title: P10_Setdb1_cKO_scRNAseq

data_processing:
Raw sequencing data (fastq files) were aligned to the reference genome mm10 (cellranger reference 2020-A, and Ensembl v98 gene annotation) using the Cell Ranger pipeline (v.7.1.0, 10x Genomics) with parameters: --include-introns=false. After alignment, filtering, barcode counting, and UMI counting we use feature-barcode matrices for downstream analysis.
Downstream analysis were performed using R package Seurat
Assembly: mm10
Supplementary files format and content: dg_setdb1_merge12_RPKM.bw
Supplementary files format and content: p10_dg_subcell_metadata.csv
Supplementary files format and content: p7_RNA_ko_merge_RPKM.bw
Supplementary files format and content: p7_RNA_wt_merge_RPKM.bw
Supplementary files format and content: p7_dg_ko_atac_RPKM.bw
Supplementary files format and content: p7_dg_wt_atac_RPKM.bw

extract_protocol:
Dentate gyri originating from WT and SETDB1 cKO mice at P10 were collected in PBS on ice. The dissected DG was then digested using the Neural Tissue dissociation kit (P) (Miltenyi Biotec) according to the manufacturer’s instructions. Approximately 20,000 cells were utilized as input for the 10X Genomics Chromium Controller, aiming for a targeted recovery of 10,000 cells per library.
The libraries were then prepared employing the Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3, strictly adhering to the manufacturer’s instructions. Following the cDNA clean-up, the libraries were quantified using a BioAnalyzer then were sequenced on the Illumina NovaSeq 6000.

value: postnatal day 10


title: Microglia,TBI,7dpi,Rep1

status: Public on Aug 06 2025

type: SRA

city: San Francisco

first: Susanna

last: Rosi

state: CA

address: 2200 Island Dr

country: USA

institute: Altos labs

description: Library name: F029489_A1-3

library_source: transcriptomic

data_processing:
RNA-seq FASTQ files were trimmed, aligned to the mouse reference genome (GRCm39, v108), and quantified using the nf-core/rnaseq pipeline with the star_salmon option (v3.12.0). Gene-level length-scaled counts were used for all downstream analyses.
Assembly: GRCm39
Supplementary files format and content: quant.sf files from salmon quantification.

molecule: total RNA

organism: Mus musculus

source_name: Whole Brain

extract_protocol:
MDMs (tdTomato+), microglia (CD11b+, CD45mid/low, tdTomato-) and “classical” monocytes (Ly6G-,Ly6Chi) were sorted from brain and blood of female and male Ms4a3-cre::Ai14D mice at 7 and 30 days with and without TBI. Naïve samples were collected from untreated mice.
cDNAs were generated using the SMART-Seq® mRNA LP (with UMIs) kit for sequencing (Takara bio,634765), according to the vendor protocol. cDNA amplification cycle was adjusted to 19 cycles. PCR-amplified cDNA was purified by immobilization on NucleoMag NGS Clean-up and Size Select beads. The beads were then washed with 80% ethanol, and cDNA is eluted with ~15ul of Elution Buffer. Subsequently, 8 ul of cDNA 0.125 ng/μL was used as a starting material for library preparation using the the Unique Dual Index (UDI) kits (Takara bio, 634752-5) according to the vendor protocol, with final library PCR amplification of 14 cycles. PCR-amplified library was purified individually by immobilization on NucleoMag NGS Clean-up and Size Select beads. The beads were then washed with 80% ethanol and the library eluted with nuclease-free water.
Quality control and quantification was performed using the Qubit dsDNA HS Assay Kit (Thermofisher, 32854) and TapeStation D5000 Reagents (Agilent, 5067-5589) and Screentape (Agilent, 5067-5588). Samples were normalized and pooled individually for sequencing. An additional double-sided SPRI selection was performed on the pool prior to sequencing. Libraries were sequenced using the NextSeq 2000 P3, 300 cycles kit (Illumina, 20040561).

tag: tissue

value: Whole Brain

tag: cell type

value: Microglia

tag: genotype

tag: treatment

value: TBI

tag: time

tag: mouse id

tag: library prep_date

tag: lysis plate_id


title: P7_DG_Setdb1_cKO_rep1

city: Shanghai

first: Yunli

last: Xie

state: Shanghai

address: 131 Dong'an Road, Shanghai

department: Institutes of Brain Science

country: China

institute: Fudan University

data_processing:
raw data were first trimmed using Trim Galore v.0.6.7 then mapped to the mm10 genome by HISAT2 v2.2.1 with default parameters.
The number of reads mapping to each gene were counted by featureCounts v2.0.1 with parameters: -a gencode.vM20.annotation.gtf. And transcripts per million (TPM) were calculated.
Assembly: mm10
Supplementary files format and content: dg_setdb1_merge12_RPKM.bw
Supplementary files format and content: p10_dg_subcell_metadata.csv
Supplementary files format and content: p7_RNA_ko_merge_RPKM.bw
Supplementary files format and content: p7_RNA_wt_merge_RPKM.bw
Supplementary files format and content: p7_dg_ko_atac_RPKM.bw
Supplementary files format and content: p7_dg_wt_atac_RPKM.bw

source_name: brain

extract_protocol:
Total RNA was isolated from Dentate gyrus at P7 using TRIzol reagent (ThermoScientific) according to the manufacturer’s instructions.
RNA-seq was performed at Genergy Biotech Co., Ltd. Shanghai, China.

value: brain

tag: cell line

value: mouse brain cells

value: postnatal day 7


title: T-ALL Primary2

city: Gent

first: Igor

last: Fijalkowski

address: Sint-Pietersnieuwstraat 33

country: Belgium

institute: Ugent

description: Library name: Primary2

data_processing:
alignment by Dorado-integrated minimap2
Basecalled using the rna004_130bps_sup@v5.1.0 m6A_DRACH aware model.
Assembly: GRCh38
Supplementary files format and content: bedmethyl files summarizing m6A methylation information obtained using Nanoporetech modkit toolkit (https://github.com/nanoporetech/modkit)

organism: Homo sapiens

source_name: Blood

growth_protocol: The cells were not cultivated prior to the collection.

extract_protocol:
RNA was extracted from the samples by using the RNeasy Plus Micro Kit (Qiagen, 74034) according to the manufacturer’s instructions.
Direct RNA Sequencing Kit (SQK-RNA004) was used for library preparation with 1ug of total RNA as input, according to manufacturers instructions

value: Blood

value: Primary material

value: T-ALL

tag: condition

value: T-ALL Primary


title: NOVA22_Blood_Phase_2_SD1

type: RNA

city: Seattle

first: kathie

last: walters

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

description: Gene expression profiling of PBMC  from influenza infected humans

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

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

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from PBMCs in Paxgene tubes according to manufacturer's instructions.RNA quality was assessed using Agilent Bioanalyzer.

treatment_protocol: PBMCs  collected from humans  and stored in Paxgene tubes  according to manufacturer's instructions.

tag: disease state

value: influenza

value: PBMC

tag: study group

value: Vaccinated

tag: study date


title: Microglia,Naive,0dpi,Rep1

description: Library name: F029488_A1-3

value: Naive


title: mouse tumor, RNA-seq, Vehicle treated, Rep 3

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

data_processing:
Read alignment was accomplished with the STAR (2.7.11) against the mm10 version of the mouse genome [PMID: 23104886].
Assembly: mm10
Supplementary files format and content: Tab-delimited text, gene counts for each sample

source_name: hSS2 mouse tumor

growth_protocol: The mice express SS18-SSX2 in ROSA26 loci were injected with TATCRE in hindlimb at 8 days of age.

extract_protocol:
Mice were treated either TAK-981 at a dosage of 25mg/kg or vehicle for 23 days and RNA was extracted with Zymo Direct-zolTM RNA Miniprep kit.
Mouse tumor RNA-seq libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep with rRNA Depletion Kit, and sequenced on a NovaSeq using the 2 x 150 bp protocol (Illumina) for approximately 25-30 million reads per sample.

value: hSS2 mouse tumor

value: mouse synovial sarcoma tumor

value: SS18-SSX2 mouse

value: vehicle-control


title: Monocytes,Naive,0dpi,Rep1

description: Library name: F029487_A1-3

value: Monocytes


title: T-ALL Primary1

description: Library name: Primary1


title: P10_control_scRNAseq

library_source: transcriptomic single cell

molecule: polyA RNA

value: wild type

value: postnatal day 10


title: NOVA45_Blood_Phase_2_SD1


title: NOVA70_Blood_Phase_2_SD1

value: Unvaccinated


title: Microglia,SHAM,8months,Rep12

description: Library name: J189323_F1.J189323_F2.J189323_F3

extract_protocol:
CD11b+ CD45+ tdTomato+ cells (MDMs) and CD11b+, CD45mid/low, tdTomato- cells (microglia) were sorted from whole brains of Ccr2-creERT2::Ai14D mice at 8 months after TBI.
cDNAs were generated using the SMART-Seq® mRNA LP (with UMIs) kit for sequencing (Takara bio,634765), according to the vendor protocol. cDNA amplification cycle was adjusted to 19 cycles. PCR-amplified cDNA was purified by immobilization on NucleoMag NGS Clean-up and Size Select beads. The beads were then washed with 80% ethanol, and cDNA is eluted with ~15ul of Elution Buffer. Subsequently, 8 ul of cDNA 0.125 ng/μL was used as a starting material for library preparation using the the Unique Dual Index (UDI) kits (Takara bio, 634752-5) according to the vendor protocol, with final library PCR amplification of 14 cycles. PCR-amplified library was purified individually by immobilization on NucleoMag NGS Clean-up and Size Select beads. The beads were then washed with 80% ethanol and the library eluted with nuclease-free water.
Quality control and quantification was performed using the Qubit dsDNA HS Assay Kit (Thermofisher, 32854) and TapeStation D5000 Reagents (Agilent, 5067-5589) and Screentape (Agilent, 5067-5588). Samples were normalized and pooled individually for sequencing. An additional double-sided SPRI selection was performed on the pool prior to sequencing. Libraries were sequenced using the NextSeq 2000 P3, 300 cycles kit (Illumina, 20040561).

value: Whole Brain

value: Microglia

value: SHAM

tag: library prep_plate_id


title: mouse tumor, RNA-seq, Vehicle treated, Rep 1


title: NOVA75_Blood_Phase_2_SD1


title: Microglia,SHAM,8months,Rep11

description: Library name: J189323_E1.J189323_E2.J189323_E3


title: mouse tumor, RNA-seq, Vehicle treated, Rep 2


title: Microglia,SHAM,8months,Rep10

description: Library name: J189323_D1.J189323_D2.J189323_D3


title: T-ALL PDX3

description: Library name: PDX3

value: Blood

value: Primary material

value: T-ALL

value: T-ALL PDX


title: mouse tumor, RNA-seq, TAK-981 treated, Rep 6


title: THESC, hormone induced decidualization, MEK inhibitor, Day3, rep3

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road, Oxford, OX3 7LD, UK

country: United Kingdom

institute: University of Oxford

data_processing:
For long-read sequencing, base calling of fast5 files was done by Guppy and converted to fastq format.
Fastq files were processed by the pipeline (pipeline_count) implemented in the workflow TallyTriN (https://github.com/cribbslab/TallyTriN/tree/main) and raw count matrix for PCA analysis was then generated.
For isoform-level analysis, reads of each sample were then aligned to hg38 genome by Minimap2 with - - MD flag enabled and output as SAM format.
The SAM file of each sample was then processed by TALON and visualized by Swan.
For short-read sequencing, reads were initially assessed for quality using FastQ Screen v0.14.0, FastQC v0.11.9 and MulitQC v1.5.dev0.
Raw reads of each sample were then merged into a single file and pseudo-aligned to the human genome hg38 with Kallisto 0.46.0.
Using the count matrix produced by Kallisto, differential expression analysis was performed by DESeq2 v1.35.0
Assembly: Human genome hg38
Supplementary files format and content: raw count matrix for each sample (including short and long-read sequencing data)

source_name: THESC

growth_protocol: THESC cell line was incubated in DMEDM/F-12 with bicarbonate and HEPES (Sigma Cat# D 2906) supplemented with 10% fetal bovine serum (FBS, Charcoal stripped F6765-500ML), puromycin (500 ng/ml), and 1% ITS Premix Universal Culture Supplement (Corning 354350).

