title: patch-seq, virus-infected, replicate 135

description:
Library name: 5_1H7
SMART-seq3


title: WT_CL_S1000

status: Public on Jun 09 2025

type: SRA

city: Tianjin

first: Hanzhi

last: Yu

address: 22 Meteorology Station Road, Heping District, Tianjin

country: China

institute: Tianjin Medical University

library_source: transcriptomic

data_processing:
Raw base calls from the sequencer were demultiplexed and converted to FASTQ format using the bcl2fastq2 (v2.2.0, illumina) command mkfastq. FASTQ files were aligned to the mouse reference genome assembly mm10 and a count matrix was generated using the SeekSpace tools (v1.0.0, Seekgene) .
Assembly: mm10
Supplementary files format and content: WTH946_masked_feature_bc_matrix.zip/WTH994_masked_feature_bc_matrix.zip/WT_L7_heAuto.zip/KO_L7_heAuto.zip
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Mus musculus

source_name: Lung

extract_protocol:
The lung tissue samples from CL WT and CL Ncf2-/- were embedded in OCT. After cutting these samples into 10-micron thick slices, RNA was extracted, and its quality was assessed to ensure that the RNA Integrity Number (RIN) > 7
BMKMANU S1000 Gene Expression Kit(S1000)

tag: tissue

value: Lung

tag: cell type

value: lung cell

tag: genotype

value: WT


title: Synchronized culture - sample 6h_3_S47_R1_001

city: paris

first: yuping

last: dia

address: 4 pl.jussieu

country: France

institute: sorbonne university

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 6h_3_S47_R1_001

data_processing:
The amount of reads per gene was counted with featureCounts91 with default parameters. Data was then processed using R and the EdgeR library92. Read counts per gene were standardized to counts per million and filtered to eliminate all of the genes which did not have at least one read per million in all 15 samples.
Assembly: S. islandicus REY15A genome (RefSeq accession number: NC_017276)
Supplementary files format and content: Comma-delimited text file includes raw counts for each sample

organism: Saccharolobus islandicus

source_name: archaeal cell

growth_protocol: Saccharolobus islandicus strain REY15A was grown aerobically at 76ºC with shaking in 25 ml of MTSV medium containing mineral salts (M), 0.2% (wt/vol) tryptone (T), 0.2% (wt/vol) sucrose (S) and a mixed vitamin solution (V); the pH was adjusted to 3.5 with sulfuric acid, as described previously

extract_protocol:
RNA was then isolated from each batch on different days, no variance between batches was found using principal component analysis. The total RNA was extracted from the 15 biological replicates at three different time-points after synchronization: 2h30, 4h and 6h. The time points were selected based on the results of the flow cytometry analysis which showed that samples at these three time points are enriched in cells in the M-G1, S and G2 phases, respectively. Total RNA was extracted using TRI Reagent (SIGMA-Aldrich), following the manufacturer’s protocol, and treated with DNase (TURBO DNA-free kit; Invitrogen) following the manufacturer’s instructions. DNase treated samples were further purified with RNeasy Mini Kit (Qiagen). RNA samples were quantified using a Qubit Fluorometer (Thermo Fischer Scientific) and assessed for quality with a BioAnalyzer (Agilent)
Analyzer (Agilent). Sequencing was performed on an Illumina NextSeq 2000 sequencer with a P3 50-cycle kit and a target of 30 to 40 million reads per sample. The reads obtained were mapped to the reference S. islandicus REY15A genome (RefSeq accession number: NC_017276) with Bowtie-290 using default parameters.

treatment_protocol: Cells were plated on solid media and 15 single colonies were inoculated in liquid media. forming 15 cultures that represent completely independent biological replicates. The 15 biological replicates were grown in 3 different batches (5 cultures per batch), each batch was grown and synchronized at a different time (5 cultures at a time). RNA was then isolated from each batch on different days, no variance between batches was found using principal component analysis (see supplementary table S1 for batch number for each sample). The total RNA was extracted from the 15 biological replicates at three different time-points after synchronization: 2h30, 4h and 6h (Fig. 1B). The time points were selected based on the results of the flow cytometry analysis which showed that samples at these three time points are enriched in cells in the M-G1, S and G2 phases, respectively (Figure 1C). Total RNA was extracted using TRI Reagent (SIGMA-Aldrich), following the manufacturers protocol, and treated with DNase (TURBO DNA-free kit; Invitrogen) following the manufacturers instructions. DNase treated samples were further purified with RNeasy Mini Kit (Qiagen). RNA samples were quantified using a Qubit Fluorometer (Thermo Fischer Scientific) and assessed for quality with a BioAnalyzer (Agilent) (see supplementary table S1 for quality control parameters for each sample).  Libraries were prepared using the Illumina Stranded Total RNA Prep, Ligation with Illumina Ribo-Zero Plus kit, with custom ribodepletion. Following PCR amplification, all samples underwent two rounds of purification with AMPure beads (Beckman Coulter) to remove small fragments. Libraries were subsequently validated using both the Qubit Fluorometer and the Fragment Analyzer (Agilent). Sequencing was performed on an Illumina NextSeq 2000 sequencer with a P3 50-cycle kit and a target of 30 to 40 million reads per sample. The reads obtained were mapped to the reference S. islandicus REY15A genome (RefSeq accession number: NC_017276) with Bowtie-290 using default parameters.

tag: strain

value: archaeal cell

tag: time


title: NCF2-/-_CL_SeekSpace

data_processing:
Raw base calls from the sequencer were demultiplexed and converted to FASTQ format using the bcl2fastq2 (v2.2.0, illumina) command mkfastq. FASTQ files were aligned to the mouse reference genome assembly mm10 and a count matrix was generated using the SeekSpace tools (v1.0.0, Seekgene) .
Assembly: mm10
Supplementary files format and content: WTH946_masked_feature_bc_matrix.zip/WTH994_masked_feature_bc_matrix.zip
Library strategy: Spatial Transcriptomics

molecule: nuclear RNA

extract_protocol:
The lung tissue samples from CL WT and CL Ncf2-/- were embedded in OCT. After cutting these samples into 10-micron thick slices, RNA was extracted, and its quality was assessed to ensure that the RNA Integrity Number (RIN) > 7
SeekSpace sc-Spatial Labeling Kit V1.0(SeekSpace)

tag: cell line


title: RIMD2210633_vpa1360 deletion mutant_1

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on HiSeq 3000 platform in a 75-base single-end mode.
Generated reads were mapped to the Vibrio parahaemolyticus RIMD 2210633 reference genome (GCF_000196095.1_ASM19609v1_genomic.fna, NCBI) using TopHat v2.1.1 in combination with Bowtie2 ver.2.2.8 and SAMtools ver.0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffnorm 2.2.1.
Assembly: the Vibrio parahaemolyticus RIMD 2210633 genome (GCF_000196095.1_ASM19609v1_genomic.fna, NCBI)
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

organism: Vibrio parahaemolyticus

source_name: Bacterial cutlure

growth_protocol: Bacteria were cultured in 0.5% NaCl LB broth at 37°C, standing for 3h.

extract_protocol:
The total RNA in bacteria was stabilized by RNAprotect® Bacteria Reagent (Qiagen) and then was extracted using RNeasy Mini Kit (Qiagen).
From extracted total RNA, ribosomal RNA was removed and the remaining RNA was fragmented, using the Ribo-Zero Plus rRNA Depletion Kit (Illumina). RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina) without the Purify and Fragment mRNA step.

value: Bacterial cutlure

value: vpa1360 deletion


title: Total_RNAseq_MCF7_sgControl_6hours_R,R-GL-373_Replicate_1

city: La Jolla

first: Garrett

middle: Lee

last: Lindsey

state: CA

address: 10650 N Torrey Pines Rd

department: Chemistry

country: USA

institute: Scripps Research

description: Library name: Sample 1

data_processing:
Transcript abundance was quantified using Salmon [v1.3.0] with GENCODE v37 annotation.
Gene level quantification was performed using tximeta [v1.8.4].
Differential gene expression was analyzed by DESeq2 [v1.30.1]
Assembly: HG19
Supplementary files format and content: Feature counts for differential expression

organism: Homo sapiens

source_name: Breast

growth_protocol: Cells were grown in vitro under standard culture conditions

extract_protocol:
QIAGEN Rneasy Plus mini
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).

treatment_protocol: Samples were treated in biological triplicate in the presence of small molecules, as indicated, for 6 hours prior to collection.

value: Breast

value: Breast carcinoma

value: single guide - Control

tag: treatment


title: patch-seq, virus-infected, replicate 132

city: madison

first: Xinyu

last: Zhao

state: WI

address: 1500 Highland Ave

department: Waisman Center

institute: University of Wisconsin-Madison

description:
Library name: 5_1H11
SMART-seq3

library_source: transcriptomic single cell

data_processing:
snATAC/RNA-seq: The 10x Multiome ATAC(snATAC-seq) + Gene Expression(snRNA-seq) dataset was processed using the Cell Ranger ARC pipeline. To analyze the macaque data, we used the Cell Ranger ARC mkref to create a rheMac10 reference. Subsequently, we performed a quality check on the output of the Cell Ranger ARC pipeline, and then used it for downstream analysis.
SMART-seq:The SMART-seq3 RNA-seq reads from human were aligned to reference genome GRCh38 and the reads from rhesus macaque were aligned to reference genome rheMac10. Trim Galore was used for the adaptor trimming. We used STAR (v2.7.2b) (69) in two pass Mode for the alignment and removed PCR duplicates. STAR quantMode was used for gene counts on uniquely aligned reads, and the intergenic regions were excluded.
Assembly: rheMac10; GRCh38
Supplementary files format and content: snATAC-seq: fragments files are generated from Cell Ranger ARC pipeline. ; snRNA-seq: barcodes, features and matrix files are generated from Cell Ranger ARC pipeline. SMART-seq3: "AcuteRhesusPatchseq.csv" and "OrganotypicCHD8Patchseq.csv" are normalized gene expression data files.

source_name: dlPFC

extract_protocol:
Macaque brain specimens were collected from postconceptional day (PCD) 87 to PCD155. All experiments using non-human primates were carried out in accordance with a protocol approved by the University of Wisconsin’s Institutional Animal Care and Use Committee and NIH guidelines.
snMultiomes:The libraries were constructed in accordance with the guidelines provided in the "Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide" (10x Genomics, CG000338); SMART-seq3: follow the protocol according to publication "Single-cell RNA counting at allele and isoform resolution using Smart-seq3" (PMID: 32518404).

value: dlPFC

value: tissue

value: organotypic dlPFC slice cells

value: lentivirus infected

value: shNC

tag: batch

value: patch-seq, virus-infected


title: LUNG_WT_SPF

data_processing:
After sequencing, raw data were processed with the SeekSpace tools (v1.0.0, Seekgene) to align reads to the mouse reference genome (mm10) and generate a gene-cell expression matrix for subsequent analysis.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix

extract_protocol:
After harvested, tissues were washed in ice-cold RPMI1640 and dissociated using Tissue Dissociation Reagent A (Seekone K01301-30) from SeekGene as instructions. DNase Ⅰ (Sigma 9003-98-9) treatment was optional according to the viscosity of the homogenate.
The SeekOne® Digital Droplet Single Cell 3’ Library Preparation Kit (SeekGene, No.K00202) was used to prepare the single-cell RNA-Seq library.

