title: pig ovary

city: Ansung

first: SangHwan

last: Kim

state: Gyeonggi-do

address: 327, Jungang-ro

department: School of Animal Life Convergence Science

institute: Hankyong National University

description: Differentially expression of genes in minipig ovary vs. pig ovary

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >5.0 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 Pocine Genome Oligo Microarrays (G2519F-026440) for 17 hours at 65°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 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2505C) 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 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 026440_D_20100525) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: PO-ovary-tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng 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:
animal collection protocol: Ovarian tissue samples were harvested following the method of Kim et al. (2012). (PLoS One. 2012;7(10):e46194. doi: 10.1371/journal.pone.0046194.)
Total RNA was extracted from the pocine tissue using the TRI REAGENT (MRC, OH) according to the manufacturer’s instructions. The total RNA quality and quantity was assessed by Agilent bioanalyzer 2100 analysis.

tag: breed

value: pig

value: Ovary

tag: gender

value: Female

value: estrous cycle 15 days


title: Minipig ovary

status: Public on Jun 15 2024

type: RNA

country: South Korea

molecule: total RNA

organism: Sus scrofa

source_name: MO-ovary-tissue

value: minipig

tag: tissue

tag: developmental stage


title: intestinal organoids from Adipfl/flpVilli-CreT mice (Adip KO)

status: Public on Jun 14 2024

type: SRA

city: Tianjin

first: Yun Huan

last: Gao

address: 94 Weijin Road, Nankai District, Tianjin

country: China

institute: Nankai University

library_source: transcriptomic

data_processing:
Library preparation and transcriptome sequencing on an MGISEQ-2000 platform were performed to generate 100-bp paired-end reads.
MGISEQ-2000 was used in counting the numbers of read mapping to each gene, and fragments per kilobase of transcript per million fragments mapped (FPKM) of each gene were calculated.
Data were analyzed after choosing an analysis tool on http://biosys.bgi.com. FC (fold change) was used to describes the difference of gene expression
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

organism: Mus musculus

source_name: intestine

growth_protocol: The prepared DMEM/F12-ENR medium (50 ng/ml EGF, 100 ng/ml Noggin and 500 ng/ml R-spondin) was added, and changed every other day.

extract_protocol:
Fresh small intestinal (5–10 cm length) was cut longitudinally, and flushed three times with cold PBS containing penicillin–streptomycin. After the villi were gently scraped with a sterile cover glass, the intestine tissue was cut into small pieces. After 2 mM EDTA incubation for 30 min on ice, crypts were dispersed by pipette, and then filtered using 70 mm cell strainer and collected in a tube, and counted and mixed with Matrigel
Total RNAs from cells were extracted according to the manual of TRIzol®reagent (Invitrogen, Shanghai, China)

value: intestine

tag: cell line

value: Intestinal epithelial cells

tag: genotype

value: Adipfl/flpVilli-CreT


title: Sep, scRNAseq

city: Wuhan

first: Mengyuan

last: Wang

state: Hubei

address: NO.1277 JieFang Avenue

department: Department of Critical Care Medicine

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing data were aligned to the Macaca fascicularis 5.0 genome by STAR （v2.7.4a）. Counts of aligned UMI were used to quantify downstream gene expression levels. For scRNA-seq data, cells with less than 200 genes and top 10% of cells with the highest number of genes were removed. Additionally, cells with more than 15% mitochondrion reads were filtered out. We applied DoubletFinder to remove potential doublets.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: small intestine

extract_protocol:
The small intestines were carefully cleaned and opened longitudinally, washed with PBS, cut into 1.0–1.5 cm pieces and incubated in 20 ml of HBSS/10 mM HEPES, 8% FBS, 4 mM EDTA, and 0.5 mM dithiothreitol at 37 ℃ with constant agitation for 15 minutes twice. After washing with Ca2+ /Mg2+ -PBS to remove EDTA, the remaining pieces of small intestines were minced and digested in RPMI-1640 medium containing fetal bovine serum (FBS), collagenase Ⅳ (0.1 mg/mL) and DNase I (0.1 mg/mL) at 37 ℃ for 40 minutes. The tissue digestion was filtered through a 40 μm cell strainer, following by centrifugation at 400g for 5 min at 4 °C. CD45+ Cells were collected using FACS, and resuspended in PBS. Cell concentration was adjusted to 1000 cells /μl for library preparation.
Prepared single-cell suspensions were loaded on a chip of the Single Cell 3' Chip Kit (10X Genomics) and subjected to a Chromium Single Cell Instrument (10X Genomics) to generate single-cell gel beads in emulsions (GEMs). cDNA amplification and library construction underwent using a Chromium Single Cell 3' Reagent Kits v2 (10x Genomics).

value: small intestine

tag: cell type

value: CD45+ cells

tag: treatment

value: septic


title: Pig heart tissue, Day28, Sample 3,Sequencing by CD Genomics

city: Scottsdale

first: Wuqiang

last: Zhu

state: AZ

address: 13400 E shea blvd

department: Cardiovascular Medicine

country: USA

institute: Mayo Clinic

data_processing:
Assembly: Sscrofa10.2
Cross sample quality control check using metrics like percentage of uniquely mapped reads and GC content.
QC visualization was done using MultiQC (v1.11)
Index generation and paired-end alignment of each sample were performed using STAR (v2.7.9a).
Ensemble's reference genome Sscrofa10.2 was used for alignment.
circRNAs were called using CIRCexplorer2
Supplementary files format and content: tab delimited rawcounts files(txt). Each row is circRNA, and each column is a sample( total of 3 files, one from each batch)
Supplementary files format and content: tab seperated value(tsv) of miRNA expression count. Each row is a miRNA, and each column is a sample
Supplementary files format and content: tab seperated value(tsv) of mRNA expression count. Each row is a mRNA, and each column is a sample
Supplementary files format and content: Compressed zip files from CircAtlas databased, used for circRNA naming annotation.

source_name: heart

growth_protocol: neonatal pigs were fed normally

extract_protocol:
The RNeasy Mini Kit (Qiagen) was used to extract total RNA from pig heart tissue
Construction of the library was performed according to the instructions provided by the manufacturer for the NEBNext Ultra II RNA (Directional) kit.
Plant and Animal Whole Transcriptome Sequencing

treatment_protocol: Heart tissue samples were harvested from neonatal pigs on days 1, 3, 7, and 28 after birth.

value: heart


title: Pig heart tissue, Day28, Sample 2, Sequencing by CD Genomics


title: R2_DNA_replicate1

city: Seattle

first: Christopher

last: Yin

state: WA

address: 3946 W Stevens Wy NE

department: Electrical & Computer Engineering

institute: University of Washington

description:
Escherichia coli episomal DNA, not transfected
R2_processed_data.csv

library_source: other

data_processing:
Sequence reads were trimmed for 3' adaptor sequence/low-quality sequencing using cutadapt package. (parameters: maximum error rate = 0.8, minimum length = 10, maximum length = 10, no_indels)
UMIs from trimmed sequences were collapsed using starcode (parameters: seq_trim=0, umi_len=10)
Number of unique UMIs per barcode sequence calculated, and UMI counts summed across all barcodes corresponding to the same enhancer, using a custom Python script
Assembly: n/a, synthetic DNA used
Supplementary files format and content: csv containing enhancer sequence, barcode sequences for this enhancer, and unnormalized read counts for each library

molecule: other

organism: synthetic construct

growth_protocol: HepG2 cells were obtained from ATCC (HB-8065) and cultured in EMEM (ATCC 30-2003) + 10% FBS + 1% Pen/Strep at 37°C and 5% CO2. K562 cells were obtained from ATCC (CCL-243) and cultured in RPMI (Gibco 11875093) + 10% FBS + 1% Pen/Strep at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted from cells 48h after transfection using the Monarch total RNA miniprep kit (NEB T2010S). For DNA libraries, barcode region of plasmid was extracted via PCR.
mRNA was isolated from total RNA extracts using the magnetic mRNA Isolation Kit (NEB S1550S) then reverse transcribed with the Maxima H Minus Reverse Transcriptase (Thermo EP0753) using a UMI-containing RT primer. Plasmid DNA was prepared with the same UMI-containing primer.

treatment_protocol: For HepG2 libraries, 600k (R1 libraries) or 1 million (R2) cells were seeded in 6-well plates or 6 cm plates respectively. 24 hours later, cells were transfected with Lipofectamine 3000 (Invitrogen L3000001) and 5 (R1) or 10 (R2) ug of library DNA following the manufacturer’s instructions. For R2, media was replaced 6 hours later. Cells were then grown for 48 hours after transfection. For K562 libraries, 1.5 million K562 cells per replicate were electroporated with 10 ug DNA using the Neon Transfection System (Invitrogen MPK5000), transferred to 6-well plates (R1) or 6 cm plates (R2) with RPMI + FBS (no Pen/Strep), and incubated for 48 hours.


title: R1-MPRA_DNA

description:
Escherichia coli episomal DNA, not transfected
R1-MPRA_processed_data.csv


title: Pig heart tissue, Day7, Sample 2, Sequencing by Novogene, Round2


title: Pig heart tissue, Day7, Sample 3, Sequencing by Novogene, Round2


title: Pig heart tissue, Day28, Sample 1, Sequencing by Novogene, Round1


title: Pig heart tissue, Day28, Sample 3, Sequencing by Novogene, Round2


title: Pig heart tissue, Day7, Sample 1, Sequencing by Novogene, Round2


title: Pig heart tissue, Day3, Sample 3, Sequencing by CD Genomics


title: Pig heart tissue, Day7, Sample 2, Sequencing by Novogene, Round1


title: Pig heart tissue, Day3, Sample 2, Sequencing by CD Genomics


title: Pig heart tissue, Day3, Sample 1, Sequencing by CD Genomics


title: Pig heart tissue, Day3, Sample 3, Sequencing by Novogene, Round2


title: Pig heart tissue, Day1, Sample 2, Sequencing by CD Genomics


title: WT_sedentary_HFD_689

city: Stockholm

first: Carolina

last: Nylén

address: Karolinska University Hospital

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Samples were processed according to the standard Affymetrix protocol

data_processing: Data were analyzed in R Bioconductor v3.17 with the packages oligo v1.66.0 and limma v3.58.1

label: biotin

source_name: EDL muscle from WT animals without access to a running wheel

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: wild-type sedentary (WT; n=5), MLC_DGKδ2 transgenic sedentary mice (TG; n=6), wild-type exercised (WT exercised; n=5) and MLC_DGKδ2 transgenic exercised mice (TG exercised; n=5)

value: WT

value: EDL

tag: training

value: sedentary


title: TG_sedentary_HFD_687

scan_protocol: Samples were processed according to the standard Affymetrix protocol

source_name: EDL muscle from TG animals without access to a running wheel

value: TG


title: Pig heart tissue, Day3, Sample 1, Sequencing by Novogene, Round2


title: Pig heart tissue, Day28, Sample 2, Sequencing by Novogene, Round2


title: Pig heart tissue, Day28, Sample 3, Sequencing by Novogene, Round1


title: Pig heart tissue, Day3, Sample 2, Sequencing by Novogene, Round1


title: Pig heart tissue, Day28, Sample 1, Sequencing by Novogene, Round2


title: R2_DNA_replicate2


title: Pig heart tissue, Day28, Sample 2, Sequencing by Novogene, Round1


title: Pig heart tissue, Day3, Sample 1, Sequencing by Novogene, Round1


title: TG_sedentary_HFD_650

label_protocol: Samples were processed according to the standard Affymetrix protocol


title: WT_sedentary_HFD_665


title: TG_sedentary_HFD_666


title: R1-DHS_DNA

description:
Escherichia coli episomal DNA, not transfected
R1-DHS_processed_data.csv


title: Pig heart tissue, Day1, Sample 3, Sequencing by Novogene, Round2


title: Pig heart tissue, Day1, Sample 2, Sequencing by Novogene, Round2


title: TG_sedentary_HFD_667


title: Pig heart tissue, Day1, Sample 1, Sequencing by Novogene, Round2


title: TG_sedentary_HFD_688


title: Pig heart tissue, Day7, Sample 3, Sequencing by Novogene, Round1


title: Pig heart tissue, Day7, Sample 1, Sequencing by Novogene, Round1


title: Pig heart tissue, Day1, Sample 2, Sequencing by Novogene, Round1


title: Pig heart tissue, Day3, Sample 2, Sequencing by Novogene, Round2


title: Pig heart tissue, Day3, Sample 3, Sequencing by Novogene, Round1


title: WT PC #2

city: New York

first: Anthony

last: Tao

state: NY

address: 550 1st Ave Smilow 506

department: Pathology

institute: New York University Grossman School of Medicine

data_processing:
Reads were aligned to the mouse reference genome (GRCm38.85/mm10) using STAR aligner (v.2.5.0c)
Read counts were generated with featureCounts
Assembly: mm10
Supplementary files format and content: Tab-delimited text file containing gene counts for each sample

molecule: polyA RNA

source_name: B cells

growth_protocol: Slc4a7-/- and WT naive B cells were purified from splenocytes using CD43 magnetic selection beads. Cells were seeded into the 40LB feeder cell system in the presence of IL-4 (2 ng/mL) for 3 days and then IL-21 (10 ng/mL) for 3 days, after which CD138+ plasma cells and CD138- non-plasma cells were sorted.

