title: Control_1

city: Los Angeles

first: Jeffrey

last: Harding

address: 405 Hilgard Avenue

institute: University of California Los Angeles

description: Library name: Sample_C_1

data_processing:
Deseq2 pipeline
Assembly: GRCm38
Supplementary files format and content: Tab deliominated file of raw counts for each sample

growth_protocol: 4T1 cells were injected to the right flank of female BALB/c mice (4-6 weeks old)

extract_protocol:
Lung tissues were collected, and RNA was then extracted with the QIAamp RNA blood mini kit.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: The mice were treated with PBS, anti-PD1, or nanocapsules of anti-PD1 (150 µg/mouse) at day 7 and day 14 after tumor engraftment. On day 21, lung tissues were collected for RNA sequencing.

value: Lung


title: ET-1_P03_D05

status: Public on Jun 25 2026

type: SRA

city: Brisbane

first: James

last: Hudson

state: Queensland

address: 300 Herston Rd, Herston QLD 4006

country: Australia

institute: QIMR Berghofer Medical Research Institute

description: Library name: LigandScreen-P03-20230901-036_S132

library_source: transcriptomic

data_processing:
Sequence reads were aligned using STAR (version 2.7.9a)
Counts matrix was generated using RSEM (version 1.3.1)
Assembly: Human reference, GRCh38 (Ensembl 98)
Supplementary files format and content: RSEM_Counts_Cardiopedia-Ligand.xlsx file includes raw counts for each sample

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Total RNA was isolated using the NuceloMag RNA kit (Macherey-Nagel) on the EpMotion 5075t
RNA libraries were prepared using the Illumina Stranded mRNA Prep Ligation kit (polyA RNA selection) on the EpMotion 5075t

treatment_protocol: hCO were stimulated with a library of 90 ligands (n = 2-5 hCO per ligand in final RNA-seq dataset after passing all quality control). After 24 hours, media was aspirated and hCO were washed with ice cold PBS- and lysed for RNAseq.

tag: cell line


title: DMSO, TPO/FL/SCF, 5d, donor1, batch3

city: Edogawa-ku

first: Kyungtaek

last: Lim

state: Tokyo

address: 1-16-13, Kitakasai

country: Japan

institute: Daiichi Sankyo Co., Ltd.

description: 10X Genomics

library_source: genomic single cell

data_processing:
The cell ranger ATAC pipeline (v2.0) was used for demultiplexing, barcode processing, read mapping against GRCh38, generation of a fragment file (a file contains coordinates of tagmented fragments), peak calling, and peak-cell count matrix construction.
ArchR (v1.0.1) was applied to the resulting fragment files to collect per-cell quality control metrics in addition to those provided from the cell ranger ATAC pipeline.
Assembly: GRCh38
Supplementary files format and content: h5. Barcode-peak count matrix
Supplementary files format and content: TSV, Fragments
Supplementary files format and content: CSV, cellranger-atac per-barcode stats
Supplementary files format and content: CSV, ArchR per-barcode stats

molecule: genomic DNA

source_name: bone marrow

growth_protocol: Primary human bone marrow CD34+ cells were cultured in StemSpan serum-free expansion medium (STEMCELL Technologies) in the presence of thrombopoietin (TPO, 50 ng/mL), TPO (50 ng/mL)/FLT3 ligand (FL, 100 ng/mL)/SCF (100 ng/mL), interleukin 3 (IL3, 20 ng/mL)/ interleukin 6 (IL6, 100 ng/mL), TPO (50 ng/mL)/IL3 (20 ng/mL)/IL6 (100 ng/mL), or TPO (50 ng/mL)/FL (100 ng/mL)/SCF (100 ng/mL)/IL3 (20 ng/mL)/IL6 (100 ng/mL) at 37 ℃ in a 5% CO2 incubator.

extract_protocol:
Cell nuclei were isolated following the standard protocol provided by 10x Genomics (Protocol number CG000169). In brief, 10,000 to 20,000 cells were lysed using 100 µL of lysis buffer (Tris-HCl pH7.4 10mM, NaCl 10mM, MgCl2 3mM, BSA 1%, Tween-20 0.1%, IGEPAL 0.1%, and Digitonin 0.01%) on ice for 5 minutes. Subsequent to lysis, cells were washed with chilled wash buffer (Tris-HCl pH7.4 10mM, NaCl 10mM, MgCl2 3mM, BSA 1%, Tween-20 0.1%). The cell suspension was centrifuged to pellet the nuclei, which were then resuspended in Nuclei Buffer (Chromium Single Cell ATAC Reagent Kits, 10x Genomics). The concentration of isolated nuclei was determined using a TC20 Automated Cell Counter (Bio-Rad).
Library preparation for scATAC-seq was performed by Chromium Next GEM Single Cell ATAC Reagent Kits v1.1 (10x Genomics) with manufacturer’s protocol.

treatment_protocol: Valemetostat or dimethyl sulfoxide was treated during the cell culture.

tag: tissue

value: bone marrow

tag: cell type

value: bone marrow CD34+ cells

tag: treatment

value: dimethyl sulfoxide 0.01%

tag: stimulation

value: TPO/FL/SCF

tag: time

tag: donor id

tag: experimental batch


title: iCAR, 4-hydroxybenzophenone, Ci10, 6h, D09

city: Mason

first: Yuqing

last: Shan

state: Ohio

address: 8700 mason montgomery road

country: USA

institute: Procter & Gamble

description: Library name: Ci10_T6_D1_D09

data_processing:
TempO-Seq data are analyzed using the Tempo-SeqR software package using the statistical computing language R.
The input for TempO-Seq data analysis is a folder of zipped FASTQ files. Each FASTQ file contains the reads and quality scores for one sample.
Each FASTQ file is aligned using the Bowtie algorithm to a pseudo-transcriptome input by the user.
The output for TempO-Seq data analysis is a table of counts with each column representing a sample and each row representing a gene.
Assembly: hWTv2
Supplementary files format and content: txt file

source_name: heart muscle cells

extract_protocol:
6h after treatment, 100uL of TempoSeq lysis buffer used to lyse cells per 96-well, which were then frozen and 2ul used for TempO-Seq library building
In TempO-Seq, each Detector Oligo (DO) consists of a sequence complementary to an mRNA target plus a universal (i.e. same for every targeted gene) primer binding site. They anneal in immediate juxtaposition to each other on the targeted RNA template such that they can be ligated together. Ligated detector oligos are PCR-amplified using a primer set (single-plex PCR reaction, with a single primer pair for each sample) that introduces both the adaptors required for sequencing and a sample-specific barcode. The barcode sequences flank the target sequence and are inserted appropriately into the standard Illumina adaptors to permit standard dual-index sequencing of the barcodes and deconvolution of sample-specific reads from the sequencing data using the standard Illumina software. All the PCR-amplified and barcoded samples are pooled into a single library for sequencing. Sequencing reads are demultiplexed using the standard sequencing instrument software for each sample using the barcodes to give a FASTQ file for each.

value: heart muscle cells

value: iCAR

value: human induced pluripotent stem cells (iPSCs)

tag: genotype

value: iPSC-derived cardiomyocytes

value: test

tag: batch


title: Control_2

state: CA

description: Library name: Sample_C_2

molecule: polyA RNA

organism: Mus musculus

source_name: Lung


title: cd8a5

city: Stanford

first: Julien

last: Couthouis

address: 279 Campus Dr

department: Genetics

institute: Stanford University

data_processing:
illumina basecalling
STAR alignment
RSEM counts
DESeq2 normalization and analyzis
Full pipeline with settings used available on https://github.com/emc2cube/Bioinformatics/blob/master/sh_RNAseq.sh
Assembly: mm10
Supplementary files format and content: comma separated value text files with normalized abundance measurements (output from DESeq2)

source_name: hippocampus

extract_protocol:
RNA extracted using Qiagen Rneasy extraction
polyA enriched mRNA libraries (SureSelect Automated Strand-Specific RNA Library Prep, mRNA Library Prep for Illumina Paired-End Multiplexed Sequencing)

treatment_protocol: For CD8 depletion, Aged (22-24 months) mice were treated i.p. with 200 μm of InVivoMAb anti-mouse CD8a (2.43, BioXCell, BE0061) or InVivoMAb rat IgG2b isotype control (LTF-2, BioXCell, BE0090) in 200 μL PBS every 4 days until time of sacrifice. For adoptive transfer, B6.SJL-Ptprca Pepcb/BoyJ (4 months) mice were treated i.p. with 200 μm of InVivoMAb anti-mouse CD8a in 200 μL PBS day -11 and -7 to deplete resident CD8+ T cells. CD8+ T cells were isolated from single cell suspensions of spleenocytes and PBMCs from young (3-4 months) or aged (22-28 months) C57BL/6J mice using the CD8a+ T cell Isolation Kit (Miltenyi Biotech, 130-104-075) according to manufacturer instructions. For adoptive transfer of young or aged CD8+ T cells, cells were immediately resuspended at concentrations of 3e5 (first injection) or 3e6 (second injection) in 100 μL saline and injected via tail vein. Mice were anesthetized with 87.5 mg per kg ketamine and 12.5 mg per kg xylazine and transcardially perfused with ice-cold phosphate-buffered saline. To process the brains, the whole brain was sectioned in half along the sagittal plane. The hippocampus from one hemisphere was subdissected and flash frozen.

value: hippocampus

tag: Sex

value: male

value: WT

tag: age

value: Aged

value: CD8a depleting antibody


title: cd8a23


title: 37_144-07_Day_10_S278_L004

city: Durham

first: Andrew

state: NC

address: 1328 Campus Drive

department: Surgery

institute: Duke University

description: Library name: 37_144-07_Day_10_S278_L004

data_processing:
Alignment was performed using STAR algorithm version 2.5.2b as described [Aid et al. Front Cell Infect Microbiol 2020]
Transcripts were annotating as described [Aid et al. Front Cell Infect Microbiol 2020]
Assembly: MacaM Assembly (Available at https://www.unmc.edu/rhesusgenechip/index.htm#NewRhesusGenome)
Supplementary files format and content: Tab delimited text file containing raw read counts for each sample (in columns) and each annotated transcript (in rows).

organism: Macaca mulatta

source_name: Peripheral Blood

extract_protocol:
Peripheral NK cells were isolated from PBMC by fluorescence-activated cell sorting. RNA extraction was conducted as described [Aid et al. Front Cell Infect Microbiol 2020]. Quality control was performed using an Agilent BioAnalyzer.
Libraries were validated by capillary electrophoresis on an Agilent 4200 TapeStation, pooled at equimolar concentrations, and sequenced on an Illumina HiSeq3000 at 100SR

treatment_protocol: Macaques were infected with SIVmac239 intravenously as described [Aid et al. Front Cell Infect Microbiol 2020]

value: Peripheral Blood

value: NK cells


title: iCAR, 4-hydroxybenzophenone, Ci10, 6h, C12

description: Library name: Ci10_T6_D1_C12


title: cd8a11


title: Val-1k, TPO/FL/SCF/IL3/IL6, 3d, donor1, batch3

description: 10X Genomics

value: valemetostat 1uM


title: 37_144-07_Day_10_S278_L003

description: Library name: 37_144-07_Day_10_S278_L003


title: DMSO, TPO/FL/SCF/IL3/IL6, 3d, donor1, batch3

description: 10X Genomics

value: bone marrow


title: AT9

value: Young

value: Aged CD8+ T Cell transfer


title: 37_144-07_Day_10_S278_L002

description: Library name: 37_144-07_Day_10_S278_L002


title: iCAR, 4-hydroxybenzophenone, Ci10, 6h, E09

description: Library name: Ci10_T6_D2_E09


title: Val-1k, TPO/FL/SCF, 3d, donor1, batch3

description: 10X Genomics

value: bone marrow CD34+ cells

value: TPO/FL/SCF


title: iCAR, 2-hydroxybenzophenone, Ci10, 6h, E06

description: Library name: Ci10_T5_D3_E06

value: heart muscle cells

value: iCAR


title: AT22


title: 36_144-07_Day_8_S277_L004

description: Library name: 36_144-07_Day_8_S277_L004


title: iCAR, 2-hydroxybenzophenone, Ci10, 6h, C09

description: Library name: Ci10_T5_D3_C09

value: human induced pluripotent stem cells (iPSCs)

value: iPSC-derived cardiomyocytes


title: DMSO, TPO/FL/SCF, 3d, donor1, batch3

description: 10X Genomics

value: dimethyl sulfoxide 0.01%


title: aLSL, rep2

city: Princeton

first: Yuri

last: Pritykin

state: NJ

address: 245 Carl Icahn Lab

department: QCB

institute: Princeton

description: Hi-C on sorted T cells

library_source: genomic

data_processing:
Hi-C reads were aligned to the mouse UCSC mm10 GRCm38 genome (chromosomes 1-19, X, Y) downloaded from the 4DNucleome (4DNFI2493SDN) using bwa mem version 0.7.17, with settings --SP5M. Pairs files were generated using pairtools parse version 0.3.0 with a min-mapq cutoff of 30 and --walks-policy 5unique, followed by pairtools dedup with default parameters, and pairtools select for the following pair types: UU, UR, and UR. Pairs files were mapped into cool files using cooler version 0.8.11. Hi-C data in these cool files was normalized using cooler balance with default parameters for each sample separately and for merged biological replicates of each condition across all conditions. This way, balancing normalization was applied to both intrachromosomal and interhcromosomal Hi-C signal.
Assembly: mm10
Supplementary files format and content: mcool: hi-c pairs at different resolutions

