title: xMG-7days, rep1

value: Xenotransplanted iPSC-microglia


title: PTEN null DN1 scRNA-seq

status: Public on Aug 14 2023

type: SRA

city: Beijing

first: Zihan

last: Xu

address: No.5 Yiheyuan Road Haidian District

country: China

institute: Peking University

library_source: transcriptomic

data_processing:
For ATAC-seq and RNA-seq data, quality assessment of raw reads was achieved with FastQC and contaminants were removed using Trimgalore with parameters ‘-q 30 --length 30 --stringency 5’.
ATAC-seq: The clean paired-end reads were aligned to the mm10 reference genome by Bowtie2 with the parameters -D 20 -R 3 -N 0 -L 20 -i S,1,0.50. All unmapped reads, reads mapped to the mitochondrial genome, PCR duplicates and nonuniquely mapped reads were discarded. Peaks were called using the above filtered reads by MACS with the parameters --nolambda–nomodel.
RNA-seq: The clean paired-end reads were aligned to the mm10 reference genome by Tophat with the parameter --no-novel-juncs. Gene expression levels and differentially expressed genes between samples were calculated with Cuffdiff and visualized with the R package cummeRbund.
For scRNA-seq data, sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads. TopHat was applied to align clean reads to the mm10 reference genome. Uniquely aligned reads were counted by the tool ‘htseq-count’ of HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: peak text files
Supplementary_files_format_and_content: text files include FPKM values for each sample
Supplementary_files_format_and_content: text files include UMI counts for each single cell

molecule: polyA RNA

organism: Mus musculus

source_name: thymus

extract_protocol:
Single cells were sorted into 96-well plates with lysis buffer.
Single cell RNA-seq barcoded libraries were generated and sequenced as previously described (Li et al., 2017)

tag: cell type

value: DN1 T

tag: genotype

value: Ptennull


title: SNRNP200 cytoplasmic eCLIP rep 1 (IP)

city: La Jolla

first: Brian

last: Yee

state: CA

address: 9500 Gilman Dr

department: Health

country: USA

institute: UCSD

description: SNRNP200_cyto.reproducible_enriched_windows.tsv.gz.bed

data_processing:
Data was processed using the eCLIP pipeline and available at https://github.com/YeoLab/skipper
Unique Molecular Identifiers (UMIs) were extracted using fastp 0.11.5 (https://github.com/OpenGene/fastp)
Post-umi-extracted reads were trimmed for adapter sequences and barcode sequences (eCLIP samples)
Mapping was then performed against the full human genome (hg38) including a database of splice junctions with STAR (v 2.7.6) allowing up to 100 multimapped regions.
Reads were then PCR deduplicated using UMIcollaps (https://github.com/Daniel-Liu-c0deb0t/UMICollapse
Enriched “windows” (IP versus SM-Input) was called on deduplicated reads using a GC-bias aware beta-binomial model. Each window (~100 b.p.) were partitioned from Gencode v38 and associated with a specific type of genomic region (CDS, UTR, proximal introns near splice site… etc). Windows are filtered using FDR < 0.2 and only reproducible windows between two replicates were used.
Data was processed using the eCLIP pipeline and available at https://github.com/YeoLab/skipper
Assembly: hg38
Supplementary files format and content: bed files contain Skipper windows.

molecule: total RNA

organism: Homo sapiens

source_name: Human epithelial cell

growth_protocol: DMEM + glutamine + 10% FBS

extract_protocol:
Cells were lysed and and sonicated in eCLIP lysis buffer, and RNA was fragmented using RNase I (Ambion) and RBP:RNA complexes were immunoprecipitated with RBP-specific antibody (A301-902A)
RNA was reverse transcripted with Superscript III, and adaptor was ligated with T4 RNA Ligase 1, then libraries were constructed with Q5 High-Fidelity 2x Master Mix (NEB)

treatment_protocol: 500 µM of arsenic

tag: tissue

value: Human epithelial cell

tag: cell line

value: Human epithelial kidney

tag: treatment

tag: fraction

value: IP


title: PTEN null CLP scRNA-seq

source_name: bone marrow

value: CLP


title: oMG, rep1

first: Christopher

last: Glass

address: 9500 Gilman Dr.

department: CMM

institute: University of California, San Diego

library_source: genomic

data_processing:
ATAC libraries were trimmed to 30bp and were mapped to hg38 genome using bowtie2 (Langmead and Salzberg, 2012) with default parameters. HOMER (Heinz et al., 2010) tag directories were created for mapped samples. Peaks were called using HOMER’s findPeaks command with the following parameters: “-style factor -size 200 - minDist 200” for ATAC-seq experiments. Peaks were merged with HOMER’s mergePeaks and annotated using HOMER’s annotatePeaks.pl using all tag directories.
Assembly: hg38
Supplementary files format and content: tab-delimited text files of peak files per each sample

molecule: genomic DNA

extract_protocol:
For iMGs, cells were carefully manually scraped from the Matrigel coated plate and were concentrated by a 300 rcf x 5 minutes. For oMGs, organoids were carefully collected, allowed to settle by gravity, and then dissociated mechanically in staining buffer (HBSS 1x with 1mM EDTA and 1% BSA) using a 2 ml polytetrafluoroethylene pestle. iMGs and oMGs were stained with the following Biolegend antibodies/dyes: CD64-APC (305014), CX3CR1 PCP-Cy5.5 (341614), CD14-488 (325610), CD11b-PE (301309), HLADR PE-Cy7 (307616), CD45-APC-CY7 (368516), and Zombie Violet (1:1000, Biolegend) for live/dead discrimination. xMGs were isolated and sorted at indicated time points following xenotransplantation. Briefly, mouse brains were homogenized as previously described by gentle mechanical dissociation (Gosselin et al., 2014) and stained with DAPI, CX3CR1-APC (Biolegend 149008), anti-human CD11b-PE (Biolegend 301306), anti-human CD45-FITC (Biolegend 368508). Microglia were purified with either a BD Influx  or FACS  AriaFusion.
Approximately 30,000-50,000 isolated microglia were lysed in 50 µl lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL, CA-630, in water). Resulting nuclei were centrifuged at 500 rcf for 10 minutes. Pelleted nuclei were resuspended in 50 µl transposase reaction mix (1x Tagment DNA buffer (Illumina 15027866), 2.5 µl Tagment DNA enzyme I (Illumina 15027865), and incubated at 37C for 30 min on a heat block. For isolations resulting in under 30,000 microglia, microglia directly placed in 50 µl transposase reaction mix, as indicated above and incubated for 37C for 30 min. DNA was purified with Zymo ChIP DNA concentrator columns (Zymo Research D5205), eluted with 11 µl of elution buffer, and amplified using NEBNext High-Fidelity 2x PCR MasterMix (New England BioLabs M0541) with the Nextera primer Ad1 (1.25 µM) and a unique Ad2.n barcoding primer (1.25 µM) for 8-12 cycles. Libraries were size-selected through gel excision for fragments that were 175-255 bp and single-end sequenced for 51 cycles on a HiSeq 4000 or NextSeq 500.

value: iPSC-microglia co-cultured with cerebral organoid


title: R13

city: Rensselaer

first: Farhad

last: Farjood

state: NY

address: 1 Discovery Drive

institute: Neural Stem Cell Institute

data_processing:
Bam files were then read into R using the GenomicAlignments package to generate a counts matrix for further analysis
Assembly: hg19
Supplementary files format and content: Rdata file with count matrices for each sample

source_name: RPE

growth_protocol: Cultures were maintained in RPE medium: MEM-a modified medium (Sigma-Aldrich), 2 mM L-glutamine, penicillin/streptomycin (1:100), 1% Na-Pyruvate, 10% fetal bovine serum supplemented with THT (Taurine, Hydrocortisone, Triiodo-thyronin), and N1 medium supplement (Sigma-Aldrich). Cells were incubated in a humidified incubator at 37oC and 5% CO2 and the medium was replaced every 3 days

extract_protocol:
RNA was harvested using Direct-zol RNA kit (Zymo Research)
Library preparation was then carried out with the TruSeq Stranded Total RNA kit (Illumina)

value: RPE

value: WT

tag: time

value: 4 weeks


title: R12


title: oMG, rep2


title: SNRNP200 whole cell eCLIP rep 2 (IP)

description: SNRNP200_HEK.reproducible_enriched_windows.tsv.gz.bed


title: iMG, rep5

value: iPSC-microglia


title: PTEN null MPP scRNA-seq

value: MPP


title: R11


title: SNRNP200 whole cell eCLIP rep 1 (IP)


title: iMG, rep4


title: R16

value: 5 weeks


title: SNRNP200 cytoplasmic stress eCLIP rep 2 (input)

description: SNRNP200_stress.reproducible_enriched_windows.tsv.gz.bed

value: 500 µM of arsenic

value: input


title: R10

value: 3 Weeks


title: iMG, rep3


title: PTEN null HPC1 scRNA-seq


title: R09


title: iMG, rep2


title: iMG, rep1


title: PTEN null CD38 high prepro-B RNA-seq Rep 2

description: alldata.txt

extract_protocol:
Total RNA was extracted from FACS-sorted cells using RNeasy Micro Kit (Qiagen, 74004)
RNA-seq barcoded libraries were generated and sequenced as previously described (Zhu et al., 2018)

value: CD38+ prepro-B


title: R07


title: SNRNP200 whole cell stress eCLIP rep1 (input)

description: SNRNP200_HEKstress.reproducible_enriched_windows.tsv.gz.bed


title: CH02 ONT-junctions

city: New York

first: Dan

middle: A.

last: Landau

address: 101 6th Ave

department: Molecular Pharmacology Program

institute: New York Genome Center

data_processing:
0X Illumina data was processed using Cell Ranger (v.3.1.0) with default parameters and reads were aligned to the human reference sequence.
Genotyping of single cells was carried out with the IronThrone (v.2.1) pipeline. In brief, individual amplicon reads were assessed for the appropriate structure (i.e. presence of the primer sequence and the expected sequence between the primer and given mutation site) and all reads were assessed for a matching cell barcode to the list generated from the 10X paired GEX dataset. A Levenshtein distance of 0.1 was allowed for all sequence matching and collapsing steps and only UMIs with a minimum of 2 supporting reads were retained for final genotyping. Following UMI collapse, genotype assignment of individual UMIs was conducted as described previously with majority rule of supporting reads for wildtype or mutant status (using a 0.7 PCR read ratio, above which the majority of PCR reads must be in order for a UMI to be called definitively). Rare UMIs that did not pass this threshold were removed as ambiguous. Additionally, to remove reads that result from PCR recombination, UMIs in the amplicon library that match UMIs of non-SF3B1 genes in the gene expression library were discarded. Each single cell was assigned as either mutant or wildtype as follows: cells with at least 1 mutant UMI were assigned as mutant cells and cells with 0 mutant UMIs and at least 1 wildtype UMI were assigned as wildtype.
scRNA-seq ONT long-read sequencing data processing, alignment, junction calling and annotation
Guppy v3.0.6 - 4.0.11 was used for basecalling output from ONT sequencing to create FAST5 files that were then converted to FASTQ files. After generating FASTQ files from the long-read ONT sequencing, we then filtered for only reads containing a polyA tail within 100 base pairs of either 5’ or 3’ end using the `NanoporeReadScanner-0.5.jar` within the SiCeLoRe-1.0 workflow. Filtered reads are aligned to the primary human genome, assembly GRCh38.p12 using minimap2 (v.2.17). Minimap2 was used with the `-ax splice` flag to prioritize annotated splice junctions. Additionally we made use of the `--junc-bed` option, to increase alignment scores for those splice junctions found in the reference junction bed file. For our reference junctions, we used splice junctions from single-cell SMART-seq2 data from human CD34+ cells obtained from a CH sample with no SF3B1 mutation. Additionally we used `--secondary=no` to suppress multi-mappings.
In preparation to identify the cell barcodes and UMI’s present in the long-read sequencing, we used the `IlluminaParser-1.0.jar` in SiCeLoRe to parse the cell barcodes and UMI’s present in the complementary short-read sequencing library. We continued to use SiCeLoRe to tag the aligned bam files with cell barcodes and UMI’s identified in the short-read library, and generate consensus sequences for each unique cell barcode and UMI combination. Consensus sequences were used to create a gene by cell count matrix.Intron-junction calling is then performed on consensus sequence BAM files, adapted from the method used in the LeafCutter pipeline for short read RNA-seq data. In brief, the Intron junction calling pipeline utilizes the pysam.fetch() function and iterates through each transcript in the bam file, noting its cell barcode (CB) tag as well as the coordinates of each intron-junction for that transcript. On iterating through the bam file, counts for the usage of each unique intron-junction and the corresponding CB are recorded. This ultimately generates an Intron-Junction x Cell Barcode count matrix for the given bam file. Each intron-junction is then identified using annotations available in the GENCODE GRCh38.p12 v31 basic annotation reference file as either canonical 3’, canonical 5’, alternative 3’, alternative 5’. This outputs a metadata file with annotations for each junction corresponding to the junctions of the Intron-Junction x Cell Barcode count matrix.
Assembly: hg38
Supplementary files format and content: Processed 10X data is matrix table of  gene counts per cell for each sample
Supplementary files format and content: Output matrices processed from amplicon data have five columns: number of wildtype calls (WT.calls),  number of mutant calls (MUT.calls) , genotype (Genotype), cell assignments (Cell.Assignment). Row names are the corresponding barcodes..
Supplementary files format and content: Junction files contain a junction (rows) per cell barcode (columns) matrix of read counts.

