title: Clam UF46S-0635

description: UF Phase II

source_name: Clam UF46S-0635


title: Control PDC085

status: Public on Feb 26 2025

type: SRA

city: London

first: Carolina

last: Barcellos Machado

address: 4-8 Maple St

country: United Kingdom

institute: BenevolentAI

description: Library name: 194017-R02

library_source: transcriptomic

data_processing:
Reads were aligned to the GRCh38 (hg38) genome. The data were mapped to RefSeq gene model, using a professional website DNAnexus (https://dnanexus.com/).
sequencing QC was run with FastQC version 3.0.1
adaptors trimmed with Trim Galore version 0.6.0
alignment was run with STAR version 2.0.0
aligned sequencing reads were quantified with RSEM version 1.0.0
Assembly: GRCh38 (hg38)
Supplementary files format and content: csv file per sample including count, TPM and FPKM

molecule: total RNA

organism: Homo sapiens

source_name: brain

extract_protocol:
Total RNA was isolsted from tissue using the RNeasy Plus Universal Mini Kit (Qiagen) according to the manufacturer's protocol with an additional DNAse digestion step using DNase I, RNase-free (Roche). 100ng of Total RNA was used for the construction of sequencing libraries.
rRNA depletion was performed using the NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (NEB). RNA sequencing library preparation used the NEBNext Ultra II RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (NEB).

tag: tissue

value: brain

tag: disease

value: Control

tag: batch

tag: which cingulate_gyrus

value: Anterior

tag: age

tag: Sex

value: female

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: End stage heart failure, atrial fibrillation, cerebral ataxia, dementia

tag: classification of_ms

value: Non-MS control

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: Subject OU03

type: protein

city: Stanford

first: Allan

last: Feng

state: CA

address: 269 Campus Dr

department: Imm/Rheum

country: USA

institute: Stanford School of Medicine

description:
raw data file: ACA Array version 3 Platform Raw MFI.xlsx
Antibodies in samples bind to barcoded beads conjugated to antigens. Antibody reactivity was quantified by the fluorescence measured as MFI from the secondary antibody.

hyb_protocol: A fluorescent secondary antibody was added to a PBS solution containing conjugated beads bound to antibodies.

scan_protocol: A Luminex FlexMAP 3D instrument was used to quantify autoantibody levels in each sample by measuring fluorescence (in MFI) from each barcoded bead.

data_processing: Barebeed MFI values were subtracted from the MFI values for all analytes in each sample and  replicate MFI values were averaged.

label: R-PE conjugated goat anti-human IgG secondary antibody

molecule: protein

source_name: Serum/Plasma

label_protocol: Secondary antibody with a conjugated fluorophore was added to a PBS solution containing conjugated beads bound to antibodies from samples.

extract_protocol: Blood was collected from iMCD patients, Hodgkin lymphoma patients, and healthy controls. Blood was then processed into serum or plasma.

tag: condition

value: iMCD patient


title: Subject UP37 F


title: MS MS129

description: Library name: 194017-R03

tag: tissue

tag: disease

value: MS

tag: batch

tag: which cingulate_gyrus

value: Posterior

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Carcinoma of lung, multiple sclerosis

tag: classification of_ms

value: PPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Muscle weakness

tag: first presented_symptom_category

value: Motor

tag: history of_motor_weakness

value: Yes

tag: history of_sensory_loss

value: No

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?


title: Clam UF41S-0616

type: genomic

city: Stony Brook

first: Denis

last: Grouzdev

address: 100 Nicolls Rd

institute: Stony Brook University

description: UF Phase II

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: Genotyping was performed at Neogen (Lincoln, Nebraska) on the Axiom 384HT arrays (Axiom HD Array [60K] Clam) following protocols outlined in the Axiom Assay 384HT Array Format Automated Workflow User Guide.

data_processing:
The raw genotyping data in CEL format was downloaded from the CAT website after the service and genotype annotation was analyzed using the Axiom software (v 5.4, Thermo Fisher) following the Best Practices Workflow with recommended threshold settings (DishQC ≥ 0.82, QC call rate ≥ 97%).
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

molecule: genomic DNA

organism: Mercenaria mercenaria

source_name: Clam UF41S-0616

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Adults M. mercenaria (12-14 months old) were collected from three farms in Cedar Key, Florida with one whole bag from each farm (1000-1200 clams). The clam seeds of each farm were originally sourced from different hatcheries. After purchase, the quahogs from each bag were cleaned at the farms using fresh water to remove sediment before being transported to the laboratory in a cooler (1 hr driving). After arriving at the laboratory, all quahogs were maintained in an indoor recirculating artificial seawater system equipped with a bead filter (Endurance 4000, Aquaculture Systems Technologies, Baton Rouge, LA) at 24 ± 0.55°C, 25 ppt salinity, and pH = 8.35. Quahogs were fed daily with a combination of microalgae, including Tetraselmis spp., Isochrysis spp., and Chaetoceros spp., at 50,000 cells/ml supplemented with commercial algal paste (Instant algae, Reed Mariculture, San Jose, CA, USA). System water quality was checked daily using a saltwater combination kit (AQ-4, Lamotte, Maryland, USA) for ammonia (< 0.01 mg/L), nitrite (< 0.01 mg/L), and nitrate levels (< 10 mg/L).

extract_protocol: The quahogs that died earliest (n = 330) were categorized as “dead” under the dichotomous phenotype, and the quahogs that died latest (n = 144) and survivors (n =231) were considered as “survived”. Genotyping of samples was performed on the previously described SNP microarray chip (Grouzdev et al., 2024). Fixed samples were shipped to the Center for Aquaculture Technologies (CAT, https://aquatechcenter.com, San Diego, CA) for this service. The total genomic DNA was extracted from sample sources (adductor muscle or hemocytes) using a magnetic bead-based extraction protocol. Briefly, fixed tissues (~10-15 mg) were subsampled and processed using mag-bind blood and tissue DNA kits (Omega BioTek, Norcross, GA) according to the manufacturer’s guidelines. Automated processing and liquid handling steps associated with the extraction protocol were performed using PurePrep 96 units (Molgen, San Diego, CA) according to kit and instrument-specific guidelines. Extracted gDNAs were assessed for yields and quality by spectrophotometry (Nanodrop, ThermoFisher) and 2% agarose gels targeting a minimum of 35 µl at >20 ng/µl of largely intact DNA (minimum 5KB).

treatment_protocol: The heat shock challenge was applied by increasing water temperature at 1°C per day from 24°C to a final temperature of 35°C using a heat pump with a temperature controller (Model No. DC24S, Aqualogic, San Diego, CA, USA). When the total dead quahog numbers reached about 50% of the total initial clam number, the temperature decreased from 35°C to 27°C within 24 hr and gradually to 24°C within another 24 hr. For easy reading, the heat challenge was separated into three phases (Figure 1): Phase I (13 days) – temperature increased from 24°C to 35°C and stayed at 35°C; Phase II (9 days) – temperature decreased from 35°C to 24°C with more clams died, and Phase III – temperature was maintained at 24°C and no quahog mortality was found in two days. Two HOBO pendant temperature loggers (UA-001–64, Onset, MA, USA) were submerged in the tank to record the temperature changes. No feeding was conducted after the temperature reached 28°C, and water quality was monitored twice a day.

tag: tissue

value: Adductor muscle


title: Clam UF42D-0385

description: UF Phase I

source_name: Clam UF42D-0385


title: KELLY-BPTF-R5

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

country: Spain

institute: CNIO

library_source: genomic

data_processing:
*library strategy: CUT&RUN
Data were analyzed using cut and run nfcore pipeline: https://nf-co.re/cutandrun
Peak calling was performed using MACS2 software with mnase-treated chromatin as control sample. Only FDR-significant peaks <0.05 with signalValue > 3 were kept for analysis.
For down-stream analyses, regions found in at least 3 (KELLY) or 2 (LAN1, SK-N-AS, and KPNYN) replicates were used and annotated using the HOMER annotatePeaks.pl command.
Assembly: UCSC hg19
Supplementary files format and content: Bigwig files and called peaks output of MACS2 for each replicate.

source_name: Neuroblastoma

growth_protocol: KELLY and LAN-1 cells were cultured in RPMI  supplemented with 10% FBS and 1% sodium pyruvate. SK-N-AS cells were grown in DMEM  supplemented with 10% FBS and 0.1% non-essential amino acids. KP-N-YN cells expressing an inducible PRRX1 transgene were cultured in  control conditions or in the presence of doxycycline (0.5mg/ml)  in RPMI  supplemented with 10% FBS and 2mM L-glutamine. Cells were grown at 37 °C with 5% CO2.

extract_protocol:
500,000 cells/sample were harvested and bound to concanavalin A–coated magnetic beads. Cells were permeabilized with 5% digitonin. After overnight incubation with echa antibody, beads were washed and incubated with pAG-MNase produced at CNIO (Protein Production Unit). Cells were chilled to 0 °C and digestion was initiated by adding Ca2+. Reactions were stopped by chelation including spike-in DNA and the DNA fragments released by cleavage were extracted from the supernatant.
Library preparation and paired end sequencing for KELLY, LAN-1, and SK-N-AS  cells were performed at the CNIO Genomics Unit; experiments with the KP-N-YN inducible cells were performed at the Center for Applied Genomics (CHOP).
DNA samples were processed through subsequent enzymatic treatments for end-repair, dA-tailing, and ligation to adapters with "NEBNext Ultra II DNA Library Prep Kit for Illumina" (NEB ref.E7645). Adapter-ligated libraries were completed by a limited-cycle PCR, with 63º T(ann/ext) for 10s, and extracted with a [single] double-sided SPRI size selection. Resulting average fragment size is 325 bp from which 120 bp correspond to adaptor sequences. Libraries were applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument by following manufacturer's recommendations.

value: Neuroblastoma

tag: cell line

value: KELLY

tag: cell type

value: Cancer cell

tag: antibody

tag: antibody amount


title: KELLY-BPTF-R4


title: MS MS542

description: Library name: 194017-R01

value: brain

tag: disease

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Pulmonary embolism, DVT

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Brainstem relapse

tag: first presented_symptom_category

value: Brainstem

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: Clam UF40S-0645

description: UF Phase III

source_name: Clam UF40S-0645

tag: tissue

value: Hemocytes in ethanol


title: KELLY-BPTF-R3

tag: cell line

tag: cell type

tag: antibody

tag: antibody amount


title: Subject UP35 F

tag: condition

value: iMCD patient


title: Clam UF400D-0437

description: UF Phase I


title: MS MS403

description: Library name: 194017-R05

tag: disease

value: MS

tag: batch

tag: which cingulate_gyrus

value: Posterior

tag: age

tag: Sex

value: female

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: End stage of Multiple Sclerosis

tag: classification of_ms

value: SPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Numbness

tag: first presented_symptom_category

value: Sensory

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion


title: Clam UF39S-0611

description: UF Phase II

source_name: Clam UF39S-0611

tag: tissue

value: Adductor muscle


title: Subject UP34 F

tag: condition


title: Clam UF3S-0628

description: UF Phase II

source_name: Clam UF3S-0628


title: KELLY-BPTF-R2

value: Neuroblastoma

tag: cell line

tag: cell type

tag: antibody

tag: antibody amount


title: KELLY-BPTF-R1

value: KELLY


title: Clam UF394D-0405

description: UF Phase I


title: Subject UP33 F


title: Retina PLX5622 rep4

city: Boston

first: Gracia

middle: M.

last: Bonilla

state: MA

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
Transcriptome mapping was performed with STAR using the Ensembl annotation of the mm10 reference genome.
Read counts for individual genes were generated using HTSeq. Only genes with CPM > 1 for at least one sample were included in the analyses.
Analysis of differential expression was performed using only genes with normalized counts (CPM) >=1 for at least one sample
Assembly: mm10
Supplementary files format and content: Table with RPKM values for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: retina

growth_protocol: No in vitro culture was involved.

