title: Contralateral Day 7, biological rep 5

city: Aurora

first: Joseph

middle: Alan

last: Hippensteel

state: Colorado

department: Medicine

institute: University of Colorado Anschutz Medical Campus

description: Gene expression data from brain tissue contralateral to controlled cortical impact 7d after injury

hyb_protocol: Following fragmentation, 5.5ug of cDNA were hybridized for per Affymetrix protocol.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000 7G.

data_processing: CEL Files were generated using GeneChip Command Console Software.  Data were analyzed with the Transcriptome Analysis Console version 4.0 available through Thermo Fisher Scientific. Significant genes were determined based upon an FDR p-value < 0.05.

label: biotin

source_name: Mouse brain contralateral to controlled cortical impact, 7 days

label_protocol: Single stranded cDNA were prepared according to the standard Affymetrix protocol from isolated RNA (per GeneChip® WT PLUS Reagent Kit, Affymetrix 2013).

growth_protocol: Adult male and female mice (8-12 weeks old) were purchased from Charles River Laboratory and kept in the University animal facility for at least a week for acclimation. Animals remained in standard housing until day of euthanasia for tissue harvest.

extract_protocol: Total RNA was isolated from brain tissue using Qiagen RNeasy kit according to manufacturer's instructions.

treatment_protocol: All animals were between 8 and 12 weeks old. A 2mm controlled cortical impact injury was applied to one hemisphere. Seven days later tissue was taken ipsilateral to injury and a region contralateral corresponding to brain injury site. Tissues were flash frozen in liquid nitrogen.

tag: laterality

value: Contralateral

value: brain


title: C034

status: Public on Aug 30 2024

type: SRA

city: Jena

first: Alberto

last: Garcia Lopez

state: Thuringia

address: Adolf-Reichwein-Straße 23

department: Microbiome Dynamics

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute

library_source: transcriptomic

data_processing:
Quality of raw read data was checked using FastQC (v0.11.8).
Reads were quality- and adapter-trimmed using Trimmomatic (v0.39)
Reads were rRNA-filtered using SortMeRNA version (v2.1b) with a single rRNA database concatenated from all rRNA databases shipped with SortMeRNA.
Reads were mapped against the human reference genome and corresponding annotation GRCh38.99 (obtained from www.ensembl.org) using HiSAT2 (v2.1.0).
Differentially expressed genes (DEGs) were determined if significance was reported by either DESeq2 (v1.22.1), or edgeR (v3.24.3) and a |log2(fold change)|≥ 0.25.
Assembly: GRCh38.99
Supplementary files format and content: raw_counts.tsv = Raw counts of sequencing reads (matrix table)
Supplementary files format and content: mrn_counts.tsv = MRN (Median Ratio Normalization) counts of sequencing reads (matrix table)

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
Total RNA was extracted from whole blood pre-operative samples and preserved with RNAlater (ThermoFisher). 1.8 mL of RNAlater-preserved blood was used for manual RNA extraction using the RiboPure-Blood Kit (Thermofisher) and following the manufacturer’s instructions.
mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs(dUTP, dATP, dGTP and dCTP), RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Purification followed by AMPure XP beads, terminal repair, polyadenylation, sequencing adapter ligation, size selection and degradation of second-strand U-contained cDNA by the USER enzyme. The strand-specific cDNA library was generated after the final PCR enrichment. QC of the constructed library included testing library concentration preliminary with Qubit 2.0 Fluorometer (ThermoFisher), insert size with BioAnalyzer 2100 (Agilent) and qPCR to quantify effective library concentration. Qualified QC checked libraries were loaded on a NovaSeq 6000 S4 (Illumina) for sequencing using paired end mode with 150 bp read length (2x150 cycles)

tag: tissue

value: Whole blood

tag: condition

value: SIRS-

tag: organ dysfunction

value: yes

tag: Sex

value: Male


title: Contralateral Day 7, biological rep 4

type: RNA

country: USA

organism: Mus musculus


title: PC-9_YVMA-5_BI01810631_BIDx3_10mpg_2h_in_vivo_rep5

city: Vienna

first: Malgorzata

middle: Emilia

last: Kamuda

address: Dr.Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer-Ingelheim

data_processing:
Multiplexed samples were sequenced on an Illumina NextSeq 500 system or Illlumina NextSeq 2000. Base-calling was performed using the Real-Time Analysis (RTA) software version 2.4.11. Conversion of the raw bcl2 output files to gzipped FASTQ files was performed using the bcl2fastq2 software version 2.20.0 provided by Illumina.
Quality control was performed on samples using FASTQC (v.0.11.5), multiqc (v.1.12), picardmetrics(v0.2.4), and bioconductor-dupRadar (v1.0.0) at respective steps. Single-end reads were mapped against Homo sapiens genome (GRCh38) using the STAR (v2.5.2b) aligner. Samples were quantified with the transcript abundances using featureCount (v1.5.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw featureCounts values for each Sample

source_name: lung

growth_protocol: Cell were seeded 24 h prior to treatment start at 500000 cells per 6-well plate in RPMI medium supplemented with 10 % FCS 0.5 µg/mL puromycin and 0.6 mg/mL G418. Cells were incubated in a humidified incubator at 5 % CO2 at 37 °C. Compounds were added for the indicated timepoints.

extract_protocol:
In vivo: Frozen tumours were cut into 5x5 mm pieces and ground using one steel bead (#69989 Qiagen) per 2 mL vial in 1 mL Trizol using a tissue lyser II (Quiagen) at 4 °C (1/s frequency, 30 sec, 30 cycles). Lysates were processed using the RNeasy Plus Universal Mini Kit (Qiagen Cat No 73404) following the manufacturer’s instructions. ; In vitro: After treatment, cells were washed with ice cold PBS and RNA extracted using the RNeasy Plus Universal Mini Kit (Qiagen Cat No 73404) following the manufacturer’s instructions using 1 mL Trizol per 6-well. RNA was eluted in 50 µL of ddH2O for further processing
Quant-seq libraries were prepares using the QuantSeq 3’ mRNA-Seq Library Prep Kit for Illumina from Lexogene according to manufacturer's instructions.

treatment_protocol: Engineered PC-9 cells cancer cells were tested in an in-vivo experiment involving 11 groups with 5 animals per group, totaling 55 animals. The treatments administered included Natrosol and BI01810631 (HER2-EXON20i). The sampling time points were set at 2h, 6h, and 24h. The samples were harvested either at day 1 or day 3 of the experiment. Also PC9 YVMA cl5 cells were tested in an in-vitro experiment where we treateded them with the HER2 inhibitor, BI01810631, as a mono-agent for 24 hours. The NCI-N87 cells were tested in an in-vitro experiment where they were treated with BI01810631 (HER2 inhibitor) at concentrations of 5nM and 250nM in monotherapy. The data was retrieved for the time points 2h and 24h.

value: lung

tag: cell line

tag: cell type

value: epithelial cell

tag: genotype

value: xenograft

tag: treatment

tag: time


title: PC-9_YVMA-5_BI01810631_BIDx3_10mpg_2h_in_vivo_rep4


title: Tregs, mir342KO, rep 3

city: Chicago

first: Booki

last: Min

state: IL

address: 300 E. Superior Street

department: Microbiology-Immunology

institute: Northwestern University

description: 2x150 paired-end sequence reads

data_processing:
Raw data was uploaded to and processed remotely using the Galaxy platform.
Read qualities for each sample were checked and passed using FastQC v0.11.9.
Read alignments were created and BAM files were generated using RNA STAR v2.7.8a.
Bam files were used for generating count tables of each sample by FeatureCounts v2.0.1.
Counts were combined and normalized by DESeq2 v2.11.40.7.
Assembly: Reads were aligned to mouse genome (GRCm38.p4, M10)
Supplementary files format and content: Tab-delimited text file includes normalized counts.

source_name: CNS

extract_protocol:
RNA was isolated using the RNeasy Micro kit (Qiagen cat#74004). All subsequent sample quality assessment was performed on a Fragment Analyzer electrophoresis system (Agilent). Total RNA was normalized prior to oligo-dT capture and cDNA synthesis with SMART-Seq v4 (Takara cat#634892). The resulting cDNA was quantified using a Qubit 3.0 fluorometer (Life Technologies).
Libraries were generated using the Nextera XT DNA library prep kit (Illumina). 25 million reads per sample was performed using a HiSeq2500 (Illumina) on a Rapid run flow cell using a 100 base pairs, paired end run.

value: CNS

value: regulatory T cells

value: KO


title: Tregs, mir342KO, rep 2

description: 2x150 paired-end sequence reads


title: Contralateral Day 7, biological rep 2


title: Tregs, mir342KO, rep 1

description: 2x150 paired-end sequence reads


title: PC-9_YVMA-5_BI01810631_BIDx3_10mpg_2h_in_vivo_rep3


title: C012

value: no


title: C015

value: Female


title: Tregs, wildtype (mir342KO control), rep 3

description: 2x150 paired-end sequence reads

value: WT


title: PC-9_YVMA-5_BI01810631_BIDx3_10mpg_2h_in_vivo_rep2


title: C036


title: C033


title: PC-9_YVMA-5_BI01810631_BIDx3_10mpg_2h_in_vivo_rep1


title: Contralateral Day 7, biological rep 1


title: Ipsilateral Day 7, biological rep 5

description: Gene expression data from brain tissue at site of controlled cortical impact 7d after injury

source_name: Mouse brain ipsilateral to controlled cortical impact, 7 days

value: Ipsilateral


title: PC-9_YVMA-5_BI01810631_BIDx3_10mpg_24h_in_vivo_rep5


title: Ipsilateral Day 7, biological rep 3


title: S022

value: UInf+


title: Contralateral Day 7, biological rep 3

value: Contralateral


title: Ipsilateral Day 7, biological rep 4

value: brain


title: Tregs, wildtype (mir342KO control), rep 1

description: 2x150 paired-end sequence reads


title: Ipsilateral Day 7, biological rep 2


title: Ipsilateral Day 7, biological rep 1


title: S037

value: Whole blood

value: Sepsis+


title: lung, BLM+GC1, 21d(11d), rep3 [BG128]

city: Xinxiang

first: Guoying

last: Yu

state: Henan

address: East of Construction Road

country: China

institute: Henan Normal University

description:
gene_count.csv
gene_fpkm.csv

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In 1 this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm10
Supplementary files format and content: comma-delimited csv file includes raw counts for each Sample
Supplementary files format and content: comma-delimited csv file includes FPKM values for each Sample

source_name: lung tissue

extract_protocol:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). Firststrand cDNA wassynthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: strain

value: lung tissue


title: lung, BLM+GC1, 21d(11d), rep1 [BG120]

description:
gene_count.csv
gene_fpkm.csv


title: S036

value: yes


title: PC-9_YVMA-5_BI01810631_BIDx3_10mpg_24h_in_vivo_rep3

value: lung


title: lung, BLM, 21d, rep3 [B127]

description:
gene_count.csv
gene_fpkm.csv

value: BLM


title: Tregs, Lag3cKO, rep 4

description: 2x150 paired-end sequence reads

extract_protocol:
RNA was isolated using the RNeasy Micro kit (Qiagen cat#74004). All subsequent sample quality assessment was performed on a Fragment Analyzer electrophoresis system (Agilent). Total RNA was normalized prior to oligo-dT capture and cDNA synthesis with SMART-Seq v4 (Takara cat#634892). The resulting cDNA was quantified using a Qubit 3.0 fluorometer (Life Technologies).
Libraries were generated using the Nextera XT DNA Library Prep kit (Illumina cat#FC-131-1096). Paired End run.

treatment_protocol: Lag3cKO (Foxp3Cre Lag3fl/fl) and wild type mice were induced for EAE by immunization with MOG peptide in CFA followed by pertussis toxin injection. At the peak of the disease, the mice were sacrificed and Foxp3+ Tregs were FACS sorted from the central nervous sytem (brain and spinal cords).


