title: Tumour, 100 mg/kg STC-15, 1 h, rep3

description:
Library name: TS1_3
rRNA depleted total RNA-seq


title: Ct_AML_K

status: Public on May 03 2026

type: SRA

city: New York

first: Bettina

last: Nadorp

state: NY

address: 500 1st Ave

department: Medicine/Pathology

country: USA

institute: NYU Langone Health

library_source: transcriptomic

data_processing:
RNA-seq data were processed using the EnFusion ensemble approach of seven fusion detection algorithms
Transcripts per million (TPM) values were generated from paired-end RNA sequence data using Salmon with bootstrapping set to 100
Assembly: Homo sapiens GRCh38.p12
Supplementary files format and content: HTSeq cov

molecule: total RNA

organism: Homo sapiens

source_name: bone marrow

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA-seq were prepared using TruSeq Stranded Total with Rebo Zero Gold library preparation kit following manufacturer's protocols.
Tumor derived RNA was subjected to 0.8x SPRI bead cleanup and size selection prior to DNase treatment and ribodepletion prior to using the NEBNext Ultra II Directional kit preparation. The library was constructed for whole transcriptome sequencing (RNA-seq). Paired-end 151-bp reads were generated on the Illumina NovaSeq (Illumina, Inc.)

tag: tissue

value: bone marrow


title: Tumour, Vehicle, 120 h, rep2

city: Cambridge

first: Harry

last: Fischl

address: Babraham Research Campus

country: United Kingdom

institute: Storm Therapeutics

description:
Library name: TV120_2
rRNA depleted total RNA-seq

data_processing:
Paired-end RNA-seq fastq files were trimmed of adapters using Trim Galore (Krueger et al., 2023) and then aligned to either the mouse GRCm39 genome using the STAR aligner (Dobin et al., 2013). Normalised bigwig tracks were generated by dividing the signal at each nucleotide by the total genome signal and multiplying by 1 billion.
Assembly: GRCm39
Supplementary files format and content: .bw files show normalized signal for positive and negative strands

organism: Mus musculus

source_name: Tumour

growth_protocol: Female C57Bl/6 mice (Envigo UK), were implanted subcutaneously (s.c.) on the left flank with 1x107 MC38 cells in serum free DMEM.  Tumours were measured three times weekly by digital calipers.

extract_protocol:
For RNA-seq, blood and tumour samples for were collected at termination. Up to 500 μL of blood was collected by cardiac puncture, stored in RNAprotect tubes (Qiagen, 76554) and left at RT. Tumours were cut in half, placed in cryovials and snap frozen.
RNA from in vivo whole blood and tumour samples were generated into RNA-seq libraries by Novogene using their rRNA-depletion strand-specific sequencing service. Blood samples were also depleted for Globin RNA. Libraries were sequenced to a depth of greater than 40 million PE150 reads on a NovaSeq X plus Illumina machine. Data from five biological replicates were collected for each in vivo condition.

treatment_protocol: Mice were randomised into 7 groups (5 mice/group). Six groups were orally dosed with 100 mg/kg STC-15 once daily, for sample collection at T=0, T=1h, T=4h, T=12h, T= 48h and T=120h. One group was orally dosed once daily with vehicle control, for sample collection at T=120h. The mice in the T=0 group received 6 treatment doses and were terminated 24h after the 6th dose. The mice in the other groups received 7 treatment doses and were collected at the indicated time following the 7th dose.

value: Tumour

tag: cell line

tag: cell type

value: C57BL6 murine colon adenocarcinoma cells

tag: treatment

value: Vehicle


title: Ct_Pt_D


title: Ct_AML_G


title: Ct_AML_F


title: Blood, 100 mg/kg STC-15, 48 h, rep3

description:
Library name: BS48_3
rRNA and Globin depleted total RNA-seq

source_name: Blood

value: Blood

value: 100 mg/kg QD STC-15


title: Ct_Pt_B


title: Blood, 100 mg/kg STC-15, 120 h, rep2

description:
Library name: BS120_2
rRNA and Globin depleted total RNA-seq


title: Blood, 100 mg/kg STC-15, 48 h, rep5

description:
Library name: BS48_5
rRNA and Globin depleted total RNA-seq


title: Ct_AML_H


title: Ct_AML_J


title: Ct_AML_E


title: Blood, 100 mg/kg STC-15, 120 h, rep3

description:
Library name: BS120_3
rRNA and Globin depleted total RNA-seq


title: Blood, 100 mg/kg STC-15, 120 h, rep1

description:
Library name: BS120_1
rRNA and Globin depleted total RNA-seq


title: Blood, 100 mg/kg STC-15, 120 h, rep4

description:
Library name: BS120_4
rRNA and Globin depleted total RNA-seq


title: Blood, 100 mg/kg STC-15, 120 h, rep5

description:
Library name: BS120_5
rRNA and Globin depleted total RNA-seq


title: EFO21 cells, DMSO, 24 h, rep1

description:
Library name: EFO21_DMSO_24h_rep1
GLORI on polyA+ RNA
mean_DMSO_m6A_proportion_ag20_m6ap25_EFO21_pos.bw
mean_DMSO_m6A_proportion_ag20_m6ap25_EFO21_neg.bw
data_table_m6a_proportion_table_filter_ag20_m6a25.csv

data_processing:
Read 1 fastq files of paired end reads were trimmed of adapters using cutadapt (-O 10 -m 20 –trimmed-only -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) (Martin, 2011). Reads with greater than 3 As were removed and As in remaining reads (indicative of m6A modification) were converted to Gs and aligned using the STAR aligner (--outFilterMultimapNmax 10 --outFilterMismatchNmax 2) (Dobin et al., 2013)  to a STAR index generated from the A-to-G converted sequences of the positive and reverse complemented negative strands of the GRCh38 genome and ensembl gene annotations. Reads were also aligned using the STAR aligner (--outFilterMultimapNmax 1 --outFilterMismatchNmax --alignIntronMin 1 --alignIntronMax 1 --alignEndsType EndToEnd) to a STAR index generated from A-to-G converted spike-in sequences. Previously converted A-to-G positions in aligned reads were converted back to As and the number of As and Gs were counted at each A position in the mRNA and lncRNA transcriptome using bcftools mpileup. The m6A proportion (A count/(A + G count)) at each site was then calculated. For each comparison the mean m6A proportion and mean A + G count across both replicates has to be greater or equal to 0.25 and 20, respectively, across all samples being compared. “MANE Select” canonical transcript exon annotations were used to determine the m6A levels in particular exon types.
Assembly: GRCh38
Supplementary files format and content: .bw files show m6A proportions for positive and negative strands
Supplementary files format and content: data_table_m6a_proportion_table_filter_ag20_m6a25.csv.zip

molecule: polyA RNA

extract_protocol:
GLORI (glyoxal and nitrite-mediated deamination of unmethylated adenosines) sequencing was carried out as described in Liu et al., 2023. Total RNA was purified by adding Trizol directly to cultured cells and then extracting RNA using Qiagen miRNeasy columns according to the manufacturer’s instructions including a DNase treatment step on column. Polyadenylated RNA was purified from 7.5 μg total RNA using the NEBNext PolyA mRNA magnetic isolation module (NEB E7490) according to the manufacturer's instructions but eluting in 18 μl nuclease-free water and fragmented by incubating (8 min, 94 °C) with 2 μl 10x NEBNext RNA fragmentation buffer. The fragmentation reaction was stopped by adding 2 μl 10x NEBNext RNA fragmentation stop solution and RNAs were purified using an RNA clean and concentrator column (Zymo, R1015) eluting in 14 μl. 1 ng of spike-in probe mix consisting of 5 different sequences each with an m6A modification site modified to 5, 20, 50, 80 or 100 % was added to each sample. To convert unmodified A positions to Gs, RNA was first incubated (30 min, 50 °C) with 6 μl glyoxal solution (8.8 M in H2O, Sigma, 50649-25 ml) and 20 μl DMSO and then incubated (30 min, 50 °C) with 10 μl saturated H3BO3 and finally incubated (8h, 16 °C) with 50 μl deamination buffer (750 mM NaNO2, 40 mM MES pH 6, 10 μl glyoxal solution [8.8 M in H20]). RNAs were precipitated by incubating (overnight, -80 °C) with 300 μl ethanol and 1.5 μl Glycoblue (ThermoFisher, AM9515) and centrifuging (20000g, 30 min, 4°C). RNA pellets were washed, dried, incubated (10 min, 95 °C) with 50 μl deprotection buffer (25 μl 1 M TEAA pH 8.6, 22.5 μl formamide) and purified using an RNA clean and concentrator column. RNA was incubated (30 min, 37 °C) with 5 μl T4 PNK buffer, 5 μl ATP, 1 μl Superase.In, 2 μl T4 PNK in a final 50 μl volume.
RNAs were purified using an RNA clean and concentrator column, eluting in 6 μl, and generated into libraries for sequencing using the NEBNext multiplex small RNA library kit for Illumina according to the manufacturer’s instructions. Final libraries were pooled and size-selected by gel electrophoresis selecting for bands from 160-250 bp. Libraries were sequenced to a depth of greater than 100 million PE150 reads on a NovaSeq X plus Illumina machine.

treatment_protocol: A549, CAOV3, COV644, EFO21, OE21 and SKOV3 treated with DMSO and CAOV3 cells treated with 1 uM STM3675 for 24h

value: Ovarian carcinoma

value: DMSO 24h


title: OE21 cells, DMSO, 24 h, rep2

description:
Library name: OE21_DMSO_24h_rep2
GLORI on polyA+ RNA
mean_DMSO_m6A_proportion_ag20_m6ap25_OE21_pos.bw
mean_DMSO_m6A_proportion_ag20_m6ap25_OE21_neg.bw
data_table_m6a_proportion_table_filter_ag20_m6a25.csv

value: Oesophageal carcinoma


title: EFO21 cells, DMSO, 24 h, rep2

description:
Library name: EFO21_DMSO_24h_rep2
GLORI on polyA+ RNA
mean_DMSO_m6A_proportion_ag20_m6ap25_EFO21_pos.bw
mean_DMSO_m6A_proportion_ag20_m6ap25_EFO21_neg.bw
data_table_m6a_proportion_table_filter_ag20_m6a25.csv


title: SKOV3 cells, DMSO, 24 h, rep1

description:
Library name: SKOV3_DMSO_24h_rep1
GLORI on polyA+ RNA
mean_DMSO_m6A_proportion_ag20_m6ap25_SKOV3_pos.bw
mean_DMSO_m6A_proportion_ag20_m6ap25_SKOV3_neg.bw
data_table_m6a_proportion_table_filter_ag20_m6a25.csv


title: CAOV3 cells, STM3675, 24 h, rep2

description:
Library name: CAOV3_STM3675_24h_rep2
GLORI on polyA+ RNA
mean_STM3675_m6A_proportion_ag20_m6ap25_CAOV3_pos.bw
mean_STM3675_m6A_proportion_ag20_m6ap25_CAOV3_neg.bw
data_table_m6a_proportion_table_filter_ag20_m6a25.csv


title: SKOV3 cells, DMSO, 24 h, rep2

description:
Library name: SKOV3_DMSO_24h_rep2
GLORI on polyA+ RNA
mean_DMSO_m6A_proportion_ag20_m6ap25_SKOV3_pos.bw
mean_DMSO_m6A_proportion_ag20_m6ap25_SKOV3_neg.bw
data_table_m6a_proportion_table_filter_ag20_m6a25.csv


title: COV644 cells, DMSO, 24 h, rep2

description:
Library name: COV644_DMSO_24h_rep2
GLORI on polyA+ RNA
mean_DMSO_m6A_proportion_ag20_m6ap25_COV644_pos.bw
mean_DMSO_m6A_proportion_ag20_m6ap25_COV644_neg.bw
data_table_m6a_proportion_table_filter_ag20_m6a25.csv


title: OE21 cells, DMSO, 24 h, rep1

description:
Library name: OE21_DMSO_24h_rep1
GLORI on polyA+ RNA
mean_DMSO_m6A_proportion_ag20_m6ap25_OE21_pos.bw
mean_DMSO_m6A_proportion_ag20_m6ap25_OE21_neg.bw
data_table_m6a_proportion_table_filter_ag20_m6a25.csv


title: CAOV3 cells, STM3675, 24 h, rep1

description:
Library name: CAOV3_STM3675_24h_rep1
GLORI on polyA+ RNA
mean_STM3675_m6A_proportion_ag20_m6ap25_CAOV3_pos.bw
mean_STM3675_m6A_proportion_ag20_m6ap25_CAOV3_neg.bw
data_table_m6a_proportion_table_filter_ag20_m6a25.csv


title: Pt_8_BM


title: Blood, 100 mg/kg STC-15, 48 h, rep1

description:
Library name: BS48_1
rRNA and Globin depleted total RNA-seq


title: Tumour, Vehicle, 120 h, rep1

description:
Library name: TV120_1
rRNA depleted total RNA-seq


title: Ct_Pt_C


title: COV644 cells, DMSO, 24 h, rep1

description:
Library name: COV644_DMSO_24h_rep1
GLORI on polyA+ RNA
mean_DMSO_m6A_proportion_ag20_m6ap25_COV644_pos.bw
mean_DMSO_m6A_proportion_ag20_m6ap25_COV644_neg.bw
data_table_m6a_proportion_table_filter_ag20_m6a25.csv