source_name: SLO

extract_protocol:
A cell suspension was made from pooled secondary lymphoid organs (spleen, pLNs and mLNs) of Foxp3GFP/LSL mice (cite PMID 15780990; 34426690) by meshing the organs through a 100-μm strainer (Corning, 07-201-432) with a syringe plunger. CD4+ T cells were enriched with the Dynabeads Flowcomp Mouse CD4 Kit (Thermo Fisher, 11461D) according to the manufacturer’s instructions, stained with antibodies, washed extensively, resuspended in isolation buffer (PBS with 2% FBS, 10 mM HEPES buffer, 1% l-glutamine and 2 mM EDTA), and sorted on a FACSAria (BD) instrument. Treg cells were sorted as TCRβ+CD4+CD8−NK1.1−Foxp3-GFP+Thy-1.1−, and naïve conventional CD4+ T cells as TCRβ+CD4+CD8−NK1.1−Foxp3-GFP−Thy-1.1−CD44loCD62Lhi. Wannabe Treg cells were sorted from Foxp3GFP/LSL mice as follows: naïve wannabe Treg cells: TCRβ+CD4+CD8−NK1.1−Foxp3-GFP−Thy-1.1+ CD44loCD62Lhi; activated wannabe Treg cells: TCRβ+CD4+CD8−NK1.1−Foxp3-GFP−Thy-1.1+CD44hiCD62L−; Treg cells and conventional CD4+ T cells were sorted from Foxp3DTR mice as follows: naïve Treg cells: TCRβ+CD4+CD8−NK1.1−Foxp3-DTR+ CD44loCD62Lhi; activated Treg cells: TCRβ+CD4+CD8−NK1.1−Foxp3-DTR+ CD44hiCD62L−; naïve conventional CD4+ T cells: TCRβ+CD4+CD8−NK1.1−Foxp3-DTR−CD44loCD62Lhi; activated conventional CD4+ T cells: TCRβ+CD4+CD8−NK1.1−Foxp3-DTR− CD44hiCD62L−. 100,000 cells were sorted for each population per replicate.
Hi-C for Tcon and Treg cells: Hi-C was performed as previously described (Viny et al., 2019). Briefly, sorted T cell populations (approximately 1x105) were cross-linked in 1% formaldehyde for 10 minutes and quenched in 125mM glycine. Cross-linked cells were lysed and chromatin was digested using the Arima HiC+ kit (Arima Genomics, San Diego, CA) using protocol adaptations for low cell input. Digested and reverse crosslinked DNA was eluted in 100uL and fragmented to 350 bps using a Covaris LE220Rsc sonicator (Covaris, Woburn, MA). Sheared genomic material was enriched for biotinylated DNA using streptavidin beads followed by library preparation using Arima protocol modifications for Accel-NGS 2S DNA plus library kit (IDT, Coralville, IA). After end repair and ligation, libraries were quantified using the KAPA library quantification kit (Roche, Indianapolis, IN) and PCR amplified for the number of cycles required to generate >4nM per library. Hi-C libraries were sequenced on an Illumina NovaSeq and raw sequencing data in the FASTQ format were obtained.

value: SLO

value: Active Foxp3-KO (LSL) Treg


title: Nanocapsule_Anti-PD1_2

description: Library name: Sample_N_2

value: Lung


title: AT20

value: hippocampus

value: male

value: WT


title: 36_144-07_Day_8_S277_L003

description: Library name: 36_144-07_Day_8_S277_L003

value: Peripheral Blood

value: NK cells


title: DMSO, TPO/FL/SCF/IL3/IL6, 7d, donor2, batch2

description: 10X Genomics

value: bone marrow


title: AT1

value: Young

value: Aged CD8+ T Cell transfer


title: iCAR, 2-hydroxybenzophenone, Ci10, 6h, A12

description: Library name: Ci10_T5_D3_A12

value: test


title: 36_144-07_Day_8_S277_L002

description: Library name: 36_144-07_Day_8_S277_L002


title: iCAR, 2-hydroxybenzophenone, Ci10, 6h, H11

description: Library name: Ci10_T5_D2_H11

value: heart muscle cells


title: Val-1k, TPO/IL3/IL6, 7d, donor2, batch2

description: 10X Genomics

value: bone marrow CD34+ cells

value: valemetostat 1uM


title: AT18


title: 35_144-07_Day_6_S276_L004

description: Library name: 35_144-07_Day_6_S276_L004


title: iCAR, 2-hydroxybenzophenone, Ci10, 6h, E03

description: Library name: Ci10_T5_D2_E03

value: iCAR

value: human induced pluripotent stem cells (iPSCs)

value: iPSC-derived cardiomyocytes


title: DMSO, TPO/IL3/IL6, 7d, donor2, batch2

description: 10X Genomics

value: dimethyl sulfoxide 0.01%


title: Human macrophages, Uninfected, 6 hr, replicate 3

city: Paris

first: Alexandre

last: Giraud-Gatineau

address: 25-28 rue du docteur roux

department: Microbiology

country: France

institute: Institut Pasteur

description:
Library name: Sample 3
N89DPD_3_Uninfected_rep_3

data_processing:
Quality of the fastq files was assessed using FastQC v0.12.1. Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp. Quality-filtered reads were aligned to the reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, followed by coordinate sorting using samtools v1.22.1. PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0. Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3, with results aggregated into a comprehensive quality control report using MultiQC v1.32. Gene-level expression quantification was performed using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id. Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file.  Sample-sample correlations for sample-sample heatmap and PCA were calculated on normalized counts (TMM, trimmed mean of M-values) using Pearson correlation. Differential expression was done with edgeR v4.0.16 using standard practice including filtering for low-expressed genes with edgeR::filterByExprwith default values. Functional enrichment, when available, is performed using gene set enrichment analysis with gseapy v0.12 using the MSigDB Hallmark gene set.
Assembly: Human samples: GRCh38_114; Murine samples: GRCm39_114
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNAs from human and murine macrophages at 6 hr post-infection were extracted using QIAzol lysis reagent (Qiagen) and purified using RNeasy mini kit (Qiagen) with a DNAse treatment.
RNA-seq libraries were prepared by Plasmidsaurus using their proprietary transcriptomics workflow. Briefly, mRNA was reverse-transcribed into complementary DNA (cDNA), followed by second-strand synthesis. The resulting cDNA was subjected to tagmentation, indexing, and PCR amplification to generate sequencing-ready libraries. This protocol is based on a 3′-end counting strategy, in which reads are generated from the 3′ end of transcripts to enable accurate and efficient quantification of gene expression while minimizing transcript length bias.

treatment_protocol: THP-1 cells (a human monocyte cell line; ATCC TIB-202) and Raw 264.7 cells (a murine macrophage cell line) were cultured in RPMI 1640 medium (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (Sigma) and 2 mM L-glutamine (Gibco). THP-1 cells were differentiated/activated into macrophages by a treatment with 50 nM PMA for 2 days following by a 24 hr incubation without PMA. Macrophages were infected with L. interrogans at a multiplicity of infection (MOI) of 50 bacteria-per-cell during 6 hr. Cells were incubated in 5% CO2 at 37°C.


title: pir2-1_clr4∆_clr4+_H3K9me2

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

description:
Library name: pir2-1_clr4∆_clr4+
pir2-1_clr4∆_clr4+_H3K9me2

data_processing:
Single ended fastq format sequences derived from ChIP-seq data were quality-trimmed using fastp (Chen et al. 2018).
Trimmed fastqs were aligned to the S. pombe reference (Wood et al. 2002) using the BWA aligner (Li H. and Durbin R. 2009) and fold enrichment bedgraphs were generated using Macs2 (Zhang Y et al, 2008).
Assembly: S. pombe V2 reference with the sequence of the full 40 kb mat region provided on a separate contig (MAT).
Supplementary files format and content: Bedgraph format of either Fold Enrichment vs Input-normalized Untagged control (IP), or RPM normalized pileups (Input)

organism: Schizosaccharomyces pombe

source_name: Yeast Whole Cells

growth_protocol: Growth in YEA 26°C, shifted to 36°C for 5 hrs

extract_protocol:
Cells were crosslinked using 3% PFA at room temperature for 30 min, quenched with 125 mM glycine and cells were spun at 2,000g for 5 min. The cells were then washed with 1X PBS.  Cells pellets were lysed using glass beads and lysis buffer (50mM Hepes/KOH, 140mM NaCl, 1 mM EDTA, 1% Triton X100, 0.1% DOC plus protease inhibitors). Cell lysates were sheared using a Bioruptor-300 (Diagenode) to an approximate size of 300–600 bp.
ChIPseq sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer’s protocol and analyzed using an Agilent 4200 TapeStation system (Agilent).

tag: strain

value: Msmt0 leu1-32 ade6-210 his2 ura4DS/E pir2-1-FLAG<<KanMX clr4D::KanMX otr1R(Sph1)::ura+ pAK70clr4+

value: Yeast Whole Cells

tag: chip antibody

value: Anti-Histone (di methyl K9) antibody_ab115159

tag: growth

tag: fixation

value: 3% PFA


title: 35_144-07_Day_6_S276_L003

description: Library name: 35_144-07_Day_6_S276_L003

value: Peripheral Blood


title: iCAR, 2-hydroxybenzophenone, Ci10, 6h, C06

description: Library name: Ci10_T5_D2_C06


title: Val-1k, IL3/IL6, 7d, donor2, batch2

description: 10X Genomics


title: pir2-1_clr4∆_vec_H3K9me2

description:
Library name: pir2-1_clr4∆_vec
pir2-1_clr4∆_vec_H3K9me2

value: Msmt0 leu1-32 ade6-210 his2 ura4DS/E pir2-1-FLAG<<KanMX clr4D::KanMX otr1R(Sph1)::ura+ pREP1

value: Growth in YEA 26°C, shifted to 36°C for 5 hrs


title: aTcon, rep1

description: Hi-C on sorted T cells

value: SLO

value: Active Tcon

value: WT


title: 35_144-07_Day_6_S276_L002

description: Library name: 35_144-07_Day_6_S276_L002

value: NK cells


title: DMSO, IL3/IL6, 7d, donor2, batch2

description: 10X Genomics

value: bone marrow

value: bone marrow CD34+ cells


title: Treg, rep3

description: Hi-C on sorted T cells

value: Treg


title: iCAR, 2-hydroxybenzophenone, Ci10, 6h, B09

description: Library name: Ci10_T5_D2_B09

value: heart muscle cells

value: iCAR

value: human induced pluripotent stem cells (iPSCs)

value: test


title: clr4∆_clr4+_H3K9me2

description:
Library name: clr4∆_clr4+
clr4∆_clr4+_H3K9me2

value: Msmt0 leu1-32 ade6-210 his2 ura4DS/E clr4D::KanMX otr1R(Sph1)::ura+ pAK70clr4+

value: Yeast Whole Cells


title: iCAR, Kaempferol, Ci10, 6h, A10

description: Library name: Ci10_T7_D3_A10

value: iPSC-derived cardiomyocytes


title: 34_144-07_Day_3_S275_L004

description: Library name: 34_144-07_Day_3_S275_L004

value: Peripheral Blood


title: Val-1k, TPO/FL/SCF, 7d, donor2, batch2

description: 10X Genomics

value: valemetostat 1uM

value: TPO/FL/SCF


title: iCAR, 2-hydroxybenzophenone, Ci10, 6h, G11

description: Library name: Ci10_T5_D1_G11


title: clr4∆_vec_H3K9me2

description:
Library name: clr4∆_vec
clr4∆_vec_H3K9me2

value: Msmt0 leu1-32 ade6-210 his2 ura4DS/E  clr4D::KanMX otr1R(Sph1)::ura+ pREP1

value: Anti-Histone (di methyl K9) antibody_ab115159

value: Growth in YEA 26°C, shifted to 36°C for 5 hrs

value: 3% PFA


title: 34_144-07_Day_3_S275_L003

description: Library name: 34_144-07_Day_3_S275_L003

value: NK cells


title: DMSO, TPO/FL/SCF, 7d, donor2, batch2

description: 10X Genomics

value: bone marrow

value: bone marrow CD34+ cells

value: dimethyl sulfoxide 0.01%


title: iCAR, 2-hydroxybenzophenone, Ci10, 6h, D03

description: Library name: Ci10_T5_D1_D03

value: heart muscle cells

value: iCAR


title: 34_144-07_Day_3_S275_L002

description: Library name: 34_144-07_Day_3_S275_L002


title: pir2-1_H3K9me2

description:
Library name: Pir2-1
pir2-1_H3K9me2

value: Msmt0 leu1-32 ade6-210 his2 ura4DS/E pir2-1-FLAG<<KanMX otr1R(Sph1)::ura+


title: Tcon, rep3

description: Hi-C on sorted T cells

value: SLO

value: Tcon

value: WT


title: Val-1k, TPO/FL/SCF/IL3/IL6, 7d, donor1, batch2

description: 10X Genomics


title: iCAR, 2-hydroxybenzophenone, Ci10, 6h, B06

description: Library name: Ci10_T5_D1_B06

value: human induced pluripotent stem cells (iPSCs)

