title: Embryo, 18 hours post fertilization

city: DURHAM

last: Berrio

state: NC

address: 124 Science Dr

department: Biology

institute: Duke University

description: 10X Genomics

data_processing:
Raw sequencing data was processed using the Cellranger 3.1.0  pipeline (10X Genomics) to generate FASTQ files.
FASTQ files were aligned to the reference genome (Lvar_3.0 Genome) and gene expression matrices were generated using Cell Ranger.
Quality control, normalization, and clustering were performed using Seurat (v4.0).
Differential expression analysis was conducted using the FindMarkers function in Seurat.
Assembly: GCF_018143015.1 (Davidson et al., 2020)
Supplementary files format and content: Processed data files are provided in TSV and MTX format, containing gene expression matrices. TSV files include  files with cell metadata and gene annotations.

organism: Lytechinus variegatus

source_name: Embryonic

extract_protocol:
Single-cell suspensions were prepared, to do this,  embryos were surgically treated to remove micormeres, then they were washed twice in calcium-free artificial seawater (CFASW) then resuspended in dissociation buffer [1.0 M glycine and 0.25 mM EDTA (pH 8.0)] at 4°C. The embryos were then dissociated by gentle trituration. Following dissociation, cells were resuspended in CFASW, and fixed at a final concentration of 80% methanol in CFASW for 1 h, at 4°C. Following fixation, cells were stored at −20°C and all cell libraries were processed within 1 month of dissociation.
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Reagent Kits v3.1 (10X Genomics) according to the manufacturer's protocol. Briefly, single cells were encapsulated into Gel Bead-In-Emulsions (GEMs) using the Chromium Controller, followed by reverse transcription, cDNA amplification, and library construction.
Libraries were titered and pooled at Duke University’s Sequencing and Genomic Technologies Core Facility, then sequenced in one S1 flow cell on an Illumina NovaSeq 6000 S-Prime 50bp PE Full flow cell

value: Embryonic

tag: age

value: 18 hours post fertilization


title: HK-2 cells,  DMEM medium containing 5mg/mL recombinant S100A8/S100A9-1, 48h

status: Public on Nov 06 2024

type: SRA

city: Guiyang

first: Qing

last: Wang

state: Guizhou

address: Zhongshan Road 83

department: Department of Urology

country: China

institute: Guizhou Provincial People's Hospital

library_source: transcriptomic

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 cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Ensembl_release100
Supplementary files format and content: tab-delimited text files include RPKM values for all Samples

molecule: total RNA

organism: Homo sapiens

source_name: Kidney

growth_protocol: In a humidified atmosphere of 37°C and 5% CO2, HK-2 cells were cultured with DMEM medium (HyClone, USA)  containing 10% fetal bovine serum (Gibico, USA).

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, USA) according to the manufacturer’s protocol.
Eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing  adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China)

treatment_protocol: We cultured the HK-2 cells with 5mg/mL recombinant S100A8, recombinant S100A9, or recombinant S100A8/S100A9 protein for 48h and then sequenced the total cellular mRNAS. mRNAS from HK-2 cells cultured with DMEM medium containing corresponding amount of PBS was set as the control group.

tag: tissue

value: Kidney

tag: cell line

tag: cell type

value: Epithelial Cells

tag: genotype

value: WT

tag: treatment

tag: time point


title: Phase I 11C × Phase II 7±5C, 41 day_rep2

city: Geneva

first: Hongrui

state: NY

address: 630 W. North Street

department: School of Integrative Plant Science, Horticulture section

country: USA

institute: Cornell University

description:
Second_F06_N138_T6_11V_AAGTGG
ControlAcclimation_gene_count_geo.csv

data_processing:
FastQC for quality control
BBDuk for removing adaptors and poly-A following the pipeline suggested by the manufacturer (https://www.lexogen.com/quantseq-data-analysis/)
STAR for gene level quantification using ‘-quantMode GeneCounts’
Low count gene filterig based on 'total gene count greater than sample number'
DESeq2 for variance stabilization transformation and gene expression normalization
WGCNA for gene co-expression analysis, noise gene filtering, module eigengene visualization and contrast generation
GSEA for pathway enrichment analysis
Assembly: Vitis vinifera 12X.v2 genome with VCost.v3 annotation
Supplementary files format and content: One matrix table with raw gene counts for every gene and every sample without any filtering

organism: Vitis vinifera

source_name: bud

extract_protocol:
Total RNA was extracted using SpectrumTM Plant Total RNA Kit (Sigma Aldrich, St Louis, MO, USA) following the protocol suggested by the manufacturer
Libraries were constructed with Lexogen QuantSeq 3’mRNA-Seq Prep Kit (Lexogen, Greenland, NH, USA) following standard practices as a service provided by Cornell University Institute of Genomic Diversity (Ithaca, NY, USA). Sequencing of the libraries was accomplished using NextSeq500 (Illumina, Inc., San Diego, CA, USA) with 95 samples per lane at Cornell University Institute of Biotechnology (Ithaca, NY, USA). The read length was 85 bp.

value: bud

tag: cultivar

value: Cabernet Sauvignon

tag: time in_treatment_(day)

tag: phase

value: Phase II

tag: phase i_treatment_(°c)

tag: phase ii_treatment_(°c)

tag: replication


title: heart, Control_05

city: Fuzhou City

first: Shaodan

last: Feng

state: Fujian Province

address: Taijiang District

department: Emergency Department

institute: First Affiliated Hospital of Fujian Medical University

data_processing:
Trimmomatic (version 0.36)
Raw sequencing data was filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean data were mapped to the reference genome of Rattus norvegicus using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated.
Assembly: Rattus_norvegicus.Rnor_6.0
Supplementary files format and content: Complete raw counts: All_reads_counts.xls
Supplementary files format and content: Normalized abundance measurements for all samples: All_samples_rpkm.txt
Supplementary files format and content: Diff-expressed data file: RPKM_of_all_diff_genes.xls

molecule: polyA RNA

organism: Rattus norvegicus

source_name: heart

growth_protocol: Each of sprague-dawley male rats, was maintained at 21±2 °C and a cycle of 12 hours of light followed by 12 hours of darkness. Rats received access to food and water ad libitum.

extract_protocol:
TRIzol reagent (Invitrogen, China) was used to extract total RNA from the myocardial tissue. Then, a wide range of RNA was measured and assayed using the QubitTM RNA Wide Range Assay Kit (Life Technologies, Q10210) and Qubit 3.0.
Total RNAs (2 μg) were utilized for library construction with a KCTM Stranded mRNA Library Prep Kit for Illumina®. High-quality total RNA was used to construct cDNA libraries.

treatment_protocol: Following one week of adaptation, rats were given an intraperitoneal dose of 10 mg/kg LPS to cause SCM. Further, they were injected intraperitoneally with or without a dose of 50 μg/kg CGRP or a body weight-matched 0.3 mL/100 g dose of saline 1 hour before LPS injection.

value: heart


title: Embryo, 16 hours post fertilization

first: Alejandro

description: 10X Genomics

library_source: transcriptomic single cell

value: 16 hours post fertilization


title: D1Pas1 KO 3

city: Bethesda

first: Heejin

last: Choi

state: Maryland

address: 50 South drive, Building 50, Room 3131

department: NIDDK

institute: NIH

data_processing:
Fastq files of technical replicates were concatenated when applicable.
Fastq files were preprocessed with cutadapt (v3.4).
RNA-seq data were analyzed using piPipes rna pipeline (v1.1.0).
Small-RNA data were analyzed using piPipes small pipeline (v1.1.0).
R-loop data were analysed following the BisMapR methods (Wulfridge & Sarma, 2021,  eLife 10:e65146).
eCLIP-seq data were analyzed using htseq-clip and DEWSeq workflow (Schwarzl & Sahadevan et al., 2024 NAR)
Assembly: mm10/Gencode M25
Supplementary files format and content: tab-delimited text files of eXpress estimated number of fragments for each RNA-seq sample
Supplementary files format and content: cluster abundance normalized by uniquexmirna per small RNA-seq sample
Supplementary files format and content: normalized bigwig files for forward and reverse strand per R-loop sample.
Supplementary files format and content: htseq-clip counts based on Gencode M25 annotation.

organism: Mus musculus

source_name: Testis

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2.0 ug of total RNA was used for the construction of sequencing libraries.
RNA and BisMapR libraries were prepared using NEB protocols. Small RNA libraries were prepared using the QIAseq miRNA Library Kit for small RNA-seq. eCLIP-seq libraries were prepared using the Yeo group's protocol (Nostrand et al., 2016 Nat Methods)

treatment_protocol: To enrich the piRNA population for the small RNA-seq, b-oxidization was subjected to a total of 20 ug of RNA.

value: Testis

value: male germ cell

value: D1Pas1 KO

value: b-elimination

tag: experiment type

value: small RNA


title: HK-2 cells,  DMEM medium containing 5mg/mL recombinant S100A9-3, 48h


title: D1Pas1 KO 2


title: HK-2 cells,  DMEM medium containing 5mg/mL recombinant S100A9-2, 48h


title: Phase I 7C × Phase II 7±5C, 69 day_rep3

description:
Second_F05_N130_T8_7V_CATCTA
ControlAcclimation_gene_count_geo.csv


title: WT sham, rep3

city: Spokane

first: Jason

middle: Robert

last: Gerstner

state: WA

address: 412 E Spokane Falls BLVD

department: Translational Medicine and Physiology

institute: Washington State Univ. Spokane

description:
columns for WT-M vs WT diffexpr_results.xlsx are: Gene , baseMean , log2FoldChange , lfcSE , stat , pvalue , padj , WT1-M , WT2-M , WT3-M , WT4-M , WT5-M , WT1 , WT2 , WT3 , WT4 , WT5
WT-M vs WT diffexpr_results.xlsx

data_processing:
DNA was sequenced from both ends (paired-end) with a read length of 150 bp.  The raw bcl files were converted to fastq files using the software program bcl2fastq, and adaptors were trimmed from the fastq files during the conversion.
Sequence data (FASTQ files) were processed by trimming low-quality reads using Trimmomatic (version 0.39) (PMID:24695404) and removing rRNA sequences using SortMeRNA (version 4.3.5) (PMID:23071270).
The remaining reads were aligned to the Mus musculus reference genome (mm10, UCSC) using HISAT2 (version 2.2.1) (PMID: 25751142).
Gene expression quantification was analyzed using featureCounts (part of the Subread package, version 2.0.3) (PMID: 24227677).
Differential expression was analyzed using DESeq2 (version 1.36.0) (PMID: 25516281).
Assembly: Mus musculus reference genome (mm10, UCSC)
Supplementary files format and content: Excel .xlsx files with rows are gene symbols. columns: Gene, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, normalized reads for each smaple

source_name: Hippocampus + cortex segment

growth_protocol: 12h ligh:12h dark. Food and water ad libitum

extract_protocol:
Total RNA was purified using an RNeasy Mini Kit (Qiagen). The integrity of total RNA was assessed using Fragment Analyzer (Advanced Analytical Technologies, Ankeny, IA) with the High Sensitivity RNA Analysis Kit. RNA Quality Numbers (RQNs) from 1 to 10 were assigned to each sample to indicate its integrity or quality. “10” stands for a perfect RNA sample without any degradation, whereas “1” marks a completely degraded sample.
RNA samples with RQNs ranging from 8 to 10 were used for RNA library preparation with the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA). Briefly, mRNA was isolated from 1-2.5 µg of total RNA using poly-T oligo attached to magnetic beads and then subjected to fragmentation, followed by cDNA synthesis, dA-tailing, adaptor ligation and PCR enrichment. The sizes of RNA libraries were assessed by Fragment Analyzer with the High Sensitivity NGS Fragment Analysis Kit. The concentrations of RNA libraries were measured using the StepOnePlus Real-Time PCR System (ThermoFisher Scientific, San Jose, CA) with the KAPA Library Quantification Kit (Kapabiosystems, Wilmington, MA).

treatment_protocol: At ZT20, Eight hours after lights-out, wild-type (WT) mice and FABP7 knockout (Fabp7KO) mice were teted for seizure threshold. Mice were tested with a single electric shock delivered via ear clip electrodes once per day. Sham mice received the same handling, but did not receive the shock. We used a constant current electroshock unit (model No. 7801, Ugo Basile, Varese, Italy) in which the initial current level was set at 20 mA and increased by 2 mA with each successive daily trial until a maximal seizure was observed. Other parameters of the stimulus were held constant (60 Hz, 0.4 ms pulse width, 0.2 s duration). Upon maximal electroshock seizure threshold (MEST) defined by bilateral tonic hind limb extension, mice were euthanized and a block of brain tissue was collected from one hemisphere encompassing the hippocampus and cortex from about Bregma 0 to -4 sagittal and about 2.5 horizontal.

