title: 231spheres_4IC_20ug_mL_PDX_dECM_Replicate3

city: New Orleans

first: Elizabeth

middle: Carol

last: Martin

state: LA

address: 1430 Tulane Avenue

institute: Tulane University

description: Library name: Sample 15

data_processing:
STAR aligner v2.7.11 was used to map short sequencing reads to the reference genome
Assembly: Reads were aligned to Ensembl
Supplementary files format and content: Data files represent relative gene abundance as counts per million (CPMs). CPM values were determined by STAR

source_name: MDA-MB-231+decelled PDX tumor

growth_protocol: TNBC cell line, MDA-MB-231, (ATCC, Manassas, VA, USA) was cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Gibco, Waltham, MA, USA) supplemented with 10% HyClone Cosmic Calf Serum (Cytiva), 1% minimal essential amino acids (Gibco, Waltham, MA), 1% non-essential amino acids (Gibco, Waltham, MA, USA), 1% antibiotic/anti-mycotic (Gibco, Waltham, MA, USA) and insulin (Gibco, Waltham, MA, USA) under mycoplasma-free conditions at 37 °C and 5% v/v CO2.

extract_protocol:
Total RNA was extracted from the cell lines using Quick RNA Miniprep Kit from Zymo Research (Irvine, CA, USA) and sent to Plasmidsaurus (Burlington, MA, USA) for RNA sequencing.
The RNA sequencing workflow after RNA isolation included generation of cDNA using a poly(dT)VN primer.  Illumina sequencing and a 3’ end counting approach was carried out. Molecular identifiers (UMIs) were used to duplicate, and unique dual indices (UDIs) to prevent index hopping. The read length is ~90bp and all of the reads align within the last ~400nt of the transcript.

treatment_protocol: No treatments were used in this study

value: MDA-MB-231+decelled PDX tumor

value: breast cancer cell line

value: WT


title: 231spheres_4IC_20ug_mL_PDX_dECM_Replicate2

status: Public on Jul 01 2026

type: SRA

department: Medicine

country: USA

description: Library name: Sample 14

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

tag: sample group


title: 8-week untreated control mouse dorsal skin

city: Vienna

first: Hannes

last: Kühtreiber

state: Vienna

address: Lazarettgasse 14

department: Department of Dermatology

country: Austria

institute: Medical University Vienna

description:
Library name: 8wk_ctrl
10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw base call files were demultiplexed and converted to FASTQ files using the 10x Genomics Cell Ranger pipeline.
Sequencing reads were aligned to the mouse reference genome using Cell Ranger count. The 10x Genomics mouse reference refdata-gex-mm10-2020-A was used, corresponding to mm10/GRCm38 with GENCODE vM23/Ensembl 98 gene annotation.
Cell Ranger was used for cellular barcode detection, UMI counting, and generation of gene-barcode count matrices for each sample.
Assembly: Mus musculus mm10/GRCm38 reference genome assembly using the 10x Genomics refdata-gex-mm10-2020-A reference package with GENCODE vM23/Ensembl 98 annotation.
Supplementary files format and content: Tab separated value files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: Dorsal skin

growth_protocol: Male C57BL/6 mice were maintained under standard animal facility conditions until 8, 26 or 52 weeks of age.

extract_protocol:
Three animals were pooled per condition. Immediately after collection, tissues were enzymatically dissociated using the gentleMACS Whole Skin Dissociation Kit (Miltenyi Biotec, Bergisch-Gladbach, Germany) according to the manufacturer's instructions on a gentleMACS Octo Dissociator (Miltenyi Biotec). Cell suspensions were filtered sequentially through 100 µm and 40 µm strainers and washed in PBS containing 0.04% bovine serum albumin (BSA; Sigma-Aldrich, St. Louis, MO, USA). Cell viability and concentration were assessed with the Acridine Orange/Propidium Iodide (AO/PI) Cell Viability Kit (Logos Biosystems, Anyang-si, Gyeonggi-do, Korea) on a LUNA-FL Dual Fluorescence Cell Counter (Logos Biosystems), and the concentration was adjusted to 0.7–1.2 × 10⁶ cells/ml.
Gel beads-in-emulsion (GEMs) were generated, and GEM formation, barcoding, clean-up, cDNA amplification, and library preparation were performed according to the manufacturer's instructions using the Chromium Next GEM Single Cell 3′ GEM, Library and Gel Bead Kit v3.1, the Chromium Next GEM Chip G Single Cell Kit, and the Single Index Kit T Set A (10x Genomics, Pleasanton, CA, USA). Sequencing, demultiplexing, and read counting were performed by the Biomedical Sequencing Facility of the Center for Molecular Medicine (CeMM, Vienna, Austria).

treatment_protocol: For untreated control samples, dorsal skin from 8-week, 26-week and 52-week-old C57BL/6 mice was processed directly after collection. For treatment samples, freshly collected dorsal skin from age-matched mice was treated ex vivo with the secretome of γ-irradiated peripheral blood mononuclear cells (PBMC-sec) prior to tissue dissociation and single-cell RNA-sequencing. Following treatment, tissue was enzymatically dissociated using the same protocol as untreated samples. Three animals were pooled per condition.

tag: tissue

value: Dorsal skin

value: Whole skin cells

value: wildtype

tag: treatment

value: Untreated

tag: Sex

value: male

tag: age


title: 231spheres_4IC_10ug_mL_PDX_dECM_Replicate3

description: Library name: Sample 12


title: 8-week PBMC-sec-treated mouse dorsal skin

description:
Library name: 8wk_Apo
10x Genomics

value: PBMCsec


title: 231spheres_4IC_10ug_mL_PDX_dECM_Replicate2

description: Library name: Sample 11


title: 231spheres_4IC_20ug_mL_PDX_dECM_Replicate1

description: Library name: Sample 13


title: Spiderbgal-high cells from mouse acylic ovaries

city: New York

first: Jiping

last: Yang

state: NY

department: OBGYN

institute: Columbia University

description:
Library name: mouse_post-estropause_ovary_Spiderbgal-high
10x Genomics

data_processing:
Raw data processing was performed using Cellranger  (version 7.2.0)
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: Tab=seperated values and matrix files generated by cellranger 7.2.0

source_name: Ovary

extract_protocol:
Ovary samples were collected separately from each individual at different days. Two ovaries were isolated and immersed in chilled M2 medium (Sigma, M7167). Surrounding fat and connective tissue were trimmed and removed. Two intact ovaries were minced in 1.5 ml Eppendorf tube and treated by enzymatic digestion in dissociation buffer (M2 medium supplemented with 30 ug/ml Liberase DH (Roche, LIBDH-RO) and 1000U/mL DNase (Thermo Fisher)) at 37°C for 15 min with shaking on thermomixer (1000 rpm). The tube was briefly spun at 1000 rpm and the supernatant was collected in a 15 ml centrifuge tube. Next, the remaining tissues were cut and incubated in a dissociation buffer for 10 min with shaking. The cell suspension was pooled with the supernatant in a 15 mL tube and neutralized with M2 medium with 1% BSA. The pooled cell suspension was filtered with a 45-um cell strainer  and was centrifuged. Cell pellets were incubated with RBC Lysis Buffer (Thermo Fisher) to remove red blood cells and subsequently washed with 1%BSA in PBS and 10% FBS in EMEM. Pelleted cells were resuspended in 10% FBS in EMEM and further submitted to Columbia Genomic Core for scRNA-seq library construction.
library was performed by Columbia Genome Center according to the manufacter's instructions (3' single cell, 10x Genomics).

value: Ovary

value: wild-type


title: CD45 positive immune cells from melanoma tumors during targeted therapy-tolerant residual disease

city: Ithaca

first: Andrew

middle: C

last: White

address: 930 CAMPUS RD

institute: Cornell University

description: Library name: Immune_Residual

data_processing:
Sequencing reads were processed with 10x Genomics Cell Ranger (v7.2.0) using the mouse GRCm39 reference genome to generate feature-barcode matrices.
Sequencing reads were processed with 10x Genomics Cell Ranger (v7.2.0) using the mouse GRCm39 reference genome to generate feature-barcode matrices.
The resulting filtered feature-barcode matrices (barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz) were used for downstream analysis.
Assembly: Mus musculus (GRCm39, Ensembl release 110)
Supplementary files format and content: Processed data files include filtered gene-barcode matrices (*_barcodes.tsv.gz, *_features.tsv.gz, *_matrix.mtx.gz) for each condition (regressing and residual). Files contain cell barcodes, gene features, and sparse gene count matrices generated by Cell Ranger.

source_name: melanoma tumor

extract_protocol:
Tumors were mechanically and enzymatically dissociated into single-cell suspensions. CD45⁺ immune cells were isolated using magnetic bead enrichment and filtered through a 40 μm strainer. Cell viability was confirmed prior to library preparation.
Single-cell libraries were generated using the 10x Genomics Chromium Next GEM Single Cell 3′ RNA-Seq Assay v3.1 (Dual Index) according to the manufacturer’s protocol (CG000416, RevC). Libraries were sequenced on an Illumina NovaSeq 6000 instrument.

treatment_protocol: Mice bearing melanoma tumors were treated with a combination of BRAF and MEK inhibitors until defined tumor regression or therapy-tolerant residual stages were reached. Tumors were collected at each stage for single-cell RNA sequencing.

value: melanoma tumor

value: CD45 positive immune cells

value: 14-day BRAF/MEK inhibitors


title: 231spheres_4IC_10ug_mL_PDX_dECM_Replicate1

description: Library name: Sample 10


title: CD45 positive immune cells from melanoma tumors during targeted therapy–induced regression

description: Library name: Immune_Regression

value: 3-day BRAF/MEK inhibitors


title: 231spheres_adipose_20ug_mL_dECM_Replicate3

description: Library name: Sample 9

source_name: MDA-MB-231+decelled breast tissue

value: MDA-MB-231+decelled breast tissue


title: PD1_F

city: Lexington

first: Avery

middle: R

last: Childress

state: KY

address: 800 Rose Street

department: Toxicology and Cancer Biology

institute: University of Kentucky

description:
Library name: Sample 5
Count data

data_processing:
Sequencing reads were trimmed and filtered using Trimmomatic (V0.39) to remove adapters and low quality reads. Reads from samples were mapped to Ensembl mm10 transcripts annotation, using RSEM (v1.3.2) and STAR (2.6.1d) with default settings.
Assembly: mm10
Supplementary files format and content: Count data: gene.count.annotated.tsv

source_name: Neutrophil

growth_protocol: Neutrophils were grown in the bone marrow of mice through the processes of normal cellular development

extract_protocol:
Bone marrow from femur and tibia of mice was flushed using 1mL of Mg2+ and Ca2+ free PBS (Cytiva cat# SH30256.01). 1.5 ml of histopaque 1077 was pipette on top of histopaque 1119 carefully to preserve the interface between the two layers. Total bone marrow (1mL) was then added on top of histopaque gradient and the tube wa centrifuged at 1000x g for 25 minutes with zero acceleration and zero brake. Once centrifuged, the upper low-density and lower high-density bands of cells were collected and washed with excess PBS. high density band was frozen and used for the RNA sequence protocol
RNA libraries were prepared for sequencing using Innomics protocol

treatment_protocol: These mice were then placed on the four treatment groups, placebo, anti-PD1, valemetostat, or combination treatment.  Valemetostat tosylate provided by Daiichi Sankyo was prepared in sterile distilled water to a concentration 13.5mg/ml and administer via oral gavage at 135 mg/kg (equivalent to 100mg/kg valmetotstat).  Anti-PD1 clone RMP1-14 (BioXCell #BP0146) and IgG2a isotype control (BioXCell #BP0089) were diluted with InVivoPure pH 7.0 dilution buffer (BioXCell #IP0070) or InVivoPure pH 6.5 dilution buffer (BioXCell # IP0065) to a concentration of 1.25μg/μL. Both antibodies were administered 7mg/kg 3 days a week via intraperitoneal injection

value: Neutrophil

value: Female


title: 231spheres_adipose_20ug_mL_dECM_Replicate1

description: Library name: Sample 7

value: breast cancer cell line


title: Combo_M

description:
Library name: Sample 8
Count data

value: Male

value: Combo


title: Rej_F

description:
Library name: Sample 9
Count data

value: No treat


title: Combo_F

description:
Library name: Sample 7
Count data


title: 231spheres_adipose_10ug_mL_dECM_Replicate2

description: Library name: Sample 5

value: WT


title: Naive_F

description:
Library name: Sample 11
Count data


title: 231spheres_adipose_10ug_mL_dECM_Replicate1

description: Library name: Sample 4


title: 231spheres_adipose_20ug_mL_dECM_Replicate2

description: Library name: Sample 8


title: PD1_M

description:
Library name: Sample 6
Count data


title: 231spheres_CNTL_noECM_Replicate3

description: Library name: Sample 3


title: Rej_M

description:
Library name: Sample 10
Count data


title: Placebo_F

description:
Library name: Sample 1
Count data

value: Placebo


title: Val_M

description:
Library name: Sample 4
Count data

value: Valemetostat


title: 231spheres_CNTL_noECM_Replicate2

description: Library name: Sample 2


title: L9 C

city: Boston

first: Ke

last: Zhang

state: MA

address: 360 Huntington Ave

institute: Northeastern University

description:
Library name: Sample 5
Column name in raw_counts_all_samples.csv: L9_DM1_63

data_processing:
Index of the reference genome was built usingHisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome (GRCm39/mm39) with Hisat2 v2.0.5. using standard workflows (Novogene)
Additional analysis was conducted in Rstudio using the DEseq2, clusterProfiler, fgsea, and gsva packages
Assembly: mm39
Supplementary files format and content: csv file of raw counts for each sample titled raw_counts_all_samples.csv

source_name: quadricep

extract_protocol:
Individual muscle sections were homogenized in a lysis buffer containing 10% BME on a Beadblaster 24R Microtube Homogenizer (Benchmark scientific, NJ, USA.). Total cellular RNA was extracted using the RNeasy® Fibrous Tissue Mini Kit (Qiagen), and RNA quality and quantity were assessed on a NanoDrop® ND-1000 UV-Vis Spectrophotometer.
Messenger RNA was purified from total RNA using poly-T oligo-attachedmagnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis. After polyA enrichment and quality control, libraries were sequenced on an Illumina NovaSeq6000 PE150 system to obtain paired-end reads of 150 bp.

