title: PBMCs, Son

city: Rochester

first: Cheng

last: Zhang

state: MN

address: 200 1st street SW

institute: Mayo Clinic

data_processing:
Fastq files of pair-end RNA-Seq reads were aligned with STAR to the reference human genome GRCh38 with default parameters.
Reads that aligned to the mouse genome.
Gene level counts were obtained using featureCounts 1.4.6 from the subRead package with gene models from corresponding UCSC annotation packages.
Assembly: GRCh38
Supplementary files format and content: raw counts in tab-delimited text file

source_name: Peripheral Blood Mononuclear Cells

growth_protocol: Extraction of Peripheral Blood Mononuclear Cells

extract_protocol:
RNA was column-extracted using Rneasy Mini kit (Qiagen #74104). DNA removed by addition of on-column DNase I treatment (#EN0521). Further RNA purification and concentration were performed using Concentrator-5 (Zymo #R1013). DNA removed by addition of on-column DNase I treatment (#EN0521). Further RNA purification and concentration were performed using Concentrator-5 (Zymo #R1013)
RNA-seq libraries were prepared from 100-200 ng high-quality RNA using TruSeq RNA Library Prep Kit v2 (Illumina)

value: Peripheral Blood Mononuclear Cells

value: Heterozygous IRF8 variant c.1279dupT (p.*427Leuext*42)


title: SARS-CoV-2 infection, PBS treatment-4

status: Public on Dec 02 2025

type: SRA

city: Xi’an

first: Ping

last: Zhu

address: Changle Xi Road

country: China

institute: Fourth Military Medical University

description:
Library name: Ctrl_4
10x genomics

library_source: transcriptomic

data_processing:
For rhesus macaques data, spaceranegr (v1.2.1) was used to process spatial sequencing data for mapping to reference genome. SCTransform function in Seurat (v4.1.0) was used to process the gene expression matrix. The pathologists preliminarily divided the pathological areas of the sections in virus-infected group, integrated the matrix and gene expression matrix after stlearn sorted out the H&E sections, and then performed dimensionality reduction clustering, which was defined according to the data of pathological spots in each cluster.
For mouse data, spaceranegr (v1.3.1) was used to process mouse spatial sequencing data for mapping to reference genome. SCTransform function in Seurat (v4.1.0) was used to process the gene expression matrix. Spots with SARS-CoV-2 genes was defined as infected spots; otherwise, defined as uninfected spots. On this basis, the two uninfected positions closest to the infected positions are defined as border positions. runRCTD function in spacexr (v2.2.1) was used for assigning single cell types to spatial transcriptomics spots and defining a spot where the proportion of a certain cell type exceeds 50% as that cell type.
Assembly: macaque reference Ensembl_release105 and mouse reference Ensembl_release111
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: tissue images.gz
Library strategy: Spatial Transcriptomics

molecule: polyA RNA

organism: Macaca mulatta

source_name: lung

extract_protocol:
The spatial transcriptome sequencing was performed by Genedenovo Biotechnology Co., Ltd. The lung tissues of rhesus macaques (Healthy, n=4; Ctrl, n=4; MPZ, n=4; 3E8, n=4; MPZ+3E8, n=4; at 7dpi) and virus-infected hCD147 mice (n=4; at 3dpi) were used to perform spatial transcriptome sequencing. The tissues were embedded in the OCT-filled mold and cut into slices by cryo-sectional technology. Subsequently, the samples were barcoded through 10× Genomics Platform using Visium Spatial Tissue Optimization Reagent Kit and Slide Kit (PN-1000192, PN-1000191, 10× Genomics), Visium Spatial Gene Expression Reagent Kit and Slide Kit (PN-1000189, PN-1000188, 10× Genomics), Library Construction Kit (PN-1000196, 10× Genomics), and Dual Index Kit (PN-1000215, 10× Genomics). Each sequencing library was sequenced using Illumina sequencing platform.
10× Genomics Visium Spatial

tag: tissue

value: lung

tag: age

value: 3-4 years

tag: Sex

value: male

tag: virus

value: SARS-CoV-2 (Beta strain)

tag: treatment

value: PBS


title: HSC-2, CDDP-exposure, rep3

city: Sendai

first: Yuki

last: Nakayama

address: 2-1 Seiryo-machi,Aoba

department: Biochemistry and Molecular Biology

country: Japan

institute: Tohoku Medical Megabank Organization, Tohoku University

description:
Library name: 44
Column name in txi_counts.csv: 2CR_3

data_processing:
Sequence reads were trimmed for adopter sequence/low-quality sequence using fastp
Read counts data were generated by trimmed sequence reads using Sarmon Quant
Assembly: GRCh38
Supplementary files format and content: txi_counts.csv

molecule: total RNA

organism: Homo sapiens

growth_protocol: All cell lines were maintained  RPMI1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics in humidified atmosphere  with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNeasy plus kit (Qiagen). 11 ng/μL RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using MGIEasy RNA directional library prep kit (MGI) following manufacture's protocol.

tag: cell line

tag: cell type

value: Head and neck squamous cell carcinoma

value: CDDP exposure


title: AKO-MOCK1-IP

city: Suzhou

first: Anqi

last: Dong

address: 199 Ren'ai Road

institute: Soochow university

description: Library name: sample6

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Raw reads would be processed to get high quality clean reads according to four stringent filtering standards: i Removing reads containing adapters; ii Removing reads containing more than 10% of unknown nucleotides (N); iii Removing reads that are all A bases；ⅳ Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The rRNA removed reads of each sample were then mapped to reference genome, respectively.
MACS2 (version: 2.1.2) software was used to identify read-enriched regions from MeRIP-seq data. Dynamic Poisson Distribution was used to calculated p-value of the specific region based on the unique mapped reads. The region would be defined as a peak when q-value<0.05.
The distribution of peak on different function regions, such as 5’UTR, CDS and 3’UTR, was performed.
All peak related genes were mapped to GO terms in the Gene Ontology database.
Pathway enrichment analysis identified significantly enriched metabolic pathways or signal transduction pathways in peak related genes comparing with the whole genome background.
MEME suit (http://meme-suite.org/) and DREME (http://memesuite.org/tools/dreme) were used to detect the significant sequence motif in the transcript sequence associated with peaks.
The DiffBind (version 2.8) software was used to combine peaks of every group, and obtained the union of peaks among groups. Peak abundance was shown by calculating rpm-values of each sample.
Peaks distant from peak-related gene (which locates farther upstream than 2k or downstream 300bp) were removed, and the remaining peak related genes were used for subsequent GO and KO enrichment analysis.
The DiffBind (version 2.8) software was used to analysis RNA methylation rate between groups.
Assembly: GRCm39
Supplementary files format and content: all_samples.expression.Annot.xls includes raw counts for each sample
Library strategy: MeRIP-Seq

organism: Mus musculus

source_name: peritoneal cavity

growth_protocol: Peritoneal macrophages (PMs) were isolated from WT and Adap-/- mice via peritoneal lavage using 5 ml of phosphate-buffered saline (PBS), 3 days after injection of 3% thioglycolate. The PMs were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin-streptomycin.

extract_protocol:
Total RNA was extracted and purified with TRIzol reagent (Invitrogen, USA) following the manufacturer’s procedure. The RNA amount and purity were examined using a Nanodrop 2000 (Thermo Fisher Scientific, USA).
After total RNA was extracted, the enriched RNA was fragmented into short fragments (about 100nt) by using fragmentation buffer. RNA was divided into two parts, one of which was used as the input (no IP experiment was performed). The other RNA was enriched with m6A specific antibody. The enriched RNA was reverse transcripted into cDNA with random primers. Next, the cDNA fragments was end repaired, and ligated to Illumina sequencing adapters. Finally we got qualified library for sequencing, sequenced using Illumina HiSeqTM 4000 (or other platforms) by Gene Denovo Biotechnology Co. (Guangzhou, China)

treatment_protocol: PMs isolated from WT and Adap-/- mice were treated or untreated with 1 ug/ml LPS for 6 h.

value: peritoneal cavity

value: primary cell

value: peritoneal macrophage

tag: genotype

value: ADAP knockout

value: mock


title: PBMCs, Mother

country: USA


title: SARS-CoV-2 infection, PBS treatment-3

description:
Library name: Ctrl_3
10x genomics


title: AKO-LPS2-IP

description: Library name: sample4

value: LPS stimulation (1ug/ml, 6h)


title: HSC-2, CDDP-exposure, rep2

description:
Library name: 43
Column name in txi_counts.csv: 2CR_2


title: Healthy-4

description:
Library name: Healthy_4
10x genomics

value: 3-5 years


title: PBMCs, Control

value: Wild-type IRF8


title: HSC-2, CDDP-exposure, rep1

description:
Library name: 42
Column name in txi_counts.csv: 2CR_1


title: HSC-3, non-treatment, rep1

description:
Library name: 45
Column name in txi_counts.csv: 3P_1

value: No


title: SARS-CoV-2 infection, PBS treatment-2

description:
Library name: Ctrl_2
10x genomics


title: RT_Amp rep2

city: shanghai

first: Xu

last: Chu

address: Dong'an Road

institute: Fudan University Shanghai Cancer Center

description:
eAMOUR_rep2
RT_Amp_TPM.txt

data_processing:
Reads were trimmed using Cutadapt
mapped to hg38  use STAR
Gene count were generated using featureCounts
Gene TPM were generated using kallisto
Assembly: hg38
Supplementary files format and content: tab-delimited text file include TPM for each Sample

source_name: kidney

growth_protocol: HEK 293T cells were cultured in DMEM high glucose (GIBCO) supplemented with 10% heat-inactivated FBS, 100 U/mL penicillin and 100 μg/mL of streptomycin. Cells were kept under standard 37 ℃ and 5% CO2 conditions

extract_protocol:
RNA was amplified in-situ, not extracted from the cultured cells.
For AMOUR: Cells (> 97% viability) were fixed with 4% PFA and immobilized with Concanavalin A beads. The bead-bound cells underwent three washes with AMOUR-wash buffer (PBS, 1 mM ATP, 0.2 U μL-1 RNase inhibitor). Subsequently, the beads were resuspended in PBS with RNase Inhibitor (40 U μL-1) and annealed with T7N9 oligo (0.25 μM). The reaction mixture was incubated at 42 °C for 2 min, followed by ramping to 25 °C and a 5-min hold. After washing, linear amplification with T7 RNA Polymerase occurred at 37 °C for 2 h with shaking at 1,200 rpm. The resulting RNA was purified using Dynabeads MyOne Silane beads. For GWA-Pd and WGA-T: HEK293T cells were collected with (WGA-T) or without 0.25% trypsin treatment (WGA-Pd), and blocked with Egg white avidin and yeast tRNA. Following buffer removal, 500 µg of biotin-WGA was added to the cells and incubated at 37 ℃ for 15 min. After centrifugation at 500 × g, 4 ℃ for 5 min to eliminate excess biotin-WGA, cells were washed with PBS. Lysis was performed with ice-cold lysis buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 1% DDM, and 0.001% GDN with 0.1% CHS, 200 U mL-1 RNase inhibitor, 1 × proteinase inhibitor). Dynabeads MyOne Streptavidin C1 were utilized for capturing membrane-associated RNA, extracted using Buffer RLT, and subsequently purified using silane beads. For RT-Amp: Cells were harvested, fixed, and immobilized utilizing ConA beads, followed by T7N9 oligo annealing through the "AMOUR" strategy. Reverse transcription (RT) was performed on beads employing HiScript II Reverse Transcriptase. Following RT, the cDNA product underwent purification with the DNA Clean Concentrator. Subsequent second-strand synthesis was achieved with Klenow exo- and P5N6 Oligo, and dsDNA was purified using silane beads. Linear amplification was executed using T7 RNA Polymerase. The resulting amplified RNA was purified with silane beads. The purified RNA was ligated to 3'adapter and reverse transcribed. The cDNA was ligated with cDNA adapter and subjected to limited cycle PCR, ready for sequencing.

treatment_protocol: HEK 293T cells were subjected to different strategies of AMOUR, WGA-Pd,WGA-T, and RT-Amp to profile surface RNAs.

