title: xylA, NusG-myc, replicate 2

city: Seoul

first: Sang Woo

last: Seo

address: 1, Gwanak-ro, Gwanak-gu

institute: Seoul National University

data_processing:
The quality of the sequence reads obtained from ChIP-exo was checked by FastQC (version 0.11.8).
The sequence reads were aligned to the reference genome using bowtie (version 1.2.2) with the following options to generate SAM output files: -X 5000 -n 2 -p 3 -3 9 -S. For the raw data generated from NovaSeq 6000, the bowtie options were as follows: -X 5000 -n 2 -p 3 -3 69 -S.
For Bowtie alignment, we updated the reference genome by applying innate mutations in our lab strain. Strains for the lacZ-related experiment are lack of lacY and lacA gene, which, however, does not affect lacZ expression. prepared multiple variants of the reference genome in advance by updating some of the sequences on the genome, such as dRBSdATG and modified UTR, to properly map the sequence reads generated from different genotype samples.
In the xylA samples, the aligned reads were manually normalized by dividing 10^9 × (reads on the xylAB operon and its upstream region) into total reads aligned to genome. The reads from the other gene samples, galE, galP, lacZ, and rhaB, were also normalized respectively in accordance with their operon sequences.
Assembly: NC_000913.3
Supplementary files format and content: gff, normalized counts of sequencing reads around the target region

source_name: bacterial cell

extract_protocol:
E. coli cells induced for 4 hours with proper inducer were cross-linked by 1% formaldehyde at room temperature for 30 min. The cross-linked cells were harvested and lysed, followed by sonication for DNA fragmentation. If necessary, cells were treated with 50 μg/mL bicyclomycin (BCM) for 30 minutes or 150 μg/mL rifampicin for 15 minutes prior to harvest.
The sheared DNA was immunoprecipitated by proper antibodies (anti-RNAP β or c-Myc). After binding to chromatin beads, immunoprecipitated DNA was end-repaired, dA-tailed, and ligated with the first adapter using the KAPA HyperPrep Kit (KAPA Biosystems). Adapter-ligated DNA samples were then nick-repaired and exonuclease-treated. The DNA samples were eluted from the beads by reversing protein-DNA crosslinking at 65 °C. Primer extension and second adapter ligation were performed in sequence. Finally, the DNA samples were enriched by PCR, using KAPA HotStart ReadMix in HyperPrep Kit (KAPA Biosystems). DNAs after each reaction were purified and size-selected using either AMPure XP beads (Beckman Coulter, Brea, CA, USA) or Zymo DNA Clean & Concentrator (Zymo, Irvine, CA, USA).

value: bacterial cell

tag: substrain

value: c-Myc Antibody (9E10) (Santa Cruz Biotech, #sc-40)

value: 8-myc-tagged NusG

value: 0.4% D-xylose induction for 4 hours


title: ATAC Biol rep 2; KO, CD62L+ TPEX

status: Public on Sep 12 2025

type: SRA

city: Melbourne

first: Lachlan

last: Dryburgh

state: Victoria

address: 792 Elizabeth Street

department: The Department of Microbiology and Immunology,  The University of Melbourne

country: Australia

institute: The Peter Doherty Institute for Infection and Immunity

description: Sample 13 KO CD62L+ TPEX

library_source: genomic

data_processing:
Alignment by BWA-mem2, to GRCm39.
Alignments sorted with SAMTools and peak called MACS2.
Peaks merged with Homer and counts matrix generated with FeatureCounts.
Peaks with log2 counts-per-million < 1 in all samples were filtered.
Assembly: GRCm39
Supplementary files format and content: Tab delimitted table of raw counts of filtered genes.
Supplementary files format and content: Rows represent MACS2 called peaks and columns samples.

molecule: genomic DNA

organism: Mus musculus

source_name: Spleen

extract_protocol:
Cells were lysed using cold ATAC buffer (10 mM Tris–HCl pH 7.5, 10 mM NaCl and 3 mM MgCl2 in UltraPure DNase/RNase-free distilled water (Thermo Fisher Scientific)) comprising NP40 (Millipore-Sigma, 0.1 %), Tween-20 (Millipore-Sigma, 0.1 %) and digitonin (Promega, 0.01 %) for 3 min. Nuclei were pelleted at 500 g for 10 min 4 °C and resuspended in Transposition Mix (Tagment DNA buffer and Tn5 Tagment DNA TDE1 Enzyme from Illumina, PBS, UltraPure DNase/RNase-free distilled water, 0.001 % digitonin, 0.1 % Tween-20). Enzymatic transposition of DNA was achieved by incubation at 37 °C for 30 min at 1000 rpm. DNA was purified using the DNA Clean and Concentrator-5 Kit (Zymo Research).
Fragments were barcoded in a PCR reaction with unique Adapter sequences using the NEBNext Ultra II Q5 2x Master Mix (New England Biolabs). Library concengtrations were quantified using the NEBNext Libary Quant Master Mix Kit (New England Biolabs) by qPCR. Individual samples were further amplified to obtain unified library concentrations.

tag: tissue

value: Spleen

tag: cell type

value: CD8 T Lymphocytes

tag: genotype

tag: treatment


title: TrafficJam-Upd H3K9me3 Input Replicate 2

city: Baltimore

first: Daniel

last: Ringwalt

state: MD

address: 3400N Charles St

department: Biology

country: USA

institute: Johns Hopkins University

description: Library name: Sample 26

data_processing:
Reads were aligned to dm6 using Bowtie 2 (version 2.4.5), and filtered for proper pairs (SAM flag 2), MAPQ at least 20, and mated fragment length between 100 and 200 bp.
Fragments were called as putative nucleosome locations, using the single bp midpoint between the two proper pairs as the location estimate.
Pileup data frames were created to identify monosome density, as the count of nucleosome locations in a 40 bp window with 20 bp sliding step (50% overlap).
Each pileup series is divided by a normalization factor: A fragment count subsetted to the 2L, 2R, 3L, 3R, and 4 (autosomes) smoothed to 1 kb window and then taking the genome-wide median.
Assembly: dm6
Supplementary files format and content: CSV: Chromosome (dm6), start and end sliding window coordinates using BED file format semantics, and each series pileup of fragments divided by a normalization factor.

organism: Drosophila melanogaster

source_name: testis tumor

growth_protocol: Fly crosses were maintained on standard molasses media at 25C.

extract_protocol:
Tesis tumors were dissected in sterile Schnieder's media supplemented with 10% fetal bovine serum (FBS). Testis tissue was digested to completion in TrypLE supplemented with 2mg/mL collagenase by incubating with intermittent agitation at 37C. Digested tissue was filtered first through at 40um filter, then a 10um filter before pelleting cells by centrifugation at 1,200rpm. After removing the supernatant, cells were resuspended in Schnieder's media + FBS and fixed in 1% formaldehyde for 5 minutes followed by quencing the reaction with glycine for an addition 5 minutes. Fixed cells were pelleted and washed with cold PBS before starting the chromatin immunocleavage (ChIC) protocol.  For a single ChIC sample, the anti-GFP + Protein A (PA)-MNase complex was prepared and incubated with fixed cells, allowing the complex to bind to chromatin. A series of washes removed excess PA-MNase-GFP complex. Chromatin from the targeted cell type was then digested by activation of the MNase enzyme. The soluble chromatin was separated from insoluble chromatin by centrifugation. A small portion of the solubilized chromatin was set aside to function as input and the remainder of the chromatin used to perform immunoprecipitation.  Immunoprecipitation for a specific histone modification was performed overnight. The next day, protein-bound beads were washed in a series of low salt washes. The DNA was eluted from beads and processed alongside the input samples to reverse the crosslinks. The DNA from both samples was then purified using the Qiagen MinElute Cleanup Kit before proceeding with library preparation.
Purified DNA from the Input and Immunoprecipitation samples were prepared for sequencing following the instructions included in the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB#7645).

value: testis tumor

value: w[1118]; traffic Jam - GAL4 / UAS - Upd ; + / UAS-FRT-H3-GFP-FRT-H3-mKO

tag: chromatin type

value: CySC-like chromatin

tag: chic-antibody

value: anti-GFP PA-Mnase

tag: chip antibody

tag: batch


title: TrafficJam-Upd H3K9me3 IP Replicate 1

description: Library name: Sample 27

value: H3K9me3, Diagenode #C15410056


title: Plasma exosomal miRNA, Dengue with warning sign, patient 03

type: RNA

city: Kubang Kerian, Kota Bharu

first: Gokulakannan

last: Venkatesan

state: Kelantan

address: Kampus Kesihatan Universiti Sains Malaysia, Jalan Raja Perempuan Zainab 2, Kubang Kerian, 16150 Kota Bharu, Kelantan

department: School of Dental Sciences

country: Malaysia

institute: Universiti Sains Malaysia

description: miRNA expression analysis in plasma exosome of dengue with warning sign.

hyb_protocol: 1.65 µg of Cy3-labeled cRNA in hybridization buffer was hybridized onto the Agilent Human miRNA Microarray (release/version) using the Agilent Gene Expression Hybridization Kit (Agilent Technologies, United States) according to the manufacturer’s protocol. Arrays were hybridized in an Agilent hybridization oven at 55°C for 20 hours with rotation at 20 rpm.

scan_protocol: After hybridization, microarrays were washed using the Agilent Gene Expression Wash Buffers according to the manufacturer’s instructions. Arrays were scanned using the Agilent Microarray Scanner System (Agilent Technologies, United States) at 5 µm resolution, using default one-color settings.

data_processing: GeneSpring GX software (Agilent Technologies, United States) was used for data analysis. The differential expression was determined using the moderated t-test with Benjamin-Hochberg multiple testing corrections. The cut-off for significantly expressed miRNAs were fixed to a probability value of less than 5% (p<0.05), and the fold change was set to be greater than 2.0 (FC > 2).

molecule: total RNA

organism: Homo sapiens

source_name: Human plasma exosomes

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Approximately two to three millilitres of left over peripheral venous blood in an ethylenediaminetetraacetic acid tube was used to isolate plasma.  The blood was centrifuged at 2,000 X g for 15 minutes and 12,000 X g for 45 minutes at 4◦C for plasma isolation. Exosomes were isolated at 110,000 x g at 4o C for two hours from the isolated plasma. The total RNA was extracted using miRNeasy micro kit (Qiagen, United States) according to manufacturer’s protocol, and quantified using NanoDrop (Thermo Fisher Scientific, United States). The quality of total RNA and the presence of miRNAs were confirmed using RNA 6000 Pico chip and small RNA chip (Agilent Technologies, United States), respectively.

value: Plasma

tag: gender

value: Male

tag: age


title: Siberian Hamster, Pituitary, LD, Rep 2

city: Glasgow

first: Calum

last: Stewart

address: Jarrett Building, University of Glasgow

country: United Kingdom

institute: University of Glasgow

description:
Pit205
PitExpressedGenesTranscripts.CSV

library_source: transcriptomic

data_processing:
Raw reads were demultiplexed and basealled using guppy basecaller
Porechop was used to trim adapters
Filtlong used to select long reads (>25 reads)
Minimap2 used to align reads to Mus musculus genome (GCRm39)
Transcript expression levels generated  using Salmon
Assembly: GRCmm39
Supplementary files format and content: Transcript expression levels generated  using Salmon

molecule: polyA RNA

organism: Phodopus sungorus

source_name: Pituitary Dissection

extract_protocol:
RNA was extracted using the Qiagen RNEasy plus mini-kit
RNA Libraries were constructed using the PCR_cDNA sequencing barcoding kit (SQK-PCB109, Oxford Nanopore) as per manufacturers instructions

value: Pituitary Dissection


title: TrafficJam-Upd H3K9me3 Input Replicate 1

description: Library name: Sample 25


title: 10 day old seedling, Atplh1_control_R1

city: Gautam Buddha Nagar

first: Rohini

last: Garg

state: UP

address: Shiv Nadar University, NH - 91, Tehsil Dadri

country: India

institute: Shiv Nadar University

data_processing:
The FASTQ files obtained from RNA-seq were pre-processed using NGS QC Toolkit (v2.3.3) to remove adapters and low-quality reads.
Filtered high-quality reads were mapped on the Arabidopsis thaliana genome using HISAT2.
The mapped reads were aligned into transcripts using StringTie followed by identification of DEGs using Cuffdiff.
FPKM for each sample is reported in processed file
Assembly: Arabidopsis thaliana genome (TAIR10)
Supplementary files format and content: Excel file containing fpkm values of all genes in all the samples across all combinations (WT_control Vs Atplh1_control; WT_control Vs Atplh2_control; WT_control Vs Atplh3_control; WT_control Vs WT_ABA;  Atplh1_control Vs Atplh1_ABA;   Atplh2_control Vs Atplh2_ABA;  Atplh3_control Vs Atplh3_ABA;  WT_control Vs WT_NaCl; Atplh1_control Vs Atplh1_NaCl; Atplh2_control Vs Atplh2_NaCl; Atplh3_control Vs Atplh3_NaCl)