treatment_protocol: 8 week old HSA-LR20b or FVB/N wildtype mice were injected by tail vein with drug or control. Mice were humanely sacrificed by carbon dioxide two weeks after the final injection and muscle sections were immediately harvested and flash frozen in liquid nitrogen.

value: quadricep

value: 5.3 mg/kg L9


title: 231spheres_CNTL_noECM_Replicate1

description: Library name: Sample 1


title: NEG_EVT_Rep2

status: Public on Jul 03 2026

city: Seattle

first: Meagan

middle: Nicole

last: Esbin

state: WA

address: 850 Republican St. S280

department: Obstetrics & Gynecology

institute: University of Washington School of Medicine

description: Library name: Sample 7

data_processing:
Plasmidsaurus performed read-filtering using FastP v0.24.0: poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp
Plasmidsaurus aligned reads to the human hg38 reference genome using STAR aligner v2.7.1181 with non-canonical splice junction removal and output of unmapped reads.
Plasmidsaurus performed gene-expression quantification using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id.
Differential gene expression analysis was performed with EdgeR in Jupyter Notebook with filtering for low-expressed genes with edgeR::filterByExpr. Statistical comparisons between individual sample conditions were made using EdgeR makeContrasts and then glmQLFit. The reported P-values and FDR values were corrected with adjust.method = “BH,” and differentially expressed genes are reported with an adjusted FDR of <0.05.
Assembly: hg38
Supplementary files format and content: Comma separated values file containing CPM-normalized count data for each Sample by Ensembl Gene ID
Supplementary files format and content: Comma separated values file containing differential gene expression analysis output from EdgeR with the Log2 Fold-Change (logFC), p-value (pValue) and Benjamini-Hochberg (BH) corrected False Discovery Rate (FDR) comparing NEG (non-targeting sgRNA transfected) hTSCs to ZBTB10 KO hTSCs in Undifferentiated, STB-differentiated, and EVT-differentiated conditions. Comparisons are noted as (_KOvsWT) where positive FC values indicates higher gene expression in ZBTB10 KO cells compared to NEG control.

source_name: hTSC

growth_protocol: Naïve-derived human trophoblast stem cells were established previously and cultured in hypoxic conditions (37°C, 5% CO2, 5% O2) in TSC Media (DMEM/F12 supplemented with 0.1 mM β-mercaptoethanol, 0.2% FBS (Sigma, F4135), 0.5% Penicillin-Streptomycin (P/S; Gibco, 15140122), 0.3% BSA, 1% ITS-X (Gibco, 41400045), 1.5 μg/mL L-ascorbic acid, 50 ng/mL EGF, 2 μM CHIR99021, 0.5 μM A83-01, 1 μM SB431542, 0.8 mM VPA, and 5 μM Y-27632).51 Media was changed every other day and TSCs were passaged using TrypLE Express (Gibco, 12605010) when 80% confluent (approximately every 4 days) at a ratio of 1:4–6 on Cultrex-coated plates. Cells from passage 10-25 were used.

extract_protocol:
hTSC RNA was harvested using the RNeasy mini kit (Qiagen, 74104).
RNA-sequencing was performed by Plasmidsaurus using Illumina Sequencing Technology with custom analysis and annotation.

treatment_protocol: Human hTSCs were plated at a density of 1E5 cells/well in Cultrex-coated 6-well plates and differentiated for 6 days into EVT or STB and harvested at Day 7, or if undifferentiated were harvested when confluent at Day 4. For the induction of EVTs, Cells were allowed to adhere overnight in TSC medium, then differentiation was initiated by switching to EVT1 medium (DMEM/F12, 0.1 mM β-mercaptoethanol, 0.5% Pen/Strep, 0.3% BSA, 1% ITS-X, 100ng/mL NRG1, 7.5uM A83-01, 2.5 μM Y-27632, and 4% Knockout Serum Replacement) supplemented with 1% Geltrex (Day 1). On day 3, the medium was replaced with EVT2 medium (EVT1 medium without NRG1) supplemented with 0.5% Geltrex. On day 5, the medium was replaced with EVT2 medium. For the induction of STBs, TSCs were seeded identically as above. Cells were allowed to adhere overnight in TSC medium, then differentiation was initiated by switching to STB medium (DMEM/F12, 0.1 mM β-mercaptoethanol, 0.5% Pen/Strep, 0.3% BSA, 1% ITS-X, 2.5 μM forskolin, 2.5 μM Y-27632, and 4% Knockout Serum Replacement) on Day 1. The medium was replaced on day 4.

value: hTSC

value: naive pluripotent stem cell derived human trophoblast stem cells

value: NEG (polyclonal nucleofected with Cas9+non-targeting sgRNA)

value: 6 day EVT differentiation

tag: batch


title: CUTTAG_H3K4me3_KMS11_NSD2dTAG#11_dTAGv1_21d_Rep2

city: Miami

first: sanxiong

last: liu

state: FL

address: 1501 NW 10th Avenue

department: Human Genetics

institute: University of Miami Miller School of Medicine

description: Library name: Sample 8

library_source: genomic

data_processing:
Raw paired-end sequencing reads (FASTQ) were first assessed for quality and cleaned using fastp (v0.24.0). Cleaned reads were then aligned to the human reference genome (hg38) using Bowtie2 with parameters --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. The resulting alignments were converted to BAM format, sorted, and indexed using Samtools. PCR duplicates were marked using Picard MarkDuplicates. Alignments were subsequently filtered using Samtools to retain properly paired reads and exclude reads mapping to ENCODE blacklisted regions. For visualization and downstream analysis, signal tracks in bigWig format were generated using deepTools (v3.5.1) bamCoverage, normalizing signal to Reads Per Kilobase per Million mapped reads (RPKM) with a bin size of 50 bp. Peak calling for the H3K27me3 modification was performed using MACS3 (v3.0.2) callpeak with parameters --format BAMPE -g hs --broad --broad-cutoff 0.1 --keep-dup all. Consensus peak sets were generated by merging reproducible peaks across replicates. Differential binding analysis between conditions was performed using DESeq2 on read counts within the consensus peak set (obtained via chromVAR), and resulting differentially bound regions were annotated using the ChIPseeker R package (v 1.42.1).
Assembly: hg38
Supplementary files format and content: Processed data files are provided for each H3K27me3 CUTTAG sample in two formats: 1) bigWig (.bw) files containing genome-wide signal enrichment, normalized as Reads Per Kilobase per Million mapped reads (RPKM) using deepTools, suitable for visualization; and 2) BED (.broadPeak) files generated by MACS3 (using --broad --broad-cutoff 0.1), defining genomic regions significantly enriched for the H3K27me3 mark. And processed bigwig files for H3K27ac and H3K4me3 CUTTAG.
Library strategy: CUT&Tag

molecule: genomic DNA

growth_protocol: KMS-11 cells are cultured in RPMI-1640 supplemented with 10% FBS and 1% Penicillin-Streptomycin.

extract_protocol:
CUTTAG was performed starting with 50,000 nuclei per sample. Nuclei were isolated, resuspended in Wash Buffer, and loaded onto a silica column. On-column incubations were performed sequentially with primary antibody (anti-H3K27me3, CST #9733; anti-H3K27ac, Abcam#ab4729; anti-H3K4me3, Active Motif #39159), secondary antibody (Antibodies-Online ABIN101961), and pAG-Tn5 transposase complex (Epicypher #15-1017), with buffer washes performed after antibody and transposase incubation steps. Tagmentation was carried out on-column by adding MgCl2 in Wash Buffer and incubating at 4°C for 1 hour. Following tagmentation, nuclei were lysed using SDS and Proteinase K. DNA fragments were then extracted and purified using the DNA Clean & Concentrator-5 kit (Zymo Research #D4014) and eluted in H2O.
Sequencing libraries were prepared from the purified tagmented DNA obtained via the Extract Protocol. Library amplification was performed by PCR for 13 cycles using NEBNext HiFi 2 × PCR Master mix (NEB #M0541). Following PCR amplification, the libraries were purified using HighPrep beads (MagBio genomics #AC-60500).

treatment_protocol: NSD2dTAG KMS-11 cells were treated with dTAGV-1 (100 nM) to induce NSD2 degradation.The specific duration of each treatment varied according to the experimental condition and is indicated in the metadata associated with each sample.

value: NSD2_dTAG knockin

value: dTAGv1 for 21d


title: hESC derived teratoma, HS1332, batch 1

first: Devin

last: Bready

address: Placantonakis Lab, 33rd and East River Drive, Smilow 1306H

department: Neurosurgery

institute: NYU School of Medicine

description:
Library name: HS1332 Deleted hESCS Batch 1
teratoma_allcells_.RDS
terataoma_ectoderm_only_subset.rds

data_processing:
Data were processed, normalized, integrated for all specimens, and clustered together using Seurat packages based on RNA. Only cells with greater than 750 features and fewer than 0.10% mitochondrial genes were included in the analysis. Initial labeling of all cells was performed using the reference mapping feature of Seurat against data from McDonald and colleagues.
Assembly: hg38
Supplementary files format and content: Seurat R Objects of All Cells and Only Ectoderm
Supplementary files format and content: barcodes, features, matrix files

molecule: nuclear RNA

source_name: H9 hESC

growth_protocol: H9 (WA09) human embryonic stem cells (hESCs) stably nucleofected with a Hes5::GFP reporter were  cultured as colonies on a layer of mouse embryonic fibroblasts (MEFs, Invitrogen) in hESC medium, consisting of 1:1 DMEM/F12 (Invitrogen), 20% KSR (Invitrogen), 5 ng/mL FGF2 (R&D), 2 mM glutamine (Invitrogen), 0.1 mM non-essential amino acids (Invitrogen), and 0.1 mM β-mercaptoethanol (Invitrogen). Male NSG mice at 6 to 8 weeks of age were anesthetized using an anesthetic of ketamine and xylazine diluted in PBS at 100 mg/kg and 20 mg/kg, respectively. After induction of anesthesia, each flank was sterilized with 70% ethanol and shaved. Subsequently, 1x10^6 dissociated hESCs in 50 mL of a 1:1 mixture of DMEM/F12 (Invitrogen) and Matrigel (Corning) was drawn into a 17-gauge needle and injected into the flank. Teratomas were allowed to grow for 6 weeks. Teratoma tissue was harvested following euthanasia through injection with 50 mg/kg of pentobarbitol (Euthasol, Virbac). Procedures were performed according to IACUC protocol number 160403 at NYU Grossman School of Medicine.

extract_protocol:
Previously harvested, flash-frozen teratoma tissue samples were lysed by addition of 0.1 mL of freshly prepared 0.1X lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP40, 0.01% digitonin, 1% BSA, 1 mM DTT, and 1 U/mL Sigma protector RNase inhibitor), tissue homogenized with microfuge tube pestles, and incubated on ice for 10 minutes. One mL of chilled wash buffer (10 mM Tris757 HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween-20, 1 mM DTT, and 1 U/mL of RNase inhibitor) was added and the mixture was strained through 70 and 40 µm filters. The resulting solution of nuclei and debris was stained with 5-AAD and the mixture sorted for 5-AAD-positive nuclei on a FACSAria cell sorter.
Resulting nuclei were immediately processed to generate single cell RNA-sequencing libraries using the 10X Genomics protocols in the Single Cell 3’ Reagent Kits v2 User Guide.

