title: MDA-MB-453 cells, DES 10μM + cadmium 10μM, rep2

city: Washington

first: Mary Beth

last: Martin

state: DC

address: 3970 Reservoir Rd. NW

department: Oncology

institute: Georgetown University

description: Library name: DES_Cd2

data_processing:
Raw data (raw reads) of fastq format were first 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 of 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 1 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool because Hisat2 can generate a database of splice junctions based on the gene model annotation file, thus providing a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and the reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: GRCh38.p14
Supplementary files format and content: csv file includes FPKM values for each sample

growth_protocol: MDA-MB-453 cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM; Corning) containing 10% FBS. 6.0e5 MDA-MB-453 cells were plated in six-well plates with 3 ml of DMEM containing 10% FBS overnight, the media was changed to 3 ml of lipoic acid- and phenol red-free IMEM (Crystalgen) containing 5% charcoal-stripped serum (CSS) for 24 h.

extract_protocol:
Total RNA was isolated from cell pellets using the TRIZOL reagent (Life Technologies). >2 μg total RNA was used for the construction of sequencing libraries.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: For calcium treatment, the media was replaced by 5 ml IMEM (Crystalgen) without serum and cells were treated with 10 mM calcium,  or 5 µM GSK4716 (in ethanol) in the absence or presence of 10 µM DES (in ethanol) for 24 h. For cadmium treatment, the serum concentration was diluted to 1% CSS in 5 ml IMEM (Crystalgen) and cells were treated with 10 µM cadmium in the absence or presence of 10 µM DES (in ethanol) for 24 h. Any combination treatment with DES was performed 3 h after the addition of DES.

value: breast cancer cells

value: DES 10μM for 3hrs then cadmium 10μM for 24hrs


title: MDA-MB-453 cells, DES 10μM + calcium 10mM, rep1

status: Public on Jan 14 2026

type: SRA

country: USA

description: Library name: DES_Ca1

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

value: WT

tag: treatment

value: DES 10μM for 3hrs then calcium 10mM for 24hrs


title: MDA-MB-453 cells, GSK4716 5μM, rep3

description: Library name: GSK3

value: GSK4716 5μM for 24hrs


title: MDA-MB-453 cells, GSK4716 5μM, rep1

description: Library name: GSK1


title: MDA-MB-453 cells, GSK4716 5μM, rep2

description: Library name: GSK2


title: MDA-MB-453 cells, DES 10μM + calcium 10mM, rep3

description: Library name: DES_Ca3


title: MDA-MB-453 cells, DES 10μM + cadmium 10μM, rep3

description: Library name: DES_Cd3


title: MDA-MB-453 cells, cadmium 10μM, rep3

description: Library name: Cd3

value: Cadmium 10μM for 24hrs


title: MDA-MB-453 cells, DES 10μM, rep1

description: Library name: DES1

value: DES 10μM for 24hrs


title: MDA-MB-453 cells, calcium 10mM, rep3

description: Library name: Ca3

value: Calcium 10mM for 24hrs


title: MDA-MB-453 cells, cadmium 10μM, rep1

description: Library name: Cd1


title: MDA-MB-453 cells, DES 10μM, rep2

description: Library name: DES2


title: MDA-MB-453 cells, cadmium 10μM, rep2

description: Library name: Cd2


title: MDA-MB-453 cells, DES 10μM, rep3

description: Library name: DES3


title: MDA-MB-453 cells, control, rep2

description: Library name: Ctrl2

value: No treatment


title: MDA-MB-453 cells, calcium 10mM, rep2

description: Library name: Ca2


title: MDA-MB-453 cells, DES 10μM + cadmium 10μM, rep1

description: Library name: DES_Cd1


title: MDA-MB-453 cells, DES 10μM + calcium 10mM, rep2

description: Library name: DES_Ca2


title: MDA-MB-453 cells, control, rep3

description: Library name: Ctrl3


title: MDA-MB-453 cells, control, rep1

description: Library name: Ctrl1


title: HEK293_dCas13d_gNT_m6A_rep1

city: Chicago

first: Chuan

last: He

state: Illinois

address: 929 E 57th St., GCIS E319

institute: The University of Chicago

description: Library name: HEK293_dCas13d_gNT_m6A_rep1

data_processing:
The FASTQ file was trimmed using Cutadapt (v4.6) and aligned to ribosomal RNA (rRNA) sequences with Bowtie2 (v2.4.2) to filter out rRNA reads. The remaining non-rRNA reads were aligned to the reference genome using STAR (v2.7.3a), and PCR duplicates were removed with UMI-tools (v1.1.1).
Assembly: GRCh38.p13, GENCODE Release 39; GRCm38.p6, GENCODE Release M25
Supplementary files format and content: bigWig files

source_name: Embryonic kidney

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and  100 U/mL penicillin-streptomycin (Gibco). Mouse embryonic stem cells were cultured in DMEM (Invitrogen) supplemented with 20% FBS (GeminiBio), 1 mmol/L L-glutamine (Gibco), 1% nonessential amino acid (Gibco), 100 U/mL penicillin-streptomycin (Gibco), 1,000 U/mL leukemia inhibitory factor (LIF, Millipore), 0.1 mmol/L 2-mercaptoethanol (Sigma), 3 μmol/L CHIR99021 (Stemcell), 1 μmol/L PD0325901 (Stemcell), and 1% EmbryoMax nucleosides (100×, Millipore). All cell lines were cultured in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Cells were fixed with 1.5% paraformaldehyde for 10 minutes, quenched with 125 mM glycine at room temperature for 5 minutes, and permeabilized with 0.5% Triton X-100 on ice for 10 minutes. Samples were then blocked with 1 mg/ml BSA, followed by sequential staining with a primary antibody, a secondary antibody, and protein A/G-reverse transcriptase. In situ reverse transcription was performed at 37°C for 1 h. Subsequently, cells were digested with proteinase K at 37°C for 2 h. Total nucleic acids were extracted using phenol-chloroform and concentrated by ethanol precipitation.
Biotinylated cDNA was enriched using streptavidin beads. A 3' cDNA adapter (5′Phos-NNNNNNNNAGATCGGAAGAGCGTCGTGT-3′SpC3) was ligated using T4 RNA ligase 1 by incubating at 25°C for 16 h. The cDNA was then recovered from the beads. The library was prepared through PCR amplification using NGS sequencing primers, followed by gel purification to isolate fragments between 180 bp and 400 bp.

tag: tissue

value: Embryonic kidney

value: Transformed embryonic kidney cell

value: NT ginde RNA

tag: antibody

value: m6A antibody (CST,Cat #56593)


title: P1405

city: La Jolla

first: Mariko

last: Horii

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

description:
Library name: sample5
column name in raw_counts.csv:P1405

data_processing:
Quality control was performed using multiQC (v1.17). Strand specificity analysis using RSeQC confirmed that the RNA-seq libraries were stranded, with the majority of reads aligning to the antisense strand. Adapter trimming and quality filtering were performed using BBDuk (BBMap suite) with the following parameters: ktrim=r, k=16, mink=11, hdist=1, tpe, tbo, qtrim=rl, and trimq=20, using a custom adapter reference file. Reads were mapped to the human genome (GRCh38, GENCODE release with ERCC spike-in sequences added) using STAR (v.2.7.11) with the following parameters: --runMode alignReads, --outSAMtype BAM SortedByCoordinate, --outSAMunmapped Within, and --quantMode GeneCounts. Feature quantification was performed using featureCounts (subread v.2.0.1)28 with parameters -p --countReadPairs -t exon -T 13 -g gene_id. Only Ensembl genes with ≥10 counts in at least 25% of samples were retained for downstream analysis. Normalization and differential expression analysis were performed using the R (v. 4.4.1) package DESeq2 (v. 1.44.0). BiomaRt (v. 2.60.1) was used to convert Ensembl gene IDs to HUGO gene names, and gene set enrichment analysis was done using the R (v. 4.4.1) package FGSEA (v. 1.30.0).
Assembly: GRCh38, GENCODE release 44
Supplementary files format and content: txt file for raw counts
Supplementary files format and content: txt file for vst data

source_name: Placenta

extract_protocol:
Total RNA was isolated using mirVana RNA Isolation Kit (ThermoFisher). RNA concentration was measured using Qubit RNA BR assay kit (ThermoFisher). RNA integrity was checked using RNA 6000 Nano chip read by Aligent 2100 bioanalyzer.
RNA-seq libraries were prepared using either the TruSeq Stranded Total RNA Sample preparation kit with Ribo-Zero Gold (Illumina) by IGM Genomics Center at UC San Diego, or the KAPA RNA HyperPrep Kit with RiboErase (Roche).