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Arabidopsis thaliana wild type (Col 0) and mutants (Atplh1, Atplh2, Atplh3 ) seedlings were grown in growth chamber for 10 days in MS media with and without ABA, NaCl

extract_protocol:
Total RNA was isolated using TRIzol. The extracted RNA samples were quantified using Qubit 2.0 Fluorometer.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 5 day old seedlings were grown in MS media with and without ABA, NaCl for  another 5 days. 10 day old seedlings were harvested from wild type and mutant under control and treatment conditions.

value: whole seedling

value: 10 day old seedling

value: control


title: xylA, NusG-myc, replicate 1

country: South Korea

organism: Escherichia coli

value: bacterial cell

tag: strain


title: ATAC Biol rep 2; KO, CD62L- TPEX

description: Sample 14 KO CD62L- TPEX


title: Plasma exosomal miRNA, Dengue with warning sign, patient 01

value: Female


title: Plasma exosomal miRNA, Dengue with warning sign, patient 04


title: dRBSdATG, xylA, NusG-myc, replicate 1

value: c-Myc Antibody (9E10) (Santa Cruz Biotech, #sc-40)

value: Deletion of RBS & start codon of xylA; 8-myc-tagged NusG


title: ATAC Biol rep 2; Ctrl, CD101+ TEX

description: Sample 12 Wt CD101+ TEX

value: Spleen


title: Cardiac fibroblasts, serum-free media, Day7woTGFb Biol Rep1

city: Pamplona

first: Laura

last: Pilar Aguado Alvaro

address: Av. de Pío XII, 55

country: Spain

institute: Center for Applied Medical Research (CIMA)- University of Navarra

description: Primary Cas9 cardiac fibroblasts were grown on serum-free media for 7 days without fibrotic stimulation with TGFb

data_processing:
Sequencing reads in FASTQ format  were processed with Cutadapt (v2.10), trimming adapters and filtering based on quality.
Alignment to the mm10 mouse reference genome was conducted using STAR (v2.7.3a), employing default parameters for optimal mapping
Gene expression quantification and matrix generation were conducted using featureCounts, a component of the Rsubread package (v2.0.1)
Gene annotations were based on GENCODE gene symbols
Pre-analysis filtering for genes with adequate counts was performed using filterByExpr from the edgeR package (v3.32.1)
Subsequent data transformation, normalization, and differential gene expression analysis were carried out with the DESeq2 package (v1.30.0) in R
Assembly: mm10
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: csv file includes normalized values for each sample

source_name: Heart

growth_protocol: Cardiac fibroblasts were isolated from Cas9-mice and seeded either on serum-free media (DMEM KO + 20% knockout serum replacement (KSR) (Gibco) + 1% non-essential amino acids (NEAA) (Gibco) + 100 μM beta-mercaptoethanol (Gibco) + 1% P/S + 1% L-Glutamine) or on serum-containing media (DMEM + 10% fetal bovine serum (FBS) + 1% P/S + 1% L-Glutamine)

extract_protocol:
Poly-A RNA was extracted with Dynabeads Oligo dT (Ambion)
PCR amplification with NPM PCR Master Mix (Illumina) using P5NEXTPT5 primer and i7 indexed primers

treatment_protocol: Primary Cas9 cardiac fibroblasts were treated or not with pro-fibrotic cytokine TGFb (2.5 ng/ml)

value: Heart

tag: media

value: serum-free media

value: Fibroblast

value: Unstimulated


title: Siberian Hamster, Pituitary, 24wk SD, Rep 1

description:
Pit178
PitExpressedGenesTranscripts.CSV


title: ATAC Biol rep 2; Ctrl, CX3CR1+ TEX

description: Sample 11 Wt CX3CR1+ TEX

value: CD8 T Lymphocytes


title: Siberian Hamster, Pituitary, 28wk SD, Rep 1

description:
Pit175
PitExpressedGenesTranscripts.CSV


title: WT_7D_1

city: Nangang

first: Kreeti

last: Kajal

state: Taipei City

address: R337, Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan

country: Taiwan

description: Library name: WT_7D_1

data_processing:
TRimmomatic v0.36 was used for adaptor clipping and sequence quality trimming with a sliding-window approach. HISAT2 was used for transcriptome alignment.
Differential expression analysis was performed using StringTie (StringTie v2.1.4) and DEseq (DEseqv1.39.0) or DEseq2 (DEseq2v1.28.1) via an in-house pipeline from Welgene Biotech.
Assembly: RNA reads were aligned to the reference genome Release 6 plus ISO1 MT NCBI RefSeq ID GCF_000001215.4
Supplementary files format and content: PRJNA1264666_rawcount.txt, tab-delimited text files, raw count of all samples
Supplementary files format and content: PRJNA1264666_DeSeq2_results.txt, tab-delimited text files, result od DESeq2 analysis.

source_name: Gut

extract_protocol:
Fly guts were dissected and frozen by dipping in liquid nitrogen, then stored at -80°C until use. Total RNA was extracted using a standard Trizol (Novel-Gene) extraction protocol. In brief, 20-30 frozen guts were homogenized in 200 μl of Triazol, followed protocol. In brief, 20-30 frozen guts were homogenized in 200 μl of Triazol, followed by a phase separation step with 200 μl 1-bromo-3-chloropropane (Sigma-Aldrich). RNA was precipitated using 500 μl isopropanol. The pellet was washed with 75% ethanol twice and re-suspended in 40 μl RNAse-free water. RNA-seq was performed according to the standard Illumina protocol (Welgene, Taiwan). In brief, RNA was quantified.
Then, library preparation was carried out by SureSelect XT HS2 mRNA Library Preparation kit (Agilent), followed by AMPure XP beads (Beckman Coulter, USA) for size selection.

value: Gut

value: yw


title: Nanos-Upd H3K9me3 IP Replicate 1

description: Library name: Sample 23

value: testis tumor

value: y[1] w[1118] P{hs70FLP} ; P{w[+mC]=GAL4::VP16-nanos.UTR} / UAS - Upd ; + / UAS-FRT-H3-GFP-FRT-H3-mKO

value: GSC-like chromatin

value: H3K9me3, Diagenode #C15410056


title: xylA, BCM-treated, replicate 1

value: anti-E. coli RNA Polymerase β (Biolegend, #663006)

value: WT

value: 0.4% D-xylose induction for 4 hours; 50 μg/mL BCM treatment for 30 min


title: Nanos-Upd H3K9me3 IP Replicate 2

description: Library name: Sample 24


title: Siberian Hamster, Pituitary, 32wk SD, Rep 1

description:
Pit161
PitExpressedGenesTranscripts.CSV

value: Pituitary Dissection


title: ATAC Biol rep 1; KO, CD101+ TEX

description: Sample 8 KO CD101+ TEX


title: TrafficJam-Upd H3K27me3 IP Replicate 3

description: Library name: Sample 20

value: w[1118]; traffic Jam - GAL4 / UAS - Upd ; + / UAS-FRT-H3-GFP-FRT-H3-mKO

value: CySC-like chromatin

value: H3K27me3, EMD Millipore #07-449


title: Siberian Hamster, Pituitary, 8wk SD, Rep 1

description:
Pit305
PitExpressedGenesTranscripts.CSV


title: Siberian Hamster, Pituitary, 20wk SD, Rep 1

description:
Pit213
PitExpressedGenesTranscripts.CSV


title: ATAC Biol rep 1; KO, CX3CR1+ TEX

description: Sample 7 KO CX3CR1+ TEX

value: Spleen


title: Fucoidan 6

city: Ås

first: Byron

last: Morales Lange

address: Arboretveien 6

country: Norway

institute: Norwegian University of Life Sciences

description: Library name: Sample 12

data_processing:
RNA-seq raw data analysis was performed in Orion-HPC (NMBU - High-Performance Computing cluster). Briefly, through nf-core rnaseq v3.3, cleaned reads were aligned to Salmo salar genome SSAL_v3.1 (GenBank assembly accession: GCA_905237065.2). The fragments obtained were counted using FeatureCounts (subread v1.5.1). Then, by SARTools R package (v1.7.3) in RStudio (v4.2.3), differentially expressed genes (DEGs) were detected when adjusted p-value (padj) was < 0.05.
Assembly: Salmo salar genome SSAL_v3.1 (GenBank assembly accession: GCA_905237065.2).
Supplementary files format and content: Count files (counted genes using FeatureCounts)

organism: Salmo salar

source_name: Distal Intestine

extract_protocol:
Total RNA was extracted from samples (6 fish per dietary group) using Qiazol Lysis Reagent (Qiagen) for standard extraction method (based on chloroform and isopropanol extraction). Total RNA was eluted in 30 µL of ultra-pure water and concentration and integrity were measured through Nanodrop (Nanodrop Technologies) and BioAnalyzer (Agilent), respectively. All samples had ≥ 200 ng of mRNA and RIN ≥ 8
Library preparation was performed by NovoGene (Cambridge, UK)

value: Distal Intestine

value: Diet containing 0.2% fucoidan

tag: dietary group

tag: time

value: Week 5


title: Siberian Hamster, Pituitary, 4wk SD, Rep 1

description:
Pit356
PitExpressedGenesTranscripts.CSV


title: ATAC Biol rep 1; KO, CD62L- TPEX

description: Sample 6 KO CD62L- TPEX

value: CD8 T Lymphocytes


title: ATAC Biol rep 2; Ctrl, CD62L- TPEX

description: Sample 10 Wt CD62L- TPEX


title: Fucoidan 3

description: Library name: Sample 9


title: TrafficJam-Upd H3K27me3 Input Replicate 3

description: Library name: Sample 17

value: anti-GFP PA-Mnase


title: PA_VM-D45-rep2

city: Cheongju

first: Sang-Hwan

last: Hyun

state: Please select your state

address: 1 Chungdae-ro, Seowon-gu

department: Veterinary Medical Center and College of Veterinary Medicine

institute: Chungbuk national university

description:
Library name: Sample 16
Day 45 of differentiation

data_processing:
Paired-end sequencing reads were generated on the Illumina sequencing NovaSeq platform. Before starting analysis, Trimmomatic v0.38 was used to remove adapter sequences and trim bases with poor base quality. The cleaned reads were aligned to the Sus scrofa (Sscrofa11.1) using HISAT v2.1.0 29. The reference genome sequence and gene annotation data were downloaded from NCBI Genome assembly and NCBI RefSeq database respectively.
Aligned data (SAM file format) were sorted and indexed using SAMtools v 1.9. After alignment, the transcripts were assembled and quantified using StringTie v2.1.3b 30,31. Gene-level and Transcript-level quantification were calculated as raw read count, FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Million).
Assembly: Sscrofa11.1 (GCA_000003025.6)
Supplementary files format and content: To normalize sequencing depth among samples, FPKM and TPM values were calculated.

organism: Sus scrofa

source_name: Midbrain

extract_protocol:
mRNA molecules were purified and fragmented from 1μg of total RNA using QIAzol® Lysis Reagent (Cat. No. 79306), RNeasy® Mini Kit.
A library was independently prepared with 1μg of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA, #20020595)

value: Midbrain

tag: cell line

value: PA_3_ pESC_FIW

value: midbrain dopaminergic neurons


title: dRBSdATG, xylA, BCM-treated, replicate 2

value: bacterial cell

value: Deletion of RBS & start codon of xylA


title: TrafficJam-Upd H3K27me3 Input Replicate 2

description: Library name: Sample 16

value: testis tumor


title: dRBSdATG, xylA, BCM-treated, replicate 1

value: anti-E. coli RNA Polymerase β (Biolegend, #663006)

value: 0.4% D-xylose induction for 4 hours; 50 μg/mL BCM treatment for 30 min


title: Nanos-Upd H3K9me3 Input Replicate 2

description: Library name: Sample 22

value: y[1] w[1118] P{hs70FLP} ; P{w[+mC]=GAL4::VP16-nanos.UTR} / UAS - Upd ; + / UAS-FRT-H3-GFP-FRT-H3-mKO

value: GSC-like chromatin


title: Fucoidan 1

description: Library name: Sample 7


title: Siberian Hamster, Pituitary, 16wk SD, Rep 1

description:
Pit244
PitExpressedGenesTranscripts.CSV

value: Pituitary Dissection


title: PA_VM-D28-rep2

description:
Library name: Sample 14
Day 28 of differentiation


title: ATAC Biol rep 1; Ctrl, CD62L- TPEX

description: Sample 2 Wt CD62L- TPEX

value: Spleen


title: ATAC Biol rep 1; Ctrl, CD62L+ TPEX

description: Sample 1 Wt CD62L+ TPEX


title: Nanos-Upd H3K27me3 IP Replicate 2

description: Library name: Sample 13

value: H3K27me3, EMD Millipore #07-449


title: Biol rep 2; KO, CD101+ TEX

description: Sample 16: KO CD101+ TEX

data_processing:
Alignment with STAR.
Sorted with SAMTools, gene counts with FEatureCounts using GRCm39/Ensmbl build 105.
Filtered with edgeR filterByExpr min.counts 200 and min.total.count 300 and any gene without counts per million greater than 15 in at least 2 samples.
Assembly: GRCm39
Supplementary files format and content: Tab delimitted table of raw counts of filtered genes.
Supplementary files format and content: Rows representing gens Symbols and columns representing samples.