value: H9 hESC


title: hESC derived teratoma, nMotif, batch 1

description:
Library name: nMotif Deleted hESCs Batch 1
teratoma_allcells_.RDS
terataoma_ectoderm_only_subset.rds


title: hESC derived teratoma, nMotif, batch 2

description:
Library name: nMotif Deleted hESCs Batch 2
teratoma_allcells_.RDS
terataoma_ectoderm_only_subset.rds


title: FRDA heart only replaced with FRDA macrophages_2 (FA sham 2)

status: Public on Jul 02 2026

city: Stanford

first: Natalia

last: Gomez-Ospina

address: 265 Campus Drive

institute: Stanford

description: Library name: FR_FR_RNA2_FPKM

data_processing:
Quality control and read alignment were performed by MedGenome. Data quality control was performed via FastQC (v0.11.9). Low-quality sequence reads were excluded, and adapter sequences were trimmed using fastq-mcf (v1.05) and cutadapt (v4.7). Removal of other unwanted sequences (mitochondrial genome sequences, ribosomal RNA, transfer RNA, adapter sequences, etc.) was performed via Bowtie2 (v2.5.3). Paired-end reads were aligned to the Ensembl Mus musculus genome (GRCm39) via STAR (2.7.11b). Raw read counts were estimated from the aligned reads using HTSeq (v2.0.5). FPKM (Fragments per kilobase per million) expression values for each gene were estimated from the aligned reads using cufflinks (v2.2.1).
Assembly: GRCm39
Supplementary files format and content: Raw_Counts_HTSEQ_heart.xlsx contains the raw counts for gene expression (calculated with HTSeq) for all eight samples, with each sample corresponding to one row. The file also contains the Ensembl gene ID, gene names, and biotype as rows.
Supplementary files format and content: FPKM_heart.xlsx contains the FPKM units for gene expression for all eight samples, with each sample corresponding to one row. The file also contains the Ensembl gene ID, gene names, and biotype as rows.

source_name: whole heart

extract_protocol:
Total RNA was extracted from one minced mouse heart tissue for bulk RNA-seq
Whole heart tissue was collected from WT and YG8s800 mice at 20- and 22-weeks post-bone marrow transplantation (BMT), following conditioning with Busulfan (BU) and PLX3397. The time points corresponded to an age of 7–8 months for each group. Following two washes with cold 1x PBS, the heart tissues were dissected in cold 1x PBS using a sterile knife to facilitate efficient RNA extraction. Total RNA was extracted from the minced heart tissue of each mouse group using the Invitrogen™ PureLink™ RNA Mini Kit (#12-183-018A), following the manufacturer's instructions for RNA purification.
Library preparation and sequencing was conducted by MedGenome Inc. (Foster City, CA, USA) using the Illumina Stranded mRNA Prep kit and Novaseq 6000 sequencer (Illumina, San Diego, CA) with paired-end 100 base pair (bp) reads.

value: whole heart

value: Busulfan + PLX3397 + Bone Marrow Transplant


title: Nthy, EZH2 WT, RNA, rep1

city: Seoul

first: Hanbyeol

last: Kim

address: Daehak-ro 103

country: South Korea

institute: Seoul National University

description: Library name: Nthy_EZH2_WT_RNA_rep1

data_processing:
For data analysis, adapter sequences were trimmed using Trimmomatic, and reads were aligned to the human reference genome (hg38) using HISAT2. Transcript assembly was performed using StringTie. Differential gene expression analysis was carried out using DESeq2, with significance defined as a p-value < 0.05 and log2 |fold change| > 1. Normalized RNA expression values were derived from DESeq2. Pathway enrichment analysis and z-scores were calculated using the limma package.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Nthy-ori 3-1

growth_protocol: RPMI, 10% fetal bovine serum, 2mM glutamine, 1x antibiotics/antimycotics. Cells were cultured at 37°C at 5% CO2.

extract_protocol:
Cells were resuspended in 1 mL of TRIzol and incubated for 5 min at room temperature. After incubation, 0.2 mL of chloroform was added, and the mixture was vortexed vigorously. The samples were centrifuged at 13,000 x g for 15 min at 4°C, and the upper aqueous phase was transferred to a fresh tube. RNA was precipitated with isopropanol and washed with ice-cold 70% ethanol. The RNA pellet was resuspended in DEPC-treated water, and the concentration was measured.
Sequencing libraries were prepared using TruSeq Stranded Total RNA Ribo-Zero H/M/R Gold kit.

value: Nthy-ori 3-1

value: Thyroid follicular epithelial cell

value: EZH2 WT overexpression


title: pacDNA-L9 4C

description:
Library name: Sample 4
Column name in raw_counts_all_samples.csv: S2_2

value: 21.2 mg/kg pacDNA-L9


title: CUTTAG_H3K4me3_KMS11_NSD2dTAG#11_dTAGv1_0d_Rep2

description: Library name: Sample 6

value: No


title: CUTTAG_H3K4me3_KMS11_NSD2dTAG#11_dTAGv1_21d_Rep1

description: Library name: Sample 7


title: pacDNA-L9 1C

description:
Library name: Sample 3
Column name in raw_counts_all_samples.csv: S1_2

value: 5.3 mg/kg pacDNA-L9


title: NT8

description:
Library name: Sample 2
Column name in raw_counts_all_samples.csv: S4_2

value: quadricep

value: no treatment


title: pacDNA-L9 1D

description:
Library name: Sample 6
Column name in raw_counts_all_samples.csv: S1_1


title: Female,FR,Saline,Adult,rep10

city: Verdun

first: Nicholas

last: O'Toole

state: QC

address: 6875 Boulevard Lasalle

country: Canada

institute: Douglas Mental Health University Institute

description:
Library name: 5B.7_Female_FR_Saline_mPFC_Adult
5B.7_Female_FR_Saline_mPFC_Adult
Adult_mPFC_counts.txt

data_processing:
Reads were aligned to the rat genome with STAR
Read counts per gene were computed with STAR
Assembly: Rnor_6.0
Supplementary files format and content: Ensembl gene Ids and read counts, tab delimited
Supplementary files format and content: Differential expression data, tab delimited

organism: Rattus norvegicus

source_name: Medial prefrontal cortex

extract_protocol:
Qiagen AllPrep RNA minikit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Medial prefrontal cortex


title: hESC derived teratoma, ROSA26, batch 2

description:
Library name: ROSA26 Control hESCs Batch 2
teratoma_allcells_.RDS
terataoma_ectoderm_only_subset.rds


title: hESC derived teratoma, ROSA26, batch 1

description:
Library name: ROSA26 Control hESCs Batch 1
teratoma_allcells_.RDS
terataoma_ectoderm_only_subset.rds


title: NT7

description:
Library name: Sample 1
Column name in raw_counts_all_samples.csv: S4_1


title: CUTTAG_H3K27ac_KMS11_NSD2dTAG#11_dTAGv1_21d_Rep2

description: Library name: Sample 4


title: CUTTAG_H3K27ac_KMS11_NSD2dTAG#11_dTAGv1_21d_Rep1

description: Library name: Sample 3


title: TAC.WT.024352

city: Munich

first: Stefanie

last: Fenske

address: Butenandtstr. 7

department: Department of Pharmacy - Center for Drug Research

country: Germany

institute: Ludwig-Maximilians-Universität München

description:
Library name: TAC_WT 3
Column name in raw_counts.csv: TAC.WT.024352

data_processing:
evaluate sequence quality
trim reads
map reads to genome
generate hit counts for genes
compare gene hit counts
analyze gene ontology
Assembly: GRCm38
Supplementary files format and content: raw data in fastq format and differential gene expression analysis results as raw gene hit counts as .csv file

source_name: Left Ventricle

extract_protocol:
Left ventricular heart tissue was isolated from mice and shock-frozen in liquid nitrogen. RNA was extracted using a RNeasy Fibrous Tissue Kit (Qiagen) according to protocol.
mRNA sequencing via polyA selection

value: Left Ventricle

value: WT

value: TAC


title: TAC.WT.024353

description:
Library name: TAC_WT 2
Column name in raw_counts.csv: TAC.WT.024353


title: TAC.KI.022502

description:
Library name: TAC_KI 3
Column name in raw_counts.csv: TAC.KI.022502


title: CUTTAG_H3K27ac_KMS11_NSD2dTAG#11_dTAGv1_0d_Rep2

description: Library name: Sample 2

value: NSD2_dTAG knockin


title: TAC.KI.021462

description:
Library name: TAC_KI 4
Column name in raw_counts.csv: TAC.KI.021462


title: CUTTAG_H3K27ac_KMS11_NSD2dTAG#11_dTAGv1_0d_Rep1

description: Library name: Sample 1


title: peaks HeLa cells, 24hrs Oligomycin + Antimycin, H3K27Me3 CUT&RUN, rep 2

city: South San Francisco

first: Daniel

last: Le

state: CA

address: 1 DNA Way

institute: Genentech

description: Library name: SAM24437147_OA2_H3K27Me3_bed

data_processing:
ChIP Seq: The ENCODE analysis pipeline (v2.2.1) was used, with Bowtie2 (v2.3.4.3) employed to align reads to the reference genome (hg38). Duplicated or low-quality reads were filtered out using Picard (Broad Institute - v2.20.7) and samtools (v1.9), with further filtering to remove regions where genome assembly introduces erroneous signal. The SPP data processing pipeline was used to call peaks, with the level of background signal assessed via reference to input sample. DiffBind (v3.12.0) was used to identify differential peaks as follows. RPKM-normalized ChIP Seq data was visualized using IGV (2.18.4) genome browser
CUT&RUN: Indexed libraries generated using NEBNext library prep kit 32 (NEB) and NEBNext Multiplex Oligos for Illumina (NEB) as per manufacturers instructions. Paired-end reads were aligned to the reference genome (hg38) using Bowtie2 (-p 24 -X2000 -t -x) and sorted with Samtools (view -bS -F 4 -q 30 -u - | sort -T). PCR duplicates were marked using Picard MarkDuplicates (MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000 REMOVE_DUPLICATES=true ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT). Genome-wide coverage was determined using Bedtools genomecov (-ibam -bg -scale -g), converted to a BigWig file with wigToBigWig -clip.
Assembly: hg38
Supplementary files format and content: bigwig files for each sample
Supplementary files format and content: bed files for each sample
Library strategy: CUT&Run

source_name: HeLa Cells

extract_protocol:
ChIP-Seq samples were extracted as follows: 50mM DSG (disuccinimidyl glutarate, #C1104 - ProteoChem) for 30 mins followed by 10 mins of 1% formaldehyde was used to double crosslink HeLa or iPSC-derived NGN2 neurons (5x106), followed by the addition of glycine to quench formaldehyde. Nuclei were released using ChIP Nuclear Isolation Buffer (20 mM Tris pH 8.0, 1% Triton X-100, 0.1% SDS, 150 mM NaCl and 1mM EDTA), and chromatin sheared via sonication (Covaris sonicator: Fill level – 10, Duty Cycle – 15, PIP – 350, Cycles/Burst – 200, Time – 8-mins). Solutions containing sheared chromatin were mixed with relevant antibodies and rotated at 4°C overnight before protein A magnetic beads were then added to isolate antibody-bound chromatin. The beads were washed twice in each of the following buffers: ChIP Wash Buffer #1 (20 mM Tris pH 8.0, 1% Triton X-100, 0.1% SDS, 150 mM NaCl, 1 mM EDTA, and 0.1% NaDOC), ChIP Wash Buffer #2. (20 mM Tris pH 8.0, 1% Triton X-100, 0.1% SDS, 500 mM NaCl, 1 mM EDTA, and 0.1% NaDOC) and ChIP Wash Buffer #3 (0.25 M LiCl, 0.5% NP-40, 1mM EDTA, 20 mM Tris, pH 8.0, 0.5% NaDOC), followed by single wash in TE buffer (200 mM Tris pH 8.0 and 10 mM EDTA). The mixtures were then shaken for 20 mins in Elution Buffer (100mM NaHCO3, 1% SDS), before overnight incubation at 65°C to de-crosslink DNA. The DNA fragments were purified with MinElute PCR purification kit (Qiagen), then quantified by Qubit. CUT&RUN was performed using the CUTANA ChIC/CUT&RUN Kit (Epicypher) as per manufacturers instructions with the addition of DUB inhibitor PR-619 (100μM) to Wash and Antibody buffers.
ChIP-Seq libraries were generated using Ovation Ultralow Library System V2 (Tecan) using 2ng of each sample according to the manufacturer’s instructions, then sequenced using paired-end 50bp read configuration. CUT&RUN libraries were generated using NEBNext library prep kit 32 (NEB) and NEBNext Multiplex Oligos for Illumina (NEB) as per manufacturers instructions.

