title: Lefty2KO_75

city: New Haven

first: Minming

state: CT

address: 10 Amistad

department: BBS

institute: Yale University

description: 10x Genomics

data_processing:
Raw base call (BCL) files generated by Illumina sequencers were demultiplexed into FASTQ files using 10X Genomics' Single-Cell Gene Expression Software Cell Ranger ("mkfastq" pipeline, version 6.0.1, default parameters).
FASTQ files were aligned, filtered, barcode and UMI counted using 10X Genomics' Single-Cell Gene Expression Software Cell Ranger ("count pipeline", version 6.0.1, default parameters).
Assembly: mm10
Supplementary files format and content: The tar archive contains the raw gene-barcode matrix as produced by the Cell Ranger pipeline and the MEX-formatted UMI count matrix. 10x Genomics explains their MEX-formatted UMI counts as follows: "The cellranger pipeline generates a gene-barcode matrix... Each matrix is stored in Market Exchange Format (MEX). It also contains TSV files with genes and barcode sequences corresponding to row and column indices, respectively." More information on the formatting can be found at https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices.

source_name: Whole embryo, Embryonic Day (E)7.5

growth_protocol: Preimplantation embryos were cultured in pre-gassed 25 ul KSOM supplemented with 1/2 amino acids (Millipore) under mineral oil at 37ºC and 5% CO2. After ~84 hours post-fertilization, cavitated blastocysts were transferred into the uterine horns of pseudopregnant females in clutches of 10-15 per horn.

extract_protocol:
Embryos were isolated from surrogate mice. Outermost extraembryonic tissues (yolk sac, trophectoderm derived tissues) were preserved if possible. Undamaged embryos isolated experiment were washed in 1xPBS/0.4%BSA, pooled without pre-selection and subjected to tissue dissociation in 200 µl TrypLE Express (Gibco) for 20-30 minutes at 37ºC, with pipetting in 5 minute intervals. The cell suspension was filtered using Scienceware Flowmi Cell Strainers, 40 µM. Cells were washed twice with 1ml 1xPBS/0.4%BSA and centrifugation for 5 minutes at 1200 rpm. The cell concentration was determined using a hemocytometer and cells were subjected to single-cell RNA sequencing (10x Genomic, Chromium™ NextGem 3’ v3.1) with dual barcodes.
Single-cell libraries were generated following the manual instructions of 10x Genomic (Chromium™ Single Cell 3’ v3), with the exception of fewer PCR cycles in cDNA amplification and sample index PCR than recommended in order to increase complexity of libraries. Libraries were sequenced with a minimum of 230 Mio paired end reads and parameters as described in the manual.

treatment_protocol: B6D2F1 oocytes were isolated from 5-10-week-old female mice ~12 hours after a hormone priming superovulation regimen (5 IU PMSG and 5 IU hCG delivered 46 hours later) and stored in 25 µl droplets of pre-gassed KSOM media with 1/2 amino acids (Millipore) at 37ºC and 5% CO2. Zygotes were generated by intracytoplasmic sperm injection of decapitated CAST/B6 F1 strain sperm (scRNA-seq). Cas9 mRNA with gRNA sets were injected at 4 hpf, and the zygotes were cultured to E3.5 blastocysts prior to uterine transfer into pseudopregnant CD-1 strain females (~25-35 g). Post-implantation embryos were isolated according to the embryonic day with a 24-hour offset to accommodate developmental delay as a result of uterine transfer (see extract protocol).

value: Whole embryo, Embryonic Day (E)7.5

value: Embryonic Day (E)7.5

tag: progeny

value: F2 progeny generated from crossing Cast/EiJ/B6 F1 sperm with B6D2F1 oocytes


title: UPN827 cells, TN1326 TrailNet 3or6 month T1D plasma

status: Public on Jun 01 2026

type: RNA

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

country: USA

institute: Medical College of Wisconsin

description: Gene expression data from UPN827 cells stimulated with T1D plasma

hyb_protocol: The Affymetrix GeneChip Human Genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios.  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA function in Partek GS.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: UPN827 cells stimulated with TN1326 TrailNet 3or6 month T1D plasma

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Commercial cryopreserved PBMCs of healthy Caucasian male donor UPN827 were thawed and washed per the manufacturer’s protocol (Cellular Technology Ltd., Shaker Heights, OH).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% of participant plasma  that was sampled at baseline or the 3-6 months post-baseline from six TrailNet new-onset T1D intervention trails, or from our local Recent onset T1DM cohort. Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl.  After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

tag: responder cells

value: UPN827 cells

tag: sample timepoint

value: TrailNet 3 or 6 month


title: RP11-33O4.1_D_LP5

type: SRA

city: Ghent

first: Xin

last: Wang

address: Corneel Heymanslaan 10, B

country: Belgium

institute: University Gent

description: Library name: RNA017562

library_source: other

data_processing:
High performance computing 3'-RNAseq analysis pipeline (Quantseq)
QC via FASTQC 0.11.9
Quality related trimming via bbduk (BBMap v38.87, k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20)
read mapping via STAR 2.7.6a
bam file indexing via SAMtools 1.15
count tables generated via HTSeq 0.11.3
Assembly: hg38
Supplementary files format and content: tab-delimited text files including raw count tables

molecule: other

growth_protocol: HEK293T-dCas9 cells were maintained in RPMI medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin at 37 °C in the incubator with 5% CO₂.

extract_protocol:
Cells were lysed directly in the culture plate using the SingleShot™ Cell Lysis Kit (Bio-Rad) according to the manufacturer’s instructions. Cell lysates were used directly for downstream RNA-seq library preparation.
Libraries were prepared using the QuantSeq 3′ mRNA-Seq Library Prep Kit (Lexogen) .

treatment_protocol: Cells were transfected with a total of 40 ng purified sgRNA per well using Lipofectamine™ CRISPRMAX™ Cas9 Transfection Reagent (Invitrogen, Cat. #CMAX00003).

tag: cell line

tag: cell type

value: embryonic kidney cell

tag: genotype

tag: treatment

tag: batch


title: Lefty2KO_65

description: 10x Genomics

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Mus musculus

source_name: Whole embryo, Embryonic Day (E)6.5

tag: tissue

value: Whole embryo, Embryonic Day (E)6.5

tag: age

value: Embryonic Day (E)6.5


title: NK cells, resting state, person 46

city: Boston

first: Zachary

middle: D

last: Nagel

state: MA

address: 655 Huntington Avenue

department: Environmental Health

institute: Harvard University

description: Library name: NK_46

library_source: transcriptomic

data_processing:
RNA-seq data were processed using the bcbio-nextgen pipeline with the hg38 genome build. The FASTQ files underwent pre-processing, where UMIs were incorporated into R2, and R1 was discarded, resulting in single FASTQ files per library. Reads were quality trimmed with Trim Galore and aligned to hg38 using TopHat2. Transcript quantification was performed with DEXSeq to produce a count matrix.
Assembly: hg38
Supplementary files format and content: csv file in .gz containing raw read counts for each sample

source_name: Blood

growth_protocol: RPMI 1640 medium supplemented with 20% FBS at 37C/5%CO2

extract_protocol:
RNA isolation was performed using PureLinkTM RNA Mini Kit protocol (Invitrogen, Cat no. 12183018A). 25 ng of isolated total RNA was used for constructing sequencing libraries
RNA samples were quantified and assessed using the Advanced Analytical Fragment Analyzer. Libraries were prepared using the 3’ Digital Gene Expression (DGE) sequencing protocol, following established methods. Custom 3’ DGE primers with barcodes and Unique Molecular Identifiers (UMIs) were incorporated to tag transcripts uniquely. After reverse transcription and template switching, cDNA was pooled, cleaned, amplified, and tagmented using Nextera tagmentation. Libraries were sequenced on an Illumina NextSeq500 platform. For more details on library construction, refer to the published protocol in the reference (doi: https://doi.org/10.1101/003236)

treatment_protocol: PBMCs and T cells were stimulated by 10ng/ml of Phytohemagglutinin-L and B cells were stimulated by human B cell Expansion kit for 3 days

value: Blood

value: Primary NK cells

value: Natural killer cells


title: UPN827 cells, TN1324 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1324 TrailNet 3or6 month T1D plasma


title: RP11-33O4.1_C_LP5

description: Library name: RNA017561


title: Monocytes, resting state, person 46

description: Library name: M_46

value: Primary Monocytes

value: Monocytes


title: UPN827 cells, TN1321 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1321 TrailNet 3or6 month T1D plasma


title: RP11-33O4.1_B_LP5

description: Library name: RNA017560


title: Lefty1KO_85

description: 10x Genomics

source_name: Whole embryo, Embryonic Day (E)8.5

value: Whole embryo, Embryonic Day (E)8.5

value: Embryonic Day (E)8.5


title: B cells, proliferative state, person 46

description: Library name: BS_46

value: Primary B Cells

value: B cells

value: Human B cell Expansion kit in 20%FBS


title: RP11-575F12.2_C_LP5

description: Library name: RNA017573


title: UPN827 cells, TN1317 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1317 TrailNet 3or6 month T1D plasma


title: RP11-33O4.1_A_LP5

description: Library name: RNA017559


title: B cells, resting state, person 46

description: Library name: B_46


title: Lefty1KO_75

description: 10x Genomics

value: Whole embryo, Embryonic Day (E)7.5

value: Embryonic Day (E)7.5


title: RP11-527F13.1_D_LP5

description: Library name: RNA017558


title: UPN827 cells, TN1316 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1316 TrailNet 3or6 month T1D plasma

value: UPN827 cells


title: CD8 T cell, rim-enriched, WT (H877)

city: Leuven

first: Lisa

middle: M

last: Becker

address: Herestraat 49

institute: VIB KU Leuven Center for Cancer Biology

data_processing:
Quality trimming: We trimmed low quality ends (< Q20) with FastX 0.0.14. Reads that are shorter than 35bp after trimming are removed.
Adapter trimming: The adapters are trimmed only at the end (at least 10bp overlap and 90% match) with cutadapt 3.2. Reads that are shorter than 35bp after adapter trimming are removed.
Quality filtering: Using FastX 0.0.14 and ShortRead 1.52.0, we remove polyA-reads (more than 90% of the bases equal A), ambiguous reads (containing N), low quality reads (more than 50% of the bases < Q25) and artifact reads (all but 3 bases in the read equal one base type).
Removal of contaminants: Using bowtie 2.4.5, we identify reads that align to phix illumina and remove them
Assembly: GRCm3882
Supplementary files format and content: Counts.csv coma separated file containing raw counts. Fastq files were aligned with HISAT2 vesrsion 2.1.0 for the M.musculus reference GRCm38 downloaded from HISAT2 website, Counting was done with subread-2.0.0 FeatureCounts for the reference mm10.ncbiRefSeq.gtf

source_name: lung tumor (rim-enriched)

extract_protocol:
RNA was harvested using the Qiagen RNeasy Micro Kit
Libraries were prepared with the TruSeq RNA Library Prep Kit (Illumina) following manufacturer's protocols

value: lung tumor (rim-enriched)

value: CD8 T cells

value: WT


title: Bulk PBMCs, proliferative state, person 47

description: Library name: PS_47

value: Primary PBMCs

value: Peripheral blood mononuclear cells

value: Phytohemagglutinin-L + 20%FBS


title: UPN827 cells, TN1360 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1360 TrailNet 3or6 month T1D plasma

value: TrailNet 3 or 6 month


title: Lefty1KO_65

description: 10x Genomics

value: Whole embryo, Embryonic Day (E)6.5

value: Embryonic Day (E)6.5

value: F2 progeny generated from crossing Cast/EiJ/B6 F1 sperm with B6D2F1 oocytes


title: UPN827 cells, TN1308 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1308 TrailNet 3or6 month T1D plasma


title: CD8 T cell, core-enriched, WT ((H876)

source_name: lung tumor (core-enriched)

value: lung tumor (core-enriched)


title: RP11-527F13.1_B_LP5

description: Library name: RNA017556

value: embryonic kidney cell


title: UPN827 cells, TN1304 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1304 TrailNet 3or6 month T1D plasma


title: EO771_LCN2,replicate 2

city: Guangzhou

first: Qidong

last: Xia

state: Guangdong

address: No.107, Yangjiangxi Road, Guangzhou

department: Breast Tumor Center

country: China

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

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 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: GRCm38.91
Supplementary files format and content: csv files include count values for each Sample