extract_protocol:
RNA was isolated from sorted populations using the RNeasy Plus Micro Kit according to the manufacturer’s instructions (QIAGEN)
DNA libraries were constructed using the TruSeq® RNA Sample Preparation v2 kit (Illumina)


title: ATAC Biol rep 2; Ctrl, CD62L+ TPEX

description: Sample 9  Wt CD62L+ TPEX


title: Nanos-Upd H3K9me3 Input Replicate 1

description: Library name: Sample 21


title: Fucoidan 5

description: Library name: Sample 11

value: Distal Intestine

value: Diet containing 0.2% fucoidan


title: TrafficJam-Upd H3K27me3 IP Replicate 2

description: Library name: Sample 19

value: w[1118]; traffic Jam - GAL4 / UAS - Upd ; + / UAS-FRT-H3-GFP-FRT-H3-mKO

value: CySC-like chromatin


title: Biol rep 2; KO, CX3CR1+ TEX

description: Sample 15: KO CX3CR1+ TEX

value: CD8 T Lymphocytes


title: Biol rep 2; KO, CD62L- TPEX

description: Sample 14: KO CD62L- TPEX


title: Nanos-Upd H3K27me3 Input Replicate 3

description: Library name: Sample 11

value: anti-GFP PA-Mnase


title: TrafficJam-Upd H3K27me3 IP Replicate 1

description: Library name: Sample 18


title: Fucoidan 4

description: Library name: Sample 10

value: Week 5


title: Control 3

description: Library name: Sample 3

value: Control diet


title: Siberian Hamster, Pituitary, LD, Rep 1

description:
Pit417
PitExpressedGenesTranscripts.CSV


title: ATAC Biol rep 1; KO, CD62L+ TPEX

description: Sample 5 KO CD62L+ TPEX


title: Biol rep 2; KO, CD62L+ TPEX

description: Sample 13: KO CD62L+ TPEX


title: ATAC Biol rep 1; Ctrl, CX3CR1+ TEX

description: Sample 3 Wt CX3CR1+ TEX


title: Fucoidan 2

description: Library name: Sample 8


title: Nanos-Upd H3K27me3 Input Replicate 1

description: Library name: Sample 9


title: ATAC Biol rep 1; Ctrl, CD101+ TEX

description: Sample 4 Wt CD101+ TEX


title: IVF_VM-D45-rep2

description:
Library name: Sample 8
Day 45 of differentiation

value: Midbrain

value: IVF_1_ pESC_FIW

value: midbrain dopaminergic neurons


title: Siberian Hamster, Pituitary, 12wk SD, Rep 1

description:
Pit277
PitExpressedGenesTranscripts.CSV


title: Control 1

description: Library name: Sample 1


title: Control 6

description: Library name: Sample 6


title: PA_VM-D28-rep1

description:
Library name: Sample 13
Day 28 of differentiation

value: PA_3_ pESC_FIW


title: Nanos-Upd H3K27me3 IP Replicate 3

description: Library name: Sample 14

value: testis tumor

value: y[1] w[1118] P{hs70FLP} ; P{w[+mC]=GAL4::VP16-nanos.UTR} / UAS - Upd ; + / UAS-FRT-H3-GFP-FRT-H3-mKO


title: Control 5

description: Library name: Sample 5


title: Control 4

description: Library name: Sample 4


title: RG11N, male foreleg, biol rep 3

city: New York

first: Anna

last: Ryba

state: New York

address: 1230 York Avenue

institute: Rockefeller University

description: Library name: RG11N_3

data_processing:
Sequencing reads were basecalled and demultiplexed using basecallQC and trimmed for adapter/low quality sequences using Rfastp.
Reads aligned to the D. melanogaster reference genome, dm6 using the subjunc function in Rsubread and counts extracted using the summarizeOverlaps function in Genomic Alignments.
Assembly: dm6
Supplementary files format and content: Space-delimited text file includes raw counts for each Sample.

source_name: male foreleg

extract_protocol:
RNA was extracted from disrupted foreleg tissue using PicoPure kit (Thermo Fisher), except TriZol reagent was used for cell lysis instead of the kit's lysis buffer. Total RNA underwent polyA selection prior to library preparation.
Libraries were constructed by the Rockefeller University Genomics Resource Center using Nextera XT DNA library preparation kit (Illumina) following manufacturer's protocols.

value: male foreleg


title: PA_VM-D16-rep2

description:
Library name: Sample 12
Day 16 of differentiation


title: Biol rep 2; Ctrl, CX3CR1+ TEX

description: Sample 11: WT CX3CR1+ TEX

value: Spleen


title: Nanos-Upd H3K27me3 IP Replicate 1

description: Library name: Sample 12

value: GSC-like chromatin

value: H3K27me3, EMD Millipore #07-449


title: TrafficJam-Upd H3K27me3 Input Replicate 1

description: Library name: Sample 15


title: PA_VM-D16-rep1

description:
Library name: Sample 11
Day 16 of differentiation


title: PA_VM-D45-rep1

description:
Library name: Sample 15
Day 45 of differentiation


title: Biol rep 2; Ctrl, CD62L- TPEX

description: Sample 10: WT CD62L- TPEX


title: Control 2

description: Library name: Sample 2

value: Distal Intestine


title: PA_VM-D0-rep2

description:
Library name: Sample 10
Day 0 of differentiation

source_name: Embryonic stem cell culture

value: Embryonic stem cell culture

value: stem cell


title: PA_VM-D0-rep1

description:
Library name: Sample 9
Day 0 of differentiation


title: Biol rep 2; Ctrl, CD101+ TEX

description: Sample 12: WT CD101+ TEX

value: CD8 T Lymphocytes


title: Biol rep 1; KO, CD101+ TEX

description: Sample 8: KO CD101+ TEX


title: CS/CO13N hybrid, male foreleg, biol rep 2

description: Library name: hyb_2

value: CS/CO13N hybrid


title: Nanos-Upd H3K27me3 Input Replicate 2

description: Library name: Sample 10

value: anti-GFP PA-Mnase


title: TrafficJam-Upd H3K4me3 IP Replicate 2

description: Library name: Sample 8

value: w[1118]; traffic Jam - GAL4 / UAS - Upd ; + / UAS-FRT-H3-GFP-FRT-H3-mKO

value: CySC-like chromatin


title: IVF_VM-D45-rep1

description:
Library name: Sample 7
Day 45 of differentiation

value: Midbrain

value: IVF_1_ pESC_FIW


title: RG11N, male foreleg, biol rep 2

description: Library name: RG11N_2


title: TrafficJam-Upd H3K4me3 IP Replicate 1

description: Library name: Sample 7


title: IVF_VM-D28-rep2

description:
Library name: Samlpe 6
Day 28 of differentiation

value: midbrain dopaminergic neurons


title: IVF_VM-D16-rep1

description:
Library name: Sample 3
Day 16 of differentiation


title: Biol rep 1; KO, CX3CR1+ TEX

description: Sample 7: KO CX3CR1+ TEX


title: Nanos-Upd H3K4me3 IP Replicate 1

description: Library name: Sample 3

value: testis tumor


title: RG11N, male foreleg, biol rep 1

description: Library name: RG11N_1


title: TrafficJam-Upd H3K4me3 Input Replicate 2

description: Library name: Sample 6


title: IVF_VM-D28-rep1

description:
Library name: Sample 5
Day 28 of differentiation


title: CS/CO13N hybrid, male foreleg, biol rep 3

description: Library name: hyb_3


title: Nanos-Upd H3K4me3 Input Replicate 2

description: Library name: Sample 2

value: y[1] w[1118] P{hs70FLP} ; P{w[+mC]=GAL4::VP16-nanos.UTR} / UAS - Upd ; + / UAS-FRT-H3-GFP-FRT-H3-mKO


title: TrafficJam-Upd H3K4me3 Input Replicate 1

description: Library name: Sample 5


title: CS, male foreleg, biol rep 3

description: Library name: CS_3

value: male foreleg

value: CS


title: IVF_VM-D0-rep1

description:
Library name: Sample 1
Day 0 of differentiation


title: Biol rep 2; Ctrl, CD62L+ TPEX

description: Sample 9: WT CD62L+ TPEX

value: Spleen


title: IVF_VM-D16-rep2

description:
Library name: Sample 4
Day 16 of differentiation


title: CS/CO13N hybrid, male foreleg, biol rep 1

description: Library name: hyb_1


title: IVF_VM-D0-rep2

description:
Library name: Sample 2
Day 0 of differentiation


title: CS, male foreleg, biol rep 2

description: Library name: CS_2


title: Nanos-Upd H3K4me3 Input Replicate 1

description: Library name: Sample 1

value: GSC-like chromatin


title: Replicate 4 NanoDam

city: Heidelberg

first: Stefan

last: Peidli

state: BW

address: Meyerhofstraße 1

department: Genome Biology

country: Germany

institute: European Molecular Biology Laboratory

description:
Library name: DS-002C5
NanoDan Cph Rep4

data_processing:
Reads were trimmed using trim_galore (v0.6.10, DOI:10.5281/zenodo.7598955) with settings for illumina reads, removing 10bp from both the 5’ and 3’ ends of all reads, and requiring a minimal read length of 36bp.
Trimmed reads were then aligned to the Drosophila Melanogaster genome using a precompiled bowtie index (BDGP6) and bowtie2 (v2.5.4, DOI:10.1038/nmeth.1923) while allowing for maximum single mismatches. Resulting alignment files were filtered for uniquely mapped reads, converted to bam, sorted, and indexed using samtools (v1.20, DOI:10.1093/bioinformatics/btp352).
We used MACS2 (v2.2.9.1, DOI:10.1101/496521) for peak calling while filtering out peaks with FDR>0.05. Peaks were then annotated with CHIPseeker (v1.38.0, DOI:10.1093/bioinformatics/btv145) and a genome annotation file from Ensembl (index BDGP6.46.110). Additionally, a GATC signal was obtained by binning the genome into consecutive GATC sites using a custom python script and a GFF of sites obtained from damidseq_pipeline doi:10.1093/bioinformatics/btv386, then calculating fold-changes of the NanoDam Cph signal with respect to the control for each replicate respectively.
Tracks were plotted using pyGenomeTracks doi:10.1038/s41467-017-02525-w, doi: 10.1093/bioinformatics/btaa692. The entire workflow was implemented using snakemake (v8.14.0, DOI: 10.12688/f1000research.29032.1).
Assembly: BDGP6
Supplementary files format and content: SAMPLE_ID_peaks.broadPeak contains broad peaks called by MACS2. Filtered versions are available.
Supplementary files format and content: SAMPLE_ID_peaks.xls also contains broad peaks called by MACS2
Supplementary files format and content: SAMPLE_ID_vs_CONTROL_ID_peaks.broadPeak and similar files contain MACS2 peaks with the respective control samples as a contrast.

source_name: intestine

extract_protocol:
To perform Cph NanoDam in the intestine, we crossed a CphYFP; UAS-NanoDam line with esgTS. As control, we crossed UAS-NanoDam line with esgTS. Flies were reared at 18°C. Adult flies aged between 3-5 days were shifted to 29°C for 17hrs.
30 Midguts where dissected in ice-cold PBS, taking care to remove Malpighian tubules, hindgut and proventriculus and samples were frozen in -80°C. DNA was extracted from dissected midgut and methylated fragments were isolated with DpnI and DpnII digestion. Methylated fragments were then amplified with PCR and sonicated in order to generate libraries suitable for sequencing. Sequencing was performed using single end 86 bp reads with a using a Nextseq 550 at the Deep Sequencing Facility, BioQuant, Heidelberg University.

value: intestine

value: intestinal epithelium

value: CphYFP x UAS-NanoDam x esgTS

value: Cph NanoDam


title: Biol rep 1; KO, CD62L- TPEX

description: Sample 6: KO CD62L- TPEX

value: CD8 T Lymphocytes


title: Biol rep 1; KO, CD62L+ TPEX

description: Sample 5: KO CD62L+ TPEX


title: Biol rep 1; Ctrl, CD62L- TPEX

description: Sample 2: WT CD62L- TPEX


title: Replicate 3 NanoDam

description:
Library name: DS-002C2
NanoDan Cph Rep3


title: Nanos-Upd tumor Replicate 2

description:
Library name: Sample 2
10X Genomics
nos.2

library_source: transcriptomic single cell

data_processing:
Reads were aligned, using CellRanger v7.0.0, and including intronic alignments, to the following reference: dm6 genome, FlyBase r6.47 GTF file, and the H3-GFP coding sequence and corresponding genomic range as GTF.
In the processed data files, each sample was filtered for mitochondrion genome percentage less than 10% and ribosomal protein transcript percentage less than 40%, and then normalized and clustered, by Seurat v5.0.3 and sctransform v0.4.1.
Doublet clusters were detected, and removed, on the basis of both Nanos and Traffic Jam expression >50%, and also by scDblFinder v1.16.0.
Remaining cells with excessively low or high sequencing depth were also detected, and removed, by UMI count <2200 or >7500, or by number of genes with a UMI <500 or >2500.
Seurat's Integrate Data workflow was applied to the 4 samples, and the entire clustering workflow was repeated on the integrated gene expression, to label the clusters that are identified in the metadata.
Assembly: dm6
Supplementary files format and content: Cells and UMIs are counted using CellRanger v7.0.0, with a reference of H3-GFP as well as FlyBase r6.47.  A matrix entry represents the UMI count for a particular cell barcode and gene.
Supplementary files format and content: For cells in the final expression matrix, we save our 5 named Seurat clusters (label), the UMI count (nCount_RNA), the quantified gene count (nFeature_RNA), the percent of mitochondrion genome UMIs (pct.mito), the percent of ribosomal protein UMIs (pct.ribo), an identifier of the 10X Genomics sample (batch), and the integrated sctransform UMAP coordinates (umap_1, umap_2).

