title: 122_TGGT1_320300_midS_norm

description: Library name: 122_BRM_midS

data_processing:
Paired-end reads were trimmed using Trim Galore (v0.6.7) with a Phred quality cutoff of 20 and discarding reads shorter than 30  bp. Trimmed reads were aligned to the Toxoplasma gondii ME49 reference genome (ToxoDB v68) using Bowtie2 (v2.4.2) with the parameters: --end-to-end -D 15 -R 2 -N 1 -L 22 -i S,1,0.50 --no-mixed --no-discordant --phred33 -I 10 -X 700. BigWig files were generated using bamCoverage (v3.5.4.post1) with CPM normalization and a fixed bin size of 10 bp to normalize for sequencing depth.
Assembly: ToxoDB v68
Supplementary files format and content: bigwig
Library strategy: CUT&Run

growth_protocol: Toxoplasma gondii parasites were cultured with human foreskin fibroblasts (HFFs, ATCC SRC-1041) in Dulbecco’s Modified Eagle Medium (DMEM, GIBCO 11965118) supplemented 10 μg/ml gentamicin (Thermo Fisher Scientific), 2 mM L-glutamine (Gemini Bioproducts) and 10 % inactivated fetal bovine serum (IFS). Tachyzoites and HFFs were grown at 37 °C and 5 % CO2.

treatment_protocol: At 24 hr post-infection, the media was exchanged for fresh media containing DMEM (GIBCO 11965118) supplemented with 10 μg/ml gentamicin (Thermo Fisher Scientific), 2 mM L-glutamine (Gemini Bioproducts), 10 % IFS, and 40 µM thymidine (Sigma-Aldrich) to synchronize the population. After 6 hr or 7 hr of growth in thymidine media, early S or mid S phase parasites were harvested, respectively. For G1 and M/C phase parasites, the thymidine containing media was aspirated followed by two washes with pre-warmed PBS and the addition of fresh DMEM (GIBCO 11965118) supplemented with 10 μg/ml gentamicin (Thermo Fisher Scientific), 2 mM L-glutamine (Gemini Bioproducts) and 10 % IFS. After 1 hr or 5 hr of post-wash growth, M/C or G1 phase parasites were harvested.

tag: sample group

value: T. gondii cells

value: 7 hr 40 µM thymidine


title: 132_TGGT1_320300_MC_norm

status: Public on Apr 26 2026

type: SRA

city: Cambridge

first: Dominic

last: Schwarz

state: MA

address: 455 Main St

department: Biology

country: USA

institute: Massachusetts Institute of Technology

description: Library name: 132_BRM_MC

library_source: genomic

molecule: genomic DNA

organism: Toxoplasma gondii

extract_protocol:
Intracellular parasites were harvested by mechanical disruption through a 27-gauge needle and filtration through a 5  μm membrane. A total of ~5 x 10⁷ parasites were pelleted (1500 x g, 10  min) and resuspended in wash buffer (20 mM HEPES-NaOH pH 7.5, 150  mM NaCl, 0.5  mM Spermidine, 1x EDTA-free Protease Inhibitor Cocktail) and attached to 100 μl BioMag Plus Concanavalin A beads (Polysciences) activated in bead activation buffer (20 mM HEPES-KOH pH 7.9, 10  mM KCl, 0.1  mM CaCl2, 0.1 mM MnCl2). Parasites were bound to the beads by incubation for 15 min at room temperature and rotation. Bead-bound parasites were blocked with wash buffer supplemented with 2 mM EDTA for 5 min at room temperature followed by binding of 1 µg NbALFA-MNase per sample in ice-cold wash buffer supplemented with 0.025 % Digitonin (Invitrogen) for 1 hr at 4 °C. After NbALFA-MNase binding, bead-bound parasites were washed three times with ice-cold wash buffer supplemented with 0.025 % Digitonin for 5 min at 4 °C. The cutting reaction was started by the addition of ice-cold wash buffer supplemented with 0.025 % Digitonin and 2 mM CaCl2 and incubation for 60 min on ice. The reaction was stopped by the addition of 4xSTOP buffer (400 mM NaCl, 40 mM EDTA, 8 mM EGTA, 100 µg/ml RNaseA, 80 µg/ml Glycogen and 0.025 % Digitonin) to 1x and incubation at 37 °C for 20 min. The DNA was extracted using a modified organic extraction and ethanol precipitation protocol.
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) and NEBNext Multiplex Oligos for Illumina (NEB) according to the manufacturer’s instructions with 11–12 PCR amplification cycles. Size selection and clean-up steps were performed with AMPure XP beads (Beckman Coulter).

tag: cell line

tag: cell type

tag: treatment

value: 7 hr 40 µM thymidine, 1 hr washout


title: 125_TGGT1_278440_earlyS_norm

description: Library name: 125_BRG1_earlyS

value: 6 hr 40 µM thymidine


title: 128_TGGT1_320300_G1_norm

description: Library name: 128_BRM_G1

value: 7 hr 40 µM thymidine, 5 hr washout


title: 123_TGGT1_278440_midS_norm

description: Library name: 123_BRG1_midS


title: genomic DNA from 201B7 tNCCs

type: genomic

city: Saitama

first: Kyosuke

last: Mukae

state: Kitaadachi-gun

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

country: Japan

institute: Saitama Cancer Center

description: genomic DNA from LP6 treated with 5-aza-dC and rosiglitazon

hyb_protocol: Standard Illumina Protocol

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing:
The data were analyzed using GenomeStudio Methylation Module Software. Beta values were obtained after background correction and normalization to internal controls.
processed value definition: Average Beta, intensity, Detection P-value

label: Cy5 and Cy3

organism: Homo sapiens

source_name: Cell line of tNCCs differentiated from 201B7 iPSCs

label_protocol: Standard Illumina Protocol

growth_protocol: The human iPSCs were maintained on feeder layers of mitomycin C-treated embryonic mouse fibroblasts in primate embryonic stem cell medium (REPROCELL, Tokyo, Japan) supplemented with 4 ng/mL recombinant human fibroblast growth factor 2 (FUJIFILM, Tokyo, Japan). Differentiation of iPSCs into cNCCs or tNCCs was induced using a previously described protocol (PMID: 25464501, 30150715).

extract_protocol: High-quality DNA was extracted by the phenol/chloroform method.

treatment_protocol: The cNCC werecollected at the third passage afted sorting of NGFR-expressing cells. The tNCCs were at Day 10 after induction of differentiation.


title: eDS071_TGGT1_320300_Rep1

description: Library name: eDS071_81

data_processing:
Paired-end reads were trimmed using Trim Galore (v0.6.7) with a Phred quality cutoff of 20 and discarding reads shorter than 30? bp. Trimmed reads were aligned to the Toxoplasma gondii ME49 reference genome (ToxoDB v68) using Bowtie2 (v2.4.2) with the parameters: --end-to-end -D 15 -R 2 -N 1 -L 22 -i S,1,0.50 --no-mixed --no-discordant --phred33 -I 10 -X 700. Bedgraph files were generated using E. coli carryover DNA as an internal spike-in control between sample/control pairs indicated by the eDS number using genomecov (v2.29.2). eDS082_TGGT1_203950_Rep2 was used as control for eDS082_TGGT1_286920_Rep2 and eDS082_TGGT1_278440_Rep2. The matching normalized TGGT1_203950 bedgraph file is indicated by _for103_ for eDS082_TGGT1_286920_Rep2 or _for104_ for eDS082_TGGT1_278440_Rep2.
Assembly: ToxoDB v68
Supplementary files format and content: bedgraph
Library strategy: CUT&Run

growth_protocol: Toxoplasma gondii parasites were cultured with human foreskin fibroblasts (HFFs, ATCC SRC-1041) in Dulbecco’s Modified Eagle Medium (DMEM, GIBCO 11965118) supplemented 10 μg/ml gentamicin (Thermo Fisher Scientific), 2 mM L-glutamine (Gemini Bioproducts) and 3 % inactivated calf serum (ICS). Tachyzoites and HFFs were grown at 37 °C and 5 % CO2.

treatment_protocol: Parasites were grown for 24 hr.

value: Toxoplasma gondii cell


title: eDS072_PARENTAL_Rep1

description: Library name: eDS072_82


title: eDS082_TGGT1_203950_Rep2

description: Library name: eDS082_102


title: 129_TGGT1_278440_G1_norm

description: Library name: 129_BRG1_G1


title: genomic DNA from 201B7 cNCCs

description: genomic DNA from LP6 treated with 5-aza-dC

source_name: Cell line of cNCCs differentiated from 201B7 iPSCs


title: Adult DRG neurons from Pten heterozygous mutant - sample 2

status: Public on Apr 27 2026

city: Portland

first: Kevin

middle: M

last: Wright

state: Oregon

address: 3181 SW Sam Jackson Rd.

department: Vollum Institute

institute: Oregon Health & Science University

description: Library name: PtenHet-2

library_source: transcriptomic

data_processing:
IlluminaMiSeq platform with 2× 150–base pair (bp) read length
Assembly: Mus musculus GRCm38
Supplementary files format and content: csv file includes raw counts of each sample
Supplementary files format and content: Each text file includes FPKM values for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: Dorsal Root Ganglia

extract_protocol:
Whole DRGs along the entire rostro-caudal axis from 4 animals of each genotype were dissected, collected in 1.5 mL Eppendorf tubes, pelleted and snap frozen in dry ice. Frozen tissue was shipped on dry ice to Genewiz (Azenta Life Sciences) for RNA sequencing.
PolyA selection-based mRNA enrichment, mRNA fragmentation and complementary DNA (cDNA) synthesis were performed at Genewiz.

tag: tissue

value: Dorsal Root Ganglia

value: Sensory neurons and satelite glia

tag: genotype

value: Pten heterozygous


title: 124_TGGT1_320300_earlyS_norm

description: Library name: 124_BRM_earlyS


title: 133_TGGT1_278440_MC_norm

description: Library name: 133_BRG1_MC


title: eDS082_TGGT1_278440_Rep2

description: Library name: eDS082_104


title: eDS076_PARENTAL_Rep1

description: Library name: eDS076_90


title: genomic DNA from 414C2 tNCCs

description: genomic DNA from well-differentiated liposarcoma cell line

source_name: Cell line of tNCCs differentiated from 414C2 iPSCs


title: eDS071_PARENTAL_Rep1

description: Library name: eDS071_80


title: genomic DNA from 604A3 tNCCs

description: genomic DNA from dedifferentiated liposarcoma cell line

source_name: Cell line of tNCCs differentiated from 604A3 iPSCs


title: genomic DNA from 201B7 iPSCs

description: genomic DNA from LP6 treated with mockline

source_name: Induced pluripotent stem cell

value: Induced pluripotent stem cell


title: genomic DNA from 414C2 iPSCs

description: genomic DNA from peripheral blood mononuclear cells of healthy femal


title: genomic DNA from 414C2 cNCCs

description: genomic DNA from peripheral blood mononuclear cells of health male

source_name: Cell line of cNCCs differentiated from 414C2 iPSCs


title: genomic DNA from 604A3 cNCCs

source_name: Cell line of cNCCs differentiated from 604A3 iPSCs


title: genomic DNA from 604A3 iPSCs


title: PBMC_macrophage_LPS_3h_rep3

type: RNA

city: Boston

first: DAIKI

last: HOSOKAWA

address: 3 Blackfan Street, 17th Floor

department: Center for Interdisciplinary Cardiovascular Sciences

institute: Brigham and Women's Hospital

description: Human PBMC-derived macrophages treated with LPS for 3 hours, biological replicate 3

hyb_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol with minor modifications. One microgram of each labeled cRNA was fragmented by adding 5 μl of 10× Blocking Agent and 1 μl of 25× Fragmentation Buffer and heating at 60°C for 30 minutes. Then, 25 μl of 2× GE Hybridization Buffer was added. Fifty microliters of hybridization solution was dispensed into the gasket slide and assembled to the Arraystar Human LncRNA Microarray V3.0 slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed and fixed before scanning.

