title: lung #28826, tumor-derived, rep# 6

description: Library name: 28826-6


title: Astrocytes_healthy_BBN002.35107

status: Public on Aug 23 2025

type: genomic

city: Maastricht

first: Ehsan

last: Pishva

state: Limburg

address: Universiteitssingel 40

department: Psychiatry and Neuropsychology

country: Netherlands

institute: Maastricht University

hyb_protocol: Illumina Infinium protocol

scan_protocol: Illumina Infinium protocol scanned using Illumina HIScan System

data_processing: wateRmelon package (v2.10.0) in R environment (v4.4.1)

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Brain (Prefrontal Cortex)

label_protocol: Illumina Infinium protocol

extract_protocol: Phenol-chloroform DNA extraction

tag: Sex

value: Male

tag: tissue

value: Brain (Prefrontal Cortex)

tag: cell type

value: Astrocytes


title: Astrocytes_healthy_BBN002.29170

value: Female


title: brown adipose tissue, HFD 1w, rep2

type: SRA

city: Toyama

first: Makito

last: Oku

address: 2630 Sugitani

department: Research Center for Pre-Disease Science

country: Japan

institute: University of Toyama

description: Library name: bat_1w_2

library_source: transcriptomic

data_processing:
FastQC version 0.11.7 was used for quality checking of the sequenced reads.
Trimmomatic version 0.38 was used to trim low-quality sequences and adapter sequences.
HISAT2 version 2.1.0 was used to map the trimmed reads to the reference genome mm10.
Samtools version 1.9 was used to convert Sequence Alignment Map (SAM) format to Binary Alignment Map (BAM) format.
featureCounts version 1.6.3 was used to count the mapped reads using BAM files.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Comma-separated values (CSV) file includes raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: brown adipose tissue

growth_protocol: The mice were housed in groups of up to six per cage at 23 ± 3 °C on a 12-hour light (starting at 7:00 a.m.) and 12-hour dark cycle.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit and RNase-Free DNase Set (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
Total RNA was then subjected to polyadenylated mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (Cat No. E7490, New England Biolabs, Ipswich, Massachusetts, USA). Strand-specific RNA-seq libraries were then prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (Cat No. E7760, New England Biolabs).

treatment_protocol: The mice were fed HFD (60 kcal% fat, D12492, Research Diets Inc., New Brunswick, New Jersey, USA) from eight weeks of age until the time of dissection.

value: brown adipose tissue

tag: strain

tag: genotype

value: wild type

value: male

tag: treatment

value: HFD 1w


title: Microglia_healthy_BBN002.35107

value: Microglia


title: lung #28826, tumor-derived, rep# 13

city: Tampa

first: Joseph

last: Kissil

state: FL

address: 12902 Magnolia Dr

department: Molecular Oncology

country: USA

institute: H Lee Moffitt Cancer Center and Research Institute

description: Library name: 28826-13

library_source: genomic

data_processing:
Raw sequencing reads were first trimmed with cutadapt 1.8.1 and aligned to the target genes with bwa 0.7.10-r789. Duplicate reads were removed with GATK 4.1.0.0. Variants were then called using Mutect2 based on tumor-only mode. Variant allele frequency no less than 0.01 was applied to selected confident SNPs and 98 InDels. SNPs and InDels that were found at consecutive loci within each sample or across samples were further merged to define highly mutated spots.
Assembly: GCF_000247695.1_HetGla_female_1.0_genomic.gff
Supplementary files format and content: The oncoplots were generated based on the appearance of the highly mutated spots using ComplexHeatmap. The selected variants (MuTect2 AF >=0.01) were annotated using tool SnpEff (Version 4.3t)

organism: Heterocephalus glaber

source_name: Lung

extract_protocol:
Laser capture microscopy (LCM) was completed using the Arcturus XT Laser Capture Microdissection System. Individual tumors were identified from the scanned H&E slides. An unstained, 10μm thick section of FFPE tissue was mounted on PEN membrane slides (2μm; Leica). Once tissue was cut, forceps were used to pick out dissected tissue from the slide and place in 1.5mL microcentrifuge tubes for DNA or RNA extraction.
Following PCR amplification (primers listed in Table 1 in the supplemental methods), amplicons were sequenced using the Illumina Nextera XT kit following the manufacturer’s protocol (Illumina). Briefly, following the quality control screening of 100ng of each amplicon on a 1% agarose gel, both amplicons for each sample were pooled equimolar and 1ng of input DNA was used for the Nextera tagmentation reaction, followed by PCR amplification and sample indexing. The libraries were purified, quantitated with the Qubit Fluorometer (ThermoFisher Scientific), and screened on the Agilent TapeStation 4200 using the TapeStation High-Sensitivity D1000 Screen Tape (Agilent Technologies). The final libraries were normalized, denatured, and sequenced on the Illumina MiSeq sequencer using a Nano flow cell to generate approximately 20,000 150-base read pairs per sample.

value: Lung


title: lung #015-11, tumor-derived, rep# 19

description: Library name: 015-11-19


title: lung #015-11, tumor-derived, rep# 9

description: Library name: 015-11-9


title: lung #28826, tumor-derived, rep# 5

description: Library name: 28826-5


title: lung #28383, tumor-derived, rep# 10

description: Library name: 28383-10


title: brown adipose tissue, HFD 1w, rep1

description: Library name: bat_1w_1


title: brown adipose tissue, HFD 3d, rep4

description: Library name: bat_3d_4

value: HFD 3d


title: lung #28383, tumor-derived, rep# 2

description: Library name: 28383-2


title: lung #28826, normal, rep# 1

description: Library name: 28826-WT1


title: brown adipose tissue, HFD 1w, rep3

description: Library name: bat_1w_3


title: brown adipose tissue, HFD 3d, rep3

description: Library name: bat_3d_3


title: lung, tumor-derived, rep# 8

description: Library name: 015-11-8


title: lung, tumor-derived, rep# 18

description: Library name: 015-11-18


title: Oligodendrocytes_healthy_BBN002.29170

value: Oligodendrocytes


title: Microglia_healthy_BBN002.29170


title: brown adipose tissue, HFD 3d, rep1

description: Library name: bat_3d_1


title: Oligodendrocytes_healthy_BBN002.35107


title: brown adipose tissue, HFD 3d, rep6

description: Library name: bat_3d_6


title: brown adipose tissue, HFD 3d, rep2

description: Library name: bat_3d_2


title: brown adipose tissue, HFD 3d, rep5

description: Library name: bat_3d_5


title: Normal_MAT_1 (HTO)

city: Stanford

first: Benjamin

last: Pham

state: CA

address: 257 Campus Drive

institute: Stanford University

description:
10x Genomics
NRMM1_barcodes.tsv.gz
NRMM1_matrix.mtx.gz
NRMM1_features.tsv.gz

library_source: other

data_processing:
Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. Libraries were sequenced on a HiSeq 4000 Illumina platform targeting 50,000 reads per cell. Case calls were converted to reads using the Cell Ranger (10X Genomics; version 3.1) implementation mkfastq and then aligned against the GRCh38 v3.0.0 human reference genome, available at: http://cf.10xgenomics.com/supp/cell-exp/, or using Cell Ranger’s count function with SC3Pv3 chemistry and 5,000 expected cells per sample. Hashtag oligos (HTOs) for human samples were demultiplexed using Seurat’s implementation HTODemux. Briefly, k-medoid clustering is performed on the normalized HTO values, after which a “negative” HTO distribution is calculated. For each HTO, the cluster with the lowest average value is treated as the negative group and a negative binomial distribution is fit to this cluster. Using the 0.99 quantile of this distribution as a threshold, each cell is classified as positive or negative for each HTO. Sample tubes contained cells from either bowel or mesentery with a similar disease state. Cells for which ambiguous HTO identity could not be clearly established were preserved and assigned to the hashtag for which it was most highly expressed.
Assembly: GCRh38 (human)
Supplementary files format and content: Tab-separated values files and matrix files

molecule: protein

source_name: Mesenteric Adipose Tissue

extract_protocol:
CD tissue from ileocecectomies and non-CD ostomy takedowns were placed in ice-cold PBS. As before, CD samples were divided into Stricture and Uninvolved bowel and MAT. MAT was dissected away from the bowel as close to the bowel wall as possible and digested using 2mg/mL of Collagenase IV in digest media (DMEM/F12, 1% Pluronics, CaCl2, DNase I, HEPES) at 37C for 30 minutes. The bowel was separated digested in a GentleMACS using the 37C_MultiA program. Both digests were quenched in quenching media (DMEM/F12, 20% FBS, and 2.5mM EDTA). The cell suspensions were then filtered through a 70um filter and centrifuged at 300g for 5 minutes. The supernatant was removed and the pellets were treated with RBC Lysis Buffer (Roche) according to the manufacturer’s instructions. Samples were washed with PBS and centrifuged. The pellet was resuspended in Bambanker’s solution and stored at -80C until they were ready to be sequenced.
Performed at the Stanford Genomics Facility (SGF) using the 10x Genomics platform. The relevant protocols were followed per manufacturer’s guidelines.

value: Mesenteric Adipose Tissue

value: all cells (hashed)

tag: disease state

value: Non-CD

tag: library type

value: HTO

tag: hto

value: TotalSeq-B-0258 HumanHashTag8--LNH-94_2M2-TSB, TotalSeq-B-0259 HumanHashTag9--LNH-94_2M2-TSB, TotalSeq-B-0257 HumanHashTag7--LNH-94_2M2-TSB


title: lung #28826, tumor-derived, rep# 4

description: Library name: 28826-4


title: Stricture_MAT_1 (HTO)

description:
10x Genomics
STRM1_barcodes.tsv.gz
STRM1_matrix.mtx.gz
STRM1_features.tsv.gz

value: CD


title: Neurons_healthy_BBN002.32844

value: Brain (Prefrontal Cortex)

value: Neurons


title: Normal_Bowel_MAT (HTO)

description:
10x Genomics
NRMBM_barcodes.tsv.gz
NRMBM_matrix.mtx.gz
NRMBM_features.tsv.gz

value: TotalSeq-B-0251 HumanHashTag1--LNH-94_2M2-TSB, TotalSeq-B-0252 HumanHashTag2--LNH-94_2M2-TSB, TotalSeq-B-0254 HumanHashTag4--LNH-94_2M2-TSB, TotalSeq-B-0253 HumanHashTag3--LNH-94_2M2-TSB


title: Neurons_healthy_BBN002.29170

value: Female


title: Microglia_healthy_BBN002.32844


title: lung #28383, tumor-derived, rep# 9

description: Library name: 28383-9


title: lung #28383, tumor-derived, rep# 1

description: Library name: 28383-1


title: Oligodendrocytes_healthy_BBN002.29471


title: Stricture_Bowel_2 (HTO)

description:
10x Genomics
STRB2_barcodes.tsv.gz
STRB2_matrix.mtx.gz
STRB2_features.tsv.gz

source_name: Bowel

value: Bowel

value: TotalSeq-B-0258 HumanHashTag8--LNH-94_2M2-TSB, TotalSeq-B-0257 HumanHashTag7--LNH-94_2M2-TSB


title: lung #28826, tumor-derived, rep# 12

description: Library name: 28826-12


title: V3

city: Urumqi

first: Banghao

last: Sun

address: No. 8, Xinyi Road, Xinshi District

country: China

institute: Xinjiang Medical University School of Basic Medicine

data_processing:
Library construction was performed using TruSeq Stranded Total RNA with Ribo-Zero Gold (Illumina, Cat. No. RS-122-2301). The amount of RNA used to construct the library was 1 µg. First, ribosomal RNA (rRNA) removal was performed by using the Ribo-Zero Gold rRNA Removal Kit (Illumina) and RNA was fragmented. Subsequently, sequencing libraries were constructed using rRNA-depleted RNA. Finally, products were purified (Agencourt AMPure XP, BECKMAN COULTER), and library quality was assessed using the Agilent Bioanalyzer 2100 system.
Assembly: NCBI_GRCh38.p13
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
After induction of THP-1 into macrophages, Mycobacterium tuberculosis infection was added for 24 h. Total RNA was extracted using the TRIZOL method.
RNA libaraies were prepared for sequencing using standard Illumina protocols.