source_name: Bone marrow aspirate from patient

extract_protocol:
Cryopreserved mononuclear cells isolated from bone marrow biopsies or peripheral blood from myelodysplastic syndrome patients with SF3B1 mutations were retrieved from Memorial Sloan Kettering, and University of Manchester. Additionally, cryopreserved G-CSF mobilized stem cell grafts (without additional mobilizing agents such as plerixafor or cyclophosphamide) from CH patients with SF3B1 mutations were retrieved from the Dana Farber Cancer Institute. Cryopreserved mononuclear cells and grafts were thawed and stained using standard procedures. Cells were first incubated with Human FcX blocking solution (Biolegend, #422302) and then incubated with the surface antibody CD34-PE-Vio770 (clone AC136, lot #5180718070, dilution 1:50, Miltenyi Biotec) and DAPI (Sigma-Aldrich) for 10 minutes at 4°C. Cells were then sorted for DAPI-negative, CD34+ cells using BD Influx at the Weill Cornell Medicine flow cytometry core.
The standard 10x Genomics Chromium 3’ (v.3.1 chemistry) and CITE-seq protocols35,36 were carried out according to manufacturer’s recommendations for the generation of scRNA-seq and ADT libraries (Fig. 1A). At the cDNA amplification step in the 10x Genomics protocol, 1 μL of 1 μM spike-in primer (5’ –GATCCTCGTCCTCATTGAACCGC– 3’) was added to increase the yield of SF3B1 cDNA and 1 µL of 0.2 µM ADT PCR additive primer (5’ – CCTTGGCACCCGAGAATTCC – 3’) was added to amplify ADT. After cDNA amplification and a double-sided cleanup with SPRI beads to separate cDNA and ADT fractions, the ADT fraction was amplified for 10 cycles with SI-PCR oligo (10x Genomics) and TruSeq Small RNA RPI-x (Illumina) primers to index the samples. SPRI was used to clean up the ADT final products.In both samples in which CITE-seq was conducted and not conducted, cDNA was allocated for gene expression library creation (standard 10x protocol; 25% of cDNA), targeted genotyping (10% of cDNA), and ONT on-bead library preparation (10ng of cDNA). Any remaining cDNA was stored.For locus-specific amplification (GoT), two serial PCRs were performed with nested reverse primers, based on the SF3B1 mutation of interest. For mutations upstream of K700E, (5’ – GATCCTCGTGGTCATTGAACCGC – 3’ and 5’ – CACCCGAGAATTCCAGGCTACTATGATCTCTACCATGAGACCTG – 3’) and, for K700E mutations, (5’ – GTGCAAAAGCAAGAAGTCCT – 3’ and 5’ –CACCCGAGAATTCCATGAACATGGTCTTGTGGATGAGC – 3’) were used as reverse primers. These reverse primers and the generic forward SI-PCR amplify the site of interest from the cDNA template (10 PCR cycles each). The second locus-specific reverse primers contain a partial Illumina TruSeq Small RNA read 2 handle and a locus-specific region to allow SF3B1 specific priming. The SI-PCR oligo (10x Genomics) anneals to the partial Illumina TruSeq read 1 sequence, preserving the cell barcode (CB) and unique molecule identifier (UMI). After these rounds of amplification and SPRI purification to remove unincorporated primers, a third PCR was performed with a generic forward PCR primer (P5_generic, 5’ – AATGATACGGCGACCACCGAGATCTACAC – 3’) to retain the CB and UMI together with an RPI-x primer (Illumina) to complete the P7 end of the library and add a sample index (6 PCR cycles).Gene expression, ADT, and SF3B1 amplicon libraries were pooled to receive 25,000, 5,000, and 5,000 reads per cell, respectively, during Illumina sequencing. The cycle settings were as follows: 28 cycles for read 1, 90 cycles for read 2, 10 cycles for i7, and 10 cycles for i5 sample index. To examine splicing patterns broadly in the whole transcriptome, full length cDNA was sequenced using the Oxford Nanopore Technology sequencing platform on PromethION flow cells. To enrich for transcripts that contain CBs and UMIs and decrease the presence of PCR artifacts, on-bead PCR with a biotinylated primer selecting for an adapter upstream of the CB was completed. In brief, 10ng of full length cDNA was amplified with LongAmp master mix (NEB) and TSO (5’ – NNNAAGCAGTGGTATCAACGCAGAG – 3’) and biotinylated read 1 (5’ – /5Biosg/AAAAACTACACGACGCTCTTCCGATCT – 3’) primers for 5 cycles. After cleanup with SPRI, 1X and 5X SSPE-washed M270 streptavidin beads (ThermoFisher) were added to the PCR product. After a 15 minute incubation and washes with 1X SSPE and 10mM Tris-HCl (pH 8, the bead-bound PCR products and beads were resuspended in PCR master mix for further amplification. Samples were amplified with LongAmp master mix and TSO and read 1 (5’ – NNNCTACACGACGCTCTTCCGATCT – 3’) primers for 5 cycles. After cleanup with SPRI, 1000ng of each full length cDNA library was sequenced on one the PromethION flow cell.
Single-cell RNA-seq (10X and long-read ONT) with targeted amplification of a mutation of interest. Two runs of the experiment, A and B, were completed for sample MDS02.

tag: disease

value: Clonal Hematopoesis

value: CD34+ sorted GCSF mobilized stem cell graft


title: PTEN null CD38 high prepro-B RNA-seq Rep 1

description: alldata.txt

value: Ptennull


title: R06

value: 2 Weeks


title: R05


title: CAPRIN eCLIP rep 2 (input)

description: CAPRIN.reproducible_enriched_windows.tsv.gz.bed

value: Human epithelial cell

value: Human epithelial kidney


title: PTEN null CD38 low prepro-B RNA-seq Rep 3

description: alldata.txt

value: CD38- prepro-B


title: CH01 ONT-junctions


title: CAPRIN eCLIP rep 1 (input)


title: MDS06 ONT-junctions

value: CD34+ and CD34-

value: Myelodysplatic syndrome

value: EPO + GCSF

value: Bone marrow


title: PTEN null CD38 low prepro-B RNA-seq Rep 2

description: alldata.txt


title: G3BP1 eCLIP rep 2 (input)

description: KR_G3BP1_HEK.reproducible_enriched_windows.tsv.gz.bed


title: PTEN null HPC2 scRNA-seq


title: PTEN null CD38 low prepro-B RNA-seq Rep 1

description: alldata.txt


title: R04

value: RPE

value: WT


title: G3BP1 eCLIP rep 1 (input)


title: WT CD38 high prepro-B RNA-seq Rep 3

description: alldata.txt


title: SNRNP200 cytoplasmic stress eCLIP rep 1 (input)

value: 500 µM of arsenic


title: R03


title: PTEN null CD38 high prepro-B RNA-seq Rep 3

description: alldata.txt


title: R08


title: SNRNP200 cytoplasmic eCLIP rep 2 (input)

value: input


title: SNRNP200 whole cell stress eCLIP rep2 (input)


title: Surgery alone, tumor sample, scRNAseq (S9478T)

city: Ningbo

first: Yanguo

last: Li

state: zhejaing

address: fenghua road 818

department: IDDT

institute: Ningbo university

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2
scDblFinder was used to identify doublets across all cells in R v3.6. The Seurat package (v4.0) was used for downstream analysis. The complexity of single cells was calculated by the number of detected genes (nFeature_RNA) divided by the read count (nCount_RNA) on a log10 scale. The values were used to estimate ambient RNA droplets and filtrate low complexity cells such as dead cells and granulocytes. Cells with complexity values higher than 0.8 were reserved according to the data distribution. Then, cells with singlet annotation and high quality (count/cell > 500, genes/cell >600, <15% mitochondrial genes, <0.1% erythrocytic genes and complexity > 0.80) were used for further analysis with default parameters unless otherwise stated. Principal component analysis (PCA) and the Harmony package (v1.0) were used to remove batch effects (each sample was seen as a batch) and integrate data after normalization (SCTransform function with 1500 variable features). For unsupervised clustering, we applied the FindNeighbors function with a reduction in Harmony (dims=1:34, k.param=50), and the FindClusters function with a resolution array and clustering tree were plotted with the clustree package to subjectively evaluate the robustness resolution (0.8). We used an elbow plot to determine the optimal number of principal components for reduction and clustering, and a more quantitative approach developed by members of the teaching team at the Harvard Chan Bioinformatics Core (HBC) was used to calculate where the principal components started to elbow by taking the larger value of 1) the point where the principal components only contributed 5% of the standard deviation and the principal components cumulatively contributed 80% of the standard deviation and 2) the point where the percent change in variation between the consecutive principal components was less than 0.1%.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: esophagus

extract_protocol:
The samples for scRNA-seq were washed with phosphate-buffered saline (PBS; Thermo Fisher Scientific, Waltham, MA, USA), placed on ice, cut into small pieces (< 2 mm3) and transferred to 5 mL Roswell Park Memorial Institute 1640 (RPMI; Thermo Fisher Scientific) containing collagenase IV (1 μg/mL), collagenase I (2 μg/mL) and DNase (1 μg/mL) (Thermo Fisher Scientific). The samples were incubated for 40 min at 37 °C with manual shaking every 5 min and then filtered through both 70-µm and 40-µm nylon mesh (Thermo Fisher Scientific). Following centrifugation (300 × g, 4 °C, and 5 min), the samples were then resuspended in PBS containing 0.04% bovine serum albumin (BSA; Sigma). Next, the cells were counted and assessed for viability using Trypan blue staining with a hemocytometer. During the dissociation procedure, the cells were kept on ice whenever possible, and the entire procedure was completed in < 90 min (generally ~70 min) to avoid the dissociation-associated artifacts recently described. A positive signal for dissociation signatures that reflects dissociation-associated changes in gene expression was obtained in < 1% of the cells.
Droplet-based scRNA-seq, a chromium single-cell 3′-library, was constructed using the Chromium Single-cell 3′-Library, Gel Bead & Multiplex Kit and Chip Kit (10× Genomics, Pleasanton, CA, USA) according to the manufacturer’s instructions. Cell suspensions were loaded onto a chromium single-cell chip along with reverse transcription (RT) master mix and single-cell 3′-gel beads, aiming for 2,000–8,000 single cells per reaction. The samples were processed using 10× Genomics V3 barcoding chemistry kits (Supplementary information, Table S2). Following cell lysis, first-strand cDNA synthesis and amplification were carried out according to the manufacturer’s instructions with cDNA amplification set for 12 cycles.

tag: individual

tag: disease state

value: ESCC

value: tumor sample

value: Surgery alone


title: WT CD38 high prepro-B RNA-seq Rep 2

description: alldata.txt

value: CD38+ prepro-B


title: SNRNP200 cytoplasmic eCLIP rep 1 (input)


title: Surgery alone, adjacent normal sample, scRNAseq (S9478N)

description: 10x Genomics

value: adjacent normal sample


title: MDS04 ONT-junctions

value: G-CSF


title: WT CD38 high prepro-B RNA-seq Rep 1

description: alldata.txt


title: MDS05 ONT-junctions

value: Lenalidomide and darbopoietin


title: WT CD38 low prepro-B RNA-seq Rep 3

description: alldata.txt


title: SNRNP200 whole cell eCLIP rep 2 (input)

value: Human epithelial cell

value: Human epithelial kidney


title: Surgery alone, adjacent normal sample, scRNAseq (S6417N)

description: 10x Genomics


title: WT CD38 low prepro-B RNA-seq Rep 2

description: alldata.txt

value: CD38- prepro-B


title: Chemoradiotherapy, tumor sample, scRNAseq (S6829T)

description: 10x Genomics

value: Chemoradiotherapy


title: CH02 10X

value: Clonal Hematopoesis

value: CD34+ sorted GCSF mobilized stem cell graft


title: MDS01 ONT-junctions

value: Myelodysplatic syndrome

value: Bone marrow


title: MDS02 ONT-junctions


title: CH01 10X


title: KaryoCreate-sgChr18 Clone 14, Replicate 2

first: Joseph

middle: Charles

last: Mays

address: 435 E 30th St

department: Institute for Systems Genetics

institute: NYU School of Medicine

description:
processed data files header: D29_g18-4_14_B
Raw_Counts.txt
Normalized_Counts.txt

data_processing:
RNA sequencing reads were processed, quality controlled, aligned, and quantified using the Seq-N-Slide software
total RNA sequencing reads were trimmed using Trimmomatic73 and mapped to the GENCODE human genome hg38 by STAR
featureCounts was used to quantify reads and generate a genes-sample counts matrix.
Normalization was completed with DESeq2 in R
Assembly: hg38
Supplementary files format and content: Raw_Counts.txt matrix contains raw gene level counts for each sample
Supplementary files format and content: Normalized_Counts.txt matrix contains all gene level counts for each sample after normalization with DESeq2

source_name: hCEC

extract_protocol:
RNA was purified for bulk sequencing using the Qiagen RNeasy Mini Kit (Qiagen 74106).
Sequencing libraries were constructed using the TruSeq Stranded Total RNA Library Prep Gold (Illumina, San Diego, CA) with an input of 250ng and 13 cycles final amplification.

