title: SH-SY5Y, WT, Untreated, Rep 1

city: Worcester

first: Job

last: Dekker

address: 368 Plantation Street

department: Program in Systems Biology

institute: University of Massachusetts Medical School/HHMI

data_processing:
Hi-C data processing was performed as previously described (Abramo et al. , 2019) to the hg38 human reference genome using the nextflow based distiller-nf pipeline. The number of valid pairs was normalized within each replicate using cooltools (v0.5.1) random-sample with the –exact argument on 1kb resolution .cool files (Venev et al. , 2022).  MultiQC was used for quality control of the Hi-C libraries (Ewels et al. , 2016). Read normalized valid pairs were binned into .mcool formatted contact matrices using the python package cooler (v0.8.11), and were iteratively balanced (Abdennur et al. , 2021, Abdennur and Mirny, 2020). Hi-C analysis was performed using Hi-C specific python packages such as cooler (v0.8.11), cooltools (v0.5.1), bioframe (v0.3.3) and pairtools (v0.3.0)   (Abdennur et al. , 2022, Abdennur et al., 2021, Goloborodko et al. , 2019, Venev et al., 2022). Other python packages used included pandas (v1.4.2), numpy (v1.22.3), scipy (v1.8.0), scikit-image (v0.19.2), seaborn (v0.11.2) and matplotlib (v3.5.2) (Harris et al. , 2020, Hunter, 2007, McKinney, 2010, Reback et al. , 2021, van der Walt et al. , 2014, Virtanen et al. , 2020). Only chromosomes without major translocations were used for most analysis (chr1-chr6, chr9-chr14, chr16, chr18-chr21).
Distance Decay: Contact frequency (P) as a function of genomic distance (s) and the derivative (slope) of this P(s) curve were calculated using cooltools compute-expected followed by cooltools logbinned-expected using only intrachromosomal reads from the read normalized cooler files, binned at 1Kb .
TAD Insulation: Insulation between topologically associating domains was calculated on 10kb binned .cool files using the cooltools API function calculate_insulation_score, with a 250kb diamond sliding window (Venev et al., 2022). Domain boundaries were found by locating minima in each profile, and thresholding using skimage threshold_otsu (van der Walt et al., 2014). Boundaries were then filtered to remove boundaries that overlapped with changes in compartment type, to analyze TAD only boundary strength. Aggregate insulation plots were made by plotting the average insulation in 500kb windows around all called TAD boundaries in the WT Control Hi-C library (Hunter, 2007).
Compartment Analysis: Active and inactive compartment regions were identified using eigenvector decomposition on 250kb binned Hi-C .mcool files using cooltools, as previously described (Abramo et al., 2019, Imakaev et al. , 2012, Venev et al., 2022). The eigenvector was phased such that positive values corresponded to the more gene-dense regions of the genome (the ‘A’, or active compartment), while negative values corresponded to the gene-poor regions of the genome (the ‘B’ or inactive compartment). To measure the strength of compartmentalization, we used cooltools saddleplot analysis on observed/expected Hi-C data, as previously described, where the expected matrix corresponds to the average distance decay (Abramo et al., 2019, Imakaev et al., 2012, Venev et al., 2022). Observed/expected matrix bins within or between chromosomes were sorted and aggregated into 50 bins according to their eigenvalue. Strength of compartmentalization for each distance was calculated as the ratio of AA/AB or BB/AB interactions, where AA is the average of the corner 10 bins with positive, positive eigenvector values, BB is the average of the 10 corner bins with negative, negative eigenvector values, and AB is the average of the 10 bins in the corner with positive, negative eigenvector values.
Differential gene expression comparison: Differential compartment bins were called and compared to differentially expressed genes using dcHiC (https://www.biorxiv.org/content/10.1101/2021.02.02.429297v2), with E1 values calculated using cooltools. The fraction of differential compartment bins was calculated compared to all bins in the genome with non-NA compartment values. A hypergeometric distribution test was used to calculate the p value of as many or more genes than observed overlapping between the RNA-seq differential genes and the genes in differential compartment domains using scipy.phyper. The eigenvector values for all bins overlapping differentially expressed genes in different classes were plotted as a boxplot using seaborn. Correlated changes in gene expression and compartment eigenvector value in the WT ATRA differentiation were identified, and the E1 for these regions was plotted for both WT and Top2BKO cell lines.
Assembly: hg38
Supplementary files format and content: Multiresolution cooler files (multires.cool) containing high quality (Mapq>30) read normalized pairwise interactions for each sample, and for both replicates combined.

source_name: bone marrow

growth_protocol: Wildtype SH-SY5Y and TOP2B null clone BKO98 (Khazeem et al., 2022) clones were maintained in a 50:50 mixture of Minimum Essential Medium (MEM) and F12 (Hams) medium (Gibco by Life Technologies, Invitrogen, UK) with 10% v/v fetal bovine serum (FBS) (Gibco by Life Technologies, Invitrogen, UK) and 1% v/v Penicillin and Streptomycin solution (10,000 units/ml penicillin, 10,000 mg/ml streptomycin, Gibco by Life Technologies, Invitrogen, UK). Cells were passaged using 0.5mM EDTA in PBS; after 2-4 minutes incubation at room temperature cells were dislodged by knocking the side of the flask, and then triturating using a 10ml serological pipette to encourage suspension into single cells. Typically, cells were passages at a 1:4 ratio.

extract_protocol:
For each Hi-C library, approximately 5 million cells were used as input. Cells were crosslinked for 10 minutes at room temperature in a final concentration of 1% formaldehyde. Glycine was added to quench crosslinking. Cells were then crosslinked with 3mM DSG for 45 minutes at room temperature, and DSG crosslinking was quenched with Tris. Cell pellets were frozen at -80C until Hi-C library generation. Flash-frozen cross-linked cells were thawed on ice for Hi-C, and were then lysed and digested with DpnII following the Hi-C 2.0 protocol (Belaghzal et al., 2017). Crosslinked chromatin was digested with DpnII (NEB, R0543M) at 37 degrees C overnight, following the Hi-C 2.0 protocol (Belaghzal et al., 2017). The overhanging DNA ends were filled in using biotin-14-dATP (LifeTech, 19524016) at 23 degrees C for four hours, and ligated with T4 DNA ligase (Life Technologies, 15224090) at 16 degrees C for four hours. Chromatin was then treated with proteinase K (ThermoFisher, 25530031) at 65 degrees C overnight to remove all cross-linked proteins. Ligation products were purified by phenol:chloroform extraction with ethanol precipitation, fragmented by sonication, and size-selected using SPRI beads to retain fragments of 100-350bp.
We performed end repair and then selectively purified biotin-tagged DNA using streptavidin coated beads (DYNAL™ MyOne™ Dynabeads™ Streptavidin C1, Invitrogen 65001). A-tailing and Illumina TruSeq adapter ligation (Illumina, 20015964) were performed on the bead-bound ligation products, and samples were amplified using the TruSeq Nano DNA Sample Prep kit (Illumina, 20015964). PCR primers were removed using SPRI beads (1.1x ratio) before sequencing the final Hi-C libraries using PE50 bases on an Illumina HiSeq 4000.

treatment_protocol: Retinoic acid treatment: WT and BKO98 SH-SY5Y cells were plated into 20cm culture dishes in medium containing 10µM ATRA in ethanol or the same volume of ethanol (0.1% v/v final concentration of ethanol). Cell were cultures for 5 days and medium was changed on days 2 and 4 to maintain ATRA concentration.

value: bone marrow

tag: disease

value: neuroblastoma

value: SH-SY5Y (ATCC CRL-2266)

tag: hi-c enzyme

value: DpnII

value: Untreated


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_KO_19

status: Public on Mar 27 2025

type: SRA

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

library_source: transcriptomic

data_processing:
RNA-Seq datasets were aligned to the Mus musculus genome assembly (GRCm38/mm10 Dec. 2011) as single-end (Smart-Seq2 polyA datasets) or paired-end (total random primed datasets) using STAR (Dobin et al. 2013) with parameters “-outFilterMultimapNmax 300 -outMultimapperOrder Random -outSAMmultNmax 1 -alignIntronMin 20 -alignIntronMax 1000000”
RNA-Seq samples for hybrid Bl6 x JF1 F1 2-cell embryos were separately aligned to Bl6 and JF1 genomes obtained by injecting JF1 single-nucleotide polymorphisms (SNPs) into reference mm10 genome using previously published SNP table (Takada et al. 2013). RNA-seq reads were categorized as maternal (Bl6), paternal (JF1) or undefined based on minimal number of mismatches in alignments to both genomes.
Assembly: mm10
Supplementary files format and content: BigWig (.bw) processed files were generated from BAM files using the function qExportWig from QuasR package selecting uniquely mapped reads. BigWig processed files for hybrid Bl6 x JF1 2-cell embryos were generated separately for maternal (files ending with MAT.bw), paternal (files ending with PAT.bw) and total alignments normalized by total number of mapped allelic reads (MAT and PAT) or total number of mapped reads.

molecule: polyA RNA

organism: Mus musculus

source_name: growing oocyte day 14

extract_protocol:
After removing the zona-pellucida by treating with acid tyrode’s solution, oocytes and F1 hybrid 2-cell embryos were washed in PBS supplemented with 0.05% Polyvinyl alcohol and lysed in Smartseq2 lysis buffer.
Libraries were prepared by Smartseq2 protocol. cDNAs were prepared by oligo dT based reverse transcription and template switching using Superscript II reverse transcriptase followed by the pre-amplification PCR using KAPA HiFi HotStart ReadyMix PCR Kit and the purification using AMPure Xp beads. 1ng of pre-amplified cDNA was tagmented by Tn5 transposase and adapter-ligated fragments were amplified with adding Nextera XT indexes followed by the purification using AMPure XP beads. Libraries with different indexes were pooled and submitted to sequencing. For total RNA sequencing GOs were isolated from the d14.0 mice. 60-80 oocytes were pooled and frozen in 100μl of Buffer RL. 4 and 3 biological replicates were prepared for ctrl and Kdm2aKOKdm2bKO, respectively. RNA was purified by using Single Cell RNA Purification Kit (NORGEN; 51800). Libraries were prepared according to Illumina Stranded total RNA-seq protocol with Illumina IDT DNA/RNA UDI indexes.

tag: cell type

value: growing oocyte day 14

tag: genotype

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ;Zp3-cre

tag: strain


title: SH-SY5Y, TOP2BKO, Untreated, Rep 1

state: MA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: tissue

tag: cell line

value: TOP2B KO

tag: treatment


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep2, H2A.Z, Abcam

city: Trento

first: Sara

last: Lago

address: Via Sommarive 9

department: CIBIO

country: Italy

institute: University od Trento

description: Library name: tIMEC-ANP32E-H1_CUTnRUN_H2AZ_Abcam_R2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic tool with Illumina:HEADCROP
Bam files were aligned on the reference genome, and downsampled randomly to obtain the same reads number for every sample.
Peaks were called using MACS2 tool
Assembly: hg38
Supplementary files format and content: bigWig files of aligned reads
Library strategy: CUT&RUN

source_name: tIMEC

growth_protocol: tIMEC, tIMEC-ANP32E and tIMEC-ANP32E-H1 cells were maintained in DMEM-F12 supplemented with hEGF 10 ng/ml, Insulin 5 μg/ml, Hydrocortisone 0.5 μg/ml, Bovine Pituitary Extract 35 μg/ml and antibiotics Penicillin/Streptomycin 1:100 in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were permeabilized using Digitonin wash buffer and functionalized on Concanavalin coated beads as described in Skene et al. dx.doi.org/10.17504/protocols.io.mgjc3un
Library preparation was performed as described in Skene et al. dx.doi.org/10.17504/protocols.io.mgjc3un by adapting NEBNext Ultra II DNA Library Prep kit and Unique Dual Index.

