title: POOL1_S1

description:
CRISPR-seq
MUCIG_pools_readCounts.txt.gz

library_source: other

data_processing:
*library strategy: CRISPR-seq
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 with --expect-cells=5000 --nosecondary commands. Raw paired-end fastq read files were filtered and demultiplexed using Cutadapt. Raw fastq read files were then trimmed to the 23 bp sgRNA spacer sequences. The 23 bp sgRNA spacer sequences from each demulitplexed sample were mapped the sgRNA spacers to the custom library using Bowtie 1.3.1. Using the resultant mapping output, we quantitated the number of reads that had mapped to each sgRNA within the library.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

molecule: other

organism: synthetic construct

source_name: plasmid

extract_protocol:
Single-cell suspensions from tumor were collected. The cells were labeled with an antimouse-CD45-Percp/Cy5.5 antibody and a live/dead dye. FACS-sorted cells were gated on CD45+ live cells. Sorted cells from 5 mice were combined and were washed with PBS, and cell numbers and viabilities were assessed by trypan blue staining. The 10,000 CD45+ cells isolated from the lung were used for scRNA-seq library prep. The MUCIG pool plasmids were extratced by the Takara Maxi-prep kit.
scRNA-seq library prep was  following the protocol from 10x Genomics Chromium Next GEM Single Cell 5’ Reagent Kits V2. The sgRNA library readout was performed using readout PCR strategy

value: plasmid


title: BALF1_TCR

status: Public on Dec 05 2024

type: SRA

city: Columbia

first: John

last: Driver

state: MO

address: 1201 Rollins Street

country: USA

institute: University of Missouri

library_source: transcriptomic

data_processing:
The gene matrix data was obtained using Cell Ranger (v8.0.0).
Assembly: Sscrofa 11.1
Supplementary files format and content: matrix files, and fasta files

molecule: total RNA

organism: Sus scrofa

source_name: Lung

extract_protocol:
Approximately 1 g of tissue collected from the left cranial, middle, and caudal lung lobes, were combined, and then digested with 2.5 mg/mL of Liberase TL (Roche, Indianapolis, IN) in Dulbecco’s Modified Eagle Medium (Thermo Fisher, Waltham, MA) at 37oC for 45 minutes. The digested tissue was dispersed into single cells as previously described30, and then passed through a 70 um cell strainer (Thermo Fisher, Waltham, MA). Cells were immediately cryopreserved in freezing media (90% FBS 10% dimethylsulfoxide (DMSO)) in temperature-controlled freezing containers at 3 x 107 cells per/mL and stored at -80oC until use. To obtain T cells from lung washes, lavage fluid was filtered first through a 70 m cell strainer (Thermo Fisher, Waltham, MA) and then a 40 um pipette tip cell strainer, washed in RPMI medium with 10 % FBS, counted, stained with PE-Cy7-conjugated anti-porcine CD3 antibody. live CD3 positive cells were sorted.
All samples underwent cDNA amplification upon which cDNA concentration and quality were assessed using a Fragment Analyzer 5200 (Agilent, Santa Clara, CA). V(D)J libraries were constructed using pig-specific primers for two successive enrichments of TCR and BCR transcripts.
scRNA-seq, scTCR-seq, and scBCR-seq

tag: tissue

value: Lung

tag: cell line

value: leucocytes

tag: cell type


title: Cas13d_Cd274-1

city: New Haven

first: Chuanpeng

last: Dong

state: CT

address: 850 West Campus Dr

department: Genetics

institute: Yale University School of Medicine

description: Library name: 3_1

data_processing:
FASTQ files were aligned to the mouse reference genome GRCm39 (version Ensembl 112) by STAR 2.7.10b . Reads mapped to each gene were counted using STAR --quantMode.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include read counts for each Sample

organism: Mus

extract_protocol:
RNA was  extracted by TRIZOL.
The RNA sequencing library was prepared using the NEBNext polyA mRNA isolation kit and NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina

value: Breast cancer

tag: treatment

tag: batch


title: FLU2_T2_TCR


title: FLU1_T2_TCR


title: Cas13d_Scramble-3

description: Library name: 2_3

value: Scramble


title: Cas13d_Scramble-2

description: Library name: 2_2


title: FLU2_T2_GEX


title: BALF1_GEX


title: Cas13d_Scramble-1

description: Library name: 2_1


title: Cas13d_Vec-3

description: Library name: 1_3

value: Vector


title: FLU1_T2_GEX


title: Cas13d_Lgals3-2

description: Library name: 5_2


title: FLU2_T1_TCR


title: FLU2_T1_GEX


title: FLU1_T1_TCR


title: H6013 Cells, H2073 EVs, Rep 2

city: Vancouver

first: Cathie

last: Garnis

state: BC

address: 675 West 10th Avenue

department: Integrative Oncology

country: Canada

institute: British Columbia Cancer Research Centre

description: column 9 in in raw count matrix from featureCounts and ComBat_seq

data_processing:
Sequencing was performed on the Illumina NextSeq2000 with Paired End 59bp × 59bp reads.
Sequencing data was demultiplexed using Illumina's BCL Convert
De-multiplexed read sequences were then aligned to the Homo sapiens (hg38 no Alts, with decoys) /Mus Musculous (mm10) reference sequence using DRAGEN RNA app on Basespace Sequence Hub
Differential expression analysis was performed using DESeq2 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html) in R.
Assembly: Homo sapiens (UCSC hg38)
Supplementary files format and content: DESeq2 differential analysis results files for each treatment type compared to cells treated with PBS as a control

organism: Homo sapiens

growth_protocol: Cells were cultured on coated surfaces using  gelatin (Cell Biologics Cat # 6950) and in complete Fibroblast Medium (Cell Biologics Cat # M2267) supplemented with 5% FBS. The H6013s were used for no more than passage ten. All cells were cultured in a 37oC, 5% CO2 incubator

extract_protocol:
Qiagen miRNeasy Mini Kit
Standard protocol for the Illumina Stranded mRNA prep (Illumina)

treatment_protocol: H6013 were seeded in twenty four well plates with 1 ml of media until reaching 15% confluency. EVs isolated from lung cancer cell lines were added to the culture media (7.13x1011 EV particles per well per day). To the PBS control, 131 µl of PBS was added per well  and to the TGFβ control, 10 ng/well of TGF-beta 1 protein with carrier  (R&D systems, final concentration 20 ug/mL after reconstitution) resuspended in 131 ul PBS was added per well. For samples co-cultured with EVs, a quarter of the media was replaced per well with EV supplemented fresh media at 24 hours (7.13x1011 EV particles per well), EVs resuspended in 131 ul PBS are added at 48 hours and 72 hours (7.13x1011 EV particles per wel) after the first EV incubation. PBS control wells were replaced with 250 ul/well of PBS-supplemented fresh media at same first time point and 131 ul of PBS was added at 48 hours and 72 hours. For the TGFβ control, 10 ng/well TGFβ (final concentration 10 ng/ml) was supplemented in 250 ul/well of fresh media at the same first time point and then TGFB resuspended in 131 ul PBS is added  as H6013 co-cultured with EVs in the second and third time points. EVs, PBS, or TGFβ was thus added three times with 24 hour intervals in between and they were left to incubate an extra day with no additions (total time of co-culture: 96 hours).

value: fibroblast

value: H2073 Evs


title: Cas13d_Vec-1

description: Library name: 1_1


title: Cas13d_Vec-2

description: Library name: 1_2


title: H6013 Cells, H1437 EVs, Rep 2

description: column 7 in in raw count matrix from featureCounts and ComBat_seq

value: H1437 Evs


title: H6013 Cells, H2073 EVs, Rep 1

description: column 8 in in raw count matrix from featureCounts and ComBat_seq


title: FLU1_T1_GEX


title: H6013 Cells, H1437 EVs, Rep 1

description: column 6 in in raw count matrix from featureCounts and ComBat_seq


title: KO_Two_BCR_3


title: BALF2_TCR


title: KO_Two_TCR_3


title: H6013 Cells, TGFB, Rep 2

description: column 5 in in raw count matrix from featureCounts and ComBat_seq

value: TGFB


title: KO_Two_BCR_2


title: KO_Two_TCR_2


title: H6013 Cells, PBS, Rep 2

description: Used as the comparator in the differential analysis in each treatment, each processed data; column 3 in raw count matrix from featureCounts and ComBat_seq

value: PBS (Control)


title: KO_Two_GEX_2


title: KO_One_BCR_3


title: KO_One_TCR_3


title: KO_Two_BCR_1


title: KO_One_GEX_3


title: Het_One_TCR_3


title: Patus_8988s_MEKi

city: Verona

first: Davide

last: Pasini

state: VR

address: Piazzale Ludovico Antonio Scuro 10

country: Italy

institute: University of Verona

description:
Patus_8988s_T2
counts_human_cl.tsv

data_processing:
Reads were aligned to the GRCh38 genome using STAR v2.7 and expression quantification were performed with RSEM
Assembly: GRCh38
Supplementary files format and content: tab-delimited file containing raw counts for each sample

molecule: polyA RNA

extract_protocol:
RNA were isolated using the TRIzol® Reagent (Life Technologies), followed by the column based PureLink RNA Mini Kit (Thermo Fisher Scientific). Purified RNA quality was evaluated using RNA 6000 Nano kit on a Bioanalyzer 2100 (Agilent) and only RNA with an RNA Integrity Number (RIN) greater than 7.5 were used.
RNA-seq library were obtained using poly(A) enrichment with TrueSeq Stranded mRNA Library Prep kit (Illumina).

tag: read length

value: 75 bp

value: Trametinib


title: Patus_8988s_vehicle

description:
Patus_8988s_V2
counts_human_cl.tsv

value: vehicle


title: Panc1_vehicle

description:
Panc1_V2
counts_human_cl.tsv


title: Hs766t_Meki

description:
Hs766t_T2
counts_human_cl.tsv


title: Panc1_MEKi

description:
Panc1_T2
counts_human_cl.tsv


title: Het_One_GEX_3


title: Miapaca_MEKi

description:
Miapaca_T2
counts_human_cl.tsv

source_name: Miapaca

value: Miapaca


title: Het_Two_BCR_3


title: H6013 Cells, TGFB, Rep 1

description: column 4 in in raw count matrix from featureCounts and ComBat_seq


title: H6013 Cells, PBS, Rep 1

description: Used as the comparator in the differential analysis in each treatment, each processed data; column 2 in raw count matrix from featureCounts and ComBat_seq


title: KO_Two_TCR_1


title: Miapaca_vehicle

description:
Miapaca_V2
counts_human_cl.tsv


title: KO_Two_GEX_1


title: Hpaf_II_MEKi

description:
Hpaf_II_T2
counts_human_cl.tsv


title: Het_One_BCR_3


title: hF2_vehicle

description:
hF2_V2
counts_human_cl.tsv


title: KO_Two_GEX_3


title: Het_Two_TCR_3


title: Hpaf_II_vehicle

description:
Hpaf_II_V2
counts_human_cl.tsv


title: Suit2_vehicle

description:
Suit2_V2
counts_human_cl.tsv


title: Het_Two_GEX_3


title: Suit2_MEKi

description:
Suit2_T2
counts_human_cl.tsv


title: Hs766t_vehicle

description:
Hs766t_V2
counts_human_cl.tsv


title: hF2_MEKi

description:
hF2_T2
counts_human_cl.tsv


title: Colo357_vehicle

description:
Colo357_V2
counts_human_cl.tsv


title: Het_Two_TCR_2


title: Colo357_MEKi

description:
Colo357_T2
counts_human_cl.tsv


title: Het_Two_BCR_1


title: Bxpc3_vehicle

description:
Bxpc3_V2
counts_human_cl.tsv


title: Aspc1_MEKi

description:
Aspc1_T2
counts_human_cl.tsv


title: Aspc1_vehicle

description:
Aspc1_V2
counts_human_cl.tsv


title: Het_One_TCR_2


title: Het_Two_GEX_1


title: Het_One_GEX_2


title: Het_One_BCR_2


title: PDAC3_C1

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequence were aligned to GRCh38 genome to gene expression count using Space Ranger's default settings
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz : list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of genes ID
Supplementary files format and content: matrix.mtx.gz: gene expression count data
Supplementary files format and content: aligned_fiducials.jpg : aligned fiducial of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spot
Supplementary files format and content: scalefactors.json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png : hi-res image of the tissue
Supplementary files format and content: tissue_lowres_image.png : low-res image of the tissue
Supplementary files format and content: tissue_position_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial transcriptomics

