title: C57BL/6J Female liver 1 control

description: Library name: Sample 1


title: HEK293FT, DNA, Variant MPRA, Replicate 1

status: Public on Mar 18 2026

type: SRA

city: Huntsville

first: Jesse

middle: Nicholas

last: Cochran

state: AL

address: 601 Genome Way

country: USA

institute: HudsonAlpha Institute for Biotechnology

description:
Library name: HEK_Variant_MPRA1_DNA
Column title in counts file dna_count_1

library_source: genomic

data_processing:
Count files were generated using MPRAsnakeflow with a min oligo threshold of 10.
The barcode association dictionary was generated using MPRAflow for each size present in the design (219bp, 218bp, 216bp, 214bp, 212bp, 210bp, 208bp) using ---mapq 0 and a cigar score flag for the length of the oligo to require an exact match (ex: --cigar 219M) dictionaries were converted to tsvs, combined, and repeat barcodes were removed.
Assembly: hg38
Supplementary files format and content: Count files are tsvs of total barcode counts for RNA and DNA.
Supplementary files format and content: The barcode association dictionary is a tsv file of barcodes and oligo names.
Supplementary files format and content: The design file is the fasta file sent to Twist biosciences to generate the oligo pool.

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Qiagen Allprep RNA/DNA mini kit for MPRA output sequencing, Qiagen Plasmid Plus Mega kit for Barcode Association Sequencing
Libraries constructed according to LentiMPRA protocol Gordon et al. 2020

tag: cell line

tag: cell type

value: human embryonic kidney cells


title: C2-STING_3

city: Boston

first: Chong

last: Zuo

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

description: Library name: C2-STING_3

library_source: transcriptomic

data_processing:
Sample data was analyzed in R with Seurat 95. The 10x Cellranger pipeline (v7.0.0) was used to align reads to the Mm10 Mus musculus genome (from 10x Genomics). CITE-seq-Count was used to count hashtag reads. Hashtag reads were used to demultiplex samples with the Seurat ‘HTODemux’ function using the default settings. Only cells classified as a “singlet”, but not as a “doublet” or “negative” by hashtag demultiplexing were kept. Following hash demultiplexing, cells were further filtered out if they contained more than 20% mitochondrial (mt-) reads. ZsGreen- and ZsGreen+ tumor-draining lymph node samples were integrated together and clusters identified in a similar manner as human samples (see below). Three clusters of lower quality cells or doublets were removed after cluster identification. Genes from the Molecular Signatures Database (MSigDB) “Hallmark Interferon Gamma Response” and “Hallmark Interferon Alpha Response” (v7.2) were z-scaled and summed to visualize an IFN score.
The three CD4 T cell clusters from the main tumor-draining lymph node dataset were subset, and new variable features were discovered. The dataset was scaled, and top 15 PCs used for UMAP embedding and clusters identified. Following cluster identification, two clusters consisting of dendritic cells and B cells were removed, and the process of generating the UMAP and clustering was repeated. The “DCs” cluster from the main tdLN dataset were subset, new variable features identified, a new UMAP generated from the top 15 PCs, and clusters identified as above. This new sub-clustered object had 2 clusters comprised of either T cells or B cells; these clusters were subsequently removed as well as any cell with Cd79b expression. This filtered, subclustered dataset was reprocessed with the above steps. Differentially expressed genes between treatment groups were identified with the ‘FindMarkers’ function.
Assembly: mm10
Supplementary files format and content: matrix files

molecule: polyA RNA

organism: Mus musculus

source_name: tumor

extract_protocol:
Mice bearing ZsGreen-expressing 6694c2 tumors were treated as described above. 48 hours after treatment, tumors, spleens, and tumor-draining lymph nodes were harvested from mice. Spleens and lymph nodes were macerated. Tumors were macerated and digested in collagenase IV (Sigma #C5138) and soybean trypsin inhibitor (Life Technologies #17075029). Tumor chunks were removed via filtration with a 40 μM filter, and the resulting single cell suspension was washed with PBS. Part of the tumor, lymph node, and spleen sample was taken for flow cytometry analysis. The rest of the samples were hashed, sorted based on ZsGreen expression on a BD FACS Aria, and analyzed via single-cell sequencing analysis. 6694c2 and B16F10 tumor cells were treated with IFNγ (100 ng/mL) (Peprotech #315-05), IFNβ (1000 U/mL) (BioLegend #581302), and STING agonist (225 ug/mL) in culture for 24 hrs. Cells were harvested and RNA isolated with a QIAGEN RNAeasy Plus Mini Kit (#74134). RNA was sent to Genewiz for paired-end RNA sequencing.
Cells were then loaded onto a Chromium X with the Single Cell K Chip (PN-2000182), the Chromium Next GEM Single Cell 5ʹ GEM Kit v2 reagents, and beads (PN-1000244). Library preparation was performed with the Library Construction Kit (PN-1000190). Libraries were pooled and sequenced on an Illumina NovaSeq 6000 instrument with 2x150bp sequencing (Azenta Life Sciences).

tag: tissue

value: tumor

tag: genotype

tag: treatment

value: STING agonist (225 ug/mL)


title: HEK293FT, RNA, Variant MPRA, Replicate 1

description:
Library name: HEK_Variant_MPRA1_RNA
Column title in counts file rna_count_1

molecule: total RNA


title: C2-STING_1

description: Library name: C2-STING_1


title: pThr4 ChIP-seq, SCP1 D96A mutant treatment, biological replicate 1

city: Austin

first: Qian

last: Zhang

state: TX

address: 2515 Speedway

institute: The Unibersity of Texas at Austin

description:
Library name: pThr4_ChIP_SCP1_D96A_rep1
pThr4 ChIP-seq performed in HEK293 cells

data_processing:
After initial quality assessment with FastQC, paired-end pT4 ChIP-seq reads from SCP1 or mutant treated samples were trimmed using cutadapt v.4.6 (paramters: -m 20 -q 20), and then mapped onto human reference genome, hg38, using bowtie2 v.2.5.2.
Assembly: hg38
Supplementary files format and content: Processed data files include broadPeak files containing enriched regions identified from ChIP-seq data and bigWig files containing normalized genome-wide coverage/signal tracks. Raw data files are paired-end FASTQ files.

source_name: kidney

growth_protocol: Cells were routinely cultured in Dulbecco’s modified Eagle’s media, supplemented with 10% fetal bovine serum at 37 °C in humidified atmosphere with 5% CO2.

extract_protocol:
Cells were fixed by 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Biorupter UCD-200, and then anti-pThr4 antibody (6D7) was used for immunoprecipitation (IP).
ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Kit for Illumina and sequenced as paired-end 150-bp reads on a Illumina NovaSeq 6000

value: kidney

value: epithelial cell


title: C2-STING_2

description: Library name: C2-STING_2


title: Neurons, DNA, Variant MPRA, Replicate 2

description:
Library name: Neuron_Variant_MPRA2_DNA
Column title in counts file dna_count_2

value: Neurons


title: Neurons, RNA, Variant MPRA, Replicate 4

description:
Library name: Neuron_Variant_MPRA4_RNA
Column title in counts file rna_count_4


title: Neurons, DNA, Variant MPRA, Replicate 3

description:
Library name: Neuron_Variant_MPRA3_DNA
Column title in counts file dna_count_3


title: Neurons, RNA, Variant MPRA, Replicate 2

description:
Library name: Neuron_Variant_MPRA2_RNA
Column title in counts file rna_count_2


title: Neurons, DNA, Variant MPRA, Replicate 4

description:
Library name: Neuron_Variant_MPRA4_DNA
Column title in counts file dna_count_4


title: pThr4 ChIP-seq, SCP1 WT treatment, biological replicate 2

description:
Library name: pThr4_ChIP_SCP1_WT_rep2
pThr4 ChIP-seq performed in HEK293 cells


title: pThr4 ChIP-seq, SCP1 WT treatment, biological replicate 3

description:
Library name: pThr4_ChIP_SCP1_WT_rep3
pThr4 ChIP-seq performed in HEK293 cells


title: C2-IFNb_3

description: Library name: C2-IFNb_3

value: IFNβ (1000 U/mL)


title: Neurons, RNA, Variant MPRA, Replicate 1

description:
Library name: Neuron_Variant_MPRA1_RNA
Column title in counts file rna_count_1


title: Neurons, DNA, Variant MPRA, Replicate 1

description:
Library name: Neuron_Variant_MPRA1_DNA
Column title in counts file dna_count_1


title: pThr4 ChIP-seq, SCP1 WT treatment, biological replicate 1

description:
Library name: pThr4_ChIP_SCP1_WT_rep1
pThr4 ChIP-seq performed in HEK293 cells


title: C2-IFNb_2

description: Library name: C2-IFNb_2


title: Neurons, RNA, Variant MPRA, Replicate 3

description:
Library name: Neuron_Variant_MPRA3_RNA
Column title in counts file rna_count_3


title: MAHS:AcGFP human adipose-derived stem cells replicate 2

city: Riverside

first: Joshua

last: Morgan

state: CA

address: 900 University Ave

department: Bioengineering

institute: University of California, Riverside

description: Library name: JLRM2

data_processing:
Raw image data were converted to sequence reads by base calling and stored in FASTQ format.
Raw reads were filtered by removing reads with adapter contamination, reads containing more than 10% uncertain nucleotides (N), and reads in which low-quality bases (base quality <5) constituted more than 50% of the read.
Clean reads were aligned to the human reference genome using HISAT2 v2.0.5 with default parameters.
Gene-level read counts were generated using featureCounts v1.5.0-p3 with default parameters and are provided in the file gene_count.txt.
Gene expression levels were normalized as FPKM values and are provided in the file gene_fpkm.txt.
Assembly: hg38
Supplementary files format and content: gene_count.txt: tab-delimited table of gene-level raw read counts for all samples. Rows correspond to genes and columns correspond to individual samples.
Supplementary files format and content: gene_fpkm.txt: tab-delimited table of gene-level normalized expression values (FPKM) for all samples. Rows correspond to genes and columns correspond to individual samples.

extract_protocol:
Total RNA was extracted using GeneJET™ RNA Purification Kit  according to the manufacturer’s instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, first-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis. Libraries were prepared by end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Library quality was assessed using Qubit, real-time PCR, and bioanalyzer, and libraries were sequenced on an Illumina platform.

value: MAHS


title: C2-IFNb_1

description: Library name: C2-IFNb_1


title: MAHS:AcGFP human adipose-derived stem cells replicate 3

description: Library name: JLRM3


title: MAHS:AcGFP human adipose-derived stem cells replicate 1

description: Library name: JLRM1


title: Day 40 human iPSC derived organoids, ,CUT&RUN, H3K4me3

city: Geneva

first: Awais

last: Javed

address: Chemin des mines, 9

department: Fundamental Neurosciences

country: Switzerland

institute: University of Geneva

description:
Library name: Org_H3K4me3_CR
CUT&RUN

library_source: other

data_processing:
Data preprocessing and quality controls. Fastq files were mapped on the standard 10X mouse reference genome GRCm38 using cellranger (v7.2.0) for the E16 collected snRNA-seq dataset. For the E16 collected scRNA-seq, fastq files were mapped with the mouse reference genome including hEGR1 and hIRF1 sequences. For the P0 collected scRNA-seq, fastq files were mapped with the mouse reference genome including PBase, TurboRFP-NLS and JUNB sequences for quality control purposes. Counts due to ambient RNA and random barcode swapping were removed from the raw matrix using remove-background function of cellbender (v0.3.0) with epochs = 150, expected-cells=2000 for the E16 snRNA-seq dataset and epochs = 50, expected-cells=6000 for the E16 collected scRNA-seq. The newly generated sn/scRNA-seq cellbender count matrix was used for subsequent analysis. Single-cell RNA-seq P0 collected dataset was not processed through cellbender. Briefly, for the JUNB overexpression E16 collected dataset, cells with nCount_RNA < 25’000, nFeature_RNA > 1’500 and percent.mt < 0.25 were included. For the IRF1/EGR1 overexpression E16 collected dataset, cells with nCount_RNA > 500, nCount_RNA < 20’000, nFeature_RNA > 1’000 and percent.mt < 5 were included. For the P0 collected dataset, nCount_RNA < 30’000, nFeature_RNA > 1’000 and percent.mt < 10 were included. scDblFinder package (v1.16.0) was used to remove doublets by simulating ncol(sce)/1000*0.008 doublet ratio. A small number of microglia and vasculature cells were removed from the analysis.
CUT&RUN. Fastqs files were processed as outlined by 4DN CUT&RUN processing pipeline. Briefly, Fastqs files were trimmed using trimmomatic (v0.39) (ILLUMINACLIP:2:30:10; LEADING:3; TRAILING:3; SLIDINGWINDOW:4:15; MINLEN:25). Trimmed reads were then aligned with human (GRCh38-noalt) and yeast (R64-1-1) spike-in reference genomes using bowtie2 (v2.5.4) using the –dovetail option. Sambamba (v1.0.1) was used to generate indices, SAM to BAM conversion and sorting. CUT&Tag. Fastqs files were aligned with either human (GRCh38-noalt), mouse (mm10) or E.coli genome using bowtie2 (v2.5.4). Spike-in depth was quantified to normalize in later steps. Duplicates were removed using Picard (v3.4.0). Reads mapped to ENCODE blacklist regions were excluded using bedtools (v2.31.1). Samtools (v1.22.1) was used to generate indices, SAM to BAM conversion and sorting. Once the CUT&RUN/CUT&Tag bam files were preprocessed, Deeptools (v3.5.6) bamCoverage function was used to generate spike-in normalized bigwig files for visualization. SEACR (v1.3) was used to call peaks with 0.01 threshold of pvalue. The .bed peaks were then uploaded to GREAT to generate peak to gene associations. IGV genome browser (v2.18.2) was used to visualize bigwig and generate coverage plots.
Assembly: refdata-gex-mm10-2020-A (cellranger reference); refdata-gex-mm10-2020-A with RFP-NLS reporter and hJUNB (custom reference); refdata-gex-mm10-2020-A with hIRF1 and hEGR1 (custom reference) used for cellranger (sn/scRNA-seq analysis) human (GRCh38-noalt), yeast (R64-1-1), mouse (mm10) or E.coli genome used for bowtie2 (CUT&Tag/RUN analysis)
Supplementary files format and content: .h5 raw matrix files for the sn/scRNAseq, processed .rds for TrackerSeq datasets, .bed SEACR and .bigwig files for the CUT&Tag/RUN datasets
Library strategy: CUT&Run

