title: patient vtr22 on d56 treated with 20bcg, vaccination via po administration

description:
GCAGACT_vtr22_d56_20bcg_po
vtr22_d56_20bcg_po

tag: tissue

value: patient vtr22

value: Cytoplasmic RNA

value: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio


title: 1231A3-COL10A1KO-#20-day42-Ex2

status: Public on Dec 01 2023

type: SRA

city: Sakyoku, Kyoto

first: takeshi

last: kamakura

state: Kyoto

address: Shogoin Kawaharacho 53

country: Japan

institute: Kyoto University

library_source: transcriptomic

data_processing:
long-rna-seq-pipeline v2.3.4 (ENCODE) with R v4.2.1 (The R Foundation)
the sequenced reads were mapped to the human reference genome GRCh38 v105 using STAR 2.5.1b with GENCODE v39 gene annotations
the expected gene counts and normalized gene expression values (TPM) were obtained using RSEM 1.2.23.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include count values for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: hiPSCs were maintained on iMatrix511 silk coated dish in AK02N medium with P/S

extract_protocol:
RNA was isolatd using RNeasy micro kit (Qiagen). 100ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Gold following manufacturer's protocols.

treatment_protocol:
Sclerotome cells were induced by bFGF, CHIR99021, Activin-A, SB431542, LDN193189, PD173074, XAV939, SAG in CDMi medium
Chondrogenic differentiation was induced by PDGF-BB, Dex, TGFβ3, BMP4, T3, β-GP in chondrogenic medium

tag: cell line

tag: cell type

value: hiPSC

tag: genotype

tag: treatment

value: chondrogenic differentiation

tag: time

value: day 42


title: Pancreatic Tumor Tissue, IPI-926, 2 days, KA003

city: New York City

first: Lukas

last: Vlahos

state: New York

address: 1130 St Nicholas Ave

department: Systems Biology

country: USA

institute: Columbia University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: Pancreatic Tumor Tissue

growth_protocol: Tumor tissue was collected following humane euthanasia and trimmed of healthy pancreas tissue in a sterile petri dish. The tumor pieces were dissociated using a modified protocol based on Miltenyi (mouse) Tumor Dissociation Kit (Miltenyi Biotec, 130-096-730)

extract_protocol:
Tumor tissue was placed in a digestion buffer containing trypsin, DNase, and an enzymatic cocktail (Supplementary Table 7) and digested at 37°C for 42 minutes (37C_m_TDK_2 program) on a gentleMACS Octo Dissociator (Miltenyi Biotec, 130-096-427). Cell suspensions were then filtered through a 40 μm cell strainer (Corning, 431750) and red blood cells were removed by incubation with red cell lysis buffer (Millipore Sigma, 11814389001), before a final resuspension in 100 μL PBS + 0.01% BSA.
Single Cell 3' v3, 10x Genomics

treatment_protocol: Treatment with the vehicle hydroxypropyl-beta-cyclodextrin (HPBCD, Acros Organics; 5% w/w in water for injection (WFI)), or IPI-926 (kindly provided by PellePharm; 5 mg/ml) was performed daily via oral gavage at 40 mg/kg. Tumor tissue was collected 2 hours after final dose.

value: Pancreatic Tumor Tissue

value: IPI-926, 2 days


title: plasma, subject 3380e771T4

type: protein

city: New York

first: Pushkala

last: Jayaraman

address: 1 Gustave Levy Pl

department: Charles Bronfman Institute of Personalized Medicine

institute: Icahn School of Medicine at Mount Sinai

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

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

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

molecule: protein

source_name: serum

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

tag: subject id

tag: blood sample id

tag: Sex

value: Male

tag: age

tag: days since first sample

tag: patient classification at first sample

tag: covid-19 status

value: Positive

value: Yes

tag: instrument model

value: Somascan discovery platform v4


title: patient vtr165 on d56 treated with 20bcg, vaccination via po administration

city: Cleveland

first: Richard

last: Silver

state: OH

address: 10900 Euclid Ave

department: Division of Pulmonary, Critical Care and Sleep Medicine

institute: Case Western Reserve University and the Louis Stokes Cleveland VA Medical Center

description:
CACTGTG_vtr165_d56_20bcg_po
vtr165_d56_20bcg_po

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4.b
Gene counts quantitated with Subread:featureCount 1.45 with CPM transformation added with custom Rscripting.
Assembly: Ensembl GRCh38.76
Supplementary files format and content: Gene counts-per-million in tab-delimitted text format

source_name: Peripheral Blood

growth_protocol: Blood was drawn into CPT tubes and PBMC isolated, aliquoted and frozen.  Following thawing, CD4+ T cells were isolated using Miltenyi positive selection kits. Autologous monocyte-derived dendritic cells (MDDC) were prepared as described.

extract_protocol:
After overnight treatment with BCG/media, supernatants were harvested, frozen and stored for lysis and RNA extraction.
RiboZero v1

treatment_protocol: Autologuous CD4+ T cells cultured overnight with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio either in the presence of Danish BCG (Statens Serum Institut, Copenhagen, MOI 20:1), or medium alone.

value: Peripheral Blood

value: patient vtr165

tag: treatment/time point

tag: molecule


title: RNASeq_SRSF2_rep3

city: San Antonio

first: Pinpin

last: Sui

state: TX

address: 8403 Floyd Curl Dr., STRF

department: Molecular Medicine

institute: UT health San Antonio

data_processing:
The fastq files were quality controlled by fastqc and trimmed by Trimmomatic(v0.38)
Clean reads were aligned to the reference genome using STAR(v 2.7.0e)
The raw read counts of each gene were calculated using HTSeq(v 0.11.2)
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Bone marrow

growth_protocol: The BM cells were harvested from the mice directly

extract_protocol:
Total RNA from individual mice was isolated with RNeasy Plus Mini Kit (QIAGEN)
The RNA libraries were prepared with the NEB Ultra RNA kit and followed by paired-end sequencing with a read length of 100 bp

treatment_protocol: The Lineage-cKit+Sca-1+ cells were purified from mouse bone marrow cells using beads sorting

value: Bone marrow

tag: strain

value: Lin-cKit+Sca-1+ bone marrow cells


title: 1231A3-COL10A1KO-#20-day42-Ex1


title: patient vtr32 on d56 treated with 20bcg, vaccination via po administration

description:
TAGCTCG_vtr32_d56_20bcg_po
vtr32_d56_20bcg_po

tag: tissue

value: patient vtr32


title: patient vtr15 on d56 treated with 20bcg, vaccination via po administration

description:
GACCGAA_vtr15_d56_20bcg_po
vtr15_d56_20bcg_po

value: patient vtr15


title: patient vtr26 on d56 treated with 20bcg, vaccination via po administration

description:
TGAGGTT_vtr26_d56_20bcg_po
vtr26_d56_20bcg_po

value: patient vtr26

value: Cytoplasmic RNA


title: RNASeq_SRSF2_rep2


title: patient vtr136 on d56 treated with 20bcg, vaccination via po administration

description:
TTTAACT_vtr136_d56_20bcg_po
vtr136_d56_20bcg_po

value: patient vtr136

value: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio


title: plasma, subject 3380e771T1

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

value: No


title: RNASeq_SRSF2_rep1


title: BT549-SNHG15 (Pull down)

city: Shantou

first: Zhou

last: Yanchun

state: Guangdong

address: Xinling Road

department: Pathophysiology

country: China

institute: Shantou University Medical College

description: miRNA profiling by RNA sequencing

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using Fastx.
Clean reads were compared with GRCh38.The analysis was performed by the Shanghai Biotechnology Corporation.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited files include TPM values  for each Sample

growth_protocol: BT549-SNHG15-MS2  Cells were cultured in  DMEM supplemented with 10% fetal bovine serum, 100U/ml penicillin,  and 100 µg/ml streptomycin at 37 °C in a humid environment with 5 % CO2

extract_protocol:
the co-precipitated RNAs were extracted using mirVana™ miRNA Isolation Kit following the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using QIAseq miRNA Library Kit.

treatment_protocol: Cell lysates were prepared and then incubated with Amylose resin coated with MBP-MCP (MS2 coat protein) or Amylose resin at 4°C for 5 h in the presence of RNasin (200 U/mL) and protease inhibitors. After incubation, the supernatant was removed by a short centrifugation and the beads were washed three times in ice-cold lysis buffer.

tag: cell line

value: breast cancer cells

value: SNHG15-MS2 overexpression

value: Amylose resin- MBP-MCP


title: 1231A3-COL10A1KO-#38-day42-Ex2

tag: cell type

value: hiPSC

value: chondrogenic differentiation

value: day 42


title: plasma, subject 334d7085T1

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

value: Male

value: Positive

value: Yes

value: Somascan discovery platform v4


title: patient vtr159 on d56 treated with 20bcg, vaccination via po administration

description:
CATCGCG_vtr159_d56_20bcg_po
vtr159_d56_20bcg_po

value: Peripheral Blood

value: patient vtr159


title: RNASeq_ASXL1_rep4

value: Bone marrow

value: Lin-cKit+Sca-1+ bone marrow cells

tag: genotype


title: 1231A3-COL10A1KO-#38-day42-Ex1

tag: treatment


title: 1231A3-COL10A1KO-#38-day42-Ex3

tag: time


title: RNASeq_ASXL1_rep3


title: plasma, subject 32cc1628T4

tag: subject id

value: Negative


title: plasma, subject 32cc1628T8

tag: blood sample id


title: RNASeq_SRSF2_rep4


title: patient vtr110 on d56 treated with 20bcg, vaccination via po administration

description:
TTCGCTG_vtr110_d56_20bcg_po
vtr110_d56_20bcg_po

value: patient vtr110

value: Cytoplasmic RNA

value: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio


title: 1231A3-COL10A1KO-#10-day42-Ex3


title: RNASeq_ASXL1_rep2


title: plasma, subject 32cc1628T12

tag: Sex

value: No


title: patient vtr121 on d56 treated with 20bcg, vaccination via po administration

description:
AAACCTT_vtr121_d56_20bcg_po
vtr121_d56_20bcg_po

value: patient vtr121


title: RNASeq_ASXL1_rep1


title: plasma, subject 32cc1628T1

tag: age


title: plasma, subject 31e42f3bT1

tag: days since first sample


title: 1231A3-COL10A1KO-#04-day42-Ex3

value: hiPSC


title: 1231A3-COL10A1KO-#10-day42-Ex1

value: chondrogenic differentiation


title: RNASeq_WT_rep4

value: wild type


title: 1231A3-COL10A1KO-#04-day42-Ex2

value: day 42


title: plasma, subject 318dda84T8

value: Male

tag: patient classification at first sample

value: Positive


title: RNASeq_WT_rep3


title: RNASeq_WT_rep2


title: plasma, subject 318dda84T4

tag: covid-19 status

value: Yes

value: Somascan discovery platform v4


title: 1231A3-COL10A1KO-#04-day42-Ex1


title: patient vtr144 on d56 treated with 0bcg, vaccination via po administration

