title: wild-type Col-0, 4d, root, +P, +N [WT_F_K]

city: Jena

first: Ralf

last: Oelmüller

address: Dornburger Str. 159

department: Plant Physiology

institute: Friedrich-Schiller-University Jena

data_processing:
RNAseq libraries were filtered and quality-trimmed with fastp v0.23.2
Read qualities were monitored by FastQC v0.11.3
Hisat2 v2.2.1 was used with default parameters to map the quality-trimmed RNAseq libraries to the A. thaliana reference genome (TAIR10, Ensembl release 51). The mapping allowed spliced reads and single-read mapping to multiple best-fitting locations.
FeatureCounts v1.5.3 was applied to perform read counting based on the A. thaliana reference annotation (TAIR10, Ensembl release 51).
The Bioconductor DESeq2 (v1.10.0) package was utilized to identify DEGs in the different pairwise wild type comparisons.
Benjamini and Hochberg’s False Discovery Rate (FDR) approach was employed to adjust the calculated p-values for multiple testing.
Assembly: TAIR10, Ensembl release 51
Supplementary files format and content: excel sheets show comparisons to the respective control condition (-N vs +N), E_G vs E_J, E_H vs E_K, F_G vs F_J and F_H vs F_K.

organism: Arabidopsis thaliana

source_name: whole root

growth_protocol: Arabidopsis thaliana seeds (Col-0) were surface-sterilized and sown on N-free MGRL medium supplemented with 2.5 mM NH4NO3 and 3 g/L gelrite. The KNO3 and Ca(NO3)2 in the MGRL medium were replaced by KCl and CaCl2 to ensure ion equilibrium. After 48 h of stratification at 4 °C in the dark, the seeds were transferred to long-day conditions with 22 °C, 16 h light/8 h dark, 80 μmol m−2 s−1 for 10 days. Piriformospora indica was cultured on Kaefers medium as described before (Johnson et al., 2011, Johnson et al., 2013). As described previously, plugs of a 4-week old fungal culture were used for co-cultures with the seedlings. The fungus was pre-grown for 7 days on PNM medium (PNM+N) with a nylon membrane in the dark at 22 °C. For N limiting conditions (0 mM total N, PNM-N), KNO3 and Ca(NO3)2 were replaced by KCl and CaCl2. For control plates without fungus, only empty KM plugs were placed on top of the membrane.

extract_protocol:
Samples of root or shoot material was stored in -80 °C. For homogenization, the samples were ground with mortar and pistil in liquid nitrogen. A maximum of 100 mg material was used for RNA extraction. RNA was extracted with TrizolTM (ThermoFisher Scientific, Waltham, USA) and chloroform according to the manufacturers protocol. The RNA isolation was followed by an additional cleaning step to remove access salts originating from the fungus tissue. For that, the sample was mixed with 3 M sodium acetate [1/10 (v/v) in RNAse-free water, pH= 5.2] and 600 µL of ice-cold 100 % ethanol and incubated at -20 °C for at least 1 hr. After centrifugation and 2 cleaning steps with 80 % ethanol the sample was resuspended in RNAse-free water.
Library construction was done by Novogene Genomics Service (Cambridge, UK).

treatment_protocol: For plant-fungus co-cultures for 4 days, 4 plants (per petri dish) were placed on top of the pre-grown fungal lawn as described previously (Johnson et al., 2013), with some adaptations. Plates were sealed with 3MTM Micropore tape to reduce the condensation and 10 d-old plants were used for co-cultivation, to reduce the amount of N which accumulates in the plants on MGRL medium before the co-culture. In pilot experiments, we showed that the reduced age did not affect the establishment of the symbiosis with the fungus. The co-cultures were incubated at 22 °C, 16 h light/8 h dark, 80 μmol m−2 s−1 with light from the top. After 2 days, roots and shoots of the plants were harvested separately. For that, 5 plates (= 20 plants) were harvested as 1 sample. Both roots and shoots were washed in sterile distilled water and carefully dried before weighing and direct freezing in liquid nitrogen. Samples were stored in - 80 °C until further use. These experiments were repeated 3-4 times independently.

value: root

value: whole root

value: w fungus, w N


title: RSB241-76 [Epinephrine Bitartrate]

status: Public on Oct 19 2023

type: SRA

city: Boston

first: Zhiyun

last: Wei

state: Massachusetts

address: 60 Fenwood Road

department: Neurology

country: USA

institute: Brigham and Women's Hospital

library_source: transcriptomic

data_processing:
FastQ files were trimmed of adapter sequences using Cutadapt with the following parameters: cutadapt -u 1 -a TGGAATTCTCGGGTGCCAAGG -m 15.
Trimmed reads were aligned to miRBase 21 (hg38) by using Bowtie.
Assembly: hg38
Supplementary files format and content: tab-delimited Excel files include read count for each Sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: Induced pluripotent stem cell (iPSC) lines were retrieved and differentiated into neurons with NGN2 expression, as previously reported. Briefly, iPSCs were plated in mTeSR1 media at a density of 9.5x104 cells/cm2 on Matrigel (Corning #354234)-coated plates. Cells were then transduced with the following virus: pTet-O-NGN2-puro (Addgene #52047): 0.1 μL per 5x104 cells; Tet-O-FUW-eGFP (Addgene #30130): 0.05μL per 5x104 cells; Fudelta GW-rtTA (Addgene #19780): 0.11 μL per 5x104 cells. Transduced cells were dissociated with Accutase (StemCell Technologies) and plated onto Matrigel-coated plates in mTeSR1 (StemCell Technologies) at 5x104/cm2 (Day 0). On day 1, media was changed to KSR media (Knockout DMEM, 15% KOSR, 1x MEM-NEAA, 55 μM beta-mercaptoethanol, 1x GlutaMAX; Gibco) with doxycycline (2 μg/ml, Sigma-Aldrich). Doxycyline was maintained in the media for the remainder of the differentiation. On day 2, the media was changed to 1:1 KSR: N2B media with puromycin (5 μg/ml, Gibco), where N2B was composed of DMEM/F12, 1x GlutaMAX, 1x N2 supplement B (StemCell Technologies) and 0.3% dextrose (Sigma-Aldrich). Puromycin was maintained in the media throughout the differentiation. On day 3, the media was changed to N2B media + 1:100 B-27 supplement (GIBCO) and puromycin (10 μg/ml). From day 4 on, cells were cultured in NBM media (Neurobasal medium, 0.5x MEM-NEAA, 1x GlutaMAX, 0.3% dextrose) + 1:50 B-27 + BDNF, GDNF, CNTF (10 ng/ml each, Peprotech). After day 4, half of the media was replaced by fresh media twice per week. Cells were stocked on day 4 at 1~2x106 cells in 200 μL freezing media (50% day 4 media + 40% FBS + 10% DMSO) per cryovial in -80oC overnight, followed by liquid nitrogen storage. Twenty-five 96-well plates (Corning) were coated with Matrigel solution (0.2 mg/mL in DMEM/F12) at 60 μL per well for 1.5 hours at 37oC. Then, the Matrigel solution was completely removed, and 100 μL PBS (Gibco) was added per well using electronic 12-channel pipettes in speed 3 (e12c-pip; Eppendorf). The plates were temporality incubated at 37oC. Frozen day 4 iPSC-iNs were thawed in 500 μL pre-warmed resuspension media per vial, which was composed of NBM, 1:100 B27, and 1:1000 ROCKi (StemCell Technologies), and were kept in a warm metal bath to facilitate the thawing. Multiple vials were pooled into one 50 mL conical tube, then pre-warmed resuspension media were added drop-wisely to reach the volume of 40 mL. After gently mixing by reverting the tube, viable cell concentration was counted with trypan blue (Bio-Rad). The cells were spun down (220 g, 5 min, room temperature) and resuspended in day 4 media at 1x105 cells/mL. Then, PBS was completely removed from the plates, and 100 μL cell suspension was added per well, using e12c-pip at speed 3. The cells were incubated at 37oC after shaking the plates for even distribution (day 4). To reduce evaporation during incubation, plates were kept in plastic containers lined with sterile wet paper towels. On day 5, an additional 100 μL pre-warmed day 4 medium was added per well using e12c-pip in speed 1. On days 7/10/14/18, 95 μL conditioned medium was removed, and 100 μL pre-warmed day 4 medium was added per well, both using e12c-pip.

extract_protocol:
On day 20, four 10x photos were taken per well automatically using the ImageXpress Micro Confocal microscope (Molecular Devices). Then, the media in the plates was removed with approximately 20 μL media left, using a 24-channel stainless steel manifold (Drummond #3-000-101) linked with a vacuum at a low speed. With the help of Multidrop™ Combi Reagent Dispenser (Thermo Scientific) and the standard cassette (speed: low), 250 μL ice-cold DPBS (Wisent) was added per well. The DPBS was removed with approximately 20 μL liquid left, using another 24-channel stainless steel manifold linked with the vacuum at a low speed. The residual DPBS was completely removed using a mechanic 12-channel pipette. Next, 45 μL lysing solution was added per well using another Multidrop™ Combi Reagent Dispenser with the small cassette (speed: low), where the lysing solution is composed of single-cell lysis buffer (Takara #635013): 1x RNase Inhibitor Murine (NEB): nuclease-free water (Exiqon) = 19:1:190. Thorough lysis was achieved by shaking the plates on a shaker for 5 min at room temperature. The lysis samples were transferred from four 96-well plates to each 384-square-well plate using the 96-well module-coupled VPrep liquid handler (Agilent) with 30 μL tips (twice without changing tips). After sealing, the 384-square-well plates were spun down at 4000 rpm for 5 min, and 10 μL supernatant was aliquoted to a 384-well plate (Eppendorf) using the 384-well module-coupled VPrep liquid handler. The plates were finally sealed with the PlateLoc Heat Sealer (Agilent) and stored at -20oC.
To avoid RNA purification, we used RealSeq-T technology (RealSeq Biosciences) following manufacturer recommendations. In summary, cell lysates were incubated at 70C for 5 minutes on RealSeq hybridization buffer (100 mM NaCl, 50 mM Tris-HCl, 10 mM MgCl2, 1mM DTT, pH 7.9) with 1x RealSeq biotinylated DNA probes to target all miRNAs in miRbase 21. After 2 hours of incubation at 37C, 10 μL of RealSeq Beads were added, and miRNAs were captured using a 384-well Magnet Plate (Alpaqua, MA). Following three washes with RealSeq Wash buffer, miRNA was eluted from beads in 10uL of RNase-free water. All the miRNA elusion was input to prepare sequencing libraries with RealSeq-Biofluids following manufacturer instructions (RealSeq Biosciences). In summary, a single adapter and circularization approach was used. Libraries were barcoded with dual indexes and sequenced with a NextSeq 550 (Illumina, CA).

treatment_protocol: On day 19, half (three 384-well plates) of the Selleck bioactive compound library (N=1902 compounds) were pin transferred (V&P Scientific) to twelve NGN2-iN plates using the Seiko Compound Transfer Robot at 200 nL per well (final concentration at 10 μM). Positive control (Forskolin) and negative control (DMSO) were also pin transferred to the wells without library compound. The other half (three and a quarter 384-well plates) of the compound library were added to the remaining thirteen 96-well plates after one day delay (on day 20), using the identical protocol due to the time consumption.

tag: cell line

tag: cell type

value: Human NGN2-driven iPSC-derived neurons

tag: treatment

value: Epinephrine Bitartrate


title: RSB241-91 [Cyclocytidine HCl]

value: Cyclocytidine HCl


title: WT, midlog, fructose, A

city: Edinburgh

first: Peter

middle: S

last: Swain

address: CH Waddington Building, Mayfield Road

department: School of Biological Sciences

country: United Kingdom

institute: University of Edinburgh

data_processing:
The data processing pipeline is written in Nextflow and the repository is available at: https://git.ecdf.ed.ac.uk/s1856140/rnaseq-paired-end
Run FastQC v0.11.9 to produce a quality control report for the input data for every sample
Cut sequencing adapters from 3' end of gene with Cutadapt v1.18
Align reads to genome with HISAT2 v2.1.0
Turn unsorted aligned SAM files into sorted indexed compressed BAM files with SAMtools v1.11
Make bedgraphs showing coverage of aligned reads with BEDTools v2.30.0.
Run featureCounts (in Subread v2.0.0) to count aligned reads to genes for all processed samples
Run multiQC v1.13 to collate single quality control report across all samples.
Assembly: R64-1-1
Supplementary files format and content: CSV file that includes the counts per million reads (CPM) of each gene in each sample in a tidy format.