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

value: tumor cells


title: Bulk PBMCs, proliferative state, person 45

description: Library name: PS_45

value: Blood


title: RP11-527F13.1_A_LP5

description: Library name: RNA017555


title: EO771_LCN2,replicate 1


title: Bulk PBMCs, resting state, person 45

description: Library name: P_45


title: UPN827 cells, TN1303 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1303 TrailNet 3or6 month T1D plasma


title: RP11-326A19.4_D_LP5

description: Library name: RNA017554


title: EO771_Control,replicate 3

value: Control


title: T cells, proliferative state, person 46

description: Library name: TS_46

value: Primary T cells

value: T cells


title: RP11-326A19.4_C_LP5

description: Library name: RNA017553


title: NK cells, resting state, person 45

description: Library name: NK_45

value: Primary NK cells

value: Natural killer cells


title: UPN827 cells, TN582 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN582 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: Monocytes, resting state, person 45

description: Library name: M_45

value: Primary Monocytes

value: Monocytes


title: UPN827 cells, TN1342 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1342 TrailNet 3or6 month T1D plasma

value: TrailNet 3 or 6 month


title: EO771_Control,replicate 2


title: Bulk PBMCs, resting state, person 46

description: Library name: P_46

value: Primary PBMCs

value: Peripheral blood mononuclear cells


title: UPN827 cells, TN580 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN580 TrailNet Baseline T1D plasma


title: UPN827 cells, TN1327 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1327 TrailNet 3or6 month T1D plasma


title: B cells, proliferative state, person 45

description: Library name: BS_45

value: Primary B Cells

value: B cells

value: Human B cell Expansion kit in 20%FBS


title: RP11-326A19.4_A_LP5

description: Library name: RNA017551

value: embryonic kidney cell


title: Fracture callus, scRNA-seq

city: New York

first: Ugur

last: Ayturk

state: NY

address: 533 East 70th St.

institute: Hospital for Special Surgery

description: 10X Genomics

data_processing:
Demultiplexing, gene expression quantification and aggregate analysis were performed with Cellranger.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bone and muscle

extract_protocol:
Femoral fracture calluses and intact diaphyses with surrounding muscle were collected from n=3 littermate male mice 3 weeks post-fracture surgery. Following dissection with scissors and forceps, fracture and intact specimens were separately pooled inside petri dishes with sterile PBS on ice. The specimens were then moved to a tissue-culture hood, finely cut with a razor blade, and put in a 15 mL tube with 10 mL collagenase solution (4000 units in αMEM with 1% anti-mycotic; type II, Worthington Biochemical Corp, Lakewood, NJ, USA). The tubes were transferred to a shaking incubator for 2x30 minutes at 37°C. Cells were filtered, pelleted and resuspended in cell culture media (αMEM with 10% FBS and 1% anti-mycotic). Cells were tested for viability with an automated fluorescent cell counter and then sorted on an Aria II flow cytometer (BD Biosciences, San Jose, CA, USA) to separate tdTomato expressing cells.
The purified cells were loaded on the 10X Chromium platform and processed for single cell RNA-seq using the 3’ single cell RNA sequencing kit V3.

value: bone and muscle

value: sorted primary bone and muscle cells

value: Clec3b.creERT2; Ai14.R26.tdTomato

value: Fracture


title: B cells, resting state, person 45

description: Library name: B_45

source_name: Blood

value: Blood


title: RP11-498C9.15_D_LP5

description: Library name: RNA017550


title: UPN827 cells, TN579 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN579 TrailNet Baseline T1D plasma


title: UPN827 cells, TN578rehyb TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN578rehyb TrailNet Baseline T1D plasma


title: T cells, proliferative state, person 44

description: Library name: TS_44

value: Primary T cells

value: T cells

value: Phytohemagglutinin-L + 20%FBS


title: Intact bone & muscle, scRNA-seq

description: 10X Genomics


title: RP11-498C9.15_C_LP5

description: Library name: RNA017549


title: UPN827 cells, TN577 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN577 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: RP11-498C9.15_B_LP5

description: Library name: RNA017548


title: E15.5, En1/2 CKO cerebellum, replicate 1

first: Alexandra

middle: L.

last: Joyner

state: New York

address: 430 E 67th St

department: Developmental Biology Program

institute: Sloan Kettering Institute

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (v6.1.0)
Assembly: Customized genome (mm10 and tdTomato sequence)
Supplementary files format and content: Tab-separated value files and matrix files.

source_name: tdT+ sorted cells from cerebellum

extract_protocol:
Animals were dissected in ice cold Hank’s balanced salt solution (HBSS) (Gibco) and were pooled together for downstream steps. Two replicate experiments were performed. On ice, cerebella were detached from the rest of the brain using forceps and dissociated in Accutase (Innovative Cell Technologies) at 37°C for 7-10 minutes. Following dissociation, accutase was washed out using neural stem cell (NSC) media (Neurobasal, supplemented with N2, B27 and non-essential amino acids, Gibco). Samples were triturated by pipetting up and down using a P1000, filtered through a 35um cell strainer (Falcon)and then centrifuged at 500g at 4°C for 5 minutes. Cells were washed again in NSC media and were finally filtered into polypropylene round bottom tubes (Falcon) prior to sorting for tdT+ cells. tdT+ cells were sorted into polypropylene round bottom tubes, spun down at 500g at 4°C for 5 minutes and resuspended in NSC media prior to single cell library preparation.
Single cell libraries were prepared using 10X Genomics’ Chromium Next GEM Single Cell 3’ Reagent Kits, v3.1 according to manufacturer’s instructions. Prior to loading the 10X Genomics chip, the limited sample preparation protocol was used. Cell viability was quantified using 0.2% (w/v) Trypan Blue on a hemocytometer, and 10,000 viable cells were targeted per pooled sample.

value: tdT+ sorted cells from cerebellum

value: Ptf1aCre/+; En1lox/lox, En2lox/lox; R26LSL-tdT/+


title: UPN827 cells, TN576 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN576 TrailNet Baseline T1D plasma


title: Bulk PBMCs, proliferative state, person 44

description: Library name: PS_44

value: Primary PBMCs

value: Peripheral blood mononuclear cells


title: E15.5, control cerebellum, replicate 2

description: 10X Genomics

value: Ptf1aCre/+; R26LSL-tdT/+


title: Bulk PBMCs, resting state, person 44

description: Library name: P_44


title: UPN827 cells, TN575 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN575 TrailNet Baseline T1D plasma


title: RP11-2B6.3_D_LP5

description: Library name: RNA017546


title: NK cells, resting state, person 44

description: Library name: NK_44

value: Primary NK cells

value: Natural killer cells


title: UPN827 cells, TN574 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN574 TrailNet Baseline T1D plasma


title: B16F10 + mLNVs-DOX + MH, biol rep 3

city: Braga

first: Juan

last: Gallo

address: avda Mestre Jose Veiga sn

department: Health

country: Portugal

institute: International Iberian Nanotechnology Laboratory

data_processing:
HISAT2 software
Raw reads were filtered as follows: (1)Remove reads with adaptor contamination. (2)Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%). (3)Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
HISAT2 is selected to map the filtered sequenced reads to the reference genome (Grcm38.p3 GCA_000001635.5)
Read counts were normalized to FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced)
Differential expression analysis (log2FoldChange) of two conditions/groups was performed using the DESeq2 R package
Benjamini and Hochberg's approach for controlling the false discovery rate  was applied to identify statistically significant alterations in the transcriptome.
Assembly: Grcm38.p3 GCA_000001635.5
Supplementary files format and content: Tab-delimited text files with: gene id;  normalized readcounts of all samples form group A; normalized readcounts of all samples form group B; log2FoldChange;  P value; padj; gene name; Chrom: name of chromosome in which the gene is located; Strand: chain information of the gene; Start: start position of the gene at the chromosome; End: end position of the gene at the chromosome.; gene length; gene type; GeneDescription: gene function description;  tf_family: TF family annotation; readcounts of all samples form group A;  readcounts of all samples form group B; fpkm of all samples form group A; Samples form group B: fpkm of all samples form group B

extract_protocol:
RNA was harvestes using RNeasy Mini Kit (Qiagen). A total amount of 1 µg RNA per sample was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® Ultra RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: melamona cells

value: mLNVs-DOX + MH


title: UPN827 cells, TN573 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN573 TrailNet Baseline T1D plasma


title: Monocytes, resting state, person 44

description: Library name: M_44

value: Primary Monocytes

value: Monocytes


title: RP11-2B6.3_C_LP5

description: Library name: RNA017545

value: embryonic kidney cell


title: UPN827 cells, TN572 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN572 TrailNet Baseline T1D plasma


title: RP11-2B6.3_A_LP5

description: Library name: RNA017543


title: B cells, proliferative state, person 44

description: Library name: BS_44

value: Blood

value: Primary B Cells

value: B cells

value: Human B cell Expansion kit in 20%FBS


title: RP11-2B6.3_B_LP5

description: Library name: RNA017544


title: B cells, resting state, person 44

description: Library name: B_44


title: B16F10 + mLNVs-DOX + MH, biol rep 1


title: NT_B_LP4

description: Library name: RNA017542

value: NT


title: UPN827 cells, TN571 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN571 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: B16F10 + mLNVs + MH, biol rep 3

value: mLNVs + MH


title: T cells, proliferative state, person 42

description: Library name: TS_42

value: Primary T cells

value: T cells

value: Phytohemagglutinin-L + 20%FBS


title: NT_A_LP4

description: Library name: RNA017541


title: UPN827 cells, TN570 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN570 TrailNet Baseline T1D plasma


title: UPN827 cells, TN569 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN569 TrailNet Baseline T1D plasma


