title: 62224_R

city: Bar Harbor

first: Michael

last: MacLean

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: Library name: 62224_R

data_processing:
The resulting ~40 M read pairs per sample were processed following standard quality control practices and high-quality read pairs were aligned to the mouse genome (mm10) using STAR 2.7.9a (Dobin et al., 2013; Wingett and Andrews, 2018). Read pair counts per gene were summed with the featureCounts function in subread 2.0.1 (Liao et al., 2013; 2014).
Assembly: mm10

source_name: retina

extract_protocol:
Mouse eyes were harvested at 2 days following injection and retinas were freshly dissected in ice-cold PBS and frozen on dry ice and stored at -80º C prior to homogenization at the University of Rochester. Samples were shipped overnight to the Jackson Laboratory for RNA sequencing studies. Tissues were homogenized in MR1 buffer (Macherey-Nagel) using a Pellet Pestle Motor (Kimbal).  Total RNA was isolated from tissue using the NucleoMag RNA Kit (Macherey-Nagel) and the KingFisher Flex purification system (ThermoFisher) as per the manufacturer’s protocol. An additional DNase treatment was done using the RNeasy Mini kit (Qiagen). RNA concentration and quality were assessed using the Nanodrop 8000 spectrophotometer (Thermo Scientific) and the RNA 6000 Nano Assay (Agilent Technologies).
Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol. The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions. Libraries were sequenced 150 bp paired-end on an Illumina NovaSeq 6000 using the S4 Reagent Kit v1.5.

value: retina

tag: time

tag: side

value: R


title: 62224_L

status: Public on Feb 04 2026

type: SRA

country: USA

description: Library name: 62224_L

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: Sex

value: Male

tag: genotype

value: WT

tag: batch

value: L

tag: treatment

value: PBS


title: whole_blood_203824800064_R06C01

type: genomic

city: Oslo

first: Lasse

last: Pihlstrøm

address: Sognsvannsveien 20

department: Department of Neurology

country: Norway

institute: Oslo University Hospital

description: Human whole blood

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using and Illumina array scanner with standard recommended Illumina settings

data_processing:
Raw signal intensity data were imported into R using the minfi package. CpG sites with a beadcount < 3 in 5% of samples or detection p-value > 0.05 in 1% of samples were filtered out using the pfilter function in the wateRmelon package. Samples failing sex-checks, samples with low median signal intensities as flagged by the minfi getQC function and samples flagged as outliers by the wateRmelon outlyx function were filtered out. The wateRmelon dasen method was used for normalization. After mapping of methylation data to the genome we removed probes on sex chromosomes, probes  overlapping loci with known single-nucleotide polymophisms (SNPs) and probes previously reported  as cross-reactive. We removed probes showing predominantly  technical variation (ICC < 0.1), leaving 502,261 CpGs in the dataset.
Normalized average Beta using the dasen method implemented in the wateRmelon R package

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted by a commercial provider using a standard method, exact protocol unknown