value: SPF


title: Synchronized culture - sample 4h_20_S44_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 4h_20_S44_R1_001


title: Synchronized culture - sample 6h_4_S48_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 6h_4_S48_R1_001


title: Synchronized culture - sample 6h_1_S46_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 6h_1_S46_R1_001


title: RIMD2210633_vpa1360 deletion mutant_2


title: Synchronized culture - sample 4h_19_S43_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 4h_19_S43_R1_001


title: patch-seq, virus-infected, replicate 134

description:
Library name: 5_1H6
SMART-seq3


title: patch-seq, virus-infected, replicate 133

description:
Library name: 5_1H12
SMART-seq3


title: patch-seq, virus-infected, replicate 131

description:
Library name: 5_1H10
SMART-seq3


title: Ncf2-/-_3

data_processing:
During the analysis of transcriptome sequencing data, we initially utilize the TrimGalore software (version 0.6.7) to preprocess the raw sequencing data, removing low-quality reads and adapter sequences. Subsequently, the processed data undergo quality control using FastQC (version 0.11.9). The sequencing fragments are then mapped to the mouse reference genome using the Hisat2 (version 2.2.0) alignment tool. The featureCounts tool (version 2.0.1) is used to efficiently count the reads mapped to exons, thereby constructing the raw count matrix needed for subsequent analysis. The raw count matrix is loaded into R version 4.2.0, and gene reads are normalized using TPM (Transcripts Per Million) for further analysis.
Assembly: mm10
Supplementary files format and content: all.id.xlsx include raw data for each sample

source_name: bone marrow

extract_protocol:
RNA was prepared from BM Lin-cell suspension sorted by magnetic beads.
The RNA-seq library was then prepared using the Illumina Stranded mRNA Prep, Ligation kit and sequenced on the Illumina NovaSeq 6000 platform.

value: bone marrow

value: BM Lin- cell


title: RIMD2210633_vpa1359 deletion mutant_2

value: vpa1359 deletion


title: RIMD2210633_vpa1359 deletion mutant_1


title: Total_RNAseq_MCF7_sgControl_6hours_R,R-GL-373_Replicate_3

description: Library name: Sample 3


title: Total_RNAseq_MCF7_sgControl_6hours_R,R-GL-373_Replicate_2

description: Library name: Sample 2


title: patch-seq, virus-infected, replicate 137

description:
Library name: 5_1H9
SMART-seq3


title: RIMD2210633_vpa1360 deletion mutant_3


title: NCF2-/-_CL_S1000

value: Lung

value: lung cell


title: Synchronized culture - sample 4h_21_S45_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 4h_21_S45_R1_001

value: archaeal cell


title: RIMD2210633_vpa1359 deletion mutant_3

value: Bacterial cutlure


title: Synchronized culture - sample 4h_17_S42_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 4h_17_S42_R1_001


title: patch-seq, virus-infected, replicate 130

description:
Library name: 5_1G9
SMART-seq3


title: Synchronized culture - sample 6h_6_S50_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 6h_6_S50_R1_001


title: Synchronized culture - sample 4h_11_S40_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 4h_11_S40_R1_001


title: WT_CL_SeekSpace


title: patch-seq, virus-infected, replicate 129

description:
Library name: 5_1G8
SMART-seq3


title: RIMD2210633_WT_2

value: WT


title: WT_3


title: patch-seq, virus-infected, replicate 128

description:
Library name: 5_1G7
SMART-seq3


title: RIMD2210633_WT_1


title: Synchronized culture - sample 4h_12_S39_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 4h_12_S39_R1_001


title: WT_1


title: patch-seq, virus-infected, replicate 127

description:
Library name: 5_1G12
SMART-seq3


title: Ncf2-/-_2


title: patch-seq, virus-infected, replicate 126

description:
Library name: 5_1G11
SMART-seq3


title: Synchronized culture - sample 4h_10_S38_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 4h_10_S38_R1_001


title: WT_2


title: RIMD2210633_vpa1369 deletion mutant_2

value: vpa1369 deletion


title: Vav1Cre Xpr1fl/fl CD45+CD19-CD3-B220-Ter119-CD49b-CD90.2- liver cells

city: Zurich

first: Sebastian

middle: A

last: Stifter

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich

description: 10x Genomics

data_processing:
Read alignment, cell-calling, and feature-barcode count matrix generation were performed using the 10x Genomics Cell Ranger v7.1.0 pipeline.
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix files

source_name: E15.5 fetal liver

extract_protocol:
Livers were collected from E15.5 embryos and digested for 30 minutes at 37°C in HBSS (containing Mg2+ and Ca+), supplemented with 2%FCS, 0.4mg/ml Collagenase IV and 0.04mg/ml DnaseI. Following digestion, samples were thoroughly dissociated using a P200 pipette. Red blood cells were lysed with RBC-lysis solution (155mM Nh4CL, 11mM KHCO3) and washed with PBS containing 2%FCS, 2mM EDTA. Following genotyping of embryos, three control (Xpr1fl/fl) and three Cre (Vav1Cre Xpr1fl/fl) samples were pooled. Samples were stained in the dark with antibodies and live/dead vialibity dye for 30 minutes at 4°C. CD45+CD19-CD3-B220-Ter119-CD49b-CD90.2- cells were sorted into 100% FCS on a BD S6 sorter using a 100um nozzle. Cells were washed and resuspended in 50ul of PBS containing 0.02%BSA.
The quality of the single-cell suspensions was assessed using a hemocytometer under a Leica DM IL LED Fluo microscope, and the quantity was determined using an automated cell counter (LUNA-FX7, Logos). Approximately 17,000 cells per sample were loaded onto the 10x Chromium X platform. Library preparation followed the manufacturer's guidelines specified in the Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry Dual Index). For sequencing, the resulting libraries were processed on an Illumina NovaSeq 6000 SP Flow Cell. Sequencing parameters were set according to 10x Genomics recommendations, using paired-end reads with the following specifications: R1=28, i7=10, i5=10, R2=90. An average depth of around 50,000 reads per cell was achieved during sequencing.

value: fetal liver

value: Vav1Cre Xpr1fl/fl

tag: developmental stage


title: Synchronized culture - sample 4h_9_S37_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 4h_9_S37_R1_001


title: patch-seq, virus-infected, replicate 125

description:
Library name: 5_1G10
SMART-seq3

value: dlPFC

value: tissue


title: RIMD2210633_vpa1369 deletion mutant_3


title: Synchronized culture - sample 4h_8_S36_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 4h_8_S36_R1_001


title: RIMD2210633_vpa1369 deletion mutant_1


title: Xpr1fl/fl control CD45+CD19-CD3-B220-Ter119-CD49b-CD90.2- liver cells

description: 10x Genomics


title: RIMD2210633_WT_3


title: Synchronized culture - sample 4h_13_S41_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 4h_13_S41_R1_001


title: patch-seq, virus-infected, replicate 124

description:
Library name: 5_1F9
SMART-seq3

value: organotypic dlPFC slice cells

value: lentivirus infected


title: LPM_PAC KO Ecoli 3

city: Baltimore

first: Henry Yi

last: Cheng

state: MD

address: 725 N Wolfe st, WBSB216

institute: Johns Hopkins University

data_processing:
Reads were mapped to mm10 reference mouse genome with Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Fragments per kilobase per million mapped reads (FPKM) of each gene were calculated based on the length of the gene and reads count mapped to this gene. Further differential expression analysis, Gene Ontology enrichment analysis, and KEGG pathway analysis were carried out by clusterProfiler R package.
Assembly: mm10
Supplementary files format and content: xls
Supplementary files format and content: excel with differential expressed genes between two groups, count, fpkm

molecule: polyA RNA

source_name: LPM

extract_protocol:
Mice were subjected to intraperitoneal infection for 30 minutes and underwent peritoneal lavage to acquire peritoneal cells. Cells were washed with ice-cold PBS and collected in FACS buffer. Cells further underwent surface staining for LPM sorting. Subsequently, the Sony MA900 Multi-Application Cell Sorter was used for isolating LPM cells. 3 samples from PBS- and infection-treated mice from control or Cx3cr1-PAC−/− mice were collected. Total RNA was extracted using the RNeasy Micro kit (Qiagen). Total RNA quality was determined by the A260/A280 and A260/A230 as well as the Agilent 2100 Bioanalyzer.
NEBNext Ultra II RNA Library Prep Kit

value: LPM

value: primary mouse large peritoneal macrophage

value: E. coli infection


title: RIMD2210633_3


title: Ncf2-/-_1

value: bone marrow

value: BM Lin- cell


title: patch-seq, virus-infected, replicate 123

description:
Library name: 5_1F8
SMART-seq3

value: shNC

value: patch-seq, virus-infected


title: Synchronized culture - sample 4h_6_S35_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 4h_6_S35_R1_001

value: archaeal cell


title: Synchronized culture - sample 4h_5_S34_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 4h_5_S34_R1_001


title: patch-seq, virus-infected, replicate 122

description:
Library name: 5_1F7
SMART-seq3


title: RIMD2210633_1

value: Bacterial cutlure


title: patch-seq, virus-infected, replicate 121

description:
Library name: 5_1F12
SMART-seq3


title: LPM_PAC KO Ecoli 1


title: Synchronized culture - sample 4h_4_S33_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 4h_4_S33_R1_001


title: LPM_PAC KO Ecoli 2


title: patch-seq, virus-infected, replicate 120

description:
Library name: 5_1F11
SMART-seq3


title: Synchronized culture - sample 4h_3_S32_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 4h_3_S32_R1_001


title: LPM_WT Ecoli 3

value: PAC F/F


title: Synchronized culture - sample 4h_1_S31_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 4h_1_S31_R1_001


title: patch-seq, virus-infected, replicate 119

description:
Library name: 5_1F10
SMART-seq3


title: patch-seq, virus-infected, replicate 118

description:
Library name: 5_1E9
SMART-seq3


title: Col_Glu2

city: Taipei

first: Yi-Jie

last: Hung

address: 128 Section 2, Academia Road, Nankang

department: IPMB

country: Taiwan

institute: Academia Sinica

description: Library name: Sample 5

data_processing:
Low quality reads, which are shorter than 35 base pairs or have an error probability greater than 0.05, were filtered out.
Mapping reads to the Arabidopsis reference genome TAIR10 by using BLAT method.
Reverse R1 BAM file of each sample under SAMtools.
For each sample, pick up R1-reversed BAM file and R2 BAM file for reads per kilo-base-pair gene model per million mapped reads (RPKM) computation.
TMM normalization is applied to normalize all RPKM files.
Assembly: TAIR 10
Supplementary files format and content: tab-delimited text file include normalized RPKM values for each sample

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Arabidopsis seeds were surface sterilized and grown on 1/2 MS-modified basal salt mixture without N (M531, PhytoTechnology Laboratories) containing 0.05% (w/v) 2-(N-morpholine)-ethanesulfonic acid (MES), 0.5% (w/v) Suc, 0.8% (w/v) agar, adjusted to pH 5.7 with 1 N KOH, and supplemented with 5 mM NH4NO3 or 5 mM Glu. The plates were sealed with parafilm, kept at 4℃ for 2 days and then transferred to the growth room on a 16-h-light/8-h-dark cycle at 22°C for 12 days.

extract_protocol:
Total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole seedling

value: Columbia (Col) ecotype


title: Col_Glu1

description: Library name: Sample 4


title: Synchronized culture - sample 2h30_21_S30_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 2h30_21_S30_R1_001


title: LPM_WT Ecoli 1


title: Col_NN3

description: Library name: Sample 3


title: Young

city: Charleston

first: Mohamed Faisal

last: Kassir

state: SC

address: 86 Jonathan Lucas St HO509

institute: Medical University of South Carolina

data_processing:
Partek
Sequence reads were aligned using STAR - 2.7.8a tool in Partek.
Sequence reads were quantified to Ensembl Transcripts annotation model with strict paired-end compatibility and a minimum 100% read overlap with feature using Partek.
Read count extraction and and normalization were performed using Partek.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw count for each sample

source_name: Spleen

growth_protocol: T-cells were activated with plate-bound anti-CD3 (2ug/ml) and anti-CD28 (5ug/ml) in the presence of 100IU/ml IL-2 for 3 days in IMDM supplemented with 10% fetal bovine serum, antibiotics, and b-mercaptoethanol.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 500ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNAseq were constructed using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocol.

treatment_protocol: Mice were treated with vehicle or fumarate (10mg/kg) three times/week for two months before T-cell isolation.

