title: NovaSeq Ribo-seq, Late set, 5 dpi, rep 2

description:
Ribo-seq, Late set, 5 dpi, rep 2
D5b

value: Lung

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

tag: treatment

tag: time

value: 5 days post-infection

tag: library type


title: F_ctrl_18_567F

status: Public on Dec 01 2023

type: SRA

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Freiburg

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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).

tag: genotype

value: control

tag: brain region

value: frontal lobe

tag: tissue type

value: fresh frozen


title: plasma, subject 67905ea6T1

type: protein

city: New York

first: Pushkala

last: Jayaraman

state: New York

address: 1 Gustave Levy Pl

department: Charles Bronfman Institute of Personalized Medicine

country: USA

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: age

tag: days since first sample

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: T_ctrl_15_476T

value: temporal lobe


title: T_ctrl_14_697T


title: 10-Male60-Hypo-24

city: Dublin

first: Paul

last: McLoughlin

address: Belfield, Dublin 4

country: Ireland

institute: University College Dublin

description:
raw_counts_male_hypo_vs_fem_hypo_24h
normCounts_male_hypo_vs_fem_hypo_24h

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

tag: cell type

value: pulmonary microvascular endothelial cells

tag: age (years)

value: hypoxia (1% oxygen)

value: 24 hours

tag: supplier

value: Promocell

tag: lot number


title: NovaSeq Ribo-seq, Late set, 5 dpi, rep 1

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

description:
Ribo-seq, Late set, 5 dpi, rep 1
D5a

library_source: other

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

organism: Mus musculus

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 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.

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).

tag: tissue

value: Lung

tag: strain

tag: treatment

value: SARS-CoV-2 infection

tag: time

tag: library type

value: Ribo-seq


title: 9-Male60-Norm-24

description:
raw_counts_male_norm_vs_fem_norm_24h
normCounts_male_norm_vs_fem_norm_24h

value: normoxia (21% oxygen)


title: 8-Male65Pr-Hypo-48

description:
normCounts_male_hypo_vs_fem_hypo_48h
normCounts_male_hypo_vs_fem_hypo_48h

value: 48 hours


title: H_ctrl_13_1502H

tag: genotype

value: control

tag: brain region

value: hippocampus

tag: tissue type

value: fresh frozen


title: 7-Male65Pr-Norm-48

description:
normCounts_male_norm_vs_fem_norm_48h
normCounts_male_norm_vs_fem_norm_48h

tag: Sex

value: Male


title: H_ctr_12_1456H


title: plasma, subject 66a9b205T1

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

tag: subject id

tag: blood sample id

tag: age

tag: days since first sample

tag: patient classification at first sample

value: Positive

value: Yes


title: T_ADAR1_11_1261T

value: temporal lobe


title: NovaSeq Ribo-seq, Late set, control, rep 2

description:
Ribo-seq, Late set, control, rep 2
Ctl2b

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


title: plasma, subject 667ae48eT1

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

tag: covid-19 status

tag: instrument model

value: Somascan discovery platform v4


title: 6-Male65Pr-Hypo-24

tag: cell line

value: primary

tag: cell type

value: pulmonary microvascular endothelial cells

tag: age (years)

value: hypoxia (1% oxygen)

tag: supplier

tag: lot number


title: NovaSeq Ribo-seq, Late set, control, rep 1

description:
Ribo-seq, Late set, control, rep 1
Ctl2a

tag: tissue

value: Lung

tag: strain

tag: treatment

tag: time

tag: library type


title: 5-Male65Pr-Norm-24

tag: Sex

value: 24 hours

value: Promocell


title: H_ADAR1_10_1261H

tag: genotype

tag: brain region

tag: tissue type


title: 4-Fem53-Hypo-48

value: Female


title: NovaSeq Ribo-seq, Early set, 2 dpi, rep 4

description:
Ribo-seq, Early set, 2 dpi, rep 4
D2d

value: SARS-CoV-2 infection

value: 2 days post-infection

value: Ribo-seq


title: F_ADAR1_09_1261F

value: frontal lobe

value: fresh frozen


title: plasma, subject 667ae48eT0

tag: subject id

tag: blood sample id

value: Male

tag: age

tag: days since first sample

tag: patient classification at first sample

value: Positive

value: No


title: NovaSeq Ribo-seq, Early set, 2 dpi, rep 3

description:
Ribo-seq, Early set, 2 dpi, rep 3
D2c

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


title: plasma, subject 677c858dT1

tag: covid-19 status

value: Yes

tag: instrument model

value: Somascan discovery platform v4


title: T_Trex1_08_480T

value: temporal lobe


title: 3-Fem53-Norm-48

tag: cell line

value: primary

tag: cell type

value: pulmonary microvascular endothelial cells

tag: age (years)

value: normoxia (21% oxygen)

value: 48 hours

tag: supplier

tag: lot number


title: NovaSeq Ribo-seq, Late set, control, rep 4

description:
Ribo-seq, Late set, control, rep 4
Ctl2d

tag: tissue

value: Lung

tag: strain

tag: treatment

tag: time

tag: library type


title: plasma, subject 6579a1aeT4

tag: subject id

tag: Sex


title: NovaSeq Ribo-seq, Early set, 2 dpi, rep 2

description:
Ribo-seq, Early set, 2 dpi, rep 2
D2b

value: SARS-CoV-2 infection


title: plasma, subject 66535e14T1

tag: blood sample id

tag: age


title: 1-Fem53-Norm-24

value: Female

value: 24 hours

value: Promocell


title: NovaSeq Ribo-seq, Late set, control, rep 3

description:
Ribo-seq, Late set, control, rep 3
Ctl2c

value: Ribo-seq


title: H_Trex1_07_480H

tag: genotype

tag: brain region

value: hippocampus

tag: tissue type

value: fresh frozen


title: F_Trex1_06_480F

value: frontal lobe


title: plasma, subject 6579a1aeT1

value: Male

tag: days since first sample

tag: patient classification at first sample

tag: covid-19 status

value: Positive

value: No

tag: instrument model


title: plasma, subject 677c538eT1

value: Yes

value: Somascan discovery platform v4


title: NovaSeq Ribo-seq, Early set, 1 dpi, rep 4

description:
Ribo-seq, Early set, 1 dpi, rep 4
D1d

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

value: 1 day post-infection


title: C_ADAR1_05_1261C

value: cerebellum

value: FFPE


title: NovaSeq Ribo-seq, Early set, 1 dpi, rep 3

description:
Ribo-seq, Early set, 1 dpi, rep 3
D1c

value: Lung

value: SARS-CoV-2 infection


title: plasma, subject 64eb2619T8


title: C_ctrl_04_624C

value: control


title: 374-A

city: Cincinnati

first: Konrad

last: Thorner

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

library_source: transcriptomic single cell

data_processing: 10x Genomics

molecule: nuclear RNA

source_name: intestinal organoid

extract_protocol:
Organoids were harvested, and a portion of the graft was flash frozen in liquid nitrogen. Human duodenal surgical sample was dissected and flash frozen in liquid nitrogen. Single nucleus extractions were performed on flash frozen organoids using the Minute Detergent Free Single Nucleus Isolation Kit (Invent Biotechnologies, Inc.). The manufacturer’s instructions were followed, with a few modifications. Buffer A was supplemented with 100 Units of Protector RNAse Inhibitor (Roche), 1 μM DTT (Invitrogen), and 8x10-5 M Leptomycin B (Cell Signaling). Buffer B was supplemented with 110 Units of Protector RNAse Inhibitor and 8x10-5 M Leptomycin B. After the final spin in Buffer A, the nuclei were fixed in Riley’s Buffer (PBS supplemented with 1% BSA,146 mM NaCl, 10 mM Tris-HCl, 1 mM CaCl2, 21 mM Mg Cl2, 20 Units of SUPERaseIn (Invitrogen), and 8x10-5 M Leptomycin B) supplemented with 0.1% PFA. After fixation, the nuclei were centrifuged at 500g for four minutes, resuspended in Riley’s Buffer without PFA, and centrifuged again at 500g for four minutes. After centrifuging the nuclei in Buffer B as directed by the manufacturer’s protocol, the nuclei were resuspended in Nuclear Storage Buffer (PBS supplemented with 1% BSA, 200 Units of Protector RNAse Inhibitor, and 8x10-5 M Leptomycin B). An aliquot of the nuclei was stained with Trypan Blue, and nuclear concentration was determined using a TC20 Automated Cell Counter. Nuclei were assessed for intactness using a Nikon Eclipse Ti prior to submission to the Single Cell Genomics Core at CCHMC for 10x sequencing.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics).

value: intestinal organoid

tag: cell line

tag: cell type

value: mixed

value: WT

value: Conventional HIO


title: 262-B

tag: tissue

value: SI Groove


title: NovaSeq Ribo-seq, Early set, 1 dpi, rep 2

description:
Ribo-seq, Early set, 1 dpi, rep 2
D1b

tag: strain

tag: treatment

value: Ribo-seq


title: C_TREX1_03_480C


title: C_ctrl_02_350C


title: plasma, subject 64eb2619T4

value: Male

value: Positive


title: plasma, subject 64eb2619T1

value: No

value: Yes


title: d14 HCO_3

description: run0337_lane99_read1_indexUDI0030-UDI003_d14-HCO-3

data_processing: Individual libraries were quantified using Qubit® dsDNA HS assay and run on the Agilent Fragment Analyzer for library bp size. Libraries were pooled using the percent range adjusted concentration of fragments 175-650 bp. Sequencing was run on Nova-SeqTM 6000 PE-100.

extract_protocol:
Bulk RNA was extracted using an RNeasy Plus Micro Kit (Qiagen) according to manufacturer guidelines.
200 ng of RNA prepared into libraries following Illumina Stranded mRNA Prep protocol with all recommended reagents. Final library amplification step using 5 uL index anchors and 13 PCR cycles.

