title: Aging3

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Tree shrew genome sequence
Supplementary files format and content: Tab-separated values files and matrix files


title: ED7.5 embryo SL (obese) replicate 2

status: Public on Mar 12 2025

type: RNA

city: L'Hospitalet

first: Josep

last: Jimenez-Chillaron

state: Barcelona

address: c/ Feixa Llarga s/n, Pavello de Govern, 4a planta, Biophysics Unit

department: Physiological Sciences

country: Spain

institute: University of Barcelona

description: Gene expression data from embryos from SL mice.

hyb_protocol: The hybridization was conducted at 45°C for 16-18 hours with rotary agitation (60-70 rpm). Hybridization volume was around 200 µL.

scan_protocol: Clariom S plates from Affymetrix were scanned using the GeneChip Scanner 3000 7G. Images were acquired with the Affymetrix GeneChip Command Console (AGCC) software to handle the image acquisition and data analysis process.

data_processing: Raw expression values were obtained directly from .CEL files and were processed using the RMA method in oligo R package to get normalized expression values (log2 scale) summarized at the gene level. A complete quality report was obtained using arrayQualityMetrics R package. The analysis to select differentially expressed genes was based on adjusting a linear model with empirical Bayes moderation of the variance.  P-values are adjusted to obtain strong control over the false discovery rate using the Benjamini and Hochberg method.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Whole embryo at day 7.5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: All samples were collected from euthanized animals (CO2) and rapidly snap-frozen at liquid nitrogen until RNA was extracted.

tag: strain

tag: tissue

value: Whole embryo

tag: age

value: Embryonic day 7.5 (ED7.5)


title: ED7.5 embryo SL (obese) replicate 4


title: CF-78-A022644-L001

type: SRA

city: Toronto

first: Claudia

middle: Chimisso

last: dos Santos

state: ON

address: 30, Bond Street, room 4-011

department: University of Toronto

country: Canada

institute: Saint Michaels Hospital

description:
Library name: 1436-A022644_1_S41_L001_R1_001.fastq.gz
VLP00436 Sample ID Key

library_source: transcriptomic

data_processing:
Raw read counts were imported into R to perform differential expression analyses with the R package DESeq2 11. Variance stabilization transformation was used to prepare data for analyses. Significance analyses of microarrays (SAM) was ran using one class analysis approach to identify miRNAs over-represented in EVs derived from control hMSCs based on the normalized data using Variance stabilization transformation. The delta value was set to 7 (the best delta parameter value selected by the software with the lowest False Discovery Rate (FDR]) using 1000 permutations, FDR cut-off was 0 (%).
Assembly: OP-00037
Supplementary files format and content: The HTG EdgeSeq Parser (v. 5.0.535.3181, HTG Molecular, Tucson, AZ, USA) was used to align the FASTQ files to the probe list to collate the data.
Supplementary files format and content: Data file  include compiled for all groups Raw data, QC Raw, QC summary, CMP and Median

organism: Homo sapiens

source_name: Extracellular vesicles (EVs)

growth_protocol: The hMSCs have been previously characterized according to criteria from the International Society for Cell and Gene Therapy - cultured in MEM/EBSS medium supplemented with 1% penicillin/streptomycin and 20% fetal bovine serum in standard tissue culture incubators. hMSCs were utilized at passages 3-5

extract_protocol:
EVs obtained either from hMSCs exposed to serum-free medium or experimental samples. Evs were prepared in accordance with recent recommendations from the International Society for Extracellular Vesicles (ISEV). EV-derived miRNAs were prepared from the conditioned medium and BALF samples using the exoRNeasy Serum/Plasma Maxi/Maxi Midi Kit (Qiagen, Germantown, MD, USA), according to manufacturer’s instructions.
microRNA sequence was outsource to HTG and performed according to manufacture's protocols. A total of 35 ul (35 ng/µl) of eRNA (EV preparation-derived RNA) was used for miRNA sequencing performed using the HTG EdgeSeq miRNA Whole Transcriptome Assay (miRNA WTA, as per manufacturer’s instructions as published). The miRNA library was sequenced on a NextSeq (Illumina, Inc., San Diego, CA) using a V3 150-cycle kit with two index reads. PhiX (Roche, Mississauga, ON, CAN). Data were returned from the sequencer in the form of demultiplexed FASTQ files, with one file per original well of the assay. The HTG EdgeSeq Parser (v. 5.0.535.3181, HTG Molecular, Tucson, AZ, USA) was used to align the FASTQ files to the probe list to collate the data. Raw read counts were imported into R to perform differential expression analyses with the R package DESeq2. The miRNA library was sequenced on a NextSeq (Illumina, Inc., San Diego, CA) using a V3 150-cycle kit with two index reads. PhiX (Roche, Mississauga, ON, CAN). Data were returned from the sequencer in the form of demultiplexed FASTQ files, with one file per original well of the assay. The HTG EdgeSeq Parser (v. 5.0.535.3181, HTG Molecular, Tucson, AZ, USA) was used to align the FASTQ files to the probe list to collate the data.

treatment_protocol: hMSCs were seeded into 6-well plates (Corning, 2 x 105 cells/well, 2 wells/BALF sample or control) in cell culture conditions outlined above and incubated overnight. The next day, cells were washed twice with PBS and synchronized for 24 hours in serum-free medium. After synchronization, the serum-free medium was replaced with 1 ml of serum-free medium containing either individual ARDS or individual HV (healthy vlunteer) BALF samples at a 20% (v/v) concentration. Control hMSCs were exposed to serum-free medium only. After 5 hours incubation at 37°C in a standard tissue culture incubator, cell culture medium was removed, cells were washed once with PBS, and 2 ml serum-free medium added per well. After 48 hours incubation (37°C), the conditioned medium was collected, passed through a 0.8 μm syringe filter, and processed for EV preparation, NTA, and miRNA assessments, as described below.

value: Extracellular vesicles (EVs)

tag: cell type

value: BM-MSCs

tag: disease

value: Cystic Fibrosis


title: Aging2

city: kunming

first: Rui-ze

last: Niu

address: Chunrong West Road

country: China

institute: kunming medical university

description: 10x Genomics

library_source: transcriptomic single cell

organism: Tupaia belangeri

source_name: Hippocampus

extract_protocol:
The hippocampus was carefully dissected out from TS with strict compliance to the ethical guidelines. In detail, the dissected tissues were washed with cold phosphate buffered saline (PBS; Invitrogen, Carlsbad, USA), quickly frozen and then stored in liquid nitrogen before use. Preceding the library construction process, the tissues were first thawed, cut into small pieces, and then transferred to 1.5 mL tube contained with 1× homogenization buffer containing 30 mmol/L CaCl2, 18 mmol/L Mg(Ac)2, 60 mmol/L Tris-HCl (pH 7.8), 320 mmol/L sucrose, 0.1% nonidet P-40, and 0.1 mmol/L ethylene diamine tetraacetic acid (Invitrogen). The tissue pieces werethen transferred to a 2 mL Dounce homogenizer and stroke on the ice with loose pestles and then with tight pestles for 15 times. The nucleus extraction was filtered with 40 mm strainer and spanned down at the speed of 500 g for 10 min at 4 ℃ to carefully discard the supernatant. The pellets were resuspended with PBS containing 0.1% bovine serum albumin (Invitrogen) and 20 U/mL RNase Inhibitor for later 10x Genomics 30 library construction (10x Genomics, Pleasanton, USA).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Hippocampus


title: NP45-A022640-L004

description:
Library name: 1436-A022640_1_S32_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Uns SRE-A022642-L003

description:
Library name: 1436-A022642_1_S71_L003_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Unstimulated


title: ED7.5 embryo SL (obese) replicate 3


title: ED14.5 embryo SL (obese) replicate 1

source_name: Whole embryo at day 14.5

value: Embryonic day 14.5 (ED14.5)


title: C2C12 cells, WN, 24h, biol rep 2

city: Kyoto

first: Masahiro

last: Kumeta

address: Yoshidakonoe

department: Graduate School of Biostudies

country: Japan

institute: Kyoto University

data_processing:
Trimming of noise signals (poly G), low-quality reads (~30 bases), and additional base at 76th position were performed by Cutadapt and Trimmomatic.
Mapping and identification of differentially expressed genes were performed using CLC Genomics Workbench 21.
Assembly: mm10
Supplementary files format and content: raw counts for each Sample
Supplementary files format and content: TPM values for each Sample

growth_protocol: C2C12 cells were maintained in DMEM supplimented with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was harvested usint RNeasy kit (Quiagen).
RNA libraries were prepared using NEB Next Ultra II Directional RNA Library Prep Kit for Illumina, following manufacture's instruction.

treatment_protocol: A vibrational transducer attached on a laboratory scissor jack was inversely fixed to a small metal shelf. Diaphragm custom made with polyether ether ketone was atached to the transducer. Position of the head of the diaphragm was adjusted to attach to the culture medium to generate acoustic wave directly in the medium. Sound signal was output by a conventional MP3 player, adjusted by an amplifier, and input into the transducer.

tag: cell line

value: myoblast

tag: treatment


title: NP45-A022640-L003

description:
Library name: 1436-A022640_1_S32_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: C2C12 cells, 14k, 24h, biol rep 1


title: Uns SRE-A022642-L002

description:
Library name: 1436-A022642_1_S71_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: C2C12 cells, 14k, 24h, biol rep 3


title: C2C12 cells, WN, 24h, biol rep 1


title: Infancy4

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Tree shrew genome sequence
Supplementary files format and content: Tab-separated values files and matrix files


title: NP45-A022640-L002

description:
Library name: 1436-A022640_1_S32_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: NP45-A022640-L001

description:
Library name: 1436-A022640_1_S32_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: C2C12 cells, 14k, 24h, biol rep 2


title: Infancy3

description: 10x Genomics


title: Root_Ga-L_rep3

city: Guangzhou

first: Shaopeng

last: Zhao

state: Guangdong

address: Tianhe District, Wushan Road

department: College of Natural Resources and Environment

institute: South China Agricultural University

description: Sample D3

data_processing:
Oligo (dT) magnetic beads are used to select mRNA with polyA tail.
Remove reads with adaptors;Remove reads in which unknown bases are more than 10%;Remove low quality reads (the percentage of low quality bases is over 50% inaread,we define the low quality base to be the base whose sequencing quality is no more than 5).
We use Bowtie2 to map clean reads to reference gene and use HISAT to reference genome.
RSEM is a quantification tool and FPKM method is used in calculated expression level.
Screening DEGs using NOISeq.
Genome_build: Glycine max Wm82.a2.v1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .

organism: Glycine max

source_name: Root

extract_protocol:
Ethanol precipitation protocol and CTAB-PBIOZOL reagent for the purification of total RNA from the plant tissue
BGI RNA-Seq kit

value: Root

tag: am type

value: Glomus aggregatum with low AM colonization


title: C2C12 cells, 440Hz, 24h, biol rep 1


title: Aging1

description: 10x Genomics


title: ED7.5 embryo Control replicate 1

description: Gene expression data from embryos from Control mice.


