title: WT-3, FA model (14 days), scRNAseq

city: Shanghai

first: Zhenkai

last: Wu

address: No. 639, Zhizaoju Road, Huangpu District, Shanghai, China.

institute: Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

description: 10x Genomics

data_processing:
Sequencing of the libraries was performed on a NovaSeq6000 (Illumina) using paired-end 2×150 bp sequencing. Raw sequencing data were processed following the Chromium's Cell Ranger 3.1.0 pipeline with default parameters. The raw sequencing data (FASTQs files) were aligned to the mouse genome using STAR algorithm. Then gene-barcode matrices containing the barcoded cells and gene expression counts were generated and imported into the Seurat (version 4.2.0) R toolkit for quality control and subsequent analysis. Unless specified, the default parameters were used for all functions. For quality control, cells with detected genes between 200 to 5000, mitochondrial gene percentages less than 30%, unique gene counts between 200 to 20000 were kept. In the remaining cells, gene expression matrices were log normalized for each cell by the total expression and multiplied this by a scale factor (10000 by default). Principal component analysis (PCA) for dimensional reduction was performed based on the highly variable genes (top 2000). Clusters were then visualized using the Uniform Manifold Approximation and Projection (UMAP) (ArXive-prints1802.03426,2018). Cell type identification were performed based on the expression of known cell markers.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: kidney

extract_protocol:
The kidney tissues were harvested after cardiac perfusion with cold PBS, then weighed, minced and incubated with 1 mg/ml type IV collagenase and 10μg/ml DNase I (both from Sigma, USA) for 40 minutes at 37℃ shaker. The digested tissue suspensions were then passed through a 40μm cell strainer and washed in PBS with 1% FBS. Erythrocytes were lysed and single cell suspension was acquired. Cells were stained with 0.4% trypan blue solution (Thermo Fisher, USA), and cell viability was was examined by Countess®II Automated Cell Counter (Thermo Fisher, USA).
Single-cell RNA sequencing libraries were prepared using the Chromium Single Cell 3′ v2 Reagent Kit (10x Genomics) according to the manufacture’s protocol. Briefly, single cells were encapsulated in oil beads with a unique molecular identifier (UMI) barcode to generate single-cellGelBeads-in-Emulsion(GEMs). Then cells were lysed and the released RNA was barcoded through reverse transcription in individual GEMs. After the reverse transcription step, cDNAs were amplified, fragmented and used for 3’ gene expression library construction.

value: kidney

value: WT

value: 6-8 weeks old


title: IL-4, rep2 [P2.L4]

status: Public on Dec 01 2023

type: SRA

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

country: USA

institute: The Ohio State University

library_source: transcriptomic

data_processing:
genome build/assembly: grch38
Human data: Raw fastq was aligned to human reference genome GRCh38 with hisat2 v2.1.0 [1]. Gene wise counts were generated with featureCounts from the subread package v1.5.1 [2] for genes annotated by ensembl Homo_sapiens.GRCh38.101, counting the primary alignment in the case of multimapped reads.
Mouse data: Individual FASTQ files were trimmed for adapter sequences and filtered using fastp v0.20.0. Mouse reference genome GRCm38.p6 and gene annotation described by Gene Transfer Format (GTF) were downloaded from Ensembl release 99 (January 2020). Reads alignment was performed against the reference genome using HISAT2 v2.1.0. Gene expression values for genes were quantified using the featureCounts tool of the Subread package v1.5.0-p2 in unstranded mode.
Supplementary files format and content: human_featurecounts.txt
Supplementary files format and content: mouse_counts.csv

molecule: total RNA

organism: Homo sapiens

source_name: Bone Marrow

extract_protocol:
RNA was harvested using total RNA purifcation plus kit (Biotek Corp). 200 ng per sample was used for the construction of sequencing libraries.
RNA-Seq libraries were prepared using NEBNext Ultra II directional RNA library prep kit following manufacturer's instruction

treatment_protocol: Both mouse Ly6G+ neutrophils, and human CD34+, bone marrow cells were cultured with media and with cytokines IL-4 and/or G-CSF

tag: tissue

value: Bone Marrow

tag: cell type

value: Stem Cell


title: KO-3, FA model (14 days), scRNAseq

country: China

description: 10x Genomics

library_source: transcriptomic single cell

organism: Mus musculus

tag: genotype

value: Aoah-/-

tag: age


title: RNA_AKPS_Day5_STAR-neg-to-neg_1

city: Utrecht

first: Maria

middle: Christine

last: Heinz

address: Heidelberglaan 100

department: Molecular Cancer Research

country: Netherlands

institute: University Medical Center Utrecht

description: STAR- cells derived from 5-day-old AKPS organoids were sorted and STAR- cells were collected for bulk RNA-seq.

data_processing:
Reads were aligned with Hisat2 (version 2.0.4) with enabled alignment tailoring for transcript assemblers.
Reads per gene were counted with htseq-count script (Hisat2 software suite, strandness disabled, identification attribute set to gene_id).
Genes with no reads in any of the samples were excluded from analysis.
Differential gene expression was performed with DESeq2 package.
Significantly changing genes were called after Walt test followed by correction for multiple testing (Benjamini-Hochberg method).
Data visualisation was performed upon normalisation, log2 transformation, and noise-stabilisation using the rlogTransformation function of the DESeq2 package.
Assembly: hg38
Supplementary files format and content: txt files containing transcript counts (PCR duplicates have been removed)

source_name: AKPS organoid

growth_protocol: Engineered human colorectal cancer organoids (APCKO/KO; KRASG12D/-; TP53KO/KO; SMAD4 KO/KO) were grown from single STAR+ or STAR- cells for 5-12 days in Matrigel (Corning). Growth media was refreshed every 2-3 days. Growth media contained Advanced DMEM/F12 (Invitrogen), supplemented with 10 mM Hepes (Invitrogen), 1% GlutaMAX (Invitrogen), 1% Penicillin-Streptomycin (Lonza) as well as 1x B27 supplement (Invitrogen), 1.25 mM N-Acetyl-L-cysteine (Sigma-Aldrich), 10 mM Nicotinamide (Sigma-Aldrich), 500 nM A83-01 (Tocris), and 10 µM SB202190 (Gentaur).

extract_protocol:
RNA was extracted using the RNeasy Mini RNA extraction kit (Qiagen, Cat. No. 74106) according to the manufacturer’s instructions with DNaseI treatment.
Up to 73ng RNA per sample was used for the preparation of the RNA sequencing libraries using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (KAPA Biosystems). In short, oligo hybridisation and rRNA depletion, rRNA depletion cleanup, DNase digestion, DNase digestion cleanup, and RNA elution were performed according to protocol. Fragmentation and priming were performed at 94⁰C for 6:30 min. First strand synthesis, second strand synthesis, and A-tailing were performed according to protocol. For the adapter ligation, a 1.5μM stock was used (NextFlex DNA barcodes, Bioo Scientific). First and second post-ligation cleanup were performed according protocol. The library was amplified in 13 cycles and the subsequent cleanup was performed using a 0.8x bead-based cleanup. Library size was determined using the High Sensitivity DNA bioanalyzer (Agilent Technologies) and the library concentration was measured using the KAPA Library Quantification Kit (KAPA Biosystems). Sequencing was performed using an Illumina NextSeq 500, while 50‐bp paired‐end reads were generated.

treatment_protocol: Organoids were harvested with 1 mg/mL Dispase II (Life Technologies) and pelleted by  spinning at 500xg, 4 min, 4°C.  Organoids  were trypsinized to single cells using TrypsinEDTA (Sigma-Aldrich), trypsin activity was blocked with trypsin inhibitor (Sigma-Aldrich) at a 1:1 ratio, and single cells were pelleted by spinning at 500xg, 4min, 4°C. To visualise dead cells on FACS, 1.5 µM DRAQ7 (Cell Signaling Technologies) was added to growth medium containing 10 µM Y-27632 (Gentaur). On FACS, alive cells with STAR expression being positive (pos) or negative (neg) were collected duplicates or triplicates (10,000-20,000 cells each). Samples were pelleted and snap-frozen until processed further.

value: AKPS organoid

value: Colorectal cancer

tag: time

value: Day 5

tag: star day 0

value: neg

tag: star day 5/12

tag: technical replicate


title: G-CSF, rep1 [P1.G]


title: ATAC_AKPS_Day12_STAR-pos-to-neg_2

description: STAR+ cells derived from 12-day-old AKPS organoids were sorted and STAR- cells were collected for bulk ATAC-seq.

library_source: genomic

data_processing:
Reads were aligned with BWA mem.
PCR duplicates were removed with picard tools version 1.129.
Reads were further filtered for a quality score of >= 1 and for not mapping to the mitochondrial chromosome.
Accesible sites were identified in each sample with macs2 using a Q value of 0.001. A union of all identified peaks was used for subsequent analyses.
Differential site accessibility was performed with DESeq2 package.
Significantly accessible sites were called after Wald test followed by correction for multiple testing (Benjamini-Hochberg method).
Data visualisation was performed upon normalisation, log2 transformation, and noise-stabilisation using the rlogTransformation function of the DESeq2 package.
Assembly: hg19
Supplementary files format and content: Single txt file containing read counts per peak of all samples (PCR duplicates have been removed)

molecule: genomic DNA

extract_protocol:
Cells were lysed and DNA was extracted after performing the transposition reaction with a Tn5 enzyme for 30 min at 37°C. Subsequently, the reaction was stopped through addition of 44 mM EDTA, 131 mM NaCl, 0.3 % SDS, and 600 µg/mL proteinase K. DNA was extracted using the Quiagen MinElute PCR Purification Kit. For further details, please refer to (Lindeboom et al., 2018).
Transposed DNA fragments were amplified using Custom Nextera PCR Primers 1 and 2 together with 10 µl DNA input. Subsequent clean-up was performed using reverse 0.65x SPRI beads (AMPure). An Illumina NextSeq 500 was used for sequencing of 50 bp paired-end reads. For further details, please refer to (Lindeboom et al., 2018).

treatment_protocol: Organoids were harvested with 1 mg/mL Dispase II (Life Technologies) and pelleted by  spinning at 500xg, 4 min, 4°C.  Organoids  were trypsinized to single cells using TrypsinEDTA (Sigma-Aldrich), trypsin activity was blocked with trypsin inhibitor (Sigma-Aldrich) at a 1:1 ratio, and single cells were pelleted by spinning at 500xg, 4min, 4°C. To visualise dead cells on FACS, 1.5 µM DRAQ7 (Cell Signaling Technologies) was added to growth medium containing 10 µM Y-27632 (Gentaur). On FACS, alive cells with STAR expression being positive (pos) or negative (neg) were collected duplicates or triplicates (10,000-20,000 cells each). Samples were pelleted and frozen in Recovery Cell Culture Freezing Medium (Gibco) prior to processing.

value: Day 12

value: pos


title: G-CSF, rep2 [P2.G]


title: plasma, subject 7d976da9T8

type: protein

city: New York

first: Pushkala

last: Jayaraman

state: New York

address: 1 Gustave Levy Pl

department: Charles Bronfman Institute of Personalized Medicine

institute: Icahn School of Medicine at Mount Sinai

description: See https://www.synapse.org/#!Synapse:syn35874390/ for full clinical data and associated metadata including detailed description for process workflow.

hyb_protocol: As described in https://www.somalogic.com/wp-content/uploads/2016/08/SSM-002-Rev-3-SOMAscan-Technical-White-Paper.pdf

data_processing:
As described in Su, C.-Y. et al. Circulating proteins to predict adverse COVID-19 outcomes. medRxiv, 2021.2010.2004.21264015, doi:10.1101/2021.10.04.21264015 (2021).
Preliminary normalization (no log2 transformation) procedure as per Somalogic guidelines. The code workflow creates the normalizations prior to running the linear model.  More details, see Data-Preprocessing section as described in Su, C.-Y. et al. Circulating proteins to predict adverse COVID-19 outcomes. medRxiv, 2021.2010.2004.21264015, doi:10.1101/2021.10.04.21264015 (2021).
Script used to analyze the data is available at:
https://github.com/Nadkarni-Lab/aki_covid_proteomics

molecule: protein

source_name: serum

extract_protocol: Blood samples were collected in Serum Separation Tubes (SST) with a polymer gel for serum separation as previously described in Del Valle DM, Kim-Schulze S, Huang HH, et al. An inflammatory cytokine signature predicts COVID-19 severity and survival. Nat Med. 2020. Samples were centrifuged at 1200 g for 10 minutes at 20°C. After centrifugation, serum was pipetted to a 15 mL conical tube. Serum was then aliquoted into cryovials and stored at -80°C.