value: conventional


title: plasma, subject 64dd6b5eT1

value: Somascan discovery platform v4


title: 2-Fem53-Hypo-24

value: primary

value: pulmonary microvascular endothelial cells

value: Female

tag: age (years)

value: hypoxia (1% oxygen)

tag: time

value: 24 hours

tag: supplier

value: Promocell

tag: lot number


title: NovaSeq Ribo-seq, Early set, 1 dpi, rep 1

description:
Ribo-seq, Early set, 1 dpi, rep 1
D1a

value: Lung

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

value: SARS-CoV-2 infection

value: 1 day post-infection

tag: library type


title: NovaSeq Ribo-seq, Early set, 2 dpi, rep 1

description:
Ribo-seq, Early set, 2 dpi, rep 1
D2a

value: 2 days post-infection

value: Ribo-seq


title: NovaSeq Ribo-seq, Early set, control, rep 3

description:
Ribo-seq, Early set, control, rep 3
Ctl1c


title: C_ctrl_01_162C

tag: genotype

value: control

value: cerebellum

value: FFPE


title: d14 HCO_2

description: run0337_lane99_read1_indexUDI0029-UDI0029_d14-HCO-2

value: intestinal organoid

value: mixed

value: WT

value: conventional


title: d14 HCO_1

description: run0337_lane99_read1_indexUDI0028-UDI0028_d14-HCO-1


title: BJ_MLC2V_1

city: Singapore

first: Boon Seng

last: SOH

address: 61 Biopolis Drive, Proteos

department: Institute of Molecular and Cell Biology (IMCB)

country: Singapore

institute: A*STAR

description: Strand-specific RNA-Seq

data_processing:
Gene expression profiling have been performed by using CSI NGS Portal (PMID: 32481589).
Briefly, raw fastq files were trimmed by Trimmomatic for adapter removal. The clean reads were aligned to the reference human genome (hg19) by using STAR (v2.7.3a) with default parameters.
The gene expression quantification was done by using HTSeq-count (v0.11.2) in strand-specific mode “-s reverse” to obtain raw read counts for each gene, and read counts only from the sense strand are used.
First, hierarchical clustering was performed with regionReport to compare the gene expression profiles of the samples, by using the top 500 genes with the highest variance across the samples.
Then the differential gene expression analysis was performed by using DESeq2 (v1.24.0) starting from the raw read counts by comparing BJ MLC2V samples to BJ MLC2A samples after collapsing the samples within each group (2 for BJ MLC2V and 3 for BJ MLC2A samples) as replicates.
The genes that are not expressed or lowly expressed (read counts <= 2 on average per sample) were removed from the analysis. In total, 1349 and 1516 genes were significantly up- and down-regulated, respectively, in the BJ MLC2V samples compared to BJ MLC2A samples, after correction for multiple hypothesis testing (log2 Fold Change >1, Padj < 0.05, using Benjamini-Hochberg method).
The same analysis was repeated to for ESO3 MLC2V and BJ MLC2A samples; 1904 and 2811 genes were significantly up- and down-regulated, respectively.
Genes that were up-regulated in both sets of comparisons, and were found to encode for surface markers were identified as potential surface marker candidates for ventricular specification.The top 30 genes were then used for heatmap plotting in R.
Assembly: hg19
Supplementary files format and content: Spreadsheet including raw and normalized read counts for each sample, differential expression analysis results and top 30 genes identified as potential surface marker candidates for ventricular specification

source_name: BJ MLC2V cells

growth_protocol: Cells were grown in RPMI-1640 Medium (1x) (Hyclone) supplemented with B27

extract_protocol:
Total RNA was extracted using Trizol LS (Invitrogen) and subjected to DNase treatment with Turbo DNA-free (Ambion).
Strand-specific cDNA library according to Illumina's TruSeq Stranded mRNA Library Prep Kit

value: BJ

value: MLC2V-expressing cells


title: BJ_MLC2V_2

description: Strand-specific RNA-Seq


title: 262

value: SI Groove


title: NovaSeq Ribo-seq, Early set, control, rep 4

description:
Ribo-seq, Early set, control, rep 4
Ctl1d


title: plasma, subject 648cd6e5T1

tag: subject id

tag: blood sample id

tag: Sex

value: Male

tag: age

value: Negative

value: No

value: Yes

value: Somascan discovery platform v4


title: plasma, subject 650d88a1T1

tag: days since first sample

tag: patient classification at first sample

tag: covid-19 status

value: Positive


title: plasma, subject 6463f11bT4

tag: instrument model


title: plasma, subject 6463f11bT1


title: BJ_MLC2A_3

description: Strand-specific RNA-Seq

source_name: BJ MLC2A cells

tag: cell line

tag: cell type

value: MLC2A-expressing cells


title: NovaSeq Ribo-seq, Early set, control, rep 2

description:
Ribo-seq, Early set, control, rep 2
Ctl1b

tag: tissue

value: Lung

tag: strain

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

tag: treatment

value: Ribo-seq


title: d14 c-groove_2

description: run0337_lane99_read1_indexUDI0032-UDI0032_d14-c-groove-2

value: intestinal organoid

value: scaffolding tray


title: D-CNO+MitoQCre+_rep6

city: Milwaukee

first: Justin

middle: L

last: Grobe

state: WI

address: 8701 W Watertown Plank Road

department: Physiology

institute: Medical College of Wisconsin

data_processing:
Raw reads were demultiplexed and quality of pre-aligned data was computed by FastQC
Reads were aligned to the Gencode vM23 (GRCm38.p6) mouse reference genome with Star
Data was then further processed in the MAPRSeq3 workflow to obtain read counts at the gene and exon levels
Aligned data was inspected via RSeQC modules
Differential gene expression was tested in EdgeR with a pairwise approach comparing: CNO Cre+ vs. Saline Cre-, CNO Cre+ vs. CNO Cre-, and CNO+MitoQ Cre+ vs. CNO Cre+
Assembly: Gencode vM23 (GRCm38.p6)
Supplementary files format and content: Excel file (.xlsx) with individual raw counts, individual RPKM values, and pairwise comparisons

source_name: placenta

growth_protocol: All mice were housed in a temperature and humidity-controlled facility with ad libitum access to 2029x Teklad diet and water.

extract_protocol:
RNA was harvested using Trizol in a bullet blender, chloroform was added, and aqueous phase was transferred to Invitrogen RNAeasy kit (per manufacture instructions)
RNA libraries were prepared using Takara low-input, SMART-seq stranded preparation kit according to manufacture protocol

value: placenta

value: hM3Dq+ Gcm1Cre+

value: CNO+MitoQ


title: BJ_MLC2A_2

description: Strand-specific RNA-Seq

value: BJ


title: d14 c-groove_1

description: run0337_lane99_read1_indexUDI0031-UDI0031_d14-c-groove-1

value: mixed

value: WT


title: plasma, subject 645c5881T8

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

value: Male


title: D-CNO+MitoQCre+_rep5


title: d14 HIO_3

description: run0337_lane99_read1_indexUDI0027-UDI0027_d14-HIO-3

value: conventional


title: plasma, subject 645c5881T4

value: No

value: Yes


title: D-CNO+MitoQCre+_rep4


title: BJ_MLC2A_1

description: Strand-specific RNA-Seq


title: ES03_MLC2V_2

description: Strand-specific RNA-Seq

source_name: ES03 MLC2V cells

value: MLC2V-expressing cells


title: d14 c-groove_3

description: run0337_lane99_read1_indexUDI0033-UDI0033_d14-c-groove-3


title: plasma, subject 645c5881T12

value: Positive

value: Somascan discovery platform v4


title: ES03_MLC2V_1

description: Strand-specific RNA-Seq


title: D-CNO+MitoQCre+_rep3


title: d14 HIO_2

description: run0337_lane99_read1_indexUDI0026-UDI0026_d14-HIO-2


title: plasma, subject 645c5881T1


title: d14 HIO_1

description: run0337_lane99_read1_indexUDI0025-UDI0025_d14-HIO-1


title: ABP-sample3

city: Shenzhen

first: Jing

last: Guo

address: 1098 Xueyuan Street

country: China

institute: Shenzhen University

data_processing:
Mapped and normalized with DESeq2 with default paramters
Supplementary files format and content: gene_count.DESeq2.normalized.txt

source_name: Liver

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 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: Liver


title: d14 si groove_3

description: run0208_lane91_read1_indexD706-D507_d14-si-groove-3


title: NovaSeq Ribo-seq, Early set, control, rep 1

description:
Ribo-seq, Early set, control, rep 1
Ctl1a

value: Lung

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

tag: time

value: Ribo-seq


title: D-CNO+MitoQCre+_rep2

value: placenta


title: plasma, subject 62deb59cT12


title: D-CNO+MitoQCre+_rep1

value: hM3Dq+ Gcm1Cre+


title: ABP-sample2


title: d14 si groove_2

description: run0208_lane91_read1_indexD705-D507_d14-si-groove-2

value: intestinal organoid

value: scaffolding tray


title: plasma, subject 62deb59cT1


title: C-CNOCre+_rep6 (paired to Cre- within dam)

value: CNO


title: ABP-sample1


title: plasma, subject 6295c70bT1


title: d14 si groove_1

description: run0208_lane91_read1_indexD704-D507_d14-si-groove-1

value: mixed

value: WT


title: B-CNOCre-_rep6 (paired to Cre+ within dam)

value: hM3Dq+ Gcm1Cre-


title: plasma, subject 626935c9T4

value: Female

value: No


title: SKF-sample3


title: d6 si groove_3

description: run0208_lane991_read1_indexD712-D506_d6-si-groove-3


title: C-CNOCre+_rep5 (paired to Cre- within dam)


title: SKF-sample2


title: plasma, subject 626935c9T1

value: Yes


title: d6 si groove_2

description: run2676_lane12_read1_indexD711-D506_d6-si-groove_2


title: B-CNOCre-_rep5 (paired to Cre+ within dam)


title: d6 si groove_1

description: run2676_lane12_read1_indexD710-D506_d6-si-groove_1


title: plasma, subject 60e2038dT4

value: Positive


title: Control-sample3


title: C-CNOCre+_rep4 (paired to Cre- within dam)


title: plasma, subject 60e2038dT20

value: Somascan discovery platform v4


title: spheroid_3

description: run2676_lane12_read1_indexD709-D506_spheroid_3

value: conventional


title: B-CNOCre-_rep4 (paired to Cre+ within dam)


title: plasma, subject 60e2038dT1


title: spheroid_2

description: run2676_lane12_read1_indexD708-D506_spheroid_2


title: C-CNOCre+_rep3 (paired to Cre- within dam)


title: Control-sample1

value: Liver


title: spheroid_1

description: run2676_lane12_read1_indexD707-D506_spheroid_1


title: plasma, subject 604d660eT1

value: Male


title: B-CNOCre-_rep3 (paired to Cre+ within dam)