source_name: PDAC

extract_protocol:
Surgical resected  FFPE samples. Section (thickness=5μm) from each sample were used
visium ffpe v2

value: PDAC

tag: tissue preparation

value: Paraffin embedded


title: Het_Two_BCR_2


title: PDAC4_D1


title: Bxpc3_MEKi

description:
Bxpc3_T2
counts_human_cl.tsv


title: PDAC2_B1


title: PDAC1_A1


title: Het_One_BCR_1


title: KO_One_GEX_2


title: PBMCs, Cov-43

city: Tampa

first: Theodoros

last: Karampitsakos

address: 560 Channelside D

institute: University of South Florida

description:
Covid19 library
Cov-43

library_source: transcriptomic single cell

data_processing:
scRNA-seq feature count matrices were constructed using Cell Ranger (v7.1.0), aligning reads to 165 the GRCh38 2020 reference genome. Subsequent quality control and data processing were performed with 166 the Seurat package (v4.3.0)
Assembly: Cells with less than 200 detected genes were discarded, as well as cells with more than 15% mitochondrial genes. DropletUtils (v1.14.2) identified empty droplets, while doublets were detected using Scrublet (v0.2.3-0). DecontX was used to detect ambient RNA contamination. Subsequently, we excluded identified empty droplets, doublets, and those with a contamination score above 0.2, alongside cells with more than 9 UMIs mapping to the hemoglobin subunit beta (HBB) gene (representing red blood cells) for further analysis. For cell type annotation, we used SCTransform for data normalization and identification of variable features. This was followed by principal component analysis (PCA) and batch effect correction using Harmony. Graph-based clustering and UMAP embedding were generated based on Harmony embeddings. Cell types were assigned to each cluster guided by canonical marker gene expression. For cell type proportions analysis, we normalized the number of cells within a given cell type by the total number of cells per subject. For Differentially Expressed Gene (DEG) analysis, we used the Seurat software (v4.3.0) “FindMarkers" function to identify differentially expressed DEGs across disease groups.
Supplementary files format and content: Tab separated values and matrix files (samples Clinic-10 and Clinic-13 not analyzed due to sample quality issues)

extract_protocol:
GEM generation and barcoding, POST GEM RT cleanup and cDNA amplification, 3' gene library construction
3' gene expression

value: pbmcs

tag: disease state


title: PBMCs, Cov-55

description:
Covid19 library
Cov-55


title: KO_One_BCR_2

value: Lung


title: Het_Two_GEX_2

value: leucocytes


title: Het_One_GEX_1


title: KO_One_BCR_1


title: PBMCs, Clinic-8

description:
post covid 19 library
Clinic-8

value: Post Covid-19 ILD


title: KO_One_TCR_1


title: Het_Two_TCR_1


title: PBMCs, Cov-14

description:
Covid19 library
Cov-14


title: Het_One_TCR_1


title: PBMCs, Clinic-1

description:
post covid 19 library
Clinic-1


title: PBMCs, Clinic-15

description:
post covid 19 library
Clinic-15


title: KO_One_GEX_1


title: PBMCs, Clinic-12

description:
post covid 19 library
Clinic-12


title: KO_One_TCR_2


title: ANE01_27-EOS-MAST

city: Guilford

first: Anna Eleonora

last: Karagianni

address: Daphne Jackson Road

country: United Kingdom

institute: Surrey University

description: Pmn ≤ 5%; Mast > 2%; EOS > 1%

data_processing:
Raw sequencing reads were processed to remove adaptors and poor-quality sequences (Q25 and below) using the Cutadapt program
Quality control of trimmed data was assessed using FASTQC
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Equus caballus reference genome EquCab3.0 available on ENSEMBL using the STAR aligner v.2.5.2b
The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences
Assembly: EquCab3.0
Supplementary files format and content: Matrix table with gene counts for every gene and every sample
Supplementary files format and content: Matrix table with gene counts for every gene and every sample

organism: Equus caballus

source_name: Bronchoalveolar lavage cells

extract_protocol:
Fresh bronchoalveolar lavage cells were isolated, and total RNA was harvested using Qiagen reagents.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bronchoalveolar lavage cells


title: ANE01_25-EOS-MAST

description: Pmn ≤ 5%; Mast > 2%; EOS > 1%


title: ANE01_26-EOS-MAST

description: Pmn ≤ 5%; Mast > 2%; EOS > 1%


title: PBMCs, Clinic-10

description:
post covid 19 library
Clinic-10
Not analyzed, due to sample quality issues.


title: PBMCs, IPF-12

description:
IPF  library
IPF-12

value: IPF


title: PBMCs, IPF-13

description:
IPF  library
IPF-13


title: PBMCs, IPF-8

description:
IPF  library
IPF-8


title: ANE01_21-CASE-PMN-MAST

description: Pmn > 5%; Mast > 2%; Eos ≤ 1%


title: ANE01_23-CASE-PMN-MAST

description: Pmn > 5%; Mast > 2%; Eos ≤ 1%


title: PBMCs, Clinic-5

description:
post covid 19 library
Clinic-5


title: ANE01_20-Mast-Cell

description: Pmn ≤ 5%; Mast > 2%; Eos ≤ 1%


title: PBMCs, IPF-3

description:
IPF  library
IPF-3


title: ANE01_19-Mast-Cell

description: Pmn ≤ 5%; Mast > 2%; Eos ≤ 1%


title: PBMCs, IPF-1

description:
IPF  library
IPF-1


title: ANE01_18-Mast-Cell

description: Pmn ≤ 5%; Mast > 2%; Eos ≤ 1%


title: PBMCs, IPF-6

description:
IPF  library
IPF-6


title: PBMCs, CTRL-4

description:
1 control library
CTRL-4

value: control


title: PBMCs, CTRL-3

description:
1 control library
CTRL-3


title: ANE01_17-Mast-Cell

description: Pmn ≤ 5%; Mast > 2%; Eos ≤ 1%


title: ANE01_16-Mast-Cell

description: Pmn ≤ 5%; Mast > 2%; Eos ≤ 1%


title: PBMCs, Clinic-13

description:
post covid 19 library
Clinic-13
Not analyzed, due to sample quality issues.


title: PBMCs, CTRL-2

description:
1 control library
CTRL-2


title: ANE01_15-Mast-Cell

description: Pmn ≤ 5%; Mast > 2%; Eos ≤ 1%


title: PBMCs, CTRL-1

description:
1 control library
CTRL-1


title: ANE01_14-Mast-Cell

description: Pmn ≤ 5%; Mast > 2%; Eos ≤ 1%


title: ANE01_24-CASE-PMN-MAST

description: Pmn > 5%; Mast > 2%; Eos ≤ 1%


title: ANE01_13-Mast-Cell

description: Pmn ≤ 5%; Mast > 2%; Eos ≤ 1%


title: Sertoli cell only sample 1 [SCO_1]

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides). Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl human genome version hg38 (GRCh38.27) using STAR 2.6.1d with the parameter “outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with feature Counts 1.6.5 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
The Ensemble annotation was enriched with UniProt data (release 06.06.2014) based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt).
Assembly: hg38
Supplementary files format and content: library size normalized counts

source_name: Human testis tissue

extract_protocol:
Total RNA was extracted using the PeqGOLD total RNA kit following the manufacturer’s protocol (PeqGOLD total RNA kit, VWR Life Sciences).
10ng of total RNA was used as input for SMARTer® Stranded Total RNA-Seq Kit - Pico Input Mammalian (Takara Clontech).

treatment_protocol: Testis biopsies obtained after surgeries were stored in liquid nitrogen

value: Testis

tag: condition

value: Sertoli cell only


title: Sertoli cell only sample 2 [SCO_2]


title: ANE01_22-CASE-PMN-MAST

description: Pmn > 5%; Mast > 2%; Eos ≤ 1%


title: ANE01_11-PMN

description: Pmn > 5%; Mast ≤ 2%; Eos ≤ 1%


title: Spermatid Arrest sample 1 [SDA_1]

value: Spermatid Arrest


title: M2

city: Hohhot

first: Hao

last: Wang

address: Inner Mongolia Medical University

country: China

institute: Inner Mongolia Medical University

description:
Library name: Sample7
7-FPKM

data_processing:
1) Trim Smart-seq2 public primer sequence from the Reads (If the length of trimmed Reads is lower than 30bp, reads should be discarded. If it is PE sequence, both of the reads must be removed );2) Remove the contaminated reads for adapters (The contaminated reads for adapters was defined that the Read Bases contained more than 5bp of adapter sequences. If either one of the PE Reads was polluted, we will remove bothends of the reads);3) Remove the low quality reads (The low quality reads was defined that the number of Reads Bases whose phred Quality value was less than or equal to 19 accounted for more than 15% . If either one of the PE Reads defined as low quality, we will remove both ends of the reads);4) Remove the reads whose N base more than 5% for total bases (If either one of the PE Reads had high Ns bases, we will remove both ends of the reads);
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
DEGseq was used for differential gene expression analysis between two samples with non biological replicates. Under the assumption that the number of reads derived from a gene (or transcript isoform) follows abinomial distribution, DEGseq is proposed based on MA-plot and widely used for differential gene expression analysis. The P-value could be assigned to each gene and adjusted by the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with q≤0.05 and |log2Foldchange |≥1 are identified as differentially expressed genes (DEGs).DESeq2 was designed for differential gene expression analysis between two samples with biological replicates under the theoretical basis obeys the hypothesis of negative binomial distribution for the value of count. Differing from DESeq, DESeq2 estimates the depth parameters of samples and gene-specific, as well as uses "linear regression" for dispersion to "shrink", which was mainly considering genes of the same expression level may share the similarity deviations or own their the expression characteristics. DESeq2 estimates the expression level of each gene in per sample by the linear regression, then calculates the p-value with Wald test. Finally the p-value was corrected by the BH method. Genes with q≤0.05 and |log2Foldchange |≥1 are identified as differentially expressed genes (DEGs).
The GO (Gene Ontology, http://geneontology.org/) enrichment analysis of differential genes wasimplemented by the R package clusterProfiler, version v4.6.0. For enrichment analysis with this package, the corrected p.adjust ≤ 0.05 by BH method was selected as the threshold, and GO term that satisfies this condition is defined as GO term that is significantly enriched in differentially expressed genes. GO functional significance enrichment analysis can identify the main biological functions performed by differentially expressed genes.KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.kegg.jp/) is adatabase for genome deciphering. Given a complete set of genes in a chromosome, it can make predictions about the role of protein interaction (interaction) networks in various cellular activities. The software used is also the R package clusterProfiler, version v4.6.0. The screening threshold is also p.adjust≤ 0.05 corrected by the BH method.
Assembly: Rnor_6.0.89.chr
Supplementary files format and content: processed data.xlsx include FPKM values for each Sample

organism: Rattus

source_name: liver

extract_protocol:
After the total RNA samples were tested and qualified, they were purified according to the characteristics of mRNA from different sources. Eukaryotic mRNA has a polyA tail structure at the 3' end, and magnetic beads with Oligo (dT) are used for enrichment and purification.
Add Fragmentation Bufer to the purified mRNA to make it fragmented into short fragments. The fragmented RNA is then used as a template for reverse transcription using random primers to synthesize the first strand of cDNA, and the second strand of cDNA is synthesized by adding 2nd Strand Marking Bufer and 2nd Strand/End Repair Enzyme Mix. After end repair, addition of base A, addition of sequencing connector, recovery of target fragments by magnetic bead screening, and PCR amplification, thus completing the entire library preparation.

