title: mouse_Organoid_12

data_processing:
Quality filtering of sequencing data were performed using cutadapt v2.1.0. Filtered reads were mapped to GRCm38 Refseq RNA using Bowtie2-2.4.2 with the following parameters: -p 2 -L 16 --very-sensitive-local -N 1 -nofw -seed 656565 -reorder. Tag numbers of each gene were quantified as the expression level of each gene.
Between-sample normalization was performed against raw count data using Microsoft R open 3.5.1 (https://cran.r-project.org/) and TCC package (EEE-E method). Genes for which adjusted P < 0.05, fold change ≥ 2, and maximum expression ≥ 100 were identified as statistically significant differentially expressed genes.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw tag-count values for each sample

extract_protocol:
Lungs were minced into 0.5 mm^2 with a razor blade and digested with Collagenase solution [RPMI-1640 (Nacalai Tesque) supplemented with 10% FBS (MP Bio Japan), 10 mM HEPES pH7.2-7.4 (Cytiva (Global Life Sciences Technologies Japan)), 0.2% Collagenase (Fujifilm Wako Pure Chemicals), 2 kU/mL DNase I (Merck)] , and 0.96 mg/mL Dispase (Roche) at 37 ºC for 50 minutes. Cell suspensions were washed and resuspended with 25% Percoll PLUS (Cytiva). After under layered 65% Percoll PLUS, cell suspensions were centrifuged at 20ºC for 1,000 ×g for 20 minutes, and the middle layer was collected. Resultant cell suspensions were washed and resuspended with 1000 μL of preparation medium [RPMI-1640 supplemented with 5% FBS and 10 mM HEPES]. Each single-cell suspension cell concentration was counted using Flow-count fluorospheres (Beckman Coulter) and a Cytoflex flow cytometer (Beckman Coulter).
Transcriptome libraries were prepared on cell lysate resolved in lysis buffer. PolyA RNAs were isolated using Dynabeads M-270 Streptavidin (Thermo Fisher Scientific) conjugated with biotin-3’ WTA-EcoP-dT25 according to the previous report with some modifications (GSE110711). To perform reverse transcription, beads were then suspended in 10 μL of RT mix [5× Superscript IV buffer (Thermo Fisher Scientific), 1 mM dNTP (Roche), 5 mM DTT (Thermo Fisher Scientific), 1 M betaine (Sigma), 6 mM MgCl2, 1 U/μL RNaseIn Plus Rnase Inhibitor (Promega), 10 U/μL Superscript IV (Thermo Fisher Scientific)], and incubated for 5 min at 35ºC, 30 min at 42ºC, and immediately cooled on ice. Beads were washed once with B&W-T buffer [5 mM Tris-HCl (pH 8.0) (Nippon Gene), 1 M NaCl (Merck), 1 mM EDTA (Nippon Gene) and 0.05% Tween-20 (Merck)], and once with Tris-HCl (pH 8.0). To digest free-primer, beads were then suspended in 10 μL of Exo I mix [10× Exo I buffer (New England Biolabs), 2 U/μL Exonuclease I (New England Biolabs)], and incubated for 30 min at 37ºC and immediately cooled on ice. Beads were washed twice with B&W-T buffer, and once with Tris-HCl (pH 8.0). To add polyC tail, beads were then suspended in 10 μL of polyC tailing mix [10× Thermopol buffer (New England Biolabs), 2 mM dCTP (Roche), 0.1 mM ddCTP (GE Healthcare), 1 mM CoCl2 (Roche), RNaseH (Invitrogen), 15 U/ul TdT enzyme (Roche)], and incubated for 30 min at 37ºC and immediately cooled on ice. Beads were washed once with B&W-T buffer, and once with Tris-HCl (pH 8.0). To synthesis 2nd strand, beads were then suspended in 10 μL of 2nd strand mix [1x KAPA Hifi Hotstart ReadyMix (KAPA Biosystems), 0.4 μM of primer (illumina-i7-9G)], and the thermal cycling was performed as following condition: for 3 min at 95°C, 20 sec at 98°C, 16 cycles of 1 min at 47°C and 2 min at 72°C, followed by 5 min at 72°C, and hold at 4°C. To amplify the total cDNA, 10 μL of beads containing cDNA was added with 15 μL of first PCR mix [0.32 μM of primer (illumina-i7), 0.48 μM of primer (NH2-3’ WTA), and 1x KAPA Hifi Hotstart ReadyMix], and the thermal cycling was performed as following condition: for 3 min at 95°C, 12 cycles of 20 sec at 98°C, 15 sec at 65°C, and 5 min at 72°C, followed by 5 min at 72°C, and hold at 4°C. The first PCR products were purified by AmPure XP beads (Beckman-Coulter) at a 0.6:1 ratio of reagents to sample and eluted with 25 μL of nuclease-free water. 6.3uL of purified first PCR product was mixed with the 8.7 μL of second PCR mix [0.4 μM of primers (illumina-i7, NH2-3’ WTA), and 1× KAPA Hifi Hotstart ReadyMix], and the thermal cycling was performed as following condition: for 3 min at 95°C, 5 cycles of 20 sec at 98°C, 15 sec at 65°C, and 5 min at 72°C, followed by 5 min at 72°C, and hold at 4°C. The second PCR products were purified by AmPure XP beads at a 0.6:1 ratio of reagent to sample and eluted with 15 μL of 10 mM Tris-HCl (pH 8.0). 100 ng of the whole-transcriptome library was subjected to fragmentation/end-repair/A-tailing using NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs) with some modifications. The thermal cycling was performed as following condition: for 7 min at 32ºC, 30 min at 65ºC, and hold at 4ºC. Then, 1.25 μL of 1.5 μM illumine adapter was used for adapter ligation. Ligated products were purified by double size selection with 0.4× → 0.7× (final 1.1×) AmPure XP beads and eluted with 10 μL of nuclease-free water. The barcoding PCR was performed with 22.5 uL of barcoding mix [7.5 μL of the resulted eluates, 1 μM primers (ILMN_[UDI]_i5 and ILMN_[UDI]_i7), and 1× NEBNext Ultra II Q5 (New England Biolabs)], and the thermal cycling was performed as following condition: for 30 sec at 98°C, 9 cycles of 10 sec at 98°C and 75 sec at 65°C, followed by 5 min at 65°C, and hold at 4°C. Resultant products were purified twice by double size selection with 0.5× → 0.8 × (final 1.3×) AmPure XP beads and eluted with 12 μL of 10 mM Tris-HCl pH8.0. Size distribution of amplified products was analyzed by MultiNA system (Shimazu) with appropriate dilutions. Final transcriptome libraries, whose lengths were around 300 base pairs, were quantified using the KAPA Library Quantification Kit (KAPA Biosystems). Pooled libraries were sequenced by Illumina Novaseq 6000 sequencer (Illumina).

treatment_protocol: Alveolopheres were stimulated with variant concentration of  bleomycin started with 0, 0.01, 0.1, and 1.0 ug/ml Bleomycin for 48 hours from day 8 post co-culture.

value: C57BL/6 and C57BL/6-Tg

value: WT and CAG-EGFP

value: Bleomycin 0.01 ug/ml


title: NaraCOVID_TP3_CD4_041_TCR

status: Public on Apr 01 2024

type: SRA

city: Noda

first: Hiroyasu

last: Aoki

state: Chiba

address: 2669 Yamazaki

department: Research Institute for Biomedical Sciences

country: Japan

institute: Tokyo University of Science

library_source: transcriptomic

data_processing:
Data processing of Bulk TCRseq was performed as described in Aoki et al. (Aoki et al., 2021).
Adapter trimming and quality filtering of sequencing data were performed using Cutadapt-3.2 and PRINSEQ-0.20.4. Sequencing data were processed by MiXCR-3.0.5. In MiXCR, filtered reads were aligned to reference mouse TCR V/D/J sequences registered in the international ImMunoGeneTics (IMGT) information system. The Variable (V) and Joining (J) segments of TCRs were represented in IMGT gene nomenclature. T-cell clones were determined as TCR reads with the same TCR V segment, J segment, and CDR3 nucleotide sequence.
Inter-sample contamination within samples using same UDIs were excluded by "Decontaminate" function of vdjtools with the parameter "-r 10".
For bulk TCRseq data, we regarded the CD4+-CD8+ overlapping clones in the same participant as contamination during T-cell isolation from PBMC because CD4+ and CD8+ T-cell repertoire are mutually exclusive (Aoki 2021). Thus, these overlapping clones were categorized into either CD4+ or CD8+ according to their dominance in CD4+ and CD8+ repertoire using VDJtools-1.2.1. The sequencing reads of bulk TCR-seq samples were normalized to 100,000 reads by the ?DownSample? command of VDJtools-1.2.1. To preserve the minor clonotypes, we performed the normalization ten times and pooled these down-sampled repertoire data for each sample, by ?JoinSamples? command of VDJtools-1.2.1.
Assembly: IMGT reference sequences of human TRA and TRB
Supplementary files format and content: Text files in VDJtools format include read count and frequency, complementarity determining region 3 (CDR3) nucleotide and amino acid sequences, Variable(V)/ Diversity(D)/ Joining(J) segment names, and V, D and J segment boundaries within CDR3 nucleotide sequence of individual clones

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood T cells

extract_protocol:
PBMCs were isolated from whole blood with BD vacutainer CPT tubes (BD), resuspended in CELLBANKER 1 (Takara), and stored in -80°C
CD4+ and CD8+ T cells were magnetically isolated from PBMC. PBMC were thawed by warming frozen cryovials in a 37°C water bath. Cells were stained for 20 minutes at 4°C with 1st antibody mix (Antibody Mix 1 in Supplementary Table S1). After washing with MACS buffer [0.5% BSA (Nacalai), 2 mmol/L EDTA (NIPPON GENE) in PBS (Nacalai)], Cells were stained for 20 minutes at 4°C with 2nd antibody mix; BD IMag anti-PE Magnetic Particles-DM (Clone E31-1459, BD) and anti-APC-Biotin (clone APC003, BioLegend). Then, the cell suspension was diluted with MACS buffer and set on a magnet plate (DynaMag96SideSkirted, Veritas). The positive fraction was collected as CD4+ T cells. The negative fraction was stained with BD IMag Streptavidin Particles Plus-DM (BD) for 20 minutes at 4°C. Then, the cell suspension was diluted with MACS buffer and set on a magnet plate. The positive fraction was collected as CD8+ T cells and B cells. The counts of CD4+ T cells, CD8+ T cells, and B cells were determined using Flow-Count fluorospheres (Beckman) and a Cytoflex flow cytometer (Beckman) and FlowJo software (version 10.8.1; BD Biosciences).
Bulk TCR sequencing library was prepared according to the previous report (Aoki et al., 2023).  In brief, mRNA in T-cell lysates were captured by incubating with 10 ?L of Dynabeads M270 streptavidin (Thermo Fisher Scientific) bound to 2.5 pmol of BioEcoP-dT25-adapter primers for 30 minutes at room temperature under gentle rotation. mRNA-trapped beads were suspended in 10 µL of RT mix and incubated for 60 min at 42ºC to perform reverse transcription (RT) and template-switching. The composition of the RT mix was as follows; 1× First Strand buffer (Thermo Fisher Scientific), 1 mM dNTP (Roche), 2.5 mM DTT (Thermo Fisher Scientific), 1 M betaine (Sigma-Aldrich), 9 mM MgCl2 (NIPPON GENE), 1 U/µL RNaseIn Plus RNase Inhibitor (Promega), 10 U/µL Superscript II (Thermo Fisher Scientific), and 1 µM of i5-TSO. To amplify the TCR cDNA containing complementarity determining region 3 (CDR3), nested PCR of the TCR locus was performed using KAPA Hifi Hotstart ReadyMix (KAPA Biosystems), followed by the purification of PCR product using an AM Pure XP kit (Beckman Coulter) at a 0.7:1 beads-to-sample ratio. The third PCR was performed to amplify TCR libraries and add adaptor sequences for the next-generation sequencer. The third-PCR products were purified as second PCR. Final TCR libraries, whose lengths were about 600 base pairs, were quantified using a KAPA SYBR Fast qPCR Kit (KAPA Biosystems), and size distribution was analyzed by Microchip Electrophoresis System MultiNA (Shimadzu). TCR libraries were sequenced using an Illumina Novaseq 6000 S4 flowcell (67 bp read 1 and 140 bp read 2) (Illumina) using NovaSeq 6000 S4 Reagent Kit v1.5 (200 cycles, Illumina). Only read2 contained the sequence regarding the definition of T-cell clones. Oligonucleotides and reaction conditions for library preparation were summarized in Table S2 and S3, respectively.

treatment_protocol: Thirty-eight healthcare workers (≥20 years old) at Nara Medical University in Japan received two doses of Pfizer-BNT162b2 vaccine between 10 March and 30 March 2021.

tag: treatment

value: Three shots of Pfizer-BNT162b2 vaccine

tag: cell type

value: CD4+ T cells

tag: age

tag: Sex

value: male

tag: date

value: 1 week after receiving the second dose


title: VUMC0125

type: RNA

city: Nashville

first: Cong

last: Wang

state: TN

address: 2525 West End Ave

country: USA

institute: Vanderbilt University

hyb_protocol: NanoString nCounter miRNA Expression Assay manufacturer's protocol

data_processing: miRNAs were normalized in the following steps: 1) background correction to remove non-specific binding. The background level was calculated as an aggregate summary of seven negative control probes with no target transcript. Mean of the calculated background level for each sample was then subtracted from the adjusted probe value to remove background noise. 2) Normalization of miRNA counts using mean counts of three spike-in synthetic control miRNAs (ath-miR159a, cel-miR-248, and osa-miR414) to control for variances on the starting material and the miRNA purification efficiency. 3) Sample content normalization using geometric mean counts of the top 50 miRNAs expressed excluding hsa-miR-320e, hsa-miR-16-5p and hsa-miR-451a because these miRNAs may be related to red blood cell contamination or hemolysis. After these steps, the expression level of each miRNA was calculated.