value: kidney

value: Human embryonic kidney

value: WT

tag: assay

value: AMOUR (RT_Amp)


title: AKO-MOCK1-INPUT

description: Library name: sample5


title: RT_Amp rep1

description:
eAMOUR_rep1
RT_Amp_TPM.txt


title: AKO-LPS2-INPUT

description: Library name: sample3


title: SARS-CoV-2 infection, PBS treatment-1

description:
Library name: Ctrl_1
10x genomics

value: lung

value: 3-4 years

value: male

value: SARS-CoV-2 (Beta strain)


title: AKO-LPS1-IP

description: Library name: sample2

value: peritoneal cavity


title: Healthy-1

description:
Library name: Healthy_1
10x genomics

value: female


title: HSC-2, non-treatment, rep1

description:
Library name: 15
Column name in txi_counts.csv: 2P_1

value: Head and neck squamous cell carcinoma


title: AsPC-1 treated with Isotype, rep2

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center

description: Library name: AsPC-1_ISO2

data_processing:
raw sequence reads were mapped to hg38 transcriptome using STAR2 v2.7.10b and salmon v1.10.2
Raw counts were collected using htseq v0.11.0 and TPM calculated using salmon reported effective gene lengths
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes log2 converted TPM values for each sample

extract_protocol:
RNA was harvested using Qiagen Rneasy Mini Kit. 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were generated from cDNA using the Illumina Nextera XT DNA Sample Preparation Kit. cDNA library quality was assessed using an Agilent 2100 Bioanalyzer

value: Human PDAC cell


title: Healthy-3

description:
Library name: Healthy_3
10x genomics


title: WGA-T rep1

description:
T-WGA_rep1
WGAT-WGA_TPM.txt

value: WGA-T


title: HSC-2, non-treatment, rep3

description:
Library name: 41
Column name in txi_counts.csv: 2P_3


title: RPMI2650, CDDP-exposure, rep3

description:
Library name: 14
Column name in txi_counts.csv: 1CR_3

value: CDDP exposure


title: AsPC-1 treated with 22B, rep2

description: Library name: AsPC-1_22B2


title: AKO-LPS1-INPUT

description: Library name: sample1

value: primary cell

value: peritoneal macrophage

value: ADAP knockout

value: LPS stimulation (1ug/ml, 6h)


title: AsPC-1 treated with 22B, rep1

description: Library name: AsPC-1_22B1


title: WGA-Pd rep2

description:
WGA_rep2
WGAT-WGA_TPM.txt

value: kidney

value: Human embryonic kidney

value: WGA-Pd


title: AMOUR rep2

description:
Rep2
AMOUR_TPM.txt

value: WT

value: AMOUR


title: A549, shGLI1 SMARCB1, bigwig

city: Tlalnepantla

first: Armas

middle: López

last: Leonel

state: Estado de México

address: Av. de los reyes

department: UBIMED

country: Mexico

institute: Universidad Nacional Autónoma de México

description: Library name: A549_shGLI1_SMARCB1.bigwig

library_source: genomic

data_processing:
For the cleaning of adapter and quality readings, the parameters provided by default by Trim Galore version 0.6.7 For the alignment and quality analysis, BWA-MEM version 0.7.17, included in Galaxy was used against the hg19 GRCh37 human reference genome The data was filtered considering a mapping quality of less than 20 (p>0.02) with the SAMtools version 1.8 tool The significant peaks (Meox2 binding sites) of mapped reads were identified using the program ‘findPeaks’ from the software suite HOMER with the following parameters: false discovery rate = 0.001, Poisson p-value over input required = 1.00e-04, fold over input required = 4.00, maximum fold under expected unique positions for tags = 2.00, and normalization to 10 million mapped tags per experiment The significant peaks of the aligned reads were identified with MACS version 2.1.1.20160309.6 with the parameters FDR=0.05, minimum mfold=5, maximum mfold=50 and band width=300 We used the web-based ChIP-Seq analysis tool ChIPseek to obtain the genomic annotation and visualization of Meox2 TFBSs.  Supplementary files format and content: The bed files include Meox2 values in 100bp bins for each ChIP-seq sample. The bam files contain information about sequence reads after they have been aligned against a reference genome.
Assembly: hg19
Supplementary files format and content: bw

molecule: genomic DNA

extract_protocol: A549 cells were fixed with 1% formaldehyde for 10 minutes, then glycine at 0.125 M was added. After cellular lysis, chromatin was sonicated using a VCX130PB vibra cell (Sonics). The DNA size profile was evaluated in a bioanalyzer 2100 (kit High Sensitivity DNA Reagent Agilent No. Cat. 50674626), for the libraries assemble the kit Truseq Chip de Illumina (No. Cat. IP-202-1012) was used, using a total of 10 ng. Cutted DNA fragments were performed from 300 to 500 bp, the distribution of the amplified libraries were evaluated by TapeStation 4200 (kit High Sensitivity DNA Reagent Agilent Technologies No. Cat. 5067- 5585), the final loading concentration was of 1.5 pM and a 30% of control PhiX was included. For the sequenciation we used a kit Nextseq 500/550 High Output (150-cycles) Flow Cell (No. Cat. FC-404-202, 20024904).

value: Human lung cancer


title: RPMI2650, CDDP-exposure, rep2

description:
Library name: 13
Column name in txi_counts.csv: 1CR_2


title: WGA-Pd rep1

description:
WGA_rep1
WGAT-WGA_TPM.txt


title: WGA-T rep2

description:
T-WGA_rep2
WGAT-WGA_TPM.txt


title: SARS-CoV-2 infection, Meplazumab and 3E8 treatment-3 [scRNA-seq]

description:
Library name: MPZ_3E8_3
10x genomics

library_source: transcriptomic single cell

data_processing:
Cellranger (v7.1.0) was used to process scRNA-seq data with macaque reference Ensembl_release105. Seurat (v4.1.0) was used for processing expression matrices. The cells with less than 200 and more than 5000 genes were filtered. Cells with less than 25000 nUMI detected and less than 10 percent of detected reads coming from mitochondrial genes were finally retained. DoubletFinder (v2.0.3) and harmony (v0.1.0) was set to default parameter.
ScRNA-seq data was aligned and quantified using Seeksoultools (v1.2.0) and STAR (v2.7.1a) against the Ensembl_release111 added with SARS-CoV-2 Beta reference genome. The mouse CD147 sequence in the reference genome was replaced with human CD147 sequence. Raw counts were then used for downstream analysis. Seurat (v4.1.0) was used to process the gene expression matrix. Cells with SARS-CoV-2 genes detected were labeled as infected cells. Cells with less than 200 and more than 5600 genes were filtered. Cells with less than 12000 nUMI detected and less than 33 percent of detected reads coming from mitochondrial genes were finally kept. To remove the deviation of double cells, DoubletFinder (v2.0.3) was used with pN parameter of 0.25 and nExp parameter of 4×10-6. The remaining cells were then used for gene expression matrix logarithmic normalization and scaling. To integrate cells into a shared space from different datasets for unsupervised clustering, harmony (v0.1.0) was used to correct the batch effect by default parameters.
Assembly: macaque reference Ensembl_release105 and mouse reference Ensembl_release111
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
The scRNA-seq was performed by Genedenovo Biotechnology Co., Ltd. The lung tissues of rhesus macaques (Healthy, n=4; Ctrl, n=4; MPZ, n=4; 3E8, n=4; MPZ+3E8, n=4; at 7dpi) and virus-infected hCD147 mice (n=4; at 3dpi) were cut into 1–2 mm3 pieces in DPBS buffer and digested with collagenase I and DNase I at 37°C for 30–60 min with persistent shaking every 10 min. The digested tissues were then passed through a 70 μm mesh filter, and the cell suspension was centrifuged at 4 °C for 5 min (350 g). The cell pellet was suspended in red blood cell removal solution at 4 °C for 10 min and then resuspended in DPBS buffer (0.04% BSA and 0.01 mM EDTA) after being washed by DPBS buffer. Following the depletion of the dead cells, the cell suspensions were directly performed for scRNA-seq according to the manufacturer's instructions.
For the samples from rhesus macaques, the cells in single-cell suspension were counted by trypan blue dye at a proper concentration of 1000–2000 cells/μL. Single-cell suspensions were loaded onto 10× Genomics Chromium v3.1 system to generate single-cell Gel Beads-In-Emulsions (GEMs), where all generated full-length cDNA share a common 10× barcode. Then, GEMs were disrupted and cDNA was amplified via PCR. The quality control of the sequencing libraries was performed by High Sensitivity DNA assay Kit (5067-4626, Agilent Technologies), and the concentration quantification was conducted using ABI StepOnePlus Real-Time PCR System. Finally, the sequencing was performed on Illumina sequencing platform in PE150 mode. For the samples from hCD147 mice, cell suspensions were barcoded through the SeekOne single cell platform.

value: lung

value: 3-4 years

value: male

value: SARS-CoV-2 (Beta strain)

value: MPZ, 5 mg/kg; 3E8, 5 mg/kg


title: control mimics transfection replicate2

city: Shanghai

first: Haiyang

last: Hu

address: 320 Yueyang Road

institute: PICB

description:
Library name: 4
control mimics transfection replicate2

data_processing:
Basecalling based on Illumina Casava1.7 software
After RNA sequencing reads quality checking, RNA-seq data were mapped to the human genome using Hisat2 using default parameters
The gene expression abundance was estimated by counting number of reads mapped to the cognate gene exons using featurecount
Assembly: hg38 (human)
Supplementary files format and content: tab-delimited text files include gene ID and expression level in reads count for each sample

source_name: Calu-3 cells

growth_protocol: Calu-3 cells were cultured in Dulbecco Modified Eagle Medium (DMEM; Gibco, Cat#12100046) supplemented with 1% penicillin–streptomycin (Gibco Cat#15070063) and 10% Fetal Bovine Serum (FBS; Gibco, Cat#A5256701) at 37 °C in a 5% CO2 incubator, according to according to the manufacturer’s instructions.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen Cat# 15596018CN) from Calu-3 cells with miR-4485-3p|+1 mimics or control mimics transfection
Total RNA subjected to polyA+ RNA enrichment with TruSeq RNA Library Preparation Kit v2 (Illumina) and prepared into the cDNA library according to the Illumina RNA-Seq instruction.

treatment_protocol: For transfection experiment, Calu-3 cells were transfected with miR-4485-3p|+1 mimics or control mimics (60 nM final concentration) using the siRNA-Mate plus transfection reagent (Genepharma Cat#G04026) without pre-infected with SARS-CoV-2, according to the manufacturer’s protocol. After 24 h, the transfection medium was replaced with fresh complete DMEM. Cells were harvested at 72 h post-transfection for RNA-seq experiments.

value: Calu-3 cells

value: human epithelial cell line

value: control mimics transfection


title: RPMI2650, CDDP-exposure, rep1

description:
Library name: 4
Column name in txi_counts.csv: 1CR_1

value: Head and neck squamous cell carcinoma

value: CDDP exposure


title: A549, SCR SMARCB1, bigwig

description: Library name: A549_SCR_SMARCB1.bigwig


title: AMOUR rep1

description:
Rep1
AMOUR_TPM.txt


title: RPMI2650, non-treatment, rep3

description:
Library name: 3
Column name in txi_counts.csv: 1P_3

value: No


title: SARS-CoV-2 infection, Meplazumab and 3E8 treatment-1 [scRNA-seq]

description:
Library name: MPZ_3E8_1
10x genomics


title: RPMI2650, non-treatment, rep2

description:
Library name: 2
Column name in txi_counts.csv: 1P_2


title: Healthy-2

description:
Library name: Healthy_2
10x genomics

value: 3-5 years


title: HSC-2, non-treatment, rep2

description:
Library name: 16
Column name in txi_counts.csv: 2P_2


description:
Library name: 2
miR-4485-3p|+1 mimics transfection replicate2

value: miR-4485-3p|+1 mimics transfection


title: A549, SCR EZH2, bigwig

description: Library name: A549_SCR_EZH2.bigwig


description:
Library name: 1
miR-4485-3p|+1 mimics transfection replicate1


title: SARS-CoV-2 infection, Meplazumab and 3E8 treatment-2 [scRNA-seq]

description:
Library name: MPZ_3E8_2
10x genomics


title: AsPC-1 treated with Isotype, rep1

description: Library name: AsPC-1_ISO1

value: Human PDAC cell


title: SARS-CoV-2 infection, 3E8 treatment-2 [scRNA-seq]

description:
Library name: 3E8_2
10x genomics


title: SARS-CoV-2 infection, 3E8 treatment-4 [scRNA-seq]

description:
Library name: 3E8_4
10x genomics


title: F81-B

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

description: Library name: F81-B

data_processing:
Genome alignment, quality control, and differential gene expression were analyzed using Partek Flow (Partek, St. Louis, MO, USA).
The trimming of raw reads (both ends) was based on a minimum quality score of 20 and a minimum read length of 25.
Contaminants were removed using Bowtie 2 v2.2.5, and the reads were aligned to the human genome (hg38) using STAR 2.7.3 a.
Aligned reads were quantified using RefSeq Transcripts 96. Features (genes) were filtered to retain only those with at least five reads in ≥ 80% of the samples.
Assembly: hg38
Supplementary files format and content: txt files contaning raw and normalized counts

source_name: Breast

extract_protocol:
Qiagen All Prep DNA/RNA FFPE Kit (Qiagen, Hilden, Germany) and MagMAX®FFPE RNA Ultra Kit  (Applied Biosystems®, Foster City, CA, USA)
Illumina TruSeq RNA Exome Library prep kit was used to prepare genomic libraries according to the manufacturer’s protocol, with minor modifications, including increasing RNA input to 300ng, selecting samples with DV200 >30%, reducing the PCR to between 9 cycles, and extending the hybridization time to 16 h.