molecule: other

source_name: Human iPSC-derived organoids

growth_protocol: Cerebral organoids were generated from induced pluripotent stem cells (iPSCs) PC1505 line at ~80% confluency according to STEMdiff Cerebral organoid kit from STEMCELL Technologies (a standardized implementation of unguided cerebral organoid differentiation). Cells were dissociated with Accutase and resuspended in Organoid formation medium with 50 μM ROCK inhibitor. Live cells (5,000 per well) were seeded into low-attachment 96-well plates, forming embryoid bodies (EBs) after 24 hours. EBs were cultured for 5 days and subsequently transferred to Neural Induction Medium and cultured for 2 days. Neuroepithelial tissues formed, showing radially organized pseudo-stratified epithelium. On day 7, aggregates were embedded in Matrigel in Expansion Medium and cultured further. By day 10, organoids were placed in Maturation Medium, with medium changes every 3-4 days, supporting cerebral tissue development.

extract_protocol:
E16.5 dataset. Twenty-four hours following electroporation, pregnant female was anaesthetized and sacrificed. Embryos from the pregnant mouse were harvested. Embryos were first separated based on electroporated plasmids, decapitated and the cortex was dissected out in 1X HBSS. JUNB: The GFP+ cortices were separated, and the electroporated region was dissected and frozen straight away in 2 ml Eppendorf tubes. Four cortices were collected per condition. On the day of the snRNA-seq, samples were first gently thawed on ice and resuspended in 100 ul of lysis buffer composed of: 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.01% NP-40, 1% BSA and 1 mM DTT. After 5 minutes of lysis on ice, 1 mL of HBSS was added. The samples were then centrifuged at 500 g for 5 minutes. After removing supernatant, the pellet was resuspended in 1 mL washing buffer composed of: 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 1% BSA, 1 mM DTT and 0.5 U/μl RNAase inhibitor. Then, using the P1000 pipette, the samples were pipetted up and down 10 times. The samples were then centrifuged again for 5 minutes at 500 g. Supernatant was removed, 1 mL of additional washing buffer was added, and the pellet was resuspended. At this point, no clumps were seen, and the samples were passed through a 30-μm filter before FANS. Hoechst was used as a positive nuclei marker and 25’000 events representing Hoechst+GFP+ nuclei were sorted directly into empty 1.5 mL Eppendorf-tubes using Beckman Coulter MoFlo Astrios. Exactly 42.8 μL of the sorted nuclei were loaded on the first step of the 10x Next GEM v3.1 reagent kit on the Chromium controller. IRF1/EGR1: The TagBFP2-NLS+ cortices were separated, and the electroporated region was dissected and processed for cell dissociation using the Miltenyi Neural dissociation kit as described previously 87. Single cell suspensions were then passed through a 70-μm filter before FACS. Only 20,000 BFP+ cells were sorted into separate tubes for either Control, IRF1, EGR1, or IRF1+EGR1. The FAC-sorted cells were centrifuged for 5 min at 300 g and all but 42.8 μL was removed from the tube before resuspending once more and loading on the Chip G for 10x capture with Next GEM v3.1 reagent kit on the 10x Chromium X controller. P0 dataset. Four days after electroporations and after birth of pups, four litter-mates per condition were sacrificed by decapitation and the cortex was dissected out of the head in cold 1x HBSS in less than 5 mins. The electroporated region was microdissected in a fresh petri dish containing 1x HBSS and transferred into an eppendorf tube. Dissociations were performed using the Neural Dissociation kit (130-092-628; Miltenyi) by treating the microdissected tissue with Enzyme mix 1 for 7mins and then Enzyme mix 2 for 3mins. Cells were washed in sorting buffer (1x PBS, 1% BSA and 0.5 U/μl SUPERase-In RNase inhibitor (AM2694; ThermoFisher Scientific)) twice at 4 C with 300 g. 16,000 for Control and 50,000 JUNB electroporated RFP+ cells were sorted into separate tubes containing sorting buffer. Sorted cell suspension was centrifuged again for 5 min at 4 C with 300 g and all but around 43.2 μL was removed. The cell suspension was resuspended gently and processed with 10X Genomics Chromium Single Cell 3’ v3 reagent kit on the Chromium X controller.
Gene expression libraries were constructed according to the manufacturer’s guidelines (10x Genomics NextGEM v3.1 reagent kit). TrackerSeq libraries were constructed as previously described (Bandler et al. 2022).

value: Human iPSC-derived organoids

value: iPSC line:PC1505

value: Mixed brain cell types

value: WT

value: No treatment

tag: batch


title: C2-IFNy_3

description: Library name: C2-IFNy_3

value: IFNγ (100 ng/mL)


title: C2-IFNy_2

description: Library name: C2-IFNy_2


title: Day 40 human iPSC derived organoids, ,CUT&RUN, Irf1

description:
Library name: Org_Irf1_CR
CUT&RUN


title: Control (AcGFP) human adipose-derived stem cells replicate 3

description: Library name: JLRA3

value: AcGFP


title: C2-IFNy_1

description: Library name: C2-IFNy_1


title: Control (AcGFP) human adipose-derived stem cells replicate 2

description: Library name: JLRA2


title: Day 40 human iPSC derived organoids, ,CUT&RUN, Rabbit IgG

description:
Library name: Org_RabbitIgG_CR
CUT&RUN


title: C2-vehicle_3

description: Library name: C2-vehicle_3


title: N33 cells, treated with MK+WP, 48h, rep1

city: Beijing

first: Xiaolong

last: Fan

address: No.19, Xinjiekouwai St, Haidian District

country: China

institute: BeiJing Normal University

description: Library name: N33_MKWP_1

data_processing:
Raw reads were filtered by fastp (v0.23.2) and mapped to the human reference genome (hg38, UCSC) by HISAT2 (2.2.1). The mapped reads numbers of each gene were counted by featureCounts (2.0.6). The FPKM of each gene was calculated by gene length and reads count.
Assembly: GRCh38
Supplementary files format and content: Matrix of FPKM values for each gene in each sample

source_name: brain

growth_protocol: Cells were cultured in DMEM F12 (Gibco, # 11330032) supplemented with 10% fetal bovine serum (Gemini, # 900-108) and 1% penicillin streptomycin (Gibco, # 15140122) at 37 °C in a 5% CO2.

extract_protocol:
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads
After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The  library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: Cells were treated with two-drug (combination of MK and WP) or three-drug (combination of MK, WP, and RA) for 48h.

value: brain

value: IDH-wildtype GBM cell

value: treated with MK+WP


title: N33 cells, treated with MK+WP, 48h, rep3

description: Library name: N33_MKWP_3


title: Control (AcGFP) human adipose-derived stem cells replicate 1

description: Library name: JLRA1


title: Day 40 human iPSC derived organoids, ,CUT&Tag, Junb

description:
Library name: Org_Junb_CT
CUT&Tag

data_processing:
Data preprocessing and quality controls. Fastq files were mapped on the standard 10X mouse reference genome GRCm38 using cellranger (v7.2.0) for the E16 collected snRNA-seq dataset. For the E16 collected scRNA-seq, fastq files were mapped with the mouse reference genome including hEGR1 and hIRF1 sequences. For the P0 collected scRNA-seq, fastq files were mapped with the mouse reference genome including PBase, TurboRFP-NLS and JUNB sequences for quality control purposes. Counts due to ambient RNA and random barcode swapping were removed from the raw matrix using remove-background function of cellbender (v0.3.0) with epochs = 150, expected-cells=2000 for the E16 snRNA-seq dataset and epochs = 50, expected-cells=6000 for the E16 collected scRNA-seq. The newly generated sn/scRNA-seq cellbender count matrix was used for subsequent analysis. Single-cell RNA-seq P0 collected dataset was not processed through cellbender. Briefly, for the JUNB overexpression E16 collected dataset, cells with nCount_RNA < 25’000, nFeature_RNA > 1’500 and percent.mt < 0.25 were included. For the IRF1/EGR1 overexpression E16 collected dataset, cells with nCount_RNA > 500, nCount_RNA < 20’000, nFeature_RNA > 1’000 and percent.mt < 5 were included. For the P0 collected dataset, nCount_RNA < 30’000, nFeature_RNA > 1’000 and percent.mt < 10 were included. scDblFinder package (v1.16.0) was used to remove doublets by simulating ncol(sce)/1000*0.008 doublet ratio. A small number of microglia and vasculature cells were removed from the analysis.
CUT&RUN. Fastqs files were processed as outlined by 4DN CUT&RUN processing pipeline. Briefly, Fastqs files were trimmed using trimmomatic (v0.39) (ILLUMINACLIP:2:30:10; LEADING:3; TRAILING:3; SLIDINGWINDOW:4:15; MINLEN:25). Trimmed reads were then aligned with human (GRCh38-noalt) and yeast (R64-1-1) spike-in reference genomes using bowtie2 (v2.5.4) using the –dovetail option. Sambamba (v1.0.1) was used to generate indices, SAM to BAM conversion and sorting. CUT&Tag. Fastqs files were aligned with either human (GRCh38-noalt), mouse (mm10) or E.coli genome using bowtie2 (v2.5.4). Spike-in depth was quantified to normalize in later steps. Duplicates were removed using Picard (v3.4.0). Reads mapped to ENCODE blacklist regions were excluded using bedtools (v2.31.1). Samtools (v1.22.1) was used to generate indices, SAM to BAM conversion and sorting. Once the CUT&RUN/CUT&Tag bam files were preprocessed, Deeptools (v3.5.6) bamCoverage function was used to generate spike-in normalized bigwig files for visualization. SEACR (v1.3) was used to call peaks with 0.01 threshold of pvalue. The .bed peaks were then uploaded to GREAT to generate peak to gene associations. IGV genome browser (v2.18.2) was used to visualize bigwig and generate coverage plots.
Assembly: refdata-gex-mm10-2020-A (cellranger reference); refdata-gex-mm10-2020-A with RFP-NLS reporter and hJUNB (custom reference); refdata-gex-mm10-2020-A with hIRF1 and hEGR1 (custom reference) used for cellranger (sn/scRNA-seq analysis) human (GRCh38-noalt), yeast (R64-1-1), mouse (mm10) or E.coli genome used for bowtie2 (CUT&Tag/RUN analysis)
Supplementary files format and content: .h5 raw matrix files for the sn/scRNAseq, processed .rds for TrackerSeq datasets, .bed SEACR and .bigwig files for the CUT&Tag/RUN datasets
Library strategy: CUT&Tag