title: C2C12 cells, silent, 2h, biol rep 3

value: silent, 2h


title: Adult2

description: 10x Genomics


title: ED7.5 embryo Control replicate 4


title: ED7.5 embryo SL (obese) replicate 1


title: F_C_18

city: Baton Rouge

first: Jaroslaw

last: Staszkiewicz

state: LA

address: 6400 Perkins Rd

department: Genomics Core Facility

country: USA

institute: Pennington Biomedical Research Center

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, R V4.0.3, Rstudio V1.4.1106 and biomaRt V2.46.0
edgeR V3.38.4 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Assembly: Mouse GRCm38.84 mm10
Supplementary files format and content: tab-delimited text containing rawcounts for all Samples

source_name: Gastrocnemius Muscle Tissue

growth_protocol: Mice were maintained on chow 5015 diet with or without exposure to voluntary wheel running from 10 to 20 weeks of age

extract_protocol:
Gastrocs were collected, snap frozen in liquid nitrogen, and tissue homogenization was done using Trizol reagent. Total RNA was isolated using RNeasy Mini kit from Qiagen.
Quant-Seq  3' mRNA-Seq Library Prep Kit
indexed and pooled samples, 50bp forward read

treatment_protocol: 14 Control and 14 HuR Skeletal Muscle Knockout mice (7 males and 7 females each) at 5 months of age were exposed to running wheels for 10 weeks, while 14 Control and 14 HuR Skeletal Muscle Knockout mice (7 males and 7 females each) at 5 months of age were exposed to locked wheels

value: Gastrocnemius Muscle Tissue

tag: group

value: Controls

tag: Sex

value: Female

value: Baseline


title: Root_Ga-L_rep1

description: Sample D1


title: AE106-A022639-L002

description:
Library name: 1436-A022639_1_S26_L002_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Healthy Control


title: C2C12 cells, 440Hz, 24h, biol rep 3


title: ED7.5 embryo Control replicate 3

value: Whole embryo


title: AE106-A022639-L001

description:
Library name: 1436-A022639_1_S26_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: ED7.5 embryo Control replicate 2

value: Embryonic day 7.5 (ED7.5)


title: C2C12 cells, 440Hz, 24h, biol rep 2


title: Adult1

description: 10x Genomics


title: Root_Ga-L_rep2

description: Sample D2


title: AE106-A022639-L003

description:
Library name: 1436-A022639_1_S26_L003_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)


title: Infancy2

description: 10x Genomics


title: Infancy1

description: 10x Genomics


title: Root_Ga-H_rep1

description: Sample C1

value: Glomus aggregatum with high AM colonization


title: C2C12 cells, silent, 2h, biol rep 2


title: C2C12 cells, WN, 2h, biol rep 2


title: Root_Ri_rep3

description: Sample B3

value: Rhizophagus irregularis


title: Root_Ga-H_rep3

description: Sample C3


title: 500nm_transcripts

city: Bonn

first: Maria Francesca

last: Viola

address: Carl Troll Str 32

country: Germany

institute: LIMES Institute

hyb_protocol: Slides were fixed and permeabilized as per the Xenium In Situ for Fresh Frozen Tissues – Fixation & Permeabilization protocol (10X Genomics). Probe hybridization was performed at 50°C overnight using the pre-designed, 247-probe Xenium Mouse Brain Gene Expression panel (Cat. #1000462, 10X Genomics). Next, slides underwent wash steps to remove any unhybridized probes, followed by a 2-hour ligation step at 37°C to anneal probes to their specific mRNA target. The probes were then enzymatically amplified via rolling circle amplification PCR for 2 hours at 37°C. After washing, quenching steps were performed to reduce background autofluorescence, followed by a DAPI nuclear stain.

data_processing:
The slide cassettes were subsequently loaded onto the Xenium Analyzer instrument (10x Genomics). Following instrument initialization, slides and consumables were loaded onto the Xenium Analyzer, and regions of interest were selected after a preliminary sample scan. mRNA-specific puncta were decoded into their corresponding gene IDs and assigned a quality score. Using the DAPI nuclear stain, cell boundaries were segmented and transcripts were spatially assigned to cells at a sub-50nm XY localization precision.
For each sample, the full output from the Xenium Analyzer is provided.

source_name: Brain

extract_protocol: After PS administration according to the chronic plastic administration model, mice were anaesthetized and perfused trans-cardially with ice-cold PBS. Dissected brain hemispheres were embedded into OCT and snap-frozen in liquid nitrogen. Samples were processed according to recommendations in the Xenium In Situ for Fresh Frozen Tissues – Tissue Preparation Guide (10X Genomics). Briefly, 10 μm slices located between bregma -2.155 and bregma -2.48 were sectioned using a cryostat and placed within the 12x24mm sample frame on a Xenium slide. Slides were subsequently stored at -80°C until use.

treatment_protocol: Mice were treated weekly with 100mg/kg of 50nm PS, 500nm PS or PBS as a control, for 12 weeks.

value: Brain

tag: section area

value: Between bregma -2.155 and -2.48.

value: Brain cells

tag: genotype

value: WT

value: Male


title: Root_Ri_rep2

description: Sample B2

value: Root


title: BRW110-A022638-HC-L001

description:
Library name: 1436-A022638_1_S30_L001_R1_001.fastq.gz
VLP00436 Sample ID Key

value: BM-MSCs


title: 50nm_transcripts

description: 247-probe Xenium Mouse Brain Gene Expression panel (Cat. #1000462, 10X Genomics)

value: 50 nm


title: AE106-A022639-L004

description:
Library name: 1436-A022639_1_S26_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Root_Ri_rep1

description: Sample B1


title: Root_Ga-H_rep2

description: Sample C2


title: C2C12 cells, silent, 2h, biol rep 1

value: myoblast

value: silent, 2h


title: BRW110-A022638-HC-L004

description:
Library name: 1436-A022638_1_S30_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: C2C12 cells, 14k, 2h, biol rep 3


title: C2C12 cells, WN, 2h, biol rep 3


title: Ctrl_transcripts

value: PBS


title: BRW110-A022638-HC-L003

description:
Library name: 1436-A022638_1_S30_L003_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Healthy Control


title: C2C12 cells, WN, 2h, biol rep 1


title: IVT, Po, rep1

city: Singapore

first: Roland

middle: G

last: Huber

address: 30 Biopolis Street

department: Bioinformatics Institute (BII)

country: Singapore

institute: Agency for Science, Technology and Research (A*STAR)

library_source: other

data_processing:
SPLASH libraries were sequenced using NovaSeq X Plus PE 150.Computational analysis was performed similarly to the published protocol (Aw et al, 2016). Briefly, paired-end reads were merged using SeqPrep (v1.3.2). Merged reads were mapped to a reference of Po or Gv PIE Gluc precursor sequence using BWA MEM (v0.7.17). Reads with identical CIGAR string were considered as duplicates and were collapsed into one read. Primary alignments with “SA” tag were identified as chimeric reads. Reads that mapped to E1-E2 ligated junction were omitted to rule out reads that the E1-E2 junction in circular confirmation. Lastly, chimeric reads with mapping quality higher than 20 and arm span higher than 10bp were used for downstream analysis.
Gv PIE Gluc Sequence: GGGAAAAAAACAAAAAAAAAAGAGAGCAGAUCUCUGAUUGGCCAUGCGUGCAGUUCACAGACUAGAUGUGGGUGGGGGGUUGUACCCCUUAAGAUAUAGUCGAAGCCCAGUGUGAAAGCCUGGGAUUAGUUGCAGAUACCGUCGUAGUCUUACGCGAAACGCCAAUAUGCUGAAAAACAAAAAACAAAAAACAAAAAAACCAAAAAACAAAACACAGGUACCCGGGGAUCCUCUAGAGCCACCAUGGGAGUCAAAGUUCUGUUUGCCCUGAUCUGCAUCGCUGUGGCCGAGGCCAAGCCCACCGAGAACAACGAAGACUUCAACAUCGUGGCCGUGGCCAGCAACUUCGCGACCACGGAUCUCGAUGCUGACCGCGGGAAGUUGCCCGGCAAGAAGCUGCCGCUGGAGGUGCUCAAAGAGAUGGAAGCCAAUGCCCGGAAAGCUGGCUGCACCAGGGGCUGUCUGAUCUGCCUGUCCCACAUCAAGUGCACGCCCAAGAUGAAGAAGUUCAUCCCAGGACGCUGCCACACCUACGAAGGCGACAAAGAGUCCGCACAGGGCGGCAUAGGCGAGGCGAUCGUCGACAUUCCUGAGAUUCCUGGGUUCAAGGACUUGGAGCCCAUGGAGCAGUUCAUCGCACAGGUCGAUCUGUGUGUGGACUGCACAACUGGCUGCCUCAAAGGGCUUGCCAACGUGCAGUGUUCUGACCUGCUCAAGAAGUGGCUGCCGCAACGCUGUGCGACCUUUGCCAGCAAGAUCCAGGGCCAGGUGGACAAGAUCAAGGGGGCCGGUGGUGACUAACCUGCAGGAAAAAACAAAAAACAAAACAGCAUAUUGAUGCGUUACCGUUAGGGGAUCGAAGACGAUUUAAGAAGGGUCCGCGCCCCCCCCGGUGGGGGCCGGCUCGGUAUUUGGUCGUUAAAAGUAAGCUCAAAGUGUCUUGCUAGUCGCCGCGACCGCGGGGGCAACACCGUCAAACUGCGGGAACGUCCUAAAGCCUGAACUACCAAGCCGACGCCGAAAGGCGCCGGUGGCCGGGGUAAUGACCCAGGGUACGGUAACAACGUUCAGGAUGCGCCAAUGGAUAACCUGCAACCAAGCGCUACCGCCUCAGAGAUCUGCUCUCUAAAAAACAAAAAAAAACAAACUCGA
Po PIE Gluc Sequence: GGGAAAAAAACAAAAAAAAAAGAGAGCAGAUCUCUGCCGGGGACCACGCGUGCAGUUCACAGACUAGAUGUCGGUGGGGGAUCCGUCUCCUAAGAUAUAGUCGAGGCCCAGCGCGAAAGCCUGGGAGUAUCCGCAGAUACCGUCGUAGUCUUACGCGAAACGCCAAUAUGCUGAAAAACAAAAAACAAAAAACAAAAAAACCAAAAAACAAAACACAGAGCUCGGUACCCGGGGAUCCUCUAGAGCCACCAUGGGAGUCAAAGUUCUGUUUGCCCUGAUCUGCAUCGCUGUGGCCGAGGCCAAGCCCACCGAGAACAACGAAGACUUCAACAUCGUGGCCGUGGCCAGCAACUUCGCGACCACGGAUCUCGAUGCUGACCGCGGGAAGUUGCCCGGCAAGAAGCUGCCGCUGGAGGUGCUCAAAGAGAUGGAAGCCAAUGCCCGGAAAGCUGGCUGCACCAGGGGCUGUCUGAUCUGCCUGUCCCACAUCAAGUGCACGCCCAAGAUGAAGAAGUUCAUCCCAGGACGCUGCCACACCUACGAAGGCGACAAAGAGUCCGCACAGGGCGGCAUAGGCGAGGCGAUCGUCGACAUUCCUGAGAUUCCUGGGUUCAAGGACUUGGAGCCCAUGGAGCAGUUCAUCGCACAGGUCGAUCUGUGUGUGGACUGCACAACUGGCUGCCUCAAAGGGCUUGCCAACGUGCAGUGUUCUGACCUGCUCAAGAAGUGGCUGCCGCAACGCUGUGCGACCUUUGCCAGCAAGAUCCAGGGCCAGGUGGACAAGAUCAAGGGGGCCGGUGGUGACUAACCUGCAGGAAAAAACAAAAAACAAAACAGCAUAUUGAUGCGUUACCGUUAGGGGAUCGAAGACGAUUUAAGGAAGCCUCCCGGCCUGGUUUCCGUGGAAAUCAGGCCGGAGAUGGUAUUUGGUCGUCCAAAGUAAGCCUGAAAGGACUUGCUAGUCUCGGCCGUGGCCGAGGCGACACCGUCAAAUUGCGGGGACCUCCUAAAGCCUGGACUACCAAGCCGACGCCGAAAGGCGCCGGUGGCCGGGGUAAUGACCUAGGGUAUGGUAACAACGUCCGGGAUGUGACAAUGGACAAUCCGCAGCCAAGCGCUACCGCCCCUCAGAGAUCUGCUCUCUAAAAAACAAAAAAAAACAAACUCGA
Assembly: In-house references for Gv and Po Gluc IVT products
Supplementary files format and content: csv format
Supplementary files format and content: called chimeric reads from SPLASH crosslinking

molecule: other

organism: synthetic construct

source_name: synthetic, IVT

extract_protocol:
In-vitro transcribed RNA samples
For details, please refer to Aw JG, Shen Y, Wilm A, Sun M, Lim XN, Boon KL, Tapsin S, Chan YS, Tan CP, Sim AY, Zhang T, Susanto TT, Fu Z, Nagarajan N, Wan Y. In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation. Mol Cell. 2016 May 19;62(4):603-17. doi: 10.1016/j.molcel.2016.04.028. Epub 2016 May 12. PMID: 27184079.
Sequencing of Psoralen crosslinked, Ligated, and Selected Hybrids (SPLASH)

value: synthetic, IVT

tag: sample group

value: IVT, Po

tag: molecule type

value: In-vitro transcribed RNA

value: biotinylated psoralen


title: Muscle GFP-, WT (7dpi)