label: NanoString

source_name: plasma

extract_protocol: Qiagen’s miRNeasy Plasma Kit manufacturer's protocol

tag: study site (plco=1 swmhs=2 sccs=3 mec=4)

tag: case control status (control=0 case=1)

tag: sets

tag: sex (female=0 male=1)

tag: age at diagnosis

tag: race (white=1 black=2 other=3)


title: VUMC0124


title: mouse_Organoid_11

city: Kashiwa

first: BIN

last: WU

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

department: Research

institute: ImmunoGeneTeqs

organism: Mus musculus

source_name: Alveolospheres

growth_protocol: Alveolopheres were generated by co-culturing murine lung fibroblasts and epithelial cells. Briefly, single-cell suspension was obtained from murine lungs by enzymatic digestion by collagenase and DNase I as described previously (Tsukui et al., 2015), and lung fibroblasts and epithelial cells were isolated by cell sorting. Resulted cells were suspended in MTEC Plus medium (described below) to yield 4 x 10^6 cells/ml of fibroblasts and 2 x 10^5 cells/ml of lung epithelial cells per well. 1x10^5 lung fibroblast and 5 x 10^3 lung epithelial cells/25µL were combined and suspended with an equal volume of Matrigel (BD Biosciences) at 4°C, and 90µL of the suspension was seeded onto each insert (BD Biosciences or Greiner) placed on a 24-well culture dish. Then, cells were cultured at 37°C for 30 min, 500 µL of MTEC Plus medium were added, and further cultured at 37°C with 5% CO2 in a humidified atmosphere. The MTEC Plus medium used for culture consisted of medium DMEM/F-12 (Sigma-Aldrich), mouse epidermal cell growth factor (25 ng/mL; R&D Systems), pituitary extract (30 µg/mL; Sigma-Aldrich), and insulin-transferrin-sodium selenite (1×; Thermo Fisher Scientific), penicillin/streptomycin (1×; Sigma-Aldrich), cholera toxin (100 ng/mL; Sigma-Aldrich), and fetal bovine serum (5%). Retinoic acid (Sigma-Aldrich) was added at the time of medium addition, and Y-27632 Rho-associated kinase inhibitor (10 μM; Fujifilm Wako Pure Chemicals) only immediately after seeding. The culture medium was changed every two days for 14 days.

tag: strain

tag: genotype

tag: tissue

value: lung


title: P. nyererei, testes, rep2

city: Cambridge

first: Miguel

middle: Vasconcelos

last: Almeida

address: Tennis Court Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Cambridge

description:
Pny_tes_rep2
rawCounts_mRNA_GenesAndTEs_Pnye.txt
NormCounts_mRNA_TEs_Pnye.txt

data_processing:
Illumina adapters and reads with low-quality calls were filtered out with Trimmomatic v0.39 (Bolger et al., 2014) using options SLIDINGWINDOW:4:28 MINLEN:36.
We mapped trimmed reads to the genome, using STAR v2.5.4b (Dobin et al., 2013) with options --outTmpDir --readFilesCommand zcat ‑‑genomeDir ‑‑readFilesIn {R1} {R2} --outSAMtype BAM SortedByCoordinate ‑‑outFilterType BySJout --outFilterMultimapNmax 150 ‑‑winAnchorMultimapNmax 150 --alignSJoverhangMin 8 --alignSJDBoverhangMin 3 ‑‑outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 10000000 --alignMatesGapMax 100000000 --outFileNamePrefix. Reads from Lake Malawi cichlid species (A. calliptera, M. zebra, T. sp. "mauve") were all mapped to the A. calliptera genome fAstCal1.2. A. burtoni, P. nyererei, and O. niloticus reads were mapped to their genomes: AstBur1.0, PunNye1.0, and  O_niloticus_UMD_NMBU respectively. All these genomes are available at Ensembl.
The resulting BAM files were used as inputs for TEtranscripts v2.2.1 (Jin et al., 2015) with options -t -c --GTF --TE --stranded reverse ‑‑project --SortByPos.
For A. calliptera samples, gene expression (without TEs) was quantified from trimmed reads using salmon v1.5.1 (Patro et al., 2017), with options --seqBias --gcBias - validateMappings -l A -1 ‑2 -o -i.
DESeq2 (Love et al., 2014) and custom scripts were used to calculate log-normalized and TPM counts, generate plots and conduct statistical tests on an R framework (R Core Team, 2021).
Assembly: fAstCal1.2; AstBur1.0; PunNye1.0; O_niloticus_UMD_NMBU
Supplementary files format and content: rawCounts_mRNA_GenesAndTEs_Acal.txt: Tab-delimited file includes raw counts for genes and TEs in each A. calliptera sample. Output of TEtranscripts.
Supplementary files format and content: NormCounts_mRNA_TEs_Acal.txt: Tab-delimited file includes DESeq2 normalized counts for TEs in each A. calliptera sample.
Supplementary files format and content: rawCounts_mRNA_GenesAndTEs_Malawi_curatedTEAnnotation.txt: Tab-delimited file includes raw counts for genes and TEs in each Lake Malawi cichlid sample. Output of TEtranscripts, using a curated TE annotation.
Supplementary files format and content: NormCounts_mRNA_TEs_Malawi_curatedTEAnnotation.txt: Tab-delimited file includes DESeq2 normalized counts for TEs in each Lake Malawi cichlid sample. Using a curated TE annotation.
Supplementary files format and content: rawCounts_mRNA_Acal_brain_gonads.txt: Tab-delimited file includes raw counts in each A. calliptera sample. From Salmon output.
Supplementary files format and content: lengthScaledTPM_mRNA_Acal_brain_gonads.txt: Tab-delimited file includes length scaled TPM counts in each A. calliptera sample. From Salmon output.
Supplementary files format and content: rawCounts_mRNA_GenesAndTEs_Abur.txt: Tab-delimited file includes raw counts for genes and TEs in each A. burtoni sample. Output of TEtranscripts.
Supplementary files format and content: NormCounts_mRNA_TEs_Abur.txt: Tab-delimited file includes DESeq2 normalized counts for TEs in each A. burtoni sample.
Supplementary files format and content: rawCounts_mRNA_GenesAndTEs_Pnye.txt: Tab-delimited file includes raw counts for genes and TEs in each P. nyererei sample. Output of TEtranscripts.
Supplementary files format and content: NormCounts_mRNA_TEs_Pnye.txt: Tab-delimited file includes DESeq2 normalized counts for TEs in each P. nyererei sample.
Supplementary files format and content: rawCounts_mRNA_GenesAndTEs_Onil.txt: Tab-delimited file includes raw counts for genes and TEs in each O. niloticus sample. Output of TEtranscripts.
Supplementary files format and content: NormCounts_mRNA_TEs_Onil.txt: Tab-delimited file includes DESeq2 normalized counts for TEs in each O. niloticus sample.

organism: Pundamilia nyererei

source_name: Testes

extract_protocol:
Tissue pieces were transferred to BeadBug tubes prefilled with 0.5 mm Zirconium beads (Merck, #Z763772) and 500-600 µl of TRIzol (Life Technologies, #15596026) was added to the tubes and mixed vigorously. Afterwards, we conducted the homogenisation using a BeadBug microtube homogeniser (Sigma, #Z764140) at approximately 4oC (in cold room). Each sample was homogenised with five BeadBug runs at maximum speed (4000 rpm) for 60 seconds each. Supernatant was then removed into a clean 1.5 mL tube. Centrifuged the lysates again, this time at maximum speed (approximately 21,000 G) for 5 minutes at 4oC. Transferred supernatant into a clean tube without disturbing the pellet and tissue debris. Mixed supernatant thoroughly 1:1 with 100% ethanol, pipetted the mix into a column provided in the Direct-zol RNA Miniprep Plus kit (Zymo Research, #R2072) and followed manufacturer’s instructions, using the recommended in-column DNase I treatment.
Quality control, library preparation (directional, with poly-A enrichment), and mRNA sequencing (Illumina, PE150) was performed by Novogene. A. calliptera brain libraries and P.nyererei gonad libraries were prepared differently with the following protocol. We used 50-250 ng of total RNA for library production with the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490), in conjunction with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB, #E7760) and the NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs, NEB #E6440). Samples were then pooled in equimolar amounts and sequenced on a NovaSeq 6000 system (PE150 on one lane of an S1 Flowcell).

value: Testes

value: wild-type


title: NaraCOVID_TP3_CD4_040_TCR


title: mouse_Organoid_10


title: VUMC0122


title: VUMC0123


title: NaraCOVID_TP3_CD4_038_TCR


title: P. nyererei, ovary, rep3

description:
Pny_ov_rep3
rawCounts_mRNA_GenesAndTEs_Pnye.txt
NormCounts_mRNA_TEs_Pnye.txt

source_name: Ovary

value: Ovary


title: mouse_Organoid_9

value: Bleomycin 0.1 ug/ml


title: P. nyererei, testes, rep1

description:
Pny_tes_rep1
rawCounts_mRNA_GenesAndTEs_Pnye.txt
NormCounts_mRNA_TEs_Pnye.txt


title: mouse_Organoid_8


title: NaraCOVID_TP3_CD4_039_TCR


title: P. nyererei, ovary, rep2

description:
Pny_ov_rep2
rawCounts_mRNA_GenesAndTEs_Pnye.txt
NormCounts_mRNA_TEs_Pnye.txt


title: VUMC0121


title: VUMC0119


title: P. nyererei, ovary, rep1

description:
Pny_ov_rep1
rawCounts_mRNA_GenesAndTEs_Pnye.txt
NormCounts_mRNA_TEs_Pnye.txt


title: NaraCOVID_TP3_CD4_036_TCR


title: NaraCOVID_TP3_CD4_035_TCR

value: female


title: mouse_Organoid_6

value: Bleomycin 1.0 ug/ml


title: VUMC0118


title: P. nyererei, testes, rep4 [smallRNA-seq]

data_processing:
The data resides within R1 so R2 was discarded. CutAdapt v1.15 (Martin, 2011) was used to remove adapters and reads shorter than 18 nucleotides with options -a TGGAATTCTCGGGTGCCAAGG   minimum-length 18 -o.
We selected small RNAs in the piRNA size range, between 24 and 35 nucleotides long, for further analysis. We have done this size selection using CutAdapt v1.15 (Martin, 2011) with options ‑‑minimum-length 24 --maximum-length 35.
We mapped the 24-35 nucleotide long reads to the genome using STAR v2.5.4b (Dobin et al., 2013), with options --outTmpDir --genomeDir   --readFilesIn --readFilesCommand zcat   outMultimapperOrder Random --outFilterMultimapNmax 100   outFilterMismatchNmax 2 --alignIntronMax 1 --outSAMtype BAM SortedByCoordinate --outFilterType BySJout --winAnchorMultimapNmax 100 --alignEndsType EndToEnd   scoreDelOpen -10000 --scoreInsOpen -10000 --outSAMmultNmax 1   outFileNamePrefix. Reads from Lake Malawi cichlid species (A. calliptera, M. zebra, T. sp. "mauve") were all mapped to the A. calliptera genome fAstCal1.2. A. burtoni, P. nyererei, and O. niloticus reads were mapped to their genomes: AstBur1.0, PunNye1.0, and  O_niloticus_UMD_NMBU respectively. All these genomes are available at Ensembl.
To quantify piRNA counts mapping to TEs, we used featureCounts v1.6.0 (Liao et al., 2014) with options -a -o -t exon -M. The 24-35 nucleotide long BAM file was used as input. For Lake Malawi cichlids, featureCounts analysis was performed twice, using A. calliptera default and curated TE annotations. DESeq2 (Love et al., 2014) and custom scripts  were used to calculate normalized counts, generate plots and conduct statistical tests on an R framework (R Core Team, 2021).
Assembly: fAstCal1.2; AstBur1.0; PunNye1.0; O_niloticus_UMD_NMBU
Supplementary files format and content: Abur_sRNA_NormTEcounts_GEO.txt. Tab-delimited file includes DESeq2 normalized counts for piRNAs mapping to  TEs in each A. burtoni sample.
Supplementary files format and content: Malawi_sRNA_NormTEcounts_CuratedAnnotation_GEO.txt. Tab-delimited file includes DESeq2 normalized counts for piRNAs mapping to TEs in each Lake Malawi cichlid sample. Using a curated TE annotation.
Supplementary files format and content: Malawi_sRNA_NormTEcounts_GEO.txt. Tab-delimited file includes DESeq2 normalized counts for piRNAs mapping to TEs in each Lake Malawi cichlid sample.
Supplementary files format and content: Onil_sRNA_NormTEcounts_GEO.txt. Tab-delimited file includes DESeq2 normalized counts for piRNAs mapping to  TEs in each O. niloticus sample.
Supplementary files format and content: Pnye_sRNA_NormTEcounts_GEO.txt. Tab-delimited file includes DESeq2 normalized counts for piRNAs mapping to  TEs in each P. nyererei sample.