tag: subject id

tag: blood sample id

tag: Sex

value: Male

tag: days since first sample

tag: patient classification at first sample

tag: covid-19 status

value: Positive

value: Yes

tag: instrument model

value: Somascan discovery platform v4


title: KO-2, FA model (14 days), scRNAseq

description: 10x Genomics


title: plasma, subject 7ef61ea8T4

scan_protocol: As described in https://www.somalogic.com/wp-content/uploads/2016/08/SSM-002-Rev-3-SOMAscan-Technical-White-Paper.pdf

value: Female


title: ATAC_AKPS_Day12_STAR-neg-to-pos_3

description: STAR- cells derived from 12-day-old AKPS organoids were sorted and STAR+ cells were collected for bulk ATAC-seq.


title: ATAC_AKPS_Day12_STAR-pos-to-neg_1


title: plasma, subject 7d976da9T1

label_protocol: As described in https://www.somalogic.com/wp-content/uploads/2016/08/SSM-002-Rev-3-SOMAscan-Technical-White-Paper.pdf

value: No


title: plasma, subject 7d976da9T4


title: IL-4+G-CSF, rep1 [P1.L4plusG]


title: Unpolarized, rep1 [P1.Up]


title: Left kidney, ischemic reperfusion 2

city: Baltimore

first: Emily

last: Lo

state: MD

address: 733 N Broadway

institute: Johns Hopkins

data_processing:
10X Visium data was preprocessed using the default settings. SpaceRanger was used for alignment and quantification with reference genome mm10.
Assembly: mm10
Supplementary files format and content: Tab-separated values barcode and feature files, matrix expression files, H&E png images, csv tissue position files, json scale factor files
Library strategy: Spatial Transcriptomics

source_name: Kidney

extract_protocol:
24 hours after ischemia, mice were anesthetized. Immediately after dissection and de-capsulation, kidneys were snap-frozen in liquid nitrogen and embedded in optimal cutting temperature (OCT) at -80°C. 10 µm thick sections were cut on a cryostat at -15°C.
Spatial transcriptomics was performed using 10X Visium Spatial Gene Expression Slide and Reagent Kit according to manufacturer’s instructions, with the following sample-specific parameters: tissue sections were permeabilized for 12 minutes at 37°C. cDNA was amplified using 14 cycles based on Cq values obtained using qPCR. Based on post-amplification cDNA yield, final libraries were amplified using 13 cycles during sample index PCR. Each sample was indexed with a unique well from the Dual Index Kit TT Set A. Libraries were sequenced on an Illumina NovaSeq with an SP200 flowcell, 4 samples per lane, in paired-end mode.

treatment_protocol: All experiments were performed using experimental protocols approved by the Animal Care and Use Committee of Johns Hopkins University. An established model of bilateral renal ischemia-reperfusion in mice was used. Briefly, mice were anesthetized with an intraperitoneal injection of sodium pentobarbital (75 mg/kg). After an abdominal medial incision, both renal pedicles were dissected, and a microvascular clamp was placed on each renal pedicle for 30 minutes. Animals were kept well-hydrated with warm saline and at constant body temperature (37°C). After 30 minutes of ischemia, the clamps were removed and wounds were sutured. The animals were allowed to recover with free access to food and water. Serum creatinine levels were determined at baseline and 24 hours after renal ischemia to confirm the injury.

value: Kidney

value: M

value: 7-8 weeks

value: WT C57BL/6J

tag: treatment

value: Ischemic reperfusion injury

tag: slide serial_number


title: Left kidney, ctrl 2

tag: tissue

value: Normal ctrl


title: ATAC_AKPS_Day12_STAR-neg-to-pos_2

value: AKPS organoid

tag: cell type

value: Colorectal cancer


title: plasma, subject 7d941f1cT3


title: Left kidney, ischemic reperfusion 1

tag: genotype


title: plasma, subject 7d941f1cT4

tag: age


title: ATAC_AKPS_Day12_STAR-neg-to-pos_1

tag: time

value: neg


title: SCC-4 cells, NC1_3

city: Beijing

first: Yi

last: Qu

address: NO.4 Tian Tan Xi Li

institute: Beijing Stomatological Hospital, Capital Medical University

description: processed data.txt

data_processing:
Quality control Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean
Reads mapping to the reference genome Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools
Novel transcripts prediction The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
Quantification of gene expression level featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene
Differential expression analysis (For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value
Assembly: GRCH.38.p12
Supplementary files format and content: processed data.txt represents FPKM and count values for all samples

source_name: Tongue

extract_protocol:
①RNA degradation and contamination was monitored on 1% agarose gels. ② RNA purity was checked using the NanoPhotometer ® spectrophotometer (IMPLEN, CA, USA) . ③ RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H - ). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 syste
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: Tongue

tag: cell line

value: Oral squamous cell carcinoma cell

value: WT


title: SCC-4 cells, KD1_1

description: processed data.txt

value: SRSF1 knockdown


title: plasma, subject 7d941f1cT2

value: Male

value: Positive

value: Yes


title: SCC-4 cells, KD1_2

description: processed data.txt


title: ATAC_AKPS_Day12_STAR-neg-to-neg_3

description: STAR- cells derived from 12-day-old AKPS organoids were sorted and STAR- cells were collected for bulk ATAC-seq.

value: Day 12

tag: star day 0

tag: star day 5/12


title: SCC-4 cells, KD1_3

description: processed data.txt


title: Left kidney, ctrl 1

value: Kidney


title: Ischemic reperfusion injury DN

data_processing:
10X Chromium scRNA-Seq data was preprocessed using the default settings. CellRanger (version 6.0.1) was used for alignment and quantification with reference genome mm10.
Assembly: mm10
Supplementary files format and content: Tab-separated values barcode and feature files, matrix expression files

extract_protocol:
Kidneys were minced and incubated in collagenase D solution for 30 minutes at 37°C. Single-cell suspensions of kidney digestions were obtained by mechanical disruption of tissues using 70-μm strainers and KMNC were isolated using Percoll density gradient centrifugation. The numbers of viable lymphocytes in each sample were determined using trypan blue exclusion dye under a light microscope.   T lymphocyte cell staining was performed using standard methods. Briefly, cells were stained in FACS buffer (PBS, 2% FBS, 0.1% sodium azide) and preincubated with anti-CD16/CD32 antibody for 10 minutes to minimize nonspecific binding through Fc-receptors. We used the following mAbs: mCD45–APC- Cyanine7 (30-F11), mTCR- BV421 (H57-597), mCD8α-APC (53–6.7), mCD4- PerCP-Cyanine5.5 (GK1.5), and live/ dead fixable aqua dead cell stain kit for 405 nm excitation.   Cells were stained by incubation with the appropriate cocktails of fluorochrome-conjugated monoclonal antibodies for 30 min at 4°C, washed, and stained with live/ dead aqua followed by incubation for 30 minutes. Cells were then sorted with a FACS Aria II Cell Sorter. After sorting purified CD4+, CD8+, and DN T cells from normal and ischemic mice were used for single cell RNA-Seq analysis.
To capture and barcode individual cells using 10X Chromium technology, purified sorted cells were processed for high-throughput droplet encapsulation. Cell counts and viability were determined using the Cell Countess II with Trypan Blue.  A maximum volume of 43.3 uL/sample was used for processing to target up to 10,000 cells.  Cells were combined with RT reagents and loaded onto 10X Next GEM Chip G along with 3’ v3.1 gel bead. The NextGEM protocol was run on the 10X Chromium Controller to create GEMs, composed of a single cell, uniquely barcoded gel bead, and RT reagents.  100uL of emulsion was retrieved from the chip and incubated (45 min at 53°C, 5 min at 85°C, cool to 4°C), generating barcoded cDNA from each cell.  The GEMs were broken using Recovery Agent and cDNA was cleaned, following manufacturer’s instructions using MyOne SILANE beads.  cDNA was amplified for 11-12 cycles, depending on input cell number (3 min at 98°C, 11-12 cycle: 15sec at 98°C, 20sec at 63°C, 1min at 72°C; 1min at 72°C, cool to 4°C).  Samples were cleaned using 0.6X SPRIselect beads. QC was completed using Qubit and Bioanalyzer to determine size and concentrations.  10uL of amplified cDNA was carried into library prep.  Fragmentation, end repair and A-tailing were completed (5 min at 32°C, 30min at 65°C, cool to 4°C), and samples cleaned up using double sided size selection (0.6X, 0.8X) with SPRIselect beads.  Adaptor ligation (15min at 20°C, cool to 4°C), 0.8X cleanup and amplification were performed, with PCR using unique i7 index sequences.  Libraries underwent a final cleanup using double sided size selection (0.6X, 0.8X) with SPRIselect beads.  Library QC was performed using Qubit, Bioanalyzer and KAPA library quantification qPCR kit.  Libraries were sequenced on the Illumina NovaSeq 6000 using v1.5 kits, targeting 50K reads/cell, at read lengths of 28 (R1), 8 (i7), 91 (R2).  Demultiplexing and FASTQ generation was completed using Illumina’s BaseSpace software.

value: T cells

value: M


title: ATAC_AKPS_Day12_STAR-neg-to-neg_2

tag: technical replicate


title: SCC-4 cells, NC1_1

description: processed data.txt


title: plasma, subject 7cf00ea9T8

tag: subject id

tag: blood sample id

value: No

value: Somascan discovery platform v4


title: Ischemic reperfusion injury CD8+

tag: Sex

value: 7-8 weeks

value: WT C57BL/6J

value: Ischemic reperfusion injury


title: plasma, subject 7cf00ea9T4

tag: days since first sample

tag: patient classification at first sample


title: ATAC_AKPS_Day12_STAR-neg-to-neg_1

value: AKPS organoid

value: Colorectal cancer

value: neg


title: CAL-27 cells, KD2_3

description: processed data.txt

value: Tongue

value: Oral squamous cell carcinoma cell


title: Ischemic reperfusion injury CD4+


title: ATAC_AKPS_Day5_STAR-pos-to-pos_3

description: STAR+ cells derived from 5-day-old AKPS organoids were sorted and STAR+ cells were collected for bulk ATAC-seq.

value: Day 5

value: pos


title: CAL-27 cells, KD2_2

description: processed data.txt

value: SRSF1 knockdown


title: ATAC_AKPS_Day5_STAR-pos-to-pos_2


title: Ctrl DN

value: Normal ctrl


title: CAL-27 cells, KD2_1

description: processed data.txt


title: plasma, subject 7cf00ea9T1

value: Male

tag: covid-19 status

value: Positive

value: Yes

tag: instrument model


title: ATAC_AKPS_Day5_STAR-pos-to-pos_1


title: plasma, subject 7cf00ea9T12

value: No


title: Ctrl CD8+

value: Kidney

value: T cells

value: M

tag: treatment


title: Ctrl CD4+

tag: tissue

value: 7-8 weeks

value: WT C57BL/6J


title: SCC-4 cells, NC1_2

description: processed data.txt

tag: cell type

value: WT


title: CAL-27 cells, NC2_3

description: processed data.txt

tag: genotype


title: plasma, subject 7ca6fb9fT1

value: Female

tag: age

value: Somascan discovery platform v4


title: ATAC_AKPS_Day5_STAR-pos-to-neg_3

description: STAR+ cells derived from 5-day-old AKPS organoids were sorted and STAR- cells were collected for bulk ATAC-seq.