title: CAOV3 cells, DMSO, 24 h, rep2

description:
Library name: CAOV3_DMSO_24h_rep2
GLORI on polyA+ RNA
mean_DMSO_m6A_proportion_ag20_m6ap25_CAOV3_pos.bw
mean_DMSO_m6A_proportion_ag20_m6ap25_CAOV3_neg.bw
data_table_m6a_proportion_table_filter_ag20_m6a25.csv


title: CAOV3 cells, DMSO, 24 h, rep1

description:
Library name: CAOV3_DMSO_24h_rep1
GLORI on polyA+ RNA
mean_DMSO_m6A_proportion_ag20_m6ap25_CAOV3_pos.bw
mean_DMSO_m6A_proportion_ag20_m6ap25_CAOV3_neg.bw
data_table_m6a_proportion_table_filter_ag20_m6a25.csv


title: Blood, 100 mg/kg STC-15, 24 h, rep5

description:
Library name: BS24_5
rRNA and Globin depleted total RNA-seq


title: Pt_20_MS

source_name: myeloid sarcoma

value: myeloid sarcoma

tag: tissue site

value: sigmoid colon mass


title: A549 cells, DMSO, 24 h, rep2

description:
Library name: A549_DMSO_24h_rep2
GLORI on polyA+ RNA
mean_DMSO_m6A_proportion_ag20_m6ap25_A549_pos.bw
mean_DMSO_m6A_proportion_ag20_m6ap25_A549_neg.bw
data_table_m6a_proportion_table_filter_ag20_m6a25.csv

value: Lung carcinoma


title: A549 cells, DMSO, 24 h, rep1

description:
Library name: A549_DMSO_24h_rep1
GLORI on polyA+ RNA
mean_DMSO_m6A_proportion_ag20_m6ap25_A549_pos.bw
mean_DMSO_m6A_proportion_ag20_m6ap25_A549_neg.bw
data_table_m6a_proportion_table_filter_ag20_m6a25.csv


title: Pt_9A_MS

value: maxilla


title: Pt_16_MS

value: sphenoid; sellar; suprasellar tissue


title: Blood, 100 mg/kg STC-15, 24 h, rep3

description:
Library name: BS24_3
rRNA and Globin depleted total RNA-seq


title: Nasal-TT-M3

first: Stefan

last: Worgall

state: New York

address: 413 East 69th Street

department: Pediatrics

institute: NewYork Presbyterian- Weill Cornell Medicine

description: Library name: Nasal-TT-M3

data_processing:
The raw sequencing reads in BCL format were processed through bcl2fastq 2.20 (Illumina) for FASTQ conversion and demultiplexing.
After trimming the adaptors with cutadapt (version1.18), RNA reads were aligned and mapped to the GRCh38 human reference genome by STAR (Version2.7.10).
Raw read counts per gene were extracted using HTSeq-count v0.13.5. Differential gene expression analysis was performed using R package limma voom with an interaction model (genome type vs. cell type) for multi-level experimental designs.
To model the within-subject variability, we treated donor as a random effect using limma’s duplicatedCorrelation function. Three contrasts were designed to reported differential gene expression, which were (1) “Nasal_CC_vs_TT”: expression of CC genotype – expression of TT genotype in nasal cells; (2) “PBMC_CC_vs_TT”: expression of CC genotype – expression of TT genotype in PBMCs; (3) “SourceDiff_CC_vs_TT”: “PBMC_CC_vs_TT” – “Nasal_CC_vs_TT”, i.e., the interaction term.
GSEA analysis of KEGG pathways was performed using R package fgsea, R packages ggplot2 and ComplexHeatmap were used to produce related figures
Assembly: GRCh38
Supplementary files format and content: text file includes raw counts for each sample
Supplementary files format and content: xlxs file includes FPKM values for each sample

source_name: Nasal

growth_protocol: The brushed primary nasal epithelial cells were seeded in 12-well plates pre-coated with bovine type I collagen in PneumaCult-Ex Plus medium (STEMCELL) with 50 IU/mL PenStrep, 50µg/mL of Gentamicin and 1.25µg/mL of Amphotericin B at 37 °C under a 5% CO2 atmosphere. The cells were propagated once to expand the basal cell progenitors, and the sub-cultured cells were maintained in the PneumaCult-Ex Plus medium until semi-confluent. To initiate mucociliary differentiation at the air-liquid interface (ALI), 150,000 cells were seeded onto Transwell 0.4µm Pore Polyester Membrane 6.5mm inserts pre-coated with human type IV collagen. The seeded cells were submerged in PneumaCult-Ex Plus medium until the cells were completely confluent and then air-lifted by removing media in the upper chambers and switching media in the lower chambers to PneumaCult ALI maintenance medium (STEMCELL). The cells were cultured at ALI for 4 weeks until beating cilia and mucous production were observed by light microscopy. PBMCs were isolated from whole blood by density gradient centrifugation using Lymphoprep (STEMCELL).

extract_protocol:
The fully differentiated cells on the inserts were washed three times with PBS and then lysed in TRIzol (Invitrogen) for RNA extraction. The isolated PBMCs were frozen in a BamBanker cell freezing medium (Bulldog Bio). The stored PBMCs were thawed in RPMI medium and washed with PBS and then lysed in TRIzol for RNA extraction. Total RNA was extracted using chloroform phase separation followed by purification using Direct-zol RNA Microprep (Zymo Research) according to the manufacturer’s instructions. The samples were all DNaseI treated.
PBMC RNAseq libraries of polyadenylated RNA were prepared using the NEB Ultra II Directional RNA Library Prep following manufacturer’s ptotocols. Nasal cell RNAseq libraries of polyadenylated RNA were prepared using the Illumina Stranded mRNA Prep following manufacturer’s ptotocols.

value: Nasal

tag: genotype

value: TT

tag: Sex

value: Male


title: Pt_8_MS-4

value: common bile duct


title: Nasal-TT-F2

description: Library name: Nasal-TT-F2

value: Female


title: Nasal-CC-M3

description: Library name: Nasal-CC-M3

value: CC


title: Nasal-TT-M2

description: Library name: Nasal-TT-M2


title: Pt_8_MS-3


title: Blood, 100 mg/kg STC-15, 24 h, rep2

description:
Library name: BS24_2
rRNA and Globin depleted total RNA-seq


title: Pt_10_MS

value: stomach


title: Nasal-TT-F3

description: Library name: Nasal-TT-F3


title: Blood, 100 mg/kg STC-15, 24 h, rep1

description:
Library name: BS24_1
rRNA and Globin depleted total RNA-seq

value: Blood


title: Nasal-CC-M1

description: Library name: Nasal-CC-M1


title: Nasal-TT-F1

description: Library name: Nasal-TT-F1


title: Nasal-TT-M1

description: Library name: Nasal-TT-M1


title: Nasal-CC-M2

description: Library name: Nasal-CC-M2


title: Blood, 100 mg/kg STC-15, 12 h, rep4

description:
Library name: BS12_4
rRNA and Globin depleted total RNA-seq

value: 100 mg/kg QD STC-15


title: Nasal-CC-F3

description: Library name: Nasal-CC-F3


title: Nasal-CC-F2

description: Library name: Nasal-CC-F2


title: Pt_2_MS

value: breast mass


title: Nasal-CC-F1

description: Library name: Nasal-CC-F1


title: Blood, 100 mg/kg STC-15, 12 h, rep3

description:
Library name: BS12_3
rRNA and Globin depleted total RNA-seq


title: Pt_8_MS-2


title: PBMC-TT-M3

description: Library name: PBMC-TT-M3

source_name: PBMC

value: PBMC


title: PBMC-TT-M2

description: Library name: PBMC-TT-M2


title: Pt_8_MS-1


title: Ct_AML_I

value: bone marrow


title: Blood, 100 mg/kg STC-15, 12 h, rep2

description:
Library name: BS12_2
rRNA and Globin depleted total RNA-seq


title: Blood, 100 mg/kg STC-15, 12 h, rep1

description:
Library name: BS12_1
rRNA and Globin depleted total RNA-seq


title: PBMC-CC-M2

description: Library name: PBMC-CC-M2


title: Blood, 100 mg/kg STC-15, 4 h, rep5

description:
Library name: BS4_5
rRNA and Globin depleted total RNA-seq


title: PBMC-CC-M3

description: Library name: PBMC-CC-M3


title: PBMC-CC-F3

description: Library name: PBMC-CC-F3


title: Blood, 100 mg/kg STC-15, 4 h, rep4

description:
Library name: BS4_4
rRNA and Globin depleted total RNA-seq


title: PBMC-TT-F3

description: Library name: PBMC-TT-F3


title: PBMC-CC-M1

description: Library name: PBMC-CC-M1


title: PBMC-TT-F1

description: Library name: PBMC-TT-F1


title: NCM460 TRIB3-OE-3

city: Beijing

first: jing

last: liu

address: tian qiao

country: China

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: mucosal epithelial cells

value: TRIB3 overexprssion


title: PBMC-TT-M1

description: Library name: PBMC-TT-M1


title: PBMC-TT-F2

description: Library name: PBMC-TT-F2


title: Blood, 100 mg/kg STC-15, 4 h, rep2

description:
Library name: BS4_2
rRNA and Globin depleted total RNA-seq


title: Blood, 100 mg/kg STC-15, 24 h, rep4

description:
Library name: BS24_4
rRNA and Globin depleted total RNA-seq


title: NCM460 TRIB3-OE-2


title: NCM460 Ctrl-3

value: Control


title: Blood, 100 mg/kg STC-15, 4 h, rep3

description:
Library name: BS4_3
rRNA and Globin depleted total RNA-seq


title: OCI/AML3_3

type: RNA

city: Hangzhou

first: Jingbo

last: Lai

address: Xihu district

institute: Zhejiang University

description: lncRNA expression

hyb_protocol: Labeled cRNA hybridized at 65°C for 17 hours with rolling agitation.

scan_protocol: Slides washed and scanned using Agilent Scanner G5761A to obtain raw images.

data_processing:
Raw images processed by Feature Extraction; quantile normalization, filtering (≥80% Detected in one group), t-test (p≤0.05), GO/KEGG enrichment, unsupervised hierarchical clustering with heatmap.
Raw signal, normalized signal, detection call (Detected/Not Detected), and detailed annotation from Genespring output.

source_name: exosomes

label_protocol: 250 ng purified RNA reverse-transcribed to cDNA using AffinityScript-RT and Promoter Primer, second-strand synthesized, cRNA amplified with T7 RNA polymerase and labeled with Cyanine-3-CTP, then purified.

extract_protocol: Total RNA extracted using Trizol (Invitrogen), quantified by NanoDrop ND-2000, integrity assessed by Agilent Bioanalyzer 2100, then purified with QIAGEN RNeasy Kit.

value: exosomes


title: PBMC-CC-F2

description: Library name: PBMC-CC-F2


title: OCI/AML3_1

description: lncRNA expression


title: OCI/AML3_2

description: lncRNA expression


title: NCM460 TRIB3-OE-1


title: NCM460 Ctrl-1


title: Blood, 100 mg/kg STC-15, 1 h, rep5

description:
Library name: BS1_5
rRNA and Globin depleted total RNA-seq


title: Blood, 100 mg/kg STC-15, 4 h, rep1

description:
Library name: BS4_1
rRNA and Globin depleted total RNA-seq


title: Blood, 100 mg/kg STC-15, 48 h, rep2

description:
Library name: BS48_2
rRNA and Globin depleted total RNA-seq


title: control_2

description: lncRNA expression


title: PBMC-CC-F1

description: Library name: PBMC-CC-F1


title: Blood, 100 mg/kg STC-15, 1 h, rep4

description:
Library name: BS1_4
rRNA and Globin depleted total RNA-seq


title: Patient7

city: Miami

first: Shanta

last: Dhar

state: Florida

address: 1011 NW 15th Street, Room 437

department: Biochemistry

institute: University of Miami

description:
Newly Diagnosed Patient 7
Patient 5-7_count.csv
Patient 5-7_fpkm.csv

data_processing:
Quality Control and adapter trimming was performed with FastQC and fastp. The filtered clean reads were mapped to reference genome by HISAT2. HTseq-count was used to quantify transcripts and gene expression levels using mapped reads’ positional information on the reference genome and we used DESeq to analyze the Differentially Expressed Genes (DEGs) for samples with biological replicates. Functional annotation for DEGs was performed with HMMER, DIAMOND, EggNOG-mapper, clusterProfiler and KofamKOALA. Gene Ontology (GO) and Kyoto Encycloepedia of Genes and Genomes (KEGG) analysis was done with clusterProfiler and KofamKOALA.
Assembly: hg38
Supplementary files format and content: Text file include raw counts and fpkm for each sample

source_name: Cancer tissue

growth_protocol: The isolated patient derived glioblastoma stem cells (GSCs) of varied background were grown in serum free glioma neural stem cell (GNS) media. The GNS media was prepared using additional components and supplements. Firstly, the N2 supplement was prepared using 7.5% solution of bovine serum albumin (BSA) fraction V, 25 mg/mL human-recombinant insulin reconstituted in 0.01 M HCl, 100 mg/mL apo-transferrin, 0.6 mg/mL progesterone reconstituted in ethanol, 160 mg/mL putrescine, and 3 mM sodium selenite. All the components were dissolved in DMEM:F12 medium. To prepare the complete growth medium for the patient derived GSCs, neurocult NS-A basal media was externally supplemented with 2% B27 supplement, 1% prepared N2 supplement, 1% penicillin/streptomycin, 1% L-glutamine, 1% sodium pyruvate, 20 ng/mL EGF, and 20 ng/mL bFGF. For the patient derived GSCs to grow as adherent single layer cell culture, an additional laminin coating of the tissue culture vessel is required. Laminin coating was prepared at 10 μg/mL concentration in 1X PBS and the vessels were coated for at least 3 h at 37 °C. The GSCs were routinely passaged using accutase and were splitted at a ratio of 1:3 or 1:5. Usually these cells become confluent within 3-5 days depending upon the cell density.

