title: 143B_shPRRX1_1_rep2

city: okayama

first: Takeshi

last: Takarada

state: okayama

address: 2-5-1 Shikata-cho

department: Graduate School of Medicine, Dentistry and Pharmaceutical Sciences

country: Japan

institute: Okayama university

data_processing:
All sequence reads were extracted in FASTQ format using the CASAVA 1.8.4 pipeline.
Filtered reads were mapped to hg19 using HISAT2 (v2.1.0).
Genome_build: hg19
Supplementary_files_format_and_content: DESeq output

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM; Nacalai Tesque, Inc., Kyoto, Japan). All culture media were supplemented with 10% fetal bovine serum (FBS; Hyclone, Victoria, Australia), penicillin (100 U/mL), and streptomycin (100 mg/mL) (NACALAI TESQUE, Inc.) in a humidified atmosphere containing 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN).
Sequencing libraries were KAPA RNA HyperPrep Kit with RiboErase (HMR) (Kapa Biosystems) and SeqCap Adapter Kit (Set A or Set B, Roche) following manufacture`s instruction. The initial amount of total RNA was 1000 ng.

treatment_protocol: pLKO.1puro, a lentiviral vector plasmid purchased from Addgene (#8453; Watertown, MA, USA), was digested with AgeI and EcoRI and then ligated with annealed primers using Ligation High ver 2 (Takara Bio). The following primers were used: shPRRX1#1 forward 5ʹ-CCG GTG ACA TTT AGG GTA TAA AGA TCT TCA AGA GAG ATC TTT ATA CCC TAA ATG TCT TTT TTG-3ʹ, shPRRX1#1 reverse 5ʹ-AAT TCA AAA AAG ACA TTT AGG GTA TAA AGA TCT CTC TTG AAG ATC TTT ATA CCC TAA ATG TCA-3ʹ; shPRRX1#2 forward 5ʹ-CCG GTG CAG CGA AGG AAT AGG ACA ACT TCA AGA GAG TTG TCC TAT TCC TTC GCT GCT TTT TTG-3ʹ, shPRRX1#2 reverse 5ʹ-AAT TCA AAA AAG CAG CGA AGG AAT AGG ACA ACT CTC TTG AAG TTG TCC TAT TCC TTC GCT GCA-3ʹ. For lentiviral production, pLKO.1 puro constructs were transfected together with packaging vectors, including pMDLg/pRRE, pRSV-Rev, and pMD2.G, to lentiX293T cells using PEI-MAX reagent (Polysciences, Warrington, PA, USA). Culture media were replaced with fresh media 12 h after transfection. Cells were cultured for 48 h, and culture supernatants containing lentivirus were passed through a 0.45 µM PVDF filter (Hawach Scientific, Xi’an, China). Lentivirus solutions were stored at −80°C until use. For lentiviral infection, 143B cells were treated with the lentiviral solution for 24 h. After culturing for another 24 h without lentivirus, cells were treated with 1 µg/mL puromycin (Wako) to select lentivirus-infected cells.

tag: source tumor type

value: osteosarcoma

value: human osteosarcoma cell line

tag: genotype/variation


title: HIV CD4 med_H37

status: Public on Oct 29 2020

type: RNA

city: Rome

first: Nicola

last: Cotugno

address: via Montpellier 1

department: Department of Systems Medicine

country: Italy

institute: University of Rome "Tor Vergata"

description:
legenda: HIV= study group; NR= Non responder to Influenza Vaccination; R=Responder to Influenza vaccination; Rem/AM/PBMC/DN/Naïve/Total B/CD4/TFH/NTF= cell subset identifier (please check source name for acronym interpretetion); med=unstimulated sample; stim= stimulated sample with H1N1 peptides for 16 hours; _HX= identifier of the subject. When patient responsiveness is not referenced please refer to this list: NR= H19  H37  H38  H40  H46  H48  H55  H58  H60  H69  H70  H83;                                                                                and Responder (R)= H3  H7  H8  H26  H41  H44  H47  H56  H75  H80  H52.
500 fixed numbers of live cell sorted by ARIA IICs, derived from human PBMCs from frozen samples.Every sample is identified according to study group, cell subset, condition and patient identifier.

data_processing:
Previously amplified samples were loaded on a Fluidigm 96.96 standard chip following manufacturer’s instructions. Briefly, assay pre-mix was prepared 1:1 20X TaqMan Gene Expression Assay (Applied Biosystems) and Assay Loading Reagent (Fluidigm). The sample pre-mix was prepared with TaqMan Universal PCR Master Mix (2X)(Applied Biosystems), 20XGE Sample Loading Reagent (Fluidigm), and cDNA. Full list of the two panels of gene probes (B subsets and T subsets is shown in supplemental table 1 and 2). 5ul of Assay and Sample mix were loaded into the chip according to manufacturers instructions. Genes’ selection has been made according to previous analysis on RNA Sequencing on HIV infected children from a different cohort (data not shown), the literature and online gene banks and biological queries.  Cycle threshold value (Ct) deriving from exported files was corrected according to number of cells sorted if lower than 500. Calculations were made following the expression 67,5 / 500 = Y / X where X is the number of cells sorted and Y is the cells equivalent cDNA of cell sorted. The dilution factor (n) was calculated as n= 67,5/Y, and base 2 log of n was subsequently subtracted to Ct value in order to get Corrected Cycle Threshold (c-Ct). Expression threshold (Et), which was  used for the main analysis was finally obtained with 40-cCT. Once exported and corrected, data were analyzed through Fluidigm SingluaR (SingulaR analysis toolset 3.0) package, loaded on R (software R 3.0.2 GUI 1.62). As previously described (De Armas LR, 2017) gene expression differences between different groups within same subset and condition were used to identify Differentially Expressed Genes (DEGs). Alternatively, paired gene expression differences between stimulated (stim) and unstimulated samples (med) (stim-med) within the same subset were used to define Differentially Induced Genes (DIGs).
Cycle threshold value (Ct) deriving from exported files was corrected according to number of cells sorted if lower than 500. Calculations were made following the expression 67,5 / 500 = Y / X where X is the number of cells sorted and Y is the cells equivalent cDNA of cell sorted. The dilution factor (n) was calculated as n= 67,5/Y, and base 2 log of n was subsequently subtracted to Ct value in order to get Corrected Cycle Threshold (c-Ct). Expression threshold (Et), which was  used for the main analysis was finally obtained with 40-cCT. Once exported and corrected, data were analyzed through Fluidigm SingluaR (SingulaR analysis toolset 3.0) package, loaded on R (software R 3.0.2 GUI 1.62). As previously described (De Armas LR, 2017) gene expression differences between different groups within same subset and condition were used to identify Differentially Expressed Genes (DEGs). Alternatively, paired gene expression differences between stimulated (stim) and unstimulated samples (med) (stim-med) within the same subset were used to define Differentially Induced Genes (DIGs).

label: FAM-MGB

molecule: total RNA

organism: Homo sapiens

source_name: HIV CD4 med_H37

growth_protocol: PBMC were thawed and cells were counted with Countess Automated Cell counter (Life technology). Cells were resuspended in complete RPMI medium at a concentration of 5 x 106 PBMCs/mL and left at 37°C for 16 hours in the presence or absence of of H1N1 A/California /09 HA peptides in a final concentration 20uL/mL. PMBCs were stained for surface markers, Vivid (Pacific Blue), CD10 (PECy7), CD20 (PE), CD27 (APC), IgD (FITC), CD21 (PECy5) for the B cell panel for 15 minutes and for CD3 (AmCyan), CD4 (PerCP Cy5.5), CD45RO (ECD), CCR7 (Alexa Fluor 700), and CXCR5 (Alexa Fluor 647) and a live/dead marker (ViViD; Molecular Probes) for the T cell panel for 15 minutes. Subsequently, stained PBMCs were washed twice in PBS, finally filtered with a 40 uM mesh and sorted by FACSAriaII (BD Biosciences). The purity of the sorted cell populations were typically >99%. All antibodies were previously titrated. Viable lymphocytes were identified as live dead amine dye negative (ViViD-) cells (Invitrogen).   500 live cells per B and T cell subset were sorted into tubes previously loaded with 9uL of PCR buffer (see also Figure 1 for gating strategy). After sorting, cells were immediately centrifuged (3000RPM for 3 minutes) and kept on ice. Samples were subsequently transferred in PCR tubes and 18 PCR cycles were performed on a C1000 Thermal Cycler (Bio Rad) with the following scheme (50°C for 20’, 95°C for 2’, 95°C 15’’, 60°C for 4’. Last step repeated 18 times). Cells were finally kept at -20 until further analysis. PCR buffer premix for cell sorting contained the following: Cells Direct Reaction mix 5uL, DEPC water 1,4, Superscript III + Taq 1ul, 0.2x diluted assay (96 primer mix) 2,5uL, Superasein 0,1uL.

extract_protocol: 500 live cells per B and T cell subset were sorted into tubes previously loaded with 9uL of PCR buffer for RNA extraction. After sorting, cells were immediately centrifuged (3000RPM for 3 minutes) and kept on ice. Samples were subsequently transferred in PCR tubes and 18 PCR cycles were performed on a C1000 Thermal Cycler (Bio Rad) with the following scheme (50°C for 20’, 95°C for 2’, 95°C 15’’, 60°C for 4’. Last step repeated 18 times). Cells were finally kept at -20 until further analysis. PCR buffer premix for cell sorting contained the following: Cells Direct Reaction mix 5uL, DEPC water 1,4, Superscript III + Taq 1ul, 0.2x diluted assay (96 primer mix) 2,5uL, Superasein 0,1uL.

treatment_protocol: PBMCs were isolated by Ficoll

tag: group

value: HIV CD4 med


title: HEK293T rescue NSUN6 C373A rep2

type: SRA

city: Guangzhou

first: Rui

last: Zhang

address: No. 135, Xingang Xi Road

country: China

institute: Sun Yat-sen University

library_source: genomic

data_processing:
Adapters were trimmed with cutadapt-1.13 (-e 0.25 -q 25 –trim-n -a NNNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A NNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAG). Adapter-trimmed reads were quality trimmed with Trimmomatic-0.36 (PE mode, HEADCROP:10 SLIDINGWINDOW:4:22 AVGQUAL:25 MINLEN:40).
Clean reads were mapped to Ensembl GRCh37.75 genome and transcriptome with hisat2-2.10 (-k 10, --fr, --rna-strandness FR --no-mixed), uniquely alignment only0. Unmapped reads were further mapped to transcriptome with bowtie2-2.2.9 (-end-to-end, --fr --gbar 5, --mp 5, -k 10, -R 2, -D 5). Unique alignments mapped to the same gene location were used. Transcriptome alignments were liftOver to genomic coordinates with a custom script. Hisat2 alignmets and bowtie2 alignmets were merged.
Pileup was performed using samtools API pysam to get base counts.
Custom scripts were used to call m5C sites from samples:  (i) C+T coverage >= 20; (ii) C count >= 3; (iii) m5C level >= 0.1; (iv) signal ratio >= 0.9 at certain C-cutoff (mostly at 2-5) and (v) one-side binomial P value < 0.001
Genome_build: hg19
Supplementary_files_format_and_content: CSV for the position, coverage, and methylation level for the samples

molecule: genomic DNA

growth_protocol: Cell lines were maintained in DMEM (Gibco) supplemented with 10% FBS (HyClone).

extract_protocol:
Total RNA was isolated with TRIzol reagent and Direct-zol RNA MiniPrep kit; for cytoplasm/nuclear fractions, cells were fractionated using the PARIS kit (Ambion) according to the manufacturer’s instructions. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads (Vazyme).
100ng-1μg of polyadenylated RNA was converted using the EZ RNA methylation kit (Zymo Research) with 3 cycles of [70 C 10 min, 64 C 45 min] and 37 C 30 min for desulfonation. The converted RNA was fragmented into 150~200 nt fragments by incubation at 94 °C for 8 minutes in fragmentation buffer (NEBNext Ultra II Directional RNA Library Prep Kit, NEB). The fragmented RNA was then used for library construction, following the manufacturer’s protocol (NEBNext Ultra II Directional RNA Library Prep Kit, NEB).

tag: genotype

value: NSUN6 knockout

tag: transfected vector

value: NSUN6 C373A

tag: cell line


title: 143B_Empty_control_rep2

library_source: transcriptomic

tag: cell type

value: Ctrl


title: 143B_shPRRX1_2_rep1


title: HIV CD4 med_H38

source_name: HIV CD4 med_H38

label_protocol: After sorting, cells were immediately centrifuged (3000RPM for 3 minutes) and kept on ice. Samples were subsequently transferred in PCR tubes and 18 PCR cycles were performed on a C1000 Thermal Cycler (Bio Rad) with the following scheme (50°C for 20’, 95°C for 2’, 95°C 15’’, 60°C for 4’. Last step repeated 18 times). Cells were finally kept at -20 until further analysis. PCR buffer premix for cell sorting contained the following: Cells Direct Reaction mix 5uL, DEPC water 1,4, Superscript III + Taq 1ul, 0.2x diluted assay (96 primer mix) 2,5uL, Superasein 0,1uL.


