title: gd 13.5 placental tissue from wild type rats, replicate 3

value: Placenta


title: Prm2 knockout testis

status: Public on Apr 22 2026

type: SRA

city: New Haven

first: Bluma

middle: J

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

country: USA

institute: Yale University

description: Library name: Prm2KO

library_source: transcriptomic single cell

data_processing:
Raw count matrices were generated using CellRanger (10X Genomics) and imported to Seurat 4.1.0 (Hao et al., 2021) and combined into one Seurat object. Reads were filtered to exclude doublets (nCount_RNA < mean + one standard deviation), dead or dying cells (nFeature_RNA > mean – one standard deviation) or high mitochondrial content (present.mt < mean + standard deviation). This filtered subset was log normalized and scaled. A linear dimensional reduction was performed using principal component analysis (PCA). Clusters were identified at a resolution of 0.5, and the “RunUMAP()” function was used to further investigate the dataset.
Assembly: mm10
Supplementary files format and content: index (.tsv), feature (.tsv), and matrix (.mtx) files

molecule: polyA RNA

organism: Mus musculus

source_name: whole testis

extract_protocol:
A polypropylene collection tube was coated with 3 ml Collection Buffer (20% FBS in 1X PBS) for 2 hours at RT with end-over-end mixing. Seminiferous tubules were mechanically isolated from the tunica and transferred to a 15ml conical tube containing 5ml Digestion Solution I [0.75 mg/ml collagenase type IV (Gibco, 17104-019) in Dulbecco’s modified Eagle’s media (DMEM, Gibco, 11965092) supplemented with 1:1000 with 1 mg/ml DNase I (StemCell Technologies, 07900)] warmed to 37 °C, followed by incubation at 37 °C for 10 mins with end-over-end rotation. 5ml of cold DMEM was added and tubules allowed to settle on ice. The supernatant was discarded and the tubules were washed again with 5ml cold DMEM to deplete Leydig cells. 5ml of DMEM was added followed by centrifugation at 500xg for 5 mins at 4°C. The supernatant was removed and 5ml of Digestion Solution II [Accutase (Gibco, A1110501) supplemented with 1 mg/ml DNase I at 1:1000 at room temperature)] was added to the tubules followed by incubation with end-over-end rotation for 10 mins at RT with gentle pipetting after 5 mins to disperse the tubules. 5ml of cold Complete Media (10% FBS in DMEM) was added and the sample was centrifuged at 500 xg for 5 mins at 4 °C. The cell pellet was then resuspended in 5 ml of cold Complete Medium, filtered through a 100 μm strainer, and the cell suspension was transferred to a fresh 15 ml conical tube and centrifuged at 500 xg for 5 mins at 4 °C.
15,000 dissociated testis cells were processed using a Chromium Next GEM Single Cell 3’ v3.1 kit (10X Genomics) and sequenced using an Illumina NovaSeq machine with 150 base pair paired-end reads at a depth of 250 million reads.

tag: tissue

value: whole testis

tag: cell type

value: mixed testicular cells

tag: genotype


title: gd 13.5 placental tissue from wild type rats, replicate 2

city: Ames

first: Geetu

last: Tuteja

state: IA

address: 2106 Molecular Biology Building

department: Genetics, Development and Cell Biology

institute: Iowa State University

library_source: transcriptomic

data_processing:
Raw data obtained from the sequencing facility was converted to fastq format using bcl2fastq (v2.20.0.422) and data quality was inspected using FastQC (v0.11.9)
Read mapping was performed by using the STAR’s (v2.7.10b) alignReads subcommand and was optimized for short reads with the options --outFilterScoreMinOverLread 0.3 and --outFilterMatchNminOverLread 0.3
featureCounts from the subread package to generate a combined count file
The raw count files were imported into R (v4.2.2) and analyzed to obtain differentially expressed genes by using DESeq2 (v1.38.3)
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text files include raw counts values for each Sample (each column represent the condition and each row represents the gene)

molecule: total RNA

organism: Rattus norvegicus

source_name: Placenta

extract_protocol:
Total RNA was isolated using the Trizol reagent according to the manufacturer’s instructions (Thermo-Fisher)
Extracted RNA was used as template for cDNA isolation with the High Capacity cDNA Reverse Transcription kit (Applied Biosystems). cDNA libraries were prepared and sequenced using a NovaSeq 6000 by the KUMC Genomics Core

treatment_protocol: Placentas were removed at gestational age 13.5, flash frozen on dry ice,

tag: strain

value: Holtzman Sprague-Dawley

tag: developmental stage

value: gestation day 13.5

value: PLAC1 Wild type

tag: treatment


title: Human TS cells (CT27), control shRNA treated, replicate 3

data_processing:
Raw data obtained from the sequencing facility was converted to fastq format using bcl2fastq (v2.20.0.422) and data quality was inspected using FastQC (v0.11.9)
Read mapping was performed by using the STAR’s (v2.7.10b) alignReads subcommand and was optimized for short reads with the options --outFilterScoreMinOverLread 0.3 and --outFilterMatchNminOverLread 0.3
featureCounts from the subread package to generate a combined count file
The raw count files were imported into R (v4.2.2) and analyzed to obtain differentially expressed genes by using DESeq2 (v1.38.3)
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include raw counts values for each Sample (each column represent the condition and each row represents the gene)

organism: Homo sapiens

source_name: human trophoblast stem cells- CT27 (Okae et.al)

growth_protocol: Human Triophoblast Stem cells  were grown and differentiated in the dish for 6 days into syncytiotrophoblast

treatment_protocol: Human Triophoblast Stem cells  were treated with control shRNA or PLAC1 shRNA before differentiation into syncytiotrophoblast

tag: cell line

value: syncytiotrophoblast

value: Control shRNA


title: control_iLS_Day6_1

city: Suita

first: Masaki

last: Nomura

state: Osaka

address: 2-2, Yamadaoka

department: Department of Cancer Pathology

country: Japan

institute: Graduate School of Medicine, The University of Osaka

description:
Library name: Smaple 1
iLS_D6_Mock_1

data_processing:
The FASTQ-sequenced reads were mapped to the mm10 genome using STAR.
Raw gene counts were calculated by RSEM.
Batch corrected data counts by ComBat were normalized and differentially expressed genes were identified with Adjusted p value < 0.05 by DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

source_name: Bone marrow

extract_protocol:
FACS sorted cells were proceeded to RNA extraction using RNeasy columns (Qiagen).
RNA libraries were prepared using TruSeq Stranded mRNA Library Prep Kit.

value: Bone marrow

value: CD45.2+ bone marrow cells


title: WT_MM_F_4

city: SAN ANTONIO

first: YI

last: ZOU

state: TX

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

description: Library name: WT_MM_F_4

data_processing:
Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were processed following nf-core RNAseq pipeline (Ewels et al, Nat Biotechnol, 2020).  The raws reads were trimmed by TrimGalore and  then aligned with the reference genome (UCSC mouse genome build mm10) by star default settings.
The BAM files obtained after alignment were processed using RSEM to quantify per gene expression in all samples.
Assembly: UCSC mouse genome build mm10
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols, the second column contain transcript ID,  and 3rd to 7th columns inclcude:   gene length, gene effective_length,  expected_count, TPM and FPKM values

source_name: masseter muscle (MM)

extract_protocol:
Dissection of dura mater and masseter muscle
Approximately 500ng Total RNA was used for RNA-seq library preparation by following TruSeq stranded mRNA-seq library preparation kit ( Cat. No: 20020595, Illumina, USA). Following mRNA enrichment by oligodT beads,  the RNA was fragmented into small pieces using divalent cautions under elevated temperature and magnesium. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM). The incorporation of dUTP in second strand synthesis effectively quenches the second strand during amplification, since the polymerase used in the assay will not incorporate past this nucleotide. These cDNA fragments then went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products were then purified and enriched with PCR to create the final RNA-Seq library for sequencing by 50bp single-end protocol with Illumina HiSeq 2500 platform, or 100bp pair-end protocol with Illumina NovaSeq 6000 platform.

treatment_protocol:
Injection into masseter muscle (MM) or temporal muscle (TM)
Mice were treated by injection of 10U Collagenase type I into temporal muscle and performing bulk RNA-seq on samples of dura mater at 2d post -injection. Mouse temporal muscle were inected multiple time (once every 4th day), and massetr muscle were used for bulk RNA-seq 28 days post-injection.

value: masseter muscle (MM)

value: Wild-type

value: Saline in MM

tag: time


title: CRE sample 9

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description: Library name: UFM1CreSAMPLE58

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20.0.422
STAR version 2.7.8a was used to align the reads to the GRCm39 genome using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes in GRCm39 version 110
Assembly: GRCm39 version 110
Supplementary files format and content: Tab-delimited gene counts

source_name: brain

growth_protocol: Mouse primary hippocampal neuron cultures were prepared as previously described (62, 63). Briefly, P0 mice brains were dissected and hippocampi were isolated and digested for 1 h at 37°C in Dulbecco's modified Eagle's medium (DMEM) containing 2.5 U/ml papain (Worthington Biomedical Corporation), 0.2 mg/ml L-cysteine, 1 mM CaCl2, and 0.5 mM EDTA. Papain digestion was stopped by incubation with DMEM supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS), 2.5 mg/ml albumin, and 2.5 mg/ml trypsin inhibitor. Hippocampi were triturated in Neurobasal medium (Neurobasal medium-A) containing 2% (v/v) B27, 100 U/ml penicillin and 100 μg/ml streptomycin. Neurons were seeded in Poly-L-Lysine (PLL)-coated plates or 12 mm glass coverslips with the following densities: 50,000 cells/well of a 24-well-plate for immunocytochemistry assays, 2 hippocampi (~150,000 cells/10 cm plate) for protein and RNA extraction or 25,000 cells/well in 8-well IBIDIs for live-imaging assays. For autaptic neuron culture (62), neurons were plated at 3,000 cells/plate (see below). Neurons were maintained at 37°C and 5% CO2 in Neurobasal medium supplemented with 2% (v/v) B27, 100 U/ml penicillin and 100 μg/ml streptomycin. The day of dissection was counted as day in vitro 0 (DIV 0). At DIV 1, primary hippocampal neurons were infected with viruses (see Table 1). All reagents are from Gibco or Sigma-Aldrich, except if otherwise stated.

extract_protocol:
Neurons were homogenized in 300 µl of DNA/RNA Shield (Zymo Research) and stored at -80 °C until RNA extraction and purification using the RNeasy Mini Kit (QIAGEN) and according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

tag: expression

value: CRE

value: primary neurons


title: Human TS cells (CT27), control shRNA treated, replicate 2

value: human trophoblast stem cells- CT27 (Okae et.al)


title: gd 13.5 placental tissue from Plac1 mutant rats, replicate 2

value: Placenta

value: PLAC1 Null


title: WT_MM_F_3

description: Library name: WT_MM_F_3


title: WT_MM_F_2

description: Library name: WT_MM_F_2


title: Human TS cells (CT27), control shRNA  treated, replicate 1


title: RFP sample 8

description: Library name: UFM1RFPSAMPLE56

value: RFP


title: gd 13.5 placental tissue from wild type rats, replicate 1

value: Holtzman Sprague-Dawley


title: Human TS cells (CT27), PLAC1 shRNA treated, replicate 3

value: PLAC1 shRNA


title: gd 13.5 placental tissue from Plac1 mutant rats, replicate 1

value: gestation day 13.5


title: gd 18.5 junctional zone tissue from Plac1 mutant rats, replicate 5

treatment_protocol: Placentas were removed at gestational age 18.5 and the  junctional zone was dissected and flash frozen on dry ice

tag: tissue region

value: JZ

value: gestation day 18.5


title: WT_MM_F_1

description: Library name: WT_MM_F_1


title: CRE sample 8

description: Library name: UFM1CreSAMPLE55


title: Human TS cells (CT27), PLAC1 shRNA treated, replicate 2

value: syncytiotrophoblast


title: CRE sample 7

description: Library name: UFM1CreSAMPLE54


title: dura_WC_4

description: Library name: dura_WC_4

source_name: dura mater

value: dura mater

value: Saline in TM


title: gd 18.5 junctional zone tissue from wild type rats, replicate 4

value: PLAC1 Wild type


title: dura_WC_3

description: Library name: dura_WC_3

value: Wild-type


title: RFP sample 7

description: Library name: UFM1RFPSAMPLE53

value: brain


title: dura_WC_2

description: Library name: dura_WC_2


title: Human TS cells (CT29), PLAC1 shRNA treated, replicate 3

source_name: human trophoblast stem cells- CT29 (Okae et.al)


title: RFP sample 9

description: Library name: UFM1RFPSAMPLE57


title: gd 18.5 junctional zone tissue from wild type rats, replicate 3


title: Human TS cells (CT29), PLAC1 shRNA treated, replicate 2

value: human trophoblast stem cells- CT29 (Okae et.al)


title: dura_WC_1

description: Library name: dura_WC_1


title: gd 18.5 junctional zone tissue from Plac1 mutant rats, replicate 4


title: RFP sample 6

description: Library name: UFM1RFPSAMPLE51

value: primary neurons


title: CRE sample 6

description: Library name: UFM1CreSAMPLE52

value: CRE


title: gd 18.5 junctional zone tissue from Plac1 mutant rats, replicate 3

value: Placenta


title: Human TS cells (CT27), PLAC1 shRNA treated, replicate 1

value: human trophoblast stem cells- CT27 (Okae et.al)


