title: eS6A-Δ6SA_rep2


title: PitNET5

status: Public on Jan 24 2024

type: genomic

city: Hamburg

first: Matthias

last: Dottermusch

address: Martinistr. 52

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description: Somatotroph PitNET

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the iScan System and standard recommended Illumina scanner setting

data_processing: Data analyses were conducted using the minfi package (v1.46.0), IlluminaHumanMethylationEPICanno.ilm10b4.hg19 (v.0.6.0) and IlluminaHumanMethylationEPICmanifest (v.0.3.0) in R (v4.3.1). The data was read into an RGChannelSet. P-values for every individual probe were calculated using the detectionP()-function of minfi. Methylated and unmethylated signal intensities were extracted without using normalization (preprocessRaw). Functional normalization (preprocessFunnorm) was applied in order to obtain normalized beta-values.

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: PitNET

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated from FFPE tissue using the ReliaPrep™ FFPE gDNA Miniprep System (Promega) according to manufacturer’s instructions. About 100-500 ng DNA was used for bisulfite conversion by the EZ DNA Methylation Kit (Zymo Research). Afterwards, the DNA Clean & Concentrator-5 (Zymo Research) and the Infinium HD FFPE DNA Restore Kit (Illumina) were employed to clean and restore the converted DNA. Finally, the Infinium MethylationEPIC BeadChip Kit Illumina) was used to quantify the methylation status of 850,000 CpG sites on an iScan device (Illumina).

tag: Sex

value: male

tag: granulation

value: dense

tag: sf1 immunostaining

value: positive


title: CB_Control2

type: SRA

city: Calgary

first: Jiami

last: Guo

address: 2500 University Dr NW

department: Cell Biology and Anatomy

country: Canada

institute: University of Calgary

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation was done using CellRanger3.1.0 pipeline
Assembly: mm10
Supplementary files format and content: Comma-separated file: gene expression matrix
Supplementary files format and content: Comma-separated file: metadata

molecule: total RNA

organism: Mus musculus

source_name: Cerebellum

extract_protocol:
Aldh1l1-CreERT2 (Control), Arl13blox/lox; Aldh1l1-CreERT2 (Arl13bcKO), Smolox/lox; Aldh1l1-CreERT2 (SmocKO), and SmoM2lox/+; Arl13blox/lox; Aldh1l1-CreERT2 (SmoM2-Arl13bcKO) mice were administrated with tamoxifen (20mg/mL) from P7 to P9. Cortices and the cerebellum were dissected at P52~55. Samples from two male mice of each genotype were combined. Tissue was cut into small pieces and digested in 5mL enzyme buffer (1 x EBSS media, 0.36% D(+) glucose, 26mM NaHCO3, 0.5mM EDTA) containing papain (~34 units/mL, Worthington), DNase I (20 units/ml, Sigma) for 30 min at 37 °C in a cell culture incubator (5% CO2, 95% air). Tissue pieces were then gently triturated into single cells after stopping the enzyme reaction by adding 10mL DMEM (Gibco) supplied with 10% FBS (Gibco). Cells were spun down and resuspended in 13mL of Percoll solution [23% Percoll (Sigma), 36mM NaCl in PBS], and carefully topped with 8mL of PBS. Cells were then centrifuged at 900g (accelerate: 4, break: 0), resuspended and washed once with FACS buffer (PBS supplied with 3% FBS). Blocked with FcBlock (Biorad) for 5 min at room temperature, cells were then stained with ACSA2-PE (Miltenyi Biotec) for 30min at 4 °C, followed by Viability Dye eFluor™ 780 (eBioscience) incubation for 5 min at room temperature. Cells were then washed with PBS solution supplied with 3% FBS (Gbico) once, and live ACSA2+ cells were sorted using flow cytometry. The RNase inhibitor (Sigma) was supplied in the solutions from the staining to the end of sorting.
A total of 15, 000 single cells of each sample were loaded for partitioning using 10x Genomics NextGEM Gel Bead emulsions (3’ gene expression kit, version 3.1) and processed according to the manufacturer’s protocol. The PCR amplification steps were run 12x.

tag: tissue

value: Cerebellum

tag: age


title: IP_yeastCrispr_Hybrid_RS182

city: Rehovot

first: Ran

last: Shachar

address: 234 Herzl St.

department: Department of Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: Synaptic Systems (Cat# 202003; RRID: AB_2279214)  + Cell Signaling D9D9W

library_source: transcriptomic

data_processing:
alignment using STAR (V. 2.5.3a)
Read coverages were obtained using the R package txtools (https://github.com/AngelCampos/txtools)
Assembly: SK1-YPS138, hg19-mm9, CAST-HOUS
Supplementary files format and content: rds

molecule: polyA RNA

organism: Saccharomyces cerevisiae x Saccharomyces paradoxus

source_name: Saccharomyces Hybrid: sk1-YPS138

growth_protocol: All yeast strains used in this work were grown in YPD (2% dextrose) at 30C. To induce synchronous sporulation, cells were grown for 24 h in 1% yeast extract, 2% peptone, 4% dextrose at 30C, diluted in BYTA (1% yeast extract, 2% tryptone, 1% potassium acetate, 50 mM potassium phthalate) to OD600 = 0.2 and grown for another 16 h at 30C, 250 rpm. Cells were then washed two times with water and re-suspended in Sporulation medium (0.3% potassium acetate) at OD600 = 2.0 and incubated at 30C at 190 rpm. Human monochromosome hybrid cells JCRB2201, JCRB2202 and JCRB2203 were purchased from the Japanese Collection of Research Bioresources (JCRB), and cultured in DMEM (GIBCO) supplemented with 10% fetal bovine serum (FBS) and 0.8mg/ml G418(Gibco,79N9555) 37. mESCs, BJ, and NIH 3T3 cells were cultured in DMEM (GIBCO) supplemented with 10% FBS and 1% Penicillin and Streptomycin.

extract_protocol:
Yeast total RNA samples were prepared by adjusting previously published protocols. After fast freezing the yeast cells in liquid nitrogen, yeast cells were resuspended in equal amounts of phenol:Chloroform:Isoamyl alcohol (Sigma Aldrich), buffer AE (50mM sodium acetate, 10mM EDTA 1% SDS), and glass beads in Eppendorf tube. The tube was vortexed for 15 minutes in a bullet blender, heated to 65 °C for 30 minutes, followed by another round of 5 minutes vortex and 30 minutes heating to 65 °C. Samples were placed on ice for 5 minutes and centrifuged for 10 minutes (12000g, 4 °C). The supernatant was isolated, re-extracted with phenol:Chloroform:Isoamyl alcohol, and precipitated with sodium acetate and isopropanol. For all types of mammalian cell lines, total RNA was extracted with BIO TRI RNA reagent (Bio-lab). Enrichment for mRNA was done by two rounds of poly-A selection using Oligo(dT) beads (Dynabeads mRNA DIRECT) in both total RNAs from yeast and mammals.
m6A-seq2: Fragmentation, 3' adapter ligation, pooled(m6A-IP, cDNA synthesis, second adapter ligation and enrichment)
m6A-seq2

tag: cell type

value: yeast cell

tag: treatment

tag: fraction

value: IP


title: PitNET27

description: Somatotroph PitNET

value: female


title: PitNET70

description: Somatotroph PitNET

value: negative


title: IP_yeastCrispr_Hybrid_RS181


title: IP_yeastCrispr_Hybrid_RS180


title: eS6A-Δ6SA_rep1

city: Philadelphia

first: Aman

middle: Yebio

last: Husbands

state: PA

address: 103B Caroline Lynch Bldg, 433 S University Ave

department: Biology

country: USA

institute: The University of Pennsylvania

data_processing:
Reads were aligned using STAR 2.7.6a intron size was set to 6000nt
Reads were counted using featureCounts 2.0.0 at the meta feature (gene) level, chimeric reads and multimapping reads were filtered out
Genes without at least one count in all three replicates of a single condition were removed
Read counts were normalized using DESeq2_1.26.0 with a pairwise comparison design between all genotypes
Assembly: TAIR10.1 (Genome) Araport 11 (Reference)
Supplementary files format and content: Processed data file is a matrix containing the DESeq2 normalized counts for each sample. Each row is a gene (AGI) and each column is a sample.

organism: Arabidopsis thaliana

source_name: Seedling Shoot

growth_protocol: Seedlings were grown for 12 days  on 1/2-strength MS medium under long-day (16h light, 8h dark) conditions (80uE/m2/sec fluorescent white light).

extract_protocol:
Seedling shoots were harvested by flooding the plants with liquid nitrogen and scraping off the seedling shoots. Total RNA was extracted using a commercial kit
Illumina total RNA with Ribo-Zero depletion plus ERCC spike in RNAs, Paired-end 75 chemistry

value: Seedling Shoot

tag: genotype

value: rps6a rps6b; eS6A-{delta}6SA


title: CB_Control1

description: 10x Genomics


title: PitNET41

description: Somatotroph PitNET


title: IP_yeastCrispr_Hybrid_RS179


title: CTX_Control

description: 10x Genomics

source_name: Brain Cortex

value: Brain Cortex


title: IP_yeastCrispr_Hybrid_RS176


title: eS6A-HA_rep3

value: rps6a rps6b; eS6A-HA


title: IP_yeastCrispr_Hybrid_RS178


title: eS6A-HA_rep2


title: IP_yeastCrispr_Hybrid_RS177


title: IP_yeastCrispr_Hybrid_RS174


title: MRTX1133 treated, scRNAseq

city: Buffalo

first: Jianxin

last: Wang

state: NY

address: 665 Elm Street

department: Molecular and Cellular Biology

institute: Roswell Park Comprehensive Cancer Center

description:
RS-03928730_AKB6-MRTX1133_RS-03928346
10X Genomics

data_processing:
cellranger-6.1.2
Assembly: mm10-2020-A
Supplementary files format and content: data matrix in hd5 format

source_name: AKB6 xenografts developed in  C57BL/6 strain

growth_protocol: AKB6 cell line  cultured in RPMI media supplemented with 10% FBS and were maintained in 37°C with 5% CO2. The xenografts were developed in C57BL/6 strain by subcutaneously injecting 500,000 cells/mouse.The mice were always maintained in Doxycycline water to induce the oncogenic KRAS

extract_protocol: Single cells were isolated from the tumor tiisues by digesting the tissues in Liberase (Sigma, 5401020001) according to mannusfacturer's protocol. The RBC cells were eliminated using the ACK lysis buffer.

treatment_protocol: Mice were treated with MRTX1133 once per day for 9 days. The drug was administed intraperitoneally . MRTX1133 was dissolved in 50 mM citrate buffer and 10% Captisol. The control mice received the vehicle (50 mM citrate buffer and 10% Captisol) treatement, which was adminsitered intraperitoneally.


title: IP_yeastTimeCourse_2


title: eS6A-HA_rep1


title: IP_yeastCrispr_Hybrid_RS164


title: Vehicle, scRNAseq

description:
RS-03928729_AKB6-vehicle_RS-03928345
10X Genomics

value: AKB6 xenografts developed in  C57BL/6 strain

value: Vehicle


title: AKB6, MRTX1133, ROI 023

library_source: other

data_processing:
GeoMx_NGS_Pipeline_2.3.3.10
Assembly: Mm_R_NGS_WTA_v1.0.pkc
Supplementary files format and content: DCC files: count data for each barcode.
Supplementary files format and content: Sample_Annotation.xlsx

molecule: other

extract_protocol: RNAs with barcode are prepared using GeoMx DSP instrument, nanoString, Inc.

treatment_protocol: Mice were treated with MRTX1133 once per day for three weeks. The drug was administed intraperitoneally . MRTX1133 was dissolved in 50 mM citrate buffer and 10% Captisol. The control mice received the vehicle (50 mM citrate buffer and 10% Captisol) treatement, which was adminsitered intraperitoneally.