tag: cell line

value: macrophages

value: infected with H37Rv


title: Astrocytes_healthy_BBN002.29471

value: Astrocytes


title: Oligodendrocytes_healthy_BBN002.32844


title: Uninvolved_MAT_1 (HTO)

description:
10x Genomics
ADJM1_barcodes.tsv.gz
ADJM1_matrix.mtx.gz
ADJM1_features.tsv.gz

value: TotalSeq-B-0251 HumanHashTag1--LNH-94_2M2-TSB, TotalSeq-B-0252 HumanHashTag2--LNH-94_2M2-TSB, TotalSeq-B-0254 HumanHashTag4--LNH-94_2M2-TSB


title: Astrocytes_healthy_BBN002.32844


title: Normal_Bowel_1 (HTO)

description:
10x Genomics
NRMB1_barcodes.tsv.gz
NRMB1_matrix.mtx.gz
NRMB1_features.tsv.gz


title: brown adipose tissue, HFD 1d, rep5

description: Library name: bat_1d_5

value: brown adipose tissue

value: wild type

value: male

value: HFD 1d


title: brown adipose tissue, HFD 1d, rep4

description: Library name: bat_1d_4


title: Uninvolved_Bowel_1 (HTO)

description:
10x Genomics
ADJB1_barcodes.tsv.gz
ADJB1_matrix.mtx.gz
ADJB1_features.tsv.gz

value: all cells (hashed)

value: HTO


title: brown adipose tissue, HFD 1d, rep3

description: Library name: bat_1d_3


title: Stricture_Bowel_1 (HTO)

description:
10x Genomics
STRB1_barcodes.tsv.gz
STRB1_matrix.mtx.gz
STRB1_features.tsv.gz

value: CD

value: TotalSeq-B-0258 HumanHashTag8--LNH-94_2M2-TSB, TotalSeq-B-0259 HumanHashTag9--LNH-94_2M2-TSB, TotalSeq-B-0257 HumanHashTag7--LNH-94_2M2-TSB


title: V2


title: Neurons_healthy_BBN002.29471

value: Brain (Prefrontal Cortex)

value: Neurons


title: brown adipose tissue, HFD 1d, rep2

description: Library name: bat_1d_2


title: brown adipose tissue, HFD 1d, rep1

description: Library name: bat_1d_1


title: V1


title: Normal_Human_MAT_LPCH3 (mRNA)

library_source: transcriptomic single cell

value: Mesenteric Adipose Tissue

tag: age

value: 2 years

value: Non-CD

value: mRNA


title: brown adipose tissue, HFD 1d, rep6

description: Library name: bat_1d_6


title: L5

value: macrophages

value: infected with clinical isolates of Mycobacterium tuberculosis from Xinjiang, China


title: Astrocytes_healthy_BBN002.30886

value: Female

value: Astrocytes


title: Microglia_healthy_BBN002.29471

value: Microglia


title: Normal_Human_MAT_LPCH8 (mRNA)

value: >1 year


title: Normal_Human_MAT_LPCH2 (mRNA)

value: 3 years


title: L6


title: Oligodendrocytes_healthy_BBN002.30886

value: Oligodendrocytes


title: L4


title: brown adipose tissue, HFD 0d, rep4

description: Library name: bat_0d_4

value: brown adipose tissue

value: wild type

value: male

value: HFD 0d


title: Normal_Human_MAT_LPCH1 (mRNA)

value: 5 years

value: all cells (hashed)


title: Microglia_healthy_BBN002.30886

value: Brain (Prefrontal Cortex)


title: L3


title: brown adipose tissue, HFD 0d, rep2

description: Library name: bat_0d_2


title: C3

value: not infected


title: brown adipose tissue, HFD 0d, rep3

description: Library name: bat_0d_3


title: Uninvolved_Human_MAT_LPCH5 (mRNA)

value: Mesenteric Adipose Tissue

value: 18 years

value: IM + Biologics

value: CD

value: mRNA


title: Neurons_healthy_BBN002.30886

value: Female

value: Neurons


title: Uninvolved_Human_MAT_LPCH4 (mRNA)

value: 19 years

value: Biologics


title: Oligodendrocytes_healthy_BBN002.35541

value: Male

value: Oligodendrocytes


title: Stricture_Human_MAT_LPCH6 (mRNA)

value: 15 years


title: brown adipose tissue, HFD 0d, rep1

description: Library name: bat_0d_1

value: brown adipose tissue

value: wild type

value: male

value: HFD 0d


title: C2

value: macrophages

value: not infected


title: C1


title: Heart, E18.5, R3

city: Shanghai

first: Chanyi

last: Li

address: 168 Changhai Road

institute: The First Affiliated Hospital of Naval Military Medical University

description: Library name: H1803

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: mm9
Supplementary files format and content: text files include FPKM values for each Sample

source_name: ICR mouse

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: heart

value: WT


title: Stricture_Human_MAT_LPCH5 (mRNA)

value: Mesenteric Adipose Tissue

value: 18 years

value: all cells (hashed)

value: IM + Biologics

value: CD


title: brown adipose tissue, HFD 0d, rep6

description: Library name: bat_0d_6


title: brown adipose tissue, HFD 0d, rep5

description: Library name: bat_0d_5


title: Stricture_Human_MAT_LPCH4 (mRNA)

value: 19 years

value: Female

value: Biologics

value: mRNA


title: Neurons_healthy_BBN002.35541

value: Male

value: Brain (Prefrontal Cortex)

value: Neurons


title: AURKBi, rep5

city: Durham

first: Nenad

last: Bursac

state: NC

address: 101 Science Dr. Rm. 1169

department: Biomedical Engineering

institute: Duke University

description: Library name: Sample 10

data_processing:
The RNA-seq data was mapped with the GRCh38 reference genome assembly using HISAT2. Differential gene expression analysis was performed with the edgeR package in R. The volcano plot was generated with the EnhancedVolcano package in R.  The Gene Ontology (GO) analysis was performed with the clusterProfiler package in R.
Assembly: GRCh38 reference genome assembly
Supplementary files format and content: Excel file showing differential gene expression analysis used to generate other figures in the manuscript. Shows Log2FC in gene expression and related p values.

molecule: polyA RNA

source_name: DU11 iPSC

growth_protocol: hiPSCs were differentiated into CMs via small-molecule-based modulation of Wnt signaling. Briefly, DU11 hiPSCs were dissociated into single cells using Accutase and plated into ESC-Matrigel coated dishes at 4 × 105/cm2 with 5 µM Y27632 (ROCK inhibitor). Maintenance media was changed daily prior to differentiation. To induce cardiac differentiation (day 0), cells were incubated in 6 μM CHIR99021 in RPMI-1640 with B27(−) insulin. Exactly 48 h later, CHIR was removed and replaced with basal RPMI/B27(−) medium. On day 3, the cells were incubated in RB- containing 5 uM IWR-1, which was switched to basal RPMI/B27(−) medium on day 5. From day 7 onward, cells were cultured in RPMI/B27(+)-insulin with media changed every 2–3 days. Spontaneous contractions of hiPSC-CMs started on day 7–10 of differentiation. Differentiating CM cultures were purified via metabolic selection between days 10 and 14 (Tohyama et al., 2013), by incubation in “no glucose” medium (glucose-free RPMI supplemented with 4 mM lactate, 0.5 mg/mL recombinant human albumin, and 213 μg/mL L-ascorbic acid 2-phosphate) for 48h. At the end of the selection period, cultures were dissociated into single cells using 0.05% trypsin/EDTA followed by quenching with stop buffer (DMEM, 20% FBS, 20 μg/mL DNAse I (Millipore 260913)) and replated onto fresh Matrigel-coated dishes to remove dead cells and debris.

extract_protocol:
Total RNA was isolated using the Qiagen Rneasy Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols, RNA was enriched for polyA prior to library prep.

value: DU11 iPSC

value: iPSC-cardiomyocytes


title: Normal_Human_Bowel_LPCH9 (mRNA)

value: Bowel

value: >1 year

value: Non-CD


title: Heart, E18.5, R2

description: Library name: H1802

value: heart

value: WT


title: AURKBi, rep4

description: Library name: Sample 9


title: Heart, E18.5, R1

description: Library name: H1801


title: Microglia_healthy_BBN_11072

value: Microglia


title: AURKBi, rep3

description: Library name: Sample 8


title: Normal_Human_Bowel_LPCH8 (mRNA)

value: all cells (hashed)


title: Neurons_healthy_BBN_11072


title: Heart, E16.5, R2

description: Library name: H1602


title: Oligodendrocytes_healthy_BBN_11072

value: Oligodendrocytes


title: Heart, E16.5, R1

description: Library name: H1601


title: AURKBi, rep1

description: Library name: Sample 6


title: Normal_Human_Bowel_LPCH2 (mRNA)

value: 3 years


title: Astrocytes_healthy_BBN002.35541

value: Astrocytes


title: Control, rep5

description: Library name: Sample 5

value: Vehicle control


title: Astrocytes_healthy_BBN_11072


title: Mouse islets, control, 16 months, rep3

city: Indianapolis

first: Xiaocheng

middle: Charlie

last: Dong

state: IN

address: 635 Barnhill Dr, MS 1021D

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

description:
Library name: 16M-I_8_S13_L007
Column name in raw_counts_All_Samples.txt: 16M-I_8_S13

data_processing:
Sequence reads were quality-trimmed, adapter sequences removed, and short or low-quality reads filtered using Trim Galore (v0.6.10) with a minimum read length of 20, a quality trimming threshold of 5, a stringency level of 5 for adapter trimming, and an error rate of 0.1 for adapter matching.
Trimmed reads were aligned to the GRCm38/M25 genome using STAR (v2.7.11a), retaining only uniquely mapped reads (--outSAMmapqUnique 60), with a minimum alignment length of 16 and a maximum mismatch rate of 3%.
Mapped reads were filtered to exclude low-quality alignments (MAPQ < 10) using ngsutilsj (v0.4.21).
Gene-level read counts were quantified using featureCounts (v2.0.0) with GENCODE annotation (vM25), employing strand-specific mode and a minimum mapping quality threshold of 10.
Assembly: mm10
Supplementary files format and content: The tab-delimited text file contains the raw counts for each sample.

source_name: pancreatic islets

growth_protocol: Freshly isolated primary islets were used. No culture.

extract_protocol:
Qiagen RNeasy Plus Mini Kit
Illumina stranded mRNA prep kit

treatment_protocol: No treatment

value: pancreatic islets

value: alpha, beta, delta, and other islet cells

value: No

tag: batch


title: Oligodendrocytes_healthy_BBN002.33675

value: Male

value: Brain (Prefrontal Cortex)


title: Microglia_healthy_BBN002.35541


title: Normal_Human_Bowel_LPCH1 (mRNA)

value: 5 years

value: mRNA


title: Mouse islets, SIRT6 transgenic, 16 months, rep3

description:
Library name: 16M-I_7_S12_L007
Column name in raw_counts_All_Samples.txt: 16M-I_7_S12

value: SIRT6 transgenic


title: Uninvolved_Human_Bowel_LPCH5 (mRNA)

value: Bowel

value: 18 years

value: Female

value: IM + Biologics

value: CD


title: Control, rep4

description: Library name: Sample 4

value: DU11 iPSC

value: iPSC-cardiomyocytes

value: WT


title: Control, rep3

description: Library name: Sample 3

value: Vehicle control


title: Microglia_healthy_BBN002.33675

value: Microglia


title: Uninvolved_Human_Bowel_LPCH4 (mRNA)

value: 19 years

value: all cells (hashed)

value: Biologics


title: Astrocytes_healthy_BBN002.33675

value: Male

value: Brain (Prefrontal Cortex)

value: Astrocytes


title: Control, rep2

description: Library name: Sample 2


title: Mouse islets, control, 16 months, rep2

description:
Library name: 16M-I_5_S11_L007
Column name in raw_counts_All_Samples.txt: 16M-I_5_S11

value: pancreatic islets

value: alpha, beta, delta, and other islet cells

value: No


title: Neurons_healthy_BBN002.33675

value: Neurons


title: Stricture_Human_Bowel_LPCH7 (mRNA)

value: Bowel

value: 16 years

value: Female

value: mRNA


title: AURKBi, rep2

description: Library name: Sample 7

value: DU11 iPSC

value: iPSC-cardiomyocytes

value: WT


title: Mouse islets, control, 16 months, rep1

description:
Library name: 16M-I_3_S9_L007
Column name in raw_counts_All_Samples.txt: 16M-I_3_S9


title: Heart, E16.5, R3

description: Library name: H1603

value: heart


title: Normal_Human_Bowel_LPCH3 (mRNA)

value: 2 years

value: all cells (hashed)

value: Non-CD


title: Mouse islets, SIRT6 transgenic, 16 months, rep2

description:
Library name: 16M-I_2_S8_L007
Column name in raw_counts_All_Samples.txt: 16M-I_2_S8