title: C2-vehicle_2

description: Library name: C2-vehicle_2

value: tumor


title: N33 cells, treated with MK+WP+RA, 48h, rep3

description: Library name: N33_MKWPRA_3

value: treated with MK+WP+RA


title: 4B_Donors 289, 292, 310, and 313 with DPI only

city: Brest

first: Marie

last: Frutoso

address: 9 rue Félix le Dantec

country: France

institute: LBAI, UMR1227

description: Library name: Cartridge_4_B

library_source: transcriptomic single cell

data_processing:
Fastq files were processed via the standard Rhapsody analysis pipeline (BD Biosciences) on Seven Bridges (www.sevenbridges.com). In brief, after read filtering, reads are aligned to a reference genome and annotated, barcodes and UMIs are counted, followed by determining putative cells. The final output (molecule per cell count matrix) was analysed in R using Seurat.
Assembly: GRCh38
Supplementary files format and content: A Seurat Object in RDS format combining all donors, tissues and cell types (data.integrated)
Supplementary files format and content: A Seurat Object in RDS format containing only NK cells, without chorioamnionitis donors and without cordblood (data.NK.pure)

source_name: mfPLAC (renamed DPI in the paper)

extract_protocol:
After thawing, cells from maternal blood, cordblood, DPI and decidua were stained with a cytometry panel and one specific Sample-Tag for multiplexing (BD Biosciences SMK).  Live, CD45+ immune cells were sorted (using the BD Symphony S6 cell sorter equipped with a 70um nozzle for batches 1 and 2 and the FACSAria III equiped with a 100um nozzle). For batches 1 and 2, Live CD45+ cells were enriched for ILC (CD45+CD19-CD14-CD3-CD127+CD34-), NK cells (CD45+CD19-CD14-CD3-CD127-NKp46+) and myeloid cells (CD45+CD3-CD19-NKp46-HLA-DR+). For batch 3 CD45+ were sorted without enrichment of specific cell type. After sorting, cells from all donors and tissues were pooled and stained with 56 oligo-proteins. Stained cells were then loaded on the BD Rhapsody cartridges (between 35 - 45,000 cells were loaded per cartridges).
Libraries were performed according to manufacturer's instructions (BD RhapsodyTM System, mRNA WTA, Abseq and Sample Tag library Preparation protocol). In brief, after sorting, single cells were stained with AbSeq antibodies, washed three times, pooled and counted and subsequently loaded onto a nano-well cartridge (BD Rhapsody), lysed inside the wells followed by mRNA capture on cell capture beads according to manufacturer instructions. Cell Capture Beads were retrieved and washed prior to performing reverse transcription and treatment with Exonuclease I. cDNA underwent random priming extension and amplification using the human primer xtension mix and via PCR (10–11 cycles). PCR products were purified, and mRNA PCR products were separated from Sample-Tag and AbSeq. PCR products with double-sided size selection using SPRIselect magnetic beads (Beckman Coulter). mRNA and Sample Tag products were further amplified using PCR (10 cycles). PCR products were then purified using SPRIselect magnetic beads.Quality of PCR products was determined by using an Agilent 2200TapeStation with High Sensitivity D5000 ScreenTape (Agilent) in the Fred Hutch Genomics Shared Resource laboratory. The quantity of PCR products was determined by Qubit with Qubit dsDNA HS Assay (Q32851). Whole transcriptome mRNA product was diluted at less than 2 nM (8 pcr cycles), and the Sample Tag and AbSeq PCR products were diluted to 0.25 ng μl−1 to prepare final libraries. Final libraries were indexed using PCR (8 cycles for WTA and 7 cycles for SampleTag and AbSeq libraries). Index PCR products were purified using SPRIselect magnetic beads. Quality of all final libraries was assessed by using Agilent 2200 TapeStation with High Sensitivity D5000 ScreenTape and quantified using a Qubit Fluorometer using the Qubit dsDNA HS Kit (ThermoFisher). Final libraries were diluted to 3 nM and multiplexed for paired-end (100 bp) sequencing on a NovaSeq 6000 (Illumina) using S1 and S2 flow cells. For the gene expression library, we targeted 35,000 reads per cell, for the AbSeq library 22,000 reads per cell, and for the Sample-Tag libraries 2,000 reads per cell.

value: mfPLAC (renamed DPI in the paper)

tag: donor

value: PRI289 PRI313 PRI292 PRI310

tag: group

value: Healthy (PRI289 PRI313) and Chorioamniontis (PRI292 PRI310)

tag: annotation

value: PRI289_mfPLAC; PRI313_mfPLAC; PRI292_mfPLAC; PRI310_mfPLAC

tag: sample tag

value: PRI289_mfPLAC (SMK9); PRI313_mfPLAC (SMK10); PRI292_mfPLAC (SMK11); PRI310_mfPLAC (SMK12)


title: N33 cells, CONT, 48h, rep3

description: Library name: N33_CONT_3

value: cont


title: N33 cells, treated with MK+WP+RA, 48h, rep1

description: Library name: N33_MKWPRA_1


title: N33 cells, CONT, 48h, rep2

description: Library name: N33_CONT_2


title: N33 cells, treated with MK+WP, 48h, rep2

description: Library name: N33_MKWP_2


title: N9 cells, treated with MK+WP+RA, 48h, rep3

description: Library name: N9_MKWPRA_3


title: 3B_Donors 289, 292, 310, and 313 with DPI only

description: Library name: Cartridge_3_B


title: B16-STING_3

description: Library name: B16-STING_3

value: STING agonist (225 ug/mL)


title: 2B_Donors 289, 292, 310, and 313 with DPI only

description: Library name: Cartridge_2_B


title: 1B_Donors 289, 292, 310, and 313 with DPI only

description: Library name: Cartridge_1_B


title: Day 40 human iPSC derived organoids, ,CUT&Tag, Rabbit IgG

description:
Library name: Org_RabbitIgG_CT
CUT&Tag

value: Human iPSC-derived organoids

value: iPSC line:PC1505

value: Mixed brain cell types


title: N9 cells, treated with MK+WP+RA, 48h, rep1

description: Library name: N9_MKWPRA_1


title: N33 cells, CONT, 48h, rep1

description: Library name: N33_CONT_1


title: N9 cells, treated with MK+WP+RA, 48h, rep2

description: Library name: N9_MKWPRA_2


title: N9 cells, treated with MK+WP, 48h, rep3

description: Library name: N9_MKWP_3


title: N33 cells, treated with MK+WP+RA, 48h, rep2

description: Library name: N33_MKWPRA_2


title: B16-STING_2

description: Library name: B16-STING_2


title: N9 cells, treated with MK+WP, 48h, rep2

description: Library name: N9_MKWP_2


title: C2-vehicle_1

description: Library name: C2-vehicle_1


title: B16-STING_1

description: Library name: B16-STING_1


title: 4A_Donors 289, 292, 310, and 313 with DPI only

description: Library name: Cartridge_4_A


title: B16-IFNb_3

description: Library name: B16-IFNb_3

value: IFNβ (1000 U/mL)


title: B16-IFNb_2

description: Library name: B16-IFNb_2


title: 1A_Donors 289, 292, 310, and 313 with DPI only

description: Library name: Cartridge_1_A


title: N9 cells, treated with MK+WP, 48h, rep1

description: Library name: N9_MKWP_1


title: N9 cells, CONT, 48h, rep1

description: Library name: N9_CONT_1


title: N9 cells, CONT, 48h, rep3

description: Library name: N9_CONT_3


title: B16-IFNy_3

description: Library name: B16-IFNy_3

value: IFNγ (100 ng/mL)


title: FA2ic, FRDA, iPSC-derived lower motor neuron, rep2

city: Wollongong

first: Marnie

last: Maddock

state: NSW

address: Northfields Ave

department: Molecular Horizons, School of Medical and Indigenous Health Sciences

country: Australia

institute: University of Wollongong

description:
Library name: FA2ic_LowerMotorNeuron_REP2
column name in all processed data files: FA2ic_LMN_REP2

data_processing:
Raw FASTQ files were processed using the nf-core RNA-seq pipeline (version 3.18.0)
Initial read quality of FASTQ files was assessed using FastQC (v0.12.1)
Adapter and quality trimming was performed using TrimGalore! (v0.6.10; cutadapt v4.9) with default parameters which automatically detect and remove adapter sequences, trim low-quality bases (Phred < 20) and remove short reads (< 20 bp).
Trimmed reads were aligned to the human reference genome (GRCh38, Ensembl release 113) using STAR (v2.8.11b).
Gene and transcript level quantification was performed using Salmon (v1.10.3) to generate raw count matrices and transcripts per million (TPM) normalised expression values.
Alignment and further quality control metrics were summarised and checked with MultiQC.
Assembly: GRCh38.113
Supplementary files format and content: Maddock_gene_counts.csv and Maddock_transcript_counts.csv are comma separated value files with the raw gene/transcript counts derived from STAR/Salmon. All samples are given in these files.
Supplementary files format and content: Maddock_gene_tpm.csv and Maddock_transcript_tpm.csv are comma separated value files with the gene/transcript transcripts per million (TPM) derived from STAR/Salmon. All samples are given in these files.

extract_protocol:
To extract total cellular RNA for RNA sequencing, the PureLink RNA Mini Kit (ThermoFisher Scientific) was implemented according to the manufacturer’s instructions
rRNA depleted libraries were prepared using the Illumina Stranded Total RNA Ribo-Zero Plus kit and sequenced on the Illumina NovaSeq X Plus platform to generate 100 bp paired-end reads

value: iPSC-derived lower motor neurons

value: Control isogenic corrected

tag: replicate

tag: days of_differentiation


title: 2_Donors 302 and 316 with DPI Decidua mBlood CordBlood

description: Library name: Cart_2

source_name: mfPLAC (renamed DPI in the paper), decidua, maternal blood and cordblood

value: PRI316 and PRI302

value: Healthy (PRI316) and Chorioamniontis (PRI302)

value: PRI316_mfPLAC; PRI316_Decidua; PRI316_mBlood; PRI316_CordBlood; PRI302_mfPLAC; PRI302_Decidua; PRI302_mBlood; PRI302_CordBlood

value: PRI316_mfPLAC (SMK6); PRI316_Decidua (SMK8); PRI316_mBlood (SMK5); PRI316_CordBlood (SMK7); PRI302_mfPLAC (SMK10); PRI302_Decidua (SMK12); PRI302_mBlood (SMK9); PRI302_CordBlood (SMK11)


title: FA2, FRDA, iPSC-derived lower motor neuron, rep4

description:
Library name: FA2_LowerMotorNeuron_REP4
column name in all processed data files: FA2_LMN_REP4

value: Diseased Friedreich's ataxia


title: FA2ic, FRDA, iPSC-derived lower motor neuron, rep4

description:
Library name: FA2ic_LowerMotorNeuron_REP4
column name in all processed data files: FA2ic_LMN_REP4


title: 2A_Donors 289, 292, 310, and 313 with DPI only

description: Library name: Cartridge_2_A

value: mfPLAC (renamed DPI in the paper)

value: PRI289 PRI313 PRI292 PRI310

value: Healthy (PRI289 PRI313) and Chorioamniontis (PRI292 PRI310)


title: 3A_Donors 289, 292, 310, and 313 with DPI only

description: Library name: Cartridge_3_A

value: PRI289_mfPLAC; PRI313_mfPLAC; PRI292_mfPLAC; PRI310_mfPLAC

value: PRI289_mfPLAC (SMK9); PRI313_mfPLAC (SMK10); PRI292_mfPLAC (SMK11); PRI310_mfPLAC (SMK12)


title: B16-IFNb_1

description: Library name: B16-IFNb_1

value: tumor


title: N9 cells, CONT, 48h, rep2

description: Library name: N9_CONT_2

value: brain

value: IDH-wildtype GBM cell

value: cont


title: FA2, FRDA, iPSC-derived lower motor neuron, rep3

description:
Library name: FA2_LowerMotorNeuron_REP3
column name in all processed data files: FA2_LMN_REP3


title: FA2, FRDA, iPSC-derived lower motor neuron, rep2

description:
Library name: FA2_LowerMotorNeuron_REP2
column name in all processed data files: FA2_LMN_REP2


title: FA2ic, FRDA, iPSC-derived lower motor neuron, rep3

description:
Library name: FA2ic_LowerMotorNeuron_REP3
column name in all processed data files: FA2ic_LMN_REP3


title: FA2, FRDA, iPSC-derived lower motor neuron, rep1

description:
Library name: FA2_LowerMotorNeuron_REP1
column name in all processed data files: FA2_LMN_REP1


title: FA2ic, FRDA, iPSC-derived lower motor neuron, rep1

description:
Library name: FA2ic_LowerMotorNeuron_REP1
column name in all processed data files: FA2ic_LMN_REP1


title: B16-vehicle_2

description: Library name: B16-vehicle_2


title: FA2ic, isogenic corrected, iPSC-derived neural crest cell, rep1

description:
Library name: FA2ic_NeuralCrest_REP1
column name in all processed data files: FA2ic_NCC_REP1

value: iPSC-derived neural crest cells


title: FA2ic, isogenic corrected, iPSC-derived neural crest cell, rep4

description:
Library name: FA2ic_NeuralCrest_REP4
column name in all processed data files: FA2ic_NCC_REP4