value: Placenta

tag: gestational age_(week)

tag: Sex

value: female

tag: condition

value: nonPE-SGA

tag: batch


title: MDA-MB-453 cells, calcium 10mM, rep1

description: Library name: Ca1


title: P1098

description:
Library name: sample2
column name in raw_counts.csv:P1098

value: male


title: P1149

description:
Library name: sample3
column name in raw_counts.csv:P1149


title: P1419

description:
Library name: sample6
column name in raw_counts.csv:P1419


title: B3

city: Tongling

first: Wumei

last: Hua

state: Anhui

address: Tongguan District

country: China

institute: Tongling People's Hospital

description: Library name: sample 6

data_processing:
Raw data (raw reads) were processed using Trimmomatic The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count. DEGs were identified using the DESeq(2012) R package functions estimateSizeFactors and nbinomTest. Pvalue < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: orbital tissue

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
Then these libraries were sequenced on the Illumina sequencing  platform (HiSeqTM 2500 ) and 125bp/150bp paired-end reads were generated.

value: orbital tissue


title: P1570

description:
Library name: sample7
column name in raw_counts.csv:P1570


title: A1

description: Library name: sample 1


title: F_14

city: shanghai

first: Jun

last: Zhang

address: No.197, Ruijin road

department: Department of Oncology

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description:
Library name: library 4
Peritoneal metastasis samples, scRNA-seq

library_source: transcriptomic single cell

data_processing:
Raw reads were trimmed of adapters and low-quality bases using Fastp (v0.20.1) and processed with the SeekSoul Tools pipeline to generate a gene-expression matrix. Downstream analyses were performed in Seurat v3: nuclei or cells of high or low quality were filtered based on gene counts, UMI counts, and mitochondrial gene proportions; after normalization, PCA was applied for dimensionality reduction followed by graph-based clustering. Intestinal mucosal cell subpopulations were extracted, and differentially expressed genes (DEGs) between conditions were identified using the Wilcoxon rank-sum test (adjusted p < 0.05). Finally, GO and KEGG pathway enrichment analyses of these DEGs were conducted using ClusterProfiler to elucidate the molecular mechanisms underlying PEDV-induced changes in intestinal mucosal cells.
Assembly: hg38
Supplementary files format and content: tab-separated values files and matrix files

source_name: stomach

extract_protocol:
An appropriate number of cells were loaded into the flow channel of the SeekOne MM chip and allowed to settle into microwells by gravity. Unsettled cells were removed, and cell-barcoded magnetic beads (CBBs) were pipetted into the flow channel and allowed to settle into microwells under a magnetic field. Excess CBBs were rinsed away, and cells on the MM chip were lysed to release and capture RNA.
Reverse transcription was carried out at 37 °C for 30 min. The barcoded cDNA on CBBs was hybridized with a random primer containing read-2 SeqPrimer sequences at the 5′ end, enabling extension to form the second strand with a 3′ cell barcode. The resulting second-strand DNA was denatured off the CBBs, purified, and amplified by PCR. The cDNA product was cleaned, ligated to adapters and sample indices, and the indexed sequencing libraries were purified with SPRI beads, quantified, and sequenced on an Illumina NovaSeq.

value: stomach

value: gastric cancer peritoneal metastasis


title: Ca3

description:
Library name: library 3
Primary gastric cancer samples, scRNA-seq

value: gastric carcinoma in situ


title: TE13-si-rna2-3

city: taiyuan

first: Li

last: wenjin

state: Shanxi

address: No. 56, Xinjian South Road, Yingze District

institute: Shanxi medical university

description: Library name: sample9

data_processing:
Raw reads were quality-checked, adapter-trimmed, and aligned to GRCh38. Gene expression counts were obtained using featureCounts for downstream analysis.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: Gene-level read counts per sample are provided in CSV files, with genes in rows and samples in columns. Raw reads are provided as gzipped FASTQ files.

source_name: esophagus, squamous cell carcinoma

extract_protocol:
Total RNA was extracted from TE13 cells using TRIzol and quantified/assessed for quality with NanoDrop
For each sample, 1 μg total RNA was used for library preparation. Poly(A)+ mRNA was isolated using a magnetic oligo(dT) capture module and converted to sequencing libraries according to the manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq 6000 system

value: esophagus, squamous cell carcinoma

value: epithelial carcinoma cells (TE13)


title: TE13-si-rna2-2

description: Library name: sample8


title: Ca1

description:
Library name: library 1
Primary gastric cancer samples, scRNA-seq


title: B2

description: Library name: sample 5


title: Ca2

description:
Library name: library 2
Primary gastric cancer samples, scRNA-seq


title: B1

description: Library name: sample 4


title: TE13-si-rna1-3

description: Library name: sample6


title: F_15

description:
Library name: library 5
Peritoneal metastasis samples, scRNA-seq


title: P1086

description:
Library name: sample1
column name in raw_counts.csv:P1086


title: A2

description: Library name: sample 2


title: TE13-si-control-3

description: Library name: sample3


title: A3

description: Library name: sample 3


title: TE13-si-rna1-1

description: Library name: sample4


title: TE13-si-control-1

description: Library name: sample1


title: TE13-si-control-2

description: Library name: sample2


title: F_16

description:
Library name: library 6
Peritoneal metastasis samples, scRNA-seq


title: TE13-si-rna1-2

description: Library name: sample5


title: HBL1 cells, Rhosin treated for 10hrs, Replicate 1

city: Frankfurt am Main

first: Sebastian

last: Scheich

address: Theodor-Stern-Kai 7

department: Hematology/Oncology

country: Germany

institute: University Hospital Frankfurt

description: Library name: HBL1_Rhosin_R1_10hr

data_processing:
Raw sequencing reads were generated on the Illumina NovaSeq 6000 platform and demultiplexed using Illumina’s standard software (bcl2fastq or bcl-convert, depending on the run). Reads were aligned to the human reference genome GRCh37 (hg19) using the STAR aligner at the DKFZ Genomics Core Facility. The resulting aligned BAM files were used for downstream analysis. For the WT and KI RhoA samples, generated at the NIH/CCR sequencing core unit, reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (hg19) and the annotated transcripts using STAR. Gene-level quantification was performed using STAR/RSEM to produce raw read counts and normalized expression values. Duplicate marking and mapping statistics were generated using Picard.
Assembly: hg19
Supplementary files format and content: TMD8_Samples.xlsx, raw counts excel file for all TMD8 10hr inhibitor treated samples
Supplementary files format and content: RIVA_Samples.xlsx, raw counts excel file for all RIVA 10hr inhibitor treated samples
Supplementary files format and content: HBL1_Samples.xlsx, raw counts excel file for all HBL1 10hr inhibitor treated samples
Supplementary files format and content: KI_RHOA_RNAseq.xlsx, normalized/log2-transformed counts excel file for TMD8 RHOA WT and p.R5W Copanlisib treated samples

growth_protocol: All cells were maintained in Advanced RPMI supplemented with 10% FCS and antibiotics in 5% CO2 at 37C.

extract_protocol:
RNA was harvested using miRNeasy Mini Kit (Qiagen) using QIAshredder homogenizers and on-column Dnase digests.
Total RNA samples were processed at the DKFZ Core Facility using the Illumina TruSeq Stranded RNA Library Prep Kit with IDT-ILMN TruSeq DNA/RNA Unique Dual Index (UDI) adapters. Libraries were sequenced on an Illumina NovaSeq 6000 platform with paired-end 2×50 bp reads. Base calling and quality control were performed with standard Illumina software. WT and KI RhoA samples were generated at the NIH/CCR sequencing core unit and sequenced on NovaSeq 6000 S1 using Illumina® Stranded mRNA Prep and paired-end sequencing.

treatment_protocol: DMSO, Ibrutinib (10nM), or Rhosin (60uM) for 10hrs. Copanlisib treatment (50nM) occurred overnight.

