title: Fish 4 Kidney, 1.5 month juvenile fish

city: Auckland

first: Alan

last: Davidson

address: 85 Park Road

department: Molecular Medicine and Pathology

country: New Zealand

institute: The University of Auckland

description: Library name: K2

data_processing:
Data was demultplexed, barcoded and gene counted using the Cell Ranger software (cellranger-6.0.1)
Assembly: GRCz11
Supplementary files format and content: rds files and comma-separated value files

molecule: nuclear RNA

organism: Danio rerio

extract_protocol:
Nuclei were isolated with Nuclei EZ Lysis buffer (NUC-101, Sigma) supplemented with protease inhibitor (5892791001, Sigma) and RNase inhibitors (N2615, Promega; AM2696, Life Technologies). Zebrafish brain, muscle and kidney tissue were dissected and quickly rinsed with ice-cold PBS before snap-froze. Samples were minced into <2-mm pieces with 500 µL of ice-cold NLB buffer (10 mL Nuclei EZ lysis buffer supplemented with 1 tablet of protease inhibitor and 10 µl of each RNase inhibitors) and incubated on ice for 5 min with an additional 500 µl of NLB. The tissue and NLB buffer mix was then transferred to the Dounce tissue grinder (D8938, Sigma), gently grind 30 times with Pestle A and 15 times with Pestle B. The homogenate was then incubated on ice for an additional 5 min. The homogenate was filtered through a mini-40-µm and a subsequent mini 20-µm cell strainer (43-10040-50 & 43-10020-50; PluriSelect) and then centrifuged at 500 x g for 5 min at 4°C. The pellet was resuspended and washed twice with 1 mL of NLB buffer to remove residue cytoplasmic RNAs. After another centrifugation, the nuclei pellet was resuspended in Nuclei Suspension Buffer (1XPBS, supplemented with 2% BSA and 2 µl Promega RNase inhibitor), filtered through a mini-10-µm cell strainer (43-10010-50, PluriSelect). Nuclei were counted on hemocytometers (KIMA211710, Vetriplast-10).
The quantified brain and muscle nuclei were pooled together in 1:2 ratio, kidney nuclei were processed on its own. The nuclei were partitioned into each droplet with a barcoded gel bead using the 10X Chromium instrument with the Chromium Single Cell 3′ Reagent Kit v.3.1 to generate transcriptome libraries.

value: Kidney


title: Mix4_0-001_R2_P2_F_pool1

status: Public on Jun 30 2025

type: SRA

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

library_source: other

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

molecule: other

organism: Homo sapiens

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

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

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

tag: cell line

tag: plate

tag: chemical

value: Mix 4

tag: dose


title: TDP43-FL, DMSO, 24hr, replicate 4

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

country: USA

institute: Denali Therapeutics

library_source: transcriptomic

data_processing:
Sequencing adapters were trimmed from the raw reads with skewer. Reads were aligned to the human genome version GRCh38_p126. A STAR index (version 2.7.1a) was built with the –sjdbOverhang=50 argument. Splice junctions from Gencode gene models (release M28) were provided via the –sjdbGTFfile argument. STAR alignments were generated with the following parameters: –outFilterType BySJout, –quantMode TranscriptomeSAM, –outFilterIntronMotifs RemoveNoncanonicalUnannotated, –outSAMstrandField intronMotif, –outSAMattributes NH HI AS nM MD XS and –outSAMunmapped Within. Alignments were obtained with the following parameters: –readFilesCommand zcat –outFilterType BySJout –outFilterMultimapNmax 20 –alignSJoverhangMin 8 –alignSJDBoverhangMin 1 –outFilterMismatchNmax 999 –outFilterMismatchNoverLmax 0.6 –alignIntronMin 20 –alignIntronMax 1000000 –alignMatesGapMax 1000000 –quantMode GeneCounts –outSAMunmapped Within –outSAMattributes NH HI AS nM MD XS –outSAMstrandField intronMotif –outSAMtype BAM SortedByCoordinate –outBAMcompression 6. Alignments sharing the same UMI and genomic coordinate were deduplicated using the collapse_UMI_bam tool (Lexogen). The raw gene expression matrix was constructed from the 'forward' column of STAR's ReadsPerGene.out.tab output files using R. Gene symbols and biotype information were extracted from the Gencode GTF file. To calculate normalized counts per million (CPM) TMM normalization was applied across all genes annotated as protein_coding with the edgeR R package.
Assembly: GRCh38
Supplementary files format and content: File raw_and_normalized_counts.xlsx is a microsoft excel file with three worksheets: 1. sample information 2. raw count table 3. normalized count table (log2 counts per million)

molecule: polyA RNA

growth_protocol: Lentiviruses encoding G3BP1-mCherry in a pLVX-CMV-IRES-Hygro vector (Clontech) and GFP-tagged RBPs [GFP-TDP-43(WT), GFP-TDP-43(86-414), GFP-TDP-43(86-414, M337V) in a pLVX-TetOne_IRES_Puro vector (Clontech) were first expressed in HEK293T-17 cells to produce virus using Lenti-x Single Shot (ClonTech, #631275). H4 cells, a human neuroglioma cell line, (ATCC HTB-148) were transduced with these viruses under the selection of hygromycin B (Invitrogen, #10687010) and puromycin (Gibco, #A1113803) to generate stable cell clones. All inducible cell lines were grown in DMEM (Gibco, #11965-092), supplemented with 10% FBS (Clontech, #631106) and 1X sodium pyruvate (Gibco, #11360-070), 1µg/mL puromycin and 150 µg/mL hygromycin B at 37°C in 5% CO2.

extract_protocol:
Total RNA was harvested from cells using the RNeasy Micro Kit (Qiagen), following the manufacturer’s protocol. RNA integrity (RIN) and concentration were measured by High Sensitivity RNA Screen Tape Analysis (Agilent) on a 4200 TapeStation System (Agilent).
RNA-Seq libraries were generated using the QuantSeq 3’ mRNA-seq Library Prep Kit FWD for Illumina (Lexogen A01173) with high quality total RNA (RINe>8) as input template.  Briefly, total RNA was primed with oligo(dT) for reverse transcription, followed by RNA removal.  Lexogen’s UMI Second Strand Synthesis Module was added to introduce unique molecular identifiers to identify and remove PCR duplicates.  Amplified cDNA was purified using magnetic beads followed by 12 cycles of PCR with dual indexes and PCR purification.  Library quantity and quality were assessed with High Sensitivity D1000 ScreenTape (Agilent 5067-5584).  Libraries were pooled in equimolar ratios and the sequencing pool was purified with magnetic beads to remove residual adaptor dimers.  Sequencing reads were generated on an Illumina NovaSeq 6000 instrument (75 bp single end) by SeqMatic (Fremont, CA, USA).

treatment_protocol: Protein expression was induced in each cell line with 1 μg/mL doxycycline (Clontech, #NC0424034) and the cells were grown for 8 or 24 h. Afterwards, the cells were treated with either 1 μM DNL343 or DMSO for 2.5 h at 37°C in 5% CO2.

tag: cell type

value: neuroglioma cells

tag: genotype

tag: treatment

value: DMSO

tag: batch

tag: induction duration

value: 24 hours


title: 2nd_Batch_cell-Hashing-5

city: GOSSELIES

first: Abdulkader

last: AZOUZ

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

description: Library name: Sample21

library_source: transcriptomic single cell

data_processing:
RNA data were filtered by mouse sample with the following thresholds: number of genes expressed > 1000 (between 800 and 1200 depending on the mouse sample), fraction of mitochondrial content < 20%, and total counts per cell > 1800 (between 1600 and 2400). The new single-cell gene expression profiles were normalized with the NormalizeData function using the "LogNormalize" normalization method and were scaled with the ScaleData function from Seurat package.
Assembly: mm10
Supplementary files format and content: tsv.gz count and mtrix files

organism: Mus musculus

source_name: CD11b and/or CD11c

extract_protocol:
Tumors were perfused with a solution containing DNase I and Liberase , cut in smaller pieces and incubated for 30 min at 37°C. The suspension was washed with RPMI, 5% FBS and 2 mM ethylenediaminetetraacetic acid , mashed and filtered through a 70 μm cell strainer, twice. Lymph nodes were mashed, filtered and washed in HBSS. Spleen were mashed and red blood cells were lysed by ACK lysing buffer (Ammonium-Chloride-Potassium, home-made). Suspension was neutralized by adding RPMI, 5% FBS and filtered before further manipulation.
Librairies were performed using Reagent Kits v3.1 (Dual Index) with surface protein from 10X according to manufactur's instruction

value: CD11b and/or CD11c


title: 2nd_Batch_cell-Hashing-3

description: Library name: Sample19


title: Mix3_50_R2_P2_F_pool1

value: Mix 3


title: GFP, DMSO, 24hr, replicate 4

value: GFP


title: Fish 4 Brain and Muscle, 1.5 month juvenile fish

description: Library name: BM2

source_name: Brain and Muscle

tag: tissue

value: Brain and Muscle


title: 2nd_Batch_cell-Hashing-2

description: Library name: Sample18


title: Mix3_10_R2_P2_F_pool1


title: TDP43-CYTO, DNL343, 8hr, replicate 3

value: 8 hours


title: CLS 24h-2

city: Chengdu

first: Ben

last: Ma

address: Huimin Street 211

country: China

institute: Sichuan Agricultural University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit. 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost 2 insertion cost 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using Cl _C genomic benchwork
Assembly: Stuberosum_686_v6.1
Supplementary files format and content: Excel file includes fpkm for each Sample

molecule: total RNA

organism: Solanum tuberosum

source_name: Potato leaf

growth_protocol: After being disinfected with carbendazim for 15 minutes, CLS and WYY varieties were planted in a greenhouse under 24℃ light culture for 16h and 20℃ dark culture for 8h.

extract_protocol:
RNA was extracted from the leaves of CLS and WYY by standard extraction methods.
The starting RNA for library construction is total RNA, which is enriched with polyA tailed mRNA using Oligo (dT) magnetic beads. Subsequently, the resulting mRNA is randomly interrupted with divalent cations in the Fragmentation Buffer. Using fragmented mRNA as a template and random oligonucleotides as primers, the first strand of cDNA was synthesized in the M-MuLV reverse transcriptase system. Subsequently, the RNA strand was degraded using RNaseH, and the second strand of cDNA was synthesized using dNTPs as raw material in the DNA polymerase I system. The purified double stranded cDNA undergoes end repair, A-tailed addition, and sequencing connections. cDNA of approximately 370-420 bp was screened using AMPure XP beans, amplified by PCR, and the PCR product was purified again using AMPure XP beans, ultimately obtaining a library.

treatment_protocol: Under normal growth conditions, samples were taken after 0h and 24h infection with Phytophthora infestation.

value: Potato leaf

tag: cultivar

value: CLS

value: Potato leaf cells

value: WT

value: 24h after infection with Phytophthora infestans


title: 2nd_Batch_cell-Hashing-1

description: Library name: Sample17


title: Mix3_5_R2_P2_F_pool1


title: Fish 2 Kidney, 1.5 month juvenile fish

description: Library name: S4

source_name: Kidney


title: 2nd_Batch_GEX-8

description: Library name: Sample16


title: L7295

city: Leiden, The Netherlands

first: Siddh

last: van Oost

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: Leiden University Medical Center

description: Library name: 104320-001-020

data_processing:
Raw RNA-seq data was processed by the RNA-seq BioWDL pipeline using default settings, developed by the SASC (https://biowdl.github.io/, LUMC, Leiden, the Netherlands)
Reads were aligned against hg38 with STAR and expression quantification was performed using HTseq-count
Assembly: hg38
Supplementary files format and content: Tab-delimited tsv file with raw counts for each sample

source_name: USTS

extract_protocol:
RNA was isolated from tissue sections (thickness = 20 µm) in TRIzol (15596018, Ambion) according to manufacturer’s instructions. RNA purification was performed using RNaesy mini kit (74104, Qaigen) and included DNAse treatment according to manufacturer’s instructions
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the samples.