title: B16-IFNy_1

description: Library name: B16-IFNy_1

value: IFNγ (100 ng/mL)


title: 3_Donors 302 and 316 with DPI Decidua mBlood CordBlood

description: Library name: Cart_3

value: mfPLAC (renamed DPI in the paper), decidua, maternal blood and cordblood


title: B16-IFNy_2

description: Library name: B16-IFNy_2


title: 2_Donors 306 and 307 with DPI Decidua mBlood CordBlood

description: Library name: Placenta_1_Cart2

value: PRI307 and PRI306

value: Healthy (PRI307) and Chorioamniontis (PRI306)

value: PRI307_mfPLAC; PRI307_Decidua; PRI307_mBlood; PRI307_CordBlood; PRI306_mfPLAC; PRI306_Decidua; PRI306_mBlood; PRI306_CordBlood

value: PRI307_mfPLAC (SMK2); PRI307_Decidua (SMK4); PRI307_mBlood (SMK1); PRI307_CordBlood (SMK3); PRI306_mfPLAC (SMK6); PRI306_Decidua (SMK8); PRI306_mBlood (SMK5); PRI306_CordBlood (SMK7)


title: FA2, FRDA, iPSC-derived neural crest cell, rep2

description:
Library name: FA2_NeuralCrest_REP2
column name in all processed data files: FA2_NCC_REP2

value: Diseased Friedreich's ataxia


title: B16-vehicle_3

description: Library name: B16-vehicle_3


title: FA1ic, isogenic corrected, iPSC-derived neural crest cell, rep4

description:
Library name: FA1ic_NeuralCrest_REP4
column name in all processed data files: FA1ic_NCC_REP4

value: Control isogenic corrected


title: FA2, FRDA, iPSC-derived neural crest cell, rep4

description:
Library name: FA2_NeuralCrest_REP4
column name in all processed data files: FA2_NCC_REP4


title: FA2ic, isogenic corrected, iPSC-derived neural crest cell, rep3

description:
Library name: FA2ic_NeuralCrest_REP3
column name in all processed data files: FA2ic_NCC_REP3


title: FA1, FRDA, iPSC-derived neural crest cell, rep5

description:
Library name: FA1_NeuralCrest_REP5
column name in all processed data files: FA1_NCC_REP5


title: FL_PBMC_C2_TCR

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

description: Library name: FL_PBMC_C2_TCR

data_processing:
The raw scRNA-seq and paired scTCR-seq data were simultaneously processed using 10× Genomics software CellRanger. The raw sequencing data were mapped into the human reference genome and VDJ database (GRCh38).
Assembly: Homo sapiens
Supplementary files format and content: "barcodes.tsv" files include scRNA-seq barcode information, "features.tsv" files include scRNA-seq gene features, and "matrix.mtx" files include scRNA-seq gene expression.
Library strategy: TCR-seq

molecule: cytoplasmic RNA

source_name: PBMC (peripheral blood mononuclear cell)

extract_protocol:
PBMCs and BMCs were isolated from EDTA anticoagulated venous blood and bone marrow of the patient, respectively, using a FicollR Paque Plus (Sigma Aldrich) solution according to standard density gradient centrifugation methods. Cells were harvested and counted via Cellaca MX high-throughput cell counter (Nexcelom Bioscience). The PBMCs were resuspended in 90% fetal bovine serum (FBS, HyClone), 10% DMSO freezing media and frozen using a Nalgene Mr. Frosty Cryo 1oC Freezing Container (Thermo Fisher Scientific) in a -80oC freezer for 24 h before being transferred to liquid nitrogen for long-term storage.
The ChromiumTM Single cell 5’ Reagent Kit and Chromium Single Cell Human TCR Amplification Kit of the Chromium platform (10× Genomics, California, USA) were used to create the scRNA-seq and paired single-cell TCR libraries in accordance with the Chromium Single Cell 5’ Reagent Kits User Guide (v2 Chemistry Dual Index). On the Illumina HiSeq X Ten platform, generated scRNA-seq libraries were sequenced.

tag: treatment stage

value: C2 (2-month)


title: Mus musculus, Model3-C39_muscle

city: Taiyuan

first: Huan

last: Xue

state: Shanxi

address: No. 56 Xinjian South Road

institute: Shanxi Medical University

description: Library name: Samlpe7

data_processing:
Raw data (raw reads) of fastq format were firstly processed using Trimmomatic and the low quality reads were removed to obtain the clean reads.The clean reads were mapped to the human genome (GRCh38) using HISAT2. FPKM of each gene was calculated using Cufflinks, and the read counts of each gene were obtained by HTSeq_x0002_count. Differential expression analysis was performed using the DESeq (2012) R package.
Assembly: GRCh38
Supplementary files format and content: processed data.xls includes FPKM and count for each sample

source_name: skeletal muscle

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA).
RNA libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: skeletal muscle


title: Mus musculus, Model1-C73_muscle

description: Library name: Samlpe5


title: Mus musculus, Model4-C45_muscle

description: Library name: Samlpe8


title: 4_Donors 306 and 307 with DPI Decidua mBlood CordBlood

description: Library name: Placenta_1_Cart4


title: 1_Donors 302 and 316 with DPI Decidua mBlood CordBlood

description: Library name: Cart_1

value: PRI316 and PRI302

value: Healthy (PRI316) and Chorioamniontis (PRI302)

value: PRI316_mfPLAC; PRI316_Decidua; PRI316_mBlood; PRI316_CordBlood; PRI302_mfPLAC; PRI302_Decidua; PRI302_mBlood; PRI302_CordBlood

value: PRI316_mfPLAC (SMK6); PRI316_Decidua (SMK8); PRI316_mBlood (SMK5); PRI316_CordBlood (SMK7); PRI302_mfPLAC (SMK10); PRI302_Decidua (SMK12); PRI302_mBlood (SMK9); PRI302_CordBlood (SMK11)


title: B16-vehicle_1

description: Library name: B16-vehicle_1

value: tumor


title: FL_PBMC_C1_TCR

description: Library name: FL_PBMC_C1_TCR

value: PBMC (peripheral blood mononuclear cell)

value: C1 (1-month)


title: 3_Donors 306 and 307 with DPI Decidua mBlood CordBlood

description: Library name: Placenta_1_Cart3


title: 1_Donors 306 and 307 with DPI Decidua mBlood CordBlood

description: Library name: Placenta_1_Cart1


title: FL_PBMC_C4_TCR

description: Library name: FL_PBMC_C4_TCR

value: C4 (4-month)


title: FA2ic, isogenic corrected, iPSC-derived neural crest cell, rep2

description:
Library name: FA2ic_NeuralCrest_REP2
column name in all processed data files: FA2ic_NCC_REP2

value: iPSC-derived neural crest cells


title: Mus musculus, Model2-C38_muscle

description: Library name: Samlpe6


title: FA1, FRDA, iPSC-derived neural crest cell, rep4

description:
Library name: FA1_NeuralCrest_REP4
column name in all processed data files: FA1_NCC_REP4


title: FA2, FRDA, iPSC-derived neural crest cell, rep3

description:
Library name: FA2_NeuralCrest_REP3
column name in all processed data files: FA2_NCC_REP3


title: FA1ic, isogenic corrected, iPSC-derived neural crest cell, rep3

description:
Library name: FA1ic_NeuralCrest_REP3
column name in all processed data files: FA1ic_NCC_REP3


title: FA2, FRDA, iPSC-derived neural crest cell, rep1

description:
Library name: FA2_NeuralCrest_REP1
column name in all processed data files: FA2_NCC_REP1


title: FL_PBMC_C0_TCR

description: Library name: FL_PBMC_C0_TCR

value: C0 (0-month)


title: FA1ic, isogenic corrected, iPSC-derived neural crest cell, rep1

description:
Library name: FA1ic_NeuralCrest_REP1
column name in all processed data files: FA1ic_NCC_REP1


title: FA1, FRDA, iPSC-derived neural crest cell, rep3

description:
Library name: FA1_NeuralCrest_REP3
column name in all processed data files: FA1_NCC_REP3


title: FA1ic, isogenic corrected, iPSC-derived neural crest cell, rep2

description:
Library name: FA1ic_NeuralCrest_REP2
column name in all processed data files: FA1ic_NCC_REP2


title: FA2ic, isogenic corrected, iPSC-derived sensory neuron, rep4

description:
Library name: FA2ic_SensoryNeuron_REP4
column name in all processed data files: FA2ic_SN_REP4

value: iPSC-derived sensory neurons


title: FA1, FRDA, iPSC-derived neural crest cell, rep1

description:
Library name: FA1_NeuralCrest_REP1
column name in all processed data files: FA1_NCC_REP1


title: FA1, FRDA, iPSC-derived neural crest cell, rep2

description:
Library name: FA1_NeuralCrest_REP2
column name in all processed data files: FA1_NCC_REP2


title: FA2ic, isogenic corrected, iPSC-derived sensory neuron, rep3

description:
Library name: FA2ic_SensoryNeuron_REP3
column name in all processed data files: FA2ic_SN_REP3


title: FL_PBMC_C4_RNA

description: Library name: FL_PBMC_C4_RNA

data_processing:
The raw scRNA-seq and paired scTCR-seq data were simultaneously processed using 10× Genomics software CellRanger. The raw sequencing data were mapped into the human reference genome and VDJ database (GRCh38).
Assembly: Homo sapiens
Supplementary files format and content: "barcodes.tsv" files include scRNA-seq barcode information, "features.tsv" files include scRNA-seq gene features, and "matrix.mtx" files include scRNA-seq gene expression.


title: FA2ic, isogenic corrected, iPSC-derived sensory neuron, rep1

description:
Library name: FA2ic_SensoryNeuron_REP1
column name in all processed data files: FA2ic_SN_REP1


title: Mus musculus, Liraglutide2-C20_muscle

description: Library name: Samlpe2


title: Mus musculus, Liraglutide1-C19_muscle

description: Library name: Samlpe1


title: FA2, FRDA, iPSC-derived sensory neuron, rep2

description:
Library name: FA2_SensoryNeuron_REP2
column name in all processed data files: FA2_SN_REP2


title: FA2, FRDA, iPSC-derived sensory neuron, rep4

description:
Library name: FA2_SensoryNeuron_REP4
column name in all processed data files: FA2_SN_REP4


title: FL_BMMC_C0_RNA

description: Library name: FL_BMMC_C0_RNA

source_name: BMC (bone marrow cell)

value: BMC (bone marrow cell)


title: Mus musculus, Liraglutide4-C31_muscle

description: Library name: Samlpe4


title: FL_PBMC_C1_RNA

description: Library name: FL_PBMC_C1_RNA


title: Cerebellum_cKO1

city: SAN FRANCISCO

first: Xiaoxin

last: Chen

state: California

address: 555 mission bay blvd. south, RM382A

department: Cardiovascular Research Institute

institute: University of California, San Francisco

description: Library name: Tox3_P1_Cerebellum_Nestin-cre;Tox3f/f_1

data_processing:
Adapter sequences were removed from the raw reads using Trimgalore v0.6.7. Reads were aligned to the primary assembly of the mm10 mouse genome using Bowtie v2.5.0 with default parameters.
Duplicates were removed using Sambamba v1.0. Blacklisted regions identified by the ENCODE project were filtered out from the final BAM files. Signal files were generated with deeptools bamCoverage v3.5.1. Signals from two controls or two conditional knockout samples were merged, respectively.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Cerebellum

growth_protocol: The mice were maintained according to the University of California, San Francisco institutional guidelines with free access to water and fed ad libitum with regular chow.

extract_protocol:
Chromatin from the cerebellum was prepared from P1 Nestin-cre;Tox3f/f and Tox3f//f or Tox3f/+ cerebella. Frozen cerebella were dissociated with a 1 mL pipette until no large tissue chunks were visible and then fixed in 1% formaldehyde in PBS for 20 min at room temperature. The fixation was stopped by adding glycine to a final concentration of 125 mM for 5 min at room temperature.
The samples were incubated with cell lysis buffer (50 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NonidetP-40 substitute (Fluka #74385), 0.25% Triton X-100, 1:200 protease inhibitor cocktail (Sigma-Aldrich #P8340)) and homogenized using a glass Dounce homogenizer with a type "B" pestle, performing 15 strokes. After centrifugation, the nuclear pellet was resuspended in nuclear lysis buffer (10mM Tris-Cl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 0.2% SDS, 1:200 protease inhibitor cocktail) and incubated for 20 min on ice. Samples were sonicated for 12 cycles of 20s on and 60s off using Branson Digital Sonifier model 450 at 9% amplitude to generate fragments of 200-500 bp.
ChIP was performed using 2 µg of anti-TOX3 antibody (Sigma). Following ChIP, ChIP-seq libraries were generated using the NEBNext® Ultra™ II DNA Library Prep Kit and sequenced using 150 bp paired-end reads on an Illumina Hiseq X platform.

