title: WT Control mouse 3; Day 6

description:
Library name: Control-3
Column name in MJU4200_genecounts.csv: MJU4200.3


title: HM009

status: Public on Jun 08 2026

type: RNA

city: Melbourne

first: Andrea

last: Di Pietro

state: VIC

address: 305 Grattan Street

department: Cancer Immunology program

country: Australia

institute: Peter MacCallum Cancer Centre

hyb_protocol: Total RNA was hybridised to a custom nCounter CodeSet that includes the commercial PanCancer Immune Profiling Panel plus a Panel Plus (PLS) extension targeting TRM-related genes. Hybridisations were performed per manufacturer instructions using the NanoString nCounter system. RNA Hybridization was performed following the manufacturer's protocol (Nanostring).

scan_protocol: nCounter

data_processing:
NanoString Gene Expression Data Analysis Guidelines
Data were normalised and quality-controlled using NanoString nSolver and further analysed to identify differentially expressed genes and pathway enrichment associated with treatment response.

label: not provided

molecule: total RNA

organism: Homo sapiens

source_name: lymph node

label_protocol: 150 ng of purified RNA were hybridized with the gene probes

growth_protocol: RNA extracted from FFPE blocks

extract_protocol: The RNA was extracted from 10 µm scrolls. Deparaffinisation was condicted by dissolving the scrolls into xylene solution. The RNA was purified using the AllPrep DNA/RNA FFPE Kit (QIAGEN) and quantified at the RNA-TapeStation (Agilent).

treatment_protocol: FFPE blocks from patients that were treatment-naïve (n=13), ICI-resistant (n=5), or ICI-responsive (n=6).

tag: treatment


title: WT Control mouse 2; Day 6

type: SRA

city: Charlottesville

first: G. Brett

last: Moreau

state: Virginia

address: 345 Crispell Drive

country: USA

institute: University of Virginia

description:
Library name: Control-2
Column name in MJU4200_genecounts.csv: MJU4200.2

library_source: transcriptomic

data_processing:
RNA-Seq reads were first processed using Cutadapt to trim the adapter sequences and then the quality of the reads was assessed by FastQC  and MultiQC. After these processes, the reads were aligned to the mouse mm10 using STAR v2.5.3a  in a 2-passing mode to generate a gene matrix for differential gene expression.
Assembly: mm10
Supplementary files format and content: CSV file including DESeq2-normalized counts for genes identified in this study.

organism: Mus musculus

source_name: Lung

extract_protocol:
A snip from the lower inferior lobe was taken and RNA was extracted from murine lung tissue preserved in trizol by bead beating (TissueLyserII, Qiagen), followed by a phenol-chloroform extraction and RNA Isolation Kit (Qiagen). RNA quality was assessed using Agilent Tape Station RNA kit.
cDNA libraries were prepared using the NEB ultra-directional library preparation kit 2.0 following manufacturer's protocol

treatment_protocol: Wildtype mice were either mock infected (saline) or infected with the mouse adapted SARS-CoV-2 strain MA10. After six days mice were euthanized and lung tissue was collected for RNA isolation.

tag: tissue

value: Lung

tag: genotype

value: WT

value: No infection

tag: time

value: Day 6


title: Unc93b1 3d/3d TAM,  αMARCO, rep1

city: Solna

first: Mikael

last: Karlsson

address: Solnavägen 9

country: Sweden

institute: Karolinska Institutet

description: Library name: ED31_KO_1

data_processing:
Raw data of fastq format were first processed through fastp software. In this step, clean data were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools. FeatureCounts v1.5.0 was used to count the reads numbers mapped to each gene, and then TPM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis for two conditions was performed using the DESeq2 R package (1.40.2). DESeq2 provides statistical programs for determining differential expression in digital gene expression data using models based on negative binomial distribution. The resulting P-value is adjusted using the Benjamini and Hochberg's methods to control the error discovery rate. The corrected P-value≤0.05& |log2(foldchange)| ≥ 0.5 was set as the threshold of significant differential expression. GO and KEGG enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package (4.10.1), in which gene length bias was corrected. GO and KEGG terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes.
Assembly: GRCm38
Supplementary files format and content: Each file contains FPKM expression values per gene across samples. Rows represent genes and columns represent samples.

source_name: Tumor

extract_protocol:
Total RNA was extracted and isolated following TRIzol Reagent User Guide.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. RNA integrity was assessed using the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. After library quality control, different libraries were pooled based on the effective concentration and targeted data amount, then subjected to Illumina sequencing by using the NovaSeq 6000 platform. As each sequencing cluster extends its complementary strand, the addition of each fluorescently labeled dNTP releases a corresponding fluorescence signal. The sequencer captures these fluorescence signals and converts them into sequencing peaks through computer software, thereby obtaining the sequence information of the target fragment.

treatment_protocol: For αMARCO treatment, the rat anti-MARCO IgG1 (Clone: ED31) was obtained from Mabtech. Mice were treated with 100μg of anti-MARCO antibody (rat IgG1, clone ED31) or IgG1 isotype control antibody (BioXCell, rat IgG1, clone TNP6A7) on day 3,6, 9 and 12.

value: Tumor

tag: cell type

value: Macrophages

value: Unc93b1 3d/3d (Absence of endosomal Toll-like receptors (TLRs))

value: αMARCO


title: WT Control mouse 1; Day 6

description:
Library name: Control-1
Column name in MJU4200_genecounts.csv: MJU4200.1


title: HM007

value: Untreated


title: Fast_(+Tetra); rabbit IgG; H3K9ac; CUT&Tag

city: HOUSTON

first: Ajay

middle: Kumar

last: Saw

state: TX

address: 7900 Cambdrige St

department: Department of Genomic Medicine

institute: University Of Texas MD Anderson Cancer Center, Houston, Texas, USA.

description: Library name: Tetra-Fast_H3K9ac

library_source: genomic

data_processing:
Raw fastq reads for all CUT&Tag-seq experiments were processed using FastQC  and aligned to the mm10 reference genome using Bowtie, and  sorted and indexed using samtools
Model based analysis of CUT&Tag-seq (MACS) used for  peak calling
Assembly: mm10
Supplementary files format and content: bed peak file
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: small intesitnal crypt

growth_protocol: mice were grown in normal contion before the tetracycline treatment

extract_protocol:
small intestinal crypt were isolated by shacking in HBSS+edta, followed by trypsin treatment to make single cells
CUT&Tag libraries were prepared using Epicypher CUTANA CUT&Tag Kit

treatment_protocol: Mice were treated with tetracycline for 21 days, fed or fasted for 24hrs.

value: small intesitnal crypt

value: small intestinal epithelial cells

tag: strain

tag: age

value: 9 weeks

tag: Sex

value: male

tag: cut&tag antibody

value: H3K9ac(ThermoFisher Scientific); rabbit IgG (Epicypher)

value: (+Tetra)


title: WT TAM,  αMARCO, rep2

description: Library name: ED31_WT_2


title: HM006


title: Fast_(+Tetra); mouse IgG; H3K27ac; CUT&Tag

description: Library name: Tetra-Fast_H3K27ac

value: H3K27ac(ThermoFisher Scientific); mouse IgG (Epicypher)


title: Fed_(+Tetra); rabbit IgG; H3K9ac; CUT&Tag

description: Library name: Tetra-Fed_H3K9ac


title: WT TAM,  αMARCO, rep1

description: Library name: ED31_WT_1


title: HM005


title: Fed_(+Tetra); mouse IgG; H3K27ac; CUT&Tag

description: Library name: Tetra-Fed_H3K27ac


title: WT_Pos470

city: Birmingham

first: Andrew

last: Arrant

state: AL

address: 1825 University Blvd SHEL 1106

institute: University of Alabama at Birmingham

description: Library name: 470

data_processing:
Reads were aligned to a custom genome composed from Gencode vM32 genome with vH43 TARDBP using STAR with the following settings: (--twopassMode Basic --outSAMstrandField intronMotif --outSAMunmapped Within --outSAMtype BAM Unsorted SortedByCoordinate --quantMode TranscriptomeSAM).
Bam files were indexed with samtools.
Aligned transcripts were quantified using Salmon.
Salmon quantification files were imported into R using tximport.
Non-protein coding genes and genes where there were fewer than three samples with normalized counts less than or equal to five were filtered out.
Normalization and differential expression analysis were performed using the R package DESeq2.
After initial principal component analysis, one mouse (WT_Pos470) was excluded as an outlier from all further analysis.
Assembly: Gencode vM32 with vH43 TARDBP
Supplementary files format and content: .sf files with TPM for each sample

molecule: polyA RNA

source_name: Frontal Cortex

growth_protocol: Grn+/- mice and hTDP transgenic mice were crossed to generate littermates of four genotypes: Grn+/+:hTDP-, Grn+/+:hTDP+, Grn+/-:hTDP-, and Grn+/-:hTDP+. Mice were housed in standard conditions to an average age of around 10 months. Brains were collected by anesthetizing mice with pentobarbital, transcardially perfusing with 0.9% saline, removing brains, and flash freezing. Brains were later thawed for dissection of frontal cortex.

extract_protocol:
RNA was isolated from frontal cortex using the Qiagen RNeasy mini kit. Samples were further processed with the Zymo Research RNA clean and concentrate kit.
After poly-A selection, RNA was fragmented and subjected to first strand cDNA synthesis using random hexamers. Second strand DNA was synthesized using dUTPs for the directional library and dTTPs for the non-directional library. The directional library was then prepared by end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The non-directional library was prepared by end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Frontal Cortex

tag: grn genotype

tag: htdp genotype

value: Female

tag: age (months)


title: HM035


title: mdx:Utrn+/- treated with saline3

city: Kansas city

first: Jian

last: Huang

state: KS

address: 3901 Rainbow Boulevard

department: Cardiovascular Medicine

institute: KUMC

description: Library name: Sample_N2696

data_processing:
NextSeq System Suite v2.2.0
The gene differential expressions were analyized using EdgeR
Assembly: mm10
Supplementary files format and content: tab delimited text file includes raw counts for each sample

source_name: Heart

extract_protocol:
Frozen cell pellets (isolated cardiomyocytes) were thawed at room temperature, and total RNA was extracted using the RNeasy Fibrous Tissue Mini Kit (74704, QIAGEN) according to the manufacturer's instructions.
Samples were run on the Agilent Tapestation 4200 to determine level of degradation thus ensuring only high quality was used (RIN Score>=8). The Qubit fluorimeter was used to determine the concentration prior to starting library prep. 1.0 μg of total RNA (DNAse treated) was then prepared with the TruSeq Stranded mRNA Library Prep Kit from Illumina. Poly-A RNA was purified and fragmented before strand specific cDNA synthesis. cDNA were then a-tailed and indexed adapters were ligated. After adapter ligation, samples were PCR amplified and purified with AmpureXP beads, then validated again.

treatment_protocol: Animals received PB1046 (0.75 or 1.5 mg/kg) or saline every other day from 4 to 12 weeks of age. Cardiac function was assessed weekly by echocardiography, and hearts were collected at 14 weeks of age for histological and molecular analyses.