value: Spleen

value: T-cells

value: Vehicle


title: patch-seq, virus-infected, replicate 117

description:
Library name: 5_1E8
SMART-seq3

value: dlPFC

value: tissue

value: organotypic dlPFC slice cells


title: Old + Fumarate

value: Fumarate


title: Synchronized culture - sample 2h30_19_S28_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 2h30_19_S28_R1_001


title: RIMD2210633_2

value: WT


title: Synchronized culture - sample 2h30_20_S29_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 2h30_20_S29_R1_001


title: patch-seq, virus-infected, replicate 116

description:
Library name: 5_1E7
SMART-seq3

value: lentivirus infected


title: Old


title: patch-seq, virus-infected, replicate 115

description:
Library name: 5_1E12
SMART-seq3


title: Col_NN1

description: Library name: Sample 1


title: GCN5-GFP Schizont CUT&Tag control rep1

city: Tampa

first: JUN

last: MIAO

state: Florida

address: 3720 Spectrum Boulevard, MDC84

department: Internal Medicine

institute: University of South Florida

description:
Library name: GCN5 CUT_Tag control rep1
CUT&Tag-seq

library_source: genomic

data_processing:
The adaptor trimming and initial quality control were performed using FASTP for all CUT&Tag-seq and ChIP-seq FASTQ files. The resulting reads were mapped to the P. falciparum 3D7 genome version 67. Peak calling was performed using ‘macs2 callpeak’ with default parameters.
For ChIP-seq samples, no peaks could be called from ChIP-seq profiles.
Assembly: the malaria parasite genome (pf3D7_V67)
Supplementary files format and content: processed data in BAM format which including all H3K9ac and GCN5 chromatin coverage values for each sample.
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Plasmodium falciparum

growth_protocol: 3D7 strains of P. falciparum were cultured in type O+ human RBCs at 5% hematocrit in RPMI 1640 medium supplemented with 25 mM HEPES, 50mg/L hypoxanthine, 25 mM NaHCO3, 0.5% Albumax II and 40 mg/ml gentamicin sulfate. The culture was maintained at 37°C in a gas mixture of 5% CO2, 3% O2 and 92% N2.

extract_protocol:
For ChIP-seq, synchronized WT 3D7 parasites at the schizont stage were harvested and crosslinked with 1% paraformaldehyde and then neutralized by glycine (0.125 M). The fixed iRBCs were lysed with saponin (0.06% final concentration) and parasites were treated with a lysis buffer (10 mM KCl, 0.1 mM EDTA, 0.1 mM EGTA, 1 mM DTT, 10 mM Hepes, pH 7.9, 1 × protease inhibitor) and then were homogenized using a douncer to free the nuclei. Pelleted nuclei were sonicated in a shearing buffer (0.1% SDS, 5 mM EDTA, 50 mM Tris-HCl, pH 8.1, 1× protease inhibitor) using a rod bioruptor (Microson ultrasonic cell disruptor, Misonix, Inc. USA) at high power for 20 cycles of 30 sec ON/30 sec OFF, resulting in sheared chromatin of approximately 100–1000 bps. Fifty μl of input samples were set aside, and the remaining chromatin was diluted in an incubation buffer (0.01% SDS, 1.5% Triton X-100, 0.5 mM EDTA, 200 mM NaCl, 5 mM Tris-HCl, pH 8.1). The chromatin (75 μl/400 ng) was incubated with rabbit anti-H3K9ac (Diagenode pAb-004-050) followed by the addition of 20 μl of agarose beads. Beads were then washed with the following: buffer 1 (0.1% SDS, 1% Triton X-100, 150 mM NaCl, 2 mM EDTA, 20 mM Tris HCl, pH 8.1); buffer 2 (0.1% SDS, 1% Triton X-100, 500 mM NaCl, 2 mM EDTA, 20 mM Tris HCl, pH 8.1), buffer 3 (250 mM LiCl, 1% NP-40, 1% Na-deoxycholate, 1 mM EDTA, 10 mM Tris HCl, pH 8.1) and finally twice with buffer 4 (10 mM EDTA, 10 mM Tris HCl, pH 8). The immunoprecipitated (IPed) chromatin was eluted with the elution buffer (1% SDS, 0.1 M NaHCO3) at room temperature. The eluted chromatin and input samples were reverse crosslinked in 10% SDS, 1MNaHCO3, 5MNaCl, and 10% Triton X-100 at 45˚C overnight while shaking and purified by the phenol:chloroform method. For CUT&Tag-seq, parasites at the schizont stage were harvested and fixed with 1% formaldehyde followed by saponin lysis. The parasite pellet was suspended in a nuclear extraction buffer. Ten μl of Activated Concanavalin A-coated magnetic beads (EpiCypher # 21-1401) were added to each sample (~0.5 × 106 nuclei). For H3K9ac CUT&Tag-seq, the bead-bound WT parasite nuclei were resuspended in 50 μl Antibody150 buffer containing 0.5 μg of rabbit anti-H3K9ac (Diagenode pAb-004-050) as the primary antibody and rabbit IgG (Cell Signaling Technology #2729S) serving as a control. For PfGCN5 CUT&Tag-seq, the bead-bound PfGCN5::GFP nuclei were incubated with 0.5 μg of goat anti-GFP (Novus biologicals NB100-1770) while WT 3D7 nuclei were used as control.  Following primary antibody incubation, nuclei were incubated with the secondary antibodies, donkey anti-goat IgG (Abcam ab6885).
For ChIP-seq, the immunoprecipitated gDNA (~20 ng/sample) was then used to generate libraries using the KAPA Hyper prep kit for the Illumina sequencing platform according to the manufacturer's protocol (KAPA Biosystems). For CUT&Tag-seq, the nuclei were resuspened in Digitonin300 Buffer containing CUTANA pAG-Tn5 (EpiCypher #15-1017). Next, the nuclei were resuspended in Tagmentation buffer (10 mM MgCl2 in Digitonin300) at 37 °C for 1 h followed by washing with 50 µl TAPS buffer, quenching tagmentation with 5 µL SDS release buffer, incubating at 58ºC to release tagmented chromatin into the solution, and quenching SDS by adding 0.67% Triton-X. PCR with appropriate barcoded primers was performed using the CUTANA High Fidelity 2x PCR Master Mix (EpiCypher #15-1018) according to the manufacturer's recommendations. Amplified DNA libraries were captured by Kapa pure beads (Roche #KK8001) according to the manufacturer's recommendations, and 150 bp paired-end sequencing was performed on the NextSeq 550 platform.

value: Schizont (S) stage

tag: antibody

value: anti-GFP (Novus biologicals NB100-1770)


title: Synchronized culture - sample 2h30_12_S25_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 2h30_12_S25_R1_001


title: PfGCN5-GFP Schizont CUT&Tag rep1

description:
Library name: GCN5 CUT_Tag rep1
CUT&Tag-seq


title: Col_Glu3

description: Library name: Sample 6


title: Col_NN2

description: Library name: Sample 2


title: patch-seq, virus-infected, replicate 114

description:
Library name: 5_1E11
SMART-seq3

value: shNC

value: patch-seq, virus-infected


title: patch-seq, virus-infected, replicate 113

description:
Library name: 5_1E10
SMART-seq3


title: LN_Th17_4

type: RNA

city: Atlanta

first: Chrystal

last: Paulos

state: GA

address: 1365 Clifton Rd NE

department: Surgery

institute: Emory University

hyb_protocol: Samples were hybridized according to Nanostring protocol

scan_protocol: Samples were scanned according to Nanostring protocol

data_processing: Data was processed usign nSolver 4.0 software. It was normalized using positive controls and housekeeping genes with the default software settings.

label: Nanostring oligonucleotide probe

source_name: Lymph node from B16F10 bearing mouse

label_protocol: Samples were labelled by Nanostring (nCounter Mouse PanCancer Immune Profiling Panel)

extract_protocol: Samples were stored in RNAlater

tag: sample

value: Lymph Node


title: LN_Th17_3


title: LPM_WT Ecoli 2

value: LPM

value: primary mouse large peritoneal macrophage

value: PAC F/F

value: E. coli infection


title: 3D7 H3K9Ac Schizont CUT&Tag control rep2

description:
Library name: H3K9ac CUT_Tag control rep2
CUT&Tag-seq

value: IgG (Cell Signaling Technology #2729S)


title: patch-seq, virus-infected, replicate 112

description:
Library name: 5_1D9
SMART-seq3


title: LN_Th17_2


title: 3D7 H3K9Ac Schizont CUT&Tag rep2

description:
Library name: H3K9ac CUT_Tag rep2
CUT&Tag-seq

value: H3K9ac (Diagenode pAb-004-050)


title: Synchronized culture - sample 2h30_10_S23_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 2h30_10_S23_R1_001

value: archaeal cell


title: patch-seq, virus-infected, replicate 111

description:
Library name: 5_1D8
SMART-seq3

value: dlPFC

value: tissue


title: 3D7 H3K9Ac Schizont CUT&Tag control rep1

description:
Library name: H3K9ac CUT_Tag control rep1
CUT&Tag-seq


title: Synchronized culture - sample 2h30_9_S22_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 2h30_9_S22_R1_001


title: Synchronized culture - sample 2h30_17_S27_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 2h30_17_S27_R1_001


title: LN_Th17_1


title: Synchronized culture - sample 2h30_13_S26_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 2h30_13_S26_R1_001


title: patch-seq, virus-infected, replicate 110

description:
Library name: 5_1D7
SMART-seq3

value: organotypic dlPFC slice cells


title: 3D7 H3K9Ac Schizont CUT&Tag rep1

description:
Library name: H3K9ac CUT_Tag rep1
CUT&Tag-seq


title: LN_NT_4

value: NT


title: Synchronized culture - sample 2h30_8_S21_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 2h30_8_S21_R1_001


title: patch-seq, virus-infected, replicate 109

description:
Library name: 5_1D12
SMART-seq3

value: lentivirus infected


title: LN_NT_3


title: 3D7 H3K9Ac Schizont Input rep1

description:
Library name: H3K9ac Schizont Input
ChIP-seq

data_processing:
The adaptor trimming and initial quality control were performed using FASTP for all CUT&Tag-seq and ChIP-seq FASTQ files. The resulting reads were mapped to the P. falciparum 3D7 genome version 67. Peak calling was performed using ‘macs2 callpeak’ with default parameters.
For ChIP-seq samples, no peaks could be called from ChIP-seq profiles.
Assembly: the malaria parasite genome (pf3D7_V67)
Supplementary files format and content: processed data in BAM format which including all H3K9ac and GCN5 chromatin coverage values for each sample.

value: Schizont (S) stage


title: patch-seq, virus-infected, replicate 108

description:
Library name: 5_1D11
SMART-seq3


title: patch-seq, virus-infected, replicate 107

description:
Library name: 5_1D10
SMART-seq3


title: Synchronized culture - sample 2h30_5_S19_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 2h30_5_S19_R1_001


title: LN_NT_2


title: 3D7 H3K9Ac Schizont ChIP rep1

description:
Library name: H3K9Ac Schizont ChIP
ChIP-seq


title: Synchronized culture - sample 2h30_4_S18_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 2h30_4_S18_R1_001


title: -aTc TetR-PfGCN::GFP S rep3

description:
Library name: Sample 24
RNA-seq

data_processing:
Illumina adapter sequence removal and quality trimming of reads were performed using Trimmomatic. Reads were then mapped to the P. falciparum 3D7 strain reference genome with HISAT2. Using an optimized data analysis workflow, we mapped about 5 million sequence reads per sample to the malaria parasite genome (pf3D7_V3.0.)
Assembly: the malaria parasite genome (pf3D7_V3.0.)
Supplementary files format and content: Table 1 contains the processed data in excel format which including all TPM values for every gene from every sample.

source_name: whole organism

extract_protocol:
Parasites of designated developmental stages were harvested after lysis of the RBC membrane with 0.1% (v/v) saponin in PBS. Total RNA was isolated from the purified parasites using Quick-RNA MiniPrep kit (Zymo Research). The RNA was treated with the ezDNaseTM Enzyme (Invitrogen) to remove contaminating genomic DNA. RNA pellets were dissolved in 50 µL RNase-free water, and the RNA integrity was checked using the Agilent Bioanalyzer.
RNA sequencing libraries were prepared using the KAPA stranded RNA-seq library preparation kit (Roche) with 500 ng RNA from each sample. RNA was fragmented by heating at 94 °C for 8 min, and cDNA was synthesized using reverse transcriptase with random primers. Afterward, 3’ dTMP adapters were ligated to the 3’ dAMP library fragments. The quality of the barcoded libraries was validated using the Agilent Bioanalyzer. The DNA 1000 Reagents were used to quantify the library sizes and confirm the absence of primer dimers. Libraries were quantified using a KAPA Universal Library Quantification Kit (Roche), and library concentrations were adjusted for library size. Libraries were sequenced on an Illumina NextSeq 550 in the Rapid Run mode using 150 ntsingle end read sequencing .