tag: slide

value: N

tag: age

value: PD


title: whole_blood_203824800055_R08C01

description: Human whole blood


title: 62221_L

description: Library name: 62221_L


title: whole_blood_203824800056_R06C01

description: Human whole blood


title: whole_blood_203824800055_R04C01

description: Human whole blood

value: Female

value: CONTR


title: whole_blood_203824800055_R06C01

description: Human whole blood


title: 62221_R

description: Library name: 62221_R


title: whole_blood_203810640039_R08C01

description: Human whole blood


title: whole_blood_203824800055_R02C01

description: Human whole blood


title: whole_blood_203810640039_R06C01

description: Human whole blood


title: 61927_R

description: Library name: 61927_R


title: whole_blood_203810640039_R02C01

description: Human whole blood


title: 61926_R

description: Library name: 61926_R


title: 61924_R

description: Library name: 61924_R


title: 61926_L

description: Library name: 61926_L


title: whole_blood_203810640039_R04C01

description: Human whole blood


title: whole_blood_203810640032_R08C01

description: Human whole blood


title: whole_blood_203810640032_R04C01

description: Human whole blood


title: whole_blood_203810640032_R02C01

description: Human whole blood


title: 61765_L

description: Library name: 61765_L


title: 61722_R

description: Library name: 61722_R


title: 61927_L

description: Library name: 61927_L


title: 61924_L

description: Library name: 61924_L


title: whole_blood_203810640032_R06C01

description: Human whole blood


title: 61722_L

description: Library name: 61722_L


title: 61721_L

description: Library name: 61721_L


title: whole_blood_203829800022_R06C01

description: Human whole blood


title: 61721_R

description: Library name: 61721_R


title: 61765_R

description: Library name: 61765_R


title: whole_blood_203829800022_R04C01

description: Human whole blood


title: whole_blood_203829800022_R02C01

description: Human whole blood


title: whole_blood_203829800022_R08C01

description: Human whole blood


title: whole_blood_203824910118_R08C01

description: Human whole blood


title: whole_blood_203824910118_R04C01

description: Human whole blood


title: 61564_R

description: Library name: 61564_R


title: whole_blood_203824910118_R06C01

description: Human whole blood


title: 61720_R

description: Library name: 61720_R


title: 61719_L

description: Library name: 61719_L


title: 61564_L

description: Library name: 61564_L


title: whole_blood_203824800017_R08C01

description: Human whole blood


title: 60782_R

description: Library name: 60782_R


title: 61720_L

description: Library name: 61720_L


title: whole_blood_203824910118_R02C01

description: Human whole blood


title: 61561_L

description: Library name: 61561_L


title: whole_blood_203824800017_R04C01

description: Human whole blood


title: whole_blood_203824800017_R02C01

description: Human whole blood


title: 60782_L

description: Library name: 60782_L


title: 60781_L

description: Library name: 60781_L


title: whole_blood_203810640011_R08C01

description: Human whole blood


title: 61561_R

description: Library name: 61561_R


title: whole_blood_203810640011_R06C01

description: Human whole blood


title: 60780_L

description: Library name: 60780_L


title: 60780_R

description: Library name: 60780_R


title: whole_blood_203824800017_R06C01

description: Human whole blood


title: 60779_R

description: Library name: 60779_R


title: whole_blood_203808570006_R08C01

description: Human whole blood


title: whole_blood_203808570006_R06C01

description: Human whole blood


title: whole_blood_203808570006_R04C01

description: Human whole blood


title: 60642_L

description: Library name: 60642_L


title: 60779_L

description: Library name: 60779_L


title: whole_blood_203808570006_R02C01

description: Human whole blood


title: 60641_R

description: Library name: 60641_R


title: 60640_R

description: Library name: 60640_R


title: whole_blood_203810640011_R04C01

description: Human whole blood


title: 60639_L

description: Library name: 60639_L


title: whole_blood_203824800100_R04C01

description: Human whole blood


title: 60639_R

description: Library name: 60639_R

value: TNF


title: whole_blood_203810640011_R02C01

description: Human whole blood


title: whole_blood_203824800100_R08C01

description: Human whole blood


title: whole_blood_203824800100_R06C01

description: Human whole blood


title: whole_blood_203824800100_R02C01

description: Human whole blood


title: 60641_L

description: Library name: 60641_L


title: whole_blood_203824800092_R07C01

description: Human whole blood


title: 60637_R

description: Library name: 60637_R


title: 60638_L

description: Library name: 60638_L


title: whole_blood_203824800092_R05C01

description: Human whole blood


title: 60588_L

description: Library name: 60588_L


title: 60588_R

description: Library name: 60588_R


title: whole_blood_203824800092_R01C01

description: Human whole blood


title: 60636_L

description: Library name: 60636_L


title: whole_blood_203824800092_R03C01

description: Human whole blood


title: whole_blood_203824800080_R07C01

description: Human whole blood


title: 60587_L

description: Library name: 60587_L


title: whole_blood_203824800080_R03C01

description: Human whole blood


title: 60585_R

description: Library name: 60585_R


title: 60586_R

description: Library name: 60586_R


title: whole_blood_203824800080_R05C01

description: Human whole blood


title: 60587_R

description: Library name: 60587_R


title: whole_blood_203824800080_R01C01

description: Human whole blood


title: 60585_L

description: Library name: 60585_L


title: whole_blood_203824800079_R07C01

description: Human whole blood


title: 60637_L

description: Library name: 60637_L


title: whole_blood_203824800079_R03C01

description: Human whole blood


title: whole_blood_203824800070_R07C01

description: Human whole blood


title: 60584_R

description: Library name: 60584_R


title: whole_blood_203824800070_R05C01

description: Human whole blood


title: 60584_L

description: Library name: 60584_L


title: 60583_R

description: Library name: 60583_R


title: whole_blood_203824800079_R01C01

description: Human whole blood


title: 60580_L

description: Library name: 60580_L


title: whole_blood_203824800070_R03C01

description: Human whole blood


title: 60583_L

description: Library name: 60583_L


title: whole_blood_203824800070_R01C01

description: Human whole blood


title: 60582_R

description: Library name: 60582_R


title: whole_blood_203824800079_R05C01

description: Human whole blood


title: 60228_R

description: Library name: 60228_R


title: 60579_R

description: Library name: 60579_R


title: whole_blood_203808570038_R01C01

description: Human whole blood


title: whole_blood_203808570038_R03C01

description: Human whole blood


title: whole_blood_203808570038_R05C01

description: Human whole blood


title: whole_blood_203808570036_R07C01

description: Human whole blood


title: 60227_L

description: Library name: 60227_L


title: whole_blood_203808570036_R05C01

description: Human whole blood


title: 60220_R

description: Library name: 60220_R


title: 60219_R

description: Library name: 60219_R


title: 60217_L

description: Library name: 60217_L


title: 60216_R

description: Library name: 60216_R


title: whole_blood_203808570038_R07C01

description: Human whole blood


title: whole_blood_203808570036_R03C01

description: Human whole blood


title: whole_blood_203808570032_R05C01

description: Human whole blood


title: 60220_L

description: Library name: 60220_L


title: whole_blood_203829800018_R03C01

description: Human whole blood


title: 60216_L

description: Library name: 60216_L


title: 60215_R

description: Library name: 60215_R


title: whole_blood_203829800018_R05C01

description: Human whole blood


title: 60215_L

description: Library name: 60215_L


title: 60214_R

description: Library name: 60214_R


title: 60214_L

description: Library name: 60214_L


title: whole_blood_203808570032_R07C01

description: Human whole blood


title: whole_blood_203808570036_R01C01

description: Human whole blood


title: 60217_R

description: Library name: 60217_R


title: whole_blood_203829800018_R01C01

description: Human whole blood


title: whole_blood_203824800016_R07C01

description: Human whole blood


title: 60213_L

description: Library name: 60213_L


title: whole_blood_203808570032_R03C01

description: Human whole blood


title: whole_blood_203824800016_R05C01

description: Human whole blood


title: 60228_L

description: Library name: 60228_L


title: whole_blood_203829800018_R07C01

description: Human whole blood


title: 60212_R

description: Library name: 60212_R


title: 60213_R

description: Library name: 60213_R


title: 60212_L

description: Library name: 60212_L


title: whole_blood_203824910117_R07C01

description: Human whole blood


title: 60033_R

description: Library name: 60033_R


title: 60033_L

description: Library name: 60033_L


title: whole_blood_203824800016_R01C01

description: Human whole blood


title: whole_blood_203824910117_R03C01

description: Human whole blood


title: 60032_R

description: Library name: 60032_R

value: F


title: whole_blood_203824910117_R05C01

description: Human whole blood


title: 60032_L

description: Library name: 60032_L


title: 59896_R

description: Library name: 59896_R


title: whole_blood_203824800014_R05C01

description: Human whole blood


title: whole_blood_203824800016_R03C01

description: Human whole blood


title: 59897_L

description: Library name: 59897_L


title: whole_blood_203824910117_R01C01

description: Human whole blood


title: whole_blood_203824800014_R07C01

description: Human whole blood


title: 59897_R

description: Library name: 59897_R


title: whole_blood_203824800014_R03C01

description: Human whole blood


title: 59895_R

description: Library name: 59895_R


title: 59895_L

description: Library name: 59895_L


title: whole_blood_203824800012_R05C01

description: Human whole blood


title: whole_blood_203824800014_R01C01

description: Human whole blood


title: whole_blood_203824800012_R07C01

description: Human whole blood


title: whole_blood_203824800012_R01C01

description: Human whole blood


title: whole_blood_203824850080_R07C01

description: Human whole blood


title: whole_blood_203824850080_R06C01

description: Human whole blood


title: 59894_L

description: Library name: 59894_L


title: 59833_R

description: Library name: 59833_R


title: 59892_L

description: Library name: 59892_L


title: whole_blood_203824850080_R03C01

description: Human whole blood


title: whole_blood_203824850080_R05C01

description: Human whole blood


title: 59833_L

description: Library name: 59833_L


title: 59894_R

description: Library name: 59894_R


title: 59830_R

description: Library name: 59830_R


title: 59830_L

description: Library name: 59830_L


title: whole_blood_203824800012_R03C01

description: Human whole blood


title: whole_blood_203824850080_R04C01

description: Human whole blood


title: whole_blood_203824850080_R02C01

description: Human whole blood


title: 59738_R

description: Library name: 59738_R

value: M


title: 59737_L

description: Library name: 59737_L


title: whole_blood_203829800173_R07C01

description: Human whole blood


title: 59736_R

description: Library name: 59736_R


title: 59736_L

description: Library name: 59736_L


title: whole_blood_203829800173_R06C01

description: Human whole blood


title: whole_blood_203829800173_R08C01

description: Human whole blood


title: 59896_L

description: Library name: 59896_L


title: 59734_L

description: Library name: 59734_L


title: whole_blood_203829800173_R04C01

description: Human whole blood


title: whole_blood_203829800173_R05C01

description: Human whole blood


title: whole_blood_203824850080_R01C01

description: Human whole blood


title: 59733_L

description: Library name: 59733_L


title: 59732_R

description: Library name: 59732_R


title: 59733_R

description: Library name: 59733_R


title: 59829_L

description: Library name: 59829_L


title: 59732_L

description: Library name: 59732_L


title: whole_blood_203829800173_R02C01

description: Human whole blood


title: whole_blood_203829800173_R01C01

description: Human whole blood


title: whole_blood_203829800173_R03C01

description: Human whole blood


title: whole_blood_203829800171_R08C01

description: Human whole blood


title: 59731_L

description: Library name: 59731_L


title: whole_blood_203829800171_R06C01

description: Human whole blood


title: whole_blood_203829800171_R04C01

description: Human whole blood


title: 59712_L

description: Library name: 59712_L


title: 59730_L

description: Library name: 59730_L


title: 59712_R

description: Library name: 59712_R


title: whole_blood_203829800171_R05C01

description: Human whole blood


title: whole_blood_203829800171_R07C01

description: Human whole blood


title: whole_blood_203829800171_R03C01

description: Human whole blood


title: whole_blood_203829800171_R02C01

description: Human whole blood


title: 59709_L

description: Library name: 59709_L


title: whole_blood_203829800168_R08C01

description: Human whole blood


title: 59708_R

description: Library name: 59708_R


title: whole_blood_203829800171_R01C01

description: Human whole blood


title: 59710_L

description: Library name: 59710_L


title: whole_blood_203829800168_R07C01

description: Human whole blood


title: 59710_R

description: Library name: 59710_R


title: 59708_L

description: Library name: 59708_L


title: Sox10 KO YUMM1.1, technical replicate 1

city: Ottawa

first: Luc

last: Sabourin

state: Ontario

address: 501 Smyth Rd

department: Cancer Research

country: Canada

institute: Ottawa Hospital Research Institute

description:
Library name: sgSox10-1
MSg10_1

data_processing:
Transcript quantification was executed using Kallisto (v0.45.0) with the GRCh38 build of the transcriptome and the -b 50 bootstrap option. Following alignment, raw abundance counts were analyzed and genes with fewer than 10 counts across samples were filtered out. Differential gene expression was done using DESeq2.
Assembly: GRCm37 - mm9
Supplementary files format and content: The processed data file (.txt) contains transcript-per-million (TPM) values.

molecule: total RNA

source_name: Melanoma

extract_protocol:
Total RNA was isolated using TRIzol Reagent (Invitrogen; 155960118) according to the manufacturers protocol. RNA was purified using the RNeasy Mini Kit (Qiagen; 74106) by following the RNA cleanup protocol with on-column DNase digestion.
polyA-enriched RNA (stranded)

value: Melanoma

tag: strain

tag: cell type

value: Braf V600E; Pten-Null; Cdkn2-Null

value: Sox10 CRISPR Knockout


title: whole_blood_203829800168_R06C01

description: Human whole blood


title: Sox10 KO YUMM1.1, technical replicate 3

description:
Library name: sgSox10-3
MSg10_3


title: whole_blood_203829800168_R05C01

description: Human whole blood


title: Sox10 KO YUMM1.1, technical replicate 2

description:
Library name: sgSox10-2
MSg10_2


title: whole_blood_203829800168_R03C01

description: Human whole blood


title: whole_blood_203939360056_R08C01

description: Human whole blood


title: whole_blood_203829800168_R01C01

description: Human whole blood


title: whole_blood_203939360056_R07C01

description: Human whole blood


title: Vemurafenib-resistant YUMM1.1, clone A, technical replicate 2

description:
Library name: ResA-2
MResA_2

value: Resistant


title: Vemurafenib-resistant YUMM1.1, clone A, technical replicate 1

description:
Library name: ResA-1
MResA_1


title: Vemurafenib-resistant YUMM1.1, clone A, technical replicate 3

description:
Library name: ResA-3
MResA_3


title: whole_blood_203829800168_R04C01

description: Human whole blood


title: whole_blood_203939360056_R05C01

description: Human whole blood


title: whole_blood_203939360056_R06C01

description: Human whole blood


title: Wildtype YUMM1.1, technical replicate 3

description:
Library name: NTC-3
MNTC_3

value: Wildtype


title: Wildtype YUMM1.1, technical replicate 1

description:
Library name: NTC-1
MNTC_1


title: Wildtype YUMM1.1, technical replicate 2

description:
Library name: NTC-2
MNTC_2


title: 59730_R

description: Library name: 59730_R

value: retina

value: R


title: whole_blood_203939360056_R04C01

description: Human whole blood

value: Male


title: whole_blood_203939360056_R02C01

description: Human whole blood


title: aorta, ApoE-KO, sST2-KO, AngII, 28 days, rep3

city: Shanghai

first: Chenfeng

last: Wang

address: West Huaihai Road

country: China

institute: Shanghai Chest Hospital

description: Library name: B5

data_processing:
The clustered, index-coded samples were sequenced on an Illumina Novaseq platform with 150 bp paired-end reads. Data processing and differential expression visualization was carried out using the R Studio (https://www.r-project.org/).
Assembly: mm39
Supplementary files format and content: gene counts file

source_name: aorta

extract_protocol:
Total RNA was extracted from cells and tissues using the TRI Reagent (Molecular Research Center, TR118), following the manufacturer's protocol.
Total RNA was used for library preparation, where mRNA was purified using poly-T oligo-attached magnetic beads and fragmented for cDNA synthesis. First-strand cDNA synthesis was carried out using random hexamer primers and M-MuLV Reverse Transcriptase. Second-strand cDNA synthesis was then performed using DNA Polymerase I and RNase H, followed by conversion of remaining overhangs to blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, adaptors with hairpin loop structures were ligated for hybridization. cDNA fragments between 370-420 bp in length were selected and purified using the AMPure XP system (Beckman Coulter). PCR amplification was performed using Phusion High-Fidelity DNA Polymerase, universal PCR primers, and an index primer. The PCR products were purified (AMPure XP system) and assessed for library quality on the Agilent Bioanalyzer 2100 system.

value: aorta


title: aorta, ApoE-KO, sST2-KO, AngII, 28 days, rep2

description: Library name: B4


title: aorta, ApoE-KO, AngII, 28 days, rep3

description: Library name: A4


title: whole_blood_203939360056_R03C01

description: Human whole blood


title: whole_blood_203824900050_R07C01

description: Human whole blood


title: aorta, ApoE-KO, AngII, 28 days, rep1

description: Library name: A1


city: Beijing

first: fengzhi

last: li

address: Bldg.3, NO.9, YIKE Rd, Zhongguancun Life Science Park, Changping District,

institute: Chinese Institute for Brain Research, Beijing

description:
Library name: neuron-P-NP4
RNA-seq of mus musculus: mouse brain cortex, Neuron_40_10

data_processing:
RNA-seq raw data were initially filtered with “FastQC” to obtain clean data after quality control. Clean data were aligned to the reference genome (Version: GRCm38) downloaded from Gencode by HISAT. Raw counts for each gene were calculated by FeatureCounts.
The expression level of detected genes was estimated by DESeq2.A volcano plot was generated by ggplot2 in R, with a cutoff of p-value less than 0.01 and the absolute value of log2 (Foldchange) more than 4, measured by DESeq2.
The heat map was generated by heatmap with the z-score of each gene. Gene Set Enrichment Analysis (GSEA) was performed using the ClusterProfiler package in R, with an adjusted p-value less than 0.05
Assembly: Hisat2 GRCm38
Supplementary files format and content: p30 cell mRNA counts.csv
Supplementary files format and content: gpx1_5fad_Mg12m_RNA.csv
Supplementary files format and content: Ast-12month mRNA counts.csv

source_name: Brain, P40

extract_protocol:
Total RNA was extracted from microglia, astrocytes or neurons using RNeasy Micro Kit (Qiagen, 74004) following the manufacturer's protocol
DNA library for sequencing was prepared following the protocol of TruePrep DNA Library Prep Kit V2

value: Brain, P40

value: neuron


title: whole_blood_203824900050_R08C01

description: Human whole blood

value: N


title: aorta, ApoE-KO, sST2-KO, AngII, 28 days, rep1

description: Library name: B2


title: whole_blood_203824900050_R01C01

description: Human whole blood

value: PD


title: whole_blood_203824900050_R02C01

description: Human whole blood


description:
Library name: neuron-P-NP3
RNA-seq of mus musculus: mouse brain cortex, Neuron_40_9


description:
Library name: neuron-P-NP2
RNA-seq of mus musculus: mouse brain cortex, Neuron_40_8


description:
Library name: neuron-P-77
RNA-seq of mus musculus: mouse brain cortex, Neuron_40_6


description:
Library name: neuron-P-NP5
RNA-seq of mus musculus: mouse brain cortex, Neuron_40_11


title: whole_blood_203939360046_R06C01

description: Human whole blood

value: CONTR


title: whole_blood_203939360056_R01C01

description: Human whole blood


title: aorta, ApoE-KO, AngII, 28 days, rep2

description: Library name: A2


description:
Library name: neuron-P-75
RNA-seq of mus musculus: mouse brain cortex, Neuron_40_4


title: whole_blood_203824900050_R04C01

description: Human whole blood


title: whole_blood_203939360046_R07C01

description: Human whole blood

value: Female


title: whole_blood_203939360046_R08C01

description: Human whole blood


description:
Library name: neuron-P-76
RNA-seq of mus musculus: mouse brain cortex, Neuron_40_5


title: whole_blood_203824900050_R06C01

description: Human whole blood


title: whole_blood_203824900050_R05C01

description: Human whole blood


description:
Library name: neuron-P-69
RNA-seq of mus musculus: mouse brain cortex, Neuron_40_3


title: whole_blood_203939360046_R03C01

description: Human whole blood


description:
Library name: astrocyte-P-A5
RNA-seq of mus musculus: mouse brain cortex, Astrocyte_40_5

value: astrocyte


description:
Library name: neuron-P-67
RNA-seq of mus musculus: mouse brain cortex, Neuron_40_2


title: whole_blood_203939360046_R02C01

description: Human whole blood


description:
Library name: neuron-P-44
RNA-seq of mus musculus: mouse brain cortex, Neuron_40_1


description:
Library name: neuron-P-NP1
RNA-seq of mus musculus: mouse brain cortex, Neuron_40_7