organism: Saccharomyces cerevisiae

growth_protocol: (1) FY4 (Brachmann et al, Yeast, 1998) cells were pre-cultured in media supplemented with 2% (w/v) sodium pyruvate in a 30C shaking incubator at 180 rpm for 40 hours, and diluted 6-fold with fresh media 6 hours before the experiment. (2) When the experiment began, the cells were washed twice with minimal (Delft) media without carbon sources and then inoculated into 250 mL flasks with 25 mL minimal (Delft) media supplemented with desired concentrations of fructose and palatinose. The volume of inoculated cells was calculated such that the initial OD was 0.05, and then the volume of each culture was topped up to 26 mL. (3) The cultures were then incubated in a 30C shaking incubator at 180 rpm.

extract_protocol:
For each sample, we harvested x mL of cells, such that the value of OD*x is around 4, by centrifuging the cells at 3500 rpm for 3 minutes at 4C. The supernatant was then removed and the cell pellets were stored in -80C. (2) We followed a column-based protocol on protocol.io to extract RNA: dx.doi.org/10.17504/protocols.io.beetjben, starting from Step 16 without using the deep well plate. Sample quality control was performed on the Fragment Analyser Automated Capillary Electrophoresis System (Agilent Technologies Inc, #5300) with the Standard Sensitivity RNA Analysis Kit (#DNF-471-0500) for quality, and on the Qubit 2.0 Fluorometer (Thermo Fisher Scientific Inc, #Q32866) with the Qubit RNA broad range assay kit (#10210) for quantification. The Qubit dsDNA HS assay kit (#Q32854) was used to quantify DNA contamination.
Libraries were generated from 400 ng of each total RNA sample with the QuantSeq 3' mRNA Library Prep Kit REV for Illumina (Lexogen Inc, #016) according to the manufacturer's protocol. A Custom Sequencing Primer (CSP Version 5, included in the kit) was used for Read 1. The libraries were then quantified by fluorometry with the Qubit dsDNA High Sensitivity assay, followed by assessment of quality and fragment size with the Agilent Fragment Analyser with the SS NGS Fragment 1--6000bp kit (#DNF-473-33). Sequencing was  performed  on  the  NextSeq 2000 platform (Illumina  Inc, #20038897) using NextSeq 1000/2000 P2 Reagents (100 Cycles) v3 (#20046811).

tag: genotype

value: wildtype

value: 0.1% fructose

tag: time

value: mid-log


title: wild-type Col-0, 4d, root, -P, +N [WT_F_J]

country: Germany

tag: tissue

value: w/o fungus, w N


title: RSB241-225 [Ibuprofen]

value: Ibuprofen


title: L506-34C-ATAC-rep2

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

library_source: genomic

data_processing:
(read alignment, ATAC-seq and MeDIP-seq data)  Bowtie 1.0.1
(bigWig file generation)  custom code
(read alignment, SMF data)  bwa-meth
(read alignment, 5-hmU chemical conversion data)  slamdunk
Assembly: custom and GCA_000507305.1_ASM50730v1 for Breviolum minutum, hg38 for human, sacCer3 for S. cerevisiae; C_glabrata_CBS138 for Candida albicans
Supplementary files format and content: bedGraph of read coverage, normalized to RPM for bigWig files for ATAC-seq and MeDIP-seq; slamdunk output for 5-hmU conversion datasets; MethylDacket bedGraph output for SMF datasets

molecule: genomic DNA

organism: Bigelowiella natans

growth_protocol:
(B. minutum)  The clonal axenic Symbiodinium/Breviolum minutum strain SSB01 was used. Stock cultures were grown in Daigo's IMK medium for marine microalgae (Wako Pure Chemicals) supplemented with casein hydrolysate (IMK+Cas) at 27C at a light intensity of 10 µmol photons m-2s-1 from Philips ALTO II 25-W bulbs on a 12-h-light:12-h-dark cycle. The medium was prepared in artificial seawater (ASW).
(yeast)  Standard yeast cell culture practices were followed. Cells were grown in YPD media at 30C until harvesting.

extract_protocol:
ATAC-seq experiments were performed following the omniATAC protocol. Briefly, ∼100K B. minutum cells were centrifuged at 1,000 g, then resuspended in 500 µL 1× PBS and centrifuged again. Cells were then resuspended in 50 µL ATAC-RSB-Lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630, 0.1% Tween-20, 0.01% Digitonin) and incubated on ice for 3 minutes. Subsequently 1 mL ATAC-RSB-Wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.01% Digitonin) were added, the tubes were inverted several times, and nuclei were centrifuged at 500 g for 5 min at 4◦C. Transposition was carried out by resuspending nuclei in a mix of 25 µL 2× TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2, 20% Dimethyl Formamide), 2.5 µL transposase (custom produced) and 22.5 µL nuclease-free H2O, and incubating at 37◦C for 30 min in a Thermomixer at 1000 RPM.
Transposed DNA was isolated using the MinElute PCR Purification Kit (Qiagen Cat# 28004/28006), and PCR amplified for 10 cycles using the usual ATAC-seq settings. Libraries were purified using the MinElute kit, then sequenced on a Illumina NextSeq 550 instrument as 2x36mers.

value: whole flagellate

tag: sample type

value: B. minutum 34C ATAC-seq

tag: chip antibody


title: SD rats 1 (S1), DON implant, 2 week

city: Guangzhou

first: Rongjie

last: Wu

address: Yuexiu District, 106, Zhongshan Road

country: China

institute: Guangdong Pronvincial People's Hospital

description:
1DON_2W_1
Gene expression.csv

data_processing:
The raw data was handled by Skewer and data quality was checked by FastQC (v0.11.2).
Clean reads were aligned to the referance genome using STAR(2.5.3a).
The expression of the transcript was calculated by FPKM (Fragments Per Kilobase of exon model per Million mapped reads) using StringTie (v1.3.1c).
Differentially expression genes(DEGs) were determined by DEGseq2(v1.16.1).
Assembly: rn6
Supplementary files format and content: Gene expression.csv contain FPKM value for each sample

organism: Rattus norvegicus

source_name: spinal cord

extract_protocol:
Total RNA was isolated from each sample using RNAiso Plus (TARAKA).
Libraries were constructed using VAHTS Stranded mRNA-seq Library Prep Kit for Illumina (Vazyme, China), and sequencing was carried out using the Illumina Novaseq 6000 instrument by the commercial service of Genergy Biotechnology Co. Ltd. (Shanghai, China).

value: spinal cord

tag: strain

value: Sprague-Dawley

value: DON implant


title: wt90m, biol rep 1, injury

city: Irapuato

first: Alfredo

last: Herrera Estrella

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León

department: LANGEBIO

country: Mexico

institute: CINVESTAV

data_processing:
Non-barcoded sequencing reads were trimmed to remove the first ten bases from the start of the read.
Trimmed sequence reads were mapped to a new version of Trichoderma atroviride assembled genome (accession number: JAEAGS000000000) using HISAT2 (V. 2.2.1). Then, reads overlapping each gene model were counted using HTseq (V 2.0.2).
Gene expression analysis was performed using the edgeR package in R.
Assembly: JAEAGS000000000
Supplementary files format and content: The text file, raw_counts.txt, contains a raw count (CPM) matrix.
Supplementary files format and content: Text files contain raw count (CPM) values for each sample.

organism: Trichoderma atroviride

source_name: Mycelium

growth_protocol: All strains were propagated in potato dextrose agar (PDA; Difco) at 27 °C in complete darkness, before and after injury.

extract_protocol:
Harvested mycelium was immediately frozen with liquid nitrogen. Then, total RNA was extracted with Trizol.
RNA libraries for RNA-seq were prepared using MGIEasy RNA Library Prep Set following the manufacturer's protocols.

treatment_protocol: 36 h old vegetative mycelium (grown in PDA) was damaged using a sterile scalpel to generate injury squares of 0.5 cm x 0.5 cm. Then, damaged mycelium was harvested after 90 min and 4 h (injury), or 0 h (undamaged mycelium or control).

value: Mycelium

tag: background strain

value: 90 minutes

value: WT

value: injury


title: wild-type Col-0, 4d, root, +P, -N [WT_F_H]

value: root

value: whole root

value: w fungus, w/o N


title: L504-27C-ATAC-rep2

value: B. minutum 27C ATAC-seq


title: RSB241-216 [Vildagliptin (LAF-237)]

value: Human NGN2-driven iPSC-derived neurons

value: Vildagliptin (LAF-237)


title: L505-34C-ATAC-rep1


title: wtc, biol rep 1, control

value: 0 h

value: control


title: L1921-GM19_rep2

organism:
Saccharomyces cerevisiae
Candida albicans

extract_protocol:
M.CviPI Reaction Buffer), by resuspending nuclei with 25 µL 2× TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2, 20% Dimethyl Formamide), 2.5 µL transposase (custom produced) and 22.5 µL nuclease-free H2O, and incubating at 37◦C for 30 min in a Thermomixer at 1000 RPM.
Transposed DNA was isolated using the MinElute PCR Purification Kit (Qiagen Cat# 28004/28006), and PCR amplified for 10 cycles using the usual ATAC-seq settings. Libraries were purified using the MinElute kit, then sequenced on a Illumina NextSeq 550 instrument as 2x36mers.

value: whole yeast

value: yeast expressing Hematodinium sp. DVNP.12 ATAC


title: RSB241-130 [Brompheniramine hydrogen maleate]

value: Brompheniramine hydrogen maleate


title: wild-type Col-0, 4d, root, -P, -N [WT_F_G]

value: w/o fungus, w/o N


title: L503-27C-ATAC-rep1

value: whole flagellate


title: L1920-GM19_rep1

extract_protocol:
ATAC-seq was carried out on the nuclei isolated the same way as for SMF (before resuspension in
Transposed DNA was isolated using the MinElute PCR Purification Kit (Qiagen Cat# 28004/28006), and PCR amplified for 10 cycles using the usual ATAC-seq settings. Libraries were purified using the MinElute kit, then sequenced on a Illumina NextSeq 550 instrument as 2x36mers.


title: RSB241-254 [Solifenacin succinate]

value: Solifenacin succinate


title: RSB241-149 [Moexipril HCl]

value: Moexipril HCl


title: L1919-GM18_rep2

value: yeast expressing B. minutum DVNP symbB.v1.2.006931 ATAC


title: wild-type Col-0, 4d, shoot, -P, +N [WT_E_J]

source_name: whole rosette

value: shoot

value: whole rosette

value: w/o fungus, w N


title: RSB241-239 [Ipratropium Bromide]

value: Ipratropium Bromide


title: L1918-GM18_rep1


title: PZH, replicate2

city: fuzhou

first: yangfan

last: zhang

address: Fujian Normal University Qishan Campus, College Town, Fuzhou, Fujian Province

institute: FJNU

data_processing:
The sequencing quality were assessed with FastQC (v0.11.5) and then low quality data were filtered using NGSQC (v2.3.3)
The clean reads were then aligned to the reference genome using HISAT2 (v2.1.0)  with default parameters
The processed reads from each sample were aligned using HISAT2 against the reference genome.
The gene expression analyses were performed with StringTie (v1.3.3b). DESeq(v1.28.0) was used to analyze the DEGs between samples.
Assembly: mm 10
Supplementary files format and content: tab-delimited text files including raw counts data for each samples

source_name: Human colon

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) and assessed with Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and Qubit Fluorometer (Invitrogen),1 μg total RNA meet the following requirements were used in subsequent experiments: RNA integrity number (RIN) > 7.0 and a 28S:18S ratio > 1.8.RNA-seq libraries were generated and sequenced
The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) was used to construct the libraries for sequencing. NEB Next Poly(A) mRNA Magnetic Isolation Module (NEB) kit was used to enrich the poly(A) tailed mRNA molecules from 1 μg total RNA. The mRNA was fragmented into ~200 base pair pieces

value: Human colon

value: epithelial cells

value: ras mutation

value: PZH treatment


title: L1917-GM17_vehcile_DVNP_ON_rep2

value: yeast empty vehicle control (turned on) ATAC


title: RSB241-288 [Naloxone HCl]

