title: H3K27ac_ChIPseq_control_repA

description: Library name: H3K27ac_ChIPseq_control_A

data_processing:
Adapter trimming was performed using fastp, followed by alignment to the hg38 reference genome using BWA-MEM. Aligned reads were sorted and indexed with samtools, and duplicate reads were marked using picard MarkDuplicates. Normalized signal tracks were generated using deepTools (bamCoverage) with reads per genomic content (RPGC) normalization.
Assembly: GRCh38/hg38
Supplementary files format and content: bigwig files for normalized signal visualization.

source_name: Brain tumor

extract_protocol:
ChIP–seq was performed essentially as described in (Schmidl et al. Nature Methods 2015) using a dual crosslinking method and in situ tagmentation. In brief, ~1 million cells per replicate were first crosslinked in 1.5 mM ethylene glycol bis(succinimidyl succinate) (EGS) for 30 min, followed by 1% formaldehyde for 10 min, then quenched with 125 mM glycine. After washing, cell pellets were snap-frozen in liquid nitrogen and stored at −80 °C. Pellets were lysed in the presence of protease and deacetylase inhibitors, and the chromatin was sonicated to the desired size range. Drosophila spike-in chromatin (Active Motif) was added at 2% by mass for normalization, and immunoprecipitation was carried out with protein A magnetic beads (ThermoScientific #10001D) conjugated to H3K27ac (2.5uL per 1x106 cells) (Abcam #ab4729), or spike-in antibody (2% of ug of target Ab, Active Motif #104597).
After extensive washing, in situ tagmentation was performed on bead-bound chromatin to incorporate sequencing adapters, and crosslinks were reversed by overnight proteinase K treatment. DNA was purified by column-based methods, then PCR-amplified to produce the final libraries. Libraries were size-selected with AMPure beads, checked for concentration and fragment distribution (Qubit and Tapestation), and quantified by qPCR prior to multiplexed sequencing on an Illumina NovaSeq 6000.

value: control

tag: chip antibody

value: H3K27ac Abcam #ab4729


title: RNA library from 12 weeks IVF single oocyte 22

status: Public on Jun 01 2026

type: SRA

city: Philadelphia

first: Eric

middle: Alejandro

last: Rhon Calderon

state: Pennsylvania

address: 3400 Civic Center Blvd, Bldg 421, Floor 9-175

department: Cell and Developmental Biology

country: USA

institute: University of Pennsylvania

description:
Library name: 126_4_6
126_4_6
summary_count_12weeks_single_oocytes.txt

library_source: transcriptomic

data_processing:
RNA-seq reads were trimmed for quality using Trimmomatic (version 0.32). Illumina TruSeq3-PE primers, leading and trailing low-quality (below quality 3) and N base calls were trimmed, and reads were scanned using a 4-bp sliding window and trimmed when the average quality per base dropped below 15. Reads of at least 30-bp in length following this quality control process were retained and used for subsequent analyses.
The resulting reads were then aligned to mm10 reference genome assembly using STAR (version 2.3.0e), allowing read pairs to align no farther than 2000-bp apart and keeping alignments with a mapping quality score (MAPQ) greater than 1 for genome-wide transcript counting.
FeatureCounts (version 1.5.0) was used to generate a matrix of mapped fragments per RefSeq annotated gene.
Analysis for differential gene expression was performed using DESeq2 with the cutoff of FDR < 0.05. Clustering and heatmaps of differentially expressed genes were generated using heatmaply R package. Chord plots were done using complexheatmap, clusterprofiler and circlize packages in R. WGCNA was done using the WGCNA package for R.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: 12 week single oocyte

growth_protocol: All animals were housed in polysulfone cages containing drinking water and chow (Laboratory Irradiated Rodent Diet 5LG4, LabDiet) ad libitum.

extract_protocol:
For tissue: RNA was extracted using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries. For single oocytes and cumulus cells: a modified SMART-seq extraction protocol was used using TCL and BME for cell lysis
For tissue: RNA libraries for RNA-seq were prepared using KAPA Stranded mRNA-Seq Kit (Illumina Platforms) and KAPA Single-Indexed adapter kit following manufacturer's protocols. For single oocytes and cumulus cells: Nextera Library prep and Nextera sequencing indexes (Illumina) were used.

treatment_protocol: E18.5 ovaries, 12 weeks ovaries, 39 weeks ovaries, 12 weeks single oocytes, 39 weeks single oocytes, 12 cumulus cells pools, 39 weeks cumulus cells pools, F2 12 weeks testis, F2 12 weeks male livers, F2 12 weeks ovaries, F2 weeks female livers awere collected, snap frozen in liquid nitrogen and stored at -80C for RNA extraction.

tag: cell type

value: 12 week single oocyte

tag: genotype

value: Female

tag: treatment

value: IVF


title: RNA library from 12 weeks IVF single oocyte 21

description:
Library name: 126_4_5
126_4_5
summary_count_12weeks_single_oocytes.txt


title: H3K27ac_ChIPseq_c483_2wk_repB

city: Los Angeles

first: Aram

last: Modrek

state: Ca

address: 1441 EastLake Ave

institute: USC

description: Library name: H3K27ac_ChIPseq_c483_2wk_B

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Patient derived glioma stem-like cultures (GSCs) were cultured in serum free media, as detailed in a publication from (Bhat et al. Cancer Cell 2013).

treatment_protocol: Treated with 10 ng/uL doxycycline for 3 hours to induce CRISPR-Cas9 guide RNA expression.

tag: tissue

value: Brain tumor

tag: cell line

value: human glioblastmoma (patient derived)

value: mtgRNA


title: Lung cells, LPS

city: hangzhou

first: REN

last: YICHAO

state: zhejiang

address: zhejianghangzhou

country: China

institute: zhejiang university

description:
Library name: Sample_2
10x Genomics scRNA-seq

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were converted to FASTQ format using Illumina bcl2fastq (v5.0.1). Demultiplexing, barcode processing, and gene counting were performed using Cell Ranger (v9.0.1) with alignment to the Ensembl mouse reference genome.
Putative doublets were identified using DoubletFinder (v2.0.4). Downstream analysis was conducted with the Seurat package (v4.4.0). Low-quality cells detecting fewer than 500 genes or exhibiting >25% mitochondrial transcript content were excluded.
Gene expression data were normalized using NormalizeData. Highly variable genes were identified via FindVariableFeatures (2,000 genes), and data scaling was performed using ScaleData. Principal component analysis was carried out with RunPCA. Batch effects were corrected using Harmony (v1.1.0).
Unsupervised clustering was performed using FindNeighbors and FindClusters. Dimensionality reduction and visualization were performed using RunUMAP and RunTSNE. Marker genes for each cluster were identified using FindAllMarkers (log₂FC > 0.26, p-value < 0.05, bimod likelihood-ratio test, expressed in ≥10% of cells within the cluster). Cell types were annotated using SingleR and ImmGen reference databases.
Alveolar macrophage subclustering was performed by subsetting AM populations and repeating dimensionality reduction and clustering based on 2,000 highly variable genes. Differential expression analysis between treatment groups was conducted using FindMarkers (|log₂FC| > 0.26, p-value < 0.05, bimod test, expressed in ≥10% of cells in one group). Pathway enrichment was performed using KEGG and Hallmark GSEA.
Pseudotime trajectory analysis of AM subsets was performed using Monocle2 (v2.22.0). Differential gene expression across pseudotime was assessed with differentialGeneTest, and cells were ordered using orderCells.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of cell barcodes；
Supplementary files format and content: features.tsv.gz: list of gene IDs (Ensembl gene annotation)；
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format

molecule: polyA RNA

source_name: Lung

growth_protocol: C57BL/6 mice were maintained under specific pathogen-free (SPF) conditions with a 12-hour light/dark cycle, at constant temperature and humidity, with free access to standard chow and water.

extract_protocol:
Mouse lungs were harvested, minced on ice, and digested with Liberase (Sigma-Aldrich) at 37 °C for 15 min. Following enzymatic dissociation, cells were pelleted by centrifugation at 500 × g for 5 min, and residual erythrocytes were removed using RBC Lysis Buffer (Beyotime). Single-cell suspensions were filtered through a 40-μm cell strainer and stained for 30 min at 4 °C in the dark using fluorophore-conjugated antibodies against CD45 (PE-Cy5), Ly6G (AF700), F4/80 (PE), CD11b (PerCP-Cy5.5), and CD11c (BV605) (BioLegend). DAPI was added 10 min before sorting to exclude nonviable cells. Fluorescence-activated cell sorting was performed on a BD FACSAria Fusion flow cytometer, and lung macrophages were identified as DAPI⁻CD45⁺Ly6G⁻F4/80⁺CD11b/CD11c⁺ cells. Sorted cells were collected in culture medium supplemented with 20% FBS. To ensure sufficient cell yield for downstream scRNA-seq analysis, each biological replicate consisted of pooled cells from three mice.
Sorted cells were washed and resuspended in 1× PBS containing 0.04% BSA. Cell concentration was adjusted to 700–1,200 cells/μL and viability was confirmed by acridine orange/propidium iodide staining and CountStar counting. Cells were loaded into the Chromium Controller (10x Genomics, PN-120270) on a Chromium GEM-X Single Cell 3′ Chip (10x Genomics, PN-1000690) to generate single-cell gel beads in emulsion (GEMs) according to the manufacturer's protocol (10x Genomics, CG000732). cDNA amplification and library construction were performed using the Chromium GEM-X Single Cell 3′ Reagent Kit v4 (10x Genomics, PN-1000691). Constructed libraries were quality-controlled using the Agilent dsDNA 915 Reagent Kit (Agilent, DNF-915-K0500) and quantified using the VAHTS Library Quantification Kit for Illumina (VAHTS, NQ101). Libraries were sequenced on the Illumina NovaSeq™ X Plus platform with 2 × 150 paired-end kits. Read 1 (28 bp) was used for cell barcode and UMI, and Read 2 (91 bp) for transcript sequence, with a minimum sequencing depth of 20,000 reads per cell.

treatment_protocol: For the LPS-induced acute lung injury model, anesthetized mice underwent cervical incision for tracheal exposure followed by intratracheal instillation of phosphate-buffered saline (PBS, 50 µL) or LPS (4 mg/kg in 50 µL; Sigma). In the LPS + Reg3g group, Reg3g (6 µg) was co-administered intratracheally with LPS. Mice were randomly assigned to three treatment groups for 24 hours: (1) PBS control; (2) LPS alone; (3) LPS + Reg3g.

value: Lung

value: mixed (macrophage-enriched)

value: wild type

value: LPS ( 4mg/kg )


title: UPN827 cells, TN22 TrailNet Baseline T1D plasma

type: RNA

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description: Gene expression data from UPN827 cells stimulated with T1D plasma

hyb_protocol: The Affymetrix GeneChip Human Genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios.  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA function in Partek GS.

