ip

value: synovial tissues

value: primary cell

value: rheumatoid arthritis fibroblast synoviocytes

value: NAT10 knockdown

value: shNAT10-lentivirus infection


title: circRNA profile of case [90T]

value: tumor

value: hepatocellular carcinoma


title: BC16151,TIL non response

value: Breast cancer


title: T cells, DMSO, biol rep 3 [RNA-Seq]

value: DMSO


title: RA7 shNAT10 input


title: T cells, DMSO, biol rep 2 [RNA-Seq]


title: circRNA profile of case [89T]


title: BC16127,TIL reaction

value: Tumor-infiltrating lymphocyte

value: Post-REP TILs


title: circRNA profile of case [83T]


title: circRNA profile of case [87T]


title: RA7 control  ip

value: WT

value: control lentivirus infection


title: RA9 shNAT10 input


title: WholeHeart-ISO-KO-4

city: Charlottesville

first: Caitlin

last: Pavelec

state: VA

address: 1340 Jefferson Park Ave

department: Pharmacology

institute: University of Virginia School of Medicine

data_processing:
One hundred fifty-base paired-end sequencing was performed using an Illumina NovaSeq platform according to manufacture instructions. Fastq files were processed using in-house perl scripts from Novogene to obtain clean reads.  FeatureCounts was used to calculate read numbers for each gene and fragments of per kilobase of transcript sequence per millions base pairs sequenced (FPKM) were calculated.
Assembly: Clean reads were aligned to the mouse reference genome using Hisat2 v2.0.5.
Supplementary files format and content: all samples are included with fpkm values in a xlsx format

source_name: Heart

extract_protocol:
For some experiments, isolated cardiomyocytes were suspended in 1mL of TRIzolTM (Invitrogen) and stored at -80oC for further analysis75. After chloroform incubation and centrifugation per manufacture instructions RNA-containing phase was diluted with 70% ethanol 1:1 and RNA isolation was performed using RNeasy Mini Kit (Qiagen). For tissues, Total RNA was isolated using RNeasy Mini Kit (Qiagen) after lysis in RLT buffer with bead homogenization. Total RNA quantity and quality were then assessed on a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific).
Library preparation including quality metrics, sequencing, and clustering were performed by Novogene (Sacramento, CA).

value: Heart

value: ISO


title: BC16126,TIL non response

value: Non reactive to autologous breast cancer cells


title: RA7 control input


title: WholeHeart-ISO-WT-5


title: BC16110,TIL reaction

value: Reactive to autologous breast cancer cells


title: RA1 shNAT10 ip

value: synovial tissues


title: circRNA profile of case [82T]


title: BC16092,TIL reaction


title: RA1 shNAT10 input

value: primary cell


title: WholeHeart-ISO-WT-3


title: RA1 control  ip

value: rheumatoid arthritis fibroblast synoviocytes


title: BC16147,TIL reaction


title: T cells, DMSO, biol rep 1 [RNA-Seq]

value: from mouse spleen

value: primary CD8+ T cells

value: T cells

value: wildtype


title: circRNA profile of case [6T]

value: tumor

value: hepatocellular carcinoma


title: circRNA profile of case [76T]


title: WholeHeart-ISO-KO-3


title: RA1 control input


title: circRNA profile of case [69T]


title: BC1544,TIL non response

value: Breast cancer

value: Tumor-infiltrating lymphocyte


title: circRNA profile of case [67T]


title: RA9 shNAT10

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC hg19) with hisat2 software (v2.0.4). Then, HTSeq (v0.9.1) was used to obtain the original count of transcripts as mRNA expression profile. EdgeR software (v3.16.5) was used to standardize and calculate the multiple change and p-value between the two groups of samples or two samples to screen the differentially expressed mRNAs. And GO and Pathway analysis were performed on these differentially expressed genes.
Assembly: UCSC hg19
Supplementary files format and content: excel format for each processed data file

extract_protocol:
Briefly, total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions.
RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina NovaSeq 6000 instrument with 150bp paired end reads.

value: NAT10 knockdown

value: shNAT10-lentivirus infection


title: WholeHeart-ISO-KO-2

value: Heart


title: WholeHeart-ISO-WT-4

value: ISO


title: RA9 control

value: WT

value: control lentivirus infection


title: ChIP-seq_input_Asyn

data_processing:
For ChIP-seq analysis; fastq files were aligned to hg19 using Bowtie2 and read depth and input normalised using SAM tools, followed by processing the BAM files with MACS2 (default with broad mode) and bigwig conversion. The regions were called a using a method involving stitching of sliding window bins in genome based on H3S10p coverage.
For ATAC-seq analysis; fastq files were trimmed for adapter sequence and aligned to hg19 using Bowtie2 with read depth normalisation using SAM tools, followed by processing the BAM files with MACS2 and bigwig conversion.
For RNA-seq analysis; fastq files were subjected to Trimmomatic and FASTQC was done to check read quality. The reads were then aligned to hg19 using HISAT2. BAM files obtained were read depth normalised and FeatureCounts was used with default settings to get coverage at all GeneIDs. The fold changes between different lines were calculated using DeSeq2.
Assembly: hg19
Supplementary files format and content: bigwig: coverage file
Supplementary files format and content: bed, tabular: coordinate/ text file