extract_protocol:
Cells were harvested using Direct-zol RNA MiniPrep kit (Cambridge Bioscience, R2052)
For long-read sequencing, 50 ng RNA of each sample were reverse transcribed and barcoded by using the PCR-cDNA barcoding kit (SQK-PCB111.24) and NEBNext Companion Module (NEB E7180L).
For short-read sequencing, Approximately 100 ng of each RNA sample was used to create Illumina sequencing libraries using a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) according to the manufacturer’s instructions.

treatment_protocol:
For the three days experiment of decidualization, cells were seeded at 6-well plates for 40,000 cells per well and incubated overnight.
At the next day (Day 0), the decidualization were induced by adding the following reagents into cell medium: Medroxyprogesterone 17-acetate (Sigma, M1629; final conc. 1.0 µM), E2 (estradiol, final conc. 10 nM; Sigma E1024), 8-Br cAMP (8-Bromoadenosine 3′,5′-cyclic monophosphate, final conc. 500 µM; Sigma B6386-100mg).
In addition to stimulation for decidualization, cells were further treated with DMSO as mock, TGF-beta (10 ng/ml; Millipore GF346) together with or without MEK inhibitor (BAY 1076672, 100 ng/ml) since Day 0, depending on the experimental design.

value: THESC

value: Endometrial Stromal Cells

value: hTERT-immortalized

value: hormone induced decidualization and MEK inhibitor


title: mouse tumor, RNA-seq, TAK-981 treated, Rep 5

value: hSS2 mouse tumor

value: mouse synovial sarcoma tumor

value: SS18-SSX2 mouse


title: THESC, hormone induced decidualization, MEK inhibitor, Day3, rep2


title: NOVA77_Blood_Phase_2_SD1

value: influenza

value: PBMC


title: mouse tumor, RNA-seq, TAK-981 treated, Rep 4


title: THESC, hormone induced decidualization, MEK inhibitor, Day3, rep1


title: Microglia,TBI,8months,Rep12

description: Library name: J189323_C1.J189323_C2.J189323_C3

value: TBI


title: NOVA80_Blood_Phase_2_SD1

value: Unvaccinated


title: NOVA63_Blood_Phase_2_SD1


title: Microglia,TBI,8months,Rep11

description: Library name: J189323_B1.J189323_B2.J189323_B3

value: Whole Brain

value: Microglia


title: THESC, hormone induced decidualization, TGF-beta with MEK inhibitor, Day3, rep3

value: hormone induced decidualization, TGF-beta and MEK inhibitor


title: mouse tumor, RNA-seq, TAK-981 treated, Rep 3


title: T-ALL PDX2

description: Library name: PDX2

value: Blood

value: Primary material


title: NOVA79_Blood_Phase_2_SD1


title: T-ALL PDX1

description: Library name: PDX1

value: T-ALL

value: T-ALL PDX


title: Macrophages,TBI,8months,Rep10

description: Library name: J189323_A5.J189323_A6

value: Monocyte-derived Macrophages


title: NOVA20_Blood_Phase_2_SD1

value: Vaccinated


title: mouse tumor, RNA-seq, TAK-981 treated, Rep 2


title: THESC, hormone induced decidualization, TGF-beta with MEK inhibitor, Day3, rep2

value: THESC

value: Endometrial Stromal Cells

value: hTERT-immortalized


title: mouse tumor, RNA-seq, TAK-981 treated, Rep 1

value: hSS2 mouse tumor

value: mouse synovial sarcoma tumor

value: SS18-SSX2 mouse


title: NOVA25_Blood_Phase_2_SD1

value: influenza

value: PBMC


title: Microglia,TBI,8months,Rep10

description: Library name: J189323_A1.J189323_A2.J189323_A3

value: Whole Brain

value: TBI


title: Macrophages,TBI,8months,Rep11

description: Library name: J189323_C5.J189323_C6


title: THESC, hormone induced decidualization, TGF-beta with MEK inhibitor, Day3, rep1

value: hormone induced decidualization, TGF-beta and MEK inhibitor


title: THESC, hormone induced decidualization, TGF-beta, Day3, rep3

value: hormone induced decidualization and TGF-beta


title: Microglia,SHAM,8months,Rep9

description: Library name: J189322_F1.J189322_F2.J189322_F3

value: Microglia

value: SHAM


title: KCL-HO-1i/Gemcitabine treated, rep 4

city: London

first: James

middle: N

last: Arnold

address: New Hunt’s House, Great Maze Pond

department: Cancer and Pharmaceutical Sciences

institute: King's College London

data_processing:
Sample read quality was checked using FastQC v0.11.9
Read alignment was done using the STAR aligner v2.7.9a
Count table was generated using the quant function from Salmon v1.9.0
Transcript level counts was summarized to Gene level counts using the tximport package in R
Differential Analysis was done using the DeSeq2 package in R
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing raw counts for all the samples

source_name: Breast

growth_protocol: FVB/N-Tg(MMTV-PyVT)634Mul/J mice used in this study were housed under specific pathogen-free conditions in individually ventilated cages at a temperature of 21°C with water and food ad libitum.

extract_protocol:
RNA was collected using The RNeasy Mini Kit  manufactured by Qiagen and RNA extraction was performed according to manufacturer’s protocol.
Library was prepared using the NEBNext Ultra II Directional RNA Library Prep Kit according to the manufacturer's instructions

treatment_protocol: The mice were treated in a acute setting for 72 hours prior tumor collection. For drug treatments, drugs were freshly prepared on the day of injection and administered by intraperitoneal (i.p.) injection using a 26 G needle. KCL-HO-1i was produced in house and administrated at 25 µmol/kg/daily. 5-fluorouracil (Sigma-Aldrich) was prepared fresh and dissolved in saline at 6 mg/mL and injected to mice i.p. at 40 mg/kg/4 days. Gemcitabine (Sigma-Aldrich) was prepared fresh and dissolved in saline at 6 mg/mL and injected to mice i.p. at 64 mg/kg/7 days.

value: Breast

tag: strain

value: WT

value: KCL-HO-1i & Gemcitabine


title: NOVA11_Blood_Phase_2_SD1

value: Vaccinated


title: THESC, hormone induced decidualization, TGF-beta, Day3, rep2

value: THESC

value: Endometrial Stromal Cells


title: Microglia,SHAM,8months,Rep8

description: Library name: J189322_E1.J189322_E2.J189322_E3


title: Microglia,SHAM,8months,Rep7

description: Library name: J189322_D1.J189322_D2.J189322_D3


title: KCL-HO-1i/Gemcitabine treated, rep 3


title: NOVA76_Blood_Phase_2_SD1

value: Unvaccinated


title: THESC, hormone induced decidualization, TGF-beta, Day3, rep1

value: hTERT-immortalized


title: Macrophages,TBI,8months,Rep9

description: Library name: J189322_C5.J189322_C6

value: Monocyte-derived Macrophages


title: NOVA64_Blood_Phase_2_SD1

value: influenza


title: THESC, hormone induced decidualization, DMSO, Day3, rep3

value: hormone induced decidualization and DMSO


title: KCL-HO-1i/Gemcitabine treated, rep 2


title: NOVA16_Blood_Phase_2_SD1

value: PBMC


title: Microglia,TBI,8months,Rep9

description: Library name: J189322_C1.J189322_C2.J189322_C3

value: Whole Brain

value: TBI


title: KCL-HO-1i/Gemcitabine treated, rep 1


title: THESC, hormone induced decidualization, DMSO, Day3, rep2


title: KCL-HO-1i/Gemcitabine treated, rep 5


title: KCL-HO-1i/5-FU treated, rep 5

value: KCL-HO-1i & 5-Fluorouracil


title: Macrophages,TBI,8months,Rep8

description: Library name: J189322_B5.J189322_B6


title: THESC, no hormone induction, Ctrl, Day0, biol rep3

value: before hormone induced decidualization


title: THESC, hormone induced decidualization, DMSO, Day3, rep1


title: Microglia,TBI,8months,Rep8

description: Library name: J189322_B1.J189322_B2.J189322_B3

value: Microglia


title: KCL-HO-1i/5-FU treated, rep 4

value: Breast


title: Macrophages,TBI,8months,Rep7

description: Library name: J189322_A5.J189322_A6


title: NOVA30_Blood_Phase_2_SD1


title: KCL-HO-1i/5-FU treated, rep 3

value: WT


title: THESC, no hormone induction, Ctrl, Day0, biol rep2


title: Microglia,TBI,8months,Rep7

description: Library name: J189322_A1.J189322_A2.J189322_A3


title: THESC, no hormone induction, Ctrl, Day0, biol rep1


title: KCL-HO-1i/5-FU treated, rep 2


title: NOVA34_Blood_Phase_2_SD1


title: Microglia,SHAM,8months,Rep6

description: Library name: J189321_F1.J189321_F2.J189321_F3

value: SHAM


title: NOVA05_Blood_Phase_2_SD1

value: Vaccinated


title: NOVA36_Blood_Phase_2_SD1


title: KCL-HO-1i/5-FU treated, rep 1


title: human cell grafts in mouse stroke model

city: Los Angeles

first: Ruslan

last: Rust

address: 1501 San Pablo Street

institute: University of Southern California

description:
sex of human cells: female (pooled)
sex of mouse cells: pooled male and female

data_processing:
Alignment and gene quantification of single-nucleus RNA sequencing (snRNAseq) data were carried out using Cellranger v3.1.0, adhering to the default settings, and using the human and mouse (GRCh38 & mm10) 2020-A datasets as reference. Cells exhibiting more than 5% mitochondrial gene expression and less than 500 nFeature_RNA were excluded. Gene counts underwent normalization and scaling to account for the total unique molecular identifier counts per barcode using Seurat v5.0.193. All analysis steps were performed according to the guidelines in the Seurat package93
Assembly: GRCh38 & mm10
Supplementary files format and content: csv

molecule: nuclear RNA

organism:
Homo sapiens
Mus musculus

source_name: IPSC-NPC were transplanted in mice one week after stroke.

extract_protocol: cortical brain tissue was removed and flash frozen using liquid nitrogen. Cortices were then homogenized using a Dounce homogenizer in lysis buffer (10mM Tris-HCl, ph 7.5, 10mM NaCl, 3mM MgCl2, and 0.1% Nonidet P40 in nucleuase-free water). Homogenized tissue was incubated for 15 minutes and subsequently filtered through a 30 μm cell strainer. The filtered cell suspension was centrifuged (to pellet the nuclei. Nuclei were washed and filtered twice through a 40 μm cell strainer using 2% BSA in sterile PBS with 0.2 U/μl RNase inhibitor (nuclei wash). After resuspension in 500 μl nuclei wash and 900 μl 1.8M sucrose, nuclei were carefully layered on top of 500 μl of 1.8M sucrose and centrifuged (13000g, 45 min, 4°C) to remove myelin debris. The pellet was resuspended in nuclei wash and filtered again through a 40 μm Cell Strainer.

tag: transplanted cells

value: IPSC-NPC

tag: host tissue

value: cortical brain stroke tissue


title: KCL-HO-1i treated, rep 5

tag: tissue


title: Microglia,SHAM,8months,Rep4

description: Library name: J189321_D1.J189321_D2.J189321_D3

tag: cell type


title: KCL-HO-1i treated, rep 4

tag: genotype


title: TU212-2

city: Shandong Province

first: ren

middle: yan

last: ru

address: Rencheng District, Jining City, Shandong Province

institute: School of Clinical Medicine, Jining Medical University

description: Library name: Experimental_2

data_processing:
Data quality control was performed using the fastp (version 0.23.0) [@fastp] software. The specific quality control procedures were as follows:  - Adapter sequences in reads were trimmed, and reads shorter than 15 bp were filtered out. - Low-quality reads were removed: reads were discarded if the proportion of bases with quality scores below Q15 exceeded 40%. - Reads containing ambiguous "N" bases were filtered: reads were discarded if the number of "N" bases was more than 5.
During library construction, a unique UID sequence is randomly added to each molecule. Therefore, after data quality control, Kangce's internal UID processing software (kcUID) is used to merge similar reads under the same UID, aiming to correct read errors and remove duplicate reads, thereby obtaining more accurate molecular sequence information and expression levels.  The data processing method of kcUID is as follows:  1. First, identify and extract the UID sequence from reads according to the UID library construction method. 2. Reads with the same UID sequence are grouped into a cluster. During library construction, the same UID sequence may be ligated to different molecules. In each cluster, reads with sequence differences below the threshold (default: 5 nt) are further clustered into sub-clusters by calculating sequence differences between reads. 3. Multiple sequence alignment is performed on reads within each sub-cluster. During alignment and calculation, duplicate reads from the same source are finally merged into a single consensus sequence to achieve error correction and deduplication. 4. Since UID sequences may also introduce errors during PCR or sequencing, sequence differences of UID sequences with the same consensus sequence are calculated. UIDs with differences below the threshold (default: 1 nt) are merged to correct UID errors.
Bowtie was used to map the length-filtered sRNA to the reference sequence, and analyze the distribution of small RNA on the reference sequence.
Assembly: GRCh38

source_name: Cell line-TU212

growth_protocol: TU212 cells were cultured in 1640 medium containing 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (double antibody). The culture was maintained in a 37°C incubator with 5% CO₂.