description:
TTGAGTG_vtr144_d56_0bcg_po
vtr144_d56_0bcg_po

value: Peripheral Blood

value: patient vtr144


title: patient vtr56 on d56 treated with 0bcg, vaccination via po administration

description:
GTGTAGT_vtr56_d56_0bcg_po
vtr56_d56_0bcg_po

value: patient vtr56


title: patient vtr33 on d56 treated with 20bcg, vaccination via po administration

description:
TATCTTA_vtr33_d56_20bcg_po
vtr33_d56_20bcg_po

value: patient vtr33


title: patient vtr20 on d56 treated with 20bcg, vaccination via po administration

description:
GTTCTCA_vtr20_d56_20bcg_po
vtr20_d56_20bcg_po

value: patient vtr20


title: plasma, subject 310c5346T1

value: Female

tag: instrument model


title: RNASeq_WT_rep1

value: Bone marrow

value: Lin-cKit+Sca-1+ bone marrow cells


title: 1231A3-day42-Ex2


title: 1231A3-day42-Ex3


title: plasma, subject 318dda84T1

value: No


title: 5xFAD, habenula, 6m

city: Daegu

first: Jaemyung

last: Jang

address: 61, Cheomdan-ro, Dong-gu

country: South Korea

institute: Korea Brain Research Institute

description: inDropTM

data_processing:
The previously published pipeline in Python available at [https://github.com/indrops/indrops] was used to read raw sequencing data under modified settings (Bowtie 1.2.3, m = 200, n = 1, l = 15, e = 1000) and align them to the Ensembl mouse reference genome (GRCm39 release 102) to obtain a cell-gene expression matrix.
Seurat package (version 4.3) (Butler et al., 2018;Stuart et al., 2019;Hao et al., 2021) in R environment (version 4.3.0) were used to filter cells, reduce dimensionality, cluster with Louvain, and project cells with UMAP. We removed cells with low quality (less than 1,000 reads and 500 UMI-filtered mapped read) and doublets using ScDblFinder package (Germain et al., 2021). The G2M phase score, S-phase score, UMI count, and mitochondrial gene proportion were regressed out using the SCTransform wrapper. cells were annotated using the top most significant upregulated cluster-specific genes. Microglia was isolated preferentially expressed markers of microglia or macrophages. The subset of microglia was processed though dimensionality reduction, Louvain clustering, and projection into UMAP.
Assembly: GRCm38 (release 102)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: habenula

extract_protocol:
Mice were euthanized by carbon dioxide gas overdose, and the brains were rapidly dissected out. The hippocampus of 3-, 9-, and 12-month-old mice, the septum of 6-month-old mice, and the Hb of 3-, 9-, and 12-month-old were collected from 5xFAD mice and WT mice. The samples were cut into small pieces, placed in digestion media (Neurobasal media containing 1 mg/mL Collagenase type 1, 2, 4 (Worthington Biochemical Corp., United States) or papain (Worthington Biochemical Corp., United States), and 20 U/mL of DNaseⅠ (Sigma)), and incubated in a shaking incubator at 37 °C for 45 min. The digested tissues were mechanically dissociated and filtered through a 40 µm cell strainer. The single-cell suspension was centrifuged at 500 g for 15 min at 4°C and the resulting pellet was suspended in ice cold neurobasal media containing B27. This neurobasal media wash was repeated twice with two different spins at 100 g and 200 g centrifugation to remove dead cells and cellular debris. The single-cell suspension was finally suspended in an ice cold Hanks’ balanced salt solution with 0.04 % bovine serum albumin (A3294, Sigma-Aldrich, United States) at approximately 2 ⅹ 105 cells/mL cell population.
The single cells were profiled using inDropTM barcoded beads in a home-made microfluidic device connected to the Drop-seq apparatus in the Korea Brain Research Institute. Libraries from isolated single cells were generated according to the inDropTM Protocol with the following modifications (Zilionis et al., 2017). Amplified cDNAs were not fragmented, and cDNA cleanup and size selection were performed using SPRIselect beads (B23317, Beckman Coulter, United States). Amplified cDNAs and final libraries were assessed on an Agilent BioAnalyzer using the High Sensitivity DNA Kit (Agilent Technologies, United States). The libraries were pooled and sequenced on a NovaSeq 6000 system / a NextSeq500 system at two sequencer companies (Macrogen, Korea / LAS Science, Korea).

value: habenula

value: 06 months-old


title: patient vtr15 on d56 treated with 0bcg, vaccination via po administration

description:
AATGACT_vtr15_d56_0bcg_po
vtr15_d56_0bcg_po

value: patient vtr15

tag: treatment/time point

value: Cytoplasmic RNA

value: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio


title: patient vtr32 on d56 treated with 0bcg, vaccination via po administration

description:
CGGTTTG_vtr32_d56_0bcg_po
vtr32_d56_0bcg_po

value: patient vtr32

tag: molecule


title: 1231A3-COL10A1KO-#10-day42-Ex2

value: hiPSC

value: chondrogenic differentiation

value: day 42


title: patient vtr61 on d56 treated with 0bcg, vaccination via po administration

description:
TTACCGT_vtr61_d56_0bcg_po
vtr61_d56_0bcg_po

value: Peripheral Blood

value: patient vtr61


title: mESC_Tdg_KO05_Rep4

city: Basel

first: Faiza

last: Noreen

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
RNA-seq data was quantified with Salmon v0.8.1 on the GRCm39 v108 transcriptome.
Transcripts with less counts than 20, after library depth normalization, were removed
Counts were further corrected by surrogate variable analysis with 3 surrogate variables using Setools 1.9.3
Assembly: GRCm39
Supplementary files format and content: quant.sf; Name, Length, EffectiveLength,TPM,NumReads
Supplementary files format and content: SE.rds.zip; count-matrix

growth_protocol: mESCs were grown on gelatin plates in serum free medium (2i and LIF)

extract_protocol:
RNA was harvested using RNeasy Plus Kit (Qiagen)
Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

value: Embryonic Stem Cells

value: male

value: Tdg-/-


title: 1231A3-day42-Ex1


title: plasma, subject 30f3e5beT8

value: Male

value: Positive

value: Yes

value: Somascan discovery platform v4


title: patient vtr98 on d56 treated with 0bcg, vaccination via po administration

description:
ATACCCG_vtr98_d56_0bcg_po
vtr98_d56_0bcg_po

value: patient vtr98


title: plasma, subject 30f3e5beT4

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

value: No


title: 414C2-COL10A1KO-#25-day42-Ex3


title: mESC_Tdg_KO04_Rep3


title: patient vtr22 on d56 treated with 0bcg, vaccination via po administration

description:
CCCGCTA_vtr22_d56_0bcg_po
vtr22_d56_0bcg_po

value: patient vtr22

value: Cytoplasmic RNA


title: 414C2-COL10A1KO-#25-day42-Ex2


title: plasma, subject 30f3e5beT12


title: plasma, subject 30f3e5beT1


title: patient vtr165 on d56 treated with 0bcg, vaccination via po administration

description:
CAGTTGT_vtr165_d56_0bcg_po
vtr165_d56_0bcg_po

value: patient vtr165

value: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio


title: 414C2-COL10A1KO-#25-day42-Ex1

value: hiPSC

value: chondrogenic differentiation


title: patient vtr26 on d56 treated with 0bcg, vaccination via po administration

description:
CTGGTGG_vtr26_d56_0bcg_po
vtr26_d56_0bcg_po

value: Peripheral Blood

value: patient vtr26


title: plasma, subject 30efa05eT8


title: 414C2-COL10A1KO-#19-day42-Ex2

value: day 42


title: mESC_Tdg_HET13_Rep3

value: Embryonic Stem Cells

value: male

value: Tdg+/-


title: 414C2-COL10A1KO-#19-day42-Ex3


title: mESC_Tdg_HET12_Rep2


title: 414C2-COL10A1KO-#19-day42-Ex1


title: patient vtr136 on d56 treated with 0bcg, vaccination via po administration

description:
CATTTAG_vtr136_d56_0bcg_po
vtr136_d56_0bcg_po

value: patient vtr136


title: patient vtr110 on d56 treated with 0bcg, vaccination via po administration

description:
CTCACCC_vtr110_d56_0bcg_po
vtr110_d56_0bcg_po

value: patient vtr110


title: mESC_Tdg_HET11_Rep1


title: patient vtr159 on d56 treated with 0bcg, vaccination via po administration

description:
GGTCCTC_vtr159_d56_0bcg_po
vtr159_d56_0bcg_po

value: patient vtr159


title: plasma, subject 30efa05eT1

value: Male

value: Positive

value: Yes

value: Somascan discovery platform v4


title: plasma, subject 30efa05eT4

value: No


title: patient vtr20 on d56 treated with 0bcg, vaccination via po administration

description:
GGCAAGA_vtr20_d56_0bcg_po
vtr20_d56_0bcg_po

value: patient vtr20

value: Cytoplasmic RNA

value: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio


title: mESC_Tdg_WT23_Rep3

value: Tdg+/+


title: plasma, subject 302cac50T1

value: Female


title: mESC_Tdg_KO03_Rep2

value: Tdg-/-


title: 414C2-COL10A1KO-#09-day42-Ex2

value: hiPSC

value: chondrogenic differentiation

value: day 42


title: patient vtr121 on d56 treated with 0bcg, vaccination via po administration

description:
TCCCAGC_vtr121_d56_0bcg_po
vtr121_d56_0bcg_po

value: Peripheral Blood

value: patient vtr121


title: 414C2-COL10A1KO-#09-day42-Ex1


title: mESC_Tdg_WT21_Rep1

value: Embryonic Stem Cells

value: male


title: patient vtr33 on d56 treated with 0bcg, vaccination via po administration

description:
TCAACTG_vtr33_d56_0bcg_po
vtr33_d56_0bcg_po

value: patient vtr33


title: mESC_Tdg_KO02_Rep1


title: plasma, subject 2e801d88T4

value: Male

value: Positive

value: Yes


title: male, WT, no-running control, tricpes [6902]

city: Washington

first: Adam

last: Bittel

state: DC

address: 111 Michigan Ave, NW

institute: CHildren's National Hospital

data_processing:
Reads were processed using cutadapt v1.16, analyzed using FastQC v0.11.7, and aligned to the spike-in complemented Ensembl release 90 of the Mus musculus assembly GRCh38 from the Genome Reference Consortium using the splice-aware aligner STAR version 2.5.3a.
Alignments were quantified based on the annotations of Ensembl GRCm38.90 and the spike-in specific annotations of Lexogen with the featureCounts software program version 1.6.2 of the subread analysis package
Assembly: Ensembl release 90 of the Mus musculus assembly GRCh38 from the Genome Reference Consortium
Supplementary files format and content: Tab-delimited text files including non-normalzied read counts for each sample, counts of all samples normalized for sequencing depth, and outputs from DEseq2

source_name: Triceps

extract_protocol:
Triceps were homogenized under liquid nitrogen by mortar and pestle. The fine powder was transferred to a 1.5 mL Eppendorf tube with a spatula and mixed with 1 ml trizol reagent for RNA extraction. RNA was separated with chloroform, precipitated with isopropanol, and washed with 75% ethanol. Genomic DNA was removed and RNA was purified using the Qiagen RNeasy Plus Mini Kit (Qiagen, Hilden, Germany). Purified RNA was submitted to Lexogen Gmbh (Vienna, Austria) for 3’ mRNA sequencing.
Sequencing-ready libraries were produced using a QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (015UG009V0252) using 50 ng RNA per sample.
Sequencing was performed on an Illumina NextSeq 500 sequencer with a v2 SR75 High Output kit at Lexogen GmbH.

