title: 44_091_P12_TCZ + RPMI_2h [0700835891]

data_processing:
Raw RNA-seq reads were aligned with UCSC human genome assembly version hg38, with STAR aligner (Dobin et al., 2013).
HTseq-count (Anders et al., 2015) was used to count the reads mapping to each gene feature. Downstream analysis and heatmap generation were performed with an in-house script in R [R Core Team (2018). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.], with DESEq2 (Love et al., 2014), and ComplexHeatmap (Gu et al., 2016)
Downstream analysis and heatmap generation were performed with an in-house script in R [R Core Team (2018). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.], with DESEq2 (Love et al., 2014), and ComplexHeatmap (Gu et al., 2016)
Assembly: hg38
Supplementary files format and content: HTSeq-count is used to get the count files, followed by quantile  normalization.

extract_protocol: RNeasy plus micro kit (Qiagen): cDNA was prepared with the SMART-Seq RNA kit (Takara Bio) for low-input RNA and DNA library preparation and used the Nextera XT DNA Library Preparation Kit (Illumina) and the Nextera XT Index Kit v2 set A (Illumina), respectively


title: Meningioma 614

status: Public on Jan 31 2025

type: genomic

city: Boston

first: Scott

middle: Thomas

last: Ryall

state: Massachusetts

address: 75 Francis Street

country: USA

institute: Brigham and Women's Hospital

description: Hybridized to OncoScanHD

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: Arrays were then washed using Affymetrix GeneChip Fluidics Station 450, and scanned using the Gene Chip Scanner 3000.

data_processing:
Data analysis was performed using Chromosome Analysis Suite software version 1.2.2
[primary data description] Fluorescent intensity values across SNP probes

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Meningioma Tissue

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Not applicable

extract_protocol: DNA was extracted using the QIAamp DNA FFPE Tissue Kit and stored at 4˚C

treatment_protocol: Not applicable

tag: tissue

value: Brain

tag: Sex

value: F

tag: age


title: WT PI #7264 biol rep 4

type: SRA

city: OKLAHOMA CITY

first: Susan

middle: E

last: Kovats

state: OK

address: 825 NE 13TH ST.

institute: OKLAHOMA MEDICAL RESEARCH FOUNDATION

description:
Library name: 14A
WT_7624_P1
DESeq2_DE_WT_CD103_vs_WT_P1.xlsx
DESeq2_DE_WT_P2_vs_WT_P1.xlsx

library_source: transcriptomic

data_processing:
Raw sequencing reads were trimmed, and aligned using the Bluebee FWD-UMI Mouse (GRCm38) Lexogen QuantSeq 2.6.1 Pipeline. Gene annotation was done using biomaRt in R. Principal component analysis of the sample groups were made for further quality control using R.
Differentially expressed analyses were performed using the empirical Bayes approach implemented in the R package DESeq2. Genes were removed from analysis if all reads from any sample were 0 or the sum across samples was less than 10. Genes were considered differentially expressed if the absolute value of the fold-change ≥ 2 and the False Discovery Rate (FDR) P-value adjusted ≤ 0.05.
Assembly: Bluebee FWD-UMI Mouse (GRCm38)
Supplementary files format and content: normalized counts for each sample after DESeq2, plus DESeq2 analysis results

molecule: polyA RNA

organism: Mus musculus

source_name: lung

extract_protocol:
Arcturus PicoPure RNA isolation kit, Ovation Pico SL WTA system V2 kit (Nugen)
Lexogen Quantseq RNAseq 3' mRNA kit

treatment_protocol: cells isolated from collagenase-digested lungs on day 5 post IAV infection, stained with fluorochrome-labeled Abs specific for surface proteins, and sorted on a FACS ARIA

value: lung

tag: cell type

value: dendritic cell cDC2A

tag: genotype

tag: treatment

value: IAV infection


title: Meningioma 613

description: Hybridized to OncoScanHD

value: M


title: P4O2 COVID-19, stimulation, patient 6 long COVID

city: Amsterdam

first: Anke-Hilse

last: Maitland-van der Zee

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

description: Library name: S18

data_processing:
To remove low quality reads/read-ends and sequencing adapters, readouts were trimmed using Trim-Galore v0.6.10, which acts as a wrapper around FastQC v0.12.1 and cutadapt v4.3
Transcripts were aligned against the human genome (GRCh38.p14) using Salmon v1.10.1
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

source_name: nasal epithelial cells

extract_protocol:
RNA was harvested using the Bioline ISOLATE II mini kit.
KAPA mRNA Hyperprep capture according to the manufacturer's protocol
S4.300 (PE150)

value: nasal epithelial cells

tag: time

value: 3-6 months post-COVID


title: WT P1 #7588 biol rep 3

description:
Library name: 10A
WT_7588_P1
DESeq2_DE_WT_CD103_vs_WT_P1.xlsx
DESeq2_DE_WT_P2_vs_WT_P1.xlsx


title: 46_091_P12_TCZ+ IL1B_2h [0700835911]

city: Doha

first: nico

last: marr

email: nico_marr@outlook.com, tkhan@sidra.org

address: AL RAYYAN

department: Research

country: Qatar

institute: Sidra Medicine

source_name: PBMCs

value: PBMCs

tag: donor

value: Patient

value: mut/mut

value: Tocilizumab + IL1B

tag: timepoint


title: 42_091_P07_TCZ + LPS _2h [0700835871]

value: Tocilizumab + LPS


title: P4O2 COVID-19, stimulation, patient 5 long COVID

description: Library name: S16


title: P4O2 COVID-19, baseline, patient 5 long COVID

description: Library name: S15


title: Meningioma 612

description: Hybridized to OncoScanHD


title: WT P1 #7579  biol rep 1

description:
Library name: 2A
WT_7579_P1
DESeq2_DE_WT_CD103_vs_WT_P1.xlsx
DESeq2_DE_WT_P2_vs_WT_P1.xlsx


title: 41_091_P07_TCZ + RPMI_2h [0700835861]

value: Tocilizumab + RPMI


title: P4O2 COVID-19, baseline, patient 6 long COVID

description: Library name: S17


title: 39_953_E030_IL1B _2h [0700835841]

value: Healthy control

value: WT/WT


title: RPE cells from 1mo wt (C57BL/6J) mice - replicate 6

city: Irvine

first: Aleksander

last: Tworak

state: CA

address: 837 Health Sciences Rd

department: Ophthalmology

institute: University of California Irvine

description: Library name: WT6

data_processing:
Sequence data were de-multiplexed using bcl2fastq2 software (Illumina) and their quality was assessed using FastQC (Babraham Bioinformatics). Reads were aligned to the reference mouse genome assembly (mm10) and quantified using the Rsubread software package with standard parameters (54). Data normalization and differential expression analyses were performed with DESeq2 (55), with a Benjamini–Hochberg adjusted P-value (Padj) <0.05 considered as statistically significant.
Assembly: mm10
Supplementary files format and content: MFRP-results.csv (CSV file) contains output of DESeq2 analysis and includes Ensembl gene identifiers, assigned MGI gene symbols, differential expression data including fold changes (log2foldchange) and adjusted P values, and normalized read counts for each sample

source_name: Retinal pigment epithelium (RPE)

extract_protocol:
To isolate RPE from the enucleated mouse eyes, anterior segment and the neural retina were removed from the eyecup, which was then incubated in RNAprotect cell reagent (Qiagen), following a previously established protocol (Xin-Zhao Wang et al. Exp Eye Res. 2012 Sep:102:1-9. doi: 10.1016/j.exer.2012.06.003. ) Total RNA was isolated from RPE pooled from both eyes per sample using RNeasy Micro kit (Qiagen) according to the manufacturer's directions and analyzed using Bioanalyzer assay (Agilent) to ensure good quality of the obtained samples (RNA integrity number, RIN ≥8).
RNA samples were processed in Transcriptomics and Deep Sequencing Core (Johns Hopkins University) for library preparation and sequencing. Briefly, total RNA (~100ng per sample) was used for library preparation by following Illumina TruSeq Stranded Total RNA Library Prep Kit protocol. Libraries were then sequenced (paired-end 100 cycles) with the Illumina NextSeq 500 platform, yielding approximately 40 million raw reads per library.

value: Retinal pigment epithelium (RPE)

value: wt


title: P4O2 COVID-19, stimulation, patient 4 long COVID

description: Library name: S14


title: Meningioma 610

description: Hybridized to OncoScanHD

value: Brain


title: RPE cells from 1mo wt (C57BL/6J) mice - replicate 5

description: Library name: WT5


title: P4O2 COVID-19, baseline, patient 4 long COVID

description: Library name: S13


title: 38_953_E030_R848_2h [0700835831]


title: smallRNA_3end_globalseq_totalRNA_rep3

city: La Jolla

first: Cody

last: Ocheltree

address: 9500 Gilman Drive

institute: UCSD

description:
Library name: totalRNA_3
D501, D703

library_source: other

data_processing:
FASTQ files were first subjected to 3’ adaptor and PCR duplicate removal using custom python scripts (https://pypi.org/project/jla-demultiplexer/).
Residual Illumina adaptor sequence was removed with Cutadapt (62).
Reads were mapped to the human genome (version hg38) using STAR 2.7.11b (63).
Gene-specific 3’ end information and graphs were subsequently generated using Tailer (https://github.com/TimNicholsonShaw/tailer) (Nicholson-Shaw, RNA, 2022) using the global alignment mode.
A three-pass alignment strategy against a small RNA genome which was developed in the lab and described previously (Ma et. al. 2024), but with a modification in order to improve the local alignment step which provides post-transcriptional nucleotide modification information. After performing a three-pass end-to-end alignment, which includes a 5’-hard clip of 10 nucleotides to facilitate alignment of reads with post-transcriptional nucleotide modifications, the aligned reads were grouped by gene and re-converted into individual fastq files for each gene detected using bedtools and samtools. Individual-gene fastq files were then re-aligned with a three-pass local alignment to single-gene genomic sequences corresponding to the gene each file was previously aligned to in the end-to-end alignment. Gene-specific 3’ end information and graphs were subsequently generated using Tailer (https://github.com/TimNicholsonShaw/tailer) using the global alignment mode.
Assembly: human genome (version hg38)
Supplementary files format and content: comma separated variable table with RNA counts, 3' end position, and 3' post-transcriptional nucleotides

molecule: other

source_name: HEK 293T-REx

growth_protocol: All cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Gibco) supplemented with 10% Fetal Bovine Serum (FBS, Gibco) and 1% penicillin/streptomycin (Gibco) at 37°C, 5% CO2.

extract_protocol:
Small RNA (100-500 bp) was isolated with a 9% polyacrylamide/6M urea denaturing gel. Ribosomal (r)RNAs were depleted using RiboCOP rRNA depletion kit (Lexogen) per manufacturer’s recommendations. A 3' adaptor containing a 15 or 16 bp randomer was ligated to RNAs. Nascent RNA was isolated with Click-it nascent RNA capture kit (Thermo Fisher). A fraction of material was prepared as total RNA and was not processed with nascent capture. A 5' adaptor was ligated following reverse transcription using a primer against the 3' adaptor.
The cDNA was amplified in two stages of Polymerase Chain Reaction (PCR) using Q5 DNA polymerase (NEB). For the first PCR reaction, the cDNA library was amplified using 3’ adaptor primer (AR17) and a primer complementary to the 5’ adaptor (RC_3Tr3) for 8 cycles. The PCR product was purified by AMPure XP beads (Beckman Coulter) per manufacturer’s recommendation. The second PCR reaction was performed using Illumina Trueseq D50X and D70X primers for 18 cycles.

treatment_protocol: HEK293 T-REx cells were incubated with either 0.5 mM 5-ethynyl uridine (EU; Thermo Fisher) or an equivalent volume of DMSO for 2 hours and harvested in TRIzol reagent (Thermo Fisher).