extract_protocol:
RNeasy Mini Kit
Total RNA proceeds to library construction. The Poly-A containing mRNA molecules are purified using poly-T oligo attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. Cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA. Adapter ligation prepares the ds cDNA for hybridization onto a flow. The products are enriched with PCR and purified to create the final cDNA library. Final library was quantified and library quality was evaluated by TapeStation D1000 ScreenTape. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina NovaSeq S4 with a read length configuration of 150 PE for 20M PE reads per sample (20M in each direction)
TruSeq Stranded mRNA Library

treatment_protocol: Tissues obtained from patient tumor were direclty used for RNA sequencing for Patient 5, Patient 6 and Patient 7

value: Cancer tissue

value: GBM cancer tissue

value: Glioblastoma cell

value: WT


title: NCM460 Ctrl-2


title: Patient 6

description:
Recurrent Patient 6
Patient 5-7_count.csv
Patient 5-7_fpkm.csv


title: control_3

description: lncRNA expression


title: control_1

description: lncRNA expression


title: Liver,white-type,rep3

city: Harbin

first: Yicheng

last: Duan

address: No.26 Hexing Road, Xiangfang District, Harbin, P.R.China

institute: Northeast Forestry University

description:
Library name: Sample 27
RD_W_L3

data_processing:
Raw reads in FASTQ format were processed using Trimmomatic to remove reads containing poly-N sequences and low-quality reads, yielding clean reads.
Clean reads were de novo assembled into transcripts using Trinity (v2.4) with the paired-end method. Based on sequence similarity and length, the longest transcript for each locus was selected as a unigene for downstream analyses.
Unigene functional annotation was performed by alignment against NCBI non-redundant (NR), Swiss-Prot, eggNOG, and KOG databases using DIAMOND with an E-value threshold of 1e-5. Unigenes were also mapped to the KEGG database for pathway annotation. Gene Ontology (GO) classification was derived from Swiss-Prot to GO term mappings.
Bowtie2 was used to align clean reads from each sample to the assembled unigenes. Expression levels (FPKM) were quantified using eXpress software. Read counts per unigene were obtained for differential expression analysis.
Differential expression analysis between color morphs within each tissue was performed using DESeq2. Significantly differentially expressed unigenes (DEGs) were defined with q-value < 0.05 and log2FoldChange > 1 (fold change > 2).
Supplementary files format and content: raw read counts and gene annotation for each sample.
Supplementary files format and content: FPKM normalized expression values and gene annotation for each sample.

organism: Rana dybowskii

source_name: Liver

extract_protocol:
TRlzol
Sequencing libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme) following the manufacturer's protocol. Library quality was validated on an Agilent 2100 Bioanalyzer. The libraries were sequenced on the Illumina NovaSeq 6000 platform, generating 150 bp paired-end reads. Transcriptome sequencing and analysis were performed by OE Biotech Co., Ltd. (Shanghai, China).

value: Liver

tag: body color_morphs

value: white-type


title: Liver,white-type,rep1

description:
Library name: Sample 25
RD_W_L1


title: Liver,white-type,rep2

description:
Library name: Sample 26
RD_W_L2


title: Skin(back),white-type,rep3

description:
Library name: Sample 24
RD_W_B3

source_name: Skin of back

value: Skin of back


title: Blood, 100 mg/kg STC-15, 1 h, rep3

description:
Library name: BS1_3
rRNA and Globin depleted total RNA-seq


title: Patient 5

description:
Recurrent Patient 5
Patient 5-7_count.csv
Patient 5-7_fpkm.csv


title: Skin(back),white-type,rep2

description:
Library name: Sample 23
RD_W_B2


title: GSC1R

description:
Recurrent Patient 1
ALL_FPKM.csv

source_name: Cancer stem cells

value: Cancer stem cells

value: Patient 1 derived glioblastoma stem cells

value: Glioblastoma stem cell


title: oviduct,white-type,rep3

description:
Library name: Sample 21
RD_W_O3

source_name: oviduct

value: oviduct


title: Skin(back),white-type,rep1

description:
Library name: Sample 22
RD_W_B1


title: Blood, 100 mg/kg STC-15, 1 h, rep1

description:
Library name: BS1_1
rRNA and Globin depleted total RNA-seq

value: Blood

value: 100 mg/kg QD STC-15


title: GSC2R

description:
Recurrent Patient 2
ALL_FPKM.csv

value: Patient 2 derived glioblastoma stem cells


title: Pt_24_MS

value: myeloid sarcoma

value: axillary LN


title: Liver,black-type,rep2

description:
Library name: Sample 17
RD_B_L2

value: black-type


title: Blood, 100 mg/kg STC-15, 1 h, rep2

description:
Library name: BS1_2
rRNA and Globin depleted total RNA-seq


title: Blood, Vehicle, 120 h, rep3

description:
Library name: BV120_3
rRNA and Globin depleted total RNA-seq

value: Vehicle


title: Liver,black-type,rep3

description:
Library name: Sample 18
RD_B_L3


title: Blood, 100 mg/kg STC-15, 12 h, rep5

description:
Library name: BS12_5
rRNA and Globin depleted total RNA-seq


title: GSC4N

description:
Newly Diagnosed Patient 4
ALL_FPKM.csv

value: Patient 4 derived glioblastoma stem cells


title: Blood, Vehicle, 120 h, rep5

description:
Library name: BV120_5
rRNA and Globin depleted total RNA-seq


title: Blood, Vehicle, 120 h, rep2

description:
Library name: BV120_2
rRNA and Globin depleted total RNA-seq


title: GSC3N

description:
Newly Diagnosed Patient 3
ALL_FPKM.csv

value: Patient 3 derived glioblastoma stem cells


title: oviduct,white-type,rep1

description:
Library name: Sample 19
RD_W_O1


title: AMLMSPB3052_AMLMSPB3268_AMLMSPB2922

description:
Single Cell RNAseq, CITEseq
library name:: 2021-11-09-MS-PB
hashed library - hastag annotation can be found in feature_ref.csv file

library_source: transcriptomic single cell

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment to GRCh38 (version 5.0.1) was performed with 10x Genomics Cell Ranger Single Cell Gene Expression Software (version 2020-A).
HTOs each cell were normalized using a centered log ratio (CLR) transformation across cells.
Samples were demultiplexed based on HTOs using the HTODemux function in Seurat.
3' libraries were filtered for incorrectly assigned hash tags using Souporcell, doublet filtered using scDblFinder, and ambient RNA contamination was removed using SoupX.  Please see publication for detailed processing steps.
Assembly: hg38

source_name: peripheral blood

extract_protocol:
Cryopreserved bone marrow aspirates were obtained from Ohio State University’s sample bank. All subjects provided written consent for banking and research use of these specimens, in accordance with the regulations of the institutional review boards of all participating institutes. Frozen human bone marrow samples were thawed and transferred into 50mL conical tubes containing PBS + 2% fetal bovine serum (FBS). Cell suspensions were centrifuged at 350 x g for 5 minutes at 4C, and the supernatant was discarded. Samples were then subjected to dead cell depletion, using a dead cell removal kit (Miltenyi Biotec, 130-090-101), or stained with DAPI (0.5mg/mL) and sorted for live cells (DAPIlow), using a FACSAria IIu SORP cell sorter (BD Biosciences). For cell sorting, all samples were gated based on forward and side scatter, followed by doublet exclusion, and then gated on DAPIlow for viable cells. Samples were sorted into 5mL poly-propylene tubes containing 300mL ice-cold PBS + 2% FBS. Following cell sorting, samples were centrifuged at 350 x g for 5 minutes at 4C. For CITE-seq, enriched live cells were first tagged with cell-hashing oligo-tagged antibodies (Biolegend) according to the manufacturer’s instructions. Samples were than counted, and a maximum of 105 cells for each sample was pooled together and stained with a CITE-Seq antibody cocktail (Biolegend) according to the manufacturer’s instructions. For scTCR-Seq, T cells were enriched using a pan T cell isolation kit (Miltenyi Biotec, 130-096-535) or sorted for live CD45+ CD3+ cells. For cell sorting, samples were stained with PerCP-conjugated anti-human CD45 (1:400, Biolegend, 304025), FITC-conjugated anti-human CD3 (1:100, Biolegend,  300452). And DAPI (0.5mg/mL). Sorted samples were gated based on forward and side scatter, followed by doublet exclusion and then gated on DAPIlow for viable cells. CD45+ CD3+ cells were sorted into 5mL poly-propylene tubes containing 300mL ice-cold PBS + 2% FBS. Following cell sorting, samples were centrifuged at 350 x g for 5 minutes at 4C. Libraries were prepared using the Chromium Single Cell 3’ Reagent Kits (v3 and v3.1, CITE-Seq).  Hashtag and antibody-derived tag (ADT) libraries were prepared according to the New York Genome Center CITE-Seq and hashing protocol (https://citeseq.files.wordpress.com/2019/02/cite-seq_and_hashing_protocol_190213.pdf). Libraries were run on an Illumina NovaSeq 6000.
Chromium Single Cell 3’ Reagent Kits (v3 )

value: peripheral blood

value: mononuclear cells


title: oviduct,black-type,rep3

description:
Library name: Sample 12
RD_B_O3


title: Blood, Vehicle, 120 h, rep4

description:
Library name: BV120_4
rRNA and Globin depleted total RNA-seq


title: oviduct,white-type,rep2

description:
Library name: Sample 20
RD_W_O2

value: white-type


title: Skin(back),black-type,rep1

description:
Library name: Sample 13
RD_B_B1_S3723252

value: Skin of back


title: Blood, Vehicle, 120 h, rep1

description:
Library name: BV120_1
rRNA and Globin depleted total RNA-seq


title: Liver,black-type,rep1

description:
Library name: Sample 16
RD_B_L_1

value: Liver


title: Skin(back),black-type,rep3

description:
Library name: Sample 15
RD_B_B3


title: Skin(back),black-type,rep2

description:
Library name: Sample 14
RD_B_B2_S3723253


title: MSBM0648_MSBM2011_MSBM1504_AMLMSPB2010

description:
Single Cell RNAseq, CITEseq
library name:: 2021-11-09-MS-BM-PB
hashed library - hastag annotation can be found in feature_ref.csv file

source_name: bone marrow / peripheral blood

value: bone marrow / peripheral blood


title: Liver,red-type,rep3

description:
Library name: Sample 9
RD_R_L3

value: red-type


title: Skin(back),red-type,rep3

description:
Library name: Sample 6
RD_R_B3


title: AMLMSPB5726

description:
Single Cell RNAseq, CITEseq
library name:: 2021-11-09-AMLMS5726


title: oviduct,black-type,rep2

description:
Library name: Sample 11
RD_B_O2

value: oviduct


title: twist mutant head (neoplasm-like) replicate 3

city: Vienna

first: Patricio

last: Ferrer Murguia

state: Vienna

address: Djerassiplatz 1

country: Austria

institute: University of Vienna

description: Library name: twist_neoplasm_rep3

data_processing:
Sequencing reads were aligned to the Nematostella vectensis genome (Zimmermann et al., 2023) using a standard RNA-seq alignment pipeline. Gene-level read counts were generated using featureCounts v2.0.0 with the Nematostella vectensis NV2 gene annotation. Differential gene expression analysis was performed using the edgeR package in R. Downstream analyses and visualizations were carried out using custom R scripts.
Assembly: Nematostella vectensis genome assembly NV2 (Zimmermann et al., 2023)
Supplementary files format and content: Tab-delimited text file containing gene-level raw read counts generated using featureCounts

organism: Nematostella vectensis

source_name: head (including tentacles)

extract_protocol:
Bulk RNA-seq libraries were prepared from head tissue (including tentacles) of Nematostella vectensis wild-type animals and twist mutants exhibiting neoplasm-like development. RNA was extracted from three biological replicates per condition. Libraries were sequenced as paired-end reads on an Illumina platform.
Libraries for bulk RNA-seq were prepared from total RNA extracted from head tissue (including tentacles) of Nematostella vectensis wild-type and twist mutant animals, following standard library preparation protocols for Illumina sequencing.