value: SIRT6 transgenic


title: Control, rep1

description: Library name: Sample 1

value: Vehicle control


title: Stricture_Human_Bowel_LPCH6 (mRNA)

value: 15 years

value: Male

value: Biologics

value: CD


title: DGKazDKO-Tcons sample 6

first: Xiaoping

last: Zhong

address: Rm 133, 203 Research Drive, MSRB-1

department: Pediatrics

institute: Duke University Medical Center

description:
XPZ-TconKO-DKO-6
TregDGKazDKO_Tconv_vs_WT-Tconv_Exp.xlsx

data_processing:
Raw sequencing reads were processed with FASTQC to screen eligible samples, and then single-end reads were trimmed for adaptor sequences and filtered with the Soapnuke tool. Trimmed reads were aligned by STAR (2.5.1b) to the mouse Ensembl genome (Ensembl, GRCm38.p5) with Ensembl annotation (Mus_musculus.GRCm38.84.gtf). Counting of reads on annotated transcripts was performed with htseq-count (0.6.0). The limma (3.38.3) Biconductor library has been used for counts normalization and differential analysis between the transcriptomes of the four WT and DKO Tregs.
Assembly: Ensembl, GRCm38.p5
Supplementary files format and content: Excel file with RPKM of genes in individual samples, Log2FC, P values, adjusted P values

source_name: Spleen and LN

extract_protocol:
RNA was isolated using the RNeasy Plus Mini kit (Qiagen)
Libraries were prepared using Truseq stranded mRNA kit (Illumina)

value: Spleen and LN

value: CD4+ conventional T cells

value: DGKazDKO


title: Oligodendrocytes_healthy_BBN002.35108

value: Female

value: Brain (Prefrontal Cortex)

value: Oligodendrocytes


title: DGKazDKO-Tcons sample 5

description:
XPZ-TconKO-DKO-5
TregDGKazDKO_Tconv_vs_WT-Tconv_Exp.xlsx


title: Stricture_Human_Bowel_LPCH5_1 (mRNA)

value: Bowel

value: 18 years

value: IM + Biologics

value: mRNA


title: Stricture_Human_Bowel_LPCH5_2 (mRNA)

value: all cells (hashed)


title: Astrocytes_healthy_BBN002.35108

value: Astrocytes


title: DGKazDKO-Tcons sample 4

description:
XPZ-TconKO-DKO-4
TregDGKazDKO_Tconv_vs_WT-Tconv_Exp.xlsx


title: Mouse islets, SIRT6 transgenic, 10 months, rep1

description:
Library name: 3_S11_L001
Column name in raw_counts_All_Samples.txt: 3_S11

value: pancreatic islets

value: alpha, beta, delta, and other islet cells

value: SIRT6 transgenic

value: No


title: Neurons_healthy_BBN002.35108

value: Neurons


title: Stricture_Human_Bowel_LPCH4 (mRNA)

value: 19 years

value: Biologics

value: CD


title: DGKazDKO-Tcons sample 3

description:
XPZ-TconKO-DKO-3
TregDGKazDKO_Tconv_vs_WT-Tconv_Exp.xlsx

value: Spleen and LN

value: CD4+ conventional T cells

value: DGKazDKO


title: Mouse islets, control, 10 months, rep1

description:
Library name: 1_S9_L001
Column name in raw_counts_All_Samples.txt: 1_S9

value: WT


title: DGKazDKO-Tcons sample 1

description:
XPZ-TconKO-DKO-1
TregDGKazDKO_Tconv_vs_WT-Tconv_Exp.xlsx


title: Mouse islets, control, 10 months, rep2

description:
Library name: 2_S10_L001
Column name in raw_counts_All_Samples.txt: 2_S10


title: Sham_Mouse (mRNA and HTO)

description:
10x Genomics
Sham_barcodes.tsv.gz
Sham_matrix.mtx.gz
Sham_features.tsv.gz

data_processing:
Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. Libraries were sequenced on a HiSeq 4000 Illumina platform targeting 50,000 reads per cell. Case calls were converted to reads using the Cell Ranger (10X Genomics; version 3.1) implementation mkfastq and then aligned against the Cell Ranger mm10 reference genome, available at: http://cf.10xgenomics.com/supp/cell-exp/, or using Cell Ranger’s count function with SC3Pv3 chemistry and 5,000 expected cells per sample. Hashtag oligos (HTOs) for human and mouse samples were demultiplexed using Seurat’s implementation HTODemux. Briefly, k-medoid clustering is performed on the normalized HTO values, after which a “negative” HTO distribution is calculated. For each HTO, the cluster with the lowest average value is treated as the negative group and a negative binomial distribution is fit to this cluster. Using the 0.99 quantile of this distribution as a threshold, each cell is classified as positive or negative for each HTO. Sample tubes contained cells from either bowel or mesentery with a similar disease state. Cells for which ambiguous HTO identity could not be clearly established were preserved and assigned to the hashtag for which it was most highly expressed.  Spatial Transcriptomics: The libraries were sequenced using NextSeq (Illumina) and Bcl files were demultiplexed. Raw FASTQ files and histology images were processed by sample with the Space Ranger software, which uses STAR v2.5.1b for genome alignment against the Cell Ranger mm10 reference genome.
Bam raw file does contain both the HTO and mRNA libraries.
Assembly: mm10 (mouse)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: mixed sample (Bowel and Mesenteric Adipose Tissue)

extract_protocol:
Mouse bowel and MAT were both digested using digest media at 37C, with the bowel digested in two 30-minute fractions and MAT digested in 30 minutes. Samples were quenched using quenching media, filtered through a 70um filter, and centrifuged for 300g for 5 minutes. The supernatant was discarded and the pellet was resuspended in staining media (StemCell Tech) containing a 1:50 concentration of anti-human hashtag antibodies corresponding to the sample tube. The cells were washed and pelleted three times with staining media. The cells were resuspended at a concentration of 100 cells / uL in 0.25% BSA in PBS.
Performed at the Stanford Genomics Facility (SGF) using the 10x Genomics platform. The relevant protocols were followed per manufacturer’s guidelines.

value: 8-12 weeks

tag: time

value: POD 14

value: Sham

value: mRNA and HTO

value: TotalSeq-B-0301 anti-mouseHashTag1--M1-42_30-F11-TSB, TotalSeq-B-0302 anti-mouseHashTag2--M1-42_30-F11-TSB


title: Neurons_healthy_BBN002.28121

value: Male

value: Brain (Prefrontal Cortex)


title: KO Sham3

first: Shun

last: Zhang

state: Shanghai

address: 1665, Kongjiang Road, Yangpu

department: Urology

institute: Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University

data_processing:
Purified libraries were quantified by Qubit®2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration.
Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA).
Paired-end sequence files (fastq) were mapped to the reference genome using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5)
Gene abundance was expressed as fragments per kilobase of exon per million reads mapped (FPKM). Stringtie software was used to count the fragment within each gene, and TMM algorithm was used for normalization.
Supplementary files format and content: tab-delimited text files include RPKM values and counts for each sample

source_name: kidney

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following  TruSeq™ RNA Sample Preparation Guide.

treatment_protocol: I/R AKI was induced by ischemia for 30 minutes at 37℃ in the left kidney using the flank approach  and contralateral nephrectomy. Animals in the sham group were performed with the same procedure except for the ischemia

value: kidney

value: Lrrk2 knockout


title: Microglia_healthy_BBN002.35108

value: Female

value: Microglia


title: Astrocytes_healthy_BBN002.28121

value: Astrocytes


title: DGKazDKO-Tcons sample 2

description:
XPZ-TconKO-DKO-2
TregDGKazDKO_Tconv_vs_WT-Tconv_Exp.xlsx


title: Zn200_3

city: taigu

first: Huizhen

last: Yang

address: Num 1 Ming Xian South Road

department: College of Veterinary Medicine

institute: Shanxi Agricultural University

description:
Library name: sample 12
Zn200 group, replicate biosample 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to ChlAethiops_1.0 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: ChlAethiops_1.0
Supplementary files format and content: tab-delimited text file includes gene counts for each sample

organism: Chlorocebus aethiops

source_name: cell culture

extract_protocol:
RNA was extracted from cell lines using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: cell culture


title: WT Tcons sample 3

description:
XPZ-TconKO-WT-3
TregDGKazDKO_Tconv_vs_WT-Tconv_Exp.xlsx

value: Spleen and LN


title: Microglia_healthy_BBN002.28121


title: Colotomy_Mouse (mRNA and HTO)

description:
10x Genomics
Colo_barcodes.tsv.gz
Colo_matrix.mtx.gz
Colo_features.tsv.gz

value: mixed sample (Bowel and Mesenteric Adipose Tissue)

value: all cells (hashed)

value: Colotomy


title: KO Sham2


title: Mouse islets, SIRT6 transgenic, 16 months, rep1

description:
Library name: 16M-I_1_S7_L007
Column name in raw_counts_All_Samples.txt: 16M-I_1_S7

value: pancreatic islets

value: alpha, beta, delta, and other islet cells

value: SIRT6 transgenic

value: No


title: Mouse islets, SIRT6 transgenic, 10 months, rep2

description:
Library name: 4_S12_L001
Column name in raw_counts_All_Samples.txt: 4_S12


title: WT Tcons sample 4

description:
XPZ-TconKO-WT-4
TregDGKazDKO_Tconv_vs_WT-Tconv_Exp.xlsx

value: CD4+ conventional T cells

value: WT


title: KO Sham1

value: Sham


title: Zn200_2

description:
Library name: sample 11
Zn200 group, replicate biosample 2


title: Astrocytes_healthy_BBN002.29416

value: Male

value: Brain (Prefrontal Cortex)


title: WT Tcons sample 2

description:
XPZ-TconKO-WT-2
TregDGKazDKO_Tconv_vs_WT-Tconv_Exp.xlsx


title: Zn200_1

description:
Library name: sample 10
Zn200 group, replicate biosample 1


title: WT Sham3

value: kidney


title: WT Tcons sample 1

description:
XPZ-TconKO-WT-1
TregDGKazDKO_Tconv_vs_WT-Tconv_Exp.xlsx


title: Zn50_2

description:
Library name: sample 8
Zn50 group, replicate biosample 2


title: WT Sham2


title: Oligodendrocytes_healthy_BBN002.28121

value: Oligodendrocytes


title: Microglia_healthy_BBN002.29416

value: Microglia


title: DGKazDKO-Treg sample 4

description:
XPZ-TrgKO-DKO-4
TregDGKazDKO_Treg_vs_WT-Treg_Exp.xlsx

value: Regulatory T cells

value: DGKazDKO


title: WT Sham1


title: Zn50_1

description:
Library name: sample 7
Zn50 group, replicate biosample 1

value: cell culture


title: DGKazDKO-Treg sample 3

description:
XPZ-TrgKO-DKO-3
TregDGKazDKO_Treg_vs_WT-Treg_Exp.xlsx

value: Spleen and LN


title: KO I/R3

value: Lrrk2 knockout

value: I/R


title: V3

description:
Library name: sample 6
V group, replicate biosample 3


title: DGKazDKO-Treg sample 2

description:
XPZ-TrgKO-DKO-2
TregDGKazDKO_Treg_vs_WT-Treg_Exp.xlsx


title: V2

description:
Library name: sample 5
V group, replicate biosample 2


title: KO I/R1


title: Neurons_healthy_BBN002.29416

value: Neurons


title: DGKazDKO-Treg sample 1

description:
XPZ-TrgKO-DKO-1
TregDGKazDKO_Treg_vs_WT-Treg_Exp.xlsx


title: KO I/R2


title: Cebpa Fl/Fl, Spc-CreER, iSuReCre, Perinatal_1b (ATAC-seq)

city: Rochester

first: Douglas

middle: Glenn

last: Brownfield

state: MN

address: 200 First St. SW

institute: Mayo Clinic

description:
Library name: Cebpa_Floxed_AT2_sample1b
Active Motif ATAC

data_processing:
ATAC-seq analysis was performed with HOMER(v 4.11). Tag directories were made for each ATAC-seq run using HOMER “makeTagDirectory”. Peaks for individual replicates were identified using the “findPeaks” command. To generate high-confidence peak lists across both replicate samples for downstream analysis, ATAC-seq peaks were identified using the HOMER “getDifferentialPeaksReplicates.pl” command. This command uses DESeq2 and identifies peaks that pass 2-fold enrichment and false discovery rate (FDR) < 0.05 cutoffs.
Assembly: GRCm38/mm10
Supplementary files format and content: bigwig

source_name: perinatal mouse lung

extract_protocol:
Cells from PN25 SftpcCreER;iSuReCre;Cebpawt/fl and SftpcCreER;iSuReCre;Cebpafl/fl mice (2 weeks after TMX) were isolated and enriched (EpCAM+) as per protocol described below.
Raw sequencing reads were trimmed of sequencing adapters and bad quality bases with cutadapt version 2.8 in Trim Galore version 0.6.6 using default parameters. Bowtie2 version 2.5.0 (parameters: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700) was used to map trimmed reads to the reference genome Mus_musculus.GRCm38.