value: Heart

value: Cardiomyocytes

value: Saline (control)

tag: batch

value: mdx:Utrn+/- control


title: Het_Pos465

description: Library name: 465

value: Male


title: HM020


title: Fast_(-Tetra); rabbit IgG; H3K9ac; CUT&Tag

description: Library name: SPF-Fast_H3K9ac

value: (-Tetra)


title: HM004


title: Unc93b1 3d/3d TAM, untreated, rep2

description: Library name: PBS_KO_2

value: Tumor

value: Macrophages

value: Unc93b1 3d/4d (Absence of endosomal Toll-like receptors (TLRs))

value: untreated


title: Fed_(-Tetra); rabbit IgG; H3K9ac; CUT&Tag

description: Library name: SPF-Fed_H3K9ac

value: small intesitnal crypt

value: small intestinal epithelial cells

value: 9 weeks


title: Fast_(-Tetra); mouse IgG; H3K27ac; CUT&Tag

description: Library name: SPF-Fast_H3K27ac

value: male


title: Fed_(-Tetra); mouse IgG; H3K27ac; CUT&Tag

description: Library name: SPF-Fed_H3K27ac

value: H3K27ac(ThermoFisher Scientific); mouse IgG (Epicypher)


title: Unc93b1 3d/3d TAM, untreated, rep1

description: Library name: PBS_KO_1

value: Unc93b1 3d/3d (Absence of endosomal Toll-like receptors (TLRs))


title: KO

city: Suzhou

first: Peng

last: Xu

state: Jiangsu

address: Office3625 Building703, RENAI ROAD No.199, INDUSTRIAL PARK DISTRICT

department: Suzhou Medical College

country: China

institute: Soochow University

description: Library name: sample4

library_source: transcriptomic single cell

data_processing:
Raw read alignment to the reference genome mm10-3.0.0 was performed by cellranger-7.1.0 . CAB implements these steps in AutoMapper, a pipeline uses the most recent versions of the reference sequence and annotation files AutoMapper Reference Library (https://wiki.stjude.org/display/CAB/Reference+Library). For more information, please see the CAB scRNA-seq (https://wiki.stjude.org/display/CAB/scRNAseq+mapping+and+QC). mapping & QC wiki page
Assembly: mm10
Supplementary files format and content: matrix files

source_name: murine bone marrow

extract_protocol:
First, a single-cell suspension is prepared and subjected to viability assessment, with cell viability >85%, good monodispersity, and low impurity content being ideal. Subsequently, microfluidic water-in-oil droplet library preparation and sequencing operations are performed. To ensure efficient single-cell capture, the cell concentration should generally be maintained within the range of 700–1,200 cells/μL.
During library preparation, individual gel beads and single cells are encapsulated within isolated water-in-oil droplets to form Gel Bead-in-Emulsions (GEMs). Each gel bead contains a unique barcode, a UMI sequence, and a poly-dT primer for initiating reverse transcription. Within the GEM reaction system, cells are lysed to release mRNA, which then binds to the poly-dT primers and undergoes reverse transcription catalyzed by reverse transcriptase to generate full-length cDNA. The cDNA is then amplified and used to construct the final sequencing library.

value: murine bone marrow

tag: cell line

value: bone marrow


title: mdx mice treated with saline2

description: Library name: Sample_N2701

value: Heart

value: Cardiomyocytes

value: mdx

value: mdx control


title: HM003-Large

value: Untreated


title: HM003-Small


title: WT

description: Library name: sample3


title: WT TAM, untreated, rep2

description: Library name: PBS_WT_2

value: Tumor

value: WT


title: mdx mice treated with saline1

description: Library name: Sample_N2668

value: Saline (control)


title: KO222

description: Library name: sample2

value: ckit+


title: WT214

description: Library name: sample1


title: WT TAM, untreated, rep1

description: Library name: PBS_WT_1

value: Macrophages

value: untreated


title: HM002


title: WT MA10-infected mouse 3; Day 6

description:
Library name: MA10-3
Column name in MJU4200_genecounts.csv: MJU4200.8

value: Lung

value: MA-10 infection

value: Day 6


title: PROTAC_H3K27me3_Rep1

city: Cambridge

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

country: United Kingdom

institute: The Babraham Institute

description: Library name: library12

data_processing:
Reads were trimmed with trim_galore v0.6.10 using default parameters.
Trimmed reads were aligned to GRCh38 using bowtie2 v2.4.1 using default parameters
Reads were sorted and indexed with samtools
BigWig files were created with deeptools bamCoverage using options --normalizeUsing CPM  --binSize 10
Assembly: GRCh38
Supplementary files format and content: BigWig quantitated with CPM
Library strategy: CUT&Tag

growth_protocol: HNES1 hPSCs were maintained in the naive state as described in (Rostovskaya 2022). In brief, cells were cultured on irradiated mouse embryonic fibroblast (MEF) feeder cells in N2B27 supplemented with 1 µM PD0325901, 10 ng/ml human LIF (made in-house), 2 µM Gö6983 (Tocris Bio-Techne, Cat. 2285), and 2 µM XAV939 (Tocris Bio-Techne, Cat. 3748). N2B27 basal medium was prepared as follows: Neurobasal and DMEM-F12 in the ratio 1:1; 0.5% N2 supplement; 1 % B27 supplement (with vitamin A); 2 mM L-glutamine; 100 mM 2-mercaptoethanol (all from ThermoFisher Scientific). Cells were passaged through single-cell dissociation using TrypLE Express (Cat. 12604021, ThermoFisher Scientific). 0.5 µL/mL Geltrex (A1413302, ThermoFisher Scientific) was added to the medium during passaging. 10 µM ROCK inhibitor (Y-27632, Cat. 688000, Millipore) was added for 24 hours after replating.

extract_protocol:
Cells were harvested by incubation with TrypLE for 5-7 minutes at 37C. TrypLE was quenched by wash buffer (0.1 % BSA in DMEM/F12) and cells were collected by centrifugation at 300 x g for 3 min. Cells were washed in 1X PBS without Calcium or Magnesium (PBS -/-) and collected by centrifugation at 300 x g for 3 minutes. Cells were resuspended in PBS -/- before addition of 2X nuclear extraction buffer (25 mM HEPES pH 7.5 (Gibco, Cat. 15630), 12.5 mM Potassium Chloride, 0.25 mM Spermidine, 0.13 % Triton X-100 (Sigma, Cat. T9284), 25% Glycerol  and 1 x Protease inhibitor cocktail (Roche) in water) to 1X and incubation on ice for 10 minutes with intermittent vortexing. Nuclei were collected by centrifugation at 1300 x g for 4 min at 4 °C. Nuclei were resuspended in cold PBS -/- and fresh 16% PFA was added to a final concentration of 0.1% followed by rocking gently at room temperature for 2 min. Fixation was stopped by addition of 1.25 M glycine. Nuclei were collected by centrifugation at 1300 x g for 4 min at 4°C and resuspended in Wash buffer. Human cells (n = 20,000) were mixed with Drosophila S2 cells (n = 8,000) per reaction prior to addition of concanavalin-beads. Concanavalin A beads (10 µL per 100,000 cells; Stratech, Cat. BP531-BAN-3ml) were first activated in Binding Buffer (20 mM HEPES pH 7.5, 10 mM KCl, 10 mM CaCl₂, 10 mM MnCl₂) and incubated with cells at room temperature for 10 min with agitation. Bead-cell complexes were resuspended in Antibody Buffer (2 mM EDTA pH 8, 0.1 % BSA in Dig-Wash Buffer) containing primary antibodies (1:100) and incubated overnight at 4 °C on a tube rotator. The following antibodies were used at a 1:50 dilution H3K27me3 (CST, Cat. 9733) and H2AK119Ub (Cell Signalling, Cat. D27C4). After a wash in Dig-Wash Buffer (0.05 % digitonin in Wash Buffer), complexes were incubated with a secondary antibody (guinea pig α-rabbit IgG, 1:100; Rockland, Cat. ABIN101961) for 30 min at room temperature on a tube rotator. After three washes in Dig-Wash Buffer, bead-cell complexes were incubated with pAG-Tn5 (1:250; EpiCypher, Cat. 15-1117) in Dig300-Wash Buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine, protease inhibitors, 0.01 % digitonin) for 1 h at room temperature. After three washes in Dig300-Wash Buffer, tagmentation was activated in Tagmentation Buffer (10 mM MgCl₂ in Dig300-Wash Buffer) for 1 h at 37 °C. The tagmentation reaction was stopped by the addition of 10 µL 0.5 M EDTA, 3 µL 10 % SDS, and 2.5 µL 20 mg/mL proteinase K, and incubated for 1 h at 55 °C. DNA was purified with 1 X AMPure XP beads (Beckman Coulter) to enrich for ≥ 100 bp fragments.
Libraries were amplified using KAPA HiFi HotStart polymerase (Roche Sequencing Store, Cat. KK2601) with 14 and 18 PCR cycles for H3K27me3 and H2AK119ub, respectively.

treatment_protocol: Naive HNES1 cells were seeded at a density of 1.6 x 104/cm2 on plates coated with 1 % Geltrex and cultured in PXGL conditions. After 24 h in PXGL, either 1 µM UNC1999 (a catalytic inhibitor of the EZH1/2 subunits of PRC2), 2.5 µM UNC6852 (a PROTAC degrader of the EED subunit of PRC2), or an equivalent volume of DMSO (control) was added. After 24 h, cells were withdrawn from PXGL and cultured in N2B27 medium supplemented with XAV939 supplemented with either 1 µM UNC1999, 2.5 µM UNC6852, or DMSO. This time point was designated “day 0” of the transition experiment. Medium and inhibitors were replaced every day until day 5. Cells were harvested on day 5

value: Human pluripotent stem cell

value: Wild-type

value: PROTAC


title: HM014


title: HSPC_KO_ATAC_Rep3

city: New York

first: Varun

middle: Saichandan

last: Sudunagunta

state: NY

address: 650 W 168th, Black Building, 1110B

department: Division of Hematology/Oncology, Department of Medicine

institute: Columbia University Vagelos College of Physicians and Surgeons

description: Library name: AD006 ATAC

library_source: genomic single cell

data_processing:
Demultiplexed data was processed using the Cellranger count pipeline
Assembly: mm10
Supplementary files format and content: .rds object using ArchR to analyze scATAC portion only. Within .rds object are the annotated cell types.

source_name: HSPC

extract_protocol:
Nuclei were isolated from sorted HSPCs (Lineage negative) as per 10X Genomics protocol
As per 10X multiome protocol

value: HSPC

value: KO

value: ATAC


title: HSPC_KO_GEX_Rep3

description: Library name: AD006 RNA

value: mRNA


title: UNC_H3K27me3_Rep2

description: Library name: library11

value: UNC


title: UNC_H3K27me3_Rep1

description: Library name: library10


title: HSPC_KO_ATAC_Rep2

description: Library name: AD005 ATAC


title: M_2

city: Kunming

first: shouyao

last: zhang

state: Yunnan

address: No.1076, yuhua road, chenggong district

institute: Yunnan University of Chinese Medicine

description: children with cerebral palsy, replicate biosample 2

hyb_protocol: The biotinylated cRNA targets were then hybridized with the slides.  scan protocol After hybridization, slides were scanned on the Agilent Microarray Scanner G5761A (Agilent technologies, Santa Clara, CA, US).

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data were extracted with Feature Extraction software 12.0.3.1 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm. The microarray experiments were performed by following the protocol of Agilent technologies at LC Sciences Corporation （Hangzhou，China）

source_name: circRNAs in peripheral blood

label_protocol: RNA samples of each group were then used to generate biotinylated cRNA targets for the LC Human ceRNA array V1.0（4*180K, Design ID:085202; GPL30304）.

growth_protocol: Healthy volunteers coming to this hospital for medical visits and ethically approved Cerebral Palsy patients.

extract_protocol: Total RNA was isolated using RNA Isolation Kit #58000(Norgen, Canada) according to the manufacturer’s instructions, and purified by using a RNeasy Mini Kit (Qiagen, Germany) .Total RNA was checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: none tratment

value: blood

tag: subject group

value: children with cerebral palsy


title: M_3

description: children with cerebral palsy, replicate biosample 3


title: UNC_H2AK119ub_Rep2

description: Library name: library9


title: HSPC_KO_GEX_Rep2

description: Library name: AD005 RNA


title: undescended testis (UD), French bulldog, age 17 months

city: Poznań

first: Arkadiusz

last: Kajdasz

state: wielkopolskie

address: ul. Z. Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry PAS

description: Library name: 6978_UD

data_processing:
Quality of raw reads were checked with fastqc (v0.11). Reads were mapped to the dog genome (CanFam3.1, downloaded from Ensembl database) with bowtie2 including --local setting (v2.4.2). SAM files were converted to BAM files with samtools (v1.11). Reads mapped to miRNA sequences were counted with featureCounts (v2.0.1) using annotation file downloaded from miRBase (v22, annotation file release date 2018-03-05).
Assembly: CanFam3.1
Supplementary files format and content: tab-delimited text files includes raw counts of miRNA for each Sample

organism: Canis lupus familiaris

source_name: testis

extract_protocol:
Total RNA from testicular tissue was isolated using an miRNeasy Mini Kit (Qiagen) according to manufacturer protocol.
The concentration of miRNA was measured with Qubit RNA BR Assay Kit (Invitrogen) on a Qubit 2.0 fluorometer (Invitrogen). The purity was analyzed using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific). The RNA integrity number (RIN) values were checked on a 2100 Bioanalyzer instrument (Agilent) using RNA 6000 Nano kit (Agilent). For each sample, 200 ng of total RNA was used for library preparation with NEXTflex Small RNA-Seq Kit v3 (Bioo Scientific).