scan_protocol: The arrays were scanned using the Agilent DNA Microarray Scanner G2505C. Acquired array images were analyzed using Agilent Feature Extraction software version 11.0.1.1.

data_processing: Raw signal intensities were extracted using Agilent Feature Extraction software version 11.0.1.1. Quantile normalization and subsequent data processing were performed using GeneSpring GX version 11.5.1. The matrix table contains log2-transformed quantile-normalized signal intensities. After quantile normalization, lncRNAs and mRNAs with Present or Marginal flags in at least 4 out of 8 samples were retained for further analysis.

molecule: total RNA

source_name: PBMC-derived macrophages, LPS-treated, 3 h

label_protocol: ArrayStar

growth_protocol: PBMCs were isolated from human blood buffy coat and cultured in RPMI-1640 medium supplemented with 5% human serum and penicillin/streptomycin at 37℃ with 5% CO2 for 7–10 days to generate PBMC-derived macrophages before treatment.

extract_protocol: Total RNA was extracted from human PBMC-derived macrophages. RNA quantity and purity were measured using the NanoDrop ND-1000, and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Human PBMC-derived macrophages were either left untreated as controls or stimulated with 10 ng/mL LPS for 3 hours before RNA extraction.

value: LPS

tag: biological replicate


title: PBMC_macrophage_LPS_3h_rep1

description: Human PBMC-derived macrophages treated with LPS for 3 hours, biological replicate 1


title: PBMC_macrophage_LPS_3h_rep2

description: Human PBMC-derived macrophages treated with LPS for 3 hours, biological replicate 2


title: PBMC_macrophage_LPS_3h_rep4

description: Human PBMC-derived macrophages treated with LPS for 3 hours, biological replicate 4


title: PBMC_macrophage_control_3h_rep4

description: Human PBMC-derived macrophages used as untreated control sample, biological replicate 4

source_name: PBMC-derived macrophages, control

value: untreated control


title: PBMC_macrophage_control_3h_rep3

description: Human PBMC-derived macrophages used as untreated control sample, biological replicate 3


title: PBMC_macrophage_control_3h_rep2

description: Human PBMC-derived macrophages used as untreated control sample, biological replicate 2


title: MDA-MB-231 CTR200 cells-Replicate 3

first: Eunbee

last: Choi

address: 440 Brookline Ave, Mayer-434

institute: Dana farber cancer institute

description: Library name: Sample 6

data_processing:
1. Raw data quality control: The quality of the raw FASTQ files was assessed using FastQC. 2. Read aignment: Paired-end reads were aligned to the human reference genome (GRCh38) usng STAR (2.7.10a) with the following parameters: --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within. Mapping statistics were reviewed to confirm data integrity. 3. Quantification of gene expression: Gene-level counts were generated concurrently with alignment using the --quantMode GeneCounts option in STAR. The raw counts were normalized to TPM (Transcripts Per Million). 4. Differential expression analysis: DESeq2 was used to normalize the raw counts and identify differentially expressed genes (DEGs) between groups.
Assembly: GRCh38 (hg38)
Supplementary files format and content: csv file includes TPM values for each sample

source_name: Breast

growth_protocol: MDA-MB-231 cells were grown in RPMI-1640 medium (Gibco) supplemented with 10% fetal bovine serum (FBS, BenchMark, GeminiBio), 100 units/mL penicillin, and 100 μg/mL streptomycin (Gibco).

extract_protocol:
Total RNA was collected using the PureLink RNA Mini kit (Life Technologies) according to the manufacturer's instructions.
High quality RNA samples were submitted to Azenta (Genewiz, USA) for DNase treatment, rRNA depletion-based library preparation, and next-generation sequencing .

treatment_protocol: Parental cells were untreated as a control and CTR200 cells were maintained in the presence of 200 nM CT7311.

value: Breast

value: Triple-negative breast cancer (TNBC) cells

value: WT


title: MDA-MB-231 CTR200 cells-Replicate 2

description: Library name: Sample 5


title: MDA-MB-231 parental cells (Par)-Replicate 3

description: Library name: Sample 3


title: MDA-MB-231 parental cells (Par)-Replicate 1

description: Library name: Sample 1


title: MDA-MB-231 parental cells (Par)-Replicate 2

description: Library name: Sample 2


title: Human Follicle stem cells - Control, biological replicate 1

city: Guangzhou

first: shizhao

last: liu

address: guangzhou avenue north

country: China

institute: southern medical university

description: Library name: Sample 1

data_processing:
Raw sequencing reads were filtered using FastQC and Trimmomatic to remove adapter sequences and low-quality reads.
Trimmed reads were aligned to the human reference genome (GRCh38.p13) using HISAT2 v2.2.1 with default parameters.
Gene-level read counts were quantified using featureCounts from the Subread package v2.0.3.
Differential expression analysis was performed using DESeq2 v1.34.0 in R.
Assembly: Homo sapiens (GRCh38.p13, NCBI)
Supplementary files format and content: Comma-separated values (CSV) file contains raw gene count matrix with gene annotations for each sample.
Supplementary files format and content: Comma-separated values (CSV) file contains normalized gene expression values (FPKM) with gene annotations for each sample.
Supplementary files format and content: Comma-separated values (CSV) file contains unfiltered differential gene expression results, including log2 fold change, p-value, and adjusted p-value for all detected genes.

source_name: Hair follicle

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) following the manufacturer's instructions. RNA integrity was assessed using an Agilent 2100 Bioanalyzer, and only samples with RIN ≥ 7.0 were used for library construction.
mRNA was enriched from total RNA using oligo(dT) magnetic beads. RNA-seq libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit for Illumina according to the manufacturer's instructions, and paired-end sequencing (150 bp) was performed on the Illumina NovaSeq 6000 platform.

value: Hair follicle

value: Human Follicle stem cells

value: control


title: B16F10_tumor, CD45+, Pmel-1_CTL_transfer, day_14

city: Osaka

first: Koji

last: Nagaoka

address: 377-2 Ohno-Higashi, Osaka-Sayama

department: Department of Immunology

institute: Kindai University Faculty of Medicine

description:
Library name: CD45+_day_14
10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw FASTQ files were processed with Cell Ranger (version 4.0.0, 10x Genomics) using the cellranger count pipeline. Reads were aligned to the mouse reference genome (mm10), and unique molecular identifiers (UMIs) were counted to generate gene-barcode matrices. Default parameters were used for alignment and quantification.
Assembly: mm10
Supplementary files format and content: Tab-separated barcodes, features and matrix files

source_name: Tumor tissue

extract_protocol:
For preparation of tumor-infiltrating immune cells, tumor tissues were cut into small pieces and incubated in RPMI-1640 medium containing 0.2% collagenase (Fujifilm Wako Pure Chemical Corporation) and 2 KU/mL DNase I (Sigma-Aldrich) at 37 °C for 40 minutes. The digested tissues were passed through a 70 μm cell strainer. Single-cell suspensions were stained with anti-mouse CD45 antibody and viable CD45⁺ cells were isolated using a cell sorter. Equal numbers of CD45⁺ cells from three mice were pooled for each time point and used for single-cell RNA sequencing.
Single-cell suspensions were loaded onto the 10x Genomics Chromium Controller using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index), following the manufacturer's instructions. After GEM generation and reverse transcription, cDNA was amplified and sequencing libraries were constructed. Libraries were quantified using Kapa library quantification kit (Roche).

value: Tumor tissue

value: Pmel-1 CTL transfer


title: Human dental papilla cells; D3-cd24-neg-vitro

city: chengdu

first: Cheng

last: Liang

state: sichuan

address: 14, Section 3, South Renmin Road, Chengdu, Sichuan, China

institute: Sichuan University West China School of Stomatology

description: Library name: D3-cd24-neg-vitro

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2.
Assembly: hg18 for sample1 and sample2; MM10 for sample3 and sample4
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes raw FPKM for each sample

source_name: dental papilla

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
RNA libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: dental papilla

value: mesenchymal stem cells

value: in vitro culture


title: B16F10_tumor, CD45+, Pmel-1_CTL_transfer, day_7

description:
Library name: CD45+_day_7
10x Genomics


title: Human Follicle stem cells - Control, biological replicate 3

description: Library name: Sample 3


title: Human Follicle stem cells - Control, biological replicate 2

description: Library name: Sample 2


title: Mouse colon tissue 6

city: Yangzhou

first: Yimin

last: Zhuang

state: Jiangsu

address: No. 88, Daxue South Road

institute: Yangzhou University

description:
Library name: COZ859
DNBelab C-TaiM 4

data_processing:
Reads were processed using the DNBc4tools v2.1.1 pipeline with default and recommended parameters.
Assembly: Mus musculus reference genome
Supplementary files format and content: Processed data include nucleus-level gene expression count matrices in tab-delimited text format, with rows representing genes and columns representing individual nuclei. Additional metadata files provide information on nucleus barcodes, UMI counts, and quality control metrics.

source_name: colon

extract_protocol:
Mus musculus colon tissue were cut into pieces <0.5 cm and homogenized using a glass Dounce tissue grinder (Sigma, cat. no. D8938). The tissue was homogenized 25 times with pestle A and 25 times with pestle B in 2 ml of ice-cold nuclei EZ lysis buffer. The sample was then incubated on ice for 5 min, with an additional 3 ml of cold EZ lysis buffer. Nuclei were centrifuged at 500g for 5 min at 4 C, washed with 5 ml ice-cold EZ lysis buffer and incubated on ice for 5 min. After centrifugation, the nucleus pellet was washed with 5 ml nuclei suspension buffer (NSB; consisting of 1 PBS, 0.01% BSA and 0.1% RNase inhibitor (Clontech, cat. no. 2313A)). Isolated nuclei were resuspended in 2 ml NSB, filtered through a 35 μm cell strainer (Corning-Falcon, cat. no. 352235) and counted.
The SC libraries were constructed according to the instructions of the DNA Nanoball (DNB) elab C4 scRNA Preparation Kit.  Briefly,  the cells were diluted to a concentration of 1,000 cells/mL and loaded into the cell reservoir of the microfluidic chip.  Barcoded beads  and droplet-generation oil were successively added to the beads and oil reservoirs.  Encapsulated droplets were generated and  collected using a DNBelab C4 system.  Beads that captured the mRNA were recovered for reverse transcription (RT).  Following  polymerase chain reaction (PCR) amplification by polymerase chain reaction, complementary DNA (cDNA) was purified and quantified using a Qubit dsDNA kit (Invitrogen, #Q32854).  Libraries of 30 -end transcripts were subsequently constructed through cDNA  fragmentation, size selection, end repair and A-tailing, adapter ligation, PCR for indexing libraries, and cyclisation of sequencing  libraries, according to the manufacturer’s instructions.  Sequencing libraries were purified and quantified using the Qubit ssDNA  kit (Thermo Fisher Scientific, #Q10212).The sequencing library was performed on DNBSEQ-T7 platform(PE150) using DNBSEQ-T7RS Reagent Kit (FCL PE150) version 3.0.