title: lung, BLM, 21d, rep2 [B126]

description:
gene_count.csv
gene_fpkm.csv


title: Dex_RNA_rep3

city: Seoul

first: Do Young

last: Hyeon

state: Select State

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Illumina BCL files were demultiplexed and converted to FASTQ files using cellranger mkfastq in Cell Ranger software (v.6.1.2) (10x Genomics).
The resulting FASTQ files were used to perform alignment to mouse GRCm38 genome, filtering, and UMI counting, as well as to produce gene-barcode matrices using cellranger count.
The subsequent data analysis was performed using the R package Seurat (v.4.0.4).
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

growth_protocol: All mice were housed under specific pathogen-free conditions until the start of each experiment.

extract_protocol:
Cellular suspensions were loaded onto a Chromium Controller (10x Genomics) to generate nanoliter-sized gel bead-in-emulsions (GEMs) containing single cells, reagents, and a single gel bead containing barcoded oligonucleotides. Lysis and barcoded reverse transcription of polyadenylated mRNA from single cells were performed inside each GEM.
Barcoded sequencing libraries were prepared using Chromium Next GEM Single Cell 3’ v3.1 Dual Index (10X Genomics) according to the manufacturer’s protocol.

value: Lung

value: CD45+ cells

value: Wild Type

value: OVA+LPS/OVA+Dex


title: S033

value: no


title: PC-9_YVMA-5_BI01810631_BIDx3_10mpg_24h_in_vivo_rep2

value: epithelial cell

value: xenograft


title: Tregs, wildtype (mir342KO control), rep 2

description: 2x150 paired-end sequence reads

value: CNS

value: regulatory T cells

value: WT


title: PBS_RNA_rep3

description: 10x Genomics

value: OVA+LPS/PBS


title: SIRS S223

value: Whole blood

value: SIRS+

value: Female


title: S035

value: Sepsis+

value: yes

value: Male


title: lung, BLM, 21d, rep1 [B125]

description:
gene_count.csv
gene_fpkm.csv

value: lung tissue

value: BLM


title: PC-9_YVMA-5_BI01810631_BIDx3_10mpg_24h_in_vivo_rep1

value: lung


title: Tregs, Lag3cKO, rep 3

description: 2x150 paired-end sequence reads

value: KO


title: lung, BLM+GC1, 21d(11d), rep2 [BG123]

description:
gene_count.csv
gene_fpkm.csv


title: PC-9_YVMA-5_BI01810631_BIDx3_10mpg_24h_in_vivo_rep4


title: Tregs, Lag3cKO, rep 2

description: 2x150 paired-end sequence reads


title: PC-9_YVMA-5_BI01810631_BIDx1_5mpg_24h_in_vivo_rep5


title: lung, PBS, 21d, rep3 [S160]

description:
gene_count.csv
gene_fpkm.csv

value: PBS


title: PC-9_YVMA-5_BI01810631_BIDx1_5mpg_24h_in_vivo_rep4

value: epithelial cell


title: S008


title: PC-9_YVMA-5_BI01810631_BIDx1_5mpg_24h_in_vivo_rep3

value: xenograft


title: lung, PBS, 21d, rep2 [S157]

description:
gene_count.csv
gene_fpkm.csv


title: Tregs, Lag3cKO, rep 1

description: 2x150 paired-end sequence reads

value: CNS


title: S012


title: S010

value: UInf+

value: no


title: lung, PBS, 21d, rep1 [S155]

description:
gene_count.csv
gene_fpkm.csv


title: S016


title: PC-9_YVMA-5_BI01810631_BIDx1_5mpg_24h_in_vivo_rep1


title: Wildtype treated with TPA

first: Irina

last: Budunova

address: 303 E. Chicago Ave, WARD 9-015

department: Dermatology

data_processing:
Trimmed with trim_galore --stringency 5 -e 0.1 --length 20 -q 20
Aligned to mouse with STAR --readFilesCommand zcat --outFilterType BySJout --outSJfilterCountUniqueMin -1 2 2 2 --outSJfilterCountTotalMin -1 2 2 2 --outFilterIntronMotifs RemoveNoncanonical --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 2 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.3
Raw counts extracted using htseq-count -r pos -s no -f bam -t exon -i gene_id -m union --nonunique none
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text containing raw counts

source_name: Skin

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Vehicle control: animals were treated topically with acetone, 200ul/animal; TPA group with  4 ug in 200 ul of acetone; or 3) TPA+FA. Some TPA-treated animals were pretreated with glucocorticoid fluocinolone acetonide (FA, 2 ug in 200 ul acetone) one hr before TPA application

value: Wildtype

value: Skin

value: TPA (4 ug/animal)


title: PC-9_YVMA-5_BI01810631_BIDx1_5mpg_24h_in_vivo_rep2


title: Tregs, wildtype, rep 2

description: 2x150 paired-end sequence reads

value: regulatory T cells

value: WT


title: S020

value: Whole blood


title: PC-9_YVMA-5_BI01810631_BIDx1_10mpg_24h_in_vivo_rep4


title: DN_rep3

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
Adaptor sequences and the ends of reads less than Phred quality score 20 were removed using Cutadapt v1.18.
The resulting reads were then mapped to the Mus musculus reference genome (GRCm38) using HISAT2 v2.2.1.
PCR or optical duplicate reads were filtered out using Picard v2.25.5.
The remaining reads were counted for gene features (GTF file of GRCm38) using HTSeq v0.11.3.
Assembly: GRCm38
Supplementary files format and content: A tab-delimited text file including read counts for all samples

extract_protocol:
Total RNA was isolated from CD39+CD9+ IMs (n = 3) and CD39-CD9- monocytes (n = 3) under OVA+LPS/OVA+αIL-23p19 condition using TRIzol RNA Isolation Reagent (Life technologies, Carlsbad, CA, USA), and purified according to the manufacturer’s instructions.
The libraries were prepared for 151 bp paired-end sequencing using RNA Prep with Enrichment, (L) Tagmentation (96 Samples) (Illumina). These cDNA libraries were qualified with the Agilent 4200 Tapestation (Agilent) and quantified with the Qubit Flex Fluorometer (Thermo Fisher Scientific) according to the manufacturer’s library protocol.

value: Lung

value: CD39-CD9- monocytes

value: Wild Type


title: Wildtype Vehicle 1

value: vehicle (acetone)


title: Wildtype treated with FA+TPA

value: FA (2ug/animal) followed by TPA (4 ug/animal)


title: PC-9_YVMA-5_BI01810631_BIDx1_10mpg_24h_in_vivo_rep5

value: lung


title: Tregs, wildtype, rep 1

description: 2x150 paired-end sequence reads


title: S019

value: Male


title: Wildtype Vehicle 2


title: PC-9_YVMA-5_BI01810631_BIDx1_10mpg_24h_in_vivo_rep3

value: epithelial cell

value: xenograft


title: REDD1 Knockout treated with TPA

value: REDD1 Knockout


title: DN_rep2


title: S003

value: Sepsis+

value: yes

value: Female


title: Tregs, wildtype, rep 4

description: 2x150 paired-end sequence reads

value: CNS


title: PC-9_YVMA-5_BI01810631_BIDx1_10mpg_24h_in_vivo_rep1


title: S001

value: UInf+

value: no


title: DN_rep1


title: PC-9_YVMA-5_BI01810631_BIDx1_10mpg_24h_in_vivo_rep2


title: Tregs, wildtype, rep 3

description: 2x150 paired-end sequence reads

value: regulatory T cells

value: WT


title: DP_rep3

value: Lung

value: CD39+CD9+ interstitial macrophages


title: REDD1 Knockout Vehicle 2

value: Skin

value: vehicle (acetone)


title: S005

value: Whole blood


title: C005

value: SIRS-


title: DP_rep2

value: Wild Type


title: RNA_201_veh

city: woolloongabba

first: laura

last: sormani

state: QLD

address: 37 kent street

department: Diamantina Institute

country: Australia

institute: The University of Queensland Diamantina Institute

data_processing:
Read sequences in compressed (gzipped) FASTQ files were aligned to the human genome (GRCh38) in the Rsubread (v2.8.0) package. The alignment produces a BAM file for each library. The featureCounts function of Rsubread takes all the BAM files and produces the gene count matrix. Each sample is a separate column and each row is a gene. Entrez Gene ID was converted to gene symbol using biomaRt (v 2.56.1) package. Gene counts were TMM normalised in the edgeR package (version 3.42.4) for downstream analysis.
Assembly: human genome (GRCh38)
Supplementary files format and content: Comma-separated values; raw counts of sequencing reads; matrix table
Supplementary files format and content: Comma-separated values; normalized abundance measurments; matrix table

source_name: placenta

growth_protocol: ECFC cells were maintained in EGM2 supplemented with antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen)
RNA-Seq libraries were prepared using the Illumina stranded total RNA prep ligation with Ribo-Zero plus kit (Illumina, 20040529) and IDT for Illumina RNA UD Indexes (Illumina, 20040553/20040554/20040555/20040556) according to the standard manufacturer’s protocol (Illumina, Document # 1000000124514 v01).The libraries were quantified on the Perkin Elmer LabChip GX Touch with the DNA High Sensitivity Reagent kit (Perkin Elmer, CLS760672). Libraries were pooled in equimolar ratios, and the pool was quantified by qPCR using the KAPA Library Quantification Kit – Illumina/Universal (KAPA Biosystems, KK4824) in combination with the Life Technologies Viia 7 real time PCR instrument.

treatment_protocol: Endothelial to mesenchymal transition was induced by treatment of 5-day with 25ug/ul oxLDL

value: placenta

value: Endothelial colony-forming cells

value: vehicle 5 days


title: RNA_MG_veh


title: S015

value: Sepsis+

value: yes


title: MDA-MB-231 cells, HA-DVL1 , 3

city: Chapel Hill

first: Dalia

last: Martinez-Marin

state: NC

address: 450 West Dr

department: Dept of Pharmacology

institute: University of North Carolina

data_processing:
trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: breast

growth_protocol: MDA-MB-231 cells were maintined in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated using Aurum™ Total RNA Mini Kit (Bio-Rad)
RNA libraries for RNA-seq were prepared by AZENTA-GENEWIZ

value: breast

value: triple-negative breast cancer

value: DVL1 knock-in


title: DP_rep1


title: PP VS2-SIV-Treated-PBMC

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
FastQC v0.11.7 was used to QC the raw sequencing reads.
Trimmomatic 0.38 was used to trim reads.
HISAT2 v2.1.0 and Bowtie2 v 2.3.4.1 were used to quantitate expression.
Limma-voom v 3.50.3 was used for differential expression of genes analysis.
fgsea v.1.20.0 was used for GSEA analysis, and L2P was used for enrichment analysis (L2P, https://github.com/ccbr/l2p).
Assembly: GCF_000772875.2_Mmul_8.0.1
Supplementary files format and content: Comma-separated values (CSV) files provided for raw counts, DEG, GSEA, and L2P results.

organism: Macaca

source_name: PBMC

growth_protocol: PBMC /Monocyte cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
TruSeq Stranded mRNA kit was used.

treatment_protocol: 1:100 diluted SIV was added to SIV-treated PBMC or SIV-treated Monocyte samples for 18hrs.