value: USTS

tag: tumor grade

value: high

tag: tumor depth

value: deep


title: WYY 0h-1

value: WYY

value: 0h after infection with Phytophthora infestans


title: Fish 2 Brain and Muscle, 1.5 month juvenile fish

description: Library name: S3


title: TDP43-FL, DNL343, 8hr, replicate 3

value: neuroglioma cells


title: Mix3_1_R2_P2_F_pool1


title: 2nd_Batch_GEX-7

description: Library name: Sample15


title: GFP, DNL343, 8hr, replicate 3


title: Fish 1 Kidney, 1.5 month juvenile fish

description: Library name: S2

value: Kidney


title: Mix3_0-5_R2_P2_F_pool1


title: TDP43-CYTO, DMSO, 8hr, replicate 3

value: DMSO


title: 2nd_Batch_GEX-6

description: Library name: Sample14

value: CD11b and/or CD11c


title: Fish 1 Brain and Muscle, 1.5 month juvenile fish

description: Library name: S1


title: TDP43-FL, DMSO, 8hr, replicate 3


title: Mix3_0-1_R2_P2_F_pool1

value: Mix 3


title: Fish 3 Brain and Muscle, 1.5 month juvenile fish

description: Library name: BM1

value: Brain and Muscle


title: GFP, DMSO, 8hr, replicate 3

value: GFP

value: 8 hours


title: 2nd_Batch_GEX-5

description: Library name: Sample13


title: TDP43-CYTO, DNL343, 24hr, replicate 3

value: 24 hours


title: Arabidopsis thaliana smxl678 mutant RNA-seq sample replicate 3

city: Changsha

first: Ruifeng

last: Yao

state: Hunan

address: TianMa Road #27

department: College of Biology

institute: Hunan University

data_processing:
RNA extraction: total RNA was extracted using TRizol (Thermo Fisher Scientific, 15596018)
Library construction: NEBNext UltraTM RNA Library Prep Kit (NEB #E7490)
Library purification: AMPure XP system beads
Sequencing: Illumina Novaseq 6000, PE150
Assembly: Arabidopsis reference genome TAIR10
Supplementary files format and content: text file for each sample

organism: Arabidopsis thaliana

source_name: whole plant

growth_protocol: The seeds were surface-sterilized and sown on standard half-strength Murashige and Skoog (½MS) medium (0.8% agar, pH 5.8, without sucrose) plates and kept at 4 °C in the dark for 3 days before being transferred to long photoperiod conditions (16 h light/8 h dark)

extract_protocol:
Approximately 100-mg whole seedlings were harvested and frozen in liquid nitrogen as independent biological samples. Total RNAs were isolated using a TRIzol kit (Invitrogen)
Illumina sequencing libraries were constructed and sequenced using the Illumina system.

value: whole plant


title: Mix3_0-01_R2_P2_F_pool1


title: 2nd_Batch_GEX-4

description: Library name: Sample12


title: Arabidopsis thaliana smxl678 mutant RNA-seq sample replicate 2


title: Mix3_0-001_R2_P2_F_pool1


title: Mix2_50_R2_P2_F_pool1

value: Mix 2


title: Arabidopsis thaliana smxl678 mutant RNA-seq sample replicate 1


title: Arabidopsis thaliana SMXL7d53 overexpression RNA-seq sample replicate 3


title: 2nd_Batch_GEX-2

description: Library name: Sample10


title: TDP43-CYTO, DMSO, 24hr, replicate 3


title: Arabidopsis thaliana SMXL7d53 overexpression RNA-seq sample replicate 2


title: 1st_Batch_cell-Hashing-D

description: Library name: Sample8


title: 2nd_Batch_GEX-1

description: Library name: Sample9


title: 2nd_Batch_GEX-3

description: Library name: Sample11


title: 1st_Batch_cell-Hashing-C

description: Library name: Sample7


title: TDP43-FL, DMSO, 24hr, replicate 3


title: GFP, DMSO, 24hr, replicate 3


title: 1st_Batch_cell-Hashing-B

description: Library name: Sample6


title: GFP, DNL343, 24hr, replicate 3


title: TDP43-CYTO, DNL343, 8hr, replicate 2


title: Mix2_0-1_R2_P2_F_pool1


title: Mix2_5_R2_P2_F_pool1


title: Mix2_1_R2_P2_F_pool1


title: Arabidopsis thaliana SMXL7d53 overexpression RNA-seq sample replicate 1


title: Mix2_0-001_R2_P2_F_pool1


title: Arabidopsis thaliana wild-type RNA-seq sample replicate 3


title: 1st_Batch_GEX-C

description: Library name: Sample3


title: Mix2_0-5_R2_P2_F_pool1


title: Arabidopsis thaliana smxl678 mutant  Hi-C sample replicate 1

library_source: genomic

data_processing:
Library type: Normal Hi-C libraries
Library number: 6
Raw data size per library: 66 Gb
Sequencing platform: Illumina Novaseq PE150
Total raw data: 396 Gb raw data
Assembly: Arabidopsis reference genome TAIR10
Supplementary files format and content: bigWig for each sample

molecule: genomic DNA

extract_protocol:
1-3g 3-week-old seedlings were harvested and fixed with 20 ml 2% formaldehyde solution for 15 min in vacuum conditions at room temperature and quenched by adding 2.162 ml of 2.5 M glycine. Fixed samples were rinsed with water three times and homogenized with liquid nitrogen and resuspended in nuclei isolation buffer (0.25 M sucrose, 10 mM Tris-HCl pH 8.0, 10 mM MgCl2, 40% glycerol, 0.25% Triton X-100, 5 mM β-mercaptoethanol, 0.1 mM PMSF) and then filtered through two layers of miracloth
The nuclei were resuspended in 0.5% SDS, applied to permeabilize at 65 °C for 10 min. Then chromatin was digested with 400 units of MboI overnight at 37 °C with gentle rocking. MboI was denatured to cease activity. Digested chromatin underwent DNA end-repair with biotin-14-dCTP insertion followed by blunt-end ligation. After decrosslinking with proteinase K at 65 °C, DNA was purified using a phenol–chloroform extraction method. Biotin-14-dCTP was removed from non-ligated DNA fragment ends using T4 DNA polymerase. DNA was sheared to a range of 200–600 bp by sonication. Next, the fragments underwent end-repair and were pulled down by streptavidin C1 magnetic beads to enrich for fragments containing contact information. Fragment ends were then A-tailed, sequencing adapters were ligated and libraries were amplified by PCR for 12 cycles. Following purification, libraries were sequenced using an Illumina HiSeq X Ten platform with 2× 150 bp length reads.


title: GFP, DNL343, 8hr, replicate 2


title: Arabidopsis thaliana wild-type RNA-seq sample replicate 1


title: TDP43-CYTO, DMSO, 8hr, replicate 2


title: Mix2_0-01_R2_P2_F_pool1


title: 1st_Batch_GEX-D

description: Library name: Sample4


title: Arabidopsis thaliana wild-type RNA-seq sample replicate 2


title: TDP43-FL, DNL343, 8hr, replicate 2


title: Mix1_10_R2_P2_F_pool1

value: Mix 1


title: Arabidopsis thaliana smxl678 mutant  Hi-C sample replicate 2


title: Arabidopsis thaliana SMXL7d53 overexpression  Hi-C sample replicate 1


title: Mix1_50_R2_P2_F_pool1


title: Mix1_5_R2_P2_F_pool1


title: Mix2_10_R2_P2_F_pool1


title: 1st_Batch_GEX-A

description: Library name: Sample1


title: Arabidopsis thaliana wild-type Hi-C sample replicate 2


title: 1st_Batch_cell-Hashing-A

description: Library name: Sample5


title: Ctrl_CMO

city: San Francisco

first: Nathan

middle: A

last: Ewing-Crystal

state: CA

address: 513 Parnassus Ave, HSW12 Room 1201A

department: Laboratory Medicine

institute: University of California, San Francisco

description:
Library name: 1_Ctrl_CMO
10x Genomics snRNASeq (Gene Expression)

data_processing:
Sequencing data were aligned to mouse genome Grcm39 with CellRanger version 9.0.0 (10x Genomics).
Assembly: Grcm39
Supplementary files format and content: barcodes.tsv.gz: list of cell barcodes (provided for each barcode-multiplexed microanatomical region)
Supplementary files format and content: features.tsv.gz: list of gene IDs (provided for each barcode-multiplexed microanatomical region)
Supplementary files format and content: matrix.tsv.gz: gene expression count data in Matrix Market Exchange Format (provided for each barcode-multiplexed microanatomical region)
Supplementary files format and content: feature_reference.csv: Reference table linking barcodes (CMO) with subsamples (microanatomical regions) (provided for each region)

source_name: Brain

extract_protocol:
Immediately following euthanasia, mice were transcardially perfused (10mL DPBS), and brains were removed and placed in iMED+ (15mM HEPES and 0.6% glucose in HBSS with phenol red). Dura, lesion, and perilesional cortex were dissected and processed separately. Tissue from male and female mice within experimental conditions were combined. Tissue was minced for 10 minutes in 100mL of TST buffer (146 mM NaCl, 10 mM Tris-HCl pH 7.5, 1 mM CaCl2, 21 mM MgCl2, 0.03% Tween-20, and 0.01% BSA in nuclease-free water), followed by filtration (40mm), and washing with TST and ST buffer (146 mM NaCl, 10 mM Tris-HCl pH 7.5, 1 mM CaCl2, and 21 mM MgCl2). Samples were centrifuged (500g 10 minutes), resuspended (PBS/1% BSA/0.2UmL Protector RNAse inhibitor), filtered (35mm), and counted. A maximum of 2x10^6 nuclei were multiplexed and washed (CellPlex, 10X Genomics), per manufacturer’s instructions.  Immediately before sorting, multiplexed microanatomical regions (lesion, parenchyma, and dural meninges) from individual mice were combined at desired ratios (75% lesion, 25% parenchyma). Nuclei were subsequently sorted (FSC/SSC/DAPI). All samples were centrifuged (500g 15 minutes) and resuspended to a maximum of 16,500 nuclei in 50uL.
Up to 1.6 x 10^4 nuclei were loaded onto the Chromium Controller (10X Genomics). Chromium Single Cell 3’ v3.1 reagents were used for library preparation according to the manufacturer’s protocol.