value: iPSC-derived cardiomyocytes

value: test


title: 33_144-07_Day_1_S274_L004

description: Library name: 33_144-07_Day_1_S274_L004

value: Peripheral Blood


title: WT_H3K9me2

description:
Library name: WT
WT_H3K9me2

value: Msmt0 leu1-32 ade6-216 his2 ura4DS/E otr1R(Sph1)::ura+

value: Yeast Whole Cells

value: Anti-Histone (di methyl K9) antibody_ab115159


title: iCAR, 2-hydroxybenzophenone, Ci10, 6h, A09

description: Library name: Ci10_T5_D1_A09


title: DMSO, TPO/FL/SCF/IL3/IL6, 7d, donor1, batch2

description: 10X Genomics


title: IP-Input-1

description:
Library name: IP-Input-1
IP-Input-1

value: Growth in YEA 26°C, shifted to 36°C for 5 hrs

value: 3% PFA


title: 33_144-07_Day_1_S274_L003

description: Library name: 33_144-07_Day_1_S274_L003

value: NK cells


title: iCAR, 2-hydroxybenzophenone, Ci10, 6h, F03

description: Library name: Ci10_T5_D3_F03


title: iCAR, 3-hydroxybenzophenone, Ci10, 6h, H08

description: Library name: Ci10_T4_D3_H08


title: Val-1k, TPO/IL3/IL6, 7d, donor1, batch2

description: 10X Genomics

value: bone marrow

value: bone marrow CD34+ cells

value: valemetostat 1uM


title: 33_144-07_Day_1_S274_L002

description: Library name: 33_144-07_Day_1_S274_L002


title: rOPCs_CTK+GAL3

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

country: Italy

institute: European Brain Research Institute

description: Library name: Sample12

data_processing:
Quality control of FASTQ raw data files was done using FastQC. FASTQ files were downloaded from the service provider with reads already quality trimmed and filtered.
STAR was used to align FASTQ files to rat genome with GTF annotations
Quality control of aligned BAM files was accomplished by Qualimap ver 2.2.2
Expression gene fragments (gene pia counts) were extracted from aligned BAM files by featurecounts
Differential expression analysis was performed using DESeq2 package in R-Bioconductor.
Assembly: Ensemble Rattus Norvegicus release 112
Supplementary files format and content: Text files containing in the last column fragment (read pairs) counts of filtered data, aggregated by Ensemble Gene ID. Files were obtained by the tool featurecounts.

organism: Rattus norvegicus

source_name: brain cortex

growth_protocol: Primary oligodendrocytes were obtained from a mixed glial rat primary culture as described previously (Fumagalli et al., 2011). After brain cortex isolation of P0-P2 postnatal days rat pups, tissue was mechanically and chemically dissociated and kept in culture with medium change every other day. Upon confluence (eight days in vitro), flasks were shaken uto remove microglia followed by an additional 3-hour shaking to obtain OPCs. OPCs were seeded in proliferation medium and cultured for three days until treatments.

extract_protocol:
Cells were lysed using Trizol™ reagent 24 hours after galinex stimulation. Total RNA was extracted using the Direct-zol RNA Microprep Kit (ZymoResearch, R2062).
Quality control of raw sequencing reads was performed using FastQC. Genome indexation and alignment from the Rattus norvegicus reference was performed using STAR R package. A comprehensive filtering strategy was applied to improve data quality: unannotated features were removed, and low-abundance genes were filtered out using the "Average" method with an abundance threshold of 5. Additionally, to exclude invariable features, a variance filter was applied to remove the lowest 15% of features based on interquartile range. Following filtration, data normalization was performed using the Log2-counts per million (logCPM) transformation to adjust for sequencing depth and stabilize variance prior to downstream analysis.

treatment_protocol: Treatments were performed when cells were switched to differentiating condition, . Cells initially received ¾ of the volume of medium containing a pro-inflamatory cytokine cocktail (CTK) with 2 ng/mL of each TNF-α, IL-1β and IFN-γ, and, after 6 hours, cells received the remaining ¼ of media containing media with four time-concentrated GAL or equivalent DMSO to reach the final desired concentration (10 nM).

value: brain cortex

value: postnatal day 2 primary cells

value: oligodendrocytes

value: pooled male and female

value: wild-type

value: Cytokines + Galinex


title: DMSO, TPO/IL3/IL6, 7d, donor1, batch2

description: 10X Genomics

value: dimethyl sulfoxide 0.01%


title: D3_cerv_DMSO_1

first: Paul

last: Khavari

address: 269 Campus Dr

department: Dermatology

description: Library name: D3_cerv_DMSO_1

data_processing:
UMI extraction with UMI tools
read alignment to reference genome using STAR
featureCount generation
DESeq2 with apeGLM shrinkage,
Assembly: GRCh38
Supplementary files format and content: feature counts

source_name: cornea

growth_protocol: Cells were aquired from ATCC (PCS-480-011, grown in ATCC PCS-480-032 and PCS-480-042) (PCS-700-010, grown in ATCC PCS-700-040 and ATCC PCS-700-030)

extract_protocol:
Cells previously transfected with siRNA or treated with pharmacologic compounds were collected in RLT plus lysis buffer supplemented with 10uL/mL Beta-mercaptoethanol (ß-ME) and passed through QIAshredder (Qiagen) column. RNA was then extracted using the RNeasy Plus mini kit (Qiagen).
Libraries were prepared with 10-500ng input to the QuantSeq mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) following the manufacturer’s protocol. Libraries were quantified with KAPA Library Quantification Kit Illumina® Platforms (Roche) and sequenced on NovaSeq X+ with ~30 M paired-end, 150 bp reads per sample.

treatment_protocol: cells were treated with DMSO or NEDD8i for 16hrs then harvested

value: cornea

value: cervical epithelial cells


title: rOPCs_CTK+GAL2

description: Library name: Sample11


title: iCAR, 3-hydroxybenzophenone, Ci10, 6h, F11

description: Library name: Ci10_T4_D3_F11

value: heart muscle cells

value: iCAR

value: human induced pluripotent stem cells (iPSCs)

value: iPSC-derived cardiomyocytes

value: test


title: 31_349-09_Day_14_S272_L004

description: Library name: 31_349-09_Day_14_S272_L004

value: Peripheral Blood

value: NK cells


title: Val-1k, IL3/IL6, 7d, donor1, batch2

description: 10X Genomics

value: bone marrow

value: bone marrow CD34+ cells

value: valemetostat 1uM


title: iCAR, 3-hydroxybenzophenone, Ci10, 6h, C03

description: Library name: Ci10_T4_D3_C03


title: rOPCs_CTK+GAL1

description: Library name: Sample10

value: brain cortex

value: postnatal day 2 primary cells

value: oligodendrocytes


title: DMSO, IL3/IL6, 7d, donor1, batch2

description: 10X Genomics


title: 31_349-09_Day_14_S272_L003

description: Library name: 31_349-09_Day_14_S272_L003


title: rOPCs_CTK3

description: Library name: Sample9

value: pooled male and female

value: wild-type

value: Cytokines


title: iCAR, 3-hydroxybenzophenone, Ci10, 6h, A06

description: Library name: Ci10_T4_D3_A06


title: 31_349-09_Day_14_S272_L002

description: Library name: 31_349-09_Day_14_S272_L002


title: Val-1k, TPO, 7d, donor1, batch2

description: 10X Genomics

value: TPO


title: rOPCs_CTK2

description: Library name: Sample8


title: iCAR, 3-hydroxybenzophenone, Ci10, 6h, H05

description: Library name: Ci10_T4_D2_H05

value: heart muscle cells


title: DMSO, TPO, 7d, donor1, batch2

description: 10X Genomics

value: dimethyl sulfoxide 0.01%


title: YT2

value: hippocampus

value: male

value: WT

value: Young

value: Young CD8+ T Cell transfer


title: 30_349-09_Day_10_S271_L004

description: Library name: 30_349-09_Day_10_S271_L004

value: Peripheral Blood

value: NK cells


title: iCAR, 3-hydroxybenzophenone, Ci10, 6h, F08

description: Library name: Ci10_T4_D2_F08

value: iCAR

value: human induced pluripotent stem cells (iPSCs)

value: iPSC-derived cardiomyocytes

value: test


title: iCAR, 3-hydroxybenzophenone, Ci10, 6h, E11

description: Library name: Ci10_T4_D2_E11


title: rOPCs_GAL3

description: Library name: Sample6

value: brain cortex

value: postnatal day 2 primary cells

value: oligodendrocytes

value: pooled male and female

value: Galinex


title: 30_349-09_Day_10_S271_L003

description: Library name: 30_349-09_Day_10_S271_L003


title: 30_349-09_Day_10_S271_L002

description: Library name: 30_349-09_Day_10_S271_L002


title: DMSO, TPO/IL3/IL6, 3d, donor2, batch2

description: 10X Genomics

value: bone marrow

value: bone marrow CD34+ cells

value: dimethyl sulfoxide 0.01%


title: 29_349-09_Day_7_S270_L004

description: Library name: 29_349-09_Day_7_S270_L004


title: DMSO, IL3/IL6, 3d, donor2, batch2

description: 10X Genomics


title: iCAR, 3-hydroxybenzophenone, Ci10, 6h, G05

description: Library name: Ci10_T4_D1_G05

value: heart muscle cells


title: rOPCs_GAL1

description: Library name: Sample4

value: wild-type


title: rOPCs_GAL2

description: Library name: Sample5


title: iCAR, 3-hydroxybenzophenone, Ci10, 6h, E08

description: Library name: Ci10_T4_D1_E08


title: rOPCs_CTRL3

description: Library name: Salmple3


title: DMSO, TPO/FL/SCF, 3d, donor2, batch2

description: 10X Genomics

value: TPO/FL/SCF


title: 29_349-09_Day_7_S270_L002

description: Library name: 29_349-09_Day_7_S270_L002

value: Peripheral Blood


title: iCAR, 3-hydroxybenzophenone, Ci10, 6h, D11

description: Library name: Ci10_T4_D1_D11


title: rOPCs_CTRL2

description: Library name: Sample2


title: 28_349-09_Day_3_S269_L004

description: Library name: 28_349-09_Day_3_S269_L004

value: NK cells


title: rOPCs_CTRL1

description: Library name: Sample1


title: iCAR, 3-hydroxybenzophenone, Ci10, 6h, A03

description: Library name: Ci10_T4_D1_A03

value: iCAR


title: 28_349-09_Day_3_S269_L003

description: Library name: 28_349-09_Day_3_S269_L003


title: DMSO, TPO/IL3/IL6, 3d, donor1, batch2

description: 10X Genomics


title: 28_349-09_Day_3_S269_L002

description: Library name: 28_349-09_Day_3_S269_L002


title: TGFB1-overexpressing lens epithelium (OVE918) replicate 4

city: Sydney

first: Frank

last: Lovicu

address: K25 - Medical Foundation Building

department: Molecular and Cellular Biomedicine

institute: University of Sydney

description:
Library name: Sample 10
918-d

data_processing:
Adapter trimming performed using Cutadapt v5.2.
Reads aligned to the Mus musculus reference genome (mm39) using STAR v2.7.11b.
Gene-level read counts generated using featureCounts v2.0.8 with NCBI RefSeq gene annotation.
Genes with FPKM ≥2 in at least half of the samples were retained for downstream analyses.
Differential expression analysis was performed using edgeR v4.6.3 following TMM normalization (|log2FC| ≥1, FDR ≤0.05).
Assembly: mm39
Supplementary files format and content: Tab-delimited text file includes gene-level raw read counts for each sample.

source_name: lens epithelium

growth_protocol: Three-week-old wild-type and transgenic mice overexpressing human TGF-β1 in the lens  (OVE853 and OVE918 lines) were maintained under standard animal care conditions. Lens epithelial tissues were isolated from mouse eyes for RNA extraction.

extract_protocol:
For OVE853 mice, three biological replicates were collected for RNA extraction and sequencing, with each replicate consisting of up to 18 freshly isolated lens epithelial explants from 9 mice exhibiting anterior subcapsular cataract plaques. For OVE918 mice, four biological replicates were collected, with each replicate consisting of up to 14 freshly isolated lens epithelial explants from 7 mice. For WT controls, three biological replicates were collected, each consisting of lens epithelial tissues pooled from up to 9 mice. Tissues for each replicate were immediately pooled in 500 µL TRIzol reagent and stored at -80°C. Total RNA was extracted according to the manufacturer's instructions. RNA samples (2.5 µg) were treated with TURBO DNA-free Kit (Invitrogen) to remove genomic DNA contamination. RNA quantity and quality were assessed using the RNA 6000 Nano Kit on an Agilent Bioanalyzer. Samples with RNA Integrity Number (RIN) values greater than 7.0 were used for sequencing.
mRNA sequencing libraries were prepared according to the manufacturer's protocol.