value: AKPS organoid

value: Colorectal cancer

tag: time

value: neg


title: ATAC_AKPS_Day5_STAR-pos-to-neg_2

value: Day 5

value: pos


title: CAL-27 cells, NC2_2

description: processed data.txt

value: Tongue

tag: cell line

value: Oral squamous cell carcinoma cell


title: plasma, subject 7b86ffe2T8

value: Male

value: Positive

value: Yes


title: BM4_BM_cage2_genderM_mouse8

city: Nashville

first: Justin

last: Jacobse

state: Tennessee

address: 2215 Garland Avenue

institute: Vanderbilt University Medical Center

data_processing:
For eosinophil RNA-seq, limma was used for differential expression analysis. The tissue of origin for eosinophils, i.e. esophagus, colon, or bone marrow, was used as metadata in the linear model. Cage or which mouse the cells originated from did not measurably affect gene expression as assessed by consensus correlation coefficient.
For differential expression analysis, limma (version 3.50.3) was used on log-CPM transformed counts with prior count set to 3.
Annotation was done with AnnotationDbi (version 1.56.2) using org.Mm.eg.db (version 3.14.0).
Assembly: Mus musculus Gencode version 21
Supplementary files format and content: Raw counts.

source_name: bone marrow

extract_protocol:
Eosinophils were extracted from lamina propria/bone marrow (see manuscript related to this submission). Cells were further processed using the Ovation Ovation RNA-seq System V2 (Tecan, Mannëdorf, Switzerland) by the Vanderbilt Technologies for Advanced Genomics core.
NEB Library prep

value: bone marrow

value: eosinophils

value: pre-cancer


title: BM3_BM_cage2_genderM_mouse7


title: plasma, subject 7b86ffe2T4

value: No


title: ATAC_AKPS_Day5_STAR-pos-to-neg_1

tag: star day 0


title: BM2_BM_cage1_genderF_mouse6

value: WT


title: plasma, subject 7cf00ea9T13


title: plasma, subject 7b86ffe2T20


title: ATAC_AKPS_Day5_STAR-neg-to-pos_2

description: STAR- cells derived from 5-day-old AKPS organoids were sorted and STAR+ cells were collected for bulk ATAC-seq.

tag: star day 5/12


title: cartilage, combined HP-T stimulation, rep2

city: Lausanne

first: Dominique

middle: P.

last: Pioletti

state: Vaud

address: EPFL

department: STI IBI

country: Switzerland

institute: EPFL

data_processing:
For data analyses, Truseq adapter sequences were trimmed from FASTQ files using bcl2fastq (Illumina, US). Sequences were aligned to the human genome (GRCh38) using STAR [10.1093/bioinformatics/bts635].
Duplicates were marked with Picard [http://broadinstitute.github.io/picard/index.html] and then FeatureCounts [10.1093/bioinformatics/btt656] was used to count reads in features annotated in Gencode (v42) [10.1093/nar/gky955] with the following parameters: paired end mode (-p), --ignoreDup, reverse-strand (-s 2), minimum quality (-Q 10).
Genes were considered expressed if they had greater than 10 reads in at least 2 of the samples.
Differential expression was performed using DESeq2 (v1.36.0) default parameters [10.1186/s13059-014-0550-8] and genes were considered differentially expressed if they were significantly (adjusted p-value ≤ 0.05) changed by more than 2-fold (log2FoldChange ≥ 1 or log2FoldChange ≤ -1).
Already all mentioned above
Assembly: GRCh38
Supplementary files format and content: .txt gene counts of 8 samples

molecule: polyA RNA

source_name: cartilage

extract_protocol:
Explant samples were snap-frozen in liquid nitrogen and subsequently ground into powder using a mortar and pestle, ensuring the continued presence of liquid nitrogen. The tissue powder was then combined with 300 µL of TRIzol (ThermoFisher, US), followed by the addition of 100 µL of chloroform (Sigma-Aldrich, US). After centrifugation, the RNA-rich aqueous phase was separated. RNA isolation and purification were carried out using the Nucleospin® RNA XS kit (Macherey-Nagel, Germany) according to the manufacturer’s guidelines.
First, non-ribosomal RNAs were enriched using the NEBNext rRNA Depletion Kit (New England Biolabs, US), starting from 15 ng RNA. Then, libraries were prepared with NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, US), according to manufacturer’s instructions.

value: cartilage

value: chondrocyte

value: combined HP-T stimulation


title: BM1_BM_cage1_genderF_mouse5


title: ATAC_AKPS_Day5_STAR-neg-to-pos_1

value: AKPS organoid

value: Colorectal cancer

tag: technical replicate


title: ATAC_AKPS_Day5_STAR-neg-to-neg_1

description: STAR- cells derived from 5-day-old AKPS organoids were sorted and STAR- cells were collected for bulk ATAC-seq.

value: Day 5

value: neg


title: COL4_COLON_cage2_genderM_mouse8

source_name: colon

value: colon


title: plasma, subject 7b86ffe2T1

tag: subject id

value: Somascan discovery platform v4


title: plasma, subject 7af92afbT4

tag: blood sample id

value: Male


title: cartilage, isolated T stimulation, rep1

value: isolated T stimulation


title: COL2_COLON_cage1_genderF_mouse6


title: cartilage, isolated T stimulation, rep2


title: cartilage, isolated HP stimulation, rep2

value: isolated HP stimulation


title: CAL-27 cells, NC2_1

description: processed data.txt

value: Tongue

value: Oral squamous cell carcinoma cell


title: COL1_COLON_cage1_genderF_mouse5

value: eosinophils

value: pre-cancer


title: T2DN_5

city: Bergen

first: Philipp

last: Strauss

address: Haukeland Universitetssykehus Laboratoriebygget, 7. etg. Heis øst

country: Norway

institute: University of Bergen

data_processing:
Assembled reads were aligned to the Homo sapiens hg38 reference genome using Gencode (https://www.gencodegenes.org/)
In R LIMMA, genes with at least 3 cpm in at least four samples were used in consecutive analysis.
Differential expression was defined as absolute fold-change (FC) value >2, and adjusted p-value <0.05
Genome_build: hg38
Supplementary_files_format_and_content: txt, log2 transformed, normalized counts in cpm

extract_protocol:
Total RNA was extracted from whole FFPE renal biopsy sections (10 μm thickness) using the High Pure FFPE-tissue RNA Isolation kit (catalogue no. 06650775001; Roche Holding AG, Basel, Switzerland)
RNA inputs of 38 to 1324 ng total RNA per sample were used for library preparation using the TruSeq RNA Access Library Preparation Kit (Illumina, Inc., San Diego, CA, USA). RNA sequencing was performed on an Illumina NextSeq500 system (Illumina, Inc., San Diego, CA, USA) as 75-bp paired ends, at the Genomics Core Facility, Norwegian University of Science and Technology (NTNU, Trondheim, Norway).

tag: diagnosis

value: Type 2 diabetic nephropathy

tag: gender

tag: hypertension

value: yes

tag: systolic bp

tag: diastolic bp

tag: diabetes

tag: egfr (ml/min/m2)

tag: proteinuria (g/d)

tag: arb/acei

value: Non


title: T2DN_6

source_name: whole FFPE renal biopsy sections (10 μm thickness)

tag: age

value: Female

value: ARB

tag: tissue


title: cartilage, unstimulated, rep2

value: cartilage

tag: cell type

value: chondrocyte

tag: treatment

value: unstimulated


title: T2DN_4

value: whole FFPE renal biopsy sections (10 μm thickness)


title: plasma, subject 7a916a79T1

tag: Sex

tag: days since first sample

tag: patient classification at first sample

tag: covid-19 status

value: Positive

value: Yes

tag: instrument model

value: Somascan discovery platform v4


title: cartilage, combined HP-T stimulation, rep1

value: combined HP-T stimulation


title: T2DN_3

tag: diagnosis

tag: gender

value: ACEI, ARB


title: ESO7_ESOPHAGUS_cage2_genderM_mouse8

source_name: Esophagus

value: Esophagus

tag: genotype

value: WT


title: plasma, subject 7a602d10T4

tag: subject id

tag: blood sample id

value: Male


title: plasma, subject 7a602d10T1

value: No


title: ESO6_ESOPHAGUS_cage2_genderM_mouse7

value: eosinophils

value: pre-cancer


title: T2DN_2

value: Type 2 diabetic nephropathy

tag: hypertension

value: yes

tag: systolic bp

tag: diastolic bp

tag: diabetes

tag: egfr (ml/min/m2)

value: ACEI


title: plasma, subject 7b86ffe2T12

tag: age


title: ESO5_ESOPHAGUS_cage1_genderF_mouse6

tag: tissue

tag: cell type

tag: treatment


title: cartilage, unstimulated, rep1

value: cartilage

value: chondrocyte


title: plasma, subject 79ee3c9dT1

tag: Sex

tag: days since first sample

tag: patient classification at first sample


title: NFA2, APA2 and APA3 (Sample 2, Hashtag)

city: Kashiwa

first: BIN

last: WU

state: Chiba

address: #304, 6-6-2, Kashiwanoha

department: Research

country: Japan

institute: ImmunoGeneTeqs

library_source: other

data_processing:
Pair-end Fastq files (R1: cell barcode reads, R2: RNA reads) of sample 1 and sample 2 were processed as follows. Adapter trimming of sequencing data was performed by using Cutadapt 3.4. Filtered reads were chunked to 16 parts for parallel processing by using Seqkit 0.15.0. Filtered cell barcode reads were annotated by Python script provided by BD with minor modification for compatible to Python3.8. Associated cDNA reads were mapped to reference RNA (build GRCh38 release-101) by using bowtie2-2.4.2 by the following parameters: -p 2 –very-sensitive-local -N 1 –norc –seed 656565 –reorder.Then, cell barcode information of each read were added to the bowtie2-mapped BAM files, and read counts of each gene in each cell barcode were counted by using mawk. Resulted count data was converted to genes x cells matrix file and inflection threshold of the knee-plot was detected by using DropletUtils package in R version 4.1.2.
For assignment of each tags to each cell barcodes, read counts of each tag in each valid cell barcode, which defined by the cDNA matrix, were extracted from tag/cell barcode expression matrix. Unassigned cell barcodes were labeled as “not-detected” cells. Then, sum of the total read counts of each tags were normalized to 10M reads, and log2 fold-change between first most counted tags and second most counted tags within each cell barcode. Doublet cells (double-positive cells of any pair of Tags (identified by flowDensity package) and log2 fold-change between first and second most counted tags < 0.30108 were identified as doublets. Finally, remained cell barcodes were assigned to the first most counted tags. Each tag expression in each cell barcode were log2(x+1)-transformed, z-scaled by each cell barcode, and visualized by using pheatmap package in R version 4.1.2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw tag-count values for each sample

source_name: adrenal adenoma

extract_protocol:
Adrenocortical tumor samples were obtained at the time of surgery and stored at −80°C. The nuclei were isolated from snap-frozen tissue using a previously described procedure.20 The Single Nuclei and Cytosol Isolation Kit for Adipose Tissues/Cultured Adipocytes (Invent Biotechnologies, Plymouth, MN, USA) was used to extract the nuclei according to the manufacturer's instructions. Approximately 20 mg of frozen adrenal specimen was utilized for each sample.
Hashtag-stained single nuclei suspension was pooled and approximately 20,000 cells were loaded onto the BD Rhapsody system (BD Biosciences, San Jose, CA, USA). After loading unique cell barcode-immobilized magnetic beads, cells were lysed. Next, reverse transcription of polyA RNA and hashtag oligos derived from each single cell was performed according to the manufacturer’s instructions. Exonuclease I treatment and cDNA/hashtag amplification were performed as per the TAS-seq protocol. Sequencing libraries were prepared using the NEBNext Ultra II FS Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA) and quantified using the KAPA Library Quantification Kit (KAPA Biosystems, Wilmington, MA, USA) and a MultiNA system (Shimazu, Kyoto, Japan).
BD Rhapsody WTA

value: Adrenocortical tumor

value: surgery


title: plasma, subject 7af92afbT1

tag: covid-19 status

value: Positive

value: Yes

tag: instrument model


title: ESO4_ESOPHAGUS_cage1_genderF_mouse5

tag: genotype


title: cartilage, isolated HP stimulation, rep1

value: isolated HP stimulation


title: COL3_COLON_cage2_genderM_mouse7

value: colon


title: T2DN_1

tag: diagnosis

tag: gender

tag: proteinuria (g/d)

tag: arb/acei

value: ARB

value: whole FFPE renal biopsy sections (10 μm thickness)


title: HN_5

value: hypertensive nephropathy without other comorbidities

value: Male

tag: hypertension

tag: systolic bp

tag: diastolic bp

value: no

value: Non


title: hRGC day42

first: Weifeng

last: Li

state: Maryland

address: 400 N Broadway

institute: Johns hopkins university

data_processing:
data was processedaccording to the Drop-seq data processing protocol.
Assembly: hg38
Supplementary files format and content: txt

source_name: h9 ESC

extract_protocol:
Differentiated RGCs were dissociated with Accumax for 60 min in total and went through 40 um cell strainer to achieve single cell.
single-cell RNA-seq library was constructed according to the Drop-seq protocol.