value: Brain

tag: microanatomical region

tag: condition

value: PT injury

value: WT

tag: timepoint


title: Mix1_1_R2_P2_F_pool1


title: cKO_CMO

description:
Library name: 2_cKO_CMO
10x Genomics snRNASeq (Gene Expression)

value: Col1a2(creER); Cxcl12(flox)


title: TDP43-FL, DNL343, 24hr, replicate 3


title: GFP, DMSO, 8hr, replicate 2


title: Arabidopsis thaliana wild-type Hi-C sample replicate 1


title: 1st_Batch_GEX-B

description: Library name: Sample2


title: TDP43-CYTO, DNL343, 24hr, replicate 2


title: GFP, DNL343, 24hr, replicate 2


title: Mix1_0-1_R2_P2_F_pool1


title: DAP-seq_SMXL7_Col-0_2_IP_2

description: DAP-seq was performed by purified SMXL7 proteins incubated with prepared Col-0 gDNA library 8

data_processing:
DNA extraction and fragmentation: gDNA was extracted and sheared into fragments
Library construction: NEBNext DNA Library Prep Master Mix Set for Illumina (NEB, #E6040S)
Protein expression: SMXL7 was expressed in TnT SP6 High-Yield Wheat Germ Protein Expression System (L3260, Promega) and purified using Magne HaloTag Beads (G7281, Promega)
DNA-protein binding: purified proteins were incubated with DNA library in PBS at 4°C for 1.5h
DNA elution: bound DNA was eluted with 10 mM Tris-HCl (pH 8.5) at 98°C
Assembly: Arabidopsis reference genome TAIR10
Supplementary files format and content: bigWig for each sample
Library strategy: DAP-seq

extract_protocol:
Briefly, gDNA was extracted from 3-week-old wild-type seedlings and sheared into fragments
Then a gDNA DAP-seq library was prepared by attaching a short DNA sequencing adaptor to the purified and fragmented gDNA. The adapter sequences were truncated Illumina TruSeq adapters; the TruSeq Universal and Index adapters corresponded to the DAP-seq Adapter A and Adapter B. The DAP gDNA library was prepared using a kit from NEBNext® DNA Library Prep Master Mix Set for Illumina (NEB, #E6040S/L, Ipswich, MA, USA). Separately, the coding sequence of SMXL7 was cloned into pFN19K HaloTag® T7 SP6 Flexi® vector (Promega #G184A) with HaloTag fused in the N-terminus. The Halo-tagged SMXL7 expressed in a TnT SP6 High-Yield Wheat Germ Protein Expression System (L3260, Promega, Madison, WI, USA), and was purified using Magne HaloTag Beads (G7281, Promega). Subsequently, the purified proteins were incubated with 500 ng DNA library in 40 μL PBS (Phosphate Buffered Saline) buffer with slow rotation in a 4°C for 1.5 h, followed by washing away the unbound DNA fragments with PBS. 30 μL of 10 mM Tris–HCl (pH 8.5) buffer was added to the beads and incubated for 10 min at 98°C to elute the bound DNA fragments from the beads. The correct DAP-seq library concentration to achieve a specific read count was calculated on the basis of on library fragment size.


title: Ctrl_GEX

description:
Library name: 1_Ctrl_GEX
10x Genomics snRNASeq (Gene Expression)


title: TDP43-FL, DNL343, 24hr, replicate 2


title: Arabidopsis thaliana SMXL7d53 overexpression Hi-C sample replicate 2


title: Mix1_0-5_R2_P2_F_pool1


title: TDP43-FL, DMSO, 8hr, replicate 2


title: Mix1_0-01_R2_P2_F_pool1


title: DAP-seq_SMXL7_Col-0_2_IP_1

description: DAP-seq was performed by purified SMXL7 proteins incubated with prepared Col-0 gDNA library 7


title: TDP43-FL, DMSO, 24hr, replicate 2


title: Memory B Cells, Hashtag Oligos

city: Darlinghurst

first: Wunna

last: Kyaw

state: NSW

address: 384 Victoria St

country: Australia

institute: Garvan Institute of Medical Research

description:
Library name: MBC_HTO
Hashtag library: Read 1 contains UMI and cell barcode, Read 2 contains hashtag oligonucleotide reads.

data_processing:
For gene expression library, the binary base call (BCL) raw data from the sequencer were demultiplexed and converted to FASTQ format using Cell Ranger v6.0.1 (10x Genomics) mkfastq pipeline. For antibody-derived tag (ADT) and hashtag libraries, Illumina Conversion Software bcl2fastq was used to convert BCL file to FASTQ format. The Cell Ranger multi pipeline was used for alignment, filtering, barcode counting, and unique molecular identifier (UMI) counting from FASTQ files against mouse reference genome mm10-2020-A. The sequence of fluorescence reporters Tdtomato (tdTomato CDS-WPRE-bGH poly(A) signal) and cyan fluorescence protein (Cfp) genes were incorporated into the reference genome using Cell Ranger mkref to allow distinguish tdTomato-SWHEL B cells and cyan OT-II T cells from recipient mice cells. Intronic mapped reads were also included in Cell Ranger multi pipeline. The pipeline was executed on a high-performance cluster with a Linux 4.15.0-143-generic operating system.
Assembly: mm10-2020-A
Supplementary files format and content: Cellranger output files: matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz, and feature_reference.csv denoting sample names.
Library strategy: CITE-seq

molecule: protein

source_name: lymph node, spleen mixed sample

extract_protocol:
Cells were first incubated with Fc receptor blockers anti-CD16/CD32 mAb and labelled with HEL at 200 ng/ml in PBA, after which cells were washed three times with PBA. Cells were then stained with anti-B220 BV786, anti-CD4 PE-Cy7, anti-Vα2 TCR FITC, anti-Vβ5.1/5.2 TCR PerCP-Cy5.5 mAbs, as well as TotalSeq-A (anti-CD19, CD38, CCR6, CD4, CD45.1, CD45.2) and hashtag oligonucleotide antibodies. Cells from different organs/conditions were stained with different TotalSeq-A hashtag antibodies: dLN (hashtag 1), ndLN (hashtag 2), spleen (hashtag 3), naïve LN (hashtag 4), and naïve spleen (hashtag 6). After staining with mAbs, cells were washed three times with PBA and finally resuspended in 500μl PBA. DAPI was added to each sample just before sorting at a final concentration 0.1μg/ml. HEL-binding B cells and Vα2+ Vβ5.1/2+ cells were sorted into RPMI 1640 with 10% FBS.
The Garvan-Weizmann Centre for Cellular Genomics (GWCCG) performed the single-cell capture, library preparation, and sequencing as an in-house commercial service, using the Chromium Single-Cell v2 3’ Kits (10x Genomics). The libraries were sequenced on Illumina NovaSeq 6000 (NovaSeq Control Software v1.7.0 / Real Time Analysis v3.4.4) using NovaSeq S2 130 cycles kit (Illumina, 20497313 as follows: 28 bp (Read 1), 91 bp (Read 2) and 8 bp (Index)). The sequencing of the libraries was performed by the Ramaciotti Centre for Genomics.

treatment_protocol: For primary immunization, recipient mice were immunized subcutaneously with 10μg adjuvanted HEL-OVA on one side of the lower flank. For secondary immunization, >28 days after primary immunisation mice were reimmunized subcutaneously with 20μg adjuvanted HEL-OVA either on the same lower flank side or on the other side of the lower flank. HEL3X-OVA and HEL-gp61 were prepared and administered similarly. For PE immunization, PE (ProZyme RPE, Agilent) at 1mg/ml was mixed with equal volume of SAS. Mice were subcutaneously primed and boosted with 15μg and 30μg of adjuvanted PE, respectively.

value: lymph node, spleen mixed sample

value: Memory B Cells


title: Mix1_0-001_R2_P2_F_pool1


title: DAP-seq_SMXL7_Col-0_2_input_1

description: DAP-seq was performed by purified SMXL7 proteins incubated with prepared Col-0 gDNA library 5


title: Memory B Cells, CiteSeq

description:
Library name: MBC_CITE
ADT library: Read 1 contains UMI and cell barcode, Read 2 contains antibody derived tag reads


title: TDP43-CYTO, DMSO, 24hr, replicate 2

value: neuroglioma cells


title: PC_B_R1_P1_E_pool1

value: No cells; Brain positive control


title: GFP, DMSO, 24hr, replicate 2

value: DMSO


title: Memory B Cells, Gene Expression

description:
Library name: MBC_GE
Gene Expression (5' mRNA) library. Read 1 contains UMI and cell Barcode information, Read 2 contains transcript

data_processing:
For gene expression library, the binary base call (BCL) raw data from the sequencer were demultiplexed and converted to FASTQ format using Cell Ranger v6.0.1 (10x Genomics) mkfastq pipeline. For antibody-derived tag (ADT) and hashtag libraries, Illumina Conversion Software bcl2fastq was used to convert BCL file to FASTQ format. The Cell Ranger multi pipeline was used for alignment, filtering, barcode counting, and unique molecular identifier (UMI) counting from FASTQ files against mouse reference genome mm10-2020-A. The sequence of fluorescence reporters Tdtomato (tdTomato CDS-WPRE-bGH poly(A) signal) and cyan fluorescence protein (Cfp) genes were incorporated into the reference genome using Cell Ranger mkref to allow distinguish tdTomato-SWHEL B cells and cyan OT-II T cells from recipient mice cells. Intronic mapped reads were also included in Cell Ranger multi pipeline. The pipeline was executed on a high-performance cluster with a Linux 4.15.0-143-generic operating system.
Assembly: mm10-2020-A
Supplementary files format and content: Cellranger output files: matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz, and feature_reference.csv denoting sample names.


title: TDP43-CYTO, DNL343, 8hr, replicate 1


title: DAP-seq_SMXL7_Col-0_1_IP_2

description: DAP-seq was performed by purified SMXL7 proteins incubated with prepared Col-0 gDNA library 4


title: cKO_GEX

description:
Library name: 2_cKO_GEX
10x Genomics snRNASeq (Gene Expression)


title: PC_UH_R1_P1_E_pool1

value: No cells; Universal human positive control


title: TDP43-FL, DNL343, 8hr, replicate 1


title: DAP-seq_SMXL7_Col-0_1_IP_1

description: DAP-seq was performed by purified SMXL7 proteins incubated with prepared Col-0 gDNA library 3


title: Trem1 KO 24hr Transplant Cd45.1/2

city: Saint Louis

first: Daniel

last: Kreisel

state: MO

address: 425 S Euclid Ave

department: Department of Surgery

institute: Washington University School of Medicine

description:
Library name: Trem1 KO 24hr Transplant Cd45.1/2
Sequencing with antibodies targeted to CD45.1 and CD45.2

data_processing:
Alignment with Cell Ranger V3, aligned to mm10 transcriptome
QC and Filtering with Seurat V4
Unsupervised Clustering with Seurat V4
Assembly: mm10
Supplementary files format and content: Clustered and annotated data in R objects (.rds)

source_name: Heart

extract_protocol:
Transplanted hearts were collected, perfused, and enzymatically digested to a single cell supsension. Monocytes and macrophages were sorted via FACS.
Chromium Single Cell 3′ Library & Gel Bead Kit from 10X Genomics

value: Heart

value: Trem1 KO

value: syngeneic heart transplant


title: TMBPF_50_R1_P1_E_pool1

value: Tetramethyl bisphenol F


title: DAP-seq_SMXL7_Col-0_1_input_2

description: DAP-seq was performed by purified SMXL7 proteins incubated with prepared Col-0 gDNA library 2

value: whole plant


title: TDP43-CYTO, DMSO, 8hr, replicate 1

value: 8 hours


title: DAP-seq_SMXL7_Col-0_1_input_1

description: DAP-seq was performed by purified SMXL7 proteins incubated with prepared Col-0 gDNA library 1


title: TMBPF_5_R1_P1_E_pool1


title: Trem1 KO 24hr Transplant

description:
Library name: Trem1 KO 24hr Transplant
n/a


title: TMBPF_10_R1_P1_E_pool1


title: Control 24hr Transplant

description:
Library name: Control 24hr Transplant
n/a

value: Trem1 WT


title: DAP-seq_SMXL7_Col-0_2_input_2

description: DAP-seq was performed by purified SMXL7 proteins incubated with prepared Col-0 gDNA library 6