value: HeLa Cells

value: Epithelial

value: 24hrs Oligomycin (1µM) + Antimycin (1µM)


title: Sham.WT.025962

description:
Library name: Sham_WT 4
Column name in raw_counts.csv: Sham.WT.025962

value: Sham


title: peaks HeLa cells, 24hrs Oligomycin + Antimycin, H3K4Me3 CUT&RUN, rep 2

description: Library name: SAM24437146_OA2_H3K4Me3_bed


title: peaks HeLa cells, 24hrs Oligomycin + Antimycin, H3K27Me3 CUT&RUN, rep 1

description: Library name: SAM24437139_OA1_H3K27Me3_bed


title: CD8+ T cells, WMS-64-10

city: Oldenburg

first: Katharina

last: Hoffmann

address: Carl-von-Ossietzky-Straße 9-11,

institute: Carl von Ossietzky Universität

description:
Library name: CD8+ T cells_WMS-64-10
Column name in gene_count.xls: Tc1_WT2_64

data_processing:
RNA-seq was performed on an Illumina NovaSeq platform generating 150 bp paired-end reads with a minimum of 20 million read pairs per sample. Raw sequencing reads were filtered to remove adapters and low-quality reads using fastp.
Assembly: Clean reads were aligned to the reference genome using Hisat2 and the read numbers mapped to each gene were quantified using featureCounts.
Supplementary files format and content: data file gene_count.xls provides raw read counts per gene for each sample.

source_name: CD8+ T cells

growth_protocol: Polarization of mouse T cells was performed according to standard protocols (https://www.biolegend.com/en-gb/technical-protocols/polarization-activation-protocols)

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were performed using a poly(A) enrichment.

treatment_protocol: Purified T cells were treated with either vehicle DMSO or 0.1 µM of the respective KOR agonist WMS-200-01, WMS-64-07, WMS-75-13, WMS-76-04A and WMS-83-02.

value: CD8+ T cells


title: Sham.WT.025963

description:
Library name: Sham_WT 3
Column name in raw_counts.csv: Sham.WT.025963


title: Sham.WT.025964

description:
Library name: Sham_WT 2
Column name in raw_counts.csv: Sham.WT.025964


title: peaks HeLa cells, 24hrs Oligomycin + Antimycin, H3K4Me3 CUT&RUN, rep 1

description: Library name: SAM24437138_OA1_H3K4Me3_bed


title: Sham.WT.026095

description:
Library name: Sham_WT 1
Column name in raw_counts.csv: Sham.WT.026095


title: peaks NGN2 iNeurons, 24hrs Oligomycin + Antimycin, pS65Ub ChIPseq, rep 1

description: Library name: SAM24449815_OA1_pS65Ub_bed

data_processing:
ChIP Seq: The ENCODE analysis pipeline (v2.2.1) was used, with Bowtie2 (v2.3.4.3) employed to align reads to the reference genome (hg38). Duplicated or low-quality reads were filtered out using Picard (Broad Institute - v2.20.7) and samtools (v1.9), with further filtering to remove regions where genome assembly introduces erroneous signal. The SPP data processing pipeline was used to call peaks, with the level of background signal assessed via reference to input sample. DiffBind (v3.12.0) was used to identify differential peaks as follows. RPKM-normalized ChIP Seq data was visualized using IGV (2.18.4) genome browser
CUT&RUN: Indexed libraries generated using NEBNext library prep kit 32 (NEB) and NEBNext Multiplex Oligos for Illumina (NEB) as per manufacturers instructions. Paired-end reads were aligned to the reference genome (hg38) using Bowtie2 (-p 24 -X2000 -t -x) and sorted with Samtools (view -bS -F 4 -q 30 -u - | sort -T). PCR duplicates were marked using Picard MarkDuplicates (MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000 REMOVE_DUPLICATES=true ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT). Genome-wide coverage was determined using Bedtools genomecov (-ibam -bg -scale -g), converted to a BigWig file with wigToBigWig -clip.
Assembly: hg38
Supplementary files format and content: bigwig files for each sample
Supplementary files format and content: bed files for each sample

source_name: iPSC-derived NGN2-type cortical neurons

value: iPSC-derived NGN2-type cortical neurons

value: Neuronal


title: Sham.KI.021252

description:
Library name: Sham_KI 3
Column name in raw_counts.csv: Sham.KI.021252


title: peaks NGN2 iNeurons, 24hrs DMSO, pS65Ub ChIPseq, rep 1

description: Library name: SAM24449807_V1_pS65Ub_bed

value: 24hrs DMSO


title: Sham.KI.013915

description:
Library name: Sham_KI 4
Column name in raw_counts.csv: Sham.KI.013915


title: Sham.KI.021254

description:
Library name: Sham_KI 2
Column name in raw_counts.csv: Sham.KI.021254


title: HeLa cells, 24hrs Oligomycin + Antimycin, H3K27Me3 CUT&RUN, rep 2

description: Library name: SAM24437147_OA2_H3K27Me3_bw


title: HeLa cells, 24hrs Oligomycin + Antimycin, H3K4Me3 CUT&RUN, rep 2

description: Library name: SAM24437146_OA2_H3K4Me3_bw


title: DLA mouse model treated with sp11 drug rep 2

city: Bengaluru

first: Bibha

last: Choudhary

state: Karnataka

address: Biotech Park, GN Ramachandran Rd, Electronics City Phase 1, Electronic City,

country: India

institute: Institute of Bioinformatics and Applied Biotechnology

description: Library name: sclib_DLA_SP11_rep2

data_processing:
Raw sequencing data were processed using the Cell Ranger pipeline, which included demultiplexing, alignment, barcode processing, and gene counting. Reads were mapped to the mouse reference genome (mm10), and gene expression matrices were generated for downstream analysis.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

extract_protocol:
The DLA tumor tissue was collected under sterile conditions and transferred to ice-cold HBSS with 1% penicillin-streptomycin. The tissue was minced and enzymatically digested using collagenase IV (2 mg/mL) and DNase I (0.1 mg/mL) at 37 °C for 30-45 minutes with gentle agitation. The digested suspension was filtered through a 70 µm strainer and centrifuged at 300 × g for 5 minutes at 4 °C. The cell pellet was washed with PBS containing 0.04% BSA. RBCs were removed using lysis buffer. Cell viability and concentration were assessed by Trypan Blue staining. The final single-cell suspension was resuspended in PBS +0.04% BSA at 700-1200 cells/µL for loading onto the 10x Genomics platform.
Single-cell RNA-seq libraries were generated using the 10x Genomics Chromium Single Cell 3′ platform as per the manufacturer’s protocol. Cells were encapsulated into GEMs, where mRNA was reverse transcribed into cDNA incorporating cell-specific barcodes and unique molecular identifiers (UMIs), enabling accurate transcript quantification at single-cell resolution. The cDNA was subsequently recovered, amplified, fragmented, and ligated with sequencing adapters and sample indices to generate final libraries.

value: Tumor

value: DLA

value: Lymphoma

value: SP11 treated


title: HeLa cells, 24hrs DMSO, H3K27Me3 CUT&RUN, rep 2

description: Library name: SAM24437143_V2_H3K27Me3_bw


title: DLA mouse model treated with sp11 drug rep 1

description: Library name: sclib_DLA_SP11_rep1


title: DLA mouse model untreated rep 1

description: Library name: sclib_DLA_CONTROL_rep1

value: untreated


title: HeLa cells, 24hrs Oligomycin + Antimycin, H3K4Me3 CUT&RUN, rep 1

description: Library name: SAM24437138_OA1_H3K4Me3_bw


title: HeLa cells, 24hrs Oligomycin + Antimycin, H3K27Me3 CUT&RUN, rep 1

description: Library name: SAM24437139_OA1_H3K27Me3_bw


title: HeLa cells, 24hrs DMSO, H3K4Me3 CUT&RUN, rep 1

description: Library name: SAM24437134_V1_H3K4Me3_bw


title: High Phosphate Exercised Sample 3

city: Columbus

first: Kedryn

last: Baskin

state: OH

address: 460 W 12th Ave

department: Physiology and Cell Biology

institute: The Ohio State University

description:
Library name: XJD947_6_HP18_22_HPE
HPE_3

data_processing:
Fastq files were trimmed using TrimGalore, and aligned using the STAR aligner. Count matrices were analyzed in pairwise comparisons using DESeq2.
Assembly: GRCm39
Supplementary files format and content: excel file containing CPM values and pairwise comparison output from DESeq2

source_name: GP

extract_protocol:
RNA was extracted using the TRI-zol kit and manufacterer instructions. At minumum, 500ng of RNA, quality determined by RIN, was used to generate libraries for each sample.
Libraries were generated by Plasmidsaurus sequencing service. Poly-A mRNA capture, second strand synthesis and tagmentation, and Illumina library amplification.

value: GP

value: High Phosphate Exercised


title: High Phosphate Exercised Sample 5

description:
Library name: XJD947_6_HP18_26_HPE
HPE_5


title: Normal Phosphate Exercised Sample 5

description:
Library name: XJD947_2_HP18_14_NPE
NPE_5

value: Normal Phosphate Exercised


title: NGN2 iNeurons, 24hrs Oligomycin + Antimycin, pS65Ub ChIPseq, rep 1

description: Library name: SAM24449815_OA1_pS65Ub_bw

value: WT


title: Normal Phosphate Exercised Sample 4

description:
Library name: XJD947_2_HP18_13_NPE
NPE_4


title: NGN2 iNeurons, 24hrs DMSO, pS65Ub ChIPseq, rep 1

description: Library name: SAM24449807_V1_pS65Ub_bw


title: Single-cell RNAseq of iMGLs exposed to Interferon-Beta or PBS_IFN_2

city: Dublin

first: Michael John

last: Dolan

state: Dublin 2

address: Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin

country: Ireland

institute: Trinity College Dublin

description: Library name: sample4

data_processing:
iAstrocyte: FastQC (v.0.12.1) and MultiQC (v.1.23) were to generate initial quality control (QC) reports. STAR (v.2.7.10b) was used to build the reference index (based on GRCh38) and align reads, then the quality of the generated BAM files was assessed with Samtools (v.1.6) quickcheck (all samples had greater than 94% alignment). The count matrix was generated using featureCounts (v.2.0.6). R (v.4.3.1) was used for subsequent analyses.  iMGL scRNAseq: Cellranger (version 6, 10X Genomics) was used for demultiplexing, barcode preprocessing, generation of fastq files, alignment and the counting of unique molecular identifiers (UMI). We applied Cellranger’s aggr function to all samples to merge and normalize by sequencing depth. We then applied CellBender to remove ambient RNA and technical artifacts due to barcode swapping (Fleming et al. 2023).
Assembly: GRCh38
Supplementary files format and content: Seurat object of iMGL scRNAseq data

source_name: cell line

growth_protocol: iMGL Differentiation: Human H1 embryonic stem cells were cultured in Essential 8 media on Matrigel, dissociated with Accutase, and aggregated in low-adherence plates with ROCK inhibitor. Cells were differentiated through sequential exposure to hematopoietic cytokines (FGF2, BMP4, VEGF, TPO, SCF, IL6, IL3) in HPC medium under hypoxic and then normoxic conditions. By day 10, cells were cryopreserved and later thawed for microglia maturation in iMG media containing M-CSF, IL-34, and TGF-β1. Final maturation occurred between days 30–45 with additional supplementation of CD200 and CX3CL1.  iAstro Differentiation: H1 hESCs were genetically engineered to express doxycycline-inducible NFIB and SOX9 from the AAVS1 locus. After transfection, cells were selected with geneticin and expanded. iAstrocyte induction was initiated with doxycycline in E8 medium, followed by sequential exposure to expansion, FGF, and maturation media containing BMP4, CNTF, and dbcAMP. Cells were dissociated on day 7, replated, and matured in MM medium until day 20 before use.

extract_protocol:
RNA was extracted either with Qiagen RNeasy Mini extraction kit (iAstrocytes) or subjected to single-cell RNA sequencing (iMGLs)
iAstrocye RNA underwent library preparation based on PolyA sequencing. iMGL underwent single-cell library preparation according to 10X Genomics protocol

treatment_protocol: Cells were treated with PBS or 25ng/ml Interferon Beta

value: stemcell microglia


title: Normal Phosphate Exercised Sample 3

description:
Library name: XJD947_2_HP18_12_NPE
NPE_3


title: Normal Phosphate Exercised Sample 2

description:
Library name: XJD947_2_HP18_11_NPE
NPE_2


title: Single-cell RNAseq of iMGLs exposed to Interferon-Beta or PBS_PBS_2

description: Library name: sample3


title: Single-cell RNAseq of iMGLs exposed to Interferon-Beta or PBS_PBS_1

description: Library name: sample1


title: Tail Tip Fibroblasts, Ad-GFP

first: Jethro

middle: WANG

last: Zih-Shuo

state: Ohio

address: 460 W 12th Ave.

department: Department of Surgery

institute: Ohio State University

description:
Library name: TTF_Ad_GFP
Column name in MG53_ageing_Mus_SCs_gene_counts_matrix: TTF_GFP_01

data_processing:
Raw reads were quality-checked and trimmed to remove adapters and low-quality bases.
Clean reads were aligned to the reference genome using STAR (v2.0.7).
Gene-level raw counts were quantified based on Ensembl gene annotations.
Assembly: mm39
Supplementary files format and content: 260319_GSExBulk_Gata4KO_6samples_RawCountsMatrix.tsv: Tab-delimited text file containing raw read counts for all samples, with Ensembl Gene IDs as row names.

source_name: tail tip fibroblast (TTF)

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS under standard incubation conditions.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) following the manufacturer's protocol.
RNA-seq libraries were generated using standard protocols.