extract_protocol:
Tesis tumors were dissected in sterile Schnieder's media supplemented with 10% fetal bovine serum. Testis tissue was digested to completion in TrypLE supplemented with 2mg/mL collagenase by incubating with intermittent agitation at 37C. Digested tissue was filtered first through at 40um filter, then a 10um filter before pelleting cells by centrifugation at 1,200rpm. After removing the supernatant cells were washed once in HBSS followed by centrifugation. After the second wash, cells were resuspended in HBSS and cell count/viability was obtained with Trypan blue.
Library preparation for RNA-seq was performed following the instructions for 10X Genomics Chromium Next GEM Single Cell 3'Kit v3.1.


title: Biol rep 1; Ctrl, CD101+ TEX

description: Sample 4: WT CD101+ TEX


title: Biol rep 1; Ctrl, CD62L+ TPEX

description: Sample 1: WT CD62L+ TPEX


title: Nanos-Upd H3K4me3 IP Replicate 2

description: Library name: Sample 4


title: CS, male foreleg, biol rep 1

description: Library name: CS_1


title: TrafficJam-Upd tumor Replicate 2

description:
Library name: Sample 4
10X Genomics
tj.2


title: Replicate 4 Control

description:
Library name: DS-002C4
NanoDan Control Input Rep4

value: UAS-NanoDam x esgTS

value: Control NanoDam


title: Biol rep 1; Ctrl, CX3CR1+ TEX

description: Sample 3: WT CX3CR1+ TEX


title: CO13N, male foreleg, biol rep 3

description: Library name: CO13N_3


title: TrafficJam-Upd tumor Replicate 1

description:
Library name: Sample 3
10X Genomics
tj.1

value: w[1118]; traffic Jam - GAL4 / UAS - Upd ; + / UAS-FRT-H3-GFP-FRT-H3-mKO


title: CO13N, male foreleg, biol rep 2

description: Library name: CO13N_2


title: Replicate 3 Control

description:
Library name: DS-002C1
NanoDan Control Input Rep3


title: sample 192 Control

status: Public on Sep 11 2025

city: Los Angeles

first: Noah

last: Zaitlen

state: CA

address: 675 Charles E Young Dr S

department: Neurology

institute: UCLA

description:
Library name: Control192
cell-free DNA

data_processing:
UMIs were extracted from the index read and added to R1/R2 FASTQ headers using umi_tools. Adapters were trimmed with trim_galore, and reads were aligned, processed, and methylation-called using BsBolt v1.6.1 following an adapted Morselli et al. pipeline. Reads were aligned in paired-end mode to a bisulfite-converted hg38 genome (generated with BsBolt Index from UCSC hg38). After alignment (BsBolt Align, default parameters), reads were processed with samtools fixmate and sorted, and duplicates removed with umi_tools dedup in paired-end mode. CpG methylation was then called for both cohorts using BsBolt CallMethylation with parameters -BG -CG -remove-ccgg, restricting to CpGs, outputting to bedGraph, and excluding CCGG sites.
at UCSF, the paired end read data was represented by R1 and R3, and R2 was the UMI. I1 contains one Illumina adapter. Complete Illumina adapter information is in read header
at UQ, the paired end read data was represented by R1 and R2, and I2 contained the UMI and one Illumina adapter. I1 was the Illumina adapter represented in the header
Assembly: hg38
Supplementary files format and content: chromosome, position, methylation read count, total read count

source_name: whole blood

extract_protocol:
cfDNA was extracted and prepared for sequencing using a harmonized protocol at UCSF and UQ. Plasma (2–8 ml) was thawed at room temperature, and cfDNA was isolated with the QIAGEN Circulating Nucleic Acid kit (Cat. No. 55114). DNA was quantified with the Qubit dsDNA HS assay and assessed using the Agilent TapeStation 4200 (UCSF) or Bioanalyzer 2100 HS kit (UQ). Bisulfite conversion was performed with the Zymo Lightning kit, and libraries were prepared using the Accel-NGS Methyl-Seq kit (Swift Biosciences) with one major modification: denatured, bisulfite-converted cfDNA underwent adaptase, extension, and ligation, followed by ligation cleanup and primer extension (98 °C 1 min; 70 °C 2 min; 65 °C 5 min; 4 °C hold) with UMIs and i5 barcodes to enable duplicate removal and accurate methylation estimation.After exonuclease I treatment and purification, libraries were amplified with a universal P5 primer and custom i7-barcoded P7 primers (98 °C 30 s; 15 cycles of 98 °C 10 s, 60 °C 30 s, 68 °C 60 s; final 68 °C 5 min; 4 °C hold).
Unique-dual indexed libraries were purified, quantified (Qubit HS-dsDNA), quality-checked (Agilent D1000-HS assay), and pooled in 12-plex. Pools underwent hybridization capture (xGen Hybridization Capture Kit, IDT) using custom probes targeting ~5,000 regions. Captured libraries were re-amplified (98 °C 30 s; 10 cycles of 98 °C 10 s, 60 °C 30 s, 68 °C 60 s; final 68 °C 5 min; 4 °C hold), purified with SPRI beads, and quantified. Identical probes were used across sites for consistency. Final pools were sequenced on an Illumina NovaSeq 6000 (S4 lane, 150 bp PE, 8 bases i7, 17 bases i5) at UCLA (USA) and UNSW Ramaciotti (Australia).