value: liver

value: Sprague-Dawley

tag: group

value: pomegranate-high


title: M9

description:
Library name: Sample9
9-FPKM


title: SG4

description:
Library name: Sample6
6-FPKM

value: model


title: SG3

description:
Library name: Sample5
5-FPKM


title: SG1

description:
Library name: Sample4
4-FPKM


title: ANE01_9-PMN

description: Pmn > 5%; Mast ≤ 2%; Eos ≤ 1%


title: KB3

description:
Library name: Sample3
3-FPKM

value: normal control


title: Normal spermatogenesis sample 2 [NSP_2]

value: Normal spermatogenesis


title: ANE01_8-Control

description: Pmn ≤ 5%; Mast ≤ 2%; Eos ≤ 1%


title: KB1

description:
Library name: Sample1
1-FPKM


title: Normal spermatogenesis sample 1 [NSP_1]


title: Upp1-800-GFP(-) cells, Day 2, biol rep 2, RNA-seq

city: Athens

first: Dimitris

last: Valakos

address: Soranou Ephessiou 4

department: Center of Basic Research

country: Greece

institute: Biomedical Reasearch Foundation Academy of Athens

data_processing:
The quality of the sequenced samples was evaluated by the FastQC tool (Andrews, 2010).
The FASTQ files were aligned to the UCSC mm10 genome version with the HISAT2 tool (v2.1.0) using the options -5 4 -3 4 to trim the 5’ and 3’ ends of the reads and --rna-strandness R (Kim et al, 2019).
Annotation of the SAM files to produce the raw counts was performed with the HTSeq htseq-count tool (v0.6.1p1 and 2.0.3) (Anders et al, 2015) and the options -s reverse -m intersection-nonempty, using the UCSC mm10refGene.gtf genome annotation file.
DEGs (Differentially Expressed Genes) and normalized counts were calculated using DESeq2 (v1.30.1, estimateSizeFactors) (Love et al, 2014).
Assembly: mm10
Supplementary files format and content: The file Day2_Upp1-800-GFP_raw-counts.xlsx contains the raw counts produced by the HTSEq algorithm, as described in data processing step.
Supplementary files format and content: The file Day2_Upp1-800-GFP_norm-counts.xlsx contains the normalized counts produced by DESeq2 (v1.30.1, estimateSizeFactors).

organism: Mus musculus

source_name: Mouse Embryonic Fibroblasts (MEFs)

growth_protocol: MEFs (Mouse Embryonic Fibroblasts) were cultured at 37ο C and 5% CO2 concentration, in high-glucose DMEM (Sigma-Aldrich, D6429) supplemented with heat-inactivated FBS at 10% final concentration (Pan Biotech, P30-1985), 1x GlutaMAX™ Supplement (Gibco™, #35050-061), 1x MEM Non-Essential Amino Acids Solution (Gibco™, #11140-050) and Penicillin-Streptomycin mix (Gibco™, #15140-122) diluted at 1/100. For cellular reprogramming MEF medium was used, as described above, but supplemented with 15% FBS.

extract_protocol:
Upp1-800-GFP(+) and (-) cells collected after sorting were subjected to RNA extraction using the NucleoSpin RNA kit (740955, Macherey-Nagel). The DNA was removed by a DNAseI on-column step, as instructed by the kit’s manual.
RNA-seq libraries were prepared using the NEBNext® Ultra II™ Directional RNA Library prep Kit for Illumina® (E7760, NEB). Sequencing was performed  in the Illumina NovaSeq 6000 sequencer to obtain single-end, reverse-stranded, 100bp-long reads.

treatment_protocol: We transduced ~0.8-1x10^6 early-passage MEFs with lenti-viral particles bearing the Upp1-800-GFP construct in the presence of polybrene at a final concentration of 6ug/ml (Sigma-Aldrich, H9268) overnight, followed by change of medium. After 2-3 days, 1.5-3x10^6 transduced-MEFs were plated in 10cm plates and reprogramming was initiated after 24 hours (day 0) with the addition of doxycycline (DOX) at 2ug/ml (Sigma-Aldrich, D9891) for OKSM expression induction. At day 2 cells were harvested using 1x Trypsin solution (Gibco™, 15090046) and prepared for sorting as follows: the cells were washed with PBS, stained with 0.3uM DAPI for 5-10 min (Roche, 236276), washed again with PBS and resuspended in cold Sorting buffer [1x PBS, 5% FBS, 1mM EDTA] to a final concentration of 5-10x10^6 cells/ml. Cell aggregates were removed prior to sorting with 50um strainer cap filters (BD Biosciences, 340629). Upp1-800-GFP(+) and GFP(-) sorted cells were used directly for RNA extraction (100-200.000 per sample). The experiment was performed in two biological replicates.

value: Mouse Embryonic Fibroblasts (MEFs)

tag: genotype

value: transduced with lenti-viral particles bearing the Upp1-800-GFP construct, treated with doxycyclin for 2 days and sorted


title: Upp1-800-GFP(+) cells, Day 2, biol rep 2, RNA-seq


title: ANE01_7-Control

description: Pmn ≤ 5%; Mast ≤ 2%; Eos ≤ 1%


title: ANE01_12-PMN

description: Pmn > 5%; Mast ≤ 2%; Eos ≤ 1%


title: Upp1-800-GFP(+) cells, Day 2, biol rep 1, RNA-seq


title: Spermatid Arrest sample 2 [SDA_2]


title: M4

description:
Library name: Sample8
8-FPKM


title: ANE01_4-Control

description: Pmn ≤ 5%; Mast ≤ 2%; Eos ≤ 1%


title: WS3，brain organoid，day56 - scRNA-seq

city: hangzhou

first: zhao

last: xingsen

address: kaixuan road268

institute: zhejiang university

description: Library name: WS3

data_processing:
Initial processing was done using Cell Ranger(3.0.2)
data analysis including standardization, cell subpopulation, difference of gene expression, and marker gene screening were achieved by Seurat software
Assembly: Genome_build: GRCh38
Supplementary files format and content: matrix.mtx, matrix file exported by cellranger

source_name: brain organoids

extract_protocol:
Three sets of human D56 forebrain organoids derived from three sets of CTRL and WS iPSCs were dissociated with 3 mL Tryp-LE (Sigma-Aldrich) and for 15 minutes at 37°C, followed by 2 washes with 3% FBS in DPBS and gentle titration using a P1000 pipette. A single-cell suspension was subsequently collected into 2 mL microtubes with a cell density of 1000 cells/μL. Then the suspensions were added to a 10X Genomics GemCode Single-cell instrument to generates a single-cell Gel Bead-In-EMlusion
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.

value: brain organoids


title: ANE01_5-Control

description: Pmn ≤ 5%; Mast ≤ 2%; Eos ≤ 1%


title: WS2，brain organoid，day56 - scRNA-seq

description: Library name: WS2


title: WS1，brain organoid，day56 - scRNA-seq

description: Library name: WS1


title: Normal spermatogenesis sample 3 [NSP_3]


title: ANE01_10-PMN

description: Pmn > 5%; Mast ≤ 2%; Eos ≤ 1%


title: 1640-E4F1NesKO-E14_5-tot-cyto-fraction

city: Montpellier

first: Pierre-François

last: Roux

address: 208 rue des Apothicaires

country: France

institute: Inserm

data_processing:
Polysome profiling datasets were pre-processed using the nf-core RNA-seq pipeline v3.11.0
Assembly: GRCm38
Supplementary files format and content: Tab-delimited file containing Salmon pseudo-counts at the gene or the transcript level

molecule: cytoplasmic RNA

source_name: Brain

extract_protocol:
Total RNAs were isolated from various organs or from cells using TRIzol Reagent (Invitrogen).
For RNA-seq, mRNA libraries were generated following the manufacturer recommendations (mRNA hyper prep from ROCHE)

value: Brain

tag: animal id

tag: fraction

value: tot-cyto-fraction


title: ANE01_3-Control

description: Pmn ≤ 5%; Mast ≤ 2%; Eos ≤ 1%

value: Bronchoalveolar lavage cells


title: CTRL2，brain organoid，day56 - scRNA-seq

description: Library name: CTRL2


title: CTRL3，brain organoid，day56 - scRNA-seq

description: Library name: CTRL3


title: 1640-E4F1NesKO-E14_5-heavy-fraction

value: heavy-fraction


title: 1639-E4F1NesWT-E14_5-tot-cyto-fraction


title: CTRL1，brain organoid，day56 - scRNA-seq

description: Library name: CTRL1


title: ANE01_1-Control

description: Pmn ≤ 5%; Mast ≤ 2%; Eos ≤ 1%


title: KB2

description:
Library name: Sample2
2-FPKM


title: 1639-E4F1NesWT-E14_5-light-fraction

value: light-fraction


title: ANE01_2-Control

description: Pmn ≤ 5%; Mast ≤ 2%; Eos ≤ 1%


title: POOL4_S4

value: plasmid


title: ANE01_6-Control

description: Pmn ≤ 5%; Mast ≤ 2%; Eos ≤ 1%


title: Upp1-800-GFP(-) cells, Day 2, biol rep 1, RNA-seq


title: 1631-E4F1NesWT-E14_5-light-fraction


title: 1640-E4F1NesKO-E14_5-light-fraction


title: Deeply Senescent fibroblasts grown in 2D

city: London

first: Beth

last: Hughes

address: Blizard Institute, 4 Newark Street, Whitechapel

institute: Queen Mary University London

description: 10X Genomics

data_processing:
Demultiplexing, counts generation and barcode processing was carried out using Cell Ranger.
Assembly: GRCh37
Supplementary files format and content: Counts, Features, and barcodes file

source_name: Facelift skin

growth_protocol: 2D growth in 6-well plates, or 3D growth in HDFs in collagen 1 (Corning) supplemented with Matrigel (Corning), FCS (1001/500, Biosera), 10X DMEM (11430-030, Invitrogen), and pH balanced with 4M NaOH in the absence of antibiotics.

extract_protocol:
Cells grown in 2D collected following trypsinisation, and cells grown in 3D collected after incubation with 2.25μg/mL collagenase D (Sigma) at 37C for 1hr. Collagenase activity was subsequently inhibited by HBSS addition (Thermofisher).
Library construction was performed as per manufacturers instructions, using the chromium 10X 3' kit, v2.