extract_protocol:
Retinas were dissected in ice-cold PBS and embryonic hylaoid blood vessels were removed. Retinas were immediately transfered to 1 ml of RNA STAT-60 and the retinal tissue was homogenized using 26 guage needle syringe and RNA was harvested using as recommended by the manufacturer (amsbio, LLC). As recommended by the manufacturer (New England BioLabs, Inc) poly (A) mRNA was isolated (using NEBNext®) and 500ng of RNA was used for construction of sequencing libraries (using NEBNext ultra II directional library prep kit for Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Timed-pregnant females were maintained on control or PLX5622 diet from gestational day 13/14. Retinal were collected from pups at P10 for RNA-seq studies.

value: retina

tag: strain

tag: treatment

value: PLX5622 (microglia depleted)


title: Subject UP32 F


title: Subject UP31 R


title: Clam UF38D-0371

description: UF Phase I

source_name: Clam UF38D-0371


title: Subject UP30 R


title: Retina PLX5622 rep3


title: Retina PLX5622 rep2


title: Subject UP29 R


title: Clam UF37S-0613

description: UF Phase II

source_name: Clam UF37S-0613


title: Subject UP36 F


title: Retina PLX5622 rep1


title: Clam UF371D-0469

description: UF Phase I


title: Retina control rep4

value: Control


title: Subject UP28 R


title: Clam UF36D-0412

description: UF Phase I

source_name: Clam UF36D-0412


title: Subject UP27 F


title: Clam UF369D-0468

description: UF Phase I


title: Retina control rep3


title: Retina control rep2


title: Clam UF35P-0490

description: UF Phase I

source_name: Clam UF35P-0490


title: Subject UP26 R


title: Retina control rep1


title: Clam UF34S-0615

description: UF Phase II

source_name: Clam UF34S-0615


title: Clam UF348P-0499

description: UF Phase I


title: Subject UP24 F


title: Subject UP25 R


title: Splenocyte, lib74671

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

data_processing:
Sequencing of pooled libraries was carried out on a NextSeq 2000 sequencer (Illumina) with paired-end 59-base reads, using NextSeq P2 sequencing kits (Illumina) with a target depth of 5 million reads per sample. Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads. The FASTQs were aligned to the GRCm38.91  mouse reference genome, using STAR v.2.4.2a40 and gene counts were generated using htseq-count41. Quality control (QC) and metrics analysis was performed using the Picard family of tools (v1.134, http://broadinstitute.github.io/picard/).
Assembly: GRCm38.91
Supplementary files format and content: Gene counts in text file.

source_name: Splenocyte

growth_protocol: Rag1-/- (#002216), Dyrk1aflox (#027801), and Dyrk1aBAC (#019460) were obtained from Jackson Laboratories. Transgenic distal Lck-Cre (dLckCre) mice were previously reported. Mice were housed in the Benaroya Research Institute Vivarium in a speciﬁc-pathogen-free (SPF) animal room with unrestricted access to food and water. All murine experiments were performed on male and female mice between 7 and 24 weeks of age, with the approval of the IACUC of Benaroya Research Institute (Seattle, WA).

extract_protocol:
Cells were harvested at 0 and 5 hours and RNA isolated using Qiagen RNeasy kits (Qiagen). RNA was used to construct libraries using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara), with reverse transcription followed by polymerase chain reaction amplification to generate full length amplified cDNA.
Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina) to generate Illumina-compatible barcoded libraries. Libraries were pooled and quantified using a Qubit Fluorometer (Life Technologies).

treatment_protocol: Splenocytes were obtained from 8- to 12-week-old mice by crushing spleens through a 100-mm ﬁlter. Naïve CD4+CD62L+ T cells were isolated from splenocytes using CD4 negative enrichment kits (Stemcell Technologies, Vancouver, Canada) and CD62L microbeads (Miltenyi Biotec, San Diego, CA) per manufacturer’s instructions. Purity (>90%) was verified by ﬂow cytometry. Cells were cultured on polystyrene 96-well plates (Corning, Corning, NY) precoated with anti-CD3 and anti-CD28 antibody (5 mg/ml each, antibodies from BioXcell). Cells (105/well) were cultured in the presence of 5 mg/ml each anti-IL-12, anti-IFN-g, and anti-IL-4 antibody, 0.25 ng/ml TGF-b,  20 ng/ml each IL-6 and IL-1b (all cytokines from Peprotech).  Cells were fed with equal volumes of medium split 1:2 at day 3, and analyzed at day 4. If chemicals (harmine, LCTB-21, iso-LCTB-21) were used, these were added at start and day 2 of culture. These conditions were also used to assess STAT1/STAT3/STAT5 phosphorylation.

tag: Sex

value: male

tag: donor id

value: Splenocyte

value: CD4+ T cell

value: 10uM Harmine

tag: stimulation

value: Il-6, Il-1B, anti-Il-4, anti-Il-12, anti-IFNg, TGFb

tag: time point


title: Clam UF347D-0370

description: UF Phase I


title: Subject UP23 F

value: iMCD patient


title: Splenocyte, lib74670


title: A549_SARS2_nucleocapsid_rep2_heavy_digest

city: Tallahassee

first: Jonathan

middle: H

last: Dennis

state: FL

address: 319 Stadium Drive

department: Biological Science

institute: Florida State University

description:
Library name: A549_SARS2_rep2_heavy_digest
A549 cells expressing SARS2 nucleocapsid

data_processing:
Raw reads were demultiplexed with Cassava, and adapter sequences and low-quality reads were removed using Trimmomatic (version 0.39) (Bolger et al. 2014). BSequences were aligned to the T2T human genome using Bowtie2 with the --end-to-end --no-mixed --no-discordant flags (Langmead and Salzberg 2012). Mitochondrial and duplicate reads were filtered using Samtools (version 1.10) and Picardtools (version 2.27.3) (Li et al. 2009). Read-depth normalization was performed using Picardtools, based on the number of paired-end reads mapping to a 2 kb window centered on the TSS of RefSeq genes. Normalized light and heavy digests were merged using Picardtools to generate total nucleosome profiles. Nucleosome footprints for merged, light, and heavy digests were calculated using DANPOS (version 3.1.1) (Chen et al. 2013b). The log₂ ratio of light to heavy digests was computed at each time point to determine nucleosome sensitivity using deepTools (version 3.5.1) (Ramírez et al. 2014).
Nucleosome distribution changes were extracted from DANPOS output using a custom R script with defined cutoffs for repositioning and occupancy alterations. Repositioned nucleosomes were defined as shifts in summit positions >80 bp between conditions. Changes in nucleosome occupancy were identified as log₂ fold changes >5 with a p-value and FDR <0.05 compared to empty vector controls. Only nucleosomes consistently altered across replicates were considered high-confidence and used for further analysis. Statistically significant sensitive and resistant nucleosomes were extracted using another custom R script. Sensitivity was defined by a log₂ fold change in summit score >1.0, while resistance was defined by a fold change <−1.0, with a p-value and FDR <0.05.
Assembly: hs1/T2T
Supplementary files format and content: bigwig files of nucleosome distribution and nuclease sensitivity singal

growth_protocol: Mammalian expression vectors encoding nucleocapsid genes from SARS-CoV-2, OC43, NL63, HKU1, and 229E, driven by a CMV promoter, were obtained from the Ginkgo Bioworks COVID-19 Plasmid Collection via Addgene. Custom plasmids for MERS-CoV and SARS-CoV nucleocapsids were synthesized by Twist Biosciences using the same backbone. An empty vector control was generated by Q5-directed mutagenesis (New England BioLabs, #E0554S) of the NL63 construct to remove the nucleocapsid gene. A549 lung epithelial cells (ATCC, CCL-185) were cultured in F-12K media (Gibco) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin and maintained at 37°C with 5% CO₂. Cells were transfected with nucleocapsid or empty vector plasmids using Turbofect (Thermo Scientific) following the manufacturer’s protocol. Stably transfected clones were selected with puromycin (Gibco), screened by PCR, and confirmed by Sanger sequencing.

extract_protocol:
Cells were crosslinked with 1% v/v formaldehyde (Sigma-Aldrich) and incubated for 10 minutes at room temperature while rocking. Excess formaldehyde was quenched with 125mM glycine and cells were washed twice in PBS. Cells were resuspended in nuclei isolation buffer (10 mM HEPES at pH 7.8, 2 mM MgOAc2, 0.3 M sucrose, 1 mM CaCl2 and 1% Triton-X) and pelleted by centrifugation at 1000 × g for 10 min at 4 °C. Nuclei were washed twice in nuclei isolation buffer and nuclei purity was confirmed by DAPI staining.  Each condition was processed in biological replicates. For each reaction, 2.5 × 10⁶ nuclei were resuspended in 500 µL of nuclei isolation buffer and digested with Micrococcal Nuclease (MNase) (Worthington) under light (5U) or heavy (200U) conditions for 10 minutes at 37°C. Digestion was stopped with 50 mM EDTA. Protein-DNA crosslinks were reversed by treating MNase-digested nuclei with 0.2 mg/mL proteinase K and 1% SDS, followed by overnight incubation at 65°C. DNA was purified using a guanidinium-isopropanol and ethanol on a silica column.
Mononucleosomal and sub-mononucleosomal DNA (<200 bp) was isolated from a 2% agarose gel and purified by glycogen precipitation. MNase sequencing libraries were prepared using the Accel-NGS®2S Plus DNA Library Kit (Swift) for Illumina®, with a minimum of 10 ng input DNA per digestion. Libraries were indexed using the Accel-NGS 2S Unique Dual Indexing Kit, normalized with Normalase, and quality-checked via D1000 Tapestation. Library molar concentrations were determined via KAPA qPCR and size-corrected using Tapestation data. We used a previously validated Roche NimbleGen SeqCap EZ Library (Sexton et al. 2016; Druliner et al. 2016) to capture 2kb regions flanking the transcription start site (TSS) of all human genes. TSS sequences were repeat masked with human COT DNA, and library adapters were blocked using universal oligos. Biotinylated capture oligos were hybridized to input libraries for 48 hours and purified with streptavidin beads. Enriched sequences were amplified via 15-cycle PCR using TruSeq primers. Final libraries were assessed via Tapestation, and molar concentrations were determined using KAPA qPCR. Paired-end 50 bp sequencing was performed on an Illumina NovaSeq 6000 at the FSU College of Medicine.

value: lung  epithelial cell


title: A549_SARS1_nucleocapsid_rep2_heavy_digest

description:
Library name: A549_SARS1_rep2_heavy_digest
A549 cells expressing SARS1 nucleocapsid


title: A549_SARS2_nucleocapsid_rep1_heavy_digest

description:
Library name: A549_SARS2_rep1_heavy_digest
A549 cells expressing SARS2 nucleocapsid


title: Clam UF344B-0698

description: UF Phase III

value: Hemocytes in ethanol


title: A549_SARS1_nucleocapsid_rep1_heavy_digest

description:
Library name: A549_SARS1_rep1_heavy_digest
A549 cells expressing SARS1 nucleocapsid


title: Clam UF342D-0476

description: UF Phase I


title: Splenocyte, lib74668


title: A549_MERS_nucleocapsid_rep2_heavy_digest

description:
Library name: A549_MERS_rep2_heavy_digest
A549 cells expressing MERS nucleocapsid


title: Splenocyte, lib74667


title: Clam UF341B-0697

description: UF Phase III


title: A549_MERS_nucleocapsid_rep1_heavy_digest

description:
Library name: A549_MERS_rep1_heavy_digest
A549 cells expressing MERS nucleocapsid


title: Splenocyte, lib74666


title: Subject UP19 R


title: Subject UP18 R


title: Clam UF340D-0369

description: UF Phase I


title: A549_null_nucleocapsid_rep1_heavy_digest

description:
Library name: A549_null_rep1_heavy_digest
A549 cells expressing empty vector nucleocapsid

value: empty vector


title: Splenocyte, lib74665


title: Clam UF33D-0422

description: UF Phase I

source_name: Clam UF33D-0422


title: Splenocyte, lib74669


title: Subject UP22 R


title: Subject UP17 R


title: Clam UF339D-0436

description: UF Phase I


title: Subject UP21 R


title: A549_NL63_nucleocapsid_rep2_heavy_digest

description:
Library name: A549_NL63_rep2_heavy_digest
A549 cells expressing NL63 nucleocapsid