tag: cell line

value: HEK 293T-REx

tag: molecule type

value: totalRNA


title: Meningioma 608

description: Hybridized to OncoScanHD


title: RPE cells from 1mo wt (C57BL/6J) mice - replicate 4

description: Library name: WT4


title: 43_091_P07_TCZ+ IL1B_2h [0700835881]


title: P4O2 COVID-19, baseline, patient 3 post-COVID

description: Library name: S05


title: Meningioma 607

description: Hybridized to OncoScanHD


title: Meningioma 611

description: Hybridized to OncoScanHD


title: P4O2 COVID-19, stimulation, patient 2 post-COVID

description: Library name: S04


title: 36_953_E030_RPMI_2h [0700835811]

value: RPMI


title: P4O2 COVID-19, baseline, patient 2 post-COVID

description: Library name: S03


title: 40_953_E030_TNFa_2h [0700835851]

value: TNFa


title: 35_953_E029_TNFa_2h [0700835801]


title: RPE cells from 1mo wt (C57BL/6J) mice - replicate 2

description: Library name: WT2


title: Meningioma 605

description: Hybridized to OncoScanHD

value: F


title: RPE cells from 1mo wt (C57BL/6J) mice - replicate 1

description: Library name: WT1


title: P4O2 COVID-19, stimulation, patient 1 post-COVID

description: Library name: S02

value: nasal epithelial cells

value: 3-6 months post-COVID


title: Meningioma 604

description: Hybridized to OncoScanHD


title: WT P1 #7580 biol rep 2

description:
Library name: 6A
WT_7580_P1
DESeq2_DE_WT_CD103_vs_WT_P1.xlsx
DESeq2_DE_WT_P2_vs_WT_P1.xlsx

value: lung

value: dendritic cell cDC2A

value: IAV infection


title: P4O2 COVID-19, baseline, patient 1 post-COVID

description: Library name: S01


title: 33_953_E029_R848_2h [0700835781]

value: PBMCs


title: RPE cells from 1mo rd6 mice - replicate 6

description: Library name: MFRP6

value: Mfrp rd6/rd6


title: Meningioma 603

description: Hybridized to OncoScanHD

value: M


title: Meningioma 602

description: Hybridized to OncoScanHD


title: RPE cells from 1mo rd6 mice - replicate 4

description: Library name: MFRP4


title: 32_953_E029_LPS_2h [0700835771]

value: Healthy control

value: WT/WT

value: LPS


title: COVID-2T_Patient_1_Memb

city: Houston

first: Rachel

middle: A

last: Keuls

email: Rachel.Keuls@bcm.edu, rkeuls@gmail.com

state: TX

address: One Baylor Plaza

department: MCB

institute: Baylor College of Medicine

description:
Library name: 105.34p
sci-rna-seq3 run 3

library_source: transcriptomic single cell

data_processing:
Demultiplexing using the BBI pipeline command bbi-demux (https://github.com/bbi-lab/bbi-dmux)
Aligment and count matrix generation using the BBI pipeline command bbi-sci (https://github.com/bbi-lab/bbi-sci/)
To ensure high-quality snRNA-seq data, we implemented several quality control measures. To address potential cross-contamination between wells, we used SoupOrCell (Heaton et al. 2020) on the merged BAM file of 17 samples from 9 donors. This method assigns barcodes to their donor of origin based on variants detected in snRNA-seq reads. Any barcodes not assigned as singlets to the predominant donor per sample were filtered out. Doublets were identified and removed using Scrublet (Wolock et al. 2019) with a threshold of 0.3. Further quality filtering retained barcodes with 200–10,000 detected features (genes), <5% mitochondrial content, and genes expressed in at least 50 nuclei. This resulted in a dataset of 47,889 nuclei and 18,932 features.
Sequencing depth differences were equalized using multiBatchNorm from the batchelor package (v1.20.0) (Haghverdi et al. 2018), scaling library size factors according to the ratio of mean counts. Variance trends were modeled separately for each library using modelGeneVarByPoisson and combined across batches with combineVar from the scran package (Lun et al. 2016). We then merged the three preprocessed feature-barcode matrices into a single object, log-normalized UMI counts, and selected 17,774 genes with positive biological variance components. Principal component analysis (PCA) was performed on this gene set using denoisePCA, followed by batch correction with Harmony (v1.2.1) (Korsunsky et al. 2019); Uniform Manifold Approximation and Projection for Dimension Reduction (UMAP) dimensional reduction on the Harmony-corrected PCs was used for visualizations. Cell type identification was performed in Seurat (v4.3.0) (Butler et al. 2018) using shared nearest-neighbor clustering (k=20) based on Harmony-corrected PCs (resolution = 0.4).
Assembly: human GRCh38 build and annotation from Ensembl (release 99)
Supplementary files format and content: Filtered Feature Matrix Files
Supplementary files format and content: Monocle3 CDS and Seurat RDS file

molecule: nuclear RNA

source_name: Chorionic Membranes

growth_protocol: Placentas were delivered via cesarian section

extract_protocol:
Tissue samples were manually pulverized on dry ice, transferred to pre-chilled tubes, and stored at -80°C. Nuclei isolations were performed with the ‘hypotonic lysis buffer solution B’ [Martin et al. 2023]. Up to 200 mg of tissue was added to 5 mL of ‘hypotonic lysis buffer B’ for 5 to 25 minutes on ice with periodic agitation. For samples under 50 mg, 500 uL of ‘hypotonic lysis buffer B’ was added directly to the 1.5 mL sample tubes and a RNase-free pestle was used for 6 to 12 strokes to further dissociate the tissue. Released nuclei were passed through a 70-micron cell strainer, pelleted (500xg, 5 minutes, 4°C), and resuspended in 1 mL of cold ‘0.3 M SPBSTM’ (Martin et al. 2023). Pre-chilled fixative (5 mg of DSP resuspended in 100 uL DMSO per 4 mL of methanol) was incrementally added for every 1 mL of nuclei resuspended in ‘0.3 M SPBSTM’ and fixed on ice for 5 to 10 minutes. The nuclei were rehydrated by gradually adding 10 mL of ‘0.3 M SPBSTM’ for every 5 mL of fixed nuclei suspension prior to centrifugation (500xg, 5 minutes, 4°C) and resuspended in 1 mL of ‘0.3 M SPBSTM’. Nuclei suspensions processed in the third sci-RNA-seq3 experimental batch were additionally  overlaid on 7 mL of a 1.4 M sucrose buffer (1.4 M sucrose, 1X phosphate buffered saline (8 mM Na2HPO4 (pH 7.4), 2 mM KH2PO4, 2.7 mM KCl, 137 mM NaCl), 3 mM MgCl2) and centrifuged at 3,000xg, 20 minutes, 4°C to remove excess debris; the pelleted nuclei were again resuspended in 1 mL of ‘0.3 M SPBSTM’ and passed through a 20-micron cell strainer. After counting, nuclei aliquots were centrifuged (500xg, 5 minutes, 4°C), supernatant aspirated, and pelleted nuclei stored at -80°C until use.
Methods for the first two sci-RNA-seq3 experimental batches largely followed those described by Cao et al. [Cao et al. 2019] with the following modifications: samples were counted with the ImageExpress Pico System (Molecular Devices), 2 μl of oligo(dT) primers were added to each well with 80,000 nuclei for reverse transcription, and tagmentation was performed using 1/40 μl per well of i7-loaded TDE1 enzyme prepared at the BAT-Lab following published protocols [Hennig et al. 2-18]. Libraries were sequenced on an Illumina Nextseq 200 cycles P3 kit with the following cycles: read 1, 34 cycles; read 2, 100 cycles; index 1, 10 cycles; index 2, 10 cycles. Methods for the third sci-RNA-seq3 experimental batch largely followed the optimized protocol described by Martin et al. (Martin et al. 2023) with the following modifications: samples were counted with the ImageExpress Pico System (Molecular Devices), 20,000 nuclei were loaded per reverse transcription well, tagmentation with N7 adaptor-loaded Tn5 transposases (Diagenode cat. no. C01070010-20) was performed at 1/80 uL per well across PCR plates, final library clean up was 0.5X AMPure XP supernatant followed by Qiagene GeneRead Size Selection purification column. The library was sequenced on an Illumina NovaSeq S4 flow cell at the University of Washington Northwest Genomics Center core sequencing facility with the following cycles: read 1, 34 cycles; read 2, 100 cycles; index 1, 10 cycles; index 2, 10 cycles. Read alignment and gene count matrix generation was performed using the Brotman Baty Institute (BBI) pipeline for sci-RNA-seq3 (https://github.com/bbi-lab/bbi-dmux; https://github.com/bbi-lab/bbi-sci). The human GRCh38 build and annotation from Ensembl (release 99) was used as the reference genome. The 3’ UTR annotations of genes and transcripts were extended by 500 bp to avoid misclassifying genic reads as intergenic, and haplotype sequences were removed from the FASTA to avoid mapping inefficiencies due to multimapping.
single-nuclei RNA libaries (sci-RNA-seq3)

treatment_protocol: Placental biopsy tissue was washed extensively to remove maternal blood and maternal uterine tissue was largely removed and rolled membranebiopsies were washed to remove maternal blood

value: Chorionic Membranes

value: COVID-19 (2T)


title: RPE cells from 1mo rd6 mice - replicate 5

description: Library name: MFRP5

value: Retinal pigment epithelium (RPE)


title: COVID-2T_Patient_1_Plac

description:
Library name: 105.31
sci-rna-seq3 run 3

source_name: Chorionic Villi

value: Chorionic Villi


title: 31_953_E029_RPMI_2h [0700835761]

value: RPMI


title: Meningioma 600

description: Hybridized to OncoScanHD

value: Brain


title: 37_953_E030_LPS_2h [0700835821]


title: Meningioma 599

description: Hybridized to OncoScanHD

value: F


title: RPE cells from 1mo rd6 mice - replicate 2

description: Library name: MFRP2


title: Tumoroids, HuCo021320-p27

city: Frederick

first: Pradip

last: Shahi Thakuri

state: Maryland

address: 7305 Executive Way

department: Cell Biology

institute: Thermo Fisher Scientific

description:
Library name: Sample4
10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were perfromed using the Cell Ranger Software v 7.1.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Colon

extract_protocol:
Dissociated tumor cells were purchased from Discovery Life Sciences. Vials of cryopreserved HuCo021320 and HuCo3209 were used for the experiment. Tumoroid lines were derived from one of the original DTC vials and were expanded in OncoPro media. Cell banks were generated throughout the culture by resuspending dissociated tumoroids at 2×10^6 cells/ml in Gibco™ Recovery™ Cell Culture Freezing Medium (Thermo Fisher Scientific, cat# 12648-010), freezing overnight at -80°C in a Mr. Frosty™ Freezing Container (Thermo Scientific™, 5100-001), and storing in a liquid nitrogen dewar. Cryopreserved HuCo021320 at passages 10 and 27, and cryopreserved HuCo3209 at passage 10, were used for single-cell RNA sequencing experiments.
Cryopreserved single cells from dissociated colorectal tumors and tumoroids were submitted to Azenta Life Sciences (Burlington, MA, USA) for scRNA-seq. The sample libraries were prepared in a single batch using the Chromium Single-Cell 3′ v3 Library and Gel Bead Kit (10x Genomics). Briefly, gel bead-based emulsions (GEM) were generated by combining barcoded single-cell 3′ Gel Beads, cells, and partitioning oil. Ten times barcoded, full-length cDNAs generated from GEMs were amplified by polymerase chain reaction (PCR). Enriched libraries were enzymatically digested, size selected, and adaptor ligated for sequencing. Sequencing libraries were generated with unique sample indices for each sample and quantified using the Kapa library kit. Quantified libraries were sequenced on an Illumina NovaSeq™ 6000.

