title: Anti-PD1+GSK2_scRNA

description:
Library name: Anti-PD1+GSK2_scRNA
Machine and cDNA libraries were amplified according to the operating instructions of 10×Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (1000268). The constructed library was sequenced using the Illumina Nova 6000 platform in PE150 sequencing platform.

data_processing:
we add the exogenous sequence of plasmids into mm10 genome reference. The cellranger (v5.0.1) was used to generate the index of genome reference and to align the raw data with the mm10 genome reference, removing duplicated reads by adjusting unique molecules identities (UMIs), estimating single-cell by splitting barcodes, quantify the gene counts on single-cell levels and summarize the sequencing reads information, mapping ratio, and cells and genes’ detection.
The FindVariableFeatures was implemented to identify 4,000 high-variable genes with vst model for data scaling and subsequent clustering and dimension reducing. The 25 principal component analysis factors were used to embedding calculation and the 20 principal component analysis factors were used to neighbors’ estimation. The openTSNE, t-SNE, UMAP and force atlas2 (fa2) were used to reduce the dimension following previously reported methods. The major population and subpopulation were identified by classical signatures, and top markers were calculated by FindAllMarkers with wilcox.test.
Assembly: mm10
Supplementary files format and content: mtx,tsv

extract_protocol:
The lung cancers tissues were collected from Anti-PD1 (n=2) and Anti-PD1+GSK (n=2) SCLC groups and washed with PBS supplemented with 2% fetal bovine serum (FBS). The lung tumors were digested by Collagenase I and IV into single cells and filtered through a 100um filter to obtain a single-cell suspension. Cell numbers were counted and the concentration of single-cell suspension was about 1000 cells/μl. The cell activity of single-cell suspension was more than 85%.
Machine and cDNA libraries were amplified according to the operating instructions of 10×Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (1000268). The constructed library was sequenced using the Illumina Nova 6000 platform in PE150 sequencing platform.


title: SCLC3

status: Public on Dec 31 2025

type: SRA

city: Chengdu, Cihna

first: Xiangmeng

last: Luo

state: Sichuan

address: No.17 Renmin road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

country: China

institute: Sichuan University

description:
Library name: SCLC3
RNA-seq libraries were generated using an Illumina stranded mRNA sample preparation kit (NEB, E7770) following the manufacturer's protocol. The libraries were subsequently sequenced on an Illumina NovaSeq 6000 sequencing machine, producing paired end reads with a length of 150 base pairs (bp).

library_source: transcriptomic

data_processing:
The RNA-seq reads were aligned to the mouse reference genome (GRCm39) using STAR (v2.7.9a).
Assembly: GRCm39
Supplementary files format and content: csv

molecule: total RNA

organism: Mus musculus

source_name: SCLC

tag: tissue

value: SCLC

tag: cell type


title: Normal3

description:
Library name: Normal3
RNA-seq libraries were generated using an Illumina stranded mRNA sample preparation kit (NEB, E7770) following the manufacturer's protocol. The libraries were subsequently sequenced on an Illumina NovaSeq 6000 sequencing machine, producing paired end reads with a length of 150 base pairs (bp).

source_name: Normal lung

value: Normal lung


title: Anti-PD1+GSK1_scRNA

description:
Library name: Anti-PD1+GSK1_scRNA
Machine and cDNA libraries were amplified according to the operating instructions of 10×Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (1000268). The constructed library was sequenced using the Illumina Nova 6000 platform in PE150 sequencing platform.

library_source: transcriptomic single cell

molecule: polyA RNA


title: wt_3+21h_2

city: Hamburg

first: Jiabin

last: Huang

address: Martinistr. 52

country: Germany

institute: University Medical Center Hamburg-Eppendorf

data_processing:
Sequencing reads containing adapters and bases with less than Q20 were trimmed using TrimGalore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and aligned to the human reference assembly hg38 using STAR [28]. RseQC [29] and Preseq [30] reports were used for quality metrics such as alignment statistics and library complexity.
The number of uniquely mapped reads per gene was calculated applying FeatureCounts [31].
Normalization and differential expression analyses were carried out with DESeq2 [32], thereby defining differentially expressed genes (DEGs) if a fold change ≥ 2.0 and adjusted P-value ≤ 0.05 was detected.
Gene Ontology (GO) analyses were performed with the web tool DAVID (http://david.abcc.ncifcrf.gov) using default parameters. The heatmaps were generated with the online tool HeatMapper. Volcano plots were generated with GraphPad.
Assembly: hg38
Supplementary files format and content: wig files were generated using bedGraphToBigWig

organism: Homo sapiens

growth_protocol: HeLa Tet-On 3G cells (Clontech, 631183) were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM; Gibco, 41965039) supplemented with 10% fetal bovine serum (FBS; Gibco, 10270106) or tetracycline-free FBS (tet-FBS; Clontech, 631106), GlutaMAX (Gibco, 35050061) and 1% penicillin/streptomycin (P/S; Gibco, 15140122).

extract_protocol:
Total RNA of triplet replicates were isolated from control and stably expressing GFP-TFEB Hela 3G cells using QIAschredder (Qiagen, 79645) and RNeasy extraction kit (Qiagen, 74104) according to the manufacturer’s instruction. RNA integrity was analyzed with the RNA 6000 Nano Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies) and mRNA was extracted using the NEBNext Poly(A) mRNA Magnetic Isolation module (New England Biolabs). RNA-Seq libraries were generated using the NEXTFLEX Rapid Directional qRNA-Seq Kit (Bioo Scientific) according to the manufacturer's recommendations.
All samples' concentration was measured with a Qubit 2.0 Fluorometer (ThermoFisher Sci), and fragment lengths distribution of the final libraries were analyzed with the DNA High Sensitivity Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies). Libraries were multiplexed sequenced on the NextSeq500 (Illumina) with 1x75bp, with 20 to 22 Mio reads per sample.

treatment_protocol: The cells were co-transfected with pTRE3G-IRES-MSC1-EGFP-TFEB-wild-type (wt) or TEFEB mutants and a linear puromycin marker (Clontech, 631626) using JetPEI (Polyplus, 101-40N) according to the manufacture’s protocol. After 48 h puromycin (2 µg/mL; Sigma, P-7255) was added to the medium. Multiple puromycin-resistant cell colonies were selected and analyzed by western blotting 24 h after doxycycline (1 µg/mL; Clontech, 631311) treatment. When indicated the cells were transiently transfected with GFP-TFEB cDNAs.

tag: cell line

value: HeLa cells

value: cervical epithelioid carcinoma-derived

tag: genotype

value: wt

tag: treatment

value: 3h dox/21 h chase

tag: time

value: Hour 24


title: MCF7-2h-1

city: Durham

first: Christopher

middle: R

last: Day

state: NC

address: 111 TW Alexander Dr.

department: ERBL

country: USA

institute: NIH/NIEHS

data_processing:
Cell barcodes and UMI information was parsed for each read and filtered based on the parameters described in Hoffman et al., Commun Biol., 2020. Reads that were past this filtering step were aligned to hg19 using STAR version 2.5.2b. Unique read counts were assigned to genes using featureCounts v1.5.3.
Assembly: hg38
Supplementary files format and content: Raw counts matrix and meta data.

source_name: Cell Line

growth_protocol: MCF-7 cells (ATCC) were grown in MEM supplemented with 10% FBS (Sigma), 2mM Glutamine and 1X Pen/strep (Gibco).

extract_protocol:
Cells were induced with E2 for 2, 8, or 24h and single-cell suspensions were generated by dissociating cells using 0.25% Trypsin-EDTA (Gibco).
Single-cell emulsions were generated using the BioRad ddSeq Single-Cell Isolator and libraries were generated using the Illumina SureCell WTA 3′ Library Prep kit.

treatment_protocol: MCF7 cells were hormone depleted for 2d prior to treatment. Cells were then treated with 1nM E2 for 2, 8 or 24h.

value: Cell Line

value: ER+ Breast Cancer

value: 2h E2


title: Pt2 Aganglionic colon, scRNAseq

city: Salt Lake City

first: Xiaomeng

state: Utah

department: Department of Human Genetics

institute: University of Utah

description:
Library name: Pt2_aganglionic_colon
10X Genomics 3'

data_processing:
Raw reads were processed using the 10X cellranger pipepline (v3.1.0)
Assembly: GRCh38-3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Colon section

extract_protocol:
Surgically resected tissue was collected in RPMI 1640 medium (Gibco). The sample is minced into small pieces (~2 mm). The pieces were put into a Miltenyi C-tube with 4.75 ml of RPMI 1640 medium with 250 μl of 100 mg/ml dispase/collagenase mixture (Roche 11–097-1130–001). The C-tube is placed on the gentleMACS Dissociator and the program m_intestine_01 was executed. The C-tube was attached to the MACSmix Tube Rotator for 30 min at 37°C. This procedure was repeated again, and followed by one final agitation cycle performed on the gentleMACS Dissociator. The cell suspension was applied to a 70 μm MACS SmartStrainer and washed with 5 ml of RPMI 1640 into a 15 ml conical tube. The cells were counted to determine viability using 0.4% Trypan blue on a Countess II (Thermo Fisher). Cells were centrifuged at 300×g for 5 min at 4°C. The cells were resuspended in cryopreservation media (50% RPMI 1640, 40% FBS, 10% DMSO) and cryopreserved prior to sequencing. Cell viability was assessed prior to 10X Genomics preparation for droplet sequencing.
The 10x Genomics Single Cell 3’ Gene Expression Library Prep v3 was used.

value: Colon section

value: Various cell types

value: Bypass surgery


title: Pt2 Healthy colon, scRNAseq

description:
Library name: Pt2_healthy_colon
10X Genomics 3'


title: human_rpe_cell_rna_2

city: Madison

first: Finn

last: Kuusisto

state: WI

address: 1205 University Ave

institute: University of Wisconsin-Madison

description: Library name: human_rpe_cell_rna_2

data_processing:
Skop Lab - We use fastp (ver 0.23.4) quality filtering, adapter trimming, and quality profiling with default settings for paired-end. We use kallisto (ver 0.46.1) for quantification with an index k-mer size of 31, and otherwise default settings. We build the index against the Ensembl human cDNA FASTA for all genes, release 109.
Iwasaki Lab - Sequencing reads were processed as previously described (Kashiwagi et al. 2021; Mito et al. 2023). fastp (ver. 0.21.0) for the read quality filtering and adapter trimming. cutadapt (ver. 3.7) for demultiplexing by linker barcodes. UMI-tools (ver. 1.1.2) for deduplication based on unique molecule identifier. Alignment to genome with STAR v2.7.0a.
Assembly: hg38
Supplementary files format and content: Skop Lab - text files contain output of kallisto quant, five columns: 1. Ensembl transcript ID; 2. transcript length; 3. adjusted transcript length; 4. read counts; 5. TPM
Supplementary files format and content: Iwasaki Lab - text files contain three columns: 1. transcript name; 2. CDS region used for read counting; 3. read counts

source_name: RPE

extract_protocol:
Skop Lab - Cells were harvested when 80% confluent with Trypsin or Versene, counted, washed with 2 mL PBS and cell pellets used for RNA extraction using the Qiagen RNeasy mini kit. RNA was eluted in RNase free water. MBRs were isolated by ultracentrifugation of cleared culture media. Cells were cultured until 80% confluent. Culture media was collected and centrifuged at 1,000×g for 10 min to clear cell debris. Cleared culture media was transferred to ultracentrifuge tubes and centrifuged at 10,000×g for 30 min at 4°C. MBR pellets were washed with 2mL sterile PBS, centrifuged at 10,000×g for 30 min at 4°C and MBR pellets used for RNA extraction using the Qiagen RNeasy mini kit. RNA was eluted in RNase free water.
Iwasaki Lab - Cells were directly lysed in lysis buffer on culture dishes. Purification of desthiobiotinylated ribosomes and RNAs were performed. For ribosome profiling, RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion, reverse transcription and PCR amplification.
Skop Lab - For RNA-seq, libraries were prepared by Azenta Life Sciences using standard protocols to assess integrity, remove contaminants, and deplete ribosomal RNA. For RNA sequencing library preparation, the NEBNext Ultra II RNA Library Preparation Kit for Illumina was used according to the manufacturer’s instructions. Detailed steps and reagents are available from Azenta documentation upon request.
Iwasaki Lab - For Ribo-Seq, lysates were used for Thor‑Ribo‑Seq library preparation (Mito et al. 2023).