value: Hippocampus + cortex segment

tag: strain

tag: age (weeks)

tag: Sex

value: male

tag: time

value: sham handling


title: D1Pas1 KO 1

tag: tissue


title: Embryo, 14 hours post fertilization

description: 10X Genomics

value: Embryonic

tag: age

value: 14 hours post fertilization


title: Phase I 7C × Phase II 7±5C, 41 day_rep1

description:
Second_F04_N122_T6_7V_CGATCT
ControlAcclimation_gene_count_geo.csv


title: HK-2 cells,  DMEM medium containing 5mg/mL recombinant S100A9-1, 48h

value: Kidney

tag: cell line

tag: cell type

value: Epithelial Cells


title: D1Pas1 WT control 3

tag: genotype

value: D1Pas1 WT

tag: treatment


title: Embryo, 10 hours post fertilization

description: 10X Genomics

value: 10 hours post fertilization


title: Phase I 2C × Phase II 7±5C, 69 day_rep3

description:
Second_F03_N115_T8_2V_GCGAAT
ControlAcclimation_gene_count_geo.csv

value: bud

tag: cultivar

value: Cabernet Sauvignon

value: Phase II


title: Embryo, 12 hours post fertilization

description: 10X Genomics

value: 12 hours post fertilization


title: Phase I 2C × Phase II 7±5C, 41 day_rep1

description:
Second_F02_N107_T6_2V_AGAATC
ControlAcclimation_gene_count_geo.csv

tag: time in_treatment_(day)


title: HK-2 cells,  DMEM medium containing 5mg/mL recombinant S100A8-3, 48h

value: WT

tag: time point


title: Embryo, 8 hours post fertilization

description: 10X Genomics

value: 8 hours post fertilization


title: HK-2 cells,  DMEM medium containing 5mg/mL recombinant S100A8-2, 48h


title: HK-2 cells,  DMEM medium containing 5mg/mL recombinant S100A8-1, 48h


title: Embryo, 6 hours post fertilization

description: 10X Genomics

value: 6 hours post fertilization


title: Phase I 4C × Phase II 4C, 34 day_rep1

description:
Second_E09_N161_T5_4_ACAGAT
ControlAcclimation_gene_count_geo.csv

tag: phase

tag: phase i_treatment_(°c)


title: Phase I 4C × Phase II 4C, 55 day_rep3

description:
Second_E10_N169_T7_4_AGACCA
ControlAcclimation_gene_count_geo.csv

tag: phase ii_treatment_(°c)

tag: replication


title: HK-2 cells, DMEM medium containing corresponding amount of PBS-2, 48h

value: Ctrl


title: WT

city: Edmonton

first: Colin

last: Anderson

state: Alberta

department: Surgery

country: Canada

institute: University of Alberta

description:
10X Genomics
CDR3AAdiversity.csv
CDR3length.csv

library_source: other

data_processing:
Reads mapping and contig annotations were conducted using the 10x Genomics Cell Ranger 7.2.0 vdj pipeline via 10x Genomics Cloud Analysis (https://www.10xgenomics.com/, accessed 2024-April-10).
Single-cell TCR repertoires were analyzed using scRepertoire package v2.0.0.
Assembly: Alignment of reads was performed using the prebuilt Cell Ranger v7.2.0 mouse reference GRCm38 v7.0.0.
Supplementary files format and content: The files WT_filtered_contig_annotations.csv and KO_filtered_contig_annotations.csv contain annotations of each high-confidence cell barcode. CDR3AAdiversity.csv contains the Shannon diversity index for each CDR3 amino acid residual position. CDR3length.csv contains the amino acid sequence and CDR3 length of each clone. VDJclones.csv includes the proportion of VDJ clones. VgenesUsage.csv contains the percentage of V gene usage.
Library strategy: TCR-seq

molecule: other

source_name: CD4 SP Thymocytes

extract_protocol:
CD4 SP T cells were isolated by negative selection using the EasySep™ Mouse Naïve CD4+ T Cell Isolation Kit (# 19765, STEMCELL Technologies, Vancouver, Canada) according to the manufacturer's instructions, from single cell thymocyte suspensions prepared from B6.Btla WT and B6.Btla-/- mice (aged 8-12 weeks).
TCR sequencing was conducted using the 10x Genomics V(D)J workflow. Briefly, single-cell TCR libraries were prepared using the Chromium Single Cell Mouse TCR Amplification Kit (Catalog #1000254). Libraries were pooled to achieve desired quantities for appropriate sequencing depths, as recommended by 10x Genomics, and were sequenced on an Illumina NovaSeq 6000 (v1.5) instrument.

value: CD4 SP Thymocytes

tag: strain

value: Wild Type


title: KO

value: C57BL/6-Btla KO

value: Btla KO


title: Phase I 4C × Phase II 4C, 13 day_rep2

description:
Second_E08_N153_T2_4_TGACAC
ControlAcclimation_gene_count_geo.csv

value: Phase I


title: HK-2 cells, DMEM medium containing corresponding amount of PBS-3, 48h

value: Kidney


title: HK-2 cells, DMEM medium containing corresponding amount of PBS-1, 48h

value: Epithelial Cells


title: 22-159

city: Coventry

first: Jan

last: Brosens

address: University Hospital Coventry and Warwickshire

department: Warwick Medical School

country: United Kingdom

institute: University of Warwick

description: 10X Genomics

data_processing:
Cell Ranger v6.1.2 pipelines 'mkfastq' and 'count' were used to process sequencing data using default parameters.
Assembly: Hg38
Supplementary files format and content: h5 format

source_name: Endometrial biopsy

extract_protocol:
Endometrial pipelle biopsies were washed in DMEM/F12, then finely minced and digested in Collagenase TypeI/TypeIV with DNaseI for 90 minutes at 37C, with periodic shaking. Cell suspensions were filtered through a 40uM cell sieve, and the flowthrough was treated with RBC lysis solution. After extensive washing, cells were resuspended in 0.1% BSA in PBS before proceeding to single-cell captures.
Single cell captures and library preparation was performed using the 10X Genomics  Chromium Next GEM Single Cell 3' (v3.1) workflow.

value: Endometrial biopsy

tag: lab id

tag: live-births

tag: lh+

tag: secretory cycle_phase

value: early

tag: bmi

tag: number of_previous_loss(es)


title: Pancreatic tumors, PPSSC

city: Houston

first: Yang

last: Chen

state: TX

address: 6565 MD Anderson Blvd

department: Translational Molecular Pathology

institute: MD Anderson Cancer Center

data_processing:
Raw sequencing data from the Illumina platform were converted into Fastq files
Fastq files from the Illumina platform were aligned to the reference genome mm10 using the 10X Genomics Cell Ranger Pipeline
After the alignment, a matrix file containing the cell barcode identity and gene values was exported by the 10X Genomics Cell Ranger Pipeline
Matrix files for the samples were then processed and analyzed by Seurat R software
Assembly: mm10
Supplementary files format and content: Processed data are in the CSV matrix format. All samples combined matrix CSV file as processed data was provided, while individual mouse/sample can be identified by the barcode.

source_name: Pancreatic tumors

extract_protocol:
Fresh tumor tissue was minced with sterilized lancets, digested with collagenase IV (17104019, Gibco, 4 mg/mL)/dispase II (17105041, Gibco, 4 mg/mL)/RPMI at 37°C for 0.5 hour, filtered by 70 mm cell strainers, and resuspended in PBS/2%FBS as single cell suspension. The single cell suspension was stained with Live/Dead viability dye eFluor 780 (65-0865-14, eBioscience), filtered through a 40 mm mesh
Cells were captured with the 10X Genomics’ Chromium controller and Single Cell 3’ Reagent Kits v3. cDNA was synthesized and amplified to construct Illumina sequencing libraries.

tag: tissue

value: Pancreatic tumors

tag: cell type

value: Mixture of various cell types

value: PPSSC

tag: detailed genotype


title: Pancreatic tumors, KPPC

tag: genotype

value: KPPC


title: Phase I 11C × Phase II 7±5C, 41 day_rep1

description:
Second_E06_N137_T6_11V_CCGACC
ControlAcclimation_gene_count_geo.csv

value: bud

tag: cultivar

value: Cabernet Sauvignon

tag: time in_treatment_(day)

value: Phase II


title: DonorD_CocultureTGFB

city: Cincinnati

first: Marc

middle: E

last: Rothenberg

state: OH

address: 3333 Burnet Ave.

department: Allergy & Immunology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
quality control with fastqc
mapped using STAR
Gene expression quantified using HOMER; analyzeRepeats
Raw count data aggregated with: -rna hg38 -condenseGenes -count exons -noadj
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes counts for each gene per sample.

source_name: Eosinophil

growth_protocol: Eosinophils were grown in media consisting of 1:1 mix of KSFM and RPMI + 10% FBS. Monocultures were maintained with 50 ng/mL GM-CSF. Cocultures were conducted with confluent EPC2 cells.

extract_protocol:
Eosinophils were lysed in 700uL TriPure and frozen. RNA eas extracted from the aqueous layer resulting from chloroform extraction using the Zymogen Quick RNA MicroPrep Kit.
RNAseq libraries were generated as described in PMID 28041958 and 32362324.

treatment_protocol: Where indicated, media were supplemented with 10ng/mL IL-13 or 10 ng/mLTGFB.

value: Eosinophil

tag: cell line

value: Primary

tag: treatment

value: Coculture with TGFB


title: Phase I 11C × Phase II 7±5C, 69 day_rep3

description:
Second_E07_N145_T8_11V_TATGTC
ControlAcclimation_gene_count_geo.csv

tag: phase

tag: phase i_treatment_(°c)

tag: phase ii_treatment_(°c)


title: 22-128

description: 10X Genomics

tag: lab id

tag: age

value: late


title: D1Pas1 WT control 2

value: Testis

value: male germ cell

value: D1Pas1 WT

value: b-elimination

tag: experiment type

value: small RNA


title: 22-121

description: 10X Genomics

value: Endometrial biopsy

tag: live-births

tag: lh+

tag: secretory cycle_phase


title: Phase I 7C × Phase II 7±5C, 69 day_rep2

description:
Second_E05_N129_T8_7V_CGCCTG
ControlAcclimation_gene_count_geo.csv

tag: tissue

tag: replication


title: DM_3

city: Jinan

first: Duan

last: Gao

address: Jinan

institute: Jinan

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Mus_musculus.GRCm38 V99
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: spleen

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: spleen

tag: cell type

value: CD4+ T cells

value: DM


title: DonorD_CocultureIL13

value: Coculture with IL-13


title: Phase I 22C × Phase II 22C, 41 day_rep2

description:
Second_F01_N99_T6_22_GAAGTG
ControlAcclimation_gene_count_geo.csv

value: bud


title: 22-120

description: 10X Genomics

value: mid

tag: bmi

tag: number of_previous_loss(es)


title: DM_2

tag: genotype


title: DonorD_Coculture

tag: cell line

value: Coculture


title: Phase I 7C × Phase II 7±5C, 34 day_rep3

description:
Second_E04_N121_T5_7V_GCAGCC
ControlAcclimation_gene_count_geo.csv

tag: cultivar

value: Cabernet Sauvignon

tag: time in_treatment_(day)

value: Phase II


title: D1Pas1 WT control 1

tag: treatment


title: DM_1


title: 22-117

description: 10X Genomics

value: early


title: Phase I 2C × Phase II 7±5C, 69 day_rep2

description:
Second_E03_N114_T8_2V_TGGATT
ControlAcclimation_gene_count_geo.csv

tag: phase

tag: phase i_treatment_(°c)

tag: phase ii_treatment_(°c)


title: DonorD_GMCSF

value: Eosinophil

value: Primary

value: GM-CSF


title: CONT_3

value: CONT


title: 22-082

description: 10X Genomics

tag: lab id

tag: age


title: DonorD_Baseline


title: CONT_2


title: DonorC_CocultureTGFB

value: Coculture with TGFB


title: CONT_1


title: DonorC_CocultureIL13


title: Phase I 4C × Phase II 4C, 55 day_rep2

description:
Second_D10_N168_T7_4_ACGTCT
ControlAcclimation_gene_count_geo.csv


title: Phase I 22C × Phase II 22C, 41 day_rep1

description:
Second_E01_N98_T6_22_AGGCAT
ControlAcclimation_gene_count_geo.csv


title: Phase I 2C × Phase II 7±5C, 34 day_rep3

description:
Second_E02_N106_T5_2V_ACCTAC
ControlAcclimation_gene_count_geo.csv


title: 22-074

description: 10X Genomics

tag: live-births

tag: lh+


title: Auriside_m10_rep1

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Morway RD

department: ICBR

institute: UNIVERSITY OF FLORIDA

data_processing:
Reads acquired from the Illumina NovaSeq 6000 platform were cleaned up with the cutadapt program (version 3.4) to trim off sequencing adaptors and low-quality bases.
The cleaned reads were mapped to the reference sequences (mm10 and GRCh38) using the read mapper of the STAR package (Spliced Transcripts Alignment to a Reference, v2.7.9a). The mapping results were processed with the HTSeq (High-Throughput Sequence Analysis in Python, v2.03), samtools, and scripts developed in house at ICBR of UF to remove potential PCR duplicates and count uniquely mapped reads for gene expression analysis.
The gene express levels were analyzed by a DESeq2-based R pipeline.
Assembly: mm10 and GRCh38
Supplementary files format and content: Tab-delimited text files include the mapped read counts for each Sample.