value: PBMC

value: PBMC-Treated with SIV

value: protected

value: Before Challenge


title: S021

value: Female


title: RNA_137_veh


title: p19_RNA_rep2

description: 10x Genomics

value: Lung

value: CD45+ cells


title: RNA_MG_oxLDL

value: oxLDL(25ug/ul) 5 days


title: MDA-MB-231 cells, HA-DVL1 , 1


title: p19_RNA_rep3

description: 10x Genomics

value: Wild Type


title: REDD1 Knockout treated with FA + TPA

value: REDD1 Knockout

value: Skin

value: FA (2ug/animal) followed by TPA (4 ug/animal)


title: MDA-MB-231 cells, HA-DVL1 , 2


title: p19_RNA_rep1

description: 10x Genomics


title: RNA_137_oxLDL

value: placenta

value: Endothelial colony-forming cells


title: MDA-MB-231 cells, Plasmid Control, 3

value: breast

value: WT


title: PM VS2-SIV-Treated-Monocyte

value: Monocytes-treated with SIV


title: PP S6-SIV-Treated-PBMC

value: PBMC


title: RNA_201_oxLDL


title: Dex_RNA_rep2

description: 10x Genomics

value: OVA+LPS/OVA+Dex


title: PM S6-SIV-Treated-Monocyte

value: protected


title: PM S5-SIV-Treated-Monocyte

value: Before Challenge


title: MDA-MB-231 cells, Plasmid Control, 2

value: triple-negative breast cancer


title: PP S5-SIV-Treated-PBMC

value: PBMC-Treated with SIV


title: RNA_KK_veh

value: vehicle 5 days


title: MDA-MB-231 cells, Plasmid Control, 1


title: RNA_KK_oxLDL

value: oxLDL(25ug/ul) 5 days


title: pE7:GFP_DEX_1μM_3

first: Hee-Seung

last: Choi

state: Seoul

address: 1 Gwanak-ro, Gwanak-gu, Seoul, School of Biological Sciences,, room 506, bdg 502

data_processing:
Raw sequencing reads were filtered to get clean reads by using SOAPnuke (v1.5.2, parameters -l 15, -q 0.4, -n 0.01, -A 0.25). Subsequent analysis of differentially expressed genes was performed in R using the DEseq2 package (Love, M. I. et al. Genome Biology 15, (2014))
For sequencing data, HISAT (Kim et al., 2015) pipeline was applied to align reads against reference genome.
StringTie (Pertea et al., 2015) was then used for transcript reconstruction.
Subsequently, Cuffcompare (Cufflinks tools; Trapnell et al., 2012) was utilized to compare reconstructed transcripts and the reference annotation of Arabidopsis. Since Arabidopsis thaliana has been fully sequenced; read alignment/mapping was achieved by the TAIR 10.
Genome_build: TAIR10
Supplementary_files_format_and_content: .txt files including FPKM values for each sample

organism: Arabidopsis thaliana

source_name: roots

growth_protocol: Three days cold treated seeds of the pE7:shy2-1:GR lines were germinated on cellophane membranes (KOMABIOTECH) on 0.5 X MS medium with hygromycin (30 μg/ml).

extract_protocol:
Root sample were flash frozen in liquid nitrogen, RNA was extracted with the Rneasy Mini Kit (QIAGEN) following manufacturer protocol. Extra DNase I (TAKARA BIO INC., Japan) treatment was necessary to remove any genomic DNA.
In total, approximately 1 μg total RNA was initially used for BGISEQ-500 library construction. Then, RNA integrity number (RIN) was obtained from Agilent 2100 Bioanalyzer, these samples were qualified for RNA-seq for downstream sequencing process.

treatment_protocol: three-day old seedlings were transferred to plates containing 0.1 nM DEX, 1 μM DEX or EtOH control for 24h.

value: 1000 DEX nM

tag: replicate


title: REDD1 Knockout Vehicle 1

value: REDD1 Knockout

value: vehicle (acetone)


title: Dex_RNA_rep1

description: 10x Genomics

value: Lung

value: CD45+ cells

value: Wild Type


title: ATAC_MG_veh

library_source: genomic

data_processing:
Raw paired-end sequencing reads were aligned to the hg19 reference genome using Bowtie273(version 2.2.9), after removing sequencing adapters with Cutadapt (version 1.13). Samtools (version 1.9) and Picard were used to filter duplicates, remove reads with mapping quality < 30, unmapped reads, reads aligning to the mitochondrial chromosome and unplaced contigs. Quality of library enrichment was evaluated using ENCODE metrics, including Transcription Start Site signal > 10, and sample concordance examined using clustering analysis. Peaks were called for each sample using MACS2 (version 2.1.2), with parameters“-p 0.01–-nomodel–-shift 0–-extsize 14”. Differentially accessible regions between treated and untreated samples were called using DiffBind version 2.14.0, where treatment-dependent peaks were selected as those exhibiting a log fold change > 1. Over-represented transcription factor binding motifs within ATAC-seq peaks were identified using HOMER version 4.8. We also employed a permutation-based strategy using ENCODE dNase-seq footprinting data
Assembly: human hg19
Supplementary files format and content: Narrowpeak file

molecule: genomic DNA

extract_protocol:
50,000 ECFCs were trypsinized and washed twice in cold PBS. Pelleted cells were lysed and then directly transposed using the TDE1 DNA Enzyme and Buffer kit (Illumina, CA, US). The transposition reaction was completed with thermomixing at 37°C for 30 minutes at 300 rpm. Transposed DNA was purified with MinElute column cleanup (Qiagen, Valencia, CA)
Prepared libraries were purified with MinElute column clean-up (Qiagen). The ATAC-seq library pool was quantified on the Agilent Bioanalyzer with the High Sensitivity DNA kit (Agilent Technologies, 4067-4626). Sequencing was performed using the Illumina NextSeq500 (NextSeq control software v4.0.0 / Real Time Analysis v2.11.3). The library pool was diluted and denatured according to the standard NextSeq protocol (Document # 15048776 v16) and sequenced to generate paired-end 76 bp reads using a 150 cycle NextSeq500/550 Mid Output reagent Kit v2.5 (Illumina, 20024904). After sequencing, fastq files were generated using bcl2fastq2 (v2.20.0.422).

value: placenta

value: Endothelial colony-forming cells


title: OVA_RNA_rep3

description: 10x Genomics

value: OVA+LPS/OVA


title: OVA_RNA_rep2

description: 10x Genomics


title: pE7:GFP_DEX_1μM_1


title: ATAC_KK_veh


title: ATAC_137_veh


title: NP N2-SIV-Treated-PBMC

value: PBMC

value: infected


title: NP N5-SIV-Treated-PBMC


title: PBS_RNA_rep2

description: 10x Genomics

value: OVA+LPS/PBS


title: ATAC_201_veh


title: pE7:GFP_DEX_0.1nM_3

value: 0.1 DEX nM


title: OVA_RNA_rep1

description: 10x Genomics


title: NP N1-SIV-Treated-PBMC

value: Before Challenge


title: pE7:GFP_DEX_1μM_2


title: PBS_RNA_rep1

description: 10x Genomics


title: CY-3

city: Lanzhou

first: shaoke

last: guo

state: Gansu

address: West Lake Street

department: Lanzhou institute of husbandry and pharmaceutical sciences

description: ribosome footprints

data_processing:
Fastp filters low-quality readings.
The short reading comparison tool Bowtie2 is used to map readings to ribosomal RNA (rRNA) databases, GenBank, and Rfam databases. Remove readings of rRNA, transfer RNA (tRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), and miRNA.
Compare the processed RNA seq readings with the genome.
A trinucleotide cycle diagram was drawn using the riboWaltz R software package.
Assembly: LU_Bosgru_v3.0
Supplementary files format and content: Calculate the number of reads in the open reading frame of coding genes using software RSEM, and normalize gene expression levels using FPKM method
Library strategy: Ribo-seq

organism: Bos grunniens x Bos taurus

source_name: cattle-yak

growth_protocol: In this study, all animal-related procedures conformed to the China Council on Animal Care and the Ministry of Agriculture of the People’s Republic of China guidelines. All yak-handling procedures were approved by The Animal Care and Use Committee of the Lanzhou Institute of Husbandry and Pharmaceutical Sciences Chinese Academy of Agricultural Sciences (Permit No: LIHPS-2022-0144).

extract_protocol:
Grind the frozen tissue into powder using a mortar and pestle in liquid nitrogen, and then dissolve it in 400 μ L lysis buffer. The ribosomal profiling technique was carried out according to the report. Add short (50-80 base) antisense DNA probes complementary to rRNA sequences to a solution containing RFs, and then add RNase H and DNase I to digest rRNA and residual DNA probes. Finally, further purification of RFs was carried out using magnetic beads.
Add adapters to both ends of RFs and perform reverse transcription and PCR amplification. Enrich PCR products with sizes of 140-160bp to generate cDNA libraries, and sequence using Illumina HiSeqTM X10.

treatment_protocol: Three 6-month-old (6M), 18-month-old (18M), 4-year-old (4Y) male yaks and 4-year-old (4Y)  cattle-yaks were selected from the same cooperative in Xiahe County, Gannan Tibetan Autonomous Prefecture, Gansu Province (N34 ° 51'50 ', E102 ° 26'9') for castration to collect testicular tissue

value: testis

tag: developmental stage

value: sexual maturity


title: pE7:GFP_DEX_0.1nM_1


title: NM N5-SIV-Treated-Monocyte

value: Monocytes-treated with SIV


title: ATAC_MG_oxLDL

value: oxLDL(25ug/ul) 5 days


title: ATAC_KK_oxLDL


title: NM N2-SIV-Treated-Monocyte


title: pE7:GFP_mock_2

value: 0 DEX nM


title: NM N1-SIV-Treated-Monocyte


title: pE7:GFP_mock_3


title: ATAC_137_oxLDL


title: ATAC_201_oxLDL


title: IP VS5-SIV-Treated-PBMC

value: PBMC-Treated with SIV


title: Si3, Cut & Tag

city: guiyang

first: Dijie

last: Zheng

address: No.8 beijing road

institute: guizhou medical universuty

data_processing:
Low-quality reads were filtered out using Fastp.
The high-quality reads were then aligned to the mm10 genome using Bowtie2.
Duplicates were removed with Picard.
The peaks were identified using MACS2.
Assembly: mm10
Supplementary files format and content: bedgraph, nrrowpeak
Library strategy: CUT&Tag

source_name: Vascular Smooth Muscle

growth_protocol: Mouse primary VSMCs were obtained from Procell Life Science & Technology Co., Ltd. (WuHan, China. CP-M076) and grown in medium at 37 °C and 5% CO2. To establish the in vitro AAA model, VSMCs were treated with 10–7 mol/L Ang II for 36 h, and the cells in the control group were treated with the same medium without Ang II.

extract_protocol:
For the Cut&Tag experiments, we utilized the UT&Tag Assay Kit (Abclonal, RK20265) and 10,000 cells. The cells were captured using ConA beads and then permeabilized with digitonin. Next, the primary antibody was added to bind the target protein, followed by an overnight incubation at 4°C with rotation. Afterward, the secondary antibody was added and incubated at room temperature for 1 hour. To fragment the genomic DNA, pAG-Tn5 was introduced. The fragmented DNA was then collected using AFTMag NGS DNA Clean Beads.
The purified DNA, now equipped with adaptors, was amplified via PCR. The resulting PCR product was further purified using DNA Clean Beads.

treatment_protocol: VSMC cells are uniformly seeded to achieve a density of about 30% at the time of transfection. Diluted siRNA (supplied by Guangzhou Ruibo) is combined with riboFECTTM CP Buffer and Reagent, allowed to incubate at room temperature for 15 minutes, and then applied to the cell-plated wells. Following this, the cells are incubated at 37°C for 24 hours, with transfection efficiency subsequently evaluated through qRT-PCR and Western Blot analysis.

value: Vascular Smooth Muscle

value: VSMC

value: Mouse Vascular Smooth Muscle Cells

tag: chip antibody


title: CLL6 post-HSCT - scDNA-seq

city: Boston

first: Livius

last: Penter

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: single cell DNA sequencing amplicons

data_processing:
Demultiplexing of llumina sequencer's base call files (BCLs).
Alignment of raw reads to hg19, extraction of cell barcodes, DNA amplicons and oligotags using Tapestri pipeline.
Extraction of called variants and surface marker expression using Tapestri Insights v3.0.2.
Assembly: GRCh19
Supplementary files format and content: Allele frequencies and surface marker expression in tsv file format.
Library strategy: Single cell DNA sequencing and CITE-seq using Total-seq D oligotags.