city: Ann Arbor

first: Susan

middle: V

last: Brooks

state: Michigan

address: 109 Zina Pitcher Pl

department: Molecular and Integrative Physiology

institute: University of Michigan

description: Library name: NC_GFP-

data_processing:
Base calling, alignment, filtering, barcode counting, and UMI counting: CellRanger v7.1.0 (10X Genomics) was used to process raw data. The CellRanger count command was run with default parameters.
Data filtering and quality control process: Data filtering and quality control process: Barcodes, features, and count matrices were uploaded into Seurat (v4.30) using the ReadMtx() function. We filtered out cells with fewer than 200 UMIs and those with over 10% mitochondrial genes. Ambient RNA was removed using decontX with default settings. After consolidating Seurat objects from all samples into one, we normalized and scaled this merged object. Dimensional reduction was then executed using RunUMAP and FindNeighbors. Cells were annotated manually using upregulated markers distinctive to each cluster.
Assembly: mm10
Supplementary files format and content: Filtered features, barcodes, count matrices (h5 format)

source_name: skeletal muscle

extract_protocol:
For tissue collection, mice were anesthetized with 3% isoflurane, then euthanized by cervical dislocation, bilateral pneumothorax, and removal of the heart. Hind limb muscles (TA and GTN) of control and experimental mice were quickly harvested using sterile surgical tools and placed in separate plastic petri dishes containing cold phosphate-buffered saline (PBS). Using surgical scissors, muscle tissues were minced and transferred into 50 mL conical tubes containing 20 mL of digest solution (2.5 U/mL Dispase II and 0.2% [~1000 U/mL] Collagenase Type II, 1 mg/mL of hyaluronidase in Dulbecco’s modified Eagle medium [DMEM] per mouse). Samples were incubated on a rocker placed in a 37 ̊C incubator for 60 min with manual pipetting the solution up and down to break up tissue every 30 min using an FBS-coated 10 mL serological pipette. Once the digestion was completed, 20 mL of F12 media containing 20% heat inactivated FBS was added into each sample to inactivate enzyme activity. The solution was then filtered through a 70 mm cell strainer into a new 50 mL conical tube and centrifuged again at 300g for 5 min. Live cells were sorted from the suspension via addition of 1 μg of propidium iodide (PI) stain into each experimental sample and all samples were filtered through 70 mm cell strainers before the FACS. Cell sorting was done using a BD FACS Aria III Cell Sorter (BD Biosciences, San Jose, CA). GFP+ PI- and GFP- PI- cells were sorted into 0.02% BSA PBS solution for immediate processing. RNA libraries for RNA Seq were prepared using GEM Single Cell 3' HT Reagent Kits v3 kits from 10X Genomics according to the manufacturer’s protocols.
Library preparation and next-generation sequencing was carried out in the Advanced Genomics Core at the University of Michigan. Cells were loaded into the 10X Genomics chromium single cell controller for each sample and captured into nanoliter-scale gel bead-in-emulsions. cDNAs were prepared using the single cell protocol as per manufacturer’s instructions.

value: skeletal muscle

value: sciatic nerve injury


title: Root_NM_rep3

description: Sample A3


title: IVT, Gv, rep2

value: IVT, Gv


title: Muscle GFP+, WT (7dpi)

description: Library name: NC_GFP+


title: Unstim 20190117-L002

description:
Library name: 1436-A022637_1_S52_L002_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)

value: Unstimulated


title: Unstim 20190117-L004

description:
Library name: 1436-A022637_1_S52_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: IVT, Po, rep2


title: C2C12 cells, 14k, 2h, biol rep 2


title: Unstim 20190117-L003

description:
Library name: 1436-A022637_1_S52_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Unstim 20190117-L001

description:
Library name: 1436-A022637_1_S52_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: C2C12 cells, 14k, 2h, biol rep 1


title: C2C12 cells, 440Hz, 2h, biol rep 2


title: BRW110-A022638-HC-L002

description:
Library name: 1436-A022638_1_S30_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Root_NM_rep2

description: Sample A2


title: CF59-A022636-L004

description:
Library name: 1436-A022636_1_S81_L004_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Cystic Fibrosis


title: CF59-A022636-L003

description:
Library name: 1436-A022636_1_S81_L003_R1_001.fastq.gz
VLP00436 Sample ID Key


title: CF59-A022636-L002

description:
Library name: 1436-A022636_1_S81_L002_R1_001.fastq.gz
VLP00436 Sample ID Key


title: Root_NM_rep1

description: Sample A1

value: Root


title: FN_RNA_rep3

city: Seoul

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

department: Department of Tropical Medicine

country: South Korea

institute: Yonsei University College of Medicine

data_processing:
Raw reads were trimmed to remove adaptor sequences and low quality bases by using Trim Galore v0.6.8dev (https://github.com/FelixKrueger/TrimGalore) with Cutadapt v4.1 (https://doi.org/10.14806/ej.17.1.200).
The trimmed reads were mapped to T.vaginalis genome downloaded from TrichDB v68 (https://trichdb.org/trichdb/app/) using STAR v2.7.10a with --sjdbGTFtagExonParentTranscript Parent and --twopassMode Basic options.
The expression levels of each transcript were estimated using RSEM (v1.3.1) with --estimate-rspd option.
Bigwig files were generated from BAM files using deeptools (v3.5.3) bamCoverage function with --normalizeUsing CPM option.
Assembly: Trichomonas vaginalis G3
Supplementary files format and content: RSEM output files including raw counts, FPKM, TPM values
Supplementary files format and content: normalized bigwig

organism: Trichomonas vaginalis

growth_protocol: The T016 strain of T. vaginalis was axenically subcultivated at 37°C in Diamond’s trypticase–yeast extract–maltose (TYM) medium with 10% heat-inactivated horse serum and 0.5% penicillin/streptomycin.

extract_protocol:
RNA was harvested using Hybrid-R total RNA kit (GeneAll Biotechnoloty).
RNA libraries for RNA-seq were prepared using TruSeq RNA Sample Prep Kit (Illumina) following manufacturer's protocol.

treatment_protocol: Iron-restricted conditions were supplemented with 50 μM 2’-2-dipyridy for 18hr

value: 50 μM 2’-2-dipyridyl

tag: time


title: IVT, PoGv, rep1

value: IVT, PoGv


title: YHIM-2018 (1)

first: Dongkwon

address: Yonsei ro 50-1

institute: Yonsei university

description:
SJ1RNAMFF003522
humanized mouse (human)

data_processing:
We used RNA expression level (count data only)
Assembly: hg38
Supplementary files format and content: Bulk-RNA-Seq_PDX.xlsx

organism:
Homo sapiens
Mus musculus

source_name: Tumor

growth_protocol: We established a patient-derived tumor xenograft (PDTX) model by implanting tumors into humanized mice, and we did not culture the tumors in vitro.

extract_protocol:
We sent the tissue samples to MACROGEN company in a fresh frozen state.
Illumina NovaSeq 6000 was used to process bulk-RNA-sequencing
Bulk-RNAseq

tag: host organism

value: mouse

tag: xenograft organism

value: human

value: Tumor

value: Patient-derived xenograft

value: Lung cancer cell

value: WT


title: C2C12 cells, 440Hz, 2h, biol rep 3

value: myoblast


title: C2C12 cells, 440Hz, 2h, biol rep 1


title: YHIM-2018 (2)

description:
SJ1RNAMFF003591
humanized mouse (human)


title: YHIM-2018 (3)

description:
SJ1RNAMFF003595
humanized mouse (human)


title: FN_RNA_rep1

tag: strain


title: CF77-A022635-L004

description:
Library name: 1436-A022635_1_S16_L004_R1_001.fastq.gz
VLP00436 Sample ID Key

tag: tissue

value: BM-MSCs


title: IVT, Gv, rep1

value: synthetic, IVT

value: In-vitro transcribed RNA

value: biotinylated psoralen


title: YHIM-1013 (2)

description:
SJ1RNAMFF262111
humanized mouse (human)


title: CF77-A022635-L002

description:
Library name: 1436-A022635_1_S16_L002_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Extracellular vesicles (EVs)


title: CF59-A022636-L001

description:
Library name: 1436-A022636_1_S81_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: YHIM-1013 (1)

description:
SJ1RNAMFF262109
humanized mouse (human)


title: CF77-A022635-L001

description:
Library name: 1436-A022635_1_S16_L001_R1_001.fastq.gz
VLP00436 Sample ID Key


title: IVT, GvPo, rep1

value: IVT, GvPo


title: YHIM-1018 (3)

description:
SJ1RNAMFF001403
humanized mouse (human)


title: YHIM-1013 (3)

description:
SJ1RNAMFF262113
humanized mouse (human)


title: CF77-A022635-L003

description:
Library name: 1436-A022635_1_S16_L003_R1_001.fastq.gz
VLP00436 Sample ID Key

value: Cystic Fibrosis


title: FN_H3K9me3_rep2

library_source: genomic

data_processing:
Raw reads were trimmed to remove adaptor sequences and low quality bases by using Trim Galore v0.6.8dev (https://github.com/FelixKrueger/TrimGalore) with Cutadapt v4.1 (https://doi.org/10.14806/ej.17.1.200).
The trimmed reads were mapped to TrichDB v68 using bwa v0.7.17 in default options.
Duplicate reads were removed using PICARD v2.18.23 (https://gith6+9ub.com/broadinstitute/picard).
Read counts from the genebody were calculated for each gene using deeptools (v3.5.3) multiBigwigSummary
Peaks were called using macs2 v2.2.7.1 with input reference bam file and the following setting: -f BAMPE -g 181470000 (--broad for H3K27me3 and H3K9me3 ChIP-seq peak calling)
Assembly: Trichomonas vaginalis G3
Supplementary files format and content: narrowPeak, broadPeak, CPM normalized bigwig

molecule: genomic DNA

extract_protocol:
Cell were fixed with 1% formaldehyde for 10 minutes at room temperature. After quenching and cell lysis, chromatin was sonicated using a Bioruptor sonication device (Diagenode).
Chip-seq libraries were prepared using the 1 ul Tagment DNA Enzyme from Nextera DNA Sample Prep Kit (Illumina). 10ng of DNA was used as starting material for input samples. Post amplification libraries were size selected at 200-400bp in length using Agencourt AMPure XP beads from Beckman Coulter.

tag: chip antibody

value: H3K9me3 (Abcam #Ab8898)


title: FN_RNA_rep2

value: 50 μM 2’-2-dipyridyl


title: FN_H3K27me3_rep2

value: H3K27me3 (Abcam #Ab6002)


title: YHIM-1018 (2)

description:
SJ1RNAMFF001401
humanized mouse (human)

value: mouse

tag: cell type


title: CF76-A022634-L003

description:
Library name: 1436-A022634_1_S31_L003_R1_001.fastq.gz
VLP00436 Sample ID Key

tag: disease


title: FN_H3K9me3_rep1


title: IVT, GvPo, rep2


title: CF76-A022634-L004

description:
Library name: 1436-A022634_1_S31_L004_R1_001.fastq.gz
VLP00436 Sample ID Key


title: YHIM-1018 (1)

description:
SJ1RNAMFF001488
humanized mouse (human)

value: human

tag: cell line


title: FN_H3K27me3_rep1

tag: treatment


title: FN_H3K4me3_rep1

value: H3K4me3 (Abcam #Ab8580)


title: YHIM-1062 (2)

description:
SJ1RNAHFF570728
humanized mouse (human)

value: Tumor

value: Patient-derived xenograft


title: FN_H3K4me3_rep2


title: Mouse naïve CD4+ T cells, WT, rep2

city: Shanghai

first: Haixin

last: Li

state: Shanghai

address: 36 Yunxin Rd

department: Shanghai Tenth People's Hospital, School of Medicine

institute: Tongji University

description:
Library name: Sample5
C4NWT2

data_processing:
About 50 million raw reads for each sample were generated, raw reads were processed by Trimmomatic.
Assembly: After processing raw reads by Trimmomatic, the high-quality clean reads were mapped to the mouse genome (GRCm38.p6) using HISAT2.
Supplementary files format and content: FPKM of each gene was calculated by Cufflinks, and the read counts of each gene were obtained by HTSeq-count. The DESeq2 was used to normalize the raw counts and identify differentially expressed genes (DEGs; |fold change| ≥ 2; p-value < 0.05)

source_name: Peripheral lymphoid organs

growth_protocol: Male mice aged 8-12 weeks were utilized in experiments

extract_protocol:
Total RNA was extracted by the TRIzol reagent (Invitrogen) according to the manufacturer’s protocol.
RNA libraries were prepared with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.

treatment_protocol: Naïve CD4+ T cells were purified using the EasySep Mouse Naïve CD4+ T Cell Isolation Kit (STEMCELL Technologies) following the provided instructions.