value: ABC DLBCL

value: WT

value: Rhosin


title: TE13-si-rna2-1

description: Library name: sample7


title: HBL1 cells, Rhosin treated for 10hrs, Replicate 3

description: Library name: HBL1_Rhosin_R3_10hr


title: TMD8 cells, WT RHOA, 50nM Copanlisib treatment overnight, Replicate 1

description: Library name: TMD8_WT_50nM_COPA_O-N__R1

value: Copanlisib


title: HBL1 cells, Ibrutinib treated for 10hrs, Replicate 2

description: Library name: HBL1_Ibrutinib_R2_10hr

value: Ibrutinib


title: HBL1 cells, Ibrutinib treated for 10hrs, Replicate 1

description: Library name: HBL1_Ibrutinib_R1_10hr


title: HBL1 cells, DMSO treated for 10hrs, Replicate 2

description: Library name: HBL1_DMSO_R2_10hr

value: DMSO


title: HBL1 cells, DMSO treated for 10hrs, Replicate 3

description: Library name: HBL1_DMSO_R3_10hr


title: TMD8 cells, WT RHOA, 50nM Copanlisib treatment overnight, Replicate 2

description: Library name: TMD8_WT_50nM_COPA_O-N__R2


title: TMD8 cells, RHOA p.R5W, 50nM Copanlisib treatment overnight, Replicate 2

description: Library name: TMD8_RHOA_R5W_50nM_COPA_O-N__R2

value: RHOA p.R5W


title: HBL1 cells, Ibrutinib treated for 10hrs, Replicate 3

description: Library name: HBL1_Ibrutinib_R3_10hr


title: RIVA cells, Rhosin treated for 10hrs, Replicate 1

description: Library name: RIVA_Rhosin_R1_10hr

source_name: RIVA

value: RIVA


title: TMD8 cells, RHOA p.R5W, 50nM Copanlisib treatment overnight, Replicate 1

description: Library name: TMD8_RHOA_R5W_50nM_COPA_O-N__R1


title: RIVA cells, Rhosin treated for 10hrs, Replicate 2

description: Library name: RIVA_Rhosin_R2_10hr


title: RIVA cells, Ibrutinib treated for 10hrs, Replicate 2

description: Library name: RIVA_Ibrutinib_R2_10hr


title: RIVA cells, Ibrutinib treated for 10hrs, Replicate 3

description: Library name: RIVA_Ibrutinib_R3_10hr


title: RIVA cells, Rhosin treated for 10hrs, Replicate 3

description: Library name: RIVA_Rhosin_R3_10hr


title: RIVA cells, DMSO treated for 10hrs, Replicate 3

description: Library name: RIVA_DMSO_R3_10hr


title: RIVA cells, DMSO treated for 10hrs, Replicate 2

description: Library name: RIVA_DMSO_R2_10hr


title: RIVA cells, Ibrutinib treated for 10hrs, Replicate 1

description: Library name: RIVA_Ibrutinib_R1_10hr


title: HBL1 cells, Rhosin treated for 10hrs, Replicate 2

description: Library name: HBL1_Rhosin_R2_10hr


title: TMD8 cells, Rhosin treated for 10hrs, Replicate 2

description: Library name: TMD8_Rhosin_R2_10hr


title: HBL1 cells, DMSO treated for 10hrs, Replicate 1

description: Library name: HBL1_DMSO_R1_10hr


title: TMD8 cells, Ibrutinib treated for 10hrs, Replicate 2

description: Library name: TMD8_Ibrutinib_R2_10hr


title: TMD8 cells, Rhosin treated for 10hrs, Replicate 1

description: Library name: TMD8_Rhosin_R1_10hr


title: TMD8 cells, Rhosin treated for 10hrs, Replicate 3

description: Library name: TMD8_Rhosin_R3_10hr


title: TMD8 cells, Ibrutinib treated for 10hrs, Replicate 1

description: Library name: TMD8_Ibrutinib_R1_10hr


title: TMD8 cells, DMSO treated for 10hrs, Replicate 1

description: Library name: TMD8_DMSO_R1_10hr


title: Case3 primary

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description:
Library name: GA61118
Thyroid cancer primary site

data_processing:
Sequencing was performed on NovaSeq 6000 or NovaSeq X Plus platform in a 101+101 base paired-end mode.
Illumina RTA v3.4.4 or RTA4 software was used for base calling.
Generated reads were mapped to the human (GRCh38.p13) reference genome using HISAT2 v2.1.0.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using cuffdiff of Cufflinks 2.2.1.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Thyroid

extract_protocol:
Total RNA was isolated from the human thyroid FFPE using a QIAGEN RNeasy FFPE Kit.
The cDNA library was prepared using a SMART-Seq stranded Kit (Takara Bio).

value: Thyroid

tag: disease state

value: Primary site

tag: tumor stage


title: RIVA cells, DMSO treated for 10hrs, Replicate 1

description: Library name: RIVA_DMSO_R1_10hr


title: TMD8 cells, DMSO treated for 10hrs, Replicate 2

description: Library name: TMD8_DMSO_R2_10hr


title: Case2 primary

description:
Library name: GA61115
Thyroid cancer primary site


title: TMD8 cells, DMSO treated for 10hrs, Replicate 3

description: Library name: TMD8_DMSO_R3_10hr


title: TMD8 cells, Ibrutinib treated for 10hrs, Replicate 3

description: Library name: TMD8_Ibrutinib_R3_10hr


title: Case1 metastasis

description:
Library name: GA61113
Thyroid cancer metastasis site

value: Metastasis site


title: Case8 primary

description:
Library name: GA69751
Thyroid cancer primary site


title: Case7 primary

description:
Library name: GA69748
Thyroid cancer primary site


title: Case1 primary

description:
Library name: GA61111
Thyroid cancer primary site


title: Case6 primary

description:
Library name: GA69745
Thyroid cancer primary site


title: Case7 Normal

description:
Library name: GA69749
Normal thyroid tissue

value: Normal


title: S2_OCCPTEMP

city: Durham

first: Amanda

middle: S

last: MacLeod

state: North Carolina

address: 40 Duke Medicine

department: Dermatology

institute: Duke University

description:
Library name: S2_OCCPTEMP
Fresh frozen Spatial transcriptome sequencing

data_processing:
Raw Visium spatial transcriptomics RNA-seq data and the histological hematoxylin and eosin (H&E) and immunoflouresence staining (IF) .tiff images were processed using the Space Ranger software (v 1.1.0) and Loupe Browser softwares.
Sequences were aligned to the GRCh38-3.0.0 reference transcriptome and their gene expression was summarized and quantified using the default settings in the Space Ranger software.
Assembly: GRCh38-3.0.0
Supplementary files format and content: matrix , tsv ,csv, image and json files
Library strategy: Spatial Transcriptomics

source_name: Post-mortem fresh frozen brain

extract_protocol:
Fresh frozen tissue blocks were embedded in OCT and equilibrated in the cryostat chamber prior to sectioning. Each block was trimmed and an 8mm x 8mm region of interest was scored and 10um thick section thaw-mounted on to the Visium gene expression slide. Sections that were 10um interior and posterior to the gene expression section were thaw-mounted onto charged slides for H&E and IF staining.
Library construction was carried out following the 10x Visium Spatial Gene Expression Reagent Kits User Guide (#CG000239 RevC).

value: Post-mortem fresh frozen brain

tag: tissue section

value: OCCPTEMP

tag: disease

value: Alzheimer's Disease


title: Case2 Normal

description:
Library name: GA61116
Normal thyroid tissue


title: Case3 Normal

description:
Library name: GA61119
Normal thyroid tissue


title: Case6 Normal

description:
Library name: GA69746
Normal thyroid tissue


title: S2_PFC

description:
Library name: S2_PFC
Fresh frozen Spatial transcriptome sequencing

value: PFC


title: S1_STR

description:
Library name: S1_STR
Fresh frozen Spatial transcriptome sequencing

value: STR


title: S1_PFC

description:
Library name: S1_PFC
Fresh frozen Spatial transcriptome sequencing


city: Lund

first: Ilia

last: Kurochkin

state: Skane

address: BMC A12, Sölvegatan 17

country: Sweden

institute: Lund University

description:
Library name: 48TF_Day 9_CD45+_10_BD Rhapsody_Pooled_exp5, Brd
brd_target_divergentDC.48TF_Pooled_SP_exp5.csv.gz

data_processing:
For 10X Genomics: The Cell Ranger v6.0.1 pipeline was used to process data generated using the 10x Chromium platform. Using Cell Ranger, the reads were converted to fastq format, processed, filtered, and then the aligned reads were generated.
For BD Rhapsody: BD Rhapsody™ Sequence Analysis Pipeline was used to process fastq files and performed alignment to human (hg38) genome assemblies using STAR.
The sparse expression matrix generated by Cellranger and BD Rhapsody Seven Bridges analysis pipeline was used as input to the Seurat library v4.3.0.
Assembly: hg38
Supplementary files format and content: Gene Expression matrix
Supplementary files format and content: TF Barcode Expression matrix

molecule: polyA RNA

source_name: HEF

growth_protocol: After transduction with lentivirus, HEFs were culture in gelatin-coated plates in DMEM+10%FBS.

extract_protocol:
For 10X Genomics: Single cells were isolated using 10x Chromium by 10x Genomics. For BD Rhapsody: sorted cells were loaded per lane onto the BD Rhapsody 8-Lane Cartridge. Subsequent steps were performed using the BD Rhapsody Cartridge Reagent Kit or the BD Rhapsody Enhanced Cartridge Reagent Kit, as specified in the manufacturer’s protocol.
For 10X Genomics: scRNA-seq libraries were prepared with Dual Index Chromium Next GEM Single Cell 3ʹ Kit v3.1 (Dual Index) (10x Genomics) according to manufacturer’s instructions. For BD Rhapsody: Following cell capture bead retrieval, cDNA synthesis was immediately initiated using the BD Rhapsody cDNA Kit, and the BD Rhapsody WTA Amplification Kit was used to prepare the scRNA-seq libraries. Library size and quality check was performed using High Sensitivity D1000 ScreenTape with High Sensitivity D1000 Reagents (Agilent) in a 4200 TapeStation System (Agilent), according to the manufacturer’s protocol.

treatment_protocol: Cells were sorted by FACS, 2 or 9 days after lentiviral transduction.