label: biotin

source_name: UPN827 cells stimulated with TN22 TrailNet Baseline T1D plasma

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Commercial cryopreserved PBMCs of healthy Caucasian male donor UPN827 were thawed and washed per the manufacturer’s protocol (Cellular Technology Ltd., Shaker Heights, OH).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% of participant plasma  that was sampled at baseline or the 3-6 months post-baseline from six TrailNet new-onset T1D intervention trails, or from our local Recent onset T1DM cohort. Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl.  After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

tag: responder cells

value: UPN827 cells

tag: sample timepoint

value: TrailNet Baseline


title: Lung cells, PBS

description:
Library name: Sample_1
10x Genomics scRNA-seq

value: PBS


title: H3K27ac_ChIPseq_c483_2wk_repA

description: Library name: H3K27ac_ChIPseq_c483_2wk_A


title: UPN827 cells, TN21RH2 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN21RH2 TrailNet Baseline T1D plasma


title: UPN827 cells, TN20 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN20 TrailNet Baseline T1D plasma


title: RNA library from 12 weeks IVF single oocyte 19

description:
Library name: 126_4_3
126_4_3
summary_count_12weeks_single_oocytes.txt


title: H3K27ac_ChIPseq_c483_3hr_repB

description: Library name: H3K27ac_ChIPseq_c483_3hr_B


title: WT3 24hr stim with 0.5nM GP33 peptide/anti-CD28

city: Indianapolis

last: Richer

state: IN

address: R2 Rm 366 950W Walnut St

department: Microbiology and Immunology

institute: Indiana University School of Medicine

description:
Library name: sample 30
24hr-WT3-GP-lo_S42

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina NovaSeq 6000
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the mouse genome using STAR (v2.7.11a) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to mm10 genes using featureCounts (from subread v2.0.0).
Differential gene expression analysis was performed using the edgeR package (v3.40.2).
Assembly: mm10
Supplementary files format and content: raw counts

source_name: Spleen

growth_protocol: CD8 T cells were isolated and enriched using the StemCell easy step CD8 enrichment kit. Cells were counted and 100 uL containing 4.5x105 cells were added to each well of a 96 well plate. Cells were activated with 2 ug/ml of anti-CD28 and 0.05 nM GP33-41 peptide or 20 nM GP33-41 peptide. Cell cultures were supplemented with recombinant mouse 10 ng/mL IL-2 peptide to support T cell proliferation and survival.

extract_protocol:
RNA was extracted from CD8 T cells using the Qiagen RNeasy mini kit.
10 nanograms of total RNA was used for library preparation with the SMARTer Stranded Total RNA-Seq Kit v3 -Pico kit, following the manufacturer’s instruction. Each resulting uniquely dual-indexed library was quantified and quality accessed by Qubit and Agilent TapeStation. Multiple libraries were pooled in equal molarity.

value: Spleen

value: CD8 T cells


title: RNA library from 12 weeks IVF single oocyte 18

description:
Library name: 126_4_2
126_4_2
summary_count_12weeks_single_oocytes.txt


title: H3K27ac_ChIPseq_c483_3hr_repA

description: Library name: H3K27ac_ChIPseq_c483_3hr_A


title: UPN827 cells, TN19 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN19 TrailNet Baseline T1D plasma


title: WT2 24hr stim with 0.5nM GP33 peptide/anti-CD28

description:
Library name: sample 29
24hr-WT2-GP-lo_S41


title: RNA library from 12 weeks IVF single oocyte 17

description:
Library name: 126_4_1
126_4_1
summary_count_12weeks_single_oocytes.txt


title: H3K27ac_ChIPseq_c142_2wk_repB

description: Library name: H3K27ac_ChIPseq_c142_2wk_B


title: WT1 24hr stim with 0.5nM GP33 peptide/anti-CD28

description:
Library name: sample 28
24hr-WT1-GP-lo_S40


title: RNA library from 12 weeks IVF single oocyte 16

description:
Library name: 126_3_8
126_3_8
summary_count_12weeks_single_oocytes.txt


title: UPN827 cells, TN18 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN18 TrailNet Baseline T1D plasma


title: UPN827 cells, TN17 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN17 TrailNet Baseline T1D plasma


title: WT3 24hr stim with 20nM GP33 peptide/anti-CD28

description:
Library name: sample 27
24hr-WT3-GP-hi_S39


title: H3K27ac_ChIPseq_c142_2wk_repA

description: Library name: H3K27ac_ChIPseq_c142_2wk_A


title: RNA library from 12 weeks IVF single oocyte 15

description:
Library name: 126_3_7
126_3_7
summary_count_12weeks_single_oocytes.txt


title: RNA library from 12 weeks IVF single oocyte 25

description:
Library name: 127_2_1
127_2_1
summary_count_12weeks_single_oocytes.txt


title: WT2 24hr stim with 20nM GP33 peptide/anti-CD28

description:
Library name: sample 26
24hr-WT2-GP-hi_S38


title: UPN827 cells, TN16 TrailNet Baseline T1D plasma

description: Gene expression data from UPN827 cells stimulated with T1D plasma

source_name: UPN827 cells stimulated with TN16 TrailNet Baseline T1D plasma


title: DNAseq_ChIPseq_c142_3hr_repA

description: Library name: DNAseq_ChIPseq_c142_3hr_A

data_processing:
To assess the frequency and distribution of small insertions and deletions (indels) and large structural variants (SVs) arising from CRISPR–Cas9-induced DNA double-strand breaks, we used separate, tailored analysis pipelines based on the sequencing assay. In both analysis pipelines, we constricted the analysis to verified cut sites and the pulled down regions that achieved coverage levels exceeding 100X. ENCODE defined blacklisted regions were filtered out. For small indel analysis, we applied the crispr-DART (Downstream Analysis and Reporting Tool) pipeline (9). Paired-end Illumina reads were subjected to quality control using FastQC (version 0.11.7) and trimmed with Trim Galore, followed by alignment to the human reference genome (hg38) using BBMap. To enhance detection sensitivity, reads overlapping putative indels were realigned using the Genome Analysis Toolkit GATK (version 3.8.0) for local realignment around indels and base quality score recalibration. Indel frequency profiles were visualized using IGV (version 2.18) and aggregated into heatmaps with deeptools (v3.5.1) using BigWig files output by crispr-DART.
For large SV analysis, we followed a parallel preprocessing workflow. Raw paired-end reads underwent quality control using FastQC (version 0.11.7) and adapter trimming via Trimmomatic (version 0.36). Reads were aligned to hg38 with BWA-MEM (version 0.7.17), and duplicates were removed using sambamba (version 0.6.8). BAM files were processed with GATK (v3.8.0) for local realignment around indels and base quality score recalibration. These realigned and recalibrated BAMs were used for structural variant calling with DELLY (version 0.8.1). DELLY identified deletions, duplications, inversions, and translocations using split-read and paired-end evidence from tumor-versus-control BAM comparisons. Output .bcf files were converted to .vcf using bcftools, and high-confidence SVs were annotated and visualized using Circos and other genome plotting tools.
Assembly: GRCh38/hg38
Supplementary files format and content: Small indels are represented in .bigwig files as scores (deletions, insertions and indels). Large structural variants are represented in .vcf files, wherin the control acts as the control baseline comparison.

extract_protocol:
genomic DNA was extracted using the AllPrep genomic DNA/RNA extraction kit (Qiagen)
Two custom biotin-tagged capture panels (xGen DNA panels, Integrated DNA Technologies) were designed to enrich specific DNA regions, each featuring 120 bp probes with one to four probes flanking each targeted cut site, see Supplemental Table S5-6. One panel contained 402 probes (mtg142) and another contained 979 probes (mtg483). The degeneracy of genomic sequences around cut sites prevented the design of probes with high enough specificity to target all sites, therefore only probe/site combinations which could be targeted without significant overlap were included in the panel. Following library construction, the prepared libraries were hybridized with the panels according to the manufacturer’s guidelines, subjected to stringent washes to remove nonspecific fragments, and subsequently PCR-amplified. The enriched libraries were purified and assessed for quality with a tapestation prior to sequencing. Sequencing was multiplexed and performed on a MiSeq 2000 with 10% PhiX spike-in.


title: H3K27ac_ChIPseq_c142_3hr_repB

description: Library name: H3K27ac_ChIPseq_c142_3hr_B


title: RNA library from 12 weeks IVF single oocyte 24

description:
Library name: 126_4_8
126_4_8
summary_count_12weeks_single_oocytes.txt


title: RNA library from 12 weeks IVF single oocyte 14

description:
Library name: 126_3_6
126_3_6
summary_count_12weeks_single_oocytes.txt


title: H3K27ac_ChIPseq_c142_3hr_repA

description: Library name: H3K27ac_ChIPseq_c142_3hr_A


title: UPN827 cells, TN15 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN15 TrailNet Baseline T1D plasma


title: H3K27ac_ChIPseq_control_repB

description: Library name: H3K27ac_ChIPseq_control_B

value: control


title: WT1 24hr stim with 20nM GP33 peptide/anti-CD28

description:
Library name: sample 25
24hr-WT1-GP-hi_S37


title: RNA library from 12 weeks IVF single oocyte 13

description:
Library name: 126_3_5
126_3_5
summary_count_12weeks_single_oocytes.txt


title: DNA_Me_GSC20 vector control rep B

description: Library name: DNA_Me_control_B

data_processing:
Partial genome bisulfite sequencing data from TruSeq Methyl Capture was trimmed for adapters and low-quality bases using Trimmomatic, then aligned to the bisulfite-converted hg38 reference genome via Bismark and Bowtie2. Duplicate reads were removed in Bismark, and methylation calls were subsequently extracted. Further processing was conducted in methylKit, beginning with coverage-based filtering to remove bases below 10× coverage and above the 99.9th percentile. Samples were merged and used to calculate percent methylation. Differential methylation analyses were performed on the merged data, considering only CpGs that had adequate coverave among all samples. We applied thresholds for q-values (e.g., <0.01) and methylation differences (≥25%), and the resulting differentially methylated bases or regions were stored for further downstream interpretation.
Assembly: hg38
Supplementary files format and content: Bigwig (.bw) files containing DNA methylation values for coverered CpGs. Differentially methylated CpGs (p<0.01) that were covered by sequencing in all samples are in bedGraph format (Rep A and B combined).

growth_protocol: Cells were grown in serum-free stem cell media in non-adherant plates.

extract_protocol:
DNA was extracted using the Qiagen AllPrep genomic DNA/RNA extraction kit (Qiagen). Experiments were performed in duplicates (n=2).
Genomic DNA was processed using the TruSeq Methyl Capture EPIC Library Prep Kit (Illumina) according to the manufacturer’s protocol. Briefly, high-quality DNA (as determined by tapestation analysis) was fragmented via a Covaris S220, followed by end-repair, 3′ adenylation, and ligation of methylation-compatible adapters. The resulting fragments underwent bisulfite conversion to convert unmethylated cytosines to uracils, while preserving methylated cytosines. The libraries were then hybridized to the TruSeq Methyl Capture EPIC probes for targeted enrichment of methylated regions, followed by bead-based capture. Finally, the enriched libraries were PCR-amplified, purified, and assessed for quality with a tapestation prior to sequencing. Sequencing multiplexed and performed on an Illumina NovoSeq 6000.


