title: HiC_8C_TripleKD_rep2

description: Library name: HiC_8C_TripleKD_rep2

data_processing:
Hi-C and Micro-C sequencing reads were mapped, processed and iteratively corrected using HiC-Pro. Micro-C reads were processed without considering the restriction enzyme fragment. Valid read pairs were then converted to Cool format and balanced using Cooler. Directionality index and insulation scores were calculated using balanced cool files at 10 kilobase (kb) resolution and 100–500 kb surroundings using Cooltools. To visualize the 2D interaction neighbourhood around cohesin islands and CTCF sites, all cis combinations between GCI genes and CTCF sites located within a defined range (>50 kb and <500 kb) were generated using BEDtools. The pile-up matrix was generated using Coolpuppy on cool files with 5 kb or 10 kb resolution.
Assembly: mm9
Supplementary files format and content: Balanced mcool files generated by cooler and cooltools based on validpairs

extract_protocol:
For Adnp knockout, three single guide RNAs (sgRNAs) targeting the last exon were designed. To assemble Cas9–sgRNA ribonucleoproteins, 200 ng μl−1 sgRNAs was mixed with 0.3 μl of Alt-R S.p. HiFi Cas9 protein (Integrated DNA Technologies, 1081060) and incubated at room temperature for 15 min in 15 μl assembly buffer (1 mM Tris-HCl pH 7.5, 0.1 mM EDTA). The injection mix was centrifuged at 12,000g for 10 min, and the supernatant was used for injection into PN3 zygotes. Embryos were then cultured in G1 medium (Vitrolife). Blastocyst-stage embryos were collected for RNA-seq, CUT&RUN and Hi-C. For DRB treatment, 8C embryos (68–70 h after hCG injection) were collected and cultured in CZB medium supplemented with DRB (final concentration 120 μM) for 2 or 4 h.For the cohesin-KD experiment, PN3 zygotes were injected with 20 μM siRNAs (targeting Rad21 (Rad21 KD) or Nipbl, Smc3 and Rad21 (triple KD; Supplementary Table 2). The PN3 zygotes in the control group were injected with an equal volume of 20 μM scramble siRNAs. Then the embryos were cultured in G1 medium (Vitrolife) for 45 h.
Embryos were crosslinked with 1% formaldehyde at room temperature for 10 min and then quenched by glycine for 10 min at room temperature. Embryos were then washed by PBS and lysed on ice and solubilized with 0.5% SDS. The nuclei were digested with MboI at 37 °C for 12 h. The resulting fragments were filled with biotin-14-dATP and then ligated. After ligation, crosslink reversal, DNA purification and sonication were performed sequentially, and the biotin-14-dATP-labelled targets were pulled down by Dynabeads MyOne Streptavidin C1 (Life Technology). The purified DNA was subjected to the True-seq library construction process.


title: HiC_8C_TripleKD_rep1

status: Public on Aug 22 2025

type: SRA

city: Beijing

first: Wei

last: Xie

state: Beijing

address: Qinghuayuan

department: School of Life Science

country: China

institute: Tsinghua University

description: Library name: HiC_8C_TripleKD_rep1

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: developmental stage

tag: cell type

tag: genotype

value: WT

tag: treatment

value: Triple KD


title: RNA_8C_Rad21KD_rep2

description: Library name: RNA_8C_Rad21KD_rep2

library_source: transcriptomic

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

molecule: polyA RNA

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

value: Rad21 KD


title: HiC_8C_Rad21KD_rep1

description: Library name: HiC_8C_Rad21KD_rep1


title: HiC_8C_Rad21KD_rep2

description: Library name: HiC_8C_Rad21KD_rep2


title: RNA_Blastocyst_AdnpKO_rep3

description: Library name: RNA_Blastocyst_AdnpKO_rep3

source_name: Blastocyst

value: Blastocyst

value: Adnp KO


title: HiC_8C_cohesinKD_control_rep2

description: Library name: HiC_8C_cohesinKD_control_rep2

value: Control


title: HiC_8C_cohesinKD_control_rep1

description: Library name: HiC_8C_cohesinKD_control_rep1


title: HiC_8C_DRB_4h_rep1

description: Library name: HiC_8C_DRB_4h_rep1

value: DRB 4h


title: HiC_8C_DMSO_control_for_4hDRB

description: Library name: HiC_8C_DMSO_control_for_4hDRB

value: DMSO 4h


title: RNA_Blastocyst_control_rep1

description: Library name: RNA_Blastocyst_control_rep1


title: HiC_8C_DRB_4h_rep2

description: Library name: HiC_8C_DRB_4h_rep2


title: HiC_Blastocyst_ADNPKO_rep1

description: Library name: HiC_Blastocyst_ADNPKO_rep1

source_name: E3.5 blastocyst

value: E3.5 blastocyst


title: HiC_Blastocyst_ADNPKO_control

description: Library name: HiC_Blastocyst_ADNPKO_control

value: untreated


title: HiC_Blastocyst_ADNPKO_rep2

description: Library name: HiC_Blastocyst_ADNPKO_rep2


title: RNA_DRB_4h_rep2

description: Library name: RNA_DRB_4h_rep2


title: Both_10Cyp_4, Female

city: Iowa City

first: Benjamin

last: Hing

state: IA

address: 51 Newton Road, BSB 6-509

country: USA

institute: University of Iowa

description:
Library name: Sample70
Column name  in Raw_Gene_Level_Counts.csv: Sample70

data_processing:
Ilumina adapters were trimmed using TrimGalore (v0.5.0)
Trimmed data was aligned to mm10 using Salmon (v1.10.1) with options –seqBias and –gcBias.
Data was summarized to gene level using tximport (v1.30.0)
Assembly: mm10
Supplementary files format and content: comma separated value of raw count for each sample

molecule: total RNA

source_name: E16 dorsal forebrain

extract_protocol:
RNA was extracted using RNAeasy Mini Kit (Qiagen)
RNA libraries was prepared by Novogene

treatment_protocol: Treatment lasted for 28 days (7 days of treatment, followed by three cycles of alternating 2 days of no treatment, and 5 days treatment). Immediately after, mice were paired using either male and female mice treated with vehicle (control), male mice exposed to a-cypermethrin and female exposed to vehicle (paternal exposure), female mice exposed to a-cypermethrin while male mice exposed to vehicle (maternal exposure) or both male and female were exposed to the same dose of a-cypermethrin (both parental exposure). At embryonic day 16 (E16), female pregnant mice were euthanized for embryo tissue collection.

tag: tissue

value: E16 dorsal forebrain

tag: Sex

value: Female

tag: batch


title: Both_10Cyp_2, Female

description:
Library name: Sample68
Column name  in Raw_Gene_Level_Counts.csv: Sample68


title: RNA_Blastocyst_AdnpKO_rep1

description: Library name: RNA_Blastocyst_AdnpKO_rep1


title: Both_10Cyp_3, Male

description:
Library name: Sample69
Column name  in Raw_Gene_Level_Counts.csv: Sample69

value: Male


title: Paternal_10Cyp_9, Female

description:
Library name: Sample65
Column name  in Raw_Gene_Level_Counts.csv: Sample65


title: Both_10Cyp_1, Male

description:
Library name: Sample67
Column name  in Raw_Gene_Level_Counts.csv: Sample67


title: Paternal_10Cyp_8, Female

description:
Library name: Sample64
Column name  in Raw_Gene_Level_Counts.csv: Sample64


title: Paternal_10Cyp_7, Male

description:
Library name: Sample63
Column name  in Raw_Gene_Level_Counts.csv: Sample63


title: Paternal_10Cyp_6, Female

description:
Library name: Sample62
Column name  in Raw_Gene_Level_Counts.csv: Sample62


title: Paternal_10Cyp_5, Male

description:
Library name: Sample61
Column name  in Raw_Gene_Level_Counts.csv: Sample61


title: Paternal_10Cyp_4, Female

description:
Library name: Sample60
Column name  in Raw_Gene_Level_Counts.csv: Sample60


title: Both_10Cyp_6, Male

description:
Library name: Sample72
Column name  in Raw_Gene_Level_Counts.csv: Sample72


title: Both_10Cyp_10, Male

description:
Library name: Sample76
Column name  in Raw_Gene_Level_Counts.csv: Sample76


title: Both_10Cyp_8, Female

description:
Library name: Sample74
Column name  in Raw_Gene_Level_Counts.csv: Sample74


title: Paternal_10Cyp_3, Female

description:
Library name: Sample59
Column name  in Raw_Gene_Level_Counts.csv: Sample59


title: Both_10Cyp_9, Female

description:
Library name: Sample75
Column name  in Raw_Gene_Level_Counts.csv: Sample75


title: Both_10Cyp_7, Male

description:
Library name: Sample73
Column name  in Raw_Gene_Level_Counts.csv: Sample73


title: Paternal_10Cyp_2, Male

description:
Library name: Sample58
Column name  in Raw_Gene_Level_Counts.csv: Sample58


title: Maternal_10Cyp_8, Female

description:
Library name: Sample56
Column name  in Raw_Gene_Level_Counts.csv: Sample56


title: Maternal_10Cyp_7, Male

description:
Library name: Sample55
Column name  in Raw_Gene_Level_Counts.csv: Sample55


title: Maternal_10Cyp_6, Male

description:
Library name: Sample54
Column name  in Raw_Gene_Level_Counts.csv: Sample54


title: Maternal_10Cyp_5, Female

description:
Library name: Sample53
Column name  in Raw_Gene_Level_Counts.csv: Sample53


title: Both_10Cyp_5, Male

description:
Library name: Sample71
Column name  in Raw_Gene_Level_Counts.csv: Sample71