extract_protocol:
RNA was purified with with the RNeasy Micro RNA Isolation Kit (Qiagen)
Libraries were prepared using the Clonetech SMART-Seq HT Kit (Takara). The amplified libraries were purified using AMPure beads (Beckman Coulter), quantified by Qubit 2.0 fluorometer (Life Technologies), and visualized on an Agilent Tapestation 2200.

value: B cells

value: 40LB feeder cells (NIH3T3 cells expressing CD40L and BAFF in the presence of IL-4 or IL-21)


title: WT PC #1


title: WT_sedentary_HFD_686


title: WT_sedentary_HFD_668


title: WT_exercise_HFD_656

source_name: EDL muscle from WT animals with access to a running wheel

value: exercise


title: WT_exercise_HFD_653


title: TG_exercise_HFD_651

source_name: EDL muscle from TG animals with access to a running wheel


title: TG_sedentary_HFD_648


title: WT_sedentary_HFD_649


title: Slc4a7-KO PC #2


title: TG_exercise_HFD_658


title: WT_exercise_HFD_673


title: K562_H3K27me3_Tuba_rep3

city: Amsterdam

first: Ruben

last: Schep

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

library_source: genomic

data_processing:
All ChIP-seq samples were processed using the SPACCa pipeline (available at https://github.com/sebastian-gregoricchio/SPACCa) using default parameters.
FASTQ reads were mapped to the reference genome Hg38/GRCh38, using the accelerated version of the Burrows-Wheeler Aligner (BWA-MEM2 v0.5.10)
Peaks were called using MACS2 using the corresponding input of each condition as background/control.
For the normalization of the ChIP-seq signal at the plasmid, scaling factors for the different samples were calculated on the signal across the human genome and applied then to the signal across the plasmid using deepTools.
Signal of three biological replicates was averaged per condition using the bigwigAverage function from deepTools.
Assembly: Hg38/GRCh38
Supplementary files format and content: .broadPeak (peaks in broadPeak/bed format)
Supplementary files format and content: .narrowPeak (peaks in narrowPeak/bed format)
Supplementary files format and content: .bw (bigWig files)

molecule: genomic DNA

organism: Homo sapiens

source_name: K562 clone #5

growth_protocol: Cells were cultured in tissue culture flasks in RPMI 1640 (GIBCO) supplemented with 10% fetal bovine serum (FBS, HyClone) and 1% penicillin/streptomycin. Cells were kept at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Cells were fixed using 1% formaldehyde and incubated while stirring for 10 minutes at room temperature. Fixation was stopped by adding 0.15 mM glycine and stirred for 1-2 minutes. Fixed cells were then pelleted by three consecutive centrifugations (6 minutes at 500 g) and washes with PBS, and subsequently snap frozen and kept at -80 °C until further processing. For ChIP processing, cell pellets were thawed on ice, resuspended in lysis buffer 1 (LB1: 50 mM Hepes, 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Tx100, KOH to pH 7.5; 10x10e6 cells/ml) and incubated on ice for 10 minutes. Nuclei were pelleted at 800 g for 10 minutes at 4°C. Pellets were resuspended in lysis buffer 2 (LB2: 10 mM Tris, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, HCl to pH 8; 10 x10e6 cells/ml), incubated 10 minutes on ice and centrifuged at 800 g for 10 minutes at 4°C. Pelleted nuclei were resuspended in lysis buffer 3 (LB3: 10 mM Tris, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-DOC, 0.5% lauroylsarcosine, HCl to pH 8; 30x10e6 cells/ml). Nuclei were sonicated for 4 cycles (30s ON, 30s OFF) using the PicoBioruptor (Diagenode). Triton X100 was added to the sheared chromatin at a final concentration of 1% and debris were pelleted for 15 minutes at 20,000 g at 4°C. The supernatant was then incubated overnight under rotation at 4°C with 50 µL (1.5 mg) of Protein A Dynabeads (Invitrogen), previously incubated with 3 µg of either H3K27ac (acm39133, Active Motif; lot #06921014) or H3K27me3 (C15410195, Diagenode, lot #A0824D) antibody. Beads were then washed 10 times with RIPA-ChIP buffer (50 mM HEPES, 500 mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-DOC, pH = 7.6), washed once in TBS, reverse cross-linked at 65°C in 500 µl of Elution Buffer (EB: 0.1M NaHCO3, SDS 1%, 200mM NaCl) for 4 hours. Upon 30 minutes treatment with 40 µg RNase A (Life Technologies), 1 hour treatment with PK buffer (10 µL 0.5M EDTA, 20 µL 1M Tris-HCl pH 6.5, 40 µg Proteinase K (Invitrogen)), ChIP DNA was purified using phenol/chloroform and precipitated with 0.7 volumes of 2-propanol.
Illumina, Paired-End 51bp (with UMIs)

treatment_protocol: Per condition, 20x10e6 clone #5 K562 cells were cultured for 16 hours in 15 cm dishes in drug-supplied medium (DMSO (1:1000), PCI-24781 (100 nM), or tubastatin A (10 µM)).

value: K562 clone #5

value: Human immortalised myelogenous leukemia cell line

tag: chip antibody

value: 16h 10uM Tubastatin A


title: K562_H3K27me3_PCI_rep1


title: K562_H3K27me3_DMSO_rep3

value: 16h DMSO


title: K562_H3K27me3_DMSO_rep1


title: TG_exercise_HFD_657


title: K562_H3K27me3_Tuba_rep1


title: K562_H3K27ac_Tuba_rep3

value: H3K27ac (acm39133, Active Motif; lot #06921014)


title: WT_exercise_HFD_671


title: Slc4a7-KO non-PC #1


title: Pig heart tissue, Day1, Sample 1, Sequencing by Novogene, Round1


title: K562_H3K27ac_Tuba_rep1


title: Akt2 KI

city: Pittsburgh

first: Dhivyaa

last: Rajasundaram

state: PA

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh

description: Retinal Pigmented Epithelium (RPE)

data_processing:
The Bioinformatics analysis was performed to identify differentially changing autophagy genes using previously published gene sets. Average expression values of the particular genes in each sample were then calculated by the function “AverageExpression” in Seurat package.
Assembly: Mm10
Supplementary files format and content: counts_data provided as csv file

source_name: Retina

growth_protocol: N/A (RPE cells were isolated from mice)

extract_protocol:
Trizol method
Performed as a paid service from Novogene Inc. Briefly, the polyA enrichment library preparation procedure was used for RNASeq data and results in the construction of 250-300 bp insert cDNA library.

treatment_protocol: N/A (genetic engineered animal RPE cells was isolated)

value: Retina

value: Retinal Pigmented Epithelium (RPE)

value: Akt2 KI


title: WT

description: Retinal Pigmented Epithelium (RPE)


title: WT PC #3


title: TG_exercise_HFD_654


title: K562_H3K27ac_PCI_rep3


title: K562_H3K27me3_Tuba_rep2


title: Pig heart tissue, Day1, Sample 3, Sequencing by Novogene, Round1


title: Slc4a7-KO PC #3


title: K562_H3K27ac_DMSO_rep3


title: Slc4a7-KO PC #1


title: WT_exercise_HFD_652


title: K562_H3K27me3_PCI_rep3


title: K562_H3K27me3_PCI_rep2


title: K562_H3K27ac_DMSO_rep2


title: WT non-PC #3


title: TG_exercise_HFD_655


title: WT non-PC #2


title: Slc4a7-KO non-PC #3


title: WT non-PC #1


title: K562_H3K27me3_DMSO_rep2


title: Slc4a7-KO non-PC #2


title: 19957x2, WT Cerebellum, Social 35, M

city: Salt Lake City

first: Nicholas

middle: Alonzo

last: Frost

state: UT

address: 383 Colorow Dr.

department: Neurology

institute: University of Utah

description: 10X Genomics

data_processing:
Processed data files are filtered_feature_bc_matrix outputs from Cell Ranger 7.0.1 with default parameters
Assembly: mm39
Supplementary files format and content: Tab separated values and matrix files

molecule: nuclear RNA

source_name: Brain

extract_protocol:
mPFC and cerebellum were microdisected from C57Bl6/J mice after isoflurane anesthesia and decapitation. The brains were removed and quickly submerged in ice cold PBS with 15 uM actinomycin-D. Nuclei were then isolated through manual homogenation with lysis buffer containing Triton-X and 15 uM actinomycin-D. Myelin was removed via sucrose gradient and nuclei resuspended in buffer containing BSA and RNAse inhibitor.
Library construction was performed by the university of Utah high-throughput sequencing core following the manufacturor's instructions (single cell 3' v3.1 protocol, 10X genomics)

value: Brain

tag: region

value: Cerebellum

tag: strain

value: Social 35

tag: age (months)


title: K562_H3K27ac_Tuba_rep2


title: 20375x10, WT Cerebellum, Not, F

description: 10X Genomics

value: Not


title: 20778X4, WT Cerebellum, Social 10, F

description: 10X Genomics

value: Social 10


title: hos_zdk641502

city: changsha

first: ruijiang

last: Zeng

address: No.139 Renmin Road Central

institute: The Second Xiangya Hospital of Central South University

data_processing:
Total RNA qualification
mRNA enrichment
Double-strand cDNA synthesis
End repair, ploy-A & adaptor addition
Fragment selection and PCR
Library qualty assessement
illumina sequencing
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: skeleton

growth_protocol: HOS cells were cultured in MEM medium supplemented with 10% fetal bovine serum (FBS) and incubated at 37 °C in 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: skeleton

value: HOS cells

value: osteosarcoma cells

value: the treat group of cells treated with PRKDC inhibitor

value: transfection infection


title: K562_H3K27ac_PCI_rep2

value: K562 clone #5

value: Human immortalised myelogenous leukemia cell line


title: 20053x4, WT Cerebellum, Not, F

description: 10X Genomics


title: K562_H3K27ac_PCI_rep1


title: hos_zdk64NC3

value: the control group of cells treated with DMSO


title: 20778X6, WT Cerebellum, Social 10, F

description: 10X Genomics


title: 20053x6, WT Cerebellum, Not, F

description: 10X Genomics


title: hos_zdk64NC2


title: K562_Input_mixed_Tuba_rep1-3

value: 16h 10uM Tubastatin A


title: hos_si3

value: the control group of knockdown of siPRKDC by siRNA


title: K562_H3K27ac_DMSO_rep1

value: H3K27ac (acm39133, Active Motif; lot #06921014)

value: 16h DMSO


title: 20778X3, WT PFC, Social 10, F

description: 10X Genomics

value: Brain

value: medial prefrontal cortex


title: 20053x2, WT Cerebellum, Not, M

description: 10X Genomics

value: Cerebellum


title: 20053x3, WT Cerebellum, Social 35, F

description: 10X Genomics

value: Social 35


title: 20053x1, WT Cerebellum, Social 35, M

description: 10X Genomics


title: 20778X2, WT Cerebellum, Social 10, M

description: 10X Genomics

value: Social 10


title: 20778X1, WT PFC, Social 10, M

description: 10X Genomics


title: K562_Input_mixed_PCI_rep1-3


title: 20053x5, WT Cerebellum, Social 35, F

description: 10X Genomics


title: hos_si2

value: skeleton


title: K562_Input_mixed_DMSO_rep1-3


title: 20523x4, WT Cerebellum, Not, M

description: 10X Genomics

value: Not


title: hos_zdk641503

value: HOS cells

value: osteosarcoma cells


title: 20521x4, WT Cerebellum, Social 35, F

description: 10X Genomics


title: hos_zdk641501

value: the treat group of cells treated with PRKDC inhibitor

value: transfection infection


title: 20778X5, WT PFC, Social 10, F

description: 10X Genomics


title: hos_zdk64NC1


title: 20042x2, WT PFC, Not, M

description: 10X Genomics


title: 20251x3, WT Cerebellum, Social 35, M

description: 10X Genomics


title: 19957x3, WT PFC, Not, M

description: 10X Genomics


title: hos_siNC1


title: 20521x1, WT PFC, Social 35, F

description: 10X Genomics


title: hos_si1


title: Patient 24, BMMC CD45+ CD14-, 5' TCR scV(D)Jseq

city: Essen

first: Björn

last: Scheffler

address: Hufelandstrasse 55

department: DKTK Division Translational Neurooncology at the WTZ

country: Germany

institute: DKFZ (German Cancer Research Center)