title: B16F10 + mLNVs + MH, biol rep 2


title: T cells, resting state, person 42

description: Library name: T_42


title: Mock_B_LP4

description: Library name: RNA017540

value: Mock


title: UPN827 cells, TN568 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN568 TrailNet Baseline T1D plasma


title: B16F10 + mLNVs + MH, biol rep 1

value: melamona cells


title: B16F10 + mLNVs-DOX + MH, biol rep 2

value: mLNVs-DOX + MH


title: Embryo, LibA_DKOAxin1Axin2

city: Cambridge

first: Bertie

last: Gottgens

email: bg200@cam.ac.uk, nkw22@cam.ac.uk

address: Jeffrey Cheah Biomedical Centre

country: United Kingdom

institute: University of Cambridge

description: 10x genomics scRNA-seq

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were carried out using the Cell Ranger software (version cellranger-7.0.1).
All downstream analysis is described in the methods section as well as in the associated code
Assembly: mm10 (refdata-cellranger-mm10-1.2.0)
Supplementary files format and content: Seurat object containing metadata, raw counts, processes counts, and more

source_name: Whole mouse embryo

extract_protocol:
(15) E6.5 control and (10) E6.5 Axin1DEpi;Axin2-/-  double mutant embryos were single cell dissociated to generate the sc-RNA libraries. Control and mutant embryos were dissected at the same time. Control embryos were obtained by crossing FVB females (Jackson) to the same males used to obtain the Axin1DEpi;Axin2-/-  double mutant embryos (Sox2-Cre+; Axin1DEpi/+;Axin2+/- ). Mutant embryos were identified by distinctive morphology (see Supplementary Figure) and dissected in DMEM-F12 + 5% Newborn Calf Serum (NCS) (Gibco). Individual embryos were washed three times in 40µl drops of DMEM-F12 media. Thereafter, batches of 4 embryos were digested in 40µl of a solution of 2:1 0.25% Trypsin (Gibco): Accutase (StemCell Technologies) at 37C for 15 minutes. After partial digestion, 40µl of (DMEM-F12 + 20% NCS + 4mM EDTA) solution was added to each batch of embryos which were mechanically dissociated by hand pipetting, followed by mouth pipetting with pulled glass capillaries of different diameters to obtain a single cell suspension. The cell suspension was collected in DMEM-F12 + 10% NCS and filtered through a FlowMi cell strainer (4mM Millipore, Sigma). Cells were centrifugated at 2,200 rpm for 4 minutes and washed twice with DMEM-F12 + 10% NCS. Cells were counted and diluted in DMEM-F12 + 10% NCS.
Cells were loaded on a Chromium Controller microfluidic chip for encapsulation with a target number of 10,000 cells for the generation of generate single cell 3’ RNA-seq libraries. Libraries were generated following the manufacturer’s instructions (10x Genomics Chromium Single Cell 3’ Reagent Kit User Guide v2 Chemistry), as previously (Nowotschin et al., 2019).

value: Whole mouse embryo

tag: time

value: Axin1/Axin2 double KO

tag: replicate


title: Bulk PBMCs, proliferative state, person 42

description: Library name: PS_42

value: Primary PBMCs

value: Peripheral blood mononuclear cells


title: Mock_A_LP4

description: Library name: RNA017539

value: embryonic kidney cell


title: Lefty2KO_85

description: 10x Genomics

source_name: Whole embryo, Embryonic Day (E)8.5

value: Whole embryo, Embryonic Day (E)8.5

value: Embryonic Day (E)8.5

value: F2 progeny generated from crossing Cast/EiJ/B6 F1 sperm with B6D2F1 oocytes


title: B16F10 + free DOX, biol rep 3

value: free DOX


title: Bulk PBMCs, resting state, person 42

description: Library name: P_42

value: Blood


title: UPN827 cells, TN555 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN555 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: PoolCTL_B_LP4

description: Library name: RNA017538

value: PoolCTL


title: B16F10 + free DOX, biol rep 2


title: NK cells, resting state, person 42

description: Library name: NK_42

source_name: Blood

value: Primary NK cells

value: Natural killer cells


title: UPN827 cells, TN554 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN554 TrailNet Baseline T1D plasma


title: PoolCTL_A_LP4

description: Library name: RNA017537


title: Lefty1KO_90

description: 10x Genomics

source_name: Whole embryo, Embryonic Day (E)9.0

value: Whole embryo, Embryonic Day (E)9.0

value: Embryonic Day (E)9.0


title: B16F10 + free DOX, biol rep 1

value: melamona cells


title: Monocytes, resting state, person 42

description: Library name: M_42

value: Primary Monocytes

value: Monocytes


title: UPN827 cells, TN553 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN553 TrailNet Baseline T1D plasma


title: GAL4_B_LP4

description: Library name: RNA017536


title: B16F10  (Control), biol rep 3

value: Control


title: GAL4_A_LP4

description: Library name: RNA017535

value: embryonic kidney cell


title: UPN827 cells, TN552 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN552 TrailNet Baseline T1D plasma


title: B cells, proliferative state, person 42

description: Library name: BS_42

value: Primary B Cells

value: B cells

value: Human B cell Expansion kit in 20%FBS


title: B16F10  (Control), biol rep 2


title: B cells, resting state, person 42

description: Library name: B_42


title: NEAT1_B_LP4

description: Library name: RNA017534


title: UPN827 cells, TN551 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN551 TrailNet Baseline T1D plasma


title: RP11-527F13.1_C_LP5

description: Library name: RNA017557


title: T cells, proliferative state, person 45

description: Library name: TS_45

value: Primary T cells

value: T cells

value: Phytohemagglutinin-L + 20%FBS


title: B16F10  (Control), biol rep 1


title: T cells, proliferative state, person 41

description: Library name: TS_41

value: Blood


title: EO771_LCN2,replicate 3

value: tumor cells


title: NEAT1_A_LP4

description: Library name: RNA017533


title: UPN827 cells, TN550 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN550 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: brain, PRVABC-59

city: Jinan

first: Chi

last: Zhang

address: 44 Wenhua West Road

institute: Shandong University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: brain

extract_protocol:
Briefly, single cells were suspended in PBS containing 0.04% BSA. Approximately 10,000 cells were added to each channel and approximately 6,000 target cells were recovered. Captured cells were lysed and the released RNA was barcoded through reverse transcription in individual GEMs. Reverse transcription was conducted on a S1000TM Touch Thermal Cycler (BioRad) at 53 °C for 45 min, followed by 85°C for 5 min and a hold at 4°C. Complementary DNA was generated and amplified, after which, quality was assessed using an Agilent 2100 (performed by Bestopcell, Beijing, China)
According to the manufacturer’s introduction, scRNA-seq libraries were constructed using a Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10X Genomics, 1000268)
The libraries were sequenced using an Illumina Novaseq 6000 sequencer with a paired-end 150-bp (PE150) reading strategy (performed by Bestopcell, Beijing, China)

tag: strain

value: ICR

value: brain

tag: infection

value: ZIKV PRVABC-59


title: T cells, resting state, person 45

description: Library name: T_45


title: T cells, resting state, person 41

description: Library name: T_41


title: UPN827 cells, TN549 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN549 TrailNet Baseline T1D plasma


title: UPN827 cells, TN1301 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1301 TrailNet 3or6 month T1D plasma

value: TrailNet 3 or 6 month


title: DPH1_B_LP4

description: Library name: RNA017532


title: brain, FSS13025

value: ZIKV FSS13025


title: Bulk PBMCs, proliferative state, person 41

description: Library name: PS_41

value: Primary PBMCs

value: Peripheral blood mononuclear cells


title: DPH1_A_LP4

description: Library name: RNA017531

value: embryonic kidney cell


title: UPN827 cells, TN548 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN548 TrailNet Baseline T1D plasma


title: brain, PBS

value: MOCK


title: Bulk PBMCs, resting state, person 41

description: Library name: P_41


title: RP11-2B6.2_D_LP4

description: Library name: RNA017530


title: UPN827 cells, TN547 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN547 TrailNet Baseline T1D plasma


title: RP11-2B6.2_C_LP4

description: Library name: RNA017529


title: NK cells, resting state, person 41

description: Library name: NK_41

value: Primary NK cells

value: Natural killer cells


title: RP11-326A19.4_B_LP5

description: Library name: RNA017552


title: Tomato positive alveolar macrophages, ATACseq, rep1

city: Iowa City

first: Jennifer

middle: Rachelle

last: Bermick

state: IA

address: 431 Newton Road, 505 EMRB

institute: University of Iowa

library_source: genomic

data_processing:
ATAC-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.39, discarding reads left with < 35 bp
ATAC-seq reads were aligned to the mm10 genome using default parameters in Bowtie2 version 2.3.4.2.
Peaks were called uing MACS2 V2.1.1.20160309 with the significance cut-off q-value <=0.05
bedgraph and narrowPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: bedgraph, narrowPeak

molecule: genomic DNA

extract_protocol: According to previously published ATAC-seq protocol (Buenrostro J, Wu B, Chang H, Greenleaf W. ATAC-seq: A method for assaying chromatin accessibility genome-wide. Curr Protoc Mol Biol, 2015, 109: 21.29.1-21.29.9). 20,000 cells were used as starting material.

value: Tomato positive (directly infected with RSV)

value: RSV infection 30 days prior


title: Tomato positive alveolar macrophages, ATACseq, rep2


title: UPN827 cells, TN546 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN546 TrailNet Baseline T1D plasma


title: Monocytes, resting state, person 41

description: Library name: M_41

value: Blood

value: Primary Monocytes

value: Monocytes


title: RP11-2B6.2_B_LP4

description: Library name: RNA017528


title: UPN827 cells, TN545 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN545 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: UPN827 cells, TN581 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN581 TrailNet Baseline T1D plasma


title: Tomato negative alveolar macrophages, ATACseq, rep2

value: Tomato negative (not directly infected with RSV)


title: EO771_Control,replicate 1

value: tumor cells

value: Control


title: UPN827 cells, TN544 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN544 TrailNet Baseline T1D plasma


title: RP11-2B6.2_A_LP4

description: Library name: RNA017527


title: B cells, proliferative state, person 41

description: Library name: BS_41

value: Primary B Cells

value: B cells

value: Human B cell Expansion kit in 20%FBS


title: Tomato negative alveolar macrophages, ATACseq, rep1


title: RP11-11N9.4_D_LP4

description: Library name: RNA017526

value: embryonic kidney cell


title: B cells, resting state, person 41

description: Library name: B_41


title: Heart, CLP 24h, replicate 2, scRNA-seq

city: Chongqing

first: Chenyang

last: Duan

address: Changjiang Road

department: Department of Anaesthesiology

institute: Chongqing Medical  University

description: 10x Genomics

data_processing:
The final library pool was sequenced on the Illumina NovaSeq 6000 platform and the sequencing data were processed using the Cell Ranger software (10X Genomics).
cellranger (v5.0.1) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20%  passed the cell quality filtering and mitochondria genes were removed in the expression table.   Seurat package (version: 3.1.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.   PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Heart

