title: PitaZAD276FLAG_ad_2_FLAG

city: Moscow

first: Natalia

last: Klimenko

address: 34/5 Vavilova Street

country: Russia

institute: Institute of Gene Biology (IGB) of the Russian Academy of Sciences

description: Library name: Sample 11

data_processing:
Trimming Illumina adapters with cutadapt
Trimming low quality tails with sickle (https://github.com/najoshi/sickle) (with -q 20 option)
Alignment with bowtie2 against version dm6 of the Drosophila melanogaster genome
Filtration of PCR duplicates and non-unique mapping with picard (https://broadinstitute.github.io/picard/)
Blacklist filtration with bedtools
Reproducible peaks calling was conducted against corresponding preimmune controls with IDR pipeline (https://sites.google.com/site/anshulkundaje/projects/idr).  A soft p value threshold for MACS2 in IDR of 0.01, the IDR reproducibility threshold was set to 0.05 for true replicates and 0.01 for pseudoreplicates. All samples showed good reproducibility (the rescue ratio or/and the self consistency ratio were <2).
ChiP-Seq coverage tracks were obtained using deepTools (Ramírez et al. 2014) bamCoverage functions  with a bin width of 50 bps and RPKM normalization.
Assembly: dm6
Supplementary files format and content: Processed data was obtained by IDR and MACS2 and deeptools bamCoverage and includes: extended bed (narrowPeak) peak calls regions and coverage (bedGraph)

organism: Drosophila melanogaster

source_name: whole organism

growth_protocol: Drosophila strains were maintained on standard medium at 25°C and 50-60% humidity.

extract_protocol:
After 3 rounds of washing with lysis buffer supplemented with 500 mM NaCl, and TE buffer (10 mM Tris-HCl, pH 8; 1 mM EDTA), the DNA was eluted with elution buffer (50 mM Tris-HCl, pH 8.0; 1 mM EDTA, 1% SDS), the cross-links were reversed, and the precipitated DNA was extracted by the ChIP DNA Clean &Concentrator kit (Zymoresearch).
Libraries were prepared according to manufacturers recommendations with small modifications. In short, 1-10ng of purified, RNase treated, and reverse cross-linked genomic DNA was end-repaired and terminal adenosine residues were added using the NEBNext reagents. Custom-made indexed adapters were ligated, after which the material was size selected at ~200-600 bp with MagSelect XP beads (Magen). PCR amplification was performed using PE1.0 and PE2.0 primers (custom-made) for 12 cycles for Input samples and 14 to 15 cycles for IP-ed samples using the Q5 Hot Start HiFi PCR Master Mix (NEB). The PCR-amplified library was purified using Ampure XP beads and its quality was assessed on a Bioanalyzer 2100 system (Agilent). The libraries were sequenced on aNovaSeq 6000 (Illumina) in pair-end mode.

treatment_protocol: Chromatin was prepared from two- to three-day-old adult flies. A 1 g of adult flies was ground in a mortar in liquid nitrogen and resuspended in 20 mL of buffer A (15 mM HEPES-KOH, pH 7.6, 60 mM KCl, 15 mM NaCl, 13 mM EDTA, 0.1 mM EGTA, 0.15 mM spermine, 0.5 mM spermidine, 0.5% NP-40, 0.5 mM DTT) supplemented with 0.5 mM PMSF and Calbiochem Cocktail V. The suspension was then homogenized subsequently in a Potter and Dounce homogenizer with tight pestle, filtered through 100 µm Nylon Cell Strainer (Miltenyi Biotec, United States), and cross-linked with 1% formaldehyde for 15 min at room temperature. Cross-linking was stopped by adding glycine to a final concentration of 125 mM. The nuclei were washed with three 10-mL portions of wash buffer (15 mM HEPES-KOH, pH 7.6, 60 mM KCl, 15 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 0.1% NP-40, protease inhibitors), one 5-mL portion of nuclear lysis basic buffer (15 mM HEPES, pH 7.6, 140 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 1% Triton X-100, 0.5 mM DTT, 0.1% sodium deoxycholate, protease inhibitors) and resuspended in 1 mL of nuclear lysis buffer (15 mM HEPES, pH 7.6, 140 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 1% Triton X-100, 0.5 mM DTT, 0.1% sodium deoxycholate, 0.5% SLS, 0.1% SDS, protease inhibitors). The suspension was sonicated in a Covaris ME220 focused-ultrasonicator (40 alternating 15-s ON and 45-s OFF intervals, peak power 75, duty % factor 25), and 50-µL aliquots were used to test extent of sonication and to measure DNA concentration. Debris was removed by centrifugation at 14 000 g, 4°C, for 10 min, and chromatin was pre-cleared with Protein A Dynabeads (Invitrogen). Corresponding antibodies were incubated for 1 hour at room temperature with 20 µL aliquots of Protein A (anti-Pita C, 1:100; anti-Flag, 1:200) Dynabeads (Invitrogen) mixed with 200 µL of PBST. Then antibodies-Dynabeads complexes were washed and equilibrated in nuclear lysis buffer. Chromatin samples containing 10–20 µg of DNA equivalent in 200 µL of nuclear lysis buffer (2 µL aliquots of such pre-cleared chromatin being stored as input material) were incubated overnight, at 4°C, with antibodies-Dynabeads complexes.

value: whole organism

value: pita1attP PitaZ276

tag: development stage

value: adult

tag: antibody source

value: rabbit

tag: antibody

value: FLAG


title: PBMC_LEP_5

status: Public on Dec 09 2025

type: RNA

city: Palma

first: Paula

last: Oliver

address: Cra. Valldemossa km 7.5

country: Spain

institute: University of the Balearic Islands

hyb_protocol: After 16 h hybridization, the arrays were washed and stained using the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The arrays were scanned at 0.7 μm resolution using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Normalization and data analysis were executed by the “Bioinformatics and Biostatistics Unit” from the “Príncipe Felipe Research Center” (Valencia, Spain). The raw data background was corrected following Robust Multichip Average (RMA). All statistical analyses were performed with R version 4.0.4 and R Studio version 1.4.1717 software. Differences in expression were calculated with a moderate t statistic of the limma package, and the contrasts studied were HF vs CTRL, LEP vs CTRL and LEP vs HF group.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: PBMC

label_protocol: Probing of Affymetrix GeneChip Rat Clariom S microarrays 10+30 (Affymetrix UK Ltd., High Wycombe, UK) was performed as described in the manufacturer’s protocols. The probes were prepared from aliquots of 100 ng total RNA by the instructions supplied with the Affymetrix WT PLUS Reagent Kit.

extract_protocol: Total RNA from the PBMC and hippocampus samples of young 3.5-month-old animals were isolated using Tripure reagent (Roche Diagnostics Barcelona, Spain) following the manufacturer’s protocol. Before analysis, RNA integrity and purity were determined using the RNA Nano 6000 Chip on an Agilent Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA). RNA integrity numbers (RIN) were evaluated using a Bioanalyzer (Agilent Technologies Inc.) and were between 7 and 10 for all the samples.

treatment_protocol: Two-month-old virgin female Wistar rats were mated with male rats. After matching, females were placed in individual cages with free access to water and food. On day 1 after delivery, excess pups in each litter were removed to keep 10 pups per dam. Male pups from a total of 8 litters were randomly assigned into 2 groups receiving different experimental treatments from day 1 to day 20 of lactation during the first 2 h of the beginning of the light cycle: Control (n = 16), leptin (n = 10). All treatments were administered orally. A solution of recombinant murine leptin (PeproTech, London, UK) dissolved in Captisol® was administered to leptin group. The amount of leptin administered to the animals was calculated as five times the average amount of daily leptin intake from breast milk; the Control group received the same volume of the vehicle, Captisol®. On day 21, after weaning, male rats were single-caged and kept on a normolipidic control balanced diet (D12450B, Research Diets). On day 23, the Control group rats were randomly assigned to two groups: normal-weight, CTRL group (n = 8), fed ad libitum a standard chow diet with 10% calories from fat (D12450B, Research Diets); and MONW, HF group (n = 8), fed a chow diet with 60% calories from fat (D12492, Research Diets), administered under isocaloric conditions to CTRL, to prevent development of obesity. Moreover, the leptin treated group, LEP group (n=10) received the same hyperlipidic diet as the HF group, also administered under isocaloric conditions relative to the CTRL group.

tag: tissue

value: PBMC

tag: gender

value: male

tag: diet

value: Hyperlipidic diet with 60% calories from fat (D12492, Research Diets) administered under isocaloric conditions to the CTRL group


title: HiC_LOS_#6

type: SRA

city: Columbia

first: Rocío

middle: Melissa

last: Rivera

state: MO

address: 920 East Campus Drive

department: Division of Animal Sciences

country: USA

institute: University of Missouri, Columbia

description:
Library name: Sample_11
Original fetal ID: 664

library_source: genomic

data_processing:
The processing of Hi-C raw sequencing reads was based on the ‘Hi-C Processing Pipeline’ from 4D Nucleome Data Portal. Briefly, reads were aligned to the corresponding reference genome using bwa 0.7.17 with parameters ‘mem -SP5M’. Reads with mapping quality (MAPQ) equal or greater than 30 were kept for analysis. Then, pairtools 0.3.0 was used to parse, sort, and deduplicate aligned reads, and pair types ‘UU’, ‘UR’, and ‘RU’ were selected. Cooler and Juicer were used to convert contact matrix to .cool and .hic files.
Hi-C data was also used to identify genomic variants following the pipeline for 1000 bull genome project. Briefly, Read groups were added using AddOrReplaceReadGroups function of picard 2.25.5 for aligned Hi-C sequencing reads. Duplicated reads were marked using MarkDuplicates function of picard with parameter ‘--OPTICAL_DUPLICATE_PIXEL_DISTANCE 2500’. For bovine, the dataset of known variants was acquired from the 1000 bull genome project, namely ARS1.2PlusY_BQSR_v3.vcf.gz. GATK 4.2.6.1 was used to recalibrate base quality and identify genomic variants in the Hi-C data with the known variant dataset as reference. Parameters used for BaseRecalibrator were ‘–bqsr-baq-gap-open-penalty 45 --read-filter MappingQualityReadFilter --minimum-mapping-quality 20’ for bovine. In addition, for bovine, our previously generated genomic sequencing data for semen DNA of the bull used to sire all the fetuses in this study was included for joint genotyping in order to assign alleles for the genomic variants (GEO: GSE197130). HaplotypeCaller was used with parameter ‘-ERC GVCF’, and GenomicsDBImport and GenotypeGVCFs were used with default settings. For bovine, raw SNP and INDEL were separately scored using VariantRecalibrator with parameter ‘--resource:1000G,known=false,training=true,truth=true,prior=10.0 known_variant -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR’. Scored variants were filtered using ApplyVQSR with parameter ‘--truth-sensitivity-filter-level 99.0’.
For bovine, variants used for allele assignment met the following criteria: 1) marked as PASS by ApplyVQSR, 2) GQ>=40 in the bull and the fetus, 3) DP>=10 in the bull, 4) no read supports not assigned alleles in the bull and the fetus, 5) only one allele of the bull is shown in the fetus. In addition, variants on chrX identified in male fetuses were excluded from analyses, since which is likely due to the lack of chrY in the reference genome. Alleles were assigned for bovine Hi-C reads based on qualified variants using custom Perl scripts. For SNP, the nucleotide in the reads at the SNP location was directly used for allele assignment. For INDEL, local maternal and paternal allele pseudo genomes were generated, and the reads were realigned to both pseudo genomes. The reads were assigned to the alleles with more aligned bases, or less mismatches if aligned base numbers were the same. Next, variants with biased allelic ratio of Hi-C reads (one allele is less than 15%) were excluded from analyses. Lastly, reads that cover multiple variants and have conflicting allele assignments were excluded from the analyses.
Assembly: ARS-UCD1.2
Supplementary files format and content: Chromosomal contacts in pairs, cool, and hic format. Genomic variants in vcf format. Genomic variants for allele assignment in txt format.

molecule: genomic DNA

organism: Bos indicus x Bos taurus

source_name: skin fibroblast primary cell

growth_protocol: Day 105 Bos taurus indicus (B. t. indicus; Brahman breed) x Bos taurus taurus (B. t. taurus; Angus breed) F1 hybrid fetuses were generated by our laboratory in 2019 (PMID: 35542046) and used as tissue donors. Fetal skins were collected to establish fibroblast primary cell line using protocol adapted from a publication (PMID: 24198123). Fibroblast cells were cultured in bovine embryonic fibroblast medium (89% (v/v) DMEM (Gibco, 11885084), 10% (v/v) fetal bovine serum (Atlanta Biologicalsa, S11150H), and 1% (v/v) Antibiotic-antimycotic (Gibco, 15240062)) at 38.5°C with 5% CO2.