value: colon

tag: Sex

value: female

tag: strain


title: Human Follicle stem cells - Palmitic acid (PA) treated, biological replicate 3

description: Library name: Sample 6

value: palmitic acid (PA)


title: PBMC_macrophage_control_3h_rep1

description: Human PBMC-derived macrophages used as untreated control sample, biological replicate 1


title: Human dental papilla cells; D2-cd24-neg-vitro

description: Library name: D2-cd24-neg-vitro


title: B16F10_tumor, CD45+, Pmel-1_CTL_transfer, day_3

description:
Library name: CD45+_day_3
10x Genomics


title: MDA-MB-231 CTR200 cells-Replicate 1

description: Library name: Sample 4


title: Human Follicle stem cells - Palmitic acid (PA) treated, biological replicate 2

description: Library name: Sample 5


title: Mouse colon tissue 5

description:
Library name: COZ851
DNBelab C-TaiM 4


title: Human dental papilla cells; C3-cd24-pos-vitro

description: Library name: C3-cd24-pos-vitro


title: Mouse colon tissue 4

description:
Library name: COZ900
DNBelab C-TaiM 4


title: Human dental papilla cells; D1-cd24-neg-vitro

description: Library name: D1-cd24-neg-vitro


title: Mouse colon tissue 3

description:
Library name: COZ849
DNBelab C-TaiM 4


title: Human Follicle stem cells - Palmitic acid (PA) treated, biological replicate 1

description: Library name: Sample 4


title: Mouse colon tissue 1

description:
Library name: COZ826
DNBelab C-TaiM 4


title: TGGT1_320300_24h_vehicle_3

description:
Library name: L311_610
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_320300_24h_vehicle_3

data_processing:
Reads were trimmed using Trim Galore (v0.6.7) and aligned to the Toxoplasma gondii ME49 reference genome (ToxoDB v68) with STAR (v2.7.1a) using the --quantMode GeneCounts option and the parameters --outFilterMismatchNoverLmax 0.04 and --outFilterMatchNminOverLread 0.4 to control alignment stringency.
Assembly: ToxoDB v68
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Monolayers were aspirated, rinsed with PBS, and parasites mechanically released by scraping and passage through a 27-gauge needle, followed by filtration through a 5  μm membrane. Parasite suspensions were centrifuged at 1,500 x g for 5  min, and RNA was extracted from parasite pellets by double extraction using TRIzol (Invitrogen). Therefore, the pellet was resuspended in 800 µl TRIzol Reagent (Invitrogen), vortexed, and split into two different tubes to retain one technical replicate. Phase separation was performed in phase lock heavy tubes (Quantabio) by addition of 100  μl chloroform:isoamyl alcohol (24:1, Sigma-Aldrich), vigorous vortexing (1 min), and centrifugation at 16,000 x g for 5  min at 4 °C. The aqueous phase was isolated, and TRIzol extracted again using 400 µl TRIzol. The resulting aqueous phase was supplemented with 1 μl Glycogen (20 mg/ml, Thermo Fisher Scientific) and 500 μl isopropanol, and RNA was precipitated at room temperature for 12 min. Pellets were recovered by centrifugation (12,000 x g, 12  min) at 4 °C, washed twice with 70 % ethanol, air-dried for 10  min at room temperature, and resuspended in 20 μl RNase-free dH2O.
RNA-seq libraries were prepared with the Rapid Directional RNA-Seq Kit 2.0 (NEXTFLEX) using Poly(A) Beads 2.0 (NEXTFLEX).

treatment_protocol: The media was replaced with DMEM (GIBCO 11965118) supplemented with 10 μg/ml gentamicin (Thermo Fisher Scientific), 2 mM L-glutamine (Gemini Bioproducts), 3 % ICS and 50 µM auxin or vehicle (PBS), respectively. Parasites were cultured for an additional 6, 12, or 24 hr before harvest.

value: Toxoplasma gondii cell

value: vehicle

tag: time


title: TGGT1_278440_24h_vehicle_3

description:
Library name: L311_608
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_278440_24h_vehicle_3


title: Human dental papilla cells; C2-cd24-pos-vitro

description: Library name: C2-cd24-pos-vitro


title: Human dental papilla cells; C1-cd24-pos-vitro

description: Library name: C1-cd24-pos-vitro


title: K562, CTCFi, rep2

city: Busan

first: Jin

last: Kang

address: 2, Busandaehak-ro 63beon-gil, Geumjeong-gu

department: Department of Molecular Biology

country: South Korea

institute: Pusan National University

description: Library name: RNA-seq_CTCFi_R2

data_processing:
ChIP-seq raw reads were trimmed and  filtered using Trimmomatic to remove input read ends with poor quality values (quality score 20) and then aligned to hg19 Canonical genome using Bowtie2. Aligned BAM files were filtered by Minimum MAPQ quality score 20 and sorted by chromosomal coordinates. Potential PCR duplicates were removed from BAM files. CTCF-enriched peaks were identified with MACS2 using input data as controls. Bigwig files generated from BAM files using BamCoverage, followed by normalization with scaling factors to adjust for read counts aligned to the dm3 genome (spike-in control) and the hg19 genome (sample).
RNA-seq raw reads were trimmed and filtered using Trimmomatic.Filtered reads were aligned to hg19 reference genome using RNA STAR with a gene annotation GTF file obtained from UCSC database.Reads aligned to genic regions were counted using featureCounts.The transcription levels were quantified as counts per million (CPM) using edgeR.
Assembly: hg19
Supplementary files format and content: bigwig

growth_protocol: K562 cells were cultured in RPMI mediun containing 10% FBS, 20 mM HEPES, 10% P/S, and 2 mM L-Glutamine.

extract_protocol:
For ChIP assay, nuclei were digested with 100 units of MNase at 37°C for 15 min. Mono or di-nucleosomes sized chromatin was incubated with antibodies for 3 h at 4°C and recovered with protein A agarose beads. Spike-in chromatin (Active Motif; 25 ng for CTCF and 50 ng for the others) and spike-in antibody (Active Motif; 1 μg for CTCF and 2 μg for the others) were included as internal controls. RNA was extracted using Rneasy Mini Kit (Qiagen). Ribosomal RNAs (rRNAs) were removed using Invitrogen RiboMinus Transcriptome Isolation Kit (human/mouse) (Invitrogen). 125 ng of rRNA-removed RNA was used for the construction of sequencing libraries.
ChIP DNA (0.5 ng for CTCF, 1 ng for H3K9ac, and 10 ng for H3K9me2 and H3K9me3) and input DNA (10 ng) were processed using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) with manufacturer’s instructions. The ends of ChIP DNA were repaired by NEBNext Ultra II End Prep enzyme mix and ligated with NEBNext adaptors. Adaptor-ligated DNA was selected at 175 bp size using NEBNext sample purification bead and amplified using the adaptor primers. The fragments are purified using NEBNext sample purification beads. RNA-seq libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) following manufacturer's protocols.

treatment_protocol: Lentiviral vectors containing a shRNA gene against CTCF mRNA were transduced into K562 cells. Empty vectors were used as experimental control.

value: erythroleukemia cells

value: shCTCF


title: K562, CTCFi, H3K9me3, ChIP, rep1

description: Library name: ChIP-seq_CTCFi_H3K9me3_R1

tag: chip antibody


title: K562, CTCFi, H3K9ac, ChIP, rep2

description: Library name: ChIP-seq_CTCFi_H3K9ac_R2


title: TGGT1_320300_12h_IAA_3

description:
Library name: L311_605
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_320300_12h_IAA_3

value: auxin


title: K562, CTCFi, rep1

description: Library name: RNA-seq_CTCFi_R1


title: K562, CTCFi, H3K9ac, ChIP, rep1

description: Library name: ChIP-seq_CTCFi_H3K9ac_R1


title: K562, CTCFi, H3K9me2, ChIP, rep1

description: Library name: ChIP-seq_CTCFi_H3K9me2_R1


title: TGGT1_278440_24h_IAA_3

description:
Library name: L311_609
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_278440_24h_IAA_3


title: TGGT1_320300_6h_IAA_3

description:
Library name: L311_602
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_320300_6h_IAA_3


title: K562, Con, Input, ChIP, rep2

description: Library name: ChIP-seq_Con_Input_R2

value: Control


title: K562, CTCFi, H3K9me3, ChIP, rep2

description: Library name: ChIP-seq_CTCFi_H3K9me3_R2


title: K562, Con, Input, ChIP, rep1

description: Library name: ChIP-seq_Con_Input_R1


title: TGGT1_320300_12h_vehicle_3

description:
Library name: L311_604
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_320300_12h_vehicle_3


title: K562, Con, H3K9me3, ChIP, rep2

description: Library name: ChIP-seq_Con_H3K9me3_R2


title: TGGT1_278440_12h_IAA_3

description:
Library name: L311_603
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_278440_12h_IAA_3


title: TGGT1_RH_Tir1_24h_IAA_3

description:
Library name: L311_607
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_RH_Tir1_24h_IAA_3


title: K562, CTCFi, H3K9me2, ChIP, rep2

description: Library name: ChIP-seq_CTCFi_H3K9me2_R2


title: TGGT1_278440_6h_vehicle_3

description:
Library name: L311_599
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_278440_6h_vehicle_3


title: Mouse colon tissue 2

description:
Library name: COZ829
DNBelab C-TaiM 4


title: TGGT1_320300_24h_IAA_2

description:
Library name: L311_598
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_320300_24h_IAA_2


title: TGGT1_278440_6h_IAA_3

description:
Library name: L311_600
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_278440_6h_IAA_3


title: K562, Con, H3K9me2, ChIP, rep2

description: Library name: ChIP-seq_Con_H3K9me2_R2


title: TGGT1_320300_6h_vehicle_3

description:
Library name: L311_601
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_320300_6h_vehicle_3


title: TGGT1_278440_24h_IAA_2

description:
Library name: L311_596
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_278440_24h_IAA_2


title: K562, Con, H3K9me3, ChIP, rep1

description: Library name: ChIP-seq_Con_H3K9me3_R1


title: TGGT1_RH_Tir1_24h_vehicle_3

description:
Library name: L311_606
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_RH_Tir1_24h_vehicle_3


title: K562, Con, H3K9me2, ChIP, rep1

description: Library name: ChIP-seq_Con_H3K9me2_R1


title: TGGT1_320300_24h_vehicle_2

description:
Library name: L311_597
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_320300_24h_vehicle_2


title: K562, CTCFi, CTCF, ChIP, rep1

description: Library name: ChIP-seq_CTCFi_CTCF


title: K562, Con, H3K9ac, ChIP, rep1

description: Library name: ChIP-seq_Con_H3K9ac_R1


title: TGGT1_RH_Tir1_24h_IAA_2

description:
Library name: L311_594
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_RH_Tir1_24h_IAA_2


title: TGGT1_RH_Tir1_24h_vehicle_2

description:
Library name: L311_593
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_RH_Tir1_24h_vehicle_2


title: K562, Con, CTCF, ChIP, rep1

description: Library name: ChIP-seq_Con_CTCF


title: K562, Con, H3K9ac, ChIP, rep2

description: Library name: ChIP-seq_Con_H3K9ac_R2


title: TGGT1_320300_12h_vehicle_2

description:
Library name: L311_591
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_320300_12h_vehicle_2


title: TGGT1_320300_12h_IAA_2

description:
Library name: L311_592
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_320300_12h_IAA_2


title: TGGT1_278440_24h_vehicle_2

description:
Library name: L311_595
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_278440_24h_vehicle_2


title: SUM149_Tunicamycin_A196_ATACseq_rep1

first: Kornelia

last: Polyak

address: 450 Brookline Ave. S1070

institute: Dana-Farber Cancer Institute

description: Library name: Sample127

data_processing:
ChIP-seq and ATAC-seq data processing were based on chips pipeline (Qiu et al., 2021; Taing et al., 2021). Peak calling was performed using MACS2 v2.1.2 with FDR<0.01 as the cutoff (Feng et al., 2012).
Reads were aligned to hg19 genome using BWA-MEM aligner (Li, 2013) and bigwig files were called after normalization to the corresponding input control.
Assembly: hg19
Supplementary files format and content: .bw files

source_name: Human breast cancer

growth_protocol: SUM149 cells were cultrued in DMEM-F12 medium +5% FBS, 10 mM HEPES pH7.4, 1 μg/ml hydrocortisone, 5 μg/ml insulin and 100U/ml Penicillin-Streptomycin. MDA-MB-231 and MDA-MB-468 cells were cultured in DMEM medium with 10% FBS and 100U/ml Penicillin-Streptomycin.