title: Subject UP16 R


title: Splenocyte, lib74663


title: Clam UF337P-0502

description: UF Phase I


title: Clam UF338S-0696

description: UF Phase III


title: A549_OC43_nucleocapsid_rep2_heavy_digest

description:
Library name: A549_OC43_rep2_heavy_digest
A549 cells expressing OC43 nucleocapsid


title: Subject UP15 R


title: A549_NL63_nucleocapsid_rep1_heavy_digest

description:
Library name: A549_NL63_rep1_heavy_digest
A549 cells expressing NL63 nucleocapsid


title: Subject UP20 R


title: Splenocyte, lib74662


title: Splenocyte, lib74661


title: Subject UP14 R


title: A549_OC43_nucleocapsid_rep1_heavy_digest

description:
Library name: A549_OC43_rep1_heavy_digest
A549 cells expressing OC43 nucleocapsid


title: Subject UP13 R


title: Clam UF335D-0419

description: UF Phase I


title: A549_null_nucleocapsid_rep2_heavy_digest

description:
Library name: A549_null_rep2_heavy_digest
A549 cells expressing empty vector nucleocapsid


title: Splenocyte, lib74660


title: A549_229E_nucleocapsid_rep2_heavy_digest

description:
Library name: A549_229E_rep2_heavy_digest
A549 cells expressing 229E nucleocapsid


title: Clam UF332D-0435

description: UF Phase I


title: Splenocyte, lib74664


title: Subject UP12 R


title: Clam UF329D-0467

description: UF Phase I


title: A549_229E_nucleocapsid_rep1_heavy_digest

description:
Library name: A549_229E_rep1_heavy_digest
A549 cells expressing 229E nucleocapsid


title: Subject UP11 R


title: DicerM KO cells and AIV

city: Nanjing

first: Yaotang

last: Wu

address: Nanjing Agricultural University, Wei gang 1

country: China

institute: Nanjing Agricultural University

description: Library name: Group7

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates. The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: GCA_016699485.1
Supplementary files format and content: excel,expression profiles

organism: Gallus gallus

source_name: cell line

growth_protocol: HD11 knockout cells were commercially obtained from American Type Culture Collection (ATCC) and maintained in RPMI 1640  supplemented with 10% FBS, penicillin (100 U/ml), and streptomycin (100 mg/mL) at 37℃ in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (v4.2) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: Macrophages

tag: genotype

value: knockout cells

value: AIV-infection


title: Dicer KO cells and AIV

description: Library name: Group6


title: A549_HKU1_nucleocapsid_rep1_heavy_digest

description:
Library name: A549_HKU1_rep1_heavy_digest
A549 cells expressing HKU1 nucleocapsid


title: Subject UP09 R


title: Subject UP10 R


title: Clam UF320D-0445

description: UF Phase I

value: Adductor muscle


title: HD11 cells and AIV

description: Library name: Group5

value: WT


title: Subject UP08 R


title: Clam UF31D-0448

description: UF Phase I

source_name: Clam UF31D-0448


title: Ago2 KO cells

description: Library name: Group4

value: Non-infection


title: A549_SARS2_nucleocapsid_rep1_light_digest

description:
Library name: A549_SARS2_rep1_light_digest
A549 cells expressing SARS2 nucleocapsid


title: DicerM KO cells

description: Library name: Group3


title: Subject UP07 F

description:
raw data file: ACA Array version 3 Platform Raw MFI.xlsx
Antibodies in samples bind to barcoded beads conjugated to antigens. Antibody reactivity was quantified by the fluorescence measured as MFI from the secondary antibody.

source_name: Serum/Plasma


title: A549_SARS1_nucleocapsid_rep2_light_digest

description:
Library name: A549_SARS1_rep2_light_digest
A549 cells expressing SARS1 nucleocapsid


title: Clam UF316S-0693

description: UF Phase III


title: Subject UP06


title: Clam UF315S-0692

description: UF Phase III


title: Dicer KO cells

description: Library name: Group2


title: Ago2 KO cells and AIV

description: Library name: Group8


title: A549_HKU1_nucleocapsid_rep2_heavy_digest

description:
Library name: A549_HKU1_rep2_heavy_digest
A549 cells expressing HKU1 nucleocapsid


title: Clam UF325D-0475

description: UF Phase I


title: Clam UF314D-0375

description: UF Phase I


title: Clam UF323S-0614

description: UF Phase II


title: Subject UP05


title: HD11 cells AIV-H9N2

description: Library name: H9N2

growth_protocol: HD11 cells were commercially obtained from American Type Culture Collection (ATCC) and maintained in RPMI 1640  supplemented with 10% FBS, penicillin (100 U/ml), and streptomycin (100 mg/mL) at 37℃ in a humidified atmosphere with 5% CO2.

value: AIV-H9N2 infection


title: A549_MERS_nucleocapsid_rep2_light_digest

description:
Library name: A549_MERS_rep2_light_digest
A549 cells expressing MERS nucleocapsid


title: Subject UP04


title: Clam UF313S-0691

description: UF Phase III


title: A549_MERS_nucleocapsid_rep1_light_digest

description:
Library name: A549_MERS_rep1_light_digest
A549 cells expressing MERS nucleocapsid


title: A549_SARS2_nucleocapsid_rep2_light_digest

description:
Library name: A549_SARS2_rep2_light_digest
A549 cells expressing SARS2 nucleocapsid


title: Clam UF312P-0494

description: UF Phase I


title: Subject UP03


title: A549_null_nucleocapsid_rep2_light_digest

description:
Library name: A549_null_rep2_light_digest
A549 cells expressing empty vector nucleocapsid


title: HD11 cells Blank

description: Library name: Blank

value: Blank


title: Subject UP02


title: A549_null_nucleocapsid_rep1_light_digest

description:
Library name: A549_null_rep1_light_digest
A549 cells expressing empty vector nucleocapsid


title: A549_SARS1_nucleocapsid_rep1_light_digest

description:
Library name: A549_SARS1_rep1_light_digest
A549 cells expressing SARS1 nucleocapsid


title: TJK085_207492260081_R08C02

city: Central Jakarta

first: Rafika

middle: Indah

last: Paramita

address: Salemba Raya

country: Indonesia

institute: Faculty of Medicine Universitas Indonesia

description: Genomic DNA extracted from blood buffy coat of breast cancer patient was genotyped using Infinium Asian Screening Array BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48℃, single-base extension and allele-specific staining was performed on a VWR chamber rack system (Blanchardstown, Dublin, Ireland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with PB1/XC4, dried for 1 hour and scanned on a iScan (Illumina).

data_processing:
Genomic DNA extracted from sample was genotyped using Infinium Asian Screening Array BeadChips (Illumina).
Genotype: AA,AB,BB

label: Cy3, Cy5

source_name: Breast cancer

label_protocol: 50 ng of genomic DNA was whole-genome amplified in an overnight reaction at 37℃ using amplification master mix (MSM) and amplifiaction mix (MA2). After incubation the amplified DNA was fragmented with fragmentation mix (FMS), precipitated with isopropanol and precipitation mix (PM1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood buffy coat was performed using QIAmp DNA Mini Kit (Qiagen Sciences, Germantown, Maryland).

tag: disease state

value: Breast cancer patient

tag: gender

value: Female

value: Blood

tag: subtype

value: TNBC


title: Subject UP01


title: HD11 cells

description: Library name: Group1


title: HD11 DicerM KD Blank

description: Library name: NO5

value: Knockdown


title: A549_NL63_nucleocapsid_rep2_light_digest

description:
Library name: A549_NL63_rep2_light_digest
A549 cells expressing NL63 nucleocapsid


title: Clam UF309D-0359

description: UF Phase I


title: TJK084_207492260081_R07C02

value: LMNA


title: TJK082_207492260081_R06C02


title: HD11 Dicer KD IBV-QX

description: Library name: NO4

value: IBV-QX infection


title: A549_NL63_nucleocapsid_rep1_light_digest

description:
Library name: A549_NL63_rep1_light_digest
A549 cells expressing NL63 nucleocapsid

value: lung  epithelial cell


title: HD11 Dicer KD Blank

description: Library name: NO3


title: A549_OC43_nucleocapsid_rep2_light_digest

description:
Library name: A549_OC43_rep2_light_digest
A549 cells expressing OC43 nucleocapsid


title: Clam UF308D-0364

description: UF Phase I


title: HD11 cells IBV-QX

description: Library name: NO2


title: TJK079_207492260081_R05C02


title: Clam UF307P-0501

description: UF Phase I


title: A549_OC43_nucleocapsid_rep1_light_digest

description:
Library name: A549_OC43_rep1_light_digest
A549 cells expressing OC43 nucleocapsid


title: TJK076_207492260081_R04C02


title: HD11 cells Blank

description: Library name: NO1


title: A549_229E_nucleocapsid_rep2_light_digest

description:
Library name: A549_229E_rep2_light_digest
A549 cells expressing 229E nucleocapsid


title: Clam UF311D-0387

description: UF Phase I


title: Clam UF306D-0453

description: UF Phase I


title: TJK075_207492260081_R12C02


title: Clam UF303S-0690

description: UF Phase III

value: Hemocytes in ethanol


title: PANC1，OE-REG3A，Rep3

first: Kunxin

last: Xie

state: China

address: 101Longmian Avenue, Jiangning District, Nanjing

institute: Nanjing Medical University

description: Library name: OE-REG3

data_processing:
DEseq2 and limma
Assembly: hg18
Supplementary files format and content: tab-delimited text file including the count and fpkm matrix

extract_protocol:
After RNA was extracted, 1.5ug of it was used for subsequent library building experiments
We built libraries according to the requirements provided by the sequencing machine


title: Clam UF30S-0644

description: UF Phase III

source_name: Clam UF30S-0644


title: Clam UF302S-0639

description: UF Phase II


title: TJK064_207492260081_R02C02

value: LMNB


title: A549_229E_nucleocapsid_rep1_light_digest

description:
Library name: A549_229E_rep1_light_digest
A549 cells expressing 229E nucleocapsid


title: PANC1，OE-REG3A，Rep1

description: Library name: OE-REG1


title: TJK070_207492260081_R03C02


title: A549_HKU1_nucleocapsid_rep1_light_digest

description:
Library name: A549_HKU1_rep1_light_digest
A549 cells expressing HKU1 nucleocapsid


title: Clam UF301S-0626

description: UF Phase II


title: Clam UF29P-0600

description: UF Phase II

source_name: Clam UF29P-0600


title: TJK063_207492260081_R01C02


title: HD11 DicerM KD IBV-QX

description: Library name: NO6

value: Macrophages


title: A549_SARS2_nucleocapsid_rep2_merged

description:
Library name: A549_SARS2_rep2_merged
A549 cells expressing SARS2 nucleocapsid


title: TJK062_207492260081_R12C01


title: A549_SARS2_nucleocapsid_rep1_merged

description:
Library name: A549_SARS2_rep1_merged
A549 cells expressing SARS2 nucleocapsid


title: PANC1，WT，Rep2

description: Library name: WT2


title: Clam UF299D-0360

description: UF Phase I


title: A549_HKU1_nucleocapsid_rep2_light_digest

description:
Library name: A549_HKU1_rep2_light_digest
A549 cells expressing HKU1 nucleocapsid


title: PANC1，WT，Rep3

description: Library name: WT3


title: TJK061_207492260081_R11C01


title: A549_SARS1_nucleocapsid_rep2_merged

description:
Library name: A549_SARS1_rep2_merged
A549 cells expressing SARS1 nucleocapsid


title: Clam UF297P-0489

description: UF Phase I


title: TJK060_207492260081_R10C01


title: PANC1，WT，Rep1

description: Library name: WT1


title: RNA-Seq CDK6-K43M, replicate 3

city: Vienna

first: Thorsten

last: Klampfl

address: Veterinaerplatz 1

country: Austria

institute: University of Veterinary Medicine Vienna

data_processing:
Alignment to genome version GRCm38 was done using STAR with a Gencode M13 gene model
Adapter trimming and removing of low quality bases was performed using Trimmomatic
Counting of reads was done using featureCounts
Assembly: GRCm38/mm10
Supplementary files format and content: the processed data file contains raw (not normalised) read counts for each gene in each sample