treatment_protocol: to knockdown of PfGCN5, aTc was removed from culture for 48h

value: whole organism

tag: Stage

value: knockdown S

value: without aTc


title: Tumor_Th17_4

source_name: Tumor from B16F10 bearing mouse

value: Tumor


title: Synchronized culture - sample 2h30_11_S24_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 2h30_11_S24_R1_001


title: patch-seq, virus-infected, replicate 106

description:
Library name: 5_1C9
SMART-seq3

value: shNC

value: patch-seq, virus-infected


title: Synchronized culture - sample 2h30_3_S17_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 2h30_3_S17_R1_001


title: -aTc TetR-PfGCN::GFP S rep2

description:
Library name: Sample 23
RNA-seq


title: LN_NT_1

value: Lymph Node


title: Tumor_Th17_3


title: -aTc TetR-PfGCN::GFP S rep1

description:
Library name: Sample 22
RNA-seq


title: patch-seq, virus-infected, replicate 105

description:
Library name: 5_1C8
SMART-seq3


title: +aTc TetR-PfGCN::GFP S rep3

description:
Library name: Sample 21
RNA-seq

value: control S

value: with aTc


title: Synchronized culture - sample 2h30_1_S16_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 2h30_1_S16_R1_001


title: patch-seq, virus-infected, replicate 103

description:
Library name: 5_1C12
SMART-seq3


title: Tumor_Th17_2


title: Synchronized culture - sample 2h30_6_S20_R1_001

description: Library name: RNA-seq of Saccharolobus islandicus synchronized culture - sample 2h30_6_S20_R1_001


title: +aTc TetR-PfGCN::GFP S rep2

description:
Library name: Sample 20
RNA-seq


title: HEK293FT, Rest, CLIP, replicate 2

city: Baton Rouge

first: Anastasios

middle: A.

last: Vourekas

state: LA

address: 202 life sciences building

institute: Louisiana State University

data_processing:
sequence reads were trimmed for adapter sequence/ low quality sequences using cutadapt version 4.1 with python 3.9.13 with the options -n 1 -e 0.15.
Trimmed sequence reads were mapped to hg38 using STAR aligner version 2.7.0d and UCSC gene transfer format for annotations.
Read counts table extraction using CLIPSEQTOOLS with the option count_reads_on_genic_elements.
Normalization and other data processing for the count reads tables were performed using custom python scripts which can be found in the following GitHub page: https://github.com/Abdelmonsif/DDX3X.
Assembly: hg38
Supplementary files format and content: Tab-delimited file containing raw counts for each sample
Supplementary files format and content: Tab-delimited file containing TPM values for each sample

growth_protocol: Human embryonic  kidney  were maintained in DMEM supplemented with 10% defined FBS, 1X Glutamax, 1X MEM non-essential amino acids,   and 1 mM sodium Pyruvate in humidified atmosphere with 5% CO2  at 37C.

extract_protocol:
Cells were grown to ~80% confluency and treated with control (DMSO) or Thapsigargin (400 nM) containing full medium to induce ER stress. The cells where then collected by trypsinization and kept in ice-cold HBSS during UV crosslinking (254 nm, 3x400 mJ/cm2). For the IP step our own custom rabbit polyclonal DDX3X antibody was used. The rest of the CLIP-Seq procedure was performed as previously described (Vourekas and Mourelatos, 2014).
RNA  libraries  for RNA-seq were prepared using Illumina Stranded mRNAs prep Ligation Reference Guide, Document # 1000000124518 V03 protocol without changes.

treatment_protocol: No treatment

value: Human embryonic kidney

value: Wt

value: DMSO


title: HEK293FT, Rest, CLIP, replicate 1


title: patch-seq, virus-infected, replicate 102

description:
Library name: 5_1C11
SMART-seq3

value: dlPFC

value: tissue


title: Tumor_Th17_1


title: patch-seq, virus-infected, replicate 101

description:
Library name: 5_1C10
SMART-seq3

value: organotypic dlPFC slice cells


title: Tumor_NT_3

value: NT


title: -aTc TetR-PfGCN::GFP LT rep3

description:
Library name: Sample 18
RNA-seq

value: Late trophozoite (LT) stage

value: knockdown LT


title: Tumor_NT_4


title: Group 3 innate lymphoid cell, wildtype ILC3s rep1, scRNAseq

city: hangzhou

first: lie

last: wang

state: zhejiang

address: Zijingang Campus, Zhejiang University，Yuhangtang Road 866

department: immunology

institute: zhejiang universiry

description: BD Rhapsody

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
The FASTQ files were processed using the BD Rhapsody Targeted analysis pipeline v1.9.1 on the Seven Bridges platform (https://www.sevenbridges.com).
First of all, read pairs with low mean base quality scores (less than 20) were removed. The filtered R1 reads were analyzed to identify the cell label sequences and unique molecular identifiers(UMIs). R2 reads were aligned to the mice reference genome(GRCm38) using Bowtie2. Valid reads with the same cell label, the same UMI sequence, and the same gene were collapsed into a single raw molecule. Recursive substation error correction (RSEC) and distribution-based error correction (DBEC) algorithms were applied to correct sequencing and PCR errors of raw UMI counts. The final single-cell expression matrices containing DBEC-adjusted molecules were used for downstream analysis.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Csv files include readcount values for each Sample with different sample tag

source_name: small intestine

extract_protocol:
Small intestinal ILC3s were sorted from siLP of IRF4flox/floxRorccre mice and control C57BL/6 mice(6-8 weeks-old) . All samples were uniformly resuscitated and washed twice by PBS (with 0.1% BSA), then the cells were 1 ml stain buffer (with 0.1% BSA) and counted. The viability of cells in all samples was assessed >80%.
Cells for all samples were labeled with sample tags (BD Mouse Single-Cell Multiplexing Kit, USA), counted, and multiplexed, ready for single-cell capture. Single-cell capture and cDNA synthesis were performed by the BD Rhapsody Single-Cell Analysis System (BD, USA), according to the manufacturer's instructions.
scRNA-seq (BD Rhapsody)

value: small intestine

value: Group 3 innate lymphoid cell

value: C57BL/6 mice

tag: age

value: 6-8 weeks-old

tag: sample tag

value: sample tag 5

tag: index

value: i7    GCTACGCT        i5 TATAGCCT


title: patch-seq, virus-infected, replicate 100

description:
Library name: 5_1B9
SMART-seq3

value: lentivirus infected

value: patch-seq, virus-infected


title: +aTc TetR-PfGCN::GFP S rep1

description:
Library name: Sample 19
RNA-seq

value: whole organism

value: Schizont (S) stage

value: control S

value: with aTc


title: Group 3 innate lymphoid cell, wildtype ILC3s rep2, scRNAseq

description: BD Rhapsody

value: sample tag 8

value: i7  GCTACGCT        i5    TATAGCCT


title: Tumor_NT_2

value: Tumor

value: NT


title: -aTc TetR-PfGCN::GFP LT rep2

description:
Library name: Sample 17
RNA-seq

value: Late trophozoite (LT) stage

value: knockdown LT

value: without aTc


title: Group 3 innate lymphoid cell, IRF4-deficient  ILC3s rep2, scRNAseq

description: BD Rhapsody

value: small intestine

value: Group 3 innate lymphoid cell

value: sample tag 9

value: i7    AAGAGGCA     i5    TATAGCCT


title: -aTc TetR-PfGCN::GFP LT rep1

description:
Library name: Sample 16
RNA-seq


title: Tumor_NT_1


title: GCGR-L24 PDX brain, terminal tumour, Section 2

city: London

first: Simona

last: Parrinello

address: 72 Huntley Street

country: United Kingdom

institute: UCL Cancer Institute

description: Fresh frozen spatial transcriptomic sequencing

data_processing:
Reads from PDX experiments were aligned to reference genomes GRCh38-2020-A (human) and mm10-2020-A (mouse) using10x Genomics Space Ranger 2.0.1. To assign reads to either species, they were mapped three times: i) to the human genome, ii) to the mouse genome, iii) to a combination of both genomes. Reads mapping consistently to a single species using this procedure were selected and remapped to the combined genome as in point iii) to form the final dataset. Reads from normal mouse brain were filtered as above and remapped to mouse genome for downstream analysis.
Assembly: GRCh38-2020-A; mm10-2020-A
Supplementary files format and content: *tar.gz: output from spaceranger
Library strategy: Spatial transcriptomics

organism: Homo sapiens/Mus musculus xenograft

source_name: Brain

growth_protocol: Human glioblastoma PDX cell lines were implanted into the striatum of 8-12 week NOD.CB17-Prkdcscid/NCrCrl mice.

extract_protocol:
Fresh frozen tissue were OCT embedded and 10mm sections cut on a cryostat onto 10xGenomics Visium Spatial Gene Expression Slides
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent Kit according to manufacturer's instructions

treatment_protocol: Brains were collected when mice showed evidence of disease, snap frozen in methylbutane cooled in a bath of dry ice and liquid nitrogen.

value: Brain

tag: model

value: GCGR-L24 PDX brain xenograft

tag: tumour stage

value: Terminal


title: patch-seq, virus-infected, replicate 99

description:
Library name: 5_1B8
SMART-seq3

tag: tissue

value: dlPFC

value: tissue

value: organotypic dlPFC slice cells

value: lentivirus infected

value: patch-seq, virus-infected


title: patch-seq, virus-infected, replicate 98

description:
Library name: 5_1B7
SMART-seq3

tag: cell type


title: Group 3 innate lymphoid cell, IRF4-deficient  ILC3s rep1, scRNAseq

description: BD Rhapsody

value: 6-8 weeks-old

value: sample tag 7

value: i7  CGAGGCTG       i5TATAGCCT


title: patch-seq, virus-infected, replicate 104

description:
Library name: 5_1C7
SMART-seq3

tag: genotype


title: +aTc TetR-PfGCN::GFP LT rep3

description:
Library name: Sample 15
RNA-seq

value: whole organism

value: Late trophozoite (LT) stage

value: control LT

value: with aTc


title: GCGR-L24 PDX brain, terminal tumour, Section 1


title: patch-seq, virus-infected, replicate 97

description:
Library name: 5_1B12
SMART-seq3

value: shNC


title: Wild type bulk 2

data_processing:
Reads were pre-processed and mapped to the mm10-2020-A mouse genome using 10x Genomics Cell Ranger 7.0.1. The tdTomato sequence, expressed by transformed cells, was added to the reference genome.
Assembly: mm10
Supplementary files format and content: *.tar.gz: output from Cell Ranger 7.0.1

extract_protocol:
Brains were collected into ice-cold HBSS media and dissected into 1mm coronal sections using a brain matrix (WPI, RBMS200C). Tumour regions were dissected out and mechanically dissociated into small pieces. Cells were isolated by papain dissociation.
RNA libraries prepared using Chromium Next GEM Chip G Single Cell Kit (10x genomics; 1000127) and sequenced on Nova Seq X Plus PE 150.