tag: cell line

value: h9 ESC

value: retinal ganglion cell


title: plasma, subject 79d7a9e5T2

tag: subject id

tag: blood sample id

value: Female

tag: age

value: No

value: Somascan discovery platform v4


title: NFA1 and APA1 (Sample 1, Hashtag)

tag: tissue

value: Adrenocortical tumor

tag: treatment


title: ESO3_ESOPHAGUS_cage2_genderM_mouse3

value: Esophagus

tag: cell type

value: eosinophils

value: WT

value: pre-cancer


title: NFA2, APA2 and APA3 (Sample 2, GEX)

value: surgery


title: NFA1 and APA1 (Sample 1, GEX)


title: HN_4

value: yes

tag: diabetes

tag: egfr (ml/min/m2)


title: plasma, subject 79d7a9e5T1

tag: Sex

tag: days since first sample

tag: patient classification at first sample

tag: covid-19 status

value: Positive

value: Yes

tag: instrument model


title: ESO1_ESOPHAGUS_cage1_genderF_mouse1

tag: genotype


title: plasma, subject 79c38c5eT4


title: HN_3

tag: diagnosis

value: hypertensive nephropathy without other comorbidities

tag: gender

value: Male

tag: hypertension

tag: systolic bp

tag: proteinuria (g/d)

tag: arb/acei

value: whole FFPE renal biopsy sections (10 μm thickness)


title: plasma, subject 79c38c5eT20

tag: subject id

tag: blood sample id

tag: age


title: sgMYG1 rep3

city: Guangzhou

first: Jianxiong

last: Chen

state: Guangdong

address: No. 1023-1063, Shatai South Road, Baiyun District, Guangzhou

institute: Southern Medical University

data_processing:
Filtering of Clean Reads
Alignment with Ribosome RNA (rRNA)
Alignment with Reference Genome
Quantification of Gene Abundance
Relationship analysis of samples
Differentially expressed genes (DEGs)
Assembly: Ensembl_release 106
Supplementary files format and content: Count and PFKM value of each samples

source_name: LoVo

extract_protocol:
Total RNA of cells were extracted with Trizol.RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT)beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).And polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).
The enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).And polymerase chain reaction (PCR) amplified.

tag: cell line

value: LoVo

tag: cell type

value: CRC

value: MYG1 KD


title: HN_2

tag: diastolic bp

tag: diabetes

value: no

tag: egfr (ml/min/m2)

value: ARB

tag: tissue


title: sgMYG1 rep2


title: Esophagus, KO6

data_processing:
For tissue bulk RNA-seq, analysis was performed as previously described.(PMID 36807140)
DESEq2 (version 1.34.0) was used on non-normalized counts. Published normalized counts are from DESEq2.
Ingenuity pathway analysis (IPA) was used for pathway assessment. Genes with an adjusted p value of <0.05 were used as input.
Annotation was done with AnnotationDbi (version 1.56.2) using org.Mm.eg.db (version 3.14.0).
Assembly: Mus musculus Gencode version 21
Supplementary files format and content: Absolute and DE-seq2 normalized counts.
Supplementary files format and content: IPA pathway results.

extract_protocol:
Extraction of RNA from whole tissue was performed on tissue stored in RNA-later (Sigma-Aldrich)until homogenization using a Tissue-Tearor (Dremel, Racine, WI), followed by phenol/chloroform extraction as described (28085883) and clean-up with the Rneasy Mini Kit with on-column DNAse digestion according to manufacturers’ instruction.
RNA QC (average RIN 8.8). mRNA enrichment and cDNA library prep utilizing the stranded mRNA (poly-A selected) library preparation kit.

value: whole tissue

value: dblGATA (Jackson #005653)

tag: treatment


title: HN_1

value: Non


title: plasma, subject 79c38c5eT1

tag: Sex

value: Female

tag: days since first sample

tag: patient classification at first sample

tag: covid-19 status

value: No

tag: instrument model

value: Somascan discovery platform v4


title: sgMYG1 rep1

tag: genotype


title: HN_6

tag: diagnosis

tag: gender

tag: hypertension

value: yes

tag: systolic bp

tag: proteinuria (g/d)

tag: arb/acei


title: Ctrl_6

value: control (normal or non-significantly altered renal tisue)

tag: age

tag: diastolic bp


title: Esophagus, KO5

value: Esophagus

tag: cell type

value: pre-cancer


title: plasma, subject 78e0c551T8

tag: subject id

tag: blood sample id

value: Positive

value: Yes


title: sgCtrl rep3

tag: cell line

value: LoVo

value: Control


title: Esophagus, KO4

tag: tissue

tag: treatment


title: Ctrl_5

value: Male

tag: diabetes

tag: egfr (ml/min/m2)

value: whole FFPE renal biopsy sections (10 μm thickness)


title: plasma, subject 78e0c551T4

tag: Sex

tag: days since first sample

tag: patient classification at first sample

tag: covid-19 status

tag: instrument model


title: sgCtrl rep2

value: CRC

tag: genotype


title: Ctrl_4

tag: diagnosis

tag: gender

tag: hypertension

tag: systolic bp

value: no

tag: proteinuria (g/d)

tag: arb/acei

value: ARB


title: plasma, subject 79c38c5eT8

tag: subject id

tag: blood sample id

tag: age


title: ESO2_ESOPHAGUS_cage1_genderF_mouse2

tag: tissue

tag: cell type

value: eosinophils

value: WT

tag: treatment


title: plasma, subject 78e0c551T12

tag: Sex

value: Female

tag: days since first sample


title: Esophagus, KO3

value: whole tissue

value: dblGATA (Jackson #005653)


title: Ctrl_3

value: control (normal or non-significantly altered renal tisue)

tag: diastolic bp

tag: diabetes

tag: egfr (ml/min/m2)

value: Non


title: Esophagus, KO2

value: Esophagus

tag: genotype

value: pre-cancer


title: sgCtrl rep1

tag: cell line


title: plasma, subject 78e0c551T1

tag: patient classification at first sample

tag: covid-19 status

value: Positive

value: No

value: Yes

tag: instrument model

value: Somascan discovery platform v4


title: Esophagus, KO1


title: SKMES sh714, biol rep 3 [sample_6-3]

city: Poznan

first: Marta

last: Machnik

state: Wielkopolska

address: Rokietnicka 8

department: Chair of Medical Biotechnology

country: Poland

institute: Poznan University of Medical Sciences

description:
SKMES shZNF714 Expression_Profile.GRCh38.gene.xlsx
SKMES shZNF714 Expression_Profile.GRCh38.transcript.xlsx

data_processing:
Trimmed reads were mapped to the UCSC hg38 human reference genome with HISAT2.
Known genes and transcripts were assembled with StringTie based on the reference genome model.
After assembly, the abundance of gene/transcript was calculated in the read count and normalized value as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) for a sample.
Assembly: USCS hg38
Supplementary files format and content: xlsx data file containing read counts, FPKMs and TPMs for all samples for each analyzed gene
Supplementary files format and content: xlsx data file containing read counts, FPKMs and TPMs for all samples for each analyzed transcript

source_name: SKMES

growth_protocol: Lung cancer cells received DMEM F-12 medium (Biowest, Nuaillé, France) with 10% FBS (EURx, Gdansk, Poland) and 1% penicillin-streptomycin (Biowest, Nuaillé, France). The cells were cultured in a suitable incubator at 37°C in 5% CO2. Trypsin (Biowest, Nuaillé, France) at the appropriate concentration was used to detach the cells during passaging.

extract_protocol:
RNA was isolated from 3 biological replicates of H2073 and SKMES cells (WT, shLUC, sh714) with GeneMATRIX Universal RNA Purification Kit (EurX) according to the manufacturer’s protocol.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LT Sample Prep Kit according to TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E.

treatment_protocol: shZNF714 and shLUC cancer cells were transduced with lentiviral vectors carrying shRNA sequences complementary to ZNF714 mRNA or complementary to luciferase (5’-CAGCGATGACGAAATTCTTAG-3’) as a control (respectively). We used a mix of two different shZNF714 sequences (5’-ACACCTACATCAACATAAAAG-3’; 5’-CAAATGTGGTTGAGTGTAAGG-3’) to obtain the most efficient level of gene knockdown (shZNF714). Lentiviral particles were prepared by 2nd generation system in HEK-293T cells, using psPAX2 and pMD2.G packaging plasmid and pLV-THEM-GP transfer vector.

value: SKMES

value: established cell line of human lung squamous cell carcinoma

value: trated with shRNA targeting  ZNF714 mRNA


title: Esophagus, KO7


title: plasma, subject 77e6b633T4

value: Male


title: SKMES sh714, biol rep 2 [sample_6-2]


title: Ctrl_1

tag: diagnosis

tag: gender

tag: hypertension

value: no

tag: systolic bp

tag: proteinuria (g/d)

tag: arb/acei

value: whole FFPE renal biopsy sections (10 μm thickness)


title: Esophagus, WT6

tag: tissue

tag: cell type

value: Wt

tag: treatment


title: Ctrl_2

tag: age

value: Female

tag: diastolic bp


title: plasma, subject 77e6b633T1

tag: subject id

tag: blood sample id

tag: Sex

tag: days since first sample


title: SKMES sh714, biol rep 1 [sample_6-1]

tag: cell line


title: Esophagus, WT5

value: whole tissue

tag: genotype


title: plasma, subject 772dda97T4

tag: patient classification at first sample

tag: covid-19 status

tag: instrument model


title: SKMES shLUC, biol rep 3 [ctrl_2-3]

value: trated with control shRNA sequence


title: PDAC_Hot_stroma_5

city: Philadelphia

first: Gregory

middle: L.

last: Beatty

state: PA

address: 3400 Civic Center Blvd, South Pavilion, Rm 8-107

department: Medicine

institute: University of Pennsylvania

data_processing:
FASTQ files uploaded to the BaseSpace Suite (Illumina) were aligned using its RNA-Seq Alignment application (version 2.0.0).
Output files were then analyzed using RNA-Seq Differential Expression application (version 1.0.1) in the BaseSpace suite.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited file contains TPM values of all samples.

source_name: RNA isolated from FFPE block

extract_protocol:
FFPE blocks containing human primary tumors were serially sectioned onto Superfrost Plus microscope slides and glass slides with PEN membrane (Leica, catalog 11505158). Sections on Superfrost Plus microscope slides were used for automated immunohistochemistry to identify tumor epithelium and other cell types. PEN membrane slides were air dried and stored at -80 °C until analysis. These slides were thawed at room temperature prior to use and deparaffinized in fresh xylene for 30 seconds twice, followed by rehydration in ethanol (30 seconds each in 100%, 100%, 95%, and 70% ethanol). Slides were then transferred to RNase-free water and stained with Mayer’s hematoxylin for 10 seconds. Slides were washed with RNase-free water and dehydrated by submerging them in 95% ethanol, 100% ethanol, and xylene, twice in each solution for 30 seconds. Specific regions of dehydrated slides were then microdissected by laser capture using a LMD7000 microscope (Leica). RNA from cold and hot tumor stroma and epithelium was collected using a NucleoSpin total RNA FFPE XS kit (Takara, catalog 740969.50).
Sequencing libraries were prepared using a SMARTer stranded total RNA-Seq kit v2 (Takara) following manufacturer’s protocol and analyzed on a NextSeq 500 sequencing system (Illumina).