treatment_protocol: Mice underwent 6 weeks of voluntary hweel running, or a n wheel running control condition

value: Triceps

tag: gender

value: WT

value: no-wheel-running control


title: patient vtr160 on d56 treated with 20bcg, vaccination via id administration

description:
CACATAT_vtr160_d56_20bcg_id
vtr160_d56_20bcg_id

tag: tissue

value: patient vtr160

value: Cytoplasmic RNA

value: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio


title: 414C2-COL10A1KO-#03-day42-Ex3

tag: cell line

value: hiPSC


title: 414C2-COL10A1KO-#09-day42-Ex3

tag: cell type

value: chondrogenic differentiation


title: patient vtr162 on d56 treated with 20bcg, vaccination via id administration

description:
ATCGTCA_vtr162_d56_20bcg_id
vtr162_d56_20bcg_id

value: patient vtr162


title: 414C2-COL10A1KO-#03-day42-Ex2

tag: genotype

value: day 42


title: plasma, subject 2e7e0b48T1

value: Female

value: Somascan discovery platform v4


title: male, FLExDUX4, no-running control, tricpes [6805]

value: male

tag: treatment


title: male, WT, no-running control, tricpes [102]


title: male, WT, no-running control, tricpes [6795]


title: patient vtr106 on d56 treated with 20bcg, vaccination via id administration

description:
ATCCAAA_vtr106_d56_20bcg_id
vtr106_d56_20bcg_id

value: Peripheral Blood

value: patient vtr106


title: 414C2-COL10A1KO-#03-day42-Ex1

tag: time


title: plasma, subject 2db62a52T4

tag: subject id

value: Male

value: Positive


title: 414C2-day42-Ex3


title: mESC_Tdg_WT22_Rep2

value: Embryonic Stem Cells

value: Tdg+/+


title: plasma, subject 2db62a52T1

tag: blood sample id

value: No

value: Yes


title: male, FLExDUX4, no-running control, tricpes [6802]

value: Triceps

value: no-wheel-running control


title: plasma, subject 2e801d88T8

tag: Sex


title: patient vtr17 on d56 treated with 20bcg, vaccination via id administration

description:
GGACATT_vtr17_d56_20bcg_id
vtr17_d56_20bcg_id

value: patient vtr17

value: Cytoplasmic RNA

value: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio


title: male, FLExDUX4, no-running control, tricpes [6776]


title: 414C2-day42-Ex2

value: hiPSC

value: chondrogenic differentiation

value: day 42


title: male, WT, 6 weeks wheel running, triceps [6901]

value: male

value: WT

value: 6 weeks wheel running


title: plasma, subject 2d3ac920T1

value: Male

tag: age

value: Somascan discovery platform v4


title: plasma, subject 2bdfdc7cT1

value: Female

tag: days since first sample

value: Positive


title: THP-1-4L

city: Shanghai

first: Yiwen

last: Wang

address: 2005, Songhu Road, Yangpu District

institute: Fudan University

data_processing:
The Cell Ranger software pipeline (v3.1.0) provided by 10x Genomics
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
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.

value: foamy macrophage

value: oxLDL incubation


title: patient vtr72 on d56 treated with 20bcg, vaccination via id administration

description:
CTTGCTC_vtr72_d56_20bcg_id
vtr72_d56_20bcg_id

value: Peripheral Blood

value: patient vtr72


title: plasma, subject 2e801d88T1

tag: patient classification at first sample

value: No

value: Yes


title: male, WT, 6 weeks wheel running, triceps [6862]

value: Triceps


title: patient vtr55 on d56 treated with 20bcg, vaccination via id administration

description:
GGTTTCG_vtr55_d56_20bcg_id
vtr55_d56_20bcg_id

value: patient vtr55

value: Cytoplasmic RNA

value: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio


title: plasma, subject 2ba3e340T1

tag: covid-19 status


title: plasma, subject 2b5aef5bT8

tag: instrument model


title: humanizedNeutrophils_WT_4

city: London

first: Dominique

last: Bonnet

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Obtained FASTQ files were uploaded to the R environment where adapter and quality trimming was performed, and a quality control report was generated. Alignment was performed using the Salmon strategy under the R environment where FASTQ files were aligned to the grch38 human genome under the Salmon reference format.
Obtained raw counts were then uploaded and analyzed using the package Deseq2 on R.
Assembly: grch38 human
Supplementary files format and content: Normalized counts

source_name: Human Neutrophils

extract_protocol:
RNA was isolated using RNAeasy microkit (Qiagen)
Libraries were prepared using KAPA Stranded with RiboErase RNA-seq kit (according to the manufacturer’s instructions). Briefly, 17–25 ng of starting RNA were subjected first to cytoplasmic and mitochondrial ribosomal RNA (rRNA) depletion by hybridization of complementary DNA oligonucleotides, followed by treatment with RNase H and DNase to remove rRNA duplexed to DNA and original DNA oligonucleotides. Samples depleted of rRNA were then subjected to 94 °C for 6 min in the 2×Fragment, Prime, and Elute Buffer in order to obtain 200–300 bp fragments. cDNA synthesis was run in two steps following the manufacturer’s instructions. The ligation step consisted of a final volume of 110 μl of the adaptor ligation reaction mixture with 60 μl of input cDNA, 5μl of diluted adaptor, and 45 μl of ligation mix (50 μl of ligation buffer + 10 μl of DNA ligase). The Kapa Dual- Indexed Adaptors stock concentration was diluted to 1.5mM to get the best adaptor concentration for library construction. The ligation cycle was run according to the manufacturer’s instructions. To remove short fragments such as adaptor dimers, 2X AMPure XP bead clean-ups were done (0.63 SPRI and 0.7 SPRI).

value: Human Neutrophils


title: male, WT, 6 weeks wheel running, triceps [64]

value: male

value: WT


title: patient vtr150 on d56 treated with 20bcg, vaccination via id administration

description:
CAGAGTC_vtr150_d56_20bcg_id
vtr150_d56_20bcg_id

value: patient vtr150

tag: treatment/time point


title: patient vtr68 on d56 treated with 20bcg, vaccination via id administration

description:
TTTTCGG_vtr68_d56_20bcg_id
vtr68_d56_20bcg_id

value: patient vtr68

tag: molecule


title: plasma, subject 2b5aef5bT4

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

value: Male

value: Somascan discovery platform v4


title: humanizedNeutrophils_TET2_3


title: humanizedNeutrophils_WT_3


title: patient vtr3 on d56 treated with 20bcg, vaccination via id administration

description:
ACAGATA_vtr3_d56_20bcg_id
vtr3_d56_20bcg_id

value: patient vtr3


title: plasma, subject 2b5aef5bT13

value: Positive


title: male, FLExDUX4, 6 weeks wheel running, triceps [6796]

tag: gender

value: 6 weeks wheel running


title: plasma, subject 2b5aef5bT12


title: 414C2-day42-Ex1

value: hiPSC

value: chondrogenic differentiation

value: day 42


title: male, FLExDUX4, 6 weeks wheel running, triceps [6787]

tag: tissue

value: Triceps


title: humanizedNeutrophils_TET2_2


title: patient vtr140 on d56 treated with 20bcg, vaccination via id administration

description:
CGAAAGT_vtr140_d56_20bcg_id
vtr140_d56_20bcg_id

value: Peripheral Blood

value: patient vtr140


title: male, FLExDUX4, 6 weeks wheel running, triceps [6784]


title: plasma, subject 2b5aef5bT1

value: No

value: Yes


title: patient vtr28 on d56 treated with 20bcg, vaccination via id administration

description:
TACAGAC_vtr28_d56_20bcg_id
vtr28_d56_20bcg_id

value: patient vtr28

value: Cytoplasmic RNA

value: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio


title: humanizedNeutrophils_WT_2

value: Human Neutrophils

value: WT


title: male, FLExDUX4, 6 weeks wheel running, triceps [6773]

value: male


title: humanizedNeutrophils_TET2_4


title: patient vtr109 on d56 treated with 20bcg, vaccination via id administration

description:
CTCCCGA_vtr109_d56_20bcg_id
vtr109_d56_20bcg_id

value: patient vtr109


title: patient vtr23 on d56 treated with 20bcg, vaccination via id administration

description:
GTACGGC_vtr23_d56_20bcg_id
vtr23_d56_20bcg_id

value: patient vtr23


title: plasma, subject 2b440626T4

value: Male

value: Positive

value: Somascan discovery platform v4


title: humanizedNeutrophils_TET2_1


title: male, WT, 6 weeks wheel running, triceps [6775]

value: 6 weeks wheel running


title: patient vtr43 on d56 treated with 20bcg, vaccination via id administration

description:
GCCTCCC_vtr43_d56_20bcg_id
vtr43_d56_20bcg_id

value: patient vtr43


title: humanizedNeutrophils_WT_1


title: FHBT9_B10_URO

city: Seattle

first: John

middle: K.