treatment_protocol: No experimental treatment was administered. Samples were collected from wild-type mice and transgenic mice overexpressing human TGF-β1 in the lens

value: lens epithelium

value: lens epithelial cells

value: TGFB1 overexpression (OVE918)


title: iCAR, Avobenzone, Ci10, 6h, G04

description: Library name: Ci10_T1_D3_G04

value: human induced pluripotent stem cells (iPSCs)

value: iPSC-derived cardiomyocytes

value: test


title: TGFB1-overexpressing lens epithelium (OVE918) replicate 3

description:
Library name: Sample 9
918-c


title: 27_349-09_Day_1_S268_L004

description: Library name: 27_349-09_Day_1_S268_L004


title: Val-1k, TPO/FL/SCF, 14d, donor3, batch1

description: 10X Genomics

value: valemetostat 1uM


title: TGFB1-overexpressing lens epithelium (OVE918) replicate 2

description:
Library name: Sample 8
918-b


title: 27_349-09_Day_1_S268_L003

description: Library name: 27_349-09_Day_1_S268_L003


title: Val-330, TPO/FL/SCF, 14d, donor3, batch1

description: 10X Genomics

value: valemetostat 0.33uM


title: TGFB1-overexpressing lens epithelium (OVE918) replicate 1

description:
Library name: Sample 7
918-a


title: iCAR, Avobenzone, Ci10, 6h, A02

description: Library name: Ci10_T1_D3_A02


title: DMSO, TPO/FL/SCF, 14d, donor3, batch1

description: 10X Genomics

value: bone marrow


title: 27_349-09_Day_1_S268_L002

description: Library name: 27_349-09_Day_1_S268_L002


title: iCAR, Avobenzone, Ci10, 6h, H01

description: Library name: Ci10_T1_D2_H01


title: TGFB1-overexpressing lens epithelium (OVE853) replicate 3

description:
Library name: Sample 6
853-c

value: TGFB1 overexpression (OVE853)


title: iCAR, Avobenzone, Ci10, 6h, E10

description: Library name: Ci10_T1_D3_E10


title: 25_94-09_Day_14_S266_L004

description: Library name: 25_94-09_Day_14_S266_L004


title: iCAR, Avobenzone, Ci10, 6h, F04

description: Library name: Ci10_T1_D2_F04


title: TGFB1-overexpressing lens epithelium (OVE853) replicate 2

description:
Library name: Sample 5
853-b


title: 25_94-09_Day_14_S266_L003

description: Library name: 25_94-09_Day_14_S266_L003


title: iCAR, Avobenzone, Ci10, 6h, E07

description: Library name: Ci10_T1_D2_E07


title: Val-1k, TPO, 7d, donor3, batch1

description: 10X Genomics

value: bone marrow CD34+ cells

value: TPO


title: 25_94-09_Day_14_S266_L002

description: Library name: 25_94-09_Day_14_S266_L002


title: TGFB1-overexpressing lens epithelium (OVE853) replicate 1

description:
Library name: Sample 4
853-a


title: iCAR, Avobenzone, Ci10, 6h, D10

description: Library name: Ci10_T1_D2_D10

value: heart muscle cells


title: Val-330, TPO, 7d, donor3, batch1

description: 10X Genomics


title: Wild-type lens epithelium replicate 3

description:
Library name: Sample 3
WT-c

value: Wild-type


title: 24_94-09_Day_10_S265_L004

description: Library name: 24_94-09_Day_10_S265_L004

value: Peripheral Blood


title: DMSO, TPO, 7d, donor3, batch1

description: 10X Genomics

value: dimethyl sulfoxide 0.01%


title: iCAR, Avobenzone, Ci10, 6h, G01

description: Library name: Ci10_T1_D1_G01

value: iCAR


title: Wild-type lens epithelium replicate 2

description:
Library name: Sample 2
WT-b

value: lens epithelium


title: Val-1k, TPO/FL/SCF, 7d, donor3, batch1

description: 10X Genomics

value: TPO/FL/SCF


title: 24_94-09_Day_10_S265_L003

description: Library name: 24_94-09_Day_10_S265_L003

value: NK cells


title: Wild-type lens epithelium replicate 1

description:
Library name: Sample 1
WT-a

value: lens epithelial cells


title: iCAR, Avobenzone, Ci10, 6h, E04

description: Library name: Ci10_T1_D1_E04

value: human induced pluripotent stem cells (iPSCs)

value: iPSC-derived cardiomyocytes


title: 24_94-09_Day_10_S265_L002

description: Library name: 24_94-09_Day_10_S265_L002


title: Val-330, TPO/FL/SCF, 7d, donor3, batch1

description: 10X Genomics


title: iCAR, Avobenzone, Ci10, 6h, D07

description: Library name: Ci10_T1_D1_D07

value: test


title: Murine macrophages, Infected L. interrogans Pomona 202100004, 6 hr, replicate 2

description:
Library name: Sample 42
QWX6CG_21_POm4_2

growth_protocol: THP-1 cells (a human monocyte cell line; ATCC TIB-202) and Raw 264.7 cells (a murine macrophage cell line) were cultured in RPMI 1640 medium (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (Sigma) and 2 mM L-glutamine (Gibco). THP-1 cells were differentiated/activated into macrophages by a treatment with 50 nM PMA for 2 days following by a 24 hr incubation without PMA.

value: WT


title: 23_94-09_Day_8_S264_L004

description: Library name: 23_94-09_Day_8_S264_L004


title: Val-110, TPO/FL/SCF, 7d, donor3, batch1

description: 10X Genomics

value: bone marrow

value: valemetostat 0.11uM


title: iCAR, Avobenzone, Ci10, 6h, B10

description: Library name: Ci10_T1_D1_B10


title: DMSO, TPO, 14d, donor3, batch1

description: 10X Genomics

value: bone marrow CD34+ cells


title: DMSO, IL3/IL6, 3d, donor1, batch2

description: 10X Genomics


title: Murine macrophages, Infected L. interrogans Pomona 202100004, 6 hr, replicate 1

description:
Library name: Sample 41
QWX6CG_20_POm4_1


title: 23_94-09_Day_8_S264_L003

description: Library name: 23_94-09_Day_8_S264_L003


title: DMSO, TPO/FL/SCF, 7d, donor3, batch1

description: 10X Genomics


title: iCAR, DMSO, Ci10, 6h, G08

description: Library name: Ci10_DMSO_G08

value: vehicle


title: iCAR, Avobenzone, Ci10, 6h, F07

description: Library name: Ci10_T1_D3_F07

value: heart muscle cells


title: Murine macrophages, Infected L. interrogans Pomona 201902969, 6 hr, replicate 2

description:
Library name: Sample 40
QWX6CG_19_POm3_2


title: 23_94-09_Day_8_S264_L002

description: Library name: 23_94-09_Day_8_S264_L002


title: Val-1k, TPO/FL/SCF, 3d, donor3, batch1

description: 10X Genomics

value: valemetostat 1uM


title: Murine macrophages, Infected L. interrogans Pomona 201902969, 6 hr, replicate 1

description:
Library name: Sample 39
QWX6CG_18_POm3_1


title: iCAR, DMSO, Ci10, 6h, F05

description: Library name: Ci10_DMSO_F05


title: iCAR, DMSO, Ci10, 6h, D02

description: Library name: Ci10_DMSO_D02


title: Murine macrophages, Infected L. interrogans Pomona 201700303, 6 hr, replicate 2

description:
Library name: Sample 38
QWX6CG_17_POm2_2


title: Val-330, TPO/FL/SCF, 3d, donor3, batch1

description: 10X Genomics

value: valemetostat 0.33uM


title: iCAR, DMSO, Ci10, 6h, C10

description: Library name: Ci10_DMSO_C10


title: Val-110, TPO/FL/SCF, 3d, donor3, batch1

description: 10X Genomics


title: 22_94-09_Day_3_S263_L003

description: Library name: 22_94-09_Day_3_S263_L003

value: Peripheral Blood


title: Murine macrophages, Infected L. interrogans Pomona 201700303, 6 hr, replicate 1

description:
Library name: Sample 37
QWX6CG_16_POm2_1


title: 22_94-09_Day_3_S263_L004

description: Library name: 22_94-09_Day_3_S263_L004


title: 22_94-09_Day_3_S263_L002

description: Library name: 22_94-09_Day_3_S263_L002


title: DMSO, TPO/FL/SCF, 3d, donor3, batch1

description: 10X Genomics

value: dimethyl sulfoxide 0.01%


title: Murine macrophages, Infected L. interrogans Pomona 201801210, 6 hr, replicate 2

description:
Library name: Sample 36
QWX6CG_15_POm1_2


title: iCAR, DMSO, Ci10, 6h, B12

description: Library name: Ci10_DMSO_B12

value: iCAR


title: No treatment, No cytokine, 0d, donor3, batch1

description: 10X Genomics

value: No treatment

value: No cytokine


title: 20_94-09_Day_6_S261_L004

description: Library name: 20_94-09_Day_6_S261_L004

value: NK cells


title: Val-1k, TPO/FL/SCF, 10d, donor3, batch1

description: 10X Genomics

value: TPO/FL/SCF


title: Val-330, TPO/FL/SCF, 10d, donor3, batch1

description: 10X Genomics


title: Murine macrophages, Infected L. interrogans Pomona 201801210, 6 hr, replicate 1

description:
Library name: Sample 35
QWX6CG_14_POm1_1


title: 20_94-09_Day_6_S261_L003

description: Library name: 20_94-09_Day_6_S261_L003


title: HepG2, Myricetin, CH11, 6h, F07

description: Library name: CH11_T8_D3_F07

source_name: liver

value: liver

value: epithelial cell

value: hepatocellular carcinoma


title: Murine macrophages, Infected L. interrogans Icterohaemorrhagiae 202102907, 6 hr, replicate 2

description:
Library name: Sample 34
QWX6CG_13_ICm5_2

value: WT


title: 20_94-09_Day_6_S261_L002

description: Library name: 20_94-09_Day_6_S261_L002


title: Val-110, TPO/FL/SCF, 10d, donor3, batch1

description: 10X Genomics

value: bone marrow

value: valemetostat 0.11uM


title: HepG2, Myricetin, CH11, 6h, E10

description: Library name: CH11_T8_D3_E10

value: test


title: 19_231-09_Day_14_S260_L004

description: Library name: 19_231-09_Day_14_S260_L004


title: Murine macrophages, Infected L. interrogans Icterohaemorrhagiae 202102907, 6 hr, replicate 1

description:
Library name: Sample 33
QWX6CG_12_ICm5_1


title: DMSO, TPO/FL/SCF, 10d, donor3, batch1

description: 10X Genomics

value: bone marrow CD34+ cells


title: HepG2, Myricetin, CH11, 6h, A02

description: Library name: CH11_T8_D3_A02


title: Murine macrophages, Infected L. interrogans Icterohaemorrhagiae 202100001, 6 hr, replicate 2

description:
Library name: Sample 32
QWX6CG_11_ICm4_2


title: 19_231-09_Day_14_S260_L003

description: Library name: 19_231-09_Day_14_S260_L003


title: HepG2, Myricetin, CH11, 6h, H01

description: Library name: CH11_T8_D2_H01


title: Murine macrophages, Infected L. interrogans Icterohaemorrhagiae 202100001, 6 hr, replicate 1

description:
Library name: Sample 31
QWX6CG_10_ICm4_1


title: Val-1k, TPO/FL/SCF, 7d, donor3

description: 10X Genomics

data_processing:
STAR (v2.5.3a) and RSEM (v1.0.3) were used for read mapping and transcriptome quantification with GENCODE release 32, respectively.
Assembly: GRCh38
Supplementary files format and content: TSV, gene read counts
Supplementary files format and content: TSV, isoform read counts

growth_protocol: Primary human bone marrow CD34+ cells were cultured in StemSpan serum-free expansion medium (STEMCELL Technologies) in the presence of thrombopoietin (50 ng/mL)/FLT3 ligand (FL, 100 ng/mL)/SCF (100 ng/mL) at 37 ℃ in a 5% CO2 incubator.

extract_protocol:
Cells were stained with anti-human CD41 and CD61 antibodies (BioLegend), and double positive fraction was collected by BD FACS Aria (BD Biosciences). RNA extraction was performed with Maxwell (Promega).
RNA-seq libraries were constructed with the ribosomal RNA depletion method with QIAseq FastSelect (Qiagen), NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) and NEBNext Multiplex Oligos for Illumina (New England Biolabs). Biomek i7 instruments (Beckman Coulter, Inc) programmed according to the manufacture’s protocols were used for library construction with the following parameters: 5 minutes of fragmentation, RNA quantity ≦ 20 ng, and 14 cycles of polymerase chain reaction amplification.