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3’ V3.1 Reagent Kits (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ V3.1 Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols

value: Heart

value: CLP 24h


title: RP11-11N9.4_C_LP4

description: Library name: RNA017525


title: UPN827 cells, TN543 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN543 TrailNet Baseline T1D plasma


title: T cells, resting state, person 40

description: Library name: T_40

source_name: Blood

value: Primary T cells

value: T cells


title: Heart, CLP 24h, replicate 1, scRNA-seq

description: 10x Genomics


title: RP11-11N9.4_B_LP4

description: Library name: RNA017524


title: T cells, proliferative state, person 40

description: Library name: TS_40

value: Phytohemagglutinin-L + 20%FBS


title: Bulk PBMCs, proliferative state, person 40

description: Library name: PS_40

value: Blood

value: Primary PBMCs

value: Peripheral blood mononuclear cells


title: UPN827 cells, TN541 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN541 TrailNet Baseline T1D plasma

value: UPN827 cells


title: Heart, CLP 12h, replicate 2, scRNA-seq

description: 10x Genomics

value: CLP 12h


title: UPN827 cells, TN542 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN542 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: UPN827 cells, TN540 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN540 TrailNet Baseline T1D plasma


title: RP11-11N9.4_A_LP4

description: Library name: RNA017523


title: Heart, CLP 12h, replicate 1, scRNA-seq

description: 10x Genomics


title: E15.5, En1/2 CKO cerebellum, replicate 2

description: 10X Genomics

source_name: tdT+ sorted cells from cerebellum

value: tdT+ sorted cells from cerebellum

value: Ptf1aCre/+; En1lox/lox, En2lox/lox; R26LSL-tdT/+


title: UPN827 cells, TN539 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN539 TrailNet Baseline T1D plasma


title: Bulk PBMCs, resting state, person 40

description: Library name: P_40


title: RP11-244M2.1_D_LP4

description: Library name: RNA017522


title: T cells, resting state, person 44

description: Library name: T_44


title: Heart, control, replicate 2, scRNA-seq

description: 10x Genomics

value: control


title: NK cells, resting state, person 40

description: Library name: NK_40

value: Primary NK cells

value: Natural killer cells


title: Heart, control, replicate 1, scRNA-seq

description: 10x Genomics


title: Monocytes, resting state, person 40

description: Library name: M_40

value: Primary Monocytes

value: Monocytes


title: RP11-244M2.1_C_LP4

description: Library name: RNA017521

value: embryonic kidney cell


title: UPN827 cells, TN538 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN538 TrailNet Baseline T1D plasma


title: RP11-244M2.1_B_LP4

description: Library name: RNA017520


title: UPN827 cells, TN537 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN537 TrailNet Baseline T1D plasma


title: B cells, proliferative state, person 40

description: Library name: BS_40

value: Primary B Cells

value: B cells

value: Human B cell Expansion kit in 20%FBS


title: RP11-244M2.1_A_LP4

description: Library name: RNA017519


title: MJR_DC-OVA +LCMV_003

city: Indianapolis

last: Richer

state: IN

address: R2 Rm 366 950W Walnut St

department: Microbiology and Immunology

institute: Indiana University School of Medicine

description: OT-I CD8 T cells isolated day 5 post DC-OVA +LCMV immunization

hyb_protocol: The resulting biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer (Affymetrix, Inc., Santa Clara, CA), placed onto Affymetrix Mouse EXON 1.0 ST Arrays, and incubated at 45º C for 18 hr with 60 rpm rotation in an Affymetrix Model 640 Genechip Hybridization Oven. The Mouse EXON 1.0 ST Array interrogates over 1 million exon clusters within the known and predicted transcribed regions of the entire genome. Following hybridization, the arrays will be washed, stained with streptavidin-phycoerythrin (Molecular Probes, Inc., Eugene, OR), signal amplified with antistreptavidin antibody (Vector Laboratories, Inc., Burlingame, CA) using the Affymetrix Model 450 Fluidics Station.

scan_protocol: Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade and data collected using the using the GeneChip operating software (GCOS) v1.4.

data_processing:
Data were imported into Partek GS v. 6.12. The normalized log2 data was compared using an ANOVA model. Individual comparisons were done using a linear model function. Genes with a p-value of <0.01 and a fold-change >1.5 were analyzed further.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.mps

label_protocol: Microarray hybridizations were performed at the University of Iowa DNA Facility. Briefly, 50 nanograms total RNA was converted to SPIA amplified cDNA using the WT-Ovation Pico RNA Amplification System, v1 (NuGEN Technologies, San Carlos, CA, Cat. #3300) according to the manufacturer’s recommended protocol. The amplified SPIA cDNA product was purified through a QIAGEN MinElute Reaction Cleanup column (QIAGEN Cat #28204) according to modifications from NuGEN. 3.3 ug of SPIA amplified DNA was then used to generate ST-cDNA using the WT-Ovation EXON Module v1 (NuGEN Technologies, Cat #2000) and again cleaned up with the Qiagen column as above. Five micrograms of this product was fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module, v2 (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol.

extract_protocol: Rneasy (Qiagen) according to manufacturer's instructions

treatment_protocol: CD8 T cells were enriched via automacs followed by cell sorting

value: spleen

value: OT-I TCR transgenic CD8 T cells


title: B cells, resting state, person 40

description: Library name: B_40

value: Blood


title: UPN827 cells, TN536 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN536 TrailNet Baseline T1D plasma

value: UPN827 cells


title: RP11-1094M14.11_D_LP4

description: Library name: RNA017518


title: T cells, proliferative state, person 38

description: Library name: TS_38

value: Primary T cells

value: T cells

value: Phytohemagglutinin-L + 20%FBS


title: UPN827 cells, TN535 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN535 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: RP11-1094M14.11_C_LP4

description: Library name: RNA017517


title: T cells, resting state, person 38

description: Library name: T_38


title: RP11-1094M14.11_B_LP4

description: Library name: RNA017516


title: Bulk PBMCs, proliferative state, person 38

description: Library name: PS_38

value: Primary PBMCs

value: Peripheral blood mononuclear cells


title: RP11-1094M14.11_A_LP4

description: Library name: RNA017515


title: MJR_DC-OVA_003

description: OT-I CD8 T cells isolated day 5 post DC-OVA immunization


title: MJR_DC-OVA +LCMV_001

source_name: OT-I CD8 T cells isolated day 5 post DC-OVA +LCMV immunization


title: UPN827 cells, TN533 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN533 TrailNet Baseline T1D plasma


title: MJR_DC-OVA_002

source_name: OT-I CD8 T cells isolated day 5 post DC-OVA immunization


title: Bulk PBMCs, resting state, person 38

description: Library name: P_38


title: RP11-218F10.3_D_LP4

description: Library name: RNA017514


title: UPN827 cells, TN532 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN532 TrailNet Baseline T1D plasma


title: MJR_DC-OVA_001


title: UPN827 cells, TN531 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN531 TrailNet Baseline T1D plasma


title: RP11-218F10.3_C_LP4

description: Library name: RNA017513


title: NK cells, resting state, person 38

description: Library name: NK_38

value: Primary NK cells

value: Natural killer cells


title: MJR_Naive_003

description: naïve OT-I CD8 T cells

source_name: naïve OT-I CD8 T cells


title: RP11-218F10.3_B_LP4

description: Library name: RNA017512


title: Monocytes, resting state, person 38

description: Library name: M_38

value: Primary Monocytes

value: Monocytes


title: B cells, proliferative state, person 38

description: Library name: BS_38

value: Primary B Cells


title: MJR_Naive_002

description: naïve OT-I CD8 T cells


title: WB5

city: Shanghai

first: dahai

last: Yang

address: No.130, Meilong Road, Xuhui District

institute: East China University of Science and Technology

description:
Library name: Sample 6
WB5

data_processing:
Raw reads were quality-trimmed and filtered using fastp.
Clean reads were then aligned to the reference genome (GRCz11.109) with HISAT2 to obtain mapping information.
Assembly: GRCz11.109
Supplementary files format and content: xls files include FPKM values for each Sample

organism: Danio rerio

source_name: whole body

growth_protocol: Zebrafish larvae were were maintained in E3 medium at 28℃

extract_protocol:
Total RNA was isolated from 8 larvae at the indicated time points using TRIzol reagent (Invitrogen), following the manufacturer's protocol.
Library preparation were carried out by Tsingke (Beijing, China). Sequencing was performed on an Illumina NovaSeq platform.

treatment_protocol: At 2 dpf, WT and cldc1-/- zebrafish larvae were subjected to training via yolk sac microinjection of β-glucan. After a four-day resting period, the larvae were challenged by immersion with E. piscicida.

value: whole body

value: WT

value: BG


title: RP11-218F10.3_A_LP4

description: Library name: RNA017511

value: embryonic kidney cell


title: B cells, resting state, person 38

description: Library name: B_38

source_name: Blood

value: Blood

value: B cells


title: UPN827 cells, TN528 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN528 TrailNet Baseline T1D plasma

value: UPN827 cells


title: T cells, proliferative state, person 36

description: Library name: TS_36

value: Primary T cells

value: T cells


title: WB4

description:
Library name: Sample 5
WB4


title: MJR_Naive_001

description: naïve OT-I CD8 T cells

value: spleen

value: OT-I TCR transgenic CD8 T cells


title: UPN827 cells, TN527 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN527 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: RP11-1055B8.9_C_LP4

description: Library name: RNA017509


title: UPN827 cells, TN526 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN526 TrailNet Baseline T1D plasma


title: WB3

description:
Library name: Sample 4
WB3


title: T cells, resting state, person 36

description: Library name: T_36


title: RP11-1055B8.9_B_LP4

description: Library name: RNA017508


title: UPN827 cells, TN525 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN525 TrailNet Baseline T1D plasma


title: CB5

description:
Library name: Sample 3
CB5

value: cldc1 KO


title: Bulk PBMCs, proliferative state, person 36

description: Library name: PS_36

value: Primary PBMCs

value: Peripheral blood mononuclear cells

value: Phytohemagglutinin-L + 20%FBS


title: Bulk PBMCs, resting state, person 36

description: Library name: P_36


title: CB4

description:
Library name: Sample 2
CB4


title: RP11-196G18.24_D_LP4

description: Library name: RNA017506


title: UPN827 cells, TN524 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN524 TrailNet Baseline T1D plasma


title: UPN827 cells, TN523 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN523 TrailNet Baseline T1D plasma


title: NK cells, resting state, person 36

description: Library name: NK_36

value: Primary NK cells

value: Natural killer cells


title: CB1

description:
Library name: Sample 1
CB1

value: whole body


title: UPN827 cells, TN522 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN522 TrailNet Baseline T1D plasma


title: Monocytes, resting state, person 36

description: Library name: M_36

value: Primary Monocytes

value: Monocytes


title: RP11-196G18.24_B_LP4

description: Library name: RNA017504

value: embryonic kidney cell


title: B cells, proliferative state, person 36

description: Library name: BS_36

value: Blood

value: Primary B Cells

value: B cells

value: Human B cell Expansion kit in 20%FBS


title: RP11-196G18.24_A_LP4

description: Library name: RNA017503


title: KO_L2C_RNA-seq_r2

first: Xinyu

address: Siping Road 1239

institute: Tongji University

description:
Library name: Sample24
KO L2C RNA-seq replicate2

data_processing:
RNA-seq: For raw paired-end RNA-seq reads, trim_galore v0.4.5 was used to remove low-quality bases and adapter sequences. HISAT2 was used to align the clean sequence data to the mouse reference genome (mm10). StringTie was used to quantify gene expression from the aligned sequences for each gene, and htseq-count was used to count reads number for each gene. The mouse gene annotation file was obtained from the mouse GENCODE release (GRCm38.99).
Assembly: mm10
Supplementary files format and content: gene fpkm file

source_name: late 2-cell

growth_protocol: Specific pathogen-free (SPF) mice were housed in the animal facility at Tongji University,Shanghai, China, and they were fed a standard diet. The temperature and light were strictly controlled (24 °C; 12 h light and 12 h dark). Smarca4flox/flox mice are from previous study(Qi et al. 2021). All animal experiments were performed in accordance with the University of Health Guide for the Care and Use of Laboratory Animals and were approved by the Biological Research Ethics Committee of Tongji University. To get MII oocytes for ICSI, B6D2F1 or Smarca4flox/flox Gdf9 Cre C57BL/6 female mice (8–12-weeks old) were superovulated by injection with 7 IU each of pregnant mare serum gonadotropin (PMSG), followed by injection of 5 IU of human chorionic gonadotropin (hCG) (San-Sheng Pharmaceutical) 48 h later.