value: testis

tag: disease

value: undescended testis (UD)

tag: breed

value: French bulldog

value: 17 months


title: descended testis (D), French bulldog, age 17 months

description: Library name: 6978_D

value: descended testis (D)


title: descended testis (D), Yorkshire terrier, age 23 months

description: Library name: 7030_D

value: Yorkshire terrier

value: 23 months


title: B_2

description: healthy contro, replicate biosample 2

value: healthy control


title: B_3

description: healthy contro, replicate biosample 3


title: M_1

description: children with cerebral palsy, replicate biosample 1


title: B_1

description: healthy contro, replicate biosample 1


title: UNC_H2AK119ub_Rep1

description: Library name: library8

value: Human pluripotent stem cell

value: Wild-type

tag: treatment


title: Unc93b1 3d/3d TAM,  αMARCO, rep2

description: Library name: ED31_KO_2

tag: tissue

value: Tumor

value: Macrophages

value: Unc93b1 3d/3d (Absence of endosomal Toll-like receptors (TLRs))

value: αMARCO


title: HSPC_WT_ATAC_Rep3

description: Library name: AD004 ATAC

value: HSPC

tag: genotype

value: WT

value: ATAC


title: descended testis (D), Chihuahua, age 46 months

description: Library name: 6968_D

value: testis

value: Chihuahua

value: 46 months


title: undescended testis (UD), Chihuahua, age 46 months

description: Library name: 6968_UD

value: undescended testis (UD)


title: PROTAC_H3K27me3_Rep2

description: Library name: library7

value: PROTAC


title: HSPC_WT_GEX_Rep3

description: Library name: AD004 RNA

value: mRNA


title: scrotal testis (C), Shih-tzu, age 35 months

description: Library name: 6976_C

value: scrotal testis (C)

value: Shih-tzu

value: 35 months


title: scrotal testis (C), French bulldog, age 21 months

description: Library name: 6975_C

value: French bulldog

value: 21 months


title: PROTAC_H2AK119ub_Rep2

description: Library name: library6

value: Human pluripotent stem cell

value: Wild-type


title: HSPC_KO_ATAC_Rep1

description: Library name: AD003 ATAC

value: KO


title: scrotal testis (C), French bulldog, age 23 months

description: Library name: 7182_C

value: 23 months


title: PROTAC_H2AK119ub_Rep1

description: Library name: library5


title: HSPC_KO_GEX_Rep1

description: Library name: AD003 RNA

value: HSPC


title: undescended testis (UD), Yorkshire terrier, age 36 months

description: Library name: 6983_UD

value: Yorkshire terrier

value: 36 months


title: DMSO_H3K27me3_Rep2

description: Library name: library4

value: DMSO


title: HSPC_WT_ATAC_Rep2

description: Library name: AD002 ATAC

value: WT

value: ATAC


title: scrotal testis (C), Chihuahua, age 29 months

description: Library name: 6923_C

value: testis

value: Chihuahua

value: 29 months


title: DMSO_H3K27me3_Rep1

description: Library name: library3


title: scrotal testis (C), Pug, age 11 months

description: Library name: 6901_C

value: scrotal testis (C)

value: Pug

value: 11 months


title: DMSO_H2AK119ub_Rep2

description: Library name: library2


title: scrotal testis (C), Maltese, age 11 months

description: Library name: 7114_C

value: Maltese


title: HSPC_WT_ATAC_Rep1

description: Library name: AD001 ATAC


title: descended testis (D), Shih-tzu, age 30 months

description: Library name: 6906_D

value: descended testis (D)

value: Shih-tzu

value: 30 months


title: scrotal testis (C), Yorkshire terrier biewer, age 18 months

description: Library name: 7113_C

value: Yorkshire terrier biewer

value: 18 months


title: scrotal testis (C), Shih-tzu, age 10 months

description: Library name: 7005_C

value: 10 months


title: HSPC_WT_GEX_Rep1

description: Library name: AD001 RNA

value: HSPC

value: mRNA


title: descended testis (D), Maltese, age 11 months

description: Library name: 7021_D


title: UNC_Day5_Rep3

description: Library name: library9

data_processing:
Reads were trimmed with trim_galore v0.6.10 using default parameters.
Trimmed data was mapped to GRCh38 using hisat2 v2.2.1 with options --n0-discordant --no-softclip --no-mixed guided by introns taken from Ensembl v87
Data was quantitated in SeqMonk v1.48.1 using the RNA-Seq quantitation pipeline in opposing strand specific mode. Geome annotations were taken from Ensembl v113
Assembly: GRCh38
Supplementary files format and content: Tab delimited text file of raw directional overlap counts per gene and sample

extract_protocol:
Total RNA was extracted from PRC2-perturbed cells treated with DMSO, PROTAC, or UNC1999 at day 5 of the transition, with three biological replicates per condition. Cells were washed with PBS and harvested in RLT buffer from the RNeasy Mini Kit (Qiagen Cat No: 74104) and stored at -80C. Once thawed, the suspension was passed through a QIAshredder (Qiagen Cat no: 79656) and the RNA purified using the RNeasy Mini Kit following manufacturer’s instructions. Contaminating DNA was removed using the Turbo DNA free kit (ThermoFisher Scientific Cat No: AM1907) following manufacturer’s instructions.
RNA-seq libraries were prepared using the Watchmaker RNA Library Prep Kit with ribosomal RNA depletion following manufacturer’s instructions.

value: Human pluripotent stem cell

value: Wild-type

value: UNC


title: UNC_Day5_Rep2

description: Library name: library8


title: descended testis (D), French bulldog, age 22 months

description: Library name: 7022_D

value: testis

value: French bulldog

value: 22 months


title: UNC_Day5_Rep1

description: Library name: library7


title: GRA knockin, Dex, biol rep4

city: RTP

first: Thomas

last: Randall

state: NC

address: 101 TW Alexander

institute: NIEHS

description: Library name: Sample 19

data_processing:
Alignment using STAR (V 2.5.1).
Read count was produced with featureCount (subread, Version 1.5.1)
Statistical analysis done with DEseq2 (v 1.38.3)
DEG was obtained using adjusted pvalue <0.05
Assembly: mm39/genecode_vM34
Supplementary files format and content: readcounts in txt format

source_name: hippocampus

extract_protocol:
The hippocampus was collected after the 6 hour PBS or Dex treatment.  Total RNA was isolated from the hippocampus using Qiagen RNeasy mini kit.
The integrity of the total RNA was determined using the TapeStation (Agilent Technologies), and RNA concentration was assessed using a Qubit (ThermoFisher Scientific).  A TruSeq RNA kit (Illumina, San Diego, CA) was utilized to prepare the poly(A)-enriched RNA-seq libraries that were sequenced on the Illumina NovaSeq 6000 in a 75-base paired-end mode according to the manufacturer’s protocol.

treatment_protocol: Adrenalectomized wild-type and homozygous GRA knockin mice were injected IP with PBS (vehicle) or dexamethasone (Dex) (1mg/kg).  After a 6-hour treatment time, mice were euthanized and the hippocampus removed.

value: hippocampus

value: male

value: GRA knockin

value: Dex


title: descended testis (D), Pug, age 17 months

description: Library name: 7040_D

value: descended testis (D)

value: Pug

value: 17 months


title: undescended testis (UD), Yorkshire terrier, age 23 months

description: Library name: 7030_UD

value: undescended testis (UD)

value: Yorkshire terrier

value: 23 months


title: 014_Week_8

city: Rochester

first: Emma

last: Durrenberger

state: Minnesota

address: 200 First St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

description:
Library name: sample_30
014_Week_8

data_processing:
Libraries were multiplexed and sequenced in a single lane using the standard protocol for the Illumina NovaSeq 6000 and the NovaSeq XP 4-Lane kit for individual lane loading. The flow cell was sequenced as 100 X 2 paired-end reads using the NovaSeq S4 sequencing kit and NovaSeq Control Software v1.8.0. Base-calling was performed with Illumina’s RTA version 3.4.4.
The raw RNA sequencing paired-end reads were processed through the Mayo RNA-Seq bioinformatics pipeline, MAP-RSeq version 3.1.5. MAP-RSeq uses STAR to align reads to the reference human genome build hg38. Gene and exon expression quantification were performed using the Subread package to obtain both raw and normalized (FPKM – Fragments Per Kilobase per Million mapped reads) reads. Finally, comprehensive analyses were run on the aligned reads to assess the quality of the sequenced libraries.
Assembly: hg38
Supplementary files format and content: merged_gene_count.tsv tsv file containing merged raw gene counts for all samples
Supplementary files format and content: merged_gene_count_fpkm_by_read.tsv tsv file containing gene count fpkm by read for all samples

source_name: blood

extract_protocol:
Total RNA concentration and quality were determined using Qubit fluorometry (ThermoFisher Scientific, Waltham, MA) and the Agilent Fragment Analyzer (Santa Clara, CA). The total RNA underwent globin depletion using GLOBINclear (ThermoFisher Scientific, Waltham, MA) and a clean-up with DNase I (Zymo Research, Irvine, CA) treatment.
cDNA libraries were prepared using 100 ng of total RNA according to the manufacturer’s instructions for the Illumina Stranded mRNA Prep, Ligation (Illumina, San Diego, CA). The concentration and size distribution of the completed libraries were determined with the Agilent TapeStation and Qubit fluorometry.

value: blood

value: PBMCs

tag: time point


title: PROTAC_Day_5_Rep_1

description: Library name: library6

tag: cell type

value: Human pluripotent stem cell

value: Wild-type

value: PROTAC


title: PROTAC_Day5_Rep3

description: Library name: library5


title: GRA knockin, Dex, biol rep1

description: Library name: Sample 16

tag: strain


title: PROTAC_Day5_Rep2

description: Library name: library4


title: 4851, HIGH RFI

city: Guelph

first: Victoria

last: Asselstine

state: Ontario

address: 553 Gordon St #501

country: Canada

institute: University of Guelph

description: Library name: Sample 37

data_processing:
Data was processed using CLC genomics workbench
the raw sequence data was trimmed using the automatic trimmer function of CLC Genomics Workbench (CLC Bio, Aarhus, Denmark) using a quality trimming score = 0.05.
After the reads were trimmed, quality control was performed using the NGS quality control tool of CLC Genomics Workbench
The trimmed sequence reads were then aligned to the annotated ARS_UCD1.2 bovine reference genome using the CLC Genomics Workbench
Alignment parameters included a length fraction of 0.8 and a similarity of 0.8, mismatch cost = 2, deletion cost = 3, insert cost = 3, minimum contig length = 200 base pairs (bp) were allowed
Read cound and normalization was performed using CLC genomics workbench
Assembly: ARS_UCD1.2
Supplementary files format and content: csv file with raw counts per gene and sample

organism: Bos taurus

source_name: Milk Somatic Cells

extract_protocol:
Milk samples were collected using a 3 cm plastic cannula to ensure no bacteria contaminated the sample. Milk was kept on ice and immediately processed for RNA extraction using Trizol reagent to preserve the integrity of RNA.
Library construction was performed using the TruSeq RNA sample preparation kit

value: Milk Somatic Cells

value: Holstein dairy


title: 4843, HIGH RFI

description: Library name: Sample 36


title: 4838, LOW RFI

description: Library name: Sample 35


title: DMSO_Day5_Rep3

description: Library name: library3

value: DMSO


title: GRA knockin, PBS, biol rep4

description: Library name: Sample 14

value: hippocampus

value: male

value: PBS


title: DMSO_Day5_Rep2

description: Library name: library2


title: C. sardiniense with subsequent C. difficile prdB mutant 24 hours post infection Mouse 7

status: Public on Jun 09 2026

city: Boston

first: Lynn

last: Bry

state: MA

address: 75 Francis St.

department: Pathology

institute: Brigham and Women's Hospital

data_processing:
Bowtie2 was used to align filtered and trimmed reads to a library consisting of C. diffcile, C. saridiniense, and Mus musculus DNA sequences for all reactions to ensure specific alignments to C. difficile gene features.
Reads were assigned to features in alignments using HTSeq. Reads overlapping multiple features were assigned to both to account for polycistronic RNAs.
Reads were also analyzed with Kraken2 to check for contaminants. Note - mouse chow contains RNAs which are present in caecal contents.
A 10 read average cutoff was applied. C. difficile genomic features were analyzed.
DESeq2 was used to normalize read counts and for subsequent differential expression analyses.
Assembly: C. difficile ATCC 43255 https://www.bv-brc.org/view/Genome/1496.5150, M. musculus GRCm39 https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001635.27/, C. sardiniense DSM 599 https://www.bv-brc.org/view/Genome/29369.14
Supplementary files format and content: HTSeq CDS read counts per gene.