tag: diagnosis

value: Pancreatic ductal adenocarcinoma

value: Pancreas


title: plasma, subject 772dda97T1


title: Esophagus, WT4

value: Esophagus

value: pre-cancer


title: SKMES shLUC, biol rep 2 [ctrl_2-2]


title: PDAC_Hot_stroma_4


title: SKMES shLUC, biol rep 1 [ctrl_2-1]


title: PDAC_Hot_stroma_2


title: Esophagus, WT3


title: plasma, subject 772d4e98T1

value: Positive


title: SKMES WT, biol rep 3 [ctrl_1-3]

value: unmodified


title: Esophagus, WT2


title: plasma, subject 76a9f3fcT1

value: Yes

value: Somascan discovery platform v4


title: PDAC_Hot_stroma_1


title: Esophagus, WT1


title: SKMES WT, biol rep 2 [ctrl_1-2]

value: SKMES

value: established cell line of human lung squamous cell carcinoma


title: SKMES WT, biol rep 1 [ctrl_1-1]


title: plasma, subject 74d9ca69T8

value: Male

value: No


title: plasma, subject 7535c499T1


title: plasma, subject 74d9ca69T4


title: PDAC_Hot_epithelium_5


title: H2073 sh714, biol rep 3 [S6_3]

description:
H2073 shZNF714 Expression_Profile.GRCh38.gene
H2073 shZNF714 Expression_Profile.GRCh38.transcript

value: established cell line of human lung adenocarcinoma

value: trated with shRNA targeting  ZNF714 mRNA


title: shROBO1_3_RNA-seq

first: Jiaying

last: Zhang

state: Shanghai

address: 320 Yue Yang Road

department: CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences

data_processing:
Raw reads were filtered by fastp(0.22.0) with default set, clean sequenced reads were alignmented to mm10 by hisat2(2.2.1), suppress unpaired alignments for paired reads,suppress discordant alignments for paired reads.(RNA-seq)
Aligned reads were extracted by featureCounts(2.0.1) with default parameters and normalized by DEseq2(1.32.0).(RNA-seq)
Assembly: mm10 for RNA-seq
Supplementary files format and content: normalized files were calculated by DEseq2(1.32.0).(RNA-seq)

extract_protocol:
8 months after poly (I:C) injection, hematopoietic stem progenitor cells were selected by fluorescence-activated cell sorting (FACS).
Libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina #RS-122-2001) and sequenced with Illumina NovaSeq6000.(RNA-seq)

value: bone marrow

value: hematopoietic stem progenitor cells

value: ROBO1 knockdown

value: ROBO3 knockdown


title: shROBO1_2_RNA-seq

value: ROBO2 knockdown


title: shROBO1_1_RNA-seq


title: PDAC_Hot_epithelium_3

value: Pancreatic ductal adenocarcinoma

value: Pancreas


title: PDAC_Hot_epithelium_4


title: plasma, subject 74d9ca69T13

value: Positive


title: plasma, subject 74d9ca69T12


title: PDAC_Hot_stroma_3


title: shCtrl-3_RNA-seq

value: WT

value: scramble shRNA control


title: PDAC_Hot_epithelium_2


title: H2073 sh714, biol rep 1 [S6_1]


title: shCtrl-2_RNA-seq


title: H2073 sh714, biol rep 2 [S6_2]


title: PDAC_Hot_epithelium_1


title: H2073 shLUC, biol rep 3 [K2_3]

value: trated with control shRNA sequence


title: plasma, subject 737d5052T21

value: Negative

value: Yes

value: Somascan discovery platform v4


title: H2073 shLUC, biol rep 2 [K2_2]


title: PDAC_Cold_stroma_5


title: shCtrl-1_RNA-seq


title: plasma, subject 74d9ca69T1

value: Male

value: No


title: transduced_prostate_cell_MOI_ctrl

city: Seattle

first: John

middle: K.

last: Lee

state: Washington

address: 1100 Fairview Ave N Rm E2-430

institute: Fred Hutch Cancer Research Ctr

data_processing:
library strategy: scDNA-seq
Raw sequencing reads were trimmed to the amplicon regions using the awk command. Barcode sequences in the reads were filtered and extracted using UMI-tools
Processed reads were aligned to custom references containing all amplicon sequences using bwa-mem
Samtools was used to extract amplicon counts for each barcode
Assembly: custom built with reference amplicon
Supplementary files format and content: tab-delimited text files include raw count values for each amplicon

source_name: primary mouse prostate epithelial cells

extract_protocol:
Single cells (3,000 to 4,000 cells per μl) were resuspended in Tapestri cell buffer and encapsulated using a Tapestri microfluidics cartridge, lysed, and barcoded.
Libraries were generated either from cryopreserved or freshly dissociated tumor cells using the Mission Bio Tapestri Single-cell DNA Custom Kit according to the manufacturer’s recommendations

value: primary mouse prostate epithelial cells

value: primary prostate cells

tag: lentivirus moi


title: H2073 shLUC, biol rep 1 [K2_1]

value: established cell line of human lung adenocarcinoma


title: PDAC_Cold_stroma_4


title: plasma, subject 737d5052T20


title: plasma, subject 7378f344T8


title: PDAC_Cold_stroma_3


title: H2073 WT, biol rep 3 [K1_3]

value: unmodified


title: transduced_prostate_cell_MOI_0.5


title: transduced_prostate_cell_MOI_1


title: plasma, subject 7378f344T4


title: transduced_prostate_cell_MOI_2


title: H2073 WT, biol rep 2 [K1_2]


title: PDAC_Cold_stroma_1


title: H2073 WT, biol rep 1 [K1_1]


title: plasma, subject 7378f344T1


title: plasma, subject 735b4b95T4

value: Female


title: AZD5153_48h_3

city: Birmingham

first: Rintaro

last: Hashizume

state: Alabama

address: 1670 University Blvd

department: Pediatrics

institute: UAB

description: AZD5153_vs_DMSO_all-results-with-normalized.csv

data_processing:
FASTQ files were aligned to the hg38 genome using RNA-STAR and genes were quantified using HTSeq-count. Differential gene expression analysis was performed using DESeq2 with default parameters.
Supplementary files format and content: Matrix table containing DESeq2 output and DESeq2 normalized abundance measurements for each sample
Assembly: hg38
Supplementary files format and content: bigwig

source_name: Cell line

growth_protocol: SF8628 cells were propagated as monolayers in complete medium consisting of Dulbecco's Modified Eagle's medium (DMEM, 11965092) supplemented with 10% fetal bovine serum (FBS, A31604-02) and non-essential amino acids (11140-050) from ThermoFisher

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions
NEBNext Ultra II RNA Library Prep Kit for Illumina
NovaSeq sequencing, 150 bp, paired-end reads

treatment_protocol: Cells were treated with vehicle (DMSO) or 1 uM AZD5153 for 24 or 48 hours

value: Cell line (DIPG)

value: SF8628 (DIPG)


title: PDAC_Cold_epithelium_5

value: Pancreatic ductal adenocarcinoma

value: Pancreas


title: plasma, subject 730b8862T1

value: Positive


title: AZD5153_48h_2


title: PDAC_Cold_epithelium_4


title: AZD5153_48h_1


title: plasma, subject 735b4b95T1


title: PDAC_Cold_epithelium_3


title: FHBT9_B10_URO

data_processing:
UCSC TOIL processing pipeline was used to align the reads to the reference genome and generating count matrix files.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: primary mouse bladder urothelial cells

extract_protocol:
RNA was harvested using RNeasy FFPE kit (Qiagen).
The RNA-seq library was prepared using Takara SMARTer Pico kit and sequenced on NovaSeq S4 PE100 by Medgenome company

value: primary mouse bladder urothelial cells

value: bladder tumor cells

tag: histology

value: Urothelial


title: AZD5153_24h_3

tag: tissue


title: PDAC_Cold_stroma_2


title: FHBT8a_B9_papillary

tag: cell type

value: Papillary


title: AZD5153_24h_2

tag: treatment


title: FHBT6_B6

value: Squamous


title: plasma, subject 72b71371T20

data_processing:
As described in Su, C.-Y. et al. Circulating proteins to predict adverse COVID-19 outcomes. medRxiv, 2021.2010.2004.21264015, doi:10.1101/2021.10.04.21264015 (2021).
Preliminary normalization (no log2 transformation) procedure as per Somalogic guidelines. The code workflow creates the normalizations prior to running the linear model.  More details, see Data-Preprocessing section as described in Su, C.-Y. et al. Circulating proteins to predict adverse COVID-19 outcomes. medRxiv, 2021.2010.2004.21264015, doi:10.1101/2021.10.04.21264015 (2021).
Script used to analyze the data is available at:
https://github.com/Nadkarni-Lab/aki_covid_proteomics

extract_protocol: Blood samples were collected in Serum Separation Tubes (SST) with a polymer gel for serum separation as previously described in Del Valle DM, Kim-Schulze S, Huang HH, et al. An inflammatory cytokine signature predicts COVID-19 severity and survival. Nat Med. 2020. Samples were centrifuged at 1200 g for 10 minutes at 20°C. After centrifugation, serum was pipetted to a 15 mL conical tube. Serum was then aliquoted into cryovials and stored at -80°C.

tag: age

value: Yes

value: Somascan discovery platform v4


title: FHBT8b_B9_PAP_SQU

value: Papillary Squamous


title: PDAC_Cold_epithelium_2


title: FHBT8_B8_papillary


title: FHBT5_B5


title: 81723T_PDAC_stroma

extract_protocol:
FFPE blocks containing human primary tumors were serially sectioned onto Superfrost Plus microscope slides and glass slides with PEN membrane (Leica, catalog 11505158). Sections on Superfrost Plus microscope slides were used for automated immunohistochemistry to identify tumor epithelium and other cell types. PEN membrane slides were air dried and stored at -80 °C until analysis. These slides were thawed at room temperature prior to use and deparaffinized in fresh xylene for 30 seconds twice, followed by rehydration in ethanol (30 seconds each in 100%, 100%, 95%, and 70% ethanol). Slides were then transferred to RNase-free water and stained with Mayer’s hematoxylin for 10 seconds. Slides were washed with RNase-free water and dehydrated by submerging them in 95% ethanol, 100% ethanol, and xylene, twice in each solution for 30 seconds. Specific regions of dehydrated slides were then microdissected by laser capture using a LMD7000 microscope (Leica). RNA from tumor stroma and epithelium was isolated using a RNeasy FFPE kit (Qiagen, catalog 73504).
Sequencing libraries were prepared using a QuantSeq 3’ mRNA-Seq library prep kit FWD for Illumina (Lexogen) following manufacturer’s protocol and analyzed on a NextSeq 500 sequencing system (Illumina).


