title: Monocytes, 125D+LPS, non-primed, ATAC replicate 3

description: Library name: DL-np_ATAC_R3

data_processing:
ATAC-seq: Paired-end reads were aligned using the STAR aligner. ENCODE-identified blacklisted regions and reads with mapping quality score < 2 were filtered out. Duplicates were identified and marked with samtools markdup. Peak calling done with MACS3 (version 3.0.1) utilizing callpeak function with the parameters -F BAM, --shift 75 --extsize 150 -g hs -q 0.01. Consensus peak summits matrix generated with DiffBind utilizing dba.count function with summits parameter set to 75.
Assembly: GRCh38.p13
Supplementary files format and content: Consensus_summit_matrix.csv - Matrix of raw values corresponding to each specific peak summit (rows) across all samples (columns) generated by DiffBind,

extract_protocol:
ATAC-seq: nuclei were isolated from 1.25 × 10⁶ cells using Buffer A (15 mM Tris-HCl, pH 8.0; 15 mM NaCl; 60 mM KCl; 1 mM EDTA; 0.5 mM EGTA; 0.5 mM spermidine; 1% protease inhibitor) supplemented with 0.04% IGEPAL. A total of 100,000 nuclei were subjected to transposition using a Tn5 transposase reaction mix (Illumina), containing Tn5 transposase, 0.01% digitonin, and 0.1% Tween-20. The reaction was incubated for 30 minutes at 37 °C in a Thermomixer. Following purification with the DNA Clean & Concentrator-5 Kit (Zymo Research), the ATAC-seq libraries were amplified via PCR, purified, and size-selected using SPRISelect purification beads (Beckman Coulter). Library quality was assessed with a Bioanalyzer (Agilent High-Sensitivity DNA Kit), and the quantified, indexed libraries were pooled for sequencing.
ATAC-seq  libraries were sequenced on an Illumina NextSeq500 system (Illumina) at 75 bp read length using standard protocols at the Gene Core facility of the EMBL (Heidelberg, Germany).


title: 27_D11_Ad26.MVA

status: Public on Jun 13 2025

type: SRA

city: Oxford

first: Daniel

last: O'Connor

state: Oxfordshire

address: Churchill Hospital

department: Paediatrics

country: United Kingdom

institute: University of Oxford

library_source: transcriptomic

data_processing:
The sequencing data were aligned against the whole human (Homo sapiens) genome build GRCh38 (https://ccb.jhu.edu/software/hisat2/index.shtml), using STAR (version 2.6.1d). Gene features were counted using HTSeq (version 0.11.1), using human gene annotation general transfer format version GRCh38.92 (www.ensembl.org).  Genes with low counts across most libraries were removed by only retaining genes with abundance greater than 3 counts per million in 4 or more samples. Ribosomal RNA (rRNA), sex chromosome genes, mitochondrial RNA and haemoglobin genes were excluded from downstream analysis.
Assembly: human (Homo sapiens) genome build GRCh38 (
Supplementary files format and content: The expression E value is the gene expression value derived from the voom‐limma workflow

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
Venous peripheral blood (up to 3ml) was collected directly in TempusTM RNA tube immediately pre-vaccination, then 10 days post-first vaccine and 7 days post-second vaccine. RNA was extractedusing theTempus™spin RNAisolationkit(Invitrogen, USA).Eluted RNA was quantifiedusingQubit™ RNA BR Assay Kit(Invitrogen, USA) and quality control was conducted usingthe Agilent RNA ScreenTape assay on the 4200 TapeStation System (Agilent, USA). RNA was ribodepleted and globin depleted usingRibo-ZeroTM Gold rRNA removal Kit (Illumina, USA).
RNA was converted to cDNA, second-strand cDNA synthesis incorporated dUTP. The cDNA was end-repaired, A-tailed and adapter-ligated and prior to amplification, samples underwent uridine digestion. The prepared libraries were size selected, multiplexed and quality controlled before 75bp paired-end sequencing (HiSeq4000). Sequencing was conducted at the Wellcome Trust Centre for Human Genetics (Oxford, UK).

tag: tissue

value: Whole blood

tag: Sex

value: Female

tag: cell type

value: blood cells

tag: visit

tag: treatment


title: Plate2_A04

city: Palo Alto

first: Rebeca

last: Arroyo Hornero

state: California

address: Campus Drive

country: USA

institute: Stanford

library_source: transcriptomic single cell

data_processing:
Data was processed with STAR
Assembly: hg19
Supplementary files format and content: feature_counts.csv (csv file)

source_name: blood

extract_protocol:
Plasmocytoid dendritic cells were magnetically enriched from peripheral blood of a healthy donor, cultured with IL-3 and CD40L for two days and single-cell FACS-sorted on a FACS Aria Fusion (BD Biosciences) into Takara Smart-Seq Single Cell kit lysis buffer and frozen at -80C.
The Illumina Nextera XT DNA Library Prep and Unique Dual Index Kits (Illumina) were used for library preparation according to manufacturer's instructions.

value: blood

value: plasmacytoid dendritic cell

value: sorted as:day2_pDC_donor 1


title: 5xFAD 40Hz 1hr Rep2 VC

city: Atlanta

first: Levi

middle: B.

last: Wood

state: GA

address: 315 Ferst Dr NW Rm 3303

institute: Georgia Institute of Technology

description: 231 VC

data_processing:
Alignment was performed by Molecular Research Lab (https://mrdnalab.com) and data was validated for fastq integrity and quality. Each library was split between four lanes and .fastq.gz files were merged using DNAstar ArrayStar. Next, Qseq reads were mapped using the mouse reference genome GRCm39 (GCF_000001635.27). For the read assignment, the threshold was set at 20bp and 80% of the bases matching within each read. Duplicated reads were eliminated and genes with less than 20 total raw counts were removed from analysis. Gene counts were normalized using DESeq2 in R.
Assembly: mouse reference genome GRCm39 (GCF_000001635.27)
Supplementary files format and content: Raw count values in csv format.

organism: Mus musculus

source_name: Brain Tissue

extract_protocol:
RNAwasisolated from mouse brain tissue  tissues using Qiagen RNeasy kit(217804; Qiagen; Hilden, Germany)according to the manufacturer’s protocols.
Libraries were sequenced for paired-end mRNA using the NovaSeq 6000 sequencing system to obtain a sequencing depth of 30 to 40 million reads per sample. Before sequencing, quality control was performed using a bioanalyzer for RNA integrity number greater than seven. The NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit were used to prepare sequencing libraries.

value: Brain Tissue

tag: tissue region

value: VC

tag: age

value: Male

tag: genotype

value: 5xFAD 40Hz 1hr


title: 5xFAD 40Hz 1hr Rep2 Hip

description: 231 Hip

value: Hip


title: Monocytes, 125D+LPS, non-primed, ATAC replicate 2

city: Olsztyn

first: Mariusz

last: Jankowski

address: Trylińskiego

country: Poland

institute: Institute of Animal Reproduction and Food Research

description: Library name: DL-np_ATAC_R2

library_source: genomic

molecule: genomic DNA

source_name: peripheral blood

treatment_protocol: Cells treated with either 10 nM 1,25(OH)2D3 or 100 ng/ml LPS (both from Sigma-Aldrich), or with the respective vehicle controls (0.1% ethanol [EtOH] or 0.1% dimethyl sulfoxide [DMSO]).

value: peripheral blood

tag: cell line

value: monocytes


title: Plate2_A02


title: 26_D11_Ad26.MVA


title: 5xFAD 40Hz 1hr Rep1 VC

description: 216 VC


title: 26_D1_Ad26.MVA


title: 5xFAD 40Hz 1hr Rep1 Hip

description: 216 Hip


title: 28_D1_Ad26.MVA


title: Plate2_A01


title: Plate2_A03


title: Monocytes, 125D+LPS, non-primed, ATAC replicate 1

description: Library name: DL-np_ATAC_R1


title: 5xFAD 40Hz 1hr Rep3 VC

description: 241 VC


title: Monocytes, solvent, 48 hours, RNA replicate 2

description: Library name: Solvent_48_RNA_R2

data_processing:
RNA-seq: Single-end reads were aligned using STAR aligner. Read quantification performed with FeatureCounts (version 2.0.6) with settings for reverse-strand.
Assembly: GRCh38.p13
Supplementary files format and content: Gene_count_matrix.csv - raw gene counts matrix with counts of protein coding genes with an expression level > 0.5 CPM, without mitochondrially encoded genes and genes missing HGNC symbols

extract_protocol:
RNA-seq: cells were preserved in TRIzol (1 ml per 5 × 10⁶ cells; Zymo Research) at -80 °C overnight before RNA extraction. Total RNA was isolated using the High Pure RNA Isolation Kit (Roche) with minor modifications. Chloroform (1:5 ratio) was added to thawed TRIzol samples to induce phase separation. Phase-lock gel heavy tubes (5Prime) were used to efficiently separate proteins into the organic phase, DNA at the interface, and RNA in the aqueous phase. RNA quality and quantity were assessed using a Bioanalyzer (Agilent 2100; RNA Nano 6000 Assay), ensuring a RIN (RNA integrity number) > 8. Ribosomal RNA (rRNA) was depleted using the NEBNext rRNA Depletion Kit, and complementary DNA (cDNA) libraries were prepared from the rRNA-depleted RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, following the manufacturer’s protocol. Library quality was confirmed using the Agilent DNA 1000 Chip, and indexed libraries were pooled prior to sequencing.
RNA-seq libraries were sequenced on an Illumina NextSeq500 system (Illumina) at 75 bp read length using standard protocols at the Gene Core facility of the EMBL (Heidelberg, Germany).