extract_protocol:
The Small RNA Sample Pre Kit was used to construct the library.
Taking advantage of the special structures at the 3' and 5' ends of small RNAs (with a complete phosphate group at the 5' end and a hydroxyl group at the 3' end), total RNA was used as the starting sample. Small RNAs were directly ligated with adapters at both ends, followed by reverse transcription to synthesize cDNA. Subsequently, cDNA was amplified by PCR, and target DNA fragments were separated by PAGE gel electrophoresis. The gel-cut and recovered products were the cDNA library.

treatment_protocol: After adhering to the culture flask for two days, TU212 cells were treated with 2 μmol/L arsenic trioxide. The cells were continuously cultured in the presence of arsenic trioxide to observe the subsequent changes.

tag: treatment

value: Arsenic trioxide treatment

tag: batch

value: batch 1


title: NOVA37_Blood_Phase_2_SD1

value: Unvaccinated


title: NOVA10_Blood_Phase_2_SD1

value: influenza


title: TU212-3

description: Library name: Experimental_3


title: NOVA39_Blood_Phase_2_SD1


title: NOVA33_Blood_Phase_2_SD1


title: NOVA49_Blood_Phase_2_SD1


title: KCL-HO-1i treated, rep 3


title: Macrophages,TBI,8months,Rep6

description: Library name: J189321_C5.J189321_C6

value: Monocyte-derived Macrophages

tag: time

tag: mouse id


title: TU212-1

description: Library name: Experimental_1


title: KCL-HO-1i treated, rep 2


title: Microglia,TBI,8months,Rep6

description: Library name: J189321_C1.J189321_C2.J189321_C3

tag: lysis plate_id


title: Ctrl-3

description: Library name: Control_3

tag: cell line

value: Control


title: NOVA04_Blood_Phase_2_SD1

description: Gene expression profiling of PBMC  from influenza infected humans

value: PBMC


title: KCL-HO-1i treated, rep 1


title: Ctrl-2

description: Library name: Control_2


title: Microglia,SHAM,8months,Rep5

description: Library name: J189321_E1.J189321_E2.J189321_E3

value: Whole Brain


title: Microglia,TBI,8months,Rep5

description: Library name: J189321_B1.J189321_B2.J189321_B3

value: TBI


title: NOVA32_Blood_Phase_2_SD1


title: Gemcitabine treated, rep 5

value: Gemcitabine


title: Macrophages,TBI,8months,Rep4

description: Library name: J189321_A5.J189321_A6


title: NOVA41_Blood_Phase_2_SD1


title: Gemcitabine treated, rep 4


title: NOVA28_Blood_Phase_2_SD1


title: Microglia,TBI,8months,Rep4

description: Library name: J189321_A1.J189321_A2.J189321_A3

value: Microglia


title: Gemcitabine treated, rep 3

value: Breast


title: Microglia,SHAM,8months,Rep2

description: Library name: J189319_E1.J189319_E2.J189319_E3


title: Gemcitabine treated, rep 2

value: WT


title: NOVA61_Blood_Phase_2_SD1


title: Macrophages,TBI,8months,Rep5

description: Library name: J189321_B5.J189321_B6


title: NOVA53_Blood_Phase_2_SD1


title: 5-FU treated, rep 5


title: NOVA12_Blood_Phase_2_SD1


title: Ctrl-1

description: Library name: Control_1


title: Microglia,SHAM,8months,Rep1

description: Library name: J189319_D1.J189319_D2.J189319_D3

value: SHAM


title: Macrophages,TBI,8months,Rep3

description: Library name: J189319_C5.J189319_C6


title: 5-FU treated, rep 4


title: 5-FU treated, rep 3


title: Microglia,TBI,8months,Rep3

description: Library name: J189319_C1.J189319_C2.J189319_C3


title: 5-FU treated, rep 2


title: Macrophages,TBI,8months,Rep2

description: Library name: J189319_B5.J189319_B6


title: Microglia,SHAM,8months,Rep3

description: Library name: J189319_F1.J189319_F2.J189319_F3


title: NOVA81_Blood_Phase_2_SD1


title: PrimThyTissue_normal_adjacent_PTC_positiveLN_RAIrefractive_RAIR5

city: Cheras

first: Nurul Syakima

last: Ab Mutalib

state: Kuala Lumpur

address: Jalan Yaacob Latiff

department: UKM Medical Molecular Biology Institute

country: Malaysia

institute: Universiti Kebangsaan Malaysia

description: Gene expression of adjacent normal thyroid tissue from PTC patient with positive lymph node and RAI-refractive.

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μL containing 10× Gene Expression Blocking Agent and 25× Fragmentation Buffer following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μL of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent One-Colour SurePrint G3 Human Gene Expression V3 Microarray (G4858A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 1 minute with Gene Expression Wash Buffer 2 (Agilent) at elevated temperature.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan MicroArray Scanner (G2600D, Agilent Technologies) using AgilentG3_GX_1color (for G3 format, standard mode) protocol.

data_processing: Scanned microarray images were analyzed using Agilent Feature Extraction software v11.5.1.1 (Agilent Technologies, Santa Clara, CA) with protocol GE1_1200_Jun14 and grid layout 072363_D_F_20150612. The resulting raw Feature Extraction text files were processed using AltAnalyze v2.1.4, employing the “Process Feature Extraction Files” workflow. Expression data from the green channel were extracted, log2-transformed, and subjected to quantile normalization to minimize inter-array variability. Gene annotation was based on the EnsMart72 gene database for Homo sapiens.

source_name: Adjacent normal thyroid tissue from patient RAIR5 with papillary thyroid carcinoma, positive lymph node metastasis

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from extracted total RNA using the Low Input Quick Amp Labeling Kit, One-Color (Agilent) according to the manufacturer's instructions, followed by column purification using the RNeasy Mini Kit (Qiagen, Hilden, Germany). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 5 primary tumor thyroid tissues were collected from PTC patients with no lymph node metastasis and RAI-avid, 5 tumor thyroid tissues were collected from PTC patients with lymph node metastasis and RAI-refractive and 4 adjacent normal thyroid tissues were acquired from the Hospital Canselor Tuanku Muhriz UKM (HCTM). The tissues were dissected, snap-frozen and stored in liquid nitrogen.

extract_protocol: Total RNA was extracted from fresh frozen primary thyroid tissues using AllPrep® DNA/RNA/miRNA Universal Kit and QIAshredder (Qiagen, Hilden, Germany). Total RNA was quantified using a Nanodrop 2000c Spectrometer (Thermo Fisher Scientific, Pittsburgh, PA, USA) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Tissue samples were cryosectioned and stained with hematoxylin and eosin and the percentage of tumor cells and normal cells contents were confirmed by a pathologist. Only tumor samples with at least 80% cancerous cells and normal adjacent thyroid tissues with less than 20% necrosis were selected for RNA extraction.

value: Primary thyroid tissue

tag: tissue types

value: Normal

tag: patient diagnosis

value: Papillary thyroid cancer

tag: gender

value: Female

tag: race

value: Malay

tag: age

value: 35 years

tag: disease stage

value: I

tag: ata risk

value: Intermediate

tag: primary tumor

tag: histological variant

value: Classic

tag: tumor size

value: 12 mm

tag: tumor focality

value: Multifocal

tag: tumor laterality

value: Bilateral

tag: extrathyroidal extension

value: No

tag: vascular invasion

tag: lymph node metastasis

tag: number lymph node metastasis

tag: lymph node metastasis ratio

tag: distant metastasis

tag: organ-specific metastasis

tag: surgical type

value: Completion thyroidectomy

tag: lymph node dissection

value: Lateral and central node

tag: rai therapy

value: Yes

tag: rai response

value: Refractive

tag: rai-refractory type

value: Tumor tissue that no longer takes up RAI despite previous uptake

tag: FDG avid

tag: disease remission


title: NOVA82_Blood_Phase_2_SD1

tag: disease state

value: influenza

tag: tissue

value: PBMC

tag: study group

value: Unvaccinated

tag: study date


title: NOVA78_Blood_Phase_2_SD1


title: Microglia,TBI,8months,Rep2

description: Library name: J189319_B1.J189319_B2.J189319_B3

value: Whole Brain

tag: cell type

value: Microglia

tag: genotype

tag: treatment

value: TBI

tag: time

tag: mouse id

tag: library prep_plate_id

tag: lysis plate_id


title: PrimThyTissue_normal_adjacent_PTC_positiveLN_RAIrefractive_RAIR1

source_name: Adjacent normal thyroid tissue from patient RAIR1 with papillary thyroid carcinoma, positive lymph node metastasis

value: Primary thyroid tissue

tag: tissue types

value: Normal

tag: patient diagnosis

value: Papillary thyroid cancer

tag: gender

value: Female

tag: race

value: Chinese

tag: age

value: 79 years

tag: disease stage

value: II

tag: ata risk

value: Intermediate

tag: primary tumor

tag: histological variant

value: Tall cell

tag: tumor size

value: 35 mm

tag: tumor focality

value: Unifocal

tag: tumor laterality

value: Unilateral

tag: extrathyroidal extension

tag: vascular invasion

tag: lymph node metastasis

tag: number lymph node metastasis

tag: lymph node metastasis ratio

tag: distant metastasis

tag: organ-specific metastasis

tag: surgical type

value: Total thyroidectomy

tag: lymph node dissection

value: Central node


title: PrimThyTissue_normal_adjacent_PTC_negativeLN_RAIavid_RAIA2

description: Gene expression of adjacent normal thyroid tissue from PTC patient with negative lymph node and RAI-avid.

source_name: Adjacent normal thyroid tissue from patient RAIA2 with papillary thyroid carcinoma, negative lymph node metastasis

tag: tissue

tag: tissue types

tag: patient diagnosis

tag: gender

tag: race

value: Malay

tag: age

value: 61 years

value: I

value: Low

value: Classic

value: 30 mm

value: No

tag: rai therapy

value: Yes

tag: rai response

value: Avid

tag: rai-refractory type

value: Not applicable

tag: FDG avid

tag: disease remission


title: Control, rep 5

value: Breast

tag: strain

tag: genotype

value: WT

tag: treatment

value: Vehicle


title: Macrophages,TBI,8months,Rep1

description: Library name: J189319_A5.J189319_A6

value: Whole Brain

tag: cell type

value: Monocyte-derived Macrophages

value: TBI

tag: time

tag: mouse id

tag: library prep_plate_id

tag: lysis plate_id


title: PrimThyTissue_normal_adjacent_PTC_negativeLN_RAIavid_RAIA1

source_name: Adjacent normal thyroid tissue from patient RAIA1 with papillary thyroid carcinoma, negative lymph node metastasis

tag: tissue

value: Primary thyroid tissue

tag: tissue types

value: Normal

tag: patient diagnosis

value: Papillary thyroid cancer

value: Female

value: Chinese

value: 59 years

tag: disease stage

tag: ata risk

tag: primary tumor

tag: histological variant

tag: tumor size

value: 22 mm

tag: tumor focality

value: Unifocal

tag: tumor laterality

value: Unilateral

tag: extrathyroidal extension

tag: vascular invasion

tag: lymph node metastasis

tag: number lymph node metastasis

tag: lymph node metastasis ratio

tag: distant metastasis

tag: organ-specific metastasis

tag: surgical type

value: Total thyroidectomy

tag: lymph node dissection

value: Central node


title: PrimThyTissue_tumor_PTC_positiveLN_RAIrefractive_RAIR4

description: Gene expression of cancerous thyroid tissue from PTC patient with positive lymph node and RAI-refractive.