title: whole_blood_203939360046_R04C01

description: Human whole blood


title: whole_blood_203939360046_R01C01

description: Human whole blood


title: whole_blood_203939360046_R05C01

description: Human whole blood


description:
Library name: astrocyte-P-A4
RNA-seq of mus musculus: mouse brain cortex, Astrocyte_40_4


title: whole_blood_203939360037_R07C01

description: Human whole blood


description:
Library name: astrocyte-P-A3
RNA-seq of mus musculus: mouse brain cortex, Astrocyte_40_3


title: whole_blood_203939360037_R08C01

description: Human whole blood


description:
Library name: astrocyte-P-A2
RNA-seq of mus musculus: mouse brain cortex, Astrocyte_40_2


title: whole_blood_203939360037_R05C01

description: Human whole blood


description:
Library name: astrocyte-P-A1
RNA-seq of mus musculus: mouse brain cortex, Astrocyte_40_1


description:
Library name: microglia-P-1-1225
RNA-seq of mus musculus: mouse brain cortex, Microglia_40_2

value: microglia


title: whole_blood_203939360037_R04C01

description: Human whole blood


title: whole_blood_203939360037_R06C01

description: Human whole blood


description:
Library name: microglia-P-MP5
RNA-seq of mus musculus: mouse brain cortex, Microglia_40_4


title: whole_blood_203939360037_R03C01

description: Human whole blood


description:
Library name: microglia-P-2-1216
RNA-seq of mus musculus: mouse brain cortex, Microglia_40_3


title: whole_blood_203829800030_R08C01

description: Human whole blood


title: whole_blood_203939360037_R02C01

description: Human whole blood


description:
Library name: microglia-P-1-1216
RNA-seq of mus musculus: mouse brain cortex, Microglia_40_1


title: whole_blood_203939360037_R01C01

description: Human whole blood


title: Uninjured, P3, Rep1

city: Cambridge

first: Ragnhildur

middle: Thora

last: Karadottir

address: Puddicombe Way

country: United Kingdom

institute: Cambridge Stem Cell Institute

description:
Library name: P3_Uninj1
10x Genomics

library_source: transcriptomic single cell

data_processing:
Each scRNAseq library were mapped with cellranger v.8.0 using the default parameters.
Scanpy
optional: Cellbender or SoupX
Assembly: mm10
Supplementary files format and content: H5, or tab-separated values files and matrix files

source_name: Adult non-regenerating digit tip

extract_protocol:
Digit amputations were performed on 6-8-week-old mice as described previously.Briefly, mice were orally administered meloxicam for analgesia and anesthetized with 5% isoflurane immediately before digit tip amputation surgeries. Then, using sterile scalpels, the distal one-third of terminal phalanges 2, 3, and 4 were amputated to induce a regenerative response. For non-regenerative amputations, the distal one-third of the second phalanx was amputated. Cells were dissociated with...and were pooled from N=3-5 unique mice, centrifuged and filtered with a succession of 40µm and 30µm filter. Cell concentration was determined and resuspended to 372 cells/µL in 2% FBS in PBS.
Libraries were prepared by using Chromium Next GEM Single cell 3'mRNA v3.1 as per the company’s protocol, and sequenced on NovaSeq 6000

value: Adult non-regenerating digit tip

value: 6-8 week old

tag: diet

value: normal

tag: number of_digits

value: Control


title: whole_blood_203829800030_R04C01

description: Human whole blood


title: Uninjured, P3, Rep2

description:
Library name: P3_Uninj2
10x Genomics


title: whole_blood_203829800030_R05C01

description: Human whole blood


title: Uninjured, P2, Rep2

description:
Library name: P2_Uninj2
10x Genomics

source_name: Adult regenerating digit tip

value: Adult regenerating digit tip


title: T_290719 Macrophages from microdissected tumours

city: Glasgow

first: Robin

last: Shaw

address: Switchback Road

institute: CRUK Scotland Institute

description: Library name: NoPool__7_6

data_processing:
Alignment was performed with Cell Ranger v3.1.0 against a custom transgenic reference.
Assembly: Custom transgenic reference based on GRCm38 (mouse genome and sequence for iRFP, human MYC and KRAS-G12D).
Supplementary files format and content: Tab-separated values and matrix files.

source_name: Lung

extract_protocol:
Lungs from SPC-Cre+ and SPC-Cre- KrasG12D+/-;MYC+/+ (KM) genetically engineered mice were microdissected under a stereomicroscope. For obtaining single cell suspensions of lung macrophages, microdissected tissue was incubated at 37C with agitation in RPMI with 10% FBS (without enzymatic digestion), before mashing through a 70 um filter. Before sorting, single cell suspensions were layered onto a Percoll (GE Healthcare) gradient 40/80 to eliminate debris and epithelial cells. Lung macrophages (CD64+F4/80+ cells), including both AMs SiglecF+CD11b and IMs CD64+CD11b+, were sorted using a FACSAria II cell sorter (BD).
For single-cell RNA-Seq, 40,000 cells were loaded per channel onto a Chromium Chip G using reagents from the 10x Genomics Chromium Single Cell 3′ v3 chemistry according to the manufacturer’s instructions. Libraries were constructed following the standard 10x Genomics Chromium 3 prime protocol. Library quality and fragment size distributions were evaluated using the Agilent Bioanalyzer High Sensitivity DNA kit. The prepared scRNA-seq libraries were then sequenced on an Illumina NovaSeq 6000 platform using paired-end 150 bp reads.

value: Lung

value: Macrophages

value: SPC-Cre+ KM


title: Tissue cells from the infected joint

city: Omaha

first: Prabhakar

last: Arumugam

state: Nebraska

address: 985900 Nebraska Medical Center

department: Department of Pathology, Microbiology and Immunology

institute: University of Nebraska Medical Center

description:
Library name: Tissue cells from the infected joint
10x Genomics

data_processing:
The demultiplexing, barcode processing, and gene counting were done using 10X Genomics Cell Ranger ().
Partek Genomics Suite was used for annotation, clustering and differential expression analysis.
Assembly: Mouse (GRCm39) 2024-A
Supplementary files format and content: CellRanger output files: Sample1_barcodes.tsv.gz, Sample1_features.tsv.gz, Sample1_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: Sample2_barcodes.tsv.gz, Sample2_features.tsv.gz, Sampl2_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: Sample3_barcodes.tsv.gz, Sample3_features.tsv.gz, Sample3_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: Sample4_barcodes.tsv.gz, Sample4_features.tsv.gz, Sample4_matrix.mtx.gz

source_name: Tissue surrounding the infected knee

extract_protocol:
Infected knee tissues were homogenized in phosphate-buffered saline (PBS) to generate a single-cell suspension. Cells were stained with Zombie Live/Dead dye and CD45-APC for 30 minutes at 4 °C, followed by washing and resuspension in PBS supplemented with 10% fetal bovine serum (FBS). Live CD45⁺ cells were sorted using a FACSAria cell sorter and subsequently resuspended in PBS containing 10% FBS.
Library was prepared using a GEM-X Universal 3' Gene Expression v4 4-plex kit (10x Genomics) according to the manufacturer's instruction.

treatment_protocol: Mice with Staphylococcus aureus prosthetic joint infection

value: Tissue surrounding the infected knee

value: CD45-positive Leukocytes

value: 6-8 weeks old

value: S. aureus LAC-13C

tag: mouse strain


title: Uninjured, P2, Rep1

description:
Library name: P2_Uninj1
10x Genomics


title: whole_blood_203829800030_R03C01

description: Human whole blood

value: N

value: Male

value: PD


title: FFT_290719 Macrophages from microdissected tumour-distant tissue

description: Library name: NoPool__7_5


title: whole_blood_203829800030_R07C01

description: Human whole blood

value: Female

value: CONTR


title: whole_blood_203829800030_R06C01

description: Human whole blood


title: Uninjured, P2, Rep3

description:
Library name: P2_Uninj3
10x Genomics


title: whole_blood_203829800030_R01C01

description: Human whole blood


title: whole_blood_203829800128_R08C01

description: Human whole blood


title: N1_290719 Macrophages from tumour-free lungs

description: Library name: NoPool__7_3

value: KM


title: N2_290719 Macrophages from tumour-free lungs

description: Library name: NoPool__7_4


title: whole_blood_203829800128_R07C01

description: Human whole blood


title: whole_blood_203829800128_R05C01

description: Human whole blood


title: whole_blood_203829800128_R04C01

description: Human whole blood


title: whole_blood_203829800128_R03C01

description: Human whole blood


title: whole_blood_203829800030_R02C01

description: Human whole blood


title: T_260619 Macrophages from microdissected tumours

description: Library name: NoPool__7_1


title: rep2, 24hr, input

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description: Library name: Rep2_24hr_input

library_source: genomic

data_processing:
RELACS ChIP-Seq, 100 bp paired-end
Data were processed using the snakePipes DNA-mapping and ChIP–seq pipelines (version 3.1.0) with parameters  --dedup --mapq 1
Assembly: mm10
Supplementary files format and content: bigWigs, broadPeaks (except for input samples)

growth_protocol: INTS11-degron mESCs (E14) were cultured on gelatin-coated dishes in High Glucose DMEM (Sigma) supplemented with 15% FBS (Gibco), 2 mM L-glutamine (Sigma), 1x non-essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), 100 U/mL penicillin-streptomycin, 0.1 mM 2-mercaptoethanol (Gibco), 1000 U/ml mouse recombinant LIF (Stemcell, 78056) and 10 µM Trimethoprim (Cayman Chemical, 16473).

extract_protocol:
ChIP sequencing was performed by the Deep Sequencing unit of the MPI-IE using the RELACS nuclei barcoding protocol. INTS11-degron mESCs (E14) were fixed by double cross-linking (2 mM DSG and 1% formaldehyde), snap-frozen in liquid nitrogen and stored at -150°C.
Digested chromatin inside nuclei is end-repaired and A-tailed using end-repair and A-tailing components from NEBNext Ultra II DNA library preparation kit (E7645L, NEB) with the following modifications: 1.5 µL of end prep enzyme mix and 3.5 µL of reaction buffer are added to each 25 µL digested nuclei aliquot. Samples are mixed and incubated at 20 °C for 30 min followed by heat inactivation at 65 °C for 5 min. 1.2 µL of hairpin adapter nuclear barcodes is added to each sample. Ligation of barcodes to A-tailed chromatin is performed using components from NEBNext Ultra II DNA library preparation kit, with the following modifications: per sample 15 µL of ligation master mix and 0.5 µL of ligation enhancer is added, followed by 15 min incubation at 30 °C and 15 min incubation at 20 °C. Libraries with insert of 200-1000 bp were generated. The average library size is approximately 300-400 bp. Libraries were sequenced paired-end with a read length of 100 bp on the Illumina NovaSeq 6000 instrument.

treatment_protocol: For INTS11-degron depletion, cells were washed twice with PBS to remove Trimethoprim and then cultivated in fresh ESC medium that contained DMSO (1 µL/ml).