title: 143B_shPRRX1_1_rep1


title: 143B_Empty_control_rep1


title: HEK293T rescue NSUN6 C373A rep1


title: 143B_shPRRX1_2_rep2


title: HEK293T rescue NSUN6 K159AR181A rep1

value: NSUN6 K159AR181A


title: CEA-TCB, B7

city: Basel

first: Andreas

last: Roller

address: Grenzacherstrasse 124

country: Switzerland

institute: Roche

description:
Experimental (treated) animal
B7_L4

data_processing:
Reads were aligned to the human and mouse transcriptome (based on Ensembl v60) using Bowtie2 with sensitive settings. Unmapped reads were aligned to the Human and mouse genome (hg19). Both mappings to genome and transcriptome were combined using in-house software. Reads mapped to both transcriptomes at the same time were discarded from further analysis.
Raw counts were used to create an R DGEList object [edgeR version 3.24.3].
Normalization factors were calculated using the calcNormFactors function. Genes were normalized by Trimmed Mean of M-values (TMM), and were subjected to DE analyses using the voom and lmFit functions in the limma package (version 3.38.3).
Gene set enrichment analysis was conducted using the fgsea R package [Version 1.8.0] with minsize=55, maxSize=500 an nperm=100000.
Genes were ranked by the corresponding log2 fold-change and GO gene sets (C5) from MsigDB signaling database were used.
Genome_build: Ensembl v60, hg19
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

source_name: Tumor tissue

growth_protocol: MKN-45 human gastric adenocarcinoma cell lines were purchased from DSMZ (Braunschweig, Germany; Cat No.: ACC 409). MKN-45 cells were cultured in RPMI containing 10% FCS (PAA Laboratories, Pasching, Austria) and 1% Glutamax (Gibco, Zug, Switzerland) at 37 °C in a water-saturated atmosphere at 5% CO2. Afterwards, 1 × 10^6 cells were injected s.c. into hematopoietic stem cell humanized NOG mice (HSC-NOG) using a 1:1 mixture of RPMI medium and matrigel in a total volume of 100 μL. All mice were maintained under specific-pathogen-free condition with daily cycles of 12 hours light /12 hours darkness according to international (Federation of European Laboratory Animal Science Associations) and national (Gesellschaft für Versuchstierkunde / Society of Laboratory Animal Science [GV-Solas] and Tierschutzgesetz [TierSchG]) guidelines.

extract_protocol:
High molecular weight RNA (>200 base pairs) was extracted from Xenograft samples using the miRNeasy Mini kit as per manufacturer’s instructions (QIAGEN®). Residual genomic DNA was removed during the extraction using the RNase-free DNase set (QIAGEN®). RNA quality was analyzed using Eukaryote Total RNA Nano chips (Agilent Technologies), and all samples used for analysis had an RNA integrity number > 7.
RNAseq libraries were generated from 0.1 μg total RNA using the TruSeq® Stranded mRNA kit (Illumina®) as per manufacturer’s instructions. Sequencing libraries were quantified using the Kapa Library Quantification kit (Kapa Biosystems), and quality was assessed on the Agilent Bioanalyzer using DNA 1000 chips (Agilent Technologies). Libraries were sequenced on the HiSeq® 2000 sequencer (Illumina) for 2 × 50 cycles using the TruSeq® PE Cluster Kit v3-cBot-HS and TruSeq® SBS Kit v3-HS sequencing reagents (Illumina®) at Expression Analysis Inc [Q2Solutions]. Each lane was spiked with the PhiX Control v3 library (Illumina®) at a final concentration of 1 % (v/v) as a sequencing control.

treatment_protocol: Mice were treated with either 200 µL of Histidine buffer (20 mM Histidine, 140 mM NaCl, pH 6.0; vehicle; n=12) or with 2.5 mg/kg i.v. of CEA-TCB diluted with Histidine buffer to a volume of 200 µL (n=12) twice weekly, starting with a tumor volume of ~150 mm^3 (Day 8). At termination (Day 32), tumor tissue was harvested for analysis.

value: human gastric adenocarcinoma cell line

tag: treatment

value: CEA-TCB (cibisatamab)


title: HEK293T cytoplasm BS

value: wildtype


title: HIV CD4 med_H3

source_name: HIV CD4 med_H3


title: CEA-TCB, B9

description:
Experimental (treated) animal
B9_L3


title: HEK293T rescue NSUN6 WT rep1

value: WT NSUN6


title: HEK293T NSUN2/6 KO rep2

value: NSUN2/NSUN6 knockout


title: CEA-TCB, B4

description:
Experimental (treated) animal
B4_L5


title: HEK293T NSUN2/6 KO rep1


title: HIV CD4 med_H19

source_name: HIV CD4 med_H19


title: CEA-TCB, B5

description:
Experimental (treated) animal
B5_L7


title: HEK293T NSUN2 KO rep2

value: NSUN2 knockout


title: CEA-TCB, B3

description:
Experimental (treated) animal
B3_L6


title: HEK293T NSUN2 KO rep1


title: BEAS-2B cells, PRMT1_3

city: Yangling

first: ZHAI

middle: Wei

last: Qi

state: Shaanxi

address: No.3 Taicheng Road

institute: Northwest A&F University

data_processing:
Eliminate the low-quality reads, adaptors and other contaminants to get clean reads.Summarize the length distribution of the clean tags, common and specific sequences between samples.
Annotate the clean tags into different categories.Reads are use HISAT to compared to the reference genome.
Filtering use the software SOAPnuke.Remove low quality tags, tags with 5' primer contaminants, tags without3' primer,tags without insertion,tags with polyA. Then summarize the length distribution of the clean tags.
Use Bowtie2 to compare clean reads to the reference gene sequence, and then use RSEM to calculate the expression levels of genes and transcripts
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: TPM values for each Sample

extract_protocol:
Total RNA was processed by mRNA enrichment or rRNA removal. Enriched mRNA with polyA tail by magnetic beads with OligodT; hybridized rRNA with DNA probe, RNaseH selectively digested DNA / RNA Hybridize the strand and digest the DNA probe with DNaseI to obtain the desired RNA after purification
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BEAS-2B cells treat with pcDNA3.1 and pcDNA-PRMT1 for 48h

value: bronchial epithelial cells

value: PRMT1 over-expression


title: BEAS-2B cells, PRMT1_1


title: BEAS-2B cells, pc3_1_3

value: control


title: CEA-TCB, B11

description:
Experimental (treated) animal
B11_L3_Human


title: HIV CD4 med_H26

source_name: HIV CD4 med_H26


title: CEA-TCB, B1

description:
Experimental (treated) animal
B1_L7


title: BEAS-2B cells, PRMT1_2


title: HEK293T WT rep2


title: BEAS-2B cells, pc3_1_2


title: HEK293T rescue NSUN6 WT rep2


title: BEAS-2B cells, pc3_1_1


title: HEK293T WT rep1


title: Vehicle, A7

description:
Control animal
A7_L5

value: Vehicle


title: HepG2 WT rep2


title: Vehicle, A5

description:
Control animal
A5_L5


title: HepG2 WT rep1


title: Vehicle, A4

description:
Control animal
A4_L7


title: MIC3_3

city: Nanchang

first: tian

last: Yu

address: 999 Xuefu Rd.

institute: Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In 1 this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC   content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean   reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time.
Genome_build: Escherichia coli NC_010468.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Escherichia coli

source_name: E. coli ATCC8739

growth_protocol: E. coli ATCC8739, provided by the Strain Preservation Center, was cultured in Luria-Bertani (1% sodium chloride, 1% peptone, and 0.5% yeast extract).

extract_protocol:
After treating E. coli with lysozyme, total RNA was extracted from E. coli using TRIzol reagent (Invitrogen, USA)
A total amount of 1 μg RNA per sample was used as input material for the RNA sample   preparations. 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 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, Adaptor with hairpin loop structure were ligated to   prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in   length, the library fragments were purified with AMPure XP system (Beckman Coulter,   Beverly, USA). 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.

tag: source

value: human feces

tag: strain

tag: agent

value: treated with 1/2MIC camphor essential oil


title: MIC3_2


title: MIC3_1


title: HEK293T rescue C373A tRNA BS

description: tRNA

data_processing:
Adapters were first trimmed with Cutadapt (--max-n 1 -m 18 -e 0.25 --trim-n -q 20). Only reads containing adapters were retained.
Clean reads were first C-to-T (read 1) or G-to-A (read2) converted and mapped to C-to-T converted reference sequences containing tRNA (with CCA tail), mRNA, and rRNA with bowtie2 (--end-to-end --no-mixed --norc -k 50 -X 80). Read pairs were ranked by alignment scores (sum of AS and YS tags in the BAM file). Only read pairs with the highest alignment score and uniquely mapped to one tRNA type (multiple alignment on tRNA isodecoders was allowed) were used. For details, see github page: https://github.com/SYSU-zhanglab/tRNA-m5C
Original reads were recovered with a custom script and piled up to call m5C sites and calculate their methylation levels.
Genome_build: GtRNAdb Release 18.1 (hg19)
Supplementary_files_format_and_content: TXT, pileup file recording the tRNA position, coverage, methylation level of the samples

extract_protocol:
20 ug total RNA was first loaded into 15% denaturing TBE-Urea PAGE Gels and separated based on the molecular weight. The gel slice corresponding to 70-90 nucleotides was excised from the PAGE gel and the RNA fragments were recovered using ZR small-RNA™ PAGE Recovery Kit (Zymo Research) following the manufacturer’s protocol.
100ng-1μg of RNA was converted using the EZ RNA methylation kit (Zymo Research) with 3 cycles of [70 C 10 min, 64 C 45 min] and 37 C 30 min for desulfonation. End-repair was performed with T4 PNK (NEB) to phosphorylate 5’-hydroxyl termini and remove 2’,3’-Cyclic phosphate produced during the bisulfite/desulfonation reaction. The tRNA BS-seq library was generated using VAHTSTM Small RNA Library Prep Kit for Illumina (Vazyme) according to the manufacturer’s protocol.


title: MIC2_3

value: treated with 1/4MIC camphor essential oil


title: MIC2_2


title: MIC2_1


title: HEK293T rescue WT tRNA BS

description: tRNA

value: NSUN6 knockout


title: Vehicle, A12

description:
Control animal
A12_L4


title: Vehicle, A3

description:
Control animal
A3_L3


title: HEK293T NSUN6 KO tRNA BS

description: tRNA


title: Vehicle, A10

description:
Control animal
A10_L5


title: Vehicle, A6

description:
Control animal
A6_L1_Human


title: Vehicle, A11

description:
Control animal
A11_L3


title: Vehicle, A1

description:
Control animal
A1_L4_Human


title: MIC1_2

value: treated with 1/8MIC camphor essential oil


title: 293T_polysome_poly_2

description: RNA with >5 ribosomes bound.

molecule: polyA RNA

extract_protocol:
Cells were collected and lysed with lysis buffer (10 mM Tris-HCl (pH 7.4), 5 mM MgCl2, 100 mM KCl, 1% Triton X-100, 2mM DTT, 100μg/ml CHX (CST), 50U/ml RNasin Plus RNase Inhibitor (Thermo fisher) and cOmplete EDTA-free protease inhibitor (1 mini tablet per 10ml, Roche)). 10–50% sucrose gradients were prepared in gradient buffer (20mM HEPES-KOH, pH7.4, 5mM MgCl2, 100mM KCl, 2mM DTT, 100μg/ml CHX, 50U/ml RNasin Plus RNase Inhibitor) using a Gradient Master (Biocomp). 400μl lysates were loaded on the gradients. Gradients were centrifuged at 36,000 rpm for 2 hours at 4 ℃ in an SW-40 Ti rotor and then fractionated using the Gradient Master. RNA was then isolated using TRIzol reagent. Polyadenylated RNA of each fraction was separated from total RNA using Oligo dT Magnetic Beads (Vazyme).
10-50 ng of polyadenylated RNA was converted using the EZ RNA methylation kit (Zymo Research) with 3 cycles of [70 C 10 min, 64 C 45 min] and 37 C 30 min for desulfonation. The converted RNA was fragmented into 150~200 nt fragments by incubation at 94 °C for 8 minutes in fragmentation buffer (NEBNext Ultra II Directional RNA Library Prep Kit, NEB). The fragmented RNA was then used for library construction, following the manufacturer’s protocol (NEBNext Ultra II Directional RNA Library Prep Kit, NEB).

tag: fraction group

value: F


title: HEK293T WT tRNA BS

description: tRNA


title: 293T_polysome_mono

description: RNA with 1 ribosome (monosome) bound.