extract_protocol:
20-30 blastomere per replicate were isolated and washed before they were placed into 1.4 μL of lysis buffer (10 mM Tris-HCl, pH 8.5, 5 mM MgCl2, 0.6% NP-40) for individual reactions. Then, 1.8 μL of MNase master mix (MNase buffer, 0.125 U/μL MNase (NEB, M0247S), 2 mM DTT, and 5% PEG 6000) was added into each tube, and the reaction was incubated at 25 °C for 10 min for chromatin fragmentation. The reaction was stopped by the addition of 0.4 μL of 100 mM EDTA, and then 0.4 μL of 2% Triton X-100 was added to the reaction to release the fragmented chromatin. Then, 0.2 μL of 20 mg/mL protease (Qiagen) was added, and the reaction was incubated at 50 °C for 90 min for protein digestion followed by incubation at 75 °C for 30 min for protease inactivation. The sequencing libraries were prepared using the KAPA Hyper Prep kit for the Illumina platform (Roche, kk8504) following the manufacturer’s instructions. After standard procedures including end repair and A-tailing, adapter ligation, post-ligation cleanup, and library amplification, the resulting products were subjected to a second round of PCR amplification with the same provided primers to generate sufficient DNA materials for highthroughput sequencing.
For mouse embryos, the sequencing libraries were prepared using KAPA Stranded RNA-Seq Kit with RiboErase(Kapa Biosystems, KK8483) and KAPA HyperPrep Kit for the Illumina platform (Roche, kk8504) following manufacturer’s protocol. Paired-end sequencing with 150-bp read length was performed on the HiSeq X Ten (Illumina) platform.

value: late 2-cell

value: Smarca4 KO


title: UPN827 cells, TN521 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN521 TrailNet Baseline T1D plasma

value: UPN827 cells

value: TrailNet Baseline


title: UPN827 cells, TN520 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN520 TrailNet Baseline T1D plasma


title: KO_L2C_RNA-seq_r1

description:
Library name: Sample23
KO L2C RNA-seq replicate1


title: B cells, resting state, person 36

description: Library name: B_36


title: UPN827 cells, TN519 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN519 TrailNet Baseline T1D plasma


title: RP11-1017G21.5_D_LP4

description: Library name: RNA017502


title: WT_L2C_RNA-seq_r3

description:
Library name: Sample22
WT L2C RNA-seq replicate3

value: wild type


title: RP11-1017G21.5_C_LP4

description: Library name: RNA017501


title: UPN827 cells, TN534 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN534 TrailNet Baseline T1D plasma


title: T cells, proliferative state, person 35

description: Library name: TS_35

value: Primary T cells

value: T cells


title: WT_L2C_RNA-seq_r2

description:
Library name: Sample21
WT L2C RNA-seq replicate2


title: T cells, resting state, person 35

description: Library name: T_35


title: UPN827 cells, TN518 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN518 TrailNet Baseline T1D plasma


title: MJR_DC-OVA +LCMV_002

source_name: OT-I CD8 T cells isolated day 5 post DC-OVA +LCMV immunization

value: spleen

value: OT-I TCR transgenic CD8 T cells


title: RP11-1017G21.5_B_LP4

description: Library name: RNA017500


title: UPN827 cells, TN517 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN517 TrailNet Baseline T1D plasma


title: WT_L2C_RNA-seq_r1

description:
Library name: Sample20
WT L2C RNA-seq replicate1


title: Bulk PBMCs, proliferative state, person 35

description: Library name: PS_35

value: Primary PBMCs

value: Peripheral blood mononuclear cells

value: Phytohemagglutinin-L + 20%FBS


title: RP11-1017G21.5_A_LP4

description: Library name: RNA017499

value: embryonic kidney cell


title: UPN827 cells, TN516 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN516 TrailNet Baseline T1D plasma


title: UPN827 cells, TN530 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN530 TrailNet Baseline T1D plasma


title: Bulk PBMCs, resting state, person 35

description: Library name: P_35

source_name: Blood

value: Blood


title: RP11-171I2.4_D_LP4

description: Library name: RNA017498


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 027 | Full ROI

first: Emmanuel

last: Ogbonna

address: 200 Longwood Ave

department: Laboratory of Systems Pharmacology

institute: Harvard Medical School; Tufts University School of Medicine

description:
Library name: LSP16102_Scan2 | 027 | Full ROI
FFPE

data_processing:
Raw sequencing data were processed to generate FASTQ files
demultiplexed fastqs according to nanostring pipeline
Process FASTQ files through GeoMx NGS pipeline and convert to DCC files
Retreive DCC files
Transfer DCC files to GeoMx DSP for QC and normalisation by DSP software
Then we have Q3 normalised count matrix file (available with the publication as Supplementary File)
Supplementary files format and content: DCC files are digital count files which have been processed from FASTQ files by nanostring pipeline
Library strategy: Spatial Transcriptomics

source_name: tuberculosis-infected human lung tissue

extract_protocol:
5uM thickness section was processed according to GeoMx protocol provided by Nanostring
the libraries were prepared according to manufacturer's protocol (Nanostring)

value: tuberculosis-infected human lung tissue

tag: histopathological region

value: TLS

tag: patient id


title: KO_E2C_RNA-seq_r3

description:
Library name: Sample19
KO E2C RNA-seq replicate3

source_name: early 2-cell

value: early 2-cell


title: UPN827 cells, TN515 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN515 TrailNet Baseline T1D plasma


title: KO_E2C_RNA-seq_r2

description:
Library name: Sample18
KO E2C RNA-seq replicate2


title: NK cells, resting state, person 35

description: Library name: NK_35

value: Primary NK cells

value: Natural killer cells


title: RP11-171I2.4_C_LP4

description: Library name: RNA017497


title: UPN827 cells, TN529 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN529 TrailNet Baseline T1D plasma

value: UPN827 cells


title: KO_E2C_RNA-seq_r1

description:
Library name: Sample17
KO E2C RNA-seq replicate1

value: Smarca4 KO


title: UPN827 cells, TN514 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN514 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: RP11-171I2.4_B_LP4

description: Library name: RNA017496


title: RP11-620J15.3_A_LP5

description: Library name: RNA017579


title: UPN827 cells, TN513 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN513 TrailNet Baseline T1D plasma


title: Monocytes, resting state, person 35

description: Library name: M_35

value: Primary Monocytes

value: Monocytes


title: WT_E2C_RNA-seq_r3

description:
Library name: Sample16
WT E2C RNA-seq replicate3

value: wild type


title: RP11-1055B8.9_D_LP4

description: Library name: RNA017510


title: B cells, proliferative state, person 35

description: Library name: BS_35

value: Primary B Cells

value: B cells

value: Human B cell Expansion kit in 20%FBS


title: RP11-171I2.4_A_LP4

description: Library name: RNA017495


title: WT_E2C_RNA-seq_r2

description:
Library name: Sample15
WT E2C RNA-seq replicate2


title: B cells, resting state, person 35

description: Library name: B_35


title: UPN827 cells, TN512 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN512 TrailNet Baseline T1D plasma


title: WT_E2C_RNA-seq_r1

description:
Library name: Sample14
WT E2C RNA-seq replicate1


title: HeLa, replicate 3

city: Yayoi, Bunkyo-ku

first: Hiroki

last: Ono

state: Tokyo

department: Research Division for Applied Life Sciences

country: Japan

institute: Institute for Quantitative Biosciences, The University of Tokyo

description: Library name: HeLa_R3_S8_R1_001

data_processing:
Adapter sequences were trimmed from raw reads using cutadapt 1.16 with options: cutadapt -a TGGAATTCTCGGGTGCCAAGG -o ${library_name}_trim1.fastq ${library_name}.fastq.gz
Four-nt long degenerate sequences at the 3′ and 5′ end were trimmed using cutadapt 1.16 with options: cutadapt -u 4 -u -4 -m 18 -o ${library_name}_trim2.fastq ${library_name}_trim1.fastq
Low-quality reads (Phred quality score <20 in >95% of the bases) were removed using FASTX-Toolkit 0.0.14 with options: fastq_quality_filter -q 20 -p 95 -Q 33 -i ${library_name}_trim2.fastq -o ${library_name}_trim3.fastq
Low-quality reads (Phred quality score <30 in >50% of the bases) were removed using FASTX-Toolkit 0.0.14 with options: fastq_quality_filter -q 30 -p 50 -Q 33 -i ${library_name}_trim3.fastq -o ${library_name}_trim4.fastq
Artifact reads were eliminated with FASTX-Toolkit 0.0.14 with options: fastx_artifacts_filter -v -i ${library_name}_trim4.fastq -o ${library_name}_trim5.fastq
Raw read counts and normalized abundance (RPM) of miRNAs were obtained using miRge 2.0 (ver. 2.0.6) with options: (for HeLa) miRge2.0 annotate -s ${library_name}_trim5.fastq -d miRBase -pb ${path_to_bowtie} -lib ${path_to_library} -sp human -ai -gff -cpu 4 (for mouse ES cells) miRge2.0 annotate -s ${library_name}_trim5.fastq -d miRBase -pb ${path_to_bowtie} -lib ${path_to_library} -sp mouse -ai -gff -cpu 4
Assembly: miRBase v22
Supplementary files format and content: csv files including raw read counts
Supplementary files format and content: csv files including normalized abundance (RPM)

source_name: HeLa

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol
miRNA-seq libraries were prepared according to the AQ-seq method (Kim et al., Nucleic Acids Res. 2019, doi: 10.1093/nar/gky1293) with some modifications.

value: HeLa


title: UPN827 cells, TN510 TrailNet Baseline T1D plasma

institute: Medical College of Wisconsin

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios.  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA function in Partek GS.