title: Maternal_10Cyp_3, Female

description:
Library name: Sample51
Column name  in Raw_Gene_Level_Counts.csv: Sample51


title: Maternal_10Cyp_4, Male

description:
Library name: Sample52
Column name  in Raw_Gene_Level_Counts.csv: Sample52


title: Maternal_10Cyp_1, Male

description:
Library name: Sample49
Column name  in Raw_Gene_Level_Counts.csv: Sample49


title: Paternal_10Cyp_10, Male

description:
Library name: Sample66
Column name  in Raw_Gene_Level_Counts.csv: Sample66


title: Both_0.3Cyp_12, Male

description:
Library name: Sample48
Column name  in Raw_Gene_Level_Counts.csv: Sample48


title: Both_0.3Cyp_11, Male

description:
Library name: Sample47
Column name  in Raw_Gene_Level_Counts.csv: Sample47


title: Both_0.3Cyp_9, Female

description:
Library name: Sample45
Column name  in Raw_Gene_Level_Counts.csv: Sample45


title: Both_0.3Cyp_8, Male

description:
Library name: Sample44
Column name  in Raw_Gene_Level_Counts.csv: Sample44


title: Both_0.3Cyp_7, Female

description:
Library name: Sample43
Column name  in Raw_Gene_Level_Counts.csv: Sample43


title: Both_0.3Cyp_10, Male

description:
Library name: Sample46
Column name  in Raw_Gene_Level_Counts.csv: Sample46


title: Both_0.3Cyp_5, Male

description:
Library name: Sample41
Column name  in Raw_Gene_Level_Counts.csv: Sample41


title: Both_0.3Cyp_6, Female

description:
Library name: Sample42
Column name  in Raw_Gene_Level_Counts.csv: Sample42


title: Paternal_10Cyp_1, Female

description:
Library name: Sample57
Column name  in Raw_Gene_Level_Counts.csv: Sample57


title: Both_0.3Cyp_4, Female

description:
Library name: Sample40
Column name  in Raw_Gene_Level_Counts.csv: Sample40


title: Maternal_0.3Cyp_12, Male

description:
Library name: Sample36
Column name  in Raw_Gene_Level_Counts.csv: Sample36


title: Both_0.3Cyp_1, Female

description:
Library name: Sample37
Column name  in Raw_Gene_Level_Counts.csv: Sample37


title: Maternal_0.3Cyp_11, Female

description:
Library name: Sample35
Column name  in Raw_Gene_Level_Counts.csv: Sample35


title: Maternal_0.3Cyp_10, Female

description:
Library name: Sample34
Column name  in Raw_Gene_Level_Counts.csv: Sample34


title: Both_0.3Cyp_3, Male

description:
Library name: Sample39
Column name  in Raw_Gene_Level_Counts.csv: Sample39


title: Maternal_0.3Cyp_7, Male

description:
Library name: Sample31
Column name  in Raw_Gene_Level_Counts.csv: Sample31


title: Both_0.3Cyp_2, Male

description:
Library name: Sample38
Column name  in Raw_Gene_Level_Counts.csv: Sample38


title: Maternal_10Cyp_2, Female

description:
Library name: Sample50
Column name  in Raw_Gene_Level_Counts.csv: Sample50


title: Maternal_0.3Cyp_5, Male

description:
Library name: Sample29
Column name  in Raw_Gene_Level_Counts.csv: Sample29


title: Maternal_0.3Cyp_6, Female

description:
Library name: Sample30
Column name  in Raw_Gene_Level_Counts.csv: Sample30


title: Maternal_0.3Cyp_8, Female

description:
Library name: Sample32
Column name  in Raw_Gene_Level_Counts.csv: Sample32


title: Maternal_0.3Cyp_3, Female

description:
Library name: Sample27
Column name  in Raw_Gene_Level_Counts.csv: Sample27


title: Maternal_0.3Cyp_4, Female

description:
Library name: Sample28
Column name  in Raw_Gene_Level_Counts.csv: Sample28


title: Maternal_0.3Cyp_1, Male

description:
Library name: Sample25
Column name  in Raw_Gene_Level_Counts.csv: Sample25


title: Paternal_0.3Cyp_12, Female

description:
Library name: Sample24
Column name  in Raw_Gene_Level_Counts.csv: Sample24


title: Maternal_0.3Cyp_2, Male

description:
Library name: Sample26
Column name  in Raw_Gene_Level_Counts.csv: Sample26


title: Paternal_0.3Cyp_11, Male

description:
Library name: Sample23
Column name  in Raw_Gene_Level_Counts.csv: Sample23


title: Paternal_0.3Cyp_10, Female

description:
Library name: Sample22
Column name  in Raw_Gene_Level_Counts.csv: Sample22


title: Paternal_0.3Cyp_9, Male

description:
Library name: Sample21
Column name  in Raw_Gene_Level_Counts.csv: Sample21


title: Paternal_0.3Cyp_8, Male

description:
Library name: Sample20
Column name  in Raw_Gene_Level_Counts.csv: Sample20


title: Paternal_0.3Cyp_6, Male

description:
Library name: Sample18
Column name  in Raw_Gene_Level_Counts.csv: Sample18


title: Paternal_0.3Cyp_5, Male

description:
Library name: Sample17
Column name  in Raw_Gene_Level_Counts.csv: Sample17


title: Paternal_0.3Cyp_4, Female

description:
Library name: Sample16
Column name  in Raw_Gene_Level_Counts.csv: Sample16


title: Paternal_0.3Cyp_7, Female

description:
Library name: Sample19
Column name  in Raw_Gene_Level_Counts.csv: Sample19


title: Paternal_0.3Cyp_3, Female

description:
Library name: Sample15
Column name  in Raw_Gene_Level_Counts.csv: Sample15


title: Maternal_0.3Cyp_9, Male

description:
Library name: Sample33
Column name  in Raw_Gene_Level_Counts.csv: Sample33


title: Paternal_0.3Cyp_2, Male

description:
Library name: Sample14
Column name  in Raw_Gene_Level_Counts.csv: Sample14


title: Paternal_0.3Cyp_1, Female

description:
Library name: Sample13
Column name  in Raw_Gene_Level_Counts.csv: Sample13


title: Ctrl_12, Male

description:
Library name: Sample12
Column name  in Raw_Gene_Level_Counts.csv: Sample12

value: Ctrl


title: Ctrl_5, Male

description:
Library name: Sample5
Column name  in Raw_Gene_Level_Counts.csv: Sample5


title: Ctrl_8, Male

description:
Library name: Sample8
Column name  in Raw_Gene_Level_Counts.csv: Sample8


title: Ctrl_4, Male

description:
Library name: Sample4
Column name  in Raw_Gene_Level_Counts.csv: Sample4


title: Ctrl_2, Male

description:
Library name: Sample2
Column name  in Raw_Gene_Level_Counts.csv: Sample2


title: Ctrl_10, Male

description:
Library name: Sample10
Column name  in Raw_Gene_Level_Counts.csv: Sample10


title: Ctrl_3, Female

description:
Library name: Sample3
Column name  in Raw_Gene_Level_Counts.csv: Sample3


title: Ctrl_6, Female

description:
Library name: Sample6
Column name  in Raw_Gene_Level_Counts.csv: Sample6


title: MuSC_iEzh2KO_quiescent_3

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

description: Library name: t17

data_processing:
Illumina runs were converted from BCL and demultiplexed to generate FastQ files using bcl2fastq v2.20.0.422
FastQ files were mapped to mm10 using Tophat 2.1.1
RPKM values were computed using Partek Genomic Suites 7.0
ANOVA comparisons were generated using Partek Genomic Suites 7.0
Assembly: mm10
Supplementary files format and content: Excel files containing RPKM values
Supplementary files format and content: Excel files containing ANOVA results

source_name: Mouse muscle

extract_protocol:
RNA was extracted using QIAmp DNA micro kit (Qiagen, #56304). 250 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA library preparation kit for Illumina (NEB #E7775) according to manufacturer’s instructions.

treatment_protocol: MuSCs and FAPs from either control or Ezh2-/- mice were FACS-isolated at 0 (quiescent), 3 and 7 days post injury, and RNA was extracted and processed for RNAsequencing.

value: Mouse muscle

value: MuSCs

value: Quiescent


title: MuSC_iEzh2KO_quiescent_2

description: Library name: t13


title: Ctrl_11, Female

description:
Library name: Sample11
Column name  in Raw_Gene_Level_Counts.csv: Sample11


title: Ctrl_1, Female

description:
Library name: Sample1
Column name  in Raw_Gene_Level_Counts.csv: Sample1


title: MuSC_iEzh2KO_quiescent_1

description: Library name: s15


title: MuSC_Ctrl_quiescent_3

description: Library name: t04


title: MuSC_Ctrl_quiescent_2

description: Library name: s13


title: Liver, Hoip_fl/fl.AdipoQ.Cre_negative, 16 weeks CD 14%, biol rep 5

city: Stuttgart

first: Nieves

last: Peltzer

address: Allmandring 31

department: Institute of Biomedical Genetics

country: Germany

institute: Universität Stuttgart

description:
Library name: XH336
X222766

data_processing:
The dataset was processed using the nextflow rnaseq pipeline (version 3.13.2) using default options
The reads were mapped to the mouse genome (NCBI RefSeq assembly GCF_000001635.27)
The count data was analyzed using the Bioconductor package DESeq2 (version 1.46.0) in R (version 4.4.2) and normalized using the size factors derived from the median of ratios.
Two different negative binomial generalized linear models were used for differential gene expression analysis: ~ genotype + diet for estimation of diet or genotype effect and ~ “genotype_diet” for between group comparisons. Log2FoldChanges and p-values were obtained using a Wald test with Benjamini-Hochberg correction for multiple testing
Assembly: GRCm39
Supplementary files format and content: csv file denoting the raw counts for each sample
Supplementary files format and content: csv file denoting the raw counts scaled by gene length
Supplementary files format and content: csv file outputting the result of the differential expression analysis for the comparison of genotypes
Supplementary files format and content: csv file outputting the result of the differential expression analysis for the comparison of diets
Supplementary files format and content: csv file providing the normalized counts obtained from DESeq using the median of ratios. The raw counts scaled by gene length were used for this normalization