title: plasma, subject 602c8cc5T4


title: 184337_B001orig_3

city: Vienna

first: Maria

last: Novatchkova

address: Dr Bohrgasse

country: Austria

institute: IMP/IMBA

description: 10x Genomics

data_processing:
ScRNA-seq reads were processed with Cell Ranger multi v6.1.1 using the prebuilt 10X GRCh38 reference refdata-gex-GRCh38-2020-A, and including introns. Further processing such as dimensionality reduction, clustering, and visualization of the scRNA-seq data was performed in R v4.2.2 with Seurat v4.3.0.
Identification of non-telencephalic clusters. Non-telencephalic cells were separated at clustering resolution 0.02 (“FindClusters”). One non-telencephalic cluster (cluster 2) was removed for downstream analysis, based on absent/low FOXG1 expression. A total of 1.76% of cells were excluded by this filter.
Removal of low-quality cells. After exclusion of non-telencephalic cells, genes located on the Y-chromosome and those not detected in at least 5 cells were excluded. We used the Gruffi algorithm to identify and remove cells presenting a transcriptional signature of cellular stress (Vértesy et al., 2022). Cells were removed if they were identified as stressed, the gene number metric was below a MAD (median absolute deviation) based threshold (library: 178119 <900, 178120 <1100, 184337 <1200, 177136 <1500), the percentage of mitochondrial reads was 10% or above, and the percentage ribosomal RNAs was 25% or above. Count data was log-normalized and scaled. Dimensionality reduction was performed using PCA on the top 3000 most variable genes. Batch correction across libraries was performed using Harmony v0.1.1, and the 40 harmony embeddings were used for UMAP visualizations.
Identification of telencephalic clusters. The first 10 Harmony dimensions were used to identify neuronal subclusters with a resolution of 0.2. Clusters were assigned to cell types using known neuron markers and the developing human neocortex reference (PMID: 31303374): INs (cluster 5), dividing progenitors (cluster 3), RGs (cluster 4), IPCs (cluster 2), ExN1 (cluster 0), ExN2 (cluster 1), and ExN3 (cluster 6).
Assembly: hg38
Supplementary files format and content: Seurat object containing counts and metadata of the filtered object (removal of non-telencephalic clusters, Gruffi, and quality filter), in .rds format
Supplementary files format and content: Tab-separated CMO, count, and metadata files

source_name: Neural organoid

growth_protocol: Human telencephalic brain organoids.

extract_protocol:
Multiplexing was performed using the 10x Genomics 3’ CellPlex Kit.
Library preparation was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: Neural organoid

value: Pat.1 clone1a

value: Neural progenitors and neurons

value: 120 days


title: C-CNOCre+_rep2 (paired to Cre- within dam)

value: placenta

value: hM3Dq+ Gcm1Cre+


title: Tub B rep1

city: wuhan

first: Jie

last: Yao

state: 湖北

address: wuhan hubei province

institute: wuhan university

data_processing:
Illumina RTA software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR 2.7.0 with default parameters
The gene expression level was calculated by featureCounts with default parameters.
Assembly: hg19
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: HepG2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted by using EASYspin RNA Mini Kit (Aidlab RN07).
RNA-seq libraries were constructed by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB E6111).

treatment_protocol: HepG2 cells were treated with DMSO or 80 μM Tub B for 48 h.

value: Human hepatoblastoma

value: Tub B


title: plasma, subject 602c8cc5T1


title: 184337_B001orig_2

description: 10x Genomics


title: Tub B rep2

value: WT


title: B-CNOCre-_rep2 (paired to Cre+ within dam)

value: hM3Dq+ Gcm1Cre-

value: CNO


title: SKF-sample1


title: DMSO rep2

value: DMSO


title: 184337_B001orig_1

description: 10x Genomics


title: C-CNOCre+_rep1 (paired to Cre- within dam)


title: 184337_F10_3

description: 10x Genomics

value: HD.1 clone3b


title: DMSO rep1


title: plasma, subject 5f88502fT4

value: Positive

value: No

value: Yes

value: Somascan discovery platform v4


title: 184337_F10_2

description: 10x Genomics

value: Neural organoid


title: B-CNOCre-_rep1 (paired to Cre+ within dam)


title: Control-sample2

value: Liver


title: plasma, subject 5f88502fT2

value: Male


title: GSC827_GSC_Brunello_Day8_unsorted_R2

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

description:
Post-selection Day 8 (p27Hi unsorted) for GSC827 transduced with Brunello library (Doench et al. 2016); replicate 2
827_Day8_Unsorted_R2

data_processing:
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and  employed a single-end, 50 base read length (SE50) sequencing strategy.
Reads were aligned to the guide library  using Bowie and counted for gene associations against the guide library used.
Raw counts for each guide are supplied for every sample
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample.

growth_protocol: GSC827 were grown on laminin-coated substrate in N2B27 media supplemented by EGF and FGF in subconfluent conditions.

extract_protocol:
Cells were harvested at Day 0 post-selection and at the final timepoint and DNA was extracted using DNA Blood Mini Kit (Qiagen).
Guides were PCR-amplified and sequencing adapters for standard illumina sequencing and sample indices for multiplexing were attached through two rounds of PCR.

treatment_protocol: Cells were transduced with lentiCRISPR v2 plasmids (Zhang lab)  for each of the libraries at a MOI <1 (.2-.6) at a representation >250x. Two days after transdution, infected cells were selected using treatment with 1 ug/mL puromycin for 3 days.

tag: library

value: Brunello

tag: timepoint

value: unsorted


title: 184337_F10_1

description: 10x Genomics

value: Neural progenitors and neurons

tag: genotype

value: 120 days


title: plasma, subject 5f88502fT1

tag: subject id


title: 184337_176_3

description: 10x Genomics

value: HD.1 clone3a

value: Control


title: A-SalineCre-_rep4

value: placenta

value: hM3Dq+ Gcm1Cre-

value: Saline


title: plasma, subject 5f81193aT12

tag: blood sample id


title: GSC827_GSC_Brunello_Day8_R3

description:
Post-selection Day 8 (p27Hi sorted) for GSC827 transduced with Brunello library (Doench et al. 2016); replicate 3
827_Day8_pos_R3

value: sorted


title: 184337_176_2

description: 10x Genomics


title: A-SalineCre-_rep3


title: GSC827_GSC_Brunello_Day8_R2

description:
Post-selection Day 8 (p27Hi sorted) for GSC827 transduced with Brunello library (Doench et al. 2016); replicate 2
827_Day8_pos_R2


title: plasma, subject 5fee91b3T1

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

tag: Sex

value: Positive


title: plasma, subject 5f88502fT3

tag: age

value: No


title: plasma, subject 5f456924T3

value: Female

tag: days since first sample

value: Yes


title: 184337_176_1

description: 10x Genomics

value: Neural organoid


title: A-SalineCre-_rep2


title: GSC827_GSC_Brunello_Day8_R1

description:
Post-selection Day 8 (p27Hi sorted) for GSC827 transduced with Brunello library (Doench et al. 2016); replicate 1
827_Day8_pos_R1


title: 178120_A3rep_2

description: 10x Genomics

value: Pat.2 clone2d


title: plasma, subject 5f456924T2

tag: patient classification at first sample

value: Somascan discovery platform v4


title: A-SalineCre-_rep1


title: 178120_A3rep_3

description: 10x Genomics


title: plasma, subject 5f456924T1

tag: covid-19 status


title: GSC827_GSC_Brunello_Day8_unsorted_R3

description:
Post-selection Day 8 (p27Hi unsorted) for GSC827 transduced with Brunello library (Doench et al. 2016); replicate 3
827_Day8_Unsorted_R3

value: Brunello


title: MVTT-treated, replicate 1, scRNAseq

city: Hong Kong

first: Zhiwu

last: Tan

address: 21 Sassoon Road, Pokfulam

department: Microbiology

country: Hong Kong

institute: University of Hong Kong

description: BD Rhapsody

data_processing:
Targeted transcriptomics sequencing files were processed via the BD Rhapsody Targeted Analysis Pipeline on SevenBridges (https://www.sevenbridges.com) according to the manufacturer's recommendations.
Supplementary files format and content: Tab-separated values files and matrix files
BD_Rhapsody_Immune_Response_Panel_Mm.fasta contains mRNA/transcript barcodes.
BDAbSeq_allReference_mm.fasta contains antibody barcodes.
Rhapsody_cell_labels.fasta contains cell label barcodes.
Please note that:
Information on the cell label is captured by bases in three sections (CLS1, CLS2, CLS3) along each R1 read. And after  each cell label section is identified, the three-part cell label is converted into a single integer with the following calculation:
(CLS1 - 1) * 96 * 96 + (CLS2 - 1) * 96 + CLS3

source_name: innoculated tumor

extract_protocol:
solid tumors were cut into pieces and digested with Tumor Dissociation Kit (Miltenyi Biotec) according to the manufacturer’s instructions under a gentleMACS Octo Dissociator (Miltenyi Biotec). After 40%/80% Percoll gradient (Sigma), leukocytes at the interphase were recovered after centrifugation and stained with Zombie Aqua dye and CD45+ antibody for isolation of total CD45+ cells
Library was performed according to the manufacter’s instructions (Targeted Library Preparation, BD Rhapsody). Briefly, cells were first labelled with AbSeq Ab-Oligos (including CD3e (clone 500A2), CD4 (clone RM4-5), CD8a (clone 53-6.7), CD19 (1D3), CD11c (N418), F4/80 (T45-2342), CD11b (clone M1/70), Ly6G/6C (clone RB6-8C5) antibodies) strictly following the manufacturer's protocol. Cells were then pooled and loaded on BD Rhapsody System at a cell number of <= 20, 000 cells of each Cartridge, and were processed according to the manufacturer's protocol. All steps were confirmed to pass Quality Control Requirements by BD Rhapsody System before processing to reverse transcription and library construction. cDNA Libraries were sequentially prepared using BD Rhapsody cDNA Kit (#633773) and BD Rhapsody Targeted Amplification Kit (#633734) supplemented with Mouse Immune Response Panel primers (#633753). Quality of final libraries was assessed by using Fragment Analyzer Automated CE System (Agilent) with High Sensitivity NGS Fragment Analysis Kit (Agilent, #DNF-474)

value: innoculated tumor

value: MVTT

value: tumor-infiltrating CD45+ cells


title: GSC827 invitro model with KAT5 ko

description:
GSC827_KAT5KO
GSC827 invitro model with KAT5 ko

data_processing:
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and used a standard Illumina dual-index, paired-end constructs with the single Cell 14 bp barcode  in the i7 index read (14 nt), sample  index sequences in the i5 index read (8 nt), and Read 1 (98 nt) and Read 2 (10 nt) with standard Illumina sequencing primers in paired-end sequencing.
raw bcl files were processed using cellranger mkfastq and cellranger count
bam files from output of  cell ranger count are submitted as raw files
Assembly: hg38
Supplementary files format and content: barcodes.tsv, genes.tsv and matrix.mtx ( 3 files per sample, output from cellranger count) are submitted as processed files.