treatment_protocol: For TOP2A and TOP2B sample preparation: tIMEC, tIMEC-ANP32E and tIMEC-ANP32E-H1 cells were treated for 1h with Etoposide 5 μM (MedChemExpress HY-13629) in order to inhibit the release of Topoisomerases IIA and IIB and improve their immunoprecipitation as reported in Nat Genet. 2019 Jun;51(6):1011-1023.doi: 10.1038/s41588-019-0421-z

value: tIMEC

value: Basal-like breast cancer

value: ANP32E overexpression, RNaseH1 overexpression


title: SH-SY5Y, TOP2BKO, 5 Day ATRA Treatment, Rep 1

value: 5 day ATRA treatment


title: Female Kidney Control Biol Rep 3

city: Cologne

first: Sebastian

last: Grönke

address: Joseph-Stelzmann Str. 9b

department: Biological Mechanisms of Ageing

country: Germany

institute: Max-Planck Institute for Biology of Ageing

description: Library name: Sample 66

data_processing:
Libraries read processing was automated using Flaski (v3.11.34) [88], developed by the Bioinformatics Core Facility at the MPI for Biology of Ageing (Cologne, Germany).
Differential gene expression was analysed using DESeq2 (v1.24.0)  in R (v3.6.3).
Assembly: Raw reads were mapped to the mm39 ENSEMBL build 105 using kallisto (v0.46.1). Gene counts were quantified in the same step
Supplementary files format and content: Excel file containing FPKM and differential expression analysis

source_name: Kidney

extract_protocol:
Total RNA was isolated from 4-10mg of spleen, muscle and kidney using TrIzol. Samples were treated with DNAase using the Turbo DNAse kit (ThermoFisher Scientific) to remove genomic DNA.
poly(A)+ mRNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation kit (New England BioLabs, Prior to first strand synthesis, samples were randomly primed (5’ d(N6) 3’ [N=A,C,G,T]) and fragmented. First strand synthesis was done using the Protoscript II Reverse Transcriptase for approximately 40 minutes at 42⁰C. All remaining steps for library construction were done according to the NEBNext Ultra™ II Non- Directional RNA Library Prep Kit for Illumina, RNA Seq with 50 million 150 bp paired-end reads/sample

value: Kidney

tag: age

value: 24 months

tag: Sex

value: Female

value: C3B6F1 wild type

value: control


title: Male Kidney Control Biol Rep 1

description: Library name: Sample 69

value: Male


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep2, acH2A.Z

description: Library name: tIMEC-ANP32E-H1_CUTnRUN_acH2AZ_R2


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_KO_16


title: tIMEC cells, rep3, Rloop

description: Library name: tIMEC_CUTnRUN_Rloop_R3

value: WT


title: tIMEC cells, rep3, pRPA32(S33)

description: Library name: tIMEC_CUTnRUN_pRPA32_R3


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_KO_18


title: SH-SY5Y, WT, 5 Day ATRA Treatment, Rep 1

value: bone marrow

value: neuroblastoma

value: SH-SY5Y (ATCC CRL-2266)


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_KO_17

value: growing oocyte day 14


title: SH-SY5Y, WT, 5 Day ATRA Treatment, Rep 2

value: DpnII


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep2, pS5RNApolII

description: Library name: tIMEC-ANP32E-H1_CUTnRUN_totRNApolII_R2


title: Female Kidney Control Biol Rep 4

description: Library name: Sample 67


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_KO_13

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ;Zp3-cre


title: Female Kidney Trametinib Biol Rep 5

description: Library name: Sample 63

value: trametinib


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep2, Rloop

description: Library name: tIMEC-ANP32E-H1_CUTnRUN_Rloop_R2

value: tIMEC

value: Basal-like breast cancer


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep2, TOP2A

description: Library name: tIMEC-ANP32E-H1_CUTnRUN_TOP2A_R2

value: ANP32E overexpression, RNaseH1 overexpression

value: Etoposide 5 μM 1h MedChemExpress HY-13629


title: SH-SY5Y, TOP2BKO, Untreated, Rep 2

value: TOP2B KO

value: Untreated


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_KO_11


title: ARP1-P28-RZ, pig 1

city: Birmingham

first: Thanh

middle: Minh

last: Nguyen

state: AL

address: 1670 University Blvd, Volker Hall G094

department: Department of Biomedical Engineering

institute: University of Alabama at Birmingham

description: Library name: 8030_RZ

library_source: transcriptomic single cell

data_processing:
Sample demultiplexing, barcode processing, and gene counting were performed with Cell Ranger Single-Cell Software v.3.10 (https://support.10xgenomics.com/single-cell-gene expression/software). Reads were aligned to the Sscrofa11.1 pre-mRNA reference genome, and the pre-mRNA portion of the reference genome was extracted for single nucleus unique molecular identifier (UMI) mapping with Cell Ranger mkref pre-mRNA. Only confidently mapped reads with valid barcodes and UMIs were used to generate the gene-barcode matrix. DoubletFinder, including Seurat preprocessing, was applied to filter out doublets
Assembly: Sscrofa11.1
Supplementary files format and content: 10X genomics format for each sample, including the barcode file (barcodes.tsv.gz), feature gene file (features.tsv.gz) and sparse-matrix of gene expression file (matrix.mtx.gz)
Supplementary files format and content: All data (combined all samples) processed file: AllData_cellBarcode.csv.gz (barcode), AllData_geneList.csv.gz (gene list), AdjustedCount.txt.gz (raw expression), NormalizedExpression.txt.gz (normalized expression via Seurat)

molecule: nuclear RNA

organism: Sus scrofa

source_name: ARP1 heart, explanted on postnatal day 2, border zone

growth_protocol: All experimental protocols were approved by The Institutional Animal Care and Use Committee (IACUC) of the University of Alabama, Birmingham, and performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals (NIH publication No 85-23). Pigs were purchased from Prestage Farm, Inc. Pigs were housed in an incubator at 30 oC with room air through P14 and then transferred to normal housing at 22 oC. Animals were fed bovine colostrum every 4 hours for the first 2 days of life, a 1:1 mixture of colostrum:goat milk on day 3, and then a 1:1 mixture of goat/sow milk. Supplemental iron was provided on day 7

extract_protocol:
Tissues were cut while submerged in cold phosphate-buffered saline (PBS) or UW solution, washed to remove blood, transferred into 1 mL lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% Nonidet™ P40 Substitute, and 50 U/mL RNase inhibitor in DEPC-treated water), cut into smaller pieces, and aspirated with the lysis buffer into a 50-mL tube; then, 10 mL of lysis buffer was added, the tissues were ground for 20-30 seconds, and more lysis buffer was added. The mixture was placed on ice for 10 minutes, filtered with 100-μm and 70-μm strainers, and centrifuged for 5 minutes at 700 relative centrifugal force (rcf) and 4 °C; then, the supernatant was removed, and the pellet was resuspended in 10 mL nuclei wash and resuspension buffer (1× PBS, 1.0% bovine serum albumin [BSA], and 50 U/mL RNase inhibitor). The suspension was passed through a 40-μm strainer, and the nuclei were centrifuged again for 5 minutes at 700 rcf and 4 °C; then, the supernatant was removed, the pellet was resuspended in 1 mL nuclei wash and resuspension buffer, and the nuclei were centrifuged a third time for 5 minutes at 700 rcf and 4 °C. The supernatant was removed; then, the pellet was resuspended in 5 mL sucrose cushion buffer I (2.7 mL Nuclei PURE 2 M Sucrose Cushion Solution and 300 μL Nuclei PURE Sucrose Cushion Buffer) and mixed with 10 mL sucrose buffer. The mixture was layered over 5 mL of sucrose cushion buffer in a second Eppendorf tube and then centrifuged for 60 minutes at 13000 g and 4 °C. All but 100 μL of the supernatant was removed, the nuclei were resuspended in nuclei wash and resuspension buffer, and the solution was passed through a 40-μm strainer; then, the nuclei concentration was determined with a cell counter or hemocytometer and adjusted to 1000 nuclei/μL. The nuclei were placed on ice, stained with propidium iodide for 5 minutes, and then immediately processed via the 10× Genomics® Single-Cell Protocol.
The nuclei were placed on ice, stained with propidium iodide for 5 minutes, and then immediately processed via the 10× Genomics® Single-Cell Protocol.

treatment_protocol: Apical resection was performed on the first neonate day. Briefly, pigs were anesthetized with isoflurane and placed on a heating pad in a dorsal recumbent position; then, a median sternotomy was performed to expose the heart. AR was performed by removing 4-5 mm of tissue from the ventricular apex; then, the sternum was re-approximated, the chest was closed in layers, and air was evacuated from the mediastinum.

value: Heart, left ventricle

value: All cell


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep2, p400

description: Library name: tIMEC-ANP32E-H1_CUTnRUN_p400_R2


title: ARP1-P15-RZ, pig 3

description: Library name: 8400_RZ


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep2, pS2RNApolII, Abcam

description: Library name: tIMEC-ANP32E-H1_CUTnRUN_pS2RNApolII_Abcam_R2


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_KO_15


title: GVO_scRNA_KO.Kdm2b_dCxxC_2

source_name: fully grown germinal vesicle oocytes

value: fully grown germinal vesicle oocytes

value: Kdm2b flox-CxxC/flox-CxxC; Zp3-cre


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_KO_9


title: Female Kidney Control Biol Rep 2

description: Library name: Sample 65

value: Kidney

value: 24 months

value: Female

value: C3B6F1 wild type

value: control


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep3, acH2A.Z

description: Library name: tIMEC-ANP32E-H1_CUTnRUN_acH2AZ_R3


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep2, ANP32E, LSBio

description: Library name: tIMEC-ANP32E-H1_CUTnRUN_ANP32E_LSBio_R2


title: Female Kidney Control Biol Rep 5

description: Library name: Sample 68


title: CHLA06_DMSO_3

city: Boston

first: Robert

last: Fisher

address: 609 Albany St

department: Dermatology

institute: Boston University

description:
Library name: CHLA06_DMSO_3
DEG_p05_CHO6.csv

data_processing:
Reads were trimmed and low-quality reads were removed using fastp
Reads were quasi-aligned to the GRCh38 reference genome using Salmon
Salmon quant files were used for differential analysis using DESeq2. The Wald test was used to generate p-values and log2 fold changes.
Assembly: hg38/Gencodev44
Supplementary files format and content: CSV files; DESeq2 outputs of differential gene expression p <0.05; salmon quant files for the processed raw unnormalized counts

growth_protocol: BT37 cell lines were cultured in RPMI (Invitrogen, Thermo Fisher Scientific) supplemented with 10% FBS, 2 mM L-glutamine, and 1% penicillin/streptomycin. CHLA06 cells were cultured in EF Media containing 30% Hams F12 (Invitrogen, Thermo Fisher Scientific), 70% DMEM (Invitrogen, Thermo Fisher Scientific), 1x antibiotic/antimycotic (#A5955, Sigma-Aldrich), 2 mM L-glutamine (#25030-081, Life Technologies), 2% B27 with vitamin A (#12586-010, Gibco), 20 ng/mL EGF (#AF-100-15-1MG, PeproTech), 20 ng/mL FGF-2 (#100-18B-1MG, PeproTech), and 5 ug/mL heparin (#H3149-100KU, Sigma). Media was passed through a 0.22 um filter before use. All cell lines were maintained in a 37°C incubator at 5% CO2.