title: plasma, subject 724467b7T1

value: Male

value: Negative

value: No


title: DMSO_48h_3

value: DMSO


title: transduced_prostate_cell_MOI_4

value: primary mouse prostate epithelial cells

value: primary prostate cells


title: 81723T_PDAC_epithelium

value: Pancreatic ductal adenocarcinoma


title: plasma, subject 7213a9b9T8


title: FHBT4b_B3_SARQ

value: Sarcomatoid


title: 81070T_PDAC_stroma

value: Pancreas


title: plasma, subject 7213a9b9T4

value: Positive


title: DMSO_48h_2

value: Cell line (DIPG)

value: SF8628 (DIPG)


title: 81070T_PDAC_epithelium


title: FHBT4a_B3_URO

value: primary mouse bladder urothelial cells

value: bladder tumor cells


title: DMSO_48h_1


title: plasma, subject 7213a9b9T1

value: Yes


title: PDAC_Cold_epithelium_1


title: plasma, subject 72b71371T4

value: Female

value: Somascan discovery platform v4


title: FHBT3_B2_URO

value: Urothelial


title: 80728T_PDAC_stroma


title: AZD5153_24h_1


title: DMSO_24h_3


title: 80728T_PDAC_epithelium


title: plasma, subject 710f4410T1

value: Negative


title: plasma, subject 70c4857cT4

value: Male


title: FHBT2_B1


title: DMSO_24h_2

value: DMSO


title: DMSO_24h_1


title: FHBT1c_B7_papillary

value: Papillary


title: FHBT1a_B7_SARQ


title: 79823T_PDAC_stroma


title: plasma, subject 70c4857cT1

value: No


title: 79856T_PDAC_epithelium

value: Pancreatic ductal adenocarcinoma


title: plasma, subject 7085fdb1T1


title: plasma, subject 701db55aT8


title: 12J-naked-DNA

city: Albuquerque

first: Peng

last: Mao

state: NM

address: 2325 Camino de Salud

institute: University of New Mexico

description: UV treatment of naked DNA

data_processing:
Fastq files were separated into individual libraries using barcodes. Adaptors were trimmed using Trimmomatic.
Fastq files were aligned to the human genome (hg19) using bowtie2-2.2.6 software to generate SAM files. The genomic DNA samples were mixed with spike-in UV-damaged pUC19 plasmid DNA to quantify repair efficiency. These libraries were aligned to the  hg19+pUC19 reference genome using bowtie2-2.2.6.
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS bamtoBed
Damage coordinates and dinucleotide sequences were obtained using the flank and getfasta functions of BEDTOOLS. The reverse complementary sequence of the dinucleotide on the opposite strand, which was the CPD damage sequence, was obtained using a custum Python script
Only reads mapped to C-containing di-pyrimidines such as TC, CT, and CC, corresponding to UV-induced mutagenic CPD (mCPD) lesions were retained in BED file using a custom python script. Because each mCPD lesion was formed between two adjacent bases, the lesion was split and asigned to each of the two bases.
BED files were split to plus and minus strands, sorted, and converted to 1-based WIG files using COUNT function of IGVTools
Assembly: Hg19
Supplementary files format and content: WIG files containing counts of UV damage reads filtered for TC, CT, and CC di-nucleotides.
Library strategy: CPD-seq

growth_protocol: Human skin fibroblast cells were grown in DMEM/F-12 (Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12) containing 10% fetal bovine serum (FBS) at 37 °C and 5% CO2.

extract_protocol:
Genomic DNA was isolated using Sigma GenElute™ Mammalian Genomic DNA Miniprep Kit by following the mannual.
CPD-seq 2.0 library was prepared by following our published protocol (Mao and Wyrick, The Nucleus 79–94 (2020), but with some modifications. Briefly, For each time point (e.g., no UV, 0, 6, and 24 h repair), 10 μg of genomic DNA was mixed with 1 ng UV-irradiated pUC19 plasmid DNA. The pUC19 plasmid DNA serves as a spike-in control for library sequencing depths and subsequent repair quantifications. The DNA was incubated with TdT and dideoxy-ATP (ddATP) to block free 3’ ends that were generated during DNA isolation step. However, because the genomic DNA was not sheared by sonication, it should contain significantly lower number of nicks and breaks compared to the original CPD-seq protocol. The genomic DNA was treated by the glycosylase T4 endonuclease V (T4 endo V) and AP endonuclease 1 (APE1). T4 endo V is a glycosylase that specifically cleaves a CPD lesion on the 5’ side. APE1 further processes the DNA product by T4 endo V and generates a new ligatable 3’-OH group 1 nucleotide upstream of the CPD lesion. After T4 endo V and APE1 digestion, DNA was denatured for single-stranded fragments and the 3’-OH group was immediately ligated to a splint adaptor DNA. After sonication to smaller DNA fragments (~300-400 bp on average), the ligation product was purified with the Streptavidin beads, which recognize the biotin on the adaptor DNA, thus separating CPD fragments from the rest of the genomic DNA. The purified fragments were further processed to add the second adaptor for Illumina sequencing. After PCR amplification for 12 cycles using primers complementary to the two adaptors, the library was sequenced on an Illumina Novaseq platform.

treatment_protocol: For UV treatment, cells were grown to ~80% confluent. Medium was removed and the residual medium was rinsed off with sterile 1 × Phosphate Buffered Saline (PBS). Cells were wetted with 2 ml of fresh PBS in a 10-cm petri dish and irradiated with UV light. For repair, pre-warmed fresh medium was added and cells were incubated to desired repair time points. Negative control (i.e., no UV) was taken before UV irradiation. To analyze CPDs in naked DNA, genomic DNA was first isolated from unirradiated cells. The purified genomic DNA was exposed to UV light to induce DNA damage when DNA was not bound by proteins.

value: Skin fibroblast

value: WT

value: 12J UV-C, naked (i.e., purified) genomic DNA


title: 8J-24h

description: 8J UV treatment, 24 h repair

value: 8J UV-C, repair for 24 h


title: 79823T_PDAC_epithelium

value: Pancreas


title: plasma, subject 701db55aT4

value: Positive


title: 8J-0h

description: 8J UV treatment, 0 h repair

value: 8J UV-C, no repair


title: Glomeruli podocytes, Pfn1 KO rep3

city: New Haven

first: Xuefei

last: Tian

state: CT

address: 300 Cedar Street

department: Nephrology/Internal Medicine

institute: Yale University School of Medicine

data_processing:
The raw TRAPseq fastq files were processed using fastp tool (version 0.20)
With a default setting, sequencing reads wit low-quality bases were trimmed or filtered. Alignment was performed for cleaned reads using STAR (version 2.7.9) and mouse reference genome (gencode version GRCm38.p6 with vM25 gene annotation).
Expression quantification was performed for alignment results using featureCounts (version 2.0.0)
As genes with low expression levels that represent noise to be excluded before downstream analysis, we defined low expression filtering as expressed gene should have >= 6 read counts in at least 20% of samples
The filtered read counts matrix was then normalized by transcripts per million (TPM) method. Detection of differentially expressed genes was performed using R package DESeq2 (version 1.30.1) and The Benjamin-Hochberg procedure was used for multiple test correction
Assembly: GRCm38.p6
Supplementary files format and content: Tab-delimited text files include TPM normalized expression values for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNAseq poly(A)

value: Kidney

value: Glomeruli podocytes

value: 3 weeks-old

value: Pfn1 KO

value: Podocyte-specific KO


title: 6J-24h

description: 6J UV treatment, 24h repair

value: 6J UV-C, repair for 24 h


title: plasma, subject 701db55aT1

value: Male

value: Yes

value: Somascan discovery platform v4


title: Glomeruli podocytes, Pfn1 KO rep1


title: plasma, subject 6f7d59ddT12

value: No


title: 79746T_PDAC_epithelium

value: Pancreatic ductal adenocarcinoma


title: 6J-6h

description: 6J UV treatment, 6h repair

value: Skin fibroblast

value: WT

value: 6J UV-C, repair for 6 h


title: Glomeruli podocytes, control rep2

value: Control (WT)

value: No treatment


title: 79856T_PDAC_stroma

value: Pancreas


title: 79359T_PDAC_stroma


title: FHBT1b_B7_URO

value: primary mouse bladder urothelial cells

value: bladder tumor cells

value: Urothelial


title: Glomeruli podocytes, control rep1

value: Kidney

value: Glomeruli podocytes

value: 3 weeks-old


title: Glomeruli podocytes, Pfn1 KO rep2

value: Pfn1 KO

value: Podocyte-specific KO


title: 79746T_PDAC_stroma


title: 79359T_PDAC_epithelium


title: 6J-0h

description: 6J UV treatment, 0 h repair

value: 6J UV-C, no repair


title: plasma, subject 6f7be7b4T1

value: Female

value: Positive

value: Yes

value: Somascan discovery platform v4


title: No-UV-control

description: no UV control

value: Skin fibroblast

value: WT

value: no treatment


title: plasma, subject 6e29f9d9T12

value: Male

value: No


title: RNA-seq, Late set, 7 dpi, rep 4

city: Seoul

first: Hyeshik

last: Chang

state: South Korea

address: Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

data_processing:
RNA-seq reads that are mapped to the contaminant sequences, including rRNA, tRNA, and srpRNA, using hisat2 were filtered out.
Filtered RNA-seq reads (forward strand only) were mapped to both mouse (GRCm39) and SARS-CoV-2 genome (NC_045512.2) using hisat2.
RNA-seq reads that are mapped within the repeat regions (repeatmasker) were filtered out.
The number of RNA-seq reads mapped to CDS regions of host nuclear genes was counted using featureCounts.
Assembly: Mouse (GRCm39) and SARS-CoV-2 (NC_045512.2)
Supplementary files format and content: Comma-delimited text files include read count values for each sample

source_name: Lung

extract_protocol:
Quick-freeze-applied lung tissue samples were homogenized within the lysis buffer (10 mM/mL Tris-HCl pH 7.4 (AM9850G, AM9855G Invitrogen), 5 mM/mL MgCl2 (#AM9530G Ambion), 100 mM/mL KCl (#AM9640G Ambion), 2 mM/mL dithiothreitol (DTT, #707265ML ThermoFisher), 300 μg/mL cycloheximide  (CHX, #C1988-1G Sigma-Aldrich), 1% Triton X-100 (#T8787 Sigma-Aldrich), 1X protease inhibitor (#P3100-001 GenDEPOT), 2 μL/mL SUPERase inhibitor (#AM2696, Invitrogen) and 2 μL/mL RNase inhibitor (#AM2694 Invitrogen)) for five minutes on ice followed by incubation at 4°C for 30 minutes with the additional lysis buffer which contained 3 times less amount of CHX. After incubation, samples were spun down and the supernatant was divided into two parts each for RNA-seq and Ribo-seq. The half for RNA-seq was treated with TRIzol LS (#10296028 Invitrogen).
After the purification of RNA from TRIzol-treated samples, libraries were constructed with TruSeq Stranded Total RNA Library Prep Gold (#20020599 Illumina) as per the manufacturer’s protocol, and then sequenced by the NovaSeq 6000 system.

treatment_protocol: The mice were lightly anaesthetized with ketamine (20 mg/kg) and xylazine (10 mg/kg) during the infection. All mice were infected intranasally with viruses in a total volume of 50 ìl DMEM. The mice were sacrificed with a CO2 chamber on 0, 1st, 2nd, 5th, and 7th days post-infection (DPI).

value: Lung

tag: strain

value: B6.Cg-Tg(K18-ACE2)2Prlmn/J (The Jackson Laboratory, #034860)

value: SARS-CoV-2 infection

tag: time

value: 7 days post-infection

tag: library type

value: RNA-seq


title: UBTF-ITD primary AML  cells, Day 12, SNDX-3

city: UTRECHT

first: Olaf

last: Heidenreich

state: UTRECHT

address: Prinses Máxima Centrum voor kinderoncologie | Postbus 113| 3720 AC BILTHOVEN | Heidelberglaan 25 |  3584CS UTRECHT | Nederland

data_processing:
For RNAseq data, the fastq files were trimmed using trim_galore 0.6.5.
The data were mapped to the Homo_sapiens GRCh38 reference sequence using STAR 2.7.10a.
The read counts were retrieved with subread/1.6.5.
Assembly: GRCh38
Supplementary files format and content: Matrix table, raw counts

source_name: Bone Marrow

extract_protocol:
RNA was harvested using MACHEREY‑NAGEL kit (MN). 0.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Bone Marrow

value: UBTF-TD

value: Primary AML cells

value: UBTF-TD, FLT3-ITD, WT1

value: Day 12


title: 78280T_PDAC_epithelium

value: Pancreatic ductal adenocarcinoma

value: Pancreas


title: RNA-seq, Late set, 7 dpi, rep 3


title: plasma, subject 6e29f9d9T1

first: Pushkala

last: Jayaraman

address: 1 Gustave Levy Pl

institute: Icahn School of Medicine at Mount Sinai

source_name: serum

tag: subject id

tag: blood sample id

tag: Sex

value: Positive

value: Yes

value: Somascan discovery platform v4


title: UBTF-ITD primary AML  cells, Day 12, Mock-3

institute: Prinses Máxima Centrum voor kinderoncologie

tag: cell line

tag: genotype

value: DMSO


title: RNA-seq, Late set, 7 dpi, rep 2


title: 76863T_PDAC

extract_protocol:
For isolation of RNA from whole slides, FFPE sections on Superfrost Plus microscope slides were collected via mechanical scrapping, and RNA was isolated using a RNeasy FFPE kit (Qiagen, catalog 73504) following the manufacturer’s protocol.
Sequencing libraries were prepared using a QuantSeq 3’ mRNA-Seq library prep kit FWD for Illumina (Lexogen) following manufacturer’s protocol and analyzed on a NextSeq 500 sequencing system (Illumina).


