title: patient vtr160 on d0 treated with 0bcg, vaccination via id administration

description:
CCTCAAG_vtr160_d0_0bcg_id
vtr160_d0_0bcg_id

value: Peripheral Blood

value: patient vtr160

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: S6 GFI1_KD_3

status: Public on Dec 01 2023

type: SRA

city: Luebeck

first: Pradeep

middle: Kumar

last: Patnana

state: Schleswig-Holstein

address: Ratzeburger Allee 160

country: Germany

institute: Universitätsklinikum Schleswig-Holstein

library_source: genomic

data_processing:
Trim Galore was used to remove adapters
BWA-MEM was used for read alignment
Reads were mapped to mm10 genome assembly
Low-quality reads were removed by Samtools
PCR duplicates were removed using Picard tool
Peaks were called by MACS2 based on the 5' end's read count
Peaks located within ENCODE black list regions were removed
DiffBind was used to identify consensus peaks, to count reads, to normalize read counts for consensus peaks, and to perform differential binding analysis
ChIPseeker was applied for peak annotation. Enhancers were annotated based on curated enhancer regions from EnhancerAtlas 2.0.
Pathway over-representation analysis was done using clusterProfiler on the basis of significant differential binding genes (FDR threshold: 0.05).
Motif analysis was done using HOMER on the basis of significant differential binding genes.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files and consensus peak normalised counts

molecule: genomic DNA

organism: Mus musculus

source_name: GMPs

extract_protocol:
The GMPs were isolated from the total bone marrow cells using FACS sorting.
Transposition was performed using Nextera DNA Library Prep Kit (FC-121–1030, Illumina)

value: GMPs

tag: strain

tag: treatment

value: Untreated

tag: gentopye

value: GFI1 KD /KD


title: patient vtr162 on d0 treated with 0bcg, vaccination via id administration

city: Cleveland

first: Richard

last: Silver

state: OH

address: 10900 Euclid Ave

department: Division of Pulmonary, Critical Care and Sleep Medicine

country: USA

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

description:
TCTGCTT_vtr162_d0_0bcg_id
vtr162_d0_0bcg_id

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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.

tag: tissue

tag: subject id

value: patient vtr162


title: plasma, subject 1c55de37T1

type: protein

city: New York

first: Pushkala

last: Jayaraman

state: New York

address: 1 Gustave Levy Pl

department: Charles Bronfman Institute of Personalized Medicine

institute: Icahn School of Medicine at Mount Sinai

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

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

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

molecule: protein

source_name: serum

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

tag: blood sample id

tag: Sex

value: Female

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: ADC_2, scRNA-seq

city: Shanghai

first: Xinyu

last: Qu

address: 419 Fangxie Road

department: Department of Gynecology

country: China

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

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

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: positive

tag: hpv subtype

tag: library

value: 10x Genomics 5' GEX library


title: S5 GFI1_KD_2

tag: cell type

tag: strain


title: ADC_1, scRNA-seq


title: plasma, subject 1b1361b3T1

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: patient vtr106 on d0 treated with 0bcg, vaccination via id administration

description:
AGCTTAT_vtr106_d0_0bcg_id
vtr106_d0_0bcg_id

value: Peripheral Blood

value: patient vtr106

tag: treatment/time point

tag: molecule


title: plasma, subject 1a5ad058T4

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

tag: subject id


title: S4 GFI1_KD_1

tag: treatment

tag: gentopye


title: SCC_3, scRNA-seq

tag: tissue

value: SCC

value: HPV 16


title: plasma, subject 1cca9f81T20

tag: blood sample id

tag: Sex

tag: age

tag: days since first sample


title: patient vtr17 on d0 treated with 0bcg, vaccination via id administration

description:
CTACGTG_vtr17_d0_0bcg_id
vtr17_d0_0bcg_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: S3 GFI1_KI_3

value: GMPs

value: Untreated

value: GFI1 KI /KI


title: SCC_2, scRNA-seq

tag: disease state


title: patient vtr72 on d0 treated with 0bcg, vaccination via id administration

description:
TGGCTGC_vtr72_d0_0bcg_id
vtr72_d0_0bcg_id

value: patient vtr72


title: SCC_1, scRNA-seq

value: cervical cancer

tag: histologic type

value: HPV  58


title: plasma, subject 188edafaT1

value: Female

tag: patient classification at first sample

tag: covid-19 status

value: Positive

value: Yes

tag: instrument model

value: Somascan discovery platform v4


title: S1 GFI1_KI_1

tag: cell type


title: patient vtr68 on d0 treated with 0bcg, vaccination via id administration

description:
ACCCACT_vtr68_d0_0bcg_id
vtr68_d0_0bcg_id

value: Peripheral Blood

value: patient vtr68


title: S6_Gfi_36N_MLL_AF9_1_TMZ

description:
normalized_counts_Gfi1_36N_with_or_without_TMZ.txt
normalized_counts_TMZ_treated_leukemic_Gfi1_36N_vs_36S.txt

data_processing:
Transcript quantification was done using Salmon against cDNA sequences of mouse genome assembly mm10.
ComBat-seq was used to adjust the batch effect in the case of two batches.
Read count normalization was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files and normalised read counts

source_name: Bonemarrow cells

extract_protocol:
RNA was extracted from 5x106 total bone marrow cells of leukemic mice using RNeasy Mini Kit (74104, Qiagen, Germany) as per manufacturer instructions.
The samples were sent to core facility genomics (CFG MFM) in University Hospital Münster for library preparation and sequencing. The NEBNext  Poly(A) mRNA Magnetic Isolation module (NEB #E7490) protocol was used for library preparation.  Module (NEB #E7490)

treatment_protocol: In case of the temozolomide (TMZ) treated samples: leukemic bone marrow cells were treated with 50 µg/ml temozolomide 20 h before RNA isolation

value: Leukemic bonemarrow cells

tag: genotpye

tag: strain

value: TMZ Treatment (50 µg/ml)


title: plasma, subject 1874c2cfT8


title: D72IFNa14

city: Aurora

first: Kejun

last: Guo

state: Colorado

department: Division of Infectious Diseases

institute: University of Colorado Anschutz Medical Campus

description: Donor 72_IFNa14

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality screened and adapter removal using cutadapt (v1.15).
Mapped to GRch38 human genome using HiSat2 (v2.1.0).
Raw gene counts were extracted using featureCounts (v1.6.5, the Subread package).
Gene Raw count matrix and Transcript per Million (TPM) table for samples was generated using custom Perl scripts.
Genome_build: Human GRch38
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt: Matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: gene_counts_TPM_matrix.txt: Matrix table with TPM normalized counts.
Supplementary_files_format_and_content: *_geneCounts.txt: Tab-delimited text files include abundance measurements.

source_name: PBMC

extract_protocol:
Qiagen RNeasy Plus kit according to the manufacturer’s instruction.
Lexogen QuantSeq 3’ mRNA-Seq Library (FWD) Prep kit according to the manufacturer’s instruction.

treatment_protocol: Mock treated with PBS or ISRE activity normalized doses of IFNa1, IFNa2, IFNa4, IFNa5, IFNa8, IFNa14, or IFNb for 18 hrs.

value: PBMC

tag: subject

value: Donor 72


title: plasma, subject 188edafaT4

tag: subject id


title: D72IFNb

description: Donor 72_IFNb


title: S5_Gfi_36N_MLL_AF9_1_TMZ

tag: treatment


title: D72IFNa8

description: Donor 72_IFNa8


title: patient vtr150 on d0 treated with 0bcg, vaccination via id administration

description:
TGCTGGG_vtr150_d0_0bcg_id
vtr150_d0_0bcg_id

value: patient vtr150

tag: treatment/time point

tag: molecule

value: Cytoplasmic RNA

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


title: plasma, subject 1874c2cfT4

tag: blood sample id

value: No


title: patient vtr55 on d0 treated with 0bcg, vaccination via id administration

description:
TGAAGGC_vtr55_d0_0bcg_id
vtr55_d0_0bcg_id

tag: tissue

value: patient vtr55


title: S4 Gfi_36N__MLL_AF9_1_TMZ


title: plasma, subject 1874c2cfT1

tag: Sex

tag: age


title: patient vtr140 on d0 treated with 0bcg, vaccination via id administration

description:
ACCTGAA_vtr140_d0_0bcg_id
vtr140_d0_0bcg_id

value: patient vtr140


title: D72IFNa5

description: Donor 72_IFNa5


title: D72IFNa4

description: Donor 72_IFNa4


title: plasma, subject 1a5ad058T1

tag: days since first sample


title: S3 GFI1_36S_S_MLL_AF9_3_TMZ

value: GFI1 KI /KI


title: patient vtr28 on d0 treated with 0bcg, vaccination via id administration

description:
TGGTCTC_vtr28_d0_0bcg_id
vtr28_d0_0bcg_id

value: patient vtr28


title: plasma, subject 17abecb0T8

value: Female

value: Positive


title: S2 GFI1_36S_S_MLL_AF9_2_TMZ


title: S2 GFI1_KI_2

value: GMPs

value: Untreated

tag: gentopye


title: plasma, subject 17abecb0T4

tag: patient classification at first sample

value: Yes

value: Somascan discovery platform v4


title: patient vtr109 on d0 treated with 0bcg, vaccination via id administration

description:
ACGTCTG_vtr109_d0_0bcg_id
vtr109_d0_0bcg_id

value: Peripheral Blood

value: patient vtr109


title: D72IFNa2

description: Donor 72_IFNa2

value: PBMC

value: Donor 72


title: S1 GFI1_36S_S_MLL_AF9_1_TMZ

value: Leukemic bonemarrow cells

value: TMZ Treatment (50 µg/ml)