value: Human NGN2-driven iPSC-derived neurons

value: Naloxone HCl


title: PZH, replicate4


title: wild-type Col-0, 4d, shoot, +P, -N [WT_E_H]

value: w fungus, w/o N


title: wild-type Col-0, 4d, shoot, -P, -N [WT_E_G]

value: w/o fungus, w/o N


title: PZH, replicate3


title: RSB241-272 [BML-190]


title: DMSO, replicate4

value: DMSO as control


title: RSB241-203 [Cefoperazone]

value: Cefoperazone


title: L1915-GM17_vehcile_DVNP_rep2

value: whole yeast

value: yeast empty vehicle control (not turned on) ATAC


title: DMSO, replicate3


title: PZH, replicate1


title: L1914-GM17_vehcile_DVNP_rep1


title: Tumor-derived cell line from 690108 (TOPCDS), HA-tag ChIP

city: Durham

last: Hendrickson

state: North Carolina

address: 308 Research Drive

institute: Duke University

data_processing:
Raw sequencing reads were trimmed using Trimmomatic v0.39 (ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 MINLEN:36).
Trimmed reads were aligned to the mm10 reference genome using Bowtie 2 (-q -t --no-mixed --no-discordant).
Duplicate reads were marked and removed using Picard tools v2.18.2 and peaks were called with MACS3 (-B -f BAMPE -g 1.87e9 -q 0.01).
bigWig files were generated using bamCoverage (-of bigwig --numberOfProcessors max/2 --effectiveGenomeSize 2652783500 --normalizeUsing CPM)
Assembly: mm10 (GRCm38.102)
Supplementary files format and content: rawCounts.txt
Supplementary files format and content: normalizedCounts.txt

organism: Mus musculus

growth_protocol: Using aspetic technique, tumors were resected from euthanized animals and divided into two. Half of the tissue was enzymatically and mechanically digested by serial pipetting. Washed cells were resupeneded in PBS and filtered through a 70um cell strainer before plating in DMEM medium containing 10%FBS and 1X GA-1000 (standard growth medium). Viable adherent cells were maintainined in standard growth medium and passaged with 0.25% trypsin-EDTA.

extract_protocol:
ChIP was performed using the Active Motif ChIP-IT High Sensitivity kit (ActiveMotif, CA, USA). In brief, cells were seeded into 150mm dishes and cultured in standard growth medium. At 80% confluency, the cells were crosslinked in 37% formaldehyde (with methanol) for 15 minutes on plate and quenched with glycine.  Washed cell pellets were manually lysed using a dounce homogenizer and the chromatin was fragmented using a Q125 sonicator (Qsonica, CT, USA) with the following settings: 25% amplitude, 30 seconds ‘ON’/30 seconds ‘OFF’ for 20 minutes total. Separate immunoprecipitation reactions using an Anti-HA tag antibody (Abcam; ab9110) or anti-Histone H3K27ac antibody (ActiveMotif, 39134) were setup for overnight immunoprecipitation reactions at 4C. ChIP DNA was bound to Protein G agarose beads, column purified, and eluted.
1-10ng of purified ChIP DNA (or input) was used to make 150bp paired-end libraries for sequencing using the TruSeq DNA library Prep Kit (Illumina, CA, USA)

value: Anti-HA tag (Abcam; ab9110)


title: Tumor-derived cell line from 690108 (TOPCDS), H3K27Ac ChIP

value: Anti-Histone H3K27ac (ActiveMotif, 39134)


title: DMSO, replicate2


title: L1916-GM17_vehcile_DVNP_ON_rep1


title: RSB241-55 [Potassium Iodide]

value: Potassium Iodide


title: wild-type Col-0, 4d, shoot, +P, +N [WT_E_K]

value: shoot

value: whole rosette

value: w fungus, w N


title: L1913-GM16_Haematodinium_DVNP_ON_rep2

value: yeast expressing Hematodinium sp. DVNP.5 (turned on) ATAC


title: RSB241-262 [Semaxanib (SU5416)]

value: Semaxanib (SU5416)


title: Tumor-derived cell line from 690001 (Ai9CDS), H3K27Ac ChIP


title: Tumor-derived cell line from 690001 (Ai9CDS), HA-tag ChIP


title: L1912-GM16_Haematodinium_DVNP_ON_rep1


title: RSB241-177 [Almotriptan Malate]

value: Almotriptan Malate


title: shNCDDP3

city: Beijing

first: Xiaoyang

last: Han

address: Qihelou

department: Beijing Obstetrics and Gynecology Hospital

institute: Capital Medical University

data_processing:
Data filter
Comparative analysis
Expression analysis
Enrichment analysis
Assembly: GRCh38.100.chr
Supplementary files format and content: count
Supplementary files format and content: fpkm

extract_protocol:
RNA was extracted using Trizol method. Total RNA with nuclease free water to final volume of 50µl is used for construction of sequencing library.
Using the fragmented RNA as a template, a random primer was used for reverse transcription to achieve the synthesis of the first strand of cDNA, and the addition of 2nd Strand Marking Bu er and 2nd StrandAfter end repair, addition of base A, sequencing connector, magnetic bead screening and recovery of the target fragment, PCR amplification were carried out to complete the entire library preparation work. Enzyme Mix to synthesize the second strand of cDNA.After the library construction is completed, preliminary quantification is performed using Qubit3.0, the library is diluted to 1ng/ul, and then Agilent is used 2000.The raw off machine sequences (Raw Reads) obtained from Illumina platform sequencing are processed through processes such as removing low-quality sequences and connector contamination to obtain high-quality sequences (Clean Reads). All subsequent analyses are based on Clean Reads

value: ovarian cancer

value: shNCDDP


title: L1911-GM16_Haematodinium_DVNP_rep2

value: yeast expressing Hematodinium sp. DVNP.5 (not turned on) ATAC


title: shNCDDP1


title: Tumor-derived cell line from 690001 (Ai9CDS), Input


title: RSB241-238 [Clindamycin]

value: Human NGN2-driven iPSC-derived neurons

value: Clindamycin


title: Tumor-derived cell line from 690108 (TOPCDS), Input


title: L1605-DVNP_GM06_rep2

value: yeast expressing Hematodinium sp. DVNP.12 ATAC


title: shNCDDP2


title: Tumor KP sarcoma

data_processing:
Raw sequencing reads were trimmed using Trimmomatic v0.39 (ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 MINLEN:36).
Trimmed reads were aligned to the mm10 reference genome using default parameters in STAR v2.7.10a
FeatureCounts (Subread v2.0.3) was used to compile a raw count table from sorted and indexed BAM files
Raw counts were loaded into DESeq2 for normalization and differential expression analysis.
Assembly: mm10 (GRCm38.102)
Supplementary files format and content: rawCounts.xlsx
Supplementary files format and content: normalizedCounts.xlsx

source_name: Tumor

extract_protocol:
RNA was extracted and purified from flash frozen tumors/normal tissues and cells using a Qiagen RNeasy kit following the manufacturer’s instructions for fibrous tissue (Qiagen, Hilden, Germany).
High quality RNA (RIN >7) was divided into triplicate and used to make 150bp paired-end, rRNA-depleted, libraries using the Illumina TruSeq RNA library Prep Kit (Illumina, CA, USA).

value: Tumor

value: KrasG12D, p53fl/fl


title: L1910-GM16_Haematodinium_DVNP_rep1

value: whole yeast


title: Tumor from 690108 (TOPCDS)


title: RSB241-104 [Sulbactam sodium]

value: Sulbactam sodium


title: Normal skeletal muscle from hindlimb

source_name: Tissue

value: Tissue

value: Skeletal muscle

value: WT


title: RSB241-168 [RS-127445]


title: DMSO, replicate1

value: Human colon

value: epithelial cells

value: ras mutation

value: DMSO as control


title: L1604-DVNP_GM06_rep1


title: L1602-DVNP_GM05_rep1

value: yeast expressing B. minutum DVNP symbB.v1.2.006931 ATAC


title: Tumor from 690001 (Ai9CDS)


title: L1603-DVNP_GM05_rep2


title: RSB241-100 [Acetanilide]

value: Acetanilide


title: RSB241-338 [Ulipristal]

value: Ulipristal


title: L1601-Control_MS47_rep2

value: yeast control ATAC


title: shFLOT2-2

city: Changsha

first: caiping

last: ren

address: No 87 Xiangya Road

institute: Xiangya Hospital, Central South University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions
The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts
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
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Assembly: reference sequence used for read alignment
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes RPKM counts for each sample

source_name: nasopharynx

growth_protocol: 5-8F cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (Gibico) and 1% antibiotics (100 U/ml penicillin and 0.1mg/ml streptomycin)

extract_protocol:
RNA was extrated using TRIZOL reagent.  A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
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

treatment_protocol: 5-8F cells were transfected by shCD109 and shFLOT2 plasmids respectively, and treated by 2 μg/ml of puro solution

value: nasopharynx

value: nasopharyngeal carcinoma cell line

value: FLOT2 knockdown


title: shCD109-2

value: CD109 knockdown


title: Tumor-derived cell line from KP sarcoma

source_name: Cell line

value: Cell line

value: Tumor

value: KrasG12D, p53fl/fl


title: shCD109-3


title: RSB241-273 [DL-Carnitine HCl]

value: Human NGN2-driven iPSC-derived neurons

value: DL-Carnitine HCl


title: L1600-Control_MS47_rep1

value: whole yeast


title: C2C12 Cells

value: Myoblasts

value: WT


title: RSB241-68 [Bupivacaine HCl]

value: Bupivacaine HCl


title: L1635-DVNP_GM06_dSMF_EM-seq

data_processing:
(read alignment, ATAC-seq and MeDIP-seq data)  Bowtie 1.0.1
(bigWig file generation)  custom code
(read alignment, SMF data)  bwa-meth
(read alignment, 5-hmU chemical conversion data)  slamdunk
Assembly: custom and GCA_000507305.1_ASM50730v1 for Breviolum minutum, hg38 for human, sacCer3 for S. cerevisiae; C_glabrata_CBS138 for Candida albicans
Supplementary files format and content: bedGraph of read coverage, normalized to RPM for bigWig files for ATAC-seq and MeDIP-seq; slamdunk output for 5-hmU conversion datasets; MethylDacket bedGraph output for SMF datasets
Library strategy: SMF

extract_protocol:
Yeast SMF experiments were carried out as follows. A 1:1 mixture of S. cerevisiae cells expression DVNPs and Candida albicans cells (used as a control for normalization) amounting to a total of 2.5×108 cells was used as input. Cells in log phase (OD660 ≤ 1.0) were first centrifuged at 13,000 rpm for 1 minute, then washed with 100 µL Sorbitol Buffer(1.4 M Sorbitol, 40 mM HEPES-KOH pH 7.5, 0.5 mM MgCl2), and centrifuged again at 13,000 rpm for 1 minute. Cells were then spheroplasted by resuspending in 200 µL Sorbitol Buffer with DTT added at a final concentration of 10 mM and 0.5 mg/mL 100T Zymolase, followed by incubating for 5 minutes at 30◦C at 300 rpm in a Thermomixer. The pellet was centrifuged for 2 minutes at 5,000 rpm, washed in 100 µL Sorbitol Buffer, and centrifuged again at 5,000 rpm for 2 minutes. Cells were then resuspended in 100 µL ice-cold Nuclei Lysis Buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1 mM EDTA, 0.5% NP-40) and incubated on ice for 10 minutes. Nuclei were then centrifuged at 5000 rpm for 5 min at 4◦C, resuspended in 100 µL cold Nuclei Wash Buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1 mM EDTA), and centrifuged again at 5,000 rpm for 5 min at 4◦C. Finally, nuclei were resuspended in 100 µL M.CviPI Reaction Buffer (50 mM Tris-HCl pH 8.5, 50 mM NaCl, 10 mM DTT). Nuclei were then first treated with M.CviPI (GpC methyltransferase) by adding 200 U of M.CviPI (NEB), SAM at 0.6 mM and sucrose at 300 mM, and incubating at 30◦C for 7.5 min. After this incubation, 128 pmol SAM and another 100 U of enzymes were added, and a further incubation at 30◦C for 7.5 min was carried out. Immediately after, M.SssI treatment (CpG methyltransferase) followed, by adding 60 U of M.SssI (NEB), 128 pmol SAM, MgCl2 at 10 mM and incubation at 30◦C for 7.5 min. The reaction was stopped by adding an equal volume of Stop Buffer (20 mM Tris-HCl pH 8.5, 600 mM NaCl, 1% SDS, 10 mM EDTA). HMW DNA was isolated using the MagAttract HMW DNA Kit (Qiagen; cat # 67563) following the manufacturer’s instructions.
Enzymatically labeled DNA was then sheared on a Covaris E220 and converted into sequencing libraries following the EM-seq protocol, using the NEBNext Enzymatic Methyl-seq Kit (NEB, Cat # E7120L).