source_name: bone marrow cells

growth_protocol: Cells were cultured in RPMI incl. 10% FCS,50 μmol/l 2-mercaptoethanol, 100 u/ml penicillin and 100 μg/ml streptomycin

extract_protocol:
QIAGEN RNeasy extraction kit
SENSE mRNA-Seq Library Prep kit, 50 bp single-end

value: bone marrow cells

value: Pre/Pro-B-cells


title: A549_SARS1_nucleocapsid_rep1_merged

description:
Library name: A549_SARS1_rep1_merged
A549 cells expressing SARS1 nucleocapsid


title: PANC1，OE-REG3A，Rep2

description: Library name: OE-REG2


title: Clam UF295D-0466

description: UF Phase I

value: Adductor muscle


title: RNA-Seq CDK6-K43M, replicate 2


title: A549_MERS_nucleocapsid_rep2_merged

description:
Library name: A549_MERS_rep2_merged
A549 cells expressing MERS nucleocapsid


title: Clam UF294D-0374

description: UF Phase I


title: RNA-Seq CDK6-K43M, replicate 1


title: TJK055_207492260081_R08C01


title: A549_MERS_nucleocapsid_rep1_merged

description:
Library name: A549_MERS_rep1_merged
A549 cells expressing MERS nucleocapsid


title: TJK054_207492260081_R07C01


title: A549_null_nucleocapsid_rep2_merged

description:
Library name: A549_null_rep2_merged
A549 cells expressing empty vector nucleocapsid

value: empty vector


title: TJK053_207492260081_R06C01


title: scRNAseq 10x VDJ immunoprofiling, NOD BDC2.5mi/IAg7-NP-treated, Tet+ T cells

city: Barcelona

first: Josep

last: Garnica

address: Rosselló, 149

institute: IDIBAPS

library_source: transcriptomic single cell

data_processing:
Cellranger v6 (10X Genomics)
Downstream - Seurat, Signac
Assembly: GRCm38.p6
Supplementary files format and content: Seurat object, feature count matrices

source_name: Spleen

extract_protocol:
Cells were partitioned into Gel Bead‑In‑Emulsions with a Target Cell Recovery of 5.000 total cells.Cell number and viabilitywere verified using a TC20™ Automated Cell Counter (Bio-Rad Laboratories, Hercules, CA, USA).
cDNA sequencing libraries were prepared using the NextGEM Single-cell 3’ mRNA kit (V3.1; 10X Genomics) following manufacturer's instructions. Briefly, after GEM-RT clean up, cDNA was amplified during 13 cycles and cDNA QC and quantification were performed on anAgilent Bioanalyzer High Sensitivity chip (Agilent Technologies).
cDNA libraries were indexed by PCR using thePN-220103 Chromiumi7 Sample Index Plate.Size distribution and concentration of 3'cDNAlibraries were verified on an Agilent Bioanalyzer High Sensitivity chip(Agilent Technologies). Finally, sequencing ofcDNA libraries was carried out on a Illumina HiSeq 2500 (Illumina) to obtain approximately25,000-50,000paired-end 75bpreads per cell, respectively.

value: Spleen

value: CD4+ Tet+

value: NOD mouse


title: scRNAseq, B6 Tbx21Cre.Il10.loxP EAE mice treated with pMOG38-49/I-Ab-NP, Tet+ PD1hi ICOShi cells

value: CD4+ Tet+ PD1hi ICOShi

value: B6 mouse


title: Clam UF288D-0382

description: UF Phase I


title: A549_null_nucleocapsid_rep1_merged

description:
Library name: A549_null_rep1_merged
A549 cells expressing empty vector nucleocapsid


title: TJK051_207492260081_R05C01

description: Genomic DNA extracted from blood buffy coat of breast cancer patient was genotyped using Infinium Asian Screening Array BeadChips (Illumina).

value: Breast cancer patient

value: Female

value: Blood

value: TNBC


title: scRNAseq, Tet+ T cells from BDC2.5mi/IAg7-NP-treated NOD CD4Cre.IRF4.loxP mice


title: Clam UF284D-0444

description: UF Phase I


title: TJK047_207492260081_R04C01


title: A549_NL63_nucleocapsid_rep2_merged

description:
Library name: A549_NL63_rep2_merged
A549 cells expressing NL63 nucleocapsid

value: lung  epithelial cell


title: Clam UF283D-0443

description: UF Phase I


title: scRNAseq, pancreatic islets Tet+ T cells from NOD mice treated with BDC2.5mi/IAg7-NP

source_name: pancreatic islets

value: pancreatic islets


title: A549_NL63_nucleocapsid_rep1_merged

description:
Library name: A549_NL63_rep1_merged
A549 cells expressing NL63 nucleocapsid


title: TJK059_207492260081_R09C01

value: LMNB


title: A549_OC43_nucleocapsid_rep2_merged

description:
Library name: A549_OC43_rep2_merged
A549 cells expressing OC43 nucleocapsid


title: TJK044_207492260081_R11C02

value: LMNA


title: Clam UF281D-0418

description: UF Phase I


title: scRNAseq, NOD.SCID  transfused with CXCR5+/PD1+CD4+ from CD4.cre+Blimp1-loxp+/+, Tet+ T cells

value: NOD.SCID mouse


title: TJK043_207492260081_R02C01


title: A549_OC43_nucleocapsid_rep1_merged

description:
Library name: A549_OC43_rep1_merged
A549 cells expressing OC43 nucleocapsid


title: Clam UF292D-0479

description: UF Phase I


title: scRNAseq, B6 EAE mice treated with pMOG38-49/I-Ab-NP, Tet+ PD1hi ICOShi cells


title: Clam UF280S-0688

description: UF Phase III

value: Hemocytes in ethanol


title: Clam UF27D-0447

description: UF Phase I

source_name: Clam UF27D-0447

value: Adductor muscle


title: scRNAseq, NOD.SCID transfused with CXCR5+/PD1+CD4+ from NOD.CD4Cre, Tet+ T cells


title: A549_229E_nucleocapsid_rep2_merged

description:
Library name: A549_229E_rep2_merged
A549 cells expressing 229E nucleocapsid


title: scRNAseq, NOD.SCID transfused with CXCR5+/PD1+CD4+ from NOD, Tet+ T cells


title: TJK041_207492260081_R01C01


title: Clam UF289S-0632

description: UF Phase II


title: TJK040_207492260152_R12C02


title: A549_229E_nucleocapsid_rep1_merged

description:
Library name: A549_229E_rep1_merged
A549 cells expressing 229E nucleocapsid


title: scRNAseq, NOD BDC2.5mi/IAg7-NP-treated Withdrawal 10wk Tet+ T cells


title: Clam UF279P-0493

description: UF Phase I


title: A549_HKU1_nucleocapsid_rep2_merged

description:
Library name: A549_HKU1_rep2_merged
A549 cells expressing HKU1 nucleocapsid


title: Clam UF277D-0434

description: UF Phase I


title: TJK038_207492260152_R11C02


title: Clam UF278D-0381

description: UF Phase I


title: TJK046_207492260081_R03C01


title: scRNAseq, NOD BDC2.5mi/IAg7-NP-treated Withdrawal 5wk Tet+ T cells


title: A549_HKU1_nucleocapsid_rep1_merged

description:
Library name: A549_HKU1_rep1_merged
A549 cells expressing HKU1 nucleocapsid


title: Clam UF275D-0377

description: UF Phase I


title: scRNAseq, NOD BDC2.5mi/IAg7-NP-treated Withdrawal 0wk Tet+ T cells


title: TJK037_207492260152_R10C02


title: PC9_WT_osi_TOP2B rep2

city: New Haven

first: Eric

last: Sun

state: CT

address: 10 Amistad St

department: Genetics

institute: Yale University

description:
Library name: PC9_WT_osi_TOP2B_rep2
CUT&RUN Antibody: TOP2B

data_processing:
Adapter sequences from paired-end sequencing reads were trimmed with Trimmomatic and quality control was performed using FastQC. Bowtie2 version 2.4.2 was used to align reads to the GRCh37 genome using the –very-sensitive flag and allowing for one mismatch. SAMtools version 1.16 was used to remove unmapped reads, secondary alignment reads, and reads with a Phred score of <30.For SEACR was used to call peaks. bigWig signal was normalized via E. coli spike-in DNA, and normalized bigWig signals were used as inputs for SEACR using the “stringent” settings. BEDTools was used to intersect peaks between biological replicates. Deeptools version 3.5.1 was used for data visualization. Plots depicting CUT&RUN signal were generated by using Deeptools bamCompare to normalize signal by CPM and to H2A, and duplicates were ignored. In all plots, the mean normalized bigWig signal between two biological replicates is plotted. Signal is Peak intersections were performed using BEDTools v2.30.
Assembly: GRCh37
Supplementary files format and content: Raw .fq.gz files are provided. bigWig files are mean files derived from two biological replicates that were derived from Counts Per Million normalization and normalization to spike-in E. coli DNA. BED files are intersections of SEACR stringent peak calls between two biological replicates.
Library strategy: CUT&RUN

source_name: Lung

growth_protocol: Cells were cultured in RPMI-1640 medium (Thermo Fisher, 11875119) with 1% penicillin-streptomycin (pen-strep, Thermo Fisher, 15140122) and 10% fetal bovine serum (FBS).

extract_protocol:
CUT&RUN was performed using the CUTANA ChIC/CUT&RUN Kit (EpiCypher 141048) according to the manufacturer’s instructions. Approximately 5 x 105 cells were used per reaction. The following antibodies were used: Histone H2A (12349), and TOP2B (abcam ab72334). One microliter of chromatin was analyzed via Agilent TapeStation to determine fragment size. DNA concentration was measured using Qubit (Invitrogen Q32854). Library preparation was performed using the CUTANA CUT&RUN Library Prep Kit (EpiCypher 14-1001) using 2.5 ng chromatin as input. Pooled libraries were sequenced by Novogene with NovaSeq with 20 million paired-end reads sequenced per library.
Library preparation was performed using the CUTANA CUT&RUN Library Prep Kit (EpiCypher 14-1001) using 2.5 ng chromatin as input. Pooled libraries were sequenced by Novogene with NovaSeq with 20 million paired-end reads sequenced per library.

treatment_protocol: Osimertinib-treated cells were treated with osimertinib over the course of 6-8 weeks via dose escalation starting from 100nM Osimertinib.

value: Lung

value: lung adenocarcinoma

value: Wild-type

value: Osimertinib


title: TJK035_207492260152_R09C02


title: Clam UF271D-0433

description: UF Phase I


title: TJK033_207492260152_R08C02


title: HC, Day 28, RNA-Seq, Replicate 4

city: Frankfurt am Main

first: Marcel

last: Schulz

address: Theodor-Stern-Kai 7, Haus 26

country: Germany

institute: Goethe University and Uniklinikum Frankfurt

data_processing:
Adaptor sequences were trimmed with TrimGalore [https://github.com/FelixKrueger/ TrimGalore] based on the library preparation protocol. Salmon was used for the estimation of gene expression values using transcript alignments from STAR v2.28
Assembly: mm10
Supplementary files format and content: salmon TPM

source_name: Hematopoietic cells

growth_protocol: see Methods in manuscript

extract_protocol:
Cardiomyocytes were enriched by performing repeated centrifugation steps (20 x g, 2 minutes). The supernatant of the centrifugation step was used to isolate hematopoietic cells, endothelial cells, and fibroblasts. Hematopoietic and endothelial cells were isolated by magnetic separation. Cells not bound to the magnetic beads or columns were used for cardiac fibroblast enrichment by a plating step with uncoated dishes. After 40 minutes, predominantly DDR2-positive fibroblasts adhered and were used for RNA isolation. Cells extracted from three mice were pooled to generate enough cells for one of four biological replicate sequencing samples for each timepoint. Total RNA was isolated from CM, EC, HC and FB using the Qiagen (Hilden, Germany) miRNeasy Kit involving column DNAse digestion. RNA quantity was fluorometrically measured using the Qubit 4 (Thermo Fisher) RNA HS Assay Kit and integrity of the RNA was verified using the Agilent Bioanalyzer RNA Pico chips.
Long RNA was converted into Illumina compatible libraries using the CATS Total RNA-seq Kit v2 with rRNA depletion (Diagenode). After the depletion, this procedure involves the fragmentation of RNA, 3 ́-polyadenylation and cDNA synthesis primed by oligo-T. Addition of a template switch oligo allows in combination with a suitable reverse transcriptase allows then the generation of double stranded cDNA with adaptor sequences for further amplification.