treatment_protocol: Tamoxifen induce Cebpa deletion and lineage labeling

value: perinatal mouse lung

value: Alveolar type 2

value: Cebpa Fl/Fl, Spc-CreER, mTmG


title: Zn50_3

description:
Library name: sample 9
Zn50 group, replicate biosample 3


title: Cebpa Fl/Fl, Spc-CreER, iSuReCre, Perinatal_2a (ATAC-seq)

description:
Library name: Cebpa_Floxed_AT2_sample2a
Active Motif ATAC


title: WT-Treg sample 4

description:
XPZ-TrgKO-WT-4
TregDGKazDKO_Treg_vs_WT-Treg_Exp.xlsx

value: WT


title: V1

description:
Library name: sample 4
V group, replicate biosample 1


title: C3

description:
Library name: sample 3
C group, replicate biosample 3


title: WT-Treg sample 3

description:
XPZ-TrgKO-WT-3
TregDGKazDKO_Treg_vs_WT-Treg_Exp.xlsx


title: C2

description:
Library name: sample 2
C group, replicate biosample 2


title: Cebpa Fl/Fl, Spc-CreER, iSuReCre, Perinatal_1a (ATAC-seq)

description:
Library name: Cebpa_Floxed_AT2_sample1a
Active Motif ATAC


title: WT I/R2


title: Cebpa WT/Fl, Spc-CreER, iSuReCre, Perinatal_1b (ATAC-seq)

description:
Library name: Control_AT2_sample1b
Active Motif ATAC

value: Cebpa WT/Fl, Spc-CreER, mTmG


title: Cebpa WT/Fl, Spc-CreER, iSuReCre, Perinatal_2a (ATAC-seq)

description:
Library name: Control_AT2_sample2a
Active Motif ATAC


title: WT-Treg sample 2

description:
XPZ-TrgKO-WT-2
TregDGKazDKO_Treg_vs_WT-Treg_Exp.xlsx


title: WT I/R1


title: Cebpa WT/Fl, Spc-CreER, iSuReCre, Perinatal_1a (ATAC-seq)

description:
Library name: Control_AT2_sample1a
Active Motif ATAC


title: WT-Treg sample 1

description:
XPZ-TrgKO-WT-1
TregDGKazDKO_Treg_vs_WT-Treg_Exp.xlsx


title: Oligodendrocytes_healthy_BBN002.29416

value: Male


title: C1

description:
Library name: sample 1
C group, replicate biosample 1


title: C-ES-I Passage 13

status: Public on Aug 22 2025

city: Essen

first: Maximilian

last: Kerkhoff

address: Hufelandstrasse 55

department: Pediatrics III

country: Germany

institute: University Hospital Essen

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC v2.0 Beadchip using Illumina Infinium methylation assay protocol.

scan_protocol: Microarrays were scanned using the Illumina iScan-Scanner according to Illumina Infinium methylation assay protocol

data_processing: Data was normalized with ENmix version 1.40.1. Beta values were calculated with minfi package version 1.50.0

source_name: C-ES-I

label_protocol: 200-500 ng genomic DNA from each sample was bisulfite converted using the EZ-96 DNA Methylation Kit (Zymo Research Corporation, Orange, US) according to the manufacturer recommendations. Each sample was whole genome amplified and enzymatically fragmented following the instructions in the Illumina Infinium HD Assay Methylation Protocol Guide .

growth_protocol: Cells were grown in DMEM (high glucose, pyruvate)+ 10% FBS in rat collagen (6mg/mL) coated T25 flasks in a ratio of 6000 cells/cm^2 for 96h

extract_protocol: Cells were processed with Macherey-Nagel Nucelospin Tissue protocol for DNA extraction

treatment_protocol: Cells got a media exchange after 48h, were washed after 96h with 1xPBS and then harvested in 200µL Buffer T1 for DNA extraction

tag: disease

value: Ewing sarcoma

value: C-ES-I


title: C-ES-I Passage 53


title: SK-N-MC Passage 15

source_name: SK-N-MC

value: SK-N-MC


title: C-ES-M Passage 53

source_name: C-ES-M

value: C-ES-M


title: C-ES-M Passage 11


title: C-ES-Y Passage 10

source_name: C-ES-Y

value: C-ES-Y


title: STA-ET-1 Passage 54


title: C-ES-P Passage 54

source_name: C-ES-P

value: C-ES-P


title: C-ES-P Passage 17


title: C-ES-Y Passage 55


title: STA-ET-1 Passage 22


title: WT I/R3

value: kidney


title: V6.5 mESC, primed KO8 rep1

city: Giessen

first: Johannes

last: Groos

state: Hessen

address: Heinrich-Buff-Ring 58-62

department: Institute of Genetics

institute: Justus-Liebig-University Giessen

description: Library name: Sample 14

data_processing:
Raw sequencing files (FASTQ) were adaptor and quality trimmed using trimGalore v0.6.7
Alignment of the trimmed sequencing reads to the mm9 reference genome (Illumina’s iGenomes) was performed using Hisat2 v.2.2
Read counts per gene were obtained from BAM files using featureCounts from the Rsubread v2.20.0 package and the mouse mm9 GTF.
Normalization of read counts and detection of differentially expressed genes (DEGs) was performed with DESeq2 v1.46.0
Assembly: mm9
Supplementary files format and content: csv files of DESEQ2 result of all Replicates per Sample

growth_protocol: Naïve mESCs were cultivated in 2iLIF condition as previously described Herchenrother et al. 2023. Specifically, naïve mESCs were cultured on 6-well plates coated with 0.1% gelatine in 2iLIF Medium (N2B27 medium supplemented with 50 μM β-mercaptoethanol, 2 mM L-glutamine, 0.1% sodium bicarbonate, 0.11% bovine serum albumin fraction V, 1000 units/ml recombinant mouse leukemia inhibitory factor (LIF), 1 µM PD0325901 (MEK inhibitor), 3 µM CHIR99021 (GSK3 inhibitor)). Every two days, cells were passaged using Accutase (Stemcell) at a density of 1x105 cells/well.

extract_protocol:
total RNA was extracted using the RNeasy Mini Kit (QIAGEN) with on column DNase digest (RNase-Free DNase Set, QIAGEN) according to the manufacturer’s instructions.
Library construction was performed by Biomarker Technologies (Germany).

treatment_protocol: Embryoid body (EB)-mediated differentiation into cardiomyocytes (CMs) was performed as previously described Herchenrother et al. 2023. Briefly, naïve mESCs (Day 0) were primed using differentiation media (DMEM, Gibco supplemented with 10% FCS, 2 mM L-glutamine, 1% nonessential amino acids, 0.1 mM β-mercaptoethanol, 1000 U/mL LIF) for 2 days. Hanging drops containing 1000 cells in 25 µl of differentiation medium (without LIF, supplemented with 50 µg/ml vitamin C) were prepared and cultured for 4 days. Afterwards, droplets containing EBs were carefully transferred to a 24-well plate coated with 0.1% gelatine and further cultured for 1.5 days in differentiation medium supplemented with 50 µg/ml vitamin C. Beating cardiomyocytes were observed starting from differentiation Day 7. Neural progenitor cell (NPC) differentiation was carried out based on the protocol by Bibel et al. 2007. Briefly, naïve mESCs were primed as mentioned above. Hanging drops containing 1,000 cells were prepared in 25 µl differentiation media (without LIF) for 4 days. Then, EBs were pooled and cultured on 100/20mm bacterial plates in suspension in differentiation media (without LIF) supplemented with 5 µM retinoic acid (RA) for 4 days. Medium was changed every two days. On differentiation Day 10, the generated EBs containing NPCs were collected for further analyses.

value: mESC

value: primed


title: V6.5 mESC, CM WT rep1

description: Library name: Sample 16

value: CM


title: V6.5 mESC, NPC KO8 rep2

description: Library name: Sample 27

value: NPC


title: V6.5 mESC, NPC WT rep2

description: Library name: Sample 23


title: V6.5 mESC, NPC KO8 rep1

description: Library name: Sample 26


title: V6.5 mESC, CM KO4 rep2

description: Library name: Sample 19


title: V6.5 mESC, CM KO8 rep2

description: Library name: Sample 21


title: V6.5 mESC, CM KO4 rep1

description: Library name: Sample 18


title: V6.5 mESC, NPC KO4 rep2

description: Library name: Sample 25


title: V6.5 mESC, NPC WT rep1

description: Library name: Sample 22


title: V6.5 mESC, CM WT rep2

description: Library name: Sample 17


title: V6.5 mESC, primed WT rep2

description: Library name: Sample 11


title: V6.5 mESC, primed KO8 rep2

description: Library name: Sample 15


title: V6.5 mESC, primed WT rep1

description: Library name: Sample 10


title: V6.5 mESC, NPC KO4 rep1

description: Library name: Sample 24


title: V6.5 mESC, CM KO8 rep1

description: Library name: Sample 20


title: V6.5 mESC, primed KO4 rep1

description: Library name: Sample 12


title: V6.5 mESC, primed KO4 rep2

description: Library name: Sample 13


title: V6.5 mESC, naive KO4 rep1

description: Library name: Sample 4

value: naive


title: V6.5 mESC, naive KO8 rep1

description: Library name: Sample 7


title: V6.5 mESC, naive KO4 rep2

description: Library name: Sample 5


title: V6.5 mESC, naive KO4 rep3

description: Library name: Sample 6


title: Mouse CD8+ T cells, treated with 5μM Zeaxanthin, 24 hour,replicate3

city: Chicago

first: Jiacheng

state: IL

address: 900 E 57th Street,

department: Medicine

institute: University of Chicago

description: Library name: Zea3

data_processing:
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-p3 was used to count the reads numbers mapped  to each gene. And then FPKM of each gene was calculated based on the  length of the gene and reads count mapped to this gene. FPKM, expected  number of Fragments Per Kilobase of transcript sequence per Millions base  pairs sequenced, considers the effect of sequencing depth and gene length for  the reads count at the same time, and is currently the most commonly used  method for estimating gene expression levels
Assembly: mm10
Supplementary files format and content: csv. file with raw gene counts

source_name: Mouse spleen

growth_protocol: Mouse naïve CD8+ T cells were isolated from the spleen of C57BL/6 mice (6-8 weeks) by magnetic bead purification using EasySep™ Mouse naïve CD8+ T Cell Isolation Kit (Stemcell Technologies) according to the manufacturer’s instructions. Naïve CD8+ T cells were activated in vitro for 18 hours with plate-bound anti-mouse CD3 (1μg/mL; Biolegend) and soluble anti-mouse CD28 (0.5 μg/mL; Biolegend) antibodies in complete Click’s media (Fujifilm Irvine Scientific) at 37℃ and 5% CO2 incubator for further experiments.

extract_protocol:
RNeasy Mini Kit; Qiagen
Messenger RNA was purified from total RNA using poly-T oligo-attached  magnetic beads. After fragmentation, the first strand cDNA was synthesized  using random hexamer primers, followed by the second strand cDNA  synthesis using either dUTP for directional library or dTTP for non-directional  library.For the non-directional library, it was ready after end repair, A-tailing,  adapter ligation, size selection, amplification, and purification.For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, andpurification.