value: head (including tentacles)

value: twist-/-

value: neoplasm-like phenotype


title: MS0137

description:
Single Cell RNAseq, CITEseq
library name:: 2021-02-05-MS0137

value: myeloid sarcoma


title: oviduct,red-type,rep3

description:
Library name: Sample 3
RD_R_O3


title: oviduct,black-type,rep1

description:
Library name: Sample 10
RD_B_O1_S3723251


title: twist mutant head (neoplasm-like) replicate 2

description: Library name: twist_neoplasm_rep2


title: oviduct,red-type,rep2

description:
Library name: Sample 2
RD_R_O2


title: Liver,red-type,rep2

description:
Library name: Sample 8
RD_R_L2


title: WT head tissue replicate 1

description: Library name: WT_head_rep1

value: wild-type

value: control


title: AMLMS1053 library 3

description:
Single Cell RNAseq, CITEseq
library name:: 2021-03-09-Z-1-3
hashed library - hastag annotation can be found in feature_ref.csv file, hashtag marked as AMLD=AMLMS0114, and AMLD_R=AMLMS1053

value: bone marrow


title: AMLMS1053 library 1

description:
Single Cell RNAseq, CITEseq
library name:: 2021-03-09-Z-1-1
hashed library - hastag annotation can be found in feature_ref.csv file, hashtag marked as AMLD=AMLMS0114, and AMLD_R=AMLMS1053


title: WT head tissue replicate 3

description: Library name: WT_head_rep3


title: Skin(back),red-type,rep2

description:
Library name: Sample 5
RD_R_B2


title: twist mutant head (neoplasm-like) replicate 1

description: Library name: twist_neoplasm_rep1


title: AMLMS1053 library 2

description:
Single Cell RNAseq, CITEseq
library name:: 2021-03-09-Z-1-2
hashed library - hastag annotation can be found in feature_ref.csv file, hashtag marked as AMLD=AMLMS0114, and AMLD_R=AMLMS1053


title: Tooth germ, gene modification, Edarfl/fl, rep1

city: Shanghai

first: Wenyu

last: Xu

address: 500 Quxi Road

department: Department of second dental center

institute: Shanghai ninth people's hospital

description:
Library name: Sample 1
single cell RNA-Seq

data_processing:
The feature-barcode matrices were obtained by aligning reads to the mouse genome (mm10) using STARsolo with default parameter
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tooth germ

extract_protocol:
The tissue samples were processed as described below. Briefly, samples were first washed with 1640 culture solution, minced into small pieces (approximately 1mm3) on ice and enzymatically digested with 1mg/ml Collagenase I , 0.5mg/ml Collagenase II, 0.4% 1mg/ml Dispase, 50U/mL DNase I for 30~40 min at 37°C, the supernatant was added to an equal volume of 1640 culture solution containing 10% FBS to terminate digestion; After digestion, samples were sieved through a 70µm cell strainer. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec) to lyse red blood cells. Dissociated single cells were then stained with AO/PI for viability assessment using Countstar Fluorescence Cell Analyzer. The single-cell suspension was further enriched with a MACS dead cell removal kit (Miltenyi Biotec).
BD Rhapsody system  were used to capture the single cells and construct the scRNA-Seq libraries

value: tooth germ


title: Skin(back),red-type,rep1

description:
Library name: Sample 4
RD_R_B1


title: NOZ cells, control, biological replicate 1

city: shanghai

first: Jun

last: Chen

state: shanghai

address: renji hostipial

institute: shanghai jiao tong university

description: Library name: NOZ-NC1

data_processing:
CLC Genomics Workbench y 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: NOZ

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for theconstruction of sequencing libraries.
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kitfollowing manufacturer's protocols

value: NOZ

value: gallbladder cancer cells

value: WT

value: adipogenic differentiation


title: NOZ cells, ETBF-infected, biological replicate 2

description: Library name: NOZ-ET2

value: ETBF-infected


title: NOZ cells, ETBF-infected, biological replicate 3

description: Library name: NOZ-ET3


title: WT head tissue replicate 2

description: Library name: WT_head_rep2


title: oviduct,red-type,rep1

description:
Library name: Sample 1
RD_R_O1_S3723254


title: Tooth germ, gene modification, K14cre;Edarfl/fl, rep1

description:
Library name: Sample 2
single cell RNA-Seq


title: MSBM5433_AMLMS5710

description:
Single Cell RNAseq, CITEseq
library name:: 2020-06-24-MSBM5433_AMLMS5710_0.90
hashed library - hastag annotation can be found in feature_ref.csv file

source_name: bone marrow

value: mononuclear cells


title: NOZ cells, control, biological replicate 3

description: Library name: NOZ-NC3


title: NOZ cells, control, biological replicate 2

description: Library name: NOZ-NC2


title: MS5433 library 1

description:
Single Cell RNAseq, CITEseq
library name:: 2019-10-16-MS5433


title: NOZ cells, ETBF-infected, biological replicate 1

description: Library name: NOZ-ET1


title: MS5433 library 2

description:
Single Cell RNAseq, CITEseq
library name:: 2020-03-18-MS5433


title: CD8 T cells with low 2-NBDG uptake

city: Barcelona

first: Cristina

last: Lopez-Rodriguez

address: Carrer Dr. Aiguader, 88

department: Medicine and Life Sciences

country: Spain

institute: Universitat Pompeu Fabra

data_processing:
The quality of the raw data was checked using FastQC (version 0.11.5) and trimmed using Skewer (version 0.2.2). The percentage of reads mapping to ribosomal RNA was assessed using riboPicker (version 0.4.3). RNA-seq raw reads (31 to 36 x 106 reads/sample) were mapped to the Mus musculus reference genome (Gencode M21 release; mm10; files GRCm38.primary_assembly.genome.fa.gz and gencode.vM21.annotation.gtf) and counted at the gene level using STAR (version 2.5.3a) and parameters '--outSAMunmapped None --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts'. As the library preparation protocol was reverse stranded, the 4th column of the STAR gene counts output of each sample was taken as input for DESeq2. Qualimap (version 2.2.1) was used to check the quality of the aligned reads.
Assembly: RNA-seq raw reads (31 to 36 x 106 reads/sample) were mapped to the Mus musculus reference genome (Gencode M21 release; mm10; files GRCm38.primary_assembly.genome.fa.gz and gencode.vM21.annotation.gtf)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: subcutaneous LLC tumor

growth_protocol: Samples are primary T cells isolated from in vivo mouse tumors. Details are provided under "treatment protocol" below

extract_protocol:
RNA was extracted with the RNeasy Microkit (Qiagen, Catalog: 74004).
cDNA libraries were prepared from poly A RNA (mRNA) using the Smart-Seq2 single-cell protocol with some modifications. Briefly, reverse transcription was done with SuperScript™ II reverse transcriptase (Invitrogen, Catalog: 18064014), oligo-dT30VN (1 µM; 5′-AAGCAGTGGTATCAACGCAGAGTACT30VN-3′), template-switching oligonucleotides (1 µM) and betaine (1 M). Template switching was done using a locked nucleic acid (LNA) without the purification step before preamplification PCR to obtain an increased cDNA yield. cDNA concentration was measured with the Qubit dsDNA High Sensitivity assay (Invitrogen, Catalog: Q32851) and analyzed with Agilent Bioanalyzer or Fragment analyzer High Sensitivity assay (Agilent, Catalog: 5067‐4626 or DNF‐474) to check the size distribution profile. cDNA libraries were prepared using NEBNext® Ultra DNA Library Prep for Illumina® kit (NEB, catalog: E7370) according to the manufacturer's protocol. Briefly, 5 ng of cDNA were fragmented at a range size of 200‐500bp using Covaris S2, then subjected to end repair and addition of “A” bases to 3′ ends, ligation of adapters and USER excision. All purification steps were performed using AgenCourt AMPure XP beads (Beckman Coulter, catalog: A63882,). Library amplification was performed by PCR using NEBNext® Multiplex Oligos for Illumina (Index Primers Set 1, Catalog E7335), (Index Primers Set 2, Catalog: E7500), (Index Primers Set 3, Catalog E7710) or/and (Index Primers Set 4, Catalog: E7730). Final libraries were analyzed with Agilent Bioanalyzer or Fragment analyzer High Sensitivity assay to estimate the quantity and check size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit (KapaBiosystems, Catalog: KK4835,) prior to amplification with Illumina’s cBot. Libraries were sequenced 1 x 50 + 8 bp on Illumina's HiSeq2500.

treatment_protocol: Effector CD4 or CD8 TILs from LLC tumor-bearing mice were sorted as 2-NBDG Hi or 2-NBDG Lo from 4 independent mice. The 15% of effector TILs with the highest 2-NBDG staining were sorted as 2-NBDG Hi cells, and the lowest 15% were sorted as 2-NBDG Lo. For each population, a pool of 2000 cells (500 cells per mouse) was done.

value: subcutaneous LLC tumor

value: C57BL/6 male mice

value: Effector (CD44+, CD62L-) CD8 T cells isolated from LLC tumors (day 14 post-inoculation)


title: CD4 T cells with high 2-NBDG uptake

value: Effector (CD44+, CD62L-) CD4 T cells isolated from LLC tumors (day 14 post-inoculation)


title: MS3730

description:
Single Cell RNAseq, CITEseq
library name:: 2021-01-22-MS3730


title: CD8 T cells with high 2-NBDG uptake


title: CD4 T cells with low 2-NBDG uptake


title: AMLMS8235 library 2

description:
Single Cell RNAseq, CITEseq
library name:: 2019-08-29-count-2
hashed library - hastag annotation can be found in feature_ref.csv file


title: Brain cells, APP-KI Fit2-Mut, scRNAseq

city: Singapore

first: James

middle: Alastair

last: Miller

address: 11 Mandalay Road

department: Lee Kong Chian School of Medicine

country: Singapore

institute: Nanyang Technological University

description: 10X Genomics

data_processing:
Sample was mapped to transcriptome mm10-2020-A via cellranger pipeline version 7.0.0 using chemistry Single Cell 3' v3
Assembly: mm10
Supplementary files format and content: Tab-separated barcode, features, and matrix files

source_name: Whole brain

extract_protocol:
Various brain cells were isolated from APP-KI brain accodiring to the manufacturer's instruction. (Adult Brain Dissociation Kit, mouse and rat, Miltenyi)
The library was performed according to the manufacturer's instructions (10x Genomics Single Cell Gene Expression 3’ v3.1).

value: APP-KI Fit2-Mut

value: Whole brain

value: all cell types in the brain


title: mESC_d6_DMSO_rep3

status: Public on May 02 2026

city: Hong Kong

first: Jian

last: Yan

state: Hong Kong Special Administrative Region

address: 83 Tat Chee Avenue, Kowloon

department: Department of Biomedical Sciences

institute: City University of Hong Kong

data_processing:
The quality control of the raw reads from RNA-seq on day 0/2/4/6 during mESC differentiation were performed by FastQC (v0.11.7).
The sequencing reads were then mapped to the human reference genome (mm10) using hisat2 (v2.1.0) with default parameters.
The raw count matrix of quantified gene expression was created using featureCounts (v2.0.1).
Then DESeq2 was used to analyze the differentially expressed genes.
Assembly: mm10
Supplementary files format and content: tab-delimited text files were generated by featureCounts (v2.0.1) which include gene expression values for each Sample

source_name: mESC

growth_protocol: Mouse embryonic stem (mES) cells were cultured in mouse ES cell medium containing KnockOut Serum Replacement: DMEM 85%, 15% KnockOut Serum Replacement (Gibco),  penicillin–streptomycin (Gibco), 1× non-essential amino acids (Gibco), 1× GlutaMax (Gibco), 1000 U ml–1 LIF (Millipore), 0.4 mM β-mercaptoethanol (Gibco). The cells were typically grown  on 0.1% gelatin-coated plates with irradiated mouse embryonic fibroblasts (MEFs) (Thermo Fisher).