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (Qiagen)
Libraries were constructed by Azenta Inc. Paired end

value: ATRT

value: DMSO


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep2, Rabbit IgG

description: Library name: tIMEC-ANP32E-H1_CUTnRUN_RabbitIgG_R2

value: tIMEC


title: Male Kidney Trametinib Biol Rep 5

description: Library name: Sample 58

value: Male

value: trametinib


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_KO_8

value: growing oocyte day 14

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ;Zp3-cre


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_KO_10


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_KO_14


title: ARP1-P15-BZ, pig 2

description: Library name: 8399_BZ


title: tIMEC cells, ANP32E overexpression, rep2, Rabbit IgG

description: Library name: tIMEC-ANP32E_CUTnRUN_RabbitIgG_R2

value: Basal-like breast cancer

value: ANP32E overexpression


title: SH-SY5Y, TOP2BKO, 5 Day ATRA Treatment, Rep 2

value: bone marrow

value: neuroblastoma

value: SH-SY5Y (ATCC CRL-2266)

value: DpnII

value: TOP2B KO

value: 5 day ATRA treatment


title: Female Kidney Control Biol Rep 1

description: Library name: Sample 64

value: Kidney

value: 24 months

value: Female

value: C3B6F1 wild type


title: SH-SY5Y, WT, Untreated, Rep 2

value: WT

value: Untreated


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_KO_12


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep2, pRPA32(S33)

description: Library name: tIMEC-ANP32E-H1_CUTnRUN_pRPA32_R2

value: tIMEC

value: ANP32E overexpression, RNaseH1 overexpression


title: Female Kidney Trametinib Biol Rep 3

description: Library name: Sample 61

value: trametinib


title: Female Kidney Trametinib Biol Rep 4

description: Library name: Sample 62


title: tIMEC cells, ANP32E overexpression, rep2, H2A.Z, Abcam

description: Library name: tIMEC-ANP32E_CUTnRUN_H2AZ_Abcam_R2

value: Basal-like breast cancer


title: tIMEC cells, ANP32E overexpression, rep2, acH2A.Z

description: Library name: tIMEC-ANP32E_CUTnRUN_acH2AZ_R2

value: ANP32E overexpression


title: ARP1-P15-BZ, pig 1

description: Library name: 8398_BZ

value: Heart, left ventricle

value: All cell


title: Female Kidney Trametinib Biol Rep 2

description: Library name: Sample 60


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_KO_5

value: growing oocyte day 14

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ;Zp3-cre


title: ARP1-P15-RZ, pig 2

description: Library name: 8399_RZ


title: Female Kidney Trametinib Biol Rep 1

description: Library name: Sample 59


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep2, pH2A.X

description: Library name: tIMEC-ANP32E-H1_CUTnRUN_pH2A.X_R2


title: Male Kidney Trametinib Biol Rep 4

description: Library name: Sample 57

value: Male


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_KO_7


title: tIMEC cells, ANP32E overexpression, rep2, pS2RNApolII, Abcam

description: Library name: tIMEC-ANP32E_CUTnRUN_pS2RNApolII_Abcam_R2


title: ARP1-P15-BZ, pig 3

description: Library name: 8400_BZ


title: ARP1-P8-RZ, pig 3

description: Library name: 8401_RZ


title: tIMEC cells, ANP32E overexpression, rep2, pS5RNApolII

description: Library name: tIMEC-ANP32E_CUTnRUN_totRNApolII_R2


title: Female Kidney Rapamycin/Trametinib Biol Rep 5

description: Library name: Sample 53

value: rapamycin/trametinib


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_KO_4


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_KO_6


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_KO_2


title: ARP1-P15-RZ, pig 1

description: Library name: 8398_RZ


title: Male Kidney Trametinib Biol Rep 3

description: Library name: Sample 56

value: Kidney


title: Male Kidney Trametinib Biol Rep 2

description: Library name: Sample 55

value: 24 months


title: ARP1-P8-BZ, pig 2

description: Library name: 8381_BZ


title: Male Kidney Trametinib Biol Rep 1

description: Library name: Sample 54


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_KO_3


title: Female Kidney Rapamycin/Trametinib Biol Rep 3

description: Library name: Sample 51

value: Female


title: tIMEC cells, ANP32E overexpression, rep2, Rloop

description: Library name: tIMEC-ANP32E_CUTnRUN_Rloop_R2


title: PGE_3h_Rep1

city: New York

first: HSS Genomics

last: Research Center

state: New York

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

description:
EC.US.5351_Male_PGE_3h_Rep1
rawcounts_PGE.txt

data_processing:
Read quality was assessed and adapters trimmed using FastQC and cutadapt.
Reads were then mapped to the human genome (hg38) and reads in exons were counted against Gencode v27 with STAR Aligner.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: CD14+ monocytes

growth_protocol: Monocytes were cultured overnight before treatment at 37°C, 5% CO2 in RPMI-1640 medium supplemented with 10% heat-inactivated defined FBS, penicillin-streptomycin, L-glutamine and 20 ng/ml human M-CSF.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1Ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNextUltraII RNA Library Prep Kit following manufacturer’s protocols

treatment_protocol: Human CD14+ monocytes were treated with PGE2, TNF or PGE2 + TNF co-stimulation for 3 or 24 hours. For the IFNg priming experiment, CD14+ monocytes were primed with IFNg, and subsequently treated with TNF, PGE2 or TNF+PGE2 for 3h.

value: CD14+ monocytes


title: ARP1-P8-BZ, pig 3

description: Library name: 8401_BZ


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_KO_1


title: tIMEC cells, ANP32E overexpression, rep2, pRPA32(S33)

description: Library name: tIMEC-ANP32E_CUTnRUN_Prpa32_R2


title: ARP1-P8-RZ, pig 2

description: Library name: 8381_RZ


title: Female Kidney Rapamycin/Trametinib Biol Rep 2

description: Library name: Sample 50

value: C3B6F1 wild type


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_22

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ


title: ARP1-P8-RZ, pig 1

description: Library name: 8379_RZ


title: tIMEC cells, ANP32E overexpression, rep2, p400

description: Library name: tIMEC-ANP32E_CUTnRUN_p400_R2

value: tIMEC


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_23


title: Female Kidney Rapamycin/Trametinib Biol Rep 1

description: Library name: Sample 49


title: tIMEC cells, ANP32E overexpression, rep2, ANP32E, LSBio

description: Library name: tIMEC-ANP32E_CUTnRUN_ANP32E_LSBio_R2


title: ARP1-P4-RZ, pig 2

description: Library name: 8351_RZ


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_21


title: Female Kidney Rapamycin/Trametinib Biol Rep 4

description: Library name: Sample 52


title: ARP1-P4-BZ, pig 2

description: Library name: 8351_BZ


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_20


title: Male Kidney Rapamycin/Trametinib Biol Rep 4

description: Library name: Sample 48


title: tIMEC cells, ANP32E overexpression, rep2, pH2A.X

description: Library name: tIMEC-ANP32E_CUTnRUN_pH2A.X_R2


title: Male Kidney Rapamycin/Trametinib Biol Rep 3

description: Library name: Sample 47


title: ARP1-P4-RZ, pig 1

description: Library name: 8350_RZ


title: tIMEC cells, rep2, Rabbit IgG

description: Library name: tIMEC_CUTnRUN_H2AZ_RabbitIgG_R2

value: WT


title: tIMEC cells, ANP32E overexpression, rep2, TOP2A

description: Library name: tIMEC-ANP32E_CUTnRUN_TOP2A_R2

value: Etoposide 5 μM 1h MedChemExpress HY-13629


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_19


title: ARP1-P4-BZ, pig 1

description: Library name: 8350_BZ


title: tIMEC cells, rep2, H2A.Z, Abcam

description: Library name: tIMEC_CUTnRUN_H2AZ_Abcam_R2

value: Basal-like breast cancer


title: Male Kidney Rapamycin/Trametinib Biol Rep 1

description: Library name: Sample 45


title: Male Kidney Rapamycin/Trametinib Biol Rep 2

description: Library name: Sample 46


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_18


title: ARP1-P8-BZ, pig 1

description: Library name: 8379_BZ


title: tIMEC cells, rep2, acH2A.Z

description: Library name: tIMEC_CUTnRUN_acH2AZ_R2


title: ARP1-P2-RZ, pig 2

description: Library name: 8382_RZ


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_17


title: GVO_scRNA_Ctrl.Kdm2b_dCxxC_1

value: fully grown germinal vesicle oocytes

value: Kdm2b flox-CxxC/flox-CxxC


title: Female Kidney Rapamycin Biol Rep 4

description: Library name: Sample 44

value: rapamycin


title: tIMEC cells, rep2, pS2RNApolII, Abcam

description: Library name: tIMEC_CUTnRUN_pS2RNApolII_Abcam_R2


title: ARP1-P2-BZ, pig 2

description: Library name: 8382_BZ

value: Heart, left ventricle

value: All cell


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_14

value: growing oocyte day 14


title: ARP1-P2-BZ (ARP1 pig, explanted on postnatal day 2, remote zone), pig 1

description: Library name: 8380_RZ


title: tIMEC cells, rep2, pRPA32(S33)

description: Library name: tIMEC_CUTnRUN_pRPA32_R2


title: Female Kidney Rapamycin Biol Rep 2

description: Library name: Sample 42


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_12


title: Female Kidney Rapamycin Biol Rep 3

description: Library name: Sample 43


title: Naïve heart, postnatal day 2 (CTL-P2)

description: Library name: 7696

source_name: Naïve heart, postnatal day 2


title: ARP1-P2-BZ (ARP1 pig, explanted on postnatal day 2, border zone), pig 1

description: Library name: 8380_BZ


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_13


title: tIMEC cells, rep2, pS5RNApolII

description: Library name: tIMEC_CUTnRUN_totRNApolII_R2


title: tIMEC cells, rep2, TOP2A

description: Library name: tIMEC_CUTnRUN_TOP2A_R2


title: Female Kidney Rapamycin Biol Rep 1

description: Library name: Sample 41


title: tIMEC cells, rep2, Rloop

description: Library name: tIMEC_CUTnRUN_Rloop_R2


title: C29_W8_good

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
Overall quality of the next-generation sequencing data was evaluated automatically and manually with fastQC v0.11.9 (Andrews 2010) and multiQC v1.10 (Ewels et al. 2016).
Reads from all passing samples were adapter trimmed and quality filtered using cutadapt v3.3 (Martin 2011) and filtered for a minimum length of 17nt.
Mapping steps were performed with bowtie v1.3.0 (Langmead et al. 2009) and miRDeep2 v2.0.1.2 (Friedländer et al. 2012), whereas reads were mapped first against the genomic reference GRCh38.p12 provided by Ensembl (Zerbino et al. 2018) allowing for two mismatches and subsequently miRBase v22.1 (Griffiths-Jones 2004), filtered for miRNAs of mmu only, allowing for one mismatch.
Assembly: Rnor.6.0; miRBase v22.1
Supplementary files format and content: CSV file containing read counts of miRDeep2 mapped miRNAs

molecule: total RNA

organism: Rattus norvegicus

source_name: blood plasma

growth_protocol: Rat calvarial defect regeneration after treatment with 3 groups plus control, blood was collected and processed for miRNA analyis

extract_protocol:
Total RNA extraction from 200 µl plasma using miRNeasy Mini Kit (Cat 217004)
RealSeq single-adapter ligation protocol for small RNA-sequening of biofluids