source_name: peripheral blood

extract_protocol:
Single cell suspensions were stained with Total-seq D surface marker oligotags followed loading onto Tapestri cartridge.
Single cell DNA and oligotag sequencing according to manufacturer's instructions (Mission Bio) using custom panels for mitochondrial and somatic nuclear DNA mutations.

value: peripheral blood

tag: pool

tag: library type

value: amplicon

value: relapse post-HSCT


title: pE7:GFP_mock_1


title: IP VS1-SIV-Treated-PBMC

value: PBMC


title: CLL5 post-HSCT - scDNA-seq

description: single cell DNA sequencing amplicons


title: IM VS5-SIV-Treated-Monocyte

value: infected


title: pE7:shy2-1:GR_DEX_1μM_2

value: 1000 DEX nM


title: Si1, Cut & Tag


title: IP S4-SIV-Treated-PBMC


title: pE7:shy2-1:GR_DEX_1μM_1


title: NC2, Cut & Tag

value: Negative Control


title: Arc Morphine1

city: Solna

first: Patrik

last: Ernfors

address: Biomedicum, Solnavägen 9

department: MBB/Molneuro

country: Sweden

institute: Karolinska Institutet

description:
10x Genomics Chromium 3' v.3
rvm_arc_counts.tsv.gz
rvm_arc_metadata.tsv.gz
barcode-1_1

data_processing:
CellRanger (version 7.07.1) pipeline and mouse transcriptome version mm10 were used to align reads and generate gene expression data.
Assembly: mm10
Supplementary files format and content: .tsv.gz files containing raw expression counts and corresponding metadata in separate .tsv.gz (meta) files

source_name: Arc Morphine

extract_protocol:
Single nucleus suspensions were prepared from isolated RVM and spinal cord samples via dounce homogenization in Tris buffer containing 0.1% Triton X-100, as well as protease/RNAse inhibitors, and where appropriate, Actinomycin D at a concentration of 15µM. Debris was removed via gradient centrifugation. To obtain enriched neuronal samples, nuclei suspensions were subjected to Fluorescence-activated cell sorting (FACS) for either NeuN (Figure 2a, Figure 5a), or tdTomato (Figure 2f). FACS was performed using a BD FACSAria III Sorter (BD Biosciences, Franklin Lakes, NJ USA). Single cell suspensions were prepared from WT mice previously injected intraspinally with AAVretro-EGFP to label descending projections from the RVM. The RVM was then sectioned via Vibratome and gently dissociated with Papain and DNase. Neurons were enriched and debris was removed via gradient centrifugation. Single EGFP-positive cells were selected via FACS.
Sorted nuclei or cells were loaded onto a 10X Genomics Chromium Chip and single nuclei/cell droplets were obtained. Reverse transcription, cDNA amplication and Library preparation were all performed according to the manufacturer's instructions.

value: Rostral ventromedial medulla

value: Neuron


title: Arc Morphine3

description:
10x Genomics Chromium 3' v.3
rvm_arc_counts.tsv.gz
rvm_arc_metadata.tsv.gz
barcode-1_3


title: NC3, Cut & Tag


title: PO VS2-SIV-Treated-PBMC

value: protected

value: Before Challenge


title: CY-2

institute: Chinese Academy of Agricultural Sciences

description: ribosome footprints

value: testis

value: sexual maturity


title: Arc Morphine2

description:
10x Genomics Chromium 3' v.3
rvm_arc_counts.tsv.gz
rvm_arc_metadata.tsv.gz
barcode-1_2


title: pE7:GFP_DEX_0.1nM_2

value: 0.1 DEX nM


title: CY-1

description: ribosome footprints


title: Si2, Cut & Tag

value: Vascular Smooth Muscle


title: PO S6-SIV-Treated-PBMC


title: pE7:shy2-1:GR_DEX_0.1nM_1


title: IM S4-SIV-Treated-Monocyte

value: Monocytes-treated with SIV


title: pE7:shy2-1:GR_DEX_0.1nM_2


title: pE7:shy2-1:GR_mock_1

description: Control for DEX 0.1 nM treatment of pE7:shy2-1:GR

value: 0 DEX nM


title: IM VS1-SIV-Treated-Monocyte


title: pE7:shy2-1:GR_mock_3

description: control for DEX 0.1 nM and 1 μM treatment of pE7:shy2-1:GR


title: Si1

data_processing:
Low-quality reads were filtered out using Fastp.
The high-quality reads were then aligned to the mm10 genome using Bowtie2.
Duplicates were removed with Picard.
The peaks were identified using MACS2.
Assembly: mm10
Supplementary files format and content: bedgraph, nrrowpeak

extract_protocol:
For the ATAC-seq experiments, 50,000 cells and Hyperactive ATAC-Seq Library Preparation Kit for Illumina (Vazyme, TD711) were utilized. The cells were lysed using Lysis Buffer to isolate nuclei. Subsequently, the nuclei were incubated with Tn5 transposase at 37°C for 30 minutes to fragment the genomic DNA. The DNA was then extracted using ATAC DNA Extraction Beads.
The purified DNA was used to construct the sequencing library through PCR amplification. The size selection of the PCR products was performed through two rounds of purification using ATAC DNA Extraction Beads.

value: VSMC

value: Mouse Vascular Smooth Muscle Cells


title: NC1, Cut & Tag


title: NO N5-orginal


title: Descending 3

description:
10x Genomics Chromium 3' v.3
Descmerge1_counts.tsv.gz
Descmerge1_metadata.tsv.gz
barcode-1_3

source_name: RVM, Descending


title: Arc Control3

description:
10x Genomics Chromium 3' v.3
ArcCmerge1_counts.tsv.gz
ArcCmerge1_metadata.tsv.gz
barcode-1_3

source_name: Arc Control


title: pE7:shy2-1:GR_mock_2

description: control for DEX 1 μM treatment of pE7:shy2-1:GR


title: PO S5-SIV-Treated-PBMC


title: AB5075_c.Δ2208_rep2

city: Southampton

first: Lyuboslava

last: Harkova

address: Building 85, University Road

country: United Kingdom

institute: University of Southampton

description: 37⁰C, 180 rpm, grown to mid- exponential phase (OD600 0.7 approx.) with 1mM IPTG

data_processing:
Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (4.1.5)
Read mapping was performed with HISAT2 (2.2.0)
Read quantification was performed using Subread’s featureCounts functionality (2.0.1)
Read counts loaded into R (4.0.2) were normalized using edgeR’s (1.14.5) Trimmed Mean of M values (TMM) algorithm. Subsequent values were then converted to counts per million (cpm)
Differential expression analysis was performed using edgeR’s glmQLFTest
Assembly: NZ_CP008706.1
Supplementary files format and content: Matrix table (tab-delimited file) with raw gene counts for every gene and every sample
Supplementary files format and content: Individual tab-delimited files with normalize counts (cpm) for every sample.

organism: Acinetobacter baumannii AB5075

source_name: VIR-O colony morphology

growth_protocol: A. baumannii AB5075 (6 independent replicates) was inoculated from a pure VIR-O type stock and incubated overnight in LB (37 C, 180 rpm). Then, cultures were diluted in LB (suplemented wth acesulfame K or with a mock treatment) to OD600 0.05 and incubated at 37 C, 180 rpm until reaching mid-exponential phase (OD600 0.6 approx.).

extract_protocol:
Cultures were harvested by centrifugation and washed in RNAlater to preserve RNA integrity. RNA was isolated using athe Qiagen RNAeasy Kit with on-column DNAase digestion (Qiagen). RNA quality was assessed using a Bioanalyzer.
Samples were additionally treated with RNAse-free DNAse (Invitrogen). cDNA library was prepared with Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices.

treatment_protocol: The treatment (1.33% or a water control) was applied as a supplement in the LB medium and was present since the beginning of the growth.

value: VIR-O colony morphology


title: Si2


title: NC2


title: NO N2-orginal

value: PBMC


title: NC1


title: Descending 2

description:
10x Genomics Chromium 3' v.3
Descmerge1_counts.tsv.gz
Descmerge1_metadata.tsv.gz
barcode-1_2


title: NO N1-orginal

value: infected


title: AB5075_c.Δ2208_rep1


title: NC3


title: Si3


title: Descending 1

description:
10x Genomics Chromium 3' v.3
Descmerge1_counts.tsv.gz
Descmerge1_metadata.tsv.gz
barcode-1_1


title: Arc Control2

description:
10x Genomics Chromium 3' v.3
ArcCmerge1_counts.tsv.gz
ArcCmerge1_metadata.tsv.gz
barcode-1_2


title: Arc Control1

description:
10x Genomics Chromium 3' v.3
ArcCmerge1_counts.tsv.gz
ArcCmerge1_metadata.tsv.gz
barcode-1_1


title: IO VS5-orginal


title: AB5075_Δ2208EV_rep3


title: RVM, Reference 3

description:
10x Genomics Chromium 3' v.3
rvm_ref_counts.tsv.gz
rvm_ref_metadata.tsv.gz
barcode-1_3

source_name: RVM, Reference


title: AB5075_c.Δ2208_rep3


title: IO VS1-orginal


title: Lcn2CreErt2;Ai9, 42dpi, scRNAseq

city: Riverside

first: Emma

middle: H

last: Wilson

state: CA

address: 900 University Avenue

institute: UC Riverside

description: 10x Genomics

data_processing:
We used the Cell Range software v5.0.1 to process raw sequencing data, and then Seurat v5.0 was applied for downstream analysis.
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Whole Brain

extract_protocol:
To isolate astrocytes, brains were intracardially perfused with sterile 1x PBS at respective time points and placed in RPMI media (Gibco, 11875101) containing 1% Fetal Bovine Serum (FBS) (Corning, MT35015CV) and 25 mM HEPES. Perfused brains were transferred to a chilled 60 mm petri dish, dissociated with a razor blade, and treated with 4 ml of 0.25% trypsin. Brain suspension was digested at 37C for 30 minutes in 50 ml conical tubes. During digestion, the mixture was inverted every 5 minutes. Trypsin digestion was stopped with the addition of 30 ml of RPMI containing 20% FBS and centrifuged at 1000 RCF (g) for 5 minutes at 4C. Supernatant was decanted, and the pellet resuspended in 1% FBS RPMI to a total volume of 7 ml. The suspension was transferred to a 15 ml conical tube with 3 ml of 100% Percoll (Sigma Aldrich, P1644), gently mixed and underlaid with 1 ml of 70% Percoll made in 1% FBS RPMI. Samples were centrifuged at 2500 RCF (g) for 20 minutes at 4C. Following density separation, glial cells were harvested from the interphase and washed in 1% FBS RPMI and resuspended in FACS buffer for flow cytometry staining. To identify transcriptional astrocyte subsets, single cell RNA sequencing (scRNAseq) was performed from murine cells. To obtain a pure astrocyte sample, extracellular staining with anti-astrocyte cell surface antigen-2 (ACSA-2) was performed (Miltenyi Biotec, 130-117-535). The viability stain 7-aminoactinomycin (ThermoFischer, A1310), was added to the FACS buffer to identify dead cells. ACSA-2+ astrocytes were sorted and collected in a flow tube containing 10% FBS complete astrocyte RPMI with the Beckman Coulter MoFlo Astrios EQ Cell Sorter. For reporter experiments, sorting was performed on live cells via DAPI and tdTomato expression to collect live Lcn2CreERT2+ RAs for sequencing. A maximum of 16,000 astrocytes from each time point following the astrocyte cell suspension protocol was collected and pre-loaded on a 10X Chromium chip and Chromium controller for barcoding. Single cell RNA sequencing steps from the 10X Genomics 3' kit (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 PN-1000128) were followed according to supplier instructions to extract RNA for sequencing
Cell purity throughout preparation was verified on the Agilent 2100 Bioanalyzer following cDNA amplification and library construction. When submitting samples to the 10X Genomics Core at UCSD, 1 billion reads per sample were requested to achieve a saturation level above 90%. After sequencing, the Cell Ranger program (v5.0.1) was utilized to align reads from the sequencing fastq data files to a mouse reference genome mm10 and generate gene-barcode expression matrices. Mean reads and median genes per cell were reviewed for statistical relevance and then aligned sequences were uploaded to R (v4.3.2) package to generate plots and obtain gene statistics per cell and cluster.