value: Colon

value: Tumoroid line

value: Patient derived tumoroid cell line

tag: diagnosis

value: Colorectal adenocarcinoma

tag: tumor site

tag: Stage

value: IVC

value: Female

tag: race

value: White

tag: height (in)

tag: weight (lb)

tag: treatment status

value: Pre-treatment

tag: tobacco history

value: Never Used

tag: alcohol history

value: No history


title: Tumoroids, HuCo3209-p10

description:
Library name: Sample5
10x Genomics

tag: tissue

tag: cell type

value: Sigmoid colon

value: I

tag: Sex

tag: age


title: 30_953_E028_TNFa_2h [0700835751]

value: PBMCs

tag: donor

value: Healthy control

tag: genotype

value: WT/WT

tag: treatment

value: TNFa


title: 29_953_E028_IL1B _2h [0700835741]

tag: timepoint


title: Meningioma 598

description: Hybridized to OncoScanHD

value: Brain

value: M


title: RPE cells from 1mo rd6 mice - replicate 1

description: Library name: MFRP1

value: Retinal pigment epithelium (RPE)

value: Mfrp rd6/rd6


title: 28_953_E028_R848_2h [0700835731]


title: Meningioma 597

description: Hybridized to OncoScanHD


title: Meningioma 596

description: Hybridized to OncoScanHD

value: F


title: 27_953_E028_LPS_2h [0700835721]

value: LPS


title: Tumoroids, HuCo021320-P10

description:
Library name: Sample3
10x Genomics

value: Colon

tag: cell line

value: Tumoroid line

value: Patient derived tumoroid cell line

tag: diagnosis

value: Colorectal adenocarcinoma

value: IVC

value: Female


title: GEFH1-G-3

city: Dallas

first: Lei

last: Guo

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center

data_processing:
Blc2fastq2 Conversion software (Illumina) was used to generate demultiplexed Fastq files. The adaptors were trimmed using Trim Galore (v0.6.4). The trimmed reads were aligned to the human genome (GRCH38) or mouse genome (mm10) using STAR (2.7.3a). Subsequently, the mapped reads were quantified using the featureCounts of the Subread (v1.6.3) package. Genes with low expression (genes with an expression value of zero in more than 30% of the samples) were removed before subsequent analysis. Gene expression was normalized using the Voom method in the R package “limma” (v 3.50.3). Differentially expressed genes were also identified using this software. Gene set enrichment analysis of differentially expressed genes was performed using the R package “clusterProfiler” (v4.2.2). Volcano plots were generated using R package ggplot2 (v3.5.1). Heat maps were generated using R package pheatmap (v1.0.12).
Assembly: hg38 & mm10
Supplementary files format and content: Text file for count tables

source_name: BMDM

growth_protocol: BMDM cells were generated by flushing bone marrow cells from femurs and tibia of wild type or Arhgef2-/-, Pglyrp-1-/- and Nod2-/- mice and red blood cells were removed by using ACK lysis buffer. Then, 70 µm cell strainers were used to filter BMDM cells, followed by resuspension in complete DMEM supplemented with 10% FBS and 0.5% penicillin/streptomycin mixture, and 200 ng M-CSF.

extract_protocol:
RNeasy Mini Plus kit (Qiagen)
Libraries were synthesized using TruSeq Stranded mRNA sample preparation kit from 500 ng of purified total RNA and indexed adapters according to the manufacturer’s protocol (Illumina). The final libraries were quantified using a Qubit fluorometer (Agilent Technologies), and RT-qPCR was performed using the Kapa Biosystems library quantification kit according to the manufacturer’s protocol. Pooled libraries were subjected to 35 bp paired-end sequencing according to the manufacturer’s protocol (Illumina NextSeq 500). The targeted sequencing depth was set at 30 million paired-end reads per sample

value: BMDM

value: macrophage

value: GMTP


title: Meningioma 595

description: Hybridized to OncoScanHD


title: Dissociated Tumor Cells, HuCo021320_P0

description:
Library name: Sample1
10x Genomics

value: Dissociated tumor cells

value: Tumor

tag: tumor site

tag: Stage

value: White

value: Pre-treatment

value: Never Used

value: No history


title: GEFH1-G-2


title: GEFH1-G-1


title: thp1_ko823_cf009

city: Santa Cruz

last: Carpenter

address: Biomedical Sciences Building First Floor, Red Hill Road

department: MCD

institute: UC Santa Cruz

data_processing:
150 x 150 paired end reads. Sequencing libraries were strand-specific (read2 is the coding strand).
Reads were trimmed to 100X100
Reads were mapped with Bowtie2 to the RepeatMasker library of human repeat elements.
After removing reads with both ends mapped to repeat elements, the remaining reads were mapped to the Hg38 genome assembly using STAR.
Potential PCR duplicates were removed with samtools rmdup.
The coverage for each gene was extracted, then divided by 200 (based on 100x 100bp mappings) for input as mapping counts to DESeq2
The DESeq2 sizeFactors were used to extract normalized read counts per gene for each sample
Assembly: Hg38
Supplementary files format and content: Deseq2_results.tsv, Deseq2 results of all condition-by-conditions comparisons.

growth_protocol: All THP1 cell lines were cultured in RPMI 1640 supplemented with 10% low-endotoxin fetal bovine serum (ThermoFisher), 1X penicillin/streptomycin, and incubated at 37°C in 5% CO2.

extract_protocol:
Total RNA was extracted using Zymo Kit
1 µg total RNA used to generate RNA-Seq libraries using the Bioo kit.
mRNA library preparation and sequenicng paired end 150X150bp

treatment_protocol: Lentivirus with sgrna against OLMALINC or LNCRMP were used to infect THP1 cells expressing dcas9

value: human monocytic cell line

value: OLMALINC knockdown


title: 26_953_E028_RPMI_2h [0700835711]

value: PBMCs

value: Healthy control

value: WT/WT

value: RPMI


title: Meningioma 594

description: Hybridized to OncoScanHD

value: Brain

value: F


title: GEFH1-M-3

value: BMDM

value: MDP


title: thp1_ko823_cf008


title: GEFH1-M-2

value: macrophage


title: Meningioma 590

description: Hybridized to OncoScanHD

value: M


title: thp1_ko823_cf007


title: thp1_ko667_cf006

value: LNCRMP knockdown


title: GEFH1-M-1


title: Dissociated Tumor Cells, HuCo3209_P0

description:
Library name: Sample2
10x Genomics

value: Colon

value: Dissociated tumor cells

value: Tumor

value: Colorectal adenocarcinoma

value: Sigmoid colon

value: I

value: Female

tag: race

value: White

tag: height (in)


title: GEFH1-0-3

value: non


title: Meningioma 589

description: Hybridized to OncoScanHD


title: 21_953_E002_RPMI_2h [0700835661]

value: PBMCs

value: Healthy control

value: WT/WT

value: RPMI


title: RPE cells from 1mo rd6 mice - replicate 3

description: Library name: MFRP3

value: Retinal pigment epithelium (RPE)

value: Mfrp rd6/rd6


title: GEFH1-0-2

value: BMDM

value: macrophage


title: thp1_ko667_cf004

value: human monocytic cell line

value: LNCRMP knockdown


title: Meningioma 587

description: Hybridized to OncoScanHD

value: Brain

value: M


title: 20_091_S05_TNFa_2h [0700835651]

value: Sibling

value: WT/mut

value: TNFa


title: 25_953_E002_TNFa_2h [0700835701]


title: GEFH1-0-1


title: thp1_cntrl_cf003

value: WT


title: 19_091_S05_IL1B _2h [0700835641]


title: Meningioma 593

description: Hybridized to OncoScanHD

value: F


title: Meningioma 586

description: Hybridized to OncoScanHD


title: WT-M-3

value: MDP


title: 24_953_E002_IL1B _2h [0700835691]

value: PBMCs

value: Healthy control


title: 22_953_E002_LPS_2h [0700835671]

value: WT/WT

value: LPS


title: thp1_cntrl_cf002


title: WT-M-2


title: thp1_cntrl_cf001


title: 23_953_E002_R848_2h [0700835681]


title: 18_091_S05_R848_2h [0700835631]


title: Meningioma 588

description: Hybridized to OncoScanHD


title: Meningioma 585

description: Hybridized to OncoScanHD


title: 17_091_S05_LPS_2h [0700835621]


title: WT-M-1


title: Meningioma 584

description: Hybridized to OncoScanHD


title: 16_091_S05_RPMI_2h [0700835611]

value: RPMI


title: Meningioma 583

description: Hybridized to OncoScanHD


title: HaCaT cells, D_3

city: hangzhou

first: zhiqi

last: xie

address: huzhou street 51

country: China

institute: Hangzhou city university

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM and count values for each samples

source_name: HaCaT cells

growth_protocol: Human immortalized keratinocytes HaCaT was cultured in DMEM containing 10% fetal bovine serum and placed in a cell incubator with 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were 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 then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. 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. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

treatment_protocol: treated with TNF-α/IFN-γ  (10 ng/ml) for 48h

value: HaCaT cells


title: WT-G-3

value: BMDM

value: macrophage

value: GMTP


title: Meningioma 582

description: Hybridized to OncoScanHD

value: Brain


title: 15_091_S05_TNFa_2h [0700835601]


title: HaCaT cells, D_2

value: treated with TNF-α/IFN-γ  (10 ng/ml) for 48h


title: WT-G-2


title: Meningioma 581

description: Hybridized to OncoScanHD

value: M


title: HaCaT cells, D_1


title: 14_091_S03_IL1B _2h [0700835591]

value: Sibling

value: WT/mut


title: WT-G-1


title: HaCaT cells, A_3

value: untreat


title: 13_091_S03_R848_2h [0700835581]


title: Meningioma 580

description: Hybridized to OncoScanHD


title: WT-0-3

value: non


title: HaCaT cells, A_2


title: Meningioma 578

description: Hybridized to OncoScanHD

value: F


title: 12_091_S03_LPS_2h [0700835571]

value: PBMCs


title: WT-0-2


title: HaCaT cells, A_1


title: 11_091_S03_RPMI_2h [0700835561]


title: Meningioma 577

description: Hybridized to OncoScanHD


title: WT-0-1


title: Meningioma 576

description: Hybridized to OncoScanHD


title: 10_091_P12_TNFa_2h [0700835551]

value: Patient

value: mut/mut

value: TNFa


title: Pglyrp1-M-3

value: PGLYRP-/-

value: MDP


title: GSC cells treated with ferroptosis inducer RSL3 (3uM) incubated for 24h in hypoxic oxygen conditions (1% O2, 5% CO2)_4

city: Warsaw

first: Barbara

last: Olejniczak

address: Pawinskiego 5

department: Department of Neurooncology

country: Poland

institute: Mossakowski Medical Research Institute, Polish Academy of Sciences

data_processing:
Raw sequences were trimmed according to quality using Trimmomatic (Bolger, Lohse, and Usadel 2014) (version 0.39) using the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:20.
Trimmed sequences were mapped to the human reference genome provided by ENSEMBL, (version grch38_snp_tran) using Hisat2 (Kim, Langmead, and Salzberg 2015) with default parameters.
Optical duplicates were removed using MarkDuplicates tool from GATK (McKenna et al. 2010) package (version 4.2.3.0) with default parameters except OPTICAL_DUPLICATE_PIXEL_DISTANCE set to 12000.
Mapped reads were associated with transcripts from grch38 database (Zerbino et al. 2018) (Ensembl, version 112) using HTSeq-count (Anders, Pyl, and Huber 2015) (version 0.9.1) with default parameters except –stranded set to “reverse”.
Differentially expressed genes were selected using the DESeq2 package (Love, Huber, and Anders 2014) (version1.38.3).
Assembly: grch38 database, Ensembl version 112
Supplementary files format and content: Count normalized with "counts" function from Deseq2 package. Genes that haven't  reach 32 normalized counts in any group were removed.

source_name: glioblastoma

growth_protocol: GSCs were cultured in Neurobasal medium with 1% GlutaMax, B27 minus Vit A and EGF/bFGF (20 ng/ml each) in 5% CO2 incubator. Before experiments single cells suspension was plated on ultra low attachment 6-well plates in concentration 400 000 cells.

extract_protocol:
RNA from snap frozen pellets were isolated with phenol-chloroform method. RNA was precipitated overnight using ice-cold isopraponol at -80C and washed with 70% ethanol. Resuspended in water and frozen in -80C for further analysis.
RNA samples (1000 ng) were treated with KAPA RNA HyperPrep Kit with Riboerase to remove ribosomal RNA. To create libraries adapters KAPA_UDI_Indexes were used. Further fragmentation was performed in 94 C for 5 min. PCR amplification was done for 10 cycles, acording to Kapa Biosystems protocol).

treatment_protocol: Control cells treated with DMSO (0.1% final concentration), and ferroptosis inducer at 3 uM (RSL3 in DMSO) and cultured for 24h in either Normoxia (20% oxygen and 5% CO2) or Hypoxia (1% oxygen, 5% CO2).