value: Facelift skin

value: Human dermal fibroblast

tag: age of_donor

tag: sex of_donor

value: Female

value: Grown in 6-well plate


title: Deeply Senescent fibroblasts grown in 3D

description: 10X Genomics

value: Grown in matrigel/collagen matrix


title: 1631-E4F1NesWT-E14_5-heavy-fraction


title: 1630-E4F1NesKO-E14_5-tot-cyto-fraction


title: POOL2_S2


title: 1630-E4F1NesKO-E14_5-light-fraction


title: 1628-E4F1NesKO-E14_5-tot-cyto-fraction


title: Early Proliferative fibroblasts grown in 3D

description: 10X Genomics


title: 1628-E4F1NesKO-E14_5-heavy-fraction


title: D12 experiment 2

city: La Jolla

first: Wolfgang

last: Busch

state: CA

address: 10010 N Torrey Pines Rd

department: Plant Biology

institute: Salk Institute for Biological Studies

description:
12 day old A.thaliana Col-0 whole root less tip
A.thaliana_periderm_snRNAseq_atlas_Seurat_object.rds
D12_experiment_2_barcodes.tsv.gz
D12_experiment_2_features.tsv.gz
D12_experiment_2_matrix.mtx.gz

data_processing:
CellRanger (v.6.0.1) was used to perform sample-demultiplexing, barcode processing and single-nuclei gene-UMI counting. An expression matrix was obtained for each experiment by aligning to the A. thaliana genome (TAIR 10) using CellRanger with default parameters. For initial quality-control filtering, aligned nuclei and transcript counts from each experiment were processed by Seurat (Version 4.3) by removing outlier nuclei in terms of the distribution of number of detected genes (nFeature) and transcripts (nCount) (Cutoffs: nFeature>4k & nCount>10k for data from Day 6&7; nFeature>3k & nCount>5k for data from Day 8 to 12; nFeature>2k & nCount>5k for data from Day 12). Low quality nuclei containing a high abundance of mitochondrial reads (>5% of total transcripts) and chloroplast reads (>5% of total transcripts) were also filtered. After initial filtering, 22,445 out of 23,747 cells were retained. Expression data of nuclei passing these thresholds were log normalized with NormalizeData() function and the top 2K variable genes were identified with the FindVariableFeatures() function. Next, data from all experiments were integrated using Seurat’s Reciprocal Principal component analysis (RPCA) and FindIntegrationAnchors() functions, to identify integration features and correct for potential batch effects. The integrated data was then scaled with ScaleData() function. PCA was carried out with the RunPCA() function and the top 30 principal components (PCs) were retained. Clusters were identified with the FindClusters() function by use of the shared nearest neighbour modularity optimization with a clustering resolution set to 0.5. Clusters with only one nucleus were removed. This method resulted in 26 initial clusters. To further check the quality of remaining nuclei, doublets were detected by applying the hybrid estimation scores from R package scds() 29. After doublet removal, the remaining nuclei were re-clustered with the top 30 PCs and a clustering resolution at 0.5. This resulted 19,755 nuclei distributed in 23 clusters. Pseudotime analysis was performed using Monocle 3 30. This was performed including just periderm-related clusters and using cluster 3, comprising pericycle-related nuclei as the progenitor cluster.
Assembly: TAIR10
Supplementary files format and content: A.thaliana_periderm_snRNAseq_atlas_Seurat_object.rds: data and analysis encapsulated as a Seurat object (R programming language)
Supplementary files format and content: *.features.tsv.gz, *.barcodes.tsv.gz, *.matrix.mtx.gz: Cellranger count output

organism: Arabidopsis thaliana

source_name: whole root less tip

growth_protocol: Seeds of A. thaliana (ecotype Col-0) were sterilized for 1.5h using chlorine gas (250ml 6% bleach with 3.5ml HCL) in an airtight chamber. Seeds were stratified at 4°C for three days before being sown on half-strength Murashige and Skoog (1/2 MS) media without sucrose at pH5.7. The plants were grown vertically at 21°C under 16/8 day-night cycle conditions. Seeds were densely sown onto 1/2 MS plates with a mesh layer. This facilitated efficient root harvesting with minimal agarose carry over. Roots were harvested at 6, 7, 8, 9, 10, 11, 12 and 14 days after germination (DAG) into liquid nitrogen and stored at -80°C until further processing. For each timepoint, 30 plates were harvested.

extract_protocol:
Nuclei extraction was performed as described by Lee et al., 2023. Briefly, roots were ground to a fine powder in liquid nitrogen and then homogenised in Nuclei Extraction Buffer (NEB) (20mM MOPS pH7, 40mM NaCl, 90mM KCL, 2mM EDTA, 0.5 mM EGTA, 1% SUPERASE inhibitor (Invitrogen), 0.5mM spermadine, 0.2mM spermine, 1 x Roche Complete Protease inhibitor tablet) before being filtered through a 70μm filter. Nuclei were then further filtered through a 40μm filter and then centrifuged at 700 rcf for 5min at 4°C. Supernatant was discarded and the pellet resuspended in NEB supplemented with 0.1% triton. Samples were centrifuged again to wash. This was repeated for a total of two washes and the samples resuspended in 2ml NEB (without triton). Two solutions were made for the density gradients - a sucrose solution (400mM sucrose, 25mM KCL, 5mM MgCl2, 10mM Tris-Cl (pH8)) and a diluent buffer (120mM Tris-Cl (pH8), 150mM KCL, 30mM MgCl2). Prior to preparing the two density fractions, 1 volume of the diluent buffer was mixed with 5 volumes of Optiprep (Sigma). Density gradients were prepared in 15ml tubes with a 2ml 45% layer (1.8ml sucrose solution and 0.2ml dilutant buffer) and a 1ml 15% layer (0.3ml sucrose solution per 0.7ml dilutant buffer). The 2ml sample was added carefully to the top of the gradient and centrifuged at 1500 rcf for 5min without breaks. Nuclei were collected at the 45% interface and resuspended in NEB and centrifuged at 1000 rcf to collect nuclei. Samples were submitted to cell sorting in fresh NEB. Nuclei were stained using Hoechst. Stringent gating was used to remove debris and chloroplast signals were also detected and omitted from the sorted nuclei portion. Following the sorting of nuclei, samples were centrifuged at 1000 rcf and resuspended in the appropriate volume of 1xPBS for the 10X Genomics single-nuclei sequencing workflow
10X Genomics single-nuclei sequencing workflow

value: whole root less tip

value: nucleus


title: POOL3_S3


title: SHED_PPi_Day1 [S4_3]

city: Bangkok

first: Ravipha

last: Suwittayarak

address: Wang mai

department: Dentistry

country: Thailand

institute: Chulalongkorn University

description: RNA-Seq of homo sapiens

data_processing:
Read quality was checked, trimmed, and filtered with a FastQC and FastX-toolkit.
Reads were mapped with Homo sapiens UCSC hg38 using TopHat2.
FPKM estimation of reference genes and transcripts was performed using DeSeq2 analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

source_name: exfoliated tissue derived from primary teeth

growth_protocol: The cells were migrated out of the tissue and cultured in High glucose Dulbecco’s Modified Eagle Medium supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine, 1% of Penicillin (100 U/mL), Streptomycin (100 mg/mL) and incubated at 37°C in a humidified 5% CO2 atmosphere.

extract_protocol:
total RNA was isolated using a RNeasy kit. DNase treatment was performed in columns. Total RNA quantity and quality were examined using a Nanodrop and Aligent 2100 Bioanalyzer system.
Library quality assurance was conducted using an Aligent 2100 Bioanalyzer system and Qubit 3.0 fluorometer.

treatment_protocol: Cells were treated with 10uM inorgnaic pyrophosphate in 10% FBS-DMEM for 1 day

value: dental mesenchymal cell

value: stem cell from human exfoliated deciduous teeth

value: wild-type

value: pyrophopshate treatment


title: 1631-E4F1NesWT-E14_5-tot-cyto-fraction

value: Brain


title: 1590-E4F1NesWT-E14_5-tot-cyto-fraction

value: tot-cyto-fraction


title: Early Proliferative fibroblasts grown in 2D

description: 10X Genomics


title: D10 experiment 2

description:
10 day old A.thaliana Col-0 whole root less tip
A.thaliana_periderm_snRNAseq_atlas_Seurat_object.rds
D10_experiment_2_barcodes.tsv.gz
D10_experiment_2_features.tsv.gz
D10_experiment_2_matrix.mtx.gz


title: D14 experiment 2

description:
14 day old A.thaliana Col-0 whole root less tip
A.thaliana_periderm_snRNAseq_atlas_Seurat_object.rds
D14_experiment_2_barcodes.tsv.gz
D14_experiment_2_features.tsv.gz
D14_experiment_2_matrix.mtx.gz


title: 1627-E4F1NesWT-E14_5-tot-cyto-fraction


title: SHED_control_Day1 [S4_1]

description: RNA-Seq of homo sapiens

value: exfoliated tissue derived from primary teeth

value: untreatement


title: SHED_PPi_Day1 [S1_3]

description: RNA-Seq of homo sapiens


title: 1627-E4F1NesWT-E14_5-light-fraction

value: light-fraction


title: 1627-E4F1NesWT-E14_5-heavy-fraction

value: heavy-fraction


title: 1589-E4F1NesKO-E14_5-light-fraction


title: 1589-E4F1NesKO-E14_5-tot-cyto-fraction


title: Barcoded hiPSC pilot, GEX+BC+HTO

city: St Lucia

first: Sophie

last: Shen

state: Queensland

address: 306 Carmody Road

department: Institute for Molecular Bioscience

country: Australia

institute: The University of Queensland

data_processing:
Raw BCL files generated by Illumina sequencers were demultiplexed into FASTQ files using cellranger mkfastq, which wraps Illumina's bcl2fastq software (cellranger version 3.0.2 and bcl2fastq v2.19.0.316). The cellranger count pipeline was used to align, filter and count barcodes and UMIs from the fastq files to generate feature-barcode (raw count) matrices.
For barcoded samples, barcode sequences were both appended to the GrCh38 reference genome with "BC01-18" identifiers to allow their expression to be recognised as custom "gene" expression, as well as sequenced as independent libraries with exclusively the barcode sequences as the reference. For HTO libraries, CITE-seq-Count was used to generate a count matrix for the hashing reads from the fastq files.
Cellranger aggr was used in the analysis for comparing the three time course datasets.
For sample demultiplexing, 'HTODemux' from the Seurat package in R was used for both HTO and barcode (BC) demultiplexing. Doublets identified from 'HTODemux' and the scds doublet detection package were removed. The Seurat package was also used for cell filtering and count normalisation. Where relevant, the R package RISC was used for dataset integration. See methods for further details and downstream analysis.
Assembly: GrCh38, BC reference file
Supplementary files format and content: All files containing 'raw_count' and 'raw_barcode' in the name are direct output from cellranger count, which provides three files: cell barcodes (*barcodes.tsv.gz), gene names (*features.tsv.gz) and the count matrix (*matrix.mtx.gz).
Supplementary files format and content: Files containing "raw_hto" in the name are direct output from CITE-seq-count, which provides three files: cell barcodes (*barcodes.tsv.gz), HTO barcode sequence (*features.tsv.gz) and the HTO count matrix (*matrix.mtz.gz)
Supplementary files format and content: Supplemental files containing "integrated_sig_time" are from RISC integration of raw counts from the three signalling dataset libraries and the control time course dataset after cell filtering as detailed in the methods. The .mtx file contains batch-corrected (integrated) and normalised values. The metadata file additionally contains cell type annotations with reference to three in vivo datasets (columns "PijuanSala_LabelTransfer", "Hutchins_CTDomains" and "Tyser_GastrulaLT". See methods for more details), as well as final clusters, annotations, and anchor genes presented in the accompanying manuscript.
Supplementary files format and content: Supplemental files containing "integrated_tm88" are from RISC integration of raw counts from cellranger aggr processing of the three time course datasets and cell quality filtering as detailed in the methods. The .mtx file contains batch-corrected (integrated) and normalised values. The metadata additionally contains label transfer results against one in vivo dataset (column: "LT_PijuanSala2019"), initial cell clusters, filtered cell clusters, as well as final cell type annotations, marker genes, and anchor genes presented in the accompanying manuscript.
Supplementary files format and content: Supplemental files "barcode.fa" and "barcode.gtf" are the fasta and gtf files added to the GrCh38 genome reference for the samples utilising the barcoded iPSC lines for sample multiplexing. The barcode.fa file contains more sequence flanking each of the unique 15bp barcodes in each cell line for better mapping.

source_name: barcoded hiPSCs (WTC WT background/RRID: CVCL_Y803)

growth_protocol: Mesendoderm directed iPSC differentiation protocol (used as the control in this study) was adapted from a small molecule-directed cardiomyoycte differentiation protocol (https://doi.org/10.1038/nmeth.2999). In brief, undifferentiated cells are cultured in mTeSR+ pluripotency media and seeded onto vitronectin-coated plates the day prior to differentiation (day -1) with ROCK inhibitor to promote survival. The following day, once cells have formed an ~80% confluent monolayer, differentiation is induced (day 0) by changing culture media to RPMI containing 3uM CHIR99021 (small molecule Wnt agonist), 500mg/mL bovine serum albumin (BSA), and 213mg/mL ascorbic acid (AA). Media is changed every second day, maintaining the RPMI, BSA and AA backbone until day 7 and onwards where the BSA and AA are replaced with 1x B27 supplement plus insulin.