tag: cell line

value: mouse embryonic stem cells

value: INTS11-degron depletion for 24 hrs

value: INTS11-degron depletion


title: rep2, 24hr, HP1 IP

description: Library name: Rep2_24hr_HP1 IP


title: whole_blood_203829800128_R01C01

description: Human whole blood


title: rep1, 24hr, HP1 IP

description: Library name: Rep1_24hr_HP1 IP


title: rep2, 0hr, HP1 IP

description: Library name: Rep2_0hr_HP1 IP

value: INTS11-degron without depletion

value: untreated


title: rep1, 24hr, input

description: Library name: Rep1_24hr_input


title: rep2, 0hr, input

description: Library name: Rep2_0hr_input


title: FFT_260619 Macrophages from microdissected tumour-distant tissue

description: Library name: NoPool__7_2

value: Lung

value: Macrophages


title: whole_blood_203829800128_R06C01

description: Human whole blood


title: whole_blood_203824900021_R05C01

description: Human whole blood


title: whole_blood_203824900021_R06C01

description: Human whole blood


title: rep1, 0hr, input

description: Library name: Rep1_0hr_input


title: whole_blood_203824900021_R07C01

description: Human whole blood


title: whole_blood_203829800128_R02C01

description: Human whole blood


title: rep1, 0hr, HP1 IP

description: Library name: Rep1_0hr_HP1 IP


title: whole_blood_203824900021_R08C01

description: Human whole blood


title: rep2, 24hr, H3K9me3 IP

description: Library name: Rep2_24hr_H3K9me3 IP


title: rep2, 0hr, H3K9me3 IP

description: Library name: Rep2_0hr_H3K9me3 IP


title: rep1, 24hr, H3K9me3 IP

description: Library name: Rep1_24hr_H3K9me3 IP


title: whole_blood_203824900021_R02C01

description: Human whole blood


title: whole_blood_203824900021_R04C01

description: Human whole blood


title: whole_blood_203824900021_R01C01

description: Human whole blood


title: whole_blood_203824900019_R08C01

description: Human whole blood


title: rep1, 0hr, H3K9me3 IP

description: Library name: Rep1_0hr_H3K9me3 IP


title: whole_blood_203824900021_R03C01

description: Human whole blood


title: whole_blood_203824900019_R07C01

description: Human whole blood


title: whole_blood_203824900019_R05C01

description: Human whole blood


title: whole_blood_203824900019_R02C01

description: Human whole blood


title: whole_blood_203824900019_R06C01

description: Human whole blood


title: Mitochondria-transferred  G-MDSC, Unstimulated, biol rep 3

description:
Library name: Sample 9
Column name in Normalized_counts.txt: 1_1_MDSC_US_3

data_processing:
Partek Genomics Suite
Sequence reads were trimmed for adaptor sequence and Phred score less than 35 using Partek Genomics Suite
Trimmed sequence reads were aligned to mm10 using STAR-2.7.8a
The aligned reads were quantified and normalized using Partek E/M
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized read counts for each sample

source_name: Bone marrow derived G-MDSC

growth_protocol: Bone marrow cells were cultured in RPMI supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 10 mM HEPES, 1x antimycotic/antibiotic, 50 µM β-mercaptoethanol, G-CSF, and GM-CSF (40 ng/mL each) for 3 days, whereupon IL-6 (40 ng/mL) was added at day 3. At day 4, G-MDSCs were isolated using anti-mouse Ly6G microbeads (Miltenyi Biotec).

extract_protocol:
Total RNA was extracted using Quick-RNA Microprep Kit (Zymo Research). 10 ng of total RNA was used to prepare cDNA using the SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio).
cDNA libraries were prepared using Nextera XT DNA Library Prep Kit (Illumina).

treatment_protocol: Control and mitochondria-transferred G-MDSCs were either co-cultured with Staphylococcus aureus biofilm or unstimulated for 2 h.

value: Bone marrow derived G-MDSC

value: Unstimulated


title: Mitochondria-transferred  G-MDSC, Biofilm, biol rep 2

description:
Library name: Sample 11
Column name in Normalized_counts.txt: 1_1_MDSC_BF_2

value: S. aureus Biofilm


title: Mitochondria-transferred  G-MDSC, Biofilm, biol rep 1

description:
Library name: Sample 10
Column name in Normalized_counts.txt: 1_1_MDSC_BF_1


title: whole_blood_203824900019_R01C01

description: Human whole blood


title: whole_blood_203824850083_R07C01

description: Human whole blood


title: Mitochondria-transferred  G-MDSC, Unstimulated, biol rep 2

description:
Library name: Sample 8
Column name in Normalized_counts.txt: 1_1_MDSC_US_2


title: whole_blood_203824850083_R06C01

description: Human whole blood


title: whole_blood_203824850083_R03C01

description: Human whole blood


title: Mitochondria-transferred  G-MDSC, Biofilm, biol rep 3

description:
Library name: Sample 12
Column name in Normalized_counts.txt: 1_1_MDSC_BF_3


title: Control G-MDSC, Biofilm, biol rep 3

description:
Library name: Sample 6
Column name in Normalized_counts.txt: MDSC_BF_3


title: whole_blood_203824850083_R04C01

description: Human whole blood


title: Mitochondria-transferred  G-MDSC, Unstimulated, biol rep 1

description:
Library name: Sample 7
Column name in Normalized_counts.txt: 1_1_MDSC_US_1


title: Control G-MDSC, Biofilm, biol rep 1

description:
Library name: Sample 4
Column name in Normalized_counts.txt: MDSC_BF_1


title: whole_blood_203824850083_R05C01

description: Human whole blood


title: Control G-MDSC, Biofilm, biol rep 2

description:
Library name: Sample 5
Column name in Normalized_counts.txt: MDSC_BF_2


title: whole_blood_203824850083_R01C01

description: Human whole blood


title: whole_blood_203824840064_R08C01

description: Human whole blood


title: whole_blood_203824840064_R07C01

description: Human whole blood


title: Control G-MDSC, Unstimulated, biol rep 3

description:
Library name: Sample 3
Column name in Normalized_counts.txt: MDSC_US_3


title: Control G-MDSC, Unstimulated, biol rep 1

description:
Library name: Sample 1
Column name in Normalized_counts.txt: MDSC_US_1


title: whole_blood_203824840064_R05C01

description: Human whole blood


title: Control G-MDSC, Unstimulated, biol rep 2

description:
Library name: Sample 2
Column name in Normalized_counts.txt: MDSC_US_2


title: whole_blood_203824840064_R04C01

description: Human whole blood


title: rep2, mESCs, input

description:
Library name: INPUT_rep2
RELACS ChIP-Seq, 100 bp paired-end

data_processing:
Data were processed using the snakePipes DNA-mapping and ChIP–seq pipelines (version 3.1.0) with parameters  --dedup --mapq 1
Assembly: mm10
Supplementary files format and content: broad peaks, bigwigs

growth_protocol: Wild type (WT26) mouse embryonic stem cells (mESC) (129/Sv x C57Bl/6J, male) and Suv39h double-null (DN57) mESC (129/Sv x C57Bl/6J, male) were generated as previously described61. WT26 and DN57 mESC were cultured on gelatin-coated dishes in High Glucose DMEM (Sigma) supplemented with 15% serum replacement (Thermo Fisher), 2 mM L-glutamine (Sigma), 1x non-essential amino acids (Sigma), 1 mM sodium pyruvate (Sigma), 0.1 mM 2-mercaptoethanol (Gibco), and 1 ml supernatant (per 500 ml medium) from LIF-producing COS-7 cells (in-house production). Cells were cultured at 37°C in 5% CO2 and were routinely verified to be mycoplasma free.

extract_protocol:
ChIP sequencing was performed by the Deep Sequencing unit of the MPI-IE using the RELACS nuclei barcoding protocol. WT26 mESCs were fixed by double cross-linking (2 mM DSG and 1% formaldehyde), snap-frozen in liquid nitrogen and stored at -150°C.
Digested chromatin inside nuclei is end-repaired and A-tailed using end-repair and A-tailing components from NEBNext Ultra II DNA library preparation kit (E7645L, NEB) with the following modifications: 1.5 µL of end prep enzyme mix and 3.5 µL of reaction buffer are added to each 25 µL digested nuclei aliquot. Samples are mixed and incubated at 20 °C for 30 min followed by heat inactivation at 65 °C for 5 min. 1.2 µL of hairpin adapter nuclear barcodes is added to each sample. Ligation of barcodes to A-tailed chromatin is performed using components from NEBNext Ultra II DNA library preparation kit, with the following modifications: per sample 15 µL of ligation master mix and 0.5 µL of ligation enhancer is added, followed by 15 min incubation at 30 °C and 15 min incubation at 20 °C. Libraries with insert of 200-1000 bp were generated. The average library size is approximately 300-400 bp. Libraries were sequenced paired-end with a read length of 100 bp on the Illumina NovaSeq 6000 instrument.

treatment_protocol: Wild type mESCs, no treatment.


title: rep2, mESCs, INTS11 IP

description:
Library name: INTS11_rep2
RELACS ChIP-Seq, 100 bp paired-end


title: whole_blood_203824840064_R01C01

description: Human whole blood


title: rep1, mESCs, INTS11 IP

description:
Library name: INTS11_rep1
RELACS ChIP-Seq, 100 bp paired-end


title: rep1, mESCs, input

description:
Library name: INPUT_rep1
RELACS ChIP-Seq, 100 bp paired-end


title: whole_blood_203824840064_R06C01

description: Human whole blood


title: whole_blood_203824900059_R08C01

description: Human whole blood


title: M3

city: Hangzhou

first: Yuepeng

last: Jiang

address: binwen road

institute: zhejiang chinese medical university

description: Library name: sample6

data_processing:
Raw sequencing data was first filtered by fastp (version 0.23.1), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean reads were mapped to the reference genome of Homo sapiens using bowtie2 (version 2.2.6) with default parameters.
Sambamba (version 0.7.1) is used for sam/bam format conversion and PCR duplicate reads removal. The RSeQC (version 2.6) was used for reads distribution analysis. The insert length was counted by Collect Insert Size Metrics tools from picard software (version 2.8.2). DeepTools (version 2.4.1) was used to visualize the distribution of reads on upstream and downstream of TSS. The MACS2 software (Version 2.2.7.1) was used for peak calling.
The bedtools (version 2.30.0) was used for peaks annotation and peak distribution analysis. The different peaks were identified by csaw (version 1.24.3). The Homer (version 4.10) was used for motifs analysis.
Assembly: mm39
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: CD4+T cell

extract_protocol:
A total of 50,000 cells were subject to the CUT&Tag assay performed by SeqHealth (Wuhan, China) using a commercial kit (Vazyme, China, TD903) according to the manufacturer's protocol. Briefly, cells were incubated with Concanavalin A-coated magnetic beads. Subsequently, anti-NFATC2 or IgG control antibody were added, and the cells were incubated on a nutator overnight at 4℃. After that, secondary antibody was performed on a nutator for 1h at room temperature followed by incubation with hyperactive pG-Tn5 transposonase. After transposon activation and tagmentation, DNA was extracted, amplified, and purified to construct library.
To amplify libraries, 21μL DNA was mixed with 2μL of a universal i5 and auniquely barcoded i7 primer. A volume of 25 μL NEBNext HiFi 2× PCR Master mix was added and mixed. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and hold at 8 °C. libraried clean-up was performed XP beads (Beckman Counter).