value: glioblastoma

value: GSCs

value: control

tag: condition

value: hypoxia


title: Meningioma 575

description: Hybridized to OncoScanHD

value: Brain


title: 9_091_P12_IL1B _2h [0700835541]


title: Pglyrp1-M-2

value: BMDM

value: macrophage


title: GSC cells treated with ferroptosis inducer RSL3 (3uM) incubated for 24h in hypoxic oxygen conditions (1% O2, 5% CO2)_3


title: Meningioma 574

description: Hybridized to OncoScanHD

value: M


title: Pglyrp1-M-1


title: 8_091_P12_R848_2h [0700835531]


title: 7_091_P12_LPS_2h [0700835521]

value: LPS


title: Meningioma 573

description: Hybridized to OncoScanHD


title: GSC cells treated with ferroptosis inducer RSL3 (3uM) incubated for 24h in hypoxic oxygen conditions (1% O2, 5% CO2)_1


title: Pglyrp1--G-3

value: GMTP


title: Pglyrp1--G-2


title: Meningioma 572

description: Hybridized to OncoScanHD

value: F


title: GSC cells treated with ferroptosis inducer RSL3 (3uM) incubated for 24h in normal oxygen conditions (21% O2, 5% CO2)_5

value: normoxia


title: GSC cells treated with ferroptosis inducer RSL3 (3uM) incubated for 24h in hypoxic oxygen conditions (1% O2, 5% CO2)_5


title: 5_091_P07_TNFa_2h [0700835501]

value: PBMCs

value: Patient


title: Meningioma 571

description: Hybridized to OncoScanHD


title: Pglyrp1--G-1


title: GSC cells treated with ferroptosis inducer RSL3 (3uM) incubated for 24h in normal oxygen conditions (21% O2, 5% CO2)_4


title: 4_091_P07_IL1B _2h [0700835491]

value: mut/mut


title: GSC cells treated with ferroptosis inducer RSL3 (3uM) incubated for 24h in normal oxygen conditions (21% O2, 5% CO2)_3


title: Meningioma 569

description: Hybridized to OncoScanHD


title: 3_091_P07_R848_2h [0700835481]


title: Pglyrp1-0-2

value: PGLYRP-/-

value: non


title: GSC cells treated with ferroptosis inducer RSL3 (3uM) incubated for 24h in normal oxygen conditions (21% O2, 5% CO2)_2

value: glioblastoma


title: 2_091_P07_LPS_2h [0700835471]


title: Meningioma 568

description: Hybridized to OncoScanHD


title: Pglyrp1-0-1


title: GSC cells treated with ferroptosis inducer RSL3 (3uM) incubated for 24h in normal oxygen conditions (21% O2, 5% CO2)_1

value: GSCs


title: 1_091_P07_RPMI_2h [0700835461]

value: RPMI


title: 6_091_P12_RPMI_2h [0700835511]


title: Meningioma 567

description: Hybridized to OncoScanHD


title: GSC cells control (with DMSO) incubated for 24h in hypoxic oxygen conditions (1% O2, 5% CO2)_5

value: control

value: hypoxia


title: NOD2-M-3

value: BMDM

value: MDP


title: Meningioma 566

description: Hybridized to OncoScanHD

value: Brain


title: Meningioma 565

description: Hybridized to OncoScanHD


title: Meningioma 570

description: Hybridized to OncoScanHD

value: M


title: NOD2-M-2

value: macrophage


title: Health control 2

city: Sao Paulo

first: Guilherme

last: Cebinelli

address: Elias Jafet, 755

country: Brazil

institute: Hospital Israelita Albert Einstein

description:
Library name: Sample 10
10x genomics

data_processing:
Single-cell RNA sequencing data pre-processing: Base call files were converted in the Cell Ranger to FASTQ files using the mkfastq function. The reads were then aligned to the mm10 Mus musculus transcriptome using the Cell Ranger software pipeline (version 6.1.2) provided by the 10x Genomics to generate raw genes by cell matrices of unique molecular identifier counts for each sample. The samples were then grouped in health controls, survived, and non-survived, and were read into R using the read10x function (Hao et al., 2021), resulting in a count matrix with 32285 genes and 8248 cells. A Seurat object was then created, and a filter was applied to remove the low-quality cells by excluding those based on unique molecular identifier counts (nCount_RNA < 10000), the number of unique genes (nFeature_RNA between 200 and 3000), and the percentage of mitochondrial gene expression (percent.mt < 10). The remaining expression values were then normalized using the SCTransform (Hafemeister & Satija, 2019).
Assembly: The reads were then aligned to the mm10 Mus musculus transcriptome using the Cell Ranger software pipeline (version 6.1.2) provided by the 10x Genomics to generate raw genes by cell matrices of unique molecular identifier counts for each sample.
Supplementary files format and content: The samples were then grouped in health controls, survived, and non-survived, and were read into R using the read10x function (Hao et al., 2021), resulting in a count matrix with 32285 genes and 8248 cells. A Seurat object was then created, and a filter was applied to remove the low-quality cells by excluding those based on unique molecular identifier counts (nCount_RNA < 10000), the number of unique genes (nFeature_RNA between 200 and 3000), and the percentage of mitochondrial gene expression (percent.mt < 10). The remaining expression values were then normalized using the SCTransform (Hafemeister & Satija, 2019).

source_name: Peripheral blood

extract_protocol:
Leukocytes from each mouse were the multiplexed with a molecular tag following the 10x Genomics 3’ CellPlex Kit (10x Genomics, cat#1000261), and cells from 10 mice were encapsulated in two lanes of a 10× Chromium instrument, each 5 mice per lane.
Libraries were constructed using the Chromium Next GEM Single Cell 3' Kit v3.1 following the manufacturer’s instructions (10x Genomics, cat#1000269), and were subsequently sequenced on the HiSeq 4000 (Illumina).

treatment_protocol: Isolation of leukocytes and single-cell RNA sequencing: Sepsis was induced using the cecal ligation and puncture (CLP) model, as previously described (Rittirsch et al., 2009). The mice were anesthetized by inhalation of 1.5 % of isoflurane, and two punctures were made through the ligated cecum using an 18-gauge needle. After the surgery, 1 mL of saline and tramadol 25 mg/kg was injected subcutaneously. After 6 hours of the surgery, antibiotic treatment with 30 mg/kg ertapenem (Merck Sharp & Dohme) was administered, followed by six additional doses every 12 hours. After 12 hours of the CLP-sepsis induction, 50 uL of blood samples were collected from the retro-orbital plexus of anesthetized mice, and the sepsis survival rate was monitored for up to 7 days. Leukocytes were isolated using positive magnetic isolation of CD45+ cells, following the manufacturer’s instructions (Miltenyi Biotec, cat#130-052-301).

value: Peripheral blood

value: CD45+ cells

value: male

tag: disease model

value: Control

tag: disease outcome

value: survived

tag: batch 10x

tag: cmo


title: Pglyrp1-0-3

tag: tissue

tag: cell type

value: PGLYRP-/-


title: Health control 1

description:
Library name: Sample 9
10x genomics

tag: age

tag: Sex


title: GSC cells control (with DMSO) incubated for 24h in hypoxic oxygen conditions (1% O2, 5% CO2)_4

tag: treatment


title: CLPsepsis, non-survived 4

description:
Library name: Sample 8
10x genomics

value: CLP-sepis induction


title: GSC cells control (with DMSO) incubated for 24h in hypoxic oxygen conditions (1% O2, 5% CO2)_3

value: glioblastoma


title: Meningioma 564

description: Hybridized to OncoScanHD

value: F


title: NOD2-G-3

tag: genotype

value: GMTP


title: GSC cells control (with DMSO) incubated for 24h in hypoxic oxygen conditions (1% O2, 5% CO2)_2

value: GSCs

value: control


title: Meningioma 563

description: Hybridized to OncoScanHD


title: NOD2-G-2

value: BMDM


title: CLPsepsis, non-survived 3

description:
Library name: Sample 7
10x genomics


title: 34_953_E029_IL1B _2h [0700835791]

value: PBMCs

tag: donor

value: Healthy control

value: WT/WT

tag: timepoint


title: GSC cells treated with ferroptosis inducer RSL3 (3uM) incubated for 24h in hypoxic oxygen conditions (1% O2, 5% CO2)_2

value: hypoxia


title: CLPsepsis, non-survived 2

description:
Library name: Sample 6
10x genomics

value: Peripheral blood


title: Meningioma 562

description: Hybridized to OncoScanHD

value: Brain


title: NOD2-G-1

value: macrophage


title: GSC cells control (with DMSO) incubated for 24h in normal oxygen conditions (21% O2, 5% CO2)_5

value: normoxia


title: CLPsepsis, non-survived 1

description:
Library name: Sample 5
10x genomics

value: CD45+ cells

value: male


title: Meningioma 561

description: Hybridized to OncoScanHD


title: GSC cells control (with DMSO) incubated for 24h in hypoxic oxygen conditions (1% O2, 5% CO2)_1


title: NOD2-0-3

value: non


title: NOD2-M-1

value: MDP


title: GSC cells control (with DMSO) incubated for 24h in normal oxygen conditions (21% O2, 5% CO2)_4

value: glioblastoma


title: Meningioma 560

description: Hybridized to OncoScanHD

value: F


title: GSC cells control (with DMSO) incubated for 24h in normal oxygen conditions (21% O2, 5% CO2)_3

value: GSCs


title: CLPsepsis, survived 4

description:
Library name: Sample 4
10x genomics

value: CLP-sepis induction

value: survived


title: NOD2-0-2

value: BMDM


title: CLPsepsis, survived 3

description:
Library name: Sample 3
10x genomics


title: NOD2-0-1


title: thp1_ko667_cf005

tag: cell line

value: human monocytic cell line

value: LNCRMP knockdown


title: RPE cells from 1mo wt (C57BL/6J) mice - replicate 3

description: Library name: WT3

value: Retinal pigment epithelium (RPE)

value: wt


title: CLPsepsis, survived 2

description:
Library name: Sample 2
10x genomics

value: Peripheral blood


title: GSC cells control (with DMSO) incubated for 24h in normal oxygen conditions (21% O2, 5% CO2)_2

value: control


title: NOD2-GMTP-2

value: macrophage

value: GMTP


title: GSC cells control (with DMSO) incubated for 24h in normal oxygen conditions (21% O2, 5% CO2)_1

value: normoxia


title: Meningioma 609

description: Hybridized to OncoScanHD

value: Brain

value: M


title: CLPsepsis, survived 1

description:
Library name: Sample 1
10x genomics

value: CD45+ cells

value: male


title: RNA_1292_HOXBLINC_KD2

city: Hershey

first: Suming

last: Huang

state: PA

address: 500 University Dr.

department: Pediatrics

institute: Penn State College of Medicine

data_processing:
Adaptor sequences were trimed by cutadaptSequenced reads were trimmed and quality filtered using cutadapt (Martin 2011) version 1.18 and aligned to human (hg19) or mouse genome (mm10) using HISAT2 (Kim, Paggi et al. 2019) version 2.2.1. The read counts were calculated by featureCounts (Liao, Smyth et al. 2014) ver.2.0.3. Normalized counts, fold change and p-value between cell condition were generated by DEseq2 (Love, Huber et al. 2014) ver.1.40.2.
Assembly: mm10 or hg19
Supplementary files format and content: Tabular file of raw counts (output from featureCounts) and/or .bigwig file

source_name: Bone marrow cells

growth_protocol: BaF3 cells were cultured in in IMDM supplemented with heat inactivated fetal bovine serum and penicillin/streptomycin. 961C were maintained in IMDM supplemented with heat inactivated fetal bovine serum and penicillin/streptomycin (Gough, Lee et al. 2014). A1929 cells were maintained RPMI supplemented with 10% FBS, 50uM 2-ME and 10ng/ml mouse recombinant IL-7(Yin, Chung et al. 2018). Patient samples were maintained in StemSpan™ SFEM II supplemented with StemSpan™ CD34+ Expansion Supplement (10X) and 10ng/ml of Human Recombinant GM-CSF, ACF.

extract_protocol:
RNA is extracted using Quick-RNA miniprep kit (ZYMO research) according to manufacturer’s protocol.
1ug of RNA which have high RIN value (more than 8) were used as input for RNA-seq library preparation. We used NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) for enrichment mRNA and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) for library preparation according to manufacturer’s protocol.

value: Bone marrow cells

value: patient AML

value: NUP98-HOXA9 with HOXBLINC KD


title: NOD2-MDP-2

value: BMDM

value: MDP


title: Meningioma 555

description: Hybridized to OncoScanHD


title: 237_WT

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute (CCRI)

data_processing:
nf-core/rnaseq v3.14.0
Assembly: GRCm38.p6
Supplementary files format and content: bigWig
Supplementary files format and content: STAR/RSEM merged counts, TSV

source_name: MSCLCs

extract_protocol:
To prepare samples for RNA sequencing, total RNA was isolated using RNeasy Mini Kit (#74106, QIAGEN). The RNA quality was checked using Bioanalyzer 2100 (Agilent) with RNA 6000 Pico Chips (#5067-1513, Agilent) according to the manufacturers’ instructions
The library was prepared from these samples by poly(A) enrichment (E7490S, New England Biolabs).