treatment_protocol: treat cells with 5 µM ZEA, 5 µM LUT, or DMSO for 24 hours

value: Mouse spleen

value: Primary CD16+ T cell

value: Mouse primaty T cell

value: Wild type

value: treated with 5μM Zeaxanthin, 24 hour


title: KDM5C_rep1,ChIP

city: San Juan de Alicante

first: Sergio

last: Niñerola

state: Alicante

address: Avenida Santiago Ramon y Cajal, s/n

department: Molecular Neurobiology and Neuropathology

country: Spain

institute: CSIC-Instituto de Neurociencias de Alicante

description: Library name: KDM5C_WT_1

data_processing:
Reads obtained were aligned to the mouse genome (mm10) using Bowtie2 (v 2.3.4.3; (Langmead and Salzberg, 2012). For posterior analysis, only reads with mapq > 30 were selected. For data processing, Samtools v1.9 (Li et al., 2009), Bedtools v2.27.1 (Quinlan and Hall, 2010), and DeepTools v3.5.0 (Ramirez et al., 2016)were used. To generate BigWigs Deeptools was used to normalize reads by reads per genomic content.
Assembly: mm10
Supplementary files format and content: Bigwig

source_name: Hippocampus

extract_protocol:
Nuclei from hippocampal cells were extracted in a dounce homogenizer as explained for the FANS method. For KDM5C (Bethyl Laboratories, A301-034A), nuclei were fixed in 1% formaldehyde for 15 min at room temperature, and fixation was blocked with 0.1 M glycine for 5 min. The nuclei pellet was resuspended in RIPA lysis buffer (containing: SDS 0,1%, IGEPAL 1%, sodium deoxycholate 0,5%, in PBS) and sonicated in a Bioruptor Pico (Diagenode) for 22 cycles of 30 s with 30 s off. Samples were centrifuged for 6 min at 13000 rpm at room temperature and the supernatants were kept in LoBind Eppendorf tubes. 10% of the samples were saved for quality control analysis (DNA concentration measurement and visualization of smir DNA in an electrophoresis gel) and the rest was diluted in ChIP Dilution buffer (containing, in mM: SDS 0.01%, Triton X-100 1.1%, EDTA 1.2, Tris-HCl 16.7, NaCl 167; pH 8). 5% of the sample was saved as Input and the rest incubated overnight at 4°C with the Dynabeads (Invitrogen) bound to the antibody. Samples were rinsed with several washes, 5 minutes each, as follows: 2x in RIPA-150 buffer (containing, in mM: Tris-HCl 50, NaCl 150, EDTA 1, SDS 0.1%, Triton X-100 1%, and sodium deoxycholate 0.1%; pH 8), 2x in RIPA-500 buffer (containing, in mM: Tris-HCl 50, NaCl 500, EDTA 1, SDS 0.1%,  Triton X-100 1%, sodium deoxycholate 0.1%; pH 8), 2x in RIPA LiCl buffer (containing, in mM: Tris-HCl 50, EDTA 1, NP-40 1%, sodium deosycholate 0.7%, LiCl2 500), and 2x in TE buffer (containing, in mM: Tris-HCl 10, pH 8.0, EDTA 1; pH 8.0). Samples were diluted in Elution buffer (containing, in mM: Tris-HCl 10, 5 mM EDTA, NaCl 300, SDS 0.5%; pH 8) and incubated with 1 μL of RNase A 10 mg/mL (Fermentas) overnight at 65°C in agitation to reverse crosslink. Samples were then placed on a magnetic rack, allowing beads to clump. Supernatants were transferred to new tubes and incubated with 2 μL of Proteinase K 20 mg/mL (Thermo Scientific) for 4 h at 55°C, in agitation. Quality controls and Inputs were also incubated with RNase A and Proteinase K. Finally, DNA was precipitated using phenol-chloroform-isoamil alcohol.
ChIP-seq

value: Hippocampus

value: WT

value: TMX


title: V6.5 mESC, naive WT rep2

description: Library name: Sample 2


title: V6.5 mESC, naive WT rep3

description: Library name: Sample 3


title: V6.5 mESC, naive WT rep1

description: Library name: Sample 1


title: Mouse CD8+ T cells, treated with 5μM Zeaxanthin, 24 hour,replicate2

description: Library name: Zea2

value: Primary CD15+ T cell


title: Mouse CD8+ T cells, treated with DMSO, 24 hour,replicate3

description: Library name: CT3

value: Primary CD10+ T cell

value: treated with DMSO, 24 hour,


title: Mouse CD8+ T cells, treated with 5μM Lutein, 24 hour,replicate1

description: Library name: Lut1

value: Primary CD11+ T cell

value: treated with 5μM Lutein, 24 hour


title: V6.5 mESC, naive KO8 rep2

description: Library name: Sample 8

value: mESC


title: Mouse CD8+ T cells, treated with 5μM Zeaxanthin, 24 hour,replicate1

description: Library name: Zea1

value: Primary CD14+ T cell


title: Mouse CD8+ T cells, treated with DMSO, 24 hour,replicate2

description: Library name: CT2

value: Primary CD9+ T cell


title: Medaka_6p5h_Bckdk_R1

city: Kansas City

first: Ariel

middle: Alejandro

last: Bazzini

state: Missouri

institute: Stowers Institute for Medical Research

description: instrument model: Singular Genomics G4

data_processing:
sgdemux 1.2.0 was run to demultiplex reads for all libraries and generate FASTQ files.
Assembly: oryLat2
Supplementary files format and content: tab-delimited txt file includes raw counts for each Sample

organism: Oryzias latipes

source_name: whole embryo

extract_protocol:
Total RNA was extracted using standard TRIzol protocol as described in the manufacturer’s instructions (ThermoFisher Scientific).
Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, Cat. No. E7760L), t

value: whole embryo

value: 6.5 hpf

value: Knockdown


title: Medaka_8h_Bckdk_KD_R2

description: instrument model: Singular Genomics G4

value: 8 hpf


title: Medaka_8h_Cas13d_R1

description: instrument model: Singular Genomics G4

value: Cas13d Control


title: Medaka_6p5h_Cas13d_R2

description: instrument model: Singular Genomics G4


title: Medaka_6p5h_Bckdk_R2

description: instrument model: Singular Genomics G4


title: V6.5 mESC, naive KO8 rep3

description: Library name: Sample 9

value: naive


title: Mouse CD8+ T cells, treated with 5μM Lutein, 24 hour,replicate2

description: Library name: Lut2

value: Mouse spleen

value: Primary CD12+ T cell

value: Mouse primaty T cell

value: Wild type

value: treated with 5μM Lutein, 25 hour


title: KDM5C_rep2,ChIP

description: Library name: KDM5C_WT_2

value: Hippocampus

value: WT

value: TMX


title: Medaka_8h_Cas13d_R2

description: instrument model: Singular Genomics G4


title: Medaka_8h_Bckdk_KD_R1

description: instrument model: Singular Genomics G4


title: Medaka_6p5h_Cas13d_R1

description: instrument model: Singular Genomics G4


title: pvfC mutant, rep1

city: Perth

first: Hussain

last: Alattas

address: 90 South St

country: Australia

institute: Murdoch University

description: Library name: pvfC mutant, rep1

data_processing:
We used the nf-core RNA-seq pipeline (version 3.7; doi: https://doi.org/10.5281/zenodo.1400710) within the Nextflow framework (version 22.04.0). This pipeline facilitated fastq preprocessing, quality assessment, transcriptome alignment using STAR aligner, and transcript quantification using salmon. Differential gene expression analysis between WT and ΔpvfC strains was performed using R (version 2024.04.0). For each functional category, a paired Wilcoxon signed-rank test was conducted to determine statistical significance of expression differences between conditions. This non-parametric test was selected to avoid assumptions about normal distribution of gene expression values. In cases where the Wilcoxon test could not be applied, a paired t-test was used as an alternative approach. P-values less than 0.05 were considered statistically significant. Genes were categorized into functional superclasses, including Metabolism, Energy, RNA Processing, Membrane Transport, Protein Processing. Gene functional annotations were obtained from The Bacterial and Viral Bioinformatics Resource Center (BV-BRC). Genes that appeared in multiple pathways were included in all relevant functional categories for comprehensive analysis. Fold changes were calculated as the median ratio of ΔpvfC to WT expression values for each gene within a functional category.
Assembly: Pseudomonas sp. MUP55 (NZ CP138214.1)
Supplementary files format and content: csv file which includes gene abundance for each sample

organism: Pseudomonas sp. MUP55

extract_protocol:
The RNA from frozen lysates extracted using the Qiagen RNAeasy extraction kit as per the standard kit protocol. Subset of extracted RNA samples are analysed for quality by Agilent RNA Tapestation and RIN scores obtained. RIN values were >6.5. For RNAseq, the samples were DNAse treated and ribosomal RNA depletion was performed on all samples
All the rRNA depleted RNA samples were taken through for cDNA conversion with OligodT primers using an adapted Smartseq assay. Briefly, the first strand of the cDNA is synthesized with the addition of a few untemplated C nucleotides using SuperScript™ IV Reverse Transcriptase (Thermo Fisher Scientific). The poly(C) overhang is added exclusively to full-length transcripts. An oligonucleotide primer (TSO - Transfer Switching Oligo) is hybridized to the poly(C) overhang and used to synthesize the second strand. The Full-length cDNAs were then amplified using KAPA HiFi DNA Polymerase (Roche Diagnostics), purified, and quantified using Promega Quantus Fluorometer. The double-stranded cDNA was further prepared for sequencing using the NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina (New England Biolabs) and sequenced on the Novaseq 6000 using 150bp PE Chemistry (Illumina Inc).

value: pvfC knockout


title: WT, rep2

description: Library name: WT, rep2


title: WT, rep1

description: Library name: WT, rep1


title: Bckdk_KD_4h_R1

data_processing:
ATAC-seq reads were aligned to the GRCz11 (danRer11) zebrafish genome assembly using Bowtie2 2.3.5 and those pairs separated by more than 2 kb were removed
The Tn5 cutting site was determined as the position -4 (minus strand) or +5 (plus strand) from each read start, and this position was extended 5 bp in both directions
Conversion of SAM alignment files to BAM was performed using Samtools 1.9
Conversion of BAM to BED files, and peak analyses, such as overlaps or merges, were carried out using the Bedtools 2.29.2 suite (51). Conversion of BED to BigWig files was performed using the genomecov tool from Bedtools and the wigToBigWig utility from UCSC
ATAC peaks were called using MACS2
Assembly: danrer11
Supplementary files format and content: narrowPeak files with peaks called with macs2 and bigwig files.

organism: Danio rerio

extract_protocol:
DNA was purified using the MinElute PCR Purification Kit (Qiagen)
Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) experiments were performed as described in Buenrostro et al., 2015. Curr. Protoc. Mol. Biol. 109, 21.29.1-9. doi:10.1002/0471142727.mb2129s109

value: 4 hpf


title: pvfC mutant, rep2

description: Library name: pvfC mutant, rep2


title: Bckdk_KD_4h_R2


title: Cas13d_4h_R2


title: Cas13d_4h_R1


title: 4 Pvt1a MUT2, biol rep 2, RNAseq

city: New Haven

first: Nadya

last: Dimitrova

state: CT

address: 260 Whitney Ave YSB211

department: MCDB

institute: Yale University

description: Library name: Sample 8

data_processing:
Reads were mapped with the STAR (2.7.11a) alignment tool.
Reads were mapped first to custom tandem repeat assembly (satellite DNA, rDNA, telomere) allowing no mismatches.
Reads that did not map perfectly to tandem repeat sequences were then mapped to the mm10 genome.
Number of mapped reads per gene in each sample was quantified using HTseq and the mouse gencode (vM25) gene annotation.
Differential Gene Expression (DEG) analysis was done with the DESeq2.
BigWig files were generated with deeptools (V3.5.2) using bin size 20.
Assembly: mm10
Supplementary files format and content: BigWig files for forward and reverse reads for each sample.
Supplementary files format and content: DEseq2 output with normalized gene counts (250710_Pvt1_RNAseqSummaryTableFull.txt).

source_name: E13.5 MEFs

growth_protocol: Primary MEFs were grown in DMEM supplemented with 15% FBS, Pen/Strep, non-essential amino acids, L-glutamine, and b-mercaptoethanol.

extract_protocol:
For RNA-seq, total RNA was extracted using Qiagen Rneasy Kit. For ATAC-seq and Hi-C, 0.5x10^6 and 1x10^6 cells, respectively were cryopreserved and submitted for library prep.
PolyA RNAseq libraries were prepared using oligo-dT beads followed by random priming.

treatment_protocol: Not applicabel.

value: E13.5 MEFs

value: Primary MEFs

value: litter 2


title: 2 Pvt1a MUT1, biol rep 2, RNAseq

description: Library name: Sample 6

value: litter 1


title: 3 Pvt1a MUT2, biol rep 1, RNAseq

description: Library name: Sample 7


title: WT HAP1, GSK-3484862, Biol Rep2

city: Zurich

first: Shana

last: Sturla

address: Schmelzbergstrasse 9

department: Department of Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

hyb_protocol: DNA was bisulphite converted  with Zymo EZ-96 DNA Methylation-Lightning Kit (D5033), amplified, fragmented and hybridized to human Infinium MethylationEPIC BeadChip v2.0 (Illumina) using standard Illumina protocol.