value: D


title: MIC1_1


title: gBT-I TM, Infl rep2

city: Bronx

first: gregoire

last: lauvau

state: New York

address: 1300 morris park avenue

department: microbiology and immunology

country: USA

institute: AECOM

description: Lm-Ova stimulated memory CD8 T cells

data_processing:
RNAseq reads were aligned to the Mouse reference mm10 with STAR (v2.4.2a)
Gene quantification was performed using featureCounts (v1.4.3) / Transcripts were quantified using Kalisto
Normalization and Comparative analysis were performed with DESeq2 (v 1.10.1)

organism: Mus musculus

source_name: Spleen

extract_protocol:
1,000 memory OT-I and 1,000 gBT-I memory cells were flow-sorted into lysis buffer (Takara Bio USA) based on congenic markers after enrichment for CD8+ T cells (negative selection).  cDNA was synthesized and amplified directly from intact cells using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio USA) according to the manufacturer protocol.
Illumina cDNA library was prepared using Nextera XT DNA Library Preparation Kits according to manufacturer protocol.

value: Lymphocyte

value: WT


title: HeLa NSUN6 KO

source_name: HeLa

value: HeLa


title: gBT-I TM, Infl rep3

description: Lm-Ova stimulated memory CD8 T cells


title: gBT-I TM, Infl rep1

description: Lm-Ova stimulated memory CD8 T cells


title: HEK293T rescue K159AR181A tRNA BS

description: tRNA

value: NSUN6 K159AR181A7


title: Vehicle, A2

description:
Control animal
A2_L6

value: human gastric adenocarcinoma cell line


title: OT-I TM, Ag/Infl rep3

description: Lm-Ova stimulated memory CD8 T cells


title: 293T_polysome_large

description: RNA with a ribosome large subunit bound.

value: wildtype

value: C


title: MIC1_3


title: con_ac

value: treated with acetone


title: OT-I TM, Ag/Infl rep2

description: Lm-Ova stimulated memory CD8 T cells


title: 293T_polysome_poly_1

description: RNA with 2-5 ribosomes bound.

value: E


title: 293T_polysome_free

description: RNA without ribosomes bound.

value: A


title: gBT-I TM, steady state rep3

description: unstimulated memory CD8 T cells


title: P8 prefrontal cortex, Male, DEP+MS, L22631-2

city: Durham

first: Wei

last: Chen

state: NC

address: 101 Science Drive

department: Center for Genomic and Computational Biology

institute: Duke University

data_processing:
Illumina NovaSeq 6000 reads were processed using the TrimGalore toolkit v0.4.1 to trim low quality bases and Illumina sequencing adapters from the 3’ end of the reads.  Only reads that were 20nt or longer after trimming were kept for further analysis. Read quality was checked for each sample using FastQC v0.11.2.
Reads were mapped to the GRCm38v73 version of the mouse genome and transcriptome using the STAR RNA-seq alignment tool v2.5.0c.  Reads were kept for subsequent analysis if they mapped to a single genomic location.
Gene counts were compiled using the HTSeq tool v0.6.1.  Only genes that had at least 10 reads in any given library were used in subsequent analysis.
Normalization and differential expression was carried out using the DESeq2 Bioconductor package v1.16.1 with the R statistical programming environment v3.4.1_3.
Genome_build: GRCm38v73
Supplementary_files_format_and_content: DESeq2 normalized expression matrix in csv format

source_name: Brain

extract_protocol:
Animals were perfused with TBS+heparin, brain was extracted and PFC was dissected, tissue was flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. KAPA Stranded mRNA-Seq Kit  was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: prefrontal cortex

tag: age

tag: Sex

value: Male

tag: condition

value: DEP+MS


title: con_wa2

value: human feces

value: treated with water


title: scRNA-seq TLE sample 20188

city: NEW YORK

first: Nadejda

middle: M

last: Tsankova

state: NY

address: 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B

department: Pathology

institute: Icahn School of Medicine at Mount Sinai

description:
10X Genomics, v3
Sample name: 476
I1: Sample Index
R1: 16bp Cell Barcode + 12bp UMI + following ignorable bases (which would be trimmed automatically by Cellranger)
R2: RNA

data_processing:
For bulk RNA-seq data analysis (EGFR+,PAX6+,OLIG2+,NEUN+), sequenced output FASTQ files were assessed for quality using the FASTQC package. Reads were aligned to the human genome (GENCODE GRCh38) using STAR with default settings (Dobin et al., 2013). Gene counts were obtained using the featureCount utility (Liao, Smyth, & Shi, 2014). The counts data were rld (rlogtransformed counts)-normalized. Differential expression analysis was performed using the DESeq2 R package (Love, Huber, & Anders, 2014), modeling the data with a negative binomial distribution and using Empirical Bayes shrinkage for dispersion and fold change estimation.
For single cell RNA-seq data analysis, the Cell Ranger v3 software was first used to demultiplex cellular barcodes to produce raw 3’ end read  profiles for individual cells, and then performed alignment, filtering, barcode counting, and UMI (unique molecular  identifier) counting, producing a feature-barcode matrix per sample. Unsupervised clustering analysis was  performed by three independent methods: Cell Ranger (10X Genomics), Seurat v2.3.4 (Butler, Hoffman, Smibert,  Papalexi, & Satija, 2018), and MetaCell (Giladi et al., 2018). Batch correction and integration of cell populations  between samples was done using mnnCorrect (Haghverdi, Lun, Morgan, & Marioni, 2018). For Seurat analysis, the  final data matrix was produced by removing unwanted cells (with too few UMIs, set at default value) from the  dataset, and applying a global-scaling normalization method that normalizes the feature expression measurements  for each cell by the total expression, multiplies this by a scale factor (10,000 by default), and log-transforms the  result. For MetaCell analysis, the raw data matrix was filtered to remove specific mitochondrial genes, and then cells  with less than 500 UMIs or total fraction of mitochondrial gene expression exceeding 60%.
Genome_build: GrCh38
Supplementary_files_format_and_content: For bulk RNA-seq data (EGFR+,PAX6+,OLIG2+,NEUN+), the included processed data file represents rld (rlogtransformed counts)-normalized read counts.  For single-cell RNA-seq data, the processed file represents feature-barcode matrix per sample, which was previously demultiplexed, aligned, filtered, and barcode and UMI counted.

growth_protocol: All material was extracted from fresh-frozen or fresh dissociated tissue

extract_protocol:
1) Single cell RNA-seq, TLE tissue from five different de-identified patients was obtained from the operating room and immersed in freshly prepared live cell buffer for single cell dissociation.    2) For NEUN+/PAX6+/OLIG2+ RNA-seq, 200-500mg of frozen tissue was manually homogenized in a hypotonic lysis buffer (0.32M Sucrose/5mM CaCl2/3mM Mg(Ac)2/0.1mM  EDTA, 10mM Tris-HCL pH8/1mM DTT/0.1% Triton X-100). Nuclei were collected in this buffer and purified  from cellular debris by ultracentrifugation in a sucrose gradient, resuspended in 1X PBS, simultaneously incubated with fluorescently-conjugated primary antibodies to NEUN, OLIG2, and PAX6, and isolated by FACS. 3) For EGFR+ RNA-seq, fresh tissue was  enzymatically dissociated with papain, debris was removed by passage through 22% Percoll, and dissociated cells were incubated for 30 min on ice with EGF-APC for positive selection of EGF-bound (i.e. EGFR+) populations and with  inflammatory and endothelial cell markers for exclusion: CD45-PE, CD34-PE, CD24-PE. EGFR+CD34-CD45-CD24-DAPI- cells were isolated by FACS.
1) Single cell RNA-seq was performed using the Chromium platform (10x Genomics) with the 3’ gene expression (3’ GEX) V1-V3 chemistry, using an input of ~10,000 single cells. Gel-Bead in Emulsions (GEMs) were generated on the sample chip in the Chromium controller.   2) For NEUN+/PAX6+/OLIG2+ RNA-seq library preparation (SMARTer Stranded Total RNA-Seq Kit Pico Input  Mammalian), 2952pg of total nuclear RNA were amplified into cDNA with  fragmentation times of 2.5 min for autopsy and 3.5 min for TLE cases (14 cycles total amplification for all).  Ribosomal RNA depletion was performed using human-specific R-Probes. 3) For EGFR+ RNA-seq library preparation  (SMART-seq v4, Clontech Laboratories), 165-234pg total RNA was converted to cDNA (8-13 cycles).  Libraries were generated using Nextera XT (FC-131-1024) and validated using Agilent 2100 Bioanalyzer.
1) For single cell RNA-seq, Barcoded cDNA was extracted from the GEMs by Post-GEM RT-cleanup and  amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly A-tailing, adapter  ligation, and 10X-specific sample indexing following the manufacturer’s protocol.

treatment_protocol: FACS was performed for the isolation of EGFR+, NEUN+, PAX6+, and OLIG2+ populations from tissue

value: Temporal lobe epilepsy (TLE)

value: Temporal neocortex

value: Unsorted, freshly dissociated cells


title: P8 prefrontal cortex, Male, VEH/CON, L22621-2

value: VEH/CON


title: P8 prefrontal cortex, Male, DEP+MS, L22630-2


title: OT-I TM, Ag/Infl rep1

description: Lm-Ova stimulated memory CD8 T cells

value: Lymphocyte

value: WT


title: gBT-I TM, steady state rep1

description: unstimulated memory CD8 T cells


title: scRNA-seq TLE sample 19619

description:
10X Genomics, v2
Sample name: 441
I1: Sample Index
R1: 16bp Cell Barcode + 10bp UMI + following ignorable bases (which would be trimmed automatically by Cellranger)
R2: RNA


title: con_wa1


title: P8 prefrontal cortex, Female, DEP+MS, L22631-3

value: Female


title: gBT-I TM, steady state rep2

description: unstimulated memory CD8 T cells


title: P8 prefrontal cortex, Female, DEP+MS, L22630-5


title: scRNA-seq TLE sample 13059

description:
10X Genomics, v1
Sample name: CL48K
I1: Sample Index
R1: RNA
R2: 14bp Cell Barcode
R3: 10bp UMI


title: OT-I TM, steady state rep3

description: unstimulated memory CD8 T cells


title: scRNA-seq TLE sample 14431

description:
10X Genomics, v2
Sample name: 172
I1: Sample Index
R1: 16bp Cell Barcode + 10bp UMI + following ignorable bases (which would be trimmed automatically by Cellranger)
R2: RNA


title: P8 prefrontal cortex, Female, VEH/CON, L22621-4


title: OT-I TM, steady state rep2

description: unstimulated memory CD8 T cells


title: scRNA-seq TLE sample 12814

description:
10X Genomics, v1
Sample name: CL37K
I1: Sample Index
R1: RNA
R2: 14bp Cell Barcode
R3: 10bp UMI


title: P8 prefrontal cortex, Male, VEH/CON, L22690-1


title: 293T_polysome_small

description: RNA with a ribosome small subunit bound.

value: wildtype

value: B


title: Healthy donor 3 CD28-CD57+CD8+ LD  (late differentiated)

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

description:
sample name:
HD3

data_processing:
Basecalls performed using RTA 2.7.3
Bad quality reads were filtered out using Trimmomatic (v 0.36) with the following paramters: HEADCROP:5 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
paired-end reads were aligned to the mm9 genome assembly using STAR (v2.5.2b), and read count per gene was subsequently estimated with the following parameters: --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999  --outFilterMismatchNoverLmax 0.05 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMatchNmin 16   --quantMode GeneCounts
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited txt file including read count per gene for each sample

source_name: peripheral blood

extract_protocol:
RNA was isolated using the Qiagen RNAeasy microkit
Barcoded RNA-sequencing libraries were prepared from 100 ng total RNA using the Ovation Human RNA-Seq system for small amounts of RNA (Nugen, San Carlos, CA). For selective depletion of rRNAs, the insert-dependent adapter cleavage method from Nugen was used prior to cDNA synthesis. To control sources of variability during sample and data processing, a common set of external spike-in RNA controls, developed by the external RNA controls consortium (ERCC), was used (Ambion).

value: T cells

value: peripheral blood

value: wildtype FAS

tag: diagnosis

value: healthy individual


title: OT-I TM, steady state rep1

description: unstimulated memory CD8 T cells


title: P8 prefrontal cortex, Female, VEH/CON, L22620-5

value: prefrontal cortex


title: Healthy donor 2 CD28-CD57+CD8+ LD  (late differentiated)

description:
sample name:
HD2


title: P8 prefrontal cortex, Male, VEH/CON, L22620-3

value: Male


title: R10_S06_Old_CD34All_FoxO1,3a,4KO

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

data_processing:
Convert from BCL and demultiplex using bcl2fastq 2.17.1
Adapter trimming of 50 and 61 base reads with Trimgalore
FastQ reads were mapped to mm10 using Tophat 2.1.1
Expression was quantitated to counts using HTCount or RPKM using Partek 7.0
Genome_build: mm10
Supplementary_files_format_and_content: HTSeq counts or normalized RPKM values

source_name: skeletal muscle

growth_protocol: Cells were processed for RNA extraction right after sorting. No cell culture was performed.