value: Breast

tag: response

value: No Response (NR)

tag: subtype

value: TNBC

tag: time

value: Baseline


title: control mimics transfection replicate1

description:
Library name: 3
control mimics transfection replicate1


title: SARS-CoV-2 infection, 3E8 treatment-3 [scRNA-seq]

description:
Library name: 3E8_3
10x genomics

value: lung

value: 3-4 years


title: pol-ADSC-3

first: Yating

last: Yin

address: Zhizaoju Road#693

institute: Shanghai ninth people’s hospital

description: Library name: Sample 6

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: adipose tissue

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

value: adipose tissue

value: pol-ADSC


title: A549, shGLI1 EZH2, bigwig

description: Library name: A549_shGLI1_EZH2.bigwig

value: Human lung cancer


title: SARS-CoV-2 infection, 3E8 treatment-1 [scRNA-seq]

description:
Library name: 3E8_1
10x genomics

value: male

value: SARS-CoV-2 (Beta strain)


title: F70Q-Bn

description: Library name: F70Q-Bn

value: FollowUp


title: pol-ADSC-2

description: Library name: Sample 5


title: SARS-CoV-2 infection, Meplazumab and 3E8 treatment-4 [scRNA-seq]

description:
Library name: MPZ_3E8_4
10x genomics

value: MPZ, 5 mg/kg; 3E8, 5 mg/kg


title: SARS-CoV-2 infection, Meplazumab treatment-4 [scRNA-seq]

description:
Library name: MPZ_4
10x genomics

value: MPZ, 10 mg/kg


title: F70B-Bn

description: Library name: F70B-Bn


title: pol-ADSC-1

description: Library name: Sample 4


title: F58B-Tn

description: Library name: F58B-Tn


title: F58Q-Tn

description: Library name: F58Q-Tn


title: MAC-ADSC-4

description: Library name: Sample 3

value: MAC-ADSC


title: SARS-CoV-2 infection, Meplazumab treatment-3 [scRNA-seq]

description:
Library name: MPZ_3
10x genomics


title: RPMI2650, non-treatment, rep1

description:
Library name: 1
Column name in txi_counts.csv: 1P_1

value: Head and neck squamous cell carcinoma

value: No


title: SARS-CoV-2 infection, Meplazumab treatment-2 [scRNA-seq]

description:
Library name: MPZ_2
10x genomics


title: MAC-ADSC-3

description: Library name: Sample 2


title: F53-Q

description: Library name: F53-Q

value: Breast


title: SARS-CoV-2 infection, Meplazumab treatment-1 [scRNA-seq]

description:
Library name: MPZ_1
10x genomics


title: F51B-Bn

description: Library name: F51B-Bn

value: No Response (NR)


title: MAC-ADSC-2

description: Library name: Sample 1


title: SARS-CoV-2 infection, PBS treatment-2 [scRNA-seq]

description:
Library name: Ctrl_2
10x genomics

value: PBS


title: old HGPS fibroblast P003 cells

city: Garching bei München

first: Felix

middle: Quirin

last: Fenzl

address: Boltzmannstraße 11

country: Germany

institute: Technische Universität München

data_processing:
Raw reads were analyzed using ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA), and repeats
Unique sequences with length in 18~26 nucleotide were mapped to human precursors in miRBase 22.0 (http://mirbase.org/) by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at 3’ and 5’ ends and one mismatch inside the sequence were allowed in the alignment
The unique sequences mapping to specific species of mature miRNAs in hairpin arms were identified as known miRNAs (http://mirbase.org/). The unique sequences mapping to the other arm of known human precursor hairpin opposite the annotated mature miRNA-containing arm were considered novel 5p- or 3p-derived miRNA candidates.
The mapped pre-miRNAs were further BLASTed (http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi) against the genome to determine their genomic locations. As Dillies et al. (2012) described, all expressed miRNAs were listed, and the normalization of sequence counts in each sample was achieved by dividing the counts by the library size parameter of the corresponding sample (Dillies et al., 2012).
The library size parameter was a median value of the ratio between the counts of a specific sample and a pseudo-reference sample. A count number in the pseudo-reference sample was the count geometric mean across all samples.
Assembly: GRCh38/hg38

growth_protocol: primary dermal fibroblaste maintained in DEMEM supplemented with 15% fetal bovine serum) and antibiotics in humified atmosphere CO2 at 37°C

extract_protocol:
RNA was harvested using miRNeasy Mini Kit (Qiagen, 217004)
1ug of total RNA was used to prepare a small RNA library according to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA)

treatment_protocol: no treatment

value: dermal fibrobalst

value: heterozygous c.1824C > T (p.Gly608Gly)


title: young HGPS fibroblast P003 cells


title: metM-Wnt-lung_tumor_from_DIO+Sulindac_C57BL6J_mouse_4

type: RNA

city: Chapel Hill

first: Michael

last: Coleman

state: NC

address: 135 Dauer Dr

institute: University of North Carolina

description: metM-Wnt-lung

hyb_protocol: Labeled cDNA was hybridized to the plate using GeneTitan Hybridization Wash and Stain Kit for WT Arrays (Affymetrix)

scan_protocol: arrays were scanned using GeneTitan

data_processing: Quality control and differential gene expression was conducted using TAC4 software (Affymetrix)

label: biotin

source_name: tumor

label_protocol: The GeneChip® WT PLUS Reagent Kit (Affymetrix, Santa Clara, CA) was used to prepare the samples

growth_protocol: C57BL/6J mice were randomized to receive a control diet D12450J, or a 60% high fat diet (D12492) to promote diet induced obesity. Once obese, mice were randomized to either remain on their respective diets or the same diet supplemented with 140ppm of sulindac.

extract_protocol: RNA was isolated by bead beating in TRIzol reagent, followed by isolation with EZNA HP Total RNA kit (omega bio-tek)

treatment_protocol: 5 weeks after initial randomization mice were orthotopically injected with one of three cells lines into the 4th mammary fat pad and tumors were allowed to grow till endpoint. At endpoint tumor was removed and total RNA isolated.

tag: strain

tag: group

value: DIO+Sulindac


title: F51Q-Bn

description: Library name: F51Q-Bn


title: F50Q-Bn

description: Library name: F50Q-Bn


title: old HGPS fibroblast P178 cells


title: F34-Q

description: Library name: F34-Q


title: metM-Wnt-lung_tumor_from_DIO+Sulindac_C57BL6J_mouse_5

description: metM-Wnt-lung


title: Healthy-4 [scRNA-seq]

description:
Library name: Healthy_4
10x genomics

value: lung

value: 3-5 years


title: old HGPS fibroblast P127 cells


title: SARS-CoV-2 infection, PBS treatment-4 [scRNA-seq]

description:
Library name: Ctrl_4
10x genomics

value: 3-4 years


title: Healthy-3 [scRNA-seq]

description:
Library name: Healthy_3
10x genomics

value: male


title: F31Q-Bn

description: Library name: F31Q-Bn


title: metM-Wnt-lung_tumor_from_DIO+Sulindac_C57BL6J_mouse_2

description: metM-Wnt-lung


title: metM-Wnt-lung_tumor_from_DIO_C57BL6J_mouse_6

description: metM-Wnt-lung

value: DIO


title: metM-Wnt-lung_tumor_from_DIO+Sulindac_C57BL6J_mouse_3

description: metM-Wnt-lung


title: SARS-CoV-2 infection, PBS treatment-3 [scRNA-seq]

description:
Library name: Ctrl_3
10x genomics

value: SARS-CoV-2 (Beta strain)


title: metM-Wnt-lung_tumor_from_DIO+Sulindac_C57BL6J_mouse_7

description: metM-Wnt-lung


title: metM-Wnt-lung_tumor_from_DIO_C57BL6J_mouse_7

description: metM-Wnt-lung


title: metM-Wnt-lung_tumor_from_DIO+Sulindac_C57BL6J_mouse_6

description: metM-Wnt-lung


title: metM-Wnt-lung_tumor_from_DIO+Sulindac_C57BL6J_mouse_1

description: metM-Wnt-lung


title: metM-Wnt-lung_tumor_from_DIO_C57BL6J_mouse_4

description: metM-Wnt-lung


title: metM-Wnt-lung_tumor_from_DIO_C57BL6J_mouse_5

description: metM-Wnt-lung


title: Healthy-1 [scRNA-seq]

description:
Library name: Healthy_1
10x genomics

value: female


title: F31B-Bn

description: Library name: F31B-Bn

value: Baseline


title: Healthy-2 [scRNA-seq]

description:
Library name: Healthy_2
10x genomics


title: F08Q-Bn

description: Library name: F08Q-Bn

value: FollowUp


title: young HGPS fibroblast P127 cells


title: old control fibroblast 3349 cells

value: WT


title: F08B-Bn

description: Library name: F08B-Bn


title: young control fibroblast 3349 cells


title: metM-Wnt-lung_tumor_from_DIO_C57BL6J_mouse_2

description: metM-Wnt-lung


title: old control fibroblast 1652 cells


title: SARS-CoV-2 infection, PBS treatment-1 [scRNA-seq]

description:
Library name: Ctrl_1
10x genomics


title: F34-B

description: Library name: F34-B


title: 95T_brain_CD45,acute-infection,rep1

city: Omaha

first: Howard

middle: S

last: Fox

state: Nebraska

address: 42nd and Emile

institute: University of Nebraska Medical Center

description: Library name: 95T_brain_CD45_1

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation for brain and blood samples were made using the Cell Ranger software v7.1.0
The demultiplexing, barcoded processing, gene counting and aggregation for cell cocultivation were made using the Cell Ranger software v9.0.1
Assembly: For brain and blood samples from rhesus macaques, Mmul10, NCBI RefSeq assembly and SIVmac251 were used. For cell cocultivation experiment, GRCh38 GENCODE v44/Ensembl110 annotations were used
Supplementary files format and content: H5 files contain feature and cell barcode matrix

source_name: Brain

growth_protocol: For cocultivation study, the monocytes were isolated from the peripheral blood mononuclear cells (PBMC) of healthy donors. They were cultured in 6-well plates (3 million cells per well) using macrophage-derived macrophage (MDM) culture medium for one week before the experiment. The MDM culture medium consisted of 50 mL macrophage serum-free medium (Catalog# 12065-074, Gibco, Grand Island, NY, USA), 500 μL HEPES (Catalog# 15630-080, Gibco, Grand Island, NY, USA), 50 μL Gentamicin (Catalog# G1397, Sigma-Aldrich, St. Louis, MO, USA), 5 μL Ciprofloxacin (20 mg/mL dissolved in 1% HCL, Catalog# 16626133, Honeywell Fluka, Charlotte, NC, USA), 500 μL Nutridoma (Catalog# 21952600, Roche, Indianapolis, IN), and 5 μL M-CSF (Catalog# 300-25-250UG, Gibco, Grand Island, NY, USA), which was filtered using Millipore Steriflip filter (Catalog# SCGP00525, Sigma-Aldrich, St. Louis, MO, USA) before use. The jurkat cells (a human T-cell cell line) was obtained from ATCC and cultured in RPMI 1640 medium (Catalog# SH30027.02, Hyclone, Logan, UT, USA) supplemented with 10% fetal bovine serum (Catalog# F8067, Sigma-Aldrich, St. Louis, MO, USA) and 1% antibiotic-antimycotic (Catalog# SV30079.01, Hyclone, Logan, UT, USA). The Jurkat cells were seeded in 24-well plates at a density of 300,000 cells per well one day before the experiment.