value: HEF

value: human embryonic fibroblasts

value: wildtype

tag: virus production

value: Pooled

tag: single-cell method

value: BD Rhapsody

tag: tf transduction

tag: cp number

tag: time

value: Day 9

tag: sorted cells


title: S1_OCCPTEMP

description:
Library name: S1_OCCPTEMP
Fresh frozen Spatial transcriptome sequencing


title: S2_ENT

description:
Library name: S2_ENT
Fresh frozen Spatial transcriptome sequencing

value: ENT


title: S1_ENT

description:
Library name: S1_ENT
Fresh frozen Spatial transcriptome sequencing


description:
Library name: 48TF_Day 9_CD45+_10_BD Rhapsody_Pooled_exp5, GEX
sc_divergentDC.48TF_Pooled_exp5.h5ad.gz
brd_divergentDC.48TF_Pooled_exp5.csv.gz

tag: cell line

tag: cell type

tag: genotype


description:
Library name: 48TF_Day 9_CD45+_10_BD Rhapsody_Arrayed_exp4, GEX
sc_divergentDC.48TF_Arrayed_exp4.h5ad.gz
brd_divergentDC.48TF_Arrayed_exp4.csv.gz

value: Arrayed


description:
Library name: 48TF_Day 9_CD45+_10_BD Rhapsody_Arrayed_exp4, Brd
brd_target_divergentDC.48TF_Arrayed_SP_exp4.csv.gz


description:
Library name: 48TF_Day 2_10_BD Rhapsody_Arrayed_exp4, GEX
sc_divergentDC.48TF_Arrayed_exp4.h5ad.gz
brd_divergentDC.48TF_Arrayed_exp4.csv.gz

value: Day 2

value: Live


description:
Library name: 48TF_Day 2_10_BD Rhapsody_Pooled_exp5, GEX
sc_divergentDC.48TF_Pooled_exp5.h5ad.gz
brd_divergentDC.48TF_Pooled_exp5.csv.gz


title: P637

description: Library name: sample40

data_processing:
Quality control was performed using multiQC (v1.17). Strand specificity analysis using RSeQC confirmed that the RNA-seq libraries were stranded, with the majority of reads aligning to the antisense strand. Adapter trimming and quality filtering were performed using BBDuk (BBMap suite) with the following parameters: ktrim=r, k=16, mink=11, hdist=1, tpe, tbo, qtrim=rl, and trimq=20, using a custom adapter reference file. Reads were mapped to the human genome (GRCh38, GENCODE release with ERCC spike-in sequences added) using STAR (v.2.7.11) with the following parameters: --runMode alignReads, --outSAMtype BAM SortedByCoordinate, --outSAMunmapped Within, and --quantMode GeneCounts. Feature quantification was performed using featureCounts (subread v.2.0.1)28 with parameters -p --countReadPairs -t exon -T 13 -g gene_id. Only Ensembl genes with ≥10 counts in at least 25% of samples were retained for downstream analysis. Normalization and differential expression analysis were performed using the R (v. 4.4.1) package DESeq2 (v. 1.44.0). BiomaRt (v. 2.60.1) was used to convert Ensembl gene IDs to HUGO gene names, and gene set enrichment analysis was done using the R (v. 4.4.1) package FGSEA (v. 1.30.0) and gene set variation analysis was done using GSVA (v. 1.4.4). Gene ontology analysis was done through Enrichr.
Assembly: GRCh38, GENCODE release 44
Supplementary files format and content: txt file for raw counts
Supplementary files format and content: txt file for vst data

tag: tissue

value: Placenta

value: siPE

value: male

tag: gestational age_(weeks)

tag: placental pathology

value: nonMVM


title: P1879

description: Library name: sample38

value: gHTN

tag: Sex

value: MVM

tag: batch


title: P1675

description: Library name: sample36


title: P1667

description: Library name: sample35

value: female


title: P666

description: Library name: sample41


title: P1626

description: Library name: sample34


title: P1478

description: Library name: sample33


title: P1221

description: Library name: sample30


title: P1280

description: Library name: sample32


title: P1266

description: Library name: sample31

value: Normal


description:
Library name: 48TF_Day 9_CD45-HLA-DR-_10_BD Rhapsody_Pooled_exp5, GEX
sc_divergentDC.48TF_Pooled_exp5.h5ad.gz
brd_divergentDC.48TF_Pooled_exp5.csv.gz

value: HEF

value: human embryonic fibroblasts


title: P771

description: Library name: sample28


title: P2005

description: Library name: sample39

value: cHTN


title: P1065

description: Library name: sample29


title: P547

description: Library name: sample25


title: P1763

description: Library name: sample23


title: P1744

description: Library name: sample22


title: P1687

description: Library name: sample37


title: P1314

description: Library name: sample20


title: P991

description: Library name: sample19


title: P1713

description: Library name: sample21


title: P934

description: Library name: sample17


title: P971

description: Library name: sample18


title: P861

description: Library name: sample14


title: P540

description: Library name: sample24


title: P853

description: Library name: sample13


title: P920

description: Library name: sample16


title: P810

description: Library name: sample11


title: P915

description: Library name: sample15


title: P597

description: Library name: sample8


title: P684

description: Library name: sample10


title: P1250

description: Library name: sample3


title: P1350

description: Library name: sample4


title: P1517

description: Library name: sample5


title: P533

description: Library name: sample6


title: P1094

description: Library name: sample1


description: Library name: 48TF_Day 9_CD45+_10_BD Rhapsody_exp3_rep2, Brd

value: wildtype

value: BD Rhapsody


title: P832

description: Library name: sample12


description: Library name: 48TF_Day 9_CD45+_10_BD Rhapsody_exp2_rep4, Brd

value: Day 9


description: Library name: 48TF_Day 9_CD45-HLA-DR-_10_BD Rhapsody_exp3_rep1, Brd

value: Arrayed


description: Library name: 48TF_Day 9_CD45+_10_BD Rhapsody_exp3_rep2, GEX


title: P584

description: Library name: sample7


description: Library name: 48TF_Day 9_CD45+_10_BD Rhapsody_exp3_rep1, Brd


description: Library name: 48TF_Day 9_CD45+_10_BD Rhapsody_exp2_rep3, Brd


description: Library name: 48TF_Day 9_CD45+_10_BD Rhapsody_exp2_rep1, Brd


description: Library name: 48TF_Day 9_CD45+_10_BD Rhapsody_exp3_rep1, GEX


description: Library name: 48TF_Day 9_CD45+_10_BD Rhapsody_exp2_rep4, GEX


description: Library name: 48TF_Day 9_CD45+_10_BD Rhapsody_exp2_rep3, GEX


description: Library name: 48TF_Day 9_CD45-HLA-DR-_10_BD Rhapsody_exp2_rep1, Brd


title: P1112

description: Library name: sample2


description: Library name: 48TF_Day 9_CD45+_10_BD Rhapsody_exp2_rep2, Brd


description: Library name: 48TF_Day 9_CD45-HLA-DR-_10_BD Rhapsody_exp2_rep1, GEX


description: Library name: 48TF_Day 9_CD45+_10_BD Rhapsody_exp2_rep2, GEX


description: Library name: 48TF_Day 9_CD45+_10_BD Rhapsody_exp2_rep1, GEX


title: Case1 Normal

description:
Library name: GA61112
Normal thyroid tissue

value: Thyroid

tag: disease state

tag: tumor stage


description: Library name: 48TF_Day 9_CD45-HLA-DR-_10_BD Rhapsody_exp3_rep1, GEX


description: Library name: 48TF_Day 9_CD45-HLA-DR-_10_BD Rhapsody_exp2_rep2, GEX


title: RNA-seq of human iPSC-derived neurons, MECP2 overexpression, biol rep 3

city: Milan

first: Michal

last: Kubacki

address: Via Olgettina 58

country: Italy

institute: San Raffaele Scientific Institute

description:
Library name: hNeuron_MECP2_rep3
Transcriptome analysis of human iPSC-derived neurons transduced with MECP2 to induce overexpression.

data_processing:
Quality Control and Trimming: Raw sequencing reads from all experiments underwent quality control using FastQC. Adapters and low-quality bases were removed using Trim Galore or Trimmomatic.
RNA-seq reads were aligned to the human (hg38/GRCh38) reference genome using STAR. Post-alignment filtering removed PCR duplicates and low-quality mapped reads.
Gene expression was quantified using featureCounts.
Differential gene expression was analyzed using DESeq2. Statistical significance was determined using FDR < 0.05.
Assembly: GRCh38/hg38
Supplementary files format and content: Raw gene count matrices (genes x samples) and normalized expression tables. Tables of differentially expressed genes include log2 fold change, p-value, and FDR for each gene.