last: Lee

state: Washington

address: 1100 Fairview Ave N Rm E2-430

institute: Fred Hutch Cancer Research Ctr

library_source: genomic

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

molecule: genomic DNA

source_name: primary mouse bladder urothelial cells

extract_protocol:
DNA was extracted using a GeneRead DNA FFPE Kit (Qiagen)
Two-step PCR for amplification and sequencing library adaptor ligation was performed using of 2x KAPA HiFi HotStart ReadyMix

tag: cell line

value: primary mouse bladder urothelial cells

value: bladder tumor cells

tag: histology

value: Urothelial


title: plasma, subject 2b440626T1

value: No

value: Yes


title: plasma, subject 2a548e63T1


title: patient vtr160 on d56 treated with 0bcg, vaccination via id administration

description:
TAAACGA_vtr160_d56_0bcg_id
vtr160_d56_0bcg_id

value: Peripheral Blood

value: patient vtr160

value: Cytoplasmic RNA

tag: cell type


title: FHBT8_B8_PAP

value: Papillary Squamous


title: plasma, subject 2a142bf4T12

value: Female


title: ATACSeq_DIPG4_with_AZD_Radiation 2

city: Aurora

first: Nathan

middle: A

last: Dahl

state: CO

department: Pediatrics

institute: University of Colorado School of Medicine

data_processing:
The quality of fastq files was accessed using FastQC
The Illumina adapters and low quality reads were filtered using BBDuk with the parameters for paired-end reads
The ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 (v. 2.3.2).
Samtools (v. 1.9) was used to convert the sam files into bam files, to filter out unmapped reads and to sort the bam files.
The total number of reads used for peak calling was normalized using samtools view -hs (random extraction of a specified percentage of reads).
Samtools sort was used to sort the bam files after read extraction.
Bam files were indexed using samtools index.
Bedtools genomecov was used to create bedgraph files from the bam files.
Igvtools toTDF was used to create tdf files from the bedgraph files.
Peaks were called using MACS2 (v. 2.1.1.20160309) with default parameters using Python (v. 2.7.14).
Peak locations were further annotated and analyzed using the clusterProfiler, ChIPseeker and ngs.plot tools.
Assembly: hg38
Supplementary files format and content: Bigwig files were created using deepTools bamCoverage (v. 3.5.0)

source_name: Diffuse intrinsic pontine glioma

growth_protocol: DIPG4 cell lines were cultured in 50% Neurobasal-A medium (Invitrogen), 50% DMEM/F12(Invitrogen) supplemented with, 1 mM sodium pyruvate (Gibco), 10mM HEPES Buffer Solution, 1mM MEM Non-Essencial Amino Acids, GlutaMAX-I Supplement. 1× penicillin/streptomycin solution, 1x B-27 Supplement Minus Vitamin A, H-EGF, H-FGF basic 154, H-PDGFAA, H-PGF -BBa and Heparin Solution 0.25%. Cells were cultured at 37 °C with 95% air and 5% CO2.

extract_protocol:
100,000 cells were spined down at 500 xg, 5min at 4oC, pellet was washed once with 500ul of cold 1x PBS, and spined down at 500 xg, 5min at 4oC. Pellet was resuspended in 450ul of cold hypotonic buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2) and immediately added 50ul of 1% IGEPAL CA-630 (0.1% final) and inverted to mix. Cells were incubated on ice for 15 min, spined down at 500 xg for 10 min at 4oC. Pellet was set on ice and the transposition reaction was performed following the ATAC-seq Kit instructions (Cell Biologics, Cat No. CB6936). Pellet cells were resuspended in 50ul of transposition reaction mix (25ul 2X Reaction Buffer, 2.5ul Transposome, 22.5ul Nuclease free water) and incubated at 37oC for 1 hour. DNA was purified using Qiagen MinElute kit (Qiagen, #28004) and eluted in 15ul of Elution Buffer, followed by the Library Generation to amplify transposed DNA fragments.
10ul of Transposed DNA, 10ul of Nuclease free water, 2.5ul of Ad1.noMX (Oligo 1), 2.5 ul Ad2._Barcode (Oligo 2) and 25ul of High Fidelity 2x PCR Master Mix and ran on a thermocycler using the following cycle: 98oC 30sec, (98oC 10sec, 63oC 30sec, 72oC 1min) x 10 times and hold at 4oC.  Followed by the Library Purification. For double-sided bead purification (to remove primer dimers and large >1,000 bp fragments), each PCR sample was transferred to a 1.5ml tube and 0.5X volume (25ul) of AMPure XP beads was added, mixed by pipetting 10 times and incubated at room temperature for 10min. Tubes were placed in a magnetic rack for 5min and the supernatant was transferred to a new tube. 1.3X of the original volume (65ul) of AMPure XP beads was added, mixed by pipetting 10x and incubated at room temperature for 10 min. Tubes were placed in a magnetic rack for 5min, supernatant was discarded, and beads were washed with 200ul 80% EtOH. EtOH was removed and tubes were left on magnetic rack with cap open for 10 min or until the pellet was totally dry. Beads were resuspended in 20ul of nuclease-free water and mixed thoroughly, tubes were placed in the magnetic rack for 5min and the supernatant was transferred to a new tube.

treatment_protocol: Cells were treated with DMSO or 40nM AZD, after 2hs cell were irradiated at 6Gy and collected after 4hs.

tag: treatment

value: AZD (40nM) and 6Gy radiation


title: ATACSeq_DIPG4_with_AZD_Radiation 1


title: patient vtr162 on d56 treated with 0bcg, vaccination via id administration

description:
TCATGTA_vtr162_d56_0bcg_id
vtr162_d56_0bcg_id

value: patient vtr162

value: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio


title: plasma, subject 2a142bf4T1

value: Positive


title: patient vtr106 on d56 treated with 0bcg, vaccination via id administration

description:
CGGGCTT_vtr106_d56_0bcg_id
vtr106_d56_0bcg_id

value: patient vtr106


title: FHBT6_B6

value: Squamous


title: ATACSeq_DIPG4_with_DSMO_Radiation 2

value: DMSO and 6Gy radiation


title: FHBT8b_B9_PAP_SQ

value: primary mouse bladder urothelial cells


title: plasma, subject 29703e49T1

value: Negative

value: Somascan discovery platform v4


title: ATACSeq_DIPG4_with_DMSO_Radiation 1


title: FHBT8a_B9_PAP

value: bladder tumor cells

value: Papillary


title: patient vtr17 on d56 treated with 0bcg, vaccination via id administration

description:
ATAGGCT_vtr17_d56_0bcg_id
vtr17_d56_0bcg_id

value: Peripheral Blood

value: patient vtr17


title: FHBT5_B5


title: patient vtr55 on d56 treated with 0bcg, vaccination via id administration

description:
CTTATCG_vtr55_d56_0bcg_id
vtr55_d56_0bcg_id

value: patient vtr55

value: Cytoplasmic RNA


title: ATACSeq_DIPG4_with_DMSO 2

value: DMSO


title: plasma, subject 293f835aT8

value: Male

value: No

value: Yes


title: FHBT4b_B3_SARCQ

value: Sarcomatoid


title: patient vtr72 on d56 treated with 0bcg, vaccination via id administration

description:
GATGTGA_vtr72_d56_0bcg_id
vtr72_d56_0bcg_id

value: patient vtr72

value: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio


title: FHBT4a_B3_URO


title: plasma, subject 293f835aT4

value: Positive


title: Input_DIPG4_with_AZD_Radiation_2

extract_protocol:
Cells were crosslinked with 1% formaldehyde added to the growth media for 10min, followed by quenching with 0.125M glycine for 5min. Cells were washed twice with cold PBS, collected in ice-cold PBS by scrapping, pelleted, and resuspended in cell lysis buffer (5mM PIPES, pH 8.0; 85mM KCl; 0.5% NP-40). Following incubation on ice for 10 min, a nuclear-enriched fraction was collected by centrifugation for 5min at 2500 xg at 4oC. Pellet was resuspended in ChIP lysis buffer (50mM Tris-HCl, pH 8.0; 10mM EDTA; 1%SDS) containing COmplete EDTA free protease inhibitors (Sigma) and quantified with BCA. 2ug/ul of lysates were sonicated with a Bioruptor Plus (Diagenode) for 20 cycles (30 seconds ON and 30 seconds OFF). The size of the sonicated DNA fragments was checked on an 1X TAE1 % agarose gel electrophoresis and ranged between 250 to 500 bp. After removing the debris via centrifugation, chromatin extracts were collected.   For immunoprecipitation, chromatin extracts were diluted with Chip Dilution Buffer (16.7mM Tris-HCl, pH8.1, 1.2Mm EDTA, 167mM NaCl, 0.01%SDS and 1.1% Triton x100) incubated with primary antibodies anti-K27Ac (#39133, Active Motif) overnight at 4ºC.  After incubation with the primary antibody, 20 uL of pre-washed magnetic beads (Magna ChIP Protein A+G Magnetic Beads, Millipore Sigma) were added to each sample for 2 hours at 4ºC. Using a magnetic rack, the immunoprecipitates were washed successively with 1 ml of low salt buffer (20 mM Tris-HCl [pH 8.0], 150 mM NaCl, 0.1% SDS, 1% triton X-100, 2 mM EDTA), high salt buffer (20 mM Tris-HCl [pH 8.0], 500 mM NaCl, 0.1% SDS, 1% triton X-100, 2 mM EDTA), LiCl washing buffer (10 mM Tris-HCl [pH 8.0], 250 mM LiCl, 1.0% NP40, 1.0% deoxycholate, 1 mM EDTA) and twice with TE buffer. The DNA-protein complexes were eluted with 300 µl of IP elution buffer (1% SDS, 0.1 M NaHCO3). The cross-links were reversed by adding NaCl (a final concentration 0.2 M) into the eluents and incubating them at 65 ºC overnight. The DNAs were recovered by proteinase K and RNase A digestion, followed by phenol/chloroform extraction and ethanol precipitation. Pellets were resuspended in 25ul of RNase and DNase free water and ChIP-DNA was quantified using the Qubit dsDNA High Sensitivity Assay kit (Thermo Fisher Scientific), followed by library preparation.
The NEBNext Ultra DNA Library Prep Kit for Illumina (NEB #E7645S) with Dual Index Primers (NEB #E7600) were used to library preparation for ChiPseq and Cut and Run samples sequencing.    NEBNext End Prep  1x TE was added to the DNA to get final volume of 50ul and mixed with 3ul of NEBNext Ultra II End Prep Enzyme Mix and 7ul of NEBNext Ultra II End Prep Reaction Buffer, placed in thermocycler with heated lid set to 75oC and run the program 30 minutes at 20oC, 60 minutes at 50oC and hold at 4oC.  Adaptor Ligation  The adaptor ligation reaction was performed with 60ul of Prep Reaction Mixture, 2.5ul of NEBNext Adaptor for Illumina diluted following the manufacture recommendations, 30ul of NEBNext Ultra Ligation Master Mix and 1ul of NEBNext Ligation Enhancer, incubated at 20oC for 15min with heated lid off. 3ul of USER Enzyme was added to the reaction and incubated at 37oC for 15min with heated led set to 47oC.  Cleanup of Adaptor-Ligated DNA without size selection  1.1x of AMPure XP Beads were added to the Adaptor Ligation reaction and samples were incubated for 5min at room temperature. Tubes were placed on a magnetic stand to separate beads from supernatant, after 5 min, supernatant was removed, and beads were washed 2 times with 200ul of 80% freshy prepared ethanol. Beads were air dried for up 5 min while tubes were on magnet with lid open. DNA was eluted from the beads by adding 17ul of 0.1XTE buffer.   PCR Enrichment of Adaptor-ligated DNA  To 15ul of the Adaptor Ligated DNA fragments was added 25ul of NEBNext Ultra Q5 Master Mix, 5ul of Index primer i7 and 5ul Universal PCR Primer i5, and PCR amplification was performed following the cycling conditions: 98oC for 45s, 98oC 15s and 60oC 10s for 16 cycles, 72oC for 1min and hold at 4oC. Followed by a Clean Up of the PCR reaction using AMPure XP Beads.   The DNA was quantified using Qubit and the quality and size of libraries were checked at the  Bioanalyzer and sent for sequencing at Novogene Corporation Inc.