extract_protocol:
Total RNA was isolated using the MiniBEST Universal RNA Extraction Kit (TaKaRa, Japan). RNA concentration was measured by a Nanodrop 2000 spectrophotometer (Thermo Fisher) .
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: mESC

value: mouse embryonic stem cells (mESC)

tag: time

value: Day 6

value: DMSO


title: mESC_d6_IAA_rep2

value: IAA


title: mESC_d6_IAA_rep3


title: Brain cells, APP-KI Fit2-WT, scRNAseq

description: 10X Genomics

value: APP-KI Fit2-WT


title: mESC_d6_IAA_rep1


title: mESC_d6_BPK25_rep1


title: mESC_d6_DMSO_rep1


title: mESC_d6_DMSO_rep2


title: AMLMS8235 library 1

description:
Single Cell RNAseq, CITEseq
library name:: 2019-08-29-count-1
hashed library - hastag annotation can be found in feature_ref.csv file

value: bone marrow


title: mESC_d6_BPK25_rep3


title: mESC_d4_BPK25_rep2

value: Day 4


title: mESC_d4_BPK25_rep1


title: mESC_d4_BPK25_rep3


title: mESC_d4_IAA_rep2


title: mESC_d2_IAA_rep1

value: Day 2


title: mESC_d6_BPK25_rep2


title: mESC_d4_DMSO_rep3


title: mESC_d4_IAA_rep3


title: mESC_d2_DMSO_rep2


title: mESC_d4_IAA_rep1


title: mESC_d4_DMSO_rep2


title: mESC_d4_DMSO_rep1


title: mESC_d0_DMSO_rep2

value: Day 0


title: mESC_d2_DMSO_rep1


title: mESC_d2_IAA_rep2


title: mESC_d2_BPK25_rep1


title: mESC_d2_BPK25_rep3


title: mESC_d0_IAA_rep1


title: mESC_d0_DMSO_rep1


title: mESC_d0_BPK25_rep1


title: mESC_d0_IAA_rep2


title: mESC_d0_BPK25_rep2


title: mESC_d2_DMSO_rep3


title: mESC_d6_IP_MBD3_rep3

library_source: genomic

data_processing:
The raw ChIP-Seq data were quality-controlled using FastQC (v0.11.7) with default parameters.
ChIP-seq reads were aligned to mouse genome (mm10) using bowtie2 (v2.3.4) with default parameters and only the uniquely mapped reads were kept for the subsequent analyses.
Sam files were converted to bam files by using samtools (v1.9) with default parameters.
Binding peaks for each sample were identified by using MACS2 software (v2.1.2) with default parameters.
Peaks were annotated by using bedtools (v2.25.0).
All peaks and reads distribution were visualized by using IGV software (v2.4.14).
Assembly: mm10
Supplementary files format and content: narrowPeak (except for input sample)  were generated by MACS2 (v2.1.2) which include the detail informations for all binding peaks;

molecule: genomic DNA

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody (CTCF (abcam, Cat. #ab128873), MBD3 (abcam, Cat. #ab157464),TET1 (GeneTex, Cat No. GTX125888),TET2 (GeneTex, Cat No. GTX124205)).
Sequencing libraries were made following the protocol of NEB Next ChIP-Seq DNA Sample Prep Kit with minor modifications. To perform end repair of DNA fragments, 12 μL mixture (5µL NEB T4 DNA ligase buffer with 10mM ATP, 2µL dNTPs mix 10mM each, 2µL T4 DNA polymerase 3u/µL, 1µL Klenow DNA polymerase 5u/µL, 2µL T4 PNK 10u/µL) was added to 38 μL of IP DNA and input DNA (20 ng in 38 μL) and incubated for 30 min at 20 °C. The DNA was then purified using VAHTS® DNA Clean Beads (N411-01, Vazyme) and eluted in 41 μL H2O, following the manufacturer’s instructions. To prepare the DNA fragments for ligation to adapters by adding an “A” base to the 3' end, 9 μL mix (5µL NEB Buffer 2, 1µL dATP 100mM, 3µL Klenow 3'-5' exo minus 5u/µL) was added to 41 μL DNA from previous step and incubated for 30 min at 37 °C. After “A” base addition, the DNA was then purified using VAHTS® DNA Clean Beads (N411-01, Vazyme) and eluted in 42 μL H2O. To ligate adapters to DNA fragments, 8 µL reaction mixture (1µL adapter mix (1uM) (1000005282, MGI), 5µL NEB T4 DNA ligase buffer, 2µL NEB T4 DNA ligase) was added to 42 μL DNA from the previous step and incubated at 16 °C overnight. Size selection (200–500 bp) was achieved using a 1.5% agarose gel and NEB Monarch DNA Gel Extraction Kit (T1020S), and the DNA was eluted in 20 μL H2O. Finally, the libraries were amplified by 18 PCR cycles using Phusion High-Fidelity DNA Polymerases (M0530L, NEB) with the DNA from size selection and purified as size selection. The libraries were sequenced with an MGIseq2000 instrument (BGI, Shenzhen) using a paired-end scheme (PE100).

tag: chip antibody


title: mESC_d6_IP_MBD3_rep2


title: mESC_d0_IAA_rep3


title: mESC_d0_DMSO_rep3


title: mESC_d0_BPK25_rep3


title: mESC_d6_IP_CTCF_rep2

value: Anti-CTCF


title: mESC_d6_IP_CTCF_rep1


title: mESC_d2_IAA_rep3


title: mESC_d6_INPUT_rep3

value: INPUT

value: Input


title: mESC_d6_IP_MBD3_rep1


title: mESC_d6_INPUT_rep2


title: mESC_d6_IP_CTCF_rep3


title: mESC_d4_IP_MBD3_rep2


title: mESC_d2_BPK25_rep2


title: mESC_d4_IP_CTCF_rep2


title: mESC_d4_INPUT_rep3


title: mESC_d6_INPUT_rep1


title: mESC_d4_IP_MBD3_rep3


title: mESC_d4_IP_MBD3_rep1


title: mESC_d4_IP_CTCF_rep3


title: mESC_d4_IP_CTCF_rep1


title: mESC_d4_INPUT_rep2


title: mESC_d2_INPUT_rep1


title: mESC_d2_IP_MBD3_rep1


title: mESC_d0_IP_MBD3_rep2


title: mESC_d2_IP_MBD3_rep3


title: mESC_d0_IP_CTCF_rep3


title: mESC_d2_IP_CTCF_rep3


title: mESC_d2_IP_CTCF_rep2


title: mESC_d4_INPUT_rep1


title: mESC_d2_IP_MBD3_rep2


title: mESC_d0_IP_CTCF_rep1


title: mESC_d2_INPUT_rep3


title: mESC_d6_rep1

value: day 6


title: mESC_d0_INPUT_rep1


title: mESC_d2_IP_CTCF_rep1


title: mESC_d4_rep3

value: day 4


title: mESC_d4_rep1


title: mESC_d0_IP_MBD3_rep3


title: mESC_d0_INPUT_rep3


title: mESC_d0_IP_CTCF_rep2


title: mESC_d2_rep3

value: day 2


title: mESC_d0_IP_MBD3_rep1


title: mESC_d2_INPUT_rep2


title: mESC_d6_rep2


title: mESC_d0_INPUT_rep2


title: mESC_d6_rep3


title: mESC_d4_rep2


title: mESC_d2_rep1


title: mESC_d2_rep2


title: mESC_d0_rep2

value: day 0


title: mESC_d0_rep1

value: mESC


title: HFD, PCCA ff, replicate 4

city: Baltimore

first: Michael

middle: J.

last: Wolfgang

state: MD

address: 855 N Wolfe Street

department: Institute for Basic Biomedical Sciences

institute: The Johns Hopkins University School of Medicine

description:
Library name: Sample 16
Sample name for raw files: Col_ff_4

data_processing:
The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.
From Novogene's provided methods: "Data quality control: Raw data (raw reads) of fastq format were firstly processed throughfastpsoftware. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-Nandlowquality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality."
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
For DESeq2 with biological replicates: Differential expression analysis for two conditions/groups was performed using the DESeq2 R package(1.20.0). DESeq2 provides statistical programs for determining differential expression in digital gene expression data using models based on negative binomial distribution. The resulting P-value is adjusted using the Benjamini and Hochberg’s methods to control theerror discovery rate. The corrected P-value ≤ 0.05 & |log2(foldchange)|≥ 1 was set as the threshold of significant differential expression. For edgeR without biological replicates: Prior to differential gene expression analysis, for each sequencing library, read counts wereadjusted using the edgeR R package (3.22.5) by scaling normalization factors to eliminate differences in sequencing depth between samples, followed by differential expression analysis. The resulting P value is adjusted using the Benjamini and Hochberg’s methods to control the error discovery rate. The corrected P-value ≤ 0.05 & |log2(foldchange)| ≥ 1 was set as the threshold of significant differential expression
GO and KEGG enrichment analysis of differentially expressed genes: Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the cluster Profiler R package, in which gene length bias was corrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions andutilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways. The Reactome database brings together the various reactions and biological pathways of human model species. Reactome pathwayswith corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. The DO (Disease Ontology) database describes the function of human genes and diseases. DO pathways with corrected Pvalue less than 0.05were considered significantly enriched by differential expressed genes. The DisGeNETdatabase integrates human disease-related genes. DisGeNET pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. We used clusterProfiler software to test the statistical enrichment of differentially expressed genes in the Reactome pathway, the DO pathway, and the DisGeNETpathway.
Assembly: mm39
Supplementary files format and content: Excel file (.xls) including tab-delimited raw counts for each sample, fkpm, log2FoldChange, pvalue, padj, and gene names.

source_name: Colon

growth_protocol: Mice were sacrificed at either 9 weeks (chow) or 18 weeks (HFD) of age.

extract_protocol:
Colon sections were dissected from mice and flushed with chilled PBS before transfer to 2ml eppendorf tubes and flash-freezing in liquid nitrogen. Samples were stored at -80 degrees Celsius until RNA extraction. Tissues were bead homogenized in Trizol reagent (11596018, Invitrogen) and processed according to manufacturer protocol. Total RNA was extracted by isopropanol precipitation followed by ethanol washes, drying of the pellet, and resuspension in RNAse-free water. RNA quality was assessed by Nanodrop before packaging and submission for RNAseq analysis at Novogene Corporation Inc.
RNA was submitted to Novogene Corporation Inc for library construction and sequencing according to their protocol: "Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification."

treatment_protocol: For the group fed standard chow (5V75, Labdiets), 9-week old mice were fasted for 4 hours prior to sacrifice at 9 weeks of age. For HFD samples, male mice were fed standard chow until 6 weeks of age, at which point they were fed High Fat Diet (60% kcal derived from fat, #D12492, Research Diets). Mice were provided a high-fat diet for 12 weeks until sacrifice at 18 weeks followign a 4-hour fast.

value: Colon

value: Pcca ff

value: High Fat Diet


title: HFD, PCCA ff, replicate 3

description:
Library name: Sample 15
Sample name for raw files: Col_ff_3


title: HFD, PCCA ff, replicate 1

description:
Library name: Sample 13
Sample name for raw files: Col_ff_1


title: HFD, PCCA Vill, replicate 4

description:
Library name: Sample 20
Sample name for raw files: Col_Vill_4

value: Pcca Vill


title: HFD, PCCA Vill, replicate 3

description:
Library name: Sample 19
Sample name for raw files: Col_Vill_3


title: mESC_d0_rep3

value: mouse embryonic stem cells (mESC)


title: HFD, PCCA Vill, replicate 2

description:
Library name: Sample 18
Sample name for raw files: Col_Vill_2


title: HFD, PCCA Vill, replicate 1

description:
Library name: Sample 17
Sample name for raw files: Col_Vill_1


title: Chow, PCCA Alb, replicate 3

description:
Library name: Sample 11
Sample name for raw files: Alb3

value: Pcca Alb

value: Standard Chow


title: Chow, PCCA Alb, replicate 2

description:
Library name: Sample 10
Sample name for raw files: Alb2


title: Chow, PCCA Alb, replicate 4

description:
Library name: Sample 12
Sample name for raw files: Alb4


title: Chow, PCCA ff, replicate 2

description:
Library name: Sample 2
Sample name for raw files: ff2


title: Chow, PCCA Vill, replicate 2

description:
Library name: Sample 6
Sample name for raw files: Vill2


title: Chow, PCCA ff, replicate 4

description:
Library name: Sample 4
Sample name for raw files: ff4


title: Chow, PCCA ff, replicate 3

description:
Library name: Sample 3
Sample name for raw files: ff3


title: Chow, PCCA Vill, replicate 4

description:
Library name: Sample 8
Sample name for raw files: Vill4


title: Chow, PCCA Vill, replicate 3

description:
Library name: Sample 7
Sample name for raw files: Vill3


title: Chow, PCCA Alb, replicate 1

description:
Library name: Sample 9
Sample name for raw files: Alb1


title: HFD, PCCA ff, replicate 2

description:
Library name: Sample 14
Sample name for raw files: Col_ff_2


title: Chow, PCCA Vill, replicate 1

description:
Library name: Sample 5
Sample name for raw files: Vill1


title: Chow, PCCA ff, replicate 1

description:
Library name: Sample 1
Sample name for raw files: ff1


title: Neutral For dMpp8 Clone13

city: Stanford

first: Joanna

last: Wysocka

state: California

address: 265 Campus Drive

institute: Stanford University

description: Library name: Neutral_For_dMpp8_Clone13

data_processing:
A custom genome with Cast and 129 SNPs and appropriate insertions based on the genetic modifications were created.
FastQ files were aligned to the corresponding custom references with bwa-mem.
All aligned reads were parsed, phased, sorted and deduplicated with pairtools v1.1.2 .
For each sample and replicate, we converted pair files into single-resolution .cool contact matrices with cooler v0.10.3,
For visualization, reads from biological replicates were merged.
Assembly: mm39
Supplementary files format and content: mcool
Supplementary files format and content: 2 mcool files were provided per each insert line. Each mcool file corresponds to either 129 or Cast allele.

growth_protocol: F123 (Cast/129 Hybrid) mESCs were grown in monolayer in 2i + LIF medium

extract_protocol:
Cells were fixed with 3 mM DSG for 35 minutes, followed by an additional 10 minutes with 1% formaldehyde. Following quenching, nuclei were prepared from fixed cells. Chromatin was digested in situ using MNase, DNA 3' ends were chewed back and biotinylated, and then free DNA ends were proximity ligated. Unligated ends were digested, and followed by reverse crosslinking of the chromatin and Protease K digestion. DNA was purified by phenol chloroform extraction and DNA Clean and Concentrator kit (Zymo), and then size selected for dinucleosomal fragments on an agarose gel. Following end polishing of DNA fragments, a streptavidin pulldown was used to enrich for ligated dinucleosomal fragments.
From bead-bound DNA fragments, Micro-C libraries were generated using NEBNext Ultra II DNA Library Prep (NEB, E7645S) on-bead following the manufacturer’s instructions, and amplified by 8 cycles of PCR followed by 0.95x AMPure XP bead purification (Beckman Coulter).

