title: 8_305123V03-0_Naive

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

description: Library name: 8_305123V03-0_Naive

data_processing:
Sequencing data was demultiplexed using Illumina bcl2fastq version 2.20.0.422 BCL to FastQ file converter. The quality of raw reads was assessed with FastQC version 0.11.8.
Reads were aligned using the STAR aligner (v2.4.2a)
Abundance estimation was done with HTSeq (v0.6.1)
Assembly: GRCh38.p7
Supplementary files format and content: Tab delimited text with raw read counts of samples in columns for annotated transcripts in rows.

source_name: Blood

extract_protocol:
Cells were sorted on a FACS Aria III (BD, Franklin Lakes, NJ). Markers used for sorting are shown in supplementary table 3. Cells were sorted into CD4+ Tnaive (CCR7+CD45RA+), TEM (CCR7-CD45RA-), and TCM (CCR7+CD45RA-) subsets. Total CD4+ T cells refers to data combining normalized gene expression from these subsets. An average of 15,000 cells were sorted at 4° C into RNAse-free eppendorf tubes containing RPMI. Cells were then centrifuged at 600 x g for 10 minutes and supernatant was removed. 350uL RLT buffer (Qiagen, Hilden, Germany) plus 1% BME was added, and cells were vortexed for 1 min. Cells were lysed in 350 μL of Buffer RLT and then extracted using the RNeasy Micro kit (Qiagen) with on-column DNase digestion.
RNA quality was assessed using a Bioanalyzer 2100 (Agilent) and then 500 picograms of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed barcodes using the Nextera XT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on a TapeStation 4200 (Agilent), pooled at equimolar concentrations, and sequenced with SE100 reads on an Illumina NovaSeq 6000, yielding ~25 million reads per sample on average.

value: Blood

value: CD4 T cell

tag: cell subset

value: Naive

value: male

tag: days post_esitimate_date_of_infection

tag: log10 viral_load


title: RNA-Seq of Leptinotarsa decemlineata: fat body female Sample2

status: Public on Jan 07 2025

type: SRA

city: Mainz

first: Shuqing

last: Xu

address: Hanns-Dieter-Hüsch-Weg 15

country: Germany

institute: University of Mainz

description: Library name: FbF2

library_source: transcriptomic

data_processing:
Trimmomatic was used to remove the Illumina adapters, drop the reads with a low quality or a short length (SLIDINGWINDOW:4:15 MINLEN:36) and remove the first ten bases of the reads (HEADCROP:10). To assess the quality both before and after this filtering process, we utilized FastQC (v0.11.9, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The reads were mapped to a chromosome-level genome assembly 31 using STAR 35 (version 2.7.8a). FeatureCounts (Subread 2.0.5) was used to count the reads mapped to the annotated genes, with the parameters "-p –countReadPairs" which indicates that the reads are paired. The genes that were not expressed were filtered out based on their transcript per million (TPM) values. We kept only the transcript having a TPM value above one in at least two samples (https://github.com/Xu-lab-Evolution/CPB_gene_expression_atlas/blob/main/TPMfiltration.R).
Assembly: JANJPO000000000, https://cpb-atlas.uni-mainz.de/media/genome_annotation/Leptinotarsa_decemlineata_01.fa
Supplementary files format and content: tab-delimited text file includes counts in transcript per million (TPM) information for each gene and each Sample

molecule: total RNA

organism: Leptinotarsa decemlineata

source_name: testis

growth_protocol: The insects were maintained in a climate chamber with 24°C, 70% humidity and a photoperiod of 16 h light and 8 h dark per day. Larvae as well as adults were fed with leaves from organically grown potato plants (Annabelle variety, purchased from Ellenberg´s Kartoffelvielfalt GmbH & Co. KG, Barum, Germany).

extract_protocol:
RNA was extracted using the RNeasy Mini kit from Qiagen (Venlo, The Netherlands), following the manufacturer’s protocol. Lysis was performed with micro pestles.
For RNA-seq library preparation, the Novogene NGS RNA Library Prep Set (PT042) was used. The magnetic beads of oligos d(T)25 were used to enrich the mRNA. Subsequently, mRNA was randomly fragmented and cDNA synthesis was carried out using random hexamers and the reverse transcriptase enzyme. The second chain was synthesized with the addition of an Illumina buffer (non-directional library preparation). The resulting products were purified, end-repaired, and ligated with adapters. Fragments of the appropriate size are enriched by PCR, where indexed P5 and P7 primers are introduced, and final products are purified. The libraries were checked with Qubit 2.0 and real-time PCR for quantification and bioanalyzer Agilent 2100 for size distribution detection.

treatment_protocol: Tissues from fourth instar larvae (L4) and adults, as well as the whole body from different stages, from egg to third instar larva (figure 2) were collected. The tissues were dissected in PBS under a stereoscopic microscope. Dissection time was limited to 10 min to avoid RNA degradation and the tissues were subsequently snap-frozen in liquid nitrogen and stored in a -80°C freezer. The whole-body samples were similarly snap-frozen before being stored to ensure identical processing of the entire dataset. The eggs were pooled into groups of five. Three L1, L2, and L3 larvae were pooled to create each sample, respectively. We pool individuals because the extracted RNA from each individual was not sufficient for sequencing. The L4 larvae and adult tissues are from single individuals. The L4 larvae were dissected on the 19th day of development from egg laying. Adults were kept in individual petri dishes from emergence and dissected seven days later.

tag: tissue

value: testis

tag: genotype

value: WT

tag: treatment

value: No treatment


title: Motor neurons, ALS,  Day 52, rep 2

city: Trondheim

first: Anna

middle: Mikalsen

last: Kollstrøm

address: Edvard Griegs gate 8

department: Department of Neuromedicine and Movement Science

country: Norway

institute: NTNU

data_processing:
FASTQ files quality controlled with fastqc (v0.11.9), and filtered and trimmed by fastp (v0.20.0).
Trimmed sequence reads were aligned to the human GRCh38 reference genome using STAR (v2.7.3).
Read counts and normalization were performed using Salmon (v1.3.0) and R statistical software.
Assembly: GRCh38
Supplementary files format and content: tab-separated text file containing raw gene counts for each sample
Supplementary files format and content: tab-separated text file containing TPM normalized gene counts for each sample

organism: Homo sapiens

source_name: human fibroblasts

growth_protocol: hiPSCs were differentiated to motor neurons according to the protocol by Nijssen et al. (2019), and maintained on PEI and laminin-coated dishes in Neurobasal medium supplemented with 1% PenStrep, 10 ng/mL BDNF and GDNF, and 200 uM L-Ascorbic Acid.

extract_protocol:
Qiagen RNeasy Mini Kit.
Illumina Stranded mRNA Prep kit

value: human fibroblasts

tag: cell line

tag: cell type

value: hiPSC-derived motor neurons

tag: disease

value: ALS C9orf72


title: CBh>FLEX[Ascl1] (2w)

city: Seattle

first: Thomas

last: Reh

state: Washington

address: 1959 NE Pacific Street, UW School of Medicine, Seattle, WA 98195

department: Department of Neurobiology and Biophysics

country: USA

institute: University of Washington

description:
Library name: SCR174
Chromium Next GEM single Cell 3’ Reagent kits v3.1

library_source: transcriptomic single cell

data_processing:
fastq files were generated using cellranegr mkfastq
fastq files were aligned to custom mm10 reference genome using cellranger 7.2 or 8.0
Assembly: Custom mm10 genome containing TurboGFP sequence
Supplementary files format and content: filtered_feature_bc_matrix.h5, expression matrix with feature names and barcodes generated by cellranger in h5 format

molecule: polyA RNA

organism: Mus musculus

source_name: retina

extract_protocol:
Following euthanasia, pools of >4 retinas were dissociated using the Worthington Papain Dissociation System (catalog no. LK003150) according to the manufacturer’s instructions. Cells were then spun at 4 °C at 400 × g for 10 min and resuspended in neurobasal medium (Gibco no. 21103049), 10% fetal bovine serum (Clontech), B27 (Invitrogen), N2 (Invitrogen), 1 mM l-glutamine (Invitrogen), and 1% penicillin-streptomycin (Invitrogen). The cell suspension was passed through a 35-μm filter and then sorted using a BD FACSAria III cell sorter (BD Bioscience) to retrieve TdT+ cells.
Following FACS purification, TdT+ cells were centrifuged at 300g at 4ºC for 5 mins. Supernatant was removed to achieve an approximate concentration of 1000 cells per µl. scRNA-seq libraries were constructed with a targeted cell recovery of 6,000-8,000 cells using the Chromium Next GEM single Cell 3’ Reagent kits v3.1 (Dual Index) following the manufacturer’s instructions.

value: retina

value: FACS TdT+ cells


title: 6_235072V03-0_Naive

description: Library name: 6_235072V03-0_Naive

tag: Sex


title: untreated

description:
Library name: SCR173
Chromium Next GEM single Cell 3’ Reagent kits v3.1


title: Dox treated ATACSeq YAPCA TechRep 3

city: Philadelphia

first: Madhura

last: Nijsure

state: Pennsylvania

address: 3450 Hamilton Walk

institute: University of Pennsylvania

library_source: genomic

data_processing:
RNA quality was evaluated using a BioAnalyzer. RNA libraries were prepared using Illumina truSeq polyA high-throughput kit and single-end reads were sequenced to 100 base pairs using an Illumina NovaSeq. Reads were aligned to the mm10 genome using Hisat2. Picard was used to generate bam files and sorted by chromosomal coordinates. FeatureCounts was used to generate count files. Deseq2 was used for differential expression analysis between groups (n=3 biological replicates/group). Gene Set Variation Analysis was performed using a previously established method (Hänzelmann et al, 2013)
Paired-end reads were mapped to the mm10 genome using bowtie2. Picard SortSam was used to convert SAM files to BAM files. PCR duplicates were removed using Picard MarkDuplicates. Mitochondrial reads were removed after indexing BAM files with SAMtools. Processed BAM files were used to call peaks using MACS2. Peaks in the blacklisted regions of the genome were discarded from subsequent analysis using SAMtools as described previously. Peaks were visualized using Integrative Genomics Viewer (IGV, Broad Institute, MA). Bedtools was used to generate bigwig files suitable for IGV. Diffbind was used to identify differentially accessible loci. Motif analysis was completed using Homer
Assembly: mm10
Supplementary files format and content: RNASeq DiffExp_YAPCA.xlsx, RNASeq_DiffExp_WT.xlsx, Gene Set Enrichment Scores_WT.xlsx, Gene Set Enrichment Scores_YAPCA.xlsx, Differentially bound sites_WT Comparisons.xlsx, Differentially bound sites_YAPCA Comparisons.xlsx, BigWig files for each replicate of ATACSeq

molecule: genomic DNA

source_name: Periosteum

growth_protocol: Cells were maintained in  -MEM, 15% FBS, 1% Penicillin-Streptomycin, 1% Gluta-MAX I, 0.1% β-Mercaptoethanol.