extract_protocol:
Qiagen microkit or SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara)
0.2-0.4 ng of total RNA (or 400 cells) were used to amplify the cDNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara). 1 ng of amplified cDNA was used to generate barcoded libraries using the Nextera XT DNA library preparation kit (Illumina). Basically, cDNA was fragmented, and adapters were added in a single reaction followed by amplification and clean up. The size of the libraries was checked using the Agilent 2100 Bioanalyzer High Sensitivity DNA chip and their concentration was determined using the Qubit® fluorometer (ThermoFisher Scientific).

treatment_protocol: Cells were isolated form resting non-injured muscles of young and geriatric WT mice without previous treatment

value: skeletal muscle

tag: mice age

value: Old


title: Healthy donor 1 CD28-CD57+CD8+ LD  (late differentiated)

description:
sample name:
HD1


title: P8 prefrontal cortex, Female, VEH/CON, L22740-8


title: R10_S05_Old_CD34All_FoxO1,3a,4KO


title: R10_S04_Old_CD34All_FoxO1,3a,4KO


title: patient 3 CD28-CD57+CD8+ LD (late differentiated)

description:
sample name:
P3_TEMRA

source_name: spleen

value: spleen

value: mutated FAS

value: ALPS-FAS, untreated


title: R10_S03_Old_CD34All_FoxO1,3a,4WT


title: P8 prefrontal cortex, Female, DEP+MS, L22710-6

value: DEP+MS


title: P8 prefrontal cortex, Male, DEP+MS, L22710-2


title: P8 prefrontal cortex, Female, DEP+MS, L22700-7


title: patient 3 CD28+CD57+CD8+ DNT-like

description:
sample name:
P3_pDNT


title: patient 3 DNT (CD3+TCRab+CD4-CD8-)

description:
sample name:
P3_DNT


title: patient 3 CD28+CD57-CD8+ N+ED (naive and early differentiated)

description:
sample name:
P3_ED


title: R10_S02_Old_CD34All_FoxO1,3a,4WT


title: patient 2 CD28+CD57+CD8+ DNT-like

description:
sample name:
P2_pDNT


title: patient 2 CD28-CD57+CD8+ LD (late differentiated)

description:
sample name:
P2_TEMRA


title: P8 prefrontal cortex, Female, VEH/CON, L22690-7

value: VEH/CON


title: R09_S03_Old_CD34All_FoxO1,3a,4KO


title: patient 2 CD28+CD57-CD8+ N+ED (naive and early differentiated)

description:
sample name:
P2_ED


title: patient 2 DNT (CD3+TCRab+CD4-CD8-)

description:
sample name:
P2_DNT


title: R09_S02_Old_CD34All_FoxO1,3a,4WT


title: R09_S01_Old_CD34All_FoxO1,3a,4WT


title: R08_S05_Young_CD34All_FoxO1,3a,4KO

value: Young


title: P8 prefrontal cortex, Male, VEH/CON, L22740-1


title: patient 1 CD28-CD57+CD8+ LD (late differentiated)

description:
sample name:
P1_TEMRA


title: 958236-15

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

institute: ETH/University of Zurich

data_processing:
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR  v2.7.1, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Mus Musculus, Ensembl GRCm38 P5
Supplementary_files_format_and_content: tad-delimited, raw counts

source_name: ZH3_5 months_FT2Fc_sciatic nerve

growth_protocol: Mice were housed in animal facilities at the University Hospital Zurich (OHC) in groups of 3–5, under a 12 h light/12 h dark cycle, with sterilized chow food and water ad libitum.

extract_protocol:
RNA was extracted using TRIzol according to the manufacturers instructions.
TruSeq RNA stranded; PolyA, TruSeq RNA Kit

treatment_protocol: Mice in the chronic treatment experiment were i.p. injected 3x/week for a total of 4 months. Mice were sacrificed by cervical dislocation. Sciatic nerves were immediately extracted and immersed into TRIzol. Sciatic nerves were stored in TRIzol at 4°C until RNA extraction.

value: ZH3 (C57BL/6J-Prnp<em1Aag)

value: 5 months

value: sciatic nerve


title: 958235-7

description: 20200206.A-958235-7_CAATAGGAAT-GCGGCTTACA


title: 958236-13

description: 20200206.A-958236-13_CGTGTCGTGG-TGTTAGCACA

source_name: ZH3_5 months_buffer_sciatic nerve

value: buffer


title: 958236-14

description: 20200206.A-958236-14_CAACGTTCGG-CGCGGTGATC

source_name: ZH3_5 months_IgG_sciatic nerve

value: IgG


title: patient 1 CD28+CD57-CD8+ N+ED (naive and early differentiated)

description:
sample name:
P1_ED

value: T cells

value: peripheral blood


title: R10_S01_Old_CD34All_FoxO1,3a,4WT


title: R08_S03_Young_CD34All_FoxO1,3a,4WT


title: P8 prefrontal cortex, Male, DEP+MS, L22700-1

value: prefrontal cortex


title: R08_S02_Young_CD34All_FoxO1,3a,4WT


title: R08_S01_Young_CD34All_FoxO1,3a,4WT


title: R09_S04_Old_CD34All_FoxO1,3a,4KO


title: 958234-9


title: 958235-4

description: 20200206.A-958235-4_AACGTTAGTT-ACAACGCTCA


title: R07_S04_Young_CD34All_FoxO1,3a,4KO-Pax7ROSAYFP


title: R07_S03_Young_CD34All_FoxO1,3a,4KO-Pax7ROSAYFP


title: patient 1 CD28+CD57+CD8+ DNT-like

description:
sample name:
P1_pDNT


title: 958234-12


title: 958234-10

description: 20200206.A-958234-10_AATTCCATCT-TATGCCTTAC


title: R07_S02_Young_CD34All_FoxO1,3a,4WT-Pax7ROSAYFP


title: R08_S04_Young_CD34All_FoxO1,3a,4KO


title: 958233-2


title: 958235-6


title: R07_S01_Young_CD34All_FoxO1,3a,4WT-Pax7ROSAYFP


title: patient 1 DNT (CD3+TCRab+CD4-CD8-)

description:
sample name:
P1_DNT


title: 958235-5

description: 20200206.A-958235-5_AAGACATTAG-CTTCAACCAC


title: Plasma Heroin2

city: 宁波

first: Haixiong

last: Liu

state: Zhejiang

address: 浙江省宁波市江北区

department: Ningbo Institute of Medical Science

institute: Ningbo University

description:
S13020_NS
Total miRNAs from plasma from heroin addict

hyb_protocol: Sample hybridization was performed as per the manufacturer’s standard protocols by using the Agilent miRNA Complete Labeling and Hyb Kit. Resuspend the dried sample in nuclease-free water. Add 4.5 μL of the 10X GE Blocking Agent to each sample. Add 22.5 μL of 2X Hi-RPM Hybridization Buffer to each sample for a total of 45 μL. Mix well but gently on a vortex mixer. Incubate at 100°C for 5 minutes. Immediately transfer to an ice water bath for 5 minutes. Quickly spin in a centrifuge to collect any condensation at the bottom of the tube, followed by preparing the hybridization assembly to process the miRNA system microarray. Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar. Slowly dispense all of the volume of the hybridization sample onto the gasket well in the center. Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces. Firmly hand-tighten the clamp onto the chamber. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles. If necessary, tap the assembly on a hard surface to move stationary bubbles. Place assembled slide chamber in rotisserie in a hybridization oven set to 55°C. Set your hybridization rotator to rotate at 20 rpm. Hybridize at 55°C for 20 hours.

scan_protocol: Slides were scanned immediately after washing. Assemble the slides into slide holder of the Agilent Scanner G2505C. Verify scan settings for miRNA. Select the protocol AgilentG3_miRNA for the 8x60K format. All the appropriate settings are set as default s (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Peripheral Blood plasma

label_protocol: Sample labeling was performed as per the manufacturer’s standard protocols by using the Agilent miRNA Complete Labeling and Hyb Kit. After the 16°C labeling reaction or sample purification, samples were completely dried by using a vacuum concentrator.

extract_protocol: When extraction, miRNA from 200 μl plasma was purified using the miRNeasy Serum/Plasma Kit, according to the manufacturer’s specifications (Qiagen, Germany). Briefly, samples were supplemented (after addition of QIAzol) with 3.5 μl miRNeasy Serum/Plasma Spike-In Control (1.6×108 copies/μl working solution) (Qiagen, Germany). Subsequently, after addition of chloroform and centrifugation, the upper, aqueous phase is extracted, and ethanol is added to provide appropriate binding conditions for all RNA molecules from approximately 18 nucleotides upwards. The samples are then applied to the RNeasy MinElute spin column, where the total RNA binds to the membrane and contaminants are washed away. RNA is then eluted in a 13 μl of nuclease-free water.

treatment_protocol: Peripheral blood samples (2 ml) were collected into EDTA-containing tubes. Whole blood was centrifuged at 1200 g for 15 min at room temperature within 30 min after blood collection, and the supernatant fluid was transferred into microcentrifuge tubes, followed by a second centrifugation at 12, 000 g for 10 min at 4°C to remove cellular debris. Plasma was then aliquoted and stored at −80°C until use.

value: plasma

tag: gender

value: male


title: Plasma Heroin4

description:
S13006.3.28_NS
Total miRNAs from plasma from heroin addict


title: Plasma Heroin1

description:
S13008.3.31_NS
Total miRNAs from plasma from heroin addict


title: Plasma Heroin3

description:
S13036_NS
Total miRNAs from plasma from heroin addict


title: 958233-1


title: 840017-13

description: 20200206.A-840017-13_AGAATTCGCC-GTATTGACGT

value: 13-15 months

value: untreated


title: R06_S07_21d_CD34All_FoxO1,3a,4KO

value: skeletal muscle


title: R06_S05_21d_CD34All_FoxO1,3a,4KO


title: Plasma Control5

description:
S86_NS
Total miRNAs from plasma from healthy control


title: 840015-9

description: 20200206.A-840015-9_TCGAGCCATA-TCGCTATGAG


title: R06_S06_21d_CD34All_FoxO1,3a,4KO


title: Plasma Control2

description:
S78_NS
Total miRNAs from plasma from healthy control


title: R06_S04_21d_CD34All_FoxO1,3a,4KO


title: 840015-10

description: 20200206.A-840015-10_CACAGCGGTC-GAGAATGGTT

source_name: WT_13-15 months_untreated_sciatic nerve

value: WT (C57BL/6J)


title: Plasma Control3

description:
S85_NS
Total miRNAs from plasma from healthy control


title: Plasma Control4

description:
S100_NS
Total miRNAs from plasma from healthy control


title: Plasma Control1

description:
S60_NS
Total miRNAs from plasma from healthy control


title: 828579-10


title: EGFR+ TLE sample 14431

description:
Sample name: E+ 14431
rldnormalized_EGFR.txt
A2-E2

value: Temporal lobe epilepsy (TLE)

value: Temporal neocortex

value: EGFR+(CD34-CD45-CD24-) sorted

tag: sorting strategy

value: EGF-APC (Life Technologies, E-35351, 1μg/10e6 live cells)


title: EGFR+ TLE sample 12433

description:
Sample name: E+ 12433
rldnormalized_EGFR.txt
A3-E4

value: Temporal lobe epilepsy (TLE) / TS


title: R06_S02_21d_CD34All_FoxO1,3a,4WT

tag: genotype


title: R06_S03_21d_CD34All_FoxO1,3a,4WT


title: 828579-9

description: 20200206.A-828579-9_GGTCTATTAA-ATTCCATAAG

value: ZH3 (C57BL/6J-Prnp<em1Aag)

value: sciatic nerve


title: EGFR+ TLE sample 10308

description:
Sample name: E+ 10308
rldnormalized_EGFR.txt
A1-E1


title: R05_S10_8d_CD34All_FoxO1,3a,4KO


title: R06_S01_21d_CD34All_FoxO1,3a,4WT


title: 828465-3

description: 20200206.A-828465-3_GAGCTTGCCG-GTGACACGCA


title: Epilepsy OLIG2+ TLE sample 10308

description:
Sample name: E3 O3
rldnormalized_nuclei.txt
A3-E4-TS-ATTCAGAA-ATAGAGGC

molecule: nuclear RNA

value: OLIG2+ sorted OPCs

value: OLIG2-AF488 antibody (Millipore, MABN50A4, 1:1000)


title: Epilepsy PAX6+ TLE sample 10308

description:
Sample name: E3 P3
rldnormalized_nuclei.txt
A3-E4-TS-GAATTCGT-ATAGAGGC

value: PAX6+ sorted astrocytes

value: anti-PAX6-APC (Novus Biologicals, NBP2-34705APC, 1:1000)