value: valemetostat 1uM


title: 19_231-09_Day_14_S260_L002

description: Library name: 19_231-09_Day_14_S260_L002


title: HepG2, Myricetin, CH11, 6h, F04

description: Library name: CH11_T8_D2_F04


title: 18_231-09_Day_10_S259_L004

description: Library name: 18_231-09_Day_10_S259_L004


title: Murine macrophages, Infected L. interrogans Icterohaemorrhagiae 202102995, 6 hr, replicate 2

description:
Library name: Sample 30
QWX6CG_9_ICm3_2


title: Val-1k, TPO/FL/SCF, 7d, donor2

description: 10X Genomics


title: HepG2, Myricetin, CH11, 6h, E07

description: Library name: CH11_T8_D2_E07


title: 18_231-09_Day_10_S259_L003

description: Library name: 18_231-09_Day_10_S259_L003


title: Murine macrophages, Infected L. interrogans Icterohaemorrhagiae 202102995, 6 hr, replicate 1

description:
Library name: Sample 29
QWX6CG_8_ICm3_1


title: Murine macrophages, Infected L. interrogans Icterohaemorrhagiae 202102576, 6 hr, replicate 2

description:
Library name: Sample 28
QWX6CG_7_ICm2_2


title: HepG2, Myricetin, CH11, 6h, D10

description: Library name: CH11_T8_D2_D10


title: 18_231-09_Day_10_S259_L002

description: Library name: 18_231-09_Day_10_S259_L002


title: DMSO, TPO/FL/SCF, 7d, donor2

description: 10X Genomics


title: Val-1k, TPO/FL/SCF, 7d, donor1

description: 10X Genomics


title: Murine macrophages, Infected L. interrogans Icterohaemorrhagiae 202102576, 6 hr, replicate 1

description:
Library name: Sample 27
QWX6CG_6_ICm2_1


title: HepG2, Myricetin, CH11, 6h, G01

description: Library name: CH11_T8_D1_G01


title: 17_231-09_Day_8_S258_L004

description: Library name: 17_231-09_Day_8_S258_L004


title: HepG2, Myricetin, CH11, 6h, E04

description: Library name: CH11_T8_D1_E04


title: Murine macrophages, Infected L. interrogans Icterohaemorrhagiae 202101402, 6 hr, replicate 2

description:
Library name: Sample 26
QWX6CG_5_ICm1_2


title: DMSO, TPO/FL/SCF, 7d, donor1

description: 10X Genomics


title: 17_231-09_Day_8_S258_L003

description: Library name: 17_231-09_Day_8_S258_L003


title: CHIP062, Input, CRISPRi , rep1_part1

city: Philadelphia

first: Ricardo

middle: A

last: Linares Saldana

state: PA

address: 3400 civic center blvd

institute: University of Pennsylvania

description: H3K9me2_iFXN_3_AK59_AK60.inpLg2_1kb.woTNR.e100.S10Kb.bw

data_processing:
Basecalls were performed using bcl2fastq v2.20.
ChIP-seq reads were deduplicated and trimmed using fastp v0.23.2. Low complexity reads were discarded.
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 2.5.1. Only uniquely mapping reads with a MAPQ >20 were retained using sambamba 1.0.0.
To create ChIP-seq coverage plots of LB1 and H3K9me2, the locations of the mapped ChIP-seq reads were extended to 100 bp to represent sequenced fragments, normalized (to counts per million, cpm) and log2 normalized against their corresponding inputs. The resulting bigwig files were generated using deeptools v3.1.3. Bigwigs for RAD21 were generated using macs2 version 2.2.6 representing a fold enrichment over their corresponding inputs. ENCODE blacklisted regions (hg38-blacklist.v2.bed) were excluded from analysis.
RAD21 peaks were called using MACS v2.2.6 with the significance cut-off q-value <=0.01. Broad domains for LB1 or H3K9me2 were identified using HMMDomainCaller doi:10.1038/s41588-021-00821-2.
Assembly: hg38
Supplementary files format and content: bigWig files with input normalized ChIP-seq signal for each condition as described above. Bed and narrowPeak files with domain calls per condition as described above.

source_name: WT fibroblast

growth_protocol: Human skin non-treatment control (NTC) fibroblasts and fibroblasts from a Freidrich's Ataxia patient (FRDA) fibroblast cells were cultured in DMEM (Gibco #11965084) supplemented with 10% fetal bovine serum (Cytiva SH30910.03), 1% penicillin/streptomycin (Invitrogen #15140122), and 1% non-essential amino acids (Invitrogen # 11140050) at 37C with 20% O2 and 5% CO2. RAD21-mAID-HCT116 cells were cultured in McCoys (Invitrogen #16600082) supplemented with 10% fetal bovine serum, and 1% penicillin/streptomycin at 37C with 20% O2 and 5% CO2.

extract_protocol:
Samples for ChIP were processed as previously described (3). Human NTC and FRDA fibroblasts and Rad21-mAID-HCT116 cells were cultured in 10cm dishes and crosslinked in culture using methanol-free formaldehyde for 10 min at RT with gentle rotation (final 1% v/v). Crosslinking was quenched by addition of glycine for 5 min at RT with gentle rotation (final 125mM). Cells were washed with 1x PBS once before collection via scraping and PBS removal by centrifugation (250xg for 5 minutes at RT). Resulting pellets were flash frozen on dry ice and stored at -80C. For each ChIP sample, 30µL protein G magnetic beads (Invitrogen #10004D) were washed 3 times in blocking buffer (0.5% BSA in 1x PBS) before beads were resuspended in 250µL blocking buffer and 2µg (anti-LaminB1 [Abcam #ab16048], anti-H3K9me2 [Active Motif #39239]) or 4µg (anti-RAD21 [Abcam, #ab992]) antibody and rotated at 4C overnight. Nuclei were isolated from frozen pellets as follows: pellets were resuspended in 10mL cold Lysis Buffer 1 (50mM HEPES-KOH pH7.5, 1mMEDTA, 140mM NaCl, 10% Glycerol, 0.5% NP-40, 0.25% TritonX-100, and protease inhibitor) and rotated at 4C for 10 min. Resuspended cells were centrifuged at 250xg for 5 min at RT and supernatant discarded. Remaining pellet was resuspended in 10mL cold Lysis buffer (220mM NaCl, 10mM Tris-HCl pH 8.0, 1mM EDTA, 0.5mM EGTA, and protease inhibitor) and rotated at 4C for 10 min. Resuspended cells were centrifuged at 250xg for 5 min at RT and supernatant discarded. Nuclei were resuspended in 1mL cold Lysis Buffer 3 (10mM Tris-HCl pH8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, and protease inhibitor). Samples were transferred to a pre-chilled 1mL Covaris AFA tube (Covaris #520130) and sonicated using a Covaris S220 sonicator (high cell chromatin shearing for 15 minutes). TrintonX-100 (final 1%) was added to lysates and centrifuged at top speed for 10 min at 4C. Supernatant was collected and protein concentration measured via Bradford assay. Antibody-conjugated beads were washed 3 times in blocking buffer and resuspended in 50µL blocking buffer before 500µg protein lysate was added and allowed to rotate overnight at 4C. For inputs, 50µg protein lysate was aliquoted and stored at -20C. The next day, antibody-conjugated beads with lysate were washed 5 times for 2 min each at 4C with rotation in 1mL RIPA buffer (50mM HEPES-KOH pH7.5, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate). Beads were washed in 1mL Final Wash buffer (1XTE, 50mM NaCl) for 2 min with rotation at RT. Lastly, beads were resuspended in 210µL Elution Buffer (50mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65C for 30 min with agitation. 200µL eluate was removed and all samples were incubated at 65C with agitation for a minimum of 12 h, but no more than 18 h. 200µL of 1X TE was added the resulting samples followed by addition of RNase (final 0.2mg/mL, Sigma #10109169001) and incubated at 37C for 2 h. Proteinase K was subsequently added (final 0.2mg/mL, Roche #3115879001) and incubated at 55C for 2 h. DNA was isolated via phenol:chloroform extraction and resuspended in 10mM Tris-HCl pH8.0. DNA was quantified by Qubit.
ChIP-seq libraries were prepared using NEBNext Ultra II DNA library prep kit (NEB #E7770L). Samples were prepared with dual unique indices for multiplex sequencing using NEBNext Multiplex Oligos (NEB #E7630). Library quality was determined by BioAnalyzer or 2% agarose gel electrophoresis and quantified by qPCR using NEBNext Library Quant Kit (NEB #E7630S). Libraries were pooled, re-quantified, and single-end sequenced on the Illumina NextSeq500 or NextSeq1000/2000 platforms
Libraries were quantified and pooled for sequencing; input libraries were always run with associated ChIP samples. If possible, replicate samples were run together on the same sequencing run.

treatment_protocol: Human fibroblasts were grown in complete media (DMEM, 10% FBS, 1% penicillin/streptomycin) and plated at 40% confluency. The next day, dCas9-KRAB-FXN guide or dCas9-KRAB-Scramble guide was introduced into NTC fibroblasts for 2d followed by 2d selection in blasticidin. RAD21-mAID-HCT116 cells were propagated in standard medium (McCoy’s with 10% FBS and 1% penicillin/streptomycin) and plated in 10cm dishes at 40% density and grown overnight. The following morning, a time course was started for three conditions (DMSO control, triptolide-only, and auxin + triptolide). At time 0, DMSO control and triptolide-only cells were incubated in fresh media alone; auxin + triptolide cells were incubated in fresh media + 1μM auxin (5-Ph-IAA, Tocris Bioscience). After 1 hour, 200nM final triptolide (Selleckchem) was added to triptolide-only and auxin + triptolide cells. 12 hours post-triptolide, all cells were harvested for ChIP (see “ChIP and library preparation for sequencing”). DMSO was used as a vehicle control.

value: WT fibroblast

value: Human fibroblast

value: Input

value: CRISPRi


title: Murine macrophages, Infected L. interrogans Icterohaemorrhagiae 202101402, 6 hr, replicate 1

description:
Library name: Sample 25
QWX6CG_4_ICm1_1


title: HepG2, Myricetin, CH11, 6h, D07

description: Library name: CH11_T8_D1_D07


title: CHIP060, H3K9me2, CRISPRi , rep1_part1

value: H3K9me2 (Active Motif, #39239)


title: 17_231-09_Day_8_S258_L002

description: Library name: 17_231-09_Day_8_S258_L002

value: Peripheral Blood


title: HepG2, Myricetin, CH11, 6h, B10

description: Library name: CH11_T8_D1_B10


title: Murine macrophages, Uninfected, 6 hr, replicate 3

description:
Library name: Sample 24
QWX6CG_3_UNIm_3


title: 16_231-09_Day_6_S257_L004

description: Library name: 16_231-09_Day_6_S257_L004

value: NK cells


title: HepG2, DMSO, CH11, 6h, G08

description: Library name: CH11_DMSO_G08

value: vehicle


title: CHIP011, Input, CRISPRi , rep2_part1

description:
LB1_iFXN.inpLg2_1kb.woTNR.e100.S10Kb.bw
LB1_iFXN.inpLg2_15kb.woTNR.e100.S75Kb.znormChr_15_woBlklst_domains.bed


title: 16_231-09_Day_6_S257_L003

description: Library name: 16_231-09_Day_6_S257_L003


title: Murine macrophages, Uninfected, 6 hr, replicate 2

description:
Library name: Sample 23
QWX6CG_2_UNIm_2


title: HepG2, DMSO, CH11, 6h, F05

description: Library name: CH11_DMSO_F05

value: liver


title: CHIP009, Input, CRISPRi , rep1_part1


title: Murine macrophages, Uninfected, 6 hr, replicate 1

description:
Library name: Sample 22
QWX6CG_1_UNIm_1


title: 16_231-09_Day_6_S257_L002

description: Library name: 16_231-09_Day_6_S257_L002


title: HepG2, Myricetin, CH11, 6h, G04

description: Library name: CH11_T8_D3_G04

value: epithelial cell


title: HepG2, DMSO, CH11, 6h, D02

description: Library name: CH11_DMSO_D02

value: hepatocellular carcinoma


title: CHIP007, LMNB1, CRISPRi , rep2_part1

value: LMNB1 (abcam, #ab16048)


title: 15_231-09_Day_3_S256_L004

description: Library name: 15_231-09_Day_3_S256_L004


title: CHIP005, LMNB1, CRISPRi , rep1_part1


title: NEDD8_KO_1

description: Library name: N8

library_source: transcriptomic single cell

data_processing:
Raw sequencing data was mapped to the mm10 mouse genome using the Cell Ranger pipeline (10X Genomics, Inc.) to generate a feature-barcode counts matrix. The resulting count matrices were then analyzed using the Seurat R package (v5.1.0). Cells which had < 200 detected genes and > 10% of mitochondrial genes were filtered out for downstream analyses. The standard Seurat analysis pipeline was performed on all data. Briefly, the top 2000 most variable genes were determined using the FindVariableFeatures function and used for principal component analysis (PCA). The first 30 principal components (PCs) were used for dimensionality reduction and uniform manifold approximation and projection (UMAP) generation. All samples were merged and integrated into one Seurat object using the Seurat merge function followed by the Seurat V5 Integration Pipeline. Harmony Integration Method from the Harmony R package (v1.2.1) was used to integrate all layers. The FindNeighbors and FindCluster functions from Seurat were used for clustering analysis and cell type annotation.
Assembly: GRCm38
Supplementary files format and content: Seurat object

source_name: skin

extract_protocol:
full thickness skin sections were isolated from mice, digested overnight with dispase at 4C, then digested with trypsin at 37C for 1hr with agitation, filtered, dead cells and debris was removed using a MACS column
Libraries were prepared using the 10x Genomics Chromium 3' single cell workflow according to manufactuers recommendations.