extract_protocol:
RNA was isolated from cultured cells using the RNeasy Mini Kit (74106, Qiagen, Germantown, MD), and quantified using a NanoDrop 2000 (ThermoFisher Scientific, Waltham, MA, USA)Open chromatin was isolated using a previously established protocol (Corces MR, et al 2017)
RNA libraries were prepared using Illumina truSeq polyA high-throughput kit. ATAC libraries were generated according to a previously published protocol (Corces MR, et al, 2017)

treatment_protocol: 1 μM Doxycycline treatment was done in 10% FBS. Dox was dissolved in Water, therefore, untreated cells were used as controls. There was no vehicle.

value: Periosteum

value: Primary cells

value: Periosteal Cells


title: 33_235092V03-0_CM

description: Library name: 33_235092V03-0_CM

value: CM


title: Dox treated ATACSeq YAPCA TechRep 1


title: 5_235095V00-1_Naive

description: Library name: 5_235095V00-1_Naive

value: female


title: Motor neurons, ALS,  Day 52, rep 1


title: CBh>FLEX[Ascl1-Atoh1] (6w)

description:
Library name: SCR181
Chromium Next GEM single Cell 3’ Reagent kits v3.1


title: Untreated Control ATACSeq YAPCA TechRep 3


title: CBh>FLEX[Ascl1] (6w)

description:
Library name: SCR180
Chromium Next GEM single Cell 3’ Reagent kits v3.1


title: Motor neurons, ALS,  Day 52, rep 3


title: PRCC-TFE3KI_1

city: Kumamoto

first: Masaya

last: Baba

state: Kumamoto

address: 1-1-1 Honjo, Chuo-ku

department: Urology

country: Japan

institute: Kumamoto University

description: Library name: Sample 17

data_processing:
Trim Galore! (version 0.6.6, incorporating cutadapt version 2.5) was used to remove adapter sequences and trim low-quality ends.
The trimmed reads were aligned to the human genome (UCSC hg38 assembly) using STAR (version 2.7.9a).
Assembly: GRCm38
Supplementary files format and content: tsv

source_name: Kidney

extract_protocol:
Total RNA was extracted using TRIzol reagent, and its quality was assessed using a BioAnalyzer 2100.
Library preparation was performed using the TruSeq Stranded mRNA Library Prep kit, following the manufacturer's protocol.

value: Kidney

value: lsl-PRCC-TFE3 KI, KSP-Cre(+)


title: 30_305123V03-0_CM

description: Library name: 30_305123V03-0_CM

value: Blood

value: CD4 T cell


title: PRCC-TFE3KI_2

description: Library name: Sample 20


title: 32_235036V00-1_CM

description: Library name: 32_235036V00-1_CM


title: Motor neurons, ALS,  Day 38, rep 1


title: 3_235074V03-0_Naive

description: Library name: 3_235074V03-0_Naive

value: Naive


title: Motor neurons, ALS,  Day 38, rep 3


title: Mouse_SI_day8_xcr1_dtr

type: RNA

city: La Jolla

first: Ananda

middle: W

last: Goldrath

state: CA

address: 9500 Gilman Drive

department: Molecular Biology

institute: University of California, San Diego

description: FFPE block

scan_protocol: Xenium analyzer was used to image target RNA positions and cell boundaries. Proprietary software was used to decode and return RNA positions as outputs from each machine, along with raw images of cell nucleus and boundary stainings.

data_processing:
Cell nuclei were segmented using Cellpose 2.0 (Pachitariu et al. 2022). Cell boundaries were predicted using the nuclear staining and transcript positions using Baysor (Petukhov et al. 2021). Experiments was integrated with the timecourse data in GSE: using scVI (Lopez et al 2018). Celltypes were assigned manually, and the processed object is stored as an Anndata object in h5ad format containing both metadata and raw gene expression counts (Wolf et al 2018).
Raw detected RNA counts per cell

source_name: Small Intestine

extract_protocol: 5 um-thick microtome sections of Formalin-Fixed Paraffin-Embedded tissues.

value: Small Intestine

tag: strain

value: C57BL/6, XCR1 DTR/Venus

value: LCMV infection and P14 CD8 T cell transfer. 500 ng/mouse of DT was administered by intraperitoneal injection days 4-7 after infection.

tag: time point

value: day 8 after infection


title: Motor neurons, ALS,  Day 18, rep 3

value: human fibroblasts

value: hiPSC-derived motor neurons

value: ALS C9orf72


title: Untreated Control ATACSeq YAPCA TechRep 1

value: Periosteum


title: PRCC-TFE3KI/HIF1a/HIF2a DKO_2

description: Library name: Sample 15

value: lsl-PRCC-TFE3 KI, HIF1af/f,HIF2af/f, KSP-Cre(+)


title: 28_235072V03-0_CM

description: Library name: 28_235072V03-0_CM

value: male


title: Untreated Control ATACSeq YAPCA TechRep 2

value: Primary cells

value: Periosteal Cells


title: PRCC-TFE3KI/HIF1a/HIF2a DKO_3

description: Library name: Sample 16

value: Kidney


title: Motor neurons, ALS,  Day 38, rep 2


title: PRCC-TFE3KI/HIF2aKO_3

description: Library name: Sample 12

value: lsl-PRCC-TFE3 KI, HIF2af/f, KSP-Cre(+)


title: Dox treated ATACSeq YAPCA TechRep 2


title: Motor neurons, ALS,  Day 18, rep 1


title: PRCC-TFE3KI/HIF1a/HIF2a DKO_1

description: Library name: Sample 11


title: 25_235074V03-0_CM

description: Library name: 25_235074V03-0_CM

value: Blood

value: CM

value: female


title: Wildtype Dox treated ATACSeq TechRep 3


title: WTA2

city: Kobe

first: Katsuya

last: Sato

address: 7-5-2, Kusunoki-cho, Chuo-ku

institute: Kobe University

description: BD Rhapsody

data_processing:
Rhapsody Sample Sequencing QC: The library, with quantified Illumina adapters attached, was sequenced using the NovaSeq 6000 S4 flow cell. The sequencing parameters were set at 67 cycles for Read1 and 155 cycles for Read2. Subsequently, the sequencing data underwent adapter trimming, homopolymer trimming, and quality filtering utilizing Cutadapt.
Rhapsody Sample Sequencing Results: Raw fastq files, post-adapter trimming and quality filtering, were subjected to cell barcode mapping. Mapping to GRCm38 release-101 was performed using Bowtie2, and the results were consolidated based on gene symbols to generate a gene count table. The cell barcode mapping efficiency was approximately 82%, and the mapping rate to GRCh38 release-104 was around 87%. These satisfactory values indicate the library quality was satisfactory.
Rhapsody Single-Cell RNA-Seq Data QC: Based on the read count for each cell, the inflection point was identified using the DropletUtils package. This was set as the threshold for distinguishing between signal and background (Inflection threshold). Cell barcodes were then filtered based on this inflection threshold. Approximately 74% of the reads were deemed usable when using the inflection point as the threshold.
Rhapsody Single-Cell RNA-Seq Data Demultiplexing: Demultiplexing based on tags was performed on the Rhapsody single-cell RNA-seq data.

source_name: hiPSCs and Leydig-like cells generated from hiPSCs

extract_protocol:
Initially, the LLCs were detached by adding 0.5X TrypLE Select to the culture dishes and incubating at 37°C for 2 minutes. In accordance with the protocol, the cells were resuspended in 1X PBS and transferred into cartridges, along with beads. Subsequent to this, reverse transcription reaction and PCR were performed.
Using the Rhapsody system, cells and beads were loaded. The cells were lysed to dissolve them, allowing the mRNA derived from each cell to be captured by barcoded beads. Following this, beads were collected, and cDNA was synthesized through reverse transcription. The mRNA that served as a template for cDNA was then degraded using RNase. Terminal transferase was employed to add a homopolynucleotide to the cDNA end using a single type of dNTP and terminated with the same type of ddNTP. A second strand was synthesized on the cDNA using a primer containing a single type of dNTP. This double-stranded DNA was then amplified via PCR, referred to as the first WTA. After PCR amplification, the sample underwent size selection, or purification, using beads. The size-selected sample was then amplified again using PCR, marking the second WTA. Following this, the sample was subjected to another round of size selection using beads. The size distribution of the sample was then measured using the MultiNA microchip electrophoresis device from Shimadzu Corporation.


title: Motor neurons, ALS,  Day 18, rep 2


title: PRCC-TFE3KI_3

description: Library name: Sample 21

value: lsl-PRCC-TFE3 KI, KSP-Cre(+)


title: PRCC-TFE3KI/HIF2a KO_2

description: Library name: Sample 10


title: Wildtype untreated ATACSeq TechRep 3


title: 27_235095V00-1_CM

description: Library name: 27_235095V00-1_CM

value: CD4 T cell


title: 24_235216V03-0_CM

description: Library name: 24_235216V03-0_CM


title: Wildtype Dox treated ATACSeq TechRep 1


title: STag2

description: BD Rhapsody

value: hiPSCs and Leydig-like cells generated from hiPSCs


title: 22_235092V03-0_EM

description: Library name: 22_235092V03-0_EM

value: EM


title: TetON_day40

data_processing:
Raw sequence files (fastq) were aligned to the human genome build 38 (hg38) reference sequences using the Strand NGS software program with default parameters.
All aligned reads were normalized using Transcripts per million (TPM).
TPM values were log2-transformed with an offset value of 1.0. Baseline transformation was not performed.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include Gene Symbol, Entrez Gene ID and TPM values (log2-transformed with an offset value of 1.0) for each Sample.