source_name: UPN827 cells stimulated with TN510 TrailNet Baseline T1D plasma

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.


title: RNU11_C_LP4

institute: University Gent

description: Library name: RNA017493

data_processing:
High performance computing 3'-RNAseq analysis pipeline (Quantseq)
QC via FASTQC 0.11.9
Quality related trimming via bbduk (BBMap v38.87, k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20)
read mapping via STAR 2.7.6a
bam file indexing via SAMtools 1.15
count tables generated via HTSeq 0.11.3
Assembly: hg38
Supplementary files format and content: tab-delimited text files including raw count tables

extract_protocol:
Cells were lysed directly in the culture plate using the SingleShot™ Cell Lysis Kit (Bio-Rad) according to the manufacturer’s instructions. Cell lysates were used directly for downstream RNA-seq library preparation.
Libraries were prepared using the QuantSeq 3′ mRNA-Seq Library Prep Kit (Lexogen) .

value: embryonic kidney cell


title: HeLa, replicate 2

description: Library name: HeLa_R2_S7_R1_001


title: UPN827 cells, TN509 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN509 TrailNet Baseline T1D plasma


title: RNU11_B_LP4

description: Library name: RNA017492


title: UPN827 cells, TN511 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN511 TrailNet Baseline T1D plasma


title: RNU11_A_LP4

description: Library name: RNA017491


title: HeLa, replicate 1

description: Library name: HeLa_R1_S6_R1_001


title: KO_PN3_RNA-seq_r3

description:
Library name: Sample12
KO PN3 RNA-seq replicate3

source_name: PN3 stage zygote

value: PN3 stage zygote


title: KO_PN3_RNA-seq_r2

description:
Library name: Sample11
KO PN3 RNA-seq replicate2


title: PKP2 mutant hiPSC-cardiomyocytes rep2

city: Utrecht

first: Su Ji

last: Han

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: Library name: Sample 4

data_processing:
During sequencing, Read 1 was assigned 26 base pairs and was used for identification of the Illumina library barcode, cell barcode and UMI. R2 was assigned 60 base pairs and used to map to the reference transcriptome of Hg19 with BWA. Data was demultiplexed.Raw read counts (included as count tables "ReadCounts") were converted to umi counts (referred to as "barcode counts"); an additional correction was performed based on binominal statistics, resulting in "transcript counts".
Assembly: hg19
Supplementary files format and content: Count tables of raw reads ("readcounts"). Columns are single cells, rows indicate genes and chromosomal origin using HGNC symbols and "chrX" where X indicates chromosome of origin. Files are labeled by identifiers described above, R1 and R2 indicate to read 1 and read 2. s001-2 and s006-7 enumerates the samples. (HUB = Hubrecht, SH = Su Ji Han)
Supplementary files format and content: umi counts ("barcode counts") Columns are single cells (and each file corresponds to one sample), rows indicate genes and chromosomal origin using HGNC symbols and "chrX" where X indicates chromosome of origin. Files are labeled by identifiers described above, R1 and R2 indicate to read 1 and read 2. s001-2 and s006-7 enumerates the samples. (HUB = Hubrecht, SH = Su Ji Han)
Supplementary files format and content: corrected umi counts ("transcript counts"): Columns are single cells (and each file corresponds to one sample), rows indicate genes and chromosomal origin using HGNC symbols and "chrX" where X indicates chromosome of origin. Files are labeled by identifiers described above, R1 and R2 indicate to read 1 and read 2. s001-2 and s006-7 enumerates the samples. (HUB = Hubrecht, SH = Su Ji Han)

source_name: hiPSC-derived cardiomyocytes

growth_protocol: The hiPSCs were cultured on Geltrex™ LDEV-Free, hESC-Qualified, Reduced Growth Factor Basement Membrane Matrix-coated wells (Gibco: A1413302) in Essential 8™ Medium (Gibco: A1517001). For directed differentiation to cardiomyocytes, hiPSCs were cultured until they reached 80-90% cell confluency. Differentiation was started (day 0) using RPMI-1640-Medium-GlutaMAX™ Supplement-HEPES (Gibco: 72400021) supplemented with 4µM CHIR99021, 0.5 mg/mL human recombinant albumin and 0.2 mg/mL L-Ascorbic Acid 2-Phosphate. After 48 hours, the medium was aspirated and cells were incubated in RPMI-1640-Medium-GlutaMAX™ Supplement-HEPES (Gibco: 72400021) supplemented with 5µM IWP2, 0.5 mg/mL human recombinant albumin and 0.2 mg/mL L-Ascorbic Acid 2-Phosphate for another 48 hours. On day 4 and 6 the medium was changed to RPMI-1640-Medium-GlutaMAX™ Supplement-HEPES (Gibco: 72400021) supplemented with 0.5 mg/mL human recombinant albumin and 0.2 mg/mL L-Ascorbic Acid 2-Phosphate. On day 8, cells were refreshed with RPMI-1640-Medium-GlutaMAX™ Supplement-HEPES (Gibco: 72400021) supplemented with B-27™Supplement (50x)-serum free (Gibco: 17504001). When spontaneously beating cardiomyocytes were observed cells were dissociated using TrypLE™ Select Enzyme (10x), no phenol red (Gibco: A1217703) and seeded for experiments in Geltrex-coated plates using RPMI-1640-Medium-GlutaMAX™ Supplement-HEPES (Gibco: 72400021) supplemented with B-27™Supplement (50x)-serum free (Gibco: 17504001) and 2μM Thiazovivin. The day after the cells were maintained in RPMI-1640-Medium-GlutaMAX™ Supplement-HEPES (Gibco: 72400021) supplemented with B-27™Supplement (50x)-serum free (Gibco: 17504001) until they were used for experiments.

extract_protocol:
hiPSC-cardiomyocytes were dissociated using TrypLE™ Select Enzyme (10x), no phenol red (Gibco: A1217703) and single-cell sorted using the FACSJazz™ Cell Sorter (BD Biosciences) into 384-well plates provided by Single Cell Discoveries. After sorting, plates were centrifuged at 4 °C, put on dry ice and stored at -80 °C until they were processed for library preparation.
The plates were prepared for single-cell mRNA sequencing by Single Cell Discoveries according to an adapted version of the SORT-seq protocol.

value: hiPSC-derived cardiomyocytes


title: RP11-147L13.15_D_LP4

description: Library name: RNA017490


title: UPN827 cells, TN507 TrailNet Baseline T1D plasma

first: Martin

last: Hessner

address: 8701 Watertown Plank Road

description: Gene expression data from UPN827 cells stimulated with T1D plasma

source_name: UPN827 cells stimulated with TN507 TrailNet Baseline T1D plasma


title: UPN827 cells, TN508 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN508 TrailNet Baseline T1D plasma


title: KO_PN3_RNA-seq_r1

last: Wang

description:
Library name: Sample10
KO PN3 RNA-seq replicate1


title: RP11-147L13.15_C_LP4

first: Xin

address: Corneel Heymanslaan 10, B

description: Library name: RNA017489


title: PKP2 mutant hiPSC-cardiomyocytes rep1

description: Library name: Sample 3


title: WT_PN3_RNA-seq_r4

description:
Library name: Sample9
WT PN3 RNA-seq replicate4


title: RP11-147L13.15_B_LP4

description: Library name: RNA017488


title: PKP2 control hiPSC-cardiomyocytes rep1

description: Library name: Sample 1


title: RP11-147L13.15_A_LP4

description: Library name: RNA017487


title: UPN827 cells, TN505 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN505 TrailNet Baseline T1D plasma


title: WT_PN3_RNA-seq_r2

description:
Library name: Sample7
WT PN3 RNA-seq replicate2


title: S3026

city: Ann Arbor

first: Adam

last: Abraham

state: MI

address: 2800 Plymouth Rd

department: Orthopaedic Surgery

institute: University of Michigan

description:
Library name: 9S
Column name in TENDONseq__counts.tsv: S3526

data_processing:
The reads were trimmed using Cutadapt v2.3
FastQC v0.11.8 was used to ensure the quality of data
Fastq Screen v0.13.0 was used to screen for various types of contamination
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a  and assigned count estimates to genes with RSEM v1.3.3.  Alignment options followed ENCODE standards for RNA-seq.
Assembly: hg38
Supplementary files format and content: tab delimited text file includes raw counts for each sample

source_name: Tendon

extract_protocol:
RNA extraction was performed using RNeasy Mini Fibrous Tissue Kit with on-column deoxyribonuclease I treatment according to manufacturer’s instructions
The NEBNext Ultra II RNA Library Preparation for Illumina Kit was used to prepare the samples for sequencing following the manufacturer protocol.

value: Tendon

value: T


title: WT_PN3_RNA-seq_r1

description:
Library name: Sample6
WT PN3 RNA-seq replicate1


title: T2697

description:
Library name: 7T
Column name in TENDONseq__counts.tsv: T2697

value: H


title: UPN827 cells, TN504 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN504 TrailNet Baseline T1D plasma


title: UPN827 cells, TN503 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN503 TrailNet Baseline T1D plasma


title: PVT1_C_LP4

description: Library name: RNA017485


title: KO_MII_RNA-seq_r2

description:
Library name: Sample5
KO MII RNA-seq replicate2

source_name: MII oocytes

value: MII oocytes


title: T3704

description:
Library name: 6T
Column name in TENDONseq__counts.tsv: T3704


title: UPN827 cells, TN501 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN501 TrailNet Baseline T1D plasma

value: UPN827 cells


title: KO_MII_RNA-seq_r1

description:
Library name: Sample4
KO MII RNA-seq replicate1

value: Smarca4 KO


title: T3078

description:
Library name: 5T
Column name in TENDONseq__counts.tsv: T3078


title: PVT1_A_LP4

description: Library name: RNA017483


title: WT_MII_RNA-seq_r3

description:
Library name: Sample3
WT MII RNA-seq replicate3


title: T3094

description:
Library name: 4T
Column name in TENDONseq__counts.tsv: T3094


title: UPN827 cells, TN500 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN500 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: UPN827 cells, TN499 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN499 TrailNet Baseline T1D plasma


title: NT_B_LP3

description: Library name: RNA017482

value: NT


title: WT_MII_RNA-seq_r2

description:
Library name: Sample2
WT MII RNA-seq replicate2


title: NT_A_LP3

description: Library name: RNA017481


title: WT_MII_RNA-seq_r1

description:
Library name: Sample1
WT MII RNA-seq replicate1


title: UPN827 cells, TN498 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN498 TrailNet Baseline T1D plasma


title: T0887

description:
Library name: 3S
Column name in TENDONseq__counts.tsv: S0889


title: UPN827 cells, TN497 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN497 TrailNet Baseline T1D plasma


title: Mock_B_LP3

description: Library name: RNA017480

value: Mock


title: EDS615, ltv1∆/ltv1∆, experimental, replicate 3

city: Highland Heights

first: Erin

last: Strome

state: KY

address: Nunn Drive, Northern Kentucky University

department: Department of Biological Sciences

institute: Northern Kentucky University

description: Library name: ES615_LTV1_KO_Rep3

data_processing:
FASTQ files were processed using the nf-core/rnaseq v3.11.1 pipeline. Quality control was performed with FastQC, adapters trimmed using Trim Galore, and reads aligned with STAR to the Saccharomyces cerevisiae S288C reference genome (R64-1-1, GCA_000146045.2). Transcript quantification was performed using Salmon, and gene-level counts were summarized using tximport. Differential expression analysis was conducted with DESeq2 (v1.34.0, R v4.1.3). Genes with adjusted p-value (FDR) < 0.05 and |log2 fold change| > 0.58 were considered significantly differentially expressed.
Assembly: Saccharomyces cerevisiae S288C, R64-1-1 (GCA_000146045.2)
Supplementary files format and content: FASTQ files were processed using the nf‑core/rnaseq pipeline (v3.11.1). Quality control was performed with FastQC, adapters trimmed with Trim Galore, and reads aligned using STAR against the Saccharomyces cerevisiae S288C reference genome. Quantification was conducted using Salmon with tximport summarization at the gene level. Differential expression analysis was performed with DESeq2 (v1.34.0, R v4.1.3). Genes with adjusted p‑value (FDR) < 0.05 and |log2 fold change| > 0.58 were considered significantly differentially expressed.