treatment_protocol: Fibroblasts (CF, LF, TTF) were transduced with either Ad-GFP (control) or Ad-Cre (GATA4 KO) adenoviruses and incubated for 48 hours prior to harvest.

value: tail tip fibroblast (TTF)

value: Ad-GFP (Control)


title: Cardiac Fibroblasts, Ad-Cre

description:
Library name: CF_Ad_Cre
Column name in MG53_ageing_Mus_SCs_gene_counts_matrix: CF_Cre_01

source_name: cardiac fibroblast (CF)

value: cardiac fibroblast (CF)

value: Ad-Cre (GATA4 KO)


title: Bulk RNAseq of iAstros exposed to Interferon-Beta or PBS_PBS3

description: Library name: PBS_3

value: stemcell astrocyte


title: Tail Tip Fibroblasts, Ad-Cre

description:
Library name: TTF_Ad_Cre
Column name in MG53_ageing_Mus_SCs_gene_counts_matrix: TTF_Cre_01


title: Bulk RNAseq of iAstros exposed to Interferon-Beta or PBS_PBS2

description: Library name: PBS_2


title: Cardiac Fibroblasts, Ad-GFP

description:
Library name: CF_Ad_GFP
Column name in MG53_ageing_Mus_SCs_gene_counts_matrix: CF_GFP_01


title: Lung Fibroblasts, Ad-GFP

description:
Library name: LF_Ad_GFP
Column name in MG53_ageing_Mus_SCs_gene_counts_matrix: LF_GFP_01

source_name: lung fibroblast (LF)

value: lung fibroblast (LF)


title: Bulk RNAseq of iAstros exposed to Interferon-Beta or PBS_IFN3

description: Library name: IFN_3


title: Lung Fibroblasts, Ad-Cre

description:
Library name: LF_Ad_Cre
Column name in MG53_ageing_Mus_SCs_gene_counts_matrix: LF_Cre_01


title: Phgdh WT with Serine/Glycine in medium with hepatocytes rep3

first: Jason

middle: Rodencal

last: Terrell

address: 530 1st Avenue

institute: NYU Langone Health

description: Library name: WT_12

data_processing:
File RNAseq_Exp1-gene_fpkm.txt was generated using the standard Novogene RNA-seq analysis pipeline. Raw paired-end reads were produced on an Illumina NovaSeq 6000 platform. Adapter sequences and low-quality reads were removed to obtain clean reads. Clean reads were aligned to the reference genome using HISAT2, and gene-level read counts were quantified. Gene expression levels were normalized and reported as FPKM values.
Assembly: GRCm38 (mm10)
Supplementary files format and content: RNAseq_Exp1-gene_fpkm.txt

extract_protocol:
RNA was extracted using RNeasy mini kit per manufacturer's protcols and RNA quality was validated.
As per Novogene protocols

value: PDAC

value: Phgdh WT

value: hepatocyte coculture


title: Bulk RNAseq of iAstros exposed to Interferon-Beta or PBS_IFN1

description: Library name: IFN_1


title: Phgdh WT with Serine/Glycine in medium with hepatocytes rep2

description: Library name: WT_11


title: CUTTAG_H3K27m3_KMS11_NSD2KO#12_Rep2

description: Library name: Sample 32

data_processing:
Raw paired-end sequencing reads (FASTQ) were first assessed for quality and cleaned using fastp (v0.24.0). Cleaned reads were then aligned to the human reference genome (hg38) using Bowtie2 with parameters --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. The resulting alignments were converted to BAM format, sorted, and indexed using Samtools. PCR duplicates were marked using Picard MarkDuplicates. Alignments were subsequently filtered using Samtools to retain properly paired reads and exclude reads mapping to ENCODE blacklisted regions. For visualization and downstream analysis, signal tracks in bigWig format were generated using deepTools (v3.5.1) bamCoverage, normalizing signal to Reads Per Kilobase per Million mapped reads (RPKM) with a bin size of 50 bp. Peak calling for the H3K27me3 modification was performed using MACS3 (v3.0.2) callpeak with parameters --format BAMPE -g hs --broad --broad-cutoff 0.1 --keep-dup all. Consensus peak sets were generated by merging reproducible peaks across replicates. Differential binding analysis between conditions was performed using DESeq2 on read counts within the consensus peak set (obtained via chromVAR), and resulting differentially bound regions were annotated using the ChIPseeker R package (v 1.42.1).
Assembly: hg38
Supplementary files format and content: Processed data files are provided for each H3K27me3 CUTTAG sample in two formats: 1) bigWig (.bw) files containing genome-wide signal enrichment, normalized as Reads Per Kilobase per Million mapped reads (RPKM) using deepTools, suitable for visualization; and 2) BED (.broadPeak) files generated by MACS3 (using --broad --broad-cutoff 0.1), defining genomic regions significantly enriched for the H3K27me3 mark.
Library strategy: CUT&Tag

extract_protocol:
CUTTAG was performed starting with 50,000 nuclei per sample. Nuclei were isolated, resuspended in Wash Buffer, and loaded onto a silica column. On-column incubations were performed sequentially with primary antibody (anti-H3K27me3, Cell Signaling Technology #9733), secondary antibody (Antibodies-Online ABIN101961), and pAG-Tn5 transposase complex (Epicypher #15-1017), with buffer washes performed after antibody and transposase incubation steps. Tagmentation was carried out on-column by adding MgCl2 in Wash Buffer and incubating at 4°C for 1 hour. Following tagmentation, nuclei were lysed using SDS and Proteinase K. DNA fragments were then extracted and purified using the DNA Clean & Concentrator-5 kit (Zymo Research #D4014) and eluted in H2O.
Sequencing libraries were prepared from the purified tagmented DNA obtained via the Extract Protocol. Library amplification was performed by PCR for 13 cycles using NEBNext HiFi 2 × PCR Master mix (NEB #M0541). Following PCR amplification, the libraries were purified using HighPrep beads (MagBio genomics #AC-60500).

value: NSD2 KO

value: No


title: Phgdh WT without Serine/Glycine in medium with hepatocytes rep3

description: Library name: WT_9

value: serine/glycine free medium and hepatocyte coculture


title: CUTTAG_H3K27m3_KMS11_NSD2KO#3_Rep2

description: Library name: Sample 30


title: Phgdh WT without Serine/Glycine in medium with hepatocytes rep2

description: Library name: WT_8


title: CUTTAG_H3K27m3_KMS11_NSD2KO#3_Rep1

description: Library name: Sample 29


title: N2

city: CAMBRIDGE

first: Giulia

last: Biffi

state: Cambridgeshire

address: Cancer Research UK, Robinson Way

country: United Kingdom

institute: University of Cambridge

description: Library name: SITSB8

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
binned at 8um
Assembly: mm10(2020-A)
Supplementary files format and content: raw_feature_bc_matrix.h5
Supplementary files format and content: aligned_fiducials.jpg
Supplementary files format and content: detected_tissue_image.jpg
Supplementary files format and content: scalefactors_json.json
Supplementary files format and content: tissue_hires_image.png.gz
Supplementary files format and content: tissue_lowres_image.png
Supplementary files format and content: cytassist_image.tiff
Supplementary files format and content: aligned_tissue_image.jpg
Library strategy: Spatial Transcriptomics

source_name: Normal

extract_protocol:
FFPE tissues, 5 micron-thick sections
Spatial transcriptomic Illumina-compatible libraries were prepared with 10x Genomics Visium HD Probe-based Spatial Gene Expression assay according to manfacturer's instructions. sequencer: Illumina NovaSeq X using a 25B flow cell 300 cycle kit

value: Normal


title: Phgdh WT without Serine/Glycine in medium with hepatocytes rep1

description: Library name: WT_7


title: CUTTAG_H3K27m3_KMS11_NSD2KOparental_Rep2

description: Library name: Sample 28


title: Phgdh WT with Serine/Glycine in medium without hepatocytes rep3

description: Library name: WT_6

value: standard conditions


title: CUTTAG_H3K27m3_KMS11_NSD2KOparental_Rep1

description: Library name: Sample 27


title: CUTTAG_H3K27m3_KMS11_NSD2dTAG#11_dTAGv1_21d_Rep2

description: Library name: Sample 26

value: NSD2_dTAG knockin

value: dTAGv1 for 21d


title: Phgdh WT with Serine/Glycine in medium without hepatocytes rep1

description: Library name: WT_4


title: CUTTAG_H3K27m3_KMS11_NSD2dTAG#11_dTAGv1_21d_Rep1

description: Library name: Sample 25


title: CUTTAG_H3K27m3_KMS11_NSD2dTAG#11_dTAGv1_14d_Rep2

description: Library name: Sample 24

value: dTAGv1 for 14d


title: Phgdh WT without Serine/Glycine in medium without hepatocytes rep2

description: Library name: WT_2

value: serine/glycine free medium


title: CUTTAG_H3K27m3_KMS11_NSD2dTAG#11_dTAGv1_14d_Rep1

description: Library name: Sample 23


title: Phgdh WT without Serine/Glycine in medium without hepatocytes rep1

description: Library name: WT_1


title: CUTTAG_H3K27m3_KMS11_NSD2dTAG#11_dTAGv1_7d_Rep2

description: Library name: Sample 22

value: dTAGv1 for 7d


title: Phgdh KO with Serine/Glycine in medium with hepatocytes rep3

description: Library name: KO_12

value: Phgdh KO


title: 231spheres_adipose_10ug_mL_dECM_Replicate3

city: New Orleans

first: Elizabeth

last: Martin

address: 1430 Tulane Avenue

institute: Tulane University

description: Library name: Sample 6

data_processing:
STAR aligner v2.7.11 was used to map short sequencing reads to the reference genome
Assembly: Reads were aligned to Ensembl
Supplementary files format and content: Data files represent relative gene abundance as counts per million (CPMs). CPM values were determined by STAR

source_name: MDA-MB-231+decelled breast tissue

extract_protocol:
Total RNA was extracted from the cell lines using Quick RNA Miniprep Kit from Zymo Research (Irvine, CA, USA) and sent to Plasmidsaurus (Burlington, MA, USA) for RNA sequencing.
The RNA sequencing workflow after RNA isolation included generation of cDNA using a poly(dT)VN primer.  Illumina sequencing and a 3’ end counting approach was carried out. Molecular identifiers (UMIs) were used to duplicate, and unique dual indices (UDIs) to prevent index hopping. The read length is ~90bp and all of the reads align within the last ~400nt of the transcript.

value: MDA-MB-231+decelled breast tissue

value: breast cancer cell line

value: WT


title: Val_F

first: Avery

last: Childress

address: 800 Rose Street

institute: University of Kentucky

description:
Library name: Sample 3
Count data

data_processing:
Sequencing reads were trimmed and filtered using Trimmomatic (V0.39) to remove adapters and low quality reads. Reads from samples were mapped to Ensembl mm10 transcripts annotation, using RSEM (v1.3.2) and STAR (2.6.1d) with default settings.
Assembly: mm10
Supplementary files format and content: Count data: gene.count.annotated.tsv

source_name: Neutrophil

extract_protocol:
Bone marrow from femur and tibia of mice was flushed using 1mL of Mg2+ and Ca2+ free PBS (Cytiva cat# SH30256.01). 1.5 ml of histopaque 1077 was pipette on top of histopaque 1119 carefully to preserve the interface between the two layers. Total bone marrow (1mL) was then added on top of histopaque gradient and the tube wa centrifuged at 1000x g for 25 minutes with zero acceleration and zero brake. Once centrifuged, the upper low-density and lower high-density bands of cells were collected and washed with excess PBS. high density band was frozen and used for the RNA sequence protocol
RNA libraries were prepared for sequencing using Innomics protocol