treatment_protocol: mice were treated with topical tamoxifen for 3 days the recovered for 2 days

value: skin

value: mixed

value: Tamoxifen


title: HepG2, DMSO, CH11, 6h, C10

description: Library name: CH11_DMSO_C10


title: NEDD8_Ctrl_2

description: Library name: N8_ctrl


title: 15_231-09_Day_3_S256_L003

description: Library name: 15_231-09_Day_3_S256_L003


title: Killifish bud stage (96 hpf)

city: Seattle

first: Sydney

middle: Marie

last: Sattler

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description:
Library name: 96 hpf
V4 T20 PIPseq

data_processing:
Reads were aligned to the N. furzeri (Nfu_20140520) or the D. rerio (GRCz11.108) genomes and gene-count matrices were generated using PIPseeker software (v1.1.7, Fluent Bio). For the 115hpf timepoint only, cells with >90% reads mapping to the killifish genome were labelled killifish cells and computationally isolated from the barnyard mix. Doublets were removed using scrublet (v0.2.3). Cells with >12% mitochondria reads and >5000 reads/cell were removed. The downstream analysis was performed with Seurat (v5.4.0).
Assembly: Nfu_20140520, GRCz11.108
Supplementary files format and content: Single Cell Experiment .RDS files

organism: Nothobranchius furzeri

source_name: whole embryo

growth_protocol: An inbred strain of Nothobranchius furzeri, originating from Gonarezhou National Park, Zimbabwe was used in each experiment. An inbred strain (AB or WIK) of Danio rerio was used in each experiment. Both species were maintained at 28°C under 15:9 light:dark cycles including a 1-hour ramp up/down period. Killifish (GRZ) were crossed for 2 hours. Zebrafish (WIK) were crossed for 30 minutes. Using the mid-point as 0 hours post fertilization, clutches of killifish embryos from 52, 72, 96, and 115hpf, and zebrafish embryos at 12 hpf, consisting of 132, 90, 80, 35, and 35 embryos, respectively, were visually confirmed to be at 100% dispersed, incipient aggregate, bud, and 8-somite stages.

extract_protocol:
Embryos were manually dechorionated with forceps in ice cold DMEM/F12 (Gibco, 21-041-025) and transferred to lo-bind 1.5 mL Eppendorf tubes on ice. Cells were spun down at 500xg for 3 min at 4°C. Cells were dissociated in Accutase (Innovative Cell Technologies, AT104) at 37°C for 7-20 min depending on embryo stage (older embryos required longer dissociation). Percent viability was determined by counting DAPI+, Calcein-AM+ (Invitrogen, C1430) live cells and DAPI+, Calcein-AM- dead cells on a disposable hemocytometer (Bulldog Bio, DHC-N420). 40,000 cells were loaded onto the V4 T20 PIP-seq kit (formerly Fluent Bio, now the Illumina Single Cell 3’RNA Prep Kit) for each timepoint except for the 115hpf timepoint which consisted of a 1:1 mix of killifish and stage-matched zebrafish cells used to initially assess the efficacy of the PIP-seq kit which, at that time, had not yet been used on teleosts.
Followed V4 P20 PIPseq protocol. cDNA fragment analysis of scRNAseq libraries was performed using the 4200 TapeStation System. Libraries were sequenced with a NextSeq 2000 P3 100 cycle kit (52hpf, 72hpf, 96hpf) or NovaSeq 6000 S4 300 cycle kit (115hpf, a gift from Fluent Biosciences) using the following configuration: read 1: 54, i7 index: 8, i5 index: 8, read 2: 68.

value: whole embryo

value: GRZ

tag: hours post_fertilization

tag: Stage

value: Bud


title: DMSO, TPO/FL/SCF/IL3/IL6, 3d, donor2, batch2

description: 10X Genomics

tag: tissue

value: bone marrow

value: bone marrow CD34+ cells

value: dimethyl sulfoxide 0.01%


title: rOPCs_CTK1

description: Library name: Sample7

value: brain cortex

tag: cell line

value: postnatal day 2 primary cells

tag: cell type

value: oligodendrocytes

value: pooled male and female

value: wild-type

value: Cytokines


title: NEDD8_Ctrl_1

description: Library name: CTL_backup

tag: treatment


title: 15_231-09_Day_3_S256_L002

description: Library name: 15_231-09_Day_3_S256_L002

value: Peripheral Blood

value: NK cells


title: HepG2, DMSO, CH11, 6h, B12

description: Library name: CH11_DMSO_B12

value: liver

value: epithelial cell

value: hepatocellular carcinoma

value: vehicle


title: Killifish incipient aggregate stage (72 hpf)

description:
Library name: 72 hpf
V4 T20 PIPseq

value: whole embryo

value: GRZ

value: Incipient Aggregate


title: iCAR, 3-hydroxybenzophenone, Ci10, 6h, B03

description: Library name: Ci10_T4_D2_B03

value: heart muscle cells

value: iCAR

value: human induced pluripotent stem cells (iPSCs)

value: iPSC-derived cardiomyocytes

value: test


title: HepG2, Kaempferol, CH10, 6h, H12

description: Library name: CH10_T7_D3_H12


title: SUMO2_Ctrl

description: Library name: S2

value: skin

value: mixed

value: Tamoxifen


title: 14_231-09_Day_1_S255_L004

description: Library name: 14_231-09_Day_1_S255_L004

value: Peripheral Blood


title: Killifish dispersed stage (52 hpf)

description:
Library name: 52 hpf
V4 T20 PIPseq

value: Dispersed


title: SUMO2_KO

description: Library name: S2C


title: 14_231-09_Day_1_S255_L003

description: Library name: 14_231-09_Day_1_S255_L003

value: NK cells


title: Sample39

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

institute: Nagoya University

description: Library name: Sample39

data_processing:
The CLC Genomics Workbench version 9.5.3 program (Qiagen) was used for adaptor trimming and mapping to the miRbase 21 database allowing two base mismatches. Then, the data was normalized using reads per million mapped reads.
Assembly: miRBase 21
Supplementary files format and content: a tab-spaced txt file includes RPM counts of each sample

source_name: EVs

extract_protocol:
Tissue samples from both the tumor and the normal mammary gland were collected and immediately stored at -80°C. Nipple discharge EVs, intracystic fluid (ICF) EVs, and tissue surface EVs were collected using cellulose nanofiber (CNF) sheets.
To obtain tissue RNA, tissues were shredded and crushed with QIAzol (Qiagen, Hilden, Germany) in a gentleMACS M tube (Miltenyi Biotec, Bergisch Gladbach, Germany). The total RNA was extracted using the miRNeasy®Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions.
Small RNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) according to the manufacturers' protocol.

tag: patient no.

value: EVs

tag: sample type

value: Intracystic fluid EVs

tag: disease status

value: DCIS

tag: er status

tag: her2 status


title: HepG2, Kaempferol, CH10, 6h, D04

description: Library name: CH10_T7_D3_D04

value: liver

value: epithelial cell

tag: genotype

value: hepatocellular carcinoma

tag: batch


title: 29_349-09_Day_7_S270_L003

description: Library name: 29_349-09_Day_7_S270_L003


title: HepG2, Kaempferol, CH10, 6h, C07

description: Library name: CH10_T7_D3_C07


title: DMSO, TPO/FL/SCF/IL3/IL6, 3d, donor1, batch2

description: 10X Genomics

value: bone marrow

value: bone marrow CD34+ cells

value: dimethyl sulfoxide 0.01%

tag: stimulation

tag: time

tag: donor id

tag: experimental batch


title: HepG2, Kaempferol, CH10, 6h, A10

description: Library name: CH10_T7_D3_A10


title: 14_231-09_Day_1_S255_L002

description: Library name: 14_231-09_Day_1_S255_L002


title: NRF2_KO

description: Library name: NRF2_KO


title: Sample38

description: Library name: Sample38

tag: age

value: Nipple discharge EVs


title: NEDD8_KO_2

description: Library name: N8_KO


title: 12_283-09_Day_14_S253_L004

description: Library name: 12_283-09_Day_14_S253_L004


title: Sample37

description: Library name: Sample37

tag: Stage

value: Tissue surface EVs

value: Normal


title: HepG2, Kaempferol, CH10, 6h, H09

description: Library name: CH10_T7_D2_H09

tag: tissue

value: test


title: NEDD8_KO, NEF2_KO

description: Library name: N8_NRF2_KO

value: skin

value: mixed

value: Tamoxifen


title: 12_283-09_Day_14_S253_L003

description: Library name: 12_283-09_Day_14_S253_L003

value: Peripheral Blood

value: NK cells


title: Sample36

description: Library name: Sample36

value: Tissue


title: HepG2, Kaempferol, CH10, 6h, G12

description: Library name: CH10_T7_D2_G12

tag: cell line


title: 12_283-09_Day_14_S253_L002

description: Library name: 12_283-09_Day_14_S253_L002

tag: cell type


title: NEDD8i_2

description: Library name: NEDD8i_2

data_processing:
UMIs were extracted using UMItools
Adapter trimming and polyA sequence removal were carried out with bbduk
Reads were aligned to the GRCm38 reference genome using STAR
gene-level counts were obtained using featureCounts with GENCODE m32 annotations.
Differential expression analysis was performed using DESeq2 with apeGLM shrinkage
Assembly: GRCm39
Supplementary files format and content: FeatureCounts

extract_protocol:
Cells previously treated with pharmacologic compounds were collected homogenized in RLT plus lysis buffer supplemented with 10uL/mL Beta-mercaptoethanol (ß-ME) and passed through QIAshredder (Qiagen) column. RNA was then extracted using the RNeasy Plus mini kit (Qiagen)
QuantSeq mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen)

treatment_protocol: mice were treated with topical DMSO or NEDD8i for 3 days then full thickness skin sections were harvested

tag: strain

value: wild type

tag: treatment

value: NEDD8i 10µM


title: Sample35

description: Library name: Sample35

tag: patient no.

value: EVs

tag: sample type

value: DCIS


title: HepG2, Kaempferol, CH10, 6h, C04

description: Library name: CH10_T7_D2_C04

value: liver

value: epithelial cell

value: hepatocellular carcinoma


title: HepG2, Kaempferol, CH10, 6h, B07

description: Library name: CH10_T7_D2_B07


title: Sample34

description: Library name: Sample34

tag: disease status

tag: er status


title: NEDD8i_1

description: Library name: NEDD8i_1

tag: genotype


title: DMSO_2

description: Library name: DMSO_2

value: DMSO


title: 11_283-09_Day_10_S252_L004

description: Library name: 11_283-09_Day_10_S252_L004


title: HepG2, Kaempferol, CH10, 6h, G09

description: Library name: CH10_T7_D1_G09

tag: batch


title: Sample33

description: Library name: Sample33

value: Nipple discharge EVs

tag: her2 status


title: DMSO_1

description: Library name: DMSO_1


title: 11_283-09_Day_10_S252_L003

description: Library name: 11_283-09_Day_10_S252_L003


title: 11_283-09_Day_10_S252_L002

description: Library name: 11_283-09_Day_10_S252_L002


title: Sample32

description: Library name: Sample32

value: IDC


title: HepG2, Kaempferol, CH10, 6h, F12

description: Library name: CH10_T7_D1_F12

value: test


title: N8_K14pos_3

description: Library name: N8_K14pos_3

extract_protocol:
Cells previously treated with pharmacologic compounds were collected in RLT plus lysis buffer supplemented with 10uL/mL Beta-mercaptoethanol (ß-ME) and passed through QIAshredder (Qiagen) column. RNA was then extracted using the RNeasy Plus mini kit (Qiagen)
QuantSeq mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen)

treatment_protocol: mice were treated with topical tamoxifen for cre induction for 5 days then allowed to recover for 5 days before skin harvest