treatment_protocol: see Methods in manuscript

value: Hematopoietic cells

value: Day 28


title: Clam UF270S-0685

description: UF Phase III


title: HC, Day 28, RNA-Seq, Replicate 3


title: PC9_WT_osi_TOP2B rep1

description:
Library name: PC9_WT_osi_TOP2B_rep1
CUT&RUN Antibody: TOP2B


title: H1975.H3K27ac

city: HOUSTON

first: Yonathan

last: Lissanu

state: TEXAS

address: 1515 Holcombe Blvd

department: Cardiovascular and Thoracic Surgery

institute: md anderson cancer centre

description: Library name: Chip

data_processing:
ChIPseq reads were aligned to reference genome hg38 using BWA 0.7.9a-r786
Assembly: hg38
Supplementary files format and content: bw file

growth_protocol: The cells were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin–streptomycin at 37 °C with 5% CO2.

extract_protocol:
ChiP DNA was prepared according to "Blecher-Gonen, R. et al. High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states. Nat Protoc 8, 539-554, doi:10.1038/nprot.2013.023 (2013)."
Libraries were prepared using the NEBNext Ultra II DNA library prep kit (Cat# E7645S, NEB) according to manufacturer's instructions.

treatment_protocol: No treatment

value: Lung cancer

value: WT

value: No treatment


title: HC, Day 28, RNA-Seq, Replicate 2


title: PC9_WT_osi_H2A rep2

description:
Library name: PC9_WT_osi_H2A_rep2
CUT&RUN Antibody: H2A


title: TJK030_207492260152_R06C02

value: Breast cancer patient

value: Female

value: Blood


title: Clam UF269S-0684

description: UF Phase III


title: PC9_WT_osi_H2A rep1

description:
Library name: PC9_WT_osi_H2A_rep1
CUT&RUN Antibody: H2A


title: HC, Day 28, RNA-Seq, Replicate 1


title: TJK029_207492260152_R05C02

value: LMNB


title: HC, Day 14, RNA-Seq, Replicate 4

value: Day 14


title: PC9_WT_TOP2B rep2

description:
Library name: PC9_WT_TOP2B_rep2
CUT&RUN Antibody: TOP2B

value: Untreated


title: Clam UF267S-0631

description: UF Phase II


title: TJK028_207492260152_R04C02


title: PC9_WT_TOP2B rep1

description:
Library name: PC9_WT_TOP2B_rep1
CUT&RUN Antibody: TOP2B


title: TJK026_207492260152_R03C02


title: HC, Day 14, RNA-Seq, Replicate 3


title: HC, Day 14, RNA-Seq, Replicate 2


title: Clam UF266S-0682

description: UF Phase III

value: Hemocytes in ethanol


title: PC9_WT_H2A rep2

description:
Library name: PC9_WT_H2A_rep2
CUT&RUN Antibody: H2A


title: TJK025_207492260152_R02C02

value: LMNA


title: PC9_WT_H2A rep1

description:
Library name: PC9_WT_H2A_rep1
CUT&RUN Antibody: H2A

value: Lung


title: TJK031_207492260152_R07C02

description: Genomic DNA extracted from blood buffy coat of breast cancer patient was genotyped using Infinium Asian Screening Array BeadChips (Illumina).


title: TJK022_207492260152_R01C02


title: Clam UF261D-0432

description: UF Phase I

value: Adductor muscle


title: HC, Day 14, RNA-Seq, Replicate 1


title: PC9_M7A_KO_osi_TOP2B rep2

description:
Library name: PC9_M7A_KO_osi_TOP2B_rep2
CUT&RUN Antibody: TOP2B

value: lung adenocarcinoma

value: METTL7A knockout


title: HC, Day 7, RNA-Seq, Replicate 4

value: Hematopoietic cells

value: Day 7


title: TJK019_207492260152_R12C01


title: Clam UF26S-0643

description: UF Phase III

source_name: Clam UF26S-0643


title: HC, Day 7, RNA-Seq, Replicate 3


title: Clam UF260S-0607

description: UF Phase II


title: PC9_M7A_KO_osi_TOP2B rep1

description:
Library name: PC9_M7A_KO_osi_TOP2B_rep1
CUT&RUN Antibody: TOP2B

value: Osimertinib


title: TJK018_207492260152_R11C01


title: HC, Day 7, RNA-Seq, Replicate 2


title: Clam UF25D-0421

description: UF Phase I

source_name: Clam UF25D-0421


title: PC9_M7A_KO_osi_H2A rep2

description:
Library name: PC9_M7A_KO_osi_H2A_rep2
CUT&RUN Antibody: H2A


title: Clam UF268S-0683

description: UF Phase III


title: HC, Day 7, RNA-Seq, Replicate 1


title: PC9_M7A_KO_osi_H2A rep1

description:
Library name: PC9_M7A_KO_osi_H2A_rep1
CUT&RUN Antibody: H2A


title: Clam UF259S-0680

description: UF Phase III


title: TJK016_207492260152_R10C01


title: PC9_M7A_KO_TOP2B rep2

description:
Library name: PC9_M7A_KO_TOP2B_rep2
CUT&RUN Antibody: TOP2B


title: TJK015_207492260152_R09C01


title: HC, Day 3, RNA-Seq, Replicate 4

value: Day 3


title: PC9_M7A_KO_TOP2B rep1

description:
Library name: PC9_M7A_KO_TOP2B_rep1
CUT&RUN Antibody: TOP2B


title: HC, Day 3, RNA-Seq, Replicate 3


title: Clam UF257P-0598

description: UF Phase II


title: TJK014_207492260152_R08C01

value: TNBC


title: Clam UF262S-0681

description: UF Phase III


title: PC9_M7A_KO_H2A rep2

description:
Library name: PC9_M7A_KO_H2A_rep2
CUT&RUN Antibody: H2A


title: Clam UF255D-0452

description: UF Phase I


title: HC, Day 3, RNA-Seq, Replicate 2


title: TJK012_207492260152_R06C01

value: Breast cancer patient


title: PC9_M7A_KO_H2A rep1

description:
Library name: PC9_M7A_KO_H2A_rep1
CUT&RUN Antibody: H2A


title: HC, Day 3, RNA-Seq, Replicate 1


title: Clam UF254D-0368

description: UF Phase I


title: TJK017_207492260081_R10C02

value: Female


title: TJK011_207492260152_R07C01

value: Blood


title: Clam UF253S-0610

description: UF Phase II


title: HC, Day 1, RNA-Seq, Replicate 3

value: Day 1


title: TJK008_207492260152_R05C01


title: PC9_OR_EV_MYC_rep2

description: Library name: PC9_OR_EV_MYC_rep2

data_processing:
Adapter sequences from paired-end sequencing reads were trimmed with Trimmomatic and quality control was performed using FastQC. Bowtie2 version 2.4.2 was used to align reads to the GRCh37 genome using the –very-sensitive flag and allowing for one mismatch. SAMtools version 1.16 was used to remove unmapped reads, secondary alignment reads, and reads with a Phred score of <30. Macs2 version 2.2.7.1 was used to call peaks with default peak-calling settings. Peaks were called against input chromatin. Peaks from 2 biological replicates were merged. Deeptools version 3.5.1 was used for ChIP-seq data visualization. Plots depicting ChIP-seq signal were generated by using Deeptools bamCoverage to normalize signal by CPM and duplicates were ignored. Peak intersections were performed using BEDTools v2.30 and quantified using BEDTools Fisher. The mean bigWig signal between biological replicates was plotted.
Assembly: GRCh37
Supplementary files format and content: .fq.gz files are provided raw files. .bigWig files are mean count per million signal files. BED files are merged MACS2 narrowPeak files from biological replicates.

extract_protocol:
ChIP-seq was performed using the Active Motif ChIP-IT Express Kit (Active Motif 53008) according to the manufacturer’s instructions. Approximately 2 x 107 cells were used per biological replicate. Chromatin was sheared using a Covaris S220 using a peak power of 175W, duty factor of 10%, 200 cycles/burst, and 160 seconds per run. One uL of decrosslinked chromatin was analyzed via Agilent TapeStation to determine fragment size, and DNA concentration was measured using Qubit (Invitrogen Q32854). c-MYC-tag (Cell Signaling Technologies 2276S) antibody was used. 20 ug of chromatin was pre-incubated with antibody overnight at 4ºC. Protein G beads were subsequently added to antibody-bound chromatin and incubated for 4 hours at 4ºC.
2.5 ng of immunoprecipitated chromatin was subject to library preparation using EpiCypher CUT&RUN Library Kit (EpiCypher 141001) according to the manufacturer’s instructions. Pooled libraries were sequenced by Novogene with NovaSeq 6000 with 20 million paired-end reads sequenced per library.

treatment_protocol: Osimertinib-resistant cells were grown in 1uM osimertinib.

value: EV-MYC-tag-FLAG (empty vector) Overexpression

tag: chip antibody

value: MYC-tag


title: Clam UF252D-0409

description: UF Phase I

tag: tissue


title: TJK007_207492260081_R09C02

value: LMNB


title: PC9_OR_EV_MYC_rep1

description: Library name: PC9_OR_EV_MYC_rep1


title: Clam UF258P-0488

description: UF Phase I


title: Clam UF251S-0625

description: UF Phase II


title: PC9_OR_EV_input_rep2

description: Library name: PC9_OR_EV_input_rep2

value: input


title: HC, Day 1, RNA-Seq, Replicate 2


title: Clam UF24P-0496

description: UF Phase I

source_name: Clam UF24P-0496


title: PC9_OR_EV_input_rep1

description: Library name: PC9_OR_EV_input_rep1

value: Lung


title: HC, Day 0, RNA-Seq, Replicate 4

value: Day 0


title: TJK003_207492260152_R03C01


title: Clam UF248D-0417

description: UF Phase I

value: Adductor muscle


title: TJK004_207492260152_R04C01


title: TJK002_207492260152_R02C01


title: HC, Day 0, RNA-Seq, Replicate 3


title: PC9_OR_K86A_MYC_rep1

description: Library name: PC9_OR_K86A_MYC_rep1

value: lung adenocarcinoma


title: TJK001_207492260152_R01C01


title: HC, Day 1, RNA-Seq, Replicate 4

value: Hematopoietic cells


title: PC9_OR_K86A_input_rep2

description: Library name: PC9_OR_K86A_input_rep2


title: Clam UF245S-0679

description: UF Phase III

value: Hemocytes in ethanol


title: NJK074_207492260024_R12C02

description: Genomic DNA extracted from blood buffy coat of healthy woman (as control) was genotyped using Infinium Asian Screening Array BeadChips (Illumina).