source_name: GSC827 invitro model with KAT5 ko

extract_protocol:
5000 cells from subconfluent GSC827 (matched for density and media changes) were loaded on a a GemCode Single Cell Instrument (10x Genomics) to generate single-cell GEMs for library preparation using Single Cell Gel Bead Kit (P/N 120217) according to manufacturer's guidelines. G0/G1 cells were first sorted on an FACSAria II (BD Biosciences) for the cells postive only for mCherry-hCDT1(aa30/120).
RNA libraries were prepared for sequencing using Single Cell Library Kit from 10x Genomics (P/N 120218) according to manufacturer's guidelines.

treatment_protocol: CRISPR KO was performed through lentiviral transduction (lentiCRISPR v2 (Zhang lab)) and KO samples were collected at least 14 days post-selection.

tag: crispr status

value: invitro


title: GSC827 invitro model

description:
GSC827_CD8KO
GSC827 invitro model

source_name: GSC827 invitro model


title: GSC827_GSC_Brunello_Day8_unsorted_R1

description:
Post-selection Day 8 (p27Hi unsorted) for GSC827 transduced with Brunello library (Doench et al. 2016); replicate 1
827_Day8_Unsorted_R1

tag: cell line

value: unsorted


title: mock-treated, replicate 1, scRNAseq

description: BD Rhapsody

value: mock

tag: cell type


title: 178120_B002_F7_3

description: 10x Genomics

tag: tissue

value: Pat.2 clone2b

value: Neural progenitors and neurons

value: 120 days


title: GSC827 Dox+ / Kat5+ tumor

description:
GSC827_Dox+_KAT5+
GSC827 Dox+ / Kat5+ tumor

source_name: GSC827 Dox+ / Kat5+ tumor

value: Dox+ / Kat5+


title: 178120_A3rep_1

description: 10x Genomics

value: Control


title: plasma, subject 5ea543fdT1

value: Female

value: Positive

value: No

tag: instrument model


title: plasma, subject 5ea543fdT4

value: Yes


title: plasma, subject 5e2f7e89T4

value: Male

value: Somascan discovery platform v4


title: podocyte, TFEB siRNA-3

city: Guangzhou

first: Cuili

last: Li

address: No.106 Zhongshan Road 2

department: Nephrology

institute: South China University of Technology

data_processing:
The amount and purity of total RNA were quantified using NanoDrop ND-1000
Poly (A) RNA was purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 with two rounds of purification.
The poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module under 94℃ for 5-7min.
The RNA fragments were reverse-transcribed to cDNA using SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution.
The U-labeled second-stranded DNAs were added poly (A),  treated with the heat-labile UDG enzyme（NEB, MA, US) and ligated to the indexed adapters
Assembly: mm10
Supplementary files format and content: RPKM values for each Sample
Supplementary files format and content: The average insert size for the final cDNA library was 300±50 bp.

source_name: kidney

growth_protocol: Podocytes were cultured in 33°C with Roswell Park Memorial Institute-1640 medium supplemented with 10% fetal bovine serum  and recombinant interferon -γ  for proliferation. podocytes were cultured in 37°C with Roswell Park Memorial Institute-1640 medium supplemented with 5% fetal bovine serum and 12 mg/ml of type-I collagen for differentiation.The duration of podocyte differentiation lasts 10-14 days.

extract_protocol:
Total RNA was isolated and purified from podocytes of each independent group using TRIzol reagent (Thermo Fisher Scientific, MA, USA) following the manufacturer's procedure
RNA libraries were prepared for sequencing using standard illumina protocols

value: kidney

value: immortalized mouse podocyte

value: podocyte

value: TFEB knockdown

tag: treatment

value: Transfection of siRNA


title: GSC827 Dox- / Kat5- tumor

description:
GSC827_Dox-_KAT5-
GSC827 Dox- / Kat5- tumor

source_name: GSC827 Dox- / Kat5- tumor

value: Dox- / Kat5

value: invitro


title: plasma, subject 5e2f7e89T1


title: 178120_B002_F7_1

description: 10x Genomics

value: Neural organoid

value: Pat.2 clone2b

value: Neural progenitors and neurons


title: 178119_E11rep_3

description: 10x Genomics

value: Pat.2 clone2c

value: Control

value: 120 days


title: podocyte, TFEB siRNA-2


title: podocyte, TFEB siRNA-1


title: replicate3 for   GSC827 tumor

description:
GSC827 REF REP3
replicate3 for  invivo GSC827

source_name: invivo GSC827

tag: sample type

value: intergrated ref

value: invivo


title: plasma, subject 5e2f7e89T0

source_name: serum

value: Male

value: Positive

value: No

value: Yes


title: replicate2 for   GSC827 tumor

description:
GSC827 REF REP2
replicate2 for  invivo GSC827


title: 81418_HP_K2 [WT]

city: Cologne

first: Muhammad Sajid

last: Hussain

address: Weyertal 115b

department: Cologne Center for Genomics

institute: University of Cologne

data_processing:
Illumina Casava software used for basecalling
RNA-Seq data were processed through the QuickNGS analysis pipeline  version 1.2.7, based on Ensembl 87
Sequenced reads mapped to Homo sapiens
Fragment Per Kilobase of exon per Million (FPKM) were calculated using a Cufflinks
Genome_build: Ensembl version 87 ( Homo sapiens )
Supplementary_files_format_and_content: Text file include FPKM values for each Sample

source_name: Primary fibroblast cells

growth_protocol: We generated dermal primary fibroblast cells by getting biopsies from patient and age matched control. Obtained cells were grown in DMEM Medium supplemented with fetal bovine serum, L-glutamine and antibiotics (Penicillin/Streptomycin).

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

value: Patient derived primary fibroblasts

value: Skin

value: Wild type


title: 178119_E11rep_2

description: 10x Genomics


title: podocyte, scramble-3

value: kidney

value: immortalized mouse podocyte

value: podocyte

value: WT

value: Transfection of scrambled siRNA


title: podocyte, scramble-2


title: podocyte, scramble-1


title: 65142_YHF_K [WT]


title: 178119_E11rep_1

description: 10x Genomics

value: Neural organoid

value: Pat.2 clone2c

value: Neural progenitors and neurons


title: 178119_B002orig_3

description: 10x Genomics

value: Pat.2 clone2a

value: 120 days


title: plasma, subject 5d55118bT4

value: Male

value: Negative

value: Somascan discovery platform v4


title: plasma, subject 5d04a912T8

value: Female

value: Positive

value: No

value: Yes


title: plasma, subject 5d55118bT1


title: 177136_E11rep_2

description: 10x Genomics

value: Control


title: 81417_HF_P2 [mutant]

value: Patient derived primary fibroblasts

value: Skin

value: Mutant


title: CD4+ T cells, 10 μM acacetin  treatment, biol rep 3

city: Zhengzhou

first: yang

last: lu

address: Zhengzhou

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
Under the action of reverse transcriptase, six-base random primers (random hexamers) are added to synthesize one-stranded cDNA using mRNA as a template, followed by two-stranded synthesis to form a stable double-stranded structure
The double-stranded cDNA structure is sticky-terminated. End Repair Mix is added to make it flat-terminated, followed by the addition of an "A" base at the 3' end, which is used to join the Y-junction.
Bridge PCR amplification was performed on the cBot to generate clusters
Illumina platform sequencing (PE library, read length 2×150bp)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: CD4+ T cells

growth_protocol: CD4+ T cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere at 37°C and 5% CO2.

extract_protocol:
The total RNA was extracted from the tissue samples, and the concentration and purity of the extracted RNA were examined using Nanodrop2000, the RNA integrity was examined by agarose gel electrophoresis, and the RIN value was determined by Agilent2100. A single library build required total RNA ≥ 1ug, concentration ≥ 35ng/μL, OD260/280 ≥ 1.8, OD260/230 ≥ 1.0 .
Library construction using Illumina TruseqTM RNA sample prep Kit method

treatment_protocol:
Isolated CD4+ T cells were treated with 5 μg/ml CD3/CD28 antibody precoated culture plates to induce activation.
Cells were cultured for 3 days in the presence of acacetin supplemented with 0,5,10 μM

value: CD4+ T cells

value: WT

value: CD3/CD28 antibody

tag: time

value: Day 3


title: replicate1 for   GSC827 tumor

description:
GSC827 REF REP1
replicate1 for  invivo GSC827

value: intergrated ref

value: invivo


title: 178119_B002orig_2

description: 10x Genomics

value: Neural organoid

value: Pat.2 clone2a

value: Neural progenitors and neurons

value: 120 days


title: plasma, subject 5d362febT1

value: Male

value: Positive

value: Somascan discovery platform v4


title: 178120_B002_F7_2

description: 10x Genomics

value: Pat.2 clone2b


title: plasma, subject 5d04a912T12

value: Female

value: Yes


title: plasma, subject 5d04a912T4

value: No


title: plasma, subject 5e152c59T1


title: plasma, subject 5d04a912T1


title: 65141_YHFLEF1_P [mutant]

value: Patient derived primary fibroblasts

value: Skin

value: Mutant


title: CD4+ T cells, 10 μM acacetin  treatment, biol rep 1

value: CD4+ T cells

value: WT

value: CD3/CD28 antibody

value: Day 3


title: 177136_E11rep_1

description: 10x Genomics

value: Neural organoid

value: Pat.2 clone2c

value: Control


title: Control gingival group1

city: Zunyi

first: chen

last: bin

address: Xuefu West street num 6

institute: Zunyi Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Read alignment software,software HISAT,version2.0
perform expression level for mRNAs by calculating FPKM. stimate the expression leveles of all transcripts.software StringTie,version1.3.0,parameters-bdta-q phred33-quals.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

source_name: Gingival tissue

extract_protocol:
mRNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Using Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC: RNA concentration, RIN value, 28S/18S and the fragment length distribution. For plant and fungi samples, we use NanoDropTMto identify the purity of the RNA samples.

value: Gingival tissue


title: plasma, subject 5bc2c935T4

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.