value: AZD (40nM) and 6Gy radiation

tag: chip antibody


title: patient vtr109 on d56 treated with 0bcg, vaccination via id administration

description:
TGCCCAT_vtr109_d56_0bcg_id
vtr109_d56_0bcg_id

tag: subject id

value: patient vtr109


title: plasma, subject 293f835aT1

tag: blood sample id

value: Somascan discovery platform v4


title: plasma, subject 293f835aT12

tag: Sex


title: patient vtr68 on d56 treated with 0bcg, vaccination via id administration

description:
TGATTAC_vtr68_d56_0bcg_id
vtr68_d56_0bcg_id

value: patient vtr68


title: Input_DIPG4_with_AZD_Radiation_1


title: patient vtr150 on d56 treated with 0bcg, vaccination via id administration

description:
ACCATAC_vtr150_d56_0bcg_id
vtr150_d56_0bcg_id

value: patient vtr150


title: FHBT2_B1

value: primary mouse bladder urothelial cells

value: bladder tumor cells


title: plasma, subject 2899c4b8T1

tag: age

value: Negative


title: patient vtr3 on d56 treated with 0bcg, vaccination via id administration

description:
AACGGAG_vtr3_d56_0bcg_id
vtr3_d56_0bcg_id

value: Peripheral Blood

value: patient vtr3

value: Cytoplasmic RNA


title: H3K27Ac_histone H3_acetyl K27_DIPG4_with_AZD_Radiation 2

value: H3K27Ac_histone H3_acetyl K27; Abcam Cat. #ab4729


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

city: Seoul

first: Hyeshik

last: Chang

state: South Korea

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

department: School of Biological Sciences

institute: Seoul National University

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

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

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).

value: Lung

tag: strain

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

value: SARS-CoV-2 infection

tag: time

value: 7 days post-infection

tag: library type

value: Ribo-seq


title: H3K27Ac_histone H3_acetyl K27_DIPG4_with_AZD_Radiation 1

value: AZD (40nM) and 6Gy radiation


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

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


title: ATACSeq_DIPG4_with_DMSO 1

value: DMSO


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

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


title: plasma, subject 26ced899T1

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

value: Male

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: patient vtr140 on d56 treated with 0bcg, vaccination via id administration

description:
AGGACCT_vtr140_d56_0bcg_id
vtr140_d56_0bcg_id

tag: tissue

value: patient vtr140

tag: treatment/time point

tag: molecule

value: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio


title: patient vtr28 on d56 treated with 0bcg, vaccination via id administration

description:
TACATGG_vtr28_d56_0bcg_id
vtr28_d56_0bcg_id

value: Peripheral Blood

value: patient vtr28

tag: cell type


title: Input_DIPG4_with_DMSO_Radiation_1

tag: cell line

tag: treatment

value: DMSO and 6Gy radiation


title: plasma, subject 273dc7aeT1

tag: subject id

value: Female

value: Negative


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

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

value: Lung

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

value: SARS-CoV-2 infection


title: patient vtr23 on d56 treated with 0bcg, vaccination via id administration

description:
TTTTGTC_vtr23_d56_0bcg_id
vtr23_d56_0bcg_id

value: patient vtr23

value: Cytoplasmic RNA


title: plasma, subject 266e2348T8

tag: blood sample id


title: H3K27Ac_histone H3_acetyl K27_DIPG4_with_DSMO_Radiation 2

tag: chip antibody

value: H3K27Ac_histone H3_acetyl K27; Abcam Cat. #ab4729


title: FHBT3_B2

value: primary mouse bladder urothelial cells

value: bladder tumor cells

tag: histology

value: Urothelial


title: H3K27Ac_histone H3_acetyl K27_DIPG4_with_DMSO_Radiation 1


title: patient vtr43 on d56 treated with 0bcg, vaccination via id administration

description:
GTCGATA_vtr43_d56_0bcg_id
vtr43_d56_0bcg_id

value: patient vtr43


title: plasma, subject 266e2348T4

tag: Sex

tag: age

value: Positive

value: No

value: Yes

value: Somascan discovery platform v4


title: plasma, subject 266e2348T13


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

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

tag: strain

tag: time

value: 5 days post-infection

tag: library type

value: Ribo-seq


title: Input_DIPG4_with_DMSO

value: DMSO


title: patient vtr144 on d0 treated with 20bcg, vaccination via po administration

description:
ACTCTTT_vtr144_d0_20bcg_po
vtr144_d0_20bcg_po

value: Peripheral Blood

value: patient vtr144

value: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio


title: NextSeq 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)

value: SARS-CoV-2 infection


title: H3K27Ac_histone H3_acetyl K27_DIPG4_with_DMSO 2

value: H3K27Ac_histone H3_acetyl K27; Abcam Cat. #ab4729


title: Input_DIPG4_with_DMSO_Radiation_2

value: DMSO and 6Gy radiation


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

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


title: patient vtr56 on d0 treated with 20bcg, vaccination via po administration

description:
AAACGAC_vtr56_d0_20bcg_po
vtr56_d0_20bcg_po

value: patient vtr56

value: Cytoplasmic RNA


title: plasma, subject 266e2348T1

value: Female

tag: days since first sample

tag: patient classification at first sample

tag: covid-19 status

value: Positive


title: plasma, subject 26ced899T4

value: Male

value: Yes

tag: instrument model


title: H3K27Ac_histone H3_acetyl K27_DIPG4_with_DMSO 1


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

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

tag: tissue


title: patient vtr15 on d0 treated with 20bcg, vaccination via po administration

description:
ATACTTC_vtr15_d0_20bcg_po
vtr15_d0_20bcg_po

value: patient vtr15

tag: treatment/time point

tag: molecule

tag: cell type


title: plasma, subject 262cc412T1

tag: subject id

value: Negative

value: No

value: Somascan discovery platform v4


title: plasma, subject 26221f93T1

tag: blood sample id


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

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

tag: treatment

value: Ribo-seq


title: Tissue, Glioblastoma, No injection, T1 (day 0)

city: Beijing

first: Lixin

last: Ma

address: Haidian District

department: Neurosurgery

institute: Sanbo Brain Hospital

description: Tumor tissue samples were collected before the two surgical injections of the oncolytic virus, so there were only uninjected tissue sample and tissue sample before the second injection. In other words, no tumor tissue samples were collected for mRNA sequencing after the second injection of the oncolytic virus.

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the human reference genome (HG19) with hisat2 software (v2.0.4).
Then, HTSeq software (v0.9.1) was used to get the raw count, and edgeR was used to perform normalization, then differentially expressed mRNAs were identified by p-value and fold change.
Assembly: hg19
Supplementary files format and content: Excel format, raw counts, normalized counts

source_name: tumor tissue

extract_protocol:
Briefly, total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions. RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions.
Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina NovaSeq 6000 instrument with 150bp paired end reads.

value: female

tag: genotype

value: H3K27M mutant, IV

tag: disease state

value: Glioblastoma

value: tumor tissue

value: no

value: Day 0


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

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

value: Lung

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

value: SARS-CoV-2 infection

value: 5 days post-infection


title: Tissue, Glioblastoma, First injection, T3 (day 70)

tag: Sex

value: oncolytic virus, first injection

value: Day 70


title: patient vtr61 on d0 treated with 20bcg, vaccination via po administration

description:
GTGATTT_vtr61_d0_20bcg_po
vtr61_d0_20bcg_po

value: Peripheral Blood

value: patient vtr61

value: Cytoplasmic RNA

value: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio


title: patient vtr98 on d0 treated with 20bcg, vaccination via po administration

description:
GGCCTAC_vtr98_d0_20bcg_po
vtr98_d0_20bcg_po

value: patient vtr98


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

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

tag: strain

value: Ribo-seq


title: Tissue, Normal, No injection, N

source_name: normal brain tissue

value: female

value: control

value: normal brain tissue

tag: time


title: plasma, subject 245ec65eT8

value: Male

tag: age

value: Positive

value: No

value: Yes

value: Somascan discovery platform v4


title: patient vtr32 on d0 treated with 20bcg, vaccination via po administration

description:
GCGTTCA_vtr32_d0_20bcg_po
vtr32_d0_20bcg_po

value: patient vtr32


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

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

value: Lung

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

tag: library type


title: patient vtr22 on d0 treated with 20bcg, vaccination via po administration

description:
TAGGATG_vtr22_d0_20bcg_po
vtr22_d0_20bcg_po

value: Peripheral Blood

value: patient vtr22


title: plasma, subject 245ec65eT4

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

tag: days since first sample

tag: patient classification at first sample


title: patient vtr165 on d0 treated with 20bcg, vaccination via po administration

description:
CTCCTAG_vtr165_d0_20bcg_po
vtr165_d0_20bcg_po

value: patient vtr165

value: Cytoplasmic RNA


title: plasma, subject 266e2348T12

value: Female

tag: covid-19 status

tag: instrument model


title: Cerebrospinal fluid, Glioblastoma, No injection, G1, Input

data_processing:
Briefly,  raw data were generated after sequencing,  image analysis, base calling and quality filtering on Illumina NovaSeq 6000 sequencer.
Q30 was used to perform quality control. After adaptor-trimming and low quality reads removing by cutadapt (v1.9.3) software, high quality clean reads were generated. Then these clean reads were aligned to Human reference genome  (HG19) using bowtie2  software  (v2.2.4) with default parameters.
Peak calling was performed with MACS software (v2.0). Differentially methylated regions were identified by diffReps software (v1.55.4).The methylated regions were then annotated with the latest UCSC RefSeq database to connect the peak information with the gene annotation.
Assembly: hg19
Supplementary files format and content: excel format

source_name: cerebrospinal fluid

extract_protocol:
Genomic DNA was isolated using phenol–chloroform, precipitated with ethanol and sonicated to 100–500 bp using Bioruptor (Diagenode). Sonicated DNA was end repaired, A tailed, and ligated to adapters by using NEBNext® Ultra™ DNA Library Prep Kit (NEB). Then, MeDIP was performed with a monoclonal antibody against 5-methylcytosine by following the standard manufacturer’s protocol (Active Motif).
MeDIP DNA libraries were quantified using Quant-iT PicoGreen dsDNA Kits (Life Technologies), and subjected to high-throughput 150 base paired-end sequencing on Illumina Hiseq sequencer according to the manufacturer’s recommended protocol.