value: RPE

tag: lab

value: Skop


title: Anti-PD1-2_scRNA

description:
Library name: Anti-PD1-2_scRNA
Machine and cDNA libraries were amplified according to the operating instructions of 10×Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (1000268). The constructed library was sequenced using the Illumina Nova 6000 platform in PE150 sequencing platform.


title: Pt3 Healthy colon, scRNAseq

description:
Library name: Pt3_healthy_colon
10X Genomics 3'


title: Normal2

description:
Library name: Normal2
RNA-seq libraries were generated using an Illumina stranded mRNA sample preparation kit (NEB, E7770) following the manufacturer's protocol. The libraries were subsequently sequenced on an Illumina NovaSeq 6000 sequencing machine, producing paired end reads with a length of 150 base pairs (bp).


title: human_rpe_mbr_rna_4

description: Library name: human_rpe_mbr_rna_4


title: CPC_Vector_2

city: Guangzhou

first: Yuning

last: Lin

address: No. 603 Huangpu Avenue, Tianhe District, Guangzhou City, Guangdong Province

department: State Key Laboratory of Bioactive Molecules and Druggability Assessment

institute: Jinan University

description:
Library name: Sample2
All_sample_FPKM.txt

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GRCh38/hg38 using CLC genomic benchwork (parameters- mismatch cost: 2; insertion cost: 3; deletion cost: 3; length fraction: 0.8; similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Trimmed sequence reads were mapped to GRCh38/hg38 using CLC genomic benchwork (parameters- mismatch cost: 2; insertion cost: 3; deletion cost: 3; length fraction: 0.8; similarity fraction: 0.8)
Supplementary files format and content: raw counts for each Sample
Supplementary files format and content: FPKM values for each Sample

source_name: Colorectal cancer

growth_protocol: Cancer pericyte cells were maintained in PM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNeasy Mini Plus Kit (Qiagen). 1.5 μg of total RNA was used for the construction of sequencing libraries
CLC Genomics Workbench v20.0.4

treatment_protocol: For QPRT overexpression, human cancer pericyte cells were transfected when reaching 70-80% confluency: cells were divided into two groups (control group: empty vector-transfected; experimental group: QPRT-overexpression plasmid-transfected) using Lipofectamine 3000 reagent (Invitrogen) following the manufacturer’s instructions. Transfected cells were cultured for 4 days (logarithmic growth phase) before subsequent experiments (designated as the sampling time point)

value: Colorectal cancer

value: cancer pericyte cell

value: stromal cell

value: WT

value: Vector

tag: batch


title: 1_Chronic_postAC

city: Los Angeles

first: Xiuju

last: Wu

state: CA

address: 650 Charles Young Dr East, CHS A2-237

institute: University of California, Los Angeles

description: Library name: 1_Chronic_postAC

data_processing:
The demultiplexing and gene counting were performed using Cell Ranger software v7.2.0.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Cells adhering to the acupuncture needles

extract_protocol:
Tissues were placed in tissue collection buffer immediately after collection and snap frozen in dry ice. For nuclei isolation, tissues were thawed in 500 μL homogenization buffer and incubated at room temperature with gentle rotation for 5 minutes. Samples were then transferred to ice to cool rapidly, then were homogenized to harvest the nuclei. Nuclei concentration was determined using the Countess II Automated Cell Counter (Thermo Fisher Scientific) with 0.4% Trypan Blue staining.
snRNA libraries were constructed according to the manufacturer's instructions (Chromium™ Single Cell 3’ Kit v3.1 protocol, 10x Genomics).


title: Pt1 Aganglionic colon, scRNAseq

description:
Library name: Pt1_aganglionic_colon
10X Genomics 3'


title: Pt3 Aganglionic colon, scRNAseq

description:
Library name: Pt3_aganglionic_colon
10X Genomics 3'


title: Normal1

description:
Library name: Normal1
RNA-seq libraries were generated using an Illumina stranded mRNA sample preparation kit (NEB, E7770) following the manufacturer's protocol. The libraries were subsequently sequenced on an Illumina NovaSeq 6000 sequencing machine, producing paired end reads with a length of 150 base pairs (bp).

value: Normal lung


title: human_rpe_mbr_rna_1

description: Library name: human_rpe_mbr_rna_1


title: wt_3+21h_3

description: WT_C8_3h_dox_plus_21h_chase_3_S12_R1_001

value: HeLa cells

value: cervical epithelioid carcinoma-derived

value: wt


title: human_rpe_cell_rna_3

description: Library name: human_rpe_cell_rna_3


title: wt_24h_2

value: 24 h continuous dox

value: Hour 24


title: wt_3+21h_1

value: 3h dox/21 h chase


title: MCF7-0h-2

value: Cell Line

value: ER+ Breast Cancer

value: 0h E2


title: brown adipose tissue, male, wild-type4

city: Iowa City

first: Renata

middle: O

last: Pereira

state: Iowa

address: 169 Newton Rd

department: Internal Medicine

institute: University of Iowa

description: Library name: 9_5_S15

data_processing:
reads quantified using Kallisto (v0.46.2)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files with TPM values assembled from individual abundance files created by Kallisto

source_name: brown adipose

extract_protocol:
Total RNA was extracted from tissues using TRIzol reagent (Invitrogen) and purified with the RNeasy kit (Qiagen)
TruSeq Stranded mRNA Library Prep

value: brown adipose

tag: Sex

value: Male


title: human_mcf7_cell_rna_3

description: Library name: human_mcf7_cell_rna_3

value: Skop


title: human_rpe_cell_rna_1

description: Library name: human_rpe_cell_rna_1

value: RPE


title: brown adipose tissue, male, knockout3

description: Library name: 9_3_S13

value: GDF15 KO


title: human_mcf7_cell_rna_2

description: Library name: human_mcf7_cell_rna_2


title: K3R_3+21h_2

description: K3R_C8_3h_dox_plus_21h_chase_2_S9_R1_001


title: Anti-PD1-1_scRNA

description:
Library name: Anti-PD1-1_scRNA
Machine and cDNA libraries were amplified according to the operating instructions of 10×Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (1000268). The constructed library was sequenced using the Illumina Nova 6000 platform in PE150 sequencing platform.

value: SCLC


title: human_mcf7_mbr_rna_6

description: Library name: human_mcf7_mbr_rna_6


title: wt_24h_3


title: HUVECs, VEGF+DZNep, 01

city: Shanghai

first: Sok I

last: Sok I

address: No. 639, Zhizaoju Road, Shanghai.

institute: shanghai jiaotong university

description: Library name: Sample 4

data_processing:
Raw FASTQ files were quality-controlled using fastp (default parameters) to remove adapter sequences, low-quality bases, and reads with undetermined bases. Clean reads were then aligned to the human reference genome (Homo sapiens GRCh38) using HISAT2 with default settings. Gene and transcript assemblies were generated with StringTie, and transcriptomes from all samples were merged using gffcompare to reconstruct a comprehensive transcriptome. Expression levels were quantified as FPKM using StringTie. Differentially expressed genes were identified using edgeR with fold change > 2 or < 0.5 and p-value < 0.05. These normalized counts and FPKM values constitute the processed data deposited in GEO.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
otal RNA was extracted using 1 mL of TRIzol reagent per well of a 6-well plate.
Library preparation was carried out using the TruSeq RNA Sample Prep Kit (Illumina, USA) according to the manufacturer’s instructions.

value: HUVECs

value: endothelial cells

value: WT

value: VEGF+DZNep


title: brown adipose tissue, female, knockout4

description: Library name: 9_9_S16

value: Female


title: Pt1 Healthy colon, scRNAseq

description:
Library name: Pt1_healthy_colon
10X Genomics 3'

value: Colon section

value: Various cell types

value: Bypass surgery


title: HUVECs, VEGF, 01

description: Library name: Sample 1

value: VEGF


title: HUVECs, VEGF+DZNep, 03

description: Library name: Sample 6


title: human_ipsc_mbr_rna_3

description: Library name: human_ipsc_mbr_rna_3

source_name: iPSC

value: iPSC


title: human_mcf7_mbr_rna_5

description: Library name: human_mcf7_mbr_rna_5


title: wt_24h_1

value: HeLa cells

value: cervical epithelioid carcinoma-derived

value: wt

value: 24 h continuous dox

value: Hour 24


title: HUVECs, VEGF, 03

description: Library name: Sample 3


title: brown adipose tissue, male, knockout2

description: Library name: 9_2_S12

value: brown adipose

value: Male

value: GDF15 KO


title: HUVECs, VEGF+DZNep, 02

description: Library name: Sample 5

value: HUVECs

value: endothelial cells


title: K3R_24h_2


title: brown adipose tissue, male, knockout4

description: Library name: 9_4_S14


title: K3R_3+21h_1

description: K3R_C8_3h_dox_plus_21h_chase_1_S4_R1_001

value: 3h dox/21 h chase


title: HUVECs, VEGF, 02

description: Library name: Sample 2

value: WT


title: brown adipose tissue, male, wild-type3

description: Library name: 9_1_S11


title: K3R_3+21h_3

description: K3R_C8_3h_dox_plus_21h_chase_3_S14_R1_001


title: human_ipsc_mbr_rna_2

description: Library name: human_ipsc_mbr_rna_2

value: Skop


title: human_mcf7_cell_rna_1

description: Library name: human_mcf7_cell_rna_1


title: human_mcf7_mbr_rna_4

description: Library name: human_mcf7_mbr_rna_4


title: brown adipose tissue, female, knockout3

description: Library name: 8b_17_S10

value: Female


title: brown adipose tissue, female, wild-type3

description: Library name: 8b_14_S8


title: K3R_24h_3


title: shPRAME replicate 2

city: Seoul

first: Hyeon Ho

last: Heo

address: 209 Neungdong-ro, Gwangjin-gu

department: Department of Integrative Bioscience and Biotechnology

country: South Korea

institute: Sejong University

description:
Library name: shPRAME_2
PRAME knockdown sample 2

data_processing:
Raw FASTQ files were adapter-trimmed and quality-filtered using fastp. Filtered reads were aligned to the human reference genome (GRCh38) using STAR. Gene-level read counts were quantified using salmon and processed with ExDEGA for normalization and differential expression analysis.
Assembly: Homo sapiens GRCh38 (hg38)
Supplementary files format and content: Tab-delimited text files containing raw gene-level read counts and normalized expression values (CPM/TMM).

source_name: skin

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions. RNA concentration and purity were measured using a Nanodrop spectrophotometer. Additional RNA quality control for sequencing was performed by DarwinBio.
PolyA-enriched RNA-seq libraries were prepared using an Illumina-compatible library preparation kit according to the manufacturer’s protocol. Libraries were quantified, pooled, and sequenced on an Illumina NovaSeq platform (paired-end 150 bp).