value: Wild type (C57BL/6NCrl)


title: GBM2 PDX brain, mid-point of disease, Section 2

value: Brain

value: GBM2 PDX brain xenograft

value: Mid-point of disease


title: +aTc TetR-PfGCN::GFP LT rep2

description:
Library name: Sample 14
RNA-seq


title: Wild type bulk 1


title: patch-seq, virus-infected, replicate 96

description:
Library name: 5_1B11
SMART-seq3

value: dlPFC


title: GBM2 PDX brain, mid-point of disease, Section 1


title: +aTc TetR-PfGCN::GFP LT rep1

description:
Library name: Sample 13
RNA-seq


title: Sarm1-/- bulk 3


title: patch-seq, virus-infected, replicate 95

description:
Library name: 5_1B10
SMART-seq3

value: tissue


title: GCGR-L22 PDX brain, mid-point of disease, Section 2

value: GCGR-L22 PDX brain xenograft


title: -aTc TetR-PfGCN::GFP ET rep3

description:
Library name: Sample 12
RNA-seq

value: Early trophozoite (ET) stage

value: knockdown ET

value: without aTc


title: -aTc TetR-PfGCN::GFP ET rep2

description:
Library name: Sample 11
RNA-seq


title: Sarm1-/- bulk 2


title: GCGR-L22 PDX brain, mid-point of disease, Section 1


title: patch-seq, virus-infected, replicate 93

description:
Library name: 5_1A8
SMART-seq3

value: organotypic dlPFC slice cells

value: lentivirus infected

value: patch-seq, virus-infected


title: Sarm1-/- bulk 1


title: -aTc TetR-PfGCN::GFP ET rep1

description:
Library name: Sample 10
RNA-seq

value: whole organism


title: GL23E PDX brain, early tumour, Section 2

description:
Library name: GL23E-2
Fresh frozen spatial transcriptomic sequencing

data_processing:
Reads from PDX experiments were aligned to reference genomes GRCh38-2020-A (human) and mm10-2020-A (mouse) using10x Genomics Space Ranger 2.0.1. To assign reads to either species, they were mapped three times: i) to the human genome, ii) to the mouse genome, iii) to a combination of both genomes. Reads mapping consistently to a single species using this procedure were selected and remapped to the combined genome as in point iii) to form the final dataset. Reads from normal mouse brain were filtered as above and remapped to mouse genome for downstream analysis.
Assembly: GRCh38-2020-A; mm10-2020-A
Supplementary files format and content: *tar.gz: output from spaceranger
Library strategy: Spatial Transcriptomics

organism:
Homo sapiens
Mus musculus

value: GL23E PDX brain xenograft

value: Early


title: GCGR-E20 PDX brain, terminal tumour, Section 2

value: GCGR-E20 PDX brain xenograft

value: Terminal


title: GCGR-E20 PDX brain, terminal tumour, Section 1

value: Brain


title: +aTc TetR-PfGCN::GFP ET rep3

description:
Library name: Sample 9
RNA-seq

value: control ET

value: with aTc


title: patch-seq, virus-infected, replicate 92

description:
Library name: 5_1A7
SMART-seq3

value: dlPFC


title: GL23E PDX brain, early tumour, Section 1

description:
Library name: GL23E-1
Fresh frozen spatial transcriptomic sequencing


title: +aTc TetR-PfGCN::GFP ET rep2

description:
Library name: Sample 8
RNA-seq


title: GCGR-L1 PDX brain, terminal tumour, Section 2

value: GCGR-L1 PDX brain xenograft


title: patch-seq, virus-infected, replicate 90

description:
Library name: 5_1A11
SMART-seq3

value: tissue


title: patch-seq, virus-infected, replicate 91

description:
Library name: 5_1A12
SMART-seq3


title: +aTc TetR-PfGCN::GFP ET rep1

description:
Library name: Sample 7
RNA-seq

value: Early trophozoite (ET) stage


title: GCGR-L1 PDX brain, terminal tumour, Section 1


title: GCGR-L24E PDX brain, early tumour, Section 2

description:
Library name: GCGR-L24E-2
Fresh frozen spatial transcriptomic sequencing

value: GCGR-L24E PDX brain xenograft


title: patch-seq, virus-infected, replicate 89

description:
Library name: 5_1A10
SMART-seq3

value: shNC


title: GCGR-L5 PDX brain, terminal tumour, Section 2

value: GCGR-L5 PDX brain xenograft


title: -aTc TetR-PfGCN::GFP Ring rep3

description:
Library name: Sample 6
RNA-seq

value: Ring (R) stage

value: knockdown Ring

value: without aTc


title: GCGR-L24E PDX brain, early tumour, Section 1

description:
Library name: GCGR-L24E-1
Fresh frozen spatial transcriptomic sequencing


title: patch-seq, virus-infected, replicate 88

description:
Library name: 1_3D10
SMART-seq3

value: organotypic dlPFC slice cells

value: lentivirus infected

value: patch-seq, virus-infected


title: GCGR-L5E PDX brain,early tumour, Section 2

description:
Library name: GCGR-L5E-2
Fresh frozen spatial transcriptomic sequencing

value: GCGR-L5E PDX brain xenograft

value: Early


title: GCGR-L5 PDX brain, terminal tumour, Section 1

value: Brain

value: Terminal


title: GCGR-E43E PDX brain, early tumour, Section 2

description:
Library name: GCGR-E43E-2
Fresh frozen spatial transcriptomic sequencing

value: GCGR-E43E PDX brain xenograft


title: MP317 fibroid/leiomyoma

city: Grand Rapids

first: Jose

middle: M

last: Teixeira

state: MI

address: 400 Monroe Ave NW

department: Ob/Gyn

institute: Michigan State University

data_processing:
HiC reads were aligned with BWA
ATAC-seq reads were aligned with MACS2
Assembly: HiC reads were aligned to GRCh38
Assembly: ATAC-seq reads were aligned to GRCh38
Supplementary files format and content: Processed data files for HiC include HiCExplorer feature matrix files (.h5).
Supplementary files format and content: Processed data files for ATAC-seq are peak calls (*.*broadPeak) using  MACS2

source_name: uterus

extract_protocol:
Chromatin was prepared from flash frozen tissue samples using Corces et al doi.org/10.1038/nmeth.4396 methods.
HiC libraries were made with a kit from Arima; ATAC libraries were made using Corces et al doi.org/10.1038/nmeth.4396 methods.

value: uterus

tag: patient id

value: fibroid smooth muscle

tag: fibroid subtype

value: MED12 mutant

tag: biological replicate

value: Not applicable


title: GCGR-L21 PDX brain, terminal tumour, Section 1

value: GCGR-L21 PDX brain xenograft


title: -aTc TetR-PfGCN::GFP Ring rep1

description:
Library name: Sample 4
RNA-seq

value: whole organism

tag: treatment


title: MP317 matched myometrium

value: myometrial smooth muscle


title: +aTc TetR-PfGCN::GFP Ring rep3

description:
Library name: Sample 3
RNA-seq

value: Ring (R) stage

value: control Ring

value: with aTc


title: GCGR-L21 PDX brain, terminal tumour, Section 2


title: GCGR-E43E PDX brain, early tumour, Section 1

description:
Library name: GCGR-E43E-1
Fresh frozen spatial transcriptomic sequencing


title: -aTc TetR-PfGCN::GFP Ring rep2

description:
Library name: Sample 5
RNA-seq

value: knockdown Ring

value: without aTc


title: GCGR-L5E PDX brain, early tumour, Section 1

description:
Library name: GCGR-L5E-1
Fresh frozen spatial transcriptomic sequencing

value: GCGR-L5E PDX brain xenograft


title: TNF alpha and IFN gamma priming cainine stem cell derive extracellular vesicle 3

city: Chuncheon si

first: JuHyun

last: AN

address: 1 Kangwondaehak-gil

country: South Korea

institute: Kangwon National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to cfa (mirbase) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: cfa
Supplementary files format and content: tab-delimited text files include read count values for each Sample

organism: Canis lupus familiaris

source_name: adipose tissue

growth_protocol: To summarize briefly, the canine adipose-derived mesenchymal stem cells (cASCs) were seeded in 6-well plates at a density of 5 × 105 cells per well and cultured in Dulbecco’s modified Eagle’s medium with 4.5 g/L glucose (DMEM; PAN-Biotech, Aidenbach, Germany) supplemented with 10% Exo-free fetal bovine serum (FBS; PAN-Biotech) and 1% penicillin-streptomycin (PS; PAN-Biotech). After 6 hours, the cells were stimulated for 24 hours with TNF-α (20 ng/mL; PROSPEC, Ness Ziona, Israel) and IFN-γ (20 ng/mL; Kingfisher Biotech, Saint Paul, MN). Then, the conditioned media in the 6-well plate was discarded and washed three times with DPBS (PAN-Biotech). To isolate EVs, cASCs were cultured for 48 h in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 5% exosome-depleted fetal bovine serum (FBS; Thermo Fisher Scientific, MA, USA). Following incubation, the medium from each cultured cASC sample was harvested and centrifuged at 100 × g for 5 min. Then, to exclude cells and cellular debris, each supernatant was transferred to a fresh tube and ExoQuick-CG Exosome Precipitation Solution (System Biosciences, CA, USA) was added at a 3:1 ratio of supernatant to ExoQuick-CG Exosome Precipitation Solution. After incubation in the refrigerator for 12 hours, the ExoQuick-CG/supernatant mixture was centrifuged at 1500 × g for 30 minutes. After centrifugation, exosomes were identified as white pellets, and these exosomes were used in experiments.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). Total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext Multiplex Small RNA Library Prep kit (New England BioLabs, Inc., USA) according to the manufacturer’ instructions.

value: adipose tissue

tag: cell line

value: primary cell

value: NF alpha and IFN gamma priming


title: TNF alpha and IFN gamma priming cainine stem cell derive extracellular vesicle 2

treatment_protocol: canine adipose-derived mesenchymal stem cells (cASCs) were seeded in 6-well plates at a density of 5 × 105 cells per well and cultured in Dulbecco’s modified Eagle’s medium with 4.5 g/L glucose (DMEM; PAN-Biotech, Aidenbach, Germany) supplemented with 10% Exo-free fetal bovine serum (FBS; PAN-Biotech) and 1% penicillin-streptomycin (PS; PAN-Biotech). After 6 hours, the cells were stimulated for 24 hours with TNF-α (20 ng/mL; PROSPEC, Ness Ziona, Israel) and IFN-γ (20 ng/mL; Kingfisher Biotech, Saint Paul, MN). Then, the conditioned media in the 6-well plate was discarded and washed three times with DPBS (PAN-Biotech).


title: Hela-ORF3-3

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

description: Library name: Hela-ORF3-3

data_processing:
Raw data were trimmed to 50 bp and mapped to the human genome (hg19) using TopHat (V2.1.1) with default parameters. Only uniquely mapped reads were kept for downstream analysis. Gene counts were generated using HTSeq-count (v 0.9.1). For each sample, the gene count matrices were merged together and then the "edgeR" package in Bioconductor was used to perform differentially expressed genes analysis.
Assembly: hg19
Supplementary files format and content: txt

source_name: HeLa

growth_protocol: To culture HeLa cells, DMEM media supplemented with 10% fetal bovine serum (FBS) were employed, maintained at 37°C in an atmosphere containing 5% CO2 (v/v).

extract_protocol:
Total RNA was extracted from GFP and pORF3 OE HeLa cells using the RNA Isolation Kit (Yeasen), following the manufacturer’s protocol.
10 ng of total RNA was then subjected to cDNA synthesis and amplification using the Smart-seq2 method as described previously (Picelli et al., 2013). Sequencing libraries were constructed from 500 pg of amplified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) according to the manufacturer’s instructions. Libraries were sequenced on the Illumina HiSeq X Ten platform to generate 150 bp paired-end reads.

treatment_protocol: HeLa with stable expression of GFP and pORF3s were obtained through transduction with a lentiviral vector, pBobi, which was selected using puromycin at a concentration of 1 μg/mL for 48 h.

value: HeLa

value: wild type

value: pORF3 OE


title: GCGR-E43 PDX brain, terminal tumour, Section 1

value: Brain

value: GCGR-E43 PDX brain xenograft

value: Terminal


title: +aTc TetR-PfGCN::GFP Ring rep2

description:
Library name: Sample 2
RNA-seq

value: whole organism


title: +aTc TetR-PfGCN::GFP Ring rep1

description:
Library name: Sample 1
RNA-seq


title: Hela-ORF3-2

description: Library name: Hela-ORF3-2


title: patch-seq, virus-infected, replicate 94

description:
Library name: 5_1A9
SMART-seq3

data_processing:
snATAC/RNA-seq: The 10x Multiome ATAC(snATAC-seq) + Gene Expression(snRNA-seq) dataset was processed using the Cell Ranger ARC pipeline. To analyze the macaque data, we used the Cell Ranger ARC mkref to create a rheMac10 reference. Subsequently, we performed a quality check on the output of the Cell Ranger ARC pipeline, and then used it for downstream analysis.
SMART-seq:The SMART-seq3 RNA-seq reads from human were aligned to reference genome GRCh38 and the reads from rhesus macaque were aligned to reference genome rheMac10. Trim Galore was used for the adaptor trimming. We used STAR (v2.7.2b) (69) in two pass Mode for the alignment and removed PCR duplicates. STAR quantMode was used for gene counts on uniquely aligned reads, and the intergenic regions were excluded.
Assembly: rheMac10; GRCh38
Supplementary files format and content: snATAC-seq: fragments files are generated from Cell Ranger ARC pipeline. ; snRNA-seq: barcodes, features and matrix files are generated from Cell Ranger ARC pipeline. SMART-seq3: "AcuteRhesusPatchseq.csv" and "OrganotypicCHD8Patchseq.csv" are normalized gene expression data files.