title: plasma, subject 6f7d59ddT1

value: Male

tag: days since first sample

tag: patient classification at first sample

tag: covid-19 status

value: No


title: plasma, subject 6decc33dT1

value: Negative

tag: instrument model


title: 76802T_PDAC

tag: diagnosis


title: plasma, subject 6dba65a2T8

value: Female


title: RNA-seq, Late set, 7 dpi, rep 1

tag: tissue

value: Lung

value: B6.Cg-Tg(K18-ACE2)2Prlmn/J (The Jackson Laboratory, #034860)

value: SARS-CoV-2 infection

value: 7 days post-infection


title: UBTF-ITD primary AML  cells, Day 12, SNDX-2

value: Bone Marrow

value: UBTF-TD

tag: cell type

value: Primary AML cells


title: UBTF-ITD primary AML  cells, Day 12, Mock-1

value: UBTF-TD, FLT3-ITD, WT1

tag: treatment

value: Day 12


title: 75755T_PDAC

value: Pancreatic ductal adenocarcinoma

value: Pancreas


title: plasma, subject 6dba65a2T1

tag: age

value: Positive

value: Yes

value: Somascan discovery platform v4


title: UBTF-ITD primary AML  cells, Day 12, Mock-2

value: DMSO


title: UBTF-ITD primary AML  cells, Day 12, SNDX-1


title: RNA-seq, Late set, 5 dpi, rep 4

tag: strain

value: 5 days post-infection

value: RNA-seq


title: RNA-seq, Late set, 5 dpi, rep 3

value: Lung

tag: time


title: plasma, subject 6dba65a2T4

value: Female

value: No


title: 75561T_PDAC


title: 70204T_PDAC


title: UBTF-ITD primary AML  cells, Day 7, Mock-3

value: Day 7


title: UBTF-ITD primary AML  cells, Day 7, SNDX-3

value: Bone Marrow


title: plasma, subject 6daa375cT2


title: RNA-seq, Late set, 5 dpi, rep 1

value: B6.Cg-Tg(K18-ACE2)2Prlmn/J (The Jackson Laboratory, #034860)

value: SARS-CoV-2 infection

tag: library type


title: UBTF-ITD primary AML  cells, Day 7, SNDX-2

value: UBTF-TD

value: Primary AML cells

value: UBTF-TD, FLT3-ITD, WT1


title: 75675T_PDAC

value: Pancreatic ductal adenocarcinoma

value: Pancreas


title: RNA-seq, Late set, control, rep 4


title: 76151T_PDAC


title: RNA-seq, Late set, control, rep 3


title: 78280T_PDAC_stroma


title: plasma, subject 6daa375cT3

tag: subject id

value: Positive

value: Yes


title: RNA-seq, Late set, 5 dpi, rep 2


title: UBTF-ITD primary AML  cells, Day 7, Mock-2

value: DMSO


title: 69032T_PDAC


title: plasma, subject 6ce79fdfT1

tag: blood sample id

value: Somascan discovery platform v4


title: UBTF-ITD primary AML  cells, Day 7, SNDX-1


title: plasma, subject 6daa375cT1

tag: Sex


title: RNA-seq, Late set, control, rep 2

value: RNA-seq


title: RNA-seq, Early set, 2 dpi, rep 4

value: Lung

value: 2 days post-infection


title: RNA-seq, Early set, 2 dpi, rep 3


title: plasma, subject 6b587132T1

value: Female

value: No


title: RNA-seq, Late set, control, rep 1


title: 27-Fem64-Norm-48

city: Dublin

first: Paul

last: McLoughlin

address: Belfield, Dublin 4

country: Ireland

institute: University College Dublin

description:
normCounts_male_norm_vs_fem_norm_48h
normCounts_male_norm_vs_fem_norm_48h

data_processing:
The sequencing libraries were multiplexed and loaded on the flowcell on the Illumina NovaSeq 6000 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration v1.5, 10M read pairs. Image analysis and base calling were conducted by the NovaSeq Control Software v1.7 on the NovaSeq instrument.
Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
The STAR aligner is a splice aligner that detects splice junctions andincorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: GRCh38
Supplementary files format and content: Raw counts and normalised counts from DESeq2 for four comparisons ("male normoxia 24 hours" vs "female normoxia 24 hours", "male hypoxia 24 hours" vs "female hypoxia 24 hours", "male normoxia 48 hours" vs "female normoxia 48 hours", "male hypoxia 48 hours" vs "female hypoxia 48 hours")

source_name: primary

growth_protocol: Cells were grown in a standard medium MV2 (Promocell) with 1% Penicillin-Streptomycin. At passage 5 cells were exposed to physiological shear stress using an orbital shaker approach as previously described (PMID: 36730645)

extract_protocol:
RNA was extracted using RNeasy Mini Kit (QIAGEN). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA sequencing library was prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).

treatment_protocol: After 24 hours of expreriencing physiological shear stress in normoxia (PMID: 36730645), cells were either placed into hypoxic conditions (1%oxygen chamber, Coy Labs) or remained in normoxic conditions (21% oxygen) for a further 24or 48 hours while shear stress continued.

tag: cell line

value: primary

value: pulmonary microvascular endothelial cells

tag: age (years)

value: normoxia (21% oxygen)

value: 48 hours

tag: supplier

value: Promocell

tag: lot number


title: plasma, subject 6ccf5fd9T1

city: New York

value: Male

tag: days since first sample

tag: patient classification at first sample

tag: covid-19 status


title: SC104041

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

institute: NIH

description: single cells

data_processing:
For single cell RNA-Seq analysis,reads were filtered by cutadapt with phred score threshold 20 and trimmed Ns.
Reads were mapped to human genome (hg38, UCSC) via STAR (2.5.2b).
Clean reads with same UMI were combined and then annotated to ensemble genes by featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: csv,gene expression matrix for single cell RNASeq

source_name: ascending aorta

extract_protocol:
For isolation of primary cells from human artery tissues,aorta samples were chopped into small pieces and digested with Aorta Dissociation Enzyme stock solution (125 mg/ml Collagenase type I in high glucose DMEM) for 2 hour at 37°C. After incubation, the digested aorta were rigorously pipetted up and down for several times, and then filtered through a 70-μm cell strainer into 15ml tubes. Then, isolated cells were maintained in 10% FBS/DMEM.
RNA was extracted from cells, and libraries were generated using the using the ICELL8 platform (Takara) according to the manufacturer’s instructions.

tag: disease state

value: normal ascending aorta

value: adult

tag: tissue

value: ascending aorta


title: plasma, subject 6b1b752dT12

value: Positive

value: Yes

tag: instrument model


title: SC103973

description: single cells

tag: age


title: RNA-seq, Early set, 2 dpi, rep 1

tag: strain

value: B6.Cg-Tg(K18-ACE2)2Prlmn/J (The Jackson Laboratory, #034860)

tag: treatment

value: SARS-CoV-2 infection


title: SC104021

description: single cells

value: thoracic aortic aneurysm ascending aorta


title: SC113557

description: single cells


title: 25-Fem64-Norm-24

description:
raw_counts_male_norm_vs_fem_norm_24h
normCounts_male_norm_vs_fem_norm_24h

tag: cell type

tag: time

value: 24 hours


title: plasma, subject 6c8d28e2T1

tag: subject id

tag: blood sample id

value: Female

value: Somascan discovery platform v4


title: SC113508

description: single cells


title: 70133T_PDAC

tag: diagnosis

value: Pancreatic ductal adenocarcinoma

value: Pancreas


title: plasma, subject 6b1b752dT1

tag: Sex

value: No


title: 26-Fem64-Hypo-24

description:
raw_counts_male_hypo_vs_fem_hypo_24h
normCounts_male_hypo_vs_fem_hypo_24h

tag: cell line

value: primary

value: pulmonary microvascular endothelial cells

tag: age (years)

value: hypoxia (1% oxygen)

tag: supplier


title: plasma, subject 6d81a52bT1

value: Male

tag: days since first sample

tag: patient classification at first sample


title: SC101932

description: single cells

tag: disease state

value: normal ascending aorta

value: adult


title: RNA-seq, Early set, 1 dpi, rep 4

tag: tissue

value: Lung

value: 1 day post-infection

tag: library type

value: RNA-seq


title: UBTF-ITD primary AML  cells, Day 7, Mock-1

value: Bone Marrow

value: UBTF-TD

value: Primary AML cells

tag: genotype

value: UBTF-TD, FLT3-ITD, WT1

value: DMSO

value: Day 7


title: plasma, subject 6ac7cb7bT8

tag: age

tag: covid-19 status

value: Positive

value: Yes

tag: instrument model

value: Somascan discovery platform v4


title: 24-Fem56-Hypo-48

description:
normCounts_male_hypo_vs_fem_hypo_48h
normCounts_male_hypo_vs_fem_hypo_48h

value: primary

tag: cell type

value: pulmonary microvascular endothelial cells

value: Female

tag: treatment

tag: time

value: 48 hours

value: Promocell

tag: lot number


title: 28-Fem64-Hypo-48

tag: Sex

value: hypoxia (1% oxygen)


title: RNA-seq, Early set, 1 dpi, rep 3

value: Lung

tag: strain

value: B6.Cg-Tg(K18-ACE2)2Prlmn/J (The Jackson Laboratory, #034860)

value: SARS-CoV-2 infection

value: 1 day post-infection


title: plasma, subject 6ac7cb7bT4

tag: subject id

tag: blood sample id

value: Male


title: RNA-seq, Early set, 2 dpi, rep 2

value: 2 days post-infection

value: RNA-seq


title: 23-Fem56-Norm-48

tag: cell line

tag: age (years)

value: normoxia (21% oxygen)

tag: supplier


title: plasma, subject 6ac7cb7bT1

tag: days since first sample

tag: patient classification at first sample

value: Positive

value: No


title: 21-Fem56-Norm-24

value: 24 hours


title: plasma, subject 6968e8c2T8

value: Yes

value: Somascan discovery platform v4


title: RNA-seq, Early set, 1 dpi, rep 2

tag: tissue

tag: library type


title: RNA-seq, Early set, control, rep 4


title: RNA-seq, Early set, 1 dpi, rep 1


title: plasma, subject 6968e8c2T4

value: Female

tag: age

tag: covid-19 status


title: RNA-seq, Early set, control, rep 3


title: plasma, subject 6a0f70fdT1

value: Negative

tag: instrument model


title: 20-Fem70-Hypo-48

value: primary

tag: cell type

value: pulmonary microvascular endothelial cells

tag: treatment

value: 48 hours

value: Promocell


title: RNA-seq, Early set, control, rep 2

value: Lung

value: B6.Cg-Tg(K18-ACE2)2Prlmn/J (The Jackson Laboratory, #034860)

tag: time


title: 19-Fem70-Norm-48

tag: Sex

tag: lot number


title: plasma, subject 6968e8c2T1

tag: subject id


title: 18-Fem70-Hypo-24

value: hypoxia (1% oxygen)


title: plasma, subject 695f8fdcT8

tag: blood sample id


title: 17-Fem70-Norm-24

tag: cell line


title: RNA-seq, Early set, control, rep 1

tag: strain


title: 22-Fem56-Hypo-24

tag: age (years)