source_name: liver

growth_protocol: Hoip A-KO mice where generated using Hoip (Rnf31) flox flox line and crossed with Adiponectin Cre (AdipoQ.Cre) to generate mature adipocyte Hoip deletion

extract_protocol:
At 16 weeks of diet, livers were collected, snap frozen in liquid nitrogen, and kept at -80 degrees until RNA extraction. The liver samples were processed according to the manufacturer's instructions using the RNeasy Midi kit (Qiagen, 75142). For tissue disruption 100 mg of liver were resuspended in 2 ml of lysis buffer RLT plus with β-mercaptoethanol (10 ul β-ME were added to every 1 ml RLT buffer) samples were homogenised in TissueLyser II using a 5 mm bead in two rounds for 2 minutes at 30 1/s. For both tissues a DNase digest kit was employed, involving the addition of 350 µl of Buffer RW1 to the RNeasy Mini spin column, followed by the addition of DNase I. The resulting RNA was evaluated for purity and concentration using a Nanodrop spectrophotometer from TECAN Reader
For RNA sequencing, we used 2 μg of total RNA per sample concentration range 50-200 ng/µL, at least 10µL volume, checking the quality by RIN > 7, OD260/280 = 1,8-2,1 and OD260/230 >1,5. mRNA libraries were prepared by mRNA Seq (Poly A+ selection) using ERCC RNA Spike-In controls. Libraries were prepared using the Illumina® Stranded TruSeq® RNA sample preparation kit. ERCC RNA Spike-In Mix (Thermo Fischer) was added to the samples before library preparation. Library preparation started with 1000 ng total RNA. After poly-A selection (using poly-T oligo-attached magnetic beads), mRNA was purified and fragmented using divalent cations under elevated temperature. The RNA fragments underwent reverse transcription using random primers. This was followed by second strand cDNA synthesis with DNA Polymerase I and RNase H. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified (15 cycles) to create the final cDNA libraries. After library validation and quantification (Agilent Tape Station), equimolar amounts of the library were pooled. The pool was quantified by using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System. The pool was sequenced on an Illumina NovaSeq6000 sequencing instrument with a PE100 protocol aiming for 40 million clusters per sample.

treatment_protocol: At 6 weeks of age mice start the diet with 14% fat (Control diet or CD) or 60% fat (High fat diet or HFD). Mice were fed for 16 weeks prior to tissue harvesting

value: liver

value: 16 weeks CD 14%

value: male

tag: age


title: MuSC_Ctrl_quiescent_1

description: Library name: s09


title: Liver, Hoip_fl/fl.AdipoQ.Cre_negative, 16 weeks CD 14%, biol rep 3

description:
Library name: XH330
X222762


title: Liver, Hoip_fl/fl.AdipoQ.Cre_positive, 16 weeks CD 14%, biol rep 4

description:
Library name: XH337
X222756


title: Liver, Hoip_fl/fl.AdipoQ.Cre_negative, 16 weeks CD 14%, biol rep 1

description:
Library name: XH327
X222758


title: Liver, Hoip_fl/fl.AdipoQ.Cre_negative, 16 weeks CD 14%, biol rep 2

description:
Library name: XH328
X222760


title: Liver, Hoip_fl/fl.AdipoQ.Cre_positive, 16 weeks CD 14%, biol rep 3

description:
Library name: XH333
X222754


title: Ctrl_9, Male

description:
Library name: Sample9
Column name  in Raw_Gene_Level_Counts.csv: Sample9


title: Liver, Hoip_fl/fl.AdipoQ.Cre_positive, 16 weeks CD 14%, biol rep 2

description:
Library name: XH332
X222752


title: Ctrl_7, Female

description:
Library name: Sample7
Column name  in Raw_Gene_Level_Counts.csv: Sample7


title: Liver, Hoip_fl/fl.AdipoQ.Cre_negative, 16 weeks HFD 60%, biol rep 3

description:
Library name: XH315
X222744

value: 16 weeks HFD 60%


title: Liver, Hoip_fl/fl.AdipoQ.Cre_positive, 16 weeks CD 14%, biol rep 1

description:
Library name: XH329
X222750


title: Liver, Hoip_fl/fl.AdipoQ.Cre_negative, 16 weeks HFD 60%, biol rep 4

description:
Library name: XH316
X222746


title: Liver, Hoip_fl/fl.AdipoQ.Cre_negative, 16 weeks HFD 60%, biol rep 2

description:
Library name: XH314
X222742


title: Liver, Hoip_fl/fl.AdipoQ.Cre_positive, 16 weeks HFD 60%, biol rep 4

description:
Library name: XH324
X222736


title: Liver, Hoip_fl/fl.AdipoQ.Cre_positive, 16 weeks HFD 60%, biol rep 2

description:
Library name: XH321
X222732


title: Liver, Hoip_fl/fl.AdipoQ.Cre_negative, 16 weeks HFD 60%, biol rep 1

description:
Library name: XH313
X222740


title: Liver, Hoip_fl/fl.AdipoQ.Cre_positive, 16 weeks HFD 60%, biol rep 3

description:
Library name: XH323
X222734


title: Liver, Hoip_fl/fl.AdipoQ.Cre_positive, 16 weeks HFD 60%, biol rep 5

description:
Library name: XH325
X222738


title: ATAC-C-1

first: Chenliang

last: Wang

address: Medical Science Building, Room D307, Tsinghua University

description: Library name: ATAC-C1

data_processing:
Hisat2 tools soft were used to map with reference genome.
Bulk RNAseq: Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample.
Bulk RNAseq: RNA-SeQC 2 was used for assessing sequencing depth and mapping quality.
ATACseq: Reference genome and gene annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA(v 0.7.12) and clean reads were aligned to the reference genome using BWA mem.
ATACseq: All peak calling was performed with MACS2 (v 2.2.7.1) using ‘macs2 -q 0.05 --call-summits -- nomodel --shift -100 --extsize 200 --keep-dup all’. By default, peaks with q-value threshold of 0.05 was used for all data sets.
Assembly: mm10
Supplementary files format and content: RNAseq: FPKM values for each sample
Supplementary files format and content: ATACseq: Peak for each sample, narrowpeak format

source_name: Th17 cell

extract_protocol:
RNeasy Plus Micro Kit(Qiagen)
Bulk RNAseq: A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. ATACseq: ATAC-seq was performed as previously reported. Briefly, nucleus was extracted from samples, and the nucleus pellet was resuspended in the Tn5 transposase reaction mix.The transposition reaction was incubated at 37 ℃ for 30 min. Equimolar Adapter1 and Adatper 2 were added after transposition, PCR was then performed to amplify the library(ATAC-seq_Novogene Kit). After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit.

value: Th17 cell

value: CTRL


title: ATAC-C-2

description: Library name: ATAC-C2


title: Liver, Hoip_fl/fl.AdipoQ.Cre_negative, 16 weeks CD 14%, biol rep 4

description:
Library name: XH331
X222764


title: ATAC-IS-2

description: Library name: ATAC-IS2


title: ATAC-IS-1

description: Library name: ATAC-IS1


title: ATAC-IN-2

description: Library name: ATAC-IN2


title: C-2

description:
Library name: C2
bulk RNA-seq
CELL_All_gene_fpkm.txt


title: C-1

description:
Library name: C1
bulk RNA-seq
CELL_All_gene_fpkm.txt


title: IN-2

description:
Library name: IN2
bulk RNA-seq
CELL_All_gene_fpkm.txt


title: IN-1

description:
Library name: IN1
bulk RNA-seq
CELL_All_gene_fpkm.txt


title: IS-1

description:
Library name: IS1
bulk RNA-seq
CELL_All_gene_fpkm.txt


title: Skin-ABX-3

description:
Library name: ABX-3
bulk RNA-seq
SKIN_All_gene_fpkm.txt

source_name: skin

value: skin

value: ABX


title: MicroC_8C

description: Library name: MicroC_8C

data_processing:
*library strategy: Micro-C
Hi-C and Micro-C sequencing reads were mapped, processed and iteratively corrected using HiC-Pro. Micro-C reads were processed without considering the restriction enzyme fragment. Valid read pairs were then converted to Cool format and balanced using Cooler. Directionality index and insulation scores were calculated using balanced cool files at 10 kilobase (kb) resolution and 100–500 kb surroundings using Cooltools. To visualize the 2D interaction neighbourhood around cohesin islands and CTCF sites, all cis combinations between GCI genes and CTCF sites located within a defined range (>50 kb and <500 kb) were generated using BEDtools. The pile-up matrix was generated using Coolpuppy on cool files with 5 kb or 10 kb resolution.
Assembly: mm9
Supplementary files format and content: Balanced mcool files generated by cooler and cooltools based on validpairs

value: WT


title: Skin-WAT-3

description:
Library name: WAT-3
bulk RNA-seq
SKIN_All_gene_fpkm.txt

value: WAT


title: Skin-ABX-1

description:
Library name: ABX-1
bulk RNA-seq
SKIN_All_gene_fpkm.txt


title: Skin-WAT-1

description:
Library name: WAT-1
bulk RNA-seq
SKIN_All_gene_fpkm.txt


title: Skin-WAT-2

description:
Library name: WAT-2
bulk RNA-seq
SKIN_All_gene_fpkm.txt


title: Liver, Hoip_fl/fl.AdipoQ.Cre_negative, 16 weeks HFD 60%, biol rep 5

description:
Library name: XH317
X222748


title: Liver, Hoip_fl/fl.AdipoQ.Cre_positive, 16 weeks HFD 60%, biol rep 1

description:
Library name: XH319
X222729


title: IS-2

description:
Library name: IS2
bulk RNA-seq
CELL_All_gene_fpkm.txt


title: E16.5 thoracic spinal cord, replicate 4, chromium reaction 1 of 2

first: Brian

last: Roome

address: 35 Convent Drive

department: NINDS

institute: National Institutes of Health

description: Library name: 16TG

library_source: transcriptomic single cell

data_processing:
Cellranger versions 6 and 7 - mkfastq and count
Assembly: GRCm39
Supplementary files format and content: All samples are made available in MEX format (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) as outputs from Cellranger Count
Supplementary files format and content: Fully processed data are available as an integrated Seurat v4 object with annotations metadata (.RDS file)

source_name: E16.5 thoracic spinal cord

growth_protocol: A breeding pair of mice was set to mate for one overnight period, and were separated the following morning. Embryos were extracted from pregnant female mice either 14 or 16 days post-mating.