extract_protocol: Hi-C sequencing for fibroblast cells was conducted by CD Genomics (Shirley, NY, USA). Information on library preparation and sequencing obtained from the company is as follows: Cells were cross-linked with 1% formaldehyde at room temperature and quenched with glycine. The cross-linked cells were subsequently lysed. Endogenous nucleases were inactivated with 0.3% SDS, then chromatin DNA were digested by MboI (NEB), marked with biotin-14-dCTP (Invitrogen), and ligated by T4 DNA ligase (NEB). After reversing cross-links, the ligated DNA was extracted through QIAamp DNA Mini Kit (Qiagen) according to manufacturers’ instructions. Purified DNA was sheared to 300-500 bp fragments and were further blunt-end repaired, A-tailed and adaptor-added, followed by purification and PCR amplification. Finally, equimolar pooling of libraries was performed based on QC values and sequenced on Novaseq6000 sequencer (Illumina) with a read length configuration of 150 bp for 1,000M PE reads per sample (1,000M in each direction).

treatment_protocol: For bovine fetuses, artificial insemination was used to generate the control group and assisted reproductive technologies (ART) were used to generate the ART group (PMID: 35732675). The large offspring syndrome (LOS) group was defined as individuals from the ART group with body weight greater than 97th centile of controls.

tag: cell type

value: skin fibroblast primary cell

tag: developmental stage

value: D105 fetus

tag: conception method

value: Assisted reproductive technology

tag: disease status

value: LOS

tag: Sex

value: Male


title: PitaZAD276FLAG_ad_1_Pita

description: Library name: Sample 10

tag: genotype

tag: strain

value: Pita


title: C57BL/6_17W_3

city: Beijing

first: Zhiying

last: Gao

state: Beijing

address: Peking Union Medical College Hospital (Dongdan campus), No.1 Shuaifuyuan Wangfujing Dongcheng District, Beijing,China 100730

department: Department of Nephrology

country: China

institute: Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences

description: Library name: SAMPLES_3

library_source: transcriptomic

data_processing:
V2-Dr.TOM Ⅱ
Data filtering: The raw sequencing data are called raw tags. We obtained clean tags using the SOAPnuke[1]. The filtering rules were as follows: removed low quality tags; removed tags with 5’ primer contaminants; remove tags without 3’ primer; removed tags without insertion; removed tags with poly A; removed tags shorter than 15nt.
Small RNA Annotation and miRNA Identification: After filtering, the clean tags were mapped to the reference genome and other sRNA database including miRbase, siRNA, piRNA and snoRNA with Bowtie2[2]. Particularly, cmsearch[3] was performed for Rfam mapping. In the annotation information of different RNAs, to ensure that each small RNA was mapped to a unique category, we set the following rules: MiRbase(v22) > pirnabank(v1.0) > snoRNA(v1.2 human/plant ) > Rfam (v12.1)> other sRNA. The miRDeep-P2 [4] or miRDeep2[5] package was used to identify potentially novel miRNAs. The potentially novel miRNAs and were named novel_mirXXX, in which XXX is a unique number specified for each novel miRNA candidate.
miRNA quantification: The small RNA expression level is calculated by counting absolute numbers of molecules using unique molecular identifiers [11]. The expression formula is:C is the number of UMIs of reads that were mapped to the small RNA, T is the UMI number of total clean reads of the sample.
Differential Expression Analysis: Differential expression analysis was performed using the DEGseq [12] (or DESeq2[13] or PoissonDis[14]) on Dr. Tom Multi-omics Data Mining System (https://biosys.bgi.com). Q value≤ 0.05 (or FDR value≤0.001) was used to judge the significance of expression difference.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: txt files include TPM values for each Sample

organism: Mus musculus

source_name: Kidney

extract_protocol:
RNA was harvested using TRIzol (Invitrogen, Carlsbad, California, USA). 2 ug of total RNA was used for the construction of sequencing libraries.
The library was constructed using the MGIEasy MiRNA Library Prep Kit (BGI-Shenzhen). RNA was sequentially ligated with 3' and 5' adapters, followed by reverse transcription into cDNA and amplification via PCR. Fragment size selection was performed using polyacrylamide gel electrophoresis to ensure quality control. The single-stranded library was then denatured and circularized, with uncyclized linear DNA molecules removed. The circularized DNA was amplified through phi29 and rolling circle amplification (RCA) to generate DNA nanoballs (DNBs), each containing over 300 copies of the original single-stranded circularized molecule. DNA nanoballs (DNBs) were deposited onto a patterned nanoarray, and paired-end 50-base sequencing reads were generated using the G400 platform (BGI-Shenzhen, China).

value: Kidney


title: PBMC_LEP_3


title: C57BL/6_17W_2

description: Library name: SAMPLES_2


title: PitaZAD276FLAG_ad_1_FLAG

description: Library name: Sample 9


title: PitawtFLAG_ad_2_Pita

description: Library name: Sample 8

value: pita1attP Pitawt


title: Preimmune

description: Library name: Sample 13

value: IgG


title: HiC_LOS_#4

description:
Library name: Sample_9
Original fetal ID: 512


title: PitawtFLAG_ad_2_FLAG

description: Library name: Sample 7

value: whole organism


title: MRL/lpr_17W_3

description: Library name: MRL/lpr_17W_3

data_processing:
V2-Dr.TOM Ⅱ
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1). Differential expression analysis was performed using the DESeq2(v1.34.0) (or DEGseq（v1.48.0 or PoissonDis) with Q value ≤ 0.05 (or FDR ≤ 0.001).
The normalized expression values for each gene were compiled into a tab-delimited text file (rna_expression.txt), with each row corresponding to a gene and each column representing a sample.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: csv files include FPKM values for each Sample

extract_protocol:
RNA was harvested using TRIzol (Invitrogen, Carlsbad, California, USA). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seg were prepared using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China) following manufacturer's protocols.

value: MRL/MpJ-Fas<lpr>/J


title: PitawtFLAG_ad_1_Pita

description: Library name: Sample 6

value: adult


title: PitaZAD276FLAG_ad_2_Pita

description: Library name: Sample 12

value: pita1attP PitaZ276

value: rabbit


title: HiC_LOS_#3

description:
Library name: Sample_8
Original fetal ID: 604B

value: Female


title: PBMC_LEP_2

value: PBMC

value: male


title: C57BL/6_17W_1

description: Library name: SAMPLES_1


title: MRL/lpr_17W_1

description: Library name: SAMPLES_4


title: MRL/lpr_17W_2

description: Library name: MRL/lpr_17W_2


title: HiC_LOS_#1

description:
Library name: Sample_6
Original fetal ID: 616

value: skin fibroblast primary cell


title: PitawtFLAG_ad_1_FLAG

description: Library name: Sample 5

value: FLAG


title: HiC_LOS_#5

description:
Library name: Sample_10
Original fetal ID: 602

value: D105 fetus

value: Assisted reproductive technology


title: PBMC_LEP_4

value: Hyperlipidic diet with 60% calories from fat (D12492, Research Diets) administered under isocaloric conditions to the CTRL group


title: PBMC_HF_8


title: PBMC_HF_7


title: HiC_CON_B_#5

description:
Library name: Sample_5
Original fetal ID: 527

value: Artificial insemination

value: Healthy

value: Male


title: MRL/lpr_17W_1

description: Library name: MRL/lpr_17W_1

value: Kidney


title: PBMC_LEP_1


title: PitadZADFLAG_ad_2_Pita

description: Library name: Sample 4

value: whole organism

value: y1w1118; pita1attP PitadeltaZ

value: pita1attP PitadeltaZ

value: Pita


title: MRL/lpr_8W_3

description: Library name: MRL/lpr_8W_3

value: MRL/MpJ-Fas<lpr>/J


title: MRL/lpr_8W_2

description: Library name: MRL/lpr_8W_2


title: HiC_CON_B_#4

description:
Library name: Sample_4
Original fetal ID: 648


title: PitadZADFLAG_ad_2_FLAG

description: Library name: Sample 3

value: adult

value: rabbit


title: HiC_CON_B_#3

description:
Library name: Sample_3
Original fetal ID: 640


title: HiC_LOS_#2

description:
Library name: Sample_7
Original fetal ID: 656

value: LOS

value: Female


title: PBMC_HF_5

value: PBMC

value: male


title: PBMC_HF_4


title: PitadZADFLAG_ad_1_Pita

description: Library name: Sample 2


title: MRL/lpr_8W_1

description: Library name: MRL/lpr_8W_1


title: HiC_CON_B_#2

description:
Library name: Sample_2
Original fetal ID: 647

value: skin fibroblast primary cell

value: D105 fetus


title: C57BL/6_17W_3

description: Library name: C57BL/6_17W_3


title: PBMC_HF_6

value: Hyperlipidic diet with 60% calories from fat (D12492, Research Diets) administered under isocaloric conditions to the CTRL group


title: HiC_CON_B_#1

description:
Library name: Sample_1
Original fetal ID: 533

value: Artificial insemination

value: Healthy


title: PBMC_HF_3


title: PitadZADFLAG_ad_1_FLAG

description: Library name: Sample 1

value: FLAG


title: C57BL/6_17W_2

description: Library name: C57BL/6_17W_2

value: Kidney


title: Rhesus macaque spleen CD45+ cells, multiplexed run 1

city: Quebec

first: Jerome

last: Estaquier

state: Quebec

address: 2705 Boul Laurier

department: Maladies infectieuses et immunitaires

country: Canada

institute: Centre de recherche du CHU - Université Laval

description:
Library name: Mix1
BD Rhapsody scRNA-seq, multiplexed with SampleTags (3100 Treated, 3101 Treated, 3106 Infected, 09071222 Naive)

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were processed using the BD Rhapsody Whole Transcriptome Analysis (WTA) pipeline. Reads were filtered for quality, demultiplexed by sample tag, and aligned to the Macaca mulatta reference genome (Ensembl GCA_003339765.3). Unique molecular identifiers (UMIs) were used to collapse PCR duplicates, and cell barcodes were used to generate cell-by-gene count matrices in Market Exchange (MEX) format (matrix.mtx, barcodes.tsv, features.tsv).
Processed matrices were analyzed using the Seurat R package (v5.2.1). Data were log-normalized (NormalizeData, method = "LogNormalize", scale.factor = 10,000), scaled (ScaleData), and dimensionality reduction was performed with PCA on highly variable genes.
Clustering was performed with a shared nearest neighbor approach (FindNeighbors, FindClusters, resolutions 0.3–0.5). Visualization was done with UMAP (dims = 1:20, n.neighbors = 50, min.dist = 0.3).
Marker genes were identified using FindAllMarkers with thresholds min.pct = 0.35 and logfc.threshold = 1, followed by Benjamini-Hochberg FDR correction. Differential expression gene (DEG) analysis between conditions was performed using FindMarkers, with results visualized by volcano plots (EnhancedVolcano v1.22.0).
Functional enrichment analyses were performed using ToppFun and g:Profiler.
Assembly: Macaca mulatta reference genome Mmul_10, Ensembl release (GCA_003339765.3).
Supplementary files format and content: Processed data are provided in the 10x MEX) format. The file matrix.mtx.gz contains the sparse gene–cell expression matrix, with rows corresponding to genes and columns corresponding to cell barcodes; the values represent raw UMI counts (molecules per cell) prior to any normalization. The file features.tsv.gz lists the features corresponding to the rows of the matrix, including Ensembl gene IDs and gene symbols. The file barcodes.tsv.gz lists the unique cell barcodes corresponding to the columns of the matrix.

molecule: polyA RNA

organism: Macaca mulatta

source_name: Spleen

growth_protocol: Rhesus macaques (Macaca mulatta, Chinese origin, females, ~40 months old, 4.5 ± 0.3 kg) were housed in compliance with French and European animal care regulations (Directive 2010/63/EU). All animals were seronegative for STLV-1, SRV-1, Herpes-B viruses, and SIV. Animals were intravenously inoculated via the saphenous vein with Leishmania infantum promastigotes (clone MHOM/MA/67/ITMAP-263; 2×10^7 parasites/kg). At day one post-infection, macaques received miltefosine (HePC, 5 mg/kg) for 21 days. Animals were sacrificed at defined time points (weeks 5, 9, and 12 post-infection). Tissues including spleen were collected at necropsy.