title: RFP sample 5

description: Library name: UFM1RFPSAMPLE50

value: RFP


title: ST_Naive_M_2C

description: Library name: ST_Naive_M_2C

value: Saline


title: Human TS cells (CT29), PLAC1 shRNA treated, replicate 1

value: PLAC1 shRNA


title: Human TS cells (CT29), control shRNA  treated, replicate 3

value: Control shRNA


title: gd 18.5 junctional zone tissue from wild type rats, replicate 2

value: JZ

value: Holtzman Sprague-Dawley


title: CRE sample 5

description: Library name: UFM1CreSAMPLE49


title: Human TS cells (CT29), control shRNA  treated, replicate 2

value: syncytiotrophoblast


title: gd 18.5 junctional zone tissue from wild type rats, replicate 1

value: gestation day 18.5


title: Human TS cells (CT29), control shRNA  treated, replicate 1


title: CRE sample 4

description: Library name: UFM1CreSAMPLE48


title: ST_Naive_M_3C

description: Library name: ST_Naive_M_3C

value: dura mater


title: ST_Naive_F_3C

description: Library name: ST_Naive_F_3C


title: gd 18.5 junctional zone tissue from Plac1 mutant rats, replicate 1

value: PLAC1 Null


title: gd 18.5 junctional zone tissue from Plac1 mutant rats, replicate 2


title: ST_Naive_F_1C

description: Library name: ST_Naive_F_1C

value: Wild-type


title: CRE sample 2

description: Library name: UFM1CreSAMPLE45

value: brain


title: ST_Naive_F_2C

description: Library name: ST_Naive_F_2C


title: ST_Naive_M_1C

description: Library name: ST_Naive_M_1C


title: Hep3B, sub2, DNA,

city: Singapore

first: Benson

last: Chen

address: 60 Biopolis Street, Genome, #04-01

department: Genome Institute of Singapore

country: Singapore

institute: A*STAR

description:
Library name: AHH23096
Column name in Hep3B_Sub2_Counts: AHH23096

library_source: genomic

data_processing:
Sequencing reads were aligned to the oligonucleotide library using BWA (PMID: 20080505). After alignment, any oligonucleotides with fewer than 10 reads in either the DNA or RNA samples were excluded from downstream analysis.
To assess oligonucleotide activity and identify robust functional Cis-Regulatory Elements (fCREs), three statistical tools were employed within the R programming environment (version 4.3.3): DESeq2 (version 1.42.1), EdgeR (version 4.0.16), MPRAnalyzer (version 1.20.0).
Assembly: hg38
Supplementary files format and content: processed files include counts >10 for each tested elements for each replicate
Supplementary files format and content: annotation of column names in counts file to associate column names with replicate number and condition

molecule: genomic DNA

growth_protocol: Human liver cancer cell line HepG2 was cultured in DMEM-high glucose (Thermo Fisher) with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen) from HepG2 or Rneasy midi kit (Qiagen) from mouse liver. DNA was extracted using mini-prep kit (Qiagen)
Plasmid DNA library preparation: we used 200 ng DNA as a template and each library was assigned unique i5 and i7 primers to aid in demultiplexing post-sequencing. The library was PCR amplified using 2X KAPA HiFi HotStart ReadyMix (Roche) with the following program (98°C for 3min; 98°C for 15s, 65°C for 30s, 7°2C for 45s and repeat for 17 cycles); 72°C for 2min). PCR reactions from each sample were combined and purified using 0.8X KAPA HyperPure Beads (Roche). RNA library preparation: we first isolated mRNA from 40 ug of total RNA from each sample using Dynabead Oligo-dT25 beads (Invitrogen) for HepG2 samples. We used 600 ug of total RNA to isolate mRNA for mouse liver samples. RNA was treated with Turbo DNase (Thermo Fisher Scientific) to remove contaminating DNA, and reverse-transcribed with SuperScript III (Thermo Fisher Scientific) using gene-specific RT primers. The library was PCR amplified using 2X KAPA HiFi HotStart ReadyMix (Roche) and 10 uM P7_UMI_Primer with the following program (98°C for 60s; 65°C for 30s; 72°C for 45s). Samples were purified using 1.4X KAPA HyperPure Beads (Roche) and eluted with 20uL water at 37°C for 3 min at 300 rpm on the thermomixer. Purified samples from the earlier step were used as a template per PCR reaction. The library was PCR amplified using 2X KAPA HiFi HotStart ReadyMix (Roche), 10 uM junction_fwd primer, and 10 uM P7_junction_rev primer with the following program (98°C for 90s; 98°C for 15s, 65°C for 30s, 72°C for 40s and repeat for 22 cycles; 72°C for 2min). Samples were purified using 0.8X KAPA HyperPure Beads (Roche) and eluted with 20uL water at 37°C for 3 min at 300 rpm on the thermomixer. Lastly, each library was assigned a unique i5 primer to aid in demultiplexing post-sequencing The library was PCR amplified using 2X KAPA HiFi HotStart ReadyMix (Roche) and 10uM P7_seqready rev primers with the following program (98°C for 90s; 98°C for 15s, 65°C for 30s, 72°C for 40s and repeat for 8 cycles; 72°C for 2min). PCR reactions from each sample were combined and purified using 0.8X KAPA HyperPure Beads (Roche). Samples were eluted with an appropriate amount of water at 37°C for 3 min at 300 rpm on the thermomixer. Sample concentration post-purification was measured using Qubit™ dsDNA Quantification Assay Kits (Invitrogen).

tag: batch


title: RFP sample 4

description: Library name: UFM1RFPSAMPLE47


title: Embryo 17.5, Tmla mutant for HP1B  Replicate 3

city: NYC

first: Martin

last: Escamilla

address: 3227 Broadway

institute: Columbia

description:
Library name: RNAseq_CbxTmla_mut_7275-2
RNA-seq

data_processing:
libraries were quality checked. KAPA, bioanalyzer
To generate .bam files, .fastq.gz were aligned to mouse mm10 with hisat2, sorted with samtools and indexed with samtools index. The .bw files were generated with deeptools "bamCoverage".
Assembly: mm10
Supplementary files format and content: bw

source_name: Main olfactory epithelium

growth_protocol: mice had access to food and water ad libitum

extract_protocol:
Cells come from micro disections. Cells were isolated using papain enzymatic treatment (Worthington).
Nugen NuQuant RNA-seq library system

value: Main olfactory epithelium

value: Embryo 17.5


title: Choriocarcinoma-derived BeWo cells, PLAC1 shRNA treated, replicate 3

data_processing:
Raw data obtained from the sequencing facility was converted to fastq format using bcl2fastq (v2.20.0.422) and data quality was inspected using FastQC (v0.11.9)
Read mapping was performed by using the STAR’s (v2.7.10b) alignReads subcommand and was optimized for short reads with the options --outFilterScoreMinOverLread 0.3 and --outFilterMatchNminOverLread 0.3
featureCounts from the subread package to generate a combined count file
The raw count files were imported into R (v4.2.2) and analyzed to obtain differentially expressed genes by using DESeq2 (v1.38.3)
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts values for each Sample (each column represent the condition and each row represents the gene)

source_name: BeWo

growth_protocol: BeWo cells  were grown and differentiated in the dish into syncytiotrophoblast with 20 μM forskolin

treatment_protocol: BeWo cells  were treated with control shRNA or PLAC1 shRNA before differentiation into syncytiotrophoblast

value: BeWo

value: Trophoblast


title: Choriocarcinoma-derived BeWo cells, PLAC1 shRNA treated, replicate 1


title: Choriocarcinoma-derived BeWo cells, PLAC1 shRNA treated, replicate 2


title: CRE sample 1

description: Library name: UFM1CreSAMPLE44

value: CRE

value: primary neurons


title: Embryo 17.5, Tmla mutant for HP1B  Replicate 2

description:
Library name: RNAseq_CbxTmla_mut_7275-1
RNA-seq


title: Embryo 17.5, Tmla mutant for HP1B  Replicate 1

description:
Library name: RNAseq_CbxTmla_mut_7077-1
RNA-seq


title: Hep3B, sub2, RNA, Rep2

description:
Library name: AHH23127
Column name in Hep3B_Sub2_Counts: AHH23127


title: Choriocarcinoma-derived BeWo cells, control shRNA  treated, replicate 2


title: Embryo 17.5, Tmla(ctrl) mouse Replicate 3

description:
Library name: RNAseq_CbxTmla_Ctrl_7707-3
RNA-seq


title: Choriocarcinoma-derived BeWo cells, control shRNA  treated, replicate 3


title: RFP sample 3

description: Library name: UFM1RFPSAMPLE43

value: RFP


title: RFP sample 2

description: Library name: UFM1RFPSAMPLE42


title: HepG2, sub5, RNA, Rep3

description:
Library name: AHH23117
Column name in HepG2_Sub5_Counts: AHH23117


title: RFP sample 1

description: Library name: UFM1RFPSAMPLE41


title: Embryo 17.5, Tmla(ctrl) mouse Replicate 2

description:
Library name: RNAseq_CbxTmla_Ctrl_7275-6
RNA-seq


title: HepG2, Sorafenib, rep4

city: Maastricht

first: Han

last: Jin

address: P. Debyelaan 25

country: Netherlands

institute: Maastricht University

data_processing:
Raw sequencing data (.bcl) was demultiplexed and converted to FASTQ files with DRAGEN Software (v3.9.5).
Kallisto (v0.48.0)16 was used to quantify the count and transcripts per million (TPM) values of transcripts based on the Homo sapiens reference cDNA (version GRCh38, Ensembl release 110)
The transcript read counts and TPM values were assembled to gene level using the R package tximport (v1.28.0), with only protein-coding transcripts and genes included.
The lowly expressed genes with an average count below 5 were filtered out, resulting in a total of 14,592 genes for the downstream analysis.
Assembly: Ensembl GRCh38, release 110
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

growth_protocol: Every 2days subculture with Growth media (RPMI-1640-R2405 10%FBS 1%P/S).

extract_protocol:
RNA samples for RNA sequencing were extracted with RNeasy Plus Mini Kit (74134, QIAGEN).
The Ilumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit was used for the construction of NGS libraries from the samples with acceptable quality parameters.

treatment_protocol: Treat 1:1000 10mM DMSO stock solution into media to make 10μM.

value: Hepatocellular carcinoma

value: WT

value: 10μM Sorafenib, 2days


title: Embryo 17.5, Tmla(ctrl) mouse Replicate 1

description:
Library name: RNAseq_CbxTmla_Ctrl_7275-4
RNA-seq


title: HepG2, sub5, RNA, Rep2

description:
Library name: AHH23116
Column name in HepG2_Sub5_Counts: AHH23116


title: HepG2, Sorafenib, rep3


title: HepG2, sub5, RNA, Rep1

description:
Library name: AHH23115
Column name in HepG2_Sub5_Counts: AHH23115


title: Input_CTCF-Nm_rep2

city: East Lansing

first: Yu

last: Zhang

state: MI

address: 567 Wilson Rd, Biomedical and Physical Sciences Building, Rm 5176

department: Microbiology, Genetics and Immunology

institute: Michigan State University

description: Library name: Sample41

data_processing:
Reads were aligned using bowtie 2.2.8 with --non-deterministic flag.
Samples were deduplicated using Picard, normalized and converted to bigWig files using bamCoverage with the --SPMR flag.
Assembly: mm9
Supplementary files format and content: bigWig including peak information for samples.

source_name: v-Abl transformed pro-B cell line

growth_protocol: v-Abl pro-B lines were maintained in RPIM1640 medium supplemented with 10% FBS, 50 uM 2-Mercaptoethanol, 100 U/ml Penicillin-Streptomycin and 2 mM L-Glutamine.

extract_protocol:
20 million cells were crosslinked in 37o prewarmed culture medium with 1% formaldehyde for 10 min at RT.  Cells were then treated with cell lysis buffer (5mM PIPES pH 8, 85mM KCl, 0.5% NP-40) for 10 min on ice, followed by treatment with nuclei lysis buffer (50mM TrisCl pH 8.1, 10mM EDTA, 1% SDS) for 10 min at RT. Chromatin was subjected to sonication with Diagenode Bioruptor at 4o to achieve an average size of 200-300 bp (30 sec on, 30 sec off, 20 cycles with high energy input). Chromatin were then precleared with Dynabeads Protein A at 4o for 2 hours. 1/30 lysates were kept as input and the rest incubated with 2.5ug SMC3 antibody  or CTCF antibody overnight at 4o. IP samples were then captured by Dynabeads Protein A at 4o for at least 2 hours, followed by bead washing and elution. IP and Input DNA were then de-crosslinked at 65o overnight and purified via Qiagen PCR purification columns.
Purified DNA was subjected to ChIP-Seq library preparation with the NEBNext Ultra II DNA Library Prep Kit for Illumina from New England Biolabs and sequenced via paired end 150-bp sequencing on a Illumina NovoSeq 6000 machine.