value: hCEC

tag: clone

value: Clone 14

value: with chromosome 18q loss


title: WT CD38 low prepro-B RNA-seq Rep 1

description: alldata.txt

value: WT


title: KaryoCreate-sgChr18 Clone 14, Replicate 1

description:
processed data files header: D29_g18-4_14_A
Raw_Counts.txt
Normalized_Counts.txt


title: MDS03 ONT-junctions


title: Chemoradiotherapy and Immunotherapy, tumor sample, scRNAseq (S2487T)

description: 10x Genomics

value: ESCC

value: tumor sample

value: Chemoradiotherapy and Immunotherapy


title: Chemoradiotherapy, tumor sample, scRNAseq (S2423T)

description: 10x Genomics


title: MDS06 10X

value: CD34+ and CD34-

value: EPO + GCSF


title: PTEN null CD38 high prepro-B ATAC-seq Rep 3

extract_protocol:
ATAC-seq libraries were generated using 1000 sorted cells
ATAC-seq barcoded libraries were constructed as previously described (Wu et al., 2018)

value: CD38+ prepro-B

value: Ptennull


title: KaryoCreate-sgChr18 Clone 13, Replicate 2

description:
processed data files header: D29_g18-4_13_B
Raw_Counts.txt
Normalized_Counts.txt

value: Clone 13

value: without chromosome 18q loss


title: Chemoradiotherapy, tumor sample, scRNAseq (S1535T)

description: 10x Genomics

value: Chemoradiotherapy


title: KaryoCreate-sgChr18 Clone 13, Replicate 1

description:
processed data files header: D29_g18-4_13_A
Raw_Counts.txt
Normalized_Counts.txt


title: PTEN null CD38 high prepro-B ATAC-seq Rep 2


title: Surgery alone, tumor sample, scRNAseq (S6417T)

description: 10x Genomics

value: Surgery alone


title: SNRNP200 whole cell eCLIP rep 1 (input)

value: Human epithelial cell

value: Human epithelial kidney

value: input


title: MDS05 10X

value: Myelodysplatic syndrome

value: Lenalidomide and darbopoietin

value: Bone marrow


title: Anti-angiogenesis, tumor sample, scRNAseq (S1315TS)

description: 10x Genomics

value: ESCC

value: Anti-angiogenesis


title: MDS04 10X

value: G-CSF


title: PTEN null CD38 low prepro-B ATAC-seq Rep 3

value: CD38- prepro-B


title: MDS03 10X


title: MDS02 10X


title: PTEN null CD38 high prepro-B ATAC-seq Rep 1


title: 1wk ATAC

city: Helsinki

first: Biswajyoti

last: Sahu

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

data_processing:
Raw sequencing data were processed using the Cell Ranger ARC pipeline (version 2.0.1) with the GRCh38 reference (refdata-cellranger-arc-GRCh38-2020-A-2.0.0) for demultiplexing, alignment, barcode and feature counting to generate GEX and ATAC feature-barcode matrices
Assembly: hg38
Supplementary files format and content: Raw feature barcode sparse matrix. Rows are the gene (GEX) and peak (ATAC) features and columns are cell barcodes. Values are number of  UMI counts (GEX) or number of ATAC transposition events in peaks (ATAC).

source_name: Human foreskin fibroblasts

growth_protocol: HFFs (ATCC, #CRL-2429) were cultured in fibroblast medium (DMEM supplemented with 10% FBS, 2 mM L-Glutamine, 1 mM Sodium pyruvate and 1% penicillin-streptomycin).

extract_protocol:
Nuclei isolation for snRNA-seq & ATAC-seq was optimized and performed following the demonstrated protocol CG000365 from 10x Genomics. The capture of mRNA and transposed DNA fragments was performed following 10xGenomics user guide CG000338.
The snRNA-seq & ATAC-seq libraries were prepared following the 10xGenomics user guide CG000338. The custom libraries for TF barcode analysis was prepared using pre-amplified cDNA from Step 4 in protocol CG000338 by a two-step PCR process (See Methods).

treatment_protocol: Early-passage HFFs were transduced with constructs for TF expression and kept in defined reprogramming medium to induce cell fate convertion (See Methods). The reprogramming cells were collected at different time points for single-cell gene expression and chromatin accessibility analysis. HFFs only transduced with GFP were used as control.

value: Human foreskin fibroblasts

value: Transduced with 6-TF cocktail

tag: time point


title: 2wk ATAC


title: Chemoradiotherapy, tumor sample, scRNAseq (S1265T)

description: 10x Genomics

value: tumor sample


title: Chemotherapy, tumor sample, scRNAseq (S0520T)

description: 10x Genomics

value: Chemotherapy


title: PTEN null CD38 low prepro-B ATAC-seq Rep 2

value: Ptennull


title: HFF-GFP&48h ATAC

value: Sample 48h, transduced with 6-TF cocktail; Sample HFF-GFP used as control


title: PTEN null CD38 low prepro-B ATAC-seq Rep 1


title: CH02 Amplicon

value: Clonal Hematopoesis

value: CD34+ sorted GCSF mobilized stem cell graft


title: Custom library_2wk

description: The custom libraries contain the cell and TF barcodes, and corresponding information can be found in the cell annotation file (cellInfo.tsv, column "TF").


title: PTEN null CLP ATAC-seq Rep 2

value: CLP


title: vHip,Susceptible,Rep6

city: Mainz

first: Susanne

last: Gerber

address: Staudinger Weg 9

department: Institute for Human Genetics

country: Germany

institute: University Medicine Mainz

data_processing:
RNA-Seq data quality was checked using FastQC. STAR aligner was used to align raw reads to reference genome.
HTSeq was used to count reads per gene. To perform differential experssion analysis DESeq2 library was used.
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw read counts of each sample.

molecule: nuclear RNA

source_name: ventral Hippocampus

extract_protocol:
Following nuclei isolation, Ten thousand GFP+ or GFP- FANS-sorted nuclei were collected in 100 μL of RLT buffer followed by flash freezing. RNA was purified using the RNeasy Micro kit (Qiagen 74004, Hilden, Germany) following the manufacturer’s instructions.
For the nuclear RNA-seq library preparation, we used  the Ovation® SoLo RNA-Seq System following NuGEN’s standard protocol (NuGEN M01406v2, Redwood City, CA, USA).

value: ventral Hippocampus

tag: phenotype

value: susceptible


title: Custom library_1wk


title: MDS01 10X

value: Myelodysplatic syndrome


title: vHip,Susceptible,Rep5


title: PTEN null CLP ATAC-seq Rep 1


title: vHip,Susceptible,Rep4


title: CH01 Amplicon


title: Custom library_48h


title: PTEN null LMPP ATAC-seq Rep 2

value: LMPP


title: MDS06 Amplicon

value: CD34+ and CD34-

value: EPO + GCSF

value: Bone marrow


title: PTEN null LMPP ATAC-seq Rep 1


title: 1wk GEX


title: MDS05 Amplicon

value: Lenalidomide and darbopoietin


title: 2wk GEX

value: Human foreskin fibroblasts


title: vHip,Susceptible,Rep3


title: vHip,Susceptible,Rep2


title: PTEN null HSC ATAC-seq Rep 2

value: HSC


title: vHip,Resilience,Rep7

value: resilient


title: MDS03 Amplicon


title: MDS02 Amplicon


title: HFF-GFP&48h GEX


title: R-IgG replicate 2

data_processing:
The quality metrics of the fastq files were checked with FastQC. The reads were mapped to the human reference genome (UCSC GRCh38/hg38) by Bowtie2 (v2.2.5) with option ‘--very-sensitive’. Duplicates were marked using Picard MarkDuplicates and removed using samtools (v1.9) view with option ‘-F 1024’. Reads were subsequently filtered for alignment quality of less than 20.
The peaks were called using MACS2 (2.1.1) with the parameter ‘--keep-dup all’ and the blacklisted regions downloaded from ENCODE were removed.
To generate the bigwig signal tracks from the aligned bam files, deeptools (3.1.3) bamCoverage was used with options ‘--normalizeUsing RPKM --binSize 10’.
Assembly: hg38
Supplementary files format and content: narrowPeak and bigwig (except for IgG sample)

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed as previously described (Sahu et al. EMBO J 2011). Cells were ﬁxed in 1% formaldehyde for 10 min at RT. Glycine was added to a final concentration of 0.125 M and incubated for 5 min to quench the reaction. Cells were then washed twice with ice-cold PBS and collected for lysis in RIPA buffer with protease inhibitors. Cross-linked chromatin was sonicated to an average fragment size of 200-500 bp, then it was immunoprecipitated with either H3K27ac antibody (Diagenode, #C15410196) or normal rabbit IgG (Santa Cruz, #sc-2027), 2μg of antibody per reaction.
Libraries were prepared as previously described (Sahu et al. EMBO J 2011) according to Illumina’s instructions.

treatment_protocol: Early-passage HFFs were transduced with constructs for TF expression and kept in defined reprogramming medium to induce cell fate convertion (See Methods).  The reprogramming cells were collected at different time points for H3K27ac enrichment analysis. HFFs only transduced with GFP were used as control.

value: Transduced with 6-TF cocktail

tag: antibody

value: IgG


title: vHip,Susceptible,Rep1


title: MDS01 Amplicon


title: R-IgG replicate 1


title: vHip,Resilience,Rep6


title: PTEN null HSC ATAC-seq Rep 1

value: Ptennull


title: WT CD38 high prepro-B ATAC-seq Rep 3

value: CD38+ prepro-B

value: WT


title: vHip,Resilience,Rep5


title: RM-1wk replicate 2


title: WT CD38 high prepro-B ATAC-seq Rep 1


title: Liver 4_TCR

city: Oxford

first: Lucy

last: Garner

address: Experimental Medicine, Level 5, John Radcliffe Hospital

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Library strategy: TCR-seq
BCL files were converted to FASTQ files using cellranger mkfastq (v2.1.1-3.0.1).
Alignment, filtering, barcode counting and UMI counting were performed using cellranger count (v3.0.1).
Single-cell V(D)J sequences and annotations were generated using cellranger vdj (v3.0.1).
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered_feature_bc_matrix.h5 output file from cellranger count (v3.0.1) - filtered feature-barcode matrices containing only cellular barcodes in HDF5 format. filtered_contig_annotations.csv output file from cellranger vdj (v3.0.1) - high-level annotations of each high-confidence, cellular contig.
Supplementary_files_format_and_content: all_samples_counts.txt: raw gene counts after QC (i.e. after removal of poor quality cells, lowly expressed genes etc.) for combined analysis of MAIT cells from all samples (n = 7). all_samples_metadata.txt: metadata for cells in all_samples_counts.txt, including cluster identity of each cell. blood_counts.txt: raw gene counts after QC for combined analysis of MAIT cells from blood samples (n = 3). blood_metadata.txt: metadata for cells in blood_counts.txt, including cluster identity of each cell. liver_counts.txt: raw gene counts after QC for combined analysis of MAIT cells from liver samples (n = 4). liver_metadata.txt: metadata for cells in liver_counts.txt, including cluster identity of each cell.