value: Male

value: Positive


title: Impacted wisdom tooth group3

source_name: Gingival tissue of impacted teeth

value: Gingival tissue of impacted teeth


title: 178119_B002orig_1

description: 10x Genomics

value: Pat.2 clone2a

value: Neural progenitors and neurons

value: 120 days


title: 177136_B002orig_2

description: 10x Genomics


title: CD4+ T cells, 10 μM acacetin  treatment, biol rep 2


title: Control gingival group2


title: CD4+ T cells, 5 μM acacetin  treatment, biol rep 1


title: CD4+ T cells, 5 μM acacetin  treatment, biol rep 2


title: CD4+ T cells, 5 μM acacetin  treatment, biol rep 3


title: Impacted wisdom tooth group1


title: plasma, subject 5bc2c935T1

value: No

value: Yes

value: Somascan discovery platform v4


title: CD4+ T cells, 0 μM acacetin  treatment, biol rep 2

value: CD4+ T cells


title: CD4+ T cells, 0 μM acacetin treatment, biol rep 3

value: WT


title: plasma, subject 5bbbd4c9T4

value: Female


title: plasma, subject 5bbbd4c9T20


title: CD4+ T cells, 0 μM acacetin treatment, biol rep 1

value: CD3/CD28 antibody

value: Day 3


title: PDGC CD97 splice variant 3 overexpression (GBML83 CD97iso3 Rep2)

first: Niklas

last: Ravn-Boess

state: NY

address: 550 1st Avenue

institute: NYU Langone

description:
GBML83 CD97iso3 Rep2
GBML83_rawcounts

data_processing:
STAR (v2.5.0c)
aligned to the reference genome (hg19)
Seq-N-Slide (rna-star-groups-dge) software
Assembly: hg19
Supplementary files format and content: raw count values

source_name: patient-derived glioblastoma culture

growth_protocol: PDGCs were kept in serum-free GBM media and were lentivirally infected with shRNA or overexpression constructs. Overexpression infected PDGCs were treated with doxycycline.

extract_protocol:
RNA was extracted using a RNeasy Mini Kit (Cat# 74104, Qiagen) according to the manufacturer’s protocol
Samples were submitted to the NYU Langone Genome Technology Core (GTC)

value: patient-derived glioblastoma culture

value: GBM

value: CD97 overexpression


title: 177136_B002orig_1

description: 10x Genomics

value: Neural organoid


title: PDGC CD97 splice variant 2 overexpression (GBML83 CD97iso2 Rep2)

description:
GBML83 CD97iso2 Rep2
GBML83_rawcounts


title: plasma, subject 5bbbd4c9T1

value: Positive


title: PDGC CD97 splice variant 3 overexpression (GBML83 CD97iso3 Rep1)

description:
GBML83 CD97iso3 Rep1
GBML83_rawcounts


title: Siglec-15 knockout, pOC2

city: Sapporo

first: Hideyuki

last: Kobayashi

department: epartment of Orthopaedic Surgery, Faculty of Medicine and Graduate School of Medicine

country: Japan

institute: Hokkaido university

description: Sample 11

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped by alignment to mouse genome (mm10) using STAR, gene expression level was quantified using RSEM, and then differential expression analysis was performed with the edgeR package within the R programming environment.
Assembly: GRCm38
Supplementary files format and content: tab-delimited test files include TPM values for each Sample

source_name: Pre Osteoclasts

growth_protocol: Bone marrow macrophages were maintained in αMEM supplemented with 10% fetal bovine serum (FBS), M-CSF 30ng/ml and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were lysed with TRIzol Reagent and harvested for RNA purification. RNA was purified using Rneasy Mini kit columns according to the manufacturer's instructions, and integrity of samples was assessed by determining 28S/18S ribosomal RNA bands with an Aglient 2100 bioanalyzer.
High-quality DNA-free RNA with integrity score > 9.0 was further used for RNA-seq. Each library was generated from 0.5-1 μg pooled RNA of 3 donors (equal quantity) using the TruSeq® Stranded mRNA Sample Preparation Kit. Quality of libraries was examined by Bioanalyzer High sensitivity DNA kit, and then paired-end reads (101 bp) were obtained by Illumina NovaSeq 6000, with an average of 69 million reads per sample.

treatment_protocol: Osteoclast differentiation was induced by treatment of 60%confluent cells (designated day 0, D0) with M-CSF 30ng/ml and RANKL 100ug/ml .

value: Pre Osteoclasts

value: Siglec-15 knockdown

value: Osteoclast differenciation


title: PDGC CD97 splice variant 2 overexpression (GBML83 CD97iso2 Rep1)

description:
GBML83 CD97iso2 Rep1
GBML83_rawcounts


title: Siglec-15 knockout, pOC3

description: Sample 12


title: Impacted wisdom tooth group2

value: Gingival tissue of impacted teeth


title: PDGC CD97 splice variant 1 overexpression (GBML83 CD97iso1 Rep2)

description:
GBML83 CD97iso1 Rep2
GBML83_rawcounts


title: plasma, subject 5badd4f1T1

first: Pushkala

last: Jayaraman

institute: Icahn School of Medicine at Mount Sinai

value: No


title: plasma, subject 5ae80188T4

value: Male

value: Yes


title: Siglec-15 knockout, BMM3

description: Sample 9

source_name: Bone marrow macrophages

value: Bone marrow macrophages

value: Day 0


title: PDGC CD97 splice variant 1 overexpression (GBML83 CD97iso1 Rep1)

description:
GBML83 CD97iso1 Rep1
GBML83_rawcounts


title: Siglec-15 knockout, pOC1

description: Sample 10


title: PDGC empty vector overexpression (GBML83 EV Rep2)

description:
GBML83 EV Rep2
GBML83_rawcounts

value: EV


title: CD34_CHD7

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

description: Ordered from Fred Hutchinson Cancer Research Center

library_source: genomic

data_processing:
Reads were aligned to human reference genome hg19 using Bowtie Version 0.12.9 with parameters -n 2 -S -k 2 -m 2 -best
Regions enriched for CHD7 were identified using SICER with parameters -w 200 -I 200 -g 400 -e 1e1
Regions enriched for histone H3K27ac were identified using MACS with input control and parameters -p 1e-9 -keep-dup=auto
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Alignment and bed files of binding peaks

molecule: genomic DNA

source_name: CD34+ cells

growth_protocol: Human mobilized peripheral CD34+ cells were thawed and grown in StemSpan SFEM media supplemented with 2% pen/strep and 1% StemSpan CC100 cocktail (Stem Cell Technologies) for 5 days. Cells were fixed and collected on day 5 for ChIP-seq.

extract_protocol:
CD34+ cells were fixed in 1% formaldehyde for 10 minutes and lysed to collect nuclei for sonication, followed by ChIP with antibody.
Library synthesis was performed using TruSeq ChIP Library Prep Kit (Illumina).

treatment_protocol: None.

value: mobilized peripheral blood

value: CD34 positive cells

tag: antibody

value: Anti-CHD7 (Bethyl,A301-223A)


title: CD34_H3K27ac

value: Anti-histone H3K27ac (Abcam,ab4729)


title: Siglec-15 knockout, BMM2

description: Sample 8

tag: genotype


title: plasma, subject 5ae80188T1

city: New York

address: 1 Gustave Levy Pl

tag: subject id

value: Somascan discovery platform v4


title: PDGC empty vector overexpression (GBML83 EV Rep1)

description:
GBML83 EV Rep1
GBML83_rawcounts

value: patient-derived glioblastoma culture

value: GBM


title: CD34_CHD7_Input


title: Siglec-15 knockout, BMM1

description: Sample 7


title: WT, pOC3

description: Sample 6

value: Pre Osteoclasts

value: WT

value: Day 3


title: plasma, subject 5ab88658T12

tag: blood sample id

value: Positive


title: plasma, subject 5ab88658T1

tag: Sex

value: No


title: plasma, subject 5aabb512T4

value: Female

tag: age


title: A-SalineCre-_rep6

source_name: placenta

value: placenta

value: hM3Dq+ Gcm1Cre-

value: Saline


title: PDGC CD97 knockdown (GBML83 CD97sh Rep2)

description:
GBML83 CD97sh Rep2
GBML83_rawcounts
GBML83_DESeq


title: PDGC CD97 knockdown (GBML83 CD97sh Rep1)

description:
GBML83 CD97sh Rep1
GBML83_rawcounts
GBML83_DESeq


title: Vari068 Docetacel non-PGCC

city: Pittsburgh

first: Yu-Chih

last: Chen

state: Pennsylvania

address: 5115 Centre Ave

institute: UPMC Hillman Cancer Center/University of Pittsburgh

data_processing:
Drop-Seq 2.5.1 alignment and read processing
Assembly: GRCh38.p13
Supplementary files format and content: DGE file

molecule: polyA RNA

source_name: Breast Cancer

extract_protocol:
Based on the Drop-Seq biochemistry, cells and barcoded beads were paired in microwells, so the mRNA from lysed cells can hybridize onto the barcoded beads. After barcoded beads captured cellular mRNA, we performed RT (Thermofisher Maxima RT kit), PCR (Kapa HiFi Hotstart PCR Readymix).
Library preparation is based on the Illumina Nextera XT Library Prep Kit.

value: Breast Cancer

tag: cell population

value: non-PGCC

value: TNBC

value: Docetaxel


title: WT, pOC1

description: Sample 4

value: Osteoclast differenciation


title: Vari068 Control non-PGCC


title: plasma, subject 5aabb512T3

tag: days since first sample

tag: patient classification at first sample

value: Yes

value: Somascan discovery platform v4


title: PDGC scrambled control (GBML83 SCRsh Rep3)

description:
GBML83 SCRsh Rep3
GBML83_rawcounts
GBML83_DESeq

value: patient-derived glioblastoma culture

value: GBM

value: SCRshRNA


title: Vari068 Control PGCC

value: PGCC


title: PDGC scrambled control (GBML83 SCRsh Rep2)

description:
GBML83 SCRsh Rep2
GBML83_rawcounts
GBML83_DESeq


title: plasma, subject 5badd4f1T12

tag: covid-19 status

value: Positive


title: SUM159 Docetacel non-PGCC

tag: cell line


title: SUM159 Docetacel PGCC


title: WT, BMM3

description: Sample 3

tag: cell type

value: Bone marrow macrophages

value: WT

value: Day 0


title: PDGC scrambled control (GBML83 SCRsh Rep1)

description:
GBML83 SCRsh Rep1
GBML83_rawcounts
GBML83_DESeq

tag: tissue


title: plasma, subject 5aabb512T1

value: Female

value: No

tag: instrument model


title: plasma, subject 5a8ceac6T1

value: Male


title: WT, BMM1

description: Sample 1

tag: treatment


title: PDGC CD97 knockdown (GBML83 CD97sh Rep3)

description:
GBML83 CD97sh Rep3
GBML83_rawcounts
GBML83_DESeq


title: plasma, subject 5a184e56T1

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


title: SUM159 Control

value: Breast Cancer

value: Control


title: PDGC CD97 knockdown (GBML91 CD97sh)

description:
GBML91 CD97sh
GBML128L90L91_rawcounts


title: Vari068 Docetacel PGCC

value: TNBC

value: Docetaxel


title: WT, pOC2

description: Sample 5

value: Pre Osteoclasts

value: Osteoclast differenciation

value: Day 3


title: MDA-MB-231 Docetacel non-PGCC

value: non-PGCC


title: BR10BPA_rep2 [Sample_15851]