treatment_protocol: 3 uM STI571 induced G1 arrest for 4 days.

value: v-Abl transformed pro-B cell line

value: 3 uM STI-571 treated for 4 days


title: HepG2, sub5, DNA

description:
Library name: AHH23092
Column name in HepG2_Sub5_Counts: AHH23092


title: mOSN, CbxSwap mouse Replicate 1

description:
Library name: RNA.B23_Cbx1Cbx5ck1_foxg1cre_4w.180108
RNA-seq

value: OMP-GFP+ mature OSN cell sorted


title: HepG2, sub4, RNA, Rep3

description:
Library name: AHH23114
Column name in HepG2_Sub4_Counts: AHH23114


title: HepG2, Sorafenib, rep1


title: mOSN, CbxSwap mouse Replicate 2

description:
Library name: RNA.B27_Cbx1Cbx5ck1_foxg1cre_4w.180108
RNA-seq


title: Input_CTCF-Nm_rep1

description: Library name: Sample40


title: Input_Stag2KO_rep2

description: Library name: Sample39

value: Stag2KO, Emu-Bcl2+, RAG1(D708A)


title: HepG2, Sorafenib, rep2


title: Input_Stag2KO_CTCF-Nm_rep2

description: Library name: Sample43

value: Stag2KO, CTCF(Y226A/F228A), Emu-Bcl2+, RAG1(D708A)


title: Input_Stag2KO_CTCF-Nm_rep1

description: Library name: Sample42


title: mOSN, Cbx(ctrl) mouse Replicate 3

description:
Library name: RNA.B9_Cbx1Cbx5ck1_wt_4w.180108
RNA-seq

value: Cbx*/*;OMP-GFP


title: HepG2, Regorafenib, rep4

value: 10μM Regorafenib, 2days


title: HepG2, Regorafenib, rep3


title: mOSN, Cbx(ctrl) mouse Replicate 2

description:
Library name: RNA.B11_Cbx1Cbx5ck1_wt_4w.180108
RNA-seq

value: Main olfactory epithelium


title: Input_Stag2KO_rep1

description: Library name: Sample38


title: mOSN, Cbx(ctrl) mouse Replicate 1

description:
Library name: RNA.B10_Cbx1Cbx5ck1_wt_4w.180108
RNA-seq


title: HepG2, sub4, RNA, Rep1

description:
Library name: AHH23112
Column name in HepG2_Sub4_Counts: AHH23112


title: HepG2, Regorafenib, rep2


title: HepG2, sub4, DNA

description:
Library name: AHH23091
Column name in HepG2_Sub4_Counts: AHH23091


title: Input_Stag1KO_rep2

description: Library name: Sample37

value: Stag1KO, Emu-Bcl2+, RAG1(D708A)


title: HepG2, sub4, RNA, Rep2

description:
Library name: AHH23113
Column name in HepG2_Sub4_Counts: AHH23113


title: Tissue zone 5, CbxSwap mouse Replicate 3

description:
Library name: 8_RNAseq_CBXompFC.Zone5.
RNA-seq


title: HepG2, Regorafenib, rep1


title: Input_Stag1KO_rep1

description: Library name: Sample36


title: HepG2, sub3, RNA, Rep3

description:
Library name: AHH23110
Column name in HepG2_Sub3_Counts: AHH23110


title: Tissue zone 5, CbxSwap mouse Replicate 2

description:
Library name: 2_RNAseq_CBXompFC.Zone5.
RNA-seq


title: Input_WT_rep2

description: Library name: Sample35

value: Emu-Bcl2+, RAG1(D708A)


title: HepG2, JNK-IN-5A, rep3

value: 10μM JNK-IN-5A, 2days


title: Tissue zone 5, CbxSwap mouse Replicate 1

description:
Library name: 12_RNAseq_CBXompFC.Zone5.
RNA-seq


title: HepG2, sub3, RNA, Rep2

description:
Library name: AHH23109
Column name in HepG2_Sub3_Counts: AHH23109


title: Input_WT_rep1

description: Library name: Sample34


title: Tissue zone 1, CbxSwap mouse Replicate 3

description:
Library name: 7_RNAseq_CBXompFC.Zone1.
RNA-seq


title: HepG2, sub3, RNA, Rep1

description:
Library name: AHH23111
Column name in HepG2_Sub3_Counts: AHH23111


title: HepG2, JNK-IN-5A, rep4


title: IP_STAG1_Stag2KO_CTCF-Nm_rep2

description: Library name: Sample33


title: HepG2, JNK-IN-5A, rep1


title: HepG2, sub2, RNA, Rep3

description:
Library name: AHH23108
Column name in HepG2_Sub2_Counts: AHH23108


title: IP_STAG1_Stag2KO_CTCF-Nm_rep1

description: Library name: Sample32


title: HepG2, sub2, RNA, Rep2

description:
Library name: AHH23107
Column name in HepG2_Sub2_Counts: AHH23107


title: IP_SMC3_CTCF-Nm_rep2

description: Library name: Sample26


title: HepG2, SET172, rep3

value: 10μM SET172, 2days


title: Tissue zone 1, CbxSwap mouse Replicate 2

description:
Library name: 11_RNAseq_CBXompFC.Zone1.
RNA-seq


title: HepG2, sub3, DNA

description:
Library name: AHH23090
Column name in HepG2_Sub3_Counts: AHH23090


title: IP_SMC3_CTCF-Nm_rep1

description: Library name: Sample25


title: HepG2, SET172, rep4


title: HepG2, JNK-IN-5A, rep2


title: Tissue zone 5, Cbx(ctrl) mouse Replicate 3

description:
Library name: 6_RNAseq_CBXomp.Zone5.
RNA-seq


title: Tissue zone 5, Cbx(ctrl) mouse Replicate 2

description:
Library name: 4_RNAseq_CBXomp.Zone5.
RNA-seq


title: HepG2, SET172, rep2


title: HepG2, SET172, rep1


title: HepG2, sub1, RNA, Rep2

description:
Library name: AHH23105
Column name in HepG2_Sub1_Counts: AHH23105


title: IP_SMC3_WT_rep3

description: Library name: Sample23


title: IP_SMC3_WT_rep4

description: Library name: Sample24


title: HepG2, sub2, RNA, Rep1

description:
Library name: AHH23106
Column name in HepG2_Sub2_Counts: AHH23106


title: HepG2, SET171, rep4

value: 10μM SET171, 2days


title: Tissue zone 1, CbxSwap mouse Replicate 1

description:
Library name: 1_RNAseq_CBXompFC.Zone1.
RNA-seq


title: HepG2, sub1, RNA, Rep1

description:
Library name: AHH23104
Column name in HepG2_Sub1_Counts: AHH23104


title: Tissue zone 5, Cbx(ctrl) mouse Replicate 1

description:
Library name: Cbx.Swap.Zones5.fpkm+results.txt
RNA-seq


title: HepG2, SET171, rep3


title: Tissue zone 1, Cbx(ctrl) mouse Replicate 2

description:
Library name: 5_RNAseq_CBXomp.Zone1.
RNA-seq


title: HepG2, sub1, DNA

description:
Library name: AHH23088
Column name in HepG2_Sub1_Counts: AHH23088


title: Tissue zone 1, Cbx(ctrl) mouse Replicate 3

description:
Library name: 3_RNAseq_CBXomp.Zone1.
RNA-seq


title: IP_CTCF_CTCF-Nm_rep1

description: Library name: Sample21


title: Tissue zone 1, Cbx(ctrl) mouse Replicate 1

description:
Library name: 9_RNAseq_CBXomp.Zone1.
RNA-seq

data_processing:
libraries were quality checked. KAPA, bioanalyzer
To generate .bam files, the .fastq.gz were aligned to mouse mm10 with hisat2, sorted with samtools and indexed with samtools index. The .bw files were generated with deeptools "bamCoverage".
Assembly: mm10
Supplementary files format and content: bw


title: HepG2, sub2, DNA

description:
Library name: AHH23089
Column name in HepG2_Sub2_Counts: AHH23089


title: IP_CTCF_WT_rep2

description: Library name: Sample20


title: HepG2, SET171, rep1


title: HepG2, SET171, rep2


title: IP_CTCF_WT_rep1

description: Library name: Sample19


title: H3K9me3 ChIP, OMP-GFP- Peaks Reference Control for Cut and Run

description:
Library name: ChIP.TK9.B3_Cbx1Cbx5ck1_wt_4w.180108
ChIP-seq

data_processing:
libraries were quality checked. KAPA, bioanalyzer
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
Cells come from micro disections. Cells were isolated using papain enzymatic treatment (Worthington).
10x Barcode (Cell Barcode)

value: OMP-GFP- immature OSN cell sorted

value: Cbx*/*;OMP;FC


title: H3K9me3 ChIP, OMP-GFP- InPut Control for Cut and Run

description:
Library name: ChIP.TK9.B1_Cbx1Cbx5ck1_IP_4w.180108
ChIP-seq


title: Hep3B, sub2, RNA, Rep1

description:
Library name: AHH23126
Column name in Hep3B_Sub2_Counts: AHH23126


title: H3K9me3 ChIP, OMP-GFP- Tissue zone 5, Swap mouse Replicate 3

description:
Library name: tk9_ChIP_zone_5_swap-154-OMPneg
ChIP-seq


title: EGF (10ng/mL)+ LA3IK (80 µM) treated PC3 cells 6h Replicate 2

city: West haven

first: Antariksh

last: Tyagi

address: 830 West Campus Dr

data_processing:
Low quality reads were trimmed and adaptor contamination were removed using Trim Galore
Trimmed reads were mapped to the human reference genome (hg38) using HISAT2
Gene expression levels were quantified using StringTie
Assembly: hg38
Supplementary files format and content: csv file of raw read counts

growth_protocol: PC3 prostate cancer cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. Cells were maintained at 37°C in a humidified atmosphere with 5% CO₂

extract_protocol:
Total RNA was extracted using the TRIzol method . RNA quality such as RIN value estimation and concentration were assessed using the Qubit RNA assay.
RNAseq libraries were prepared using Illumina Stranded mRNA Library Prep kits (Illumina, Cat. No. 20040534) following the manufacturer’s instruction.

treatment_protocol: PC3 cells were grown in RPMI-1640 with 10% FBS and 1% penicillin-streptomycin at 37°C with 5% CO₂. Cells were serum-starved for 24 hours, then treated with EGF (10 ng/mL) and LA3IK peptide (80 µM). RNA was collected at 0h, 30 min, 1h, and 6h.

value: Prosate Cancer Cells

value: Wild type

value: EGF+LA3IK co-treatment 6 hours


title: HepG2, SET159, rep3

value: Hepatocellular carcinoma

value: WT

value: 10μM SET159, 2days


title: IP_SMC3_Stag2KO_rep2

description: Library name: Sample18

value: v-Abl transformed pro-B cell line

value: Stag2KO, Emu-Bcl2+, RAG1(D708A)

value: 3 uM STI-571 treated for 4 days


title: HepG2, SET159, rep4


title: LA3IK(80µM) treated PC3 cells 6h Replicate 1

value: LA3Ik only Treatment 6hours


title: IP_SMC3_Stag2KO_rep1

description: Library name: Sample17


title: EGF (10ng/mL)+ LA3IK (80 µM) treated PC3 cells 6h Replicate 3


title: EGF (10ng/mL) treated PC3 cells 6h Replicate 3

value: EGF treatment 6h


title: HepG2, SET159, rep2


title: HepG2, SET159, rep1


title: H3K9me3 ChIP, OMP-GFP- Tissue zone 5, Swap mouse Replicate 1

description:
Library name: tk9_ChIP_zone_5_swap-150-OMPneg
ChIP-seq

value: Main olfactory epithelium


title: IP_SMC3_Stag1KO_rep2

description: Library name: Sample16

value: Stag1KO, Emu-Bcl2+, RAG1(D708A)


title: EGF (10ng/mL) treated PC3 cells 6h Replicate 2


title: IP_SMC3_Stag1KO_rep1

description: Library name: Sample15


title: H3K9me3 ChIP, OMP-GFP- Tissue zone 5, Swap mouse Replicate 2

description:
Library name: tk9_ChIP_zone_5_swap-153-OMPneg
ChIP-seq


title: EGF (10ng/mL)+ LA3IK (80 µM) treated PC3 cells 6h Replicate 1


title: H3K9me3 ChIP, OMP-GFP- Tissue zone 1, Swap mouse Replicate 3

description:
Library name: tk9_ChIP_zone_1_swap-154-OMPneg
ChIP-seq


title: HepG2, SET158, rep4

value: 10μM SET158, 2days


title: Choriocarcinoma-derived BeWo cells, control shRNA  treated, replicate 1

value: BeWo

value: Trophoblast

value: Control shRNA


title: EGF (10ng/mL) treated PC3 cells 6h Replicate 1

value: Prosate Cancer Cells


title: IP_SMC3_WT_rep2

description: Library name: Sample14

value: Emu-Bcl2+, RAG1(D708A)