extract_protocol:
Spleen mononuclear cells were isolated by Ficoll-Paque density gradient centrifugation (Sigma). Cell suspensions were stained with a CD45 antibody. Four samples (Naive, Infected, and two treated RMs) were pooled and loaded onto a single BD Rhapsody cartridge (~40,000 cells per cartridge). Cells were lysed and polyadenylated mRNAs were captured on barcoded magnetic beads according to the BD Rhapsody protocol. Each transcript was tagged with a unique molecular identifier (UMI) and a cell-specific barcode. cDNA was synthesized and amplified following the manufacturer’s instructions prior to library preparation
Single-cell cDNA libraries were generated using the BD Rhapsody Single-Cell RNA-Seq Library Preparation Kit according to the manufacturer’s instructions. After reverse transcription and second-strand synthesis, cDNAs containing unique molecular identifiers (UMIs) and cell barcodes were amplified by PCR. Sequencing libraries were prepared following the BD Rhapsody workflow, including fragmentation, end repair, A-tailing, adaptor ligation, and sample index PCR. Library quality and size distribution were assessed using the Agilent 4200 TapeStation, and concentrations were measured with the Qubit dsDNA HS assay kit (Invitrogen). Pooled libraries were sequenced on an Illumina NovaSeq 6000 platform with paired-end reads, targeting a depth of ~50,000 reads per cell and ~600 reads per cell for sample tag libraries.

treatment_protocol: Naïve animals are controls. Infected animals were intravenously inoculated with Leishmania infantum promastigotes. Treated animals were infected and treated with a daily dose of miltefosine starting at day one post-infection. HePC was adminitrated by nasogastric gavage at 5 mg/kg for 21 consecutive days.

value: Spleen

tag: cell line

value: CD45+ cells

tag: characteristics [condition]

value: multiplexed

tag: characteristics [multiplex_tag]

tag: characteristics [sampletag]

tag: treatment

value: HePC/Naive/Infected

tag: batch


title: Rhesus macaque spleen CD45+ cells, multiplexed run 2

description:
Library name: Mix2
BD Rhapsody scRNA-seq, multiplexed with SampleTags (3100 Treated, 3101 Treated, 3106 Infected, 09071222 Naive)


title: C57BL/6_17W_1

description: Library name: C57BL/6_17W_1


title: MelFemale_dsx_neurons

city: Philadelphia

first: Justin

last: Walsh

state: PA

address: 3740 Hamilton Walk

institute: University of Pennsylvania

description:
Library name: MelFemale_dsxNeurons
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using CellRanger software v7.1.0
Assembly: GCA_000001215.4
Assembly: GCA_016746365.2
Assembly: GCA_016746245.2
Assembly: GCA_016746235.2
Supplementary files format and content: tab-separated value files, matrix files, and Rds files

source_name: central nervous system

extract_protocol:
For each replicate, the central nervous system of approximately 100 doublesex-GAL4 x UAS-nls::tdTomato flies were dissected in ice cold Schneider's medium and digested in a solution containing Liberase DH for 45 mins. The tissue was washed with Schneider's medium and broken apart via pipetting before FACS sorting out the tdTomato+ cells.
Library was constructed according to the manufacter's instructions (single cell 3' V2 protocol, 10X Genomics)

value: central nervous system

value: neurons

value: female

tag: age

value: 4-8 days


title: Mel2_dsx_neurons

description:
Library name: Mel2_dsxNeurons
10X Genomics

tag: tissue


title: PBMC_HF_2

value: PBMC

tag: gender


title: S15

city: Wuhan

first: Pengbo

last: Wang

state: Hubei

address: hongshan street

institute: Huazhong university of science and technology

data_processing:
Fastp software was used to filter raw reads by quality, and STAR was used to align clean reads to the reference genome of E. coli BL21 (DE3).
The expression abundance of each gene in each sample was identified by sequence similarity comparison. Stringtie was used to obtain the number of reads aligned to the gene in each sample and calculate gene count.
The number of gene count of each sample was normalized by DESeq2 software, when p-value and fold change (FC) of difference comparison were calculated.
The differentially expressed genes (DGEs) were screened based on false discovery rate (FDR) < 0.05 and FC > 2.
The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the differential genes were performed by clusterProfiler.
Assembly: NCBI Genome assembly ASM2266v1
Supplementary files format and content: Files include FPKM values for each sample and gene changes for different treatments.

organism: Escherichia coli

growth_protocol: E.coli was cultivated at 37 ℃ and 200rpm in 50ml LB for 2.5h. Then IPTG was added to achiece a final concentration of 1 mmol/L. After induction,  flask was transferred to 20℃ and 200rpm, and continue cultivating for 16h.

extract_protocol:
RNA was exacted using Bacteria RNA Extraction Kit (Vazyme).
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II RNA Library Prep with Sample Purification Beads (NEW ENGLAND biolabs).

treatment_protocol: The culture was centrifuged and resuspended in equal volume sterile phosphate buffer solution (PBS, pH 7.2). Multiple bottles of cluture medium were mixed and then divided into 50ml centrifuge tubes, making all the sample same before treatment.Samples  were placed on ice until HI-PMF treatment. The sham group was in the same environment without HI-PMF treatment. After treatment, the samples were placed on ice again until centrifuging and removing the supernatant. The cells were placed on dry ice until extracting mRNA.

value: HI-PMF at 2.5 T and 15 pulses


title: C57BL/6_8W_3

description: Library name: C57BL/6_8W_3


title: PBMC_CTRL_8

value: male

tag: diet

value: Standard chow diet with 10% calories from fat (D12450B, Research Diets)


title: PBMC_HF_1

value: Hyperlipidic diet with 60% calories from fat (D12492, Research Diets) administered under isocaloric conditions to the CTRL group


title: S1

tag: cell type


title: PBMC_CTRL_6


title: PBMC_CTRL_7


title: C6

value: control


title: Subcutaneous fat SVF-derived single-cell clone 4, SF4

city: BLACKSBURG

first: Zhendong

last: Tan

state: VA

address: 175 West Campus Drive

institute: Virginia Tech

description: Library name: sample 8

data_processing:
The raw RNA-seq reads were filtered using Trimmomatic v0.39 to remove low-quality reads and reads containing adapters. Clean reads were aligned to the bovine reference genome ARS-UCD 2.0 using STAR v2.7.11a.
Gffread v0.12.18 was used to convert the genomic annotation files from gff to gtf format
FeatureCounts (v2.0.2) was used to estimate the read counts
Differential expression analysis was performed using the DESeq2 (v1.42.0) R package
Genes with Benjamini–Hochberg approach adjusted P value < 0.05 and |log2fold change| ≥ 1 were designated as differentially expressed genes (DEGs)
Assembly: ARS-UCD 2.0
Supplementary files format and content: Comma separated file includes raw counts for each sample and list of all genes that are differentially expressed

organism: Bos taurus

source_name: Adipose tissue

extract_protocol:
Total RNA was extracted using TRIzol reagent (Zymo Research, Irvine, CA) and the Direct-zol RNA MiniPrep Plus Kit (Zymo Research)
Total RNA was extracted and fragmented, followed by first-strand cDNA synthesis using random hexamer primers. Second-strand cDNA synthesis was performed using a dUTP mix. The resulting double-stranded cDNA was purified using the AMPure XP system. After end repair and adaptor ligation, the adaptor-linked cDNA was again purified with the AMPure XP system and enriched through 10 cycles of PCR. The final cDNA library was purified using the AMPure XP system, pooled, and paired-end sequenced on an Illumina platform.

treatment_protocol: Intramuscular and subcutaneous adipose tissue was collected from five adult Angus cross breed steers.

value: Adipose tissue

tag: Stage

value: Adult

value: SF-derived preadipocytes


title: Subcutaneous fat SVF-derived single-cell clone 3, SF3

description: Library name: sample 7


title: C57BL/6_8W_2

description: Library name: C57BL/6_8W_2

value: Kidney


title: C57BL/6_8W_1

description: Library name: C57BL/6_8W_1


title: Mel3_dsx_neurons

description:
Library name: Mel3_dsxNeurons
10X Genomics


title: C13


title: Subcutaneous fat SVF-derived single-cell clone 2, SF2

description: Library name: sample 6


title: PBMC_CTRL_5


title: peak phase EAE2

city: Xian

first: Jiaji

last: Lin

address: No. 1. XinSi Road

department: Neurology

institute: Forth Military Medicial University

description: Library name: peak phase EAE2

data_processing:
*1. Raw FASTQ reads were quality-checked by FastQC and trimmed to remove adapters and low-quality bases. 2. Clean reads were aligned to the Mus musculus reference genome (GRCm38/NCBIM38) using HISAT2 v2.0.5. 3. Gene-level quantification was performed using HTSeq-count. 4. Expression normalization was performed using FPKM. 5. Differential expression analysis was conducted using DESeq2 with thresholds
Assembly: Mus musculus GRCm38 (NCBIM38), GENCODE vM29 annotation.
Supplementary files format and content: Processed data include gene-level count matrices in tab-delimited text format with rows representing genes and columns representing samples, and normalized expression values (FPKM). Metadata files include sample group (EAE/control), time point (5 dpi / 15 dpi), and sequencing platform (NovaSeq / DNBSEQ-T7).

source_name: Liver

growth_protocol: Female C57BL/6J mice (6–8 weeks old) were obtained from the Laboratory Animal Center of Fourth Military Medical University. Mice were maintained under SPF conditions with a 12 h light/dark cycle, 40–70% humidity, and 20–26 °C ambient temperature, with ad libitum access to food and water.

extract_protocol:
Liver tissue was perfused via the portal vein with cold PBS to remove blood, then dissected and snap-frozen in liquid nitrogen. Total RNA was extracted using TRIzol reagent (Invitrogen) with on-column DNase I treatment, followed by quality control: A260/A280 1.8–2.1, A260/A230 ≥ 2.0, RIN ≥ 7.0.
Liver transcriptome profiling was conducted at two distinct timepoints during EAE progression. For the first analysis, total RNA was extracted from liver tissues collected at theEAE peak phase (approximately 15 days post-immunization, dpi) and compared with baseline controls (pre-immunization). Libraries were constructed using the Illumina NEBNext® Ultra™ RNA Library Prep Kit following the manufacturer’s protocol. Qualified libraries were pooled and subjected to 150-bp paired-end sequencing on an Illumina NovaSeq 6000 platform. The second transcriptomic study focused on the EAE pre-onset phase (approximately 5 dpi), again comparing livers with baseline controls. RNA extraction was followed by library preparation using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina. Library quality was assessed using an Agilent 2200 system, and sequencing was performed on a DNBSEQ-T7 platform with a 150-bp paired-end configuration.

treatment_protocol: Experimental autoimmune encephalomyelitis (EAE) was induced by immunizing mice with 200 μg MOG35–55 peptide emulsified in CFA containing 500 μg M. tuberculosis, followed by intraperitoneal injection of 200 ng pertussis toxin on days 0 and 2. Neurological scores were assessed daily using a 0–5 scale. Samples were collected at two time points: pre-onset phase (5 days post-immunization) and peak phase (15 days post-immunization). For each time point, both EAE-induced and non-immunized control groups were included, resulting in four experimental groups in total.

value: Liver

value: wild type

value: MOG35-55 peptide-induced EAE


title: Subcutaneous fat SVF-derived single-cell clone 1, SF1

description: Library name: sample 5


title: PBMC_CTRL_4


title: peak phase EAE3

description: Library name: peak phase EAE3


title: Intramuscular fat SVF-derived single-cell clone 4, IMF4

description: Library name: sample 4

value: IMF-derived preadipocytes


title: PCSC+, Rep2

city: Gustavo A. Madero

first: ROSAURA

middle: HERNANDEZ

last: RIVAS

state: Ciudad de México

address: Av. Instituto Politécnico Nacional 2508

department: Molecular Biomedicine

country: Mexico

institute: CINVESTAV

description: miRNAs expression data from PANC-1 PCSC+.

hyb_protocol: The microarray was placed in a hybridization oven (Affymetrix)and was incubated at 48°C and 60 rpm for 16 to 18 hours. After, the array was removed from the oven. The hybridization cocktail was removed and transferred to a new tube for storage at -80°C. The array was equilibrated to room temperature with Array Holding Buffer before washing and staining. To perform the staining and washing process, the microarray was placed in a fluidic station and the protocol was continued.    Abrir en Google Traductor  •  C

scan_protocol: It was used a A Model 3000 7G microarray scanner with autoloader and workstation  (Affymetrix)

data_processing: Microarray data were normalized using RMA and background adjustment was performed following a linear additive model. Statistical analysis was conducted with empirical Bayes and limma, a parametric method based on linear models

organism: Homo sapiens

source_name: PANC-1 PCSC+

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 130 ng of total RNA.