organism: Saccharomyces cerevisiae S288C

growth_protocol: Yeast were grown in 8ml of YPD overnight with agitation at 30°C and harvested at mid-exponential phase (OD600 0.5-0.6).

extract_protocol:
RNA was extracted using the hot phenol method. Cells were grown to mid-exponential phase (OD600 0.5–0.6), pelleted, washed twice with ddH2O, and stored at -80°C. Pellets were resuspended in buffer (50 mM sodium acetate, 10 mM EDTA, 1% SDS, pH 5.2), mixed with hot phenol (65°C), vortexed, incubated at 65°C for 5 min with periodic inversion, and centrifuged at 15,000 x g for 5 min. Aqueous phase was collected and re-extracted with phenol:chloroform, followed by ethanol precipitation, 70% ethanol washes, air-drying, and resuspension in RNase-free water. RNA quality and concentration were checked by OD260/280 and 1% agarose gel electrophoresis.
Batch-Tag-Sequencing (Batch-Taq-Seq) libraries were prepared at the UC Davis Genome Center with inline UMIs and sample indexes for multiplexing. Sequencing used single-end 84–90 cycle chemistries on NextSeq 500 instruments, generating ~3–6 million reads per sample. The core returned only reads passing Illumina quality filters.


title: UPN827 cells, TN496 TrailNet Baseline T1D plasma

city: Milwaukee

source_name: UPN827 cells stimulated with TN496 TrailNet Baseline T1D plasma


title: T3074

description:
Library name: 2T
Column name in TENDONseq__counts.tsv: T3674


title: Mock_A_LP3

city: Ghent

description: Library name: RNA017479


title: EDS615, ltv1∆/ltv1∆, experimental, replicate 2

description: Library name: ES615_LTV1_KO_Rep2


title: UPN827 cells, TN495 TrailNet Baseline T1D plasma

description: Gene expression data from UPN827 cells stimulated with T1D plasma

source_name: UPN827 cells stimulated with TN495 TrailNet Baseline T1D plasma


title: PoolCTL_B_LP3

description: Library name: RNA017478

value: PoolCTL


title: T1435

description:
Library name: 1T
Column name in TENDONseq__counts.tsv: T1435


title: UPN827 cells, TN494 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN494 TrailNet Baseline T1D plasma


title: EDS615, ltv1∆/ltv1∆, experimental, replicate 1

description: Library name: ES615_LTV1_KO_Rep1


title: PoolCTL_A_LP3

description: Library name: RNA017477


title: EDS76, wildtype, control, replicate 3

description: Library name: ES76_WT_Rep3

value: WT


title: UPN827 cells, TN493 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN493 TrailNet Baseline T1D plasma


title: GAL4_B_LP3

description: Library name: RNA017476


title: S2929

description:
Library name: 15S
Column name in TENDONseq__counts.tsv: S2929


title: UPN827 cells, TN492 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN492 TrailNet Baseline T1D plasma


title: S2892

description:
Library name: 14S
Column name in TENDONseq__counts.tsv: S2892


title: GAL4_A_LP3

description: Library name: RNA017475


title: S2912

description:
Library name: 13S
Column name in TENDONseq__counts.tsv: S2912


title: UPN827 cells, TN491 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN491 TrailNet Baseline T1D plasma


title: S3027

description:
Library name: 10S
Column name in TENDONseq__counts.tsv: S3527


title: UPN827 cells, TN490 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN490 TrailNet Baseline T1D plasma


title: scRNA-Seq of impact of HIV on latent TB infection in a rhesus macaque model of Mtb/SIV co-infection [35974_N]

city: SAN ANTONIO

first: YI

last: ZOU

state: TX

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mmul10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Macaca mulatta

source_name: BAL cells

extract_protocol:
BAL was performed with 80 mL of sterile saline in BSL3 on NHPs at weeks 5, 11, 15 and necropsy after Mtb infection. The BAL was filtered, centrifuged (1,200 rpm, 10 min at 4C), lysed for red blood cells (RBCs) using ACK lysis buffer (GibcoTM) and resuspended in 2 mL final volume of RPMI 1640 media (GibcoTM). The cells were counted and stored in internally threaded cryovials in liquid nitrogen for downstream scRNA-seq processing using 10x Genomics platform.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Target about 5-10K cells per sample.

treatment_protocol: Coinfected NHPs received a drug regimen consisting of 20 mg/kg of (R)-9-(2-phosphonylmethoxypropyl) adenine (PMPA, tenofovir, Gilead Sciences), 30 mg/kg of 2′,3′-dideoxy-5-fluoro-3′-thiacytidine (FTC, emtricitabine, Gilead Sciences), and 2.5 mg/mL of the integrase inhibitor DTG (ViiV Healthcare).

value: BAL cells

tag: time point

value: necropsy, end point

value: 4.40 years


title: UPN827 cells, TN489 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN489 TrailNet Baseline T1D plasma


title: scRNA-Seq of impact of HIV on latent TB infection in a rhesus macaque model of Mtb/SIV co-infection [35974_wk15]

description: 10x Genomics


title: Healthy quadricep biopsy

city: Lexington

first: Alexander

middle: Romano

last: Keeble

address: 900 S Limestone st

institute: Northwestern University

description: Input

data_processing:
The single-end 75-nt sequence reads were mapped to the GRCh38/hg38 genome using the Burrows-Wheeler Aligner (BWA) algorithm with default settings. Only reads that passed Illumina’s purity filter, aligned with no more than 2 mismatches, and mapped uniquely to the genome were used in the subsequent analysis. In addition, duplicate reads were removed. Peak calling was completed using MACS2 to identify significant enrichments in the ChIP data file from each condition when compared to the Input data file
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Skeletal muscle

extract_protocol:
DNA was prepared for sequencing using the ChIP-IT ChIP-seq kit
Immunoprecipitation was achieved using 4 µl of anti-HDAC4 antibody against 8 µg of chromatin for immunoprecipitation. The resultant DNA was prepared for sequencing using the ChIP-IT ChIP-seq kit (Active Motif).

value: Skeletal muscle

tag: antibody

value: input


title: DPH1_B_LP3

description: Library name: RNA017472

value: embryonic kidney cell


title: scRNA-Seq of impact of HIV on latent TB infection in a rhesus macaque model of Mtb/SIV co-infection [35974_wk11]

description: 10x Genomics


title: ACL injured post recon quadricep biopsy


title: DPH1_A_LP3

description: Library name: RNA017471


title: UPN827 cells, TN487 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN487 TrailNet Baseline T1D plasma

tag: responder cells


title: ACL injured quadricep biopsy


title: UPN827 cells, TN486 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN486 TrailNet Baseline T1D plasma

tag: sample timepoint


title: NORAD_D_LP3

description: Library name: RNA017470

tag: cell line

value: NORAD


title: UPN827 cells, TN485 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN485 TrailNet Baseline T1D plasma


title: EDS76, wildtype, control, replicate 1

description: Library name: ES76_WT_Rep1


title: scRNA-Seq of impact of HIV on latent TB infection in a rhesus macaque model of Mtb/SIV co-infection [34741_N]

description: 10x Genomics

tag: cell type

value: 5.30 years


title: ACL non injured quadricep biopsy


title: Human Erythroid cells,DZNep, Day11

city: zhengzhou

first: Hengchao

state: Henan

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

institute: zzu

description:
scRNA_human_DNZep
10x Genomics

data_processing:
After obtaining the expression matrix through the Cellranger software, low-quality cells were filtered, and PCA was applied for dimensionality reduction of the highly variable gene expression matrix. Using a graph-based clustering algorithm, the clustering results were also visualized with UMAP in two dimensions. Cell annotation was followed using the R package SingleR version 2.5.0 (https://bioconductor.org/packages/devel/bioc/html/SingleR.html). Cells of interest were selected for subset analysis. Next, single-cell trajectory analysis was performed using the R package Monocle3 version 1.3.1 (https://bioconductor.org/packages/ devel/bioc/html/monocle.html).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cord blood

growth_protocol: CD34+ cells were puriﬁed from cord blood by positive selection using the magnetic-activated cell sorting magnetic beads system, according to the manufacturer’sinstructions. The purity of isolated CD34+ cells was 95% to 98%. The cell culture procedure was comprised of 3 phases. Composition ofthe base culture medium was Iscove’sModiﬁed Dulbecco’s Medium, 2%human peripheral blood plasma, 3% human AB serum, 200 mg/mL Holo-human transferrin, 3 IU/mL heparin, and 10 mg/mL insulin. In the ﬁrst phase(day 0 to day 6), CD34+ cells at a concentration of 105/mL were cultured inthe presence of 10 ng/mL stem cell factor, 1 ng/mL IL-3, and 3 IU/mL erythropoietin. In the second phase (day 7 to day 11), IL-3 was omitted from the culture medium. In the third phase that lasted until day 21, the cell concentration was adjusted to 106/mL on day 11 and to 5 3 106/mL on day 15, respectively, the medium for this phase was the base medium plus 3 IU/mL erythropoietin, and the concentration of transferrin was adjusted to 1mg/mL. The cells were cultured at 37°C in the presence of 5% CO2.

extract_protocol:
Adherent and suspended cells were collected after treatment with 0.5μM DZNep and used for single-cell suspension preparation and quality inspection.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Here, we set 0.5μM DZNep dosing which was an inhibitor of AHCY to inhibit AHCY activity. After treated with 0.5μM DZNep for four days, we performed a scRNA sequencing of DMSO and DZNep treated cells.