source_name: Leydig-like cells

extract_protocol:
Total RNA from each cell was isolated using Trizol reagent (Life Technologies) according to the manufacturer's instructions.
RNA libraries were prepared for TruSeq Stranded mRNA Sample Preparation Guide (Part#15031047 Rev.3).

value: Leydig-like cells


title: Cre(-)_3

description: Library name: Sample 7

value: lsl-PRCC-TFE3 KI, KSP-Cre(-)


title: 21_235036V00-1_EM

description: Library name: 21_235036V00-1_EM


title: PRCC-TFE3KI/HIF2a KO_1

description: Library name: Sample 9


title: Wildtype untreated ATACSeq TechRep 2


title: TetON_day30


title: Htag2

description: BD Rhapsody


title: Cre(-)_4

description: Library name: Sample 8


title: Wildtype untreated ATACSeq TechRep 1


title: Dox treated RNASeq YAPCA TechRep 2


title: Dox treated RNASeq YAPCA TechRep 3


title: Cre(-)_1

description: Library name: Sample 5

value: lsl-PRCC-TFE3 KI, HIF1af/f, KSP-Cre(-)


title: 2_235216V03-0_Naive

description: Library name: 2_235216V03-0_Naive

value: Naive


title: Cre(-)_2

description: Library name: Sample 6


title: Dox treated RNASeq YAPCA TechRep 1

value: Periosteum


title: TetON_day14


title: Wildtype Dox treated ATACSeq TechRep 2


title: 17_235072V03-0_EM

description: Library name: 17_235072V03-0_EM

value: male


title: Untreated Control RNASeq YAPCA  TechRep 3

value: Primary cells


title: TetON_day20


title: Untreated Control RNASeq YAPCA  TechRep 2

value: Periosteal Cells


title: 19_305123V03-0_EM

description: Library name: 19_305123V03-0_EM


title: PRCC-TFE3KI/HIF1a KO_4

description: Library name: Sample 4

value: Kidney

value: lsl-PRCC-TFE3 KI, HIF1af/f, KSP-Cre(+)


title: PRCC-TFE3KI/HIF1a KO_3

description: Library name: Sample 3


title: 16_235095V00-1_EM

description: Library name: 16_235095V00-1_EM

value: Blood


title: 23_235086V03-0_CM

description: Library name: 23_235086V03-0_CM

value: CM


title: Untreated Control RNASeq YAPCA  TechRep 1


title: 13_235216V03-0_EM

description: Library name: 13_235216V03-0_EM


title: TetOFF_day35

source_name: hiPSCs

value: hiPSCs


title: Subcutaneous adipose tissue, GA-3

city: Dallas

first: Christine

middle: M

last: Kusminski

state: Texas

address: 5323 Harry Hines Boulevard

department: Internal Medicine, Touchstone Diabetes Center

institute: The University of Texas Southwestern Medical Center

data_processing:
Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5).
The reads were counted using featureCounts (v.1.4.6)
Differential expression analysis was performed using edgeR (v.3.18.1)
Assembly: UCSC genome mm10
Supplementary files format and content: Processed Data gencode.vM4_TRANSCRIPTS_counts.feature_count: count

source_name: Subcutaneous adipose tissue

extract_protocol:
RNA isolated from subcutaneous adipose tissue was used to prepare an RNAseq library by enrichment from total RNA using oligo(dT) beads
TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat
RNA-seq. Samples are run on the Agilent Tapestation 4200 to determine level of degradation thus ensuring only high quality RNA is used (RIN Score 8 or higher).   The Qubit® 4.0 Fluorimeter from ThermoFisher is used to determine the concentration prior to staring library prep.  One microgram of total DNAse treated RNA is then prepared with the TruSeq Stranded Total RNA Sample Prep Kit from Illumina. Total RNA is depleted of its rRNA and fragmented before strand-specific cDNA synthesis.  cDNA are then a-tailed and indexed adapters are ligated.   After adapter ligation, samples are PCR amplified and purified with AmpureXP beads, then validated again on the Agilent Tapestation 4200.  Before being normalized and pooled, samples are quantified by Qubit then run on the Illumina NextSeq 500 using V2.5 reagents.

value: Subcutaneous adipose tissue

value: (2-weeks) Dox-HFD regimen


title: PRCC-TFE3KI/HIF1a KO_2

description: Library name: Sample 2


title: Wildtype Dox treated TechRep 2


title: 14_235074V03-0_EM

description: Library name: 14_235074V03-0_EM

value: CD4 T cell

value: female


title: PRCC-TFE3KI/HIF1a KO_1

description: Library name: Sample 1


title: Wildtype Dox treated TechRep 3


title: DKD01

city: Jinan

first: jinxiu

last: Hu

address: jingwuweiqi

country: China

institute: Shandong Provincial Hospital

description: 10x Genomics

data_processing:
The Cell Ranger software pipeline (version 5.0.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells.
Cells were clustered using a graph-based clustering approach and visualized in two dimensions using t-distributed stochastic neighbor embedding (t-SNE)
Differentially expressed genes (DEGs) were identified using the FindMarkers function of Seurat.
Assembly: GRCH38-2020-A
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: renal cortex

extract_protocol:
Each fresh kidney sample was cut into millimeter-sized pieces and enzymatically digested in Dulbecco’s modified Eagle’s medium (Gibco, 11995065) containing 5% fetal bovine serum (HyClone), 0.2% collagenase type IV (#C5138; Sigma–Aldrich), and 0.002% DNase I (Applichem, A3778.0050) for 5 min at 37°C with slight shaking. Digested tissues were then filtered through a 40μm pore size nylon mesh and centrifuged at 300g for 5min. The pellets were resuspended by culture medium and erythrocytes were lysed using a red blood cell lysis solution (MACS, 130-094-183) at 4℃ for 10 min, and then the cell suspension was centrifuged at 300g for 5min. After washed once in culture medium, the pellets were centrifuged at 300g for 5min, and the supernatant was removed. The pellets were then resuspended by 100μl culture medium, and the cell concentration and viability were assessed using Luna cell counter. The sequencing was performed on Illumina Nova 6000 PE150.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, cells  were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane magnetic beads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: renal cortex

tag: disease state

value: non-diabetic renal cancer patients undergoing surgical resection


title: 12_235086V03-0_EM

description: Library name: 12_235086V03-0_EM

value: EM


title: DKD03

description: 10x Genomics


title: Subcutaneous adipose tissue, GA-1


title: TetON_day6

value: Leydig-like cells


title: Wildtype Dox treated TechRep 1

value: Periosteum


title: 10_235036V00-1_Naive

description: Library name: 10_235036V00-1_Naive

value: Naive


title: Subcutaneous adipose tissue, WT-3

value: Wild-type


title: Subcutaneous adipose tissue, GA-2


title: Subcutaneous adipose tissue, WT-2


title: Wildtype untreated RNASeq TechRep 3

value: Primary cells

value: Periosteal Cells


title: 1_235086V03-0_Naive

description: Library name: 1_235086V03-0_Naive


title: Wildtype untreated RNASeq TechRep 1


title: Subcutaneous adipose tissue, WT-1


title: NM01

description: 10x Genomics

value: diabetic kidney disease


title: Wildtype untreated RNASeq TechRep 2


title: NM03

description: 10x Genomics


title: C.elegans_ac4C

city: Fuzhou

first: lele

last: Yang

address: Fujian Medical University, 1 Xuefubei Road, Minhou, Fuzhou, Fujian province, China

institute: Fujian Medical University

data_processing:
The raw ac4C-RIP-seq data were aligned to genome reference sequences by Hisat2. The aligned reads were used for ac4C-modification peak calling and the significant methylation was identified by exomepeak2 , and the ac4C peak calling can be visualized by IGV software.
The MetaTX was used to examine the distribution pattern of epitranscriptome profiles. The STREME  was used to determine if the ac4C peaks contained the consensus of ac4C motif sequences.
For mRNA-seq, the mRNA expression level was analyzed by StringTie, and differentially expressed mRNAs were calculated by DEseq.
The substrates of ac4C regulators were obtained from starBase v2.0.
The statistical enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for differentially expressed genes (DEGs) and differentially methylated mRNAs were applied by DAVID.
Assembly: danRer10 or WBcel235
Supplementary files format and content: The processed data files is in CSV format, containing the expression levels and ac4C status changes for each gene.

organism: Caenorhabditis elegans

source_name: Animal organ cells

extract_protocol:
Total RNA was extracted according to manufacturer’s instruction.
The stranded RNA sequencing library was constructed by KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched

value: Animal organ cells

value: Wild type

tag: rip antibody

value: anti-ac4C  (Abcam  catalog No. ab252215)


title: iPSC

value: hiPSCs


title: C.elegans_input

value: none (input)


title: Control and trained cells, mixed sample (non-demultiplexed)

status: Public on Jan 06 2025

city: Rehovot

first: Roi

last: Avraham

address: Herzl St 234

country: Israel

institute: Weizmann Institute of Science

description: Control and trained cells

data_processing:
MARS-seq pipeline (https://www.nature.com/articles/s41596-019-0164-4) was used for demultiplexing, alignment to the genome, and gene counting by unique molecular identifier (UMI).
Demultiplexing into samples is based on 4bp pool-barcode for each sample which is located at R1 base-pairs 6-9 (see sc_samples_barcodes.xlsx tab:amp_batches for pool-barcodes sequences of each sample)
Demultiplexing into cells is based on 7bp  cell-barcode for each cells which is located at R2 base-pairs 1-7 (see sc_samples_barcodes.xlsx tab:well cells for cell-barcodes sequences of each cell)
Overall, we sequenced 1536 cells (768 from control mouse and 768 from trained mouse), with 1474 median UMI count per cell and 668 median genes per cell.
Only genes with at least one UMI count detected in at least one cell were used.
Data was normalized to a library size factor. Factors were calculated by dividing total UMI counts in each cell to the median of the total UMI counts across all cells
Cells with less than 200 UMIs were excluded due to low coverage (24 cells, 9 from naïve mouse and 15 from trained mouse). Data was transformed to log2 scale (log2(UMI count+1))
Assembly: mm9
Supplementary files format and content: Text files include UMI counts table for each gene in each cell in the sample

source_name: Spleen

extract_protocol:
Two weeks post injection, mice were sacrificed with CO2, and spleens were isolated whole. Extracted spleens were mashed on 70um screens with 5mL FACs buffer (1% FBS, 5uM EDTA). Cells were pelleted, treated with RBS lysis buffer, and washed 2x with FACs buffer before sorting in a FACs Aria III.
Cells were sorted into MARs-seq lysis plates containing barcoded primers and frozen in the -80C. Libraries were prepared according to the MARs-seq 2.0 protocol.