value: skin

value: NEDD8fl/fl, K14-CreERT pos

value: tamoxifen, topical


title: 10_283-09_Day_8_S251_L004

description: Library name: 10_283-09_Day_8_S251_L004

value: Peripheral Blood


title: HepG2, Kaempferol, CH10, 6h, B04

description: Library name: CH10_T7_D1_B04


title: N8_K14pos_2

description: Library name: N8_K14pos_2


title: Sample31

description: Library name: Sample31

value: No malignancy


title: Sample30

description: Library name: Sample30

value: Tissue surface EVs

value: Normal


title: 10_283-09_Day_8_S251_L003

description: Library name: 10_283-09_Day_8_S251_L003

value: NK cells


title: 10_283-09_Day_8_S251_L002

description: Library name: 10_283-09_Day_8_S251_L002


title: HepG2, Kaempferol, CH10, 6h, A07

description: Library name: CH10_T7_D1_A07


title: N8_K14pos_1

description: Library name: N8_K14pos_1


title: HepG2, 4-hydroxybenzophenone, CH10, 6h, H06

description: Library name: CH10_T6_D3_H06


title: N8_K14neg_3

description: Library name: N8_K14neg_3

value: NEDD8fl/fl, K14-CreERT neg


title: Sample29

description: Library name: Sample29

value: Tissue


title: 9_283-09_Day_3_S250_L004

description: Library name: 9_283-09_Day_3_S250_L004


title: Sample28

description: Library name: Sample28

value: EVs

value: IDP


title: HepG2, 4-hydroxybenzophenone, CH10, 6h, F09

description: Library name: CH10_T6_D3_F09

value: liver

value: epithelial cell

value: hepatocellular carcinoma


title: N8_K14neg_2

description: Library name: N8_K14neg_2


title: 9_283-09_Day_3_S250_L003

description: Library name: 9_283-09_Day_3_S250_L003


title: Sample27

description: Library name: Sample27


title: HepG2, 4-hydroxybenzophenone, CH10, 6h, E12

description: Library name: CH10_T6_D3_E12


title: 9_283-09_Day_3_S250_L002

description: Library name: 9_283-09_Day_3_S250_L002


title: Sample26

description: Library name: Sample26

value: Intracystic fluid EVs


title: S2_K14pos_3

description: Library name: S2_K14pos_3

value: SUMO2fl/fl, K14-CreERT pos


title: 8_283-09_Day_1_S249_L004

description: Library name: 8_283-09_Day_1_S249_L004


title: N8_K14neg_1

description: Library name: N8_K14neg_1

value: skin


title: HepG2, 4-hydroxybenzophenone, CH10, 6h, A04

description: Library name: CH10_T6_D3_A04

value: test


title: Sample25

description: Library name: Sample25

value: Nipple discharge EVs


title: HepG2, 4-hydroxybenzophenone, CH10, 6h, H03

description: Library name: CH10_T6_D2_H03


title: S2_K14pos_2

description: Library name: S2_K14pos_2

value: tamoxifen, topical


title: 8_283-09_Day_1_S249_L003

description: Library name: 8_283-09_Day_1_S249_L003

value: Peripheral Blood


title: HepG2, 4-hydroxybenzophenone, CH10, 6h, G06

description: Library name: CH10_T6_D2_G06


title: Sample24

description: Library name: Sample24

value: No malignancy


title: S2_K14pos_1

description: Library name: S2_K14pos_1


title: HepG2, 4-hydroxybenzophenone, CH10, 6h, E09

description: Library name: CH10_T6_D2_E09


title: 8_283-09_Day_1_S249_L002

description: Library name: 8_283-09_Day_1_S249_L002


title: S2_K14neg_3

description: Library name: S2_K14neg_3

value: SUMO2fl/fl, K14-CreERT neg


title: Sample23

description: Library name: Sample23


title: 6_173-09_Day_14_S247_L004

description: Library name: 6_173-09_Day_14_S247_L004

value: NK cells


title: S2_K14neg_2

description: Library name: S2_K14neg_2


title: Sample22

description: Library name: Sample22


title: HepG2, 4-hydroxybenzophenone, CH10, 6h, D12

description: Library name: CH10_T6_D2_D12


title: 6_173-09_Day_14_S247_L003

description: Library name: 6_173-09_Day_14_S247_L003


title: Sample21

description: Library name: Sample21


title: HepG2, 4-hydroxybenzophenone, CH10, 6h, G03

description: Library name: CH10_T6_D1_G03


title: S2_K14neg_1

description: Library name: S2_K14neg_1


title: Sample20

description: Library name: Sample20


title: B6_DMSO_2

description: Library name: B6_DMSO_2

treatment_protocol: Mice of various genotypes were topically treated daily with Aldara cream (5% Imiquimod) starting day 0 until termination (day 7). Knockout mice were induced for five consecutive days prior to experiment start. The cream was applied on the shaved backs or on the right ears of all the mice. \

value: wild type C57BL/6J

value: DMSO


title: HepG2, 4-hydroxybenzophenone, CH10, 6h, F06

description: Library name: CH10_T6_D1_F06


title: 5_173-09_Day_10_S246_L004

description: Library name: 5_173-09_Day_10_S246_L004


title: CAL27_NEDD8i_2

description: Library name: CAL27_NEDD8i_2

data_processing:
UMIs were extracted using UMItools
Adapter trimming and polyA sequence removal were carried out with bbduk
Reads were aligned to the GRCh38 reference genome using STAR
gene-level counts were obtained using featureCounts with GENCODE v39 annotations.
Differential expression analysis was performed using DESeq2 with apeGLM shrinkage
Assembly: GRCh38
Supplementary files format and content: FeatureCounts

source_name: cell line

growth_protocol: Cells were grown subconfluently in appropriate cell culture media. Fresh media was added with drug treatments.

treatment_protocol: 16hr drug treatments

value: cell line

value: squamous cell carcinoma


title: 6_173-09_Day_14_S247_L002

description: Library name: 6_173-09_Day_14_S247_L002


title: Sample19

description: Library name: Sample19

value: EVs


title: B6_DMSO_1

description: Library name: B6_DMSO_1


title: HepG2, 4-hydroxybenzophenone, CH10, 6h, D09

description: Library name: CH10_T6_D1_D09

value: liver

value: epithelial cell


title: 5_173-09_Day_10_S246_L003

description: Library name: 5_173-09_Day_10_S246_L003


title: Sample18

description: Library name: Sample18

value: DCIS


title: B6_IMQ_2

description: Library name: B6_IMQ_2

value: IMQ


title: HepG2, 4-hydroxybenzophenone, CH10, 6h, C12

description: Library name: CH10_T6_D1_C12

value: hepatocellular carcinoma


title: HepG2, 2-hydroxybenzophenone, CH10, 6h, F03

description: Library name: CH10_T5_D3_F03

value: test


title: 5_173-09_Day_10_S246_L002

description: Library name: 5_173-09_Day_10_S246_L002


title: Sample17

description: Library name: Sample17

value: Tissue surface EVs

value: Normal


title: 4_173-09_Day_1_S245_L004

description: Library name: 4_173-09_Day_1_S245_L004

value: Peripheral Blood


title: Sample16

description: Library name: Sample16

value: Tissue


title: HepG2, 2-hydroxybenzophenone, CH10, 6h, E06

description: Library name: CH10_T5_D3_E06


title: B6_IMQ_1

description: Library name: B6_IMQ_1

value: skin


title: K14neg_IMQ_2

description: Library name: K14neg_IMQ_2

value: NEDD8fl/fl, K14-CreERT neg


title: 4_173-09_Day_1_S245_L003

description: Library name: 4_173-09_Day_1_S245_L003

value: NK cells


title: Sample15

description: Library name: Sample15


title: HepG2, 2-hydroxybenzophenone, CH10, 6h, C09

description: Library name: CH10_T5_D3_C09


title: K14pos_DMSO_3

description: Library name: K14pos_DMSO_3

value: NEDD8fl/fl, K14-CreERT pos

value: DMSO


title: 4_173-09_Day_1_S245_L002

description: Library name: 4_173-09_Day_1_S245_L002


title: HepG2, 2-hydroxybenzophenone, CH10, 6h, A12

description: Library name: CH10_T5_D3_A12


title: Sample14

description: Library name: Sample14


title: K14pos_DMSO_2

description: Library name: K14pos_DMSO_2


title: 3_173-09_Day_7_S244_L004

description: Library name: 3_173-09_Day_7_S244_L004


title: K14pos_DMSO_1

description: Library name: K14pos_DMSO_1


title: Sample13

description: Library name: Sample13

value: Nipple discharge EVs

value: 2+(FISH not performed)


title: HepG2, 2-hydroxybenzophenone, CH10, 6h, H11

description: Library name: CH10_T5_D2_H11

value: liver


title: K14neg_DMSO_3

description: Library name: K14neg_DMSO_3


title: 3_173-09_Day_7_S244_L003

description: Library name: 3_173-09_Day_7_S244_L003


title: 3_173-09_Day_7_S244_L002

description: Library name: 3_173-09_Day_7_S244_L002


title: Sample11

description: Library name: Sample11

value: EVs


title: HepG2, 2-hydroxybenzophenone, CH10, 6h, E03

description: Library name: CH10_T5_D2_E03

value: epithelial cell


title: Sample12

description: Library name: Sample12

value: Intracystic fluid EVs

value: DCIS


title: HepG2, 2-hydroxybenzophenone, CH10, 6h, C06

description: Library name: CH10_T5_D2_C06

value: hepatocellular carcinoma

value: test


title: K14neg_DMSO_2

description: Library name: K14neg_DMSO_2


title: 2_173-09_Day_3_S243_L004

description: Library name: 2_173-09_Day_3_S243_L004


title: Sample10

description: Library name: Sample10

value: IDP


title: HepG2, 2-hydroxybenzophenone, CH10, 6h, B09

description: Library name: CH10_T5_D2_B09


title: K14neg_DMSO_1

description: Library name: K14neg_DMSO_1


title: Sample9

description: Library name: Sample9

value: IDC


title: 2_173-09_Day_3_S243_L003

description: Library name: 2_173-09_Day_3_S243_L003

value: Peripheral Blood


title: HepG2, 2-hydroxybenzophenone, CH10, 6h, G11

description: Library name: CH10_T5_D1_G11


title: K14pos_IMQ_2

description: Library name: K14pos_IMQ_2

value: skin

value: IMQ


title: 2_173-09_Day_3_S243_L002

description: Library name: 2_173-09_Day_3_S243_L002

value: NK cells


title: Sample8

description: Library name: Sample8

value: 2+(FISH no amplification)


title: HepG2, 2-hydroxybenzophenone, CH10, 6h, B06

description: Library name: CH10_T5_D1_B06


title: HepG2, 2-hydroxybenzophenone, CH10, 6h, D03

description: Library name: CH10_T5_D1_D03


title: K14neg_IMQ_1

description: Library name: K14neg_IMQ_1

value: NEDD8fl/fl, K14-CreERT neg


title: R32_25_3

city: Pamplona

first: Maite

middle: G

last: Fernandez-Barrena

address: Pio XII 55

country: Spain

institute: CIMA

description: Library name: R32_25_3

data_processing:
Alignment with STAR 2.7
Read counts with Feature count (SubRead 2.0.6)
Assembly: GRCm39
Supplementary files format and content: Microsoft Excel file with raw counts

source_name: Liver (CCA tumor)

growth_protocol: C57BL/6J mice were transfected with HTVI of plasmids coding for NICD1 (10 µg/mouse), myr-AKT (10 µg/mouse), and the Sleeping Beauty transposase. C57BL/6J mice without HTVI injection were used as healthy controls (C).

extract_protocol:
Automated Maxwell system (Promega)
Illumina Stranded mRNA Prep Ligation kit

treatment_protocol: Mice were sacrificed at 2 and 3 weeks after HTVI. Healthy liver (C) and CCA tumors were excised and stored at -80ºC until the RNA extraction step.

value: Liver (CCA tumor)

value: NICD/myr-AKT

value: 3 weeks post-HTVI


title: K14pos_IMQ_1

description: Library name: K14pos_IMQ_1

value: NEDD8fl/fl, K14-CreERT pos


title: Sample7

description: Library name: Sample7

value: EVs

value: Nipple discharge EVs


title: Sample6

description: Library name: Sample6

value: DCIS

value: 2+(FISH not performed)


title: R32_25_2

description: Library name: R32_25_2


title: HepG2, 2-hydroxybenzophenone, CH10, 6h, A09

description: Library name: CH10_T5_D1_A09

data_processing:
TempO-Seq data are analyzed using the Tempo-SeqR software package using the statistical computing language R.
The input for TempO-Seq data analysis is a folder of zipped FASTQ files. Each FASTQ file contains the reads and quality scores for one sample.
Each FASTQ file is aligned using the Bowtie algorithm to a pseudo-transcriptome input by the user.
The output for TempO-Seq data analysis is a table of counts with each column representing a sample and each row representing a gene.
Assembly: hWTv2
Supplementary files format and content: txt file

extract_protocol:
6h after treatment, 100uL of TempoSeq lysis buffer used to lyse cells per 96-well, which were then frozen and 2ul used for TempO-Seq library building
In TempO-Seq, each Detector Oligo (DO) consists of a sequence complementary to an mRNA target plus a universal (i.e. same for every targeted gene) primer binding site. They anneal in immediate juxtaposition to each other on the targeted RNA template such that they can be ligated together. Ligated detector oligos are PCR-amplified using a primer set (single-plex PCR reaction, with a single primer pair for each sample) that introduces both the adaptors required for sequencing and a sample-specific barcode. The barcode sequences flank the target sequence and are inserted appropriately into the standard Illumina adaptors to permit standard dual-index sequencing of the barcodes and deconvolution of sample-specific reads from the sequencing data using the standard Illumina software. All the PCR-amplified and barcoded samples are pooled into a single library for sequencing. Sequencing reads are demultiplexed using the standard sequencing instrument software for each sample using the barcodes to give a FASTQ file for each.