source_name: Liver

extract_protocol:
Liver tissue and matched blood were obtained from patients (50-65 years old) undergoing liver resection for metastatic colorectal cancer (n = 1; male), haemangioma (n = 1; female), or hepatocellular carcinoma (n = 2; one male and one female). Disease-free liver tissue was collected from the resection margin. Liver tissue was cut into small pieces with a scalpel and ground through a 70 μm cell strainer. Cells were washed with R10 (RPMI-1640 [Sigma-Aldrich] + 10% FCS [Sigma-Aldrich] + 1% Penicillin-Streptomycin [Thermo Fisher Scientific]; 2000 rpm [931 g], 10 min, 4°C) and mononuclear cells isolated by density gradient centrifugation on a discontinuous 35%/70% Percoll (GE Healthcare) gradient (2000 rpm [931 g], 20 min, room temperature, no brake). Mononuclear cells were collected from the interface and washed with R10 (1600 rpm [596 g], 10 min, 4°C). Residual red blood cells were lysed with ammonium-chloride-potassium (ACK) for 3-5 min. Cells were washed twice (1600 rpm [596 g], 10 min, 4°C) and cryopreserved (90% FCS, 10% DMSO [Sigma-Aldrich]) in liquid nitrogen. PBMCs were isolated from fresh whole blood by density gradient centrifugation (Lymphoprep, Axis-Shield) at 2000 rpm (931 g) for 30 min with no brake. Cells were cryopreserved (90% FCS, 10% DMSO) in liquid nitrogen. Blood and liver cells were thawed, stained, and live MAIT cells (CD3+MR1/5-OP-RU+) and memory T cells (CD3+MR1/5-OP-RU-CCR7-; donor 2 and 3 only) sorted by fluorescence-activated cell sorting (BD FACSAria III, 70 μm nozzle).
scRNA-seq and scTCR-seq libraries were generated using Chromium Single Cell V(D)J Reagent Kits (v1.0 Chemistry) following manufacturer's instructions.

tag: donor

value: Liver

value: MAIT


title: vHip,Resilience,Rep4

value: ventral Hippocampus


title: Liver 3.B_TCR

description:
Processed data file on GSM5830300
615171_02_S5_L003


title: RM-1wk replicate 1


title: vHip,Resilience,Rep3


title: WT CD38 low prepro-B ATAC-seq Rep 3

value: CD38- prepro-B


title: RM-96h replicate 2


title: MDS04 Amplicon

value: Myelodysplatic syndrome

value: G-CSF


title: Liver 3.A_TCR


title: Blood 3.B_TCR

description:
Processed data file on GSM5830298
615171_04_S7_L003

source_name: Blood

value: Blood


title: RM-96h replicate 1


title: vHip,Resilience,Rep2


title: RM-48h replicate 2


title: Blood 3.A_TCR


title: vHip,Resilience,Rep1


title: vHip,Control,Rep6

value: control


title: WT CD38 high prepro-B ATAC-seq Rep 2


title: RM-48h replicate 1


title: vHip,Control,Rep5


title: vHip,Control,Rep4


title: HFF-GFP replicate 2

value: Transduced with GFP


title: Liver 2.B_TCR

description:
Processed data file on GSM5830296
615171_06_S9_L003


title: Blood 2.B_TCR

description:
Processed data file on GSM5830294
615171_08_S11_L003


title: WT LMPP ATAC-seq Rep 2

value: LMPP


title: WT LMPP ATAC-seq Rep 1


title: WT CLP ATAC-seq Rep 1

value: CLP


title: HFF-GFP replicate 1

value: Human foreskin fibroblasts


title: vHip,Control,Rep3


title: Blood 2.A_TCR


title: RM-1wk replicate 2

data_processing:
The quality metrics of the fastq files were checked with FastQC. The reads were mapped to the human reference genome (UCSC GRCh38/hg38) by Bowtie2 (v2.2.5) with option ‘--very-sensitive’. The reads that mapped to mitochondrial DNA were discarded. Duplicates were marked using Picard MarkDuplicates and removed using samtools (v1.9) view with option ‘-F 1024’. Reads were subsequently filtered for alignment quality of less than 10.
The peaks were called using MACS2 (2.1.1) with the parameter ‘--keep-dup all’ and the blacklisted regions downloaded from ENCODE were removed.
To generate the bigwig signal tracks from the aligned bam files, deeptools (3.1.3) bamCoverage was used with options ‘--normalizeUsing RPKM --binSize 10’.
Assembly: hg38
Supplementary files format and content: narrowPeak and bigwig (except for IgG sample)

extract_protocol:
The cells were extracted and processed as per ATAC-seq protocol (Buenrostro et al. Curr Protoc Mol Biol. 2015, Corces et al. Nature Methods. 2017).
The ATAC-seq library was prepared as per the ATAC-seq protocol (Buenrostro et al. Curr Protoc Mol Biol. 2015, Corces et al. Nature Methods. 2017).

treatment_protocol: Early-passage HFFs were transduced with constructs for TF expression and kept in defined reprogramming medium to induce cell fate convertion (See Methods).  The reprogramming cells were collected at different time points for chromatin accessibility analysis. HFFs only transduced with GFP were used as control.

value: Transduced with 6-TF cocktail


title: WT HSC ATAC-seq Rep 2

value: HSC


title: WT CD38 low prepro-B ATAC-seq Rep 2


title: RM-1wk replicate 1


title: WT CD38 low prepro-B ATAC-seq Rep 1


title: vHip,Control,Rep2


title: Liver 1_TCR


title: WT HSC ATAC-seq Rep 1


title: vHip,Control,Rep1


title: Blood 1_TCR


title: RM-96h replicate 2


title: WT CLP ATAC-seq Rep 2


title: Liver 2.A_TCR


title: Liver 4_GEX

data_processing:
BCL files were converted to FASTQ files using cellranger mkfastq (v2.1.1-3.0.1).
Alignment, filtering, barcode counting and UMI counting were performed using cellranger count (v3.0.1).
Single-cell V(D)J sequences and annotations were generated using cellranger vdj (v3.0.1).
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered_feature_bc_matrix.h5 output file from cellranger count (v3.0.1) - filtered feature-barcode matrices containing only cellular barcodes in HDF5 format. filtered_contig_annotations.csv output file from cellranger vdj (v3.0.1) - high-level annotations of each high-confidence, cellular contig.
Supplementary_files_format_and_content: all_samples_counts.txt: raw gene counts after QC (i.e. after removal of poor quality cells, lowly expressed genes etc.) for combined analysis of MAIT cells from all samples (n = 7). all_samples_metadata.txt: metadata for cells in all_samples_counts.txt, including cluster identity of each cell. blood_counts.txt: raw gene counts after QC for combined analysis of MAIT cells from blood samples (n = 3). blood_metadata.txt: metadata for cells in blood_counts.txt, including cluster identity of each cell. liver_counts.txt: raw gene counts after QC for combined analysis of MAIT cells from liver samples (n = 4). liver_metadata.txt: metadata for cells in liver_counts.txt, including cluster identity of each cell.


title: RM-96h replicate 1


title: liver of mice under microgravity in space for 30 days, replicate 3

city: Yokohama

first: Ryo

last: Kurosawa

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN

description:
MG8
Counts.xlsx
TPMs.xlsx
DE_GC_MG.xlsx
DE_A1G_MG.xlsx

data_processing:
These data were analyzed with the RaNA-Seq58 cloud platform for the rapid analysis and visualization of RNASeq data to perform FASTQ preprocessing (fastp 0.19.4) and quantification (salmon 0.9.1) of the samples.
Total reads obtained for each library ranged between 18 and 26 million, and properly matched reads/read pairs were between 81 and 94%.
Differentially expressed genes were detected by means of DESeq cloud using a Wald test, a parametric fit type, and setting an adjusted p-value cutoff of 0.05.
Assembly: Mouse, Mus musculus (GRCm38)
Supplementary files format and content: Excel file includes raw counts for each sample
Supplementary files format and content: Excel file includes TPMs for each sample
Supplementary files format and content: Excel file includes DEGs between two groups

source_name: liver

extract_protocol:
A piece of liver weighing 20–30 mg was cut from each liver sample on dry ice. Homogenization was performed using a disposable homogenizer (Biomasher II, AS ONE CORPORATION, Osaka, Japan) on ice. RNA was isolated and purified using NucleoSpin RNA (Takara, Kusatsu, Shiga, Japan) according to the manufacturer’s instructions. RNA was eluted in 40 μl RNase-free water per sample. The concentration and absorbance ratios of all RNA samples were measured using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA).
The messenger RNA (mRNA) obtained from the livers of mice was sequenced using NovaSeq 6000 (Illumina Inc., San Diego, CA). We used the Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA) for poly(A) RNA preparation, and NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA) for library preparation.

value: liver

value: liver cells (homogenate)

tag: strain

tag: Sex

value: male

value: microgravity in space for 30 days


title: liver of mice under microgravity in space for 30 days, replicate 2

description:
MG2
Counts.xlsx
TPMs.xlsx
DE_GC_MG.xlsx
DE_A1G_MG.xlsx

tag: cell type

value: WT


title: PFC,Susceptible,Rep4

source_name: Prefrontal cortex

value: Prefrontal cortex

value: susceptible


title: Liver 3.B_GEX

value: Liver

value: MAIT


title: liver of mice under microgravity in space for 30 days, replicate 1

description:
MG1
Counts.xlsx
TPMs.xlsx
DE_GC_MG.xlsx
DE_A1G_MG.xlsx

tag: genotype


title: RM-48h replicate 2


title: PFC,Susceptible,Rep3

tag: tissue


title: RM-48h replicate 1


title: PFC,Susceptible,Rep2


title: Liver 3.A_GEX


title: liver of mice under artificial earth gravity (1 g) in space for 30 days, replicate 3

description:
A1G6
Counts.xlsx
TPMs.xlsx
DE_GC_A1G.xlsx
DE_A1G_MG.xlsx


title: liver of mice under artificial earth gravity (1 g) in space for 30 days, replicate 2

description:
A1G5
Counts.xlsx
TPMs.xlsx
DE_GC_A1G.xlsx
DE_A1G_MG.xlsx


title: HFF-GFP replicate 2


title: HFF-GFP replicate 1


title: Blood 3.A_GEX

value: Blood


title: PFC,Susceptible,Rep1


title: Blood 3.B_GEX


title: PFC,Resilient,Rep5

value: resilient


title: liver of mice under artificial earth gravity (1 g) in space for 30 days, replicate 1

description:
A1G4
Counts.xlsx
TPMs.xlsx
DE_GC_A1G.xlsx
DE_A1G_MG.xlsx


title: liver of control mice on Earth, replicate 3

description:
GC6
Counts.xlsx
TPMs.xlsx
DE_GC_A1G.xlsx
DE_GC_MG.xlsx

value: control mice on Earth


title: fibroblast replicate 3

data_processing:
The sample quality of the RNA-seq datasets were evaluated by the tool FastQC. Sequence reads were aligned to the human reference genome (UCSC GRCh38/hg38) using STAR aligner (v2.7.5c) with default parameters. Samtools (v1.9) was used to sort the bam files.
Gene counts were quantified using HTSeq-count (v0.11.2).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

extract_protocol:
Total RNA was isolated using RNeasy Plus Mini Kit (Qiagen, #74134) following manufacturer’s instruction.
Libraries were prepared from 500ng of total RNA for each sample using KAPA mRNA HyperPrep Kit for Illumina (Roche, #KR1352) following manufacturer’s instruction.

treatment_protocol: Early-passage HFFs were transduced with constructs for TF expression and kept in defined reprogramming medium to induce cell fate convertion (See Methods). The reprogramming cells were collected at different time points for gene expression analysis. Mock HFFs were used as control.

value: Mock


title: fibroblast replicate 2


title: Liver 2.B_GEX


title: Liver 2.A_GEX


title: PFC,Susceptible,Rep5


title: liver of control mice on Earth, replicate 2

description:
GC5
Counts.xlsx
TPMs.xlsx
DE_GC_A1G.xlsx
DE_GC_MG.xlsx


title: PFC,Resilient,Rep3


title: PFC,Resilient,Rep2


title: Blood 2.B_GEX


title: 6F-TERT replicate 3

value: Transduced with 6-TF cocktail and hTERT


title: Blood 2.A_GEX


title: 6F-TERT replicate 2

value: Human foreskin fibroblasts


title: Liver 1_GEX


title: PFC,Control,Rep5

value: control


title: 6F-TERT replicate 1


title: PFC,Control,Rep4


title: Blood 1_GEX


title: 6F-6wk replicate 3

value: Transduced with 6-TF cocktail


title: CD4 T cells from spleen transduced with retroviruses encoding TOX replicate 2

city: West Lafayette

first: D. Alejandro

last: Canaria

state: IN

address: 201 S University St

institute: Purdue University

data_processing:
Raw sequencing quality was checked using fastqc. Adapters were trimmed later.
Alignment and RNA expression level calculation was carried out using bowtie2 and RSEM (--bowtie-n 1 --bowtie-m 100). Reference transcript used in alignment was mm10.
DESeq2 was used to identify the differential expressed genes between CD4+ T cells transduced with TOX retrovirus and with Empty Vector retrovirus with default parameters.
Differentially expressed genes (DEGs) were sorted based on significant level (log2(fold change)*-log2(p-value)).
Assembly: mm10
Supplementary files format and content: tab-delmited file including TPM from all samples and separte RSEM result for each sample.