treatment_protocol: C57/BL6J mice were inoculated with 5*10^6 BCG (Pasteur) or PBS i.p in a volume of 200ul.

value: Spleen

value: Splenocytes

value: PBS or BCG


title: DKD02

description: 10x Genomics

value: renal cortex

value: non-diabetic renal cancer patients undergoing surgical resection


title: 11_235092V03-0_Naive

description: Library name: 11_235092V03-0_Naive

value: Blood

value: CD4 T cell

value: male


title: cep1fed3

city: Vancouver

first: Stefan

last: Taubert

state: BC

address: 950 W 28th Ave, CMMT Room 2024

department: Medical Genetics

country: Canada

institute: UBC

description: Sex: hermaphrodite

data_processing:
Construction of strand-specific mRNA sequencing libraries and sequencing (75bp PET) on an Illumina HiSeq 2500 machine was done at the Sequencing Services facility of the Genome Sciences Centre, BC Cancer Agency, Vancouver BC, Canada. >20 million reads were sequenced per sample.
The raw FASTQ reads obtained from the facility were trimmed using Trimmomatic version 0.36 with parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
Trimmed reads were aligned to the NCBI reference genome WBcel235 WS277 using Salmon version 0.9.1 with parameters -l A -p 8 --gcBias.
Transcript-level read counts were imported into R and summed into gene-level read counts using tximport. Genes not expressed at a level greater than 1 count per million (CPM) reads in at least three of the samples were excluded from further analysis. The gene-level read counts were normalized using the trimmed mean of M‐values (TMM) in edgeR to adjust samples for differences in library size.
Differential expression analysis was performed using the quasi-likelihood F-test with the generalized linear model (GLM) approach in edgeR.
Assembly: C. elegans Ensembl transcriptome build WBcel235
Supplementary files format and content: Comma seperated value sheet containing raw counts for all genes in WBcel235 for all conditions and repeats.
Supplementary files format and content: Microsoft Excel spreadsheet containing logCPM values for all conditions and repeats.

source_name: whole worm

growth_protocol: Synchronized L1 wild-type, efk-1(ok3609), zip-2(tm4248), and cep-1(gk138) worms were allowed to grow on OP50 plates to mid-L4 stage. Fed samples was collected immediately by flash-freezing. Starved samples were washed 5 times in sterile M9, starved for 8 hours on unseeded plates, and then collected.

extract_protocol:
For total RNA extraction, L4 worms were thawed in Trizol and sonicated. Total RNA was extracted from the mixture using a Trizol and 1-bromo-3-chloropropane extraction, as described (PMID 35285794). RNA integrity and quantity were assessed on an Agilent Technologies 2100 Bioanalyzer System.
Construction of strand-specific mRNA sequencing libraries and sequencing (75bp PET) on an Illumina HiSeq 2500 machine was done at the Sequencing Services facility of the Genome Sciences Centre, BC Cancer Agency, Vancouver BC, Canada.

value: whole worm

value: fed


title: cep1starved2

description: Sex: hermaphrodite

value: starved


title: cep1starved1

description: Sex: hermaphrodite


title: cep1fed2

description: Sex: hermaphrodite


title: zip2starved3

description: Sex: hermaphrodite


title: zip2starved2

description: Sex: hermaphrodite


title: cep1fed1

description: Sex: hermaphrodite


title: zip2starved1

description: Sex: hermaphrodite


title: zip2fed3

description: Sex: hermaphrodite


title: zip2fed2

description: Sex: hermaphrodite


title: efk1starved2

description: Sex: hermaphrodite


title: efk1starved3

description: Sex: hermaphrodite


title: NM02

description: 10x Genomics

value: diabetic kidney disease


title: zip2fed1

description: Sex: hermaphrodite


title: efk1starved1

description: Sex: hermaphrodite


title: efk1fed3

description: Sex: hermaphrodite


title: efk1fed1

description: Sex: hermaphrodite


title: efk1fed2

description: Sex: hermaphrodite


title: N2starved3

description: Sex: hermaphrodite

value: Wild type (strain N2)


title: N2starved1

description: Sex: hermaphrodite


title: N2starved2

description: Sex: hermaphrodite


title: N2fed3

description: Sex: hermaphrodite


title: N2fed2

description: Sex: hermaphrodite


title: N2fed1

description: Sex: hermaphrodite


title: cep1starved3

description: Sex: hermaphrodite


title: training kinetics - mixed sample (non-demultiplexed)

description: Training kinetics

data_processing:
MARS-seq pipeline (https://www.nature.com/articles/s41596-019-0164-4) was used for demultiplexing, alignment to the genome, and gene counting
Demultiplexing into plates is based on 4bp pool-barcode for each plate which is located at R1 base-pairs 6-9 (see samples_barcodes.xlsx tab:amp_batches for pool-barcodes sequences of each plate)
Demultiplexing into samples is based on 7bp  sample-barcode for each sample which is located at R2 base-pairs 1-7 (see samples_barcodes.xlsx tab:well_cells for sample-barcodes sequences of each sample)
Data was normalized to a library size factor. Factors were calculated by dividing the total number of reads from each sample to the median total number of reads across all samples.
Data was transformed to log2 scale, and minimal expression threshold was set to 3
Replicate samples of each condition were averaged, except for 1 sample that was excluded due to low coverage (<100k reads; BCG 30d replicate 3).
Assembly: mm9
Supplementary files format and content: data_matrix_raw_counts.txt: tab-delimited text files include raw number of reads (linear scale) for each sample
Supplementary files format and content: normalized_data_matrix_kinetics.txt: tab-delimited text files include normalized number of reads (linear scale) for each sample

extract_protocol:
3, 5, 14, 30, 45, or 60 days post inoculation, mice were sacrificed with CO2, and spleens were isolated whole. Extracted spleens were mashed on 70um screens with 5mL FACs buffer (1% FBS, 5uM EDTA). Cells were pelleted, treated with RBS lysis buffer, and washed 2x with FACs buffer before lysing pellet directly with 350uL RLT buffer.
Libraries were prepared according to the MARs-seq 2.0 protocol.


title: Case233

city: Seoul

first: Jaemoon

last: Koh

state: Seoul

address: Jongnogu 101 Seoul National University hospital, B1, Department of Pathology

country: South Korea

institute: Seoul National University Hospital

description:
Library name: Case233
Case 233

data_processing:
Barcoded libraries were pooled and sequenced on the Illumina HiSeq 2500 generating 50 bp paired end reads
Sequencing reads were mapped using STAR v2.5.2 and RSEM ver 1.3.0 pipeline with the parameters  as in the ENCODE Phases 3. Hg19 human genme from Ensenbl was used as the treference genome
Sindce we used two different kits in RNA-seq library preparation, we checked for any systematic biases between the two kits and found substantial batch effect using ComBat in sva R package (version 3.34.0)
Gene level abundance was quantitated from the filtered human alignments in R using the GenomicAlignments Bioconductor package (version 1.22.1)
Assembly: hg38
Supplementary files format and content: count

source_name: Lung

extract_protocol:
RNA extracted by column purification using an RNA isolation kit Rneasy (Qiagen) according to the manufacturer's protocol
RNAseq libraries were constructed from 1ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit or TruSeq RNA Access Library Prep Kit

value: Lung

value: cancer

value: wt


title: Case232

description:
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Case 232


title: Case234

description:
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title: Case231

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title: Case1

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title: BE_MA1001_pre_Batch2

first: Kimberly

middle: A

last: Dill-McFarland

state: WA

address: 750 Republican St

department: Allergy and Infectious Diseases

data_processing:
Reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of 30 (Galaxy FASTQ Trimmer tool v1.0.0). FastqMcf (v1.1.2) was used to remove adapter sequences.
Reads were aligned using the STAR aligner (v2.4.2) with the GRCh38 reference genome and gene annotations from ensembl release 91."
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134), FASTQC (v0.11.3), Samtools (v1.2), and HTSeq-count (v0.4.1).
Libraries were quality filtered by median coefficient of variation (CV) coverage < 0.65, duplicate mapped reads > 0.8, total aligned sequences > 1 million, and the first two principal components
Counts were normalized for RNA composition using the trimmed mean of M-values normalization method, filtered to protein coding genes with at least 1 count per million (CPM) in at least 10% of samples, and converted to log2 CPM with quality weights using voom in R (v4.0.2)
Assembly: hg38
Supplementary files format and content: CSV: normalized counts in genes (ensembl_gene_id) for each sample (libID)

source_name: airway cells

extract_protocol:
Total RNA was extracted from BE cell pellets using QIAshredder homogenizer columns followed by RNeasy purification using manufacturer’s instructions (QIAGEN). RNA quality and concentration were assessed using RNA electrophoresis (Agilent) and NanoDrop 1000 (NanoDrop Products, Thermo Fisher Scientific)
Sequencing libraries were constructed from total RNA using SMART-Seq v4 Ultra Low Input RNA Kit (Takara) and clustered onto a flowcell using a cBOT amplification system with a HiSeq SR v4 Cluster Kit (Illumina). Single-read sequencing was carried out on a HiSeq2500 sequencer (Illumina), using a HiSeq SBS v4 Kit to generate 58-base reads, with a target of approximately 5 million reads per sample.