growth_protocol: RAW264.7 cells (175,000 cells/well) and HCT116 cells (300,000cells/well) were seeded in 12-well plates and allowed to attach overnight. After overnight incubation, the media (DMEM, 10% FBS) in each well were replaced with fresh media prior to treatment with compound.

extract_protocol:
RNA was extracted after 12h using RNeasy Mini Kit (Qiagen) according to manufacturer instructions.
Illumina RNA library construction and sequencing were performed at the Interdisciplinary Center for Biotechnology Research (ICBR) Gene Expression Core, University of Florida (UF).

treatment_protocol: Cells were treated with solvent control (DMSO, 0.5%) and LPS (1 µg/mL), solvent control (DMSO, 0.5%) alone, the compound (32, 10 µM) and LPS (1 µg/mL), the compound alone (32, 10 µM).

value: Mouse Macrophage

value: Compound (10 uM) + LPS (1 ug/mL)

tag: replicate

value: Biol rep 1


title: 22-036

description: 10X Genomics

tag: tissue

value: Endometrial biopsy

tag: secretory cycle_phase

value: late


title: DonorC_Baseline

tag: cell type


title: Phase I 4C × Phase II 4C, 13 day_rep1

description:
Second_D08_N152_T2_4_CTCCAT
ControlAcclimation_gene_count_geo.csv

value: Phase I

tag: replication


title: Phase I 11C × Phase II 7±5C, 69 day_rep2

description:
Second_D07_N144_T8_11V_CCGCAA
ControlAcclimation_gene_count_geo.csv

value: bud


title: DonorB_CocultureTGFB


title: Phase I 4C × Phase II 4C, 26 day_rep3

description:
Second_D09_N160_T4_4_GTCAGG
ControlAcclimation_gene_count_geo.csv


title: 22-030

description: 10X Genomics

tag: bmi

tag: number of_previous_loss(es)


title: 22-080

description: 10X Genomics

value: mid


title: 22-025

description: 10X Genomics


title: Auriside_m32_rep1

tag: cell line

value: Compound (32 uM) + LPS (1 ug/mL)


title: control_m_rep2

value: vehicle control (0.5%DMSO)

value: Biol rep 2


title: DonorB_Coculture

value: Coculture


title: DonorB_CocultureIL13

value: Eosinophil

value: Coculture with IL-13


title: WiT49, PRC, Rep3

city: Madison

first: Wei

last: Xu

state: WI

address: 7459 WIMR II

department: McArdle Laboratory for Cancer Research

institute: University of Wisconsin-Madison

data_processing:
RNA-seq fragments were aligned by STAR (version 2.5.2b) to the human genome (hg38) with GENCODE basic gene annotations (version 27)
Gene expression levels were quantified by RSEM (version 1.3.0)
Assembly: hg38
Supplementary files format and content: TSV: RSEM quantification results at the gene level

extract_protocol:
Total RNA was extracted from cancer cells by using the E.Z.N.A® Total RNA Kit I (Omega BioTEK, Cat#R6834-02).
The RNA library was constructed using SMARTer® Stranded RNA-Seq Kit (TakaraBio, Cat#634839) according to the manufacturer’s instructions.  Equal amounts of polyA-purified RNA (100ng) were used for first-strand cDNA synthesis. Subsequently, the synthesized first strand-cDNA was incubated with AMPure XP beads (Beckman Coulter, Cat#A63881) at room temperature for 30 min, washed with 80% ethanol, and eluted in resuspension buffer. The purified first-strand cDNA is amplified into RNA-seq libraries using SeqAmp DNA Polymerase, the Universal Forward PCR Primer, and the Reverse PCR Primers from the Illumina Indexing Primer Set. Samples were re-purified by using AMPure XP beads, quantified by a Qubit fluorometer (Invitrogen, Cat#Q33231), and sent to the NUSeq Core at Northwestern University for RNA-seq.

value: Kidney

value: Wilms tumor cell line

tag: genotype

value: Partial reprogrammed iPSC

value: No treatment


title: Phase I 11C × Phase II 7±5C, 34 day_rep3

description:
Second_D06_N136_T5_11V_TCTTAA
ControlAcclimation_gene_count_geo.csv

tag: cultivar

value: Cabernet Sauvignon

tag: time in_treatment_(day)

value: Phase II


title: Auriside_m10_rep2

value: Mouse Macrophage

tag: treatment

value: Compound (10 uM) + LPS (1 ug/mL)


title: control_m_rep1

value: Biol rep 1


title: DonorC_Coculture

value: Primary


title: DonorB_GMCSF

value: GM-CSF


title: WiT49, PRC, Rep2


title: Auriside_m32_rep2

value: Compound (32 uM) + LPS (1 ug/mL)


title: Phase I 7C × Phase II 7±5C, 34 day_rep2

description:
Second_D04_N120_T5_7V_CAGCGT
ControlAcclimation_gene_count_geo.csv

value: bud

tag: phase

tag: phase i_treatment_(°c)

tag: phase ii_treatment_(°c)


title: control_lm_rep2

value: vehicle control (0.5%DMSO) + LPS (1 ug/mL)

value: Biol rep 2


title: WiT49, PRC, Rep1


title: Phase I 2C × Phase II 7±5C, 69 day_rep1

description:
Second_D03_N113_T8_2V_CACACT
ControlAcclimation_gene_count_geo.csv


title: DonorA_CocultureTGFB

value: Eosinophil

value: Coculture with TGFB


title: control_lm_rep1


title: Phase I 2C × Phase II 7±5C, 34 day_rep2

description:
Second_D02_N105_T5_2V_GACGAT
ControlAcclimation_gene_count_geo.csv


title: WiT49, Parental, Rep2

value: Kidney

value: Wild type


title: WiT49, Parental, Rep3

value: Wilms tumor cell line


title: DonorB_Baseline


title: Phase I 22C × Phase II 22C, 34 day_rep3

description:
Second_D01_N97_T5_22_AGTTGA
ControlAcclimation_gene_count_geo.csv


title: mBMSCs, Ocn-Cre

city: Rochester

first: Alexandra

last: Krivonos

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

data_processing:
Raw data were analyzed using the Galaxy platform.
FastQC (Galaxy Version 0.74+galaxy0) was used to assess read quality
Trimmomatic (Galaxy Version 0.38.1) was used for read trimming
HISAT2 (Galaxy Version 2.2.1+galaxy1) was used for alignment to the mouse mm10 genome
FeatureCounts (Galaxy Version 2.0.3+galaxy2) was used for counting the genome-aligned reads
DEseq2 (Galaxy Version 2.11.40.8+galaxy0) was used to generate the normalized counts (CPM)
Assembly: mm10
Supplementary files format and content: TSV file containing normalized gene expression values. Generated using the default ‘median of ratios’ method from DESeq2.

source_name: Bone Marrow

growth_protocol: Mouse bone marrow stromal cells (mBMSCs) were grown in MEMα medium (ThermoFisher Scientific, Waltham, MA) supplemented with 15% (v/v) BenchMark Fetal Bovine Serum (GeminiBio, West Sacramento, CA), 1% (v/v) Antibiotic-Antimycotic (ThermoFisher Scientific), and 50 µg/mL gentamycin (Sigma-Aldrich, St. Louis, MO) in a 37oC incubator with 5% CO2  and 3% O2 (hypoxic conditions)

extract_protocol:
RNA was isolated using the RNeasy Plus Kit (Qiagen) and 100 ng of total RNA used in making the sequencing libraries.
mRNA samples from the mBMSC culture were sent to Azenta Life Sciences (South Plainfield, NJ) for next-generation sequencing. Briefly, RNA sequencing libraries were prepared from 100 ng RNA using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), The libraries were multiplexed and clustered onto a flowcell on the Illumina NovaSeq 6000 (San Diego, CA) and sequenced using an 2x150bp paired-end configuration. Approximately 20 million paired-end reads were sequenced per sample. Image analysis and base calling were conducted by the NovaSeq Control Software. Raw sequence data was converted into fastq files, de-multiplexed using Illumina bcl2fastq v2.20 software, and provided to us for analysis.

treatment_protocol: mBMSCs were treated for 3 days with All-EVs, Ocn-EVs or Prx1-Evs

value: Bone Marrow

value: Mouse Bone Marrow Stromal Cells (mBMSCs)

value: WT

value: Ocn-EV treated


title: WiT49, Parental, Rep1

value: No treatment


title: Phase I 7C × Phase II 7±5C, 69 day_rep1

description:
Second_D05_N128_T8_7V_TGCTAT
ControlAcclimation_gene_count_geo.csv

value: Cabernet Sauvignon

value: Phase II


title: mBMSCs, All-EV

value: All-EV treated


title: Pancreatic tumors, PPSSC-3

data_processing:
The raw sequencing data was filtered and aligned to the mouse genome assembly GRCm39 using HISAT2.
The Fastq reads were processed by quality control and adaptor trimming, alignment, check strandness, and gene count.
Different expression gene (DEG) analysis was performed using DESeq2. TPM normalized counts were calculated with the DGEobj.utils package.
Assembly: mm39
Supplementary files format and content: Processed data files format and content included RPKM value for each sample.

extract_protocol:
Fresh tumor tissue rom KPPC and PPSSC mice were minced with sterilized lancets, digested with collagenase IV (17104019, Gibco, 4 mg/mL)/dispase II (17105041, Gibco, 4 mg/mL)/RPMI at 37°C for 0.5 hour, filtered by 70 mm cell strainers, and resuspended in PBS/2%FBS as single cell suspension. The single cell suspension was stained with Live/Dead viability dye eFluor 780 (65-0865-14, eBioscience), filtered through a 40 mm mesh.The cells were cultured in a DMEM medium containing 20% FBS and 1% penicillin-streptomycin-amphotericin B (PSA) antibiotic mixture.
Total RNA samples were used to prepare the DNA library and were sequenced on the Illumina Hiseq 2000/2500 platform using the paired-end sequencing method.

value: Pancreatic tumors

value: Cancer cell

value: PPSSC

tag: detailed genotype


title: Phase I 4C × Phase II 4C, 55 day_rep1

description:
Second_C10_N167_T7_4_ACCGTG
ControlAcclimation_gene_count_geo.csv

value: bud


title: DonorA_Coculture

value: Eosinophil

value: Primary

value: Coculture


title: DonorA_GMCSF

value: GM-CSF


title: Phase I 4C × Phase II 4C, 26 day_rep2

description:
Second_C09_N159_T4_4_TGTGCA
ControlAcclimation_gene_count_geo.csv

value: Phase I


title: 075A

city: Cambridge

first: Baohong

last: Zhang

state: MA

address: 225 Binney St

institute: Biogen Inc.

data_processing:
BCL files were converted to fastq files with Space Ranger mkfastq pipeline. The fastq files were then mapped to the mouse reference genome using Space Ranger count pipeline that produces spot-barcoded expression matrix
Assembly: mm10
Supplementary files format and content: h5, UMI counts
Supplementary files format and content: csv: spot locations; png: image
Library strategy: Spatial Transcriptomics

source_name: Brain

growth_protocol: Age 6-8 weeks-old male mice were used for the cuprizone model study. Research animals were housed under specific-pathogen-free conditions in an AAALAC accredited facility according to an approved institutional animal care and use committee (IACUC) protocol with a 12 hr - 12 hr light - dark cycle and environmental conditions controlled at 21°C and 40–60% humidity.

extract_protocol:
At 4 (CPZ) and 6 weeks (Control and Recovery), mice were euthanized by carbon dioxide (CO2) inhalation, and their brains were subsequently dissected. Each brain was sagittally cut into left and right hemispheres. One hemisphere was then further divided into three coronal segments, which were embedded in OCT for spatial transcriptomic analysis.
Frozen sections of mouse brain hemispheres embedded in OCT (TissueTek) were collected using a Leica CM1520 cryostat equipped with a Leica Surgipath high-profile blade at -23°C. The 10 µm tissue sections were placed onto Visium Spatial Gene Expression slides (10X Genomics Slide Kit, Ref No. 1000185). The tissue sections were processed using the 10X Genomics Visium platform following manufacturer’s instructions. Library construction was carried out using the 10X Genomics Library Construction Kit (PN-1000190) following the manufacturer's instructions.
The libraries were then sequenced on an Illumina NovaSeq 6000 S2 flowcell, employing paired-end sequencing with the parameters Read1-28bp, i7-10bp, i5-10bp, and Read2-120bp.

treatment_protocol: In the cuprizone (CPZ) group, male mice aged 6-8 weeks were administered a 0.3% Cuprizone diet for 4 weeks to induce demyelination in the brain (n = 3). In the recovery group, mice were administered CPZ diet for 4-weeks and then switched to a control diet for an additional 2 weeks (n = 3). In the control group, mice received the control diet throughout the entire 6-week study period (n = 4).