extract_protocol:
For ChIP-seq, 150 mm plates tissue culture plates were fixed in 1% formaldehyde (Electron Microscopy Sciences, 15714) containing fixing buffer (50 mM HEPESKOH pH7.5, 100 mM NaCl, 1 mM EDTA pH8 and 0.5 mM EGTA pH8) for 10 min at 37°C.  Crosslinking was quenched by adding glycine to a final concentration of 0.125 M and further rocking the plates for 5 min. Cell monolayers were washed twice with ice-cold PBS and scrapped off the plate in 10 ml PBS, spun at 200g for 5 min, and flash frozen after removing the supernatant. Frozen pellets were resuspended in 1 ml of Cell Lysis Buffer (50 mM HEPES pH8, 140 mM NaCl, 1 mM EDTA pH8, 10 % glycerol, 0.5% NP-40, 0.25% Triton X-100 and PPI) and incubated for 10 min at 4°C with gentle rotation. Nuclei were then centrifuged at 1,700g for 5 min at 4°C. Pelleted nuclei were washed twice with 1 ml Wash Buffer (10 mM Tris-HCl pH8, 200 mM NaCl, 1mM EDTA pH8, 0.5 mM EGTA pH8 and PPI) and then resuspended in 1 ml of Shearing Buffer (10 mM Tris-HCl pH7.4, 1 mM EDTA pH8, 0.1% SDS, 1% Triton-X100, 0.1% Sodium Deoxycholate, 0.25% NLauroylsarcosine, 1 mM DTT and PPI) and sonicated in a Covaris E220 focused-ultrasonicator (peak intensity: 140, 5% duty cycle, 200 cycles per burst, 10-12 min) using 1 ml AFA fiber tubes. An equivalent of 5 x 106 cells was sonicated in each tube and used for each ChIP. Lysates were centrifuged for 15 min at 10,000g in a refrigerated centrifuge. Cleared supernatants were transferred to new tubes and NaCl was added to a final concentration of 150 mM. Samples were then incubated with Dynabeads Protein G (LifeTechnologies,10003D, 40 µl/ml of lysate) for 1 hour at 4°C, with constant rotation (pre-clearing). After magnetic separation of the beads, the appropriate primary antibody was added to each tube for an overnight immunoprecipitation, at 4°C, with gentle rotation. Antibody-bound cross-linked chromatin was precipitated with prewashed Dynabeads Protein G for 2 h at 4°C and with constant rotation. Beads were then washed sequentially with low salt wash buffer (20 mM Tris-HCl pH 8, 150 mM NaCl, 10 mM EDTA, and 1% SDS), high salt wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS), LiCl wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) and twice with 1X TE buffer. Each wash was performed for 5 min at 4°C with gentle rotation. DNA was eluted from the beads with 300 µl of 100 mM sodium bicarbonate and 1% SDS for 30 min at RT with constant shaking. Crosslinking was reversed overnight at 65°C and RNA and protein were then sequentially digested by adding 0.2 mg/ml RNase A for 30 min at 37°C followed by 0.2 mg/ml Proteinase K for 1 h at 55°C. DNA was extracted with 300 µl of phenol/chloroform/isoamyl-alcohol (Calbiochem, #516726) and centrifuged at 20,000g for 5 min at RT. DNA in the upper layer was then precipitated with 1 volume isopropanol, 1/3 volume of 2 M sodium perchlorate and 5 µl glycogen and centrifuged at 20,000g for 10 min at RT. Pelleted DNA was washed twice with 70% ethanol and resuspended in 20 µl low TE. For ATAC-seq: Fifty thousand cells were resuspended in 1ml of cold ATAC-seq resuspension buffer (RSB) (10mM Tris-HCl (pH 7.4), 10mM NaCl and 3mM MgCl2 in water). Cells were centrifuged at maximum speed for 10min in a prechilled (4 °C) fixed-angle centrifuge. After centrifugation, supernatant was carefully aspirated. Cell pellets were then resuspended in 50μl of ATAC-seq RSB containing 0.1% NP40, 0.1% Tween-20 and 0.01% digitonin by pipetting up and down three times and incubated on ice for 3min. After lysis, 1ml of ATAC-seq RSB containing only 0.1% Tween-20 was added and the tubes were inverted to mix. Nuclei were then centrifuged for 5min at max speed in a prechilled fixed-angle centrifuge. Supernatant was removed and nuclei were resuspended in 50μl of transposition mix (25μl 2X TD buffer, 2.5μl transposase (100nM final), 16.5μl PBS, 0.5μl 1% digitonin, 0.5μl 10% Tween20 and 5μl water46) by pipetting up and down six times. Transposition reactions were incubated at 37 °C for 30min in a thermomixer with shaking at 1,000 r.p.m. Reactions were cleaned up with Qiagen MinElute columns.
ChIP-seq/Hi-ChIP: Libraries were prepared using the ThruPLEX DNA-seq Kit (Rubicon Genomics, R400427) according to the manufacturer’s protocol. Library fragments were size-selected by PAGE within a 150kb and 700kb range. ATAC-seq: Libraries were amplified as previously described (Buenrostro et al., 2015).

treatment_protocol: For in vitro experiment, cells were profield under three different designs: 1) baseline charaterization without any treatment; 2) 0,1% DMSO (vehicle) or 1μM A196 treatment for 5 days; 3) wiuth or without pretreatment of 1μM A196 treatment for 5 days and further in the presence or absence of 1μM Tunicamycin treatment for 12 hours.

value: Human breast cancer

value: Human breast cancer epithelial cell

value: Wild-type

value: 1μM A196 pretreatment 5 days+1μM Tunicamycin 12hours


title: SUM149_Tunicamycin_A196_ATACseq_rep2

description: Library name: Sample128


title: SUM149_A196_ATACseq_rep1

description: Library name: Sample125

value: 1μM A196 5 days


title: SUM149_A196_ATACseq_rep2

description: Library name: Sample126


title: TGGT1_278440_12h_vehicle_2

description:
Library name: L311_589
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_278440_12h_vehicle_2


title: TGGT1_320300_6h_IAA_2

description:
Library name: L311_588
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_320300_6h_IAA_2


title: SUM149_Tunicamycin_ATACseq_rep1

description: Library name: Sample123

value: 1μM Tunicamycin 12hours


title: SUM149_Tunicamycin_ATACseq_rep2

description: Library name: Sample124


title: TGGT1_278440_6h_IAA_2

description:
Library name: L311_586
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_278440_6h_IAA_2


title: TGGT1_278440_12h_IAA_2

description:
Library name: L311_590
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_278440_12h_IAA_2


title: TGGT1_320300_6h_vehicle_2

description:
Library name: L311_587
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_320300_6h_vehicle_2


title: TGGT1_320300_24h_IAA_1

description:
Library name: L311_584
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_320300_24h_IAA_1


title: SUM149_Control_ATACseq_rep1

description: Library name: Sample121

value: 0.1% DMSO 5 days


title: SUM149_Control_ATACseq_rep2

description: Library name: Sample122


title: TGGT1_278440_24h_IAA_1

description:
Library name: L311_582
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_278440_24h_IAA_1


title: TGGT1_278440_6h_vehicle_2

description:
Library name: L311_585
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_278440_6h_vehicle_2


title: SUM149_Tunicamycin_A196_ATF4_ChIP_rep2

description: Library name: Sample118


title: SUM149_Tunicamycin_A196_E2F4_ChIP_rep2

description: Library name: Sample120


title: SUM149_Tunicamycin_A196_ATF4_ChIP_rep1

description: Library name: Sample117


title: SUM149_Tunicamycin_A196_E2F4_ChIP_rep1

description: Library name: Sample119


title: TGGT1_278440_24h_vehicle_1

description:
Library name: L311_581
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_278440_24h_vehicle_1


title: SUM149_Tunicamycin_A196_Input_rep2

description: Library name: Sample116


title: TGGT1_320300_12h_IAA_1

description:
Library name: L311_578
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_320300_12h_IAA_1


title: TGGT1_RH_Tir1_24h_IAA_1

description:
Library name: L311_580
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_RH_Tir1_24h_IAA_1


title: TGGT1_320300_24h_vehicle_1

description:
Library name: L311_583
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_320300_24h_vehicle_1


title: SUM149_Tunicamycin_A196_Input_rep1

description: Library name: Sample115


title: TGGT1_RH_Tir1_24h_vehicle_1

description:
Library name: L311_579
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_RH_Tir1_24h_vehicle_1


title: SUM149_A196_E2F4_ChIP_rep1

description: Library name: Sample113


title: SUM149_A196_ATF4_ChIP_rep2

description: Library name: Sample112


title: TGGT1_278440_12h_IAA_1

description:
Library name: L311_576
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_278440_12h_IAA_1


title: TGGT1_320300_12h_vehicle_1

description:
Library name: L311_577
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_320300_12h_vehicle_1


title: SUM149_A196_E2F4_ChIP_rep2

description: Library name: Sample114


title: SUM149_A196_ATF4_ChIP_rep1

description: Library name: Sample111


title: TGGT1_278440_12h_vehicle_1

description:
Library name: L311_575
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_278440_12h_vehicle_1


title: SUM149_A196_Input_rep2

description: Library name: Sample110


title: SUM149_Tunicamycin_E2F4_ChIP_rep2

description: Library name: Sample108


title: TGGT1_320300_6h_IAA_1

description:
Library name: L311_574
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_320300_6h_IAA_1


title: TGGT1_320300_6h_vehicle_1

description:
Library name: L311_573
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_320300_6h_vehicle_1


title: SUM149_Tunicamycin_ATF4_ChIP_rep2

description: Library name: Sample106


title: TGGT1_278440_6h_vehicle_1

description:
Library name: L311_571
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_278440_6h_vehicle_1


title: SUM149_Tunicamycin_Input_rep1

description: Library name: Sample103


title: TGGT1_278440_6h_IAA_1

description:
Library name: L311_572
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_278440_6h_IAA_1


title: TGGT1_321450_12h_vehicle_3

description:
Library name: L311_387
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_321450_12h_vehicle_3


title: TGGT1_RH_Tir1_12h_IAA_1

description:
Library name: L311_386
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_RH_Tir1_12h_IAA_1


title: SUM149_Tunicamycin_ATF4_ChIP_rep1

description: Library name: Sample105


title: SUM149_Control_ATF4_ChIP_rep1

description: Library name: Sample99


title: TGGT1_203950_12h_vehicle_2

description:
Library name: L311_389
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_203950_12h_vehicle_2


title: TGGT1_275480_6h_vehicle_2

description:
Library name: L311_385
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_275480_6h_vehicle_2


title: SUM149_Tunicamycin_Input_rep2

description: Library name: Sample104


title: TGGT1_203950_12h_IAA_1

description:
Library name: L311_388
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_203950_12h_IAA_1


title: SUM149_Control_Input_rep1

description: Library name: Sample97


title: TGGT1_203950_12h_vehicle_3

description:
Library name: L311_383
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_203950_12h_vehicle_3


title: SUM149_Tunicamycin_E2F4_ChIP_rep1

description: Library name: Sample107


title: TGGT1_203950_12h_IAA_3

description:
Library name: L311_384
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_203950_12h_IAA_3


title: TGGT1_203950_12h_IAA_2

description:
Library name: L311_380
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_203950_12h_IAA_2


title: SUM149_Control_E2F4_ChIP_rep1

description: Library name: Sample101


title: SUM149_HP1gamma_rep2

description: Library name: Sample96

value: No treatment


title: SUM149_Control_E2F4_ChIP_rep2

description: Library name: Sample102


title: SUM149_Control_ATF4_ChIP_rep2

description: Library name: Sample100


title: SUM149_A196_Input_rep1

description: Library name: Sample109


title: TGGT1_286920_12h_IAA_3

description:
Library name: L311_382
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_286920_12h_IAA_3


title: TGGT1_286920_12h_vehicle_3

description:
Library name: L311_381
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_286920_12h_vehicle_3


title: TGGT1_286920_12h_IAA_2

description:
Library name: L311_378
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_286920_12h_IAA_2