value: yeast expressing Hematodinium sp. DVNP.12 SMF


title: RSB241-241 [Irinotecan HCl Trihydrate]

value: Irinotecan HCl Trihydrate


title: shCD109-1


title: Tumor-derived cell line from 690065 (Ch7CDS)


title: shFLOT2-1


title: Tumor from  690065 (Ch7CDS)


title: L1634-DVNP_GM05_dSMF_EM-seq

value: yeast expressing B. minutum DVNP symbB.v1.2.006931 SMF


title: Tumor-derived cell line from 690108 (TOPCDS)


title: control-2


title: RSB241-140 [ICG-001]


title: control-1


title: RSB241-248 [Cinepazide maleate]

value: Cinepazide maleate


title: L529-dhmU-MeDIP

description:
L529-dhmU-MeDIP
Homo sapiens gDNA was used as an internal control.

organism:
Homo sapiens
Breviolum minutum

extract_protocol:
B. minutum genomic DNA was isolated as follows. Briefly, cells were centrifuged at 1,000 g for 5 minutes, then resuspended in 500 µL 1× Cell Lysis Buffer (prepared by mixing equal volumes of 2× Cell Lysis Buffer – 2% SDS, 400 mM NaCl, 40 mM EDTA, 100 mM Tris-HCl, pH 8.0 – and H2O) and vortexed. The lysed cells were mixed with an equal 500 µL volume Phenol:Chloroform:Isoamyl alcohol (25:24:1), and mixed well by inverting a few times. The phases were centrifugation at 13,000 g for 5 minutes, then the top phase was transferred to a new tube and treated with 4 µL Ribonuclease A (20 mg/mL) by incubating for 30 minutes at 37◦C. DNA was purified by adding an equal volume Phenol:Chloroform:Isoamyl alcohol (25:24:1), mixing well and centrifuging at 13,000 g for 5 minutes, then transferring the top layer to a new tube, to which Phenol:Chloroform:Isoamyl alcohol (25:24:1) was added again, and the centrifugation and top phase isolation was repeated. Then 2.5× volumes of 100% EtOH were added and the mixture was incubated on ice for 30 minutes or at -20◦C overnight. The solution was then centrifuged at 13,000 g at room temperature for 20 minutes, the pellet was washed with 70% EtOH, dried on air and resuspended in 50 µL H2O. To prepare inputs for MeDIP-seq experiments, gDNA was first sonicated using a Qsonica S-4000 with a 1/16” tip for 3 minutes, with 10 second pulses at intensity 3.5, and 20 seconds rest between pulses. For each reaction, 100 µL of Protein A Dynabeads (ThermoFisher Cat # 10002D) were washed 3 times with a 5 mg/mL BSA solution. Beads were then resuspended in 1 mL BSA solution and 5 µL of α-5-hmU antibody (Abcam Cat # ab19735) were added. Coupling of antibodies to beads was carried out overnight on a rotator at 4◦C. Beads were again washed 3 times with BSA solution and resuspended in 100 µL of BSA solution. Sheared genomic DNA (∼1 µg 1:1 mix of B. minutum and Homo sapiens) was end repaired and adapters were ligated to it following the procedure of the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S), purified using AMPure XP beads and eluted in 50 µL of H2O, and then denatured at 98◦C for 10 minutes. DNA was then immediately placed on ice, resuspended in 850 µL RIPA buffer (1× PBS, 1% IGEPAL, 0.5% Sodium Deoxycholate, 0.1% SDS, Roche Protease Inhibitor Cocktail) and added to the beads, then incubated overnight on a rotator at 4◦C. Beads were washed 5 times with LiCl buffer (10 mM Tris-HCl pH 7.5, 500 mM LiCl, 1% NP-40/IGEPAL, 0.5% Sodium Deoxycholate) by incubating for 10 minutes at 4◦C on a rotator, then rinsed once with 1× TE buffer. Beads were then resuspended in 200 µL IP Elution Buffer (1% SDS, 0.1 M NaHCO3) and incubated at 65◦C in a Thermomixer (Eppendorf) with interval mixing to dissociate antibodies. Beads were separated from the DNA solution by centrifugation, and DNA was purified using the MinElute kit.
Library generation was completed by carrying out PCR following the rest of the steps of the NEBNext Ultra II DNA Library Prep Kit protocol, using 15 cycles of amplification. Final libraries were purified using AMPure XP beads.

value: whole dinoflagellate

value: B. minutum 5-hmU MeDIP-seq

value: anti-5-hmU Abcam ab19735


title: Tumor-derived cell line from 690001 (Ai9CDS)


title: Xrn1 knock-out cells in SL media_2

city: Dallas

first: Benjamin

last: Tu

state: TEXAS

address: 5323 Harry Hines Blvd.

department: Biochemistry

institute: UT Southwestern Medical Center

description:
30x Genomics
MM14

data_processing:
Read quality assessments and trimming using FastQC and TrimGalore, respectively.
Indexing reference genome using both reference genome (S288C) and reference annotations (R64-1-1) for more accurate alignment of the reads using STAR version 2.7.3a. Following parameters were used in mapping reads  --outFilterMultimapNmax 20 \  --alignSJoverhangMin 8 \  --alignSJDBoverhangMin 1 \  --outFilterMismatchNmax 999 \  --alignIntronMin 10 \  --alignIntronMax 5000 \  --alignMatesGapMax 5000 \  --outSAMattrIHstart 0 \  --outSAMattributes Standard \
Reads with MAPQ less than 5 were removed with samtools. Using Sambamba we marked duplicates, and got alignment statistics using flagstat.
Uniquely mapped reads were quantified using featureCounts from Subread package
We used “--ignoreDup” and set “-s” to 1 for strand-specific read counting
Assembly: S288C (S. cerevisiae)
Supplementary files format and content: One tab-delimited text file include all read count values for each sample per geneid

source_name: Saccharomyces cerevisiae

growth_protocol: Strains were grown in YPL and switched to SL media for 1 hour

extract_protocol:
RNA was extracted using phenol/chloroform protocol.
RNA libraries for RNA-seq were prepared using rRNA depletion and directional library preparation by Novogene.

treatment_protocol: 2 ug total RNA was used in the construction of sequencing libraries

value: Xrn1 KO

value: SL

value: 1 hour

value: Saccharomyces cerevisiae


title: 2057-AB-6

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

library_source: transcriptomic single cell

data_processing:
data processing including quality control, read alignment and gene quantification were conducted using the 10X Cell Ranger software
Seurat was then used for normalization, data integration, and clustering analysis
Assembly: GRCh38
Supplementary files format and content: 10x cellranger output

molecule: polyA RNA

source_name: skin

extract_protocol:
Skin was harvested via punch biopsy
Samples were incubated overnight in 0.4% dispase (Life Technologies) in Hank’s Balanced Saline Solution (Gibco) at 4°C.
scRNA-seq was performed by the University of Michigan Advanced Genomics Core on the 10 Chromium system. Libraries were sequencing on the Illumina NovaSeq sequencer.

value: skin

value: Control


title: RSB241-233 [Enalaprilat Dihydrate]

value: Human NGN2-driven iPSC-derived neurons

value: Enalaprilat Dihydrate


title: Xrn1 knock-out cells in SL media_1

description:
30x Genomics
MM12


title: RSB241-337 [Tangeretin]

value: Tangeretin


title: 2057-AB-5


title: L527-Depleted

description:
L527-Depleted
Homo sapiens gDNA was used as an internal control.

value: B. minutum 5-hmU MeDIP-seq depleted control


title: L528-IgG

description:
L528-IgG
Homo sapiens gDNA was used as an internal control.

value: B. minutum 5-hmU MeDIP-seq IgG control


title: control-3

value: nasopharynx

value: nasopharyngeal carcinoma cell line

value: WT


title: Xrn1 knock-out cells in YPL media_2

description:
30x Genomics
MM13

value: YPL


title: RSB241-166 [XL335]


title: Xrn1 knock-out cells in YPL media_1

description:
30x Genomics
MM11


title: 2057-AB-3


title: L1633-Control_MS47_dSMF_EM-seq

value: whole yeast

value: yeast control SMF


title: RSB241-60 [4-Aminohippuric Acid]

value: 4-Aminohippuric Acid


title: 4902-AB-2

value: Pansclerotic Morphea Nonlesional


title: WT cells in SL media_2

description:
30x Genomics
MM10

value: SL

value: 1 hour


title: m69

city: Fukuoka

first: Tappei

last: Mishina

address: 744 Motooka Nishi-ku

country: Japan

institute: Kyushu University

description:
count_tenodera.txt.gz
tpm_tenodera.txt.gz
SuperTranscripts_tenodera.fasta
SuperTranscripts_tenodera.gff.gz

data_processing:
de novo assembly was obtained using Trinity
Clustering of assembled transcripts using Corset
Building reference SuperTranscripts using Lace
fastq files were aligned to assembled transcripts using the Hisat2 v2.1.0.
BAM files resulting from the alignments were summarized to genes using the featureCounts v1.5.1 with the parameters '-p --countReadPairs'
Assembly: SuperTranscripts for C. fukuii and T. angustipennis
Supplementary files format and content: tab-delimited text files include raw counts values for each sample; fasta files for reference SuperTranscripts; gtf annotation files for exon boundary

organism: Tenodera angustipennis

source_name: whole brain of a T. angustipennis

extract_protocol:
Total RNA was extracted from dissected praying mantis brains or whole bodies of hairworms according to the standard protocol of the RNeasy spin column kit (Qiagen). The eluted total RNA was treated with DNase I (TAKARA) and purified by ethanol precipitation with 0.3 M sodium acetate. The precipitate was dissolved in nuclease-free water.
The RNA-seq libraries were prepared using the NEBNext Ultra II RNA library Prep Kit for Illumina (NEB) according to manufacturer's protocol.

tag: manipulation status

value: before

tag: sampling year

tag: Sex

value: female

tag: c. fukuii weight (g)

tag: t. angustipennis chest length (mm)

tag: host  t. angustipennis sample name

tag: c. fukuii sample name in the host

tag: number of infected c. fukuii in the same host


title: L526-Input

description:
L526-Input
Homo sapiens gDNA was used as an internal control.

value: whole dinoflagellate

value: B. minutum 5-hmU MeDIP-seq input control


title: RSB241-49 [Deflazacort]

extract_protocol:
On day 20, four 10x photos were taken per well automatically using the ImageXpress Micro Confocal microscope (Molecular Devices). Then, the media in the plates was removed with approximately 20 μL media left, using a 24-channel stainless steel manifold (Drummond #3-000-101) linked with a vacuum at a low speed. With the help of Multidrop™ Combi Reagent Dispenser (Thermo Scientific) and the standard cassette (speed: low), 250 μL ice-cold DPBS (Wisent) was added per well. The DPBS was removed with approximately 20 μL liquid left, using another 24-channel stainless steel manifold linked with the vacuum at a low speed. The residual DPBS was completely removed using a mechanic 12-channel pipette. Next, 45 μL lysing solution was added per well using another Multidrop™ Combi Reagent Dispenser with the small cassette (speed: low), where the lysing solution is composed of single-cell lysis buffer (Takara #635013): 1x RNase Inhibitor Murine (NEB): nuclease-free water (Exiqon) = 19:1:190. Thorough lysis was achieved by shaking the plates on a shaker for 5 min at room temperature. The lysis samples were transferred from four 96-well plates to each 384-square-well plate using the 96-well module-coupled VPrep liquid handler (Agilent) with 30 μL tips (twice without changing tips). After sealing, the 384-square-well plates were spun down at 4000 rpm for 5 min, and 10 μL supernatant was aliquoted to a 384-well plate (Eppendorf) using the 384-well module-coupled VPrep liquid handler. The plates were finally sealed with the PlateLoc Heat Sealer (Agilent) and stored at -20oC.
To avoid RNA purification, we used RealSeq-T technology (RealSeq Biosciences) following manufacturer recommendations. In summary, cell lysates were incubated at 70C for 5 minutes on RealSeq hybridization buffer (100 mM NaCl, 50 mM Tris-HCl, 10 mM MgCl2, 1mM DTT, pH 7.9) with 1x RealSeq biotinylated DNA probes to target all miRNAs in miRbase 21. After 2 hours of incubation at 37C, 10 μL of RealSeq Beads were added, and miRNAs were captured using a 384-well Magnet Plate (Alpaqua, MA). Following three washes with RealSeq Wash buffer, miRNA was eluted from beads in 10uL of RNase-free water. All the miRNA elusion was input to prepare sequencing libraries with RealSeq-Biofluids following manufacturer instructions (RealSeq Biosciences). In summary, a single adapter and circularization approach was used. Libraries were barcoded with dual indexes and sequenced with a NextSeq 550 (Illumina, CA).