value: skin

value: melanoma cell

value: shPRAME


title: shPRAME replicate 3

description:
Library name: shPRAME_3
PRAME knockdown sample 3


title: shPRAME replicate 1

description:
Library name: shPRAME_1
PRAME knockdown sample 1


title: control_3

value: HeLa cells

value: control

value: untreated

value: Hour 0


title: brown adipose tissue, female, wild-type4

description: Library name: 8b_16_S9


title: brown adipose tissue, female, wild-type2

description: Library name: 8b_13_S7


title: K3R_24h_1

value: cervical epithelioid carcinoma-derived

value: 24 h continuous dox

value: Hour 24


title: human_ipsc_mbr_rna_1

description: Library name: human_ipsc_mbr_rna_1

value: iPSC


title: control_2


title: human_ipsc_cell_rna_3

description: Library name: human_ipsc_cell_rna_3


title: control_1


title: brown adipose tissue, male, wild-type2

description: Library name: 5_22_S5

value: brown adipose

value: Male


title: shCtrl replicate 1

description:
Library name: shCtrl_1
control shRNA sample 1

value: shCtrl


title: brown adipose tissue, male, wild-type1

description: Library name: 5_20_S4

value: WT


title: HCC827 cells in 2D culture, rep2

city: La Jolla

first: Sandra

middle: L.

last: Leibel

address: 9500 Gilman Dr

department: Pediatrics

institute: University of California, San Diego

data_processing:
Illumina sequencing reads were preprocessed to remove Truseq adapter, polyA, and polyT sequences using cutadapt v2.3 (Martin 2011). Trimmed reads were aligned to human genome version 38 (hg38) using STAR aligner v2.7.0d_0221 (Dobin, Davis et al. 2013) with parameters according to ENCODE long RNA-seq pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline). Gene expression levels were quantified using RSEM v1.3.1 (Li and Dewey 2011) and Ensembl gene annotations version 84.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes Transcripts Per Million (TPM).

growth_protocol: 2D Culture of the HCC827 cells: The HCC827 cell line (ATCC) was grown in a T-75 flask (Corning) and cultured in 10 mL of RPMI 1640 medium with GlutaMAX supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin, and 100U/mL streptomycin (complete media). Cells were grown in an incubator at 37°C and 5% CO2. Cells were cultured for 4-6 days before passaging. Cells were passaged once they reached 80% confluency. For passaging, 5 ml of dissociation enzyme, TrypLE was added to the HCC827 cells in a T-75 flask and allowed to incubate at 37 degrees for 12-15 minutes until the cell layer was dispersed. The dissociation was quenched with 10mL of DMEM-F12 with 2% FBS. Cells were dissociated by washing gently with a 10ml pipette and collected into a 15 ml conical tube. The cells were spun down at 400 g for 5 min and the supernatant was discarded. The cells were resuspended in 5mL of fresh and warm complete media and counted. One million cells were passaged into a fresh uncoated T-75 flask with 10mL of complete media.3D Culture of the HCC827 cells: To make 3D tumoroids, HCC827 monolayer cells were passaged into growth factor reduced (GFR) Matrigel droplet (Catalog #354230). After monolayer dissociation, the cells were pelleted after spinning down at 400 g for 5 min. The supernatant was discarded, and the cells were resuspended in 5mL of complete media and 50,000 cells were aliquoted into 1.5 ml centrifuge tubes. The tubes were spun down the supernatant discarded. 100 µL of GFR matrigel was added to the cells on ice, resuspended carefully to avoid bubbles, and placed into a 12-well plate as a droplet. The plate was placed in the incubator for gelling to occur for 30 min. 1 mL of 1640 medium with Glutamax supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin, and 100U/mL streptomycin was added to each well. The 3D tumoroids embedded in Matrigel were maintained in an incubator at 37°C and 5% CO2 for 12-16 days or until they were 80% confluent and fed every 2-3 days.

extract_protocol:
Total RNA from the 2D and 3D HCC827 cell lines was purified using the Direct-zol RNA MicroPrep kit (Genesee Scientific: 11-330MB) using the manufacturer’s recommendations, including DNase treatment. RNA concentration and RNA integrity number (RIN) were determined using an Agilent microfluidic RNA 6000 Nano Chip kit (Agilent Technologies, Santa Clara, CA) on the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Those samples with RIN greater than 9 were used for RNAseq.
PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich MA). Libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA). Read data was processed in BaseSpace (basespace.illumina.com).

treatment_protocol: To passage confluent tumoroids onto a new Matrigel droplet, fresh Matrigel was cool thawed on ice into a liquid. The cell media was aspirated from the well and 1mL of Dispase (+Rock Inhibitor (Tocris REF 1254)) was added to each well. The cells were incubated at 37°C for 30 minutes and triturated at 15-minute increments. Dissociated 3D tumoroids were transferred into a new 15mL conical and chilled PBS was added to wash down and “melt” the Matrigel. The conical was spun down at 400 x g for 5 minutes and a P-1000 pipette was used to remove the supernatant. If residual “gray Matrigel” was present, the PBS step was repeated. The Matrigel-free cells were then spun down at 400 x g for 5 minutes and the supernatant was discarded. 1-2mL of TrypLE was added and the cells were incubated at 37°C for 15 minutes. The reaction was quenched by adding 2x volume of stop media (DMEM-F-12 with 2% FBS). The cells were centrifuged at 400 x g for 5 minutes and resuspended in 1mL of complete media and counted. After calculating the number of cells required for a seeding of 50,000 cells per Matrigel drop, the cells were transferred into 1.5mL centrifuge tubes and spun down at 400 x g for 5 minutes. Supernatant was removed and the cells were carefully resuspended in 100uL of Matrigel and transferred into a 12-well plate as a droplet. The plate was placed in the incubator for gelling to occur for 30 min. After the droplets have gelled, 1 mL of complete media was added to each droplet.

value: 2D culture


title: human_hepg2_mbr_rna_2

description: Library name: human_hepg2_mbr_rna_2

value: Skop


title: brown adipose tissue, female, knockout1

description: Library name: 10_6_S3

value: Female

value: GDF15 KO


title: HCC827 cells in 2D culture, rep1


title: ScRNA-seq of CR#2 patient after CACAG-VEN

city: Beijing

first: Yanan

last: Wen

state: Beijing

address: Fuxing Street 28th, Haidian District, Beijing, China

institute: Chinese PLA General Hospital

description: Library name: CR2-postreatment

data_processing:
To ensure data quality, an initial assessment of the sequenced reads was conducted using FastQC. Subsequently, FASTQ sequenced files were aligned to the human reference genome using CellRanger, and the transcript expression of each cell was quantified. The resulting expression matrix from all samples was imported into R (v4.3.2) and further analyzed using Seurat (v4.3.2). Cells with unique feature counts exceeding 9,000 or falling below 200, and those with mitochondrial counts exceeding 15%, were excluded. Genes detected in at least three cells were retained for subsequent analysis. The combined dataset was normalized using Seurat’s “NormalizedData” function, applying a global-scaling normalization method referred to as “LogNormalize,” and then multiplied by a default scale factor of 10,000. Data integration and batch effect removal were performed using Seurat’s “RPCA” method. Dimension reduction analysis was conducted using Seurat’s “RunPCA” function, followed by nonlinear dimensional reduction using the “RunUMAP” function. Stemness and lineage priming scores for hematopoietic stem cells and granulocyte-macrophage progenitors (HSCs/GMPs) were computed using the Seurat package’s “AddModuleScore” function. Radar plots were used to visualize the average HSC/GMP subpopulation scores at different time points. Differential analysis to identify differentially expressed genes (DEGs) between distinct clusters was conducted using the “FindAllMarkers” function in Seurat. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed using ClusterProfiler for DEGs identified within each cluster.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger software output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Bone marrow

extract_protocol:
BM cells from patients with AML were collected in EDTA tubes and diluted 2:1 in ice-cold FACS buffer. Mononuclear cell separation was accomplished using density centrifugation media (Ficoll-Paque; GE Healthcare Life Sciences) at a 1:1 ratio with BM cells. Subsequently, the cell suspension, with a concentration ranging from 700 to 1,200 cells/µl and a cell viability exceeding 85%, was loaded onto the Chromium Single Cell Controller (10× Genomics) to generate single-cell gel beads in the emulsion, following the manufacturer’s protocol and employing the Chromium Single Cell 3' Library and Gel Bead Kit V3.1 (10× Genomics, PN1000268).
The libraries were sequenced on an Illumina NovaSeq 6,000 sequencer.

value: Bone marrow

value: mononuclear cells

value: Bone marrow mononuclear cells


title: shCtrl replicate 3

description:
Library name: shCtrl_3
control shRNA sample 3

value: skin

value: melanoma cell


title: brown adipose tissue, female, knockout2

description: Library name: 5_23_S6


title: human_ipsc_cell_rna_2

description: Library name: human_ipsc_cell_rna_2


title: shCtrl replicate 2

description:
Library name: shCtrl_2
control shRNA sample 2


title: human_hepg2_mbr_rna_1

description: Library name: human_hepg2_mbr_rna_1


title: human_ipsc_cell_rna_1

description: Library name: human_ipsc_cell_rna_1


title: human_hepg2_mbr_rna_3

description: Library name: human_hepg2_mbr_rna_3


title: ScRNA-seq of CR#2 patient before CACAG-VEN

description: Library name: CR2-pretreatment


title: HCC827 cells in 3D culture, rep3

value: 3D culture


title: brown adipose tissue, male, knockout1

description: Library name: 10_2_S1


title: brown adipose tissue, female, wild-type1

description: Library name: 10_4_S2


title: human_hepg2_cell_rna_1

description: Library name: human_hepg2_cell_rna_1


title: ScRNA-seq of CR#1 patient after CACAG-VEN

description: Library name: CR1-postreatment


title: HCC827 cells in 3D culture, rep2


title: CDAHFD-2

city: Hangzhou

first: Sike

last: Yu

address: No.1 Xiangshan Branch Lane, Xihu District

institute: Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences

description: Library name: Sample 5

data_processing:
The sequence alignment, and counts were made using the STAR software v2.7.11a (https://github.com/alexdobin/STAR)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes TPM for each sample

source_name: Liver

extract_protocol:
Total RNA was extracted from the tissue using TRlzol® Reagent according the manufacturer's instructions.
RNA libraries was prepared following llumina® Stranded mRNA Prep, Ligation from llumina (San Diego, CA) using 1ug of total RNA.

value: Liver


title: ScRNA-seq of PR patient before CACAG-VEN

description: Library name: PR-pretreatment


title: human_hela_mbr_rna_3

description: Library name: human_hela_mbr_rna_3

source_name: HeLa

value: HeLa


title: HCC827 cells in 2D culture, rep3


title: ScRNA-seq of CR#1 patient before CACAG-VEN

description: Library name: CR1-pretreatment


title: CDAHFD-3

description: Library name: Sample 6


title: human_hela_mbr_rna_2

description: Library name: human_hela_mbr_rna_2


title: ScRNA-seq of PR patient after CACAG-VEN

description: Library name: PR-postreatment


title: HCC827 cells in 3D culture, rep1


title: TOP1 ICEseq Input, VEH, 45 min

city: Madrid

first: Felipe

last: Cortés Ledesma

state: Madrid

address: Melchor Fernández Almagro 3

department: Molecular Oncology

country: Spain

institute: CNIO

library_source: genomic

data_processing:
Tags were aligned to human genome (hg19) using Rsubread for the aligment of uniquely mapped tags (type =1, TH1 =2)
Peaks were called using MACS2 and broad peak mode. Peaks from differente biological repeats were merged.
For genome tracks, bamCoverage (deepTools) was used to convert aligned reads to signal tracks (bigwig) using RPKM normalization (bin size of 50 bps and 300 bps read extension)
Assembly: hg19
Supplementary files format and content: bigWig (Coverage files)
Supplementary files format and content: bed (called peaks)

molecule: genomic DNA

growth_protocol: MEM with Earle´s salts supplemented with 50 U/ml Penicillin, 50 µg/ml Streptomycin, 2 mM L-Glutamine, 10% FBS and non-essential amino acids. Cells maintained in HEPA class 100 incubators at 37ºC and 5% CO2.