organism:
Clostridioides difficile
Mus musculus
Clostridium sardiniense

source_name: Mouse caecal contents

growth_protocol: 6-7 week-old male and female gnotobiotic (germ-free) mice were pre-colonized by gavage (C. sardiniense) with 10^8 cfu 1 week before inoculation by gavage with10^3 C. difficile ATCC43255 spores.

extract_protocol:
Mice were sacrificed at the indicated timepoint and dissected. Cecal contents were immediately cryogenically stored for RNA extraction.
Purified RNAs were rRNA depleted and eukaryotic (mouse) poly-A mrRNA depleted. Illumina NovaSeq S4-300 with paired-end 150 nucleotide runs were performed.

value: Mouse caecal contents


title: 4829, HIGH RFI

description: Library name: Sample 32


title: Control experiment 2, 24 hrs of vehicle treatment

city: Ulm

first: Pallab

last: Maity

address: Meyerhofstrasse/James Franck Ring

department: Dermatology

country: Germany

institute: University of Ulm

description: Library name: Co_24h_2

data_processing:
Raw reads (fastq) were pseudoaligned and quantified with Kallisto quant with bootostrap set to 100. Transcript abundance counts from kallisto quant for all the samples were merged to a single transcript expression count matrix. This transcript expression count matrix was applied for differential transcript expression analyses using DESeq2. Visualization and representation of the transcriptome data were performed by custom R scripts in R-Studio environment.
Assembly: GRCh38
Supplementary files format and content: tab delimited txt file for count data

source_name: adipose tissue derived mesenchymal stromal cell

growth_protocol: cells were cultured in Mesenchymal Stem Cell Growth Medium 2 at 37C and 5% CO2

extract_protocol:
RNA was isolated from the cells using Rneasy plus kit (Qiagen). 1 µg of total RNA was used for the rRNA depletion and library preparation.
Library was prepared using NEBNext Ultra II Directional RNA Library Preparation kit (NEB)

treatment_protocol: Cells were treated either with vehicle or S100A8_A9 (0.5 µg/ml) for 6, 12 or 24 hrs

value: vehicle


title: Control experiment 3, 12 hrs of vehicle treatment

description: Library name: Co_12h_3

value: adipose tissue derived mesenchymal stromal cell


title: GRA knockin, PBS, biol rep3

description: Library name: Sample 13

value: GRA knockin


title: 4825, LOW RFI

description: Library name: Sample 31


title: 4824, LOW RFI

description: Library name: Sample 30


title: GRA knockin, PBS, biol rep2

description: Library name: Sample 12


title: 4821, LOW RFI

description: Library name: Sample 29


title: Pomalidomide, 100uM, Bonsai, 3

city: Lausanne

first: Nicolas

last: Thomä

address: Rte Cantonale

country: Switzerland

institute: EPFL

description:
Library name: Pomalidomide 100 Bonsai 3
Bonsai_Pomalidomide_processed.txt
B_100_3_S18

library_source: other

data_processing:
Data was processed and matched to its expected sequence with Mutscan. Then the logFC was calculated with edgeR and Limma (Singe/Dual) or Loess (DMS). Additional details in the corresponding manuscript.
Assembly: Reference sequences were used for alignment
Supplementary files format and content: Tab delimmited text files. Contains count, logFC, Pvalues and dna sequence for alignment.

molecule: other

organism: Saccharomyces cerevisiae

extract_protocol:
For all Single ZF, Dual Z and Bonsai libraries, DNA was extracted using a custom yeast Miniprep protocol. For the DMS library, DNA was extracted using a custom yeast Midiprep protocol.
Sequencing libraries wer constructed by PCR with primers containing the illumina adapters

value: Pomalidomide, 100uM, Bonsai


title: 4820, HIGH RFI

description: Library name: Sample 28


title: GRA knockin, PBS, biol rep1

description: Library name: Sample 11


title: Pomalidomide, 100uM, Bonsai, 2

description:
Library name: Pomalidomide 100 Bonsai 2
Bonsai_Pomalidomide_processed.txt
B_100_2_S17


title: 4819, LOW RFI

description: Library name: Sample 27


title: NEMODK, Stimulated, 2 days, H3K27me3, rep2

city: Milwaukee

first: Demin

last: Wang

state: WI

address: 8727 W Watertown Plank Rd

institute: 1Versiti Blood Research Institute

description: Library name: Stim_14_H3K27me3

data_processing:
For data analysis, reads were aligned to the mm10 mouse genome, and peaks were identified using SEACR v1.3  in stringent mode with IgG controls. Data normalization and differential peak analysis were conducted using DESeq2 v1.32.0
Assembly: mm10
Supplementary files format and content: bigWig files after peakcalling
Library strategy: CUT&Tag

source_name: primary cells

extract_protocol:
Splenic B cells were isolated from WT and NEMODK mice, stimulated with anti-CD40 and IL-4 for two days, then washed and resuspended in wash buffer. Cells were bound to ConA-coated beads, incubated overnight with anti-RelA (Cell Signaling, 8242), anti-H3K4me3 (Active Motif, 39159), anti-H3K27ac (Active Motif, 39034), and anti-H3K27me3 (Cell Signaling, 9733) antibodies, followed by secondary incubation with anti-rabbit IgG antibodies (Antibodies Online). After washing, the cells were incubated with the pA-Tn5 adapter complex (Epicypher) at room temperature for 1 hour.
Tagmentation was performed at 37°C, after which DNA was extracted and PCR-amplified to generate sequencing libraries. Libraries were sequenced on an Illumina NovaSeq platform to produce paired-end 150 bp reads.

value: Spleen

value: B cells

value: NEMODK

value: Anti-CD40 and IL-4


title: C. sardiniense with subsequent C. difficile prdB mutant 24 hours post infection Mouse 2


title: 4817, HIGH RFI

description: Library name: Sample 26


title: 4815, HIGH RFI

description: Library name: Sample 25


title: wild-type, Dex, biol rep5

description: Library name: Sample 10

value: wild-type

value: Dex


title: Pomalidomide, 100uM, Bonsai, 1

description:
Library name: Pomalidomide 100 Bonsai 1
Bonsai_Pomalidomide_processed.txt
B_100_1_S16


title: 4810, HIGH RFI

description: Library name: Sample 24

value: Milk Somatic Cells


title: wild-type, Dex, biol rep4

description: Library name: Sample 9


title: 4808, LOW RFI

description: Library name: Sample 23

value: Holstein dairy


title: Pomalidomide, 0.1uM, Bonsai, 3

description:
Library name: Pomalidomide 0.1 Bonsai 3
Bonsai_Pomalidomide_processed.txt
B_0-1_3_S9

value: Pomalidomide, 0.1uM, Bonsai


title: DMSO_Day5_Rep1

description: Library name: library1

value: Human pluripotent stem cell

value: Wild-type

value: DMSO


title: 4807, HIGH RFI

description: Library name: Sample 22


title: wild-type, Dex, biol rep3

description: Library name: Sample 8

value: hippocampus

value: male


title: 4804, HIGH RFI

description: Library name: Sample 21


title: Pomalidomide, 0.1uM, Bonsai, 2

description:
Library name: Pomalidomide 0.1 Bonsai 2
Bonsai_Pomalidomide_processed.txt
B_0-1_2_S8


title: 4803, HIGH RFI

description: Library name: Sample 20


title: Control experiment 3, 6 hrs of vehicle treatment

description: Library name: Co_6h_3

value: adipose tissue derived mesenchymal stromal cell

value: vehicle


title: wild-type, Dex, biol rep2

description: Library name: Sample 7


title: 4798, LOW RFI

description: Library name: Sample 19


title: Pomalidomide, 0.1uM, Bonsai, 1

description:
Library name: Pomalidomide 0.1 Bonsai 1
Bonsai_Pomalidomide_processed.txt
B_0-1_1_S7


title: descended testis (D), French bulldog, age 23 months

description: Library name: 7223_D

value: testis

value: descended testis (D)

value: French bulldog

tag: age

value: 23 months


title: undescended testis (UD), French bulldog, age 23 months

description: Library name: 7223_UD

value: undescended testis (UD)


title: 4797, HIGH RFI

description: Library name: Sample 18


title: wild-type, Dex, biol rep1

description: Library name: Sample 6

tag: Sex

value: wild-type


title: 4795, HIGH RFI

description: Library name: Sample 17


title: descended testis (D), Yorkshire terrier, age 36 months

description: Library name: 6983_D

value: Yorkshire terrier

value: 36 months


title: DMSO, Bonsai, 3

description:
Library name: DMSO Bonsai 3
Bonsai_Pomalidomide_processed.txt
B_DMSO_3_S6

value: DMSO, Bonsai


title: 4789, LOW RFI

description: Library name: Sample 16

value: Milk Somatic Cells

value: Holstein dairy


title: 4786, LOW RFI

description: Library name: Sample 15


title: HSPC_WT_GEX_Rep2

description: Library name: AD002 RNA

value: HSPC

value: WT

value: mRNA


title: wild-type, PBS, biol rep5

description: Library name: Sample 5

value: hippocampus

value: male

value: PBS


title: DMSO, Bonsai, 2

description:
Library name: DMSO Bonsai 2
Bonsai_Pomalidomide_processed.txt
B_DMSO_2_S5


title: 4785, LOW RFI

description: Library name: Sample 14


title: wild-type, PBS, biol rep4

description: Library name: Sample 4


title: 4783, LOW RFI

description: Library name: Sample 13


title: DMSO_H2AK119ub_Rep1

description: Library name: library1

value: Human pluripotent stem cell

value: Wild-type

value: DMSO


title: 4781, LOW RFI

description: Library name: Sample 12


title: DMSO, Bonsai, 1

description:
Library name: DMSO Bonsai 1
Bonsai_Pomalidomide_processed.txt
B_DMSO_1_S4


title: wild-type, PBS, biol rep3

description: Library name: Sample 3


title: 4775, LOW RFI

description: Library name: Sample 11


title: Pomalidomide, 15uM, DMS, 3

description:
Library name: Pomalidomide 15 DMS 3
DMS_Pomalidomide_processed.txt
M-POM-15-3_S12

data_processing:
Data was processed and matched to its expected sequence with Mutscan. Then the logFC was calculated with edgeR and Limma (Singe/Dual) or Loess (DMS). Additional details in the corresponding manuscript.
Assembly: Reference sequences were used forr alignment
Supplementary files format and content: Tab delimmited text files. Contains count, logFC, Pvalues and dna sequence for alignment.

extract_protocol:
For all Single ZF and Dual ZF libraries, DNA was extracted using a custom yeast Miniprep protocol. For the DMS library, DNA was extracted using a custom yeast Midiprep protocol.
Sequencing libraries wer constructed by PCR with primers containing the illumina adapters

value: Pomalidomide5uM, DMS


title: undescended testis (UD), Maltese, age 11 months

description: Library name: 7021_UD

value: testis

value: undescended testis (UD)

value: Maltese

value: 11 months


title: 4774, LOW RFI

description: Library name: Sample 10


title: wild-type, PBS, biol rep2

description: Library name: Sample 2

value: wild-type


title: GRA knockin, Dex, biol rep5

description: Library name: Sample 20

value: GRA knockin

value: Dex


title: undescended testis (UD), Pug, age 17 months

description: Library name: 7040_UD

value: Pug

value: 17 months


title: undescended testis (UD), French bulldog, age 22 months

description: Library name: 7022_UD

value: French bulldog

value: 22 months


title: Pomalidomide, 15uM, DMS, 2

description:
Library name: Pomalidomide 15 DMS 2
DMS_Pomalidomide_processed.txt
M-POM-15-2_S11


title: 4773, HIGH RFI

description: Library name: Sample 9

value: Milk Somatic Cells

value: Holstein dairy


title: 4764, LOW RFI

description: Library name: Sample 8


title: GRA knockin, Dex, biol rep3

description: Library name: Sample 18

value: hippocampus

value: male


title: 4762, LOW RFI

description: Library name: Sample 7


title: 4755, HIGH RFI

description: Library name: Sample 6


title: Mammary glands, Oxtr flox rep (1-4); Adipo-specific-Oxtr KO rep(1-4), HTO

first: NORC

last: Boston

address: 3 Blackfan Circle, CLS0733

institute: Beth Israel Deaconess Medical Center

description:
Library name: Multiplexed_Samples_HTO
10x Genomics

data_processing:
The QC for the RNA-Seq data was perfomed using fastp
The demultiplexing, barcoded processing, were made using the Cell Ranger software v7.2.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm39
Supplementary files format and content: Cell Ranger output files: mRNA_barcodes.tsv.gz, mRNA_features.tsv.gz, mRNA_matrix.mtx.gz
Supplementary files format and content: Count HTOs output: hto.stat.csv.gz

molecule: nuclear RNA

source_name: Mammary glands

growth_protocol: Breeding cages were established using 8-week-old male and female mice, with all animals maintained on a standard chow diet. To prevent further mating, males were removed from the cages once pregnancy was confirmed.