tag: cell line

tag: cell type

value: Human NGN2-driven iPSC-derived neurons

value: Deflazacort


title: m66


title: 2330-AB-3

value: skin


title: RSB241-231 [Phenylbutazone]

tag: treatment

value: Phenylbutazone


title: 2330-AB-1

value: Pansclerotic Morphea Lesional


title: WT cells in YPL media_2

description:
30x Genomics
MM9

tag: genotype

value: WT

value: Saccharomyces cerevisiae


title: RSB241-132 [Pioglitazone]

value: Pioglitazone


title: m62


title: WT cells in YPL media_1

description:
30x Genomics
MM7

value: YPL


title: M14A GP after print rep2

city: 北京

first: yixue

last: Luo

state: 北京市

address: Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Department of Mechanical Engineering, Tsinghua University, Beijing 100084, China

institute: 清华大学

data_processing:
Sequencing was performed with an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Reads were filtered and mapped to the reference genome sequence with Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
The fragments per kilobase of exon per million fragments mapped (FPKM) method was used to calculated gene expression levels.
Assembly: Homo_sapiens_Ensemble_94
Supplementary files format and content: gene fpkm.txt

source_name: liver

extract_protocol:
The samples for RNA-seq were collected in TriZol. 1 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

tag: tissue

value: liver

value: hepaRG

value: hepatic stem cells

value: FoxM1/HNF4A transfected

value: bioprinted


title: m63

value: uninfected

value: female


title: m37

value: during


title: M14A GP after print rep1


title: RSB241-123 [Dyclonine HCl]

value: Human NGN2-driven iPSC-derived neurons

value: Dyclonine HCl


title: m9_S19


title: WT cells in SL media_1

description:
30x Genomics
MM8

value: SL

tag: time

value: 1 hour


title: M14A 2D rep2

value: planar cell culture


title: RSB241-128 [Pirfenidone]

value: Pirfenidone


title: M14A 2D rep3


title: RSB241-138 [TAK-875]


title: m4_S17


title: M14A 2D rep1


title: 4902-AB-1

value: skin

value: Pansclerotic Morphea Lesional


title: RSB241-37 [Dovitinib (TKI-258, CHIR-258)]

value: Dovitinib (TKI-258, CHIR-258)


title: HepaRG 2D rep3

value: liver

value: WT


title: RSB241-267 [Nisoldipine]

value: Nisoldipine


title: m11_S10


title: MUT_E15.5 kidney 1

city: Chapel Hill

first: Lori

last: O'Brien

state: NC

address: 111 Mason Farm Rd

department: Cell Biology and Physiology

institute: University of North Carolina at Chapel Hill

data_processing:
Alignment and analysis were performed following a modified Tuxedo workflow.
Alignment was done with STAR aligner
Cufflinks/cuffmerge was used for assembled transcripts.
FPKM was calculated with CuffDiff
CuffDiff results were analyzed with the R package
Assembly: mm10
Supplementary files format and content: tab delimited text file contains FPKM values for all samples

source_name: Whole kidney

extract_protocol:
Kidneys were placed in RNAlater (Thermo Fisher) until all samples were collected. RNA was extracted with TRIzol (Invitrogen)
RNA samples were converted to sequencing libraries using the TruSeq Stranded mRNA kit (Illumina Cat. #20020595)

value: Whole kidney


title: WT_E15.5 kidney 3


title: MUT_E15.5 kidney 3


title: MUT_E15.5 kidney 2


title: HepaRG 2D rep2

value: hepaRG

value: hepatic stem cells


title: WT_E15.5 kidney 1


title: RSB241-222 [Pravastatin sodium]

value: Pravastatin sodium


title: RSB241-257 [Hydrocortisone]

value: Hydrocortisone


title: HET_E15.5 kidney 3


title: uninf_67_S26

value: uninfected

value: female


title: WT_E15.5 kidney 2


title: HepaRG 2D rep1


title: m8_S18

value: during


title: RSB241-197 [Olmesartan Medoxomil]

value: Human NGN2-driven iPSC-derived neurons

value: Olmesartan Medoxomil


title: uninf_21_S25


title: HET_E15.5 kidney 2


title: RSB241-249 [(-)-Epigallocatechin Gallate]

value: (-)-Epigallocatechin Gallate


title: inf_dur94_S24


title: HET_E15.5 kidney 1


title: siRNA-3

first: Wei

last: Chen

state: Beijing

address: No. 95 Yong’an road, Xicheng District

department: Beijing Friendship Hospital

data_processing:
Raw reads were further processed with a bioinformatic pipeline tool, BMKCloud (www.biocloud.net) online platform
Clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data
Clean reads were aligned to human reference genome (hg19) and the obtained read counts were scaled to reads per kilo-base of exon model per million mapped reads (RPKM)
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read counts and RPKM values for each Sample

growth_protocol: Human HSC line LX-2 cells were cultured in minimum essential medium (MEM) supplemented with 10% fetal bovine serum (Thermo Scientific) and 100 U/mL penicillin and streptomycin (Thermo Scientific) in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA from LX-2 cells was extracted and purified using Trizol reagent (Invitrogen, USA).
A total amount of 1 μg RNA per sample was used to generated sequencing libraries using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd., China) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Human AEBP1 gene specific siRNA (50 nM, Ribobio, China) or scrambled siRNA (50 nM, Ribobio, China) were transfected into LX-2 cells using Lipofectamine 3000 regent (Invitrogen, USA)  and cultured for 48 hours.

value: hepatic stellate cell

value: AEBP1 knockdown

value: AEBP1 siRNA


title: siRNA-2


title: m3_S16


title: siRNA-1


title: RSB241-303 [Fenoprofen Calcium]

data_processing:
FastQ files were trimmed of adapter sequences using Cutadapt with the following parameters: cutadapt -u 1 -a TGGAATTCTCGGGTGCCAAGG -m 15.
Trimmed reads were aligned to miRBase 21 (hg38) by using Bowtie.
Assembly: hg38
Supplementary files format and content: tab-delimited Excel files include read count for each Sample

value: Fenoprofen Calcium


title: NC-2

value: WT

value: scrambled siRNA


title: RSB241-107 [Dexamethasone (DHAP)]

value: Dexamethasone (DHAP)


title: RSB241-38 [Geniposide]

value: Geniposide


title: NC-3


title: inf_bef18_S22

value: before


title: h69

description:
count_chordodes.txt.gz
tpm_chordodes.txt.gz
SuperTranscripts_chordodes.fasta.gz
SuperTranscripts_chordodes.gff.gz

organism: Chordodes fukuii

source_name: whole body of a C. fukuii

value: male


title: R022

city: Cleveland

first: Vladimir

last: Makarov

state: OH

address: 9500 Euclid Ave

institute: CLEVELAND CLINIC LERNER COM-CWRU

description: Single-Arm Phase II Trial

data_processing:
Raw reads in the FASTQ format were aligned to the mm10 reference genome using STAR aligner v2.7.6a. The featureCounts read summarization program was used to count mapped reads for each gene in the annotation file (Human GENECODE: Release 42 (GRCh38.p13)). Count files were then merged by an in-house R script and differential gene expression analysis was performed using DESeq2. DESeq2 normalizes the count data to account for differences in sequencing depth and composition. This is done using the median of ratios method, which involves dividing each gene's raw count by a size factor that accounts for library size and composition. DESeq2 models the variation in gene expression using a negative binomial distribution. The dispersion estimates are used to model the relationship between mean expression and variance, which is critical for accurate detection of differentially expressed genes.
Assembly: Human GENECODE: Release 42 (GRCh38.p13)
Supplementary files format and content: Raw (raw_count_matrix.csv) and DESeq normalized (DeseqNormalizedCount.csv) matrices are made available along with the FASTQ files used in current study.

source_name: Metastatic Triple-Negative Breast Cancer PRE treatment

extract_protocol: RNA was isolated from frozen core biopsies of primary or metastatic TNBC tissue using the Qiagen AllPrep DNA/RNA kit.Libraries were prepared using the Takara SMART-Seq v4 Ultra Low Input RNA kit and sequenced on an Illumina NovaSeq for a target of 40 million reads per sample.

treatment_protocol: Pre-treatment samples were collected from patients with stage IV triple negative breast cancer prior to receiving chemo-immunotherapy with the following regimen which was administered intravenously on a 21 day cycle: carboplatin (C) day 1 (AUC 4.5), nab-paclitaxel (N) days 1,8,15 (75 mg/m2), and pembrolizumab (P) 200 mg on day 15. An optional post-therapy biopsy was obtained after the 3rd cycle of CNP chemo-immunotherapy

value: metastatic tissue biopsy

value: Carboplatin, Nab-Paclitaxel, and Pembrolizumab

tag: overall response

value: Complete Response

tag: os

tag: pfs

tag: os event

tag: pfs event

tag: age

tag: biomaterial provider

tag: collection date

tag: geo loc_name

value: Cleveland, OH, USA

value: chestwall

tag: race

value: White


title: R020

description: Single-Arm Phase II Trial

tag: Sex

value: female

value: mediastinum

tag: disease

value: TNBC

tag: disease stage

value: stage IV

value: Asian


title: RSB241-240 [Epiandrosterone]

tag: cell line

tag: cell type

value: Human NGN2-driven iPSC-derived neurons

tag: treatment

value: Epiandrosterone


title: inf_dur48_S23

tag: manipulation status

value: during

tag: sampling year

tag: c. fukuii weight (g)

tag: t. angustipennis chest length (mm)

tag: host  t. angustipennis sample name

tag: c. fukuii sample name in the host

tag: number of infected c. fukuii in the same host


title: R021

description: Single-Arm Phase II Trial

tag: tissue

tag: overall response

value: Stable Disease

tag: os

tag: pfs

tag: os event

tag: pfs event

tag: age

tag: biomaterial provider

value: lung


title: NC-1

tag: cell line

tag: cell type

value: hepatic stellate cell

tag: genotype

value: WT

value: scrambled siRNA


title: h66_2

tag: manipulation status

value: before

tag: sampling year

tag: Sex


title: h66_1

tag: c. fukuii weight (g)

tag: t. angustipennis chest length (mm)

tag: host  t. angustipennis sample name


title: RSB241-172 [Dovitinib (TKI-258) Dilactic Acid]

tag: treatment

value: Dovitinib (TKI-258) Dilactic Acid


title: RSB241-201 [Methimazole]

value: Methimazole


title: R018_PRE

description: Single-Arm Phase II Trial

tag: tissue

value: metastatic tissue biopsy

value: Carboplatin, Nab-Paclitaxel, and Pembrolizumab

tag: overall response

value: Partial Response

tag: collection date

tag: geo loc_name

value: Cleveland, OH, USA

value: lymph node

tag: disease

tag: disease stage

tag: race

value: Black or African American


title: P138_MRT_M221AAD_T_ATAC

city: Utrecht

first: Irene

middle: Evelyn Karla

last: Paassen

address: Heidelberglaan 25

country: Netherlands

institute: Prinses Maxima Centrum

description: 10X Genomics - Single Cell Multiome ATAC + Gene Expression User Guide (CG000338 Rev D)