extract_protocol:
Cells were dissociated with EDTA/Trypsin. For hashtagged samples, 1e6 cells were stained with their corresponding TotalSeq-A anti-human Hashtag antibody (see HTO antibody details above). Cells were sorted for viability using propidium iodide before being pooled for 10X Genomics Chromium Single Cell 3' V3 capture, targeting 2e4 cells.
mRNA libraries were constructed according to manufacturer's instructions (Chromium Single Cell 3' V3). The barcoding (BC) libraries were generated from a portion of the cleaned up full length amplified cDNA from each mRNA sample pool. In brief, the cDNA regions containing the barcode cassette were amplified and partial P5 and P7 sequencing adaptors were appended in one round of PCR. After clean-up to remove primers, additional PCR was performed as per the SI-PCR protocol in the Chromium gene expression library construction workflow  with a unique i7 indexed R primer from Chromium i7 Multiplex Kit for a total of 14 cycles. For more details, see methods. The HTO libraries were generated following additional methods from Stoeckius et al., (2018) to capture the fraction of droplets containg HTO-derived cDNA and generate the hashing libraries.

treatment_protocol: Treatments in the signalling dataset were each added to the differentiation media on day 3 and removed on day 5 of differentiation. Likewise, the XAV treatment for the XAV-treated time course dataset was also added to the differentiation backbone media on day 3 and removed on day 5. For the TMEM88 knockdown sample, doxycycline was added from day 0 of differentiation for the entire duration to induce the tetracycline-inducible CRISPRi-mediated TMEM88 knockdown of expression.

value: barcoded hiPSCs (WTC WT background/RRID:CVCL_Y803)

value: undifferentiated hiPSC

tag: library type

value: mRNA/HTO/BC


title: 1590-E4F1NesWT-E14_5-heavy-fraction


title: D10 experiment 1 replicate 2

description:
10 day old A.thaliana Col-0 whole root less tip
A.thaliana_periderm_snRNAseq_atlas_Seurat_object.rds
D10_experiment_1_barcodes.tsv.gz
D10_experiment_1_features.tsv.gz
D10_experiment_1_matrix.mtx.gz


title: D9 experiment 1 replicate 2

description:
9 day old A.thaliana Col-0 whole root less tip
A.thaliana_periderm_snRNAseq_atlas_Seurat_object.rds
D9_experiment_1_barcodes.tsv.gz
D9_experiment_1_features.tsv.gz
D9_experiment_1_matrix.mtx.gz


title: 1588-E4F1NesWT-E14_5-tot-cyto-fraction


title: 1628-E4F1NesKO-E14_5-light-fraction


title: D9 experiment 1 replicate 1


title: HT1_vehicle

description:
HT1V2
counts_human_cl.tsv

value: vehicle


title: 1588-E4F1NesWT-E14_5-light-fraction


title: SHED_control_Day1 [S1_1]

description: RNA-Seq of homo sapiens


title: 1590-E4F1NesWT-E14_5-light-fraction


title: D8 experiment 1 replicate 2

description:
8 day old A.thaliana Col-0 whole root less tip
A.thaliana_periderm_snRNAseq_atlas_Seurat_object.rds
D8_experiment_1_barcodes.tsv.gz
D8_experiment_1_features.tsv.gz
D8_experiment_1_matrix.mtx.gz


title: HT1_MEKi

description:
HT1_T2
counts_human_cl.tsv

value: Trametinib


title: 1588-E4F1NesWT-E14_5-heavy-fraction


title: D8 experiment 1 replicate 1

value: whole root less tip


title: HM1_MEKi

description:
HM1_T2
counts_human_cl.tsv


title: 1587-E4F1NesKO-E14_5-heavy-fraction


title: D7 experiment 1 replicate 2

description:
7 day old A.thaliana Col-0 whole root less tip
A.thaliana_periderm_snRNAseq_atlas_Seurat_object.rds
D7_experiment_1_barcodes.tsv.gz
D7_experiment_1_features.tsv.gz
D7_experiment_1_matrix.mtx.gz

value: nucleus


title: HM1_vehicle

description:
HM1V2
counts_human_cl.tsv


title: VR23-2D

data_processing:
Reads were aligned to the GRCh38 genome using STAR v2.7 and expression quantification were performed with RSEM
GRCh38
tab-delimited file containing raw counts for each sample

source_name: pancreatic ductal adenocarcinoma

value: pancreatic ductal adenocarcinoma

value: baseline


title: 1573-E4F1NesWT-E14_5-light-fraction


title: 1572-E4F1NesKO-E14_5-tot-cyto-fraction


title: 1589-E4F1NesKO-E14_5-heavy-fraction


title: 1572-E4F1NesKO-E14_5-light-fraction


title: 1573-E4F1NesWT-E14_5-tot-cyto-fraction


title: 1573-E4F1NesWT-E14_5-heavy-fraction


title: D10 experiment 1 replicate 1


title: D7 experiment 1 replicate 1


title: VR20-2D


title: 1572-E4F1NesKO-E14_5-heavy-fraction


title: D6 experiment 1 replicate 2

description:
6 day old A.thaliana Col-0 whole root less tip
A.thaliana_periderm_snRNAseq_atlas_Seurat_object.rds
D6_experiment_1_barcodes.tsv.gz
D6_experiment_1_features.tsv.gz
D6_experiment_1_matrix.mtx.gz


title: VR09-2D


title: Hepa1-6 RIP, sgUsp5, YTHDF1 _CST

city: Chongqing

first: Tianshu

last: Fang

state: China

address: 临江路74号（重医附二院渝中院区）

institute: 重医附二院渝中院区第二临床学院

data_processing:
RIP RNA samples were collected and subjected to strand-specific library preparation. The libraries were then sequenced using the Illumina high-throughput sequencing platform (NovaSeq 6000) at PE150 read length. The sequencing data was processed using Bioptic Qsep100. The software Hisat2 (v2.1.0) was utilized to align the clean data, which represents the valid sequencing reads, to the reference genomes of mouse (mm10).Read counts were calculated using featureCounts (v1.6.3).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample: All.count.txt

source_name: Hepa 1-6

extract_protocol:
Collect cell pellets, add 1 ml of IP lysis buffer (pre-supplemented with PIC and RNAse inhibitor), vortex or pipette mix thoroughly, perform on-ice lysis or rotate at 4°C for 30 minutes, centrifuge at 12, 000 x g for 10 minutes, and transfer the supernatant to a new 1.5 ml EP tube.Take 10% of the lysate volume as the input sample for RNA extraction, and assess its integrity.Take 40 μl of protein G magnetic beads, wash twice with IP buffer, add the lysateand the antibody, and incubate overnight at 4°C. Transfer the supernatant to a new 1.5 ml EP tube.Place the bead mixture on a magnetic stand, discard the supernatant once it becomes clear, add 1 ml of wash buffer, mix thoroughly, and rotate at 4°C for 10 minutes. Place the bead mixture on a magnetic stand, discard the supernatant, and repeat the washing step three times.Place the bead mixture on a magnetic stand, discard the supernatant once it becomes clear, add 1 ml of TRIzol™ Reagent (Invitrogen™, cat. no15596018), and perform RNA extraction using the phenol-chloroform method.
Fragment the obtained RNA sample and prepare libraries using the EpiTM mini longRNA-seq kit:Remove ribosomal RNA using 5XRT Buffer and rRNA probes. After rRNA removal, add random primers, TSO, reverse transcriptase, and perform a 40°C reaction for 90 minutes. Inactivate the enzyme at 70°C for 15 minutes to synthesize the first-strand cDNA based on the SMART principle. Purify the cDNA using magnetic beads, add 2xpfuMax HiFi PCR ProMix and index primers for PCR amplification to enrich library fragments. Purify the DNA using magnetic beads to select library fragments.

value: Hepa 1-6

value: murine hepatocellular carcinoma

value: Usp5 Knockdown

tag: rip antibody


title: Hepa1-6 RIP, sgcontrol, YTHDF1 _CST

address: 临江路74号（重医附二院渝中院区）

institute: 重医附二院渝中院区第二临床学院

value: WT


title: 1587-E4F1NesKO-E14_5-tot-cyto-fraction

tag: tissue

value: Brain

value: tot-cyto-fraction


title: D6 experiment 1 replicate 1


title: Hepa1-6 input, sgUsp5

address: 临江路74号（重医附二院渝中院区）

institute: 重医附二院渝中院区第二临床学院

tag: cell line


title: E9.5 WT mouse embryo WT6

city: Oklahoma City

first: Anthony

middle: C

last: Johnson

state: OK

address: 1122 NE 13th St, O'Donoghue Research Building 332

department: Neurosurgey

institute: University of Oklahoma Health Sciences

data_processing:
Standard bioinformatics analyses were conducted by Novogene Co., LTD (Beijing, China).
Assembly: GRCm38
Supplementary files format and content: matrix table containg gene ID, sample ID, gene name, chromosome, gene start, gene end, strand, gene length, gene biotype, gene description, transcription factor family

source_name: embryo

extract_protocol:
Day 9.5 embryos were collected and stored in Invitrogen™ RNAlater™ Stabilization Solution (Fisher Scientific, AM7023) before RNA extraction. Total RNA was purified using the RNeasy Lipid Tissue Mini Kit (QIAGEN, Redwood City, CA, USA, 74804) according to the manufacturer’s instructions, quantified by NanoDrop and stored at -80ºC.
Preparation of cDNA libraries, sequencing, and Standard bioinformatics analyses were conducted by Novogene Co., LTD (Beijing, China).

value: embryo

tag: strain

tag: age

value: Embryo day 9.5


title: VR06-2D

tag: cell type


title: Hepa1-6 input, sgcontrol

address: 临江路74号（重医附二院渝中院区）

institute: 重医附二院渝中院区第二临床学院


title: VR02-2D


title: E9.5 WT mouse embryo WT5


title: TA_D3_3

city: Cambridge

first: Jianfeng

last: Ge

state: Cambridgeshire

address: 37, ST THOMAS'S SQUARE

institute: University of Cambridge

data_processing: deseq output data for both L1475 and A549 on condition of OSKM vs TA control

source_name: lung

growth_protocol: L1475 and A549 were cultured in DMEM+10% FBS medium

extract_protocol: RNA was havested using Rnaset mini plus kit (Qiagen). 1 ug of total RNA was used for the library prep

treatment_protocol: Both L1475 and A549 was expressed OSKM fators, TA was plasmid control

value: lung

value: cell line

tag: treatment

value: control


title: E9.5 WT mouse embryo WT4


title: TA_D3_1


title: E9.5 WT mouse embryo WT2


title: E9.5 WT mouse embryo WT3


title: female mouse spinal cord tissue, Nkx6.1 cKO, GFP astrocytes, replicate 3

city: Houston

first: Zhung-Fu

last: Lee

state: Texas

address: 2300 Old Spanish Trl, Apt1013

institute: Baylor College of Medicine

description: Library name: NB017_Female_cKO3

data_processing:
Quality control was performed using fastQC (v0.10.1) and MultiQC (v0.9).
Reads were mapped to the mouse genome mm10 assembly using STAR (v2.5.0a). Mapped reads were used to build count matrices using Bioconductor packages GenomicAlignments (v1.26.0) and GenomicFeatures (v1.42.2).
UCSC transcripts were downloaded from Illumina iGenomes in GTF file format.
DESeq2 (v1.20.0) was used for normalization and differential gene expression analysis.
Assembly: mm10
Supplementary files format and content: xlsx files include RPM values

source_name: spinal cord

extract_protocol:
Total RNA was extracted using the RNeasy Micro Kit (Qiagen #74004)
cDNA synthesis and library construction with 8-bp single indices were done from 10 ng total RNA using TRIO-RNA SEQ V2 kit (Nugen #0506.0507.0357). A final library dilution of 2 nM was subjected to paired-end sequencing.