treatment_protocol: To induce chronic T. gondii infection, mice were infected interperitoneally (I.P.) with the cyst forming Me49 Type II T. gondii strain. Parasites were maintained in vivo by passaging alternatively in Swiss Webster (SW) and CBA mice (JAX). Following at least three weeks post infection, brains from CBA mice were harvested, homogenized in 3ml sterile 1X Phosphate Buffered Saline (PBS) through needle passing, and cysts were counted using a 30ul aliquot and a light microscope (average cyst burden/brain ~3000). Cyst homogenate was diluted in sterile 1X PBS and 10 Me49 cysts were injected in experimental mice via 200ul I.P. injections. To selectively activate reporter fluorescence of Lcn2CreERT2+ cells at chosen time points, mice were I.P. administered 150 ug/g of tamoxifen (Millipore Sigma, T5648) diluted in corn oil at the appropriate time points prior to the respective brain collections. Mice were then scarified via IACUC approved methods. For acute infection, I.P. TAM injections start on 5 days post infection (dpi) and are given every other day until collection at 14 dpi. This timeline was decided due to astrocyte activation starting around 5 days after initial T. gondii infection. For chronic infection, Lcn2CreERT2+ RA tdTomato red fluorescent protein expression was activated with TAM treatments starting on 14 dpi and given 3 times a week (MWF) until 42 dpi. To investigate how labeled Lcn2CreERT2+ RAs may change over time following long term infection, tamoxifen-rested RAs were labeled from day 14 dpi to 42 dpi, tamoxifen was then withdrawn, and the phenotype of the labeled Lcn2CreERT2+ RAs were analyzed after two additional weeks of infection.

value: Whole Brain

tag: age

value: 6-8 weeks old

value: Astrocytes/Endothelial Cells

value: Lcn2CreERT2;Ai9 C57BL/6J

value: Toxoplasma gondii chronic infection


title: IO S4-orginal

value: Before Challenge


title: AB5075_Δ2208EV_rep1


title: sciMETv3, brain, 4 donors, Ultima UG100

city: Portland

first: Andrew

last: Adey

state: OR

address: 3181 S.W. Sam Jackson Park Rd, RHH, L103

department: MMG

institute: Oregon Health & Science University

description: Cell-level methylation calls and amethyst analysis object for Ultima-sequenced sciMETv3 dataset

data_processing:
Reads were processed using Premethyst and aligned to hg38
Methylation calls were analyzed using Amethyst
Assembly: hg38
Supplementary files format and content: Methylation calls in h5 format or a tar file with multiple h5 files included
Supplementary files format and content: Methylaiton metadata in amethyst object format, integrated with sciMETv3-only dataset

source_name: Brain BA46

extract_protocol:
Nuclei were extracted using nuclei isolation buffer and gentle dounce homogenization
sciMETv3 libraries were prepared using 3-level single-cell combinatorial indexing workflows

value: Brain BA46


status: Public on Aug 29 2024

city: Suita

first: Yukiko

last: Ueyama-Toba

state: Osaka

address: 1-6 Yamadaoka

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Osaka University

description: human liver organoid-derived hepatocyte_2_S6

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic.
Trimmed sequence reads were mapped to GRCh38 using HISAT2.
Read count extraction and nomalization were performed using samtools and featureCounts.
Supplementary files format and content: tab-delimited text file includes raw conuts for each Sample.

source_name: human liver organoid

growth_protocol: Human liver organoids culture medium was prepared according to the previous report [Huch et al., Cell, 2015]. Briefly, Advanced DMEM/F12 was supplemented with 1% Antibiotic Antimycotic Solution and 1% GlutaMAX (GIBCO), 10 mM HEPES (Nacalai Tesque), 2% B27 supplement (GIBCO), 1.25 mM N-Acetylcysteine (Sigma), 10 mM Nicotinamide (Sigma), 10 nM recombinant gastrin (Merk), 50 ng/ml EGF (R&D), 10% R-Spondin1 conditioned medium (homemade), 100 ng/ml recombinant human FGF10 (PeproTech), 25 ng/ml recombinant human HGF (R&D), 5 M A83-01 (Wako), and 10 M Forskolin (Wako). During cultivation, medium was refreshed every three days. For the establishment of human liver organoids, the medium was supplemented with 25 ng/ml recombinant Noggin (R&D), 7.5 ng/mL recombinant Wnt3a (R&D) and 10 M Y27632 (Wako) for the first 3-4 days. Passage was performed in a 1:3 split ratio once every 10–14 days. Human liver organoids passaged for 3-15 times were used in all experiments.

extract_protocol:
RNA was extracted using RNeasy Mini Kit.
According to the manufacturer's instructions, library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA). Libraries were converted to libraries for DNBSEQ using MGIEasy Universal Library Conversion Kit (App-A).

treatment_protocol: human liver organoids-derived hepatocytes; Human liver organoids were collected and incubated in TrypLE select at 37°C for 7–10 min to dissolve the Matrigel. After incubation, the cells were pipetted up and down to dissociate organoids into single cells. The cell suspension was filtered through a 40-μm cell strainer (Corning). The suspension was centrifuged at 2000 rpm for 5 min at room temperature. The cells were seeded at 2.0x105 cells/cm2 in hepatocyte culture medium (HCM; Lonza) on collagen-coated 48-well plates (IWAKI), and cultured with HCM supplemented with 10 M Y27632, 2 M SB431542, 0.5  M PD0325901, and 50 ng/mL BMP7 for 3 days. From days 3 to 6, the cells were cultured in HCM containing 10 M Y27632, 2 M SB431542, 0.5 M PD0325901, and 100 ng/mL FGF19. Finally, from day 6 to day 9, the cells were cultured with HCM supplemented with 10 M Y27632, 2 M SB431542, 0.5 M PD0325901, 100 ng/mL FGF19, and 10 M DEX. The resulting cells were named Org-HEPs.

tag: individual

value: donor 2

value: human liver organoid

value: liver organoid-derived hepatocyte

value: hepatic differentiation


title: human liver organoid_2

description: human liver organoid_2_S5

value: cultured cell

value: control


title: Intact mandible, An2 (Replicate 2)

city: Dresden

first: Tatiana

last: Sandoval-Guzmán

state: Saxony

address: Fetscherstrasse 74

department: Department of Internal Medicine III, Center for Healthy Aging, Medical Faculty Carl Gustav Carus

institute: Technische Universität Dresden

data_processing:
Generated lower jaw reads and the downloaded limb fastq files were trimmed of adapter sequences and low quality bases via the programs cutadapt (https://journal.embnet.org/index.php/embnetjournal/article/view/200) and fastq_quality_filter from the FASTX-Toolkit (Hannon, G.J. (2010) FASTX-Toolkit. http://hannonlab.cshl.edu/fastx_toolkit), respectively. The reads were then mapped against the current axolotl reference genome (www.axolotl-omics.org, AmexG_v6.0-DD), using HISAT2 ver. 2.2.1 (Pertea et al., 2015) with standard parameters and a known-splicesite-infile created from the current axolotl annotation file (AmexT_v47-AmexG_v6.0-DD.gtf) via the hisat2_extract_splice_sites.py command. Reads aligned with an average mapping rate of 96.02% for the jaw and 78.06% for the limb. Transcript quantification was then conducted using StringTie (Pertea et al., 2015) with standard parameters and the option of assembling novel transcripts. Finally, normalized CPM values for each sample were calculated using the Bioconductor package edgeR (Robinson et al., 2009) for R.
Assembly: AmexG_v6_DD
Supplementary files format and content: tab-delimited text files include CPM values for each sample
Supplementary files format and content: tab-delimited text files include raw count values for each sample

organism: Ambystoma mexicanum

source_name: Intact mandible

extract_protocol:
RNA extraction was performed using RNAeasy Mini Kit according to the manufacturer's instructions. Samples were disrupted and homogenized using the NG010 Tissue Grinder Mixy Professional (NIPPON Genetics) in 600 µl of RLT Buffer containing β-mercaptoethanol (M625, Sigma). Extracted RNA was stored at -80 until processed for sequencing.
RNA sequencing libraries were prepared using NEBNext Ultra II Directional RNA Lib Prep (Biomek i7) with estimated fragment sizes of 300 - 400 bp. Poly-dT pull down enrichment of mRNA was performed before sequencing 101 bp paired-end reads on an Illumina NovaSeq 6000 (Illumina), generating between 37 and 57 million read pairs per sample.

treatment_protocol: The mandible (lower jaw) of 12 cm ST long juvenile d/d axolotls was resected to create a 5 mm defect in the  paramedial left side. Tissue was collected at intact (0 dpa)5-, 14-, and 35 days post-amputation (dpa). 2 mandibles (biological replicates) were used per time point for sequencing.

tag: tissue

value: Intact mandible

tag: time point

value: Intact

tag: size

value: 12 cm snout-to-tail (ST)

value: DD

value: 5 mm of intact mandible


title: Patient 1

type: genomic

city: Liège

first: Maria

middle: Valeria

last: Freire

address: Av. Hippocrate 1/11

department: Human Genetics

country: Belgium

institute: Uliege

description:
ch1: patient, ch2: control
Agilent, ISCA CGH 180K+SNP (AMADID 029830)

hyb_protocol: Prepare the 10× Blocking Agent. Prepare labeled gDNA for hybridization. Prepare the hybridization assembly. Hybridize.

scan_protocol: Put assembled slide holders into the scanner cassette. Select Protocol AgilentG3_CGH for G3 microarrays. Select Protocol  AgilentHD_CGH for HD microarrays. Verify that the Scanner status in the main window says Scanner Ready. Click Start Scan.

data_processing:
After scanning is completed, extract features and analyze. Feature extraction is the process by which data is extracted from the scanned microarray image (.tif) and translated into log ratios, allowing researchers to identify aberrations in their samples. Agilent provides Feature Extraction software as a standalone program and as an integral part of CytoGenomics software (Windows version only).
Set up Analysis Workflow in the CytoGenomics program to analyze your data. You can use the Agilent Euro Female or Agilent Euro Male files as the Reference. The dbSNP141 files contain all of the active SNP probes of the Euro files, plus 50,000 new probes.

source_name: Blood from cancer patient

label_protocol: Spin the samples in a centrifuge for 1 minute at 6,000 × g to drive the contents off the walls and lid. Add Random Primers.  Set the thermal cycler to run the program. Transfer the plate or tubes into the thermal cycler, and then start the program. Remove the samples from the thermal cycler. Spin the samples in a centrifuge for 1 minute at 6,000 × g to drive the contents off the walls and lid. Mix the components on ice in the order indicated to prepare one cyanine-3 and one cyanine-5 Labeling Master Mix. Add 19 μL (or 21 μL) of Labeling Master Mix to each reaction tube containing the gDNA to make a total volume of 50 μL. Mix well by gently pipetting up and down. Set the thermal cycler to run the program. At the end of the thermal cycler program, remove the samples from the thermal cycler. Spin them briefly in a centrifuge to drive the contents off the walls and lid. Put samples on ice.