source_name: spleen

extract_protocol:
Resulting cells were washed twice with 1x sterile PBS the pellets were resuspended in 500uL of Trizol reagent (Applied Biosystems) and RNA-isolation was carried out as per manufacturer’s instructions.
RNA from these cells was sent to Novogene for library preparation and sequencing.

value: spleen

value: CD4 T cells

value: anti-CD3, soluble anti-CD28 and recombinant human anti-CD28, transduced with retrovirus encoding TOX


title: CD4 T cells from spleen transduced with retroviruses encoding TOX replicate 1


title: PFC,Control,Rep3


title: PFC,Resilient,Rep4


title: 6F-6wk replicate 2


title: fibroblast replicate 1


title: PFC,Control,Rep2


title: liver of control mice on Earth, replicate 1

description:
GC4
Counts.xlsx
TPMs.xlsx
DE_GC_A1G.xlsx
DE_GC_MG.xlsx

value: liver

value: liver cells (homogenate)

value: male


title: 6F-6wk replicate 1


title: Kidneys: CM + NTCI, biol rep 3 [9324-HQ-0009]

city: Nashville

first: Jozef

last: Zienkiewicz

state: TN

address: 1161 21st Ave. South, T2220, MCN

department: Medicine

institute: Vanderbilt University

description:
Sample_18_KCN_3
9324-HQ-0009
KNcomparison_vs_KScontrol.genes.counts.csv
KNcomparison_vs_KScontrol.genes.res.csv

data_processing:
DRAGEN RNA Pipeline 3.6.3 (DRAGEN Host Software Version 05.021.572.3.6.3 and Bio-IT Processor Version 0x04261818); DRAGEN Differential Expression 4.0.3; Illumina DRAGEN Secondary Analysis
Sequence reads were trimmed to remove adapter sequences and low-quality tails using DRAGEN RNA Pipeline 3.6.3
Trimmed sequences were aligned and mapped to GRCm38 using STAR2.3 and RefSeq annotations built-in DRAGEN RNA Pipeline 3.6.3
After alignment, the read counts were used as input for differential expression analysis between test (comparison) and control groups using R and DESeq2 built-in DRAGEN Differential Expression 4.0.3
The Illumina DRAGEN Secondary Analysis were used to generate processed data files.
Assembly: Mus_musculus.GRCm38.99
Supplementary files format and content: genes.counts.csv - comma separated values (CSV) file describing the number of reads mapped to each gene for each sample in the control and comparison groups.
Supplementary files format and content: genes.res.csv - CVS file containing DESeq2 results: the mean expression, log2 (fold change), standard error of log2 (fold change), p-value, adjusted p-value, and the expression status of each gene.

source_name: kidneys

growth_protocol: Unlimited acess to regular irradiated rodent chow diet and water.

extract_protocol:
lungs and kidneys were disrupted in lysis buffer on ice using a Dounce hand homogenizer. Total RNA was isolated using NucleoSpin RNA Plus kit (Macherey-Nagel, Germany) according to the manufacturer’s instructions. RNA concentration and purity were determined using a NanoDrop One spectrophotometer (Thermo Fisher Scientific, Hampton, NH). RNA integrity numbers (RIN) were measured using TapeStation system (Agilent Technologies, Santa Clara, CA)
total RNA was processed into Stranded mRNA (NEB) Library folowing manufacturer's protocols

treatment_protocol: The experimental groups (Sham (5% dextrose) + Saline, n = 5; CM + Saline, n = 5; and CM + NTCI, n = 5) were comprised of randomly assigned 8 – 10-week-old female C57Bl/6J mice (The Jackson Laboratory, Bar Harbor, ME). The mice were infected by a single intraperitoneal (i.p.) injection of a cecal microbiome (CM) stock corresponding to 4.5x10^5 CFU/kg (between 9 - 11.5 µl/g of 80mg/ml CM stock). Mice were treated with the i.p. injection of nuclear transport checkpoint inhibitor (NTCI) (cSN50.1 peptide, 33 μg/g/injection in 200 μl 0.45% NaCl) or 0.45% NaCl (200 μl) as vehicle control, at 30 min before and 30 min, 1.5h, 2.5h, 3.5h, and 5h after CM challenge. Mice were euthanized at 6 hrs. post CM challenge. Circulation system was washed with cold PBS (2 ml to each ventricle) and lungs ang kidneys were removed for total RNA extraction.

value: kidneys

value: female

tag: condition

value: polymicrobial sepsis - onset

value: CM + NTCI

value: 6 hrs post CM challenge


title: PFC,Control,Rep1

value: Prefrontal cortex


title: Kidneys: CM + NTCI, biol rep 2 [9324-HQ-0008]

description:
Sample_17_KCN_2
9324-HQ-0008
KNcomparison_vs_KScontrol.genes.counts.csv
KNcomparison_vs_KScontrol.genes.res.csv

tag: treatment


title: PFC,Resilient,Rep1

value: resilient


title: 6F-4wk replicate 3


title: 6F-4wk replicate 2


title: CD4 T cells from spleen transduced with empty vector replicate 1

value: WT

value: anti-CD3, soluble anti-CD28 and recombinant human anti-CD28


title: CD4 T cells from spleen transduced with empty vector replicate 2


title: Kidneys: CM + Saline, biol rep 3 [9324-HQ-0006]

description:
Sample_15_KCS_3
9324-HQ-0006
KScomparison_vs_KShamControl.genes.counts.csv
KScomparison_vs_KShamControl.genes.res.csv
KNcomparison_vs_KScontrol.genes.counts.csv
KNcomparison_vs_KScontrol.genes.res.csv

value: CM + Saline


title: Kidneys: CM + Saline, biol rep 2 [9324-HQ-0005]

description:
Sample_14_KCS_2
9324-HQ-0005
KScomparison_vs_KShamControl.genes.counts.csv
KScomparison_vs_KShamControl.genes.res.csv
KNcomparison_vs_KScontrol.genes.counts.csv
KNcomparison_vs_KScontrol.genes.res.csv


title: tumorspheroid_017-1_Group1

city: Philadelphia

first: Nelson

last: Freeburg

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

data_processing:
Fastq file quality checked with FastQC version 0.11.9
Reads pseudoaligned with Kallisto version 0.46.2
Assembly: mm10
Supplementary files format and content: tab separated value file containing read abundance for each gene as measured by Kallisto pseudoaligner

source_name: mouse lung adenocarcinoma

growth_protocol: Tumor spheroid cells were grown in solid matrigel plugs immersed in DMEM/F12 media with 10% FBS for 10 days prior to collection.

extract_protocol:
Extraction using Qiagen RNeasy Micro Plus Kit according to manufacturer protocol with elution in 14 uL RNAse free H2O
Illumina Stranded mRNA library preparation kit following manufacturer protocol using 250 ng input RNA

value: mouse lung adenocarcinoma

tag: cell line

value: tumor spheroid


title: 27_Mix_high_3

type: RNA

city: Chapel Hill

first: Anastasia

middle: Natalie

last: Freedman

state: NC

address: 135 Dauer Dr

department: Environmental Sciences and Engineering

institute: University of North Carolina at Chapel Hill

hyb_protocol: not provided

scan_protocol: not provided

data_processing: The data were analyzed using Transcriptome Analysis Console (TAC) 4.0.2

label: WT Plus reagent Kit

source_name: HTR-8/SVneo cells exposed to 1.5microM iAs and 20microM Mn  for 24 hrs

label_protocol: not provided

growth_protocol: The HTR-8/SVneo (SVneo) cell line was purchased from the American Type Culture Collection (Manassas, VA). SVneo cells were grown in Gibco RMPI 1940, supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37C in 5% CO2.

extract_protocol: Cells were harvested in 350uL of buffer RLT plus, and RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA), according to manufacturer’s protocol

treatment_protocol: Cells were seeded at 100,000 cells/well in 12-well plates, and incubated at 37C in 5% CO2 for 24-hours, until reaching ~80% confluency. Inorganic arsenic (iAs), and manganese (II) chloride tetrahydrate (MnCl2) were dissolved in cell culture media on day of treatment. Cells were treated with 0.3µM (22.5 ppb), 1µM (74.9 ppb), and 1.5µM (112.4 ppb) iAs, and 5µM (274.7 ppb), 10µM (549.5 ppb), and 20µM (1,098 ppb) MnCl2. Three co-exposure groups were tested yielding final concentrations of 0.3µM iAs + 5µM MnCl2, 1µM iAs + 10µM MnCl2, and 1.5µM iAs + 20µM MnCl2.

value: placenta


title: 28_Control_1

source_name: HTR-8/SVneo cell control sample, no chemical exposure


title: 29_Control_2


title: 30_Control_3


title: Kidneys: CM + Saline, biol rep 1 [9324-HQ-0004]

description:
Sample_13_KCS_1
9324-HQ-0004
KScomparison_vs_KShamControl.genes.counts.csv
KScomparison_vs_KShamControl.genes.res.csv
KNcomparison_vs_KScontrol.genes.counts.csv
KNcomparison_vs_KScontrol.genes.res.csv

tag: time


title: tumorspheroid_776-5_Group1


title: Kidneys: CM + NTCI, biol rep 1 [9324-HQ-0007]

description:
Sample_16_KCN_1
9324-HQ-0007
KNcomparison_vs_KScontrol.genes.counts.csv
KNcomparison_vs_KScontrol.genes.res.csv


title: tumorspheroid_817-6_Group1


title: 6F-2wk replicate 2

value: Human foreskin fibroblasts

value: Transduced with 6-TF cocktail


title: Kidneys: Sham + Saline, biol rep 3 [9324-HQ-0003]

description:
Sample_12_KSS_3
9324-HQ-0003
KScomparison_vs_KShamControl.genes.counts.csv
KScomparison_vs_KShamControl.genes.res.csv

value: Sham + Saline


title: tumorspheroid_793-14_Group2


title: 6F-2wk replicate 1


title: 6F-1wk replicate 3


title: tumorspheroid_017-7_Group2


title: tumorspheroid_860-7_Group1


title: Kidneys: Sham + Saline, biol rep 2 [9324-HQ-0002]

description:
Sample_11_KSS_2
9324-HQ-0002
KScomparison_vs_KShamControl.genes.counts.csv
KScomparison_vs_KShamControl.genes.res.csv


title: Kidneys: Sham + Saline, biol rep 1 [9324-HQ-0001]

description:
Sample_10_KSS_1
9324-HQ-0001
KScomparison_vs_KShamControl.genes.counts.csv
KScomparison_vs_KShamControl.genes.res.csv


title: 6F-4wk replicate 1


title: 25_Mix_low_3

source_name: HTR-8/SVneo cells exposed to 0.3microM iAs and 5microM Mn  for 24 hrs


title: 24_Mix_high_2


title: 6F-1wk replicate 2


title: tumorspheroid_817-5_Group2


title: 6F-2wk replicate 3


title: Lungs: CM + NTCI, biol rep 3 [9064-HQ-0009]

description:
Sample_09_LCN_3
9064-HQ-0009
LNcomparison_vs_LScontrol.genes.counts.csv
LNcomparison_vs_LScontrol.genes.res.csv

source_name: lungs

value: lungs


title: 21_Mix_high_1


title: 26_Mix_med_3

source_name: HTR-8/SVneo cells exposed to 1.0microM iAs and 10microM Mn  for 24 hrs


title: tumorspheroid_776-1_Group2


title: 23_Mix_med_2


title: 6F-1wk replicate 1


title: Lungs: CM + NTCI, biol rep 2 [9064-HQ-0008]

description:
Sample_08_LCN_2
9064-HQ-0008
LNcomparison_vs_LScontrol.genes.counts.csv
LNcomparison_vs_LScontrol.genes.res.csv


title: 6F-96h replicate 3


title: 22_Mix_low_2


title: Microglia, Low Sodium Diet r3

first: Justin

middle: Shaun Arnold

last: Perry

state: New York

address: 408 East 69th Street, 408-15

department: Immunology Program

institute: Sloan Kettering Institute for Cancer Research

data_processing:
Adapter trimming via ea-utils.1.1.2-537
FastQC for read quality check
Alignment with STAR -RNAseq Data (variables P=24; BAMRAM=$(($P*8 * 1000000000 - (30*1000000000))); INDEX=INDEX; GTF=GTF)
Quantitation via featureCounts (featureCounts -a GTF -o counts.txt -p -B -T 16 -t exon -g gene_id *.bam)
Assembly: GRCm38 - M. musculus
Supplementary files format and content: .tsv file with correct gene names, generated using DESeq2, with normalized read counts