title: patient vtr23 on d0 treated with 0bcg, vaccination via id administration

description:
AAATGCA_vtr23_d0_0bcg_id
vtr23_d0_0bcg_id

value: patient vtr23

value: Cytoplasmic RNA

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


title: D72IFNa1

description: Donor 72_IFNa1


title: plasma, subject 17abecb0T13

tag: covid-19 status


title: patient vtr43 on d0 treated with 0bcg, vaccination via id administration

description:
GGTGAAT_vtr43_d0_0bcg_id
vtr43_d0_0bcg_id

value: patient vtr43


title: S9 Gfi_KD_MLL_AF9_1

value: GFI1 KD /KD


title: patient p057 on d0 treated with 20bcg, ltbi

description:
CGGATAC_p057_d0_20bcg_ltbi
p057_d0_20bcg_ltbi

value: patient p057

value: d0 treated with 20bcg, ltbi


title: D72Mock

description: Donor 72_Mock


title: plasma, subject 17a77dd8T4

value: Male

value: Positive

tag: instrument model


title: D35IFNb

description: Donor 35_IFNb

tag: cell type

value: Donor 35


title: patient p062 on d0 treated with 20bcg, ltbi

description:
CTGCGCA_p062_d0_20bcg_ltbi
p062_d0_20bcg_ltbi

value: patient p062


title: D35IFNa14

description: Donor 35_IFNa14


title: patient vtr3 on d0 treated with 0bcg, vaccination via id administration

description:
GACACAG_vtr3_d0_0bcg_id
vtr3_d0_0bcg_id

value: Peripheral Blood

value: patient vtr3


title: S7 Gfi_KD_MLL_AF9_1

tag: genotpye

value: Untreated


title: D35IFNa5

description: Donor 35_IFNa5

value: PBMC


title: S6_Gfi_36N_MLL_AF9_1

value: Leukemic bonemarrow cells

tag: strain


title: S4 Gfi_36N__MLL_AF9_1


title: patient p066 on d0 treated with 20bcg, ltbi

description:
AGATCAG_p066_d0_20bcg_ltbi
p066_d0_20bcg_ltbi

value: patient p066


title: patient p069 on d0 treated with 20bcg, ltbi

description:
GCTATAG_p069_d0_20bcg_ltbi
p069_d0_20bcg_ltbi

value: patient p069


title: plasma, subject 1758a4b0T1

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

value: Female

value: No

value: Yes

value: Somascan discovery platform v4


title: plasma, subject 175135feT4


title: plasma, subject 175135feT8


title: D35IFNa8

description: Donor 35_IFNa8

tag: subject


title: plasma, subject 175135feT12

tag: subject id


title: D35IFNa4

description: Donor 35_IFNa4


title: S3 GFI1_36S_S_MLL_AF9_3

value: GFI1 KI /KI

tag: treatment


title: D35IFNa2

description: Donor 35_IFNa2


title: plasma, subject 175135feT1


title: S8 Gfi_KD_MLL_AF9_1

value: GFI1 KD /KD


title: plasma, subject 17a77dd8T1

value: Male


title: S2 GFI1_36S_S_MLL_AF9_2


title: patient p025 on d0 treated with 20bcg, ltbi

description:
CTAATGC_p025_d0_20bcg_ltbi
p025_d0_20bcg_ltbi

value: patient p025

tag: treatment/time point

value: d0 treated with 20bcg, ltbi

value: Cytoplasmic RNA

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


title: D35IFNa1

description: Donor 35_IFNa1

value: Donor 35


title: S1 GFI1_36S_S_MLL_AF9_1

value: Untreated


title: patient p009 on d0 treated with 20bcg, ltbi

description:
GCACTAA_p009_d0_20bcg_ltbi
p009_d0_20bcg_ltbi

value: Peripheral Blood

value: patient p009

tag: molecule


title: plasma, subject 16ae238fT4

tag: blood sample id

value: Positive


title: plasma, subject 15dd9db5T1


title: D35Mock

description: Donor 35_Mock

value: PBMC


title: patient p050 on d0 treated with 20bcg, ltbi

description:
CGTGATA_p050_d0_20bcg_ltbi
p050_d0_20bcg_ltbi

tag: tissue

value: patient p050


title: patient p065 on d0 treated with 20bcg, ltbi

description:
AGATACT_p065_d0_20bcg_ltbi
p065_d0_20bcg_ltbi

value: patient p065


title: S5_Gfi_36N_MLL_AF9_1

value: Leukemic bonemarrow cells


title: plasma, subject 15dcbdd1T1

tag: Sex

value: Yes

value: Somascan discovery platform v4


title: plasma, subject 15a8b3acT4

value: Female

tag: age

value: No


title: D21IFNb

description: Donor 21_IFNb

value: Donor 21


title: patient p047 on d0 treated with 20bcg, ltbi

description:
TTGCCCC_p047_d0_20bcg_ltbi
p047_d0_20bcg_ltbi

value: patient p047

value: d0 treated with 20bcg, ltbi


title: WT-ND2

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

description:
WT-ND
215MH16_DGE_Matrix.txt
AGATTA

data_processing:
Create bam file without alignment with Picard: java -jar PATHTOPICARD/picard.jar' FastqToSam F1=FORWARDREAD  F2=REVERSEREAD O=RUNNAME.bam' SM=RUNNAME
Sort bam file according to read ID with Picard: java -jar PATHTOPICARD/picard.jar' SortSam I=RUNNAME.bam O=RUNNAME_sorted.bam SORT_ORDER=queryname
Map data with Drop-seq tools and default settings: PATHTODROPSEQTOOLS/Drop-seq_alignment.sh -g PATHTOSTARINDEX -r PATHTOREFERENCEGENOME -d PATHTODROPSEQTOOLS -s STAREXECUTABLE -o OUTPUTNAME RUNNAME_sorted.bam
Get countmatrix by invoke command 'DigitalExpression' as implemented in Drop-seq tools: PATHTODROPSEQTOOLS/DigitalExpression I=star_gene_exon_tagged.bam O=DGE_Matrix.txt CELL_BARCODE_TAG=XC MOLECULAR_BARCODE_TAG=XM CELL_BC_FILE=BARCODEINFOFILE
Genome_build: GRCm38
Supplementary_files_format_and_content: *_DGE_Matrix.txt: Matrix tables with raw gene counts for every gene and every sample.

source_name: small intestine

extract_protocol:
300-1000 cells were sorted for each sample directly in a well (low binding Eppendorf) containing 5μl lysis buffer (500μl lysis buffer: 250 μl of 2X TCL buffer (Qiagen, cat.no.1070498) plus 245 μl of RNase-free water and 5 μl (1% of total volume) of b-mercaptoethanol). Nucleic acids of the lysates were purified with AMPure XP beads (Beckman Coulter). 1.8 volume of reagent and lysate were mixed thoroughly by pipette, followed and kept for 5 min at room temperature (RT). The mix was then placed onto Magnet Plate for 3 min to separate beads from the solution. The resulted cleared solution was aspirated from the reaction plate and discarded. Then were dispensed 150 μL of 80% ethanol to each well; 30 seconds at RT, aspirated out and discarded, followed by one repetition, and let it dry for 5 min at RT. Off the magnet plate, were added 6 μL of elution buffer (RNase free water), pipette and mixed 10 times. On the magnet plate 1 min to separate beads from the solution. The eluate was then transferred to the retrotranscription mix for RNA-Seq processing. For the RNA-Seq, library preparation for bulk-sequencing of poly(A)-RNA was done as described previously (Parekh et al., 2016). Briefly, barcoded cDNA of each sample was generated with a Maxima RT polymerase (Thermo Fisher) using oligo-dT primer containing barcodes, unique molecular identifiers (UMIs) and an adaptor. Ends of the cDNAs were extended by a template switch oligo (TSO) and full-length cDNA was amplified with primers binding to the TSO-site and the adaptor. NEB UltraII FS kit was used to fragment cDNA. After end repair and A-tailing a TruSeq adapter was ligated and 3’-end-fragments were finally amplified using primers with Illumina P5 and P7 overhangs. In comparison to Parekh et al. (2016)5, the P5 and P7 sites were exchanged to allow sequencing of the cDNA in read1 and barcodes and UMIs in read2 to achieve a better cluster recognition. The library was sequenced on a NextSeq 500 (Illumina) with 63 cycles for the cDNA in read1 and 16 cycles for the barcodes and UMIs in read2. Data was processed using the published Drop-seq pipeline (v1.0) to generate sample- and gene-wise UMI tables6. Reference genome (GRCm38) was used for alignment. Transcript and gene definitions were used according to the GENCODE Version M25.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Small intestines were harvested and cleaned of fat residue and Peyer’s patches. To obtain lamina propria cells (LPC), the small intestine was cut longitudinally and scraped in PBS 1X to clean the mucus and feces. The clean tissue was fragmented into pieces in 20ml HBSS 2% FCS. The pieces were filtered through a 100μm mesh and were incubated in 10ml HBSS 2mM EDTA in a shaker at 37°C for 20 min. The pieces were rinsed with HBSS through a 100μm mesh and incubated in 10ml HBSS 2mM EDTA in a shaker at 37°C for 20 min. The pieces were rinsed with HBSS, filtered through a 100μm mesh and incubated in 15 ml IMDM +10% FCS containing 1mg/ml collagenase VIII (Sigma) in a shaker at 37°C for 15 min in order to disaggregate the tissue. Single cell suspensions were then washed and filtered (100 and 40μm cell strainer). Staining was performed using Live/Dead discrimination by using DAPI or ZombieDyeNIR according to the manufacturer´s instructions. After washing (~400g, 5min, 4°C), cells were stained with anti-CD19 (PE/Cy7-conjugated, cat.no.115520, Biolegend), anti-CD20 (PE-conjugated, cat.no.152105, Biolegend), anti-CD3 (APC-conjugated, cat.no100236, Biolegend), anti-CD45 (AlexaFluor700-conjugated, cat.no.103128, Biolegend), for 20min at 4°C and washed again. Samples for flow cytometry were fixed using eBioscience IC fixation (cat.no.00-8222-49) according to the manufacturer´s instruction. For sorting, a FACS Aria II and a FACSAria FUSION were used.