title: HepG2, SET158, rep3


title: H3K9me3 ChIP, OMP-GFP- Tissue zone 1, Swap mouse Replicate 2

description:
Library name: tk9_ChIP_zone_1_swap-150-OMPneg
ChIP-seq

value: OMP-GFP- immature OSN cell sorted

value: Cbx*/*;OMP;FC


title: EGF (10ng/mL)+ LA3IK (80 µM) treated PC3 cells 1h Replicate 3

value: Wild type

value: EGF+LA3IK co-treatment 1 hour


title: H3K9me3 ChIP, OMP-GFP- Tissue zone 1, Swap mouse Replicate 1

description:
Library name: tk9_ChIP_zone_1_swap-144-OMPneg
ChIP-seq


title: HepG2, SET158, rep1

value: Hepatocellular carcinoma

value: WT


title: EGF (10ng/mL)+ LA3IK (80 µM) treated PC3 cells 1h Replicate 2


title: IP_STAG2_Stag2KO_rep2

description: Library name: Sample12

value: v-Abl transformed pro-B cell line

value: Stag2KO, Emu-Bcl2+, RAG1(D708A)

value: 3 uM STI-571 treated for 4 days


title: H3K9me3 ChIP, OMP-GFP- Tissue zone 5, control mouse Replicate 3

description:
Library name: tk9_ChIP_zone_5_wt-149-OMPneg
ChIP-seq

value: Main olfactory epithelium

value: Cbx*/*;OMP


title: IP_CTCF_CTCF-Nm_rep2

description: Library name: Sample22


title: H3K9me3 ChIP, OMP-GFP- Tissue zone 5, control mouse Replicate 2

description:
Library name: tk9_ChIP_zone_5_wt-148-OMPneg
ChIP-seq


title: HepG2, SET156, rep4

value: 10μM SET156, 2days


title: HepG2, SET158, rep2

value: 10μM SET158, 2days


title: HepG2, SET156, rep3


title: IP_STAG2_Stag1KO_rep2

description: Library name: Sample10

value: Stag1KO, Emu-Bcl2+, RAG1(D708A)


title: IP_SMC3_WT_rep1

description: Library name: Sample13


title: IP_STAG2_Stag1KO_rep1

description: Library name: Sample9


title: EGF (10ng/mL)+ LA3IK (80 µM) treated PC3 cells 1h Replicate 1


title: EGF (10ng/mL) treated PC3 cells 1h Replicate 1

value: EGF treatment 1 hour


title: HepG2, SET156, rep1


title: H3K9me3 ChIP, OMP-GFP- Tissue zone 5, control mouse Replicate 1

description:
Library name: tk9_ChIP_zone_5_wt-143-OMPneg
ChIP-seq


title: EGF (10ng/mL)+ LA3IK (80 µM) treated PC3 cells 30 minutes Replicate 3

value: Prosate Cancer Cells

value: EGF+LA3IK co-treatment 30 minutes


title: IP_STAG2_WT_rep2

description: Library name: Sample8

value: Emu-Bcl2+, RAG1(D708A)


title: H3K9me3 ChIP, OMP-GFP- Tissue zone 1, control mouse Replicate 2

description:
Library name: tk9_ChIP_zone_1_wt-147-OMPneg
ChIP-seq

value: OMP-GFP- immature OSN cell sorted


title: H3K9me3 ChIP, OMP-GFP- Tissue zone 1, control mouse Replicate 3

description:
Library name: tk9_ChIP_zone_1_wt-149-OMPneg
ChIP-seq


title: EGF (10ng/mL) treated PC3 cells 1h Replicate 3

value: Wild type


title: EGF (10ng/mL)+ LA3IK (80 µM) treated PC3 cells 30 minutes Replicate 2


title: CRE sample 3

description: Library name: UFM1CreSAMPLE46

value: brain

value: CRE

value: primary neurons


title: HepG2, SET156, rep2

value: Hepatocellular carcinoma

value: WT


title: EGF (10ng/mL) treated PC3 cells 1h Replicate 2


title: IP_STAG2_WT_rep1

description: Library name: Sample7

value: v-Abl transformed pro-B cell line

value: 3 uM STI-571 treated for 4 days


title: HepG2, SET135, rep4

value: 10μM SET135, 2days


title: H3K9me3 ChIP, OMP-GFP- Tissue zone 1, control mouse Replicate 1

description:
Library name: tk9_ChIP_zone_1_wt-143-OMPneg
ChIP-seq

value: Main olfactory epithelium

value: Cbx*/*;OMP


title: IP_STAG2_Stag2KO_rep1

description: Library name: Sample11

value: Stag2KO, Emu-Bcl2+, RAG1(D708A)


title: Input control_2

description:
Library name: tk9_ChIP_zone_5_Imput-OMPneg
ChIP-seq


title: HepG2, SET135, rep3


title: pool of 4 samples (WT_1, WT_2, Notch_KO_1, Notch_KO_2)

city: Epalinges

first: Nagham

last: Alouche

address: Chemin des Boveresses 155

department: Immunobiology

country: Switzerland

institute: University of Lausanne

description:
Library name: poolNA1
3' end mRNA (Single-Cell Fixed 10X Genomics): read1 contains sample barcodes (BC009, BC010, BC011, BC012); read2 contains transcript sequence

data_processing:
To generate single-cell feature counts, Cell Ranger (v7.1.0) was used to process FASTQ files and align reads to the Chromium Mouse Transcriptome Probe Set v1.0 (mm10-2020-A). The assay was based on the Fixed RNA Profiling (Flex) chemistry, and probe annotations were provided via the Chromium_Mouse_Transcriptome_Probe_Set_v1.0_mm10-2020-A.csv file, following the manufacturer’s guideline. Demultiplexing was performed with the bcl2fastq2 conversion software (v2.20, Illumina)
analysis was done using suerat V (4.3.0)
Assembly: mm10
Supplementary files format and content: Tab-separated values file and matrix files

source_name: Lymph node (pooled from 2 mice per sample)

extract_protocol:
For each sample, peripheral lymph nodes (axillary, brachial, and inguinal) were cut into small pieces and digested in RPMI 1640 supplemented with recombinant Collagenase D (1 mg/ml; Roche) and DNase I (0.01 mg/ml) at 37°C for 30 min with gentle stirring.  Live immune cells were sorted using a MoFlo Astrios EQ cell sorter, with the following final proportions: 20% CD45⁺ CD19⁺, 20% CD45⁺ CD3e⁺, 30% CD45⁺ CD19⁻ CD3e⁻ CD11c⁺ MHCII^hi, and 30% CD45⁺ CD19⁻ CD3e⁻ CD11c⁻ MHCII^low.
after sorting, cells were fixed and were mulitplexed and processed for single cell libraries using the Chromium Fixed RNA profiling reagent kits (user guide CG000527 revC 2022),

tag: Sex

value: Female

value: Immune cells

value: Notch2^fl/fl and Notch2fl/fl X Ccl19-Cre


title: Input control_1

description:
Library name: tk9_ChIP_zone_1_Imput-OMPneg
ChIP-seq


title: EGF (10ng/mL)+ LA3IK (80 µM) treated PC3 cells 30 minutes Replicate 1

value: Prosate Cancer Cells

value: EGF+LA3IK co-treatment 30 minutes


title: EGF (10ng/mL) treated PC3 cells 30 minutes Replicate3

value: Wild type

value: EGF treatment 30 minutes


title: Ccl19-Cre_Notch2^fl/fl_N2KO_Batch2

description:
Library name: B3_N2_FRC
10X Genomics

data_processing:
To generate single cell feature counts, Cellranger (v5.0.1 and v7.1.0) was run to align FASTQ files to the mm10 genome version.
Assembly: mm10
Supplementary files format and content: Tab-separated values file and matrix files

source_name: Lymph node (pooled from 3 mice)

extract_protocol:
For each sample, peripheral lymph nodes (axillary, brachial, and inguinal) were cut into small pieces and digested for 30 min at 37°C with gentle stirring in 1.5 mL RPMI 1640 medium (Gibco) containing 0.3 mg/ml Collagenase P (Roche) and 0.8 mg/ml Dispase II (Sigma Aldrich), and 0.1 mg/ml DNase I and 2% (vol/vol) Fetal Calf Serum (FCS). The small LN pieces were digested for 20 min at 37°C with gentle stirring in 2 mL digestion mix. After incubation, fragments were gently dissociated using a 1 mL pipette equipped with a wide-bore tip and allowed to settle for 30 seconds. The supernatant was transferred to a collection tube containing cold PBS supplemented with 2% FCS and 5 mM ethylenediaminetetraacetic acid (EDTA). 1 mL of fresh digestion media was added to the remaining fragments, which were incubated for an additional 10 minutes at 37°C under stirring. Following this, the single-cell suspension was added to the collection tube containing the first supernatant. Cells were then washed and resuspended in RPMI-2% FCS.  Cell suspensions were depleted of CD45⁺ cells using magnetic-activated cell sorting (MACS, Miltenyi Biotec) according to the manufacturer’s instructions. Live propidium iodide⁻ Hoechst⁺ CD45⁻ CD31⁻ stromal cells were then sorted using a MoFlo Astrios EQ cell sorter (Beckman Coulter).
Single-cell RNA sequencing libraries were prepared using the Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 with Dual Index (10x Genomics), following the manufacturer's protocol.

value: Lymph node (pooled from 3 mice)

value: Fibroblasts

value: Ccl19-Cre x Notch2^fl/fl

tag: age

value: 12 weeks


title: HepG2, SET135, rep2

value: Hepatocellular carcinoma

value: WT


title: Ccl19-Cre_WT_Batch2

description:
Library name: B3_WT_FRC
10X Genomics


title: HepG2, SET135, rep1

value: 10μM SET135, 2days


title: H3K9me3 ChIP, Tissue zone 5, control mouse Replicate 2

description:
Library name: chip_TK9_OMP_Zone5_wt5
ChIP-seq

value: Main olfactory epithelium

value: OMP-GFP+ mature OSN cell sorted


title: Ccl19-Cre x Notch2^fl/fl FRC N2KO2

description:
Library name: Ccl19-Cre x Notch2^fl/fl FRC N2KO2
Loess normalized peak counts calculated in csaw

data_processing:
FASTQ files were trimmed for adapter and low-quality sequences using TrimGalore (v0.6.7) and Cutadapt, with default parameters. The trimmed files were aligned to the mm10 genome using Bowtie2 (v2.4.5) with the --very-sensitive parameter. Bam file downstream processing was performed with Samtools (version1.14) and duplicates were marked using Picard (v2.27.5). Finally, read positions were adjusted using the default ATACshift parameters in DeepTools alignmentSieve (v3.5.1). Peak calling was performed using csaw (v1.30.1) on 300 bp windows. Windows showing a 3-fold increase in enrichment over the 2 kb surrounding neighborhood were retained. The remaining peaks were normalized using the csaw loess normalization method
Assembly: mm10
Supplementary files format and content: table of peak counts organized by sample (columns) and peak locations (rows)

source_name: Lymph node (pooled from 6 mice)

extract_protocol:
For each sample, peripheral lymph nodes were cut into small pieces and digested for 30 min at 37°C with gentle stirring in 1.5 mL RPMI 1640 medium (Gibco) containing 0.3 mg/ml Collagenase P (Roche) and 0.8 mg/ml Dispase II (Sigma Aldrich), and 0.1 mg/ml DNase I and 2% (vol/vol) Fetal Calf Serum (FCS). The small LN pieces were digested for 20 min at 37°C with gentle stirring in 2 mL digestion mix. After incubation, fragments were gently dissociated using a 1 mL pipette equipped with a wide-bore tip and allowed to settle for 30 seconds. The supernatant was transferred to a collection tube containing cold PBS supplemented with 2% FCS and 5 mM ethylenediaminetetraacetic acid (EDTA). 1 mL of fresh digestion media was added to the remaining fragments, which were incubated for an additional 10 minutes at 37°C under stirring. Following this, the single-cell suspension was added to the collection tube containing the first supernatant. Cells were then washed and resuspended in RPMI-2% FCS.Cell suspensions were then depleted of CD45⁺ cells using magnetic-activated cell sorting (MACS, Miltenyi Biotec) according to the manufacturer’s instructions. Live  5x10^4 flow sorted (BP3hi Pdpn+ CD31- CD45-) FRCs were washed with cold 1X PBS and resuspended in 50mL of ice-cold lysis buffer (10mM Tris-Cl (PH7.4),10mM NaCl, 3mM MgCl2 and 0.1%(v/v) of NP-40. Cells were centrifuged immediately, and the resulting pellet (nuclei) was resuspended in 50mL of transposase reaction mix, containing 25mL 2x TD buffer (Illumina), 2.5mL Tn5 transposase (Illumina) and 22.5mL of nuclease-free water, followed by incubation at 37°C for 30 min (while gently shaking). Tagmented DNA was cleaned using QIAGEN MinElute PCR Purification kit as described in the kit’s protocol.
Library preparation was performed using Illumina’s Unique Dual (UD) Indexes and NEB Next High-Fidelity 2x PCR Master Mix (New England Biolabs), using the following program: 5min at 72°C, 30 sec at 98°C; then 10 cycles of: 10 sec at 98°C, 30 sec at 63°C, 1min at 72°C; ending at 4°C. The libraries were then cleaned using AMPureXP magnetic beads (Beckman Coulter). To remove both excess adaptor primers and big DNA fragments we performed double-sided magnetic bead purification. Finally, libraries were quantified using Fragment Analyzer (Advanced Analytical) and sequenced on an Illumina NovaSeq 6000, with paired end 150 nucleotides.