title: Lung cells, LPS + Reg3g

description:
Library name: Sample_3
10x Genomics scRNA-seq

value: LPS ( 4mg/kg ) + Reg3g ( 6ug )


title: UPN827 cells, TN14rehyb TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN14rehyb TrailNet Baseline T1D plasma


title: UPN827 cells, TN23 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN23 TrailNet Baseline T1D plasma


title: WT3 6hr stim with 0.5nM GP33 peptide/anti-CD28

description:
Library name: sample 24
6hr-WT3-GP-lo_S36


title: DNA_Me_GSC20 vector control rep A

description: Library name: DNA_Me_control_A


title: RNA library from 12 weeks IVF single oocyte 12

description:
Library name: 126_3_4
126_3_4
summary_count_12weeks_single_oocytes.txt

value: 12 week single oocyte


title: UPN827 cells, TN13 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN13 TrailNet Baseline T1D plasma


title: WT2 6hr stim with 0.5nM GP33 peptide/anti-CD28

description:
Library name: sample 23
6hr-WT2-GP-lo_S35


title: RNA library from 12 weeks IVF single oocyte 20

description:
Library name: 126_4_4
126_4_4
summary_count_12weeks_single_oocytes.txt

value: Female


title: RNA library from 12 weeks IVF single oocyte 11

description:
Library name: 126_3_3
126_3_3
summary_count_12weeks_single_oocytes.txt

value: IVF


title: UPN827 cells, TN12 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN12 TrailNet Baseline T1D plasma


title: WT1 6hr stim with 0.5nM GP33 peptide/anti-CD28

description:
Library name: sample 22
6hr-WT1-GP-lo_S34


title: DNA_Me_GSC20 mtg483 3hr rep B

description: Library name: DNA_Me_c483_3hr_B

value: Brain tumor


title: DNA_Me_GSC20 mtg483 2wk rep B

description: Library name: DNA_Me_c483_2wk_B

value: human glioblastmoma (patient derived)


title: RNA library from 12 weeks IVF single oocyte 10

description:
Library name: 126_3_2
126_3_2
summary_count_12weeks_single_oocytes.txt


title: WT3 6hr stim with 20nM GP33 peptide/anti-CD28

description:
Library name: sample 21
6hr-WT3-GP-hi_S33


title: DNA_Me_GSC20 mtg483 3hr rep A

description: Library name: DNA_Me_c483_3hr_A

value: mtgRNA


title: RNA library from 12 weeks IVF single oocyte 9

description:
Library name: 126_3_1
126_3_1
summary_count_12weeks_single_oocytes.txt


title: UPN827 cells, TN11 TrailNet Baseline T1D plasma

description: Gene expression data from UPN827 cells stimulated with T1D plasma

source_name: UPN827 cells stimulated with TN11 TrailNet Baseline T1D plasma


title: RNA library from 12 weeks IVF single oocyte 8

description:
Library name: 126_2_8
126_2_8
summary_count_12weeks_single_oocytes.txt


title: DNA_Me_GSC20 mtg483 2wk rep A

description: Library name: DNA_Me_c483_2wk_A

source_name: Brain tumor


title: WT2  6hr stim with 20nM GP33 peptide/anti-CD28

description:
Library name: sample 20
6hr-WT2-GP-hi_S32


title: UPN827 cells, TN9 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN9 TrailNet Baseline T1D plasma


title: UPN827 cells, TN10 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN10 TrailNet Baseline T1D plasma


title: WT 1 6hr stim with 20nM GP33 peptide/anti-CD28

description:
Library name: sample 19
6hr-WT1-GP-hi_S31


title: RNA library from 12 weeks IVF single oocyte 7

description:
Library name: 126_2_7
126_2_7
summary_count_12weeks_single_oocytes.txt

source_name: 12 week single oocyte


title: DNA_Me_GSC20 mtg142 3hr rep B

description: Library name: DNA_Me_c142_3hr_B


title: AFF3 KO3 24hr stim with 0.5nM GP33 peptide/anti-CD28

description:
Library name: sample 18
24hr-KO3-GP-lo_S30


title: DNA_Me_GSC20 mtg142 2wk rep B

description: Library name: DNA_Me_c142_2wk_B


title: RNA library from 12 weeks IVF single oocyte 6

description:
Library name: 126_2_6
126_2_6
summary_count_12weeks_single_oocytes.txt


title: AFF3 KO2 24hr stim with 0.5nM GP33 peptide/anti-CD28

description:
Library name: sample 17
24hr-KO2-GP-lo_S29


title: RNA library from 12 weeks IVF single oocyte 5

description:
Library name: 126_2_5
126_2_5
summary_count_12weeks_single_oocytes.txt


title: UPN827 cells, TN6 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN6 TrailNet Baseline T1D plasma


title: DNA_Me_GSC20 mtg142 3hr rep A

description: Library name: DNA_Me_c142_3hr_A


title: UPN827 cells, TN8 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN8 TrailNet Baseline T1D plasma


title: RNA library from 12 weeks IVF single oocyte 4

description:
Library name: 126_2_4
126_2_4
summary_count_12weeks_single_oocytes.txt


title: UPN827 cells, TN7 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN7 TrailNet Baseline T1D plasma


title: DNA_Me_GSC20 mtg142 2wk rep A

description: Library name: DNA_Me_c142_2wk_A


title: AFF3 KO3 24hr stim with 20nM GP33 peptide/anti-CD28

description:
Library name: sample 15
24hr-KO3-GP-hi_S27

source_name: Spleen


title: RNA library from 12 weeks IVF single oocyte 3

description:
Library name: 126_2_3
126_2_3
summary_count_12weeks_single_oocytes.txt


title: UPN827 cells, TN5 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN5 TrailNet Baseline T1D plasma


title: isBLISS GSC20 vector control rep B

description: Library name: isBLISS_GSC20_vector_control_rep_B

data_processing:
Raw sequencing data was first processed by author instructions. Briefly, the blissNP pipeline (Yan Nat. Comm. 2017) was used to generate a BED file that averaged both replicates with counts of every unique double-strand break that had been sequenced. Signals from the isBLISS data were normalized to achieve a mean signal of 1 across all bases. We calculated the total signal by multiplying each region’s length by its signal value and divided by the total number of bases to determine the current average signal. We then applied a normalization factor to each region’s signal, bringing the average signal across each sample per base to 1. To define the final set of mtgRNA-CRISPR-cas9 cut sites we defined a potential ‘universe’ of theoretical guide-RNA landing sides that includes a perfect match (0 mis-matches to the genome with the guide RNA sequence), 1 mis-match (1 nucleotide is not matched) or 2 mis-matches (2 nucleotides do not match), up to two RNA bulges on the genome and up to two DNA bulges on the guideRNA. This universe of potential target sites was intersected with the normalized isBLISS signals to only include sites that had a double-strand break.
Assembly: hg38
Supplementary files format and content: bigwig files ending in "all_isBLISSsignals_norm.bw" signify all normalized isBLISS counts across the entire genome. Bedgraph files ending in "DefinedCuts_isBLISSsignals_norm.bedgraph" signify the normalized and defined isBLISS counts that represent cut sites used in this dataset and manuscript.

extract_protocol:
Double-strand break sequencing in-suspension breaks labeling in situ and sequencing, or sBLISS or isBLISS) was performed as described in detail in (Bouman Nature Protocols 2020). Summarized here, the protocol begins with the crosslinking of cells with 2% PFA. Cells are lysed to expose the DSB ends, which are subsequently blunted in situ and ligated to the sBLISS adaptor. Genomic DNA is then extracted and sonicated.
Library preparation proceeds with in vitro transcription for linear amplification of the template. The library is then ligated to a new adaptor and annealed to a complimentary oligonucleotide to enable reverse transcription of each template. The entire library is amplified with sequencing primers that include indexes and unique barcodes. Following quantification and quality control checks via tapestation analysis, the libraries are sequenced via an Illumina NovoSeq6000 with 10% PhiX spiked in.


title: UPN827 cells, TN3 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN3 TrailNet Baseline T1D plasma


title: RNA library from 12 weeks IVF single oocyte 2

description:
Library name: 126_2_2
126_2_2
summary_count_12weeks_single_oocytes.txt


title: AFF3KO2 24hr stim with 20nM GP33 peptide/anti-CD28

description:
Library name: sample 14
24hr-KO2-GP-hi_S26


title: isBLISS GSC20 vector control rep A

description: Library name: isBLISS_GSC20_vector_control_rep_A


title: UPN827 cells, TN4 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN4 TrailNet Baseline T1D plasma


title: AFF3 KO1 24hr stim with 20nM GP33 peptide/anti-CD28

description:
Library name: sample 13
24hr-KO1-GP-hi_S25


title: isBLISS GSC20 mtg483 3hr rep B

description: Library name: isBLISS_GSC20_mtg483_3hr_rep_B


title: RNA library from 12 weeks IVF single oocyte 1

description:
Library name: 126_2_1
126_2_1
summary_count_12weeks_single_oocytes.txt


title: AFF3 KO3 6hr stim with 0.5nM GP33 peptide/anti-CD28

description:
Library name: sample 12
6hr-KO3-GP-lo_S24


title: UPN827 cells, TN2 TrailNet Baseline T1D plasma

description: Gene expression data from UPN827 cells stimulated with T1D plasma

source_name: UPN827 cells stimulated with TN2 TrailNet Baseline T1D plasma


title: RNA library from 12 weeks Natural single oocyte 36

description:
Library name: 92_5_8
92_5_8
summary_count_12weeks_single_oocytes.txt

value: Natural


title: SNU1196 cells, afatinib rep3

city: Beijing

first: Huishan

last: Sun

state: Beijing

address: No.1 Shuaifuyuan Wangfujing Dongcheng District, Beijing,China

institute: Peking union medical college hospital

description:
Library name: Sample9
S96_3_3

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Differential expression analysis of two groups (three biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: ensembl_110_homo_sapiens_grch38_primary
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

growth_protocol: All cells were maintained in RPMI-1640 supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37 ℃

extract_protocol:
RNA was extracted using TRNzol Universal total RNA kit (TiANGEN) according to the manufacturer's instructions.
RNA library was prepared using Fast RNA-seq Lib Prep Kit V2 following manufacture's protocals

value: Biliary Tract Cancer Cell Line

value: WT

value: afatinib


title: isBLISS GSC20 mtg483 3hr rep A

description: Library name: isBLISS_GSC20_mtg483_3hr_rep_A


title: UPN827 cells, TN1 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN1 TrailNet Baseline T1D plasma

value: UPN827 cells


title: AFF3 K02 6hr stim with 0.5nM GP33 peptide/anti-CD28

description:
Library name: sample 11
6hr-KO2-GP-lo_S23


title: RNA library from 12 weeks Natural single oocyte 35

description:
Library name: 92_5_7
92_5_7
summary_count_12weeks_single_oocytes.txt


title: AFF3 KO1 6hr stim with 0.5nM GP33 peptide/anti-CD28

description:
Library name: sample 10
6hr-KO1-GP-lo_S22


title: PYIVA-13

city: Hong Kong

first: Huaping

last: Li

address: 21 Sassoon Rd, Pok Fu Lam

country: Hong Kong

institute: The University of Hong Kong

description: gene expression from FFPE sample

hyb_protocol: The Affymetrix Human U133 GeneChip (Affymetrix, Santa Clara, CA, USA) was used for microarray gene expression analysis

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing: The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: locoregionally advanced NPC FFPE sample

label_protocol: RNA integration using an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). Total RNA was amplified using an Ovation FFPE WTA System (NuGEN, San Carlos, CA, USA), and an Encore Biotin Module (NuGEN) was used for fragmentation and labeling.

growth_protocol: All paraffin was removed from freshly cut FFPE tissue before RNA purification, and the sample was briefly heated in RNeasy lysis bugger

extract_protocol: RNA was extracted from FFPE samples using the QIAGEN FFPE RNeasy kit (QIAGEN GmbH, Hilden, Germany).