scan_protocol: Arrays were imaged using iScan System and standard recommended Illumina scanning settings.

data_processing: R library minfi version 1.50.0

label: biotin (ddCTP and ddGTP) and 2,4-dinitrophenol (DNP) (ddATP and ddTTP)

label_protocol: Standard Illumina Protocol

growth_protocol: HAP1 cells (RRID:CVCL_Y019, Horizon Discovery) were cultivated in Iscove's Modified Dulbecco's Medium supplemented with 10% fetal bovine serum (Gibco) and 1% penicillin-streptomycin (Gibco). U2OS cells (RRID:CVCL_0042) were cultivated in McCoy‘s general cell culture medium, modified with high glucose, L-glutamate, bacto-peptone and phenol red, and lacking sodium pyruvate and HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) (McCoy‘s 5A, Gibco 16600082), supplemented with 10% fetal bovine serum (Gibco) and 1% penicillin-streptomycin (Gibco). 10 mL of cell culture medium was supplemented by 4 μL GSK-3484862 (MedChemExpress, 10 mM dissolved in DMSO) (final concentration 4 μM). Control medium was prepared by adding 4 μL of DMSO to 10 mL of cell culture medium. The treatment and control media were filtered with a sterile syringe filter (0.22 μm) and added to the cells, followed by 72-h incubation at 37 °C, 5% CO2, 3% O2, with the treatment and control media being refreshed after every 24 hours.

extract_protocol: Cells were harvested by removing the medium, washing once with 10 mL DPBS followed by addition of 1 mL 0.25% Trypsin EDTA solution (Gibco). After an incubation of 5 min at 37°C, 9 mL medium was added, cells resuspended and transferred to a Falcon centrifugal tube. Cells were centrifuged (4°C, 0.3 rcf, 5 min) and the supernatant removed. gDNA was extracted from  cell pellets using the Monarch Genomic DNA Extraction Kit following the manufacturer’s instructions. In order to avoid artefactual oxidation, DPBS used in the cell pellet resuspension  was supplemented with 1 mM deferoxamine and 50 µM n-tert-butyl-α-phenylnitrone.

treatment_protocol: 10 mL of cell culture medium was supplemented by 4 μL GSK-3484862 (MedChemExpress, 10 mM dissolved in DMSO) (final concentration 4 μM); control medium was prepared by adding 4 μL of DMSO to 10 mL of cell culture medium.

value: wild type


title: 3 Pvt1a WT2, biol rep 1, RNAseq

description: Library name: Sample 3


title: 2 Pvt1a WT1, biol rep 2, RNAseq

description: Library name: Sample 2


title: 4 Pvt1a WT2, biol rep 2, RNAseq

description: Library name: Sample 4


title: 1 Pvt1a WT1, biol rep 1, RNAseq

description: Library name: Sample 1


title: 1 Pvt1a MUT1, biol rep 1, RNAseq

description: Library name: Sample 5


title: Mouse CD8+ T cells, treated with 5μM Lutein, 24 hour,replicate3

description: Library name: Lut3

value: Primary CD13+ T cell

value: treated with 5μM Lutein, 26 hour


title: Mouse CD8+ T cells, treated with DMSO, 24 hour,replicate1

description: Library name: CT1

value: Mouse spleen

value: Primary CD8+ T cell

value: treated with DMSO, 24 hour,


title: 2 Pvt1a WT1, biol rep 2, HiC

description: Library name: Sample 2

data_processing:
Paired-end reads were processed with the Juicer command tool (V1.6) to generate hic files.
The juicer_tools.3.0.0.jar tool was used to run the HICCUPS and HiCCUPSdiff algorithms.
Assembly: mm10
Supplementary files format and content: Hi-C contact matrices (.hic) for each sample (for MAPQ >= 30).
Supplementary files format and content: HiCCUPSdiff output in bedpe files.

extract_protocol:
For ATAC-seq and Hi-C, 0.5x10^6 and 1x10^6 cells, respectively were cryopreserved and submitted for library prep.
Hi-C library preparation was performed using Arima-HiC kit, according to the manufacturer's instructions.


title: 1 Pvt1a MUT1, biol rep 1, HiC

description: Library name: Sample 3


title: 2 Pvt1a MUT1, biol rep 2, HiC

description: Library name: Sample 4


title: WT U2OS, GSK-3484862, Biol Rep2


title: 1 Pvt1a WT1, biol rep 1, HiC

description: Library name: Sample 1


title: 4 Pvt1a WT2, biol rep 2, ATACseq

description: Library name: Sample 4

data_processing:
Reads were mapped with the STAR (2.7.11a) alignment tool.
Reads were mapped first to custom tandem repeat assembly (satellite DNA, rDNA, telomere) allowing no mismatches.
Reads that did not map perfectly to tandem repeat sequences were then mapped to the mm10 genome.
MACS2 (Zhang et al. 2008) was used to call peaks with default parameters.
All peaks (signalValue > 2 and -log10(FDR) > 2) were merged into a single bed file for count quantification. Significantly different peaks were determinded using DESeq2
BigWig files were generated with deeptools (V3.5.2) using bin size 20.
Assembly: mm10
Supplementary files format and content: BigWig files for each sample.
Supplementary files format and content: MACS2 peak calling output for each sample.
Supplementary files format and content: DEseq2 output with normalized gene counts (250710_Pvt1_ATACseqSummaryTableFull.txt).

extract_protocol:
For ATAC-seq and Hi-C, 0.5x10^6 and 1x10^6 cells, respectively were cryopreserved and submitted for library prep.
ATAC-seq library preparation was performed using the Active Motif Library preparation kit, according to the manufacturer's instructions.

treatment_protocol: Not applicable.


title: 4 Pvt1a MUT2, biol rep 2, ATACseq

description: Library name: Sample 8


title: 3 Pvt1a MUT2, biol rep 1, ATACseq

description: Library name: Sample 7


title: WT HAP1, DMSO, Biol Rep1

value: DMSO


title: WT U2OS, DMSO, Biol Rep3


title: 1 Pvt1a MUT1, biol rep 1, ATACseq

description: Library name: Sample 5


title: 2 Pvt1a MUT1, biol rep 2, ATACseq

description: Library name: Sample 6


title: 2 Pvt1a WT1, biol rep 2, ATACseq

description: Library name: Sample 2


title: 3 Pvt1a WT2, biol rep 1, ATACseq

description: Library name: Sample 3


title: 1 Pvt1a WT1, biol rep 1, ATACseq

description: Library name: Sample 1


title: Wild-type mice (B6), infection day 14, nasal mucosa, CITE-Seq

city: Philadelphia

first: Lauren

last: Springer

state: PA

address: 1020 Locust St

institute: Thomas Jefferson University

description:
Library name: D14_B6_NM_CITE-seq
10x Genomics

data_processing:
CITE-seq reads were processed with 10X Genomics cellranger (version 8.0.1) tool
The mouse reference genome (mm10) was used for mapping RNA reads
Known barcodes were used for mapping reads from the ADTs
Quality control, cell and feature selection was performed using Seurat R package (v5.1.0)
RNA (SCTransform2) and ADT (CLR) data were normalized, then integrated using IntegrateData (RNA) and Reciprocal PCA (ADT). Assessed RNA vs. protein utility using weighted-nearest neighbor.
Annotated cell types with SingleR (ImmGen reference, celldex)
Assembly: Mouse mm10
Supplementary files format and content: C57BL/6
Supplementary files format and content: matrix files
Library strategy: CITE-seq

source_name: nasal mucosa

extract_protocol:
C57BL/6 mice and BLT1-/- mice were infected intransally with 1 million pfu of strain K181 MCMV. 0 days, 3 days, and 14 days post infection, target cells from nasal mucosa and lungs were isolated by FACs. Target cells were positively sorted as live, IV+ cells, and cells expressing Siglec-F, CD19, and FcεRIα were excluded. Cells for single cell RNA sequencing groups were pooled from four mice per group.
Library was performed accoriding to the manufacter's instructions ( Next GEM Single Cell 3’ Reagent Kits v3.1 protocol, 10x Genomics). Briefly, immune cells were resuspended in master mix and loaded with partitioning oil and gel beads into the chip to mak GEM (gel bead-in-emulsion). The poly-A RNA from the cell lysate in the GEMs were retrotranscripted to cDNA. The barcoded cDNA was cleaned by Silane DynaBeads, aplified by PCR and the appropriate size fragmet was selected with SPRIselect for subsequent library contruction.

treatment_protocol: MCMV K181 strain intranasal infection

value: nasal mucosa

value: immune cells

value: MCMV infection


title: Knockout mice (BLT), infection day 14, lung, CITE-Seq

description:
Library name: D14_BLT_L_CITE-seq
10x Genomics

source_name: lung

value: lung


title: WT U2OS, DMSO, Biol Rep1


title: Knockout mice (BLT) infection day 14, lung

description:
Library name: D14_BLT_L_gene
10x Genomics

data_processing:
CITE-seq reads were processed with 10X Genomics cellranger (version 8.0.1) tool
The mouse reference genome (mm10) was used for mapping RNA reads
Known barcodes were used for mapping reads from the ADTs
Quality control, cell and feature selection was performed using Seurat R package (v5.1.0)
RNA (SCTransform2) and ADT (CLR) data were normalized, then integrated using IntegrateData (RNA) and Reciprocal PCA (ADT). Assessed RNA vs. protein utility using weighted-nearest neighbor.
Annotated cell types with SingleR (ImmGen reference, celldex)
Assembly: Mouse mm10
Supplementary files format and content: C57BL/6
Supplementary files format and content: matrix files


title: Wild-type mice (B6), infection day 14, lung, CITE-Seq

description:
Library name: D14_B6_L_CITE-seq
10x Genomics


title: WT U2OS, DMSO, Biol Rep2


title: Wild-type mice (B6), infection day 14, lung

description:
Library name: D14_B6_L_gene
10x Genomics


title: Wild-type Mice (B6), infection day 3, nasal mucosa

description:
Library name: D3_B6_NM_gene
10x Genomics


title: Knockout mice (BLT), infection day 14, nasal mucosa, CITE-Seq

description:
Library name: D14_BLT_NM_CITE-seq
10x Genomics


title: Wild-type mice (B6), infection day 14, nasal mucosa

description:
Library name: D14_B6_NM_gene
10x Genomics


title: WT U2OS, GSK-3484862, Biol Rep3


title: Knockout mice (BLT) infection day 0 (uninfected), lung

description:
Library name: D0_ BLT_L_gene
10x Genomics


title: Knockout mice (BLT) infection day 0 (uninfected), nasal mucosa

description:
Library name: D0_ BLT_NM_gene
10x Genomics


title: Wild-type Mice (B6), infection day 3, lung, CITE-Seq

description:
Library name: D3_B6_L_CITE-seq
10x Genomics


title: Wild-type Mice (B6), infection day 0 (uninfected), lung, CITE-Seq

description:
Library name: D0_ B6_L_CITE-seq
10x Genomics


title: Knockout mice (BLT) infection day 14, nasal mucosa

description:
Library name: D14_BLT_NM_gene
10x Genomics


title: Wild-type Mice (B6), infection day 3, lung

description:
Library name: D3_B6_L_gene
10x Genomics


title: WT HAP1, DMSO, Biol Rep2


title: WT HAP1, DMSO, Biol Rep3


title: Knockout mice (BLT), infection day 0 (uninfected), lung, CITE-Seq

description:
Library name: D0_ BLT_L_CITE-seq
10x Genomics


title: Knockout mice (BLT), infection day 0 (uninfected), nasal mucosa, CITE-Seq

description:
Library name: D0_ BLT_NM_CITE-seq
10x Genomics


title: Wild-type Mice (B6), infection day 0 (uninfected), nasal mucosa, CITE-Seq

description:
Library name: D0_ B6_NM_CITE-seq
10x Genomics


title: Pol2_8C_heatshock_62

city: Beijing

first: Wei

last: Xie

state: Beijing

address: Qinghuayuan

department: School of Life Science

institute: Tsinghua University

description: Library name: Pol2_8C_heatshock_control_62

data_processing:
The paired-end CUT&RUN reads were aligned to the mouse reference genome (mm9) using Bowtie2 with the parameters: -t –q –N 1 –L 25 –X 1000 --no-mixed --no-discordant. All unmapped reads, non-uniquely mapped reads, reads with low mapping quality (MAPQ < 20) and PCR duplicates were removed. For downstream analysis, we normalized the read counts by computing the number of reads per kilobase of bin per million reads sequenced (RPKM) for 100-bp bins of the genome. To minimize the batch and cell type variation, RPKM values across the whole genome were further Z-score-normalized. Spike-in normalization was performed as previously described. Briefly, reads were aligned to the yeast (sacCer3) reference genome, with those unmapped or derived from PCR duplicates excluded. A scaling factor was then calculated using an arbitrary number to divide the number of reads mapped to the yeast genome and the total cell number used to prepare the library (scaling factor = 100,000/(spike-in reads number × cell number)). For downstream analysis and visualization, the genomecov function of BEDtools was used to generate normalized read counts for the whole genome with the parameters: -scale scaling factor -bg -pc.
Assembly: mm9
Supplementary files format and content: bw files generated by bedtools with or without spike-in normalization
Library strategy: CUT&Run