title: Control 24hr Transplant Cd45.1/2

description:
Library name: Control 24hr Transplant Cd45.1/2
Sequencing with antibodies targeted to CD45.1 and CD45.2


title: Wild type Arabidopsis H3K27me3 ChIP-seq IP

data_processing:
Sample fixation: cross-linked with 1% formaldehyde (sigma,47608)
DNA fragmentation: sheared to 100-400bp, 5% was taken as input
Library construction: IP DNA and input DNA were purified using QIAquick PCR Purification Kit (28106), then prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S)
Library quality control: quality assessment using DNA-based fluorometric assay and electrophoresis
Sequencing: Illumina Novaseq PE150
Assembly: Arabidopsis reference genome TAIR10
Supplementary files format and content: bigWig for each sample

extract_protocol:
3g 14-day-old plants were ground into fine powder in liquid nitrogen and suspended with 10 ml nuclei extraction buffer (10 mM Tris-HCl pH 8.0, 1 M sucrose, 5 mM KCl, 5 mM EDTA, 0.6% Triton X-100, 0.4 mM PMSF, and protease inhibitor cocktail). The homogenate was cross-linked with 1% formaldehyde for 15 min and stopped with 125 mM glycine. The extract was filtered through double layers of wet gauze and centrifuged at 1,500 g for 10 min at 4 °C. The nuclei pellet was washed 3 times with 10 ml nuclei extraction buffer. The pellet was resuspended in 0.2 ml nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS, and protease inhibitor cocktail) and sonicated for 3 times for 10 min, 30s on 30s off at high setting, and then diluted 10-fold to 2 ml with ChIP dilution buffer (1.1 % Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, and protease inhibitor cocktail).
Chromatin was immunoprecipitated with an antibody at 4 °C overnight with rotation. Each antibody, against H3 (Abcam,1:1,000) and H3K27me3 (Abcam, 07-,1:200), was bound to the pre-washed Dynabeads Protein G magnetic beads (50 μL) for 3 h at 4 °C with rotation. The beads were washed twice with each of the following solutions for 5 min at 4 °C: 1 mL of low-salt buffer, high-salt buffer, LiCl buffer and TE buffer. Protein complexes were eluted from beads with 400 µl of elution buffer (1% SDS and 0.1 M NaHCO3) at 65 °C for 10 min. The eluted chromatin was reverse crosslinked with 0.2 M NaCl at 65 °C overnight, and treated with Protease K at 50 °C for 1 h, and boiled for 10 min at 95 °C, then purified with phenol- chloroform. The enriched DNA was subjected to library construction and Illumina sequencing for ChIP–seq analysis.


title: TMBPF_1_R1_P1_E_pool1


title: Wild type Arabidopsis H3K27me3 ChIP-seq input


title: GFP, DMSO, 8hr, replicate 1

value: GFP


title: TDP43-FL, DMSO, 8hr, replicate 1


title: TMBPF_0-01_R1_P1_E_pool1


title: TDP43-CYTO, DNL343, 24hr, replicate 1

value: 24 hours


title: TMBPF_0-1_R1_P1_E_pool1


title: N2AInput_F2

city: Hangzhou

first: Xiang

last: Yuhang

address: Yuhang Tang street

description:
Library name: Sample 2
Cells overexpressing pFOXF1, infected with HSV-1 for 5 hours

data_processing:
Libraries were analyzed for size distribution by an Agilent 5400 system (Agilent, USA) and quantified by qPCR. The quantified libraries were pooled and sequenced on an Illumina Novaseq600 platform to obtain raw data with 150 bp paired-end reads. Reads containing adapter contamination, low-quality nucleotides and unrecognizable nucleotides were discarded to obtain clean reads using fastp (version 0.23.1). The 136 k bp genome of HSV-1 strain KOS (JQ673480.1) with one copy of the repeat sequences deleted was concatenated to the mouse reference genome (mm10 assembly version) resulting in a combined genome named mm10+KOSnorepeat. The clean reads were aligned to the mm10+KOSnorepeat genome using Bowtie2 (version 2.3.4.3) with default parameters. Then the virus and mouse reads were splited. DeepTools (verison 3.5.1) bamCoverage was used to calculate read coverages. PlotProfiles and ComputeMatrix were utilized to plot signals around the TSS. The peak calling algorithm MACS2 (version 2.2.7.1) was used to identify significant peaks representing DNA binding sites for mouse and virus separately. The peaks were annotated to known genomic features using ChIPseeker (version 1.32.1). Homer2 (version 4.11.1) findMotifsGenome.pl was used to identify enriched known and de novo motifs. Integrative Genomics Viewer (version 2.16.2) was used to visualize read coverages and identified peaks.
Assembly: mm10 and KOS
Supplementary files format and content: bigwig

extract_protocol:
Each immunoprecipitation reaction was conducted in ChIP dilution buffer for 3 h at 4 °C using 150 µg of chromatin and 40 µl FLAG Affinity Gels (catalogue no. F2426; Merck Millipore). After the gels were washed as above, the crosslinked DNA-protein complexes were eluted by incubation with 90 µg of 3XFlag peptide (catalogue no.P9801; Beyotime) at 4 °C for 1 h.
DNA libraries were constructed and sequenced by Tianjin Novogene Bioin_x0002_formatic Technology Co., Ltd. Briefly, an NEBNext® Ultra™ II DNA Library Prep kit (catalogue no. E7645L; NEB) was used for library preparation.

treatment_protocol: For infection, cells were infected with ICP0-null HSV-1 (strain 7134) for 5hpi (MOI = 5) before ChIP

value: Brain

value: Infect cells with HSV-1 virus for five hours


title: GFP, DNL343, 24hr, replicate 1


title: TDP43-FL, DNL343, 24hr, replicate 1


title: GFP, DNL343, 8hr, replicate 1


title: 44BPF_50_R1_P1_E_pool1

value: 4,4'-Bisphenol F


title: Wild type Arabidopsis H3 ChIP-seq input


title: N2AInput_F1

description:
Library name: Sample 1
Cells overexpressing pFOXF1, infected with HSV-1 for 5 hours


title: SMXL7d53 overexpression Arabidopsis H3K27me3 ChIP-seq IP


title: SMXL7d53 overexpression Arabidopsis H3K27me3 ChIP-seq input


title: TDP43-CYTO, DMSO, 24hr, replicate 1


title: SMXL7d53 overexpression Arabidopsis H3 ChIP-seq IP


title: N2ApFOXF1 1_ATAC

description:
Library name: Sample 3
Cells overexpressing pFOXF1, infected with HSV-1 for 3 hours

data_processing:
For 10X Genomics ATAC-seq library, we integrated the concatenated barcode at the beginning of the read name in the demultiplexed FASTQ using Drop-seq tools
snaptools was used to pre-process the 10X Genomics ATAC data. Demultiplexed sequencing reads are aligned to the mouse reference (mm10 genome) and HSV-1 reference (KOS genome)using bwa-mem.
Assembly: mm10 and KOS
Supplementary files format and content: bigwig

extract_protocol:
Genomic DNA  was extracted according to TruePrepTM DNA Library Prep Kit V2 for Illumina®（Vazyme TD501）
ATAC libraries were prepared for sequencing using TruePrepTM Index Kit V2 for Illumina® (Vazyme TD202)

treatment_protocol: For infection, cells were infected with ICP0-null HSV-1 (strain 7134) for 3hpi (MOI = 1) before ATAC


title: 44BPF_10_R1_P1_E_pool1


title: N2ApFOXF1 2_ATAC

description:
Library name: Sample 4
Cells overexpressing pFOXF1, infected with HSV-1 for 3 hours


title: TDP43-FL, DMSO, 24hr, replicate 1


title: 44BPF_5_R1_P1_E_pool1


title: N2ApcDNA 2_ATAC

description:
Library name: Sample 2
Cells overexpressing pcDNA, infected with HSV-1 for 3 hours


title: Wild type Arabidopsis H3 ChIP-seq IP


title: SMXL7d53 overexpression Arabidopsis H3 ChIP-seq input


title: N2AIP_F1

description:
Library name: Sample 3
Cells overexpressing pFOXF1, infected with HSV-1 for 5 hours


title: 44BPF_0-5_R1_P1_E_pool1


title: 44BPF_1_R1_P1_E_pool1


title: GFP, DMSO, 24hr, replicate 1


title: N2AIP_F2

description:
Library name: Sample 4
Cells overexpressing pFOXF1, infected with HSV-1 for 5 hours


title: N2ApcDNA 1_ATAC

description:
Library name: Sample 1
Cells overexpressing pcDNA, infected with HSV-1 for 3 hours


title: AC_pool2_RNA

city: URBANA

first: Ullas

middle: Valiya

last: Chembazhi

state: Illinois

address: 600 S Mathews Avenue

department: Biochemistry

institute: UIUC

data_processing:
demultiplexing, barcode processing and feature counting were performed using Cellranger and Cellranger-ARC
The data was integrated using the Seurat pipeline and batch-corrected using harmony. Seurat and Signac pipelines were used to perform dimensionality reduction, cluster determination and cell type annotation.
Assembly: hg38
Supplementary files format and content: Combined Seurat object with counts and metadata for all samples

source_name: Liver

extract_protocol:
Intact nuclei were isolated from human liver samples based on a protocol adapted from 10X genomics CG000375.  Briefly, frozen tissue was homogenized in a Dounce homogenizer with homogenization Buffer, filtered through a 15 μm strainer and resuspended in 1ml PBS + 1% BSA + 1U/μl RNase Inhibitor and used for library preparation.
Single-nuclei sequencing libraries for multi-omic profiling using scRNA-seq and scATAC-seq were prepared individually from pools of human liver samples from Normal individuals, AH patients and AC patients using the 10x Genomics Chromium Single Cell Kit and sequenced with Illumina NovaSeq 6000 on a SP/S4 flow cell to obtain 150bp paired reads.

value: Liver

tag: disease state

value: AC


title: 44BPF_0-1_R1_P1_E_pool1

tag: cell line


title: In vitro differentiated murine pathogenic TH17 cells treated with NorUDCA for 4 hours replicate 4

city: Vienna

first: Wilfried

last: Ellmeier

address: Lazarettgase 19

department: Institute of Immunology

country: Austria

institute: Medical University of Vienna

description:
Library name: Nor_4
Column name in rnaseq_deseq_global_counts_raw.tsv: Nor_4_S160528

data_processing:
Illumina NovaSeq Control Software (NCS) 1.8.1 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling was performed by the Illumina Real-Time Analysis (RTA) software 3.4.4.
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/epigen/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Spliced genome alignments to GRCm39 (UCSC Genome Browser mm39) and basic Gencode reference transcriptome vM35 (May 2024) with STAR 2.7.11b and options recommended by the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Differential expression modelling with Bioconductor 3.18 package DESeq2 1.40.2, running under R 4.3.3.
Assembly: UCSC mm39 based on GRCm39
Supplementary files format and content: Per gene and sample raw (integer) counts and DESeq2-calculated FPKMs in tab-separated value (TSV) format

source_name: Primary cell culture

growth_protocol: Primary mononuclear cells were isolated from peripheral lymph nodes and spleens of C57BL/6 mice and magnetically enriched for CD4+TNaïve cells using a Naïve CD4+T cell isolation kit (Miltenyi). The purity of the CD4+TNaïve cells was routinely >98% when assessed by flow cytometry. Approximately 0.3×106 CD4+TNaïve cells were stimulated in vitro with plate-bound αCD3 (clone 17A2; 1µg/ml) and αCD28 (clone 37.51, 3µg/ml) antibodies. For pathogenic TH17 conditions, T cells were cultured with the addition of IL6 (20ng/ml, Biolegend), IL1β (20ng/ml, Biolegend), IL23 (20ng/ml, Biolegend), αIFNγ (10μg/ml, BioxCell) and αIL4 (10μg/ml, Biolegend).