value: Cerebellum

value: conditional knockout

tag: chip antibody

value: TOX3 (Sigma,#HPA040376)


title: FL_PBMC_C2_RNA

description: Library name: FL_PBMC_C2_RNA

value: C2 (2-month)


title: FA2ic, isogenic corrected, iPSC-derived sensory neuron, rep2

description:
Library name: FA2ic_SensoryNeuron_REP2
column name in all processed data files: FA2ic_SN_REP2

value: Control isogenic corrected


title: Cerebellum_Ctrl1

description: Library name: Tox3_P1_Cerebellum_Ctrl1

value: control littermate


title: FA1, FRDA, iPSC-derived sensory neuron, rep4

description:
Library name: FA1_SensoryNeuron_REP4
column name in all processed data files: FA1_SN_REP4

value: Diseased Friedreich's ataxia


title: FA1ic, isogenic corrected, iPSC-derived sensory neuron, rep3

description:
Library name: FA1ic_SensoryNeuron_REP3
column name in all processed data files: FA1ic_SN_REP3


title: FA1ic, isogenic corrected, iPSC-derived sensory neuron, rep4

description:
Library name: FA1ic_SensoryNeuron_REP4
column name in all processed data files: FA1ic_SN_REP4


title: FL_PBMC_C0_RNA

description: Library name: FL_PBMC_C0_RNA


title: FL_BMMC_C0_TCR

description: Library name: FL_BMMC_C0_TCR


title: FA2, FRDA, iPSC-derived sensory neuron, rep1

description:
Library name: FA2_SensoryNeuron_REP1
column name in all processed data files: FA2_SN_REP1


title: H-A-H02

city: Portland

first: Priya

last: Chaudhary

state: OR

address: 1225 NE 2nd Avenue

department: Devers Eye Institute

institute: Legacy Research Institute

description:
Library name: DSP-1001660022236-A-H02
spatial WTA sequencing

data_processing:
Raw sequencing data were processed using the Nanostring's pipeline to generate DCC files.
Hs_R_NGS_WTA_v1.0.pkc = 46ed2c63a88f12c64e9ba6f7841b0d27
Assembly: Human NGS Whole Transcriptome Atlas RNA version 1.0
Supplementary files format and content: .dcc and .pkc
Library strategy: Spatial transcriptomics

growth_protocol: Control and Experimental glaucoma ONH samples were used.

extract_protocol:
Paraformaldehyde fixed tissue was paraffin embedded and 5 micron sections were cut.
Spatial transcriptomics sequencing libraries were prepared using Nanostring GeoMx NGS pipeline according to manufacturer's instructions.

treatment_protocol: Laser treatment was used to induce experimental glaucoma.

tag: glaucoma

value: Controls


title: Cerebellum_cKO2

description: Library name: Tox3_P1_Cerebellum_Nestin-cre;Tox3f/f_2


title: FA1ic, isogenic corrected, iPSC-derived sensory neuron, rep2

description:
Library name: FA1ic_SensoryNeuron_REP2
column name in all processed data files: FA1ic_SN_REP2


title: FA1ic, isogenic corrected, iPSC-derived sensory neuron, rep5

description:
Library name: FA1ic_SensoryNeuron_REP5
column name in all processed data files: FA1ic_SN_REP5


title: FA2, FRDA, iPSC-derived sensory neuron, rep3

description:
Library name: FA2_SensoryNeuron_REP3
column name in all processed data files: FA2_SN_REP3


title: Mus musculus, Liraglutide3-C28_muscle

description: Library name: Samlpe3

value: skeletal muscle


title: FA1ic, isogenic corrected, iPSC-derived sensory neuron, rep1

description:
Library name: FA1ic_SensoryNeuron_REP1
column name in all processed data files: FA1ic_SN_REP1


title: Cerebellum_Ctrl3

description: Library name: Tox3_P1_Cerebellum_Ctrl3


title: H-A-G12

description:
Library name: DSP-1001660022236-A-G12
spatial WTA sequencing


title: FA1, FRDA, iPSC-derived sensory neuron, rep2

description:
Library name: FA1_SensoryNeuron_REP2
column name in all processed data files: FA1_SN_REP2


title: WWP2 PTCKO UIR 3

city: Nanjing

first: Mengqiu

last: Miao

state: Jiangsu

address: Children's Hospital of Nanjing Medical University

description: Library name: Sample 12

data_processing:
A propriety Sub-pixel Registration algorithm developed by MGI was used for base call.
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows:1) Remove the reads containing the adaptor(adaptor pollution);2) Remove reads whose N content is greater than 5%;3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).
Bowtie2 was used to map the clean reads to the reference gene sequence (transcriptome), and then RSEM was used to calculate the gene expression level of each sample.
The DEseq2 was used to perform differential expression analysis.DESeq2: Qvalue (Adjusted Pvalue) <= 0.05
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: xls, include FPKM values for each Sample

source_name: Kidney

extract_protocol:
Kidney tissues were harvested and rapidly frozen in liquid nitrogen. Total RNA was extracted from the tissues using Trizol (Invitrogen) according to the instruction manual.
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25μL~100μL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).

value: Kidney


title: FA1, FRDA, iPSC-derived sensory neuron, rep3

description:
Library name: FA1_SensoryNeuron_REP3
column name in all processed data files: FA1_SN_REP3


title: FA1, FRDA, iPSC-derived sensory neuron, rep1

description:
Library name: FA1_SensoryNeuron_REP1
column name in all processed data files: FA1_SN_REP1


title: FA1, FRDA, iPSC-derived sensory neuron, rep5

description:
Library name: FA1_SensoryNeuron_REP5
column name in all processed data files: FA1_SN_REP5


title: Cerebellum_Input

description: Library name: Tox3_P1_Cerebellum_Input

value: Input control


title: H-A-G11

description:
Library name: DSP-1001660022236-A-G11
spatial WTA sequencing

source_name: Liver

value: Liver


title: H-B-H04

description:
Library name: DSP-1001660033923-B-H04
spatial WTA sequencing


title: WWP2 PTCKO UIR 1

institute: Children's Hospital of Nanjing Medical University

description: Library name: Sample 10


title: WWP2 PTCKO UIR 2

description: Library name: Sample 11


title: H-B-H02

description:
Library name: DSP-1001660033923-B-H02
spatial WTA sequencing


title: H-A-G09

description:
Library name: DSP-1001660022236-A-G09
spatial WTA sequencing


title: H-A-H01

description:
Library name: DSP-1001660022236-A-H01
spatial WTA sequencing


title: H-B-H03

description:
Library name: DSP-1001660033923-B-H03
spatial WTA sequencing


title: WWP2 PTCKO Sham 3

description: Library name: Sample 9


title: H-B-G06

description:
Library name: DSP-1001660033923-B-G06
spatial WTA sequencing


title: H-B-G09

description:
Library name: DSP-1001660033923-B-G09
spatial WTA sequencing

source_name: Raji

value: Raji


title: H-B-G12

description:
Library name: DSP-1001660033923-B-G12
spatial WTA sequencing


title: H-A-G07

description:
Library name: DSP-1001660022236-A-G07
spatial WTA sequencing

source_name: Jurkat

value: Jurkat


title: H-B-G10

description:
Library name: DSP-1001660033923-B-G10
spatial WTA sequencing


title: H-A-G06

description:
Library name: DSP-1001660022236-A-G06
spatial WTA sequencing


title: WWP2 PTCKO Sham 2

description: Library name: Sample 8


title: WWP2 PTCKO Sham 1

description: Library name: Sample 7


title: H-B-G07

description:
Library name: DSP-1001660033923-B-G07
spatial WTA sequencing


title: H-B-H01

description:
Library name: DSP-1001660033923-B-H01
spatial WTA sequencing


title: H-B-G05

description:
Library name: DSP-1001660033923-B-G05
spatial WTA sequencing


title: H-A-G05

description:
Library name: DSP-1001660022236-A-G05
spatial WTA sequencing


title: H-A-G10

description:
Library name: DSP-1001660022236-A-G10
spatial WTA sequencing

source_name: PBMC+PHA

value: PBMC+PHA


title: H-B-G02

description:
Library name: DSP-1001660033923-B-G02
spatial WTA sequencing

source_name: Spleen

value: Spleen


title: H-B-G04

description:
Library name: DSP-1001660033923-B-G04
spatial WTA sequencing


title: WT UIR 3

description: Library name: Sample 6


title: H-A-G08

description:
Library name: DSP-1001660022236-A-G08
spatial WTA sequencing


title: WT UIR 2

description: Library name: Sample 5


title: H-B-G11

description:
Library name: DSP-1001660033923-B-G11
spatial WTA sequencing


title: H-B-G03

description:
Library name: DSP-1001660033923-B-G03
spatial WTA sequencing


title: WT Sham 2

description: Library name: Sample 2


title: WT UIR 1

description: Library name: Sample 4


title: H-A-G04

description:
Library name: DSP-1001660022236-A-G04
spatial WTA sequencing


title: H-B-G08

description:
Library name: DSP-1001660033923-B-G08
spatial WTA sequencing


title: H-B-G01

description:
Library name: DSP-1001660033923-B-G01
spatial WTA sequencing


title: H-A-G01

description:
Library name: DSP-1001660022236-A-G01
spatial WTA sequencing


title: H-A-G02

description:
Library name: DSP-1001660022236-A-G02
spatial WTA sequencing


title: N-B-F02

description:
Library name: DSP-1001660033923-B-F02
spatial WTA sequencing

tag: animal#

value: YES


title: N-B-F04

description:
Library name: DSP-1001660033923-B-F04
spatial WTA sequencing


title: WT Sham 1

description: Library name: Sample 1


title: N-B-E11

description:
Library name: DSP-1001660033923-B-E11
spatial WTA sequencing


title: N-B-F05

description:
Library name: DSP-1001660033923-B-F05
spatial WTA sequencing


title: H-B-F12

description:
Library name: DSP-1001660033923-B-F12
spatial WTA sequencing


title: N-B-E12

description:
Library name: DSP-1001660033923-B-E12
spatial WTA sequencing


title: H-B-F11

description:
Library name: DSP-1001660033923-B-F11
spatial WTA sequencing


title: N-B-E10

description:
Library name: DSP-1001660033923-B-E10
spatial WTA sequencing


title: H-A-G03

description:
Library name: DSP-1001660022236-A-G03
spatial WTA sequencing


title: N-B-E07

description:
Library name: DSP-1001660033923-B-E07
spatial WTA sequencing


title: N-A-F04

description:
Library name: DSP-1001660022236-A-F04
spatial WTA sequencing


title: WT Sham 3

description: Library name: Sample 3


title: HT_hTERT_T6_R1 [array]

type: genomic

city: Saskatoon

first: Franco

middle: J

last: Vizeacoumar

state: Saskatchewan

address: 4D40 Health Sciences Building, 107 Wiggins Road

department: Oncology

country: Canada

institute: University of Saskatchewan

description:
HT1080 TERT overexpressing
T6 Timepoint Replicate 1

hyb_protocol: Hybridizing was done as described in Blakely et al. Methods in Molecular Biology. 2011 PMID: 2187728.

scan_protocol: Scanning was done as described in Blakely et al. Methods in Molecular Biology. 2011 PMID: 2187728.

data_processing: The raw intensity data extracted from the CEL files were normalized with cyclic loess normalization and log transformed.

label: biotin

source_name: Fibrosarcoma

label_protocol: Labeling was done as described in Blakely et al. Methods in Molecular Biology. 2011 PMID: 2187728.

growth_protocol: Cells were collected as described in the manuscript Abuhussein et al.

extract_protocol: Genomic DNA was extracted as described in Blakely et al. Methods in Molecular Biology. 2011 PMID: 2187728.

treatment_protocol: Cells were treated as described in the manuscript Abuhussein et al.

value: Infection with the 90k shRNA libraries

tag: time point

tag: condition

value: TERT overexpressing


title: N-B-E05

description:
Library name: DSP-1001660033923-B-E05
spatial WTA sequencing


title: N-B-E09

description:
Library name: DSP-1001660033923-B-E09
spatial WTA sequencing


title: H-A-F12

description:
Library name: DSP-1001660022236-A-F12
spatial WTA sequencing


title: H-A-F10

description:
Library name: DSP-1001660022236-A-F10
spatial WTA sequencing

source_name: Tonsil

value: Tonsil


title: U2OS shFTSJ3 Day 10

description: TERRA Seq

data_processing:
Sequenced files were demultiplexed from MinION Mk1B
Sequencing data was processed using a method adapted from Rodrigues et al
Assembly: sub-telomeric regions of T2T CHM13v2.0/hs1 genome assembly
Supplementary files format and content: Matrix table with RPMK for each sub-telomeric regions are provided

source_name: Bone

growth_protocol: 7x10^8 cells were infected at an MOI of 0.3 with a viral constucts of (shFTSJ3 and shRFP) to yield a coverage of 300x.  Infected cells were selected for with puromycin.