extract_protocol:
For isolating brain lymphocytes, a necropsy was performed on deeply anesthetized (ketamine plus xylazine) animals, following intracardial perfusion with sterile PBS containing 1 U/ml heparin. Brains were harvested, and approximately half of the brain was taken for cell isolation.The brain was minced and homogenized in cold Hank’s Balanced Salt Solution (HBSS, Invitrogen, Carlsbad, CA, USA). After being centrifuged, the brain tissue was digested at 37° C in HBSS containing 28 U/ml DNase I and 8 U/ml papain for 30 minutes. After digestion, the enzymes were inactivated by adding 2.5% FBS, and the cells were centrifuged and resuspended in cold HBSS. The cell suspension was brought to a final concentration of 20% Percoll by the addition of 90% Percoll (GE HealthCare, Pittsburg, PA, USA) and centrifuged at 4° C for 15 minutes at 550 x g. The cell pallet at the bottom was resuspended in HBSS and passed through a 40 μm strainer to remove cell clumps and/or aggregates. Cells were again pelleted by centrifugation. A final wash was performed before the resulting cells were quantified on a hemocytometer and Coulter Counter Z1.The brain cells were cryopreserved before the cell sorting and scRNA-seq. To isolate the brain lymphocytes, samples of cryopreserved brain cell isolates, stored in liquid nitrogen , were rapidly thawed in a 37° C water bath. After the recovery, cells were washed and counted by Coulter Counter Z1. Once cell concentration was known, cells were transferred to ice-cold PBS, staining with Live/Dead and PE-labeled anti-CD45 antibody (Biolegend, San Diego, CA). The live cells that were CD45+ were collected for scRNA-seq capture and library preparation. For isolating blood CD4+ lymphocytes, freshly isolated EDTA-anticoagulated blood was centrifuged, and the cells washed with PBS and then stained with UV-blue live/dead for 30 minutes at 4° C. After being blocked with FACS buffer for 3 minutes, the cells were centrifuged and resuspended in the antibody cocktail mixed in Brilliant Stain buffer (Catalog# 563794, BD Biosciences, San Jose, CA, USA) for 45 minutes. After incubation, red blood cell (RBC) lysing buffer was added to the sample and the cells were pelleted at 300 x g for 8 minutes. After centrifugation, the cells were resuspended in RBC lysing buffer, which was repeated to completely remove RBCs. The cells were then pelleted and resuspended in MACS buffer for FACS sorting. The antibody cocktail included V500-labeled anti-CD3 antibody (Catalog# 561417, BD Biosciences, San Jose, CA, USA), BV786-labeled anti-CD4 antibody (Catalog# 563881, BD Biosciences, San Jose, CA, USA), PE-CF594-labeled anti-CD20 antibody (Catalog# 562295, BD Biosciences, San Jose, CA, USA) The selection of cells was based on the size, singlet, live, and expression of CD20, CD3, and CD4. The CD20-positive cells were excluded, and the CD20-negative cells that were positive for CD3 and CD4 were collected for scRNA-seq library preparations.  For cell cocultivation experiment, MDM or MDM-jurkats cocultivation system was harvested by incubating with trypLE (Catalog# 12605-010, Gibco, Grand Island, NY, USA)  for 10 minutes at 37 ℃, then after one step of washing with 1mL PBS, another 1 mL PBS (Catalog# 14190-136, Gibco, Grand Island, NY, USA) with 0.04% BSA (Catalog# 130-091-376, Miltenyi Biotec, Bergisch Gladbach, Germany) was added for scraping the cells from the plate. For the cocultivation groups,  the harvested cells were directly used for library preparations. For the non-cocultivation group, the MDM was mixed with jurkat cells for library preparations.
Post-sorting, isolates were concentrated to approximately 1000 cells per µL and assessed by trypan blue for viability and concentration. Brain immune cells and blood CD4+ T cells are isolated from the acutely infected macaques that were processed using the 10× Genomics (Pleasanton, CA, USA) Chromium 3’ v3 GEM kit targeting 8000 cells. And cocultivation study used 10× Genomics GEM-X Universal 3' Gene Expression v4 4-plex kit targeting 5000 cells. Based on the targeting cell number, the ideal volume of cells was loaded onto the 10× Genomics Chromium GEM Chip and placed into the Chromium Controller for cell capturing and library preparation. In short, this occurs through microfluidics and combining with Single Cell 3’ Gel Beads containing unique barcoded primers with a unique molecular identifier (UMI), followed by lysis of cells and barcoded reverse transcription of RNA, amplification of barcoded cDNA, fragmentation of cDNA to 200 bp, 5’ adapter attachment, and sample indexing as the manufacturer instructed with version 3 reagent kits. The prepared libraries were sequenced using Illumina (San Diego, CA, USA) Nextseq550 and Novaseq6000 sequencers.

treatment_protocol: For three acute-infected rhesus macaques (93T, 94T, and 95T), they were intravenously inoculated with SIVmac251. For cell cocultivation experiment, we cocultured MDMs and jurkat cells in NoApop, CD95, and Campto groups for 1 hour. The jurkats in CD95 and Campto groups were treated with apoptotic agents (i.e. CD95 and camptothecin) for 3 hours prior to cocultivation . The MDMs and jurkats in NoCoCul group did not receive any cocultivation, and they were mixed before library preparations to assess the the artefactual dual capture.

value: Brain

value: CD45+ cells

value: 12-days of SIVmac251 infection


title: young HGPS fibroblast P178 cells


title: 314B-Bn

description: Library name: 314B-Bn

value: Breast

value: No Response (NR)


title: metM-Wnt-lung_tumor_from_DIO_C57BL6J_mouse_3

description: metM-Wnt-lung


title: young control fibroblast 1652 cells

value: dermal fibrobalst


title: 94T_brain_CD45,acute-infection,rep2

description: Library name: 94T_brain_CD45_2


title: 314-Q

description: Library name: 314-Q


title: 277B-Bp

description: Library name: 277B-Bp


title: 94T_brain_CD45,acute-infection,rep1

description: Library name: 94T_brain_CD45_1


title: old control fibroblast 1651 cells


title: 93T_brain_CD45,acute-infection,rep2

description: Library name: 93T_brain_CD45_2


title: young control fibroblast 1651 cells


title: metM-Wnt-lung_tumor_from_Control+Sulindac_C57BL6J_mouse_5

description: metM-Wnt-lung

value: Control+Sulindac


title: CRC Patient Derived Organoid (PDO5) IKKa KO rep2

city: Barcelona

first: Lluis

last: Espinosa

state: Barcelona

address: Dr. Aiguader 88

department: Institut Municipal d'Investigacions Mèdiques, (IMIM)

country: Spain

institute: Hospital del Mar

data_processing:
Raw reads were trimmed to remove adapters presence with Trimgalore (v0.6.6) (Krueger et al., 2020). Default parameters were used except for a minimum quality of 15 (Phred score) and an adapter removal stringency of 3bp overlap
Trimmed reads were aligned to reference genome (hg38 release 106 from Ensembl) with STAR aligner tool (v2.7.8). STAR was executed with default parameters except for the number of allowed mismatches which was set to 1
Uniquely mapped reads were considered for further analysis. Raw gene expression was quantified using featureCounts tool from subRead software (v2.0.1) with exon as feature.
Raw counts matrix was imported into R Statistical software (v4.3.1). Prior to statistical analysis, those genes with less than 5 raw counts across the 6 samples per timepoint were discarded
For visualization purposes, counts were normalized by variance-stabilizing transformation method as implemented in DESeq2 R package (v1.40.2)
Assembly: hg38
Supplementary files format and content: Tab-separated value file: RNAseq_RawCounts_PD05_Ikka_KO_CTL.txt: RNAseq Raw expression levels for each gene (61,552 rows) in each individual sample as calculated using featureCounts. This data is prior to conducting any pre-filtering step.
Supplementary files format and content: Tab-separated value file: RNAseq_NormCounts_PD05_Ikka_KO_CTL.txt. Normalized expression levels including the expression of 20,826 genes (rows) per all individual samples. Normalization carried out with VST from DESeq2 (v1.40.2)

source_name: Colorectal Tumoroid

growth_protocol: PDOs cultured in matrigel at 37 °C, 5% CO2 and medium changed every week.

extract_protocol:
Tumor spheres were collected and digested with an adequate amount of trypsin to single cells. Then were sorted (DAPI (-)) to purify >95% viable cells without debris. Total RNA was extracted from cells using Qiagen RNeasy Micro Kit (#74004) following manufacturer's instructions. RNA quality was measured by Nanodrop and Agarose gel.
Library was prepared according to manufacturer's instructions (PE 50bp paired-end reads)

value: Colorectal Tumoroid

value: IKKa-/-

value: knock-out untreated


title: 275Q-A

description: Library name: 275Q-A

value: LumA


title: 277-Q

description: Library name: 277-Q


title: 93T_brain_CD45,acute-infection,rep1

description: Library name: 93T_brain_CD45_1


title: 95T_brain_CD45,acute-infection,rep2

description: Library name: 95T_brain_CD45_2


title: 275B-A

description: Library name: 275B-A


title: 92T_brain_CD45,non-infection,rep2

description: Library name: 92T_brain_CD45_2


title: CRC Patient Derived Organoid (PDO5) IKKa KO rep1


title: metM-Wnt-lung_tumor_from_Control+Sulindac_C57BL6J_mouse_6

description: metM-Wnt-lung


title: CRC Patient Derived Organoid (PDO5) WT rep2

value: IKKa+/+

value: wildtype untreated


title: 247Q-A

description: Library name: 247Q-A


title: CRC Patient Derived Organoid (PDO5) WT rep1


title: metM-Wnt-lung_tumor_from_Control+Sulindac_C57BL6J_mouse_2

description: metM-Wnt-lung


title: A375 2μM vemurafenib 48h

city: GUANGZHOU

first: JIEYU

last: LIU

address: Shatainanlu

institute: South Medical University

description:
Library name: Sample4
X4_TPM

data_processing:
After obtaining the raw sequencing data (Raw Data), you first need to filter the data, remove the adapter sequence, and process low-quality reads, and then evaluate the sequencing quality to obtain high-quality data (Clean Data). And compare the Clean Data with the reference genome to get the BAM file.
Use the HISAT2 software to compare the sequencing data with the reference genome, and make a comprehensive evaluation of the coverage area and coverage depth of the sequencing data. HISAT2 is the successor of TopHat2/Bowtie2. It uses an improved BWT algorithm (FM index). HISAT uses a large number of FM indexes to cover the entire genome, and combines several comparison strategies to achieve an efficient and faster comparison of RNA-seq data.
In RNA sequencing, RPKM (expected number of Reads Per Kilobase of transcript sequence per Millions basepairs sequenced) is the number of reads from a gene per kilobase length per million reads, which also considers the sequence depth and gene length pair The influence of read count is currently the most commonly used method for estimating gene expression levels. Map the bam file obtained by sequencing to the gtf file of the reference species to obtain the gene expression level, and perform regional statistics on the gene expression level of the genome according to the statistical method to reflect the overall expression level of the sample.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include counts and TPM values for each Sample.

source_name: skin cancer

growth_protocol: A375 and A375R cells were cultured in Dulbecco’s modified Eagle medium supplemented with 10% fetal bovine serum and maintained at 37°C with 5% CO2 in a humidified atmosphere

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment. Then 10 ug of total RNA for the construction was used as sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A375 with untreated, A375R treated with gradient concentration vemurafenib constantly, A375 treated with 1‰ DMSO and 2μM vemurafenib for 48h

value: skin cancer

value: human melanoma cells

value: Wild Type

value: treated with vemurafenib for 48h

tag: batch


title: metM-Wnt-lung_tumor_from_Control+Sulindac_C57BL6J_mouse_3

description: metM-Wnt-lung


title: metM-Wnt-lung_tumor_from_Control+Sulindac_C57BL6J_mouse_4

description: metM-Wnt-lung


title: metM-Wnt-lung_tumor_from_DIO_C57BL6J_mouse_1

description: metM-Wnt-lung

value: DIO


title: 247B-A

description: Library name: 247B-A

value: Baseline


title: metM-Wnt-lung_tumor_from_Control+Sulindac_C57BL6J_mouse_1

description: metM-Wnt-lung


title: A375 DMSO 48h

description:
Library name: Sample3
X3_TPM

value: treated with DMSO for 48h


title: A375 vemursfenib_resistence

description:
Library name: Sample2
X2_TPM

value: treated with vemurafenib continuously


title: 239Q-Bn

description: Library name: 239Q-Bn

value: Breast

value: No Response (NR)

value: FollowUp


title: 92T_brain_CD45,non-infection,rep1

description: Library name: 92T_brain_CD45_1

value: Brain

value: CD45+ cells


title: male SMG H3K4me3 ChIP

city: Buffalo

first: Rose-Anne

last: Romano

state: NY

address: Main Cir

institute: SUNY University at Buffalo

data_processing:
Reads were aligned to the Homo sapiens (hg38 build) using Bowtie2 (v2.3.4.1). Resulting sam files were converted to sorted bam files using samtools (v1.3). BigWig files (bw) were generated using the deepTools suite with the following flags: --binSize 20 --normalizeUsing BPM --smoothLength 60 --extendReads 150 --scaleFactorsMethod None --centerReads -p 6. Peaks were called via MACS2 v(2.1.0). Flags for H3K4me1 were -f BAM --broad --broad-cutoff 0.1 --nomodel -p 0.01. Flags for sharp peaks (all other marks) -f BAM --nomodel -p 0.01.
Assembly: Hg38
Supplementary files format and content: BigWig and Peak Files

source_name: Human Submandibular Gland

extract_protocol:
Salivary gland samples were dissected and subjected to chemical and enzymatic digestion to generate single cell suspensions which were then cross-linked and processed for downstream applications. For histone ChIP-seq the Chromatin Shearing Optimization Kit-Low SDS (Diagenode) was used with 10 million cells per cell line and 40 cycles sonication in the Bioruptor Plus (Diagenode). After RNase and proteinase K incubation, chromatin shearing was confirmed as a DNA smear between 100-300 bp on a 1.5% agarose gel. Histone ChIP DNA was prepared with the Auto Histone ChIP-seq kit protein G Kit (Diagenode), 2.4 μg H3K27ac, with 3 μg H3K4me1, 2 μg H3K4me3, and 2 μg H3K4me2 of premium polyclonal antibody (Diagenode) per 1 million cells with the SX-8G IP-Star® Compact System (Diagenode). 1% input sample for each cell line was used as a control for background experimental noise. ChIP-sequencing on ilumina HiSeq2500.
Libraries were prepared using ThruPLEX DNA-seq kits from Rubicon Genomics. The samples were then 50 bp single-end sequenced on an Illumina HiSeq 2500.