extract_protocol:
Tissue pieces were transferred to BeadBug tubes prefilled with 0.5 mm Zirconium beads (Merck, #Z763772) and 500-600 µl of TRIzol (Life Technologies, #15596026) was added to the tubes and mixed vigorously. Afterwards, we conducted the homogenisation using a BeadBug microtube homogeniser (Sigma, #Z764140) at approximately 4oC (in cold room). Each sample was homogenised with five BeadBug runs at maximum speed (4000 rpm) for 60 seconds each. Supernatant was then removed into a clean 1.5 mL tube. Centrifuged the lysates again, this time at maximum speed (approximately 21,000 G) for 5 minutes at 4oC. Transferred supernatant into a clean tube without disturbing the pellet and tissue debris. Mixed supernatant thoroughly 1:1 with 100% ethanol, pipetted the mix into a column provided in the Direct-zol RNA Miniprep Plus kit (Zymo Research, #R2072) and followed manufacturer’s instructions, using the recommended in-column DNase I treatment.
Samples were processed according to the NEXTFLEX® Small RNA-Seq Kit v4 with UDIs (PerkinElmer, #NOVA-5132-32) with a 1 µg starting input and 12 cycles of PCR. Samples were then pooled in equimolar amounts according to the TapeStation results and sequenced on a Novaseq 6000 system (PE50 on one lane of an SP Flowcell).


title: P. nyererei, testes, rep3

description:
Pny_tes_rep3
rawCounts_mRNA_GenesAndTEs_Pnye.txt
NormCounts_mRNA_TEs_Pnye.txt


title: mouse_Organoid_5


title: P. nyererei, testes, rep3 [smallRNA-seq]


title: NaraCOVID_TP3_CD4_033_TCR


title: VUMC0117


title: mouse_Organoid_4


title: NaraCOVID_TP3_CD4_032_TCR


title: P. nyererei, testes, rep2 [smallRNA-seq]


title: VUMC0116


title: NaraCOVID_TP3_CD4_037_TCR


title: NaraCOVID_TP3_CD4_031_TCR


title: VUMC0113


title: mouse_Organoid_7


title: P. nyererei, testes, rep1 [smallRNA-seq]


title: mouse_Organoid_2

value: Bleomycin 0 ug/ml


title: mouse_Organoid_1


title: NaraCOVID_TP3_CD4_030_TCR


title: NaraCOVID_TP3_CD4_029_TCR


title: P. nyererei, ovary, rep1 [smallRNA-seq]


title: VUMC0111


title: VUMC0110


title: NaraCOVID_TP3_CD4_027_TCR


title: VUMC0108


title: mouse_Organoid_3


title: NaraCOVID_TP3_CD4_024_TCR


title: CRF518

city: Swansea

first: April

last: Rees

address: Room 203 ILS1, Singleton Park

institute: Swansea University

hyb_protocol: RNA samples stored at -80°C were thawed on ice prior to hybridisation reactions. Reporter probes were diluted in 70 μl of hybridisation buffer and gently mixed to create a master mix. To set up the hybridisation reactions, 5 μl of each sample was added to 8 μl of master mix. Hybridisation reactions were then completed by adding 2 μl of Capture ProbeSet and incubation at 65°C for 20 h. Probe set-target RNA hybridisation solution is then further diluted to a final volume of 35 μl. 33 μl of the diluted hybridisation solution is loaded onto a SPRINT microfluidic cartridge, with an air bubble also inserted to the stop point.

scan_protocol: Detection and scanning were performed by the nCounter® SPRINT Profiler analysis system (Nanostring).

data_processing: Data analysis was performed using the advanced analysis package (2.0.134) within the nSolver© analysis software (Version 4.0, NanoString©), and differential expression p-value adjustment was done with Benjamini-Hochberg. Significant gene changes were determined to be p  ≤ 0.05 with a fold change of ≤ -0.5 or ≥0.5.

source_name: Human peripheral blood

label_protocol: Sample RNA is hybridised with target-specific capture and reporter probes in order to create a library of unique target-probe complexes. Each target is labelled with a specific molecular barcode, which can then be detected and counted using an automated fluorescence microscope

extract_protocol: Sample processing: 1 x 106 of monocytes were washed with 1 ml RPMI 1640/Glutamax and centrifuged at 8,000 x g for 4 mins. The cells were re-suspended with diluted RLT buffer (Qiagen, UK) (1/3 with RNase-free water; Invitrogen) to 10,000 cells / μl, and frozen at -80°C.

value: Peripheral blood

value: Monocytes

tag: participant group

value: Non-pregnant


title: VUMC0107


title: NaraCOVID_TP3_CD4_026_TCR


title: CRF468


title: CRF509


title: VUMC0109


title: P. nyererei, ovary, rep2 [smallRNA-seq]


title: VUMC0106


title: NaraCOVID_TP3_CD4_022_TCR


title: CRF433


title: VUMC0105


title: NaraCOVID_TP3_CD4_021_TCR


title: VUMC0112


title: CRF072


title: VUMC0104


title: NaraCOVID_TP3_CD4_020_TCR


title: CRF381


title: VUMC0103


title: CAT1647

value: Pregnant


title: NaraCOVID_TP3_CD4_025_TCR


title: CAT1646


title: VUMC0102


title: NaraCOVID_TP3_CD4_019_TCR


title: VUMC0101


title: NaraCOVID_TP3_CD4_023_TCR


title: CAT1645


title: NaraCOVID_TP3_CD4_018_TCR


title: VUMC0100


title: NaraCOVID_TP3_CD4_017_TCR


title: NaraCOVID_TP3_CD4_015_TCR


title: NaraCOVID_TP3_CD4_014_TCR


title: VUMC0098


title: G-IH24h_2

city: Nanjing

first: jun

last: Zhang

address: 1 Weigang, Nanjing City, Jiangsu Province

country: China

institute: Nanjing Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
we use Cutadapt(v1.15) software to filter the sequencing data to get high quality sequence（Clean Data）forfurther analysis .
Thefiltered reads were mapping to the reference genome using HISAT2 v2.0.5
we used HTSeq(0.9.1) statistics to compare the Read Count values on each gene as the originalexpression of the gene, and then used FPKM to standardize the expression.
Assembly: https://fungidb.org/fungidb/app/downloads/Current_Release/Poryzae70-15/
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

organism:
Oryza sativa
Pyricularia oryzae

source_name: Infected leaves

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: Infected leaves

tag: cell line

value: Pyricularia oryzae and Oryza sativa L.

value: Collected infected leaves at 24 hpi


title: VUMC0097


title: CAT1624


title: CAT1642


title: VUMC0099


title: G-IH24h_1


title: CAT1643


title: NaraCOVID_TP3_CD4_013_TCR

value: Three shots of Pfizer-BNT162b2 vaccine

value: CD4+ T cells


title: NaraCOVID_TP3_CD4_012_TCR

value: male

value: 1 week after receiving the second dose


title: VUMC0096


title: VUMC0095


title: NaraCOVID_TP3_CD4_011_TCR


title: Chip_002122-IFN-KO

city: Marseille

first: Lionel

last: Spinelli

address: Avenue de Luminy

country: France

institute: CIML

data_processing:
Sequencing,  read  alignment,  de-multiplexing,  quality  control  and  normalization was performed using an Ion S5 system (A27212; Ion Torrent).
Supplementary files format and content: For Chip001, 001_Iontorrent_RNAseq_211006_Metadata_Chip001.xlsx contains the library metadata information, Auto_Zanoni_LP1_093021_Trx_MOUSE_s5-torrent-server-vm_247.bcmatrix.xls contains the  raw count of aligned reads and Auto_Zanoni_LP1_093021_Trx_MOUSE_s5-torrent-server-vm_247.rpm.bcmatrix.xls contains the normalized read counts.
Supplementary files format and content: For Chip002, 001_Iontorrent_RNAseq_211006_Metadata_Chip002.xlsx contains the library metadata information, Auto_Zanoni_LP2_093021_Trx_MOUSE_s5-torrent-server-vm_249.bcmatrix.xls contains the  raw count of aligned reads and Auto_Zanoni_LP2_093021_Trx_MOUSE_s5-torrent-server-vm_249.rpm.bcmatrix.xls contains the normalized read counts.

source_name: Small intestine

extract_protocol:
For targeted transcriptome sequencing, RNA (15ng) isolated from  small  intestinal crypts was retro-transcribed to cDNA using SuperScript VILO cDNA Synthesis Kit  (11754-05; Invitrogen).
Barcoded libraries were prepared using the Ion  AmpliSeq Transcriptome Mouse  Gene  Expression  Panel,  Chef-Ready  Kit  (A36412; Thermo  Scientific)  as  per  the  manufacturer’s  protocol

value: Small intestine

value: epithelial cells

value: Vil CRE IFNLR1 fl/fl

value: IFNL

tag: sample id


title: Chip_002123-IFN-KO

tag: treatment


title: Chip_002124-IFN-KO

tag: cell type


title: VUMC0094


title: NaraCOVID_TP3_CD4_010_TCR

tag: age


title: Chip_002121-IFN-KO


title: VUMC0093


title: VUMC0092


title: NaraCOVID_TP3_CD4_016_TCR

tag: Sex

value: female


title: NaraCOVID_TP3_CD4_008_TCR

tag: date


title: Fli1 KO Notch1 OE Lineage depleted cells1

city: NY

first: Tomer

last: Itkin

state: NY

address: 1300 York Avenue, A-869

department: Medicine

institute: Weill Cornell Medicine

description:
FN1
Polyadenylated mRNA
single-cell RNAseq
FN.tar

data_processing:
FastQC (v0.11.8) to check FASTQ quality.
Single cell feature counts were generated using cellranger (v3.0.2).
Monocole 3 (v.3_0.2.3.0) for downstream analysis.
Batchelor (v.1.2.4) to project data and remove batch effects.
Garnette (v.0.2.15) for cell type specification.
ggplo2 (v3.3.2) for generation of violin plots comparing gene-set scores.
Genome_build: mm10 (refdata-cellranger-mm10-3.0.0)
Supplementary_files_format_and_content: *.tar: Filtered feature-barcode matrix; barcodes.tsv, features.tsv, matrix.mtx files

source_name: BM

growth_protocol: Cells were isolated from in vivo BM and depleted from lineage positive populations.

extract_protocol:
Lineage negative CD45.2 positive HSPCs were isolated by fluorescence-activated cell sorting and subjected to RNA extraction using Arcturus PicoPure RNA isolation kit (Applied Biosystems).
RNA-seq cDNA libraries were constructed using the 10X Chromium single-cell 3′ Library Kit according to the manufacturer’s original protocol.

treatment_protocol: LSK cells were sorted and co-cultured with E4orf1 vascular niche cells in StemSpan serum free media supplemented with SCF, Flt3, and TPO and with knockout serum replacement media, Fli-1 alleles deletion was induced using 4-OHT, then cells were resorted and transplanted into recipient mice and isolated following 4 months of engraftment.

tag: organ

value: BM

value: Fli-1 knockout Notch1 overexpression


title: VUMC0091

tag: study site (plco=1 swmhs=2 sccs=3 mec=4)

tag: case control status (control=0 case=1)


title: Chip_002029-IFN-WT

value: WT


title: NaraCOVID_TP3_CD4_007_TCR


title: WT Lineage depleted cells2

description:
Control2
Polyadenylated mRNA
single-cell RNAseq
Control.tar


title: Chip_002027-IFN-WT


title: ZEA30_3 RNA-seq

city: Qingdao

first: JunLin

last: Song

address: Changcheng Road

institute: JunLin Song

data_processing:
Illumina Casava1.7 software used for basecalling.
Index of the reference genome was built using Hisat2 v2.0.4 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.4.
HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. Then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: ASM130575v1
Supplementary_files_format_and_content: gene_fpkm.xlsx: Excel file includes gene expression count for each Sample.
Supplementary_files_format_and_content: gene.fa
Supplementary_files_format_and_content: Equus_asinus_NCBI_novel_gene.fa

organism: Equus asinus

source_name: endometrium cells

extract_protocol:
Cultured endometrium cells were dissected and stored in liquid nitrogen individually. Total RNA from each tank was isolated by TRIzol reagent (Invitrogen, UK).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: primary cultured endometrium cells

value: 30 uM ZEA


title: Fli1 KO Notch1 OE Lineage depleted cells2

description:
FN2
Polyadenylated mRNA
single-cell RNAseq
FN.tar


title: NaraCOVID_TP3_CD4_004_TCR


title: VUMC0090

tag: sets

tag: sex (female=0 male=1)


title: ZEA30_2 RNA-seq


title: NaraCOVID_TP3_CD4_005_TCR


title: Chip_002_026-IFN-WT


title: Chip_001_113-NT-KO

value: NT


title: VUMC0087

tag: age at diagnosis

tag: race (white=1 black=2 other=3)