extract_protocol:
genomic DNA was extracted using the QIAamp Blood Maxi kit (Qiagen #51194)
TERRA-seq libraries were constructed using Native Barcoding Kit 24 V14 (Oxford Nanopore Technologies)

treatment_protocol: MIA PaCa-2 cells and U-2 OS cells were transduced with shRFP and shFTSJ3 virus separately. Day 5 and Day 10 cell pellets

value: Bone

tag: cell line

tag: cell type

value: ALT Cells

value: shFTSJ3 KD Day 10


title: N-A-F02

description:
Library name: DSP-1001660022236-A-F02
spatial WTA sequencing

tag: tissue


title: H-A-F11

description:
Library name: DSP-1001660022236-A-F11
spatial WTA sequencing


title: N-A-F01

description:
Library name: DSP-1001660022236-A-F01
spatial WTA sequencing


title: MiaPaCa shFTSJ3 Day10

description: TERRA Seq

source_name: Pancreatic

value: Pancreatic

value: TERT positive Cells

tag: genotype

tag: treatment


title: N-B-E08

description:
Library name: DSP-1001660033923-B-E08
spatial WTA sequencing

tag: batch


title: N-B-F01

description:
Library name: DSP-1001660033923-B-F01
spatial WTA sequencing


title: N-B-D12

description:
Library name: DSP-1001660033923-B-D12
spatial WTA sequencing


title: Klebsiella pneumoniae ΔdksA mutant strain (ΔdksA), biological replicate 3

city: Please Select

first: 佳

last: 万

state: Please Select

address: 广东省广州市越秀区中山二路中山医学院科技楼301

institute: 中山医学院

description: Library name: ΔdksA-3

data_processing:
Data were employed to assemble the transcriptome using Trinity RNA-Seq software, and RNA-Seq reads were aligned according to the genome sequences of Klebsiella pneumoniae subsp. pneumoniae ATCC43816 KPPR1 (CP009208. 1) using the Subread aligner. A volcano map was constructed with R studio (version 3.6.1) to show the comprehensive differences between WT group and ΔdksA group. The differential transcription genes were mapped to KEGG database (http://geneontology.org/) and gene ontology (GO) terms (with Blast2GO software) for enrichment analysis, and the results were plotted by R studio (version 3.6.1).
DksA_RNAseq_expression_matrix.txt
WT_vs_ΔdksA_DEGs.csv
Assembly: Klebsiella pneumoniae ATCC 43816 KPPR1 (NCBI: CP009208.1)
Supplementary files format and content: WT_vs_ΔdksA_DEGs.csv : Differentially expressed gene list with columns for gene ID, log2 fold change, p-value, adjusted p-value, and gene annotation; DksA_RNAseq_expression_matrix.txt: Tab-delimited text file containing raw gene counts for all 6 samples. Rows represent genes, columns represent samples.

organism: Klebsiella pneumoniae

source_name: Bacteria

extract_protocol:
Total RNA was extracted from Klebsiella pneumoniae using TRIzol reagent (Invitrogen, USA) following the manufacturer's protocol. Genomic DNA was removed by DNase I treatment.
Sequencing libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Cat# E7530L) following manufacturer's recommendations. Index codes were added to multiplex samples.

value: Bacteria

value: Klebsiella pneumoniae


title: H-B-F10

description:
Library name: DSP-1001660033923-B-F10
spatial WTA sequencing

value: Controls


title: MiaPaCa shRFP Day10

description: TERRA Seq

value: Control Day 10

value: shRFP


title: HT_hTERT_T12_R2 [array]

description:
HT1080 TERT overexpressing
T12 Timepoint Replicate 2


title: Klebsiella pneumoniae control (WT), biological replicate 2

address: 广东省广州市越秀区中山二路中山医学院科技楼301

description: Library name: WT-2


title: N-A-F05

description:
Library name: DSP-1001660022236-A-F05
spatial WTA sequencing


title: N-A-E12

description:
Library name: DSP-1001660022236-A-E12
spatial WTA sequencing


title: Klebsiella pneumoniae control (WT), biological replicate 1

address: 广东省广州市越秀区中山二路中山医学院科技楼301

description: Library name: WT-1


title: N-B-E06

description:
Library name: DSP-1001660033923-B-E06
spatial WTA sequencing


title: HT_P_T0 [array]

description:
HT1080 Parental
T0 Timepoint

value: Parental


title: N-A-E09

description:
Library name: DSP-1001660022236-A-E09
spatial WTA sequencing


title: HT_P_T12_R2 [array]

description:
HT1080 Parental
T12 Timepoint Replicate 2


title: LN_AMP-dT_48h_1

type: RNA

first: Martin

middle: P

last: Steinbuck

state: Massachusetts

address: 451D Street, Ste 501

department: Research

institute: Elicio Therapeutics

hyb_protocol: Performed by Canopy Biosciences following the NanoString protocols

data_processing:
NanoString generated raw values of 24h and 48h samples were analyzed and compared to baseline (0h) samples using Rosalind software. Volcano plots show Rosalind-generated p-values (log2) and fold-changes (-log10). For heat maps, Z-scores were calculated for the raw expression data. These were then averaged among biological duplicates and mock-subtracted.
Rosalind computed expression values.

label: NanoString Probes

organism: Macaca mulatta

extract_protocol: Inguinal lymph node fine needle aspirates were obtained from immunized NHP at the indicated time points and lysed with RLT buffer (Qiagen, cat# 79216)

treatment_protocol: In vivo - vaccine injection into NHP

value: AMP-dT

tag: time

tag: subject


title: LN_AMP-dT_24h_2

scan_protocol: Performed by Canopy Biosciences following the NanoString protocols


title: N-A-E10

description:
Library name: DSP-1001660022236-A-E10
spatial WTA sequencing


title: Klebsiella pneumoniae ΔdksA mutant strain (ΔdksA), biological replicate 1

address: 广东省广州市越秀区中山二路中山医学院科技楼301

description: Library name: ΔdksA-1


title: HT_P_T6_R1 [array]

description:
HT1080 Parental
T6 Timepoint Replicate 1


title: HT_hTERT_T12_R1 [array]

description:
HT1080 TERT overexpressing
T12 Timepoint Replicate 1


title: HT_P_T12_R1 [array]

description:
HT1080 Parental
T12 Timepoint Replicate 1


title: LN_AMP-dT_24h_1

label_protocol: Performed by Canopy Biosciences following the NanoString protocols


title: HT_hTERT_T0 [array]

description:
HT1080 TERT overexpressing
T0 Timepoint


title: GM_hTERT_T14_R2 [array]

description:
GM0847 TERT overexpressing
T14 Timepoint Replicate 2

source_name: Skin


title: N-B-F03

description:
Library name: DSP-1001660033923-B-F03
spatial WTA sequencing


title: N-A-F03

description:
Library name: DSP-1001660022236-A-F03
spatial WTA sequencing


title: GM_hTERT_T6_R2 [array]

description:
GM0847 TERT overexpressing
T6 Timepoint Replicate 2


title: GM_hTERT_T14_R1 [array]

description:
GM0847 TERT overexpressing
T14 Timepoint Replicate 1


title: Shade, phyA-211, sucrose, replication 1

first: Lin

last: Li

address: 2005 Songhu Road,Yangpu District

department: school of life sciences

description: Library name: SH_PU_1

data_processing:
Raw sequence reads were initially processed by fastp for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT
Quality filitered reads were then mapped to Tair10 using Hisat2
Differential gene expression analysis was done using R package DESeq2
Assembly: Tair 10
Supplementary files format and content: all_genes_expresson_TPM.csv

organism: Arabidopsis

source_name: leaves

growth_protocol: 10-day-white-light grown seedlings were treated with 30 mM sorbitol or 30 mM sucrose under shade for 6 h.

extract_protocol:
Total RNA was extracted from tissue samples, and the concentration and purity of the extracted RNA were detected by Nanodrop2000. The integrity of RNA was detected by agarose gel, and the RIN value was determined by Agilent 2100. Using magnetic beads with Oligo (dT) and ployA for A-T base pairing, mRNA can be isolated from total RNA for analysis of transcriptome information. Under the action of reverse transcriptase, six random primers were added to reverse synthesize a single strand of cDNA using mRNA as a template, followed by a two-strand synthesis to form a stable double-stranded structure. The structure of double-stranded cDNA is sticky end. Add End Repair Mix to repair it into a flat end, and then add an "A" base at the 3 'end to connect the Y-shaped connector.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treated by 6 h shade (R/FR=0.17) together with 30 mM sorbitol or 30 mM sucrose.

value: leaves

value: Mutuan, phyA-211

value: 30 mM sucrose


title: Shade, Col-0, sucrose, replication 2

description: Library name: SH_CU_2

value: Wild type


title: N-A-E05

description:
Library name: DSP-1001660022236-A-E05
spatial WTA sequencing

value: YES


title: HT_hTERT_T6_R2 [array]

description:
HT1080 TERT overexpressing
T6 Timepoint Replicate 2

value: Infection with the 90k shRNA libraries

value: TERT overexpressing


title: LN_AMP-dT_48h_2


title: GM_P_T14_R2 [array]

description:
GM0847 Parental
T14 Timepoint Replicate 2


title: N-A-E11

description:
Library name: DSP-1001660022236-A-E11
spatial WTA sequencing


title: N-A-D11

description:
Library name: DSP-1001660022236-A-D11
spatial WTA sequencing

value: NO


title: LN_AMP-dT_0h_2


title: Shade, phyA-211, sorbitol, replication 1

description: Library name: SH_PO_1

value: 30 mM sorbitol


title: Shade, phyA-211, sucrose, replication 2

description: Library name: SH_PU_2


title: Shade, Col-0, sorbitol, replication 2

description: Library name: SH_CO_2


title: GM_P_T8_R2 [array]

description:
GM0847 Parental
T8 Timepoint Replicate 2


title: N-A-E07

description:
Library name: DSP-1001660022236-A-E07
spatial WTA sequencing


title: N-A-E08

description:
Library name: DSP-1001660022236-A-E08
spatial WTA sequencing


title: Shade, phyA-211, sucrose, replication 3

description: Library name: SH_PU_3


title: GM_P_T14_R1 [array]

description:
GM0847 Parental
T14 Timepoint Replicate 1


title: HT_P_T6_R2 [array]

description:
HT1080 Parental
T6 Timepoint Replicate 2


title: GM_hTERT_T0 [array]

description:
GM0847 TERT overexpressing
T0 Timepoint


title: N-A-D09

description:
Library name: DSP-1001660022236-A-D09
spatial WTA sequencing


title: LN_AMP-dT_0h_1


title: N-A-D12

description:
Library name: DSP-1001660022236-A-D12
spatial WTA sequencing


title: Aealbo treatment replicate 03

city: Hamilton

first: Lucas

last: Tirloni

state: MT

address: 903 S 4th Street

department: LB

institute: NIAID

description: Library name: Aealbo treatment replicate 03

data_processing:
RNA-Seq reads underwent quality control, adapter trimming, mapping, counting and differential expression analysis via the mRNAseq pipeline from the snakePipes package (v2.7.3). Mapping was performed using the software STAR (v2.7.10b) and the AalbF5 (GCF_035046485) version of the A. albopictus genome as reference. Read count for each gene was done using featureCounts (v2.0.1).
Assembly: GCF_035046485
Supplementary files format and content: aa_dmso_stm_counts.tsv

organism: Aedes albopictus

extract_protocol:
Total RNA was isolated from cells using TRIzol reagent according to the manufacturer’s instructions and analyzed with an Agilent High Sensitivity RNA ScreenTape System in an TapeStation 4150 (Agilent).
The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: Klebsiella pneumoniae ΔdksA mutant strain (ΔdksA), biological replicate 2

address: 广东省广州市越秀区中山二路中山医学院科技楼301

description: Library name: ΔdksA-2


title: Shade, Col-0, sucrose, replication 1

description: Library name: SH_CU_1


title: Heart, Normal, rep5

city: Paris

first: Jean-Sébastien

last: Hulot

address: Rue Leblanc

institute: Paris Centre de Recherche Cardiovasculaire

hyb_protocol: A total of 100 ng of RNA were incubated with the Capture and Reporter ProbeSets for 18 hours at 65 °C.

scan_protocol: Post-hybridization processing and data collection were performed using the nCounter Prep Station and Digital Analyzer (nCounter Max System) as indicated by the manufacturer.