source_name: Thyroid tumor tissue from patient RAIR4 with papillary thyroid carcinoma, positive lymph node metastasis

tag: tissue

tag: tissue types

value: Tumor

tag: patient diagnosis

tag: gender

value: Male

tag: race

value: Malay

tag: age

value: 64 years

value: IVB

value: High

value: Classic

value: 25 mm

value: Multifocal

value: Bilateral

value: Yes

value: Lung

value: Lateral and central node

tag: rai therapy

tag: rai response

value: Refractive

tag: rai-refractory type

value: Tumor tissue that no longer takes up RAI despite previous uptake

tag: FDG avid

tag: disease remission

value: No


title: PrimThyTissue_tumor_PTC_positiveLN_RAIrefractive_RAIR5

source_name: Thyroid tumor tissue from patient RAIR5 with papillary thyroid carcinoma, positive lymph node metastasis

value: Primary thyroid tissue

value: Papillary thyroid cancer

value: Female

value: 35 years

tag: disease stage

value: I

tag: ata risk

value: Intermediate

tag: primary tumor

tag: histological variant

tag: tumor size

value: 12 mm

tag: tumor focality

tag: tumor laterality

tag: extrathyroidal extension

tag: vascular invasion

tag: lymph node metastasis

tag: number lymph node metastasis

value: Completion thyroidectomy


title: PrimThyTissue_tumor_PTC_positiveLN_RAIrefractive_RAIR3

source_name: Thyroid tumor tissue from patient RAIR3 with papillary thyroid carcinoma, positive lymph node metastasis

tag: tissue

tag: tissue types

value: Tumor

tag: patient diagnosis

tag: gender

value: Male

tag: race

value: Malay

tag: age

value: 74 years

value: IVB

value: High

value: Classic

value: 55 mm

tag: lymph node metastasis ratio

tag: distant metastasis

tag: organ-specific metastasis

value: Lung, pleura, bones, mediastinal nodes

tag: surgical type

value: Total thyroidectomy

tag: lymph node dissection

value: RAI uptake in some lesions only


title: PrimThyTissue_tumor_PTC_positiveLN_RAIrefractive_RAIR2

source_name: Thyroid tumor tissue from patient RAIR2 with papillary thyroid carcinoma, positive lymph node metastasis

value: Primary thyroid tissue

value: Papillary thyroid cancer

value: Female

value: Chinese

value: 54 years

tag: disease stage

tag: ata risk

tag: primary tumor

tag: histological variant

tag: tumor size

value: 42 mm

tag: tumor focality

value: Unifocal

value: Unilateral

value: No

value: Lung

value: Lateral and central node

tag: rai therapy

value: Yes

tag: rai response

value: Refractive

tag: rai-refractory type

value: Tumor tissue that no longer takes up RAI despite previous uptake

tag: FDG avid

tag: disease remission


title: NOVA31_Blood_Phase_2_SD1

tag: disease state

value: influenza

tag: tissue

value: PBMC

tag: study group

value: Vaccinated

tag: study date


title: NOVA17_Blood_Phase_2_SD1


title: NOVA59_Blood_Phase_2_SD1

value: Unvaccinated


title: NOVA62_Blood_Phase_2_SD1


title: Control, rep 4

value: Breast

tag: strain

tag: genotype

value: WT

tag: treatment

value: Vehicle


title: Control, rep 3


title: NOVA46_Blood_Phase_2_SD1


title: Pancreas, ADM, 18

city: Edinburgh

first: Carla

last: Salomo Coll

address: Crewe Rd S

department: Institute of Genetics and Cancer - CRUK Scotland Centre

institute: University of Edinburgh

description: NanoString GeoMx Digital Spatial Profiler(DSP)

data_processing:
FastQ files were transformed into digital count conversion (DCC) files using Nanostring GeoMx NGS pipeline and uploaded to the GeoMX DSP for analysis following the GeoMx DSP Data Analysis User Manual. Outlier probes were removed from all segments when the limit of quantitation (LOQ) was higher than 2. Targets were filtered and only genes with an expression greater than the LOQ in at least 5% of the segments were used. Q3 normalisation was performed on the remaining genes.
Assembly: GeoMx Mouse WholeTranscriptome Atlas
Supplementary files format and content: GeoMX_Q3Norm_values.xlxs: Includes a matrix with Q3 normalised gene expression values for each sample
Supplementary files format and content: GeoMX_Segment_properties.xlx: List of segments and spatial information of each
Supplementary files format and content: .DCC files, digital count conversion files for the GeoMX Analysis
Library strategy: Spatial transcriptomics

source_name: Pancreas

extract_protocol:
Slides were prepared following NanoString GeoMx DSP Manual RNA Assay Slide Preparation. In the scan area of each slide, two 5-μm-thick FFPE tissue sections were placed, for a total of four mice. Slides were incubated with Whole Transcriptome Atlas Probe Mix overnight. For segmentation of the different cell populations, slides were incubated with the following morphology markers: Reg3a/g (B-10) (Santacruz biotechnologies, sc-377038), Amylase (D55H10) XP (CST, 3796), PanCK AlexaFluor 532 (Novus Biologicals, NBP2-33200AF532) and SYTO 13 (Invitrogen, S7575) for nuclear staining. Slides were then scanned with GeoMx Digital Spatial Profiler (Nanostring). Regions of interest (ROIs) were selected based the morphology markers and a total of 95 segments were collected for analysis.
After the GeoMx DSP system has completed collection, the DSP collection plate can be removed from the instrument. Each GeoMx DSP aspirate in the plate contains photocleaved DNA oligos comprised of an analyte identifier, a unique molecular identifier (UMI) barcode, and primer binding sites. 95 ROIs were dried down at 65C for 1 hour on a PCR block and resuspended in 10ul of Nuclease-Free water for 10 minutes. PCR was then performed with the matching primers from the primer plate Seq Code C. When PCR is performed on the aspirates, Illumina adapter sequences and unique dual sample indices are added. After the PCR step, 4ul of each library were pooled, size selected and clean-up using AMPure XP beads (Beckman Coulter, #A63881). 4ul of each library was pooled, creating a volume of 380ul. 456ul of Ampure was added to the first step of the size selection. The final elution volume was 48ul. The final library had an average peak size of 153bp. The library pool was quantified by fluorometry using the Qubit dsDNA HS assay and assessed for quality and fragment size using the Agilent Bioanalyser with the DNA HS Kit (#5067-4626). Fragment size and quantity measurements were used to calculate molarity. The pool had a molarity of 29.7nM.

value: Pancreas

tag: cell type

value: ADM

value: LSL-KrasG12D; Pdx1-Cre


title: 5-FU treated, rep 1


title: PrimThyTissue_tumor_PTC_negativeLN_RAIavid_RAIA5

description: Gene expression of cancerous thyroid tissue from PTC patient with negative lymph node and RAI-avid.

source_name: Thyroid tumor tissue from patient RAIA5 with papillary thyroid carcinoma, negative lymph node metastasis

value: Primary thyroid tissue

tag: tissue types

value: Tumor

tag: patient diagnosis

value: Papillary thyroid cancer

tag: gender

value: Female

tag: race

value: Malay

tag: age

value: 27 years

tag: disease stage

value: I

tag: ata risk

value: Intermediate

tag: primary tumor

value: Classic

value: 55 mm

value: Unifocal

tag: tumor laterality

value: Unilateral

tag: extrathyroidal extension

tag: vascular invasion

tag: lymph node metastasis

tag: number lymph node metastasis

tag: lymph node metastasis ratio

tag: distant metastasis

tag: organ-specific metastasis

tag: surgical type

value: Total thyroidectomy

tag: lymph node dissection

value: Avid

value: Not applicable


title: Control, rep 2

tag: tissue

value: Breast

tag: strain

tag: genotype

value: WT

tag: treatment

value: Vehicle


title: Pancreas, ADM_REG3, 7

value: Pancreas

tag: cell type

value: LSL-KrasG12D; Pdx1-Cre


title: Control, rep 1


title: Pancreas, Acini_Distal, 19


title: Pancreas, ADM, 17

value: ADM


title: 3T3-rep3

city: Wuhan

first: Zhen-Xia

last: Chen

state: Hubei

address: No.1 Shizishan Street

department: College of Life Science and Technology

institute: Huazhong Agricultural University

library_source: genomic

data_processing:
CUT&Tag: Raw fastq files were subjected to quality control using FastQC (v0.11.9) and Trim Galore (v0.6.0).
CUT&Tag: Reads were aligned with bowtie2 (v2.3.5.1) and samtools (v1.3.1, options: -Sb -q 20).
CUT&Tag: BAM files were deduplicated with picard (v2.25.7) MarkDuplicates
CUT&Tag: MACS2 (v2.2.7.1) subcommand callpeak was used for peak calling
Assembly: hg19, mm10, Sscrofa11
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

molecule: genomic DNA

extract_protocol:
Living cells with a 10 minutes’ incubation at room temperature
Cleavage Under Targets and Tagmentation (CUT&Tag) have been described in detail (KayaOkur et al. 2019; Wang et al. 2019) with some modifications. Briefly, cells were incubated with activated concanavalin A-coated magnetic beads (Smart-Lifesciences). The bead-bound cells were permeabilized and incubated first with BG4 primary antibody, followed by anti-Flag M2 antibody (Sigma-Aldrich), and lastly with rabbit antimouse IgG antibody. Diluted pA-Tn5 adapter complex was then added followed by the tagmentation reaction. Extracted DNA fragments were used for library preparation. More details of this experiment and data analysis are described in following.

tag: cell line

value: Mouse embryonic fibroblasts

tag: chip antibody


title: Arabidopsis thaliana,odr1-2, imbibition seeds, rep3

city: Shenzhen

first: Ling

last: Ding

address: No 7,Pengfei Road,Dapeng District

institute: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences

description:
Library name: m49_6HAI_3
Column name in allSample.count.xls and allSample.FPKM.xls: m49_6HAI_3

data_processing:
Quality control and filtering of raw sequencing data were performed using fastp (version 0.14.0)
Filtered reads were aligned to the reference genome using HISAT (version 0.1.6)
Gene expression levels were quantified using HTSeq (version 0.6.1)
Assembly: Arabidopsis Information Resource 10 genome (TAIR10)
Supplementary files format and content: The FPKM expression matrix file includes gene IDs and corresponding expression values for each sample.
Supplementary files format and content: The Gene Count Matrix file comprises gene IDs and the raw counts of reads that mapped to each gene in every sample.

organism: Arabidopsis thaliana

source_name: mature seeds

growth_protocol: Arabidopsis thaliana were grown in a controlled environment at 22°C with a 16-hour light and 8-hour dark cycle.

extract_protocol:
The extraction of RNA was carried out with the FastPure Plant Total RNA Isolation Kit (Vazyme, RC401), strictly following the protocol provided by the manufacturer.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: RNA was extracted directly from dry seeds. For imbibed seeds, RNA extraction was performed after a 6-hour soaking period in distilled water.