title: WT Lineage depleted cells1

description:
Control1
Polyadenylated mRNA
single-cell RNAseq
Control.tar

tag: genotype


title: NaraCOVID_TP3_CD4_002_TCR


title: ZEA30_1 RNA-seq


title: NaraCOVID_TP3_CD4_001_TCR


title: Chip_001_112-NT-KO

tag: tissue


title: VUMC0084


title: Chip_001_111-NT-KO


title: VUMC0086


title: ZEA10_2 RNA-seq

value: 10 uM ZEA


title: VUMC0089


title: NaraCOVID_TP3_CD4_006_TCR


title: Chip_002028-IFN-WT


title: NaraCOVID_TP2_CD8_041_TCR

value: CD8+ T cells and CD19+ B cells

value: 1 week after receiving the first dose


title: Chip_001_114-NT-KO


title: DON30_3 RNA-seq

value: 30 uM DON


title: Chip_001_012-NT-WT


title: NaraCOVID_TP3_CD4_003_TCR

value: Three shots of Pfizer-BNT162b2 vaccine

value: CD4+ T cells

value: male


title: Chip_001_014-NT-WT

value: Small intestine

value: epithelial cells


title: VUMC0085


title: ZEA10_1 RNA-seq


title: VUMC0081


title: Chip_001_011-NT-WT


title: ZEA10_3 RNA-seq


title: NaraCOVID_TP2_CD8_037_TCR


title: NaraCOVID_TP2_CD8_036_TCR


title: DON30_2 RNA-seq


title: NaraCOVID_TP2_CD8_040_TCR


title: VUMC0083


title: Chip_001_013-NT-WT


title: DON30_1 RNA-seq


title: VUMC0080


title: dor_reg_unc_plex-12hpa-rep1

city: Kansas City

first: Alejandro

last: Sanchez Alvarado

state: MO

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

description: 12hpa amputated dorsal fin

library_source: transcriptomic single cell

data_processing:
Fastqs were demultiplexed using cellranger mkfastq (cellranger 6.0.1) with default settings. Cellranger multi (cellranger 6.0.1) was used to align the fastqs against Ensembl 104 Nfu_20140520 and filter, count barcodes and UMIs
Demultiplexed sample feature count matrices were loaded into R using Seurat (Seurat_4.3.0), mitochondrial percentages were calculated using the PercentageFeatureSet function and a median + 2 sd threshold was use to filter out cells with high mitochondrial gene expression, the resulting percent.mt distribution in the integrated object had a median of 3.9% and the highest value was 21.5%. Low nFeature_RNA count was filtered with median - 1.2 sd and high nFeature_RNA count was filtered with median + 4 sd, the resulting nFeature_RNA distribution in the integrated object had a median of 1536 and the highest value was 5259 nFeature_RNA. We decided to apply relative statistical thresholds to compensate between batch effects and sequencing depth between samples considering doublets were removed during demultiplexing on the previous step. After quality control, all samples were normalized individually using the SCTransform function regressing percent.mt from the model. All the samples for integration were put on a list and anchor features were identified with SelectIntegrationFeatures (nfeatures = 8000), samples were prepared for integration using the function PrepSCTIntegration and the anchor features, and integration anchors were identified with the function FindIntegrationAnchors using the list containing the samples, SCT as the normalization method and the anchor features. Finally, all samples were integrated using the function IntegrateData with the integration anchors and SCT as the normalization method. Once integrated, RunPCA, RunUMAP and FindNeighbors functions were run on the integrated assay, and clusters were computed with the FindClusters function by iteratively changing the cluster resolution from 0.2 to 2 in 0.1 intervals. Cell markers of differential expression analysis was done using the FindMarkers function and selecting the subset of cells to compare to each other.
Differential analysis with MiloR. To understand the enrichment of certain cell types between conditions, differential abundance between the cell neighborhoods for a given condition were tested using MiloR16. We tested for differential abundance between the conditions (proximal vs distal, regenerated vs homeostasis). Using Seurat generated graph, a K-nearest neighborhood (KNN) graph was precomputed which assigned the cells to a neighborhood with the parameters (k=20, d=30, prop = 0.1). Cells within each neighborhood for a given sample were then counted and tested for differential abundance using a generalized linear design framework while accounting for multiple comparison testing using the spatial FDR in MiloR. We then annotated the neighborhoods with the cell clusters and neighborhoods with a fraction less than 0.7 were annotated to be “mixed”.
Assembly: Nfu_20140520
Supplementary files format and content: h5 file containing counts matrix
Supplementary files format and content: per 10x recommendations cell_counts.txt contains cell counts per sample

organism: Nothobranchius furzeri

source_name: dorsal fin

growth_protocol: African killifish Nothobranchius furzeri were reared at the Stowers Institute and all animal procedures were performed with IACUC approval (Protocol ID: 2022-137).

extract_protocol:
Freshly collected fin tissue was dissociated with 1mg/mL collagenase type II, for 5 mins, 70μm filtered, labeled with CellPlex reagents (10x Genomics), counted, stained with and 1μg/mL DAPI, 500 nM Draq5 at 4e6 cells/mL and sorted on a 6-laser BD S6 FACSymphony with a 100-μm nozzle chilled to 4°C at all times, sorting was done on Draq5 positive DAPI negative gates, samples with post-sort viability >96% were used for library preparation and sequencing.
Libraries were prepared using the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 with Feature Barcode technology for Cell Multiplexing (10x Genomics) according to manufacturer’s directions. Resulting cDNA, short fragment libraries, and CMO libraries were checked for quality and quantity using a 2100 Bioanalyzer (Agilent Technologies) and Qubit Fluorometer (Thermo Fisher Scientific). Multiplexed gene expression and CMO libraries were pooled, as specified by manufacturer, and sequenced to a depth necessary to achieve at least 26,000 mean reads per cell on an Illumina NovaSeq 6000 instrument utilizing RTA and instrument software versions current at the time of processing with the following paired read lengths: 28*10*10*90bp

treatment_protocol: Anesthetized fish were amputated using a disposable razor blade at the plane of amputation (Supplementary Figure S1A).

value: dorsal fin

tag: group

value: 12 hours post-amputation


title: NaraCOVID_TP2_CD8_038_TCR


title: VUMC0088


title: DON10_3 RNA-seq

value: 10 uM DON


title: BM SLAM LSK HSPCs (multiome-scATAC)

library_source: genomic

data_processing:
cellranger-arc-2.0.0 to process snRNAseq and scATACseq multiome
Assembly: refdata-cellranger-arc-mm10-2020-A-2.0.0
Supplementary files format and content: atac_fragments.tsv.gz (10x cellranger-arc ATACseq fragments file)
atac_fragments.tsv.gz.tbi (Tabix index of fragments interval )
filtered_feature_bc_matrix.h5 (Multiomimodal h5 object containing filtered gene expression and peak counts)

molecule: genomic DNA

organism: Mus

source_name: SLAM LSK HSPCs isolated from BM of C57Bl/6 mice

extract_protocol: Femurs and tibias were harvested from C57Bl/6 mice, flushed, crushed, filtered, and washed. Total BM cells were labeled and CD150+/CD48-/Lineage-/Sca-1+/c-Kit+/CD45+ HSPCs sorted and processed for 10X multiome analysis.

tag: strain

tag: time points

value: 2-4 months old mice

value: Bone marrow (BM)

value: SLAM LSK HSPCs


title: VUMC0075


title: BM SLAM LSK HSPCs (multiome-snRNA)

molecule: nuclear RNA


title: DON10_2 RNA-seq

value: primary cultured endometrium cells

tag: treatment


title: NaraCOVID_TP2_CD8_039_TCR

tag: cell type


title: VUMC0077


title: NaraCOVID_TP2_CD8_032_TCR

tag: age


title: NaraCOVID_TP2_CD8_035_TCR

tag: Sex

value: female


title: DON10_1 RNA-seq


title: VUMC0076


title: CON2 RNA-seq


title: dor_reg_unc_plex-unc-rep1

description: trimmed uncut dorsal fin

value: uncut


title: NaraCOVID_TP2_CD8_033_TCR

value: CD8+ T cells and CD19+ B cells

tag: date


title: reg_unc_plex-12hpa-rep3

description: 12hpa amputated caudal fin

source_name: caudal fin

value: caudal fin


title: NaraCOVID_TP2_CD8_031_TCR

value: 1 week after receiving the first dose


title: CON1 RNA-seq


title: CON3 RNA-seq


title: dor_reg_unc_plex-unc-rep2

description: trimmed uncut dorsal fin


title: NaraCOVID_TP2_CD8_030_TCR

value: Three shots of Pfizer-BNT162b2 vaccine


title: VUMC0079


title: VUMC0071


title: Fusobacterium nucleatum+metformin 5mm rep_2

city: Shanghai

first: Xiaowen

last: Huang

address: 145 Middle Shandong Road, Shanghai 200001, China

institute: Shanghai Jiao Tong University, Shanghai Cancer Institute,Shanghai Institute of Digestive Disease

data_processing:
The mappings of all samples were conducted with HISAT2 v2.1.0 and read numbers were counted using the HTSeq version 0.10.019.
Genome_build: AE009951.2
Supplementary_files_format_and_content: FPKM

organism: Fusobacterium nucleatum subsp. nucleatum ATCC 25586

source_name: Fusobacterium nucleatum

growth_protocol: Fusobacterium nucleatum strain ATCC 25586 were cultured overnight at 37‘C under anaerobic conditions in brain heart infusion (BHI) broth supplemented with hemin, K2HPO4, Vitamin K1, and L-Cysteine.

extract_protocol:
Total RNA of F. nucleatum was stabilized with RNA protect Bacteria Reagent (QIAGEN, Germany) and extracted using a QIAGEN RNeasy kit (QIAGEN, Germany) following the manufacturer’s instructions. Any remaining genomic DNA was digested by On-column RNase-Free DNase kit (Qiagen, Germany).
Ribosomal RNA removal, cDNA library construction, and paired-end sequencing with the Illumina HiSeq 2000 were completed by Guangdong Magigene Biotechnology Co. Ltd.

treatment_protocol: F. nucleatum was incubated with 1 mM or 5 mM metformin for 7 hours, when the bacterium were under logarithmic phase.

value: metformin 5 mm


title: Fusobacterium nucleatum+metformin 5mm rep_1


title: VUMC0070


title: VUMC0078


title: reg_unc_plex-unc-rep3

description: trimmed uncut caudal fin


title: Fusobacterium nucleatum+metformin 1mm rep_3

value: metformin 1mm


title: NaraCOVID_TP2_CD8_026_TCR

value: male


title: VUMC0074


title: Fusobacterium nucleatum+metformin 1mm rep_2


title: reg_unc_plex-12hpa-rep2

description: 12hpa amputated caudal fin


title: reg_unc_plex-12hpa-rep1

description: 12hpa amputated caudal fin


title: Fusobacterium nucleatum+metformin 5mm rep_3


title: NaraCOVID_TP2_CD8_029_TCR


title: VUMC0072


title: Fusobacterium nucleatum control rep_3

value: control


title: 50K_plex-dist-rep3

description: uncut dorsal fin belonging to fish with distal amputation in caudal fin

value: dorsal fin

value: distal amputation in caudal fin


title: NaraCOVID_TP2_CD8_023_TCR


title: VUMC0067


title: NaraCOVID_TP2_CD8_027_TCR


title: reg_unc_plex-unc-rep4

description: trimmed uncut caudal fin


title: 30K_plex-dist-rep3


title: Fusobacterium nucleatum control rep_2


title: reg_unc_plex-unc-rep2

description: trimmed uncut caudal fin


title: NaraCOVID_TP2_CD8_025_TCR


title: VUMC0069


title: VUMC0068


title: NaraCOVID_TP2_CD8_024_TCR


title: reg_unc_plex-unc-rep1

description: trimmed uncut caudal fin


title: NaraCOVID_TP2_CD8_021_TCR


title: Fusobacterium nucleatum+metformin 1mm rep_1


title: VUMC0064


title: 50K_plex-prox-rep3

description: uncut dorsal fin belonging to fish with proximal amputation in caudal fin

value: proximal amputation in caudal fin


title: 30K_plex-prox-rep3


title: VUMC0063


title: NaraCOVID_TP2_CD8_019_TCR


title: PQ4w3

first: LU

last: FAN

state: Jiangsu

address: No. 300 Guangzhou Road

department: Department of Emergency

institute: Jiangsu Province Hospital, the First Aﬃliated Hospital of Nanjing Medical University

data_processing:
Library building and sequencing were performed on a BGISEQ 500 by Genomic institution (www.genomics.org.cn, BGI, Shenzhen, China).
The sequencing data was filtered by SOAPnuke software (v1.5.2, -l 15 -q 0.5 -n 0.1) then compared with the whole genome by HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) software (v2.0.4, -p 8 --phred64 --sensitive -I 1 -X 1000).
Clean reads were compared to referred sequence by Bowite2 (v2.2.5, -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200). The FPKM value was calculated by RSEM (v1.2.12).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample. Matrix table with raw gene counts for every gene and every sample

source_name: lung

extract_protocol:
RNA was extracted from homogenized lung tissue. RNA integrity numbers (RIN) and 28S/18S ratio were measured by Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) for RNA quality assessment. Samples with RIN above 7.0 and 28S/18S ratio above 1.0 were used for sequencing.
Library building and sequencing were performed on a BGISEQ 500 by Genomic institution (www.genomics.org.cn, BGI, Shenzhen, China).