value: Brain

value: Recovery


title: Pancreatic tumors, PPSSC-2


title: Phase I 4C × Phase II 4C, 7 day_rep3

description:
Second_C08_N151_T1_4_CGTCGC
ControlAcclimation_gene_count_geo.csv


title: Pancreatic tumors, PPSSC-1


title: mBMSCs, Prx1-Cre

value: Bone Marrow

value: Mouse Bone Marrow Stromal Cells (mBMSCs)

value: WT

value: Prx1-EV treated


title: Auriside_h10_rep2

value: Human colon cancer cells

value: Compound (10 uM)

value: Biol rep 2


title: DonorA_CocultureIL13

value: Coculture with IL-13


title: DonorA_Baseline


title: Fabp7 KO MEST, rep2

description:
columns for KO_vs_KO_S_2_diffexpr_results.xlxs are: Gene , baseMean , log2FoldChange , lfcSE , stat , pvalue , padj , KO1-M , KO2-M , KO3-M , KO4-M , KO5-M , KO2 , KO3 , KO4 , KO5
KO_vs_KO_S_2_diffexpr_results.xlxs

value: Hippocampus + cortex segment

tag: strain

tag: age (weeks)

tag: Sex

value: male

tag: time

value: Fabp7 KO

value: electroshock


title: Phase I 11C × Phase II 7±5C, 69 day_rep1

description:
Second_C07_N143_T8_11V_TTCGAG
ControlAcclimation_gene_count_geo.csv

tag: tissue

value: bud

value: Cabernet Sauvignon

value: Phase II


title: 076B

value: Brain


title: Phase I 11C × Phase II 7±5C, 34 day_rep2

description:
Second_C06_N135_T5_11V_CCAATT
ControlAcclimation_gene_count_geo.csv

tag: replication


title: Auriside_h10_rep1

tag: cell type

tag: replicate

value: Biol rep 1


title: Auriside_h32_rep2

tag: cell line

value: Compound (32 uM)


title: Pancreatic tumors, KPPC-2

value: Pancreatic tumors

value: Cancer cell

tag: genotype

value: KPPC


title: Pancreatic tumors, KPPC-3


title: 072C

value: Recovery


title: 075C


title: Auriside_h32_rep1

value: Human colon cancer cells


title: Phase I 7C × Phase II 7±5C, 34 day_rep1

description:
Second_C04_N119_T5_7V_GTTACC
ControlAcclimation_gene_count_geo.csv

tag: cultivar


title: Phase I 2C × Phase II 7±5C, 55 day_rep3

description:
Second_C03_N112_T7_2V_CAAGCA
ControlAcclimation_gene_count_geo.csv

tag: time in_treatment_(day)


title: Veh-4-1

data_processing:
Bulk RNA analysis was aligned to mm10 using STAR & RSEM pipeline
Assembly: mm10
Supplementary files format and content: csv: TPM and raw counts and gene annotation table

extract_protocol:
At 4 (CPZ) and 6 weeks (Control and Recovery), mice were euthanized by carbon dioxide (CO2) inhalation, and their brains were subsequently dissected. Each brain was sagittally cut into left and right hemispheres. One hemisphere was promptly frozen for bulk RNA-seq investigation.
Bulk RNA-seq libraries were generated using the Kapa mRNA HyperPrep Kit (Kapa Biosystems KK8581) following the manufacturer's instructions.
The libraries were sequenced on an Illumina HiSeq2500 platform, generating paired-end reads of 50 base pairs with an average sequencing depth of 9 million reads.

tag: treatment


title: control_h_rep2

value: vehicle control (0.5%DMSO)

value: Biol rep 2


title: 074B


title: 107D


title: Veh-3-1


title: control_h_rep1


title: Phase I 2C × Phase II 7±5C, 34 day_rep1

description:
Second_C02_N104_T5_2V_GCGCTG
ControlAcclimation_gene_count_geo.csv

tag: phase


title: 106D


title: Veh-2-1


title: FLD041FLD029FLD030 TCR library 2

city: New York

first: Alex

last: George

address: 960 Broadway, 2nd Floor, Room 203AC

institute: Columbia University

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript.
filtered_contig_annotations.TCR.txt.gz

data_processing:
scRNA-seq reads were analyzed by pseudoalignment using kallisto v0.46.2 (GRCh38 with Gencode v24 annotation) and bustools v0.40.0. CITE-seq and hashtag barcodes were demultiplexed and extracted using DropSeqPipeline8 (https://github.com/simslab/DropSeqPipeline8). GEX count matrix was filtered for cell barcodes with >1000 molecules/cell. These cell barcodes were used to filter ADT hashtag/CITE-seq count matrix from DropSeq8. Hashtags were demultiplexed on filtered HTO/ADT count matrix using the HashSolo (https://github.com/calico/solo/blob/master/solo/hashsolo.py) implementation in ScanPy (https://github.com/scverse/scanpy, scanpy.external.pp.hashsolo function) where prior cell frequency arguments for HashSolo function were based on theoretical doublet rate in 5’v2 HT 10x chip based on cell input (e.g. 0.08 doublet rate, 0.01 negative, 0.91 singlet rate, for 20k cell input).
Immune receptor libraries (TCR and BCR) were aligned using Cell Ranger 7.0.1 (vdj function) using reference vdj_GRCh38_alts_ensembl-7.0.0.
A mitochondrial gene filter was applied for any cells above a 95% confidence interval for MT pseudo-alignment rate on a per library basis. A hemoglobin gene filter was applied to all libraries for cells > 0.01 pseudo-alignment rate for HB genes.
MultiModal Classifier Hierarchy (MMOCHI, https://github.com/donnafarberlab/MMoCHi), which is trained using events selected by thresholding of user-defined marker genes and proteins, was implemented to define immune cell subsets across sites. MMOCHI classification legend: (CD4N = Naive CD4 T cell, CD4Treg = CD4 Regulatory T cell, CD4CM = Central Memory CD4 T Cell, CD4EM = Effector Memory CD4 T cell, CD8EM = Effector Memory CD8 T cell, CD8N = Naive CD8 T Cell, CD8CM = Central Memory CD8 T Cells, B_cell_N = Naive B Cells, B_cell_Innate_M = Innate Memory B Cells (IgD+CD27+), B_cell_CD27-IgD- =  CD27-IgD- B cells, Plasma_cluster = Plasma Cells identified by GEX clustering, Myeloid_cluster = Myeloid Cells identified by GEX clustering, NK_Cluster = NK Cells identified by GEX clustering). Memory B cell classifications are subtyped by receptor isotype.
Assembly: GRCh38/Ensembl93
Supplementary files format and content: GEX and ADT libraries: tab-delimited text files with cell-identifying barcodes, hashtags, donor, tissue site, MMOCHI immune cell classification, stimulation condition (w/ applicable sort information), and count matrix
Supplementary files format and content: TCR and BCR libraries: tab-delimited text files with cell-identifying barcodes, immune receptor chain, VDJ genes, cdr3 amino acid sequence, cdr3 nucleotide sequence, raw clonotype id and other alignment statistics/metadata outputted from CellRanger.
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

source_name: blood

extract_protocol:
Organ donor samples in saline or University of Wisconsin solution were placed on ice, transported to the laboratory, and processed within 2 to 4 hours of procurement. Single cell suspensions were obtained from blood, bone marrow, spleen, lungs, and associated lymph nodes (LN) using mechanical and enzymatic digestion as previously described (Nat Med 22, 72-77. 10.1038/nm.4008). Blood and bone marrow samples were diluted with wash buffer (PBS (Corning, cat #20-030-CV) + 2mM EDTA (Corning, cat #46-034-CI) + 5% FBS (GeminiBio, cat #100-106)), and mononuclear cells were isolated by density centrifugation using Ficoll-Paque PLUS (GE Healthcare, catalog no. 17-1440-03). Lymph nodes were isolated by dissection from the mesentery of the small and large intestine, the tracheobronchial tree of the lung, and inguinal fat. Tissue samples were first mechanically disrupted with scissors. Isolated LNs and lung were then placed into digestion media (IMDM + Collagenase D 1mg/mL (Millipore Sigma cat# 11088882001) and + DNAse 0.1mg/mL (Millipore Sigma cat# DN25-5G)) on a shaker at 37C for 30 minutes followed by addition of 0.5M EDTA (pH 8.0). Digested LNs and lung as well as mechanically disrupted spleen were then pushed through 100m filters and washed with buffers. The samples then underwent density centrifugation as above to isolate live leukocytes. For healthy blood samples, we obtained peripheral blood from a consenting, healthy volunteers by venous puncture. Peripheral blood mononuclear cells (PBMCs) were isolated using Ficoll-Paque PLUS, following manufacturer's protocols for density gradient centrifugation. Single cell mononuclear suspensions isolated from blood and tissue samples prepared as above were plated in 96 well U-bottom plates (1X10^6 cells per well) in 200uL of complete media (RPMI (Corning, catalog no. 10-040-CM), 10% inactivated human AB serum (Gemini, catalog no. 507533010) and penicillin-streptomycin-glutamate (Thermo Fisher Scientific, catalog no. 10378016)) and incubated overnight at 37C in 5% CO2. The next day, the wells were split (5x10^5 cells per well) and topped up with complete media to 200uL. Cells were then blocked for 15 minutes with anti-CD40 monoclonal antibody (0.5g/mL) (Miltenyi Biotec, catalog no. 130-094-133). Subsequently, a SARS-CoV-2 Spike Megapool (S MP) (1g/mL), designed and synthesized as previously described (Cell 181, 1489-1501 e1415. 10.1016/j.cell.2020.05.015), was added to the cell culture for 24 hours. The S MP consists of 253 15-mer peptides overlapping by 10 residues and covering the entire S protein. As controls, additional cells were stimulated with an equimolar amount of DMSO, or a combination of 3 Influenza peptide Mega pools at 1g/mL (CD4 HA, CD4 Other, and CD8), synthesized as previously described (Curr Protoc. 2023 Nov;3(11):e934. doi: 10.1002/cpz1.934.). Following 24-hour stimulation, each tissue and stimulation condition combination for a particular donor was combined, treated with 10uL each of Trustain FcX (BioLegend) and FcR Blocking Reagent (Miltenyi) at 4C for 10 minutes, and then incubated with 2 uL (1 ug) of a unique TotalSeq-C anti-human DNA-barcoded hashtag for 30 minutes at 4C and washed 3 times with FACS buffer) as described. Subsequently all peptide-stimulated samples from a single donor were combined and all DMSO-stimulated samples from a single donor were combined. These samples were stained with BV421 labeled full length Spike protein and a panel of fluorescently labeled antibodies and washed as described above. These samples were sorted using the BD FACSAria III Cell Sorter. Peptide-stimulated samples were sorted for AIM+ CD4 T cells (Live, CD45+, CD19-, CD3+, CD4+, OX40 & 4-1BB++), AIM+ CD8 T cells (Live, CD45+, CD19-, CD3+, CD8+, CD25 & 4-1BB++), and Spike B cells (Live, CD45+, CD19+, CD3-, Spike-BV421+). DMSO-stimulated cells were sorted for AIM-CD4 T cells (Live, CD45+, CD19-, CD3+, CD4+, OX40 & 4-1BB--), AIM-CD8 T cells (Live, CD45+, CD19-, CD3+, CD8+, CD25 & 4-1BB--), and Total B cells (Live, CD45+, CD19+, CD3-, Spike-BV421-). Each sample of sorted cells was counted, and for each donor, a fraction of AIM-CD4 T, AIM-CD8 T, and Total B cells were spiked into the AIM+CD4+T, AIM+CD8+T, and Spike B cell samples to reach ~80K cells for per donor to have adequate cell numbers to manipulate for CITE-seq staining and have sufficient cell numbers after washing for input into 10x microfluidics chip (e.g. spike in cells to achieve 80k cells, yielding ~50k out post-wash for 33.3k cell requirement to achieve 20k cell capture on chip). The samples were then stained with TotalSeq C Human Universal Cocktail V1.0 and washed 3 times with FACS buffer by centrifugation or with a Curiox HT2000 Laminar Wash System (Curiox, 5 uL/sec speed, 27 cycles, 50 uL loading volume). The resultant stained cells (33.3K) were resuspended in 10x genomics recommended loading buffer (1X DPBS w/ 0.04% BSA) for loading into 10x Genomics single sequencing workflows with a target of 20K cell captured per lane on chip. To investigate the role of Tregs in the AIM assay, we performed CD25 depletion on our single cell LLN suspension from D616 prior to the above peptide stimulation and sorting protocols. For depletion, single cell suspensions were pre-incubated with 10uL each of Trustain FcX (BioLegend, catalog no. 422322) and FcR Blocking Reagent (Miltenyi, catalog no. 130-059-901) at 4C for 10 minutes followed by addition of 10uL of biotinylated anti-CD25 for 30 minutes on ice and washed with FACS buffer three times. Washed BioMag Plus Streptavidin Beads (BangsLabs catalog no. BP628) were resuspended in 100uL of FACS buffer and incubated with the single cell suspension at room temperature for 5 minutes. 1.5mL of DPBS was added to the tube and placed on the EasySep magnet (STEMCELL Technologies catalog no. 18000) for 5 minutes. The supernatant was collected and set aside. The remaining beads were combined with DPBS and placed back on the magnet for an additional 5 minutes prior to collecting the supernatant and combining with the supernatant from the first separation. This sample was then plated at 1X10^6 cells per well in 96-well U bottom plates for in vitro peptide stimulations as above. DMSO control, SARS or Flu peptide stimulated, and CD25 depleted SARS or Flu stimulated were FACS sorted with AIM+ gates described above. SARS or Flu peptide stimulated CD4 T cells were also sorted using an altenative AIM+ gating strategy (Live, CD45+, CD19-, CD3+, CD4+, OX40 & CD40LG) while maintaining original CD8 gating strategy. Stimulated and sorted single cell-suspensions were loaded onto a 5v2 high throughput (HT) Chromium Next GEM Single Cell Chip N (10x Genomics) for co-encapsulation with barcoded GelBeads with a target capture of 20-30k cells per sample.
Organ donor samples: Captured mRNA was reverse transcribed to cDNA, amplified, and converted to libraries using the Chromium Next GEM Single Cell 5 HT Reagent kit v2 (10X genomics) protocol and recommended reagents with a 5 Feature Barcode kit (10x genomics) for antibody-derived tag amplification, a Chromium Single Cell Human TCR Amplification kit (10x Genomics) for targeted TCR amplification, and a Chromium Single Cell Human BCR Amplification kit (10x Genomics) for targeted BCR amplification. The scRNA-seq gene expression (GEX) libraries, antibody derived tag (ADT) CITE-seq/hashtag libraries, scTCR-seq and, scBCR-seq libraries were sequenced on S4 flow cells (ADT, GEX libraries pooled together and TCR/BCR libraries pooled on independent flow cell lanes) with an Illumina NovaSeq 6000 (~2.5 billion, 2 x 100-bp, reads per lane). The scTCR-seq and sc-BCRseq libraries for D561 and D574 were sequenced with a 150-cycle high-output kit on an Illumina NextSeq 550 (read 1: 26 bp; read 2: 114 bp; index read 1: 10 bp; index read 2: 10 bp). Hashtag IDs for D534,D559,D561,D564,D568,D574: (HTO1: Donor blood AIM+ SARS, HTO2: Donor blood AIM+ Flu, HTO3: Donor blood AIM- DMSO control, HTO4: Donor bone marrow AIM+ SARS, HTO5: Donor bone marrow AIM+ Flu, HTO6: Donor bone marrow AIM- DMSO control, HTO7: Donor spleen AIM+ SARS, HTO8: Donor spleen AIM+ Flu, HTO9: Donor spleen AIM- DMSO control, HTO10: Donor lung AIM+ SARS, HTO12: Donor lung AIM+ Flu, HTO13: Donor lung AIM- DMSO control, HTO14: Donor lung lymph node AIM+ SARS, HTO15: Donor lung lymph node AIM+ Flu, HTO16: Donor lung lymph node AIM- DMSO control). For D561D564 library, only LNG sample is from D564, all other tissues are from D561. (BLD = blood, BM = bone marrow, SPL = spleen, LNG = lung, LLN = lung lymph node, CITE-seq = cellular indexing of transcriptomes and epitopes).
Healthy blood samples: Captured mRNA was reverse transcribed to cDNA, amplified, and converted to libraries using the Chromium Next GEM Single Cell 5 HT Reagent kit v2 (10X genomics) protocol and recommended reagents with a 5 Feature Barcode kit (10x genomics) for antibody-derived tag amplification, a Chromium Single Cell Human TCR Amplification kit (10x Genomics) for targeted TCR amplification, and a Chromium Single Cell Human BCR Amplification kit (10x Genomics) for targeted BCR amplification. The scRNA-seq gene expression (GEX) libraries, antibody derived tag (ADT) CITE-seq/hashtag libraries, scTCR-seq and, scBCR-seq libraries were sequenced on S4 flow cells (ADT, GEX libraries pooled together and TCR/BCR libraries pooled on independent flow cell lanes) with an Illumina NovaSeq 6000 (~2.5 billion, 2 x 100-bp, reads per lane).  Hashtag IDs for healthy blood donors FLD032,FLD040,FLD015,FLD041,FLD029,FLD030: (HTO1: Donor 1 blood AIM+ SARS, HTO2: Donor 1 blood AIM+ Flu, HTO3: Donor 1 blood AIM- DMSO control, HTO4: Donor 2 blood AIM+ SARS, HTO5: Donor 2 blood AIM+ Flu, HTO6: Donor 2 blood AIM- DMSO control, HTO7: Donor 3 blood AIM+ SARS, HTO2: Donor 3 blood AIM+ Flu, HTO3: Donor 3 blood AIM- DMSO control). Donors 1-3 in hashtag IDs correspond to FLD-prefixed donors in corresponding order in library ID. (BLD = blood, BM = bone marrow, SPL = spleen, LNG = lung, LLN = lung lymph node, CITE-seq = cellular indexing of transcriptomes and epitopes).
Donor 616: Captured mRNA was reverse transcribed to cDNA, amplified, and converted to libraries using the Chromium Next GEM Single Cell 5 HT Reagent kit v2 (10X genomics) protocol and recommended reagents with a 5 Feature Barcode kit (10x genomics) for antibody-derived tag amplification. The scRNA-seq gene expression (GEX) libraries and antibody derived tag (ADT) CITE-seq/hashtag libraries libraries were sequenced on S4 flow cells (ADT, GEX libraries pooled together on independent flow cell lanes) with an Illumina NovaSeq 6000 (~2.5 billion, 2 x 100-bp, reads per lane). Hashtag IDs for D616: (HTOs 1,3,4,5,6,7: Donor 616 LLN AIM- DMSO control, HTO8: Donor 616 LLN AIM+ Flu peptide stimulation, HTO9: Donor 616 LLN AIM+ SARS peptide stimulation, HTO13: Donor 616 LLN CD25 depletion AIM+ Flu peptide stimulation, HTO14: Donor 616 LLN CD25 depletion AIM+ SARS peptide stimulation, HTO10: Donor 616 LLN CD40LG+/OX40+ alternate CD4 AIM+ gate Flu peptide stimulation, HTO12: Donor 616 LLN CD40LG+/OX40+ alternate CD4 AIM+ gate SARS peptide stimulation).  (BLD = blood, BM = bone marrow, SPL = spleen, LNG = lung, LLN = lung lymph node, CITE-seq = cellular indexing of transcriptomes and epitopes).