value: embryonic stem cell

value: Neutral-For


title: Neutral Rev dMpp8 Clone13A

description: Library name: Neutral_Rev_dMpp8_Clone13A

value: Neutral-Rev


title: Rpl13a For Clone3X

description:
Library name: Rpl13a_For_Clone3X
.mcool files are combination of Rpl13aFor Clone3X and 5


title: Rpl13a Rev Clone7X

description:
Library name: Rpl13a_Rev_Clone7X
.mcool files are combination of Rpl13aRev Clone7X and 22A


title: Rpl13a Rev Clone22A

description: Library name: Rpl13a_Rev_Clone22A


title: Neutral Rev dMpp8 Clone3

description:
Library name: Neutral_Rev_dMpp8_Clone3
.mcool files are combination of NeutralRev Clone3 and 13A


title: Ef1a Rev dMpp8 Clone8

description:
Library name: Ef1a_Rev_dMpp8_Clone8
.mcool files are combination of Ef1aRev clone 8 and 8A


title: Rpl13a For Clone5

description: Library name: Rpl13a_For_Clone5


title: Ef1a Rev dMpp8 Clone8A

description: Library name: Ef1a_Rev_dMpp8_Clone8A


title: Neutral For dMpp8 Clone10

description:
Library name: Neutral_For_dMpp8_Clone10
.mcool files are combination of NeutralFor Clone10 and 13


title: Ef1a For dMpp8 Clone9

description: Library name: Ef1a_For_dMpp8_Clone9


title: Ef1a For dMpp8 Clone6

description:
Library name: Ef1a_For_dMpp8_Clone6
.mcool files are combination of Ef1aFor clone 6 and 9


title: Rpl41 For Input

description: Library name: Rpl41_For_Input

data_processing:
An N-masked genome was generated using SNPSplit (v0.6.0)
The reads were trimmed using skewer (v0.2.2) and  were aligned to the N-masked mouse genome (mm39) using bowtie2(v2.5.1).
The reads were assigned to either Cast or 129 allele with SNPSplit  (v0.6.0).
For visualization, allele specific bigwig files were generated using deeptools (v3.5.1) bamCoverage.
Assembly: mm39
Supplementary files format and content: bigWig
Supplementary files format and content: Three bigWig files per sample provided, one for Cast allele, one for 129 allele and one for leftover reads that were unassigned due to lack of informative SNPs in the region

extract_protocol:
Cells were fixed on plate in 1% formaldehyde (in PBS) at room temperature for 10 mins with agitation. After quenching and cell lysis, chromatin was sheared using E220 Focused Ultrasonicator (Covaris) for 10 minutes.
Libraries were prepared using the NEBNext Ultra II DNA kit (NEB, E7645S) using up to 50 ng of input or ChIP DNA, with ~4-8 cycles of amplification, with no pre-PCR size selection but a post-PCR double-sided 0.5x/0.9x Ampure XP bead clean-up. Final quantification and QC were assessed by Qubit(Thermo) and Tapestation (Agilent), respectively, and libraries were pooled for sequencing on NovaSeq X Plus (Illumina) platform

tag: batch


title: Rpl41 Rev Pol2

description: Library name: Rpl41_Rev_Pol2

value: RNA polymerase II (BioLegend, 664906)


title: Rpl41 Rev Input

description: Library name: Rpl41_Rev_Input


title: Rpl41 Rev Rad21

description: Library name: Rpl41_Rev_Rad21

value: Rad21 (abcam, ab992)


title: Liver,red-type,rep1

description:
Library name: Sample 7
RD_R_L1

value: Liver

value: red-type


title: Rpl41 For Rad21

description: Library name: Rpl41_For_Rad21


title: Rpl41 For Pol2

description: Library name: Rpl41_For_Pol2


title: Ef1a Rev Input

description: Library name: Ef1a_Rev_Input


title: Ef1a For Rad21

description: Library name: Ef1a_For_Rad21


title: Neutral Rev Rad21

description: Library name: Neutral_Rev_Rad21


title: Ef1a Rev Pol2

description: Library name: Ef1a_Rev_Pol2


title: Neutral For Rad21

description: Library name: Neutral_For_Rad21


title: Neutral For Input

description: Library name: Neutral_For_Input


title: Neutral Rev Input

description: Library name: Neutral_Rev_Input


title: Neutral For Pol2

description: Library name: Neutral_For_Pol2


title: Ef1a For Pol2

description: Library name: Ef1a_For_Pol2


title: Ef1a For Input

description: Library name: Ef1a_For_Input


title: hESC_H9_d4_BPK25_RNA_Seq_rep2

description:
H9_4day_BPK25_rep2
1_hESC_H9_BPK25_RNA_Seq_samples.featureCounts.s1.cut.forDESeq2.txt

data_processing:
The quality control of the raw reads from RNA-seq on Day 0/4/9 during NPC differentiation were performed by FastQC (v0.11.7).
The sequencing reads were then mapped to the human reference genome (hg19) using hisat2 (v2.1.0) with default parameters.
The raw count matrix of quantified gene expression was created using featureCounts (v2.0.1).
Then DESeq2 was used to analyze the differentially expressed genes for Day 4 vs Day 0, Day 9 vs Day 0 and Day 9 vs Day 4.
The union set of the differentially expressed genes was made, and standardized to z-scores.
Finally, the ComplexHeatmap package of R was used to visualize the expression data by k-means clustering, and the gene list of each cluster was extracted for GO and KEGG analyses.
Assembly: hg19
Supplementary files format and content: tab-delimited text files were generated by featureCounts (v2.0.1) which include gene expression values for each Sample

growth_protocol: Human embryonic stem (hES) cell line (H9) cells were routinely cultured under feeder-free condition in mTeSR1 medium (Stem cell technologies) on Matrigel (Corning) coated tissue culture dishes, under the regular tissue culture condition, i.e. 5% CO2 at 37°C.

extract_protocol:
Total RNA was isolated using the MiniBEST Universal RNA Extraction Kit (TaKaRa, Japan). RNA concentration was measured by a Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific).1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using LM-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Human embryonic stem (hES) cell line (H9) were dissociated into single cell suspension using Gentle Cell Dissociation Reagent. Cells were collected by centrifugation at 300×g for 5 min. Careful aspiration of the supernatant was conducted followed  by resuspension of cells in STEMdiff™ Neural Induction Medium supplemented with SMADi and 10 μM Y-27632 (Stem cell technologies, USA), to obtain a final concentration of 1 × 106 cells/mL (i.e. 2 × 105 cells/cm2). Two milliliters of cell suspension (2 x 106 cells/well) were added into one well of a Matrigel-coated 6-well plate. Place the plate in a 37 °C CO2 (5%) incubator. Warm (37°C) STEMdiff™ Neural Induction Medium with SMADi was used to replace the full medium once a day on Days 1-5. On day 6, the medium was aspirated from the wells containing NPCs and 1 mL of ACCUTASE™ (Stem cell technologies, USA) was add and incubated at 37 °C for 10 min. Then the remaining attached cells were removed by pipetting up and down the cell suspension. Five mL of DMEM/F-12 was added to each well to suspend the pellet and transferred to a 15 mL conical tube for centrifuge at 300×g for 5 min. Next, the supernatant was carefully aspirated in which 1 mL of complete STEMdiff™ Neural Induction Medium containing SMADi was added. Cells were plated at the desired density (e.g., 1.5 - 2 x 105 cells/cm2) into a single well of a newly Matrigel-coated 6-well plate containing 2 mL of STEMdiff™ Neural Induction Medium with SMADi. STEMdiff™ Neural Induction Medium containing SMADi was daily replaced with the fresh medium.Human embryonic stem (hES) cell line (H9) cells were treated with 20 μM of BPK-25 and induced to differentiate by STEMdiff Neural Induction Medium at 24 hours. During differentiation, the medium was replaced daily with STEMdiff™ Neural Induction Medium supplemented with SMADi and 20 μM BPK-25.

value: human embryonic stem cells (hESC) H9

value: day 4


title: Ef1a Rev Rad21

description: Library name: Ef1a_Rev_Rad21


title: hESC_H9_d9_BPK25_RNA_Seq_rep3

description:
H9_9day_BPK25_rep3
1_hESC_H9_BPK25_RNA_Seq_samples.featureCounts.s1.cut.forDESeq2.txt

value: day 9


title: hESC_H9_d4_BPK25_RNA_Seq_rep1

description:
H9_4day_BPK25_rep1
1_hESC_H9_BPK25_RNA_Seq_samples.featureCounts.s1.cut.forDESeq2.txt


title: hESC_H9_d9_BPK25_RNA_Seq_rep1

description:
H9_9day_BPK25_rep1
1_hESC_H9_BPK25_RNA_Seq_samples.featureCounts.s1.cut.forDESeq2.txt


title: hESC_H9_d4_BPK25_RNA_Seq_rep3

description:
H9_4day_BPK25_rep3
1_hESC_H9_BPK25_RNA_Seq_samples.featureCounts.s1.cut.forDESeq2.txt


title: hESC_H9_d9_BPK25_RNA_Seq_rep2

description:
H9_9day_BPK25_rep2
1_hESC_H9_BPK25_RNA_Seq_samples.featureCounts.s1.cut.forDESeq2.txt


title: hESC_H9_d4_DMSO_RNA_Seq_rep3

description:
H9_4day_DMSO_rep3
1_hESC_H9_BPK25_RNA_Seq_samples.featureCounts.s1.cut.forDESeq2.txt

value: DMSO


title: hESC_H9_d4_DMSO_RNA_Seq_rep2

description:
H9_4day_DMSO_rep2
1_hESC_H9_BPK25_RNA_Seq_samples.featureCounts.s1.cut.forDESeq2.txt


title: hESC_H9_d9_DMSO_RNA_Seq_rep1

description:
H9_9day_DMSO_rep1
1_hESC_H9_BPK25_RNA_Seq_samples.featureCounts.s1.cut.forDESeq2.txt


title: Neutral Rev Pol2

description: Library name: Neutral_Rev_Pol2


title: hESC_H9_d0_DMSO_RNA_Seq_rep3

description:
H9_0day_DMSO_rep3
1_hESC_H9_BPK25_RNA_Seq_samples.featureCounts.s1.cut.forDESeq2.txt

value: day 0


title: hESC_H9_d9_WT_RNA_Seq_rep3

description:
H9_9day_rep3
1_hESC_H9_WT_RNA_Seq_samples.featureCounts.s1.cut.forDESeq2.txt

value: WT


title: hESC_H9_d9_DMSO_RNA_Seq_rep2

description:
H9_9day_DMSO_rep2
1_hESC_H9_BPK25_RNA_Seq_samples.featureCounts.s1.cut.forDESeq2.txt


title: hESC_H9_d0_BPK25_RNA_Seq_rep1

description:
H9_0day_BPK25_rep1
1_hESC_H9_BPK25_RNA_Seq_samples.featureCounts.s1.cut.forDESeq2.txt


title: hESC_H9_d0_BPK25_RNA_Seq_rep2

description:
H9_0day_BPK25_rep2
1_hESC_H9_BPK25_RNA_Seq_samples.featureCounts.s1.cut.forDESeq2.txt


title: hESC_H9_d4_DMSO_RNA_Seq_rep1

description:
H9_4day_DMSO_rep1
1_hESC_H9_BPK25_RNA_Seq_samples.featureCounts.s1.cut.forDESeq2.txt


title: hESC_H9_d0_DMSO_RNA_Seq_rep1

description:
H9_0day_DMSO_rep1
1_hESC_H9_BPK25_RNA_Seq_samples.featureCounts.s1.cut.forDESeq2.txt


title: hESC_H9_d0_BPK25_RNA_Seq_rep3

description:
H9_0day_BPK25_rep3
1_hESC_H9_BPK25_RNA_Seq_samples.featureCounts.s1.cut.forDESeq2.txt


title: hESC_H9_d0_DMSO_RNA_Seq_rep2

description:
H9_0day_DMSO_rep2
1_hESC_H9_BPK25_RNA_Seq_samples.featureCounts.s1.cut.forDESeq2.txt


title: hESC_H9_d9_WT_RNA_Seq_rep2

description:
H9_9day_rep2
1_hESC_H9_WT_RNA_Seq_samples.featureCounts.s1.cut.forDESeq2.txt


title: hESC_H9_d0_WT_RNA_Seq_rep3

description:
H9_0day_rep3
1_hESC_H9_WT_RNA_Seq_samples.featureCounts.s1.cut.forDESeq2.txt


title: hESC_H9_d4_WT_RNA_Seq_rep2

description:
H9_4day_rep2
1_hESC_H9_WT_RNA_Seq_samples.featureCounts.s1.cut.forDESeq2.txt


title: hESC_H9_d9_WT_RNA_Seq_rep1

description:
H9_9day_rep1
1_hESC_H9_WT_RNA_Seq_samples.featureCounts.s1.cut.forDESeq2.txt


title: hESC_H9_d4_WT_RNA_Seq_rep1

description:
H9_4day_rep1
1_hESC_H9_WT_RNA_Seq_samples.featureCounts.s1.cut.forDESeq2.txt


title: hESC_H9_d0_WT_RNA_Seq_rep1

description:
H9_0day_rep1
1_hESC_H9_WT_RNA_Seq_samples.featureCounts.s1.cut.forDESeq2.txt


title: hESC_H9_d9_BPK25_IP_TET3_rep2

description: H9_d9_BPK25_IP_TET3_rep123_TvsC_peaks.narrowPeak

data_processing:
The raw ChIP-Seq data were quality-controlled using FastQC (v0.11.7) with default parameters.
ChIP-seq reads were aligned to human genome (hg19) using bowtie2 (v2.3.4) with default parameters and only the uniquely mapped reads were kept for the subsequent analyses.
Sam files were converted to bam files by using samtools (v1.9) with default parameters.
Binding peaks for each sample were identified by using MACS2 software (v2.1.2) with default parameters.
Peaks were annotated by using bedtools (v2.25.0).
All peaks and reads distribution were visualized by using IGV software (v2.4.14).
Assembly: hg19
Supplementary files format and content: narrowPeak (except for input sample)  were generated by MACS2 (v2.1.2) which include the detail informations for all binding peaks;