extract_protocol:
MCF-7 cells were lysed with 1% Sarkozyl and subjected to conventional ICE assay. Samples were then subjected to IP.
Libraries were prepared by ChIPmentation as described by Schmidl et al. 2015 using NEBNext HF Polymerase and sequenced using Illumina NextSeq 500.

treatment_protocol: MEM with Earle's salts without phenol-red and supplemented with 50 U/ml Penicillin, 50 µg/ml Streptomycin, 2 mM L-Glutamine, 5% Charcoal-stripped FBS and non-essential amino acids. Cells maintained in HEPA class 100 incubators at 37ºC and 5% CO2 for 48 hours prior treatments.

value: ER positive breast cancer cell line

value: 45 min EtOH


title: human_hela_mbr_rna_1

description:
Library name: human_hela_mbr_rna_1
[removed from analysis]


title: Normal diet-2

description: Library name: Sample 2


title: Normal diet-3

description: Library name: Sample 3


title: TOP1 ICEseq Input, E2, 45 min

value: 45 min 10 nM E2


title: TOP1 ICEseq , VEH, 45 min


title: human_hepg2_cell_rna_3

description: Library name: human_hepg2_cell_rna_3


title: ScRNA-seq of NR patient after CACAG-VEN

description: Library name: NR-postreatment


title: human umbilical cord mesenchymal stem cells，2d cultivation，sus3

city: JinZhong

first: Haichao

last: Diao

state: 山西省

address: 55 Wenhua Street, Yuci District, Jinzhong City, Shanxi Province, China

institute: Shanxi Medical University

description: Library name: sus3

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
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 reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: umbilical cord

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using Fast RNA-seg Lib Prep Kit V2 (Cat.No.RK20306) following manufacturer's protocols.

value: umbilical cord

value: primary cell

value: mesenchymal stem cell

value: 2d cultivation


title: ScRNA-seq of NR patient before CACAG-VEN

description: Library name: NR-pretreatment


title: human_hela_cell_rna_3

description: Library name: human_hela_cell_rna_3

value: Skop


title: TOP2A ICEseq Input, VEH, 45 min, rep2


title: human_hela_cell_rna_2

description: Library name: human_hela_cell_rna_2


title: TOP1 ICEseq, E2, 45 min


title: human umbilical cord mesenchymal stem cells，2d cultivation，sus1

description: Library name: sus1

value: WT


title: Sen_ko, rep3

city: TIANJIN

first: hong

last: lei

address: WEIJIN STREET

institute: nankai university

description: Library name: Sample 12

data_processing:
Approximately 10 million reads were obtained by Illumina sequencing. Differential expression analysis was performed using Bluebee (Lexogen).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Primary MEF

growth_protocol: Primary MEF were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated and purified by using a total RNA extraction kit (Promega), according to the manufacturer’s protocols, and then was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the QuantSeq 3’ mRNASeq Library Prep Kit (Lexogen) following manufacturer's protocols.

treatment_protocol: Cellular senescence was induced by treatment of Etoposide for 48 hours in NRF1-knockout (KO) Primary MEF or wild-type (WT) Primary MEF; Cellular proliferation was induced by treatment of DMSO for 48 hours in NRF1-knockout (KO) Primary MEF or wild-type (WT) Primary MEF.

value: embryo

value: mouse embryonic fibroblasts

value: Etoposide


title: human_hela_cell_rna_1

description: Library name: human_hela_cell_rna_1


title: Normal diet-1

description: Library name: Sample 1


title: human_hepg2_cell_rna_2

description: Library name: human_hepg2_cell_rna_2


title: human umbilical cord mesenchymal stem cells，2d cultivation，sus2

description: Library name: sus2


title: TOP2B ICEseq Input, VEH, 45 min, rep2


title: CDAHFD-1

description: Library name: Sample 4


title: Sen_ko, rep2

description: Library name: Sample 11


title: TOP2A ICEseq Input, E2, 45 min, rep2


title: human_esc_mbr_rna_6

description: Library name: human_esc_mbr_rna_6


title: TOP2B ICEseq Input, E2, 45 min, rep2


title: human umbilical cord mesenchymal stem cells，3d cultivation，sph3

description: Library name: sph3

value: 3d cultivation


title: human umbilical cord mesenchymal stem cells，3d cultivation，sph2

description: Library name: sph2


title: human umbilical cord mesenchymal stem cells，3d cultivation，sph1

description: Library name: sph1


title: human_esc_mbr_rna_5

description: Library name: human_esc_mbr_rna_5


title: A549 shNNMT 2

city: Chongqing

first: He

last: Xiao

state: Chongqing

address: No. 10, Changjiang Branch Road, Yuzhong District, Chongqing 400042, China

department: Department of Cancer Center

institute: Daping Hospital, Army Medical University

description: Library name: A549 shNNMT 2

data_processing:
Low quality raw reads were filtered with fastp (version 0.23.2) before aligned to hg19 human genome reference with Bowtie2 in Bismark. Differentially methylated regions (DMRs) were identified using the R package DSS (version 2.48.0). The significance of differential methylation at single base level was inferred with DMLtest with smoothing = T. DMRs were identified with callDMR setting parameter p.thrshold = 0.01. A differential methylation > 0.2 was defined as a hypermethylated, while a difference < -0.2 was defined as a hypomethylated
Assembly: hg19
Supplementary files format and content: EXCEL file includes raw counts for each sample. Each row in the file represents <chromosome> <position> <methylated_count><unmethylated_count>

extract_protocol:
Bisulfite conversion (EZ DNA Methylation Gold Kit, Zymo Research)
Amplify 24 μL of bisulfite-converted DNA with 25 μL of KAPA HiFi Uracil+ readymix (Roche, Basel, Switzerland) and 1 μL of 25 μM Illumina compatible primers

value: shNNMT


title: Sen_wt, rep1

description: Library name: Sample 7

value: wt


title: TOP2A ICEseq, VEH, 45 min, rep2


title: A549 shNNMT 1

description: Library name: A549 shNNMT 1


title: TOP2A ICEseq, VEH, 45 min, rep1


title: Sen_wt, rep3

description: Library name: Sample 9


title: Prol_ko, rep3

description: Library name: Sample 6

value: DMSO


title: human_esc_cell_rna_1

description: Library name: human_esc_cell_rna_1


title: Prol_ko, rep2

description: Library name: Sample 5


title: TOP2A ICEseq, E2, 45 min, rep2


title: human_esc_cell_rna_2

description: Library name: human_esc_cell_rna_2


title: HUVEC CELLS, HPDM group, 3days 3

city: 南充市

first: Cai-Ping

last: Yan

state: sichuan

address: No. 1 The South of Maoyuan Road

department: orthopedics

institute: North sichuan medical college

description:
Library name: Hu-H-3
HUVECs_ref_trans_full_table.txt

data_processing:
After passing the library quality inspection, high-throughput sequencing was performed using the Illumina NovaSeq6000 platform in paired-end 150bp (PE150) mode.
Assembly: The sequencing data was analyzed through the BMK Cloud platform (www.biocloud.net).
Supplementary files format and content: FPKM, count valus for each Sample

source_name: HUVEC

growth_protocol: The third-generation cells were seeded at 5×10^3 cells/well in a 96-well plate, with 200μL of material extract added to each well. After 48 hours of incubation (5% CO2, 37°C), the extract was aspirated and discarded, followed by washing the cells with PBS three times.

extract_protocol:
Upon reaching the predetermined time points, the cells were lysed with TRIzol, cooled in liquid nitrogen for 5-10 minutes, and stored at −80°C.
The NanoDrop 2000 spectrophotometer was used to measure the purity and concentration of RNA, while the Agilent 2100/LabChip GX assessed RNA integrity. After passing sample quality control, library construction and quality control were performed.

value: HUVEC

value: Endothelial

value: HPDM


title: Sen_ko, rep1

description: Library name: Sample 10


title: A549 OV-LKB1 2

description: Library name: A549 OV-LKB1 2

value: Overexpression LKB1


title: HUVEC CELLS, HPDM group, 3days 2

description:
Library name: Hu-H-2
HUVECs_ref_trans_full_table.txt


title: TOP2A ICEseq, E2, 45 min, rep1

value: ER positive breast cancer cell line

value: 45 min 10 nM E2


title: A549 shNC 2

description: Library name: A549 shNC 2

value: shNC


title: Prol_wt, rep3

description: Library name: Sample 3


title: human_esc_mbr_rna_4

description: Library name: human_esc_mbr_rna_4


title: TOP2B ICEseq, VEH, 45 min, rep2

value: 45 min EtOH


title: A549 shNC 1

description: Library name: A549 shNC 1


title: TOP2B ICEseq, E2, 45 min, rep1


title: Prol_ko, rep1

description: Library name: Sample 4


title: TOP2B ICEseq, E2, 45 min, rep2


title: A549 OV-LKB1 1

description: Library name: A549 OV-LKB1 1


title: HUVEC CELLS, HP group, 3days 3

description:
Library name: Hu-B-3
HUVECs_ref_trans_full_table.txt

value: HP


title: TOP2B ICEseq, VEH, 45 min, rep1


title: HUVEC CELLS, HP group, 3days 2

description:
Library name: Hu-B-2
HUVECs_ref_trans_full_table.txt

value: WT


title: HUVEC CELLS, HPDM group, 3days 1

description:
Library name: Hu-H-1
HUVECs_ref_trans_full_table.txt


title: Sen_wt, rep2

description: Library name: Sample 8

value: embryo


title: Prol_wt, rep2

description: Library name: Sample 2

value: mouse embryonic fibroblasts


title: human_esc_cell_rna_3

description: Library name: human_esc_cell_rna_3

value: Skop


title: CHB donor Hu-P-005524  spatial transcriptomics

city: Foster City

first: Ricardo

last: Ramirez

address: 333 Lakeside Drive

institute: Gilead Sciences

description: Library name: SAM006188_LIB006621

data_processing:
Illumina Fastq files were aligned to 10x Visium human transcriptome probe set v2.0_GRCh38-2020-A using Spaceranger-3.0.1
Count data were merged in R using the Seurat package and normalized using SCTransform
Cell-type estimation was performed using RCTD from spacexr version 2.2.1
Assembly: hg38
Supplementary files format and content: compressed Seurat R data objects
Library strategy: Spatial Transcriptomics

extract_protocol:
10X Visium FFPE Kit
FFPE sections of 5µm thickness were prepared using a Leica RM2255 microtome and placed on Superfrost Plus glass slides (Epredia, Cat#22-042-941), as per guidance outlined in 10X Genomics Visium CytAssist Tissue preparation guide (CG000518). Slides were subjected to H&E staining as outlined in guidance provided by 10X Genomics (CG000518). Following H&E staining, slides were imaged using Aperio AT2 DX scanner (Leica Biosystems, Cat#23AT2100) at 40X magnification. Following imaging, coverslips were removed, and tissues were decrosslinked. Library construction was conducted as described in 10X Genomics, CG000495. Post library construction QC was performed on the 2100 Bioanalyzer Instrument (Agilent) with the High Sensitivity DNA Kit (Agilent Technologies, Cat#5067-4626). Library concentrations were measured using the Qubit dsDNA High Sensitive Assay Kit (Invitrogen, Cat#Q32854). Sequencing was performed on the Illumina NovaSeq6000, following the guidance outlined in the 10X Genomics Visium CytAssist Spatial Gene Expression User Guide (CG000495). Sequencing was performed to meet a targeted sequencing depth of 50,000 read pairs per tissue-covered spot.