value: Peripheral lymphoid organs

value: T cell

value: WT


title: Mouse naïve CD4+ T cells, WT, rep1

description:
Library name: Sample4
C4NWT1


title: FN_H3K27ac_rep2

value: H3K27ac (Abcam #Ab4729)


title: YHIM-1062 (1)

description:
SJ1RNAHFF570726
humanized mouse (human)

value: Lung cancer cell


title: YHIM-1062 (3)

description:
SJ1RNAHFF570729
humanized mouse (human)


title: FN_H3K27ac_rep1


title: Mouse naïve CD4+ T cells, Nat10 KO, rep3

description:
Library name: Sample3
C4N10KO3

value: Nat10 KO


title: YHIM- 2004 (3)

description:
SJ1RNAMFF004645
humanized mouse (human)


title: FN_input_rep2

value: Not applied


title: Mouse naïve CD4+ T cells, Nat10 KO, rep1

description:
Library name: Sample1
C4N10KO1


title: HALO_CTEP2_ampDNA

status: Public on Mar 11 2025

city: Barcelona

first: Arnau

last: Sebé-Pedrós

address: C/ Dr. Aiguader, 88

department: Systems and Synthetic Biology

institute: Centre for Genomic Regulation (CRG)

data_processing:
Raw reads were filtered and trimmed with Trimmomtic (version 0.39) before mapping to the genome with bwa mem (version 0.7.17).
Duplicated reads were marked with bamsormadup from biobambam2 (https://github.com/gt1/biobambam2)
DAP-seq peaks were called with MACS2.
Assembly: Mnemiopsis leidyi genome assembly Mlei_v1
Supplementary files format and content: BigWig
Library strategy: DAP-seq

organism: Mnemiopsis leidyi

source_name: Whole-organism

extract_protocol:
The DNA-binding domains of CTEP1 and CTEP2 proteins were cloned from cDNA library of M. leidyi into the pIX-HALO vector using NEBuilder HiFi DNA Assembly Master Mix (NEB, E2621). The obtained HALO-fusion constructs were translated using the TnT SP6High-Yield Wheat Germ Protein Expression System (Promega, L3260)
Adapter-ligated DNA library was prepared from native genomic DNA of M. leidyi using NEBNext UltraII FS DNA library prep kit (NEB, E7805) or PCR amplified genomic DNA. Incubation of 1h was done to allow the binding of the HALO-CTEP fusion proteins and adapter-ligated genomic DNA library (100 ng). The unbound fragments were washed away and the reactions were boiled to release the DNA into solution. The barcoded DAP-seq libraries were created and sequenced in paired-end mode on an Illumina NextSeq 500 using High-Output 75 cycles.

value: Whole-organism

value: wild type


title: YHIM-2004 (1)

description:
SJ1RNAMFF004639
humanized mouse (human)


title: YHIM-2004 (2)

description:
SJ1RNAMFF004644
humanized mouse (human)


title: Mouse naïve CD4+ T cells, Nat10 KO, rep2

description:
Library name: Sample2
C4N10KO2


title: HALO_CTEP1_gDNA


title: FN_input_rep1


title: HALO_CTEP1_ampDNA


title: Mlei_ChIP_input

data_processing:
Raw reads were filtered and trimmed with Trimmomtic (version 0.39) before mapping to the genome with bwa mem (version 0.7.17).
Duplicated reads were marked with bamsormadup from biobambam2 (https://github.com/gt1/biobambam2)
ATAC peaks were called with MACS2.
Assembly: Cladtertia collaboinventa genome assembly HoiH23_v2, Hormiphora californensis genome assembly GCA_020137815.1; Nematostella vectensis genome assembly GCA_932526225.1; Sphaeroforma arctica genome assembly Sarc_v2, Salpingoeca rosetta genome assembly Sros_v2
Supplementary files format and content: BigWig

source_name: Mnemiopsis leidyi

growth_protocol: Sphaeroforma arctica culture was grown in Marine Broth (37.4 g/L) at 12 ºC. Salpingoeca rosetta culture was kept in artificial sea water with salinity 33 ppt supplemented with 4 % CGM3 and 4 % SWC at 23 ºC. Nematostella vectensis specimens were grown in 1/3 artificial sea water with salinity 14 ppt at 25 ºC. Cladtertia collaboinventa colonies were grown in artificial sea water (Red Sea, R11055) with salinity 33 ppt at 21 ºC.

extract_protocol:
S. arctica and S. rosetta cells were double crosslinked with 1% formaldehyde and 3 mM DSG (Thermo Scientific, A35392). H.californensis specimens were flash-frozen in liquid nitrogen. Frozen tissues were then pulverized, cells and nuclei were collected by centrifugation for 15 min at 2,000 g. Collected cells were filtered through a 40 µm cell strainer and double crosslinked with 1% formaldehyde and 3 mM DSG. N. vectensis 1.5-2 month old specimens were crosslinked with 1 % formaldehyde under vacuum. Crosslinked tissues were dissociated into single cells in Ca2+/Mg2+-free artificial sea water in the presence of Protease XIV (Sigma-Aldrich, P5147). Dissociated cells were filtered through 40 µm cell strainer, stained with 2 µg/ml Hoechst 33342, and FACS sorted to isolate mOrange-positive neuronal cells. FACS-sorted cells were additionally crosslinked with 3 mM DSG. C. collaboinventa specimens were dissociated into single cells in Ca2+/Mg2+-free artificial sea water. Dissociated cells were filtered through a 40 µm cell strainer and double crosslinked with 1% formaldehyde and 3 mM DSG.
Chromatin immunoprecipitation was performed as previously described by Lara-Astiaso et al. (PMID: 25103404) with following modifications. For each species, 100 ng chromatin was used for immunoprecipitation.

treatment_protocol: To synchronize cells in G1/early S phase, S. arctica cells were treated with 200 mM hydroxyurea (Sigma-Aldrich, H8627) for 18 hours, S. rosetta culture was treated with 0.05 mM aphidicolin for 18 hours.


title: HALO_control_ampDNA


title: HALO_control_gDNA


title: Mlei_ChIP_SMC1

data_processing:
Raw reads were filtered and trimmed with Trimmomtic (version 0.39) before mapping to the genome with bwa mem (version 0.7.17).
Duplicated reads were marked with bamsormadup from biobambam2 (https://github.com/gt1/biobambam2)
peaks were called with MACS2.
Assembly: Capsaspora owzarzaki genome assembly Cowc_v2, Mnemiopsis leidyi genome assembly Mlei_v1; Ephydatia muelleri genome assembly Emue_v2; Trichoplax adhaerens genome assembly TadhH1_v1
Supplementary files format and content: BigWig

growth_protocol: Capsaspora owczarzaki strain ATCC30864 was maintained in axenic culture at 23 ºC in the ATCC medium 1034 (modified PYNFH medium). Mnemiopsis leidyi specimens were kept in artificial sea water (Red Sea, R11055) with salinity 27 ppt at 21 ºC. For experiments we used adult lobate animals that were starved for 2 days.  Ephydatia muelleri sponge gemmules were hatched and grown for one week in Strekal’s media.  Trichoplax adhaerens colonies were grown in artificial sea water (Red Sea, R11055) with salinity 33 ppt at 21 ºC.

extract_protocol:
Capsaspora owczarzaki cells were double crosslinked with 1% formaldehyde and 3 mM DSG (Thermo Scientific, A35392).  Mnemiopsis leidyi specimens were dissociated into single cells in Ca2+/Mg2+-free artificial sea water by triturating every 2 min for a total of 10 min. Dissociated cells were filtered through a 40 µm cell strainer and double crosslinked with 1% formaldehyde and 3 mM DSG. Seven days post hatching sponges Ephydatia muelleri were fed with 0.5 µm fluorescent carboxylate-modified FluoSpheres (Invitrogen, F8813). Next, animal tissues were dissociated into cells and double crosslinked with 1% formaldehyde and 3 mM DSG. Crosslinked cells were filtered through 40 µm cell strainer, stained with 2 µg/ml Hoechst 33342, and FACS sorted to isolate choanocytes. Trichoplax adhaerens specimens were dissociated into single cells in Ca2+/Mg2+-free artificial sea water. Dissociated cells were filtered through a 40 µm cell strainer and double crosslinked with 1% formaldehyde and 3 mM DSG.
Chromatin immunoprecipitation was performed as previously described by Lara-Astiaso et al. (PMID: 25103404) with following modifications. For each species, 100 ng chromatin was used for immunoprecipitation. The pool of chromatin was incubated for 14 - 16 hours at 4 ºC with 6 µL (3.4 µg) anti-H3K4me2 (Abcam, ab32356), 2.5 µL anti-H3K4me3 (Millipore, 07-473), 5 µL (5 µg) anti-SMC1 (ThermoFisher , A300-055A) or 2 µL (2 µg) anti-H3 (Abcam, ab1791).

treatment_protocol: To synchronize cells in G1/early S phase, C. owczarzaki cells were treated with 100 mM hydroxyurea (Sigma-Aldrich, H8627) for 18 hours. Synchronised cells were scraped off the surface and pelleted at 2,200 g for 5 min at room temperature (RT).

value: SMC1, ThermoFisher  A300-055A


title: Mlei_ChIP_H3K4me3

value: H3K4me3, Millipore, 07-473


title: Mouse naïve CD4+ T cells, WT, rep3

description:
Library name: Sample6
C4NWT3


title: dCas13b_ROBO1 rep1

city: Haining

first: Huanchang

last: Tu

address: 718 East Haizhou Rd., Haining, Zhejiang

institute: Zhejiang University

description:
Library name: dCas13b_ROBO1 rep1
the column 'dCas13b_ROBO1_rep1'
dCas13b_count_matix.csv

data_processing:
The original fluorescence image files obtained from Illumina platform are transformed to short reads (Raw data) by base calling and these short reads are recorded in FASTQformat, which contains sequence information and corresponding sequencing quality information.
For the initial RNA-seq data, quality evaluation was performed using the FastQC tool (version 0.11.9). This step assessed the overall integrity of the RNA-seq fastq files and identified any potential issues.
The bulk RNA-seq libraries were processed with paired-end sequencing. This was followed by trimming the sequences using cutadapt (version 4.1).
The trimmed reads were aligned to the human genome (hg38) using STAR (version 2.7.10a), organized with samtools (version 1.6), and the read counts were quantified against Gencode (version 41) annotations with featureCounts (version 2.0.1).
Assembly: hg38
Supplementary files format and content: csv: matrix of gene counts of updated samples

molecule: polyA RNA

source_name: hESC

extract_protocol:
Total RNA was extracted from hESCs with AG RNAex Pro Reagent (Accurate Biology, AG21101), adhering to the manufacturer’s protocol
Total RNA worked as input for the RNA sample preparation. Sequencing libraries were generated using NEBNext Ultra Libraries Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s protocol and index codes were added to attribute sequences to each sample. Sepecifically, poly-T oligo-attached magnetic beads were used to purified mRNA from total RNA. Fragmentation was applied with divalent cations under elevated temperature in NEB Next First Strand Synthesis Reaction Buffer(5X). M-MuLV Reverse Transcriptase (RNase H) and random hexamer primers were used to create first strand cDNA. RNase H and DNA Polymerase I were then used to synthesise second strand cDNA. The remaining overhangs were transformed into blunt ends by polymerase and exonuclease reactions. To become ready for hybridization, NEB Next Adaptors with hairpin loop structures were ligated after the 3' ends of DNA fragments had been adenylated. Purification of the library fragments was done using the AMPure XP system (Beverly, USA) to select cDNA fragments that were preferably 370–420 bp in length. Subsequently, 3 μL USER Enzyme (NEB, USA) was employed with adaptor-ligated, size-selected cDNA at 37°C for 15 min, and then 5 min at 95 °C before PCR. After that, Phusion High-Fidelity DNA polymerase, Universal PCR primers, and Index (X) primer were used to carry out PCR. Finally, the PCR products were purified using the AMPure XP system, and the Agilent 5400 system (Agilent USA) was used to evaluate the library quality and quantify the results using QPCR (1.5 nM). The qualified libraries were pooled and sequenced using PE150 technique on Illumina platforms in Novogene Bioinformatics Technology Co., Ltd (Beijing, China), according to effective library concentration and necessary data amount.