tag: supplier


title: 16-Male69-Hypo-48

value: Male


title: NovaSeq Ribo-seq, Late set, 7 dpi, rep 3

description:
Ribo-seq, Late set, 7 dpi, rep 3
D7c

data_processing:
Ribo-seq reads were trimmed for adaptors and low-quality sequences using cutadapt.
Ribo-seq reads sequenced on the NextSeq and NovaSeq platforms were merged.
Ribo-seq reads that are mapped to the contaminant sequences, including rRNA, tRNA, and srpRNA, using hisat2 were filtered out.
Filtered Ribo-seq were mapped to both mouse (GRCm39) and SARS-CoV-2 genome (NC_045512.2) using hisat2.
Ribo-seq reads mapped within the repeat regions (repeatmasker) were filtered out.
The number of canonical Ribo-seq (30–34 nt) reads mapped to CDS regions of host nuclear genes was counted using an in-house script.
Assembly: Mouse (GRCm39) and SARS-CoV-2 (NC_045512.2)
Supplementary files format and content: Comma-delimited text files include read count values for each sample

molecule: other

extract_protocol:
Quick-freeze-applied lung tissue samples were homogenized within the lysis buffer (10 mM/mL Tris-HCl pH 7.4 (AM9850G, AM9855G Invitrogen), 5 mM/mL MgCl2 (#AM9530G Ambion), 100 mM/mL KCl (#AM9640G Ambion), 2 mM/mL dithiothreitol (DTT, #707265ML ThermoFisher), 300 μg/mL cycloheximide  (CHX, #C1988-1G Sigma-Aldrich), 1% Triton X-100 (#T8787 Sigma-Aldrich), 1X protease inhibitor (#P3100-001 GenDEPOT), 2 μL/mL SUPERase inhibitor (#AM2696, Invitrogen) and 2 μL/mL RNase inhibitor (#AM2694 Invitrogen)) for five minutes on ice followed by incubation at 4°C for 30 minutes with the additional lysis buffer which contained 3 times less amount of CHX. After incubation, samples were spun down and the supernatant was divided into two parts each for RNA-seq and Ribo-seq. The half for Ribo-seq was treated with 0.1 U/mL of RNase I (#EN0601 ThermoFisher) for 30 minutes at 25°C to digest the exposed mRNA from the ribosome-protected mRNA. To remove the digested mRNA fragments and collect the ribosome-protected mRNA containing lysis, samples were passed through an illustraTM MicroSpin S400 HR Columns (#27-5140-01 Cytiva) which were pre-washed with a polysome buffer (20 mM HEPES KOH pH 7.4 (#BP299100 Fisher BioReagents), 5mM MgCl2, 100 mM KCl, 2mM DTT and 100μg/mL CHX) prior to TRIzol LS treatment. Ribosomal RNAs were depleted using the RiboZero Gold Kit of TruSeq Stranded Total RNA Library Prep Gold (#20020599 Illumina) as per the manufacturer’s protocol and precipitated in 100% ethanol (#100983 Supelco) at -80°C. Samples were labeled with radioisotope γ-P32 ATP (#NEG-502H-1 PerkinElmer) via T4 Polynucleotide kinase (T4 PNK, #M0201L New England Biolabs) and separated on a 10% denaturing Urea-PAGE (#U5128 Sigma-Aldrich) gel followed with signal exposure on Fujifilm imaging plates (#28956478 GE Healthcare). The radioisotope signals were visualized with an Amersham Typhoon Biomolecular imager (v2.0.0.6 GE Healthcare) and analyzed using MultiGauge (v3.0) software. Based on the separation, gel excision was performed around the ~30nt length and continued with RNA purification. Purified samples were then dephosphorylated by Antarctic Phosphatase (#M0289S New England Biolabs) and biochemically re-labeled with γ-P32 ATP using T4 PNK reaction to attach the phosphate to the free hydroxyl 5′ end of the mRNA. Additional 10mM ATP (#P0756S New England Biolabs) was supplemented to compensate for the lack of γ-P32 ATP. Samples were separated from the remaining free ATP with 10% denaturing Urea-PAGE gel followed by excision and purification, as mentioned above.
Adapter ligation and PCR amplification were done by Somagenics RealSeq®-AC miRNA Library Kit (#500-00048 RealSeq Biosciences) as per the manufacturer's protocol. Desired adapter-ligated PCR products were purified through SPRIselect magnetic beads as per manufacturer’s protocol, left side selection. Libraries were sequenced by the NextSeq 500 and NovaSeq 6000 systems.

value: SARS-CoV-2 infection

value: 7 days post-infection

value: Ribo-seq


title: NovaSeq Ribo-seq, Late set, 7 dpi, rep 4

description:
Ribo-seq, Late set, 7 dpi, rep 4
D7d


title: PE-pLVB4_cells

data_processing:
library strategy: DNA-seq
Sequencing reads were trimmed by cutadapt and aligned to reference using Bowtie2
Samtools were used to extract read counts for each sample.
Assembly: customized barcode reference sequences.
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

extract_protocol:
DNA was extracted using a GeneJET Genomic DNA Purification Kit (Thermo Scientific)
Two-step PCR for amplification and sequencing library adaptor ligation was performed using of 2x KAPA HiFi HotStart ReadyMix

value: primary mouse prostate epithelial cells

value: primary prostate cells

tag: pooled lentivirus_batch_number


title: plasma, subject 695f8fdcT4

tag: days since first sample

tag: patient classification at first sample

value: Positive

value: No

value: Yes


title: 15-Male69-Norm-48

value: normoxia (21% oxygen)


title: PE-pLVB1_cells


title: 14-Male69-Hypo-24

value: primary

value: 24 hours


title: plasma, subject 695d5202T1

tag: age

value: Somascan discovery platform v4


title: NovaSeq Ribo-seq, Late set, 7 dpi, rep 2

description:
Ribo-seq, Late set, 7 dpi, rep 2
D7b

tag: tissue

tag: library type


title: NovaSeq Ribo-seq, Late set, 7 dpi, rep 1

description:
Ribo-seq, Late set, 7 dpi, rep 1
D7a


title: plasma, subject 68b25dd2T4

tag: covid-19 status

tag: instrument model


title: 13-Male69-Norm-24

tag: cell type

value: pulmonary microvascular endothelial cells

tag: treatment

tag: time

value: Promocell


title: HGN376, control

type: RNA

city: Chicago

first: Rizaldy

middle: Paz

last: Scott

state: IL

address: 303 E. Superior St.

department: Medicine (Division of Nephrology & Hypertension)

institute: Northwestern University Feinberg School of Medicine

description: Gene expression data from embryonic E14.5 kidneys

hyb_protocol: Hybridization was carried out using a Mouse Gene 2.0 ST array. Microarrays were washed and stained in the Affymetrix Fluidics Station 450 using script FS450_002.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: Data analysis was done using Applied Biosystems Transcriptome Analysis Console (TAC) 4.0.2.

label: biotin

source_name: E14.5 kidneys, control

label_protocol: 200 ng total RNA were amplified from each sample. Samples were prepared using Ambion WT Kit according to manufacturer's instruction.

extract_protocol: Total RNA was extracted from dissected E14.5 embryonic kidneys (contralateral kidneys from each embryo were pooled together into one sample) using Purelink RNA Micro Scale Kit (Cat# 12183016; Invitrogen) following manufacturer's instruction.

tag: genotype

value: wild-type control


title: HGN373, Grb2-cKO

source_name: E14.5 kidneys, Grb2-cKO

value: Grb2 UB-cKO


title: HGN375, control


title: HGN372, Grb2-cKO


title: HGN369, Grb2-cKO


title: HGN363, Grb2-cKO


title: NovaSeq Ribo-seq, Late set, 5 dpi, rep 4

description:
Ribo-seq, Late set, 5 dpi, rep 4
D5d

value: Lung

value: B6.Cg-Tg(K18-ACE2)2Prlmn/J (The Jackson Laboratory, #034860)

value: 5 days post-infection


title: HGN366, control


title: H_ctrl_17_531H

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Freiburg

data_processing:
The sequencing run was performed on a HiSeq 1000 instrument using the indexed, 2x50 cycles paired end (PE) protocol and TruSeq SBS v3 Reagents according to the Illumina HiSeq 1000 System User Guide. Image analysis and base calling resulted in .bcl files, which were converted into .fastq files by the CASAVA1.8.2 software.
Fastq files were aligned to the Gencode 25 / GRCh38 genome annotation using STAR aligner version 2.5.2b with options STAR --runThreadN 10 --genomeDir /xxx/Annotations/Gencode_v25/STAR_50bp --genomeLoad LoadAndKeep --limitBAMsortRAM 20000000000 --readFilesIn .R1, .R2 --readFilesCommand zcat --outFileNamePrefix yyy --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --seedSearchStartLmax 30 --outSAMtype BAM SortedByCoordinate --outBAMcompression 10 --quantMode GeneCounts
Gene counts were generated using featureCounts v1.5.1 with command: featureCounts -a /xxx/Annotations/Gencode_v25/gencode.v25.annotation.gtf -G /xxx/Annotations/GRCh38/GRCh38.primary_assembly.genome.fa -o counts.tsv -p -F GTF -g gene_name -t exon -T 10 --largestOverlap
Genome_build: Grch38
Supplementary_files_format_and_content: counts.tsv – tab delimited file containing gene level counts

source_name: human brain tissue

extract_protocol:
For fresh frozen samples, tissue was homogenized and total RNA extracted using the Qiagen RNAeasy Mini Kit as per the product manual. For FFPE samples 10µm sections of FFPE blocks were cut and immediately processed using the Covaris FFPE RNA extraction kit as per the product manual.
Library preparation and RNAseq were carried out as described in the Illumina TruSeq RNA Access Library Prep Guide, the Illumina HiSeq 1000 System User Guide (Illumina, Inc., San Diego, CA, USA), and the KAPA Library Quantification Kit - Illumina/ABI Prism User Guide (Kapa Biosystems, Inc., Woburn, MA, USA).  In brief, 200 ng of cryosection-derived RNA was fragmented using divalent cations under elevated temperature (94°C for 8 minutes). For FFPE-derived RNA the starting amount was 150 ng, omitting the initial fragmentation step. Next, the RNA was reverse transcribed into first strand cDNA using reverse transcriptase and random hexamer primers. Actinomycin D was added to improve strand specificity by preventing spurious DNA-dependent synthesis. Blunt-ended second strand cDNA was synthesized using DNA Polymerase I, RNase H and dUTP nucleotides. The incorporation of dUTP, in place of dTTP, quenched the second strand during the later PCR amplification, because the polymerase does not incorporate past this nucleotide. The resulting cDNA fragments were adenylated at the 3' ends, the indexing adapters were ligated and subsequently specific cDNA libraries were created by PCR enrichment. After pooling of 3 to 4 libraries each, the pools were hybridized to biotin-labeled probes specific for coding RNA regions. Specific targets within the pool were then captured by adding streptavidin beads that bound to the biotinylated probes. Magnets pulled the bound RNA fragments from the solution. Captured RNA fragments were eluted from the beads and hybridized for a second enrichment reaction. After a final PCR amplification, the targeted libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit. Equimolar amounts of each library were used for cluster generation on the cBot (TruSeq SR Cluster Kit v3). Library preparation and RNAseq were performed at the service facility “KFB - Center of Excellence for Fluorescent Bioanalytics” (Regensburg, Germany; www.kfb-regensburg.de).

value: control

tag: brain region

value: hippocampus

tag: tissue type

value: fresh frozen


title: plasma, subject 68b25dd2T1

state: New York

tag: subject id

tag: blood sample id

tag: Sex

value: Male

value: Positive


title: F_ctrl_16_476F

value: frontal lobe


title: 12-Male60-Hypo-48

tag: cell line

tag: age (years)

value: hypoxia (1% oxygen)

value: 48 hours

tag: supplier

tag: lot number


title: NovaSeq Ribo-seq, Late set, 5 dpi, rep 3

description:
Ribo-seq, Late set, 5 dpi, rep 3
D5c

tag: tissue

tag: strain

value: SARS-CoV-2 infection

value: Ribo-seq


title: 11-Male60-Norm-48

value: primary

value: pulmonary microvascular endothelial cells

value: normoxia (21% oxygen)


title: plasma, subject 67dec94dT1

value: Female

tag: age

tag: days since first sample

tag: patient classification at first sample

tag: covid-19 status

value: Yes

value: Somascan discovery platform v4


title: HGN367, control

value: wild-type control


title: plasma, subject 695f8fdcT12

tag: instrument model


title: plasma, subject 67905ea6T12

value: No