treatment_protocol: PQ group was treated with a single intratracheal shot of paraquat-saline solution. Control mice were treated with saline

value: lung

value: 8 week

value: wild type

value: PQ 4w


title: NaraCOVID_TP2_CD8_018_TCR


title: VUMC0066


title: 30K_plex-unc-rep3

description: uncut dorsal fin belonging to fish with uncut caudal fin

value: uncut caudal fin


title: NaraCOVID_TP2_CD8_022_TCR


title: Fusobacterium nucleatum control rep_1


title: VUMC0061


title: PQ4w1


title: NaraCOVID_TP2_CD8_020_TCR

value: female


title: 50K_plex-dist-rep2


title: PQ1w3

value: PQ 1w


title: NaraCOVID_TP2_CD8_017_TCR

value: CD8+ T cells and CD19+ B cells


title: 50K_plex-unc-rep3


title: VUMC0065


title: PQ4w2


title: PQ1w2


title: VUMC0073


title: VUMC0062


title: VUMC0058


title: 30K_plex-prox-rep2


title: NaraCOVID_TP2_CD8_014_TCR

value: 1 week after receiving the first dose


title: VUMC0060


title: 30K_plex-dist-rep2


title: 50K_plex-prox-rep2


title: PQ1w1


title: NaraCOVID_TP2_CD8_016_TCR

value: Three shots of Pfizer-BNT162b2 vaccine


title: NaraCOVID_TP2_CD8_012_TCR


title: control4w1

value: control 4w


title: VUMC0059


title: control4w3


title: control1w3

value: control 1w


title: VUMC0057


title: VUMC0056


title: NaraCOVID_TP2_CD8_008_TCR


title: NaraCOVID_TP2_CD8_013_TCR


title: VUMC0052


title: control4w2


title: 30K_plex-unc-rep2


title: control1w1


title: 50K_plex-unc-rep2


title: VUMC0051


title: 50K_plex-dist-rep1


title: VUMC0054


title: 50K_plex-prox-rep1


title: NaraCOVID_TP2_CD8_010_TCR

value: male


title: 30K_plex-dist-rep1


title: 50K_plex-unc-rep1


title: control1w2


title: VUMC0050


title: VUMC0053


title: NB4 CTR-2

first: Chenhui

last: Luo

address: Shanghai Jiao Tong University School of Medicine

data_processing:
Paired-end reads were aligned to GRCh38 with HISAT.
Assembly: hg38
Supplementary files format and content: excel file includes FPKM values for each Sample

extract_protocol:
Total RNA was extracted from HH, Hut78 and NB4 cells by TRIzol reagent.
RNA-seq libraries were prepared by BGI Genomics

tag: cell line

value: Acute promyelocytic leukemia

value: CTR


title: NB4 ATRA-2

institute: Shanghai Jiao Tong University School of Medicine

value: ATRA


title: NaraCOVID_TP2_CD8_015_TCR


title: NB4 ATRA-1


title: NaraCOVID_TP2_CD8_006_TCR


title: VUMC0048

tag: study site (plco=1 swmhs=2 sccs=3 mec=4)


title: NaraCOVID_TP2_CD8_011_TCR


title: NaraCOVID_TP2_CD8_005_TCR


title: VUMC0055

tag: case control status (control=0 case=1)


title: VUMC0049

tag: sets


title: 30K_plex-unc-rep1

value: dorsal fin


title: NaraCOVID_TP2_CD8_004_TCR


title: Hut78 ATRA-2

value: Cutaneous T-cell lymphoma


title: NB4 CTR-1


title: NaraCOVID_TP2_CD8_007_TCR


title: NaraCOVID_TP2_CD8_002_TCR


title: prox_dist_10x-prox-rep2

description: 12hpa proximal amputation in caudal fin

value: caudal fin

value: 12 hours post-proximal amputation


title: prox_dist_plex-dist-rep1

description: 12hpa distal amputation in caudal fin

value: 12 hours post-distal amputation


title: VUMC0044

tag: sex (female=0 male=1)


title: NaraCOVID_TP2_CD8_003_TCR


title: VUMC0047

tag: age at diagnosis


title: Hut78 ATRA-1


title: NaraCOVID_TP2_CD8_001_TCR


title: 206796510113_R06C02

type: genomic

city: Providence

first: Alexey

middle: V

last: Fedulov

state: Rhode Island

address: 593 Eddy St.

department: RIH / Surgical Research

institute: Alpert Medical School of Brown University

description: SAMPLE 39_MK896

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEpic using standard Illumina protocol

scan_protocol: Standard Illumina

data_processing: Illumina Bead Studio (beta-values) and Partek Genomic Suite (m-values)

label: Cy5 and Cy3

source_name: RcpCAPsterilized

label_protocol: Standard Illumina

extract_protocol: Qiagen Dneasy

tag: asthma predisposed or not

value: no

value: CD11c+ dendritic cell


title: NaraCOVID_TP2_CD4_040_TCR

value: CD4+ T cells


title: Hut78 CTR-2


title: VUMC0045

tag: race (white=1 black=2 other=3)


title: prox_dist_plex-prox-rep1

description: 12hpa proximal amputation in caudal fin

tag: tissue


title: NaraCOVID_TP2_CD4_041_TCR


title: VUMC0043


title: 206796510113_R05C02

description: SAMPLE 38_MK895


title: HH ATRA-2

source_name: HH

value: HH


title: Hut78 CTR-1


title: NaraCOVID_TP2_CD4_037_TCR

source_name: Peripheral blood T cells

value: female

value: 1 week after receiving the first dose


title: HH ATRA-1


title: NaraCOVID_TP2_CD4_039_TCR

value: Three shots of Pfizer-BNT162b2 vaccine


title: VUMC0042

source_name: plasma


title: 206796510113_R04C02

description: SAMPLE 37_MK894


title: 30K_plex-prox-rep1

tag: group

value: proximal amputation in caudal fin


title: NaraCOVID_TP2_CD4_036_TCR

value: male


title: 206796510113_R01C02

description: SAMPLE 28_MK851

source_name: RcpCAPfresh

value: yes


title: VUMC0038


title: VUMC0041


title: 206796510113_R06C01

description: SAMPLE 27_MK819


title: prox_dist_10x-dist-rep2

description: 12hpa distal amputation in caudal fin


title: gastric mucosa, pylorus G7_2

city: Shenzhen

first: Yuhao

last: An

state: Guangdong Province

address: 16 Lanjing Road, Kengzi Street, Pingshan District

institute: Shenzhen Bay Lab

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence, which were mapped to GRCh38 by HISAT2 and counted by RSEM.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files includes TPM values for each sample.

source_name: healthy gastric mucosa

extract_protocol:
Put samples into a pre-cooled agate mortar, while adding the liquid nitrogen to maintain a low temperature, and gradually grind the tissue into powder. The pre-cooled ethanol was poured into the mortar for the powder resuspending. Transfer the suspension into two 1.5 mL centrifuge tubes at a ratio of 1:2, and the former was placed at -20 ℃ or -80 °C for more than 2 hours for protein extraction, the latter for RNA extraction. The suspension was removed from the -20 ℃ or -80 ℃, 14,000 g, 4 ℃ centrifuged for 30 min, the supernatant was discarded. Place the powder on ice and air dry it. The powder was used to extract RNA by the Trizol method
mRNA-seq Library Prep Kit follwing the manufacturer's protocols.

value: healthy gastric mucosa


title: VUMC0037


title: NaraCOVID_TP2_CD4_038_TCR


title: VUMC0040


title: NaraCOVID_TP2_CD4_033_TCR


title: gastric mucosa, antrum G6


title: 206796510113_R03C02

description: SAMPLE 33_MK883


title: 206796510113_R05C01

description: SAMPLE 26_MK818


title: 206796510113_R02C02

description: SAMPLE 32_MK882


title: HH CTR-1

value: CTR


title: HH CTR-2


title: NaraCOVID_TP2_CD4_035_TCR


title: VUMC0039


title: 206796510113_R03C01

description: SAMPLE 15_MK856


title: gastric mucosa, pylorus G7_1


title: VUMC0035


title: 206796510113_R04C01

description: SAMPLE 25_MK817


title: NaraCOVID_TP2_CD4_030_TCR


title: VUMC0036


title: VUMC0033


title: gastric mucosa, angular incisure G5_2


title: gastric mucosa, greater curvature G4


title: NaraCOVID_TP2_CD4_031_TCR


title: VUMC0034


title: gastric mucosa, fundus G2


title: NaraCOVID_TP2_CD4_032_TCR


title: 206796510113_R02C01

description: SAMPLE 14_MK855


title: 206796510113_R01C01

description: SAMPLE 13_MK854


title: 206796510059_R05C02

description: SAMPLE 11_MK815

source_name: CAP


title: gastric mucosa, cardia G1


title: gastric mucosa, lesser curvature G3


title: NaraCOVID_TP2_CD4_027_TCR


title: VUMC0031


title: NaraCOVID_TP2_CD4_025_TCR


title: VUMC0030


title: 206796510059_R06C02

description: SAMPLE 12_MK816


title: gastric mucosa, pylorus F7


title: gastric mucosa, antrum F6


title: VUMC0026


title: NaraCOVID_TP2_CD4_026_TCR


title: NaraCOVID_TP2_CD4_029_TCR


title: gastric mucosa, angular incisure F5


title: gastric mucosa, angular incisure G5_1


title: VUMC0029


title: VUMC0025


title: VUMC0028


title: 206796510059_R01C02

description: SAMPLE 7_MK805


title: 206796510059_R03C02

description: SAMPLE 9_MK807


title: NaraCOVID_TP2_CD4_021_TCR


title: NaraCOVID_TP2_CD4_024_TCR


title: gastric mucosa, greater curvature F4_2


title: 206796510059_R02C02

description: SAMPLE 8_MK806


title: 206796510059_R06C01

description: SAMPLE 6_MK802

source_name: PBS


title: 206796510059_R04C02

description: SAMPLE 10_MK814


title: 206796510059_R05C01

description: SAMPLE 5_MK801


title: gastric mucosa, lesser curvature F3


title: 206796510059_R04C01

description: SAMPLE 4_MK800


title: VUMC0021


title: gastric mucosa, pylorus E7


title: VUMC0018


title: VUMC0023


title: NaraCOVID_TP2_CD4_016_TCR


title: 206796510059_R01C01

description: SAMPLE 1_MK795


title: VUMC0017


title: VUMC0022


title: VUMC0015


title: NaraCOVID_TP2_CD4_020_TCR


title: Cortex_A1M_controll_7dpi_rep3 [SAMPLE 60]

city: Gothenburg

first: Charlotte

last: Andersson

address: Gula Stråket 2B

department: Department of Medical Radiation Science

country: Sweden

institute: University of Gothenburg

description: controll

data_processing:
Sham-treated samples were used as a control. We compared the relative expression in kidney tissue between the controls and three treatment groups (177Lu-octreotate, 177Lu-octreotate+A1M, A1M) at one and seven days after administration. For data analysis, we used Microsoft Excel to calculate fold-expression of the target genes based upon the 2-ΔΔCt method (Livak and Schmittgen 2001). The relative expression compared to controls were analyzed by Welch T-test, and p<0.05 was considered significant. For differentially expressed genes in at least one group, one-way ANOVA followed by Welch T-test was used to determine significant differences between the 177Lu-octreotate, 177Lu-octreotate+A1M and A1M group. Target gene signals in all samples (test and controls) are normalized to geometric average of housekeeping genes provided in the same array, resulting in ΔCt values, where ΔCt=(Ct_Target-Ct_HKG). ΔCt values for all test replicates (at 1dpi and 7 dpi) were normalized against the average of corresponding control replicates, resulting in ΔΔCt, where ΔΔCt= ΔCt_test replicate– average ΔΔCt_control. 2^-ΔΔCT values for each condition were considered as fold change expression of test samples compared to controls (untreated). Fold change is determined for target genes in all replicates of test samples as 2^-ΔΔCt where -ΔΔCt= ΔCt_test replicate– average ΔΔCt_control
Non-normalized raw data matrix reports Ct values for target and housekeeping genes in all control and test replicates. Normalized Ct and fold change worksheet reports ΔCt and 2^-ΔΔCt, respectivly, calculates as indicated in the data processing

label: SYBR Green

source_name: Cortex, A1M, controll, 7dpi, replicate3

label_protocol: For each reaction, a final volume of 25 µl was used which contained 12.5 µl of RT2 SYBR Green Mastermix (QIAGEN), 11.5 µl of nuclease free water and 1 µl of cDNA (1.7 µg of total RNA). Quantitative real-time PCR were performed (7500 Fast Real-120 Time PCR system, Applied Biosystem) with thermal profile starting by activation of HotStart DNA Taq polymerase at 95°C for 10 min followed by 40 cycles of 95°C for 15 sec and 60°C for 1min.

extract_protocol: According to the manufacturer's protocol, total RNA was extracted from frozen kidney tissue samples using the RNeasy Lipid Tissue Mini Kit (QIAGEN) or AllPrep® DNA/RNA/Protein Kit (QIAGEN). The purity, integrity and concentration of isolated RNA were assessed with Nanodrop 1000 Spectrometer (Thermo Scientific), RNA 6000 Nano LabChip Kit and Agilent 2100 Bioanalyzer (both from Agilent Technologies) and Qubit 3.0 Fluorometer (Thermo Fisher Scientific), respectively. Reverse transcription was performed from 200 ng total RNA using the RT2 First Strand Kit (QIAGEN).

treatment_protocol: Samples of kidney medulla and kidney cortex were collected from mice that had received i.v. injection of a) 150 MBq 177Lu-octreotate and phosphate buffered saline solution (PBS), b) 5 mg/kg A1M and PBS, or c) 150 MBq 177Lu-octreotate and 5 mg/kg  A1M. Samples were also collected from control mice that had received either two injections of PBS or PBS and A1M vehicle solution. Collection of the samples was performed at the time of death; three animals in each group were killed one day after injection and another three after seven days.