extract_protocol: DNA extracted and purified by different methods (extraction on Qiagen columns and purification on Amicon columns, extraction with DNA extractor robots [STARLET, QIACube]). The sample is measured (BMO.NANO.APP or BMO.QB.APP) and diluted in Nuclease Free water to obtain the desired final concentration in an amber Eppendorf: generally 500-400ng or 200ng depending on the protocol used in a volume of 20.2µL for 180K Agilent method chips and in a volume of 10µL for 60K ENZO method chips. At the same time, a “control” sample is prepared for each patient using the same process as the “patient” sample (same concentration, same sex).

tag: gender

value: Male

value: cancer

source_name: Agilent control


title: RVM, Reference 1

description:
10x Genomics Chromium 3' v.3
rvm_ref_counts.tsv.gz
rvm_ref_metadata.tsv.gz
barcode-1_1

value: Rostral ventromedial medulla

value: Neuron


description: human liver organoid-derived hepatocyte_1_S3

value: donor 1

tag: cell line


title: Lcn2CreErt2;Ai9, Tamoxifen Rested, scRNAseq

description: 10x Genomics

value: Whole Brain

value: 6-8 weeks old

tag: cell type

value: Astrocytes/Endothelial Cells

value: Lcn2CreERT2;Ai9 C57BL/6J

value: Toxoplasma gondii chronic infection


title: Regenerating mandible, 5 dpi, An2 (Replicate 2)

source_name: Regenerating mandible

value: Regenerating mandible

value: 5 days post-injury

tag: genotype

value: Paramedial mandible resection (5 mm)


title: Regenerating mandible, 35 dpi, An2 (Replicate 2)

value: 35 days post-injury

tag: treatment


title: Regenerating mandible, 35 dpi, An1 (Replicate 1)

value: 12 cm snout-to-tail (ST)


title: Regenerating mandible, 5 dpi, An1 (Replicate 1)

value: DD


title: Regenerating mandible, 14 dpi, An1 (Replicate 1)

value: 14 days post-injury


title: Patient 9

description:
ch1: patient, ch2: control
Agilent, ISCA CGH 60K (AMADID 031746)

value: Male


title: Patient 7

value: Female

value: cancer


title: Regenerating mandible, 14 dpi, An2 (Replicate 2)


title: RVM, Reference 2

description:
10x Genomics Chromium 3' v.3
rvm_ref_counts.tsv.gz
rvm_ref_metadata.tsv.gz
barcode-1_2

value: Rostral ventromedial medulla

value: Neuron


title: Patient 8


title: Patient 5


title: Patient 3


title: Patient 4


title: Patient 6


title: Patient 2


title: Lcn2CreErt2;Ai9, 14dpi, scRNAseq

description: 10x Genomics

value: Whole Brain

value: Toxoplasma gondii acute infection


title: AC1P, 72hr, 3

city: Berkeley

first: Joshua

last: Tworig

address: Weill Hall, Frank Schlessinger Way

department: Molecular and Cell Biology

institute: University of California, Berkeley

data_processing:
Reads were aligned to the human genome via Hisat2 with default parameters.
Genomic features were counted using Subread featurecounts with default parameters.
Assembly: Homo sapiens GRCh38.84
Supplementary files format and content: Individual CSV file for each sample contains raw counts.

molecule: polyA RNA

growth_protocol: HEK293 cells were maintained in suspension in Expi293™ expression medium on an orbital shaker (125 rpm,19 mm orbital throw) in a 37°C, 5% CO2 incubator.

extract_protocol:
Total RNA was extracted from cell pellets before and during AAV production. RNA was extracted using Direct-zol-96 RNA Kit.
mRNA libraries were constructed by SeqMatic using the Illumina Stranded mRNA prep kit.

treatment_protocol: HEK293 cells were resuspended in fresh Expi293™ expression medium at a density of 2.5M/ml and triple-transfected with TransIT-VirusGEN and a pHelper plasmid, a RepCap9 plasmid and an ITR containing reporter plasmid.

value: WT, polyclonal

value: 72hr post-transfection


title: human liver orgnaoid_1

description: human liver organoid_1_S2

value: donor 1

value: human liver organoid

value: cultured cell

value: control


title: AC1P, 72hr, 1


title: AC1P, 72hr, 2


title: No Template Control 2

city: Jefferson

first: Elijah

middle: F

last: Edmondson

state: MD

address: 4310 Mountville Rd

institute: Frederick National Laboratory for Cancer Research

description: FFPE (v1.0) Mouse NGS Whole Transcriptome Atlas RNA

data_processing:
Raw data was evaluated in R (version 4.1.2). ROI segment and probe quality control (QC) was performed according to NanoString’s Whole Transcriptome Atlas Normalization guidelines. ROI QC was performed using the GeomxTools (V3.2.0) package. ROIs were flagged using the following settings: raw reads threshold 1000 reads, percent trimmed 80%, percent stitched 80%, percent aligned reads 80%, percent sequencing saturation 50%, negative probe count geomean 1, no template PCR control count > 60, minimum nuclei 20, and minimum surface area of 1000 µm². Of the 190 AOIs, one was flagged for a low negative probe count and low sequencing alignment. Probe QC was performed with default settings excluding probes from target count calculation in all segments if (geomean probe in all segments)/(geomean probes within target) ≤ 0.1 and if it fails Grubbs’ outlier test in ≥20% of the segments. The limit of quantification (LOQ) was calculated using two SDs of the geomean of the negative probes. Quartile 3 count (Q3) normalization was performed to account for technical effects between AOIs. Gene filtering was used to filter and select only genes detected in at least 10% of AOIs. Following QC, the resulting gene expression matrix consisted of 189 AOIs that passed QC and a total of 14,882 genes. Q3-normalised expression data was exported from the DSP Analysis Suite. Dimension-reduction of the expression matrix was performed using t-Distributed Stochastic Neighbor Embedding by R package Rtsne (V.0.16), umap (V.0.2.10.0), and visualized using ggplot2 (V.3.4.3).
Sequences were aligned to mm10 genome using Space Ranger default settings
Assembly: mm10
Supplementary files format and content: Mm_R_NGS_WTA_v1.0.pkc
Library strategy: Spatial Transcriptomics

organism: blank sample

source_name: blank sample

extract_protocol:
Slides were processed within 5 days after the microtomy for the NanoString GeoMx DSP RNA assay following the GeoMx NGS Slide Preparation User Manual (NanoString, MAN-10 115-04). After 30 min baking at 60oC, dewaxing, heat-induced epitope retrieval (ER2 for 20 min at 100oC) and proteinase K treatment (1 mg/mL proteinase K in 1X phosphate-buffered saline (PBS) at 37°C for 15 min) was performed on Leica Biosystems BOND RX according to the FFPE RNA Slide Preparation Protocol. Slides were hybridized with the GeoMx Whole Transcriptome Atlas Mouse RNA for Illumina Panel (GMX[1]RNA-NGSMsWTA) overnight at 37oC, followed by a series of stringent washes and morphology staining: Syto 13 for nuclei, pancytokeratin- AF532 to visualize epithelial cells and smooth muscle actin (aSMA-AF647) to visualize stroma. The staining was visualized on the GeoMx DSP instrument using a 20X objective on FITC, CY3, Texas Red and CY5 channels. A total of 190 regions of interest (ROI) were selected from 13 mouse uterus sections (6 Thra1 PV/+ and 7 wild-type mice), which included endometrial mucosa, glands, and stroma; a minimum of 5 ROIs were taken per category per mouse. Annotations were selected by a board-certified veterinary pathologist based on morphology and marker staining using HALO (Indica Labs). ROI masks were imported to the GeoMx and used to guide UV light cleavage of the barcode linkers of the prebound RNA probes in each area of illumination, and the cleaved probes were deposited in DSP collection plates.
Library construction and sequencing (NextSeq2000) was performed according to Nanostring’s Guidelines at the Genomics Core (OSTR, CCR). Processed data was uploaded to the DSP analysis suite for visualization and quality control while detailed data analysis was performed using an R-package from Nanostring.

value: blank sample


title: 293F, 72hr, 2

value: WT


title: Intact mandible, An1 (Replicate 1)

value: Intact mandible

value: Intact

value: 12 cm snout-to-tail (ST)

value: DD

value: 5 mm of intact mandible


title: No Template Control 1


title: AC1.203, 72hr, 3

value: WT, clonal


title: 293F, 72hr, 1


title: AC1.203, 72hr, 2


title: AC1.112, 72hr, 3


title: AC1.203, 72hr, 1


title: AC1.230, 72hr, 3


title: AC1.112, 72hr, 2


title: AC1.230, 72hr, 2


title: AC1P, 24hr, 3

value: 24hr post-transfection


title: AC1P, 24hr, 1


title: AC1.230, 72hr, 1


title: 293F, 24hr, 1


title: 293F, 24hr, 2


title: AC1P, 24hr, 2


title: AC1.203, 24hr, 3


title: 293F, 72hr, 3


title: AC1.203, 24hr, 2


title: AC1.112, 24hr, 3


title: AC1.112, 24hr, 1


title: AC1.203, 24hr, 1


title: AC1.112, 24hr, 2


title: AC1.230, 24hr, 2


title: AC1.112, 72hr, 1


title: AC1P, 0hr, 2

value: pre-transfection


title: AC1P, 0hr, 1


title: 293F, 0hr, 2


title: AC1.230, 24hr, 1


title: 293F, 0hr, 1


title: AC1.203, 0hr, 3


title: AC1.203, 0hr, 1


title: AC1.112, 0hr, 3


title: AC1.203, 0hr, 2


title: AC1.230, 24hr, 3


title: AC1.112, 0hr, 1


title: AC1.230, 0hr, 3


title: 293F, 24hr, 3


title: AC1.230, 0hr, 2


title: AC1.112, 0hr, 2


title: AB5075_Δ2208EV_rep2

value: VIR-O colony morphology


title: 293F, 0hr, 3


title: AC1.230, 0hr, 1


title: AC1P, 0hr, 3

value: WT, polyclonal


title: HaCaT cells, FGFR2 KO, rep3

city: ZÜRICH

first: Luca

last: Ferrarese

state: Zürich

address: Otto-Stern-Weg 7, HPL F23.2

department: Institute of Molecular Health Sciences (IMHS)

country: Switzerland

institute: ETH Zürich

data_processing:
The raw reads were first cleaned by removing adapter sequences and poly-x sequences (> 9 nt used for detection) using fastp (Version 0.20.0) [fastp].
Sequence pseudo alignment of the resulting high-quality reads to the Human reference genome (build GRCh38.p13) and quantification of gene level expression (gene model definition from GENCODE release 37) was carried out using Kallisto (Version 0.46.1) [Kallisto].
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: HaCaT cells

growth_protocol: Low-passage HaCaT keratinocytes (Boukamp et al., 1988) were cultured in high-glucose Dulbecco’s Modified Eagle Medium® (DMEM, Thermo Fisher Scientific, Waltham, MA) supplemented with 10% FBS (Life Technologies, Carlsbad, CA) under standard conditions at 37°C with 5% CO2.

extract_protocol:
Cells were lysed in RB lysis buffer, and stored at -80°C until further use. RNA extraction was performed using the Mini Total Tissue RNA kit (IBI Scientific, Dubuque, IO), including a DNase digestion step.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA (Illumina, Inc, California, USA) following manufacturer's protocols.

value: HaCaT cells

value: Keratinocyte

value: FGFR2 KO


title: TAMs_EVs_rep3

city: Chengdu

first: Tian

last: Lan

state: Sichuan

address: No. 37 of Guoxue Lane

department: Department of Liver Surgery & Liver Transplantation

institute: West China Hospital

description: circRNA expression profile of EVs from TAMs

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

scan_protocol: Raw images were obtained using Agilent Scanner G5761A (Agilent).