value: control


title: Plate2_A05


title: Monocytes, 1,25D+LPS, LPS-primed, ATAC replicate 3

description: Library name: DL-Lp_ATAC_R3


title: Plate1_E08

value: sorted as:fresh tDC_donor 1


title: 26_D92_Ad26.MVA


title: Plate1_E07


title: 5xFAD 40Hz 0.5hr Rep7 Hip

description: 294 Hip

value: 5xFAD 40Hz 0.5hr


title: 5xFAD 40Hz 0.5hr Rep6 VC

description: 280 VC


title: 25_D11_Ad26.MVA


title: Monocytes, 1,25D+LPS, LPS-primed, ATAC replicate 1

description: Library name: DL-Lp_ATAC_R1


title: 27_D1_Ad26.MVA


title: Monocytes, 1,25D+LPS, LPS-primed, ATAC replicate 2

description: Library name: DL-Lp_ATAC_R2


title: Plate1_E06


title: 25_D1_Ad26.MVA


title: Monocytes, 1,25D+LPS 1,25D-primed, ATAC replicate 3

description: Library name: DL-Dp_ATAC_R3


title: Plate1_E05


title: 25_D36_Ad26.MVA


title: 5xFAD 40Hz 0.5hr Rep5 VC

description: 210 VC


title: Monocytes, 1,25D+LPS 1,25D-primed, ATAC replicate 2

description: Library name: DL-Dp_ATAC_R2


title: Plate1_E04


title: 24_D64_Ad26.MVA


title: 5xFAD 40Hz 0.5hr Rep5 Hip

description: 210 Hip


title: Monocytes, 1,25D+LPS 1,25D-primed, ATAC replicate 1

description: Library name: DL-Dp_ATAC_R1


title: 24_D11_Ad26.MVA


title: Monocytes, LPS, non-primed, ATAC replicate 2

description: Library name: L-np_ATAC_R2

value: LPS


title: 24_D1_Ad26.MVA

value: Whole blood


title: Plate1_E03


title: 5xFAD 40Hz 0.5hr Rep4 VC

description: 152 VC


title: Monocytes, LPS, non-primed, ATAC replicate 3

description: Library name: L-np_ATAC_R3


title: Monocytes, LPS, non-primed, ATAC replicate 1

description: Library name: L-np_ATAC_R1


title: Monocytes, LPS, LPS-primed, ATAC replicate 3

description: Library name: L-Lp_ATAC_R3


title: 5xFAD 40Hz 0.5hr Rep4 Hip

description: 152 Hip


title: Plate1_E02


title: 23_D64_Ad26.MVA


title: 23_D1_Ad26.MVA


title: 5xFAD 40Hz 0.5hr Rep3 VC

description: 127 VC


title: Monocytes, LPS, LPS-primed, ATAC replicate 2

description: Library name: L-Lp_ATAC_R2


title: 5xFAD 40Hz 0.5hr Rep3 Hip

description: 127 Hip


title: 5xFAD 40Hz 0.5hr Rep2 VC

description: 122 VC


title: 23_D11_Ad26.MVA


title: 5xFAD 40Hz 0.5hr Rep6 Hip

description: 280 Hip


title: 5xFAD 40Hz 0.5hr Rep2 Hip

description: 122 Hip


title: Plate1_D10


title: 22_D11_Ad26.MVA

value: Female


title: 22_D1_Ad26.MVA

value: blood cells


title: 5xFAD 40Hz 0.5hr Rep1 VC

description: 104 VC


title: Monocytes, LPS, LPS-primed, ATAC replicate 1

description: Library name: L-Lp_ATAC_R1


title: 22_D64_Ad26.MVA


title: Plate1_D09

value: blood


title: Monocytes, LPS 1,25-primed, ATAC replicate 3

description: Library name: L-Dp_ATAC_R3


title: Plate1_D07

value: plasmacytoid dendritic cell

value: sorted as:fresh pDC_donor 1


title: Plate1_E01


title: Plate1_D11


title: 21_D1_Ad26.MVA


title: 5xFAD 20Hz 4hr Rep3 VC

description: 247 VC

value: Brain Tissue

value: 5xFAD 20Hz 4hr


title: Monocytes, LPS 1,25-primed, ATAC replicate 1

description: Library name: L-Dp_ATAC_R1


title: Plate1_D08


title: 21_D11_Ad26.MVA

value: Male


title: Plate1_D06


title: 5xFAD 20Hz 4hr Rep3 Hip

description: 247 Hip


title: Monocytes, 1,25D, non-primed, ATAC replicate 3

description: Library name: D-np_ATAC_R3


title: 21_D92_Ad26.MVA


title: Plate1_D05


title: Monocytes, 1,25D, non-primed, ATAC replicate 2

description: Library name: D-np_ATAC_R2


title: 20_D11_Ad26.MVA


title: Plate1_D04


title: 5xFAD 20Hz 4hr Rep2 Hip

description: 237 Hip


title: Monocytes, 1,25D, non-primed, ATAC replicate 1

description: Library name: D-np_ATAC_R1


title: Monocytes, LPS 1,25-primed, ATAC replicate 2

description: Library name: L-Dp_ATAC_R2


title: 5xFAD 40Hz 0.5hr Rep1 Hip

description: 104 Hip


title: Plate1_D03


title: Monocytes, 1,25D, LPS-primed, ATAC replicate 3

description: Library name: D-Lp_ATAC_R3


title: 20_D1_Ad26.MVA


title: 5xFAD 20Hz 4hr Rep1 VC

description: 225 VC

value: VC


title: 5xFAD 20Hz 4hr Rep1 Hip

description: 225 Hip

value: Hip


title: Plate1_D01


title: 20_D92_Ad26.MVA


title: Monocytes, 1,25D, LPS-primed, ATAC replicate 2

description: Library name: D-Lp_ATAC_R2

value: peripheral blood


title: 5xFAD 20Hz 4hr Rep2 VC

description: 237 VC


title: 19_D11_Ad26.MVA


title: Monocytes, 1,25D, LPS-primed, ATAC replicate 1

description: Library name: D-Lp_ATAC_R1

value: monocytes


title: 5xFAD 20Hz 1hr Rep12 VC

description: 1 VC

value: 5xFAD 20Hz 1hr


title: Plate1_C12


title: 5xFAD 20Hz 1hr Rep12 Hip

description: 1 Hip


title: Monocytes, 1,25D, 1,25D-primed, ATAC replicate 3

description: Library name: D-Dp_ATAC_R3


title: Monocytes, 1,25D, 1,25D-primed, ATAC replicate 2

description: Library name: D-Dp_ATAC_R2


title: 19_D92_Ad26.MVA


title: 5xFAD 20Hz 1hr Rep11 VC

description: 8 VC


title: 19_D1_Ad26.MVA


title: Plate1_C11


title: Plate1_C10


title: Monocytes, 1,25D, 1,25D-primed, ATAC replicate 1

description: Library name: D-Dp_ATAC_R1


title: 5xFAD 20Hz 1hr Rep10 VC

description: 528 VC


title: 18_D11_Ad26.MVA


title: 5xFAD 20Hz 1hr Rep11 Hip

description: 8 Hip


title: Plate1_C09


title: Plate1_D02


title: 18_D92_Ad26.MVA


title: Plate1_C08


title: Monocytes, solvent 24 hours, ATAC replicate 3

description: Library name: Solvent_24_ATAC_R3

value: control


title: 18_D1_Ad26.MVA


title: 5xFAD 20Hz 1hr Rep10 Hip

description: 528 Hip


title: Plate1_C07


title: Monocytes, solvent 24 hours, ATAC replicate 2

description: Library name: Solvent_24_ATAC_R2


title: 17_D64_Ad26.MVA


title: 5xFAD 20Hz 1hr Rep9 VC

description: 517 VC


title: Plate1_C06


title: 5xFAD 20Hz 1hr Rep9 Hip

description: 517 Hip


title: Plate1_C05


title: 17_D11_Ad26.MVA


title: 17_D1_Ad26.MVA


title: Monocytes, solvent 48 hours, ATAC replicate 3

description: Library name: Solvent_48_ATAC_R3


title: Monocytes, solvent 48 hours, ATAC replicate 2

description: Library name: Solvent_48_ATAC_R2


title: 5xFAD 20Hz 1hr Rep8 VC

description: 302 VC


title: 16_D92_Ad26.MVA


title: Monocytes, solvent 48 hours, ATAC replicate 1

description: Library name: Solvent_48_ATAC_R1


title: Plate1_C03


title: 5xFAD 20Hz 1hr Rep7 VC

description: 279 VC


title: 16_D11_Ad26.MVA


title: Plate1_C02


title: 16_D1_Ad26.MVA


title: 15_D11_Ad26.MVA


title: 5xFAD 20Hz 1hr Rep7 Hip

description: 279 Hip


title: K27m3_ScPD_WT_r2

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

description: Library name: Sample24

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore
Trimmed sequence reads were mapped to mm10 using STAR
Duplicated reads were removed using SAMtools
Read count extraction and normalization were performed using QuasR/limma
Assembly: mm10
Supplementary files format and content: BigWig files created using the function qExportWig from the QuasR package for 100bp  tiles in the mm10 genome.

source_name: Testis

extract_protocol:
To profile histone modifications in spermatogonia cells we followed the previously published ULI-NChIP protocol (Brind'Amour, Liu et al. 2015) with minor modifications. Briefly 5000-7500 spermatogonia cells were FACS-sorted directly in 20 μl nuclear isolation buffer (Sigma-Aldrich NUC101) in Eppendorf® LoBind microcentrifuge tubes. The nuclei were centrifuged at 500g for 5 minutes at 4°C in a swing bucket centrifuge and the volume of the sample was reduced to 10 μl. The sample was snap frozen in liquid nitrogen and stored at –80°C freezer until further processing. The sample was thawed on ice and 1 μl of TS buffer (5% Triton X-100, 5% Sodium deoxycholate) was added for 10 minutes to ensure permeabilization of nuclei. 40 μl of MNAse digestion buffer (3.33 gelUnits/μl Micrococcal Nuclease (NEB M0247S), 1.25X Micrococcal Nuclease buffer, 6.25% PEG 6000, 0.85mM DTT) was added to the sample for 10 minutes at 25 °C to fragment the chromatin. Reaction was stopped by addition of 5 μl 100 uM EDTA and the sample was placed on ice. The sample was diluted by addition of 145 μl ChIP buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 150 mM NaCl, 0.1% Triton X-100, 1X EDTA-free protease inhibitor cocktail). To ensure release of chromatin fragments, the sample was sonicated using the Diagenode Bioruptor Plus® for 3 cycles of 5 seconds ON and 30 seconds OFF at low output. Then chromatin was pre-cleared with 10 μl of 1:1 protein A:protein G Dynabeads (Thermo Fisher Scientific, 10001D and 10003D). The precleared chromatin sample was incubated with 0.5 μg of anti-H3K4me3 or 1 μg anti-H3K36me2 or 1 μg anti-H3K27me3 conjugated with 10 μl of 1:1 protein A: protein G Dynabeads overnight at 4 °C on a rotator. Chromatin-Antibody-Dynabeads complexes were washed once with 500 μl of ChIP buffer, 3 times with 1ml of Low Salt wash buffer (20 mM Tris-HCl (pH 8.0), 0.05% SDS, 1% Triton X-100, 2 mM EDTA and 150 mM NaCl) and 3 times with 1 ml High Salt buffer (20 mM Tris-HCl (pH 8.0), 0.05% SDS, 1% Triton X-100, 2 mM EDTA and 250 mM NaCl). Chromatin was eluted in 40 μl of Elution buffer (100 mM NaHCO3 and 1% SDS) for 90 minutes at 65 °C. DNA from eluted material was purified by 2X volumes of Ampure XP DNA purification beads (Beckman Coulter, A63881) and resuspended in 25 μl nuclease free H2O.
For library construction the ChIP purified DNA was used as input for the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB E7645L) with modifications of the manufacturer instruction as we assembled half volume reactions and we doubled reaction incubation times. For adaptor ligation we used 1:15 adaptor dilution. We amplified the ligated fragments for 12 cycles using single indexed primers.

treatment_protocol: Activation of the CreERT2 was achieved by tamoxifen administration (Sigma-Aldrich #T5648; 1mg, dissolved in corn oil, per 20g mouse body weight, dosed by IP injection) on 5 consecutive days. Testis were collected 10 days after the first injection. Differentiated spermatogonia cells (SgD) were isolated from single-cell testicular suspension by FACS (BD FACSAria II; Hoechst 33342 mid/ CD117 positive /CD324 negative/ CD49f negative)

value: Testis

tag: antibody

value: anti-H3K27me3 (Cell Signaling 9733)

value: Pachytene/Diplotene Spermatocytes

value: Kdm2a F/F ; cre-ERt2 -

value: No treatment


title: K27m3_ScPD_WT_r1

description: Library name: Sample23

value: Kdm2a F/F ; cre-ERt2 +


title: Monocytes, solvent 24 hours, ATAC replicate 1

description: Library name: Solvent_24_ATAC_R1


title: Plate1_C04

value: blood

value: plasmacytoid dendritic cell


title: 5xFAD 20Hz 1hr Rep6 VC

description: 271 VC

value: Brain Tissue


title: Plate1_B12

value: sorted as:fresh pDC_donor 1


title: 15_D1_Ad26.MVA

value: Whole blood

value: Male

value: blood cells


title: 5xFAD 20Hz 1hr Rep6 Hip

description: 271 Hip

value: Hip


title: Plate1_C01


title: K27m3_SgD_WT_r2

description: Library name: Sample20

value: Differentiated Spermatogonia

value: Kdm2a +/+ ; cre-ERt2 -


title: Plate1_B11


title: 15_D92_Ad26.MVA


title: 5xFAD 20Hz 1hr Rep8 Hip

description: 302 Hip

value: 5xFAD 20Hz 1hr


title: K27m3_ScLZ_WT_r1

description: Library name: Sample21

value: Testis

value: Leptotene/Zygotene Spermatocytes


title: 5xFAD 20Hz 1hr Rep5 VC

description: 254 VC

value: VC


title: K27m3_SgD_WT_r1

description: Library name: Sample19

value: anti-H3K27me3 (Cell Signaling 9733)


title: Plate1_B10


title: 14_D92_Ad26.MVA

value: Female


title: 5xFAD 20Hz 1hr Rep5 Hip

description: 254 Hip


title: K27m3_SgU_WT_r1

description: Library name: Sample17

value: Undifferentiated Spermatogonia

value: No treatment


title: 14_D11_Ad26.MVA


title: 5xFAD 20Hz 1hr Rep4 VC

description: 252 VC


title: RRBS_SgD_KDM2A_iKO_r4

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore
Trimmed sequence reads were mapped to mm10 using QuasR/RBowtie
Methylation extraction was performed using QuasR
Assembly: mm10

extract_protocol:
DNA was extracted from 5000-10000 Differentiated Spermatogonia (SgD) by QIAamp DNA Micro Kit (Qiagen # 56304)
Libraries were prepared using 10-20 μg of DNA and following the previously publish method (Smallwood, Tomizawa et al. 2011) . Briefly, DNA was digested with 0.9μl MspI Fast Digest (Thermo Scientific FD0544) in 1X Tango buffer in a volume of 18 μl for 6 hours at 37oC. DNA ends were repaired by adding 1 μl Klenow Fragment, exo– (Thermo Scientific EP0421) and 1µl of nucleotide end-repair mix (1mM dATP; 0.1mM dGTP; 0.1mM dCTP prepared in 2X Tango buffer) and incubated for 45min at 37ᵒC, followed by enzyme heat inactivation at 75ᵒC for 15min. Then 6.25nM of 5mC sequencing adapter (NEB E7535S) was ligated with 1 μl T4 DNA Ligase, HC (Thermo Scientific EL0013) and 0.5 μl ATP solution (Thermo Scientific R0441) for 16 hours at room temperature. The looped adaptor ligated DNA fragments were subjected to USER (NEB M5508) digestion at 37 ᵒC for 20 minutes and used directly for bisulfite treatment using the Imprint DNA Modification Kit (Sigma MOD50) according to the manufacturer’s 2-step modification procedure. The modified DNA was amplified with 13 cycles of PCR using Kapa U+ polymerase (Roche 07959052001) and indexed primers (NEB) and purified with 1.8X Ampure XP beads.10-20ng of DNA

treatment_protocol: Activation of the CreERT2 was achieved by tamoxifen administration (Sigma-Aldrich #T5648; 1mg, dissolved in corn oil, per 20g mouse body weight, dosed either by IP injection or oral gavage) on 5 consecutive days. Testis were collected 10 days after the first injection. Differentiated spermatogonia cells (SgD) were isolated from single-cell testicular suspension by FACS (BD FACSAria II; Hoechst 33342 mid/ CD117 positive /CD324 negative/ CD49f negative)