title: R05_S09_8d_CD34All_FoxO1,3a,4WT


title: R05_S08_8d_CD34All_FoxO1,3a,4KO


title: 828474-6

description: 20200206.A-828474-6_TCACCAACTT-CGCTCCACGA


title: 828474-4


title: 2988-540-7_ZH3

source_name: ZH3_4 months_untreated_sciatic nerve

value: 4 months


title: 2988-532-4_WT

source_name: WT_4 months_untreated_sciatic nerve


title: R05_S06_8d_CD34All_FoxO1,3a,4KO


title: Epilepsy OLIG2+ TLE sample 12321

description:
Sample name: E2 O2
rldnormalized_nuclei.txt
A2-E2-14431-ATTCAGAA-ATAGAGGC


title: 2988-540-8_WT


title: Epilepsy NEUN+ TLE sample 10308

description:
Sample name: E3 N3
rldnormalized_nuclei.txt
A3-E4-TS-GAGATTCC-ATAGAGGC

value: NEUN+ sorted neurons

value: NeuN-AF555 antibody (Millipore, MAB377A5, 1:1000)


title: Epilepsy PAX6+ TLE sample 12321

description:
Sample name: E2 P2
rldnormalized_nuclei.txt
A2-E2-14431-GAATTCGT-ATAGAGGC


title: Epilepsy NEUN+ TLE sample 12321

description:
Sample name: E2 N2
rldnormalized_nuclei.txt
A2-E2-14431-GAGATTCC-ATAGAGGC


title: 2988-532-3_ZH3

value: untreated


title: R05_S05_8d_CD34All_FoxO1,3a,4KO

value: skeletal muscle


title: Epilepsy PAX6+ TLE sample 12726

description:
Sample name: E1 P1
rldnormalized_nuclei.txt
A1-E1-10308-GAATTCGT-ATAGAGGC


title: R05_S04_8d_CD34All_FoxO1,3a,4WT


title: 2988-496-7_ZH3


title: Epilepsy OLIG2+ TLE sample 12726

description:
Sample name: E1 O1
rldnormalized_nuclei.txt
A1-E1-10308-ATTCAGAA-ATAGAGGC


title: 2988-496-4_WT

value: WT (C57BL/6J)


title: R05_S02_8d_CD34All_FoxO1,3a,4WT


title: R05_S01_8d_CD34All_FoxO1,3a,4KO


title: Autopsy PAX6+ TL Control sample 10997

description:
Sample name: A3 P3
rldnormalized_nuclei.txt
A3-E4-TS-CGCTCATT-ATAGAGGC

value: Temporal lobe autopsy control (TL)


title: R05_S07_8d_CD34All_FoxO1,3a,4KO


title: CITE-seq HTO

city: Dallas

first: Siyuan

address: 6001 Forest Park Rd

department: Department of Pathology

institute: UT Southwestern Medical Center

data_processing:
Demultiplexing: cellranger mkfastq
10x genomics Cellranger V3.1 was used for alignment, filtering, barcoding Counting and UMI Counting.
HTO1-8 were used for sample level demultiplexing and group assignment. (1) HTO1: Control/Non-treated (2) HTO2: Control/Non-treated ; (3) HTO3: Control/Non-treated ; (4) Control/Non-treated ; (5) HTO5: Dual TX; (6) Dual TX; (7) HTO7: Dual TX; (8) HTO8: Dual TX. The following sample comparisons were made: HTO1 - HTO4 were compared to HTO5 - HTO8.
After generating the digital gene expression data matrices, the Seurat R package V3.1.1 (Satija, 2015) was used to perform data normalization, dimension reduction, clustering and differential expression analysis.
Genome_build: mm10-3.0.0
Supplementary_files_format_and_content: tab-delimited text files that include UMI values for gene UMI, HTO and ADT counts

source_name: brain immune cells

extract_protocol:
Mice were  perfused with PBS and brains extracted. Brains digested with a multi-tissue dissociation kit (Miltenyi). Brain infiltrating immune cells were enriched by 70%/37%/30% percoll gradient centrifugation.
For RNA expression (cDNA), we followed 10x genomics single cell 3’ v3 assay standard protocol. For ADT and HTO, we followed CITE-seq and Cell hashing protocol as provided here:https://citeseq.files.wordpress.com/2019/02/cite-seq_and_hashing_protocol_190213.pdf
10x genomics single cell 3’ v3 assay

tag: mouse strain

tag: 1 brain or pooled

value: 3 brain hemisphere per biological sample


title: CITE-seq ADT

description: ADT

value: 2 brain hemisphere per biological sample


title: R04_S12_Young_CD34Lo_Pax7-ROSAYFP

value: Young


title: Autopsy NEUN+ TL Control sample 10997

description:
Sample name: A3 N3
rldnormalized_nuclei.txt
A3-E4-TS-ATTACTCG-ATAGAGGC

value: Temporal neocortex

tag: cell type


title: Autopsy OLIG2+ TL Control sample 10997

description:
Sample name: A3 O3
rldnormalized_nuclei.txt
A3-E4-TS-TCCGGAGA-ATAGAGGC


title: Epilepsy NEUN+ TLE sample 12726

description:
Sample name: E1 N1
rldnormalized_nuclei.txt
A1-E1-10308-GAGATTCC-ATAGAGGC

value: Temporal lobe epilepsy (TLE)


title: R13_S14_Young_CD34Hi_IGF1

tag: treatment


title: CITE-seq mRNA/cDNA

description: mRNA/cDNA

value: 1 brain hemisphere per biological sample


title: Autopsy PAX6+ TL Control sample 10355

description:
Sample name: A2 P2
rldnormalized_nuclei.txt
A2-E2-14431-CGCTCATT-ATAGAGGC


title: R13_S13_Young_CD34Hi_IGF1


title: R04_S10_Young_CD34Hi_Pax7-ROSAYFP


title: R04_S11_Young_CD34Med_Pax7-ROSAYFP


title: R13_S11_Young_CD34Hi_IGF1


title: R13_S12_Young_CD34Hi_IGF1


title: Autopsy NEUN+ TL Control sample 10355

description:
Sample name: A2 N2
rldnormalized_nuclei.txt
A2-E2-14431-ATTACTCG-ATAGAGGC


title: Autopsy OLIG2+ TL Control sample 10355

description:
Sample name: A2 O2
rldnormalized_nuclei.txt
A2-E2-14431-TCCGGAGA-ATAGAGGC

value: OLIG2+ sorted OPCs


title: R04_S09_Young_CD34Lo_Pax7-ROSAYFP


title: R13_S10_Young_CD34Lo_IGF1


title: Autopsy PAX6+ TL Control sample 10662

description:
Sample name: A1 P1
rldnormalized_nuclei.txt
A1-E1-10308-CGCTCATT-ATAGAGGC


title: R04_S07_Young_CD34Hi_Pax7-ROSAYFP


title: R04_S08_Young_CD34Med_Pax7-ROSAYFP


title: R04_S06_Young_CD34Lo_Pax7-ROSAYFP


title: Autopsy OLIG2+ TL Control sample 10662

description:
Sample name: A1 O1
rldnormalized_nuclei.txt
A1-E1-10308-TCCGGAGA-ATAGAGGC

value: OLIG2-AF488 antibody (Millipore, MABN50A4, 1:1000)


title: R04_S05_Young_CD34Med_Pax7-ROSAYFP


title: Autopsy NEUN+ TL Control sample 10662

description:
Sample name: A1 N1
rldnormalized_nuclei.txt
A1-E1-10308-ATTACTCG-ATAGAGGC


title: R13_S09_Young_CD34Lo_IGF1


title: R13_S08_Young_CD34Lo_IGF1


title: R04_S04_Young_CD34Hi_Pax7-ROSAYFP


title: R04_S03_Young_CD34Lo_Pax7-ROSAYFP


title: R13_S06_Young_CD34Lo_WT

value: WT


title: R13_S07_Young_CD34Lo_IGF1


title: R13_S05_Young_CD34Lo_WT


title: R13_S04_Young_CD34Lo_WT


title: R13_S03_Young_CD34Hi_WT


title: R13_S02_Young_CD34Hi_WT


title: R04_S02_Young_CD34Med_Pax7-ROSAYFP


title: R03_S05_Young_CD34Lo_WT


title: R04_S01_Young_CD34Hi_Pax7-ROSAYFP


title: R03_S03_Young_CD34Hi_WT


title: R03_S04_Young_CD34Lo_WT


title: R03_S02_Young_CD34Hi_WT


title: R12_S06_Ger_CD34All_FoxO1,3a,4KO

value: Ger


title: R13_S01_Young_CD34All_WT


title: R03_S01_Young_CD34Hi_WT


title: R02_S14_Young_CD34Lo_WT


title: R12_S04_Ger_CD34All_FoxO1,3a,4KO


title: R12_S03_Ger_CD34All_FoxO1,3a,4WT


title: R02_S13_Young_CD34Hi_WT


title: R12_S02_Ger_CD34All_FoxO1,3a,4WT


title: R12_S01_Ger_CD34All_FoxO1,3a,4WT


title: R11_S16_Young_CD34Lo_WT_Wort

value: Wort


title: R11_S15_Young_CD34Hi_WT_Wort


title: Man12_HLC_BPS_repB

city: Dortmund

first: Jan

middle: G.

last: Hengstler

address: Ardeystrasse 67

institute: Leibniz Research Centre for Working Environment and Human Factors at the TU Dortmund University (IfADo)

hyb_protocol: For washing and staining, Affymetrix HWS kit and GeneChip Fluidics Station 450 were used, according to the manufacturer’s instructions.

scan_protocol: After staining, arrays were scanned with Affymetrix GeneChip Scanner 3000 7G and Affymetrix GCOS software was used for quality control analysis.

data_processing: Summarized probe set data were generated using R/Bioconductor and the fRMA algorithm.

label: biotin

source_name: Man12 derived HLC

label_protocol: For microarray labelling, 100 ng total RNA was taken as a starting material, and after amplification, 12.5 μg-amplified RNA was hybridized on Affymetrix Human Genome U133 Plus 2.0 arrays (Affymetrix, Santa Clara, CA, USA).

growth_protocol: The human pluripotent stem cell lines H9 and Man12 were maintained on pre-coated laminin 521 in serum-free medium mTeSR1 and maintained in a humidified 37°C, 5% CO2 incubator. Differentiation was initiated at 40% confluence by replacing serum-free medium with endoderm differentiation medium: RPMI 1640 containing 1× B27 supplement, 100 ng/mL Activin A, and 50 ng/mL Wnt3a. The medium was changed every 24 hours for 72 hr. On day 3, endoderm differentiation medium was replaced with hepatoblast differentiation medium, and this was renewed every second day for a further 5 days. The medium consisted of knockout (KO)-DMEM, Serum replacement, 0.5% Glutamax, 1% non-essential amino acids, 0.2% β-mercaptoethanol, and 1% DMSO. On day 8, differentiating cells were cultured in the hepatocyte maturation medium HepatoZYME containing 1% Glutamax, supplemented with 10 µM hydrocortisone, 10 ng/ml hepatocyte growth factor and 20 ng/ml oncostatin M.

extract_protocol: Total RNA was isolated from HLC using the Phenol/Chloroform method (Trizol®).

treatment_protocol: On day 9, the supplemented maturation media hepatocyte maturation medium was replaced every 48 hr by fresh media supplemented with a 0.1% solution in DMSO containing different concentrations of bisphenol A, F or S for 8 days.