value: small intestine

value: B cells

tag: genotype

value: wildtype

tag: diet

value: normal


title: patient p052 on d0 treated with 20bcg, ltbi

description:
ATGAGCC_p052_d0_20bcg_ltbi
p052_d0_20bcg_ltbi

value: Peripheral Blood

value: patient p052

value: Cytoplasmic RNA

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


title: WT-ND3

description:
WT-ND
215MH16_DGE_Matrix.txt
CTTTAA


title: patient p049 on d0 treated with 20bcg, ltbi

description:
CGTCGCT_p049_d0_20bcg_ltbi
p049_d0_20bcg_ltbi

value: patient p049


title: D21IFNa14

description: Donor 21_IFNa14

value: PBMC


title: WT-ND1

description:
WT-ND
215MH16_DGE_Matrix.txt
GTGCGC


title: patient p067 on d0 treated with 20bcg, ltbi

description:
CCGATTA_p067_d0_20bcg_ltbi
p067_d0_20bcg_ltbi

value: patient p067


title: plasma, subject 1562a93cT12

value: Male

tag: days since first sample

tag: patient classification at first sample

value: Positive

value: Yes

value: Somascan discovery platform v4


title: D21IFNa5

description: Donor 21_IFNa5

value: Donor 21


title: D21IFNa8

description: Donor 21_IFNa8


title: plasma, subject 15a8b3acT1

value: Female

tag: covid-19 status

value: No

tag: instrument model


title: uMT-CFR-HFD3

description:
uMT-CFR-HFD
215MH16_DGE_Matrix.txt
TCCCGC

value: small intestine

tag: cell type

value: B cells

value: uMT-KO

value: choline-deficient high-fat


title: patient p060 on d0 treated with 20bcg, ltbi

description:
ATCGAGC_p060_d0_20bcg_ltbi
p060_d0_20bcg_ltbi

value: Peripheral Blood

value: patient p060

value: d0 treated with 20bcg, ltbi


title: D21IFNa4

description: Donor 21_IFNa4


title: D21IFNa2

description: Donor 21_IFNa2


title: uMT-CFR-HFD1

description:
uMT-CFR-HFD
215MH16_DGE_Matrix.txt
CGCTGC


title: uMT-CFR-HFD2

description:
uMT-CFR-HFD
215MH16_DGE_Matrix.txt
GCGAGC


title: patient p061 on d0 treated with 20bcg, ltbi

description:
GCTTAGA_p061_d0_20bcg_ltbi
p061_d0_20bcg_ltbi

value: patient p061

value: Cytoplasmic RNA

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


title: plasma, subject 15170ae3T1

value: Negative


title: plasma, subject 1516340bT8

value: Male

value: Positive


title: patient p042 on d0 treated with 20bcg, ltbi

description:
AATACGC_p042_d0_20bcg_ltbi
p042_d0_20bcg_ltbi

value: patient p042


title: D21IFNa1

description: Donor 21_IFNa1

value: PBMC

value: Donor 21


title: patient p057 on d0 untreated, ltbi

description:
AGCTCGC_p057_d0_0bcg_ltbi
p057_d0_0bcg_ltbi

value: patient p057

value: d0 untreated, ltbi


title: CD-HFD3

description:
CD-HFD
215MH16_DGE_Matrix.txt
AGGGGC

value: small intestine

value: B cells

value: wildtype


title: CD-HFD2

description:
CD-HFD
215MH16_DGE_Matrix.txt
CACCAA

value: choline-deficient high-fat


title: D21Mock

description: Donor 21_Mock


title: plasma, subject 1516340bT4

value: No

value: Yes

value: Somascan discovery platform v4


title: plasma, subject 1516340bT1


title: D20IFNb

description: Donor 20_IFNb

value: Donor 20


title: plasma, subject 1516340bT20


title: D20IFNa14

description: Donor 20_IFNa14


title: patient p062 on d0 untreated, ltbi

description:
GATAAGG_p062_d0_0bcg_ltbi
p062_d0_0bcg_ltbi

value: Peripheral Blood

value: patient p062

value: Cytoplasmic RNA

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


title: patient p050 on d0 untreated, ltbi

description:
AATGGTA_p050_d0_0bcg_ltbi
p050_d0_0bcg_ltbi

value: patient p050


title: patient p069 on d0 untreated, ltbi

description:
AAGAAGT_p069_d0_0bcg_ltbi
p069_d0_0bcg_ltbi

value: patient p069


title: plasma, subject 14eb8045T4

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

value: Female

value: Positive


title: CD-HFD1

description:
CD-HFD
215MH16_DGE_Matrix.txt
TCATAT


title: plasma, subject 1562a93cT1

value: Male


title: plasma, subject 14eb8045T1


title: WT-ND-CD20-BR3

description:
WT-ND-CD20
157MH11_DGE_Matrix.txt
GCGAGC

value: small intestine

value: normal


title: WT-ND-CD20-BR4

description:
WT-ND-CD20
157MH11_DGE_Matrix.txt
TCCCGC

value: B cells

value: wildtype


title: D20IFNa5

description: Donor 20_IFNa5

value: PBMC


title: patient p066 on d0 untreated, ltbi

description:
GACTTGC_p066_d0_0bcg_ltbi
p066_d0_0bcg_ltbi

value: patient p066

value: d0 untreated, ltbi


title: plasma, subject 148ddee7T1

value: Yes

value: Somascan discovery platform v4


title: patient p052 on d0 untreated, ltbi

description:
CATACTG_p052_d0_0bcg_ltbi
p052_d0_0bcg_ltbi

value: Peripheral Blood

value: patient p052


title: D20IFNa4

description: Donor 20_IFNa4

value: Donor 20


title: WT-ND-CD20-BR1

description:
WT-ND-CD20
157MH11_DGE_Matrix.txt
AGGGGC


title: D20IFNa2

description: Donor 20_IFNa2


title: plasma, subject 130b19cdT1

value: No


title: WT-ND-CD19-BR4

description:
WT-ND-CD19
157MH11_DGE_Matrix.txt
CACCAA


title: WT-ND-CD19-BR3

description:
WT-ND-CD19
157MH11_DGE_Matrix.txt
TCATAT


title: D20IFNa1

description: Donor 20_IFNa1


title: plasma, subject 12eac067T1


title: patient p009 on d0 untreated, ltbi

description:
TTCTTCG_p009_d0_0bcg_ltbi
p009_d0_0bcg_ltbi

value: patient p009

value: Cytoplasmic RNA

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


title: patient p065 on d0 untreated, ltbi

description:
GTCTGAT_p065_d0_0bcg_ltbi
p065_d0_0bcg_ltbi

value: patient p065


title: plasma, subject 12c04870T4

value: Female

value: Positive


title: D20Mock

description: Donor 20_Mock


title: WT-ND-CD19-BR2

description:
WT-ND-CD19
157MH11_DGE_Matrix.txt
CTTTAA

value: small intestine

value: B cells

value: normal


title: D20IFNa8

description: Donor 20_IFNa8

value: PBMC


title: D15IFNb

description: Donor 15_IFNb

value: Donor 15


title: WT-ND-CD20-BR2

description:
WT-ND-CD20
157MH11_DGE_Matrix.txt
CGCTGC

value: wildtype


title: patient p049 on d0 untreated, ltbi

description:
ACTGTCG_p049_d0_0bcg_ltbi
p049_d0_0bcg_ltbi

value: patient p049

value: d0 untreated, ltbi


title: plasma, subject 128d09dcT8

value: Male

value: Yes

value: Somascan discovery platform v4


title: D15IFNa14

description: Donor 15_IFNa14


title: patient p067 on d0 untreated, ltbi

description:
TAGGTAA_p067_d0_0bcg_ltbi
p067_d0_0bcg_ltbi

value: Peripheral Blood

value: patient p067


title: WT-CDHFD-CD20-BR3

description:
WT-CDHFD-CD20
157MH11_DGE_Matrix.txt
GCGCTG

value: choline-deficient high-fat


title: plasma, subject 12c04870T1

value: No


title: WT-CDHFD-CD20-BR4

description:
WT-CDHFD-CD20
157MH11_DGE_Matrix.txt
TCGGGC


title: patient p025 on d0 untreated, ltbi

description:
CGCCGTA_p025_d0_0bcg_ltbi
p025_d0_0bcg_ltbi

value: patient p025

value: Cytoplasmic RNA

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


title: plasma, subject 128639afT1

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

value: Positive


title: D15IFNa8

description: Donor 15_IFNa8


title: patient p061 on d0 untreated, ltbi

description:
TCCGGGA_p061_d0_0bcg_ltbi
p061_d0_0bcg_ltbi

value: patient p061


title: D15IFNa5

description: Donor 15_IFNa5

value: PBMC


title: patient p060 on d0 untreated, ltbi

description:
ACTCCAA_p060_d0_0bcg_ltbi
p060_d0_0bcg_ltbi

value: patient p060


title: WT-CDHFD-CD20-BR1

description:
WT-CDHFD-CD20
157MH11_DGE_Matrix.txt
CACGGC

value: small intestine

value: B cells

value: wildtype


title: D15IFNa4

description: Donor 15_IFNa4

value: Donor 15


title: plasma, subject 1228d709T8

value: Male

value: Yes


title: patient p042 on d0 untreated, ltbi

description:
ACTGGAT_p042_d0_0bcg_ltbi
p042_d0_0bcg_ltbi

value: Peripheral Blood

value: patient p042

value: d0 untreated, ltbi


title: WT-ND-CD19-BR1

description:
WT-ND-CD19
157MH11_DGE_Matrix.txt
AGATTA

value: normal


title: WT-CDHFD-CD19-BR4

description:
WT-CDHFD-CD19
157MH11_DGE_Matrix.txt
CCACAT

value: choline-deficient high-fat


title: plasma, subject 1228d709T4

value: No

value: Somascan discovery platform v4


title: patient p047 on d0 untreated, ltbi

description:
GCCGTTT_p047_d0_0bcg_ltbi
p047_d0_0bcg_ltbi

value: patient p047

value: Cytoplasmic RNA

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


title: plasma, subject 1228d709T1

value: Positive


title: D15IFNa2

description: Donor 15_IFNa2

value: PBMC


title: D15IFNa1

description: Donor 15_IFNa1


title: patient 02BAL006, mtb_infected_in_vitro, po_group

description:
02BAL006_mtb_infected_po
CACTGTG-GAACCGT_02BAL006_mtb_infected_po

source_name: Bronchoalveolar Lavage (BAL) fluid

growth_protocol: Bronchoscopy with BAL was performed by instillation and recovery of up to eight 30 mL aliquots of saline. Following centrifugation, cell pellets were combined, counted and aliquoted.

extract_protocol:
Cell pellets were flash-frozen and stored at -80 for eventual RNA extraction.
RiboZero v1

treatment_protocol: Frozen stocks of virulent Mtb strain H37Rv (#NR-123, BEI resources, Manassas VA) were thawed, cleared of bacterial clumps, and suspended in infecting medium. BAL cells were cultured with H37Rv (3:1 MOI) or medium alone and incubated at 37degC for twenty-four hours.

value: Bronchoalveolar Lavage (BAL) fluid

value: patient 02BAL006

tag: group


title: plasma, subject 128d09dcT1


title: patient 02BAL004, mtb_infected_in_vitro, po_group

description:
02BAL004_mtb_infected_po
CGGATAC-TCTTTGG_02BAL004_mtb_infected_po

value: patient 02BAL004


title: plasma, subject 11dc6956T1

value: Female


title: patient 02BAL005, mtb_infected_in_vitro, po_group

description:
02BAL005_mtb_infected_po
TTGAGTG-AGGTAGG_02BAL005_mtb_infected_po

value: patient 02BAL005


title: WT-CDHFD-CD19-BR2

description:
WT-CDHFD-CD19
157MH11_DGE_Matrix.txt
GATAAT

value: small intestine

value: B cells

value: wildtype


title: WT-CDHFD-CD19-BR3

description:
WT-CDHFD-CD19
157MH11_DGE_Matrix.txt
TCTTAA


title: WT-CDHFD-CD20-BR2

description:
WT-CDHFD-CD20
157MH11_DGE_Matrix.txt
CGGCCA


title: plasma, subject 1147dbe5T1

value: Yes


title: D15Mock

description: Donor 15_Mock

tag: subject

value: Donor 15


title: D10IFNb

description: Donor 10_IFNb

value: Donor 10


title: patient 02BAL007, mtb_infected_in_vitro, po_group

description:
02BAL007_mtb_infected_po
ATCGTCA-ACTCCTA_02BAL007_mtb_infected_po

tag: subject id

value: patient 02BAL007


title: WT-CDHFD-CD19-BR1

description:
WT-CDHFD-CD19
157MH11_DGE_Matrix.txt
ATAAAC

value: choline-deficient high-fat


title: D10IFNa14

description: Donor 10_IFNa14


title: plasma, subject 112e879cT4

value: Somascan discovery platform v4


title: uMT-CDHFD-CD20-BR4

description:
MT-CDHFD-CD20
157MH11_DGE_Matrix.txt
CTAGTG

value: uMT-KO


title: patient 02BAL008, mtb_infected_in_vitro, id_group

description:
02BAL008_mtb_infected_id
CACAGCA-GCTCCTC_02BAL008_mtb_infected_id

value: patient 02BAL008

tag: treatment

value: Cytoplasmic RNA


title: uMT-CDHFD-CD20-BR3

description:
MT-CDHFD-CD20
157MH11_DGE_Matrix.txt
TGATTT


title: plasma, subject 112d83e0T1

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

value: Male

value: Negative

value: No


title: D10IFNa8

description: Donor 10_IFNa8

value: PBMC


title: uMT-CDHFD-CD20-BR2

description:
MT-CDHFD-CD20
157MH11_DGE_Matrix.txt
GTAATA


title: plasma, subject 11244d58T21

value: Positive


title: patient 02BAL009, mtb_infected_in_vitro, id_po_group

description:
02BAL009_mtb_infected_id_po
CAGTTGT-GCAATAT_02BAL009_mtb_infected_id_po

value: Bronchoalveolar Lavage (BAL) fluid

value: patient 02BAL009


title: D10IFNa5

description: Donor 10_IFNa5


title: patient 02BAL010, mtb_infected_in_vitro, id_group

description:
02BAL010_mtb_infected_id
AAACGAC-GGACCGA_02BAL010_mtb_infected_id

value: patient 02BAL010


title: uMT-CDHFD-CD20-BR1

description:
MT-CDHFD-CD20
157MH11_DGE_Matrix.txt
ATACAA

value: small intestine

value: B cells


title: plasma, subject 11244d58T20

value: Yes


title: D10IFNa4

description: Donor 10_IFNa4

value: Donor 10


title: patient 02BAL011, mtb_infected_in_vitro, po_group

description:
02BAL011_mtb_infected_po
CCTCAAG-GTGCTCT_02BAL011_mtb_infected_po

value: patient 02BAL011


title: Pancreas tumor: Hot_5 [S5]