tag: cell line

value: KRAS G12D


title: IP_yeastCrispr_Hybrid_RS161


title: rps6b_rep_3


title: AKB6, MRTX1133, ROI 019


title: IP_yeastCrispr_Hybrid_RS160


title: rps6b_rep_2


title: IP_yeastCrispr_Hybrid_RS162


title: IP_Yeast_HYBRIDmu_REP3


title: IP_Yeast_HYBRIDmu_REP2


title: AKB6, MRTX1133, ROI 018


title: AKB6, MRTX1133, ROI 016


title: IP_Yeast_HYBRIDmu_REP1


title: rps6a_rep_3


title: IP_Yeast_HYBRID_REP3


title: rps6a_rep_2


title: IP_Yeast_HYBRID_REP2


title: IP_yeastCrispr_Hybrid_RS163


title: IP_Yeast_HYBRID_REP1


title: AKB6, MRTX1133, ROI 014


title: Input_yeastTimeCourse_11

value: input


title: Input_yeastTimeCourse_9.5


title: rps6a_rep_1


title: AKB6, MRTX1133, ROI 012


title: WT_rep_3

value: WT


title: IP_yeastCrispr_Hybrid_WT


title: Input_yeastTimeCourse_7


title: Input_yeastTimeCourse_8


title: rps6b_rep_1


title: WT_rep_2


title: Input_yeastTimeCourse_5


title: Input_yeastTimeCourse_6


title: AKB6, MRTX1133, ROI 010


title: Input_yeastTimeCourse_4


title: WT_rep_1


title: AKB6, MRTX1133, ROI 015


title: IP_yeastTimeCourse_9.5


title: AKB6, MRTX1133, ROI 009


title: Input_yeastTimeCourse_2


title: patient_#114107_nonpAstro_3

city: Planegg-Martinstied

first: Giacomo

last: Masserdotti

address: Groshaderner Strasse 9

department: ISF

institute: Helmholtz Zentrum

description:
E3V7_S1_H6_m_STAR_hg38
allStar_res_both.csv

data_processing:
Aligment STAR-2.5.3a, hg38, ensembl90
Assembly: hg38, ensembl90
Supplementary files format and content: CSV file with raw data per line

source_name: cell line

growth_protocol: Briefly, confluent iPSC cultures were dissociated with collagenase, collected with a cell scraper and cultured in suspension to form embryoid bodies. Cells were cultured in mTESR1 with 1× mTESR1 supplement and 10 μM Rock Inhibitor Y-27632 for 24 hours. Then, medium was changed to Astrocyte Medium (AM) supplemented with 20ng/ml Noggin and 10ng/mL PDGFAA for the next two weeks and an additional week with only PDGFAA. Embryoid bodies were then manually dissociated by pipetting and the resulting pAstros were plated on poly-L-ornithine (PLO) and laminin-coated dishes in AM supplemented with 10ng/ml bFGF and 10ng/ml EGF. Upon reaching ~80% confluency, pAstros were passaged using Accutase. pAstros were maintained in culture until ~day 45-50 of glial differentiation and subsequently terminally differentiated into nonpAstros in AM supplemented with 10ng/ml LIF. Media was changed every second day.

extract_protocol:
Cells at iPSC, pAstro and nonpAstro stages were collected and RNA was isolated on column using the PicoPureTM RNAextraction kit (Applied Biosystems). RNA quality and concentration were evaluated with an Agilent BioAnalyzer 2100 (Agilent). All samples had a RIN > 9
10 ng of RNA from each sample was used to generate the RNA-seq libraries using bulk-adapted mcSCRB-seq protocol (Bagnoli et al., 2018): cDNA was generated by oligo-dT primers containing well-specific (e.g. sample specific) barcodes and unique molecular identifiers (UMIs). Unincorporated barcode primers were digested using Exonuclease I (Thermo Fisher)
cDNA was pre-amplified using KAPA HiFi HotStart polymerase (Roche) and pooled before Nextera libraries were constructed from 0.8 ng of pre-amplified cleaned up cDNA using Nextera XT Kit (Illumina). 3’ ends were enriched with a custom P5 primer (P5NEXTPT5, IDT) and libraries were size selected using 2% E6 Gel Agarose EX Gels (Life Technologies), cut out in the range of 300–800 bp, and extracted using the Monarch DNA Gel Extraction Kit (New England Biolabs)

value: cell line

value: nonpAstro

value: patient

tag: replicate


title: Input_yeastTimeCourse_3


title: AKB6, MRTX1133, ROI 008


title: Input_yeastTimeCourse_0


title: Input_yeastTimeCourse_KO


title: control_HMGU-1_nonpAstro_2

description:
E3V7_S1_H5_m_STAR_hg38
allStar_res_both.csv

value: control


title: PitNET1

description: Somatotroph PitNET

value: male

value: dense


title: control_ULERi82a-R1-002_pAstro_1

description:
E3V7_S1_H4_m_STAR_hg38
allStar_res_both.csv

value: pAstro


title: AKB6, MRTX1133, ROI 011


title: patient_#114107_nonpAstro_2

description:
E3V7_S1_H3_m_STAR_hg38
allStar_res_both.csv


title: Input_yeastCrispr_Hybrid_RS184

value: yeast cell


title: Input_yeastCrispr_Hybrid_RS185


title: Input_yeastCrispr_Hybrid_RS183


title: AKB6, MRTX1133, ROI 006


title: Input_yeastCrispr_Hybrid_RS182


title: Input_yeastCrispr_Hybrid_RS181


title: AKB6, MRTX1133, ROI 005


title: Input_yeastCrispr_Hybrid_RS180


title: Input_yeastCrispr_Hybrid_RS179


title: AKB6, MRTX1133, ROI 003


title: Input_yeastTimeCourse_1


title: control_HMGU-1_pAstro_3

description:
E3V7_S1_H1_m_STAR_hg38
allStar_res_both.csv


title: Input_yeastCrispr_Hybrid_RS177


title: AKB6, MRTX1133, ROI 001


title: Input_yeastCrispr_Hybrid_RS176


title: AKB6, MRTX1133, ROI 007


title: Input_yeastTimeCourse_WT


title: AKB6, Vehicle, ROI 006


title: Input_yeastCrispr_Hybrid_RS174


title: Input_yeastCrispr_Hybrid_RS163


title: Input_yeastCrispr_Hybrid_RS164


title: Input_yeastCrispr_Hybrid_RS162


title: AKB6, Vehicle, ROI 005


title: Input_yeastCrispr_Hybrid_RS161


title: AKB6, MRTX1133, ROI 004


title: patient_#79787_nonpAstro_3

description:
E3V7_S1_G3_m_STAR_hg38
allStar_res_both.csv


title: Input_yeastCrispr_Hybrid_RS160


title: patient_#114107_pAstro_3

description:
E3V7_S1_G5_m_STAR_hg38
allStar_res_both.csv


title: control_HMGU-1_nonpAstro_1

description:
E3V7_S1_H2_m_STAR_hg38
allStar_res_both.csv


title: control_HMGU-1_pAstro_2

description:
E3V7_S1_G4_m_STAR_hg38
allStar_res_both.csv


title: AKB6, Vehicle, ROI 004


title: Input_yeastCrispr_Hybrid_RS178


title: Input_yeastCrispr_Hybrid_WT


title: AKB6, Vehicle, ROI 003


title: patient_#114107_pAstro_2

description:
E3V7_S1_G2_m_STAR_hg38
allStar_res_both.csv


title: Input_Yeast_HYBRIDmu_REP3


title: patient_#87971_iPSC_4

description:
E3V7_S1_G7_m_STAR_hg38
allStar_res_both.csv

value: iPSC


title: patient_#114107_nonpAstro_1

description:
E3V7_S1_G6_m_STAR_hg38
allStar_res_both.csv


title: Input_Yeast_HYBRIDmu_REP2


title: Input_Yeast_HYBRID_REP3


title: AKB6, Vehicle, ROI 002


title: control_HMGU-1_pAstro_1

description:
E3V7_S1_G1_m_STAR_hg38
allStar_res_both.csv


title: Input_Yeast_HYBRIDmu_REP1


title: AKB6, Vehicle, ROI 001


title: patient_#114107_iPSC_3

description:
E3V7_S1_F7_m_STAR_hg38
allStar_res_both.csv


title: Input_Yeast_HYBRID_REP2


title: Input_Yeast_HYBRID_REP1


title: patient_#79787_nonpAstro_2

description:
E3V7_S1_F6_m_STAR_hg38
allStar_res_both.csv


title: ATAC_Tdt_Neg_2

city: Hangzhou

first: DANYANG

last: HE

state: Zhejiang

address: 600 Dunyu Road Sandun Town

department: School of Life Sciences

country: China

institute: Westlake Univeristy

library_source: genomic

data_processing:
For bulk RNA-Seq, FASTQ files were trimmed using cutadapt (v2.10) with ‘-q 30’ and aligned to the mouse genome/transcriptome (GENCODE GRCm38 vM25, mm10) using STAR (v2.7.5c) with ‘twopassModeBasic’. The expression abundances were estimated (expected counts and TPM values) using RSEM (v1.3.3). COMBAT was used to correct for batch effects. The count matrix was processed with the edgeR package (v3.32.0) in R to calculate DEGs with the default parameters. Principal component analysis (PCA) was run on the centered expression matrix  of the top 2000 variable genes. Gene set enrichment analyses (Broad, GSEA 4.2.3 build 10) and TopGO (v2.40.0) were used for pathway analysis with graphical rendering using clusterProfiler (v3.16.1). Heatmaps were plotted with Complexheatmap (v2.6.2).
For single cell RNA-Seq, Reads processing, alignment to the mm10 transcriptome and unique molecular identifier(UMI) counting/collapsing were performed using Cellranger toolkit (v7.0.0, 10x Genomics) with ‘—include-introns false’. Main downstream analysis like ‘Demultiplexing with hashtag oligos (HTOs)’, clustering and filtering were run with Seurat (v4.1.1) in R(v4.1.3)/Rstudio.
For ATAC-Seq, Cutadapt(v2.10) trimmed reads were aligned to mouse genome (ENCODE, GRCh38 GCA_000001405.15) with bowtie2(v2.2.5) “-I10 -X2000 --very-sensitive-local --no-mixed --no-discordant”. For advanced filtering, samtools(v1.10), bedtools(v2.29.2) and picard(v2.23.8) MarkDuplicates were used to remove bad-quality, blacklist-region reads and duplicates as mentioned in kundajelab pipeline(github.com/kundajelab/atac_dnase_pipelines). Then the clean bam files were used to generate normalized bigwig files with deeptools(v3.5.0)  “bamCoverage -e250 -bs100 --normalizedUsing RPKM”. And Genome-wide signal correlation of each two samples were processed and plotted using ‘multiBigwigSummary bins -bs 5000’ and ‘plotCorrelation’.
Assembly: mm10
Supplementary files format and content: csv file includes raw tpm for each sample (bulk RNA-Seq)
Supplementary files format and content: CellRanger output matrix files and HTO setting csv file packaged in format .zip (single cell RNA-Seq)
Supplementary files format and content: Final Seurat Object in format .rds (single cell RNA-Seq)
Supplementary files format and content: Final nodup, clean and normalized genomic signal in format .bigwig (ATAC-Seq)

source_name: cortex, stroke

extract_protocol:
For bulk RNA-Seq,  2,000 freshly sorted microglia were lysed in 10μL TCL buffer (QIAGEN) supplemented with 1% 2-mercaptoethanol.   For single cell RNA-Seq, cell hashing was performed by incubating the single cell suspensions with antibody cocktails containing FACS antibodies and TotalSeq antibody (Biolegend) at 1:100 final dilution for each antibody, followed by incubation for 30min on ice. Next, cells were washed and CD45+CD11b+CX3CR1+ were sorted for single cell capturing and library preparations. Briefly, 70,000 cells pooled from 10 biological samples (with 1-8 mice pooled per sample) were partitioned into nanoliter Gel-bead-inEmulsions (GEMs) droplets using the Chromium Single Cell 3′ V3.1 Kits (10x Genomics).   For ATAC-Seq, 15,000 to 20,000 freshly sorted microglia per sample were lysed for 4 min on ice in 50μl lysis buffer. The nuclei were then collected and incubated with Tn5 transposase and tagmentation buffer at 37°C for 20 min, followed by DAN purification using Tagment DNA extract beads.   For single cell RNA-Seq, cell hashing was performed by incubating the single cell suspensions with antibody cocktails containing FACS antibodies and TotalSeq antibody (Biolegend) at 1:100 final dilution for each antibody, followed by incubation for 30min on ice. Next, cells were washed and CD45+CD11b+CX3CR1+ were sorted for single cell capturing and library preparations. Briefly, 70,000 cells pooled from 10 biological samples (with 1-8 mice pooled per sample) were partitioned into nanoliter Gel-bead-inEmulsions (GEMs) droplets using the Chromium Single Cell 3′ V3.1 Kits (10x Genomics). In brief, 15,000 to 20,000 freshly sorted microglia per sample were lysed for 4 min on ice in 50μl lysis buffer. The nuclei were then collected and incubated with Tn5 transposase and tagmentation buffer at 37°C for 20 min, followed by DAN purification using Tagment DNA extract beads.
For bulk RNA-Seq, full-length RNA-seq libraries were prepared following a modified SMART-Seq2 protocol. The cDNA libraries were generated using the TruePrep RNA Library Prep Kit for Illumina and pair-end sequenced (150 bp × 2) with Novaseq 6000 (Illumina).Single cell gene expression libraries and feature barcoding libraries were generated as recommended by the 10x Genomics Chromium Single Cell 30 Reagent Kits User Guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. Libraries were pair-end (150bp x2) sequenced on a NovaSeq 6000 system (Illumina). ATAC-Seq libraries were prepared with Chromatin Profile Kit (Novoprotein; N248) following the manufacturer’s instructions. The complete DNA elute was then amplified for 13 PCR cycles with indexed primers. Following DNA clean-up with Ampure XP beads, the libraries were analyzed with Bioanalyzer for quality control, and subsequently pair-end sequenced (150 bp x 2) with a Novaseq6000 system (Illumina).

treatment_protocol: Brains were homogenized in ice-cold HBSS supplemented with 15mM HEPES and 0.5% glucose by 5 gentle strokes in a 7 mL glass Dounce homogenizer. Myelin debris were removed by density gradient separation; pellet was resuspended in 40% Percoll and centrifuged in 800G for 20 min at 4°C. Isolated microglia were labeled with a combination of conjugated antibodies, and Flow-sorted for subsequent library construction.