value: hESC

value: ectoderm


title: dCas13b_ROBO1 rep2

description:
Library name: dCas13b_ROBO1 rep2
the column 'dCas13b_ROBO1_rep2'
dCas13b_count_matix.csv


title: Mlei_ChIP_H3

value: H3, Abcam ab1791


title: Histone PTM library, 2rep

city: Baltimore

first: Taekjip

last: Ha

state: Maryland

address: 3400 N. Charles Street

institute: Johns Hopkins University

description:
Library name: PTMlib_2rep
Synthetic PTM library experiment

data_processing:
Bowtie2 alignment
Coverage and read counts were computed using custom python scripts
Nucleosome peak calling using custom python scripts
Condensabilities for each genomic bins and each nucleosomes were computed
Assembly: hg38 (Human), mm10 (Mouse)
Supplementary files format and content: Condensability scores for 10kb, 1kb genomic bins and individual nucleosome resolution
Library strategy: Condense-seq

source_name: synthetic construct

extract_protocol:
DNA library were prepared using NEBNext Ultra II kit
Condense-seq

treatment_protocol: Native nuclesomes were purified from cells using HAP (hydroxy apartite purification) protocol and genomic DNA were purified by phenol chloroform extraction

value: synthetic construct


title: Histone PTM library, 13ep

description:
Library name: PTMlib_3rep
Synthetic PTM library experiment


title: dCas13b_Ctrl rep2

description:
Library name: dCas13b_Ctrl rep2
the column 'dCas13b_Ctrl_rep2'
dCas13b_count_matix.csv


title: Histone PTM library, 1rep

description:
Library name: PTMlib_1rep
Synthetic PTM library experiment


title: dCas13b_Ctrl rep1

description:
Library name: dCas13b_Ctrl rep1
the column 'dCas13b_Ctrl_rep1'
dCas13b_count_matix.csv


title: ARPE-19 infected 144hpi rep3

city: Chicago

first: Adam

last: Oberstein

state: IL

address: 835 South Wolcott Ave.

department: Microbiology and Immunology

institute: University of Illinois

description:
Library name: OBE082120-048_S432_L004
Sample S432 in GeTMM_allData_TMM_expValues_rpkm.tab

data_processing:
A concatenated human/HCMV transcripts file was created for mapping and feature counting by combining sequences and annotations from gencode human genome Release 34 (GRCh38.p13) and TB40E-BAC4 (EF999921.1). HCMV long non-coding RNA's were annotated in TB40/E by querying the TB40/E genome with the corresponding sequences from HCMV strain Merlin (NC_006273.2) with tblastn.
Fastq files were pseudo-aligned to a combined homo sapiens + HCMV transcriptome and converted to pseudo-counts using Kallisto version 0.45.0
Gene-level read counts were summed from the Kallisto transcript pseudocounts using tximport. The count matrices for all runs were joined and normalized for transcript length (within sample normalization) and compositional bias (cross-sample normalization) using the GeTMM procedure (BMC Bioinformatics. 2018;19: 236. Doi:10.1186/s12859-018-2246-7) and the R-package limma.
Assembly: gencode human genome Release 34 (GRCh38.p13) and TB40E-BAC4 (EF999921.1).
Supplementary files format and content: Tab delimited text file (.tab): GeTMM_allData_TMM_expValues_rpkm.tab.This file contains TMM-normalized RPKM values. Rows are genes and columns are samples.

source_name: Retina

growth_protocol: Cells were seeded at 2e5 per well into a 24-well dish, 24 hours prior to infection. Cells were just confluent at the start of infection.  ARPE-19 cells were grown in DMEM supplemented with 10% fetal bovine serum, 1 mM sodium pyruvate, 2 mM Glutamax (Gibco), 10 mM Hepes pH 7.4, 0.1 mM MEM Non-Essential Amino Acids (Gibco), 100 units/mL Penicillin G, and 100 μg/mL Streptomycin Sulfate. MCF10A cells were cultured in DMEM supplemented with 5% horse serum, 10 mM Hepes pH 7.4, 20 ng/ml EGF, 10 ug/ml Insulin, 1 nM Forskolin, 500 ng/ml Hydrocortisone, 100 units/ml Penicillin G, and 100 μg/ml Streptomycin Sulfate.

extract_protocol:
Total RNA was isolated using RNAeasy columns (Qiagen) and treated with Turbo Dnase (Thermo) prior to library preparation.
RNA was quantified and quality-controlled using an Agilent TapeStation 4200. Sequencing libraries were prepared by the UIC College of Medicine Genomics Research Core Facility using a CORALL Total RNA-seq Kit with Ribosomal RNA depletion (Lexogen) and sequenced on an Illumina NovaSeq DNA sequencer in paired-end, rapid mode (50 bp x 2).

treatment_protocol: Control wells were counted just prior to infection, to determine the volume of virus to add to cells at the indicated multiplicities. The medium on the cells was changed to 0.7 mL complete medium and vius was added to the cell medium. For mocks, virus resuspension medium (PBS containing 7% sucrose and 1% BSA) was added to the cell medium. Virus was allowed to adsorb onto the cell monolayers for 2h in a standard tissue culture incubator, with gentle tapping every 30 minutes. At 2 hpi, cells were washed one time with warm PBS before returning to complete medium (2.0 mL per well). At the indicated time points, the medium was aspirated, the cell monolayer were scraped into 1 mL trizol, and lysates were frozen at -80C to coordinate samples for RNA isolation.

value: Retina

value: Epithelial (Phenotypically mesenychmal)

value: HCMV-infected

tag: batch


title: ARPE-19 infected 24hpi rep2

description:
Library name: OBE082120-035_S419_L004
Sample S419 in GeTMM_allData_TMM_expValues_rpkm.tab


title: Mlei_ATAC

data_processing:
Raw reads were filtered and trimmed with Trimmomtic (version 0.39) before mapping to the genome with bwa mem (version 0.7.17).
Duplicated reads were marked with bamsormadup from biobambam2 (https://github.com/gt1/biobambam2)
Aligned reads were filtered with deeptools alignmentSieve  and shifted with -ATACshift, which corresponds to mate reads being shifted +4 bp and -5 bp for positive and negative strands, respectively. To generate nucleosome-position data tracks, nucleosome-free and nucleosome-bound regions were defined using the following length thresholds 0 – 120 bp and 150 – 240 bp, respectively.
ATAC peaks were called with MACS2.
Assembly: Capsaspora owzarzaki genome assembly Cowc_v2, Mnemiopsis leidyi genome assembly Mlei_v1
Supplementary files format and content: BigWig with ATAC-seq nucleosome-free read coverage

growth_protocol: Mnemiopsis leidyi specimens were kept in artificial sea water (Red Sea, R11055) with salinity 27 ppt at 21 ºC. For experiments we used adult lobate animals that were starved for 2 days. Ephydatia muelleri sponge gemmules were hatched and grown for one week in Strekal’s media.

extract_protocol:
Two M. leidyi adult specimens were dissociated using CMFSW with 0.25% α-Chymotrypsin (Sigma-Aldrich, C8946). To isolate nuclei, dissociated cells were transferred into cold hypotonic ATAC lysis buffer adjusted for marine animals (10 mM Tris-HCl (pH 7.5), 35 mM NaCl, 3 mM MgCl2, 0,1% Tween-20, 0.01% NP-40, 0.01% digitonin, 70 µM Pitstop (Abcam, AB1206875MG)). Cell lysis was stopped after 2 min by adding marine ATAC wash buffer (10 mM Tris-HCl (pH 7.5), 35 mM NaCl, 3 mM MgCl2, 0,1% Tween-20, 1% BSA).  To isolate choanocytes of E. muelleri, 7 days post hatching sponges were fed with 0.5 µm fluorescent carboxylate-modified FluoSpheres (Invitrogen, F8813). After 10 min incubation, sponges were washed twice with Strekal’s media, collected and dissociated for 15 min at 28 ºC using Protease XIV (Sigma-Aldrich, P5147). Cells were pelleted at 800 g for 5 min at RT and resuspended in Strekal’s media with 2 mM EDTA (pH 8.0). Further dissociation and trituration of sponge tissue continued for additional 15 min at RT. Cells were filtered through 40 µm cell strainer, stained with 2 µg/ml Hoechst 33342, and FACS sorted.
ATAC-seq libraries were prepared using Omni-ATAC protocol as described in Corces et al. 2017 (PMID: 28846090).


title: Mlei_ChIP_H3K4me2

value: H3K4me2, Abcam ab32356


title: ARPE-19 infected 144hpi rep2

description:
Library name: OBE082120-047_S431_L004
Sample S431 in GeTMM_allData_TMM_expValues_rpkm.tab

value: WT


title: HALO_CTEP2_gDNA


title: ARPE-19 infected 96hpi rep3

description:
Library name: OBE082120-045_S429_L004
Sample S429 in GeTMM_allData_TMM_expValues_rpkm.tab


title: ARPE-19 infected 96hpi rep2

description:
Library name: OBE082120-044_S428_L004
Sample S428 in GeTMM_allData_TMM_expValues_rpkm.tab


title: ARPE-19 infected 144hpi rep1

description:
Library name: OBE082120-046_S430_L004
Sample S430 in GeTMM_allData_TMM_expValues_rpkm.tab


title: ARPE-19 infected 6hpi rep1

description:
Library name: OBE082120-028_S412_L004
Sample S412 in GeTMM_allData_TMM_expValues_rpkm.tab


title: ARPE-19 infected 96hpi rep1

description:
Library name: OBE082120-043_S427_L004
Sample S427 in GeTMM_allData_TMM_expValues_rpkm.tab


title: Mlei_ChIP_H3K4me1

value: H3K4me1, Cell Signaling, 5326S


title: ARPE-19 mock 6hpi rep2

description:
Library name: OBE082120-026_S410_L004
Sample S410 in GeTMM_allData_TMM_expValues_rpkm.tab

value: Mock-infected


title: MCF10A infected 144hpi rep2

description:
Library name: OBE082120-023_S407_L004
Sample S407 in GeTMM_allData_TMM_expValues_rpkm.tab

source_name: Mammary

value: Mammary

value: Epithelial


title: ARPE-19 mock 96hpi rep3

description:
Library name: OBE082120-042_S426_L004
Sample S426 in GeTMM_allData_TMM_expValues_rpkm.tab


title: ARPE-19 mock 96hpi rep1

description:
Library name: OBE082120-040_S424_L004
Sample S424 in GeTMM_allData_TMM_expValues_rpkm.tab


title: MCF10A infected 96hpi rep3

description:
Library name: OBE082120-021_S405_L004
Sample S405 in GeTMM_allData_TMM_expValues_rpkm.tab


title: ARPE-19 mock 96hpi rep2

description:
Library name: OBE082120-041_S425_L004
Sample S425 in GeTMM_allData_TMM_expValues_rpkm.tab


title: ARPE-19 infected 48hpi rep2

description:
Library name: OBE082120-038_S422_L004
Sample S422 in GeTMM_allData_TMM_expValues_rpkm.tab


title: ARPE-19 infected 48hpi rep3

description:
Library name: OBE082120-039_S423_L004
Sample S423 in GeTMM_allData_TMM_expValues_rpkm.tab


title: ARPE-19 infected 48hpi rep1

description:
Library name: OBE082120-037_S421_L004
Sample S421 in GeTMM_allData_TMM_expValues_rpkm.tab


title: ARPE-19 infected 24hpi rep3

description:
Library name: OBE082120-036_S420_L004
Sample S420 in GeTMM_allData_TMM_expValues_rpkm.tab


title: MCF10A infected 96hpi rep1

description:
Library name: OBE082120-019_S403_L004
Sample S403 in GeTMM_allData_TMM_expValues_rpkm.tab


title: MCF10A mock 96hpi rep3

description:
Library name: OBE082120-018_S402_L004
Sample S402 in GeTMM_allData_TMM_expValues_rpkm.tab


title: ARPE-19 infected 12hpi rep3

description:
Library name: OBE082120-033_S417_L004
Sample S417 in GeTMM_allData_TMM_expValues_rpkm.tab


title: ARPE-19 mock 6hpi rep3

description:
Library name: OBE082120-027_S411_L004
Sample S411 in GeTMM_allData_TMM_expValues_rpkm.tab


title: ARPE-19 infected 24hpi rep1

description:
Library name: OBE082120-034_S418_L004
Sample S418 in GeTMM_allData_TMM_expValues_rpkm.tab


title: MCF10A infected 48hpi rep1

description:
Library name: OBE082120-013_S397_L004
Sample S397 in GeTMM_allData_TMM_expValues_rpkm.tab


title: ARPE-19 infected 12hpi rep2

description:
Library name: OBE082120-032_S416_L004
Sample S416 in GeTMM_allData_TMM_expValues_rpkm.tab