value: whole blood

tag: location

value: UQ


title: sample 182 Control

description:
Library name: Control182
cell-free DNA


title: sample 181 Control

description:
Library name: Control181
cell-free DNA


title: CO13N, male foreleg, biol rep 1

description: Library name: CO13N_1


title: sample 184 Control

description:
Library name: Control184
cell-free DNA


title: sample 191 Control

description:
Library name: Control191
cell-free DNA


title: sample 189 Control

description:
Library name: Control189
cell-free DNA


title: Nanos-Upd tumor Replicate 1

description:
Library name: Sample 1
10X Genomics
nos.1


title: sample 179 Control

description:
Library name: Control179
cell-free DNA


title: sample 180 Control

description:
Library name: Control180
cell-free DNA


title: sample 188 Control

description:
Library name: Control188
cell-free DNA


title: sample 190 Control

description:
Library name: Control190
cell-free DNA


title: sample 183 Control

description:
Library name: Control183
cell-free DNA


title: sample 176 Control

description:
Library name: Control176
cell-free DNA


title: sample 187 Control

description:
Library name: Control187
cell-free DNA


title: sample 186 Control

description:
Library name: Control186
cell-free DNA


title: sample 171 Control

description:
Library name: Control171
cell-free DNA


title: sample 178 Control

description:
Library name: Control178
cell-free DNA


title: sample 173 Control

description:
Library name: Control173
cell-free DNA


title: sample 174 Control

description:
Library name: Control174
cell-free DNA


title: sample 170 Control

description:
Library name: Control170
cell-free DNA


title: sample 177 Control

description:
Library name: Control177
cell-free DNA


title: sample 185 Control

description:
Library name: Control185
cell-free DNA


title: sample 169 Control

description:
Library name: Control169
cell-free DNA


title: sample 167 ALS

description:
Library name: ALS167
cell-free DNA


title: sample 168 ALS

description:
Library name: ALS168
cell-free DNA


title: sample 165 ALS

description:
Library name: ALS165
cell-free DNA


title: sample 172 Control

description:
Library name: Control172
cell-free DNA


title: sample 163 ALS

description:
Library name: ALS163
cell-free DNA


title: sample 161 ALS

description:
Library name: ALS161
cell-free DNA


title: sample 157 ALS

description:
Library name: ALS157
cell-free DNA


title: sample 158 ALS

description:
Library name: ALS158
cell-free DNA


title: sample 164 ALS

description:
Library name: ALS164
cell-free DNA


title: sample 156 ALS

description:
Library name: ALS156
cell-free DNA


title: sample 162 ALS

description:
Library name: ALS162
cell-free DNA


title: sample 159 ALS

description:
Library name: ALS159
cell-free DNA


title: sample 154 ALS

description:
Library name: ALS154
cell-free DNA


title: sample 153 ALS

description:
Library name: ALS153
cell-free DNA


title: sample 175 Control

description:
Library name: Control175
cell-free DNA


title: sample 150 ALS

description:
Library name: ALS150
cell-free DNA


title: sample 149 ALS

description:
Library name: ALS149
cell-free DNA


title: sample 155 ALS

description:
Library name: ALS155
cell-free DNA


title: sample 152 ALS

description:
Library name: ALS152
cell-free DNA


title: sample 148 ALS

description:
Library name: ALS148
cell-free DNA


title: sample 145 ALS

description:
Library name: ALS145
cell-free DNA


title: sample 146 ALS

description:
Library name: ALS146
cell-free DNA


title: sample 143 ALS

description:
Library name: ALS143
cell-free DNA


title: sample 147 ALS

description:
Library name: ALS147
cell-free DNA


title: sample 142 ALS

description:
Library name: ALS142
cell-free DNA


title: sample 141 ALS

description:
Library name: ALS141
cell-free DNA


title: sample 166 ALS

description:
Library name: ALS166
cell-free DNA


title: sample 139 ALS

description:
Library name: ALS139
cell-free DNA


title: sample 144 ALS

description:
Library name: ALS144
cell-free DNA


title: sample 160 ALS

description:
Library name: ALS160
cell-free DNA


title: sample 137 ALS

description:
Library name: ALS137
cell-free DNA


title: sample 135 Control

description:
Library name: Control135
cell-free DNA


title: sample 133 Control

description:
Library name: Control133
cell-free DNA


title: sample 132 Control

description:
Library name: Control132
cell-free DNA


title: sample 134 Control

description:
Library name: Control134
cell-free DNA


title: sample 131 Control

description:
Library name: Control131
cell-free DNA


title: sample 128 ALS

description:
Library name: ALS128
cell-free DNA


title: sample 151 ALS

description:
Library name: ALS151
cell-free DNA


title: sample 130 Control

description:
Library name: Control130
cell-free DNA


title: sample 129 Control

description:
Library name: Control129
cell-free DNA


title: sample 126 Control

description:
Library name: Control126
cell-free DNA


title: sample 127 ALS

description:
Library name: ALS127
cell-free DNA


title: sample 125 Control

description:
Library name: Control125
cell-free DNA


title: sample 122 Control

description:
Library name: Control122
cell-free DNA


title: sample 121 Control

description:
Library name: Control121
cell-free DNA


title: sample 140 ALS

description:
Library name: ALS140
cell-free DNA


title: sample 124 ALS

description:
Library name: ALS124
cell-free DNA


title: sample 119 ALS

description:
Library name: ALS119
cell-free DNA


title: sample 120 ALS

description:
Library name: ALS120
cell-free DNA


title: sample 113 Control

description:
Library name: Control113
cell-free DNA


title: sample 116 ALS

description:
Library name: ALS116
cell-free DNA


title: sample 114 Control

description:
Library name: Control114
cell-free DNA


title: sample 123 ALS

description:
Library name: ALS123
cell-free DNA


title: sample 138 ALS

description:
Library name: ALS138
cell-free DNA


title: sample 117 Control

description:
Library name: Control117
cell-free DNA


title: sample 136 Control

description:
Library name: Control136
cell-free DNA


title: sample 111 ALS

description:
Library name: ALS111
cell-free DNA


title: sample 109 Control

description:
Library name: Control109
cell-free DNA


title: sample 107 ALS

description:
Library name: ALS107
cell-free DNA


title: sample 108 ALS

description:
Library name: ALS108
cell-free DNA


title: sample 105 Control

description:
Library name: Control105
cell-free DNA


title: sample 104 ALS

description:
Library name: ALS104
cell-free DNA


title: sample 106 Control

description:
Library name: Control106
cell-free DNA


title: sample 102 Control

description:
Library name: Control102
cell-free DNA


title: sample 103 ALS

description:
Library name: ALS103
cell-free DNA


title: sample 101 Control

description:
Library name: Control101
cell-free DNA


title: sample 99 ALS

description:
Library name: ALS99
cell-free DNA


title: sample 100 ALS

description:
Library name: ALS100
cell-free DNA


title: sample 98 Control

description:
Library name: Control98
cell-free DNA


title: sample 97 Control

description:
Library name: Control97
cell-free DNA


title: sample 96 BS Control

description:
Library name: BS Control96
cell-free DNA

value: UCSF

value: UCLA


title: sample 118 Control

description:
Library name: Control118
cell-free DNA


title: sample 95 ALS

description:
Library name: ALS95
cell-free DNA


title: sample 94 ALS

description:
Library name: ALS94
cell-free DNA


title: sample 115 ALS

description:
Library name: ALS115
cell-free DNA


title: sample 92 ALS

description:
Library name: ALS92
cell-free DNA


title: sample 112 ALS

description:
Library name: ALS112
cell-free DNA


title: sample 89 ALS

description:
Library name: ALS89
cell-free DNA


title: sample 90 ALS

description:
Library name: ALS90
cell-free DNA


title: sample 93 ALS

description:
Library name: ALS93
cell-free DNA


title: sample 110 Control

description:
Library name: Control110
cell-free DNA


title: sample 88 ALS

description:
Library name: ALS88
cell-free DNA


title: sample 84 ALS

description:
Library name: ALS84
cell-free DNA


title: sample 85 ALS

description:
Library name: ALS85
cell-free DNA


title: sample 86 ALS

description:
Library name: ALS86
cell-free DNA


title: sample 91 ALS

description:
Library name: ALS91
cell-free DNA


title: sample 87 ALS

description:
Library name: ALS87
cell-free DNA


title: sample 83 ALS

description:
Library name: ALS83
cell-free DNA


title: sample 81 ALS

description:
Library name: ALS81
cell-free DNA


title: sample 82 ALS

description:
Library name: ALS82
cell-free DNA


title: sample 80 ALS

description:
Library name: ALS80
cell-free DNA


title: sample 77 ALS

description:
Library name: ALS77
cell-free DNA


title: sample 78 ALS

description:
Library name: ALS78
cell-free DNA


title: sample 74 ALS

description:
Library name: ALS74
cell-free DNA


title: sample 79 ALS

description:
Library name: ALS79
cell-free DNA


title: sample 76 ALS

description:
Library name: ALS76
cell-free DNA


title: sample 75 ALS

description:
Library name: ALS75
cell-free DNA


title: sample 73 ALS

description:
Library name: ALS73
cell-free DNA


title: sample 72 ALS

description:
Library name: ALS72
cell-free DNA


title: sample 68 ALS

description:
Library name: ALS68
cell-free DNA


title: sample 69 ALS

description:
Library name: ALS69
cell-free DNA


title: sample 65 ALS

description:
Library name: ALS65
cell-free DNA


title: sample 66 ALS

description:
Library name: ALS66
cell-free DNA


title: sample 64 ALS

description:
Library name: ALS64
cell-free DNA


title: sample 62 ALS

description:
Library name: ALS62
cell-free DNA


title: sample 60 ALS

description:
Library name: ALS60
cell-free DNA


title: sample 63 ALS

description:
Library name: ALS63
cell-free DNA


title: sample 59 ALS

description:
Library name: ALS59
cell-free DNA


title: sample 58 ALS

description:
Library name: ALS58
cell-free DNA


title: sample 61 ALS

description:
Library name: ALS61
cell-free DNA


title: sample 55 ALS

description:
Library name: ALS55
cell-free DNA


title: sample 56 ALS

description:
Library name: ALS56
cell-free DNA


title: sample 54 ALS

description:
Library name: ALS54
cell-free DNA


title: sample 57 ALS

description:
Library name: ALS57
cell-free DNA


title: sample 53 ALS

description:
Library name: ALS53
cell-free DNA


title: sample 51 ALS

description:
Library name: ALS51
cell-free DNA


title: sample 52 ALS

description:
Library name: ALS52
cell-free DNA


title: sample 50 ALS

description:
Library name: ALS50
cell-free DNA


title: sample 45 Control

description:
Library name: Control45
cell-free DNA


title: sample 44 Control

description:
Library name: Control44
cell-free DNA


title: sample 47 ALS

description:
Library name: ALS47
cell-free DNA


title: sample 43 Control

description:
Library name: Control43
cell-free DNA


title: sample 71 ALS

description:
Library name: ALS71
cell-free DNA


title: sample 70 ALS

description:
Library name: ALS70
cell-free DNA


title: sample 46 ALS

description:
Library name: ALS46
cell-free DNA


title: sample 48 ALS

description:
Library name: ALS48
cell-free DNA


title: sample 67 ALS

description:
Library name: ALS67
cell-free DNA


title: sample 42 Control

description:
Library name: Control42
cell-free DNA


title: sample 41 Control

description:
Library name: Control41
cell-free DNA


title: sample 37 Control

description:
Library name: Control37
cell-free DNA


title: sample 39 Control

description:
Library name: Control39
cell-free DNA


title: sample 40 Control

description:
Library name: Control40
cell-free DNA


title: sample 38 Control

description:
Library name: Control38
cell-free DNA


title: sample 35 Control

description:
Library name: Control35
cell-free DNA


title: sample 34 Control

description:
Library name: Control34
cell-free DNA


title: sample 36 Control

description:
Library name: Control36
cell-free DNA


title: sample 33 Control

description:
Library name: Control33
cell-free DNA


title: sample 29 Control

description:
Library name: Control29
cell-free DNA


title: sample 32 Control

description:
Library name: Control32
cell-free DNA


title: sample 31 Control

description:
Library name: Control31
cell-free DNA


title: sample 27 Control

description:
Library name: Control27
cell-free DNA


title: sample 26 Control

description:
Library name: Control26
cell-free DNA


title: sample 24 Control

description:
Library name: Control24
cell-free DNA


title: sample 49 ALS

description:
Library name: ALS49
cell-free DNA


title: sample 28 Control

description:
Library name: Control28
cell-free DNA


title: sample 22 Control

description:
Library name: Control22
cell-free DNA


title: sample 21 Control

description:
Library name: Control21
cell-free DNA


title: sample 20 Control

description:
Library name: Control20
cell-free DNA


title: sample 16 Control

description:
Library name: Control16
cell-free DNA


title: sample 18 Control

description:
Library name: Control18
cell-free DNA


title: sample 19 Control

description:
Library name: Control19
cell-free DNA


title: sample 17 Control

description:
Library name: Control17
cell-free DNA


title: sample 14 Control

description:
Library name: Control14
cell-free DNA


title: sample 13 Control

description:
Library name: Control13
cell-free DNA


title: sample 12 Control

description:
Library name: Control12
cell-free DNA


title: sample 11 Control

description:
Library name: Control11
cell-free DNA


title: sample 9 Control

description:
Library name: Control9
cell-free DNA


title: sample 10 Control

description:
Library name: Control10
cell-free DNA


title: sample 8 Control

description:
Library name: Control8
cell-free DNA


title: sample 6 Control

description:
Library name: Control6
cell-free DNA


title: sample 7 Control

description:
Library name: Control7
cell-free DNA


title: sample 5 Control

description:
Library name: Control5
cell-free DNA


title: sample 30 Control

description:
Library name: Control30
cell-free DNA


title: sample 3 Control

description:
Library name: Control3
cell-free DNA


title: sample 25 Control

description:
Library name: Control25
cell-free DNA


title: sample 1 Control

description:
Library name: Control1
cell-free DNA


title: sample 23 Control

description:
Library name: Control23
cell-free DNA


title: sample 2 Control

description:
Library name: Control2
cell-free DNA


title: sample 15 Control

description:
Library name: Control15
cell-free DNA


title: Stroma 10 Hypoxia

city: Brussels

first: Eline

last: Menu

address: Bd de la Plaine 2

country: Belgium

institute: Vrije Universiteit Brussel

description: Library name: Sample 10

data_processing:
Reads were mapped to the human genome GRCh38 using the software STAR (version 2.7.11a)
Read counts were compiled using the function featureCounts within the Rsubread package (version 2.20.0)
Assembly: GRCh38
Supplementary files format and content: csv file of unnormalized counts for all samples

source_name: Bone Marrow

growth_protocol: RPMI-8226 cells were cultured in RPMI-1640 medium, and HS-5 cells were cultured in DMEM medium. Both media were supplemented with 10% FBS, 2 mM L-glutamine, and 100 Units/mL penicillin/streptomycin

extract_protocol:
Supernatant was concentrated using Millipore filters after which the Qiagen ExoRNeasy maxi kit was used to isolate RNA from sEVs.
Takara Bio's SMART-Seq® Stranded Kit was used to prepare libraries

treatment_protocol: Cells (RPMI-8226 or HS5) were cultured for 48 hours in either normoxia (21% oxygen) or hypoxia (1% oxygen). For hypoxic cultures, the Whitley H35 hypoxia workstation was used. Following settings were applied: 1% O2, 5% CO2, and 94% N2. Supernatant was used to collect EVs

value: Bone Marrow

value: fibroblast

value: wt

value: Hypoxia


title: Stroma 12 Hypoxia

description: Library name: Sample 12


title: MM 2 Hypoxia

description: Library name: Sample 2

value: plasma cell (malignant)


title: MM 6 Hypoxia

description: Library name: Sample 6


title: Stroma 8 Hypoxia

description: Library name: Sample 8


title: Stroma 9 Normoxia

description: Library name: Sample 9

value: Normoxia


title: MM 5 Normoxia

description: Library name: Sample 5


title: MM 1 Normoxia

description: Library name: Sample 1


title: MM 3 Normoxia

description: Library name: Sample 3


title: MM 4 Hypoxia

description: Library name: Sample 4


title: Stroma 7 Normoxia

description: Library name: Sample 7


title: sample 4 Control

description:
Library name: Control4
cell-free DNA


title: scPMT-6

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

description: Library name: Sample6

data_processing:
Sequenced reads were processed with Cellranger v8.0.1
Expression matrices were filtered to have at least 500 molecules per cell (100 in case of scPMT-8) and analyzed with Seurat v5.0.0.
Samples were combined and integrated by using Harmony v1.2.3.
Assembly: refdata-gex-GRCh38-2024-A provided by 10x Genomics
Supplementary files format and content: Filtered expression matrices from Cellranger output in h5 format and a Seurat object for integrated data.

source_name: Phosphaturic mesenchimal tumor

extract_protocol:
Approximately 100-200 mg of tissue samples were washed in HBSS (Gibco, Thermo Fisher Scientific, United States). Tissue samples were dissociated using 25 uL of enzyme D Multi Tissue Dissociation Kit (MTDK) (Miltenyi Biotec, Bergisch Gladbach, Germany) and enzyme A Neural Tissue Dissociation Kit P (NTDK) (Miltenyi Biotec, Bergisch Gladbach, Germany) in a solution of 870 mM HBSS (Capricorn scientific, Ebsdorfergrund, Germany), 10% FBS (Gibco, Thermo Fisher Scientific, Waltham, MA, USA), and 20 mM HEPES (Gibco, Thermo Fisher Scientific, Waltham, MA, USA) for 50-60 min. The resulting homogenate was filtered through a pre-wetted 70 μm cell culture filter (Miltenyi Biotec, Germany) into 3–5 mL of Wash Buffer (1xDPBS without Ca & Mg (Capricorn Scientific, Germany) containing 10% FBS (HyClone, Thermo Fisher Scientific, United States), 20 mM HEPES (Gibco, Thermo Fisher Scientific, United States), and 6 mM glucose (Gibco, Thermo Fisher Scientific, United States) and then centrifuged for 5 min at 300xg at 4°C. RNA extractions were performed using an AllPrep DNA/RNA Mini Kit (QIAGEN, United States) following the manufacturer’s protocol. For methanol fixation, 200 µL of enzyme-dissociated cells in Wash buffer (as described in the Methods section, Enzymatic dissociation) supplemented with 0.5 u/µL of the RNase Inhibitor RiboLock (Thermo Fisher Scientific, United States) were used. Ice-cold 100% methanol in a volume of 800 µL (Sigma-Aldrich, United States) was added dropwise to the cells while gently vortexing to prevent cell clumping. The fixed cells were then stored at -80°C. Methanol-fixed cells were thawed and centrifuged at 2000×g for 5 min at 4°C to remove the 3xSSC*/DMSO and methanol. 3xSSC* buffer  is composed of 3xSSC (Invitrogen, Thermo Fisher Scientific, United States), 40 mM DTT (Wuhan Servicebio Technology, China), 1% BSA (Thermo Fisher Scientific, United States), and RNase-free water[15]. The resulting pellet was then resuspended in cold 3xSSC* buffer to a concentration of approximately 2000 cells/µL.
Single cells were captured and barcoded, and cDNA libraries were generated using the Chromium Next GEM Single Cell 3ʹGEM, Library & Gel Bead Kit v3.1 (10X Genomics, United States). For each sample, approximately 10,000 cells (∼2000 cells per 1µL, as calculated using the cell suspension volume calculator from 10X Genomics) in cold 3xSSC* buffer were mixed with RT-PCR master mix and immediately loaded, along with Single-Cell 3′Gel Beads and Partitioning Oil, into a Chromium Chip G. cDNA and gene expression libraries were then generated following the manufacturer’s instructions (10x Genomics, United States). cDNA and gene expression libraries were quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, United States), and fragment sizes were assessed with the Agilent 5,200 Fragment Analyzer (Agilent Technologies, United States) using the DNA HS (1–6,000 bp) Kit (Agilent Technologies, United States).