value: cortex, stroke

tag: disease state

value: stroke

value: Tdt- microglia


title: patient_#79787_nonpAstro_1

description:
E3V7_S1_F3_m_STAR_hg38
allStar_res_both.csv


title: ATAC_Tdt_Pos_1

value: Tdt+ microglia


title: patient_#114107_iPSC_2

description:
E3V7_S1_F4_m_STAR_hg38
allStar_res_both.csv


title: ATAC_Tdt_Pos_2


title: ATAC_Tdt_Neg_1


title: ATAC_contra_2

source_name: cortex, contralateral

value: cortex, contralateral

value: microglia


title: patient_#79787_pAstro_3

description:
E3V7_S1_F2_m_STAR_hg38
allStar_res_both.csv


title: ATAC_contra_1


title: patient_#114107_iPSC_1

description:
E3V7_S1_F1_m_STAR_hg38
allStar_res_both.csv


title: patient_#114107_pAstro_1

description:
E3V7_S1_F5_m_STAR_hg38
allStar_res_both.csv


title: hashed_Tdt_dpi6_dpi30_GEX

source_name: cortex

value: cortex

tag: library type

value: mRNA


title: patient_#79787_iPSC_3

description:
E3V7_S1_E7_m_STAR_hg38
allStar_res_both.csv

value: cell line


title: CD8+_Memory_Tcell_39

type: RNA

city: Tartu

first: Lehte

last: Turk

address: Ravila 19

country: Estonia

institute: University of Tartu

description: Gene expression data from CD8+ memory T cells

hyb_protocol: 30 μl of fragmented and labeled ds-cDNA was mixed with Hybridization Master Mix and the mix was incubated for 5 minutes at 95C and then for 5 min at 45C in a thermal cycler. The final concentration of ds-cDNA in the mix was 50 ng/μl. After the incubation, 90 μl of centrifuged supernatant hybridization cocktail was placed into the appropriate well of the hybridization tray (GeneChip Clariom S Human HT).

scan_protocol: Microarray plates were read on the GeneTitan (Thermo Fisher Scientific) instrument.

data_processing: The data was analysed with the TAC 4.0 software using default settings and SST-RMA for normalization.

label: biotin

source_name: sorted CD8+ T cells from PBMC

label_protocol: 5.5 μg of ds-cDNA was mixed with Fragmentation and Labeling Master Mix and incubated for 1h at 37C, for 2 minutes at 95C and then for 2 minutes at 4C according to the GeneChip 3' IVT Pico Kit Manual Workflow.

extract_protocol: RNA was isolated with RNeasy Micro kit (Qiagen) and the concentration and quality of RNA was measured with NanoDrop (Thermo Fisher Scientific) and Bioanalyzer (Agilent) using RNA 6000 Pico kit (Agilent), respectively

value: blood

tag: gender

value: female


title: CD8+_Temra_141

description: Gene expression data from CD8+ Temra cells


title: CD8+_Temra_147


title: CD8+_Temra_80


title: CD8+_Memory_Tcell_147


title: CD8+_Memory_Tcell_35


title: CD8+_Temra_77


title: hashed_Tdt_dpi6_dpi30_FB

value: HTO


title: CD8+_Temra_18


title: CD8+_Memory_Tcell_54


title: IP_yeastCrispr_Hybrid_RS183

description: Synaptic Systems (Cat# 202003; RRID: AB_2279214)  + Cell Signaling D9D9W

value: IP


title: CD8+_Temra_35

value: male


title: CD8+_Memory_Tcell_11


title: CD8+_CMV+_Tcell_1

description: Gene expression data from CD8+ CMV-reactive T cells


title: patient_#87971_nonpAstro_3

description:
E3V7_S1_E6_m_STAR_hg38
allStar_res_both.csv

value: nonpAstro

value: patient


title: patient_#87971_nonpAstro_2

description:
E3V7_S1_E3_m_STAR_hg38
allStar_res_both.csv


title: LPS_dpi28_Tdt_Pos_2

tag: development stage


title: CD8+_CMV+_Tcell_58


title: patient_#79787_pAstro_2

description:
E3V7_S1_E5_m_STAR_hg38
allStar_res_both.csv

value: pAstro


title: CD8+_Memory_Tcell_9


title: patient_#79787_pAstro_1

description:
E3V7_S1_E2_m_STAR_hg38
allStar_res_both.csv


title: patient_#79787_iPSC_1

description:
E3V7_S1_E1_m_STAR_hg38
allStar_res_both.csv

value: iPSC


title: CD8+_Memory_Tcell_164


title: LPS_dpi28_Tdt_Pos_4

value: cortex, stroke

value: stroke


title: patient_#87971_iPSC_3

description:
E3V7_S1_D7_m_STAR_hg38
allStar_res_both.csv


title: LPS_dpi28_Tdt_Neg_4

value: Tdt- microglia


title: CD8+_Memory_Tcell_159


title: LPS_dpi28_Tdt_Pos_3

value: Tdt+ microglia


title: CD8+_Memory_Tcell_141


title: CD8+_CMV+_Tcell_37


title: CD8+_Temra_54


title: LPS_dpi28_Tdt_Neg_3


title: LPS_dpi28_Tdt_Neg_2


title: CD8+_CMV+_Tcell_116


title: CD8+_Naive_Tcell_168

description: Gene expression data from CD8+ naive T cells


title: CD8+_Temra_19


title: LPS_dpi28_Tdt_Pos_1


title: patient_#79787_iPSC_2

description:
E3V7_S1_E4_m_STAR_hg38
allStar_res_both.csv


title: CD8+_Naive_Tcell_77


title: CD8+_Naive_Tcell_1


title: patient_#87971_nonpAstro_1

description:
E3V7_S1_D6_m_STAR_hg38
allStar_res_both.csv


title: CD8+_Naive_Tcell_164


title: patient_#87971_pAstro_3

description:
E3V7_S1_D5_m_STAR_hg38
allStar_res_both.csv


title: LPS_dpi28_contra_4

value: cortex, contralateral

value: microglia


title: LPS_dpi28_Tdt_Neg_1


title: CD8+_Memory_Tcell_168


title: CD8+_Naive_Tcell_58


title: patient_#87971_iPSC_2

description:
E3V7_S1_D4_m_STAR_hg38
allStar_res_both.csv


title: CD8+_Naive_Tcell_147


title: CD8+_CMV+_Tcell_35


title: LPS_dpi28_contra_3


title: control_HMGU-12_nonpAstro_3

description:
E3V7_S1_D3_m_STAR_hg38
allStar_res_both.csv

value: control


title: LPS_dpi28_contra_2


title: patient_#87971_pAstro_2

description:
E3V7_S1_D2_m_STAR_hg38
allStar_res_both.csv

value: cell line


title: CD8+_Memory_Tcell_77

description: Gene expression data from CD8+ memory T cells

value: blood


title: LPS_dpi28_contra_1


title: patient_#87971_iPSC_1

description:
E3V7_S1_D1_m_STAR_hg38
allStar_res_both.csv


title: Tdt_Pos_dpi28_4


title: control_HMGU-12_iPSC_3

description:
E3V7_S1_C7_m_STAR_hg38
allStar_res_both.csv


title: CD8+_Naive_Tcell_141

value: female


title: CD8+_Memory_Tcell_22


title: CD8+_Naive_Tcell_116


title: Tdt_Pos_dpi28_3


title: CD8+_Temra_60

description: Gene expression data from CD8+ Temra cells


title: Tdt_Pos_dpi28_2


title: CD8+_Naive_Tcell_37


title: CD8+_Memory_Tcell_32


title: CD8+_Naive_Tcell_36


title: patient_#87971_pAstro_1

description:
E3V7_S1_C5_m_STAR_hg38
allStar_res_both.csv


title: Tdt_Pos_dpi28_1


title: CD8+_Temra_164


title: CD8+_Temra_159


title: CD8+_Temra_22


title: Tdt_Pos_dpi14_5


title: control_HMGU-12_iPSC_2

description:
E3V7_S1_C4_m_STAR_hg38
allStar_res_both.csv


title: CD8+_Memory_Tcell_92


title: CD8+_Memory_Tcell_1


title: control_HMGU-12_nonpAstro_1

description:
E3V7_S1_C3_m_STAR_hg38
allStar_res_both.csv


title: CD8+_Naive_Tcell_86


title: Tdt_Pos_dpi14_4


title: control_HMGU-12_nonpAstro_2

description:
E3V7_S1_C6_m_STAR_hg38
allStar_res_both.csv


title: CD8+_Temra_32


title: CD8+_Memory_Tcell_36


title: control_HMGU-12_pAstro_3

description:
E3V7_S1_C2_m_STAR_hg38
allStar_res_both.csv


title: CD8+_Temra_11


title: Tdt_Pos_dpi14_3


title: control_ULERi82a-R1-002_nonpAstro_3

description:
E3V7_S1_B6_m_STAR_hg38
allStar_res_both.csv


title: Tdt_Pos_dpi14_1


title: CD8+_Memory_Tcell_86


title: control_HMGU-12_iPSC_1

description:
E3V7_S1_C1_m_STAR_hg38
allStar_res_both.csv


title: Tdt_Pos_dpi14_2


title: CD8+_CMV+_Tcell_69

description: Gene expression data from CD8+ CMV-reactive T cells


title: Tdt_Pos_dpi7_4


title: Tdt_Pos_dpi7_5


title: control_HMGU-12_pAstro_2

description:
E3V7_S1_B5_m_STAR_hg38
allStar_res_both.csv


title: CD8+_Temra_116


title: control_ULERi82a-R1-002_iPSC_2

description:
E3V7_S1_B4_m_STAR_hg38
allStar_res_both.csv


title: control_ULERi82a-R1-002_iPSC_3

description:
E3V7_S1_B7_m_STAR_hg38
allStar_res_both.csv


title: CD8+_CMV+_Tcell_77


title: control_ULERi82a-R1-002_nonpAstro_2

description:
E3V7_S1_B3_m_STAR_hg38
allStar_res_both.csv


title: CD8+_Naive_Tcell_92

description: Gene expression data from CD8+ naive T cells


title: CD8+_Naive_Tcell_60


title: CD8+_Naive_Tcell_80


title: CD8+_Memory_Tcell_72

description: Gene expression data from CD8+ memory T cells


title: CD8+_Naive_Tcell_28


title: CD8+_Temra_69


title: CD8+_CMV+_Tcell_168


title: CD8+_Naive_Tcell_69


title: CD8+_Memory_Tcell_37


title: CD8+_Temra_39


title: CD8+_Temra_92


title: CD8+_Temra_1


title: CD8+_Memory_Tcell_28


title: Tdt_Pos_dpi7_3


title: Tdt_Pos_dpi7_2


title: control_HMGU-12_pAstro_1

description:
E3V7_S1_B2_m_STAR_hg38
allStar_res_both.csv


title: control_HMGU-1_iPSC_3

description:
E3V7_S1_A7_m_STAR_hg38
allStar_res_both.csv


title: Tdt_Pos_dpi7_1


title: Tdt_Pos_dpi3_4


title: Tdt_Pos_dpi3_3


title: Tdt_Pos_dpi3_5


title: control_ULERi82a-R1-002_nonpAstro_1

description:
E3V7_S1_A6_m_STAR_hg38
allStar_res_both.csv


title: Tdt_Pos_dpi3_1


title: CD8+_Temra_58

description: Gene expression data from CD8+ Temra cells


title: CD8+_Memory_Tcell_18


title: CD8+_Naive_Tcell_11


title: CD8+_Naive_Tcell_35


title: CD8+_Memory_Tcell_58


title: CD8+_Temra_72


title: CD8+_Memory_Tcell_80


title: control_ULERi82a-R1-002_pAstro_2

description:
E3V7_S1_A2_m_STAR_hg38
allStar_res_both.csv


title: dpi28_Tdt_Pos_3


title: control_HMGU-1_iPSC_1

description:
E3V7_S1_A1_m_STAR_hg38
allStar_res_both.csv


title: CD8+_Naive_Tcell_54


title: CD8+_Naive_Tcell_22


title: CD8+_Naive_Tcell_25


title: control_HMGU-1_nonpAstro_3

description:
E3V7_S1_A3_m_STAR_hg38
allStar_res_both.csv


title: CD8+_Temra_37


title: CD8+_Naive_Tcell_72


title: CD8+_Naive_Tcell_32


title: CD8+_Temra_25


title: CD8+_Naive_Tcell_159


title: dpi28_Tdt_Pos_2


title: young LSECs, rep 2.4

city: Warsaw

first: Michal

last: Mikula

address: Roentgena 5

department: Experimental Oncology

country: Poland

institute: Maria Skłodowska-Curie National Research Institute of Oncology

data_processing:
The raw reads were processed with Ion Torrent RNASEQAnalysis pipeline (Torrent Suite version 5.0.4)
htseq-count, version 0.6.0, default parameters
DESeq2, version 1.18.1, normalization
Assembly: AmpliSeq Mouse Transcriptome v1
Supplementary files format and content: htseq normalized count

source_name: Liver

extract_protocol:
RNA from sorted LSECs was extracted using TRIzol™ LS Reagent (ThermoScientific, #10296028) according to the manufacturer’s instructions with an additional step of RNA precipitation with glycogen (ThermoScientific, #R0551).
Library was prepared using Ion AmpliSeq™ Transcriptome Mouse Gene Expression Kit according to the manufacturer’s protocol (Thermo Fisher Scientific)

value: Liver

value: LSECs

value: FAC-sorted LSECs (CD45-dim, STAB2-high, CD146-high)

value: wild type

value: young (8-10 weeks old)

tag: strain


title: dpi28_Tdt_Pos_1


title: dpi28_Tdt_Neg_4


title: CD8+_Temra_168


title: CD8+_CMV+_Tcell_54


title: aged LSECs, rep 2.3

value: aged (10-11 months old)


title: aged LSECs, rep 2.4


title: CD8+_CMV+_Tcell_11


title: CD8+_Memory_Tcell_116


title: dpi28_Tdt_Neg_3


title: CD8+_Memory_Tcell_60


title: dpi28_Tdt_Neg_2


title: ASPC1-MRTX-6-p11-A

data_processing:
Adapter trimming with trimGalore!, followed by runing mageck(v.5.9) using the Toronto KnockOut (TKO) CRISPR Library - Version 3.
Assembly: NA
Supplementary files format and content: ASPC1-UM53-TKOv3.count.txt, raw count, tab delimited text file.
Supplementary files format and content: ASPC1-UM53-TKOv3.count_normalized.txt, normalized counts, tab delimited text file.