value: MSC

tag: flowcell

value: MSCLCs

tag: lane


title: NOD2-GMTP-1


title: Meningioma 559

description: Hybridized to OncoScanHD


title: Meningioma 606

description: Hybridized to OncoScanHD

value: F


title: Meningioma 554

description: Hybridized to OncoScanHD


title: RNA_1292_HOXBLINC_KD1


title: 234_WT


title: Meningioma 553

description: Hybridized to OncoScanHD


title: 229


title: NOD2-UT-2

value: non


title: 225


title: NOD2-UT-1


title: Meningioma 558

description: Hybridized to OncoScanHD


title: NOD2-MDP-1


title: RNA_1265_HOXBLINC_KD1


title: RNA_1265_HOXBLINC_KD2


title: Meningioma 552

description: Hybridized to OncoScanHD


title: Meningioma 551

description: Hybridized to OncoScanHD


title: 221


title: Meningioma 556

description: Hybridized to OncoScanHD


title: PG1-GMTP-2

value: PGLYRP-/-


title: PG1-GMTP-1

value: macrophage


title: AC replicate 3

city: Chengdu

first: Yuxi

last: Gu

address: No.17, Section 3, Renmin South Road, Wuhou District, Chengdu

institute: West China hospital of stomatology, Sichuan University

library_source: genomic

data_processing:
After harvesting paired-end reads, quality control was performed by Q30. Cutadapt software (v1.9.1) was used for low quality reads removal and bwa software v(v0.7.12) was used for reference genome (Feb. 2009 GRCh37 / hg19) alignment of the clean reads of the high quality
Next, eccDNAs in all samples were detected using circle-map software (v1.1.4), and raw soft-clipped read counts of the break poin were obtained by samtools (v0.2).
Annotation of eccDNAs was conducted with bedtools (v2.27.1).
Assembly: hg19
Supplementary files format and content: excel format include number of raw junction read
Library strategy: Circle-seq

source_name: ACs

extract_protocol:
For each sample, cells were mixed with proteinase K (ThermoFisher, E00491) in L1 solution (A&A Biotechnology, 010-50) before incubation at 50°C for 16h with agitation. Then samples were prepared for eccDNA enrichment with column chromatography on an ion exchange membrane column (Plasmid Mini AX; A&A Biotechnology). DNA from uhBMSCs, OBs, CCs and ACs was purified using FastDigest MssI (Thermo Scientifific, ER1341) at 37 °C for 16h and Plasmid-Safe ATP-dependent DNase (E3110K, Plasmid-Safe ATP-dependent DNase, Lucigen) at 37 °C for 1 week. Every 24h, 30 units of ATP and ATP-dependent DNase were added. GenSeq® RCA DNA Amplification Kit was used for phi29 amplification (Genseq Inc., GS-MB-002S) at 30 °C for 46–48h.
Library preparation was conducted using GenSeq® Rapid DNA Lib Prep Kit (GenSeq Inc.)

value: ACs


title: 202


title: Meningioma 549

description: Hybridized to OncoScanHD


title: PG1-MDP-1


title: RNA_1292_WT


title: AC replicate 2


title: AC replicate 1


title: 221-Combi-T1

value: ha


title: PG1-MDP-2


title: Meningioma 548

description: Hybridized to OncoScanHD

value: Brain


title: PG1-0-2


title: 221-Combi-uns-1-1

value: hr


title: CC replicate 3

source_name: CCs

value: CCs


title: Meningioma 547

description: Hybridized to OncoScanHD

source_name: Meningioma Tissue


title: Meningioma 545

description: Hybridized to OncoScanHD


title: 221-Combi-T2


title: 221-Combi-uns-1-2


title: CC replicate 2


title: RNA_1265_WT


title: Meningioma 544

description: Hybridized to OncoScanHD


title: WT-GMTP-2

value: GMTP


title: Meningioma 546

description: Hybridized to OncoScanHD


title: CC replicate 1


title: WT-GMTP-1


title: OB replicate 3

source_name: OBs

value: OBs


title: Meningioma 550

description: Hybridized to OncoScanHD


title: PG1-0-1


title: 219


title: 221-Combi-uns-2-1


title: 221-Combi-uns-2-2


title: Meningioma 543

description: Hybridized to OncoScanHD

value: M


title: Meningioma 542

description: Hybridized to OncoScanHD


title: WT-MDP-2


title: OB replicate 2


title: WT-MDP-1


title: 221-1

value: EF


title: Meningioma 541

description: Hybridized to OncoScanHD


title: OB replicate 1


title: 221-2


title: uBMSC replicate 3

source_name: uBMSCs

value: uBMSCs


title: WT-UT-2

value: BMDM


title: Meningioma 540

description: Hybridized to OncoScanHD


title: S_221_IGF1_xeno

data_processing:
Raw sequencing data were processed using pypiper v0.10.0 and PEPATAC v0.8.6
Assembly: GRCm38.p3
Supplementary files format and content: bigWig
Supplementary files format and content: MACS2 narrowPeak

extract_protocol:
20,000 to 50,000 cells were lysed in the transposase reaction mix (12.5 μl 2xTD buffer, 2 μl TDE1 [Illumina], 10.25 μl nuclease-free water, and 0.25 μl 1% digitonin [Promega]) for 30 min at 37 °C.
Tagmented DNA was purified and enriched and ATAC-seq libraries were prepared sequencing in 50 bp single-end read mode on an Illumina HiSeq instrument at the Biomedical Sequencing Facility (BSF) at the CeMM Research Center of Molecular Medicine of the Austrian Academy of Sciences.


title: uBMSC replicate 1


title: Meningioma 539

description: Hybridized to OncoScanHD


title: Meningioma 538

description: Hybridized to OncoScanHD


title: mESC, Tead4, nexus, 2

city: Overland Park

first: Khyati

middle: Sudhir

last: Dalal

state: KS

address: 75th street, APT 106, 6329 W

institute: Stowers Institute for Medical Research

description:
mesc_tead4_nexus_combined_peaks.narrowPeak
mesc_tead4_nexus_combined_positive.bw
mesc_tead4_nexus_combined_negative.bw

data_processing:
ChIP-nexus adapter fragments were trimmed from the 3’ end of the fragments using cutadapt (v.2.5)
ChIP-nexus reads were aligned using bowtie (v.1.1.2) to the Mus musculus genome assembly mm10. Aligned ChIP-nexus BAM files were deduplicated based on unique fragment coordinates and barcode assignments.
Genome-wide coverage was calculated and saved in BigWig format.
ChIP-nexus peaks were called using MACS2 (v.2.2.6) with parameters designed to resimulate the full fragment length coverage rather than the single stop base coverage (--keep-dup=all -f=BAM --shift=-75 --extsize=150).
Genome-wide coverage was calculated and saved in BigWig format.
Assembly: UCSC mm10
Supplementary files format and content: BigWig, narrowPeak (except for Input sample)

growth_protocol: R1 ESCs were cultured on 0.1% gelatin-coated plates without feeder cells in N2B27 medium (DMEM/F12 with 1:1 mix of GlutaMax/N2 and Neurobasal medium/B27, Invitrogen) supplemented with 2 mML-glutamine (Stemcell Technologies), 1× 2-mercaptoethanol (Millipore), 1× NEAA (Stemcell Technologies), 3 µM CHIR99021 (Stemcell Technologies), 1 µM PD0325901 (Stemcell Technologies), 0.033% BSA solution (Invitrogen) and 107U ml–1LIF (Millipore).

extract_protocol:
For each ChIP experiment, 10 million TSCs were used. Cells were washed with PBS and cross-linked with 1% formaldehyde (Fisher Scientific) in PBS for 10 minutes at room temperature. The reaction was quenched with 125 mM glycine. Fixed cells were washed twice with cold PBS and resuspended in cold lysis buffer (15 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.5% N-lauroylsarcosine, 0.1% sodium deoxycholate and 0.1% SDS), incubated for 10 min on ice and sonicated with a Bioruptor Pico (Diagenode) for five cycles of 30s on and 30 s off.  The following antibodies were used: anti-Tfap2c (R & D systems, no. AF5059), anti-Tead4 (Abcam, no. ab58310), anti-Cdx2 (Bethyl Laboratories, no. A300-692A), anti-Gata3 (Cell Signaling, no. 5852T), anti-Yap1 (Cell Signaling, no. 14074S), anti-Pol II (Cell Signaling, no. D8L4Y), anti-H3K27ac (ChIP–seq) (Active motif, no. 39135).
ChIP-nexus was performed according to He et al., 2015. ChIP-seq was performed as previously described in He et al., 2011, and included a whole cell extract (WCE).
ChIP-nexus for transcription factors and ChIP-seq for histone modifications using standard Illumina protocols.
ChIP-nexus reads were pre-processed by trimming off fixed and random barcodes and reassigning them to FASTQ read names.

value: Wild-type

value: mouse embryonic stem cells

tag: chip antibody

value: Tead4, Abcam, no. ab58310


title: mESC, Tead4, nexus, 3


title: S_220_IGF1

value: MSCLCs


title: lung, infected, donor7, adult, scRNAseq

city: Rochester

first: Raven

middle: M.

last: Osborn

state: NY

address: 601 Elmwood Ave

department: Microbiology

institute: University of Rochester School of Medicine and Dentistry

description: 10x Genomics

data_processing:
Samples were demultiplexed and counted using 10x cellranger version 6.0.1 with standard parameters.
Bowtie2 (v. 2.2.9) to align against combined reference containing the 10x provided human reference (GRCh38-2020-A) and NCBI GenBank reference sequence MT644268
Assembly: GRCh38-2020-A and NCBI GenBank reference sequence MT644268
Supplementary files format and content: Tab-separated values, files, and matrix files

source_name: lung

extract_protocol:
The protocol described is published on protocols.io (https://dx.doi.org/10.17504/protocols.io.kqdg3999eg25/v1) and is included for printing purposes as supplementary file in a article published by PlosONE (https://doi.org/10.1371/journal.pone.0281898). Briefly, cultured cells were washed by dispensing and aspirating 37°C HEPES buffered saline solution (Lonza, CC-5022), and then dissociated with 0.025% Trypsin/EDTA (Lonza,CC-5012) for 10 min at 37°C. Dissociated cells were aspirated using a wide-bore pipette tip and placed in a tube containing ice-cold Trypsin Neutralization Solution (Lonza, CC5002); this was repeated to maximize cell collection. Cells were then pelleted by centrifugation, resuspended in chilled HEPES, and centrifugally pelleted once more. Using a wide-bore pipette tip, the supernatant was then removed and the cell pellet was resuspended in 100ul chilled 1X DPBS. Next, 1ml of a chilled 1:1 methanol acetone mixture was added to the cells in a dropwise manner with continuous gentle agitation. Cells were incubated on ice for 1 hour, washed in PBS++, counted, and finally resuspended in cold SSC cocktail (3× Lonza AccuGENE SSC, BMA51205 + 0.04% BSA + 1mM DTT + 0.2 U/ul RNase1 inhibitor).
Following SARS-CoV-2 inactivation and rehydration, cell suspensions were processed to generate single-cell RNA-Seq libraries using Chromium Next GEM Single Cell 3′ GEM, Library and Gel Bead Kit v3.1 (10x Genomics), per the manufacturer’s recommendations, as summarized below. To minimize the addition of the rehydration buffer, a maximum of 4ul cell suspension was used in the GEM (Gel Bead-in-Emulsion) generation step. Subsequently, samples were loaded on a Chromium Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell GEMs. GEM reverse transcription (GEM-RT) was performed to produce a barcoded, full-length cDNA from poly-adenylated mRNA. After incubation, GEMs were broken, the pooled GEM-RT reaction mixtures were recovered, and cDNA was purified with silane magnetic beads (DynaBeads MyOne Silane Beads, PN37002D, ThermoFisher Scientific). The purified cDNA was further amplified by PCR to generate sufficient material for library construction. Enzymatic fragmentation and size selection was used to optimize the cDNA amplicon size and indexed sequencing libraries were constructed by end repair, A-tailing, adaptor ligation, and PCR. Final libraries contain the P5 and P7 priming sites used in Illumina bridge amplification.