source_name: Cervix; Uterus

extract_protocol:
For ChIP-seq, genomic DNA was isolated as per standard ChIP-seq protocol. For ATAC-seq, genomic DNA was isolated as per standard ATA-seq protocol, following viable nuclei isolation. For RNA-seq, total RNA was isolated using trizol as per the reagent manual.
ChIP-seq and ATAC-seq library was prepared using the NEBNext® Ultra™II DNA Library Prep kit with Sample Purification Beads (Catalogue-E7103L) following the manufacturer's protocol. For total RNA-seq, rRNA depletion was done using NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) with RNA Sample Purification Beads(Catalog no-E7405L) and library was prepared using NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads(Catalog no-E7765L).

value: Cervix; Uterus

value: HeLa

value: epithelial cell

value: DMSO 24h

value: none (input)


title: circRNA profile of case [65T]


title: WholeHeart-ISO-WT-1


title: ChIP-seq_H3S10p_Mit_Repeat_3

value: Nocodazole 24h

value: anti-H3S10p (Abcam ab5176)


title: RA7 shNAT10

value: synovial tissues

value: primary cell

value: rheumatoid arthritis fibroblast synoviocytes


title: BC16043,TIL non response

value: Breast cancer

value: Tumor-infiltrating lymphocyte

value: Post-REP TILs

value: Non reactive to autologous breast cancer cells


title: WholeHeart-ISO-KO-1

value: Heart

value: ISO


title: circRNA profile of case [62T]

value: tumor

value: hepatocellular carcinoma


title: RA7 control

value: WT

value: control lentivirus infection


title: ChIP-seq_H3S10p_Mit_Repeat_2

value: Cervix; Uterus

value: HeLa

value: epithelial cell


title: Cardiomyocyte-ISO-WT-4

value: Cardiomyocyte


title: ChIP-seq_H3S10p_Mit_Repeat_1

value: Nocodazole 24h

value: anti-H3S10p (Abcam ab5176)


title: RA1 shNAT10

value: synovial tissues

value: primary cell

value: rheumatoid arthritis fibroblast synoviocytes

value: NAT10 knockdown

value: shNAT10-lentivirus infection


title: Cardiomyocyte-ISO-KO-4

value: Heart


title: RA1 control


title: WholeHeart-ISO-WT-2

value: ISO


title: Cardiomyocyte-ISO-KO-3


title: ChIP-seq_input_Mit

value: none (input)


title: ChIP-seq_H3S10p_Asyn_Repeat_3

value: DMSO 24h


title: norrin and nutlin3 - replicate 4

city: Minneapolis

first: Harald

middle: J

last: Junge

state: Minnesota

address: Room 310A LRB, 2001 6th Street SE

department: OVNS

institute: University of Minnesota

data_processing:
Data were processed using the DNASTAR Lasergene (version 15) Seqman NGen RNA-Seq module. Differential gene expression analysis, gene ontology analysis, and statistical tests were performed in the DNA STAR Lasergene (version 15) Arraystar module.
Assembly: human genome 38p12
Supplementary files format and content: Processed data were exported from the DNASTAR Arraystar module  in xlsm format. The exported table contains the number of reads per gene, RPKM values, and the RPKM fold change between groups.

source_name: primary human retinal microvascular endothelial cells

growth_protocol: Human retinal microvascular endothelial cells (ACBRI 181) were cultured and maintained in EBM2 medium (CC-3156, Lonza) supplemented with single-quot growth factors (CC-4176, Lonza). Approximately 325K cells were seeded per well into a gelatin coated 6-well plate.

extract_protocol:
Trizol (Invitrogen, 15596026) was used to extract total RNA. DNA was digested (Turbo DNAse free, Invitrogen™ AM1907), and RNA was ribodepleted (Ribozero RNA removal kit, Illumina). The samples RNA integrity values were >8.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit (RS-122–2202), and 300 bp fragments were isolated. High output 150 bp paired-end sequencing was performed at Novogene, resulting in approximately 20 million reads per sample.

treatment_protocol: 24 hrs after seeding, cells were treated with R+D norrin (R+D Systems, 3014‐NR-025, 200 ng/ml), nutlin-3 (EMD Millipore, 444151-1MG, 10 µM), or their combination for 24 hr before harvest for RNA extraction. DMSO concentration in all samples was 0.1%.