growth_protocol: UM53 and ASPC1  cell lines were  grown in RPMI media supplemented with 10% FBS. The cellswere maintained in 37°C with 5% CO2 and tested to be mycoplasma-free.

extract_protocol:
Genomic DNA exptration was carried out using the Wizard Genomic DNA purification kit (Promega, A1120)  according to the manufacturer's protocol
A two step PCR was performed to enrich guide RNA regions in the genome and to amplify the guide RNAs with Illumina TruSeq adapters with i5 and i7 indices.

treatment_protocol: The positive and negative selections of the guide sequences in ASPC1 cells were carried out using 0.1% DMSO and MRTX1133 (6.25 nM). For the UM53 the selectio was performed using 0.1% DMSO and MRTX849 (500 nM)


title: CD8+_Memory_Tcell_69


title: dpi28_Tdt_Neg_1


title: young LSECs, rep 2.3


title: ASPC1-MRTX-6-p11


title: CD8+_CMV+_Tcell_25


title: aged LSECs, rep 2.2


title: CD8+_Temra_9


title: CD8+_CMV+_Tcell_32


title: ASPC1-DMSO-p11-A


title: ASPC1-DMSO-p11


title: CD8+_Memory_Tcell_25


title: dpi28_contra_4


title: young LSECs, rep 2.2


title: UM53-TKO-MRTX-T2-P8


title: dpi28_contra_3


title: UM53-TKO-MRTX-T3-P8


title: caBRAF-2wk-sample3

city: Durham

first: Nenad

last: Bursac

state: NC

address: 101 Science Dr. Rm. 1169

department: Biomedical Engineering

institute: Duke University

data_processing:
RNAseq reads were aligned to Rnor_6.0 genome assembly using Rsubread package from Bioconductor version 3.14
Feature counts obtained using Rsubread package as above
Genes for which the average feature count was less than 1 per replicate were filtered out prior to analysis
Differential expression analysis was performed using Bioconductor (v3.14) package DESeq2
Gene Ontology analysis was conducted using Bioconductor package ViSEAGO
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: tab delimited text file containing feature counts for each sample

organism: Rattus norvegicus

source_name: P2 neonatal rat ventricles

growth_protocol: Engineered cardiac tissues were generated from 3.25e5 P2 neonatal rat ventricular cardiomyocytes isolated from pooled male and female pups. Tissues were cultured for one or two weeks in Low Glucose DMEM, 10% horse serum, 0.5% chick embryo extract, aminocaproic acid (1 mg/ml), ascorbic acid 2-phosphate sesquimagnesium salt hydrate (50 µg/ml), penicillin (5 U/ml), vitamin B12 (2 µg/ml).

extract_protocol:
Total RNA was isolated using the Qiagen RNEasy Fibrous Tissue Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Engineered cardiac tissues were transduced with lentiviral particles on the day of tissue generation, either with a mCherry-only lentivirus (Ctrl LV) or BRAF-V600E (caBRAF) lentivirus.

value: cardiomyocyte

value: Engineered cardiac tissue

tag: culture duration


title: dpi28_contra_2

value: stroke


title: caBRAF-2wk-sample2


title: young LSECs, rep 2.1


title: UM53-TKO-DMSO-T3-P8

value: DMSO


title: caBRAF-2wk-sample1


title: dpi28_contra_1


title: UM53-TKO-DMSO-T2-P8


title: Ctrl LV-2wk-sample3


title: CD8+_Memory_Tcell_19


title: dpi7_Tdt_Pos_3

value: cortex, stroke

value: Tdt+ microglia


title: aged LSECs, rep 1.3


title: young LSECs, rep 1.3


title: CD8+_Temra_28


title: UM53-TKO-MRTX-500-P8


title: dpi7_Tdt_Pos_2


title: aged LSECs, rep 1.2


title: Ctrl LV-2wk-sample2


title: UM53-TKO-DMSO-P8


title: dpi7_Tdt_Pos_1


title: CD8+_Temra_86

value: male


title: Ctrl LV-2wk-sample1


title: young LSECs, rep 1.1


title: dpi7_Tdt_Neg_3

value: Tdt- microglia


title: caBRAF-1wk-sample3


title: HepG2 CYP3A4 cells, compound 6, day 1

city: Mainz

first: Federico

last: Marini

address: Obere Zahlbacher Strasse 69

department: Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI)

institute: University Medical Center - Mainz

data_processing:
Quality control on the sequencing data was performed with the FastQC tool (0.12.0, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Transcript abundance estimates were computed with Salmon (version 1.5.0) with a transcriptome index generated from the GENCODE (version 38), and subsequently summarized to gene level with the tximeta R package (version 1.16.0).
The exploration, modelling, and interpretation of the expression data followed previously described protocols (Ludt et al., 2022).
Exploratory data analysis was executed with the pcaExplorer package (version 2.24.0).
Differential expression analysis was performed with DESeq2 package (version 1.38.3) [31], setting the false discovery rate (FDR) cutoff to 0.05. Accurate estimation of the effect sizes (described as log2FoldChange) was finalized using the apeglm shrinkage estimator (version 1.20.0).
Subsequent analyses included Gene Ontology pathway enrichment by topGO (version 2.50.0) - using all expressed genes as background dataset and the ideal package (version 1.22.0) and clusterProfiler (version 4.6.0) with default settings.
The enrichment results were the foundation for visualization and summarization with the GeneTonic package (version 2.2.0).
Gene expression profiles were plotted as heatmaps (color-coded standardized Z scores for the expression values, after variance stabilizing transformation) to simplify comparison across samples.
Assembly: GRCh38
Supplementary files format and content: comma-delimited text file include the expression values for all genes as a count matrix, used for the statistical modeling

source_name: liver

growth_protocol: Cells were grown in DMEM medium (DMEM, 31966021, Gibco™) at 37 °C and 5% CO2 in a humidified incubator. DMEM media were supplemented with 10% fetal bovine serum (FBS) and with 3 μg/mL blasticidin (ant-bl-05, InvivoGen).

extract_protocol:
RNA extraction was performed with the InviTrap®Spin Cell RNA Mini Kit (Invitek Molecular GmbH, Berlin, Germany), according to the manufacturer's instruction. Briefly, the cell pellet was lysed with 350 μL Lysis Solution and treated with β-mercaptoethanol. After DNA removal, 350 μL 70% ethanol were added and the sample applied onto the RNA-RTA Spin Filter. After several washing steps, RNA was eluted with 60 μL of Elution Buffer R and the concentration and purity measured with NanoDrop.
Library preparation using the NEBNext© Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, MA, USA),

treatment_protocol: Aliquots of 5×10^5 CYP3A4-overexpressing HepG2 cells were seeded into 6-well-plates 24 h before treatment. Cells were treated with previously calculated IC50 concentrations of the compounds of interest. Control cells were treated with 0.2% DMSO.

value: liver

value: cytochrome P450 3A4-overexpressing HepG2

value: liver cell line

value: cyclohexil

tag: time

value: day 1


title: young LSECs, rep 1.2

value: Liver

value: LSECs

value: FAC-sorted LSECs (CD45-dim, STAB2-high, CD146-high)

value: female


title: dpi7_Tdt_Neg_2


title: caBRAF-1wk-sample2

value: cardiomyocyte


title: HepG2 CYP3A4 cells, compound 5, day 1

value: tetrabut


title: dpi7_Tdt_Neg_1

value: stroke


title: HepG2 CYP3A4 cells, compound 5, day 2

value: day 2


title: LSECs; iron citrate-injected mouse, rep. 3

description: female Balb/c mouse

value: wild type

value: intravenous injection with iron citrate (150 ug) for 5 hours


title: Ctrl LV-1wk-sample3

value: Engineered cardiac tissue


title: dpi7_contra_3

value: cortex, contralateral

value: microglia


title: LSECs; iron citrate-injected mouse, rep. 2

description: female Balb/c mouse


title: HepG2 CYP3A4 cells, compound 4, day 2

value: liver

value: cytochrome P450 3A4-overexpressing HepG2

value: metylcresol


title: caBRAF-1wk-sample1


title: LSECs; iron citrate-injected mouse, rep. 1

description: female Balb/c mouse


title: HepG2 CYP3A4 cells, compound 4, day 1

value: liver cell line

value: day 1


title: dpi7_contra_2


title: HepG2 CYP3A4 cells, compound 6, day 2

value: cyclohexil


title: Ctrl LV-1wk-sample2


title: aged LSECs, rep 1.1

value: Liver

value: LSECs

value: FAC-sorted LSECs (CD45-dim, STAB2-high, CD146-high)

value: aged (10-11 months old)


title: dpi7_contra_1

value: stroke


title: Ctrl LV-1wk-sample1

value: cardiomyocyte


title: LSECs; iron citrate-injected mouse, rep. 4

description: female Balb/c mouse

value: wild type


title: control_HMGU-1_iPSC_2

description:
E3V7_S1_A4_m_STAR_hg38
allStar_res_both.csv

value: cell line

value: iPSC

value: control


title: HepG2 CYP3A4 cells, DMSO control, day 2

value: DMSO

value: day 2


title: LSECs; citrate buffer-injected mouse, rep. 4

description: female Balb/c mouse

value: intravenous injection with citrate buffer (0,05M) for 5 hours


title: hashed_5xFAD_SIMPLE_EAE_GEX

data_processing:
For bulk RNA-Seq, FASTQ files were trimmed using cutadapt (v2.10) with ‘-q 30’ and aligned to the mouse genome/transcriptome (GENCODE GRCm38 vM25, mm10) using STAR (v2.7.5c) with ‘twopassModeBasic’. The expression abundances were estimated (expected counts and TPM values) using RSEM (v1.3.3). COMBAT was used to correct for batch effects. The count matrix was processed with the edgeR package (v3.32.0) in R to calculate DEGs with the default parameters. Principal component analysis (PCA) was run on the centered expression matrix  of the top 2000 variable genes. Gene set enrichment analyses (Broad, GSEA 4.2.3 build 10) and TopGO (v2.40.0) were used for pathway analysis with graphical rendering using clusterProfiler (v3.16.1). Heatmaps were plotted with Complexheatmap (v2.6.2).
For single cell RNA-Seq, Reads processing, alignment to the mm10 transcriptome and unique molecular identifier(UMI) counting/collapsing were performed using Cellranger toolkit (v7.0.0, 10x Genomics) with ‘—include-introns false’. Main downstream analysis like ‘Demultiplexing with hashtag oligos (HTOs)’, clustering and filtering were run with Seurat (v4.1.1) in R(v4.1.3)/Rstudio.
Assembly: mm10
Supplementary files format and content: csv file includes raw tpm for each sample (bulk RNA-Seq)
Supplementary files format and content: CellRanger output matrix files and HTO setting csv file packaged in format .zip (single cell RNA-Seq)
Supplementary files format and content: Final Seurat Object in format .rds (single cell RNA-Seq)

source_name: cortex for SIMPLE, spinal cord for EAE, brain w/o cerebellum for 5xFAD

extract_protocol:
"For bulk RNA-Seq,  2,000 freshly sorted microglia were lysed in 10μL TCL buffer (QIAGEN) supplemented with 1% 2-mercaptoethanol.   For single cell RNA-Seq, cell hashing was performed by incubating the single cell suspensions with antibody cocktails containing FACS antibodies and TotalSeq antibody (Biolegend) at 1:100 final dilution for each antibody, followed by incubation for 30min on ice. Next, cells were washed and CD45+CD11b+CX3CR1+ were sorted for single cell capturing and library preparations. Briefly, 70,000 cells pooled from 10 biological samples (with 1-8 mice pooled per sample) were partitioned into nanoliter Gel-bead-inEmulsions (GEMs) droplets using the Chromium Single Cell 3′ V3.1 Kits (10x Genomics).
For bulk RNA-Seq, full-length RNA-seq libraries were prepared following a modified SMART-Seq2 protocol. The cDNA libraries were generated using the TruePrep RNA Library Prep Kit for Illumina and pair-end sequenced (150 bp × 2) with Novaseq 6000 (Illumina).