growth_protocol: PANC-1 cell line was grown in DMEM high glucose medium (Sigma D-5030), supplemented with Fetal Bovine Serum (FBS, Gibco 10437028) at a final concentration of 10% and in presence of 1X Penicillin/Streptomycin (100x) (Gibco, 10378016) at 37°C under a humidified 5% CO2 atmosphere. Then, PDAC-1 cells (5000/well) were seed in Ultra-low attachment surface 96-well plates (Sigma CLS3474) in serum-free media supplemented with FGF-2 (10 ng/mL) and EGF (20 ng/mL). The spheres were collected after seven days for FACS assays.

extract_protocol: Total RNA was extracted with TRIzol according to the manufacturer's instructions.

treatment_protocol: PCSC+ and PCSC- cells were selected using surface makers (CD24, CD44 and CD133) throught FACS assays.


title: PBMC_CTRL_3


title: peak phase EAE1

description: Library name: peak phase EAE1


title: Intramuscular fat SVF-derived single-cell clone 3, IMF3

description: Library name: sample 3


title: peak phase NC3

description: Library name: peak phase NC3


title: Intramuscular fat SVF-derived single-cell clone 2, IMF2

description: Library name: sample 2


title: PCSC-, Rep2

description: miRNAs expression data from PANC-1 PCSC-.

source_name: PANC-1 PCSC-


title: PBMC_CTRL_2


title: PCSC+, Rep1


title: TSC_AML

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: GA74233

data_processing:
Sequencing was performed on DNBSEQ-G400 platform in 28+100 or 28+50-base paired-end mode.
Raw sequencing data were converted to matrices of expression using Space Ranger (version spaceranger-2.0.0 or 2.1.1, 10X Genomics).
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: ('title name')_filtered_('file name'): files in Space Ranger output folder "filtered_feature_bc_matrix"
Supplementary files format and content: ('title name')_raw_('file name'): files in Space Ranger output folder "raw_feature_bc_matrix"
Supplementary files format and content: ('title name')_spatial_('file name'): files in Space Ranger output folder "spatial"
Library strategy: Spatial Transcriptomics

source_name: Angiomyolipoma associated with Tuberous Sclerosis Complex

extract_protocol:
Visium Human Transcriptome Probe Set v2.0 and Visium V4 Slide - FFPE v2 chemistry were used to extract total RNA and hybridize transcriptomic probes to the Visium slide.
Sequencing library preparation were performed according to standard protocol of the Visium CytAssist Spatial Gene Expression for FFPE.


title: PBMC_CTRL_1


title: Sporadic_AML

description: Library name: GA74232

source_name: Sporadic Angiomyolipoma

value: Sporadic Angiomyolipoma


title: peak phase NC2

description: Library name: peak phase NC2


title: Intramuscular fat SVF-derived single-cell clone 1, IMF1

description: Library name: sample 1


title: OSA4_Long_Treat_T2_D8

status: Public on Dec 08 2025

type: genomic

city: Cincinnati

first: Bala S. C.

last: Koritala

state: Ohio

address: 3333 Burnet Avenue

department: Division of Pediatric Otolaryngology

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: Standard Illumina protocol

scan_protocol: DNA methylation in PBMCs was evaluated in bisulfite-converted genomic DNA using the Illumina Infinium® Methylation EPIC Bead Chip array (Illumina, San Diego, CA, USA) and scanned on an Illumina iScan using standard Illumina protocol.

data_processing:
Quality control, preprocessing, and normalization of DNA methylation data were performed using R packages, minfi (v1.38.0), watermelon (v2.2.0), and FlowSorted.Blood.EPIC (v2.0.0)
Average Beta value

label: Cy3 and Cy5

source_name: Blood

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted from PBMCs using GeneJET Genomic DNA Purification Kit (#K0792, Thermo ScientificTM), according to the manufacturer’s instructions.

value: Blood

value: Peripheral Blood Mononuclear Cells

value: Patients with long-term CPAP


title: SI-GA-D11, scRNA-seq

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

description:
10x Genomics
SYMASYM_B2019_2019_011

data_processing:
The demulitplexing, barcoded processing, counting and aggregation were made using Cell Ranger software (v5.0.0).
Assembly: Gallus gallus ensembl 96
Supplementary files format and content: Files from raw_feature_bc_matrix directory
Supplementary files format and content: tabulated files

organism: Gallus gallus

source_name: spinal cord

extract_protocol:
Three chick embryos at 66 hours of embryonic development were collected and dissected in ice-cold 1X PBS, transferred into ice-cold L15 medium for further dissection to retain only the cervical spinal region (spanning 5 somites starting from somite n°8). To generate single-cell suspension solution dissection products were then transferred in 250µL of 37°C pre-heated papain/L15 solution (Worthington, REF: LS003126 – Stock solution = 41,6mg/mL in 100mL; Working solution = 50µL of stock solution diluted in 1,5mL of L15 medium) and incu-bated at 37°C for 15 minutes.  Papain was then replaced with ice-cold L15 medium, and clus-ters of cells were disaggregated through gentle up-and-down pipetting. Cells were then cen-trifuged at 300g for 2 minutes at 4°C. Supernatant was removed, and 500µL of new ice-cold L15 medium was added. Another round of up-and-down pipetting was performed, and cells were then applied on 30µm filters to eliminate clumps of poorly-dissociated cells. Filtered cells were then centrifuged for 4 minutes at 300g, and supernatant was replaced with 1000µL of 1X PBS containing 0.04% BSA. Cells were then centrifuged for 4 minutes at 300g, 900µL of supernatant was removed and cells were then re-suspended in remaining 100µL of solution.  Quality control was assayed by counting live vs dead cells using Trypan blue. Sam-ples with >90% viability were then used for sequencing. After viability assessment, cell concentration of samples was adjusted to 1000cells/µL.
The library construction was performed according to the manufacter's intructions (single cell 3' v3 protocol; 10x Genomics)

value: spinal cord

tag: developmental stage

value: at 66 hours of development (HH18)

value: neuroepithelium

value: no tratment


title: OSA2_Long_Treat_T2_D5


title: OSA6_Long_Treat_T2_D15


title: OSA9_Long_Treat_T2_D1


title: cMet & β-catenin 2weeks-1

city: New Brunswick

first: Xinlu

last: Han

address: 164 Frelinghuysen Road Piscataway

institute: Rutgers university

description:
Library name: 2W6855
Column name in RPKM_allSamples.txt : 2wk6855

data_processing:
The RNA-seq reads were mapped to the mouse genome reference (Mus musculus genome (UCSC mm10)) using HISAT2, Gene-level quantification was counted using FEATURE COUNTS, differentially expressed gene analysis was conducted using DEseq, heatmap was generated using iDEP online tool https://bioinformatics.sdstate.edu/idep/. Functional enrichment analysis was performed using the Metascape online tool https://metascape.org/gp/index.html#/main/step1.
Assembly: UCSC mouse genome build mm10
Supplementary files format and content: The processed data files are in txt format.  The first column contains the gene name and the other columns contain the RPKM of the gene

extract_protocol:
Total RNA was extracted from snap-frozen liver tissues using a TRIzol™ (Invitrogen #15596026) and PureLink RNA Mini Kit (Invitrogen, #12183018A) combined method.
Approximately 500 ng Total RNA was used for RNA-seq library preparation by following kapa rRNA depletion Total RNA-se sample preparation kit

value: Hepatocyte


title: peak phase NC1

description: Library name: peak phase NC1


title: cMet & β-catenin 3weeks-4

description:
Library name: 3W8125
Column name in RPKM_allSamples.txt : 3wk8125


title: cMet & β-catenin 2weeks-2

description:
Library name: 2W6863
Column name in RPKM_allSamples.txt : 2wk6863


title: cMet & β-catenin 3weeks-3

description:
Library name: 3W8122
Column name in RPKM_allSamples.txt : 3wk8122


title: Control-2

description:
Library name: 0W7682
Column name in RPKM_allSamples.txt : 0wk7682


title: Control-3

description:
Library name: 0W7684
Column name in RPKM_allSamples.txt : 0wk7684


title: PCSC-, Rep1


title: cMet & β-catenin 2weeks-4

description:
Library name: 2W8124
Column name in RPKM_allSamples.txt : 2wk8124


title: cMet & β-catenin 2weeks-3

description:
Library name: 2W8121
Column name in RPKM_allSamples.txt : 2wk8121


title: OSA9_D1

value: Patients with no treatment


title: Control-1

description:
Library name: 0W7628
Column name in RPKM_allSamples.txt : 0wk7628


title: cMet & β-catenin 3weeks-1

description:
Library name: 3W8092
Column name in RPKM_allSamples.txt : 3wk8092


title: OSA1_Long_Treat_T2_D4


title: EHU-W2

description: Library name: GA47837

source_name: Kidney Cancer

value: Kidney Cancer


title: OSA6_D15


title: OSA5_Long_Treat_T2_D11


title: OSA5_D11


title: OSA4_D8


title: OSA2_D5


title: Healthy10_C12

value: Healthy subjects with no treatment


title: OSA1_D4


title: Healthy6_CB14


title: Healthy5_CB7


title: Healthy4_F2D12


title: Healthy3_C22


title: Healthy1_AMC6


title: HiPSC-aCM-TTN-WT-1

city: Chicago

first: Mahmud

middle: Arif

last: Pavel

email: gmmahmud@uic.edu, arvindsr@uic.edu

state: Illinois

address: 840 South Wood Street, Suite 920S

department: Medicine/Cardiology

institute: University of Illinois at Chicago

description: Library name: Sample1

data_processing:
Sequenced reads were aligned to Homo sapiens reference genome GRCh38 (hg38) with STAR v. 2.7.6a
mRNA expressions were quantified from the aligned reads by using STAR from option -quantMode
Gene symbols were annotated using the biomaRt R package
Principal component analysis (PCA) was performed after normalization. DEGs were identified using DESeq2, with FDR < 0.05 and absolute log2fold-change higher than 1. DEGs for each comparison were plotted using the ComplexHeatmap R package
Assembly: To define the biological function significantly associated with the DEGs identified from each comparison, we performed gene set enrichment analysis suing the enrichGO function from clusterProfiler R package
Supplementary files format and content: Genome_build: Homo sapiens reference genome GRCh38 (hg38)
Supplementary files format and content: Supplementary_files_format_and_content: Processed data files are provided as .txt

source_name: Atrial cells

growth_protocol: HiPSCs were maintained on human recombinant vitronectin coated plates in mTeSR medium. HiPSCs were then differentiated using the cardiomyocyte differentiation kit (Gibco), and guided into atrial subtypes using 1µmol/l all-trans retinoic acid (protocol adapted from Devalla et al., 2015). At day 10, glucose starvation metabolic selection was used to enrich the iPSC-aCM culture. For matured iPSC-aCMs, thyroid hormone, insulin-like growth factor, dexamethasone, palmitic acid, and oleic acid were added to the foundational maintenance media from day 18-32, and the cells were subjected to electrical field stimulation from day 18-25.