value: Man12 derived HLC

value: BPS

tag: technical replicate

value: B


title: Man12_HLC_BPS_repC

value: C


title: R02_S10_Young_CD34Lo_WT

value: skeletal muscle


title: Man12_HLC_BPF_repC

value: BPF


title: Man12_HLC_BPS_repA

value: A


title: Man12_HLC_BPS_repD

value: D


title: Man12_HLC_BPF_repA


title: R02_S09_Young_CD34Hi_WT

value: Young


title: Man12_HLC_BPF_repB


title: Man12_HLC_BPF_repD


title: R11_S14_Young_CD34Lo_WT_CTRL

value: CTRL


title: R12_S05_Ger_CD34All_FoxO1,3a,4KO


title: Man12_HLC_BPF_repE

value: E


title: Man12_HLC_BPA_repE

value: BPA


title: R11_S13_Young_CD34Hi_WT_CTRL


title: R11_S12_Young_CD34Lo_WT_Wort


title: R02_S06_Young_CD34Lo_WT


title: R11_S11_Young_CD34Hi_WT_Wort


title: R02_S05_Young_CD34Hi_WT


title: R11_S10_Young_CD34Lo_WT_CTRL


title: R11_S09_Young_CD34Hi_WT_CTRL


title: R11_S08_Young_CD34Lo_WT_Wort


title: R11_S07_Young_CD34Hi_WT_Wort


title: R11_S06_Young_CD34Lo_WT_CTRL


title: R11_S05_Young_CD34Hi_WT_CTRL


title: R02_S02_Young_CD34Lo_WT


title: R01_S16_Ger_CD34Lo_WT


title: R01_S15_Ger_CD34Hi_WT


title: R11_S04_Young_CD34Lo_WT_Wort


title: R02_S01_Young_CD34Hi_WT


title: R01_S14_Ger_CD34Lo_WT


title: Man12_HLC_vehicle_control_repD

value: VC


title: Man12_HLC_BPA_repA


title: Man12_HLC_BPA_repB


title: Man12_HLC_untreated_control_repC

value: UC


title: R11_S03_Young_CD34Hi_WT_Wort

value: WT


title: Man12_HLC_untreated_control_repA


title: Man12_HLC_BPA_repC


title: R01_S13_Ger_CD34Hi_WT

value: Ger


title: Man12_HLC_vehicle_control_repC


title: Man12_HLC_BPA_repD


title: Man12_HLC_vehicle_control_repA


title: R11_S02_Young_CD34Lo_WT_CTRL


title: Man12_HLC_vehicle_control_repB


title: Man12_HLC_untreated_control_repD


title: Man12_HLC_untreated_control_repB


title: H9_HLC_BPS_repA

source_name: H9 derived HLC

value: H9 derived HLC


title: R11_S01_Young_CD34Hi_WT_CTRL


title: CITE-seq HTO [Mg_ex_dep_UDP02_HTO]

data_processing:
Demultiplexing: cellranger mkfastq
10x genomics Cellranger V3.1 was used for alignment, filtering, barcoding Counting and UMI Counting.
HTO1-8 were used for sample level demultiplexing and group assignment.  (1) HTO1: brain of naïve Cx3cr1CreERT mouse (non-microglia depleted); (2) HTO2: brain of metastasis-burdened  Cx3cr1CreERT mouse (non-microglia depleted); (3) HTO3: brain of metastasis-burdened  Cx3cr1CreERT mouse (non-microglia depleted); (4) HTO4: brain of naïve Cx3cr1CreERT-ROSA-iDTR mouse (microglia depleted); (5) HTO5: brain of metastasis-burdened  Cx3cr1CreERT-ROSA-iDTR mouse (microglia depleted); (6) HTO6: brain of metastasis-burdened  Cx3cr1CreERT-ROSA-iDTR mouse (microglia depleted); (7) HTO7: blood of metastasis-burdened Cx3cr1CreERT mouse (non-microglia depleted); (8) HTO8: blood of metastasis-burdened Cx3cr1CreERT-ROSA-iDTR mouse (microglia depleted).The following sample comparisons were made: HTO1 versus HTO4; HTO2 and HTO3 versus HTO5 and HTO6; HTO7 versus HTO8.
After generating the digital gene expression data matrices, the Seurat R package V3.1.1 (Satija, 2015) was used to perform data normalization, dimension reduction, clustering and differential expression analysis.
Genome_build: mm10-3.0.0
Supplementary_files_format_and_content: tab-delimited text files that include UMI values for gene UMI, HTO and ADT counts

source_name: brain immune cells or peripherial blood cells

extract_protocol:
Blood was collected in a heparin solution by cardiac puncture and RBCs were subsequently lysed with RBC lysis buffer. Mice were then perfused with PBS and brains extracted. Brains digested with a multi-tissue dissociation kit (Miltenyi). Brain infiltrating immune cells were enriched by 70%/37%/30% percoll gradient centrifugation.
For RNA expression (cDNA), we followed 10x genomics single cell 3’ v3 assay standard protocol. For ADT and HTO, we followed CITE-seq and Cell hashing protocol as provided here:https://citeseq.files.wordpress.com/2019/02/cite-seq_and_hashing_protocol_190213.pdf
10x genomics single cell 3’ v3 assay

tag: strain background

tag: genotype/variation

value: Cx3cr1CreERT or Cx3cr1CreERT-ROSA-iDTR

value: 1 brain hemisphere or periheral blood

tag: molecule subtype


title: CITE-seq mRNA/cDNA [Mg_ex_dep_SI-GA-C5]

value: brain immune cells or peripherial blood cells

value: mRNA/cDNA


title: CITE-seq ADT [Mg_ex_dep_UDI01_ADT]

value: ADT


title: R01_S10_Ger_CD34Lo_WT

tag: tissue

value: skeletal muscle


title: R01_S09_Ger_CD34Hi_WT


title: R01_S11_Ger_CD34Hi_WT


title: H9_HLC_BPS_repE

value: BPS


title: CITE-seq HTO [Cx3cr1_HTO_Nextera_i7_UDP03]

data_processing:
Demultiplexing: cellranger mkfastq
10x genomics Cellranger V3.1 was used for alignment, filtering, barcoding Counting and UMI Counting.
HTO1-8 were used for sample level demultiplexing and group assignment. (1) HTO1: brain of naïve Cx3cr1+/- mouse; (2) HTO2: brain of naïve Cx3cr1+/- mouse; (3) HTO3: brain of metastasis-burdened Cx3cr1+/- mouse; (4) HTO4: brain of metastasis-burdened Cx3cr1+/- mouse; (5) HTO5: brain of naïve Cx3cr1-/- mouse; (6) HTO6: brain of naïve Cx3cr1-/- mouse; (7) HTO7: brain of metastasis-burdened Cx3cr1-/- mouse; (8) HTO8: brain of metastasis-burdened Cx3cr1-/- mouse.The following sample comparisons were made: HTO1 and HTO2 versus HTO5 and HTO6; HTO3 and HTO4 versus HTO7 and HTO8.
After generating the digital gene expression data matrices, the Seurat R package V3.1.1 (Satija, 2015) was used to perform data normalization, dimension reduction, clustering and differential expression analysis.
Genome_build: mm10-3.0.0
Supplementary_files_format_and_content: tab-delimited text files that include UMI values for gene UMI, HTO and ADT counts

extract_protocol:
Mice were perfused with PBS and brains extracted. Brains digested with a multi-tissue dissociation kit (Miltenyi). Brain infiltrating immune cells were enriched by 70%/37%/30% percoll gradient centrifugation.
For RNA expression (cDNA), we followed 10x genomics single cell 3’ v3 assay standard protocol. For ADT and HTO, we followed CITE-seq and Cell hashing protocol as provided here:https://citeseq.files.wordpress.com/2019/02/cite-seq_and_hashing_protocol_190213.pdf
10x genomics single cell 3’ v3 assay

value: 1 brain hemisphere

value: brain immune cells


title: H9_HLC_BPS_repC

value: C


title: R01_S08_Young_CD34Lo_WT

value: Young


title: R01_S12_Ger_CD34Lo_WT


title: R01_S07_Young_CD34Hi_WT


title: P1_neu

first: David

last: Beck

address: 9000 Rockville Pike

department: NHGRI

institute: NIH

data_processing:
Quality control on the initial raw FASTQ files was performed using FastQC from Babraham Bioinformatics. Trimmomatic was used to remove paired-end reads in which one or more read had a Phred33 base call quality score average of less than 20 across the entire length of the read.8 Reads aligning to enriched hemoglobin subunit beta (HBB) gene were removed using bedtools. FASTQ files were mapped to the human reference genome build GRCh37/hg19 using STAR version 2.5.3a by manual two-pass mapping. Gene-level raw read counts were computed using featureCounts from the Subread package with a RefSeq transcript annotation set. Statistical tests on raw and processed data were performed using the SARTools R package. The DESeq2 R package from Bioconductor was used to perform differential expression analysis on raw read count data. Genes with Benjamini-Hochberg-adjusted FDRs < 0.05 were included in subsequent analyses. Raw read count data was imported into MSigDB to perform Gene Set Enrichment Analysis (GESA) using the Hallmark Gene Set Collection.
Genome_build: hg19
Supplementary_files_format_and_content: counts

source_name: RNA from sorted blood cells

extract_protocol:
Whole blood was collected from patients and controls in PAX tubes and RNA was extracted using PAXgene Blood RNA Kit (Qiagen). Patient and control blood was collected in sodium heparin BD Vacutainer tubes (Becton Dickinson) and PBMCs were isolated via density centrifugation of blood using Lympholyte-H (Cedarlane). CD14+ monocytes were purified via magnetic bead positive selection (Miltenyi) using an AutoMACS Pro, while preserving the CD14- untagged population. Neutrophils were isolated from a 30 minute sedimentation of RBC pellets in 3% dextran, washed once, with residual RBCs lysed using 30 seconds of 0.2% NaCl followed by 1.8% NaCl. For RNA-seq, after isolation, neutrophils, CD14+ monocytes, and CD14- PBMCs were immediately lysed in Trizol (Life Technologies) and frozen at -80° C. After thawing, RNA was isolated via phenol-chloroform extraction.
Library construction was performed using TrueSeq stranded mRNA workflow kit (Illumina)

tag: disease state

value: VEXAS patient

tag: cell population

value: Neutrophils


title: P1_CD14plus

value: CD14+ monocytes


title: P1_CD14dep

value: CD14+ depleted fraction


title: R01_S06_Young_CD34Lo_WT

value: WT


title: CITE-seq ADT [Cx3cr1_ADT-RPI-2]


title: H9_HLC_BPS_repD

value: H9 derived HLC

value: D


title: H9_HLC_BPF_repE

value: BPF

value: E


title: H9_HLC_BPS_repB

value: B


title: CITE-seq mRNA/cDNA [Cx3cr1_SI-GA-C12]

value: mRNA/cDNA


title: H9_HLC_BPF_repB


title: H9_HLC_BPF_repA

value: A


title: H9_HLC_BPF_repC


title: H9_HLC_BPF_repD


title: H9_HLC_BPA_repE

value: BPA


title: R01_S05_Young_CD34Hi_WT

value: skeletal muscle


title: P13_neu


title: H9_HLC_BPA_repD


title: CITE-seq HTO [CCR2_Cx3cr1B_HTO_Nextera_i7_UDP01]

data_processing:
Demultiplexing: cellranger mkfastq
10x genomics Cellranger V3.1 was used for alignment, filtering, barcoding Counting and UMI Counting.
HTO1-8 were used for sample level demultiplexing and group assignment. (1) HTO1: brain of naïve CCR2+/- mouse; (2) HTO2: brain of naïve  CCR2+/- mouse; (3) HTO3: brain of naïve CCR2-/- mouse; (4) HTO4: brain of naive CCR2-/-; (5) HTO5: blood of naïve Cx3cr1+/- mouse; (6) HTO6: blood of metastasis-burdened Cx3cr1+/- mouse; (7) HTO7: blood of naïve Cx3cr1-/- mouse; (8) HTO8: blood of metastasis-burdened Cx3cr1-/- mouse. The following sample comparisons were made: HTO1 and HTO2 versus HTO3 and HTO4; HTO5 versus HTO7; HTO6 versus HTO8.
Genome_build: mm10-3.0.0
Supplementary_files_format_and_content: tab-delimited text files that include UMI values for gene UMI, HTO and ADT counts

source_name: peripheral blood cells and brain immune cells

value: Cx3cr1+/-; Cx3cr1-/-; CCR2+/-; CCR2-/- (C57Bl/6 background)

value: 1 brain hemisphere or whole blood

tag: moelcule subtype


title: R01_S03_Young_CD34Hi_WT

value: Young


title: CITE-seq ADT [CCR2_Cx3cr1B_ADT-RPI-1]

value: peripheral blood cells and brain immune cells

value: ADT


title: R01_S02_Young_CD34Lo_WT


title: P13_CD14dep

value: VEXAS patient


title: P13_CD14plus

value: CD14+ monocytes


title: P11_neu

value: Neutrophils


title: R01_S01_Young_CD34Hi_WT

value: WT


title: H9_HLC_BPA_repC

value: H9 derived HLC

value: C


title: P11_CD14plus


title: H9_HLC_BPA_repB


title: H9_HLC_BPA_repA


title: CITE-seq Met v Naïve ADT_2

description: 1 brain hemisphere

data_processing:
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)
Demultiplexing: cellranger mkfastq
10x genomics Cellranger V3.0.2 was used for alignment, filtering, barcoding counting, cDNA UMI counting and antibody counting
HTO1-4 were used for sample level demultiplexing and group assignment. HTO1: naive brain, replicate 1; HTO2: naive brain, replicate 2; HTO3: brain metastasese-bearing brain, replicate 1; HTO4: brain metastasese-bearing brain, replicate 2
After generating the digital gene expression data matrices, the Seurat v3.0.1 R pacckage was used to perform data normalization, dimension reduction, clustering and differential expression analysis.
Genome_build: mm10-3.0.0 (10x genomics)
Supplementary_files_format_and_content: tab-delimited text files that include UMI values for gene UMI, HTO and ADT counts

source_name: brain cells and metastatic tumor cells

extract_protocol:
Mice were perfused with PBS and brains extracted. Brains digested with papain-based neural tissue dissocation kit (Miltenyi). Mononuclear cells enriched by 70%/37%/30% percoll gradient centrifugation.
For RNA expression (cDNA), we followed 10x genomics single cell 3’ v2 assay standard protocol. For ADT and HTO, we followed CITE-seq and Cell hashing protocol as provided here:https://citeseq.files.wordpress.com/2019/02/cite-seq_and_hashing_protocol_190213.pdf

value: brain cells and metastatic tumor cells

tag: molecule type


title: H9_HLC_vehicle_control_repE

value: VC

value: E


title: R01_S04_Young_CD34Lo_WT

tag: mice age


title: CITE-seq Met v Naïve mRNA/cDNA_2

description: 1 brain hemisphere

value: mRNA/cDNA


title: P10_neu


title: P11_CD14dep

value: CD14+ depleted fraction


title: P10_CD14plus


title: H9_HLC_vehicle_control_repD

value: D


title: W03

first: Hong-wei

last: Sun

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

description: Lab data ID: CWS39

data_processing:
Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. PE reads of 50 bases were mapped to the mm10 using Bowtie 1.1.1.
Peak calling: Redundant reads were removed using Fastquniq. Uniquely mapped reads from fragments less than 175 bp were used to call peaks with MACS 2.1.1 using a p-value threshold of 1 x 10-5.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files

extract_protocol:
Sorted satellite cells were directly processed for ATAC-seq library preparation without in vitro culture.
ATAC-seq was performed according to a published protocol (Buenrostro et al., 2013) with minor modification. 2000-5000 cells were processed for each sample and treated with the Tn5 transposase (Illumina) for 30 min at 37°C and PCR-purified (Qiagen) to generate library fragments.
ATAC seq data were generated on Illumina HiSeq 2500 instruments according to the manufacturer's instructions.