value: Lymph node (pooled from 6 mice)


title: HepG2, Control, rep4

value: DMSO


title: EGF (10ng/mL) treated PC3 cells 30 minutes Replicate1


title: Ccl19-Cre x Notch2^fl/fl FRC N2KO1

description:
Library name: Ccl19-Cre x Notch2^fl/fl FRC N2KO1
Loess normalized peak counts calculated in csaw

value: Female


title: H3K9me3 ChIP, Tissue zone 5, control mouse Replicate 1

description:
Library name: chip_TK9_OMP_Zone5_wt4
ChIP-seq

value: Cbx*/*;OMP


title: HepG2, Control, rep3


title: Notch2^fl/fl FRC WT2

description:
Library name: Notch2^fl/fl FRC WT2
Loess normalized peak counts calculated in csaw


title: H3K9me3 ChIP, Tissue zone 5, control mouse Replicate 3

description:
Library name: chip_TK9_OMP_Zone5_wt6
ChIP-seq


title: EGF (10ng/mL)+ LA3IK (80 µM) treated PC3 cells 0h Replicate 2

value: Prosate Cancer Cells

value: EGF+LA3IK co-treatment 0 hour


title: HepG2, Control, rep1


title: EGF (10ng/mL) treated PC3 cells 30 minutes Replicate2

value: Wild type


title: EGF (10ng/mL)+ LA3IK (80 µM) treated PC3 cells 0h Replicate 3


title: HepG2, Control, rep2


title: Notch2^fl/fl FRC WT1

description:
Library name: Notch2^fl/fl FRC WT1
Loess normalized peak counts calculated in csaw


title: H3K9me3 ChIP, Tissue zone 5, Swap mouse Replicate 3

description:
Library name: chip_TK9_OMP_Zone5_Swap18
ChIP-seq

value: Cbx*/*;OMP;FC


title: H3K9me3 ChIP, Tissue zone 5, Swap mouse Replicate 2

description:
Library name: chip_TK9_OMP_Zone5_Swap17
ChIP-seq


title: EGF (10ng/mL)+ LA3IK (80 µM) treated PC3 cells 0h Replicate 1


title: mOSN, CbxSwap mouse Replicate 3

description:
Library name: RNA.B25_Cbx1Cbx5ck1_foxg1cre_4w.180108
RNA-seq


title: H3K9me3 ChIP, Tissue zone 5, Swap mouse Replicate 1

description:
Library name: chip_TK9_OMP_Zone5_Swap16
ChIP-seq


title: 12D

description: Library name: 12D

value: dura mater

value: Wild-type

value: 10U Col in TM


title: 11D

description: Library name: 11D


title: EGF (10ng/mL) treated PC3 cells 0h Replicate3

value: EGF treatment 0h


title: H3K9me3 ChIP, Tissue zone 1, control mouse Replicate 3

description:
Library name: chip_TK9_OMP_Zone1_wt3
ChIP-seq


title: IM-4D-3  (biol rep 3)

city: Daejeon

first: In-Hwan

last: Jang

address: 125, Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea

department: Immunotherapy Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
HISAT2 software (ver. 2.2.0) was used to index the reference genome and map sequencing reads of samples.
Samtools (ver. 1.15.1) was used to convert BAM files
FeatureCounts (ver. 2.0.1) software was used to calculate the generated BAM files
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes CPM values for each Sample

growth_protocol: The culture method of NK-92 was consistent with the culture method recommended by ATCC except that the added cytokines were special

extract_protocol:
Total RNA was isolated by TRIzol Reagent
RNA libraries for RNA-seq were prepared using TruSeq Standarded Total RNA Library Prep Gold Kit following manufacturer's protocols.

treatment_protocol: Four-condition experiment, IL-2 activated NK-92 cells cultured for 2 days (IL-2-D2) or 4 days (IL-2-D4), IL-7 activated NK-IL-7R-WT cells cultured for 4 days (IL-7R-IL-7-D4), and no cytokines activated NK-IL-7R-IM cells cultured for 4 days (IL-7R-IM-D4).

value: human natural killer cell line

value: IL-7R-IM overexpression

value: Cultured without any cytokines

value: Day 4


title: EGF (10ng/mL) treated PC3 cells 0h Replicate2


title: IM-4D-2  (biol rep 2)


title: 10D

description: Library name: 10D


title: H3K9me3 ChIP, Tissue zone 1, control mouse Replicate 2

description:
Library name: chip_TK9_OMP_Zone1_wt2
ChIP-seq

value: Main olfactory epithelium

value: OMP-GFP+ mature OSN cell sorted


title: IM-4D-1  (biol rep 1)


title: H3K9me3 ChIP, Tissue zone 1, control mouse Replicate 1

description:
Library name: chip_TK9_OMP_Zone1_wt1
ChIP-seq


title: 9D

description: Library name: 9D


title: IL2-4D-3  (biol rep 3)

value: WT

value: Cultured with IL-2 (20ng/mL)


title: IL2-4D-2  (biol rep 2)


title: 7D

description: Library name: 7D


title: IL2-4D-1  (biol rep 1)


title: EGF (10ng/mL) treated PC3 cells 0h Replicate1


title: IL2-2D-3 (biol rep 3)

value: Day 2


title: H3K9me3 ChIP, Tissue zone 1, Swap mouse Replicate 1

description:
Library name: chip_TK9_OMP_Zone1_Swap13
ChIP-seq


title: H3K9me3 ChIP, Tissue zone 1, Swap mouse Replicate 2

description:
Library name: chip_TK9_OMP_Zone1_Swap14
ChIP-seq


title: 5D

description: Library name: 5D


title: H3K9me3 ChIP, Tissue zone 1, Swap mouse Replicate 3

description:
Library name: chip_TK9_OMP_Zone1_Swap15
ChIP-seq


title: Cut and Run control (IgG antibody) IP replicate 2

description: Library name: 14_CUTandRun_S14

data_processing:
libraries were quality checked. KAPA, bioanalyzer
Assembly: mm10
Supplementary files format and content: Only FASTQ are provided
Library strategy: CUT&Run

value: Mix of WT and Cbx_Swap mice


title: IL2-2D-2 (biol rep 2)


title: 6D

description: Library name: 6D


title: 4D

description: Library name: 4D


title: Cut and Run control (IgG antibody) IP replicate 1

description: Library name: 7_CUTandRun_S7


title: IL2-2D-1 (biol rep 1)


title: 3D

description: Library name: 3D


title: Cut and Run HP1a Swap mouse (.ab109028 antibody) IP replicate 2

description: Library name: 49_CUTandRun_S49


title: BM-IL27_3

city: Shanghai

first: duan

middle: cai

last: wen

address: 1678 dongfang road

country: China

institute: Shanghai Children's Medical Center

description: Library name: Sample 12

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke v1.5.2 with parameters -l 15 -q 0.2 -n 0.05
Sequenced reads were mapped to GRCm39 or GRCh38 whole genome using STAR 2.7.11a  with parameters  --runMode alignReads --runThreadN 5  --genomeLoad NoSharedMemory  --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts
The gene expression level (TPM) was calculated according to the Sequencing depth and gene length, and the DEG matrix was analyzed with the R package DESeq2.
Assembly: Mus_musculus.GRCm39 and Homo_sapiens.GRCh38
Supplementary files format and content: txt files includes raw counts for every sample

source_name: BM

extract_protocol:
Bone marrow cells and splenic cells were prepared using standard procedures. Specific cellular subsets were isolated by fluorescence-activated cell sorting (FACS) where indicated. Sorted cell populations were lysed directly in TRIzol reagent (Invitrogen) for RNA extraction. Total bone marrow cells and cultured human mesenchymal stromal cells (hMSCs) were directly lysed in TRIzol without prior sorting. Lysates were stored at −80 °C prior to RNA isolation according to the manufacturer’s instructions.
Total RNA extracted using TRIzol reagent was subjected to quality control prior to library preparation. RNA sequencing libraries were constructed using standard RNA-seq library preparation protocols by commercial service providers (BGI Genomics and OE Biotech). Libraries were prepared following manufacturer-recommended procedures and sequenced on Illumina sequencing platforms to generate paired-end reads.

value: BM

value: BM  cells


title: E. crypticus_NUCOP 500 21days_ replicate3

type: RNA

city: Aveiro

first: Susana

middle: Isabel Lopes

last: Gomes

address: Campus Universitário de Santiago, Departement of Biology, University of Aveiro

department: Biology

country: Portugal

institute: CESAM & University of Aveiro

hyb_protocol: The cRNA samples were hybridized on the Custom Gene Expression Agilent Microarrays (4 x 44k format) developed for Enchytraeus crypticus. Hybridizations were performed using the Agilent Gene Expression Hybridization Kit (Agilent Technologies, Palo Alto, CA, USA) and each biological replicate was individually hybridized on one array. The arrays were hybridized at 65ºC with a rotation of 10 rpm, during 17h. After that the microarrays were washed using Agilent Gene Expression Wash Buffer Kit (Agilent Technologies, Palo Alto, CA, USA)

scan_protocol: Scanning was performed using the Agilent DNA microarray scanner G2505B (Agilent Technologies). Fluorescence intensity data was obtained with Feature Extraction (10.5.1.1) Software (Agilent Technologies).

data_processing: Background correction was provided by Agilent Feature Extraction software and only gene probes with good signal quality (flag IsPosAndSignif = True) in all samples were employed in the analyses.

organism: Enchytraeus crypticus

source_name: Tissue: Whole body extracts (40 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: 500 mg Cu/kg soil of NUCOP, for 21 days

label_protocol: Labelling and hybridizations followed the protocol “One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling” from Agilent Technologies (Agilent Technologies, Palo Alto, CA, USA)). Briefly, 500 ng of total RNA was amplified and labelled with Agilent Low Input Quick Amp Labelling Kit (Agilent Technologies, Palo Alto, CA, USA). Positive controls were added with the Agilent one-colour RNA Spike-In Kit (Agilent Technologies, Palo Alto, CA, USA). Purification of the amplified and labelled cRNA was performed with the RNeasy columns (Qiagen, Valencia, CA, USA).

extract_protocol: Total RNA was extracted using SV Total RNA Isolation System (Promega Corporation, USA).The quantity and purity of the RNA samples was checked using the ND-1000 spectrophotometer (Nanodrop®, USA) through measurement of the 260nm/280nm and 260nm/230nm absorbance. For all used samples these ratios were approximately 2. To verify the integrity of the RNA samples, a denaturating formaldehyde agarose gel electrophoresis was performed.

value: Whole body extracts


title: 8D

description: Library name: 8D

data_processing:
Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were processed following nf-core RNAseq pipeline (Ewels et al, Nat Biotechnol, 2020).  The raws reads were trimmed by TrimGalore and  then aligned with the reference genome (UCSC mouse genome build mm10) by star default settings.
The BAM files obtained after alignment were processed using RSEM to quantify per gene expression in all samples.
Assembly: UCSC mouse genome build mm10
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols, the second column contain transcript ID,  and 3rd to 7th columns inclcude:   gene length, gene effective_length,  expected_count, TPM and FPKM values

value: dura mater


title: E. crypticus_NUCOP 100 21days_ replicate2

source_name: Tissue: Whole body extracts (40 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: 100 mg Cu/kg soil of NUCOP, for 21 days


title: E. crypticus_NUCOP 100 21days_ replicate3

value: Adult organisms with well developed clitellum


title: 2D

description: Library name: 2D

value: Wild-type

value: 10U Col in TM


title: E. crypticus_NUCOP 500 21days_ replicate1


title: 1D

description: Library name: 1D


title: BM-IL27_1

description: Library name: Sample 10


title: 13M

description: Library name: 13M

value: masseter muscle (MM)


title: Cut and Run HP1a (.ab109028 antibody) IP replicate 2

description: Library name: 9_CUTandRun_S9


title: BM-IL27_2

description: Library name: Sample 11


title: Cut and Run HP1a (.ab109028 antibody) IP replicate 1

description: Library name: 2_CUTandRun_S2


title: E. crypticus_Control 21days_ replicate3

source_name: Tissue: Whole body extracts (40 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: un-spiked soil for 21 days


title: E. crypticus_NUCOP 100 21days_ replicate1


title: E. crypticus_Control 21days_ replicate2


title: E. crypticus_Control 21days_ replicate1


title: BM-Ctrl_2

description: Library name: Sample 8

value: AAV-Ctrl


title: ATAC-Seq, tissue Zone-5 Swap mouse replicate_3

description: Library name: 12-atac-omp-zone5-swap1-BLC_fem

data_processing:
libraries were quality checked. KAPA, bioanalyzer
Assembly: mm10
Supplementary files format and content: Only FASTQ are provided

extract_protocol:
Cells come from micro disections. Cells were isolated using papain enzymatic treatment (Worthington).
OMNI-ATAC protocol