title: MCF10A mock 96hpi rep2

description:
Library name: OBE082120-017_S401_L004
Sample S401 in GeTMM_allData_TMM_expValues_rpkm.tab


title: ARPE-19 infected 12hpi rep1

description:
Library name: OBE082120-031_S415_L004
Sample S415 in GeTMM_allData_TMM_expValues_rpkm.tab


title: ARPE-19 infected 6hpi rep3

description:
Library name: OBE082120-030_S414_L004
Sample S414 in GeTMM_allData_TMM_expValues_rpkm.tab


title: MCF10A infected 24hpi rep2

description:
Library name: OBE082120-011_S395_L004
Sample S395 in GeTMM_allData_TMM_expValues_rpkm.tab


title: ARPE-19 mock 6hpi rep1

description:
Library name: OBE082120-025_S409_L004
Sample S409 in GeTMM_allData_TMM_expValues_rpkm.tab


title: ARPE-19 infected 6hpi rep2

description:
Library name: OBE082120-029_S413_L004
Sample S413 in GeTMM_allData_TMM_expValues_rpkm.tab


title: MCF10A infected 144hpi rep3

description:
Library name: OBE082120-024_S408_L004
Sample S408 in GeTMM_allData_TMM_expValues_rpkm.tab


title: MCF10A infected 6hpi rep3

description:
Library name: OBE082120-006_S390_L004
Sample S390 in GeTMM_allData_TMM_expValues_rpkm.tab


title: MCF10A mock 6hpi rep3

description:
Library name: OBE082120-003_S387_L004
Sample S387 in GeTMM_allData_TMM_expValues_rpkm.tab


title: MCF10A infected 144hpi rep1

description:
Library name: OBE082120-022_S406_L004
Sample S406 in GeTMM_allData_TMM_expValues_rpkm.tab


title: MCF10A infected 96hpi rep2

description:
Library name: OBE082120-020_S404_L004
Sample S404 in GeTMM_allData_TMM_expValues_rpkm.tab


title: MCF10A mock 96hpi rep1

description:
Library name: OBE082120-016_S400_L004
Sample S400 in GeTMM_allData_TMM_expValues_rpkm.tab


title: MCF10A infected 48hpi rep3

description:
Library name: OBE082120-015_S399_L004
Sample S399 in GeTMM_allData_TMM_expValues_rpkm.tab


title: MCF10A infected 48hpi rep2

description:
Library name: OBE082120-014_S398_L004
Sample S398 in GeTMM_allData_TMM_expValues_rpkm.tab


title: MCF10A infected 24hpi rep1

description:
Library name: OBE082120-010_S394_L004
Sample S394 in GeTMM_allData_TMM_expValues_rpkm.tab


title: MCF10A infected 24hpi rep3

description:
Library name: OBE082120-012_S396_L004
Sample S396 in GeTMM_allData_TMM_expValues_rpkm.tab


title: Patient 45 pre-treatment

city: St. Louis

first: David

last: DeNardo

state: MO

address: 660 S Euclid Ave

institute: Washington University in St. Louis

description: Library name: Pt45_Pre

data_processing:
Data were processed and aligned with BD Rhapsody WTA Analysis Pipeline (SevenBridges) using reference genome (GRCh38-PhiX-gencodev29.tar.gz).
Integrated data was analyzed using Seurat (v4). For each sample, genes expressed in less than 3 cells and cells that expressed less than 1,000 or more than 6,000 genes were excluded. Cells with greater than 15% mitochondrial RNA content were also excluded. SCTransform was used on each individual sample to normalize and scale the expression matrix against the sequence depths and percentages of mitochondrial and ribosomal genes. Variable features were calculated for every sample in the dataset independently and ranked based on the number of samples they were independently identified (SelectIntegrationFeatures). The top 3,000 variable features were then used for PCA (RunPCA). The calculated PCA embedding of each cell was then used as an input for the soft k-means clustering algorithm. Briefly, through iteration, the algorithm designated the cluster-specific centroids and cell-specific correction factors corresponding to batch effects. The correction factors were used to assign cells into clusters until the assignment was stable (RunHarmony). The first 20 PCA components were then used to refine the edge weights between any two cells based on Jaccard similarity (FindNeighbors) and were used to cluster cells through FindClusters. To characterize clusters, the FindAllMarkers function with logfold threshold = 0.25 and minimum 0.25-fold difference and MAST test were used to identify signatures alone with each cluster. Myeloid and lymphoid populations were then isolated for further downstream analysis based on their expression of CSF1R, C1QA, C1QB, FCGR3A, CD14, and CSF3R for myeloid cells and CD3E, CD8A, CD4, FOXP3, GZMA, and GZMB for lymphoid cells.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files, matrix files, and Seurat object

source_name: pancreas

extract_protocol:
Biopsies were manually minced and digested in 1x HBSS containing 2mg/mL Collagenase A (Roche) and 1x DNase I (Sigma) for 30 minutes at 37°C with stirring. Digestion was quenched with 5mL FBS (Atlanta Biologicals), filtered through 45µM filter, pelleted by centrifugation (500xg for 5 minutes), and resuspended in FACS Buffer (1% BSA solution in DPBS).
Libraries were generated according to manufacturer's instructions (BD Rhapsody Single-Cell Capture and cDNA Synthesis Analysis System, BD Biosciences).

value: pancreas


title: Patient 50 post-treatment sample 2

description: Library name: Pt50_Post_2


title: Patient 39 post-treatment sample 1

description: Library name: Pt39_Post_1


title: Patient 38 post-treatment sample 2

description: Library name: Pt38_Post_2


title: Patient 42 post-treatment

description: Library name: Pt42_Post


title: MCF10A infected 12hpi rep3

description:
Library name: OBE082120-009_S393_L004
Sample S393 in GeTMM_allData_TMM_expValues_rpkm.tab


title: MCF10A infected 6hpi rep2

description:
Library name: OBE082120-005_S389_L004
Sample S389 in GeTMM_allData_TMM_expValues_rpkm.tab


title: MCF10A infected 12hpi rep2

description:
Library name: OBE082120-008_S392_L004
Sample S392 in GeTMM_allData_TMM_expValues_rpkm.tab


title: MCF10A infected 6hpi rep1

description:
Library name: OBE082120-004_S388_L004
Sample S388 in GeTMM_allData_TMM_expValues_rpkm.tab


title: MCF10A infected 12hpi rep1

description:
Library name: OBE082120-007_S391_L004
Sample S391 in GeTMM_allData_TMM_expValues_rpkm.tab


title: Patient 51 pre-treatment

description: Library name: Pt51_Pre


title: Patient 37 post-treatment sample 2

description: Library name: Pt37_Post_2


title: Patient 51 post-treatment

description: Library name: Pt51_Post


title: MCF10A mock 6hpi rep1

description:
Library name: OBE082120-001_S385_L004
Sample S385 in GeTMM_allData_TMM_expValues_rpkm.tab


title: Patient 37 post-treatment sample 1

description: Library name: Pt37_Post_1


title: Patient 50 pre-treatment

description: Library name: Pt50_Pre


title: MCF10A mock 6hpi rep2

description:
Library name: OBE082120-002_S386_L004
Sample S386 in GeTMM_allData_TMM_expValues_rpkm.tab


title: GBM0709 cells, Control_2

first: Aidong

last: Zhou

address: Shatai North Road

department: Department of Cell Biology

institute: Southern Medical University

description:
Library name: Control Group_2
Column name in FPKMs_all_samples.txt: Control_2

data_processing:
Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1)
Hisat2 (v2.0.1) was used to index reference genome sequence.
HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

growth_protocol: GBM0709 cells were maintained under standard humidification conditions (37°C, 5% CO2) with DMEM (Gibco) supplemented by 10% fetal bovine serum (Gibco) and 1% penicillin/streptomycin (Gibco).

extract_protocol:
Total RNA of GBM0709 cells overexpressing TRAF3 was extracted using Trizol reagent (Invitrogen) and quantified at an optical density of 260 nm (Nanodrop Technology). Total RNA Library were prepared using Illumina TruSeq RNA Sample Preparation kit, and 1 μg total RNA was used for library preparation.
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

treatment_protocol: GBM0709 cells were stably transfected with TRAF3 overexpression lentivirus or the control lentivirus.

value: glioblastoma cells


title: GBM0709 cells, TRAF3 overexpressed_1

description:
Library name: TRAF3 Overexpressed Group_1
Column name in FPKMs_all_samples.txt: oeTRAF3_1


title: GBM0709 cells, TRAF3 overexpressed_2

description:
Library name: TRAF3 Overexpressed Group_2
Column name in FPKMs_all_samples.txt: oeTRAF3_2


title: GBM0709 cells, Control_1

description:
Library name: Control Group_1
Column name in FPKMs_all_samples.txt: Control_1


title: Patient 47 pre-treatment

description: Library name: Pt47_Pre


title: Patient 50 post-treatment sample 1

description: Library name: Pt50_Post_1


title: Patient 39 post-treatment sample 2

description: Library name: Pt39_Post_2


title: GM,synNCP,sp,6,2rep

description:
Library name: GM_synNCP_sp_6_2rep
Reconstituted nucleosome sample, spermine used as condensing agent


title: GM,synNCP,sp,4,2rep

description:
Library name: GM_synNCP_sp_4_2rep
Reconstituted nucleosome sample, spermine used as condensing agent


title: GM,synNCP,sp,5,2rep

description:
Library name: GM_synNCP_sp_5_2rep
Reconstituted nucleosome sample, spermine used as condensing agent


title: Patient 38 post-treatment sample 1

description: Library name: Pt38_Post_1


title: GM,synNCP,sp,1,2rep

description:
Library name: GM_synNCP_sp_1_2rep
Reconstituted nucleosome sample, spermine used as condensing agent


title: GM,NCP,sp,8,2rep

description:
Library name: GM_NCP_sp_8_2rep
Native nucleosome sample, Spermine used as condensing agent


title: GBM0709 cells, Control_3

description:
Library name: Control Group_3
Column name in FPKMs_all_samples.txt: Control_3


title: GBM0709 cells, TRAF3 overexpressed_3

description:
Library name: TRAF3 Overexpressed Group_3
Column name in FPKMs_all_samples.txt: oeTRAF3_3


title: GM,NCP,sp,3,2rep

description:
Library name: GM_NCP_sp_3_2rep
Native nucleosome sample, Spermine used as condensing agent


title: GM,synNCP,sp,7,2rep

description:
Library name: GM_synNCP_sp_7_2rep
Reconstituted nucleosome sample, spermine used as condensing agent


title: GM,synNCP,sp,3,2rep

description:
Library name: GM_synNCP_sp_3_2rep
Reconstituted nucleosome sample, spermine used as condensing agent


title: 926895

city: Munich

first: Thomas

last: Metzler

address: Trogerstr. 18

department: CEP

institute: TU Munich

data_processing:
*library strategy: Spatial Transcriptomics
Raw sequencing data were processed using bcl2fastq v2.20.0.422 to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: aligned_tissue_image.jpg: image of the aligned tissue
Supplementary files format and content: cytassist_image.tiff: image taken by the cytassist
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: spatial_enrichment.csv: table containing Moran's I value for each feature
Supplementary files format and content: tissue_hires_image.png: highres image of the tissue
Supplementary files format and content: tissue_lowres_image.png: lowres image of the tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene Ids
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange format
Supplementary files format and content: adata.h5ad: dataset containing megred spatial transcriptomic information, pathological annotations, clusters, pseudotime and scRNA integrated data of all datasets combined

extract_protocol:
Pancreata were fixed in formalin, dehydrated and embedded in Paraffin (FFPE) and 5µm sections were cut on a microtome.
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial for FFPE Gene Expression Slides & Reagent kit according to manufacterer's construction.

value: female

tag: age

value: 6 months


title: GM,synNCP,sp,9,2rep

description:
Library name: GM_synNCP_sp_9_2rep
Reconstituted nucleosome sample, spermine used as condensing agent


title: GM,synNCP,sp,8,2rep

description:
Library name: GM_synNCP_sp_8_2rep
Reconstituted nucleosome sample, spermine used as condensing agent


title: CF1038_35_3_S18

city: CHARLOTTE

first: Patricija

last: van Oosten-Hawle

state: NC

address: 9201 University City Blvd, Woodward Hall, Room 246D

department: Biological Sciences

institute: UNC Charlotte

description:
Library name: Sample 18
column name in readcounts.txt: CF1038_35_3_S18

data_processing:
WBCel235 was used as a reference genome
Assembly: WBCel235 was used as a reference genome
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Eggs were synchronized to L1 larvae overnight in M9 and 10000 larvae were grown to Day 1 adulthood on NGM seeded with OP50-1.