value: Liver


title: YUMM1.7

city: Mannheim

first: Volker

last: Ast

address: Theodor-Kutzer-Ufer 1-3

department: NGS Core Facility

institute: University Hospital Mannheim

description: Library name: Unknown_CE192-ZX01-010002

data_processing:
The cell calling and gene counting were done using the Cell Ranger software v8.0.1
Assembly: Mouse mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lymph node

extract_protocol:
Lymph nodes were collected and digested using collagenase to yield a single cell suspension. Positive enrichment of target cells was achieved using a mix of CD11b and CD11c magnetic beads. Approx. 10000 cells / condition were subjected to GEM generation using the Chromium GEM-X Single Cell 3' Kit v4
Chromium GEM-X Single Cell 3' Kit v4

value: lymph node

value: positively enriched for CD11b and/or CD11c expression

value: YUMM1.7 bearing mice


title: A549 EV-LKB1 2

description: Library name: A549 EV-LKB1 2

value: Empty vector


title: HeLa cells, GM2 treated2

city: Kolkata

first: Kaushik

last: Biswas

state: WB

address: Block EN-80 Sector V, Salt Lake, College More

department: Department of Biological Sciences

country: India

institute: Bose Institute

description: Library name: GM2_2

data_processing:
The sequenced reads were trimmed and aligned to the human genome (GRCh38, refseq). Transcript assembly was performed by Cufflinks Supplementary files format and content: Fragments Per Kilobase of transcript per Million mapped reads (FPKM) as a txt file
Assembly: GRCh38

extract_protocol:
Total RNA from GM2 treated and non-treated samples was extracted using the Trizol-chloroform method (Trizol reagent procured from Invitrogen). The extracted RNA was treated with RNase free Dnase (Ambion) to remove genomic DNA contamination.
RNA sequencing libraries were prepared with Illumina-compatible NEBNext® Ultra™ Directional  RNA Library Prep Kit (New England BioLabs, MA, USA) at Genotypic Technology Pvt. Ltd., Bangalore,India

value: HeLa

value: Epithelial cells


title: CHB donor Hu-P-005522 spatial transcriptomics

description: Library name: SAM006179_LIB006612


title: Input POLII ChIPseq, siC (siZATT), VEH, 45 min

data_processing:
Tags were aligned to human genome (hg19) using Bowtie (version 1.2.0).
Peaks were called using MACS2 and broad peak mode. Peaks from differente biological repeats were merged.
For genome tracks, we used bamCoverage (deepTools) to convert aligned reads to signal tracks (bigwig) using RPGC normalization (bin size of 50 bps and 300 bps read extension). Spike-in normalization was applied to all ChIPseq experiments to correct technical biases and global differences. Spike-in normalization was performed using mouse chromatin in our human experiments, basically as described by Minchell et al. 2020.
Assembly: hg19
Supplementary files format and content: bigWig (Coverage files)
Supplementary files format and content: bed (called peaks)

extract_protocol:
MCF-7 cells were fixed by adding formaldehyde to a final concentration of 1% and incubated at 37ºC for 10 min before quenching with 125 mM glycine. Subsequently, culture plates were washed twice with cold PBS and collected in protease inhibitor cocktail, centrifuged and lysed in two steps: 10 min incubation in 1 ml Lysis Buffer A (5 mM Pipes pH 8, 85 mM KCl, 0,5% NP40, 1 mM PMSF, 1x Complete Protease inhibitor cocktail) for nuclei isolation and then, adding 300 µl Lysis Buffer B (50 mM Tris HCl pH 8.1, 1% SDS, 10 mM EDTA, 1 mM PMSF, 1x Complete Protease inhibitor cocktail) to pelleted nuclei (4000 rpm, 5 min) for nuclear lysis. Sonication was performed using Bioruptor (Diagenode, UCD-200) at high intensity for 25 min (30” sonication, 30” pause). Chromatin was clarified by centrifugation (17,000 × g, 10 min, 4 °C).
Libraries were prepared by ChIPmentation as described by Schmidl et al. 2015 using NEBNext HF Polymerase and sequenced using Illumina NextSeq 500.

value: siC 60h + 45min EtOH


title: HeLa cells, GM2 treated1

description: Library name: GM2_1


title: ESC-CTCF/WAPL-AID, E14, IAA treated 72 hours, ATAC-Seq

city: Bethesda

first: Sergio

last: Ruiz Macias

state: Maryland

address: 37 Convent Dr, Room 1112B

department: Center for Cancer Research

institute: National Cancer Institute

description: Library name: SCAF3619_CMV118_D3_ATAC

library_source: genomic single cell

data_processing:
Base calling was performed using RTA 3.4.4
Demultiplexing was performed using cellranger-arc v2.0.2 (Bcl2fastq 2.20.0)
Alignment was performed using cellranger-arc v2.0.2 (BWA 0.7.17-r1188)
Sequenced reads were aligned to refdata-cellranger-arc-mm10-2020-A-2.0.0
Assembly: mm10
Supplementary files format and content: Cellranger-ARC output files: filtered_feature_bc_matrix.h5, raw_feature_bc_matrix.h5
Supplementary files format and content: Cellranger-ARC output files: atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi

growth_protocol: ESC were grown on 0.1% gelatin-coated plates in high-glucose DMEM (Gibco) supplemented with 15% FBS, 1:500 LIF (made in house), 0.1 mM non-essential amino acids, 1% glutamax, 1mM Sodium Pyruvate, 55 mM β-mercaptoethanol, and 1% penicillin/streptomycin (all from ThermoFisher Scientific) at 37°C and 5% CO2. Cells were routinely passaged with Trypsin 0.05% (Gibco). Media was changed every other day and passaged every 2-3 days.

extract_protocol:
The nuclei isolation was performed according to 10x Genomics guidelines. In brief, 500,000 trypsinized ESC were washed with PBS + 0.04% BSA and then lysed in 100ul Lysis Buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.01% Tween-20, 0.01% IGEPAL CA-630, 0.001% Digitonin, 1% BSA, 1mM DTT, 1 U/ul RNase inhibitor) for 5 minutes on ice. Immediately after, lysed cells were washed three times with 1ml Wash Buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 1% BSA, 0.1% Tween-20, 1mM DTT, 1 U/ul RNase inhibitor) and resuspended in 100ul Diluted Nuclei Buffer (1X Nuclei Buffer, 1mM DTT, 1 U/ul RNase inhibitor). Nuclei concentration was determined using LUNA Automated Cell Counter.
Single-nucleus multiome libraries were prepared according to the 10x Genomics Multiome User Guide (CG000338). In short, nuclei were transposed and then partitioned with barcoded gel beads on a Chromium X controller. Transposed genomic DNA fragments and reverse-transcribed mRNA were single-cell barcoded, and libraries for ATAC and RNA-Seq were separated and processed in parallel. Sequencing libraries were prepared and quantified on an Agilent BioAnalyzer before being sequenced on an Illumina NovaSeq X Plus.

treatment_protocol: ESC were untreated or treated for the indicated times with indole-3-acetic acid (IAA) at a final concentration of 500nM.

value: Embryonic stem cell

value: CTCF/WAPL-AID

value: IAA

value: 72 hours


title: Prol_wt, rep1

description: Library name: Sample 1

value: wt

value: DMSO


title: Input POLII ChIPseq, siZATT, E2, 45 min

value: ER positive breast cancer cell line

value: siZATT 60h + 45 min 10 nM E2


title: CHB donor Hu-P-003720 spatial transcriptomics

description: Library name: SAM006183_LIB006616


title: Input POLII ChIPseq, siTOP2A, E2, 45 min

value: siTOP2A 60h + 45 min 10 nM E2


title: HUVEC CELLS, HP group, 3days 1

description:
Library name: Hu-B-1
HUVECs_ref_trans_full_table.txt

value: HUVEC

value: Endothelial

value: WT

value: HP


title: A549 EV-LKB1 1

description: Library name: A549 EV-LKB1 1

value: Empty vector


title: Input POLII ChIPseq, siC (siZATT), E2, 45 min

value: siC 60h + 45 min 10 nM E2


title: healthy donor Hu-P-003752 spatial transcriptomics

description: Library name: SAM006185_LIB006618

value: Liver


title: YUMMER1.7

description: Library name: Unknown_CE192-ZX01-010003

value: lymph node

value: positively enriched for CD11b and/or CD11c expression

value: YUMMER1.7 bearing mice


title: Input POLII ChIPseq, siZATT, VEH, 45 min

value: siZATT 60h + 45min EtOH


title: Naive

description: Library name: Unknown_CE192-ZX01-010001

value: tumor-free mice


title: ESC-CTCF/WAPL-AID, E14, IAA treated 24 hours, ATAC-Seq

description: Library name: SCAF3617_CMV118_D1_ATAC

value: Embryonic stem cell

value: CTCF/WAPL-AID

value: IAA

value: 24 hours


title: MCF-7PR cell, R5020, Treated, 96 hrs, Rep 3

city: Singapore

first: Valerie Chun Ling

last: Lin

address: 60, Nanyang Dr

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

description: Library name: RHC11497

data_processing:
Trim galore was used to trim the FASTQ files for all samples. FASTQC was done on these files.
STAR was used to map the reads to the human genome GRCh38 using GENCODE 41 annotations
featureCounts were then used to generate the gene counts using GENCODE 41 annotations.
The gene counts were then used for an DESeq2 analysis
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file for raw counts, log2tpm and log2rpkm

growth_protocol: The MCF-7PR cells were maintained in DMEM with phenol red,  supplied with 7.5% of FBS and 2mM L-glutamine

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Thermo Fisher Scientific, USA) and treated with Dnase I using the DNA-free™ DNA Removal Kit (Invitrogen, Carlsbad, CA, USA) to remove any contaminating DNA.
The total RNA was sent to Genome Institute of Singapore, Agency for Science, Technology and Research for library preparation and pair-end sequencing

treatment_protocol: The cells were starved for 48 hrs before 0.1% ETOH or 10nM R5020 treatment for 96 hrs. There were triplicates for each of the treatments

value: Epithelial cell

value: R5020 treatment


title: CHB donor Hu-P-005521 spatial transcriptomics

description: Library name: SAM006184_LIB006617


title: HeLa cells, SFM (serum starved condition) Control2

description: Library name: SFM2

value: HeLa

value: Epithelial cells


title: Input POLII ChIPseq, siTOP2A, VEH, 45 min

value: ER positive breast cancer cell line

value: siTOP2A 60h + 45min EtOH


title: HeLa cells, SFM (serum starved condition) Control1

description: Library name: SFM1


title: MCF-7PR cell, R5020, Treated, 96 hrs, Rep 2

description: Library name: RHC11496


title: Input POLII ChIPseq, siC (siTOP2A), E2, 45 min

value: siC 60h + 45 min 10 nM E2


title: healthy donor Hu-P-003749 spatial transcriptomics

description: Library name: SAM006182_LIB006615

value: Liver


title: WT_SC3

city: Cincinnati

first: Konrad

last: Thorner

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: Library name: Sample54

data_processing:
Processed with the nf-core-rnaseq pipeline, version 3.13.2, with STAR/Salmon selected for the alignment/quantification.
Assembly: GRCh38
Supplementary files format and content: Length-corrected raw counts

source_name: Stem cell for endoderm differentiation

extract_protocol:
RNA was extracted from tissue samples using the Macherey-Nagel Nucleospin RNA Kit.
For library preparation, 150 to 300ng of total RNA determined by InvitrogenTM QubitTM high-sensitivity spectrofluorometric measurement was poly-A selected and reverse transcribed using Illumina’s TruSeq stranded mRNA library preparation kit.