extract_protocol:
Macaque brain specimens were collected from postconceptional day (PCD) 87 to PCD155. All experiments using non-human primates were carried out in accordance with a protocol approved by the University of Wisconsin’s Institutional Animal Care and Use Committee and NIH guidelines.
snMultiomes:The libraries were constructed in accordance with the guidelines provided in the "Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide" (10x Genomics, CG000338); SMART-seq3: follow the protocol according to publication "Single-cell RNA counting at allele and isoform resolution using Smart-seq3" (PMID: 32518404).

value: dlPFC

value: tissue

value: organotypic dlPFC slice cells

value: lentivirus infected

tag: batch

value: patch-seq, virus-infected


title: CFUE_Control_input_rep2

city: zhengzhou

first: Hengchao

last: Zhang

state: Henan

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

institute: zzu

description:
Library name: m6A_CFUE_Control_input_rep2
RNA methylation

data_processing:
For RNA-seq data analysis, raw sequencing data were filtered by fastp (0.23.4), transcript-level expression were quantified using Kallisto (v0.48.0) with the mouse reference genome (mm10), and then merged to gene-level by R package tximport. Differential expression analysis was performed by DESeq2 (v2_1.44.0) for pairwise comparisons, with the cutoff of a fold change of ≥ 1.5, adjusted P of< 0.05, and ≥ 1 transcript per million (TPM) at least in one group. Principal component analysis (PCA) was done on log-transformed normalized counts in gene expression analysis. GO enrichment analyses were applied by Metascape. GO terms and pathways with a q-value of < 0.001 were considered significant.m6A-seq:raw sequencing data from all input and immunoprecipitated (IP) samples were processed by fastp, Kallisto and tximport to quantify the gene-level abundance. To evaluate the relative m6A level of each gene, fold-change between IP and input sample read counts was calculated by DESeq2, representing m6A enrichment level. High-confidence m6A-tagged genes were identified using the following criteria: TPM > 1 in input samples, log2(fold-change) for IP/input > 0 with adjusted p< 0.05.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Tab-delimited text file includes TPM values for each Sample

source_name: Bone marrow

extract_protocol: Mouse erythroid progenitor cells and proerythroblasts were sorted, collected, and washed twice with PBS, then amplified by the Smart-Seq2 method. An Oligo-dT primer was used in the reverse transcription reaction for first-strand cDNA synthesis, followed by PCR amplification to enrich the cDNA and a magbeads purification step to clean up the product.  Next, the cDNA was randomly fragmented by ultrasonic waves prior to Illumina library preparation. After library preparation, PerkinElmer LabChip® GX Touch and Step OnePlus™ Real-Time PCR System were introduced for library quality inspection. Qualified libraries were then loaded on Illumina Hiseq platform for PE150 sequencing.For m6A-seq, m6A immunoprecipitation was performed according to the standard protocol. The cDNA was fragmented to ~300 bp using Tn5 transposase and processed using the TruePrep DNA Library Prep Kit V2 (Vazyme, TD501). Final libraries were amplified with the Tn5 adaptor and 3' primer (AATGATACGGCGACCACCGAGATCTACACTAGATCGCTCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGTAATACGACTCACTATA) and sequenced as 150-bp paired-end reads on an Illumina HiSeq X Ten platform.

value: Bone marrow

value: Erythroid progenitor cells


title: Hela-ORF3-1

description: Library name: Hela-ORF3-1


title: GL23 PDX brain, terminal tumour, Section 2

value: GL23 PDX brain xenograft


title: GL23 PDX brain, terminal tumour, Section 1


title: Naïve canine stem cell derived extracellular vesicle 3

value: adipose tissue

value: primary cell

value: canine adipose-derived mesenchymal stem cells (cASCs)

value: Naïve


title: Hela-GFP-3

description: Library name: Hela-GFP-3

value: HeLa

value: wild type

value: GFP OE


title: Naïve canine stem cell derived extracellular vesicle 2


title: CFUE_Control_input_rep1

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: m6A_CFUE_Control_input_rep1
RNA methylation


title: CFUE_Control_IP_rep2

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: m6A_CFUE_Control_IP_rep2
RNA methylation


title: GCGR-E43 PDX brain, terminal tumour, Section 2

value: Brain

value: GCGR-E43 PDX brain xenograft

value: Terminal


title: Hela-GFP-2

description: Library name: Hela-GFP-2


title: GCGR-L15 PDX brain, terminal tumour, Section 2

value: GCGR-L15 PDX brain xenograft


title: GCGR-L15 PDX brain, terminal tumour, Section 1


title: Hela-GFP-1

description: Library name: Hela-GFP-1


title: Naïve canine stem cell derived extracellular vesicle 1


title: WT organoid Rep 4

status: Public on Jun 08 2025

first: Nathaniel

last: Hyams

address: 68 President St

department: Bioengineering

institute: Clemson University

description: Library name: WT_org_4

data_processing:
RNA STAR (v.2.7.11) was used to align FASTQ files to the hg38 genome. FastQC (v.0.74) was used for quality control.
SAM-to-BAM (v.2.1.2) was used to generate .bam and .bai files.
FeatureCounts (v.2.1.1) was used to generate tab delimited files of raw counts.
DESeq2 (v.1.46.0) within R (4.4.1) was used for downstream processing and analysis.
Assembly: hg38
Supplementary files format and content: comma separated spreadsheet includes raw gene counts for each sample, tab delimited text file includes metadata information

growth_protocol: For both lines, iPSCs were maintained in mTeSR1 medium (Stemcell) and passaged with Versene (Gibco) every 3-4 days. iPSC-CMs were maintained in RPMI (Gibco) with B27 supplemented (Gibco). iPSC-ECFs were maintained in FibroGro (Sigma-Aldrich). iPSC-ECs were maintained in EGM2 (Promocell). Organoids were cultured in a mixed medium of DMEM/F12 (Gibco), EGM2 (Promocell), FGM3 (Promocell), and FBS (HyClone)

extract_protocol:
total RNA was harvested from each cell type/cell line upon confluency. Between 750,000 and 1,000,000 cells were collected to be used for each replicate (n = 4 for each cell type/line). Organoids were fabricated at 6,000 total cells/organoid, with 120 organoids used for RNA collection for each replicate.
All cells were checked for viability and sent to NovoGene for library preparation

treatment_protocol: Both wild type and hypoimmune lines were handled in the same manner.

value: Cardiac Organoid


title: WT organoid Rep 2

description: Library name: WT_org_2


title: WT organoid Rep 3

description: Library name: WT_org_3


title: DM-MuSC from patient sDM3, Differentiation day 3

city: Leuven

first: Wilhelm

last: Bouchereau

email: wilhelm.bouchereau@kuleuven.be, patrick.lomonte@univ-lyon1.fr, benedicte.chazaud@inserm.fr, armelle.corpet@univ-lyon1.fr

state: Vlaams brabant

address: ON4 - Herestraat 49 PB 804

department: Stamcelinstituut Leuven

country: Belgium

institute: KU-Leuven

description:
Library name: CRD_DM3P5
in H33_diff_DBA_peakAnno.csv: DM3

data_processing:
Sequencing was performed on a DNBSEQ Technology platform.
CUT&RUN paired-end reads were aligned to the human genome (GRCh38) using Bowtie 2 (version 2.3.5.1 by Ben Langmead) with a default setting after removing adaptor sequences and low-quality reads by cutadapt (version 4.6).
Samtools (version 1.10) was used to generate bam files and quality controls were done using deepTools.
Normalisation factors were calculated using CUT&RUN greenlist following the protocol of (de Mello et al., 2024). We use the deepTools “bamCoverage” with option --scaleFactor to generate scaled bigwig tracks. Mean bigwig files were generated using WigToBigWig (version 2.9).
Peak calling was done using SEACR (Meers et al., 2019) with the following parameters : normalisation (non), peak calling (stringent), threshold (0.01). Peaks with less than 300 bp of distance were merged using bedtools.
R (version 4.4.1) with package DiffBind (version 3.14.0) were used to perform differential binding analysis.
Peak annotation was performed with CHIPseeker package (version 1.40.0) with a TSS range of a -500, 500 bp window.
Assembly: Human genome GRCh38
Supplementary files format and content: bigwig files for each sample and mean bigwig files for either HC or DM samples in either proliferating or differentiating conditions
Supplementary files format and content: bed files for each sample and consensus bed files for HC and DM samples in either proliferating or differentiating conditions
Library strategy: CUT&Run

source_name: skeletal muscle

growth_protocol: MuSCs derived from healthy controls were directly extracted by mechanical and enzymatic digestion from fresh muscle biopsies. After an expansion period, they were frozen and stored in liquid nitrogen until further use. After thawing, MuSCs were purified at the first passage of primary culture using anti-CD56 coated magnetic beads (Miltenyi Biotech 130-050-401) to obtain pure myogenic cell cultures as described previously (Gitiaux et al., 2018). Cell purity was checked by flow cytometry (BD FACSCanto II) using anti-CD56 antibodies (APC-conjugated anti-CD56 antibodies, BD Pharmingen #555518) and isotypic control (BD Pharmingen #555751). MuSCs were cultured in complete medium (Skeletal Muscle Cell Growth Medium #23060 Promocell, supplemented with Mix C-39365, Promocell), 10% of heat-inactivated Fetal Bovine Serum (FBS, Sigma-Aldrich) and 1% of Penicillin/streptomycin (Gibco, 14190169). Cells were passaged upon reaching 80% confluency using 0.05% trypsin-EDTA (Gibco, 25300-054) digestion then seeded back onto new supports.

extract_protocol:
Samples were processed with active motif CUT&RUN kit (Active motif, 53180) following manufacturer instructions with some modifications inspired from (Ding and Braun, 2023). 1 ug of anti-H3.3 antibody (Active motif, 91191) was used for CUT&RUN. DNA was purified by phenol-chloroform extraction before library preparation.
Library preparation was performed as in Drmanac R, et al., Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science. 2010 Jan 1;327(5961):78-81. doi: 10.1126/science.1181498.

treatment_protocol: Analysis of proliferation of MuSCs was performed as follows: MuSCs were seeded at 3000 cells/cm². The next day, medium was changed with fresh medium. 24 hours later, 50% of the medium was replaced with fresh medium. Analysis of differentiation capacities of MuSCs was performed as follows: cells were seeded in labtek at 1500 cells/cm2 in growth medium. The next day, medium was changed with differentiation medium consisting of skeletal muscle cell basal medium (Promocell, C-23260) supplemented with 10 μg/mL insulin (Sigma-Aldrich, I2643), FBS 0.5% and 1% of Penicillin/streptomycin. 50% of the medium was replaced with fresh medium with cytokines every day for 3 days.