extract_protocol:
RNA was harvested using RNEASY mini kit (Qiagen). Around 250 nanogram total RNA were used for the construction of sequencing libraries.
The amount of total RNA was quantified using the Qubit 2.0 Fluorometric Quantitation assay (Thermo Fisher Scientific, Waltham, MA, USA) and the RNA integrity number (RIN) was determined using the 2100 Bioanalyzer High-Resolution Automated Electrophoresis instrument (Agilent, Santa Clara, CA, USA). RNA-seq libraries were prepared with the NEBNext UltraExpress® RNA Library Prep Kit (New England Biolabs, Inc., Ipswich, MA, USA). NGS library concentrations were quantified with the Qubit 2.0 assay and the size distribution was assessed using the 2100 Bioanalyzer instrument. Before sequencing, sample-specific NGS libraries were diluted and pooled in equimolar amounts.

treatment_protocol: To test the impact of NorUDCA differentiated pTH17 cell, culture medium was supplemented with or without NorUDCA (500μM). Concentrations of NorUDCA (500μM) for in vitro experiments were selected to mimic the in vivo serum bile acid level of mice on 0.5% (wt/wt) NorUDCA supplemented diet. Concentrations of NorUDCA selected for in vitro experiments were previously shown not to affect T cell viability.

value: Primary cell culture

value: WT

value: NorUDCA treatment (4 hours)


title: smxl678 mutant Arabidopsis H3K27me3 ChIP-seq input

value: smxl678 mutant


title: 44BPF_0-01_R1_P1_E_pool1

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

tag: plate


title: In vitro differentiated murine pathogenic TH17 cells treated with NorUDCA for 4 hours replicate 3

description:
Library name: Nor_3
Column name in rnaseq_deseq_global_counts_raw.tsv: Nor_3_S160527


title: AC_pool1_RNA


title: 44BPF_0-001_R1_P1_E_pool1

tag: chemical


title: smxl678 mutant Arabidopsis H3 ChIP-seq IP


title: In vitro differentiated murine pathogenic TH17 cells treated with NorUDCA for 4 hours replicate 2

description:
Library name: Nor_2
Column name in rnaseq_deseq_global_counts_raw.tsv: Nor_2_S160524


title: SAH_pool2_RNA

value: SAH


title: SAH_pool1_RNA


title: Normal_pool2_RNA

value: Normal


title: BPC_10_R1_P1_E_pool1

value: Bisphenol C

tag: dose


title: smxl678 mutant Arabidopsis H3K27me3 ChIP-seq IP

value: whole plant


title: Arabidopsis thaliana smxl678 mutant ATAC-seq sample replicate 2

data_processing:
Sequencing: Illumina Novaseq 6000, PE150
Nuclei isolation from frozen tissues; Sample preparation: Cell
Library construction: Tn5 transposition (40000 cells), MinElute PCR Purification
Library amplification: NEBNext High-Fidelity PCR Master Mix
Sequencing: Illumina Novaseq 6000, PE150
Assembly: Arabidopsis reference genome TAIR10
Supplementary files format and content: bigWig for each sample

extract_protocol:
The nuclei were resuspended and washed with Tris-Mg buffer (10 mM Tris-HCl, pH 8.0, 5 mM MgCl2), centrifuged using the same settings, and the supernatant removed, leaving ~10 μL in the tube. Chromatin was digested by Tn5-mediated tagmentation and adapter incorporation, according to the manufacturer’s protocol (Nextera DNA sample preparation kit; Illumina) at 37 °C for 30 min. The purified tagmented DNA underwent an initial amplification of 10 cycles as libraries. The quality of the libraries was assessed by a DNA-based fluorometric assay and by electrophoresis. The libraries subsequently sequenced using an Illumina NovaSeq 6000 paired-end reads of 2 × 50 bp.
The quality of the libraries was assessed by a DNA-based fluorometric assay and by electrophoresis. The libraries subsequently sequenced using an Illumina NovaSeq 6000 paired-end reads of 2 × 50 bp.

treatment_protocol: Briefly, 3 week old tissue was chopped on glass using a razor blade in 5 ml of ice-cold Lysis buffer (15 mM Tris-Cl pH 7.5, 0.5 mM spermine-4HCl, 80 mM KCl, 20 mM NaCl, 0.25 % Triton X-100, 5 mM β-mercaptoethanol), filtered through 40μM strainer (Falcon) into 5ml Sucrose buffer (20 mM Tris-Cl pH 8.0, 1.7M Sucrose, 5 mM MgCl2, 0.25 % Triton X-100, 2 mM EDTA, 5mM β-mercaptoethanol), and spun at 20,000xg, for 30 mins at 4oC. Pellets were resuspended in 1 ml of Lysis buffer and stained with DAPI (0.5 μg/ml final concentration) and 50,000 nuclei were collected by FACS into 0.5 ml of Lysis buffer.


title: Normal_pool1_RNA


title: In vitro differentiated murine pathogenic TH17 cells replicate 2

description:
Library name: Ctrl_2
Column name in rnaseq_deseq_global_counts_raw.tsv: Ctrl_2_S160522

tag: cell type

value: No treatment


title: BPC_1_R1_P1_E_pool1

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


title: Arabidopsis thaliana smxl678 mutant ATAC-seq sample replicate 1

tag: genotype


title: Arabidopsis thaliana SMXL7d53 overexpression ATAC-seq sample replicate 1

tag: treatment


title: In vitro differentiated murine pathogenic TH17 cells treated with NorUDCA for 4 hours replicate 1

description:
Library name: Nor_1
Column name in rnaseq_deseq_global_counts_raw.tsv: Nor_1_S160523


title: BPC_5_R1_P1_E_pool1


title: BPC_0-5_R1_P1_E_pool1


title: Arabidopsis thaliana SMXL7d53 overexpression ATAC-seq sample replicate 2


title: In vitro differentiated murine pathogenic TH17 cells replicate 1

description:
Library name: Ctrl_1
Column name in rnaseq_deseq_global_counts_raw.tsv: Ctrl_1_S160521


title: SAH_pool2_ATAC

library_source: genomic single cell


title: BPC_0-1_R1_P1_E_pool1


title: Arabidopsis thaliana wild-type ATAC-seq sample replicate 1


title: BPC_0-01_R1_P1_E_pool1


title: smxl678 mutant Arabidopsis H3 ChIP-seq input


title: CL2

city: 成都

first: ping

last: he

address: 17 Renmin South Road, Wuhou District, Chengdu

institute: sichuan university

description:
Library name: CL2
The frozen sections on Visium Spatial Gene Expression Slides were fixed with pre-chilled methanol and stained with H&E, following the Tissue Optimization Guide (CG000238 Rev A, 10X Genomics). Sections were then permeabilized using Permeabilization Enzyme for the optimal duration, after which cDNAs were reverse transcribed, spatially barcoded, and amplified for 10 cycles. Standard spatial transcriptomics libraries were prepared according to the Visium Spatial Gene Expression User Guide (CG0000239 Rev A, 10X Genomics). A total of 10 μL of amplified cDNA from each sample was used for library construction, including fragmentation, adapter ligation, index PCR, and purification. Each final library underwent quality control using the Bio-Fragment Analyzer Qseq1 (Bioptic Inc.) and was sequenced on the Illumina NovaSeq 6000 platform at Novogene, Beijing, China, with a sequencing depth of approximately 300-400 million read-pairs per sample.

data_processing:
The quality control and preprocessing of FASTQ files were implemented by fastp with default parameters. Before processing the sequencing data with SpaceRanger to obtain gene expression profiles, SCAR was used to demultiplex the human and mouse reads from the raw files. All analysis steps were seamlessly coordinated using Snakemake. The separated mouse- and human-derived fastq files were then processed with SpaceRanger to generate gene expression data. For quality control, low-quality spots—defined as those with fewer than 100 gene counts or a mitochondrial gene ratio greater than 25%—were removed. The expression matrix of the high-quality spots was then normalized, scaled, and highly variable genes were selected using SCTransform. Principal component analysis (PCA) was performed on the scaled matrix with default parameters. Shared nearest-neighbor graph construction and clustering were then performed using the FindNeighbors and FindClusters functions in Seurat, respectively. The anatomical regions of each slide were defined based on clustering results integrated with the Allen Brain Atlas map.
Assembly: hg38/mm10
Supplementary files format and content: The standard output of spaceranger
Library strategy: Spatial Transcriptomics

source_name: brain

value: brain

value: brain whole cells


title: myb68 myb84 Bio 3

city: Freiburg

first: Laura

last: Ragni

address: Schänzlerstr. 1

country: Germany

institute: University of Freiburg

data_processing:
using Galaxy Europe platform
Trim galore to remove adaptors
Hisat II: to align reads
Featurecount: to count read
Deseq2 to differentially expressed gened
Assembly: TAIR10 on Galaxy
Supplementary files format and content: tab-delimited file of count read for each sample

source_name: Root

growth_protocol: 1/2 MS  plates 22C constant light 18d old root

extract_protocol:
2cm of the upper part of the primary root. Rna extraction with Ronoklon kit
Illumina kit protocol

value: Root

value: myb68 myb84

value: no


title: BPC_50_R1_P1_E_pool1


title: In vitro differentiated murine pathogenic TH17 cells replicate 4

description:
Library name: Ctrl_4
Column name in rnaseq_deseq_global_counts_raw.tsv: Ctrl_4_S160526


title: AC_pool2_ATAC


title: myb68 myb84 Bio 2


title: Normal_pool1_ATAC


title: AC_pool1_ATAC


title: In vitro differentiated murine pathogenic TH17 cells replicate 3

description:
Library name: Ctrl_3
Column name in rnaseq_deseq_global_counts_raw.tsv: Ctrl_3_S160525


title: BPAF_50_R1_P1_E_pool1

value: Bisphenol AF


title: myb68 myb84 Bio 1


title: BPAF_10_R1_P1_E_pool1


title: Wt Bio 3

value: WT (Col)


title: human GSC1 xenografted GBM models

description:
Library name: GSC1
The frozen sections on Visium Spatial Gene Expression Slides were fixed with pre-chilled methanol and stained with H&E, following the Tissue Optimization Guide (CG000238 Rev A, 10X Genomics). Sections were then permeabilized using Permeabilization Enzyme for the optimal duration, after which cDNAs were reverse transcribed, spatially barcoded, and amplified for 10 cycles. Standard spatial transcriptomics libraries were prepared according to the Visium Spatial Gene Expression User Guide (CG0000239 Rev A, 10X Genomics). A total of 10 μL of amplified cDNA from each sample was used for library construction, including fragmentation, adapter ligation, index PCR, and purification. Each final library underwent quality control using the Bio-Fragment Analyzer Qseq1 (Bioptic Inc.) and was sequenced on the Illumina NovaSeq 6000 platform at Novogene, Beijing, China, with a sequencing depth of approximately 300-400 million read-pairs per sample.