treatment_protocol: Segmental allergen bronchial provocation (SBP-Ag) was used to provoke airway inflammation and retrieve airway cells pre and post SBP-Ag

tag: source

value: bronchoalveolar brushing

tag: visit

value: pre SBP-Ag

tag: donor

tag: batch

tag: pass-filter

value: FALSE

value: airway cells


title: BE_MA1092_post_Batch1

value: post SBP-Ag


title: BE_MA1001_post_Batch2


title: BE_MA1086_pre_Batch1

value: TRUE


title: Case18

description:
Library name: Case18
Case 18


title: Case19

description:
Library name: Case19
Case 19


title: Case17

description:
Library name: Case17
Case 17


title: Case22

description:
Library name: Case22
Case 22


title: BE_MA1083_post_Batch1


title: Case13

description:
Library name: Case13
Case 13


title: BE_MA1080_post_Batch1


title: BE_MA1067_pre_Batch1


title: Case21

description:
Library name: Case21
Case 21


title: Case5

description:
Library name: Case5
Case 5


title: Case6

description:
Library name: Case6
Case 6


title: Case15

description:
Library name: Case15
Case 15


title: Case4

description:
Library name: Case4
Case 4


title: BE_MA1072_post_Batch1


title: BE_MA1058_post_Batch1


title: BE_MA1058_pre_Batch1


title: Case3

description:
Library name: Case3
Case 3


title: BE_MA1055_post_Batch1


title: BE_MA1092_post_Batch2


title: BE_MA1092_pre_Batch2


title: BE_MA1055_pre_Batch1


title: Case8

description:
Library name: Case8
Case 8


title: BE_MA1049_pre_Batch1


title: BE_MA1028_post_Batch2


title: BE_MA1028_pre_Batch2


title: BE_MA1025_pre_Batch1b


title: BE_MA1042_pre_Batch1


title: BE_MA1038_post_Batch1


title: BE_MA1092_pre_Batch1


title: BE_MA1086_post_Batch1


title: BE_MA1028_post_Batch1


title: BE_MA1083_pre_Batch1


title: BE_MA1063_pre_Batch1


title: BE_MA1063_post_Batch1


title: BE_MA1069_pre_Batch1


title: BE_MA1069_post_Batch1


title: BE_MA1067_post_Batch1


title: BE_MA1038_pre_Batch1


title: BE_MA1025_post_Batch1b


title: BE_MA1049_post_Batch1


title: BE_MA1024_pre_Batch1


title: BE_MA1022_post_Batch1


title: BE_MA1042_post_Batch1


title: BE_MA1013_pre_Batch1


title: BE_MA1013_post_Batch1


title: BE_MA1072_pre_Batch1


title: BE_MA1012_pre_Batch1


title: BE_MA1010_pre_Batch1


title: BE_MA1080_pre_Batch1


title: BE_MA1025_post_Batch1a


title: BE_MA1010_post_Batch1


title: BE_MA1024_post_Batch1


title: BE_MA1028_pre_Batch1


title: BE_MA1022_pre_Batch1


title: BE_MA1025_pre_Batch1a


title: BE_MA1009_post_Batch1


title: BE_MA1009_pre_Batch1


title: BE_MA1007_pre_Batch1


title: BE_MA1001_post_Batch1


title: BE_MA1001_pre_Batch1


title: BE_MA1007_post_Batch1


title: VEEV, 10dpi, 12mkd, Rep3

city: Memphis

first: Evan

middle: Peter

last: Williams

state: TN

address: 858 Madison Ave

department: Dept. of Microbiology, Immunology, and Biochemistry

institute: University of Tennessee Health Science Center

data_processing:
CLC Genomics Workbench v 23.0
Sequence reads were trimmed  and filter using default parameters in CLC Genomic Workbench
Trimmed and filter sequence reads were mapped to GRCm39/virus species concatinated genome using default parameters in CLC Genomic Workbench
Assembly: GRCM39 concatinated with lab reference genome of each virus
Supplementary files format and content: tab-delimited text files include total counts for each sample
Supplementary files format and content: tab-delimited text filesthat contains gene total counts

source_name: Brain

extract_protocol:
Total RNA was isolated using MagMAX mirVana Total RNA Isolation Kit on a KingFisher Flex instrument
Libraries were constructed using NEB NEBNext Ultra II RNA Kits

value: Brain

value: Infected, 12 mk/kg/day


title: VEEV, 9dpi, 12mkd, Rep1


title: VEEV, 10dpi, 12mkd, Rep2


title: VEEV, 7dpi, 12mkd, Rep4


title: VEEV, 7dpi, 12mkd, Rep3


title: VEEV, 7dpi, 12mkd, Rep2


title: VEEV, 5dpi, 12mkd, Rep4


title: VEEV, 7dpi, 12mkd, Rep1


title: BE_MA1012_post_Batch1


title: VEEV, 5dpi, 12mkd, Rep3


title: VEEV, 5dpi, 12mkd, Rep2


title: VEEV, 5dpi, 12mkd, Rep1


title: VEEV, 3dpi, 12mkd, Rep3


title: VEEV, 3dpi, 12mkd, Rep4


title: VEEV, 3dpi, 12mkd, Rep1


title: VEEV, 3dpi, 12mkd, Rep2


title: E12.5_9,PGC,XX

city: Paris

first: Laurène

last: Syx

address: 11 rue Pierre et Marie Curie

department: Centre de recherche

country: France

institute: Institut Curie

data_processing:
Quality control: Reads characterized by at least one of the following criteria were discarded from the analysis i) >50% of low quality bases (Phred score <5) ii) >5% of N bases iii) >80% of AT rate iv) ≥30% of continuous A and/or T
Genome reconstruction: The VCF file (mgp.v5.merged.snps_all.dbSNP142.vcf) reporting all SNP sites from 36 mouse strains based on mm10 was downloaded from the Sanger database. Using SNPsplit tool (v0.3.0), these SNPs were filtered based on their quality values (FI value) and used to reconstruct the Cast genome from mm10 genome assembly.
Mapping: Single-end reads were then aligned to the mouse mm10 and Cast/EiJ genomes using the TopHat2 software (v2.1.1). Only random best alignments with less than 2 mismatches were reported for downstream analyses. The resulting mapping files for both parental genomes were then merged for each sample.
Allelic Ratio: The SAMtools mpileup utility (v1.1) was then used to extract base-pair information at each genomic position from the merged alignment file. At each SNP position, the number of paternal and maternal allele was counted. The allele-specific origin of the transcripts (or allelic ratio) has been measured by the total number of reads mapped on the paternal genome divided by the total number of reads for each gene: allelic ratio = paternal reads / (paternal+maternal) reads.
Estimation of gene expression levels: To estimate the transcript abundance, count tables of gene expression were generated using HTSeq v0.7.2 software. Read counts are then normalized based on the amplification size of each transcript (RPRT for Reads Per Retro-Transcribed length per million mapped reads)
Assembly: mm10
Supplementary files format and content: CountTable.xlsx : raw count table
Supplementary files format and content: RPRT.xlsx : RPRT expression table
Supplementary files format and content: AllelicRatio.xlsx : Allelic ratio table

source_name: embryo

growth_protocol: natural matings, no embryo culture

extract_protocol: Illumina manufacturer protocol

treatment_protocol: single cell cDNA amplification (adapted from Tang et al, 2010)

value: embryo

tag: lineage

value: PGC

tag: embryonic day

value: XX


title: E12.5_8,PGC,XX

tag: tissue

tag: genotype


title: E12.5_48,PGC,XX


title: E12.5_7,PGC,XX


title: E12.5_6,PGC,XX


title: E12.5_49,PGC,XX


title: E12.5_5,PGC,XX


title: E12.5_46,PGC,XX


title: VEEV, 10dpi, 12mkd, Rep4

tag: treatment


title: E12.5_44,Soma,XO

value: Soma

value: XO


title: E12.5_43,PGC,XO


title: E12.5_42,PGC,XO


title: E12.5_40,PGC,XX


title: E12.5_4,PGC,XX


title: E12.5_39,PGC,XX


title: E12.5_38,PGC,XX


title: E12.5_37,PGC,XY

value: XY


title: E12.5_35,PGC,XY


title: E12.5_34,Soma,XY


title: E12.5_33,PGC,XY


title: E12.5_32,PGC,XY


title: E12.5_31,PGC,XY


title: E12.5_30,PGC,XY


title: E12.5_3,PGC,XX


title: E12.5_29,PGC,XY


title: E12.5_47,PGC,XX


title: E12.5_27,PGC,XX


title: E12.5_28,PGC,XY


title: E12.5_23,PGC,XX


title: E12.5_21,PGC,XX


title: E12.5_22,PGC,XX


title: E12.5_20,PGC,XX


title: E12.5_18,PGC,XX


title: E12.5_45,PGC,XO


title: E12.5_17,PGC,XX


title: E12.5_19,PGC,XX


title: E12.5_16,Soma,XX


title: E12.5_15,Soma,XX


title: E12.5_41,PGC,XX


title: E12.5_36,PGC,XY


title: E11.5_9,PGC,XX


title: E11.5_6,Soma,XY


title: E12.5_14,PGC,XX


title: E12.5_13,PGC,XX


title: E12.5_12,PGC,XX


title: E11.5_5,PGC,XY


title: E12.5_24,PGC,XX


title: E11.5_28,Soma,XX


title: E11.5_7,PGC,XX


title: E12.5_10,PGC,XX


title: E11.5_30,Soma,XX


title: E12.5_11,Soma,XX


title: E11.5_4,Soma,XY


title: E11.5_20,PGC,XX


title: E11.5_2,PGC,XY


title: E11.5_8,PGC,XX


title: E11.5_18,PGC,XX


title: E11.5_24,PGC,XX


title: E11.5_19,PGC,XX


title: E11.5_27,PGC,XX


title: E11.5_17,PGC,XX


title: E11.5_3,Soma,XY


title: E11.5_15,PGC,XX


title: E11.5_22,PGC,XX


title: E11.5_13,Soma,XX


title: E11.5_11,PGC,XX


title: E11.5_16,PGC,XX


title: E11.5_21,PGC,XX


title: E10.5_5,PGC,XY


title: E10.5_39,PGC,XY


title: E10.5_35,Soma,XX


title: E11.5_1,PGC,XY


title: E11.5_12,PGC,XX


title: E11.5_14,PGC,XX


title: E10.5_3,PGC,XY


title: E10.5_26,PGC,XX


title: E10.5_21,PGC,XY


title: E10.5_20,PGC,XY


title: E10.5_9,PGC,XY


title: E10.5_8,PGC,XX


title: E11.5_26,PGC,XX


title: E11.5_25,PGC,XX


title: E10.5_7,PGC,XX


title: E10.5_2,PGC,XX


title: E9.5_6,PGC,XX


title: E10.5_19,PGC,XX


title: E9.5_8,PGC,XX


title: E9.5_9,Soma,XX


title: E9.5_5,PGC,XX


title: E10.5_4,PGC,XY


title: E9.5_41,PGC,XY


title: E9.5_43,PGC,XY


title: E10.5_38,Soma,XX


title: E11.5_23,PGC,XX


title: E9.5_4,PGC,XX


title: E9.5_27,PGC,XX


title: E10.5_33,Soma,XX


title: E10.5_27,Soma,XX


title: E9.5_25,PGC,XX


title: E10.5_23,PGC,XX


title: E10.5_24,PGC,XX


title: E10.5_22,PGC,XY


title: E9.5_23,PGC,XX


title: E9.5_2,PGC,XX


title: E9.5_18,PGC,XX


title: E9.5_19,PGC,XX


title: E9.5_16,PGC,XY


title: E11.5_10,PGC,XX


title: E10.5_14,PGC,XX


title: E9.5_7,PGC,XX


title: E9.5_44,PGC,XX


title: E9.5_46,Soma,XX


title: E9.5_3,PGC,XX


title: E9.5_28,PGC,XY


title: E10.5_34,Soma,XX


title: E9.5_20,PGC,XY


title: LSS_H3K27ac_Experimental Repl 2

city: Stanford

first: Jan-Renier

last: Moonen

address: 269 Campus Drive, CCSR 1220

institute: Stanford University

data_processing:
nf-core/cutandrun (https://github.com/nf-core/cutandrun/blob/master/main.nf) was used to process the data.
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: pulmonary artery endothelial cell

growth_protocol: PAEC were grown in commercial EC media containing 5% FBS (ScienCell) in a 5% CO2 air atmosphere and used at passages 3–7.  Cells were routinely tested for mycoplasma contamination.