value: liver

value: epithelial cell

value: hepatocellular carcinoma

value: test


title: R32_25_12

description: Library name: R32_25_12

source_name: Liver

value: Liver

value: WT


title: adrenal gland -female

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

description:
Library name: whole_female
Formalin-fixed paraffin-embedded (FFPE) spatial transcriptomics study
adrenal gland -female, n=4

data_processing:
Raw FASTQ files were processed using Space Ranger v4.0.0 in 10x Genomics Cloud Environment. Two capture areas were processed independently: male_pooled (4 male adrenal sections) and female_pooled (4 female adrenal sections). Alignment to Mus musculus reference genome (GRCm38/mm10) with Ensembl annotations (release 2024) using STAR aligner. Pipeline included read trimming, probe-target mapping, UMI counting, and H&E-based computational cell segmentation to achieve single-cell resolution. Cell-segmented expression data (from Space Ranger cell_segmentation output folder) were used for downstream analysis. Individual tissue sections (4 biological replicates per sex) were computationally identified and annotated based on spatial coordinates and tissue morphology. Quality control metrics included nCount_Spatial (UMIs per cell), nFeature_Spatial (genes per cell), and percent.mt (mitochondrial percentage). Data from both capture areas were merged and normalized using LogNormalize (scale factor 10,000). Batch correction was performed using Harmony v1.0 to integrate biological replicates across capture areas while preserving biological variation between sexes. Highly variable genes were identified using variance-stabilizing transformation (top 3000 features). Dimensionality reduction: PCA followed by UMAP on Harmony-corrected embeddings. Unsupervised clustering using Louvain algorithm at resolution 0.35 identified 10 distinct cell populations. Cell type annotation was based on established marker gene expression and spatial localization patterns. Final dataset: 104,032 high-quality cells (59,141 from whole male; 44,891 from whole female) representing 8 biological replicates (4 per sex) with preserved spatial information for each individual adrenal section.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5: gene expression count data, stored in an HDF5
Supplementary files format and content: male_filtered_feature_cell_matrix.h5: gene expression count data, stored in an HDF5
Supplementary files format and content: male_cell_segmentations.geo.json: polygon coordinates defining cell boundaries from H&E-based segmentation, stored in geo.json format
Supplementary files format and content: male_tissue_hires_image.png: high-resolution H&E-stained tissue image
Supplementary files format and content: male_tissue_lowres_image.png: low-resolution H&E-stained tissue image
Supplementary files format and content: male_tissue_positions_list.csv: spatial coordinates and metadata for each cell
Supplementary files format and content: female_filtered_feature_cell_matrix.h5: gene expression count data, stored in an HDF5
Supplementary files format and content: female_cell_segmentations.geo.json: polygon coordinates defining cell boundaries from H&E-based segmentation, stored in geo.json format
Supplementary files format and content: female_tissue_hires_image.png: high-resolution H&E-stained tissue image
Supplementary files format and content: female_tissue_lowres_image.png: low-resolution H&E-stained tissue image
Supplementary files format and content: female_tissue_positions_list.csv: spatial coordinates and metadata for each cell
Library strategy: Spatial Transcriptomics

source_name: adrenal gland with adjacent adipose tissue

growth_protocol: BALB/c mice were bred and maintained at the Centre for Advanced Technology, Adam Mickiewicz University, Poznan, Poland. Animals were housed in colony cages under specific pathogen-free conditions with controlled temperature (21-23°C), relative humidity (55-60%), and a 12-hour light/dark cycle. Standard rodent chow and water were provided ad libitum.

extract_protocol:
FFPE tissue blocks were sectioned at 5 µm thickness using a Leica RM2255 microtome. Four male adrenal sections were placed on a single Visium HD capture area (6.5mm × 6.5mm),  and four female adrenal sections were placed on a separate Visium HD capture area. This spatial pooling design enabled simultaneous profiling of multiple biological replicates while preserving spatial information for each individual tissue section. Sections were mounted on Visium HD slides and stored at 4°C. RNA quality was assessed using adjacent sections with Agilent 2100 Bioanalyzer; only samples with DV200 > 50% were processed. Slides were deparaffinized in xylene, rehydrated through graded ethanol series, and stained with H&E. High-resolution brightfield images were acquired at 20× magnification using Grundium Ocus 40 scanner (~300 DPI) for cell segmentation and spatial alignment.
Spatial transcriptomic profiling was performed using 10x Genomics Visium HD Spatial Gene Expression workflow for FFPE samples with CytAssist instrument (User Guide CG000684, Rev B). Each capture area (whole male, whole female) was processed independently. Protocol included: enzymatic permeabilization, RNase H-mediated probe cleavage, reverse transcription with spatially barcoded primers (bin size: 8 µm), second-strand synthesis, and cDNA amplification. Libraries were prepared according to Visium HD Spatial Gene Expression Library Preparation protocol. Each library was quantified using Qubit fluorometer, normalized, and diluted to 650 pM final concentration.

treatment_protocol: The mice were euthanized via decapitation, and the adrenal glands with surrounded adipose tissue were promptly collected and preserved in 10% buffered formalin for subsequent analysis.

tag: Sex

value: Female

value: 7 weeks

tag: stain

value: BALB/c

value: intact


title: Sample5

description: Library name: Sample5


title: adrenal gland -male

description:
Library name: whole_male
Formalin-fixed paraffin-embedded (FFPE) spatial transcriptomics study
adrenal gland -male, n=4

value: adrenal gland with adjacent adipose tissue

value: Male


title: R32_25_11

description: Library name: R32_25_11

value: 3 weeks post-HTVI


title: Sample4

description: Library name: Sample4

value: EVs


title: HepG2, 3-hydroxybenzophenone, CH10, 6h, H08

description: Library name: CH10_T4_D3_H08


title: HepG2, 3-hydroxybenzophenone, CH10, 6h, F11

description: Library name: CH10_T4_D3_F11


title: R32_25_10

description: Library name: R32_25_10


title: Sample3

description: Library name: Sample3

value: Nipple discharge EVs

value: IDC

value: 2+(FISH no amplification)


title: R32_25_1

description: Library name: R32_25_1

value: Liver (CCA tumor)

value: NICD/myr-AKT


title: HepG2, 3-hydroxybenzophenone, CH10, 6h, C03

description: Library name: CH10_T4_D3_C03

value: liver

value: epithelial cell

value: hepatocellular carcinoma


title: Monocytes, endothelial cells, atrial fibrillation 2

city: Bengbu

first: Pinfang

last: Kang

address: 801 Zhihuai Road

country: China

institute: Bengbu Medical University

description:
Library name: AF2
DNBelab C4

data_processing:
Raw sequencing reads are first processed with a tool like SOAPnuke (v.1.5.2) to remove low-quality data. The clean reads are then aligned to a reference genome. After alignment, the number of reads mapping to each gene is counted.  Finally, the count data is normalized and analyzed for differential gene expression.
Assembly: human hg19
Supplementary files format and content: Processed feature-barcode matrix in MEX format for each sample.

source_name: Left atrial appendage

extract_protocol:
The initial step is performed using standard commercial kits. Following extraction, The poly-A containing mRNA molecules were purified using poly-T oligo attached magnetic beads.
After purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. First strand synthesis is performed using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The cDNA fragments undergo the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. The final step before sequencing involves pooling samples and converting them into the sequencing-ready format: Quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle).

value: Left atrial appendage

value: Monocytes, endothelial cells


title: Sample2

description: Library name: Sample2


title: Monocytes, endothelial cells, atrial fibrillation 1

description:
Library name: AF1
DNBelab C4


title: HepG2, 3-hydroxybenzophenone, CH10, 6h, A06

description: Library name: CH10_T4_D3_A06

value: test


title: R32_25_35

description: Library name: R32_25_35

value: 2 weeks post-HTVI


title: Sample1

description: Library name: Sample1


title: PCL_C

city: Copenhagen

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description:
Library name: Sample 42
RiboMeth-seq

data_processing:
Library strategy: RiboMeth-seq
Barcode separation using python script
Adaptor trimming using Cutadapt v. 2.0
Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1
Counting read ends and calculating RiboMeth-seq scores using python scripts
Assembly: rDNA reference sequence from Krogh et al, NAR 2016 (find reference in the paper)
Supplementary files format and content: MS Excel file contains 5' and 3' read count and calculated RiboMeth-seq score at all positions in the rRNA sequence.

source_name: Peripheral blood

extract_protocol:
Tissue and tumor samples were homogenized prior to RNA extraction, otherwise was whole cell RNA extracted using Trizol according to the manufacturer.
RiboMeth-seq: 5-10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20-40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2',3' cyclic phosphate and 5' phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U, Christensen-Dalsgaard M, Krogh N, Sabarinathan R, Gorodkin J, Nielsen H. Profiling of ribose methylations in RNA by high-throughput sequencing. Angewandte Chemie. 2015;54(2):451-5 for detailed description

value: Peripheral blood

value: Tumor

value: adult

value: normal


title: HepG2, 3-hydroxybenzophenone, CH10, 6h, H05

description: Library name: CH10_T4_D2_H05


title: PCL_B

description:
Library name: Sample 41
RiboMeth-seq


title: R32_25_34

description: Library name: R32_25_34


title: PIIV-28 dpv

city: San Antonio

first: Venkatesh

last: Kumaresan

state: TX

address: 3.230, BSE Building, One UTSA circle

department: Molecular Microbiology and Immunology

institute: The University of Texas at San Antonio

description: Library name: PIIV28

data_processing:
Raw reads were aligned to the mouse reference genome (GRCm38, Ensembl) using STAR, and sorted with SAMtools. Strand-specificity was verified using RSeQC v2.6.4 in conjunction with the mouse RSeQC reference file (GRCm38_mm10_Ensembl.bed.gz). Gene-level raw counts were normalized using HTSeq with 0.75 quartile normalization and log₂-transformed. Differential gene expression (DEG) between groups was calculated using GFold, and genes exhibiting ≥3-fold change were considered significant
Assembly: GRCm38, Ensembl
Supplementary files format and content: quartile normalization and log₂-transformed count data

source_name: Spleen

growth_protocol: Whole cell vaccines of NMI (PIV) and NMII (PIIV) were prepared by inactivating purified C. burnetii NMI and NMII with 1% formaldehyde

extract_protocol:
After 7 and 28 dpv, mice were euthanized by CO2 exposure followed by cervical dislocation. Spleens were homogenized through a 70 µm cell strainer, red blood cells were lysed using ACK buffer, and cells were centrifuged at 400 × g for 10 minutes. Viable cells were counted using a hemocytometer and Trypan blue, with >98% viability for all assays. Immediately after cell separation, 5 million cells of splenocytes from each group were pooled together and total RNA was isolated using the RNeasy Mini Kit (Qiagen). Contaminating DNA was removed with the TURBO DNA-free Kit (Ambion), and RNA samples were processed for Illumina sequencing.
The integrity of isolated total RNA was assessed by capillary electrophoresis fragment analysis (University of Missouri DNA Core Laboratory), and both the 28S/18S rRNA ratio and RNA integrity number (RIN) were calculated. All samples exhibited RIN scores above 9.5 and were subsequently used for library preparation. Strand-specific RNA-seq libraries were generated using the Illumina TruSeq HT Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA) according to the manufacturer’s instructions. Libraries were normalized, pooled, and sequenced on an Illumina HiSeq 2000 using a 100-nucleotide paired-end protocol.

treatment_protocol: Mice were divided into four groups (PBS, Adjuvant, PIV, PIIV), each with four biological replicates. Vaccination was administered subcutaneously: mice were restrained by scruff, and 10 µg of PIV or PIIV in 50 µL PBS plus 50 µL aluminum hydroxide gel (Alum) adjuvant (Invivogen) was injected into the scruff skin to a depth of 0.5 cm using a sterile 25G needle. The adjuvant group received 50 µL PBS with 50 µL adjuvant, and the PBS group received 100 µL PBS.

value: Spleen

value: Splenocytes

value: PIIV-vaccinated

tag: time

value: 28 dpv


title: PCL_A

description:
Library name: Sample 40
RiboMeth-seq


title: HepG2, 3-hydroxybenzophenone, CH10, 6h, F08

first: Yuqing

address: 8700 mason montgomery road

description: Library name: CH10_T4_D2_F08


title: R32_25_33

description: Library name: R32_25_33

value: Liver (CCA tumor)


title: PIV-28 dpv

description: Library name: PIV28

value: PIV-vaccinated


title: B cell_3

description:
Library name: Sample 3
RiboMeth-seq

value: B cell


title: R32_25_32

description: Library name: R32_25_32

value: Liver

value: WT


title: Adjuvant Control-28 dpv

description: Library name: A28

value: Adjuvant-treated


title: HepG2, 3-hydroxybenzophenone, CH10, 6h, E11

description: Library name: CH10_T4_D2_E11

value: liver

value: epithelial cell

value: hepatocellular carcinoma


title: HepG2, 3-hydroxybenzophenone, CH10, 6h, B03

description: Library name: CH10_T4_D2_B03

value: test