title: CV1_81_CecalBac-RNA

city: Beltsville

first: Allen

last: Smith

state: MD

address: 10300 Baltimore Ave, BARC-East, 307C

institute: USDA ARS

description: Library name: CV1_81_CecalBac-RNA

data_processing:
CLC Genomics Workbench v.24
Assembly: GCA_000403335, GCA_003024805, GCA_001945535, GCA_910584485, GCA_003612485, GCA_013166605
Supplementary files format and content: compressed tab delimited text with gene counts for each sample

source_name: Cecal contents

extract_protocol:
RNA was extracted from cecal contents using Zymo Tri-Reagent and Qiagen Power Fecal Pro RNA isolation kits followed by further purification using Zymo RNA Clean and Concentrate kits. Qiagen QIAseq FastSelect 5S/16S/23S kit was used to deplete rRNA from the samples prior to library preparation.
Libraries were prepared using the Roche KAPA RNA HyperPrep Kit with KAPA UDI primers following manufacturer’s recommendations. Completed libraries were QC’d and quantified using a combination of Qubit dsDNA HS and Agilent 4200 TapeStation HS DNA1000 assays. The libraries were pooled in equimolar proportions and the pool quantified using the Invitrogen Collibri Quantification qPCR kit.

value: Cecal contents


title: Arabidopsis thaliana wild-type ATAC-seq sample replicate 2


title: BPAF_5_R1_P1_E_pool1


title: PANC1_siPADI2-2

city: Bunkyo-ku

first: Kentaro

last: Umemura

state: Tokyo

address: 1-5-45 Yushima

department: Department of Molecular Oncology

country: Japan

institute: Institute of Science Tokyo

data_processing:
Sequence reads were checked by using FastQC.
Reads were aligned to the human reference genome (GRCh38) using STAR (2.7.0d).
Read count extraction was performed by using RSEM.
Normalization and differential expression analysis were performed by using DESeq2.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text files include expected_count, TPM and FPKM, which were calculated by using RSEM.
Supplementary files format and content: Tab-delimited text files include expected_count, TPM and FPKM, which were calculated by using RSEM.

source_name: Pancreas

extract_protocol:
Total RNA was extracted from cells by using TRIzol Reagent (Thermo Fisher Scientific). Contaminating DNA was removed by digestion with DNA-free DNA Removal Kit (Thermo Fisher Scientific). The RNA Integrity Number (RIN) of all the samples was confirmed to be greated than 7.0 by using 2100 Bioanalyzer (Agilent Technologies).
Sequencing libraries were prepared from total RNA using the TruSeq Standard mRNA Library Kit (Cat# 20020595, Illumina, San Diego, CA, USA)

value: Pancreas

value: Pancreatic ductal adenocarcinoma

value: PADI2 knockdown


title: PANC1_siPADI2-1


title: CV1_80_CecalBac-RNA

description: Library name: CV1_80_CecalBac-RNA


title: Wt Bio 2


title: SAH_pool1_ATAC

value: Liver


title: CL1

description:
Library name: CL1
The frozen sections on Visium Spatial Gene Expression Slides were fixed with pre-chilled methanol and stained with H&E, following the Tissue Optimization Guide (CG000238 Rev A, 10X Genomics). Sections were then permeabilized using Permeabilization Enzyme for the optimal duration, after which cDNAs were reverse transcribed, spatially barcoded, and amplified for 10 cycles. Standard spatial transcriptomics libraries were prepared according to the Visium Spatial Gene Expression User Guide (CG0000239 Rev A, 10X Genomics). A total of 10 μL of amplified cDNA from each sample was used for library construction, including fragmentation, adapter ligation, index PCR, and purification. Each final library underwent quality control using the Bio-Fragment Analyzer Qseq1 (Bioptic Inc.) and was sequenced on the Illumina NovaSeq 6000 platform at Novogene, Beijing, China, with a sequencing depth of approximately 300-400 million read-pairs per sample.


title: PANC1_NC-2

value: PADI2 wild type


title: CV1_79_CecalBac-RNA

description: Library name: CV1_79_CecalBac-RNA


title: Wt Bio 1


title: PANC1_NC-1


title: Normal_pool2_ATAC

value: Normal


title: BPAF_0-5_R1_P1_E_pool1


title: CV1_78_CecalBac-RNA

description: Library name: CV1_78_CecalBac-RNA


title: BPC_0-001_R1_P1_E_pool1

value: Bisphenol C


title: KLM1_siPADI2-2


title: Bmsc-IRDC biol rep 4

city: Shanghai

first: MENGTING

last: ZHENG

address: Jumen Road

institute: Shanghai Jiaotong University

description: Library name: Sample 11

data_processing:
Fastq files were checked with Fastqc (v. 0.11.9) for quality control. The adapters were removed from the raw reads with Cutadapt (v. 1.18) and mapped to rat reference genome (rn6) with STAR (v. 2.7.1a). SAM files were converted to Bam format using Samtools (v. 1.3.1). Gene expression levels and differences were calculated using Cufflinks (v. 0.17.3) and HTseq-count (v. 0.13.5).
Assembly: rn6
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: bone marrow mesenchymal stem cells

extract_protocol:
RNA was harvested usingTRIzol reagent (Takara Biotechnology, Japan). 1.3 ug of total RNA was used for the construction of sequencing libraries.
The mRNA was isolated and fragmented using mRNA Capture Beads (VAHTS mRNA Capture Beads, N401). The resultant RNAs samples were reverse-transcribed for library construction with NEB Next® VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina, NR604. The libraries were purified by DNA clean beads (VAHTS DNA Clean Beads, N411) for size selection for 200-300 bp fragments. and analyzed on Agilent 2100 Bioanalyzer (Agilent) for measuring fragment size distribution. The qualified libraries were sequenced on Illumina Nova Seq 6000.

value: bone marrow mesenchymal stem cells


title: hNSC-TNP xenografted GBM models

description:
Library name: TNP
The frozen sections on Visium Spatial Gene Expression Slides were fixed with pre-chilled methanol and stained with H&E, following the Tissue Optimization Guide (CG000238 Rev A, 10X Genomics). Sections were then permeabilized using Permeabilization Enzyme for the optimal duration, after which cDNAs were reverse transcribed, spatially barcoded, and amplified for 10 cycles. Standard spatial transcriptomics libraries were prepared according to the Visium Spatial Gene Expression User Guide (CG0000239 Rev A, 10X Genomics). A total of 10 μL of amplified cDNA from each sample was used for library construction, including fragmentation, adapter ligation, index PCR, and purification. Each final library underwent quality control using the Bio-Fragment Analyzer Qseq1 (Bioptic Inc.) and was sequenced on the Illumina NovaSeq 6000 platform at Novogene, Beijing, China, with a sequencing depth of approximately 300-400 million read-pairs per sample.

value: iPSC-derived hNSC


title: CV1_77_CecalBac-RNA

description: Library name: CV1_77_CecalBac-RNA


title: KLM1_siPADI2-1


title: Bmsc-IRDC biol rep 2

description: Library name: Sample 9


title: BPAF_0-1_R1_P1_E_pool1

city: Ottawa

first: Matthew

last: Meier

address: 251 Sir Frederick Banting Driveway


title: KLM1_NC-2


title: BPAF_0-01_R1_P1_E_pool1


title: Bmsc-IRDC biol rep 3

description: Library name: Sample 10


title: Bmsc-IRDC biol rep 1

description: Library name: Sample 8


title: BPAF_0-001_R1_P1_E_pool1


title: CV1_47_CecalBac-RNA

description: Library name: CV1_47_CecalBac-RNA


title: BPAF_1_R1_P1_E_pool1


title: CV1_46_CecalBac-RNA

description: Library name: CV1_46_CecalBac-RNA


title: KLM1_NC-1


title: BPA_50_R1_P1_E_pool1

value: Bisphenol A


title: AsPC1_PADI2-2

value: PADI2 overexpression


title: BPA_10_R1_P1_E_pool1


title: Bmsc-imDC  biol rep 2

description: Library name: Sample 6


title: CV1_45_CecalBac-RNA

description: Library name: CV1_45_CecalBac-RNA


title: CV1_44_CecalBac-RNA

description: Library name: CV1_44_CecalBac-RNA


title: AsPC1_PADI2-1


title: BPA_5_R1_P1_E_pool1


title: Bmsc-imDC  biol rep 1

description: Library name: Sample 5


title: CV1_43_CecalBac-RNA

description: Library name: CV1_43_CecalBac-RNA


title: Bmsc biol rep 4

description: Library name: Sample 4


title: AsPC1_GFP-2

value: GFP overexpression


title: CV1_76_CecalBac-RNA

description: Library name: CV1_76_CecalBac-RNA


title: BPA_0-5_R1_P1_E_pool1


title: BPA_1_R1_P1_E_pool1


title: AsPC1_GFP-1


title: CV1_42_CecalBac-RNA

description: Library name: CV1_42_CecalBac-RNA


title: Bmsc biol rep 3

description: Library name: Sample 3


title: Bmsc biol rep 2

description: Library name: Sample 2


title: CV1_40_CecalBac-RNA

description: Library name: CV1_40_CecalBac-RNA


title: ZMAT3-KO-3

city: Bethesda

first: Javed

last: Khan

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

description:
Table_S1-KO.txt
17_ZKO_EV_unt_c

data_processing:
Basecalls performed using CASAVA version 1.8.2
RNASeq reads were aligned to Human Hg19 reference genome and Human Hg38 reference genome using TopHat2 version 2.0.8 for the 4 p53 samples and 6 ZMAT3 samples, respectively.
Fusion detection was done using TopHat2 fusion version 2.0.8
fpkm was generated using Cufflink version 2.2.1
fastqc was done using fastqc version 0.11.2
Assembly: Hg19 (for the 4 p53 samples) and Hg38 for the 6 ZMAT3 samples
Supplementary files format and content: fpkm, fusion results

growth_protocol: all cell lines were cultured in DMEM with 10% FBS, at 37 degrees C, 5% CO2

extract_protocol:
RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
The Illumina mRNASeq protocol involves Oligo(dT) magnetic beads to capture and purify RNAs with polyA tails. The RNA is fragmented into small pieces and the cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The resulting double-strand cDNA is used as the input to a standard Illumina library prep with end-repair, adapter ligation and PCR amplification being performed to give you a library that is ready to go on the sequencer.

treatment_protocol: The cells were not treated with any drug.

value: colorectal cancer


title: ZMAT3-KO-2

description:
Table_S1-KO.txt
15_ZKO_EV_unt_b


title: BPA_0-01_R1_P1_E_pool1

institute: Government of Canada


title: BPA_0-1_R1_P1_E_pool1


title: Bmsc-imDC  biol rep 3

description: Library name: Sample 7


title: CV1_39_CecalBac-RNA

description: Library name: CV1_39_CecalBac-RNA


title: Bmsc biol rep 1

description: Library name: Sample 1


title: ZMAT3-KO-1

description:
Table_S1-KO.txt
13_ZKO_EV_unt_a


title: BPA_0-001_R1_P1_E_pool1


title: CV1_38_CecalBac-RNA

description: Library name: CV1_38_CecalBac-RNA


title: Mix6_50_R1_P1_E_pool1

value: Mix 6


title: ZMAT3-WT-3

description:
Table_S1-KO.txt
5_Zwt_EV_unt_c


title: CV1_37_CecalBac-RNA

description: Library name: CV1_37_CecalBac-RNA


title: ZMAT3-WT-2

description:
Table_S1-KO.txt
3_Zwt_EV_unt_b


title: CV1_36_CecalBac-RNA

description: Library name: CV1_36_CecalBac-RNA


title: Mix6_10_R1_P1_E_pool1


title: Plasma_D14_5

city: Philadelphia

first: Theresa

last: Freeman

state: PA

address: 1015 Walnut Street

department: Orthopedic Surgery Research

institute: Thomas Jefferson University

data_processing:
The data processing steps were done by Novogene and the methods detailed here are from their report and methods files.
Raw data was processed throuh fastp software. Clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. Q20, Q30, and GC content the clean data were calculated. All downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from the genome website directly. Index fo the reference genome was built using Hisat2 v.2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v.2.0.5. Hisat2 was selected since it can create a database of splice junctions based on the gene model annotation file.
featureCounts v1.5.0-p3 was used to count the reads numebrs mapped to each gene. FPKM of each gene was calculated based on the length of the gene and the reads count mapped to the gene. FPKM, expected number of Fragments per Kilobase of transcript sequence per Millions base pair sequenced considers the effect of sequencing depth and gene length for the reads count at the same time.
Assembly: ensembl_104_rattus_norvegicus_rnor_6_0_toplevel
Supplementary files format and content: The Apyx_Manuscript_All_Raw_Counts.gz contains the raw count numbers for all samples prior to removing outliers and truncating the data for GSEA analysis. The outlier removal and data truncation thresholds are outlined in the Methods section of the manuscript.