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.
Genome_build: MM10
Supplementary_files_format_and_content: Tab delimited file contains TPM values of all samples.

source_name: Pancreas tumor

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

value: Pancreas tumor

tag: diagnosis

value: Pancreatic ductal adenocarcinoma

tag: tumor subtype

value: T cell-rich ("hot")


title: plasma, subject 0f8becc0T4

tag: blood sample id

value: Somascan discovery platform v4


title: D10IFNa1

description: Donor 10_IFNa1


title: plasma, subject 11244d58T1

value: Male


title: Pancreas tumor: Hot_6 [S6]

description: RNA isolated from tumor

tag: tissue


title: Pancreas tumor: Hot_3 [S3]

description: RNA isolated from tumor


title: patient 02BAL012, mtb_infected_in_vitro, id_po_group

description:
02BAL012_mtb_infected_id_po
GTCCCTT-CTGAGCG_02BAL012_mtb_infected_id_po

value: patient 02BAL012

tag: molecule

value: Cytoplasmic RNA


title: plasma, subject 0f8becc0T1

tag: Sex

tag: age

value: No


title: D3IFNb

description: Donor 3_IFNb

value: PBMC

value: Donor 3


title: patient 02BAL013, mtb_infected_in_vitro, id_group

description:
02BAL013_mtb_infected_id
ATACTTC-GCTTCCT_02BAL013_mtb_infected_id

value: Bronchoalveolar Lavage (BAL) fluid

value: patient 02BAL013


title: D10IFNa2

description: Donor 10_IFNa2


title: Pancreas tumor: Hot_2 [S2]

description: RNA isolated from tumor


title: patient 02BAL015, mtb_infected_in_vitro, id_group

description:
02BAL015_mtb_infected_id
GATAAGG-GTGCGAG_02BAL015_mtb_infected_id

value: patient 02BAL015


title: D10Mock

description: Donor 10_Mock


title: Pancreas tumor: Hot_4 [S4]

description: RNA isolated from tumor


title: plasma, subject 0f06b495T1

value: Positive


title: D3IFNa14

description: Donor 3_IFNa14


title: plasma, subject 0e81d28bT1

value: Female

value: Negative

value: Yes


title: patient 02BAL016, mtb_infected_in_vitro, id_group

description:
02BAL016_mtb_infected_id
AATGGTA-AGTGCAA_02BAL016_mtb_infected_id

value: patient 02BAL016


title: Pancreas tumor: Hot_1 [S1]

description: RNA isolated from tumor

value: Pancreas tumor

value: Pancreatic ductal adenocarcinoma


title: plasma, subject 0e17de76T1

value: Somascan discovery platform v4


title: patient 02BAL017, mtb_infected_in_vitro, po_group

description:
02BAL017_mtb_infected_po
GATGTGA-GGTCCAC_02BAL017_mtb_infected_po

value: patient 02BAL017


title: Pancreas tumor: Cold_6 [S12]

description: RNA isolated from tumor

value: T cell-poor ("cold")


title: D3IFNa8

description: Donor 3_IFNa8


title: Pancreas tumor: Cold_5 [S11]

description: RNA isolated from tumor


title: D3IFNa5

description: Donor 3_IFNa5


title: plasma, subject 0d28c031T1


title: D3IFNa4

description: Donor 3_IFNa4


title: patient 02BAL014, mtb_infected_in_vitro, id_group

description:
02BAL014_mtb_infected_id
TCAGCAC-ATGGAAC_02BAL014_mtb_infected_id

value: patient 02BAL014

value: Cytoplasmic RNA


title: patient 02BAL018, mtb_infected_in_vitro, id_group

description:
02BAL018_mtb_infected_id
AAGAAGT-CAAATGG_02BAL018_mtb_infected_id

value: patient 02BAL018


title: plasma, subject 0d273be0T21

value: Male

value: No


title: Pancreas tumor: Cold_4 [S10]

description: RNA isolated from tumor


title: D3IFNa2

description: Donor 3_IFNa2

value: PBMC

value: Donor 3


title: patient 02BAL001, mtb_infected_in_vitro, id_group

description:
02BAL001_mtb_infected_id
AGTCTAG-AGTAAGA_02BAL001_mtb_infected_id

value: Bronchoalveolar Lavage (BAL) fluid

value: patient 02BAL001


title: plasma, subject 0d273be0T12

value: Positive


title: plasma, subject 0d273be0T1

value: Yes


title: patient P079, mtb_infected_in_vitro, ltbi_group

description:
P079_mtb_infected_ltbi
GACTTGC-TGAGTCC_P079_mtb_infected_ltbi

value: patient P079


title: Pancreas tumor: Cold_2 [S8]

description: RNA isolated from tumor

value: Pancreas tumor


title: D3Mock

description: Donor 3_Mock


title: Pancreas tumor: Cold_3 [S9]

description: RNA isolated from tumor

value: Pancreatic ductal adenocarcinoma


title: Pancreas tumor: Cold_1 [S7]

description: RNA isolated from tumor


title: patient N175, mtb_infected_in_vitro, control_group

description:
N175_mtb_infected_control
GGACATT-TAGGTCG_N175_mtb_infected_control

value: patient N175


title: patient N162, mtb_infected_in_vitro, control_group

description:
N162_mtb_infected_control
CTCCTAG-CGTATTA_N162_mtb_infected_control

value: patient N162


title: plasma, subject 0d11bebaT1

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

value: Somascan discovery platform v4


title: RNA_tcf21_sham_12

city: Oxford

first: Paul

middle: Richard

last: Riley

address: IMS-Tetsuya Nakamura Building, Old Road Campus

country: United Kingdom

institute: University of Oxford

description:
poly-adenylated RNA
RNA_seq_tcf21_larval_vs_adult_count_table.txt

data_processing:
ATAC-seq: Sequencing reads were mapped to the zebrafish reference genome (GRCz10-91) using the bowtie aligner (v1.2.3). Duplicate reads were removed with samtools (v1.10). BAM files were converted to BED format and peaks were called using MACS (v2.2.7.1, callpeak -B -f BED -g 1.37e09 --call-summits). The Homer (v20201202) script “annotatePeaks.pl” was used to annotate peaks to the closest expressed gene in each condition and to genomic features, to do TSS enrichment analysis and to compute CpG and GC content. For this, fasta and gtf files for GRCz10 were obtained from the UCSC Genome Browser website. The R package  DiffBind (v3.0.13) was then used to construct a consensus peak set across all samples, removing peaks contained in less than two samples and peaks overlapping repetitive elements in the genome, and resizing all peak widths to 500bp. Peak names were assigned based on genomic position as “P.[chromosome].[start position]”. Peak accessibility FPKM values were computed manually.
RNA-seq: Transcriptomic data was mapped to the zebrafish reference genome (GRCz10-91) using the STAR (v2.7.3a) gapped aligner. Duplicate reads were removed with samtools (v1.10) and reads were summarized using featureCounts. Counts were transformed into FPKM expression values with the rpkm() command in the edgeR package (v3.32.1).
Genome_build: GRCz10-91
Supplementary_files_format_and_content: Tab separated text files, ATAC_seq_tcf21_larval_vs_adult_count_table.txt includes raw ATAC-seq counts ("raw" column names) and FPKM values ("fpkm" column names) summarized on peak level. ATAC_seq_tcf21_larval_vs_adult_peak_annotation.txt contains gene annotation (to all genes in the GRCz10 gtf file or only those expressed in the condition indicated in the column name), CpG and GC content of each peak. RNA_seq_tcf21_larval_vs_adult_count_table.txt contains raw gene expression counts.

molecule: polyA RNA

organism: Danio rerio

extract_protocol: Clontech SMART-SeqTm v4 UltraTm Low Input RNA Kit for Sequencing + Illumina Nextera XT

tag: developmental stage

value: Adult

value: 3 days post sham

tag: transgenic reporter

tag: cell purification

value: Nuclear pulldown


title: plasma, subject 0c02dbf2T1

value: Female

tag: days since first sample

tag: patient classification at first sample

tag: covid-19 status


title: patient P054, mtb_infected_in_vitro, ltbi_group

description:
P054_mtb_infected_ltbi
AGCTTAT-GTGTAAG_P054_mtb_infected_ltbi

value: patient P054

tag: group

value: Cytoplasmic RNA


title: RNA_tcf21_sham_4


title: patient P077, mtb_infected_in_vitro, ltbi_group

description:
P077_mtb_infected_ltbi
GCGTTCA-TTAAGGG_P077_mtb_infected_ltbi

value: patient P077


title: NC 3

city: Jinan, Shandong

first: Wenyan

last: Kang

address: No. 44-1 Wenhua Road West

institute: Shandong university

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
Genome_build: hg38

growth_protocol: Cells were cultured with 6-well plates at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA was isolated, evaluated the quality, reverse-transcribed to cDNA,
The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat.1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: Cells were treated  with BSArGO@ZIF8 NSs at a multiplicity of infection (MOI) of F. nucleatum : cell =10:1, and culured at 3d, 7d, 14d and 21d

tag: cell line

tag: cell type

value: Human oral cell line

tag: donor

value: purchased from ATCC

tag: culture time

value: negative control


title: RNA_tcf21_cryo_9

tag: treatment

value: 3 days post cryoinjury


title: plasma, subject 0b4c8b59T8

tag: subject id

tag: blood sample id

value: Male

value: Positive

value: Yes

tag: instrument model


title: patient N091, mtb_infected_in_vitro, control_group

description:
N091_mtb_infected_control
CGGGCTT-TTTCGCT_N091_mtb_infected_control

tag: tissue

value: Bronchoalveolar Lavage (BAL) fluid

value: patient N091

tag: molecule


title: plasma, subject 0d273be0T13

tag: Sex

tag: age

value: Somascan discovery platform v4


title: patient N173, mtb_infected_in_vitro, control_group

description:
N173_mtb_infected_control
ATGAGCC-TTTGCTT_N173_mtb_infected_control

value: patient N173


title: plasma, subject 0b4c8b59T4

value: No


title: D3IFNa1

description: Donor 3_IFNa1

value: PBMC

tag: subject

value: Donor 3


title: NC 2


title: plasma, subject 0d273be0T20

tag: days since first sample


title: RNA_tcf21_cryo_8

tag: developmental stage

value: Adult

tag: transgenic reporter

tag: cell purification

value: Nuclear pulldown


title: patient P080, mtb_infected_in_vitro, ltbi_group

description:
P080_mtb_infected_ltbi
CTGCGCA-CAACGTG_P080_mtb_infected_ltbi

value: patient P080

tag: group

value: Cytoplasmic RNA


title: Treat_3

tag: cell line

tag: cell type

value: Human oral cell line

value: purchased from ATCC

value: BSArGO@ZIF-8 NSs


title: plasma, subject 0b4c8b59T1

value: Male

tag: patient classification at first sample

tag: covid-19 status


title: RNA_tcf21_cryo_7

tag: treatment

value: 3 days post cryoinjury


title: patient P061, mtb_infected_in_vitro, ltbi_group

description:
P061_mtb_infected_ltbi
CTTATCG-CATCGGC_P061_mtb_infected_ltbi

tag: subject id

value: patient P061


title: NC 1

tag: donor

tag: culture time

value: negative control


title: RNA_tcf21_larval_3

value: Larval 5 days post fertilization

value: FACS


title: RNA_tcf21_larval_2


title: Treat_2


title: patient P060, mtb_infected_in_vitro, ltbi_group

description:
P060_mtb_infected_ltbi
GCAGACT-GAATACT_P060_mtb_infected_ltbi

tag: tissue

value: Bronchoalveolar Lavage (BAL) fluid

value: patient P060

tag: molecule


title: plasma, subject 0ae9858bT1

tag: blood sample id

tag: Sex

tag: age

value: Positive

value: Yes

tag: instrument model

value: Somascan discovery platform v4


title: Pulsatilla Chinensis rep3

city: beijing

first: ruijun

last: wang

address: college of life science

institute: Tsinghua university

data_processing:
Demultiplexing and basecalling performed using CASAVA version 1.8.2
QC was performed on the FASTQ files using FastQC(v0.11.5) software.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens(GRCh38) whole genome using HISAT2(v2.1.0).
Sequence reads aligned to the human genome were imported into StringTie(v1.3.3b) for sequence read counting.
Sequence reads mapped to different isoforms of individual genes were pooled together, and then were input into the DESeq2(v1.28.0) differential expression analysis program to normalize and determine expression levels and differentially expressed genes.
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for each gene per sample