data_processing: Raw counts of gene expression data were analyzed with the nSolver Analysis Software (version 4.0.70). Background correction was applied based on the negative controls, and the geometric means of the supplied positive controls and housekeeping genes were used to normalize the measured expression values. All the samples passed the QC metrics which were defined as binding density > 0.05 and < 2.25 probes/μm2, % fields of view > 0.75, positive control linearity > 0.95, and sufficient assay efficiency. Per-sample Level of Detection (LOD)  was defined as the mean of the counts of negative control probes for each sample and was ensured by using internal quality control reference probes. Raw gene expression data were normalized using the Remove Unwanted Variation (RUV) approach following quality control and housekeeping assessment.

label: Fluorescently barcoded nucleic acid probes

source_name: Heart

label_protocol: The customized nCounter Human Banff Organ Transplant gene panel probes were prepared by the manufacturer.

extract_protocol: RNA was extracted froms three 20 𝜇m FFPE sections using the tissue RNEasy FFPE kit #73504 (Qiagen, Hilden, Germany). The concentration and quality of isolated RNA were assessed using NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA, USA).

tag: myocardial infarctus or normal

value: Normal


title: Shade, phyA-211, sorbitol, replication 2

description: Library name: SH_PO_2


title: Shade, Col-0, sorbitol, replication 3

description: Library name: SH_CO_3


title: N-A-D07

description:
Library name: DSP-1001660022236-A-D07
spatial WTA sequencing


title: Shade, Col-0, sucrose, replication 3

description: Library name: SH_CU_3


title: Heart, Normal, rep3


title: N-A-D10

description:
Library name: DSP-1001660022236-A-D10
spatial WTA sequencing


title: Shade, Col-0, sorbitol, replication 1

description: Library name: SH_CO_1


title: N-A-D08

description:
Library name: DSP-1001660022236-A-D08
spatial WTA sequencing


title: Aealbo treatment replicate 02

description: Library name: Aealbo treatment replicate 02


title: N-A-D06

description:
Library name: DSP-1001660022236-A-D06
spatial WTA sequencing


title: N-A-E06

description:
Library name: DSP-1001660022236-A-E06
spatial WTA sequencing


title: Heart, Early MI, rep6

value: Early MI


title: GM_P_T0 [array]

description:
GM0847 Parental
T0 Timepoint


title: GM_P_T8_R1 [array]

description:
GM0847 Parental
T8 Timepoint Replicate 1


title: Aealbo control replicate 02

description: Library name: Aealbo control replicate 02


title: Heart, Normal, rep4


title: Heart, Early MI, rep4


title: GM_hTERT_T6_R1 [array]

description:
GM0847 TERT overexpressing
T6 Timepoint Replicate 1


title: Aealbo treatment replicate 01

description: Library name: Aealbo treatment replicate 01


title: Heart, Early MI, rep7


title: Heart, Early MI, rep3


title: Heart, Early MI, rep2


title: Heart, Late MI, rep8

value: Late MI


title: N-A-D05

description:
Library name: DSP-1001660022236-A-D05
spatial WTA sequencing


title: Shade, phyA-211, sorbitol, replication 3

description: Library name: SH_PO_3


title: N-A-C12

description:
Library name: DSP-1001660022236-A-C12
spatial WTA sequencing


title: Aealbo control replicate 03

description: Library name: Aealbo control replicate 03


title: Heart, Late MI, rep6


title: N-A-D02

description:
Library name: DSP-1001660022236-A-D02
spatial WTA sequencing


title: Heart, Late MI, rep5


title: N-A-D03

description:
Library name: DSP-1001660022236-A-D03
spatial WTA sequencing


title: N-A-D04

description:
Library name: DSP-1001660022236-A-D04
spatial WTA sequencing


title: N-A-C07

description:
Library name: DSP-1001660022236-A-C07
spatial WTA sequencing


title: Heart, Late MI, rep9


title: Heart, Early MI, rep8


title: Heart, Early MI, rep1


title: OA_DMSO_3

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

country: Germany

institute: Universitätsklinikum Düsseldorf

description: Library name: OA_DMSO_3

data_processing:
alignment via HISAT2
hisat2 -p 7 -N 1 -L 20 -i S,1,0.5 -D 25 -R 5 --mp 1,0 --sp 3,0 -x /home/ww/hisatindex/grch38_r109 -U $1 -S $x.sam  2>&1 | tee $x.hisat.log
Reads were summarized per gene with the subread (1.6.1) featurecounts software against the Homo_sapiens.GRCh38.109.gtf
CPM values were filtered for expressed genes via rowSums(cpm(x) > 1) >= 1 and normalized with the limma-voom normalization
Assembly: GRCh38 r109
Supplementary files format and content: tab-delimitted txt file contains normalized CPM values for each sample

source_name: hepatocyte-like cells

growth_protocol: iPSCs were differentiated to HLCs. From day 15-17 of HLC differentiation on, the cells were fed with complete HLC medium, supplemented with OA and or vildagliptin (VILDA)

extract_protocol:
Cells were lysed in trizol and RNA was isolated using the direct-zol RNA kit (ZYMO research), following the manufacturers instructions. Residual DNA was removed by a DNAse digestion step.
QuantSeq 3’ mRNA-Seq Library Prep Kit FWD

treatment_protocol: cells were treated with 400 µM OA or the respective volume of TRIS-BSA as mock-treatment. The medium was changed every other day for 7 days. A final concentration of 30µM VILDA (Sigma-Aldrich) dissolved in DMSO was fed to the cells after 48 h OA-/mock-induction for 5 days with medium changes every other day

value: hepatocyte-like cells

tag: disease state

value: healthy

value: oleic acid


title: N-A-C06

description:
Library name: DSP-1001660022236-A-C06
spatial WTA sequencing


title: U2OS shRFP Day 10

description: TERRA Seq

value: Bone

value: ALT Cells

value: Control Day 10

value: shRFP


title: Heart, Late MI, rep1


title: ctrl_DMSO_3

description: Library name: ctrl_DMSO_3

value: no


title: OA_DMSO_2

description: Library name: OA_DMSO_2


title: ctrl_DMSO_2

description: Library name: ctrl_DMSO_2


title: N-A-C05

description:
Library name: DSP-1001660022236-A-C05
spatial WTA sequencing


title: Overexpressing HK1-3

city: xiamen

first: feng

last: deyi

state: xiamen

address: Xiamen University

institute: xiamen university

description: Library name: sample6

data_processing:
trim-galore;subjunc and featurecount
Assembly: hg38
Supplementary files format and content: counts.txt

extract_protocol:
Extracting RNA using the TRIZOL
RNA libraries for RNA-seq were prepared using the Stranded mRNA Prep.

value: hepatocellular carcinoma

value: Overexpressing HK1


title: Overexpressing HK1-2

description: Library name: sample5


title: OA_DMSO_1

description: Library name: OA_DMSO_1


title: ctrl_DMSO_1

description: Library name: ctrl_DMSO_1


title: N-A-C03

description:
Library name: DSP-1001660022236-A-C03
spatial WTA sequencing

value: YES


title: N-A-C04

description:
Library name: DSP-1001660022236-A-C04
spatial WTA sequencing


title: OA_Vilda_3

description: Library name: OA_Vilda_3

value: oleic acid+Vildagliptin


title: OA_Vilda_2

description: Library name: OA_Vilda_2


title: N-A-C02

description:
Library name: DSP-1001660022236-A-C02
spatial WTA sequencing


title: OA_Vilda_1

description: Library name: OA_Vilda_1


title: Overexpressing HK1-1

description: Library name: sample4


title: Control-3

description: Library name: sample3

value: Control


title: ctrl_Vilda_2

description: Library name: ctrl_Vilda_2

value: Vildagliptin


title: ctrl_Vilda_3

description: Library name: ctrl_Vilda_3


title: N-A-B12

description:
Library name: DSP-1001660022236-A-B12
spatial WTA sequencing


title: Control-2

description: Library name: sample2


title: ctrl_Vilda_1

description: Library name: ctrl_Vilda_1


title: KG1A-50 nM-R1

city: Little Rock

first: Samrat

last: Roy Choudhury

state: AR

address: 13 Children's Way, Arkansas Children's Research Institute

institute: University of Arkansas for Medical Sciences

description:
207041120095_R07C01
Illumina Infinium MethylationEPIC v2.0 BeadChip (GPL33022)

hyb_protocol: Bisulfite-converted DNA was hybridized to the Illumina Infinium MethylationEPIC v2.0 BeadChip following the manufacturer's protocol (Illumina, Part # 15019519 v01). Samples were denatured and loaded onto the array using the automated Tecan system or Illumina manual procedures.

scan_protocol: Arrays were scanned using the Illumina iScan System according to the manufacturer's recommended settings. IDAT files were generated for each sample and used for downstream analysis.

data_processing:
Raw IDAT files were imported and processed using the R package minfi. Quality control and background correction were applied using standard minfi workflows. Probes failing detection p-value threshold (p > 0.01) were excluded. Probes on sex chromosomes and known cross-reactive sites were filtered out. Beta values (β-values), representing the ratio of methylated signal over the sum of methylated and unmethylated signals, were calculated for each CpG.
Processed values represent β-values, calculated as: β=MM+U+100\beta = \frac{M}{M + U + 100}β=M+U+100M, where M is the methylated signal intensity, U is the unmethylated signal intensity, and 100 is a regularization constant. Values range from 0 (completely unmethylated) to 1 (fully methylated).

label: Cy3 and Cy5

label_protocol: Genomic DNA (500 ng per sample) was bisulfite-converted using the EZ DNA Methylation Kit (Zymo Research) following the manufacturer’s standard protocol. No additional labeling step was used, as hybridization and signal detection are built into the Illumina array platform.

growth_protocol: KG1A cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified incubator with 5% CO₂. Cells were maintained in logarithmic growth phase and passaged every 2–3 days.

extract_protocol: Genomic DNA was extracted using the AllPrep DNA/RNA kit (Qiagen) according to the manufacturer’s instructions. DNA concentration and purity were assessed using a NanoDrop spectrophotometer, and DNA integrity was confirmed by agarose gel electrophoresis.

treatment_protocol: Cells were seeded at 1×10⁶ cells per well and treated with 50 nM Nanaomycin A (NanA; MedChemExpress, HY-103397) or an equivalent volume of DMSO (vehicle control) for 48 hours. Following treatment, cells were collected for DNA extraction.

value: Acute Myeloid Leukemia

value: WT

value: Treatment (NanA_50 nM)


title: S08_Cntrl_n3

description: Library name: S08_Cntrl_n3

data_processing:
alignment via HISAT2
hisat2 -p 7 -N 1 -L 20 -i S,1,0.5 -D 25 -R 5 --mp 1,0 --sp 3,0 -x /home/ww/hisatindex/grch38_r109 -U $1 -S $x.sam  2>&1 | tee $x.hisat.log
Reads were summarized per gene with the subread (1.6.1) featurecounts software against the Homo_sapiens.GRCh38.109.gtf
CPM values were for expressed genes via rowSums(cpm(x) > 1) >= 1 and normalized with the limma-voom normalization
Assembly: GRCh38 r109
Supplementary files format and content: tab-delimitted txt file contains normalized CPM values for each sample

growth_protocol: induced pluripotent stem cells (iPSC) derived hepatocyte-like cells were differentiated and treated for 7 days with 400 µM oleic acid before extracting.

treatment_protocol: hepatocyte-like cells were treated with 400 µM oleic acid bound to BSA or mock treated with only BSA as a solvent control (Cntrl/ mock)

value: hepatocyte-like cells

value: steatosis


title: KG1A-R2

description:
207041120103_R05C01
Illumina Infinium MethylationEPIC v2.0 BeadChip (GPL33022)

value: Control (DMSO)


title: Control-1

description: Library name: sample1


title: S11_OA_n3

description: Library name: S11_OA_n3

value: oleic acid


title: S11_OA_n2

description: Library name: S11_OA_n2


title: N-A-B10

description:
Library name: DSP-1001660022236-A-B10
spatial WTA sequencing


title: S11_Cntrl_n3

description: Library name: S11_Cntrl_n3


title: S11_Cntrl_n2

description: Library name: S11_Cntrl_n2


title: S11_Cntrl_n1

description: Library name: S11_Cntrl_n1


title: S11_OA_n1

description: Library name: S11_OA_n1


title: N-A-B08

description:
Library name: DSP-1001660022236-A-B08
spatial WTA sequencing


title: N-A-B09

description:
Library name: DSP-1001660022236-A-B09
spatial WTA sequencing


title: S08_OA_n2

description: Library name: S08_OA_n2


title: 04DMSO_R2

city: London

first: Allan

middle: M

last: Carrillo-Baltodano

address: Mile End

department: School of Biological and Behavioural Studies

country: United Kingdom

institute: Queen Mary University of London

description: Library name: 04DMSO_R2

data_processing:
Adapter and low-quality bases were removed using FastP v0.20.1 . Cleaned reads were mapped to the O. fusiformis genome annotation using Kallisto v.0.46.2. Read counts were normalised using the R package DESeq2 v. 1.26.0. Differential gene expression analyses were performed for each pairwise comparison between control and treatment with DESeq2.
Assembly: The genome assembly and annotation of Owenia fusiformis was downloaded from https://github.com/ChemaMD/OweniaGenome
Supplementary files format and content: The RNA-seq file are counts on genes for each sample as obtained from Kallisto

organism: Owenia fusiformis

source_name: whole-embryo

growth_protocol: Embryos were raised in glass bowls containig artificial seawater

extract_protocol:
Total RNA from these cultures were extracted using the Monarch Total RNA Miniprep Kit (New England Biolabs; Cat No.: #T2010)
mRNA fraction were selected from the total RNA before converted to cDNA. Second strand cDNA synthesis had dUTP incorporated. The cDNA was end-repaired, A-tailed and adapter-ligated. Prior to amplification, samples underwent uridine digestion. The prepared libraries were selected, multiplexed and QC’ed before paired-end sequenced over 1 of a NovaSeq v1.5 flow cell.