source_name: Wild-type iPSC line

growth_protocol: Murine Neural Progenitor Cells (NPCs): Derived from the telencephalic cortex of E13.5 mouse embryos, NPCs were cultured in adhesion on flasks coated with 1:100 Matrigel. The culture medium was Neural Inducing Medium (NIM) composed of DMEM/F12, Hormon Mix, penicillin/streptomycin, glutamine, glucose, Heparin, 10 ng/ml bFGF, and 10 ng/ml EGF. Murine Primary Neurons (Ns): Prepared from E18.5 wild-type mouse embryos, neurons were maintained in Neurobasal medium supplemented with glucose, penicillin/streptomycin, L-glutamine, and 1% B27.Human iPSC-derived Neurons (hNs): Wild-type human NPCs were differentiated into cortical neurons. Differentiation was induced in DMEM/F1 with N2 and B27 supplements, SU5402, PD0325901, and DAPT. Following dissociation, cells were plated on Poly-L-Lysine/Laminin/Fibronectin coated plates in neuronal maturation medium (Neurobasal A with B-27, Glutamine, BDNF, Ascorbic acid, Laminin, DAPT, and dbcAMP) for at least 3 weeks before experiments.

extract_protocol:
Total RNA was isolated from primary murine NPCs, Ns, and human-derived Ns using Trizol (Sigma-Aldrich) according to the manufacturer's protocol.
Library preparation and paired-end sequencing were performed by a commercial service (Genewiz).

treatment_protocol: Lentiviral particles (LV) were produced in 293T cells and concentrated by ultracentrifugation. Murine NPCs and Ns: Cells were transduced one day after seeding. NPCs were transduced with LV-Mecp2 or LV-EGFP at a Multiplicity of Infection (MOI) of 10. Ns were transduced at an MOI of 5. Cells were harvested for analysis 5 days post-transduction. Human iPSC-derived Neurons: Neurons cultured for 4 weeks were transduced with LV-MECP2 or LV-EGFP at an MOI of 10. Cells were harvested 5 days after infection.

value: Wild-type iPSC line

value: iPSC-derived neurons

value: wild-type

tag: treatment

value: lentiviral transduction with MECP2


title: RNA-seq of human iPSC-derived NPCs, MECP2 overexpression, biol rep 2

description:
Library name: hNPC_MECP2_rep2
Transcriptome analysis of human iPSC-derived NPCs transduced with MECP2 to induce overexpression.

value: iPSC-derived neuronal progenitor cells


title: RNA-seq of human iPSC-derived neurons, EGFP control, biol rep 1

description:
Library name: hNeuron_EGFP_rep1
Transcriptome analysis of human iPSC-derived neurons transduced with EGFP as a control.

value: lentiviral transduction with EGFP


title: RNA-seq of human iPSC-derived NPCs, MECP2 overexpression, biol rep 3

description:
Library name: hNPC_MECP2_rep3
Transcriptome analysis of human iPSC-derived NPCs transduced with MECP2 to induce overexpression.


description: Library name: 48TF_Day 9_CD45-HLA-DR-_10_BD Rhapsody_exp2_rep2, Brd

tag: virus production


title: RNA-seq of human iPSC-derived neurons, EGFP control, biol rep 3

description:
Library name: hNeuron_EGFP_rep3
Transcriptome analysis of human iPSC-derived neurons transduced with EGFP as a control.


title: RNA-seq of human iPSC-derived neurons, MECP2 overexpression, biol rep 1

description:
Library name: hNeuron_MECP2_rep1
Transcriptome analysis of human iPSC-derived neurons transduced with MECP2 to induce overexpression.


title: RNA-seq of human iPSC-derived NPCs, MECP2 overexpression, biol rep 1

description:
Library name: hNPC_MECP2_rep1
Transcriptome analysis of human iPSC-derived NPCs transduced with MECP2 to induce overexpression.


title: RNA-seq of human iPSC-derived NPCs, EGFP control, biol rep 2

description:
Library name: hNPC_EGFP_rep2
Transcriptome analysis of human iPSC-derived NPCs transduced with EGFP as a control.


title: RNA-seq of human iPSC-derived NPCs, EGFP control, biol rep 1

description:
Library name: hNPC_EGFP_rep1
Transcriptome analysis of human iPSC-derived NPCs transduced with EGFP as a control.


title: RNA-seq of human iPSC-derived NPCs, EGFP control, biol rep 3

description:
Library name: hNPC_EGFP_rep3
Transcriptome analysis of human iPSC-derived NPCs transduced with EGFP as a control.


title: 48TF_Day 9_CD45-HLA-DR-_10_BD Rhapsody_exp1_rep1, GEX

description:
Library name: 48TF_Day 9_CD45-HLA-DR-_10_BD Rhapsody
sc_divergentDC.48TF.h5ad.gz
brd_divergentDC.48TF.csv.gz
DN

data_processing:
For 10X Genomics: The Cell Ranger v6.0.1 pipeline was used to process data generated using the 10x Chromium platform. Using Cell Ranger, the reads were converted to fastq format, processed, filtered, and then the aligned reads were generated.
For BD Rhapsody: BD Rhapsody™ Sequence Analysis Pipeline was used to process fastq files and performed alignment to human (hg38) genome assemblies using STAR.
The sparse expression matrix generated by Cellranger and BD Rhapsody Seven Bridges analysis pipeline was used as input to the Seurat library v4.3.0.
Assembly: hg38
Supplementary files format and content: Gene Expression matrix
Supplementary files format and content: TF Barcode Expression matrix
Metadata info is stored in h5ad, brd_* are accompanying files that should be read together with h5ad files.
Here is how this info is stored:
9 TFs -> h5ad file metadata contains celltypes ('Day2', 'Day9 45+DR+', 'Day9 45-DR') and copies (20cp and 40cp)
22 TFs -> h5ad file metadata contains Type  ('Day9 45+DR+', 'Day9 45-DR-')
42 TFs -> h5ad file metadata contains Type  ('Day2 (40cp)', 'Day9 45+ (10cp)', 'Day9 45+ (15cp)', 'Day9 45+ (40cp)', 'Day9 45+ (5cp)', 'Day9 45-DR- (10cp)', 'Day9 45-DR- (15cp)', 'Day9 45-DR- (40cp)', 'Day9 45-DR- (5cp)')

tag: single-cell method


title: 42TF_Day 9_CD45+_10_10x Genomics

description:
Library name: 42TF_Day 9_CD45+_10_10x Genomics
sc_barcodedData42TF.h5ad.gz
brd_barcodedData42TF.csv.gz
10CP_45_pos

value: 10x Genomics

tag: tf transduction


title: 48TF_Day 9_CD45+_10_BD Rhapsody_exp1_rep2, GEX

description:
Library name: 48TF_Day 9_CD45+_10_BD Rhapsody_rep2
sc_divergentDC.48TF.h5ad.gz
brd_divergentDC.48TF.csv.gz
SP2

tag: cp number


title: 42TF_Day 9_CD45+_5_10x Genomics

description:
Library name: 42TF_Day 9_CD45+_5_10x Genomics
sc_barcodedData42TF.h5ad.gz
brd_barcodedData42TF.csv.gz
5CP_45_pos

tag: time


title: RNA-seq of human iPSC-derived neurons, MECP2 overexpression, biol rep 2

description:
Library name: hNeuron_MECP2_rep2
Transcriptome analysis of human iPSC-derived neurons transduced with MECP2 to induce overexpression.


title: 42TF_Day 2_Live_40_10x Genomics

description:
Library name: 42TF_Day 2_Live_40_10x Genomics
sc_barcodedData42TF.h5ad.gz
brd_barcodedData42TF.csv.gz
all_brd_D2

value: Day 2

tag: sorted cells

value: Live


title: 42TF_Day 9_CD45-HLA-DR-_15_10x Genomics

description:
Library name: 42TF_Day 9_CD45-HLA-DR-_15_10x Genomics
sc_barcodedData42TF.h5ad.gz
brd_barcodedData42TF.csv.gz
15CP_45_DRneg

tag: cell line

value: HEF


title: 42TF_Day 9_CD45+_15_10x Genomics

description:
Library name: 42TF_Day 9_CD45+_15_10x Genomics
sc_barcodedData42TF.h5ad.gz
brd_barcodedData42TF.csv.gz
15CP_45_pos_clog

tag: cell type

value: human embryonic fibroblasts


title: 42TF_Day 9_CD45-HLA-DR-_10_10x Genomics

description:
Library name: 42TF_Day 9_CD45-HLA-DR-_10_10x Genomics
sc_barcodedData42TF.h5ad.gz
brd_barcodedData42TF.csv.gz
10CP_45_DRneg

tag: genotype


title: 42TF_Day 9_CD45-HLA-DR-_40_10x Genomics

description:
Library name: 42TF_Day 9_CD45-HLA-DR-_40_10x Genomics
sc_barcodedData42TF.h5ad.gz
brd_barcodedData42TF.csv.gz
all_brd_D9_negneg


title: 22TF_Day 9_CD45+HLA-DR+_40_10x Genomics

description:
Library name: 22TF_Day 9_CD45+HLA-DR+_40_10x Genomics
sc_barcodedData22TF.h5ad.gz
brd_barcodedData22TF.csv.gz
9_14brd_D9_pospos


title: 42TF_Day 9_CD45-HLA-DR-_5_10x Genomics

description:
Library name: 42TF_Day 9_CD45-HLA-DR-_5_10x Genomics
sc_barcodedData42TF.h5ad.gz
brd_barcodedData42TF.csv.gz
5CP_45_DRneg