value: spinal cord

value: astrocyte

value: cKO


title: E9.5 WT mouse embryo WT1


title: female mouse spinal cord tissue, Nkx6.1 cKO, GFP astrocytes, replicate 2

description: Library name: NB016_Female_cKO2


title: TA_D1_3


title: E9.5 TRAF7-*/-* mouse embryo KO6

value: KO


title: E9.5 TRAF7-*/-* mouse embryo KO5


title: E9.5 TRAF7-*/-* mouse embryo KO4


title: TA_D3_2


title: female mouse spinal cord tissue, Nkx6.1 cKO, GFP astrocytes, replicate 1

description: Library name: NB013_Female_cKO1


title: TA_D1_2


title: E9.5 TRAF7-*/-* mouse embryo KO3


title: E9.5 TRAF7-*/-* mouse embryo KO2


title: female mouse spinal cord tissue, Nkx6.1 Control, GFP astrocytes, replicate 3

description: Library name: NB015_Female_Control3

value: Control


title: TA_D1_1


title: P23 male WT 7 mouse brain

source_name: whole brain

extract_protocol:
Mouse brains were collected and stored in Invitrogen™ RNAlater™ Stabilization Solution (Fisher Scientific, AM7023) before RNA extraction. Total RNA was purified using the RNeasy Lipid Tissue Mini Kit (QIAGEN, Redwood City, CA, USA, 74804) according to the manufacturer’s instructions, quantified by NanoDrop and stored at -80ºC.
Preparation of cDNA libraries, sequencing, and Standard bioinformatics analyses were conducted by Novogene Co., LTD (Beijing, China).

value: whole brain

tag: Sex

value: Male

value: Post-natal day 23


title: 4F_D3_3

value: OSKM expressing


title: female mouse spinal cord tissue, Nkx6.1 Control, GFP astrocytes, replicate 2

description: Library name: NB014_Female_Control2


title: female mouse spinal cord tissue, Nkx6.1 Control, GFP astrocytes, replicate 1

description: Library name: NB018_Female_Control1


title: P23 female WT 5 mouse brain

value: Female

value: WT


title: 4F_D3_2


title: E9.5 TRAF7-*/-* mouse embryo KO1


title: P23 female WT 4 mouse brain


title: 4F_D3_1


title: male mouse spinal cord tissue, Nkx6.1 cKO, GFP astrocytes, replicate3

description: Library name: NB011_Male_cKO3


title: P23 male WT 3 mouse brain


title: 4F_D1_3


title: male mouse spinal cord tissue, Nkx6.1 cKO, GFP astrocytes, replicate2

description: Library name: NB009_Male_cKO2


title: male mouse spinal cord tissue, Nkx6.1 cKO, GFP astrocytes, replicate1

description: Library name: NB003_Male_Cko1


title: P23 female WT 1 mouse brain


title: P23 male WT 2 mouse brain


title: male mouse spinal cord tissue, Nkx6.1 Control, GFP astrocytes, replicate3

description: Library name: NB008_Male_Control3


title: 4F_D1_2


title: P23 female RIK KO3 mouse brain

value: RIK KO


title: P23 female RIK KO7 mouse brain


title: P23 male WT 6 mouse brain


title: P23 male RIK KO4 mouse brain


title: male mouse spinal cord tissue, Nkx6.1 Control, GFP astrocytes, replicate2

description: Library name: NB005_Male_Control2


title: P23 female RIK KO1 mouse brain


title: P23 male RIK KO2 mouse brain


title: 4F_D1_1


title: skin explant day4 ZIKV.NeSt1_4

city: New Haven

first: Alejandro

last: Marin Lopez

address: 300 Cedar St

department: Internal Medicine

institute: 300 Cedar St

data_processing:
The samples were sequenced using a 2x150bp Paired-End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software.
After investigating the quality of the raw data, sequence read was trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens reference genome (GRCh38) available on ENSEMBL using the STAR aligner v.2.5.2b.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: skin explant

extract_protocol:
The RNA quality check, sequencing, and bioinformatic analysis were performed at Azenta Life Sciences (South Plainfield). RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using the manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First-strand and second-strand cDNAs were subsequently synthesized. cDNA fragments were end-repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on flow cells. After clustering, the flow cells were loaded onto the Illumina HiSeq instrument (4000 or equivalent) according to the manufacturer’s instructions.  The samples were sequenced using a 2x150bp Paired-End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS).

value: skin explant

tag: time

value: day 4


title: male mouse spinal cord tissue, Nkx6.1 Control, GFP astrocytes, replicate1

description: Library name: NB001_Male_Control1


title: skin explant day4 ZIKV.NeSt1_3


title: P14 female WT 6 mouse brain

data_processing:
Standard bioinformatics analyses were conducted by Novogene Co., LTD (Beijing, China).
Assembly: mm10
Supplementary files format and content: matrix table containg gene ID, sample ID, gene name, chromosome, gene start, gene end, strand, gene length, gene biotype, gene description, transcription factor family

value: Post-natal day 14


title: Male mouse spinal cord tissue, Nkx6.1 cKO Input

description: Library name: Nkx6.1_KO_Input

library_source: genomic

data_processing:
For Nkx6.1 ChIP-seq, reads were aligned to the mm10 reference genome using Bowtie2. Both HOMER and MUSIC were used to identify peaks, and separate peak lists were generated for control Nkx6.1 and knockout (KO) Nkx6.1 conditions using the union of peaks identified by HOMER or MUSIC.51,55 To identify condition-specific enhancers, we performed bedtools intersect -v to generate control-specific and KO-specific peak regions by removing overlapping regions between the conditions. Motif enrichment analysis of these peaks was using performed HOMER's findMotifsGenome.pl.
Assembly: mm10
Supplementary files format and content: BigWig

molecule: genomic DNA

extract_protocol:
Cell pellets were collected by centrifugation at 3500 rpm for 5 min at 4°C, washed with PBS, and frozen at 80°C until further processing. Pellets were resuspended with PBS–phenylmethylsulfonyl fluoride (PMSF) containing 0.5% Igepal to release nuclei followed by washing with cold ChIP-Buffer (0.25% Triton-X100, 10 mM EDTA, 0.5 mM EGTA,10 mM HEPES pH 6.5), and nuclei were lysed with ChIP lysis buffer (0.5% SDS, 5 mM EDTA, 25 mM Tris-HCl pH 8) for 15 to 20 min at room temperature
ChIP libraries were prepared using the TruSeq ChIP Library Preparation Kit (Illumina no. IP-202-1012), according to the manufacturer’s instructions. Libraries ranging from 250 to 350 bp were extracted from gel incisions using the QIAquick Gel Extraction Kit (Qiagen no. 28706),

tag: chip antibody

value: Nkx6.1 cKO


title: P14 female WT 3 mouse brain


title: P14 female WT 5 mouse brain


title: P14 female WT 4 mouse brain


title: P23 female RIK KO6 mouse brain


title: P14 male WT 2 mouse brain


title: skin explant day4 ZIKV.NeSt1_2


title: P14 male WT 1 mouse brain


title: P23 male RIK KO5 mouse brain


title: P14 male RIK KO7 mouse brain


title: Male mouse spinal cord tissue, Nkx6.1 Control, Input

description: Library name: Nkx6.1_Ctrl_Input

value: Nkx6.1 control


title: P14 male RIK KO8 mouse brain


title: skin explant day3 ZIKV.NeSt1_4

value: day 3


title: skin explant day3 ZIKV.NeSt1_3


title: P14 male RIK KO4 mouse brain


title: skin explant day4 ZIKV.NeSt1_1


title: P14 male RIK KO6 mouse brain


title: P14 female RIK KO5 mouse brain


title: skin explant day3 ZIKV.NeSt1_1


title: skin explant day2 ZIKV.NeSt1_4

value: day 2


title: P14 male RIK KO2 mouse brain


title: skin explant day3 ZIKV.NeSt1_2


title: lung SEG, d7, rep2

city: Chapel Hill

first: Li

last: Qian

state: North Carolina

address: 111 Mason Farm Road, MBRB

department: Department of Pathology

institute: UNC

data_processing:
Transcript expression was quantified using Salmon
DESeq2 was used to compare gene expression between conditions at each timepoint
Assembly: mm10
Supplementary files format and content: csv file of DESeq2 counts of all samples

growth_protocol: EGM2 media

extract_protocol:
Rneasy mini kit
Novogene mRNA

value: lung

value: iEC

value: Day 7


title: Male mouse spinal cord tissue, Nkx6.1 Control, H3K27ac ChIP

description: Library name: Nkx6.1_Ctrl_H3k27ac_ChIP

value: spinal cord


title: skin explant day2 ZIKV.NeSt1_3


title: lung EC, d7, rep3

value: endothelial


title: lung EC, d7, rep1


title: skin explant day2 ZIKV.NeSt1_2


title: Male mouse spinal cord tissue, Nkx6.1 cKO, H3K27ac ChIP

description: Library name: Nkx6.1_KO_H3k27ac_ChIP


title: lung SEG, d7, rep1


title: skin explant day2 ZIKV.NeSt1_1


title: lung control fibroblast, d7, rep3

value: fibroblast


title: lung control fibroblast, d7, rep1


title: lung control fibroblast, d7, rep2


title: lung EC, d7, rep2


title: skin explant day1 ZIKV.NeSt1_4

value: day 1


title: P14 male RIK KO3 mouse brain

value: whole brain

value: Male


title: P14 male RIK KO1 mouse brain

value: RIK KO


title: skin explant day1 ZIKV.NeSt1_2

value: skin explant


title: heart EC, d7, rep2

source_name: heart

value: heart


title: heart SEG, d7, rep3


title: heart control fibroblast, d7, rep3


title: skin explant day1 ZIKV.NeSt1_1


title: heart SEG, d7, rep2


title: heart control fibroblast, d7, rep1


title: skin explant day1 ZIKV.NeSt1_3


title: lung SEG, d7, rep3


title: heart EC, d7, rep1


title: skin explant day4 ZIKV.buffer_3

value: day 4


title: heart EC, d7, rep3


title: MEFs treated with doxycycline, Day 6, biol rep 2, RNA-seq

data_processing:
The FASTQ files were aligned to the UCSC mm10 genome version with the HISAT2 tool (v2.1.0) using the options -5 4 -3 4 to trim the 5’ and 3’ ends of the reads and --rna-strandness R (Kim et al, 2019).
Annotation of the SAM files to produce the raw counts was performed with the HTSeq htseq-count tool (v0.6.1p1 and 2.0.3) (Anders et al, 2015) and the options -s reverse -m intersection-nonempty, using the UCSC mm10refGene.gtf genome annotation file.
DEGs (Differentially Expressed Genes) and normalized counts were calculated using DESeq2 (v1.30.1, estimateSizeFactors) (Love et al, 2014).
Assembly: mm10
Supplementary files format and content: The file Reprogramming-timecourse_raw-counts.xlsx contains the raw counts produced by the HTSEq algorithm, as described in data processing step. Each column represents a different sample.

growth_protocol: MEFs (Mouse Embryonic Fibroblasts) were cultured at 37ο C and 5% CO2 concentration, in high-glucose DMEM (Sigma-Aldrich, D6429) supplemented with heat-inactivated FBS at 10% final concentration (Pan Biotech, P30-1985), 1x GlutaMAX™ Supplement (Gibco™, 35050-061), 1x MEM Non-Essential Amino Acids Solution (Gibco™, 11140-050) and Penicillin-Streptomycin mix (Gibco™, 15140-122) diluted at 1/100. For cellular reprogramming MEF medium was used, as described above, but supplemented with 15% FBS. The medium was refreshed every two days.

extract_protocol:
MEFs and cells undergoing reprogramming for 1, 2, 3, 4, 6 and 8 days were lysed and their RNA was extracted using NucleoZOL (740404, Macherey-Nagel), as by the manufacturer’s instructions. The RNAs were DNAseI-treated and cleaned-up using the classic phenol-chloroform procedure. Two biological replicates were prepared for each time-point.
RNA-seq libraries were prepared using the NEBNext® Ultra II™ Directional RNA Library prep Kit for Illumina® (E7760, NEB) with 1 ug of total RNA input, according to the manufacturer’s guidelines.