extract_protocol:
Female wild-type mice with a pregnancy dated to embryonic day E14.5 or E16.5 were used. Each experimental replicate consisted of a pooled litter of 3-10 spinal cords taken from embryos of one single pregnant female. The expediency of the experiment did not allow sex-typing of embryos prior to pooling and, as such, all biological replicates are a mix of sexes.
Embryos were rapidly dissected and immersed in cold 1X PBS. Spinal cords were sequentially dissected as described above and placed in cold dissection medium (50 ml HBSS-calcium/magnesium-free with phenol red (Gibco) + 750 µl HEPES (1M, Gibco)). When possible, extra care was taken to remove meninges and dorsal root ganglia from the isolated cord. From here, appropriate spinal cord segments were dissected from the cord, and then cut into fine pieces with dissecting spring scissors. Either cervical, thoracic or lumbosacral cords were isolated based on the experimental group. In either case, care was taken not to include transitional zones of the cord (e.g. where cervical tapers into thoracic or where thoracic begins to enlarge to lumbar); due to this, these regions are likely underrepresented in our data.
Pooled spinal cord tissues were then added to a 15 ml conical tube containing dissociation medium (100 units Papain (Worthington), 4.75 ml HBSS+CM (calcium and magnesium; Gibco), and 250 µl of DNAse (Worthington, 1000 units resuspended in 500 µl of HBSS+CM)). The tube was gently inverted several times every 5 minutes while leaving the tube to incubate at 37 °C between inversions. After 20 minutes, the suspension was triturated gently with a series of three fire-polished glass pipettes (Fisher Scientific) with progressively finer bores. Suspensions are then centrifuged for 8 minutes at 850 rpm; after this, the supernatant was removed and the cells were gently resuspended with a solution of 4.5 ml HBSS+CM, 600 µl ovomucoid protease inhibitor solution (Worthington, resuspended in 30 ml HBSS+CM), and 250 µl DNAse (as above). Debris is allowed to settle for 10 minutes, at which point the supernatant with suspended cells was added to a second 15 ml conical tube containing neutralizing solution (10 ml HBSS+CM + 100 mg Trypsin inhibitor (Sigma) + 100 mg bovine serum albumin (Sigma)). This suspension was centrifuged once more for 8 minutes at 850 rpm, and the supernatant was removed. The remaining cells were resuspended in approximately 1 ml of 1X PBS containing 5 µl of molecular-grade BSA (New England Biolabs) and 2 ul of RNAse-inhibitor (Biosearch Technologies). Cell concentration in this suspension was assessed using a standard hemacytometer (a 50:50 sample of cell suspension + Trypan blue). The cell suspension was diluted with the same resuspension medium until the final concentration was appropriate for loading into the 10X Genomics Chromium chip.
Produced based on manufacturer's instructions (10X Chromium 3' gene expression user guide; CG000204 Rev D)

treatment_protocol: The only experimental variable was the time of harvest (E14.5 or E16.5); no treatment otherwise occurred.

value: thoracic spinal cord

value: All cells

value: wild-type


title: E16.5 thoracic spinal cord, replicate 3, chromium reaction 2 of 2

description: Library name: 16TF


title: ATAC-IN-1

description: Library name: ATAC-IN1


title: E16.5 thoracic spinal cord, replicate 3, chromium reaction 1 of 2

description: Library name: 16TE


title: E16.5 thoracic spinal cord, replicate 2, chromium reaction 2 of 2

description: Library name: 16TD


title: E16.5 thoracic spinal cord, replicate 4, chromium reaction 2 of 2

description: Library name: 16TH


title: E16.5 thoracic spinal cord, replicate 1, chromium reaction 2 of 2

description: Library name: 16TB


title: E16.5 thoracic spinal cord, replicate 2, chromium reaction 1 of 2

description: Library name: 16TC


title: E16.5 thoracic spinal cord, replicate 1, chromium reaction 1 of 2

description: Library name: 16TA


title: E16.5 lumbosacral spinal cord, replicate 4, chromium reaction 2 of 2

description: Library name: 16LH

source_name: E16.5 lumbosacral spinal cord

value: lumbosacral spinal cord


title: E16.5 lumbosacral spinal cord, replicate 3, chromium reaction 1 of 2

description: Library name: 16LE


title: E16.5 lumbosacral spinal cord, replicate 3, chromium reaction 2 of 2

description: Library name: 16LF


title: E16.5 lumbosacral spinal cord, replicate 2, chromium reaction 2 of 2

description: Library name: 16LD


title: E16.5 lumbosacral spinal cord, replicate 4, chromium reaction 1 of 2

description: Library name: 16LG


title: E16.5 lumbosacral spinal cord, replicate 1, chromium reaction 2 of 2

description: Library name: 16LB


title: E16.5 lumbosacral spinal cord, replicate 2, chromium reaction 1 of 2

description: Library name: 16LC


title: E16.5 cervical spinal cord, replicate 4, chromium reaction 2 of 2

description: Library name: 16H

source_name: E16.5 cervical spinal cord

value: cervical spinal cord


title: E16.5 lumbosacral spinal cord, replicate 1, chromium reaction 1 of 2

description: Library name: 16LA


title: E16.5 cervical spinal cord, replicate 3, chromium reaction 2 of 2

description: Library name: 16F


title: Skin-ABX-2

description:
Library name: ABX-2
bulk RNA-seq
SKIN_All_gene_fpkm.txt


title: E16.5 cervical spinal cord, replicate 2, chromium reaction 2 of 2

description: Library name: 16D


title: E16.5 cervical spinal cord, replicate 4, chromium reaction 1 of 2

description: Library name: 16G


title: E16.5 cervical spinal cord, replicate 2, chromium reaction 1 of 2

description: Library name: 16C


title: E16.5 cervical spinal cord, replicate 1, chromium reaction 1 of 2

description: Library name: 16A


title: E14.5 cervical spinal cord, replicate 2, chromium reaction 2 of 2

description: Library name: 14D

source_name: E14.5 cervical spinal cord


title: E14.5 cervical spinal cord, replicate 3, chromium reaction 2 of 2

description: Library name: 14F


title: E14.5 cervical spinal cord, replicate 2, chromium reaction 1 of 2

description: Library name: 14C


title: E14.5 cervical spinal cord, replicate 3, chromium reaction 1 of 2

description: Library name: 14E


title: E14.5 cervical spinal cord, replicate 1, chromium reaction 1 of 2

description: Library name: 14A


title: Mouse, kidney, male, Y665F HET, IRI, rep 2

first: Jakub

last: Jankowski

address: 8 Center DR.

department: NIDDK

institute: NIH

description: Library name: IRI Y665F HET M 2

data_processing:
First, respective samlpe reads from two lanes were concatenated.
Next, samples were processed with trimmomatic (Bolger et al., Bioinformatics, 2014) in order to filter low quality reads
subsequently, samples were aligned to the reference genome mm10 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013).
Finally, HTSeq (Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
Assembly: mm10
Supplementary files format and content: .tabular files with raw read counts

source_name: Kidney

extract_protocol:
Total RNA was isolated from whole mouse kidneys using PureLink™ RNA Mini Kit (Invitrogen).
Libraries for sequencing were prepared according to the manufacturer’s instructions with TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina, RS-122-2301).Libraries were sequenced using Illumina NovaSeq 6000 using standard protocols.