description: 10x Genomics, 5' GEX+V(D)J

data_processing:
3' data read alignment of raw reads was performed to the hg38 human reference genome (2020) and feature-barcode matrices were obtained according to the Cell Ranger pipeline (7.0.1) set to default parameters. 5' data, integrating V(D)J repertoire and gene expression data were processed utilizing the cellranger multi pipeline with the hg38 human reference genome (2020), and the human V(D)J reference (GRCh38) provided by 10x Genomics. Further analyses of count matrices were performed in the R environment (v4.2.0) using the raw file output of the 3’ data and the filtered multi pipeline output of the 5’ data.
Assembly: hg38/GRCh38
Supplementary files format and content: CellRanger (7.0.1) Output, raw tab-separated feature and barcode files, raw matrix files; filtered feature bc martix; comma-separated filtered contig annotations files

source_name: BMMC

extract_protocol:
Processing of fresh samples occurred within 30 min after surgical resection and transfer in ice-cold transport media. Tumor tissues were minced and single cell suspensions prepared by homogenizing the tissue in Iscove’s Modified Dulbecco’s Medium (IMDM, Gibco) with 0.11 DMC U/mL neutral protease (NP, Nordmark Biochemicals, Germany) at 37°C for approximately 30 minutes in a shaker-incubator. Tissue dissociation was supported by gentle intermittent resuspension. Bone chips were continuously flushed with pre-warmed (37°C) 0.11 DMC U/mL NP in IMDM for 10–15 minutes in 15 mL canonical tubes to facilitate vital cell release. Cell suspensions were filtered by a 35 µm cell strainer. PBMC and BMMC were isolated from venous blood or from distal hip bone marrow. Aspirates were collected in 7.5 mL EDTA vacutainers or heparinized tubes, respectively. PBMC and BMMC were seprarated using the high-density medium Histopaque®-1077 by density centrifugation according to the manufacturer’s suggestions.  For subsequent 10x Genomics processing, respective single cell suspensions were washed in PBS supplemented with 0.04% BSA and enriched for CD45+ cells by magnetic cell separation. Indicated samples underwent additional magnetic depletion of myeloid cells (CD14 negative flowthrough) prior to 10x Genomics processing.
Samples were processed using the Chromium Next GEM Single Cell 3´ Reagent Kits v3.1 (Dual Index) (10x Genomics, #CG0000315 Rev C) or the Chromium Next GEM Single Cell 5’ Reagent Kits v2 (Dual Index) (#CG0000331 Rev E), following the manufacturer’s instructions. Following a standard quality control (2100 Bioanalyzer, Agilent), paired-end sequencing of pooled libraries was performed using a NovaSeq 6000 system (Illumina).

value: CD45+ CD14- cells

value: BMMC


title: 20042x6, WT PFC, Not, F

description: 10X Genomics


title: 20251x1, WT PFC, Social 35, M

description: 10X Genomics


title: 20042x5, WT PFC, Social 35, F

description: 10X Genomics


title: Patient 24, Cranial Bone CD45+ CD14-, 5' TCR scV(D)Jseq

description: 10x Genomics, 5' GEX+V(D)J

source_name: Cranial Bone

value: Cranial Bone


title: 20042x4, WT PFC, Not, F

description: 10X Genomics


title: Patient 24, Cranial Bone CD45+ CD14-, 5' GEX scRNAseq

description: 10x Genomics, 5' GEX+V(D)J


title: hos_siNC2

value: the control group of knockdown of siPRKDC by siRNA


title: 20042x1, WT PFC, Social 35, M

description: 10X Genomics


title: Patient 24, BMMC CD45+ CD14-, 5' GEX scRNAseq

description: 10x Genomics, 5' GEX+V(D)J


title: Patient 24, Tumor CD45+ CD14-, 5' TCR scV(D)Jseq

description: 10x Genomics, 5' GEX+V(D)J

source_name: Tumor

value: Tumor


title: 20042x3, WT PFC, Social 35, F

description: 10X Genomics


title: Patient 24, Tumor CD45+ CD14-, 5' GEX scRNAseq

description: 10x Genomics, 5' GEX+V(D)J


title: 20523x1, WT PFC, Not, M

description: 10X Genomics


title: 20375x6, WT PFC, Not, F

description: 10X Genomics


title: MH-S, ChIP

data_processing:
extracted DNA was ligated to specific adaptors followed by deep sequencing in the Illumina Novaseq 6000 using 150bp paired-end.
Quality control and trimming of the reads were done using FastQC (v0.11.9) using default parameters and Trimmomatic (v0.39)
Clean reads were aligned to the UCSC GRCm38 genome using Bowtie2(v2.4.5)
PCR duplicates were removed using Picard MarkDuplicates. Peak calling was performed using Macs2 with parameters ”-f BAMPE -B --SPMR --keep-dup all”
Peaks were filtered at a q-value threshold < 0.05. Peak calls from each replicate across both controls and treatments were merged into a union set using bedtools merge.
Assembly: GRCm38
Supplementary files format and content: bigWig, narrow peak

source_name: MH-S

growth_protocol: Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% FBS and 1% penicillin–streptomycin, followed by incubation at 37 °C in 5% CO2/95% air humidified atmosphere

extract_protocol:
DNA was extracted and purified by Universal DNA Purification Kit (#DP214)
The ChIP-seq library was prepared using ChIP-seq DNA sample preparation kit (NEBNext® Ultra™II DNA) according to the manufacturer’s instructions

treatment_protocol: MH-S cell were treated with 1000ng/ml LPS. After 24 h of incubation in cultures

value: MH-S

value: murine alveolar macrophages


title: hos_siNC3


title: Patient 22, BMMC CD45+ CD14-, 5' TCR scV(D)Jseq

description: 10x Genomics, 5' GEX+V(D)J


title: Patient 22, BMMC CD45+ CD14-, 5' GEX scRNAseq

description: 10x Genomics, 5' GEX+V(D)J


title: Patient 22, Cranial Bone CD45+ CD14-, 5' TCR scV(D)Jseq

description: 10x Genomics, 5' GEX+V(D)J


title: Patient 22, Tumor CD45+ CD14-, 5' TCR scV(D)Jseq

description: 10x Genomics, 5' GEX+V(D)J


title: CropSeq NTN, Sample 1

city: Hamburg

first: Malte

last: Hellmig

state: Hamburg

address: Martinistraße 52

department: III. Department of Medicine

institute: University Medical Center Hamburg-Eppendorf

description: 10X Genomics scRNA-seq using Chromium Single Cell 3' v3

data_processing:
10x Genomics raw sequencing data were processed using CellRanger software (version 3.1, 10x Genomics, Pleasanton, CA).
Assembly: mm10
Supplementary files format and content: Cellranger output: Tab seperated values files and Matrix table with raw gene counts

source_name: kidney

extract_protocol:
Kidneys were incubated at 37 °C for 40 min in RPMI 1640 Medium (Thermo Fisher) containing 10% heat inactivated FBS, 1% P/S, 0.4 µg/ml Collagenase D (Roche, Basel, Switzerland) and 0.2 µg/ml DNAse (Roche). Subsequently, tissue was dissociated using the GentleMACS Dissociator and C-Tubes (both Miltenyi Biotec) and leukocytes were isolated using a gradient centrifugation with 37 % Percoll (GE Healthcare). After the centrifugation, cells were washed with DPBS (Gibco). CD4+ T cells were enriched using the EasySep Mouse CD4+ T cell Isolation Kit according to manufacturer’s instructions (Stemcell Technologies, Vancouver, Canada). Enriched cells were sorted by Fluorescence-activated cell sorting (FACS) for CD4+ T cells, GFP signal and eBFP2 signal.
All steps were performed according to standard protocol of the Chromium Single Cell 3' v3 kit

value: kidney

value: T cells

value: crescentic glomerulonephritis


title: CropSeq NTN, Sample 3

description: 10X Genomics scRNA-seq using Chromium Single Cell 3' v5


title: Patient 22, Cranial Bone CD45+ CD14-, 5' GEX scRNAseq

description: 10x Genomics, 5' GEX+V(D)J


title: MLN_WT

city: Farmington

first: Kepeng

state: CT

address: 263 Farmington Ave

department: Immunology

institute: UConn Health

data_processing:
Illumina basecall (.bcl) files were converted to FASTQ using bcl2fastq from the CellRanger pipeline. Fastq files were aligned to the mm39 mouse reference genome and transcriptome and cell-counts matrices were generated using 10x Genomics CellRanger v7.0 with default parameters.
Assembly: mm39
Supplementary files format and content: tab separate values files and matrix files

source_name: mesenteric lymph node

extract_protocol:
Tissue samples were digested with 1 mg/ml collagenase IV for 20 minutes. Cells were filtered with a 70-μm cell sieve and stained with Live/Dead fixable exclusion dye, followed by fluorochrome-conjugated antibodies in PBS with 2% fetal bovine serum (FBS) and 1mM EDTA. Live/CD45+/CD3+/CD4+/YFP+ cells were sorted.
Cells were loaded for capture using the Chromium System with single-cell 3’ reagent kit v2 from 10X Genomics. After capture and lysis, cDNA synthesis and amplification were performed according to manufacturer protocol. Amplified cDNA was used to construct the Illumina sequencing library and sequenced on the NovaSeq 6000.

value: mesenteric lymph node

value: CD4+Foxp3+ Treg


title: Patient 21, Tumor CD45+ CD14-, 5' TCR scV(D)Jseq

description: 10x Genomics, 5' GEX+V(D)J


title: tumor_KO

source_name: colonic tumor

value: colonic tumor


title: CropSeq NTN, Sample 2

description: 10X Genomics scRNA-seq using Chromium Single Cell 3' v4


title: Patient 21, BMMC CD45+ CD14-, 5' TCR scV(D)Jseq

description: 10x Genomics, 5' GEX+V(D)J


title: tumor_WT


title: Patient 21, BMMC CD45+ CD14-, 5' GEX scRNAseq

description: 10x Genomics, 5' GEX+V(D)J


title: Patient 21, Tumor CD45+ CD14-, 5' GEX scRNAseq

description: 10x Genomics, 5' GEX+V(D)J


title: mimic_OE1

city: Shanghai

first: feng

last: Long

state: --- Select One

address: Department of Orthopedics, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China

institute: fudan university

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Mus_musculus.GRCm38.101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: bEnd.3 cells

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: bEnd.3 cells

value: miR-423-5p overexpressed


title: mimic_OE2


title: Patient 21, Cranial Bone CD45+ CD14-, 5' TCR scV(D)Jseq

description: 10x Genomics, 5' GEX+V(D)J


title: Patient 22, Tumor CD45+ CD14-, 5' GEX scRNAseq

description: 10x Genomics, 5' GEX+V(D)J


title: Patient 16, PBMC CD45+, 5' TCR scV(D)Jseq

description: 10x Genomics, 5' GEX+V(D)J

source_name: PBMC

value: CD45+ cells

value: PBMC


title: mimic_OE3


title: mimic_NC2

value: control


title: mimic_NC1


title: Patient 16, PBMC CD45+, 5' GEX scRNAseq

description: 10x Genomics, 5' GEX+V(D)J


title: mimic_NC3


title: Clu-Positive-Intact-2

city: Buffalo

first: Mark

middle: D

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

data_processing:
Pre-alignment quality control was performed using FASTQC v0.11.9.
Sequenced reads (fastq files) were alinged to the mouse genome GRCm39.v28 (Gencode) using STAR v2.7.9a.
counts at the gene level were quantified using subread v2.0.1 featureCounts
Assembly: GRCm39
Supplementary files format and content: raw counts (featureCounts) at the gene level for all samples

source_name: Clu+ prostate epithelial cells_Intact

growth_protocol: All animal related experimental procedures were approved by Roswell Park Comprehensive Cancer Center (RPCCC) Institutional Animal Care and Use Committee (IACUC). All mice used in these studies were male and between the ages of 7 and 13 weeks of age, as indicated in experimental outlines. Clu-CreER(T2) mice were crossed with B6.Cg-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze/J mice (RRID:IMSR_JAX:007914) to generate the Clu;tdTomato model. Nkx3.1-CreER(T2) mice were crossed with B6.129X1-Gt(ROSA)26Sortm1(EYFP)Cos/J mice (RRID:IMSR_JAX:006148) to generate the Nkx3.1;EYFP model. At 8 weeks of age, mice were either left intact or castrated via approved IACUC methods. After 4 weeks, mice were euthanized, and tissue was harvested for single-cell digestion and used in fluorescent activated cell sorting (FACS) experiments. Marker positive sorted cells were collected directly into RLT buffer from Qiagen and used for RNA extraction.