value: AD/EAE/stroke

value: microglia

value: Spp1-GFP heterozygous

value: mRNA


title: HepG2 CYP3A4 cells, DMSO control, day 1

value: liver

value: cytochrome P450 3A4-overexpressing HepG2

value: liver cell line

value: day 1


title: LSECs; citrate buffer-injected mouse, rep. 3

description: female Balb/c mouse

value: Liver

value: LSECs

value: FAC-sorted LSECs (CD45-dim, STAB2-high, CD146-high)


title: BHLHE40-41 double siRNA, biological replicate 4

city: New York

first: Anna

last: Podlesny-Drabiniok

address: 1425 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Reads QC FastQC v0.11.8
Adapter trimming Cutadapt v2.6
Alignment to the human genome STAR v2.5.3a
Assembly: hg38
Supplementary files format and content: tab-deliminated text file includes raw counts for each sample

source_name: Cell line

growth_protocol: THP-1 acute myeloid leukemia line was differentiated to THP-1 macrophages using Phorbol 12-myristate 13-acetate (PMA) for 72h followed by transient transfection with siRNA. THP1 macrophages were maintained in RPMI1640 medium in 1% BSA, 1mM Hepes and 1x PenStrept

extract_protocol:
Rneasy Mini column (Qiagen), according to the manufacturer's protocol
TruSeq RNA Sample Prep Kit v2, according to the manufacturer's protocol

treatment_protocol: siRNA treatment (40nM/sample)

value: Cell line

value: THP-1 macrophages

value: DKD

value: BHLHE40-41 double siRNA


title: LSECs; citrate buffer-injected mouse, rep. 2

description: female Balb/c mouse

value: wild type


title: BHLHE41 siRNA, biological replicate 4

value: BHLHE41 siRNA


title: hashed_P05_P28_SIMPLE_GEX

value: cortex

value: stroke


title: BHLHE40 siRNA, biological replicate 4

value: BHLHE40 siRNA


title: hashed_P05_P28_SIMPLE_FB

description:
Spp1GFP_SIMPLE.final.seur_obj.rds
Spp1GFP_SIMPLE.raw.cellranger.zip

value: microglia

value: Spp1-GFP heterozygous

value: HTO


title: Wt controls 2

city: Dallas

first: Matt

last: Sieber

state: Texas

address: 5323 Harry Hines blvd, MC 9040 ND12.214

institute: UT Southwestern Medical Center

data_processing:
fastq files were quality chekced using fastqc
Reads from each sample we maped using STAR(v2.53a)
Edge R is used to conduct differmetial expression analysis and to output normalized TPM values.
Assembly: Hg18
Supplementary files format and content: tab-delimited files with normalized TPM values

growth_protocol: Cell are grown in high-glucose DMEM +10%FBS

extract_protocol:
Tripure RNA extraction
illumina stranded mRNA library kit.

treatment_protocol: Cells are co-ciltured with ROS producing HEK293 (+DAAO) cells grow with 25uM D-alanine for 10 hrs. Samples were then FACS sorted for GFP+ cells.

value: GFP+

value: control


title: LSECs; citrate buffer-injected mouse, rep. 1

description: female Balb/c mouse

value: Liver

value: intravenous injection with citrate buffer (0,05M) for 5 hours


title: P28 SIMPLE_Spp1_Pos_4

value: cortex, stroke

value: GFP+ microglia


title: Wt controls 3


title: hashed_5xFAD_SIMPLE_EAE_FB

description:
Spp1GFP_Modelx3.final.seur_obj.rds
Spp1GFP_Modelx3.raw.cellranger.zip

value: cortex for SIMPLE, spinal cord for EAE, brain w/o cerebellum for 5xFAD

value: AD/EAE/stroke


title: Wt controls 1


title: ROS-co-cutured cells 3

value: ROS-co-cultured


title: control_ULERi82a-R1-002_pAstro_3

description:
E3V7_S1_A5_m_STAR_hg38
allStar_res_both.csv

value: cell line

value: pAstro


title: P28 SIMPLE_Spp1_Pos_3


title: control_ULERi82a-R1-002_iPSC_1

description:
E3V7_S1_B1_m_STAR_hg38
allStar_res_both.csv

value: iPSC


title: G-147

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

data_processing:
Trimmed sequence reads were mapped to mm10 using Banana Slug Analytics Platform (Slug Genomics, 203 UV Santa Cruz)
The Cuffidiff output was used to generate Venn diagram (https://goodcalculators.com/venn-diagram-maker/) using  venn-diagram-maker software.
Assembly: pneuMuri1 (https://www.ncbi.nlm.nih.gov/datasets/taxonomy/1069680/)
Supplementary files format and content: CSV files include abundance values for each sample

source_name: mouse lung

extract_protocol:
Total RNA was extracted using TRIzol LS reagent (ThermoFisher Scientific, 10296010) in accordance with the TRIzol LS Reagent manufacturer’s protocol. The total RNA was DNase treated and quantified using the Qubit RNA HS assay kit (Thermo Fisher Scientific, Q32855). RNA quality was determined on an Agilent TapeStation 4150 using an Agilent RNA ScreenTape (Agilent, 5067-5576).
Total RNA libraries were generated using the NEBNext rRNA Depletion Kit v2 (Human/Mouse/rat) (NEB #E7400) and NEBNext UltraII Direction RNA Library Prep Kit for Illumina (NEB #7760) using 10 ng of each total RNA sample.

tag: inoculation

value: Pneumocystis Murina

value: mouse lung

value: Day 14


title: G-146


title: G-145


title: BHLHE41 siRNA, biological replicate 3

value: Cell line

value: THP-1 macrophages

value: BHLHE41 siRNA


title: BHLHE40 siRNA, biological replicate 3

value: BHLHE40 siRNA


title: dpi28_Tdt_Pos_4

value: stroke

value: Tdt+ microglia


title: Tdt_Pos_dpi3_2

value: cortex, stroke


title: Day14_Naive

description: Day14_inoculated_1_2_naive_abundance.fpkm.csv

source_name: mouse PCLS

value: naive

value: mouse PCLS


title: P28 SIMPLE_Spp1_Pos_2

value: GFP+ microglia

value: Spp1-GFP heterozygous


title: ROS-co-cutured cells 1

value: GFP+

value: ROS-co-cultured


title: scrambled, biological replicate 4

value: WT

value: scrambled


title: P28 SIMPLE_Spp1_Pos_1


title: Day14_Inoculated_2

value: Pneumocystis Murina


title: scrambled, biological replicate 3

description: SCR


title: P28 SIMPLE_Spp1_Neg_4

value: GFP- microglia


title: Gb3i-Stx2-3

city: Seattle

first: Russell

last: Whelan

state: Washington

address: 850 Republican St

department: Bioengineering

institute: University of Washington

data_processing:
RNA-seq libraries were pooled (30-plex) and clustered onto a P3 flow cell. Sequencing was performed using an Illumina NextSeq 2000 employing a paired-end, 50 base read length (PE50) sequencing strategy
STAR v2.7.1  with 2-pass mapping was used to align paired-end reads to human genome build hg38 and GENCODE gene annotation V31
FastQC 0.11.9  and RSeQC 4.0.0  were used for QC including insert fragment size, read quality, read duplication rates, gene body coverage and read distribution in different genomic regions.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: kidney endothelail

growth_protocol: HKMECs grown in endothelial growth media containing 10%FBS, heparin, endothelial growth supplement and antibiotics

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared from total RNA using the TruSeq Stranded mRNA kit (Illumina)

treatment_protocol: Cells grown to confluency, media changed, and then 12h treatment with Gb3i for appropriate conditions prior to treatment with Stx1 or Stx2 for appropriate conditions, with 8h of incubation prior to lysis and RNA extaction

value: kidney endothelail

value: GCSi-Stx2 tx


title: BHLHE40-41 double siRNA, biological replicate 3

value: Cell line

value: THP-1 macrophages

value: DKD

value: BHLHE40-41 double siRNA


title: Day14_Inoculated_1

value: Day 14


title: P28 SIMPLE_Spp1_Neg_3

value: cortex, stroke

value: stroke


title: Gb3i-Stx2-2


title: BHLHE41 siRNA, biological replicate 2

value: BHLHE41 siRNA


title: Day3_Naive

description: Day3_inoculated_1_2_naive_abundance.fpkm.csv

value: naive

value: mouse PCLS

value: Day 3


title: BHLHE40 siRNA, biological replicate 2

value: BHLHE40 siRNA


title: ROS-co-cutured cells 2

value: GFP+

value: ROS-co-cultured


title: Day3_Inoculated_2

value: Pneumocystis Murina


title: P28 SIMPLE_Spp1_Neg_2

value: GFP- microglia

value: Spp1-GFP heterozygous


title: P28 SIMPLE_Spp1_Neg_1


title: scrambled, biological replicate 2

value: Cell line

value: WT

value: scrambled


title: Day3_Inoculated_1


title: Gb3i-Stx1-2

value: kidney endothelail

value: GCSi-Stx1 tx


title: P28 SIMPLE_contra_4

value: cortex, contralateral

value: microglia


title: BHLHE40-41 double siRNA, biological replicate 1

value: THP-1 macrophages

value: DKD

value: BHLHE40-41 double siRNA


title: adult cortex [W8CSR12]

city: Baltimore

first: Mollie

last: Meffert

address: 725 N. Wolfe St.

institute: Johns Hopkins University School of Medicine

description: seq library data from forebrain cortex

data_processing:
Raw reads were filtered to remove adaptor contamination, reads missing an insert or 3’adaptor, reads containing N >10% or with Qscore of over 50% bases ≥ 5.  Clean reads (~97 % of raw) were mapped (Bowtie) to the mouse mm10 reference genome and miRBase20.0 as a reference.  Following total RNA comparisons, sample miRNA expression was statistically analyzed and normalized by transcripts per million (tpm; 106 * readcount/ library miRNA readcount)(Zhao et al., 2020; Zhou et al., 2010).  Fraction of total reads at discrete TPM intervals were assessed across samples. miRNA with expression ≥ 0.5 TPM in ≥ 4 samples were removed to reduce minimal expression comparisons.  Differential expression was assessed using DESeq2 and biological replicates to calculate log2(FoldChange) with padj < 0.05(Love et al., 2014). MiRNA were analyzed using mirdeep20.0_5 ViennaRNA-2.1.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM and read count values for each Sample

source_name: brain cortex

extract_protocol:
Brain cortices from age-matched WT or Fmr1 KO males were washed in PBS and then were directly homogenized in TrizolITM Reagent (Invitrogen) and total RNA was extracted according to the manufacturer’s instructions. total RNA was cleaned using the RNA Clean & ConcentratorTM-5 Kit (Zymo Research, R1014) with on-column DNase I treatment according to the manufacturer’s instructions. RNA was resuspended in DNase/RNase-free water and its concentration determined by the Qubit® RNA BR Assay Kit (Invitrogen, Q10211).  Compared and biological replicate samples were handled in parallel following RNA integrity assessment (Bioanalyzer2100,Agilent).  Individual libraries were constructed using 3µg of total RNA isolated from each sample.   Libraries were prepared by ligation of 3’ and 5’ adaptors, reverse transcription, minimal PCR amplification, gel purification and size selection, following by library quality control and sequencing on SE50 Illumina platform.
Libraries were prepared by ligation of 3’ and 5’ adaptors, reverse transcription, minimal PCR amplification, gel purification and size selection, following by library quality control and sequencing on SE50 Illumina platform.