source_name: Pulsatilla Chinensis treated

extract_protocol:
Total RNA extracted using Trizol following manufacturer's instructions，Illumina TruSeq RNA Sample was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hepatocellular carcinoma cell line

tag: sample type

value: experimental group

value: 125ng/mL of PC  for 24 h


title: Treat_1

value: Human oral cell line


title: Pulsatilla Chinensis rep2


title: plasma, subject 0a2680d2T8

tag: days since first sample

value: No


title: patient N171, mtb_infected_in_vitro, control_group

description:
N171_mtb_infected_control
TTATGAG-TGGAGTG_N171_mtb_infected_control

value: patient N171

tag: group

value: Cytoplasmic RNA


title: RNA_tcf21_larval_1

tag: developmental stage

tag: transgenic reporter

tag: cell purification


title: Pulsatilla Chinensis rep1

tag: cell line

tag: cell type


title: patient 02BAL004, uninfected_in_vitro, po_group

description:
02BAL004_mediarested_po
ATTAGGA-TAGAGGT_02BAL004_mediarested_po

tag: subject id

value: patient 02BAL004

tag: treatment


title: RNA_tcf21_control_3


title: plasma, subject 0a2680d2T4

value: Male

tag: patient classification at first sample

tag: covid-19 status


title: patient 02BAL006, uninfected_in_vitro, po_group

description:
02BAL006_mediarested_po
ATACCCG-CTCTCGT_02BAL006_mediarested_po

tag: tissue

value: patient 02BAL006

tag: molecule


title: DMSO rep3

source_name: DMSO treated

value: control group

value: DMSO for 24 h


title: DMSO rep2


title: RNA_tcf21_control_2

value: Larval 5 days post fertilization

value: FACS


title: patient 02BAL005, uninfected_in_vitro, po_group

description:
02BAL005_mediarested_po
GTGATTT-TGGTGAC_02BAL005_mediarested_po

value: Bronchoalveolar Lavage (BAL) fluid

value: patient 02BAL005


title: RNA_tcf21_control_1


title: DMSO rep1


title: plasma, subject 0a2680d2T1

tag: blood sample id

tag: Sex

value: Positive

value: Yes

value: Somascan discovery platform v4


title: plasma, subject 0835f624T1

value: Female

tag: age

tag: instrument model


title: plasma, subject 0a7ea79eT1

tag: days since first sample

value: Negative


title: plasma, subject 0a2680d2T12


title: ATAC-tcf21-sham-2

description:
Tn5 accessible genomic DNA
ATAC_seq_tcf21_larval_vs_adult_count_table.txt, ATAC_seq_tcf21_larval_vs_adult_peak_annotation.txt

extract_protocol: Tn5 tagmentation + PCR amplification (Nextera XT adapters)

value: Adult

value: 3 days post sham


title: plasma, subject 089e98eaT1

value: No


title: patient 02BAL007, uninfected_in_vitro, po_group

description:
02BAL007_mediarested_po
GAATGGT-CCGAATT_02BAL007_mediarested_po

value: patient 02BAL007

tag: group

value: Cytoplasmic RNA


title: ATAC-tcf21-sham-1

tag: developmental stage


title: plasma, subject 06f24a67T8


title: patient 02BAL009, uninfected_in_vitro, id_po_group

description:
02BAL009_mediarested_id_po
GTTTACC-GTTTAGT_02BAL009_mediarested_id_po

value: patient 02BAL009


title: patient 02BAL011, uninfected_in_vitro, po_group

description:
02BAL011_mediarested_po
CCTTGAC-GGCGATT_02BAL011_mediarested_po

value: patient 02BAL011


title: ATAC-tcf21-cryo-4

value: 3 days post cryoinjury

tag: transgenic reporter


title: patient 02BAL010, uninfected_in_vitro, id_group

description:
02BAL010_mediarested_id
GTGTAGT-ATCCTGG_02BAL010_mediarested_id

value: patient 02BAL010


title: HDM_5_T0706P4

city: Guangzhou

first: Maojin

last: Yao

state: Guangdong

address: No.195, West Dongfeng Road, Yuexiu District

department: Guangzhou Institute of Respiratory Health

institute: Guangzhou Medical University

data_processing:
Construction of Illumina PE library
Initial quality assessment of sequencing reads using FastQC
Quality cutting and statistics of sequencing data
Compare with reference genome using TopHat (http://tophat.cbcb.umd.edu/ )
Gene coverage analysis using RSeQC-2.3.2（http://code.google.com/p/rseqc/）
Genome_build: hg38
Supplementary_files_format_and_content: txt file includes TPM values for each sample and each gene.

source_name: liver

extract_protocol:
RNA Extraction: Trizol method
RNA libraries were prepared for sequencing using standard Illumina protocol

value: paracarcinomatous liver tissue

value: Patient-derived organoids

tag: disease state

value: Hyperuricemia (HUA) model

tag: medium

value: DM

tag: passage


title: HDM_5_T0706P6

tag: cell type


title: HEM_5_T0706P8

value: EM


title: plasma, subject 06f24a67T4

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

tag: subject id

value: Positive

value: Yes

value: Somascan discovery platform v4


title: ATAC-tcf21-cryo-2

value: Adult

tag: treatment

tag: cell purification

value: FACS


title: HDM_5_T0706P8

tag: tissue


title: ATAC-tcf21-cryo-1


title: patient 02BAL012, uninfected_in_vitro, id_po_group

description:
02BAL012_mediarested_id_po
CACATAT-AAGATCC_02BAL012_mediarested_id_po

value: Bronchoalveolar Lavage (BAL) fluid

value: patient 02BAL012

tag: molecule


title: HEM_5_T0706P6


title: plasma, subject 06f24a67T21

tag: blood sample id

value: Female

tag: patient classification at first sample

tag: covid-19 status

value: No


title: plasma, subject 06f24a67T20

tag: Sex

tag: age

tag: instrument model


title: HEM_5_T0706P4


title: patient 02BAL008, uninfected_in_vitro, id_group

description:
02BAL008_mediarested_id
CACCAGG-AAGCCTT_02BAL008_mediarested_id

value: patient 02BAL008

tag: group

value: Cytoplasmic RNA


title: ATAC-tcf21-cryo-3

tag: developmental stage

value: 3 days post cryoinjury

tag: transgenic reporter


title: ATAC-tcf21-larval-1

value: Larval 5 days post fertilization


title: ATAC-tcf21-larval-2


title: patient 02BAL014, uninfected_in_vitro, id_group

description:
02BAL014_mediarested_id
AGCTCGC-GGTAGTA_02BAL014_mediarested_id

value: patient 02BAL014


title: patient 02BAL013, uninfected_in_vitro, id_group

description:
02BAL013_mediarested_id
CTAACTT-CTTCATT_02BAL013_mediarested_id

value: patient 02BAL013


title: plasma, subject 06f24a67T12

tag: days since first sample


title: plasma, subject 06f24a67T13


title: plasma, subject 06f24a67T1


title: ATAC-tcf21-control-2


title: patient 02BAL016, uninfected_in_vitro, id_group

description:
02BAL016_mediarested_id
TCTGCTT-ATGGCAT_02BAL016_mediarested_id

value: patient 02BAL016


title: patient 02BAL015, uninfected_in_vitro, id_group

description:
02BAL015_mediarested_id
GACAACC-TAGTAGA_02BAL015_mediarested_id

value: patient 02BAL015


title: plasma, subject 06cabf6cT1

value: Male

value: Positive


title: ATAC-tcf21-control-1


title: ATAC-tbx18-larval-2


title: plasma, subject 06cabf6cT8

value: Yes

value: Somascan discovery platform v4


title: plasma, subject 0631e306T20


title: ATAC-tbx18-larval-1

value: FACS


title: ATAC-tbx18-control-2


title: patient N091, uninfected_in_vitro, control_group

description:
N091_mediarested_control
ATCCAAA-TCGCAGA_N091_mediarested_control

value: Bronchoalveolar Lavage (BAL) fluid

value: patient N091


title: plasma, subject 0631e306T1


title: patient 02BAL017, uninfected_in_vitro, po_group

description:
02BAL017_mediarested_po
CGTACAA-AGTTCGG_02BAL017_mediarested_po

value: patient 02BAL017


title: pureGX_10

type: RNA

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description:
US11263921_257403611528_S01_GE2_1200_Jun14_1_1.txt
Gene expression from the colon mucosa of a female rat fed a diet containing hihgly purified GX (10% w/w)
PAm41

hyb_protocol: Labeled cRNA samples were hybridised onto the Agilent 2-colour 8x60k arrays according to the manufacturer's recommendations and hybridized for 17 hours at 65°C. After hybridization, slides were washed following the manufacturer's instructions (Agilent).

scan_protocol: Slides were scanned with Agilent microarray scanner G2505C and data were extracted using the Agilent Feature Extraction software (V12.0.2.2.)

data_processing: Raw intensity values were obtained from Agilent Feature Extraction software and quality checked according to Agilent standard procedures. The median foreground intensities were imported into R software and data were log2 transformed and normalized with quantile normalization. This experiment was performed as a two-colour experiment, but data were analyzed as single-channel arrays. Raw data files are available as a tar archive on the series record.

organism: Rattus norvegicus

source_name: Colon mucosa of a rat fed a diet containging pureGX, replicate 10

label_protocol: Samples (200 ng) were amplified using the T7 RNA polymerase method. cRNAs were labelled with Cy3 or Cy5 following the manufacturer's protocol (Agilent).

growth_protocol: The animal study protocol was approved by the Finnish National Animal Experiment Board (Eläinkoelautakunta, ELLA; permit code: ESAVI/12806/2019), and the research was carried out according to ARRIVE guidelines.

extract_protocol: For RNA extraction, the mucosa of colon mid-segment (2cm) was collected using a microscope slide and stored in RNALater for 24 hours at +4°C, after which it was transferred to -20°C. Total RNA was extracted with TRIzol Plus RNA Purification Kit (12183555, Invitrogen) according to manufactures instructions. Samples with RIN values > 8 were used for the analysis.

treatment_protocol: The four-weeks-old female and male Wistar (RccHan: WIST) rats purchased from Envigo Netherlands (Horst, The Netherlands) were fed pelleted, modified AIN-93G diets (Envigo Teklad Diets, Madison WI, The United States) containing either 10% (w/w) of cellulose (control group), 10% of polyphenol-and GX-rich extract (GXpoly), or 10% of highly purified GX (pureGX) after 12 days of acclimatization.