title: SUM149_Control_Input_rep2

description: Library name: Sample98


title: SUM149_H4K20me3_A196_rep2

description: Library name: Sample94


title: SUM149_HP1gamma_rep1

description: Library name: Sample95


title: SUM149_H4K20me1_A196_rep2

description: Library name: Sample92


title: TGGT1_286920_12h_IAA_1

description:
Library name: L311_374
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_286920_12h_IAA_1


title: TGGT1_203950_12h_vehicle_1

description:
Library name: L311_375
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_203950_12h_vehicle_1


title: TGGT1_286920_12h_vehicle_2

description:
Library name: L311_377
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_286920_12h_vehicle_2


title: SUM149_H4K20me3_A196_rep1

description: Library name: Sample93


title: TGGT1_286920_12h_vehicle_1

description:
Library name: L311_373
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_286920_12h_vehicle_1


title: SUM149_H4K20me1_A196_rep1

description: Library name: Sample91


title: TGGT1_264120_12h_IAA_3

description:
Library name: L311_372
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_264120_12h_IAA_3


title: TGGT1_264120_12h_vehicle_3

description:
Library name: L311_371
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_264120_12h_vehicle_3


title: SUM149_H4K20me1_Vehicle_rep2

description: Library name: Sample86


title: TGGT1_321450_12h_IAA_3

description:
Library name: L311_370
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_321450_12h_IAA_3


title: TGGT1_RH_Tir1_12h_vehicle_3

description:
Library name: L311_367
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_RH_Tir1_12h_vehicle_3


title: SUM149_H4K20me1_Vehicle_rep1

description: Library name: Sample85


title: SUM149_H4K20me3_Vehicle_rep1

description: Library name: Sample87


title: TGGT1_RH_Tir1_12h_IAA_3

description:
Library name: L311_368
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_RH_Tir1_12h_IAA_3


title: SUM149_A196_Input_pooled

description: Library name: Sample89


title: TGGT1_264120_12h_vehicle_2

description:
Library name: L311_365
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_264120_12h_vehicle_2


title: MDAMB468_HP1gamma_rep2

description: Library name: Sample80


title: SUM149_H4K20me3_Vehicle_rep2

description: Library name: Sample88


title: SUM149_H3K9me3_Vehicle_rep2

description: Library name: Sample84


title: TGGT1_321450_12h_IAA_2

description:
Library name: L311_364
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_321450_12h_IAA_2


title: TGGT1_264120_12h_IAA_2

description:
Library name: L311_366
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_264120_12h_IAA_2


title: MDAMB468_HP1gamma_rep1

description: Library name: Sample79


title: TGGT1_RH_Tir1_12h_vehicle_2

description:
Library name: L311_361
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_RH_Tir1_12h_vehicle_2


title: TGGT1_RH_Tir1_12h_IAA_2

description:
Library name: L311_362
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_RH_Tir1_12h_IAA_2


title: MDAMB468_H4K20me3_A196_rep2

description: Library name: Sample78


title: SUM149_Input_Vehicle_pooled

description: Library name: Sample81


title: TGGT1_264120_12h_IAA_1

description:
Library name: L311_360
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_264120_12h_IAA_1


title: MDAMB468_H4K20me3_A196_rep1

description: Library name: Sample77


title: MDAMB468_H4K20me1_A196_rep2

description: Library name: Sample76


title: mandibular condylar cartilage, aged mice(18 months)-6

city: Beijing

first: Xinyi

last: Wang

state: Ms.

address: Haidian district

department: Prosthodontics

institute: Peking University School and Hospital of Stomatology

description:
Library name: Sample13
fpkm_A_tm6

data_processing:
Raw reads were filtered using SOAPnuke (v1.5.6) to remove adapter sequences, reads with >5% unknown bases, and low-quality reads. Clean reads were aligned to reference genome (GCF_000001635.27_GRCm39) using HISAT2 (v2.1.0).
Clean reads were aligned to reference gene set using Bowtie2 (v2.3.4.3).
Gene expression quantification was performed using RSEM (v1.3.1).
Differential expression analysis was performed using DESeq2 (v1.4.5) with Q value ≤ 0.05.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file includes TPM values for each sample.
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

source_name: temporomandibular joint, mandible condylar cartilage

extract_protocol:
Total RNA was extracted from tissue samples using TRIzol reagent. Samples were homogenized, extracted with chloroform/isoamyl alcohol (24:1), precipitated with isopropanol at -20°C, washed with 75% ethanol, and dissolved in DEPC-treated water.
mRNA was enriched using oligo(dT) magnetic beads and fragmented. Double-stranded cDNA was synthesized, followed by end repair, 3' adenylation, and adapter ligation. PCR amplification was performed, and the products were circularized to generate single-stranded circular DNA. DNA nanoballs (DNBs) were generated by rolling circle replication and sequenced on DNBSEQ platform using cPAS technology (PE150, strand-specific).


title: TGGT1_321450_12h_vehicle_2

description:
Library name: L311_363
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_321450_12h_vehicle_2


title: TGGT1_321450_12h_IAA_1

description:
Library name: L311_358
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_321450_12h_IAA_1


title: MDAMB468_A196_Input_rep2

description: Library name: Sample74


title: TGGT1_321450_12h_vehicle_1

description:
Library name: L311_357
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_321450_12h_vehicle_1


title: MM_13

city: Pamplona

first: Itziar

last: Cenzano

state: Navarra

address: Avenida de Pio XII, 55

country: Spain

institute: CIMA Universidad de Navarra

description:
Library name: MM_13
Takaras SMART-Seq v4

data_processing:
Raw sequencing reads were demultiplexed using bclfastq2 v2.20 (Illumina) to convert BCL files to FASTQ format. Quality control was performed with FastQC, and reads were trimmed for adapters and low-quality bases using Trimmomatic. Reads were aligned to the human reference genome hg19 using STAR v2.6. Uniquely aligned reads were assigned to GENCODE gene annotations and quantified using HTSeq v0.11 in stranded mode with default parameters. Downstream analyses, including normalization, differential expression, and pathway analysis, were conducted in R.
Assembly: hg19
Supplementary files format and content: Tab-delimited text file including raw counts for each Sample

source_name: Bone marrow

extract_protocol:
Human bone marrow (BM) mesenchymal stem cells (MSC)were obtained from BM samples of healthy adult donors and BM aspirates of newly diganosed patients. Red blood cells were lysed twice for 15 min at room temperature with rotation using 45 ml of ACK lysis buffer per 5 ml of sample. Bone fragments were cut into small pieces, crushed, and digested with 0.3% collagenase I and 5 U/ml dispase in PBS (3 ml/sample) for 15 min at 37°C with shaking at 200 rpm. Digestion was stopped with FBS (10% of digestion volume), and the digested fractions were filtered through a 70 μm filter. Live cell concentration and viability were assessed using acridine orange/propidium iodide (AO/PI) staining on a Cellometer K2 Image Cytometer (Nexcelom Bioscience). Cells were either cryopreserved in FBS with 10% DMSO until use or immediately processed for downstream sorting. BM mesenchymal stem cells (MSC) were stained with conjugated antibodies, and TO-PRO-3-/Lin-/CD45-/CD235-/CD16-/CD56-/CD31-/CD271+/CD146+/- cells were sorted by fluorescence-activated cell sorting (FACS) into Lysis/Binding Buffer (Ambion) for bulk RNA-seq.
Libraries were prepared according to the manufacturer’s instructions (10x Genomics, Single Cell 3′ Reagent Kits v3.1). Briefly, ~15,000 cells per sample were loaded onto a Chromium Controller to generate single-cell gel bead-in-emulsions (GEMs). Poly-A RNA from each cell was reverse transcribed to cDNA containing Illumina Read 1 primer sequences, 16 bp 10x barcodes, and 12 bp Unique Molecular Identifiers (UMIs). Barcoded cDNA was amplified by PCR, size-selected using SPRIselect (Beckman Coulter), enzymatically fragmented, and subjected to end repair, A-tailing, adaptor ligation, and PCR indexing. Libraries were quantified using a Qubit 3.0 Fluorometer and Agilent 4200 TapeStation, and sequenced on an Illumina NextSeq 2000 (Read 1: 28 cycles; i7: 10; i5: 10; Read 2: 90).

value: Bone marrow

value: mesenchymal stem cells (MSC)

tag: disease

value: MM

tag: age

tag: gender

value: MALE


title: MM_6

description:
Library name: MM_6
Takaras SMART-Seq v4


title: MM_7

description:
Library name: MM_7
Takaras SMART-Seq v4


title: MDAMB468_H4K20me3_Vehicle_rep2

description: Library name: Sample72


title: mandibular condylar cartilage, aged mice(18 months)-2

description:
Library name: Sample9
fpkm_A_tm2

value: temporomandibular joint, mandible condylar cartilage


title: MM_16

description:
Library name: MM_16
Takaras SMART-Seq v4

value: FEMALE


title: MDAMB468_A196_Input_rep1

description: Library name: Sample73


title: MM_3

description:
Library name: MM_3
Takaras SMART-Seq v4


title: MDAMB468_H4K20me1_Vehicle_rep2

description: Library name: Sample70


title: MM_1

description:
Library name: MM_1
Takaras SMART-Seq v4


title: SUM149_H3K9me3_Vehicle_rep1

description: Library name: Sample83


title: TGGT1_264120_12h_vehicle_1

description:
Library name: L311_359
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_264120_12h_vehicle_1

value: Toxoplasma gondii cell

value: vehicle


title: TGGT1_275480_6h_IAA_3

description:
Library name: L311_352
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_275480_6h_IAA_3

value: auxin


title: MDAMB468_H4K20me1_Vehicle_rep1

description: Library name: Sample69

value: Human breast cancer


title: TGGT1_275480_6h_vehicle_3

description:
Library name: L311_351
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_275480_6h_vehicle_3


title: TGGT1_RH_Tir1_6h_IAA_3

description:
Library name: L311_350
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_RH_Tir1_6h_IAA_3


title: mandibular condylar cartilage, aged mice(18 months)-5

description:
Library name: Sample12
fpkm_A_tm5


title: MM_11

description:
Library name: MM_11
Takaras SMART-Seq v4


title: MDAMB468_H4K20me1_A196_rep1

description: Library name: Sample75

value: Human breast cancer epithelial cell


title: mandibular condylar cartilage, aged mice(18 months)-4

description:
Library name: Sample11
fpkm_A_tm4


title: MM_23

description:
Library name: MM_23
Takaras SMART-Seq v4


title: TGGT1_203950_6h_IAA_2

description:
Library name: L311_348
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_203950_6h_IAA_2


title: TGGT1_RH_Tir1_12h_vehicle_1

description:
Library name: L311_355
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_RH_Tir1_12h_vehicle_1


title: MDAMB468_Input_Vehicle_rep1

description: Library name: Sample65

value: Wild-type


title: TGGT1_203950_6h_IAA_3

description:
Library name: L311_354
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_203950_6h_IAA_3


title: MDAMB468_H4K20me3_Vehicle_rep1

description: Library name: Sample71


title: mandibular condylar cartilage, young mice(2 months)-2

description:
Library name: Sample2
fpkm_Y_tm2


title: MM_4

description:
Library name: MM_4
Takaras SMART-Seq v4


title: mandibular condylar cartilage, young mice(2 months)-3

description:
Library name: Sample3
fpkm_Y_tm3


title: TGGT1_203950_6h_vehicle_3

description:
Library name: L311_353
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_203950_6h_vehicle_3


title: mandibular condylar cartilage, young mice(2 months)-7

description:
Library name: Sample7
fpkm_Y_tm7


title: mandibular condylar cartilage, aged mice(18 months)-1

description:
Library name: Sample8
fpkm_A_tm1


title: TGGT1_203950_6h_vehicle_2

description:
Library name: L311_347
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_203950_6h_vehicle_2