tag: tissue type

value: Kidney cortex

value: A1M vehicle solution

tag: time

value: 7 days


title: gastric mucosa, antrum E6_1


title: NaraCOVID_TP2_CD4_019_TCR

data_processing:
Data processing of Bulk TCRseq was performed as described in Aoki et al. (Aoki et al., 2021).
Adapter trimming and quality filtering of sequencing data were performed using Cutadapt-3.2 and PRINSEQ-0.20.4. Sequencing data were processed by MiXCR-3.0.5. In MiXCR, filtered reads were aligned to reference mouse TCR V/D/J sequences registered in the international ImMunoGeneTics (IMGT) information system. The Variable (V) and Joining (J) segments of TCRs were represented in IMGT gene nomenclature. T-cell clones were determined as TCR reads with the same TCR V segment, J segment, and CDR3 nucleotide sequence.
Inter-sample contamination within samples using same UDIs were excluded by "Decontaminate" function of vdjtools with the parameter "-r 10".
For bulk TCRseq data, we regarded the CD4+-CD8+ overlapping clones in the same participant as contamination during T-cell isolation from PBMC because CD4+ and CD8+ T-cell repertoire are mutually exclusive (Aoki 2021). Thus, these overlapping clones were categorized into either CD4+ or CD8+ according to their dominance in CD4+ and CD8+ repertoire using VDJtools-1.2.1. The sequencing reads of bulk TCR-seq samples were normalized to 100,000 reads by the ?DownSample? command of VDJtools-1.2.1. To preserve the minor clonotypes, we performed the normalization ten times and pooled these down-sampled repertoire data for each sample, by ?JoinSamples? command of VDJtools-1.2.1.
Assembly: IMGT reference sequences of human TRA and TRB
Supplementary files format and content: Text files in VDJtools format include read count and frequency, complementarity determining region 3 (CDR3) nucleotide and amino acid sequences, Variable(V)/ Diversity(D)/ Joining(J) segment names, and V, D and J segment boundaries within CDR3 nucleotide sequence of individual clones

extract_protocol:
PBMCs were isolated from whole blood with BD vacutainer CPT tubes (BD), resuspended in CELLBANKER 1 (Takara), and stored in -80°C
CD4+ and CD8+ T cells were magnetically isolated from PBMC. PBMC were thawed by warming frozen cryovials in a 37°C water bath. Cells were stained for 20 minutes at 4°C with 1st antibody mix (Antibody Mix 1 in Supplementary Table S1). After washing with MACS buffer [0.5% BSA (Nacalai), 2 mmol/L EDTA (NIPPON GENE) in PBS (Nacalai)], Cells were stained for 20 minutes at 4°C with 2nd antibody mix; BD IMag anti-PE Magnetic Particles-DM (Clone E31-1459, BD) and anti-APC-Biotin (clone APC003, BioLegend). Then, the cell suspension was diluted with MACS buffer and set on a magnet plate (DynaMag96SideSkirted, Veritas). The positive fraction was collected as CD4+ T cells. The negative fraction was stained with BD IMag Streptavidin Particles Plus-DM (BD) for 20 minutes at 4°C. Then, the cell suspension was diluted with MACS buffer and set on a magnet plate. The positive fraction was collected as CD8+ T cells and B cells. The counts of CD4+ T cells, CD8+ T cells, and B cells were determined using Flow-Count fluorospheres (Beckman) and a Cytoflex flow cytometer (Beckman) and FlowJo software (version 10.8.1; BD Biosciences).
Bulk TCR sequencing library was prepared according to the previous report (Aoki et al., 2023).  In brief, mRNA in T-cell lysates were captured by incubating with 10 ?L of Dynabeads M270 streptavidin (Thermo Fisher Scientific) bound to 2.5 pmol of BioEcoP-dT25-adapter primers for 30 minutes at room temperature under gentle rotation. mRNA-trapped beads were suspended in 10 µL of RT mix and incubated for 60 min at 42ºC to perform reverse transcription (RT) and template-switching. The composition of the RT mix was as follows; 1× First Strand buffer (Thermo Fisher Scientific), 1 mM dNTP (Roche), 2.5 mM DTT (Thermo Fisher Scientific), 1 M betaine (Sigma-Aldrich), 9 mM MgCl2 (NIPPON GENE), 1 U/µL RNaseIn Plus RNase Inhibitor (Promega), 10 U/µL Superscript II (Thermo Fisher Scientific), and 1 µM of i5-TSO. To amplify the TCR cDNA containing complementarity determining region 3 (CDR3), nested PCR of the TCR locus was performed using KAPA Hifi Hotstart ReadyMix (KAPA Biosystems), followed by the purification of PCR product using an AM Pure XP kit (Beckman Coulter) at a 0.7:1 beads-to-sample ratio. The third PCR was performed to amplify TCR libraries and add adaptor sequences for the next-generation sequencer. The third-PCR products were purified as second PCR. Final TCR libraries, whose lengths were about 600 base pairs, were quantified using a KAPA SYBR Fast qPCR Kit (KAPA Biosystems), and size distribution was analyzed by Microchip Electrophoresis System MultiNA (Shimadzu). TCR libraries were sequenced using an Illumina Novaseq 6000 S4 flowcell (67 bp read 1 and 140 bp read 2) (Illumina) using NovaSeq 6000 S4 Reagent Kit v1.5 (200 cycles, Illumina). Only read2 contained the sequence regarding the definition of T-cell clones. Oligonucleotides and reaction conditions for library preparation were summarized in Table S2 and S3, respectively.

tag: treatment


title: NaraCOVID_TP2_CD4_023_TCR

tag: cell type


title: VUMC0024

data_processing: miRNAs were normalized in the following steps: 1) background correction to remove non-specific binding. The background level was calculated as an aggregate summary of seven negative control probes with no target transcript. Mean of the calculated background level for each sample was then subtracted from the adjusted probe value to remove background noise. 2) Normalization of miRNA counts using mean counts of three spike-in synthetic control miRNAs (ath-miR159a, cel-miR-248, and osa-miR414) to control for variances on the starting material and the miRNA purification efficiency. 3) Sample content normalization using geometric mean counts of the top 50 miRNAs expressed excluding hsa-miR-320e, hsa-miR-16-5p and hsa-miR-451a because these miRNAs may be related to red blood cell contamination or hemolysis. After these steps, the expression level of each miRNA was calculated.

extract_protocol: Qiagen’s miRNeasy Plasma Kit manufacturer's protocol


title: gastric mucosa, fundus F2


title: Cortex_A1M_controll_7dpi_rep2 [SAMPLE 59]

description: controll

source_name: Cortex, A1M, controll, 7dpi, replicate2


title: NaraCOVID_TP2_CD4_014_TCR

tag: age


title: gastric mucosa, greater curvature F4_1


title: VUMC0019


title: Cortex_A1M_controll_7dpi_rep1 [SAMPLE 58]

description: controll

source_name: Cortex, A1M, controll, 7dpi, replicate1


title: NaraCOVID_TP2_CD4_022_TCR

tag: Sex


title: 206796510059_R03C01

description: SAMPLE 3_MK797


title: gastric mucosa, cardia F1


title: NaraCOVID_TP2_CD4_017_TCR

tag: date


title: gastric mucosa, greater curvature E4_1


title: Cortex_150MBq_controll_7dpi_rep2 [SAMPLE 56]

description: controll

source_name: Cortex, 150MBq, controll, 7dpi, replicate2

value: phosphate buffered saline solution


title: gastric mucosa, antrum E6_2


title: NaraCOVID_TP2_CD4_011_TCR


title: 206796510059_R02C01

description: SAMPLE 2_MK796


title: NaraCOVID_TP2_CD4_008_TCR


title: NaraCOVID_TP2_CD4_015_TCR


title: Cortex_A1M_7dpi_rep3 [SAMPLE 54]

description: test

source_name: Cortex, A1M, 7dpi, replicate3

value: A1M (5 mg/kg)


title: gastric mucosa, angular incisure E5


title: gastric mucosa, fundus E2_2


title: VUMC0014


title: NaraCOVID_TP2_CD4_018_TCR


title: gastric mucosa, greater curvature E4_2


title: NaraCOVID_TP2_CD4_013_TCR


title: NaraCOVID_TP2_CD4_012_TCR


title: gastric mucosa, lesser curvature E3_2


title: VUMC0012


title: VUMC0005


title: gastric mucosa, pylorus D7_2


title: NaraCOVID_TP2_CD4_005_TCR


title: Cortex_150MBq_A1M_7dpi_rep3 [SAMPLE 51]

description: test

source_name: Cortex, 150MBq, A1M, 7dpi, replicate3

value: 150 MBq Lu-177-octreotate + A1M (5 mg/kg)


title: Cortex_150MBq_controll_7dpi_rep3 [SAMPLE 57]

description: controll

source_name: Cortex, 150MBq, controll, 7dpi, replicate3


title: VUMC0009


title: VUMC0013


title: NaraCOVID_TP2_CD4_010_TCR


title: gastric mucosa, lesser curvature E3_1


title: Cortex_150MBq_controll_7dpi_rep1 [SAMPLE 55]

description: controll

source_name: Cortex, 150MBq, controll, 7dpi, replicate1


title: NaraCOVID_TP2_CD4_006_TCR


title: gastric mucosa, antrum D6


title: NaraCOVID_TP2_CD4_003_TCR


title: gastric mucosa, angular incisure D5


title: VUMC0006


title: gastric mucosa, fundus E2_1


title: NaraCOVID_TP2_CD4_007_TCR


title: Cortex_A1M_7dpi_rep2 [SAMPLE 53]

description: test

source_name: Cortex, A1M, 7dpi, replicate2


title: gastric mucosa, cardia E1


title: Cortex_150MBq_7dpi_rep3 [SAMPLE 48]

description: test

source_name: Cortex, 150MBq, 7dpi, replicate3

value: 150 MBq Lu-177-octreotate


title: VUMC0008


title: Cortex_A1M_7dpi_rep1 [SAMPLE 52]

description: test

source_name: Cortex, A1M, 7dpi, replicate1


title: NaraCOVID_TP1_CD8_041_TCR

source_name: Peripheral blood T cells

value: CD8+ T cells and CD19+ B cells

value: before receiving the first dose


title: VUMC0010

source_name: plasma


title: R42_ams_FB23_AACGGAGTCC-GACACTCCTA

city: Urbana

first: Gene

middle: E.

last: Robinson

state: IL

address: 1206 W. Gregory Dr. M/C 195

department: Carl R. Woese Institute for Genomic Biology

description: oral antagomir treatment

data_processing:
Aligned FASTQ files to honey bee genome and deformed wing virus reference with STAR 2.7.6a
Counts were generated with the "featureCounts" function in Subread 2.0.0
Assembly: HAv3.1

organism: Apis mellifera

source_name: abdominal fat body

growth_protocol: Adult worker honey bees were collected from apiaries at the University of Illinois at Urbana-Champaign Bee Research Facility in Urbana, IL. All workers used were produced from colonies headed by queens inseminated with the sperm from a single drone.

extract_protocol:
Abdominal fat body: abdomens were separated from the bodies and placed in 500ul RNAlaterICE (Life Technologies) at -20ºC for 14 to 18 h. Abdomens were then opened and guts and sting apparatus gently removed. The remaining intact fat body tissue connected to the cuticle was placed in a 1.5ml tube and stored frozen (-80°C) until RNA extraction. Brains: bee heads were separated from the bodies and placed in a pure ethanol in a dissection dish chilled on dry ice to prevent RNA degradation during dissection. The cuticle of the anterior head capsule (frons) was removed and each head placed in 300ul of RNAlaterICE at -20ºC for 14 to 18 h. Heads were then opened, hypopharyngeal glands removed, and whole brain collected. Brains were place in 1.5ml tube and stored frozen (-80°C) until RNA extraction. Total RNA extraction for both abdominal fat body and whole brain was performed with miRNeasy Mini Kits (Qiagen) and C. elegans miR-39 spike-in (Qiagen) at the tissue homogenization step for other downstream analyses (qPCR).
RNA-Seq libraries were prepared with Kapa Hyper Stranded mRNA library kit (Roche). Libraries were pooled and sequenced on one S4 lane for 151 cycles  from both ends of the fragments on a NovaSeq 6000 (Illumina). Reads are 150 nt.

treatment_protocol: Age-matched, 1-day old adults workers were collected, paint-marked for identificiation, and replaced into a colony for typical development. As 3-days old, paint-marked bees were recaptured and food removed for 1 hr prior to oral treatment. For the antagomir treatment, bees were cold-anesthetized on wet ice, immobilized, and allowed to reanimate before being fed 1,000 pmol of antagomir (ame-miR-305 or missense construct) suspended in 4 ul of 30% sucrose solution. Bees were immediately placed in individual cages to prevent oral treatment sharing via trophallaxis and provisioned ad libitum with 30% sucrose to prevent the introduction of  plant factors in honey or pollen. Bees were placed in an incuabtor (34°C, 50% relative humidity) for 48h and then flash-frozen in liquid nitrogen.