extract_protocol: 2 nanogram total RNA was used for library preparation using the SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara Bio Inc.) following manufacturer's instructions.

value: Clu+ prostate epithelial cells

value: Intact

tag: treatment duration


title: Patient 16, Tumor CD45+, 5' GEX scRNAseq

description: 10x Genomics, 5' GEX+V(D)J


title: Nkx-Positive-Castrate-2

institute: Roswell Park Comprehensive Cancer Center

source_name: Nkx+ prostate epithelial cells_Castrate

value: Nkx+ prostate epithelial cells

value: Castrate

value: 4 weeks


title: MLN_KO


title: Patient 16, Cranial Bone CD45+, 5' TCR scV(D)Jseq

description: 10x Genomics, 5' GEX+V(D)J

value: Cranial Bone


title: Patient 16, Cranial Bone CD45+, 5' GEX scRNAseq

description: 10x Genomics, 5' GEX+V(D)J


title: MH-S, input

value: MH-S

value: murine alveolar macrophages


title: Patient 15, PBMC CD45+, 5' TCR scV(D)Jseq

description: 10x Genomics, 5' GEX+V(D)J


title: Nkx-Positive-Intact-1

source_name: Nkx+ prostate epithelial cells_Intact


title: Patient 15, Tumor CD45+, 5' TCR scV(D)Jseq

description: 10x Genomics, 5' GEX+V(D)J

value: Tumor


title: Patient 21, Cranial Bone CD45+ CD14-, 5' GEX scRNAseq

description: 10x Genomics, 5' GEX+V(D)J

value: CD45+ CD14- cells


title: Nkx-Positive-Castrate-1


title: Patient 15, PBMC CD45+, 5' GEX scRNAseq

description: 10x Genomics, 5' GEX+V(D)J


title: Patient 15, Tumor CD45+, 5' GEX scRNAseq

description: 10x Genomics, 5' GEX+V(D)J


title: DBDB 16 weeks, scRNAseq

city: Rome

first: Andrea

last: Ninni

address: Via della ricerca scientifica 1

department: Biology

country: Italy

institute: University of Rome "Tor Vergata"

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brown Adipose Tissue

extract_protocol:
Total RNAs from cells and tissues were extracted using Direct-zolTM RNA MiniPrep (ZYMO RESEARCH) according to the manufacturer’s instructions. Total RNA was quantified using the Qubit 4.0 fluorimetric Assay (Thermo Fisher Scientific).
Libraries were prepared from 50 ng of total RNA using the NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostic srl), which included library preparation, quality assessment and sequencing on a NovaSeq 6000 sequencing system using a single-end, 75 cycle strategy (Illumina Inc.).

value: Stromal Vascular Fraction

value: Brown Adipose Tissue

tag: age

value: 16 weeks old


title: Patient 15, Cranial Bone CD45+, 5' GEX scRNAseq

description: 10x Genomics, 5' GEX+V(D)J


title: Patient 4, Tumor CD45+, 5' TCR scV(D)Jseq

description: 10x Genomics, 5' GEX+V(D)J


title: WT, scRNAseq

description: 10x Genomics

value: 10 weeks old

value: WT


title: BAT_DB_DB_4 Bulk RNA-seq

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TRIMMOMATIC
Trimmed sequence reads were mapped to GrCM38/mm10 using HISAT2
Read count extraction and normalization were performed using DeSeq2 (R package)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample


title: BAT_DB_DB_3 Bulk RNA-seq


title: Patient 4, Tumor CD45+, 5' GEX scRNAseq

description: 10x Genomics, 5' GEX+V(D)J

value: CD45+ cells


title: Patient 4, Cranial Bone CD45+, 5' TCR scV(D)Jseq

description: 10x Genomics, 5' GEX+V(D)J


title: Patient 4, Cranial Bone CD45+, 5' GEX scRNAseq

description: 10x Genomics, 5' GEX+V(D)J


title: Artery, PS, rep4, run2

city: Leuven

first: Elizabeth

last: Jones

address: Herestraat 49, bus 911

department: Centre for Molecular and Vascular Biology

country: Belgium

institute: KU Leuven

description:
D6@PS@L@S41@GGACTTGG@CGTCTGCG
raw_counts_run2.txt
FPKM_values_run2.txt

data_processing:
Sequence reads were trimmed for low-quality using FastX 0.0.14 (<Q20) and for adaptor sequence using cutadapt (at least 10 bp overlap with 90% match), removal of reads < 35bp
Removal of polyA reads (>90% A), ambiguous reads (containing N), low quality reads (> 50% < Q25) and artifact reads using FastX 0.0.14 and ShortRead 1.40.0, removal of contaminants using bowtie 2.3.3.1
Trimmed and filtered sequence reads were mapped to Ovis_aries.RefSeq.Oar_v4.0 using STAR 2.5.2b (parameters: --outSAMprimaryFlag OneBestScore --twopassMode Basic --alignIntronMin 50 -- alignIntronMax 50000 --outSAMtype BAM SortedByCoordinate)
Read count extraction was performed with featureCounts 1.5.3 and normalization with EDASeq (bioconductor)
Assembly: Oar_v4.0
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

organism: Ovis aries

source_name: Pulmonary sinus

extract_protocol:
RNA was extracted using TRIzol
RNA libraries for RNA-Seq were prepared using TruSeq Library Prep Kit

value: Pulmonary sinus

value: Control


title: Artery, AS, rep4, run2

description:
D6@AS@L@S37@CCGCGGTT@CTAGCGCT
raw_counts_run2.txt
FPKM_values_run2.txt

source_name: Aortic sinus

value: Aortic sinus


title: Clu-Positive-Intact-1

value: Clu+ prostate epithelial cells

value: Intact


title: Artery, PS, rep3, run2

description:
D5@PS@L@S40@GCTTGTCA@GTATGTTC
raw_counts_run2.txt
FPKM_values_run2.txt


title: Patient c10, Control PBMC CD45+, 3' GEX scRNAseq

description: 10x Genomics, 3' GEX

value: PBMC


title: BAT_WT_4 Bulk RNA-seq


title: Artery, AS, rep3, run2

description:
D5@AS@L@S36@GACCTGAA@CTCACCAA
raw_counts_run2.txt
FPKM_values_run2.txt


title: Patient c10, Control Cranial Bone CD45+, 3' GEX scRNAseq

description: 10x Genomics, 3' GEX

value: Cranial Bone


title: HFD, scRNAseq

description: 10x Genomics

value: HFD


title: Artery, PS, rep2, run2

description:
D4@PS@L@S39@TTATAACC@TCGATATC
raw_counts_run2.txt
FPKM_values_run2.txt


title: BAT_WT_3 Bulk RNA-seq


title: Patient 15, Cranial Bone CD45+, 5' TCR scV(D)Jseq

description: 10x Genomics, 5' GEX+V(D)J


title: DBDB 8 weeks, scRNAseq

description: 10x Genomics

value: 8 weeks old


title: Patient c9, Control PBMC CD45+, 3' GEX scRNAseq

description: 10x Genomics, 3' GEX


title: Artery, PS, rep1, run2

description:
D3@PS@L@S38@ATCCACTG@ACGCACCT
raw_counts_run2.txt
FPKM_values_run2.txt


title: BAT_WT_2 Bulk RNA-seq


title: Artery, AS, rep1, run2

description:
D3@AS@L@S34@TCTCTACT@GAACCGCG
raw_counts_run2.txt
FPKM_values_run2.txt

value: Ross surgery


title: Patient c9, Control Cranial Bone CD45+, 3' GEX scRNAseq

description: 10x Genomics, 3' GEX


title: Artery, AGS, rep3, run2

description:
73422@AGS@L@S43@AAGTCCAA@TACTCATA
raw_counts_run2.txt
FPKM_values_run2.txt

source_name: Autograft sinus

value: Autograft sinus


title: BAT_DB_DB_1 Bulk RNA-seq

value: Stromal Vascular Fraction


title: BAT_DB_DB_2 Bulk RNA-seq

value: Brown Adipose Tissue


title: BAT_WT_1 Bulk RNA-seq


title: Artery, AGS, rep2, run2

description:
1204@AGS@L@S42@CAAGCTAG@CGCTATGT
raw_counts_run2.txt
FPKM_values_run2.txt


title: Patient c8, Control PBMC CD45+, 3' GEX scRNAseq

description: 10x Genomics, 3' GEX


title: KO4_CD36 Bulk RNA-seq


title: Artery, AGS, rep1, run2

description:
0676@AGS@L@S44@TGGATCGA@TATCGCAC
raw_counts_run2.txt
FPKM_values_run2.txt


title: Artery, AS, rep4, run1

description:
D6@AS@L@S37@CCGCGGTT@CTAGCGCT
raw_counts_run1.txt
FPKM_values_run1.txt


title: KO3_CD36 Bulk RNA-seq


title: Artery, AS, rep2, run2

description:
D4@AS@L@S35@AGTTCAGG@TCTGTTGG
raw_counts_run2.txt
FPKM_values_run2.txt


title: Patient c8, Control Cranial Bone CD45+, 3' GEX scRNAseq

description: 10x Genomics, 3' GEX


title: Tonsils and PBMC NK cells, HTO

city: Saint Louis

first: Marco

last: Colonna

state: Missouri

address: 660 S Euclid Ave

department: Pathology and Immunology

institute: Washington University in St Louis School of Medicine

description:
Tonsils were obtained from elective tonsillectomies (Children’s Hospital in Saint Louis) and provided as surgical waste with no identifiers attached. Briefly, tissue was mechanically disrupted, passed through a 0.0059-inch opening sieve, and filtered extensively through 70-μm cell strainers. CD56+ cells were enriched via positive selection with CD56 microbeads (Miltenyi), according to the manufacturer’s recommendations. Cells were sorted and pooled: CD3-CD19-CD45+NKp44+CD56+.
HTO-tagged tonsils and PBMC NK cells
HTO_barcodes.tsv.gz
HTO_features.tsv.gz
HTO_matrix.mtx.gz
HTO_feature_reference.csv

data_processing:
Sorted cells were sequenced using 10X Genomics Platform 3’ with chemistry version 2 or with chemistry version 3. The Cell Ranger count pipeline (version 6.0.0. and 7.0.0., 10X Genomics) was used to align reads and generate gene-cell expression matrices. Briefly, short sequencing reads were aligned to the GRCh38 reference genome. We filtered out low-quality cells from the dataset if the number of genes detected was <300-1000 or >2500-10000, depending on the dataset, and chemistry, and the percentage of mitochondrial-related reads was greater than >7.5-22%.
For barcoded samples, Seurat’s HTODemux() function was used as described previously (https://satijalab.org/seurat/articles/hashing_vignette).
Assembly: GRCh38
Supplementary files format and content: tsv.gz of Filtered feature-barcode matrix with raw counts for each sample
Supplementary files format and content: csv barcode information

source_name: mixed sample (Tonsil and blood)

extract_protocol:
Using the Chromium Single Cell 3′ Reagent Kit v3User Guide, single cell suspensions were partitioned into nanoliter droplets called Gel-bead-in-Emulsions (GEMs) to achieve single cell resolution. The cDNA generated within each individual GEM is tagged with a common 16nt 10x barcode and a 12nt unique molecular barcode during the RT reaction. Purified cDNA was amplified for 11 cycles before being purified using SPRIselect beads. Samples were then run on a Agilent Bioanalyzer to determine cDNA concentration. 10uL of purified cDNA was used to generate the Illumina library for sequencing.
For sample preparation on the 10x Genomics platform, the Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v3 16 rxns (PN-1000075), Chromium Chip B Single Cell Kit, 48 rxns (PN-1000073) and Chromium i7 Multiplex Kit (PN-120262) were used. The single cell libraries were then sequenced on the Illumina NovaSeq 6000 S4 200 cycle flow cell generating 28x98 reads. A median sequencing depth of 50,000 reads/cell was targeted for each sample.