value: Cbx*/*;Foxg1CRE; OMP-GFP


title: Cut and Run HP1a Swap mouse (.ab109028 antibody) IP replicate 1

description: Library name: 45_CUTandRun_S45


title: 10M

description: Library name: 10M


title: Cut and Run HP1B (D2F2 antibody) IP replicate 2

description: Library name: 4_CUTandRun_S4


title: 11M

description: Library name: 11M


title: BM-Ctrl_1

description: Library name: Sample 7


title: Cut and Run HP1B (D2F2 antibody) IP replicate 1

description: Library name: 11_CUTandRun_S11


title: B-ALL-IL27-3

description: Library name: Sample 6

value: B-ALL cells


title: 12M

description: Library name: 12M


title: BM-Ctrl_3

description: Library name: Sample 9


title: E. crypticus_NUCOP 500 21days_ replicate2


title: B-ALL-IL27-1

description: Library name: Sample 4


title: ATAC-Seq, tissue Zone-5 Swap mouse replicate_2

description: Library name: 9-atac-omp-zone5-BLC-swap1

value: Main olfactory epithelium


title: B-ALL-IL27-2

description: Library name: Sample 5


title: 9M

description: Library name: 9M


title: 7M

description: Library name: 7M


title: 8M

description: Library name: 8M


title: ATAC-Seq, tissue Zone-1 Swap mouse replicate_3

description: Library name: 6-atac-omp-zone1-BLC-swap2

value: OMP-GFP+ mature OSN cell sorted


title: E. crypticus_NUCOP 100 2days_ replicate1

source_name: Tissue: Whole body extracts (40 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: 100 mg Cu/kg soil of NUCOP, for 2 days


title: B-ALL-Ctrl-3

description: Library name: Sample 3


title: E. crypticus_NUCOP 500 2days_ replicate2

source_name: Tissue: Whole body extracts (40 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: 500 mg Cu/kg soil of NUCOP, for 2 days


title: E. crypticus_NUCOP 500 2days_ replicate3


title: E. crypticus_NUCOP 100 2days_ replicate2


title: B-ALL-Ctrl-2

description: Library name: Sample 2


title: ATAC-Seq, tissue Zone-1 Swap mouse replicate_2

description: Library name: 10-atac-omp-zone1-swap1-BLC_fem


title: E. crypticus_NUCOP 500 2days_ replicate1


title: ATAC-Seq, tissue Zone-1 Swap mouse replicate_1

description: Library name: 3-atac-omp-zone1-BLC-swap1


title: B-ALL-Ctrl-1

description: Library name: Sample 1


title: 5M

description: Library name: 5M


title: E. crypticus_NUCOP 100 2days_ replicate3


title: E. crypticus_Control 2days_ replicate3

source_name: Tissue: Whole body extracts (40 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: un-spiked soil for 2 days


title: ATAC-Seq, tissue Zone-5 Control replicate_3

description: Library name: 7-atac-omp-zone5-BLC-wt1

value: Cbx*/*;OMP-GFP


title: Control 074

type: genomic

city: Montreal

first: Alain

last: Moreau

state: QC

address: 3175 Côte-Ste-Catherine

country: Canada

institute: Azrieli Research Center of CHU Sainte-Justine

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing:
ChAMP package (Version 2.28.0)
[processed value definition] Beta value

label: Cy3 and Cy5

source_name: Saliva

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from saliva using the PureLink Genomic DNA Mini Kit (Thermo Fisher Scientific) according to the manufacturer's protocol.

value: Saliva

value: M

tag: bmi

tag: age at time of test

tag: subject group

value: Healthy control


title: Control 076

value: F


title: testes Rep 5

city: Cambridge

first: Amelie

last: Raz

state: MA

address: 455 Main St

institute: Whitehead Institute for Biomedical Research

description: Library name: Rep 5

data_processing:
cellranger
Assembly: DM6
Supplementary files format and content: Gene expression matrix

organism: Drosophila melanogaster

source_name: Testes

extract_protocol:
Testes were dissected and dissociated in trypsin and collagenase
scRNAseq, Illumina

value: Testes

value: Germline and Soma

value: Wildtype


title: 2M

description: Library name: 2M

source_name: masseter muscle (MM)

extract_protocol:
Dissection of dura mater and masseter muscle
Approximately 500ng Total RNA was used for RNA-seq library preparation by following TruSeq stranded mRNA-seq library preparation kit ( Cat. No: 20020595, Illumina, USA). Following mRNA enrichment by oligodT beads,  the RNA was fragmented into small pieces using divalent cautions under elevated temperature and magnesium. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM). The incorporation of dUTP in second strand synthesis effectively quenches the second strand during amplification, since the polymerase used in the assay will not incorporate past this nucleotide. These cDNA fragments then went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products were then purified and enriched with PCR to create the final RNA-Seq library for sequencing by 50bp single-end protocol with Illumina HiSeq 2500 platform, or 100bp pair-end protocol with Illumina NovaSeq 6000 platform.

value: Saline in MM


title: testes Rep 4

description: Library name: Rep 4


title: E. crypticus_Control 2days_ replicate1

value: Whole body extracts

value: Adult organisms with well developed clitellum


title: 4M

description: Library name: 4M

value: masseter muscle (MM)

value: Wild-type


title: 3M

description: Library name: 3M


title: ATAC-Seq, tissue Zone-5 Control replicate_1

description: Library name: 10-atac-omp-zone5-BLC-wt2


title: 6M

description: Library name: 6M


title: Control 069


title: ATAC-Seq, tissue Zone-5 Control replicate_2

description: Library name: 3-atac-omp-zone5-BLC-wt1_fem


title: 1M

description: Library name: 1M


title: E. crypticus_Control 2days_ replicate2


title: ATAC-Seq, tissue Zone-1 Control replicate_3

description: Library name: 4-atac-omp-zone1-wt2


title: testes Rep 3

description: Library name: Rep 3


title: ATAC-Seq, tissue Zone-5 Swap mouse replicate_1

description: Library name: 12-atac-omp-zone5-BLC-swap2

value: Cbx*/*;Foxg1CRE; OMP-GFP


title: Sp5C, CFA injection+Tributyrin via oral gavage,rep2, ATAC

city: Dallas

first: Feng

last: Tao

address: 3302 Gaston Avenue

department: Biomedical Sciences

institute: Texas A&M University College of dentistry

description: Library name: TB_2_ATAC

library_source: genomic single cell

data_processing:
Sequenced data were processed using Cell Ranger ARC software (v2.0.2) with alignment to the mouse genome (GRCm38).
Assembly: mm10
Supplementary files format and content: feature reference.csv

source_name: spinal trigeminal nucleus caudalis

extract_protocol:
Cell nuclei were isolated from Sp5C tissues using the 10X Genomics Chromium Nuclei Isolation Kit (manual CG000505 Rev A). Tissue homogenization was performed in lysis buffer, followed by debris removal and filtration (Flowmi 40-μm). Isolated nuclei were counted using a Countess 3 FL Automated Cell Counter.
Isolated nuclei were processed using the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression workflow (manual CG000338 Rev F). Nuclei were subjected to tagmentation, barcoded in the Chromium X Controller, and prepared for library construction using 10X Genomics PN-1000283. Libraries were sequenced on an Illumina NovaSeq platform.

treatment_protocol: Mice were treated with tributyrin (5 g/kg/day) via oral gavage for 10 days, starting 5 days prior to CFA injection. CFA (10 μl, 5 mg/ml) or saline was injected into the superior TMJ space on day 0 to induce inflammatory pain. Tissues were harvested on day 5 post-CFA injection.

value: spinal trigeminal nucleus caudalis


title: Control 064


title: S55L PP_EH301diet_10

city: New York

first: Nicole

last: Sayles

address: 407 East 61st Street

institute: Weill Cornell

description:
Library name: Sample30
Column name in EH301study_rawdata.txt: HGFGFBGXM_D10_EH_Preg_D03_1737_HTSeqCounts.txt

data_processing:
PP study libraries were seequenced with paired-end 86 bps. EH301 diet study libraries were sequenced with sing-end 86 bps.
Raw single-end or pair-end reads were processed using Trimmomatic (version 0.39) to trim adapters and the BBDuk program in the BBMap package (version 39.27) to trim polyA and polyG tails.
Trimmed reads were aligned to the mouse genome assembly GRCm39.p6 using the STAR aligner (version 2.7.0f).
SAM files were converted to BAM to read overlapping reads per gene using HTSeq-count (version 0.6.1)
The R package DESeq2 (version 3.21) was used to obtain both normalized and variance stabilized counts.
Assembly: GRCm39.p6
Supplementary files format and content: tab-deliminted text includes raw counts for each sample

source_name: Heart

extract_protocol:
RNA was harvested using Qiagen Rneasy Mini Kit. 500ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the Lexogegn QuantSeq 3'mRNA-Seq Library Prep Kit FWD following manufacturer's protocols.

treatment_protocol: WT or S55L mice were either aged to 100 days or bred at 65 days and euthanized 0 days postpartum (PP). S55L mice were fed either control or EH301 diet during breeding and euthanized 0 days PP.

value: Heart

value: PP + EH301 diet


title: ATAC-Seq, tissue Zone-1 Control replicate_1

description: Library name: 1-atac-omp-zone1-BLC-wt1_fem

source_name: Main olfactory epithelium

value: Main olfactory epithelium

value: OMP-GFP+ mature OSN cell sorted

value: Cbx*/*;OMP-GFP


title: testes Rep 2

description: Library name: Rep 2


title: Control 066

value: Saliva

value: Healthy control


title: S55L PP_EH301diet_9

description:
Library name: Sample29
Column name in EH301study_rawdata.txt: HGFGFBGXM_D10_EH_Preg_C03_843_HTSeqCounts.txt


title: testes Rep 1

description: Library name: Rep 1

value: Testes


title: ATAC-Seq, tissue Zone-1 Control replicate_2

description: Library name: 1-atac-omp-zone1-BLC-wt1


title: Sp5C, CFA injection+Tributyrin via oral gavage,rep1, GEX

description: Library name: TB_1_RNA


title: Control 044

value: F


title: S55L PP_EH301diet_8

description:
Library name: Sample28
Column name in EH301study_rawdata.txt: HGFGFBGXM_D10_EH_Preg_B03_320_HTSeqCounts.txt


title: Sp5C, CFA injection+Tributyrin via oral gavage,rep2, GEX

description: Library name: TB_2_RNA


title: Sp5C, CFA injection+Glycerol via oral gavage,rep2, ATAC

description: Library name: CFA_2_ATAC


title: Sp5C, CFA injection+Tributyrin via oral gavage,rep1, ATAC

description: Library name: TB_1_ATAC


title: Control 045

value: M


title: Control_replicate_1

description:
Library name: SM002_S34_L003
10x Genomics

data_processing:
libraries were quality checked with 10x Genomics software
Assembly: mm10
Supplementary files format and content: matrix.mtx

extract_protocol:
cells were isolated using papain enzymatic treatment (Worthington).
10x Barcode (Cell Barcode)

value: OSN

value: WT; Foxg1CRE


title: Control 037


title: Control 031


title: Sp5C, CFA injection+Glycerol via oral gavage,rep2, GEX

description: Library name: CFA_2_RNA


title: Control 028


title: CbxSwap;Foxg1CRE_replicate_1

description:
Library name: SM001_S33_L003
10x Genomics

value: Cbx*/*; Foxg1CRE 1


title: CbxSwap;Foxg1CRE_replicate_2

description:
Library name: SE004_S1_L003
10x Genomics

value: Cbx*/*; Foxg1CRE 2


title: S55L PP_EH301diet_7

description:
Library name: Sample27
Column name in EH301study_rawdata.txt: HGFGFBGXM_D10_EH_Preg_A03_319_HTSeqCounts.txt


title: Control_replicate_2

description:
Library name: SE005_S1_L003
10x Genomics

value: Cbx*/*


title: S55L PP_EH301diet_6

description:
Library name: Sample26
Column name in EH301study_rawdata.txt: HGFGFBGXM_D10_EH_Preg_H02_316_HTSeqCounts.txt


title: Control 027


title: S55L PP_controldiet_4

description:
Library name: Sample24
Column name in EH301study_rawdata.txt: HGFGFBGXM_D10_EH_Preg_A02_1852_HTSeqCounts.txt

value: PP + control diet


title: gg8-tTA

description:
Library name: SR006_S16_L001
10x Genomics


title: Control 025


title: Control 017


title: S55L PP_controldiet_3

description:
Library name: Sample23
Column name in EH301study_rawdata.txt: HGFGFBGXM_D10_EH_Preg_H01_1851_HTSeqCounts.txt


title: Sp5C, CFA injection+Glycerol via oral gavage,rep1, GEX

description: Library name: CFA_1_RNA

value: spinal trigeminal nucleus caudalis


title: In_vivo_GF, sub5, DNA, Rep2

description:
Library name: AML282
Column name in GF_Sub5_Counts: AML282

data_processing:
Sequencing reads were aligned to the oligonucleotide library using BWA (PMID: 20080505). After alignment, any oligonucleotides with fewer than 10 reads in either the DNA or RNA samples were excluded from downstream analysis.
To assess oligonucleotide activity and identify robust functional Cis-Regulatory Elements (fCREs), three statistical tools were employed within the R programming environment (version 4.3.3): DESeq2 (version 1.42.1), EdgeR (version 4.0.16), MPRAnalyzer (version 1.20.0).
Assembly: hg38
Supplementary files format and content: processed files include counts >10 for each tested elements for each replicate
Supplementary files format and content: annotation of column names in counts file to associate column names with replicate number and condition