extract_protocol:
All total RNA samples were isolated Trizol phenol chloroform method at 1.5 ug of RNA.
RNA-seq

value: Atrial cells

value: HiPSC-aCM

value: WT


title: HiPSC-aCM-TTN-WT-3

description: Library name: Sample3


title: HiPSC-aCM-TTN-T32756I-2

description: Library name: Sample5

value: Point mutation


title: Healthy2_C16


title: HiPSC-aCM-TTN-T32756I-1

description: Library name: Sample4


title: HiPSC-aCM-TTN-T32756I-3

description: Library name: Sample6


title: NLVspecific T cells, No Treat Control, Day1, Replicate 1

city: Bronx

first: Harris

last: Goldstein

state: NY

address: 1300 Morris Park Avenue

department: Pediatrics

institute: Albert Einstein College of Medicine

description: Library name: CH_un_L004

data_processing:
STAR 2.4.2a for alignment
subread 1.5.0.post3 (featureCount) for quantification of genes
removed zero-sum rows from raw gene counts, then excluded rows where 80% or more number of samples fall below the threshold of 10
Assembly: GRCh37
Supplementary files format and content: comma separated values gene counts per samples (column)

source_name: CD8 T cell

growth_protocol: PBMC were rested overnight in complete RPMI1640 media supplemented with 10% FBS, 1X GlutaMAX (Gibco, Ref# 35050-061), 1X Penicillin Streptomycin Solution (Corning, Ref# 30-002-CI), 100mM HEPES buffer, and 100 U/mL IL-2 before treatment

extract_protocol:
RNA was isolated using the micro RNeasy Plus kit (Qiagen, Cat# 74034)
For the day 1 experiment, Novogene's Ultra-low input mRNA non-directional library preparation was used. For the day 5 experiment, Novogene's standard mRNA library preparation was used

treatment_protocol: For the day 1 experiment, PBMC were treated in complete RPMI1640 media supplemented with 10% FBS, 1X GlutaMAX (Gibco, Ref# 35050-061), 1X Penicillin Streptomycin Solution (Corning, Ref# 30-002-CI), 100mM HEPES buffer, and 100 U/mL IL-2 using 0.01nM of TCR agonist alone (NLV-FLAG IST), TCR agonist + CD28 agonist (NLV-antiCD28 IST), TCR agonist + 4-1BB agonist (NLV-4-1BBL IST), or no treatment for 24 hours. For the day 5 experiment, PBMC were treated in RPMI1640 media supplemented with 10% FBS, 1X GlutaMAX (Gibco, Ref# 35050-061), 1X Penicillin Streptomycin Solution (Corning, Ref# 30-002-CI), 100mM HEPES buffer, and 100 U/mL IL-2 using TCR agonist alone (NLV-FLAG IST) for 4 days or no treatment. Then, some samples received no retreatment, TCR agonist alone (NLV-FLAG IST) retreatment, or TCR agonist + 4-1BB agonist (NLV-4-1BBL IST) retreatment

value: CD8 T cell

value: Male

value: No Treat

tag: time

value: Day 1


title: NLVspecific T cells, NLV41BBL retreat, Day5, Replicate 1

description: Library name: NLV_41BBL_retreat_D5_1

tag: Sex

value: NLVFLAG to NLV41BBL

value: Day 5


title: NLVspecific T cells, NLVFLAG, Day1, Replicate 1

description: Library name: CH_252_L004

value: NLVFLAG


title: NLVspecific T cells, NLVFLAG, Day5, Replicate 2

description: Library name: NLV_FLAG_D5_2


title: NLVspecific T cells, NLVFLAG, Day1, Replicate 2

description: Library name: CH_252_2


title: NLVspecific T cells, NLV41BBL retreat, Day5, Replicate 2

description: Library name: NLV_41BBL_retreat_D5_2


title: NLVspecific T cells, NLVFLAG, Day5, Replicate 1

description: Library name: NLV_FLAG_D5_1


title: NLVspecific T cells, No Treat Control, Day5, Replicate 2

description: Library name: Unstim_D5_2


title: NLVspecific T cells, NLVFLAG retreat, Day5, Replicate 2

description: Library name: NLV_FLAG_retreat_D5_2

value: NLVFLAG to NLVFLAG


title: NLVspecific T cells, No Treat Control, Day1, Replicate 3

description: Library name: CH_un_3


title: NLVspecific T cells, NLVFLAG retreat, Day5, Replicate 1

description: Library name: NLV_FLAG_retreat_D5_1


title: NLVspecific T cells, No Treat Control, Day5, Replicate 1

description: Library name: Unstim_D5_1


title: NLVspecific T cells, NLV41BBL, Day1, Replicate 3

description: Library name: CH_285_3


title: NLVspecific T cells, NLV41BBL, Day1, Replicate 2

description: Library name: CH_285_2


title: NLVspecific T cells, NLVantiCD28, Day1, Replicate 3

description: Library name: CH_304_3


title: NLVspecific T cells, NLVantiCD28, Day1, Replicate 2

description: Library name: CH_304_2


title: HiPSC-aCM-TTN-WT-2

description: Library name: Sample2

tag: genotype


title: Ishikawa_input

city: Salt Lake City

first: Alexandra

last: Richey

state: UT

address: 2000 Cir of Hope Dr

department: Biomedical Engineering

institute: University of Utah

description: Library name: Ishikawa_input

data_processing:
Read 1 was aligned to the hg19 build of the human genome using Bowtie: -m1 -t -best -q -S -l 32 -e 80 -n 2
SAMtools was used to sort and convert SAM files to BAM files
MACS2 was used to call peaks with a P-value cutoff of 1x10-10 and mfold parameter between 15 and 100
Assembly: hg19
Supplementary files format and content: BigWig files
Supplementary files format and content: narrowPeak files from MACS2

source_name: Ishikawa

growth_protocol: Cells were cultured in full serum media: RPMI-1640 with 10% fetal bovine serum and 1% penicillin-streptomycin. Cells were incubated at 37°C with 5% CO2 for the duration of all experiments. 5 days prior to treatment, cells were placed in hormone deprived media: phenol-red free RPMI-1640 media (Thermo Fisher Scientific) with 10% charcoal-dextran stripped fetal bovine serum (Thermo Fisher Scientific) and 1% penicillin-streptomycin.

extract_protocol:
Cells were fixed using 1% formaldehyde (Sigma Aldrich, 252549) for 10 minutes at room temperature to cross-link DNA and proteins. Cross-linking was stopped by addition of glycine (Fisher Scientific, BP381) to a final concentration of 125 mM. Cells were then washed with cold PBS and harvested via scraping in Farnham lysis buffer supplemented with protease and phosphatase inhibitors (Thermo Scientific, A32959).
Chromatin immunoprecipitation was performed as previously described (Reddy et al. Genome Research 2009) with 5 μg of a goat anti-SOX17 (R&D Systems, AF1924) antibody.

treatment_protocol: Cells were treated with 0.1% DMSO for one hour.

value: Ishikawa

value: endometrial adenocarcinoma

value: pooled input

tag: chip antibody


title: NLVspecific T cells, NLVantiCD28, Day1, Replicate 1

description: Library name: CH_304_L004


title: hepatocyte_Mttp_KO_CM_5

city: Mineola

first: M. Mahmood

last: Hussain

state: New York

address: 101 Mineola Blvd.

department: Foundations of Medicine

institute: NYU Grossman Long Island School of Medicine

data_processing:
Raw data in fastq format were processed by Novogene using their in-house Perl scripts  to obtain clean reads by removing adapter sequences, reads with poly-N, and low-quality reads.
Trimmed sequence reads were mapped to GRCm39/mm39 using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm39
Supplementary files format and content: tab-limited text file includes raw counts for each sample
Supplementary files format and content: tab-limited text file includes FPKM values for each sample

source_name: Hepatocytes

growth_protocol: Stromal vascular fraction (SVF) was isolated from inguinal adipose tissue collected in PBS as described previously26 from male Mttpf/f and A-Mttp–/– mice (n=3) fed an obesogenic diet for 6 months. The minced tissue was incubated with digestion buffer (1.5 U/mL of collagenase D, 2.4 U/mL of dispase II, and 10mM CaCl2) for 30 min to 1 h until the tissue and digestion buffer became homogeneous. The digestion was stopped by adding an equal volume of PBS containing 0.5 % BSA and centrifuged at 300 g for 5 min at room temperature. The cell pellet was resuspended in PBS containing 0.5% BSA and passed through a 100 µM cell strainer. The flow through was centrifuged again at 300 g for 5 min at room temperature and the pellet was re-suspended in PBS containing 0.5% BSA and passed through 40 µM cell strainer. The flow through was centrifuged at 300 g for 5 min and the resultant pellet was re-suspended in DMEM containing 10% FBS supplement with 1% antibiotics (penicillin and streptomycin) and transferred to a T75 flask. The media was changed the next day. The cells were either used for experiment or cryo-frozen in freezing media (90% FBS, and 10% DMSO). Mouse SVF was differentiated using a differentiation cocktail containing 500 μM IBMX, 5 μg/mL insulin, 1 μM dexamethasone, 200 μM indomethacin and 1 µM rosiglitazone. Cells were maintained in a differentiation cocktail media for 3 days. Differentiation media was replaced with media containing insulin 5μg/ml and maintained for 2 days. Further adipocytes were maintained DMEM containing 10% FBS supplement with 1% antibiotics (penicillin and streptomycin) for 2 days. Mice were anesthetized and sacrificed by cervical dislocation. The vena cava was canulated using 24 G butterfly syringe and connected to a peristaltic pump. A small cut was made in the portal vein and the liver was perfused with 35 mL of PBS containing 1% penicillin/streptomycin mix. The liver was further perfused with 35 mL liver perfusion medium (Gibco, #17701038) containing 1% penicillin/streptomycin mix followed by 35 mL liver digestion media (Gibco, #17703034) containing 0.25 % collagenase II (Thermo Fisher Scientific, #17101015). The liver was collected and minced in digestion media and incubated in rotor at 37 °C till the liver tissue and liver digestion media became homogenous. An equal volume of hepatocyte culture media (Gibco, #17705-021) containing 10% FBS was added to neutralize the action of collagenase and centrifuged at 300g for 10 mins. The resultant pellet was washed with hepatocyte wash buffer and again centrifuged at 300g for 10 mins. The supernatant was discarded, and the pellet was resuspended in hepatocyte culture media and filtered through 100 µM cell strainer (Thermo Fisher Scientific, Catalog No #431752). The flow through was collected, and centrifuged at 300g for 10 mins. The resultant pellet was resuspended in hepatocyte culture media and seeded in collagen coated 6 well plates (Corning #356400). The next day the media was replaced with fresh hepatocyte culture media and proceeded for experiment as mentioned in results and figure legends.

extract_protocol:
Total RNA was isolated from different organs using a TRIZOL reagent. The RNA was purified using  RNA purification kit. RNA concentrations were measured using NanoDrop (Thermo Scientific™, USA, #ND-2000).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP. It was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Wild type hepatocytes were treated over night with condition media from overnight starved Mttpflox and Mttp KO adipocytes.

value: Hepatocytes

value: Mttp KO conditioned media


title: cMet & β-catenin 3weeks-2

description:
Library name: 3W8095
Column name in RPKM_allSamples.txt : 3wk8095

value: Liver

value: Hepatocyte


title: NLVspecific T cells, NLVFLAG, Day1, Replicate 3

description: Library name: CH_252_3


title: NLVspecific T cells, No Treat Control, Day1, Replicate 2

description: Library name: CH_un_2


title: Ishikawa_SOX17_DMSO

description: Library name: Ishikawa_SOX17_DMSO

tag: cell line

value: DMSO

value: SOX17 (R&D Systems, AF1924)


title: 041_SMSCTRNRAS2_SMSCTRNRAS2

city: Baltimore

first: Michael

last: Considine

state: Maryland

address: 550 North Broadway

institute: Johns Hopkins University

description: Library name: 041_SMSCTRNRAS2_SMSCTRNRAS2

data_processing:
trimgalor-0.6.3, a wrapper for cutadapt and FastQC is used to trim the adaptors from fastq files.
rsem-1.3.0 was used for running the alignments as well as generating gene and isoform expression levels. The ‘rsem-calculate-expression’ module was used with the following options: --star --calc -ci --star-output-genome-bam --forward-prob 0
Assembly: hg38
Supplementary files format and content: tab delimited text file containing tpm normalized counts, tab delimited text files containing detailed output for each respective file (including expected counts, which are essentially raw counts)

source_name: Rhabdomyosarcoma cell line

growth_protocol: RMS cell lines were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted from cell pellets, using Trizol Phenol Chloroform extraction followed by  RNeasy (Qiagen)
Library Protocol TruSeq Stranded Total RNA Sample Prep Guide, Part # 15031048 Rev. E
Library Kit TruSeq Stranded Total RNA LT Sample Prep Kit (Human Mouse Rat)