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
Demultiplexing was perfomed using bcl2fastq2 v2.20
Adapter trimming was performed using Trimmomatic v0.36 with following parameters ILLUMINACLIP:NexteraPE-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:25 MINLEN:36 CROP:48
Alignment was performed using bowtie2 v2.4.5 against the human reference genome mm10.
Duplicated reads were removed using picard "dedup" function and the transposase-induced offset was removed using the deeptools v3.1.3 "alignmentSieve" function.
Sorting and indexing of bam files was done using samtools v1.14
Peak calling was performed using MACS2 v2.2.7.1. on sample merged .bam file
Quantification of sequencing reads in unified peak regions was performed in R 4.1.0 using the "summarizeOverlaps" function implemented in the GenomicAlignments package v1.28.0.
Assembly: mm10
Supplementary files format and content: comma separated files include raw count table

source_name: brain

extract_protocol:
Fresh frozen lung and brain tissue sections from C57BL/6J mice were collected on a UV-activated PEN slide and further tagmented in situ using an in-house Tn5 enzyme for 1 h at 37 °C. Following, LCM was applied to collect a mini bulk of randomly captured nuclei (PALM microdissection microscope, Zeiss). Two mini-bulk sizes were investigated: 50 single-captured nuclei or 10 larger captured-areas composed each of roughly 20 nuclei, for a total of ~200 nuclei. This was applied both on brain and lung samples, at least in technical duplicates and nuclei were collected in reverse-crosslinking buffer containing Proteinase K and SDS. After reverse crosslinking at 65 °C for 1 hour, tagmented fragments were amplified, purified and sequenced paired-end on a Illumina NextSeq 2000.
Barcoded Nextera i7 and i5 primers were used to amplify the tagmented gDNA and preapare it for Illumina sequencing
ATAC-seq - Paired End 50 on a NovaSeq6000 (S1 v1.5 chemistry)

value: brain

tag: cell number

tag: strain


title: plasma, subject 5a0b46e8T8

value: Yes

value: Somascan discovery platform v4


title: MDA-MB-231 Docetacel PGCC

value: PGCC


title: PDGC scrambled control (GBML91 SCRsh)

description:
GBML91 SCRsh
GBML128L90L91_rawcounts

value: patient-derived glioblastoma culture

value: GBM

value: SCRshRNA


title: PDGC CD97 knockdown (GBML90 CD97sh)

description:
GBML90 CD97sh
GBML128L90L91_rawcounts


title: BR10BPA_rep1 [Sample_15850]

value: WT


title: BR50SCA_rep2 [Sample_15848]


title: PDGC scrambled control (GBML90 SCRsh)

description:
GBML90 SCRsh
GBML128L90L91_rawcounts


title: plasma, subject 5a0b46e8T4

value: Female

value: Positive

value: No


title: plasma, subject 5a0b46e8T12


title: BR50SCA_rep1 [Sample_15847]


title: plasma, subject 5a0b46e8T1


title: MDA-MB-231 Control

value: Breast Cancer

value: Control

value: TNBC


title: PDGC CD97 knockdown (GBML128 CD97sh)

description:
GBML128 CD97sh
GBML128L90L91_rawcounts


title: Serum, control 4

city: Galveston

first: Xiaoyong

last: Bao

state: TX

address: 301 University Boulevard

department: Pediatrics

institute: University of Texas Medical Branch

data_processing:
For seq data analyses, adaptor sequences were removed using Cutadpat, and RNAs with a length ≥ 15 bp were extracted. RNAs with counts of less than ten and all rRNAs were filtered out. The remaining RNA reads, also treated as cleaned input reads, were mapped to our in-house small RNA database using bowtie2 (v2.4.1), allowing two mismatches, as we previously described. In brief, our in-house small RNA database includes 1) tRF5 and tRF3 databases using the identical sequences derived from different tRNAs [sequences downloaded from tRNA genes using the Table Browser of the UCSC genome browser, 2) tRF1 sequences using genome locations of tRNAs, 3) miR/snoR sequences downloaded from the UCSC genome browser, and 4) piRNA sequences downloaded from piRBase (https://www.pirnadb.org/browse/pirna ).
Assembly: hg38
Supplementary files format and content: tab-seperated text file of read counts (matrix file)

extract_protocol:
mirVanaTM PARISTM RNA and native protein purification kit (AM1556, Invitrogen, Waltham, MA) was used to extract total RNAs from 300 µl CSF or 250 µl serum samples, according to the manufacturer's protocol. 5 μl of 5 nM artificial microRNA (cel-miR-39) was spiked after denaturing endogenous ribonucleases to control extraction efficiency. At the elution step, samples were incubated on the column for 5 min at 65 ℃, and RNAs were eluted with 45 μl nuclease-free water. TRIzol reagents (Thermo Fisher Scientific, Hercules, CA) were used to extract RNAs from the hippocampus.
RNAs were treated with T4 PNK (New England Biolabs, Ipswich, MA, US) to make the 3’-end of tRFs homogenously with 3’-OH before the ligation with sequencing barcodes, as the ligation of the 3′-end of sncRNAs with sequencing barcodes requires the presence of 3′-OH and not all sncRNAs have 3-OH ends. The treated RNA was purified and concentrated using Zymo RNA Clean and Concentrator kit (D4060, Thomas Scientific, Swedesboro, NJ). Small RNA libraries were then prepared with NEB Next Multiplex Small RNA Library Prep Set for Illumina (Ipswich, MA, US).

value: serum


title: plasma, subject 596d3193T1

value: Male


title: Serum, control 3


title: WT, BMM2

description: Sample 2

value: Bone marrow macrophages

value: Osteoclast differenciation

tag: time

value: Day 0


title: LU10BPA_rep1 [Sample_15841]

source_name: lung

value: lung

tag: genotype


title: plasma, subject 590c4e5aT12

tag: subject id

value: Yes

value: Somascan discovery platform v4


title: LU10BPA_rep3 [Sample_15843]


title: CSF, control 2

source_name: CSF

value: CSF


title: CSF, control 1


title: IDH mutant astrocytoma, scATACseq

description: 10x Genomics

library_source: genomic single cell

data_processing:
10x Genomics CellRanger, version 7.0.1
Assembly: hg38
Supplementary files format and content: Barcode, features, and matrix files.

source_name: tumor specimen

growth_protocol: Tumor specimen

extract_protocol:
The sample was then processed as described in the “10X Genomics Nuclei Isolation from Complex Tissues for Single Cell Multiome ATAC + GEX Sequencing Demonstrated Protocol CG000375 Rev B”
nuclei were processed for sequencing by the NYU GTC on an Illumina NovaSeq 6000 flow cell
10x Genomics single cell RNAseq and ATACseq

treatment_protocol: Glioma specimen are flash frozen and single cell RNAsequencing and ATAC sequencing

value: IDH mutant

value: astrocytoma

value: neural/tumor


title: plasma, subject 590c4e5aT1

tag: blood sample id

value: Female

value: Positive


title: IDH wildtype GBM, scATACseq

description: 10x Genomics

value: IDH wildtype

value: GBM


title: LU50SCA_rep3 [Sample_15840]

value: WT


title: plasma, subject 57e835f4T1

tag: Sex

value: No


title: IDH mutant astrocytoma, scRNAseq

description: 10x Genomics


title: plasma, subject 5816588aT1

value: Male

tag: age


title: PDA_10X_mixed_HTO_rep1

city: Heidelberg

first: Leo

middle: Carl

last: Förster

state: Deutschland

address: Im Neuenheimer Feld 581

institute: DKFZ

description: GTCAACTCTTTAGCG:hashtag1 (wntrep1), TGATGGCCTATTGGG:hashtag2 (wntrep2), TTCCGCCTCTCTTTG:hashtag3 (wntrep4), AGTAAGTTCAGCGTA:hashtag4 (wntrep5), AAGTATCGTTTCGCA:hashtag5 (sfrp1_9), GGTTGCCAGATGTCA:hashtag6 (sfrp1_10), TGTCTTTCCTGCCAG:hashtag7 (sfrp1_11), CTCCTCTGCAATTAC:hashtag8 (sfrp1_13), CAGTAGTCACGGTCA:hashtag9 (unused), ATTGACCCGCGTTAG:hashtag10 (unused)

data_processing:
hashtag UMI-counts were determined using CITE-seq-Count v1.4.5
hg38
CITE-seq-count UMI-count output files in MTX format

source_name: Cortical organoid

extract_protocol:
Barcoded oligonucleotide molecules were captured using bead-bound oligo dT(30) primers in droplets.
HTO sequencing library was constructed according to the cell hashing protocol for multiplexing as previously reported (Stoeckius et al. 2018).

value: Cortical organoid

tag: library type

value: HTO


title: LU50SCA_rep2 [Sample_15839]


title: LU50SCA_rep1 [Sample_15838]


title: PDA_10X_sorted_tumor_rep2_HTO

description: TGATGGCCTATTGGG:hashtag2 (organoid1), AGTAAGTTCAGCGTA:hashtag4 (organoid2), GGTTGCCAGATGTCA:hashtag6 (organoid3), CTCCTCTGCAATTAC:hashtag8 (organoid4)


title: 10X_PDA_sorted_tumor_rep1_HTO


title: LU10BPA_rep2 [Sample_15842]


title: plasma, subject 57e3c4f6T12

tag: days since first sample


title: Patient 4 PostTreatment 4

city: Geneva

first: Phil

middle: Fang

last: Cheng

address: Rue Gabrielle-Perret-Gentil 4

department: Oncology

country: Switzerland

institute: Hopitaux universitaires de Geneve

description: 10x Genomics 5'