library_source: genomic single cell

data_processing:
Alignment, counting and peak calling was performed with CellRanger-ARC 2.0.0
Data was further filtered with seurat (4.1.1) and signac (1.7.0) with the following parameters: ATAC counts < 50000 & > 800, RNA counts < 30000 & > 800, nucleosome signal < 1.5, TSS enrichment > 1, % of blacklist regions < 3%, % of mitochondrial genes < 20%).
Assembly: Reads were mapped to GRCh38 (refdata-cellranger-arc-GRCh38-2020-A-2.0.0 from 10X Genomics)
Supplementary files format and content: count tables (.csv) of genes and genomic regions

source_name: MRT (viably frozen)

extract_protocol:
MRT tissues were processed using standard tissue processing procedure following the 10X Genomics protocol. In brief, tissues were minced into small pieces and homogenized using a dounce tissue grinder. After cell lysis, the sample was filtered once using a 70uM filter as well as a 40uM filter. Intact single nuclei were sorted and two independent samples were mixed based on different gender (male with female).
Library construction was performed following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide (CG000338 Rev D)

value: MRT (viably frozen)


title: P138_MRT_M221AAD_T_RNA

molecule: nuclear RNA


title: RSB241-286 [Ambroxol HCl]

last: Wei

address: 60 Fenwood Road

tag: cell line

value: Human NGN2-driven iPSC-derived neurons

value: Ambroxol HCl


title: h62

value: female

tag: c. fukuii sample name in the host

tag: number of infected c. fukuii in the same host


title: R018_POST

description: Single-Arm Phase II Trial

source_name: Metastatic Triple-Negative Breast Cancer POST treatment

value: metastatic tissue biopsy, post treatment

tag: os

tag: pfs

tag: os event

tag: pfs event

tag: age

tag: biomaterial provider

value: TNBC

value: stage IV

value: White


title: h37

tag: manipulation status

value: during

tag: sampling year

tag: Sex

tag: c. fukuii weight (g)

tag: t. angustipennis chest length (mm)

tag: host  t. angustipennis sample name


title: R017

description: Single-Arm Phase II Trial

tag: tissue

tag: treatment

tag: overall response

tag: collection date

tag: geo loc_name

value: liver

tag: disease

tag: disease stage


title: P041_MRT_M563AAB_T_ATAC


title: RSB241-106 [5-Aminolevulinic acid HCl]

tag: cell line

tag: cell type

value: 5-Aminolevulinic acid HCl


title: RSB241-92 [ZM 323881 HCl]


title: R016

description: Single-Arm Phase II Trial

value: metastatic tissue biopsy

value: Stable Disease

tag: os

tag: pfs

tag: os event

tag: pfs event

tag: age

value: scapula

tag: race


title: R015

description: Single-Arm Phase II Trial

value: Carboplatin, Nab-Paclitaxel, and Pembrolizumab

tag: biomaterial provider

value: Cleveland, OH, USA

tag: Sex

value: lung


title: h8_S8

tag: manipulation status

value: after

tag: sampling year

tag: c. fukuii weight (g)

tag: t. angustipennis chest length (mm)

tag: host  t. angustipennis sample name

tag: c. fukuii sample name in the host

tag: number of infected c. fukuii in the same host


title: R019

description: Single-Arm Phase II Trial

tag: tissue

tag: treatment

tag: overall response

tag: collection date

tag: geo loc_name

tag: disease

tag: disease stage

value: Black or African American


title: h3_S7


title: P041_MRT_M563AAB_T_RNA

value: MRT (viably frozen)


title: R014_PRE

description: Single-Arm Phase II Trial

value: Progressive Disease

tag: os

tag: pfs

tag: os event

tag: pfs event

tag: age

value: female

value: sternum

tag: race

value: Not specified


title: h29_2_S6

tag: manipulation status

value: before

tag: sampling year

tag: Sex

tag: c. fukuii weight (g)

tag: t. angustipennis chest length (mm)


title: P168_MRT_M378AAD_ATAC

tag: tissue


title: R014_POST

description: Single-Arm Phase II Trial

value: metastatic tissue biopsy, post treatment

tag: treatment

tag: overall response

tag: biomaterial provider

value: missing

value: TNBC

value: stage IV

value: White


title: P156_MRT_M375AAD_ATAC


title: P156_MRT_M375AAD_RNA


title: RSB241-174 [MK-2461]

tag: cell line

tag: cell type

value: Human NGN2-driven iPSC-derived neurons


title: RSB241-50 [GW5074]


title: RSB241-45 [Docetaxel]

value: Docetaxel


title: R013

description: Single-Arm Phase II Trial

value: metastatic tissue biopsy

value: Carboplatin, Nab-Paclitaxel, and Pembrolizumab

value: Partial Response

tag: os

tag: collection date

tag: geo loc_name

value: Cleveland, OH, USA

tag: disease

tag: disease stage


title: RSB241-224 [Bepotastine Besilate]

value: Bepotastine Besilate


title: RSB241-265 [Guaifenesin]

value: Guaifenesin


title: h23_S4

value: during

value: female

tag: host  t. angustipennis sample name

tag: c. fukuii sample name in the host

tag: number of infected c. fukuii in the same host


title: h29_1_S5

tag: manipulation status

tag: sampling year

tag: Sex


title: P166_MRT_M728AAD_T_ATAC

tag: tissue

value: MRT (viably frozen)


title: P168_MRT_M378AAD_RNA


title: R012

description: Single-Arm Phase II Trial

tag: treatment

tag: pfs

tag: os event

tag: pfs event

tag: age

value: lymph node

tag: race


title: h2_S3

value: before

tag: c. fukuii weight (g)

tag: t. angustipennis chest length (mm)


title: RSB241-187 [Imidapril HCl]

tag: cell line

tag: cell type

value: Imidapril HCl


title: h16_S2

value: after

tag: host  t. angustipennis sample name


title: R010_PRE

description: Single-Arm Phase II Trial

tag: overall response

tag: os

tag: biomaterial provider

tag: collection date

value: missing

tag: geo loc_name

value: unspecified metastatic site

tag: disease

value: TNBC

tag: disease stage

value: stage IV

value: Not specified


title: P116_MRT_M981AAC_T_ATAC

source_name: MRT (snapfrozen)

tag: tissue

value: MRT (snapfrozen)


title: RSB241-328 [U-104]

value: Human NGN2-driven iPSC-derived neurons

tag: treatment


title: RSB241-193 [AM1241]


title: R010_POST

description: Single-Arm Phase II Trial

value: metastatic tissue biopsy, post treatment

value: Carboplatin, Nab-Paclitaxel, and Pembrolizumab

value: Partial Response

tag: pfs

tag: os event

tag: pfs event

value: Cleveland, OH, USA

tag: Sex

value: White


title: dur_16b_S20

tag: manipulation status

value: during

tag: sampling year

value: female

tag: c. fukuii weight (g)

tag: t. angustipennis chest length (mm)

tag: c. fukuii sample name in the host

tag: number of infected c. fukuii in the same host


title: P052_MRT_M711AAA_T_ATAC


title: RSB241-48 [Forskolin]

tag: cell line

tag: cell type

value: Forskolin


title: R008_PRE

description: Single-Arm Phase II Trial

value: primary breast tissue biopsy

tag: overall response

tag: os

tag: age

tag: biomaterial provider

tag: collection date

tag: geo loc_name

value: breast

tag: race


title: R009

description: Single-Arm Phase II Trial

tag: tissue

tag: treatment

value: Progressive Disease

tag: pfs

tag: os event

tag: pfs event

tag: disease

tag: disease stage


title: dur_7a_S21

tag: manipulation status

tag: sampling year

tag: Sex

tag: c. fukuii weight (g)

tag: t. angustipennis chest length (mm)

tag: host  t. angustipennis sample name

tag: c. fukuii sample name in the host

tag: number of infected c. fukuii in the same host


title: bef_14b_S19

value: before


title: P052_MRT_M711AAA_T_RNA


title: RSB241-270 [BRL-54443]

tag: cell line

tag: cell type


title: bef_12b_S18


title: h1_S1


title: RH4_siMYCN_72h_Rep3

city: Bethesda

first: Zhihui

last: Liu

state: Maryland

address: 9000 rockville pike

institute: National Cancer Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,  then mapped to hg19 whole genome using STAR 2.5.1
Counts per million (CPM) were quantified using the Partek E/M model
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include CPM values for each Sample.

source_name: RH4 Cells

growth_protocol: RH4 cells are maintained in growth medium. Growth medium: RPMI-1640, 10% fetal calf serum, 100µg/mL streptomycin, 100U/mL penicillin, and L-glutamine.

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Plus Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: siRNAs were transiently transfected into RH4 cells using Nucleofector electroporation (Lonza) and cultured in growth medium for 72 h before RNA extraction.

value: Rhabdomyosarcoma

value: siMYCN


title: R008_POST

description: Single-Arm Phase II Trial

tag: tissue

tag: overall response

tag: os

tag: age

tag: biomaterial provider

tag: collection date

value: missing

tag: geo loc_name

value: TNBC

value: stage IV

tag: race


title: shFLOT2-3

value: nasopharynx

value: nasopharyngeal carcinoma cell line

tag: treatment

value: FLOT2 knockdown


title: RSB241-108 [Tetracaine HCl]

city: Boston

first: Zhiyun

institute: Brigham and Women's Hospital

value: Human NGN2-driven iPSC-derived neurons

value: Tetracaine HCl


title: RSB241-309 [Neohesperidin]

value: Neohesperidin


title: P116_MRT_M981AAC_T_RNA

value: MRT (snapfrozen)


title: aft_122a_S16

tag: manipulation status

value: after

tag: sampling year

tag: Sex

value: female

value: nd


title: SHEPtetMYCN_Dox_48h_Rep3

source_name: SHEP cells

growth_protocol: SHEPtetMYCN cells are maintained in growth medium. Growth medium: RPMI-1640, 10% fetal calf serum, 100µg/mL streptomycin, 100U/mL penicillin, and L-glutamine.

treatment_protocol: SHEPtetMYCN cells cultured in growth medium with or without 0.25 µg/ml doxycycline for 48 h before RNA extraction.

value: SHEP

value: Neuroblastoma

tag: transfected with

value: SHEPtetMYCN

value: doxycycline


title: RSB241-120 [Lumiracoxib]

value: Lumiracoxib


title: RH4_siMYCN_72h_Rep2

value: Rhabdomyosarcoma

value: siMYCN


title: P166_MRT_M728AAD_T_RNA

value: MRT (viably frozen)


title: SHEPtetMYCN_Dox_48h_Rep2


title: RSB241-102 [Tolterodine tartrate]

value: Tolterodine tartrate


title: RH4_siMYCN_72h_Rep1


title: SHEPtetMYCN_Dox_48h_Rep1


title: RH4_siCtrl_72h_Rep3

value: siCtrl


title: RSB241-333 [Roxatidine Acetate HCl]

value: Human NGN2-driven iPSC-derived neurons

value: Roxatidine Acetate HCl


title: P14_(miRNA-4_0)

type: RNA

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

description: Gene expression data from Malignant mucinous tumors

hyb_protocol: Samples were hybridized for 16 h at 48°C on GeneChip microRNA 4.0 Array (Affymetrix)

scan_protocol: arrays were scanned with a GC30007G scanner (Affymetrix)

data_processing: Raw data were normalized using the Expression Console (Affymetrix) with the RMA method, algorithmically based on microarrays spike-in.

label: biotin

source_name: Malignant mucinous tumors

label_protocol: Microarrays were processed according to manufacturer’s recommendations. For each sample, 200 ng of RNAs were labeled with FlashTag Biotin HSR RNA Labeling Kit (Genisphere Affymetrix UK Ltd, High Wycombe, United Kingdom).