value: Epithelial

value: lung

value: male

tag: developmental stage

value: adult

value: 69 years

tag: race

value: caucasian

value: infected with SARS-CoV-2


title: S_221_IGF1


title: Meningioma 536

city: Boston

first: Scott

last: Ryall

address: 75 Francis Street

institute: Brigham and Women's Hospital

description: Hybridized to OncoScanHD

data_processing:
Data analysis was performed using Chromosome Analysis Suite software version 1.2.2
[primary data description] Fluorescent intensity values across SNP probes

extract_protocol: DNA was extracted using the QIAamp DNA FFPE Tissue Kit and stored at 4˚C

value: Brain


title: S_221_0


title: S_220_0


title: Meningioma 535

description: Hybridized to OncoScanHD


title: mESC, Tead4, nexus, 1


title: lung, mock, donor7, adult, scRNAseq

description: 10x Genomics

value: mock


title: mTSC,wildtype,nascent_rna,3

data_processing:
To get STAR count table for RNA-seq data:  100 bp single-end sequencing reads were aligned using STAR(v.2.7.3) (Dobin et al. 2013) to the Mus Musculus genome assembly mm10  using Ensembl 102 gene models with the following parameters: outSAMtype BAM SortedByCoordinate, outSAMprimaryFlag OneBestScore ,outFilterMultimapNmax 20, outFilterMismatchNoverLmax 0.1, outFilterType BySJout ,alignSJoverhangMin 8, alignSJDBoverhangMin 1,outFilterMismatchNmax 999,alignIntronMin 20,alignIntronMax 1000000,alignMatesGapMax 1000000,limitBAMsortRAM 10000000000 ,outSAMattributes NH HI MD AS nM, quantMode TranscriptomeSAM GeneCounts.
To get TPM for RNA-seq data : Rsem-calculate-expression (v1.3.0) (Li and Dewey 2011) was used to generate an expression table with the following parameters: no-bam-output, estimate-rspd, strandedness reverse. EdgeR analysis : Pairwise differential expression analysis was performed using Bioconductor package edgeR (3.24.3 with R 3.5.2). Only protein coding genes and long non-coding RNAs (lncRNAs) were considered from the Ens_102 annotation. Only genes with counts per million expression ≥ 0 in at least 2 sample were kept for further analyses. Statistical significance was determined by fold change cutoff of 1 and false discovery rate (FDR) cutoff of 0.05 .
For Nascent RNA captured through TT-seq method : 75 bp paired-end sequencing reads were aligned using STAR(v.2.7.3) (Dobin et al. 2013) to the Mus Musculus genome assembly mm10 with the following parameters: outFilterMismatchNmax 2, outFilterMultimapScoreRange 0. SAMtools (v.1.14) (Li et al. 2009) were then used to keep alignments with mapping quality greater than 255 (-q 255), and only proper pairs (-f 2) were selected. Strand-specific BAM files for each replicate and combined were generated using the following parameters (samtools view -b -f 128 -F 16; -b -f 80; -b -f 144; -b -f 64 -F 16) and (samtools merge plus_128.bam with plus_80.bam and minus_144.bam with minus_64.bam).
Normalized TT-seq coverage was generated using bamCoverage (v.3.1.3) (Ramírez et al. 2014) parameter Reads Per Kilobase per Million mapped reads (RPKM).
Assembly: UCSC mm10
Supplementary files format and content: BigWig, CSV,TSV

source_name: cells

growth_protocol: 70% Feeder-CM plus 30% TS medium (hereafter 70cond) supplemented with FGF4, and heparin (70cond + 1.5 F4H Medium) was used to maintain TSCs in feeder-free conditions

extract_protocol:
For RNA-seq experiments : TSCs wild-type and CRISPR-mutated ezr cells were grown separately in wells of a 6-well plate and harvested at 80% confluency (~2e6 cells) using 500 μL of TRIzol reagent (Life Technologies Corp-15596026). For RNA extraction, the lysate was quickly thawed at 65°C, cooled on ice for 5 minutes, and vortexed. Then, 100 μL of chloroform was added per 0.5 mL of TRIzol lysis reagent, shaken vigorously for 15 seconds, and incubated for 3 minutes. The sample was centrifuged at 4°C and 7000 x g for 25 minutes, and the upper colorless aqueous phase was transferred to a new tube. To this, 250 μL of isopropanol was added, incubated for 10 minutes at 4°C, and centrifuged at 4°C and 12,000 x g for 10 minutes. The total RNA precipitate formed a white gel-like pellet at the bottom of the tube, which was washed with 75% ethanol, air-dried for 5-10 minutes, and resuspended in 20 μL of RNase-free water. DNase treatment was performed using the TURBO DNase kit per the manufacturer's instructions: adding 1 ul of TURBO DNase & 2 ul of DNase buffer to the dissolved RNA and incubating at 37 degrees for 30 min. To inactivate TURBO DNase, RNA samples were extracted with phenol/chloroform (Sigma-P3803). After the total RNA pellet dissolved again in 20 ul of RNase-free water. Then, incubate the sample in a water bath or heat block set at 55-60°C for 10-15 minutes.
For RNA-seq,The RNA concentration was determined using a NanoDrop spectrophotometer, and The RNA integrity was checked on a 2100 Bioanalyzer using an Agilent RNA 6000 Nano Kit. mRNA-stranded libraries were prepared using a TruSeq poly-A Stranded mRNA Library Prep Kit and sequenced on an Illumina NextSeq 2000 P2 platform with 2 x 100 bp single-end reads.
For RNA-seq: mRNA-stranded libraries were prepared using a TruSeq poly-A Stranded mRNA Library Prep Kit
For Nascent RNA-seq, we used TT-Seq method as described: https://www.protocols.io/view/transient-transcriptome-sequencing-experimental-pr-3byl42y22vo5/v1; For trophoblast stem cells: approximately 10 million cells were seeded in a 100 cm dish (~80% confluency), and 500 µM of 4sU (Sigma, T4509) was added and kept at 37 °C, 5% CO2 for 15 mins. The cells were then collected by adding 4.5 mL of TRIzol lysis reagent (Life Technologies Corp-15596026), incubated for 5 min on ice, flash-frozen, and stored at −80°C. And in the biotinylation of 4sU labeled RNA step, acid-phenol-chloroform (ThermoFisher, AM9720) was used instead of chloroform.
For Nascent RNA-seq, Nascent RNA concentration was measured using the Qubit RNA HS Kit, and RNA integrity was analyzed on Agilent Bioanalyzer RNA 6000 Pico Chip and sequenced on an Illumina NextSeq 500  with 2 x 75 bp paired-end reads.
For Nascent RNA-seq: TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold Set, which degrades rRNA with the enzyme.

value: cells

value: mouse trophoblast stem cells


title: S_203_0

value: Wt


title: Meningioma 534

description: Hybridized to OncoScanHD

value: F


title: lung, mock, donor6, adult, scRNAseq

description: 10x Genomics

value: 53 years


title: BM_IGF1


title: Meningioma 533

description: Hybridized to OncoScanHD

value: M


title: mTSC,wildtype,nascent_rna,2

value: Wild-type


title: mTSC,wildtype,nascent_rna,1


title: lung, infected, donor5, pediatric, scRNAseq

description: 10x Genomics

value: pediatric

value: 2 months

value: unknown


title: BM_unt

value: MSCLCs


title: uBMSC replicate 2

value: uBMSCs


title: Meningioma 532

description: Hybridized to OncoScanHD


title: WT-UT-1

value: BMDM

value: macrophage

value: non


title: Meningioma 531

description: Hybridized to OncoScanHD

value: Brain


title: mTSC,Patchcap,nexus,2

data_processing:
ChIP-nexus adapter fragments were trimmed from the 3’ end of the fragments using cutadapt (v.2.5)
ChIP-nexus reads were aligned using bowtie (v.1.1.2) to the Mus musculus genome assembly mm10. Aligned ChIP-nexus BAM files were deduplicated based on unique fragment coordinates and barcode assignments.
Genome-wide coverage was calculated and saved in BigWig format.
ChIP-nexus peaks were called using MACS2 (v.2.2.6) with parameters designed to resimulate the full fragment length coverage rather than the single stop base coverage (--keep-dup=all -f=BAM --shift=-75 --extsize=150).
ChIP-seq reads were aligned using bowtie2 (v.2.4.2) to theMus musculus genome assembly mm10. Aligned ChIP-seq BAM files were deduplicated based on unique fragment coordinates and fragments extended based on the average experiment fragment length as determined with an Agilent 2100 Bioanalyzer.
Genome-wide coverage was calculated and saved in BigWig format.
ChIP-seq peaks were called using MACS2 (v.2.2.6) with default parameters and either  applied background coverage using the associated WCE ChIP-seq control experiment or only performed normalization using --normalizeUsing RPKM
Assembly: UCSC mm10
Supplementary files format and content: BigWig, narrowPeak (except for Input sample)


title: lung, mock, donor5, pediatric, scRNAseq

description: 10x Genomics

value: Epithelial

value: lung

value: male

value: mock


title: mTSC,Patchcap,nexus,1

value: cells

value: mouse trophoblast stem cells


title: WT_2_1

value: Wt


title: Meningioma 530

description: Hybridized to OncoScanHD

value: M


title: WT_1_1


title: mTSC,WCE,rin3_crispr,seq


title: lung, infected, donor4, pediatric, scRNAseq

description: 10x Genomics

value: pediatric

value: 6 months

value: caucasian

value: infected with SARS-CoV-2


title: S_221_1

value: EF

value: MSCLCs


title: Meningioma 529

description: Hybridized to OncoScanHD

value: F


title: mTSC,WCE,seq,3

value: Wild-type


title: lung, infected, donor3, pediatric, scRNAseq

description: 10x Genomics

value: 2 months


title: mTSC,WCE,seq,2


title: lung, infected, donor6, adult, scRNAseq

description: 10x Genomics

value: Epithelial

value: adult

value: 53 years


title: S_220_1


title: lung, mock, donor3, pediatric, scRNAseq

description: 10x Genomics

value: lung

value: male

value: mock


title: MSI1 posCompRBNS, 100, UNK 10, rep2

city: Chapel Hill

first: Daniel

last: Dominguez

state: NC

address: 120 Mason farm

department: Pharmacology

institute: UNC Chapel Hill

description: Counts were normalized for library size prior to enrichment against pos_RNA_input_3

data_processing:
Reads were trimmed to library sequencing size (20 nt for RBNS, 33 nt for posRBNS and compPosRBNS, 100 nt for nsRBNS)
For non-nsRBNS: Duplicate reads were collapsed
Counts were generated as dictated per experiment: RBNS (6mers), posRBNS and compPosRBNS (3mers, positionally), nsRBNS (STAR mapping against .fa)
For non-nsRBNS: Counts were normalized for library size
Enrichments were calculated as the frequency of an oligo in the protein bound sample divided by the frequency in the input pool
Assembly: hg38
Supplementary files format and content: RBNS: 6mer enrichments
Supplementary files format and content: posRBNS & compPosRBNS: 3mer enrichments, positionally
Supplementary files format and content: nsRBNS: sequence enrichments

organism: synthetic construct

source_name: RBNS

extract_protocol:
Bound RNA was eluted from streptavidin magnetic beads in 0.1% SDS with 0.3 mg/mL proteinase K. RNA was concentrated via phenol-chloroform extraction.
RNA libraries for sequencing were reverse transcribed with SuperScript IV following manufacturer's protocols, PCR amplified with Phusion DNA polymerase to attach Illumina TrueSeq Small RNA adapters, then agarose gel purified.