value: brain cortex

tag: Sex

value: male

value: fmr1 WT


title: P28 SIMPLE_contra_3

tag: tissue

value: stroke


title: BHLHE40-41 double siRNA, biological replicate 2


title: Gb3i-Stx1-1


title: Gb3i-2

value: GCSi tx


title: adult cortex [W8CSR10]

description: seq library data from forebrain cortex


title: P28 SIMPLE_contra_2


title: BHLHE40 siRNA, biological replicate 1

value: BHLHE40 siRNA


title: P28 SIMPLE_contra_1

value: Spp1-GFP heterozygous


title: adult cortex [W8CSR11]

description: seq library data from forebrain cortex


title: scrambled, biological replicate 1

value: Cell line


title: Stx2-3

value: Stx2 tx


title: Gb3i-1


title: adult cortex [W8CSR9]

description: seq library data from forebrain cortex

value: fmr1 KO


title: Gb3i-Stx1-3

value: kidney endothelail


title: Stx2-2


title: P6 SIMPLE_Spp1_Pos_3

value: cortex, stroke

value: GFP+ microglia


title: Stx2-1


title: adult cortex [W8CSR8]

description: seq library data from forebrain cortex


title: BHLHE41 siRNA, biological replicate 1

value: BHLHE41 siRNA


title: adult cortex [W8CSR7]

description: seq library data from forebrain cortex


title: P6 SIMPLE_Spp1_Pos_2


title: Stx1-3

value: Stx1 tx


title: Stx1-2


title: aged LSECs, rep 2.1

value: Liver

value: LSECs

value: FAC-sorted LSECs (CD45-dim, STAB2-high, CD146-high)

value: wild type

value: aged (10-11 months old)

value: female


title: Stx1-1


title: P6 SIMPLE_Spp1_Pos_4

value: stroke


title: No_tx-3

value: no tx


title: No_tx-1


title: P6 SIMPLE_Spp1_Neg_1

value: GFP- microglia

value: Spp1-GFP heterozygous


title: P6 SIMPLE_Spp1_Neg_3


title: P6 SIMPLE_Spp1_Neg_2


title: P6 SIMPLE_Spp1_Pos_1


title: P6 SIMPLE_Spp1_Neg_4


title: TOP03-PcyM-D6b

city: Guangzhou

first: Haoyu

last: Wu

address: Kai Yuan Avenue 190

institute: GIBH

description: plate B

data_processing:
Sample demultiplexing based on the cell barcode was performed with UMI-tools v1.0.0 using the extract command which append mCherry++/GFP++s the UMI from read 2 to the ID of read 1. Demultiplexed read 1 fastq files were processed with Trim Galore v0.6.4 with default settings to remove adapters, low-quality bases, polyA and polyT repeats. PolyG sequences were removed using fastp v0.20.0 (these polyG sequences are an apparent artefact of NEXT500 sequencing) . Demultiplexed and trimmed read 1 fastq files were mapped with STAR 2.4.0j with default settings to a reference genome composed of the P. cynomolgi M PlasmoDB release 44 genome, the sequence of the mcherry-gfp transgene with 33 bp 3’UTR on both sides, the NCBI M mulatta v10 reference genome and the control ERCCs.
Bam files were filtered for a mapq of 255 and the readID was corrected with a custom script to remove the tags added in the polyA- and polyT trimming procedure by Trim Galore, this step was required such that UMI-tools could recognize the UMI again. Bam files were split per reference genome and these were then used by featureCounts  v1.6.4 (Subread package, http://subread.sourceforge.net/) to assign reads to genes with settings –s 1 for strand-specific counting in forward mode and –R bam to get output in bam file. Since 3’ UTRs are not annotated in the P. cynomolgi reference genome, we extended the 3’ end of each gene in PlasmoDB-44_PcynomolgiM.gff with 1kb, or less when this 1kb overlapped with genes on the same strand. After read-to-gene assignment, UMIs were counted with the UMI-tools count command with settings --per-gene --gene-tag=XT --per-cell and --extract-umi-method=read_id.
Downstream data analyses were performed in R. Cells from the three batches were treated separately until integration. For each batch, cells with gene counts from P. cynomolgi, M. mulatta and ERCC were imported into Seurat (Seurat package v3.1.5) and filtered for at least 400 P. cynomolgi genes. Candidate duplicate events were removed with a P. cynomolgi UMI count filter of 40.000. Genes were filtered on being detected in at least five cells per batch, resulting in a dataset of 1243 cells and 4773 genes.
P. cynomolgi gene counts were normalized per batch using the “Normalization by spike-ins” strategy, as described in the online companion of Amezquita et al. To do so, filtered counts in Seurat objects were converted to SingleCellExperiment objects and with splitAltExps (SingleCellExperiment package v1.8.037) ERCC and M. mulatta counts were placed in different alternative experiments. The ERCC alternative experiment was used by computeSpikeFactors (scran package v1.14.6) to compute the scaling factors to be used to normalize the counts with in the logNormcounts (scater package v1.14.6). This normalization was performed with and without log-transformation per batch (not across batches since the added amount of ERCC to the reaction mixture is more equal within than between batches). The ERCC-normalized counts were imported into the “RNA” assay of a new Seurat object: ERCC-corrected counts in the “counts” slot, the log-ERCC-corrected counts in the “data” slot.
The default integration workflow of Seurat was followed to integrate the counts from the three experiments. Integration was performed based on features detected by FindVariableFeatures with “vst” method and for 2000 features. Anchor finding was performed with the FindIntegrationAnchors function with default settings except for the k.filter which was set to 100 anchors. Anchor finding and integration used dims 1:30. The integrated data was scaled, PCA dimensionality reduction was run and UMAP and Louvain clustering were performed following the standard Seurat integration workflow. UMAP and clustering used PCs 1 till 15. Louvain clustering resolution was set to 0.4 resulting in 5 clusters.
The dotplot function from Seurat was used to obtain average and scaled average expression per cluster from the RNA assay of the integrated Seurat object (ERCC-scaled counts). For the heatmap of scaled average expression, genes within the lowest decile (10%) of the summed average expression were removed leaving 4295 genes. The heatmap was generated with the Morpheus tool of the broad institute (https://software.broadinstitute.org/morpheus/). Using the scaled data from the dotplot function. Coloring was set as relative to row minimum and row maximum. Rows (genes) were clustered by k-means clustering using 1-pearson correlation with 1000 iterations. Within k-means clusters, rows were ordered by hierarchical clustering (Euclidean, average linkage).
Genome_build: P. cynomolgi M PlasmoDB release 44 genome
Supplementary_files_format_and_content: Raw malaria and ERCC read count tables of each plates

organism: Plasmodium cynomolgi

source_name: pooled schizonts and hypnozoite

growth_protocol: Primary hepatocytes from Macaca mulatta were isolated freshly or thawed from frozen stocks as described previously. Hepatocytes were plated into collagen coated 96-well plates (65 x 103 hepatocytes per well; Perkin Elmer) and maintained at 5% CO2 at 37 °C in William's B medium supplemented with 2% DMSO: William’s E medium with glutamax containing 10% human serum (A+), 1% MEM non-essential amino acids, 2% penicillin/streptomycin, 1% insulin/transferrin/selenium, 1% sodium pyruvate, 50 µM β-mercapto-ethanol, and 0.05 µM hydrocortisone. After 2-3 days, hepatocytes were inoculated with 50 × 103 P. cynomolgi sporozoites per well.  Cultures were maintained at 5% CO2 at 37 °C with 2-3 medium refreshments (William’s B without DMSO) per week and were collected for FACS sorting at day 2, 3, 4 or 6 post hepatocyte infection (see "D#" in file name).  Quality of the cultures was assessed by Operetta high content imaging as described previously.

extract_protocol:
Sorting was performed using a 100 µm nozzle at 20 PSI or with a 130 µm nozzle at 11.5 PSI. GFP positive parasites (see gating strategy in article) were collected in 384 wells plates containing 100 nl primer and 5ul mineral oil with the sorting precision at “single cell” (yield mask: 0; purity mask: 32; phase mask: 16) to maximize the purity and counting accuracy. By including the index sorting function, information on parameters such as forward scatter (FSC), side scatter (SSC), GFP and mCherry signals was recorded for each well containing a sorted event. In this way, information could be traced back to specific wells of interest. As controls, single cell sorts were performed through gating on uninfected hepatocytes (performed for every plate), and by gating on GFPpositive/mCherry positive parasites  and GFP positive/mCherry negative parasites (only in batch 1, day 6). Immediately after sorting, plates were centrifuged (2 min., 350 g, 4 C) and stored at -80 C until further processing.
Cel-seq2 protocol (Tamar Hashimshony et al, 2016). In short, single cells were sorted based on their GFP signal into 384-well plates containing 100 nl of unique CEL-seq2 compatible primer (7 ng/µl) and 5 µl mineral oil (Sigma-Aldrich). Following cell lysis and denaturation, reverse transcription was performed using 3.5 units SuperScript II reverse transcriptase per well (Invitrogen, #18064014) in the presence of 20 nl ERCC spike-in per well (Ambion™ 4456740, 1:5000 diluted in H2O). Single-cell RNA-seq libraries were sequenced for 2x 42 bp on the Illumina NextSeq 500 system (read 1 is part of the 3’ end mRNA, read 2 contains the UMI and cell barcode).

treatment_protocol: no treatment

tag: experimental batch

tag: collection day

value: day 6 post-infection

tag: stage (schizonts vs hypnozoites)

value: separated based on the single cell transcriptional analysis


title: TOP03-PcyM-D6a

description: plate A


title: P6 SIMPLE_contra_4

value: cortex, contralateral

tag: cell type

value: microglia


title: P6 SIMPLE_contra_1

tag: genotype


title: P6 SIMPLE_contra_2


title: P6 SIMPLE_contra_3


title: AML6613R_K1_30_PLX51107_PD901_1

city: San Francisco

first: Benjamin

last: Huang

state: CA

address: 1450 3rd Street

institute: University of California San Francisco

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 using Bowtie v2.
Transcript quantification was performed with RNA-seq by Expectation Maximization (RSEM) protocol.
Gene set enrichment analysis was performed using the package provided by the Broad Institute.
Assembly: mm10
Supplementary files format and content: Tab-separated values files including count, FPKM, and TPM values for each gene.

source_name: Bone Marrow

extract_protocol:
Bone marrow cells were collected from moribund mice, subjected to RBC lysis, homogenized in Trizol. RNA was extracted using standard Trizol based techniques
Libraries were prepared using the TruSeq Stranded Total RNA kit. Libraries were sequenced on a HiSeq 400 using 100 bp single-end or paired-end chemistry.

treatment_protocol: Mice were transplanted with primary leukemias, treated daily, and observed daily.

value: Bone Marrow

value: Acute Myeloid Leukemia

tag: treatment

value: PLX51107 and PD901


title: AML6613R_K1_26_PLX51107_PD901_3


title: AML6613P_K1_04_VEH_4

value: Vehicle


title: AML6613R_K1_30_PLX51107_PD901_3


title: AML6613R_K1_26_PLX51107_PD901_2


title: AML6613R_K1_26_PLX51107_PD901_1


title: AML6613P_K1_04_VEH_5


title: AML6613R_K1_26_PLX51107_PD901_4


title: AML6613R_K1_26_PLX51107_PD901_5


title: AML6613R_K1_30_PLX51107_PD901_2


title: AML6613R_K1_30_PLX51107_PD901_4


title: AML6613R_K1_30_PLX51107_PD901_5


title: AML6613P_K1_04_VEH_3


title: AD_Spp1_Pos_4

source_name: brain

value: brain

value: GFP+ microglia

value: 5xFAD heterozygousand Spp1-GFP heterozygous

value: 7 month


title: TOP03-PcyM-D2b

description: plate B

value: day 2 post-infection


title: TOP02-PcyM-D6b

description: plate B


title: TOP03-PcyM-D4b

description: plate B

value: day 4 post-infection


title: TOP02-PcyM-D6a

description: plate A


title: TOP03-PcyM-D4a

description: plate A


title: TOP03-PcyM-D2a

description: plate A


title: AD_Spp1_Pos_1


title: AD_Spp1_Pos_3


title: TOP02-PcyM-D2

description: one plate


title: TOP02-PcyM-D4

description: one plate


title: AD_Spp1_Neg_4


title: AD_Spp1_Neg_3


title: AD_Spp1_Pos_2


title: TOP01-PcyM-D4

description: one plate


title: TOP01-PcyM-D3

description: one plate

value: day 3 post-infection


title: TOP01-PcyM-D2

description: one plate


title: TOP01-PcyM-D6

description: one plate


title: Pcy_M_bloodstage_INPUT

data_processing:
The quality of the resulting reads was checked with FastQC (V0.11.8) and the reads were mapped against the P. cynomolgi reference genome from PlasmoDB (www.plasmodb.org) using BWA samse (v0.7.17-r1188).
Mapped reads originating from the mitochondrial and apicoplast genome, multi-mapping reads, and reads having a mapping quality below 15 were removed (SAMtools v1.9)
Libraries were normalised to the total amount of reads, reads per million, with bedtools genomeCoverageBed 19 (v2.27.1) and the enrichment over the input sample was calculated by dividing ChIP sample with input sample read counts, which subsequently was log2 transformed (one pseudo count was added to avoid division by zero)
Genome_build: Pcy_M GCA_900180395.1
Supplementary_files_format_and_content: bedgraph

source_name: blood-stage parasites

growth_protocol: P. cynomolgi M blood stage parasites, on two sequential days, 9 ml heparin blood was collected from a donor monkey (containing 1.2 % ring stage parasites and 1.4% trophozoites respectively). P. cynomolgi M sporozoites, 6.5 x 106 salivary gland sporozoites were isolated two weeks post-mosquito-feeding, collected in PBS/glycerol and stored frozen until further processing.