value: Phosphaturic mesenchimal tumor

value: Hard palate

tag: Sex

value: Female


title: SM-102_UNR_24H_Rep6

city: Waltham

first: Sudha

last: Chivukula

state: MA

address: 200 West

department: mRNA Center of Excellence

institute: Sanofi

description:
Library name: HSK_s162_S162_001
Column name in count_nhp.txt: HSK_s162_S162_001

data_processing:
The bcl files were demultiplexed using Illumina’s bcl2fastq software.
The fastq files were processed using Array Studio software (Qiagen) and aligned to the cynomolgus Macaque CynoWashU2013 reference genome with the WashUGene2017512 gene model.
Differential gene expression analysis was performed using the Limma-Voom method, which transforms the raw read counts into log-counts per million (log-CPM) and models the mean-variance relationship of the data.
Assembly: cynomolgus Macaque CynoWashU2013 reference genome with the WashUGene2017512 gene model.
Supplementary files format and content: Tab-delimited text file including raw counts for each sample.
Supplementary files format and content: Tab-delimited text file including log-CPM for each sample.

source_name: HSMM

growth_protocol: Primary human skeletal muscle myoblasts were obtained from Lonza (Cat. No. CC-2580) and thawed and expanded following vendor recommendations. Briefly, cryopreserved cell stocks were thawed into SkGM-2 complete media (Lonza, Cat. No. CC-3245). Media was replaced 24 h after thawing and every 48 h thereafter. Cells were expanded/passaged to P6, at which point they were seeded on 24-well culture plates pre-coated with Collagen 1 at a density of 24,000 cells/cm2 in 1 mL of culture media. The next day, media in each well was replaced with 0.5 mL of fresh media before transfection mixes were prepared. Naive male and female Mauritius origin cynomolgus macaques (Macaca fascicularis) were selected from the Sanofi NHP colony at the NIRC. Animals weighed > 2 kg and were > 2 years of age at the start of the studies. Per NIRC SOPs, all animals underwent a pre-study health assessment performed by a licensed veterinarian, which included a complete blood count and clinical chemistry analysis before being cleared for entry into the study.

extract_protocol:
Muscle cells at each collection time-point, media was aspirated, and cultures were lysed on-plate using 350 µL of RLT buffer (Qiagen Cat. No. 79216) and immediately transferred to 1.5 mL tubes and stored at -80 °C. Total RNA was extracted from whole blood NHP samples collected in PAXgene Blood RNA Tubes (Qiagen, BD Diagnostics) pre- and 2 days post-immunization using the MagMAX™ for Stabilized Blood Tubes RNA Isolation Kit (Invitrogen) on an automated KingFisher Flex System (Thermo Scientific). The quality and yield of RNA were assessed on the 4200 TapeStation System (Agilent) and NanoDrop™ Eight Spectrophotometer (Thermo Scientific). Sequencing libraries were then prepared using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit and sequenced on the NovaSeq 6000 Sequencing System (Illumina) using the S4 Reagent Kit v1.5 (200 cycles).
Sequencing libraries were then prepared using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit and sequenced on the NovaSeq 6000 Sequencing System (Illumina) using the S4 Reagent Kit v1.5 (200 cycles).

treatment_protocol: Muscle cells were transfected at 2 µg of formulated RNA/million cells. For each treatment, 50 µL of transfection mix was added to the culture before an additional 0.5mL of media was added to thoroughly distribute the transfection mixture before plates were returned to the incubator for 1, 4, or 24 h. NHPs were randomized, (stratified randomization approach based on age, body weight, and sex by biostatistician) into groups of 4-6 per treatment group, were generally housed in pairs whenever possible and acclimated for at least 6 days prior to the start of the study. All NHPs were immunized with a dose of 0.5 mL of vaccine via the intramuscular (IM) route in the right forelimb on Day 0 and the left forelimb on D28 while under 10 mg/kg ketamine HCl /1 mg/kg acepromazine sedation.

value: HSMM

value: Human skeletal muscle myoblasts

value: WT

tag: timepoint

tag: dose

value: 2ug per 1 million cells

tag: biological replicate


title: scPMT-7

description: Library name: Sample7

tag: tissue

value: Subcutaneous adipose tissue of the left gluteal region


title: scPMT-8

description: Library name: Sample8

value: Subcutaneous adipose tissue of the inguinal region

value: Male


title: SM-102_UNR_24H_Rep3

description:
Library name: HSK_s159_S159_001
Column name in count_nhp.txt: HSK_s159_S159_001

tag: cell type

tag: genotype

tag: treatment


title: SM-102_UNR_24H_Rep5

description:
Library name: HSK_s161_S161_001
Column name in count_nhp.txt: HSK_s161_S161_001


title: SM-102_UNR_4H_Rep6

description:
Library name: HSK_s102_S102_001
Column name in count_hsk.txt: HSK_s102_S102_001


title: SM-102_UNR_24H_Rep1

description:
Library name: HSK_s157_S157_001
Column name in count_hsk.txt: HSK_s157_S157_001


title: SM-102_UNR_24H_Rep2

description:
Library name: HSK_s158_S158_001
Column name in count_hsk.txt: HSK_s158_S158_001


title: SM-102_UNR_4H_Rep5

description:
Library name: HSK_s101_S101_001
Column name in count_hsk.txt: HSK_s101_S101_001


title: SM-102_UNR_4H_Rep3

description:
Library name: HSK_s099_S99_001
Column name in count_hsk.txt: HSK_s099_S99_001


title: SM-102_UNR_4H_Rep2

description:
Library name: HSK_s098_S98_001
Column name in count_hsk.txt: HSK_s098_S98_001


title: Stroma 11 Normoxia

description: Library name: Sample 11


title: SM-102_UNR_4H_Rep1

description:
Library name: HSK_s097_S97_001
Column name in count_hsk.txt: HSK_s097_S97_001


title: SM-102_UNR_1H_Rep6

description:
Library name: HSK_s042_S18_001
Column name in count_hsk.txt: HSK_s042_S18_001


title: SM-102_UNR_1H_Rep5

description:
Library name: HSK_s041_S6_001
Column name in count_hsk.txt: HSK_s041_S6_001


title: SM-102_UNR_1H_Rep4

description:
Library name: HSK_s040_S89_001
Column name in count_hsk.txt: HSK_s040_S89_001


title: SM-102_UNR_1H_Rep2

description:
Library name: HSK_s038_S65_001
Column name in count_hsk.txt: HSK_s038_S65_001


title: SM-102_MNR_24H_Rep5

description:
Library name: HSK_s167_S167_001
Column name in count_hsk.txt: HSK_s167_S167_001


title: SM-102_MNR_24H_Rep4

description:
Library name: HSK_s166_S166_001
Column name in count_hsk.txt: HSK_s166_S166_001


title: SM-102_MNR_24H_Rep3

description:
Library name: HSK_s165_S165_001
Column name in count_hsk.txt: HSK_s165_S165_001


title: SM-102_MNR_24H_Rep2

description:
Library name: HSK_s164_S164_001
Column name in count_hsk.txt: HSK_s164_S164_001


title: SM-102_MNR_24H_Rep6

description:
Library name: HSK_s168_S168_001
Column name in count_hsk.txt: HSK_s168_S168_001


title: SM-102_MNR_24H_Rep1

description:
Library name: HSK_s163_S163_001
Column name in count_hsk.txt: HSK_s163_S163_001


title: SM-102_UNR_1H_Rep3

description:
Library name: HSK_s039_S77_001
Column name in count_hsk.txt: HSK_s039_S77_001


title: SM-102_MNR_4H_Rep6

description:
Library name: HSK_s108_S108_001
Column name in count_hsk.txt: HSK_s108_S108_001


title: SM-102_UNR_24H_Rep4

description:
Library name: HSK_s160_S160_001
Column name in count_nhp.txt: HSK_s160_S160_001


title: SM-102_UNR_4H_Rep4

description:
Library name: HSK_s100_S100_001
Column name in count_hsk.txt: HSK_s100_S100_001


title: SM-102_MNR_1H_Rep5

description:
Library name: HSK_s047_S78_001
Column name in count_hsk.txt: HSK_s047_S78_001


title: SM-102_MNR_4H_Rep4

description:
Library name: HSK_s106_S106_001
Column name in count_hsk.txt: HSK_s106_S106_001


title: SM-102_MNR_4H_Rep3

description:
Library name: HSK_s105_S105_001
Column name in count_hsk.txt: HSK_s105_S105_001


title: SM-102_MNR_1H_Rep6

description:
Library name: HSK_s048_S90_001
Column name in count_hsk.txt: HSK_s048_S90_001


title: SM-102_MNR_4H_Rep1

description:
Library name: HSK_s103_S103_001
Column name in count_hsk.txt: HSK_s103_S103_001


title: SM-102_MNR_1H_Rep4

description:
Library name: HSK_s046_S66_001
Column name in count_hsk.txt: HSK_s046_S66_001


title: SM-102_MNR_4H_Rep5

description:
Library name: HSK_s107_S107_001
Column name in count_hsk.txt: HSK_s107_S107_001


title: SM-102_MNR_1H_Rep2

description:
Library name: HSK_s044_S42_001
Column name in count_hsk.txt: HSK_s044_S42_001


title: SM-102_MNR_1H_Rep1

description:
Library name: HSK_s043_S30_001
Column name in count_hsk.txt: HSK_s043_S30_001


title: cKK-E10_UNR_24H_Rep6

description:
Library name: HSK_s138_S138_001
Column name in count_hsk.txt: HSK_s138_S138_001


title: cKK-E10_UNR_24H_Rep5

description:
Library name: HSK_s137_S137_001
Column name in count_hsk.txt: HSK_s137_S137_001


title: SM-102_MNR_1H_Rep3

description:
Library name: HSK_s045_S54_001
Column name in count_hsk.txt: HSK_s045_S54_001


title: cKK-E10_UNR_24H_Rep4

description:
Library name: HSK_s136_S136_001
Column name in count_hsk.txt: HSK_s136_S136_001


title: cKK-E10_UNR_24H_Rep3

description:
Library name: HSK_s135_S135_001
Column name in count_hsk.txt: HSK_s135_S135_001


title: cKK-E10_UNR_24H_Rep2

description:
Library name: HSK_s134_S134_001
Column name in count_hsk.txt: HSK_s134_S134_001


title: SM-102_UNR_1H_Rep1

description:
Library name: HSK_s037_S53_001
Column name in count_hsk.txt: HSK_s037_S53_001


title: cKK-E10_UNR_24H_Rep1

description:
Library name: HSK_s133_S133_001
Column name in count_hsk.txt: HSK_s133_S133_001


title: cKK-E10_UNR_4H_Rep4

description:
Library name: HSK_s076_S46_001
Column name in count_hsk.txt: HSK_s076_S46_001


title: cKK-E10_UNR_4H_Rep5

description:
Library name: HSK_s077_S58_001
Column name in count_hsk.txt: HSK_s077_S58_001


title: cKK-E10_UNR_4H_Rep2

description:
Library name: HSK_s074_S22_001
Column name in count_hsk.txt: HSK_s074_S22_001


title: cKK-E10_UNR_4H_Rep1

description:
Library name: HSK_s073_S10_001
Column name in count_hsk.txt: HSK_s073_S10_001


title: cKK-E10_UNR_1H_Rep6

description:
Library name: HSK_s018_S15_001
Column name in count_hsk.txt: HSK_s018_S15_001


title: cKK-E10_UNR_1H_Rep4

description:
Library name: HSK_s016_S86_001
Column name in count_hsk.txt: HSK_s016_S86_001


title: SM-102_MNR_4H_Rep2

description:
Library name: HSK_s104_S104_001
Column name in count_hsk.txt: HSK_s104_S104_001


title: cKK-E10_UNR_1H_Rep3

description:
Library name: HSK_s015_S74_001
Column name in count_hsk.txt: HSK_s015_S74_001


title: cKK-E10_UNR_1H_Rep2

description:
Library name: HSK_s014_S62_001
Column name in count_hsk.txt: HSK_s014_S62_001


title: BD10_2_32_1

city: Stanford

first: Robert

middle: Raymond

last: Butler

address: 3172 Porter Dr., MC 5475

department: Neurology & Neurological Sciences

institute: Stanford University School of Medicine

data_processing:
FASTQ files were trimmed for adapter sequences and low quality base calls with Cutadapt v1.8.1
Trimmed reads were then aligned to the GRCm38.p6 (mm10) reference genome with STAR 2.7.6a [37] using gene annotations from GENCODE release vM23
Gene counts were calculated using RSEM v1.3.1
Quality control metrics were calculated using featureCounts v1.6, PicardTools v2.23.4, and Samtools v1.11
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: hippocampus

growth_protocol: amyloid model (Thy1-hAPPLond/Swe [Line 41] mice) and C57BL/6 mice were grown to 16 months of age

extract_protocol:
Qiazol for lysis, and total RNA was extracted using miRNeasy kit (cat # 217084) following standardprotocolwith on column DNase digestion (Qiagen)
RNA sequencing libraries were prepared with 200 ng of total RNA using KAPA RiboErase Stranded RNA-Seq kit (cat # KK8483)following standardprotocol (Roche)

treatment_protocol: dosed via oral gavage with BD10-2 or vehicle for 3 months from 13-16 months of age. Afterwards, right hippocampal slices were rapidly dissected for ephysiology (stimulated or unstimulated control), subjected to 3 times theta burst stimulation consisting of 10 bursts of 4 stimuli at 100 Hz separated by 200 ms each. Unstimulated slices experienced sham procedure of the same duration without TBS. Immediately after slices were flash frozen for RNAseq processing.