tag: strain

value: Wistar

value: female

tag: date

value: purified glucuronoxylan

tag: sample type

value: pureGX

tag: tissue type

value: mucosa of colon mid-segment

tag: cage

tag: slide

tag: slide position

tag: rin


title: pureGX_11

description:
US11263921_257403611528_S01_GE2_1200_Jun14_2_4.txt
Gene expression from the colon mucosa of a female rat fed a diet containing hihgly purified GX (10% w/w)
PAm42

source_name: Colon mucosa of a rat fed a diet containging pureGX, replicate 11

tag: treatment


title: pureGX_9

description:
US11263921_257403611527_S01_GE2_1200_Jun14_1_1.txt
Gene expression from the colon mucosa of a female rat fed a diet containing hihgly purified GX (10% w/w)
PAm38

source_name: Colon mucosa of a rat fed a diet containging pureGX, replicate 9


title: patient P079, uninfected_in_vitro, ltbi_group

description:
P079_mediarested_ltbi
GGCCTAC-ATAGGAC_P079_mediarested_ltbi

tag: tissue

tag: subject id

value: patient P079

tag: molecule

value: Cytoplasmic RNA


title: control_11

description:
US11263921_257403611527_S01_GE2_1200_Jun14_2_1.txt
Gene expression from the colon mucosa of a female rat fed a control diet (10% w/w cellulose)
PAm39

source_name: Colon mucosa of a rat fed a control diet, replicate 11

tag: Sex

value: cellulose

value: control


title: GXpoly_10

description:
US11263921_257403611528_S01_GE2_1200_Jun14_1_3.txt
Gene expression from the colon mucosa of a female rat fed a diet containing polyphenol-and GX-rich extract (10% w/w)
PAm37

source_name: Colon mucosa of a rat fed a diet containging GXpoly, replicate 10

value: extract rich in polyphenol and glucoronoxylan

value: GXpoly

tag: group


title: KYSE150_ctl

city: Dalian

first: Wang

last: Yang

address: 9 Lvshun South Rd West Section, Lüshunkou District, Dalian, Liaoning, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

description: sample :RBM4 knockdown ctrl

data_processing:
Raw data(raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
The mapped reads of each sample were assembled by both Scripture (beta2) (Guttman et al. 2010) and Cufflinks (v2.1.1) (Trapnell et al. 2010) in a reference-based approach. Both methods use spliced reads to determine exons connectivity, but with two different approaches. Scripture uses a statistical segmentation model to distinguish expressed loci from experimental noise and uses spliced reads to assemble expressed segments. It reports all statistically expressed isoforms in a given locus. Cufflinks uses a probabilistic model to simultaneously assemble and quantify the expression level of a minimal set of isoforms that provides a maximum likelihood explanation of the expression data in a given locus (Cabili et al. 2011). Scripture was run with default parameters, Cufflinks was run with ‘min-frags-per-transfrag=0’ and ‘--library-type’, other parameters were set as default.
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Cuffdiff provides statistical routines for determining differential expression in digital transcript or gene expression data using a model based on the negative binomial distribution (Trapnell, C. et al. 2010). Transcripts with an P-adjust <0.05 were assigned as differentially expressed.
Genome_build: human NCBI genome build 38
Supplementary_files_format_and_content: The gene expressiong matrix from RNA-seq

source_name: esophageal cancer cells

growth_protocol: KYSE150 cells were cultured in 1640 medium containing 10% FBS and growed in the 5% carbon dioxide environment.

extract_protocol:
RNA samples were extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We generated RBM4 knockdown sample in KYSE150 esophageal cancer cells

tag: cell type

value: human esophageal cancer cells


title: ATAC-tbx18-control-1

description:
Tn5 accessible genomic DNA
ATAC_seq_tcf21_larval_vs_adult_count_table.txt, ATAC_seq_tcf21_larval_vs_adult_peak_annotation.txt

tag: developmental stage

value: Larval 5 days post fertilization

tag: transgenic reporter

tag: cell purification


title: plasma, subject 06319f12T4

tag: blood sample id

value: Female

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 02BAL001, uninfected_in_vitro, id_group

description:
02BAL001_mediarested_id
TGAAGGC-TGATACA_02BAL001_mediarested_id

value: Bronchoalveolar Lavage (BAL) fluid

value: patient 02BAL001


title: patient N162, uninfected_in_vitro, control_group

description:
N162_mediarested_control
TAAGTGC-CAGCCCA_N162_mediarested_control

value: patient N162


title: plasma, subject 06319f12T1

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

value: No


title: KYSE150_shRBM4

description: sample :RBM4 knockdown

value: RBM4 knocked down


title: plasma, subject 05fd9717T4


title: pureGX_8

description:
US11263921_257403611527_S01_GE2_1200_Jun14_2_4.txt
Gene expression from the colon mucosa of a female rat fed a diet containing hihgly purified GX (10% w/w)
PAm35

source_name: Colon mucosa of a rat fed a diet containging pureGX, replicate 8

tag: strain

value: Wistar

value: female

tag: date

value: purified glucuronoxylan

tag: sample type

value: pureGX

tag: tissue type

value: mucosa of colon mid-segment

tag: cage

tag: slide

tag: slide position

tag: rin


title: N2

city: Jinan

first: Wei

last: Li

state: Shandong

address: Wenhuaxi Road NO.44

institute: Shandong University

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM

source_name: Paracancerous tissue

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
rRNA was removed using Epicentre Ribo-Zero™ Gold Kits (Epicentre, USA).
Libraries were generated following manufacturer recommendations with varied index label by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, USA).

tag: tissue

value: lung

tag: disease state

value: Paracancerous tissue


title: patient 02BAL018, uninfected_in_vitro, id_group

description:
02BAL018_mediarested_id
GCTATAG-CCACAGG_02BAL018_mediarested_id

tag: subject id

value: patient 02BAL018

tag: treatment

tag: group

tag: molecule

value: Cytoplasmic RNA


title: pureGX_7

description:
US11263921_257403611527_S01_GE2_1200_Jun14_2_3.txt
Gene expression from the colon mucosa of a female rat fed a diet containing hihgly purified GX (10% w/w)
PAm33

source_name: Colon mucosa of a rat fed a diet containging pureGX, replicate 7

tag: Sex


title: control_10

description:
US11263921_257403611528_S01_GE2_1200_Jun14_1_2.txt
Gene expression from the colon mucosa of a female rat fed a control diet (10% w/w cellulose)
PAm36

source_name: Colon mucosa of a rat fed a control diet, replicate 10

value: cellulose

value: control


title: plasma, subject 05f57419T1

source_name: serum

tag: blood sample id

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: patient N175, uninfected_in_vitro, control_group

description:
N175_mediarested_control
CCACTCG-TGGTTCC_N175_mediarested_control

value: Bronchoalveolar Lavage (BAL) fluid

value: patient N175


title: patient P054, uninfected_in_vitro, ltbi_group

description:
P054_mediarested_ltbi
CGGTTTG-GGAGAGT_P054_mediarested_ltbi

value: patient P054


title: N4


title: plasma, subject 056d5843T4

value: No

tag: instrument model


title: N3


title: GXpoly_9

description:
US11263921_257403611527_S01_GE2_1200_Jun14_2_2.txt
Gene expression from the colon mucosa of a female rat fed a diet containing polyphenol-and GX-rich extract (10% w/w)
PAm32

source_name: Colon mucosa of a rat fed a diet containging GXpoly, replicate 9

tag: strain

value: Wistar

value: female

tag: date

value: extract rich in polyphenol and glucoronoxylan

tag: sample type

value: GXpoly

tag: tissue type

tag: cage


title: N1

tag: tissue

value: lung

tag: disease state

value: Paracancerous tissue


title: plasma, subject 056d5843T1

tag: subject id


title: plasma, subject 056d5843T8


title: GXpoly_8

description:
US11263921_257403611527_S01_GE2_1200_Jun14_1_3.txt
Gene expression from the colon mucosa of a female rat fed a diet containing polyphenol-and GX-rich extract (10% w/w)
PAm31

source_name: Colon mucosa of a rat fed a diet containging GXpoly, replicate 8

tag: treatment

value: mucosa of colon mid-segment

tag: slide

tag: slide position

tag: rin

tag: group


title: patient P077, uninfected_in_vitro, ltbi_group

description:
P077_mediarested_ltbi
TCCACGT-CGCTGGA_P077_mediarested_ltbi

source_name: Bronchoalveolar Lavage (BAL) fluid

value: patient P077

tag: molecule

value: Cytoplasmic RNA


title: patient N173, uninfected_in_vitro, control_group

description:
N173_mediarested_control
TAAACGA-ACGACTT_N173_mediarested_control

value: patient N173


title: patient P060, uninfected_in_vitro, ltbi_group

description:
P060_mediarested_ltbi
TTATAGC-GACAGCA_P060_mediarested_ltbi

value: patient P060


title: patient N171, uninfected_in_vitro, control_group

description:
N171_mediarested_control
CTAATGC-CTGGATG_N171_mediarested_control

value: patient N171


title: patient P080, uninfected_in_vitro, ltbi_group

description:
P080_mediarested_ltbi
CTCGGGT-GTAACCT_P080_mediarested_ltbi

value: patient P080


title: plasma, subject 04a0e89fT4

tag: blood sample id

tag: Sex

value: Male

tag: age

tag: days since first sample

tag: patient classification at first sample

value: Positive

value: Yes

value: Somascan discovery platform v4


title: plasma, subject 04d69a1aT1

tag: covid-19 status

tag: instrument model


title: plasma, subject 0424041dT4

value: No


title: T1

source_name: Lung adenocarcinoma tissue

value: Lung adenocarcinoma


title: T4


title: patient P061, uninfected_in_vitro, ltbi_group

description:
P061_mediarested_ltbi
TAGCTCG-GGCTGCT_P061_mediarested_ltbi

value: Bronchoalveolar Lavage (BAL) fluid

value: patient P061


title: Mbl_day3_3_180711_L2_S3

city: Waltham

first: Sebastian

last: Kadener

state: MA

address: 415 South Street

department: Biology department

institute: Brandeis University

data_processing:
Data was aligned using STAR to Drosophila melanogaster genome version dm6
Counting number of reads for each gene at the 3' end using ESAT tool (Derr A. et al 2016)
Genome_build: dm6
Supplementary_files_format_and_content: normalized read counts

organism: Drosophila melanogaster

extract_protocol:
Brains were disected in cold PBS. Total RNA was extracted using Trizol reagent (Sigma) and treated with DNase I (NEB) following the manufacturer's protocol.
Cell-seq2 library preparation was done as in Hashimshony et al 2016, adapted for bulk RNA.