value: Kdm2a F/F ; cre-ERt2 +

value: Tamoxifen


title: Plate1_B08

value: blood

value: plasmacytoid dendritic cell

value: sorted as:fresh pDC_donor 1


title: 14_D1_Ad26.MVA

value: Whole blood

value: blood cells


title: 5xFAD 20Hz 1hr Rep4 Hip

description: 252 Hip

value: Brain Tissue

value: Hip

value: Male


title: RRBS_SgD_KDM2A_iKO_r3

value: Testis

value: Differentiated Spermatogonia


title: Plate1_B07


title: 5xFAD 20Hz 1hr Rep3 VC

description: 251 VC

value: VC

value: 5xFAD 20Hz 1hr


title: 13_D92_Ad26.MVA

value: Female


title: Plate1_B06


title: RRBS_SgD_KDM2A_iKO_r2


title: 13_D11_Ad26.MVA


title: 5xFAD 20Hz 1hr Rep3 Hip

description: 251 Hip


title: Plate1_B05


title: 5xFAD 20Hz 1hr Rep2 VC

description: 206 VC


title: RRBS_SgD_KDM2A_CTR_r4

value: Corn Oil


title: Plate1_B04


title: 13_D1_Ad26.MVA


title: 12_D11_Ad26.MVA


title: 5xFAD 20Hz 1hr Rep2 Hip

description: 206 Hip


title: RRBS_SgD_KDM2A_CTR_r3


title: Plate1_B03


title: Plate1_B09


title: 5xFAD 20Hz 1hr Rep1 VC

description: 2 VC


title: RRBS_SgD_KDM2A_CTR_r2


title: 5xFAD 20Hz 1hr Rep1 Hip

description: 2 Hip


title: 12_D64_Ad26.MVA


title: Plate1_B02


title: 5xFAD 20Hz 0.5hr Rep7 Hip

description: 283 Hip

value: 5xFAD 20Hz 0.5hr


title: RRBS_SgD_KDM2A_CTR_r1

value: Kdm2a F/F ; cre-ERt2 +


title: RRBS_SgD_KDM2A_iKO_r1

value: Tamoxifen


title: 11_D11_Ad26.MVA


title: Plate1_B01

value: blood


title: 5xFAD 20Hz 0.5hr Rep7 VC

description: 283 VC


title: H3K27me3_SgD_DM2A_iKO_r4

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore
Trimmed sequence reads were mapped to mm10 using STAR
Duplicated reads were removed using SAMtools
Read count extraction and normalization were performed using QuasR/limma
Assembly: mm10

value: anti-H3K27me3 (Cell Signaling 9733)


title: Plate1_A12

value: plasmacytoid dendritic cell

value: sorted as:fresh pDC_donor 1


title: 11_D1_Ad26.MVA

value: Whole blood

value: blood cells


title: H3K27me3_SgD_KDM2A_iKO_r3


title: 5xFAD 20Hz 0.5hr Rep6 VC

description: 233 VC

value: Brain Tissue


title: 11_D64_Ad26.MVA

value: Male


title: H3K27me3_SgD_KDM2A_iKO_r2

value: Testis


title: 5xFAD 20Hz 0.5hr Rep6 Hip

description: 233 Hip

value: Hip


title: 10_D11_Ad26.MVA


title: Plate1_D12

value: sorted as:fresh tDC_donor 1


title: H3K27me3_SgD_KDM2A_iKO_r1

value: Differentiated Spermatogonia


title: 12_D1_Ad26.MVA

value: Female


title: 5xFAD 20Hz 0.5hr Rep5 VC

description: 203 VC

value: VC


title: Plate1_A10


title: 10_D1_Ad26.MVA


title: Plate1_A08


title: 10_D64_Ad26.MVA


title: 5xFAD 20Hz 0.5hr Rep5 Hip

description: 203 Hip

value: 5xFAD 20Hz 0.5hr


title: H3K27me3_SgD_KDM2A_CTR_r3

value: Kdm2a F/F ; cre-ERt2 +

value: Corn Oil


title: H3K27me3_SgD_KDM2A_CTR_r4


title: Plate1_A07

value: blood


title: Plate1_A11


title: 9_D11_Ad26.MVA


title: 9_D64_Ad26.MVA


title: 5xFAD 20Hz 0.5hr Rep4 VC

description: 148 VC


title: H3K27me3_SgD_KDM2A_CTR_r2

value: anti-H3K27me3 (Cell Signaling 9733)


title: 5xFAD 20Hz 0.5hr Rep4 Hip

description: 148 Hip


title: Plate1_A06

value: plasmacytoid dendritic cell


title: 9_D1_Ad26.MVA


title: H3K27me3_SgD_KDM2A_CTR_r1


title: 5xFAD 20Hz 0.5hr Rep3 VC

description: 126 VC


title: Plate1_A05

value: sorted as:fresh pDC_donor 1


title: 5xFAD 20Hz 0.5hr Rep3 Hip

description: 126 Hip


title: H3K36me2_SgD_KDM2A_iKO_r2

value: anti-H3K36me2 (Upstate 07-369)

value: Tamoxifen


title: 5841

city: Amsterdam

first: Joe

last: Butler

address: Meibergdreef 9

department: Infectious diseases

country: Netherlands

institute: Amsterdam UMC

data_processing:
Libraries were sequenced using the Illumina HiSeq4000 (Illumina, San Diego, CA, USA) to generate 50bp single-end reads.
The sequence read quality was assessed using FastQC methods (version 0.11.5; Babraham Institute, Babraham, Cambridgeshire, UK).
Trimmomatic version 0.39 was used to trim the Illumina adapters and filter low quality reads and ambiguous nucleotide-containing sequences.
The remaining high-quality reads were aligned against the human Genome Reference Consortium Build 38 (GRCh38, Ensembl 84) using Hisat2 (2.2.0) with default parameters
Count data were generated using the HTSeq method.
Assembly: Human Genome Reference Consortium Build 38 (GRCh38, Ensembl 84)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: N/A

extract_protocol:
Total RNA was extracted using the PAXgene blood mRNA kit (Qiagen, Venlo, the Netherlands).
Sequencing libraries were prepared by means of the KAPA RNA HyperPrep with RiboErase (Roche) as per manufacturer’s instructions.

value: Whole blood

tag: gender

value: female

tag: bsi group

value: CoNS


title: Control TINs, replicate 1, plate 14, scRNAseq

city: Bunkyo-ku

first: Osamu

last: Sugahara

state: Tokyo

address: Yushima 1-5-45

department: Advanced Research Initiative

country: Japan

institute: Institute of Science Tokyo

data_processing:
The FASTQ files obtained from CEL-seq2 analysis were processed with celseq2 software. The reads were thus “demultiplexed” and mapped to the mouse genome (Mm10, Genome Reference Consortium GRCm38) with the use of Bowtie2 software, and gene counting was then performed with HTSeq software. The resultant gene (UMI)-cell matrices for each experiment were concatenated with R software.
Assembly: mm10
Supplementary files format and content: Gene (UMI)-cell matrices

source_name: cholangiocarcinoma (CCA) tumor

extract_protocol:
For isolation of single tumor cells, tumors were mechanically dissociated with scissors and digested by incubation for 30 min at 37°C with collagenase at 1 mg/mL in HBSS. Cells were then isolated by vigorous pipetting of the tumor fragments and passage through a 70-μm cell strainer. For analysis of CCA tumors, erythrocytes were lysed with hemolysis buffer (0.14 M NH4Cl and 0.01 M Tris-HCl at pH 7.5), and the remaining cells were stained with antibodies against CD45.2 (clone 104, BioLegend), CD11b (clone M1/70, BioLegend), Ly6G (clone 1A8, BioLegend). Cell sorting was performed with a FACS Aria II instrument fitted with a 100-μm nozzle. After gating for forward scatter and side scatter and exclusion of doublets, the 7AAD–CD45+CD11b+Ly6G+ fraction was collected as neutrophils.
For single-cell RNA sequencing (scRNA-seq) library preparation, single TINs were processed and barcoded with the use of the CEL-seq2 technique as performed with minor modifications. In brief, each single cell was directly sorted into a well of a 96-well PCR plate containing primer mix including reverse transcription (RT) primers with unique molecular identifiers (UMI) and cell barcodes, deoxynucleoside triphosphates, RNase inhibitors, and 0.3% Nonidet P-40. The cells were lysed by incubation at 65°C for 5 minutes and then subjected to room temperature with SuperScript III Reverse Transcriptase. Samples from each plate were pooled into a single library, from which cDNAs were purified with the use of Agencourt AMPure XP Beads and subjected to second-strand synthesis. The resultant libraries were again bead-purified and then used as templates for in vitro transcription with a MEGAscript T7 Transcription Kit. The amplified RNAs were subjected to RT followed by PCR amplification (20 cycles) with Illumina TruSeq Small RNA primers to generate the final cDNA libraries, which were subjected to paired-end sequencing with an Illumina NovaSeq6000 instrument.

value: cholangiocarcinoma (CCA) tumor

value: tumor-infiltrating neutrophils (TINs)

value: WT

value: PBS


title: 8_D36_Ad26.MVA

value: Female

value: blood cells


title: H3K36me2_SgD_KDM2A_iKO_r1

value: Testis

value: Differentiated Spermatogonia

value: Kdm2a F/F ; cre-ERt2 +


title: Plate1_A04

value: blood


title: Plate1_A09

value: plasmacytoid dendritic cell


title: Plate1_A03

value: sorted as:fresh pDC_donor 1


title: 5xFAD 20Hz 0.5hr Rep2 VC

description: 120 VC

value: Brain Tissue

value: VC

value: Male

value: 5xFAD 20Hz 0.5hr


title: H3K36me2_SgD_KDM2A_CTR_r2

value: anti-H3K36me2 (Upstate 07-369)

value: Corn Oil


title: Plate1_A02


title: 5xFAD 20Hz 0.5hr Rep2 Hip

description: 120 Hip

value: Hip


title: 8_D11_Ad26.MVA

value: Whole blood


title: 8_D1_Ad26.MVA


title: H3K36me2_SgD_KDM2A_CTR_r1


title: Plate1_A01


title: 5xFAD 20Hz 0.5hr Rep1 VC

description: 103 VC


title: H3K4me3_SgD_KDM2A_iKO_r1

value: anti-H3K4me3 (Millipore 17-614)

value: Tamoxifen


title: 7_D11_Ad26.MVA

value: Female

value: blood cells


title: 5xFAD 20Hz 0.5hr Rep1 Hip

description: 103 Hip


title: Upf1-RIP, replicate 2

city: Paris

first: Gwenael

last: Badis

address: 46 rue d'Ulm

department: Genomique fonctionnelle (Section 2)

country: France

institute: IBENS

description:
Library name: RIP_3730_R2
SR75

data_processing:
demultiplexing using Flexbar
Mapping to the SC288 reference genome Saccer3.fa using STAR standard configuration with option  --alignIntronMax 1500 --alignMatesGapMax 1500 --alignSJoverhangMin 25
Assembly: Saccer3.fa
Supplementary files format and content: bigwig files contain the profile of each experiment (strand 1 and strand 2 per replicatre)

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: 30°C in YPD, exponential phase (OD 600=0,7)

extract_protocol:
Phenol Chloroform extraction of total RNA (hot phenol and two supbsequent phenolChloroform extraction), or Immunoprecipitated (one phenol chloroform)
Truseq mRNA stranded (Illumina)

treatment_protocol: Immunoprecipitiation of the protein A tag using rabbit IgG coupled to magnetic beads (RIP-seq only)

value: yeast

tag: strain

value: MATa, ura3delta0, his3delta1, leu2delta0, met15delta0, UPF1(YMR080W)-HTP:URA3MX6

tag: batch

value: November 2015


title: H3K4me3_SgD_KDM2A_CTR_r1

value: Testis

value: Differentiated Spermatogonia

value: Kdm2a F/F ; cre-ERt2 +


title: 7_D36_Ad26.MVA


title: 5xFAD 10Hz 4hr Rep6 Hip

description: 288 Hip

value: Brain Tissue

value: 5xFAD 10Hz 4hr


title: Single cell RNA sequencing of mouse bone marrow stromal cells at 24 months

city: Dallas

first: Zhiyu

last: Zhao

state: Texas

address: 5323 Harry Hines Blvd.

department: Children's Medical Center Research Institute

institute: University of Texas Southwestern Medical Center

description: Library name: 24M_bone_marrow_stroma

data_processing:
Sequencing data was demultiplexed using CellRanger 6.1.2 to obtain raw reads.
Raw reads were aligned to the reference genome and cell-gene raw count matrix files were obtained using CellRanger.
Cell-gene raw count matrices were filtered and normalized, cells were clustered and annotated, gene expressions were measured, and visualization plots were generated using Seurat 4.2.3 with R 4.0.2.
Assembly: mm10
Supplementary files format and content: Text files with cell barcodes. One barcode per line.
Supplementary files format and content: Tab-delimited text files with gene Ensembl IDs and symbols. One gene per line.
Supplementary files format and content: Space-delimited text files with cell-gene raw counts in the format of a sparse matrix. One entry per line.

molecule: polyA RNA

source_name: bone marrow

growth_protocol: mice at 2-month, 12-month, 24-month of age were used for the cell isolation.