value: skeletal muscle

value: Wild type

tag: age

value: young (2-4 months old)

tag: muscle state

value: resting non-injured muscle


title: W02

description: Lab data ID: CWS38


title: W01

description: Lab data ID: CWS37


title: CITE-seq mRNA/cDNA [CCR2_Cx3cr1B_SI-GA-G11]

value: Cx3cr1+/-; Cx3cr1-/-; CCR2+/-; CCR2-/- (C57Bl/6 background)

value: 1 brain hemisphere or whole blood

value: peripheral blood cells and brain immune cells


title: W04

description: Lab data ID: CWS41


title: H9_HLC_vehicle_control_repC


title: K04

description: Lab data ID: CSJ89

value: FoxO knockout


title: CITE-seq Met v Naïve HTO_2

description: 1 brain hemisphere


title: K03

description: Lab data ID: CSJ87


title: P10_CD14dep

value: VEXAS patient


title: C9_neu

value: Healthy control

value: Neutrophils


title: H9_HLC_untreated_control_repE

value: H9 derived HLC

value: UC


title: H9_HLC_vehicle_control_repB

value: VC

value: B


title: C9_CD14plus

value: CD14+ monocytes


title: C9_CD14dep

value: CD14+ depleted fraction


title: K02

description: Lab data ID: CSJ84

value: skeletal muscle


title: K01

description: Lab data ID: CSJ75


title: C8_CD14plus


title: C8_CD14dep


title: N04

description: Lab data ID: LGP_10

tag: cd34 status

value: CD34 negative


title: N05

description: Lab data ID: LGP_1

value: young (2-4 months old)


title: C7_neu


title: C7_CD14dep


title: H9_HLC_untreated_control_repD

value: D


title: H9_HLC_untreated_control_repC

value: C


title: C8_neu


title: H9_HLC_untreated_control_repA

value: A


title: H9_HLC_vehicle_control_repA


title: N06

description: Lab data ID: LGP_13

value: resting non-injured muscle


title: Renal tumor, #8

type: genomic

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

institute: National Institutes for Quantum and Radiological Science and Technology

description: Renal tumor, #8

hyb_protocol: Slides were hybridised in 1X Agilent Blocking Agent/Hi-RPM Buffer for 24 hours at 67°C in a rotating hybridization oven, then washed with the Agilent Oligo aCGH Buffer 1 and Buffer 2 in an ozone-depleted hood.

scan_protocol: Scanned on an Agilent microarray scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

organism: Rattus norvegicus

source_name: Renal tumor of gamma-irradiated rat at postnatal day 5

label_protocol: Labeling reactions with cyanine 5-UTP and cyanine 3-UTP were performed according to the Agilent SureTag DNA labeling kit (Agilent Technologies, Santa Clara, CA, USA).

growth_protocol: Rats were housed in autoclaved cages and maintained in a room with a controlled temperature (23 ± 1°C) and humidity (50 ± 5%) under a regular 12-hours light, 12-hours dark cycle. They were fed a standard laboratory animal diet (CE-2; Clea Japan, Tokyo, Japan) and sterilized water ad libitum.

extract_protocol: Genomic DNA was extarcted by QIAmp DNA Micro kit (Qiagen).

treatment_protocol: Rats were left untreated or were subjected to whole-body 137Cs gamma-irradiation (2 Gy, 0.7 Gy/min) at geatational day 19 or postnatal day 5.

value: renal Carcinoma

tag: gender

value: Male

tag: strain

value: F1 hybrid of F344 and Eker rats

source_name: Normal ear

value: Ear skin


title: Mouse mammary tumor from PyMT Wsh mouse rep7

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

institute: IRCCS Ospedale San Raffaele

hyb_protocol: Fluorescent dye-labeled cRNA was hybridized to SurePrint G3 Mouse GE v2 8x60K arrays (Agilent); hybridization and washing were performed on Agilent’s microarray platform, according to standard protocols.

scan_protocol: Microarray images were acquired using an Agilent DNA microarray scanner

data_processing: Raw gene expression data were generated using the Agilent Feature Extraction software v10.7.3.1 and were preprocessed using the limma package. Raw data were log2-transformed, background-corrected using the normexp method and quantile-normalized.

source_name: Mouse mammary tumor

label_protocol: Total RNA was amplified using the Low Input Quick Amp WT Labeling kit, according to the manufacturer’s instructions (Agilent Technologies, Santa Clara, USA). 100 ng of total RNA was reverse-transcribed into double-stranded cDNA, which was translated into cRNA in the presence of Cy3-dCTP and amplified by T7 RNA polymerase.

growth_protocol: Transgenic mice were sacrificed at 20 weeks of age and always maintained in SPF conditions

extract_protocol: Total RNA was extracted using the Rneasy Lipid Tissue Mini Kit (Qiagen) according to the manufacturer's instructions. RNA quality was assessed using Tapestation (Agilent, Santa Clara, CA, USA) and was quantified using Qubit (ThermoFisher, DE).

value: MMTV-PyMT

tag: background

value: Wsh

value: mammary tumor

value: 20 weeks


title: N03

description: Lab data ID: LGP_7

source_name: skeletal muscle


title: Mouse mammary tumor from PyMT B6 mouse rep8


title: Renal tumor, #7

description: Renal tumor, #7

value: Female


title: H9_HLC_untreated_control_repB

tag: cell type

value: H9 derived HLC

tag: treatment

value: UC

value: B


title: Renal tumor, #6

description: Renal tumor, #6


title: Mouse mammary tumor from PyMT B6 mouse rep6


title: Mouse mammary tumor from PyMT B6 mouse rep7


title: N01

description: Lab data ID: LGP_16

value: skeletal muscle

value: CD34 negative

value: young (2-4 months old)


title: Renal tumor, #5

description: Renal tumor, #5

source_name: Renal tumor of gamma-irradiated rat at gestational day 19


title: C10_neu

value: Healthy control

value: Neutrophils


title: C10_CD14plus

value: CD14+ monocytes


title: Renal tumor, #1

description: Renal tumor, #1

source_name: Renal tumor of non-irradiated rat

value: renal Carcinoma

value: Male


title: L06

description: Lab data ID: LGP_18

value: CD34 low

value: resting non-injured muscle


title: Mouse mammary tumor from PyMT Wsh mouse rep5

value: MMTV-PyMT

value: Wsh


title: Mouse mammary tumor from PyMT Wsh mouse rep6

value: mammary tumor

value: 20 weeks


title: P9.wholeblood

source_name: Whole blood RNA

value: VEXAS patient

value: Whole blood


title: L05

description: Lab data ID: LGP_15


title: Renal tumor, #2

description: Renal tumor, #2

value: F1 hybrid of F344 and Eker rats

value: Ear skin


title: P6.wholeblood


title: P5.wholeblood


title: L03

description: Lab data ID: LGP_9

value: skeletal muscle


title: N02

description: Lab data ID: LGP_4

value: CD34 negative

value: young (2-4 months old)


title: P4.wholeblood


title: P3.wholeblood


title: L02

description: Lab data ID: LGP_6


title: Renal tumor, #3

description: Renal tumor, #3

value: Female


title: Renal tumor, #4

description: Renal tumor, #4


title: L04

description: Lab data ID: LGP_12


title: L01

description: Lab data ID: LGP_3


title: P2.wholeblood


title: Mouse mammary tumor from PyMT B6 mouse rep5


title: Mouse mammary tumor from PyMT Wsh mouse rep3


title: Mouse mammary tumor from PyMT Wsh mouse rep2


title: P1B.wholeblood


title: Mouse mammary tumor from PyMT Wsh mouse rep4


title: mammary carcinoma, #16

source_name: Mammary carcinoma of gamma-irraddiated rat

treatment_protocol: Rats were left untreated or were subjected to whole-body neutron- (0.485 Gy) or 137Cs gamma-irradiation (0.5 Gy, 0.5 Gy/min) at 7 weeks of age.

value: Carcinoma

value: Sprague-Dawley rat

source_name: Normal liver

value: Liver


title: mammary carcinoma, #15


title: H05

description: Lab data ID: LGP_14

value: CD34 high


title: mammary carcinoma, #14


title: Mouse mammary tumor from PyMT B6 mouse rep4


title: mammary carcinoma, #12


title: mammary carcinoma, #13


title: P1A.wholeblood


title: Mouse mammary tumor from PyMT Wsh mouse rep1


title: H04

description: Lab data ID: LGP_11

value: resting non-injured muscle


title: Mouse mammary tumor from PyMT B6 mouse rep3

value: MMTV-PyMT


title: oschz1_input_for_MYC_rep2

city: Shanghai

first: Liufan

last: Yin

state: Shanghai

address: No. 2005, Songhu Road

department: School of Life Science

institute: Fudan University

data_processing:
Cleaned paired reads and single reads were mapped to the reference genome by Bowtie2. Samtools was used to remove reads with low mapping quality (Q< 20) and potential PCR duplicates. Reads were normalized as reads per kilobase per million mapped reads (RPKM) in windows of 10 bp using the bamCoverage tool in deepTools. MACS2 was used to call peak (parameter: -p 0.001, --nomodel). DiffBind2 was performed to obtained differentially enriched regions as OsChz1 binding sites (parameter: bFullLibrarySize=TRUE, filter=1, Fold=1, FDR<=0.05).
Genome_build: MSU7
Supplementary_files_format_and_content: bigwig files were generated using DeepTools with binsize of 10. bed files contained the enrichment regions or differentially enriched regions with the format: chrom, start, end.

organism: Oryza sativa

source_name: 30-day-old seddlings grown up under long-day condition (14 h light at 30°C and 10 h dark at 28°C)

growth_protocol: The husked rice seeds were surface-sterilized by treatment with 0.1% HgCl2 for 20 min and washed with sterilized water. After sterilization, seeds were then cultured on half-strength MS medium in artificial growth chambers under LD conditions (14 h 30 °C : 10 h 28°C, light : dark) for 10 days. Then, seedlings were transferred to MS medium and cultured under LD conditions for 20 days.

extract_protocol:
ChIP was performed as previously described (Johnson et al., 2002).
ChIP-seq libraries were prepared using the method previously described (Barski, Cuddapah et al. 2007).

value: 30-day-old seedling

tag: genotype

value: oschz1 mutant

tag: chip antibody


title: H06

description: Lab data ID: LGP_17


title: H03

description: Lab data ID: LGP_8


title: P13.wholeblood


title: Mouse mammary tumor from PyMT B6 mouse rep2

value: mammary tumor

value: 20 weeks


title: oschz1_MYC_rep2

value: anti-MYC (M20002L, Abmart)


title: P12.wholeblood

value: VEXAS patient

value: Whole blood


title: H02

description: Lab data ID: LGP_5

value: skeletal muscle


title: mammary carcinoma, #10

source_name: Mammary carcinoma of neutron-irraddiated rat


title: P10B.wholeblood


title: P11.wholeblood


title: oschz1_input_for_MYC_rep1


title: oschz1_MYC_rep1


title: mammary carcinoma, #9


title: mammary carcinoma, #11


title: com_input_rep2


title: Mouse mammary tumor from PyMT B6 mouse rep1


title: YMBR [TJb5-2]

city: Boston

first: Tatjana

last: Jakobs

state: MA

address: 20 Staniford Street

department: Howe Laboratory of Ophthalmology

institute: Massachusetts Eye and Ear Infirmary

description:
microbead injected
4BR4

data_processing:
Transcriptome mapping to full genome sequences for Mus musculus (UCSC version mm10) was performed with STAR version 2.3.0 (Dobin et al., 2013)
Read counts for individual genes were produced using FeatureCounts (Liao et al., 2014)
Differential expression analysis was performed using the DESeq2 R package after normalizing read counts and excluding  those genes with normalized read counts equal 0  (Anders et al., 2013)
Genome_build: mm10
Supplementary_files_format_and_content: featureCounts_

source_name: Optic nerve head

extract_protocol:
Optic nerve head were dissected. Qiagen microplus kit was used for total RNA extraction and Clontech SMARTer Ultra Low Input RNA Kit for Sequencing v3 (Takara, Kusatsu, Japan) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Microbeads (experimental glaucoma) or saline solution (controls) were injected into right anterior chamber of young adult mice to induce high intraocular pressure in glaucoma group. In addition, 13 week old and 40 week old naïve C57bl/6 mice were also examined.