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody (CTCF (abcam, Cat. #ab128873), MBD3 (abcam, Cat. #ab157464) and TET1 (GeneTex 125888)).
Sequencing libraries were made following the protocol of NEB Next ChIP-Seq DNA Sample Prep Kit with minor modifications. To perform end repair of DNA fragments, 12 μL mixture (5µL NEB T4 DNA ligase buffer with 10mM ATP, 2µL dNTPs mix 10mM each, 2µL T4 DNA polymerase 3u/µL, 1µL Klenow DNA polymerase 5u/µL, 2µL T4 PNK 10u/µL) was added to 38 μL of IP DNA and input DNA (20 ng in 38 μL) and incubated for 30 min at 20 °C. The DNA was then purified using VAHTS® DNA Clean Beads (N411-01, Vazyme) and eluted in 41 μL H2O, following the manufacturer’s instructions. To prepare the DNA fragments for ligation to adapters by adding an “A” base to the 3' end, 9 μL mix (5µL NEB Buffer 2, 1µL dATP 100mM, 3µL Klenow 3'-5' exo minus 5u/µL) was added to 41 μL DNA from previous step and incubated for 30 min at 37 °C. After “A” base addition, the DNA was then purified using VAHTS® DNA Clean Beads (N411-01, Vazyme) and eluted in 42 μL H2O. To ligate adapters to DNA fragments, 8 µL reaction mixture (1µL adapter mix (1uM) (1000005282, MGI), 5µL NEB T4 DNA ligase buffer, 2µL NEB T4 DNA ligase) was added to 42 μL DNA from the previous step and incubated at 16 °C overnight. Size selection (200–500 bp) was achieved using a 1.5% agarose gel and NEB Monarch DNA Gel Extraction Kit (T1020S), and the DNA was eluted in 20 μL H2O. Finally, the libraries were amplified by 18 PCR cycles using Phusion High-Fidelity DNA Polymerases (M0530L, NEB) with the DNA from size selection and purified as size selection. The libraries were sequenced with an MGIseq2000 instrument (BGI, Shenzhen) using a paired-end scheme (PE100).


title: hESC_H9_d9_BPK25_IP_TET1_rep2

description: H9_d9_BPK25_IP_TET1_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d9_BPK25_IP_TET3_rep3


title: hESC_H9_d9_BPK25_IP_TET3_rep1


title: hESC_H9_d9_BPK25_IP_MBD3_rep1

description: H9_d9_BPK25_IP_MBD3_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d9_BPK25_IP_MBD3_rep3


title: hESC_H9_d9_BPK25_IP_CTCF_rep2

description: H9_d9_BPK25_IP_CTCF_rep123_TvsC_peaks.narrowPeak

value: CTCF


title: hESC_H9_d9_BPK25_IP_CTCF_rep3


title: hESC_H9_d9_BPK25_IP_MBD3_rep2


title: hESC_H9_d9_BPK25_IP_TET1_rep1


title: hESC_H9_d9_BPK25_input_rep2

value: input


title: hESC_H9_d9_BPK25_IP_TET2_rep1

description: H9_d9_BPK25_IP_TET2_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d9_BPK25_input_rep3


title: hESC_H9_d9_DMSO_IP_TET3_rep1

description: H9_d9_DMSO_IP_TET3_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d9_DMSO_IP_TET3_rep2


title: hESC_H9_d9_BPK25_IP_TET1_rep3


title: hESC_H9_d9_DMSO_IP_TET3_rep3


title: hESC_H9_d9_BPK25_input_rep1


title: hESC_H9_d4_WT_RNA_Seq_rep3

description:
H9_4day_rep3
1_hESC_H9_WT_RNA_Seq_samples.featureCounts.s1.cut.forDESeq2.txt


title: hESC_H9_d9_DMSO_IP_TET1_rep1

description: H9_d9_DMSO_IP_TET1_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d9_DMSO_IP_TET2_rep2

description: H9_d9_DMSO_IP_TET2_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d9_BPK25_IP_TET2_rep3


title: hESC_H9_d9_DMSO_IP_TET1_rep2


title: hESC_H9_d9_DMSO_IP_TET1_rep3


title: hESC_H9_d9_BPK25_IP_TET2_rep2


title: hESC_H9_d9_BPK25_IP_CTCF_rep1


title: hESC_H9_d9_DMSO_IP_CTCF_rep3

description: H9_d9_DMSO_IP_CTCF_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d9_DMSO_IP_TET2_rep3


title: hESC_H9_d9_DMSO_IP_CTCF_rep1


title: hESC_H9_d9_DMSO_IP_MBD3_rep2

description: H9_d9_DMSO_IP_MBD3_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d9_DMSO_IP_TET2_rep1


title: hESC_H9_d9_DMSO_IP_MBD3_rep3


title: hESC_H9_d9_DMSO_input_rep1


title: hESC_H9_d4_BPK25_IP_TET3_rep1

description: H9_d4_BPK25_IP_TET3_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d9_DMSO_input_rep3


title: hESC_H9_d9_DMSO_input_rep2


title: hESC_H9_d9_DMSO_IP_CTCF_rep2


title: hESC_H9_d4_BPK25_IP_TET2_rep3

description: H9_d4_BPK25_IP_TET2_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d4_BPK25_IP_TET3_rep2


title: hESC_H9_d9_DMSO_IP_MBD3_rep1


title: hESC_H9_d4_BPK25_IP_TET3_rep3


title: hESC_H9_d4_BPK25_IP_TET2_rep1


title: hESC_H9_d4_BPK25_IP_TET1_rep3

description: H9_d4_BPK25_IP_TET1_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d4_BPK25_IP_TET2_rep2


title: hESC_H9_d4_BPK25_IP_TET1_rep2


title: hESC_H9_d4_BPK25_IP_MBD3_rep3

description: H9_d4_BPK25_IP_MBD3_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d4_BPK25_IP_CTCF_rep1

description: H9_d4_BPK25_IP_CTCF_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d4_BPK25_IP_MBD3_rep2


title: hESC_H9_d4_BPK25_IP_MBD3_rep1


title: hESC_H9_d4_BPK25_IP_CTCF_rep3


title: hESC_H9_d4_BPK25_IP_CTCF_rep2


title: hESC_H9_d4_BPK25_IP_TET1_rep1


title: hESC_H9_d4_DMSO_IP_TET3_rep1

description: H9_d4_DMSO_IP_TET3_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d4_DMSO_IP_TET3_rep2


title: hESC_H9_d4_BPK25_input_rep1


title: hESC_H9_d4_BPK25_input_rep3


title: hESC_H9_d4_DMSO_IP_TET1_rep2

description: H9_d4_DMSO_IP_TET1_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d4_BPK25_input_rep2


title: hESC_H9_d4_DMSO_IP_TET1_rep3


title: hESC_H9_d4_DMSO_IP_TET3_rep3


title: hESC_H9_d4_DMSO_IP_CTCF_rep2

description: H9_d4_DMSO_IP_CTCF_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d4_DMSO_IP_TET1_rep1


title: hESC_H9_d4_DMSO_IP_CTCF_rep1


title: hESC_H9_d4_DMSO_IP_MBD3_rep1

description: H9_d4_DMSO_IP_MBD3_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d4_DMSO_input_rep2


title: hESC_H9_d0_BPK25_IP_TET3_rep3

description: H9_d0_BPK25_IP_TET3_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d4_DMSO_IP_TET2_rep2

description: H9_d4_DMSO_IP_TET2_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d0_BPK25_IP_TET3_rep1


title: hESC_H9_d4_DMSO_input_rep3


title: hESC_H9_d4_DMSO_IP_TET2_rep1


title: hESC_H9_d4_DMSO_IP_TET2_rep3


title: hESC_H9_d0_BPK25_IP_TET2_rep3

description: H9_d0_BPK25_IP_TET2_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d0_BPK25_IP_TET2_rep1


title: hESC_H9_d0_BPK25_IP_CTCF_rep3

description: H9_d0_BPK25_IP_CTCF_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d4_DMSO_IP_CTCF_rep3


title: hESC_H9_d4_DMSO_IP_MBD3_rep3


title: hESC_H9_d0_BPK25_IP_CTCF_rep1


title: hESC_H9_d0_BPK25_IP_MBD3_rep1

description: H9_d0_BPK25_IP_MBD3_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d0_BPK25_IP_TET3_rep2


title: hESC_H9_d4_DMSO_IP_MBD3_rep2


title: hESC_H9_d0_BPK25_input_rep1


title: hESC_H9_d0_BPK25_IP_TET1_rep3

description: H9_d0_BPK25_IP_TET1_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d0_BPK25_IP_TET2_rep2


title: hESC_H9_d4_DMSO_input_rep1


title: hESC_H9_d0_DMSO_IP_TET1_rep2

description: H9_d0_DMSO_IP_TET1_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d0_BPK25_IP_TET1_rep2


title: hESC_H9_d0_BPK25_input_rep3


title: hESC_H9_d0_DMSO_IP_MBD3_rep3

description: H9_d0_DMSO_IP_MBD3_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d0_DMSO_IP_TET2_rep1

description: H9_d0_DMSO_IP_TET2_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d0_BPK25_IP_MBD3_rep2


title: hESC_H9_d0_DMSO_IP_TET2_rep2


title: hESC_H9_d0_BPK25_input_rep2


title: hESC_H9_d0_DMSO_IP_CTCF_rep3

description: H9_d0_DMSO_IP_CTCF_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d0_DMSO_IP_TET3_rep1

description: H9_d0_DMSO_IP_TET3_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d0_BPK25_IP_MBD3_rep3


title: hESC_H9_d0_BPK25_IP_CTCF_rep2


title: hESC_H9_d0_DMSO_IP_TET1_rep3


title: hESC_H9_d0_WT_RNA_Seq_rep2

description:
H9_0day_rep2
1_hESC_H9_WT_RNA_Seq_samples.featureCounts.s1.cut.forDESeq2.txt


title: hESC_H9_d9_WT_IP_MBD3_rep1

description: H9_d9_WT_IP_MBD3_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d0_DMSO_input_rep3


title: hESC_H9_d0_DMSO_IP_TET1_rep1


title: hESC_H9_d0_DMSO_IP_TET2_rep3


title: hESC_H9_d0_DMSO_IP_MBD3_rep2


title: hESC_H9_d0_DMSO_input_rep1


title: hESC_H9_d0_DMSO_IP_TET3_rep3


title: hESC_H9_d0_DMSO_IP_TET3_rep2


title: hESC_H9_d0_DMSO_IP_CTCF_rep2


title: hESC_H9_d0_DMSO_IP_CTCF_rep1


title: hESC_H9_d9_WT_IP_CTCF_rep1

description: H9_d9_WT_IP_CTCF_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d9_WT_IP_CTCF_rep2


title: hESC_H9_d9_WT_IP_MBD3_rep2


title: hESC_H9_d9_WT_IP_CTCF_rep3


title: hESC_H9_d9_WT_IP_MBD3_rep3


title: hESC_H9_d4_WT_IP_MBD3_rep2

description: H9_d4_WT_IP_MBD3_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d9_WT_input_rep3


title: hESC_H9_d0_DMSO_input_rep2


title: hESC_H9_d4_WT_IP_MBD3_rep3


title: hESC_H9_d9_WT_input_rep2


title: HEK293 sorbitol replicate 2 ATAC-seq

city: Chapel Hill

first: John Patrick

last: Flores

state: NC

address: 104 Manning Dr

institute: UNC Chapel Hill

description:
Library name: YAPP_ATAC_HEK_wt_Sorbitol_1h_S_1p2p1_S6
ATAC-seq in HEK293 cells treated with sorbitol for 1h