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/)
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz.gz, features.tsv.gz.gz, matrix.mtx.gz, SingleCellExperiment R object: FNA_SCE.rds

source_name: melanoma

extract_protocol:
FNA samples were quickly thawed in a water bath set to 37°C, re-suspended in 10 mL of ice-cold RPMI (Sigma, cat. no. R0883) with 0.04% BSA (Sigma-Aldrich, cat. no. A7906) and incubated for 10 min on ice to allow DMSO to diffuse from the tissue. Samples were spun down at 300g for 5 min, resuspended in PBS with 0.04% BSA (Sigma-Aldrich, cat. no. A7906) and cell count and viability was assessed using Luna-FLTM cell counter (Dual Fluorescence Cell counter, Logos Biosystems Inc., cat. no. L1001) using acridine orange propidium iodide (AOPI, Logos Biosystems Inc., cat. no. F23001) live/dead staining. Cell concentration was set according to 10X Genomics recommendation to 700-1000 cells/μL and 10 000 cells were targeted per sample. Cell suspensions were loaded on Chip G (10X Genomics, PN-1000120) and processed using the 10X Genomics Chromium platform with the 3' v3.1 profiling kit on 10X Genomics Chromium Single Cell Controller (10X Genomics, PN-120263).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: subject

value: Patient 4

value: melanoma


title: Patient 4 PostTreatment 3

description: 10x Genomics 5'


title: IDH wildtype GBM, scRNAseq

description: 10x Genomics


title: PTPN2 +/+ Rep 2 cytokine treated

city: Aurora

first: Kristen

last: Wells

state: CO

address: 1775 Aurora Ct,

department: Barbara Davis Center

institute: University of Colorado Anschutz

description:
TNF alpha (410-MT-010), IL-1beta (401-ML-005), INF-gamma (485-MI-100). All cytokines were dissolved in 0.1 % BSA containing PBS.  Cytokines were thawed and fully dissolved before mixing with the islet culture media (RPMI 1640, 10 % FBS, 1 % PS). All pro-inflammatory cytokine treatments were performed for 24 hours.
WT_5_CytokineTreatment

data_processing:
Fastqc (version 0.11.7) was run on the raw fastq files to check quality
Cutadapt (version 1.16) was used to trim illumina sequencing adaptors from the raw fastq files. Cutadapt was run using the following parameters -m 20 -a 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
STAR (version 2.5.2a) was used to align reads to the mouse GRCm38 genome post adaptor trimming. Star was run using the following parameters --outFilterMultimapNmax 10 --outFilterMismatchNmax 10 --outFilterMismatchNoverReadLmax 0.04 --tSAMmultNmax 1 --outMultimapperOrder Random --outSAMattrIHstart 0 --outSAMstrandField intronMotif
Reads were counted using featureCounts (version 1.6.2) from the subread package. FeatureCounts was run with the following parameters --extraAttributes 'gene_name,gene_biotype' -s 1
raw reads were loaded into the DESeq2 package (version 1.30.0). DESeq analysis was performed using the following design ~genotype + treatment + genotype:treatment to allow for interaction between the genotype and treatment.
Assembly: GRCm38
Supplementary files format and content: Tab delimited text file of counts output by feature counts and tab delimited meta data file with sample information

source_name: Pancreatic islet

extract_protocol:
Islets from 3 control and 3 Ptpn2-bKO mice were treated with pro-inflammatory cytokines. Treated and untreated islets were washed 3 times with cold-PBS. Total RNA was extracted using the RNeasy Micro Kit (QIAGEN) following instructions. We confirmed the RNA Integrity Number (RIN) value using an Agilent 2100 Bioanalyzer. RNA samples all had RIN values over 8.0. Libraries were constructed using 0.5 µg total RNA.
RNA was isolated with the RNeasy Micro kit (QIAGEN). Sequencing was performed using Illumina NovaSEQ6000.

value: PTPN2 fl/fl

value: Mixed strain background of C57BL/6J

value: 16 weeks

value: cytokine treatment


title: PTPN2 +/+ Rep 3 cytokine treated

description:
TNF alpha (410-MT-010), IL-1beta (401-ML-005), INF-gamma (485-MI-100). All cytokines were dissolved in 0.1 % BSA containing PBS.  Cytokines were thawed and fully dissolved before mixing with the islet culture media (RPMI 1640, 10 % FBS, 1 % PS). All pro-inflammatory cytokine treatments were performed for 24 hours.
WT_6_CytokineTreatment


title: PDGC scrambled control (GBML128 SCRsh)

description:
GBML128 SCRsh
GBML128L90L91_rawcounts

value: patient-derived glioblastoma culture

value: SCRshRNA


title: Patient 4 PostTreatment 2

description: 10x Genomics 5'


title: plasma, subject 572a7c65T4

source_name: serum

value: Female

tag: patient classification at first sample

tag: covid-19 status

value: Yes

value: Somascan discovery platform v4


title: PDA_10X_sorted_healthy_cells_HTO


title: Patient 4 PostTreatment 1

description: 10x Genomics 5'


title: PTPN2 +/+ Rep 3 not treated

description:
No treatment
WT_3_NonTreatment

treatment_protocol: TNF alpha (410-MT-010), IL-1beta (401-ML-005), INF-gamma (485-MI-100). All cytokines were dissolved in 0.1 % BSA containing PBS.  Cytokines were thawed and fully dissolved before mixing with the islet culture media (RPMI 1640, 10 % FBS, 1 % PS). All pro-inflammatory cytokine treatments were performed for 24 hours.

value: No treatment


title: PTPN2 +/+ Rep 1 cytokine treated

description:
TNF alpha (410-MT-010), IL-1beta (401-ML-005), INF-gamma (485-MI-100). All cytokines were dissolved in 0.1 % BSA containing PBS.  Cytokines were thawed and fully dissolved before mixing with the islet culture media (RPMI 1640, 10 % FBS, 1 % PS). All pro-inflammatory cytokine treatments were performed for 24 hours.
WT_4_CytokineTreatment


title: PDX_SS3_tumor_cells_NOTUM

data_processing:
Read1 sequences were processed to extract and trim UMIs, storing them in the FASTQ identifier field. Processed paired-end reads were trimmed using trim-galore v0.5.0 and mapped to the hg38 and mm10 genome references individually including Ensembl96 gene annotations using STAR v2.5.3a with "--bamRemoveDuplicatesType UniqueIdentical --outFilterMismatchNmax 9999 --outFilterScoreMinOverLread 0.2 --outFilterMatchNminOverLread 0.2 --alignSJoverhangMin 3 --alignSplicedMateMapLminOverLmate 0.2 --twopassMode Basic". UMI-containing readpairs were quantified with a custom script based on HTSeq to identify exonic and intronic UMIs and deduplicate them, reporting a merged UMI-counts matrix. Cell transcriptomes were subset to 1:1 human-mouse orthologs reported in Ensembl102 to be consistent with our downstream analysis. We excluded mouse cells with <1.3x reads mapped to human vs mouse genomes, and for quality-control excluded cells with fewer than 2000 UMIs or under 500 detected genes.
hg38
counts: comma separated matrix of deduplicated UMI counts per cell (columns) per gene (rows). Metadata: comma separated matrix relating metdata (columns) per cell (rows)

source_name: Brain tumor

extract_protocol:
RNA molecules were captured using an oligo dT(30) primer. mRNA was reverse-transcribed using a template switching oligonucleotide contianing an 8 bp unique molecular identifier to obtain cDNA which was subsequently amplified and purified using AMPureXP beads.
Purified cDNA was used for Illumina Nextera XP library preparation according to Hagemann-Jensen et al. 2020 with modifications reported in Cerrizuela and Kaya et al. 2022.

value: Brain tumor

value: TCF-Lef NOTUM


title: PDA_10X_mixed_HTO_rep2


title: PDX_SS3_tumor_cells_SFRP1

value: TCF-Lef SFRP1


title: Patient 4 Baseline

description: 10x Genomics 5'


title: plasma, subject 572a7c65T1

value: Positive

value: No


title: PDX_SS3_tumor_cells_wntrep

value: TCF-Lef EGFP


title: plasma, subject 56dee75fT8

value: Male


title: PDX_SS2_tumor_cells_wntrep

data_processing:
Paired-end reads were trimmed using trim-galore v0.5.0 and mapped to the hg38 and mm10 genome references individually including Ensembl96 gene annotations using STAR v2.5.3a with "--bamRemoveDuplicatesType UniqueIdentical --outFilterMismatchNmax 9999 --outFilterScoreMinOverLread 0.2 --outFilterMatchNminOverLread 0.2 --alignSJoverhangMin 3 --alignSplicedMateMapLminOverLmate 0.2 --twopassMode Basic --quantMode geneCounts". STAR-generated gene-wise read counts were merged into a counts matrix. Cell transcriptomes were subset to 1:1 human-mouse orthologs reported in Ensembl102 to be consistent with our downstream analysis. We excluded mouse cells with <1.3x reads mapped to human vs mouse genomes, and for quality-control excluded cells with fewer than 2000 UMIs or under 500 detected genes.
hg38
counts: comma separated matrix of read counts per cell (columns) per gene (rows). Metadata: comma separated matrix relating metdata (columns) per cell (rows)

extract_protocol:
RNA molecules were captured using an oligo dT(30) primer. cDNA was prepared using a template switching oligonucleotide to obtain cDNA which was subsequently amplified and purified using AMPureXP beads.
Purified cDNA was used for Illumina Nextera XP library preparation according to Picelli et al. 2014 with modifications reported in Cerrizuela and Kaya et al. 2022.


title: PTPN2 +/+ Rep 1 not treated

description:
No treatment
WT_1_NonTreatment

value: PTPN2 fl/fl


title: plasma, subject 56dee75fT4


title: plasma, subject 57e3c4f6T1


title: Patient 3 PostTreatment 3

description: 10x Genomics 5'

value: Patient 3

value: melanoma


title: PTPN2 -/- Rep 3 cytokine treated

description:
TNF alpha (410-MT-010), IL-1beta (401-ML-005), INF-gamma (485-MI-100). All cytokines were dissolved in 0.1 % BSA containing PBS.  Cytokines were thawed and fully dissolved before mixing with the islet culture media (RPMI 1640, 10 % FBS, 1 % PS). All pro-inflammatory cytokine treatments were performed for 24 hours.
KO_6_CytokineTreatment

value: PTPN2 -/-

value: Mixed strain background of C57BL/6J

value: 16 weeks

value: cytokine treatment


title: plasma, subject 572a7c65T8

value: Female

value: Yes


title: plasma, subject 56dee75fT1

value: Somascan discovery platform v4


title: Patient 3 PostTreatment 1

description: 10x Genomics 5'


title: plasma, subject 56811af1T1


title: Patient 3 Baseline

description: 10x Genomics 5'


title: PDX_SS2_tumor_cells_naive

data_processing:
Paired-end reads were trimmed using trim-galore v0.5.0 and mapped to the hg38 and mm10 genome references individually including Ensembl96 gene annotations using STAR v2.5.3a with "--bamRemoveDuplicatesType UniqueIdentical --outFilterMismatchNmax 9999 --outFilterScoreMinOverLread 0.2 --outFilterMatchNminOverLread 0.2 --alignSJoverhangMin 3 --alignSplicedMateMapLminOverLmate 0.2 --twopassMode Basic --quantMode geneCounts". STAR-generated gene-wise read counts were merged into a counts matrix. Cell transcriptomes were subset to 1:1 human-mouse orthologs reported in Ensembl102 to be consistent with our downstream analysis. We excluded mouse cells with <1.3x reads mapped to human vs mouse genomes, and for quality-control excluded cells with fewer than 2000 UMIs or under 500 detected genes.
hg38
counts: comma separated matrix of read counts per cell (columns) per gene (rows).