value: mixed sample (Tonsil and blood)

value: innate lymphoid cells

tag: library type

value: HTO


title: KO2_CD36 Bulk RNA-seq


title: Artery, PS, rep2, run1

description:
D4@PS@L@S39@TTATAACC@TCGATATC
raw_counts_run1.txt
FPKM_values_run1.txt


title: Tonsils and PBMC NK cells, GEX

value: mRNA


title: Artery, AS, rep2, run1

description:
D4@AS@L@S35@AGTTCAGG@TCTGTTGG
raw_counts_run1.txt
FPKM_values_run1.txt


title: KO1_CD36 Bulk RNA-seq


title: Artery, AS, rep1, run1

description:
D3@AS@L@S34@TCTCTACT@GAACCGCG
raw_counts_run1.txt
FPKM_values_run1.txt


title: wt_4 Bulk RNA-seq

value: WT


title: Artery, AGS, rep3, run1

description:
73422@AGS@L@S43@AAGTCCAA@TACTCATA
raw_counts_run1.txt
FPKM_values_run1.txt


title: Artery, PS, rep1, run1

description:
D3@PS@L@S38@ATCCACTG@ACGCACCT
raw_counts_run1.txt
FPKM_values_run1.txt

value: Pulmonary sinus

value: Control


title: sample 13 cNF, control and treated, adt

city: Birmingham

first: Deeann

last: Wallis

state: Al

address: 720 20th St S

department: Genetics

institute: University of Alabama at Birmingham

description:
Ch13_adt
Antibody-derived oligonucleotide (ADT)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Ch13_barcodes.tsv
Ch13_features.tsv
Ch13_matrix.mtx

data_processing:
Demultiplexing, barcoded processing, gene counting were made using Cell Ranger version 7.1.0)
Assembly: 10X Genomics refdata-gex-GRCh38-2020-A
Supplementary files format and content: Cell Ranger output files

molecule: protein

source_name: cutaneaous neurofibroma

extract_protocol: Nuclei were isolated via 10x Genomics protocol

treatment_protocol: Samples were snap frozen after being collected

value: cutaneaous neurofibroma

value: Tumor

value: Selumetinib treated and control

value: ADT

tag: adt

value: TotalSeq-B0452 anti-vertebrate Nuclear Pore Complex Proteins Sample 13v1, TotalSeq-B0453 anti-vertebrate Nuclear Pore Complex Proteins Sample 13v4


title: Artery, AGS, rep1, run1

description:
0676@AGS@L@S44@TGGATCGA@TATCGCAC
raw_counts_run1.txt
FPKM_values_run1.txt


title: sample 13 cNF, control and treated, mRNA

description:
Ch13_mRNA
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
Ch13_barcodes.tsv
Ch13_features.tsv
Ch13_matrix.mtx


title: sample 1 cNF, control and treated, adt

description:
Ch1_adt
Antibody-derived oligonucleotide (ADT)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Ch1_barcodes.tsv
Ch1_features.tsv
Ch1_matrix.mtx

value: TotalSeq-B0451 anti-vertebrate Nuclear Pore Complex Proteins Sample 1v1, TotalSeq-B0452 anti-vertebrate Nuclear Pore Complex Proteins Sample 1vc3


title: wt_3 Bulk RNA-seq


title: Artery, AGS, rep2, run1

description:
1204@AGS@L@S42@CAAGCTAG@CGCTATGT
raw_counts_run1.txt
FPKM_values_run1.txt

value: Ross surgery


title: Artery, PS, rep4, run1

description:
D6@PS@L@S41@GGACTTGG@CGTCTGCG
raw_counts_run1.txt
FPKM_values_run1.txt


title: single L7 motor neurons, AGE 3, Long-term Sensitization, replicate 4

city: Baltimore

first: Carrie

last: McCracken

state: MD

address: 670 W. Baltimore St

department: Institute for Genome Sciences

institute: Institute of Genome

description: neuron_5 A 22

data_processing:
Reads were assessed for quality, trimmed if PHRED scores fell below 20, and any remaining adapter sequences were removed
Processed paired-end reads were aligned to human reference genome GRCh38 using HISAT2, and counts were generated using the HTseq analysis package
Reads that successfully mapped to the reference genome were used for downstream analyses
Assembly: GCF_000002075.1_AplCal3
Supplementary files format and content: htseq output with gene counts for each sample

organism: Aplysia californica

source_name: single L7 motor neurons

growth_protocol: Three different age groups (8,10, 12 months old)of Aplysia california maintained at National Aplysia Resource Facility, University of Miami.

extract_protocol:
Total RNAs from single L7 motor neuron (L7MN) were isolated for RNAseq after one hour of behavior training.
Clontech SMART-Seq Ultra Low Input RNA kit, following manufacturer's protocol

treatment_protocol: Short-term sensitization, long-term sensitization, untrained controls

value: single L7 motor neurons

value: 12 months

value: Wild Type

value: Long-term Sensitization


title: single L7 motor neurons, AGE 3, Long-term Sensitization, replicate 5

description: neuron_6 A 23


title: wt_2 Bulk RNA-seq

value: Stromal Vascular Fraction

value: Brown Adipose Tissue


title: Artery, PS, rep3, run1

description:
D5@PS@L@S40@GCTTGTCA@GTATGTTC
raw_counts_run1.txt
FPKM_values_run1.txt


title: Artery, AS, rep3, run1

description:
D5@AS@L@S36@GACCTGAA@CTCACCAA
raw_counts_run1.txt
FPKM_values_run1.txt

value: Aortic sinus


title: single L7 motor neurons, AGE 3, Long-term Sensitization, replicate 3

description: neuron_5 A 16


title: wt_1 Bulk RNA-seq

value: WT


title: sample 1 cNF, control and treated, mRNA

description:
Ch1_mRNA
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
Ch1_barcodes.tsv
Ch1_features.tsv
Ch1_matrix.mtx

value: mRNA


title: single L7 motor neurons, AGE 3, Long-term Sensitization, replicate 1

description: neuron_5 A 4


title: sample 5 cNF, control and treated, adt

description:
5V14_adt
Antibody-derived oligonucleotide (ADT)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
5V14_barcodes.tsv
5V14_features.tsv
5V14_matrix.mtx

value: TotalSeq-B0451 anti-vertebrate Nuclear Pore Complex Proteins Sample 5v1, TotalSeq-B0457 anti-vertebrate Nuclear Pore Complex Proteins Sample 5v4


title: single L7 motor neurons, AGE 3, Long-term Sensitization, replicate 2

description: neuron_5 B 7


title: ATGLKO4 Bulk RNA-seq

value: ATGLKO


title: single L7 motor neurons, AGE 3, Short-term Sensitization, replicate 4

description: neuron_6 A 8

value: Short-term Sensitization


title: ATGLKO3 Bulk RNA-seq


title: single L7 motor neurons, AGE 3, Short-term Sensitization, replicate 5

description: neuron_6 A 25


title: sample 15 cNF, control and treated, adt

description:
15V14_adt
Antibody-derived oligonucleotide (ADT)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
15V14_barcodes.tsv
15V14_features.tsv
15V14_matrix.mtx

value: cutaneaous neurofibroma

value: Tumor

value: Selumetinib treated and control

value: TotalSeq-B0452 anti-vertebrate Nuclear Pore Complex Proteins Sample 15v4, TotalSeq-B0453 anti-vertebrate Nuclear Pore Complex Proteins Sample 15v1


title: sample 5 cNF, control and treated, mRNA

description:
5V14_mRNA
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
5V14_barcodes.tsv
5V14_features.tsv
5V14_matrix.mtx


title: single L7 motor neurons, AGE 3, Short-term Sensitization, replicate 3

description: neuron_6 B 6


title: ATGLKO2 Bulk RNA-seq


title: ATGLKO1 Bulk RNA-seq


title: single L7 motor neurons, AGE 3, Control, replicate 4

description: neuron_6 B S14

value: Control


title: single L7 motor neurons, AGE 3, Short-term Sensitization, replicate 1

description: neuron_5 A 10

value: single L7 motor neurons


title: Patient 16, Tumor CD45+, 5' TCR scV(D)Jseq

description: 10x Genomics, 5' GEX+V(D)J

source_name: Tumor

value: CD45+ cells


title: single L7 motor neurons, AGE 3, Control, replicate 5

description: neuron_6 A 4

value: 12 months

value: Wild Type


title: sample 15 cNF, control and treated, mRNA

description:
15V14_mRNA
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
15V14_barcodes.tsv
15V14_features.tsv
15V14_matrix.mtx


title: 20230719_KSR032_RNA_NCIH1048_FHD286_rep3

city: Boston

first: Cigall

last: Kadoch

state: Massachusetts

address: 440 Brookline Ave

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
RNAseq reads were aligned to the hg19 genome with STAR v2.5.2b, which output gene count tables to the hg19 refFlat annotation. For ATACseq data, quality read trimming was performed by Trimmmomatic v0.36, followed by alignment, duplicate read removal, and read quality filtering, using Bowtie2 v2.29, Picard v2.8.0, and SAMtools v0.1.19, respectively. For ChIP Data, reads were aligned, then duplicates removed and read quality filtered using using Bowtie2 v2.29, Sambamba v0.7.1, and SAMtools v0.1.19.
For ChIP and ATACseq data, tracks were generated using deepTools bamCoverage (--normalizeUsing CPM -bs 40), ATACseq data was first filtered insert sizes between 38 and 100 bp. For RNAseq data, tracks were generated using deepTools bamCoverage (--normalizeUsingRPKM).
Assembly: hg19
Supplementary files format and content: Cut&Run and ATACseq bigWig files give the normalized coverage of DNA fragments across the genome in RPM, and gene count tables give raw RNA read counts mapped to exons of given genes. RNAseq bigWig files give the give the normalized coverage of DNA fragments across the genome in RPKM.

extract_protocol:
For ChIP-Seq: Cells were fixed with 2mM DSG 40min RT then 1.0% PFA 10min RT, then sonicated for 12 minutes  For ATAC-Seq: 200K cells were incubated in hypotonic buffer and lysis buffer, then were resuspended in transposase reaction mixture for 30 min at 37°C with gentle shaking followed by DNA purification and 8 cycles of amplification  For RNA-Seq: All RNA was collected using the RNeasy Mini Kit (Qiagen). RNA-seq libraries were prepared using the Nebnext Poly(A) mRNA Magnetic Isolation Module and the Nebnext Ultra II Directional RNA Library Prep Kit for Illumina using standard protocols
ChIP-seq libraries were prepared with Illumina’s NEBNext Ultra II DNA library Prep Kit using standard protocols. ChIP-seq was sequenced on Illumina NextSeq 500 using 37 bp pair-end sequencing parameters.  ATAC-seq samples were sequenced on NextSeq 500 (Illumina) or NovaSeq 6000 (Illumina) using 37 bp pair-end sequencing parameters.  RNA-seq libraries were prepared using the Nebnext Poly(A) mRNA Magnetic Isolation Module and the Nebnext Ultra II Directional RNA Library Prep Kit for Illumina using standard protocols. RNA was sequenced on  NextSeq 6000 (Illumina) using 37 bp pair-end sequencing parameters.