value: Cord blood

value: Erythroid cells

value: DZNep 0.5μM


title: UPN827 cells, TN484rehyb TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN484rehyb TrailNet Baseline T1D plasma

value: UPN827 cells


title: scRNA-Seq of impact of HIV on latent TB infection in a rhesus macaque model of Mtb/SIV co-infection [34741_wk15]

description: 10x Genomics


title: NORAD_B_LP3

description: Library name: RNA017468

tag: genotype


title: scRNA-Seq of impact of HIV on latent TB infection in a rhesus macaque model of Mtb/SIV co-infection [34741_wk11]

description: 10x Genomics


title: UPN827 cells, TN483 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN483 TrailNet Baseline T1D plasma

value: TrailNet Baseline


title: UPN827 cells, TN482 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN482 TrailNet Baseline T1D plasma


title: scRNA-Seq of impact of HIV on latent TB infection in a rhesus macaque model of Mtb/SIV co-infection [34741_wk5]

description: 10x Genomics


title: S4_biorep2_techrep1

city: Palo Alto

first: Reema

last: Baskar

address: 3373 Hillview Ave

institute: Stanford University

data_processing:
FASTQ files from Illumina nextseq runs were obtained from primer de-barcoding using the bcl2fastq2 application. Else, they were obtained directly from novogene sequencing service. FASTQ files were input into pepATAC pipeline to check sequencing quality (fastqc), trim (Skewer), and align (bowtie2) to the hg38 genome for cell line data and hg19 for BM and BALL data. Duplicated reads were marked and removed using Picard MarkDuplicates tool. Peaks were called using MACS2 under parameters ‘-q 0.01 ‐‐shift 0 –nomodel’. The signal-to-noise ratio between transcription start sites and flanking regions was calculated and plotted to check data quality. All samples had TSS scores of 10 and above, as well as expected fragment length distributions as plotted for all 3 sequencing experiments with 2 technical and 2 biological replicates each.
Consensus bed file was created for each experiment across technical and biological replicates using Chraccr package. Exact code in github and zenodo as referred to in paper.
Assembly: hg19
Supplementary files format and content: Peak set output from pepATAC pipeline (bed file format)
Library strategy: InTAC-seq (variation of ATAC-seq)

source_name: Bone marrow

growth_protocol: After BM processing and lineage depletion as described in paper methods section, 1 million BMMC from 2 separate donors were washed and resuspended in PBS. Cells were stained with LIVE/DEAD Aqua kit (Invitrogen, #L34965) and incubated at RTP for 30 min protected from light. Cells were then washed and pelleted before resuspending in 100ul of PBS with Human TruStain Fc blocker (Biolegend, #422302) for 10min at RTP. Cells were then incubated with our surface marker antibody cocktail for 30min in dark and on ice (Table S5). Wash cells with 2ml CSM at 300G for 10min. Fix cells with 1.6% paraformaldehyde in PBS for 5min at RTP. Wash cells twice with 1X permeabilization buffer (from eBioscience Foxp3/Transcription Factor staining buffer set, #00-5523-00) at 600G for 5min. Add intracellular marker (TdT) into cells resuspended in 100ul of 1X permeabilization buffer and incubate for 45min at RTP. Wash cells with CSM at 600G for 5min. Cells were filtered for clumps before sorting. Cells were then washed and resuspended in 1ml CSM for FACS sorting. Cells were gated for cell size and viability on Aqua before defined epigenetic switch point populations were sorted.

extract_protocol:
Sorted cells were counted and split into 50K cells per replicate, including live, unsorted control. Samples were then processed using the InTAC-seq protocol. Briefly, cells were washed once with cold PBS at 300G for 5 minutes and then once with cold PBS+0.1% Tween-20 at 300G for 5 minutes. Transposition and lysis were carried out in 1 step with each sample cell pellet being suspended with 25ul 2x TD buffer, 2.5ul Tn5 enzyme, 0.5ul 1% digitonin, 0.5ul of 10% NP40 and 21.5ul of nuclease-free water. Cell suspensions were incubated at 37C for 30 minutes on a shaker at 800RPM. After transposition, 50ul of 2X reverse crosslinking buffer (100mM N,N-Dimethylethylenediamine, pH 6.5 (Sigma Aldrich D158003), 2% SDS, 1ul Proteinase K (NEB #P8107S) in nuclease-free water) was added to cells with an overnight incubation at 37C on a shaker at 800RPM.
DNA extracted from samples using QIAGEN MiniElute PCR purification columns and subsequent library preparation and next-generation sequencing were carried out as previously described in the InTAC-seq paper and this protocol is optimized from the published InTAC-seq method. For the preparation of live ATAC-seq samples from fresh cells as a comparison, samples were prepared as above, except DNA was purified immediately after transposition rather than performing crosslink reversal.

value: Bone marrow

value: Developing B cell


title: LINC01508_1_D_LP3

description: Library name: RNA017466

tag: treatment


title: S0864

description:
Library name: 16S
Column name in TENDONseq__counts.tsv: S0864

source_name: Tendon

value: Tendon

value: T

tag: batch


title: UPN827 cells, TN481 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN481 TrailNet Baseline T1D plasma


title: NORAD_A_LP3

description: Library name: RNA017467


title: EDS76, wildtype, control, replicate 2

description: Library name: ES76_WT_Rep2

value: WT


title: scRNA-Seq of impact of HIV on latent TB infection in a rhesus macaque model of Mtb/SIV co-infection [33994_N]

description: 10x Genomics

value: BAL cells

value: necropsy, end point

value: 7.00 years


title: S2_biorep2_techrep2

tag: tissue


title: NEAT1_B_LP3

description: Library name: RNA017474


title: LINC01508_1_C_LP3

description: Library name: RNA017465


title: UPN827 cells, TN479 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN479 TrailNet Baseline T1D plasma


title: S2_biorep2_techrep1


title: NEAT1_A_LP3

description: Library name: RNA017473


title: LINC01508_1_B_LP3

description: Library name: RNA017464


title: UPN827 cells, TN478 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN478 TrailNet Baseline T1D plasma


title: scRNA-Seq of impact of HIV on latent TB infection in a rhesus macaque model of Mtb/SIV co-infection [33994_wk11]

description: 10x Genomics

tag: age


title: S2_biorep1_techrep2


title: LINC01508_1_A_LP3

description: Library name: RNA017463


title: UPN827 cells, TN477 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN477 TrailNet Baseline T1D plasma


title: scRNA-Seq of impact of HIV on latent TB infection in a rhesus macaque model of Mtb/SIV co-infection [33994_wk5]

description: 10x Genomics


title: S2_biorep1_techrep1


title: MIR503HG_D_LP3

description: Library name: RNA017462


title: UPN827 cells, TN476 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN476 TrailNet Baseline T1D plasma


title: scRNA-Seq of impact of HIV on latent TB infection in a rhesus macaque model of Mtb/SIV co-infection [33343_N]

description: 10x Genomics

source_name: BAL cells

value: 6.30 years


title: S1_biorep2_techrep2


title: MIR503HG_C_LP3

description: Library name: RNA017461

value: embryonic kidney cell


title: scRNA-Seq of impact of HIV on latent TB infection in a rhesus macaque model of Mtb/SIV co-infection [35974_wk5]

description: 10x Genomics

value: 4.40 years


title: scRNA-Seq of impact of HIV on latent TB infection in a rhesus macaque model of Mtb/SIV co-infection [33343_wk15]

description: 10x Genomics


title: S1_biorep2_techrep1


title: UPN827 cells, TN475 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN475 TrailNet Baseline T1D plasma


title: MIR503HG_B_LP3

description: Library name: RNA017460


title: scRNA-Seq of impact of HIV on latent TB infection in a rhesus macaque model of Mtb/SIV co-infection [33343_wk11]

description: 10x Genomics


title: MIR503HG_A_LP3

description: Library name: RNA017459


title: S1_biorep1_techrep2


title: UPN827 cells, TN474 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN474 TrailNet Baseline T1D plasma


title: scRNA-Seq of impact of HIV on latent TB infection in a rhesus macaque model of Mtb/SIV co-infection [33343_wk5]

description: 10x Genomics


title: UPN827 cells, TN473RH2 TrailNet Baseline T1D plasma

source_name: UPN827 cells stimulated with TN473RH2 TrailNet Baseline T1D plasma


title: scRNA-Seq of impact of HIV on latent TB infection in a rhesus macaque model of Mtb/SIV co-infection [33994_wk15]

description: 10x Genomics


title: S1_biorep1_techrep1


title: LINC01399_1_D_LP3

description: Library name: RNA017458


title: NORAD_C_LP3

description: Library name: RNA017469

value: NORAD


title: GMB7-1_GMB6_Hypoxia treated

city: Sharjah

first: Rifat

last: Hamoudi

state: Sharjah

address: M32 Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, , Sharjah

department: Clinical Sciences

country: United Arab Emirates

institute: University of Sharjah

description:
Library name: GMB6_HI.bam
GMB_HI.txt

data_processing:
RNA-seq data analysis was performed using the Torrent Mapping Alignment Program (TMAP) (https://github.com/iontorrent/TMAP). Alignment of the raw sequencing reads generated by the Ion Torrent sequencing data against reference sequence derived from the hg19 (GRCh37) assembly was carried out using nested alignment. Each of the short alignment algorithm generates contigs of certain size which is then passed to the next alignment algorithm generating longer contigs and eventually applying de novo alignment using SMEM algorithm. Raw read counts of the targeted genes were extrapolated using samtools (samtools view –c –F 4 –L bed_file bam_file). RNA-seq data was normalized using Fragments Per Kilobase Million (FPKM) normalization prior to quality control check. Differentially expressed gene (DEGs) analysis was performed using DESeq2.
Assembly: GRCh37 (hg19)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: RCNSi003-A (RRID:CVCL_E4ER)

extract_protocol:
RNA were isolated  from GMB7-1 organoids in healthy and hypoxia-treated conditions. Three sample from each group were used. For gene expression analysis, the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit was utilized, enabling the simultaneous measurement of over 20,000 human RefSeq genes.
Genomic DNA removal from RNA samples was ensured by treating the RNA with Turbo DNase (ThermoFisher Scientific, USA). Next, whole transcriptome sequencing was performed using targeted RNA-Seq with Ion AmpliSeq whole transcriptome human gene expression kit (ThermoFisher Scientific, USA). Briefly, cDNA was synthesized using a SuperScript VILO cDNA Synthesis kit (ThermoFisher Scientific, USA) and amplified using Ion AmpliSeq human gene expression core panel primers. The amplified products were subjected to enzymatic shearing to get amplicons of ~200 bp, then ligated with the adapter and the unique barcodes. Next, the constructed library was purified using Agencourt AMPure XP Beads (Beckman Coulter, USA), quantified using an Ion Library TaqMan™ quantitation kit (Applied Biosystems, USA), further diluted to 100 pM, and pooled equally with 16 individual samples. The diluted library was amplified and enriched in Ion Chef System (ThermoFisher Scientific) according to the manufacturer’s instructions. Ion 540 Chip was used to sequence the prepared template libraries using an Ion S5 XL Semiconductor sequencer (ThermoFisher Scientific).

treatment_protocol: Hypoxia treated cell lines were exposed to 1% oxygen for 24h followed by 24h of normoxia step (reoxygenation). Healthy cell line were kept at normoxic condition.

value: RCNSi003-A (RRID:CVCL_E4ER)

value: Human induced pluripotent stem cell (hiPSC)


title: LSP_biorep2_techrep2