value: blood

value: mononuclear cells (MNCs)

tag: library type

value: mRNA


title: Phase I 22C × Phase II 22C, 34 day_rep2

description:
Second_C01_N96_T5_22_ACAACG
ControlAcclimation_gene_count_geo.csv

tag: phase i_treatment_(°c)

tag: phase ii_treatment_(°c)


title: FLD041FLD029FLD030 TCR library 1


title: 108B


title: 074A


title: Phase I 4C × Phase II 4C, 41 day_rep2

description:
Second_B10_N166_T6_4_GTGCCA
ControlAcclimation_gene_count_geo.csv


title: Phase I 7C × Phase II 7±5C, 55 day_rep3

description:
Second_C05_N127_T7_7V_CTCTCG
ControlAcclimation_gene_count_geo.csv


title: cpz4W-4-1

value: Cuprizone


title: FLD041FLD029FLD030 BCR library 2

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript.
filtered_contig_annotations.BCR.txt.gz


title: 074C


title: Phase I 4C × Phase II 4C, 26 day_rep1

description:
Second_B09_N158_T4_4_ACCAGT
ControlAcclimation_gene_count_geo.csv

value: bud

value: Phase I


title: Pancreatic tumors, KPPC-1

tag: detailed genotype


title: cpz4W-3-1


title: 076C


title: FLD041FLD029FLD030 BCR library 1


title: Phase I 4C × Phase II 4C, 7 day_rep2

description:
Second_B08_N150_T1_4_GGCTGC
ControlAcclimation_gene_count_geo.csv

value: Cabernet Sauvignon


title: 075D

value: Brain


title: cpz4W-2-1


title: Phase I 11C × Phase II 7±5C, 55 day_rep2

description:
Second_B07_N142_T7_11V_CCTAAG
ControlAcclimation_gene_count_geo.csv

value: Phase II


title: 074D


title: cpz4W-1-1


title: FLD041FLD029FLD030 GEX library 1

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript.
FLD032FLD040FLD015FLD041FLD029FLD030.GEX.matrix.txt.gz


title: Phase I 11C × Phase II 7±5C, 34 day_rep1

description:
Second_B06_N134_T5_11V_CGCGGA
ControlAcclimation_gene_count_geo.csv


title: Veh-1-1


title: FLD041FLD029FLD030 ADT library 2

description:
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C Human Universal Cocktail,TotalSeq-C0251,TotalSeq-C0252,TotalSeq-C0253,TotalSeq-C0254,TotalSeq-C0255,TotalSeq-C0256,TotalSeq-C0257,TotalSeq-C0258,TotalSeq-C0259.
FLD032FLD040FLD015FLD041FLD029FLD030.ADT.matrix.txt.gz

molecule: protein

value: ADT/HTO

tag: adt/hto

value: Antibodies/tags:TotalSeq-C Human Universal Cocktail v1.0,TotalSeq-C0251 anti-human HTO1,TotalSeq-C0252 anti-human HTO2,TotalSeq-C0253 anti-human HTO3,TotalSeq-C0254 anti-human HTO4,TotalSeq-C0255 anti-human HTO5,TotalSeq-C0256 anti-human HTO6,TotalSeq-C0257 anti-human HTO7,TotalSeq-C0258 anti-human HTO8,TotalSeq-C0259 anti-human HTO9. Hashtag IDs for healthy blood donors FLD032,FLD040,FLD015,FLD041,FLD029,FLD030:(HTO1:Donor 1 blood AIM+ SARS, HTO2:Donor 1 blood AIM+ Flu, HTO3:Donor 1 blood AIM- DMSO control, HTO4:Donor 2 blood AIM+ SARS, HTO5:Donor 2 blood AIM+ Flu, HTO6:Donor 2 blood AIM- DMSO control, HTO7:Donor 3 blood AIM+ SARS, HTO2:Donor 3 blood AIM+ Flu, HTO3:Donor 3 blood AIM- DMSO control). Donors 1-3 in hashtag IDs correspond to FLD-prefixed donors in corresponding order in library ID. (BLD = blood, BM = bone marrow, SPL = spleen, LNG = lung, LLN = lung lymph node, CITE-seq = cellular indexing of transcriptomes and epitopes).


title: control-4-1

value: Control


title: Phase I 7C × Phase II 7±5C, 55 day_rep2

description:
Second_B05_N126_T7_7V_GATCAC
ControlAcclimation_gene_count_geo.csv


title: 072D


title: 072A


title: control-5-1


title: control-3-1


title: Phase I 22C × Phase II 22C, 55 day_rep2

description:
Second_B02_N103_T7_22_CGGTTA
ControlAcclimation_gene_count_geo.csv


title: control-2-1


title: FLD041FLD029FLD030 ADT library 1


title: Phase I 2C × Phase II 7±5C, 55 day_rep2

description:
Second_B03_N111_T7_2V_AACGCC
ControlAcclimation_gene_count_geo.csv


title: FLD032FLD040FLD015 TCR library 2


title: 107B


title: FLD032FLD040FLD015 TCR library 3


title: 108A


title: BO_AD4_3

city: Groningen

last: Marmolejo

state: Groningen

address: Antonius Deusinglaan 2

country: Netherlands

institute: University of Groningen

data_processing:
GenomeScan delivers the alignment (BAM with index), feature counts, and differential expression analysis using the RNA-Seq pipeline that was developed in-house and described in standard operating procedure SOP 70 (RNA-Seq Analysis). The workflow includes library prep QC (INS 74), raw data quality control (INS 92), UMI processing (INS 78), adapter trimming (INS 88), alignment of short reads (INS 61), feature counting and differential expression (INS 79).
The reads were mapped to the reference sequence using a short read aligner based on Burrows—Wheeler Transform (Tophat v2.0.14) with default settings. The aligner is a splice-aware mapper that detects splice junctions and incorporates them to help align the entire read. The statistics of mapping the reads to the reference genome are shown in Fig. 4 and Table 5. Samples are comparable is there is uniformity of the mapping result for each sample.
BAM files were generated as a result of this step. The alignment files (BAM files sorted on coordinates and indexed with the samtools v2.0.14 package) containing the mapping information are provided in the Mapping folder.
Based on the mapped locations in the alignment file the frequency of how often a read was mapped on a transcript was determined with HTSeq v0.11.0. The hit counts were summarised and reported using the gene_id feature inthe annotation file. Only unique reads that fall within exon regions were counted. The counts were savedto count files, which serve as input for downstream RNA-Seq differential expression analysis
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited count files include count values for each Sample