title: 20230719_KSR031_RNA_NCIH1048_FHD286_rep2


title: single L7 motor neurons, AGE 3, Control, replicate 3

description: neuron_6 A 11


title: single L7 motor neurons, AGE 3, Control, replicate 1

description: neuron_5 A 5


title: WT4 Bulk RNA-seq

value: Stromal Vascular Fraction


title: WT3 Bulk RNA-seq

value: Brown Adipose Tissue


title: single L7 motor neurons, AGE 2, Long-term Sensitization, replicate 5

description: neuron_4 A 23

value: 10 months

value: Long-term Sensitization


title: 20230719_KSR030_RNA_NCIH1048_FHD286_rep1


title: single L7 motor neurons, AGE 2, Long-term Sensitization, replicate 3

description: neuron_4 B 3


title: 20230719_KSR029_RNA_NCIH1048_DMSO_rep3

value: DMSO


title: WT1 Bulk RNA-seq

value: WT


title: single L7 motor neurons, AGE 2, Long-term Sensitization, replicate 2

description: neuron_3 A 16


title: single L7 motor neurons, AGE 2, Long-term Sensitization, replicate 4

description: neuron_4 A 18


title: single L7 motor neurons, AGE 3, Short-term Sensitization, replicate 2

description: neuron_5 B 18


title: single L7 motor neurons, AGE 2, Long-term Sensitization, replicate 1

description: neuron_3 B 9


title: single L7 motor neurons, AGE 2, Short-term Sensitization, replicate 6

description: neuron_4 B 19


title: WT2 Bulk RNA-seq


title: AP2-Regenerated, replicate 2, scRNA

first: Tao

last: Liu

address: Elm and Carlton St

department: Biostatistics and Bioinformatics

institute: Roswell Park Comprehensive Cancer Institute

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0
Note: each sample has two lanes of sequenced data which were pooled/aggregated.
Assembly: mm10
Supplementary files format and content: Gene counts, barcodes, and features are packaged in the H5 format file

source_name: Prostate

extract_protocol:
Single cell tissue dissociations were performed as previously described (Lukacs et al., 2010). Briefly, in dissecting medium (DMEM (#10-027-CV, Corning) with 10% (vol/vol) FBS (#10437028, ThermoFisher), 1X glutaMAX (#35050061, ThermoFisher), and 1X penicillin-streptomycin (#15070063, ThermoFisher)) prostates were dissected away from the GU tract into individual lobes from 4-6 independent mice (N=4-6). Dorsal, lateral, and ventral prostatic lobes were pooled together, and anterior lobes were processed separately. Pooled prostatic tissue was minced and transferred to digestion solution containing 1mg/ml collagenase (#17100017, ThermoFisher Scientific). Tissue was digested at 37 °C for 2 hours with constant inversion. After digestion, tissue was spun down, resuspended in Trypsin-EDTA (#25300120, ThermoFisher), and digested for an additional 5 minutes at 37 °C. Trypsin digestions was inhibited by addition of dissecting medium supplemented with 500 U DNase I (#10104159001, Millipore-Sigma). Digested tissue was next passed through 18-G and then 20-G syringes to facilitate dissociation. Dissociated tissue was finally passed through a mesh filter with a 40 mm pore size to isolate single cells. All solutions used for tissue digestion/dissociation contained 10 mM Y-27632 dihydrochloride (#1254, Tocris) to prevent anoikis. Cell viability was greater than 80% for all downstream assays.
scRNA-Seq for dissociated mouse tissues was performed using 10X genomics Chromium Single Cell 3’ Library & Gel bead Kit V2 (ADLVP study) or the 10X genomics Chromium Single Cell 3’ Library & Gel bead Kit V3 (AP2 study) according to the manufacturer’s protocol. Briefly, approximately 17,000 viable cells were loaded into each channel of the Chromium Next GEM Chip G to capture 10,000 Gel Beads-in-emulsion (GEMs) per channel. After GEM capture, gel beads are dissolved, and cells are lysed into the cDNA master mix containing reverse transcription (RT) reagents. Post RT incubation, GEMs were broken, and first strand barcoded-cDNA was purified with magnetic beads, followed by 12-cycles of PCR-amplification. PCR-amplified barcoded-cDNA was then fragmented and purified with SPRI beads to obtain an average fragment size of 600 bp. Next, cDNA libraries were ligated to sequencing adapters followed by indexing PCR. Resulting libraries were sequenced on the Illumina NovaSeq 6000. Cell-ranger v2.1.0 (10X genomics) was used to demultiplex all mouse runs to FASTQ files, align reads to the mm10 mouse transcriptome and extract cell and UMI barcodes. The pipeline output is a cell by gene count matrix, which records the number of UMIs for each gene associated with a particular cell barcode.

value: Prostate

value: all prostatic cells

value: 96 hours of testosterone induced regeneration


title: 20230719_KSR027_RNA_NCIH1048_DMSO_rep1


title: single L7 motor neurons, AGE 2, Short-term Sensitization, replicate 5

description: neuron_4 A 10

value: Short-term Sensitization


title: single L7 motor neurons, AGE 3, Control, replicate 2

description: neuron_5 A 8


title: single L7 motor neurons, AGE 2, Short-term Sensitization, replicate 4

description: neuron_4 A 6


title: AP2-Regenerated, replicate 1, scRNA

description: 10x Genomics


title: 20230719_KSR028_RNA_NCIH1048_DMSO_rep2


title: single L7 motor neurons, AGE 2, Short-term Sensitization, replicate 2

description: neuron_3 B 28


title: single L7 motor neurons, AGE 2, Short-term Sensitization, replicate 3

description: neuron_4 B 5


title: AP2-Castrated, replicate 2, scRNA

description: 10x Genomics

value: 4 weeks of castration


title: 20230719_KSR026_RNA_NCIH526_FHD286_rep3


title: single L7 motor neurons, AGE 2, Short-term Sensitization, replicate 1

description: neuron_3 A 15


title: 20230719_KSR025_RNA_NCIH526_FHD286_rep2


title: single L7 motor neurons, AGE 2, Control, replicate 5

description: neuron_4 B 29


title: AP2-Castrated, replicate 1, scRNA

description: 10x Genomics


title: AP2-Intact, replicate 2, scRNA

description: 10x Genomics

value: left intact, sham castration


title: single L7 motor neurons, AGE 2, Control, replicate 4

description: neuron_4 A 28

value: Control


title: single L7 motor neurons, AGE 2, Control, replicate 3

description: neuron_4 B 4

value: single L7 motor neurons


title: single L7 motor neurons, AGE 2, Control, replicate 2

description: neuron_3 B 30


title: 20230719_KSR024_RNA_NCIH526_FHD286_rep1


title: 20230719_KSR023_RNA_NCIH526_DMSO_rep3


title: single L7 motor neurons, AGE 2, Control, replicate 1

description: neuron_3 B 11


title: single L7 motor neurons, AGE 1, Long-term Sensitization, replicate 6

value: 8 months


title: AP2-Intact, replicate 1, scRNA

description: 10x Genomics


title: 20230719_KSR022_RNA_NCIH526_DMSO_rep2


title: DLVP-Castrated, replicate 4, scRNA

description: 10x Genomics


title: single L7 motor neurons, AGE 1, Long-term Sensitization, replicate 4


title: single L7 motor neurons, AGE 1, Long-term Sensitization, replicate 5


title: DLVP-Castrated, replicate 3, scRNA

description: 10x Genomics


title: single L7 motor neurons, AGE 1, Long-term Sensitization, replicate 3


title: 20230719_KSR021_RNA_NCIH526_DMSO_rep1


title: single L7 motor neurons, AGE 1, Long-term Sensitization, replicate 2


title: 20230719_KSR020_RNA_CORL311_FHD286_rep3


title: single L7 motor neurons, AGE 1, Short-term Sensitization, replicate 5


title: 20230719_KSR019_RNA_CORL311_FHD286_rep2


title: DLVP-Castrated, replicate 1, scRNA

description: 10x Genomics


title: single L7 motor neurons, AGE 1, Short-term Sensitization, replicate 4


title: single L7 motor neurons, AGE 1, Short-term Sensitization, replicate 2

description: neuron_1 B 20


title: 20230719_KSR018_RNA_CORL311_FHD286_rep1


title: single L7 motor neurons, AGE 1, Short-term Sensitization, replicate 3

description: neuron_1 A 16


title: DLVP-Intact, replicate 4, scRNA

description: 10x Genomics


title: 20230719_KSR017_RNA_CORL311_DMSO_rep3


title: DLVP-Intact, replicate 3, scRNA

description: 10x Genomics


title: single L7 motor neurons, AGE 1, Short-term Sensitization, replicate 1


title: 20230719_KSR016_RNA_CORL311_DMSO_rep2


title: DLVP-Intact, replicate 2, scRNA

description: 10x Genomics


title: single L7 motor neurons, AGE 1, Control, replicate 4


title: single L7 motor neurons, AGE 1, Control, replicate 5


title: 20230719_KSR015_RNA_CORL311_DMSO_rep1


title: 20230719_KSR014_RNA_NCIH211_FHD286_rep3


title: DLVP-Intact, replicate 1, scRNA

description: 10x Genomics


title: single L7 motor neurons, AGE 1, Long-term Sensitization, replicate 1


title: single L7 motor neurons, AGE 1, Control, replicate 2


title: Nkx-Positive-Intact-2

value: Nkx+ prostate epithelial cells

value: Intact


title: single L7 motor neurons, AGE 1, Control, replicate 1

value: Wild Type


title: tumor_KO rep 2

last: Wang

data_processing:
Paired end reads in fastq format were aligned to the mm39 mouse genome and transcriptome using Hisat2. Transcripts were assembled, gtf files for all conditions were merged, and read coverage tables were generated using StringTie v2.2.1. Read counts were extracted using the prepDE python script from Stringtie, and normalization, calculation of FPKM values, and differential expression analysis were performed using the R package DESeq2 (adjusted p-value < 0.05). Replicates 1 and 2 for each condition represent technical replicates.
Assembly: mm39
Supplementary files format and content: comma separated text file of normalized counts for each sample

extract_protocol:
Tissue samples were digested with 1 mg/ml collagenase IV for 20 minutes. Cells were filtered with a 70-μm cell sieve and stained with Live/Dead fixable exclusion dye, followed by fluorochrome-conjugated antibodies in PBS with 2% fetal bovine serum (FBS) and 1mM EDTA. Live/CD45+/CD3+/CD4+/YFP+ cells were sorted.
RNA was isolated using Qiagen RNeasy Plus Mini Kit. cDNA libraries were generated for poly-A selected RNA using the Illumina TruSeq mRNA Library Kit. 100 bp paired end reads were sequenced on the Illumina NextSeq 550 v2.5.

value: colonic tumor

value: CD4+Foxp3+ Treg


title: DLVP-Castrated, replicate 2, scRNA

description: 10x Genomics


title: single L7 motor neurons, AGE 1, Short-term Sensitization, replicate 6


title: 20230719_KSR013_RNA_NCIH211_FHD286_rep2


title: tumor_KO rep 1


title: AP1-Castrated, replicate 1, scRNA

description: 10x Genomics


title: R1-scMPRA Tx

city: Seattle

first: Christopher

last: Yin

address: 3946 W Stevens Wy NE

institute: University of Washington

description: pooled HepG2 and K562 sample, single cell transcriptome

data_processing:
For both MPRA and transcriptome libraries, we initially performed anchored alignments to detect and filter the reads for correct amplicon structures using cutadapt. For MPRA libraries, we extracted and concatenated only the barcode sequences from the reads and clustered them using starcode in order to remove PCR chimerism artifacts.
We used STARsolo to align the reads to the human genome (hg38) and enhancer barcode references and to quantify the read counts. We filtered the cells based on a knee plot of per-cell transcriptome UMI counts.
Assembly: hg38
Supplementary files format and content: Matrices (row:transcript/enhancer x column:cells) containing UMI counts for each library in 10x HDF5 format

source_name: HepG2, K562

extract_protocol:
Cells were fixed using Parse Bio Evercode Fixation kit
Parse Bio Evercode Mini v2 kit with the following modifications to the kit protocol for cDNA amplification steps to prepare an additional sequencing library enriching for MPRA amplicons. First, we spiked-in a MPRA amplicon targeting primer GB39 to initial cDNA amplification reaction at the final concentration of 400nM. We performed a second PCR, starting from 50ng of the cDNA from the initial amplification round, using GB42/GB43, with the following conditions: 0.02U/uL NEB Q5 HotStart Polymerase, 1x NEB Q5 Reaction Buffer, 300nM each primers, 20uM dNTPs, 1x Biotium EvaGreen dye; 98°C 20s - 67°C 10s - 72°C 30s. The cycling was stopped after the exponential phase, and the reaction products were double size-selected using Roche KAPA Pure beads at 0.8x-1.5x. Index PCR was performed according to the kit protocol alongside the whole transcriptome library. The final indexed libraries were quantified using KAPA Library Quantification Kit (Roche 7960140001) for pooling and sequenced at 2x150 cycles on NovaSeq X Plus by Novogene.