data_processing: Raw data were extracted using Feature Extraction (Agilent), followed by normalization using the quantile algorithm, Genespring (Agilent). Limma package in R (v.3.2.2) was employed to compare the differential expressions of circRNAs and mRNAs between matched profiles, followed by false discovery rate (FDR) correction using Benjamini and Hochberg’s approach.

source_name: EVs

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA of macrophages and HCC cells was extracted and purified using a RNeasy Maxi kit (Qiagen) according to the manufacturer’s instructions. EVs-derived RNA extraction was performed using exoRNeasy Maxi kit (Qiagen) according to the manufacturer’s instructions. The purity, concentration and integrity were analyzed using NanoDrop ND-2000 (Thermo) and Agilent Bioanalyzer 2100 system (Agilent).

value: tumor-associated macrophages

tag: intervention

value: from TAMs


title: TAMs_EVs_rep2


title: C4, HWG

first: Xin

last: Wang

institute: Sichuan Agricultural University

data_processing:
To preprocess the sequencing data, the fastp software was employed to remove reads containing adaptor contamination, low-quality bases, and undetermined bases, using the default parameters. The reads were then mapped to the reference genome of the Sichuan white goose (GCA_002166845.1) using HISAT2. After the final transcriptome was generated, StringTie was used to estimate the expression levels of all transcripts, and FPKM was calculated as a measure of mRNA expression level. Differentially expressed mRNAs were identified based on a fold change > 1.5 or fold change < 0.5, and statistical significance was determined using a parametric F-test comparing nested linear models (p-value < 0.05) with the R package edgeR. Finally, both Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis were performed using DAVID software (https://david.ncifcrf.gov/).
Assembly: The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters.
Supplementary files format and content: Excel file includes FPKM values and raw counts for each Sample

organism: Anser cygnoides

source_name: jejunum

extract_protocol:
Total RNA was extracted and purified using Trizol reagent (Invitrogen, USA) following the manufacturer's procedure. The quantity and purity of each RNA sample were determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop, USA). RNA integrity was assessed using the Bioanalyzer 2100 system (Agilent, USA), ensuring a RIN number >7.0, and confirmed by denaturing agarose gel electrophoresis.
Then the poly(A) RNA was fragmented into small pieces using 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 is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads.

value: jejunum

value: HWG

value: received a diet containing 43.6% wheat germ


title: C3, HWG


title: TAMs_EVs_rep1


title: MDMs_EVs_rep3

description: circRNA expression profile of EVs from MDMs

value: monocyte-derived macrophages

value: from MDMs


title: HaCaT cells, FGFR2 KO, rep2


title: C1, HWG


title: MDMs_EVs_rep1


title: MDMs_rep3

description: circRNA expression profile of MDMs

source_name: macrophages

value: from human peripheral blood


title: HaCaT cells, WT, rep3

value: WT


title: TAMs_rep3

description: circRNA expression profile of TAMs

value: from human HCC tissues


title: HaCaT cells, FGFR2 KO, rep1


title: MDMs_rep1

description: circRNA expression profile of MDMs


title: Bird_SEM19-107_MG-protein_Day0

city: Fayetteville

first: Carson

middle: Len

last: Stacy

state: AR

address: 850 W. Dickson St. Rm 601

department: Biological Sciences

institute: University of Arkansas

description:
ES97_SEM19-107_MG-protein_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

data_processing:
nf-core rnaseq version 3.10.1 pipeline was utilized with Nextflow version 22.10.3 [parameters: -profile singularity  --featurecounts_group_type transcript_biotype --skip_markduplicates --aligner star_rsem --pseudo_aligner salmon]
Adapter trimming performed with TrimGalore! v 0.6.7 [parameters: nf-core default]
Mapping to genome performed with STAR v 2.7.10a  [parameters: nf-core default]
Counts estimated from genes with RSEM v 1.3.1 [parameters: --strandedness reverse]
Differential expression was performed in EdgeR using expected counts and the quasi-liklihood (QL) framework with Benjamini-Hochberg FDR correction. Genes with less than 0.5 count per million (CPM) in more than 12 samples were excluded from the analysis.
Assembly: serCan2020
Supplementary files format and content: All files are tab delimited text files. One file is the STAR-RSEM gene count output (serinus_canaria_rsem.merged.gene_counts.tsv) and the other is the STAR-RSEM gene tpm values (serinus_canaria_rsem.merged.gene_tpm.tsv)

organism: Serinus canaria

source_name: Whole blood

growth_protocol: Canaries were housed individually in cages and provided with either a high protein (n = 20) or high lipid (n = 22) diet for 17 days prior to inoculation and throughout the experiment. On day 0, birds were inoculated in the palpebral conjunctiva of both eyes with either 0.025 mL of MG suspended in Frey’s media or with a sham of Frey’s media alone.

extract_protocol:
Zymo Direct-zol RNA Miniprep with TRI Reagent phase separation
NEXTflex™ Rapid Directional RNA-Seq Kit 2.0

treatment_protocol: RNAlater was added to blood samples immediately upon collection. Samples were stored at 20°C for 24 hr then at -80°C until extraction. Canary RNA was extracted from whole blood on days 0, 14, and 21 post infection

value: Whole blood

tag: subject

tag: time

value: Day 0

tag: disease

value: Unexposed

value: High protein diet


title: Bird_SEM19-107_MG-protein_Day21

description:
ES99_SEM19-107_MG-protein_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Day 21

value: Exposed


title: Bird_172_Control-protein_Day0

description:
ES9_172_Control-protein_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_SEM19-107_MG-protein_Day14

description:
ES98_SEM19-107_MG-protein_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Day 14


title: MDMs_rep2

description: circRNA expression profile of MDMs


title: Hep3B_TAMs_rep3

description: circRNA expression profile of Hep3B cells

source_name: HCC cells

value: Hep3B cells

value: co-culture with TAMs


title: B4, LWG

value: jejunum

value: LWG

value: received a diet containing 21.8% wheat germ


title: MDMs_EVs_rep2

value: monocyte-derived macrophages


title: C2, HWG

value: HWG

value: received a diet containing 43.6% wheat germ


title: TAMs_rep1

description: circRNA expression profile of TAMs

value: tumor-associated macrophages


title: Hep3B_TAMs_rep2


title: Bird_610_MG-protein_Day21

description:
ES96_610_MG-protein_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: B3, LWG


title: Hep3B_alone_rep3

value: cultured alone


title: Hep3B_alone_rep1


title: Hep3B_alone_rep2


title: Bird_610_MG-protein_Day14

description:
ES95_610_MG-protein_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Whole blood


title: Hep3B_TAMs_rep1


title: B2, LWG


title: Bird_SEM19-76_MG-lipid_Day14

description:
ES93_SEM19-76_MG-lipid_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: high lipid diet


title: PF_WM_ALSP

city: Stanford

first: JAUME

last: FORES MARTOS

state: California

address: 300 Pasteur Drive

department: Pathology

institute: Stanford

data_processing:
The paired-end raw sequence reads were preprocessed using the Kallisto bustools package (kbpython:0.26.0). An alignment index was constructed based on the human reference pre-mRNA (GRCh38, Ensembl 105).  Using the Lamanno workflow, we generated separate count matrices for spliced and unspliced transcripts. These matrices were then merged to obtain the total nucleus count matrix. Downstream analysis, including quality control, integration, cell type annotation, and differential gene expression, was performed using the nuclear transcript counts. Empty droplets were removed by comparison with ambient RNA levels using the DropletUtils package. Droplets with FDR <0.05 were removed, and 80,864 non-empty droplets were retained. To identify potential doublets, we used the DoubletFinder package version 4.2. An average doublet rate of 2.53% per sample was detected. The identified doublets were labeled and retained during batch correction and data integration. Following clustering and major cell type annotation, we identified two clusters of doublets based on high doublet scores and the presence of markers specific to more than one major cell type. These clusters, containing 721 nuclei, were excluded from downstream analysis. Four additional clusters driven by low gene count nuclei, containing 15,668 nuclei, were also excluded from the analysis. We used Scanpy version 3.9.1 to analyze raw count data. First, nuclei expressing less than 100 genes were removed from the analysis. Counts were normalized and log transformed. Highly variable genes were identified using default parameters and a dispersion threshold of 0.5. Principal Component Analysis (PCA) was applied to reduce dimensionality, and the first 50 principal components were computed. Samples were integrated using Harmony with the Donor used as batch effect. After integration, the neighborhood graph was computed employing 20 PCs and 15 neighbors. Clustering was carried out employing the Leiden algorithm with a resolution parameter of 1.0. Marker genes for each cluster were determined using the Wilcoxon rank sum test with a significance threshold of adjusted p-value (padj) < 0.05. We then applied a more stringent cutoff of 400 for the minimum number of UMIs per nuclei. The final integrated dataset included 58,447 nuclei (8,724 neuronal and 49,723 non-neuronal) for downstream analysis.
Assembly: GRCh38, release-105
Supplementary files format and content: Raw counts, normalized counts, metadata, dimensionality reduction, integration and clustering, cell-type annotations

source_name: Prefrontal cortex

extract_protocol:
We isolated nuclei from fresh-frozen brain tissue blocks obtained from the ALSP donor (white and gray matter from prefrontal cortex, and white matter from medial temporal lobe, parietal cortex, and occipital cortex), and controls (white and gray matter from prefrontal cortex). The gray or white matter was dissected under a stereomicroscope, and then chopped it into small pieces (< 1 mm³) with a chilled razor blade. For tissue homogenization, a Kimble Kontes all-glass tissue grinder was utilized (Kimble, 885300-0007). Each tissue sample was dissociated using 2.4 mL of homogenization buffer containing 10 mM Tris pH 8, 5 mM MgCl2, 25 mM KCl, 250 mM sucrose, 1 μM DTT, 0.5x protease inhibitor (cOmplete, Roche #4693159001), 0.2 U/μL RNase inhibitor, and 0.1% Triton X-100. The homogenates were subsequently filtered through a 40-μm cell strainer, transferred into 1.5-mL Eppendorf tubes, and centrifuged at 1000 ×g for 8 minutes at 4°C. The supernatant was aspirated and discarded, and the pellets were resuspended in 450 μL of cold homogenization buffer. Further clean-up was carried out using iodixanol gradient centrifugation. An equal volume (450 μL) of 50% v/v iodixanol solution (41.25 mM sucrose, 24.75 mM KCl, 4.95 mM MgCl2, 9.9 mM Tris pH 8, 50% w/v iodixanol) was added to the homogenate and gently mixed with a pipette. The mixture was then transferred to a 2-mL Eppendorf tube containing 900 μL of cold 29% iodixanol solution (129.17 mM sucrose, 77.5 mM KCl, 15.5 mM MgCl2, 31 mM Tris pH 8, and 29% w/v iodixanol) by slow layering on the top. The tubes were centrifugated at 13,500 ×g for 20 minutes at 4°C, resulting in the sedimentation of nuclei at the bottom. The supernatant and top layer of myelin and cell debris were removed and discarded. The nuclei pellets were then detached with a small amount (~50 μL) of immunostaining buffer (0.1 M PBS; pH 7.4, 0.5% bovine serum albumin [BSA], 5 mM MgCl2, 2 U/mL DNAse I, 0.2 U/μL RNase inhibitor), transferred to clean tubes, and gently resuspended in a total volume of 200 μL of immunostaining buffer. After a 15-minute incubation with immunostaining buffer at 4°C, with gentle rocking, primary antibodies (NeuN; 1:1000, Millipore cat#MAB377; and/or PAX6; 1:500, Biolegend, 901301) were added, and the suspension was further incubated for 40 minutes at 4°C with gentle rocking. Subsequently, an equal volume (500 μL) of immunostaining buffer was added, and the tubes were inverted several times before being centrifuged at 500 ×g for 5 minutes at 4°C. The supernatant was removed, and the pellets resuspended in 600 μL of immunostaining buffer. Secondary antibodies (Alexa Fluor 488, Alexa Fluor 647) and a nuclear stain (Hoechst 34580; 1:1,000 of 2.5 mg/ml stock, Invitrogen cat# H21486) were subsequently added, and the solutions incubated for 30 minutes at 4°C with gentle rocking. Microscopic evaluation of the number and morphology of the nuclei was conducted after each critical step and immediately before FANS. FANS was employed to enrich single nuclei from glia. We used a Sony SH800 cell sorter with a 100-μm microfluidics sorting chip. The primary laser, at 488 nm, was utilized for the generation of forward scatter (FSC) and back scatter (BSC). Secondary lasers emitting at 405, 488, and 638 nm were utilized to detect Hoechst 34580, Alexa Fluor 488, and Alexa Fluor 647, respectively. The FSC versus BSC gates were set with permissive limits, discarding the smallest debris and largest particles. Hoechst 34580 fluorescence was used to discriminate single nuclei from doublets and clumps. We sorted Hoechst 34580 positive singlets from ALSP white matter. For ALSP gray matter, we sorted non-neuronal (NeuN-negative) nuclei. For healthy and AD control tissue, we sorted the PAX6-positive, NeuN-negative population singlets. Nuclei were collected in collection buffer (0.1 M PBS pH 7.4, 0.1 U/μL RNase inhibitor, 1% BSA) into BSA-coated Eppendorf tubes.
snRNAseq of postmortem human brain nuclei was conducted using the 10x Genomics Chromium Single Cell 3’ v3 assay. The input single nuclear suspensions were centrifuged at 400 ×g for 5 min at 4°C to achieve a concentration of ~350 nuclei per μL, determined using a hemocytometer. On average, ~12,500 nuclei were loaded to capture around 5,000 nuclei per sample, with an expected capture efficiency of ~40%. cDNA amplification and library construction were performed following the manufacturer’s instructions. The paired-end libraries were sequenced on Novaseq 6000. A total of 12 samples were sequenced in 3 batches. For each sequencing batch, the concentration of each sample was normalized to the total number of nuclei to ensure similar numbers of reads per nucleus. Nuclei were sequenced to a depth of ~75,000 reads per nucleus.