value: RBNS


title: Meningioma 526

description: Hybridized to OncoScanHD

value: Brain


title: mTSC,WCE,seq,1

value: cells

value: mouse trophoblast stem cells


title: lung, infected, donor2, pediatric, scRNAseq

description: 10x Genomics

value: pediatric

value: 5 weeks

value: caucasian


title: MSI1 posCompRBNS, 100, UNK 10, rep1


title: mTSC,H3K27ac,rin3_crispr,seq,2

value: H3K27ac (Active motif, 39135)


title: Meningioma 525

description: Hybridized to OncoScanHD

value: F


title: mTSC,H3K27ac,rin3_crispr,seq,1


title: lung, mock, donor2, pediatric, scRNAseq

description: 10x Genomics


title: MSI1 posCompRBNS, 100, UNK 100, rep1


title: lung, infected, donor1, pediatric, scRNAseq

description: 10x Genomics

value: 3 months

value: unknown

value: infected with SARS-CoV-2


title: mTSC,H3K27ac,seq,3

value: Wild-type


title: lung, mock, donor4, pediatric, scRNAseq

description: 10x Genomics

value: Epithelial

value: 6 months


title: Meningioma 521

description: Hybridized to OncoScanHD

value: M


title: MSI1 posCompRBNS, 100, UNK 1000, rep2


title: mTSC,H3K27ac,seq,2


title: MSI1 posCompRBNS, 100, UNK 100, rep2


title: Meningioma 524

description: Hybridized to OncoScanHD


title: Meningioma 520

description: Hybridized to OncoScanHD


title: lung, mock, donor1, pediatric, scRNAseq

description: 10x Genomics

value: lung

value: male

value: mock


title: mTSC,H3K27ac,seq,1

value: cells


title: Relapse1

city: beijing

first: Juan

last: Xie

address: No.11 Xizhimen South Street, Xicheng District, Beijing, P.R.China

department: hematology

institute: peking university people's hospital

data_processing:
IIIumina bcl2fastq2.0 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by limma voom was performed on normalized gene counts, using batch effects and the first two PCAs of aligning and sequencing as covariates.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes gene abundance for each sample

source_name: Bone marrow

extract_protocol:
Total RNA was extracted from each tissue sample using the Qigen mini RNA extract kit
After incubation of RNA with a biotin-modified probe, the probe was captured by a streptavidin magnetic bead to eliminate rRNA. The obtained samples were purified by AMPure XP magnetic beads, and then buffer composed of elution, fragmented, and random primers was added and the samples were incubated at 94°C. Thermal fracture led to fragments distributed between 100 and 300 bp. Using first-strand synthesis buffer and Invitrogen SuperScript IV reverse transcriptase, this fragmented RNA was used as a template to synthesize the first-strand cDNA. Actinomycin D was added to the first-strand synthesis buffer to prevent the reverse transcription of DNA templates and to ensure the reverse transcription specificity of RNA templates. After that, the double-stranded synthesis premix system was added to the synthesized first-strand cDNA, and the product was purified by Agencourt AMpure XP magnetic beads. From this reaction we obtained purified double-stranded cDNA and then added a 3' end plus "A" buffer reaction system to this system. Finally, ligation buffer and a double-stranded sequencing linker was added to the library; we used T4 DNA ligase to attach the Illumina sequencing linker to the DNA library. The library was purified using the Agencourt SPRI select Nucleic Acid Fragment Screening kit.

treatment_protocol: NK cells were sorted from Bone marrow by flow cytometry.

value: Bone marrow

value: primary NK

value: NK cells

tag: subject status

value: relapsed patient


title: pos_RNA_input_4

description: Input control for UNK posCompRBNS

value: RBNS


title: MSI1 posCompRBNS, 100, UNK 1000, rep1


title: Meningioma 527

description: Hybridized to OncoScanHD

value: Brain


title: mTSC,PolII,rin3_crispr,nexus,2

value: mouse trophoblast stem cells

value: Pol II ,Cell Signaling, no. D8L4Y


title: Meningioma 528

description: Hybridized to OncoScanHD

value: F


title: Meningioma 517

description: Hybridized to OncoScanHD


title: mTSC,PolII,rin3_crispr,nexus,1


title: HC1

value: healthy donor


title: HC2


title: Relapse2


title: UNK posCompRBNS, 100, MSI1 10, rep1

description: Counts were normalized for library size prior to enrichment against pos_RNA_input_4


title: CR2

value: complete remession patient


title: mTSC,Tead4,ezr_crispr,nexus,2

value: Tead4, Abcam, no. ab58310


title: Meningioma 516

description: Hybridized to OncoScanHD


title: Meningioma 515

description: Hybridized to OncoScanHD

value: M


title: CR1


title: mTSC,Tead4,ezr_crispr,nexus,1


title: Mut 165009, EZH2i, sample 3

city: Toronto

first: Sehyun

last: Cheon

state: Ontario

address: 101 College St., Suite 700

country: Canada

institute: Structural Genomics Consortium

data_processing:
Raw fastq files were aligned to hg38 using Nextflow nf-core/rnaseq pipeline: alignment with STAR, and QC performed using fastqc
Quantification of expression of transcripts with Salmon using gtf gencode v40 annotations
DESeq2 was used for differential gene expression
Default parameters were used for all software
Assembly: hg38
Supplementary files format and content: Comma separated values file containing gene counts (Salmon output) and results of differential expression analysis using DESeq2.

source_name: blood

growth_protocol: AML patient sample cells were cultured in IMDM media (Gibco/Wisent) with 2mM L-glutamine, 10% FBS (Wisent), 55uM β-mercaptoethanol (Gibco), 100ug/mL Primocin (InvivoGen), 100ng/mL SCF, 50ng/mL FLT3L, 40ng/mL THPO, 20ng/mL IL3, and 20ng/mL GM-CSF (Shenandoah Biotech or Custom Biologics) in 6-well plates (Greinier) seeded with confluent OP9

extract_protocol:
RNA was extracted using TRIzol (Invitrogen) and quality was assessed using a Bioanalyzer (Agilent Technologies).
Sample libraries were prepared using the Library is NEB Ultra II Directional polyA mRNA prep
Sequencing was performed using Illumina Novaseq S4 flowcell PE2x150bp at the SickKids facility TCAG.

treatment_protocol: Cells were treated with EPZ6438 1uM or DMSO for 4 days

value: blood

value: myeloid

value: Mutant

value: EZH2inhibitor EPZ6438


title: UNK posCompRBNS, 100, MSI1 100, rep1


title: mTSC,Tead4,rin3_crispr,nexus,2

value: cells


title: Mut 165009, EZH2i, sample 2


title: Meningioma 514

description: Hybridized to OncoScanHD


title: UNK posCompRBNS, 100, MSI1 1000, rep2


title: Meningioma 513

description: Hybridized to OncoScanHD


title: mTSC,Tead4,rin3_crispr,nexus,1


title: UNK posCompRBNS, 100, MSI1 10, rep2


title: UNK posCompRBNS, 100, MSI1 1000, rep1


title: Replacer milk group - Biol rep 2

city: Patna

first: Rajni

last: Kumari

state: Bihar

address: ICAR Research Complex For Eastern Region, ICAR Parisar, P. O. Bihar

country: India

institute: ICAR-RCER

data_processing:
BCL to Fastq conversion by bcl2fastq v2.19.0.316
The raw data quality was checked using FastQC v0.11.9 and MultiQC v1.12 software. The data was checked for base call quality distribution, % bases above Q30, %GC, and sequencing adapter contamination.
The raw sequence reads were processed using fastp 0.22.0 to remove adapter sequences, low quality bases and to filter reads shorter than 50 bp. The rRNA reads removed using bbmap’s bbduk algorithm.
The pre-processed reads were mapped onto an indexed Goat (Capra aegagrus hircus) reference genome (assembly: ARS1.2, GCF_001704415.2) using STAR v2.7.10a aligner.
The gene level expression values were obtained as read counts using featureCounts v2.0.0 software.
Assembly: assembly: ARS1.2, GCF_001704415.2
Supplementary files format and content: Excel format file include read counts for each sample
Supplementary files format and content: -

organism: Capra hircus

source_name: PBMC

extract_protocol:
The RNA extraction was performed using TRIzol method.
Library was prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina.

value: PBMC

value: Replacer Milk


title: pos_RNA_input_3

description: Input control for MSI2 posRBNS and MSI1 posCompRBNS


title: UNK posCompRBNS, 100, MSI1 100, rep2


title: mTSC,PolII,crispr_control,nexus,2

value: Wild-type


title: mTSC,PolII,crispr_control,nexus,1


title: mTSC,PolII,nexus,3


title: MSI2 posRBNS, 100, rep2

value: RBNS


title: Mut 162245, EZH2i, sample 2


title: MSI2 posRBNS, 100, rep1


title: Meningioma 518

description: Hybridized to OncoScanHD

value: Brain


title: mTSC,PolII,nexus,2

value: mouse trophoblast stem cells


title: Doe milk group - Biol rep 3

value: Doe Milk


title: pos_RNA_input_2

description: Input control for UNK rep2 and MSI1 posRBNS


title: Mut 165009, EZH2i, sample 1


title: Replacer milk group - Biol rep 3


title: Doe milk group - Biol rep 2


title: mTSC,Gata3,nexus,4

value: Gata3 ,Cell Signaling, no. 5852T


title: MSI1 posRBNS, 100, rep1

description: Counts were normalized for library size prior to enrichment against pos_RNA_input_2


title: Doe milk group - Biol rep 1


title: WT151311, EZH2i, sample 1

value: Wildtype


title: MSI1 posRBNS, 100, rep2


title: Mut 162245, EZH2i, sample 3


title: WT151311, EZH2i, sample 2


title: WT 150860, EZH2i, sample 3


title: Replacer milk group (post-PPR vacc.) - Biol rep 3

data_processing:
BCL to Fastq conversion by bcl2fastq v2.19.0.316
The raw data quality was checked using FastQC v0.11.9 and MultiQC v1.12 software. The data was checked for base call quality distribution, % bases above Q30, %GC, and sequencing adapter contamination.
The raw sequence reads were processed using fastp 0.22.0 to remove adapter sequences, low quality bases and to filter reads shorter than 50 bp. The rRNA reads removed using bbmap’s bbduk algorithm.
The pre-processed reads were mapped onto an indexed Goat (Capra aegagrus hircus) reference genome (assembly: ARS1.2, GCF_001704415.2) using STAR v2.7.10a aligner.
The gene level expression values were obtained as read counts using featureCounts v2.0.0 software.
Assembly: assembly: ARS1.2, GCF_001704415.2
Supplementary files format and content: Excel format file include read counts for each sample

value: PPR Vaccination


title: mTSC,Gata3,nexus,3


title: UNK posRBNS, 100, rep2


title: Replacer milk group - Biol rep 1


title: Replacer milk group (post-PPR vacc.) - Biol rep 2


title: Replacer milk group (post-PPR vacc.) - Biol rep 1


title: mTSC,Gata3,nexus,2


title: WT 150860, EZH2i, sample 2


title: mTSC,Gata3,nexus,1


title: UNK posRBNS, 100, rep1

description: Counts were normalized for library size prior to enrichment against pos_RNA_input_1


title: Mut 162245, EZH2i, sample 1


title: mTSC,Cdx2,nexus,4

value: Cdx2 ,Bethyl Laboratories, no. A300-692A


title: Doe milk group (post-PPR vacc.) - Biol rep 3


title: mTSC,PolII,nexus,1

value: Pol II ,Cell Signaling, no. D8L4Y


title: MSI2 RBNS, 50, rep2

description: Counts were normalized for library size prior to enrichment against 20mer_RNA_input_2


title: Doe milk group (post-PPR vacc.) - Biol rep 2


title: WT151311, EZH2i, sample 3

value: blood


title: mTSC,Cdx2,nexus,3


title: Mut 165009, DMSO, sample 3

value: myeloid

value: Control DMSO


title: Mut 165009, DMSO, sample 2

value: Mutant


title: Doe milk group (post-PPR vacc.) - Biol rep 1


title: MSI2 RBNS, 50, rep1


title: mTSC,Cdx2,nexus,2

value: cells


title: mTSC,Cdx2,nexus,1


title: MSI2 RBNS, 250, rep2


title: MSI2 RBNS, 250, rep1


title: GC055068_group_3_notflying

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

description: Library name: GC055068

data_processing:
Raw sequencing data was pseudo-aligned against the D. melanogaster  transcriptome (Ensembl GRCh38.105) using kallisto (v0.45.0). Gene expression was summarized from the transcripts using tximport (v1.30.0).
Assembly: Ensembl drosophila melanogaster Release 113
Supplementary files format and content: Excel file with counts summarized to gene expression using tximport (v1.30.0).

organism: Drosophila melanogaster

source_name: human skin

growth_protocol: One-day-old male flies were collected and tested for their flying ability. Flies were placed in an empty vial that was gently tapped. Flies able or unable to fly were scored one and zero, respectively [33]. For the sequencing analyses, the offspring of each parent pair that was able to fly (group 4) was separately collected from those that were not able to fly (group 3).