value: hippocampus

tag: stimulation

value: STIM

tag: mouseid

tag: batch id

value: I


title: BD10_2_32

value: D


title: cKK-E10_MNR_24H_Rep6

description:
Library name: HSK_s144_S144_001
Column name in count_hsk.txt: HSK_s144_S144_001


title: BD10_2_30


title: cKK-E10_UNR_1H_Rep1

description:
Library name: HSK_s013_S50_001
Column name in count_hsk.txt: HSK_s013_S50_001


title: cKK-E10_MNR_24H_Rep4

description:
Library name: HSK_s142_S142_001
Column name in count_hsk.txt: HSK_s142_S142_001


title: BD10_2_31

value: noSTIM


title: BD10_2_29


title: lqt_wt

city: hangzhou

first: jiuxiao

last: zhao

state: zhejiang

address: Yuhangtang Road, Hangzhou 310058

country: China

institute: zhejiang university

description: Library name: sample1

data_processing:
To investigate the underlying mechanisms, single-nuclei transcriptomic analysis was performed with myocardium of WT and L5 pigs. After quality control, the 22,342 genes from 8,103 cells in WT and 9,691 cells in L5 were analyzed
Assembly: Sscrofa11.1
Supplementary files format and content: 10 X files

source_name: heart

extract_protocol:
The ventricular myocardium of pigs from WT and LQT lines was dissected into the following layers: left ventricular endocardium, myocardium, epicardium; right ventricular endocardium, myocardium, epicardium; and interventricular septum. Samples were then collected from each layer and pooled.
The sequencing part was completed by Gideon Company

value: heart


title: cKK-E10_MNR_24H_Rep3

description:
Library name: HSK_s141_S141_001
Column name in count_hsk.txt: HSK_s141_S141_001


title: cKK-E10_MNR_24H_Rep2

description:
Library name: HSK_s140_S140_001
Column name in count_hsk.txt: HSK_s140_S140_001


title: cKK-E10_MNR_24H_Rep5

description:
Library name: HSK_s143_S143_001
Column name in count_hsk.txt: HSK_s143_S143_001


title: cKK-E10_MNR_24H_Rep1

description:
Library name: HSK_s139_S139_001
Column name in count_hsk.txt: HSK_s139_S139_001


title: BD10_2_28

value: VEH

value: C


title: BD10_2_26


title: BD10_2_27


title: cKK-E10_MNR_4H_Rep6

description:
Library name: HSK_s084_S47_001
Column name in count_hsk.txt: HSK_s084_S47_001


title: cKK-E10_UNR_4H_Rep6

description:
Library name: HSK_s078_S70_001
Column name in count_hsk.txt: HSK_s078_S70_001


title: cKK-E10_UNR_4H_Rep3

description:
Library name: HSK_s075_S34_001
Column name in count_hsk.txt: HSK_s075_S34_001


title: BD10_2_24_1


title: BD10_2_25


title: cKK-E10_UNR_1H_Rep5

description:
Library name: HSK_s017_S3_001
Column name in count_hsk.txt: HSK_s017_S3_001


title: cKK-E10_MNR_4H_Rep5

description:
Library name: HSK_s083_S35_001
Column name in count_hsk.txt: HSK_s083_S35_001


title: cKK-E10_MNR_4H_Rep4

description:
Library name: HSK_s082_S23_001
Column name in count_hsk.txt: HSK_s082_S23_001


title: BD10_2_23

value: H


title: cKK-E10_MNR_4H_Rep3

description:
Library name: HSK_s081_S11_001
Column name in count_hsk.txt: HSK_s081_S11_001


title: BD10_2_24


title: cKK-E10_MNR_4H_Rep2

description:
Library name: HSK_s080_S94_001
Column name in count_hsk.txt: HSK_s080_S94_001


title: BD10_2_22

value: B


title: cKK-E10_MNR_4H_Rep1

description:
Library name: HSK_s079_S82_001
Column name in count_hsk.txt: HSK_s079_S82_001

value: HSMM


title: BD10_2_21


title: BD10_2_20

value: G


title: cKK-E10_MNR_1H_Rep5

description:
Library name: HSK_s023_S75_001
Column name in count_hsk.txt: HSK_s023_S75_001

value: Human skeletal muscle myoblasts

value: WT


title: BD10_2_17

value: A


title: cKK-E10_MNR_1H_Rep3

description:
Library name: HSK_s021_S51_001
Column name in count_hsk.txt: HSK_s021_S51_001

value: 2ug per 1 million cells


title: cKK-E10_MNR_1H_Rep6

description:
Library name: HSK_s024_S87_001
Column name in count_hsk.txt: HSK_s024_S87_001


title: cKK-E10_MNR_1H_Rep4

description:
Library name: HSK_s022_S63_001
Column name in count_hsk.txt: HSK_s022_S63_001


title: cKK-E10_MNR_1H_Rep1

description:
Library name: HSK_s019_S27_001
Column name in count_hsk.txt: HSK_s019_S27_001


title: BD10_2_19


title: BD10_2_16_1


title: BD10_2_18


title: cKK-E10_MNR_1H_Rep2

description:
Library name: HSK_s020_S39_001
Column name in count_hsk.txt: HSK_s020_S39_001


title: BD10_2_15


title: OF-02_UNR_24H_Rep5

description:
Library name: HSK_s125_S125_001
Column name in count_hsk.txt: HSK_s125_S125_001


title: BD10_2_14


title: BD10_2_16


title: OF-02_UNR_24H_Rep4

description:
Library name: HSK_s124_S124_001
Column name in count_hsk.txt: HSK_s124_S124_001


title: BD10_2_13


title: OF-02_UNR_24H_Rep2

description:
Library name: HSK_s122_S122_001
Column name in count_hsk.txt: HSK_s122_S122_001


title: OF-02_UNR_24H_Rep3

description:
Library name: HSK_s123_S123_001
Column name in count_hsk.txt: HSK_s123_S123_001


title: BD10_2_11


title: BD10_2_12


title: OF-02_UNR_24H_Rep1

description:
Library name: HSK_s121_S121_001
Column name in count_hsk.txt: HSK_s121_S121_001


title: BD10_2_10

value: E


title: OF-02_UNR_4H_Rep6

description:
Library name: HSK_s066_S21_001
Column name in count_hsk.txt: HSK_s066_S21_001


title: BD10_2_9

value: hippocampus


title: OF-02_UNR_4H_Rep5

description:
Library name: HSK_s065_S9_001
Column name in count_hsk.txt: HSK_s065_S9_001


title: BD10_2_8_1


title: BD10_2_8

value: STIM


title: OF-02_UNR_4H_Rep3

description:
Library name: HSK_s063_S80_001
Column name in count_hsk.txt: HSK_s063_S80_001


title: OF-02_UNR_4H_Rep4

description:
Library name: HSK_s064_S92_001
Column name in count_hsk.txt: HSK_s064_S92_001


title: OF-02_UNR_4H_Rep1

description:
Library name: HSK_s061_S56_001
Column name in count_hsk.txt: HSK_s061_S56_001


title: BD10_2_7


title: BD10_2_5

value: I


title: OF-02_UNR_1H_Rep5

description:
Library name: HSK_s005_S49_001
Column name in count_hsk.txt: HSK_s005_S49_001


title: BD10_2_2


title: BD10_2_3


title: OF-02_UNR_1H_Rep3

description:
Library name: HSK_s003_S25_001
Column name in count_hsk.txt: HSK_s003_S25_001


title: OF-02_UNR_4H_Rep2

description:
Library name: HSK_s062_S68_001
Column name in count_hsk.txt: HSK_s062_S68_001


title: BD10_2_6


title: BD10_2_1


title: OF-02_UNR_1H_Rep1

description:
Library name: HSK_s001_S1_001
Column name in count_hsk.txt: HSK_s001_S1_001


title: OF-02_UNR_1H_Rep4

description:
Library name: HSK_s004_S37_001
Column name in count_hsk.txt: HSK_s004_S37_001


title: iPSC, Control, ChIP Input

city: Manchester

first: Siddharth

last: Banka

address: Oxford Road

institute: University of Manchester

description: Library name: hIPSC CTRL DS1 Input

data_processing:
Reads were trimmed to remove any adapter or poor-quality sequence using Trimmomatic v0.36, and truncated at a sliding 4bp window, starting 5’, with a mean quality <Q20, then removed if the final length was less than 35bp.
The filtered paired-reads were mapped to the human reference sequence analysis set (hg19/GRCh37) from the UCSC browser, using Bowtie2 v2.3.0.
Mapped reads were filtered using Samtools v0.1.19 to retain only high-confidence concordant pairs (-f 2 -q30), followed by the removal of reads mapping to the mitochondrial genome and to unassembled parts of the reference genome. Peak calling was performed using MACS2 v2.1.2 using the parameters ' --format BAMPE --gsize hs --keep-dup 1 --bdg --SPMR --qvalue 0.05'. Candidate regions were further filtered by fold enrichment score.
BamCompare from Deeptools v3.4.3 was used to generate BigWig files where peaks were corrected using ChIP input reads and normalised using bins per million with bin size of 20.
Assembly: hg19/GRCh37
Supplementary files format and content: BigWig files for visualisation of peaks.

extract_protocol:
ChIPseq has been performed using the True MicroChIP kit from Diagenode following the manufacturer’s protocol. Briefly, cells were collected and DNA-protein was cross-linked using 36.5% formaldehyde. Then cells were lysed and chromatin was sheared by sonication (Bioruptor NextGen). Sheared chromatin was incubated with H3K4me1 Antibody (5326, Cell signalling) overnight at 4°C.
Library preparation was performed by the Genomic Technologies Core facility at the University of Manchester.

value: iPSC

tag: time point

value: Day 0

value: Male


title: iPSC, Kabuki Syndrome 1, ChIP Input

description: Library name: hIPS KS1 DS1 Input

value: Female


title: OF-02_MNR_24H_Rep5

description:
Library name: HSK_s131_S131_001
Column name in count_hsk.txt: HSK_s131_S131_001


title: OF-02_UNR_1H_Rep2

description:
Library name: HSK_s002_S13_001
Column name in count_hsk.txt: HSK_s002_S13_001


title: Cortical neuron, Kabuki Syndrome 1, rep3

description: Library name: Neur KS1 rep3 DS1 ChIP

value: Cortical Neuron

value: Day 18


title: Cortical neuron, Kabuki Syndrome 1, rep2

description: Library name: Neur KS1 rep2 DS1 ChIP


title: OF-02_MNR_24H_Rep3

description:
Library name: HSK_s129_S129_001
Column name in count_hsk.txt: HSK_s129_S129_001


title: OF-02_MNR_24H_Rep4

description:
Library name: HSK_s130_S130_001
Column name in count_hsk.txt: HSK_s130_S130_001


title: Cortical neuron, Control, rep3

description: Library name: Neur CTRL3 DS1 ChIP


title: Cortical neuron, Kabuki Syndrome 1, rep1

description: Library name: Neur KS1 rep1 DS1 ChIP


title: OF-02_MNR_24H_Rep2

description:
Library name: HSK_s128_S128_001
Column name in count_hsk.txt: HSK_s128_S128_001


title: OF-02_MNR_24H_Rep1

description:
Library name: HSK_s127_S127_001
Column name in count_hsk.txt: HSK_s127_S127_001


title: OF-02_UNR_1H_Rep6

description:
Library name: HSK_s006_S61_001
Column name in count_hsk.txt: HSK_s006_S61_001


title: OF-02_MNR_4H_Rep6

description:
Library name: HSK_s072_S93_001
Column name in count_hsk.txt: HSK_s072_S93_001


title: Cortical neuron, Control, rep1

description: Library name: Neur CTRL1 DS1 ChIP

value: Day 17


title: Neuronal progenitor, Kabuki Syndrome 1, rep3

description: Library name: Prog KS1 rep3 DS1 ChIP

value: Neuronal Progenitor


title: OF-02_UNR_24H_Rep6

description:
Library name: HSK_s126_S126_001
Column name in count_hsk.txt: HSK_s126_S126_001