value: Kidney

value: Stat5b Y665F HET


title: Mouse, kidney, male, WT, IRI, rep 3

description: Library name: IRI Y665F WT M 3

value: Stat5b Y665F WT


title: Mouse, kidney, male, WT, IRI, rep 2

description: Library name: IRI Y665F WT M 2


title: Mouse, kidney, male, WT, IRI, rep 4

description: Library name: IRI Y665F WT M 4


title: Mouse, kidney, male, Y665F HET, IRI, rep 3

description: Library name: IRI Y665F HET M 3


title: Mouse, kidney, male, WT, IRI, rep 1

description: Library name: IRI Y665F WT M 1


title: Mouse, kidney, female, Y665F HET, IRI, rep 4

description: Library name: IRI Y665F HET F 4

value: female


title: Mouse, kidney, female, Y665F HET, IRI, rep 3

description: Library name: IRI Y665F HET F 3


title: E16.5 cervical spinal cord, replicate 3, chromium reaction 1 of 2

description: Library name: 16E


title: Mouse, kidney, female, WT, IRI, rep 1

description: Library name: IRI Y665F WT F 1


title: Mouse, kidney, female, Y665F HET, IRI, rep 2

description: Library name: IRI Y665F HET F 2


title: Mouse, kidney, female, WT, IRI, rep 3

description: Library name: IRI Y665F WT F 3


title: Mouse, kidney, female, WT, IRI, rep 4

description: Library name: IRI Y665F WT F 4


title: Mouse, kidney, female, WT, IRI, rep 2

description: Library name: IRI Y665F WT F 2


title: Mouse, kidney, female, Y665F HET, IRI, rep 1

description: Library name: IRI Y665F HET F 1


title: Mouse, kidney, male, Y665F HET, rep 1

description: Library name: Y665F HET M 1

value: male


title: Mouse, kidney, male, WT, rep 2

description: Library name: Y665F WT M 2


title: Mouse, kidney, male, Y665F HET, rep 4

description: Library name: Y665F HET M 4


title: Mouse, kidney, male, Y665F HET, rep 3

description: Library name: Y665F HET M 3


title: E14.5 cervical spinal cord, replicate 1, chromium reaction 2 of 2

description: Library name: 14B


title: Mouse, kidney, male, Y665F HET, rep 2

description: Library name: Y665F HET M 2


title: Mouse, kidney, male, WT, rep 1

description: Library name: Y665F WT M 1


title: Mouse, kidney, male, Y665F HET, IRI, rep 4

description: Library name: IRI Y665F HET M 4


title: Mouse, kidney, female, Y665F HET, rep 4

description: Library name: Y665F HET F 4


title: Mouse, kidney, male, Y665F HET, IRI, rep 1

description: Library name: IRI Y665F HET M 1


title: Mouse, kidney, female, Y665F HET, rep 2

description: Library name: Y665F HET F 2


title: Mouse, kidney, female, Y665F HET, rep 3

description: Library name: Y665F HET F 3


title: Mouse, kidney, female, Y665F HET, rep 1

description: Library name: Y665F HET F 1


title: Mouse, kidney, female, WT, rep 3

description: Library name: Y665F WT F 3


title: DRG_control_rep3

city: St Louis

first: Mikhail

last: Berezin

state: Missouri

address: 4515 McKinley  Ave

institute: Washington University in St. Louis

description:
Library name: drg_m3_control.AGGAACAGCA-ATAACCGGCA
DRG_control_rep3

data_processing:
RNA-seq reads were aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a
Aligned reads were imported to Partek Flow software for downstream analysis
Genes were filtered based on: maximum reads across all samples < 100
DEGs were identified with DESeq2 package implemented in Partek Flow
Assembly: Ensembl release 76
Supplementary files format and content: tab-delimited text file includes raw gene counts for each sample

source_name: Dorsal Root Ganglia (DRG)

growth_protocol: DRG were stored in RNALater (Thermofisher) in 4 degree overnight and transferred to -20 degree until RNA extraction

extract_protocol:
RNA was extracted with the magnetic bead based MaxwellRSC 48 instrument using the Maxwell RSC simply RNA Tissue kit
Library was prepared according to manufacturer’s protocol with Clontech SMARTer method kit

value: Dorsal Root Ganglia (DRG)

tag: strain

value: vehicle


title: DRG_control_rep4

description:
Library name: drg_m4_control.CGTAGATCGC-ATACGTCTCT
DRG_control_rep4


title: Mouse, kidney, female, WT, rep 4

description: Library name: Y665F WT F 4


title: Mouse, kidney, female, WT, rep 2

description: Library name: Y665F WT F 2


title: DRG_control_rep2

description:
Library name: drg_m2_control.AAGCTTCGAG-GATGTCATGC
DRG_control_rep2


title: Mouse, kidney, female, WT, rep 1

description: Library name: Y665F WT F 1


title: DRG_control_rep5

description:
Library name: drg_m5_control.AACCATACCG-CTTCTGTGCG
DRG_control_rep5


title: Mouse, kidney, male, WT, rep 3

description: Library name: Y665F WT M 3


title: DRG_10mg_rep5

description:
Library name: drg_m5_10mg.TCCTACGTGC-GCATTCTCGC
DRG_10mg_rep5

value: 10mg/kg oxaliplatin


title: DRG_10mg_rep4

description:
Library name: drg_m4_10mg.AGCCAAGGAC-AGGTGTCCTC
DRG_10mg_rep4


title: DRG_10mg_rep2

description:
Library name: drg_m2_10mg.CAGACGATGA-GCATGCTGGA
DRG_10mg_rep2


title: DRG_10mg_rep3

description:
Library name: drg_m3_10mg.TCGTGATCAG-ACACTACGTA
DRG_10mg_rep3


title: CD8_T_cells_ZEA_2h_KAS-seq.rep2

city: Chicago

first: Ruitu

last: Lyu

state: IL

address: 929 E 57th Street

department: Chemistry

institute: The University of Chicago

description: Library name: Sample 7

data_processing:
We used the Trim Galore package to trim low-quality sequences, adapter sequences, and primer sequences from single-end or paired-end KAS-seq raw FASTQ files. Reads shorter than 30 bp were discarded.
The remaining reads were aligned to the reference genome (mm10) using Bowtie2 (v2.3.3.1) under default parameters. The resulting SAM files were converted and sorted into BAM files using SAMtools sort (v1.9).
Duplicate reads were removed using Picard MarkDuplicates (v1.141). Uniquely mapped reads were extended to 150 bp to match the average length of DNA fragments, using the awk command. The extended data, in BED file format, were converted to BedGraph files using bedtools genomecov and subsequently transformed into BigWig files using bedGraphToBigWig.
Shell scripts for processing KAS-seq data are available on GitHub (https://github.com/Ruitulyu/KAS-Analyzer). MACS2 was used for peak calling to identify broad KAS-seq peaks.
Assembly: mm10
Supplementary files format and content: bigWig, KAS-seq reads density
Supplementary files format and content: bed, KAS-seq peak lists

source_name: T cells

growth_protocol: Primary murine CD8+ T cells were isolated from the spleens of 8-week-old female C57BL/6 mice using the EasySep™ Mouse Naïve CD8+ T Cell Isolation Kit (STEMCELL Technologies, 19858).

extract_protocol:
Cells were lysed using a lysis buffer containing 0.1% NP40, 0.1% Tween-20, 0.01% Digitonin, 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, and 3 mM MgCl2, and incubated on ice for 3 minutes. The lysed cell pellets were resuspended in 100 µL of 10 mM N3-Kethoxial in PBS and incubated at 37℃ with shaking at 500 rpm for 10 minutes. Cells were then collected for genomic DNA (gDNA) purification using the PureLink Genomic DNA Mini Kit (Invitrogen).
DNA was eluted from the beads by heating in 15 µL of H2O at 95℃ for 10 minutes. Library preparation was performed using the xGen Methyl-Seq DNA Library Prep Kit (IDT), and the final libraries were sequenced on the Illumina NovaSeq 6000 platform.

treatment_protocol: A total of 10,000,000 primary Naïve CD8+ T cells were activated overnight with aCD3/CD28 antibodies, followed by treatment with 5 µM ZEA for 40 minutes or 2 hours. DMSO-treated cells served as controls. Each condition included three biological replicates.

value: T cells

value: Zeaxanthin

tag: time


title: CD8_T_cells_ZEA_2h_KAS-seq.rep1

description: Library name: Sample 6


title: DRG_control_rep1

description:
Library name: drg_m1_control.CACACTGTTG-ATTCCACACT
DRG_control_rep1


title: CD8_T_cells_ZEA_40min_KAS-seq.rep3

description: Library name: Sample 5


title: CD8_T_cells_ZEA_40min_KAS-seq.rep2

description: Library name: Sample 4


title: scRNAseq FAPs & MuSC coculture, KO 2

description: 10x Genomics

data_processing:
The 10x Genomics Cell Ranger v7.0.0 analysis pipeline was used to generate FASTQ files and count matrices using default parameters with the 10x Genomics mm10 reference.
Assembly: mm10-2020-A
Supplementary files format and content: 10x Genomics Cell Ranger Output Files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

extract_protocol:
Freshly isolated cells were diluted to obtained a stock concentration of 1000 cells/ul. Cells were loaded into a Chromium Next GEM Chip G to generate a Gel Beads-in-emulsion (GEMs).
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 . The final libraries were diluted to 3 nM and sequenced on an Illumina NovaSeq6000 using the following read length: 28bp for Read1, 8 bp for I7 Index, and 91 bp for Read2.
10x Single Cell Genomics

treatment_protocol: TA muscles of Pax7creER and iEzh2-/-;PDGFRaEGFP  mice were injured with Notexin and FACS-sorted  7 days after injury.

value: Mouse muscle

value: FAPs & MuSC

value: iEzh2-/- + PDGFRalphaEGFP

value: 7 days post Notexin muscle injury


title: scRNAseq FAPs & MuSC coculture, Ctrl 4

description: 10x Genomics

value: Pax7creER + PDGFRalphaEGFP


title: scRNAseq FAPs & MuSC coculture, KO 3

description: 10x Genomics


title: CD8_T_cells_control_KAS-seq.rep1

description: Library name: Sample 1

value: DMSO

value: control


title: CD8_T_cells_control_KAS-seq.rep2

description: Library name: Sample 2


title: scRNAseq FAPs & MuSC coculture, Ctrl 3

description: 10x Genomics


title: scRNAseq FAPs 7 DPI, KO 1

description: 10x Genomics

value: FAPs


title: scRNAseq FAPs 7 DPI,  KO 2

description: 10x Genomics


title: scRNAseq FAPs 7 DPI, Ctrl 2

description: 10x Genomics


title: FAP_iEzh2KO_7dpi_1

description:
s09
210930_220217_combined_giulia_rna-seq_gene_rpkm.xlsx
210930_220217_combined_giulia_rna-seq_gene_FAP_ANOVA_3-25-22.xlsx

treatment_protocol: TA muscles of Pax7creER and iEzh2-/- mice were injured with Notexin and FACS-isolated at 3 and 7 dpi. RNA was extracted and samples were processed for library preparation.