source_name: Brain Organoid

growth_protocol: Human induced pluripotent stem cells (iPSCs:AD4 harbouring the PSEN1-ΔE9 mutation, isogenic control corrected for the PSEN1-ΔE9 mutation and healthy control stem cell lines were kindly provided by Dr. Šárka Lehtonen and Prof. Jari Koistinaho. iPSCs were maintained on 6-well plates coated with Matrigel (Corning, USA #356234) in Essential 8TM flex medium (E8F; GibcoTM, Thermo Fisher Scientific, Netherlands # A2858501) at 37 °C, 5% CO2. The human brain organoids were generated from the above mentioned iPSCs (AD4 harbouring PSEN1-ΔE9 mutation, isogenic control corrected for PSEN1-ΔE9 mutation and healthy control stem cell lines). At 80-90% confluency, a day before spheroid formation, iPSCs were pre-treated with 1% dimethyl sulfoxide (DMSO; Merck Life Science N.V, Sigma, Netherlands #S002D) to improve spheroid differentiation capacity (30). Cells were first washed with phosphate buffer saline (PBS; Gibco, Thermo Fisher Scientific, Netherlands #70011044) and detached with Accutase® (Stemcell Technologies, USA #07920) for 5 minutes at 37 °C. The dissociated single cells were seeded on AggreWellTM800 plates (Stemcell Technologies, USA #34850) containing 300 microwells per well, pre-treated with AggreWell™ rinsing solution (Stemcell Technologies, USA #07010), according to user’s manual. Cells were spun down at 100 rcf for 3 min and each single microwell contained at least 5,000 cells, cultured in E8F medium (without antibiotic) containing 10 μM ROCK inhibitor Y-27632 (10 mM stock, Stemcell Technologies, USA #72304). After 24 hrs of incubation, spheroids were collected from the microwells using cut 1000 μL pipette tip and transferred into a sterile 10 cm petri dishes in cortical differentiation medium [E8F with 10 μM dorsomorphin (DM; 25 mM stock, Stemcell Technologies, USA #72102), 10 μM SB-431542 (10 mM stock, Stemcell Technologies, USA #72234) and 10 μM XAV-939 (10 mM stock, Stemcell Technologies, USA #72674)]. Medium was changed every day for 6 days. At day 6, medium was changed into neuronal maintenance medium consisting of: Neurobasal (GibcoTM, Thermo Fisher Scientific, Netherlands #21103049) containing 1:50 B-27 supplement without vitamin A (GibcoTM, Thermo Fisher Scientific, Netherlands #12587010) and 1:100 GlutaMax (GibcoTM, Thermo Fisher Scientific, Netherlands #35050061). This medium was supplemented with 20 ng/mL epidermal growth factor (EGF; 100 μg/mL stock, Stemcell Technologies, USA #780061) and 20 ng/mL fibroblast growth factor 2 (FGF2; 100 μg/mL stock, Stemcell Technologies, USA #781341) from day 6 to day 16 with daily medium change. From day 16 to day 24, medium was changed every other day with fresh EGF and FGF2 added every time. At day 24, neuronal maintenance medium was supplemented with 20 ng/mL brain-derived neurotrophic factor (BDNF; 100 μg/mL stock, Stemcell Technologies, USA #78133) and 20 ng/mL Neurotrophin-3 (NT3; 100 μg/mL stock, Stemcell Technologies, USA #78074) until day 43, with media change every other day. cBOs were maintained in neuronal maintenance medium without growth factors from day 43 with media change every other day.

extract_protocol:
Isolation of RNA was performed using the Nucleospin® RNA isolation Kit (Macherey-Nagel). The samples were stored at -80°C until they were sent for transcriptomic analysis.
The quality of the samples, the construction and the sequencing of the RNA-libraries were performed by GenomeScan Bv. Data obtained from the transcriptomic analysis: quality control data, raw count files, FPKMs, RPMs and CPMs.

treatment_protocol: We treated brain organoids for 25 days with BACE inhibitor or co-cultured them with iMGLs. From day 25 of the protocol of differentiation until Day 50, when they were collected for RNAseq experiments.

tag: Sex

value: Male

value: Brain Organoid

value: Isogenic Control

value: Untreated


title: FLD041FLD029FLD030 GEX library 2


title: FLD032FLD040FLD015 TCR library 1


title: Phase I 22C × Phase II 22C, 34 day_rep1

description:
Second_B01_N95_T5_22_GAACCT
ControlAcclimation_gene_count_geo.csv

data_processing:
FastQC for quality control
BBDuk for removing adaptors and poly-A following the pipeline suggested by the manufacturer (https://www.lexogen.com/quantseq-data-analysis/)
STAR for gene level quantification using ‘-quantMode GeneCounts’
Low count gene filterig based on 'total gene count greater than sample number'
DESeq2 for variance stabilization transformation and gene expression normalization
WGCNA for gene co-expression analysis, noise gene filtering, module eigengene visualization and contrast generation
GSEA for pathway enrichment analysis
Assembly: Vitis vinifera 12X.v2 genome with VCost.v3 annotation
Supplementary files format and content: One matrix table with raw gene counts for every gene and every sample without any filtering

extract_protocol:
Total RNA was extracted using SpectrumTM Plant Total RNA Kit (Sigma Aldrich, St Louis, MO, USA) following the protocol suggested by the manufacturer
Libraries were constructed with Lexogen QuantSeq 3’mRNA-Seq Prep Kit (Lexogen, Greenland, NH, USA) following standard practices as a service provided by Cornell University Institute of Genomic Diversity (Ithaca, NY, USA). Sequencing of the libraries was accomplished using NextSeq500 (Illumina, Inc., San Diego, CA, USA) with 95 samples per lane at Cornell University Institute of Biotechnology (Ithaca, NY, USA). The read length was 85 bp.


title: Phase I 4C × Phase II 4C, 20 day_rep1

description:
Second_A09_N157_T3_4_AATGAA
ControlAcclimation_gene_count_geo.csv


title: D1Pas1 P28 KO 3

data_processing:
Fastq files of technical replicates were concatenated when applicable.
Fastq files were preprocessed with cutadapt (v3.4).
RNA-seq data were analyzed using piPipes rna pipeline (v1.1.0).
Small-RNA data were analyzed using piPipes small pipeline (v1.1.0).
R-loop data were analysed following the BisMapR methods (Wulfridge & Sarma, 2021,  eLife 10:e65146).
Assembly: mm10/Gencode M25
Supplementary files format and content: tab-delimited text files of eXpress estimated number of fragments for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2.0 ug of total RNA was used for the construction of sequencing libraries.
RNA and BisMapR libraries were prepared using NEB protocols. Small RNA libraries were prepared using the QIAseq miRNA Library Kit for small RNA-seq.

value: Testis

value: male germ cell

value: KO

value: post-natal day 28


title: D1Pas1 P28 KO 2


title: FLD032FLD040FLD015 BCR library 3

value: blood

value: mononuclear cells (MNCs)

value: mRNA


title: FLD032FLD040FLD015 BCR library 2


title: 072B


title: 075B


title: Phase I 4C × Phase II 4C, 7 day_rep1

description:
Second_A08_N149_T1_4_TTAACT
ControlAcclimation_gene_count_geo.csv

value: bud

value: Cabernet Sauvignon

value: Phase I


title: FLD032FLD040FLD015 BCR library 1


title: D1Pas1 P28 KO 1


title: Phase I 11C × Phase II 7±5C, 55 day_rep1

description:
Second_A07_N141_T7_11V_AATAGC
ControlAcclimation_gene_count_geo.csv

value: Phase II


title: 076D

value: Brain


title: D1Pas1 P28 WT control 3

value: WT


title: 108C

value: Control


title: Phase I 7C × Phase II 7±5C, 55 day_rep1

description:
Second_A05_N125_T7_7V_TAATCG
ControlAcclimation_gene_count_geo.csv


title: FLD032FLD040FLD015 GEX library 2


title: 107A


title: FLD032FLD040FLD015 GEX library 1


title: D1Pas1 P28 WT control 2


title: 106A

value: Cuprizone


title: 106B


title: control-1-1


title: Phase I 2C × Phase II 7±5C, 55 day_rep1

description:
Second_A03_N110_T7_2V_CGAAGG
ControlAcclimation_gene_count_geo.csv


title: Phase I 4C × Phase II 4C, 41 day_rep1

description:
Second_A10_N165_T6_4_GATTGT
ControlAcclimation_gene_count_geo.csv


title: D1Pas1 P28 WT control 1


title: Phase I 22C × Phase II 22C, 55 day_rep1

description:
Second_A02_N102_T7_22_GGTGAG
ControlAcclimation_gene_count_geo.csv


title: 076A


title: FLD032FLD040FLD015 ADT library 3

value: ADT/HTO

value: Antibodies/tags:TotalSeq-C Human Universal Cocktail v1.0,TotalSeq-C0251 anti-human HTO1,TotalSeq-C0252 anti-human HTO2,TotalSeq-C0253 anti-human HTO3,TotalSeq-C0254 anti-human HTO4,TotalSeq-C0255 anti-human HTO5,TotalSeq-C0256 anti-human HTO6,TotalSeq-C0257 anti-human HTO7,TotalSeq-C0258 anti-human HTO8,TotalSeq-C0259 anti-human HTO9. Hashtag IDs for healthy blood donors FLD032,FLD040,FLD015,FLD041,FLD029,FLD030:(HTO1:Donor 1 blood AIM+ SARS, HTO2:Donor 1 blood AIM+ Flu, HTO3:Donor 1 blood AIM- DMSO control, HTO4:Donor 2 blood AIM+ SARS, HTO5:Donor 2 blood AIM+ Flu, HTO6:Donor 2 blood AIM- DMSO control, HTO7:Donor 3 blood AIM+ SARS, HTO2:Donor 3 blood AIM+ Flu, HTO3:Donor 3 blood AIM- DMSO control). Donors 1-3 in hashtag IDs correspond to FLD-prefixed donors in corresponding order in library ID. (BLD = blood, BM = bone marrow, SPL = spleen, LNG = lung, LLN = lung lymph node, CITE-seq = cellular indexing of transcriptomes and epitopes).


title: Phase I 22C × Phase II 22C, 26 day_rep3

description:
Second_A01_N94_T4_22_ACATTA
ControlAcclimation_gene_count_geo.csv


title: 108D


title: Phase I 22C × Phase II 22C, 26 day_rep2

description:
First_H12_N93_T4_22_ATATCC
ControlAcclimation_gene_count_geo.csv


title: FLD032FLD040FLD015 ADT library 2


title: control for PAF1 data HEL RNA-seq rep2

city: Shanghai

first: Aiwei

last: Wu

state: Shanghai

address: 800 Dongchuan Road

department: School of Life Sciences and Biotechnology

institute: Shanghai Jiao Tong University

description: HEL.shCtrl_and_shPaf1.read_count_table.txt

data_processing:
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. RNA-seq read were aligned using hisat2 v2.1.0 with parameter --rna-strandness RF.
Read/fragment count were obtained using featureCounts v1.6.1.
Genome_build: Hg38 for RNA-seq in human cells and mm10 for RNA-seq in mouse.
Supplementary_files_format_and_content: Tab-delimited text files include read/fragment count values of genes for each sample.

source_name: HEL cell line

growth_protocol: Human cells HEL were cultured in 90% RPMI-1640 + 10% FBS + 2% Penicillin/Streptomycin.

extract_protocol:
RNA was extracted from cells using RNeasy Plus Mini Kit (Qiagen, cat. no. 74134) and Quick-RNA MiniPrep Kit (Zymo Research, cat. no. R1054)
the Illumina TruSeq RNA Library preparation protocol: PolyA RNA is captured by oligodT beads and fragmented when eluted from the beads. The first-strand cDNA was synthesized by reverse transcriptase using dNTP, whereas the second-strand cDNA was generated using a dUTP mix . After end-repair, dA-tailing and adapter ligation, the dUTP-containing second strand is digested by uracil DNA glycosylase, rendering it unamplifiable in the subsequent PCR step. Hence the resulting library contains only PCR product of the first-strand cDNA. And then, the barcoded DNA was amplified by 15-cycle PCR.  Libraries were sequenced on Illumina Genome Analyzer II, HiSeq 2000, or HiSeq 2500.
ssRNAseq

value: shCtrl


title: FLD032FLD040FLD015 GEX library 3

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript.
FLD032FLD040FLD015FLD041FLD029FLD030.GEX.matrix.txt.gz


title: FLD032FLD040FLD015 ADT library 1


title: Phase I 22C × Phase II 22C, 7 day_rep3

description:
First_H11_N85_T1_22_TAGGCT
ControlAcclimation_gene_count_geo.csv


title: control for PAF1 data HEL RNA-seq rep1


title: 106C


title: 107C


title: 9W-2mm10_asis

data_processing:
FASTQ files were generated from Illumina bcl files using CellRanger mkfastq. CellRanger count was used to identify UMI and cell barcodes
Assembly: mm10
Supplementary files format and content: h5,  filter UMI and raw UMI

extract_protocol:
At 4 (CPZ) and 6 weeks (Control and Recovery), mice were euthanized by carbon dioxide (CO2) inhalation, and their brains were subsequently dissected. Each brain was sagittally cut into left and right hemispheres. One hemisphere was then further divided into three coronal segments, which were embedded in OCT for snRNA-seq.
snRNA-seq was performed using the 10X Genomics Chromium Next GEM Single Cell 3' Kit v3.1 (PN1000268), Chromium Next GEM Chip G (PN1000127), and Dual Index Kit TT Set A (PN1000215). Nuclei suspensions were loaded onto the 10X Chromium instrument with the aim of recovering 5000 nuclei per sample.
Libraries were sequenced on an Illumina NovaSeq 6000 S4 flowcell using paired-end sequencing with the following parameters: Read1-28bp, i7-10bp, i5-10bp, Read2-90bp.