value: Stem cell for endoderm differentiation

value: WT

value: Endoderm differentiation


title: ESC-CTCF/WAPL-AID, E14, IAA treated 48 hours, RNA-Seq

description: Library name: SCAF3618_CMV118_D2_GEX

value: 48 hours


title: Input POLII ChIPseq, siTOP2B, VEH, 45 min

value: siTOP2B 60h + 45min EtOH


title: ESC-CTCF/WAPL-AID, E14, IAA untreated, ATAC-Seq

description: Library name: SCAF3616_CMV118_D0_ATAC

value: Embryonic stem cell

value: Untreated


title: ESC-CTCF/WAPL-AID, E14, IAA treated 24 hours, RNA-Seq

description: Library name: SCAF3617_CMV118_D1_GEX

value: CTCF/WAPL-AID

value: IAA


title: Input POLII ChIPseq, siC (siTOP2B), E2, 45 min


title: ESC-CTCF/WAPL-AID, E14, IAA treated 48 hours, ATAC-Seq

description: Library name: SCAF3618_CMV118_D2_ATAC


title: cell pellet array

description: Library name: SAM009165_LIB009655

value: PLC/PRF/5, PHH

value: HCC, Primary Human hepatocyte


title: Input POLII ChIPseq, siC (siTOP2A), VEH, 45 min

value: siC 60h + 45min EtOH


title: Input POLII ChIPseq, siC (siTOP2B), VEH, 45 min


title: WT_D9_RESPENDO3

description: Library name: Sample51

source_name: Ventral anterior foregut endoderm

value: Ventral anterior foregut endoderm


title: ESC-CTCF/WAPL-AID, E14, IAA untreated, RNA-Seq

description: Library name: SCAF3616_CMV118_D0_GEX


title: MCF-7PR cell, ETOH, Control, 96 hrs, Rep 1

description: Library name: RHC11492

value: Epithelial cell

value: ETOH Control


title: CD45- celll in Py8119 tumors from MTDH KO mice

city: Plainsboro

first: Yong

last: Wei

state: NJ

address: LTL227 Wathington Road

department: Molecular Biology

institute: Princeton University

description: Library name: Py8119 KO

data_processing:
The library pools were denatured and sequenced on Illumina NovaSeq 6000 using the S Prime flowcells as pair-end 65 nt reads according to the manufacturer’s protocol.  Raw sequencing reads were filtered by Illumina NovaSeq Control Software, only the Pass-Filter (PF) reads were de-multiplexed allowing 1 mismatch and used for further analysis.
Demultiplexed raw sequence file (FASTQ) were analyzed using Partek® Flow® software package. Raw reads were aligned using STAR 2.7.8a.Gene counts were obtained by quantifying against the mm39-Ensembl Transcripts release 108 annotation model. After noise filtering, counts were normalized using log2( FPKM+1).
Assembly: mm39-Ensembl Transcripts release 108
Supplementary files format and content: tab-delimited text files with  log2( FPKM+1) values

source_name: tumors

growth_protocol:
Cell preparation protocol: Py8119 tumors were harvested from mouse, and processed into single cell suspspension using tissu disscociator with tumor dissociatio kit from Milltenyi biotec. Red blood cells were removed with RBC lysis buffer.The cell suspension was filtered through a 70-μm strainer and stained with live dye and related antibodies.
FACS sorting protocol: Target cells were sorted from live cells with CD45-.

extract_protocol:
Total RNA were extracted using RNAeasy micro-prep kit from Qiagen
The integrity of total RNA samples were assessed on Bioanalyzer 2100 using RNA 6000 Pico chip (Agilent Technologies, CA).  Messenger RNA was enriched from these samples using QIAseq FastSelect - rRNA HMR Kit (Qiagen, CA), fragmented and converted to cDNA and Illumina sequencing library using the PrepX RNA-seq library preparation protocol on the Apollo 324TM NGS Library Prep System (Takara Bio, CA).

value: tumors

tag: tumor cell_mtdh_status

value: wild type

tag: host genotype

value: Mtdh knock out (KO)


title: Input POLII ChIPseq, siTOP2B, E2, 45 min

value: ER positive breast cancer cell line

value: siTOP2B 60h + 45 min 10 nM E2


title: ESC-CTCF/WAPL-AID, E14, IAA treated 72 hours, RNA-Seq

description: Library name: SCAF3619_CMV118_D3_GEX

value: 72 hours


title: MCF-7PR cell, ETOH, Control, 96 hrs, Rep 3

description: Library name: RHC11494


title: Input POLII ChIPseq, ICRF-187, E2, 45 min

value: ICRF-187 100uM 60min + 45 min 10 nM E2


title: MCF-7PR cell, R5020, Treated, 96 hrs, Rep 1

description: Library name: RHC11495

value: R5020 treatment


title: WT_SC1

description: Library name: Sample52

value: Stem cell for endoderm differentiation

value: WT

value: Endoderm differentiation


title: Input POLII ChIPseq, ICRF-187, VEH, 45 min

value: ICRF-187 100uM 60min + 45min EtOH


title: MCF-7PR cell, ETOH, Control, 96 hrs, Rep 2

description: Library name: RHC11493


title: WT_D9_RESPENDO2

description: Library name: Sample50


title: WT_SC2

description: Library name: Sample53


title: BM1 CTRL and RKIP tumors single-cell RNA-seq replicate 3

city: Chicago

first: Marsha

middle: Rich

last: Rosner

state: IL

address: 929 E 57th St

institute: University of Chicago

description: BM1-vector control (BM1-VC) and BM1-RKIP-S153E (BM1-RKIP) cells were generated from wild-type BM1 by Dangi-Garimella and colleagues. Wild-type BM1 cells were generated by Massagué and colleagues and were originally derived from MDA-MB-231.

data_processing:
For the single-cell RNA-seq experiment, the RNA sequencing data were demultiplexed using the manufacturer-supplied API script to generate individual FASTQ files for single cells based on the barcodes used (Fluidigm, mRNASeqHT_demultiplex.pl). The reads were mapped to the human genome (UCSC hg38 with GENCODE annotations) using RNA STAR. The resulting mapped reads from every single cell were counted by featureCounts to generate per-gene read counts. Gene expression data from three biological replicates were combined, and the batch effect was corrected via the “BatchCorrectedCounts” function in the CountClust package by specifying the replicate number as the variable to regress out.
For the bulk RNA-seq experiment, all ten samples were sequenced in four runs by a NovaSeq 6000 sequencer (Illumina) to generate paired-end 100bp reads. The raw FASTQ files from four flow cells were combined for each sample before downstream processing. RNA-seq data were analyzed using a local Galaxy instance. Quality and adapter trimming were applied to the raw sequencing reads using the Trim Galore! Package (Felix Krueger, github.com/FelixKrueger/TrimGalore). The reads were mapped to the human genome (UCSC hg19 with GENCODE annotation) using RNA STAR. Per gene read counts from each sample were generated by featureCounts.
Assembly: Single-cell study: Human (hg38). Bulk tumor study: Human (hg19).
Supplementary files format and content: Comma delimited text file containing a matrix table with raw gene counts for every gene and every sample.

source_name: BM1 CTRL and RKIP xenograft primary mammary tumors (one each)

growth_protocol:
BM1 cells were cultured in DMEM media (Gibco, 11965-118) with 10% fetal bovine serum (FBS, Avantor, 97068-085) and 1% penicillin-streptomycin (Gibco, 15140-122).
1 × 10^6 BM1-VC or BM1-RKIP cells were injected orthotopically into the mammary fat pad of athymic nude mice (Harlan Envigo). The mice were sacrificed three weeks after tumor cell implantation. Primary tumors were collected for single-cell isolation.

extract_protocol:
BM1 cells from one CTRL tumor and one RKIP tumor were isolated through tumor dissociation, mouse cell depletion, and dead cell removal following the manufacturer's protocols (Miltenyi Biotec, 130-095-929, 130-104-694, 130-090-101). Suspensions of single cells were processed on a Fluidigm C1 instrument using a C1 Single-Cell mRNA Seq HT IFC and Reagent Kit v2 (Fluidigm, 101-4981, 101-3743).
cDNA synthesis, barcoding, library preparation, and quality check were performed following the manufacturer’s protocol (Fluidigm, PN 101-4964 I1).
none provided by the submitter

tag: sequencing type

value: Single-cell RNA-seq


title: Islet cells from offspring of intrauterine hyperglycemia mother mouse

city: Shanghai

first: Jiahang

last: Mo

address: No.131 Dong'an Road

department: Institute of Reproduction and Development

institute: Obstetrics and gynecology Hospital of Fudan University

description: Library name: Sample 4

data_processing:
The raw data were quantified by Cell Ranger. Analyses were conducted using the Seurat program. For quality control, we removed cells for which fewer than 500 UMIs. Simultaneous data normalization/scaling and variable feature detection was performed using “LogNormalize”. Cells were integrated by canonical correlation analysis (CCA). Cells were clustered via Seurat’s shared nearest neighbor clustering algorithm (“FindNeighbors” and “FindClusters”) using the the top 10 PCs and a resolution of 0.5. The top 10 most variable PCs were used for subsequent clustering. The clustering was visualized using t-Distributed Stochastic Neighbor Embedding (tSNE).
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: pancreatic islet

extract_protocol:
Adult mouse pancreatic islets were isolated by collagenase IV (2 mg/ml; Worthington) digestion, separated by density gradient centrifugation, and handpicked under a stereomicroscope. Islets were cultured in a standard RPMI medium supplemented with 10% FBS. After isolation and extraction, each tube contained 200-300 islets; they were digested with 0.25% Trypsin-EDTA, at 37 ℃ for 2 min. Digestion was stopped using RPMI 1640 containing 10% fetal bovine serum (FBS), blowing evenly. It was centrifuged at 1360 rpm for 5 min at 4 ℃. After the supernatant was abandoned, it was resuspended with 4 ℃ PBS containing 0.2% BSA, with cell concentration control at approximately 1000 counts/μL. Debris and dead cells were removed.
Single-cell RNA-Seq libraries were prepared using SeekOne® MM Single Cell 3’ library preparation kit (cat.). Briefly, appropriate cells were loaded into the flow channel of SeekOne® MM chip. Cell Barcoded Magnetic Beads (CBBs) were pipetted into flow channel and also allowed to settle in microwells with the help of a magnetic field. Cells in MM chip were lysed to release RNA which was captured by the CBB in the same microwell. Then all CBBs were collected and reverse transcription were performed at 37℃ for 30 minutes to lable cDNA with cell barcode on the beads. Further Exonuclease I treatment were performed to remove unused primer on CBBs. Subsequently, barcoded cDNA on the CBBs was hybridized with random primer which had reads 2 SeqPrimer sequence on the 5’ end and could extend to form the second strand DNA with cell barcode on the 3’ end. The resulting second strand DNA were denatured off the CBBs, purified and amplified in PCR reaction. The amplified cDNA product was then added to full length sequencing adapter and sample index by indexed PCR. The indexed sequencing libraries were cleanup with SPRI beads, quantified by quantitative PCR and then sequenced on illumina NovaSeq 6000 with PE150 read length.

value: pancreatic islet

value: male

tag: age

value: 8 weeks

value: offspring from intrauterine hyperglycemia model


title: WT_D9_RESPENDO1

description: Library name: Sample49

value: Ventral anterior foregut endoderm


title: Islet cells from offspring of control mother mouse

description: Library name: Sample 3

value: offspring from control model


title: Islet cells from Tet2(flox/flox)Tet3(flox/flox) Pdx1 cre+ mouse

description: Library name: Sample 2


title: BM1 CTRL and RKIP tumors single-cell RNA-seq replicate 2


title: Input POLII ChIPseq, MERB, E2, 45 min

value: Merb 100uM 60min + 45 min 10 nM E2


title: WT_D9_ESOPHENDO3

description: Library name: Sample48

source_name: Dorsal anterior foregut endoderm

value: Dorsal anterior foregut endoderm


title: WT_D9_ESOPHENDO2

description: Library name: Sample47


title: Control_3

city: Guangzhou

first: Yanteng

last: Xu

state: Guangdong

address: 600# Tianhe Road

department: Centre for Nanomedicine

institute: The Third Affiliated Hospital of Sun Yat-sen University

description: Library name: Control_3

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used Ensembl (ftp://ftp.ensembl.org/pub/release-107/fasta/mus musculus c57bl6nj/dna/) to map reads to the reference genome of mus musculus Ensembl_v107. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: mus_musculus Ensembl_v112
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Tumor