value: glioblastoma

value: H3K27M mutant, IV

tag: tissue

value: cerebrospinal fluid

value: no

value: Day 0

tag: molecule type

value: ctDNA

tag: ip antibody


title: NextSeq 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: Cerebrospinal fluid, Normal, No injection, N, Input

value: control

value: female


title: plasma, subject 245ec65eT12

tag: subject id

value: Male

value: Positive

value: Yes

value: Somascan discovery platform v4


title: plasma, subject 30f3e5beT0

tag: blood sample id

value: No


title: plasma, subject 245ec65eT1


title: patient vtr136 on d0 treated with 20bcg, vaccination via po administration

description:
TCAAACA_vtr136_d0_20bcg_po
vtr136_d0_20bcg_po

value: Peripheral Blood

value: patient vtr136

tag: treatment/time point

tag: molecule

value: Cytoplasmic RNA

tag: cell type

value: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio


title: Cerebrospinal fluid, Glioblastoma, Second injection, G5 (day 82)

tag: disease state

value: glioblastoma

tag: Sex

tag: genotype

value: H3K27M mutant, IV

value: cerebrospinal fluid

tag: treatment

value: oncolytic virus, second injection

value: Day 153

value: monoclonal antibody against 5-methylcytosine


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

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

value: Lung

tag: strain

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

value: SARS-CoV-2 infection

tag: time

value: 2 days post-infection

tag: library type

value: Ribo-seq


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

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


title: patient vtr26 on d0 treated with 20bcg, vaccination via po administration

description:
TCGAGAT_vtr26_d0_20bcg_po
vtr26_d0_20bcg_po

value: patient vtr26


title: plasma, subject 24064c86T1

value: Male

tag: age

tag: days since first sample

tag: patient classification at first sample

tag: covid-19 status

value: Positive

value: Yes

value: Somascan discovery platform v4


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

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

tag: tissue


title: patient vtr110 on d0 treated with 20bcg, vaccination via po administration

description:
CTCAATG_vtr110_d0_20bcg_po
vtr110_d0_20bcg_po

value: Peripheral Blood

tag: subject id

value: patient vtr110

value: Cytoplasmic RNA

value: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio


title: plasma, subject 2424324fT1

tag: blood sample id

tag: instrument model


title: Cerebrospinal fluid, Glioblastoma, First injection, G3 (day 70)

value: glioblastoma

value: female

value: H3K27M mutant, IV

value: cerebrospinal fluid

value: oncolytic virus, first injection

value: Day 70

tag: molecule type

value: ctDNA

tag: ip antibody


title: Cerebrospinal fluid, Glioblastoma, Second injection, G4 (day 1)

tag: disease state

value: oncolytic virus, second injection

value: Day 71

value: monoclonal antibody against 5-methylcytosine


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

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

value: Lung

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

value: SARS-CoV-2 infection

value: 1 day post-infection

value: Ribo-seq


title: plasma, subject 23e92638T1

tag: Sex

value: Female

value: Positive

value: Yes

value: Somascan discovery platform v4


title: patient vtr159 on d0 treated with 20bcg, vaccination via po administration

description:
GTATCCT_vtr159_d0_20bcg_po
vtr159_d0_20bcg_po

value: Peripheral Blood

value: patient vtr159

tag: treatment/time point

tag: molecule

value: Cytoplasmic RNA

tag: cell type

value: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio


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

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

tag: strain

tag: treatment

tag: time


title: Cerebrospinal fluid, Glioblastoma, No injection, G1 (day 0)

value: glioblastoma

value: female

tag: genotype

value: H3K27M mutant, IV

value: cerebrospinal fluid

value: no

value: Day 0

value: ctDNA


title: plasma, subject 23dd0be0T12

value: Male

tag: age

tag: days since first sample

tag: patient classification at first sample


title: patient vtr20 on d0 treated with 20bcg, vaccination via po administration

description:
CCGGACC_vtr20_d0_20bcg_po
vtr20_d0_20bcg_po

tag: tissue

tag: subject id

value: patient vtr20


title: Cerebrospinal fluid, Glioblastoma, First injection, G2 (day 1)

value: oncolytic virus, first injection

value: Day 1

value: monoclonal antibody against 5-methylcytosine


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

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

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

value: Ribo-seq


title: patient vtr33 on d0 treated with 20bcg, vaccination via po administration

description:
TGTTTGT_vtr33_d0_20bcg_po
vtr33_d0_20bcg_po

value: Peripheral Blood

value: patient vtr33

value: Cytoplasmic RNA

value: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio


title: patient vtr121 on d0 treated with 20bcg, vaccination via po administration

description:
GAGTACG_vtr121_d0_20bcg_po
vtr121_d0_20bcg_po

value: patient vtr121


title: Cerebrospinal fluid, Normal, No injection, N

value: control

value: female

value: cerebrospinal fluid

value: no

value: Day 0

tag: molecule type


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

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


title: plasma, subject 23d77493T20

tag: blood sample id

value: Male

tag: covid-19 status

value: Positive

value: No

value: Yes

tag: instrument model

value: Somascan discovery platform v4


title: patient vtr144 on d0 treated with 0bcg, vaccination via po administration

description:
CACCAGG_vtr144_d0_0bcg_po
vtr144_d0_0bcg_po

value: patient vtr144

tag: treatment/time point


title: plasma, subject 23d77493T1

tag: Sex


title: plasma, subject 23c3ea62T1


title: RFL4

city: Leuven

first: Sandrine

last: Da Cruz

state: Flemish Brabant

address: ON 5 Herestraat 49

department: KU Leuven Department of Neurosciences

country: Belgium

institute: VIB-KU Leuven Center for Brain and Disease Research

data_processing:
Read mapping: The reads are aligned to the reference genome with STAR 2.5.2b
Quality filtering: With samtools 1.5 we remove reads from the alignment that are non-primary mappings or have a mapping quality ≤ 20
Sorting and indexing: With samtools 1.5 we sort the reads from the alignment according to the chromosomes and index the resulting bam-files.
Assembly: Homo sapiens.Ensembl.GRCh38.88
Supplementary files format and content: Collated count matrix derived from raw data files

source_name: Human umbilical cord endothelial cells

growth_protocol: HUVECs from pooled donors were obtained from PromoCell (C-12208) and cultured in 0,2% gelatin-coated dishes in EGM2 medium supplemented with growth factors (PromoCell, C-22111), 100 units/ml penicillin and 100ug/ml streptomycin (Gibco). HUVECs were used between passages 4 to 6, the medium was refreshed every 48h or 72h, and regularly tested for mycoplasma.

extract_protocol:
RNA was extracted using RNEasy Kits (Qiagen) according to the manufacturer’s instructions. RNA sequencing was performed by the VIB Nucleomics Core (KU Leuven, Belgium). RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyzer 2100 (Agilent).
Per sample, an amount of 250ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: # 1000000040498 v00 October 2017) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Sequence libraries of each sample were equimolarly pooled and sequenced on Illumina NovaSeq 6000 (S1 100, 100bp single-end reads (100-8-8-0)) at the VIB Nucleomics Core.

treatment_protocol: HUVECs were seeded at a density of 500.000 cells per slide in growth medium on gelatin-coated SuperFrost Excell object slides (Thermo Scientific Menzel) and were grown to confluency for 48h. Slides were placed in a custom-designed parallel plate flow chamber within a tissue culture incubator. Wall shear stress was applied (15 dynes/cm2) for 24h using a peristaltic pump (Masterflex LS 7550-30). For static controls, HUVECs were seeded on slides, cultured in the same incubator in the absence of shear stress, and collected at the same time.

tag: cell type

value: Human endothelial cells

value: Wall shear stress culture


title: RFS4

value: Static culture


title: patient vtr32 on d0 treated with 0bcg, vaccination via po administration

description:
CCTTGAC_vtr32_d0_0bcg_po
vtr32_d0_0bcg_po

value: Peripheral Blood

value: patient vtr32

tag: molecule

value: Cytoplasmic RNA


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

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

value: Lung

tag: strain

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

tag: treatment

value: Ribo-seq


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

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

tag: time


title: RFL3


title: patient vtr56 on d0 treated with 0bcg, vaccination via po administration

description:
GTCCCTT_vtr56_d0_0bcg_po
vtr56_d0_0bcg_po

value: patient vtr56

value: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio


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

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


title: plasma, subject 237edd62T20

value: Male

tag: age


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

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


title: RFL2


title: plasma, subject 237edd62T1

tag: days since first sample

value: Positive


title: RFS3


title: patient vtr61 on d0 treated with 0bcg, vaccination via po administration

description:
TAAGTGC_vtr61_d0_0bcg_po
vtr61_d0_0bcg_po

value: patient vtr61


title: patient vtr15 on d0 treated with 0bcg, vaccination via po administration

description:
CGTACAA_vtr15_d0_0bcg_po
vtr15_d0_0bcg_po

value: patient vtr15


title: plasma, subject 23dd0be0T1

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

tag: patient classification at first sample

value: No

value: Yes

value: Somascan discovery platform v4


title: plasma, subject 230ded0fT1

value: Female

value: Negative


title: RFS2

value: Human endothelial cells

value: Static culture


title: xCT knockout, mouse embryonic fibroblast, red clover extract treated group 3

first: Junpil

last: Won

state: Seoul

address: 120 Neungdong-ro

department: Food science and biotechnology of animal resources

institute: Konkuk university

data_processing:
Illumina NextSeq 500 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to mm10 whole genome using STAR (version 2.5.4) with parameters -outFilterIntronMotifs RemoveNoncanonicalUnannotated.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by Cufflinks packages (version 2.2.1).
Differentially expressed genes were detected using Cuffdiff (version 2.2.1) against Ensemble genes.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Embryonic fibroblast

extract_protocol:
Total RNA extraction was performed using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions.
The quantity and quality of the total RNA were evaluated using Agilent 2100 bioanalyzerRNA kit (Agilent). The isolated total RNA was processed for preparing mRNA sequencing library using the Illumina TruSeqStranded mRNA Sample Preparation kit (Illumina), according to the manufacturer's protocol.