extract_protocol: RNA from FFPE sample was extracted using Nucleospin® total RNA FFPE Kit (Ma-cherey-Nagel, Hoert, France). We estimated the amount of tissue of FFPE nodes according to their surface (R*r*π) and the equivalence provided by the fabricant: 1 slice of 10µm thick and 1cm² equates 1mg of material. We calculated the numbers of 20µm thick slice necessary to obtain 17-19mg of material from each node. Slices were cut by microtome and the excess of paraffin was removed with a scalpel. According to the manufacturer’s protocol, the slices were incubated 5 minutes at 56°C in paraffin dissolver provided in the kit. The deparaffined samples were next incubated with proteinase K for 3 hours at 56°C to digest the fixed tissue, release acid nucleic acids and remove the crosslinks. Optimal binding conditions for small RNA were adjusted and the lysate was applied to Nucleo-spin® RNA column. Finally, the RNA was purified by washing steps and eluted. The quantification of total RNA was assessed using Nanodrop 2000 (Thermo Scientific, Les Ulis, France). One of malignant tumor was excluded due to its low amount of RNA, which was insufficient for further analyses

tag: gender


title: RH4_siCtrl_72h_Rep2


title: SHEPtetMYCN_Ctrl_48h_Rep3

value: untreated


title: RSB241-213 [PF-4708671]


title: RSB241-352 [Vitamin C]

value: Vitamin C


title: SHEPtetMYCN_Ctrl_48h_Rep2


title: P13_(miRNA-4_0)


title: RSB241-77 [Entecavir Hydrate]

value: Entecavir Hydrate


title: RH4_siCtrl_72h_Rep1


title: KCNR_siMYCN-72h_Rep3

source_name: KCNR cells

growth_protocol: KCNR cells are maintained in growth medium. Growth medium: RPMI-1640, 10% fetal calf serum, 100µg/mL streptomycin, 100U/mL penicillin, and L-glutamine.

treatment_protocol: siRNAs were transiently transfected into KCNR cells using Nucleofector electroporation (Lonza) and cultured in growth medium for 72 hr before RNA extraction.

value: KCNR


title: RSB241-325 [Cimetidine]

value: Cimetidine


title: P3_(miRNA-4_0)

description: Gene expression data from Borderline mucinous tumors

source_name: Borderline mucinous tumors

value: female


title: KCNR_siMYCN-72h_Rep2

value: Neuroblastoma


title: P1_(miRNA-4_0)


title: KCNR_siMYCN-72h_Rep1


title: RSB241-327 [Bifonazole]

value: Bifonazole


title: RSB241-75 [Letrozole]

value: Letrozole


title: L498-dhmU-Depleted

city: Stanford

first: Georgi

last: Marinov

address: 279 Campus Drive West, Beckman Center, B-257A/259

institute: STANFORD UNIVERSITY

data_processing:
(read alignment, ATAC-seq and MeDIP-seq data)  Bowtie 1.0.1
(bigWig file generation)  custom code
(read alignment, SMF data)  bwa-meth
(read alignment, 5-hmU chemical conversion data)  slamdunk
Assembly: custom and GCA_000507305.1_ASM50730v1 for Breviolum minutum, hg38 for human, sacCer3 for S. cerevisiae; C_glabrata_CBS138 for Candida albicans
Supplementary files format and content: bedGraph of read coverage, normalized to RPM for bigWig files for ATAC-seq and MeDIP-seq; slamdunk output for 5-hmU conversion datasets; MethylDacket bedGraph output for SMF datasets

organism: Breviolum minutum

value: whole dinoflagellate

tag: sample type

value: B. minutum 5-hmU MeDIP-seq depleted control

tag: chip antibody


title: L570-5hmU_chemical_mapping_mild_oxid

data_processing:
(read alignment, ATAC-seq and MeDIP-seq data)  Bowtie 1.0.1
(bigWig file generation)  custom code
(read alignment, SMF data)  bwa-meth
(read alignment, 5-hmU chemical conversion data)  slamdunk
Assembly: custom and GCA_000507305.1_ASM50730v1 for Breviolum minutum, hg38 for human, sacCer3 for S. cerevisiae; C_glabrata_CBS138 for Candida albicans
Supplementary files format and content: bedGraph of read coverage, normalized to RPM for bigWig files for ATAC-seq and MeDIP-seq; slamdunk output for 5-hmU conversion datasets; MethylDacket bedGraph output for SMF datasets
Library strategy: 5-hmU chemical mapping

extract_protocol:
Chemical mapping of 5-hmU as carried out following the previously described by Kawasaki et al. chemical conversion method. Briefly, sheared genomic DNA was used as input and end prep and adapter ligation were carried out using the NEBNext Ultra II DNA Library Prep Kit. After the ligation step, DNA was purified using AMPure XP beads and eluted in 50 µL of H2O. DNA denaturation was performed by adding NaOH to a final concentration of 0.05M and incubating at 37◦C for 30 minutes. Oxidation was carried out by adding 2 µL of KRuO4 solution (15 mM in 0.05 M NaOH) and incubating for 30 minutes at room temperature. Oxidized DNA was purified using AMPure XP beads and extension was carried out by mixing 13.5 µL DNA, 1.6 µL 100 mM MgSO4, 2 µL NEB Index Primer, 2 µL 10× ThermoPol Reaction Buffer (NEB), 0.5 µL 10 mM dNTP mix, and 0.4 µL Bst DNA Polymerase, Large Fragment (NEB), then incubating for 1 hour at 37◦C
PCR amplification was carried out using the NEB Ultra DNA Library Prep Kit, with 12 cycles of PCR. Final libraries were purified using AMPure XP beads.

value: B. minutum 5-hmU chemical mapping


title: RSB241-72 [Xylazine HCl]

tag: cell line

tag: cell type

value: Xylazine HCl


title: L497-dhmU-MeDIP

tag: tissue

value: B. minutum 5-hmU MeDIP-seq

value: anti-5-hmU Abcam ab19735


title: SHEPtetMYCN_Ctrl_48h_Rep1

value: SHEP

value: SHEPtetMYCN


title: KCNR_siCtrl-72h_Rep2

value: siCtrl


title: P4_(miRNA-4_0)


title: KO1_2

city: Yangzhou

first: Yijun

last: Wang

state: Jiangsu

address: Wenhui

institute: Yangzhou University

data_processing:
Clean reads were aligned to the maize reference genome (AGPv4) with Tophat2.
Aligned reads of single sample were assembled to generate transcripts with Cufflinks.
FPKM (expected fragments per kilobase of transcript per million fragments sequenced) values were evaluated by the Cuffdiff utility embedded in the Cufflinks package.
Genome_build: AGPv4
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism: Zea mays

source_name: seedlings (roots removed)

growth_protocol: Maize plants were grown in normal conditions.

extract_protocol:
Total RNA was extracted with the RNeasy Plant Mini Kit.
RNA libraries were prepared according to standard Illumina protocols.

treatment_protocol: Seedlings were not treated.

tag: genotype

value: GBetaKO

value: seedlings (roots removed)

value: three-leaf stage


title: L08_Symbiodinium_minutum_SSb01_omniATAC

extract_protocol:
ATAC-seq experiments were performed following the omniATAC protocol. Briefly, ∼100K B. minutum cells were centrifuged at 1,000 g, then resuspended in 500 µL 1× PBS and centrifuged again. Cells were then resuspended in 50 µL ATAC-RSB-Lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630, 0.1% Tween-20, 0.01% Digitonin) and incubated on ice for 3 minutes. Subsequently 1 mL ATAC-RSB-Wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.01% Digitonin) were added, the tubes were inverted several times, and nuclei were centrifuged at 500 g for 5 min at 4◦C. Transposition was carried out by resuspending nuclei in a mix of 25 µL 2× TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2, 20% Dimethyl Formamide), 2.5 µL transposase (custom produced) and 22.5 µL nuclease-free H2O, and incubating at 37◦C for 30 min in a Thermomixer at 1000 RPM.
Transposed DNA was isolated using the MinElute PCR Purification Kit (Qiagen Cat# 28004/28006), and PCR amplified for 10 cycles using the usual ATAC-seq settings. Libraries were purified using the MinElute kit, then sequenced on a Illumina NextSeq 550 instrument as 2x36mers.

value: B. minutum ATAC-seq


title: KCNR_siCtrl-72h_Rep1

value: KCNR


title: P17_(miRNA-4_0)

value: female


title: RSB241-23 [nc-DMSO rep1-8]

value: Human NGN2-driven iPSC-derived neurons

value: DMSO


title: L571-5hmU_chemical_mapping_harsh_oxid

value: whole dinoflagellate


title: WT_2

value: WT

tag: age


title: IMR32_siG9a_48h_Rep3

source_name: IMR32 Cells

growth_protocol: IMR32 cells are maintained in growth medium. Growth medium: RPMI-1640, 10% fetal calf serum, 100µg/mL streptomycin, 100U/mL penicillin, and L-glutamine.

treatment_protocol: siRNAs were transiently transfected into IMR32 cells using Nucleofector electroporation (Lonza) and cultured in growth medium for 48 hr before RNA extraction.

value: Neuroblastoma


title: aft_47a_S17

value: after

tag: c. fukuii weight (g)

tag: t. angustipennis chest length (mm)

tag: host  t. angustipennis sample name

value: nd

tag: c. fukuii sample name in the host

tag: number of infected c. fukuii in the same host


title: RSB241-345 [Ammonium Glycyrrhizinate]

tag: treatment

value: Ammonium Glycyrrhizinate


title: IMR32_siG9a_48h_Rep2


title: Sebastian Zeocin 7 (SZ7)

city: Olomouc

first: Ales

last: Pecinka

address: Šlechtitelů 31

country: Czech Republic

institute: Institute of Experimental Botany of the AS CR

data_processing:
Illumina RTA3 was used for basecalling and .cbcl files were converted to .fastq using bcl2fastq2 Conversion Software v2.20
Sequenced reads were trimmed for adaptor sequence and low-quality sequence and then mapped to Morex v3 whole genome using hisat2 v2.1.0 with default parameters. Hisat2 output was converted and sorted by samtools view and samtools sort, respectively.
The number of reads falling in the exons of transcripts were counted using subread v1.5.2 with parameters -p -t exon -g Parent.
Transcripts Per Million (TPM) were calculated in R using standard formula.
Assembly: Mascher, M., Wicker, T., Jenkins, J., Plott, C., Lux, T., Koh, C. S., ... & Stein, N. (2021). Long-read sequence assembly: a technical evaluation in barley. The Plant Cell, 33(6), 1888-1906.
Supplementary files format and content: Tab-delimited text file including RAW counts for each Sample
Supplementary files format and content: Excel table including TPM values for each replicate, and calculated MEAN and SD values for each sample.

organism: Hordeum vulgare

source_name: dissected root appices

growth_protocol: mature barley seeds were sterilized and stored overnight at 4°C  in ddH2O. The following day embryos were extracted and placed onto half strength MS medium. Plants were grown for 7 days in climate controled phytochamber with long day regime (16h light, 150 µmol m-2 s-1, 21°C, 8h dark, 19°C).

extract_protocol:
Dissected root apical meristems (RAMs) were flash-frozen in liquid nitrogen and stored until use at -80 °C. RNA extraction was performed by RNeasy Mini Kit (Qiagen, Cat. no. 74104) according to manufacturer’s instructions with on column DNAse I treatment.
Novogene Ltd. (UK) performed library construction by poly A enrichment

treatment_protocol: After seven days growth in normal conditions seedlings were transfered into liquid medium without or with zeocin (500 μg/ml) for six hours treatment.

value: dissected root appices

value: Sebastian

value: zeocin 500 μg/ml, 6h


title: Sebastian Zeocin 8 (SZ8)


title: RSB241-8 [nc-DMSO rep1-7]


title: IMR32_siG9a_48h_Rep1


title: RSB241-26 [nc-DMSO rep1-6]


title: 3dpi-2, input, 1

city: nanjing

first: Han

state: jiangsu

address: weigang no.1,xuanwu district

institute: Nanjing Agricultural University

data_processing:
Clean reads were aligned to Phytophthora infestans whole genome using bowtie2 v2.3.3.1 with parameter -N 1
Bigwig files were generated by DeepTools "bamCompare" using --normalizeUsing RPKM --scaleFactorsMethod None
Assembly: Phytophthora infestans ASM14294v1 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000142945.1)
Supplementary files format and content: Bigwig files, scores represent enriched value(log2(fold-change))

organism: Phytophthora infestans

source_name: infected leaves

extract_protocol:
After antibody Immunoprecipitation, target DNA was eluted from Dynabeads and precipitated using ethanol followed by twice washes, finally the samples was dried and dissolved in 33 μl ddH2O
Qualified library for sequencing was prepared using the QIAquick PCR Purification Kit(Qiagen). Briefly, 10-300ng DNA was taken to do DNA-end repair(3'-dA overhang and ligation of methylated sequencing adaptors) followed by PCR amplication and size selection (usually 100-300bp, including adaptor sequencing).