treatment_protocol: The patients were recruited from seven oncology centers in Hong Kong between September 2006 and September 2012 and were treated with concurrent chemoradiotherapy plus (neo)-adjuvant chemotherapy. The median follow-up time for all patients was 8.4 years. Formalin-fixed paraffin-embedded (FFPE) samples from the nasopharynx were prospectively archived

tag: age

value: unknown


title: RNA library from 12 weeks Natural single oocyte 34

description:
Library name: 92_5_5
92_5_5
summary_count_12weeks_single_oocytes.txt


title: isBLISS GSC20 mtg142 3hr rep B

description: Library name: isBLISS_GSC20_mtg142_3hr_rep_B


title: isBLISS GSC20 mtg142 3hr rep A

description: Library name: isBLISS_GSC20_mtg142_3hr_rep_A


title: AFF3 KO3 6hr stim with 20nM GP33 peptide/anti-CD28

description:
Library name: sample 9
6hr-KO3-GP-hi_S21


title: RNA library from 12 weeks Natural single oocyte 33

description:
Library name: 92_5_4
92_5_4
summary_count_12weeks_single_oocytes.txt


title: HiC GSC20 vector control rep B

description: Library name: HiC_control_B

data_processing:
Standard pipelines were used to process cis-genome HiC contact data unless noted otherwise. HiC Bench was used in conjunction with standard bioinformatics tools to ensure reproducibility. Alignment was performed with bwa (version 0.7.17) using settings -A1 -B4 -E50 -L0. After alignment, reads were filtered with samtools (version 1.3) and gtools (version 3.0) using a mapping quality threshold of 20, no minimum distance, and a maximum offset of 500. Duplicate reads were also removed during this step. Filtered contact pairs were converted to hic format using juicer (version 1.5) and normalized using Knight-Ruiz (KR) normalization. These were then converted to cool format using hicexplorer (version 3.7.2) in various resolutions for further visualization and processing in GENOVA (version 1.0.0). HiC data visualization with GENOVA using cool file outputs included the following steps. Centromeres were masked from analysis. Insulation scores for Topologically Associated Domain (TAD) inference was called using hic resolutions of 20kb with replicates combined. Compartments were called using hic resolutions of 500kb using combined replicates and signing of compartments was determined using H3K27ac ChIP-seq data. Interaction scores between arms of chromosomes were visualized in saddle plots and data was exported for quantification.
Hi-C valid pairs from HiC-Pro (version 3.0.0): processing options were as follows, ligation/digestion sequences (GATCGATC, GANTGATC, GANTANTC, GATCANTC), insert size range 100 to 800 bp, min and max fragment sizes set to 10 and 1,000,000, chromosomes XY were excluded and hg38 was used as the reference genome. Time point replicates were merged into a single chromatin map to reduce sparsity and enhance detection of trans interaction frequencies. Regions containing outliers were removed, and the contact maps were balanced using the Knight-Ruiz algorithm with default parameters. Subsequently, the contact maps were scaled using Hi-C contact distance-dependent median-of-ratios size factors to bring all samples to the same scale and enable direct comparisons.
Assembly: hg38
Supplementary files format and content: BedGraph files of compartment scores, mcool files for genome contact visualization (20k, 100k and 500k resolutions), and ValidPairs that contains all Hi-C read pairs that passed all filtering steps during Hi-C data processing.

extract_protocol:
For HiC (genome-wide chromatin contact conformation), the ARIMA Standard Hi-C Kit was used following manufacturer instructions. In brief, cells were crosslinked with 2% formaldehyde for 10 minutes at room temperature, and the reaction was quenched with glycine. Chromatin was digested with the restriction enzyme mixture provided in the ARIMA Standard Hi-C Kit, followed by a biotin fill-in step and proximity ligation according to the manufacturer’s protocol. Experiments were performed in duplicates (n=2).
After reversing crosslinks and purifying the DNA, adapters were ligated to the fragment ends, and library amplification was performed. Sequencing multiplexed and performed on an Illumina NovoSeq 6000.


title: AFF3 KO2 6hr stim with 20nM GP33 peptide/anti-CD28

description:
Library name: sample 8
6hr-KO2-GP-hi_S20


title: RNA library from 12 weeks Natural single oocyte 32

description:
Library name: 92_5_3
92_5_3
summary_count_12weeks_single_oocytes.txt


title: PYIII-71

description: gene expression from FFPE sample

tag: gender

value: M


title: HiC GSC20 vector control rep A

description: Library name: HiC_control_A


title: QEIII-75

description: gene expression from FFPE sample


title: AFF3 KO1 6hr stim with 20nM GP33 peptide/anti-CD28

description:
Library name: sample 7
6hr-KO1-GP-hi_S19

value: Spleen


title: QEIII-76

description: gene expression from FFPE sample


title: Naïve AFF3 WT3

description:
Library name: sample 6
N-WT3_S6

value: CD8 T cells


title: HiC GSC20 mtg483 2wk rep B

description: Library name: HiC_c483_2wk_B


title: RNA library from 12 weeks Natural single oocyte 31

description:
Library name: 92_5_2
92_5_2
summary_count_12weeks_single_oocytes.txt


title: HiC GSC20 mtg483 2wk rep A

description: Library name: HiC_c483_2wk_A


title: Naive AFF3 WT2

description:
Library name: sample 5
N-WT2_S5


title: QEIII-61

description: gene expression from FFPE sample


title: RNA library from 12 weeks Natural single oocyte 29

description:
Library name: 92_4_8
92_4_8
summary_count_12weeks_single_oocytes.txt


title: PYIVB-49

description: gene expression from FFPE sample


title: HiC GSC20 mtg483 3hr rep B

description: Library name: HiC_c483_3hr_B


title: PYIVB-25

description: gene expression from FFPE sample


title: Donor_32_Non_neuron_SCZ

city: New York

first: Swadha

last: Singh

state: NY

address: 1470 Madison Ave

department: Psychiatry

institute: Icahn School of medicine, Mount sinai

description: Library name: Donor 32

data_processing:
• Adapter trimming using Trimmomatic v0.36
• Alignment to the human genome (GRCh38/hg38) with STAR v2.5.3a
• Gene and transcript quantification using GENCODE v27 annotations
• Quality control using QTLtools (mbv) and sex-marker validation
• Normalization and differential expression modeling using voom/limma-dream
Assembly: GRCh38 / hg38 (GENCODE v27 for gene annotation)
Supplementary files format and content: Processed data include normalized gene-level and transcript-level counts (CPM / log2CPM) and differential expression statistics. Files contain gene identifiers (GENCODE v27), expression values per sample, and model outputs.

source_name: Midbrain

growth_protocol: Postmortem human ventral midbrain (substantia nigra, A9/A10 region) tissue was obtained from established brain banks participating in the CommonMind Consortium. Donors provided informed consent for brain donation, and all tissue collection followed institutional ethical guidelines and the Declaration of Helsinki.

extract_protocol:
Nuclei were isolated from ventral midbrain tissue using Dounce homogenization in sucrose-based lysis buffer, followed by ultracentrifugation through a sucrose cushion to obtain purified nuclei. Immunotagging was performed using NeuN-Alexa488 and Nurr1-Alexa647 antibodies. Approximately 50,000 NeuN+/Nurr1+ (dopaminergic) and 50,000 NeuN-/Nurr1- nuclei were sorted on a BD FACSAria. RNA was extracted from sorted nuclei in TRIzol LS, followed by chloroform extraction and cleanup using the Zymo RNA Clean & Concentrator kit with extended DNase treatment.
RNA-seq libraries were generated using the SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara). cDNA synthesis, rRNA depletion, adapter ligation, and PCR amplification were performed following the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeq-6000 (100 bp paired-end).

treatment_protocol: No experimental treatments were applied. Tissue was collected postmortem and processed directly for nuclei isolation and downstream assays. Medication history (including antipsychotic exposure) was recorded by the brain banks but no treatments were administered as part of this study.

value: Midbrain

value: postmortem brain tissue

value: Non neuron

value: SCZ


title: SNU1196 cells, pyrotinib rep3

description:
Library name: Sample6
S96_2_3

value: pyrotinib


title: RNA library from 12 weeks Natural single oocyte 30

description:
Library name: 92_5_1
92_5_1
summary_count_12weeks_single_oocytes.txt

value: 12 week single oocyte

value: Female


title: Naïve AFF3 WT1

description:
Library name: sample 4
N-WT1_S4


title: RNA library from 12 weeks Natural single oocyte 28

description:
Library name: 92_4_7
92_4_7
summary_count_12weeks_single_oocytes.txt


title: HiC GSC20 mtg483 3hr rep A

description: Library name: HiC_c483_3hr_A

value: Brain tumor

value: human glioblastmoma (patient derived)

value: mtgRNA


title: SNU1196 cells, pyrotinib rep1

description:
Library name: Sample4
S96_2_1

value: Biliary Tract Cancer Cell Line

value: WT


title: Naïve AFF3 KO3

description:
Library name: sample 3
N-KO3_S3


title: RNA library from 12 weeks Natural single oocyte 27

description:
Library name: 92_4_6
92_4_6
summary_count_12weeks_single_oocytes.txt

value: Natural


title: HiC GSC20 mtg142 2wk rep B

description: Library name: HiC_c142_2wk_B


title: Naïve AFF3 KO4

description:
Library name: sample 2
N-KO4_S2


title: PYIII-106

description: gene expression from FFPE sample


title: RNA library from 12 weeks Natural single oocyte 26

description:
Library name: 92_4_5
92_4_5
summary_count_12weeks_single_oocytes.txt


title: HiC GSC20 mtg142 2wk rep A

description: Library name: HiC_c142_2wk_A


title: PYIII-90

description: gene expression from FFPE sample


title: Naïve AFF3 KO1

description:
Library name: Sample 1
N-KO1_S1


title: AFF3 KO1 24hr stim with 0.5nM GP33 peptide/anti-CD28

description:
Library name: sample 16
24hr-KO1-GP-lo_S28


title: RNA library from 12 weeks Natural single oocyte 25

description:
Library name: 92_4_4
92_4_4
summary_count_12weeks_single_oocytes.txt


title: PYIII-52

description: gene expression from FFPE sample


title: RNA library from 12 weeks Natural single oocyte 24

description:
Library name: 92_4_3
92_4_3
summary_count_12weeks_single_oocytes.txt


title: HiC GSC20 mtg142 3hr rep B

description: Library name: HiC_c142_3hr_B


title: HiC GSC20 mtg142 3hr rep A

description: Library name: HiC_c142_3hr_A


title: Muscle_young_WT_3

city: Durham

first: James

last: White

state: nc

address: 300 N Duke Street

institute: Duke University SOM

description: Library name: Y3

data_processing:
Data filtered by removing adapter contamination, greater than 10% N bases, or low quality nucleotides.
Read alignment in HISAT2 v2.2.1
Counts in featureCounts 2.1.1
Differential analysis in DESeq2 1.42.0
Assembly: mm39
Supplementary files format and content: RPMK-normalized read count matrix for all samples and all annotated genes in .txt format.

source_name: muscle

extract_protocol:
Trizol homogenization in bead beater with Qiagen Rneasy column extraction
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 using either dTTP for non strand specific library or dUTP for strand specific library.

value: muscle

value: Wildtype

value: young


title: Muscle_young_WT_2

description: Library name: Y2


title: PYIVB-52

description: gene expression from FFPE sample

value: M


title: RNA library from 12 weeks Natural single oocyte 23

description:
Library name: 92_4_2
92_4_2
summary_count_12weeks_single_oocytes.txt


title: vascularized human cerebral organoids at day90 after Zika virus infection

city: Suzhou

first: Hu

last: Du

state: Jiangsu

address: Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, China.