value: Rhabdomyosarcoma cell line

value: SMS-CTR

value: HRAS Q61K mutant

value: siNRAS


title: 044_SMSCTRNT2_SMSCTRNT2

description: Library name: 044_SMSCTRNT2_SMSCTRNT2

value: non-targeting control


title: 043_SMSCTRNT1_SMSCTRNT1

description: Library name: 043_SMSCTRNT1_SMSCTRNT1


title: 045_SMSCTRNT3_SMSCTRNT3

description: Library name: 045_SMSCTRNT3_SMSCTRNT3


title: 042_SMSCTRNRAS3_SMSCTRNRAS3

description: Library name: 042_SMSCTRNRAS3_SMSCTRNRAS3


title: NLVspecific T cells, NLV41BBL, Day1, Replicate 1

description: Library name: CH_285_L004

value: CD8 T cell

value: Male

value: Day 1


title: 040_SMSCTRNRAS1_SMSCTRNRAS1

description: Library name: 040_SMSCTRNRAS1_SMSCTRNRAS1


title: 039_SMSCTRHRAS3_SMSCTRHRAS3

description: Library name: 039_SMSCTRHRAS3_SMSCTRHRAS3

value: siHRAS


title: 036_RH36NT3_RH36NT3

description: Library name: 036_RH36NT3_RH36NT3


title: 033_RH36NRAS3_RH36NRAS3

description: Library name: 033_RH36NRAS3_RH36NRAS3


title: 035_RH36NT2_RH36NT2

description: Library name: 035_RH36NT2_RH36NT2


title: 032_RH36NRAS2_RH36NRAS2

description: Library name: 032_RH36NRAS2_RH36NRAS2


title: 031_RH36NRAS1_RH36NRAS1

description: Library name: 031_RH36NRAS1_RH36NRAS1


title: 009_JHERMS2NT3_JHERMS2NT3

description: Library name: 009_JHERMS2NT3_JHERMS2NT3

value: HRAS G12S mutant


title: 029_RH36HRAS2_RH36HRAS2

description: Library name: 029_RH36HRAS2_RH36HRAS2


title: 028_RH36HRAS1_RH36HRAS1

description: Library name: 028_RH36HRAS1_RH36HRAS1


title: 034_RH36NT1_RH36NT1

description: Library name: 034_RH36NT1_RH36NT1


title: 006_JHERMS2NRAS3_JHERMS2NRAS3

description: Library name: 006_JHERMS2NRAS3_JHERMS2NRAS3


title: 008_JHERMS2NT2_JHERMS2NT2

description: Library name: 008_JHERMS2NT2_JHERMS2NT2


title: 004_JHERMS2NRAS1_JHERMS2NRAS1

description: Library name: 004_JHERMS2NRAS1_JHERMS2NRAS1


title: 003_JHERMS2HRAS3_JHERMS2HRAS3

description: Library name: 003_JHERMS2HRAS3_JHERMS2HRAS3


title: 002_JHERMS2HRAS2_JHERMS2HRAS2

description: Library name: 002_JHERMS2HRAS2_JHERMS2HRAS2


title: 001_JHERMS2HRAS1_JHERMS2HRAS1

description: Library name: 001_JHERMS2HRAS1_JHERMS2HRAS1


title: SMSCTR_tipifarnibalpelisib_3

description: Library name: SMSCTR_tipifarnibalpelisib_3

value: tipifarnib+alpelisib


title: SMSCTR_tipifarnibtrametinib_2

description: Library name: SMSCTR_tipifarnibtrametinib_2

value: tipifarnib+trametinib


title: SMSCTR_tipifarnibtrametinib_1

description: Library name: SMSCTR_tipifarnibtrametinib_1


title: SMSCTR_tipifarnibalpelisib_2

description: Library name: SMSCTR_tipifarnibalpelisib_2


title: 038_SMSCTRHRAS2_SMSCTRHRAS2

description: Library name: 038_SMSCTRHRAS2_SMSCTRHRAS2


title: 030_RH36HRAS3_RH36HRAS3

description: Library name: 030_RH36HRAS3_RH36HRAS3


title: SMSCTR_alpelisib_3

description: Library name: SMSCTR_alpelisib_3

value: alpelisib


title: SMSCTR_alpelisib_2

description: Library name: SMSCTR_alpelisib_2


title: SMSCTR_tipifarnibalpelisib_1

description: Library name: SMSCTR_tipifarnibalpelisib_1


title: 037_SMSCTRHRAS1_SMSCTRHRAS1

description: Library name: 037_SMSCTRHRAS1_SMSCTRHRAS1


title: SMSCTR_trametinib_2

description: Library name: SMSCTR_trametinib_2

value: trametinib


title: SMSCTR_alpelisib_1

description: Library name: SMSCTR_alpelisib_1


title: SMSCTR_trametinib_3

description: Library name: SMSCTR_trametinib_3


title: SMSCTR_tipifarnib_1

description: Library name: SMSCTR_tipifarnib_1

value: tipifarnib


title: 005_JHERMS2NRAS2_JHERMS2NRAS2

description: Library name: 005_JHERMS2NRAS2_JHERMS2NRAS2


title: SMSCTR_tipifarnib_3

description: Library name: SMSCTR_tipifarnib_3


title: SMSCTR_trametinib_1

description: Library name: SMSCTR_trametinib_1


title: 007_JHERMS2NT1_JHERMS2NT1

description: Library name: 007_JHERMS2NT1_JHERMS2NT1


title: SMSCTR_DMSO_3

description: Library name: SMSCTR_DMSO_3

value: DMSO


title: SMSCTR_DMSO_2

description: Library name: SMSCTR_DMSO_2


title: SMSCTR_tipifarnib_2

description: Library name: SMSCTR_tipifarnib_2


title: SJRHB26_tipifarnibalpelisib_3

description: Library name: SJRHB26_tipifarnibalpelisib_3

value: HRAS G13R mutant


title: SJRHB26_tipifarnibtrametinib_3

description: Library name: SJRHB26_tipifarnibtrametinib_3

value: Rhabdomyosarcoma cell line


title: SJRHB26_tipifarnibtrametinib_2

description: Library name: SJRHB26_tipifarnibtrametinib_2


title: SJRHB26_tipifarnibalpelisib_1

description: Library name: SJRHB26_tipifarnibalpelisib_1


title: SJRHB26_tipifarnibtrametinib_1

description: Library name: SJRHB26_tipifarnibtrametinib_1


title: SMSCTR_tipifarnibtrametinib_3

description: Library name: SMSCTR_tipifarnibtrametinib_3

value: SMS-CTR


title: SJRHB26_tipifarnibalpelisib_2

description: Library name: SJRHB26_tipifarnibalpelisib_2


title: SJRHB26_alpelisib_3

description: Library name: SJRHB26_alpelisib_3


title: SJRHB26_alpelisib_2

description: Library name: SJRHB26_alpelisib_2


title: SJRHB26_trametinib_2

description: Library name: SJRHB26_trametinib_2


title: SJRHB26_tipifarnib_3

description: Library name: SJRHB26_tipifarnib_3


title: SJRHB26_trametinib_3

description: Library name: SJRHB26_trametinib_3


title: SJRHB26_trametinib_1

description: Library name: SJRHB26_trametinib_1


title: SJRHB26_DMSO_2

description: Library name: SJRHB26_DMSO_2


title: SJRHB26_DMSO_3

description: Library name: SJRHB26_DMSO_3


title: RH36_tipifarnibalpelisib_3

description: Library name: RH36_tipifarnibalpelisib_3

value: HRAS Q61K mutant


title: SJRHB26_tipifarnib_2

description: Library name: SJRHB26_tipifarnib_2


title: SJRHB26_tipifarnib_1

description: Library name: SJRHB26_tipifarnib_1


title: SMSCTR_DMSO_1

description: Library name: SMSCTR_DMSO_1


title: RH36_tipifarnibalpelisib_1

description: Library name: RH36_tipifarnibalpelisib_1


title: SJRHB26_DMSO_1

description: Library name: SJRHB26_DMSO_1


title: RH36_tipifarnibtrametinib_1

description: Library name: RH36_tipifarnibtrametinib_1


title: RH36_tipifarnibalpelisib_2

description: Library name: RH36_tipifarnibalpelisib_2


title: RH36_alpelisib_3

description: Library name: RH36_alpelisib_3


title: RH36_alpelisib_2

description: Library name: RH36_alpelisib_2


title: RH36_tipifarnibtrametinib_3

description: Library name: RH36_tipifarnibtrametinib_3


title: RH36_alpelisib_1

description: Library name: RH36_alpelisib_1


title: RH36_trametinib_1

description: Library name: RH36_trametinib_1


title: RH36_trametinib_3

description: Library name: RH36_trametinib_3


title: RH36_trametinib_2

description: Library name: RH36_trametinib_2


title: RH36_tipifarnib_3

description: Library name: RH36_tipifarnib_3


title: RH36_tipifarnib_2

description: Library name: RH36_tipifarnib_2


title: RH36_tipifarnib_1

description: Library name: RH36_tipifarnib_1


title: SJRHB26_alpelisib_1

description: Library name: SJRHB26_alpelisib_1


title: RH36_DMSO_2

description: Library name: RH36_DMSO_2


title: RH36_DMSO_3

description: Library name: RH36_DMSO_3


title: RH36_DMSO_1

description: Library name: RH36_DMSO_1


title: JHERMS2_tipifarnibalpelisib_3

description: Library name: JHERMS2_tipifarnibalpelisib_3


title: JHERMS2_tipifarnibalpelisib_1

description: Library name: JHERMS2_tipifarnibalpelisib_1


title: JHERMS2_tipifarnibtrametinib_3

description: Library name: JHERMS2_tipifarnibtrametinib_3


title: JHERMS2_tipifarnibtrametinib_2

description: Library name: JHERMS2_tipifarnibtrametinib_2


title: JHERMS2_tipifarnibtrametinib_1

description: Library name: JHERMS2_tipifarnibtrametinib_1


title: JHERMS2_tipifarnibalpelisib_2

description: Library name: JHERMS2_tipifarnibalpelisib_2


title: JHERMS2_alpelisib_3

description: Library name: JHERMS2_alpelisib_3


title: JHERMS2_trametinib_3

description: Library name: JHERMS2_trametinib_3


title: JHERMS2_trametinib_2

description: Library name: JHERMS2_trametinib_2


title: RH36_tipifarnibtrametinib_2

description: Library name: RH36_tipifarnibtrametinib_2


title: JHERMS2_trametinib_1

description: Library name: JHERMS2_trametinib_1


title: JHERMS2_DMSO_3

description: Library name: JHERMS2_DMSO_3


title: JHERMS2_alpelisib_2

description: Library name: JHERMS2_alpelisib_2


title: JHERMS2_DMSO_1

description: Library name: JHERMS2_DMSO_1


title: JHERMS2_DMSO_2

description: Library name: JHERMS2_DMSO_2


title: JHERMS2_tipifarnib_3

description: Library name: JHERMS2_tipifarnib_3


title: JHERMS2_alpelisib_1

description: Library name: JHERMS2_alpelisib_1


title: SMS-CTR_Control3_24

description: Library name: SMS-CTR_Control3_24


title: SMS-CTR_Control2_48

description: Library name: SMS-CTR_Control2_48


title: JHERMS2_tipifarnib_2

description: Library name: JHERMS2_tipifarnib_2


title: SMS-CTR_Control1_6

description: Library name: SMS-CTR_Control1_6


title: SMS-CTR_Control1_24

description: Library name: SMS-CTR_Control1_24


title: SMS-CTR_100nmTipi3_6

description: Library name: SMS-CTR_100nmTipi3_6


title: SMS-CTR_Control1_48

description: Library name: SMS-CTR_Control1_48


title: SMS-CTR_100nmTipi3_48

description: Library name: SMS-CTR_100nmTipi3_48


title: SMS-CTR_100nmTipi3_24

description: Library name: SMS-CTR_100nmTipi3_24


title: SMS-CTR_100nmTipi2_48

description: Library name: SMS-CTR_100nmTipi2_48


title: SMS-CTR_100nmTipi2_6

description: Library name: SMS-CTR_100nmTipi2_6


title: SMS-CTR_100nmTipi2_24

description: Library name: SMS-CTR_100nmTipi2_24


title: RH36_Control3_24

description: Library name: RH36_Control3_24


title: JHERMS2_tipifarnib_1

description: Library name: JHERMS2_tipifarnib_1


title: RH36_Control1_24

description: Library name: RH36_Control1_24


title: RH36_100nmTipi3_24

description: Library name: RH36_100nmTipi3_24


title: SMS-CTR_100nmTipi1_48

description: Library name: SMS-CTR_100nmTipi1_48


title: RH36_Control2_24

description: Library name: RH36_Control2_24


title: SMS-CTR_Control3_48

description: Library name: SMS-CTR_Control3_48


title: RH36_100nmTipi2_24

description: Library name: RH36_100nmTipi2_24


title: SMS-CTR_Control2_6

description: Library name: SMS-CTR_Control2_6


title: RH36_100nmTipi1_24

description: Library name: RH36_100nmTipi1_24


title: RD_100nmTipi3_24