tag: strain

value: Actin-GAL4 UAS-sh-circMbl

value: brain


title: GXpoly_7

description:
US11263921_257403611528_S01_GE2_1200_Jun14_1_4.txt
Gene expression from the colon mucosa of a female rat fed a diet containing polyphenol-and GX-rich extract (10% w/w)
PAm29

source_name: Colon mucosa of a rat fed a diet containging GXpoly, replicate 7

value: Wistar

value: female

tag: date

value: extract rich in polyphenol and glucoronoxylan

tag: sample type

value: GXpoly

tag: tissue type

value: mucosa of colon mid-segment

tag: cage


title: control_9

description:
US11263921_257403611528_S01_GE2_1200_Jun14_2_1.txt
Gene expression from the colon mucosa of a female rat fed a control diet (10% w/w cellulose)
PAm27

source_name: Colon mucosa of a rat fed a control diet, replicate 9

tag: treatment

value: cellulose

value: control

tag: slide


title: plasma, subject 04a0e89fT8

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

tag: subject id

value: Male


title: GXpoly_6

description:
US11263921_257403611527_S01_GE2_1200_Jun14_1_4.txt
Gene expression from the colon mucosa of a female rat fed a diet containing polyphenol-and GX-rich extract (10% w/w)
PAm28

source_name: Colon mucosa of a rat fed a diet containging GXpoly, replicate 6

tag: slide position

tag: rin

tag: group


title: T3

tag: tissue

value: lung

tag: disease state


title: control_8

description:
US11263921_257403611528_S01_GE2_1200_Jun14_2_3.txt
Gene expression from the colon mucosa of a female rat fed a control diet (10% w/w cellulose)
PAm26

source_name: Colon mucosa of a rat fed a control diet, replicate 8

tag: Sex


title: control_7

description:
US11263921_257403611527_S01_GE2_1200_Jun14_1_2.txt
Gene expression from the colon mucosa of a female rat fed a control diet (10% w/w cellulose)
PAm24

source_name: Colon mucosa of a rat fed a control diet, replicate 7


title: pureGX_5

description:
US11263921_257403611528_S01_GE2_1200_Jun14_1_2.txt
Gene expression from the colon mucosa of a male rat fed a diet containing hihgly purified GX (10% w/w)
PAm20

source_name: Colon mucosa of a rat fed a diet containging pureGX, replicate 5

value: male

value: purified glucuronoxylan

value: pureGX


title: Mbl_day3_2_180711_L2_S2


title: T2

value: Lung adenocarcinoma


title: DS Thyroid_2

city: Hangzhou

first: Yao

last: Chen

state: Zhejiang

address: 866 Yuhangtang Rd

department: School of Medicine

institute: Zhejiang University

description: Microwell-seq analysis

data_processing:
Data were aligned to the Homo sapiens GRCh38 genome using STAR 2.5.2a
The DGE data matrices were obtained using the Dropseq Core Computational Protocol  with default parameters
Downstream standard procedures for filtering, variable gene selection, dimensionality reduction and clustering were performed using the Seurat 2.4.3 in R3.5.0
Cellphonedb was to used to make ligand-receptor analysis
GRN analysis were performed using the CellRouter in R3.5.0
Genome_build: Homo sapiens GRCh38
Supplementary_files_format_and_content: digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

source_name: DS Thyroid

growth_protocol: untached tissues

extract_protocol:
Cold lysis buffer (0.1 M Tris-HCl pH 7.5, 0.5 M LiCl, 1% SDS, 10 mM EDTA, and 5 mM dithiothreitol) was pipetted over the surface of the plate and removed after 12 min of incubation. The beads were then collected. After reverse transcription, exonuclease I treatment and cDNA amplification, the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) was used with 1 ug of total RNA for the construction of sequencing libraries.
Library preparations were performed with the Microwell-seq protocol

treatment_protocol: Donated tissues were transported on ice, transferred to cold DPBS, and minced into ~1-mm pieces on ice using scissors. The samples were treated with various enzymes for different amounts of time.

tag: source id

value: embryo 5

tag: karyotype

value: trisomy 21

tag: age

value: 21 weeks

value: Thyroid


title: Mbl8MM_day3_3_181105_L7_S6

tag: strain

value: Actin-GAL4 UAS-sh8MM

value: brain


title: pureGX_6

description:
US11263921_257403611528_S01_GE2_1200_Jun14_2_2.txt
Gene expression from the colon mucosa of a female rat fed a diet containing hihgly purified GX (10% w/w)
PAm22

source_name: Colon mucosa of a rat fed a diet containging pureGX, replicate 6

value: Wistar

value: female

tag: date


title: DS Muscle_2

description: Microwell-seq analysis

source_name: DS Muscle

value: Muscle


title: plasma, subject 03ca6bb0T4

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: blood sample id

value: Female

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: plasma, subject 041fe111T20

tag: subject id


title: DS Thyroid_1

description: Microwell-seq analysis


title: plasma, subject 03ca6bb0T1


title: plasma, subject 041fe111T1


title: plasma, subject 03ca6bb0T8


title: control_6

description:
US11263921_257403611528_S01_GE2_1200_Jun14_1_4.txt
Gene expression from the colon mucosa of a male rat fed a control diet (10% w/w cellulose)
PAm19

source_name: Colon mucosa of a rat fed a control diet, replicate 6

value: male

tag: treatment

value: cellulose

tag: sample type

value: control

tag: tissue type

value: mucosa of colon mid-segment

tag: cage

tag: slide

tag: slide position


title: Mbl8MM_day3_2_181105_L7_S5

tag: tissue


title: mixed_cells

city: Seattle

first: John

middle: K.

last: Lee

state: Washington

address: 1100 Fairview Ave N Rm E2-430

institute: Fred Hutch Cancer Research Ctr

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

organism:
Homo sapiens
Mus musculus

source_name: 3T3 cells/HEK 293T cells

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

tag: cell line

value: 3T3 cells/HEK 293T cells

tag: cell type

value: mouse fibroblast cells/human kidey cells

tag: phenotype

value: mixed


title: control_5

description:
US11263921_257403611527_S01_GE2_1200_Jun14_1_4.txt
Gene expression from the colon mucosa of a male rat fed a control diet (10% w/w cellulose)
PAm15

source_name: Colon mucosa of a rat fed a control diet, replicate 5

tag: strain

tag: Sex

tag: date

tag: rin

tag: group


title: GXpoly_5

description:
US11263921_257403611528_S01_GE2_1200_Jun14_2_1.txt
Gene expression from the colon mucosa of a male rat fed a diet containing polyphenol-and GX-rich extract (10% w/w)
PAm18

source_name: Colon mucosa of a rat fed a diet containging GXpoly, replicate 5

value: extract rich in polyphenol and glucoronoxylan

value: GXpoly


title: DS Intestine

description: Microwell-seq analysis

source_name: DS Intestine

tag: source id

value: embryo 4

tag: karyotype

value: trisomy 21

tag: age

value: 20 weeks

value: Intestine


title: DS Male Gonad

description: Microwell-seq analysis

source_name: DS Male Gonad

value: Gonad


title: DS Lung

description: Microwell-seq analysis

source_name: DS Lung

value: Lung


title: control_4

description:
US11263921_257403611527_S01_GE2_1200_Jun14_2_3.txt
Gene expression from the colon mucosa of a male rat fed a control diet (10% w/w cellulose)
PAm14

source_name: Colon mucosa of a rat fed a control diet, replicate 4

value: Wistar

tag: treatment

tag: sample type


title: DS Muscle_1

description: Microwell-seq analysis

value: embryo 5

value: 21 weeks

value: Muscle


title: plasma, subject 03564ed9T1

source_name: serum

tag: subject id

tag: blood sample id

value: Female

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: GXpoly_4

description:
US11263921_257403611527_S01_GE2_1200_Jun14_1_1.txt
Gene expression from the colon mucosa of a male rat fed a diet containing polyphenol-and GX-rich extract (10% w/w)
PAm16

source_name: Colon mucosa of a rat fed a diet containging GXpoly, replicate 4

value: male

value: extract rich in polyphenol and glucoronoxylan

tag: tissue type

value: mucosa of colon mid-segment

tag: cage

tag: slide

tag: slide position


title: Mbl8MM_day3_2_181105_L5_S26

tag: strain

value: Actin-GAL4 UAS-sh8MM

tag: tissue

value: brain


title: plasma, subject 03564ed9T4

tag: Sex


title: Stimuli 2 Replicate 2

city: Delhi

first: Naveen

last: Arora

address: Mallroad

country: India

institute: IGIB

description: Biological replicate 2 of 2

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA™ microRNA Array 7th Gen

scan_protocol: Scanned on  Agilent G2565BA Microarray Scanner System The image analysis was carried out using the ImaGene 9.0 software

data_processing:
The quantified signals were background corrected  (Normexp with offset value 10, see Ritchie et al. 2007) and normalized using quantile normalization method, which we have found produces the best between-slide normalization to minimize the intensity-dependent differences between the samples
log2transformed normalized median intensity values (Hy3)

source_name: Lung tissue

label_protocol: 750 ng total RNA from sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™.

growth_protocol: Mice were exposed to diesel exhaust for 5 days a week for 8 weeks. Euro tier 2 (Stimuli-2), Euro tier 4 (Stimuli-1)

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: gender

value: Male


title: Normal Muscle_1

description: Microwell-seq analysis

source_name: Normal Muscle

tag: source id

value: embryo 3

tag: karyotype

value: diploidy

tag: age

value: 19 weeks


title: Mbl8MM_day3_3_181105_L5_S27


title: Stimuli 2 Replicate 1

description: Biological replicate 1 of 2


title: Normal Lung_2

description: Microwell-seq analysis

source_name: Normal Lung

value: embryo 2

value: 22 weeks

value: Lung


title: Mbl8MM_day3_1_181105_L7_S4


title: GXpoly_3

description:
US11263921_257403611527_S01_GE2_1200_Jun14_1_2.txt
Gene expression from the colon mucosa of a male rat fed a diet containing polyphenol-and GX-rich extract (10% w/w)
PAm13

source_name: Colon mucosa of a rat fed a diet containging GXpoly, replicate 3

value: Wistar

tag: date

tag: treatment

tag: sample type

value: GXpoly

tag: rin

tag: group


title: plasma, subject 02da55faT8

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: subject id

tag: blood sample id

tag: days since first sample

tag: patient classification at first sample

tag: covid-19 status

value: Positive

value: No

tag: instrument model


title: pureGX_4

description:
US11263921_257403611528_S01_GE2_1200_Jun14_1_3.txt
Gene expression from the colon mucosa of a male rat fed a diet containing hihgly purified GX (10% w/w)
PAm12

source_name: Colon mucosa of a rat fed a diet containging pureGX, replicate 4

tag: strain

value: purified glucuronoxylan

value: pureGX

tag: tissue type

tag: cage

tag: slide

tag: slide position


title: Control Replicate 2

description: Biological replicate 2 of 2

tag: gender


title: control_3

description:
US11263921_257403611527_S01_GE2_1200_Jun14_1_3.txt
Gene expression from the colon mucosa of a male rat fed a control diet (10% w/w cellulose)
PAm9

source_name: Colon mucosa of a rat fed a control diet, replicate 3

tag: Sex

value: male

tag: date

value: cellulose

value: control


title: pureGX_2

description:
US11263921_257403611527_S01_GE2_1200_Jun14_2_1.txt
Gene expression from the colon mucosa of a male rat fed a diet containing hihgly purified GX (10% w/w)
PAm5

source_name: Colon mucosa of a rat fed a diet containging pureGX, replicate 2

tag: treatment

tag: sample type

value: mucosa of colon mid-segment


title: Normal Thyroid_2

description: Microwell-seq analysis

source_name: Normal Thyroid

tag: source id

value: embryo 1

tag: karyotype

tag: age

value: 20 weeks

tag: tissue

value: Thyroid


title: pureGX_3

description:
US11263921_257403611527_S01_GE2_1200_Jun14_2_2.txt
Gene expression from the colon mucosa of a male rat fed a diet containing hihgly purified GX (10% w/w)
PAm10

source_name: Colon mucosa of a rat fed a diet containging pureGX, replicate 3

tag: rin

tag: group


title: plasma, subject 030a3354T8

tag: subject id

tag: blood sample id

value: Female

tag: days since first sample

tag: patient classification at first sample

tag: covid-19 status

value: Yes

tag: instrument model

value: Somascan discovery platform v4


title: GXpoly_2

description:
US11263921_257403611528_S01_GE2_1200_Jun14_2_4.txt
Gene expression from the colon mucosa of a male rat fed a diet containing polyphenol-and GX-rich extract (10% w/w)
PAm4