source_name: Liver

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen) from HepG2 or Rneasy midi kit (Qiagen) from mouse liver. DNA was extracted using mini-prep kit (Qiagen)
Plasmid DNA library preparation: we used 200 ng DNA as a template and each library was assigned unique i5 and i7 primers to aid in demultiplexing post-sequencing. The library was PCR amplified using 2X KAPA HiFi HotStart ReadyMix (Roche) with the following program (98°C for 3min; 98°C for 15s, 65°C for 30s, 7°2C for 45s and repeat for 17 cycles); 72°C for 2min). PCR reactions from each sample were combined and purified using 0.8X KAPA HyperPure Beads (Roche). RNA library preparation: we first isolated mRNA from 40 ug of total RNA from each sample using Dynabead Oligo-dT25 beads (Invitrogen) for HepG2 samples. We used 600 ug of total RNA to isolate mRNA for mouse liver samples. RNA was treated with Turbo DNase (Thermo Fisher Scientific) to remove contaminating DNA, and reverse-transcribed with SuperScript III (Thermo Fisher Scientific) using gene-specific RT primers. The library was PCR amplified using 2X KAPA HiFi HotStart ReadyMix (Roche) and 10 uM P7_UMI_Primer with the following program (98°C for 60s; 65°C for 30s; 72°C for 45s). Samples were purified using 1.4X KAPA HyperPure Beads (Roche) and eluted with 20uL water at 37°C for 3 min at 300 rpm on the thermomixer. Purified samples from the earlier step were used as a template per PCR reaction. The library was PCR amplified using 2X KAPA HiFi HotStart ReadyMix (Roche), 10 uM junction_fwd primer, and 10 uM P7_junction_rev primer with the following program (98°C for 90s; 98°C for 15s, 65°C for 30s, 72°C for 40s and repeat for 22 cycles; 72°C for 2min). Samples were purified using 0.8X KAPA HyperPure Beads (Roche) and eluted with 20uL water at 37°C for 3 min at 300 rpm on the thermomixer. Lastly, each library was assigned a unique i5 primer to aid in demultiplexing post-sequencing The library was PCR amplified using 2X KAPA HiFi HotStart ReadyMix (Roche) and 10uM P7_seqready rev primers with the following program (98°C for 90s; 98°C for 15s, 65°C for 30s, 72°C for 40s and repeat for 8 cycles; 72°C for 2min). PCR reactions from each sample were combined and purified using 0.8X KAPA HyperPure Beads (Roche). Samples were eluted with an appropriate amount of water at 37°C for 3 min at 300 rpm on the thermomixer. Sample concentration post-purification was measured using Qubit™ dsDNA Quantification Assay Kits (Invitrogen).

value: Liver

value: Germ-free


title: In_vivo_GF, sub5, DNA, Rep3

description:
Library name: AML284
Column name in GF_Sub5_Counts: AML284


title: Control 013


title: In_vivo_GF, sub5, DNA, Rep1

description:
Library name: AML285
Column name in GF_Sub5_Counts: AML285


title: Sp5C, CFA injection+Glycerol via oral gavage,rep1, ATAC

description: Library name: CFA_1_ATAC


title: gg8-tTA; tetOP2iresGFP

description:
Library name: SR005_S15_L001
10x Genomics

value: Main olfactory epithelium

value: gg8-tTA; tetOP2iresGFP


title: Control 009


title: S55L PP_controldiet_5

description:
Library name: Sample25
Column name in EH301study_rawdata.txt: HGFGFBGXM_D10_EH_Preg_B02_1730_HTSeqCounts.txt

value: Heart


title: Control 014

value: Saliva


title: Sp5C, Saline injection+Glycerol via oral gavage,rep2, ATAC

description: Library name: CON_2_ATAC


title: S55L PP_controldiet_2

description:
Library name: Sample22
Column name in EH301study_rawdata.txt: HGFGFBGXM_D10_EH_Preg_G01_1951_HTSeqCounts.txt


title: Sp5C, Saline injection+Glycerol via oral gavage,rep2, GEX

description: Library name: CON_2_RNA


title: In_vivo, sub5, DNA, Rep1

description:
Library name: AML251
Column name in Liver_Sub5_Counts: AML251


title: S55L PP_controldiet_1

description:
Library name: Sample21
Column name in EH301study_rawdata.txt: HGFGFBGXM_D10_EH_Preg_F01_311_HTSeqCounts.txt


title: S55L PP_5

description:
Library name: Sample20
Column name in PPstudy_rawdata.txt: polyAGtrimmed_HT1005_April2025_H02_518_10481885_232FCWLT3_L2_alignedAligned_counts.txt

value: PP


title: In_vivo, sub5, DNA, Rep2

description:
Library name: AML250
Column name in Liver_Sub5_Counts: AML250


title: tibial anterior muscle, 8w, HFD-4

city: Hangzhou

first: Senjie

last: Wang

address: No. 866, Yuhangtang Road, Sandun Town

institute: Zhejiang University

data_processing:
Reads were quality controlled with FastQC (Version 0.12.1)
Cutadapt was used to trim low quality sequences
RNA STAR (Version 2.7.11a) was used to map reads to the mouse reference genome
Gene expression quantification was performed using featureCounts (Version 2.0.3)
Differential expression analysis was conducted with the DESeq2 package (version 1.42.0)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes gene counts for each sample
Supplementary files format and content: tab-delimited text files include gene counts for each sample

source_name: tibial anterior muscle

extract_protocol:
Total RNA was isolated from the anterior tibial muscle of mice with FreeZol reagent (R711-01, Vazyme) according to the manufacturer's instruction, and was eluted in 20 µl of sterile water.
Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, followed by RNA degradation with RNase H. Second strand cDNA synthesis was subsequently performed with DNA Polymerase I and dNTP.The cDNA was then processed to create blunt ends through exonuclease/polymerase activities, followed by adenylation of the 3’ ends and ligation of adaptors with a hairpin loop structure. Next, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA), and PCR amplification was performed. The library was then quantified by Qubit2.0 Fluorometer and Agilent 2100 bioanalyzer, respectively.

treatment_protocol: 3- and 8-week-old mice were exposed to 4-week chow diet or HFD. Fresh muscle tissues were harvested from mice and immediately frozen in liquid nitrogen for further processing.

value: tibial anterior muscle

value: WT

value: 4w HFD


title: Sp5C, Saline injection+Glycerol via oral gavage,rep1, ATAC

description: Library name: CON_1_ATAC


title: Sp5C, Saline injection+Glycerol via oral gavage,rep1, GEX

description: Library name: CON_1_RNA


title: Control 008

value: M

value: Healthy control


title: S55L PP_4

description:
Library name: Sample19
Column name in PPstudy_rawdata.txt: polyAGtrimmed_HT1005_April2025_D03_903_10481885_232FCWLT3_L2_alignedAligned_counts.txt


title: In_vivo, sub5, DNA, Rep3

description:
Library name: AML249
Column name in Liver_Sub5_Counts: AML249


title: tibial anterior muscle, 8w, HFD-3


title: S55L PP_3

description:
Library name: Sample18
Column name in PPstudy_rawdata.txt: polyAGtrimmed_HT1005_April2025_C03_906_10481885_232FCWLT3_L2_alignedAligned_counts.txt


title: Control 007

value: F


title: In_vivo, sub4, DNA, Rep1

description:
Library name: AML247
Column name in Liver_Sub4_Counts: AML247


title: tibial anterior muscle, 8w, HFD-2


title: S55L PP_2

description:
Library name: Sample17
Column name in PPstudy_rawdata.txt: polyAGtrimmed_HT1005_April2025_B03_581_10481885_232FCWLT3_L2_alignedAligned_counts.txt


title: In_vivo, sub4, DNA, Rep2

description:
Library name: AML246
Column name in Liver_Sub4_Counts: AML246


title: tibial anterior muscle, 8w, HFD-1


title: In_vivo, sub4, DNA, Rep3

description:
Library name: AML244
Column name in Liver_Sub4_Counts: AML244


title: tibial anterior muscle, 8w, chow diet-4

value: 4w chow diet


title: S55L PP_1

description:
Library name: Sample16
Column name in PPstudy_rawdata.txt: polyAGtrimmed_HT1005_April2025_A03_578_10481885_232FCWLT3_L2_alignedAligned_counts.txt


title: Control 003


title: tibial anterior muscle, 8w, chow diet-3


title: S55L Naïve_4

description:
Library name: Sample14
Column name in PPstudy_rawdata.txt: polyAGtrimmed_HT1005_April2025_F02_5907_10481885_232FCWLT3_L2_alignedAligned_counts.txt

value: Naïve


title: In_vivo, sub3, DNA, Rep1

description:
Library name: AML242
Column name in Liver_Sub3_Counts: AML242


title: Case 178

tag: age of disease onset

value: EM


title: tibial anterior muscle, 8w, chow diet-2

tag: tissue


title: In_vivo, sub4, DNA, Rep4

description:
Library name: AML243
Column name in Liver_Sub4_Counts: AML243


title: Case 177


title: Control 004


title: Control 005


title: tibial anterior muscle, 8w, chow diet-1


title: In_vivo, sub3, DNA, Rep2

description:
Library name: AML241
Column name in Liver_Sub3_Counts: AML241


title: S55L Naïve_2

description:
Library name: Sample12
Column name in PPstudy_rawdata.txt: polyAGtrimmed_HT1005_April2025_D02_576_10481885_232FCWLT3_L2_alignedAligned_counts.txt


title: Case 173


title: S55L Naïve_5

description:
Library name: Sample15
Column name in PPstudy_rawdata.txt: polyAGtrimmed_HT1005_April2025_G02_5908_10481885_232FCWLT3_L2_alignedAligned_counts.txt


title: tibial anterior muscle, 3w, HFD-4


title: In_vivo, sub2, DNA, Rep2

description:
Library name: AML217
Column name in Liver_sub2_Counts: AML217


title: In_vivo, sub2, DNA, Rep1

description:
Library name: AML215
Column name in Liver_sub2_Counts: AML215


title: S55L Naïve_3

description:
Library name: Sample13
Column name in PPstudy_rawdata.txt: polyAGtrimmed_HT1005_April2025_E02_5403_10481885_232FCWLT3_L2_alignedAligned_counts.txt


title: Case 172


title: WT PP_5

description:
Library name: Sample10
Column name in PPstudy_rawdata.txt: polyAGtrimmed_HT1005_April2025_H01_579_10481885_232FCWLT3_L2_alignedAligned_counts.txt

value: Wildtype


title: Case 171


title: S55L Naïve_1

description:
Library name: Sample11
Column name in PPstudy_rawdata.txt: polyAGtrimmed_HT1005_April2025_C02_597_10481885_232FCWLT3_L2_alignedAligned_counts.txt


title: tibial anterior muscle, 3w, HFD-2


title: tibial anterior muscle, 3w, HFD-3


title: WT PP_4

description:
Library name: Sample9
Column name in PPstudy_rawdata.txt: polyAGtrimmed_HT1005_April2025_G01_583_10481885_232FCWLT3_L2_alignedAligned_counts.txt


title: Case 170


title: tibial anterior muscle, 3w, HFD-1


title: Case 167


title: Case 169


title: In_vivo, sub1, DNA, Rep2

description:
Library name: AML237
Column name in Liver_Sub1_Counts: AML237

value: Liver


title: WT PP_3

description:
Library name: Sample8
Column name in PPstudy_rawdata.txt: polyAGtrimmed_HT1005_April2025_F01_517_10481885_232FCWLT3_L2_alignedAligned_counts.txt


title: In_vivo, sub1, DNA, Rep3

description:
Library name: AML236
Column name in Liver_Sub1_Counts: AML236


title: Case 162


title: tibial anterior muscle, 3w, chow diet-4


title: tibial anterior muscle, 3w, chow diet-3


title: In_vivo, sub1, DNA, Rep4

description:
Library name: AML235
Column name in Liver_Sub1_Counts: AML235


title: WT PP_1

description:
Library name: Sample6
Column name in PPstudy_rawdata.txt: polyAGtrimmed_HT1005_April2025_A02_586_10481885_232FCWLT3_L2_alignedAligned_counts.txt


title: tibial anterior muscle, 3w, chow diet-2


title: In_vivo, sub1, DNA, Rep1

description:
Library name: AML238
Column name in Liver_Sub1_Counts: AML238


title: tibial anterior muscle, 3w, chow diet-1


title: Case 153


title: WT Naïve_5

description:
Library name: Sample5
Column name in PPstudy_rawdata.txt: polyAGtrimmed_HT1005_April2025_E01_595_10481885_232FCWLT3_L2_alignedAligned_counts.txt


title: NpatKI, dTAG, 3hr, RNA, rep3

city: Fukuoka

first: Yuichiro

last: Semba

address: 3-1-1 Maidashi

institute: Kyushu University

data_processing:
Raw sequence reads were pseudoaligned to the mm10 genome using kallisto, and transcript abundance quantified.
Assembly: mm10
Supplementary files format and content: The tab-delimited text file contains TPMs per genes.