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.  The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).  The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.   Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.  e6150, USA) under 94℃ 5-7min.   Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat.   1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.  m0209, USA), RNase H (NEB, cat.  m0297, USA) and dUTP Solution (Thermo Fisher, cat.  R0133, USA）.   An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters.   Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA.   Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads.   After the heat-labile UDG enzyme (NEB, cat.  m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min;   8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec;   and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.   At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Tumor


title: CD45- celll in Py8119 tumors from MTDH WT mice

description: Library name: Py8119 WT

value: tumors

value: wild type

value: Mtdh wild type (WT)


title: human stellate cells - Nuclear_rep2

city: Boston

first: Alan

middle: C.

last: Mullen

state: MA

address: 55 Fruit St.

department: Department of Medicine

institute: Massachusetts General Hospital

data_processing:
no processed data
Reads were quality asssed using the FASTQC (v 0.11.9).
Genome_build: GRCh38

source_name: primary human stellate cells

growth_protocol: Adult HSCs were grown in DMEM (Gibco) containing 10 percent FBS.

extract_protocol:
Cells were washed two times in PBS. Cells were then resuspended in the hypotonic buffer (20 mM Tris-HCl pH 7.4, 10 mM NaCl and 3 mM MgCl2, 0.5% NP-40) and incubated on ice for 30 mins with a gentle vortex every 10 mins. The supernatant was collected to extract RNA representing cytoplasmic fraction using Trizol LS reagent. The nuclei pellet was resuspended in the hypotonic buffer and spun down again to rinse the nuclei. A small fraction of nuclei were examined under the microscope to confirm complete isolation. The nuclei were resuspended in Trizol reagent (Thermo Fisher) to extract nuclear RNA fraction
The strand-specific RNA sequencing library was prepared by using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following the manufacturer’s instructions (NEB). Briefly, the enriched RNAs were fragmented for 8 minutes at 94°C. First strand and second strand cDNA were subsequently synthesized. The second strand of cDNA was marked by incorporating dUTP during the synthesis. The cDNA fragments were adenylated at 3’-ends, and an indexed adapter was ligated to cDNA fragments. Limited cycle PCR was used for library enrichment. The incorporated dUTP in second strand cDNA quenched the amplification of second strand, which helped to preserve the strand specificity. The sequencing library was validated on the Agilent TapeStation, and quantified by using Qubit 2.0 Fluorometer (Thermo Fisher) as well as by quantitative PCR (KAPA Biosystems).

value: Untreated

tag: molecule

value: Nuclear RNA


title: WT_D9_ESOPHENDO1

description: Library name: Sample46

value: WT

value: Endoderm differentiation


title: human stellate cells - ribominus

extract_protocol:
HSCs were rinsed with PBS and lysed using Trizol reagent (Thermo Fisher). The mixture was vortexed and incubated at room temperature to ensure complete lysis of cells and separation of protein-RNA complexes. RNA was then extracted using chloroform (Sigma) and precipitated using ethanol and centrifuged at 13,000 RPM for 20 min to form an RNA pellet. The RNA pellet was rinsed with 75% ethanol. The RNA was resuspended in nuclease free water and incubated with DNase I (Thermo Fisher) to remove potentially contaminating genomic DNA fragments. The RNA was then extracted using acidic phenol chloroform, precipitated in ethanol, and resuspended in nuclease free water. RNA samples with RIN score of >9 were sequenced.
The strand-specific RNA sequencing library was prepared by using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following the manufacturer’s instructions (NEB). Briefly, the enriched RNAs were fragmented for 8 minutes at 94°C. First strand and second strand cDNA were subsequently synthesized. The second strand of cDNA was marked by incorporating dUTP during the synthesis. The cDNA fragments were adenylated at 3’-ends, and an indexed adapter was ligated to cDNA fragments. Limited cycle PCR was used for library enrichment. The incorporated dUTP in second strand cDNA quenched the amplification of second strand, which helped to preserve the strand specificity. The sequencing library was validated on the Agilent TapeStation, and quantified by using Qubit 2.0 Fluorometer (Thermo Fisher) as well as by quantitative PCR (KAPA Biosystems).
The sequencing libraries were multiplexed and clustered onto a flow cell. After clustering, the flow cell was loaded onto the Illumina HiSeq 4000 or equivalent instrument according to the manufacturer’s instructions. The samples were sequenced using 2×100bp or 2×150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mismatch was allowed for index sequence identification.

value: rRNA-depleted RNA


title: Input POLII ChIPseq, DMSO (ICRF-187), VEH, 45 min

value: ER positive breast cancer cell line

value: DMSO 60min + 45min EtOH


title: Islet cells from Tet2(flox/flox)Tet3(flox/flox) Pdx1 cre- mouse

description: Library name: Sample 1

value: pancreatic islet

value: male

value: 8 weeks


title: WT_D6_ENDO3

description: Library name: Sample45

source_name: Anterior foregut endoderm

value: Anterior foregut endoderm


title: human stellate cells - Cytoplasmic_rep2

value: Cytoplasmic RNA


title: Input POLII ChIPseq, DMSO (Merb), E2, 45 min

value: DMSO 60 min + 45 min 10 nM E2


title: Input POLII ChIPseq, DMSO (Merb), VEH, 45 min


title: BM1 CTRL and RKIP tumors single-cell RNA-seq replicate 1

value: Single-cell RNA-seq


title: WT_D3_ENDO3

description: Library name: Sample42

source_name: Definitive endoderm

value: Definitive endoderm


title: WT_D6_ENDO2

description: Library name: Sample44


title: Lenvatinib_anti_PD1_3

description: Library name: Lenvatinib_anti_PD1_3

value: Tumor


title: WT_D6_ENDO1

description: Library name: Sample43


title: human stellate cells - Nuclear_rep1


title: Input POLII ChIPseq, MERB, VEH, 45 min

value: Merb 100uM 60min + 45min EtOH


title: Input TOP2A ChIPseq, E2, 45 min, rep2

value: 45 min 10 nM E2


title: WT_D3_ENDO1

description: Library name: Sample40


title: Input POLII ChIPseq, DMSO (ICRF-187), E2, 45 min


title: Lenvatinib_anti_PD1_1

description: Library name: Lenvatinib_anti_PD1_1


title: Input ZATT ChIPseq, E2, 45 min, rep2


title: human stellate cells - Cytoplasmic_rep1

value: Untreated


title: Control_1

description: Library name: Control_1


title: Input ZATT ChIPseq, VEH, 45 min, rep2

value: 45 min EtOH


title: 83_12_SC2

description: Library name: Sample38

value: Stem cell for endoderm differentiation

value: Endoderm differentiation


title: Input TOP2A ChIPseq, E2, 45 min, rep1

value: ER positive breast cancer cell line


title: human stellate cells-H3K27ac_rep2

data_processing:
Library strategy: Cut&Tag
The sequence data from Cut & Tag libraries were aligned to the human genome (hg38) using Bowtie2 (Langmead and Salzberg 2012). Duplicate reads were identified and filtered out using GATK markDuplicate script (https://gatk.broadinstitute.org/hc/en-us). The peaks were identified using SEACR package using relaxed option
Reads were quality asssed using the FASTQC (v 0.11.9).
Genome_build: GRCh38

extract_protocol: For each Cut & Tag reaction, 100,000 nuclei were adsorbed to activated Concanavalin A-coated magnetic beads. Nuclei-adsorbed beads were resuspended in the antibody buffer (wash buffer and 0.01% Digitonin) containing 0.5 μg antibody and allowed to incubate overnight at 4°C on a nutator. After two washing steps, the secondary antibody was added and incubated with beads for 1 hour at room temperature (RT). Beads were washed in Wash buffer 300 (Wash buffer containing 300mM NaCl) two times and resuspended in Wash buffer 300 containing Protein A/G-TN5 (EpiCypher) and incubated for an hour at RT. The tagging reaction was activated using the TN5 activation buffer (Wash buffer 300 and 10mM MgCl2) at 37°C for one hour. To extract tagmented fragments from nuclei, beads were dissolved in the sodium dodecyl sulfate (SDS) buffer (0.1% SDS). The tagged fragments were PCR amplified using Nextra-compatible primers to generate indexed ready-to-sequence libraries. The PCR products were cleaned up by AMPure beads (Beckman Coulter) and run on Agilent Tapestation (Agilent Technologies) for quality assessment. The cleaned PCR products were submitted for RNA sequencing.

tag: antibody

value: H3K27ac antibody ab4729 (Abcam)

value: Genomic DNA


title: WT_D3_ENDO2

description: Library name: Sample41

value: WT


title: Co_LenOVA_anti_PD1_2

description: Library name: Co_LenOVA_anti_PD1_2


title: 83_12_SC1

description: Library name: Sample37


title: Lenvatinib_anti_PD1_2

description: Library name: Lenvatinib_anti_PD1_2


title: Input TOP2A ChIPseq, VEH, 45 min, rep2


title: human stellate cells-IgG_rep1

value: IgG antibody 13-0047 (EpiCypher)


title: human stellate cells-IgG_rep2


title: human stellate cells-H3K4me3_rep2

value: H3K4me3 antibody 13-0041 (EpiCypher)


title: human stellate cells-H3K27ac_rep1


title: Co_LenOVA_anti_PD1_1

description: Library name: Co_LenOVA_anti_PD1_1


title: Control_2

description: Library name: Control_2


title: human stellate cells - polyA fraction

extract_protocol:
HSCs were rinsed with PBS and lysed using Trizol reagent (Thermo Fisher). The mixture was vortexed and incubated at room temperature to ensure complete lysis of cells and separation of protein-RNA complexes. RNA was then extracted using chloroform (Sigma) and precipitated using ethanol and centrifuged at 13,000 RPM for 20 min to form an RNA pellet. The RNA pellet was rinsed with 75% ethanol. The RNA was resuspended in nuclease free water and incubated with DNase I (Thermo Fisher) to remove potentially contaminating genomic DNA fragments. The RNA was then extracted using acidic phenol chloroform, precipitated in ethanol, and resuspended in nuclease free water. RNA samples with RIN score of >9 were sequenced.
The strand-specific RNA sequencing library was prepared by using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following the manufacturer’s instructions (NEB). Briefly, the enriched RNAs were fragmented for 8 minutes at 94°C. First strand and second strand cDNA were subsequently synthesized. The second strand of cDNA was marked by incorporating dUTP during the synthesis. The cDNA fragments were adenylated at 3’-ends, and an indexed adapter was ligated to cDNA fragments. Limited cycle PCR was used for library enrichment. The incorporated dUTP in second strand cDNA quenched the amplification of second strand, which helped to preserve the strand specificity. The sequencing library was validated on the Agilent TapeStation, and quantified by using Qubit 2.0 Fluorometer (Thermo Fisher) as well as by quantitative PCR (KAPA Biosystems).

value: polyA RNA


title: 83_12_D9_RESPENDO3

description: Library name: Sample36

value: Ventral anterior foregut endoderm


title: 83_12_SC3

description: Library name: Sample39


title: Input TOP2B ChIPseq, E2, 45 min


title: Input TOP2B ChIPseq, VEH, 45 min


title: Co_LenOVA_anti_PD1_3

description: Library name: Co_LenOVA_anti_PD1_3


title: C57, IR+Decursin6, Day7

first: hui

last: chen

address: 639 Zhizaoju Road, Shanghai 200011, People’s Republic of China

institute: Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

description: Library name: C-6

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: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.

source_name: Heart

growth_protocol: All adult male C57BL/6 mice (approximately 20 g;) were housed under controlled temperature conditions (20±2°C), with a 12-hour light-dark cycle, and provided with adequate food and water.