title: 42TF_Day 9_CD45+_40_10x Genomics

description:
Library name: 42TF_Day 9_CD45+_40_10x Genomics
sc_barcodedData42TF.h5ad.gz
brd_barcodedData42TF.csv.gz
all_brd_D9_pospos


title: 9TF_Day 9_CD45-HLA-DR-_40_10x Genomics

description:
Library name: 9TF_Day 9_CD45-HLA-DR-_40_10x Genomics
sc_barcodedData9TF.h5ad.gz
brd_barcodedData9TF.csv.gz
S2


title: 9TF_Day 9_CD45+HLA-DR+_40_10x Genomics

description:
Library name: 9TF_Day 9_CD45+HLA-DR+_40_10x Genomics
sc_barcodedData9TF.h5ad.gz
brd_barcodedData9TF.csv.gz
S1


title: 9TF_Day 9_CD45-HLA-DR-_20_10x Genomics

description:
Library name: 9TF_Day 9_CD45-HLA-DR-_20_10x Genomics
sc_barcodedData9TF.h5ad.gz
brd_barcodedData9TF.csv.gz
S4


title: 9TF_Day 9_CD45+HLA-DR+_20_10x Genomics

description:
Library name: 9TF_Day 9_CD45+HLA-DR+_20_10x Genomics
sc_barcodedData9TF.h5ad.gz
brd_barcodedData9TF.csv.gz
S3


title: Case8 Normal

description:
Library name: GA69752
Normal thyroid tissue

tag: tissue

value: Normal


title: 9TF_Day 2_Live_40_10x Genomics

description:
Library name: 9TF_Day 2_Live_40_10x Genomics
sc_barcodedData9TF.h5ad.gz
brd_barcodedData9TF.csv.gz
S5

value: wildtype


title: 9TF_Day 2_Live_20_10x Genomics

description:
Library name: 9TF_Day 2_Live_20_10x Genomics
sc_barcodedData9TF.h5ad.gz
brd_barcodedData9TF.csv.gz
S6


title: DA neurons, vehicle control, male line 3

city: Atlanta

first: Zhexing

last: Wen

state: GA

address: 615 Michael Street

institute: Emory University

description:
Library name: M-line3-veh
column name in raw_counts_all_samples.csv: M-line3-veh.A, M-line3-veh.B, M-line3-veh.C

data_processing:
Sequencing was performed using the paired-end 150 method that reads DNA fragments in pairs of 150 base pairs each with a reading depth of 20 million reads/direction/sample.
FastQC was used to assess adapter sequences and low-quality reads, which were subsequently trimmed with TrimGalore.
The trimmed RNA-seq reads were then aligned to the human reference genome hg38 using STAR.
Assembly: hg38
Supplementary files format and content: csv file includes raw counts for all samples

source_name: human induced pluripotent stem cells

extract_protocol:
total RNA was extracted using the Zymo RNA miniprep kit. 1 ug of total RNA was used for the construction of sequencing libraries
RNA-seq libraries were prepared using the Illumina mRNA sample prep kit following the manufacturer’s protocol

value: human induced pluripotent stem cells

value: dopaminergic neurons

value: healthy control

value: vehicle


title: DA neurons, IL6, male line 3

description:
Library name: M-line3-IL6
column name in raw_counts_all_samples.csv: M-line3-IL6.A, M-line3-IL6.B, M-line3-IL6.C


title: DA neurons, IL6, male line 1 (KOLF2.1J)

description:
Library name: M-line1-IL6
column name in raw_counts_all_samples.csv: M-line1-IL6.A, M-line1-IL6.B, M-line1-IL6.C


title: DA neurons, IL6, female line 3

description:
Library name: F-line3-IL6
column name in raw_counts_all_samples.csv: F-line3-IL6.A, F-line3-IL6.B, F-line3-IL6.C


title: RNA-seq of human iPSC-derived neurons, EGFP control, biol rep 2

description:
Library name: hNeuron_EGFP_rep2
Transcriptome analysis of human iPSC-derived neurons transduced with EGFP as a control.

value: Wild-type iPSC line


title: DA neurons, vehicle control, male line 2 (PGP1)

description:
Library name: M-line2-veh
column name in raw_counts_all_samples.csv: M-line2-veh.A, M-line2-veh.B, M-line2-veh.C


title: DA neurons, vehicle control, male line 1 (KOLF2.1J)

description:
Library name: M-line1-veh
column name in raw_counts_all_samples.csv: M-line1-veh.A, M-line1-veh.B, M-line1-veh.C


title: DA neurons, vehicle control, female line 3

description:
Library name: F-line3-veh
column name in raw_counts_all_samples.csv: F-line3-veh.A, F-line3-veh.B, F-line3-veh.C


title: DA neurons, vehicle control, female line 1

description:
Library name: F-line1-veh
column name in raw_counts_all_samples.csv: F-line1-veh.A, F-line1-veh.B, F-line1-veh.C


title: DA neurons, vehicle control, female line 2

description:
Library name: F-line2-veh
column name in raw_counts_all_samples.csv: F-line2-veh.A, F-line2-veh.B, F-line2-veh.C


title: DA neurons, IL6, female line 2

description:
Library name: F-line2-IL6
column name in raw_counts_all_samples.csv: F-line2-IL6.A, F-line2-IL6.B, F-line2-IL6.C


title: 48TF_Day 9_CD45+_10_BD Rhapsody_exp1_rep1, GEX

description:
Library name: 48TF_Day 9_CD45+_10_BD Rhapsody_rep1
sc_divergentDC.48TF.h5ad.gz
brd_divergentDC.48TF.csv.gz
SP1

value: Arrayed

value: BD Rhapsody

value: Day 9


title: DAPC_MT_10μM-3

city: Shen Zhen

first: Peng

last: Cui

state: Guang Dong

address: Futian District, Lianhua Street

institute: Peking University Shenzhen Hospital

description:
Library name: MTDAPC-3
NSCs-derived DA neural progenitor cells (DAPCs), treated with 10μM MT, rep3

data_processing:
First,Trim_galore (version0.6.6 http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used for quality control and adaptor trimming.
Then, Processed reads were mapped to GRCh38 using STAR (2.7.9a)
Gene expressions were counted by  RSEM (v1.3.1 ).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include read count, tpm and fpkm for each sample

source_name: PBMC

growth_protocol: HiPSC-derived NSCs were cultured in DMEM/F12 supplemented with 1× N2, 1× B27, 1% GlutaMAX, 1% penicillin/streptomycin, 1% nonessential amino acids, 0.1 mM β-mercaptoethanol, 10 μg/mL BSA, 10 ng/mL hLIF, 4 μM CHIR99021, and 3 μM SB431542. The NSCs were passaged using Accutase at a 1:6 dilution. NSCs-derived DA neural progenitor cells (DAPCs) were cultured in DMEM/F12, 1×N2, 1×B27, 300 ng/mL cAMP, 0.2 µM VC, 100 nM LDN-193189, 600 ng/mL +/−Noggin, 100 ng/mL SHH, and 100 ng/mL FGF8b. All cells were maintained in a CO2 incubator at 37°C.

extract_protocol:
Extract total RNA from the samples using TRIzol™ Reagent. Then, the purity of RNA was determined by Nano Drop, the concentration of RNA was determined by Qubit RNA BR (Broad-Range) Assay Kit, and the integrity of RNA was detected by RNA Screen Tape.
Based on the Total amount of Total RNA, take 0.1-1 μ g of Total RNA and use the Poly(A)mRNA Capture Module (item number: mRNA was isolated using the RK20340 Kit, and then the mRNA library was constructed using the Aibotek Fast RNA-seq Lib Prep Kit V2 (Catalog No. : RK20306) library construction kit.