extract_protocol:
CUT&RUN was performed using the CUTANA CUT&RUN kit (#14-1048, EpiCypher, USA) following manufacturer’s instructions.  Briefly, 100,000 cells were detached using Accutase (Stem Cell Technologies, USA) and centrifuged at 600 x g for 3 min.  The pellet was resuspended in 100 uL wash buffer and centrifuged for 3 min at 600 x g. This was repeated twice.  After resuspension in 100 uL wash buffer, the cells were incubated with 10 uL of activated Concanavalin A conjugated paramagnetic beads on a rotator for 10 min at RT.  Tubes were placed on a magnetic stand and the supernatant was carefully removed.  The pellet was resuspended in 50 uL cold Antibody buffer with 0.5 ug of antibodies targeting H3K27ac (ab4729, Abcam, USA), or H3K27me3 antibodies and Rabbit IgG provided with the kit as positive and negative controls, respectively.  Samples were incubated on a nutator overnight at 4ºC.  The next day, the tubes were placed on a magnetic stand and the supernatant was removed, followed by resuspension, and washing with cold cell permeabilization buffer.  The pellets were resuspended with 50 uL cell permeabilization buffer with 2.5 uL/reaction of pAG-MNase, and allowed to incubate for 10 min at RT.  Following removal of the supernatant in a magnetic stand, the pellet was washed twice with 200 uL of cold cell permeabilization buffer and resuspended in 50 uL cell permeabilization buffer.  The tubes were placed on ice and 1 uL/reaction of 100 mM calcium chloride was added to activate digestion.  Tubes were incubated on a nutator for 2 h at 4ºC. The reaction was terminated by adding 33 uL Stop Master Mix comprised of stop buffer and 1 uL of E. coli spike-in DNA and samples were placed in a thermocycler and incubated at 37ºC for 10 min.  Following a quick spin, the tubes were placed on a magnetic stand and the supernatant was transferred to fresh tubes.  DNA was purified by adding 420 uL of DNA binding buffer to each reaction and loading into DNA Cleanup Column + collection tubes provided with the kit.  Columns were centrifuged at 16,000 x g for 30 sec at RT, washed twice with 200 μL DNA wash buffer, and finally DNA was eluted using 12 uL of DNA elution buffer
Paired-end sequencing libraries were prepared using the CUTANA™ CUT&RUN Library Prep Kit (#14-1001, EpiCypher, USA) following manufacturer’s instructions.  Enrichment of mononucleosomal fragments was confirmed and library concentration was determined using Agilent Bioanalyzer.

treatment_protocol: Pulmonary artery endothelial cells were pre-conditioned by exposure to 15 dyn/cm2 of unidirectional uniform LSS for 24 h. Cells were then exposed to an additional 24 h of LSS, or 24 h of 100 dyn/cm2 unidirectional uniform HSS. Shear stress was generated using the Ibidi Perfusion System (Ibidi). Static (ST) controls were performed simultaneously with the shear stress experiments, cultured on 0.4 mm chamber slides using the same EC media.

tag: cell type

value: pulmonary artery endothelial cell

value: PAEC exposed to LSS


title: E9.5_24,PGC,XX


title: E9.5_26,PGC,XX


title: E9.5_45,PGC,XY


title: E9.5_15,PGC,XX


title: PSEN2-N141I replicate 3 [RNA-seq]

first: Shankar

last: Subramaniam

department: Department of Bioengineering

data_processing:
RNA-seq pre-processing was performed using the TrimGalore! package v0.6.4, removing adapter sequences and low-quality reads using CutAdapt v1.18.
Trimmed RNA-Seq reads were mapped to the GRCh38.99 human transcriptome using kallisto v0.46.1 with the options -bias -rf-stranded -b 100 followed by transcript level summation to the gene level using the R package tximport v1.18.0
Lowly expressed genes were filtered out using filterByExpr and counts normalized using the weighted mean trimmed of M-values (TMM) in the R package edgeR v3.32.1.
Assembly: GRCh38.99
Supplementary files format and content: Normalized count matrix for all RNA-seq samples

source_name: hiPSC-derived neurons

growth_protocol: Fibroblasts were derived from patient skin biopsies from adult human volunteers; Non-demented control (NDC) and APP_V717I were generated at the Alzheimer’s Disease Research Center at the University of California, San Diego (UCSD) in accordance with UC San Diego IRB approval, whereas PSEN1A79V and PSEN2N141I were generated at the Dominantly Inherited Alzheimer’s Network (DIAN) at Washington University in accordance with the Washington University School of Medicine Institutional Review Board and Ethics Committee (IRB 201104178, 201306108). PSEN1_A79V and PSEN2-N141I fibroblasts were transformed with retroviral transduction using OCT3/4, KLF4, SOX2 and c-MYC. NDC and APP_V717I fibroblasts were transformed using the episcopal method to introduce reprogramming factors. Neurons were differentiated from iPSCs as previously described; PA6 cells were plated in a 10 cm dish and seeded with 100,000 cells iPSC next day. To enhance neural induction, cultures were treated with 5μM dorsomorphin (Sigma) and 10μM SB431542 (Tocris) for the first 6 days of differentiation. On day 12, neural stem cells (NSCs) were sorted using cell surface signature CD24+/CD184+/CD44-/CD271-. NSCs were expanded in NSC growth medium (DMEM:F12+GlutamaxTM (Thermo Fisher Cat. 10565018), 1x B-27 (Thermo Fisher Cat. 17504044), 1x N-2 (Thermo Fisher Cat. 17502001), 1x Penicillin-Streptomycin (Thermo Fisher Cat. 15070063), and 20ng/mL human bFGF-2 (BioPioneer Cat. HRP-0011)). At 80% confluence, the medium was changed to neuron differentiation medium (DMEM:F12+GlutamaxTM, 1x B-27, 1x N-2, 1x Penicillin-Streptomycin) for 3 weeks of differentiation followed by culture dissociation with Accutase (Sigma Cat. A6964). Cells were resuspended in 200μL of iMag buffer (1x neural differentiation medium, 0.5µM EDTA, 0.5% Bovine Serum Albumin) and incubated with PE Mouse Anti-Human CD184 and CD44 antibodies (BD Biosciences Cat. 561733 and 561858, respectively) for 15min on ice in the dark. The mixture was washed with iMag buffer and subsequently incubated with anti-PE conjugated magnetic beads (BD Biosciences) for 30min at room temperature. Magnetic bead separation was carried out for 8min according to the manufacturer’s protocol (BD Biosciences). The supernatant containing purified CD184-/CD44- neurons was then removed and spun down for downstream applications.

extract_protocol:
Total RNA from magnetically purified human NDC, PSEN1_A79V, PSEN2_N141I, and APP_V717I hiPSC-derived neurons (replicates, n=3) using the RNeasy Plus Micro Kit (QIAGEN, catalog no. 74034) according to the manufacturer’s protocol. On-column deoxyribonuclease digestion was performed on total RNA extracts to remove any genomic contamination (QIAGEN, catalog no 79254)
Libraries were prepared for RNA-seq using the TruSeq Stranded Total RNA Library Prep Kit (Illumina, catalog no. RS-122-2303) by the Ribo-Zero ribosomal RNA reduction method (Illumina, catalog no. MRZG12324). Samples were sequenced at the UC San Diego Institute for Genomics Medicine (IGM) sequencing core on an Illumina HiSeq 4000 generating paired-end, 100-bp reads with an average of 25 million reads per sample (Illumina, catalog no. FC-410-1001)

value: Alzheimer's disease

value: hiPSC-derived neurons

value: F, APOE3/3


title: E9.5_13,PGC,XX


title: PSEN2-N141I replicate 2 [RNA-seq]


title: PSEN2-N141I replicate 1 [RNA-seq]


title: E9.5_12,Soma,XX


title: E9.5_11,Soma,XX


title: E9.5_10,Soma,XX


title: PSEN1-A79V replicate 1 [RNA-seq]

value: M, APOE3/4


title: E9.5_1,PGC,XX


title: ST_H3K27ac_Experimental Repl 2

value: PAEC Static control


title: ST_H3K27ac_Experimental Repl 3


title: LSS_H3K27ac_Experimental Repl 3


title: ST_H3K27ac_Experimental Repl 1


title: APP-V717I replicate 2 [RNA-seq]


title: APP-V717I replicate 1 [RNA-seq]


title: NDC replicate 3 [RNA-seq]

value: Non-demented Control

value: WT

value: M, APOE2/3


title: LSS_H3K27ac_Experimental Repl 1


title: HSS_H3K27ac_Experimental Repl 2

value: PAEC exposed to HSS


title: PSEN2-N141I replicate 3 [ATAC-seq]