value: Brain tumor

value: WT


title: plasma, subject 55d94f54T12


title: ONS76, rep 2

city: Saint Petersburg

first: Ranjan

last: Perera

state: FL

address: 600 5th St S

department: Oncology Center

institute: Johns Hopkins All Childrens Hospital

description: small RNA

data_processing:
Basecalls were performed using bcl2fastq v2.17 for nextseq output.
Small RNA-seq reads were trimmed with trim_galore retaining minimum read length 16 and average read quality 20.
Reads were aligned to reference genome using STAR aligner with maximum 10 multiple alignments allowed.
Read counts for miRNA were generated using featureCounts from subread package using gff from mirbase database.
Assembly: GRCh38
Supplementary files format and content: featureCounts files

source_name: Human medulloblastoma

growth_protocol: DAOY cells were cultured in DMEM supplemented with 10% FBS, 1% sodium pyruvate, 1% nonessential amino acids and 1% penicillin/streptomycin. ONS-76 cells were cultured in RPMI-1640 supplemented with 10% FBS, 1% nonessential amino acids and 1% penicillin/streptomycin. D341 cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin. D425 cells were cultured in DMEM/F12 supplemented with 10% FBS and 1% penicillin/streptomycin. CHLA-01-MED and CHLA-01R-MED cells were cultured in DMEM/F12 with 10% FBS, 20 ng/mL EGF, 20 ng/mL bFGF, B-27 supplement and 1% penicillin/streptomycin.

extract_protocol:
miRNA was prepared from cell lines using the miRNeasy Mini Kit (Qiagen). The quality of RNA was determined with the High Sensitivity RNA ScreenTape assay in TapeStation (Agilent Technologies).
Small RNA libraries were prepared for sequencing using standard PerkinElmer protocols of NEXTFLEX Small RNA Sequencing Kit V4.

value: Human medulloblastoma

tag: cell line

tag: cell type

value: Medulloblastoma cell line


title: ONS76, rep 1

description: small RNA

tag: tissue


title: PTPN2 -/- Rep 2 cytokine treated

description:
TNF alpha (410-MT-010), IL-1beta (401-ML-005), INF-gamma (485-MI-100). All cytokines were dissolved in 0.1 % BSA containing PBS.  Cytokines were thawed and fully dissolved before mixing with the islet culture media (RPMI 1640, 10 % FBS, 1 % PS). All pro-inflammatory cytokine treatments were performed for 24 hours.
KO_5_CytokineTreatment

tag: treatment


title: PTPN2 -/- Rep 1 cytokine treated

description:
TNF alpha (410-MT-010), IL-1beta (401-ML-005), INF-gamma (485-MI-100). All cytokines were dissolved in 0.1 % BSA containing PBS.  Cytokines were thawed and fully dissolved before mixing with the islet culture media (RPMI 1640, 10 % FBS, 1 % PS). All pro-inflammatory cytokine treatments were performed for 24 hours.
KO_4_CytokineTreatment


title: Patient 2 PostTreatment 2

description: 10x Genomics 5'

value: Patient 2


title: PTPN2 -/- Rep 3 not treated

description:
No treatment
KO_3_NonTreatment

value: No treatment


title: Patient 2 PostTreatment 1

description: 10x Genomics 5'


title: plasma, subject 55d94f54T1

value: Male

value: Positive

value: No

tag: instrument model


title: DAOY, rep 3

description: small RNA

value: DAOY


title: PTPN2 -/- Rep 2 not treated

description:
No treatment
KO_2_NonTreatment

value: PTPN2 -/-

tag: strain


title: PTPN2 +/+ Rep 2 not treated

description:
No treatment
WT_2_NonTreatment

value: PTPN2 fl/fl

value: Mixed strain background of C57BL/6J


title: D425, rep 3

description: small RNA


title: Patient 1 PostTreatment 1

description: 10x Genomics 5'

value: Patient 1

value: melanoma


title: Patient 1 Baseline

description: 10x Genomics 5'


title: D425, rep 2

description: small RNA


title: plasma, subject 558be967T4

value: Yes


title: Patient 6 followup

description: 10x Genomics 5'

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/)
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_feature_bc_matrix.h5

source_name: Peripheral blood mononuclear cells

extract_protocol:
Frozen PBMC samples were quickly thawed in a water bath set to 37°C, re-suspended in 10 mL of ice-cold RPMI (Sigma, cat. no. R0883) with 0.04% BSA (Sigma-Aldrich, cat. no. A7906) and incubated for 10 min on ice to allow DMSO to diffuse from the tissue. Samples were spun down at 300g for 5 min, resuspended in PBS with 0.04% BSA (Sigma-Aldrich, cat. no. A7906) and cell count and viability was assessed using Luna-FLTM cell counter (Dual Fluorescence Cell counter, Logos Biosystems Inc., cat. no. L1001) using acridine orange propidium iodide (AOPI, Logos Biosystems Inc., cat. no. F23001) live/dead staining. Cell concentration was set according to 10X Genomics recommendation to 700-1000 cells/μL and 10 000 cells were targeted per sample. Cell suspensions were loaded on Chip K (10X Genomics, PN- 1000286) and processed using the 10X Genomics Chromium platform with the 5P V(D)J immune profiling kit on 10X Genomics Chromium Single Cell Controller (10X Genomics, PN-120263).
Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Peripheral blood mononuclear cells

tag: time point

value: followup

tag: disease state


title: plasma, subject 55967838T1

tag: subject id

value: Female

value: Somascan discovery platform v4


title: Microglia_coculture_wo [DE43NGSUKBR117836]

first: Susanne

last: Schmidt

address: Venusberg-Campus 1

department: Institute of Clin. Chemistry and Clin. Pharmacology

institute: University Hospital Bonn

data_processing:
Alignment with STAR against the mm10 reference genome
quantification of gene counts via Partek's E/M algorithm
DEseq2 normalization
Flooring
Assembly: mm10
Supplementary files format and content: fastq

source_name: Microglia

growth_protocol: Primary microglia were generated from P0-3 pups and cultured in in DMEM (Gibco) supplemented with 10% heat-inactivated fetal calf serum (FCS; Gibco) and 1% penicillin/streptomycin (P/S; Gibco) for 7-10 days.

extract_protocol:
RNA was isolated via Qiagen RNeasy micro kit
performed by the NGS Core Facility University Hospital Bonn according to the maufacturers' user guide for the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (https://www.lexogen.com/quantseq-3mrna-sequencing/#quantseqdownloads/)

treatment_protocol: Primary cortical neurons (DIV14) were loaded for 16 h with 0.1 µM Atto488-labelled α-syn fibrils, washed with PBS and co-cultured with or without microglia for 6 hrs. Control neurons were left untreated.

value: primary Microglia

tag: passages

tag: treatment group


title: DAOY, rep 2

description: small RNA

value: Human medulloblastoma

value: Medulloblastoma cell line


title: plasma, subject 558be967T1

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

tag: blood sample id

tag: Sex

value: Male

tag: age


title: Patient 3 PostTreatment 2

description: 10x Genomics 5'

tag: subject

value: Patient 3


title: Microglia_coculture_wo [DE38NGSUKBR117829]


title: Patient 6 baseline

description: 10x Genomics 5'

value: baseline


title: Patient 5 followup

description: 10x Genomics 5'


title: CHLA01-R, rep 2

description: small RNA


title: plasma, subject 54f0f59aT1

tag: days since first sample

tag: patient classification at first sample

value: Negative

value: No


title: plasma, subject 558be967T8

tag: covid-19 status

value: Positive


title: Microglia_coculture_aSyn [DE98NGSUKBR117816]

tag: cell type


title: PTPN2 -/- Rep 1 not treated

description:
No treatment
KO_1_NonTreatment

tag: genotype

value: PTPN2 -/-

value: Mixed strain background of C57BL/6J

value: 16 weeks

value: No treatment


title: D341, rep 2

description: small RNA

tag: tissue

tag: cell line


title: Microglia_single_wo [DE22NGSUKBR117826]

tag: strain


title: plasma, subject 558be967T12

value: Yes

tag: instrument model


title: CHLA01, rep 2

description: small RNA


title: D341, rep 1

description: small RNA


title: plasma, subject 534ef1bfT4


title: 2510 [Sample_8]

first: Raymond

last: Comenzo

address: 800 Washington Street

institute: Tufts Medical Center

data_processing:
The raw reads were mapped to human refrence genome using HISAT (v2.1.0), resulting in alignment file in BAM format.
A count table is generated using the BAM files as input, and a GTF annotation files from the reference genome.
The raw count table is used as input for differential expression analysis using DESeq2
Supplementary files format and content: tab delimited file of raw read count tables from featureCounts
Supplementary files format and content: tab delimited files of differential expression analysis from DESeq2 analysis

source_name: Bone Marrow

extract_protocol:
The bone marrow cell was sorted and then lysted in RLT Plus buffer.  The RNA is isolated on a Qiagen QIASymphony with QIASymphony RNA Kit, following the manufacturer instruction.
The RNA-Seq libraries were preparing using Illumina stranded mRNA sample preparation kit, following the manufacturer instruction.

value: Bone Marrow

value: Plasma Cell

tag: disease

value: AL Amyloidosis

tag: disease state

value: intersitial amyloid in bone marrow


title: CHLA01-R, rep 1

description: small RNA

value: Human medulloblastoma


title: Microglia_single_wo [DE27NGSUKBR117833]

value: primary Microglia

tag: passages


title: Microglia_coculture_wo [DE33NGSUKBR117822]

tag: treatment group


title: Microglia_single_wo [DE12NGSUKBR117812]


title: Patient 3 followup

description: 10x Genomics 5'

value: Peripheral blood mononuclear cells

tag: time point

value: followup

value: melanoma


title: 2511 [Sample_7]

tag: Sex

value: Male


title: plasma, subject 5386f49eT1

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

value: Female

tag: age

value: Somascan discovery platform v4


title: Microglia_coculture_aSyn [DE11NGSUKBR117830]


title: 2442 [Sample_6]


title: Patient 2 followup

description: 10x Genomics 5'


title: plasma, subject 52c9ea6bT1

tag: days since first sample

tag: patient classification at first sample

value: Positive


title: Patient 2 Baseline

description: 10x Genomics 5'

tag: subject

value: Patient 2


title: 2803 [Sample_5]

tag: cell type

value: vascular amyloid in bone marrow