treatment_protocol: The cells to be sequenced were collected, lysed with TRIzol™ Reagent and then stored in a -80 ° C refrigerator

value: PBMC

value: Dopaminergic neuroprogenitors differentiated from hiPSCs

value: Neural differentiation


title: DA neurons, IL6, female line 1

description:
Library name: F-line1-IL6
column name in raw_counts_all_samples.csv: F-line1-IL6.A, F-line1-IL6.B, F-line1-IL6.C


title: 22TF_Day 9_CD45-HLA-DR-_40_10x Genomics

description:
Library name: 22TF_Day 9_CD45-HLA-DR-_40_10x Genomics
sc_barcodedData22TF.h5ad.gz
brd_barcodedData22TF.csv.gz
9_14brd_D9_negneg

value: 10x Genomics


title: DAPC_MT_10μM-1

description:
Library name: MTDAPC-1
NSCs-derived DA neural progenitor cells (DAPCs), treated with 10μM MT, rep1


title: DAPC_MT_10μM-2

description:
Library name: MTDAPC-2
NSCs-derived DA neural progenitor cells (DAPCs), treated with 10μM MT, rep2


title: DA neurons, IL6, male line 2 (PGP1)

description:
Library name: M-line2-IL6
column name in raw_counts_all_samples.csv: M-line2-IL6.A, M-line2-IL6.B, M-line2-IL6.C


title: DAPC_MT_0μM-3

description:
Library name: DAPC-D-3D3
NSCs-derived DA neural progenitor cells (DAPCs), treated with 0μM MT, rep3


title: NSC-1

description:
Library name: NSC1
neural stem cells, rep1

value: Neural stem cells differentiated from hiPSCs


title: DAPC_MT_0μM-1

description:
Library name: DAPC-D-1D3
NSCs-derived DA neural progenitor cells (DAPCs), treated with 0μM MT, rep1


title: DAPC_MT_0μM-2

description:
Library name: DAPC-D-2D3
NSCs-derived DA neural progenitor cells (DAPCs), treated with 0μM MT, rep2


title: NSC-3

description:
Library name: NSC3
neural stem cells, rep3


title: MSC(M), Adapted FBS, 2 Passage, 1 Adaptation Passage, Donor 3

city: Lisbon

first: Ana

last: Fernandes-Platzgummer

address: Av. Prof. Dr. Cavaco Silva

department: Department of Bioengineering - Instituto Superior Técnico, University of Lisbon

country: Portugal

institute: Institute for Bioengineering and Biosciences (iBB)

description: Library name: HF_99

data_processing:
Quality Control: Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads Mapping to the Reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: ensembl_homo_sapiens_grch38_p12_gca_000001405_27
Supplementary files format and content: all counts are in a single .csv file. Each column corresponds to one sample. The file contains the number of reads mapped to each gene (counts).

source_name: Bone Marrow

growth_protocol: BM-derived Mesenchymal Stromal Cells (MSC(M)) were cultured either with DMEM supplemented with 10% Fetal Bovine Serum (FBS) and 1% Antibiotic-Antimicotic (AA) or DMEM supplemented with 5% human Platelet Lysate (hPL) and 1% AA. Cells were mantained in a humidified atmospheres with 5% CO2 at 37ºC.

extract_protocol:
Total RNA was extracted using a High Pure RNA Isolation Kit (11828665001, Roche) according to the manufacturer’s instructions. Briefly, cells were resuspended in PBS and lysed by adding Lysis/-Binding Buffer, followed by centrifugation through a High Pure Filter Tube. After lysis, DNA contamination was removed by DNase I treatment, and subsequent washing steps were performed to increase purity. The isolated RNA was eluted with Elution Buffer and stored at -80ºC until further use.
Library preparation and paired-end 150 bp sequencing were performed by Novogene (Beijing, China) using an Illumina NovaSeq 6000 platform. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the directional library, it was ready after end repair, A tailing, adapter ligation, size selection, USER enzyme digestion , amplification, and purification. The library was checked with Qubit and real time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: MSC(M) underwent one of three different adaptation regimens over 4 passages. "F" denotes one passage in FBS, and "H" one passage in hPL. The conditions included Direct (continuous expansion in the same medium: F, FF, FFF, FFFF or H, HH, HHH, HHHH), Adapted (medium switch: HF, HHF, HFF, HHFF, or FH, FFH, FHH, FFHH), and Re-adapted (returned to the original medium: FHHF or HFFH).

value: Bone Marrow

value: Mesenchymal Stromal Cells

tag: adaptation condition

value: Adapted FBS

tag: culture medium_supplement

value: FBS

value: Female

tag: age

tag: donor

value: Donor 3


title: MSC(M), Adapted FBS, 4 Passage, 2 Adaptation Passages, Donor 3

description: Library name: HHFF_99

tag: Sex


title: MSC(M), Adapted FBS, 3 Passage, 1 Adaptation Passage, Donor 3

description: Library name: HHF_99


title: MSC(M), Direct hPL, 4 Passage, Donor 3

description: Library name: HHHH_99

value: Direct hPL

value: hPL


title: MSC(M), Adapted hPL, 3 Passage, 1 Adaptation Passage, Donor 3

description: Library name: FFH_99

value: Adapted hPL


title: MSC(M), Adapted hPL, 4 Passage, 2 Adaptation Passages, Donor 3

description: Library name: FFHH_99


title: MSC(M), Adapted FBS, 3 Passage, 2 Adaptation Passages, Donor 3

description: Library name: HFF_99


title: MSC(M), Re-adapted hPL, 4 Passage, Donor 3

description: Library name: HFFH_99

value: Re-adapted hPL


title: MSC(M), Re-adapted FBS, 4 Passage, Donor 3

description: Library name: FHHF_99

value: Re-adapted FBS


title: MSC(M), Direct hPL, 2 Passage, Donor 3

description: Library name: HH_99


title: NSC-2

description:
Library name: NSC2
neural stem cells, rep2


title: MSC(M), Adapted hPL, 2 Passage, 1 Adaptation Passage, Donor 3

description: Library name: FH_99


title: MSC(M), Direct hPL, 1 Passage, Donor 3

description: Library name: H_99


title: MSC(M), Direct FBS, 4 Passage, Donor 3

description: Library name: FFFF_99

value: Direct FBS


title: MSC(M), Direct FBS, 2 Passage, Donor 3

description: Library name: FF_99


title: MSC(M), Direct FBS, 1 Passage, Donor 3

description: Library name: F_99


title: MSC(M), Re-adapted hPL, 4 Passage, Donor 2

description: Library name: HFFH_86

value: Male

value: Donor 2


title: MSC(M), Adapted FBS, 2 Passage, 1 Adaptation Passage, Donor 2

description: Library name: HF_86


title: MSC(M), Direct hPL, 4 Passage, Donor 2

description: Library name: HHHH_86


title: MSC(M), Direct hPL, 3 Passage, Donor 2

description: Library name: HHH_86


title: MSC(M), Direct hPL, 2 Passage, Donor 2

description: Library name: HH_86


title: MSC(M), Direct hPL, 1 Passage, Donor 2

description: Library name: H_86


title: MSC(M), Adapted FBS, 4 Passage, 2 Adaptation Passages, Donor 2

description: Library name: HHFF_86


title: MSC(M), Direct FBS, 3 Passage, Donor 3

description: Library name: FFF_99


title: MSC(M), Re-adapted FBS, 4 Passage, Donor 2

description: Library name: FHHF_86


title: MSC(M), Adapted hPL, 2 Passage, 1 Adaptation Passage, Donor 2

description: Library name: FH_86


title: MSC(M), Direct FBS, 2 Passage, Donor 2

description: Library name: FF_86


title: MSC(M), Adapted hPL, 3 Passage, 2 Adaptation Passages, Donor 2

description: Library name: FHH_86


title: MSC(M), Direct FBS, 1 Passage, Donor 2

description: Library name: F_86


title: MSC(M), Re-adapted hPL, 4 Passage, Donor 1

description: Library name: HFFH_50

value: Donor 1


title: MSC(M), Adapted FBS, 3 Passage, 1 Adaptation Passage, Donor 1

description: Library name: HHF_50


title: MSC(M), Adapted FBS, 2 Passage, 1 Adaptation Passage, Donor 1

description: Library name: HF_50


title: MSC(M), Direct hPL, 2 Passage, Donor 1

description: Library name: HH_50


title: MSC(M), Direct hPL, 4 Passage, Donor 1

description: Library name: HHHH_50


title: MSC(M), Adapted FBS, 4 Passage, 2 Adaptation Passages, Donor 1

description: Library name: HHFF_50


title: MSC(M), Adapted FBS, 3 Passage, 2 Adaptation Passages, Donor 1

description: Library name: HFF_50


title: MSC(M), Adapted hPL, 4 Passage, 2 Adaptation Passages, Donor 1

description: Library name: FFHH_50


title: MSC(M), Direct hPL, 3 Passage, Donor 1

description: Library name: HHH_50


title: MSC(M), Adapted hPL, 3 Passage, 1 Adaptation Passage, Donor 1

description: Library name: FFH_50


title: MSC(M), Re-adapted FBS, 4 Passage, Donor 1

description: Library name: FHHF_50


title: MSC(M), Direct hPL, 1 Passage, Donor 1

description: Library name: H_50


title: MSC(M), Direct FBS, 4 Passage, Donor 2

description: Library name: FFFF_86


title: MSC(M), Adapted hPL, 4 Passage, 2 Adaptation Passages, Donor 2

description: Library name: FFHH_86


title: MSC(M), Adapted hPL, 3 Passage, 2 Adaptation Passages, Donor 1

description: Library name: FHH_50


title: S2_STR

description:
Library name: S2_STR
Fresh frozen Spatial transcriptome sequencing

value: Post-mortem fresh frozen brain

tag: tissue section

value: STR

tag: disease

value: Alzheimer's Disease


description:
Library name: 48TF_Day 9_CD45-HLA-DR-_10_BD Rhapsody_Arrayed_exp4, GEX
sc_divergentDC.48TF_Arrayed_exp4.h5ad.gz
brd_divergentDC.48TF_Arrayed_exp4.csv.gz