value: skeletal muscle

value: Primary skeletal muscle stem cell derived from dermatomyositis patient

value: Differentiation day 3

tag: patient

tag: patient sex

value: F

tag: patient age_(in_years)

tag: greenlist normalization_factor


title: HC-MuSC from patient SK230, Differentiation day 3

description:
Library name: CRD_SK230P4
in H33_diff_DBA_peakAnno.csv: SK230

value: Primary skeletal muscle stem cell derived from healthy control patient


title: DM-MuSC from patient sDM6, Differentiation day 3

description:
Library name: CRD_DM6P4
in H33_diff_DBA_peakAnno.csv: DM6

value: M


title: DM-MuSC from patient sDM5, Differentiation day 3

description:
Library name: CRD_DM5P4
in H33_diff_DBA_peakAnno.csv: DM5


title: HC-MuSC from patient SK236, Differentiation day 3

description:
Library name: CRD_SK236P4
in H33_diff_DBA_peakAnno.csv: SK236


title: HC-MuSC from patient CT6, Differentiation day 3

description:
Library name: CRD_CT6P4
in H33_diff_DBA_peakAnno.csv: CT6


title: WT iPSC Rep 4

description: Library name: WT_iPSC_4

value: iPSC


title: TNF alpha and IFN gamma priming cainine stem cell derive extracellular vesicle 1

value: adipose tissue

value: primary cell

value: canine adipose-derived mesenchymal stem cells (cASCs)

value: NF alpha and IFN gamma priming


title: WT organoid Rep 1

description: Library name: WT_org_1


title: DM-MuSC from patient sDM3, Proliferation

description:
Library name: CR_DM3P4
in CR_H33_prolif_DBA_peakAnno.csv: DM3

value: Proliferation


title: DM-MuSC from patient sDM5, Proliferation

description:
Library name: CR_DM5P3
in CR_H33_prolif_DBA_peakAnno.csv: DM5


title: DM-MuSC from patient sDM1, Proliferation

description:
Library name: CR_DM1P3
in CR_H33_prolif_DBA_peakAnno.csv: DM1


title: WT iPSC Rep 3

description: Library name: WT_iPSC_3


title: HC-MuSC from patient CT7, Proliferation

description:
Library name: CR_CT7P5
in CR_H33_prolif_DBA_peakAnno.csv: CT7


title: WT iPSC Rep 2

description: Library name: WT_iPSC_2


title: WT iPSC Rep 1

description: Library name: WT_iPSC_1


title: WT iPC Rep 4

description: Library name: WT_iPC_4

value: Pericyte


title: HC-MuSC from patient CT6, Proliferation

description:
Library name: CR_CT6P3
in CR_H33_prolif_DBA_peakAnno.csv: CT6


title: CFUE_Control_IP_rep1

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: m6A_CFUE_Control_IP_rep1
RNA methylation

value: Bone marrow

value: Erythroid progenitor cells


title: HC-MuSC from patient SK236, Proliferation

description:
Library name: CR_SK236P2
in CR_H33_prolif_DBA_peakAnno.csv: SK236


title: WT iPC Rep 1

description: Library name: WT_iPC_1


title: WT iPC Rep 2

description: Library name: WT_iPC_2


title: WT iECF Rep 4

description: Library name: WT_iECF_4

value: Cardiac Fibroblast


title: 4-cell-type organoid, rep 2

description:
Library name: L4
10X Genomics

data_processing:
Demultiplexing, barcoding, gene aggregation, and genome aligment were performed within the CellRanger (10X Genomics) software (v 8.0).
Matrix, barcode, and feature files were loaded into python (v 3.10.2) using Scanpy (v 1.10.2), preprocessed, visualized, and packaged into an .h5ad object.
Assembly: hg38
Supplementary files format and content: Tab separated matrix files
Supplementary files format and content: .h5ad object (Python readable)

source_name: Cardiac Organoid

growth_protocol: Organoids were fabricated in a two-step process. First, hPSC-CMs were dissociated into single cells using TrypLE (Gibco, 1X). hPSC-CMs were counted and resuspended to a concentration of 4 mil cells/mL. CM spheroids were formed in low-adhesion agarose molds by seeding 4,200 CMs into each microwell, then cultured for 10 days. Following spheroid formation, sequential seeding was performed, seeding hPSC-cFBs, hPSC-ECs, and hPSC-PCs into micromolds, so as to create a 70/10/15/5 ratio, respectively.

extract_protocol:
After 5 days of culture, organoids were dissociated into single cells using TrypLE (Gibco, 1X) for 60 minutes. Single cells were then ready for library preparation.
Libraries were constructed according to the manufacturer's protocol (10X Genomics, Chromium 3' v3.1 Kit).

treatment_protocol: Organoids were cultured using a mixed media, consisting of 50% DMEM/F12 (Gibco), 30% FGM3 (Promocell), 15% EGM2 (Promocell), and 5% FBS (HyClone)

value: Cardiac Organoid

value: Cardiomyocyte, Cardiac Fibroblast, Endothelial Cell, Pericyte

tag: Sex

value: male

tag: condition

value: 10 day spheroid culture, 5 day organoid culture


title: 4-cell-type organoid, rep 1

description:
Library name: L3
10X Genomics


title: WT iECF Rep 2

description: Library name: WT_iECF_2


title: WT iECF Rep 1

description: Library name: WT_iECF_1


title: PaTu 8988T cells,shOFD1,rep3

city: Shanghai

first: Peng

last: Li

address: Chongqing nanlu 280

department: Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education

institute: Shanghai JiaoTong University School of Medicine

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter - Quality limit: 0.05).
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters - mismatch cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: Hg38
Supplementary files format and content: tab-delimited text file includes FPKM for each Sample

source_name: PaTu 8990T

growth_protocol: MIA PaCa-2,PANC-1,PaTu 8988T cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTer mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Samples were collected 72 hours after doxycycline-induced OFD1 knockdown in pancreatic cancer cell lines  MIA PaCa-2,PANC-1,PaTu 8988T. These cell lines were treated with doxycycline (Dox) to induce OFD1 knockdown, as well as a control group without treatment.

value: PaTu 8990T

value: pancreatic cancer cell line

value: doxycycline-induced OFD1 knockdown


title: PaTu 8988T cells,shOFD1,rep1

source_name: PaTu 8988T

value: PaTu 8988T


title: DM-MuSC from patient sDM6, Proliferation

description:
Library name: CR_DM6P3
in CR_H33_prolif_DBA_peakAnno.csv: DM6

value: skeletal muscle

value: Primary skeletal muscle stem cell derived from dermatomyositis patient

value: M


title: 3-cell-type organoid, rep 2

description:
Library name: L2
10X Genomics

value: Cardiomyocyte, Cardiac Fibroblast, Endothelial Cell


title: WT iECF Rep 3

description: Library name: WT_iECF_3


title: 3-cell-type organoid, rep 1

description:
Library name: L1
10X Genomics


title: PaTu 8988T cells,shOFD1,rep2

source_name: PaTu 8989T

value: PaTu 8989T


title: WT iEC Rep 3

description: Library name: WT_iEC_3

value: Endothelial Cell


title: PaTu 8988T cells,shControl,rep3

value: WT

value: no treatment


title: WT iEC Rep 1

description: Library name: WT_iEC_1


title: PaTu 8988T cells,shControl,rep2


title: WT iCM Rep 4

description: Library name: WT_iCM_4

value: Cardiomyocyte


title: PaTu 8988T cells,shControl,rep1


title: PANC-1 cells,shOFD1,rep3


title: WT iCM Rep 3

description: Library name: WT_iCM_3


title: PANC-1 cells,shOFD1,rep2


title: WT iPC Rep 3

description: Library name: WT_iPC_3

value: Pericyte


title: WT iCM Rep 2

description: Library name: WT_iCM_2


title: WT iCM Rep 1

description: Library name: WT_iCM_1


title: PANC-1 cells,shOFD1,rep1


title: PANC-1 cells,shControl,rep3


title: PANC-1 cells,shControl,rep2


title: PANC-1 cells,shControl,rep1


title: UDET organoid Rep 3

description: Library name: UDET_org_3

source_name: UDET (B2M KO/HLA-E KI)

value: UDET (B2M KO/HLA-E KI)

value: Cardiac Organoid


title: UDET organoid Rep 4

description: Library name: UDET_org_4


title: WT iEC Rep 4

description: Library name: WT_iEC_4


title: UDET organoid Rep 2

description: Library name: UDET_org_2


title: WT iEC Rep 2

description: Library name: WT_iEC_2


title: UDET iPSC Rep 4

description: Library name: UDET_iPSC_4

value: iPSC


title: UDET iPSC Rep 3

description: Library name: UDET_iPSC_3


title: MIA PaCa-2 cells,shOFD1,rep1

source_name: MIA PaCa-2

value: MIA PaCa-2


title: MIA PaCa-2 cells,shOFD1,rep2

value: pancreatic cancer cell line


title: MIA PaCa-2 cells,shControl,rep2


title: MIA PaCa-2 cells,shControl,rep1


title: UDET iPSC Rep 1

description: Library name: UDET_iPSC_1


title: UDET iPSC Rep 2

description: Library name: UDET_iPSC_2


title: UDET iPC Rep 3

description: Library name: UDET_iPC_3


title: UDET iPC Rep 4

description: Library name: UDET_iPC_4


title: Arabidopsis, ssrp1-2 H3.1-3×3Flag,Flag, 12DAG, Rep1,INPUT

city: Xianyang

first: Weiye

last: Qian

state: Shanxi

address: Yangling District

institute: State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F University

description: Library name: 12DAG_ssrp1-2 H3.1-3×3Flag_Flag_Rep1,INPUT

data_processing:
(1)Filter:ChIP-seq reads were trimmed using the fastp tool (version 0.23.4)  with a quality score threshold of >20 for the final base.Reads shorter than 35 bp after trimming were discarded.(2)Alignment:The clean reads were aligned to the TAIR 10 genome (https://www.arabidopsis.org/) using Bowtie2 and sorted and indexed using the samtools suite (version 1.17).(3)Remove: PCR duplicates were removed using Picard (version 3.0.0). (4)Callpeak:Peaks were identified using the “callpeak” function of MACS2 (version 2.2.6,). (5)Coverage tracks were calculated: normalizing using RPGC (effective genome size 119482912) –bin size 10, normalization method using RPGC reads per genome coverage), creating bigwig files.(6)Plot:The metagene results were drawn using deepTools(version 3.5.2).
Assembly: TAIR 10
Supplementary files format and content: BigWig files were generated using the Deeptools  (version 3.5.2).The BigWig files for making plot were  assessed by merging results from 'bigwigcompare' of two independent biological replicates, employing the 'mean' operation.

source_name: 12DAG seedling

growth_protocol: All the lines used in this article are in Columbia-0 background.Plants were grown under standard long day conditions and ~21°C unless stated differently.

extract_protocol:
1)Crosslink protein-DNA interactions with formaldehyde; 2) Fragment chromatin via sonication or enzymatic digestion; 3) Immunoprecipitate target protein-DNA complexes using specific antibodies; 4) Reverse crosslinking and purify DNA, followed by library construction for sequencing .
ChIP-Seq libraries were prepared using Ovation® Ultralow System V2 Library Preparation Kit (PART NO. 0344, 0344NB).