extract_protocol:
Nuclei were isolated from frozen mouse mammary gland samples for 10x snRNA-seq using a slightly modified approach to what was previously described (PMID: 32888429 and PMID: 35296864). Samples were kept frozen on dry ice until immediately before nuclei isolation, and all sample handling steps were performed on ice. Each flash-frozen adipose tissue sample was placed into a gentleMACS C tube (Miltenyi Biotec, 130-096-334) with 2 ml freshly prepared TST buffer (0.03% Tween 20 (Bio-Rad 1610781), 0.01% Molecular Grade BSA (New England Biolabs B9000S), 146 mM NaCl (ThermoFisher Scientific AM9759), 1 mM CaCl2 (VWR 97062-820), 21 mM MgCl2 (Sigma Aldrich M1028), and 10 mM Tris-Hcl pH 7.5 (ThermoFisher Scientific 15567027) in Ultrapure water (ThermoFisher Scientific 10977-023)) with or without 0.2 U µl−1 of Protector RNase Inhibitor (Sigma Aldrich 3335399001). gentleMACS C tubes were then placed on the gentleMACS Dissociator (Miltenyi Biotec 130-093-235) and tissue was dissociated by running the program mr_adipose_01 twice, and then incubated on ice for 10 min. Lysate was passed through a 40 µm nylon filter (CellTreat 229481) and collected into a 50 ml conical tube (Thomas Scientific 1149Z03). Filter was rinsed with 3 ml of freshly prepared ST buffer buffer (146 mM NaCl, 1 mM CaCl2, 21 mM MgCl2; 10 mM Tris-Hcl pH 7.5) with or without 0.2 U µl−1 RNase Inhibitor, and collected into the same tube. Flow-through was centrifuged at 500g for 5 min at 4 °C with brake set to low. Following centrifugation, supernatant was removed, and the nuclear pellet was resuspended in 50–200 µl PBS pH 7.4 (ThermoFisher Scientific 10010049) with 0.02% BSA, with or without 0.2 U µl−1 RNase inhibitor. In order to reduce ambient mRNA, the nuclear pellets of some samples were washed 1–3 times with 5 ml PBS, 0.02% BSA before final resuspension. An aliquot of nuclei from each sample was stained with NucBlue (Invitrogen R37605) counted in a haemocytometer using fluorescence to identify intact nuclei, and then immediately loaded on the 10x Chromium controller (10x Genomics) according to the manufacturer’s protocol.
For each sample, 10,000–16,500 nuclei were loaded in one channel of a Chromium Chip (10x Genomics). The Single Cell 3′ v3.1 chemistry was used to process all samples. cDNA and gene expression libraries were generated according to the manufacturer’s instructions (10x Genomics). cDNA and gene expression library fragment sizes were assessed with a DNA High Sensitivity Bioanalyzer Chip (Agilent 5067-4626). cDNA and gene expression libraries were quantified using the Qubit dsDNA High Sensitivity assay kit (ThermoFisher Scientific Q32851). Gene expression libraries were multiplexed and sequenced on the Nextseq 500 (Illumina) with a 75-cycle kit and the following read structure: Read 1: 28 cycles, Read 2: 55 cycles, Index Read 1: 8 cycles.

treatment_protocol: On postnatal day 1 (P1), litter sizes were standardized to 4-5 pups per cage. Inguinal white adipose tissue (iWAT) was harvested from lactating Oxtrflox and OxtrΔAd dams on postnatal day 11 (P11). Lymph nodes were carefully removed from the iWAT fat pads, which were then flash-frozen in liquid nitrogen and stored at -80°C for subsequent single nucleus RNA-seq analysis.

value: Mammary glands

value: Oxtr flox; Adipo-specific Oxtr KO

tag: library type

value: HTO


title: wild-type, PBS, biol rep1

description: Library name: Sample 1

value: PBS


title: Pomalidomide, 15uM, DMS, 1

description:
Library name: Pomalidomide 15 DMS 1
DMS_Pomalidomide_processed.txt
M-POM-15-1_S10

value: Pomalidomide5uM, DMS


title: 4747, LOW RFI

description: Library name: Sample 4


title: DMSO, DMS, 3

description:
Library name: DMSO DMS 3
DMS_Pomalidomide_processed.txt
M-DMSO-3_S6

value: DMSO, DMS


title: DMSO, DMS, 2

description:
Library name: DMSO DMS 2
DMS_Pomalidomide_processed.txt
M-DMSO-2_S5


title: 4749, LOW RFI

description: Library name: Sample 5


title: 4742, LOW RFI

description: Library name: Sample 3


title: 4731, HIGH RFI

description: Library name: Sample 2


title: 4721, LOW RFI

description: Library name: Sample 1


title: DMSO, DMS, 1

description:
Library name: DMSO DMS 1
DMS_Pomalidomide_processed.txt
M-DMSO-1_S4


title: multiome tumor biopsy sample, replicate 3, ATAC

city: Brussels

first: Gabriel

middle: Sölvi

last: Windels

address: 808, route de Lennik

department: Faculty of Medicine

country: Belgium

institute: Université Libre de Bruxelles (ULB)

description: Library name: MU3_atac

data_processing:
The raw reads from Multiome sequencing outputs with single cell ATAC and single cell gene expression were aligned to the mm10 mouse reference genome, and then quantified by the CellRanger pipeline.
Assembly: mm10
Supplementary files format and content: CellRanger output files: MU1_filtered_feature_bc_matrix.h5, MU2_filtered_feature_bc_matrix.h5, MU3_filtered_feature_bc_matrix.h5
Supplementary files format and content: CellRanger output files: MU1_atac_fragments.tsv.gz, MU2_atac_fragments.tsv.gz, MU3_atac_fragments.tsv.gz
Supplementary files format and content: CellRanger output files: MU1_atac_fragments.tsv.gz.tbi, MU2_atac_fragments.tsv.gz.tbi, MU3_atac_fragments.tsv.gz.tbi

source_name: skin

extract_protocol:
After FACS isolation, 200.000 cells were collected in PBS, 0,04% filtered BSA using low binding 1.5 ml tubes (Eppendorf). For nuclei isolation, the protocol CG000365 Rev C, 10x Genomics was followed.
Nuclei were resuspended in nuclei buffer, counted and loaded on Chromium Next GEM Single Cell Multiome, ATAC + Gene Expression microfluidic chips (10x Genomics) was employed for Multiome. The libraries were prepared using the Chromium Single Cell 3′ Library Kit (V2-chemistry, 10x Genomics), quantified using a low coverage Illumina NextSeq 550 run and sequenced on an Illumina NovaSeq.

value: skin

value: tumor

tag: library

value: ATAC


title: Tumor5_TC

first: Yuemeng

last: Jia

address: 1 Blackfan Circle

institute: Boston Children's Hospital

description: Library name: HCC5_TC

data_processing:
The identities of the DARLIN arrays were determined using a custom MATLAB script described in the manuscript.
Assembly: mm10
Supplementary files format and content: txt.gz

source_name: Liver

extract_protocol:
Frozen tissues were embedded in OCT and sectioned at 10 μm.
DARLIN arrays were amplified by nested PCR according to the SPACE-seq protocol described in the manuscript.

value: Liver


title: multiome tumor biopsy sample, replicate 2, ATAC

description: Library name: MU2_atac


title: Tumor4_TC

description: Library name: HCC4_TC


title: multiome tumor biopsy sample, replicate 1, ATAC

description: Library name: MU1_atac


title: Tumor3_TC

description: Library name: HCC3_TC


title: Liver_YJ734_TC

description: Library name: Liver_YJ734_TC

data_processing:
The identities of the DARLIN arrays were determined using a custom MATLAB script described in the manuscript.
Assembly: mm10
Supplementary files format and content: tsv.gz
Supplementary files format and content: mtx.gz

source_name: Brain

value: Brain


title: Input, DMS, 2

description:
Library name: Input DMS 2
DMS_Pomalidomide_processed.txt
M-INP-2_S2

value: Input, DMS


title: Liver_E15_5_YJ1005_TC

description: Library name: Liver_E15_5_YJ1005_TC


title: Liver_YJ734_RC

description: Library name: Liver_YJ734_RC


title: multiome tumor biopsy sample, replicate 3, GEX

description: Library name: MU3_rna

value: mRNA


title: Input, DMS, 1

description:
Library name: Input DMS 1
DMS_Pomalidomide_processed.txt
M-INP-1_S1


title: Liver_E15_5_YJ1005_RC

description: Library name: Liver_E15_5_YJ1005_RC


title: multiome tumor biopsy sample, replicate 2, GEX

description: Library name: MU2_rna


title: Liver_E10_YJ1022_TC

description: Library name: Liver_E10_YJ1022_TC


title: paya_mng_293

type: genomic

city: Heidelberg

first: Philipp

last: Sievers

address: Im Neuenheimer Feld 224

department: Neuropathology

institute: University Hospital Heidelberg, Intitute of Pathology

description: PAYA MNG

hyb_protocol: Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing:
Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'  Average beta
Average Beta
Unmethylated and methylated signal intensities

label: cy3, cy5

source_name: PAYA MNG

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

treatment_protocol: An automated extraction was done with a Maxwell system (Promega, Fitchburg, WI, USA) and the Maxwell 16 FFPE Plus LEV DNA Purification Kit according to the manufacturer’s instructions.

tag: material

value: FFPE

value: Male

tag: age group

tag: methylation class

value: ben

tag: localisation

value: supratentoriell


title: Liver_E10_YJ1022_RC

description: Library name: Liver_E10_YJ1022_RC


title: multiome tumor biopsy sample, replicate 1, GEX

description: Library name: MU1_rna


title: Brain_LL904_right_TC

description: Library name: Brain_LL904_right_TC


title: Creb3l1KO.d8.Ep-.sample2

description:
Library name: Creb3l1KO d8 Ep- sample2
Column name in normalised_counts.csv: Creb3l1KO.d8.Ep-.sample2

data_processing:
The multiplexed libraries (11 pM or 18 pM) were loaded onto flow cells and sequences were produced using a HiSeq PE Cluster Kit v4 and TruSeq SBS Kit v3-HS (250 cycles) on a Novaseq 6000 (Illumina). Approximately 20 million paired end reads per sample were generated and quality checks were performed with FastQC.
The adapter sequences and low-quality regions were trimmed by Trimmomatic
Trimmed reads were mapped against the mouse reference genome (Grcm38/mm10) using STAR software to generate read alignments.
Duplicated reads were removed by Picard MarkDuplicates.
After transcript assembly, gene level counts were obtained using HTseq and normalized to 20 millions of aligned reads.
Assembly: mm10
Supplementary files format and content: csv file includes normalised counts for each sample

source_name: primary cell lines derived from Lgr5CreER/ KrasLSL-G12D/p53fl/fl/Rosa26-YFP+/+ primary tumor and CRISPR/Cas9-derived cell lines

extract_protocol:
After FACS isolation, cultured cells were collected in for RNA extraction. RNA was extracted from FACS-isolated cells or culture cell lines using RNeasy micro kit (QIAGEN) according to the manufacturer’s recommendations. RNA quality was evaluated by Bioanalyzer 2100 (Agilent) before sequencing.
Indexed cDNA libraries were obtained using Ovation Solo RNA-seq Systems (NuGen) according to the manufacturer’s recommendations.