source_name: Microglia

extract_protocol:
Total RNA was extracted using Qiagen RNA isolation kit
mRNA library was prepared using the Illumina TruSeq platform
RNA-seq, 75bp, paired-end sequencing

treatment_protocol: Pregnant dams were treated with control or low sodium (Na) diet

value: Low Sodium Diet (Maternal)

value: Microglia


title: Microglia, Low Sodium Diet r2


title: 6F-96h replicate 2


title: Lungs: CM + Saline, biol rep 3 [9064-HQ-0006]

description:
Sample_06_LCS_3
9064-HQ-0006
LScomparison_vs_LShamControl.genes.counts.csv
LScomparison_vs_LShamControl.genes.res.csv
LNcomparison_vs_LScontrol.genes.counts.csv
LNcomparison_vs_LScontrol.genes.res.csv

value: female

value: polymicrobial sepsis - onset


title: Lungs: CM + NTCI, biol rep 1 [9064-HQ-0007]

description:
Sample_07_LCN_1
9064-HQ-0007
LNcomparison_vs_LScontrol.genes.counts.csv
LNcomparison_vs_LScontrol.genes.res.csv

value: CM + NTCI

value: 6 hrs post CM challenge


title: Microglia, Low Sodium Diet r1


title: 6F-96h replicate 1


title: Lungs: CM + Saline, biol rep 2 [9064-HQ-0005]

description:
Sample_05_LCS_2
9064-HQ-0005
LScomparison_vs_LShamControl.genes.counts.csv
LScomparison_vs_LShamControl.genes.res.csv
LNcomparison_vs_LScontrol.genes.counts.csv
LNcomparison_vs_LScontrol.genes.res.csv


title: 19_Mix_low_1


title: Microglia, Control Diet r3

value: Control Diet (Maternal)


title: 6F-48h replicate 3


title: 6F-48h replicate 2


title: Lungs: Sham + Saline, biol rep 3 [9064-HQ-0003]

description:
Sample_03_LSS_3
9064-HQ-0003
LScomparison_vs_LShamControl.genes.counts.csv
LScomparison_vs_LShamControl.genes.res.csv


title: Lungs: CM + Saline, biol rep 1 [9064-HQ-0004]

description:
Sample_04_LCS_1
9064-HQ-0004
LScomparison_vs_LShamControl.genes.counts.csv
LScomparison_vs_LShamControl.genes.res.csv
LNcomparison_vs_LScontrol.genes.counts.csv
LNcomparison_vs_LScontrol.genes.res.csv


title: 20_Mix_med_1


title: Microglia, Control Diet r1


title: 6F-48h replicate 1


title: 17_Mn_20_2

source_name: HTR-8/SVneo cells exposed to 20microM Mn for 24 hrs


title: 16_Mn_20_1


title: karyocreate-treated cells, scrnaseq with hashtags, treatment set 2 [HT]

data_processing:
The CellRanger v6.1 pipeline (10X Genomics) was used to process single-cell RNA sequencing data. CellRanger count was used to align sequences and generate gene expression matrices. Sequences were aligned to a custom reference genome (designated 20210929-custom-ref) created with CellRanger mkref with default parameters. This custom reference was created using the pre-built GRCh38-2020-A human reference for CellRanger based on hg38, combined with sequences for dCas9, puromycin resistance, blastomycin resistance, and GFP. Gene expression matrices were generated with each column representing a cell barcode and each row representing a gene or hashtag oligo sequences (HTO).
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz together define a martrix in MEX format, containing gene-level or hashtag-level counts for each cell-associated barcode

source_name: hCEC

extract_protocol:
Cells were trypinized, collected, and hashtaged using Biolegend's protocol for cell surface protein (hashtag antibody) feature barcoding. 10 TotalSeq-B hashtag antibodies (BioLegend, San Diego, CA) were used for multiplexing samples in each sequencing run.
scRNA-seq libraries were prepared using the 10X Chromium Single-Cell 3' v3 Gene Expression kit according to the manufacturer's instructions.

value: hCEC

value: Mutant KNL1-dcas9 hCECs treated with gRNAs gNC, g7-1, g7-3, g7-1+7-3, gNC+18-4, g7-1+18-4, or g7


title: LPS, replicate 4, bulk RNA-seq

city: Bethesda

first: Thierry

last: Gauthier

state: MD

address: 30 convent drive (NIH)

institute: NIH/NIDCR

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to GRCm38.vM11 mouse genome using STAR v2.5.2a in  single-pass mode
Gene counts were generated with STAR v2.5.2a built-in counting option --quantMode GeneCounts against a GRCm38.vM11 genome annotation GTF which included ERCCs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Assembly: GRCm38.vM11
Supplementary files format and content: Raw gene counts in tab-delimited txt format.
Supplementary files format and content: Filtered raw gene counts in tab-delimited txt format, after removal of genes with less that 5 reads in at least 1 sample.
Supplementary files format and content: TMM-normalized annotated gene expression matrix in counts per million reads units, tab-delimited txt format.

source_name: Peritoneum

growth_protocol: Peritoneal elicited macrophages

extract_protocol: Library preparation was performed according to the manufacturer’s instructions for the Illumina Nextera XT unstranded library kit. The libraries were then pooled and sequenced on tow separate runs on a NextSeq2000 sequencer (Illumina) on 55x55 paired-end mode.

treatment_protocol: Cells were treated in vitro with TGFB, IL4, IL10 or LPS for 24 h

value: Peritoneum

value: Thioglycolate elicited macrophages

value: WT

value: LPS


title: 18_Mn_20_3

value: placenta


title: Lungs: Sham + Saline, biol rep 1 [9064-HQ-0001]

description:
Sample_01_LSS_1
9064-HQ-0001
LScomparison_vs_LShamControl.genes.counts.csv
LScomparison_vs_LShamControl.genes.res.csv


title: 15_Mn_10_3

source_name: HTR-8/SVneo cells exposed to 10microM Mn for 24 hrs


title: LPS, replicate 3, bulk RNA-seq


title: 14_Mn_10_2


title: LPS, replicate 2, bulk RNA-seq


title: karyocreate-treated cells, scrnaseq with hashtags, treatment set 1 [HT]


title: karyocreate-treated cells, scrnaseq with hashtags, treatment set 2


title: LPS, replicate 1, bulk RNA-seq


title: 12_Mn_5_3

source_name: HTR-8/SVneo cells exposed to 5microM Mn for 24 hrs


title: Microglia, Control Diet r2


title: karyocreate-treated cells, scrnaseq with hashtags, treatment set 1


title: IL4, replicate 4, bulk RNA-seq


title: IL4, replicate 3, bulk RNA-seq


title: Donor 322- 4W

description:
ICELL8, 3' DE kit
RPE322-4W

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cogent software v1.0 (https://www.takarabio.com/products/next-generation-sequencing/bioinformatics-tools/cogent-ngs-analysis-pipeline)
Seurat package was used to make and integrate seurat objects for downstream analysis. Code available at Github (https://github.com/neural-stem-cell-institute/RPESC_TREX/tree/main/R).
Assembly: hg38
Supplementary files format and content: rds

source_name: RPE

growth_protocol: Cultures were cultured on Transwell inserts and maintained in RPE medium: MEM-a modified medium (Sigma-Aldrich), 2 mM L-glutamine, penicillin/streptomycin (1:100), 1% Na-Pyruvate, 10% fetal bovine serum supplemented with THT (Taurine, Hydrocortisone, Triiodo-thyronin), and N1 medium supplement (Sigma-Aldrich)76. Cells were incubated in a humidified incubator at 37oC and 5% CO2 and the medium was replaced every 3 days.

extract_protocol:
RPE cells were dissociated from culture plates using 0.25% Trypsin and Takara's ICELL8 3'DE chip and reagents kit was used for single cell capture and RT-PCR
cDNA samples were concentrated and purified using a DNA Clean & Concentrator-5 kit (Zymo Research, Irvine, CA) and purified using a 0.6X proportion of AMPure XP magnetic beads (Beckman Coulter, Brea, CA) according to manufacturer protocols. Library preparation was performed using a Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA) according to the Takara’s 3’ DE chip and reagent kit instructions. Libraries were sequenced using a NovaSeq 6000 high-output flow cell generating 2 × 150-bp read lengths (GeneWiz).

value: RPE

tag: age


title: Donor 322- 8W

description:
ICELL8, 3' DE kit
RPE322-8W


title: 11_Mn_5_2


title: Lungs: Sham + Saline, biol rep 2 [9064-HQ-0002]

description:
Sample_02_LSS_2
9064-HQ-0002
LScomparison_vs_LShamControl.genes.counts.csv
LScomparison_vs_LShamControl.genes.res.csv

value: Sham + Saline


title: 13_Mn_10_1


title: Donor 322- 2W

description:
ICELL8, 3' DE kit
RPE322-2W


title: IL4, replicate 1, bulk RNA-seq


title: IL4, replicate 2, bulk RNA-seq


title: Donor 319- 8W

description:
ICELL8, 3' DE kit
RPE319-8W


title: 10_Mn_5_1


title: IL10, replicate 4, bulk RNA-seq


title: TGFB_LPS, replicate 2, bulk ATACseq

data_processing:
Reads were trimmed using Trim Galore v0.5.0
Reads were mapped to the mouse mm10 genome version using BWA 0.7.17-r1188
Peaks were called with MACS2 v2.1.2
Assembly: mm10
Supplementary files format and content: Read coverage per samples in BigWig format
Supplementary files format and content: Called peaks per sample in .narrowPeak (BED 6+4) format

extract_protocol:
Experiment was performed by Zymo Reserach Corp. Add how you froze the cells / pelleted them. Cells were thawed in a 37°C water bath and then quickly transferred to 9 mL of warm RPMI-1640 with 15% FBS and 1% P/S. The cells were centrifuged at 300 x g for 5 minutes at 25°C. The supernatant was discarded, and the cells were resuspended in 1 mL complete RPMI-1640. 10 μL of the cell suspension was mixed with 10 μL 0.4% Trypan Blue. Cells were counted, and viability was determined using a Countess II (Invitrogen). Both sides of the counting chamber were used, and the numbers reported above are an average of both reads. 300,000 cells were aliquoted to a new tube and centrifuged at 300 x g for 5 minutes at room temperature. The supernatant was removed, and the pellet was resuspended in 150 μL of room temperature ATAC-S Buffer. 50,000 cells were aliquoted to new tubes. An equal volume of cold 2x ATAC Lysis Buffer was added to each aliquot of cells and incubated on ice for 3 minutes, at which point cold ATAC Dilution Buffer was added. These mixtures were centrifuged at 1,000 x g for 10 minutes at 4°C. Nuclei were resuspended in cold Tagmentation Buffer containing the tagmentation enzyme. The tagmentation reaction was carried out at 37°C shaking at 1,000 rpm for 30 minutes. The tagmentation reaction was cleaned up with the DNA Clean & Concentrator Kit-5 (Zymo Research Corp.) and eluted with 21 μL DNA Elution Buffer.
The ATAC Seq libraries were prepared in 50 μL PCR reactions consisting of 20 μL of the cleaned up tagmentation products, 2x PCR Master Mix, and 2.5 μM of forward and reverse index primers. The PCR protocol was as follows: 72°C for 5 minutes,  98°C for 30 seconds, 11 cycles of: o 98°C for 10 seconds, 63°C for 30 seconds, 72°C for 60 seconds, Hold at 4°C. The PCR products were cleaned up using the DNA Clean & Concentrator Kit-5 (Zymo Research Corp.) and eluted with 21 μL DNA Elution Buffer. Library QC was performed by analyzing the cleaned-up library via TapeStation (Agilent Technologies). Libraries were quantified using KAPA Library Quantification (Roche) and pooled together for sequencing 150 bp paired-end on the Illumina NovaSeq platform.