source_name: Biceps Femoris

extract_protocol:
The muscle tissue was homogenized by resuspending crushed muscle in TRIzol reagent at 1 ml of reagent per 0.1 g of muscle. Then the tissue was dissociated by using M tubes and a gentleMACS tissue dissociator. The RNA was extracted using the Macherey-Nagel NucleoSpin RNA Midi Kit after chloroform phase separation.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: Biceps Femoris

value: Renuvion treated, euthanized 14 days after revision surgery


title: Plasma_D14_4


title: ZMAT3-WT-1

description:
Table_S1-KO.txt
1_Zwt_EV_unt_a


title: Mix6_5_R1_P1_E_pool1


title: CV1_35_CecalBac-RNA

description: Library name: CV1_35_CecalBac-RNA

value: Cecal contents


title: Plasma_D14_3


title: Mix6_1_R1_P1_E_pool1


title: CellDonor#3, tech. rep#1, PD1-LAG3_DEM, T cells

first: Claudio

last: Mussolino

address: Breisacherstr. 115

institute: Institute for Transfusion Medicine and Gene Therapy

data_processing:
Fastq files were processed as described in the paper from Foley et al. (2019). The unique molecular identifiers were trimmed and STAR v.2.7.10 was used for the alignment to the reference Genome.
Assembly: GRCh38
Supplementary files format and content: tab delimeted file containing raw counts.

source_name: primary T cells

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, cat. no.  74104)
Sequencing libraries were prepared using Smart3-seq protocol described in Foley et al. (2019)

value: primary T cells


title: CV1_33_CecalBac-RNA

description: Library name: CV1_33_CecalBac-RNA


title: Plasma_D14_2


title: CellDonor#3, tech. rep#1, LAG3_DEM, T cells


title: Mix6_0-5_R1_P1_E_pool1


title: CellDonor#3, tech. rep#1, PD1_DEM, T cells


title: Plasma_D14_1


title: CV1_31_CecalBac-RNA

description: Library name: CV1_31_CecalBac-RNA


title: CV1_32_CecalBac-RNA

description: Library name: CV1_32_CecalBac-RNA


title: Plasma_D14_6


title: CellDonor#3, tech. rep#1, Neg.Control, T cells


title: Mix6_0-01_R1_P1_E_pool1


title: CV1_30_CecalBac-RNA

description: Library name: CV1_30_CecalBac-RNA


title: Plasma_D4_6

value: Renuvion treated, euthanized 4 days after revision surgery


title: Mix6_0-1_R1_P1_E_pool1


title: Plasma_D4_5


title: CellDonor#2, tech. rep#1, LAG3_DEM, T cells


title: Mix6_0-001_R1_P1_E_pool1


title: CV1_29_CecalBac-RNA

description: Library name: CV1_29_CecalBac-RNA


title: CellDonor#2, tech. rep#1, PD1_DEM, T cells


title: Mix5_50_R1_P1_E_pool1

value: Mix 5


title: Plasma_D4_4


title: CV1_28_CecalBac-RNA

description: Library name: CV1_28_CecalBac-RNA


title: CellDonor#2, tech. rep#2, Neg.Control, T cells


title: Plasma_D4_3


title: Mix5_10_R1_P1_E_pool1


title: CV1_27_CecalBac-RNA

description: Library name: CV1_27_CecalBac-RNA


title: CellDonor#2, tech. rep#1, Neg.Control, T cells


title: Mix5_5_R1_P1_E_pool1


title: Plasma_D4_1


title: CellDonor#1, tech. rep#2, PD1-LAG3_DEM, T cells


title: Plasma_D4_2


title: Mix5_1_R1_P1_E_pool1


title: CV1_26_CecalBac-RNA

description: Library name: CV1_26_CecalBac-RNA


title: Mix5_0-5_R1_P1_E_pool1


title: CellDonor#1, tech. rep#1, PD1-LAG3_DEM, T cells


title: CV1_24_CecalBac-RNA

description: Library name: CV1_24_CecalBac-RNA


title: Plasma_6h_6

value: Renuvion treated, euthanized 6 hours after surgery


title: Plasma_6h_5


title: CV1_23_CecalBac-RNA

description: Library name: CV1_23_CecalBac-RNA


title: Mix5_0-1_R1_P1_E_pool1


title: Plasma_6h_4


title: CellDonor#1, tech. rep#1, LAG3_DEM, T cells


title: CellDonor#1, tech. rep#2, LAG3_DEM, T cells


title: CV1_18_CecalBac-RNA

description: Library name: CV1_18_CecalBac-RNA


title: Mix5_0-01_R1_P1_E_pool1


title: CellDonor#1, tech. rep#2, PD1_DEM, T cells


title: CV1_20_CecalBac-RNA

description: Library name: CV1_20_CecalBac-RNA


title: CV1_17_CecalBac-RNA

description: Library name: CV1_17_CecalBac-RNA


title: Plasma_6h_2


title: Plasma_6h_3


title: CellDonor#1, tech. rep#1, PD1_DEM, T cells


title: CV1_16_CecalBac-RNA

description: Library name: CV1_16_CecalBac-RNA


title: Mix5_0-001_R1_P1_E_pool1


title: Plasma_6h_1


title: CellDonor#1, tech. rep#1, Neg.Control, T cells


title: NC_R1_P1_E_pool1

value: No cells; 1X Lysis buffer


title: NC_R2_P1_E_pool1


title: CV1_15_CecalBac-RNA

description: Library name: CV1_15_CecalBac-RNA


title: Control_D14_6

value: Control euthanized 14 days after revision surgery


title: CV1_14_CecalBac-RNA

description: Library name: CV1_14_CecalBac-RNA


title: DMSO_0-1_R4_P1_E_pool1

value: Dimethyl sulfoxide


title: R

city: Los Angeles

first: Yichen

last: Zhu

address: 610 Charles E Young Drive S

institute: University of California, Los Angeles

description: 10x Genomics

data_processing:
For cell clustering and annotation, the merged digital expression matrix generated by Cellranger was analyzed using an R package Seurat (v.4.0.0) following the guidelines. Briefly, after filtering the low-quality cells, the expression matrix was normalized using NormalizeData function, followed by selecting variable features across datasets using FindVariableFeatures and SelectIntegrationFeatures functions. To correct the batch effect, FindIntegrrationAnchors and IntegrateData functions were used based on the selected feature genes. The corrected dataset was subjected to standard Seurat workflow for dimension reduction and clustering. In this study, clusters of therapeutic cells were manually merged and annotated based on gene signatures reported from previous studies. AddModuleScore was used to calculate module scores of each list of gene signatures, and FeaturePlot function was used to visualize the expression of each signature in the UMAP plots.
Assembly: Human (GRCh38) 2020-A
Supplementary files format and content: matrix.mtx.gz: Matrix Market Format, with rows representing genes and columns representing cells.
Supplementary files format and content: barcode.tsv.gz: Tab-separated values, where each row represents a unique identifier for a cell.
Supplementary files format and content: features.tsv.gz: Tab-separated values, where each row represents a gene.

source_name: Ascites

extract_protocol:
Cells were collected from primary OC patient ascites at various tumor stages (Chemonaive: Sample_01; Recurrent: Sample_02) and then sent for scRNA sequencing.
Cells were quantified using a Cell Countess II automated cell counter (Invitrogen/Thermo Fisher Scientific). A total of 10,000 cells from each experimental group were loaded on the Chromium platform (10X Genomics), and libraries were constructed using the Chromium Next GEM Single Cell 3' Kit v3.1 and the Chromium Next GEM Chip G Single Cell Kit (10X Genomics), according to the manufacturer’s instructions. Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).
Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).

value: Ascites

value: Tumor cells

value: Recurrent


title: DMSO_0-1_R3_P1_E_pool1


title: Control_D14_5


title: CV1_13_CecalBac-RNA

description: Library name: CV1_13_CecalBac-RNA


title: C

description: 10x Genomics

value: Chemonaive


title: Control_D14_4


title: DMSO_0-1_R2_P1_E_pool1


title: Control_D14_3


title: HONE-1,Input

city: Guangzhou

first: Liu

state: GuangDong

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

data_processing:
RIP-seq reads were filtered and quality-verified using Trimmomatic(v0.36).
Peaks were called using RIPSeeker(http://www.bioconductor.org/packages/release/bioc/html/RIPSeeker.html) is based on Hidden Markov Model(HMM,)and annotated with the closest hg38 genes by annotatePeaks of HOMER (v.4.7.2).
Assembly: hg19
Supplementary files format and content: fastq.gz

extract_protocol:
RNA was havest using Magna RIPTM RNA-Binding Protein Immunoprecipitation Kit.Briefly,lyse Cells in RIP Lysis Buffer.Then,Immunoprecipitate with anti-eEF1A2 with protein A/G magnetic beads;Immobilize magnetic beads bound complexes with magnet and wash off unbound materials.
Fragment the eluted and purified RNA.Purify the synthesized cDNA, perform 3' end repair, purify again, and then amplify by PCR to complete the library construction.Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

value: nasopharyngeal carcinoma cells

tag: rip antibody


title: DMSO_0-1_R1_P1_E_pool1


title: CV1_12_CecalBac-RNA

description: Library name: CV1_12_CecalBac-RNA


title: HONE-1 cells,eEF1A2,RIP-seq

value: IgG(Thermo Fisher Scientific)


title: CV1_11_CecalBac-RNA

description: Library name: CV1_11_CecalBac-RNA


title: Control_D14_1


title: E2_1_R1_P1_E_pool1


title: Epithelial ovarian cancer, rep3

city: Yiwu

first: keren

last: cheng

state: Zhejiang

address: 1575 chouzhou bei road

department: School of Medicine

institute: Zhejiang University

data_processing:
Raw fastq files were generated by using cellranger(v7.0.0)
raw counts table was generated by using cellranger(v7.0.0)
The velocyto command line interface was used to generate spliced/unspliced expression matrices from the 10x Genomics Chromium samples
Assembly: GRCh38
Supplementary files format and content: loom files with gene count, spliced, unspliced count for each sample

source_name: Epithelial ovarian cancer

extract_protocol:
Centrifuge cells at 300 rcf for 5 min at 4°C. Remove the supernatant without disturbing the cell pellet. Using a wide-bore pipette tip, add 200 ul Lysis Buffer  and gently pipette mix 5x or until cells are completely  suspended without introducing bubbles. Lyse the cells on ice for 1 min.  Using a regular-bore pipette tip, add 800 ul Nuclei Wash & Resuspension Buffer. Gently pipette mix 5x. and wash nuclei two times. Remove the supernatant without disrupting the pellet.  Using a regular-bore pipette tip, add 1 ml or an appropriate  volume Nuclei Wash & Resuspension Buffer to achieve a  target concentration of 700-1,200 nuclei/μl. Gently pipette  mix 10x or until nuclei are completely suspended.   Determine the nuclei concentration using a Countess II FL  Automated Cell Counter. Proceed immediately with the 10x Genomics Single  Cell protocol and minimize the time between nuclei  preparation and chip loading
Preparation of single nuclei from frozen human HGSOC and fallopian tube samples and constructions of 3’ single-cell gene expression libraries were conducted using the 10x Genomics Chromium system (Next GEM v3.1) following the manufacturer’s protocol. The libraries were sequenced with ~200 million PE150 reads per sample on Illumina NovaSeq at LC-BIO Co., Ltd (Hangzhou, China).