value: Recovery


title: shPAF1 CCRF-CEM RNA-seq rep2

description: CCRF-CEM.shCtrl_and_shPaf1.read_count_table.txt

source_name: CCRF-CEM cell line

growth_protocol: Human cells CCRF-CEM were cultured in 90% RPMI-1640 + 10% FBS + 2% Penicillin/Streptomycin.


title: D616 GEX library 5

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript.
D616.GEX.matrix.txt.gz

source_name: lung lymph node

value: lung lymph node


title: 9G-1mm10_asis


title: Phase I 11C × Phase II 11C, 34 day_rep3

description:
First_H09_N70_T5_11_GGTATA
ControlAcclimation_gene_count_geo.csv


title: D616 GEX library 4


title: shPAF1 CCRF-CEM RNA-seq rep1


title: Phase I 11C × Phase II 11C, 69 day_rep3

description:
First_H10_N77_T8_11_TTCCGC
ControlAcclimation_gene_count_geo.csv


title: D616 GEX library 3


title: Phase I 11C × Phase II 11C, 20 day_rep3

description:
First_H08_N62_T3_11_CCTGCT
ControlAcclimation_gene_count_geo.csv


title: 9G-2mm10_asis


title: shPAF1 HEL RNA-seq rep2


title: 9W-1mm10_asis


title: control for PAF1 data CCRF-CEM RNA-seq rep2


title: shPAF1 HEL RNA-seq rep1


title: D616 GEX library 2


title: Phase I 7C × Phase II 7C, 41 day_rep3

description:
First_H06_N46_T6_7_GGCCAA
ControlAcclimation_gene_count_geo.csv


title: D616 GEX library 1


title: control for PAF1 data CCRF-CEM RNA-seq rep1


title: Phase I 7C × Phase II 7C, 26 day_rep3

description:
First_H05_N38c_T4_7_CAGGAC
ControlAcclimation_gene_count_geo.csv


title: D616 ADT library 5

description:
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C Human Universal Cocktail,TotalSeq-C0251,TotalSeq-C0253,TotalSeq-C0254,TotalSeq-C0255,TotalSeq-C0256,TotalSeq-C0257,TotalSeq-C0258,TotalSeq-C0259,TotalSeq-C0260,TotalSeq-C0262,TotalSeq-C0263,TotalSeq-C0264.
D616.ADT.matrix.txt.gz

value: Antibodies/tags:TotalSeq-C Human Universal Cocktail v1.0,TotalSeq-C0251 anti-human HTO1,TotalSeq-C0253 anti-human HTO3,TotalSeq-C0254 anti-human HTO4,TotalSeq-C0255 anti-human HTO5,TotalSeq-C0256 anti-human HTO6,TotalSeq-C0257 anti-human HTO7,TotalSeq-C0258 anti-human HTO8,TotalSeq-C0259 anti-human HTO9,TotalSeq-C0260 anti-human HTO10,TotalSeq-C0262 anti-human HTO12,TotalSeq-C0263 anti-human HTO13,TotalSeq-C0264 anti-human HTO14. Hashtag IDs for D616:(HTOs 1,3,4,5,6,7:Donor 616 LLN AIM- DMSO control, HTO8:Donor 616 LLN AIM+ Flu peptide stimulation, HTO9:Donor 616 LLN AIM+ SARS peptide stimulation, HTO13:Donor 616 LLN CD25 depletion AIM+ Flu peptide stimulation, HTO14:Donor 616 LLN CD25 depletion AIM+ SARS peptide stimulation, HTO10:Donor 616 LLN CD40LG+/OX40+ alternate CD4 AIM+ gate Flu peptide stimulation, HTO12:Donor 616 LLN CD40LG+/OX40+ alternate CD4 AIM+ gate SARS peptide stimulation).(BLD = blood, BM = bone marrow, SPL = spleen, LNG = lung, LLN = lung lymph node, CITE-seq = cellular indexing of transcriptomes and epitopes).


title: Phase I 7C × Phase II 7C, 7 day_rep3

description:
First_H04_N30b_T1_7_GGAGGT
ControlAcclimation_gene_count_geo.csv


title: 6G-1mm10_asis


title: Phase I 2C × Phase II 2C, 55 day_rep3

description:
First_H03_N22_T7_2_CAATGC
ControlAcclimation_gene_count_geo.csv


title: 9H-1mm10_asis


title: D616 ADT library 3


title: 6G-2mm10_asis


title: Phase I 2C × Phase II 2C, 34 day_rep3

description:
First_H02_N14_T5_2_CAACAG
ControlAcclimation_gene_count_geo.csv


title: Phase I 2C × Phase II 2C, 13 day_rep3

description:
First_H01_N6b_T2_2_TTGGTA
ControlAcclimation_gene_count_geo.csv


title: D616 ADT library 2


title: 6W-2mm10_asis


title: 6W-1mm10_asis


title: 21-337

description: 10X Genomics

value: Endometrial biopsy

tag: lab id

tag: age

tag: live-births

tag: lh+

tag: secretory cycle_phase

value: early

tag: bmi

tag: number of_previous_loss(es)


title: D616 ADT library 1

tag: tissue

tag: cell type

value: mononuclear cells (MNCs)


title: 6H-1mm10_asis

tag: genotype

tag: treatment


title: Phase I 22C × Phase II 22C, 7 day_rep2

description:
First_G11_N84_T1_22_TCAGGA
ControlAcclimation_gene_count_geo.csv

value: bud

tag: cultivar

tag: time in_treatment_(day)

tag: phase

tag: replication


title: 3H-1mm10_asis


title: Phase I 22C × Phase II 22C, 26 day_rep1

description:
First_G12_N92_T4_22_ATTGGT
ControlAcclimation_gene_count_geo.csv

value: Cabernet Sauvignon

tag: phase i_treatment_(°c)

tag: phase ii_treatment_(°c)


title: D574 GEX library 4

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript.
D574.GEX.matrix.txt.gz

source_name: various

value: various

tag: library type

value: mRNA


title: Phase I 11C × Phase II 11C, 55 day_rep3

description:
First_G10_N76_T7_11_ACTCTT
ControlAcclimation_gene_count_geo.csv

source_name: bud

value: Phase II


title: 3G-1mm10_asis

value: Brain


title: G1_rep3

type: RNA

city: Nanning

first: wang

last: Cuimin

address: No. 6, Taoyuan Road, Qingxiu District

institute: Guangxi Academy of Medical Sciences

description:
G1_rep3
Serum LncRNA expression in pregnant women who did not receive antiviral therapy in the second trimester

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: Second trimester maternal serum,non-antiviral treatment,replicate 3

label_protocol: LncRNA and mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

extract_protocol: Total RNA was isolated from cartilage of KOA patients and healthy volunteers using TRIzol reagent. RNA integrity was assessed by standard denaturing agarose gel electrophoresis. The RNA samples were labeled, purified and amplified. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner

treatment_protocol: Initially, blood samples were collected from six pregnant women with high HBVL and normal liver function in the second trimester (24-28 weeks) who had not undergone antiviral therapy. Thereafter, three of these women were randomly chosen to receive antiviral treatment during pregnancy, whilst the remaining three women did not undergo antiviral intervention. Approximately 5 mL blood samples were aseptically obtained by puncturing a needle into the Cubital vein and subsequently placed in sterile centrifuge tubes, followed by 5-minute centrifugation at 300 g to separate serum. The serum samples were then aliquoted into 2 mL centrifuge tubes (0.5 mL per tube) which were labeled with sample number, date, and time. The samples were stored in a -80°C refrigerator to prevent repeated freezing and thawing for ensuring the integrity of lncRNAs in the serum

value: whole blood

tag: gender

value: female


title: D616 ADT library 4

value: ADT/HTO

tag: adt/hto


title: D574 GEX library 2


title: Phase I 11C × Phase II 11C, 34 day_rep2

city: Geneva

first: Hongrui

last: Wang

institute: Cornell University

description:
First_G09_N69_T5_11_GTGTAG
ControlAcclimation_gene_count_geo.csv


title: D1_rep2

description:
D1_rep2
Serum lncRNA expression of pregnant women who did not receive antiviral treatment before delivery

source_name: Maternal serum before delivery,non-antiviral treatment,replicate 2


title: G1_rep2

description:
G1_rep2
Serum LncRNA expression in pregnant women who did not receive antiviral therapy in the second trimester

source_name: Second trimester maternal serum,non-antiviral treatment,replicate 2


title: D2_rep3

description:
D2_rep3
Serum LncRNA expression of pregnant women receiving antiviral therapy before delivery

source_name: Maternal serum before delivery,antiviral treatment,replicate 3


title: G2_rep3

description:
G2_rep3
Serum LncRNA expression in pregnant women who did not receive antiviral therapy in the second trimester

source_name: Second trimester maternal serum,non-antiviral treatment,replicate 6


title: D574 GEX library 1


title: G2_rep2

description:
G2_rep2
Serum LncRNA expression in pregnant women who did not receive antiviral therapy in the second trimester

source_name: Second trimester maternal serum,non-antiviral treatment,replicate 5


title: D1_rep3

description:
D1_rep3
Serum lncRNA expression of pregnant women who did not receive antiviral treatment before delivery

source_name: Maternal serum before delivery,non-antiviral treatment,replicate 3


title: 3W-2mm10_asis


title: D574 ADT library 3

description:
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C Human Universal Cocktail,TotalSeq-C0251,TotalSeq-C0252,TotalSeq-C0253,TotalSeq-C0254,TotalSeq-C0255,TotalSeq-C0256,TotalSeq-C0257,TotalSeq-C0258,TotalSeq-C0259,TotalSeq-C0260,TotalSeq-C0262,TotalSeq-C0263,TotalSeq-C0264,TotalSeq-C0265,TotalSeq-C0276.
D574.ADT.matrix.txt.gz

value: Antibodies/tags:TotalSeq-C Human Universal Cocktail v1.0,TotalSeq-C0251 anti-human HTO1,TotalSeq-C0252 anti-human HTO2,TotalSeq-C0253 anti-human HTO3,TotalSeq-C0254 anti-human HTO4,TotalSeq-C0255 anti-human HTO5,TotalSeq-C0256 anti-human HTO6,TotalSeq-C0257 anti-human HTO7,TotalSeq-C0258 anti-human HTO8,TotalSeq-C0259 anti-human HTO9,TotalSeq-C0260 anti-human HTO10,TotalSeq-C0262 anti-human HTO12,TotalSeq-C0263 anti-human HTO13,TotalSeq-C0264 anti-human HTO14,TotalSeq-C0265 anti-human HTO15,TotalSeq-C0276 anti-human HTO16. Hashtag IDs for D534,D559,D561,D564,D568,D574:(HTO1:Donor blood AIM+ SARS, HTO2:Donor blood AIM+ Flu, HTO3:Donor blood AIM- DMSO control, HTO4:Donor bone marrow AIM+ SARS, HTO5:Donor bone marrow AIM+ Flu, HTO6:Donor bone marrow AIM- DMSO control, HTO7:Donor spleen AIM+ SARS, HTO8:Donor spleen AIM+ Flu, HTO9:Donor spleen AIM- DMSO control, HTO10:Donor lung AIM+ SARS, HTO12:Donor lung AIM+ Flu, HTO13:Donor lung AIM- DMSO control, HTO14:Donor lung lymph node AIM+ SARS, HTO15:Donor lung lymph node AIM+ Flu, HTO16:Donor lung lymph node AIM- DMSO control). For D561D564 library, only LNG sample is from D564, all other tissues are from D561. (BLD = blood, BM = bone marrow, SPL = spleen, LNG = lung, LLN = lung lymph node, CITE-seq = cellular indexing of transcriptomes and epitopes).


title: Phase I 11C × Phase II 11C, 13 day_rep3

description:
First_G08_N61_T2_11_AATCCG
ControlAcclimation_gene_count_geo.csv

value: Phase I


title: Phase I 7C × Phase II 7C, 20 day_rep3

description:
First_G05_N37b_T3_7_AAGCTC
ControlAcclimation_gene_count_geo.csv


title: 3W-1mm10_asis

value: Recovery


title: Phase I 7C × Phase II 7C, 41 day_rep2

description:
First_G06_N45_T6_7_TACCTT
ControlAcclimation_gene_count_geo.csv


title: D574 ADT library 2


title: D574 GEX library 3


title: Phase I 7C × Phase II 7C, 7 day_rep2

description:
First_G04_N29b_T1_7_CACTAA
ControlAcclimation_gene_count_geo.csv


title: 3G-2mm10_asis


title: 8W-1mm10_asis

value: Cuprizone


title: 8H-1mm10_asis


title: D2_rep2

description:
D2_rep2
Serum LncRNA expression of pregnant women receiving antiviral therapy before delivery

source_name: Maternal serum before delivery,antiviral treatment,replicate 2


title: Phase I 2C × Phase II 2C, 55 day_rep2

description:
First_G03_N21_T7_2_TGGCGA
ControlAcclimation_gene_count_geo.csv


title: D574 ADT library 1


title: 8G-1mm10_asis


title: 8W-2mm10_asis


title: D568 TCR library 1

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript.
filtered_contig_annotations.TCR.txt.gz


title: Cortex E15.5 FVBxBALB/c Kat6b Transgenic, rep 3

city: Parkville

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description: Samples were sequenced (NextSeq500, Illumina) to give 66 bp paired end reads.