value: CD4+T cell


title: M2

description: Library name: sample5


title: whole_blood_203824900059_R06C01

description: Human whole blood

value: N


title: whole_blood_203824900059_R05C01

description: Human whole blood

value: Male


title: M1

description: Library name: sample4


title: C2

description: Library name: sample2


title: whole_blood_203829800052_R08C01

description: Human whole blood

value: PD


title: CMO multiplexing library on WT and Hox-/- gastruloids at various stages

city: Paris

first: Hocine

last: Rekaik

address: 11, Place Marcelin Berthelot

department: CIRB

country: France

institute: College de France

description: Library name: HoxLess_CellPlex_4_CMO

library_source: other

data_processing:
All scripts are in https://github.com/hrekaik/scriptsForRekaikEtAl2025.
Mapping and demultiplexing of cell barcode were performed using RNA STARSolo v2.7.10b against the mouse reference genome mm10 and a motified gtf file based on Ensembl 102 (doi:zenodo.org/doi/10.5281/zenodo.10079672) with the following parameters --soloBarcodeReadLength 1 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 12 -- soloStrand Forward --soloFeatures Gene --soloUMIdedup 1MM_CR --soloUMIfiltering - --quantMode TranscriptomeSAM GeneCounts --outSAMattributes NH HI AS nM GX GN CB UB --outSAMtype BAM SortedByCoordinate --soloCellFilter None --soloOutFormatFeaturesGeneField3 'GeneExpression' --outSAMunmapped None --outSAMmapqUnique 60 --limitOutSJoneRead 1000 --limitOutSJcollapsed 1000000  --limitSjdbInsertNsj 1000000.Then the matrices have been filtered with DropletUtils version 1.10 (Method EmptyDrops, lower-bound threshold = 100, FDR threshold = 0.01).
Samples demultiplexing was performed using CITE-seq-Count v1.4.4 --cell_bacode_first_base 1 --cell_barcode_last_base 16 --umi_first_base 17 --umi_last_base 28 --bc_collapsing_dist 1 --umi_collapsing_dist 2 --expected_cells 24000 --whitelist '3M-february-2018.txt' --max-error 2. Subsequently the cell barcodes were translated to match the one from the gene expression. Each gene–cell count matrix was then analyzed using Seurat v5.1.0. A Seurat object was generated by filtering out barcodes with less than 200 identified gene and genes identified in less than three cells. Then, the demultiplexing from the translated CMO matrices was performed: any cell barcode with less than 5 CMO UMI was excluded as well as any cell barcode absent from the Seurat object.  Sample attribution was performed with demuxmix using the total number of gene expression UMI per cell. Then, further filtering was applied to remove low-quality cells and doublets. For each dataset, the mean RNA count was used, and cells with either less than 40% of the mean or more than 2.5-fold of the mean were removed. In addition, cells with more than 8% or less than 0.05% mitochondrial counts were removed. Then, all individual datasets were merged into a single Seurat object. The combined dataset was then normalized and, the 2,000 most variable features were identified and data scaled and regressed by cell cycle score and percentage of mitochondrial reads. Principal component analysis (PCA) was computed using variable genes falling within the 5th and 80th percentile of expression and by excludinggenes included in the regions of the deletions of the 4 Hox clusters. UMAP and k-nearest neighbours were then computed using 30 principal components. Clusters were computed at a resolution of 1.5 in order to identify the NMP population. Clusters with similar identities (using known gene markers) were then manually grouped together. For the differential gene expression analysis, the function FindMarkers from Seurat was used and the thresholds were set to adjusted p-value below 0.01 and absolute log2 fold-change above 1.5. For RNA velocity, velocyto v0.17.17 was used to pre-processes datasets and generate loom files. scVelo v1.10.2 was used to estimate and project RNA velocity and compute the pseudotime. The velocity was computed once for the whole dataset in order to sort cells by pseudotime in the heatmap. In order to compare the dataset to a single-cell atlas, matrices from E6.5 to E9.5 were downloaded from https://tome.gs.washington.edu (REF TOME). The E9.5 sample was downsampled to get only 20'000 cells. All the mouse samples were merged with the Seurat object with the gastruloids and the gene labels were unified. The cells were splitted by study (Pijuan-Sala, Cheng, Mohammed, Tome, and our study) , normalized, 2500 variable features were identified. Genes included in the regions of the deletions of the 4 Hox clusters were excluded. Data was scaled and PCA was run with 50 components. Finally all cells from all studies were integrated with the IntegrateLayers function from Seurat with CCAIntegration, recursively: ((((Pijuan-Sala with Mohammed) with Cheng) with Tome) with our study). UMAP was computed using the 30 first component of the integrated cca.
Assembly: mm10
Supplementary files format and content: tar.gz: output of STARsolo or CITE-seq-Counts (translated) as output of cellranger (genes.tsv, barcodes.tsv, matrix.mtx)
Supplementary files format and content: loom: output of velocyto
Supplementary files format and content: CMO_samples.txt.gz: tabular separated text file with for each Library (first column), the different samples (second column), with their barcodes (third column). The Pool.96h.Rep4.5 refers to GSM7890936 and GSM7890954.
Supplementary files format and content: combined_AlltimewtvsBADC_dafd6eb6.analyzed.scVelo.RDS: R object with the Seurat object with all wt and Hox-/- samples used in the study.
Supplementary files format and content: seurat.atlas.combined.E6.5-9.5.gastruloids.integrated.study.rds: R object with Seurat object with the integration of the Embryonic atlas and the samples used in this study.

molecule: other

source_name: Gastruloids

growth_protocol: For gastruloid differentiation, 300 mES cells were resuspended in 40μl of prewarmed N2B27 medium (50% DMEM/F12 and 50% Neurobasal supplemented with 0.5x N2 and 0.5x B27), and seeded into each well of a low-attachment, rounded-bottom 96-well plate. After 48h, 150µl of N2B27 medium supplemented with 3μM of GSK-3 inhibitor was added to each well. Medium was then replaced every 24h.

extract_protocol:
Control and Hox-/- gastruloid at 72h, 96h and 120h were collected, dissociated and processed.
Samples were processed following the manufacturer’s instructions of the 3' CellPlex Kit (10X Genomics). Cells were then pooled and subjected to single-cell RNA-seq using the 10x Genomics platform (V3.1 chemistry). cDNA preparations were performed according to 10X Genomics recommendations, amplified for 10–12 cycles and sequenced on a Novaseq 6000 with the cbot2 chemistry.

value: Gastruloids

tag: Stage

value: wt and Hox-/-

tag: library type

value: CMO


title: Multiplexed scRNA-seq on WT gastruloids at 120h

description: Library name: HoxLess_CellPlex_3_GEX

value: wt

value: GEX


title: CMO multiplexing library of WT gastruloids at 120h

description: Library name: HoxLess_CellPlex_3_CMO


title: whole_blood_203829800052_R07C01

description: Human whole blood


title: whole_blood_203824840064_R03C01

description: Human whole blood

value: Female

value: CONTR


title: Multiplexed scRNA-seq on WT and Hox-/- gastruloids at various stages

description: Library name: HoxLess_CellPlex_4_GEX


title: whole_blood_203824900059_R07C01

description: Human whole blood


title: whole_blood_203829800052_R06C01

description: Human whole blood


title: CMO multiplexing library of WT gastruloids at 72h

description: Library name: HoxLess_CellPlex_2_CMO


title: C3

description: Library name: sample3


title: C1

description: Library name: sample1


title: Multiplexed scRNA-seq on WT gastruloids at 72h

description: Library name: HoxLess_CellPlex_2_GEX


title: whole_blood_203824900059_R03C01

description: Human whole blood


title: whole_blood_203829800052_R02C01

description: Human whole blood


title: whole_blood_203824850034_R08C01

description: Human whole blood


title: whole_blood_203829800052_R01C01

description: Human whole blood


title: whole_blood_203824900059_R02C01

description: Human whole blood


title: Multiplexed scRNA-seq on WT gastruloids at 96h

description: Library name: HoxLess_CellPlex_1_GEX


title: whole_blood_203824900059_R04C01

description: Human whole blood


title: whole_blood_203829800052_R04C01

description: Human whole blood


title: CMO multiplexing library of WT gastruloids at 96h

description: Library name: HoxLess_CellPlex_1_CMO


title: Multiome_BADC_96h_scRNA

description: Library name: Multiome_BADC_96h_scRNA

data_processing:
All scripts are in https://github.com/hrekaik/scriptsForRekaikEtAl2025.
scRNAseq: Mapping and demultiplexing of cell barcode were performed using RNA STARSolo v2.7.10b against the mouse reference genome mm10 and a motified gtf file based on Ensembl 102 (doi:zenodo.org/doi/10.5281/zenodo.10079672) with the following parameters --soloBarcodeReadLength 1 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 12 -- soloStrand Forward --soloFeatures Gene --soloUMIdedup 1MM_CR --soloUMIfiltering - --quantMode TranscriptomeSAM GeneCounts --outSAMattributes NH HI AS nM GX GN CB UB --outSAMtype BAM SortedByCoordinate --soloCellFilter None --soloOutFormatFeaturesGeneField3 'GeneExpression' --outSAMunmapped None --outSAMmapqUnique 60 --limitOutSJoneRead 1000 --limitOutSJcollapsed 1000000  --limitSjdbInsertNsj 1000000.Then the matrices have been filtered with DropletUtils version 1.10 (Method EmptyDrops, lower-bound threshold = 100, FDR threshold = 0.01).
For scATAC data processing, first, the I2 fastq was reverse complemented with seqtk seq version 1.3.3. Then cell barcodes were added to fastq reads using Sinto barcode v0.10.1. After adapters removal with cutadapt version 4.9, mapping was performed with BWA-MEM v0.7.18 against the mouse reference genome mm10. ATAC fragments with the associated cell barcode were retrieved with Sinto fragments version 0.9.0. The barcodes were translated to match the one from the gene expression. These translated fragment files were sorted and bgzipped to be used by Signac. On the other hand, the fragment file was duplicated and attributed to the + and - strand in order to use both extremities in the peak calling. This duplicated fragment file was used to call peaks with MACS2 v 2.2.9.1 with options --format BED --gsize 1870000000 --call-summits --keep-dup all --bdg --nomodel --extsize 200 --shift -100. The peaks from wt and from Hox-/- samples were concatenated, sorted and merged with bedtools version 2.31.1 in order to create a single comprehensive peak list.
Downstream analysis was done in R with Signac. Individual chromatin assays were created using the ATAC fragment object and the comprehensive list of peaks, then added to the RNA Seurat object. wt and Hox-/- Seurat objects were then merged. The combined Seurat object was filtered to remove low quality cells using ATAC counts (below 1800 or above 100'000), RNA counts (below 1'000 and above 25'000), nucleosome signal (above 2) and TSS enrichment (below 1) values. RNA layer was normalized with SCTransform regressing the percentage of mitochondrial genes and the cell cycle. PCA was also performed on selected genes using the average expression, excluding Hox genes. For the ATAC layer, the all features with more than 5 counts were considered as top features and data normalized using the RunTFID function. The singular value decomposition (SVD) was computed with exclusion of genomic ranges spanning the deleted Hox regions. The joint neighbor graph using RNA and ATAC assays was performed with the FindMultiModalNeighbors function with the 50 first PC for SCT (RNA) and the second to fortieth for lsi (ATAC). The UMAP was computed using this 'weighted.nn' and clustering was computed using the grah 'wknn' with a resolution of 0.5. For motif analysis, chromVAR v1.26.0  was used with the JASPAR 2022 motif collection, the motifs from Berger et al. 2008, the ISMARA motif collection available at https://swissregulon.unibas.ch/data/mm10_f5/mm10_weight_matrices_v2 and the HOMER motifs.
For RNA velocity, velocyto v0.17.17 was used to pre-processes datasets and generate loom files. scVelo v1.10.2  was used to estimate and project RNA velocity and compute the pseudotime.
Assembly: mm10
Supplementary files format and content: .txt: fragment file for ATACseq generated by Sinto fragment and translated so the barcodes match the barcodes from RNAseq part
Supplementary files format and content: tar.gz: scRNAseq filtered matrix in 3 files (barcodes.tsv, genes.tsv, matrix.mtx)
Supplementary files format and content: loom: velocyto output
Supplementary files format and content: merged_peaks.bed.gz: comprehensive list of peaks
Supplementary files format and content: RDS: R seurat object with both samples

source_name: Gastruloid

extract_protocol:
Gastruloid at 96h were collected, pooled and dissociated. Nuclei isolation for the single-cell Multiome ATAC and gene expression procedure was per-formed following the manufacture’s instruction of the Chromium Nuclei Isolation Kit (10X Genomics). Dissociated cells were resuspended in cold lysis buffer and incubated for 10min on ice, then transferred to the nuclei isolation column and centrifuged at 16’000 rcf for 20sec at 4°C to re-move cellular debris. The Flowthrough was centrifuged to retrieve the nuclei pellet, then washed with cold Debris Removal Buffer and two rounds of centrifugation, and wash with cold Wash Buffer. Purified nuclei were resuspended in cold Resuspension Buffer, counted and their nuclear membrane assessed.
Samples were immediately processed according to 10X Genomics recommendations of the v1.0 Multiome ATAC + Gene Expression kit. The 10X ATAC and GEX libraries were sequenced

value: Gastruloid

value: whole gastruloid

value: Hox-/-


title: whole_blood_203824850034_R06C01

description: Human whole blood


title: whole_blood_203829800052_R05C01

description: Human whole blood


title: Multiome_wt_96h_scATAC

description: Library name: Multiome_wt_96h_scATAC

library_source: genomic single cell


title: whole_blood_203824850034_R07C01

description: Human whole blood


title: Multiome_BADC_96h_scATAC

description: Library name: Multiome_BADC_96h_scATAC


title: Multiome_wt_96h_scRNA

description: Library name: Multiome_wt_96h_scRNA


title: whole_blood_203824850034_R05C01

description: Human whole blood


title: whole_blood_203824850034_R02C01

description: Human whole blood


title: corneas, Scop_3

city: Qingdao

first: xiaoyu

state: Shandong

address: NO.5 Yanerdao Road

institute: Qingdao Eye Hospital of Shandong First Medical University

description: Library name: Sample7

data_processing:
Raw reads in fastq format were processed with fastp to remove low-quality reads, resulting in clean reads that were then mapped to the reference genome using HISAT2. Read counts were determined using HTSeq-count and gene expression levels were quantified as fragments per kilobase per million mapped reads (FPKM).
Assembly: mm10
Supplementary files format and content: csv fles include FPKM values for all samples

source_name: corneas

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug oftotal RNA was used for the construction ofsequencing libraries.
Libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme Biotech) and sequenced on an Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA) by Shanghai OE Biotech.