value: blood plasma

tag: timepoint

tag: regeneration

value: good

tag: animal


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_10


title: Male Kidney Rapamycin Biol Rep 2

description: Library name: Sample 38

value: Kidney

value: 24 months

value: Male


title: tIMEC cells, rep2, p400

description: Library name: tIMEC_CUTnRUN_p400_R2


title: Male Kidney Rapamycin Biol Rep 3

description: Library name: Sample 39

value: C3B6F1 wild type


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_8

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ


title: C23_W8_good


title: C25_W8_bad

value: bad


title: C21_W8_good


title: Male Kidney Rapamycin Biol Rep 1

description: Library name: Sample 37


title: tIMEC cells, rep2, pH2A.X

description: Library name: tIMEC_CUTnRUN_pH2A.X_R2

value: tIMEC

value: WT


title: Female Muscle Control Biol Rep 5

description: Library name: Sample 36

source_name: Muscle

value: Muscle

value: Female

value: control


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_9


title: tIMEC cells, rep2, ANP32E, LSBio

description: Library name: tIMEC_CUTnRUN_ANP32E_LSBio_R2

value: Basal-like breast cancer


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_7


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_11


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_5


title: C17_W8_good


title: Male Kidney Rapamycin Biol Rep 4

description: Library name: Sample 40

value: rapamycin


title: Female Muscle Control Biol Rep 4

description: Library name: Sample 35


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_4


title: SK-N-Be(2)_ATO_2 μM

city: Hangzhou

first: Xuejing

last: Shao

address: 866, Yuhangtang Road

department: Zhejiang University

country: China

institute: College of Pharmaceutical Sciences

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: SK-N-BE(2) cells were maintained in MEM and F12, 10% fetal bovine serum, 2 mM L-glutamine, 10 mM pyruvate and 0.1 mM non-essential amino acids, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Paired-end libraries were synthesized by using the TruSeq® RNA sample preparation kit (Illumina, USA) following TruSeq® RNA sample preparation guide.

treatment_protocol: SK-N-BE(2) cells treated with ATO for 12 h.

value: neuroblastoma

value: ATO (2 μM)


title: SK-N-Be(2)_ATO_4 μM

value: ATO (4 μM)


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_3

value: growing oocyte day 14


title: SK-N-Be(2)_Ctrl

value: Ctrl


title: C7_W8_bad

value: blood plasma


title: TNF-PGE2_Rep3

description:
Sample_US-TP-Do3
rawcounts_IFNg.txt

value: CD14+ monocytes


title: Female Muscle Control Biol Rep 3

description: Library name: Sample 34

value: 24 months

value: C3B6F1 wild type


title: C16_W8_bad

value: bad


title: C26_W8_bad


title: Female Muscle Control Biol Rep 1

description: Library name: Sample 32


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_1

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ


title: Female Muscle Control Biol Rep 2

description: Library name: Sample 33


title: Male Muscle Control Biol Rep 5

description: Library name: Sample 31

value: Male


title: C5_W8_good

value: good


title: C6_W8_bad


title: TNF-PGE2_Rep2

description:
Sample_US-TP-Do2
rawcounts_IFNg.txt


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_24

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-CxxC/flox-CxxC; Zp3-cre


title: TNF-PGE2_Rep1

description:
Sample_US-TP-Do1
rawcounts_IFNg.txt


title: C3_W8_bad


title: TNF_Rep3

description:
Sample_US-T-Do3
rawcounts_IFNg.txt

value: TNF


title: Male Muscle Control Biol Rep 4

description: Library name: Sample 30

value: Muscle

value: control


title: TNF_Rep2

description:
Sample_US-T-Do2
rawcounts_IFNg.txt


title: C2_W8_good


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_23


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_22


title: C7_W4_bad


title: Male Muscle Control Biol Rep 2

description: Library name: Sample 28


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_21


title: Male Muscle Control Biol Rep 1

description: Library name: Sample 27


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_2


title: TNF_Rep1

description:
Sample_US-T-Do1
rawcounts_IFNg.txt


title: Female Muscle Trametinib Biol Rep 5

description: Library name: Sample 26

value: Female

value: trametinib


title: C7_W1_bad


title: Resting_Rep3

description:
Sample_US-R-Do3
rawcounts_IFNg.txt

value: Resting


title: C7_BL_unknown

value: BL

value: unknown


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_20

value: growing oocyte day 14


title: Resting_Rep2

description:
Sample_US-R-Do2
rawcounts_IFNg.txt

value: CD14+ monocytes


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_19


title: Female Muscle Trametinib Biol Rep 4

description: Library name: Sample 25

value: 24 months


title: Male Muscle Control Biol Rep 3

description: Library name: Sample 29

value: C3B6F1 wild type


title: Female Muscle Trametinib Biol Rep 3

description: Library name: Sample 24


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_18


title: PGE2_Rep3

description:
Sample_US-P-Do3
rawcounts_IFNg.txt


title: C6_BL_unknown

value: blood plasma


title: C6_W4_bad

value: bad


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_17


title: C6_W1_bad


title: PGE2_Rep2

description:
Sample_US-P-Do2
rawcounts_IFNg.txt


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_16


title: PGE2_Rep1

description:
Sample_US-P-Do1
rawcounts_IFNg.txt


title: C5_W4_good


title: Female Muscle Trametinib Biol Rep 2

description: Library name: Sample 23


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_15


title: Male Muscle Trametinib Biol Rep 4

description: Library name: Sample 21

value: Male


title: C5_W1_good

value: good


title: Female Muscle Trametinib Biol Rep 1

description: Library name: Sample 22


title: IFNG-TNF-PGE2_Rep3

description:
Sample_US-GTP-Do3
rawcounts_IFNg.txt


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_14

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-CxxC/flox-CxxC; Zp3-cre


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_13


title: IFNG-TNF-PGE2_Rep1

description:
Sample_US-GTP-Do1
rawcounts_IFNg.txt


title: Male Muscle Trametinib Biol Rep 3

description: Library name: Sample 20


title: IFNG-TNF-PGE2_Rep2

description:
Sample_US-GTP-Do2
rawcounts_IFNg.txt


title: Male Muscle Trametinib Biol Rep 2

description: Library name: Sample 19


title: C3_W4_bad


title: IFNG-TNF_Rep3

description:
Sample_US-GT-Do3
rawcounts_IFNg.txt

value: IFNG-TNF


title: Resting_Rep1

description:
Sample_US-R-Do1
rawcounts_IFNg.txt


title: Male Muscle Trametinib Biol Rep 1

description: Library name: Sample 18

value: Muscle


title: Female Muscle Rapamycin/Trametinib Biol Rep 4

description: Library name: Sample 17

value: rapamycin/trametinib


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_11


title: C3_BL_unknown


title: Female Muscle Rapamycin/Trametinib Biol Rep 3

description: Library name: Sample 16

value: Female


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_10


title: C2_W1_good


title: IFNG-TNF_Rep2

description:
Sample_US-GT-Do2
rawcounts_IFNg.txt


title: C2_BL_unknown


title: C2_W4_good


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_9


title: Female Muscle Rapamycin/Trametinib Biol Rep 2

description: Library name: Sample 15


title: IFNG-PGE2_Rep3

description:
Sample_US-GP-Do3
rawcounts_IFNg.txt


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_12


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_8


title: C5_BL_unknown


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_7


title: IFNG-PGE2_Rep1

description:
Sample_US-GP-Do1
rawcounts_IFNg.txt


title: Female Muscle Rapamycin/Trametinib Biol Rep 1

description: Library name: Sample 14


title: Male Muscle Rapamycin/Trametinib Biol Rep 3

description: Library name: Sample 12


title: IFNG-PGE2_Rep2

description:
Sample_US-GP-Do2
rawcounts_IFNg.txt


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_6


title: IFNG_Rep3

description:
Sample_US-G-Do3
rawcounts_IFNg.txt

value: IFNG


title: C3_W1_bad


title: IFNG_Rep2

description:
Sample_US-G-Do2
rawcounts_IFNg.txt


title: Male Muscle Rapamycin/Trametinib Biol Rep 4

description: Library name: Sample 13


title: C29_W4_good


title: C29_BL_unknown


title: C29_W1_good


title: Male Muscle Rapamycin/Trametinib Biol Rep 1

description: Library name: Sample 10


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_5


title: IFNG-TNF_Rep1

description:
Sample_US-GT-Do1
rawcounts_IFNg.txt


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_4


title: Female Muscle Rapamycin Biol Rep 5

description: Library name: Sample 9

value: rapamycin


title: Male Muscle Rapamycin/Trametinib Biol Rep 2

description: Library name: Sample 11


title: TP3_Rep3

data_processing:
Raw data underwent adapter trimming with FastP.
Sequencing read alignments were performed against (GRCh38/hg38) reference human genome using Bowtie2.
Peak calling was performed using MACS2 with the following parameters: "macs2 callpeak -f BAMPE --nomodel --shift -37 --extsize 76 -g hs -q 0.05".
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

extract_protocol:
Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500 x g for 10 min in a refrigerated centrifuge. Immediately following the nuclei prep, the pellet was resuspended in the transposase reaction mix (25 µl 2× TD buffer, 2.5 µl transposase (Illumina) and 22.5 µl nuclease-free water). The transposition reaction was carried out for 30 min at 37 °C. Directly following transposition, the sample was purified using a MinElute PCR Purification kit.
Library fragments were amplified using 1× NEB next PCR master mix and 1.25 M of custom Nextera PCR primers as previously described, sing the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min. The libraries were purified using a Qiagen PCR cleanup kit yielding a final library concentration of ∼30 nM in 20 µl.


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_3


title: Female Muscle Rapamycin Biol Rep 4

description: Library name: Sample 8


title: C26_W1_bad


title: C26_BL_unknown

value: BL


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_1


title: C25_W4_bad


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_2


title: TP3_Rep2


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_23

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-CxxC/flox-CxxC


title: Female Muscle Rapamycin Biol Rep 3

description: Library name: Sample 7


title: C25_W1_bad


title: TP3_Rep1


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_21

value: growing oocyte day 14


title: Female Muscle Rapamycin Biol Rep 1

description: Library name: Sample 5


title: C25_BL_unknown

value: unknown


title: Male Muscle Rapamycin Biol Rep 4

description: Library name: Sample 4

value: 24 months


title: T3_Rep1

value: CD14+ monocytes

value: TNF


title: T3_Rep3


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_20


title: Female Muscle Rapamycin Biol Rep 2

description: Library name: Sample 6

value: C3B6F1 wild type


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_19


title: Male Muscle Rapamycin Biol Rep 3

description: Library name: Sample 3

value: Male


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_22


title: P3_Rep2

value: PGE


title: IFNG_Rep1

description:
Sample_US-G-Do1
rawcounts_IFNg.txt


title: C23_W4_good

value: blood plasma

value: good


title: IFNg_TP3_Rep3


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_16


title: C23_W1_good


title: AT093

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

institute: University of Zurich

description: Library name: AT093

data_processing:
Base calling was done using Illumina RTA2
Illumina bc12fastq v2.20 was used for demultiplexing and fastq file generation
Reads were pseudoaligned using kallisto to GRCm38 release 95  to get gene counts (Data-counts.txt)
Cells that passed quality control were normalized (Data-normed.tsv)
Differential gene expression was analyzed using edgeR.
Assembly: GRCm38, Ensemble release 95
Supplementary files format and content: Data-counts.tsv; raw counts
Supplementary files format and content: Data-normed.tsv; normalized counts

source_name: brain

extract_protocol:
single cell extraction via patch pipette
Nextera XT DNA Library Preparation kit