value: Epithelial ovarian cancer


title: Control_D4_6

value: Biceps Femoris

value: Control euthanized 4 days after revision surgery


title: CV1_9_CecalBac-RNA

description: Library name: CV1_9_CecalBac-RNA

value: Cecal contents


title: Mix4_50_R1_P4_H_pool1

value: Mix 4


title: CV1_10_CecalBac-RNA

description: Library name: CV1_10_CecalBac-RNA


title: CV1_8_CecalBac-RNA

description: Library name: CV1_8_CecalBac-RNA


title: Epithelial ovarian cancer, rep2


title: Control_D4_5


title: Epithelial ovarian cancer, rep1


title: E2_0-1_R1_P1_E_pool1


title: Mix4_5_R1_P4_H_pool1


title: Mix4_10_R1_P4_H_pool1


title: Fimbriae, rep3

source_name: fallopian tube

value: fallopian tube


title: CV1_45_CEC

data_processing:
CLC Genomics Workbench v.24
Assembly: mm10
Supplementary files format and content: compressed tab delimited text with gene counts for each sample

source_name: Cecum

extract_protocol:
RNA was extracted from tissues using Zymo Tri-Reagent and Invitrogen PureLink RNA isolation kits followed by further purification using Zymo RNA Clean and Concentrate kits.
Libraries were prepared using Illumina Stranded mRNA Prep, Ligation kit with IDT for Illumina Unique Dual Indexes following manufacturer’s recommendations, except that half reaction volumes were used. Completed libraries were QC’d and quantified using a combination of Qubit dsDNA HS and Agilent 4200 TapeStation HS DNA1000 assays. The libraries were pooled in equimolar amounts for multiplexed sequencing, and the pool quantified using the Invitrogen Collibri Quantification qPCR kit.

value: Cecum

tag: strain


title: Fimbriae, rep2

tag: tissue


title: CV1_46_CEC


title: Control_D4_4


title: Mix4_1_R1_P4_H_pool1


title: Control_D4_3


title: Control_D4_2


title: Fimbriae, rep1


title: CV1_42_CEC


title: Control_D14_2


title: Control_D4_1


title: CV1_44_CEC


title: Mix4_0-5_R1_P4_H_pool1


title: Ampulla, rep3


title: CV1_40_CEC


title: Control_6h_6

value: Control euthanized 6 hours after surgery


title: Mix4_0-01_R1_P4_H_pool1


title: Control_6h_5


title: CV1_80_CEC


title: Ampulla, rep1


title: CV1_37_CEC


title: Mix4_0-001_R1_P4_H_pool1


title: Control_6h_4


title: Isthmus, rep3


title: CV1_36_CEC


title: Mix3_50_R1_P3_G_pool1

value: Mix 3


title: CV1_32_CEC


title: Isthmus, rep1


title: Mix3_5_R1_P3_G_pool1


title: Mix3_10_R1_P3_G_pool1


title: Control_6h_2


title: Isthmus, rep2


title: CV1_31_CEC


title: CV1_77_CEC


title: Mix4_0-1_R1_P4_H_pool1


title: Control_6h_1


title: OVSAHO, Veh, Rep3

city: Rochester

first: Esther

last: Rodman

state: Minnesota

address: 200 1st St SW

institute: Mayo Clinic

description:
Library name: OVS_Veh_3
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

data_processing:
Reads were aligned using STAR (version 2.7.3a) and featureCounts (version 2.8.2) was used to assign mapped reads. Any gene with an RPKM < 1 in all samples were considered to be lowly expressed and removed from further analysis.
Assembly: hg38
Supplementary files format and content: .xlsx table file including raw counts and RPKM values for each sample

source_name: cell line

growth_protocol: MDAH and OVSAHO cells were maintained in phenol red free RPMI (#11835050, Gibco), containing 10% (v/v) FBS (#900-308, Gemini Bioproducts) and 1% (v/v) antibiotic/antimycotic (#15240-062, Gibco)

extract_protocol:
Total RNA was isolated using the Qiagen miRNeasy mini kit (#217004, Qiagen)
LibTruSeqStrmRNAv2(TSMRN)

treatment_protocol: MDAH and OVSAHO cells were plated at 70% confluence in maintainance media with 500nM lestaurtinib or DMSO vehicle for 24 hours

value: OVSAHO

value: High grade serous ovarian cancer

value: WT

value: Vehicle (DMSO)


title: Mix3_1_R1_P3_G_pool1


title: Mix3_0-5_R1_P3_G_pool1


title: Ampulla, rep2


title: OVSAHO, Veh, Rep2

description:
Library name: OVS_Veh_2
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: Epithelial ovarian cancer, rep4


title: CV1_76_CEC


title: Homo sapiens,Crontrol_IP _2_RNA

city: Beijing

first: xinyuan

last: chen

address: No.17, Hougou Hutong, Dongcheng District, Beijing

institute: Beijing Eye Research Institute

data_processing:
Base calling software: BCL convert
Data filter: fastp(0.19.4)，remove adapters, repeat sequences and low quality sequences
reads alignment : HISAT2(2.0.4)
Peak calling diffpeak : R package: exomePeak (1.5.0)
Peak annotation : ANNOVAR
Transcript assembly and quantification : StringTie (2.1.2)
Differential Expression Analysis :R package: edgeR(4.1)
Motif: HOMER(4.10)
Assembly: eg GRCH38
Supplementary files format and content: sh-METTL14+Hypoxia_IPVSsh-METTL14+Hypoxia_input_peak.xlsx,sh-NC+Hypoxia_IPVSsh-NC+Hypoxia_input_peak.xlsx,which contained methylation site information of m6A
Supplementary files format and content: sh-METTL14+HypoxiaVSsh-NC+Hypoxia_diffPeak_result.xlsx, which contained the result  of differential methylation sites
Supplementary files format and content: 4_genes_fpkm_expression.xlsx,which  contained the expression information of various genes in various samples (Expression profile)

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA), and the RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA). Poly (A) RNA was purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) by two rounds of purification.
the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. The cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The IP RNA was reverse-transcribed to cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which was next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base was added to the blunt ends of each strand, preparing for ligation to the indexed adapters. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. At last, we performed paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 platform(LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol
m6A-seq


title: Mix3_0-1_R1_P3_G_pool1


title: CV1_26_CEC


title: Homo sapiens,Crontrol_input_2_ RNA


title: Control_6h_3


title: CV1_20_CEC


title: OVSAHO, Veh, Rep1

description:
Library name: OVS_Veh_1
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: Mix3_0-001_R1_P3_G_pool1


title: CV1_18_CEC


title: Mix3_0-01_R1_P3_G_pool1


title: OVSAHO, Lest, Rep3

description:
Library name: OVS_Lest_3
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

value: 500nM Lestaurtinib


title: Homo sapiens,Crontrol_IP _1_RNA


title: Mix2_50_R1_P2_F_pool1

value: Mix 2


title: OVSAHO, Lest, Rep2

description:
Library name: OVS_Lest_2
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: OVSAHO, Lest, Rep1

description:
Library name: OVS_Lest_1
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: Homo sapiens,metll14 ko_IP _3_RNA


title: Homo sapiens,metll14 ko_input _3_RNA


title: Homo sapiens,Crontrol_input_3_ RNA


title: CV1_16_CEC


title: Mix2_10_R1_P2_F_pool1


title: Homo sapiens,Crontrol_IP _3_RNA


title: Mix2_5_R1_P2_F_pool1


title: CV1_15_CEC


title: MDAH, Veh, Rep3

description:
Library name: MDAH_Veh_3
Column name processed data file: Counts_LibraryName, RPKM_LibraryName

value: Endometrioid ovarian cancer


title: MDAH, Veh, Rep2

description:
Library name: MDAH_Veh_2
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: Homo sapiens,metll14 ko_IP_2_ RNA


title: CV1_14_CEC


title: MDAH, Veh, Rep1

description:
Library name: MDAH_Veh_1
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: Mix2_0-5_R1_P2_F_pool1


title: Homo sapiens,metll14 ko_input_2_ RNA


title: CV1_13_CEC


title: MDAH, Lest, Rep3

description:
Library name: MDAH_Lest_3
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: Homo sapiens,Crontrol_input _1_RNA


title: Homo sapiens,metll14 ko_IP_1_ RNA


title: Mix2_0-1_R1_P2_F_pool1


title: MDAH, Lest, Rep2

description:
Library name: MDAH_Lest_2
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: Homo sapiens,metll14 ko_input_1_ RNA


title: Geltrex_3

city: Taipei

first: Hsi

last: Chang

state: Xinyi

address: No. 250, Wuxing Street

department: Pediatrics

country: Taiwan

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

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

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

value: skeletal muscle

value: Geltrex™


title: Geltrex_2


title: MDAH, Lest, Rep1

description:
Library name: MDAH_Lest_1
Column name processed data file: Counts_LibraryName, RPKM_LibraryName


title: Mix2_0-001_R1_P2_F_pool1

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


title: IP NC_3

city: Wu'xi

first: Yu

last: Xin

state: Jiangsu

address: 1800 Lihu Road

institute: Jiangnan University

description:
NC_3
non-diabetic retinopathy

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

source_name: vitreous bodies

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

value: vitreous bodies


title: IP NC_2

description:
NC_2
non-diabetic retinopathy


title: sip53-1

description:
Table_S4-p53_si.txt
Lal 14

value: colorectal cancer


title: Mix1_50_R1_P1_E_pool1

value: Mix 1


title: CV1_17_CEC


title: Fibro_3

value: Fibronectin


title: Geltrex_1


title: IP NC_1

description:
NC_1
non-diabetic retinopathy


title: Mix2_1_R1_P2_F_pool1


title: siCTRL-2

description:
Table_S4-p53_si.txt
Lal 11

value: siCTRL


title: Mix1_5_R1_P1_E_pool1


title: Fibro_2


title: siCTRL-1

description:
Table_S4-p53_si.txt
Lal 10


title: IP DR_2

description:
DR_2
diabetic retinopathy


title: IP DR_3

description:
DR_3
diabetic retinopathy


title: Mix1_1_R1_P1_E_pool1


title: CV1_8_CEC

value: Cecum


title: Mix2_0-01_R1_P2_F_pool1


title: IP DR_1

description:
DR_1
diabetic retinopathy


title: Fibro_1


title: Mix1_0-5_R1_P1_E_pool1


title: PJS1-2_3

city: Chicago

first: Tahir

address: 255 E Chicago Street

institute: Lurie Childrens Hospital

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

source_name: Skin

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

value: Skin

value: Fibroblast

value: STK11 del


title: CollagenI_3

value: Collagen I


title: PJS1-2_2


title: Input NC_3

description:
NC_3
non-diabetic retinopathy


title: sip53-2

description:
Table_S4-p53_si.txt
Lal 15


title: Input NC_2

description:
NC_2
non-diabetic retinopathy