extract_protocol:
RNA was from whole flies using the innuPREP RNA Mini Kit 2.0.
Illumina TruSeq Stranded Total RNA Library Prep Kit

value: human skin

value: male

value: 1 day

tag: flying

value: No


title: Mut 165009, DMSO, sample 1


title: pos_RNA_input_1

description: Input control for UNK rep1 posRBNS

value: RBNS


title: GC055069_group_4_flying

description: Library name: GC055069

value: Yes


title: mTSC,Tfap2c,nexus,3

value: Wild-type

value: mouse trophoblast stem cells

value: Tfap2c ,R & D systems, no. AF5059


title: mTSC,Tfap2c,nexus,4


title: Mut 162245, DMSO, sample 2


title: Mut 162245, DMSO, sample 3


title: UNK ZnF4-6 RBNS, 500, rep2


title: GC055067_group_4_flying

description: Library name: GC055067


title: GC055066_group_3_notflying

description: Library name: GC055066


title: Mut 162245, DMSO, sample 1


title: UNK ZnF4-6 RBNS, 250, rep2


title: WT 150860, EZH2i, sample 1

value: Wildtype

value: EZH2inhibitor EPZ6438


title: mTSC,Tfap2c,nexus,2


title: GC055065_group_4_flying

description: Library name: GC055065


title: UNK ZnF4-6 RBNS, 1000, rep2


title: mTSC,Tfap2c,nexus,1


title: WT151311, DMSO, sample 3


title: 20mer_RNA_input_4

description: Input control for MSI2 RRM2 RBNS


title: GC055064_group_3_notflying

description: Library name: GC055064


title: mTSC,Yap1,nexus,5

value: Yap1 ,Cell Signaling, no. 14074S


title: WT151311, DMSO, sample 2

value: blood


title: WT151311, DMSO, sample 1

value: myeloid


title: 20mer_RNA_input_3

description: Input control for MSI2 RRM1 RBNS


title: GC055063_group_4_flying

description: Library name: GC055063

source_name: whole body

value: whole body


title: MSI2, RRM2 RBNS, 500, rep2

description: Counts were normalized for library size prior to enrichment against 20mer_RNA_input_4


title: GC055062_group_3_notflying

description: Library name: GC055062


title: mTSC,Yap1,nexus,4


title: mTSC,Yap1,nexus,3


title: MSI2, RRM2 RBNS, 500, rep1


title: mTSC,Yap1,nexus,2


title: GC055061_group_4_flying

description: Library name: GC055061


title: WT 150860, DMSO, sample 1

value: Control DMSO


title: GC055060_group_3_notflying

description: Library name: GC055060


title: MSI2, RRM2 RBNS, 250, rep1


title: WT 150860, DMSO, sample 2


title: mTSC,Yap1,nexus,1

value: cells


title: MSI2, RRM2 RBNS, 250, rep2


title: GC055059_group_4_flying

description: Library name: GC055059


title: mTSC,Tead4,crispr_control,nexus,2

value: Tead4, Abcam, no. ab58310


title: MSI2, RRM2 RBNS, 1000, rep2


title: GC055058_group_3_notflying

description: Library name: GC055058

value: male


title: COVID_Patient_4_Memb-3

city: Houston

first: Rachel

last: Keuls

address: One Baylor Plaza

institute: Baylor College of Medicine

description: sci-rna-seq3 run 3

data_processing:
Demultiplexing using the BBI pipeline command bbi-demux (https://github.com/bbi-lab/bbi-dmux)
Aligment and count matrix generation using the BBI pipeline command bbi-sci (https://github.com/bbi-lab/bbi-sci/)
Cells were clustered in Seurat using cells with 10PCs, >500 features per cell, 2000 variable features used to cluster cells, and samples in the control group were merged together while samples in the COVID-19 group were merged together and then the two groups were integrated together. The processed Seurat objects containing nuclei from all patients are included as follows: the file COVIDvControl_500Features_5pctmito_2000VariableFeature_Limit-Integrated-10PCs-CLEANED-clustsless5cellsremoved.rds was used for visualization and the file COVIDvControl_500Features_5pctmito_2000VariableFeature_Limit-Integrated-10PCs-CLEANED.rds was used for covid v control differential expression
Assembly: human GRCh38 build and annotation from Ensembl (release 99)
Supplementary files format and content: Filtered Feature Matrix Files
Supplementary files format and content: Monocle3 CDS and Seurat RDS file

source_name: Chorionic Membranes

extract_protocol:
Tissue samples were manually pulverized on dry ice, transferred to pre-chilled tubes, and stored at -80°C. Nuclei isolations were performed with the ‘hypotonic lysis buffer solution B’ [Martin et al. 2023]. Up to 200 mg of tissue was added to 5 mL of ‘hypotonic lysis buffer B’ for 5 to 25 minutes on ice with periodic agitation. For samples under 50 mg, 500 uL of ‘hypotonic lysis buffer B’ was added directly to the 1.5 mL sample tubes and a RNase-free pestle was used for 6 to 12 strokes to further dissociate the tissue. Released nuclei were passed through a 70-micron cell strainer, pelleted (500xg, 5 minutes, 4°C), and resuspended in 1 mL of cold ‘0.3 M SPBSTM’ (Martin et al. 2023). Pre-chilled fixative (5 mg of DSP resuspended in 100 uL DMSO per 4 mL of methanol) was incrementally added for every 1 mL of nuclei resuspended in ‘0.3 M SPBSTM’ and fixed on ice for 5 to 10 minutes. The nuclei were rehydrated by gradually adding 10 mL of ‘0.3 M SPBSTM’ for every 5 mL of fixed nuclei suspension prior to centrifugation (500xg, 5 minutes, 4°C) and resuspended in 1 mL of ‘0.3 M SPBSTM’. Nuclei suspensions processed in the third sci-RNA-seq3 experimental batch were additionally overlaid on 7 mL of a 1.4 M sucrose buffer (1.4 M sucrose, 1X phosphate buffered saline (8 mM Na2HPO4 (pH 7.4), 2 mM KH2PO4, 2.7 mM KCl, 137 mM NaCl), 3 mM MgCl2) and centrifuged at 3,000xg, 20 minutes, 4°C to remove excess debris; the pelleted nuclei were again resuspended in 1 mL of ‘0.3 M SPBSTM’ and passed through a 20-micron cell strainer. After counting, nuclei aliquots were centrifuged (500xg, 5 minutes, 4°C), supernatant aspirated, and pelleted nuclei stored at -80°C until use.
Methods for the first two sci-RNA-seq3 experimental batches largely followed those described by Cao et al. [Cao et al. 2019] with the following modifications: samples were counted with the ImageExpress Pico System (Molecular Devices), 2 μl of oligo(dT) primers were added to each well with 80,000 nuclei for reverse transcription, and tagmentation was performed using 1/40 μl per well of i7-loaded TDE1 enzyme prepared at the BAT-Lab following published protocols [Hennig et al. 2-18]. Libraries were sequenced on an Illumina Nextseq 200 cycles P3 kit with the following cycles: read 1, 34 cycles; read 2, 100 cycles; index 1, 10 cycles; index 2, 10 cycles. Methods for the third sci-RNA-seq3 experimental batch largely followed the optimized protocol described by Martin et al. (Martin et al. 2023) with the following modifications: samples were counted with the ImageExpress Pico System (Molecular Devices), 20,000 nuclei were loaded per reverse transcription well, tagmentation with N7 adaptor-loaded Tn5 transposases (Diagenode cat. no. C01070010-20) was performed at 1/80 uL per well across PCR plates, final library clean up was 0.5X AMPure XP supernatant followed by Qiagene GeneRead Size Selection purification column. The library was sequenced on an Illumina NovaSeq S4 flow cell at the University of Washington Northwest Genomics Center core sequencing facility with the following cycles: read 1, 34 cycles; read 2, 100 cycles; index 1, 10 cycles; index 2, 10 cycles. Read alignment and gene count matrix generation was performed using the Brotman Baty Institute (BBI) pipeline for sci-RNA-seq3 (https://github.com/bbi-lab/bbi-dmux; https://github.com/bbi-lab/bbi-sci). The human GRCh38 build and annotation from Ensembl (release 99) was used as the reference genome. The 3’ UTR annotations of genes and transcripts were extended by 500 bp to avoid misclassifying genic reads as intergenic, and haplotype sequences were removed from the FASTA to avoid mapping inefficiencies due to multimapping.

value: Chorionic Membranes


title: GC055057_group_4_flying

description: Library name: GC055057

value: 1 day


title: MSI2, RRM2 RBNS, 1000, rep1

value: RBNS


title: mTSC,Tead4,nexus,3


title: COVID_Patient_3_Memb-3

description: sci-rna-seq3 run 3


title: MSI2, RRM1 RBNS, 500, rep2

description: Counts were normalized for library size prior to enrichment against 20mer_RNA_input_3


title: GC055056_group_3_notflying

description: Library name: GC055056

value: No


title: mTSC,Tead4,nexus,2

value: Wild-type


title: GC055055_group_4_flying

description: Library name: GC055055

value: Yes


title: Control_Patient_2_Memb

description: sci-rna-seq3 run 3

value: Control


title: WT 150860, DMSO, sample 3

value: Wildtype


title: MSI2, RRM1 RBNS, 500, rep1


title: mTSC,Tead4,nexus,1

value: mouse trophoblast stem cells


title: MSI2, RRM1 RBNS, 250, rep2


title: GC055054_group_3_notflying

description: Library name: GC055054


title: GC055053_group_4_flying

description: Library name: GC055053


title: Control_Patient_4_Memb

description: sci-rna-seq3 run 3


title: mTSC,atac,2

data_processing:
ATAC-seq paired-end sequencing reads were aligned using bowtie2 (v.2.3.5.1) to the Mus musculus genome assembly mm10.
Genome-wide normalized fragment coverage was calculated and saved in BigWig format using following parameters : -bs=50 --minFragmentLength 10 --maxFragmentLength 1000 --ignoreDuplicate --extendReads --normalizeUsing RPKM
ATAC-seq peaks were called using MACS2 (v.2.2.6) with default paired-end parameters using ATAC-seq fragment coverage.
Assembly: UCSC mm10
Supplementary files format and content: BigWig, narrowPeak

extract_protocol:
100,000 or 200,000 mouse TSCs were harvested, washed with PBS, and resuspended in ATAC Resuspension Buffer (RSB, 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 3mM MgCl2) with 0.1% IGEPAL CA-630. Tn5 transposition was performed as previously described (Corces et al. 2017; Buenrostro et al. 2013). Briefly, the cells were incubated for 3 minutes on ice in ATAC RSB supplemented with 0.1% IGEPAL CA-630, 0.1% Tween-20, and 0.01% Digitonin (Promega, G9441). The reaction was quenched with ATAC RSB with 0.1% Tween-20 and centrifugation. Tagmentation took place at 37 °C and 1000 rpm for 30 minutes in a 50 μL reaction volume containing 10 μL of 5x Tagmentation Buffer (50 mM Tris-HCl pH 7.5, 25 mM MgCl2, 50% DMF), 0.5 μL 10% Tween-20, 0.5 μL 1% Digitonin, 1-2 μM assembled transposome and water. Tn5 transposase was purified in-house as previously described (Hennig et al. 2018). Tn5 was loaded with previously reported oligonucleotides Tn5ME-A/Tn5mC1.1-A1block  and  Tn5ME-B/Tn5mC1.1-A1block (Wang et al. 2013), (Picelli et al. 2014)  by mixing equal amounts of purified Tn5 protein and annealed oligonucleotides for 30 min at room temperature.
Accessible fragments were purified using the Monarch PCR & DNA Cleanup Kit (NEB). Libraries were constructed using Illumina Nextera Dual Indexing, and qPCR was used to prevent over-amplification as done in Corces et al., 2017.
ATAC-seq for chromatin accessibility using standard Illumina protocols.


title: Control_Patient_1_Memb

description: sci-rna-seq3 run 3


title: mTSC,atac,3


title: mTSC,atac,1


title: GC055052_group_3_notflying

description: Library name: GC055052


title: mTSC,Tead4,crispr_control,nexus,1


title: MSI2, RRM1 RBNS, 250, rep1


title: MSI2, RRM1 RBNS, 1000, rep1


title: MSI2, RRM1 RBNS, 1000, rep2


title: COVID_Patient_2_Memb

description: sci-rna-seq3 run 3


title: 20mer_RNA_input_2

description: Input control for MSI1 RRM2 rep2, UNK ZnF4-6 rep2, and MSI2 RBNS


title: GC055050_group_3_notflying

description: Library name: GC055050


title: GC055049_group_2_notflying

description: Library name: GC055049