treatment_protocol: Embryos from 4 hours post fertilization (hpf) to 6 hpf were treated with either 20uM DMH1, 0.2% DMSO, 1x Mock, 1000 ng/ul recombinant zBMP4 or 75 ng/ul recombinant Activin-A. Embryos from 3hpf to 6hpf were treated with either 40uM SB431542 or 0.4% DMSO.

value: whole-embryo


title: N-A-B07

description:
Library name: DSP-1001660022236-A-B07
spatial WTA sequencing


title: SB435421_R1

description: Library name: SB435421_R1


title: KG1A-R1

description:
207041120095_R05C01
Illumina Infinium MethylationEPIC v2.0 BeadChip (GPL33022)


title: SB435421_R2

description: Library name: SB435421_R2


title: KG1A-50 nM-R2

description:
207041120103_R07C01
Illumina Infinium MethylationEPIC v2.0 BeadChip (GPL33022)


title: S08_OA_n3

description: Library name: S08_OA_n3


title: S08_OA_n1

description: Library name: S08_OA_n1


title: S08_Cntrl_n1

description: Library name: S08_Cntrl_n1


title: N-A-B02

description:
Library name: DSP-1001660022236-A-B02
spatial WTA sequencing

value: NO


title: S08_Cntrl_n2

description: Library name: S08_Cntrl_n2


title: N-A-B11

description:
Library name: DSP-1001660022236-A-B11
spatial WTA sequencing


title: CO2_OA_n3

description: Library name: CO2_OA_n3

value: healthy


title: Activin_R2

description: Library name: Activin_R2

value: Activin


title: N-A-B01

description:
Library name: DSP-1001660022236-A-B01
spatial WTA sequencing


title: CO2_OA_n2

description: Library name: CO2_OA_n2


title: 04DMSO_R1

description: Library name: 04DMSO_R1


title: CO2_OA_n1

description: Library name: CO2_OA_n1


title: CO2_Cntrl_n3

description: Library name: CO2_Cntrl_n3

value: no


title: BMP_R2

description: Library name: BMP_R2

value: BMP


title: N-A-A11

description:
Library name: DSP-1001660022236-A-A11
spatial WTA sequencing


title: N-A-A12

description:
Library name: DSP-1001660022236-A-A12
spatial WTA sequencing


title: CO2_Cntrl_n2

description: Library name: CO2_Cntrl_n2


title: BMP_R1

description: Library name: BMP_R1


title: Activin_R1

description: Library name: Activin_R1


title: CO2_Cntrl_n1

description: Library name: CO2_Cntrl_n1


title: N-A-A10

description:
Library name: DSP-1001660022236-A-A10
spatial WTA sequencing


title: N-A-A09

description:
Library name: DSP-1001660022236-A-A09
spatial WTA sequencing


title: MC38 cells, wildtype, replicate 17

first: Chen

last: Qian

address: No. 227 Chongqing South Road, Huangpu District, Shanghai, China

institute: Shanghai Jiao Tong University School of Medicine

description:
Library name: WT_17
RNA-seq of MC38 cells with non-targeting CRISPR control

data_processing:
Raw sequencing reads were subjected to quality control to remove adaptor sequences and low-quality reads.
Clean reads were aligned to the mouse reference genome using HISAT2.
Gene-level read counts were quantified using featureCounts.
Gene expression levels were normalized and summarized to generate a gene expression matrix.
Assembly: GRCm39
Supplementary files format and content: The processed data file is provided in comma-separated values (CSV) format, with genes in rows and samples in columns. Each cell represents the raw read count mapped to the corresponding gene in each sample.

growth_protocol: Cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted from MC38 cells using TRIzol reagent according to the manufacturer’s instructions. RNA integrity and concentration were assessed using an Agilent Bioanalyzer.
RNA sequencing libraries were constructed using a poly(A) selection method to enrich mRNA. Libraries were prepared following the standard protocol recommended by BGI and sequenced on the DNBSEQ-T7 platform to generate paired-end reads.

treatment_protocol: MC38 cells were transduced with CRISPR-Cas9 constructs targeting RAD51D, LIMCH1, or BRD9 using gene-specific sgRNAs. A non-targeting sgRNA was used as the negative control. Stable knockout cells were selected and validated before RNA extraction.

value: colorectal cancer cell

value: CRISPR-Cas9 control


title: MC38 cells, wildtype, replicate 18

description:
Library name: WT_18
RNA-seq of MC38 cells with non-targeting CRISPR control


title: UJ_OA_n3

description: Library name: UJ_OA_n3


title: Mock_R2

description: Library name: Mock_R2

value: Mock


title: N-A-A08

description:
Library name: DSP-1001660022236-A-A08
spatial WTA sequencing


title: MC38 cells, wildtype, replicate 16

description:
Library name: WT_16
RNA-seq of MC38 cells with non-targeting CRISPR control


title: Mock_R1

description: Library name: Mock_R1


title: MC38 cells, wildtype, replicate 15

description:
Library name: WT_15
RNA-seq of MC38 cells with non-targeting CRISPR control


title: N-A-A07

description:
Library name: DSP-1001660022236-A-A07
spatial WTA sequencing


title: UJ_OA_n2

description: Library name: UJ_OA_n2


title: MC38 cells, wildtype, replicate 14

description:
Library name: WT_14
RNA-seq of MC38 cells with non-targeting CRISPR control


title: DMH1_R1

description: Library name: DMH1_R1


title: UJ_OA_n1

description: Library name: UJ_OA_n1


title: N-A-A06

description:
Library name: DSP-1001660022236-A-A06
spatial WTA sequencing


title: UJ_Cntrl_n3

description: Library name: UJ_Cntrl_n3


title: DMH1_R2

description: Library name: DMH1_R2


title: 02DMSO_R2

description: Library name: 02DMSO_R2


title: UJ_Cntrl_n2

description: Library name: UJ_Cntrl_n2


title: N-A-A05

description:
Library name: DSP-1001660022236-A-A05
spatial WTA sequencing


title: UJ_Cntrl_n1

description: Library name: UJ_Cntrl_n1


title: MC38 cells, wildtype, replicate 11

description:
Library name: WT_11
RNA-seq of MC38 cells with non-targeting CRISPR control


title: N-A-A04

description:
Library name: DSP-1001660022236-A-A04
spatial WTA sequencing


title: 02DMSO_R1

description: Library name: 02DMSO_R1


title: MC38 cells, wildtype, replicate 13

description:
Library name: WT_13
RNA-seq of MC38 cells with non-targeting CRISPR control


title: MC38 cells, wildtype, replicate 12

description:
Library name: WT_12
RNA-seq of MC38 cells with non-targeting CRISPR control


title: CUT&Tag, Free_siKDM4A.2_TGFb_H3K36me3_1

city: wuhan

first: Jie

last: Yao

state: 湖北

address: wuhan hubei province

institute: wuhan university

description: Library name: Sample5

data_processing:
We performed quality control using FastQC on all samples. The raw reads were trimmed using Trim-galore to remove adapters. The clean reads were mapped to mouse reference genome (mm39) using Bowtie2 with the “--end-to-end --very-sensitive -I 10 -X 700 --no-mixed" option.  Low-quality mapped reads and those mapped to mitochondrial reads were filtered using Samtools. The duplicated reads were removed using Sambamba. The Counts Per Million mapped reads (CPM) normalization method was used to transform alignment bam files into read coverage files in bigWig format on deepTools. Peak calling was performed using MACS2. Differentially accessible peaks were identified using the DiffBind. Motif enrichment analysis was performed using the HOMER.
Assembly: mm39
Supplementary files format and content: bigWig for each Sample
Library strategy: CUT&Tag

source_name: MLF

growth_protocol: Primary mouse lung fibroblasts (MLFs) were maintained in DMEM/F-12 medium supplemented with 10% FBS (LONSERA) and 1% penicillin-streptomycin (Gibco) at 37°C under 5% O₂ and 5% CO₂.

extract_protocol:
CUT&Tag assay was performed using CUT&Tag High‐Sensitivity Kit (Novoprotein, N259-YH01) according to the manufacturer’s recommendation.
CUT&Tag assay was performed using CUT&Tag High‐Sensitivity Kit (Novoprotein, N259-YH01) according to the manufacturer’s recommendation.

treatment_protocol: We transfected two KDM4A siRNAs into MLF cells. After 24 h of transfection, the cells were treated with 20 ng/mL TGF-β1 for 48 h, followed by CUT&Tag assay for H3K36me3.

value: MLF

value: Primary mouse lung fibroblasts


title: N-A-A03

description:
Library name: DSP-1001660022236-A-A03
spatial WTA sequencing


title: CUT&Tag, Free_siKDM4A.2_TGFb_H3K36me3_2

description: Library name: Sample6

value: WT


title: N-A-A02

description:
Library name: DSP-1001660022236-A-A02
spatial WTA sequencing


title: Antigen-specific GC B cells, GT8-IL-21-NIC DNA vaccine

city: Philadelphia

first: David

last: Weiner

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

description:
Library name: GT8-IL21-NIC
10x Genomics 5’ V(D)J library from lymph node GC B cells of VH1-2RJH2/VK1-33RCSd/hTdT mice

data_processing:
Raw FASTQs generated from Illumina NextSeq 2000 (paired-end 26x8x90)
Cell Ranger V(D)J pipeline used to produce filtered/all contig annotations, clonotypes, and metrics summary
Assembly: Custom reference derived from Mus musculus GRCm38 (mm10) and human GRCh38
Supplementary files format and content: .tar.gz archive per sample containing filtered_contig_annotations.csv, all_contig_annotations.csv, clonotypes.csv, all_contig.fasta, filtered_contig.fasta, metrics_summary.csv, airr_rearrangement.tsv

source_name: Lymph node

extract_protocol:
Lymph nodes collected from VH1-2RJH2/VK1-33RCSd/hTdT mice and antigen-specific germinal center B cells sorted by FACS
10x Genomics Chromium single-cell 5’ V(D)J library prep (GEM-X Single Cell 5’ V3 Kit) according to manufacturer’s protocol; cDNA generated and amplified; sequencing adaptors ligated; double-sided SPRIselect bead clean-ups

value: Lymph node

value: GC B cells

value: Immunized

value: Day 7


title: Antigen-specific GC B cells, GT8-60mer DNA vaccine

description:
Library name: GT8-60mer
10x Genomics 5’ V(D)J library from lymph node GC B cells of VH1-2RJH2/VK1-33RCSd/hTdT mice


title: MC38 cells, wildtype, replicate 10

description:
Library name: WT_10
RNA-seq of MC38 cells with non-targeting CRISPR control


title: MC38 cells, wildtype, replicate 9

description:
Library name: WT_9
RNA-seq of MC38 cells with non-targeting CRISPR control


title: CUT&Tag, Free_siKDM4A.1_TGFb_H3K36me3_2

description: Library name: Sample4


title: AKM56

city: AUBURN

first: Amit

middle: Kumar

last: Mitra

address: HARRISON COLLEGE OF PHARMACY

department: DRUG DISCOVERY AND DEVELOPMENT

institute: AUBURN UNIVERSITY

description: Library name: MCL37

data_processing:
Partek Genomics Suite
Read count extraction were performed from raw data using Partek Flow
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized gene counts in Samples

source_name: MCL

extract_protocol:
High quality RNA was isolated using QIAshredder columns and RNAeasy Mini kit (Qiagen)
RNA-seq libraries were constructed using Illumina TruSeq RNA Library Prep Kit v2 (poly A enrichment).

value: MCL

value: Mantle Cell Lymphoma cell line

value: IBR


title: CUT&Tag, Free_siKDM4A.1_TGFb_H3K36me3_1

description: Library name: Sample3