extract_protocol:
To isolate bone marrow stromal cells, whole femurs and tibias were crushed, then the bone marrow was collected and digested in enzymatic dissociation buffer [HBSS with Ca2+ and Mg2+ (Corning), supplemented with 200 U/mL Dnase I (Roche), 4 mg/mL Dispase (Sigma-Aldrich), and 3 mg/mL Collagenase type 1 (Worthington Biochemical)] at 37 °C for 30 min as described (2). After a brief vortex at medium speed, the samples sedimented for 1 min, then the cell suspension was transferred to a new tube containing 10 mL of staining medium (Ca2+ and Mg2+ free HBSS containing 3% heat-inactivated bovine serum) with 2 mM EDTA on ice. We then centrifuged at 500 × g for 5 min at 4 °C and resuspended the cell pellet in staining medium. Cells were then incubated with fluorophore-conjugated antibodies against CD45 (eBioscience), Ter119 (eBioscience),and hematopoietic lineage markers for 30 min at 4 °C. Cells were washed again and resuspended in staining medium containing 2 μg/mL DAPI for flow cytometric sorting using a FACSAria II (BD Bioscience) or a FACSAria Fusion (BD Bioscience).
Single cell RNA sequencing libraries were generated using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10xGenomics) according to the manufacturer’s instructions. Briefly, cells, reagents (10xGenomics, PN-1000130), gel beads (10xGenomics, 2000164), and partitioning oil (10xGenomics, 220088) were loaded into the Chromium Next GEM Chip G (10xGenomics, 200177). The chip was loaded into the Chromium Controller (10xGenomics) to generate Gel Bead-In-Emulsions (GEMs). After reverse transcription using the GEM-RT incubation protocol, cDNA was extracted from GEMs using the recovery reagent (10xGenomics, 220016), cDNA was purified with DynaBeads MyOne Silane beads (10xGenomics, 2000048), amplified by PCR for 12 cycles, and further purified with SPRIselect reagent (Beckman Coulter, B23318). The DNA concentration and amplicon size were measured using a Tapestation (Agilent) with D1000 high sensitivity screentapes (Agilent, 5067-5582), and cDNA yield was measured using the Qubit DNA high sensitivity assay (Invitrogen, Q32854), to ensure the amplified cDNA met quality control standards. After fragmentation, end-repair, A-tailing and size selection, cDNA was ligated with adaptor and purified with SPRIselect reagents, according to 10xGenomics instructions. Libraries were amplified by PCR with sample index primers from the Chromium i7 Multiplex kit (10xGenomics, PN-120262), typically for a total of 14 cycles, depending on the original cDNA yield measured by Qubit. Final PCR products were subjected to double-sided size selection with SPRIselect reagents to eliminate fragments larger and smaller than the target amplicons. Library cDNA concentration and size were determined using the Agilent Tapestation with D1000 screentapes (Agilent, 5067-5582), as well as the Qubit DNA high sensitivity assay. cDNA libraries were sequenced using a NextSeq 500 sequencer using the 150bp high output sequencing kit (Illumina), with the following pair-end sequencing settings: Read 1 - 28bp, i7 index – 10bp, i5 index – 10bp, Read 2 - 90bp, generating ~400 million raw reads per run.

treatment_protocol: Mice used for cell isolation did not get any treatment.

value: bone marrow


title: 5xFAD 10Hz 4hr Rep6 VC

description: 288 VC

value: VC

value: Male


title: upf1_delta, replicate 3

description:
Library name: del_1667_R3
SR75

value: MATa, ura3delta0, his3delta1, leu2delta0, met15delta0, upf1(ymr080c)delta::kanMX6


title: 6_D36_Placebo.Placebo

value: Whole blood


title: 6_D11_Placebo.Placebo


title: upf1_delta, replicate 2

description:
Library name: del_1667_R2
SR75


title: Single cell RNA sequencing of mouse bone marrow stromal cells at 2 months

description: Library name: 2M_bone_marrow_stroma


title: upf1_delta, replicate 1

description:
Library name: del_1667_R1
SR75


title: 5xFAD 10Hz 4hr Rep5 VC

description: 257 VC


title: 5_D11_Ad26.MVA


title: 5xFAD 10Hz 4hr Rep4 VC

description: 250 VC


title: Single cell RNA sequencing of mouse bone marrow stromal cells at 12 months

description: Library name: 12M_bone_marrow_stroma


title: 6_D1_Placebo.Placebo


title: 5_D1_Ad26.MVA


title: 5xFAD 10Hz 4hr Rep5 Hip

description: 257 Hip

value: Hip


title: 7_D1_Ad26.MVA


title: 5xFAD 10Hz 4hr Rep4 Hip

description: 250 Hip


title: 5_D64_Ad26.MVA


title: WT input, replicate 3

description:
Library name: WT_2154_R3
SR75

value: MATa, ura3delta0, his3delta1, leu2delta0, met15delta0


title: WT input, replicate 2

description:
Library name: WT_2154_R2
SR75


title: 5xFAD 10Hz 4hr Rep3 VC

description: 240 VC


title: Upf1-RIP, replicate 1

description:
Library name: RIP_3730_R1
SR75


title: Adcy5 KI 3

first: Mohamed

last: Doulazmi

state: Paris

address: 9 quai St Bernard

department: Neurocsiences

institute: Sorbonne Unversity

description:
Library name: Groupe_4-6
KI

data_processing:
feature Counts V2.0.1
Assembly: Mus_musculus.GRCm39.103.gtf
Supplementary files format and content: tab-limided text file raw counts

source_name: Striatum

extract_protocol:
Stranded mRNA prep Ligation-Illumina
RNAseq

value: Striatum

value: striatal cells

value: Adcy5 KI


title: Adcy5 WT 3

description:
Library name: Groupe_4-3
WT

value: Adcy5 WT


title: WT input, replicate 1

description:
Library name: WT_2154_R1
SR75

value: yeast

value: November 2015


title: Adcy5 KI 1

description:
Library name: Groupe_4-4
KI


title: 4_D11_Ad26.MVA

value: Female

value: blood cells


title: Adcy5 WT 2

description:
Library name: Groupe_4-2
WT


title: 4_D92_Ad26.MVA


title: 5IRDGN_1726

city: Durham

first: Liuyang

last: Wang

state: NC

address: 213 Research Drive

institute: Duke University

description: Library name: 5IRDGN_1726

data_processing:
RNA-seq data were processed using the fastp toolkit to trim low-quality bases and Illumina sequencing adapters with default parameters. Trimmed sequence reads were pseudo-aligned to GRCz11/ASM1834v1 using Salmon. Gene count was quantified by Salmon v1.4.0. Read count extraction and normalization were performed using DESeq2.
Assembly: GRCz11
Supplementary files format and content: zebrafish_bulkRNAseq_raw_count.csv; a excel csv file contains raw counts quantified by Salmon

organism: Danio rerio

source_name: Larval

growth_protocol: Zebrafish larvae were maintained at 28.5 °C in E3 medium supplemented with 1-phenyl-2-thiourea (#P7629, Sigma-Aldrich) at a final concentration of 45 μg/mL.

extract_protocol:
RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer’s instructions were followed with subsequent Single Cell RT-PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T, Chien MS, Kaleem S, Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225-51.
Illumina Sequencing Library Preparation method developed in: Zhou T, Chien MS, Kaleem S, Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225-51., was used whereby the amplified cDNA was purified with magnetic beads (Agencourt AMPure XP) and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits (Illumina Inc). Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource

treatment_protocol: Two days post-fertilization zebrafish larvae were infected with approximately 100 fluorescent expressing Mycobacterium marinum or control; Macrophages were isolated from infected or uninfected larvae after 48 hours of infection, then sorted by FACS.

value: Larval

value: macrophage

value: Infected

value: red fluorescent macrophages from infected larvae


title: Adcy5 WT 1

description:
Library name: Groupe_4-1
WT


title: Adcy5 KI 2

description:
Library name: Groupe_4-5
KI


title: 5xFAD 10Hz 4hr Rep2 Hip

description: 224 Hip

value: Brain Tissue

value: Male

value: 5xFAD 10Hz 4hr


title: 5irdgn_1358

description: Library name: 5irdgn_1358


title: 5IRDGN_1140mfap4infect

description: Library name: 5IRDGN_1140mfap4infect


title: 4_D1_Ad26.MVA

value: Whole blood


title: 3_D11_Ad26.MVA


title: 5xFAD 10Hz 4hr Rep1 VC

description: 212 VC

value: VC


title: MDM1402, EPZ-treated, Rep 2

city: Cambridge

first: Colin

middle: Emory

last: Fowler

state: MA

address: 500 Main Street

department: Biology

institute: Massachusetts Institute of Technology

description: Library name: 294005

data_processing:
To generate counts for alternative splicing analysis, raw reads were mapped to the human GRCh38 genome using STAR (--runMode alignReads --runThreadN 16 --sjdbOverhang 149 --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 70 --alignIntronMax 500000 --alignMatesGapMax 500000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outSAMstrandField intronMotif --outFilterType BySJout --twopassMode Basic) and Bowtie (-n 1 -l 30 -e 70 -t -p 4 -m 1 -X 500 -S).
Mapped reads were filtered using Bedtools to remove reads overlapping expressed repeats from the UCSC genome browser RNA repeats and Gencode hg38 and coding exons annotated in the Gencode hg38 annotations. Alternative and constitutive classifications were performed using custom Python scripts and are agnostic to existing annotations other than known gene boundaries. All three cell lines were run in parallel to ensure consistency between annotations. Alternative splicing events were quantified using DEXSeq.
Assembly: Gencode GRCh38 v33 and Gencode GRCm38 vM24
Supplementary files format and content: genes.results files are outputted raw count files from RSEM for each gene.
Supplementary files format and content: isoform.results files are outputted raw count files from RSEM for each isoform (Consensus/Coding or DI).
Supplementary files format and content: DEXSeq files are outputted exon count files from DEXSeq.
Supplementary files format and content: Supplementary files are gff files needed for DEXSeq alternative splicing analysis.

growth_protocol: All cells were cultured in Dulbecco’s modified Eagle’s media (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin, and cultured in 37℃ at 5% CO2. Η23 cells were cultured in RPMI-1640 media supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin, and cultured in 37℃ at 5% CO2. Cells were routinely tested for mycoplasma and were found to be negative.

extract_protocol:
For whole cell lysates, following 3-day treatment with either DMSO (vehicle), PRMT5i, or dTag-13, cells were harvested by scraping. RNA was purified using the RNeasy Mini Kit (Qiagen, 74106) according to manufacturer’s instructions, including the optional DNaseI addition to remove contaminating gDNA (Qiagen, 79254). For fractionated cells, after 3 days in drug, cells were harvested via trypsinization, pelleted, and separated into nuclear and cytoplasmic fractions. Briefly, cell pellets were resuspended in cytoplasmic lysis buffer [0.15% (v/v) NP40, 10 mM Tris (pH7), 150 mM NaCl] supplemented with 10 U SUPERase.IN (Thermo Fisher, AM2694) and EDTA-free protease inhibitor cocktail (MilliporeSigma, 11836170001). Cells were then incubated on ice for 5 minutes. Cell lysate was layered on top of sucrose buffer [0 mM Tris (pH7), 150 mM NaCl, 25% (w/v) sucrose] supplemented with 10 U SUPERase.IN (Thermo Fisher, AM2694) and EDTA-free protease inhibitor cocktail (MilliporeSigma, 11836170001). Cells were then centrifuged at 16,000 x g for 10 minutes at 4 °C. The supernatant contains the cytoplasmic fraction and was harvested for RNA extraction. The remaining pellet contains the nuclear fraction and was washed twice with 800 μL cold PBS, centrifuging at 16,000 x g for 1 minute at 4°C after each wash. The pellet was resuspended in cold RIPA buffer [50 mM Tris (pH 8), 150 mM NaCl, 1% (v/v) NP-40, 0.5% sodium deoxycholate, and 0.1% (w/v) SDS] supplemented with 10 U SUPERase.IN (ThermoFisher, AM2694) and EDTA-free protease inhibitor cocktail (MilliporeSigma, 11836170001). Lysate was incubated for 30 minutes on ice, with vortexing every 10 minutes, and then pelleted at 16,000 x g for 10 minutes at 4°C. The supernatant contains the nuclear fraction and was harvested for RNA extraction. The RNA from the nuclear and cytoplasmic fractions were extracted using TRIzol Reagent (Thermo Fisher, 15596026) according to manufacturer’s instructions. Briefly, to each aqueous fraction, 0.5 mL of isopropanol and 1 mL of TRIzol Reagent was added, followed by an incubation on ice for 10 minutes. Samples were then centrifuged for 10 minutes at 12,000 x g at 4 °C, pellets were washed in 1 mL 75% ethanol, and centrifuged again for 5 minutes at 7,500xg at 4 °C. Pellets were air dried for 10 minutes and resuspended in RNase-free water.
RNA-Seq libraries were prepared using the NEB Ultra II Directional RNA Kit with Poly(A) Selection per the manufacturer's protocol.

treatment_protocol: Cells were grown in the presence of PRMT5 inhibitor, dTag-13, or vehicle control.