value: seeds

value: imbibition for 6h


title: 3T3-rep2


title: Arabidopsis thaliana,odr1-2, imbibition seeds, rep2

description:
Library name: m49_6HAI_2
Column name in allSample.count.xls and allSample.FPKM.xls: m49_6HAI_2


title: NOVA03_Blood_Phase_2_SD1

tag: disease state

value: influenza

value: PBMC

tag: study group

value: Vaccinated

tag: study date


title: Pancreas, ADM, 16


title: NOVA07_Blood_Phase_2_SD1


title: PrimThyTissue_tumor_PTC_negativeLN_RAIavid_RAIA3

source_name: Thyroid tumor tissue from patient RAIA3 with papillary thyroid carcinoma, negative lymph node metastasis

value: Primary thyroid tissue

tag: tissue types

value: Tumor

tag: patient diagnosis

value: Papillary thyroid cancer

tag: gender

value: Female

tag: race

value: Malay

tag: age

value: 69 years

tag: disease stage

value: II

tag: ata risk

value: Intermediate

tag: primary tumor

tag: histological variant

value: Cribriform morular

tag: tumor size

value: 80 mm

tag: tumor focality

value: Unifocal

tag: tumor laterality

tag: extrathyroidal extension

value: No

tag: vascular invasion

value: Yes

tag: lymph node metastasis

value: Lateral and central node

tag: rai therapy

tag: rai response

tag: rai-refractory type

tag: FDG avid

tag: disease remission


title: Arabidopsis thaliana,odr1-2, imbibition seeds, rep1

description:
Library name: m49_6HAI_1
Column name in allSample.count.xls and allSample.FPKM.xls: m49_6HAI_1

tag: tissue

value: seeds

tag: genotype

tag: treatment

value: imbibition for 6h


title: PrimThyTissue_tumor_PTC_negativeLN_RAIavid_RAIA1

source_name: Thyroid tumor tissue from patient RAIA1 with papillary thyroid carcinoma, negative lymph node metastasis

tag: tissue types

tag: patient diagnosis

tag: gender

tag: race

value: Chinese

tag: age

value: 59 years

tag: disease stage

value: I

tag: ata risk

value: Low

value: Classic

value: 22 mm

value: Unilateral

tag: number lymph node metastasis

tag: lymph node metastasis ratio

tag: distant metastasis

tag: organ-specific metastasis

tag: surgical type

value: Total thyroidectomy

tag: lymph node dissection

value: Central node

value: Avid

value: Not applicable


title: 3T3-rep1

tag: cell line

tag: cell type

value: Mouse embryonic fibroblasts

tag: chip antibody


title: NOVA60_Blood_Phase_2_SD1

description: Gene expression profiling of PBMC  from influenza infected humans

tag: disease state

value: influenza

tag: tissue

value: PBMC

tag: study group

value: Unvaccinated

tag: study date


title: PrimThyTissue_tumor_PTC_negativeLN_RAIavid_RAIA2

source_name: Thyroid tumor tissue from patient RAIA2 with papillary thyroid carcinoma, negative lymph node metastasis

value: Primary thyroid tissue

tag: tissue types

value: Tumor

tag: patient diagnosis

value: Papillary thyroid cancer

tag: gender

value: Female

tag: race

value: Malay

value: 61 years

tag: primary tumor

tag: histological variant

tag: tumor size

value: 30 mm

tag: tumor focality

value: Unifocal

tag: tumor laterality

tag: extrathyroidal extension

value: No

tag: vascular invasion

tag: lymph node metastasis

tag: rai therapy

value: Yes

tag: rai response

tag: rai-refractory type

tag: FDG avid

tag: disease remission


title: PrimThyTissue_tumor_PTC_negativeLN_RAIavid_RAIA4

source_name: Thyroid tumor tissue from patient RAIA4 with papillary thyroid carcinoma, negative lymph node metastasis

tag: tissue

tag: tissue types

tag: age

value: 41 years

tag: disease stage

value: I

tag: ata risk

value: Intermediate

value: Classic

value: 40 mm

value: Unilateral

tag: number lymph node metastasis

tag: lymph node metastasis ratio

tag: distant metastasis

tag: organ-specific metastasis

tag: surgical type

value: Total thyroidectomy

tag: lymph node dissection

value: Central node


title: Pancreas, Acini_Proximal, 22

value: Pancreas

tag: cell type

tag: genotype

value: LSL-KrasG12D; Pdx1-Cre


title: PrimThyTissue_tumor_PTC_positiveLN_RAIrefractive_RAIR1

source_name: Thyroid tumor tissue from patient RAIR1 with papillary thyroid carcinoma, positive lymph node metastasis

value: Primary thyroid tissue

value: Tumor

tag: patient diagnosis

value: Papillary thyroid cancer

tag: gender

value: Female

tag: race

value: Chinese

value: 79 years

value: II

tag: primary tumor

tag: histological variant

value: Tall cell

tag: tumor size

value: 35 mm

tag: tumor focality

tag: tumor laterality

tag: extrathyroidal extension

tag: vascular invasion

tag: lymph node metastasis

tag: rai therapy

tag: rai response

value: Refractive

value: Tumor tissue that no longer takes up RAI despite previous uptake


title: NOVA01_Blood_Phase_2_SD1

tag: disease state

value: influenza

tag: tissue

value: PBMC

tag: study group

value: Vaccinated

tag: study date


title: Arabidopsis thaliana,odr1-2, dry seeds, rep2

description:
Library name: m49_ds_2
Column name in allSample.count.xls and allSample.FPKM.xls: m49_ds_2

value: seeds

tag: genotype

tag: treatment


title: NOVA02_Blood_Phase_2_SD1


title: Pancreas, Acini_REG3, 28

value: Pancreas

tag: cell type


title: C2C12-rep2

tag: cell line

value: Mouse myoblast cell

tag: chip antibody


title: NOVA40_Blood_Phase_2_SD1


title: Arabidopsis thaliana,odr1-2, dry seeds, rep3

description:
Library name: m49_ds_3
Column name in allSample.count.xls and allSample.FPKM.xls: m49_ds_3


title: C2C12-rep1


title: Pancreas, ADM, 15

value: ADM

value: LSL-KrasG12D; Pdx1-Cre


title: Microglia,TBI,8months,Rep1

description: Library name: J189319_A1.J189319_A2.J189319_A3

source_name: Whole Brain

value: Whole Brain

value: Microglia

value: TBI

tag: time

tag: mouse id

tag: library prep_plate_id

tag: lysis plate_id


title: Pancreas, Acini_Distal, 18


title: Arabidopsis thaliana,odr1-2, dry seeds, rep1

description:
Library name: m49_ds_1
Column name in allSample.count.xls and allSample.FPKM.xls: m49_ds_1


title: Arabidopsis thaliana,Col-0, imbibition seeds, rep3

description:
Library name: col_6HAI_3
Column name in allSample.count.xls and allSample.FPKM.xls: col_6HAI_3

value: imbibition for 6h


title: JLT5_15

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Bioinformatic analysis of the resulting reads contained two parts: removing duplicates using UMIs and implementing the CCseqBasicS pipeline. First, the beginning eight base pairs on the forward and reverse reads respectively were extracted using fgbio toolkit as UMIs (v0.5.0a, https://github.com/fulcrumgenomics/fgbio), which we later used for PCR duplication removal. Reads were then aligned to reference genome (mm10) using BWA MEM (v0.7.17) and default parameters. Only properly paired, primary alignments were kept for downstream analysis. Read pairs aligned to the same location which had the same UMI were removed as PCR duplicates using Picard (v2.18.15). The successfully aligned, non-duplicated read pairs were reverted to FASTQ format for Capture-C analysis using the CCseqBasicS (VS1.0.8) pipeline. FLASH (v1.2.11) was first used to merge paired-end reads from the same fragment, allowing the reads to overlap to a maximum of 250 bp (‘-M 150’). Fragments were digested with DpnII using the Python script implemented by the CCseqBasicS pipeline and mapped to mm10 reference genome using Bowtie (Langmead, 2010) (version 2.3.4.3) using default parameters and the maximum allowed insert size of 2000bp. Blacklist regions provided by the CCseqBasicS pipeline were excluded from the alignment file using bedtools toolkit (v.2.17.0). CCseqBasic tool (vCC5) was implemented with default settings (“--ampliconSize 2000 --noTrim -w 200 -i 20”) to acquire reporter reads of each designed captured probe in each sample. The tool was run in both non-SNP-specific as well as SNP-specific configurations (we designed probes so that they have B6/Cast SNPs nearby to be sequenced; the list of used SNPs is available in Supp. Table 3.3). The total read counts for each probe region (non-snp-specific) and for each SNP (Cast, B6) are provided in Supp. Table 3.5. Bigwig files were generated for each sample and each probe by piling up all reads, B6 reads and Cast reads separately, and then normalized to 10K reporter reads per designed probe for track visualization. We pooled reads from alleles in the same experimental group (WT.neonatal.maternal, WT.neonatal.paternal, WT.adult.maternal, WT.adult.paternal, [CCDIvr pKO] KO.adult.paternal) together for calling contact sites, statistical analysis and visualization. For each experimental group and for each probe, we defined contact sites in two ways: the “given coordinates” approach which we manually defined contact sites (loci with CTCF motif, Igf2 promoters, previously reported skeletal muscle enhancer and a putative skeletal muscle enhancer [see Supp. Table 5]), and the “peak calling” approach for which we used computational algorithm to call contact sites from the data. More specifically for the peak calling approach, contact sites were defined as peaks called using MACS2 (v2.1.1) with parameters “--nomodel --extsize 1200 --qvalue 1e-100 --broad --nolambda --broad-cutoff 1e-100 --minsize 5000”. The corresponding contact site visualization, for each group and each probe, was defined by fourSig (Williams et al., 2014) with parameters “window.size=1, iterations=100, fdr=0.001, fdr.prob=0.05” and normalized to 100K reporter reads per designed probe for track visualization. Signal for each contact site was quantified on each bigwig file generated from the pipeline using bwtool (v1.0) (Pohl and Beato, 2014). Differential analysis between experiment groups was then performed using DESeq2 R package (FDR 0.05). Statistics for locus-specific comparisons are provided in Supp. Table 5 for both the “peak calling” and “given coordinates” approach. Figures were generated using .bw and .longinteraction files and visualized on WashU Epigenome Browser.
Assembly: mm10
Supplementary files format and content: normalized bigwig files for each probe in on maternal, paternal and both (non-SNP-specific) strands
Library strategy: Capture-C

source_name: muscle

extract_protocol:
Briefly, muscle tissues were obtained from wildtype adult or neonate reciprocal F1 C57BL/6 (B6) and C7 F1 hybrid mice, and C7 mice bred to male or female mice with ccd knock out (KO) to generate maternal- and paternal-specific ccd KO F1 hybrids (mKO and pKO).
Capture-C was performed simultaneously with the Capture-C described by Juan et al. 2022 and followed previously described methods (Davies et al., 2016). The samples described here included nuclei isolated from neonatal and adult hindlimb muscle obtained from reciprocal hybrid wildtype mice (BxC and CxB) and mice with the maternal and paternal DCCDIvr allele (CCDIvrD/+ and CCDIvr+/D, respectively, where ‘+’ is the wildtype C allele). 3C libraries were generated from nuclei using standard methods (Naveh et al., 2021) and DnpII as the primary restriction enzyme. Before oligonucleotide capture, 3C libraries were fragmented to 200-1000 bp sizes using a second digestion with two spike-ins of NlaIII overnight and in the morning for library prep and sequencing. The xGen Prism DNA library kit with primers (IDT 10006202 & 10005975) and adapters with unique molecular identifier (UMI) sequences were incorporated during adapter ligation to minimize sequence errors and reduce PCR duplication rates (IDT, 10006914). 1 ug of indexed samples were pooled before oligonucleotide capture using biotinylated oligonucleotides designed for multiple CTCF binding sites across the Igf2/H19 locus (including the ICR), Igf2 promoters and previously identified and putative enhancer skeletal muscle enhancers using IDT Discovery Pool technology. Probe sequences are provided in Supp. Table 3.1. The first hybridization reaction included five pools describes by Juan et al. and two additional pools described herewith (one pool assayed the four neonatal muscle samples; the other pool assayed the six adult muscle [see Supp. Table 3.2]), with each hybridization pool set up using Mouse-COT DNA and 1.5 pM of Discovery Probes using reagents provided by the xGen Hybridization and Wash Kit according to the manufacturer’s instructions (IDT, 1080577). After a 16-hour hybridization step, streptavidin bead pulldown (IDT, 1080577) and multiple bead washes using IDT xGen Hybridization and Wash Kit, PCR amplification of the captured material was performed using KAPA HiFi HotStart Readymix Kit (KAPA Biosystems, KR0370) and library amplification primer (IDT, 1077676) for 14 cycles. A second capture was performed as above, with the exception that it was carried out with one-half of the Mouse-COT DNA and probe concentration used in the first capture. The material was sequenced using the Illumina NOVA-Seq platform with 250-bp paired end reads.