extract_protocol:
Total RNA was extracted using the Total RNA Extraction Kit 2.0 Plus according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: in this study, C57BL/6 mice were used to investigate the protective effects of Decursin on myocardial ischemia-reperfusion injury. A total of 18 mice were randomly divided into three groups, with 6 mice in each group:SHAM Group, IR (Ischemia-Reperfusion) Group,  IR + Decursin Group. All mice were sacrificed at 7 days post-surgery, and heart tissues were collected for RNA sequencing (RNA-seq) analysis. This design aims to elucidate the molecular mechanisms by which Decursin may confer cardioprotective effects in the context of ischemia-reperfusion injury, with a focus on gene expression changes associated with the treatment.

value: Heart

value: IR+Decursin


title: C57, IR+Decursin5, Day7

description: Library name: C-5


title: 83_12_D9_RESPENDO2

description: Library name: Sample35


title: MTCH2-D8-23: CTCF-B KO cell rep4

city: Kunming

first: Yong-Gang

last: Yao

state: Yunnan

address: 32 Jiaochang Donglu

department: Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province

institute: Kunming Institute of Zoology

description: U251-APP cell with CTCF-binding site CTCF-B knockout by CRISPR/Cas12

data_processing:
Raw RNA-seq reads were trimmed to remove sequencing adapters and low-quality reads by using the Trimmomatic (version 0.33).
The clean reads were then aligned to the reference genome (GRCh38.p7) using HISTA2.
FeatureCounts was used to generate counts for known human genes.
Gene-level differential expression analyses were performed using DESeq2.
Genes with Padjust<0.05 were defined as differentially expressed genes.
Genome_build: hg38
Supplementary_files_format_and_content: The processed data file is in plain text file format and contains normalized expression of all samples.

source_name: U251 cell with a stable expression of mutant APP 128 (M671L) (U251-APP cells)

growth_protocol: U251 cells with stable expression of mutant APP (K670N/M671L) were cultured in Roswell RPMI-1640 medium (HyClone, C11875500BT) supplemented with 10% fetal bovine serum at 37 °C in a humidified atmosphere incubator with 5% CO2

extract_protocol:
Total RNA was extracted by using the RNAeasy kit (TianGen) according to the manufacturer’s instructions. The A260/A280 ratio of total RNA was measured on a NanoDrop biophotometer (Thermo Fisher Scientific). Only samples with A260/A280 ratio of 1.8–2.0 were used for subsequent experiments. Quality and integrity of RNA samples were evaluated based on the 28S and 18S rRNA bands on a 1% agarose gel.
About 1.5 μg total RNA per sample was used to prepare library for RNA-seq. Sequencing libraries were generated using the NEBNextUltraTM RNA Library Prep kit for Illumina (NEB, USA) following the manufacturer’s recommendation and index codes were added to attribute sequence to each sample. The final library was sequenced on an IlluminaHiseq 4000 platform, and 150 bp paired-ends reads were generated.

treatment_protocol: Two guide RNAs (gRNAs) targeting to the upstream and downstream region of the CTCF-binding sites (CTCF-A and CTCF-B) were designed according to the PAM sequence “NGG” in this region. The two gRNAs were respectively sub-cloned into the pGL3-U6-sgRNA-PGK-puromycin (Addgene plasmid # 51133) plasmid and PX330-mcherry (Addgene plasmid #98750) plasmid, and were co-transfected into U251-APP cells using Lipofectamine™ 3000 (Invitrogen L3000008). U251-APP cells were cultured in Roswell Park Memorial Institute 1640 Medium (Thermo Fishers) supplemented with 10% FBS (Thermo Fishers). Forty-eight hours after transfection, single cells were picked from puromycin-resistant cells with strong mcherry fluorescence signals and were seeded and cultured in 96-well plate for 3-4 weeks to obtain single cell clones. Genomic DNA of each clone was extracted by using the AxyPrep Genomic DNA Miniprep Kit (Axygen, AP-MN-BL-GDNA-250). The target region was amplified and sequenced to confirm successful deletion of the targeted CTCF-binding site.

value: CTCF-B knockout

value: CRISPR/Cas9 editing


title: 83_12_D9_RESPENDO1

description: Library name: Sample34


title: C57, IR+Decursin4, Day7

description: Library name: C-4


title: Input ERA ChIPseq, E2, 45 min

city: Madrid

first: Felipe

last: Cortés Ledesma

address: Melchor Fernández Almagro 3

institute: CNIO

value: 45 min 10 nM E2


title: 83_12_D9_ESOPHENDO3

description: Library name: Sample33

value: Dorsal anterior foregut endoderm


title: Input ERA ChIPseq, VEH, 45 min

value: 45 min EtOH


title: Input TOP2A ChIPseq, VEH, 45 min, rep1


title: human stellate cells-H3K4me3_rep1

value: Untreated


title: MTCH2-D8-22: CTCF-B KO cell rep3

description: U251-APP cell with CTCF-binding site CTCF-B knockout by CRISPR/Cas11


title: C57, IR+Decursin3, Day7

description: Library name: C-3


title: 83_12_D9_ESOPHENDO2

description: Library name: Sample32

value: Endoderm differentiation


title: MTCH2-D8-20: CTCF-B KO cell rep1

description: U251-APP cell with CTCF-binding site CTCF-B knockout by CRISPR/Cas9


title: MTCH2-D8-21: CTCF-B KO cell rep2

description: U251-APP cell with CTCF-binding site CTCF-B knockout by CRISPR/Cas10


title: 83_12_D9_ESOPHENDO1

description: Library name: Sample31


title: U251-APP-Cas9-SP5-6: CTCF-A KO cell rep4

description: U251-APP cell with CTCF-binding site CTCF-A knockout by CRISPR/Cas9

value: CTCF-A knockout


title: Input RAD21 ChIPseq, siTOP2B, E2, 45 min

value: ER positive breast cancer cell line

value: siTOP2B 60h + 45 min 10 nM E2


title: U251-APP-Cas9-SP5-5: CTCF-A KO cell rep3


title: C57, IR6, Day7

description: Library name: B-6

value: WT

value: IR


title: Input RAD21 ChIPseq, siTOP2B, VEH, 45 min

value: siTOP2B 60h + 45min EtOH


title: C57, IR+Decursin2, Day7

description: Library name: C-2


title: Input RAD21 ChIPseq, siC, E2, 45 min

value: siC 60h + 45 min 10 nM E2


title: 83_12_D6_ENDO3

description: Library name: Sample30

value: Anterior foregut endoderm


title: Input RAD21 ChIPseq, siC, VEH, 45 min

value: siC 60h + 45min EtOH


title: C57, IR+Decursin1, Day7

description: Library name: C-1

value: Heart

value: IR+Decursin


title: U251-APP-Cas9-SP5-3: CTCF-A KO cell rep2

value: CRISPR/Cas9 editing


title: POLII ChIPseq, siZATT, E2, 45 min

value: siZATT 60h + 45 min 10 nM E2


title: C57, IR5, Day7

description: Library name: B-5


title: C57, IR4, Day7

description: Library name: B-4


title: 83_12_D6_ENDO1

description: Library name: Sample28


title: 83_12_D3_ENDO3

description: Library name: Sample27

value: Definitive endoderm


title: U251-APP-10: wild-type control cell rep4

description: wild type U251-APP cell

value: wild type


title: C57, IR3, Day7

description: Library name: B-3


title: POLII ChIPseq, siC (siZATT), E2, 45 min


title: U251-APP-9: wild-type control cell rep3

description: wild type U251-APP cell


title: 83_12_D3_ENDO2

description: Library name: Sample26


title: C57, IR2, Day7

description: Library name: B-2


title: POLII ChIPseq, siC (siZATT), VEH, 45 min


title: U251-APP-8: wild-type control cell rep2

description: wild type U251-APP cell


title: 83_12_D6_ENDO2

description: Library name: Sample29


title: C57, IR1, Day7

description: Library name: B-1


title: POLII ChIPseq, siTOP2A, E2, 45 min

value: siTOP2A 60h + 45 min 10 nM E2


title: WT-SPM-3

description: Library name: Sample24

source_name: Splanchinc mesoderm

value: Splanchinc mesoderm

value: Mesenchyme differentiation


title: U251-APP-7: wild-type control cell rep1

description: wild type U251-APP cell


title: C57, SHAM6, Day7

description: Library name: A-6

value: SHAM


title: POLII ChIPseq, siTOP2A, VEH, 45 min

value: ER positive breast cancer cell line

value: siTOP2A 60h + 45min EtOH


title: C57, SHAM5, Day7

description: Library name: A-5

value: WT


title: WT-SC-3

description: Library name: Sample21

source_name: Stem cell for mesenchyme differentiation


title: POLII ChIPseq, siC (siTOP2A), VEH, 45 min


title: WT-SPM-1

description: Library name: Sample22


title: POLII ChIPseq, siZATT, VEH, 45 min

value: siZATT 60h + 45min EtOH


title: POLII ChIPseq, siC (siTOP2A), E2, 45 min

value: siC 60h + 45 min 10 nM E2


title: dcdc73_rep2

city: Chuncheon-si, Gangwon-do

first: soojin

last: yeom

address: 1 Kangwondaehak-gil

institute: Kangwon National University

description: Library name: dcdc73-2

data_processing:
Sequencing was performed on an Illumina Hi-seq 2500 instrument to generate 101 bp paired-end reads for each sample.
Trimmomatic v.0.36 performed the sequencing adapter removal and quality-based trimming on raw data with TruSeq adapter sequence
Cleaned reads were mapped to the S. cerevisiae reference genome (SacCer3) using TopHat2 v.2.0.11 with the default parameter
featureCounts was used for counting to measure the expression level of each gene, and data were normalized by DESeq2
Assembly: sacCer3
Supplementary files format and content: bw

organism: Saccharomyces cerevisiae BY4741

source_name: Normal condition

growth_protocol: S. cerevisiae strains were grown in YPD media (1% yeast extracts, 2% peptone, 2% glucose) at 30˚C. Overnigh cultured cells were diluted to OD600 of 0.1 into fresh 10ml YPD and grown at 30˚C until OD600 of 1.0.

extract_protocol:
Total RNA was extracted using NucleoSpin® RNA (MN, MN740955) according to the protocol of the manufacturer
mRNA was captured using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, E7490). The library for sequencing was prepared following the manufacturer's instructions of NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, Cat. No: E7760).

treatment_protocol: α-Factor (9.6 μg/mL) was added to the culture and incubated for 1.5 hours at 30°C with shaking, followed by a second treatment under the same conditions

value: S. cerevisiae BY4741 (haploid)

value: CDC73 Knocoout

value: X


title: dcdc73_a_factor_rep1

description: Library name: dcdc73-a-1

source_name: α-factor induced

value: α-factor


title: U251-APP-Cas9-SP5-2: CTCF-A KO cell rep1

value: CTCF-A knockout

value: CRISPR/Cas9 editing


title: WT-SC-2

description: Library name: Sample20

value: Stem cell for mesenchyme differentiation


title: C57, SHAM3, Day7

description: Library name: A-3

value: Heart


title: POLII ChIPseq, siTOP2B, E2, 45 min

value: siTOP2B 60h + 45 min 10 nM E2


title: WT-SC-1

description: Library name: Sample19


title: C57, SHAM2, Day7

description: Library name: A-2


title: dsir2_a_factor_rep2

description: Library name: dsir2-a-2

value: SIR2 Knockout


title: dcdc73_rep1

description: Library name: dcdc73-1


title: 83_12_D3_ENDO1

description: Library name: Sample25

value: Definitive endoderm

value: Endoderm differentiation


title: C57, SHAM1, Day7

description: Library name: A-1

value: SHAM


title: POLII ChIPseq, siC (siTOP2B), E2, 45 min

value: ER positive breast cancer cell line


title: WT-RESP-3

description: Library name: Sample18

source_name: Respiratory mesenchyme

value: Respiratory mesenchyme

value: WT

value: Mesenchyme differentiation


title: WT-SPM-2

description: Library name: Sample23

value: Splanchinc mesoderm