value: 12DAG seedling

tag: chip-antibody


title: UDET iPC Rep 2

description: Library name: UDET_iPC_2


title: MIA PaCa-2 cells,shOFD1,rep3

value: doxycycline-induced OFD1 knockdown


title: Arabidopsis, ssrp1-2 H3.3-3×3Flag,Flag, 12DAG, Rep2,INPUT

description: Library name: 12DAG_ssrp1-2 H3.3-3×3Flag_Flag_Rep2,INPUT


title: UDET iECF Rep 4

description: Library name: UDET_iECF_4

value: Cardiac Fibroblast


title: UDET iPC Rep 1

description: Library name: UDET_iPC_1


title: Arabidopsis, ssrp1-2 H3.3-3×3Flag,Flag, 12DAG, Rep1,INPUT

description: Library name: 12DAG_ssrp1-2 H3.3-3×3Flag_Flag_Rep1,INPUT


title: Arabidopsis, Columbia H3.1-3×3Flag,Flag, 12DAG, Rep2,INPUT

description: Library name: 12DAG_Columbia H3.1-3×3Flag_Flag_Rep2,INPUT


title: Arabidopsis, Columbia H3.3-3×3Flag,Flag, 12DAG, Rep2,INPUT

description: Library name: 12DAG_Columbia H3.3-3×3Flag_Flag_Rep2,INPUT


title: Arabidopsis, Columbia H3.3-3×3Flag,Flag, 12DAG, Rep1,INPUT

description: Library name: 12DAG_Columbia H3.3-3×3Flag_Flag_Rep1,INPUT


title: UDET iECF Rep 1

description: Library name: UDET_iECF_1


title: UDET iEC Rep 4

description: Library name: UDET_iEC_4


title: Arabidopsis, Columbia H3.1-3×3Flag,Flag, 12DAG, Rep1,INPUT

description: Library name: 12DAG_Columbia H3.1-3×3Flag_Flag_Rep1,INPUT


title: UDET iECF Rep 2

description: Library name: UDET_iECF_2


title: UDET organoid Rep 1

description: Library name: UDET_org_1


title: MIA PaCa-2 cells,shControl,rep3


title: UDET iEC Rep 3

description: Library name: UDET_iEC_3


title: Arabidopsis, h2az-5 ssrp1-2 SSRP1-3×HA,HA, 12DAG, Rep1

description: Library name: 12DAG_h2az-5 ssrp1-2  SSRP1-3×HA_HA_Rep1,ChIP

value: 88836(Thermo USA)


title: Arabidopsis, ssrp1-2 SSRP1-3×HA,HA, 12DAG, Rep2

description: Library name: 12DAG_ssrp1-2 ssrp1-3×HA_HA_Rep2,ChIP


title: UDET iEC Rep 1

description: Library name: UDET_iEC_1


title: Arabidopsis, ssrp1-2 H3.1-3×3Flag,Flag, 12DAG, Rep2,INPUT

description: Library name: 12DAG_ssrp1-2 H3.1-3×3Flag_Flag_Rep2,INPUT


title: UDET iEC Rep 2

description: Library name: UDET_iEC_2


title: Arabidopsis, h2az-5 ssrp1-2 SSRP1-3×HA,HA, 12DAG, Rep2

description: Library name: 12DAG_h2az-5 ssrp1-2  SSRP1-3×HA_HA_Rep2,ChIP


title: UDET iCM Rep 4

description: Library name: UDET_iCM_4


title: Arabidopsis, ssrp1-2 H3.1-3×3Flag,Flag, 12DAG, Rep1

description: Library name: 12DAG_ssrp1-2 H3.1-3×3Flag_Flag_Rep1,ChIP


title: UDET iCM Rep 2

description: Library name: UDET_iCM_2


title: UDET iCM Rep 3

description: Library name: UDET_iCM_3


title: Arabidopsis, ssrp1-2 H3.3-3×3Flag,Flag, 12DAG, Rep1

description: Library name: 12DAG_ssrp1-2 H3.3-3×3Flag_Flag_Rep1,ChIP


title: Arabidopsis, Columbia H3.1-3×3Flag,Flag, 12DAG, Rep1

description: Library name: 12DAG_Columbia H3.1-3×3Flag_Flag_Rep1,ChIP


title: Arabidopsis, ssrp1-2 H3.3-3×3Flag,Flag, 12DAG, Rep2

description: Library name: 12DAG_ssrp1-2 H3.3-3×3Flag_Flag_Rep2,ChIP


title: Arabidopsis, Columbia H3.1-3×3Flag,Flag, 12DAG, Rep2

description: Library name: 12DAG_Columbia H3.1-3×3Flag_Flag_Rep2,ChIP


title: UDET iECF Rep 3

description: Library name: UDET_iECF_3


title: B1_TG CCI-ION sample 1

city: Suzhou

first: Jin

last: Tao

state: Jiangsu

address: 199 Ren-Ai Road

department: Physiology and Neurobiology

institute: Soochow University

data_processing:
Illumina HiseqX system software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn6 whole genome using bowtie v1.1.1 with parameters -f -p 20
Use cutadapt (version 1.14) software to remove the connector sequence, fastx_ Toolkit (version 0.0.13) software for quality control of sequences, NGSQCToolkit (version 2.3.3) to filter out reads containing N bases, fastx_ The toolkit (version 0.0.13) to count the number of types of clean reads.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include TPM values for each Sample ...
Supplementary files format and content: Matrix table with raw mRNA counts for every mRNA and every sample

organism: Rattus norvegicus

source_name: trigeminal ganglion

extract_protocol:
Trigeminal ganglions were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A trigeminal neuropathic pain model was produced by CCI-ION. After anesthetization, the left ION was dissected near the infraorbital foramen using glass rods. Two loose ligatures (4-0 silk) were placed around the ION using fine forceps. The sham-operated rats received only unilateral nerve exposure using the same procedure without ligation.

tag: strain

value: Sprague-Dawley

value: trigeminal ganglion

tag: age

value: 8-10 weeks

value: CCI-ION-operation


title: A2_TG sham sample 2

tag: tissue

value: sham-operation


title: Arabidopsis, Columbia H3.3-3×3Flag,Flag, 12DAG, Rep1

description: Library name: 12DAG_Columbia H3.3-3×3Flag_Flag_Rep1,ChIP

tag: genotype


title: Arabidopsis, Columbia H3.3-3×3Flag,Flag, 12DAG, Rep2

description: Library name: 12DAG_Columbia H3.3-3×3Flag_Flag_Rep2,ChIP


title: Arabidopsis, spt16-2,H3K4me3, 12DAG, Rep2

description: Library name: 12DAG_spt16-2_H3K4me3_Rep2,ChIP

value: 04-745( Millipore USA)


title: Arabidopsis, spt16-2, 12DAG, , Rep3

description:
Library name: spt16-2_R3
Treatment

data_processing:
Paired-end reads were subjected to filtering and trimming using the fastp tool (version 0.23.4).The clean reads were aligned to the TAIR 10 genome (https://www.arabidopsis.org/) using HISAT2 (VERSION 2.2.1).Quantification was performed with Rsubread package (version 2.12.0) and normalized using TPM (Transcripts Per Kilobase of exon model per Million mapped reads).
Assembly: TAIR 10
Supplementary files format and content: Tab-delimited text includes raw counts for each sample.
Supplementary files format and content: Txt files include TPM values for each sample.

growth_protocol: Plants were grown on soil mixture in a growth chamber under long-day conditions at ~21°C.  seeds were stratified for 4 days at 4°C, and seedlings were harvested 12 days after germination.

extract_protocol:
total RNA was extracted by using RNA extraction  columns (Axygen, UE-MN-MS-RNA-250) following the manufacturer’s instructions.
RNA-Seq libraries  were constructed by BGI company.


title: Arabidopsis, ssrp1-2,H3K4me3, 12DAG, Rep2

description: Library name: 12DAG_ssrp1-2_H3K4me3_Rep2,ChIP


title: Arabidopsis, ssrp1-2 SSRP1-3×HA,HA, 12DAG, Rep1

description: Library name: 12DAG_ssrp1-2 ssrp1-3×HA_HA_Rep1,ChIP


title: Arabidopsis, nrpb2-3,H3K4me3, 12DAG, Rep2

description: Library name: 12DAG_nrpb2-3_H3K4me3_Rep2,ChIP


title: Arabidopsis, spt16-2, 12DAG, , Rep2

description:
Library name: spt16-2_R2
Treatment


title: Arabidopsis, Columbia,H3K4me3, 12DAG, Rep2

description: Library name: 12DAG_Columbia_H3K4me3_Rep2,ChIP


title: A1_TG sham sample 1


title: Arabidopsis, spt16-2, 12DAG, , Rep1

description:
Library name: spt16-2_R1
Treatment


title: Arabidopsis, ssrp1-2 H3.1-3×3Flag,Flag, 12DAG, Rep2

description: Library name: 12DAG_ssrp1-2 H3.1-3×3Flag_Flag_Rep2,ChIP


title: Arabidopsis, nrpb2-3 ssrp1-2 SSRP1-3×HA, HA,12DAG, Rep2

description: Library name: 12DAG_nrpb2-3 ssrp1-2 SSRP1-3×HA_HA_G1_Rep2,ChIP


title: UDET iCM Rep 1

description: Library name: UDET_iCM_1

tag: cell type

value: Cardiomyocyte


title: B3_TG CCI-ION sample 3


title: Arabidopsis, ssrp1-2, 12DAG, , Rep3

description:
Library name: ssrp1-2_R3
Treatment


title: B2_TG CCI-ION sample 2


title: Arabidopsis, ssrp1-2, 12DAG, , Rep2

description:
Library name: ssrp1-2_R2
Treatment


title: Arabidopsis, ssrp1-2,NRPB1, 12DAG, Rep2

description: Library name: 12DAG_ssrp1-2_NRPB1_Rep2,ChIP

value: E4646 (AbClonal China)


title: Arabidopsis, ssrp1-2, 12DAG, , Rep1

description:
Library name: ssrp1-2_R1
Treatment


title: A3_TG sham sample 3


title: Arabidopsis, nrpb2-3,NRPB1, 12DAG, Rep2

description: Library name: 12DAG_nrpb2-3_NRPB1_Rep2,ChIP


title: Chip 4, Barcode: D02266B1

city: St Lucia

first: Tori

middle: Jewel

last: Millsteed

state: QLD

address: 306 Carmody rd

department: Queensland Alliance for Agriculture and Food Innovation

country: Australia

institute: The University of Queensland

description:
Library name: D02266B1
Fresh frozen spatial tramscriptomics sample

data_processing:
Raw sequencing reads were processed using the SAW pipeline to generate FASTQ files and then GEF files
Spatial gene expression clusters and spatial expression of target genes were investigated and quantified using the Stereopy library
Assembly: IWGSC CS RefSeq v2.1
Supplementary files format and content: D02266B1_chip4.gef - Gene expression matrix with spatial data, Chip 4
Supplementary files format and content: D02266A4_chip1.gef - Gene expression matrix with spatial data, Chip 1
Supplementary files format and content: D02263D4_chip2.gef - Gene expression matrix with spatial data, Chip 2
Library strategy: Spatial Transcriptomics

organism: Triticum aestivum

source_name: seed

growth_protocol: Bobwhite SH98 26 seeds were germinated and grown in pots to 2.5 months

extract_protocol:
Fresh frozen seeds were embedded in OCT media and cut to 20μm by cryostat
Spatial transcriptomics was undertaking using STOmics scStereo-seq kit according to manafacturer instructions

treatment_protocol: Seeds were collected at 14 days after anthesis (DPA)

value: seed


title: Chip 2, Barcode: D02263D4

description:
Library name: D02263D4
Fresh frozen spatial tramscriptomics sample


title: Chip 1, Barcode: D02266A4

description:
Library name: D02266A4
Fresh frozen spatial tramscriptomics sample


title: Arabidopsis, nrpb2-3,NRPB1, 12DAG, Rep1

description: Library name: 12DAG_nrpb2-3_NRPB1_Rep1,ChIP


title: LFU mediated rejuvenated late passage HFF cells, rep 3

city: Galveston

first: Steven

middle: G

last: Widen

state: Texas

address: 301 University Blvd

department: BMB

institute: University of Texas Medical Branch

data_processing:
Base calling was using Illumina's bcl2fastq2-v2.20 converter
RNA-Seq reads were aligned to the human GRCh38  reference using the STAR software version 2.7.10a with the parameters recommended for the ENCODE consortium.
Human gene read counts were obtained from the STAR quantMode GeneCounts feature using the Gencode v41 annotation file.
Assembly: GRCh38
Supplementary files format and content: Tab delimited table of raw gene read counts per sample.

source_name: Foreskin fibroblast

extract_protocol:
Qiagen RNeasy Mini Kit. (Germantown, MD).
Poly-A plus RNA was enriched from ~0.1ug of total RNA and used to generate libraries using New England Biolabs NEBNext Ultra II Kit.

value: Foreskin fibroblast

tag: passage

value: Late passage

value: Male

value: Neonatal

value: LFU


title: Arabidopsis, nrpb2-3, 12DAG, , Rep3

description:
Library name: nrpb2-3_R3
Treatment

value: 12DAG seedling


title: Arabidopsis, Columbia,NRPB1, 12DAG, Rep2

description: Library name: 12DAG_Columbia_NRPB1_Rep2,ChIP


title: Arabidopsis, Columbia,NRPB1, 12DAG, Rep1

description: Library name: 12DAG_Columbia_NRPB1_Rep1,ChIP


title: LFU mediated rejuvenated late passage HFF cells, rep 2