value: Human Submandibular Gland

value: male

tag: chip antibody


title: A375 parent

description:
Library name: Sample1
X1_TPM

value: untreated


title: 239B-Bn

description: Library name: 239B-Bn


title: male SMG H3K4me2 ChIP


title: 226Q-Tn

description: Library name: 226Q-Tn

value: TNBC


title: male SMG H3K4me1 ChIP


title: metM-Wnt-lung_tumor_from_Control_C57BL6J_mouse_3

description: metM-Wnt-lung

value: Control


title: metM-Wnt-lung_tumor_from_Control_C57BL6J_mouse_4

description: metM-Wnt-lung


title: metM-Wnt-lung_tumor_from_Control_C57BL6J_mouse_6

description: metM-Wnt-lung


title: 226B-Tn

description: Library name: 226B-Tn


title: male SMG input ChIP


title: 8H_Fiber_3

city: Boca Raton

first: Marc

last: Kantorow

state: FL

address: 777 Glades Rd

department: Biomedical Science

institute: Florida Atlantic University

description: Library name: Sample 6

data_processing:
Sequence reads were analyzed with the STAR alignment and DESeq2 software pipeline.
Cutadapt was used to remove adaptor-contaminated reads, low quality bases and undetermined bases.
Reads were mapped to galgal6 genome (ensemble version 96) using Bowtie2 and HISAT2
Comprehensive transcriptomes were generated using gffcompare and StringTie. The R package edgeR was used to estimate the expression levels of all transcripts and to identify differentially expressed genes (log2-fold change FPKM > 1.0 or <  -1.0) with parametric F test comparing nested linear models (adjusted p < 0.05)
Assembly: Galgal6
Supplementary files format and content: txt file contains FPKM, fold changes, and statistics for each sample

organism: Gallus gallus

source_name: Embryonic D13 Chick lens

growth_protocol: Embryonic chicken lens organ cultures were prepared from the lenses of Embryonic day 13 (E13) White Leghorn embryonated chicken eggs (Charles River Laboratories, Storrs, CT). Whole lenses were removed from E13 chicken eyes and placed into 35mm dishes containing Medium 199 (Invitrogen) supplemented with 10% FBS (Invitrogen) and penicillin-streptomycin antibiotic mix (50 units/ml; Invitrogen). Lenses were cultured for 2H or 8H in normoxia or hypoxia, lenses that exhibited damage or opacity were removed from the study.

extract_protocol:
For RNA-seq 10-15 lenses per n were microdissected at 0 hours or 8 hours of hypoxia treatment and the tissue stored in Tissue protect reagent® from the kit for less than 1 week at -20 °C before RNA isolation. Total RNA was isolated from biological triplicates of pooled microdissected chick E13 lens fiber cells using the RNeasy® Protect Mini Kit (Qiagen, prod no: 74124) according to the manufacturer’s instructions.
For each sample, 500ng of total RNA was used in Illumina’s TruSeq Stranded mRNA Library kit (Cat# 20020594).

treatment_protocol: Lenses untreated or were incubated for 8H in 1% O2

value: Embryonic D13 Chick lens

value: lens fiber cells

value: Incubated in hypoxia for 8H


title: 8H_Fiber_2

description: Library name: Sample 5


title: male SMG H3K27ac ChIP


title: metM-Wnt-lung_tumor_from_Control_C57BL6J_mouse_5

description: metM-Wnt-lung


title: metM-Wnt-lung_tumor_from_Control_C57BL6J_mouse_1

description: metM-Wnt-lung


title: female SMG H3K4me2 ChIP

value: female


title: female SMG H3K4me3 ChIP


title: 0H_Fiber_3

description: Library name: Sample 3

value: Untreated


title: 208Q-Bp

description: Library name: 208Q-Bp


title: female SMG H3K4me1 ChIP


title: 208B-Bp

description: Library name: 208B-Bp

value: Baseline


title: metM-Wnt-liver_tumor_from_DIO+Sulindac_C57BL6J_mouse_7

description: metM-Wnt-liver

value: DIO+Sulindac


title: female SMG input ChIP


title: 0H_Fiber_1

description: Library name: Sample 1


title: 0H_Fiber_2

description: Library name: Sample 2


title: metM-Wnt-lung_tumor_from_Control_C57BL6J_mouse_2

description: metM-Wnt-lung


title: metM-Wnt-liver_tumor_from_DIO+Sulindac_C57BL6J_mouse_5

description: metM-Wnt-liver


title: B205

description: Library name: B205

value: Breast

value: LumA


title: 8H_Fiber_1

description: Library name: Sample 4


title: female SMG H3K27ac ChIP


title: metM-Wnt-liver_tumor_from_DIO+Sulindac_C57BL6J_mouse_3

description: metM-Wnt-liver


title: metM-Wnt-liver_tumor_from_DIO+Sulindac_C57BL6J_mouse_4

description: metM-Wnt-liver


title: 219B-Bn

description: Library name: 219B-Bn

value: No Response (NR)


title: 187B-Bn

description: Library name: 187B-Bn


title: PEM-CONT-3

city: chengdu

first: donghao

last: zhang

address: No. 211, Huimin Road, Wenjiang District, Chengdu City

institute: sichuan agricultural university

description:
Library name: SAMPLES23
CONT_PEM_3

data_processing:
Differentially expressed genes (DEGs) were identified using the DESeq2 package， with thresholds of |log₂(fold change)| ≥1 and adjusted p-value ≤0.05, using the Benjamini–Hochberg method for multiple testing correction. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted using the clusterProfiler R package (v3.8.1). Gene Set Enrichment Analysis (GSEA) was also performed using the GSEA software (version 4.3.2) to identify significantly enriched functional pathways.
Assembly: GRCg6a (GCA_000002315.5)
Supplementary files format and content: A tab-delimited text file containing FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values for all expressed genes across all samples. Rows represent Ensembl gene IDs or gene symbols, and columns represent individual samples (e.g., LHFD_SOL_1, LHFD_SOL_2, etc.). FPKM values were calculated using Cufflinks based on HISAT2-aligned reads to the Gallus gallus reference genome.

source_name: PEM muscle

extract_protocol:
Total RNA was extracted from the PEM and SOL muscles using TRIzol reagent (Invitrogen, USA). RNA concentration and purity were assessed using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, USA), and RNA integrity was confirmed via agarose gel electrophoresis (Biowest, France) and the Agilent 2100 Bioanalyzer (Agilent Technologies, USA). All samples met the quality requirements for RNA sequencing, with concentrations ≥300 ng/μL, RNA integrity number (RIN) >7.0, and OD260/280 ratios between 1.8 and 2.2.
Each group included four biological replicates. Raw reads were filtered using fastp to remove adapters and low-quality sequences. Clean reads were mapped to the chicken reference genome (GRCg6a, Ensembl release April 2022) using HISAT2. Transcript assembly and quantification were performed with StringTie (v1.3.3b), and expression levels were calculated as fragments per kilobase of transcript per million mapped reads (FPKM).

value: PEM muscle

value: CONT


title: PEM-CONT-4

description:
Library name: SAMPLES24
CONT_PEM_4


title: B163

description: Library name: B163


title: peripheral blood, benign, EV66

city: Ulsan

first: Semin

last: Lee

address: 50, UNIST-gil

department: Biomedical Engineering

country: South Korea

institute: Ulsan National Institute of Science and Technology

data_processing:
The adapter sequences of the raw reads were eliminated using Cutadapt. If a read matched at least the first 5 bp of the 3′-adapter sequence, it was regarded as an adapter sequence and was trimmed from the read. (-q 10)
Trimmed reads were aligned to the human genome reference from the hg38 GATK resource bundle, and miRNAs were predicted using the miRDeep2 algorithm.
Trimmed reads were basically mapped to the GRCh38 human reference genome from GENCODE v34 using STAR v2.7.3a. The aligned reads were quantified using RSEM v1.3.1.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes RPM values of miRNAs for all samples
Supplementary files format and content: tab-delimited text file includes TPM values of lncRNAs for all samples

source_name: peripheral blood

extract_protocol:
We extracted EVs from plasma samples by using Exo2D™ EV isolation kit (EXOSOME Plus, Inc.) based on an aqueous two-phase system and then, isolated total RNAs from extracted EVs for small RNA sequencing (smRNA-seq).
The libraries were constructed by SMARTer smRNA-Seq kit.

value: peripheral blood

tag: diagnosis

value: benign

tag: Stage

tag: treatment (palliative)

tag: response to_treatment


title: 219Q-Bn

description: Library name: 219Q-Bn

tag: tissue

value: FollowUp


title: peripheral blood, benign, EV65


title: metM-Wnt-liver_tumor_from_DIO+Sulindac_C57BL6J_mouse_6

description: metM-Wnt-liver


title: metM-Wnt-liver_tumor_from_DIO+Sulindac_C57BL6J_mouse_2

description: metM-Wnt-liver


title: PEM-CONT-2

description:
Library name: SAMPLES22
CONT_PEM_2


title: peripheral blood, benign, EV64


title: PEM-CONT-1

description:
Library name: SAMPLES21
CONT_PEM_1


title: 160B-A

description: Library name: 160B-A


title: 160-Q

description: Library name: 160-Q


title: peripheral blood, benign, EV63


title: 133-Q

description: Library name: 133-Q


title: peripheral blood, benign, EV62


title: metM-Wnt-liver_tumor_from_DIO_C57BL6J_mouse_7

description: metM-Wnt-liver

value: DIO


title: PEM-SHFD-3

description:
Library name: SAMPLES19
SHFD_PEM_3

value: SHFD


title: metM-Wnt-liver_tumor_from_DIO_C57BL6J_mouse_5

description: metM-Wnt-liver


title: metM-Wnt-liver_tumor_from_DIO_C57BL6J_mouse_6

description: metM-Wnt-liver


title: PEM-SHFD-2

description:
Library name: SAMPLES18
SHFD_PEM_2


title: 117Q-Bp

description: Library name: 117Q-Bp


title: PEM-SHFD-1

description:
Library name: SAMPLES17
SHFD_PEM_1


title: peripheral blood, benign, EV61


title: metM-Wnt-liver_tumor_from_DIO_C57BL6J_mouse_4

description: metM-Wnt-liver


title: PEM-LHFD-4

description:
Library name: SAMPLES16
LHFD_PEM_4

value: LHFD


title: 117B-Bp

description: Library name: 117B-Bp


title: 115-Q

description: Library name: 115-Q


title: peripheral blood, benign, EV58


title: metM-Wnt-liver_tumor_from_DIO_C57BL6J_mouse_2

description: metM-Wnt-liver


title: PEM-LHFD-3

description:
Library name: SAMPLES15
LHFD_PEM_3


title: peripheral blood, benign, EV57


title: PEM-SHFD-4

description:
Library name: SAMPLES20
SHFD_PEM_4


title: peripheral blood, benign, EV59


title: metM-Wnt-liver_tumor_from_DIO_C57BL6J_mouse_3

description: metM-Wnt-liver


title: metM-Wnt-liver_tumor_from_DIO_C57BL6J_mouse_1

description: metM-Wnt-liver


title: PEM-LHFD-2

description:
Library name: SAMPLES14
LHFD_PEM_2


title: 115-B

description: Library name: 115-B


title: 125B-Bn

description: Library name: 125B-Bn


title: peripheral blood, benign, EV60


title: PEM-LHFD-1

description:
Library name: SAMPLES13
LHFD_PEM_1


title: 090B_Bn

description: Library name: 090B_Bn


title: peripheral blood, benign, EV56


title: metM-Wnt-liver_tumor_from_Control+Sulindac_C57BL6J_mouse_3

description: metM-Wnt-liver

value: Control+Sulindac


title: peripheral blood, benign, EV55


title: SOL-CONT-4

description:
Library name: SAMPLES12
CONT_SOL_4

source_name: SOL muscle

value: SOL muscle


title: 084Q_Bn

description: Library name: 084Q_Bn


title: metM-Wnt-liver_tumor_from_Control+Sulindac_C57BL6J_mouse_4

description: metM-Wnt-liver


title: SOL-CONT-3

description:
Library name: SAMPLES11
CONT_SOL_3


title: 084B_Bn

description: Library name: 084B_Bn


title: metM-Wnt-liver_tumor_from_Control+Sulindac_C57BL6J_mouse_2

description: metM-Wnt-liver


title: 090Q_Bn

description: Library name: 090Q_Bn


title: peripheral blood, healthy control, EV54

value: healthy control


title: 083Q-Tn

description: Library name: 083Q-Tn

value: TNBC


title: SOL-CONT-1

description:
Library name: SAMPLES9
CONT_SOL_1


title: peripheral blood, healthy control, EV53


title: peripheral blood, healthy control, EV52


title: metM-Wnt-liver_tumor_from_Control+Sulindac_C57BL6J_mouse_1

description: metM-Wnt-liver


title: 066-Q

description: Library name: 066-Q


title: SOL-CONT-2

description:
Library name: SAMPLES10
CONT_SOL_2


title: metM-Wnt-liver_tumor_from_Control_C57BL6J_mouse_7

description: metM-Wnt-liver

value: Control


title: peripheral blood, PDAC, EV51

value: PDAC

value: O

value: non-responder


title: 066-B

description: Library name: 066-B

value: Breast

value: No Response (NR)