tag: cell line

tag: time

tag: ko treatment

tag: epcam condition

value: Neg

tag: batch


title: Brain_LL904_right_RC

description: Library name: Brain_LL904_right_RC

tag: tissue


title: Brain_LL904_right_CC

description: Library name: Brain_LL904_right_CC


title: Creb3l1KO.d8.Ep+.sample2

description:
Library name: Creb3l1KO d8 Ep+ sample2
Column name in normalised_counts.csv: Creb3l1KO.d8.Ep+.sample2

value: primary cell lines derived from Lgr5CreER/ KrasLSL-G12D/p53fl/fl/Rosa26-YFP+/+ primary tumor and CRISPR/Cas9-derived cell lines

tag: genotype

value: Pos


title: Brain_LL904_left_TC

description: Library name: Brain_LL904_left_TC


title: Brain_LL904_left_RC

description: Library name: Brain_LL904_left_RC


title: paya_mng_289

description: PAYA MNG

value: Female


title: Brain_LL904_left_CC

description: Library name: Brain_LL904_left_CC


title: Creb3l1KO.d8.Ep-.sample1

description:
Library name: Creb3l1KO d8 Ep- sample1
Column name in normalised_counts.csv: Creb3l1KO.d8.Ep-.sample1


title: paya_mng_282

description: PAYA MNG

value: Frozen

value: int

value: skull base


title: Creb3l1KO.d8.Ep+.sample1

description:
Library name: Creb3l1KO d8 Ep+ sample1
Column name in normalised_counts.csv: Creb3l1KO.d8.Ep+.sample1


title: Brain_LL903_RC

description: Library name: Brain_LL903_RC


title: paya_mng_281

description: PAYA MNG


title: Brain_LL903_CC

description: Library name: Brain_LL903_CC


title: Brain_spikeIn_5_CC

description: Library name: Brain_spikeIn_5_CC


title: Nfatc1KO.d8.Ep-.sample2

description:
Library name: Nfatc1KO d8 Ep- sample2
Column name in normalised_counts.csv: Nfatc1KO.d8.Ep-.sample2


title: Brain_spikeIn_1_CC

description: Library name: Brain_spikeIn_1_CC


title: paya_mng_280

description: PAYA MNG


title: Brain_spikeIn_5_RC

description: Library name: Brain_spikeIn_5_RC


title: Nfatc1KO.d8.Ep+.sample2

description:
Library name: Nfatc1KO d8 Ep+ sample2
Column name in normalised_counts.csv: Nfatc1KO.d8.Ep+.sample2


title: Brain_spikeIn_0_CC

description: Library name: Brain_spikeIn_0_CC


title: Nfatc1KO.d8.Ep-.sample1

description:
Library name: Nfatc1KO d8 Ep- sample1
Column name in normalised_counts.csv: Nfatc1KO.d8.Ep-.sample1


title: Brain_spikeIn_1_RC

description: Library name: Brain_spikeIn_1_RC


title: Brain_spikeIn_0_RC

description: Library name: Brain_spikeIn_0_RC


title: paya_mng_276

description: PAYA MNG

value: posterior fossa


title: Brain_spikeIn_5_TC

description: Library name: Brain_spikeIn_5_TC


title: Brain_spikeIn_1_TC

description: Library name: Brain_spikeIn_1_TC


title: paya_mng_273

description: PAYA MNG


title: Klf5KO.d8.Ep-.sample2

description:
Library name: Klf5KO d8 Ep- sample2
Column name in normalised_counts.csv: Klf5KO.d8.Ep-.sample2


title: YK184_Right_superior_E15_5

description: Library name: YK184_Right_superior_E15_5

data_processing:
The data was process with our customized software (https://gitlab.com/hormozlab/carlin)
Assembly: mm10
Supplementary files format and content: text files

extract_protocol:
RNA were extracted with Qiagen RNAeasy
RNA was reverse transcribed using a CARLIN-specific UMI-tagged primer. The DARLIN from Col1a1 was was then PCR amplified by nested PCR


title: paya_mng_272

description: PAYA MNG


title: YK184_Right_inferior_E15_5

description: Library name: YK184_Right_inferior_E15_5


title: Klf5KO.d8.Ep+.sample2

description:
Library name: Klf5KO d8 Ep+ sample2
Column name in normalised_counts.csv: Klf5KO.d8.Ep+.sample2


title: paya_mng_269

description: PAYA MNG

value: ventricel


title: RNA-seq: cGFP tagged EBNA3A transient transfection Rep 2

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

description: Library name: RNA_EBNA3A_cGFP_RepB_E05649

data_processing:
RNA-seq reads were mapped to the hg38 genome using the nf-core RNA-seq pipeline with the default alignment options (STAR and Salmon).
Transcription abundance estimates were generated by Salmon
Assembly: hg38
Supplementary files format and content: Aligned reads in bigWig format. Reads were normalized using deepTools bamCoverage with the parameters --normalizeUsing CPM --binSize 10. The reads aligned to the forward strand were processed separately from the reads aligned to the reverse strand. The parameter --scaleFactor -1 was used when generating the reads on the reverse strand.

growth_protocol: Flp-In-293 cells were plated on 6 well plates in DMEM supplemented with 10% FBS, 0.1% Anti-anti, and 0.2% normocin. Two days later, the cells were transfected using Lipofectamine 2000, according to the manufacturer’s protocol, with 0.25 µg of vTR plasmid and 2.25 mg of the pOG44 Flp-Recombinase expression vector. Within three days, the media was changed to media containing hygromycin at 50 mg/mL and the hygromycin was gradually increased to 200 mg/mL to produce a pool of cells stably expressing the vTR. Doxycycline inducible Flp-In T-REx-293 cells were cultured in media also containing 100µg/mL zeocin. These cells were cultured in 1µg/mL doxycycline for overnight prior to collection.

extract_protocol:
Total RNA was isolated using the mirVana RNA extraction kit
rRNA depleted, stranded libraries were generated by the sequencing center. Samples were sequenced at either Novogene or the Cincinnati Children’s Hospital Medical Center Genomics Sequencing Facility (CCHMC)

tag: transfection type

value: Transient transfection

tag: transfection plasmid

value: cGFP tagged EBNA3A

tag: sequencing center

value: Novogene


title: Klf5KO.d8.Ep-.sample1

description:
Library name: Klf5KO d8 Ep- sample1
Column name in normalised_counts.csv: Klf5KO.d8.Ep-.sample1


title: YK184_Left_E15_5

description: Library name: YK184_Left_E15_5

value: Liver


title: paya_mng_268

description: PAYA MNG

value: FFPE

tag: Sex


title: Klf5KO.d8.Ep+.sample1

description:
Library name: Klf5KO d8 Ep+ sample1
Column name in normalised_counts.csv: Klf5KO.d8.Ep+.sample1


title: YJ775_Right_superior_E10

description: Library name: YJ775_Right_superior_E10


title: paya_mng_263

description: PAYA MNG

value: spinal


title: YJ775_Right_inferior_E10

description: Library name: YJ775_Right_inferior_E10


title: YJ775_Median_right_E10

description: Library name: YJ775_Median_right_E10


title: paya_mng_261

description: PAYA MNG

value: Male

value: ben


title: Pitx1KO.d8.Ep-.sample2

description:
Library name: Pitx1KO d8 Ep- sample2
Column name in normalised_counts.csv: Pitx1KO.d8.Ep-.sample2

value: Neg


title: YJ775_Median_left_E10

description: Library name: YJ775_Median_left_E10


title: Pitx1KO.d8.Ep+.sample2

description:
Library name: Pitx1KO d8 Ep+ sample2
Column name in normalised_counts.csv: Pitx1KO.d8.Ep+.sample2

value: primary cell lines derived from Lgr5CreER/ KrasLSL-G12D/p53fl/fl/Rosa26-YFP+/+ primary tumor and CRISPR/Cas9-derived cell lines


title: paya_mng_257

description: PAYA MNG

value: supratentoriell


title: Pitx1KO.d8.Ep-.sample1

description:
Library name: Pitx1KO d8 Ep- sample1
Column name in normalised_counts.csv: Pitx1KO.d8.Ep-.sample1


title: YJ775_Caudate_E10

description: Library name: YJ775_Caudate_E10


title: YJ775_Left2_E10

description: Library name: YJ775_Left2_E10


title: paya_mng_278

description: PAYA MNG


title: RNA-seq: nGFP tagged EBNA1 transient transfection Rep 2

description: Library name: RNA_EBNA1_nGFP_RepB_E006022

value: nGFP tagged EBNA1

value: CCHMC


title: paya_mng_256

description: PAYA MNG

value: Female


title: RNA-seq: untagged EBNA1 transient transfection Rep 1

description: Library name: RNA_EBNA1_only_RepA_E006018

value: untagged EBNA1


title: Pitx1KO.d8.Ep+.sample1

description:
Library name: Pitx1KO d8 Ep+ sample1
Column name in normalised_counts.csv: Pitx1KO.d8.Ep+.sample1

value: Pos


title: paya_mng_252

description: PAYA MNG

value: int

value: posterior fossa


title: YJ774_Median_right_E10

description: Library name: YJ774_Median_right_E10


title: paya_mng_251

description: PAYA MNG

value: Frozen


title: Control.d8.Ep+.sample2

description:
Library name: Control d8 Ep+ sample2
Column name in normalised_counts.csv: Control.d8.Ep+.sample2

value: Control


title: YJ774_Left2_E10

description: Library name: YJ774_Left2_E10

value: Liver


title: paya_mng_248

description: PAYA MNG

value: FFPE

value: skull base


title: Nfatc1KO.d8.Ep+.sample1

description:
Library name: Nfatc1KO d8 Ep+ sample1
Column name in normalised_counts.csv: Nfatc1KO.d8.Ep+.sample1


title: YJ774_Caudate_E10

description: Library name: YJ774_Caudate_E10


title: Control.d8.Ep-.sample1

description:
Library name: Control d8 Ep- sample1
Column name in normalised_counts.csv: Control.d8.Ep-.sample1


title: paya_mng_247

description: PAYA MNG


title: LL1183_Right_inferior_E15_5

description: Library name: LL1183_Right_inferior_E15_5


title: Control.d8.Ep+.sample1

description:
Library name: Control d8 Ep+ sample1
Column name in normalised_counts.csv: Control.d8.Ep+.sample1


title: LL1183_Median_right2_E15_5

description: Library name: LL1183_Median_right2_E15_5


title: LL1183_Median_right1_E15_5

description: Library name: LL1183_Median_right1_E15_5


title: LL1183_Median_left2_E15_5

description: Library name: LL1183_Median_left2_E15_5


title: paya_mng_245

description: PAYA MNG

value: Male


title: LL1183_Median_left1_E15_5

description: Library name: LL1183_Median_left1_E15_5


title: Control.d0.Ep+.sample1

description:
Library name: Control d0 Ep+ sample1
Column name in normalised_counts.csv: Control.d0.Ep+.sample1


title: YJ774_Median_left_E10

description: Library name: YJ774_Median_left_E10


title: LL1183_Left3_E15_5

description: Library name: LL1183_Left3_E15_5


title: paya_mng_242

description: PAYA MNG

value: ben


title: LL1183_Left2_E15_5

description: Library name: LL1183_Left2_E15_5


title: Mammary glands, Oxtr flox rep (1-4); Adipo-specific-Oxtr KO rep(1-4), GEX

description:
Library name: Multiplexed_Samples_mRNA
10x Genomics

value: Mammary glands

value: Oxtr flox; Adipo-specific Oxtr KO

tag: library type

value: mRNA


title: Embryo 32_3, Right side of microdissected heart field, stage E8.5i

city: Paris

first: Sigolène

middle: M

last: Meilhac

address: 24 boulevard du Montparnasse

country: France

institute: Institut Imagine, Institut Pasteur

description: Library name: 32_3_R

data_processing:
After demultiplexing, reads were trimmed to remove adapter sequences. Sequence quality was assessed using FastQC and Picard metrics. FASTQ files were mapped to the ENSEMBL Mus musculus GRCm39 reference genome using the Illumina STAR aligner and counted by featureCounts from the Subread package (v2.0.6).
Genes with low expression levels were filtered, using the filterByExpr function of edgeR R package [edgeR] with parameters min.count = 5, min.total.count = 10, large.n = 50 and min.prop = 0.2.
All differential analyses were carried out using the DESeq2 R package, with local fit type for dispersion estimation and ashr type to shrink the log2 fold changes.
An initial differential analysis was performed on wild-type samples to identify genes associated with asymmetry in wild type samples. The DESeq2 model was adjusted for the effect of the side (left/right) and embryo identifier to account for pairing. The resulting lists of differentially expressed genes (DEG) was refined by retaining “congruent” genes, defined as those exhibiting the same left-right trend across all samples. By using this list, asymmetry behaviour of mutant samples was divided into 3 laterality clusters.
A second differential analysis was then conducted to assess asymmetry variations between clusters, using a DESeq2 model adjusted for the effect of the side and embryo identifier, as well as to evaluate expression changes within each side, using a model adjusted for the cluster and sex. DEG were filtered to exclude genes not expressed in myocardial lineages and then refined to 1842 genes exhibiting diverse variation patterns.
Assembly: ENSEMBL Mus musculus GRCm39 reference genome
Supplementary files format and content: Processed data for all samples is in the file named: processed_data_file.txt
Supplementary files format and content: The file includes all available genes in the 1st column, under the column header "Geneid". To its right, there is a column per sample, with the sample name as a column header and matching "library name" in this Excel. Raw counts per gene (no filtering applied) are indicated.