value: brain

value: VTA projecting neurons in the lateral nucleus accumbens

value: HFD

tag: batch


title: C21_BL_unknown


title: AT091

description: Library name: AT091


title: IFNg_TP3_Rep1


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_14


title: C23_BL_unknown


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_18


title: C26_W4_bad

value: bad


title: Male Muscle Rapamycin Biol Rep 1

description: Library name: Sample 1

value: Muscle

value: rapamycin


title: AT087

description: Library name: AT087


title: Male Muscle Rapamycin Biol Rep 2

description: Library name: Sample 2


title: C21_W4_good


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_17

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-CxxC/flox-CxxC


title: IFNg_T3_Rep3


title: C21_W1_good


title: AT094

description: Library name: AT094


title: T3_Rep2


title: IFNg_T3_Rep1


title: C16_W4_bad


title: IFNg_TP3_Rep2


title: C17_W4_good


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_10

value: growing oocyte day 14


title: AT085

description: Library name: AT085

value: NORM


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_15


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_13


title: P3_Rep3


title: AT090

description: Library name: AT090


title: C17_W1_good


title: P3_Rep1


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_11


title: IFNg_T3_Rep2


title: AT081

description: Library name: AT081


title: C2

city: Guangzhou

first: Yuke

last: Meng

state: Guangdong

address: 1023-1063, South Shatai Road, Baiyun dictrict

institute: Southern Medical University

data_processing:
fastp software (v0.20.0) was used to trim adaptor and remove low quality reads to get high quality clean reads. STAR software (v2.7.9a) was used to align the high-quality clean reads to the mouse reference genome (mm39). featureCounts software (v2.0) was used to get the raw gene level mRNA.
Assembly: GRCm39/mm39
Supplementary files format and content: raw counts and annotations in excel format

source_name: Bone marrow

extract_protocol:
A total of 10^7 cells were prepared for cell lysis. Then, the cell medium was discarded, and the cells were washed twice with ice-cold PBS containing 100 μg/mL cycloheximide (Adooq, 66-81-9). EpiTM RiboRNA Depletion Kit (Human/Mouse/Rat) (Epibiotek, R1805) was used for rRNA depletion.
mRNA libraries were constructed by using Illumina TrueSeq mRNA sample prepa ration kit (Cat. No. RS-122-2101) according to the manufacturer’s instructions.

treatment_protocol: Using BMDMs from WT and Nat10 CKO mice after 3-day-RANKL-induced osteoclastogenesis

value: Bone marrow

value: Bone marrow derived monocytes

value: WT

value: Osteoclast differentiation


title: AT086

description: Library name: AT086


title: IFNg_P3_Rep1

value: CD14+ monocytes


title: IFNg_P3_Rep2


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_7


title: C16_W1_bad


title: IFNg_C3_Rep3

value: IFNg


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_9


title: C16_BL_unknown

value: blood plasma

value: BL

value: unknown


title: AT076

description: Library name: AT076

value: brain

value: VTA projecting neurons in the lateral nucleus accumbens


title: IFNg_C3_Rep2


title: C17_BL_unknown


title: R1

value: Nat10 conditional knockout


title: IFNg_P3_Rep3


title: R2


title: AT073

description: Library name: AT073

value: HFD


title: IFNg_C3_Rep1


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_4


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_8


title: AT082

description: Library name: AT082


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_6


title: AT078

description: Library name: AT078


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_5


title: C1


title: C3_Rep3

value: Ctrl


title: AT072

description: Library name: AT072


title: BMDMs, C2

data_processing:
Use the fastp software to trim adapters and remove low-quality reads to obtain clean reads. Use the bowtie software to align the clean reads to rRNA. Use the STAR software to align the clean reads that did not align to rRNA to the transcriptome, and count the alignment results. Since Ribo-seq sequencing data only captures fragments protected by ribosomes, we set the CDS mode here and use the htseq software to calculate the raw expression counts for all genes in each sample.
Assembly: GRCm39/mm39
Supplementary files format and content: raw counts and annotations in excel format
Library strategy: Ribo-seq

extract_protocol:
A total of 107 cells were prepared for cell lysis. Then, the cell medium was discarded, and the cells were washed twice with ice-cold PBS containing 100 μg/mL cycloheximide (Adooq, 66-81-9). EpiTM RiboRNA Depletion Kit (Human/Mouse/Rat) (Epibiotek, R1805) was used for rRNA depletion.
Sequencing libraries were constructed using QIAseq miRNA Library kit (QIAGEN, 1103679).


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_3

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-CxxC/flox-CxxC


title: AT071

description: Library name: AT071


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_2

value: growing oocyte day 14


title: AT070

description: Library name: AT070

value: NORM


title: GO_day14_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_1


title: BMDMs, R1

value: Bone marrow


title: BMDMs, R2

value: Bone marrow derived monocytes


title: AT067

description: Library name: AT067


title: tIMEC cells, RNA-Seq, ANP32E and RNaseH1 overexpression, rep4

description: The library was loaded on two lanes of the same flow cell. Merged raw data from the two flow cells are submited

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic tool with Illumina:HEADCROP and Illumina_General.fa indexes
Trimmed sequence reads were mapped to GrCh38 reference genome using STAR
Read count extraction was performed using STAR quantMode GeneCounts
Transcript abundance quantification and normalization was performed using Salmon tool
Assembly: hg38
Supplementary files format and content: tab-delimited text files including raw reads counts for each gene calculated by STAR
Supplementary files format and content: tab-delimited text files including TPM counts for each gene calculated by Salmon

extract_protocol:
RNA was harvested using TRIzol (Life Technologies) and purified with RNA-Clean adn Concentrator-25 kit (Zymo Research). 450 ng of total RNA were used for the construction of sequencing libraries.
Libraries were prepared using the TECAN Universal Plus™ Total RNA-Seq kit

value: tIMEC

value: Basal-like breast cancer

value: ANP32E overexpression, RNaseH1 overexpression


title: C3_Rep1

value: CD14+ monocytes


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_30

source_name: growing oocyte day 9

value: growing oocyte day 9

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ;Zp3-cre


title: AT063

description: Library name: AT063


title: AT066

description: Library name: AT066


title: BMDMs, C1.Input

description: macs2 IP vs Input enriched peaks

data_processing:
The adapter sequences and low-quality reads were trimmed using fastp (version 0.20.1), and the clean reads were subsequently aligned to the reference genome (mm39) using STAR (version 2.7.8a); peaks for all samples were identified using MACS2 (version 2.2.7.1).
Assembly: GRCm39/mm39
Supplementary files format and content: IP vs Input enriched peaks in bed format

extract_protocol:
The concentration of total RNA was measured by Qubit RNA HS assay kit (Invitrogen, Q32852). 100μg total RNA was fragmented into 100-200 nt RNA fragments using 10X RNA Fragmentation Buffer (100 mM Tris-HCl, 100 mM ZnCl2 in nuclease-free H2O). The reaction was stopped by adding 10X EDTA (0.5M EDTA). Acetylated RNA immunoprecipitation was performed using EpiTM ac4C immunoprecipitation kit (Epibiotek, R1815). Briefly, the fragmented RNA was incubated with Anti-N4-acetylcytidine (ac4C) antibody (abcam, ab252215) for 3 h at 4℃ and then with protein A/G magnetic beads (Thermo Fisher Scientific, 88802) at 4 ℃ for an additional 2 h to obtain immunoprecipitated RNA fragments. The ac4C-enriched RNA was purified by Zymo RNA clean and concentrator-25 kit (Zymo Research, R1017).
The library was prepared by EpiTM mini longRNA-seq kit (Epibiotek, E1802). Both the input samples without IP and the ac4C IP samples were subjected to 150-bp, paired-end sequencing on an Illumina NovaSeq 6000 sequencer.

value: WT

value: Osteoclast differentiation


title: BMDMs, C2.Input

description: macs2 IP vs Input enriched peaks


title: BMDMs, C2.IP

description: macs2 IP vs Input enriched peaks


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_28


title: tIMEC cells, RNA-Seq, ANP32E and RNaseH1 overexpression, rep3


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_27


title: tIMEC cells, RNA-Seq, ANP32E and RNaseH1 overexpression, rep2


title: tIMEC cells, RNA-Seq, ANP32E overexpression, rep4

value: ANP32E overexpression


title: AT060

description: Library name: AT060

value: brain

value: VTA projecting neurons in the lateral nucleus accumbens


title: C3_Rep2

value: Ctrl


title: tIMEC cells, RNA-Seq, ANP32E overexpression, rep3


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_24


title: AT069

description: Library name: AT069


title: BMDMs, C1


title: BMDMs, R2.IP

description: macs2 IP vs Input enriched peaks

value: Nat10 conditional knockout


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_26


title: BMDMs, C1.IP

description: macs2 IP vs Input enriched peaks


title: AT062

description: Library name: AT062

value: HFD


title: AT058

description: Library name: AT058


title: BMDMs, R1.Input

description: macs2 IP vs Input enriched peaks


title: tIMEC cells, RNA-Seq, ANP32E overexpression, rep1


title: BMDMs, R2.Input

description: macs2 IP vs Input enriched peaks


title: tIMEC cells, RNA-Seq, ANP32E overexpression, rep2


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_23


title: AT054

description: Library name: AT054

value: NORM


title: tIMEC cells, RNA-Seq, ANP32E and RNaseH1 overexpression, rep1


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_21


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_22


title: PDGFRB+ Sham 2

city: Edinburgh

first: Laura

last: Denby

state: Midlothian

address: Queen's Medical Research Institute, 47 Little France Cres

country: United Kingdom

institute: University of Edinburgh

data_processing:
FastQC was used for initial quality control (QC)
Reads were mapped to the mm10 transcriptome using RSEM and Bowtie2
DESeq2 was used for differential gene expression analysis.
Assembly: mm10
Supplementary files format and content: comma-separated value file including FPKM values for each sample.

extract_protocol:
Cells were FACS sorted ino individual cell populations.  RNA was extracted using the microRNeay kit.
Ovation RNA-Seq System V2was used as per manufactures instructions.