treatment_protocol: For HepG2, 2.5 million cells were electroporated with 11.5ug R1 library plasmid DNA in 250uL Resuspension Buffer R using the Neon Transfection System at 1230V, pulse width 20ms and 3 pulses total. 2 million cells were seeded in 2mL total media volume in a 6-well plate and fixed 24 hours later. For K562, 2.5 million cells were electroporated with 11.5ug R1 library plasmid DNA in 250uL Resuspension Buffer R using the Neon Transfection System at 1450V, pulse width 10ms and 3 pulses total. 2 million cells were seeded in 10mL total media volume in a T25 flask and fixed 24 hours later.

value: HepG2, K562


title: tumor_WT rep 2


title: 20230719_KSR012_RNA_NCIH211_FHD286_rep1


title: R1-scMPRA

description: pooled HepG2 and K562 sample, scMPRA


title: AP1-Intact, replicate 2, scRNA

description: 10x Genomics


title: AP1-Intact, replicate 1, scRNA

description: 10x Genomics


title: sample 2 10X multiome (ATAC) coronal section

first: Gert

last: Hulselmans

address: Herestraat 49 PO Box 602

department: Center for Brain and Disease Research

institute: VIB

description:
10X Single Cell Multiome ATAC
instrument model:  Illumina NextSeq 2000/Illumina NovaSeq 6000
atac_counts_matrix.mtx.gz
atac_features.tsv.gz
atac_barcodes.tsv.gz
meta_data.tsv.gz
sample_2_coronal_section_atac_fragments.tsv.gz

library_source: genomic single cell

data_processing:
Raw reads were mapped to the chicken genome assembly galGal6 (GRCg6a) with Cell Ranger ARC (v2.0.2, 10x Genomics) using an ENSEMBL 108 gene annotation as reference.
The scRNA-seq modality was processed  in SCANPY using the VSN pipelines. Cells were filtered by a maximum 5% mitochondrial genes, a minimum of 200 and a maximum of 4,500 genes per cell. Genes that were present in less than three cells were removed. Doublets were detected with Scrublet. Gene expression counts were normalized per cell to a target sum of 10,000 and log-transformed. Sample batch effects were corrected with Harmony. Clusters were identified with Louvain clustering using a resolution of 2. Celltypes were assigned to clusters based on the expression of known marker genes and transcriptome comparisons with mouse scRNAseq data using SAMap.
The scATAC-seq modality was processed with pycisTopic. Pseudobulks were generated based on assigned clusters from the gene expression modality. Consensus peaks were called with MACS2. Barcodes with less than 1,000 unique fragments, a fraction of reads in peaks (FRIP) lower than 20% and a TSS-enrichment below 2 were removed. In addition, only barcodes were kept that satisfied the filtering criteria of the gene expression modality and that were not considered doublets.
Assembly: galGal6
Supplementary files format and content: gex_counts_matrix.mtx.gz:  gene expression (GEX) count matrix in MatrixMarket format
Supplementary files format and content: gex_genes.tsv.gz: ENSEMBL gene IDs and gene names of the GEX count matrix
Supplementary files format and content: gex_barcodes.tsv.gz: cell barcodes of the GEX count matrix
Supplementary files format and content: atac_counts_matrix.mtx.gz: chromatin accessibility (ATAC) count matrix in MarketMatrix format
Supplementary files format and content: atac_features.tsv.gz: regions/genomic coordinates of the ATAC count matrix
Supplementary files format and content: atac_barcodes.tsv.gz: cell barcodes of the ATAC count matrix
Supplementary files format and content: meta_data.tsv.gz: meta data for the barcodes
Supplementary files format and content: atac_fragments.tsv.gz files: genomic coordinates, cell barcodes, and counts per ATAC-seq fragment

organism: Gallus gallus

source_name: Telencephalon

extract_protocol:
The telencephalon was dissected  from brains of 15 days old domestic chickens. Two different sample types of chicken brain were used to isolate nuclei: dissected telencephalon snap-frozen in liquid nitrogen and a cryosectioned sample (12x 50 µm sections). The following procedure was followed to extract the nuclei: the tissues were resuspended in 300 µl nuclei lysis buffer comprising 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Nonidet P40, 1 mM dithiothreitol and 1U/µl RNasin ribonuclease inhibitor (Promega) in nuclease-free water, pipeted until homogenized, 1 ml nuclei lysis buffer was added and samples were incubated on ice for 5 min. Nuclei were pelleted by centrifugation at 500 g for 5 min at 4°C and resuspended in 1x PBS, 1% BSA, 1U/µl RNasin ribonuclease inhibitor. Nuclei were centrifuged another time at 500 g for 5 min at 4°C and resuspended again in 1x PBS, 1% BSA, 1U/µl RNasin ribonuclease inhibitor. DAPI was added to the samples at a conc. of 0.5 µg/ml and incubated for 10 min. DAPI positive nuclei were sorted on a MA900 Sony cell sorter (Sony Biotechnology). The sorted nuclei were centrifuged at 500 g for 5 min at 4°C and resuspended in a 1 x nuclei buffer (10x Genomics) supplemented with 1 mM dithiothreitol and 1U/µl RNasin ribonuclease inhibitor.
Single-cell libraries were generated using the 10X Chromium Single-Cell Instrument and NextGEM Single Cell Multiome ATAC+Gene Expression kit (10X Genomics) according to the manufacturer’s protocol. In brief, the single nuclei of chicken brains were incubated for 60 min at 37°C with a transposase that fragments the DNA in open regions of the chromatin and adds adapter sequences to the ends of the DNA fragments. After generation of nanoliter-scale gel bead-in-emulsions (GEMs), GEMs were incubated in a C1000 Touch Thermal Cycler (Bio-Rad) under the following program: 37°C for 45 min, 25°C for 30 min, and hold at 4°C. Incubation of the GEMs produced 10x barcoded DNA from the transposed DNA (for ATAC) and 10x barcoded, full-length cDNA from poly-adenylated mRNA (for GEX). This was followed by a quenching step that stopped the reaction. After quenching, single-cell droplets were broken and the transposed DNA and full-length cDNA were isolated using Cleanup Mix containing Silane Dynabeads. To fill gaps and generate sufficient mass for library construction, the transposed DNA and cDNA were amplified via PCR: 72°C for 5 min; 98°C for 3 min; seven cycles of 98°C for 20 s, 63°C for 30 s, 72°C for 1 min; 72°C for 1 min; and hold at 4°C. The pre-amplified product was used as input for both ATAC library construction and cDNA amplification for gene expression library construction. Illumina P7 sequence and a sample index were added to the single-strand DNA during ATAC library construction via PCR: 98°C for 45 s; 7–9 cycles of 98°C for 20 s, 67°C for 30 s, 72°C for 20 s; 72°C for 1 min; and hold at 4°C. The sequencing-ready ATAC library was cleaned up with SPRIselect beads (Beckman Coulter). Barcoded, full-length pre-amplified cDNA was further amplified via PCR: 98°C for 3 min; 6–9 cycles of 98°C for 15 s, 63°C for 20 s, 72°C for 1 min; 72°C for 1 min; and hold at 4°C. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, and index adaptor ligated, with SPRIselect cleanup in between steps. The final gene expression library was amplified by PCR: 98°C for 45 s; 5–16 cycles of 98°C for 20 s, 54°C for 30 s, 72°C for 20 s, 72°C for 1 min; and hold at 4°C. The sequencing-ready GEX library was cleaned up with SPRIselect beads. Before sequencing, the fragment size of every library was analyzed using the Bioanalyzer high-sensitivity chip. All 10x scATAC libraries were sequenced on a NextSeq2000 instrument (Illumina) or on a NovaSeq6000 instrument (Illumina) with the following sequencing parameters: 51 bp read 1 – 8 bp index 1 – 24 bp index 2 – 51 bp read 2 and for 10x GEX libraries the following sequencing parameters were used: 28 bp read 1 - 10 bp index 1 - 10 bp index 2 - 90 bp read 2.
OTHER: scRNA-seq + scATAC-seq

value: Telencephalon

tag: tissue region

value: coronal section

tag: breed

value: broiler


title: 20230719_KSR011_RNA_NCIH211_DMSO_rep3

value: DMSO


title: MLN_KO rep 2

source_name: mesenteric lymph node

tag: tissue

value: mesenteric lymph node


title: single L7 motor neurons, AGE 1, Control, replicate 6


title: tumor_WT rep 1

source_name: colonic tumor


title: AP2-Regenerated, replicate 2, scATAC

description: 10x Genomics

data_processing:
The demultiplex, reads alignment and aggregation were made using the Cell Ranger cellranger-arc software v1.2.0
Note: each sample has two lanes of sequenced data which were pooled/aggregated.
Assembly: mm10
Supplementary files format and content: fragments.tsv.gz files are gzipped files containing the tab-seperated values of chromosome, start, end locations of the sequenced reads after alignment associated with each cell barcode

extract_protocol:
Single cell tissue dissociations were performed as previously described (Lukacs et al., 2010). Briefly, in dissecting medium (DMEM (#10-027-CV, Corning) with 10% (vol/vol) FBS (#10437028, ThermoFisher), 1X glutaMAX (#35050061, ThermoFisher), and 1X penicillin-streptomycin (#15070063, ThermoFisher)) prostates were dissected away from the GU tract into individual lobes from 4-6 independent mice (N=4-6). Dorsal, lateral, and ventral prostatic lobes were pooled together, and anterior lobes were processed separately. Pooled prostatic tissue was minced and transferred to digestion solution containing 1mg/ml collagenase (#17100017, ThermoFisher Scientific). Tissue was digested at 37 °C for 2 hours with constant inversion. After digestion, tissue was spun down, resuspended in Trypsin-EDTA (#25300120, ThermoFisher), and digested for an additional 5 minutes at 37 °C. Trypsin digestions was inhibited by addition of dissecting medium supplemented with 500 U DNase I (#10104159001, Millipore-Sigma). Digested tissue was next passed through 18-G and then 20-G syringes to facilitate dissociation. Dissociated tissue was finally passed through a mesh filter with a 40 mm pore size to isolate single cells. All solutions used for tissue digestion/dissociation contained 10 mM Y-27632 dihydrochloride (#1254, Tocris) to prevent anoikis. Cell viability was greater than 80% for all downstream assays.
Single cell ATAC-Seq libraries are generated using the 10X Genomics platform.  Isolated nuclei suspensions are treated with Transposase to preferentially fragment open DNA and add partial adapter sequences to the ends of the DNA fragments.  Nuclei are loaded into the Chromium Controller (10X Genomics) where they are partitioned into nanoliter-scale Gel Beads-in-emulsion with a single barcode per cell.  Libraries are completed by PCR amplification incorporate remaining Illumina adapter sequences and unique sample indexes.  The resulting libraries are evaluated on D1000 screentape using a TapeStation 4200 (Agilent Technologies), and quantitated using Kapa Biosystems qPCR quantitation kit for Illumina. They are then pooled, denatured, and diluted to 300pM with 1% PhiX control library added.  The resulting pool is then loaded into the appropriate NovaSeq Reagent cartridge and sequenced on a NovaSeq6000 following the manufacturer’s recommended protocol (Illumina Inc.).

value: Prostate

value: all prostatic cells

value: 96 hours of testosterone induced regeneration


title: single L7 motor neurons, AGE 1, Control, replicate 3

value: Control


title: 20230719_KSR010_RNA_NCIH211_DMSO_rep2


title: AP1-Castrated, replicate 2, scRNA

description: 10x Genomics

value: 4 weeks of castration


title: sample 1 10X multiome (ATAC) whole telencephalon

description:
10X Single Cell Multiome ATAC
instrument model:  Illumina NextSeq 2000/Illumina NovaSeq 6000
atac_counts_matrix.mtx.gz
atac_features.tsv.gz
atac_barcodes.tsv.gz
meta_data.tsv.gz
sample_1_whole_telencephalon_atac_fragments.tsv.gz

value: whole telencephalon


title: AP2-Regenerated, replicate 1, scATAC

description: 10x Genomics


title: MLN_KO rep 1


title: 20230719_KSR009_RNA_NCIH211_DMSO_rep1


title: sample 2 10X multiome (RNA) coronal section

description:
10X Single Cell Multiome RNA
gex_counts_matrix.mtx.gz
gex_genes.tsv.gz
gex_barcodes.tsv.gz
meta_data.tsv.gz


title: AP2-Castrated, replicate 2, scATAC

description: 10x Genomics


title: 20231010_KSR044_RNA_NCIH1048_FHD609_rep3


title: AP2-Castrated, replicate 1, scATAC

description: 10x Genomics


title: MLN_WT rep 2


title: sample 1 10X multiome (RNA) whole telencephalon


title: MLN_WT rep 1


title: AP2-Intact, replicate 2, scATAC

description: 10x Genomics

value: left intact, sham castration


title: 20231010_KSR043_RNA_NCIH1048_FHD609_rep2


title: R2_K562_replicate1

data_processing:
Sequence reads were trimmed for 3' adaptor sequence/low-quality sequencing using cutadapt package. (parameters: maximum error rate = 0.8, minimum length = 10, maximum length = 10, no_indels)
UMIs from trimmed sequences were collapsed using starcode (parameters: seq_trim=0, umi_len=10)
Number of unique UMIs per barcode sequence calculated, and UMI counts summed across all barcodes corresponding to the same enhancer, using a custom Python script
Assembly: n/a, synthetic DNA used
Supplementary files format and content: csv containing enhancer sequence, barcode sequences for this enhancer, and unnormalized read counts for each library

extract_protocol:
Total RNA was extracted from cells 48h after transfection using the Monarch total RNA miniprep kit (NEB T2010S). For DNA libraries, barcode region of plasmid was extracted via PCR.
mRNA was isolated from total RNA extracts using the magnetic mRNA Isolation Kit (NEB S1550S) then reverse transcribed with the Maxima H Minus Reverse Transcriptase (Thermo EP0753) using a UMI-containing RT primer. Plasmid DNA was prepared with the same UMI-containing primer.