value: HRMVECs represent a pooled population from multiple human donors

value: norrin 200 ng/ml plus nultin-3 10 µM


title: circRNA profile of case [5T]

value: tumor

value: hepatocellular carcinoma


title: ChIP-seq_H3S10p_Asyn_Repeat_2

value: Cervix; Uterus

value: HeLa

value: epithelial cell


title: circRNA profile of case [54T]


title: Cardiomyocyte-ISO-KO-2

value: Cardiomyocyte


title: nutlin-3 - replicate 4

value: primary human retinal microvascular endothelial cells

value: nultin-3 10 µM


title: circRNA profile of case [64T]


title: norrin - replicate 4

value: norrin 200 ng/ml


title: circRNA profile of case [51T]


title: circRNA profile of case [63T]


title: Cardiomyocyte-ISO-WT-2


title: VAS98

city: Armilla

first: Bioinformatics Unit

last: IPBLN-CSIC

state: GRANADA

address: Avda. del Conocimiento, 17. Instituto de Parasitología y Biomedicina Lopez-Neyra. Bioinformática

country: Spain

institute: IPBLN-CSIC

data_processing:
The paired-end sequencing was conducted on a HiSeq sequencer (Illumina, CA, USA) producing 34.6x2 M raw paired reads sample on average.
We used miARma-Seq pipeline to process the data and perform the analyses.
Raw data were evaluated using FastQC software to analyse the quality of the reads, and afterwards, sequences were aligned to the GRCh38 reference genome with STAR.
Principal component analysis (PCA) and hierarchical clustering of normalized samples were performed to check the similarity of RNA-sequencing samples.
Samples identified as outliers were filtered out from further analyses as well as duplicated samples and those presenting gender discrepancies.
Differential expression analyses were conducted using the limma package11. First, we removed the low expressed genes (CPM< 1) and calculated reads per kilobase per million mapped reads (RPKM) for downstream analyses. Then, we performed a linear model using the limma voom function12 including sex as a covariate. Finally, we carried out an eBayes test in order to identify genes that are differentially expressed between the subgroups in our study. We considered statistically differentially expressed genes (DEGs) those with a false discovery rate (FDR) < 0.05. log2 fold changes (logFC) was used to assess expression changes among groups of comparison. We also calculated TMM (trimmed mean of M-values) values for graphical representations1
All genes with a FDR < 0.05 were statistically significant and designated as differentially expressed genes (DEGs).
Subsequently, we used the online tool Enrichr14 to perform enrichment analysis of DEGs based on the following databases: BioPlanet 2019 and gene ontology (GO) for biological processes, cellular component, and molecular function. Significant enrichments were considered when p < 0.05 and a minimum count of 3 genes. Finally, we performed TF binding motif enrichment analysis of DEGs by applying the DoRothEA v2 tool15. We restricted our analyses to the most reliable interactions (A, B and C levels), and a p < 0.05 and normalized enrichment score (NES) of ± 2 were considered significantly enriched.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TMM values for each Sample

source_name: Whole blood

extract_protocol:
Peripheral blood mononuclear cells were acquired from whole blood by density gradient centrifugation using Ficoll-Paque (Rafer, Zaragoza, Spain). These cells were then incubated with CD4-APC conjugated antibodies (MiltenyiBiotec, Germany) in staining buffer (PBS with 2mM of EDTA and 4% FBS) for 20 minutes. Next, flow cytometry sorting was used to isolate CD4+ T cells through positive selection. Finally, both genomic DNA and total RNA were extracted from the same cell pellet by using AllPrep DNA/RNA/miRNA Universal kit (Qiagen, Hilden, Germany).  Total RNA quality was first determined by the 2100 Bioanalyzer System (Agilent, CA, USA),
1 ug of those samples with excellent quality RNA (RNA integrity number >7) was used for library synthesis with the TruSeq Stranded mRNA Library Prep Kit (Illumina, CA, USA) according to the manufacturer’s protocol

value: Whole blood

value: CD4+ T cells

value: T cells

tag: clasification*

value: F

tag: sorter day


title: Cardiomyocyte-ISO-KO-1

value: Heart

value: ISO


title: no treatment - replicate 4

value: HRMVECs represent a pooled population from multiple human donors

value: untreated


title: VAS97


title: nutlin-3 - replicate 3


title: VAS94


title: norrin - replicate 3


title: circRNA profile of case [49T]

value: tumor


title: circRNA profile of case [47T]

value: hepatocellular carcinoma


title: circRNA profile of case [52T]


title: circRNA profile of case [48T]


title: Cardiomyocyte-Saline-KO-3

value: Saline


title: VAS93


title: ChIP-seq_H3S10p_Asyn_Repeat_1

first: Dimple

institute: National Centre for Biological Sciences

value: Cervix; Uterus

value: HeLa

value: DMSO 24h

value: anti-H3S10p (Abcam ab5176)


title: Cardiomyocyte-Saline-WT-3

value: Cardiomyocyte


title: VAS92


title: no treatment - replicate 3

value: primary human retinal microvascular endothelial cells


title: Cardiomyocyte-Saline-KO-2


title: Cardiomyocyte-ISO-WT-3


title: VAS99

value: Whole blood

value: M


title: norrin and nutlin3 - replicate 3

value: norrin 200 ng/ml plus nultin-3 10 µM


title: nutlin-3 - replicate 2

value: nultin-3 10 µM


title: Cardiomyocyte-ISO-WT-1

value: Heart


title: Cardiomyocyte-Saline-KO-1


title: circRNA profile of case [45T]


title: circRNA profile of case [36T]


title: circRNA profile of case [43T]


title: circRNA profile of case [40T]


title: circRNA profile of case [34T]