extract_protocol:
For Adnp knockout, three single guide RNAs (sgRNAs) targeting the last exon were designed. To assemble Cas9–sgRNA ribonucleoproteins, 200 ng μl−1 sgRNAs was mixed with 0.3 μl of Alt-R S.p. HiFi Cas9 protein (Integrated DNA Technologies, 1081060) and incubated at room temperature for 15 min in 15 μl assembly buffer (1 mM Tris-HCl pH 7.5, 0.1 mM EDTA). The injection mix was centrifuged at 12,000g for 10 min, and the supernatant was used for injection into PN3 zygotes. Embryos were then cultured in G1 medium (Vitrolife). Blastocyst-stage embryos were collected for RNA-seq, CUT&RUN and Hi-C. For DRB treatment, 8C embryos (68–70 h after hCG injection) were collected and cultured in CZB medium supplemented with DRB (final concentration 120 μM) for 2 or 4 h.For the cohesin-KD experiment, PN3 zygotes were injected with 20 μM siRNAs (targeting Rad21 (Rad21 KD) or Nipbl, Smc3 and Rad21 (triple KD; Supplementary Table 2). The PN3 zygotes in the control group were injected with an equal volume of 20 μM scramble siRNAs. Then the embryos were cultured in G1 medium (Vitrolife) for 45 h. Heatshock was induced by placing the embryos or mouse ES cells at 43 °C for 30 min, followed by a recovery at 37 °C for 30 min. Control embryos or mouse ES cells were maintained at 37 °C throughout culture and were collected at the same time with heat-shock samples. Blastomere numbers and cell numbers were counted to allow downstream spike-in normalization.
Embryos without the zona pellucida were transferred into 1.5-ml conventional tubes. Cells were attached to 10 μl pre-washed concanavalin A-coated magnetic beads to allow simple handling. Samples were then incubated with 50–100 μl antibody buffer (CTCF antibody (Active Motif, 61311), SMC3 antibody (Abcam, 9263) and NIPBL antibody (Bethyl Laboratories, A301-779A) diluted at ratio of 1:100) at 4 °C on a Thermomixer for overnight at 400 r.p.m. Samples were washed twice with washing buffer before being incubated with pA-MNase (700 ng ml−1 in washing buffer) at 4 °C on the Thermomixer for 3 h at 400 r.p.m. and then washed twice and resuspended in 100 μl washing buffer. Targeted digestion was performed on ice for 30 min after adding 2 μl 100 mM CaCl2 and stopped by adding 100 μl stop buffer (containing 2 μl diluted yeast spike-in DNA). Cleaved fragments were then released to diffuse out of the nuclei through incubation at 37 °C for 20 min. After removing the intact nuclei by centrifugation, the super- natant containing released chromatin fragments was used to extract DNA directly for library construction. Purified DNA was subjected to Tru-seq library construction using a NEBNext Ultra II DNA Library Prep Kit from Illumina (NEB E7645S).

tag: developmental stage

value: WT

value: Heatshock control


title: WT HAP1, GSK-3484862, Biol Rep3


title: Wild-type Mice (B6), infection day 3, nasal mucosa, CITE-Seq

description:
Library name: D3_B6_NM_CITE-seq
10x Genomics


title: Wild-type Mice (B6), infection day 0 (uninfected), nasal mucosa

description:
Library name: D0_ B6_NM_gene
10x Genomics


title: Wild-type Mice (B6), infection day 0 (uninfected), lung

description:
Library name: D0_ B6_L_gene
10x Genomics


title: CTCF_Blastocyst_AdnpKO_rep2

description: Library name: CTCF_Blastocyst_AdnpKO_rep2

source_name: E3.5 blastocyst

value: E3.5 blastocyst

value: Adnp KO


title: WT U2OS, GSK-3484862, Biol Rep1


title: SMC3_8C_heatshock_control_75_rep2

description: Library name: SMC3_8C_heatshock_control_75_rep2


title: SMC3_8C_heatshock_control_90_rep1

description: Library name: SMC3_8C_heatshock_control_90_rep1


title: Pol2_8C_heatshock_50

description: Library name: Pol2_8C_heatshock_50

value: Heatshock 30min


title: CTCF_Blastocyst_AdnpKO_control

description: Library name: CTCF_Blastocyst_AdnpKO_control

value: KO control


title: CTCF_Blastocyst_AdnpKO_rep1

description: Library name: CTCF_Blastocyst_AdnpKO_rep1


title: SMC3_8C_GFP_OE_75_rep1

description: Library name: SMC3_8C_GFP_OE_75_rep1

value: GFP control


title: SMC3_8C_GFP_OE_70_rep2

description: Library name: SMC3_8C_GFP_OE_70_rep2


title: SMC3_8C_heatshock_75_rep2

description: Library name: SMC3_8C_heatshock_75_rep2


description: Library name: SMC3_8C_DMSO_control_for_amanitin_100_rep1

value: DMSO control


title: SMC3_8C_heatshock_120_rep1

description: Library name: SMC3_8C_heatshock_120_rep1


title: SMC3_2C_amanitin_45h_390_rep2

description: Library name: SMC3_2C_amanitin_45h_390_rep2

source_name: 2-cell arrested

value: 2-cell arrested

value: Alpha-amanitin 45h


title: SMC3_8C_DRB_20h_95

description: Library name: SMC3_8C_DRB_20h_95

value: DRB 20h


title: WT HAP1, GSK-3484862, Biol Rep1

value: wild type


title: NIPBL_8C_rep2

description: Library name: NIPBL_8C_rep2

value: untreated


title: SMC3_8C_Wapl_OE_150_rep2

description: Library name: SMC3_8C_Wapl_OE_150_rep2

value: Wapl OE


title: SMC3_8C_Rad21KD_100

description: Library name: SMC3_8C_Rad21KD_100

value: Rad21 KD


title: SMC3_8C_cohesinKD_control_93

description: Library name: SMC3_8C_cohesinKD_control_93

value: KD control


description: Library name: SMC3_8C_DMSO_control_for_amanitin_100_rep2


title: CTCF_8C_cohesinKD_control_110

description: Library name: CTCF_8C_cohesinKD_control_110


title: SMC3_8C_DMSO_control_for_DRB_20h_100

description: Library name: SMC3_8C_DMSO_control_for_DRB_20h_100


title: SMC3_Late2C_rep2

description: Library name: SMC3_Late2C_rep2

source_name: Late 2-cell

value: Late 2-cell


title: CTCF_8C_TripleKD_100

description: Library name: CTCF_8C_TripleKD_100

value: WT

value: Triple KD


title: SMC3_ICM_rep1

description: Library name: SMC3_ICM_rep1

source_name: ICM from E3.5 blastocyst

value: ICM from E3.5 blastocyst


title: SMC3_Late2C_rep1

description: Library name: SMC3_Late2C_rep1


description: Library name: RNA_spikein_mESC_ActivinA_D3_500_batch2_rep3

data_processing:
RNA-seq reads were aligned to the mouse reference genome (mm9) by STAR70 with the following parameters: --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate -outFilterMultimapNmax 20 --outSAMstrandField intronMotif. The gene expression level was normalized to FPKM values using Cufflinks. Read counts of genes were summarized with featureCounts. The read count matrices were then imported to edgeR73 to perform differential expression analysis based on the negative binomial GLM framework. Gene set enrichment analysis was performed using the FGSEA on the basis of the gene expression fold changes calculated by edgeR. ERCC spike-in normalization was performed as previously described. Briefly, reads were mapped to the ERCC reference (http://tools.invitrogen.com/downloads/ERCC92.fa), and an ERCC count matrix was generated by featureCounts. The normalizing factor was calculated using the calcNormFactors function of edgeR. Voom transformation of the Limma package was then utilized to generate the normalized RNA-seq data using normalizing factors calculated at the previous step.Single-cell Smart-seq3 sequencing reads were processed with zUMIs. Demultiplexed UMI-containing reads were extracted in zUMIs by setting: find_pattern: ATTGCGCAATG, BC (12–17), UMI (18–25) and cDNA(29–150). UMI counts were used for downstream analysis. Intron reads from each cell were used for estimation of nascent transcription.
Assembly: mm9
Supplementary files format and content: Gene read count table generated by featureCounts

source_name: mESC

extract_protocol:
For Adnp knockout, three single guide RNAs (sgRNAs) targeting the last exon were designed. To assemble Cas9–sgRNA ribonucleoproteins, 200 ng μl−1 sgRNAs was mixed with 0.3 μl of Alt-R S.p. HiFi Cas9 protein (Integrated DNA Technologies, 1081060) and incubated at room temperature for 15 min in 15 μl assembly buffer (1 mM Tris-HCl pH 7.5, 0.1 mM EDTA). The injection mix was centrifuged at 12,000g for 10 min, and the supernatant was used for injection into PN3 zygotes. Embryos were then cultured in G1 medium (Vitrolife). Blastocyst-stage embryos were collected for RNA-seq, CUT&RUN and Hi-C. For DRB treatment, 8C embryos (68–70 h after hCG injection) were collected and cultured in CZB medium supplemented with DRB (final concentration 120 μM) for 2 or 4 h.For the cohesin-KD experiment, PN3 zygotes were injected with 20 μM siRNAs (targeting Rad21 (Rad21 KD) or Nipbl, Smc3 and Rad21 (triple KD; Supplementary Table 2). The PN3 zygotes in the control group were injected with an equal volume of 20 μM scramble siRNAs. Then the embryos were cultured in G1 medium (Vitrolife) for 45 h. Short-term mouse ES cell differentiation was performed as previously described with modifications. For retinoic acid-induced differentiation, mouse ES cells were transferred to 0.1% gelatin-precoated dishes in DMEM containing 15% fetal bovine serum, EmbryoMax nucleosides, GlutaMAX, penicillin–streptomycin, 2-mercaptoethanol and non-essential amino acids, with retinoic acid (final concentration of 2 μg ml−1; catalogue no. R2625; Sigma-Aldrich). For activin A-induced differentiation, mouse ES cells were transferred to 0.1% gelatin-precoated dishes in DMEM containing 15% fetal bovine serum, EmbryoMax nucleosides, GlutaMAX, penicillin–streptomycin, 2-mercaptoethanol and non-essential amino acids, with activin A (final concentration of 100 ng ml−1). For BMP4- and FGF2-induced differentiation, mouse ES cells were transferred to 0.1% gelatin-precoated dishes in DMEM containing 15% fetal bovine serum, EmbryoMax nucleosides, GlutaMAX, penicillin–streptomycin, 2-mercaptoethanol and non-essential amino acids, with BMP4 (catalogue no. SRP3298; Sigma-Aldrich; final concentration of 50 ng ml−1) and FGF2 (catalogue no. SRP4038; Sigma-Aldrich; final concentration 5 ng ml−1). Mouse ES cells (day 0 (D0)) and differentiated cells from various time points (D1, D2 and D3) were then collected for subsequent analyses.
Smart-seq2 libraries were prepared as previously described64. Embryos or cells were lysed in hypotonic lysis buffer (Amresco, M334). After a pre-amplification step, cDNAs were purified using AMPure XP beads and then subjected to library preparation using the TruePrep DNA library Prep Kit (Vazyme, TD502). All libraries were sequenced by the Illumina Hi-Seq Xten or Novaseq 6000 according to the manufacturer’s instructions. For ERCC spike-in Smart-seq2, mouse ES cells and embryos were quantified by mouth pipette. A 1 μl volume of 1:2,000 diluted ERCC RNA Spike-In Mix (Invitrogen, 4456740) was added before cell lysis. Total RNA-seq libraries for heat-shock embryos were prepared as previously described. Briefly, RNA was extracted from mouse embryos or cells using TRIzol (Thermo, 10296028). Ribosomal RNA was then depleted using the NEB Next rRNA Depletion Kit (NEB, E6310S). NEB Next first-strand (NEB, E7771S) and second-strand synthesis modules (NEB, E7550S) were used to synthesize cDNA. Library preparation was performed using the NEBNext Ultra II DNA Library Prep Kit (NEB, E7645S) according to the manufacturer’s instructions. Mouse 2C and 8C embryos were dissected manually to obtain single blastomeres. Single-cell Smart-seq3 libraries were manually prepared as previously described66. In short, 3 μl lysis buffer (5% PEG 8000, 0.1% Triton X-100, 0.5 U μl−1 RNase inhibitor, 0.5 mM dNTPs and 0.5 μM oligodT30VN) was added to the obtained single blastomere. Following incubation of the blastomere at 72 °C for 10 min, 1 μl reverse transcription master mix (25 mM Tris-HCl pH 8.3, 30 mM NaCl, 2.5 mM MgCl2, 1 mM GTP, 8 mM dithiothreitol, 0.5 U μl−1 RNase inhibitor, 2 U μl−1 Maxima H-minus RT enzyme and 2 μM TSO (/5Biotin/AGAGACAGATTGCGCAATG[6-nt Cell barcode][8-nt UMI]rGrGrG)) was added. Reverse transcription was carried out at 42 °C for 90 min, followed by 10 cycles of 50 °C for 2 min and 42 °C for 2 min, and the reaction was inactivated by incubation at 85 °C for 5 min. Pre-amplification was then performed by adding 5 μl KAPA HiFi Hot-Start ReadyMix, 0.5 µM Smart-seq3 forward PCR primer (5′-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGATTGCGCAATG-3′) and 0.1 µM reverse PCR primer (5′-ACGAGCATCAGCAGCATACGA-3′), using the following cycles: 3 min at 98 °C, 23 cycles of 20 s at 98 °C, 30 s at 65 °C and 6 min at 72 °C, and a final elongation for 5 min at 72 °C. After the pre-amplification step, the single-cell libraries were pooled together, and cDNAs were purified using AMPure XP beads, followed by library preparation using TruePrep DNA library Prep Kit (Vazyme, TD502).