source_name: Control

value: Healthy woman

value: Control


title: HC, Day 0, RNA-Seq, Replicate 2


title: Clam UF247D-0465

description: UF Phase I


title: HC, Day 0, RNA-Seq, Replicate 1


title: PC9_OR_K86A_input_rep1

description: Library name: PC9_OR_K86A_input_rep1

value: Osimertinib


title: NJK069_207492260024_R11C02


title: Clam UF244S-0678

description: UF Phase III


title: NJK062_207492260024_R10C02


title: FB, Day 28, RNA-Seq, Replicate 4

source_name: Fibroblasts

value: Fibroblasts

value: Day 28


title: Clam UF240D-0431

description: UF Phase I


title: PC9_OR_M7A_OE_MYC_rep2

description: Library name: PC9_OR_M7A_OE_MYC_rep2

value: METTL7A-MYC-tag-FLAG Overexpression


title: PC9_OR_M7A_OE_MYC_rep1

description: Library name: PC9_OR_M7A_OE_MYC_rep1


title: FB, Day 28, RNA-Seq, Replicate 3


title: HC, Day 1, RNA-Seq, Replicate 1

value: Day 1


title: NJK061_207492260024_R09C02

value: Female

value: Blood


title: PC9_OR_K86A_MYC_rep2

description: Library name: PC9_OR_K86A_MYC_rep2

value: MYC-tag


title: FB, Day 28, RNA-Seq, Replicate 2


title: PC9_OR_M7A_OE_input_rep2

description: Library name: PC9_OR_M7A_OE_input_rep2

value: input


title: Clam UF238S-0676

description: UF Phase III


title: NJK057_207492260024_R08C02


title: PC9_OR_M7A_OE_input_rep1

description: Library name: PC9_OR_M7A_OE_input_rep1

value: Lung


title: Clam UF236D-0416

description: UF Phase I


title: FB, Day 28, RNA-Seq, Replicate 1


title: NJK056_207492260024_R07C02


title: FB, Day 14, RNA-Seq, Replicate 4

value: Day 14


title: FB, Day 14, RNA-Seq, Replicate 3


title: Clam UF235D-0464

description: UF Phase I

value: Adductor muscle


title: PC9_OR_WT_MYC_rep2

description: Library name: PC9_OR_WT_MYC_rep2

value: lung adenocarcinoma

value: Wild-Type


title: NJK052_207492260024_R06C02


title: PC9_OR_WT_MYC_rep1

description: Library name: PC9_OR_WT_MYC_rep1


title: NJK048_207492260024_R05C02


title: Clam UF239S-0677

description: UF Phase III

value: Hemocytes in ethanol


title: Clam UF232S-0675

description: UF Phase III


title: PC9_OR_WT_input_rep2

description: Library name: PC9_OR_WT_input_rep2


title: NJK041_207492260024_R03C02

value: Healthy woman


title: NJK043_207492260024_R04C02

value: Control


title: Clam UF231S-0641

description: UF Phase III


title: Clam UF227D-0373

description: UF Phase I


title: Clam UF233S-0622

description: UF Phase II


title: FB, Day 7, RNA-Seq, Replicate 4

value: Day 7


title: FB, Day 14, RNA-Seq, Replicate 2

value: Fibroblasts


title: NJK040_207492260024_R02C02


title: PC9_OR_WT_input_rep1

description: Library name: PC9_OR_WT_input_rep1

value: Osimertinib


title: FB, Day 7, RNA-Seq, Replicate 3


title: Clam UF226S-0674

description: UF Phase III


title: PC9_M7A_OE_MYC_rep1

description: Library name: PC9_M7A_OE_MYC_rep1

value: METTL7A-MYC-tag-FLAG Overexpression

value: Untreated


title: FB, Day 14, RNA-Seq, Replicate 1


title: NJK038_207492260024_R01C02

value: Female


title: FB, Day 7, RNA-Seq, Replicate 2


title: Clam UF224S-0638

description: UF Phase II


title: PC9_M7A_OE_MYC_rep2

description: Library name: PC9_M7A_OE_MYC_rep2


title: NJK037_207492260024_R12C01

value: Blood


title: FB, Day 7, RNA-Seq, Replicate 1


title: NJK033_207492260024_R11C01


title: Clam UF223D-0463

description: UF Phase I


title: FB, Day 3, RNA-Seq, Replicate 4

value: Day 3


title: PC9_WT_MYC_rep2

description: Library name: PC9_WT_MYC_rep2

value: MYC-tag


title: Clam UF222D-0404

description: UF Phase I


title: NJK030_207492260024_R10C01


title: FB, Day 3, RNA-Seq, Replicate 3


title: PC9_WT_MYC_rep1

description: Library name: PC9_WT_MYC_rep1

value: Lung


title: NJK027_207492260024_R09C01


title: FB, Day 3, RNA-Seq, Replicate 2


title: PC9_WT_input_rep2

description: Library name: PC9_WT_input_rep2

value: input


title: Clam UF220D-0474

description: UF Phase I

value: Adductor muscle


title: NJK026_207492260024_R08C01


title: FB, Day 3, RNA-Seq, Replicate 1


title: Clam UF21P-0495

description: UF Phase I

source_name: Clam UF21P-0495


title: PC9_WT_input_rep1

description: Library name: PC9_WT_input_rep1

value: lung adenocarcinoma


title: NJK024_207492260024_R07C01


title: FB, Day 1, RNA-Seq, Replicate 4

value: Day 1


title: PC9_M7A_OE_input_rep1

description: Library name: PC9_M7A_OE_input_rep1


title: PC9_M7A_OE_input_rep2

description: Library name: PC9_M7A_OE_input_rep2


title: Clam UF218P-0498

description: UF Phase I


title: Clam UF219S-0673

description: UF Phase III

value: Hemocytes in ethanol


title: Skeletal Muscle; PAD-CKD1; snRNA-seq

city: Gainesville

first: Terence

middle: E.

last: Ryan

state: Florida

address: 1864 Stadium Rd

department: Applied Physiology and Kinesiology

institute: University of Florida

description:
Library name: PAD-CKD1
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software v7.0.0
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Gastrocnemius

extract_protocol:
Nuclei were isolated using the 10x Genomics Chromium nuclei isolation kit.
Library was performed according to the manufacter's instructions (Chromium Next GEM Single Cell 3’ HT Reagent kits v3.1, 10x Genomics).

value: Skeletal Muscle

value: Gastrocnemius


title: NJK010_207492260024_R05C01

value: Healthy woman

value: Control


title: Skeletal Muscle; PAD-CKD2; snRNA-seq

description:
Library name: PAD-CKD2
10x Genomics


title: FB, Day 1, RNA-Seq, Replicate 2

value: Fibroblasts


title: NJK007_207492260024_R04C01


title: Clam UF217S-0609

description: UF Phase II


title: FB, Day 1, RNA-Seq, Replicate 1


title: Skeletal Muscle; PAD3; snRNA-seq

description:
Library name: PAD3
10x Genomics


title: Clam UF221D-0384

description: UF Phase I


title: Clam UF216D-0380

description: UF Phase I


title: NJK005_207492260024_R03C01


title: FB, Day 0, RNA-Seq, Replicate 4

value: Day 0


title: Clam UF215D-0396

description: UF Phase I


title: NJK004_207492260024_R02C01


title: FB, Day 0, RNA-Seq, Replicate 3


title: Clam UF213S-0672

description: UF Phase III


title: THP-1, anti_VEGFA_3

city: Lanzhou

first: Shi

last: Dong

address: No.222, Tianshui South Road, Chengguan District, Lanzhou City

institute: Lanzhou University

description:
Library name: Sample 12
anti_VEGFA_3_fpkm

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: Human genome build 38
Supplementary files format and content: csv files include FPKM values for each Sample

extract_protocol:
Atotal amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Acute mononuclear cell leukemia cells


title: NJK002_207492260024_R01C01

value: Female


title: THP-1, anti_VEGFA_2

description:
Library name: Sample 11
anti_VEGFA_2_fpkm


title: THP-1, anti_VEGFA_1

description:
Library name: Sample 10
anti_VEGFA_1_fpkm


title: NJK014_207492260024_R06C01

value: Blood


title: Clam UF211D-0411

description: UF Phase I


title: FB, Day 0, RNA-Seq, Replicate 1


title: EC, Day 28, RNA-Seq, Replicate 4

source_name: Endothelial cells

value: Endothelial cells

value: Day 28


title: THP-1, anti_IL_8_3

description:
Library name: Sample 9
anti_IL_8_3_fpkm


title: FB, Day 1, RNA-Seq, Replicate 3


title: GAN-DPTIP 4

city: Shanghai

first: Cen

address: 501 Haike Road

institute: Shanghai Institute of Materia Medica

description: Library name: Sample 8

data_processing:
On average, we generated > 200 million paired end reads for each sample, with more than 95% of the reads passed the QC. Sequencing reads were trimmed for adapters and low-quality bases using SeqPrep and Sickle.
Alignment to the human reference genome (GRCh38.p13) with HISTA2 (Version 2.1.0).
The quantification of gene expression was performed using RSEM tool (Version 1.3.3) and generated TPM data for all genes individually.
Assembly: GRCh38.p13
Supplementary files format and content: FPKM, counts

source_name: Liver

extract_protocol:
RNA was harvested using Plus Mini Kit (QIAGEN, Duesseldorf, Germany). 1 μg of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using Illumina TrueSeq Stranded Total RNA Library Prep (Illumina, CA, USA).

value: Liver

value: Male

value: subjected to GAN diet for 12 weeks and then those mice were randomly grouped for 15-week intragastric administration of vehicle


title: Clam UF212S-0671

description: UF Phase III

data_processing:
The raw genotyping data in CEL format was downloaded from the CAT website after the service and genotype annotation was analyzed using the Axiom software (v 5.4, Thermo Fisher) following the Best Practices Workflow with recommended threshold settings (DishQC ≥ 0.82, QC call rate ≥ 97%).
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

extract_protocol: The quahogs that died earliest (n = 330) were categorized as “dead” under the dichotomous phenotype, and the quahogs that died latest (n = 144) and survivors (n =231) were considered as “survived”. Genotyping of samples was performed on the previously described SNP microarray chip (Grouzdev et al., 2024). Fixed samples were shipped to the Center for Aquaculture Technologies (CAT, https://aquatechcenter.com, San Diego, CA) for this service. The total genomic DNA was extracted from sample sources (adductor muscle or hemocytes) using a magnetic bead-based extraction protocol. Briefly, fixed tissues (~10-15 mg) were subsampled and processed using mag-bind blood and tissue DNA kits (Omega BioTek, Norcross, GA) according to the manufacturer’s guidelines. Automated processing and liquid handling steps associated with the extraction protocol were performed using PurePrep 96 units (Molgen, San Diego, CA) according to kit and instrument-specific guidelines. Extracted gDNAs were assessed for yields and quality by spectrophotometry (Nanodrop, ThermoFisher) and 2% agarose gels targeting a minimum of 35 µl at >20 ng/µl of largely intact DNA (minimum 5KB).