data_processing:
ATAC-seq data preprocessing was performed using TrimGalore! to remove sequencing adaptors and low-quality reads.
Trimmed reads were then aligned to the GRCh38 human genome (GCA_000001405.15 with no alternative analysis) using BBMap v37.95 in the BBTools suite with the options maxindel=20 ambig=random, followed by sorting and indexing of bam files using SAMtools v1.9, and annotation of PCR duplicates using the Picard v2.23.3 MarkDuplicates function with the option VALIDATION_STRINGENCY=LENIENT. All duplicates and mitochondrial, chromosome X, chromosome Y, and EBV reads were removed using SAMtools v1.9 command view with the options -b -h -f 3 -F 4 -F 8 -F 256 -F 1024 -F 2048.
To determine open chromatin regions, HMMRATAC v1.2.5 was used to call peaks on the ATAC-seq data and determine regions of open chromatin with the options –m 50,200,400,600 --score all.
open regions of chromatin were then passed to the Diffbind R package v3.0.15 to determine regions of differential accessibility between NDC and each FAD mutant condition. Consensus peaks selection for each condition were identified (minimum overlap=3) and the subsequent peaksets for all conditions were merged using the dba.peakset function. Read coverage over the combined consensus peakset was determined using the dba.count function with the DBA_SCORE_TMM_READS_EFFECTIVE peak scoring option. Differentially accessible peaks for each FAD condition relative to NDC were determined with the edgeR method with a FDR-adjusted p-value of <0.05 and then subsequently annotated using the annotatePeak function in the ChIPseeker R package v1.26.2, defining the promoter region −1500 to 500 bp from the TSS. Enhancer-associated ATAC-seq regions were defined as differential peaks occurring within the PEREGRINE enhancer region list and then finding the intersecting non-promoter based DNA regions with the join_overlap_inner function in the plyranges R package.
Assembly: GRCh38 (GCA_000001405.15)
Supplementary files format and content: Normalized count matrix for all ATSC-seq samples

extract_protocol:
ATAC-seq transposition experiments were performed as previously described on 50,000 cells in NDC, PSEN1_A79V, PSEN2_N141I, and APP_V717I hiPSC-derived neurons (replicates, n=3) using the Illumina Nextera DNA Sample Preparation Kit (Illumina, catalog no. 15028523) and the QIAGEN MinElute PCR Purification Kit (QIAGEN, catalog no. 28004).
ATAC-seq libraries were generated from transposed DNA using the Kapa Biosystems Real-Time Library Amplification Kit (Kapa Biosystems, catalog no. 07959028001) as recommended by the manufacturer, monitoring amplification by qPCR and stopping the reaction when all samples reached a fluorescence amplification intensity between standards 1 and 3. ATAC-seq libraries were then further purified using the QIAGEN MinElute PCR Purification Kit and sequenced at the UC San Diego IGM sequencing core on an Illumina HiSeq 4000 platform generating paired-end, 50-bp reads with an average of 25 million reads per sample.


title: PSEN2-N141I replicate 1 [ATAC-seq]


title: PSEN2-N141I replicate 2 [ATAC-seq]


title: HSS_H3K27ac_Experimental Repl 1


title: PSEN1-A79V replicate 3 [RNA-seq]


title: PSEN1-A79V replicate 2 [RNA-seq]


title: APP-V717I replicate 3 [RNA-seq]


title: HSS_H3K27ac_Experimental Repl 3


title: NDC replicate 3 [ATAC-seq]


title: NDC replicate 1 [ATAC-seq]


title: NDC replicate 2 [RNA-seq]


title: NDC replicate 1 [RNA-seq]


title: PSEN1-A79V replicate 3 [ATAC-seq]


title: PSEN1-A79V replicate 1 [ATAC-seq]


title: Leaf 6 of WT plant before wounding treatment (rep 3) [0min-4]

city: Beijing

first: daoxin

last: Xie

address: Tsinghua University Haidian District

institute: Tsinghua University

description:
The mock control of wounding treatment
0min-4

data_processing:
Low-quality reads were removed from the raw reads using Cutadapt and Trimmomatic software to get clean reads.
Clean reads were mapped to the corresponding reference genome using HISAT2 software.
Gene expression levels and read count of each gene were calculated using StringTie software.
The R package DEseq2 (v1.16.1) was used to identify the differentially expressed genes based on the following criteria: padj < 0.05 & log2FoldChange > 2.
Venn diagramming and GO enrichment analysis were performed using TBtools (v2.007).
Assembly: TAIR10
Supplementary files format and content: tab-delimited text file include read count for each sample

organism: Arabidopsis thaliana

source_name: leaf

extract_protocol:
Tranzol RNA kit (TransGen Biotech, China) was used to extract total RNA from Arabidopsis plants according to manufacturer’s instructions.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: leaf

value: before wounding treatment


title: Leaf 6 of WT plant one hour after wounding leaf 1 (rep 3) [W1h-4]

value: one hour after wounding leaf 1


title: Leaf 6 of WT plant one hour after wounding leaf 1 (rep 1) [W1h-1]


title: Leaf 6 of WT plant one hour after application of 100 mM Glu to leaf 1 (rep 3) [G1h-11]


title: APP-V717I replicate 2 [ATAC-seq]


title: APP-V717I replicate 3 [ATAC-seq]


title: APP-V717I replicate 1 [ATAC-seq]


title: Leaf 6 of WT plant one hour after wounding  leaf 1 (rep 2) [W1h-2]

value: one hour after wounding  leaf 1


title: Leaf 6 of WT plant before wounding treatment (rep 2) [0min-2]

description:
The mock control of wounding treatment
0min-2


title: E9.5_22,PGC,XY

value: embryo

value: PGC


title: Leaf 6 of WT plant without small molecule treatment (rep 3) [X0min-4]

description:
The mock control of GSH/Glu treatment
X0min-4

value: without small molecule treatment


title: Leaf 6 of WT plant one hour after application of 100 mM GSH to leaf 1 (rep 1) [M1h-1]


title: Leaf 6 of WT plant one hour after application of 100 mM GSH to leaf 1 (rep 2) [M1h-3]


title: aitf1-1asr3-1_3h_rep3

city: Wuhan

first: Ying

last: Wang

address: No.1 Shizishan Street

institute: Huazhong Agricultural University

data_processing:
RNA-Seq: analysis was performed using  Hisat2 (v 2.1.0) and FeatureCounts in the Subread package (v1.6.5)
Genome_build: Arabidopsis genome (TAIR10) was obtained from Ensembl (http://plants.ensembl.org/).
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for every gene and every sample

source_name: seedling

growth_protocol: Plants were grown in soil (KEKKILA) in a growth room at 21°C, 45% humidity, and 75 μE m-2 s-1 light with a 12-hr-light/12-hr-dark photoperiod. 14-day-old seedlings were cultured on half-strength Murashige and Skoog (1/2MS) plates containing 1% sucrose and 0.8% agar, and grown under the same condition as above.

extract_protocol: Total RNA was extracted from plant leaves  by RNAprep Pure Plant Plus Kit (Polysaccharides&Polyphenolics-rich).

tag: age

value: seedling


title: aitf1-1asr3-1_3h_rep2


title: Leaf 6 of WT plant before wounding treatment (rep 1) [0min-1]

description:
The mock control of wounding treatment
0min-1


title: aitf1-1asr3-1_3h_rep1


title: aitf1-1asr3-1_1h_rep3


title: Leaf 6 of WT plant one hour after application of 100 mM Glu to leaf 1 (rep 2) [G1h-3]


title: aitf1-1asr3-1_0h_rep3


title: aitf1-1asr3-1_0h_rep2


title: aitf1-1asr3-1_0h_rep1


title: PSEN1-A79V replicate 2 [ATAC-seq]

value: Alzheimer's disease


title: Leaf 6 of WT plant one hour after application of 100 mM GSH to leaf 1 (rep 3) [M1h-6]


title: Leaf 6 of WT plant one hour after application of 100 mM Glu to leaf 1 (rep 1) [G1h-2]


title: Leaf 6 of WT plant without small molecule treatment (rep 2) [X0min-3]

description:
The mock control of GSH/Glu treatment
X0min-3


title: OXAITF1_rep2

source_name: plant

value: plant leaf


title: OXAITF1_rep1


title: NDC replicate 2 [ATAC-seq]

value: hiPSC-derived neurons


title: WT_rep1


title: brain vessels, heart-healthy diet + statin, rep3

city: Beltsville

first: Gloria

last: Solano-Aguilar

state: MD

address: 10300 Baltimore Ave

institute: USDA-ARS

data_processing:
CLC Genomics Workbench 11.0.1
Sequences were trimmed for adaptor content and low quality bases using a Quality Limit of 0.01.
Trimmed sequences were mapped to the non-redundant (NR_11-13-19) transcript library available in the Porcine Translational Research Database maintained by the Beltsville Human Nutrition Research Center, Diet, Genomics, and Immunology Laboratory,  (parameters: length fraction=0.95, similarity fraction=0.95)
Read counts ("unique gene reads") were exported to csv format.
Assembly: NR_11-13-19
Supplementary files format and content: comma delimited text file containing raw counts for each sample

organism: Sus scrofa

source_name: brain vessels

growth_protocol: Pigs were gradually acclimatized to their respective diet beginning at two months of age and at four months were exclusively fed the assigned diet in isocaloric amounts for six months. Caloric intake was adjusted to the pigs’ growing needs.

extract_protocol:
Blood microvessels were isolated from the right brain temporal region using an established method.This method is designed to purify neurovascular units which comprise small blood vessel and associated pericytes and perivascular astrocyte end-feet. Briefly, a 150-200 mg frozen slice of the temporal region was minced in sterile HBSS, 10 mM HEPES (buffer B1),  homogenized in a Dounce homogenizer, and centrifuged at 2,000 g for 10 min at 4 °C. The pellet, comprising microvessels and myelin, was resuspended in ice-cold buffer B2 (B1 containing 18 g dextran from Leuconostoc spp/100 mL). After centrifugation at 4,400 g for 15 min at 4 °C, the supernatant and myelin were discarded and the vessel pellet resuspended in ice-cold buffer B3 (B1 containing 1% BSA), filtered through a 20 µm mesh membrane (Millipore, Burlington, MA), and recentrifuged. The pellet, containing purified brain microvessels was immediately processed for RNA isolation.
Libraries were constructed using Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina, San Diego, CA, USA) and AMPure XP beads (Beckman Coulter, Hercules, CA) according to the manufacturers’ protocols. Library quantification was performed using KAPA Library Quantification kit (KAPA Biosystems, Wilmington, MA) and library fragment size was determined using Experion DNA 1K Analysis kit (Bio-Rad, Hercules, CA).