value: optic nerve head

value: 13 weeks

tag: genoptype

value: wild type

tag: group

value: 3 month, 4 weeks after microbead injection


title: YMBR [TJb5-1]

description:
microbead injected
4BR3

tag: tissue


title: C6.wholeblood

tag: disease state

value: Healthy control


title: com_input_rep1


title: mammary carcinoma, #7

source_name: Mammary carcinoma of non-irraddiated rat

value: Carcinoma

value: Female

value: Sprague-Dawley rat

value: Liver


title: com_MYC_rep2

value: 30-day-old seedling


title: C5.wholeblood


title: YMBR [TJb4-7]

description:
microbead injected
4BR2


title: H01

description: Lab data ID: LGP_2

value: CD34 high

value: young (2-4 months old)

value: resting non-injured muscle


title: mammary carcinoma, #8


title: Pol II_ChIPseq in UPF1RNAi 2

city: Birmingham

first: Anand

middle: Kumar

last: Singh

state: West Midlands

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

description:
Pol II ChIP in UPF1RNAi S2 cells-Repeat 2
AS-C17

data_processing:
The ChIP-seq BAM files were converted to bedgraph files by using the genome Coverage Bed command and options bga and ibam from the Bedtools v2.26.0 suite.
Custom Perl scripts were then used to filter the Dm6 annotations either for genes separated by a minimum distance to avoid overlapping signals or RNA-seq expression levels.
Further custom scripts were used to extract the signal from the bedgraph files for each entry in the filtered gene list.
Single base resolution was used for flanking regions, while the signal in gene bodies was binned into 16 bins to take account of different gene lengths.
Each dataset was normalized by the total mapped sequencing reads in that dataset.
Cross-referencing between different datasets was done based on the 'named' field, after filtering the annotations for multiple entries with identical name.
Genome_build: Dm6
Supplementary_files_format_and_content: bedgraph

organism: Drosophila melanogaster

source_name: S2 Cells

growth_protocol: Drosophila Embryonic S2 cells were cultured in Insect–XPRESS media (Lonza) supplemented with 10% Fetal Bovine Serum (FBS) and 1% Penicillin-Streptomycin-Glutamine mix (P/S/G) (Invitrogen) at 27°C

extract_protocol:
Lysates were clarified from sonicated cells and DNA complexes were isolated with antibody.
ChIP-DNA libraries were produced using the NEBNext Ultra II DNA Library Prep Kit (NEB E7645L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (NEB E7600S), using provided protocols with 10ng of fragmented ChIP DNA

treatment_protocol: For RNAi, dsRNA Specific for UPF1 transcripts were used

tag: cell line

value: S2 Cells

tag: cell origin

value: Embryonic cell line

tag: passages

value: Pol II (ab817, Abcam)


title: mammary carcinoma, #5


title: mammary carcinoma, #6


title: YMBR [TJb4-6]

description:
microbead injected
4BR1

tag: age


title: mammary carcinoma, #4


title: mammary carcinoma, #3


title: C4.wholeblood

value: Whole blood


title: com_MYC_rep1

value: anti-MYC (M20002L, Abmart)


title: P10A.wholeblood

value: VEXAS patient


title: YSR [TJb4-4]

description:
saline injected
4SR3

value: optic nerve head

value: 13 weeks

value: wild type

value: 3 month, 4 weeks after saline injection


title: Pol II_ChIPseq in UPF1RNAi 1

description:
Pol II ChIP in UPF1RNAi S2 cells-Repeat 1
AS-C14


title: M2: Stem MR-VP Control 2

city: Frankfurt am Main

first: Lukas

last: Jost

address: Altenhöferallee 3

institute: GenXPro GmbH

data_processing:
Library strategy: Massive Analysis of cDNA ends (MACE-Seq)
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and bad quality as well as MACE specific polyA stretches; PCR artifacts were deduplicated based on Unique Molecular Identifier sequences
Cleaned reads were mapped onto SolTub_3.0 genome using bowtie2 and raw counts were obtained using HTSeq
Genome_build: SolTub_3.0
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each group
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Solanum tuberosum

source_name: Stem

growth_protocol: Plants were clonally propagated from potato 'Golden Wonder'. Cuttings were placed in polyurethane foam imbibed with 50 ml autotrophic M+S media. Photoperiod was 18/6 hours light/dark. Growth room temperature was ~ 23 degrees Celsius. Total growth time was 6 weeks.

extract_protocol:
Plants were harvested under aseptic conditions and RNA extractions from stem tissue were carried out using the QIAGEN® RNeasy™ plant extraction kit according to the manufacturer’s specifications. To eliminate genomic DNA contamination the Ambion® TURBO™ DNAse kit was used according to manufacturer’s specifications (Life Technologies, Carlsbad, CA, USA). RNA quantification was measured using a Nanodrop™ 2000c spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). Samples were immediately stored at -80°C to prevent degradation of RNA.
MACE seq Kit was used (GenXPro-GmbH, Frankfurt Germany) for 3' end sequencing of poly-adenylated mRNAs. Sequences are generated fromm the 5' end of average 350 bp 3' mRNA fragemnts.

treatment_protocol: Plants were exposed to bacterial VOCs by dropping 20 µl of either bacterial culture, LAC2 (L) or FZB24 (F) at OD 600nm = 1.0 on the centre of a 50 mm petri dish containing either Methyl Red Voges Proskeur (MR-VP) broth (Sigma Aldrich) supplemented with 14 g agar (Sigma Aldrich) per litre

value: Stem

tag: cultivar

value: Golden Wonder

value: Axenic Media in Proximity to Plant


title: YSR [TJb4-5]

description:
saline injected
4SR4


title: M3: Stem MR-VP Control 3


title: mammary carcinoma, #1

value: Carcinoma

value: Female

value: Sprague-Dawley rat

value: Liver


title: C3.wholeblood

value: Healthy control


title: C2.wholeblood


title: C1.wholeblood


title: Pol II Ser2_ChIPseq in UPF1RNAi 2

description:
Pol II Ser2 ChIP in UPF1RNAi S2 cells-Repeat 2
AS-C11

value: S2 Cells

value: Embryonic cell line

value: Pol II Ser2 (ab5095, Abcam)


title: YSR [TJb4-2]

description:
saline injected
4SR1


title: M1: Stem MR-VP Control 1


title: Pol II_ChIPseq in Wild type 1

description:
Pol II ChIP in Normal S2 cells-Repeat 1
AS-C12

value: Pol II (ab817, Abcam)


title: YSR [TJb4-3]

description:
saline injected
4SR2


title: L3: Stem LAC-treated 3

value: Bacterial Volatile Organic Compounds


title: Pol II Ser2_ChIPseq in UPF1RNAi 1

description:
Pol II Ser2 ChIP in UPF1RNAi S2 cells-Repeat 1
AS-C8


title: Pol II_ChIPseq in Wild type 2

description:
Pol II ChIP in Normal S2 cells-Repeat 2
AS-C15


title: Adult human cardiomyocytes_SARS-CoV-2_3

city: New York

first: Shuibing

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Illumina bcl2fastq2 v2.20 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the human hg19 reference genome plus SARS-CoV-2 genome using STAR v2.5.2b.
Raw reads counts were extracted using htseq-count v0.11.2.
Genome_build: hg19
Supplementary_files_format_and_content: txt files storing raw read counts per gene per sample

source_name: Adult human cardiomyocytes

growth_protocol: For monolayer-based cardiomyocyte (CMs) differentiation, hESCs were passaged at a density of 3x105cells/well of 6-well plate and grown for 48 hours to 90% confluence in a humidified incubator with 5% CO2 at 37℃. On day 0, the medium was replaced with RPMI 1640 supplemented with B27 without insulin and 6 µM CHIR99021. On day 1, the medium was changed to RPMI 1640 supplemented with B27 without insulin for 48 hr. Day 3, medium was refreshed to RPMI 1640 supplemented with B27 without insulin and 2 µM C59 for another 48 hr. On day 5, the medium was changed back to RPMI-B27 without insulin for 48 hr, and then switched to RPMI 1640 plus normal B27 until day 12 with a medium change every 2 days. On day 12, the medium was transiently changed to RPMI 1640 without D-glucose containing ascorbic acid, human albumin and DL-Lactate for two days to allow metabolic purification of CMs. From that day on, fresh RPMI 1640-B27 was changed every two days. On day 21, cells were dissociated with Accutase at 37℃ followed by resuspending with fresh RPMI 1640-B27 plus Y-27632 and reseeding into 96-well plates. After 24 hr, then switched to RMPI 1640-B27 without Y-27632 for following virus confection tests.

extract_protocol: Libraries were prepared using Illumina TruSeq RNA Sample Preparation (Non-stranded and Poly-A selection).

treatment_protocol: hPSC-derived cardiomyocytes were dissociated with Accutase at 37℃ followed by resuspending with fresh RPMI 1640-B27 plus Y-27632 and reseeding into 96-well plates. After 24 hr, the medium was switched to RMPI 1640-B27 without Y-27632. After 24h recovery, macrophages were added into hPSC-derived cardiomyocytes and co-cultured for another 24 hr before following analysis. Adult cardiomyocytes were also seeded into plates for 48-96 hr and co-cultured with macrophages for 24 hr before following analysis.

value: Adult human cardiomyocytes


title: mammary carcinoma, #2


title: ONLR [TJb4-1]

description:
aged naïve mice
ONR4

value: optic nerve head

value: 40 weeks

value: 10 month, naive


title: Adult human cardiomyocytes_SARS-CoV-2_2


title: L2: Stem LAC-treated 2

value: Stem


title: Fly head rep2

city: Guangzhou

first: Rui

last: Zhang

address: No. 135, Xingang Xi Road

institute: Sun Yat-sen University

data_processing:
Adapters were trimmed with cutadapt-1.13 (-e 0.25 -q 25 –trim-n -a NNNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A NNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAG). Adapter-trimmed reads were quality trimmed with Trimmomatic-0.36 (PE mode, HEADCROP:10 SLIDINGWINDOW:4:22 AVGQUAL:25 MINLEN:40).
Clean reads were mapped to Ensembl GRCh37.75 genome and transcriptome with hisat2-2.10 (-k 10, --fr, --rna-strandness FR --no-mixed), uniquely alignment only0. Unmapped reads were further mapped to transcriptome with bowtie2-2.2.9 (-end-to-end, --fr --gbar 5, --mp 5, -k 10, -R 2, -D 5). Unique alignments mapped to the same gene location were used. Transcriptome alignments were liftOver to genomic coordinates with a custom script. Hisat2 alignmets and bowtie2 alignmets were merged.
Pileup was performed using samtools API pysam to get base counts.
Custom scripts were used to call m5C sites from samples:  (i) C+T coverage >= 20; (ii) C count >= 3; (iii) m5C level >= 0.1; (iv) signal ratio >= 0.9 at certain C-cutoff (mostly at 2-5) and (v) one-side binomial P value < 0.001
Genome_build: BDGP5.78
Supplementary_files_format_and_content: CSV for the position, coverage, and methylation level for the samples

source_name: Head

extract_protocol:
Total RNA was isolated with TRIzol reagent and Direct-zol RNA MiniPrep kit; for cytoplasm/nuclear fractions, cells were fractionated using the PARIS kit (Ambion) according to the manufacturer’s instructions. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads (Vazyme).
100ng-1μg of polyadenylated RNA was converted using the EZ RNA methylation kit (Zymo Research) with 3 cycles of [70 C 10 min, 64 C 45 min] and 37 C 30 min for desulfonation. The converted RNA was fragmented into 150~200 nt fragments by incubation at 94 °C for 8 minutes in fragmentation buffer (NEBNext Ultra II Directional RNA Library Prep Kit, NEB). The fragmented RNA was then used for library construction, following the manufacturer’s protocol (NEBNext Ultra II Directional RNA Library Prep Kit, NEB).

value: Wildtype

value: Head


title: ONLR [TJb3-7]

description:
aged naïve mice
ONR3

value: wild type


title: Adult human cardiomyocytes_SARS-CoV-2_1


title: Fly head rep1


title: Adult human cardiomyocytes_Mock_3


title: ONLR [TJb3-6]

description:
aged naïve mice
ONR2


title: L1: Stem LAC-treated 1

value: Golden Wonder


title: Adult human cardiomyocytes_Mock_2


title: F3: Stem FZB-treated 3