institute: university of science and technology of china

description:
Library name: H9-VBO_ZV
Singleron Biotechnologies

data_processing:
Cellranger software was used for mapping raw data to the human genome (version hg38 [v1.2.0]). Then, data were processed with Seurat (v5.1.0) under R (v4.3.3) environment. For quality control, cells expressing less than 300 genes or less than 1000 UMIs or more than 20% mitochondrial gene content were removed, and genes expressed in less than 10 cells were excluded for the following analysis. Putative doublets were removed using DoubletFinder (v2.0.4). Variance-stabilizing transformation (VST) was used for searching for the highly variable genes, and the top 2000 genes were chosen to do the downstream analysis. The cells were clustered and reduced into the UMAP space by PCA, with the principal components (PCs) selected based on ElbowPlot function.
DEGs in each cluster were identified by more than 1.4-fold change and p-value<.05 with Wilcoxon rank-sum test. GO enrichment analysis was carried out by ‘ClusterProfiler’ and org.Hs.eg.db in R software program with false discovery rate (FDR) < 0.05 considered as statistical significance. Monocle (v2.32.0) package was used to analyze the developmental trajectory of cell types (using the recommended parameters). The dynamic model of scVelo (v0.3.3 based on Python 3.10) was used for modeling. Except for the vhCO+Z.V. group, the top 20% of genes with differential kinetic were used for correction. The cell differentiation trajectories were then visualized on the UMAP embedding. Cell-cell communication analysis was performed using Cellchat (v1.6.1) with default settings. Regulon expression was analyzed using pySCENIC (v0.12.1) with default settings. Based on the computed threshold, the open/off status of each regulon in each cell was binarized. The open proportion of each regulon was then calculated for each cell type.
Assembly: GRCh38
Supplementary files format and content: .h5ad format built with python-scanpy package

molecule: nuclear RNA

source_name: cerebral organoid

extract_protocol:
Organoids were harvested and were washed in pre-cooled PBSE (PBS buffer containing 2 mM EGTA). Nuclei isolation was carried out using GEXSCOPE® Nucleus Separation Solution (Singleron Biotechnologies, Nanjing, China) according to the manufacturer's product manual. Isolated nuclei were resuspended in PBSE to 106 nuclei per 400 μL, fltered through a 40 μm cell strainer, and counted with Trypan blue. Nuclei enriched in PBSE were stained with DAPI (1:1,000) (TermoFisher Scientifc, D1306). Nuiclei were defined as DAPI-positive singlets.
The concentration of single nucleus suspension was adjusted to 3-4 × 105 nuclei/mL in PBS. Single nucleus suspension was then loaded onto a microfluidic chip (GEXSCOPE® Single NucleusRNA-seq Kit, Singleron Biotechnologies) and snRNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron Biotechnologies). The resulting snRNA-seq libraries were sequenced on an Illumina novaseq 6000 instrument with 150 bp paired end reads.

value: cerebral organoid

value: Zika virus infection


title: QEIII-72

description: gene expression from FFPE sample


title: Muscle_young_WT_1

description: Library name: Y1


title: RNA library from 12 weeks Natural single oocyte 22

description:
Library name: 92_4_1
92_4_1
summary_count_12weeks_single_oocytes.txt


title: vascularized human cerebral organoids at day90

description:
Library name: H9-vBO-day90-N
Singleron Biotechnologies


title: Muscle_old_WT_3

description: Library name: O3

value: old


title: QEIII-94

description: gene expression from FFPE sample


title: RNA library from 12 weeks Natural single oocyte 21

description:
Library name: 92_3_7
92_3_7
summary_count_12weeks_single_oocytes.txt


title: human cerebral organoids at day90

description:
Library name: H9-BO-day90
Singleron Biotechnologies


title: Muscle_old_WT_2

description: Library name: O2


title: HSC2_cells_shortRNA, C. parapsilosis-treated, high-dose 3, 6 hours

city: Szeged

first: Marton

last: Horvath

state: Csongrád

address: Közép fasor 52.

department: Microbiology

country: Hungary

institute: University of Szeged

description: Library name: H6_CP513_miR

library_source: other

data_processing:
Human sequenced reads were trimmed for standard Illumina adaptor sequences / low-quality sequences using trim-galore (v0.6.4) (parameters: -q 20 --paired --illumina), the --length cutoff was set 36 for RNA-seq and 18 for miRNA-seq samples.
Processed RNA reads were aligned using Hisat2 (v2.2.1)  (parameter: --phred33 --dta --non-deterministic --rna-strandness "RF"), sorted and indexed using Samtools (v1.20).
Mapped reads were quantified for genomic features using FeatureCounts (v2.0.6). (parameter: -p --countReadPairs -s 2)
Further analysis steps for RNA-seq samples were conducted in R, inculding differential gene expression analysis using DESeq2 (v1.46.0) packages.
Processed miRNA reads were aligned using mirdeep2 (v2.0.1.3) in two steps: mapped with the mapper.pl script (parameter: -e -h -i -j -m -k AGATCGGAAGAGCACACGTCT -l 18) and quantified with the miRDeep2.pl script.
Assembly: GRCh38 (release 96) from ENSEMBL, further references for the miRNA sequencing were downloaded from miRBase (release 22), including human mature- and hairpin sequences, and mouse and rat mature sequences for contaminant masking.
Supplementary files format and content: total_read_counts.csv
Supplementary files format and content: The 6 column miRNA quantification result tables, including detected mature-, precursor-, and normalized counts.

molecule: other

growth_protocol: HSC-2 cells were grown in EMEM medium supplemented with 10% heat inactivated FBS, 1% PS, and 4 mM L-glutamine. Cells were maintained at 37°C in the presence of 5% CO2.

extract_protocol:
After reaching 85 % confluency, total RNA and total miRNA was extracted using the miRNeasy Mini Kit, following the manufacturer’s instructions.
mRNA and miRNA sequencing libraries were prepared at Novogene (UK) Company Limited, Cambridge, UK, according to the company’s own guidelines. Briefly, mRNA was poly(A)-enriched and sequenced on an Illumina NovaSeq X Plus (2×15 bp, PE150 workflow, ≥20M read pairs/sample). miRNA libraries were sequenced on a NovaSeq 6000 (50 bp single-end, SE50 workflow, ≥10M reads/sample)

treatment_protocol: Host cells were stimulated with yeast cells at the MOI of 1:1 or 5:1 (pathogen: host ratio) in serum-free EMEM medium for 1 or 6 hours at 37C, in the presence of 5% CO2. Yeast cells were cultivated in liquid YPD medium, overnight at 30C, prior to the experiments.

value: oral epithelial

value: C.parapsilosis MOI 5(pathogen):1(host)

tag: time

value: 6 hours


title: PYIVA-20

description: gene expression from FFPE sample


title: Muscle_old_WT_1

description: Library name: O1


title: RNA library from 12 weeks Natural single oocyte 19

description:
Library name: 92_3_4
92_3_4
summary_count_12weeks_single_oocytes.txt

value: 12 week single oocyte

value: Female


title: DO iPSC line 1438, untreated

city: Bar Harbor

first: Madison

last: Armstrong

state: ME

address: 600 Main St

institute: The Jackson Laboratory

description: Library name: DO_iPSC_1438_CTRL

data_processing:
Raw RNA-seq reads were combined across lanes for each sample to obtain over 30 million raw reads per sample. Combined RNA-seq reads were processed using the Jackson Laboratory Data Science Nextflow DSL2 Workflows (version 24.10.6, https://github.com/TheJacksonLaboratory/jds-nf-workflows/wiki). Reads were aligned and quantified using EMASE (Expectation Maximization for Allele-Specific Expression)[Munger, S.C., et al., RNA-Seq alignment to individualized genomes improves transcript abundance estimates in multiparent populations. Genetics, 2014. 198(1): p. 59–73.]
Raw gbrs expected read counts were compiled into a counts matrix. Raw transcript per million counts were compiled into a tpm matrix.
Assembly: Mus musculus GRCm39
Supplementary files format and content: Count tsv file with counts per gene (rows) for each sample (columns)
Supplementary files format and content: Transcript per million tsv with tpm per gene (rows) for each sample (columns)

source_name: DO iPSC 1438

growth_protocol: 218 Diversity Outbred iPSC lines were thawed from early passage aliquots, plating ~1 million cells onto gelatinized 60mm tissue culture treated plates with mESC medium +2i/LIF (DMEM supplemented with 15% ES cell grade FBS [Gibco, 16141079], 1X GlutaMAX [100X, Gibco, 35050061], 1X penicillin/streptomycin [100X, Gibco, 15140], 1X nonessential amino acids [100X, Gibco, 11140], 1X sodium pyruvate [100X, Gibco, 11360], 0.1 mM β‐mercaptoethanol [55 mM, Gibco 21985023], and 1,000 U/ml leukemia inhibitory factor [Chemicon ESG1106 or 1107], supplemented with 2i [3 uM CHIR99021, Stemgent 04-0004, GSK3 inhibition and 1 uM PD0325901, Stemgent 04-0006, MEK/ERK inhibition]). Cells were grown to confluency in 5% CO2 at 37°C before passaging for a minimum of three passages before beginning the treament protocol.

extract_protocol:
Total RNA was isolated from tissue using the NucleoMag RNA Kit (Macherey-Nagel) and the KingFisher Flex purification system (ThermoFisher). Cells were homogenized in MR1 buffer (Macherey-Nagel) by vortexing.  RNA isolation was performed according to the manufacturer’s protocol. RNA concentration and quality were assessed using the Nanodrop 8000 spectrophotometer (Thermo Scientific) and the RNA ScreenTape Assay (Agilent Technologies).
Stranded libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol.  Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions.

treatment_protocol: Density plating experiments identified plating with 75,000 cells produced optimal numbers of cells following treatment. Cells were plated on gelatinized 12-well tissue culture treated glass-like bottom plates to reduce chemical precipitation. Following plating with 75,000 cells per well in mESC medium +2i/LIF, cells were allowed to recover from passaging and expand for 24 hours at 5% CO2 at 37°C. After 24 hours of recovery, control sample cell media was replaced with fresh mESC medium +2i/LIF while treated sample cell media was replaced with mESC medium +2i/LIF with added 80μM triphenyl phosphate (TPHP, dissolved in DMSO, Acros Organics 147672500). Cells were treated for 24 hours at 5% CO2 at 37°C. Cells were collected using trypsin (0.05%, Gibco 25300-054) and cell pellets were store at -80°C until RNA extraction.

value: DO iPSC 1438

value: iPSC

value: untreated

tag: Sex

value: male

tag: do generation

tag: batch

tag: run


title: HSC2_cells_shortRNA, C. parapsilosis-treated, high-dose 2, 6 hours

description: Library name: H6_CP512_miR


title: Muscle_old_KO_3

description: Library name: O_KO_3


title: LN229-R, DMSO, rep 2

city: New Haven

first: Sigrid

last: Nachtergaele

state: CT

address: 260 Whitney Ave

department: Molecular, Cellular, and Developmental Biology

institute: Yale University

description: Library name: LN229R-DMSO2

data_processing:
Sequencing reads were trimmed using Trimmomatic (v0.39)
Trimmed sequence reads were mapped to GRCh38 using STAR (v2.7.11a)
Read counts were determined using Salmon (v1.4.0)
Normalized read counts were calculated using DESeq2
Assembly: hg38
Supplementary files format and content: csv files include normalized read counts for each comparison

source_name: LN229, TMZ resistant

growth_protocol: U87 MG and U87-R cells were grown in EMEM with 10% fetal bovine serum and 1% penicillin/streptomycin. LN229 and LN229-R cells were grown in DMEM with 5% fetal bovine serum, 1% penicillin/streptomycin, and 1mM sodium pyruvate. Growth media for U87-R and LN229-R cells was also supplemented with 50uM temozolomide.

extract_protocol:
Cells were lysed in Trizol and RNA was extracted by pehnol/chloroform extraction as per manufacturer instructions, followed by isopropanol precipitation. For U87 MG cell lines, 90ug of total RNA was used for polyA enrichment using the Dynabeads mRNA DIRECT Purification kit (Invitrogen), followed by fractionation using RNA Fragmentation Reagents (Invitrogen).
For U87 MG cell lines, libraries were prepared using the TruSeq Stranded mRNA Library Prep (Illumina) from 30ng fragmented mRNA. For LN229 cell lines, libraries were prepared using the Watchmaker mRNA Library Prep kit from 1ug of total RNA.