value: mESC

value: Activin-A induced Day3


title: SMC3_ICM_rep2

description: Library name: SMC3_ICM_rep2


description: Library name: RNA_spikein_mESC_ActivinA_D3_50_batch2_rep2


title: SMC3_8C_Wapl_OE_122_rep1

description: Library name: SMC3_8C_Wapl_OE_122_rep1


description: Library name: RNA_spikein_mESC_ActivinA_D2_50_batch2_rep3

value: Activin-A induced Day2


description: Library name: RNA_spikein_mESC_ActivinA_D2_50_batch2_rep1


description: Library name: RNA_spikein_mESC_ActivinA_D1_50_batch2_rep3

value: Activin-A induced Day1


title: SMC3_2C_amanitin_45h_360_rep1

description: Library name: SMC3_2C_amanitin_45h_360_rep1


description: Library name: RNA_spikein_mESC_ActivinA_D1_500_batch2_rep2


description: Library name: RNA_spikein_mESC_ActivinA_D2_500_batch2_rep2


title: RNA_spikein_mESC_BMP4_D3_50_batch2_rep3

description: Library name: RNA_spikein_mESC_BMP4_D3_50_batch2_rep3

value: BMP4 induced Day3


title: RNA_spikein_mESC_BMP4_D3_50_batch2_rep1

description: Library name: RNA_spikein_mESC_BMP4_D3_50_batch2_rep1


description: Library name: RNA_spikein_mESC_BMP4_D3_500_batch2_rep2


title: RNA_spikein_mESC_BMP4_D2_50_batch2_rep3

description: Library name: RNA_spikein_mESC_BMP4_D2_50_batch2_rep3

value: BMP4 induced Day2


description: Library name: RNA_spikein_mESC_BMP4_D2_500_batch2_rep2


title: RNA_spikein_mESC_BMP4_D2_50_batch2_rep1

description: Library name: RNA_spikein_mESC_BMP4_D2_50_batch2_rep1


title: SMC3_8C_TripleKD_120

description: Library name: SMC3_8C_TripleKD_120


description: Library name: RNA_spikein_mESC_BMP4_D1_500_batch2_rep2

value: BMP4 induced Day1


title: RNA_spikein_mESC_RA_D3_500_batch2_rep3

description: Library name: RNA_spikein_mESC_RA_D3_500_batch2_rep3

value: Retinoic acid induced Day3


title: RNA_spikein_mESC_BMP4_D1_50_batch2_rep1

description: Library name: RNA_spikein_mESC_BMP4_D1_50_batch2_rep1


title: RNA_spikein_mESC_RA_D3_50_batch2_rep1

description: Library name: RNA_spikein_mESC_RA_D3_50_batch2_rep1


title: RNA_spikein_mESC_RA_D2_50_batch2_rep3

description: Library name: RNA_spikein_mESC_RA_D2_50_batch2_rep3

value: Retinoic acid induced Day2


title: RNA_spikein_mESC_RA_D2_500_batch2_rep2

description: Library name: RNA_spikein_mESC_RA_D2_500_batch2_rep2


title: RNA_spikein_mESC_RA_D1_50_batch2_rep3

description: Library name: RNA_spikein_mESC_RA_D1_50_batch2_rep3

value: Retinoic acid induced Day1


title: RNA_spikein_mESC_RA_D2_50_batch2_rep1

description: Library name: RNA_spikein_mESC_RA_D2_50_batch2_rep1


title: RNA_spikein_mESC_RA_D3_50_batch2_rep2

description: Library name: RNA_spikein_mESC_RA_D3_50_batch2_rep2


title: RNA_spikein_mESC_RA_D1_500_batch2_rep2

description: Library name: RNA_spikein_mESC_RA_D1_500_batch2_rep2


title: RNA_spikein_8C_6_batch2_rep1

description: Library name: RNA_spikein_8C_6_batch2_rep1

value: untreated


description: Library name: RNA_spikein_mESC_ActivinA_D3_500_batch2_rep1


title: RNA_spikein_mESC_RA_D1_50_batch2_rep1

description: Library name: RNA_spikein_mESC_RA_D1_50_batch2_rep1


title: RNA_spikein_L2C_15_batch2_rep2

description: Library name: RNA_spikein_L2C_15_batch2_rep2


title: RNA_spikein_8C_6_batch2_rep2

description: Library name: RNA_spikein_8C_6_batch2_rep2


description: Library name: RNA_spikein_mESC_ActivinA_D1_50_batch2_rep1


title: RNA_spikein_mESC_BMP4_D1_50_batch2_rep3

description: Library name: RNA_spikein_mESC_BMP4_D1_50_batch2_rep3


title: RNA_spikein_mESC_RA_D2_50_rep1

description: Library name: RNA_spikein_mESC_RA_D2_50_rep1


title: RNA_spikein_mESC_RA_D1_500_rep3

description: Library name: RNA_spikein_mESC_RA_D1_500_rep3


title: RNA_spikein_L2C_15_batch2_rep1

description: Library name: RNA_spikein_L2C_15_batch2_rep1


title: RNA_spikein_mESC_RA_D1_50_rep1

description: Library name: RNA_spikein_mESC_RA_D1_50_rep1


title: RNA_spikein_PN5_25_batch2_rep1

description: Library name: RNA_spikein_PN5_25_batch2_rep1

source_name: PN5 zygote

value: PN5 zygote


title: RNA_spikein_mESC_RA_D3_500_rep3

description: Library name: RNA_spikein_mESC_RA_D3_500_rep3


title: RNA_spikein_mESC_RA_D1_50_rep2

description: Library name: RNA_spikein_mESC_RA_D1_50_rep2


title: RNA_spikein_PN5_25_batch2_rep2

description: Library name: RNA_spikein_PN5_25_batch2_rep2


title: RNA_spikein_mESC_RA_D2_50_rep2

description: Library name: RNA_spikein_mESC_RA_D2_50_rep2


title: RNA_spikein_EPI_D65_80_rep1

description: Library name: RNA_spikein_EPI_D65_80_rep1

source_name: Epiblast of E6.5 blastocyst

value: Epiblast of E6.5 blastocyst


title: RNA_spikein_mESC_RA_D3_50_rep1

description: Library name: RNA_spikein_mESC_RA_D3_50_rep1


title: RNA_spikein_mESC_RA_D3_50_rep2

description: Library name: RNA_spikein_mESC_RA_D3_50_rep2


title: RNA_spikein_EPI_D55_80_rep2

description: Library name: RNA_spikein_EPI_D55_80_rep2

source_name: Epiblast of E5.5 blastocyst

value: Epiblast of E5.5 blastocyst


title: RNA_spikein_mESC_RA_D2_500_rep3

description: Library name: RNA_spikein_mESC_RA_D2_500_rep3

value: WT


title: RNA_spikein_EPI_D65_80_rep2

description: Library name: RNA_spikein_EPI_D65_80_rep2


title: RNA_spikein_ICM_D45_80_rep1

description: Library name: RNA_spikein_ICM_D45_80_rep1

source_name: ICM of E4.5 blastocyst

value: ICM of E4.5 blastocyst


title: RNA_spikein_EPI_D55_80_rep1

description: Library name: RNA_spikein_EPI_D55_80_rep1


title: RNA_spikein_8C_3_rep2

description: Library name: RNA_spikein_8C_3_rep2


description: Library name: RNA_8C_cohesinKD_control_singlecell_pool

value: Control


title: RNA_spikein_ICM_D45_80_rep2

description: Library name: RNA_spikein_ICM_D45_80_rep2


title: RNA_spikein_8C_6_rep1

description: Library name: RNA_spikein_8C_6_rep1


title: RNA_spikein_L2C_12_rep1

description: Library name: RNA_spikein_L2C_12_rep1

value: Late 2-cell


title: RNA_spikein_PN5_13_rep2

description: Library name: RNA_spikein_PN5_13_rep2


title: RNA_spikein_L2C_6_rep2

description: Library name: RNA_spikein_L2C_6_rep2


title: RNA_spikein_PN5_25_rep1

description: Library name: RNA_spikein_PN5_25_rep1


title: RNA_8C_TripleKD_singlecell_pool

description: Library name: RNA_8C_TripleKD_singlecell_pool

value: Rad21 KD


title: RNA_8C_TripleKD_rep1

description: Library name: RNA_8C_TripleKD_rep1

value: Triple KD


title: RNA_2C_singlecell_pool

description: Library name: RNA_2C_singlecell_pool


title: RNA_8C_Rad21KD_singlecell_pool

description: Library name: RNA_8C_Rad21KD_singlecell_pool


title: RNA_8C_cohesinKD_control_rep2

description: Library name: RNA_8C_cohesinKD_control_rep2


title: RNA_8C_Rad21KD_rep1

description: Library name: RNA_8C_Rad21KD_rep1


title: RNA_8C_TripleKD_rep2

description: Library name: RNA_8C_TripleKD_rep2


title: RNA_Blastocyst_AdnpKO_rep4

description: Library name: RNA_Blastocyst_AdnpKO_rep4

source_name: Blastocyst

value: Blastocyst

value: Adnp KO


title: RNA_Blastocyst_control_rep2

description: Library name: RNA_Blastocyst_control_rep2


title: RNA_Blastocyst_control_rep4

description: Library name: RNA_Blastocyst_control_rep4


title: RNA_Blastocyst_AdnpKO_rep2

description: Library name: RNA_Blastocyst_AdnpKO_rep2


title: RNA_8C_cohesinKD_control_rep1

description: Library name: RNA_8C_cohesinKD_control_rep1


title: RNA_Blastocyst_control_rep3

description: Library name: RNA_Blastocyst_control_rep3


title: RNA_DRB_8h_rep1

description: Library name: RNA_DRB_8h_rep1

value: DRB 8h


title: RNA_DMSO_8h_rep1

description: Library name: RNA_DMSO_8h_rep1

value: DMSO 8h


title: RNA_DMSO_8h_rep2

description: Library name: RNA_DMSO_8h_rep2


title: RNA_DRB_8h_rep2

description: Library name: RNA_DRB_8h_rep2


title: RNA_mESC_singlecell_pool

description: Library name: RNA_mESC_singlecell_pool

value: mESC


title: RNA_DRB_4h_rep1

description: Library name: RNA_DRB_4h_rep1

value: DRB 4h


title: RNA_DMSO_4h_rep2

description: Library name: RNA_DMSO_4h_rep2

value: DMSO 4h


title: RNA_DMSO_4h_rep1

description: Library name: RNA_DMSO_4h_rep1