treatment_protocol: Cells were treated in vitro with or without TGFB for 24h followed by LPS for 24h

value: TGFB LPS


title: Donor 319- 4W

description:
ICELL8, 3' DE kit
RPE319-4W


title: 8_iAs_1.5_2

source_name: HTR-8/SVneo cells exposed to 1.5microM iAs for 24 hrs


title: TGFB_LPS, replicate 1, bulk ATACseq


title: 9_iAs_1.5_3


title: IL10, replicate 3, bulk RNA-seq


title: Donor 319- 2W

description:
ICELL8, 3' DE kit
RPE319-2W


title: IL10, replicate 2, bulk RNA-seq


title: Donor 318- 8W

description:
ICELL8, 3' DE kit
RPE318-8W


title: LPS, replicate 3, bulk ATACseq


title: TGFB_LPS, replicate 4, bulk ATACseq


title: Donor 318- 4W

description:
ICELL8, 3' DE kit
RPE318-4W


title: TGFB, replicate 4, bulk RNA-seq

value: TGFB


title: IL10, replicate 1, bulk RNA-seq


title: LPS, replicate 2, bulk ATACseq


title: Donor 318- 2W

description:
ICELL8, 3' DE kit
RPE318-2W


title: Cytokine-stimulated 3.3_TCR

data_processing:
Library strategy: TCR-seq
BCL files were converted to FASTQ files using cellranger mkfastq (v3.0.2).
Alignment, filtering, barcode counting and UMI counting were performed using cellranger count (v3.0.2).
Single-cell V(D)J sequences and annotations were generated using cellranger vdj (v3.0.2).
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered_feature_bc_matrix.h5 output file from cellranger count (v3.0.2) - filtered feature-barcode matrices containing only cellular barcodes in HDF5 format. filtered_contig_annotations.csv output file from cellranger vdj (v3.0.2) - high-level annotations of each high-confidence, cellular contig.
Supplementary_files_format_and_content: counts.txt: raw gene counts after QC (i.e. after removal of poor quality cells, lowly expressed genes etc.) for combined analysis of all samples (n = 9). metadata.txt: metadata for cells in counts.txt, including cluster identity of each cell.

source_name: Blood

extract_protocol:
PBMCs were isolated from fresh whole blood by density gradient centrifugation (Lymphoprep, Axis-Shield) at 2000 rpm (931 g) for 30 min with no brake. Cells were cryopreserved (90% FCS, 10% DMSO [Sigma-Aldrich]) in liquid nitrogen. A Pierce streptavidin coated high capacity flat-bottom 96-well plate (Thermo Fisher Scientific) was coated with 50 μl biotinylated MR1/5-OP-RU monomer (NIH Tetramer Core Facility) at 10 μg/ml in PBS overnight at 4°C. Cryopreserved PBMCs from three healthy female donors were thawed in complete medium. CD8+ T cells were enriched using CD8 MicroBeads (Miltenyi Biotec) following manufacturer’s instructions. Enriched CD8+ T cells were washed in complete medium and resuspended at 10 million cells/ml. One million cells per well were added to the appropriate 96-well plate (MR1/5-OP-RU-coated plate for the TCR stimulation condition, round-bottom plate for the unstimulated and cytokine stimulation conditions). IL-12 (50 ng/ml; R&D Systems) and IL-18 (50 ng/ml; R&D Systems) were added to the cytokine stimulation condition, αCD28 (1 μg/ml; clone: CD28.2; BioLegend) to the TCR stimulation condition, and complete medium to the unstimulated condition (final volume 200 μl in all wells). Cells were incubated for 20 hours at 37°C, 5% CO2. Surface staining was performed in Brilliant Stain Buffer (BD Biosciences) for 30 min at 4°C. Cells were washed twice in PBS with 0.5% BSA, resuspended in pre-sort buffer containing 3-5 nM SYTOX Green Nucleic Acid Stain (Thermo Fisher Scientific), and incubated for 20 min at 4°C. MAIT cells (CD3+CD8+CD26+CD161hiVα7.2+) were sorted on a BD FACSAria III with a 70 μm nozzle. Sorted cells were collected in RPMI-1640, 10% FBS, 25 mM HEPES. Sort purity was > 99%.
scRNA-seq and scTCR-seq libraries were generated using Chromium Single Cell V(D)J Reagent Kits (v1.0 Chemistry) following manufacturer's instructions.

tag: stimulation

value: MAIT


title: GK gene silenced strain, Biological replicate C

city: BUNKYO

first: Ghulam

last: Jeelani

state: Tokyo

department: BIOMEDICAL CHEMISTRY

institute: University of Tokyo

description: gs-GK-C

data_processing:
The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq.
Sequence reads were trimmed for adapter contamination and uncertain nucleotides using cutadapt software 2.4 (default parameters) and the quality were checked by FastQC 0.11.8 software (default parameters). The sequence reads were assembled using MultiQC 1.7 software (default parameters).
Trimmed sequence reads were aligned to the reference genome using TopHat 2.1.1 (default parameters).
Mapped reads were assembled using Cufflinks 2.2.1 software (default parameters) and integrated by cuffmerge software (default parameters).
Analyzed the expression level among samples by using cuffdiff software (default parameters).
Assembly: JCVI-ESG2-1.0
Supplementary files format and content: tab-delimited text files include raw fragment counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: tab-delimited text files include expressed genes in mock vector transfected (pSAP), EhGK and EhG3PDH gene silencing strain.

organism: Entamoeba histolytica

source_name: HM1: IMSS

growth_protocol: Trophozoites of the E. histolytica clonal strain HM1: IMSS  G3 strain were maintained axenically in Diamond’s BI-S-33 medium at 35.5°C

extract_protocol:
Total RNA was purified using TRIZOL reagent (Thermo Fisher, Waltham, MA, USA) according to manufacturer’s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-seq libraries were generated by using TruSeq stranded mRNA kit

treatment_protocol: The trophozoites of G3 strain were transformed with either empty vector or silencing plasmid by liposome-mediated transfection. Transformants were initially selected in the presence of 1 μg/ml geneticin, and the geneticin concentrations were gradually increased during next two weeks prior to subjecting the transformants to analyses.

value: trophozoite

value: GK gene silenced

tag: transfected plasmid

value: pSAP-EhGK


title: GK gene silenced strain, Biological replicate B

description: gs-GK-B


title: TGFB, replicate 3, bulk RNA-seq


title: TGFB, replicate 2, bulk RNA-seq


title: 6_iAs_1.0_3

source_name: HTR-8/SVneo cells exposed to 1.0microM iAs for 24 hrs


title: 5_iAs_1.0_2


title: GK gene silenced strain, Biological replicate A

description: gs-GK-A


title: TCR-stimulated 3.3_TCR

value: MR1/5-OP-RU + alphaCD28


title: TGFB, replicate 1, bulk RNA-seq


title: Unstimulated 3.3_TCR

value: media


title: 3_iAs_0.3_3

source_name: HTR-8/SVneo cells exposed to 0.3microM iAs for 24 hrs


title: 7_iAs_1.5_1


title: TGFB, replicate 3, bulk ATACseq


title: Control, replicate 4, bulk RNA-seq

value: Control


title: G3PDH gene silenced strain, Biological replicate C

value: G3PDH gene silenced


title: Cytokine-stimulated 3.2_TCR


title: 1_iAs_0.3_1


title: 4_iAs_1.0_1


title: 2_iAs_0.3_2


title: G3PDH gene silenced strain, Biological replicate B


title: TCR-stimulated 3.2_TCR


title: Control, replicate 3, bulk RNA-seq

value: Peritoneum


title: LPS, replicate 1, bulk ATACseq

value: Thioglycolate elicited macrophages


title: G3PDH gene silenced strain, Biological replicate A


title: Control, replicate 2, bulk RNA-seq

value: WT


title: Unstimulated 3.2_TCR


title: Control, replicate 2, bulk ATACseq


title: Control, replicate 1, bulk RNA-seq


title: pSAP mock control strain, Biological replicate C

description: pSAP-C

value: pSAP (Empty)


title: Cytokine-stimulated 3.1_TCR


title: TGFB, replicate 2, bulk ATACseq


title: Control, replicate 1, bulk ATACseq


title: pSAP mock control strain, Biological replicate B

description: pSAP-B


title: CD4 T cells, Arg-2 KO, Spleen, Rep3

first: Behdad (Ben)

last: Afzali

address: 10 Center Drive, Building 10

department: NIDDK

institute: National Institutes of Health

description:
Freshly isolated in vitro activated cells
Arg2KO_d3

data_processing:
Sequence reads were assessed for quality on fastqc and mapped to mm10 using bowtie2 (--sensitive-local --no-unal)
Read count was calculated using Rsubread (with default parameter) tools while using the GTF file (mm10.ncbiRefSeq.gtf.gz, last modified on the server on 2020-01-10, 09:40) obtained from https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/genes/
Assembly: mm10
Supplementary files format and content: tab-delimited text file contain raw counts values for each Sample

source_name: Spleen

extract_protocol:
RNA was harvested from Total CD4 T cells (from the lungs or spleen of WT or flu infected WT mice) using RNAqueous Micro Kit (AM1931, Invitrogen). 100 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Poly(A) mRNA capture and Library prep Kits (E7770 and E7490, source: neb) following manufacturer's protocols.

treatment_protocol: Cells harvest protocol:  Flu infection experiment  6-10 week old mice were infected intranasally (i.n.) with 103 EID50 of recombinant PR8 influenza virus (expressing the LCMV gp33-41 eptiope (KAVYNFATM) inserted into the NA of A/PR/8/34 (H1N1) (PR8-33) (kindly provided by Dr. Rafi Ahmed (Emory University))(Mueller et al., 2010). At day 9 of infection, lymphocytes were isolated from the lungs as previously described. Briefly, the mice were perfused with PBS, lungs excised, minced and incubated in 1mg/ml Collagenase and 1mg/ml DNase (both from Sigma-aldrich) in 3ml of RPMI for 45 min at 37 degrees. Single cell suspensions were obtained by pushing the digested lung pieces through a 40uM mesh filter (BD biosciences).  Lung lymphocytes were then purified by a 44/67% percoll gradient (Sigma-Aldrich) and centrifugation at 2000rpm for 20 min at room temperature. CD4 T cells were then stained with anti-CD11a, CD49d, TCRbeta, CD4 and live dead near-IR and FACS sorted on the live CD4+ TCRbeta+ CD11a+CD49d+ cells. RNA was then extracted for RNA-seq. Processing of spleen cells: CD4 T cells were isolated from mouse spleens (day 9 p.i) using a negative selection kit (#19852 from Stem Cell Technologies (Vancouver, Canada)) according to the manufacturer’s protocol. Purity of isolated cells was >95%. RNA was then extracted for RNA-seq.    In vitro activation experiment  CD4 T cells were isolated from mouse spleens using a negative selection kit (#19852 from Stem Cell Technologies (Vancouver, Canada)) according to the manufacturer’s protocol. Purity of isolated cells was >95%, and cells were resuspended in complete RPMI medium (10% FCS, 2mM glutamine (#25030-149, Gibco), 50U/ml Penicillin + 50µg/ml streptomycin (#15070-063, Gibco) and 2-betamercaptethanol (21985-023, Gibco)). Cells were activated in plates pre-coated with 2ug/ml of anti-CD3 (clone 145-2C11, BioXcell, West Lebanon, NH) at 5x105 per well of a 48 well plate in the presence of 1ug/ml soluble anti-CD28 (clone 37.51, BioXcell, West Lebanon, NH).  After 22 hours the cells were harvested and RNA extracted for RNA-seq.

value: Spleen

value: CD4 T cells

value: Arg2 KO

value: In vitro activation

value: 22 hr


title: TCR-stimulated 3.1_TCR

value: MAIT


title: TGF_LPS, replicate 3, bulk RNAseq

extract_protocol: Library preparation was performed according to the manufacturer’s instructions for the Illumina Nextera XT unstranded library kit. The libraries were then pooled and sequenced on tow separate runs on a NextSeq 500 sequencer (Illumina) on 55x55 paired-end mode.

treatment_protocol: Cells were treated in vitro with LPS for 6h or TGF for 24h followed by LPS for 6h

value: TGF LPS


title: Unstimulated 3.1_TCR


title: CD4 T cells, Arg-2 KO, Spleen, Rep1

description:
Freshly isolated in vitro activated cells
Arg2KO_d1


title: Control, replicate 3, bulk ATACseq


title: CD4 T cells, Arg-2 KO, Spleen, Rep2

description:
Freshly isolated in vitro activated cells
Arg2KO_d2


title: TGF_LPS, replicate 1, bulk RNAseq


title: TGF_LPS, replicate 2, bulk RNAseq


title: CD4 T cells, Arg-1 KO, Spleen, Rep3

description:
Freshly isolated in vitro activated cells
Arg1KO_d3

value: Arg1 KO


title: Bmmar_0009

city: Amsterdam

first: Beatriz

last: Izquierdo Lafuente

address: De Boelelaan

country: Netherlands

institute: Vrije Universiteit

data_processing:
The readouts underwent a screening process for quality using CLC Genomics Workbench 12.Paired-end raw reads were trimmed and aligned to reference genome
Count data was then converted to reads per million (rpm) and subjected to differential analysis. Differentially gene expression was determined by FDR <0.05 and log2 Fold change ≥2.5
Assembly: Reference genome M. mairnum MUSA WT NC_010612.1
Supplementary files format and content: Tab text file containing the RPKM and the expression values of each gene

organism: Mycobacterium marinum M

source_name: Bacteria

extract_protocol:
NucleoSpin RNA kit (Macherey-Nagel). 25 optical density (OD) units per sample were isolated
Illumina sequencing (Novogene Bioinformatics Technology)

value: MUSA

value: Bacteria


title: Cmmar_0009


title: TGFB, replicate 1, bulk ATACseq

value: TGFB


title: TCR-stimulated 3.3_GEX

data_processing:
BCL files were converted to FASTQ files using cellranger mkfastq (v3.0.2).
Alignment, filtering, barcode counting and UMI counting were performed using cellranger count (v3.0.2).
Single-cell V(D)J sequences and annotations were generated using cellranger vdj (v3.0.2).
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered_feature_bc_matrix.h5 output file from cellranger count (v3.0.2) - filtered feature-barcode matrices containing only cellular barcodes in HDF5 format. filtered_contig_annotations.csv output file from cellranger vdj (v3.0.2) - high-level annotations of each high-confidence, cellular contig.
Supplementary_files_format_and_content: counts.txt: raw gene counts after QC (i.e. after removal of poor quality cells, lowly expressed genes etc.) for combined analysis of all samples (n = 9). metadata.txt: metadata for cells in counts.txt, including cluster identity of each cell.