value: Kidney

value: PDGFRB+ Stromal Cell

value: Sham


title: BMDMs, R1.IP

description: macs2 IP vs Input enriched peaks

value: Bone marrow

value: Bone marrow derived monocytes


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_25


title: tIMEC cells, RNA-Seq, rep4

value: tIMEC

value: Basal-like breast cancer


title: AT049

description: Library name: AT049


title: PDGFRB+ Sham 3


title: AT044

description: Library name: AT044


title: AT059

description: Library name: AT059


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_20

value: growing oocyte day 9

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ;Zp3-cre


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_19


title: tIMEC cells, RNA-Seq, rep2

value: WT


title: AT031

description: Library name: AT031


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_18


title: AT029

description: Library name: AT029


title: tIMEC cells, RNA-Seq, rep1

description: The library was loaded on two lanes of the same flow cell. Fastq for the single lanes are load and identified as L001 and L002


title: AT028

description: Library name: AT028


title: tIMEC cells, ATAC-Seq, ANP32E and RNaseH1 overexpression, rep3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic tool with Illumina:HEADCROP  and NexteraPE-PE.fa indexes
Bam files were either processed individually for each replicate or biological replicates were merged.
DRIP-seq reads were aligned to the UCSC hg38 genome using Bowtie.
Aligned reads were converted to bedGraph and BigWig using samtools and wigtobigwig. Duplicated reads were removed and BigWig files were scaled according to library size using samtools bamCoverage.
Peakcalling was performed with Genrich tool and PCR duplicates removal.
Assembly: hg38
Supplementary files format and content: BigWig files of individual samples scaled according to library size, Bigwig files of merged biological relicates scaled for library size and without duplicates
Supplementary files format and content: Peaks list of narrowPeaks obtained by Genrich for individual biological replicates and merged biological replicates

extract_protocol:
Nuclei extraction and sample preparation was performed as reported in Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues.NatMethods 14, 959–962 (2017). https://doi.org/10.1038/nmeth.4396
Library Construction was performed according to the protocol described with custom indiced synthesized by IDT in Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962 (2017). https://doi.org/10.1038/nmeth.4396

value: ANP32E overexpression, RNaseH1 overexpression


title: F4/80+ Sham 2

value: F4/80+ Macrophage


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_16


title: tIMEC cells, ATAC-Seq, ANP32E and RNaseH1 overexpression, rep2


title: tIMEC cells, ATAC-Seq, ANP32E and RNaseH1 overexpression, rep1


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_15


title: F4/80+ Sham 3


title: AT027

description: Library name: AT027

value: brain

value: VTA projecting neurons in the lateral nucleus accumbens


title: AT026

description: Library name: AT026


title: tIMEC cells, RNA-Seq, rep3


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_14


title: AT025

description: Library name: AT025


title: F4/80+ Sham 4


title: tIMEC cells, ATAC-Seq, ANP32E overexpression, rep2

value: ANP32E overexpression


title: tIMEC cells, ATAC-Seq, ANP32E overexpression, rep3


title: PDGFRB+ Sham 1


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_13


title: PDGFRB+ Sham 4


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_12


title: AT024

description: Library name: AT024


title: CD31+ UUO 1

value: CD31+ Endothelial Cell

value: UUO


title: F4/80+ UUO 4

value: Kidney


title: AT022

description: Library name: AT022

value: NORM


title: tIMEC cells, ATAC-Seq, ANP32E overexpression, rep1


title: AT021

description: Library name: AT021


title: CD31+ Sham 4

value: Sham


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_11


title: tIMEC cells, ATAC-Seq, rep3


title: tIMEC cells, ATAC-Seq, rep2


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_17


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_10


title: LTL+ Sham 4

value: LTL+ Proximal Tubule Cell


title: tIMEC cells, ATAC-Seq, rep1


title: AT020

description: Library name: AT020


title: F4/80+ Sham 1


title: PDGFRB+ RUUO 2

value: PDGFRB+ Stromal Cell

value: RUUO


title: tIMEC-ANP32E-H1 cells, exogenous RNaseh1 treatment, rep1

data_processing:
Basecalls were performed using bcl2fastq for Novaseq output.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic tool with Illumina:HEADCROP 8 and TrueSeq3-SE.fa indexes
Bam files coming from technical replicates were merged.
DRIP-seq reads were aligned to the UCSC hg38 genome using Bowtie.
Aligned reads were converted to bedGraph and BigWig using samtools and wigtobigwig. BigWig files were scaled according to library size using samtools bamCoverage.
Peakcalling was performed with MACS2 using broadPeaks mode and the samples treated with exogenous RNaseH1 as background reference.
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: broadPeak (except for exogenous RNaseH1 treated samples)
Library strategy: DRIP-seq

extract_protocol:
Samples extraction was performed according to the protocol published in Nat Protoc. 2019 Jun;14(6):1734-1755.doi: 10.1038/s41596-019-0159-1.
Library preparation was adapted according to the protocol published in Nat Protoc. 2019 Jun;14(6):1734-1755.doi: 10.1038/s41596-019-0159-1 using NEBNext Ultra II Unique Dual Index.

value: tIMEC

value: Basal-like breast cancer

value: exogenous RNaseH1


title: AT019

description: Library name: AT019


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_8

data_processing:
RNA-Seq datasets were aligned to the Mus musculus genome assembly (GRCm38/mm10 Dec. 2011) as single-end (Smart-Seq2 polyA datasets) or paired-end (total random primed datasets) using STAR (Dobin et al. 2013) with parameters “-outFilterMultimapNmax 300 -outMultimapperOrder Random -outSAMmultNmax 1 -alignIntronMin 20 -alignIntronMax 1000000”
RNA-Seq samples for hybrid Bl6 x JF1 F1 2-cell embryos were separately aligned to Bl6 and JF1 genomes obtained by injecting JF1 single-nucleotide polymorphisms (SNPs) into reference mm10 genome using previously published SNP table (Takada et al. 2013). RNA-seq reads were categorized as maternal (Bl6), paternal (JF1) or undefined based on minimal number of mismatches in alignments to both genomes.
Assembly: mm10
Supplementary files format and content: BigWig (.bw) processed files were generated from BAM files using the function qExportWig from QuasR package selecting uniquely mapped reads. BigWig processed files for hybrid Bl6 x JF1 2-cell embryos were generated separately for maternal (files ending with MAT.bw), paternal (files ending with PAT.bw) and total alignments normalized by total number of mapped allelic reads (MAT and PAT) or total number of mapped reads.

extract_protocol:
After removing the zona-pellucida by treating with acid tyrode’s solution, oocytes and F1 hybrid 2-cell embryos were washed in PBS supplemented with 0.05% Polyvinyl alcohol and lysed in Smartseq2 lysis buffer.
Libraries were prepared by Smartseq2 protocol. cDNAs were prepared by oligo dT based reverse transcription and template switching using Superscript II reverse transcriptase followed by the pre-amplification PCR using KAPA HiFi HotStart ReadyMix PCR Kit and the purification using AMPure Xp beads. 1ng of pre-amplified cDNA was tagmented by Tn5 transposase and adapter-ligated fragments were amplified with adding Nextera XT indexes followed by the purification using AMPure XP beads. Libraries with different indexes were pooled and submitted to sequencing. For total RNA sequencing GOs were isolated from the d14.0 mice. 60-80 oocytes were pooled and frozen in 100μl of Buffer RL. 4 and 3 biological replicates were prepared for ctrl and Kdm2aKOKdm2bKO, respectively. RNA was purified by using Single Cell RNA Purification Kit (NORGEN; 51800). Libraries were prepared according to Illumina Stranded total RNA-seq protocol with Illumina IDT DNA/RNA UDI indexes.

value: growing oocyte day 9

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ;Zp3-cre


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_9


title: AT018

description: Library name: AT018


title: CD31+ Sham 1

value: WT


title: AT016

description: Library name: AT016

value: brain

value: HFD


title: tIMEC-ANP32E cells, exogenous RNaseh1 treatment, rep1

value: ANP32E overexpression


title: F4/80+ RUUO 6

value: F4/80+ Macrophage


title: tIMEC cells, exogenous RNaseh1 treatment, rep1


title: AT015

description: Library name: AT015

value: VTA projecting neurons in the lateral nucleus accumbens


title: PDGFRB+ RUUO 6

value: Kidney


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep4

value: ANP32E overexpression, RNaseH1 overexpression

value: no


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_6


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_5


title: AT012

description: Library name: AT012


title: F4/80+ RUUO 1


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_3


title: CD31+ RUUO 2

value: CD31+ Endothelial Cell


title: AT010

description: Library name: AT010

value: NORM


title: CD31+ Sham 2

value: Sham


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_4


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_2


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep2

value: tIMEC


title: AT003

description: Library name: AT003


title: tIMEC cells, ANP32E overexpression, rep4

value: Basal-like breast cancer


title: primary Leydig cells isolated from 24-mon-old mouse's testes_2

first: Jiajie

last: Yu

state: State

address: No.58 Zhongshan Second Road

institute: The First Affiliated Hospital, Sun Yat-sen University

description: Library name: oldlc2

data_processing:
Raw RNA sequencing data were pre-processed using fastp (version 0.23.4) and FastQC (version 0.12.1). Paired-end clean reads were mapped to the mm10 mouse reference genome using HISAT2 (version 2.2.1). Gene expression profiles were quantified using featureCounts (version 2.0.6) to obtain read counts.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: primary Leydig cells

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer's protocols.

value: primary Leydig cells

value: Leydig cells


title: primary Leydig cells isolated from 24-mon-old mouse's testes_1

description: Library name: oldlc1


title: PDGFRB+ RUUO 4

value: PDGFRB+ Stromal Cell

value: RUUO


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep1


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_1

value: growing oocyte day 9

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ;Zp3-cre


title: tIMEC cells, ANP32E overexpression, rep3

value: ANP32E overexpression


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep3


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_30

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_29


title: primary Leydig cells isolated from 2-mon-old mouse's testes_2

description: Library name: younglc2


title: tIMEC cells, ANP32E overexpression, rep2


title: tIMEC cells, ANP32E overexpression, rep1


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_28


title: PDGFRB+ UUO 3

value: WT

value: UUO


title: primary Leydig cells isolated from 2-mon-old mouse's testes_1

description: Library name: younglc1


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_KO_7


title: tIMEC cells, rep4


title: MLTC-1 cells treated with Hymeglusin _3

description: Library name: H3

source_name: MLTC-1 cells

value: Hymeglusin


title: PDGFRB+ RUUO 1

value: Kidney


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_27


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_26


title: F4/80+ RUUO 4

value: F4/80+ Macrophage


title: MLTC-1 cells treated with Hymeglusin _1

description: Library name: H1


title: CD31+ RUUO 6

value: CD31+ Endothelial Cell


title: tIMEC cells, rep3

value: no


title: MLTC-1 cells treated with Hymeglusin _2

description: Library name: H2


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_25


title: PDGFRB+ UUO 2


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_24


title: tIMEC cells, rep1

value: tIMEC


title: MLTC-1 cells treated with DMSO_3

description: Library name: C3

value: DMSO


title: tIMEC cells, rep2

value: Basal-like breast cancer


title: PDGFRB+ UUO 4


title: CD31+ RUUO 1


title: MLTC-1 cells treated with DMSO_2

description: Library name: C2

value: Leydig cells


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_23


title: MLTC-1 cells treated with DMSO _1

description: Library name: C1


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep1, Rabbit IgG

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic tool with Illumina:HEADCROP
Bam files were aligned on the reference genome, and downsampled randomly to obtain the same reads number for every sample.
Peaks were called using MACS2 tool
Assembly: hg38
Supplementary files format and content: bigWig files of aligned reads
Supplementary files format and content: .broadPeak files of called peaks
Library strategy: CUT&RUN

extract_protocol:
Cells were permeabilized using Digitonin wash buffer and functionalized on Concanavalin coated beads as described in Skene et al. dx.doi.org/10.17504/protocols.io.mgjc3un
Library preparation was performed as described in Skene et al. dx.doi.org/10.17504/protocols.io.mgjc3un by adapting NEBNext Ultra II DNA Library Prep kit and Unique Dual Index.

value: ANP32E overexpression, RNaseH1 overexpression


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_22


title: LTL+ UUO 4

value: LTL+ Proximal Tubule Cell


title: F4/80+ UUO 2


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_21

value: growing oocyte day 9


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep1, H2A.Z, Abcam


title: CD31+ UUO 4


title: MN1-BEND2_2

city: Beijing

first: wei

last: Shi

address: Chinese Institute for Brain Research, Beijing(CIBR), Jianzan Building, No.26, Science Park Road, Zhongguancun Life Science Park, Changping District, Beijing, China

institute: Chinese institute for brain research

description: Library name: Sample4

data_processing:
Sequencing reads were aligned to the mm10 mouse reference genome using bowtie2 with default settings. Peak calling was performed using MACS2.
Assembly: mm10
Supplementary files format and content: csv files include peaks for samples.