title: Skeletal Muscle; PAD2; snRNA-seq

description:
Library name: PAD2
10x Genomics


title: THP-1, anti_IL_8_2

description:
Library name: Sample 8
anti_IL_8_2_fpkm


title: GAN-DPTIP 1

description: Library name: Sample 5

value: subjected to GAN diet for 12 weeks and then those mice were randomly grouped for 15-week intragastric administration of DPTIP


title: THP-1, anti_IL_8_1

description:
Library name: Sample 7
anti_IL_8_1_fpkm


title: Clam UF207S-0606

description: UF Phase II

value: Adductor muscle


title: EC, Day 28, RNA-Seq, Replicate 2


title: Skeletal Muscle; PAD1; snRNA-seq

description:
Library name: PAD1
10x Genomics


title: GAN-Veh 4

description: Library name: Sample 4


title: EC, Day 28, RNA-Seq, Replicate 3


title: Clam UF206S-0605

description: UF Phase II


title: THP-1, OE_3

description:
Library name: Sample 6
OE_3_fpkm


title: Clam UF205D-0442

description: UF Phase I


title: EC, Day 28, RNA-Seq, Replicate 1


title: FB, Day 0, RNA-Seq, Replicate 2


title: GAN-Veh 3

description: Library name: Sample 3


title: THP-1, OE_2

description:
Library name: Sample 5
OE_2_fpkm


title: Clam UF203P-0487

description: UF Phase I


title: GAN-DPTIP 3

description: Library name: Sample 7


title: EC, Day 14, RNA-Seq, Replicate 4

value: Day 14


title: Clam UF20D-0363

description: UF Phase I

source_name: Clam UF20D-0363


title: EC, Day 14, RNA-Seq, Replicate 3


title: GAN-Veh 2

description: Library name: Sample 2


title: GAN-DPTIP 2

description: Library name: Sample 6


title: THP-1, OE_1

description:
Library name: Sample 4
OE_1_fpkm


title: Clam UF202D-0408

description: UF Phase I


title: Clam UF201D-0403

description: UF Phase I


title: EC, Day 14, RNA-Seq, Replicate 2


title: GAN-Veh 1

description: Library name: Sample 1


title: THP-1, NC_3

description:
Library name: Sample 3
NC_3_fpkm


title: EC, Day 14, RNA-Seq, Replicate 1


title: THP-1, NC_2

description:
Library name: Sample 2
NC_2_fpkm


title: Clam UF1D-0378

description: UF Phase I

source_name: Clam UF1D-0378


title: THP-1, NC_1

description:
Library name: Sample 1
NC_1_fpkm


title: Liver, HKO3, HFMCD 9w

data_processing:
On average, we generated > 200 million paired end reads for each sample, with more than 95% of the reads passed the QC. Sequencing reads were trimmed for adapters and low-quality bases using SeqPrep and Sickle.
The quantification of gene expression was performed using RSEM tool (Version 1.3.3) and generated TPM data for all genes individually.
Assembly: Alignment to the human reference genome (GRCh38.p13) with HISTA2 (Version 2.1.0).
Supplementary files format and content: TPM data.txt

source_name: Liver sample

value: Liver sample

value: Alb-cre+

value: fed with HFMCD for 9 weeks


title: Liver, HKO2, HFMCD 9w


title: EC, Day 7, RNA-Seq, Replicate 3

value: Day 7


title: Liver, HKO1, HFMCD 9w


title: Clam UF197D-0383

description: UF Phase I


title: EC, Day 7, RNA-Seq, Replicate 2


title: OE_3

description:
Library name: Sample 6
OE3_fpkm

value: pancreatic cancer cells

value: MMP28 overexpression

value: Overexpression of MMP28 lentivirus transfection


title: OE_2

description:
Library name: Sample 5
OE2_fpkm


title: Liver, FLOX4, HFMCD 9w

value: Alb-cre-


title: Clam UF196D-0462

description: UF Phase I


title: OE_1

description:
Library name: Sample 4
OE1_fpkm


title: Liver, FLOX3, HFMCD 9w


title: Liver, HKO4, HFMCD 9w


title: Clam UF200D-0357

description: UF Phase I


title: Liver, FLOX2, HFMCD 9w


title: EC, Day 7, RNA-Seq, Replicate 1


title: NC_3

description:
Library name: Sample 3
NC3_fpkm

value: WT

value: empty virus transfection


title: NC_2

description:
Library name: Sample 2
NC2_fpkm


title: Clam UF191D-0395

description: UF Phase I


title: Clam UF193S-0604

description: UF Phase II


title: EC, Day 3, RNA-Seq, Replicate 4

value: Endothelial cells

value: Day 3


title: EC, Day 7, RNA-Seq, Replicate 4


title: EC, Day 3, RNA-Seq, Replicate 3


title: NC_1

description:
Library name: Sample 1
NC1_fpkm


title: Clam UF190S-0621

description: UF Phase II


title: EC, Day 3, RNA-Seq, Replicate 2


title: Liver, FLOX1, HFMCD 9w


title: Clam UF199D-0473

description: UF Phase I


title: Liver, HKO3, GAN 24w

data_processing:
On average, we generated > 200 million paired end reads for each sample, with more than 95% of the reads passed the QC. Sequencing reads were trimmed for adapters and low-quality bases using SeqPrep and Sickle.
The quantification of gene expression was performed using RSEM tool (Version 1.3.3) and generated TPM data for all genes individually.
Assembly: Alignment to the human reference genome (GRCh38.p13) with HISTA2 (Version 2.1.0).
Supplementary files format and content: TPM_data.txt

value: fed with GAN diet for 24 weeks


title: EC, Day 3, RNA-Seq, Replicate 1


title: Clam UF188S-0670

description: UF Phase III

value: Hemocytes in ethanol


title: Clam UF187D-0367

description: UF Phase I


title: Liver, HKO2, GAN 24w


title: Liver, HKO1, GAN 24w


title: EC, Day 1, RNA-Seq, Replicate 4

value: Day 1


title: JC_ATRT

city: Homburg (Saar)

first: Marc

last: Remke

state: Saarland

address: Kirrberger Straße 100, Gebäude 9

department: Pediatric Translational Oncology Lab

institute: Universitätsklinikum des Saarlandes

description:
Library name: JC_ATRT
Column in ATRT_cell_line_processed.txt: JC_ATRT

data_processing:
Fastq files were imported into Partek Flow (Partek Incorporated, St. Louis, MO, USA). Quality analysis and quality control were performed on all reads to assess read quality and to determine the amount of trimming required (both ends: 13 bases 5´ and 1 base 3´). Trimmed reads were aligned against the hg38 genome using the STAR v2.4.1d aligner. Unaligned reads were further processed using Bowtie 2 v2.2.5 aligner. Finally, aligned reads were combined before quantifying the expression against the ENSEMBL (release 84) database using the Partek Expectation–Maximization algorithm. Partek Flow default settings were used in all analyses.
Assembly: hg38
Supplementary files format and content: Tab delimited text file containing Counts per Million (CPM)

growth_protocol: Cells were grown in serum-free media

extract_protocol:
Total RNA was isolated from cell pellets lysed in TRIZol according to the manufacturer’s instructions.
the library preparation was performed using the TruSeq RNA Library Preparation Kit v2

value: ATRT cell line

tag: batch


title: EC, Day 1, RNA-Seq, Replicate 3


title: CHLA06

description:
Library name: CHLA06
Column in ATRT_cell_line_processed.txt: CHLA06

tag: cell line


title: Clam UF186S-0669

first: Denis

address: 100 Nicolls Rd

institute: Stony Brook University

description: UF Phase III


title: Liver, FLOX3, GAN 24w


title: EC, Day 1, RNA-Seq, Replicate 2

tag: cell type


title: CHLA04

description:
Library name: CHLA04
Column in ATRT_cell_line_processed.txt: CHLA04


title: Liver, FLOX2, GAN 24w


title: EC, Day 1, RNA-Seq, Replicate 1


title: Clam UF181P-0486

description: UF Phase I

value: Adductor muscle


title: Clam UF180S-0633

description: UF Phase II


title: CHLA02

description:
Library name: CHLA02
Column in ATRT_cell_line_processed.txt: CHLA02


title: CHLA-05

description:
Library name: CHLA-05
Column in ATRT_cell_line_processed.txt: CHLA-05


title: Liver, FLOX1, GAN 24w

value: Liver sample


title: EC, Day 0, RNA-Seq, Replicate 4

value: Day 0


title: EC, Day 0, RNA-Seq, Replicate 3


title: Clam UF179P-0485

description: UF Phase I


title: Clam UF17D-0454

description: UF Phase I

source_name: Clam UF17D-0454


title: BT12_SF

description:
Library name: BT12_SF
Column in ATRT_cell_line_processed.txt: BT12_SF


title: Primary hepatocytes, HKO4, PA

data_processing:
On average, we generated > 200 million paired end reads for each sample, with more than 95% of the reads passed the QC. Sequencing reads were trimmed for adapters and low-quality bases using SeqPrep and Sickle.
The quantification of gene expression was performed using RSEM tool (Version 1.3.3) and generated TPM data for all genes individually.
Assembly: Alignment to the human reference genome (GRCh38.p13) with HISTA2 (Version 2.1.0).
Supplementary files format and content: TPM data.csv

source_name: Primary hepatocytes

value: Primary hepatocytes

value: Alb-cre+

value: stimulated with 0.4 mM palmitic acid for 24h


title: EC, Day 0, RNA-Seq, Replicate 2


title: Clam UF177D-0354

description: UF Phase I


title: BT16_SF

description:
Library name: BT16_SF
Column in ATRT_cell_line_processed.txt: BT16_SF


title: CHLA266_SF

description:
Library name: CHLA266_SF
Column in ATRT_cell_line_processed.txt: CHLA266_SF


title: Primary hepatocytes, HKO2, PA


title: Clam UF176S-0620

description: UF Phase II


title: CM, Day 28, RNA-Seq, Replicate 4

source_name: Cardiomyocytes

value: Cardiomyocytes

value: Day 28


title: Primary hepatocytes, HKO1, PA


title: ATRT_HHU_01

description:
Library name: ATRT_HHU_01
Column in ATRT_cell_line_processed.txt: ATRT_HHU_01


title: Primary hepatocytes, FLOX4, PA

value: Alb-cre-


title: CM, Day 28, RNA-Seq, Replicate 3


title: Clam UF174P-0500

description: UF Phase I


title: ATRT_311_FHTC

description:
Library name: ATRT_311_FHTC
Column in ATRT_cell_line_processed.txt: ATRT_311_FHTC

value: WT


title: Primary hepatocytes, HKO3, PA


title: Primary hepatocytes, FLOX3, PA


title: Clam UF173S-0619

description: UF Phase II


title: ATRT_310

description:
Library name: ATRT_310
Column in ATRT_cell_line_processed.txt: ATRT_310


title: ATRT_13808

description:
Library name: ATRT_13808
Column in ATRT_cell_line_processed.txt: ATRT_13808


title: CM, Day 28, RNA-Seq, Replicate 2


title: CM, Day 28, RNA-Seq, Replicate 1


title: Primary hepatocytes, FLOX2, PA


title: Clam UF172S-0668

description: UF Phase III


title: Clam UF170D-0390

description: UF Phase I


title: EC, Day 0, RNA-Seq, Replicate 1


title: CM, Day 14, RNA-Seq, Replicate 4

value: Day 14


title: hFXS_3, MeRIP

city: Cincinnati

first: Ziyuan

last: Guo

address: 3333 Burnet Ave

institute: CCHMC

data_processing:
Raw reads in fastq format were trimmed to remove the adaptor sequence and the reads with adaptor contaminants and low-quality reads using Trim Galore (v 0.6.6)
Preprocessed reads were then aligned to the human genome (build GRCh38) using STAR (v2.7.9) with the default settings
m6A peaks were identified using exomePeak R package (v2.16.0), GO analysis was performed using clusterProfiler R package. m6A-RNA-related genomic features were visualized using Guitar R package (v2.14.0), de novo motif analysis was performed by homer (v4.11).
Assembly: GRCh38
Supplementary files format and content: bed
Library strategy: MeRIP-seq

source_name: Postmortem brain tissue

growth_protocol: iPSCs were expanded onto fresh vitronectin-coated plate with Essential 8 medium, passaged with ReleSRTM every 3-4 days

extract_protocol:
Total RNA was isolated from six-week-old cortical neurons and postmortem cortex tissues using TRIzol reagent and Phase Lock Gel Heavy
Purified mRNA samples were fragmented to 100-200 nucleotides.  10% fragmented RNA was set aside as an input sample, while the remaining RNA was used for m6A immunoprecipitation. The fragmented RNA was incubated with anti-m6A antibody and then with protein G magnetic beads. The m6A-enriched RNA was purified using TRIzol. The library was prepared following the instructions for Kapa RNA hyper prep kit. Both the input samples without IP and the m6A IP samples were subjected to 150-bp, paired-end sequencing on an Illumina NovaSeq 6000 sequencer.