source_name: Colon mucosa of a rat fed a diet containging GXpoly, replicate 2

tag: strain

value: extract rich in polyphenol and glucoronoxylan

tag: tissue type

tag: cage

tag: slide

tag: slide position


title: Normal Intestine_2

description: Microwell-seq analysis

source_name: Normal Intestine

tag: source id

value: diploidy

value: Intestine


title: pureGX_1

description:
US11263921_257403611528_S01_GE2_1200_Jun14_2_3.txt
Gene expression from the colon mucosa of a male rat fed a diet containing hihgly purified GX (10% w/w)
PAm3

source_name: Colon mucosa of a rat fed a diet containging pureGX, replicate 1

value: Wistar

tag: Sex

tag: date

tag: treatment

tag: sample type


title: Normal Intestine_1

description: Microwell-seq analysis

tag: karyotype

tag: age

tag: tissue


title: plasma, subject 030a3354T12

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

tag: subject id

tag: blood sample id

tag: days since first sample

value: Positive


title: control_2

description:
US11263921_257403611528_S01_GE2_1200_Jun14_2_2.txt
Gene expression from the colon mucosa of a male rat fed a control diet (10% w/w cellulose)
PAm8

source_name: Colon mucosa of a rat fed a control diet, replicate 2

tag: rin

tag: group


title: Stimuli 1 Replicate 2

description: Biological replicate 2 of 2

tag: strain

tag: gender

value: Male


title: plasma, subject 0223e0e5T1

tag: patient classification at first sample

tag: covid-19 status

value: Negative

value: No

tag: instrument model


title: 10X_scf_bleo_4w

city: Daejeon

first: Myung Jin

country: South Korea

institute: Institute for Basic Science

library_source: transcriptomic single cell

data_processing:
Cell Ranger (v3.0.0) was used to process single cell 3' RNA-seq ouput. First, cell ranger mkfastq demultiplexed illumina BCLs into fastq files.
Then, using cell ranger count, reads were aligned to mm10 mouse reference genome.
Aligned reads were then read by Seurat (v4.0.4) and cell-gene raw expression matrices were made. Then, low quality cells (expressing less than 800 genes), potential doublets (expressing more than 6000 genes),potential dead cells (>10% mitochondrial gene percentage) and contaminating CD31- cells were removed. Also, genes that are only expressed in less than 3 cells were discarded.
Expression matrices were made after quality control. Matrices were log normalized and variables such as number of UMIs and mitochondrial gene percentage were regressed out and scaled with Seurat to produce processed data files.
Dimensionality reduction, clustering and differential expression testing were performed using R package Seurat
Assembly: mm10
Supplementary files format and content: Cell-gene expression matrix of log normalized UMI counts for ECs following bleomycin administration (bleo_2w & bleo4w) or pneumonectomy (pnx_1w & pnx_4w) in WT(tdT mouse) or Kitl deleted mouse

source_name: scf-deleted Bleomycin 4 weeks lung EC

extract_protocol:
FACS sorted lung tdTomato+ cells and endothelial cells were processed on the 10X chromium system following the manufacturer's protocols
Using 10x single cell RNA sequencing 3' NEXT GEM v3.1 reagent Kit (10X genomics), cDNA libraries were constructed

treatment_protocol: Mice were pre-treated with tamoxifen to induced tdTomato expression in Apln expressing cells

tag: cell sorting

value: FACS sorted

tag: cell type

value: lung EC

tag: developmental stage

value: Adult

tag: genotype

value: scf-deleted

value: Bleomycin 4 weeks


title: 10X_scf_bleo_2w

source_name: scf-deleted Bleomycin 2 weeks lung EC

growth_protocol: 10x single cell RNA sequencing 3' NEXT GEM v3.1

tag: treatment

value: Bleomycin 2 weeks


title: A549 xenografts exposed to 15mg/kg dacomitinib,  replicate 1, scRNAseq

first: Yu

last: Yangziwei

state: Shanghai

address: 上海市浦东新区周祝公路279号

description: BD Rhapsody

data_processing:
Raw sequencing reads of the cDNA library were processed through the BD Rhapsody Whole Transcriptome Assay Analysis Pipeline.
Assembly: hg18,mm9
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung cancer

extract_protocol:
Mice were obtained from JiHui Laboratory Technology Co., Ltd. (China). All experimental protocols were approved by Shanghai University of Medicine and Health Sciences and mice were treated and sacrificed in accordance with the institutional guidelines for animal care. All mice were housed in a Specific Pathogen Free (SFP) environment at a suitable temperature (23±2 °C) and humidity (60±5 %) with a 12-h day/night cycle. 5 × 106 A549 cells were subcutaneously injected into the ventral flank of female nude mice (4 to 6 weeks old). After a few weeks，the tumors reached higher than 150 mm3 in volume calculated from the formula V = (length × width2)/2 using calipers, according to the report previously described(10). Mice were randomized into three groups gavaged through oral with vehicle (1% w/v CMC-Na, dissolved in sterile water), 7.5 mg/kg dacomitinib and 15 mg/kg dacomitinib, respectively. Mice were weighted and tumor sizes were measured every two or three days.
Single Cell preparation, library construction, sequencing and preliminary analysis were performed by Sinotech Genomics Co., Ltd. Shanghai, China. Each specimen was washed extensively in HyClone™ RPMI 1640 media, weighed, and enzymatically digested in 10 ml RPMI 1640 media supplemented with Collagenase type I (0.2 mg/mL，A004194, sangon, Shanghai, China), Collagenase type IV (0.2 mg/mL, A004186, sangon), Neutral Protease (0.1 mg/mL, A002100, sangon) and DNase I (0.01 mg/mL, B300065, sangon) for 1.5 h at 37°C with agitation. The mixture was strained consecutively through 70 μm and 40 μm cell strainers, washed twice in PBS, and centrifuged at 400 g for 5 minutes. After quenching digestion with excess RPMI-1640 medium, filtered single cell solutions were kept on ice until they were loaded into the BD Rhapsody system (BD, San Jose, CA) for single cell transcriptome isolation.   The final library was generated using microbead-captured single cell transcriptome as the manufacturer’s protocol. The final cDNA library was generated from double strand full length cDNA by random priming amplification with the BD Rhapsody cDNA Kit (633773, BD Biosciences) and the BD Rhapsody Targeted mRNA & AbSeq Amplification Kit (633774, BD Biosciences). All the libraries were sequenced in a PE150 mode (Pair-End for 150bp read) in the X Ten instrument (Illumina, San Diego, CA).

value: lung cancer

tag: age

value: 4-6 weeks old


title: plasma, subject 030a3354T1

city: New York

first: Pushkala

last: Jayaraman

institute: Icahn School of Medicine at Mount Sinai

source_name: serum

tag: Sex

value: Female

value: Yes

value: Somascan discovery platform v4


title: plasma, subject 030a3354T4

tag: subject id


title: Stimuli 1 Replicate 1

description: Biological replicate 1 of 2

source_name: Lung tissue


title: Normal Thyroid_1

description: Microwell-seq analysis

tag: source id

value: embryo 1

tag: karyotype

value: diploidy

value: 20 weeks

tag: tissue

value: Thyroid


title: A549 xenografts, replicate 1, scRNAseq

city: Shanghai

address: 上海市浦东新区周祝公路279号

institute: Shanghai University of Medicine and Health Science

description: BD Rhapsody


title: 10X_tdT_pnx_4w

source_name: Pneumonectomy 4 weeks lung EC

value: control

value: Pneumonectomy 4


title: A549 cells, replicate 1, scRNAseq

address: 上海市浦东新区周祝公路279号

description: BD Rhapsody


title: plasma, subject 02da55faT4

tag: blood sample id

value: Male

tag: days since first sample

value: Positive

value: No


title: 10X_tdT_pnx_1w

source_name: Pneumonectomy 2 weeks lung EC

tag: strain

value: FACS sorted

value: lung EC

value: Adult

value: Pneumonectomy 2 weeks


title: plasma, subject 0184426fT4

tag: patient classification at first sample

value: Negative


title: Normal Muscle_2

description: Microwell-seq analysis

source_name: Normal Muscle

value: embryo 3

value: 19 weeks

value: Muscle


title: Control Replicate 1

description: Biological replicate 1 of 2

tag: gender


title: 10X_tdT_bleo_4w

source_name: Bleomycin 4 weeks lung EC

value: Bleomycin 4 weeks


title: zmuvr8-1_White+NUVB_2

city: Shenzhen

first: Zhao

last: Zhiwei

address: 1066, Xueyuan Rd

department: College of Life Sciences and Oceanography

institute: Shenzhen univerisity

data_processing:
Illumina software used for basecalling.
Sequenced reads were processed using Trimmomatic(Version0.36), The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2(Version2.2.1.0).
Then quantified read counts per gene and normalized Fragments Per Kilobase exon per Million reads mapped (FPKM) values using Cufflinks TopHat（version:2.2.1）
FPKM and read counts valueof each transcript (protein_coding) was calculated using bowtie2 and eXpress. DEGs were identified using the DESeq(Version1.18.0)(2012) functions estimateSizeFactors and nbinomTest.
Assembly: B73_RefGen_v4_gramene_63
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Zea mays

source_name: leaf

growth_protocol: 7 days of B73 and zmuvr8-1 seedlings  grown in low white light

extract_protocol:
total RNA was isolated using RNAiso Plus kit (Takara Bio, Shiga, Japan)
The RNA library generation process followed the manufacturer’s protocol for the Illumina TruseqTM RNA sample prep Kit

treatment_protocol: treat with or without UVB treatment 1 hour

value: leaf

value: 7 DAY OLD

value: zmuvr8-1 mutant

value: 1 hour NUVB


title: zmuvr8-1_White+NUVB_3


title: Normal Male Gonad

description: Microwell-seq analysis

source_name: Normal Male Gonad

value: embryo 1

value: diploidy

value: 20 weeks

value: Gonad


title: GXpoly_1

description:
US11263921_257403611527_S01_GE2_1200_Jun14_2_4.txt
Gene expression from the colon mucosa of a male rat fed a diet containing polyphenol-and GX-rich extract (10% w/w)
PAm2

source_name: Colon mucosa of a rat fed a diet containging GXpoly, replicate 1

value: Wistar

value: male

tag: date

value: extract rich in polyphenol and glucoronoxylan

tag: sample type

value: GXpoly

tag: tissue type

value: mucosa of colon mid-segment

tag: cage

tag: slide

tag: slide position

tag: rin

tag: group


title: plasma, subject 02da55faT1

tag: subject id

tag: Sex

value: Male

tag: age

tag: covid-19 status

value: Positive

value: No

value: Yes

tag: instrument model

value: Somascan discovery platform v4


title: zmuvr8-1_White+NUVB_1

tag: tissue

value: leaf

tag: developmental stage

value: 7 DAY OLD

tag: genotype

tag: treatment


title: plasma, subject 01c05642T20

tag: blood sample id

tag: days since first sample

tag: patient classification at first sample


title: plasma, subject 028f3d47T1


title: 10X_scf_pnx_4w

source_name: scf-deleted Pneumonectomy 4 weeks lung EC

tag: strain

tag: cell sorting

value: FACS sorted

tag: cell type

value: lung EC

value: Adult

value: scf-deleted

value: Pneumonectomy 4


title: 10X_scf_pnx_1w

source_name: scf-deleted Pneumonectomy 2 weeks lung EC

value: Pneumonectomy 2 weeks


title: plasma, subject 005cd7b9T12