title: mandibular condylar cartilage, aged mice(18 months)-3

description:
Library name: Sample10
fpkm_A_tm3


title: MM_24

description:
Library name: MM_24
Takaras SMART-Seq v4


title: TGGT1_RH_Tir1_6h_IAA_2

description:
Library name: L311_346
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_RH_Tir1_6h_IAA_2


title: mandibular condylar cartilage, young mice(2 months)-6

description:
Library name: Sample6
fpkm_Y_tm6


title: MDAMB231_H4K20me3_A196_rep1

description: Library name: Sample63


title: MDAMB468_H3K9me3_Vehicle_rep1

description: Library name: Sample67


title: SMM_HR_1

description:
Library name: SMM_HR_1
Takaras SMART-Seq v4

value: SMM-HR


title: mandibular condylar cartilage, young mice(2 months)-4

description:
Library name: Sample4
fpkm_Y_tm4


title: TGGT1_RH_Tir1_6h_vehicle_2

description:
Library name: L311_345
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_RH_Tir1_6h_vehicle_2


title: MDAMB231_H4K20me1_A196_rep2

description: Library name: Sample62

value: 1μM A196 5 days


title: SMM_10

description:
Library name: SMM_10
Takaras SMART-Seq v4

value: SMM


title: MDAMB468_Input_Vehicle_rep2

description: Library name: Sample66

value: 0.1% DMSO 5 days


title: TGGT1_RH_Tir1_6h_vehicle_3

description:
Library name: L311_349
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_RH_Tir1_6h_vehicle_3


title: mandibular condylar cartilage, young mice(2 months)-5

description:
Library name: Sample5
fpkm_Y_tm5


title: TGGT1_275480_6h_IAA_2

description:
Library name: L311_344
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_275480_6h_IAA_2


title: MDAMB468_H3K9me3_Vehicle_rep2

description: Library name: Sample68


title: MGUS_9

description:
Library name: MGUS_9
Takaras SMART-Seq v4

value: MGUS-HR


title: mandibular condylar cartilage, young mice(2 months)-1

description:
Library name: Sample1
fpkm_Y_tm1


title: MDAMB231_H4K20me3_A196_rep2

description: Library name: Sample64


title: MGUS_8

description:
Library name: MGUS_8
Takaras SMART-Seq v4

value: Bone marrow

value: MGUS


title: TGGT1_RH_Tir1_6h_vehicle_1

description:
Library name: L311_341
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_RH_Tir1_6h_vehicle_1


title: MGUS_10

description:
Library name: MGUS_10
Takaras SMART-Seq v4

value: mesenchymal stem cells (MSC)


title: MDAMB231_H4K20me1_A196_rep1

description: Library name: Sample61


title: mouse intestinal organoids, DSS treatment, Day4

city: Daegu

first: Pacian

middle: Sung-Wook

last: Nam

state: Daegu

address: 90 Chilgokjoongangdaero-136-gil

department: School of Medicine

institute: Kyungpook National University

description: Library name: sample2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence.
Trimmed reads were mapped by HISAT2, to generate aligned reads.
Assembly: From the aligned reads, transcript assembly was performed by StringTie. Read count extraction and normalization were performed.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Intestine

growth_protocol: Mouse intestinal organoids were maintained in organoid growth medium supplemented with EGF, Noggin, and R-spondin.

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Inflammatory intestinal organoids were induced by treatment of dextran sulfate sodium (DSS) for 4 days.

value: Intestine

value: Organoids

value: intestinal stem cells

value: DSS treatment

tag: batch

value: Day 4


title: mouse intestinal organoids, Control, Day4

description: Library name: sample1

value: control


title: MGUS_4

description:
Library name: MGUS_4
Takaras SMART-Seq v4

value: FEMALE


title: Control_8

description:
Library name: Control_8
Takaras SMART-Seq v4

value: Healthy donor

value: MALE


title: TGGT1_203950_6h_IAA_1

description:
Library name: L311_340
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_203950_6h_IAA_1

value: Toxoplasma gondii cell

value: auxin


title: TGGT1_RH_Tir1_6h_IAA_1

description:
Library name: L311_342
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_RH_Tir1_6h_IAA_1


title: MDAMB231_A196_Input_rep2

description: Library name: Sample60

value: Human breast cancer

value: Human breast cancer epithelial cell

value: Wild-type

value: 1μM A196 5 days


title: T24 cells, siFBXL6-1

city: Wuhan

first: Yu

last: Xiao

address: Donghu Road 169

department: Department of Urology

institute: Zhongnan Hospital of Wuhan University

description:
Library name: sample4
Column name in All_reads_counts.xls: si_1

data_processing:
Raw sequencing reads were adapter-trimmed and quality-filtered using fastp (version 0.23.0) with default parameters. The resulting clean reads were uploaded to GEO. Clean reads were then aligned to the Homo sapiens reference genome (GRCh38, NCBI) using STAR aligner. Gene-level quantification was performed by counting exonic reads uniquely mapped to annotated genes using featureCounts (Subread version 1.5.1; Bioconductor).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: T24 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNAs were extracted using TRIzol Reagent (Invitrogen, cat. NO 15596026）following the methods. A total of 2 μg of high-quality RNA was used for the construction of sequencing libraries.
KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction

value: bladder cancer cell

value: FBXL6 knockdown


title: MDAMB231_HP1gamma_rep1

description: Library name: Sample57

value: No treatment


title: MGUS_5

description:
Library name: MGUS_5
Takaras SMART-Seq v4

value: Bone marrow

value: mesenchymal stem cells (MSC)

value: MGUS


title: T24 cells, siFBXL6-3

description:
Library name: sample6
Column name in All_reads_counts.xls: si_3


title: MDAMB231_A196_Input_rep1

description: Library name: Sample59


title: T24 cells, siNC-3

description:
Library name: sample3
Column name in All_reads_counts.xls: NC_3

value: WT


title: TGGT1_203950_6h_vehicle_1

description:
Library name: L311_339
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_203950_6h_vehicle_1

value: vehicle


title: T24 cells, siFBXL6-2

description:
Library name: sample5
Column name in All_reads_counts.xls: si_2


title: TGGT1_275480_6h_IAA_1

description:
Library name: L311_338
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_275480_6h_IAA_1


title: Control_18

description:
Library name: Control_18
Takaras SMART-Seq v4


title: Control_3

description:
Library name: Control_3
Takaras SMART-Seq v4


title: MDAMB231_HP1gamma_rep2

description: Library name: Sample58


title: MDAMB231_SMARCA5_rep2

description: Library name: Sample56


title: Control_15

description:
Library name: Control_15
Takaras SMART-Seq v4

value: FEMALE


title: MDAMB231_SMARCA5_rep1

description: Library name: Sample55


title: Control_7

description:
Library name: Control_7
Takaras SMART-Seq v4

value: Healthy donor


title: T24 cells, siNC-2

description:
Library name: sample2
Column name in All_reads_counts.xls: NC_2


title: TGGT1_321440_6h_IAA_3

description:
Library name: L311_303
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_321440_6h_IAA_3


title: Control_2

description:
Library name: Control_2
Takaras SMART-Seq v4


title: T24 cells, siNC-1

description:
Library name: sample1
Column name in All_reads_counts.xls: NC_1


title: TGGT1_275480_6h_vehicle_1

description:
Library name: L311_337
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_275480_6h_vehicle_1


title: Control_6

description:
Library name: Control_6
Takaras SMART-Seq v4


title: 604A3_tNCC_rep3

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 uL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 uL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851C) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the SureScan Agilent DNA Microarray Scanner (G4900DA) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Trunk neural crest cells from 604A3 hiPSC.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions (Protocol version 6.9), followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total cellular RNA for preparing RT–PCR templates was extracted using ISOGEN II (Nippon Gene KK). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was guaranteed by an RNA Integrity Number (RIN) > 8.

value: male

value: tNCC


title: MDAMB231_H4K20me3_Vehicle_rep2

description: Library name: Sample54

value: 0.1% DMSO 5 days


title: MDAMB231_H4K20me1_Vehicle_rep2

description: Library name: Sample52

value: Human breast cancer


title: TGGT1_321440_6h_vehicle_3

description:
Library name: L311_302
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_321440_6h_vehicle_3

value: Toxoplasma gondii cell


title: MDAMB231_H4K20me3_Vehicle_rep1

description: Library name: Sample53

value: Human breast cancer epithelial cell

value: Wild-type


title: TGGT1_264120_6h_IAA_3

description:
Library name: L311_301
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_264120_6h_IAA_3

value: auxin


title: 604A3_tNCC_rep2


title: Rehydration_2

description: Biological replicate 2 of 2.

hyb_protocol: 600 ng of Cy3 or Cy5-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 uL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 uL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Custom Microarrays of Physcomitrium  for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the SureScan Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides.

organism: Physcomitrium patens

label_protocol: Cyanine-3 (Cy3) or Cyanine-5 (Cy5) labeled cRNA was prepared from 200 ng RNA using the Two-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Physcomitrium protonemal colonies of wild-type (WT) and autophagy deficient (autophagy related gene 5 knockout: atg5) mutant were cultured on a nutrient-sufficient medium, BCD medium containing 5 mM ammonium tartrate and 0.5% (w/v) glucose (BCDATG medium) along with 0.8% (w/v) agar, at 25°C under continuous light. To maintain the culture, a piece of the colony comprising protonemal cells was transferred to BCDATG agar medium once a week.

extract_protocol: Total cellular RNA for preparing RT–PCR templates was extracted using NucleoSpin® RNA Kit (TAKARA). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was guaranteed by an RNA Integrity Number (RIN) > 8.

treatment_protocol: Colonies that had been cultured for 7 days were used as hydration in this study.In order to treat colonies with ABA, 7-day-old protonemal colonies were placed on fresh agar culture medium containing 50 μM cis-trans ABA (FUJIFILM, Tokyo, Japan) for 24 h under light. For dehydration treatment, the colonies were transferred onto a filter paper placed in a tightly-stoppered glass jar containing silica gel and kept for 24 h. Thereafter, the colonies were transferred onto fresh culture medium for rehydration of 24 h.

value: Rehydration

value: protonema


title: ABA_2

description: Biological replicate 2 of 2.

value: ABA


title: TGGT1_264120_6h_vehicle_3

description:
Library name: L311_300
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_264120_6h_vehicle_3


title: Control_4

description:
Library name: Control_4
Takaras SMART-Seq v4

value: Bone marrow

value: mesenchymal stem cells (MSC)

value: MALE


title: MDAMB231_H4K16ac_Vehicle_rep2

description: Library name: Sample50


title: MDAMB231_H4K20me1_Vehicle_rep1

description: Library name: Sample51


title: TGGT1_213890_6h_vehicle_3

description:
Library name: L311_298
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_213890_6h_vehicle_3

value: vehicle


title: Hydration_rep2

description: Biological replicate 2 of 2.

value: WT

value: Hydration


title: 604A3_cNCC_rep3

source_name: Cranial neural crest cells from 604A3 hiPSC.

value: male

value: cNCC


title: MDAMB231_H4K16ac_Vehicle_rep1

description: Library name: Sample49

value: 0.1% DMSO 5 days


title: TGGT1_213890_6h_IAA_3

description:
Library name: L311_299
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_213890_6h_IAA_3


title: 604A3_iPSC_rep3

source_name: 604A3 iPSC

value: iPSC


title: TGGT1_321450_6h_vehicle_3

description:
Library name: L311_296
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_321450_6h_vehicle_3

value: Toxoplasma gondii cell


title: Dehydration_2

description: Biological replicate 2 of 2.

value: Dehydration


title: TGGT1_321450_6h_IAA_3

description:
Library name: L311_297
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_321450_6h_IAA_3


title: MDAMB231_H4K12ac_Vehicle_rep2

description: Library name: Sample48

value: Human breast cancer

value: Human breast cancer epithelial cell

value: Wild-type


title: Rehydration_1

description: Biological replicate 1 of 2.