value: HSMM


title: Neuronal progenitor, Kabuki Syndrome 1, rep2

description: Library name: Prog KS1 rep2 DS1 ChIP


title: Neuronal progenitor, Kabuki Syndrome 1, rep1

description: Library name: Prog KS1 rep1 DS1 ChIP


title: OF-02_MNR_4H_Rep3

description:
Library name: HSK_s069_S57_001
Column name in count_hsk.txt: HSK_s069_S57_001

value: Human skeletal muscle myoblasts


title: Cortical neuron, Control, rep2

description: Library name: Neur CTRL2 DS1 ChIP


title: OF-02_MNR_4H_Rep2

description:
Library name: HSK_s068_S45_001
Column name in count_hsk.txt: HSK_s068_S45_001

value: WT


title: Neuronal progenitor, Control, rep3

description: Library name: Prog CTRL3 DS1 ChIP


title: BD10_2_4

value: VEH

value: A


title: Neuronal progenitor, Control, rep2

description: Library name: Prog CTRL2 DS1 ChIP


title: OF-02_MNR_4H_Rep1

description:
Library name: HSK_s067_S33_001
Column name in count_hsk.txt: HSK_s067_S33_001

value: 2ug per 1 million cells


title: OF-02_MNR_1H_Rep6

description:
Library name: HSK_s012_S38_001
Column name in count_hsk.txt: HSK_s012_S38_001


title: OF-02_MNR_24H_Rep6

description:
Library name: HSK_s132_S132_001
Column name in count_hsk.txt: HSK_s132_S132_001


title: Neuronal progenitor, Control, rep1

description: Library name: Prog CTRL1 DS1 ChIP


title: OF-02_MNR_1H_Rep5

description:
Library name: HSK_s011_S26_001
Column name in count_hsk.txt: HSK_s011_S26_001


title: OF-02_MNR_1H_Rep4

description:
Library name: HSK_s010_S14_001
Column name in count_hsk.txt: HSK_s010_S14_001


title: iPSC, Kabuki Syndrome 1, rep1

description: Library name: hiPSC KS1 rep1 DS1 ChIP


title: iPSC, Kabuki Syndrome 1, rep3

description: Library name: hiPSC KS1 rep3 DS1 ChIP


title: OF-02_MNR_1H_Rep2

description:
Library name: HSK_s008_S85_001
Column name in count_hsk.txt: HSK_s008_S85_001


title: OF-02_MNR_1H_Rep3

description:
Library name: HSK_s009_S2_001
Column name in count_hsk.txt: HSK_s009_S2_001


title: iPSC, Control, rep2

description: Library name: hiPSC CTRL2 DS1 ChIP


title: iPSC, Control, rep1

description: Library name: hiPSC CTRL1 DS1 ChIP


title: HCC, miR372_3p_3

city: Pathumwan

first: Archittapon

last: Nokkeaw

state: Bangkok

address: Padtayapatana Building, 1873, Henri Dunant Road

department: Biochemistry

country: Thailand

institute: Chulalongkorn university, faculty of medicine

description: Library name: Sample 6

data_processing:
The acquisition of clean data was achieved by filtering and removing raw data that had adapters, low-quality data, and readings with a Q-score below 30. Subsequently, the transcriptome was assembled using StringTie (V2.2.1), and the clean reads were mapped to the human-specific genome GRCH38 using HISAT2 software (V2.0.4). The DESeq2 R software (V1.38.3) was utilized to conduct differential expression analysis between two groups. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were utilized to identify gene biological function and investigate signaling networks.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM values for each Sample

growth_protocol: The JHH-4 cell line was obtained from the Japanese Collection of Research Bioresources (JCRB) Cell Bank and grown in Eagle's Minimum Essential Medium (EMEM) (Gibco™, Thermo Fisher Scientific, Massachusetts, USA), supplemented with 10% FBS, 1% L-glutamine, and 1% antibiotic-antimycotic.

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen). 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepare using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

value: Epithelial-like

value: hsa-miR-372-3p overexpress


title: HCC, miR372_3p_2

description: Library name: Sample 5


title: PIG28-ALAC-Hypo

city: Davis, CA

first: Carolyn

middle: M.

last: Slupsky

address: One Shields Ave

department: Department of Nutrition, Department of food science and technology

institute: University of California, Davis

data_processing:
Removal of low-quality reads/nucleotides and adapter sequences were performed via BBDuk from the BBTools suite (v38.72) using the recommended parameters for QuantSeq experiment (parameters: k=13, ktrim=r, useshortkmers=t, mink=5, qtrim=t, trimq=10, minlength=20, ftl=13). The trimmed-high-quality sequencing reads were then mapped to the latest reference genome for domestic pig (Sscrofa11.1) using STAR aligner (v2.7.10a) with the recommended modified-Encode settings. Quantification of per-gene counts was obtained using HT-Seq count (v2.0.2).
Assembly: Sscrofa11.1
Supplementary files format and content: Tab-delimited text file in which the first column contains the Ensembl gene ID for each reference gene, and the second column provides the corresponding gene count

source_name: Hypothalamus

extract_protocol:
Tissues were collected immediately after euthanasia, follow by snap-freezing in liquid nitrogen, and stored at -80°C until further analysis. Tissues were manually ground in liquid nitrogen using a mortar and pestle. 25-30 mg of cryoground tissue was extracted using a modified Folch extraction, and RNA was extracted from the resulting cell layer (All Prep DNA/RNA/Protein Kit, Qiagen, Germantown, MD). RNA samples were quantified using the Qubit RNA HS Assay Kit and Quibit 3.0 Fluorometer (Thermo Fisher Scientific, Waltham, MA), and sample quality was assessed using a Lab Chip GX Touch HT (Perken Elmer, Waltham, MA).
Isolated RNA was submitted to the UC Davis DNA Technologies and Expression Analysis Core to generate 3’ Tag-Seq libraries with unique molecular indices (UMIs). To generate Illumina-compatible multiplexed sequencing libraries, barcoded 3'Tag-Seq libraries were prepared using the QuantSeq FWD kit (Lexogen, Vienna, Austria) according to the manufacturer’s recommendations.  The fragment size distribution of the libraries was verified via micro-capillary gel electrophoresis via Bioanalyzer 2100 (Agilent, Santa Clara, CA).  The libraries were quantified fluorometrically on a Qubit instrument (LifeTechnologies, Carlsbad, CA), and pooled in equimolar ratios. 232 libraries were sequenced on 2.5 lanes of NextSeq500 sequencer.

tag: crossbreed

value: Hampshire x Yorkshire x Landrace cross

value: Hypothalamus

tag: age

value: Postnatal day 16

value: F

tag: diet

value: Piglet formula enriched in α-lactalbumin


title: OF-02_MNR_4H_Rep4

description:
Library name: HSK_s070_S69_001
Column name in count_hsk.txt: HSK_s070_S69_001

tag: cell line


title: OF-02_MNR_4H_Rep5

description:
Library name: HSK_s071_S81_001
Column name in count_hsk.txt: HSK_s071_S81_001


title: PIG12-ALAC-Hypo

value: M


title: HCC, miR372_3p_1

description: Library name: Sample 4


title: HCC, Control_2

description: Library name: Sample 2


title: PIG31-ALAC-Hypo


title: PIG13-WPI-Hypo

value: Piglet formula cotaining α-lactalbumin reduced, whey protein isolate


title: HCC, Control_1

description: Library name: Sample 1


title: Au_NRs_CPG-4

city: kunming

first: Shiwen

last: Zhang

address: kunming

institute: Yunnan Cancer Hospital (The Third Affiliated Hospital of Kunming Medical University, Peking University Cancer Hospital Yunnan)

description: Library name: SAMPLES12

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: GRCh38.p13
Supplementary files format and content: FASTQ Sequence Trace

source_name: Peripheral blood mononuclear cells

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using VAHTS Universal V5 RNA-seq Library Prep  Kit following manufacturer's protocols.

value: Peripheral blood mononuclear cells


title: iPSC, Control, rep3

description: Library name: hiPSC CTRL3 DS1 ChIP

value: iPSC

value: Day 0

value: Male


title: HCC, Control_3

description: Library name: Sample 3

value: WT


title: Au_NRs_CPG-3

description: Library name: SAMPLES11


title: PIG21-ALAC-Hypo


title: PIG22-SF-Hypo

value: Sow-fed


title: Au_NRs_CPG-2

description: Library name: SAMPLES10


title: PIG15-WPI-Hypo


title: Au_NRs-4

description: Library name: SAMPLES8


title: PIG25-ALAC-Hypo


title: PIG7-SF-Hypo


title: OF-02_MNR_1H_Rep1

description:
Library name: HSK_s007_S73_001
Column name in count_hsk.txt: HSK_s007_S73_001

value: HSMM

value: Human skeletal muscle myoblasts


title: PIG11-ALAC-Hypo


title: Au_NRs-3

description: Library name: SAMPLES7


title: con-4

description: Library name: SAMPLES4


title: PIG27-WPI-Hypo


title: PIG19-ALAC-Hypo


title: con-3

description: Library name: SAMPLES3


title: Au_NRs-1

description: Library name: SAMPLES5


title: PIG3-WPI-Hypo


title: PIG20-WPI-Hypo


title: con-1

description: Library name: SAMPLES1


title: PIG5-SF-Hypo


title: HC033_VDJ

city: St. Louis

first: Aaron

last: Ver Heul

state: MO

address: 660 S Euclid Ave.

department: Medicine

institute: Washington University School of Medicine

description: Full-length VDJ segments enriched from amplified cDNA

data_processing:
RTA v3.4.4 was used for base calls and quality scores
cellranger mkfastq (version 2.0.1) was used to generate FASTQ files
FASTQ files were processed using cellranger-6.0.1 to combine GEX and VDJ data.
Genome_build: GRCh38-2020-A and vdj-GRCh38-alts-ensembl-5.0.0
Supplementary_files_format_and_content: Unfiltered matrix files of raw gene counts for each sample in HDF5 format
Supplementary_files_format_and_content: List of identified TCR clonotypes by cellular barcode for each sample in csv format

growth_protocol: Fresh blood donated from patients was immediately processed

extract_protocol:
PBMC samples were isolated into into single cells and loaded into GEMs using the 10X Genomics Chromium instrument
cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps.  Purified cDNA was amplified for 10-14 cycles before being cleaned up using SPRIselect beads.  Samples were then run on a Bioanalyzer to determine the cDNA concentration.  TCR target enrichments were done on the full-length cDNA.  GEX and Enriched TCR libraries were prepared as recommended by the 10x Genomics Chromium Single Cell V(D)J Reagent Kits (v1 Chemistry) user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.  Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 151x8x151 sequencing recipe according to manufacturer protocol.  A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression Library and 5000 reads/cell for each V(D)J (Tcell) library.

treatment_protocol: PBMCs were isolated by density gradient centrifugation using a standard Ficoll protocol. PBMCs were washed three times in RPMI followed by final resuspension in PBS with 0.04% BSA

value: peripheral blood mononuclear cells

tag: disease

value: healthy control


title: PIG29-ALAC-Hypo

value: Hampshire x Yorkshire x Landrace cross

tag: Sex


title: HC032_VDJ


title: PIG16-ALAC-Hypo

value: Hypothalamus


title: HC030_VDJ


title: iPSC, Kabuki Syndrome 1, rep2

description: Library name: hiPSC KS1 rep2 DS1 ChIP

value: Female


title: HC029_VDJ


title: PIG6-ALAC-Hypo

value: Postnatal day 16


title: PIG1-ALAC-Hypo

value: F

value: Piglet formula enriched in α-lactalbumin


title: PIG14-WPI-Hypo

value: M

value: Piglet formula cotaining α-lactalbumin reduced, whey protein isolate


title: PIG10-WPI-Hypo


title: PIG23-WPI-Hypo


title: Au_NRs-2

description: Library name: SAMPLES6

value: Peripheral blood mononuclear cells


title: PIG26-WPI-Hypo


title: TMOC5 (with mregDC)

city: Harbin

first: Qiming

last: Shen

address: Thoracic Surgery, The First Hospital Of China Medical University, No.155 North Nanjing Road, Heping Area, Shenyang

description: Library name: sample5

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited xlsx file includes raw counts for each sample

source_name: Non-small cell lung cancer (organ chip)

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® following manufacturer's protocols

value: Non-small cell lung cancer (organ chip)

value: with mregDC infiltration


title: TMOC4 (with mregDC)

institute: Thoracic Surgery, The First Hospital Of China Medical University

description: Library name: sample4


title: con-2

description: Library name: SAMPLES2


title: PIG8-WPI-Hypo

value: WT


title: TMOC3

description: Library name: sample3

value: control


title: Au_NRs_CPG-1

description: Library name: SAMPLES9


title: PIG17-WPI-Hypo


title: HC027_VDJ


title: CTCL019_VDJ

value: cutaneous t cell lymphoma


title: PIG18-SF-Hypo

value: Sow-fed


title: PIG24-SF-Hypo


title: PIG9-SF-Hypo


title: TMOC6 (with mregDC)

description: Library name: sample6


title: TMOC2

description: Library name: sample2