description: Library name: RD_100nmTipi3_24

value: RD

value: NRAS Q61H mutant


title: SMS-CTR_100nmTipi1_6

description: Library name: SMS-CTR_100nmTipi1_6


title: M39_Control3_24

description: Library name: M39_Control3_24


title: RD_Control3_24

description: Library name: RD_Control3_24


title: RD_100nmTipi2_24

description: Library name: RD_100nmTipi2_24


title: SMS-CTR_Control3_6

description: Library name: SMS-CTR_Control3_6


title: M39_Control2_24

description: Library name: M39_Control2_24


title: M39_Control1_24

description: Library name: M39_Control1_24


title: RD_100nmTipi1_24

description: Library name: RD_100nmTipi1_24


title: RD_Control2_24

description: Library name: RD_Control2_24


title: SMS-CTR_Control2_24

description: Library name: SMS-CTR_Control2_24


title: M39_100nmTipi2_24

description: Library name: M39_100nmTipi2_24


title: M39_100nmTipi1_24

description: Library name: M39_100nmTipi1_24


title: M39_100nmTipi3_24

description: Library name: M39_100nmTipi3_24


title: JR_Control3_24

description: Library name: JR_Control3_24

value: NRAS Q61K mutant


title: SMS-CTR_100nmTipi1_24

description: Library name: SMS-CTR_100nmTipi1_24


title: JR_Control2_24

description: Library name: JR_Control2_24


title: JR_Control1_24

description: Library name: JR_Control1_24


title: JR_100nmTipi3_24

description: Library name: JR_100nmTipi3_24


title: JH2_Control3_48

description: Library name: JH2_Control3_48


title: JR_100nmTipi1_24

description: Library name: JR_100nmTipi1_24


title: JR_100nmTipi2_24

description: Library name: JR_100nmTipi2_24


title: JH2_Control3_24

description: Library name: JH2_Control3_24


title: JH2_Control3_6

description: Library name: JH2_Control3_6


title: JH2_Control2_6

description: Library name: JH2_Control2_6


title: JH2_Control2_48

description: Library name: JH2_Control2_48


title: JH2_Control2_24

description: Library name: JH2_Control2_24


title: JH2_Control1_6

description: Library name: JH2_Control1_6


title: JH2_Control1_48

description: Library name: JH2_Control1_48


title: JH2_100nmTipi3_6

description: Library name: JH2_100nmTipi3_6


title: JH2_100nmTipi3_48

description: Library name: JH2_100nmTipi3_48


title: RD_Control1_24

description: Library name: RD_Control1_24


title: JH2_Control1_24

description: Library name: JH2_Control1_24


title: JH2_100nmTipi3_24

description: Library name: JH2_100nmTipi3_24


title: JH2_100nmTipi2_48

description: Library name: JH2_100nmTipi2_48


title: JH2_100nmTipi2_24

description: Library name: JH2_100nmTipi2_24


title: JH2_100nmTipi1_48

description: Library name: JH2_100nmTipi1_48


title: JH2_100nmTipi2_6

description: Library name: JH2_100nmTipi2_6


title: JH2_100nmTipi1_6

description: Library name: JH2_100nmTipi1_6


title: Hepatocyte, Control sample for female, biol rep 4

city: Berkeley

first: Yuchen

last: He

state: California

address:
344 Morgan Hall, University of California
 Berkeley

department: Department of Nutritional Science and Toxicology

institute: University of California Berkeley

description: Library name: CTL4

data_processing:
FASTQ file generation was performed by Novogene using Illumina NovaSeq 6000
Original image data file from the high-throughput sequencing platform was transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files.
Alignment were performed with HISAT2
Gene expression level analysis, including PCA, hierarchical clustering
Differential expression analysis using pyDESeq2
Assembly: Homo_sapiens_Ensembl_94
Supplementary files format and content: .xlsx files includes raw gene counts info of male OCM treated Liver-MPS
Supplementary files format and content: .xlsx files includes sample metadata of female OCM treated Liver-MPS

extract_protocol:
Cells were exposed by cutting and exfoliating the cell chamber slab off the device then lysed in Trizol (#15596026, Invitrogen)
Library construction was performed by Novogene. The polyA enrichment library preparation procedure was used and resulted in the construction of 250-300 bp insert cDNA library.

value: G15.AO iPSC

value: Hepatocyte

value: WT

value: hepatocyte differentiation


title: Hepatocyte, female OCM, biol rep 4

description: Library name: OF2_4

source_name: OF2_4 Female Old

value: hepatocyte differentiation, treated with OCM


title: Hepatocyte, female OCM, biol rep 1

description: Library name: OF2_1

source_name: OF2_1 Female Old


title: Hepatocyte, female YCM, biol rep 4

description: Library name: YF1_4

source_name: YF1_4 Female Young

value: hepatocyte differentiation, treated with YCM


title: Hepatocyte, female YCM, biol rep 3

description: Library name: YF1_3

source_name: YF1_3 Female Young


title: Hepatocyte, female OCM, biol rep 2

description: Library name: OF2_2

source_name: OF2_2 Female Old


title: Hepatocyte, Control sample for female, biol rep 2

description: Library name: CTL2


title: Hepatocyte, Control sample for female, biol rep 3

description: Library name: CTL3


title: Hepatocyte, female OCM, biol rep 3

description: Library name: OF2_3

source_name: OF2_3 Female Old


title: Hepatocyte, male OCM, biol rep 3

description: Library name: Liver_M6

source_name: Liver_M6 Male Old


title: Hepatocyte, female YCM, biol rep 1

description: Library name: YF1_1

source_name: YF1_1 Female Young


title: Hepatocyte, male OCM, biol rep 2

description: Library name: Liver_M5

source_name: Liver_M5 Male Old


title: Hepatocyte, Control sample for female, biol rep 1

description: Library name: CTL1


title: Hepatocyte, male YCM, biol rep 2

description: Library name: Liver_M2

source_name: Liver_M2 Male Young


title: Hepatocyte, male YCM, biol rep 3

description: Library name: Liver_M3

source_name: Liver_M3 Male Young


title: Hepatocyte, male OCM treated WAT-MPS Knock-On, biol rep 4

description: Library name: KN_OM2_4

value: hepatocyte differentiation,connected to WAT-MPS pre-treated with OCM


title: Hepatocyte, male OCM, biol rep 1

description: Library name: Liver_M4

source_name: Liver_M4 Male Old


title: Hepatocyte, male YCM, biol rep 1

description: Library name: Liver_M1

source_name: Liver_M1 Male Young


title: Hepatocyte, male OCM treated WAT-MPS Knock-On, biol rep 3

description: Library name: KN_OM2_3


title: Hepatocyte, male OCM treated WAT-MPS Knock-On, biol rep 1

description: Library name: KN_OM2_1


title: Hepatocyte, male YCM treated WAT-MPS Knock-On, biol rep 3

description: Library name: KN_MY1_3

value: hepatocyte differentiation,connected to WAT-MPS pre-treated with YCM


title: JH2_100nmTipi1_24

description: Library name: JH2_100nmTipi1_24

value: HRAS G12S mutant

value: tipifarnib


title: Hepatocyte, male YCM treated WAT-MPS Knock-On, biol rep 2

description: Library name: KN_MY1_2


title: Hepatocyte, Control sample for male

description: Library name: CTL_1003


title: Hepatocyte, male YCM treated WAT-MPS Knock-On, biol rep 1

description: Library name: KN_MY1_1


title: Hepatocyte, female YCM, biol rep 2

description: Library name: YF1_2

source_name: YF1_2 Female Young


title: male opto-FGFR-expressing brain organoids with simGCRsim #3

first: Gabsang

last: Lee

state: MD

address: 733 N. Broadway

institute: Johns Hopkins School of Medicine

description:
Library name: 18_S18
opto-FGFR brain organoid exposed to 50 cGy simGCRsim; replicate 3 of 3

data_processing:
Batch_1:
Batch_2:
Base calling with RTA version 2.4.11
Batch_1: Alignment to human reference transcriptome with the CLCGenomicsServer 23.0.2
Batch_2:Alignment to human reference transcriptome with the CLCGenomicsServer 21.0.3
Batch_1:Gene-level count calculation with CLCGenomicsServer 23.0.2
Batch_2:Gene-level count calculation with CLCGenomicsServer 21.0.3
Batch correction with PyComBat v.0.3.3
Differential expression analysed with edgeR v.4.0.16 and limma v.3.58.1
Assembly: Batch_1: Hs_GRCh38.p14_Oct-23
Assembly: Batch_2: Hs_GRCh38.p14_Jul-22
Supplementary files format and content: Linear value .txt file, CLCGenomicsServer Expression value Total counts

source_name: brain organoids

growth_protocol: Human induced pluripotent stem cells (hiPSCs) were initially cultured on inactivated mouse embryonic fibroblasts (Gibco) in human ESC medium composed of DMEM/F-12, 20% knockout serum replacement (KSR), 0.1 mM non-essential amino acids, 2 mM L-glutamine, 55 μM β-mercaptoethanol (all from Life Technologies), and 10 ng/mL FGF2 (R&D Systems). To generate cortical brain organoids, hiPSCs were enzymatically dissociated into single cells using TrypLE, and seeded at 5 × 10⁵ cells per well in ultra-low attachment U-bottom 96-well plates (Corning) using mTeSR Plus medium (STEMCELL Technologies) supplemented with 50 μM Y-27632 (BioGems). From day 2 onward, two-thirds of the medium was refreshed every other day, omitting Y-27632. Once the aggregates reached approximately 350–450 μm in diameter, they were transferred to 24-well plates containing cortical induction medium consisting of DMEM/F-12, N2 (1:200), B27 (1:100), 0.2 mg/mL glucose, 0.15 μg/mL cAMP, 0.5% NEAA, 1% L-alanyl-L-glutamine, 10 μg/mL heparin, 180 nM LDN-193189, 500 nM A83-01, and 10 μg/mL IWR-1. Medium changes were performed every 3 days. Upon observation of neuroectodermal morphology, including brightened surfaces and radial neuroepithelial organization, aggregates were embedded in reduced growth factor Geltrex (Thermo Fisher Scientific). These were transferred to low-attachment 6-cm petri dishes containing organoid maturation medium composed of DMEM/F-12, N2 (1:200), B27 (1:100), glucose (0.2 mg/mL), cAMP (0.15 μg/mL), 0.5% NEAA, 1% L-alanyl-L-glutamine, and 2.5 μg/mL insulin. Cultures were maintained on an orbital shaker, with medium refreshed every 3–4 days.

extract_protocol:
QIAGEN miRNeasy Mini kit
Batch_1: SMART-seq mRNA v4 library prep (non-stranded)
Batch_2: Stranded mRNA Seq library prep with UDI

treatment_protocol: At day 60 of brain organoid differentiation, organoids were either left untreated (control) or exposed to 50 cGy of simulated Galactic Cosmic Radiation (simGCRsim) using a NASA GCR simulator. After irradiation, organoids were returned to standard culture conditions and harvested 48 hours post-exposure for RNA extraction.