tag: caste

value: worker

value: fat body

value: antagomir-missense

tag: colony


title: gastric mucosa, greater curvature D4_1

source_name: healthy gastric mucosa


title: gastric mucosa, pylorus D7_1


title: Cortex_150MBq_A1M_7dpi_rep1 [SAMPLE 49]

description: test

source_name: Cortex, 150MBq, A1M, 7dpi, replicate1


title: VUMC0004

tag: study site (plco=1 swmhs=2 sccs=3 mec=4)

tag: case control status (control=0 case=1)


title: Cortex_150MBq_7dpi_rep1 [SAMPLE 46]

description: test

source_name: Cortex, 150MBq, 7dpi, replicate1


title: VUMC0007

tag: sets

tag: sex (female=0 male=1)


title: NaraCOVID_TP2_CD4_001_TCR

first: Hiroyasu

last: Aoki

address: 2669 Yamazaki

value: Three shots of Pfizer-BNT162b2 vaccine

value: CD4+ T cells

value: 1 week after receiving the first dose


title: NaraCOVID_TP2_CD4_002_TCR

value: male


title: R42_ams_FB24_AGGTGTGACC-GAGTTCGGAG

institute: University of Illinois at Urbana-Champaign

description: oral antagomir treatment


title: VUMC0002

first: Cong

last: Wang

address: 2525 West End Ave

tag: age at diagnosis


title: R42_ams_FB20_ACTTCCGGCA-CGTGTAACTT

description: oral antagomir treatment


title: Cortex_150MBq_A1M_7dpi_rep2 [SAMPLE 50]

description: test

source_name: Cortex, 150MBq, A1M, 7dpi, replicate2


title: Cortex_A1M_controll_1dpi_rep3 [SAMPLE 45]

description: controll

source_name: Cortex, A1M, controll, 1dpi, replicate3

value: 1 day


title: NaraCOVID_TP1_CD8_039_TCR

institute: Tokyo University of Science


title: gastric mucosa, greater curvature D4_2

value: healthy gastric mucosa


title: VUMC0001

institute: Vanderbilt University

tag: race (white=1 black=2 other=3)


title: Cortex_150MBq_7dpi_rep2 [SAMPLE 47]

description: test

source_name: Cortex, 150MBq, 7dpi, replicate2

value: Kidney cortex


title: gastric mucosa, fundus D2_1

tag: tissue


title: Cortex_A1M_controll_1dpi_rep1 [SAMPLE 43]

description: controll

source_name: Cortex, A1M, controll, 1dpi, replicate1

value: A1M vehicle solution


title: NaraCOVID_TP1_CD8_040_TCR


title: R42_ams_FB22_GTGAAGCTGC-CTCACATTGC

description: oral antagomir treatment


title: gastric mucosa, lesser curvature D3


title: gastric mucosa, fundus D2_2


title: NaraCOVID_TP1_CD8_038_TCR


title: R42_ams_FB17_GACAGCCTTG-ATTACGGTTG

description: oral antagomir treatment


title: NaraCOVID_TP1_CD8_037_TCR

value: female


title: NaraCOVID_TP1_CD8_036_TCR


title: R42_ams_FB18_CGGTTATCTG-CAACGCATAA

description: oral antagomir treatment


title: Cortex_A1M_controll_1dpi_rep2 [SAMPLE 44]

description: controll

source_name: Cortex, A1M, controll, 1dpi, replicate2


title: Cortex_150MBq_controll_1dpi_rep2 [SAMPLE 41]

description: controll

source_name: Cortex, 150MBq, controll, 1dpi, replicate2

value: phosphate buffered saline solution


title: Cortex_150MBq_controll_1dpi_rep3 [SAMPLE 42]

description: controll

source_name: Cortex, 150MBq, controll, 1dpi, replicate3


title: NaraCOVID_TP1_CD8_033_TCR


title: gastric mucosa, antrum C6_2


title: R42_ams_FB14_CAGCCGATGT-AAGAGTTCGA

description: oral antagomir treatment


title: NaraCOVID_TP2_CD4_004_TCR


title: gastric mucosa, cardia D1_1


title: gastric mucosa, pylorus C7_2


title: gastric mucosa, cardia D1_2


title: NaraCOVID_TP1_CD8_032_TCR


title: Cortex_A1M_1dpi_rep3 [SAMPLE 39]

description: test

source_name: Cortex, A1M, 1dpi, replicate3

value: A1M (5 mg/kg)


title: R42_ams_FB19_TACTCCACGG-GTTCTCATAG

description: oral antagomir treatment


title: R42_ams_FB13_CTTGATATCC-AATGTCTGGA

description: oral antagomir treatment


title: R42_ams_FB15_TCATGCGCTA-CCGAGAAGGT

description: oral antagomir treatment


title: NaraCOVID_TP1_CD8_035_TCR


title: NaraCOVID_TP1_CD8_031_TCR


title: gastric mucosa, pylorus C7_1


title: R42_ams_FB16_ACTCCGTCCA-GTTGGCGTCT

description: oral antagomir treatment


title: NaraCOVID_TP1_CD8_030_TCR


title: Cortex_A1M_1dpi_rep2 [SAMPLE 38]

description: test

source_name: Cortex, A1M, 1dpi, replicate2


title: Cortex_150MBq_A1M_1dpi_rep3 [SAMPLE 36]

description: test

source_name: Cortex, 150MBq, A1M, 1dpi, replicate3

value: 150 MBq Lu-177-octreotate + A1M (5 mg/kg)


title: gastric mucosa, antrum C6_1


title: Cortex_150MBq_A1M_1dpi_rep2 [SAMPLE 35]

description: test

source_name: Cortex, 150MBq, A1M, 1dpi, replicate2


title: R42_ams_B24_CGGACTACTT-CCTTAATACG

description: oral antagomir treatment

source_name: whole brain

value: brain


title: NaraCOVID_TP1_CD8_027_TCR

source_name: Peripheral blood T cells

value: CD8+ T cells and CD19+ B cells

value: before receiving the first dose


title: gastric mucosa, angular incisure C5


title: Cortex_150MBq_controll_1dpi_rep1 [SAMPLE 40]

description: controll

source_name: Cortex, 150MBq, controll, 1dpi, replicate1


title: NaraCOVID_TP1_CD8_026_TCR


title: R42_ams_B23_TGAAGCATCT-GTTAGATACC

description: oral antagomir treatment

value: worker


title: NaraCOVID_TP1_CD8_029_TCR


title: gastric mucosa, fundus C2

source_name: healthy gastric mucosa


title: R42_ams_B20_TCTTAACTGG-TTCAGGCCGA

description: oral antagomir treatment

value: antagomir-missense


title: gastric mucosa, greater curvature C4_2


title: Cortex_150MBq_1dpi_rep2 [SAMPLE 32]

description: test

source_name: Cortex, 150MBq, 1dpi, replicate2

value: 150 MBq Lu-177-octreotate


title: Cortex_150MBq_1dpi_rep3 [SAMPLE 33]

description: test

source_name: Cortex, 150MBq, 1dpi, replicate3


title: Cortex_150MBq_A1M_1dpi_rep1 [SAMPLE 34]

description: test

source_name: Cortex, 150MBq, A1M, 1dpi, replicate1


title: Cortex_150MBq_1dpi_rep1 [SAMPLE 31]

description: test

source_name: Cortex, 150MBq, 1dpi, replicate1


title: R42_ams_B22_GTCACATCCG-AGAACAGTGA

description: oral antagomir treatment


title: R42_ams_B19_TAGATCCGAA-ACTTCGATAG

description: oral antagomir treatment


title: NaraCOVID_TP1_CD8_023_TCR

value: Three shots of Pfizer-BNT162b2 vaccine


title: gastric mucosa, pylorus B7


title: NaraCOVID_TP1_CD8_024_TCR


title: NaraCOVID_TP1_CD8_022_TCR


title: R42_ams_B16_GTAACATTGG-TCGTGGCCAA

description: oral antagomir treatment


title: Cortex_A1M_1dpi_rep1 [SAMPLE 37]

description: test

source_name: Cortex, A1M, 1dpi, replicate1


title: R42_ams_B18_GCGTGTCATG-CGATTGTTCT

description: oral antagomir treatment


title: gastric mucosa, cardia C1


title: R42_ams_B17_CAACAATTCG-GCGACCGATT

description: oral antagomir treatment


title: R42_ams_B15_TGTATCGCGA-CGTGTGAGTG

description: oral antagomir treatment


title: gastric mucosa, greater curvature C4_1


title: gastric mucosa, antrum B6


title: NaraCOVID_TP1_CD8_021_TCR


title: R42_ams_B14_AATGGTACCT-ACAACCGTCG

description: oral antagomir treatment


title: NaraCOVID_TP1_CD8_020_TCR


title: NaraCOVID_TP1_CD8_025_TCR


title: Medulla_A1M_controll_7dpi_rep2 [SAMPLE 29]

description: controll

source_name: Medulla, A1M, controll, 7dpi, replicate2

value: Kidney medulla

value: 7 days


title: gastric mucosa, angular incisure B5_2


title: gastric mucosa, angular incisure B5_1


title: NaraCOVID_TP1_CD8_019_TCR


title: gastric mucosa, greater curvature B4_2


title: gastric mucosa, lesser curvature C3


title: R42_a305_FB23_ACATACGTGA-TCTGTAACGC

description: oral antagomir treatment

source_name: abdominal fat body

value: fat body


title: R42_ams_B13_TGCGTGCGAA-ATCGGTATGA

description: oral antagomir treatment


title: Medulla_150MBq_controll_7dpi_rep3 [SAMPLE 27]

description: controll

source_name: Medulla, 150MBq, controll, 7dpi, replicate3


title: gastric mucosa, greater curvature B4_1

value: healthy gastric mucosa


title: R42_a305_FB22_CCTTGTAGCG-GCTGGCTCAA

description: oral antagomir treatment


title: NaraCOVID_TP1_CD8_018_TCR

value: male


title: NaraCOVID_TP1_CD8_017_TCR


title: gastric mucosa, lesser curvature B3_2


title: NaraCOVID_TP1_CD8_016_TCR


title: Medulla_150MBq_controll_7dpi_rep2 [SAMPLE 26]

description: controll

source_name: Medulla, 150MBq, controll, 7dpi, replicate2


title: Medulla_A1M_7dpi_rep3 [SAMPLE 24]

description: test

source_name: Medulla, A1M, 7dpi, replicate3


title: gastric mucosa, lesser curvature B3_1


title: R42_a305_FB21_CCATGCGTTG-GACAACACGG

description: oral antagomir treatment


title: R42_a305_FB20_ACTTGTGACG-GGAGCTTGTG

description: oral antagomir treatment


title: Medulla_150MBq_controll_7dpi_rep1 [SAMPLE 25]

description: controll

source_name: Medulla, 150MBq, controll, 7dpi, replicate1


title: Medulla_A1M_controll_7dpi_rep3 [SAMPLE 30]

description: controll

source_name: Medulla, A1M, controll, 7dpi, replicate3

value: A1M vehicle solution


title: NaraCOVID_TP1_CD8_015_TCR


title: Medulla_A1M_7dpi_rep2 [SAMPLE 23]

description: test

source_name: Medulla, A1M, 7dpi, replicate2


title: R42_a305_FB19_CGTGTAACTT-TTGTCACGTT

description: oral antagomir treatment


title: Medulla_A1M_7dpi_rep1 [SAMPLE 22]

description: test

source_name: Medulla, A1M, 7dpi, replicate1


title: gastric mucosa, fundus B2_1


title: Medulla_A1M_controll_7dpi_rep1 [SAMPLE 28]

description: controll

source_name: Medulla, A1M, controll, 7dpi, replicate1


title: gastric mucosa, fundus B2_2


title: NaraCOVID_TP1_CD8_014_TCR

source_name: Peripheral blood T cells

value: female


title: gastric mucosa, cardia B1

source_name: healthy gastric mucosa


title: NaraCOVID_TP1_CD8_013_TCR


title: Medulla_150MBq_A1M_7dpi_rep3 [SAMPLE 21]

description: test

source_name: Medulla, 150MBq, A1M, 7dpi, replicate3


title: R42_a305_FB17_TTAACGCAGA-GGCGGATCAA

description: oral antagomir treatment


title: Medulla_150MBq_A1M_7dpi_rep2 [SAMPLE 20]

description: test

source_name: Medulla, 150MBq, A1M, 7dpi, replicate2


title: R42_a305_FB18_AGGTAGTGCG-ATCAGCCTCC

description: oral antagomir treatment


title: NaraCOVID_TP1_CD8_012_TCR


title: gastric mucosa, pylorus A7_2


title: R42_a305_FB16_GGCCTTGTTA-CGTGGAACAC

description: oral antagomir treatment


title: NaraCOVID_TP1_CD8_011_TCR


title: gastric mucosa, pylorus A7_1


title: NaraCOVID_TP1_CD8_010_TCR


title: Medulla_150MBq_A1M_7dpi_rep1 [SAMPLE 19]

description: test

source_name: Medulla, 150MBq, A1M, 7dpi, replicate1


title: gastric mucosa, antrum A6


title: R42_a305_FB15_CTGAACCTCC-ACAATGCCTG

description: oral antagomir treatment


title: gastric mucosa, angular incisure A5


title: Medulla_150MBq_7dpi_rep3 [SAMPLE 18]

description: test

source_name: Medulla, 150MBq, 7dpi, replicate3


title: R42_a305_FB13_CACGAGTATG-CGCTAAGGCT

description: oral antagomir treatment


title: Medulla_150MBq_7dpi_rep2 [SAMPLE 17]

description: test

source_name: Medulla, 150MBq, 7dpi, replicate2


title: NaraCOVID_TP1_CD8_008_TCR


title: R42_a305_FB14_CCGCTACCAA-ACTGAGGTAA

description: oral antagomir treatment


title: Medulla_150MBq_7dpi_rep1 [SAMPLE 16]

description: test

source_name: Medulla, 150MBq, 7dpi, replicate1


title: gastric mucosa, greater curvature A4


title: NaraCOVID_TP1_CD8_006_TCR


title: NaraCOVID_TP1_CD8_007_TCR


title: R42_a305_B22_TTGACCTAGC-GGAACACCAA

description: oral antagomir treatment

source_name: whole brain


title: gastric mucosa, lesser curvature A3


title: NaraCOVID_TP1_CD8_005_TCR


title: Medulla_A1M_controll_1dpi_rep2 [SAMPLE 14]

description: controll

source_name: Medulla, A1M, controll, 1dpi, replicate2

value: 1 day


title: NaraCOVID_TP1_CD8_004_TCR


title: R42_a305_B21_AGGTCCTATA-GCGTGACGTT

description: oral antagomir treatment


title: Medulla_A1M_controll_1dpi_rep3 [SAMPLE 15]

description: controll

source_name: Medulla, A1M, controll, 1dpi, replicate3


title: gastric mucosa, fundus A2


title: Medulla_A1M_controll_1dpi_rep1 [SAMPLE 13]

description: controll

source_name: Medulla, A1M, controll, 1dpi, replicate1


title: NaraCOVID_TP1_CD8_003_TCR


title: R42_a305_B20_GAACACAGTT-GTGAATTCGG

description: oral antagomir treatment


title: gastric mucosa, cardia A1


title: Medulla_150MBq_controll_1dpi_rep3 [SAMPLE 12]

description: controll

source_name: Medulla, 150MBq, controll, 1dpi, replicate3

value: phosphate buffered saline solution


title: shScr-H

city: Tianjin

first: feng

last: dong

address: Qixiangtai Road 22

institute: Tianjin Medical University

description: U87 shScr Hypoxia

data_processing:
Raw data were processed using CASAVA V1.6 package
The quality control of each sample was accomplished using FASTQC V0.11.5
Clean  reads were aligned to human reference genome hg19 by HISAT
RSEM was used to calculate gene expression, differential expression was determined by BGI’s developed algorithm.
Differential expressed genes (DEGs) with log2(fold change) > 1 and FDR <0.05 were considered as significant.
Assembly: hg19
Supplementary files format and content: bigwig file for each Sample

source_name: cell line

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using NEBNext Ultra RNA library Prep Kit for Illumina.