value: WT

tag: time

value: Day 3


title: 4IRD_1726

description: Library name: 4IRD_1726


title: 3_D1_Ad26.MVA


title: 5xFAD 10Hz 4hr Rep1 Hip

description: 212 Hip

value: Hip


title: MDM1402, EPZ-treated, Rep 1

description: Library name: 294004


title: 3_D64_Ad26.MVA


title: 5xFAD 10Hz 1hr Rep6 VC

description: 303 VC

value: 5xFAD 10Hz 1hr


title: 4IRD_1140mfap4infect

description: Library name: 4IRD_1140mfap4infect


title: MDM1402, DMSO-treated, Rep 3

description: Library name: 294003

value: DMSO


title: 5xFAD 10Hz 4hr Rep3 Hip

description: 240 Hip


title: 5xFAD 10Hz 1hr Rep6 Hip

description: 303 Hip


title: 5xFAD 10Hz 4hr Rep2 VC

description: 224 VC


title: MDM1402, DMSO-treated, Rep 2

description: Library name: 294002


title: 2_D11_Ad26.MVA


title: 5xFAD 10Hz 1hr Rep5 VC

description: 268 VC


title: 2_D1_Ad26.MVA


title: 3i_1358

description: Library name: 3i_1358

value: nonfluorescent cells from infected larvae


title: MDM1402, EPZ-treated, Rep 3

description: Library name: 294006


title: MDM1402, DMSO-treated, Rep 1

description: Library name: 294001


title: 5xFAD 10Hz 1hr Rep5 Hip

description: 268 Hip


title: KP393T5, EPZ-treated, Rep 3

description: Library name: 244054


title: 3I_1140mfap4infect

description: Library name: 3I_1140mfap4infect


title: 5xFAD 10Hz 1hr Rep4 VC

description: 214 VC


title: 2CRD_1726

description: Library name: 2CRD_1726

value: Uninfected

value: red fluorescent macrophages from uninfected larvae


title: KP393T5, EPZ-treated, Rep 2

description: Library name: 244040


title: 1_D36_Ad26.MVA

value: blood cells


title: 4ird_1358

description: Library name: 4ird_1358

value: Larval

value: macrophage


title: 5xFAD 10Hz 1hr Rep4 Hip

description: 214 Hip


title: 2crd_1358

description: Library name: 2crd_1358


title: 1_D11_Ad26.MVA


title: 5xFAD 10Hz 1hr Rep3 VC

description: 154 VC


title: 2_D64_Ad26.MVA

value: Female


title: 2CRD_1140mfap4infect

description: Library name: 2CRD_1140mfap4infect


title: 5xFAD 10Hz 1hr Rep3 Hip

description: 154 Hip

value: Brain Tissue


title: KP393T5, DMSO-treated, Rep 2

description: Library name: 244039


title: KP393T5, DMSO-treated, Rep 3

description: Library name: 244053


title: Upf1-RIP, replicate 3

description:
Library name: RIP_3730_R3
SR75

value: yeast

value: MATa, ura3delta0, his3delta1, leu2delta0, met15delta0, UPF1(YMR080W)-HTP:URA3MX6

value: November 2015


title: 1C_1726

description: Library name: 1C_1726

value: nonfluorescent cells from uninfected larvae


title: Ad-RNF128_3

city: Shanghai

first: Kai

last: Huang

address: 168 Changhai Road, Yangpu District, Shanghai, China

department: Department of Cardiovascualr Surgery

country: China

institute: Changhai Hospital

description: Library name: Sample 6

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to rat genome assembly mRatBN7.2 (https://ftp.ensembl.org/pub/release-112/fasta/rattus_norvegicus/dna/Rattus_norvegicus.mRatBN7.2.dna.toplevel.fa.gz) using HISAT2.
HTSeq v0.13.5 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:https://ftp.ensembl.org/pub/release-112/gtf/rattus_norvegicus/Rattus_norvegicus.mRatBN7.2.112.gtf.gz.
Assembly: mRatBN7.2
Supplementary files format and content: File include Count and  FPKM values for each sample

organism: Rattus norvegicus

source_name: rat heart

growth_protocol: The isolation of primary cardiomyocytes from rats involves euthanizing neonatal (1-3 days old), excising the heart, and rinsing it in cold PBS or HBSS. For neonatal cardiomyocytes, the heart tissue is minced and digested with enzymes like trypsin and collagenase II at 37°C. The digested tissue is then filtered to remove debris, centrifuged to pellet the cells, and pre-plated to reduce fibroblast contamination by taking advantage of the slower attachment rate of cardiomyocytes. The purified cells are cultured in cardiac-specific medium supplemented with serum and BrdU to inhibit fibroblast overgrowth, and maintained at 37°C with 5% CO2.

extract_protocol:
After 48 hours, remove the medium and directly add 800μL Trizol into the 6-well plate to harvest samples. Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Neonatal rat cardiomyocytes were seeded into 6-well plates and treated with 500 μM palmitic acid for 24h. Cells were transfected with adenovirus to establish RNF28-overexpression cells. After validation of the overexpression efficiency of RNF128, cells were harvested for RNA sequencing.

value: rat heart

value: neonatal rat cardiomyocytes

value: RNF128 overexpression


title: 1c_1358

description: Library name: 1c_1358


title: Ad-RNF128_2

description: Library name: Sample 5


title: 1_D1_Ad26.MVA

value: Whole blood

value: Male


title: Ad-GFP_3

description: Library name: Sample 3

value: WT


title: 3I_1726

description: Library name: 3I_1726

value: Infected

value: nonfluorescent cells from infected larvae


title: 1C_1140mfap4infect

description: Library name: 1C_1140mfap4infect

value: Uninfected


title: 5xFAD 10Hz 1hr Rep2 Hip

description: 130 Hip

value: Hip

value: 5xFAD 10Hz 1hr


title: Ad-RNF128_1

description: Library name: Sample 4


title: KP393T5, DMSO-treated, Rep 1

description: Library name: 244037

value: DMSO

value: Day 3


title: 5xFAD 10Hz 1hr Rep2 VC

description: 130 VC

value: Brain Tissue

value: VC


title: SR16-005712_A1

description: Library name: SR16-005712_A1

data_processing:
Raw BCL files were demultiplexed, and then short reads from spatial snRNA-seq were mapped to human reference genome (GRCh38) using spaceranger v2.0.1 with default parameters.
Gene expression were quantified by spaceranger v2.0.1 with default parameters.
The filtered count matrix were retained for further analysis. Seurat (version 5.2.1) was used for single-cell and spatial data processing and clustering with initial clustering and visualization of spatial data conducted using Loupe Browser (version 8)
Assembly: GRCh38
Supplementary files format and content: *.tif, image of tissue and spot
Supplementary files format and content: barcode.txt.gz, list of spatial barcode
Supplementary files format and content: feature.txt.gz, list of gene ID
Supplementary files format and content: matrix.txt.gz, gene expression count matrix with Matrix Market Exchange Format
Library strategy: Spatial Transcriptomics

source_name: Lung granuloma

growth_protocol: Samples used for assay were patient derived clinical biopsy specimens.

extract_protocol:
10x Genomics Visium V2 assays were carried out following 10x Genomics protocol CG000520-Rev B. Human whole transcriptome probe panels were added to the tissue, enabling hybridization and of each probe pair across the transcriptome. Slides were processed through probe ligation and prepared for analyte transfer. Tissue slides and Visium CytAssist Spatial Gene Expression v2 Slides were then loaded into the Visium CytAssist instrument, where they were brought into proximity with one another.
Gene expression probes were released from the tissue upon CytAssist Enabled RNA Digestion & Tissue Removal, enabling capture by the spatially barcoded oligonucleotides present on the Visium slide surface. The Visium CytAssist Spatial Gene Expression v2 slides were removed from the Visium CytAssist for downstream library preparation. Barcoded products were cleaved from the slide surface and amplified. Gene expression libraries were generated from each tissue section and sequenced on an Illumina NovaSeq6000.

treatment_protocol: Patient with available tissue specimens described to contain Mycobacterium tuberculosis were evaluated for inclusion in the study. Tissue specimens were requested from the pathology department and formalin fixed paraffin embedded (FFPE) sections were cut by the Duke Pathology Research Histology Laboratory.

value: Lung granuloma

value: infected with Mycobacterium tuberculosis


title: 5xFAD 10Hz 1hr Rep1 Hip

description: 118 Hip


title: 5xFAD 10Hz 1hr Rep1 VC

description: 118 VC


title: Ad-GFP_1

description: Library name: Sample 1

value: rat heart


title: Ad-GFP_2

description: Library name: Sample 2

value: neonatal rat cardiomyocytes


title: KP393T5, EPZ-treated, Rep 1

description: Library name: 244038


title: 5xFAD 10Hz 0.5hr Rep7 VC

description: 93 VC

value: 5xFAD 10Hz 0.5hr


title: No KD (Dox-) 3

city: West Lafayette

first: Chang-Deng

last: Hu

state: IN

address: 201 S. University St, Hansen Life Sciences Building, Room 401A

department: Department of Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina HiSeq 2500
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the human genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to hg38 genes using featureCounts (from subread v1.6.5) with the following parameters: “-s2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 3 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using likelihood ratio test method in edgeR (v3.20.8).
Assembly: hg38
Supplementary files format and content: differential analysis and raw counts

source_name: LNCaP Cell Line

growth_protocol: LNCaP cells stably transfected with doxycycline-inducible shRNA targeting PRMT5 mRNA plasmid were cultured in RPMI 1640 / 10% FBS until experimental passage. After seeding experiment and allowing cells to attach to plate, doxycycline was added to PRMT5 knockdown samples (PRMT5 KD) for 4 days. No doxycycline was added to to non-knockdown samples (No KD).

extract_protocol:
RNA was extracted from cells with Trizol reagent. Two rounds of P:C extraction were performed, and mRNA was precipitated with isopropanol and washed with 75% ethanol.
Libaray construction performed by Novogene contract research organization with NEBNext Ultra II

treatment_protocol: PRMT5 Knockdown samples: doxyxycline was added and cultured for 4 days. No Knockdown samples: Cells were cultured for 4 days without doxycycline.

value: LNCaP


title: SP16-002655_A3

description: Library name: SP16-002655_A3


title: No KD (Dox-) 2


title: SP16-040417_B3

description: Library name: SP16-040417_B3


title: 5xFAD 10Hz 0.5hr Rep7 Hip

description: 93 Hip

value: Male


title: 5xFAD 10Hz 0.5hr Rep6 VC

description: 273 VC


title: No KD (Dox-) 1


title: PRMT5 KD (Dox+) 3

value: PRMT5 knockdown


title: 5xFAD 10Hz 0.5hr Rep5 VC

description: 244 VC


title: SP16_040417_B3

description: Library name: SP16_040417_B3

data_processing:
Raw BCL files were demultiplexed, and then short reads from scRNA-seq were mapped to human reference genome (GRCh38) using Cellranger v7.0 with default parameters.
Gene expression were quantified by cellranger v7.0 with default parameters.
The filtered count matrix were retained for further analysis. Seurat (version 5.2.1) was used for single-cell data processing and clustering with initial clustering.
Assembly: GRCh38
Supplementary files format and content: barcode.txt.gz, list of spatial barcode
Supplementary files format and content: feature.txt.gz, list of gene ID
Supplementary files format and content: matrix.txt.gz, gene expression count matrix with Matrix Market Exchange Format

extract_protocol:
2-4 25µM FFPE tissue sections of human TB granuloma biopsy specimens were dissociated into single cells. Nuclei and cells were isolated from formaldehyde fixed and paraffin embedded (FFPE) tissue blocks using the 10x Genomics Sample Preparation from FFPE Tissue Sections protocol. FFPE scrolls were deparaffinized then dissociated into nuclei and cells using Dissociation Enzyme mix and counted then the 10x Genomics Fixed RNA Profiling Reagent Kits protocol was followed. After the RT reaction, the GEMs are broken, full length cDNAs are cleaned with Silane Dynabeads, and then amplified via polymerase chain reaction (PCR) and purified using SPRIselect (Beckman Coulter – Brea, CA) bead size selection. Resulting cDNAs are assayed using a 4200 TapeStation System High Sensitivity D5000 ScreenTape and reagents (Agilent - Santa Clara, CA) for qualitative and quantitative analysis.
Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size for the sequencing library preparation in which Illumina P5 and P7 sequences, a sample index, and TruSeq read 2 primer sequence are added through End Repair, A-tailing, Adaptor Ligation PCR. The final libraries contain P5 and P7 primers used in Illumina bridge amplification. Following additional bead purification, libraries are assayed for quality using 4200 TapeStation System HSD1000 ScreenTape and reagents, then quantitated and checked for successful adapter ligation with the KAPA Library Quantification Kit (Roche - Indianapolis, IN) on the Applied Biosystems QuantStudio 5 (Thermo Fisher Scientific - Waltham, MA). Sequence is generated using paired end sequencing (one end to generate cell specific, barcoded sequence and the other to generate sequence of the expressed poly-A tailed mRNA).  These libraries were sequencing on an Illumina NovaSeq6000.