title: scRNAseq FAPs 7 DPI, Ctrl 1

description: 10x Genomics


title: scRNAseq FAPs & MuSC coculture, Ctrl 2

description: 10x Genomics


title: FAP_iEzh2KO_7dpi_2

description:
s10
210930_220217_combined_giulia_rna-seq_gene_rpkm.xlsx
210930_220217_combined_giulia_rna-seq_gene_FAP_ANOVA_3-25-22.xlsx


title: MuSC_iEzh2KO_7dpi_3

description:
s06
210930_220217_combined_giulia_rna-seq_gene_rpkm.xlsx
210930_220217_combined_giulia_rna-seq_gene_SC_ANOVA_3-25-22.xlsx

value: MuSCs


title: DRG_10mg_rep1

description:
Library name: drg_m1_10mg.CGCAGGAGTA-GCGACCTTGA
DRG_10mg_rep1


title: MuSC_iEzh2KO_7dpi_2

description:
s05
210930_220217_combined_giulia_rna-seq_gene_rpkm.xlsx
210930_220217_combined_giulia_rna-seq_gene_SC_ANOVA_3-25-22.xlsx


title: FAP_Ctrl_7dpi_2

description:
s08
210930_220217_combined_giulia_rna-seq_gene_rpkm.xlsx
210930_220217_combined_giulia_rna-seq_gene_FAP_ANOVA_3-25-22.xlsx


title: MuSC_Ctrl_7dpi_2

description:
s02
210930_220217_combined_giulia_rna-seq_gene_rpkm.xlsx
210930_220217_combined_giulia_rna-seq_gene_SC_ANOVA_3-25-22.xlsx


title: MuSC_iEzh2KO_7dpi_1

description:
s04
210930_220217_combined_giulia_rna-seq_gene_rpkm.xlsx
210930_220217_combined_giulia_rna-seq_gene_SC_ANOVA_3-25-22.xlsx


title: FAP_iEzh2KO_3dpi_3

description:
s20_R1
210503_210514_giulia_rna-seq_results.gene.rpkm.tx.xlsx
210503_210514_giulia_rna-seq_results.gene.FAP.ANOVA.xlsx

value: 3 days post Notexin muscle injury


title: FAP_iEzh2KO_3dpi_1

description:
s16_R1
210503_210514_giulia_rna-seq_results.gene.rpkm.tx.xlsx
210503_210514_giulia_rna-seq_results.gene.FAP.ANOVA.xlsx


title: MuSC_Ctrl_7dpi_3

description:
s03
210930_220217_combined_giulia_rna-seq_gene_rpkm.xlsx
210930_220217_combined_giulia_rna-seq_gene_SC_ANOVA_3-25-22.xlsx


title: MuSC_Ctrl_7dpi_1

description:
s01
210930_220217_combined_giulia_rna-seq_gene_rpkm.xlsx
210930_220217_combined_giulia_rna-seq_gene_SC_ANOVA_3-25-22.xlsx


title: CD8_T_cells_ZEA_40min_KAS-seq.rep1

description: Library name: Sample 3


title: FAP_Ctrl_3dpi_2

description:
s10_R1
210503_210514_giulia_rna-seq_results.gene.rpkm.tx.xlsx
210503_210514_giulia_rna-seq_results.gene.FAP.ANOVA.xlsx


title: MuSC_iEzh2KO_3dpi_1

description:
s15_R1
210503_210514_giulia_rna-seq_results.gene.rpkm.tx.xlsx
210503_210514_giulia_rna-seq_results.gene.SC.ANOVA.xlsx


title: MuSC_iEzh2KO_3dpi_2

description:
s19_R1
210503_210514_giulia_rna-seq_results.gene.rpkm.tx.xlsx
210503_210514_giulia_rna-seq_results.gene.SC.ANOVA.xlsx


title: FAP_iEzh2KO_3dpi_4

description:
s22_R1
210503_210514_giulia_rna-seq_results.gene.rpkm.tx.xlsx
210503_210514_giulia_rna-seq_results.gene.FAP.ANOVA.xlsx


title: FAP_Ctrl_3dpi_3

description:
s12_R1
210503_210514_giulia_rna-seq_results.gene.rpkm.tx.xlsx
210503_210514_giulia_rna-seq_results.gene.FAP.ANOVA.xlsx


title: FAP_Ctrl_3dpi_1

description:
s08_R1
210503_210514_giulia_rna-seq_results.gene.rpkm.tx.xlsx
210503_210514_giulia_rna-seq_results.gene.FAP.ANOVA.xlsx


title: FAP_Ctrl_3dpi_4

description:
s14_R1
210503_210514_giulia_rna-seq_results.gene.rpkm.tx.xlsx
210503_210514_giulia_rna-seq_results.gene.FAP.ANOVA.xlsx


title: MuSC_Ctrl_3dpi_3

description:
s11_R1
210503_210514_giulia_rna-seq_results.gene.rpkm.tx.xlsx
210503_210514_giulia_rna-seq_results.gene.SC.ANOVA.xlsx


title: MuSC_iEzh2KO_3dpi_3

description:
s21_R1
210503_210514_giulia_rna-seq_results.gene.rpkm.tx.xlsx
210503_210514_giulia_rna-seq_results.gene.SC.ANOVA.xlsx


title: Mouse, kidney, male, WT, rep 4

description: Library name: Y665F WT M 4

value: Kidney

value: Stat5b Y665F WT


title: FAP_Ctrl_7dpi_1

description:
s07
210930_220217_combined_giulia_rna-seq_gene_rpkm.xlsx
210930_220217_combined_giulia_rna-seq_gene_FAP_ANOVA_3-25-22.xlsx


title: SQ24007030-ZW2

city: Shanghai

first: Ziwen

last: Song

address: No. 100, Haike Road, Pudong New Area, Shanghai

institute: Chinese Academy of Sciences

data_processing:
Sequencing reads were mapped to the reference genome mm10 (GRCm38) or mm39 (GRCm39) from Gencode with hisat2 by default parameter.
The read counts for each gene were calculated by featureCounts58.
The count files were used as input to R package DESeq2 (v1.42.1) or EdgeR (v4.0.16) for normalization.
The count files were used as input to R package DESeq2 (v1.42.1) or EdgeR (v4.0.16) for differential expression genes.
The count files were used as input to R package DESeq2 (v1.42.1) for forming heatmap.
Assembly: GRCm38
Supplementary files format and content: Comma-delimited text files include read counts for each Sample.
Supplementary files format and content: Comma-delimited text files include RPKM values for each Sample.

source_name: hippocampus

growth_protocol: Two groups of transgenic mice (Ripk1D138N/D138N, Zbp1-/-) each had their own WT mice sharing the same ancestor. All animals were maintained in a specific pathogen-free environment, and animal experiments were conducted according to the protocols approved by the Standing Animal Care Committee at the Interdisciplinary Research Center on Biology and Chemistry.

extract_protocol:
Total RNA or IP RNA was extracted and purified using RNAiso Plus (TaKaRa).
RNA libraries were prepared according to instructions of Abclonal Fast RNA-seq Lib Prep Kit V2 (RK20306).

treatment_protocol: Mice aged 9 months after behavior tests were sacrificed for RNA-seq.

value: hippocampus


title: input_WT_ZBP1

value: WT

tag: antibody


title: SQ24007030-ZF3

value: Zbp1-/-, 5xFAD


title: IP_FAD_ZBP1

value: WT, 5xFAD


title: input_FAD_ZBP1


title: MuSC_Ctrl_3dpi_4

description:
s13_R1
210503_210514_giulia_rna-seq_results.gene.rpkm.tx.xlsx
210503_210514_giulia_rna-seq_results.gene.SC.ANOVA.xlsx


title: FAP_iEzh2KO_3dpi_2

description:
s18_R1
210503_210514_giulia_rna-seq_results.gene.rpkm.tx.xlsx
210503_210514_giulia_rna-seq_results.gene.FAP.ANOVA.xlsx


title: SQ24007030-ZW3


title: MuSC_Ctrl_3dpi_2

description:
s09_R1
210503_210514_giulia_rna-seq_results.gene.rpkm.tx.xlsx
210503_210514_giulia_rna-seq_results.gene.SC.ANOVA.xlsx


title: SQ24007030-ZF1


title: SQ24007030-WT1


title: SQ24007030-ZW1


title: SQ24007030-WT2


title: SQ24007030-ZF2


title: JZ24113084-WT3


title: JZ24113084-WT1


title: MuSC_Ctrl_3dpi_1

description:
s07_R1
210503_210514_giulia_rna-seq_results.gene.rpkm.tx.xlsx
210503_210514_giulia_rna-seq_results.gene.SC.ANOVA.xlsx


title: SQ24007030-WF2


title: JZ24113084-WF3


title: JZ24113084-DNF3

value: Ripk1D138N/D138N, 5xFAD


title: JZ24113084-DNF1


title: JZ24113084-WF2


title: IP_WT_ZBP1


title: JZ24113084-WF1


title: JZ24113084-DN3


title: SQ24007030-WT3


title: JZ24113084-DN2


title: JZ24113084-DNF2


title: SQ24007030-WF1


title: Mock Rep 3

city: Ann Arbor

first: Michael

middle: J

last: McFadden

state: Michigan

address: 6751 Medical Science II, 1137 Catherine Street

department: Microbiology & Immunology

institute: University of Michigan

description: 150 bp reads

data_processing:
RNA-seq reads were evaluated using FastQC
Quality reads were trimmed using cutadapt
Trimmed transcripts were aligned to the GRCm38 mouse genome and quantified using salmon alignment software
Differential gene expression analysis was performed using DESeq2
Assembly: GRCm38
Supplementary files format and content: comma separated values file with raw counts from each sample

source_name: Bone marrow

growth_protocol: Immortalized bone marrow-derived macrophage cell lines were grown in bone marrow media (BMM), containing modification of Eagle’s medium (DMEM; Thermo Fisher Scientific) supplemented with 20% fetal bovine serum (Thermo Fisher Scientific), 30% L929 conditioned media, and 1 mM sodium pyruvate (Thermo Fisher Scientific).