value: Neutrophil

value: Female

value: Valemetostat


title: CUTTAG_H3K27m3_KMS11_NSD2dTAG#11_dTAGv1_7d_Rep1

description: Library name: Sample 21


title: Placebo_M

description:
Library name: Sample 2
Count data

value: Male

value: Placebo


title: Phgdh KO with Serine/Glycine in medium with hepatocytes rep2

city: New York

description: Library name: KO_11

value: PDAC

value: hepatocyte coculture


title: CUTTAG_H3K27m3_KMS11_NSD2dTAG#11_dTAGv1_0d_Rep2

description: Library name: Sample 20

value: No


title: Phgdh WT with Serine/Glycine in medium without hepatocytes rep2

description: Library name: WT_5

value: Phgdh WT

value: standard conditions


title: Phgdh KO with Serine/Glycine in medium with hepatocytes rep1

description: Library name: KO_10


title: CUTTAG_H3K27m3_KMS11_NSD2dTAG#11_dTAGv1_0d_Rep1

description: Library name: Sample 19

value: NSD2_dTAG knockin


title: Phgdh KO without Serine/Glycine in medium with hepatocytes rep3

description: Library name: KO_9

value: serine/glycine free medium and hepatocyte coculture


title: CUTTAG_H3K27m3_KMS11_NSD2dTAG#8_dTAGv1_21d_Rep2

description: Library name: Sample 18

value: dTAGv1 for 21d


title: Phgdh KO without Serine/Glycine in medium with hepatocytes rep2

description: Library name: KO_8

value: Phgdh KO


title: Phgdh WT without Serine/Glycine in medium without hepatocytes rep3

description: Library name: WT_3

value: serine/glycine free medium


title: CUTTAG_H3K4me3_KMS11_NSD2dTAG#11_dTAGv1_0d_Rep1

description: Library name: Sample 5

data_processing:
Raw paired-end sequencing reads (FASTQ) were first assessed for quality and cleaned using fastp (v0.24.0). Cleaned reads were then aligned to the human reference genome (hg38) using Bowtie2 with parameters --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. The resulting alignments were converted to BAM format, sorted, and indexed using Samtools. PCR duplicates were marked using Picard MarkDuplicates. Alignments were subsequently filtered using Samtools to retain properly paired reads and exclude reads mapping to ENCODE blacklisted regions. For visualization and downstream analysis, signal tracks in bigWig format were generated using deepTools (v3.5.1) bamCoverage, normalizing signal to Reads Per Kilobase per Million mapped reads (RPKM) with a bin size of 50 bp. Peak calling for the H3K27me3 modification was performed using MACS3 (v3.0.2) callpeak with parameters --format BAMPE -g hs --broad --broad-cutoff 0.1 --keep-dup all. Consensus peak sets were generated by merging reproducible peaks across replicates. Differential binding analysis between conditions was performed using DESeq2 on read counts within the consensus peak set (obtained via chromVAR), and resulting differentially bound regions were annotated using the ChIPseeker R package (v 1.42.1).
Assembly: hg38
Supplementary files format and content: Processed data files are provided for each H3K27me3 CUTTAG sample in two formats: 1) bigWig (.bw) files containing genome-wide signal enrichment, normalized as Reads Per Kilobase per Million mapped reads (RPKM) using deepTools, suitable for visualization; and 2) BED (.broadPeak) files generated by MACS3 (using --broad --broad-cutoff 0.1), defining genomic regions significantly enriched for the H3K27me3 mark. And processed bigwig files for H3K27ac and H3K4me3 CUTTAG.
Library strategy: CUT&Tag

extract_protocol:
CUTTAG was performed starting with 50,000 nuclei per sample. Nuclei were isolated, resuspended in Wash Buffer, and loaded onto a silica column. On-column incubations were performed sequentially with primary antibody (anti-H3K27me3, CST #9733; anti-H3K27ac, Abcam#ab4729; anti-H3K4me3, Active Motif #39159), secondary antibody (Antibodies-Online ABIN101961), and pAG-Tn5 transposase complex (Epicypher #15-1017), with buffer washes performed after antibody and transposase incubation steps. Tagmentation was carried out on-column by adding MgCl2 in Wash Buffer and incubating at 4°C for 1 hour. Following tagmentation, nuclei were lysed using SDS and Proteinase K. DNA fragments were then extracted and purified using the DNA Clean & Concentrator-5 kit (Zymo Research #D4014) and eluted in H2O.
Sequencing libraries were prepared from the purified tagmented DNA obtained via the Extract Protocol. Library amplification was performed by PCR for 13 cycles using NEBNext HiFi 2 × PCR Master mix (NEB #M0541). Following PCR amplification, the libraries were purified using HighPrep beads (MagBio genomics #AC-60500).


title: CUTTAG_H3K27m3_KMS11_NSD2dTAG#8_dTAGv1_21d_Rep1

description: Library name: Sample 17


title: Phgdh KO without Serine/Glycine in medium with hepatocytes rep1

description: Library name: KO_7


title: CUTTAG_H3K27m3_KMS11_NSD2dTAG#8_dTAGv1_14d_Rep2

description: Library name: Sample 16

value: dTAGv1 for 14d


title: Phgdh KO with Serine/Glycine in medium without hepatocytes rep3

description: Library name: KO_6


title: peaks NGN2 iNeurons, 24hrs Oligomycin + Antimycin, pS65Ub ChIPseq, rep 2

description: Library name: SAM24449827_OA2_pS65Ub_bed

value: iPSC-derived NGN2-type cortical neurons

value: Neuronal

value: WT

value: 24hrs Oligomycin (1µM) + Antimycin (1µM)


title: TAC.KI.023919

description:
Library name: TAC_KI 1
Column name in raw_counts.csv: TAC.KI.023919

value: Left Ventricle

value: TAC


title: CUTTAG_H3K27m3_KMS11_NSD2dTAG#8_dTAGv1_14d_Rep1

description: Library name: Sample 15


title: Phgdh KO with Serine/Glycine in medium without hepatocytes rep2

description: Library name: KO_5

value: PDAC


title: TAC.KI.023917

description:
Library name: TAC_KI 2
Column name in raw_counts.csv: TAC.KI.023917


title: Phgdh KO with Serine/Glycine in medium without hepatocytes rep1

description: Library name: KO_4


title: CUTTAG_H3K27m3_KMS11_NSD2dTAG#8_dTAGv1_7d_Rep2

description: Library name: Sample 14

value: dTAGv1 for 7d


title: CUTTAG_H3K27m3_KMS11_NSD2dTAG#8_dTAGv1_7d_Rep1

description: Library name: Sample 13


title: Sham.KI.022051

description:
Library name: Sham_KI 1
Column name in raw_counts.csv: Sham.KI.022051

value: Sham


title: Phgdh KO without Serine/Glycine in medium without hepatocytes rep3

description: Library name: KO_3


title: CUTTAG_H3K27m3_KMS11_NSD2dTAG#8_dTAGv1_0d_Rep2

description: Library name: Sample 12

value: No


title: Phgdh KO without Serine/Glycine in medium without hepatocytes rep2

description: Library name: KO_2


title: peaks NGN2 iNeurons, 24hrs DMSO, pS65Ub ChIPseq, rep 2

description: Library name: SAM24449819_V2_pS65Ub_bed

value: 24hrs DMSO


title: HeLa cells, 24hrs DMSO, H3K4Me3 CUT&RUN, rep 2

description: Library name: SAM24437142_V2_H3K4Me3_bw

value: HeLa Cells

value: Epithelial


title: DLA mouse model untreated rep 2

description: Library name: sclib_DLA_CONTROL_rep2

value: Tumor

value: DLA

value: Lymphoma

value: untreated


title: CUTTAG_H3K27m3_KMS11_NSD2dTAG#8_dTAGv1_0d_Rep1

description: Library name: Sample 11

value: NSD2_dTAG knockin


title: Phgdh KO without Serine/Glycine in medium without hepatocytes rep1

description: Library name: KO_1

value: Phgdh KO

value: serine/glycine free medium


title: CUTTAG_H3K27m3_KMS11_dTAGparental_dTAGv1_21d_Rep2

description: Library name: Sample 10

value: WT

value: dTAGv1 for 21d


title: 23L001685_S89 mNSC, GF, control

city: Planegg

first: Anna

last: Danese

address: Grosshaderner strasse 9

institute: Ludwig Maximilians University

description:
Library name: 23L001685_S89
out_ct_mtx_85

data_processing:
sequencing adpaters were trimmed using trimmomatic.
data was aligned against GRCm39_M35 mouse genome from Gencode using STAR
PCR duplicates were removed using samtools rmdup
Count matrices were built using htseq counts
Assembly: GRCm39 M35 primary assembly
Supplementary files format and content: count matrices for all samples each containing  2 columns : gene_id and raw count

source_name: Neural Stem Cells

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen).
Libraries were produced using the Illumina Stranded Total Prep with Ribo-Zero Plus and the Illumina RNA UD Indexes SetA according to the manufacturer’s protocol.

value: Neural Stem Cells

value: GF, control


title: 23L001684_S88 mNSC, GF, gRNA

description:
Library name: 23L001684_S88
out_ct_mtx_84

value: GF, gRNA


title: CUTTAG_H3K27m3_KMS11_dTAGparental_dTAGv1_21d_Rep1

first: sanxiong

last: liu

address: 1501 NW 10th Avenue

institute: University of Miami Miller School of Medicine

description: Library name: Sample 9


title: NGN2 iNeurons, 24hrs Oligomycin + Antimycin, pS65Ub ChIPseq, rep 2

description: Library name: SAM24449827_OA2_pS65Ub_bw

value: iPSC-derived NGN2-type cortical neurons

value: Neuronal

value: 24hrs Oligomycin (1µM) + Antimycin (1µM)


title: CUTTAG_H3K27m3_KMS11_dTAGparental_dTAGv1_14d_Rep2

description: Library name: Sample 8

value: dTAGv1 for 14d


title: HeLa cells, 24hrs DMSO, H3K27Me3 CUT&RUN, rep 1

description: Library name: SAM24437135_V1_H3K27Me3_bw

value: HeLa Cells

value: Epithelial

value: 24hrs DMSO


title: 23L001677_S81 mNSC, GF, control

description:
Library name: 23L001677_S81
out_ct_mtx_77


title: 23L001676_S80 mNSC, GF, gRNA

description:
Library name: 23L001676_S80
out_ct_mtx_76


title: CUTTAG_H3K27m3_KMS11_dTAGparental_dTAGv1_7d_Rep2

description: Library name: Sample 6

value: dTAGv1 for 7d


title: 23L001672_S76 mNSC, GF, gRNA

description:
Library name: 23L001672_S76
out_ct_mtx_72


title: CUTTAG_H3K27m3_KMS11_dTAGparental_dTAGv1_7d_Rep1

description: Library name: Sample 5


title: 23L001673_S77 mNSC, GF, control

description:
Library name: 23L001673_S77
out_ct_mtx_73


title: CUTTAG_H3K27m3_KMS11_dTAGparental_dTAGv1_0d_Rep1

description: Library name: Sample 3

value: No


title: DE35NGSUKBD144063 mNSC, GF, control

description:
Library name: DE35NGSUKBD144063
out_ct_mtx_63


title: DE62NGSUKBD144062 mNSC, GF, control

description:
Library name: DE62NGSUKBD144062
out_ct_mtx_62


title: DE89NGSUKBD144061 mNSC, GF, control

description:
Library name: DE89NGSUKBD144061
out_ct_mtx_61


title: CUTTAG_IgG_KMS11_dTAGparental_dTAGv1_0d_Rep1

description: Library name: Sample 1


title: DE19NGSUKBD144060 mNSC, GF, gRNA

description:
Library name: DE19NGSUKBD144060
out_ct_mtx_60


title: DE73NGSUKBD144058 mNSC, GF, gRNA

description:
Library name: DE73NGSUKBD144058
out_ct_mtx_58


title: CUTTAG_IgG_KMS11_dTAGparental_dTAGv1_0d_Rep2

description: Library name: Sample 2


title: U2OS WT 0.19uM ANS 15min replicate 4

city: Lausanne

first: David

last: Gatfield

address: Genopode building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

description: Library name: PF83_GATCA

library_source: other

data_processing:
Reads were trimmed using TrimGalore (auto-detect adapter type and minimum length=30nt). Then, reads without barcodes were excluded (UMI-tools) and the remaining reads were size-filtered (26-35nt), quality-filtered, and trimmed for 2nt in the read's 5'end.
The sequential mapping was performed with STAR: rRNA and tRNA (parameters: --seedSearchStartLmax 28 --outSAMmultNmax 1 --outSAMtype BAM SortedByCoordinate Unsorted --outReadsUnmapped Fastx). The reads unmapped to tRNA were then demultiplexed (split by barcode using demuxbyname.sh from BBTools) and mapped to the genome (parameters: --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --genomeLoad NoSharedMemory --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM).
Reads were then projected to the transcriptome (*.transcript.sorted.bam) and filtered to keep only the reads mapped to the single most expressed transcript per gene (*.transcript.sorted.filtered.bam).
Assembly: Hsapiens.GRCh38.111
Supplementary files format and content: .sga, A-site count table
Library strategy: Ribo-Seq

molecule: other

growth_protocol: Cells were grown on (DMEM+glucose+L-glutamine)+10%FBS+1%Pen strep

extract_protocol:
Cellular lysates were obtained from cell pellets and RNase I digested. RPFs were then recovered after Qiazol purification (miRNeasy kit)
RPF 3'-ends were repaired with PNK and ligated to an adaptor containing UMIs and barcodes. Once pooled together, rRNA was depleted from the libraries. After RT and circularization, the libraries were PCR-amplified and sent for sequencing.

treatment_protocol: Cells were treated during 15min with DMSO or 0.19uM of anisomycin or 76uM of anisomycin

value: osteosarcoma

value: 0.19 uM Anisomycin


title: U2OS WT 76uM ANS 15min replicate 3

description: Library name: PF83_GCATA

value: 76 uM Anisomycin


title: Tb-DOX-4

city: 蚌埠市

first: aonan

last: yu

state: 安徽省

address: 龙子湖区

country: China

institute: 蚌埠医科大学

description:
Library name: Sample20
Tb-DOX-4_FPKM

data_processing:
Raw FASTQ reads were trimmed using Cutadapt and quality checked with FastQC. Clean reads were aligned to the reference genome using HISAT2. Gene counts were obtained with HTSeq, and differential expression analysis was performed using DESeq2 (|log2FC| ≥ 1, FDR < 0.05).
Assembly: GRCm39.107
Supplementary files format and content: Processed data files include a gene-by-sample count matrix generated by HTSeq (v0.6.1), containing raw read counts for each gene in each sample. Differential expression analysis results generated by DESeq2 (v1.34.0) include log2 fold changes, p-values, and adjusted p-values (FDR).