value: cell line

tag: cell line

value: glioblastoma cell line


title: NaraCOVID_TP1_CD8_002_TCR

value: CD8+ T cells and CD19+ B cells


title: Medulla_150MBq_controll_1dpi_rep1 [SAMPLE 10]

description: controll

source_name: Medulla, 150MBq, controll, 1dpi, replicate1

tag: tissue type


title: shScr-N

description: U87 shScr Normoxia


title: Medulla_150MBq_controll_1dpi_rep2 [SAMPLE 11]

description: controll

source_name: Medulla, 150MBq, controll, 1dpi, replicate2

tag: time


title: R42_a305_B18_CGGTAAGTAA-TAGATAGCTC

description: oral antagomir treatment

value: brain

tag: treatment


title: NaraCOVID_TP1_CD8_001_TCR

tag: cell type

value: before receiving the first dose


title: shPRMT2-H

description: U87 shPRMT2 Hypoxia


title: R42_a305_B23_GCTTCAATCA-TTCCACCTGG

description: oral antagomir treatment

value: worker


title: Medulla_A1M_1dpi_rep3 [SAMPLE 9]

description: test

source_name: Medulla, A1M, 1dpi, replicate3

value: A1M (5 mg/kg)


title: NaraCOVID_TP1_CD4_041_TCR

source_name: Peripheral blood T cells

value: Three shots of Pfizer-BNT162b2 vaccine

value: CD4+ T cells

tag: age


title: R42_a305_B17_ATTACGGTTG-GGTGATTCCG

description: oral antagomir treatment


title: R42_a305_B16_TCTCTAGTCG-AATCGATCCA

description: oral antagomir treatment


title: Medulla_A1M_1dpi_rep2 [SAMPLE 8]

description: test

source_name: Medulla, A1M, 1dpi, replicate2

value: Kidney medulla


title: NaraCOVID_TP1_CD4_039_TCR

tag: Sex


title: Stiff 2

city: Bryan

first: Irtisha

last: Singh

state: TX

address: 8447 Riverside Pkwy, Medical Research and Education Building II Suite 4344

department: Department of Molecular and Cellular Medicine

institute: Texas A&M University

data_processing:
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's NCS 1.0.2 and RFV 1.0.2 software with default parameter settings. Sequencer .cbcl basecall files were demultiplexed and formatted into .fastq files using bcl2fastq 2 2.19.0 script configureBclToFastq.pl.
Sequenced reads were trimmed for adaptor sequence and aligned by STAR aligner
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons (excluding 5UTR and 3UTR) of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library (only reads mapping to annotated regions of the genome were used for the total libraray size).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for all samples

source_name: MNP GelMA

growth_protocol: hMSCs were cultured under media conditions consisting of α-minimal essential media (alpha-MEM, Hyclone, GE Sciences) with 16.5% fetal bovine serum (Atlanta Biologicals, USA) and 1% penicillin/streptomycin (100 U/100 µg/mL, Gibco). After every 2-3 days, culture media was exchanged for fresh media. Cells were passaged with 0.5% trypsin-EDTA upon reaching 90% confluency and mixed with hydrogel precursor solutions at ~10,000 cells/uL. All experiments were completed with cell populations under P5.

extract_protocol:
At the end of 7 days of culture, cells were harvested from hydrogels via micropestle homogenization in cell lysis buffer. Total RNA was extracted (Zymogen, High Purity RNA Isolation kit), and then converted into cDNA (>1 μg).
RNA libraries were prepared for sequencing using standard BGI protocols for DNBseq™ rapid Whole Genome Sequencing (rWGS)

treatment_protocol: hMSCs were encapsulated within soft (5% w/v GelMA, 0.5% w/v Irgacure 5939) or stiff (MNP (5 ug/mL Fe content), 5% w/v GelMA, 0.5% w/v Irgacure 5939) hydrogel precursor solutions and UV crosslinked (30 mW/cm2, 60 seconds)

value: Bone marrow derived mesenchymal stem cells

value: encapsulated within stiff hydrogel precursor solutions


title: NaraCOVID_TP1_CD4_040_TCR

city: Noda

value: male

tag: date


title: Medulla_A1M_1dpi_rep1 [SAMPLE 7]

description: test

source_name: Medulla, A1M, 1dpi, replicate1


title: Stiff 1


title: R42_a305_B14_TCAATCGTCT-GACTATGTCA

description: oral antagomir treatment

tag: caste


title: NaraCOVID_TP1_CD4_038_TCR


title: NaraCOVID_TP1_CD4_037_TCR


title: Medulla_150MBq_A1M_1dpi_rep3 [SAMPLE 6]

description: test

source_name: Medulla, 150MBq, A1M, 1dpi, replicate3

value: 150 MBq Lu-177-octreotate + A1M (5 mg/kg)


title: Medulla_150MBq_A1M_1dpi_rep2 [SAMPLE 5]

description: test

source_name: Medulla, 150MBq, A1M, 1dpi, replicate2


title: Soft 2

source_name: Control GelMA

value: encapsulated within soft hydrogel precursor solutions


title: R3_ams_FB23_TTCATAGACC-GCATGTTGAA

description: oral antagomir treatment

source_name: abdominal fat body

value: fat body

value: antagomir-missense

tag: colony


title: NaraCOVID_TP1_CD4_036_TCR


title: NaraCOVID_TP1_CD4_035_TCR

value: female


title: NaraCOVID_TP1_CD4_033_TCR


title: R42_a305_B19_TAACGTCCGG-CTCTCGAGGT

description: oral antagomir treatment

source_name: whole brain


title: COBRA_0703H_LPS

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

data_processing:
Fastq files were assessed for quality using the FastQC package and no samples were excluded from analysis. Bowtie was used to map 100-bp paired end reads to the human transcriptome (Ensembl, GRCh37v70), and gene expression estimates were derived using the mmseq pipeline. DESeq2  was used to normalise count data and determine gene expression differences between treatments.
Assembly: hg19
Supplementary files format and content: .gene.mmseq.txt files contain counts per gene

source_name: Adolescent Human Peripheral Blood

growth_protocol: We performed two cohort studies ('COBRA' for adolescents with obesity and 'PAID' for controls) and isolated PBMCs. Following PBMC isolation we further purified the monocytes using a magnetic bead isolation method (negative isolation)

extract_protocol:
500.000 cells of the monocyte-enriched cell suspension were used for RNA extraction (250.000 for medium stimulated, 250.000 for LPS stimulated). The cells were spun down at 500g for 5 minutes. Supernatant was removed and the cell pellet was resuspended with 500µL TrIzoL solution. The resuspended solution was stored at -80C until RNA isolation. RNA was isolated using RNeasy Micro Kit (Qiagen) with adaptation of the first step for TriZOL samples, according to manufacturer’s protocol, and included on column DNAse treatment.
RNA quality was assessed on the Agilent 2100 analyzer. cDNA library construction and sequencing were performed at Beijing Genomics Institute using the BGISEQ-500 platform with a starting input of 200ng. Libraries were sequenced on the BGISeq-500 platform generating an average of 20 million reads per sample.
To infer gene expression levels, RNA-seq reads were aligned to hg19 human transcriptome using Bowtie. Quantification of gene expression levels as RPKM was performed using MMSEQ. Reads/transcripts were normalized using DEseq2 and pair-wise comparisons were performed.

value: Adolescent Human Peripheral Blood

tag: individual

value: Monocyte

tag: group

value: COBRA

value: Negatively selected circulating monocytes exposed to LPS in vitro for 4 hours


title: R42_a305_B13_TGGAGAGCCA-TTGTGCCTAA

description: oral antagomir treatment

value: worker

value: brain


title: Stiff 3


title: Soft 3


title: Medulla_150MBq_A1M_1dpi_rep1 [SAMPLE 4]

description: test

source_name: Medulla, 150MBq, A1M, 1dpi, replicate1

value: 1 day


title: R3_ams_FB24_CCAACTCCGA-GCGTTACTCC

description: oral antagomir treatment


title: NaraCOVID_TP1_CD4_030_TCR

value: Three shots of Pfizer-BNT162b2 vaccine

value: CD4+ T cells

value: before receiving the first dose


title: Medulla_150MBq_1dpi_rep1 [SAMPLE 1]

description: test

source_name: Medulla, 150MBq, 1dpi, replicate1

value: Kidney medulla

value: 150 MBq Lu-177-octreotate


title: R3_ams_FB21_CGTAACAGAA-CCGCTATAGA

description: oral antagomir treatment


title: R3_ams_FB19_TGAAGGTGAA-AACGAGGCGT

description: oral antagomir treatment


title: Soft 1

value: Bone marrow derived mesenchymal stem cells


title: R42_a305_B15_GTCGTGACAC-AGCCATACA

description: oral antagomir treatment


title: Medulla_150MBq_1dpi_rep2 [SAMPLE 2]

description: test

source_name: Medulla, 150MBq, 1dpi, replicate2


title: COBRA_0703H_RPMI

value: Negatively selected circulating monocytes exposed to media in vitro for 4 hours


title: Medulla_150MBq_1dpi_rep3 [SAMPLE 3]

description: test

source_name: Medulla, 150MBq, 1dpi, replicate3


title: R3_ams_FB18_TTGGTACGCG-TGTCCTACTA

description: oral antagomir treatment

value: fat body


title: R3_ams_FB22_AAGGCCATAA-TGTCCATCGG

description: oral antagomir treatment

value: antagomir-missense


title: COBRA_1821A_LPS


title: NaraCOVID_TP1_CD4_029_TCR

value: female


title: COBRA_1844K_RPMI

value: Adolescent Human Peripheral Blood


title: R3_ams_FB17_AATGACGCTG-GCACTCATCC

description: oral antagomir treatment


title: NaraCOVID_TP1_CD4_027_TCR

value: male


title: NaraCOVID_TP1_CD4_032_TCR


title: R3_ams_FB16_AAGCGGAGAA-AGTTCGTACA

description: oral antagomir treatment


title: R3_ams_FB20_GTAGTGGCTT-AACAGCGGTG

description: oral antagomir treatment


title: Overexp_CS8M_Vessel_rep5

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

hyb_protocol: 2 µg of the labeled cDNA were subjected to hybridization. The cDNA was not fragmented before hybridization. Hybridization was performed following the Agilent protocol at 65°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 2 µm/pixel resolution and analyzed with Mapix 8.5.0

data_processing: Raw data was further processed using R (http://www.R-project.org) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. NAR 43(7), e47). Background correction was performed with the normexp model using negative control spots and and offset of 1. Spot intensities were quantile normalized between arrays.

source_name: Microdissected structures/cells, lung vessels and septa compartment

label_protocol: Purified total RNA was amplified using the Ovation PicoSL WTA System V2 kit (NuGEN Technologies, Bemmel, Netherlands). Per sample, 2 µg amplified cDNA was Cy-labeled using the SureTag DNA labeling kit (Agilent, Waldbronn, Germany).

growth_protocol: Lung samples are harvested from animals that were exposed to cigarette smoke for 3 months.

extract_protocol: Laser microdisected septa and vessel compartment; Qiagen Rneasy Micro Kit.

treatment_protocol: 3 months time point: Room Air (RA) or Cigarette Smoke (CS) Exposure; Wt, Fgf10+/-, Fgfr2b+/- animals.  Therapeutic approach: 8 months of RA / CS Exposure followed by 1 week of treatment (+/- doxycycline)

tag: fgf10 expression

value: overexpressing

value: cigarette smoke

tag: compartment

value: Vessel


title: NaraCOVID_TP1_CD4_031_TCR


title: NaraCOVID_TP1_CD4_026_TCR


title: COBRA_1844K_LPS

value: Monocyte

value: COBRA

value: Negatively selected circulating monocytes exposed to LPS in vitro for 4 hours


title: R3_ams_FB15_GCTAGAGGTG-GTGGTTCTCC

description: oral antagomir treatment

value: worker


title: COBRA_1821A_RPMI


title: NaraCOVID_TP1_CD4_025_TCR

value: Three shots of Pfizer-BNT162b2 vaccine

value: CD4+ T cells

value: before receiving the first dose


title: Overexp_CS8M_Vessel_rep3


title: R3_ams_FB14_CTCGTTGCGT-TACGACACTT

description: oral antagomir treatment


title: NaraCOVID_TP1_CD4_024_TCR


title: COBRA_2948G_LPS


title: COBRA_2948G_RPMI


title: COBRA_2970G_LPS


title: COBRA_2970G_RPMI


title: NaraCOVID_TP1_CD4_023_TCR


title: R3_ams_B24_GATCTTGGCA-CGCTGTCTAA

description: oral antagomir treatment

value: brain


title: R3_ams_FB13_TGTAAGCACA-AGAACACATC

description: oral antagomir treatment


title: NaraCOVID_TP1_CD4_022_TCR


title: COBRA_2972E_RPMI

value: Negatively selected circulating monocytes exposed to media in vitro for 4 hours


title: NaraCOVID_TP1_CD4_021_TCR


title: R3_ams_B23_TCTGTCGTGC-ACTAGTGCTT

description: oral antagomir treatment