data_processing:
ATAC-seq reads were processed using the bagPipes Snakemake workflow (ATACpipe.snakefile; https://github.com/PhanstielLab/bagPipes). Reads were trimmed with Trim Galore (v0.6.10) and quality assessed with FastQC (v0.12.1) and MultiQC (v1.28). Trimmed reads were aligned to the hg38 reference genome using bwa mem (v0.7.17) and sorted with samtools (v1.22). PCR duplicates were removed using Picard MarkDuplicates (REMOVE_DUPLICATES=true) and mitochondrial reads were excluded with samtools idxstats and view. Per-replicate peaks were called using MACS2 (v2.2.9.1; callpeak -f BAM -q 0.01 -g hs --nomodel --shift 100 --extsize 200 --keep-dup all -B --SPMR). Peaks from all replicates were merged using bedtools merge (v2.31.1) to generate a unified peak set, and fragment counts per peak per sample were quantified using bedtools multicov. Signal tracks were generated using deepTools bamCoverage (v3.5.4). Genome build: hg38 (GRCh38).
ATAC-seq reads were processed using the bagPipes Snakemake workflow (ATACpipe.snakefile). Reads were trimmed with Trim Galore (v0.6.10) and quality assessed with FastQC (v0.12.1) and MultiQC (v1.28). Trimmed reads were aligned to the hg38 reference genome using bwa mem (v0.7.17) and sorted with samtools (v1.22). PCR duplicates were removed using Picard MarkDuplicates (REMOVE_DUPLICATES=true) and mitochondrial reads were excluded using samtools idxstats and view. Per-replicate peaks were called using MACS2 (v2.2.9.1; callpeak -f BAM -q 0.01 -g hs --nomodel --shift 100 --extsize 200 --keep-dup all -B --SPMR). Peaks from all replicates were merged using bedtools merge (v2.31.1) to generate a unified peak set, and fragment counts per peak per sample were quantified using bedtools multicov. Signal tracks were generated using deepTools bamCoverage (v3.5.4). Genome build: hg38 (GRCh38).
Assembly: hg38 (GRCh38) human reference genome.
Supplementary files format and content: bigWig (.bw) files contain per-replicate and merged ATAC-seq chromatin accessibility signal tracks for untreated (0h) and 1-hour sorbitol-treated eGFP-YAP HEK293 cells, generated with deepTools bamCoverage. Values represent normalized read coverage across the genome at hg38 coordinates.
Supplementary files format and content: TSV file (YAPP_HEK_1_peakCounts.tsv) contains the merged peak-by-sample fragment count matrix across all ATAC-seq replicates and conditions (untreated and 1h sorbitol), where rows are merged peak coordinates (chr, start, stop) and columns are individual replicate BAM-derived counts. Used as input for differential accessibility analysis with DESeq2.

growth_protocol: HEK293 cells were cultured in standard conditions (37 °C, 5% CO₂) in DMEM supplemented with 10% fetal bovine serum and penicillin/streptomycin. Cells were regularly monitored for mycoplasma contamination and maintained at 30–80% confluence prior to experimental treatments.

extract_protocol:
Cells were detached, counted, and pelleted at 4 °C. For RNA-seq, total RNA was extracted using a column-based RNA purification kit following the manufacturer’s instructions. For CUT&Tag and Hi-C, nuclei were isolated by gentle lysis in detergent-containing buffer prior to downstream processing. For ATAC-seq, 50,000 cells per sample were used. Nuclei were isolated using Omni-ATAC lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% NP-40, 0.1% Tween-20, 0.01% digitonin) on ice for 3 minutes, followed by a wash with 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% Tween-20. Isolated nuclei were used immediately for tagmentation.
ATAC-seq libraries were prepared following the Omni-ATAC protocol (Corces et al., 2017). 50,000 cells per sample were lysed in ATAC lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% NP-40, 0.1% Tween-20, 0.01% digitonin) on ice for 3 minutes. Nuclei were pelleted, washed once with wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% Tween-20), and resuspended in transposition mix containing Nextera XT transposase (Illumina) for 30 minutes at 37 °C with gentle shaking. Transposed DNA was purified using the Zymo DNA Clean and Concentrator kit. Libraries were amplified by PCR for 5 initial cycles; a qPCR side reaction on 5% of the amplified material was used to determine the number of additional cycles required (typically 4–7 additional cycles). Libraries were size-selected using a two-sided AMPure XP bead cleanup (0.5× then 1.3×), quantified by Qubit (dsDNA HS Assay) and the KAPA Library Quantification kit, and sequenced in paired-end 75 bp mode on an Illumina NextSeq 500.

treatment_protocol: Hyperosmotic stress was induced by adding sorbitol to a final concentration of 200 mM for the indicated timepoints. Untreated samples were collected in parallel as controls. Cells were harvested at the specified time after treatment and processed immediately for downstream library preparation.

value: eGFP-YAP

value: 0.2M sorbitol for 1h


title: hESC_H9_d4_WT_IP_CTCF_rep3

description: H9_d4_WT_IP_CTCF_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d4_WT_IP_MBD3_rep1


title: hESC_H9_d4_WT_input_rep3


title: hESC_H9_d9_WT_input_rep1


title: HEK293 vehicle replicate 4 ATAC-seq

description:
Library name: YAPP_ATAC_HEK_wt_Control_0h_S_2p2p1_S4
ATAC-seq in HEK293 cells with vehicle treatment

value: vehicle


title: HEK293 sorbitol replicate 3 ATAC-seq

description:
Library name: YAPP_ATAC_HEK_wt_Sorbitol_1h_S_2p1p1_S7
ATAC-seq in HEK293 cells treated with sorbitol for 1h


title: hESC_H9_d0_BPK25_IP_TET1_rep1


title: hESC_H9_d4_WT_input_rep2


title: HEK293 vehicle replicate 1 ATAC-seq

description:
Library name: YAPP_ATAC_HEK_wt_Control_0h_S_1p1p1_S1
ATAC-seq in HEK293 cells with vehicle treatment


title: hESC_H9_d4_WT_IP_CTCF_rep1


title: hESC_H9_d4_WT_input_rep1


title: hESC_H9_d0_WT_IP_MBD3_rep2

description: H9_d0_WT_IP_MBD3_rep123_TvsC_peaks.narrowPeak


title: HEK293 sorbitol replicate 1 ATAC-seq

description:
Library name: YAPP_ATAC_HEK_wt_Sorbitol_1h_S_1p1p1_S5
ATAC-seq in HEK293 cells treated with sorbitol for 1h


title: HEK293 vehicle replicate 2 ATAC-seq

description:
Library name: YAPP_ATAC_HEK_wt_Control_0h_S_1p2p1_S2
ATAC-seq in HEK293 cells with vehicle treatment


title: HEK293 sorbitol replicate 4 ATAC-seq

description:
Library name: YAPP_ATAC_HEK_wt_Sorbitol_1h_S_2p2p1_S8
ATAC-seq in HEK293 cells treated with sorbitol for 1h


title: SHED_OSR2_rep_3

city: Nanjing

first: Liwen

last: Fan

address: Hanzhong Road 140

institute: Nanjing Medical University

description: Library name: Sample 6

data_processing:
Raw reads were processed using Skewer software to dynamically remove adapter sequences and low-quality fragments from the 3' end. FastQC software was then used for quality control analysis, including assessment of Q20 and Q30 base quality scores.
For each sample, StringTie software was used to assemble transcripts guided by known transcript annotation files. Transcripts with zero expression were filtered out. Assembled transcripts from all samples were then merged for a comprehensive transcriptome reconstruction.
Gene expression levels were quantified as counts and FPKM (fragments per kilobase per million reads) values using StringTie.
Assembly: GRCh37 (hg19)
Supplementary files format and content: tab-delimited text file includes  FPKM values for each Sample.

source_name: Dental pulp

growth_protocol: SHED cells (stem cells from human exfoliated deciduous teeth) were cultured in α-MEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37°C in a humidified atmosphere with 5% CO2. Cells at passages 2-4 were used for experiments.

extract_protocol:
Total RNA was extracted using an RNA isolation kit (Vazyme, China) following the manufacturer's instructions.
RNA libraries for RNA‑seq were prepared using the SMARTER mRNA‑Seq Library Prep Kit following manufacturer’s protocols.

value: Dental pulp

value: Stem cells from human exfoliated deciduous teeth

value: Mesenchymal Stem Cells


title: hESC_H9_d4_WT_IP_CTCF_rep2


title: hESC_H9_d0_WT_IP_MBD3_rep3


title: SHED_OSR2_rep_2

description: Library name: Sample 5

treatment_protocol: SHED cells (stem cells from human exfoliated deciduous teeth) were cultured in α-MEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37°C in a humidified atmosphere with 5% CO2. Cells at passages 2-4 were used for experiments.


title: SHED_OSR2_rep_1

description: Library name: Sample 4


title: hESC_H9_d0_WT_IP_CTCF_rep2

description: H9_d0_WT_IP_CTCF_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d0_WT_IP_CTCF_rep1


title: SHED_Control_rep_3

description: Library name: Sample 3


title: SHED_Control_rep_2

description: Library name: Sample 2


title: HEK293T_IAA_plus_72h_IP_TET2_rep3

description: HEK293T_IAA_plus_72h_IP_TET2_rep123_TvsC_peaks.narrowPeak

growth_protocol: The HEK293T (ATCC, CRL-3216) and its derived edited cells were cultured with DMEM (Invitrogen) supplemented with 10% FBS and antibiotics (penicillin and streptomycin), under the regular tissue culture condition, i.e. 5% CO2 at 37°C.

treatment_protocol: For the CTCF-AID experiment, CTCF-edited HEK293T were co-transfected with 1.5 μg of pcDNA3.1-ScFv-miniIAA7-mEGFP plasmid and 1.5 μg of pcDNA3.1-AtAFB2-mCherry constructs using 9 μg of PEI (0.1%, Polysciences). At 48 h post plasmid transfection, the medium was changed to 2 mL of fresh medium without or containing 0.5 mM IAA (Indole-3-acetic acid sodium salt, Santa Cruz, sc-215171). The cells were harvested 72 hours after being treated with 0.5mM IAA for subsequent experiments.

value: human embryonic kidney (HEK) 293T cells


title: hESC_H9_d0_WT_input_rep2


title: SHED_Control_rep_1

description: Library name: Sample 1


title: HEK293T_IAA_IP_TET1_rep1

description:
HEK293T_IAA_IP_TET1_rep123_treat_pileup.bigwig
HEK293T_IAA_IP_TET1_rep123_TvsC_peaks.narrowPeak

data_processing:
The raw ChIP-Seq data were quality-controlled using FastQC (v0.11.7) with default parameters.
ChIP-seq reads were aligned to human genome (hg19) using bowtie2 (v2.3.4) with default parameters and only the uniquely mapped reads were kept for the subsequent analyses.
Sam files were converted to bam files by using samtools (v1.9) with default parameters.
Binding peaks for each sample were identified by using MACS2 software (v2.1.2) with default parameters.
Peaks were annotated by using bedtools (v2.25.0).
The ChIP signal enrichment heat map of the flank of a specific point collection (such as CTCF binding sites) was calculated using deeptools (v3.5.0).
All peaks and reads distribution were visualized by using IGV software (v2.4.14).
Assembly: hg19
Supplementary files format and content: bigwig
Supplementary files format and content: narrowPeak (except for input sample)  were generated by MACS2 (v2.1.2) which include the detail informations for all binding peaks;

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody (CTCF (abcam, Cat. #ab128873), MBD2 (abcam, Cat. #ab224827), MBD3 (abcam, Cat. #ab157464),TET1 (GeneTex, Cat No. GTX125888).
Sequencing libraries were made following the protocol of NEB Next ChIP-Seq DNA Sample Prep Kit with minor modifications. To perform end repair of DNA fragments, 12 μL mixture (5µL NEB T4 DNA ligase buffer with 10mM ATP, 2µL dNTPs mix 10mM each, 2µL T4 DNA polymerase 3u/µL, 1µL Klenow DNA polymerase 5u/µL, 2µL T4 PNK 10u/µL) was added to 38 μL of IP DNA and input DNA (20 ng in 38 μL) and incubated for 30 min at 20 °C. The DNA was then purified using VAHTS® DNA Clean Beads (N411-01, Vazyme) and eluted in 41 μL H2O, following the manufacturer’s instructions. To prepare the DNA fragments for ligation to adapters by adding an “A” base to the 3' end, 9 μL mix (5µL NEB Buffer 2, 1µL dATP 100mM, 3µL Klenow 3'-5' exo minus 5u/µL) was added to 41 μL DNA from previous step and incubated for 30 min at 37 °C. After “A” base addition, the DNA was then purified using VAHTS® DNA Clean Beads (N411-01, Vazyme) and eluted in 42 μL H2O. To ligate adapters to DNA fragments, 8 µL reaction mixture (1µL adapter mix (1uM) (1000005282, MGI), 5µL NEB T4 DNA ligase buffer, 2µL NEB T4 DNA ligase) was added to 42 μL DNA from the previous step and incubated at 16 °C overnight. Size selection (200–500 bp) was achieved using a 1.5% agarose gel and NEB Monarch DNA Gel Extraction Kit (T1020S), and the DNA was eluted in 20 μL H2O. Finally, the libraries were amplified by 18 PCR cycles using Phusion High-Fidelity DNA Polymerases (M0530L, NEB) with the DNA from size selection and purified as size selection.

treatment_protocol: HEK293T cells were treated with DMSO, IAA(0.5mM) or BPK-25 (30 μM) for 72 hr. Chromatin immunoprecipitation was conducted as mentioned above.

value: IAA


title: hESC_H9_d0_WT_input_rep1


title: hESC_H9_d0_WT_IP_MBD3_rep1


title: HEK293T_IAA_IP_MBD3_rep3

description:
HEK293T_IAA_IP_MBD3_rep123_treat_pileup.bigwig
HEK293T_IAA_IP_MBD3_rep123_TvsC_peaks.narrowPeak