extract_protocol:
Total RNA was extracted using MagZol Reagent (Magen) following the manufacturer’s protocol. RNA was purified, dissolved in RNase-free water, and treated with DNase I to remove genomic DNA contamination.
Total RNA (1 μg) was used for library preparation. mRNA was enriched using Oligo(dT) beads or rRNA depletion and fragmented. cDNA was synthesized, end-repaired, A-tailed, and ligated to adapters. Libraries were PCR-amplified, size-selected, and sequenced on an Illumina HiSeq/Novaseq/MGI2000 platform (2 × 150 bp paired-end).

tag: group

value: tumor


title: Tb-DOX-5

description:
Library name: Sample21
Tb-DOX-5_FPKM


title: U2OS WT 0.19uM ANS 15min replicate 3

description: Library name: PF83_CGTAA

value: WT


title: U2OS WT DMSO 15min replicate 4

description: Library name: PF83_AGCTA

value: DMSO 15min


title: Tb-DOX-2

description:
Library name: Sample18
Tb-DOX-2_FPKM


title: U2OS WT 76uM ANS 15min replicate 2

description: Library name: PF82_TAGAC


title: Tb-DOX-1

description:
Library name: Sample17
Tb-DOX-1_FPKM


title: Tb-6

description:
Library name: Sample16
Tb-6_FPKM


title: U2OS WT 76uM ANS 15min replicate 1

description: Library name: PF82_GCATA


title: U2OS WT 0.19uM ANS 15min replicate 2

description: Library name: PF82_GATCA


title: Tb-4

description:
Library name: Sample14
Tb-4_FPKM


title: U2OS WT DMSO 15min replicate 2

description: Library name: PF82_AGCTA


title: Tb-3

description:
Library name: Sample13
Tb-3_FPKM


title: Tb-2

description:
Library name: Sample12
Tb-2_FPKM


title: U2OS WT DMSO 15min replicate 1

description: Library name: PF82_ATCGT


title: 5-004

city: DIJON

first: François

last: Ghiringhelli

address: 1 rue du Professeur Marion

country: France

institute: UMR INSERM 1231

description:
Library name: 5-004
TPM_exp.txt

data_processing:
Raw FASTQ data were pseudo-aligned, and gene counts were quantified using Kallisto software (Bray et al). Kallisto transcript index used as reference was built from merged human cDNA and ncDNA files from the GRCh37 assembly Ensembl. Gene-level count and transcripts matrices were then created with the DESeq2 library
Assembly: GRCh37
Supplementary files format and content: tabulated txt file containing TPM values

extract_protocol:
By using the Maxwell RNA FFPE kit (Promega), fifty nanograms of total RNA were ribodepleted with the RiboCop rRNA Depletion kit (Lexogen) by following manufacturer’s protocol, and then purified using NEB kit by following manufacturer’s instructions.
By using the Maxwell RNA FFPE kit (Promega), fifty nanograms of total RNA were ribodepleted with the RiboCop rRNA Depletion kit (Lexogen) by following manufacturer’s protocol, and then purified using NEB kit by following manufacturer’s instructions.

treatment_protocol: Following dissection, tumor tissue was placed in formaldehyde for 24 hours, followed by ethanol dehydration, cleared with xylene, and embedded in paraffin wax at 60ºC to create FFPE samples

value: Tumor

value: exp


title: 5-003

description:
Library name: 5-003
TPM_exp.txt


title: Tb-1

description:
Library name: Sample11
Tb-1_FPKM


title: DOX-5

description:
Library name: Sample10
DOX-5_FPKM

value: non tumor


title: 5-001

description:
Library name: 5-001
TPM_exp.txt


title: DOX-4

description:
Library name: Sample9
DOX-4_FPKM


title: 4-019

description:
Library name: 4-019
TPM_exp.txt


title: DOX-3

description:
Library name: Sample8
DOX-3_FPKM


title: 4-017

description:
Library name: 4-017
TPM_exp.txt


title: DOX-2

description:
Library name: Sample7
DOX-2_FPKM


title: DOX-1

description:
Library name: Sample6
DOX-1_FPKM


title: 4-016

description:
Library name: 4-016
TPM_exp.txt


title: 4-013

description:
Library name: 4-013
TPM_exp.txt


title: Control-4

description:
Library name: Sample4
Control-4_FPKM


title: 4-011

description:
Library name: 4-011
TPM_exp.txt


title: Control-5

description:
Library name: Sample5
Control-5_FPKM


title: Control-2

description:
Library name: Sample2
Control-2_FPKM


title: earlyAna SHFDPCs in June, female (bio rep 2)

city: Shenyang

first: Huiling

last: Xue

address: 120 Dongling Road,110866 Shenyang,China

institute: Shenyang Agricultural University

description: Library name: Sample 2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and mapped to goat (Capra hircus) transcriptomes (GCF_001704415.1_ARS1) using Kallisto (v.0.46.1) with parameters -b 100. The gene abundances were obtained by kallisto-sleuth (v.0.30.0) pipeline in TPM (transcripts per million) (Bray NL et al. 2016).
Assembly: GCF_001704415.1_ARS1
Supplementary files format and content: tab-delimited text files include TPM values for each Sample.

organism: Capra hircus

source_name: Secondary hair follicle dermal papilla cells from goat skin

extract_protocol:
Total RNA was extracted from the hair follicle dermal papilla cells using RNAiso Plus (TRIzol method, TaKaRa Bio, Dalian, China).
Paired-end sequencing of the cDNA library construction for transcriptome sequencing was performed according to the operating instructions for the NEB Next® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA).

value: female


title: 4-002

description:
Library name: 4-002
TPM_exp.txt


title: 56_GB-N21_mCPLT

description: Library name: SLX25210_idtUDP0234

data_processing:
Estimated transcript counts were counted using Salmon (version 1.9.0)
Assembly: GRCm39 (mm39) - kmer 23
Supplementary files format and content: Raw count data in tab-delimited salmon file

extract_protocol:
Samples were collected in 1 mL of TRIzol Reagent (15596018; Invitrogen). RNA was extracted using the PureLink RNA mini kit (12183018A; Invitrogen). RNA concentration was measured using a Qubit and RNA quality was assessed on a TapeStation 4200 (Agilent) using the Agilent RNA ScreenTape kit. mRNA library preparations were performed using 55 mL of 10 ng/mL per sample (RNA integrity number, RIN ≥ 8.8)
Illumina mRNA library


title: Control-1

description:
Library name: Sample1
Control-1_FPKM


title: earlyAna SHFDPCs in June, male (bio rep 1)

description: Library name: Sample 4

value: Secondary hair follicle dermal papilla cells from goat skin

value: male


title: 4-008

description:
Library name: 4-008
TPM_exp.txt


title: PBS-2

city: Suita

first: Tomoaki

last: Hara

address: Yamadaoka 2-2

country: Japan

institute: The University of Osaka

description: Library name: Sample 6

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 platform in a 101-base paired-end mode.
The NovaSeq control software operated base calling analysis software and delivered raw sequencing data.
Sequence quality of the FASTQ files was assessed using FastQC, and reads were trimmed based on quality scores using Trimmomatic. Trimmed reads were aligned to the mouse reference genome sequences (GRCm38) using Hisat2.
SAM files were converted to BAM format with Samtools, and gene-level read counts were generated using featureCounts.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes count values for each Sample

source_name: tumor

extract_protocol:
A moderate amount of tumor was placed in ISOGEN (NIPPON GENE), crushed with a mixer, and RNA was extracted according to ISOGEN protocol.
Ribosomal RNA was depleted using Ribo-Zero Plus rRNA Depletion Kit (Illumina) and the library was prepared using a SMARTer Stranded Total RNA-Seq Kit v2- Pico Input Mammalian (TAKARA BIO) .

value: PBS-2; phosphate-buffered saline


title: 4-003

description:
Library name: 4-003
TPM_exp.txt


title: 3-002

description:
Library name: 3-002
TPM_exp.txt


title: PBS-1

description: Library name: Sample 5

value: PBS-1; phosphate-buffered saline


title: FPCRJB161-2

description: Library name: Sample 4

value: FPCRJB161-2; FPC in combination with mRNA–LNP and CJB-161


title: 2-003

description:
Library name: 2-003
TPM_exp.txt


title: FPCRJB161-1

description: Library name: Sample 3

value: FPCRJB161-1; FPC in combination with mRNA–LNP and CJB-161


title: 2-007

description:
Library name: 2-007
TPM_exp.txt


title: FPCRC

description: Library name: Sample 2

value: FPCRC; FPC in combination with mRNA–LNP and CPI-455


title: 2-001

description:
Library name: 2-001
TPM_exp.txt


title: FPC

description: Library name: Sample 1

value: FPC; 5-FU, an anti–PD-1 antibody, and an anti–CTLA-4 antibody


title: 1-039

description:
Library name: 1-039
TPM_exp.txt


title: 1-036

description:
Library name: 1-036
TPM_exp.txt


title: 24m_WTiMOS_MPP4_T2_rep3

city: Shanghai

first: Linlin

last: Zhang

address: siping road

institute: Tongji university

description: Library name: 24m_WTiMOS_MPP4_T2_rep3

data_processing:
RNA-seq reads were first trimmed to remove adapters and then mapped to the annotated mouse transcripts (mm10) using Hisat2 with the parameters `--no-unal --no-mixed --no-discordant`. Expression level of genes were calculated using Stringtie. Read counts were calculated using featureCounts. Differential gene expression analysis was performed using Bioconductor package DESeq2. Significantly genes were defined as having a fold change > 1.5 and P value < 0.05. Principal component analysis (PCA) was performed using the prcomp function of R software.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Bone Marrow

extract_protocol:
RNA was harvested using the AccuNext Single Cell/Low Input cDNA Synthesis & Amplification Kit (Accurate Biology, AG12501).
Low-input RNA-seq libraries for sequencing were prepared using the AccuNext Single Cell/Low Input cDNA Synthesis & Amplification Kit (Accurate Biology, AG12501) following the manufacturer’s protocols.