treatment_protocol: Cells were treated 50uM STM2457 for 96 hours (or an equivalent volume of DMSO in controls)

value: LN229, TMZ resistant

value: glioma cultured cells

value: DMSO control


title: HSC2_cells_shortRNA, C. parapsilosis-treated, high-dose 1, 6 hours

description: Library name: H6_CP511_miR


title: QEIII-194

description: gene expression from FFPE sample


title: Muscle_old_KO_2

description: Library name: O_KO_2

value: muscle


title: HSC2_cells_shortRNA, C. parapsilosis-treated, low-dose 3, 6 hours

description: Library name: H6_CP113_miR

value: C.parapsilosis MOI 1(pathogen):1(host)


title: RNA library from 12 weeks Natural single oocyte 17

description:
Library name: 92_3_2
92_3_2
summary_count_12weeks_single_oocytes.txt

value: Natural


title: Muscle_old_KO_1

description: Library name: O_KO_1


title: RNA library from 12 weeks Natural single oocyte 16

description:
Library name: 35_3_8
35_3_8
summary_count_12weeks_single_oocytes.txt


title: HSC2_cells_shortRNA, C. parapsilosis-treated, low-dose 2, 6 hours

description: Library name: H6_CP112_miR


title: RNA library from 12 weeks Natural single oocyte 15

description:
Library name: 35_3_7
35_3_7
summary_count_12weeks_single_oocytes.txt


title: PYIVB-24

description: gene expression from FFPE sample

value: M


title: Peyer's patch immune cells, pooled 16 mice, ScaleBio scRNA-seq multiplexed library_4

city: New Brunswick

first: Gaetan

last: Barbet

state: NJ

address: 89 French Street

department: Department of Pediatrics

institute: Rutgers University

description:
Library name: 24274FL-01-04
One multiplexed ScaleBio scRNA-seq library prepared from Peyer's patch immune cells from 16 mice (4 wild-type, 4 Trif-/-, 4 Il1r1-/-, and 4 littermate controls). Sample identity was encoded with RT barcodes (sample.csv). Run2 is additional sequencing of the same library.

data_processing:
Raw sequencing reads were processed using the ScaleBio Seq Suite: RNA pipeline. The workflow included barcode parsing, sample demultiplexing using RT barcode information in samples.csv, read trimming, genome alignment with STAR/STARsolo, transcript assignment, UMI counting, cell filtering, and generation of filtered gene expression matrices.
Mouse samples were aligned to the mm39 reference genome.
Filtered gene expression matrices were used for downstream analysis in Seurat v5.0.2.
Assembly: Mus musculus (mm39)
Supplementary files format and content: Processed data files include per-sample filtered gene-expression matrices in Matrix Market format (matrix.mtx.gz) with matching barcodes.tsv.gz and features.tsv.gz files. Sample barcode-to-biological-sample assignments are provided in sample.csv.

source_name: Peyer's patches

extract_protocol:
Trif- and Il1r1-deficient mice were crossed with wild-type C57BL/6 mice to generate F1 offspring. heterzygotes F1 were crossed to get F2 mice. Peyer's patches of Trif- and Il1r1-deficient mice and their littermate wild-type controls (4 mice per group) were digested for 15 min at 37 °C in 0.5 mg/ml collagenase D and 10 μg/ml DNase I to generate a single-cell suspension. Live cells (Zombie NIR-negative) were sorted using a Cytek Aurora CS. One million cells from each sample were fixed with the ScaleBio Sample Fixation Kit. Fixed samples were stored at -80 °C until all samples were collected.
Frozen fixed cells were thawed on ice and counted twice by hemocytometer. Using the ScaleBio Single Cell RNA Sequencing Kit v1.1 (Scale Biosciences), all 16 samples were prepared in one batch. Cells were loaded at 10,000 per well (6 wells per sample) to add RT barcodes as sample identifiers. Pooled cells were distributed across the 384-well plate for ligation barcode addition, then pooled again with 1,600 nuclei per well for second-strand synthesis. After tagmentation and indexing PCR, libraries were pooled (5 ul each), cleaned with 0.8X SPRIselect beads (Beckman Coulter B23317), and fragment size/concentration were quantified using High Sensitivity D5000 ScreenTape (Agilent).

treatment_protocol: Twelve-week-old wild-type (JAX#00664), Trif^Lps2 (JAX#005037; hereafter referred to as Trif-/-), and Il1r1-/- (JAX#003245) mice were maintained under specific pathogen-free (SPF) conditions.

value: Peyer's patches

value: immune cells

value: mixed (wild-type littermate controls, Trif-/-, and Il1r1-/-)

value: ScaleBio batch 1


title: HSC2_cells_shortRNA, C. parapsilosis-treated, low-dose 1, 6 hours

description: Library name: H6_CP111_miR

value: oral epithelial

value: 6 hours


title: HSC2_cells_shortRNA, C. albicans-treated 3, 6 hours

description: Library name: H6_CA113_miR

value: C.albicans MOI 1(pathogen):1(host)


title: Peyer's patch immune cells, pooled 16 mice, ScaleBio scRNA-seq multiplexed library_2

description:
Library name: 24274FL-01-02
One multiplexed ScaleBio scRNA-seq library prepared from Peyer's patch immune cells from 16 mice (4 wild-type, 4 Trif-/-, 4 Il1r1-/-, and 4 littermate controls). Sample identity was encoded with RT barcodes (sample.csv). Run2 is additional sequencing of the same library.


title: QEIII-136

description: gene expression from FFPE sample


title: RNA library from 12 weeks Natural single oocyte 13

description:
Library name: 35_3_5
35_3_5
summary_count_12weeks_single_oocytes.txt

data_processing:
RNA-seq reads were trimmed for quality using Trimmomatic (version 0.32). Illumina TruSeq3-PE primers, leading and trailing low-quality (below quality 3) and N base calls were trimmed, and reads were scanned using a 4-bp sliding window and trimmed when the average quality per base dropped below 15. Reads of at least 30-bp in length following this quality control process were retained and used for subsequent analyses.
The resulting reads were then aligned to mm10 reference genome assembly using STAR (version 2.3.0e), allowing read pairs to align no farther than 2000-bp apart and keeping alignments with a mapping quality score (MAPQ) greater than 1 for genome-wide transcript counting.
FeatureCounts (version 1.5.0) was used to generate a matrix of mapped fragments per RefSeq annotated gene.
Analysis for differential gene expression was performed using DESeq2 with the cutoff of FDR < 0.05. Clustering and heatmaps of differentially expressed genes were generated using heatmaply R package. Chord plots were done using complexheatmap, clusterprofiler and circlize packages in R. WGCNA was done using the WGCNA package for R.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: 12 week single oocyte

extract_protocol:
For tissue: RNA was extracted using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries. For single oocytes and cumulus cells: a modified SMART-seq extraction protocol was used using TCL and BME for cell lysis
For tissue: RNA libraries for RNA-seq were prepared using KAPA Stranded mRNA-Seq Kit (Illumina Platforms) and KAPA Single-Indexed adapter kit following manufacturer's protocols. For single oocytes and cumulus cells: Nextera Library prep and Nextera sequencing indexes (Illumina) were used.

value: 12 week single oocyte

value: Female


title: QEIII-181

description: gene expression from FFPE sample


title: Peyer's patch immune cells, pooled 16 mice, ScaleBio scRNA-seq multiplexed library_1

description:
Library name: 24274FL-01-01
One multiplexed ScaleBio scRNA-seq library prepared from Peyer's patch immune cells from 16 mice (4 wild-type, 4 Trif-/-, 4 Il1r1-/-, and 4 littermate controls). Sample identity was encoded with RT barcodes (sample.csv). Run2 is additional sequencing of the same library.


title: QEIII-107

description: gene expression from FFPE sample


title: HSC2_cells_shortRNA, C. albicans-treated 1, 6 hours

description: Library name: H6_CA111_miR


title: FF_5_WT

city: Guangzhou

first: Ximin

last: Hu

address: Department of Burn and Plastic Surgery, Guangzhou First People's Hospital, South China University of Technology, Guangzhou, Guangdong

description:
Library name: Sample_16
gene_expression_473_DTR.xlsx; sample_FF_5_fpkm

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Bray N, Pimentel H, Melsted P, et al., Near-optimal RNA-Seq quantification, 2015. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: http://ftp.ensembl.org/pub/release-107/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.toplevel.fa.gz http://ftp.ensembl.org/pub/release-107/gtf/mus_musculus/Mus_musculus.GRCm39.107.gtf.gz http://ftp.ensembl.org/pub/release-107/gtf/mus_musculus_c57bl6nj/Mus_musculus_c57bl6nj.C57BL_6NJ_v1.107.gtf.gz
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: Male and female mice (8 to 12 weeks old) were housed in individually ventilated cages under a 12-hour light/dark cycle with ad libitum access to food and water. Mice used within each experimental comparison were bred to generate littermates, cohoused under identical conditions, and randomly assigned to experimental groups by lab managers blinded to the study design.

extract_protocol:
RNA was harvested using Trizol reagent.
A total amount of 0.2 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Fast RNA-seq Lib Prep Kit V2 （Cat.No.RK20306） following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.  The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads (PE150) were generated.

treatment_protocol: Optogenetic stimulation was performed using a 473nm 100mW diode-pumped solid-state laser (Laser and Optics Century, Shanghai, China). An optical cannula aimed at the dorsal ear was placed 1 cm from the surface of the skin. Stimulation was at a frequency of 10 Hz for 30 minutes with a power density of 8 mW/mm2 for 11 consecutive days. Both PF4Cre; Ai32 and Ai32 control mice underwent photostimulation of the dorsal ear.

value: iDTR

value: MC903 treatment


title: RNA library from 12 weeks Natural single oocyte 12

description:
Library name: 35_3_4
35_3_4
summary_count_12weeks_single_oocytes.txt


title: QEIII-98

description: gene expression from FFPE sample


title: Donor_14_Non_neuron_SCZ

description: Library name: Donor 14

value: Midbrain

value: postmortem brain tissue

value: Non neuron

value: SCZ


title: DO iPSC line 1415, untreated

description: Library name: DO_iPSC_1415_CTRL

source_name: DO iPSC 1415

value: DO iPSC 1415

value: iPSC

value: untreated

value: female


title: PYIVB-13

description: gene expression from FFPE sample

value: F


title: LN229, STM2457, rep 2

description: Library name: LN229-STM2

value: glioma cultured cells

value: 50uM STM2457, 96 hours


title: LN229, DMSO, rep 1

description: Library name: LN229-DMSO1

value: DMSO control


title: RNA library from 12 weeks Natural single oocyte 10

description:
Library name: 35_3_2
35_3_2
summary_count_12weeks_single_oocytes.txt

value: Natural


title: QEIII-102

description: gene expression from FFPE sample

value: M


title: HSC2_cells_shortRNA, non-treated 2, 6 hours

description: Library name: H6_C2_miR

value: oral epithelial

value: 6 hours


title: UPN827 cells, TN138 TrailNet Baseline T1D plasma

description: Gene expression data from UPN827 cells stimulated with T1D plasma

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios.  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA function in Partek GS.