source_name: microdissected heart field

growth_protocol: Embryos were dissected at E8.5.

extract_protocol:
Total RNA was extracted in TRIzol-Chloroform and purified using the RNeasy Micro Elute Columns kit (QIAGEN) including DNAse treatment. RNA quality and quantity were measured on Fragment Analyzer (Agilent Technologies). All RQN were >9.1.
RNAseq libraries were prepared starting from 10 ng of total RNA using the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina.
The cDNAs produced from the poly-A+ fraction were PCR amplified in 2 steps (9 cycles for the first amplification and -8 cycles for the second amplification). An equimolar pool of the final indexed RNA-Seq libraries was sequenced on an Illumina NovaSeq6000, with paired-end reads of 100 bases and a mean of ~80 million of reads/clusters was obtained per sample.

treatment_protocol: The heart field of E8.5i embryos was microdissected, divided into left and right halves, and flash frozen in liquid nitrogen

value: microdissected heart field

tag: side

value: Right

tag: heart looping_direction

value: Rightward


title: LL1183_Right_superior_E15_5

description: Library name: LL1183_Right_superior_E15_5


title: LL1183_Left1_E15_5

description: Library name: LL1183_Left1_E15_5


title: paya_mng_241

description: PAYA MNG

tag: material

value: Female

tag: age group

value: supratentoriell


title: Input, DMS, 3

description:
Library name: Input DMS 3
DMS_Pomalidomide_processed.txt
M-INP-3_S3

tag: treatment

value: Input, DMS


title: LL1183_Caudate_E15_5

description: Library name: LL1183_Caudate_E15_5


title: paya_mng_246

description: PAYA MNG

tag: methylation class

tag: localisation


title: LL1176_Right_superior_E12

description: Library name: LL1176_Right_superior_E12


title: Embryo 32_3, Left side of microdissected heart field, stage E8.5i

description: Library name: 32_3_L

value: Left


title: paya_mng_240

description: PAYA MNG


title: LL1176_Right_inferior_E12

description: Library name: LL1176_Right_inferior_E12


title: Embryo 32_2, Right side of microdissected heart field, stage E8.5i

description: Library name: 32_2_R

value: Inverted


title: paya_mng_291

description: PAYA MNG


title: LL1176_Median_right2_E12

description: Library name: LL1176_Median_right2_E12


title: Control.d0.Ep+.sample2

description:
Library name: Control d0 Ep+ sample2
Column name in normalised_counts.csv: Control.d0.Ep+.sample2

tag: cell line

value: primary cell lines derived from Lgr5CreER/ KrasLSL-G12D/p53fl/fl/Rosa26-YFP+/+ primary tumor and CRISPR/Cas9-derived cell lines

tag: time

tag: ko treatment

value: Control

value: Pos


title: paya_mng_290

description: PAYA MNG

value: FFPE


title: paya_mng_237

description: PAYA MNG

value: Male

value: int


title: Embryo 32_2, Left side of microdissected heart field, stage E8.5i

description: Library name: 32_2_L

tag: tissue


title: LL1176_Median_right1_E12

description: Library name: LL1176_Median_right1_E12

value: Liver


title: LL1176_Median_left1_E12

description: Library name: LL1176_Median_left1_E12


title: LL1176_Median_left2_E12

description: Library name: LL1176_Median_left2_E12


title: Brain_LL903_TC

description: Library name: Brain_LL903_TC

value: Brain


title: Embryo 23_3, Right side of microdissected heart field, stage E8.5i

description: Library name: 23_3_R

tag: genotype


title: paya_mng_234

description: PAYA MNG

value: skull base


title: LL1176_Left3_E12

description: Library name: LL1176_Left3_E12


title: LL1176_Left2_E12

description: Library name: LL1176_Left2_E12


title: Embryo 23_3, Left side of microdissected heart field, stage E8.5i

description: Library name: 23_3_L

value: microdissected heart field


title: paya_mng_228

description: PAYA MNG

value: ben


title: LL1176_Caudate_E12

description: Library name: LL1176_Caudate_E12


title: Embryo 22_4, Right side of microdissected heart field, stage E8.5i

description: Library name: 22_4_R

value: Right

value: Rightward


title: Human PBMCs TCR-seq library, 10X Batch 5

city: Parkville

first: Davide

last: Vespasiani

address: 1G Royal Parade

institute: The Walter and Eliza Hall Institute

description:
Library name: TCR_Batch5
10x Genomics

data_processing:
Bcl2fastq (v2.20.0; Illumina) was used to convert and demultiplex CITE-seq and VDJ-seq BaseCall files into FASTQ files. Cellranger mkref and cellranger mkvdjref (v8.0.1; 10x Genomics) were used to build the hs1/T2T-CHM13v2.0 reference genome respectively for the CITE-seq and VDJ-seq data using the GCF_009914755.1_T2T-CHM13v2.0_genomic.gtf file downloaded from NCBI https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/ and the hs1.fa fasta file was downloaded from https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/. Cellranger multi and cellranger vdj (v8.0.1; 10x Genomics) were respectively used to align the CITE-seq and VDJ-seq libraries to the hs1 reference genome and to generate the cell barcode-gene UMI count matrices. Gene expression count matrices for each sequencing batch were separately processed with Seurat (v.5.4.0) in R (v. 4.4.1). HTODemux (assay = "HTO", positive.quantile = 0.99, kfunc='clara') was used to assign the donor ID and the vaccination timepoint for each single cell based on cell hashtags and to remove both doublets and negative droplets.  High-quality single-cells were identified and processed using Seurat.
Assembly: hs1 (T2T-CHM13v2.0), GCF_009914755.1_T2T-CHM13v2.0
Supplementary files format and content: GEX_matrix.mtx.gz (matrix with gene expression counts, with row names in GEX_features.tsv and column names in GEX_barcodes.tsv)
Supplementary files format and content: ADT_matrix.mtx.gz (matrix with protein expression counts, with row names in ADT_features.tsv and column names in ADT_barcodes.tsv)
Supplementary files format and content: HTO_matrix.mtx.gz (matrix with cell hashtag expression counts, with row names in HTO_features.tsv and column names in HTO_barcodes.tsv)
Supplementary files format and content: TCR_filtered_contig.fastq containing the raw sequence for the assembled VDJ contigs of high-confidence for the T cell receptor with corresponding annotations in TCR_filtered_contig_annotations.csv
Supplementary files format and content: BCR_filtered_contig.fastq containing the raw sequence for the assembled VDJ contigs of high-confidence for the B cell receptor with corresponding annotations in BCR_filtered_contig_annotations.csv
Library strategy: TCR-Seq

source_name: peripheral mononuclear blood cells

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were separated and cryopreserved from blood samples collected at baseline and 7-days post-vaccination
PBMC samples were collected from 10 patients with SAD, 10 CVID and 10 healthy controls collected before and 7 days after vaccination. All 60 samples were stained with Hash Tag Oligonucleotides (HTOs) and a panel of 130 Antibody-Derived Tags (ADTs) using TotalSeqTM antibodies (BioLegend), pooled and then split into 5 batches (12 samples each). For each batch, GEX, ADT and HTO and VDJ libraries were generateed using the 10X Genomics Chromium single-cell 5′ reagent kit v3 according to manufacturer’s protocol and then sequenced on a NovaSeq X Plus (PE150).

treatment_protocol: A single dose of Vi-polysaccharide vaccine (TYPHIM Vi; Sanofi Pasteur, Lyon France), containing 25mcg of purified Salmonella Typhi capsular Vi-polysaccharide, was administered intramuscularly on day 0 (baseline). Follow up visits were performed at 7 days and 1, 6 and 13 months post-vaccination. Serum samples collected at baseline and 1, 6 and 13 months post-vaccination were stored at -80C prior to analysis. PBMCs were separated and cryopreserved from freshly isolated blood samples collected at baseline and 7-days post-vaccination.

value: peripheral mononuclear blood cells

tag: cell type

value: alpha-beta T cells

value: Day0 and Day7 post-vaccination

value: Typhim Vi vaccine

tag: batch


title: paya_mng_279

description: PAYA MNG

value: Female

value: orbital


title: paya_mng_225

description: PAYA MNG

value: mal


title: Embryo 22_4, Left side of microdissected heart field, stage E8.5i

description: Library name: 22_4_L

value: Left


title: Human PBMCs TCR-seq library, 10X Batch 4

description:
Library name: TCR_Batch4
10x Genomics


title: paya_mng_224

description: PAYA MNG

value: FFPE

value: ventricel


title: Human PBMCs TCR-seq library, 10X Batch 2

description:
Library name: TCR_Batch2
10x Genomics


title: Human PBMCs TCR-seq library, 10X Batch 3

description:
Library name: TCR_Batch3
10x Genomics


title: Brain_spikeIn_0_TC

description: Library name: Brain_spikeIn_0_TC


title: Embryo 22_1, Right side of microdissected heart field, stage E8.5i

description: Library name: 22_1_R


title: Human PBMCs TCR-seq library, 10X Batch 1

description:
Library name: TCR_Batch1
10x Genomics


title: paya_mng_223

description: PAYA MNG

value: supratentoriell


title: Human PBMCs BCR-seq library, 10X Batch 5

description:
Library name: BCR_Batch5
10x Genomics

data_processing:
Bcl2fastq (v2.20.0; Illumina) was used to convert and demultiplex CITE-seq and VDJ-seq BaseCall files into FASTQ files. Cellranger mkref and cellranger mkvdjref (v8.0.1; 10x Genomics) were used to build the hs1/T2T-CHM13v2.0 reference genome respectively for the CITE-seq and VDJ-seq data using the GCF_009914755.1_T2T-CHM13v2.0_genomic.gtf file downloaded from NCBI https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/ and the hs1.fa fasta file was downloaded from https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/. Cellranger multi and cellranger vdj (v8.0.1; 10x Genomics) were respectively used to align the CITE-seq and VDJ-seq libraries to the hs1 reference genome and to generate the cell barcode-gene UMI count matrices. Gene expression count matrices for each sequencing batch were separately processed with Seurat (v.5.4.0) in R (v. 4.4.1). HTODemux (assay = "HTO", positive.quantile = 0.99, kfunc='clara') was used to assign the donor ID and the vaccination timepoint for each single cell based on cell hashtags and to remove both doublets and negative droplets.  High-quality single-cells were identified and processed using Seurat.
Assembly: hs1 (T2T-CHM13v2.0), GCF_009914755.1_T2T-CHM13v2.0
Supplementary files format and content: GEX_matrix.mtx.gz (matrix with gene expression counts, with row names in GEX_features.tsv and column names in GEX_barcodes.tsv)
Supplementary files format and content: ADT_matrix.mtx.gz (matrix with protein expression counts, with row names in ADT_features.tsv and column names in ADT_barcodes.tsv)
Supplementary files format and content: HTO_matrix.mtx.gz (matrix with cell hashtag expression counts, with row names in HTO_features.tsv and column names in HTO_barcodes.tsv)
Supplementary files format and content: TCR_filtered_contig.fastq containing the raw sequence for the assembled VDJ contigs of high-confidence for the T cell receptor with corresponding annotations in TCR_filtered_contig_annotations.csv
Supplementary files format and content: BCR_filtered_contig.fastq containing the raw sequence for the assembled VDJ contigs of high-confidence for the B cell receptor with corresponding annotations in BCR_filtered_contig_annotations.csv
Library strategy: BCR-Seq

value: B cells


title: Human PBMCs BCR-seq library, 10X Batch 4

description:
Library name: BCR_Batch4
10x Genomics


title: paya_mng_222

description: PAYA MNG

value: posterior fossa


title: Embryo 19_6, Right side of microdissected heart field, stage E8.5i

description: Library name: 19_6_R

value: microdissected heart field


title: paya_mng_221

description: PAYA MNG

value: ben

value: skull base


title: Human PBMCs BCR-seq library, 10X Batch 1

description:
Library name: BCR_Batch1
10x Genomics


title: Embryo 19_6, Left side of microdissected heart field, stage E8.5i

description: Library name: 19_6_L

value: Rightward


title: Human PBMCs BCR-seq library, 10X Batch 2

description:
Library name: BCR_Batch2
10x Genomics

value: peripheral mononuclear blood cells


title: WM115_3D, rep 4

city: Milan

first: Michela

last: Francesconi

state: Brescia

address: Via Giovanni Antonio Amadeo, 42

country: Italy

institute: Istituto Nazionale dei Tumori

description: Library name: WM115_3D_4

data_processing:
BlueBee Genomics Platform (Lexogen).
Assembly: GRCh38/hg38 was used as human reference genome
Supplementary files format and content: tab-delimeted text file includes raw counts for each sample

extract_protocol:
RNA was extracted using the Direct-zol RNA MicroPrep Kit (Zymo Research)
Sequencing libraries were prepared from 100 ng of total RNA using the QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD (Lexogen), as per the manufacturer’s instructions.