extract_protocol:
Native ChIP was carried out as described earlier {Hoeijmakers, 2012 }. In short: After saponin lysis of the red blood cells and/or lysis of the parasites, nuclei were separated using a 0.25 M sucrose buffer cushion. Native chromatin was prepared by MNase digestion and subsequent extraction with salt-free buffers (10 mM Tris pH 7.4, 1 mM EDTA; 1 mM Tris pH 7.4, 0.2 mM EDTA). Chromatin was diluted in 2×ChIP incubation buffer (100 mM NaCl, 20 mM Tris pH 7.4, 6 mM EDTA, 1% Triton X-100, 0.1% SDS). ∼400 ng DNA-containing chromatin was incubated with 1 µg antibody (H3K9/14ac (Diagenode, C15410005); H3K9me2 (Sigma-Aldrich, 07-441)) overnight at 4°C followed by the addition of 10 µl A/G beads (SantaCruz Biotechnology) and further incubation for 2 h. After washing with buffers containing 100, 150 and 250 mM NaCl, immuno-precipitated DNA was eluted and purified using PCR purification columns (Qiagen).
1-10 ng of ChIP-ed or input DNA were used to generate sequencing libraries. All samples were first end repaired, a 3’ A-overhang added and NextFlex 6bp barcoded adapters (Bio Scientific) were ligated as described in. Adapter ligation was followed by 2 successive Agencourt AMPure XP bead purifications (Beckman Coulter) and library amplification by an in-house Plasmodium-optimized KAPA PCR amplication protocol. First, 2x KAPA HiFi HotStart ready-mix (KAPA Biosystems) and NextFlex primers were used for 4 cycles of PCR amplification (98 °C for 2 min; 4 cycles of 98 °C for 20 sec, 62 °C for 3 min; 62 °C for 5 min). Subsequently, amplified libraries were size selected for ~270 bp (mono-nucleosomes + ~125 bp NextFlex adapter) using 2% E-Gel Size Select Agarose Gels (Thermo Fisher Scientific) and again amplified as described above for 9 cycles. To deplete adapter dimers and clean-up the DNA, libraries were subsequently purified with Agencourt AMPure XP bead (Beckman Coulter) (1:1 library beads ratio) before sequencing.
ChIP-seq and input libraries were sequenced on the Illumina NextSeq 500 system with a 20% phiX spike-in (Illumina, FC-110-3001) to generate 75 bp single-end reads (NextSeq 500/550 High Output v2 kit).

tag: barcode

value: TAGCTT

tag: Stage

value: blood-stage parasites

tag: chip antibody

value: none (input)


title: Pcy_M_bloodstage_H3K914ac_ChIP

value: GGCTAC


title: Gb3i-3

value: kidney endothelail

tag: cell line

value: GCSi tx


title: AML6606P_H0_40_VEH_5

value: Bone Marrow


title: AML6606R_H0_20_PLX51107_1

value: Acute Myeloid Leukemia


title: AML6613P_K1_04_VEH_2


title: AML6613P_K1_04_VEH_1


title: AML6606R_H0_20_PLX51107_3


title: AML6606R_H0_20_PLX51107_4


title: AML6606P_H0_40_VEH_4


title: AML6606R_H0_20_PLX51107_2


title: AD_CTRL_3

tag: disease state

value: microglia

value: WT

tag: development stage


title: AD_Spp1_Neg_1

value: brain

value: GFP- microglia


title: AD_CTRL_4


title: AD_Spp1_Neg_2

value: 5xFAD heterozygousand Spp1-GFP heterozygous


title: AML6606R_H0_20_PLX51107_5


title: Pcy_M_bloodstage_H3K9me2_ChIP

value: AGTCAA


title: AML6606P_H0_40_VEH_3

value: Vehicle


title: AD_CTRL_2

value: 7 month


title: AD_CTRL_1


title: AML6606P_H0_40_VEH_2


title: AML6606P_H0_40_VEH_1


title: Astrocytes Type 1 transplanted with BTIC mitochondria

city: Chicago

first: Jason

middle: M

last: Wood

state: IL

address: 900 S Ashland Ave rm 1057

department: Research Informatics Core

institute: University of Illinois at Chicago

data_processing:
Raw sequence data were analyzed using FastQC version 0.11.9 to assess sequence quality. Low-quality bases and adapters were trimmed from reads using cutadapt version 1.18. Ribosomal RNA content was assessed by comparing sequence data with human rRNA sequences using BWA MEM version 0.7.17. Reads were then mapped to the human reference genome (hg38) in a splice-aware manner using STAR version 2.7.6a. PCR duplicate levels were assessed using Picard MarkDuplicate. Gene expression was quantified against Ensembl gene IDs using featureCounts. To quantify alternative splicing events, isoform abundances were estimated by comparison with Ensembl transcript sequences using Kalisto version 0.46.2. Exon-level expression was quantified against flattened gene exon annotations using featureCounts and splice junctions were quantified using STAR.
Assembly: hg38
Supplementary files format and content: Tab-delimited text containing gene expression quantification for each sample

source_name: Astrocytes Type 1

growth_protocol: RG cells (LC26-10R) and BTICs (LC26-RTL(4)) were cultured in Knockout DMEM/F-12 (Gibco, 12-660012) supplemented with 2% Stempro Neural Supplements (Gibco, A1050801), 1% Hyclone Antibiotic/Antimycotic (GEHealthcare Life Sciences, SV30079.01SV3007901), 1% Glutamax (Gibco, 35-050-061) and 10 ng/ml bFGF (Sigma, GF003-AF) in laminin (Invitrogen, 23017015) coated 35 mm culture dishes. Cell lines were maintained in the exponential growth phase by passing them every 3 days with growth medium, in CO2 incubator maintained at 37°C with 5% CO2 and 20% O2. For hypoxia ex-periments O2 levels were maintained at 5%. RG Cells Differentiation into White Matter Astrocytes On day 1 of astrocyte differentiation, the RG cells (LC26-10R) were seeded at 1.5x105 cells / cm2 density on laminin coated plate in astrocyte differ-entiation medium (Gibco, A1261301 kit) supplemented with 20 ng/ml EGF. Cells were fed every 48 hrs. with fresh medium for 25 to 30 days to generate homogenous population of immature astrocytes (type 1 astrocytes).

extract_protocol:
Total RNA was isolated from cells using Invitrogen (Waltham, MA, USA) TRIzol and purified using Invitrogen (Waltham, MA) Turbo DNase following the manufacturer’s protocols. RNA was cleaned and concentrated using Zymo (Irvine, CA, USA) RNA Clean and Concentrator MagBead following the manufacturer’s protocols.
RNA-seq libraries were prepared using the Lexogen (Greenland, NH, USA) CORALL Total RNA-seq kit with UDIs (PN M11696 and PN M10096-2-0101) and the Lexogen (Green-land, NH) RiboCop rRNA Depletion kit V2 (PN K14496).
Illumina (San Diego, CA, USA) NovaSeq SP 2 × 150 was used to sequence the RNA-seq libraries following the manufacturer’s protocol.

treatment_protocol: Isolated mitochondria were added to the recipient cells followed by 7 days incubation in culture conditions.

value: Astrocytes Type 1

value: Transplanted with BTIC mitochondria


title: Pcy_M_sporozoite_INPUT

source_name: sporozoite

value: AGTTCC

value: sporozoite


title: Pcy_M_sporozoite_H3K9me2_ChIP

value: CCGTCC


title: Astrocytes Type 1

value: Control


title: Pcy_M_sporozoite_H3K914ac_ChIP

value: ATGTCA


title: Astrocytes Type 1 transplanted with RG mitochondria

value: Transplanted with RG mitochondria


title: EAE_Spp1_Pos_2

value: EAE recovered to clinical score 1-2

value: GFP+ microglia

value: Spp1-GFP heterozygous

value: 8-10 week


title: AML6606R_H0_16_PLX51107_PD901_PLX250_5

value: Bone Marrow

value: Acute Myeloid Leukemia

value: PLX51107 and PD901 (in vivo), PLX51107 250 nM (ex vivo)


title: EAE_Spp1_Pos_1

value: brain


title: AML6606R_H0_16_PLX51107_PD901_PLX250_4


title: PDAC051T PDAC  with oxaliplatin and control siRNA, tumor #13

city: Toulouse

first: Pierre

last: Cordelier

address: 2, avenue Hubert Curien

country: France

institute: Cancer Research Center of Toulouse

data_processing:
The sequencing output (bcl2 files) was demultiplexed and aligned on the human reference genome GRCh38 using the software CellRanger v6.1.1. Quality control, normalization, PCA and t-SNE/UMAP coordinate computation were assessed using the R package Seurat 4.1.0. Quality control was performed using the number of detected genes per cell, and the mitochondrial genes proportion. Enrichment scores were computed using Single-Cell Signature Scorer. These encompassed signatures downloaded from MsigDB v7.5.1. For differential pathway analysis, a Student t test or a Mann–Whitney U was applied, if the data followed a normal distribution (validated by the Shapiro-Wilk test for normal distribution). Corrected P-values were obtained using a Bonferroni correction. Figures were produced using the ggplot2 (R package). The software used in the present study for single-cell analysis is available here (https://sites.google.com/site/fredsoftwares/home).
Assembly: GRCh38/hg38
Supplementary files format and content: csv file with raw counts

source_name: Pancreas tumor

extract_protocol:
Experimental tumors were removed, maintained in PBS and processed using the Tumor dissociation kit following the provider's instructions. Total RNA was extracted with RNeasy kit (Qiagen) according to the manufacturer’s instructions; quality and quantity were measured on a Nanodrop system (ThermoFisher Scientific).
The single cell suspension was loaded onto the Chromium Controller (10x Genomics) and the single cell libraries preparation was performed using the Chromium Next GEM single Cell 3' reagent kit v3.1 Dual Index (10x genomics) according to the manufacturer's instructions. The libraries were qualified with the HS NGS kit for the Fragment Analyzer (Agilent Technologies) and quantified using the KAPA library quantification kit (Roche Diagnostics). The libraries were sequenced on the Illumina NextSeq550 instrument using a High Output 150 cycles kit and the cycling parameters: 28 (read 1), 10 (index 1), 10 (index 2),90 (read 2) to obtain more than 20000 read pairs per cell

value: Pancreas tumor

value: cancer cells

value: treated in vivo with oxaliplatin and control siRNA


title: PDAC051T PDAC  with oxaliplatin and control siRNA, tumor #11


title: AML6606R_H0_16_PLX51107_PD901_PLX250_3


title: EAE_Spp1_Neg_3

value: GFP- microglia


title: PDAC051T PDAC  with oxaliplatin and siRNA trageting cytidine deaminase (CDA),tumor #8

value: treated in vivo with oxaliplatin and siRNA trageting cytidine deaminase


title: AML6606R_H0_16_PLX51107_PD901_PLX250_2


title: EAE_Spp1_Neg_2


title: PDAC051T PDAC  with oxaliplatin and siRNA trageting cytidine deaminase (CDA),tumor #7


title: EAE_Spp1_Neg_1


title: Fatigue-143

type: protein

city: Bethesda

first: Avindra

last: Nath

state: Maryland

address: 10 Center Drive

institute: NIH/NINDS

description: Control

hyb_protocol: Hypbridization was performed according to manufacturers instructions for the SOMAscan Assay v3.2 standard protocol (SomaLogic, Boulder, CO, USA).

scan_protocol: Scanning was performed according to manufacturers instructions for the SOMAscan Assay v3.2 standard protocol (SomaLogic, Boulder, CO, USA).

data_processing: Data processing was performed according to manufacturers instructions for the SOMAscan Assay v3.2 standard protocol (SomaLogic, Boulder, CO, USA).  In brief, systematic effects on the data introduced during the hybridization step were corrected followed by median normalization (i.e., hybNorm.plateScale.medNorm).

molecule: protein

source_name: Serum

label_protocol: Labeling was performed according to manufacturers instructions for the SOMAscan Assay v3.2 standard protocol (SomaLogic, Boulder, CO, USA).

extract_protocol: Serum samples were assayed at three dilutions (40%, 1%, and 0.005%) with each sample dilution added to a corresponding subset of the 1,305 SOMAmer detection reagents binned according to manufacturer’s predicted target abundance in serum. Cerebrospinal fluid was run at a single 15% concentration dilution with protease inhibitors and polyanionic competitor reagent added.

value: Male

tag: age

tag: group


title: Fatigue-144

description: Patient

value: Female

value: Patient


title: Fatigue-142

description: Patient


title: AML6606R_H0_16_PLX51107_PD901_PLX250_1


title: Fatigue-122

description: Control

value: Control


title: Fatigue-123

description: Patient


title: Fatigue-126

description: Patient


title: Fatigue-125

description: Control


title: Fatigue-124

description: Control


title: Fatigue-128

description: Control


title: Fatigue-131

description: Patient


title: Fatigue-136

description: Control


title: Fatigue-129

description: Patient


title: Fatigue-135

description: Control


title: Fatigue-139

description: Patient


title: Fatigue-140

description: Patient


title: Fatigue-132

description: Control


title: Fatigue-134

description: Patient


title: Fatigue-137

description: Patient


title: Fatigue-138

description: Patient


title: Fatigue-127

description: Control


title: Fatigue-141

description: Control


title: Fatigue-120

description: Patient


title: EAE_CTRL_3

value: microglia

value: WT


title: AML6606R_H0_16_PLX51107_PD901_PLX100_5

value: PLX51107 and PD901 (in vivo), PLX51107 100 nM (ex vivo)


title: EAE_CTRL_2

value: 8-10 week


title: AML6606R_H0_16_PLX51107_PD901_PLX100_4

value: Bone Marrow


title: Fatigue-121

description: Control


title: HCC1806, normaxia, H3K27ac, ChIP

city: Chengdu

first: Hu

last: CHEN

state: Sichuan

address: No, 278, Baoguang Road, Xindu District, Chengdu

department: School of Clinical Medicine

institute: Chengdu Medical College

data_processing:
DNA library were sequenced on Illumina Nova Seq6000 (Gene Denovo CO., Ltd., Guangzhou, China).
The low-quality reads were filtered out by Trimmomatic (version 0.38).
All of ChIP-seq peaks were identified by MACS2 software (version 2.1.1.20160309) with default parameters (bandwidth, 300bp; model fold, 5, 50; q value, 0.05).
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: HCC1806 cells were grown in RPMI-1640 (Gibco) containing 10% FBS. All cells were cultured supplemented with penicillin (100 U/mL)/streptomycin (100 μg/mL) at 37 °C in a humidified incubator under 5% CO2.