source_name: Bone marrow

growth_protocol: Mouse AML cells were cultured in Iscove's Modified Dulbecco's Media (IMDM) (Life Technologies) supplemented with 20% Fetal Bovine Serum (FBS) (Omega Scientific), 1% penicillin streptomycin (Life Technologies), and mouse SCF (20 ng/ml), mouse IL-3 (10 ng/ml) and mouse IL-6 (10 ng/ml) (all purchased from PeproTech).

extract_protocol:
Cells were washed twice with ice-cold PBS, and total RNA extracted using the Rneasy Mini Kit (Qiagen).
To enrich for mRNA, total RNA was processed using the Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). For RNA-seq using NpatKI AML cells, total RNA was prepared using the rRNA Depletion Kit v2 (New England Biolabs) to retain histone-derived RNA. Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions.

treatment_protocol: Nutlin-3a (S8059) or dTAGV-1 were added to culture media at a final concentration of 10 μM or 500 nM, respectively.

value: Bone marrow

value: MLL::AF9 mAML

tag: cell type

value: AML

value: NpatKI


title: NpatKI, dTAG, 3hr, RNA, rep2

tag: genotype


title: Case 144

value: Saliva


title: WT PP_2

description:
Library name: Sample7
Column name in PPstudy_rawdata.txt: polyAGtrimmed_HT1005_April2025_B02_907_10481885_232FCWLT3_L2_alignedAligned_counts.txt

value: Heart

value: PP


title: H33K27M-H3K27me3-ChIP

first: Rui

last: Guo

address: 131 DongAn Road

institute: Institutes of Biomedical Sciences, Fudan University

data_processing:
ChIP-seq reads were trimmed using trim_galore
Trimmed ChIP-seq reads were aligned to mm10. Duplicated reads were removed prior to further anlysis.
Peaks were called using MACS2
Assembly: mm10
Supplementary files format and content: bw,narrowPeak(except for input sample)

source_name: Brain

growth_protocol: Minimum essential medium (Eagle) with non-essential amino acids and 4 mM L-glutamine, 90%; fetal bovine serum, 10%.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature and stopped with 125 mM glycine. The cell pellets were lysed  in a lysis buffer containing 50 mM HEPES pH7.5, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.05% SDS, 1 mM PMSF, 1 mM DTT and protease inhibitor cocktail. The lysate was sonicated to achieve an average DNA fragment length of 300-500 bp (Qsconica).
ChIP-seq libraries were prepared using VAHTS Universal DNA Library Prep Kit for Illumina® V3 Kits (Vazyme.ND607).

value: Brain

value: neural stem cell

tag: chip antibody


title: NpatKI, dTAG, 3hr, RNA, rep1


title: Case 134


title: H33K27M-inputforH3K27me3


title: WT Naïve_4

description:
Library name: Sample4
Column name in PPstudy_rawdata.txt: polyAGtrimmed_HT1005_April2025_D01_592_10481885_232FCWLT3_L2_alignedAligned_counts.txt


title: WT Naïve_2

description:
Library name: Sample2
Column name in PPstudy_rawdata.txt: polyAGtrimmed_HT1005_April2025_B01_598_10481885_232FCWLT3_L2_alignedAligned_counts.txt


title: H33WT-H3K27me3-ChIP


title: WT Naïve_3

description:
Library name: Sample3
Column name in PPstudy_rawdata.txt: polyAGtrimmed_HT1005_April2025_C01_590_10481885_232FCWLT3_L2_alignedAligned_counts.txt


title: Case 131


title: NpatKI, dTAG, 0hr, RNA, rep2


title: H33WT-CBFA2T2KO-H3K27me3-ChIP

value: H3.3WT Cbfa2t2 Knockout


title: Case 129


title: WT Naïve_1

description:
Library name: Sample1
Column name in PPstudy_rawdata.txt: polyAGtrimmed_HT1005_April2025_A01_596_10481885_232FCWLT3_L2_alignedAligned_counts.txt


title: NpatKI, dTAG, 0hr, RNA, rep3


title: Case 121


title: Case 132


title: Xpo7KO, MDM2i, RNA, rep3

value: DMSO


title: H33WT-inputforH3K27me3


title: Case 119

value: F


title: AG_3

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

institute: University of Toyama

description: Library name: Sample 9

data_processing:
Reads were mapped on GRCm38/mm10 mouse reference genome and quantified using CLC Genomics Workbench version 12.0 (Qiagen).
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software version 12.0 (Qiagen).
Filtering characteristics of fold-change and false discovery rate (FDR) were used to identify the DEGs.
Assembly: GRCm38/mm10
Supplementary files format and content: Excel file includes raw read counts and RPKM normalized values for all genes from each sample.

growth_protocol: Male mice (5-week-old, C57BL/6J) were purchased from the Jackson Laboratory (ME, USA) for the space experiments and from Charles River Laboratories (Ibaraki, Japan) for ground experiments. These mice caged in the transportation cage unit (TCU) were launched aboard the SpaceX Falcon 9 rocket (SpX9). The Dragon space vehicle from SpX9 reached the ISS, and then mice were transferred to the habitat cage unit (HCU) by the crew. Mice were divided into 2 groups of six mice each (MG space mice (microgravity)) and AG mice (artificial gravity, at a centrifugation speed of 77 rpm)), and they were caged in the ISS for about 35 days. All mice returned to the Earth (the Pacific Ocean offshore from California on 26 August 2016), and then they were sacrificed at the laboratory 2 days after splash down. For replicating the housing conditions of the space flight experiment, male mice (GC, ground controls) were reared for 35 days at the JAXA Tsukuba Space Center in Japan.

extract_protocol:
Total RNA was extracted from powder samples using ISOGEN II reagent (Nippon Gene) according to the manufacturer’s instruction. About 500 ng of total RNA were ribosomal RNA-depleted using NEBNext rRNA Depletion Kit (E6310, New England Biolabs).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Male

value: Artificial gravity (1 g in space)


title: Case 117

value: EM


title: Xpo7KO, MDM2i, RNA, rep2


title: AG_2

description: Library name: Sample 8


title: Xpo7KO, MDM2i, RNA, rep1


title: H33K27M-HA-ChIP


title: Xpo7WT, MDM2i, RNA, rep3


title: H33WT-CBFA2T2KO-H3K4me3-ChIP


title: Case 116


title: NpatKI, dTAG, 0hr, RNA, rep1


title: MG_3

description: Library name: Sample 6

value: Microgravity


title: H33WT-CBFA2T2KO-inputforH3K27me3


title: AG_1

description: Library name: Sample 7

value: Liver


title: MG_1

description: Library name: Sample 4


title: H33WT-CBFA2T2KO-inputforHAandK4me3


title: MG_2

description: Library name: Sample 5


title: Case 107


title: H33WT-CBFA2T2KO-HA-ChIP


title: Xpo7WT, MDM2i, RNA, rep2

value: Bone marrow


title: H33WT-H3K4me3-ChIP


title: Case 103


title: Xpo7KO, DMSO, RNA, rep2

value: MLL::AF9 mAML


title: Case 102


title: GC_2

description: Library name: Sample 2

value: Ground control (1 g)


title: Case 109

value: M


title: GC_3

description: Library name: Sample 3


title: H33WT-inputforHAandK4me3


title: Xpo7WT, MDM2i, RNA, rep1

value: AML


title: Case 100

value: Saliva


title: GC_1

description: Library name: Sample 1


title: H33K27M-CBFA2T2-ChIP

value: CBFA2T2 (Bethyl,A302-089A)


title: Case 097


title: H33WT-HA-ChIP

value: Brain


title: Heart, PG_3, rnaseq

description: Library name: Sample 6

growth_protocol: For the lunar gravity (0.167 g) experiment, male mice were purchased from the Charles River Laboratories Japan, Inc. (Kanagawa, Japan). The lunar gravity group was maintained in an artificial gravity environment at 0.167 g on the bottom floor of the habitat cage units (HCU) via centrifugation at 31 rpm in MARS-S (15 cm radius). The GC group comprised six age-matched male C57BL/6 J mice per mission, maintained under the same conditions as those aboard the ISS.

value: Heart

value: 8- or 9-week-old

value: Partial gravity (1/6 g)


title: Xpo7KO, DMSO, RNA, rep3

value: DMSO


title: Case 095


title: Heart, PG_2, rnaseq

description: Library name: Sample 5

value: Male


title: Xpo7KO, DMSO, RNA, rep1


title: Xpo7WT, DMSO, RNA, rep3


title: H33K27M-inputforCBFA2T2

value: neural stem cell


title: Heart, PG_1, rnaseq

description: Library name: Sample 4


title: H33WT-CBFA2T2-ChIP


title: Xpo7WT, DMSO, RNA, rep2


title: Heart, GC_3, rnaseq

description: Library name: Sample 3


title: H33WT-inputforCBFA2T2


title: Case 094

value: F

value: EM


title: Xpo7WT, DMSO, RNA, rep1


title: NpatKI, dTAG, 12hr, rep3

data_processing:
Data processing employed the nf-core atacseq pipeline. Read mapping to mitochondrial and nuclear DNA was performed using SAMtools (v1.10), with fragment sizes calculated via Picard (v2.23.1).
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
5 x 104 mouse AML cells were lysed in ice-cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630).
Transposition was then carried out using Tn5 Transposase (Tagment DNA TDE1 Enzyme, Illumina). Transposed DNA fragments were purified using a MinElute Kit (Qiagen), followed by PCR amplification with specific PCR primers. Amplified libraries were further purified with the MinElute Kit.

treatment_protocol: dTAGV-1 was added to culture media at a final concentration of 500 nM.

value: NpatKI


title: Heart, GC_2, rnaseq

description: Library name: Sample 2


title: H33WT-CBFA2T2KO-CBFA2T2-Chip

value: H3.3WT Cbfa2t2 Knockout


title: NpatKI, dTAG, 12hr, rep2

value: Bone marrow

value: MLL::AF9 mAML


title: Case 082


title: H33WT-CBFA2T2KO-input


title: Case 083

value: M


title: Case 081


title: Heat, PG_3, riboseq

description: Library name: Sample 6

extract_protocol:
The heart of mice was removed and flash frozen by liquid nitrogen. After suspending in lysis buffer, nuclear fraction, insoluble debris and mitochondria were removed by centrifugation. Extracts were digested with RNase I (Ambion). Then, monosomes were purified by ultra-centrifugation (Beckman coulter, Optima MAX-TL Ultracentrifuge) through 50% sucrose. Next, ribosome pellets were digested with Proteinase K. Finally, the ribosome protected fragments (RPFs) were size-selected (25-35 nt) by polyacrylamide gel electrophoresis, and converted to Illumina sequencing library using NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs).
RNA libraries were prepared for sequencing using standard Illumina protocols.


title: Case 077


title: NpatKI, dTAG, 3hr, rep3

value: AML


title: NE-4C, H3f3a knockout, stably expressed H3.3K27M-HA

data_processing:
Performed by GENEWIZ, Inc.
Sequence reads were trimmed by trim_galore.
Trimmed sequence reads were aligned to the reference genome using Hisat2, followed by transcript assembly and quantification using StringTie. Differential expression analysis was condected with Ballgown and Deseq.
Assembly: GRCm38
Supplementary files format and content: text file includes FPKM values for each Sample

extract_protocol:
The RNA extraction was carried out by GENEWIZ, Inc.. RNA was extracted using Trizol reagent according to the manufacturer’s protocols.1 μg of total RNA was used for the subsequent library preparation.
The process was conducted by GENEWIZ, Inc.The isolation of poly(A) mRNA was conducted using Oligo(dT) beads. The mRNA fragmentation was achieved using divalent cations and high temperature. Priming was executed using Random Primers. First strand cDNA and  second-strand cDNA were synthesized. The purified double-stranded cDNA was subsequently treated to repair both ends and add a dA-tailing in a single reaction, followed by a T-A ligation to attach adaptors to both ends. Size selection of Adaptor-ligated DNA was performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers, and the PCR products were validated.


title: NpatKI, dTAG, 12hr, rep1


title: Heat, PG_2, riboseq

description: Library name: Sample 5


title: NE-4C, H3f3a knockout, stably expressed H3.3K27M-HA, repeated


title: Case 075

value: Saliva


title: Case 074


title: Heat, PG_1, riboseq

description: Library name: Sample 4


title: NpatKI, dTAG, 3hr, rep2


title: NE-4C, H3f3a knockout, stably expressed H3.3wildtype-HA,Cbfa2t2 knockout, repeated


title: NE-4C, H3f3a knockout, stably expressed H3.3wildtype-HA,Cbfa2t2 knockout


title: Heat, GC_3, riboseq

description: Library name: Sample 3

value: Ground control (1 g)


title: Heart, GC_1, rnaseq

description: Library name: Sample 1


title: NpatKI, dTAG, 0hr, rep3


title: NpatKI, dTAG, 3hr, rep1


title: Case 073


title: Case 069