value: melanoma

value: Melanosphere enrichment protocol


title: paya_mng_217

description: PAYA MNG


title: Embryo 19_4, Right side of microdissected heart field, stage E8.5i

description: Library name: 19_4_R

value: Right


title: WM115_3D, rep 2

description: Library name: WM115_3D_2


title: paya_mng_216

description: PAYA MNG

value: Female


title: Embryo 19_4, Left side of microdissected heart field, stage E8.5i

description: Library name: 19_4_L


title: WM115_2D, rep 4

description: Library name: WM115_2D_4

value: No treatment


title: paya_mng_213

description: PAYA MNG

value: Male


title: WM115_2D, rep 3

description: Library name: WM115_2D_3


title: Embryo 18_2, Right side of microdissected heart field, stage E8.5i

description: Library name: 18_2_R

value: Inverted


title: WM115_2D, rep 2

description: Library name: WM115_2D_2


title: paya_mng_211

description: PAYA MNG

value: Frozen


title: WM115_2D, rep 1

description: Library name: WM115_2D_1


title: paya_mng_208

description: PAYA MNG

value: FFPE

value: int


title: A375_3D, rep 2

description: Library name: A375_3D_2


title: A375_3D, rep1

description: Library name: A375_3D_1


title: Embryo 18_1, Left side of microdissected heart field, stage E8.5i

description: Library name: 18_1_L

value: Left


title: A375_2D, rep4

description: Library name: A375_2D_4


title: paya_mng_203

description: PAYA MNG

value: supratentoriell


title: A375_2D, rep3

description: Library name: A375_2D_3


title: WM115_3D, rep 3

description: Library name: WM115_3D_3


title: A375_2D, rep 2

description: Library name: A375_2D_2


title: paya_mng_201

description: PAYA MNG

value: posterior fossa


title: Embryo 17_7, Left side of microdissected heart field, stage E8.5i

description: Library name: 17_7_L

value: microdissected heart field


title: paya_mng_206

description: PAYA MNG


title: WM115 stem cell-educated macrophages, rep 4

description: Library name: CM_WM115_4

value: monocyte/macrophage

value: PMA 20nM for 72 h followed by incubation with WM115 stem cell conditioned medium for 24 h


title: paya_mng_194

description: PAYA MNG

value: ben


title: WM115 stem cell-educated macrophages, rep 3

description: Library name: CM_WM115_3


title: Embryo 17_1, Right side of microdissected heart field, stage E8.5i

description: Library name: 17_1_R

value: Rightward


title: WM115 stem cell-educated macrophages, rep 2

description: Library name: CM_WM115_2


title: paya_mng_193

description: PAYA MNG


title: Embryo 17_7, Right side of microdissected heart field, stage E8.5i

description: Library name: 17_7_R


title: Embryo 17_1, Left side of microdissected heart field, stage E8.5i

description: Library name: 17_1_L


title: WM115 stem cell-educated macrophages, rep 1

description: Library name: CM_WM115_1


title: paya_mng_236

description: PAYA MNG


title: A373 stem cell-educated macrophages, rep 4

description: Library name: CM_A375_4

value: PMA 20nM for 72 h followed by incubation with A375 stem cell conditioned medium for 24 h


title: A375_2D, rep 1

description: Library name: A375_2D_1

value: melanoma


title: paya_mng_187

description: PAYA MNG


title: LL1176_Left1_E12

description: Library name: LL1176_Left1_E12

value: Liver


title: Embryo 15_5, Right side of microdissected heart field, stage E8.5i

description: Library name: 15_5_R

value: Right


title: A373 stem cell-educated macrophages, rep 3

description: Library name: CM_A375_3


title: A373 stem cell-educated macrophages, rep 2

description: Library name: CM_A375_2


title: paya_mng_186

description: PAYA MNG

value: Male

value: spinal


title: A373 stem cell-educated macrophages, rep 1

description: Library name: CM_A375_1


title: Embryo 15_5, Left side of microdissected heart field, stage E8.5i

description: Library name: 15_5_L


title: paya_mng_185

description: PAYA MNG


title: M0 macrophages, rep4

description: Library name: M0_4

value: PMA 20nM for 72 h


title: M0 macrophages, rep3

description: Library name: M0_3


title: Embryo 22_1, Left side of microdissected heart field, stage E8.5i

description: Library name: 22_1_L

value: Female


title: Embryo 10_3, Right side of microdissected heart field, stage E8.5i

description: Library name: 10_3_R

value: Inverted


title: Human PBMCs BCR-seq library, 10X Batch 3

state: VIC

description:
Library name: BCR_Batch3
10x Genomics

value: peripheral mononuclear blood cells

value: B cells

value: Day0 and Day7 post-vaccination

value: Typhim Vi vaccine


title: M0 macrophages, rep2

description: Library name: M0_2

value: monocyte/macrophage


title: paya_mng_184

description: PAYA MNG

value: FFPE

value: supratentoriell


title: M0 macrophages, rep1

description: Library name: M0_1


title: ChIP-seq: anti-GFP ZTA in Akata B cells Rep 3

description: Library name: ChIP_CL0169_Akata_ZTA_RepC_E007460

data_processing:
ChIP-seq alignment, quality control, and peak calling was performed using a version of the ChIP-Seq Transcription Factor Pipeline v2.2.0 from the ENCODE Project slightly modified to run within a Nextflow environment.
ChIP-seq reads were aligned to the human genome (hg38) using Bowtie2. Aligned reads were then sorted using samtools and duplicate reads were removed using Picard.
Peaks were called using the default parameters of MACS2.
Conservative overlap peaks, generated from the ENCODE pipeline, were obtained for each transfection plasmid and used for downstream analyses.
Assembly: hg38
Supplementary files format and content: Conservative overlap peaks in narrowPeak format.
Supplementary files format and content: Aligned reads in bigWig format. Reads were normalized using deepTools bamCoverage with the parameters --normalizeUsing CPM --binSize 10

source_name: Akata B cells

growth_protocol: EBV negative Akata B cells were added to Retronectin treated 12 well plates at 250K cells per well. Cells were transduced at an MOI of 5 with a pLenti lentiviral vector construct using a lentiviral transduction protocol. The construct contained either the GFP control or ZTA. Viral media was left on cells for 24 hours before switching to regular RPMI suspension media with 0 ug/mL of puromycin. After cell viability improved following transduction, cells were selected in 1 ug/mL of Puromycin

extract_protocol:
Cells were crosslinked and nuclei were sonicated as described previously (Lu et al. 2015).
Libraries were prepared via ChIPmentation (Schmidl et al. 2015).

treatment_protocol: 1 ug/mL of puromycin media

value: Akata B cells

tag: transfection plasmid

value: pLenti nGFP tagged ZTA

tag: chip target

value: GFP

tag: antibody

value: Abcam ab290

tag: antibody lot_number


title: Embryo 10_3, Left side of microdissected heart field, stage E8.5i

description: Library name: 10_3_L

value: microdissected heart field

tag: side

value: Left

tag: Sex

tag: heart looping_direction


title: paya_mng_180

description: PAYA MNG

tag: material

value: Male

tag: age group

value: ben


title: ChIP-seq: anti-GFP ZTA in Akata B cells Rep 2

description: Library name: ChIP_CL0169_Akata_ZTA_RepB_E007459


title: Embryo 10_1, Right side of microdissected heart field, stage E8.5i

description: Library name: 10_1_R

value: Right

value: Rightward


title: ChIP-seq: anti-GFP in GFP control Akata B cells Rep 3

description: Library name: ChIP_CL0172_Akata_GFP_RepC_E007563

value: pLenti GFP control


title: Embryo 10_1, Left side of microdissected heart field, stage E8.5i

description: Library name: 10_1_L


title: WM115_3D, rep 1

description: Library name: WM115_3D_1

value: melanoma

tag: treatment

value: Melanosphere enrichment protocol


title: ChIP-seq: anti-GFP ZTA in Akata B cells Rep 1

description: Library name: ChIP_CL0169_Akata_ZTA_RepA_E007458

tag: cell line


title: paya_mng_171

description: PAYA MNG

tag: methylation class

value: int

tag: localisation

value: skull base


title: ChIP-seq: anti-GFP in GFP control Akata B cells Rep 2

description: Library name: ChIP_CL0172_Akata_GFP_RepB_E007562


title: paya_mng_170

description: PAYA MNG

value: FFPE

value: Female


title: ChIP-seq: anti-GFP in GFP control Akata B cells Rep 1

description: Library name: ChIP_CL0172_Akata_GFP_RepA_E007561

value: Akata B cells


title: Embryo 8_1, Right side of microdissected heart field, stage E8.5i

description: Library name: 8_1_R

tag: tissue


title: Static, 120h, 3

city: Jena

first: Marc Thilo

last: Figge

state: Thuringen

address: Adolf-Reichwein-Straße 23

department: Applied System Biology

institute: HKI-Leibniz

description: Library name: Static_3

data_processing:
Raw paired-end FASTQ files were quality-checked using FastQC.
Reads were aligned to the human reference genome GRCh38 using STAR.
Gene-level read counts were generated using featureCounts with Ensembl gene annotation.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file containing featureCounts gene-level raw counts for each sample, including gene annotation columns and per-sample count columns

source_name: C2BBe1, HUVECs, primary monocyte-derived macrophages

growth_protocol: Intestine-on-chips were built according to Feile et al. (Immunocompetent Intestine-on-Chip Model for Analyzing Gut Mucosal Immune Responses. J Vis Exp. 2024 May 24;(207). doi: 10.3791/66603)

extract_protocol:
RNA-extraction was performed using tha RNeasy Kit (Qiagen) to the manufacturer's recommendation.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: Flow chips were kept under flow for 120h while static chips were only perfused for 30minutes per day. 48h before the endpoint, LPS was added to the intestinal compartment of the chip.

value: 120h static


title: paya_mng_169

description: PAYA MNG

value: ventricel


title: Embryo 18_2, Left side of microdissected heart field, stage E8.5i

description: Library name: 18_2_L

value: Inverted

tag: genotype


title: Static, 120h, 2

description: Library name: Static_2

value: C2BBe1, HUVECs, primary monocyte-derived macrophages


title: Embryo 8_1, Left side of microdissected heart field, stage E8.5i

description: Library name: 8_1_L

value: microdissected heart field

value: Left


title: Static, 120h, 1

description: Library name: Static_1


title: Flow, 120h, 3

description: Library name: Flow_3

value: 120h flow


title: paya_mng_168

description: PAYA MNG

value: Male

value: ben


title: A375_3D, rep 4

description: Library name: A375_3D_4

tag: cell type


title: A375_3D, rep 3

description: Library name: A375_3D_3


title: Embryo 7_1, Right side of microdissected heart field, stage E8.5i

description: Library name: 7_1_R

value: Right

value: Rightward


title: Flow, 120h, 2

description: Library name: Flow_2


title: Embryo 7_1, Left side of microdissected heart field, stage E8.5i

description: Library name: 7_1_L


title: paya_mng_166

description: PAYA MNG

value: supratentoriell