tag: tissue

value: Embryonic fibroblast

tag: genotype

value: xCT knockout

value: Red clover extract


title: patient vtr98 on d0 treated with 0bcg, vaccination via po administration

description:
CTCGGGT_vtr98_d0_0bcg_po
vtr98_d0_0bcg_po

value: Peripheral Blood

tag: subject id

value: patient vtr98

value: Cytoplasmic RNA


title: plasma, subject 22854ceaT1

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.


title: xCT knockout, mouse embryonic fibroblast, red clover extract treated group 1


title: patient vtr22 on d0 treated with 0bcg, vaccination via po administration

description:
CAAGAAT_vtr22_d0_0bcg_po
vtr22_d0_0bcg_po

extract_protocol:
After overnight treatment with BCG/media, supernatants were harvested, frozen and stored for lysis and RNA extraction.
RiboZero v1

value: patient vtr22

value: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio


title: RFL1

value: Wall shear stress culture


title: patient vtr165 on d0 treated with 0bcg, vaccination via po administration

description:
TTATAGC_vtr165_d0_0bcg_po
vtr165_d0_0bcg_po

value: patient vtr165


title: plasma, subject 224dc393T4

value: Male

value: Positive

value: No


title: xCT knockout, mouse embryonic fibroblast, control group 3

value: Water


title: Sorafenib treated DDX5 Wildtype rep3 [WTSOR3]

city: West Lafayette

first: Ourania

middle: M

last: Andrisani

state: IN

address: 625 Harrison Street

department: DEPARTMENT OF BASIC MEDICAL SCIENCES

institute: Purdue University

data_processing:
Sequence data quality was determined using FastQC tool (version 0.11.7).
Quality trimming and filtering were performed using Fastp2 (version 0.19.5) to remove the basecalls with a Phred33 score less than 30 and any reads shorter than 50 basepairs.
Quality trimmed reads were mapped against the indexed Homo_sapiens.GRCh38.99 reference genome using STAR3 aligner (version 2.5.4b).
STAR derived mapping results and annotation (GTF) file were fed into the HTSeq4 package (version 0.7.0).
Counts from all replicates were merged together using a custom Perl script to generate a gene counts matrix for all samples.
Differential expression analysis was performed with R-package edgeR .
Assembly: GRCh38.99 (ENSEMBL)
Supplementary files format and content: Tab delimited text file with raw and TPM counts.

source_name: HepAD38 cells

extract_protocol:
RNA extraction was performed following standard protocol from Qiagen RNeasy plus kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with Sorafenib (7.5 μM) for 3 days prior to harvesting

value: Sorafenib

tag: cell line

value: DDX5 Wildtype


title: xCT knockout, mouse embryonic fibroblast, control group 2


title: patient vtr26 on d0 treated with 0bcg, vaccination via po administration

description:
CAAGCCG_vtr26_d0_0bcg_po
vtr26_d0_0bcg_po

value: patient vtr26


title: plasma, subject 224dc393T1

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

value: Yes

value: Somascan discovery platform v4


title: xCT knockout, mouse embryonic fibroblast, control group 1

value: Embryonic fibroblast

value: xCT knockout


title: Sorafenib treated DDX5 Wildtype rep1 [WTSOR1]


title: plasma, subject 21b7ab7cT3

tag: covid-19 status


title: DMSO treated DDX5 Wildtype rep3 [WTDMSO3]

value: DMSO


title: patient vtr110 on d0 treated with 0bcg, vaccination via po administration

description:
ATGACAG_vtr110_d0_0bcg_po
vtr110_d0_0bcg_po

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4.b
Gene counts quantitated with Subread:featureCount 1.45 with CPM transformation added with custom Rscripting.
Assembly: Ensembl GRCh38.76
Supplementary files format and content: Gene counts-per-million in tab-delimitted text format

value: Peripheral Blood

value: patient vtr110

value: Cytoplasmic RNA


title: DMSO treated DDX5 Wildtype rep2 [WTDMSO2]


title: xCT knockout, mouse embryonic fibroblast, red clover extract treated group 2

value: Red clover extract


title: plasma, subject 21b7ab7cT2

tag: instrument model


title: Hot tumor, CD4 and CD8 depletion, sample 3

city: Philadelphia

first: Gregory

middle: L.

last: Beatty

state: PA

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

department: Medicine

institute: University of Pennsylvania

description: RNA isolated from tumor

data_processing:
FASTQ files uploaded to the BaseSpace Suite (Illumina) were aligned using its RNA-Seq Alignment application (version 2.0.0).
Output files were then analyzed using RNA-Seq Differential Expression application (version 1.0.1) in the BaseSpace suite.
Assembly: MM10
Supplementary files format and content: Tab delimited file contains TPM values of all samples.

source_name: Pancreas tumor

growth_protocol: Cell lines were cultured in DMEM (Corning) supplemented with 10% fetal bovine serum (FBS, VWR), 83 μg/ml gentamicin (Thermo Fisher), and 1% GlutaMAX (Thermo Fisher) at 37 °C, 5% CO2.

extract_protocol:
RNA was isolated from mouse tumors using a RNeasy mini kit (Qiagen) following the manufacturer’s protocol.
Sequencing libraries were prepared using a QuantSeq 3’ mRNA-Seq library prep kit FWD for Illumina (Lexogen) following manufacturer’s protocol and analyzed on a NextSeq 500 sequencing system (Illumina).

treatment_protocol: C57BL/6J mice were treated with a cocktail of antibiotics, including metronidazole (20 mg/kg, Sigma), ceftriaxone (50 mg/kg, Sigma), and vancomycin (20 mg/kg, Sigma), via intraperitoneal injections. After 3 days (day 0), mice were orthotopically injected with tumor cells (5e105 cells suspended in 100 uL sterile PBS). Antibiotics were administrated twice daily until mice were sacrificed, and anti-CD4 (clone GK1.5, 0.2 mg) and anti-CD8 (clone 2.43, 0.2 mg) antibodies were administered on days -3, 4, 11 and 18. Tumors were harvested 20 days after implantation. All antibodies used in in vivo experiments were obtained from BioXCell.

value: Pancreas tumor

value: Tumor cell line

value: Anti-CD4 and CD8 antibodies


title: Hot tumor, CD4 and CD8 depletion, sample 4

description: RNA isolated from tumor


title: patient vtr20 on d0 treated with 0bcg, vaccination via po administration

description:
AGCGCCG_vtr20_d0_0bcg_po
vtr20_d0_0bcg_po

value: patient vtr20

tag: treatment/time point

value: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio


title: plasma, subject 21b7ab7cT1

first: Pushkala

last: Jayaraman

institute: Icahn School of Medicine at Mount Sinai

tag: Sex

value: Male

value: Positive

value: No


title: RFS1

tag: cell type

value: Human endothelial cells

value: Static culture


title: Hot tumor, CD4 and CD8 depletion, sample 2

description: RNA isolated from tumor


title: plasma, subject 224dc393T8

value: Yes

value: Somascan discovery platform v4


title: DMSO treated DDX5 Wildtype rep1 [WTDMSO1]

value: DMSO

value: DDX5 Wildtype


title: Hot tumor, CD4 and CD8 depletion, sample 1

description: RNA isolated from tumor


title: plasma, subject 21438992T1


title: patient vtr121 on d0 treated with 0bcg, vaccination via po administration

first: Richard

last: Silver

institute: Case Western Reserve University and the Louis Stokes Cleveland VA Medical Center

description:
CTTGGAA_vtr121_d0_0bcg_po
vtr121_d0_0bcg_po

value: Peripheral Blood

value: patient vtr121

tag: molecule


title: Sorafenib treated DDX5 Wildtype rep2 [WTSOR2]

value: Sorafenib


title: Sorafenib treated DDX5 Knockdown rep3 [KDSOR3]

value: DDX5 Knockdown


title: patient vtr136 on d0 treated with 0bcg, vaccination via po administration

description:
GGGTCAA_vtr136_d0_0bcg_po
vtr136_d0_0bcg_po

value: patient vtr136

value: Cytoplasmic RNA


title: Hot tumor, antibiotics treatment, sample 4

description: RNA isolated from tumor

value: Pancreas tumor

value: Tumor cell line

value: Antibiotics


title: plasma, subject 209e82dfT12

value: Male

value: Positive


title: patient vtr33 on d0 treated with 0bcg, vaccination via po administration

description:
GATAGTT_vtr33_d0_0bcg_po
vtr33_d0_0bcg_po

value: patient vtr33

value: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio


title: patient vtr160 on d0 treated with 20bcg, vaccination via id administration

description:
ATTAGGA_vtr160_d0_20bcg_id
vtr160_d0_20bcg_id

value: patient vtr160


title: plasma, subject 21b7ab7cT4

value: No

value: Yes

value: Somascan discovery platform v4


title: patient vtr159 on d0 treated with 0bcg, vaccination via po administration

description:
GCAACGC_vtr159_d0_0bcg_po
vtr159_d0_0bcg_po

value: Peripheral Blood

value: patient vtr159


title: Hot tumor, antibiotics treatment, sample 3

description: RNA isolated from tumor


title: Sorafenib treated DDX5 Knockdown rep2 [KDSOR2]

value: Sorafenib


title: plasma, subject 209e82dfT1


title: Hot tumor, antibiotics treatment, sample 2

description: RNA isolated from tumor


title: Sorafenib treated DDX5 Knockdown rep1 [KDSOR1]

value: DDX5 Knockdown


title: DMSO treated DDX5 Knockdown rep3 [KDDMSO3]

value: DMSO


title: plasma, subject 1f485cb6T20

value: Female


title: patient vtr162 on d0 treated with 20bcg, vaccination via id administration

description:
CTAACTT_vtr162_d0_20bcg_id
vtr162_d0_20bcg_id

value: patient vtr162

value: Cytoplasmic RNA


title: patient vtr55 on d0 treated with 20bcg, vaccination via id administration

description:
AGTCTAG_vtr55_d0_20bcg_id
vtr55_d0_20bcg_id

value: patient vtr55


title: Hot tumor, antibiotics treatment, sample 1

description: RNA isolated from tumor

value: Pancreas tumor

value: Tumor cell line

value: Antibiotics


title: plasma, subject 1f485cb6T1

value: Positive


title: patient vtr106 on d0 treated with 20bcg, vaccination via id administration

description:
TCCACGT_vtr106_d0_20bcg_id
vtr106_d0_20bcg_id

value: patient vtr106

value: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio


title: Hot tumor, no treatment, sample 4

description: RNA isolated from tumor


title: DMSO treated DDX5 Knockdown rep2 [KDDMSO2]


title: DMSO treated DDX5 Knockdown rep1 [KDDMSO1]


title: Hot tumor, no treatment, sample 3

description: RNA isolated from tumor


title: patient vtr17 on d0 treated with 20bcg, vaccination via id administration

description:
CCACTCG_vtr17_d0_20bcg_id
vtr17_d0_20bcg_id

value: patient vtr17


title: ADC_5, TCR-seq

first: Xinyu

last: Qu

address: 419 Fangxie Road

department: Department of Gynecology

institute: Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University

data_processing:
Library strategy: TCR-seq
Basecalls performed using CASAVA version 1.8
cellranger (v5.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20%  passed the cell quality filtering and mitochondria genes were removed in the expression table.
Seurat package (version: 3.1.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data which was filtered below 20%.
PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Genome_build: GRCh38/Ensembl100
Supplementary_files_format_and_content: scRNA-seq samples:  Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)
Supplementary_files_format_and_content: TCR-seq samples:  contig_annotations.csv file

source_name: cervical cancer tissue

growth_protocol: Fresh surgically removed CC tissues were kept in MACS Tissue Storage Solution and further processed into single cell suspension.