source_name: UPN827 cells stimulated with TN138 TrailNet Baseline T1D plasma

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: UPN827 cells

value: TrailNet Baseline


title: FF_3_WT

department: Department of Burn and Plastic Surgery, Guangzhou First People's Hospital

institute: Guangzhou First People's Hospital, South China University of Technology

description:
Library name: Sample_14
gene_expression_473_DTR.xlsx; sample_FF_3_fpkm

value: iDTR

value: MC903 treatment


title: RNA library from 12 weeks Natural single oocyte 9

description:
Library name: 35_3_1
35_3_1
summary_count_12weeks_single_oocytes.txt

value: 12 week single oocyte

value: Female


title: HSC2_cells_shortRNA, non-treated 1, 6 hours

description: Library name: H6_C1_miR


title: RNA library from 12 weeks Natural single oocyte 8

description:
Library name: 35_1_8
35_1_8
summary_count_12weeks_single_oocytes.txt


title: QEIII-33

description: gene expression from FFPE sample


title: HSC2_cells_shortRNA, C. albicans-treated 3, 1 hour

description: Library name: H1_CA113_miR

value: C.albicans MOI 1(pathogen):1(host)

value: 1 hour


title: FF_1_WT

description:
Library name: Sample_13
gene_expression_473_DTR.xlsx; sample_FF_1_fpkm


title: RNA library from 12 weeks Natural single oocyte 7

description:
Library name: 35_1_7
35_1_7
summary_count_12weeks_single_oocytes.txt


title: HSC2_cells_shortRNA, C. albicans-treated 2, 1 hour

description: Library name: H1_CA112_miR


title: DTR_3

description:
Library name: Sample_11
gene_expression_473_DTR.xlsx; sample_DTR_3_fpkm

value: PF4 Cre; iDTR


title: PYIVB-34

description: gene expression from FFPE sample


title: HSC2_cells_shortRNA, C. albicans-treated 1, 1 hour

description: Library name: H1_CA111_miR


title: PYIVB-46

description: gene expression from FFPE sample


title: RNA library from 12 weeks Natural single oocyte 5

description:
Library name: 35_1_5
35_1_5
summary_count_12weeks_single_oocytes.txt


title: HSC2_cells_shortRNA, non-treated 3, 1 hour

description: Library name: H1_C3_miR


title: RNA library from 12 weeks Natural single oocyte 4

description:
Library name: 35_1_4
35_1_4
summary_count_12weeks_single_oocytes.txt


title: PYIII-41

description: gene expression from FFPE sample


title: DTR_1

description:
Library name: Sample_9
gene_expression_473_DTR.xlsx; sample_DTR_1_fpkm


title: DO iPSC line 1386, triphenyl phosphate treated

description: Library name: DO_iPSC_1386_TPHP

source_name: DO iPSC 1386

value: DO iPSC 1386

value: iPSC

value: triphenyl phosphate

value: female


title: HSC2_cells_shortRNA, non-treated 2, 1 hour

description: Library name: H1_C2_miR


title: CTL_6

description:
Library name: Sample_8
gene_expression_473_DTR.xlsx; sample_CTL_6_fpkm

value: Optogenetic stimulation (473nm 100mW, Laser and Optics Century, Shanghai, China)


title: DO iPSC line 3304, triphenyl phosphate treated

description: Library name: DO_iPSC_3304_TPHP

source_name: DO iPSC 3304

value: DO iPSC 3304

value: male


title: UPN827 cells, TN331 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN331 TrailNet Baseline T1D plasma


title: HSC2_cells_shortRNA, non-treated 1, 1 hour

description: Library name: H1_C1_miR

value: oral epithelial


title: QEIII-26

description: gene expression from FFPE sample

value: M


title: CTL_4

description:
Library name: Sample_7
gene_expression_473_DTR.xlsx; sample_CTL_4_fpkm


title: HSC2_cells, C. parapsilosis-treated, high-dose 3, 6 hours

description: Library name: H6_CP513

value: C.parapsilosis MOI 5(pathogen):1(host)

value: 6 hours


title: QEIII-69

description: gene expression from FFPE sample


title: CTL_2

description:
Library name: Sample_6
gene_expression_473_DTR.xlsx; sample_CTL_2_fpkm


title: QEIII-142

description: gene expression from FFPE sample


title: RNA library from 12 weeks Natural single oocyte 1

description:
Library name: 35_1_1
35_1_1
summary_count_12weeks_single_oocytes.txt

value: Natural


title: CTL_1

description:
Library name: Sample_5
gene_expression_473_DTR.xlsx; sample_CTL_1_fpkm


title: HSC2_cells, C. parapsilosis-treated, high-dose 2, 6 hours

description: Library name: H6_CP512


title: HSC2_cells, C. parapsilosis-treated, high-dose 1, 6 hours

description: Library name: H6_CP511


title: RS-M MEN_24h_rep.2

city: Warszawa

first: Michal

last: Pawlak

address: Indiry Gandhi 14

department: Department of Experimental Hematology

country: Poland

institute: Institute of Hematology

description: Library name: IHITSAMID000032

data_processing:
RNA-seq reads were aligned to GRCh37 human genome version and gene counts were generated using STAR under nextflow nf-core RNA-seq analysis pipeline.
Assembly: GRCh37
Supplementary files format and content: IHIT_raw_counts_RNAseq.csv contains raw gene counts

source_name: RS-M MEN_24h_rep.2

growth_protocol: THP-1 cells were stimulated with 250nM Phorbol-12-myristate-13-acetate (PMA, Sigma-Aldrich) in RPMI medium for three days, followed by four day resting in PMA-free RPMI medium. To generate MdM, CD14+ monocytes were incubated with 10ng/ml CSF-1 (Biolegend) in TexMACS (Miltenyi Biotec) for 7 days. To generate in vitro cHL-TAMs (RS-M), differentiated THP1-Mϕ and MdM, expressing mature macrophage marker – 25F9, were cocultured with L428 or L1236 RS cells for five days under conditions prohibiting direct contacts, using 0.4µm polycarbonate cell culture inserts (NuncTM, Thermo Fisher Scientific, cat. 140640). For unstimulated, control (M0) macrophages, THP1-Mϕ and MdM were cultured in RPMI only in parallel to the RS cell/ Mϕ cocultures.

extract_protocol:
RNAs were isolated using GeneMATRIX Universal RNA purification kit (EURx). RNA integrity was assessed using TapeStation 4200 Instrument (Agilent) and minimal RINe value of RNA samples subjected to library preparation was ≥9.7
Libraries were generated using SENSE mRNA-Seq Library Prep Kit (Lexogen, cat. 001.96)

value: macrophage


title: PYIII-95

description: gene expression from FFPE sample


title: QEIII-193

description: gene expression from FFPE sample


title: PYIII-81

description: gene expression from FFPE sample


title: 4_473

description:
Library name: Sample_3
gene_expression_473_DTR.xlsx; sample_473_4_fpkm

value: PF4 Cre; Ai32


title: HSC2_cells, C. parapsilosis-treated, low-dose 2, 6 hours

description: Library name: H6_CP112

value: C.parapsilosis MOI 1(pathogen):1(host)


title: RS-M MEN_24h_rep.1

description: Library name: IHITSAMID000031

source_name: RS-M MEN_24h_rep.1


title: 3_473

description:
Library name: Sample_2
gene_expression_473_DTR.xlsx; sample_473_3_fpkm


title: PYIVB-53

description: gene expression from FFPE sample


title: RS-M DMSO_24h_rep.3

description: Library name: IHITSAMID000030

source_name: RS-M DMSO_24h_rep.3


title: HSC2_cells, C. parapsilosis-treated, low-dose 1, 6 hours

description: Library name: H6_CP111


title: RS-M DMSO_24h_rep.2

description: Library name: IHITSAMID000029

source_name: RS-M DMSO_24h_rep.2


title: HSC2_cells, C. albicans-treated 3, 6 hours

description: Library name: H6_CA113

value: C.albicans MOI 1(pathogen):1(host)


title: QEIII-192

description: gene expression from FFPE sample

source_name: locoregionally advanced NPC FFPE sample


title: mouse colon, Bifidobacteria infantis, rep 4

city: College Station

first: Destiny

middle: A

last: Mullens

state: Texas

address: 2253 TAMU

department: Nutrition

institute: Texas A&M University

description:
Library name: 49
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregaion were made using the Cell Ranger software v. 8.0.0.
To perform the mapping using the updated genome, we created an adaptation to the "Chromium Mouse Transcriptome Probe Set v1.0.1" (provided). Alternatively, samples can be mapped using 10X Genomics provided "refdata-gex-mm10-2020-A" reference with the "Chromium_Mouse_Transcriptome_Probe_Set_v1.0.1_mm10-2020-A.csv" probe list.
Assembly: GRCm39-2024-A
Assembly: Chromium_Mouse_Transcriptome_Probe_Update2024.csv
Supplementary files format and content: tab separated value files and matrix files

source_name: colon

extract_protocol:
Flash frozen mouse colon samples were minced on dry ice and fixed according to 10X Genomics Tissue Fixation and Dissociation for Chromium Fixed RNA Profiling protocol. All samples were fixed for 18h. Samples were subsequently dissociated into single cells for the Fixed RNA Profiling (Flex) assay according to the 10X Genomics Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples user guide.
Library prepartation and construction was performed according to the 10X Genomics Chromium Fixed RNA Profiling (Flex) Reagent Kits for Multiplexed Samples protocol.

treatment_protocol: C57BL/6 germ-free mice were orally-gavaged with human milk oligosaccharides and/or Bifidobacteria infantis for 14 days.