treatment_protocol: iPSCs were differentiated into cortical neurons and cultured for 6 weeks

value: Postmortem brain tissue

value: fragile X syndrome


title: hFXS_3, Input


title: ATRT_VU397

description:
Library name: ATRT_VU397
Column in ATRT_cell_line_processed.txt: ATRT_VU397


title: Clam UF175D-0356

city: Stony Brook

last: Grouzdev

description: UF Phase I


title: Primary hepatocytes, HKO4, Veh

value: stimulated with vehicle for 24h


title: Primary hepatocytes, HKO3, Veh


title: CM, Day 14, RNA-Seq, Replicate 3


title: Primary hepatocytes, HKO2, Veh


title: Primary hepatocytes, FLOX1, PA


title: Clam UF16S-0624

description: UF Phase II

source_name: Clam UF16S-0624


title: CM, Day 14, RNA-Seq, Replicate 2


title: Clam UF168D-0456

description: UF Phase I


title: hFXS_2, Input


title: Clam UF167D-0478

description: UF Phase I


title: CM, Day 14, RNA-Seq, Replicate 1


title: hFXS_2, MeRIP


title: Primary hepatocytes, HKO1, Veh


title: CM, Day 7, RNA-Seq, Replicate 4

value: Day 7


title: hFXS_1, Input


title: Clam UF166D-0430

description: UF Phase I


title: CM, Day 7, RNA-Seq, Replicate 3


title: Primary hepatocytes, FLOX3, Veh


title: hFXS_1, MeRIP


title: Primary hepatocytes, FLOX4, Veh


title: hUHC_3, Input

value: healthy


title: Clam UF164D-0472

description: UF Phase I


title: Clam UF165D-0393

description: UF Phase I


title: CM, Day 7, RNA-Seq, Replicate 2


title: Primary hepatocytes, FLOX2, Veh


title: Clam UF163S-0667

description: UF Phase III

value: Hemocytes in ethanol


title: CM, Day 3, RNA-Seq, Replicate 4

value: Day 3


title: hUHC_3, MeRIP


title: Primary hepatocytes, FLOX1, Veh


title: Clam UF161D-0372

description: UF Phase I

value: Adductor muscle


title: hUHC_2, Input


title: CM, Day 7, RNA-Seq, Replicate 1


title: Citeseq, CD45+DAPI- alive cells, CD40, ADT

city: Saint Louis

first: Jesus

last: Jimenez

state: MO

address: Clinical Sciences Research Building, Rm. 9900 4939 Children's Place, Campus Box 8086

institute: Washington University School of Medicine

description:
Library name: CD40_adt
Antibody-derived oligonucleotide (ADT)

library_source: other

data_processing:
Alignment: Cell Ranger v3, aligned to GRCh38 transcriptome or custom pre-mRNA reference
QC and Filtering: Seurat v3/v4
Unsupervised Clustering: Seurat V3/V4
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files
Supplementary files format and content: Cell ranger output files (single combined file for GEX & ADT): matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz
Library strategy: CITE-seq

source_name: heart

extract_protocol:
At experiment termination, single cell suspensions of heart tissue from Rat IgG or anti-CD40 agonist antibody treated mice (C57BL6J) mice were generated following perfusion with cold PBS, atria removal, fine mincing, and digestion for 20 minutes at 37⁰C in DMEM (Gibco, 11965-084) containing 4500 U/ml Collagenase IV (Millipore Sigma, C5138), 2400 U/ml Hyaluronidase I (Millipore Sigma, H3506), and 6000 U/ml DNAse I (Millipore Sigma, D4527). Enzymes were deactivated with HBSS (Gibco, 14025092) containing 2% FBS and 0.2% BSA, then filtered through 40-micron strainers. For red blood cell lysis, cells were incubated with ACK lysis buffer (Gibco, A10492-01) for 5 minutes at room temperature. Cells were washed with DMEM and resuspended in FACS buffer (PBS containing 2% FBS and 2 mM EDTA).Centrifugation was repeated at above conditions, supernatant removed, and pellet resuspended in 300uL cell resuspension buffer (0.04% BSA in 1X PBS) and 1uL each of CD45-Percp-cy5.5 and allowed to incubate 30 minutes before sorting. 1ul DAPI (BD Biosciences, 564907) were added before sorting. CD45+/DAPI- cells were collected in cell resuspension buffer. Collected cells were then recentrifuged according to above parameters and resuspended in cell resuspension buffer to a target concentration of 1000 cells/μL. Cells were counted on a hemocytometer and concentration adjusted as necessary.
10X Genomics Chromium Single Cell 5’ Reagent V1.1

value: heart

value: CD45+DAPI- alive cells

value: CD40 antibody

tag: library type

value: ADT


title: hUHC_2, MeRIP


title: Citeseq, CD45+DAPI- alive cells, ISO, GEX

description:
Library name: ISO_gex
polyA RNA

value: Rat IgG antibody (isotype)

value: mRNA


title: Citeseq, CD45+DAPI- alive cells, ISO, ADT

description:
Library name: ISO_adt
Antibody-derived oligonucleotide (ADT)


title: hUHC_1, MeRIP


title: Clam UF15S-0634

description: UF Phase II

source_name: Clam UF15S-0634


title: Citeseq, CD45+DAPI- alive cells, CD40, GEX

description:
Library name: CD40_gex
polyA RNA


title: CM, Day 3, RNA-Seq, Replicate 2

value: Cardiomyocytes


title: Clam UF156S-0665

description: UF Phase III


title: Clam UF157S-0666

description: UF Phase III


title: CM, Day 3, RNA-Seq, Replicate 1


title: FXS_7, MeRIP

source_name: iPS

value: iPS

value: iPS-derived cortical neuron

value: FMR1 CGG repeats is over 200


title: hUHC_1, Input

value: Postmortem brain tissue


title: FXS_7, Input

value: fragile X syndrome


title: CM, Day 3, RNA-Seq, Replicate 3


title: CM, Day 1, RNA-Seq, Replicate 3

value: Day 1


title: Clam UF155S-0627

description: UF Phase II


title: CM, Day 1, RNA-Seq, Replicate 4


title: CM, Day 1, RNA-Seq, Replicate 2


title: FXS_6, Input


title: Clam UF154D-0379

description: UF Phase I


title: RH MET-4 replicate

city: Toronto

first: Mohsen

last: Hosseini

state: Ontario

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre

description: Library name: RH MET-4

data_processing:
The readings were mapped to the mm10 reference genome using the STAR (v2.5) program
The HTSeq v0.6.1 software was utilized to tally the number of reads that were aligned to each individual gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files including raw counts for each sample

source_name: Bone marrow

growth_protocol: Freshly isolated HSPCs from mouse bone marrow, never cultured

extract_protocol:
RNA extraction from enriched murine HSPC was performed using the RNeasy Plus Mini Kit (QIAGEN, Cat #74136) following the instructions provided by the manufacturer.
Libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina, and sequencing was performed using the NovaSeq 6000 S4 with PE150 BP sequencing system.

treatment_protocol: The dataset was derived from an in vivo competition experiment after 1 month of treatment, with 2 animals per treatment groups.

value: Bone marrow

value: Mouse HSPCs

value: Lin-ckit+ cells (hematopoietic stem and progenitor cells)

tag: sorting

value: Lin-ckit+ cells were sorted from fresh mouse BM samples and processed without culturing

value: C57BL/6(Dnmt3afl-R878H/+ mice (JAX stock #032289) crossbred with B6. CgTg(Mx1-cre)1Cgn/J mice (JAX stock #003556))

value: metformin


title: FXS_6, MeRIP


title: Clam UF153D-0366

description: UF Phase I

value: Adductor muscle


title: RH VEH-3 replicate

description: Library name: RH VEH-3

value: vehicle (control)


title: CM, Day 1, RNA-Seq, Replicate 1


title: CM, Day 0, RNA-Seq, Replicate 4

value: Day 0


title: WT MET-4 replicate

description: Library name: WT MET-4

value: C57BL/6(Dnmt3a+/+ mice crossbred with B6. CgTg(Mx1-cre)1Cgn/J mice (JAX stock #003556))


title: Clam UF149D-0362

description: UF Phase I


title: Clam UF14S-0637

description: UF Phase II

source_name: Clam UF14S-0637


title: CM, Day 0, RNA-Seq, Replicate 3

value: Cardiomyocytes


title: RH VEH-4 replicate

description: Library name: RH VEH-4


title: FXS_5, Input

value: iPS


title: WT VEH-4 replicate

description: Library name: WT VEH-4


title: FXS_5, MeRIP

value: iPS-derived cortical neuron


title: WT MET-3 replicate

description: Library name: WT MET-3


title: Clam UF148S-0664

description: UF Phase III


title: Spleen, Pb-infection

city: Beijing

first: Weixuan

last: Wang

address: No. 38 Xueyuan Road, Haidian District

institute: Peking University

description:
Library name: Pb-infection
10x Genomics

data_processing:
The Cell ranger software pipeline (version 6.0.1) provided by 10xGenomics was used to demultiplex cellular barcodes,map reads to the transcriptome, control quality and generate quantitative matrix.
The R package Seurat (version 4.3.0) was used for generation of Seurat object.
The count matrix was normalized with NormalizeData function.
tSNE and UMAP were performed by R package Seurat (version 4.3.0).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Spleen

extract_protocol:
Single cells were mixed with Gel Beads, Partitioning Oil and glycerol, using for preparation of GEMs with ChromiumTM Next GEM Chip G Single Cell Kit. The GEMs were subjected to RT-PCR, and the products were purified with Dynabeads, followed by cDNA amplification.
RNA libraries were prepared with ChromiumTM Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's protocol.

treatment_protocol: Mice were intraperitoneally injected with 1 × 10⁴ iRBCs, and on day 5 post-infection, spleens from both uninfected and Pb-infected mice were collected to isolate lymphocytes.

value: Spleen

value: WT

value: infection of 1 x 104 iRBCs for 5 days


title: CM, Day 0, RNA-Seq, Replicate 1


title: Clam UF160P-0497

description: UF Phase I


title: Clam UF146S-0402

description: UF Phase I


title: Spleen, Un-infection

description:
Library name: Un-infection
10x Genomics

value: uninfection


title: FXS_3, MeRIP

value: FMR1 CGG repeats is over 200

value: fragile X syndrome


title: FXS_2, Input


title: FXS_3, Input


title: Clam UF144D-0663

description: UF Phase III


title: HC, Day 28, smallRNA-Seq, Replicate 3

description: small RNA sequencing

data_processing:
small RNA-seq analysis pipeline from nf-core [https://nf-co.re/smrnaseq]
Small RNAs were trimmed/qualitycheck using Trimgalore and then quantified using the small RNA-seq analysis pipeline from nf-core [https://nf-co.re/smrnaseq], where the full length of the small RNA reads were used for the pipeline.
The processed file is the result of samtools idxstats run on the sorted bowtie2 alignment files, aligned wiith the reference mm10 and thereafter mapped to miRBase v21 miRNAs.
Assembly: mm10
Supplementary files format and content: tab delimited files include reference sequence name, sequence length, # mapped read-segments and # unmapped read-segments

source_name: Hematopoietic cells

extract_protocol:
Cardiomyocytes were enriched by performing repeated centrifugation steps (20 x g, 2 minutes). The supernatant of the centrifugation step was used to isolate hematopoietic cells, endothelial cells, and fibroblasts. Hematopoietic and endothelial cells were isolated by magnetic separation. Cells not bound to the magnetic beads or columns were used for cardiac fibroblast enrichment by a plating step with uncoated dishes. After 40 minutes, predominantly DDR2-positive fibroblasts adhered and were used for RNA isolation. Cells extracted from three mice were pooled to generate enough cells for one of four biological replicate sequencing samples for each timepoint.
Small RNAs were converted into Illumina compatible libraries using the NEB Next small RNA library Kit from New England Biolabs (NEB), which involves 3´-ligation and 5´-ligation to small RNAs and therefore enriches for 5´-monophosphorylated and 3 ́-hydroxylated small RNAs, such as miRNA. Due to the varying RNA amounts available for each cell type, we used the following parameters for input of total RNA and PCR cycles: CM-500ng-14cycles, EC-50ng-16cycles, HC-150ng-15cycles, FB-150ng-15-cycles. After library amplification, we cut each library from 10% TBE (Tris-Borate-EDTA) PAGE gels, extracting the library size of approx. 140-150bp which corresponds to 20-30nt miRNAs. Libraries were then quantified using the Qubit dsDNA HS Assay (Thermo Fisher).

value: Hematopoietic cells

value: Day 28


title: FXS_2, MeRIP


title: Clam UF140D-0389

description: UF Phase I


title: HC, Day 28, smallRNA-Seq, Replicate 4

description: small RNA sequencing


title: HC, Day 28, smallRNA-Seq, Replicate 2

description: small RNA sequencing