extract_protocol:
RNA was extracted using TriZol and then purified using the Direct-Zol RNA Miniprep kit (Zymo-research, Cambridge Biosciences). RNA quality was measured using an Agilent Technologies 2200 TapeStation. All samples had an RNA integrity number of > 9.5.
cDNA libraries were prepared from >1.5 μgs of total RNA

treatment_protocol: Day 1 adults were exposed to heat shock in a waterbath for 1hr at 35 degrees celsius and allowed to recover for 2 hours at 20 degrees celsius.

value: whole organism

tag: strain name

tag: developmental stage

value: Day 1 adult

value: 35 degrees celsius


title: CF1038_35_2_S17

description:
Library name: Sample 17
column name in readcounts.txt: CF1038_35_2_S17

tag: genotype


title: GM,synNCP,sp,2,2rep

description:
Library name: GM_synNCP_sp_2_2rep
Reconstituted nucleosome sample, spermine used as condensing agent


title: GM,synNCP,sp,0,2rep

description:
Library name: GM_synNCP_sp_0_2rep
Reconstituted nucleosome sample, spermine used as condensing agent


title: GM,NCP,sp,9,2rep

description:
Library name: GM_NCP_sp_9_2rep
Native nucleosome sample, Spermine used as condensing agent


title: GM,NCP,sp,5,2rep

description:
Library name: GM_NCP_sp_5_2rep
Native nucleosome sample, Spermine used as condensing agent


title: GM,NCP,sp,6,2rep

description:
Library name: GM_NCP_sp_6_2rep
Native nucleosome sample, Spermine used as condensing agent


title: GM,NCP,sp,2,2rep

description:
Library name: GM_NCP_sp_2_2rep
Native nucleosome sample, Spermine used as condensing agent


title: GM,NCP,sp,1,2rep

description:
Library name: GM_NCP_sp_1_2rep
Native nucleosome sample, Spermine used as condensing agent


title: 926983

tag: Sex


title: CF1038_20_1_S13

description:
Library name: Sample 13
column name in readcounts.txt: CF1038_20_1_S13

value: 20 degrees celsius


title: 38032


title: H1,DNA,HP1a,3,2rep

description:
Library name: H1_DNA_HP1a_3_2rep
Naked DNA sample, HP1-alpha  used as condensing agent


title: RB711_35_2_S11

description:
Library name: Sample 11
column name in readcounts.txt: RB711_35_2_S11


title: 926987


title: RB711_35_1_S10

description:
Library name: Sample 10
column name in readcounts.txt: RB711_35_1_S10


title: H1,DNA,HP1a,0,2rep

description:
Library name: H1_DNA_HP1a_0_2rep
Naked DNA sample, HP1-alpha  used as condensing agent


title: RB711_20_3_S9

description:
Library name: Sample 9
column name in readcounts.txt: RB711_20_3_S9


title: H1,NCP,HP1bSUV,4,2rep

description:
Library name: H1_NCP_HP1bSUV_4_2rep
Native nucleosome sample, HP1-beta/SUV39H1 used as condensing agent


title: H1,NCP,HP1bSUV,5,2rep

description:
Library name: H1_NCP_HP1bSUV_5_2rep
Native nucleosome sample, HP1-beta/SUV39H1 used as condensing agent


title: GM,NCP,sp,7,2rep

description:
Library name: GM_NCP_sp_7_2rep
Native nucleosome sample, Spermine used as condensing agent


title: GM,NCP,sp,4,2rep

description:
Library name: GM_NCP_sp_4_2rep
Native nucleosome sample, Spermine used as condensing agent


title: RB711_20_2_S8

description:
Library name: Sample 8
column name in readcounts.txt: RB711_20_2_S8


title: H1,NCP,HP1bSUV,3,2rep

description:
Library name: H1_NCP_HP1bSUV_3_2rep
Native nucleosome sample, HP1-beta/SUV39H1 used as condensing agent


title: H1,NCP,Ca,5,2rep

description:
Library name: H1_NCP_Ca_5_2rep
Native nucleosome sample, Calcium used as condensing agent


title: CF1038_35_1_S16

description:
Library name: Sample 16
column name in readcounts.txt: CF1038_35_1_S16


title: H1,NCP,HP1bSUV,2,2rep

description:
Library name: H1_NCP_HP1bSUV_2_2rep
Native nucleosome sample, HP1-beta/SUV39H1 used as condensing agent


title: H1,NCP,HP1a,0,2rep

description:
Library name: H1_NCP_HP1a_0_2rep
Native nucleosome sample, HP1-alpha  used as condensing agent


title: GM,NCP,sp,0,2rep

description:
Library name: GM_NCP_sp_0_2rep
Native nucleosome sample, Spermine used as condensing agent


title: H1,NCP,HP1bSUV,1,2rep

description:
Library name: H1_NCP_HP1bSUV_1_2rep
Native nucleosome sample, HP1-beta/SUV39H1 used as condensing agent


title: H1,NCP,Ca,0,2rep

description:
Library name: H1_NCP_Ca_0_2rep
Native nucleosome sample, Calcium used as condensing agent


title: RB711_20_1_S7

description:
Library name: Sample 7
column name in readcounts.txt: RB711_20_1_S7


title: H1,NCP,HP1a,2,2rep

description:
Library name: H1_NCP_HP1a_2_2rep
Native nucleosome sample, HP1-alpha  used as condensing agent


title: H1,NCP,PEG,6,2rep

description:
Library name: H1_NCP_PEG_6_2rep
Native nucleosome sample, PEG 8000 used as condensing agent


title: N2_20_3_S3

description:
Library name: Sample 3
column name in readcounts.txt: N2_20_3_S3

value: N2 Bristol


title: RB711_35_3_S12

description:
Library name: Sample 12
column name in readcounts.txt: RB711_35_3_S12


title: H1,NCP,PEG,0,2rep

description:
Library name: H1_NCP_PEG_0_2rep
Native nucleosome sample, PEG 8000 used as condensing agent


title: N2_35_1_S4

description:
Library name: Sample 4
column name in readcounts.txt: N2_35_1_S4


title: H1,NCP,CoH,0,2rep

description:
Library name: H1_NCP_CoH_0_2rep
Native nucleosome sample, Cobalt Hexammine used as condensing agent


title: CF1038_20_2_S14

description:
Library name: Sample 14
column name in readcounts.txt: CF1038_20_2_S14


title: H1,NCP,spd,6,2rep

description:
Library name: H1_NCP_spd_6_2rep
Native nucleosome sample, Spermidine used as condensing agent


title: H1,NCP,HP1bSUV,0,2rep

description:
Library name: H1_NCP_HP1bSUV_0_2rep
Native nucleosome sample, HP1-beta/SUV39H1 used as condensing agent


title: H1,NCP,HP1a,5,2rep

description:
Library name: H1_NCP_HP1a_5_2rep
Native nucleosome sample, HP1-alpha  used as condensing agent


title: H1,NCP,HP1a,4,2rep

description:
Library name: H1_NCP_HP1a_4_2rep
Native nucleosome sample, HP1-alpha  used as condensing agent


title: H1,NCP,HP1a,1,2rep

description:
Library name: H1_NCP_HP1a_1_2rep
Native nucleosome sample, HP1-alpha  used as condensing agent


title: CF1038_20_3_S15

description:
Library name: Sample 15
column name in readcounts.txt: CF1038_20_3_S15


title: H1,NCP,HP1a,3,2rep

description:
Library name: H1_NCP_HP1a_3_2rep
Native nucleosome sample, HP1-alpha  used as condensing agent


title: H1,NCP,sp,9,2rep

description:
Library name: H1_NCP_sp_9_2rep
Native nucleosome sample, Spermine used as condensing agent


title: H1,NCP,sp,8,2rep

description:
Library name: H1_NCP_sp_8_2rep
Native nucleosome sample, Spermine used as condensing agent


title: H1,NCP,sp,7,2rep

description:
Library name: H1_NCP_sp_7_2rep
Native nucleosome sample, Spermine used as condensing agent


title: H1,NCP,sp,5,2rep

description:
Library name: H1_NCP_sp_5_2rep
Native nucleosome sample, Spermine used as condensing agent


title: N2_35_3_S6

description:
Library name: Sample 6
column name in readcounts.txt: N2_35_3_S6


title: H1,NCP,sp,6,2rep

description:
Library name: H1_NCP_sp_6_2rep
Native nucleosome sample, Spermine used as condensing agent


title: N2_35_2_S5

description:
Library name: Sample 5
column name in readcounts.txt: N2_35_2_S5


title: N2_20_1_S1

description:
Library name: Sample 1
column name in readcounts.txt: N2_20_1_S1


title: N2_20_2_S2

description:
Library name: Sample 2
column name in readcounts.txt: N2_20_2_S2


title: GM,synNCP,sp,8,1rep

description:
Library name: GM_synNCP_sp_8_1rep
Native nucleosome sample, Spermine used as condensing agent


title: H1,NCP,sp,3,2rep

description:
Library name: H1_NCP_sp_3_2rep
Native nucleosome sample, Spermine used as condensing agent


title: GM,synNCP,sp,7,1rep

description:
Library name: GM_synNCP_sp_7_1rep
Native nucleosome sample, Spermine used as condensing agent


title: H1,NCP,sp,4,2rep

description:
Library name: H1_NCP_sp_4_2rep
Native nucleosome sample, Spermine used as condensing agent


title: H1,NCP,sp,2,2rep

description:
Library name: H1_NCP_sp_2_2rep
Native nucleosome sample, Spermine used as condensing agent


title: GM,synNCP,sp,6,1rep

description:
Library name: GM_synNCP_sp_6_1rep
Native nucleosome sample, Spermine used as condensing agent


title: GM,synNCP,sp,2,1rep

description:
Library name: GM_synNCP_sp_2_1rep
Native nucleosome sample, Spermine used as condensing agent


title: H1,NCP,sp,1,2rep

description:
Library name: H1_NCP_sp_1_2rep
Native nucleosome sample, Spermine used as condensing agent


title: H1,NCP,spd,0,2rep

description:
Library name: H1_NCP_spd_0_2rep
Native nucleosome sample, Spermidine used as condensing agent


title: H1,NCP,sp,0,2rep

description:
Library name: H1_NCP_sp_0_2rep
Native nucleosome sample, Spermine used as condensing agent


title: GM,synNCP,sp,4,1rep

description:
Library name: GM_synNCP_sp_4_1rep
Native nucleosome sample, Spermine used as condensing agent


title: GM,NCP,sp,9,1rep

description:
Library name: GM_NCP_sp_9_1rep
Native nucleosome sample, Spermine used as condensing agent


title: H1,NCP,CoH,5,2rep

description:
Library name: H1_NCP_CoH_5_2rep
Native nucleosome sample, Cobalt Hexammine used as condensing agent


title: GM,synNCP,sp,5,1rep

description:
Library name: GM_synNCP_sp_5_1rep
Native nucleosome sample, Spermine used as condensing agent


title: GM,synNCP,sp,9,1rep

description:
Library name: GM_synNCP_sp_9_1rep
Native nucleosome sample, Spermine used as condensing agent


title: smallRNA_TAF1C_1

city: ropar

first: srivatsava

last: naidu

state: punjab

address: bhara phool

department: biomedical engineering

country: India

institute: indian institute of technology ropar

data_processing:
Adaptor trimming using Trimmomatic-0.36, Contamination removal using Bowtie2 (version 2.2.4)
Read alignment to hg19 genome using HISAT2, miRDeep2 for miRNA reads alignment and piRBase for piRNA alignment
Expression estimation using cufflinks (version 2.2.1) and Randfold
Differential expression using DESeq2
miRNA target prediction using Miranda with query identity percentage of 100
Assembly: hg19
Supplementary files format and content: .txt file, content : raw read counts

source_name: BEAS-2B cell line

growth_protocol: BEAS-2B cell line cultured in LHC9 media supplemented with 10% FBS, stable cells cultured with G418 selection media

extract_protocol:
mirVana RNA isolation kit for RNA isolation
NEBNext RNA Ultra for long RNA libraries with ribo depletion, NEBNext Multiplex small RNA library prep kit for small RNA libraries

treatment_protocol: BEAS-2B cell line treated with empty vector and TAF1C vector with pCMV6 promoter, stable cells generated and maintained in selection media

value: TAF1C overexpression


title: GM,synNCP,sp,1,1rep

description:
Library name: GM_synNCP_sp_1_1rep
Native nucleosome sample, Spermine used as condensing agent


title: smallRNA_TAF1C_3


title: GM,NCP,sp,8,1rep

description:
Library name: GM_NCP_sp_8_1rep
Native nucleosome sample, Spermine used as condensing agent


title: JMC160-2-5, rep 3

city: Rochester

first: Tyler

last: Stahl

state: NY

address: 601 Elmwood Ave

institute: University of Rochester Medical Center School of Medicine and Dentistry

description: Library name: 9

data_processing:
Data Formatting bcltofastq-2.19.1
Data Cleaning FastP  0.23.2, --trim_poly_g -x --cut_window_size 4 -3 -l 35 -i ${SAMPLE}_R1.fastq.gz -I ${SAMPLE}_R2.fastq.gz -o synced_clt_${SAMPLE}_R1.fastq.gz -O synced_clt_${SAMPLE}_R2.fastq.gz -h ${SAMPLE}_fastp.html
Genome Alignment bowtie2 version 2.4.4, -x ${REF} -X 2000 -p ${CPUS} -1 synced_clt_${SAMPLE}_R1.fastq.gz -2 synced_clt_${SAMPLE}_R2.fastq.gz -S synced_clt_${SAMPLE}_bowtie.sam
Assembly: SC5314 assembly22
Supplementary files format and content: broad peak file containing chromosome, peak start, and peak end
Supplementary files format and content: narrow peak file containing chromosome, peak start, and peak end

organism: Candida albicans SC5314

growth_protocol: Three independent batches of C. albicans cells were grown in liquid YPD mediuam at 37 degree centigrade with shaking at 200 rpm.