source_name: mouse brian

extract_protocol:
Cells were isolated from P4 Olig2Cre;Ai14 and Olig2Cre;MN1:BEND2;Ai14 mouse forebrains by FACS, and 3× 104 cells (>95% viability) were washed with cold PBS, spun down at 500× g and 4°C for 5 minutes, and resuspended in 50 μL cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.1% IGEPAL CA-630 for 10 min on ice. Nuclei were centrifuged at 500 g and 4 °C for 10 min, resuspended in a 50 μL Tn5 transposase reaction mixture (Vazyme TD501), and incubated at 37°C for 30 minutes.
Fragments were immediately purified with 2× AMPure XP beads (Vazyme N411-01), and library amplification was performed using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme TD501). Libraries were sequenced on an Illumina Nova 6000 platform using a 150 bp paired-end setting.

value: mouse brian


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep1, acH2A.Z


title: CD31+ UUO 2


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_20


title: MN1-BEND2_1

description: Library name: Sample3


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep1, pS2RNApolII, Abcam


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_19


title: LTL+ RUUO 2

value: RUUO


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_18

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ


title: ctrl_2

description: Library name: Sample2


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep1, pS2RNApolII, ActiveMotif


title: CD31+ Sham 3

value: WT

value: Sham


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_17


title: ctrl_1

description: Library name: Sample1


title: LTL+ UUO 1

value: UUO


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep1, pS5RNApolII


title: CD31+ RUUO 4

value: Kidney


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep1, cMYC


title: LTL+ UUO 3


title: Mutant_scRNAseq_1

description: Library name: Sample3

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrices using CeleScope (https://github.com/singleron-RD/CeleScope) v1.9.0 pipeline (Singleron Biotechnologies). MN1:BEND2 fusion was constructed as an exogenous gene by CeleScope mkref pipeline, and appended to the mouse reference genome (GRCm38/mm10). UMI counts and gene counts of each cell were acquired with featureCounts (v2.0.) software, and used to generate expression matrix files for subsequent analysis.
Assembly: GRCm38/mm10
Supplementary files format and content: tar archives include matrix.mtx, barcode.tsv, and genes.tsv files.

extract_protocol:
Brains of neonatal mice were extracted and transferred into 60mm dishes with 1X Lo Ovo buffer (1% BSA in DPBS, Sigma-Aldrich #A3803) and pial membranes were carefully removed. All procedures were done at room temperature, unless otherwise stated. Forebrains from individual neonatal mice were cut into chunks and placed in papain (20U/mL in EBSS, Worthington #LK003176，Worthington #LK003188) and DNase (200U/mL in ddH2O, Worthington #LK003170) in 1X Lo Ovo. Tissue chunks were digested for 30 min at 37 °C, then washed by 1X Lo Ovo for 2-3 times and triturated by 5 mL pipette and P-1000 pipetman. The cells were centrifuged for 15 min at 300 x g, then discarded supernatant and resuspended cell pellets with 1X Lo Ovo. Cells were kept on ice before sorting. For fluorescence-activated cell sorting (FACS), the cells were incubated with DAPI (1μg/mL, Sigma-Aldrich #D9542) for 10 min and then sorted using the BD FACSAria Fusion Flow Cytometer (BD Biosciences). After gating on morphology and singlets, DAPI-negative (live) and tdTomato+ cells were collected into a 5mL tube (Eppendorf #30119401) containing 1X Lo Ovo.
The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPER® Single-Cell RNA Library Kit (Singleron 4180011). Briefly, single cell suspension loaded onto the GEXSCOPE microchip which integrates single cell capture, cell lysis, capture of the cellular mRNA and molecular labeling. The barcoded cDNA was then amplified and used for the construction of single cell NGS libraries. The loading of the GEXSCOPE microchip was performed using the Singeron Matrix instrument. Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina NovaSeq 6000 with 150 bp paired end reads.

value: brain

value: Olig2 lineage

value: postnatal day3

value: female


title: MN1-BEND2

description: Library name: Sample1

data_processing:
Sequencing reads from CUT&Tag were aligned to the mm10 mouse reference genome using bowtie2 with default settings. Peak calling was performed using MACS2. The resulting peaks were further filtered using the ENCODE ChIP-seq blacklist and CUT&RUN suspected regions.
Assembly: mm10
Supplementary files format and content: csv files include peaks.
Library strategy: CUT&Tag

source_name: mouse brain

extract_protocol:
The CUT&Tag assay was performed in accordance with the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme TD903). Briefly, concanavalin A (ConA) coated magnetic beads were pre-activated and stored on ice until use. 50,000 sorted cells were collected at 600g at room temperature for 5 minutes. Cell pellets were then lysed with the nuclear extraction buffer on ice for 10 minutes. Nuclei were centrifuged, resuspended and then incubated with activated ConA beads at room temperature for 10 minutes. The nuclei-ConA beads were sequentially incubated with the HA-antibody (Abcam 9110)，secondary antibody and pA/G-Transposon. Chromatin tagmentation and library amplification were performed according to the kit protocol. The TruePrep Index Kit V4 for Illumina (Vazyme TD204) was used for index-labeled DNA library preparation. Size distribution within the library was measured on Bioanalyzer 2100 (Agilent). The library was sequenced on a Novaseq using 150 bp paired-end sequencing.
The TruePrep Index Kit V4 for Illumina (Vazyme TD204) was used for index-labeled DNA library preparation. Size distribution within the library was measured on Bioanalyzer 2100 (Agilent). The library was sequenced on a Novaseq 6000 using 150 bp paired-end sequencing.

treatment_protocol: Cells were isolated from the forebrains of P3 Olig2Cre;MN1:BEND2;Ai14 mice.

value: mouse brain


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep1, H2A.Z, ActiveMotif

value: tIMEC

value: Basal-like breast cancer


title: Mutant_scRNAseq_2

description: Library name: Sample4


title: Control_scRNAseq_2

description: Library name: Sample2


title: LTL+ RUUO 3


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep1, pRPA32(S33)

value: ANP32E overexpression, RNaseH1 overexpression


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_14


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_16


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep1, Rloop


title: Control_scRNAseq_1

description: Library name: Sample1


title: LTL+ Sham 3

value: LTL+ Proximal Tubule Cell


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_13

value: growing oocyte day 9


title: ER-3

city: Chongqing

first: Zhe

last: Chen

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing Medical University

data_processing:
Low-quality reads and adaptor sequences were removed by Trim Galore v0.4.4 with parameters “-q 10 -length 30 -stringency 5’.”
Paired-end reads were mapped to the mm10 reference genome using Bowtie2 version 2.2.9. Reads that aligned to the mitochondrial genome were filtered, and PCR duplicates were removed with picard MarkDuplicates.
To identify peaks, the bam files containing unique, nonchrM reads were used to call peaks with MACS2 using parameters ‘‘-nomodel-keep-dup all -q 0.01-shift -100-extsize 200-call-summits -g mm’’.
For differential coverage, corresponding bam files were merged to call peaks to get a union peak set. For each peak in the peak set, raw ATACseq reads were counted by featureCounts.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

extract_protocol:
About 5,000 HSCs was resuspended in 50 µL of lysis buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween 20, 0.01% Digitonin) and incubated on ice for 5 min. After lysis, 950 µL wash buffer was added to the sample. The supernatant was removed by centrifugation (500 g, 10 min).
Then, 4 µLPBS, 0.4 µL 10% Tween 20, 0.4 µL 1% Digitonin, 13.6 µL ddH2O, 20 µl 2×TD buffer, and 1.6 µL Transposome Mix were added to the sample, which was mixed and incubated at 37°C for 30 min. The reaction was terminated by incubating with 10 µL stop buffer. Then the tagment DNA was extracted using 2×DNA Extract Beads (Novoprotein). Total 35 µL DNA was transferred to a 0.2 ml PCR tube, and 2.5 µL N5 primer, 2.5 µL N7 primer, and 10 µL 5×AmpliMix were added. PCR was performed to amplify the library for 13-16 cycles. After the PCR reaction, libraries were purified using the 1.2×DNA Clean Beads (Novoprotein).

treatment_protocol: HSCs (CD48-CD150+LSK) were sorted from wild-type C57BL/6J mice injected intraperitoneally with DMSO or Tunicamycin (2 mg/kg) and then subjected to ATAC-seq.

value: Bone marrow

value: Hematopoietic stem cell

value: Wild-type

value: Tunicamycin


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep1, TOP2B

value: Etoposide 5 μM 1h MedChemExpress HY-13629


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep1, TOP2A


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_12

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_11


title: ER-2


title: ER-1


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep1, p400


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_15


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_8


title: LTL+ RUUO 4

value: Kidney

value: WT

value: RUUO


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep1, ANP32E, LSBio


title: WT-3

value: DMSO


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep1, ANP32E, Abcam


title: LTL+ Sham 1

value: Sham


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_7


title: LTL+ SHAM 2


title: F4/80+  UUO 3

value: F4/80+ Macrophage

value: UUO


title: WT-1


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep1, pH2A.X

value: tIMEC

value: Basal-like breast cancer


title: WT-2


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_10


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_9


title: tIMEC cells, ANP32E overexpression, rep1, Rabbit IgG

value: ANP32E overexpression


title: LTL+ SHAM UUO 2

value: LTL+ Proximal Tubule Cell


title: Tunicamycin-5

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.9.
Fragments per kilobase per million (FPKM) estimation was performed with Cufflinks v2.1.1, aligned reads were counted with HTSeq (a Python framework to work with high-throughput sequencing data), and differential expression analysis was performed with DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted with miRNeasy Kit (QIAGEN).
The mRNA was reverse-transcribed and amplified according to the method Geo-seq, then the library was constructed using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) according to the manufacturer’s instruction.

treatment_protocol: HSCs (CD48-CD150+LSK) were sorted from wild-type C57BL/6J mice injected intraperitoneally with DMSO or Tunicamycin (2 mg/kg) and then subjected to RNA-seq.

value: Bone marrow


title: CD31+ UUO 3

value: CD31+ Endothelial Cell


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_5

value: growing oocyte day 9


title: Tunicamycin-4

value: Hematopoietic stem cell

value: Wild-type

value: Tunicamycin


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_6

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ


title: Tunicamycin-3


title: F4/80+ UUO 1

value: Kidney

value: WT


title: PDGFRB+ UUO 1

value: PDGFRB+ Stromal Cell


title: tIMEC cells, ANP32E overexpression, rep1, H2A.Z, Abcam


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_4


title: ep_OsmrWT, colitis, day 21, E2_2_5

city: Berlin

first: Ahmed

middle: Nabil

last: Hegazy

address: Hindenburgdamm 30

department: Department of Gastroenterology, Infectious Diseases and Rheumatology

institute: Charité - University Medicine Berlin

data_processing:
raw data were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data
The reads were aligned with HISAT2 to the GRCm39 genome annotation
The gene counts were calculated with htseq-count package
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw counts for each sample

source_name: colon

extract_protocol: Mice were euthanized via cervical dislocation, and their colons were harvested into ice-cold PBS. After longitudinal opening and cleaning, colons were sectioned into 2 mm pieces and subjected to sequential EDTA washes in RPMI with 10% FCS at 37°C to detach epithelial cells. For the sequencing of VillincreERT2 Osmrfl/fl and VillincreERT2 Osmrfl/+ epithelial cells, EpCAM+ live epithelial cells were FACS-sorted and lysed in the RLT lysis buffer and RNA was extracted using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol. RNA integrity was assessed as per the manufacturer's guidelines. The following procedures were performed at Novogene, where sequencing was carried out on a HiSeq X sequencer to generate 150 bp paired-end reads.