value: Rehydration

value: protonema


title: 604A3_cNCC_rep2


title: MDAMB231_H4K12ac_Vehicle_rep1

description: Library name: Sample47


title: MDAMB231_H4K8ac_Vehicle_rep2

description: Library name: Sample46


title: TGGT1_286920_6h_IAA_3

description:
Library name: L311_295
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_286920_6h_IAA_3

value: auxin


title: 604A3_tNCC_rep1

value: tNCC


title: Hydration_rep1

description: Biological replicate 1 of 2.


title: ABA_1

description: Biological replicate 1 of 2.

value: ABA


title: TGGT1_286920_6h_vehicle_3

description:
Library name: L311_294
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_286920_6h_vehicle_3

value: vehicle


title: MDAMB231_H4K8ac_Vehicle_rep1

description: Library name: Sample45


title: Dehydration_1

description: Biological replicate 1 of 2.

value: WT


title: TGGT1_217050_6h_IAA_3

description:
Library name: L311_293
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_217050_6h_IAA_3


title: 604A3_cNCC_rep1


title: MDAMB231_H4K5ac_Vehicle_rep2

description: Library name: Sample44


title: 604A3_iPSC_rep2


title: MDAMB231_H4K5ac_Vehicle_rep1

description: Library name: Sample43


title: 596E OD, Control, Day 28

city: Dallas

first: Katherine

last: Borner

address: 5323 Harry Hines Blvd.

department: Ophthalmology

institute: UT Southwestern Medical Center

description:
Library name: Control Day 28 Sample 2
10x Genomics

data_processing:
Cell Ranger (v5.0.1; 10x Genomics) was used to process the raw sequencing data. Raw BCL files were converted to FASTQ files and aligned to a custom Oryctolagus cuniculus (rabbit) reference transcriptome generated in-house using the Cell Ranger mkref pipeline, based on the rabbit genome annotation and formatted for 10x Genomics analysis. Gene–barcode count matrices were subsequently generated using the Cell Ranger count pipeline.
Assembly: OryCun2
Supplementary files format and content: feature-barcode matrix HDF5

organism: Oryctolagus cuniculus

source_name: Cornea

extract_protocol:
Following rabbit euthanasia with intravenous injection of sodium pentobarbital (120 mg/kg body weight), excised 8mm diameter central corneal buttons were digested in a 37 °C incubator (5 % CO2) with 2D rocking for approximately 3 h in 1 mL of media containing 2 mg/mL collagenase, and 0.5 mg/mL hyaluronidase in minimum essential medium (MEM) supplemented with 2 % penicillin/streptomycin/amphotericin. Following incubation, the solution underwent centrifugation (1500 rpm, 4 min), the supernatant was discarded, and the pellet was resuspended in 1 mL 0.05 % trypsin for incubation at 37 °C for 3 min. The trypsinization reaction was halted with 4 mL of trypsin inhibitor. After centrifugation (1500 rpm, 4 min), the supernatant was discarded, and the pellet was washed in 1 mL 4 °C chilled PBS. The cell suspension was filtered sequentially with 70 μm and 40 μm porosity Flowmi® cell strainers. Following centrifugation (1500 rpm, 4 min), the supernatant was discarded, and the single cells were resuspended in 500 μL 4 °C chilled PBS enriched with 0.4 % bovine serum albumin. Ice-cold, freshly prepared single cell suspensions were submitted for sequencing.
Single cell suspensions are washed in 1X PBS (calcium and magnesium free) containing 0.04% weight/volume BSA (400 μg/ml) and brought to a concentration of ~700-1200 cells/μl. This is accomplished by staining 10 μl of the single cell suspension with Trypan blue and reading on the Countess™ II Automated Cell Counter (ThermoFisher).  The appropriate volume of cells is loaded with Single Cell 3’ Gel Beads into a Next GEM Chip G and run on the Chromium™ Controller. GEM emulsions are incubated and then broken.  Silane magnetic beads are used to clean up GEM reaction mixture. Read one primer sequence is added during incubation and full-length, barcoded cDNA is then amplified by PCR after cleanup. Sample size is checked on the Agilent Tapestation 4200 using the DNAHS 5000 tape and concentration determined by the Qubit® 4.0 Fluorimeter from ThermoFisher using the DNA HS assay. Samples are enzymatically fragmented and undergo size selection before proceeding to library construction.  During library preparation, Read 2 primer sequence, sample index and both Illumina adapter sequences are added.  Subsequently, samples are cleaned up using Ampure XP beads and post library preparation quality control is performed using the DNA 1000 tape on the Agilent Tapestation 4200. Final concentration is ascertained using the Qubit DNA HS assay. Samples are then loaded at 650 pM on the NextSeq 2000  using a P2-100 flowcell with the run configuration of 28x90x10x10.

treatment_protocol: transcorneal freeze injury

value: Cornea

tag: time point

value: Day 28


title: TGGT1_217050_6h_vehicle_3

description:
Library name: L311_292
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_217050_6h_vehicle_3


title: 201B7_tNCC_rep1

source_name: Trunk neural crest cells from 201B7 hiPSC.

value: female


title: 595E OD, Control, Day 28

description:
Library name: Control Day 28 Sample 1
10x Genomics


title: TGGT1_321440_6h_IAA_2

description:
Library name: L311_291
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_321440_6h_IAA_2


title: 201B7_tNCC_rep2


title: 604A3_iPSC_rep1

value: male


title: MDAMB231_H3K9me3_Vehicle_rep2

description: Library name: Sample42

value: 0.1% DMSO 5 days


title: MDAMB231_H3K9me3_Vehicle_rep1

description: Library name: Sample41


title: 595E OS, FI, Day 28

description:
Library name: FI Day 28 Sample 1
10x Genomics

value: transcorneal freeze injury


title: MDAMB231_Input_Vehicle_rep2

description: Library name: Sample40


title: 596E OS, FI, Day 28

description:
Library name: FI Day 28 Sample 2
10x Genomics


title: 616E OD, Control, Day 7

description:
Library name: Control Day 7 Sample 2
10x Genomics

value: Day 7


title: TGGT1_264120_6h_vehicle_2

description:
Library name: L311_288
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_264120_6h_vehicle_2

value: Toxoplasma gondii cell


title: TGGT1_264120_6h_IAA_2

description:
Library name: L311_289
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_264120_6h_IAA_2


title: 201B7_cNCC_rep3

source_name: Cranial neural crest cells from 201B7 hiPSC.

value: cNCC


title: TGGT1_213890_6h_IAA_2

description:
Library name: L311_287
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_213890_6h_IAA_2


title: TGGT1_321440_6h_vehicle_2

description:
Library name: L311_290
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_321440_6h_vehicle_2


title: 201B7_iPSC_rep2

source_name: 201B7 iPSC

value: iPSC


title: 201B7_iPSC_rep3


title: 201B7_cNCC_rep2


title: 594E OD, Control, Day 7

description:
Library name: Control Day 7 Sample 1
10x Genomics


title: 201B7_tNCC_rep3


title: 201B7_iPSC_rep1


title: 201B7_cNCC_rep1


title: 616E OS, FI, Day 7

description:
Library name: FI Day 7 Sample 2
10x Genomics


title: MDAMB231_Input_Vehicle_rep1

description: Library name: Sample39

value: Human breast cancer

value: Human breast cancer epithelial cell

value: Wild-type


title: TGGT1_213890_6h_vehicle_2

description:
Library name: L311_286
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_213890_6h_vehicle_2


title: MDAMB231_H4K20A_HA_ChIP_rep1

description: Library name: Sample37

value: No treatment


title: 594E OS, FI, Day 7

description:
Library name: FI Day 7 Sample 1
10x Genomics


title: MDAMB231_H4K20A_Input_rep2

description: Library name: Sample36


title: TGGT1_321450_6h_IAA_2

description:
Library name: L311_285
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_321450_6h_IAA_2

value: auxin


title: TGGT1_321450_6h_vehicle_2

description:
Library name: L311_284
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_321450_6h_vehicle_2

value: vehicle


title: MDAMB231_H4K20A_Input_rep1

description: Library name: Sample35


title: MDAMB231_H4K16A_HA_ChIP_rep2

description: Library name: Sample34


title: DN1_Primary human T cells_MOCK_Day0_NONE

city: san francisco

first: Jeremy

last: Bjelajac

state: CA

address: 2190 grove st

department: Pediatrics

institute: Stanford University

description:
Library name: Sample_25
Column name in raw_counts.txt: DN1_M-DAY-0

data_processing:
Raw reads were assessed for quality using FastQC. Adapter trimming and quality filtering were performed.
Reads were aligned to the human reference genome (GRCh38/hg38) using STAR aligner.
Gene-level read counts were quantified using featureCounts or HTSeq against a GENCODE/Ensembl GTF annotation. (verify — check your counts.txt file header for the tool used)
Differential expression analysis was performed using DESeq2 or edgeR. Genes with adjusted p-value < 0.05 and |Log2 Fold Change| > 1 were considered differentially expressed.
PCA was performed using the top variable genes. Hierarchical clustering was performed on the top 100 genes driving PC1 variance.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-delimited text file (raw_counts.txt): raw gene-level read counts per sample, with Ensembl gene IDs as rows and sample names as columns.

source_name: T cells (DN1)

growth_protocol: Primary human T cells were isolated from healthy donor PBMCs and activated with anti-CD3/CD28 magnetic beads (Dynabeads). T cells were lentivirally transduced with HA.28ζ, AIR-HA.28ζ, or mutAIR-HA.28ζ CAR constructs and expanded in T cell media (RPMI + 10% FBS + IL-2).

extract_protocol:
Total RNA was extracted from CAR T cells using a standard RNA isolation kit (e.g., RNeasy Mini Kit, Qiagen). RNA quality and quantity were assessed prior to library preparation.
Bulk RNA-seq libraries were prepared from total RNA using a poly(A) selection for paired-end sequencing. Libraries were sequenced by Novogene on an Illumina platform.

treatment_protocol: On Day 7 of culture, cells were treated with either DMSO (vehicle control) or Dasatinib (1 μM) for 7 days. Cells were derived from three healthy donors. After treatment, cells were harvested for RNA extraction.

value: T cells (DN1)


title: DN2_Primary human T cells_MOCK_Day0_NONE

description:
Library name: Sample_26
Column name in raw_counts.txt: DN2_M-DAY-0

source_name: T cells (DN2)

value: T cells (DN2)


title: DN3_Primary human T cells_MOCK_Dasatinib

description:
Library name: Sample_24
Column name in raw_counts.txt: DN3_M-DAS

source_name: T cells (DN3)

value: T cells (DN3)

value: MOCK

value: Dasatinib


title: DN3_Primary human T cells_MOCK_Day0_NONE

description:
Library name: Sample_27
Column name in raw_counts.txt: DN3_M-DAY-0


title: TGGT1_286920_6h_vehicle_2

first: Dominic

last: Schwarz

address: 455 Main St

institute: Massachusetts Institute of Technology

description:
Library name: L311_282
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_286920_6h_vehicle_2


title: TGGT1_286920_6h_IAA_2

description:
Library name: L311_283
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_286920_6h_IAA_2


title: 414C2_tNCC_rep2

first: Kyosuke

last: Mukae

address: 818, Komuro, Ina-machi

institute: Saitama Cancer Center

source_name: Trunk neural crest cells from 414C2 hiPSC.

value: female

value: tNCC


title: 414C2_tNCC_rep3


title: MDAMB231_H4K16A_HA_ChIP_rep1

description: Library name: Sample33


title: 414C2_tNCC_rep1


title: 414C2_cNCC_rep3

source_name: Cranial neural crest cells from 414C2 hiPSC.