value: MR1/5-OP-RU + alphaCD28


title: LPS, replicate 3, bulk RNAseq

value: LPS


title: Ammar_0009


title: Unstimulated 3.3_GEX

value: media


title: CD4 T cells, Arg-1 KO, Spleen, Rep2

description:
Freshly isolated in vitro activated cells
Arg1KO_d2


title: LPS, replicate 2, bulk RNAseq

value: Peritoneum

value: Thioglycolate elicited macrophages


title: CmetH


title: LPS, replicate 1, bulk RNAseq

value: WT


title: ATAC-seq_Tmem cells, donor 3

data_processing:
Adapter sequences were removed using Trimmomatic (v0.36).
Reads were mapped to hg38 using Bowtie 2 (v2.3.4.1).
BAM files from multiple sequencing lanes were merged using samtools (v1.6).
Duplicate reads were removed using Picard MarkDuplicates (v2.15.0).
Reads mapping to the mitochondrial genome (samtools v1.6) and blacklisted regions (bedtools v2.26.0) were removed.
Read start sites were adjusted to correspond to the center of the tranposase binding site - reads on the forward strand were offset by +5 bp and reads on the reverse strand were offset by −4 bp using deepTools alignmentSieve (v3.1.0). Cut sites were identified as the 5′ ends of forward and reverse reads.
Peak calling was performed with MACS2 (v2.1.1).
An optimal peak list was defined using the irreproducibility discovery rate framework.
Cut sites within peaks were quantified using featureCounts (v1.6.0).
Assembly: hg38
Supplementary files format and content: peak_counts.txt (output of featureCounts, cut sites per peak)

extract_protocol:
50,000 naïve T cells (CD8+CD45RO−CCR7+), MAIT cells (CD8+CCR7−MR1/5-OP-RU+) and Tmem cells (CD8+CCR7−MR1/5-OP-RU−) were sorted per donor (n = 3) from CD8-enriched PBMCs.
ATAC-seq libraries were generated using the Fast-ATAC protocol (Corces et al., Nat. Genet., 2016).

value: Blood

value: CD8+ memory T cells


title: CD4 T cells, WT, Spleen, In vitro activation, Rep4

description:
Freshly isolated in vitro activated cells
WT_d4

value: Spleen

value: CD4 T cells


title: pSAP mock control strain, Biological replicate A

description: pSAP-A

value: trophozoite

value: pSAP (Empty)


title: BmetH


title: TCR-stimulated 3.2_GEX

value: MAIT


title: ATAC-seq_Tmem cells, donor 2


title: AmetH


title: CD4 T cells, WT, Spleen, In vitro activation, Rep3

description:
Freshly isolated in vitro activated cells
WT_d3

value: In vitro activation

value: 22 hr


title: Cytokine-stimulated 3.3_GEX


title: Unstimulated 3.2_GEX


title: Cytokine-stimulated 3.1_GEX


title: pheochromocytoma and paraganglioma, group 2, sample 9

city: Utrecht

first: Frank

last: van Steenbeek

state: Select State/Province

address: Yalelaan 104

institute: Utrecht University

description:
PPGL_g2_9
GAL6380_exon_featureCounts.raw.txt

data_processing:
perform quality control on FastQ files (using FastQC)
align reads of each sample in a run against reference genome (using STAR) and add read groups (using Picard)
perform quality control on generated BAM files (using Picard)
count reads in features (using HTSeq-count)
Assembly: CanFam3.1
Supplementary files format and content: tab-delimited text file includes raw count values for each Sample

organism: Canis lupus familiaris

source_name: pheochromocytoma and paraganglioma

extract_protocol:
RNeasy Mini Kit (Qiagen)
TruSeq Stranded mRNA Library Prep Kit (Illumina)

tag: group

value: pheochromocytoma and paraganglioma

value: tumor cells arising from the chromaffin cells


title: CD4 T cells, WT, Spleen, In vitro activation, Rep2

description:
Freshly isolated in vitro activated cells
WT_d2


title: ATAC-seq_Tmem cells, donor 1


title: ATAC-seq_MAIT cells, donor 3

value: CD8+ MAIT cells


title: pheochromocytoma and paraganglioma, group 2, sample 8

description:
PPGL_g2_8
GAL6380_exon_featureCounts.raw.txt


title: ATAC-seq_MAIT cells, donor 2


title: TCR-stimulated 3.1_GEX

value: MR1/5-OP-RU + alphaCD28


title: pheochromocytoma and paraganglioma, group 2, sample 7

description:
PPGL_g2_7
GAL6380_exon_featureCounts.raw.txt


title: ATAC-seq_MAIT cells, donor 1


title: pheochromocytoma and paraganglioma, group 2, sample 6

description:
PPGL_g2_6
GAL6380_exon_featureCounts.raw.txt


title: Cytokine-stimulated 3.2_GEX


title: CD4 T cells, WT, Spleen, In vitro activation, Rep1

description:
Freshly isolated in vitro activated cells
WT_d1


title: Unstimulated 3.1_GEX

value: media


title: CD4 T cells, Arg-1 KO, Spleen, Rep1

description:
Freshly isolated in vitro activated cells
Arg1KO_d1

value: Arg1 KO


title: CD4 T cells, WT, Spleen, Rep1

description:
Mouse infected with recombinant PR8 influenza virus (expressing the LCMV gp33-41 eptiope (KAVYNFATM) inserted into the NA of A/PR/8/34 (H1N1) (PR8-33)
Spleen-d1

tag: disease state

value: flu infection

value: Day 9


title: CD4 T cells, WT, Spleen, Rep3

description:
Mouse infected with recombinant PR8 influenza virus (expressing the LCMV gp33-41 eptiope (KAVYNFATM) inserted into the NA of A/PR/8/34 (H1N1) (PR8-33)
Spleen-d3

value: WT


title: BFD1KO9wks1

city: Pittsburgh

first: Jon

middle: P

last: Boyle

address: 4249 Fifth Avenue

department: Biological Sciences

institute: University of Pittsburgh

data_processing:
Data analyzed using CLC Genomics workbench
log-transformed normalized data generated usign "rlog" in DESeq2
Assembly: hg18
Supplementary files format and content: log2 transformed normalized counts per million reads mapped

organism:
Toxoplasma gondii
Mus musculus

source_name: Brain

extract_protocol:
Qiagen Rneasy
NEB Next Ultra II stranded mRNA seq
200 bp insert

treatment_protocol: Intraperitoneal infection

value: Brain

value: Mouse CBA/J, T. gondii strain VEG

value: 9 weeks post infection


title: pheochromocytoma and paraganglioma, group 2, sample 5

description:
PPGL_g2_5
GAL6380_exon_featureCounts.raw.txt


title: ATAC-seq_Naïve T cells, donor 3

value: Blood

value: CD8+ naive T cells


title: ROCY1KO9wks3


title: CD4 T cells, WT, Lungs, Rep3

description:
Mouse infected with recombinant PR8 influenza virus (expressing the LCMV gp33-41 eptiope (KAVYNFATM) inserted into the NA of A/PR/8/34 (H1N1) (PR8-33)
Lungs-d3

source_name: Lungs

value: Lungs

value: CD4 T cells


title: ROCY1KO9wks2


title: ATAC-seq_Naïve T cells, donor 2


title: pheochromocytoma and paraganglioma, group 2, sample 3

description:
PPGL_g2_3
GAL6380_exon_featureCounts.raw.txt


title: ATAC-seq_Naïve T cells, donor 1


title: CD4 T cells, WT, Lungs, Rep2

description:
Mouse infected with recombinant PR8 influenza virus (expressing the LCMV gp33-41 eptiope (KAVYNFATM) inserted into the NA of A/PR/8/34 (H1N1) (PR8-33)
Lungs-d2


title: pheochromocytoma and paraganglioma, group 2, sample 4

description:
PPGL_g2_4
GAL6380_exon_featureCounts.raw.txt


title: ROCY1KO9wks1


title: pheochromocytoma and paraganglioma, group 2, sample 2

description:
PPGL_g2_2
GAL6380_exon_featureCounts.raw.txt


title: BFD1KO4wks6

value: 4 weeks post-infection


title: CD4 T cells, WT, Spleen, Rep2

description:
Mouse infected with recombinant PR8 influenza virus (expressing the LCMV gp33-41 eptiope (KAVYNFATM) inserted into the NA of A/PR/8/34 (H1N1) (PR8-33)
Spleen-d2

value: Spleen


title: CD4 T cells, WT, Lungs, Rep1

description:
Mouse infected with recombinant PR8 influenza virus (expressing the LCMV gp33-41 eptiope (KAVYNFATM) inserted into the NA of A/PR/8/34 (H1N1) (PR8-33)
Lungs-d1


title: BFD1KO4wks5


title: pheochromocytoma and paraganglioma, group 2, sample 12

description:
PPGL_g2_12
GAL6380_exon_featureCounts.raw.txt

value: pheochromocytoma and paraganglioma

value: tumor cells arising from the chromaffin cells


title: Tumor tissue, FMD, replicate 1

city: Shanghai

first: Ziwen

last: Zhong

address: No. 180, Fenglin Road, Xuhui District

institute: Zhongshan Hospital Fudan University

description: 10X Genomics

data_processing:
Basecalls performed using CASAVA version 1.8.
cellranger (v3.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20%  passed the cell quality filtering and mitochondria genes were removed in the expression table.
Seurat package (version: 2.3.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.
PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Assembly: GRCm38
Supplementary files format and content: MTX file and TSV file contain counts for each barcode and gene.

source_name: colorectal cancer tissue

extract_protocol:
Briefly, the tumor bearing colons and location-matched normal colons were cleaned, cut into 0.5-cm sections, and shaken twice in a Ca and Mg-free (CMF) solution containing 10 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES), 25 mM NaHCO3, 1 mM dithiothreitol (DTT), and 1 mM ethylenediaminetetraacetic acid (EDTA) (all from Sigma-Aldrich, St. Louis, MO), and 2% fetal bovine serum (FBS) (Gibco, Portland, OR, USA) at 37 ℃. Subsequently, the cell suspension was filtered using a 70-mm nylon cell strainer (Corning, NY, USA), and the cells were collected. The residual colon pieces were digested for 60 min in Roswell Park Memorial Institute 1640 Medium (RPMI-1640 medium) containing 10% FBS, 1 mg/mL of collagenase D (Roche Applied Science, Upper, Bavaria, Germany), and 0.08 mg/mL of DNase I (Sigma-Aldrich, St. Louis, MO) at 37℃, and the cells were collected. All the collected cells were mixed, and all the immune cells from were purified using 40% and 70% discontinuous percoll gradients.
RNA libraries were generated by 10x Genomics Single Cell 3’ V3 Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols.

treatment_protocol: Male C57BL/6 mice were randomly divided into two groups (control group and FMD group). Mice in two groups were injected (day 0) intraperitoneally with 12 mg/kg body weight of azoxymethane (AOM), followed by ad libitum access to three dextran sodium sulfate (DSS) (at a final concentration of 2.5%)/water cycles (7 days of DSS and 14 days of water). Ad libitum and FMD treatment are given from the second cycle. After three cycles, the mice were sacrificed.

tag: model

value: AOM-DSS induced CRC

value: colorectal cancer tissue

value: CD45+ cells

value: Male

value: fasting-mimicking diet


title: pheochromocytoma and paraganglioma, group 2, sample 11

description:
PPGL_g2_11
GAL6380_exon_featureCounts.raw.txt


title: pheochromocytoma and paraganglioma, group 2, sample 10

description:
PPGL_g2_10
GAL6380_exon_featureCounts.raw.txt


title: Tumor tissue, ad libitum, replicate 1

description: 10X Genomics

value: ad libitum