value: brain organoids

value: pluripotent stem cell-derived brain organoid

value: male


title: male opto-FGFR-expressing brain organoids with simGCRsim #2

description:
Library name: 17_S17
opto-FGFR brain organoid exposed to 50 cGy simGCRsim; replicate 2 of 3


title: male opto-FGFR-expressing brain organoids without simGCRsim #1

description:
Library name: 13_S13
opto-FGFR brain organoid without simGCRsim; replicate 1 of 3


title: RNA-seq of female brain organoid derived from SC2131 cell lines with simGCRsim #1

description:
Library name: 10_S10
Female brain organoid exposed to 50 cGy simGCRsim; replicate 1 of 3

value: wt

value: Female


title: male mock-expressing brain organoids with simGCRsim #1

description:
Library name: 4_S4
mock brain organoid exposed to 50 cGy simGCRsim; replicate 1 of 3


title: Hepatocyte, male YCM treated WAT-MPS Knock-On, biol rep 4

description: Library name: KN_MY1_4


title: male opto-FGFR-expressing brain organoids without simGCRsim #2

description:
Library name: 14_S14
opto-FGFR brain organoid without simGCRsim; replicate 2 of 3


title: RNA-seq of female brain organoid derived from SC2131 cell lines with simGCRsim #3

description:
Library name: 12_S12
Female brain organoid exposed to 50 cGy simGCRsim; replicate 3 of 3


title: RNA-seq of female brain organoid derived from 01582 cell lines with simGCRsim #3

description:
Library name: ERa-48
Female brain organoid exposed to 50 cGy simGCRsim; replicate 3 of 3


title: Hepatocyte, male OCM treated WAT-MPS Knock-On, biol rep 2

description: Library name: KN_OM2_2


title: male mock-expressing brain organoids without simGCRsim #3

description:
Library name: 3_S3
mock brain organoid without simGCRsim; replicate 3 of 3


title: male opto-FGFR-expressing brain organoids without simGCRsim #3

description:
Library name: 15_S15
opto-FGFR brain organoid without simGCRsim; replicate 3 of 3


title: male opto-FGFR-expressing brain organoids with simGCRsim #1

description:
Library name: 16_S16
opto-FGFR brain organoid exposed to 50 cGy simGCRsim; replicate 1 of 3


title: RNA-seq of female brain organoid derived from SC2131 cell lines with simGCRsim #2

description:
Library name: 11_S11
Female brain organoid exposed to 50 cGy simGCRsim; replicate 2 of 3


title: male mock-expressing brain organoids without simGCRsim #2

description:
Library name: 2_S2
mock brain organoid without simGCRsim; replicate 2 of 3


title: RNA-seq of female brain organoid derived from 01582 cell lines with simGCRsim #1

description:
Library name: ERa-46
Female brain organoid exposed to 50 cGy simGCRsim; replicate 1 of 3


title: male mock-expressing brain organoids with simGCRsim #3

description:
Library name: 6_S6
mock brain organoid exposed to 50 cGy simGCRsim; replicate 3 of 3


title: male mock-expressing brain organoids without simGCRsim #1

description:
Library name: 1_S1
mock brain organoid without simGCRsim; replicate 1 of 3


title: RNA-seq of female brain organoid derived from 01582 cell lines without simGCRsim #1

description:
Library name: ERa-43
Female brain organoid without simGCRsim; replicate 1 of 3


title: RNA-seq of female brain organoid derived from 01582 cell lines without simGCRsim #2

description:
Library name: ERa-44
Female brain organoid without simGCRsim; replicate 2 of 3


title: male mock-expressing brain organoids with simGCRsim #2

description:
Library name: 5_S5
mock brain organoid exposed to 50 cGy simGCRsim; replicate 2 of 3


title: RNA-seq of male brain organoid derived from SC1014 cell lines with simGCRsim #3

description:
Library name: ERa-42
Male brain organoid exposed to 50 cGy simGCRsim; replicate 3 of 3

value: Male


title: RNA-seq of male brain organoid derived from SC1014 cell lines with simGCRsim #2

description:
Library name: ERa-41
Male brain organoid exposed to 50 cGy simGCRsim; replicate 2 of 3


title: RNA-seq of female brain organoid derived from 01582 cell lines without simGCRsim #3

description:
Library name: ERa-45
Female brain organoid without simGCRsim; replicate 3 of 3


title: RNA-seq of male brain organoid derived from SC1014 cell lines with simGCRsim #1

description:
Library name: ERa-40
Male brain organoid exposed to 50 cGy simGCRsim; replicate 1 of 3


title: RNA-seq of male brain organoid derived from SC1014 cell lines without simGCRsim #3

description:
Library name: ERa-39
Male brain organoid without simGCRsim; replicate 3 of 3


title: RNA-seq of female brain organoid derived from 01582 cell lines with simGCRsim #2

description:
Library name: ERa-47
Female brain organoid exposed to 50 cGy simGCRsim; replicate 2 of 3


title: RNA-seq of male brain organoid derived from SC1014 cell lines without simGCRsim #1

description:
Library name: ERa-37
Male brain organoid without simGCRsim; replicate 1 of 3


title: RNA-seq of female brain organoid derived from SC2131 cell lines without simGCRsim #1

description:
Library name: 7_S7
Female brain organoid without simGCRsim; replicate 1 of 3


title: RNA-seq of female brain organoid derived from SC2131 cell lines without simGCRsim #2

description:
Library name: 8_S8
Female brain organoid without simGCRsim; replicate 2 of 3


title: RNA-seq of female brain organoid derived from SC2131 cell lines without simGCRsim #3

description:
Library name: 9_S9
Female brain organoid without simGCRsim; replicate 3 of 3


title: RNA-seq of male brain organoid derived from KOLF2.1J cell lines with simGCRsim #3

description:
Library name: ERa-36
Male brain organoid exposed to 50 cGy simGCRsim; replicate 3 of 3

value: KOLF


title: RNA-seq of male brain organoid derived from KOLF2.1J cell lines without simGCRsim #3

description:
Library name: ERa-33
Male brain organoid without simGCRsim; replicate 3 of 3


title: RNA-seq of male brain organoid derived from KOLF2.1J cell lines with simGCRsim #1

description:
Library name: ERa-34
Male brain organoid exposed to 50 cGy simGCRsim; replicate 1 of 3


title: RNA-seq of male brain organoid derived from KOLF2.1J cell lines with simGCRsim #2

description:
Library name: ERa-35
Male brain organoid exposed to 50 cGy simGCRsim; replicate 2 of 3


title: RNA-seq of female brain organoid derived from H9 cell lines with simGCRsim #2

description:
Library name: ERa-29
Female brain organoid exposed to 50 cGy simGCRsim; replicate 2 of 3


title: RNA-seq of male brain organoid derived from KOLF2.1J cell lines without simGCRsim #1

description:
Library name: ERa-31
Male brain organoid without simGCRsim; replicate 1 of 3


title: RNA-seq of female brain organoid derived from H9 cell lines without simGCRsim #3

description:
Library name: ERa-27
Female brain organoid without simGCRsim; replicate 3 of 3


title: RNA-seq of female brain organoid derived from H9 cell lines without simGCRsim #1

description:
Library name: ERa-25
Female brain organoid without simGCRsim; replicate 1 of 3


title: RNA-seq of male brain organoid derived from ApoE cell lines with simGCRsim #2

description:
Library name: ERa-23
Male brain organoid exposed to 50 cGy simGCRsim; replicate 2 of 3

value: ApoE


title: RNA-seq of female brain organoid derived from H9 cell lines with simGCRsim #1

description:
Library name: ERa-28
Female brain organoid exposed to 50 cGy simGCRsim; replicate 1 of 3


title: RNA-seq of male brain organoid derived from KOLF2.1J cell lines without simGCRsim #2

description:
Library name: ERa-32
Male brain organoid without simGCRsim; replicate 2 of 3


title: RNA-seq of male brain organoid derived from ApoE cell lines with simGCRsim #3

description:
Library name: ERa-24
Male brain organoid exposed to 50 cGy simGCRsim; replicate 3 of 3


title: RNA-seq of male brain organoid derived from ApoE cell lines without simGCRsim #2

description:
Library name: ERa-20
Male brain organoid without simGCRsim; replicate 2 of 3


title: RNA-seq of male brain organoid derived from ApoE cell lines without simGCRsim #3

description:
Library name: ERa-21
Male brain organoid without simGCRsim; replicate 3 of 3


title: RNA-seq of female brain organoid derived from H9 cell lines without simGCRsim #2

description:
Library name: ERa-26
Female brain organoid without simGCRsim; replicate 2 of 3


title: RNA-seq of male brain organoid derived from BC1 cell lines without simGCRsim #3

description:
Library name: ERa-15
Male brain organoid without simGCRsim; replicate 3 of 3


title: RNA-seq of male brain organoid derived from BC1 cell lines with simGCRsim #2

description:
Library name: ERa-17
Male brain organoid exposed to 50 cGy simGCRsim; replicate 2 of 3


title: RNA-seq of male brain organoid derived from SC1014 cell lines without simGCRsim #2

description:
Library name: ERa-38
Male brain organoid without simGCRsim; replicate 2 of 3


title: RNA-seq of male brain organoid derived from BC1 cell lines without simGCRsim #1

description:
Library name: ERa-13
Male brain organoid without simGCRsim; replicate 1 of 3


title: RNA-seq of male brain organoid derived from CS25 cell lines with simGCRsim #2

description:
Library name: ERa-11
Male brain organoid exposed to 50 cGy simGCRsim; replicate 2 of 3


title: RNA-seq of female brain organoid derived from H9 cell lines with simGCRsim #3

description:
Library name: ERa-30
Female brain organoid exposed to 50 cGy simGCRsim; replicate 3 of 3


title: RNA-seq of male brain organoid derived from ApoE cell lines with simGCRsim #1

description:
Library name: ERa-22
Male brain organoid exposed to 50 cGy simGCRsim; replicate 1 of 3


title: RNA-seq of male brain organoid derived from BC1 cell lines without simGCRsim #2

description:
Library name: ERa-14
Male brain organoid without simGCRsim; replicate 2 of 3


title: RNA-seq of male brain organoid derived from CS25 cell lines with simGCRsim #3

description:
Library name: ERa-12
Male brain organoid exposed to 50 cGy simGCRsim; replicate 3 of 3


title: RNA-seq of male brain organoid derived from BC1 cell lines with simGCRsim #3

description:
Library name: ERa-18
Male brain organoid exposed to 50 cGy simGCRsim; replicate 3 of 3


title: RNA-seq of male brain organoid derived from ApoE cell lines without simGCRsim #1

description:
Library name: ERa-19
Male brain organoid without simGCRsim; replicate 1 of 3


title: RNA-seq of male brain organoid derived from CS25 cell lines with simGCRsim #1

description:
Library name: ERa-10
Male brain organoid exposed to 50 cGy simGCRsim; replicate 1 of 3


title: RNA-seq of male brain organoid derived from CS25 cell lines without simGCRsim #2

description:
Library name: ERa-8
Male brain organoid without simGCRsim; replicate 2 of 3


title: RNA-seq of male brain organoid derived from CS25 cell lines without simGCRsim #3

description:
Library name: ERa-9
Male brain organoid without simGCRsim; replicate 3 of 3


title: RNA-seq of male brain organoid derived from CS25 cell lines without simGCRsim #1

description:
Library name: ERa-7
Male brain organoid without simGCRsim; replicate 1 of 3


title: RNA-seq of male brain organoid derived from SC1015 cell lines with simGCRsim #1

description:
Library name: ERa-4
Male brain organoid exposed to 50 cGy simGCRsim; replicate 1 of 3


title: RNA-seq of male brain organoid derived from SC1015 cell lines with simGCRsim #3

description:
Library name: ERa-6
Male brain organoid exposed to 50 cGy simGCRsim; replicate 3 of 3


title: RNA-seq of male brain organoid derived from SC1015 cell lines with simGCRsim #2

description:
Library name: ERa-5
Male brain organoid exposed to 50 cGy simGCRsim; replicate 2 of 3


title: RNA-seq of male brain organoid derived from SC1015 cell lines without simGCRsim #2

description:
Library name: ERa-2
Male brain organoid without simGCRsim; replicate 2 of 3


title: RNA-seq of male brain organoid derived from BC1 cell lines with simGCRsim #1

description:
Library name: ERa-16
Male brain organoid exposed to 50 cGy simGCRsim; replicate 1 of 3


title: RNA-seq of male brain organoid derived from SC1015 cell lines without simGCRsim #1

description:
Library name: ERa-1
Male brain organoid without simGCRsim; replicate 1 of 3


title: RNA-seq of male brain organoid derived from SC1015 cell lines without simGCRsim #3

description:
Library name: ERa-3
Male brain organoid without simGCRsim; replicate 3 of 3


title: Pericyte transwell Mock 8hr infection rep. 3

city: Cambridge

first: Rudolf

last: Jaenisch

state: MA

address: 455 Main St.

institute: Whitehead Institute for Biomedical Research

description: Library name: PC8 Mock 3

data_processing:
Counts were tabulated for human protein coding genes, lncRNAs (ENSEMBL release 93 annotations) and viral genes (MN988713.1) using featureCounts.
Assembly: GRCh38, ENSEMBL release 93, GenBank MN988713.1
Supplementary files format and content: Raw feature counts per sample as tab delimited text.

growth_protocol: Differentiation of hPSC-derived cell types or culture of primary cells using standard tissue culture techniques

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Plus Micro Kit
Libraries for samples shown on lines 34-60 were prepared using SWIFT RNA Library Kit. Libraries for samples shown on lines 62-85 were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit.

treatment_protocol: Exposure to WNV (Nea Santa strain obtained from BEI, expanded on Vero cells) for 1 hour in minimum volume of serum-free culture media. Mock infection was done by exposing cells to a matched volume of Vero conditioned media.

value: hPSC-derived pericytes

value: Mock infection 8 hours