value: corneas

value: Scop


title: corneas, Scop_4

description: Library name: Sample8


title: corneas, Scop_2

description: Library name: Sample6


title: corneas, Scop_1

description: Library name: Sample5


title: corneas, ICI_4

description: Library name: Sample4

value: ICI


title: whole_blood_203824850034_R04C01

description: Human whole blood


title: whole_blood_203824840030_R07C01

description: Human whole blood


title: whole_blood_203824840030_R06C01

description: Human whole blood


title: whole_blood_203824840030_R08C01

description: Human whole blood


title: corneas, ICI_2

description: Library name: Sample2


title: corneas, ICI_3

description: Library name: Sample3


title: corneas, ICI_1

description: Library name: Sample1


title: whole_blood_203824840030_R05C01

description: Human whole blood


title: whole_blood_203824840030_R04C01

description: Human whole blood


title: whole_blood_203824840030_R03C01

description: Human whole blood


title: acupuncture, replicate3, scRNAseq

city: Tianjin

first: Ruping

last: Yuan

state: 天津Tianjin

address: 卫津路94号

institute: Nankai University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger softwore 5.0.0
Assembly: mm10
Supplementary files format and content: rds file with cell type annotation and count matrix
Supplementary files format and content: h5ad file with spliced and unspliced RNA count matrix

source_name: ST36 acupoint tissue

extract_protocol:
Mice were anesthetized and perfused with 10 mL of pre-chilled phosphate-buffered saline (PBS) via the left heart ventricle. Tissues from the ST36 acupoint were excised and stored in cold 1640 medium . Then, the tissues were minced on ice using small scissors and incubated in 5 mL of a digestion buffer containing 0.25 mg/mL Liberase TH Research Grade enzyme and 50 μg/mL DNase I at 37°C for 30 min, with gentle shaking twice during incubation. Digestion was halted using 5% fetal bovine serum. The digested tissue was then passed through a 70-μm cell strainer into pre-chilled PBS twice on ice. Cells were pelleted by centrifugation at 400 g at 4°C for 5 min. Following centrifugation, the cell pellet was incubated with 3 mL of red blood cell lysis buffer  on ice for 5 min and pelleted again by centrifugation at 400 g at 4°C for 5 min. Subsequently, the cells were washed, re-suspended in pre-chilled PBS twice, and filtered through a 40-μm cell strainer to remove debris or cell aggregates. Finally, the cells were centrifuged at 400 g at 4°C for 5 min, re-suspended in 500 μL of pre-chilled PBS with 0.04% bovine serum albumin, and dead cells were removed using Dead Cell Removal Micro Beads .
Libraries were prepared according to Illumina's instructions accompanying the Illumina NovaSeq 6000

value: ST36 acupoint tissue

value: 6-8 weeks old


title: whole_blood_203824850034_R03C01

description: Human whole blood

value: N

value: Male


title: control group, replicate2, scRNAseq

description: 10x Genomics


title: whole_blood_203824850034_R01C01

description: Human whole blood


title: whole_blood_203824840030_R02C01

description: Human whole blood


title: whole_blood_203824840030_R01C01

description: Human whole blood


title: acupuncture, replicate2, scRNAseq

description: 10x Genomics


title: whole_blood_203939360029_R08C01

description: Human whole blood

value: PD


title: control group, replicate1, scRNAseq

description: 10x Genomics


title: whole_blood_203939360029_R07C01

description: Human whole blood


title: acupuncture, replicate1, scRNAseq

description: 10x Genomics


title: Non-regen, 14DPA, Rep2

description: 10x Genomics

extract_protocol:
Digit amputations were performed on 6-8-week-old mice as described previously.Briefly, mice were orally administered meloxicam for analgesia and anesthetized with 5% isoflurane immediately before digit tip amputation surgeries. Then, using sterile scalpels, the distal one-third of terminal phalanges 2, 3, and 4 were amputated to induce a regenerative response. For non-regenerative amputations, the distal one-third of the second phalanx was amputated.  Cells were dissociated with...and were pooled from N=3-5 unique mice, centrifuged and filtered with a succession of 40µm and 30µm filter. Cell concentration was determined and resuspended to 372 cells/µL in 2% FBS in PBS.
Libraries were prepared by using Chromium Next GEM Single cell 3'mRNA v3.1 as per the company’s protocol, and sequenced on NovaSeq 6000

value: Adult non-regenerating digit tip

value: 6-8 week old

value: normal

tag: time

value: 14 days post amputation


title: control group, replicate3, scRNAseq

description: 10x Genomics


title: whole_blood_203939360029_R06C01

description: Human whole blood


title: Non-regen, 14DPA, Rep1

description: 10x Genomics

value: Female


title: Regen, 14DPA, Control, Rep2

description: 10x Genomics

value: Adult regenerating digit tip


title: whole_blood_203939360029_R03C01

description: Human whole blood

value: CONTR


title: Regen, 14DPA, 4MU treated, Rep1

description: 10x Genomics

value: 4-methylumbelliferone fused diet


title: whole_blood_203939360029_R02C01

description: Human whole blood


title: whole_blood_203939360029_R05C01

description: Human whole blood


title: Regen, 14DPA, Control, Rep1

description: 10x Genomics


title: Shaker_hom_Rep2

first: Fiorella

last: Grandi

address: 105 Bld d'Hopital

department: Centre de Recherche de Myologie

institute: Sorbonne Universite

description:
Shaker_Hom_R2
Shaker_allsample.salmon.gene_counts.tsv
DEGs_Shaker_HomvsHet_P10.xlsx

data_processing:
NextFlow RNA pipeline
Salmon used for counting transcripts.
DeSeq2 used for differential expression analysis.
Assembly: mm10
Supplementary files format and content: Shaker_allsample.salmon.gene_counts.tsv; raw gene counts from salmon used as input for DESEQ2
Supplementary files format and content: DEGs_Shaker_HomvsHet_P10.xlsx; differentially expressed genes from Deseq2

source_name: cochlea

extract_protocol:
cochlear tissues were homogenized with Qiagen's RLT buffer using a plastic homogenizer and RNA eas extracted using the Qiagen microRNAeasy column. Samples were tested for a RIN values >9 before sequencing.
mRNA was purfied using poly-T olgio attached magentic beads. After fragmentation, the frist strand cDNA was synthesized usign random hexamer primers, followed by second stand cDNA synthesis using dTTP primers. End repari, A-tailing was reported, before adapter ligation and size seldction.

value: cochlea

value: Homozygous


title: whole_blood_203939360029_R04C01

description: Human whole blood

extract_protocol: DNA was extracted by a commercial provider using a standard method, exact protocol unknown


title: Regen, 14DPA, 4MU treated, Rep2

description: 10x Genomics


title: whole_blood_203829800028_R06C01

description: Human whole blood


title: Shaker_hom_Rep1

description:
Shaker_Hom_R1
Shaker_allsample.salmon.gene_counts.tsv
DEGs_Shaker_HomvsHet_P10.xlsx


title: Shaker_het_Rep2

description:
Shaker_het_R2
Shaker_allsample.salmon.gene_counts.tsv
DEGs_Shaker_HomvsHet_P10.xlsx

value: Heterozygous


title: Shaker_het_Rep3

description:
Shaker_het_R3
Shaker_allsample.salmon.gene_counts.tsv
DEGs_Shaker_HomvsHet_P10.xlsx


title: whole_blood_203829800028_R03C01

description: Human whole blood


title: Shaker_hom_Rep4

description:
Shaker_Hom_R4
Shaker_allsample.salmon.gene_counts.tsv
DEGs_Shaker_HomvsHet_P10.xlsx


title: whole_blood_203829800028_R08C01

description: Human whole blood


title: whole_blood_203829800028_R02C01

description: Human whole blood


title: whole_blood_203939360029_R01C01

description: Human whole blood


title: whole_blood_203829800028_R05C01

description: Human whole blood


title: whole_blood_203829800025_R08C01

description: Human whole blood


title: whole_blood_203829800028_R04C01

description: Human whole blood


title: Endoderm_BADC_RNA-seq_rep1

description: Library name: Endoderm_BADC_rep1

data_processing:
All scripts are in https://github.com/hrekaik/scriptsForRekaikEtAl2025.
Adapter sequences were trimmed from reads using cutadapt version 1.16 (-a ‘GATCGGAAGAGCACACGTCTGAACTCCAGTCAC’ -A ‘GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT’). Trimmed reads were aligned on mm10 with STAR version 2.7.7a69 with ENCODE options using a custom gtf based on Ensembl version 102 (https://doi.org/10.5281/zenodo.7510406). Only uniquely mapped reads (tag NH:i:1) were kept using bamFilter version 2.4.171 and Cufflinks  version 2.2.1 was run with default parameters to get FPKM values
Assembly: mm10
Supplementary files format and content: counts.txt.gz: raw counts from STAR
Supplementary files format and content: FPKM.txt.gz: FPKM from cufflinks identical ensembl Ids have been summed to have a single line per ID.

source_name: Endoderm differentiation

growth_protocol: mES cells were maintained in a humidified incubator (5% CO2, 37°C), and passaged every 3 days into 2i LIF DMEM medium composed of DMEM supplemented with 10% mES certified FBS, 100ng ml-1 of mouse LIF, 3μM of GSK-3 inhibitor (CHIR99021) and 1μM of MEK1/2 inhibitor (PD0325901).

extract_protocol:
mES cells and endoderm differentiated mES cells were collected in RLT plus buffer (Qiagen) and stored at −80°C until RNA extraction. RNeasy Plus Micro kit (Qiagen) with on-column DNase digestion was used for RNA extraction.
RNA-seq library preparation with Poly-A selection was performed with 1μg of purified RNA using the TruSeq Stranded mRNA kit from Illumina. Library quality was assessed with a fragment analyzer before sequencing.

treatment_protocol: For  in vitro endoderm differentiation, round 50’000 cells of control and Hox-/- mES cells were seeded in a 6-wells plate in differentiation medium (DM) composed of DMEM/F12 with 0.2% FBS medium and 1x B27. After 24h, medium was replaced with DM supplemented with 100ng ml-1 of recombinant Activin A and 3μM of GSK-3 inhibitor (CHIR99021). The same treatment was repeated at 72h, before cells collection at 120h.