extract_protocol: ATAC-seq libraries were prepared from aliquots of 50,000 cells using the method described in Corces et al. Briefly, cells were incubated in hypotonic buffer in the presence of digitonin, washed, centrifuged to collect permeabilized samples, and resuspended in tagmentation buffer with Tn5 transposase (Illumina, San Diego, CA). Tagmented DNA was isolated with the Qiagen MinElute Reaction Cleanup kit and a dual-indexed library was prepared by subsequent PCR with Illumina-compatible primers and purified with AMPure XP beads (Beckman Coulter, Indianapolis, IN). Library quantity and quality were assessed by Qubit and Bioanalyzer (Agilent, Santa Clara, CA) assays, respectively, and paired-end sequencing performed on an Illumina NovaSeq 6000.

treatment_protocol: No treatment was given prior to nuclei extraction and tagmentation.


title: GM,synNCP,sp,0,1rep

description:
Library name: GM_synNCP_sp_0_1rep
Native nucleosome sample, Spermine used as condensing agent


title: smallRNA_eV_1

value: Empty vector


title: smallRNA_TAF1C_2


title: genomic control

description: Library name: 10


title: smallRNA_eV_2


title: HDL090-Ile-CD8-TEM

city: New York

first: Peter

middle: A

last: Sims

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

description: mRNA

data_processing:
For scRNA-seq, we aligned the reads corresponding to each sample index to the GRCh38 genome / GENCODE v.24 transcriptome annotation with STAR v2.5.0 (23104886) after removing 3’ poly(A) tails from read 2 (anything >7 A’s) and discarding any resulting fragments < 25 nts in length.
We then constructed an address for each read with a unique, strand-specific, exonic alignment comprised of the cell-identifying barcode, unique molecular identifier (UMI) barcode, and gene identifier.
Next, we applied the algorithm described by Griffiths et al. to correct of index swapping between clusters on the Illumina flow cell (29991676). Finally, we collapsed PCR duplicates using UMIs and corrected errors in both the cell-identifying and UMI barcodes to generate an initial molecular count matrix.
To identify cell barcodes associated with cells, we used the EmptyDrops algorithm (Lun et al., Genome Biol, 2019) and then further filtered the resulting count matrix to remove cells above of the 95% confidence interval for the fraction of molecules aligned to the mitochondrial genome (possible dead cells), the fraction of molecules aligned to introns (possible nuclei), and the number of molecules per gene (filters red blood cells and other artifacts). We also pre-emptively removed cells with sufficiently low coverage that they would interfere with unsupervised clustering. To identify highly variable genes for clustering, we use the drop-out curve method previously described (Levitin et al., Mol Sys Bio, 2019), removing all cells in which fewer than three highly variable genes were detected.
For bulk RNA-seq, adapter-trimmed paired-end reads were aligned to the GRCh38 reference genome with ENSEMBL transcriptome annotation using the STAR aligner v.2.5.2b. Read quantification was performed using the featureCounts program in the Subread v.1.5.2 package.
Genome_build: GRCh38
Supplementary_files_format_and_content: InfantAdult_Tcells.scrnaseq.cts.txt: For scRNA-seq, the processed data are in a single, tab-delimited text file that contains the gene expression counts for each individual cell.
Supplementary_files_format_and_content: *.counts.txt: For each bulk RNA-seq sample, there is a tab-delimited text file containing the output of featureCounts.

source_name: Ileum

extract_protocol:
For single-cell RNA-seq, RNA was extracted and poly(A) mRNA was converted into barcoded cDNA using the 10x Genomics Chromium platform. For bulk RNA-seq, RNA was extracted using the Qiagen RNeasy Micro Kit.
Single-cell RNA-seq libraries were constructed using the 10x Genomics Single Cell Gene Expression 3' v2 chemistry for donors D363, D370, Adult Donor A, Adult Donor B, HDL049, HDL055, D381 and the 10x Genomics Single Cell Gene Expression 3' v3 chemistry for donors D457, D471, HDL082. For bulk RNA-seq, library preparation was done using the SMART-Seq® ultra-low input RNA kit (Takara bio).

treatment_protocol: For both bulk and single-cell RNA-seq, cells were dissociated from each tissue. Organ donor samples (whole lungs, intestinal blocks, spleen, blood) in saline or University of Wisconsin solution were placed on ice, transported to the laboratory, and processed within 24-36 hours of procurement. Single cell suspensions were obtained from spleen, lung, intestine, and lymph node samples using mechanical and enzymatic digestion as previously described (Thome et al., Nature Med, 2016; Sathaliyawala et al., Immunity, 2013; Granot et al, Immunity, 2017). Lymph nodes were isolated by dissection from the mesentery of intestinal blocks and the tracheobronchial tree of the lung. Isolated lymph nodes and spleen samples were placed in complete media (IMDM (Gibco, ref #12440-053) +1% PSQ (100 U/ml penicillin, 100 μg/ml streptomycin, 2 mM L-glutamine, GeminiBio, cat #c400-110) + 10% FBS (GeminiBio, cat #100-106)) and mechanically disrupted with scissors and double filtered through 100μm strainers. Suspensions were washed with wash buffer (PBS (Corning, cat #20-030-CV) + 2mM EDTA (Corning, cat #46-034-CI) + 5% FBS) followed by red blood cell lysis (ACK lysing buffer, Gibco, ref A10492-01), then resuspended in complete media. Lung parenchyma were separated from the large airways (trachea) using scissors then placed into digestion media (IMDM + Collagenase D 1mg/mL (Millipore Sigma cat# 11088882001) and + DNase 0.1mg/mL (Millipore Sigma cat# DN25-5G) on a shaker at 37⁰ for 30 minutes. Intestinal tissue was washed with sterile PBS to remove luminal contents, chopped into pieces using scissors, then placed into digestion media on a shaker at 37⁰ degrees for 30 minutes. Following incubation, lung and intestinal samples were strained and washed with wash buffer. Samples were centrifuged with resultant cell pellet diluted for mononuclear cells isolation by density gradient centrifugation (Lymphocyte Separation Medium, Corning, cat #25-072-CI) followed by resuspension in complete media. Peripheral blood mononuclear cells were isolated from blood samples by density centrifugation. For bulk RNA-seq, CD4 and CD8 TEM cells were isolated by FACS. For scRNA-seq, pan T cells were isolated by negative selection using the EasySep Human T cell Enrichment Kit (STEMCELL Technologies) and dead cells were removed using a column-based Dead Cell Removal Kit (Miltenyi). T cells were rested overnight at 37C for 16 hours in complete medium or activated with Human CD3/CD28 T cell Activator (STEMCELL) 16 37C for 16 hours prior to scRNA-seq.

value: Ileum

value: T cells

tag: age (years)

value: Male

tag: stimulation

tag: donor id

tag: cell isolation

value: CD8 Effector Memory T cells by FACS

tag: assay type

value: bulk RNA-seq


title: HDL090-Jej-CD8-TEM

description: mRNA

source_name: Jejunum

tag: tissue

value: Jejunum


title: GM,NCP,sp,7,1rep

description:
Library name: GM_NCP_sp_7_1rep
Native nucleosome sample, Spermine used as condensing agent

value: WT


title: GM,synNCP,sp,3,1rep

description:
Library name: GM_synNCP_sp_3_1rep
Native nucleosome sample, Spermine used as condensing agent


title: JMC160-2-5, rep1

description: Library name: 7


title: JMC160-2-5. rep 2

description: Library name: 8


title: GM,NCP,sp,6,1rep

description:
Library name: GM_NCP_sp_6_1rep
Native nucleosome sample, Spermine used as condensing agent


title: HDL090-Col-CD8-TEM

description: mRNA

source_name: Colon

value: Colon


title: GM,NCP,sp,5,1rep

description:
Library name: GM_NCP_sp_5_1rep
Native nucleosome sample, Spermine used as condensing agent


title: HDL081-Jej-CD8-TEM

description: mRNA


title: GM,NCP,sp,4,1rep

description:
Library name: GM_NCP_sp_4_1rep
Native nucleosome sample, Spermine used as condensing agent


title: JMC200-2-5, rep 3

description: Library name: 6


title: JMC200-2-5, rep 1

description: Library name: 4


title: HDL081-Ile-CD8-TEM

description: mRNA


title: HDL081-Col-CD8-TEM

description: mRNA


title: HDL078-Ile-CD8-TEM

description: mRNA

value: Female


title: HDL078-Lg-CD8-TEM

description: mRNA

source_name: Lung

value: Lung


title: JMC200-2-5, rep 2

description: Library name: 5


title: GM,NCP,sp,2,1rep

description:
Library name: GM_NCP_sp_2_1rep
Native nucleosome sample, Spermine used as condensing agent


title: parental control, rep 3

description: Library name: 3


title: HDL074-Col-CD8-TEM

description: mRNA


title: HDL078-Jej-CD8-TEM

description: mRNA


title: HDL073-Lg-CD8-TEM

description: mRNA


title: parental control, rep 2

description: Library name: 2


title: HDL074-Jej-CD8-TEM

description: mRNA


title: HDL074-Lg-CD8-TEM

description: mRNA


title: HDL081-Lg-CD8-TEM

description: mRNA


title: HDL073-Jej-CD8-TEM

description: mRNA


title: GM,NCP,sp,1,1rep

description:
Library name: GM_NCP_sp_1_1rep
Native nucleosome sample, Spermine used as condensing agent


title: GM,NCP,sp,0,1rep

description:
Library name: GM_NCP_sp_0_1rep
Native nucleosome sample, Spermine used as condensing agent


title: parental control, rep 1

description: Library name: 1


title: HDL073-Col-CD8-TEM

description: mRNA


title: H1,DNA,HP1a,3,1rep

description:
Library name: H1_DNA_HP1a_3_1rep
Naked DNA sample, HP1-alpha  used as condensing agent


title: GM,NCP,sp,3,1rep

description:
Library name: GM_NCP_sp_3_1rep
Native nucleosome sample, Spermine used as condensing agent


title: HDL071-Lg-CD8-TEM

description: mRNA


title: HDL071-Ile-CD8-TEM

description: mRNA


title: H1,DNA,HP1a,0,1rep

description:
Library name: H1_DNA_HP1a_0_1rep
Naked DNA sample, HP1-alpha  used as condensing agent


title: H1,NCP,HP1bSUV,5,1rep

description:
Library name: H1_NCP_HP1bSUV_5_1rep
Native nucleosome sample, HP1-beta/SUV39H1 used as condensing agent


title: HDL071-Col-CD8-TEM

description: mRNA


title: HDL069-Lg-CD8-TEM

description: mRNA


title: H1,NCP,HP1bSUV,4,1rep

description:
Library name: H1_NCP_HP1bSUV_4_1rep
Native nucleosome sample, HP1-beta/SUV39H1 used as condensing agent