value: Baseline


title: metM-Wnt-liver_tumor_from_Control_C57BL6J_mouse_6

description: metM-Wnt-liver


title: SOL-SHFD-4

description:
Library name: SAMPLES8
SHFD_SOL_4


title: peripheral blood, PDAC, EV50

value: peripheral blood


title: SOL-SHFD-3

description:
Library name: SAMPLES7
SHFD_SOL_3


title: 050Q-A

description: Library name: 050Q-A

value: LumA


title: peripheral blood, PDAC, EV49


title: metM-Wnt-liver_tumor_from_DIO+Sulindac_C57BL6J_mouse_1

description: metM-Wnt-liver

value: DIO+Sulindac


title: SOL-SHFD-2

description:
Library name: SAMPLES6
SHFD_SOL_2


title: metM-Wnt-liver_tumor_from_Control_C57BL6J_mouse_5

description: metM-Wnt-liver


title: metM-Wnt-liver_tumor_from_Control_C57BL6J_mouse_4

description: metM-Wnt-liver


title: metM-Wnt-liver_tumor_from_Control_C57BL6J_mouse_3

description: metM-Wnt-liver


title: SOL-SHFD-1

description:
Library name: SAMPLES5
SHFD_SOL_1


title: peripheral blood, PDAC, EV48


title: metM-Wnt-liver_tumor_from_Control_C57BL6J_mouse_2

description: metM-Wnt-liver


title: 014Q-Tn

description: Library name: 014Q-Tn

value: FollowUp


title: 014B-Tn

description: Library name: 014B-Tn


title: peripheral blood, PDAC, EV46


title: SOL-LHFD-4

description:
Library name: SAMPLES4
LHFD_SOL_4


title: peripheral blood, PDAC, EV47

value: responder


title: 013Q_Bn

description: Library name: 013Q_Bn


title: metM-Wnt-liver_tumor_from_Control_C57BL6J_mouse_1

description: metM-Wnt-liver


title: SOL-LHFD-2

description:
Library name: SAMPLES2
LHFD_SOL_2

value: LHFD


title: peripheral blood, PDAC, EV44


title: SOL-LHFD-3

description:
Library name: SAMPLES3
LHFD_SOL_3


title: SOL-LHFD-1

description:
Library name: SAMPLES1
LHFD_SOL_1


title: IN.HD0015

city: Vienna

first: Ola

last: Grimsholm

address: Wahringer Gurtel 18-20

department: Pathophysiology and Allergy Research

country: Austria

institute: Medical University of Vienna

description:
Library name: Sample 50
naive B cells_healthy donor

data_processing:
Paired-end sequencing (2 x 75 bp) was performed on an Illumina NextSeq 500. Base calling was done by RTA software and demultiplexing to paired-end FASTQ files was performed with CASAVA (v1.8.2).
Adapter sequences were trimmed using Trimmomatic (v0.39). Filtering parameters were set to SLIDINGWINDOW:4:20 and MINLEN:25.
Reads were aligned to human GRCh38 using STAR (v2.6.1a) in 2-pass mode, and quantified at the gene level with featureCounts (v2.0.6) and Ensembl 110 GTF annotation.
Assembly: human GRCh38/Ensembl 110 GTF
Supplementary files format and content: Tab-delimited text file includes gene raw counts for each sample  obtained with featureCounts v2.0.6

extract_protocol:
Total RNA was isolated using RNeasy Plus Micro kit (QIAGEN).
Library preparation was performed using the Illumina TruSeq Stranded mRNA kit. The protocol included mRNA enrichment with oligo-dT beads, dUTP-based second-strand synthesis for strand specificity, indexing with TruSeq set A, and amplification via a 15-cycle PCR, with AMPure XP bead purification.

treatment_protocol: Naive B cells and CD27bright MBCs were stimulated with 1 μg/mL rhCD40L plus 10 μg/mL anti-IgM/IgG/IgA and 20 ng/mL rhIL-21 or 0.35 μM TLR9 agonist CpG-B ODN2006 for 48 hours in complete medium at a concentration of 2.5x106 cells/mL.

value: naive B cells

value: healthy donor

tag: treatment


title: IN.HD0014

description:
Library name: Sample 49
naive B cells_healthy donor


title: E0771_tumor_from_DIO+Sulindac_C57BL6J_mouse_7


title: RaptrCKO_ILC1_CR_3

city: Akita

first: Megumi

last: Tatematsu

department: Department of Medical Biology

institute: Akita University Graduate School of Medicine

description: Library name: Sample24

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (v. 0.23.2) (parameters - Quality >= Q15, N base limit = 10)
Trimmed sequence reads were mapped to GRCm39 using STAR aligner (v. 2.7.11a) with default parameters
Read count exxtraction were performed using featureCounts (v. 2.0.3)
Read count normalization were caliculated by R (v. 4.1.3)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes TPM for each Sample

source_name: Liver

extract_protocol:
Cells were isolated and directly brought into First-Strand cDNA Synthesis step using SMART-Seq® Stranded Kit (Takara).
Libraries were generated using SMART-Seq® Stranded Kit according to manufacturer's instruction

value: Liver

value: Raptr CKO

value: calorie restriction


title: 050B-A

description: Library name: 050B-A


title: peripheral blood, PDAC, EV43

value: PDAC


title: peripheral blood, PDAC, EV42


title: IN.HD0013

description:
Library name: Sample 48
naive B cells_healthy donor


title: E0771_tumor_from_DIO+Sulindac_C57BL6J_mouse_8


title: peripheral blood, PDAC, EV41

value: O


title: RaptrCKO_ILC1_CR_2

description: Library name: Sample23


title: RaptrCKO_ILC1_CR_1

description: Library name: Sample22


title: E0771_tumor_from_DIO+Sulindac_C57BL6J_mouse_4


title: peripheral blood, PDAC, EV45


title: peripheral blood, PDAC, EV40


title: RaptrCKO_ILC1_AL_3

description: Library name: Sample21

value: ad libitum


title: IN.HD0010

description:
Library name: Sample 45
naive B cells_healthy donor


title: peripheral blood, PDAC, EV39


title: RaptrCKO_ILC1_AL_2

description: Library name: Sample20


title: IN.HD0011

description:
Library name: Sample 46
naive B cells_healthy donor


title: peripheral blood, PDAC, EV38


title: E0771_tumor_from_DIO+Sulindac_C57BL6J_mouse_2


title: E0771_tumor_from_DIO+Sulindac_C57BL6J_mouse_1


title: E0771_tumor_from_DIO+Sulindac_C57BL6J_mouse_5


title: RaptrCKO_ILC1_AL_1

description: Library name: Sample19


title: IN.HD0008

description:
Library name: Sample 43
naive B cells_healthy donor


title: E0771_tumor_from_DIO_C57BL6J_mouse_8

value: DIO


title: E0771_tumor_from_DIO_C57BL6J_mouse_7


title: RaptrCKO_NK_CR_3

description: Library name: Sample18

value: NK cell


title: peripheral blood, PDAC, EV37


title: E0771_tumor_from_DIO+Sulindac_C57BL6J_mouse_6


title: IN.CVID49

description:
Library name: Sample 41
naive B cells_CVID

value: CVID


title: peripheral blood, PDAC, EV36

value: peripheral blood


title: E0771_tumor_from_DIO+Sulindac_C57BL6J_mouse_3


title: RaptrCKO_NK_CR_2

description: Library name: Sample17


title: IN.HD0007

description:
Library name: Sample 42
naive B cells_healthy donor


title: IN.HD0012

description:
Library name: Sample 47
naive B cells_healthy donor


title: RaptrCKO_NK_CR_1

description: Library name: Sample16


title: IN.CVID44

description:
Library name: Sample 40
naive B cells_CVID


title: peripheral blood, PDAC, EV34


title: IN.HD0009

description:
Library name: Sample 44
naive B cells_healthy donor


title: E0771_tumor_from_DIO_C57BL6J_mouse_6


title: RaptrCKO_NK_AL_3

description: Library name: Sample15


title: E0771_tumor_from_DIO_C57BL6J_mouse_5


title: IN.CVID28

description:
Library name: Sample 39
naive B cells_CVID


title: peripheral blood, PDAC, EV33


title: RaptrCKO_NK_AL_2

description: Library name: Sample14


title: IN.CVID25

description:
Library name: Sample 38
naive B cells_CVID


title: E0771_tumor_from_DIO_C57BL6J_mouse_3


title: peripheral blood, PDAC, EV32


title: E0771_tumor_from_DIO_C57BL6J_mouse_4


title: RaptrCKO_NK_AL_1

description: Library name: Sample13


title: IN.CVID21

description:
Library name: Sample 37
naive B cells_CVID


title: IN.CVID14

description:
Library name: Sample 36
naive B cells_CVID


title: peripheral blood, PDAC, EV31


title: peripheral blood, PDAC, EV30


title: WT_ILC1_CR_2

description: Library name: Sample11

value: wild type


title: peripheral blood, PDAC, EV29


title: IN.CVID13

description:
Library name: Sample 35
naive B cells_CVID


title: WT_ILC1_CR_1

description: Library name: Sample10


title: IN.CVID10

description:
Library name: Sample 34
naive B cells_CVID


title: WT_ILC1_CR_3

description: Library name: Sample12


title: peripheral blood, PDAC, EV28


title: IN.CVID08

description:
Library name: Sample 33
naive B cells_CVID


title: WT_ILC1_AL_3

description: Library name: Sample9


title: WT_ILC1_AL_2

description: Library name: Sample8


title: peripheral blood, PDAC, EV27


title: IB.HD0015

description:
Library name: Sample 32
CD27 bright memory cells_healthy donor

value: CD27 bright memory cells


title: peripheral blood, PDAC, EV26


title: IB.HD0014

description:
Library name: Sample 31
CD27 bright memory cells_healthy donor


title: WT_ILC1_AL_1

description: Library name: Sample7


title: E0771_tumor_from_Control+Sulindac_C57BL6J_mouse_6

value: Control+Sulindac


title: IB.HD0013

description:
Library name: Sample 30
CD27 bright memory cells_healthy donor


title: peripheral blood, PDAC, EV25


title: WT_NK_CR_3

description: Library name: Sample6


title: peripheral blood, PDAC, EV24

value: responder


title: E0771_tumor_from_Control+Sulindac_C57BL6J_mouse_4


title: peripheral blood, PDAC, EV23

value: non-responder


title: E0771_tumor_from_Control+Sulindac_C57BL6J_mouse_2


title: E0771_tumor_from_DIO_C57BL6J_mouse_2


title: IB.HD0012

description:
Library name: Sample 29
CD27 bright memory cells_healthy donor


title: WT_NK_CR_1

description: Library name: Sample4


title: E0771_tumor_from_Control+Sulindac_C57BL6J_mouse_5


title: IB.HD0011

description:
Library name: Sample 28
CD27 bright memory cells_healthy donor


title: E0771_tumor_from_Control+Sulindac_C57BL6J_mouse_3


title: WT_NK_AL_3

description: Library name: Sample3


title: E0771_tumor_from_Control_C57BL6J_mouse_6

value: Control


title: peripheral blood, PDAC, EV22


title: peripheral blood, PDAC, EV35


title: peripheral blood, PDAC, EV21


title: E0771_tumor_from_Control_C57BL6J_mouse_4


title: E0771_tumor_from_DIO_C57BL6J_mouse_1


title: WT_NK_AL_2

description: Library name: Sample2


title: peripheral blood, PDAC, EV20


title: IB.HD0009

description:
Library name: Sample 26
CD27 bright memory cells_healthy donor

value: healthy donor


title: WT_NK_CR_2

description: Library name: Sample5

value: Liver


title: E0771_tumor_from_Control+Sulindac_C57BL6J_mouse_1


title: E0771_tumor_from_Control_C57BL6J_mouse_2


title: peripheral blood, PDAC, EV19


title: IgG Hypoxia rep 2

description: Library name: Sample 15

data_processing:
Sequence reads were analyzed with the STAR alignment and DESeq2 software pipeline.
Reads were trimmed with Trimmomatic56 with the following settings (ILLUMINACLIP: 2:15:4:4:true SLIDINGWINDOW:4:15 MINLEN:25)
Trimmed reads were aligned to the galgal6 genome (Ensembl genome browser version 96) using Bowtie2with the following settings: (−-end-to-end,--dove-tail,--phred33).
H3K4me3 and H3K27ac genomic binding regions were identified using MACS2 by pooling the H3K4me3 or H3K27ac BAM files versus the pooled IgG BAM files as a negative control and using default broadpeak settings
ChIPseeker was used to identify relative distances of H3K4me3 and H3K27ac peaks to the nearest gene transcription start site.
Assembly: Galgal6
Supplementary files format and content: txt file contains identfied peaks for all samples
Library strategy: CUT&Run