title: 5xFAD 10Hz 0.5hr Rep6 Hip

description: 273 Hip


title: s10S_5513_H6

description: Library name: s10S_5513_H6


title: 5xFAD 10Hz 0.5hr Rep5 Hip

description: 244 Hip


title: PRMT5 KD (Dox+) 1


title: 5xFAD 10Hz 0.5hr Rep4 VC

description: 200 VC


title: RNA_SgD_KDM2A_iKO_r4

data_processing:
UMI information were added to the read name for use in downstrean deduplication.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore
Trimmed sequence reads were mapped to mm10 using STAR
Duplicated reads were removed using NUDUP
Read count extraction and normalization were performed using QuasR
Assembly: mm10

extract_protocol:
RNA was extracted from 10000 cells with Single Cell RNA Purification Kit (Norgen, 51800)
Libraries were prepared using the Ovation® SoLo RNA-Seq Library Preparation Kit (Nugen, 0501-32)

treatment_protocol: Activation of the CreERT2 was achieved by tamoxifen administration (Sigma-Aldrich #T5648; 1mg, dissolved in corn oil, per 20g mouse body weight, dosed by IP injection) on 5 consecutive days. Testis were collected 10 days after the first injection. Undifferentiated spermatogonia  cells (SgU) were isolated from single-cell testicular suspension by FACS (BD FACSAria II; Hoechst 33342 - blue MID, Hoechst 33342 - red LOW/ CD117 negative /CD324 positive/ CD49f positive). Differentiated spermatogonia cells (SgD) were isolated from single-cell testicular suspension by FACS (BD FACSAria II; Hoechst 33342 - blue MID, Hoechst 33342 - red LOW/ CD117 positive /CD324 negative/ CD49f negative). Leptotene/Zygotene spermatocytes cells (ScLZ) were isolated from single-cell testicular suspension by FACS (BD FACSAria II; Hoechst 33342 - blue HIGH, Hoechst 33342 - red LOW/ CD117 negative /CD324 negative/ CD49f negative).

value: Testis

value: Differentiated Spermatogonia

value: Kdm2a F/F ; cre-ERt2 +

value: Tamoxifen


title: SP16_002655_A3

description: Library name: SP16_002655_A3


title: RNA_SgD_KDM2A_iKO_r3


title: SP19-000120_B1

description: Library name: SP19-000120_B1


title: s10S_5513_H3

description: Library name: s10S_5513_H3


title: 5xFAD 10Hz 0.5hr Rep4 Hip

description: 200 Hip

data_processing:
Alignment was performed by Molecular Research Lab (https://mrdnalab.com) and data was validated for fastq integrity and quality. Each library was split between four lanes and .fastq.gz files were merged using DNAstar ArrayStar. Next, Qseq reads were mapped using the mouse reference genome GRCm39 (GCF_000001635.27). For the read assignment, the threshold was set at 20bp and 80% of the bases matching within each read. Duplicated reads were eliminated and genes with less than 20 total raw counts were removed from analysis. Gene counts were normalized using DESeq2 in R.
Assembly: mouse reference genome GRCm39 (GCF_000001635.27)
Supplementary files format and content: Raw count values in csv format.

value: Hip


title: PRMT5 KD (Dox+) 2


title: Usp17l_KD9_H3K9me3_rep2

city: Jinan

first: Xukun

last: Lu

address: No. 44 Wenhua West Road

institute: Shandong University

data_processing:
Paired-end reads were first processed by TrimGalore (v.0.6.4) with default parameters to remove adaptor sequences and reads of low quality. The filtered reads were then mapped to the mm9 genome using Bowtie2 (v2.2.5) (Langmead and Salzberg, 2012) with the default parameters. Duplicates were removed with MarkDuplicates.jar. The unique mapped reads were then used to calculate the RPKM (Reads per kilobase per million of sequenced reads), which was further Z-score normalized to minimize the batch and cell type variation. The Pearson correlation was calculated for each sample with two biological replicates (10-kb bin). Replicates with good reproducibility were pooled together for downstream analyses. The UCSC genome browser was used for visualization.
Assembly: mm9
Supplementary files format and content: bigWig

source_name: mESC

growth_protocol: Serum/Lif (S/L) R1 mESCs were cultured in 0.1% gelatin-coated dishes in Dulbecco’s modified Eagle’s medium (Gibco, 11995065) containing 15% FBS (Gibco, 16000-044), 1000 IU/ml leukemia inhibitory factor (Lif) (Merck Millipore, ESG1107), 100 IU/ml penicillin and 100 μg/ml streptomycin (Merck Millipore, TMS-AB2-C), 2 mM GlutaMAX (Gibco, 35050061), 1% EmbryoMax nucleosides (Merck Millipore, ES-008-D), 0.1 mM nonessential amino acids (Gibco, 25-025-CIR), and 0.1 mM 2-mercaptoethanol (Gibco, 21985023). 2i mESCs were cultured on 0.2% gelatin-coated dishes in 2i/Lif medium (N2B27 medium supplemented with 1 μm PD0325901 (Tocris, 41921), 3 μm CHIR99021 (Tocris, 4423) and 1000 IU/ml Lif). Cells were routinely propagated every 2-3 days. The formative EpiLCs were induced as previously described (Hayashi et al., 2011). Briefly, 1.0×105 2i ESCs were plated in a well of a 12-well plate coated with Matrigel (BD, 356230/356231, diluted at a ratio of 1:100 in N2B27 medium). Cells were cultured in N2B27 medium containing activin A (20 ng/ml), bFGF (12 ng/ml), XAV939 (5 μM), and KSR (1%). EpiLCs were collected for analysis at the indicated time point. Embryos were collected in vivo.

extract_protocol:
Embryos or cells were lysed in lysis buffer and subject to Mnase digestion, antibody immunoprecipitation, and subsequent library preparation.
STAR ChIP-seq was performed as previously described (Zhang et al., 2016) with modifications. Briefly, samples were suspended and lysed followed by chromatin fragmentation by micrococcal nuclease (MNase, Sigma-Aldrich, N3755-200UN) at 37°C for 5 min. After being terminated, the supernatant containing chromatin was incubated with 1 μg of primary antibody (H3K36me2, Active motif, 61019; H3K36me3, Active motif, 61021 or 61902) at 4°C overnight with rotation. The next day, 100 μg of Protein A/G dynabeads (mixed at 1:1, Thermo Fisher Scientific, 10001D for Protein A and 10004D for Protein G) was added to each sample and incubated at 4°C for 3 hours with rotation. The beads were next washed five times with 150 μl of RIPA buffer and once with 150 μl of LiCl buffer. For each sample, beads were resuspended with 28 μl of H2O, 1 μl of 10× Ex Taq buffer (Takara, RR006B), and 1 μl of proteinase K (NEB, P8107S) and incubated at 55°C for 90 min, followed by incubation at 72°C for 40 min to inactivate the proteinase K. Samples were then subjected to TruSeq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). Libraries were sequenced using the Illumina Hiseq X Ten or Novaseq 6000 system according to the manufacturer’s protocol.

value: mESC

tag: chip antibody

value: WT

tag: developmental stage

value: Usp17l KD


title: zen mutant, blastoderm stage, ATAC-seq replicate 5

city: Evanston

first: Shelby

middle: A

last: Blythe

state: IL

address: Northwestern University, Hogan Hall, 2205 Tech Drive

department: Molecular Biosciences

institute: Northwestern University

description:
Library name: zen_ATAC_rep5
ATAC-seq of a zen mutant embryo
zen_ATAC_CPM_normalized_nodups.wig

data_processing:
Barcode-split fastq files were trimmed of adapter sequences using TrimGalore
Adapter-trimmed fastq files were mapped to the dm6 Drosophila reference genome using Bowtie2, with option -X 2000.
Mapped reads were sorted using Samtools
Suspected PCR and optical duplicate mapped reads were marked using Picard MarkDuplicates
Duplicate-marked mapped reads were imported into R, discarding duplicates, and keeping only reads with map-quality scores of 10 or greater. Wiggle files were generated by calculating the average number of mapped reads within 10 bp windows, and normalizing to millions of reads in the overall sample. Peaks were called using MACS2.
Assembly: Drosophila melanogaster dm6
Supplementary files format and content: wiggle files for merged replicates are provided . Data represents counts per million normalized average reads per 10 bp genomic bin
Supplementary files format and content: Peaks lists for GFP-medea and WT ATAC-seq are provided. GFP-Med data represents MACS output for the indicated ChIP target enrichment over negative control ChIP (q=0.001, fe=5). Wild type ATAC peaks are output from MACS with no negative control (q=0.001, fe=2).

organism: Drosophila melanogaster

source_name: embryo

growth_protocol: Adult flies were placed in a cage with yeasted apple juice plates and embryos were collected prior to treatment and/or processing for ChIP.

extract_protocol:
For ChIP experiments, embryos were crosslinked (Heptane/PBS/formaldehyde, 15 minutes) and sorted by stage prior to homogenization in RIPA buffer and sonication. Sonicated chromatin samples were subjected to immunoprecipiation with the indicated antibodies. For ATAC seq, individual embryos were staged in mid cellular blastoderm stages and homogenized in ATAC lysis buffer (Buenrostro, 2013). Nuclear pellets were isolated by low-speed centrifugation prior to library preparation.
ChIP libraries: following IP but prior to washes, antibody-chromatin complexes were tagmented by incubation with Illumina Tn5 (Nextera) reagent for 40 minutes at 37 degrees C. Following tagmentation, beads were washed and subjected to PCR with barcoding primers (Buenrostro, 2013). ATAC libraries: nuclear pellets were tagmented by incubation with Illumina Tn5 (Nextera) reagent for 30 minutes at 37 degrees C. DNA was cleaned up using a Qiagen MinElute kit. Tagmented library fragments were subjected to PCR with barcoding primers (Buenrostro, 2013).

tag: tissue

value: embryo

value: cellular blastoderm


title: 5xFAD 10Hz 0.5hr Rep3 VC

description: 147 VC

extract_protocol:
RNAwasisolated from mouse brain tissue  tissues using Qiagen RNeasy kit(217804; Qiagen; Hilden, Germany)according to the manufacturer’s protocols.
Libraries were sequenced for paired-end mRNA using the NovaSeq 6000 sequencing system to obtain a sequencing depth of 30 to 40 million reads per sample. Before sequencing, quality control was performed using a bioanalyzer for RNA integrity number greater than seven. The NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit were used to prepare sequencing libraries.

value: Brain Tissue

value: VC

tag: Sex


title: RNA_SgD_KDM2A_iKO_r1

tag: cell type


title: zen mutant, blastoderm stage, ATAC-seq replicate 3

description:
Library name: zen_ATAC_rep3
ATAC-seq of a zen mutant embryo
zen_ATAC_CPM_normalized_nodups.wig


title: Usp17l_KD9_H3K9me3_rep1


title: Usp17l_KD4_H3K9me3_rep2


title: 5xFAD 10Hz 0.5hr Rep3 Hip

description: 147 Hip


title: RNA_SgD_KDM2A_CTR_r4

value: Corn Oil


title: zen mutant, blastoderm stage, ATAC-seq replicate 2

description:
Library name: zen_ATAC_rep2
ATAC-seq of a zen mutant embryo
zen_ATAC_CPM_normalized_nodups.wig


title: zen mutant, blastoderm stage, ATAC-seq replicate 1

description:
Library name: zen_ATAC_rep1
ATAC-seq of a zen mutant embryo
zen_ATAC_CPM_normalized_nodups.wig


title: 5xFAD 10Hz 0.5hr Rep2 VC

description: 125 VC

value: 5xFAD 10Hz 0.5hr


title: 5xFAD 10Hz 0.5hr Rep2 Hip

description: 125 Hip


title: WT_H3K9me3_rep2

value: ICM


title: RNA_SgD_KDM2A_CTR_r3


title: RNA_SgD_KDM2A_CTR_r2


title: 5xFAD 10Hz 0.5hr Rep1 VC

description: 101 VC

value: Male


title: Usp17l_KD_L2C_H3K27me3_rep2

source_name: late 2-cell

value: late 2-cell


title: RNA_SgD_KDM2A_iKO_r2

value: Testis


title: WT_H3K9me3_rep1


title: RNA_SgD_KDM2A_CTR_r1

value: Differentiated Spermatogonia


title: wildtype, blastoderm stage, ATAC-seq replicate 7

description:
Library name: wt_ATAC_rep7
ATAC-seq of a zen wild-type embryo
wt_ATAC_CPM_normalized_nodups.wig
wt_ATAC_peaks.narrowPeak


title: wildtype, blastoderm stage, ATAC-seq replicate 6

description:
Library name: wt_ATAC_rep6
ATAC-seq of a zen wild-type embryo
wt_ATAC_CPM_normalized_nodups.wig
wt_ATAC_peaks.narrowPeak


title: wildtype, blastoderm stage, ATAC-seq replicate 5

description:
Library name: wt_ATAC_rep5
ATAC-seq of a zen wild-type embryo
wt_ATAC_CPM_normalized_nodups.wig
wt_ATAC_peaks.narrowPeak


title: RNA_SgU_KDM2A_iKO_r4

value: Undifferentiated Spermatogonia

value: Kdm2a F/F ; cre-ERt2 +


title: RNA_SgU_KDM2A_iKO_r3

value: Tamoxifen


title: zen mutant, blastoderm stage, ATAC-seq replicate 4

description:
Library name: zen_ATAC_rep4
ATAC-seq of a zen mutant embryo
zen_ATAC_CPM_normalized_nodups.wig


title: Usp17l_KD_L2C_H3K27me3_rep1


title: wildtype, blastoderm stage, ATAC-seq replicate 4

description:
Library name: wt_ATAC_rep4
ATAC-seq of a zen wild-type embryo
wt_ATAC_CPM_normalized_nodups.wig
wt_ATAC_peaks.narrowPeak


title: SNI no stim biol rep 2

city: Philadelphia

first: Gregory

last: Corder

address: 125 S. 31st Street

institute: University of Pennsyvannia

description: 10x Genomics

data_processing:
Paired end sequencing reads were processed using 10x Genomics Cell Ranger v5.0.1.
Filtered matrices were merged and processed with the R Seurat package (5.0.1)
Assembly: Reads were aligned to the mm10 genome optimized for single cell sequencing (https://doi.org/10.1038/s41592-023-02003-w)
Supplementary files format and content: expression matrices as tsv and mtx files