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 5’ V1.1 Reagent Kits (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 5’ V1.1 Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols

tag: disease state

value: cervical cancer

value: cervical cancer tissue

tag: histologic type

value: ADC

tag: hpv infection

value: negative

tag: hpv subtype

value: not applicable

tag: library

value: 10x Genomics TCR library


title: Hot tumor, no treatment, sample 2

description: RNA isolated from tumor

tag: treatment


title: plasma, subject 1e96bcf2T20

address: 1 Gustave Levy Pl

source_name: serum

value: Female

tag: age

tag: days since first sample

tag: patient classification at first sample

value: Negative

value: No

value: Yes

value: Somascan discovery platform v4


title: ADC_4, TCR-seq

tag: tissue


title: Hot tumor, no treatment, sample 1

description: RNA isolated from tumor

value: Pancreas tumor

tag: cell line

value: Tumor cell line


title: ADC_3, TCR-seq

value: positive


title: plasma, subject 1e0265deT4

tag: subject id

tag: blood sample id

value: Male

tag: covid-19 status

value: Positive


title: plasma, subject 1e96bcf2T1

tag: Sex

tag: instrument model


title: patient vtr109 on d0 treated with 20bcg, vaccination via id administration

address: 10900 Euclid Ave

description:
CCAGGCA_vtr109_d0_20bcg_id
vtr109_d0_20bcg_id

source_name: Peripheral Blood

value: Peripheral Blood

value: patient vtr109

tag: treatment/time point

tag: molecule

value: Cytoplasmic RNA

tag: cell type

value: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio


title: Cold tumor, no treatment, sample 4

description: RNA isolated from tumor


title: ADC_2, TCR-seq

tag: disease state

value: cervical cancer

value: cervical cancer tissue

tag: histologic type

value: ADC

tag: hpv infection


title: plasma, subject 1e0265deT1

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


title: patient vtr68 on d0 treated with 20bcg, vaccination via id administration

description:
CCTAATC_vtr68_d0_20bcg_id
vtr68_d0_20bcg_id

value: patient vtr68


title: patient vtr150 on d0 treated with 20bcg, vaccination via id administration

description:
AGACTGA_vtr150_d0_20bcg_id
vtr150_d0_20bcg_id

value: patient vtr150


title: plasma, subject 1f485cb6T12

value: Female

value: No


title: Cold tumor, no treatment, sample 3

description: RNA isolated from tumor

tag: treatment


title: plasma, subject 1d5983f7T4

tag: age

value: Yes

value: Somascan discovery platform v4


title: ADC_1, TCR-seq

tag: hpv subtype

tag: library

value: 10x Genomics TCR library


title: patient vtr3 on d0 treated with 20bcg, vaccination via id administration

description:
CGGTGGC_vtr3_d0_20bcg_id
vtr3_d0_20bcg_id

tag: tissue

value: patient vtr3


title: Cold tumor, no treatment, sample 2

description: RNA isolated from tumor

value: Pancreas tumor

tag: cell line

value: Tumor cell line


title: Cold tumor, no treatment, sample 1

description: RNA isolated from tumor


title: patient vtr28 on d0 treated with 20bcg, vaccination via id administration

description:
CACCTCC_vtr28_d0_20bcg_id
vtr28_d0_20bcg_id

value: Peripheral Blood

tag: subject id

value: patient vtr28


title: SCC_3, TCR-seq

value: SCC

value: positive

value: HPV 16


title: SCC_1, TCR-seq

value: cervical cancer

value: cervical cancer tissue

value: HPV  58


title: plasma, subject 1d5983f7T1

tag: blood sample id

value: Male

tag: days since first sample

tag: patient classification at first sample

value: Positive


title: SCC_2, TCR-seq


title: Female Control

city: Boston

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

data_processing:
The sample was processed using the standard Cell ranger pipeline
Reads were mapped to GRCm38
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Doublet threshold was raised to include binucleated hepatocytes
Assembly: GRCm38
Supplementary files format and content: the processed files are the standard output from the cell ranger count pipeline:

source_name: Liver cells from females 48hrs after PBS vehicle IP injection

extract_protocol: 10X Chromium system

treatment_protocol: Cells were not sorted prior to sequencing

value: liver

tag: Sex

value: female

tag: strain

value: 12 weeks

tag: isolation method

value: Mice were anaesthetized with ketamine/xylazine and then perfused by through the inferior vena cava with 30 mL 1X Liver Perfusion Medium (Gibco by Life Technologies), while the portal vein was cut to allow the perfusate to flow out. In total, 15 mL of Earle’s Balanced Salt Solution (EBSS) containing 10mM Hepes (Ca++ and Mg++, pH 7.4) was then perfused, and finally followed with 30 mL of Liver Digest Medium (Gibco by Life Technologies) to allow complete dissociation of liver cells in situ. All solutions were pre-warmed to 40 °C and delivered at a rate of 4 ml/min. Livers were then extracted and mechanically dissociated in 10 mL of Liver Digest Medium. Cells were filtered through 100 μm cell strainer and filtrate was centrifuged at 50 × g for 2 min at 4 °C to obtain hepatocytes in the pellet while the supernatant was collected as the fraction of NPCs. The hepatocyte pellet was resuspended in wash media (Hepatocyte Wash Medium by Gibco + 0.1 mg/mL DNAse 1 + 10% FBS) and saved. The cell fraction caught in the 100 μm strainer was further digested in NPC Digest Medium (2.5 mg/mL Collagenase IV + 0.1 mg/mL DNAse 1), filtered through a 40 μm strainer, then centrifuged at 300 × g for 5 min at 4 °C. The supernatant was discarded, pellet was resuspended in wash media, and solution was added to the other collection of NPCs. This NPC fraction was used for the single-cell RNA sequencing analysis.


title: patient vtr140 on d0 treated with 20bcg, vaccination via id administration

description:
CAATATC_vtr140_d0_20bcg_id
vtr140_d0_20bcg_id

value: patient vtr140

tag: treatment/time point

tag: molecule

value: Cytoplasmic RNA

tag: cell type

value: Autologuous CD4+ T cells cultured with Autologous monocyte-derived dendritic cells (MDDC) in a 20:1 ratio


title: plasma, subject 1cca9f81T4

city: New York

value: Female

tag: covid-19 status

value: No

value: Yes

tag: instrument model

value: Somascan discovery platform v4


title: patient vtr23 on d0 treated with 20bcg, vaccination via id administration

city: Cleveland

description:
GAGGCGT_vtr23_d0_20bcg_id
vtr23_d0_20bcg_id

value: Peripheral Blood

value: patient vtr23


title: patient vtr43 on d0 treated with 20bcg, vaccination via id administration

description:
GCAGGGG_vtr43_d0_20bcg_id
vtr43_d0_20bcg_id

value: patient vtr43


title: plasma, subject 1cca9f81T13

tag: age


title: patient vtr72 on d0 treated with 20bcg, vaccination via id administration

description:
GTTTACC_vtr72_d0_20bcg_id
vtr72_d0_20bcg_id

value: patient vtr72


title: Male Control

source_name: Liver cells from males 48hrs after PBS vehicle IP injection

value: male


title: ADC_4, scRNA-seq

data_processing:
Basecalls performed using CASAVA version 1.8
cellranger (v5.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20%  passed the cell quality filtering and mitochondria genes were removed in the expression table.
Seurat package (version: 3.1.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data which was filtered below 20%.
PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Genome_build: GRCh38/Ensembl100
Supplementary_files_format_and_content: scRNA-seq samples:  Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)
Supplementary_files_format_and_content: TCR-seq samples:  contig_annotations.csv file

tag: disease state

value: cervical cancer

value: cervical cancer tissue

tag: histologic type

value: ADC

tag: hpv infection

value: negative

tag: hpv subtype

value: not applicable

value: 10x Genomics 5' GEX library


title: ADC_5, scRNA-seq

tag: tissue

tag: library


title: plasma, subject 1df07b1dT1

tag: subject id

tag: blood sample id

tag: days since first sample

value: Negative


title: Female APAP

source_name: Liver cells from females 48hrs after 400 mg/kg APAP IP injection

value: liver

tag: Sex

value: female

tag: strain

value: 12 weeks

value: Mice were anaesthetized with ketamine/xylazine and then perfused by through the inferior vena cava with 30 mL 1X Liver Perfusion Medium (Gibco by Life Technologies), while the portal vein was cut to allow the perfusate to flow out. In total, 15 mL of Earle’s Balanced Salt Solution (EBSS) containing 10mM Hepes (Ca++ and Mg++, pH 7.4) was then perfused, and finally followed with 30 mL of Liver Digest Medium (Gibco by Life Technologies) to allow complete dissociation of liver cells in situ. All solutions were pre-warmed to 40 °C and delivered at a rate of 4 ml/min. Livers were then extracted and mechanically dissociated in 10 mL of Liver Digest Medium. Cells were filtered through 100 μm cell strainer and filtrate was centrifuged at 50 × g for 2 min at 4 °C to obtain hepatocytes in the pellet while the supernatant was collected as the fraction of NPCs. The hepatocyte pellet was resuspended in wash media (Hepatocyte Wash Medium by Gibco + 0.1 mg/mL DNAse 1 + 10% FBS) and saved. The cell fraction caught in the 100 μm strainer was further digested in NPC Digest Medium (2.5 mg/mL Collagenase IV + 0.1 mg/mL DNAse 1), filtered through a 40 μm strainer, then centrifuged at 300 × g for 5 min at 4 °C. The supernatant was discarded, pellet was resuspended in wash media, and solution was added to the other collection of NPCs. This NPC fraction was used for the single-cell RNA sequencing analysis.


title: plasma, subject 1cb60f79T8

value: Male

tag: patient classification at first sample

value: Positive

value: Yes

value: Somascan discovery platform v4


title: Male APAP

source_name: Liver cells from males 48hrs after 400 mg/kg APAP IP injection

tag: isolation method


title: ADC_3, scRNA-seq

value: positive