growth_protocol: Embryonic chicken lens organ cultures were prepared from the lenses of Embryonic day 13 (E13) White Leghorn embryonated chicken eggs (Charles River Laboratories, Storrs, CT). Whole lenses were removed from E13 chicken eyes and placed into 35mm dishes containing Medium 199 (Invitrogen) supplemented with 10% FBS (Invitrogen) and penicillin-streptomycin antibiotic mix (50 units/ml; Invitrogen). Lenses were cultured for 2H  in normoxia (21% O2) or hypoxia (1% O2), lenses that exhibited damage or opacity were removed from the study.

extract_protocol:
For CUT&RUN 10-15 lenses per n were microdissected at 0 hours or 2 hours of hypoxia treatment and immediately processed for CUT&RUN using the Epicypher protocol available online.
Library prep was carried out using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7645) following the manufacturer’s instructions

treatment_protocol: Lenses  incubated in 21% or 1% O2 for 2H

value: Embryonic D13 Chick lens

value: lens fiber cells

value: Incubated in 1% O2 for 2H


title: E0771_tumor_from_Control_C57BL6J_mouse_5


title: IB.HD0007

description:
Library name: Sample 24
CD27 bright memory cells_healthy donor


title: IgG Hypoxia rep 3

description: Library name: Sample 16


title: IB.CVID31

description:
Library name: Sample 23
CD27 bright memory cells_CVID


title: E0771_tumor_from_Control_C57BL6J_mouse_3


title: IgG Hypoxia rep 1

description: Library name: Sample 14


title: peripheral blood, PDAC, EV18

value: PDAC

value: O


title: mES_WT_rep2

city: hangzhou

first: kuang

last: junqi

address: No.18 Shilongshan Road

institute: westlake University

description: Library name: Sample 2

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (hg38) transcriptome using Bowtie2 (v2.2.5) and RSEM (v1.3.0)
Gene expression level was calculated using EDASeq (v2.4.1)
Assembly: mm10
Supplementary files format and content: Myh9KO.rnaseq.csv

source_name: inner cell mass

growth_protocol: mESC were cultured by mES medium plus 2i

extract_protocol:
TRIzol, according to the manufacturers instructions
VAHTS mRNA-seq V2 Library Prep Kit for Illumina was used according to the manufacturer's instruction. Briefly, 1ug total RNA was used and mRNA was enriched using olig-dT dynabeads, followed by fragmentation by divalent cation at elevated temperature. First-strand cDNA synthesis by random hexamers and reverse transcriptase was followed by the second-strand cDNA synthesis. Then the reverse product was purified using AMPure XP beads. The cDNA was end repaired and a dA was added, followed by ligation, two round purification using AMPure XP beads, PCR amplification and PCR product purification. The library was quantified with an Invitrogen Qubit.

treatment_protocol: routinely cultured without special treatment

value: inner cell mass

tag: cell line

value: mouse embryonic stem cell

value: WT

value: cultured in mES+2i medium


title: mES_Myh9KO_rep1

description: Library name: Sample 3

tag: cell type

value: Myh9 KO


title: IB.HD0010

description:
Library name: Sample 27
CD27 bright memory cells_healthy donor

value: peripheral blood

value: CD27 bright memory cells

tag: genotype


title: IgG Nomoxia rep 3

description: Library name: Sample 13

value: Incubated in 21% O2 for 2H


title: peripheral blood, PDAC, EV16


title: IgG Nomoxia rep 2

description: Library name: Sample 12


title: IB.CVID21

description:
Library name: Sample 21
CD27 bright memory cells_CVID

value: CVID


title: peripheral blood, PDAC, EV15

value: non-responder


title: mES_WT_rep1

description: Library name: Sample 1


title: E0771_tumor_from_Control_C57BL6J_mouse_1

value: Control


title: IB.HD0008

description:
Library name: Sample 25
CD27 bright memory cells_healthy donor

value: healthy donor


title: WT_NK_AL_1

description: Library name: Sample1

value: Liver

value: NK cell

value: wild type

value: ad libitum


title: IgG Nomoxia rep 1

description: Library name: Sample 11

value: Embryonic D13 Chick lens

value: lens fiber cells


title: mES_Myh9KO_rep2

description: Library name: Sample 4

value: inner cell mass

value: mouse embryonic stem cell


title: peripheral blood, PDAC, EV14

value: PDAC

value: O

value: responder


title: IB.CVID14

description:
Library name: Sample 19
CD27 bright memory cells_CVID

value: peripheral blood

value: CD27 bright memory cells


title: H3K4me3 Hypoxia rep 3

description: Library name: Sample 10

value: Incubated in 1% O2 for 2H


title: BALF, TB_37

city: Asan

first: Jeong-An

last: Gim

address: 22 Suncheonhyang-ro

institute: Soonchunhyang University

data_processing:
The raw 16S amplicon sequences were processed by QIIME2 v1.8.0 with default parameters.
We then used SHI7 for trimming Nextera adapters and stitching paired-end reads and performed quality trimming at both ends of the stitched reads until a minimum Phred score of 32 was reached.
The OTUs were determined by de novo clustering of the sequences with a 97% sequence identity cut-off by QIIME
We performed alpha- and beta-diversity analyses in R using the vegan and phyloseq packages.
Based on the OTU table, we calculated the average richness estimate for each alpha-diversity metric (Chao1, observed OTUs, and Shannon).
Supplementary files format and content: OTU.xlsx
Library strategy: 16s rRNA seq

organism: human lung metagenome

source_name: Bronchoalveolar lavage fluid

extract_protocol:
From BALF samples, DNA was extracted by the QIAamp DNA microbiome kit (Qiagen, 51704).
We used Herculase II Fusion DNA Polymerase Nextera XT Index Kit V2, and sequencing instrument model was Illumina MiSeq.

value: Bronchoalveolar lavage fluid

tag: disease state

value: TB

tag: Sex

value: Male

tag: age

tag: bmi


title: BALF, TB_38

value: Female


title: IB.CVID13

description:
Library name: Sample 18
CD27 bright memory cells_CVID

value: CVID


title: H3K4me3 Hypoxia rep 1

description: Library name: Sample 8


title: H3K4me3 Hypoxia rep 2

description: Library name: Sample 9


title: peripheral blood, PDAC, EV11


title: BALF, NTM_28

value: NTM


title: IB.CVID08

description:
Library name: Sample 16
CD27 bright memory cells_CVID


title: peripheral blood, PDAC, EV13


title: IB.CVID10

description:
Library name: Sample 17
CD27 bright memory cells_CVID


title: peripheral blood, PDAC, EV17


title: peripheral blood, PDAC, EV10


title: H3K4me3 Normoxia rep 2

description: Library name: Sample 6

value: Incubated in 21% O2 for 2H


title: BALF, NTM_27


title: IB.CVID16

description:
Library name: Sample 20
CD27 bright memory cells_CVID


title: IB.CVID01

description:
Library name: Sample 15
CD27 bright memory cells_CVID


title: BALF, Others_41

value: Others


title: AB.HD0006

description:
Library name: Sample 14
CD27 bright memory cells_healthy donor

value: healthy donor

value: TLR9 agonist (CpG) for 48 hours


title: peripheral blood, PDAC, EV8


title: H3K4me3 Normoxia rep 1

description: Library name: Sample 5

value: Embryonic D13 Chick lens

value: lens fiber cells


title: H3K4me3 Normoxia rep 3

description: Library name: Sample 7


title: H3K27ac Hypoxia rep 2

description: Library name: Sample 4


title: BALF, TB_36


title: peripheral blood, PDAC, EV7

value: PDAC

value: O

value: non-responder


title: AB.HD0003

description:
Library name: Sample 13
CD27 bright memory cells_healthy donor

value: peripheral blood

value: CD27 bright memory cells


title: BALF, NTM_26

value: Bronchoalveolar lavage fluid


title: peripheral blood, PDAC, EV12

value: responder


title: BALF, TB_35

value: TB


title: AB.HD0002

description:
Library name: Sample 12
CD27 bright memory cells_healthy donor


title: H3K27ac Hypoxia rep 1

description: Library name: Sample 3

value: Incubated in 1% O2 for 2H


title: peripheral blood, PDAC, EV6


title: BALF, TB_34

value: Male


title: peripheral blood, PDAC, EV5


title: BALF, Others_40


title: peripheral blood, PDAC, EV9


title: H3K27ac Normoxia rep 1

description: Library name: Sample 1


title: AB.CVID53

description:
Library name: Sample 10
CD27 bright memory cells_CVID

value: CVID


title: AB.HD0001

description:
Library name: Sample 11
CD27 bright memory cells_healthy donor


title: peripheral blood, PDAC, EV4


title: AB.CVID51

description:
Library name: Sample 9
CD27 bright memory cells_CVID


title: peripheral blood, PDAC, EV3


title: AB.CVID30

description:
Library name: Sample 8
CD27 bright memory cells_CVID


title: ss8, scATACseq

city: London

first: Eva

last: Hamrud

address: Centre for Craniofacial and Regenerative Biology, King's College London, Guy's Campus, Great Maze Pond

country: United Kingdom

institute: King's College London

description: 10x Genomics

data_processing:
Demultiplexing and barcode identification was carried out using 10x Genomics Cell Ranger-ATAC 2.0.0. Generates the processed files: filtered_peak_bc_matrix.h5 (note these peaks are not used in the downstream scACE pipeline), singlecell.csv and fragments.tsv.gz
ArchR objects were made and processed using the standard processing steps of the scACE pipeline (https://github.com/Streit-lab/scACE) which uses the ArchR package. Briefly, ArchR projects were created, peaks called and cells annotated by integration with published equivalent scRNAseq data (Thiery et al 2023). Generates processed files Save-ArchR.tar.gz. To use these files untar and then load into R using the ArchR package (https://www.archrproject.com/index.html)
Assembly: GRCg6a
Supplementary files format and content: Cellranger output files: filtered_peak_bc_matrix.h5, fragments.tsv.gz, singlecell.csv
Supplementary files format and content: scACE pipeline output files: Save_ArchR.tar.gz

source_name: Embryonic ectoderm

extract_protocol:
Single nuclei were dissociated from cryopreserved tissue pieces using a the modified 10x Genomics protocol. Samples were warmed in a 37C water bath for 1 minute before adding 500 μl warmed Tyrode’s saline. Samples were spun at 4C for 5 minutes at 200 RCF, the supernatant was removed and replaced with 100 μl of 0.05X lysis buffer (see 10x protocol for composition). Samples were incubated on ice for 5 minutes before adding 1 ml wash buffer (see 10x protocol for composition). Nuclei were filtered (20 μm Miltenyi cell strainer) and recovered by spinning at 4C at 500 RCF for 5 minutes. Nuclei were resuspended in nuclei solution buffer (10x Genomics, PN 2000153/2000207).
Library preparation was carried out using the Chromium Next GEM Single Cell ATAC Kit v1.1 (10 x Genomics)