value: muscle

tag: strain

tag: age

value: adult

value: pKO


title: C2C12-rep3


title: Pancreas, Acini_Proximal, 23


title: Pancreas, Acini_Distal, 17


title: NOVA32_Blood_Phase_2_SD_-1

value: SD -1


title: JLT3_8

value: neonatal


title: Arabidopsis thaliana,Col-0, imbibition seeds, rep1

description:
Library name: col_6HAI_1
Column name in allSample.count.xls and allSample.FPKM.xls: col_6HAI_1


title: Arabidopsis thaliana,Col-0, imbibition seeds, rep2

description:
Library name: col_6HAI_2
Column name in allSample.count.xls and allSample.FPKM.xls: col_6HAI_2


title: JLT4_13


title: NOVA57_Blood_Phase_2_SD1

value: influenza

value: Unvaccinated


title: NOVA21_Blood_Phase_2_SD_-1

value: PBMC

value: Vaccinated


title: NOVA53_Blood_Phase_2_SD_-1


title: NOVA06_Blood_Phase_2_SD_-1


title: JLT2_7

value: WT


title: Arabidopsis thaliana,Col-0, dry seeds, rep3

description:
Library name: col_ds_3
Column name in allSample.count.xls and allSample.FPKM.xls: col_ds_3

value: seeds


title: Pancreas, Acini_REG3, 27

value: Pancreas


title: Pancreas, Acini_Proximal, 20

value: LSL-KrasG12D; Pdx1-Cre


title: NOVA27_Blood_Phase_2_SD_-1


title: JLT2_6


title: NOVA49_Blood_Phase_2_SD_-1


title: JLT2_5


title: Pancreas, Acini_Proximal, 19


title: Pancreas, Acini_REG3, 26


title: JLT1_4

value: mKO


title: rat cartilage, syd, rep3

city: jinan

first: xuyu

last: song

address: 47 Shanda South Road

institute: shandong university

description:
Library name: CXTB3
syd

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5。
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: gene_fpkm2.txt

organism: Rattus norvegicus

source_name: Cartilage tissue

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cartilage tissue


title: NOVA08_Blood_Phase_2_SD_-1


title: Pancreas, ADM, 14

value: ADM


title: Pancreas, Acini_REG3, 25


title: JLT1_3


title: NOVA22_Blood_Phase_2_SD_-1_a


title: NOVA52_Blood_Phase_2_SD_-1


title: JLT1_2


title: rat cartilage, syd, rep2

description:
Library name: CXTB2
syd


title: NOVA51_Blood_Phase_2_SD_-1_a


title: rat cartilage, syd, rep1

description:
Library name: CXTB1
syd


title: Arabidopsis thaliana,Col-0, dry seeds, rep1

description:
Library name: col_ds_1
Column name in allSample.count.xls and allSample.FPKM.xls: col_ds_1


title: NOVA50_Blood_Phase_2_SD_-1


title: JLT1_1


title: Pancreas, Acini_Proximal, 18


title: input_yw_rep1, dme ovary, ChIP-seq

city: Moscow

first: Anastasiya

last: Kobelyatskaya

address: Vavilov str, 32

country: Russia

institute: Engelhardt Institute of Molecular Biology, RAS

description: Library name: input_yw_rep1

data_processing:
FastQC and Trimmomatic were used for the quality control and trimming of reads. Bowtie2 aligner was used to map the reads to the reference genome (BDGP assembly R6/dm6). bamCoverage (deepTools) was used to obtain bigwig files (normalized ChIP signals - CPM).
Assembly: dme6
Supplementary files format and content: bigWig (lib size normalized CPM)

organism: Drosophila melanogaster

source_name: ovary

extract_protocol:
ChIP on Drosophila ovaries was performed according to a published procedure (PMID: 29358235). Chromatin was immunoprecipitated with the following antibodies: anti-trimethyl-histone H3 Lys9 (Millipore); anti-dimethyl-histone H3 Lys4 (Millipore); anti-BEAF32 ( PMID: 34189647); anti-Chriz/Chromator ( PMID: 15821938); anti-DREF (from P. Geogriev), anti-Rhino ( PMID: 27939293).
The libraries for ChIPseq were prepared using MGIEasy Universal DNA Library Prep Set (MGI)

value: ovary


title: NOVA42_Blood_Phase_2_SD_-1


title: Arabidopsis thaliana,Col-0, dry seeds, rep2

description:
Library name: col_ds_2
Column name in allSample.count.xls and allSample.FPKM.xls: col_ds_2


title: Pancreas, Acini_Distal, 16


title: rat cartilage, koa, rep3

description:
Library name: MOD3
koa


title: Pancreas, Acini_Proximal, 21


title: rat cartilage, koa, rep2

description:
Library name: MOD2
koa


title: rat cartilage, koa, rep1

description:
Library name: MOD1
koa


title: input_BeafKO_rep1, dme ovary, ChIP-seq

description: Library name: input_BeafKO_rep1

value: BEAF AB-KO strain, homozygotes BEAF AB-KO/BEAF AB-KO  (Roy, Gilbert and Hart 2007)


title: Rhino_yw_rep2, dme ovary, ChIP-seq

description: Library name: Rhino_yw_rep2

value: Rhino


title: rat cartilage, nc, rep3

description:
Library name: NOR3
control


title: NOVA15_Blood_Phase_2_SD_-1


title: rat cartilage, nc, rep2

description:
Library name: NOR2
control


title: Rhino_yw_rep1, dme ovary, ChIP-seq

description: Library name: Rhino_yw_rep1


title: Pancreas, Acini_Proximal, 17


title: NOVA43_Blood_Phase_2_SD_-1


title: Rhino_BeafKO_rep2, dme ovary, ChIP-seq

description: Library name: Rhino_BeafKO_rep2


title: rat cartilage, nc, rep1

description:
Library name: NOR1
control


title: Gemcitabine treated, rep 1

source_name: Breast

value: Breast

value: Gemcitabine


title: Pancreas, ADM, 13


title: Pancreas, Acini_REG3, 22


title: NOVA29_Blood_Phase_2_SD_-1

value: SD -1


title: Rhino_BeafKO_rep1, dme ovary, ChIP-seq

description: Library name: Rhino_BeafKO_rep1


title: NOVA67_Blood_Phase_2_SD_-1

value: influenza


title: H3K9me3_yw_rep2, dme ovary, ChIP-seq

description: Library name: H3K9me3_yw_rep2


title: RNA230912TZ_Tumor_38_S70

city: Portland

first: Rafael

last: Correia

address: 2730 S Moody Ave

institute: Oregon Health & Science University

description:
Library name: Sample 19
TRIzol and Quiagen miRNeasy Mini

data_processing:
The proceed data were obtain using the software Partek Flow.
The quality trimming level (Phred) was 35 (3' end)
We aligned the reads to the UCSC Rattus norvegicus (rn7) reference genome using STAR (Spliced Transcripts Alignment to a Reference)
To quantify gene expression, we used the annotation model Rn07
The gene counts were filtered using noise filter reduction filter <=10
The normalization was made using Median ratio (DESeq2) and differential analysis was made using DESeq2
Assembly: rn7 - Rn07
Supplementary files format and content: Normalized counts and DESeq2 for tibialis or tumor
Supplementary files format and content: .txt

source_name: Tumor

extract_protocol:
Snap-frozen tibialis anterior and tumor tissue were homogenized in liquid nitrogen via mortar and pestle. RNA was isolated from ∼50 mg of tissue using the miRNeasy Mini Kit (Qiagen, cat: 217004). The concentration and quality of total RNA samples were assessed using an Agilent 2100 Bioanalyzer, and an RNA Integrity Number (RIN) of 8 or higher was required to pass the quality control.
Library preparation and sequencing was completed at the Massively Parallel Sequencing Shared Resource at Oregon Health and Science University using the Illumina NovoSeq6000. 150ng of total RNA was used for each sample. cDNA library preparation includes mRNA purification/enrichment, RNA fragmentation, cDNA synthesis, and ligation of index adaptors using the KAPA mRNA Hyperprep Kit prep (cat: KK8581). Each resulting indexed library was quantified, and its quality was assessed by NovaSeq 6000. 5μL of 2nM pooled libraries per lane was denatured, neutralized, and applied to the cBot for flow cell deposition and cluster amplification before loading to 100bp paired-end sequencing (Illumina, Inc.). Approximately 30-50 million reads per library were generated.

value: Tumor

tag: Sex

value: male

value: Wild Type

value: DMBA-induced cancer with 8 weeks of aerobic physical training


title: RNA230912TZ_Tumor_39_S71

description:
Library name: Sample 20
TRIzol and Quiagen miRNeasy Mini


title: Pancreas, Acini_Distal, 15

description: NanoString GeoMx Digital Spatial Profiler(DSP)


title: Pancreas, Acini_REG3, 24


title: NOVA65_Blood_Phase_2_SD_-1

value: PBMC

value: Unvaccinated


title: Pancreas, Acini_Distal, 14

value: Pancreas

value: LSL-KrasG12D; Pdx1-Cre


title: RNA230912TZ_Tumor_33_S69

description:
Library name: Sample 18
TRIzol and Quiagen miRNeasy Mini


title: H3K9me3_BeafKO_rep2, dme ovary, ChIP-seq

description: Library name: H3K9me3_BeafKO_rep2


title: NOVA71_Blood_Phase_2_SD_-1


title: NOVA31_Blood_Phase_2_SD_-1

value: Vaccinated


title: Pancreas, Acini_Proximal, 16


title: Pancreas, Acini_Distal, 13


title: H3K9me3_BeafKO_rep1, dme ovary, ChIP-seq

description: Library name: H3K9me3_BeafKO_rep1


title: Pancreas, Acini_Proximal, 15


title: NOVA74_Blood_Phase_2_SD_-1_a


title: RNA230912TZ_Tumor_4_S67

description:
Library name: Sample 15
TRIzol and Quiagen miRNeasy Mini

value: DMBA-induced cancer and no training


title: H3K4me2_yw_rep2, dme ovary, ChIP-seq

description: Library name: H3K4me2_yw_rep2

value: ovary


title: Pancreas, Acini_REG3, 21


title: H3K4me2_yw_rep1, dme ovary, ChIP-seq

description: Library name: H3K4me2_yw_rep1


title: RNA230912TZ_Tumor_7_2_S73

description:
Library name: Sample 16
TRIzol and Quiagen miRNeasy Mini


title: NOVA25_Blood_Phase_2_SD_-1

description: Gene expression profiling of PBMC  from influenza infected humans


title: NOVA36_Blood_Phase_2_SD_-1


title: RNA230912TZ_Tumor_3_2_S72

description:
Library name: Sample 14
TRIzol and Quiagen miRNeasy Mini


title: H3K9me3_yw_rep1, dme ovary, ChIP-seq

description: Library name: H3K9me3_yw_rep1


title: RNA230912TZ_Tumor_2_S66

description:
Library name: Sample 13
TRIzol and Quiagen miRNeasy Mini


title: Pancreas, Acini_REG3, 23


title: NOVA09_Blood_Phase_2_SD_-1


title: Pancreas, Acini_Proximal, 14


title: Pancreas, ADM, 12

value: ADM


title: H3K4me2_BeafKO_rep3, dme ovary, ChIP-seq

description: Library name: H3K4me2_BeafKO_rep3

value: BEAF AB-KO strain, homozygotes BEAF AB-KO/BEAF AB-KO  (Roy, Gilbert and Hart 2007)