tag: assay

tag: donor

value: ALSP

tag: brain region

value: Prefrontal cortex

tag: gray vs_white_matter

value: wm

tag: rin

tag: sort

value: DAPI

tag: braak stage

value: IV

tag: amyloid cerad

tag: pmi hr

tag: Sex

value: M

tag: read length


title: Bird_SEM19-76_MG-lipid_Day21

description:
ES94_SEM19-76_MG-lipid_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

tag: tissue

value: Day 21

value: Exposed


title: B1, LWG

value: jejunum

tag: genotype

value: LWG

tag: treatment


title: Bird_SEM19-76_MG-lipid_Day0

description:
ES92_SEM19-76_MG-lipid_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

tag: subject

value: Day 0

value: Unexposed


title: A3, Control

value: Control

value: corn-soybean meal basal diet


title: Bird_Blue-049_Control-protein_Day21

description:
ES91_Blue-049_Control-protein_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

tag: time

value: High protein diet


title: Bird_SEM19-1354_Control-protein_Day21

description:
ES8_SEM19-1354_Control-protein_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Whole blood

tag: disease


title: Bird_Blue-049_Control-protein_Day14

description:
ES90_Blue-049_Control-protein_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Day 14


title: Bird_orange-24_Control-protein_Day21

description:
ES87_orange-24_Control-protein_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: PAR_WM_ALSP

source_name: Parietal cortex

tag: assay

value: ALSP

value: Parietal cortex

tag: age


title: PF_GM_ALSP

tag: donor

tag: brain region

value: Prefrontal cortex

value: gm

value: DAPI/NeuNneg


title: A4, Control


title: Bird_610_MG-protein_Day0

description:
ES88_610_MG-protein_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_Blue-049_Control-protein_Day0

description:
ES89_Blue-049_Control-protein_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: A2, Control


title: Bird_orange-24_Control-protein_Day14

description:
ES86_orange-24_Control-protein_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_orange-24_Control-protein_Day0

description:
ES85_orange-24_Control-protein_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_LD19-239_MG-lipid_Day0

description:
ES84_LD19-239_MG-lipid_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: high lipid diet


title: A1, Control


title: HaCaT cells, WT, rep2

tag: cell line

value: HaCaT cells

tag: cell type

value: Keratinocyte

value: WT


title: MTL_WM_ALSP

source_name: Medial temporal lobe

value: Medial temporal lobe

tag: gray vs_white_matter

value: wm

tag: rin

tag: sort

value: DAPI

tag: braak stage

value: IV

value: M


title: Bird_SEM19-1481_MG-lipid_Day0

description:
ES83_SEM19-1481_MG-lipid_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Day 0

value: Unexposed


title: Bird_Blue-047_Control-lipid_Day0

description:
ES81_Blue-047_Control-lipid_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Whole blood


title: Bird_Blue-047_Control-lipid_Day14

description:
ES82_Blue-047_Control-lipid_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Day 14


title: IgG_DIP_rep3

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

institute: Institute of Molecular Biology

description: IgG DIP, replicate 3

data_processing:
Sample demultiplexing was performed using Illumina's bcl2fastq Conversion Software v.1.8.4 and read quality was checked with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Sequence reads were aligned to the Xenopus tropicalis genome assembly version 7.1 (https://ftp.xenbase.org/pub/Genomics/JGI/Xentr7.1) using weighted multi-mapping strategy employing bowtie2 v.2.2.7 (http://bowtie-bio.sourceforge.net/bowtie2) with default parameters.
Normalized bigWig coverage tracks were generated from the mapped reads extended to average fragment size using deepTools bamCoverage v.2.5.1 (https://deeptools.readthedocs.io/) with parameters “--normalizeUsing RPKM --extendReads 250”.
Assembly: Xenopus tropicalis v.7.1 (JGI7.1)
Supplementary files format and content: bigWig coverage tracks with RPKM normalization
Library strategy: DIP-seq

organism: Xenopus tropicalis

source_name: blastula stage 9 embryos

extract_protocol:
Genomic DNA from stage 9 Xenopus tropicalis embryos was extracted using the DNeasy Blood and Tissue kit (Qiagen). 15 µg DNA was sheared to around 200 bp using a Covaris S2/E210 focused ultrasonicator. 5 pg of 5mC, 5hmC, 5fC or control unmodified amplicon were spiked in and the samples were brought to 450 μl with nuclease-free water. 5% sample was kept aside as input control. DNA was denatured for 10 min at 95°C and cooled immediately on ice. Samples were incubated in IP buffer (100 mM Na-Phosphate pH 7, 1.4 M NaCl, 0.5% Triton X-100) and 3 µg antibody overnight at 4°C with overhead shaking. Antibodies used: 5mC (MAb-5MECYT-100, Diagnode), 5hmC (39791, Active Motif), 5fC (61227, Active Motif), 5caC (61229, Active Motif) and IgG (ab46540, Abcam). Dynabeads Protein G (10004D, Thermo Scientific) were pre-washed with 0.1% BSA, PBS and resuspended in IP buffer. 40 μl Dynabeads per sample were added and the samples were incubated at 4°C for 2 h with overhead shaking. Dynabeads were collected in a magnetic rack, washed 3x in IP buffer, resuspended in Proteinase K digestion buffer (50 mM Tris pH 8, 10 mM EDTA, 0.5% SDS) and Proteinase K (0.3 mg/ml final concentration) was added. Samples were incubated for 3 h at 50°C and DNA was purified with phenol/chloroform followed by ethanol precipitation.
Library preparation was performed with Swift Bioschiences's Accel-NGS 1S Plus DNA Library Kit following Accel-NGS 1S Plus DNA Library Kit Reference Guide (15-0300, 08/15). Libraries were profiled in a High Sensitivity DNA chip on a 2100 Bioanalyzer (Agilent Technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life Technologies). All samples were pooled in equimolar ratio and sequenced on 4 HiSeq 2500 Rapid Flowcells, SR mode with 59 cycles plus 2x8 cycles for dual index reads.

value: blastula stage 9 embryos

tag: dip antibody

value: IgG


title: Bird_SEM19-1354_Control-protein_Day14

description:
ES7_SEM19-1354_Control-protein_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

tag: tissue

value: High protein diet


title: IgG_DIP_rep2

description: IgG DIP, replicate 2


title: NMP_050, POST, TP [268_S209]

city: Innsbruck

first: Theresa

last: Hautz

address: Anichstr. 45

department: Department of Visceral, Transplant and Thoracic Surgery

institute: Medical University of Innsbruck

data_processing:
Adapters were trimmed using BBDuk according to recommendations (Lexogen, Austria) and quality checked using FastQC.
Reads were mapped to the human reference genome (GRCh38/hg38) using the splice aware aligner STAR (v2.7.1a). Note, since  the specific 3'  sequencing libraries used here, only forward reads were mapped and all reverse reads were discarded since provide only limited information.
Read counts for NCBI Gene/Refseq annotation were detrmined using featureCounts (v2.0.0)
Differentially expressed genes were determined using DESeq2 based on raw counts and a negative binomial distribution
Data were normalized using DESeq2 and log-transformed (rlog).
Assembly: hg38
Supplementary files format and content: tab delimited txt file include raw counts for each sample (raw_counts.txt)
Supplementary files format and content: tab delimited txt file include log2 transformed normalized counts adding a pseudocount of 1 (DESeq2) for each sample (log2_normalized_counts_1.txt)

source_name: liver

extract_protocol:
Cryopreserved liver biopsies were homogenized using the ULTRA Turrax IKA T10 basic. Total RNA was extracted according to the Rneasy Micro Kit (Qiagen, Netherlands). RNA integrity was determined using a 2100 Bioanalyzer and RNA 6000 Nano LabChip kits (Agilent Technology, USA).
QuantSeq 3'protocol (Lexogen, Austria) according to manufacturers's recommendations

treatment_protocol: Grafts were flushed with 2000 ml histidin-tryptophan-ketoglutarate, surgically prepared for NMP and connected to the OrganOc metra® device.

value: liver

tag: transplantation

value: yes

value: POST

value: normothermic machine perfusion


title: Bird_Blue-050_Control-lipid_Day14

description:
ES80_Blue-050_Control-lipid_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

tag: treatment

value: high lipid diet


title: NMP_045, POST, TP [265_S207]


title: IgG_DIP_rep1

description: IgG DIP, replicate 1


title: Bird_Blue-043_MG-lipid_Day21

description:
ES78_Blue-043_MG-lipid_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

tag: subject

value: Day 21

value: Exposed


title: Bird_Blue-043_MG-lipid_Day14

description:
ES77_Blue-043_MG-lipid_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

tag: time


title: OCC_WM_ALSP

source_name: Occipital cortex

value: ALSP

value: Occipital cortex

value: wm

value: DAPI

tag: amyloid cerad

tag: pmi hr

tag: Sex

tag: read length


title: Bird_Blue-050_Control-lipid_Day0

description:
ES79_Blue-050_Control-lipid_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Day 0

tag: disease

value: Unexposed


title: Input_DIP_rep3

description: Input DNA, replicate 3


title: NMP_039, POST, TP [261_S205]


title: NMP_040, POST, TP [262_S206]


title: Bird_Blue-042_MG-protein_Day21

description:
ES75_Blue-042_MG-protein_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Whole blood


title: Input_DIP_rep2

description: Input DNA, replicate 2

value: blastula stage 9 embryos


title: NMP_038, POST, TP [260_S204]


title: Bird_Blue-042_MG-protein_Day14

description:
ES74_Blue-042_MG-protein_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Day 14