value: Embryonic ectoderm


title: ss4, scATACseq

description: 10x Genomics


title: BALF, Others_38

value: Others


title: peripheral blood, PDAC, EV2


title: BALF, TB_32


title: peripheral blood, PDAC, EV1


title: AB.CVID17

description:
Library name: Sample 6
CD27 bright memory cells_CVID


title: RNA-seq of BafA1 treated NPC dIV 11,Rep3

city: Bongmyeongdong

first: Vincencius

last: Vidyawan

state: Cheonan

address: 25, Bongjeong-ro, Dongnam-gu, Cheonan-si, 31151, Korea

department: Department of Integrated Biomedical Science

institute: Soonchunhyang Institute of Medi-bio Science (SIMS)

description: biological replicate 3

data_processing:
Trimmometrix 0.38
Trimmomatic performs trimming with various parameters for illumina paired-end or single-end.
Iluminaclip : Cut adapter or specific sequence from read
Sliding Window: Perform sliding window trimming. The average quality within the window is the threshold.
LEADING: If it is below the threshold, the base of the start part of the read is cut off. TRAILING: If it is below the threshold, the base at the end of the read is truncated. Truncate if less than, and CROP: truncate reads to a specific length.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file included Raw count for each sample
Supplementary files format and content: Tab-delimited text file included RFPKM each sample

source_name: NPC

growth_protocol: The dual-SMAD inhibition protocol from previous study was used to initiate midbrain dopamine neuron (DA) differentiation derived from hESC. Accutase® (Gibco Grand Island, NY) was used to dissociate the cells, which were then seeded as single cells and allowed to grow onto Matrigel (Corning, Corning, NY)-coated culture dish at density 5 x 105 per 24-well plate until confluence.KSR was supplemented with 200 nM LDN193189 (STEMCELL Technologies, Vancouver, BC, Canada) and 10 μM SB431542 (Tocris; “day 0”), 2µM Purmophamine, and 3uM CHIR 99021 were added to KSR medium at specific time exposures. Starting on day 5 of differentiation, 25% of the N2 medium was gradually added, and the proportion of N2 was raised by 50% and 75% every two days.

extract_protocol:
Total RNA was isolated using TRIZOL (Life Technology), and RNA quality was checked by OD 260/280 ratio and analyzed by Agilent 2100 Bioanalyzer
TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E

treatment_protocol: Bafilomycin (BafA1; 10nM) is treated for 6 hours on days 4-6, 6-8, 8-10, and 6-10 during the differentiation process.

value: NPC

value: Bafilomycin A1


title: BALF, TB_31

value: Female


title: H3K27ac Normoxia rep 2

description: Library name: Sample 2

value: Embryonic D13 Chick lens

value: lens fiber cells

value: Incubated in 21% O2 for 2H


title: HH6, scATACseq

description: 10x Genomics


title: HH7, scATACseq

description: 10x Genomics


title: RNA-seq of BafA1 treated NPC dIV 11,Rep2

description: biological replicate 2


title: HH5, scATACseq

description: 10x Genomics


title: AB.CVID13

description:
Library name: Sample 4
CD27 bright memory cells_CVID

value: TLR9 agonist (CpG) for 48 hours


title: BALF, NTM_25

value: NTM


title: RNA-seq of BafA1 treated NPC dIV 11,Rep1

description: biological replicate 1


title: AB.CVID14

description:
Library name: Sample 5
CD27 bright memory cells_CVID

value: peripheral blood

value: CD27 bright memory cells


title: BALF, Others_37

value: Bronchoalveolar lavage fluid


title: Leaf primordia SR1, Halo-tagged AmMIXTA, replicate 3

city: Louvain-la-Neuve

first: Charles

last: Hachez

address: Croix du Sud 4

department: LIBST

country: Belgium

institute: UCLouvain

description:
MIXTA3
DAPseq MIXTA results.xlsx
DAP_seqMIXTA_raw.xlsx

data_processing:
The DNA-seq libraries were sequenced by Macrogen using Illumina NovaSeq 6000 sequencing platform. A minimum of 50 million 150 bp paired-end reads were obtained per sample
Using CLC Genomic Workbench (Qiagen), reads were cleaned and trimmed of adaptors, ambiguous nucleotides, homopolymers in 3’ and 5’ and for quality (PHRED30) and minimum length
They were then mapped to the N. tabacum TN90 reference genome (GCF_000715135.1_Ntab- TN90_genomic)
Peak scores (>2) and p-values (<0.05) were then calculated using the Transcription Factor CHIP-seq tool from CLC Genomic Workbench comparing our samples to the negative control (DNA bound to nlsGFP).
Assembly: GCF_000715135.1_Ntab- TN90_genomic
Supplementary files format and content: "DAPseq ZFP8 results.xlsx" and "DAPseq MIXTA results.xlsx" are tab delimited text files giving the calculated Peak scores (>2) and p-values (<0.05) using the Transcription Factor CHIP-seq tool from CLC Genomic Workbench comparing our samples to the negative control (DNA bound to nlsGFP). Peaks of interest were selected based on their proximity to a gene: 3kb upstream of a START codon and 1kb downstream of a STOP codon.
Supplementary files format and content: "DAP_seqZFP8_raw.xlsx" and "DAP_seqMIXTA_raw.xlsx" are tab delimited text files providing for each detected DAPseq Peak the  following information: chromosome, genomic region, peak center, Peak length, Peak shape score and P-value calculated using the Transcription Factor CHIP-seq tool from CLC Genomic Workbench.
Library strategy: DAP-seq

organism: Nicotiana tabacum

source_name: Leaf primordia

extract_protocol:
Leaf primordia harvested from three independent WT plants were flash-frozen, grinded and DNA was extracted using the Wizard Genomic DNA Purification Kit (Promega; A1120).
DNA was fragmented using a sonicating bath for 20 min (Elam S10H Elmasonic) and fragment size was verified on gel.
the DNA fragments were subjected to end-repair (Fast DNA end repair kit, Thermoscientific, K0771), A-tail reaction using Klenow enzyme (NEB, M0212S), ligation to the adaptor (Promega, M1794) and DNA concentration measurement (Qubit dsDNA Assay kit, Qiagen, Q32850). HALO-AmMIXTA, HALO-NtZFP8 and HALO-nlsGFP (negative control) were expressed independently three times using the TnT® Coupled Wheat Germ Extract System (Promega, L41030). Expression was confirmed by Western-blot using Monoclonal Antibody Raised Against the HaloTag® Protein (Promega, G9211) and Goat anti-mouse IgG (H+L) HRP conjugated (Chemicon, AP308P).  Proteins were bound to the 20μl of Magne® HaloTag Beads (Promega, G7882) per sample, washed and put in contact with 1000 ng of DNA for 1h at 25°C. Each replicate of proteins was put in contact with one replicate of DNA. Beads were washed and DNA was eluted in EB at 98°C. Index and adaptor were added to the DNA fragments using Phusion® High-Fidelity DNA polymerase (NEB, M0530L) and NEBNext® Multiplex Oligos for Illumina® primers (NEB, E6440S), and DNA check on gel and was purified using the minelute reaction cleanup kit (Qiagen, 28204)

treatment_protocol: The DAPseq experiment was executed following the protocol from Bartlett et al. (2017) with some small modifications.

value: Leaf primordia

tag: cultivar

value: Petit Havana

tag: expressing

value: Halo-tagged AmMIXTA


title: BALF, TB_33

value: TB

value: Male


title: AB.CVID10

description:
Library name: Sample 3
CD27 bright memory cells_CVID

value: CVID


title: Leaf primordia SR1, Halo-tagged AmMIXTA, replicate 2

description:
MIXTA2
DAPseq MIXTA results.xlsx
DAP_seqMIXTA_raw.xlsx


title: BALF, Others_39

value: Others


title: RNA-seq of NPC dIV 11,Rep3

description: biological replicate 3

value: NPC

value: No-treatment


title: AB.CVID03

description:
Library name: Sample 2
CD27 bright memory cells_CVID


title: AB.CVID01

description:
Library name: Sample 1
CD27 bright memory cells_CVID


title: Leaf primordia SR1, Halo-tagged AmMIXTA, replicate 1

description:
MIXTA1
DAPseq MIXTA results.xlsx
DAP_seqMIXTA_raw.xlsx


title: RNA-seq of NPC dIV 11,Rep2

description: biological replicate 2


title: Leaf primordia SR1, Halo-tagged NtZFP8, replicate 3

description:
ZFP83
DAPseq ZFP8 results.xlsx
DAP_seqZFP8_raw.xlsx

value: Halo-tagged NtZFP8


title: BALF, TB_29

value: Female


title: RNA-seq of hESC H9,Rep3

description: biological replicate 3

source_name: Embryonic stemcell

value: Embryonic stemcell


title: BALF, NTM_23


title: DPTILs, Untransduced, Donor43

city: Durham

middle: A

last: Gersbach

address: 101 Science Drive

institute: Duke University

description: Library name: T43 DP -

data_processing:
Initial data processing was performed on FASTQ files using MiXCR using the present for the SMARTer Human TCR a/b kit
The R package immunarch was used to analyze effective number of types for TCR diversity across samples to account for both number of clones and relative abundance.
Assembly: MiXCR V-, D-, J-, and C- gene segment librar for Homo sapiens
Supplementary files format and content: .tsv files were generated from MiXCR exporClones function. File outputted includes clonotype abundances, nucleotide and amino acid clonotype sequences, Phred qualities, all or just best hit for V, D, J and C genes, corresponding alignments, nucleotide and amino acid sequences of gene regions present in sequence
Library strategy: TCR-Seq

source_name: NSCLC tumor

extract_protocol:
RNA was isolated using Norgen’s Total RNA Purification Plus Kit
Takara’s SMARTer Human TCR a/b Profiling Kit v1 was used to generate TCR-seq libraries. Library generation and purification methods were carried out according to manufacturer protocol.

value: NSCLC tumor

value: tumor-infiltrating lymphocytes

value: DP

value: Untransduced


title: Leaf primordia SR1, Halo-tagged NtZFP8, replicate 2

description:
ZFP82
DAPseq ZFP8 results.xlsx
DAP_seqZFP8_raw.xlsx


title: CD8TILs, RELB, Donor43

description: Library name: T43 CD8 RELB

value: RELB


title: RNA-seq of hESC H9,Rep2

description: biological replicate 2


title: Leaf primordia SR1, Halo-tagged GFP (Negative control), replicate 3

value: Leaf primordia

value: Halo-tagged GFP (Negative control)


title: RNA-seq of hESC H9,Rep1

description: biological replicate 1


title: BALF, Others_36

value: Bronchoalveolar lavage fluid


title: CD8TILs, Thy1.1, Donor43

description: Library name: T43 CD8 Thy1.1


title: Leaf primordia SR1, Halo-tagged NtZFP8, replicate 1

description:
ZFP81
DAPseq ZFP8 results.xlsx
DAP_seqZFP8_raw.xlsx

value: Petit Havana


title: BALF, NTM_24

value: NTM


title: CD8TILs, Untransduced, Donor43

description: Library name: T43 CD8 -


title: BALF, NTM_22

value: Male


title: Spleen sample 1

city: Zwijnaarde

first: VIB

last: Single Cell Core

address: Technologiepark-Zwijnaarde 71

department: VIB Single cell core

institute: VIB

description: 10X genomics

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger software (Cellranger-5.0.0 )
Assembly: ensembl release 101 Melopsittacus_undulatus_6.3
Supplementary files format and content: CellRanger filtered count matrix
Supplementary files format and content: CellRanger raw count matrix

organism: Melopsittacus undulatus

source_name: Spleen

extract_protocol:
An enzymatic digest was conducted for 20 min at 37°C and 1200 RPM, in the presence of 0.5 ml RPMI 1640 medium, 0.4% DNase (10 U/µl) and 2% Liberase (1 mg/ml). The resulting cell suspension was filtered through a 70 µm cell strainer and washed with HBSS at RT. Next, splenocytes were isolated through density gradient centrifugation, where cells were carefully layered onto 2 ml Lymphoprep™ and centrifuged for 20 min at 800 g and 18°C. The recovered splenocytes were washed with HBSS (RT), stained with DAPI (10 µg/ml) and subjected to cell sorting. Dead cells and cell aggregates were excluded.
Library was performed according to manufacturer's instructions (single cell 3' V2 protocol, 10X genomics).

value: Spleen

value: enzymatic digest and purification with lymphoprep gradient centrifugation


title: RNA-seq of NPC dIV 11,Rep1

description: biological replicate 1

value: NPC

value: No-treatment


title: BALF, TB_30

value: TB


title: Leaf primordia SR1, Halo-tagged GFP (Negative control), replicate 1


title: CD4TILs, Thy1.1, Donor43

description: Library name: T43 CD4 Thy1.1


title: BALF, Others_33

value: Others