value: Endoderm differentiation

value: Mixed cells

value: Hox-/-

value: endoderm differentiation


title: Shaker_het_Rep1

description:
Shaker_het_R1
Shaker_allsample.salmon.gene_counts.tsv
DEGs_Shaker_HomvsHet_P10.xlsx


title: whole_blood_203829800025_R07C01

description: Human whole blood

data_processing:
Raw signal intensity data were imported into R using the minfi package. CpG sites with a beadcount < 3 in 5% of samples or detection p-value > 0.05 in 1% of samples were filtered out using the pfilter function in the wateRmelon package. Samples failing sex-checks, samples with low median signal intensities as flagged by the minfi getQC function and samples flagged as outliers by the wateRmelon outlyx function were filtered out. The wateRmelon dasen method was used for normalization. After mapping of methylation data to the genome we removed probes on sex chromosomes, probes  overlapping loci with known single-nucleotide polymophisms (SNPs) and probes previously reported  as cross-reactive. We removed probes showing predominantly  technical variation (ICC < 0.1), leaving 502,261 CpGs in the dataset.
Normalized average Beta using the dasen method implemented in the wateRmelon R package

value: N


title: whole_blood_203829800028_R01C01

description: Human whole blood

value: Male


title: Shaker_hom_Rep3

description:
Shaker_Hom_R3
Shaker_allsample.salmon.gene_counts.tsv
DEGs_Shaker_HomvsHet_P10.xlsx


title: whole_blood_203829800028_R07C01

description: Human whole blood

value: PD


title: Endoderm_BADC_RNA-seq_rep3

description: Library name: Endoderm_BADC_rep3


title: whole_blood_203829800025_R06C01

description: Human whole blood


title: Endoderm_wt_RNA-seq_rep3

description: Library name: Endoderm_wt_rep3

value: wt


title: whole_blood_203829800025_R05C01

description: Human whole blood


title: Endoderm_BADC_RNA-seq_rep2

description: Library name: Endoderm_BADC_rep2


title: whole_blood_203829800025_R04C01

description: Human whole blood


title: mES_BADC_RNA-seq_rep2

description: Library name: mES_BADC_rep2

source_name: mES cells

value: mES cells


title: Endoderm_wt_RNA-seq_rep2

description: Library name: Endoderm_wt_rep2


title: whole_blood_203829800025_R03C01

description: Human whole blood


title: mES_BADC_RNA-seq_rep1

description: Library name: mES_BADC_rep1


title: whole_blood_203829800025_R01C01

description: Human whole blood


title: whole_blood_203824840021_R07C01

description: Human whole blood


title: Endoderm_wt_RNA-seq_rep1

description: Library name: Endoderm_wt_rep1


title: mES_wt_RNA-seq_rep2

description: Library name: mES_wt_rep2


title: whole_blood_203824840021_R06C01

description: Human whole blood


title: whole_blood_203829800025_R02C01

description: Human whole blood


title: whole_blood_203824840021_R08C01

description: Human whole blood


title: mES_wt_ATAC_rep2

description: Library name: mES_wt_ATAC_rep2

data_processing:
All scripts are in https://github.com/hrekaik/scriptsForRekaikEtAl2025. Adapter sequences and bad quality bases were removed with Cutadapt version 4.8 with options -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA -q 30 -m 15. Reads were mapped with bowtie 2.5.0 with parameters --very-sensitive on mm10. Alignments with a mapping quality below 30, discordant pairs, and reads mapping to the mitochondria, were discarded with bamtools version 2.5.2. PCR duplicates were removed with picard version 2.18.2 before the BAM to BED conversion with bedtools version 2.30.0. Coverage and peak calling were computed by MACS2 version 2.2.9.1 with options --format BED --gsize 1870000000 --call-summits --keep-dup all --bdg --nomodel --extsize 200 --shift -100. Coverages were normalized to million reads in peaks (summits +-500bp) using bigwigAverage from deeptools version 3.5.4.
Assembly: mm10
Supplementary files format and content: narrowPeaks.gz: peaks obtained with MACS2
Supplementary files format and content: bigwig: coverage normalized to the million reads in peaks

extract_protocol:
Cells were dissociated with Accutase for 5min at 37°C, washed and collected in cold resuspension buffer (RSB).
50k cells were resuspended in lysis buffer and incubated for 3min on ice. then immediately washed with RSB containing 0.01% Tween-20 and centrifuged. The pellet was gently resuspended in 50μL Tagmentation Mix (Nextera) and incubated at 37°C in a thermomixer at 1000rpm for 30min. DNA was extracted using the MinElute PCR Purification Kit (Qiagen), then fragments were amplified with Nextera Index Primers (Nextera) using the KAPA HiFi HotStart ReadyMix (Roche) for 12 cycles. After PCR the reactions were cleaned first with the MinElute PCR Purification Kit and then with AMPure XP beads (Beckman Coulter). Library quality was assessed with a fragment analyzer before sequencing.


title: mES_wt_RNA-seq_rep1

description: Library name: mES_wt_rep1


title: mES_BADC_ATAC_rep2

description: Library name: mES_BADC_ATAC_rep2


title: mES_wt_ATAC_rep1

description: Library name: mES_wt_ATAC_rep1


title: whole_blood_203824840021_R03C01

description: Human whole blood


title: mES_BADC_ATAC_rep1

description: Library name: mES_BADC_ATAC_rep1


title: whole_blood_203824900020_R07C01

description: Human whole blood


title: whole_blood_203824840021_R05C01

description: Human whole blood


title: whole_blood_203824840021_R04C01

description: Human whole blood


title: control_8cell_18

city: Philadelphia

first: Colin

last: Conine

state: Pennsylvania

address: 421 Curie Blvd BRB 1213

department: Genetics and Neonatology

institute: UPenn Perelman SOM and CHOP

description:
Library name: control_8cell_18
single embryo RNA-seq 8-cell embryo

data_processing:
Bioinformatic pipelines were assembled using Via Foundry, formerly DolphinNext, pipeline generator for all RNA-sequencing data analyzed in this study.
mRNA libraries were first aligned to the C. elegans genome (WS245) using STAR and quantified and normalized to transcripts per million (TPM) using the RSEM package. Significance calls were made based on t-tests (unpaired, two-tailed), where we identified up- and down-regulated genes using the following cutoff:  log2(fold change) >1 or less than –1 and an adjusted P-value ≤0.01. For differentially expressed genes WormBase enrichment analysis was used to determine tissue, pathway, and gene ontology enrichment.
Small RNA libraries were trimmed of adapter sequences using trimmomatic and aligned (in order) sequentially to C. elegans rRNAs, miRNAs, tRNAs, and piRNAs using Bowtie 2. STAR was used to align small RNAs to the C. elegans genome (WS245), featureCounts was then used to quantify reads mapping to genomic features (mRNA fragments, and endo siRNA). Mapped reads were normalized to reads per million using custom python scripts, to total genome mapping reads or to a specific RNA class, for subsequent analysis.
Assembly: WS245
Supplementary files format and content: csv files for small RNA data include raw count values for each Sample
Supplementary files format and content: csv files for mRNA data include TPM values for each Sample

organism: Caenorhabditis elegans

source_name: 8 cell embryo

extract_protocol:
Unless otherwise stated all RNA-seq experiments, beyond single embryo experiments (below) were conducted on adult animals. To generate rnst-2 mutant males, heterozygous rnst-2/tmc16 males and females were mated to generate progeny that’s parents had equivalent genotypes. Individual ~50 F1 L4 from these crosses, propagated at 20°C, were then picked as males and females separately to NGM OP50 plates.  These animals were then developed at 20°C for 24 hours to generate adult animals. These animals were then picked into 1X M9 media with 0.5% polyethylene glycol (mPEG) in a 1.5 mL low adhesion microcentrifuge tube. Worms were washed three times with M9/mPEG and once with cold nuclease free water before resuspending in 1 volume 2X worm lysis buffer (1% SDS, 80mM Tris HCl, 400 mM NaCl, 20 mM EDTA, 0.8 mg/mL Proteinase K). The samples were then incubated at 55°C for 15 minutes while shaking and visually inspected to ensure complete lysis. Following worm lysis, 2X volume of TRI reagent (Invitrogen, AM9738) was added followed by 1/5th volume of BCP (catalog #). This solution was mixed thoroughly and transferred a Phase Lock Gel Heavy tube (QuantaBio, 2302830; pre-spun at 14,000 RPM for 1 minute) and spun at 14,000 RPM for 4 minutes at 4°C. The aqueous layer was then transferred to a new low-adhesion microcentrifuge tube, and 15 μg of GlycoBlue coprecipitant (Invitrogen AM9515) was added prior to the addition of 1.1 volume isopropanol. Samples were then precipitated at -20°C for at least 1 hours, and up to a month in isopropanol (longer storage times at -80°C) to purify total RNA. To generate small RNA and mRNA-seq libraries RNA samples in isopropanol were centrifuged at 14,000 RPM for 15 minutes at 4°C, then washed with cold 70% ethanol, spun again at 14,000 RPM for 5 minutes at 4°C, and finally reconstituted in nuclease-free water. RNA isolation from 50 adult male and females, yields ~500ng and ~1µg, respectively.
For small RNA 200 ng of total RNA was used as input for all small RNA sequencing experiments with library construction carried out using a modified Illumina Tru-Seq small RNA library prep protocol (Illumina RS-200). Small RNAs (18 – 40 nt) were first purified by was size selection from denaturing 15% polyacrylamide 7M urea TBE gel electrophoresis. Small RNAs from eluted in 10mM Tris-HCl pH 7.5, 300mM NaCl, and 1mM EDTA shaking overnight at room temperature. Small RNAs were then precipitated by separating the gel debris using 0.45µM cellulose-acetate filters, adding 1ul GlycoBlue and 1.1 volume of isopropanol, mixing well, and placing the samples at -20°C for at least 1 hour. The samples then were centrifuged at 14,000 RPM for 15 minutes at 4°C and the supernatant was discarded before washing with 1X volume of cold 70% ethanol. Following a 14,000 RPM spin at 4°C for five minutes and after complete ethanol removal, the pellet was reconstituted in RNA 5´ Pyrophosphohydrolase (RppH - NEB M0356S) per manufacturers guidelines and incubated at 37°C for one hour. Following RppH treatment, small RNAs were precipitated and ligated to the 3´ adapter using Truncated T4 RNA ligase (Lucigen LR2D11310K). Small RNAs were then ligated to the 5´ adapter using T4 ligase, and subsequently reverse transcribed using Superscript II (Invitrogen 18064014) following the Tru-Seq small RNA protocol. Following PCR optimization, to determine the proper number of cycles for amplification, the libraries were amplified, gel purified on a 8% TBE polyacrylamide gel (to remove cloned products with no insert) and combined at equimolar concentration. Libraries were then sequenced using an Illumina NextSeq1000 (75-bp single read).
For standard  mRNA-seq library construction was carried out using the Illumina stranded mRNA kit as per manufacturer’s instructions (Illumina 20040534). In brief, poly-adenylated RNAs were captured using oligo(dT) magnetic beads from 200-800ng total RNA. The RNA was then fragmented, primed for cDNA synthesis and subsequently cleaned up using AMPure XP beads (Beckman Coulter, Cat# A63881). Following PCR optimization, to determine the proper number of cycles from amplification, the libraries were amplified and combined at equimolar concentrations before being purified using non-denaturing PAGE. Paired-end sequencing (50 bp per read) was performed using an Illumina NextSeq1000.
For single embryo RNA-seq cross plates were prepared by placing 50 WT (fog-2(q71) L4-stage females and 50 rnst-2 Δ/Δ (pen1); fog-2(q71) L4-stage males on 60 mM NGM plates seeded with OP50. The next day mated females full of eggs were picked and washed several times with M9 mPEG and then subjected to a 5-minute hypochlorite treatment. Early-stage embryos, identified under the microscope, were then transferred to 10ug/ul chitanase in M9 mPEG treatment and incubated at room temperature for 8-10 minutes. Following chitinase treatment 2-cell and 8-cell embryos, identified visually under a dissecting microscope were placed in RNA worm lysis buffer in PCR tubes and incubated at 55°C for 10 minutes. Embryo lysates were then stored at -80°C before proceeding to library preparation. Single-embryo mRNA-seq libraries were constructed using the SMART-Seq protocol, used previously for single mouse preimplantation embryos. RNA was isolated with RNAClean-XP beads (Beckman Coulter, Cat# A63987) and full-length polyadenylated RNA was reverse transcribed using Superscript II (Invitrogen, Cat# 18064014). The cDNA was then amplified using 10 cycles and subsequently 0.33 ng of cDNA was used to construct a pool of uniquely indexed samples using the Nextera XT kit (Illumina, Cat# FC-131-1096). Finally, pooled libraries were sequenced on a NextSeq1000 with paired-end sequencing (50 bp per read).