title: RNA230912TZ_Tumor_31_S68

description:
Library name: Sample 17
TRIzol and Quiagen miRNeasy Mini


title: H3K4me2_BeafKO_rep2, dme ovary, ChIP-seq

description: Library name: H3K4me2_BeafKO_rep2


title: RNA230912TZ_Tibialis_39_S41

description:
Library name: Sample 12
TRIzol and Quiagen miRNeasy Mini

source_name: Tibialis Anterior

value: Tibialis Anterior


title: NOVA33_Blood_Phase_2_SD_-1


title: NOVA24_Blood_Phase_2_SD_-1


title: RNA230912TZ_Tibialis_38_S40

description:
Library name: Sample 11
TRIzol and Quiagen miRNeasy Mini


title: Dref_yw_rep2, dme ovary, ChIP-seq

description: Library name: Dref_yw_rep2

value: Dref


title: NOVA01_Blood_Phase_2_SD_-1

value: SD -1


title: Dref_yw_rep1, dme ovary, ChIP-seq

description: Library name: Dref_yw_rep1


title: NOVA05_Blood_Phase_2_SD_-1

value: influenza


title: RNA230912TZ_Tibialis_33_S39

description:
Library name: Sample 10
TRIzol and Quiagen miRNeasy Mini


title: RNA230912TZ_Tibialis_31_S38

description:
Library name: Sample 9
TRIzol and Quiagen miRNeasy Mini


title: Chriz_yw_rep1, dme ovary, ChIP-seq

description: Library name: Chriz_yw_rep1

value: Chriz


title: RNA230912TZ_Tibialis_7_S37

description:
Library name: Sample 8
TRIzol and Quiagen miRNeasy Mini

value: male


title: Pancreas, Acini_Proximal, 13


title: NOVA35_Blood_Phase_2_SD_-1


title: Pancreas, ADM, 10


title: NOVA19_Blood_Phase_2_SD_-1


title: Beaf_yw_rep1, dme ovary, ChIP-seq

description: Library name: Beaf_yw_rep1

value: Beaf


title: Pancreas, Acini_Distal, 11


title: RNA230912TZ_Tibialis_3_S35

description:
Library name: Sample 6
TRIzol and Quiagen miRNeasy Mini

value: Wild Type


title: Pancreas, Acini_REG3, 20


title: NOVA17_Blood_Phase_2_SD_-1

value: PBMC


title: Pancreas, ADM, 11


title: NOVA28_Blood_Phase_2_SD_-1


title: Beaf_BeafKO_rep3, dme ovary, ChIP-seq

description: Library name: Beaf_BeafKO_rep3


title: RNA230912TZ_Tibialis_2_S34

description:
Library name: Sample 5
TRIzol and Quiagen miRNeasy Mini


title: Beaf_BeafKO_rep1, dme ovary, ChIP-seq

description: Library name: Beaf_BeafKO_rep1


title: Pancreas, Acini_REG3, 19


title: Pancreas, Acini_Distal, 12


title: yw_rep3, dme ovary, chromRNA-seq

description: Library name: yw_rep3

library_source: other

data_processing:
FastQC and Trimmomatic were used for the quality control and trimming of reads.The STAR splice-aware aligner was used to map the reads to the reference genome (BDGP assembly R6/dm6). The Rsamtools package was used to process bam files. FeatureCounts was used to calculate the read counts for gene (Ensembl) and repeat databases (RepeatMasker) prepared by biomaRt package.
Assembly: dme6
Supplementary files format and content: tab-delimited text files include counts for each Sample

molecule: other

extract_protocol:
Chromatin-associated RNA was extractred from the Drosophila ovaries as descirbed in (Chen et al 2016, PMID: 27292797)
chromRNA-seq; MGIEasy RNA Library Prep Set (MGI, China)


title: RNA230912TZ_Tibialis_90_S33

description:
Library name: Sample 4
TRIzol and Quiagen miRNeasy Mini

value: No cancer and no training


title: Beaf_yw_rep3, dme ovary, ChIP-seq

description: Library name: Beaf_yw_rep3


title: NOVA11_Blood_Phase_2_SD_-1


title: Pancreas, Acini_REG3, 18

value: Pancreas


title: yw_rep2, dme ovary, chromRNA-seq

description: Library name: yw_rep2


title: NOVA18_Blood_Phase_2_SD_-1


title: RNA230912TZ_Tibialis_4_S36

description:
Library name: Sample 7
TRIzol and Quiagen miRNeasy Mini


title: RNA230912TZ_Tibialis_89_S32

description:
Library name: Sample 3
TRIzol and Quiagen miRNeasy Mini


title: BeafKOhetero_rep1, dme ovary, chromRNA-seq

description: Library name: BeafKOhetero_rep1

value: BEAF AB-KO strain, heterozygotes BEAF AB-KO/CyO  (Roy, Gilbert and Hart 2007)


title: RNA230912TZ_Tibialis_88_S31

description:
Library name: Sample 2
TRIzol and Quiagen miRNeasy Mini


title: Pancreas, ADM, 9

description: NanoString GeoMx Digital Spatial Profiler(DSP)

value: LSL-KrasG12D; Pdx1-Cre


title: NOVA20_Blood_Phase_2_SD_-1

value: Vaccinated


title: Pancreas, Acini_Proximal, 12


title: BeafKO_rep2, dme ovary, chromRNA-seq

description: Library name: BeafKO_rep2

value: ovary


title: Pancreas, Acini_REG3, 17


title: NOVA48_Blood_Phase_2_SD_-1

value: Unvaccinated


title: RNA230912TZ_Tibialis_87_S30

description:
Library name: Sample 1
TRIzol and Quiagen miRNeasy Mini


title: BeafKO_rep1, dme ovary, chromRNA-seq

description: Library name: BeafKO_rep1

value: BEAF AB-KO strain, homozygotes BEAF AB-KO/BEAF AB-KO  (Roy, Gilbert and Hart 2007)


title: Pancreas, ADM, 8

value: ADM


title: NOVA12_Blood_Phase_2_SD_-1_a

description: Gene expression profiling of PBMC  from influenza infected humans


title: Hypoxic carotid body cells

city: Seville

first: Ricardo

last: Pardal

address: Avda. Manuel Siurot, s/n

department: Medical Physiology and Biophysics

country: Spain

institute: University of Seville

description:
Library name: CC4
10X Genomics

data_processing:
Cell Ranger v.7.0.1 (10x Genomics) was used to align the sequenced reads to the rat genome (mRatBN7 genome build), perform quality control on cells and generate count tables of unique molecular identifiers (UMIs) for each gene and cell.
Assembly: mRatBN7
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: whole carotid body

extract_protocol:
Rat carotid bodies (CBs) were dissociated by enzymatic and mechanical treatment. Briefly, CBs were dissociated in PBS solution containing 0.6 mg/ml collagenase type II (Sigma), 0.35 U/ml porcine elastase (Calbiochem), 0.3 mg/ml trypsin (Sigma), and 10 ul/ml of 5 mM CaCl2 solution, for 25 min at 37ºC, using a shaker. Once dissociated, single cells were resuspended in a staining solution composed by (for 50 ml): 44 ml L15 medium (Gibco), 0.5 ml penicillin/streptomycin (Gibco), 0.5 ml 1M HEPES buffer (Gibco), 0.1 g BSA (Sigma), and 5 ml distilled and deionized water. Dispersed cells were used for single cell transcriptome analysis .
Single-cell RNA sequencing (scRNA-seq) was performed with the 10x Genomics Chromium Single Cell 3′ Kit (v.3) according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing platform.

treatment_protocol: 10%O2 hypoxia

value: whole carotid body

value: primary cells

value: all cells

value: Wild type

value: Hypoxia


title: NOVA68_Blood_Phase_2_SD_-1

extract_protocol: Total RNA was isolated from PBMCs in Paxgene tubes according to manufacturer's instructions.RNA quality was assessed using Agilent Bioanalyzer.

value: influenza

value: SD -1


title: input AA96, CEW1, early stage synchronized larvae

city: New York

first: Avrami

last: Aharonoff

state: NY

address: 29 Washington Place

department: Biology

institute: New York University

description: Library name: input_AA96_CEW1_L-24hrs_ext790

data_processing:
Adapters were trimmed when necessary with trimmomatic (version 0.39). Reads were aligned with bowtie2 (version 2.4.2) using the default parameters. Sam files were converted to bam files, sorted and indexed using samtools (version 1.11). Bam files were used to generate bigwig files with the bamCoverage tool in deeptools (version 3.5.0) with the following parameters: --binsize 10 --minMappingQuality 20 --extendReads 200 --ignoreDuplicates --normalizeUsing CPM --exactScaling --ignoreForNormalization chrM.
Assembly: PRJNA982879 (S. hermaphroditum), this paper (P. pacificus), PRJNA644888 (O. tipulae)
Supplementary files format and content: bigwig

organism: Oscheius tipulae

source_name: whole worm

growth_protocol: S. hermaphroditum early stage mixed larvae were isolated by filtering mixed stage worms through a 30 micron nylon mesh filter, and collecting the flow through. Pristionchus pacificus J2-J3 larvae were isolated by filtering mixed stage worms through a 20 micron nylon mesh, and collecting the flow through. Oscheius tipulae early stage synchronized larvae were isolated by bleaching mixed stage worms (0.5 M NaOH, 1% sodium hypochlorite for 2 minutes), hatching embryos in M9, and growing synchronized L1 larvae on NGM plates supplemented with agarose at 22˚C for 24 hours.

extract_protocol:
Around 100-150 µL of pelleted larvae was removed from -80 ˚C and washed in FA Buffer (final concentrations of 50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate, 150 mM NaCl, filter sterilized) with 0.1% sarkosyl, 1 mM PMSF, and 1X protease inhibitors (protease inhibitor cocktail set I – Calbiochem, catalog # 539131) added fresh. Larvae were then dounced 30 times in a glass dounce tissue grinder (VWR, catalog number 22877-280) with pestle type B. Sonication was performed in a Biopruptor ® Pico (catalog # B01060010) to obtain fragments between 200 and 800 bp in length (30 seconds on, 30 seconds off, 10-15 cycles). Protein concentration was determined using the Bradford assay (Bio-Rad, catalog # 500-0006). For chromatin immunoprecipitation, 1-2 mg of extract and 3-5 µg of antibody were used (see supplemental file 1), and allowed to rotate overnight at 4 ˚C. nProtein A Sepharose beads (Cytiva, catalog # 17528001) were added and incubation was allowed to continue for 2 hours. Beads were washed with FA buffer, FA buffer – 1 M NaCl, FA buffer – 500 mM NaCl, TEL buffer (final concentrations of 0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl, pH 8.0, filter sterilized), and TE, respectively. Immunocomplexes were eluted twice with ChIP elution buffer (final concentrations of 1% SDS, 250 mM NaCl, 10 mM Tris, pH 8.0, 1 mM EDTA) at 65 ˚C for 15 min at 1400 rpm. The eluate was then treated with 2 µL of 10 mg/mL proteinase K for 1 hour at 50 ˚C, and reverse crosslinked overnight in a 65 ˚C waterbath. DNA was purified the next morning with Qiagen MinElute PCR Purification Kit (catalog # 28006), and fragment size was checked by agarose gel electrophoresis or TapeStation. The remaining DNA was stored at -20 ˚C.
Library preparation was performed as follows. To perform end repair, we used half the ChIP DNA and 10-30 ng of input DNA, T4 DNA Ligase Reaction Buffer (NEB, catalog #  B0202S), 0.4 mM dNTPs, 20 U PNK (Fisher, catalog # FEREK0032), 0.7 U Large Klenow Fragment (NEB, catalog # M0210S), and 6 U T4 DNA Polymerase (Fisher, catalog # FEREP0062) (total volume 33 µL). The reaction was incubated at 20 ˚C for 30 minutes, and was cleaned with Qiagen MinElute PCR Purification Kit (eluted in 21 µL). To perform A-tailing, NEBuffer 2 (catalog # B7002S), 0.2 mM dATP, and 7.5 U of Klenow Fragment (3’ → 5’ exo-) (NEB, catalog # M0212L) were added to the cleaned DNA (total volume of 25 µL), and incubated for an hour in a 37 ˚C water bath. The reaction was cleaned with Qiagen MinElute PCR Purification Kit (eluted in 17 µL). To perform adapter ligation, Quick Ligation Buffer, Illumina Truseq Adapters (see supplemental file 1), and 2 µL of Quick Ligase (NEB, catalog # M2200L) were added to cleaned DNA (total volume of 40 µL), and incubated for 20 minutes at 23 ˚C. The reaction was size selected and cleaned with Ampure XP beads (Beckman Coulter, catalog # A63881). The eluate was amplified by PCR with Phusion HF Reaction Buffer, 0.5 µM TruSeq forward and reverse primers (see supplemental file 1), 0.2 mM dNTP, and 1 U Phusion High-Fidelity DNA Polymerase (Fisher, catalog F-530L) for a total reaction volume of 50 µL under the following parameters: 98 ˚C for 1 min, 98 ˚C for 30 seconds, 60 ˚C for 30 seconds, 72 ˚C for 30 seconds, repeat steps 2-4 14 times, 72 ˚C for 5 min, 8 ˚C forever. 10 µL of 3 M sodium acetate (pH 5.2) was added to reaction, and the reaction was cleaned with Qiagen MinElute PCR Purification Kit, (eluted in 11 µL). The eluate was gel purified (1.5% agarose gel) to obtain fragments between 250-600 bp using the Qiagen MinElute Gel Extraction Kit (catalog # 28606). Library concentration was determined with the KAPA Library Quantification Kit (catalog # KK4824). Single-end (75 bp) sequencing was performed at the Genomics Core at the Center for Systems and Genome Biology, New York University using the Illumina NextSeq 500 platform.