title: TGGT1_217050_6h_vehicle_2

description:
Library name: L311_280
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_217050_6h_vehicle_2


title: MDAMB231_H4K16A_Input_rep2

description: Library name: Sample32


title: MDAMB231_H4K16A_Input_rep1

description: Library name: Sample31


title: 414C2_cNCC_rep2


title: DN3_Primary human T cells_AIR-HA_Dasatinib

description:
Library name: Sample_23
Column name in raw_counts.txt: DN3_AIR-DAS

value: AIR-HA


title: DN3_Primary human T cells_AIRMUT-HA_Dasatinib

description:
Library name: Sample_22
Column name in raw_counts.txt: DN3_AIR-MUT-DAS

value: AIRMUT-HA


title: TGGT1_217050_6h_IAA_2

description:
Library name: L311_281
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_217050_6h_IAA_2

value: Toxoplasma gondii cell


title: TGGT1_321440_6h_IAA_1

description:
Library name: L311_279
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_321440_6h_IAA_1


title: TGGT1_321440_6h_vehicle_1

description:
Library name: L311_278
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_321440_6h_vehicle_1


title: MDAMB231_H4K20A_HA_ChIP_rep2

description: Library name: Sample38


title: MDAMB231_H4K12A_HA_ChIP_rep1

description: Library name: Sample29


title: TGGT1_264120_6h_vehicle_1

description:
Library name: L311_276
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_264120_6h_vehicle_1


title: MDAMB231_H4K12A_Input_rep2

description: Library name: Sample28


title: MDAMB231_H4K12A_Input_rep1

description: Library name: Sample27


title: DN2_Primary human T cells_AIRMUT-HA_Dasatinib

description:
Library name: Sample_18
Column name in raw_counts.txt: DN2_AIR-MUT-DAS


title: 414C2_cNCC_rep1

value: cNCC


title: DN2_Primary human T cells_MOCK_Dasatinib

description:
Library name: Sample_20
Column name in raw_counts.txt: DN3_AIR-MUT-DAS


title: TGGT1_264120_6h_IAA_1

description:
Library name: L311_277
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_264120_6h_IAA_1


title: MDAMB231_H4K12A_HA_ChIP_rep2

description: Library name: Sample30

value: Human breast cancer


title: DN3_Primary human T cells_HA_Dasatinib

description:
Library name: Sample_21
Column name in raw_counts.txt: DN3_AIR-DAS

value: HA


title: DN2_Primary human T cells_AIR-HA_Dasatinib

description:
Library name: Sample_19
Column name in raw_counts.txt: DN2_AIR-DAS


title: 414C2_iPSC_rep4

source_name: 414C2 iPSC

value: iPSC


title: 414C2_cNCC_rep4


title: TGGT1_213890_6h_IAA_1

description:
Library name: L311_275
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_213890_6h_IAA_1


title: 414C2_iPSC_rep3


title: DN2_Primary human T cells_HA_Dasatinib

description:
Library name: Sample_17
Column name in raw_counts.txt: DN2_HA-DAS


title: Mouse SGZ NSCs, 0.8 μM CdCl₂, biol rep 3

city: Shanghai

first: Xiuli

last: Chang

address: No. 130, Dong'an Road, Shanghai, 200032, China

institute: Fudan University

description:
Library name: Cd_rep3
Primary SGZ-derived NSCs, passage 3

data_processing:
Raw reads were filtered and trimmed using fastp v0.20.1 with the parameter --length_required 50.
Clean reads were aligned to the Mus musculus reference genome GRCm39 using HISAT2 v2.1.0 with default parameters.
Gene-level read counts were quantified using htseq-count v0.11.2 with the parameter -s reverse.
Differential expression analysis was performed using DESeq2 v1.22.2 with thresholds of adjusted p-value < 0.05 and |log2FoldChange| > 1.
Assembly: GRCm39
Supplementary files format and content: counts_anno.txt: Tab-delimited text file containing raw gene counts for all samples.
Supplementary files format and content: FPKM_anno.txt: Tab-delimited text file containing FPKM-normalized expression values for all samples.

source_name: hippocampus

extract_protocol:
Total RNA was extracted using TRIzol reagent (Tiangen) according to the manufacturer's instructions. RNA quality and quantity were assessed before library preparation.
RNA-seq libraries were prepared using standard Illumina protocols by Shanghai OE Biotech Co., Ltd. Briefly, mRNA was enriched, fragmented, and reverse transcribed into cDNA. Libraries were amplified and purified, then sequenced on an Illumina platform.

value: hippocampus

value: neural stem cells

value: wild type

value: 0.8 μM CdCl₂ for 72 h


title: MDAMB231_H4K8A_HA_ChIP_rep2

description: Library name: Sample26

source_name: Human breast cancer

value: Human breast cancer epithelial cell

value: Wild-type

value: No treatment


title: TGGT1_213890_6h_vehicle_1

description:
Library name: L311_274
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_213890_6h_vehicle_1

value: vehicle


title: DN1_Primary human T cells_MOCK_Dasatinib

description:
Library name: Sample_16
Column name in raw_counts.txt: DN1_M-DAS

value: T cells (DN1)

value: MOCK

value: Dasatinib


title: MDAMB231_H4K8A_HA_ChIP_rep1

description: Library name: Sample25


title: MDAMB231_H4K8A_Input_rep2

description: Library name: Sample24


title: 414C2_iPSC_rep1

value: female


title: TGGT1_321450_6h_IAA_1

description:
Library name: L311_273
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_321450_6h_IAA_1

value: Toxoplasma gondii cell

value: auxin


title: Mouse SGZ NSCs, 0.8 μM CdCl₂, biol rep 2

description:
Library name: Cd_rep2
Primary SGZ-derived NSCs, passage 3


title: DN1_Primary human T cells_AIR-HA_Dasatinib

description:
Library name: Sample_15
Column name in raw_counts.txt: DN1_AIR-DAS

value: AIR-HA


title: Mouse SGZ NSCs, 0.8 μM CdCl₂, biol rep 1

description:
Library name: Cd_rep1
Primary SGZ-derived NSCs, passage 3


title: Mouse SGZ NSCs, untreated control, biol rep 3

description:
Library name: Control_rep3
Primary SGZ-derived NSCs, passage 3

value: control (untreated)


title: TGGT1_321450_6h_vehicle_1

description:
Library name: L311_272
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_321450_6h_vehicle_1


title: DN1_Primary human T cells_HA_Dasatinib

description:
Library name: Sample_13
Column name in raw_counts.txt: DN1_HA-DAS

value: HA


title: DN1_Primary human T cells_AIRMUT-HA_Dasatinib

description:
Library name: Sample_14
Column name in raw_counts.txt: DN1_AIR-MUT-DAS

value: AIRMUT-HA


title: Mouse SGZ NSCs, untreated control, biol rep 2

description:
Library name: Control_rep2
Primary SGZ-derived NSCs, passage 3

value: hippocampus

value: neural stem cells


title: MDAMB231_H4K5A_HA_ChIP_rep2

description: Library name: Sample22

value: Human breast cancer


title: 414C2_iPSC_rep2

value: iPSC


title: TGGT1_286920_6h_IAA_1

description:
Library name: L311_271
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_286920_6h_IAA_1


title: TGGT1_286920_6h_vehicle_1

description:
Library name: L311_270
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_286920_6h_vehicle_1


title: MDAMB231_H4K5A_HA_ChIP_rep1

description: Library name: Sample21

value: Human breast cancer epithelial cell

value: Wild-type


title: DN3_Primary human T cells_MOCK_DMSO

description:
Library name: Sample_12
Column name in raw_counts.txt: DN3_M

value: T cells (DN3)

value: DMSO


title: TGGT1_217050_6h_vehicle_1

description:
Library name: L311_268
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_217050_6h_vehicle_1

value: vehicle


title: MDAMB231_H4K8A_Input_rep1

description: Library name: Sample23

value: No treatment


title: DN3_Primary human T cells_AIRMUT-HA_DMSO

description:
Library name: Sample_10
Column name in raw_counts.txt: DN3_AIR-MUT


title: TGGT1_217050_6h_IAA_1

description:
Library name: L311_269
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_217050_6h_IAA_1


title: Mouse SGZ NSCs, untreated control, biol rep 1

description:
Library name: Control_rep1
Primary SGZ-derived NSCs, passage 3

value: wild type


title: DN3_Primary human T cells_AIR-HA_DMSO

description:
Library name: Sample_11
Column name in raw_counts.txt: DN3_AIR


title: MDAMB231_H4K5A_Input_rep1

description: Library name: Sample19


title: MDAMB231_H4K5A_Input_rep2

description: Library name: Sample20


title: MDAMB231_WT_H4_HA_ChIP_rep2

description: Library name: Sample18


title: TGGT1_320300_24h_IAA_3

description:
Library name: L311_611
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_320300_24h_IAA_3

value: Toxoplasma gondii cell


title: DN2_Primary human T cells_AIRMUT-HA_DMSO

description:
Library name: Sample_6
Column name in raw_counts.txt: DN2_AIR-MUT

value: T cells (DN2)


title: MDAMB231_WT_H4_HA_ChIP_rep1

description: Library name: Sample17


title: Regenerated pulp tissue; B2-cd24-neg-vivo

description: Library name: B2-cd24-neg-vivo

source_name: Regenerated pulp tissue

value: Regenerated pulp tissue

value: WT

value: in vivo transplantation


title: Regenerated pulp tissue; B3-cd24-neg-vivo

description: Library name: B3-cd24-neg-vivo


title: DN2_Primary human T cells_AIR-HA_DMSO

description:
Library name: Sample_7
Column name in raw_counts.txt: DN2_AIR

value: AIR-HA


title: DN2_Primary human T cells_HA_DMSO

description:
Library name: Sample_5
Column name in raw_counts.txt: DN2_HA

value: HA


title: Regenerated pulp tissue; A3-cd24-pos-vivo

description: Library name: A3-cd24-pos-vivo


title: DN1_Primary human T cells_MOCK_DMSO

description:
Library name: Sample_4
Column name in raw_counts.txt: DN1_M

value: T cells (DN1)

value: MOCK


title: TGGT1_278440_12h_vehicle_3

description:
Library name: L311_612
Column name in FEATURE_COUNTS_MYBs_RNAseq_cumulative_GEO.txt: TGGT1_278440_12h_vehicle_3


title: Regenerated pulp tissue; B1-cd24-neg-vivo

description: Library name: B1-cd24-neg-vivo


title: YCC-9

city: 강남구

first: Inho

last: Park

state: 서울특별시

address: Dept. of Pathology, Gangnam Severance Hospital, 20, Eonjuro 63gil

department: Yonsei University College of Medicine

institute: Yonsei University College of Medicine

description:
Library name: TN1406R1467
Column name in raw_counts_gene_49GC_cell_lines.xlsx: YCC-9

data_processing:
Sequencing reads were quality-checked using FastQC and trimmed with Trimmomatic. Clean reads were aligned to the human reference genome (hg19) using STAR (v2.7). Gene-level raw counts were generated with featureCounts (Subread v2.0.1) based on GENCODE gene annotation (release 38). No further normalization was applied before submission.
Assembly: hg19
Supplementary files format and content: excel file includes raw counts for each Sample

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen), quality-assessed with NanoDrop and Bioanalyzer.
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA integrity was assessed using the Agilent 2100 Bioanalyzer. Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit, including poly(A) mRNA enrichment, fragmentation, cDNA synthesis, adaptor ligation, and PCR amplification. Final libraries were quantified, pooled, and sequenced on an Illumina HiSeq 2500 platform (2 x 100 bp).


title: YCC-3/7

description:
Library name: TN1404R0747
Column name in raw_counts_gene_49GC_cell_lines.xlsx: YCC-3/7


title: MDAMB231_WT_H4_Input_rep2

description: Library name: Sample16

value: Human breast cancer


title: Regenerated pulp tissue; A1-cd24-pos-vivo

description: Library name: A1-cd24-pos-vivo


title: DN1_Primary human T cells_AIR-HA_DMSO

description:
Library name: Sample_3
Column name in raw_counts.txt: DN1_AIR


title: MDAMB468_H4K20me3_rep2

description: Library name: Sample14

value: Human breast cancer epithelial cell