treatment_protocol: MEFs were plated in 10cm plates and reprogramming was initiated after 24 hours (day 0) with the addition of doxycycline (DOX) at 2ug/ml (Sigma-Aldrich, D9891) for OKSM transgene expression induction. Two biological replicates were prepared for each time-point. The Day 0 sample was not treated with doxycycline.

value: Mouse Embryonic Fibroblasts (MEFs)

value: MEFs treated with doxycycline at 2ug/ml for 6 days


title: heart control fibroblast, d7, rep2


title: skin explant day4 ZIKV.buffer_2


title: skin explant day4 ZIKV.buffer_4


title: MEFs treated with doxycycline, Day 8, biol rep 2, RNA-seq

value: MEFs treated with doxycycline at 2ug/ml for 8 days


title: skin explant day4 ZIKV.buffer_1


title: MEFs treated with doxycycline, Day 2, biol rep 2, RNA-seq

value: MEFs treated with doxycycline at 2ug/ml for 2 days


title: MEFs treated with doxycycline, Day 8, biol rep 1, RNA-seq


title: skin explant day3 ZIKV.buffer_3

value: day 3


title: MEFs treated with doxycycline, Day 6, biol rep 1, RNA-seq


title: MEFs treated with doxycycline, Day 2, biol rep 1, RNA-seq


title: heart SEG, d7, rep1

value: iEC


title: MEFs treated with doxycycline, Day 4, biol rep 1, RNA-seq

value: MEFs treated with doxycycline at 2ug/ml for 4 days


title: MEFs treated with doxycycline, Day 3, biol rep 2, RNA-seq

value: MEFs treated with doxycycline at 2ug/ml for 3 days


title: MEFs treated with doxycycline, Day 4, biol rep 2, RNA-seq


title: MEFs treated with doxycycline, Day 3, biol rep 1, RNA-seq


title: skin explant day3 ZIKV.buffer_4


title: MEFs treated with doxycycline, Day 1, biol rep 2, RNA-seq

value: MEFs treated with doxycycline at 2ug/ml for 1 day


title: para09 200mpk day3 rep 4

city: South San Francisco

first: Kevin

last: Huang

state: California

address: 1 DNA Way

department: Bioinformatics

institute: Genentech

description: 10x Genomics

data_processing:
Raw sequencing reads were processed and aligned to the cynomolgus reference transcriptome (Macaca Fascicularis 5.0 Assembly) via the 10x software Cellranger (v3.1.0) using default parameters to generate the raw feature and barcodes matrices. CellBender (v0.2.0) was used to remove ambient RNA effects from raw gene-by-cell count matrices for each sample using the remove-background function with the following parameters: epochs=200, fpr=0.01, total-droplets-included=30000, and expected-cells=number of cells called by CellRanger. CellBender produces processed and filtered gene-by-cell count matrices corrected for ambient RNA.
Individual samples were merged and analyzed using Seurat (v3.1.1) following the standard workflow. Briefly, cells with less than 200 UMIs or mitochondria RNA content greater than 25% were filtered. For each cell, the feature expression counts were normalized by the total expression and log transformed.
Assembly: Macaca_fascicularis_5.0
Supplementary files format and content: H5

molecule: nuclear RNA

organism: Macaca fascicularis

source_name: Frontal Cortex

extract_protocol:
Frontal cortex samples from cynomolgus monkey were placed in the lysis buffer (20 mM NaCl, 5 mM MgCL2, 0.1% TX-100, 10 mM Tris-HCl pH7.2) containing EDTA-Free protease inhibitor, RNAse inhibitor, and RNase-free DNase. Dounce homogenization was used to dissociate all tissues. Before douncing, 1 mL HBSS containing 3% BSA Fraction VI and RNAse inhibitor in nuclei suspension buffer (NSB) was added to the 2 mL Dounce Tissue Grinder. The tissues were homogenized with an A (“loose”) pestle using 5 to 10 strokes. The homogenate was then filtered through a 70 micron filter and spun down. The pellet was resuspended in the NSB. The frozen tissues were not allowed to thaw before placing in the lysis buffer and douncing. From this homegenate, nuclei were isolated density-gradient centrifugation. The homogenate was layered over an Optiprep density (40%, 20% and 10% for primates) gradient and centrifuged at 2500 g for 20 min. Nuclei at the 20/40 interface were aspirated and mixed with an equal volume of NSB. Nuclei were re-pelleted, washed, and counted using a hemocytometer prior to loading into a 10X Genomics Chromium controller.
10x Genomics 3' v3 chemistry

value: Frontal Cortex

tag: animal

tag: day

value: Para09 200 mg/kg


title: skin explant day3 ZIKV.buffer_2


title: para09 50mpk day3 rep 4

description: 10x Genomics

value: Para09 50 mg/kg


title: skin explant day2 ZIKV.buffer_4

value: day 2


title: para09 50mpk day29 rep 4

description: 10x Genomics


title: anti-gD 200mpk day3 rep 4

description: 10x Genomics

value: Anti-gD 200 mg/kg


title: MEFs (Day 0), biol rep 1, RNA-seq

tag: genotype

value: no treatment


title: para09 50mpk day29 rep 3

description: 10x Genomics


title: MEFs (Day 0), biol rep 2, RNA-seq


title: skin explant day2 ZIKV.buffer_2

value: skin explant


title: skin explant day2 ZIKV.buffer_3


title: skin explant day3 ZIKV.buffer_1


title: ESCs, ATAC-seq

data_processing:
Reads were trimmed to 50 bp using the Trimmomatic tool (Bolger et al., 2014) in The Galaxy suite (Galaxy Community, 2022).
Sequencing reads were mapped to the mm10 version of the mouse genome using the Bowtie2 algorithm (Langmead & Salzberg, 2012) with the ‘very sensitive end to end option’.
The Samtools Fixmate command was used (Li et al, 2009) prior to duplicate removal with the MarkDuplicates command from Picard tools using the option ‘do not write duplicates to the output file’.
Reads from all samples were downsampled to the same sequencing depth using the Downsample BAM option from Picard tools.
Peaks were called using the MACS2 algorithm (Zhang et al, 2008) with the options ‘no model’, ‘extension-200’, ‘shift-100’ and a q-value cutoff of 0.05.
Bigwig files were constructed using the bamCoverage command from the Deeptools suite (Ramírez et al, 2014).
Assembly: mm10
Supplementary files format and content: The "ATAC-seq_peaks_XXX".bed files are bed-format files containing the ATAC-seq peaks, produced by the MACS2 algorithm, as described above.
Supplementary files format and content: The "ATAC-seq_XXX.bigwig" files are bigwig files, produced by bamCoverage command from the Deeptools suite, as described above.

growth_protocol: MEFs (Mouse Embryonic Fibroblasts) were cultured at 37ο C and 5% CO2 concentration, in high-glucose DMEM (Sigma-Aldrich, D6429) supplemented with heat-inactivated FBS at 10% final concentration (Pan Biotech, P30-1985), 1x GlutaMAX™ Supplement (Gibco™, 35050-061), 1x MEM Non-Essential Amino Acids Solution (Gibco™, 11140-050) and Penicillin-Streptomycin mix (Gibco™, 15140-122) diluted at 1/100. For cellular reprogramming MEF medium was used, as described above, but supplemented with 15% FBS. The medium was refreshed every two days. Bruce-4 Embryonic Stem Cells (ESCs) were cultured in complete ESC medium [Knock Out DMEM (Gibco, Cat. No. 10829018), 20% ES-tested FBS (Pansera, Cat. No. P30-2602), Penicillin/Streptomycin 1X (Thermo Fischer Scientific, Cat. No. 15140122), GlutaMAX 1X (Gibco, Cat. No. 35-050-061). Non-Essential Amino Acids 1X (Gibco, Cat. No. 11140050) and mLIF 20ng/mL (Santa Cruz Biotechnology, sc-4378).

extract_protocol:
ATAC-seq libraries from different timepoints were prepared starting from 50,000 cells, following previously published protocols (Buenrostro et al, 2013, 2015; Ackermann et al, 2016; Corces et al, 2017). Briefly, cell pellets were lysed in Lysis Buffer [10mM Tris-HCl, pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin (Promega, G9441)] for 3 min on ice, washed with Wash Buffer [10mM Tris-HCl, pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% Tween-20] and centrifuged at 500g for 10 min at 4o C.
Each pellet (nuclei) was resuspended in 50ul Transposition reaction mix [1x Tagment DNA Buffer (Illumina, 15027866), 16.5ul 1x PBS, 0.1% Tween-20, 0.01% Digitonin (Promega, G9441), 2.5ul Tn5 Transposase (Tagment DNA Enzyme 1, Illumina, 15027865)] and incubated at 37o C for 30 min on a thermomixer at 1000rpm. DNA purification was performed using the Qiagen MinElute Reaction Cleanup Kit (Qiagen, 28204). Library purification was performed with the AMPure XP beads (Beckman Coulter, A63880). The quality of libraries was assessed using an Agilent 2100 Bioanalyzer and libraries were quantified with the Qubit™ High Sensitivity (HS) spectrophotometric method (Invitrogen). Libraries were sequenced paired-end using a NovaSeq 6000 sequencer at the Greek Genome Center at BRFAA.

treatment_protocol: MEFs were plated in 10cm plates and reprogramming was initiated after 24 hours (day 0) with the addition of doxycycline (DOX) at 2ug/ml (Sigma-Aldrich, D9891) for OKSM transgene expression induction. The Day 0 and ESCs sample were not treated with doxycycline.

value: Embryonic Stem Cells (ESCs)


title: skin explant day2 ZIKV.buffer_1


title: para09 200mpk day3 rep 3

description: 10x Genomics


title: anti-gD 200mpk day3 rep 3

description: 10x Genomics


title: MEFs treated with doxycycline, Day 3, ATAC-seq

value: Mouse Embryonic Fibroblasts (MEFs)


title: para09 50mpk day29 rep 2

description: 10x Genomics


title: skin explant day1 ZIKV.buffer_3

value: day 1


title: MEFs treated with doxycycline, Day 9, ATAC-seq

value: MEFs treated with doxycycline at 2ug/ml for 9 days


title: skin explant day1 ZIKV.buffer_2


title: MEFs treated with doxycycline, Day 2, ATAC-seq

value: MEFs treated with doxycycline at 2ug/ml for 2 days


title: para09 200mpk day3 rep 2

description: 10x Genomics


title: skin explant day1 ZIKV.buffer_1


title: para09 50mpk day3 rep 3

description: 10x Genomics


title: para09 50mpk day3 rep 2

description: 10x Genomics


title: skin explant day4 NeSt1_4

value: day 4


title: anti-gD 200mpk day3 rep 2

description: 10x Genomics


title: skin explant day4 NeSt1_3


title: CD4+ T cell, HDAC1-cKO, day 10, rep3

city: Vienna

first: Philipp

last: Penninger

address: Dr. Bohr-Gasse 9

country: Austria

institute: Medical University of Vienna

data_processing:
The quality of raw reads were analyzed using FastQC (Andrews, 2010).
TrueSeq (Illumina) adapters were trimmed by using cutadapt v2.8 (https://cutadapt.readthedocs.io/en/stable/; settings: -q 30 -O 1). The reads were then mapped to Mus Musculus (GRCm38/mm10) using Hisat2 v2.0.5.
Read counting was done using featureCounts v1.5.0-p3.
Differential gene expression analysis was done using the DESeq2 v1.34.0 (Love MI, Huber W, Anders S, 2014)
Assembly: Mus Musculus (GRCm38/mm10)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample and gene annotation

source_name: Spleen

growth_protocol: Directly isolated from Mus musculus spleen using total CD4+ T cell isolation kit. During sorting process maintained in PBS containing 5% heat-inactivated fetal bovine serum (FBS) and 5mM EDTA

extract_protocol:
Total RNA extraction was done with ReliaPrep RNA cell miniprep system kit (Promega)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end pairing, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Isolated T cells from unifected or systemically infected mice with C. albicans for 4, 7 and 10 days.