extract_protocol:
RNA was extracted using TRIzol (manufacturer protocol), followed by TURBO Dnase I treatment for 1 hour at 37C, and an additional TRIzol extraction
PolyA enrichment was performed and sequencing libraries were prepared and sequenced on an Illumina NovaSeq 6000 with 150 bp paired-end reads by Novogene.

treatment_protocol: Immortalized bone marrow-derived macrophages were seeded in 6-well plates overnight in bone marrow media

value: Bone marrow

tag: cell line

value: Macrophages

value: Mock


title: Ca Rep 3

description: 150 bp reads

value: Immortalized bone marrow-derived macrophages

value: C. albicans


title: SQ24007030-WF3


title: JZ24113084-DN1


title: Pb_300ppm-1

city: Seoul

first: Yeonghoon

last: Son

address: 75, Nowon-ro

country: South Korea

institute: Korea Institute of Radiological & Medical Sciences (KIRAMS)

data_processing:
Illumina GATK software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastp), then mapped to GRCm39 whole genome using STAR
Calculation mapped reads using salmon
CPM + TMM calculation using conorm
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: striatum

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

value: striatum

value: male

value: 4 weeks after Pb exposure


title: Pb_300ppm-3


title: Pb_30ppm-3


title: Pb_300ppm-2


title: Pb_30ppm-2


title: Pb_30ppm-1


title: Mock Rep 2

description: 150 bp reads


title: Ca Rep 2

description: 150 bp reads


title: Ca Rep 1

description: 150 bp reads


title: Mock Rep 1

description: 150 bp reads


title: Pb_0ppm-3

value: sham


title: MI+Cur-2

first: YU

last: GUANYE

address: Yanchang Road No. 301

department: Cardiovascular Department

institute: Shanghai Tenth People's Hospital

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count .
Assembly: Bowtie2
Supplementary files format and content: Tab-separated values files and matrix files

source_name: heart

extract_protocol:
CD45+CD64+ macrophages within post-MI tissue were sorted out using FACS, and RNA of macrophages was extracted using the TRIzol reagent (15596018; Invitrogen) according to the manufacturer’s instructions. RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: heart

value: macrophages

value: myocardial infarction with curcumol treatement


title: Pb_0ppm-1


title: MI+Cur-1


title: MI-2

value: myocardial infarction


title: Pb_0ppm-2


title: MI+Cur-3

value: WT


title: Mouse,IL,Metformin3

city: seoul

first: jungho

last: nam

address: 50-1, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea

institute: yonsei univ

data_processing:
Paired-end sequencing reads were generated on the Illumina sequencing NovaSeq platform. Before starting the analysis, Trimmomatic v0.38 was used to remove adapter sequences and trim bases with poor base quality. The cleaned reads were aligned to the Mus musculus (mm10) using HISAT v2.1.0 (KIM et al, 2015), based on the HISAT and Bowtie2 implementations.
Aligned data (SAM file format) were sorted and indexed using SAMtools v 1.9. After alignment, the transcripts were assembled and quantified using StringTie v2.1.3b (Pertea, Mihaela, et al., 2015, 2016). Gene-level and Transcript-level quantification were calculated as raw read count, FPKM (Fragments Per Kilobase of transcript per Million mapped reads), and TPM (Transcripts Per Million).
Assembly: The reference genome sequence and gene annotation data were downloaded from the NCBI Genome assembly and NCBI RefSeq database respectively.

source_name: ileum

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen).
The libraries were quantified using KAPA Library Quantification kits for Illumina Sequencing platforms according to the qPCR Quantification Protocol Guide (KAPA BIOSYSTEMS, #KK4854) and qualified using the TapeStation D1000 ScreenTape (Agilent Technologies, # 5067-5582). Indexed libraries were then submitted to an Illumina NovaSeq (Illumina, Inc., San Diego, CA, USA), and the paired-end (2×100 bp) sequencing was performed by Macrogen Incorporated.

value: ileum

value: Metformin


title: Mouse,IL,vehicle1

value: Vehicle


title: Mouse,IL,vehicle2


title: Mouse,IL,Metformin2


title: Mouse,IL,Metformin1


title: aged_icm, scRNAseq

city: wuhan

first: ZHANGYI

middle: ZHANGYI

last: YU

state: hubei

address: donghu street

department: Frontier Science Center for Immunology and Metabolism

institute: wuhan university

description: 10x genomics

data_processing:
Raw sequencing data was initially filtered by Trimmomatic (version 0.36), with the discarding of low-quality reads and the trimming of reads contaminated with adaptor sequences.
Clean reads were mapped to the reference genome of mouse (mm10) using STRA software (version 2.5.3a) with default parameters.
The counting of reads mapped to the exon regions of each gene was carried out by featureCounts (Subread-1.5.1; Bioconductor).
Resulting BAM files were sorted and indexed using SAMtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file include FPKM values for each sample

extract_protocol:
RNA was harvested using TRIzol (Invitrogen, cat. NO15596026). 2ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Ribo-off rRNA Depletion Kit (Human/Mouse/Rat) (Catalog NO. MRZG12324, Illumina) and KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Hiseq X 10 sequencer (Illumina) with PE150 model.

value: primary cell

value: cardiac fibroblast

value: 24 months old

value: MGT


title: Mouse,IL,vehicle3


title: neo_icm, scRNAseq

description: 10x genomics


title: Neo CFs, OENr4a3 RNA replicate 2, Day10

value: Primary cell


title: Neo CFs, OENr4a3 RNA replicate 1, Day10


title: Adult CFs, MGT+shNr4a3 RNA replicate 1, Day7

value: 3 months old


title: Adult CFs, MGT+shNT RNA replicate 2, Day7

value: MGT+shNT


title: Neo CFs, OECtrl RNA replicate 2, Day10

value: OE-Ctrl


title: Neo CFs, OECtrl RNA replicate 1, Day10


title: MGT_Aged_1_RNA_replicate 1, MGT, Day3

value: 18 months old


title: MGT_Aged_2_RNA_replicate 1, MGT, Day3

value: heart


title: MI-1

value: macrophages


title: MGT_Neo_2_RNA_replicate 1, MGT, Day3


title: MGT_Neo_1_RNA_replicate 1, MGT, Day3


title: MGT_Adult_1_RNA_replicate 1, MGT, Day3


title: LacZ_Aged_1_RNA_replicate 1, MGT, Day3

value: LacZ


title: LacZ_Aged_2_RNA_replicate 1, MGT, Day3


title: LacZ_Adult_2_RNA_replicate 1, MGT, Day3


title: LacZ_Adult_1_RNA_replicate 1, MGT, Day3


title: 24m_CFs_RNA_replicate 2

value: culture 3 days


title: LacZ_Neo_1_RNA_replicate 1, MGT, Day3

value: WT


title: Adult CFs, MGT+shNT RNA replicate 1, Day7


title: LacZ_Neo_2_RNA_replicate 1, MGT, Day3


title: 12m_CFs_RNA_replicate 2

value: 12 months old


title: neo_CFs_RNA_replicate 2


title: Adult CFs, MGT+shNr4a3 RNA replicate 2, Day7


title: Adult CF, shNr4a3_2, H3K27me3 CUT&Tag

data_processing:
The raw reads were subjected to adapter removal (Fastp version 0.20.1) and mapping mouse reference genome (mm10) using Bowtie2 (version 2.2.5) using –no-unal –no-mixed –no-discordant –local –very-sensitive-local –phred33 -I 10 -X 700 parameter.
Bigwig files were generated by bam Coverage function in deepTools (version 3.4.3) with default parameter settings.
Assembly: mm10
Supplementary files format and content: Bigwig

extract_protocol:
50000 cells were harvested, and the CUT&Tag assay was performed by SeqHealth (Wuhan Seqhealth Co., Ltd. China) using a commercial kit (TD903, Vazyme, China) according to the manufacturer’s protocol. The following primary antibodies were used: Rabbit anti-H3K27ac antibody (Abcam; ab4729), anti-H3K27me3 antibody (Active Motif; Catalog No: 39155). Hyperactive pG-Tn5 transposonase was then added to perform tagmentation. The reaction was terminated, and DNA fragments were extracted by PCI, followed by PCR amplification using indexed P5 and P7 primers.
cells were incubated with Rabbit anti-H3K27ac antibody (Abcam; ab4729) and anti-H3K27me3 antibody (Active Motif; Catalog No: 39155) for 2 h, and then 1 h with secondary antibody at room temperature. Hyperactive pG-Tn5 transposonase was then added to perform tagmentation. The reaction was terminated, and DNA fragments were extracted by PCI, followed by PCR amplification using indexed P5 and P7 primers. The library products were enriched, quantified and finally sequenced on a Novaseq 6000 sequencer (Illumina) with PE150 model.