treatment_protocol: Larvae were treated with 2% formaldehyde for 30 minutes, washed with M9 (PBS was used for S. hermaphroditum), collected by centrifugation, flash frozen in liquid nitrogen, and stored at -80˚C until extract preparation

tag: source

value: whole worm

value: hermaphrodite

tag: developmental stage

value: early stage synchronized larvae


title: Normoxic carotid body cells

description:
Library name: CC3
10X Genomics

tag: tissue

value: Normoxia


title: Pancreas, Acini_Proximal, 11

source_name: Pancreas

value: Pancreas

value: LSL-KrasG12D; Pdx1-Cre


title: NOVA75_Blood_Phase_2_SD_-1

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

tag: disease state

value: PBMC

tag: study group


title: NOVA40_Blood_Phase_2_SD_-1_b

value: Vaccinated

tag: study date


title: Pancreas, Acini_REG3, 16

tag: genotype


title: Pancreas, Acini_Proximal, 10

tag: cell type


title: CFA, SRP-001, scATAC

city: New Orleans

first: Surjyadipta

last: Bhattacharjee

state: Louisiana

address: 2020 Gravier Street, Suite D, 8th floor

department: Neuroscience Center of Excellence

institute: LSU Health, New Orleans

description:
Library name: CFA_SRP001_ATAC
10x Genomics

library_source: genomic single cell

data_processing:
Cell Ranger ARC (cellranger-arc) v.2.0.2 from 10x Genomics was utilized to process Chromium Single Cell Multiome ATAC + Gene Expression (GEX) sequencing data. Initially, raw BCL files from the Illumina NovaSeq were demultiplexed into paired-end, gzip-compressed FASTQ files using the default parameters of cellranger-arc mkfastq. Subsequently, the cellranger-arc count function was employed for read alignment, filtering, barcode counting, peak calling, and the quantification of both ATAC and GEX molecules. The rat genome mRatBN7 and its annotated transcriptome served as the reference for alignment. Only confidently mapped reads with valid barcodes, unique molecular identifiers (UMIs), and non-PCR duplicates were retained
Assembly: mRatBN7
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz for each sample from filtered_feature_bc_matrix folder
Supplementary files format and content: CellRanger output files: fragments.tsv.gz for each sample

source_name: Brain, periaqueductal gray

extract_protocol:
After one hour, the rats were euthanized, and the periaqueductal gray (PAG) was dissected from their flash-frozen brains. To isolate cell nuclei from the midbrain PAG, the tissue was flash-frozen, dissected with a cryotome, minced into small pieces, homogenized, filtered through a 70 μm strainer, and centrifuged. ReadiDrop 7-AAD cell viability dye (Bio-Rad) was added, and live nuclei (7-AAD positive) were sorted using a BioRad Cell Sorter S3e in purity mode. Nuclei were counted with a Nexcelom automated Cellometer using acridine orange/propidium iodide (AOPI) staining, and the nuclei stock concentration was adjusted to target 10,000 nuclei per sample. The samples were bulk transposed, and approximately 16,100 nuclei were loaded into each channel of the microfluidic chip, with GEMs generated using the 10x Chromium controller and reagents from the Chromium Next GEM Single Cell ATAC Kit, 1,000,280 (10x Genomics), following the manufacturer’s instructions
After post-GEM cleanup with Dynabeads and SPRIselect (Beckman Coulter), samples underwent pre-amplification PCR and were then divided for constructing ATAC and GEX libraries. Quality control for the libraries was performed using an Agilent Bioanalyzer 2100 with High Sensitivity DNA chips. After verifying sample traces, each library was normalized based on the average fragment size, and concentration was determined using a Qubit 4.0 fluorometer (Thermo Fisher Scientific). The pooled libraries were subsequently sequenced using Illumina high output kits on a NovaSeq 6000 platform from Illumina

treatment_protocol: Sprague Dawley rats were injected with Complete Freund’s adjuvant (CFA) or Saline and later ApAP or SRP-001 were administered per os. The left hind paws of Sprague-Dawley rats were injected with 150 µl of 50% CFA, freshly diluted with sterile saline on the day of administration, to induce significant long-term inflammatory pain and mechanical hyperalgesia, assessed using eVF. Following this, the rats were administered either ApAP or SRP-001 at a dose of 100 mg/kg

value: Brain, periaqueductal gray

value: Sprague Dawley

value: male

value: 2 months

tag: treatment

tag: library type

value: ATAC


title: H3K4me3, ChIP, CEW1, early stage synchronized larvae, rep 3

description: Library name: H3K4me3_ab8580_CEW1_L-24hrs_ext790_AA90_rep3

tag: antibody (target)

tag: antibody (vendor,_catalog_number)

value: Abcam, ab8580

tag: antibody (host,_clonality)

value: rabbit, polylconal

tag: matching input

value: input AA96, CEW1, early stage synchronized larvae


title: Pancreas, Acini_REG3, 15


title: CFA, ApAP, scATAC

description:
Library name: CFA_ApAP_ATAC
10x Genomics

tag: strain

value: ApAP


title: CFA, Veh, scATAC

description:
Library name: CFA_Veh_ATAC
10x Genomics

tag: age

value: Saline


title: IgG, ChIP, CEW1, early stage synchronized larvae, rep 3

description: Library name: IgG_ab46540_CEW1_L-24hrs_ext790_AA91_rep3

value: whole worm

tag: Sex

value: hermaphrodite

value: IgG

value: Abcam, ab46540


title: Pancreas, Acini_REG3, 14

value: Pancreas

value: LSL-KrasG12D; Pdx1-Cre


title: NOVA63_Blood_Phase_2_SD_-1_a

city: Seattle

first: kathie

last: walters

address: 401 Terry Ave N

institute: Institute for Systems Biology

value: influenza

value: PBMC

value: Unvaccinated

value: SD -1


title: input AA111, PS312, J2

description: Library name: input_AA111_PS312_J2_ext809

organism: Pristionchus pacificus

tag: source


title: H4K20me1, ChIP, CEW1, early stage synchronized larvae, rep 3

description: Library name: H4K20me1_ab9051_CEW1_L-24hrs_ext790_AA89_rep3

tag: developmental stage

value: early stage synchronized larvae

value: Abcam, ab9051


title: Saline, SRP-001, scATAC

description:
Library name: Saline_SRP001_ATAC
10x Genomics

tag: tissue

value: Brain, periaqueductal gray

value: Sprague Dawley

value: male

value: 2 months

value: ATAC


title: Pancreas, ADM, 7

value: ADM


title: NOVA61_Blood_Phase_2_SD_-1

tag: disease state


title: NOVA47_Blood_Phase_2_SD_-1

tag: study group


title: Saline, ApAP, scATAC

description:
Library name: Saline_ApAP_ATAC
10x Genomics

value: ApAP


title: NOVA59_Blood_Phase_2_SD_-1

tag: study date


title: Pancreas, ADM, 6

tag: genotype


title: NOVA60_Blood_Phase_2_SD_-1


title: H3K4me3, ChIP, PS312, J2, rep 3

description: Library name: H3K4me3_ab8580_PS312_J2_ext809_AA106_rep3

value: whole worm

value: hermaphrodite

value: Abcam, ab8580

value: rabbit, polylconal

value: input AA111, PS312, J2


title: Saline, Veh, scATAC

description:
Library name: Saline_Veh_ATAC
10x Genomics

value: Saline


title: Pancreas, ADM_REG3, 6

value: Pancreas

tag: cell type

value: LSL-KrasG12D; Pdx1-Cre


title: NeuN+ ATAC-seq, Cow

city: Huntsville

first: J.

middle: Nicholas

last: Cochran

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description: Library name: ATAC_Cow-NEUN

data_processing:
Samples were processed using the standard ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline v.1.7.0).
Assembly: Rattus rattus (rat) assembly: mRatBN7.2 (rn7), annotation: Ensembl release 111; Oryctolagus cuniculus (rabbit) assembly: OynCun2, annotation: Ensembl release 111; Bos taurus (cow) assembly: bosTau9, annotation: GCF_002263795.2; Equus caballus (horse) assembly: equCab3, annotation: GCA_002863925.1; Danio rerio (zebrafish) assembly: danRer11, annotation: Ensembl release 109.
Supplementary files format and content: ATAC-seq peak calls, tagAlign alignment files

organism: Bos taurus

source_name: Cortex

extract_protocol:
After centrifugation to remove sucrose gradient, nuclei were labeled by resuspending the pellet in 1 mL blocking buffer with NeuN-488 antibody (Millipore, cat. no. MAB377X) at 1:4,000 and 4,6-diamidino-2-phenylindole at 1:20,000 for at least 30 minutes at 4°C with rotation. Nuclei were then centrifuged at 500 x g for 5 minutes at 4°C. The supernatant was removed the pellet was resuspended in 500 μL cold 1% BSA in PBS with RNase Inhibitor. Nuclei were then filtered through a 35 μm filter, washing the filter with an additional 100 μL 1% BSA in PBS. Nuclei were then sorted using a Sony MA900 device with a 70-μm nozzle and pressure not exceeding a pressure setting of 7. Gates were set to capture those populations that were positive for 488 signal (NeuN+). Both the NeuN+ and NeuN- populations were collected and held at 4°C . Purity of selected samples was typically >95% based on reanalysis of sorted samples.
Approximately 100,000 NeuN+ nuclei were isolated from cortex tissues and used for ATAC-seq library preparation as per standard protocols (PMID: 24097267, PMID: 25559105, PMID: 28846090) with the following modifications. Briefly, 50 μL of cold 5x lysis buffer was added to sorted nuclei to reach a final concentration of 1x (1- mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40) and incubated for 20 min on ice followed by centrifugation for 10 minutes. The transposition reaction was incubated for 30 minutes at 37°C with agitation at 1000 rpm (Illumina Tagment DNA Enzyme and Buffer kit, cat. no. 20034198). After column clean up via the QIAGEN MinElute Reaction Cleanup kit (QIAGEN, cat. no. 28204) and PCR amplification of libraries, an additional clean up with AMPure XP beads (0.8X ratio) was performed with two 80% ethanol washes before quantification using a DNA High-Sensitivity chip on a 2100 BioAnalyzer (Agilent). Libraries were sequenced paired-end with the Illumina dual indexes on a NovaSeq X Plus 10 B 300 cycle flowcell targeting 100 million reads per sample.

value: Cortex

value: Neurons


title: CFA, SRP-001, scRNA

description:
Library name: CFA_SRP001_RNA
10x Genomics

value: Brain, periaqueductal gray

tag: treatment

value: mRNA


title: NOVA72_Blood_Phase_2_SD_-1

value: influenza

value: PBMC

value: Unvaccinated

value: SD -1


title: CFA, ApAP, scRNA

description:
Library name: CFA_ApAP_RNA
10x Genomics

value: Sprague Dawley

value: male

value: 2 months

value: ApAP

tag: library type


title: NeuN+ ATAC-seq, Cat, rep1

description: Library name: ATAC_Cat2066-NEUN

organism: Felis catus


title: Pancreas, ADM_REG3, 5


title: Pancreas, ADM_REG3, 4


title: NOVA66_Blood_Phase_2_SD_-1


title: NOVA69_Blood_Phase_2_SD_-1


title: NeuN+ ATAC-seq, Horse

description: Library name: ATAC_Horse-NEUN

organism: Equus caballus


title: Saline, SRP-001, scRNA

description:
Library name: Saline_SRP001_RNA
10x Genomics


title: Pancreas, Acini_Proximal, 9


title: Saline, ApAP, scRNA

description:
Library name: Saline_ApAP_RNA
10x Genomics


title: Pancreas, Acini_REG3, 13

description: NanoString GeoMx Digital Spatial Profiler(DSP)


title: H4K20me1, ChIP, PS312, J2, rep 3

description: Library name: H4K20me1_ab9051_PS312_J2_ext809_AA105_rep3

value: whole worm

value: hermaphrodite

tag: antibody (target)

value: Abcam, ab9051

value: rabbit, polylconal


title: NOVA70_Blood_Phase_2_SD_-1

description: Gene expression profiling of PBMC  from influenza infected humans


title: CFA, Veh, scRNA

description:
Library name: CFA_Veh_RNA
10x Genomics

value: Saline


title: NOVA81_Blood_Phase_2_SD_-1


title: NOVA79_Blood_Phase_2_SD_-1


title: Pancreas, Acini_REG3, 12

value: Pancreas

value: LSL-KrasG12D; Pdx1-Cre