value: Spleen

value: primary CD4+ T cell

value: infected 10 days


title: MEFs treated with doxycycline, Day 6, ATAC-seq

source_name: Mouse Embryonic Fibroblasts (MEFs)

value: MEFs treated with doxycycline at 2ug/ml for 6 days


title: MEFs treated with doxycycline, Day 1, biol rep 1, RNA-seq

value: MEFs treated with doxycycline at 2ug/ml for 1 day


title: skin explant day4 NeSt1_2


title: para09 50mpk day29 rep 1

description: 10x Genomics

value: Frontal Cortex


title: CD4+ T cell, HDAC1-cKO, day 10, rep2


title: para09 200mpk day3 rep 1

description: 10x Genomics

value: Para09 200 mg/kg


title: skin explant day4 NeSt1_1


title: skin explant day3 NeSt1_4

value: day 3


title: para09 50mpk day3 rep 1

description: 10x Genomics

value: Para09 50 mg/kg


title: CD4+ T cell, WT, day 10, rep3

value: WT


title: anti-gD 200mpk day3 rep 1

description: 10x Genomics

value: Anti-gD 200 mg/kg


title: skin explant day3 NeSt1_3

value: skin explant


title: CD4+ T cell, WT, day 10, rep1


title: C05_PBMC_scRNA

city: Harbin

first: meng

last: cui

state: Heilongjiang

address: Xidazhi street

institute: Harbin Institute of Technology

description: Library name: sample 35

data_processing:
The demultiplexed FASTQ files were aligned and quantified using Cell Ranger (version 6.0.2, https://support.10xgenomics.com/single-cell-gene_x0002_expression/software/downloads/latest) against the GRCh38 human reference genome
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: blood

extract_protocol:
Liver biopsy tissues were obtained from donors by ultrasound-guided percutaneous liver biopsy using a 16G needle. Tissues were stored in cold HBSS buffer for subsequent dissociation. Briefly, tissues were cut into small pieces in HBSS buffer, and resuspended in 5 mL digestion buffer containing 200 U/mL type II collagenase and 10 U/mL DNase I in 1x HBSS buffer, digested at 37℃ 120 rpm for approximately 20 minutes, the cell suspension was collected and filtered through a 40-micron sterile strainer. Cells were collected for erythrocyte lysis, washed once with 2% FBS-PBS and resuspended in 50 μL of 2% FBS-PBS, and counted by Acridine Orange/ PropidiumIodide (AO/PI). For a qualified sample, the live cell ratio should be greater than 80% for 10x genomic RNA-seq.
Library construction was performed using the 10× Chromium Single-cell 5′and VDJ Library Construction Kits V2.1 (10× Genomics, Pleasanton) according to the manufacturer's protocol.

value: PBMC

tag: biomaterial provider

value: Heilongjiang Provincial Hospital and the Fourth Affiliated Hospital of Harbin Medical University

tag: geo loc_name

value: China

value: male

value: blood


title: C06_PBMC_scRNA

description: Library name: sample 36


title: CD4+ T cell, WT, day 10, rep2

value: Spleen


title: C04_PBMC_scRNA

description: Library name: sample 34

value: female


title: skin explant day3 NeSt1_1


title: MEFs (Day 0), ATAC-seq

value: Mouse Embryonic Fibroblasts (MEFs)

value: no treatment


title: CD4+ T cell, HDAC1-cKO, day 7, rep2

value: primary CD4+ T cell

value: infected 7 days


title: skin explant day2 NeSt1_3

value: day 2


title: C03_PBMC_scRNA

description: Library name: sample 33


title: skin explant day2 NeSt1_4


title: T06_PBMC_scRNA

description: Library name: sample 31


title: C01_PBMC_scRNA

description: Library name: sample 32


title: CD4+ T cell, WT, day 7, rep3


title: skin explant day2 NeSt1_2


title: skin explant day2 NeSt1_1


title: CD4+ T cell, HDAC1-cKO, day 10, rep1

value: infected 10 days


title: CD4+ T cell, WT, day 7, rep2


title: skin explant day1 NeSt1_4

value: day 1


title: CD4+ T cell, WT, day 7, rep1

value: WT


title: skin explant day1 NeSt1_3


title: CD4+ T cell, HDAC1-cKO, day 4, rep3

value: infected 4 days


title: skin explant day3 NeSt1_2

value: skin explant

value: day 3


title: T02_PBMC_scRNA

description: Library name: sample 28

value: PBMC

value: Heilongjiang Provincial Hospital and the Fourth Affiliated Hospital of Harbin Medical University


title: T05_PBMC_scRNA

description: Library name: sample 30

value: China

value: male


title: A07_PBMC_scRNA

description: Library name: sample 27

value: blood


title: skin explant day1 NeSt1_1


title: CD4+ T cell, HDAC1-cKO, day 7, rep3

value: Spleen


title: CD4+ T cell, HDAC1-cKO, day 4, rep2


title: A06_PBMC_scRNA

description: Library name: sample 26

value: female


title: skin explant day4 buffer_4

value: buffer

value: day 4


title: CD4+ T cell, WT, day 4, rep3

value: primary CD4+ T cell


title: CD4+ T cell, HDAC1-cKO, day 7, rep1

value: infected 7 days


title: A04_PBMC_scRNA

description: Library name: sample 25


title: AHB03_PBMC_scRNA

description: Library name: sample 24


title: skin explant day4 buffer_3


title: CD4+ T cell, WT, day 4, rep1


title: CD4+ T cell, WT, day 4, rep2


title: CD4+ T cell, HDAC1-cKO, day 0, rep3

value: uninfected


title: skin explant day4 buffer_1


title: skin explant day4 buffer_2


title: AHB02_PBMC_scRNA

description: Library name: sample 23


title: T04_PBMC_scRNA

description: Library name: sample 29


title: skin explant day3 buffer_4


title: AHB01_PBMC_scRNA

description: Library name: sample 22


title: CD4+ T cell, HDAC1-cKO, day 0, rep2


title: skin explant day3 buffer_3


title: HC02_LIVER_scRNA

description: Library name: sample 20

source_name: liver biopsy

value: lymphocytes/parenchymal cells

value: Anhui Provincial Hospital

value: liver


title: CD4+ T cell, HDAC1-cKO, day 0, rep1


title: skin explant day1 NeSt1_2

value: skin explant

value: day 1


title: CD4+ T cell, HDAC1-cKO, day 4, rep1

value: infected 4 days


title: HC03_LIVER_scRNA

description: Library name: sample 21


title: skin explant day3 buffer_2

value: day 3


title: HC01_LIVER_scRNA

description: Library name: sample 19

value: China


title: C06_LIVER_scRNA

description: Library name: sample 18

value: Heilongjiang Provincial Hospital and the Fourth Affiliated Hospital of Harbin Medical University

value: male


title: CD4+ T cell, WT, day 0, rep3

value: Spleen

value: WT


title: CD4+ T cell, WT, day 0, rep2


title: C05_LIVER_scRNA

description: Library name: sample 17


title: skin explant day1 ZIKV.buffer_4


title: skin explant day2 buffer_4

value: buffer

value: day 2


title: skin explant day3 buffer_1


title: skin explant day2 buffer_2


title: PRDX1 Cys52Ser-CDAHFD-8w-2

city: TIANJIN

first: Yin

last: Wen

state: TIANJIN

address: Address:No.6 North Huanrui Rd, Beichen District, Tianjin, P.R China

department: NHC Key Laboratory of Hormones and Development

institute: Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes.
Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: liver

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: PRDX1 Cys52Ser


title: C03_LIVER_scRNA

description: Library name: sample 15

value: female


title: PRDX1 Cys52Ser-CDAHFD-8w-1


title: skin explant day2 buffer_1


title: WT-CDAHFD-8w-3


title: skin explant day1 buffer_4


title: T06_LIVER_scRNA

description: Library name: sample 13


title: skin explant day1 buffer_2


title: T04_LIVER_scRNA

description: Library name: sample 11


title: T05_LIVER_scRNA

description: Library name: sample 12


title: skin explant day1 buffer_1


title: WT-CDAHFD-8w-1


title: T02_LIVER_scRNA

description: Library name: sample 10


title: TLR KO Rep 3

city: Ann Arbor

first: Michael

middle: J

last: McFadden

state: Michigan

address: 6751 Medical Science II, 1137 Catherine Street

department: Microbiology & Immunology

institute: University of Michigan

data_processing:
RNA-seq reads were evaluated using FastQC
Quality reads were trimmed using cutadapt
Trimmed transcripts were aligned to the GRCm38 mouse genome and quantified using salmon and STAR alignment software
BAM and BAI files were generated using Galaxy.org
Read density was visualized using the Interactive Genomics Viewer desktop application
Assembly: GRCm38
Supplementary files format and content: comma separated values file with raw counts from each sample

source_name: Bone marrow

growth_protocol: Immortalized bone marrow-derived macrophage cell lines were grown in bone marrow media (BMM), containing modification of Eagle’s medium (DMEM; Thermo Fisher Scientific) supplemented with 20% fetal bovine serum (Thermo Fisher Scientific), 30% L929 conditioned media, and 1 mM sodium pyruvate (Thermo Fisher Scientific).

extract_protocol:
RNA was extracted using TRIzol (manufacturer protocol), followed by TURBO Dnase I treatment for 1 hour at 37C, and an additional TRIzol extraction
PolyA enrichment was performed and sequencing libraries were prepared and sequenced on an Illumina NovaSeq 6000 with 150 bp paired-end reads by Novogene.

treatment_protocol: Immortalized bone marrow-derived macrophages were seeded in 6-well plates overnight in bone marrow media

value: Bone marrow

value: Macrophages

value: TLR KO

value: Seeded overnight in a 6-well plate


title: CD4+ T cell, WT, day 0, rep1

value: primary CD4+ T cell

value: uninfected


title: A07_LIVER_scRNA

description: Library name: sample 8

value: lymphocytes/parenchymal cells

value: liver


title: day3_TA2

value: lung

value: cell line

value: control


title: day3_TA3


title: TLR KO Rep 1

value: Immortalized bone marrow-derived macrophages


title: skin explant day2 buffer_3

value: skin explant


title: day3_TA1


title: TLR KO Rep 2


title: T01_LIVER_scRNA

description: Library name: sample 9

value: Heilongjiang Provincial Hospital and the Fourth Affiliated Hospital of Harbin Medical University

value: China

value: male


title: PRDX1 Cys52Ser-CDAHFD-8w-3

value: PRDX1 Cys52Ser


title: C04_LIVER_scRNA

description: Library name: sample 16

value: female


title: A06_LIVER_scRNA

description: Library name: sample 7


title: TLR WT Rep 3

value: Bone marrow

value: Macrophages

value: TLR WT


title: day3_4F3

value: OSKM expressing


title: A04_LIVER_scRNA

description: Library name: sample 6


title: WT-CDAHFD-8w-2

value: WT


title: TLR WT Rep 2

value: Seeded overnight in a 6-well plate


title: C01_LIVER_scRNA

description: Library name: sample 14

value: lymphocytes/parenchymal cells

value: liver


title: A02_LIVER_scRNA

description: Library name: sample 5


title: TLR WT Rep 1


title: A01_LIVER_scRNA

description: Library name: sample 4


title: day1_TA3

value: lung

value: cell line


title: skin explant day1 buffer_3

value: buffer

value: day 1


title: day3_4F1


title: AHB02_LIVER_scRNA

description: Library name: sample 2

value: Heilongjiang Provincial Hospital and the Fourth Affiliated Hospital of Harbin Medical University


title: AHB03_LIVER_scRNA

description: Library name: sample 3

value: China


title: AHB01_LIVER_scRNA

description: Library name: sample 1


title: day1_TA2

value: control


title: day1_4F3