molecule: nuclear RNA

source_name: amygdala

extract_protocol:
Nuclei were captured with the 10x Genomics Chromium controller for 3' gene expression assay (v3.1) according to manufacturer protocols
Libraries were prepared according to 10x Genomics manufacturer protocols
snRNAseq

value: amygdala

tag: injury state

value: SNI

tag: stimulation

value: no stim


title: Usp17le_OE_L2C_H3K27me3_rep1

value: WT

tag: treatment

value: Usp17le OE


title: wildtype, blastoderm stage, ATAC-seq replicate 3

description:
Library name: wt_ATAC_rep3
ATAC-seq of a zen wild-type embryo
wt_ATAC_CPM_normalized_nodups.wig
wt_ATAC_peaks.narrowPeak

value: embryo

value: cellular blastoderm


title: RNA_SgU_KDM2A_iKO_r2


title: Usp17l_KD4_H3K9me3_rep1

value: mESC

value: Usp17l KD


title: SNI no stim biol rep 1

description: 10x Genomics


title: RNA_SgU_KDM2A_iKO_r1


title: Ctrl_L2C_H3K27me3_rep2


title: Uninjured no stim biol rep 3

description: 10x Genomics

value: Uninjured


title: 5xFAD 10Hz 0.5hr Rep1 Hip

description: 101 Hip

value: Brain Tissue

tag: tissue region

value: Hip

tag: age

value: Male

value: 5xFAD 10Hz 0.5hr


title: wildtype, blastoderm stage, ATAC-seq replicate 1

description:
Library name: wt_ATAC_rep1
ATAC-seq of a zen wild-type embryo
wt_ATAC_CPM_normalized_nodups.wig
wt_ATAC_peaks.narrowPeak

tag: genotype


title: RNA_SgU_KDM2A_CTR_r4

value: Testis

value: Undifferentiated Spermatogonia

value: Corn Oil


title: GFP-Medea zen mutant, ChIP anti-GFP, Medea enrichment, replicate3

description:
Library name: zen-GFP-Medea_IP-GFP_rep3
Medea ChIP in zen mutant embryos
zen_Med-ChIP_CPM_normalized_nodups.wig

value: w[1118]; zen[7] GFP-Medea

value: GFP


title: Uninjured no stim biol rep 2

description: 10x Genomics

value: amygdala

value: no stim


title: Usp17le_OE_L2C_H3K27me3_rep2

value: late 2-cell

value: WT

value: Usp17le OE


title: Uninjured no stim biol rep 1

description: 10x Genomics


title: RNA_SgU_KDM2A_CTR_r3

value: Kdm2a F/F ; cre-ERt2 +


title: Usp17l_KD_L2C_H2AK119ub1_rep2

value: Usp17l KD


title: Usp17l_KD_L2C_H2AK119ub1_rep1


title: SNI no stim biol rep 3

description: 10x Genomics

value: SNI


title: RNA_SgU_KDM2A_CTR_r2


title: Uninjured hot water drop biol rep 3

description: 10x Genomics

value: Uninjured

value: hot water


title: GFP-Medea zen mutant, ChIP anti-GFP, Medea enrichment, replicate1

description:
Library name: zen-GFP-Medea_IP-GFP_rep1
Medea ChIP in zen mutant embryos
zen_Med-ChIP_CPM_normalized_nodups.wig

value: embryo

value: cellular blastoderm


title: GFP-Medea zen mutant, ChIP anti-GFP, Medea enrichment, replicate2

description:
Library name: zen-GFP-Medea_IP-GFP_rep2
Medea ChIP in zen mutant embryos
zen_Med-ChIP_CPM_normalized_nodups.wig


title: RNA_SgU_KDM2A_CTR_r1

value: Testis


title: Usp17le_OE_L2C_H2AK119ub1_rep2


title: RNA_ScLZ_KDM2A_iKO_r4

value: Leptotene and Zygotene Spermatocytes

value: Tamoxifen


title: Usp17le_OE_L2C_H2AK119ub1_rep1


title: wildtype, ChIP phospho-Mad, Mad enrichment, replicate3

description:
Library name: wt_IP-phosphoMad_rep3
Phospho-Mad ChIP in wild-type embryos
wt_phosphoMad-ChIP_CPM_normalized_nodups.wig

value: phospho-Mad


title: RNA_ScLZ_KDM2A_iKO_r3


title: wildtype, blastoderm stage, ATAC-seq replicate 2

description:
Library name: wt_ATAC_rep2
ATAC-seq of a zen wild-type embryo
wt_ATAC_CPM_normalized_nodups.wig
wt_ATAC_peaks.narrowPeak


title: Uninjured hot water drop biol rep 2

description: 10x Genomics

value: Male


title: wildtype, ChIP phospho-Mad, Mad enrichment, replicate2

description:
Library name: wt_IP-phosphoMad_rep2
Phospho-Mad ChIP in wild-type embryos
wt_phosphoMad-ChIP_CPM_normalized_nodups.wig


title: Uninjured hot water drop biol rep 1

description: 10x Genomics

value: amygdala


title: SNI light touch biol rep 3

description: 10x Genomics

value: Light touch


title: RNA_ScLZ_KDM2A_iKO_r2


title: wildtype, ChIP phospho-Mad, Mad enrichment, replicate1

description:
Library name: wt_IP-phosphoMad_rep1
Phospho-Mad ChIP in wild-type embryos
wt_phosphoMad-ChIP_CPM_normalized_nodups.wig


title: Ctrl_L2C_H2AK119ub1_rep1

value: late 2-cell


title: Ctrl_L2C_H2AK119ub1_rep2

value: WT


title: RNA_ScLZ_KDM2A_iKO_r1


title: SNI light touch biol rep 2

description: 10x Genomics


title: SNI light touch biol rep 1

description: 10x Genomics


title: Ctrl_L2C_H3K27me3_rep1


title: Usp17l_KD_L2C_RNA_rep2

data_processing:
Paired-end RNA-seq reads were trimmed and mapped to the mm9 genome by TopHat v2.1.1 (Trapnell et al., 2009). FPKM (Fragments per kilobase per million of sequenced reads) for gene expression was calculated using Cufflinks v2.2.1 (Trapnell et al., 2012) based on mm9 refFlat from the UCSC genome annotation database.
Assembly: mm9
Supplementary files format and content: bigWig

growth_protocol: Serum/Lif (S/L) R1 mESCs were cultured in 0.1% gelatin-coated dishes in Dulbecco’s modified Eagle’s medium (Gibco, 11995065) containing 15% FBS (Gibco, 16000-044), 1000 IU/ml leukemia inhibitory factor (Lif) (Merck Millipore, ESG1107), 100 IU/ml penicillin and 100 μg/ml streptomycin (Merck Millipore, TMS-AB2-C), 2 mM GlutaMAX (Gibco, 35050061), 1% EmbryoMax nucleosides (Merck Millipore, ES-008-D), 0.1 mM nonessential amino acids (Gibco, 25-025-CIR), and 0.1 mM 2-mercaptoethanol (Gibco, 21985023). 2i mESCs were cultured on 0.2% gelatin-coated dishes in 2i/Lif medium (N2B27 medium supplemented with 1 μm PD0325901 (Tocris, 41921), 3 μm CHIR99021 (Tocris, 4423) and 1000 IU/ml Lif). Cells were routinely propagated every 2-3 days. The formative EpiLCs were induced as previously described (Hayashi et al., 2011). Briefly, 1.0×105 2i ESCs were plated in a well of a 12-well plate coated with Matrigel (BD, 356230/356231, diluted at a ratio of 1:100 in N2B27 medium). Cells were cultured in N2B27 medium containing activin A (20 ng/ml), bFGF (12 ng/ml), XAV939 (5 μM), and KSR (1%). EpiLCs were collected for analysis at the indicated time point.

extract_protocol:
Embryos or cells were lysed and used directly as input materials for subsequent RNA-seq library prepararion.
All RNA libraries were prepared using the Smart-seq2 method as previously reported (Picelli et al., 2014), and were sequenced by the Illumina Hiseq X Ten or Novaseq 6000 system according to the manufacturer’s instructions.

value: WT, Usp17l KD


title: RNA_ScLZ_KDM2A_CTR_r3

value: Kdm2a F/F ; cre-ERt2 +

value: Corn Oil


title: GFP-Medea, ChIP anti-GFP, Medea enrichment, replicate2

description:
Library name: GFP-Medea_IP-GFP_rep2
Medea ChIP in wild-type embryos
wt_Med-ChIP_CPM_normalized_nodups.wig
wt_Med_peaks.narrowPeak

value: w[1118]; GFP-Medea

value: GFP


title: GFP-Medea, ChIP anti-GFP, Medea enrichment, replicate3

description:
Library name: GFP-Medea_IP-GFP_rep3
Medea ChIP in wild-type embryos
wt_Med-ChIP_CPM_normalized_nodups.wig
wt_Med_peaks.narrowPeak


title: Usp17l_KD_L2C_RNA_rep1


title: RNA_ScLZ_KDM2A_CTR_r4


title: Uninjured light touch biol rep 3

description: 10x Genomics

value: Uninjured


title: RNA_ScLZ_KDM2A_CTR_r2


title: Uninjured light touch biol rep 2

description: 10x Genomics


title: GFP-Medea, ChIP anti-GFP, Medea enrichment, replicate1

description:
Library name: GFP-Medea_IP-GFP_rep1
Medea ChIP in wild-type embryos
wt_Med-ChIP_CPM_normalized_nodups.wig
wt_Med_peaks.narrowPeak

value: embryo


title: Usp17le_OE_L2C_RNA_rep2

value: WT, Usp17le OE


title: Ctrl_L2C_RNA_rep2


title: HIS-24, ChIP-seq, replicate 2

first: Iva

last: Tchasovnikarova

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

data_processing:
Reads were aligned using bowtie2 and quantification was performed using deepTools.
Assembly: ce11
Supplementary files format and content: bigwig files normalised as RPKM

organism: Caenorhabditis elegans

source_name: L3 Larvae

extract_protocol:
Wild-type N2 C. elegans were cultured using standard methods as described in Brenner, S. Genetics (1974).
HIS-24 ChIP-seq libraries were prepared from EGS- and formaldehyde-fixed synchronized L3 larvae in duplicate, as described in McMurchy et al. (2017) eLife

value: L3 Larvae

value: Wild-type

tag: antibody


title: wildtype, ChIP anti-GFP, negative control, replicate3

description:
Library name: wt_Negcontrol_rep3
negative control ChIP
wt_Negcontrol-ChIP_CPM_normalized_nodups.wig

value: cellular blastoderm


title: Usp17le_OE_L2C_RNA_rep1


title: wildtype, ChIP anti-GFP, negative control, replicate1

description:
Library name: wt_Negcontrol_rep1
negative control ChIP
wt_Negcontrol-ChIP_CPM_normalized_nodups.wig


title: wildtype, ChIP anti-GFP, negative control, replicate2

description:
Library name: wt_Negcontrol_rep2
negative control ChIP
wt_Negcontrol-ChIP_CPM_normalized_nodups.wig


title: Ctrl_L2C_RNA_rep1


title: tg3

status: Public on Jun 12 2025

city: Baltimore

first: Yuji

last: Zhang

state: MD

address: 660 W. Redwood Street

institute: University of Maryland

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS).
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software.
Sequence read will be trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads will be mapped to the ZV9 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Assembly: Danio_rerio.GRCz11.cdna.all.fa
Supplementary files format and content: merged_gene_counts.txt

source_name: Heart

extract_protocol:
Total RNA was extracted from dissected ventricular tissue of 6-month-oldmtorxu015/+ mutant, Tg(cmlc2:tfeb) transgenic and corresponding  WT siblings.
Five ventricles were pooled as one sample and three biological replicates for each genotype were sequenced using the HiSeq 2000 platform. (Illumina) with a 50-bp paired-end sequencing protocol in the Mayo Clinic DNA Sequencing Core Facility

value: Heart

value: Tg(cmlc2:tfeb) transgenic


title: tg2


title: H3K4me3_SgD_KDM2A_CTR_r2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore
Trimmed sequence reads were mapped to mm10 using STAR
Duplicated reads were removed using SAMtools
Read count extraction and normalization were performed using QuasR/limma
Assembly: mm10