treatment_protocol: The WD and HHD diets were designed to be similar to typical human diets and have the same macronutrient content, consisting of 38% energy as fat, 47% energy as carbohydrates, and 15% as protein.However, the two diets differed in macronutrient composition, with the WD high in saturated fatty acids, cholesterol and refined carbohydrates and low in fiber, and the HHD high in unsaturated fatty acids, unrefined carbohydrates and fiber, low in cholesterol, and containing a freeze-dried fruit and vegetable mix (Futureceuticals, Momence, IL).18 Pigs assigned to the HHD were also supplemented with omega-3 fatty acids (one capsule containing 550 mg EPA and 200 mg DHA 3 times/week). Pigs assigned to statin treatment were given 20 mg of atorvastatin (Lipitor; Pfizer, New York, NY) each day for the first 3 months of the dietary intervention and 40 mg atorvastatin each day during the last 3 months.

value: brain vessels

tag: Sex

value: female

value: heart-healthy diet + statin


title: aitf1-1asr3-1_1h_rep2


title: brain vessels, heart-healthy diet + statin, rep2

value: male


title: brain vessels, heart-healthy diet, rep5

value: heart-healthy diet


title: brain vessels, heart-healthy diet, rep4


title: WT_0h_rep3


title: aitf1-1asr3-1_1h_rep1


title: brain vessels, heart-healthy diet, rep3


title: WT_3h_rep3


title: WT_3h_rep2


title: brain vessels, heart-healthy diet, rep2


title: brain vessels, western diet + statin, rep8

value: western diet + statin


title: WT_3h_rep1


title: WT_1h_rep3


title: WT_1h_rep2


title: brain vessels, western diet + statin, rep6


title: brain vessels, western diet + statin, rep5


title: WT_1h_rep1


title: brain vessels, western diet + statin, rep1


title: WT_0h_rep2


title: Leaf 6 of WT plant without small molecule treatment (rep 1) [X0min-2]

description:
The mock control of GSH/Glu treatment
X0min-2

value: leaf


title: WT_0h_rep1


title: 10x lib 83, donor N369, MDS

first: Liran

last: Shlush

address: 234 Herzl Street

description:
Library name: 10x_lib_83_donor_N369_blood_sample_222
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model

data_processing:
Count matrices were generated using 10x Genomics' Cell Ranger v7.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest).
As each 10x scRNA library contained pooled cells of multiple individuals, both Vireo (https://github.com/single-cell-genetics/vireo) and Souporcell (https://github.com/wheaton5/souporcell) were used (on each 10x library separately) to cluster cells based on SNPs found in the sequenced RNA. Cells that were identified as doublets by Vireo or Souporcell were discarded. Resulting clusters were matched to targeted genotype data obtained for each donor.
Cells with high mitochondrial content (>20%), platelet signature (PPBP > 0.2%), neutrophil signature (LCN2, CAMP, LTF), erythrocyte signature (HBB, HBA1, HBA2), or with low signature of nuclear RNAs were excluded. As part of additional doublet detection, cells were excluded if their UMI count was higher than 2.5-fold of their cluster median computed (thereby compensating for variable cell sizes across types), as well as if they exhibited high expression of both monocyte and MEBEMP gene programs.
Assembly: GRCh38-3.0.0
Supplementary files format and content: h5ad file (https://anndata.readthedocs.io/en/stable/) containing count matrix and cell metadata.

source_name: peripheral blood

extract_protocol:
Peripheral blood was drawn into lithium-heparin tubes. PBMCs were isolated via Ficoll, using Lymphoprep filled Sepmate tubes (StemCell technologies), followed by CD34 magnetic bead-based enrichment using the EasySep human CD34 positive selection kit II (StemCell technologies). 3-6 individual samples were pooled on each experiment day such that CD34-enrichment was performed on the entire pool of PBMCs produced. Few samples were not pooled due to logistical issues of timing blood donations, as sampling was restricted to fresh blood.
Single cell RNA libraries were generated using the 10x Genomics scRNA-seq platform (Chromium Next Gem single cell 3’ reagent kit V3.1) according to the manufacturer's instructions, except that we "super-loaded" each chromium chip lane, loading cells at a significantly higher concentration than recommended, with an expected yield of ~20-25k single cells.

value: peripheral blood

value: PBMC

value: MDS


title: WT_rep2


title: brain vessels, heart-healthy diet + statin, rep7


title: brain vessels, heart-healthy diet + statin, rep8


title: brain vessels, heart-healthy diet + statin, rep6


title: 10x lib 83, donor N180, MDS

description:
Library name: 10x_lib_83_donor_N180_blood_sample_218
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 82, donor N307, normal

description:
Library name: 10x_lib_82_donor_N307_blood_sample_215
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model

value: normal


title: brain vessels, heart-healthy diet + statin, rep5


title: brain vessels, heart-healthy diet + statin, rep4


title: brain vessels, heart-healthy diet + statin, rep1


title: brain vessels, heart-healthy diet, rep6


title: 10x lib 81, donor N357, normal

description:
Library name: 10x_lib_81_donor_N357_blood_sample_213
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 81, donor N356, normal

description:
Library name: 10x_lib_81_donor_N356_blood_sample_212
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 80, donor N356, normal

description:
Library name: 10x_lib_80_donor_N356_blood_sample_212
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 80, donor N355, normal

description:
Library name: 10x_lib_80_donor_N355_blood_sample_211
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: brain vessels, heart-healthy diet, rep1


title: 10x lib 81, donor N354, normal

description:
Library name: 10x_lib_81_donor_N354_blood_sample_210
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: brain vessels, western diet + statin, rep7


title: brain vessels, heart-healthy diet, rep7


title: 10x lib 81, donor N260, normal

description:
Library name: 10x_lib_81_donor_N260_blood_sample_209
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 80, donor N260, normal

description:
Library name: 10x_lib_80_donor_N260_blood_sample_209
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 79, donor N188, MDS

description:
Library name: 10x_lib_79_donor_N188_blood_sample_208
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: brain vessels, western diet + statin, rep4


title: 10x lib 78, donor N25, normal

description:
Library name: 10x_lib_78_donor_N25_blood_sample_207
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 81, donor N355, normal

description:
Library name: 10x_lib_81_donor_N355_blood_sample_211
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 78, donor N240, MDS/MPN

description:
Library name: 10x_lib_78_donor_N240_blood_sample_206
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model

value: MDS/MPN


title: brain vessels, western diet, rep7

value: western diet


title: brain vessels, western diet, rep5


title: brain vessels, western diet, rep4


title: brain vessels, western diet, rep2


title: brain vessels, western diet, rep3


title: 10x lib 77, donor N322, normal

description:
Library name: 10x_lib_77_donor_N322_blood_sample_203
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: brain vessels, western diet, rep1


title: 10x lib 76, donor N320, normal

description:
Library name: 10x_lib_76_donor_N320_blood_sample_201
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 76, donor N319, normal

description:
Library name: 10x_lib_76_donor_N319_blood_sample_200
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 83, donor N211, MDS

description:
Library name: 10x_lib_83_donor_N211_blood_sample_220
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 76, donor N318, normal

description:
Library name: 10x_lib_76_donor_N318_blood_sample_199
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 77, donor N317, normal

description:
Library name: 10x_lib_77_donor_N317_blood_sample_198
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 83, donor N208, cytopenia

description:
Library name: 10x_lib_83_donor_N208_blood_sample_219
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model

value: cytopenia


title: 10x lib 76, donor N317, normal

description:
Library name: 10x_lib_76_donor_N317_blood_sample_198
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 74, donor N309, normal

description:
Library name: 10x_lib_74_donor_N309_blood_sample_197
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: brain vessels, western diet + statin, rep3


title: brain vessels, western diet + statin, rep2


title: 10x lib 83, donor N368, MDS/MPN

description:
Library name: 10x_lib_83_donor_N368_blood_sample_221
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: brain vessels, western diet, rep6


title: 10x lib 82, donor N363, normal

description:
Library name: 10x_lib_82_donor_N363_blood_sample_217
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 74, donor N12, MDS

description:
Library name: 10x_lib_74_donor_N12_blood_sample_192
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 73, donor N299, cytopenia

description:
Library name: 10x_lib_73_donor_N299_blood_sample_190
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 72, donor N293, normal

description:
Library name: 10x_lib_72_donor_N293_blood_sample_185
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 72, donor N294, cytopenia

description:
Library name: 10x_lib_72_donor_N294_blood_sample_186
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 81, donor N359, MDS

description:
Library name: 10x_lib_81_donor_N359_blood_sample_214
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 82, donor N362, normal

description:
Library name: 10x_lib_82_donor_N362_blood_sample_216
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 80, donor N354, normal

description:
Library name: 10x_lib_80_donor_N354_blood_sample_210
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 80, donor N359, MDS

description:
Library name: 10x_lib_80_donor_N359_blood_sample_214
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 72, donor N291, normal

description:
Library name: 10x_lib_72_donor_N291_blood_sample_183
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 73, donor N300, normal

description:
Library name: 10x_lib_73_donor_N300_blood_sample_191
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 70, donor N285, normal

description:
Library name: 10x_lib_70_donor_N285_blood_sample_178
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 70, donor N283, cytopenia

description:
Library name: 10x_lib_70_donor_N283_blood_sample_176
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 77, donor N321, normal

description:
Library name: 10x_lib_77_donor_N321_blood_sample_202
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 78, donor N196, cytopenia

description:
Library name: 10x_lib_78_donor_N196_blood_sample_205
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 76, donor N321, normal

description:
Library name: 10x_lib_76_donor_N321_blood_sample_202
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 80, donor N357, normal

description:
Library name: 10x_lib_80_donor_N357_blood_sample_213
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 69, donor N281, MDS/MPN

description:
Library name: 10x_lib_69_donor_N281_blood_sample_174
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model


title: 10x lib 78, donor N1, normal

description:
Library name: 10x_lib_78_donor_N1_blood_sample_204
DNA of this sample (obtained by 10x Genomics scRNA-seq) was sent to Ultima Genomics and sequenced by them on an early UG model