tag: host

value: potato

value: infected leaves

tag: strain


title: KO1_3

value: GBetaKO

value: seedlings (roots removed)

value: three-leaf stage


title: RSB241-112 [Quinapril HCl]

value: Quinapril HCl


title: KO1_1


title: RSB241-10 [nc-DMSO rep1-5]

value: Human NGN2-driven iPSC-derived neurons


title: Sebastian Mock 3 (SM3)

value: zeocin 0 μg/ml, 6h


title: 3dpi-2, H3K36, 1


title: Sebastian Mock 2 (SM2)


title: WT_3


title: KCNR_siCtrl-72h_Rep3

value: KCNR

value: siCtrl


title: RSB241-11 [nc-DMSO rep1-4]

value: DMSO


title: IMR32_siWDR5_48h_Rep2

value: Neuroblastoma


title: IMR32_siWDR5_48h_Rep3


title: RSB241-24 [nc-DMSO rep1-3]


title: Sebastian Mock 1 (SM1)


title: IMR32_siWDR5_48h_Rep1


title: WT_1

value: WT


title: IMR32_siMYCN_48h_Rep3

value: siMYCN


title: Sebastian Zeocin 6 (SZ6)

value: dissected root appices


title: 3dpi-2, H3K9, 1


title: atr Zeocin 18 (AZ18)


title: IMR32_siMYCN_48h_Rep2


title: RSB241-25 [nc-DMSO rep1-2]


title: 3dpi-2, H3K27, 1


title: RSB241-7 [nc-DMSO rep1-1]


title: atr Zeocin 16 (AZ16)


title: IMR32_siMYCN_48h_Rep1


title: 3dpi-1, input, 1


title: 3dpi-1, H3K36, 1


title: atr Mock 13 (AM13)


title: 3dpi-1, H3K27, 1


title: atr Mock 12 (AM12)


title: IMR32_siCtrl_48h_Rep3


title: 3dpi-1, H3K9, 1


title: IMR32_siCtrl_48h_Rep2


title: IMR32_siCtrl_48h_Rep1


title: 3dpi-2, H3K4, 1


title: 3dpi-1, H3K4, 1


title: IgD+ B, 16C303+16C222+16C237+16C235, week -1, VDJ-derived cDNA

status: Public on Oct 18 2023

first: Chaim

middle: A

last: Schramm

state: MD

address: 40 Convent Dr

department: Vaccine Research Center

institute: NIAID, NIH

description: IGG/IGK/IGL enriched from polyA RNA via 10x Chromimum

data_processing:
The counts matrix was generated with Cellranger v3.1.0, using the protein-coding genes of the rhesus macaque reference genome from Ensembl (Mmul10, release #101). The filtered feature/barcode matrices were imported into Seurat v4.0.1 using R v4.0.4. Cells absent from either the gene expression or antibody capture datasets were eliminated, along with cells expressing zero counts of hash oligos. For hash demultiplexing, Seurat’s HTOdemux function was applied, and only singlets were retained for subsequent analyses. The filters based on percent mitochondrial genes and number of genes expressed varied between sample, but the upper threshold for percent mitochondrial genes ranged from 4-10%; the minimum for number of genes expressed was 200 genes for each sample; the upper threshold for number of genes expressed ranged from 1500-2500. The raw counts of each individual sample were merged.  For the innate cell sorts, clusters of contaminating B and T cells (identified using Seurat’s FindClusters and RunUMAP) were removed and not included in downstream analysis. The merged and filtered data matrix was then corrected for sparseness using DeepImpute with tensorflow v2.1.0 and default parameters. The imputed matrix was then re-imported into Seurat.  For both innate and T cells, Seurat was used to normalize the (imputed) count matrix, find variable genes, and regress out technical factors. Principle compents (PCs) were then calculated and used as input to Harmony to remove batch effects between samples. The integrated output was clustered using FindClusters and marker genes were identified with FindAllMarkers. Canonical marker genes were used to annotate the detected clusters.  Gene set enrichment analysis of the innate cell data was conducted using the R library fgsea. The data were broken down by cell type and time point, and differential expression analysis of all 21,369 genes was conducted using FindMarkers between each subset. Finally, the statistically significant (adjusted p < 0.05) pathways were detected by inputting the genes, ranked by average log fold change, into the function fgsea. The Hallmark gene set databases originated from MSigDB.  Signature scores for 50 pro-inflammatory genes previously determined to be predictive of antibody responses to a variety of vaccines were calculated using AddModuleScore in Seurat.
cellranger vdj (10x Genomics) was used to assign TCR annotations for each read-pair. TCR alpha recovery was minimal and not followed up further. An in-house shell script was used to filter for productive TCR betas. All subsequent analyses were done in R (v4.0.2). Cells with duplicated barcodes were discarded, and the TCR data was merged with the T cell transcriptomics Seurat (v4.0.1) object metadata for hash demultiplexing. Usage of each TRBV gene was compared between the S-specific and non-specific T cells from each animal using a paired samples Wilcoxon test in R.
SmartSeq sequencing reads were trimmed with Trimmomatic v 0.39, trimming nucleotides with Phred score below 20 and removing reads with resulting length less than 50 nucleotides. Alignment of reads to macaque protein-coding reference build Mmul10 was performed using Spliced Transcript to a Reference (STAR) v. 2.5.1b. Gene quantifications of reads as transcripts per million (TPM) were computed with Stringtie v. 1.33. Individual cells were removed from the analysis based on trimming and alignment metrics, as well as read quantity, feature quantity, quantity of mitochondrial reads, and diversity of transcripts.   Seurat was used to calculate principal component analysis, which was used as input to integrate the data by batch with Harmony. PCA, cell clustering and UMAP dimensionality reductions were conducted in Seurat. A single cluster was identified as likely T cells by its more than triple the expression of CD3E than the next highest cluster and so was removed from the analysis. Clustering and dimensionality reduction was repeated after this cell filter.   Differential expression of cell clusters was conducted with Seurat's function FindAllMarkers, and FindMarkers was used for comparison of timepoints week 2 and week 6. Those results were used as input to Gene set enrichment analysis conducted with the R package fgsea and the hallmark pathwaysfrom MSigDB.
Full-length V(D)J sequences from were reconstructed from SmartSeq data using BALDR and filtered using filterBALDR.pl (https://github.com/scharch/filterBALDR). Gene annotation and clonal assignment were done using SONAR v4.2 in single cell mode. Clonal flow diagrams were plotted using the ggalluvial package in R v4.2.1. Public clone were identified by clustering CDR H3 amino acid sequences using usearch as previously described . Members of the human public clone were identified from CovAbDab sequences downloaded as of January 24th, 2023 meeting the following criteria: (1) derived from IGHV3-30, IGHV3-30-3, or IGHV3-30-5; (2) 14 amino acid CDR H3 with Gly at position 6 and Tyr at position 8; (3) originating from a human; (4) not annotated as binding to any RBD or NTD epitope. This resulted in 326 public clone sequences, which were plotted using ggseqlogo.
Assembly: Mmul10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: tab-delimited HTO assignments for each cell
Supplementary files format and content: comma-delimited values of gene expression in TPM
Supplementary files format and content: AIRR-formated VDJ sequences recovered from B cells
Supplementary files format and content: 10x Genomics output files: TR VDJ contigs with annotations
Supplementary files format and content: RDS-formatted R data files with complete Seurat objects

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
Frozen rhesus macaque PBMCs were thawed into warm R10 media (RPMI + 10% Fetal Bovine Serum + 2 mL L-Glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin; all reagents from Gibco) containing DNase I (MilliporeSigma), followed by one wash with R10 and one wash with FACS buffer (PBS with 2% FBS). For B and innate cell staining, cells were resuspended in 100µL of Live/Dead Fixable Blue Dead Cell Stain Kit (Invitrogen, cat# L23105) diluted 1:200 in PBS for 10 min at room temperature. Cells were washed with FACS buffer and incubated for 20 min with the staining cocktail consisting of antibodies and probes. Additionally, each sample was labelled with 1µl of TotalSeq-C Hashtag antibodies (Biolegend) that was incubated together with the staining cocktail. After incubation, cells were washed twice with FACS buffer and resuspended in R10 for sort.  From each sample, 10,000-60,000 innate cells were sorted into a tube containing FBS according to the gating strategy showed in Fig. S1B. From baseline samples, 50 thousand naïve B cells were also sorted in a separate tube. From week 2 and 6 samples, antigen-specific cells were single-cell sorted into 96-well plates containing 5 µL of TCL buffer (Qiagen) with 1% b-mercaptoethanol for sequencing by SmartSeq. All sorts were performed using a BD FACSymphony S6 Cell Sorter (BD Biosciences) with BD FACSDiva Software version 9.5.1 (BD Biosciences) and data were analyzed using Flowjo v10.8.1.
Frozen rhesus macaque PBMC were thawed into warm R10 media (RPMI + 10% Fetal Bovine Serum + 2 mL L-Glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin; all reagents from Gibco) containing DNase I (MilliporeSigma) and rested for 1 hour at 37oC / 5% CO2.  Cells were stimulated with two peptide pools corresponding to S1 and S2 of the vaccine insert SARS-CoV-2 S protein (JPT Peptide Technologies) at 2 µg/mL of each peptide for 6 hours at 37oC / 5% CO2.  A DMSO only control was included for each sample.  Anti-CD154 BV421(Biolegend, clone 24-31, cat# 310824) was included during the 6-hour culture and GolgiStop (BD Biosciences) was added after 2 hours of stimulation.  Following stimulation, cells were washed and stained with Aqua LIVE/DEAD dye (ThermoFisher) for 10 minutes, and subsequently stained with antibody mix. In addition, cells were incubated with TotalSeqTM Hashtag antibodies (Biolegend) with separate antibodies applied to the DMSO only condition and the stimulated conditions. For each animal, 1000-2000 memory CD4 cells from the DMSO only condition were sorted and combined with memory cells expressing CD154 and CD69 from each S pool stimulation for processing for 10X Genomics.
Bulk-sorted cells were pooled into a tube and loaded on the 10x Genomics Chromium Chip according to the manufacturer’s protocol for the Next GEM Single Cell 5’ Kit v1.1 (10x Genomics, PN-1000165). To sequence single-cell gene expression and cell surface oligonucleotides (from Hashtag antibodies), libraries were prepared according to manufacturer’s instructions using the Chromium Single Cell 5' Library Construction Kit (10x Genomics, PN-1000020) and Chromium Single Cell 5' Feature Barcode Library Kit (10x Genomics, PN-1000080), respectively. To sequence TCR repertoire libraries were prepared using the Chromium Single Cell V(D)J Enrichment Kit (10x Genomics, PN- PN-1000005). These libraries were sequenced on an Illumina NovaSeq platform (Illumina). To sequence BCR repertoire, heavy and light chains were amplified from the cDNA using IgG_REV, IgA_REV, IgK_REV or IgL_REV primers (Table S3) with the addition of Illumina sequences as detailed in (25). These Illumina-ready libraries were sequenced using 2x300 paired-end reads on an Illumina MiSeq
Full-length transcriptomes were sequenced using a modified SMART-Seq protocol. Heavy and light chain variable regions were enriched by amplifying cDNA with a forward primer complementary to the TSO and IgA/IgG_REV or IgK/IgL_REV primer pools.
OTHER: scRNA-seq with FeatureSeq and scAIRR-seq

value: PBMC

value: IgD+ naive B cells

tag: library type

value: mRNA

tag: tags

value: mRNA-1273 vaccination

tag: time

value: week -1


title: atr Zeocin 17 (AZ17)

value: zeocin 500 μg/ml, 6h


title: IgD+ B, 16C301, week -1, VDJ-derived cDNA


title: IgD+ B, 36186, week -1, VDJ-derived cDNA


title: IgD+ B, 34941, week -1, VDJ-derived cDNA


title: atr Mock 11 (AM11)


title: RSB241-360 [pc-Forskolin rep1-4]

value: Forskolin


title: RSB241-375 [pc-Forskolin rep1-3]


title: RSB241-376 [pc-Forskolin rep1-1]


title: RSB241-359 [pc-Forskolin rep1-2]


title: IgD+ B, 16C283, week -1, VDJ-derived cDNA