extract_protocol:
To profile histone modifications in spermatogonia cells we followed the previously published ULI-NChIP protocol (Brind'Amour, Liu et al. 2015) with minor modifications. Briefly 5000-7500 spermatogonia cells were FACS-sorted directly in 20 μl nuclear isolation buffer (Sigma-Aldrich NUC101) in Eppendorf® LoBind microcentrifuge tubes. The nuclei were centrifuged at 500g for 5 minutes at 4°C in a swing bucket centrifuge and the volume of the sample was reduced to 10 μl. The sample was snap frozen in liquid nitrogen and stored at –80°C freezer until further processing. The sample was thawed on ice and 1 μl of TS buffer (5% Triton X-100, 5% Sodium deoxycholate) was added for 10 minutes to ensure permeabilization of nuclei. 40 μl of MNAse digestion buffer (3.33 gelUnits/μl Micrococcal Nuclease (NEB M0247S), 1.25X Micrococcal Nuclease buffer, 6.25% PEG 6000, 0.85mM DTT) was added to the sample for 10 minutes at 25 °C to fragment the chromatin. Reaction was stopped by addition of 5 μl 100 uM EDTA and the sample was placed on ice. The sample was diluted by addition of 145 μl ChIP buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 150 mM NaCl, 0.1% Triton X-100, 1X EDTA-free protease inhibitor cocktail). To ensure release of chromatin fragments, the sample was sonicated using the Diagenode Bioruptor Plus® for 3 cycles of 5 seconds ON and 30 seconds OFF at low output. Then chromatin was pre-cleared with 10 μl of 1:1 protein A:protein G Dynabeads (Thermo Fisher Scientific, 10001D and 10003D). The precleared chromatin sample was incubated with 0.5 μg of anti-H3K4me3 or 1 μg anti-H3K36me2 or 1 μg anti-H3K27me3 conjugated with 10 μl of 1:1 protein A: protein G Dynabeads overnight at 4 °C on a rotator. Chromatin-Antibody-Dynabeads complexes were washed once with 500 μl of ChIP buffer, 3 times with 1ml of Low Salt wash buffer (20 mM Tris-HCl (pH 8.0), 0.05% SDS, 1% Triton X-100, 2 mM EDTA and 150 mM NaCl) and 3 times with 1 ml High Salt buffer (20 mM Tris-HCl (pH 8.0), 0.05% SDS, 1% Triton X-100, 2 mM EDTA and 250 mM NaCl). Chromatin was eluted in 40 μl of Elution buffer (100 mM NaHCO3 and 1% SDS) for 90 minutes at 65 °C. DNA from eluted material was purified by 2X volumes of Ampure XP DNA purification beads (Beckman Coulter, A63881) and resuspended in 25 μl nuclease free H2O.
For library construction the ChIP purified DNA was used as input for the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB E7645L) with modifications of the manufacturer instruction as we assembled half volume reactions and we doubled reaction incubation times. For adaptor ligation we used 1:15 adaptor dilution. We amplified the ligated fragments for 12 cycles using single indexed primers.

value: Testis

value: anti-H3K4me3 (Millipore 17-614)

value: Differentiated Spermatogonia


title: tg1


title: RNA_ScLZ_KDM2A_CTR_r1

value: Leptotene and Zygotene Spermatocytes


title: HIS-24, ChIP-seq, replicate 1


title: mtor2

value: mtorxu015/+ mutant


title: mtor1


title: mtor3


title: WT2

value: WT


title: Input-2

city: Stockholm

first: Sören

last: Lehmann

address: Blickagången 16

department: the Department of Medicine

country: Sweden

institute: Karolinska Institute

description: Library name: VI-3409-Input-2

data_processing:
use nf-core-chipseq-2.0.0 for data processing
Assembly: hg19
Supplementary files format and content: xls, peak call results: MALNC_1_ChIRPseq_peaks.xls and MALNC_2_ChIRPseq_peaks.xls
Library strategy: ChIRP-Seq

source_name: Hematopoietic system

extract_protocol:
NB4 cell lysates were prepared from 20x10 to6 cells each, cross-linked with 1% glutaraldehyde and sonicated. MALNC was captured with 30 biotinylated tilling probes (Thermo Scientific) which were designed using Biosearch Technologies' Stellaris FISH Probe Designer. Probes were divided into an odd and an even probe pool (15 probes each) and separately subject to hybridization with cross-linked and sonicated chromatin. MALNC-chromatin complexes were pulled down using streptavidin magnetic beads (Thermo Scientific). MALNC pull-down was confirmed by RNA extraction followed by qRT-PCR detection of MALNC expression. Probes against LacZ were used as negative control (Magna ChIRP™ Negative Control Probe Set, Merck) accounting for non-specific binding. gDNA was extracted (Qiagen DNeasy Blood & Tissue Kit) and subject to DNA sequencing.
Sequencing libraries were prepared from the entire sample volume of ChIRP-DNA using the Smarter ThruPLEX DNA- seq Kit without Covaris fragmentation (cat# R400676, Takara) with Unique dual index Set A-D (cat# R400665/6/7/8, Takara). The library preparation was performed according to the manufacturers’ instructions (guide#112219). Paired-end 150bp read length, NovaSeq 6000 system, SP flowcell and v1.5 sequencing chemistry. A sequencing library for the phage PhiX was included as 5% spike-in in the sequencing run.

value: Hematopoietic system

tag: cell line

value: Promyelocytic leukemia cells

value: carry the t(15;17) PML-RARA fusion gene, Deletion of MALNC Exon 1.1 and exon 1.2


title: Uninjured light touch biol rep 1

description: 10x Genomics

value: amygdala

value: Male

value: Uninjured

value: Light touch


title: Input-1

description: Library name: VI-3409-Input-1


title: MALNC-2

description: Library name: VI-3409-MALNC-2


title: WT1


title: MALNC-1

description: Library name: VI-3409-MALNC-1


title: OE_RP11_3

city: Zhengzhou City

first: Xue

last: Cao

state: Henan Province

address: No. 7, Weiwu Road, Zhengzhou City, Henan Province

institute: Henan Provincial People's Hospital

description: Library name: Sample6

data_processing:
Raw reads with more than 2-N bases were discarded, and adaptors and low-quality bases were trimmed using FASTX-Toolkit (Version 0.0.13). Additionally, reads shorter than 16nt were removed.
Clean reads were then aligned to the GRCh38 genome using HISAT2, allowing for 4 mismatches. Uniquely mapped reads were utilized for gene read number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped).
The R Bioconductor package DESeq2 was employed to identify differentially expressed genes (DEGs), with a significance threshold set at a p-value < 0.05 and a fold change > 1.5 or < 0.67.
Alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) between samples were defined and quantified using the ABLas pipeline as described previously[18]. Ten types of ASEs, including exon skipping (ES), alternative 5' splice site (A5SS), alternative 3' splice site (A3SS), mutually exclusive exons (MXE), mutually exclusive 5'UTRs (5pMXE), mutually exclusive 3'UTRs (3pMXE), cassette exon, A3SS&ES, and A5SS&ES, were detected based on splice junction reads. To assess lncRNA-regulated ASEs, Student’s t-test was applied, and events significant at a p-value cutoff corresponding to a false discovery rate cutoff of 5% were considered lncRNA-regulated ASEs.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes FPKM value for each Sample.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.

source_name: BEAS-2B cells

growth_protocol: Cell culture was conducted in Dulbecco's modified Eagle's medium (DMEM) (PM150210, Procell Life Science & Technology Co., Ltd., China), supplemented with 10% fetal bovine serum (FBS) (10091148, Gibco, China), 100μg/mL streptomycin, and 100U/mL penicillin. Cells were maintained at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol Reagent and then treated with RQ1 DNase to remove DNA, followed by assessing its quality and quantity using a smartspec plus spectrophotometer (BioRad) and confirming integrity through 1.5% agarose gel electrophoresis. Each sample underwent mRNA capture using VAHTS mRNA capture Beads (Vazyme, N401), with an additional round of RQ1 DNase treatment.
Directional library preparation with the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (NR605) involved purifying, fragmenting, and converting polyadenylated mRNAs into double-stranded cDNA. This was followed by end repair, A tailing, and adaptor ligation (N323), with subsequent purification and size fractionation (300 - 500bps). Ligated products were then amplified, purified, quantified, and stored at -80℃ prior to sequencing, with strand-specific sequencing achieved by excluding amplification of the dUTP-marked strand. High-throughput sequencing was performed on an Illumina Novaseq 6000 system using 150nt paired-end sequencing, as per the manufacturer's instructions.

treatment_protocol: The pcDNA3.1-RP11-284N8.3 (ENST00000566942.1) plasmid and empty vector, sourced from Youbio Biotech (Changsha, PRC), was utilized for transfection experiments in BEAS-2B cells (CL-0496, Procell Life Science & Technology Co., Ltd., China). Transfection of BEAS-2B cells with the plasmid was carried out using Lipofectamine 3000 (L3000015, Invitrogen, Carlsbad, CA, USA), following the manufacturer's protocol. After transfection, cells were cultured for 48 hours and induced by LPS (100mg/L) for 24 hours before harvesting for RT-qPCR analysis.

value: BEAS-2B cells

value: Overexpression of RP11-284N8.3 through transfection of the pcDNA3.1-RP11-284N8.3 plasmid in BEAS-2B cells.


title: H3K4me3_SgD_KDM2A_iKO_r2

first: Antoine

last: Peters

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute

source_name: Testis

value: Kdm2a F/F ; cre-ERt2 +

value: Tamoxifen


title: OE_RP11_2

description: Library name: Sample5


title: NC_3

description: Library name: Sample3

value: Overexpression control with empty vector transfection.


title: NC_2

description: Library name: Sample2


title: OE_RP11_1

description: Library name: Sample4


title: NC_1

description: Library name: Sample1


title: WT-2

description:
Library name: UA-2818-WT-2_S2
other

data_processing:
Samples were analysed with the nf-core rnaseq pipeline release 1.4.2. In short, the pipeline does the following: The workflow processes raw data from FastQ inputs, aligns the reads, generates counts relative to genes or transcripts and performs extensive quality-control on the results. For information regarding the pipeline, folder structure and how to interpret results, please refer to the pipeline documentation: https://github.com/nf-core/rnaseq. Detailed information about standard outputs from the pipeline can be found here: https://github.com/nf-core/rnaseq/tree/1.4.2
Assembly: hg19
Supplementary files format and content: MALNC_RNAseq_merged_gene_counts.txt

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer protocol.
Sequencing libraries were prepared from 500ng total RNA using TruSeq stranded total RNA library preparation kit with ribosomal depletion using RiboZero Gold (Illumina Inc.) and samples were paired-end sequenced (150 cycles in one NovaSeq 6000 SP flowcell).

treatment_protocol: NB4 KOB clones and NB4 WT clones were treated with ATRA (1µM) for 72h

value: carry the t(15;17) PML-RARA fusion gene, MALNC Wilde type


title: WT-ATRA-3

description:
Library name: UA-2818-WT-ATRA-3_S15
other

value: all-trans retinoic acid (ATRA)


title: WT-3

description:
Library name: UA-2818-WT-3_S3
other


title: WT-ATRA-2

description:
Library name: UA-2818-WT-ATRA-2_S14
other


title: KOB-ATRA-1

description:
Library name: UA-2818-KOB-ATRA-1_S16
other

value: carry the t(15;17) PML-RARA fusion gene, Deletion of MALNC Exon 1.0, 1.1 and exon 1.4


title: WT-1

description:
Library name: UA-2818-WT-1_S1
other


title: WT-ATRA-1

description:
Library name: UA-2818-WT-ATRA-1_S13
other


title: KOB-ATRA-2

description:
Library name: UA-2818-KOB-ATRA-2_S17
other


title: KOB-ATRA-3

description:
Library name: UA-2818-KOB-ATRA-3_S18
other


title: KOB-3

description:
Library name: UA-2818-KOB-3_S9
other

value: carry the t(15;17) PML-RARA fusion gene, Deletion of MALNC Exon 1.0, 1.1 and exon 1.2


title: WT3

value: Heart

value: WT


title: KOB-2

description:
Library name: UA-2818-KOB-2_S8
other

value: Hematopoietic system

value: Promyelocytic leukemia cells


title: KOB-1

description:
Library name: UA-2818-KOB-1_S7
other


title: KOA-1

description:
Library name: UA-2818-KOA-1_S4
other

value: carry the t(15;17) PML-RARA fusion gene, Deletion of MALNC Exon 1.1 and exon 1.2


title: KOA-2

description:
Library name: UA-2818-KOA-2_S5
other


title: D7+11 samples treated with FGF9

city: Melbourne

first: Allara

last: Zylberberg

state: VIC

address: Murdoch Children's Research Institute, Royal Children's Hospital, 50 Flemington Rd, Parkville VIC 3052

department: Stem Cell Medicine

country: Australia

institute: Murdoch Children's Research Institute

description: Library name: D7_11_F9HC

library_source: other

data_processing:
10x Genomics cellranger-8.0.0 for data demultiplexing. Sample QC, integration and analysis was performed in Python using Scanpy (v.1.10.2)
Assembly: GRCh38
Supplementary files format and content: D7_5.h5ad = processed and integrated D7+5 single cell samples. D7_11.h5ad = processed and integrated D7+11 samples.

molecule: other

source_name: Kidney organoid

extract_protocol:
Suspension kidney organoids at D7+5 or D7+11 were transferred into a 15ml falcon for dissociation in 4ml of 1:1 TrypLE/Accutase solution (STEMCELL Technologies) at 37°C with occasional agitation (flicking) until large clumps were no longer visible. If the organoids were not dissociated after 20 minutes, mechanical dissociation was undertaken. The TrypLE/Accutase solution was quenched using an equal amount of TeSR-E6 and cells were run through a pre-wet 40µm cell strainer to make them into single cell suspension.
Library was constructed according to manufacturer's protocol, 10x Chromium Single Cell Expression Flex Protocol (CG00527, Revision E).

value: Kidney organoid


title: D7+5 samples treated with FGF8b and FGF10

description: Library name: D7_5_F10_F8bHC


title: D7+11 samples treated with FGF8b

description: Library name: D7_11_F8bHC