value: 8 cell embryo


title: whole_blood_203824900020_R05C01

description: Human whole blood


title: control_8cell_15

description:
Library name: control_8cell_15
single embryo RNA-seq 8-cell embryo


title: control_8cell_16

description:
Library name: control_8cell_16
single embryo RNA-seq 8-cell embryo


title: control_8cell_11

description:
Library name: control_8cell_11
single embryo RNA-seq 8-cell embryo


title: whole_blood_203824900020_R08C01

description: Human whole blood

value: Female


title: control_8cell_14

description:
Library name: control_8cell_14
single embryo RNA-seq 8-cell embryo


title: control_8cell_17

description:
Library name: control_8cell_17
single embryo RNA-seq 8-cell embryo


title: control_8cell_8

description:
Library name: control_8cell_8
single embryo RNA-seq 8-cell embryo


title: control_8cell_7

description:
Library name: control_8cell_7
single embryo RNA-seq 8-cell embryo


title: whole_blood_203824840021_R01C01

description: Human whole blood


title: whole_blood_203824840021_R02C01

description: Human whole blood


title: control_8cell_9

description:
Library name: control_8cell_9
single embryo RNA-seq 8-cell embryo


title: whole_blood_203824900020_R06C01

description: Human whole blood


title: whole_blood_203824900020_R03C01

description: Human whole blood


title: control_8cell_5

description:
Library name: control_8cell_5
single embryo RNA-seq 8-cell embryo


title: whole_blood_203824900020_R04C01

description: Human whole blood


title: control_8cell_12

description:
Library name: control_8cell_12
single embryo RNA-seq 8-cell embryo


title: control_8cell_10

description:
Library name: control_8cell_10
single embryo RNA-seq 8-cell embryo


title: control_8cell_13

description:
Library name: control_8cell_13
single embryo RNA-seq 8-cell embryo


title: whole_blood_203824900020_R02C01

description: Human whole blood


title: control_8cell_2

description:
Library name: control_8cell_2
single embryo RNA-seq 8-cell embryo


title: whole_blood_203824840014_R08C01

description: Human whole blood


title: whole_blood_203824840014_R03C01

description: Human whole blood


title: whole_blood_203824900020_R01C01

description: Human whole blood


title: whole_blood_203824840014_R07C01

description: Human whole blood


title: control_2cell_23

description:
Library name: control_2cell_23
single embryo RNA-seq 2-cell embryo

source_name: 2 cell embryo

value: 2 cell embryo


title: whole_blood_203824840014_R05C01

description: Human whole blood


title: control_8cell_4

description:
Library name: control_8cell_4
single embryo RNA-seq 8-cell embryo


title: whole_blood_203824840014_R04C01

description: Human whole blood

value: CONTR


title: control_8cell_3

description:
Library name: control_8cell_3
single embryo RNA-seq 8-cell embryo


title: whole_blood_203824840014_R02C01

description: Human whole blood


title: control_8cell_6

description:
Library name: control_8cell_6
single embryo RNA-seq 8-cell embryo


title: control_2cell_19

description:
Library name: control_2cell_19
single embryo RNA-seq 2-cell embryo


title: NM850_024

city: Miaoli County

first: Shih-Sheng

address: 35, Keyan Road, Zhunan Town

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes

hyb_protocol: The bisulfite-converted DNA was hybridized to the Illumina HumanMethylation450/EPIC/EPIC v2.0 BeadChips according to the manufacturer’s Infinium HD protocol. Hybridization was performed at 48°C for 16 hours in a humidity-controlled chamber. Following hybridization, chips were washed using Illumina-supplied buffers to remove unbound DNA prior to extension.

scan_protocol: Arrays were scanned on the Illumina iScan System using default parameters. Images were processed using Illumina GenomeStudio Methylation Module software to extract signal intensities and compute methylation beta values. Quality control was performed using internal control probes.

data_processing: For NM450 (450K), NM850 (EPIC), and NM900 (EPICv2) samples, raw intensities were background-corrected, dye-bias-equalized, and functionally normalized using the ‘preprocessFunnorm’ function in the minfi R package. CpGs on sex chromosomes, containing SNPs (MAF ≥5%), in repetitive regions, or with poor detection p-values were removed. Three processed DNA methylation datasets were generated: NM450-114 (NM450 samples), NMC-47 (combined NM850 and NM900), and NMC-161 (combined NM450, NM850, and NM900), retaining CpGs common to the platforms within each dataset (373,275 CpGs for NM450-114; 558,115 CpGs for NMC-47; 298,801 CpGs for NMC-161). For each dataset, beta values were inverse-rank transformed to a standard normal distribution and regressed on confounders including sex, age, medical operation status, batch, top genotyping PCs, and top methylation PCs. The residuals were inverse-rank transformed again to produce the final processed DNA methylation data.

source_name: lung

label_protocol: Genomic DNA (500 ng) underwent bisulfite treatment with the EZ DNA Methylation Kit (Zymo Research). Following conversion, samples were processed according to the Illumina Infinium HD Methylation Assay protocol, including amplification, fragmentation, and hybridization steps. Labeling was incorporated during the single-base extension step.

extract_protocol: Tissue DNA was extracted from lung tissues using the QIAamp DNA Mini Kit (Qiagen Inc, USA). Bisulfite conversion of tissue DNA was performed using the EpiTect Fast DNA Bisulfite Kit (Qiagen Inc, USA) according to the manufacturer’s instructions. DNA methylation of bisulfite-converted DNA was measured using the abovementioned platform, according to Illumina’s standard procedure in Genetech Biotech Co., Ltd.

value: lung

tag: gender

tag: smoking status

value: Non-smoking


title: control_8cell_1

description:
Library name: control_8cell_1
single embryo RNA-seq 8-cell embryo

tag: tissue


title: whole_blood_203824840014_R01C01

description: Human whole blood

tag: Sex


title: control_2cell_18

description:
Library name: control_2cell_18
single embryo RNA-seq 2-cell embryo

tag: genotype


title: NM850_023

tag: batch


title: control_2cell_26

description:
Library name: control_2cell_26
single embryo RNA-seq 2-cell embryo


title: NM850_031


title: control_2cell_25

description:
Library name: control_2cell_25
single embryo RNA-seq 2-cell embryo


title: control_2cell_17

description:
Library name: control_2cell_17
single embryo RNA-seq 2-cell embryo


title: control_2cell_16

description:
Library name: control_2cell_16
single embryo RNA-seq 2-cell embryo


title: NM850_030


title: NM850_022


title: NM850_021


title: control_2cell_15

description:
Library name: control_2cell_15
single embryo RNA-seq 2-cell embryo


title: NM850_020


title: control_2cell_24

description:
Library name: control_2cell_24
single embryo RNA-seq 2-cell embryo


title: NM850_028


title: NM850_029


title: control_2cell_22

description:
Library name: control_2cell_22
single embryo RNA-seq 2-cell embryo


title: NM850_027


title: control_2cell_14

description:
Library name: control_2cell_14
single embryo RNA-seq 2-cell embryo


title: NM850_019


title: control_2cell_12

description:
Library name: control_2cell_12
single embryo RNA-seq 2-cell embryo


title: control_2cell_13

description:
Library name: control_2cell_13
single embryo RNA-seq 2-cell embryo


title: NM850_017


title: NM850_016


title: control_2cell_21

description:
Library name: control_2cell_21
single embryo RNA-seq 2-cell embryo


title: NM850_026


title: control_2cell_20

description:
Library name: control_2cell_20
single embryo RNA-seq 2-cell embryo


title: control_2cell_10

description:
Library name: control_2cell_10
single embryo RNA-seq 2-cell embryo


title: NM850_014


title: control_2cell_8

description:
Library name: control_2cell_8
single embryo RNA-seq 2-cell embryo


title: NM850_012


title: NM850_010


title: NM850_025


title: control_2cell_4

description:
Library name: control_2cell_4
single embryo RNA-seq 2-cell embryo


title: control_2cell_3

description:
Library name: control_2cell_3
single embryo RNA-seq 2-cell embryo


title: NM850_007


title: NM850_018


title: NM850_006


title: control_2cell_2

description:
Library name: control_2cell_2
single embryo RNA-seq 2-cell embryo


title: control_2cell_11

description:
Library name: control_2cell_11
single embryo RNA-seq 2-cell embryo


title: control_2cell_1

description:
Library name: control_2cell_1
single embryo RNA-seq 2-cell embryo


title: NM850_004


title: anti_tRF_8cell_19

description:
Library name: anti_tRF_8cell_19
single embryo RNA-seq 8-cell embryo


title: NM850_003


title: NM850_009


title: NM850_001


title: anti_tRF_8cell_17

description:
Library name: anti_tRF_8cell_17
single embryo RNA-seq 8-cell embryo


title: anti_tRF_8cell_16

description:
Library name: anti_tRF_8cell_16
single embryo RNA-seq 8-cell embryo


title: NM850_013


title: NM850_015


title: control_2cell_9

description:
Library name: control_2cell_9
single embryo RNA-seq 2-cell embryo


title: NM850_011


title: control_2cell_7

description:
Library name: control_2cell_7
single embryo RNA-seq 2-cell embryo


title: NM850_008


title: control_2cell_5

description:
Library name: control_2cell_5
single embryo RNA-seq 2-cell embryo


title: control_2cell_6

description:
Library name: control_2cell_6
single embryo RNA-seq 2-cell embryo


title: anti_tRF_8cell_12

description:
Library name: anti_tRF_8cell_12
single embryo RNA-seq 8-cell embryo


title: anti_tRF_8cell_11

description:
Library name: anti_tRF_8cell_11
single embryo RNA-seq 8-cell embryo


title: NM850_005


title: anti_tRF_8cell_20

description:
Library name: anti_tRF_8cell_20
single embryo RNA-seq 8-cell embryo


title: anti_tRF_8cell_14

description:
Library name: anti_tRF_8cell_14
single embryo RNA-seq 8-cell embryo


title: NM850_002


title: anti_tRF_8cell_18

description:
Library name: anti_tRF_8cell_18
single embryo RNA-seq 8-cell embryo


title: TGF38, Biopsy Day15

city: Portland

first: venkatesh

last: rajamanickam

state: OR

address: 4805 NE Glisan St, Suite 2N35

institute: Earle A. Chiles Research Institute

description: Library name: TGF38_Day15

data_processing:
Expression counts were quantified using salmon-v.0.12.0
Normalization and differential gene expression analysis was conducted using edgeR
Assembly: hg19
Supplementary files format and content: comma separated file includes normalized counts for all samples and timepoint

source_name: RNA Exome

extract_protocol:
Total RNA were purified from 5 µm FFPE tumor sections on an automated QiaCube instrument using DNA/RNA AllPrep reagents (Qiagen) according to the manufacturer’s instructions.
The RNA is fragmented using divalent cations under elevated temperature. cDNA is generated from the cleaved RNA fragments using random priming during first and second strand synthesis. Then, sequencing adapters are ligated to the resulting double-stranded cDNA fragments. The coding regions of the transcriptome are captured from this library using sequence-specific probes to create the final library. Captured library pools were normalized and loaded onto a Illumina Novaseq 6000 for sequencing.

value: Tumor

tag: treatment

value: galunisertib+chemoradiation

value: Day 15


title: anti_tRF_8cell_15

description:
Library name: anti_tRF_8cell_15
single embryo RNA-seq 8-cell embryo


title: INTS11 depletion 24hrs, INTS11-degron mESCs rep1

description: Library name: Rep1_24h

data_processing:
Data were processed using the snakePipes ncRNAseq (version 3.2.0) with parameters   ncRNAseq -i fastq -o snakepipe_noncoding mm10_gencodeM19 --trim --trimmer cutadapt
Assembly: mm10
Supplementary files format and content: Rep1_0h.cntTable, Rep1_24h.cntTable, Rep2_0h.cntTable, Rep2_24h.cntTable

extract_protocol:
Total RNA was extracted using TRI Reagent and ethanol precipitated. 10 µg of total RNA was further processed to remove the remaining DNA with 4 U of TURBO DNase for 30 min and column purified prior to library construction.
Total RNA libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold (Illumina, 20020598) following manufacturer's protocol.

value: mouse embryonic stem cells

value: INTS11-degron depletion for 24 hrs

value: INTS11-degron depletion


title: TGF37, Biopsy Day0

description: Library name: TGF37_Day0


title: anti_tRF_8cell_13

description:
Library name: anti_tRF_8cell_13
single embryo RNA-seq 8-cell embryo