value: H3K27me3 (Active Motif; Catalog No:39155)


title: 3m_CFs_RNA_replicate 2


title: 3m_CFs_RNA_replicate 1


title: Adult CF, shNr4a3_1, H3K27me3 CUT&Tag


title: neo_CFs_RNA_replicate 1


title: 24m_CFs_RNA_replicate 1


title: 12m_CFs_RNA_replicate 1


title: MGT_Adult_2_RNA_replicate 1, MGT, Day3


title: Adult CF, shNT_2, H3K27me3 CUT&Tag


title: Adult CF, shNr4a3_2, H3K27ac CUT&Tag

value: H3K27ac (Abcam; ab4729)


title: Adult CF, shNT_1, H3K27me3 CUT&Tag

value: primary cell


title: Adult CF, shNT_1, H3K27ac CUT&Tag

value: cardiac fibroblast


title: Adult CF, shNr4a3_1, H3K27ac CUT&Tag


title: Adult CF, shNT_2, H3K27ac CUT&Tag


title: Adult CFs, MGT+shNr4a3 replicate 1, Day7

data_processing:
The raw reads were subjected to adapter removal (fastp 0.20.1) and mapping genome mm10 (Bowtie version 2.2.5) using –no-unal –no-mixed –no-discordant -X 2000 –local parameters. The null, unmapped and duplicated reads were removed by view and markdup functions in sambamba (version 0.7.1) with default parameter settings and mitochondrial reads were removed by SAMtools (version 1.9).
Bigwig files were generated by bam Coverage function in deepTools (version 3.4.3)
MACS2 (version 2.1.2) were used to call ATAC-seq peaks, using default parameters in -p 1e−5 –nomodel -f BAMPE –keep-dup all -g mm.
Assembly: mm10
Supplementary files format and content: narrowPeak

extract_protocol:
10000-50000 cells were treated with cell lysis buffer and nucleus were collected by centrifuging for 5 min at 2000 g.
Transposition and high-throughput DNA sequencing library were carried out by TruePrep DNA Library Prep Kit V2 for Illumina kit (Catalog No. TD501, Vazyme).


title: Adult CFs, MGT+shNT replicate 2, Day7


title: Adult CFs, MGT+shNr4a3 replicate 2, Day7


title: Adult CFs, MGT+shNT replicate 1, Day7


title: MGT_Aged_2_replicate 1, MGT, Day3


title: MGT_Neo_2_replicate 1, MGT, Day3


title: MGT_Neo_1_replicate 1, MGT, Day3


title: Lacz_Aged_2_replicate 1, Lacz, Day3


title: Lacz_Adult_2_replicate 1, Lacz, Day3


title: Lacz_Adult_1_replicate 1, Lacz, Day3


title: Lacz_Neo_2_replicate 1, Lacz, Day3


title: Lacz_Neo_1_replicate 1, Lacz, Day3


title: mouse colon cancer tissue, WT, biol rep 3

city: Suzhou

first: Xiaoqin

last: Yang

state: Jiangsu

address: NO. 199 Renai Road

institute: Soochow University

data_processing:
All libraries were sequenced on the Illumina NovaSeq 6000 instrument, and 150 bp paired-end reads were generated.
Sequencing reads were aligned back to the mouse genome (version: mm10) by TopHat 2 software.
Read count extraction was performed using GFOLD software.
The expression matrix of all samples was subjected to the Bayesian workflow for differential gene modeling based on the “edgeR” and “limma” R bioconductor packages.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include reads count for each Sample

source_name: mouse colon cancer tissue

extract_protocol:
Total RNA was isolated from the colorectal cancer tissue using Trizol reagent (Invitrogen; ThermoFisher) according to the manufacturer’s instructions. Then, the ribosomal RNA was depleted from the Trizol-harvested total RNA with the GenSeq rRNA Removal Kit (GenSeq, Inc.) by adhering to its operation guideline.
Next, RNA-seq libraries (with each treatment in triplicate) were constructed with the GenSeq Low Input RNA Library Prep Kit (GenSeq, Inc.) following the manual specifications.

value: mouse colon cancer tissue

value: colon tumor tissues from AOM/DSS-treated Trim21 +/+ mice


title: mouse colon cancer tissue, WT, biol rep 2


title: mouse colon cancer tissue, Trim21 knock out, biol rep 3

value: Trim21 knock out

value: colon tumor tissues from AOM/DSS-treated Trim21 -/- mice


title: mouse colon cancer tissue, Trim21 knock out, biol rep 2


title: mouse colon cancer tissue, Trim21 knock out, biol rep 1


title: mouse colon cancer tissue, WT, biol rep 1


title: MGT_Aged_1_replicate 1, MGT, Day3

value: Primary cell

value: MGT


title: MGT_Adult_1_replicate 1, MGT, Day3

value: 3 months old


title: MGT_Adult_2_replicate 1, MGT, Day3

value: heart


title: Lacz_Aged_1_replicate 1, Lacz, Day3

value: 18 months old


title: JZ24113084-WT2

value: hippocampus


title: HL60 cells,InputALKBH5

city: nanchang

first: zhiwei

last: wu

address: No.17, Yongwai Street, Donghu District, Nanchang City, Jiangxi Province

institute: The First Affiliated Hospital of Nanchang University

description: Library name: Ctrl_ip

data_processing:
Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis for annotated genes were conducted using KOBAS software (version 2.1.1). A corrected P-value cutoff of 0.05 was used to determine statistically significant enrichment.
Assembly: hg38
Supplementary files format and content: Ctrl_peaks_anno_kegg
Supplementary files format and content: Ctrl_peaks_anno_go

organism: Homo sapiens

source_name: HL60 cells

extract_protocol:
The RNA from both "input" (10% of the cell lysate) and "IP" (80% of the lysate used for immunoprecipitation with anti-ALKBH5 antibody) samples was extracted using TRIzol reagent (Invitrogen Bio, Waltham, USA).
Stranded RNA sequencing libraries were constructed using the KC-Digital™ Stranded mRNA Library Prep Kit for Illumina® (Wuhan Seqhealth Co., Ltd., China) following the manufacturer’s instructions. Library fragments within the range of 200–500 bp were enriched and quantified. Sequencing was performed on a DNBSEQ-T7 sequencer (MGI Tech Co., Ltd.) using the PE150 mode.

value: HL60 cells


title: HL60 cells,IPALKBH5

description: Library name: Ctrl_input


title: Cas13d_No_S4U_R1

city: Kansas City

first: Ariel

middle: Alejandro

last: Bazzini

institute: Stowers Institute for Medical Research

data_processing:
Slam-dunk pipeline
Assembly: danrer11
Supplementary files format and content: tsv files for gene counts and vcf file for snp calling on background samples
Library strategy: Slam-seq

organism: Danio rerio

source_name: whole embryo

extract_protocol:
Trizol
QuantSeq 3′ mRNA-Seq Library Prep Kit

value: whole embryo

value: 4 hpf

value: Cas13d Control

value: NO


title: Bckdk_KD_No_S4U_R1

value: Knockdown


title: Cas13d_S4U_R1


title: Bckdk_KD_S4U_R4


title: Bckdk_KD_S4U_R3


title: Bckdk_KD_S4U_R2


title: STA-ET-1_p22_affy

type: RNA

city: Essen

first: Maximilian

last: Kerkhoff

address: Hufelandstrasse 55

department: Pediatrics III

institute: University Hospital Essen

description: Gene expression data of C-ES series of Ewing sarcoma cell lines

hyb_protocol: 5,2 ug of fragmented and labeled ss-cDNA were hybridized for 17 hr at 45°C on Applied Biosystems™ human Clariom™ D Array according to GeneChip™ WT PLUS Reagent Kit User Guide.

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays.

data_processing: The data was preprocessed and normalized by the “rma” function of the R package “oligo” version 1.68.0. Data was filtered based on intensity threshold of 4.5

label: biotin

source_name: Ewing sarcoma

label_protocol: The Applied Biosystems™ GeneChip™ WT PLUS Reagent Kit is used to generate biotin-labeled ss-cDNA from input amounts of 100ng total RNA.

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

extract_protocol: Cells were processed with Macherey-Nagel Nucelospin RNA kit and protocol for RNA extraction

treatment_protocol: Cells got a media exchange after 48h, were washed after 96h with 1xPBS and then harvested in 350µL Buffer RA1 for RNA extraction


title: NIPBL_8C_rep1

first: Wei

last: Xie

address: Qinghuayuan

institute: Tsinghua University

description: Library name: NIPBL_8C_rep1

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

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

value: WT

value: untreated


title: Bckdk_KD_S4U_R1


title: C-ES-Y_p10_affy

value: C-ES-Y


title: C-ES-Y_p55_affy


title: C-ES-M_p53_affy

value: C-ES-M


title: SK-N-MC_p15_affy

value: SK-N-MC


title: C-ES-P_p17_affy

value: C-ES-P


title: Cas13d_S4U_R2


title: C-ES-P_p54_affy


title: STA-ET-1_p54_affy


title: C-ES-M_p11_affy


title: C-ES-I_p13_affy

value: C-ES-I


title: N605

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

source_name: kidney biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol: All human kidney biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

tag: disease subgroup

value: Normal

tag: in 300? (yes, no)

value: no

tag: in 280? (yes, no)


title: N606


title: N603


title: N604

value: cAKI


title: N599


title: N607


title: N595


title: N601


title: N598

value: pABMR


title: N597


title: N602


title: N596


title: N594


title: N600

value: ABMR


title: N587


title: N592


title: C-ES-I_p53_affy


title: N580


title: N588


title: N579


title: N590


title: N589


title: N584


title: N593


title: N585


title: N583


title: N582


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title: N575

value: Mixed


title: N576


title: N573


title: N566


title: N563


title: N578


title: N581


title: N561


title: N577

value: pTCMR


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value: TCMR


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value: yes


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