title: 20231010_KSR041_RNA_NCIH1048_DMSO_rep6


title: 20231010_KSR042_RNA_NCIH1048_FHD609_rep1


title: sample12, pigBAL, Ad-HA/NP, rep3

city: Cambridge

first: Andrew

last: Muir

address: B570, Babraham Instititute

country: United Kingdom

institute: Babraham Institute

description: 10x Genomics

data_processing:
Bcl files were demultiplexed using ‘cellranger mkfastq’ and aligned/counted using ‘cellranger count’ (cellranger-7.0.0) using default parameters and Sus scrofa genome (genome assembly 11.1, Ensembl release 107).
Assembly: Sscrofa11.1
Supplementary files format and content: 10X filtered and unfiltered (raw) feature h5 matrix files

source_name: bronchoalveolar lavage

extract_protocol:
Cryopreserved BAL cells were thawed, washed and resuspended in PBS. Cells were incubated with antibodies against CD4 (clone 74-12-4, PerCP-Cy5.5-conjugated, BD Biosciences), CD8β (clone PPT23, FITC-conjugated, Bio-Rad), CD3 (clone PPT3, APC-conjugated, Southern Biotech), CD16 (clone G7, AF647-conjugated, Bio-Rad), CD172a (clone 74-22-15, PE-conjugated, Bio-Rad) and Fixable Viability Dye eFluor780 (ThermoFisher). After two washes in PBS, cells were fixed, washed again and sorted on a FACSAria UIII (BD Biosciences), equipped with 405, 488, 561 and 640nm lasers and BD FACSDiva 8 software. After gating on FSC-AdimSSC-Adim cells and exclusion of doublets and dead cells, CD4+, CD8β+ and CD3-CD16- (to enrich for B cells) cells were sorted (12,000 cells per population). In addition, after gating on FSC-AbrightSSC-Abright cells, doublet and dead cell exclusion and gating on CD16+CD172a+ cells, 12,000 macrophages were sorted. Cells from each fraction were pooled and subjected to partitioning and barcoding on a 10x Genomics Chromium iX Controller.
For 10X, single cells were processed with the Chromium iX controller, using the Next GEM chip G, and single cell 3’ kit v3.1 library preparation kit (10X Genomics, Pleasanton, CA). An estimated 10,000 cells were targeted for recovery during partitioning. Samples were randomly grouped and run with two libraries per sequencing run on three NextSeq High Output 150 cycle reagent kits (Illumina, San Diego, CA), with 1% PhiX, targeting approximately 200 million reads per sample.

treatment_protocol: Three groups of 5 pigs each, were treated as follows: 1) infected intranasally with 8x106 PFU of A/swine/England/1353/2009 (pH1N1) using a mucosal atomization device (MAD); 2) immunized intranasally with 1x109 particles of recombinant adenoviral vectors expressing NP from H1N1/PR8/34 virus and HA from pH1N1/Texas/05/2009 (Ad-HA/NP) using a MAD and 3) immunized intranasally with a mix of 1x109 particles of Ad-HA/NP and 1x109 particles recombinant adenoviral vector encoding porcine IL-1β (Ad-HA/NP+Ad-IL-1β) using a MAD. Control pigs (n=3) received PBS intranasally. The animals were culled three weeks later, and bronchoalveolar lavage (BAL), tracheobronchial lymph nodes and blood collected.

value: bronchoalveolar lavage

value: tissue

value: leukocytes

value: Babraham pigs

value: wild-type

value: Ad-HA/NP

tag: Sex

value: M


title: sample11, pigBAL, PBS, rep3

description: 10x Genomics

tag: cell line

value: PBS


title: AP2-Intact, replicate 1, scATAC

description: 10x Genomics

tag: genotype


title: R2_HepG2_replicate1


title: R2_HepG2_replicate2


title: Intramuscular adipocytes, Ad_ lncFABP4 transduction, Day4, rep3 [Ad_ lncFABP4-3]

city: Nanning

first: Huang

last: JiePing

address: Xixiangtang District

institute: Guangxi University

data_processing:
To obtain clean reads, Low-quality reads, adapter reads, and those reads with more than 3% N were removed by SOAPnuke software (Chen et al. 2018).
The buffalo reference genome (GVM000043) and gene model annotation files were downloaded from the Genome Variation Map database (https://ngdc.cncb.ac.cn/gvm).
Clean reads were aligned to the reference genome by HISAT2 (Kim et al. 2019).
Mapped reads were assembled using StringTie (Pertea et al. 2015).
Expression of transcript was analyzed by StringTie (Pertea et al. 2015) and presented as fragments per kilobase of transcript per million mapped reads (FPKM).
Assembly: The river buffalo genome was assembled by our team (not published) and can be provided from corresponding authors by e-mail.
Supplementary files format and content: Excel file (.xlsx) include all the identified mRNA with FPKM values for all samples

organism: Bubalus bubalis

source_name: Intramuscular adipocytes

growth_protocol: Cells were cultured with complete culture medium containing 20% fetal bovine serum and 1% penicillin–streptomycin (Gibco, Grand Island, NY) at 37℃ with 5% CO2.

extract_protocol:
Total RNAs were isolated using a TRIzol regent according to a manufacturer’s protocol (Invitrogen, Carlsbad, CA, USA).
Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNA with poly A tail; mRNA molecules were fragmented into small pieces; The fragmented mRNA was synthesized into first strand cDNA using random primers; The second strand cDNA was synthesized; The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; PCR amplification and purification; Library quality control; Library circularization; The library was amplified to make DNA nanoball (DNB); Sequencing on DNBSEQ (DNBSEQ Technology) platform.

treatment_protocol: Intramuscular adipocytes were planted in six-well plates in triplicate. When the cells reach 80% confluence, transduction was performed. Adenovirus were added to cells at the indicated MOI. The culture media was exchanged three hours later. When transduction occurs for 48 hours, cells were treated with an inducing medium. Cells were collected for RNA sequencing after 48 hours of induction.

tag: cell type

value: Intramuscular adipocytes

value: lncFABP4 overexpress

value: adipogenic differentiation, Ad_lncFABP4 transduction


title: 20231010_KSR040_RNA_NCIH1048_DMSO_rep5

tag: treatment

value: DMSO


title: Intramuscular adipocytes, Ad_ lncFABP4 transduction, Day4, rep2 [Ad_ lncFABP4-2]


title: sample10, pigBAL, pH1N1, rep3

description: 10x Genomics


title: sample9, pigBAL, Ad-HA/NP+Ad-IL1b, rep3

description: 10x Genomics


title: R1-MPRA_K562_replicate2


title: R1-MPRA_K562_replicate1


title: 20231010_KSR036_RNA_NCIH211_FHD609_rep1


title: Intramuscular adipocytes, Ad_ lncFABP4 transduction, Day4, rep1 [Ad_ lncFABP4-1]

value: adipogenic differentiation, Ad_lncFABP4  transduction


title: sample7, pigBAL, pH1N1, rep2

description: 10x Genomics

value: F


title: 20231010_KSR037_RNA_NCIH211_FHD609_rep2


title: R2_K562_replicate2


title: 20231010_KSR038_RNA_NCIH211_FHD609_rep3


title: sample8, pigBAL, PBS, rep2

description: 10x Genomics


title: R1-MPRA_HepG2_replicate2


title: Intramuscular adipocytes,  Ad_EGFP transduction,  Day4, rep2 [Ad_EGFP-2]

value: WT


title: sample6, pigBAL, Ad-HA/NP+Ad-IL1b, rep2

description: 10x Genomics


title: R1-MPRA_HepG2_replicate1


title: Intramuscular adipocytes,  Ad_EGFP transduction,  Day4, rep1 [Ad_EGFP-1]


title: sample5, pigBAL, Ad-HA/NP+Ad-IL1b, rep1

description: 10x Genomics


title: 20231010_KSR035_RNA_NCIH211_DMSO_rep6


title: 20231010_KSR039_RNA_NCIH1048_DMSO_rep4


title: 20231010_KSR033_RNA_NCIH211_DMSO_rep4


title: sample4, pigBAL, pH1N1, rep1

description: 10x Genomics


title: 20230824_KSA072_NCIH1048_FHD609_rep3


title: sample2, pigBAL, Ad-HA/NP,  rep1

description: 10x Genomics


title: IT4 SLI-var16

first: Johannes

last: Allweier

address: Bernhard-Nocht-Straße 74

institute: Bernhard Nocht Institute for Tropical Medicine

data_processing:
Raw reads were mapped with hisat2 (version 2.2.1) to the respective reference genomes sourced from PlasmoDB (Amos et al., 2022). Mapped reads were sorted and indexed with samtools (version 1.17). Reads mapped to genomic features were counted using featureCounts (version 2.0.4). For var genes, only reads mapping to exon 1 were considered, for rifs, reads to the entire coding region were included. Python3 (version 3.11.4) and bioinfokit (version 2.1.2) were used to normalize the reads to transcripts per million (TPM).Differential gene expression analysis for panned against unpanned parasites was performed in R with the DESeq2 (version 1.42.0) package.
Assembly: IT4: Release 58; 3D7: Release 62
Supplementary files format and content: processed_data.xlsx; featureCounts, DESeq2

organism: Plasmodium falciparum

source_name: P. f. infected human erythrocytes

growth_protocol: P. falciparum parasites (3D7 (Walliker et al., 1987) and IT4 (Jensen and Trager, 1978) were cultured using standard procedures (Trager and Jensen, 1976). The parasites were maintained in RPMI1640 supplemented with 0.5% Albumax and human 0+ erythrocytes, at a haematocrit of 5% at 37°C under an atmosphere consisting of 1% O2, 5% CO2, and 94% N2.

extract_protocol:
Synchronous ring-stage parasites with a parasitemia of 3 - 5%, dissolved in 5 pellet volumes of Trizol (Thermo Fischer). RNA isolation with Qiagen miRNeasy Mini Kit according to the manufacturer’s instructions. RNA integrity was assessed using the Agilent 2100® bioanalyzer system with the RNA 6000 Pico Kit. All samples had a RIN > 8.
Ribosomal RNA was removed using QIAseq FastSelect RNA Removal Kit. Libraries were prepared with the QIASeq Stranded mRNA Library Kit and sequenced on an Illumina NextSeq 550 system with NextSeq 500/550 Mid Output Kit v2.5 (150 cycles).

value: P. f. infected human erythrocytes

value: SLI integrant


title: R1-DHS_HepG2_replicate2


title: 20231010_KSR034_RNA_NCIH211_DMSO_rep5


title: R1-DHS_HepG2_replicate1


title: IT4 SLI-var01


title: R1-DHS_K562_replicate2


title: sample3, pigBAL, Ad-HA/NP,  rep2

description: 10x Genomics

value: bronchoalveolar lavage


title: IT4 SLI-var19-K2 unpanned_4


title: 20230824_KSA071_NCIH1048_FHD609_rep2


title: sample1, pigBAL, PBS, rep1

description: 10x Genomics

value: tissue


title: IT4 SLI-var19-K2 unpanned_3


title: Intramuscular adipocytes,  Ad_EGFP transduction,  Day4, rep3 [Ad_EGFP-3]


title: 20230824_KSA070_NCIH1048_FHD609_rep1