value: colon


title: RS-M DMSO_24h_rep.1

description: Library name: IHITSAMID000028

source_name: RS-M DMSO_24h_rep.1


title: HSC2_cells, C. albicans-treated 2, 6 hours

description: Library name: H6_CA112


title: QEIII-6

description: gene expression from FFPE sample


title: QEIII-172

description: gene expression from FFPE sample


title: MdM RS-M generated using L428_rep.3

description: Library name: IHITSAMID000027

source_name: MdM RS-M generated using L428_rep.3

value: healthy-donor-derived CD14+ monocytes


title: HSC2_cells, C. albicans-treated 1, 6 hours

description: Library name: H6_CA111


title: mouse colon, Bifidobacteria infantis, rep 2

description:
Library name: 43
10x Genomics


title: QEIVA-5

description: gene expression from FFPE sample


title: PYIII-73

description: gene expression from FFPE sample


title: mouse colon, Bifidobacteria infantis, rep 1

description:
Library name: 41
10x Genomics


title: MdM  RS-M generated using L428_rep.1

description: Library name: IHITSAMID000025

source_name: MdM  RS-M generated using L428_rep.1


title: HSC2_cells, non-treated 2, 6 hours

description: Library name: H6_C2


title: mouse colon, human milk oligosaccharides + Bifidobacteria infantis, rep 4

description:
Library name: 38
10x Genomics


title: QEIII-109

description: gene expression from FFPE sample

value: F


title: MdM RS-M generated using L1236_rep.3

description: Library name: IHITSAMID000024

source_name: MdM RS-M generated using L1236_rep.3


title: PYIVB-28

description: gene expression from FFPE sample


title: MdM  RS-M generated using L1236_rep.2

description: Library name: IHITSAMID000023

source_name: MdM  RS-M generated using L1236_rep.2


title: HSC2_cells, C. albicans-treated 3, 1 hour

description: Library name: H1_CA113

value: 1 hour


title: mouse colon, Bifidobacteria infantis, rep 3

description:
Library name: 44
10x Genomics


title: mouse colon, human milk oligosaccharides + Bifidobacteria infantis, rep 2

description:
Library name: 33
10x Genomics


title: HSC2_cells, non-treated 3, 6 hours

description: Library name: H6_C3


title: MdM RS-M generated using L428_rep.2

description: Library name: IHITSAMID000026

source_name: MdM RS-M generated using L428_rep.2


title: MdM  RS-M generated using L1236_rep.1

description: Library name: IHITSAMID000022

source_name: MdM  RS-M generated using L1236_rep.1


title: HSC2_cells, C. albicans-treated 2, 1 hour

description: Library name: H1_CA112


title: QEIII-99

description: gene expression from FFPE sample


title: mouse colon, human milk oligosaccharides + Bifidobacteria infantis, rep 1

description:
Library name: 31
10x Genomics


title: MdM M0 macrophages_rep.3

description: Library name: IHITSAMID000021

source_name: MdM M0 macrophages_rep.3


title: HSC2_cells, C. albicans-treated 1, 1 hour

description: Library name: H1_CA111


title: mouse colon, control, rep 4

description:
Library name: 21
10x Genomics


title: HSC2_cells, non-treated 1, 6 hours

description: Library name: H6_C1


title: PYIII-117

description: gene expression from FFPE sample


title: mouse colon, human milk oligosaccharides + Bifidobacteria infantis, rep 3

description:
Library name: 34
10x Genomics


title: MdM M0 macrophages_rep.2

description: Library name: IHITSAMID000020

source_name: MdM M0 macrophages_rep.2


title: HSC2_cells, non-treated 3, 1 hour

description: Library name: H1_C3


title: PYIVA-14

description: gene expression from FFPE sample


title: mouse colon, control, rep 3

description:
Library name: 17
10x Genomics


title: MdM M0 macrophages_rep.1

description: Library name: IHITSAMID000019

source_name: MdM M0 macrophages_rep.1


title: HSC2_cells, non-treated 2, 1 hour

description: Library name: H1_C2


title: mouse colon, control, rep 2

description:
Library name: 16
10x Genomics


title: THP-1 derived RS-M generated using L428_rep.3

description: Library name: IHITSAMID000012


title: PYIVA-19

description: gene expression from FFPE sample


title: HSC2_cells, non-treated 1, 1 hour

description: Library name: H1_C1


title: QEIII-141

description: gene expression from FFPE sample


title: mouse colon, control, rep 1

description:
Library name: 12
10x Genomics


title: THP-1 derived RS-M generated using L428_rep.2

description: Library name: IHITSAMID000009


title: PNU282987 treated hiPSC-derived primitive macphages

city: Kyoto

first: Keiichi

last: Ishihara

state: Kyoto

address: 5 Misasagi Nakauchi-cho, Yanashina-ku

country: Japan

institute: Kyoto Pharmaceutical University

description: Library name: PNU

data_processing:
Quality check: FastQC ver.0.11.7
Trimming: Trimmomatic ver. 0.38, Low quality bases and adaptor sequences were trimmed.
Mapping: HISAT2 ver.2.1.0
Caliculation of read count and TPM: Stringtie ver.2.1.3b
Statistic analysis: exactTest with edgeR
Assembly: GRCh38
Supplementary files format and content: read count, FPKM, TPM

growth_protocol: Human induced pluripotent stem cells were maintained in essential 8 medium in humodified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was extracted using Nucleospin RNA kit (Macherey-Nagel).
The sequencing library was prepared using TruSeq stranded mRNA library prep kit (Illumina).

treatment_protocol: Primitive macrophages were induced by addtion cytokines and inhibitors for 30 days (Takata et al., Immunity 2017, 47:183-198. doi: 10.1016/j.immuni.2017.06.017), then treated 100 µM PNU282987 for 12 hours.

value: Induced pluripotent stem cell derived cells

value: wild-type

value: Differentiation into primitive macrophages and treated amiroid β


title: QEIII-47

description: gene expression from FFPE sample


title: QEIII-179

description: gene expression from FFPE sample


title: mouse colon, human milk oligosaccharides, rep 3

description:
Library name: 8
10x Genomics


title: PYIII-120

description: gene expression from FFPE sample


title: THP-1 derived RS-M generated using L428_rep.1

description: Library name: IHITSAMID000006


title: hiPSC-derived primitive macphages

description: Library name: Control

value: Differentiation into primitive macrophages


title: mouse colon, human milk oligosaccharides, rep 2

description:
Library name: 7
10x Genomics


title: Control SKHEP1 cells

city: Nanjing

first: Ying

last: Cao

address: 12 Xuefu Rd., Pukou High-Tech Zone

institute: Nanjing University

description: Library name: SKHEP1_shCtrl

data_processing:
CASAVA base recognition
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data, then mapped to GRCh38 whole genome using Hisat2 software.
The featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: GRCh38
Supplementary files format and content: Excel files including fpkm values for each sample

source_name: Cell line

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS at 37°C in 5% CO2 for desired period of time when knockdown cells underwent significant phenotypic change.

extract_protocol:
Cells were collected with trypsinization and total RNA was extract with TRIzol using the protocol from the manufacturer.
Libraries were contructed with NEBNext® Ultra™ RNA Library Prep Kit for Illumina® using the protocol from the manufacturer.

value: Hepatocellular carcinoma cell line

value: Wild type

value: SKHEP1 cells transfected with lentivirus carrying the empty knockdown vetor (shCtrl)


title: PYIII-97

description: gene expression from FFPE sample

value: M


title: THP-1 derived RS-M generated using L1236_rep.3

description: Library name: IHITSAMID000013


title: mouse colon, human milk oligosaccharides, rep 1

description:
Library name: 4
10x Genomics


title: THP-1 derived RS-M generated using L1236_rep.2

description: Library name: IHITSAMID000010


title: QEIII-46

description: gene expression from FFPE sample


title: Differentiated SKHEP1 cells induced by SETDB1 knockdown

description: Library name: SKHEP1_shSETDB1

value: SETDB1 knockdown

value: SKHEP1 cells transfected with lentivirus for SETDB1 knockdown using shor-hairpin RNA against SETDB1 (shSETDB1)


title: THP-1 derived RS-M generated using L1236_rep.1

description: Library name: IHITSAMID000007

value: macrophage


title: eWAT_PHx_D7_3

city: Portland

first: Teresa

last: Zimmers

state: OR

address: 2730 S Moody Ave

department: CDCB

institute: OHSU

description:
Library name: Sample 12
RNAs cleaned up, DNaseI treated

data_processing:
Raw FASTQ files were uploaded to Partek (Illumina). Pre allignment QC was applied to test quality of reads. All samples passed QC with an average trim score of 39. Reads were then trimmed and aligned using the STAR function using mm39 as a reference index. We next proceeded with post-alignement QA/QC. Uniquely paired percentage was superior than 70% in all samples, and average quality score was superior than 39 in all samples..
Reads were then quantified using Partek E/M function. Counts were filtered by excluding feature with a maximun median counts ≤1.0. Filtered counts were then normalized based on median ratio (DESeq2 only).
Differential analysis was applied, using a multitest correction by FDR-Step up
Differentailly expression genes (Hamidi et, al_Adipose_PHx_2025.xls) were obtained by comparing PHx-day3 vs Sham, and Phx-day7 vs Sham. Data was then used for subsequent analysis by applying defined Fold change and FDR cutoff.
Assembly: mm39
Supplementary files format and content: DEGs file contains gene annotations and correspoding fold change, Log2FC, P-value and FDR for each gene. Two differential gene expression were analyzed, gene expression changes in PHx-Day3 vs Sham, and gene expression changes in PHx-Day7 vs Sham.

source_name: Day7 post 70% hepatectomy

growth_protocol: 12 to 14 weeks old male C57bl6 mice were used

extract_protocol:
Total RNAs were extracted from nitrogen frozen bulk eWAT using QIAzol lysis reagent (Qiagen, #79306). RNA cleanup and DNAse treatment were performed using the RNeasy cleanup kit (Qiagen, #74204) and DNaseI
Library construction performed at Novogene

treatment_protocol: Animals were subjected to sham surgery or 70% partial hepatectomy. On day3, and day7 post-surgery, animals were euthanized, then epididymal white adipose tissue were collected to extract total RNA for subsequent     RNA0sequencing experiment. 4 sham control animals, 5 and 3 partial hepatectomy animals were used for day3 and day7 respectively.

value: eWAT


title: Control SKHEP1 cells

description: Library name: SKHEP1_Ctrl

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS at 37°C in 5% CO2 for desired period of time when cells with forced expression of PPARG underwent significant phenotypic change.

value: SKHEP1 cells transfected with lentivirus carrying the empty expression vector


title: PYIII-63

description: gene expression from FFPE sample

data_processing: The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

extract_protocol: RNA was extracted from FFPE samples using the QIAGEN FFPE RNeasy kit (QIAGEN GmbH, Hilden, Germany).


title: eWAT_PHx_D7_2

description:
Library name: Sample 11
RNAs cleaned up, DNaseI treated


title: PYIII-69

description: gene expression from FFPE sample


title: THP-1 derived M0 macrophages_rep.3

description: Library name: IHITSAMID000011

source_name: THP-1 derived M0 macrophages_rep.3


title: Differentiated SKHEP1 cells induced by PPARG expression

description: Library name: SKHEP1_PPARG

value: Forced expression of PPARG

value: SKHEP1 cells transfected with lentivirus for PPARG expression


title: eWAT_PHx_D7_1

description:
Library name: Sample 10
RNAs cleaned up, DNaseI treated


title: QEIII-5

description: gene expression from FFPE sample


title: HSC2_cells_shortRNA, non-treated 3, 6 hours

description: Library name: H6_C3_miR

value: oral epithelial

value: 6 hours


title: Control SKHEP1 cells

description: Library name: SKHEP1_OECTRL

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS at 37°C in 5% CO2 for desired period of time when cells with forced expression of MYOD1 underwent significant phenotypic change.


title: THP-1 derived M0 macrophages_rep.2

description: Library name: IHITSAMID000008

source_name: THP-1 derived M0 macrophages_rep.2


title: PYIII-116

description: gene expression from FFPE sample


title: THP-1 derived M0 macrophages_rep.1

description: Library name: IHITSAMID000005

source_name: THP-1 derived M0 macrophages_rep.1


title: eWAT_PHx_D3_5

description:
Library name: Sample 9
RNAs cleaned up, DNaseI treated

source_name: Day3 post 70% hepatectomy


title: Differentiated SKHEP1 cells induced by MYOD1 expression

description: Library name: SKHEP1_OEMYOD

value: Forced expression of MYOD1

value: SKHEP1 cells transfected with lentivirus for MYOD1 expression


title: eWAT_PHx_D3_4

description:
Library name: Sample 8
RNAs cleaned up, DNaseI treated


title: Control HCT116 cells for MYOD1 or PPARG expression

description: Library name: HCT116_Ctrl

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS at 37°C in 5% CO2 for desired period of time when cells with forced expression of MYOD1 or PPARG underwent significant phenotypic change.

value: Colon cancer cell line

value: HCT116 cells transfected with lentivirus carrying the empty expression vector


title: QEIVA-16

description: gene expression from FFPE sample

source_name: locoregionally advanced NPC FFPE sample


title: U2OS ZAK-KO + ZAKɑ full-length rescue, replicate 1, 30 µM Harringtonine

city: Copenhagen

first: Zhenzhen

last: Wu

address: Blegdamsvej 3B, Maersk Building,

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description: Library name: ZAK_HAR_Rep1_batch3

data_processing:
Pulled libraries were demultiplexed based on barcoded adaptor sequences using SeqKit.
Raw reads were quality filtered and Illumina adaptor trimmed using TrimGalore.
PCR duplicates removed using SeqKit.
Barcode and UMI tags were trimmed using TrimGalore.
Reads aligned using STAR and crosllink sites identified using bedtools as described Buchbender et al.
Assembly: GRCh38/hg38
Supplementary files format and content: Bedgraph
Library strategy: iCLIP

source_name: bone

growth_protocol: DMEM, clucose concentration: 4.5g/L, with L-Glutamine, 10% fetal bovine serum, sodium pyruvate, 1x penicillin/streptomycin. U-2 OS cells were cultured at 37°C supplied with 5% CO2.

extract_protocol:
Cells were subjected to 254 nm (UVC) irradiation with a dose of 150 mJ/cm². Cell pellets were lysed and sonicated using Branson Digital Sonifier.
iCLIP2-seq libraries were prepared following the protocol described by Buchbender et al. (“Improved library preparation with the new iCLIP2 protocol,” Methods 178 (2020): 33–48), with adaptations inspired by Cordiner et al. (“Temporal-iCLIP captures co-transcriptional RNA-protein interactions,” Nat Commun 14(1):696, 2023). Cells were cultured in 15 cm dishes and harvested at ~80% confluence; two plates were used as starting material per condition. Final pooled libraries were size-selected for fragments ≥155 bp using AMPure XP beads (Beckman Coulter). Library quality was assessed with the Agilent High Sensitivity D1000 ScreenTape assay.

value: bone

value: U-2 OS

value: osteosarcoma cell

value: 30 µM Harringtonine, 1 hour