value: Bone Marrow

value: Hematopoietic Progenitor Cells


title: 24m_WTiMOS_MPP4_T2_rep2

description: Library name: 24m_WTiMOS_MPP4_T2_rep2


title: 1-035

description:
Library name: 1-035
TPM_exp.txt


title: 24m_WTiMOS_MPP4_T2_rep1

description: Library name: 24m_WTiMOS_MPP4_T2_rep1


title: 1-034

description:
Library name: 1-034
TPM_exp.txt


title: 24m_WTiMOS_MPP4_T1_rep3

description: Library name: 24m_WTiMOS_MPP4_T1_rep3


title: 1-032

description:
Library name: 1-032
TPM_exp.txt


title: 24m_WTiMOS_MPP4_T1_rep2

description: Library name: 24m_WTiMOS_MPP4_T1_rep2


title: 1-031

description:
Library name: 1-031
TPM_exp.txt


title: 24m_WTiMOS_MPP3_T2_rep3

description: Library name: 24m_WTiMOS_MPP3_T2_rep3


title: 1-026

description:
Library name: 1-026
TPM_exp.txt


title: 1-025

description:
Library name: 1-025
TPM_exp.txt


title: 24m_WTiMOS_MPP4_T1_rep1

description: Library name: 24m_WTiMOS_MPP4_T1_rep1


title: 24m_WTiMOS_MPP3_T2_rep2

description: Library name: 24m_WTiMOS_MPP3_T2_rep2


title: 1-024

description:
Library name: 1-024
TPM_exp.txt


title: 1-022

description:
Library name: 1-022
TPM_exp.txt


title: 24m_WTiMOS_MPP3_T1_rep3

description: Library name: 24m_WTiMOS_MPP3_T1_rep3


title: 24m_WTiMOS_MPP3_T2_rep1

description: Library name: 24m_WTiMOS_MPP3_T2_rep1


title: 1-018

description:
Library name: 1-018
TPM_exp.txt


title: 24m_WTiMOS_MPP3_T1_rep2

description: Library name: 24m_WTiMOS_MPP3_T1_rep2


title: 24m_WTiMOS_MPP3_T1_rep1

description: Library name: 24m_WTiMOS_MPP3_T1_rep1


title: 1-015

description:
Library name: 1-015
TPM_exp.txt


title: 1-013

description:
Library name: 1-013
TPM_exp.txt


title: 1-011

description:
Library name: 1-011
TPM_exp.txt


title: 3m_WTiMOS_MPP4_T2_rep2

description: Library name: 3m_WTiMOS_MPP4_T2_rep2


title: 1-007

description:
Library name: 1-007
TPM_exp.txt


title: 3m_WTiMOS_MPP4_T2_rep1

description: Library name: 3m_WTiMOS_MPP4_T2_rep1


title: 3m_WTiMOS_MPP4_T1_rep3

description: Library name: 3m_WTiMOS_MPP4_T1_rep3


title: 1-006

description:
Library name: 1-006
TPM_exp.txt


title: 3m_WTiMOS_MPP4_T1_rep2

description: Library name: 3m_WTiMOS_MPP4_T1_rep2


title: 3m_WTiMOS_MPP4_T1_rep1

description: Library name: 3m_WTiMOS_MPP4_T1_rep1


title: 1-005

description:
Library name: 1-005
TPM_exp.txt


title: 3m_WTiMOS_MPP3_T2_rep3

description: Library name: 3m_WTiMOS_MPP3_T2_rep3


title: 2-006

description:
Library name: 2-006
TPM_exp.txt


title: 4-018

description:
Library name: 4-018
TPM_ctrl.txt

value: ctrl


title: 1-003

description:
Library name: 1-003
TPM_exp.txt


title: 3m_WTiMOS_MPP3_T2_rep2

description: Library name: 3m_WTiMOS_MPP3_T2_rep2


title: 4-014

description:
Library name: 4-014
TPM_ctrl.txt


title: 3m_WTiMOS_MPP3_T2_rep1

description: Library name: 3m_WTiMOS_MPP3_T2_rep1


title: 4-010

description:
Library name: 4-010
TPM_ctrl.txt


title: 3m_WTiMOS_MPP3_T1_rep3

description: Library name: 3m_WTiMOS_MPP3_T1_rep3


title: 3m_WTiMOS_MPP3_T1_rep2

description: Library name: 3m_WTiMOS_MPP3_T1_rep2


title: 4-006

description:
Library name: 4-006
TPM_ctrl.txt


title: 3m_WTiMOS_MPP3_T1_rep1

description: Library name: 3m_WTiMOS_MPP3_T1_rep1


title: 4-005

description:
Library name: 4-005
TPM_ctrl.txt


title: 4-004

description:
Library name: 4-004
TPM_ctrl.txt


title: 4-001

description:
Library name: 4-001
TPM_ctrl.txt


title: 3m_KOiMOS_MPP3_T2_rep3

description: Library name: 3m_KOiMOS_MPP3_T2_rep3


title: 3m_KOiMOS_MPP3_T2_rep2

description: Library name: 3m_KOiMOS_MPP3_T2_rep2


title: 3-003

description:
Library name: 3-003
TPM_ctrl.txt


title: 3m_KOiMOS_MPP3_T2_rep1

description: Library name: 3m_KOiMOS_MPP3_T2_rep1


title: 3-001

description:
Library name: 3-001
TPM_ctrl.txt


title: 3m_KOiMOS_MPP3_T1_rep3

description: Library name: 3m_KOiMOS_MPP3_T1_rep3


title: 3m_KOiMOS_MPP3_T1_rep2

description: Library name: 3m_KOiMOS_MPP3_T1_rep2


title: 2-012

description:
Library name: 2-012
TPM_ctrl.txt


title: 2-011

description:
Library name: 2-011
TPM_ctrl.txt


title: 3m_KOiMOS_MPP3_T1_rep1

description: Library name: 3m_KOiMOS_MPP3_T1_rep1


title: 1-017

description:
Library name: 1-017
TPM_exp.txt


title: Spi1_3m_KOiMOS_MPP3_T2_rep2

description: Library name: Spi1_3m_KOiMOS_MPP3_T2_rep2

data_processing:
Sequencing reads were first trimmed to remove adapters and then mapped to mouse genome (mm10) using Bowtie2 with the parameters ` -t --local --very-sensitive-local --no-mixed --no-discordant --no-unal. The alignment files were processed using SAMtools. PCR duplicates were removed using Sambamba. Peaks were called using MACS2 with the setting ‘-f BAMPE -g mm’. If a peak was detected across all three replicates, the intersection of the three locations was preserved.
Assembly: mm10
Supplementary files format and content: bigWig,narrowPeak
Library strategy: CUT&Tag

extract_protocol:
Chromatin was extracted using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme).
CUT&Tag libraries for sequencing were prepared using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme) following the manufacturer’s protocols.


title: Spi1_3m_KOiMOS_MPP3_T2_rep1

description: Library name: Spi1_3m_KOiMOS_MPP3_T2_rep1


title: 2-013

description:
Library name: 2-013
TPM_ctrl.txt


title: 2-009

description:
Library name: 2-009
TPM_ctrl.txt


title: CUTTAG_H3K27m3_KMS11_dTAGparental_dTAGv1_14d_Rep1

city: Miami

description: Library name: Sample 7

value: WT

value: dTAGv1 for 14d


title: 3m_WTiMOS_MPP4_T2_rep3

description: Library name: 3m_WTiMOS_MPP4_T2_rep3


title: 2-005

description:
Library name: 2-005
TPM_ctrl.txt

value: Tumor


title: Spi1_3m_KOiMOS_MPP3_T1_rep2

description: Library name: Spi1_3m_KOiMOS_MPP3_T1_rep2


title: 2-002

description:
Library name: 2-002
TPM_ctrl.txt


title: Spi1_3m_KOiMOS_MPP3_T1_rep1

description: Library name: Spi1_3m_KOiMOS_MPP3_T1_rep1


title: 1-038

description:
Library name: 1-038
TPM_ctrl.txt


title: CUTTAG_H3K27m3_KMS11_dTAGparental_dTAGv1_0d_Rep2

description: Library name: Sample 4

value: No


title: Spi1_3m_WTiMOS_MPP3_T2_rep3

description: Library name: Spi1_3m_WTiMOS_MPP3_T2_rep3


title: 1-037

description:
Library name: 1-037
TPM_ctrl.txt


title: Spi1_3m_WTiMOS_MPP3_T2_rep2

description: Library name: Spi1_3m_WTiMOS_MPP3_T2_rep2


title: 1-033

description:
Library name: 1-033
TPM_ctrl.txt


title: Spi1_3m_WTiMOS_MPP3_T2_rep1

description: Library name: Spi1_3m_WTiMOS_MPP3_T2_rep1


title: 1-030

description:
Library name: 1-030
TPM_ctrl.txt


title: U2OS WT 76uM ANS 15min replicate 4

description: Library name: PF83_TAGAC

value: osteosarcoma

value: 76 uM Anisomycin


title: DE46NGSUKBD144059 mNSC, GF, gRNA

description:
Library name: DE46NGSUKBD144059
out_ct_mtx_59

value: Neural Stem Cells

value: GF, gRNA


title: Spi1_3m_WTiMOS_MPP3_T1_rep3

description: Library name: Spi1_3m_WTiMOS_MPP3_T1_rep3


title: Spi1_3m_WTiMOS_MPP3_T1_rep2

description: Library name: Spi1_3m_WTiMOS_MPP3_T1_rep2


title: 1-028

description:
Library name: 1-028
TPM_ctrl.txt


title: Spi1_3m_WTiMOS_MPP3_T1_rep1

description: Library name: Spi1_3m_WTiMOS_MPP3_T1_rep1


title: 1-029

description:
Library name: 1-029
TPM_ctrl.txt


title: Bcl11a_3m_WTiMOS_MPP3_T2_rep3

description: Library name: Bcl11a_3m_WTiMOS_MPP3_T2_rep3


title: 1-023

description:
Library name: 1-023
TPM_ctrl.txt


title: Tb-DOX-3

description:
Library name: Sample19
Tb-DOX-3_FPKM

value: tumor


title: U2OS WT DMSO 15min replicate 3

description: Library name: PF83_ATCGT

value: DMSO 15min


title: 1-020

description:
Library name: 1-020
TPM_ctrl.txt


title: Bcl11a_3m_WTiMOS_MPP3_T2_rep2

description: Library name: Bcl11a_3m_WTiMOS_MPP3_T2_rep2


title: 1-027

description:
Library name: 1-027
TPM_ctrl.txt


title: Bcl11a_3m_WTiMOS_MPP3_T2_rep1

description: Library name: Bcl11a_3m_WTiMOS_MPP3_T2_rep1


title: 1-019

description:
Library name: 1-019
TPM_ctrl.txt


title: Bcl11a_3m_WTiMOS_MPP3_T1_rep3

description: Library name: Bcl11a_3m_WTiMOS_MPP3_T1_rep3


title: 1-016

description:
Library name: 1-016
TPM_ctrl.txt


title: Bcl11a_3m_WTiMOS_MPP3_T1_rep2

description: Library name: Bcl11a_3m_WTiMOS_MPP3_T1_rep2


title: Tb-5

description:
Library name: Sample15
Tb-5_FPKM


title: 1-014

description:
Library name: 1-014
TPM_ctrl.txt


title: U2OS WT 0.19uM ANS 15min replicate 1

description: Library name: PF82_CGTAA

value: 0.19 uM Anisomycin


title: 1-010

description:
Library name: 1-010
TPM_ctrl.txt


title: 3m_WTiMOS_MPP3_T2_rep2

description: Library name: 3m_WTiMOS_MPP3_T2_rep2

data_processing:
Sequencing reads were first trimmed to remove adapters and then mapped to mouse genome (mm10) using Bowtie2. Low quality mapped reads were removed using SAMtools (view -q 30) and only unique reads mapping to a single genomic location and strand were kept. We removed mitochondrial sequences using ‘grep -v chrM’. Peaks were calling using MACS2 with the setting ‘-f BAMPE -g mm’. If the overlap between replicated peaks exceeds 50%, the intersecting segment was preserved.
Assembly: mm10
Supplementary files format and content: bigWig,narrowPeak

extract_protocol:
Chromatin was extracted using the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme).
ATAC libraries for sequencing were prepared using the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme) following the manufacturer’s protocols.


title: 1-009

description:
Library name: 1-009
TPM_ctrl.txt


title: Bcl11a_3m_WTiMOS_MPP3_T1_rep1

description: Library name: Bcl11a_3m_WTiMOS_MPP3_T1_rep1


title: 3m_WTiMOS_MPP3_T2_rep1

description: Library name: 3m_WTiMOS_MPP3_T2_rep1


title: 1-002

description:
Library name: 1-002
TPM_ctrl.txt


title: 1-008

description:
Library name: 1-008
TPM_ctrl.txt


title: 3m_WTiMOS_MPP3_T1_rep2

description: Library name: 3m_WTiMOS_MPP3_T1_rep2


title: 3m_WTiMOS_MPP3_T1_rep1

description: Library name: 3m_WTiMOS_MPP3_T1_rep1


title: pig endometrium2

city: Qingda

first: yadan

last: Jin

state: 山东Shandong

address: Qingdao

institute: Qingdao Agricultural University

description: Library name: Samples2

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1(https://support 10xgenomics. com/single-cel-gene-expression/software/pipelines/latestwhat- is-cel-range)
Assembly: 10mm
Supplementary files format and content: Tab-separated values files and matrix files

organism: Sus scrofa

source_name: endometrium

extract_protocol:
About 200 mg of endometrial tissue was clipped, washed twice with precooled phosphate-buffered saline (PBS) solution, placed in tissue protection solution (BioYou, 21903-10), and transferred to the laboratory on ice for follow-up treatment. After adding enzyme digestion solution (2 mg/mL collagenase II, 1 mg/mL dispersed protease, 30 μg/mL DNase I, 2.5 mM CaCl2, containing FBS 2% dissolved in basal medium), the samples were shaken in a 37 ℃ water bath shaker at 100 rpm/min for 20 min. The enzyme-digested suspension was filtered through a 30 µm cell filter and added to 15 mL PBS, centrifuged at 500 g for 5 min at 4 ℃. The supernatant was removed and the pellet resuspended with 1 ml of 0.04% BSA, added into 3 ml of 1X RBC to lyse erythrocytes, and left at room temperature for 5 min (the time can be adjusted according to the actual situation of erythrocyte lysis). The suspension was then washed twice with PBS and centrifuged at 4 ℃, 300 g for 5 min. The supernatant was removed and the pellet resuspended in 500 μl of 0.04% BSA. Cell parameters were then tested with a cell counter (CountessTM II FL Automated Cell Counter, Thermo Fisher Scientific, Waltham, MA, USA).
The 10X Genomics 3 'transcriptome uses short-read long sequencing and microfluidic techniques to enable simultaneous transcriptomic profiling of 500-10,000 cells per sample. We combine Gel Beads containing barcode information with a mixture of cells and enzymes, which are then coated with oil surfactant droplets located in a microfluidic "double cross" system to form GEMs (Gel Beads-InEmulsions). GEMs flow into a reservoir and are collected, the gel beads dissolve to release the Barcode sequence, reverse transcrib the cDNA fragment, and label the sample. The gel beads were broken and the oil droplets were broken, and PCR amplification was performed using cDNA as template. The standard sequencing library was constructed by mixing all GEMs products

value: endometrium

value: single

value: endometrium cell