data_processing:
Base calling and quality scoring was performed by Illumina Real-Time Analysis (v2) software. FASTQ file generation and de-multiplexing was performed by bcl2fastq conversion software (v2.15.0.4).
Reads were aligned to the mouse genome by Rsubread version 1.24.1
Read counts were summarized by Entrez Gene ID using the Rsubread's featureCounts function and Rsubread's built-in NCBI annotation.
Assembly: mm10
Supplementary files format and content: tab-delimited text files (tsv). Columns represent Entrez Gene Id, Gene Symbol, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: Cortex

extract_protocol:
Total RNA was collected from cultured NSPCs, E12.5 dorsal telencephalon or E15.5 cortex tissue using a kit (RNeasy mini kit, Qiagen, 74104) according to the manufacturer’s instructions and including the optional DNase I digest step.
500 ng to 1 µg total RNA was used to generate sequencing libraries using a kit (TruSeq RNA prep kit v2, Illumina, RS-122-2002) according to the manufacturer’s instructions.

tag: mouse background

value: FVBxBALB/c

tag: gestation

value: Cortex

tag: mouse litter

tag: embryo number

value: Kat6b Tg

tag: replicate

tag: sequencing batch


title: Cortex E15.5 FVBxBALB/c Kat6b Transgenic, rep 4

tag: tissue

tag: genotype


title: D574 ADT library 4

tag: cell type

value: mononuclear cells (MNCs)


title: Phase I 2C × Phase II 2C, 13 day_rep2

address: 630 W. North Street

description:
First_G01_N5_T2_2_AACAAG
ControlAcclimation_gene_count_geo.csv

value: bud

tag: cultivar

tag: time in_treatment_(day)


title: Phase I 2C × Phase II 2C, 26 day_rep3

description:
First_G02_N13_T4_2_AACCGA
ControlAcclimation_gene_count_geo.csv

value: Cabernet Sauvignon

tag: phase

tag: replication


title: D2_rep1

description:
D2_rep1
Serum LncRNA expression of pregnant women receiving antiviral therapy before delivery

source_name: Maternal serum before delivery,antiviral treatment,replicate 1


title: D1_rep1

description:
D1_rep1
Serum lncRNA expression of pregnant women who did not receive antiviral treatment before delivery

source_name: Maternal serum before delivery,non-antiviral treatment,replicate 1


title: G2_rep1

description:
G2_rep1
Serum LncRNA expression in pregnant women who did not receive antiviral therapy in the second trimester

source_name: Second trimester maternal serum,non-antiviral treatment,replicate 4


title: G1_rep1

description:
G1_rep1
Serum LncRNA expression in pregnant women who did not receive antiviral therapy in the second trimester

source_name: Second trimester maternal serum,non-antiviral treatment,replicate 1


title: D568 ADT library 1

description:
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C Human Universal Cocktail,TotalSeq-C0251,TotalSeq-C0252,TotalSeq-C0253,TotalSeq-C0254,TotalSeq-C0255,TotalSeq-C0256,TotalSeq-C0257,TotalSeq-C0258,TotalSeq-C0259,TotalSeq-C0260,TotalSeq-C0262,TotalSeq-C0263,TotalSeq-C0264,TotalSeq-C0265,TotalSeq-C0276.
D568.ADT.matrix.txt.gz

value: various


title: Cortex E15.5 FVBxBALB/c Kat6b Transgenic, rep 2


title: Cortex E15.5 FVBxBALB/c Wild Type, rep 3

value: WT


title: Cortex E15.5 FVBxBALB/c Wild Type, rep 4


title: D568 BCR library 1

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript.
filtered_contig_annotations.BCR.txt.gz

value: mRNA


title: D568 GEX library 1

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript.
D568.GEX.matrix.txt.gz


title: 8G-2mm10_asis

source_name: Brain

value: Brain

tag: treatment


title: 2G-2mm10_asis


title: D564 TCR library 2

tag: library type


title: D564 TCR library 1


title: Phase I 11C × Phase II 11C, 55 day_rep2

description:
First_F10_N75_T7_11_GTAGAA
ControlAcclimation_gene_count_geo.csv

value: Phase II

tag: phase i_treatment_(°c)

tag: phase ii_treatment_(°c)


title: Cortex E15.5 FVBxBALB/c Wild Type, rep 2

tag: mouse background


title: Phase I 22C × Phase II 22C, 7 day_rep1

description:
First_F11_N83_T1_22_AGTACT
ControlAcclimation_gene_count_geo.csv


title: 2H-1mm10_asis


title: 2G-1mm10_asis


title: Phase I 11C × Phase II 11C, 13 day_rep2

description:
First_F08_N60b_T2_11_TCGTTC
ControlAcclimation_gene_count_geo.csv


title: 2W-1mm10_asis


title: Phase I 11C × Phase II 11C, 34 day_rep1

description:
First_F09_N68_T5_11_ACACGC
ControlAcclimation_gene_count_geo.csv


title: Phase I 22C × Phase II 22C, 20 day_rep3

description:
First_F12_N91_T3_22_GCATGG
ControlAcclimation_gene_count_geo.csv


title: Phase I 7C × Phase II 7C, 69 day_rep3

description:
First_F07_N52b_T8_7_TGCACG
ControlAcclimation_gene_count_geo.csv


title: Cortex E15.5 FVBxBALB/c Wild Type, rep 1

tag: gestation


title: D564 BCR library 2


title: 2W-2mm10_asis


title: Dorsal telencephalon E12.5 FVBxBALB/c Kat6b Transgenic, rep 4

source_name: Dorsal telencephalon

value: Dorsal telencephalon

tag: mouse litter


title: Cortex E15.5 FVBxBALB/c Kat6b Transgenic, rep 1

tag: embryo number


title: D564 BCR library 1

source_name: various


title: 5G-2mm10_asis


title: Phase I 7C × Phase II 7C, 20 day_rep2

description:
First_F05_N36b_T3_7_CATCTA
ControlAcclimation_gene_count_geo.csv

source_name: bud


title: 5H-1mm10_asis


title: D564 GEX library 2

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript.
D564.GEX.matrix.txt.gz


title: 5G-1mm10_asis


title: Dorsal telencephalon E12.5 FVBxBALB/c Kat6b Transgenic, rep 3

description: Samples were sequenced (NextSeq500, Illumina) to give 66 bp paired end reads.

tag: replicate


title: Dorsal telencephalon E12.5 FVBxBALB/c Kat6b Transgenic, rep 1

tag: sequencing batch


title: Dorsal telencephalon E12.5 FVBxBALB/c Wild Type, rep 4

tag: tissue


title: Phase I 2C × Phase II 2C, 26 day_rep2

description:
First_F02_N12b_T4_2_AGAATC
ControlAcclimation_gene_count_geo.csv


title: D564 ADT library 2

description:
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C Human Universal Cocktail,TotalSeq-C0251,TotalSeq-C0252,TotalSeq-C0253,TotalSeq-C0254,TotalSeq-C0255,TotalSeq-C0256,TotalSeq-C0257,TotalSeq-C0258,TotalSeq-C0259,TotalSeq-C0260,TotalSeq-C0262,TotalSeq-C0263,TotalSeq-C0264,TotalSeq-C0265,TotalSeq-C0276.
D564.ADT.matrix.txt.gz

value: ADT/HTO

tag: adt/hto


title: D561D564 GEX library 2

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript.
D561.GEX.matrix.txt.gz
D564.GEX.matrix.txt.gz

tag: cell type


title: Dorsal telencephalon E12.5 FVBxBALB/c Wild Type, rep 3

tag: genotype


title: Dorsal telencephalon E12.5 FVBxBALB/c Kat6b Transgenic, rep 2


title: Dorsal telencephalon E12.5 FVBxBALB/c Wild Type, rep 2


title: Phase I 7C × Phase II 7C, 41 day_rep1

description:
First_F06_N44b_T6_7_AAGTGG
ControlAcclimation_gene_count_geo.csv

tag: cultivar

tag: time in_treatment_(day)


title: D564 GEX library 1


title: Phase I 2C × Phase II 2C, 55 day_rep1

description:
First_F03_N20_T7_2_GCGAAT
ControlAcclimation_gene_count_geo.csv

tag: phase

tag: replication


title: Phase I 2C × Phase II 2C, 7 day_rep3

description:
First_F01_N4_T1_2_GAAGTG
ControlAcclimation_gene_count_geo.csv


title: 5W-1mm10_asis

tag: treatment


title: D564 ADT library 1

tag: library type

value: Antibodies/tags:TotalSeq-C Human Universal Cocktail v1.0,TotalSeq-C0251 anti-human HTO1,TotalSeq-C0252 anti-human HTO2,TotalSeq-C0253 anti-human HTO3,TotalSeq-C0254 anti-human HTO4,TotalSeq-C0255 anti-human HTO5,TotalSeq-C0256 anti-human HTO6,TotalSeq-C0257 anti-human HTO7,TotalSeq-C0258 anti-human HTO8,TotalSeq-C0259 anti-human HTO9,TotalSeq-C0260 anti-human HTO10,TotalSeq-C0262 anti-human HTO12,TotalSeq-C0263 anti-human HTO13,TotalSeq-C0264 anti-human HTO14,TotalSeq-C0265 anti-human HTO15,TotalSeq-C0276 anti-human HTO16. Hashtag IDs for D534,D559,D561,D564,D568,D574:(HTO1:Donor blood AIM+ SARS, HTO2:Donor blood AIM+ Flu, HTO3:Donor blood AIM- DMSO control, HTO4:Donor bone marrow AIM+ SARS, HTO5:Donor bone marrow AIM+ Flu, HTO6:Donor bone marrow AIM- DMSO control, HTO7:Donor spleen AIM+ SARS, HTO8:Donor spleen AIM+ Flu, HTO9:Donor spleen AIM- DMSO control, HTO10:Donor lung AIM+ SARS, HTO12:Donor lung AIM+ Flu, HTO13:Donor lung AIM- DMSO control, HTO14:Donor lung lymph node AIM+ SARS, HTO15:Donor lung lymph node AIM+ Flu, HTO16:Donor lung lymph node AIM- DMSO control). For D561D564 library, only LNG sample is from D564, all other tissues are from D561. (BLD = blood, BM = bone marrow, SPL = spleen, LNG = lung, LLN = lung lymph node, CITE-seq = cellular indexing of transcriptomes and epitopes).


title: 5W-2mm10_asis


title: D561D564 ADT library 2

description:
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C Human Universal Cocktail,TotalSeq-C0251,TotalSeq-C0252,TotalSeq-C0253,TotalSeq-C0254,TotalSeq-C0255,TotalSeq-C0256,TotalSeq-C0257,TotalSeq-C0258,TotalSeq-C0259,TotalSeq-C0260,TotalSeq-C0262,TotalSeq-C0263,TotalSeq-C0264,TotalSeq-C0265,TotalSeq-C0276.
D561.ADT.matrix.txt.gz
D564.ADT.matrix.txt.gz


title: 1G-2mm10_asis

value: Control


title: Phase I 11C × Phase II 11C, 55 day_rep1

description:
First_E10_N74_T7_11_AGACCA
ControlAcclimation_gene_count_geo.csv

tag: phase i_treatment_(°c)

tag: phase ii_treatment_(°c)


title: D561D564 GEX library 1


title: Cortex E15.5 C57BL/6 Kat6b Knock Out, rep 5

tag: mouse background

tag: gestation

value: Kat6b KO


title: 1W-1mm10_asis


title: D561D564 ADT library 1


title: Cortex E15.5 C57BL/6 Kat6b Knock Out, rep 4

tag: mouse litter

tag: embryo number


title: Phase I 11C × Phase II 11C, 26 day_rep3

description:
First_E09_N67_T4_11_ACAGAT
ControlAcclimation_gene_count_geo.csv

value: Phase I


title: D559 TCR library 2

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript.
filtered_contig_annotations.TCR.txt.gz


title: 1G-1mm10_asis


title: Phase I 11C × Phase II 11C, 13 day_rep1

description:
First_E08_N59b_T2_11_TGACAC
ControlAcclimation_gene_count_geo.csv


title: D559 TCR library 1


title: 1H-1mm10_asis


title: Cortex E15.5 C57BL/6 Kat6b Knock Out, rep 3

tag: replicate

tag: sequencing batch


title: 7W-2mm10_asis

tag: tissue


title: Phase I 7C × Phase II 7C, 69 day_rep2

description:
First_E07_N51b_T8_7_TATGTC
ControlAcclimation_gene_count_geo.csv


title: Cortex E15.5 C57BL/6 Kat6b Knock Out, rep 2