extract_protocol:
Cells wre fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, charomatin was sheared by Enzymatic Shearing (ChIP-IT Express Enzymatic, Active motif, 53009).
Immunoprecipitated DNA was used to construct sequencing libraries according to the protocol provided by the TruePrep DNA library Prep kit (Vazyme #TD501)

treatment_protocol: For hypoxia treatment, HCC1806 were transferred into an anaerobic chamber maintained at 37℃ with humidified atmosphere of 5% CO2, 10% O2, and 85% N2.

value: Human breast cancer cell

value: Normoxia (21percent O2)


title: HCC1806, normaxia, H3K27me3, ChIP

value: H3K27ac (abcam, ab4729)


title: HCC1806, normoxia, IgG, ChIP

value: Normal IgG (CST, 2927)


title: Fatigue-119

description: Patient


title: HCC1806, hypoxia, IgG, ChIP

value: hypoxia (1.5percent O2) for 24h


title: EAE_CTRL_1

value: brain


title: Fatigue-118

description: Patient


title: HCC1806, hypoxia, H3K27me3, ChIP


title: AML6606R_H0_16_PLX51107_PD901_PLX100_2

value: Acute Myeloid Leukemia


title: GBM_Spp1_Pos_3

value: CT2a inoculated for 21 days

value: GFP+ microglia

value: Spp1-GFP heterozygous


title: AML6606R_H0_16_PLX51107_PD901_PLX100_1


title: GBM_Spp1_Pos_2


title: GBM_Spp1_Pos_1


title: A375_ATACseq_HMGB2_OE3

first: Miranda

last: Hunter

address: 418 E 68th St

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Image analysis and base calling were conducted by the Control Software (CS). Raw sequence data (.bcl files) generated from Illumina instrument was converted into fastq files and de- multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Sequencing reads were trimmed and filtered for quality control using TrimGalore (version 0.6.7) with a quality setting of 15, cutadapt (version 4.0), and FastQC version 0.12.1.
Reads were aligned to the human genome assembly hg38 using bowtie282 (version 2.3.5.1) and were deduplicated using MarkDuplicates from Picard (Broad Institute; version 2.16).
Peaks were identified using MACS2 with a p-value setting of 0.001, using a publicly available melanocyte dataset (GSM3191792) as control.
To generate a global peak atlas, blacklisted regions (link) were removed, before merging all peaks within a 500 bp region and quantifying reads using featureCounts.
Assembly: GRCh38
Supplementary files format and content: Peak atlas as txt file.

extract_protocol:
Live cell samples were thawed, washed, and treated with DNAse I to remove genomic DNA contamination. Live cell samples were quantified and assessed for viability using a Countess Automated Cell Counter. After cell lysis and cytosol removal, nuclei were treated with Tn5 enzyme for 30 minutes at 37°C and purified with Minelute PCR Purification Kit to produce tagmented DNA samples.
Tagmented DNA was barcoded with Nextera Index Kit v2 and amplified via PCR prior to a SPRI Bead cleanup to yield purified DNA libraries.

value: Melanoma


title: Fatigue-117

description: Patient

value: Male

value: Patient


title: HCC1806, hypoxia, H3K27ac, ChIP


title: A375_ATACseq_HMGB2_OE2


title: Fatigue-116

description: Control

value: Female

value: Control


title: Fatigue-115

description: Patient


title: AML6606R_H0_16_PLX51107_PD901_DMSO_3

value: PLX51107 and PD901 (in vivo), DMSO (ex vivo)


title: A375_ATACseq_HMGB2_OE1


title: Fatigue-114

description: Patient


title: GBM_Spp1_Neg_4

first: DANYANG

last: HE

address: 600 Dunyu Road Sandun Town

institute: Westlake Univeristy

value: GFP- microglia

value: 8-10 week


title: Fatigue-113

description: Control


title: AML6606R_H0_16_PLX51107_PD901_PLX100_3

value: Bone Marrow

value: PLX51107 and PD901 (in vivo), PLX51107 100 nM (ex vivo)


title: AML6606R_H0_16_PLX51107_PD901_DMSO_2


title: AML6606R_H0_16_PLX51107_PD901_DMSO_4


title: GBM_Spp1_Pos_4


title: A375_ATACseq_HMGB2_EV3

value: empty vector


title: AML6606R_H0_16_PLX51107_PD901_DMSO_1


title: A375_ATACseq_HMGB2_EV2


title: AML6606R_H0_16_PLX51107_PD901_DMSO_5


title: Fatigue-112

description: Control


title: AML6606P_H0_40_VEH_PLX250_4

value: Vehicle (in vivo), PLX51107 250 nM (ex vivo)


title: A375_ATACseq_HMGB2_EV1


title: GBM_CTRL1_4

value: brain

value: microglia

value: WT


title: GBM_Spp1_Neg_2

value: CT2a inoculated for 21 days


title: Fatigue-110

description: Control


title: Fatigue-111

description: Patient


title: Fatigue-109

description: Patient


title: AML6606P_H0_40_VEH_PLX250_5

value: Acute Myeloid Leukemia


title: A375_RNAseq_HMGB2_OE3

data_processing:
Image analysis and base calling were conducted by the NovaSeq Control Software (NCS). Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification.
FASTQC was used for quality control of raw sequencing reads.
Trimmomatic was used to remove sequencing adapters.
Reads were aligned to GRCh38 using STAR and alignment checked using SeQC.
Assembly: GRCh38
Supplementary files format and content: Counts matrix for each sample in .tab format.

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Plus Universal Mini kit following manufacturer’s instructions. RNA samples were quantified using Qubit 2.0 Fluorometer and RNA integrity was checked using Agilent TapeStation 4200.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions. Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation, and quantified by using Qubit 2.0 Fluorometer as well as by quantitative PCR.

value: Melanoma


title: A375_RNAseq_HMGB2_OE2


title: GBM_CTRL1_3


title: GBM_Spp1_Neg_1

value: Spp1-GFP heterozygous


title: GBM_Spp1_Neg_3


title: AML6606P_H0_40_VEH_PLX250_2


title: Fatigue-108

description: Patient

value: Male

value: Patient


title: GBM_CTRL1_2


title: AML6606P_H0_40_VEH_PLX250_1


title: Fatigue-107

description: Patient

value: Female


title: A375_RNAseq_HMGB2_EV3

value: Empty vector


title: Cuprizone_Spp1_Pos_3

value: Cuprizone diet for 5 weeks

value: GFP+ microglia


title: Fatigue-106

description: Control

value: Control


title: A375_RNAseq_HMGB2_EV2


title: AML6606P_H0_40_VEH_PLX100_5

value: Bone Marrow

value: Vehicle (in vivo), PLX51107 100 nM (ex vivo)


title: Cuprizone_Spp1_Pos_2

value: 8-10 week


title: AML6606P_H0_40_VEH_PLX100_4


title: AML6606P_H0_40_VEH_PLX250_3

value: Vehicle (in vivo), PLX51107 250 nM (ex vivo)


title: AML6606P_H0_40_VEH_PLX100_3


title: Cuprizone_Spp1_Pos_1

value: brain


title: GBM_CTRL1_1

value: microglia

value: WT


title: Fatigue-104

description: Control


title: confined_A375_RNA_C3

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Plus Universal Mini kit following manufacturer’s instructions. RNA samples were quantified using Qubit 2.0 Fluorometer and RNA integrity was checked using Agilent TapeStation 4200.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions. Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation, and quantified by using Qubit 2.0 Fluorometer as well as by quantitative PCR).

value: confined


title: Cuprizone_Spp1_Neg_3

value: GFP- microglia


title: confined_A375_RNA_C2

value: Melanoma


title: Fatigue-105

description: Control

value: Male


title: AML6606P_H0_40_VEH_PLX100_2

value: Acute Myeloid Leukemia


title: AML6606P_H0_40_VEH_PLX100_1


title: Fatigue-103

description: Control

value: Female


title: confined_A375_RNA_C1


title: Cuprizone_Spp1_Neg_1

value: Spp1-GFP heterozygous


title: Fatigue-102

description: Control


title: confined_A375_RNA_NC3

value: unconfined


title: Fatigue-101

description: Control


title: AML6606P_H0_40_VEH_DMSO_5

value: Vehicle (in vivo), DMSO (ex vivo)


title: Cuprizone_CTRL_3


title: confined_A375_RNA_NC1


title: Cuprizone_CTRL_4


title: AML6606P_H0_40_VEH_DMSO_2


title: Cuprizone_Spp1_Neg_2

value: Cuprizone diet for 5 weeks


title: Cuprizone_CTRL_2


title: AML6606P_H0_40_VEH_DMSO_1

value: Bone Marrow


title: AML6606P_H0_40_VEH_DMSO_3


title: CD4+ T cell from BCL6fl/fl 3 4x4

city: Columbia

first: Jerod

last: Skyberg

state: MO

address: Veterinary Pathobiology, 1500 Bouchelle

institute: University of Missouri

data_processing:
OnestopRNASeq
FastQC and MultiQC were used for raw reads quality control and QoRTs for post-alignment quality control
Reads were aligned to the reference genome assembly mm10 with star_2.7.5a and annotated with gencode.vM25.
Aligned exon reads were counted toward gene expression with featureCounts_2.0.0 with default settings.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM  values for each Sample

extract_protocol:
RNA was isolated via Rneasy kit.
Stranded mRNA libaries were constructed by the University of Missouri Genomics Core facility using a poly A enrichment method

value: vaccinated and infected

tag: time

value: 28 days after vaccination, 28 days after challenge


title: CD4+ T cell from BCL6fl/fl 2 4x4


title: Cuprizone_CTRL_1

city: Hangzhou

extract_protocol:
"For bulk RNA-Seq,  2,000 freshly sorted microglia were lysed in 10μL TCL buffer (QIAGEN) supplemented with 1% 2-mercaptoethanol.   For single cell RNA-Seq, cell hashing was performed by incubating the single cell suspensions with antibody cocktails containing FACS antibodies and TotalSeq antibody (Biolegend) at 1:100 final dilution for each antibody, followed by incubation for 30min on ice. Next, cells were washed and CD45+CD11b+CX3CR1+ were sorted for single cell capturing and library preparations. Briefly, 70,000 cells pooled from 10 biological samples (with 1-8 mice pooled per sample) were partitioned into nanoliter Gel-bead-inEmulsions (GEMs) droplets using the Chromium Single Cell 3′ V3.1 Kits (10x Genomics).
For bulk RNA-Seq, full-length RNA-seq libraries were prepared following a modified SMART-Seq2 protocol. The cDNA libraries were generated using the TruePrep RNA Library Prep Kit for Illumina and pair-end sequenced (150 bp × 2) with Novaseq 6000 (Illumina).

value: 8-10 week


title: Mia PACA-2 Control Pool 5

data_processing:
RNA-seq data was processed with standard approaches. we first converted from Illumina format to fastq using bcl2fastq.
Quality control was performed with FastQC and adaptor sequences were trimmed using Trimmomatic. Quality control with FastQC was run again after adaptor removal. Gene expression was quantified at the transcript level by Salmon. Import of Transcript-level abundances and counts from Salmon and name conversion to HUGO gene symbols was performed with the tximport R package
Assembly: GRCh38/hg38
Supplementary files format and content: Text file with raw counts

source_name: pancreatic cancer

growth_protocol: cancer cells were obtained from the ATCC and cultured in Dulbecco Modified Eagle Medium (DMEM) 4.5 g/L glucose containing 10% Fetal Bovine Serum (FBS), 100 IU/mL penicillin, 100 µg/mL streptomycin and 250 ng/mL fungizone (AB) and 100 µg/mL normocin (Invivogen) to avoid mycoplasma  contamination. Cells were incubated at 37°C with 5% CO2

extract_protocol:
Total RNA was extracted with RNeasy kit (Qiagen) according to the manufacturer’s instructions; quality and quantity were measured on a Nanodrop system (ThermoFisher Scientific)
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptorligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system

treatment_protocol: Not applicable

value: pancreatic cancer

value: Mia PACA-2

value: cancerous


title: Mia PACA-2 CDA Pool 5