treatment_protocol: Col1a2creERT2 and VillincreERT2 Osmr^fl/fl mice were treated with 75 mg/kg body weight of tamoxifen intraperitoneally daily for one week, following the Jackson Laboratory protocol. Control mice, either cre+ Osmr^fl/wt or Osmr^fl/fl without creERT2, also received tamoxifen. Colitis was induced by orally inoculating the mice with 1 × 10^8 CFU of H. hepaticus for two days, followed by weekly 1 mg injections of anti-IL10R antibody.

value: colon

value: primary cells

value: epithelial cells

value: Wildtype


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep1, ANP32E, Sigma

value: tIMEC

value: Basal-like breast cancer

value: ANP32E overexpression, RNaseH1 overexpression


title: Tunicamycin-2

value: Bone marrow


title: ep_OsmrWT, colitis, day 21, E1_2_5


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_3


title: Tunicamycin-1


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_1


title: ep_OsmrWT, colitis, day 21, E1_2_4


title: ep_OsmrWT, colitis, day 21, E2_2_1


title: tIMEC cells, ANP32E overexpression, rep1, acH2A.Z

value: ANP32E overexpression


title: tIMEC cells, ANP32E overexpression, rep1, H2A.Z, ActiveMotif


title: tIMEC cells, ANP32E overexpression, rep1, pS2RNApolII, Abcam


title: DMSO-4

value: DMSO


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_2

value: growing oocyte day 9


title: ep_OsmrWT, colitis, day 21, E1_2_2


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_30

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-CxxC/flox-CxxC; Zp3-cre


title: DMSO-5

value: Hematopoietic stem cell

value: Wild-type


title: ep_OsmrKO, colitis, day 21, E2_1_3

value: IEC{delta}Osmr


title: tIMEC cells, ANP32E overexpression, rep1, pS2RNApolII, ActiveMotif


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_29


title: tIMEC cells, ANP32E overexpression, rep1, pS5RNApolII


title: DMSO-3


title: tIMEC cells, ANP32E overexpression, rep1, pRPA32(S33)


title: tIMEC cells, ANP32E overexpression, rep1, cMYC


title: ep_OsmrKO, colitis, day 21, E2_1_1


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_28


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_27


title: DMSO-1


title: ep_OsmrKO, colitis, day 21, E1_1_1


title: Emp1-ko-3

treatment_protocol: HSCs (CD48-CD150+LSK) from Emp1fl/fl and Emp1fl/fl,Tie2-Cre mice were sorted and then subjected to RNA-seq


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_26


title: tIMEC cells, ANP32E overexpression, rep1, TOP2B

value: Etoposide 5 μM 1h MedChemExpress HY-13629


title: Emp1-ko-2


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_24


title: DMSO-2


title: tIMEC cells, ANP32E overexpression, rep1, p400


title: ZT20-old-2

city: Lille

first: Joel

last: Haas

address: 1 Rue du Professeur Calmette

country: France

institute: Institut Pasteur de Lille

data_processing:
Primary analysis of raw sequencing datasets was performed using the nf-core/rnaseq v3.6 pipeline (https://doi.org/10.5281/zenodo.7998767).
Raw FastQ files were quality and adapter trimmed with Trim Galore v0.6.7. (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Ribosomal RNA reads were filtered out with SortMeRNA v 4.3.476.
Cleaned reads were aligned with STAR v2.6.1d77 against the GRCh38 genome from the Ensembl 108 database and expression for annotated genes was quantified using Salmon v1.5.278 in mapping-based mode.
Assembly: GRCm39
Supplementary files format and content: raw counts as caluclated by STAR v.2.7.6a in --quantMode GeneCounts

source_name: lung

growth_protocol: Male specific pathogen-free C57BL/6J young adult mice (2-month-old, 20-25g) and elderly mice (18-month-old, 35-45 g) were fed a standard rodent chow (SAFE A04, SAFE, Augy, France) with water ad libitum and housed in a 12-h light/dark cycle.

extract_protocol:
A frozen piece of lung was resuspended in 500 µL of TRIzol and RNA were extracted following the manufacturer protocol. RNA extracts were clean up with Macherey-Nagel nucleospin RNA column.
The quality of RNA was evaluated with a Bioanalyzer (Agilent Technologies) and the Agilent RNA 6000 nano kit. Only RNAs with RNA Integrity Number (RIN) over 7 were used. 200ng of RNA were used for library construction followed by 100 bp paired-end sequencing performed by DNBSEQ technology and DNA nanoballs.

treatment_protocol: Lungs from young mice and old mice were harvested at ZT0, ZT4, ZT8, ZT12, ZT16 and ZT20 (n=4-5/group), were perfused with 10 mL ice-cold PBS through using the right cardiac ventricule route. Lungs were incubated in RNA later for 10 minutes at room temperature, frozen in liquid nitrogen and stored at -80°C until RNA extraction.

value: lung

value: old

tag: number (zt)


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_25


title: ZT20-old-4


title: Emp1-fl-2


title: tIMEC cells, ANP32E overexpression, rep1, TOP2A

source_name: tIMEC


title: ZT20-old-1


title: ZT20-old-3


title: Emp1-fl-3


title: tIMEC cells, ANP32E overexpression, rep1, ANP32E, LSBio


title: tIMEC cells, ANP32E overexpression, rep1, ANP32E, Sigma


title: tIMEC cells, ANP32E overexpression, rep1, Rloop


title: tIMEC cells, ANP32E overexpression, rep1, ANP32E, Abcam


title: ZT20-young-5

value: young


title: ZT20-young-4


title: ep_OsmrKO, colitis, day 21, E1_1_3

value: colon

value: primary cells

value: epithelial cells


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_20


title: Emp1-ko-1


title: Emp1-fl-1


title: ZT20-young-3


title: tIMEC cells, ANP32E overexpression, rep1, pH2A.X

value: tIMEC

value: Basal-like breast cancer


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_19


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_18


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_23


title: ZT20-young-1


title: Col_Cadh5, colitis, day 21, E2_2_4_WT

source_name: colonic tissue

extract_protocol:
RNA was isolated using the Qiagen Mini RNA kit (Qiagen) following the manufacturer’s protocol.
The following procedures were performed at Novogene

value: colonic tissue

tag: tamoxifen treatment

value: Yes, day -7. to  day 0

value: whole tissue

value: wild type

value: H.h.+anti-IL10R, 3 weeks colitis


title: ZT20-young-2


title: tIMEC cells, rep1, H2A.Z, Abcam

value: WT


title: Col_a20_WT

value: untreated


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_17

value: growing oocyte day 9

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-CxxC/flox-CxxC; Zp3-cre


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_16


title: Col_a9_WT


title: Col_a10_WT


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_15


title: Col_a19_WT


title: Col_Cadh5, colitis, day 21, E2_2_3_WT


title: ZT16-old-3

value: lung


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_22


title: ZT16-old-4

value: old


title: tIMEC cells, rep1, acH2A.Z


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_14


title: tIMEC cells, rep1, pS2RNApolII, Abcam


title: Col_Villin, colitis, day 21, E2_2_5_WT


title: ZT16-old-2


title: tIMEC cells, rep1, Rabbit IgG


title: tIMEC cells, rep1, pS2RNApolII, ActiveMotif


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_13


title: tIMEC cells, rep1, H2A.Z, ActiveMotif


title: tIMEC cells, rep1, pS5RNApolII


title: Col_Villin, colitis, day 21, E1_2_4_WT


title: ZT16-young-5

value: young


title: ZT16-old-1


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_12


title: Col_Cadh5, colitis, day 21, E2_1_5

value: Endo{delta}Osmr


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_11


title: Col_Cadh5, colitis, day 21, E2_1_4


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_9


title: tIMEC cells, rep1, cMYC


title: tIMEC cells, rep1, Rloop


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_8


title: Col_Cadh5, colitis, day 21, E2_1_1


title: Col_Cadh5, colitis, day 21, E2_1_3


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_10


title: ZT16-young-3


title: tIMEC cells, rep1, pRPA32(S33)


title: Col_Villin, colitis, day 21, E2_1_3

value: IEC{delta}Osmr


title: ZT16-young-2


title: tIMEC cells, rep1, TOP2B

value: Etoposide 5 μM 1h MedChemExpress HY-13629


title: ZT16-young-1


title: ZT12-old-4


title: tIMEC cells, rep1, p400

value: tIMEC


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_6


title: Col_Villin, colitis, day 21, E2_1_2


title: Col_Villin, colitis, day 21, E2_1_1


title: ZT16-young-4


title: ZT12-old-3


title: tIMEC cells, rep1, ANP32E, LSBio

value: Basal-like breast cancer


title: Col_Villin, colitis, day 21, E1_1_3

value: colonic tissue


title: ZT12-old-2


title: tIMEC cells, rep1, TOP2A


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_5


title: tIMEC cells, rep1, ANP32E, Abcam


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_4


title: Col_Villin, colitis, day 21, E1_1_1

value: Yes, day -7. to  day 0


title: ZT12-old-1


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_2


title: Col_Col1a2, colitis, day21, E1_1_7

value: whole tissue

value: Stroma{delta}Osmr


title: Col_Col1a2, colitis, day21, E1_1_6

value: H.h.+anti-IL10R, 3 weeks colitis


title: ZT12-young-4


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_7


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_1


title: ZT12-young-3


title: ZT12-young-5


title: tIMEC cells, rep1, pH2A.X

value: WT


title: tIMEC cells, rep1, ANP32E, Sigma


title: SCC13: keratinocyte SCC BCC cell line

first: Tomonori

last: Oka

department: CBRC

institute: Massachusetts general hospital

data_processing:
The QC for the RNA samples was performed using Qubit and Bioanalyzer instruments.
Libraries were then prepared using NEBNext Ultra II non-directional RNA Library Prep kit
Library quality and concentration were assessed with Labchip and qPCR.
Libraries were sequenced on Novaseq6000 using PE150 sequencing.
Base calling was done with bcl2fastq.
Data was trimmed to remove low quality reads and adapter reads. Remaining reads were mapped to the reference genome using STAR, followed by calculation of FPKM.
genome build: Human genome/GRCh38
processed data files format and content: FPKM values

extract_protocol: Used RNAeasy mini kit (Qiagen) and followed instruction

value: cutaneous squamous cell carcinoma cell line


title: ZT12-young-2


title: Col_Col1a2, colitis, day21, E1_1_5


title: Col_Col1a2, colitis, day21, E1_1_4


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_26

first: Antoine

last: Peters

institute: Friedrich Miescher Institute

value: growing oocyte day 9

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-CxxC/flox-CxxC


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_25


title: ZT12-young-1

value: lung


title: Col_Col1a2, colitis, day21, E1_1_3


title: GO_day9_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_3

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-CxxC/flox-CxxC; Zp3-cre


title: BCC: keratinocyte SCC BCC cell line

value: basal cell carcinoma cell line

value: BCC


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_24


title: ZT8-old-5

value: old


title: GO_day9_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_23


title: GO_day14_totbulkRNA_KO.Kdm2a_KO.Kdm2b_KO_rep3

source_name: growing oocyte day 14

value: growing oocyte day 14

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ;Zp3-cre


title: GO_day14_totbulkRNA_KO.Kdm2a_KO.Kdm2b_KO_rep2


title: SCC12: keratinocyte SCC BCC cell line


title: GO_day14_totbulkRNA_KO.Kdm2a_KO.Kdm2b_KO_rep1


title: ZT8-old-4


title: ZT8-old-2