value: HEF

value: human embryonic fibroblasts

value: wildtype

tag: virus production

value: Arrayed

value: BD Rhapsody

value: Day 9


title: MSC(M), Adapted hPL, 2 Passage, 1 Adaptation Passage, Donor 1

description: Library name: FH_50

value: Bone Marrow

value: Mesenchymal Stromal Cells

value: hPL

value: Female


title: MSC(M), Direct FBS, 2 Passage, Donor 1

description: Library name: FF_50

value: Direct FBS

value: FBS


title: MSC(M), Direct FBS, 3 Passage, Donor 1

description: Library name: FFF_50


title: MSC(M), Direct FBS, 1 Passage, Donor 1

description: Library name: F_50


title: MSC(M), Adapted hPL, 3 Passage, 2 Adaptation Passages, Donor 3

description: Library name: FHH_99

value: Adapted hPL

value: Donor 3


title: PXGLN2B27.5uMEPZ rep3

city: Guangzhou

first: Man

state: Guangdong

address: No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District

department: Department of Basic Research

institute: Guangzhou Laboratory

description:
Library name: PXGLN2B27.5uMEPZ rep3
PXGLN2B27.5uMEPZ rep3

data_processing:
The raw RNA-seq reads were processed using TrimGalore to remove adapter sequences and low-quality bases. The cleaned reads were then aligned to hg38 with STAR (V2.7.6a). Gene expression values were normalized across samples using the variance modeling tool DESeq2
Assembly: hg38
Supplementary files format and content: Tab-separated values files

extract_protocol:
Cellular total RNA was collected using a Trizol extraction method
RNA libraries were constructed using the Illumina Ribo-Zero plus rRNA Depletion kit (20037135, Illumina)

value: human embryonic stem cell

value: wild-type

tag: treatment

value: N2B27+EPZ6438 for 3 days


title: MSC(M), Direct hPL, 3 Passage, Donor 3

description: Library name: HHH_99

value: Direct hPL


title: SW1990 cell ，Vector-3

city: Hangzhou

first: Mengyi

last: Lao

state: Zhejiang

address: Qingchun 79 road

institute: Zhejiang university

description: Library name: samples3

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: cell line

growth_protocol: SW1990 pancreatic cancer cells were maintained in DMEM supplemented with10% fetal bovine serum (FBS)and antibiotics in humidified atmosphere with 5%CO2 at 37℃

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes.  After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
CUT&Tag libraries were prepared using the KAPA HTP Library Preparation Kit complemented withNEXTflex DNA Barcodes from Bio Scientific.10ng of DNA was used as starting material for input and ip samples.   Libraries were amplified using 13 cycles on the thermocycler.   Post amplification libraries were size selected at250-450bp in length using AgencourtAMPure XP beads from Beckman Coulter.   Libraries were validated using the Agilent High SensitivityDNA Kit.

treatment_protocol: The control group and the treatment group cells were transfected with the vector and the SREBP1 overexpression plasmid, respectively.

value: cell line

value: Pancreatic cancer cell

value: Vector

value: lipid metabolism


title: SW1990 cell ，SREBP1-2

description: Library name: samples5

value: SREBP2 OE


title: SW1990 cell ，SREBP1-3

description: Library name: samples6

value: SREBP3 OE


title: SW1990 cell ，Vector-2

description: Library name: samples2


title: PXGLN2B27.5uMEPZ rep1

description:
Library name: PXGLN2B27.5uMEPZ rep1
PXGLN2B27.5uMEPZ rep1


title: PXGLN2B27 rep3

description:
Library name: PXGLN2B27 rep3
PXGLN2B27 rep3

value: N2B27 basal


title: SW1990 cell ，SREBP1-1

description: Library name: samples4

value: SREBP1 OE


title: PXGLN2B27.5uMEPZ rep2

description:
Library name: PXGLN2B27.5uMEPZ rep2
PXGLN2B27.5uMEPZ rep2


title: SW1990 cell ，Vector-1

description: Library name: samples1


title: PXGLN2B27 rep2

description:
Library name: PXGLN2B27 rep2
PXGLN2B27 rep2


title: PXGLN2B27 rep1

description:
Library name: PXGLN2B27 rep1
PXGLN2B27 rep1


title: PXGLH1ESC rep1

description:
Library name: PXGLH1ESC rep1
PXGLH1ESC rep1

value: PXGL medium


title: human post-mortem prostate tissue case 78

city: Montgomery

first: Gulnaz

last: Javan

state: AL

address: 915 S Jackson Street

department: Physical and Forensic Sciences

institute: Alabama State University

description: Library name: HP_78_GJ5

data_processing:
Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system.
Firstly, Cutadapt21 and perl scripts were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used HISAT222 to map reads to the genome of homo sapiens. The mapped reads of each sample were assembled using StringTie23. Then, all transcriptomes from five samples were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare (https://github.com/gpertea/gffcompare/). After the ﬁnal transcriptome was generated, StringTie23 and ballgown (http://www.bioconductor.org/packages/release/bioc/-html/ballgown.html) was used to estimate the expression levels of all transcripts.
StringTie23 was used to perform expression level for mRNAs and lncRNAs by calculating FPKM. mRNAs/lncRNAs differential expression analysis was performed by DESeq224 software between two different groups (and by edgeR25 between two samples). The genes/mRNAs/lncRNAs with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes/mRNAs/lncRNAs.
Assembly: GRCh38 - hg38
Supplementary files format and content: fpkm and count matrix

source_name: human prostate tissue

extract_protocol:
RNA was extracted using QIAGEN RNeasy Mini Kit (cat. no. 74104, Qiagen) from the prostate tissues (~ 30 mg).
The sequencing library was prepared following Illumina’s TruSeq-stranded-total-RNA-sample preparation protocol.

value: prostate

value: Male


title: human post-mortem prostate tissue case 74

description: Library name: HP_74_GJ4


title: PXGLH1ESC rep3

description:
Library name: PXGLH1ESC rep3
PXGLH1ESC rep3


title: human post-mortem prostate tissue case 56

description: Library name: HP_56_GJ3


title: human post-mortem prostate tissue case 53

description: Library name: HP_53_GJ2


title: 92F

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

description:
Library name: 92F
sam92

data_processing:
FastQC v0.11.8 for Sequencing QC
STAR 2.4.2a for alignment
subread 1.5.0.post3 (featureCount) for quantification of genes
samples that were sequenced in more than one lane, counts from L001 and L002 were summed
Assembly: GRCh37
Supplementary files format and content: raw_counts_per_gene.csv: comma separated delimited raw gene counts of each sample

source_name: Non-Lesional

extract_protocol:
Cutaneous adipose tissue biopsies were taken from lesional and non-lesional skin of 82 psoriasis patients. Samples were also collected from 15 healthy subjects using the same procedure. RNA was isolated from adipose tissue samples using the RNeasy Lipid Tissue Mini Kit (Qiagen)
Total RNA was extracted from adipose tissue using the RNeasy Lipid Tissue Mini Kit (Valencia, CA, USA). and libraries prepared using TruSeq Stranded mRNA Sample Library Preparation kit (Illumina, San Diego, CA), according to the manufacturer’s instructions. The normalized cDNA libraries were pooled and sequenced on Illumina Nova 6000.

value: Fat

tag: condition

value: Psoriasis

tag: timepoint

value: Week 12

value: Non-Lesional

value: Secukinumab

tag: subjectid


title: 93F

description:
Library name: 93F
sam93

source_name: Lesional

value: Baseline

value: Lesional


title: human post-mortem prostate tissue case 4

description: Library name: HP_4_GJ1


title: 99F

description:
Library name: 99F
sam99

value: Placebo


title: 90F

description:
Library name: 90F
sam90


title: PXGLH1ESC rep2

description:
Library name: PXGLH1ESC rep2
PXGLH1ESC rep2

value: human embryonic stem cell

value: wild-type


title: 87F

description:
Library name: 87F
sam87


title: 91F

description:
Library name: 91F
sam91


title: 89F

description:
Library name: 89F
sam89


title: 85F

description:
Library name: 85F
sam85


title: 84F

description:
Library name: 84F
sam84


title: 88F

description:
Library name: 88F
sam88


title: 82F

description:
Library name: 82F
sam82


title: 77F

description:
Library name: 77F
sam77


title: 81F

description:
Library name: 81F
sam81


title: 78F

description:
Library name: 78F
sam78


title: 83F

description:
Library name: 83F
sam83


title: 75F

description:
Library name: 75F
sam75


title: 74F

description:
Library name: 74F
sam74


title: 98F

description:
Library name: 98F
sam98


title: 8F

description:
Library name: 8F
sam8


title: 97F

description:
Library name: 97F
sam97


title: 73F

description:
Library name: 73F
sam73


title: 68F

description:
Library name: 68F
sam68


title: 64F

description:
Library name: 64F
sam64


title: 69F

description:
Library name: 69F
sam69


title: 59F

description:
Library name: 59F
sam59


title: 70F

description:
Library name: 70F
sam70


title: 61F

description:
Library name: 61F
sam61


title: 67F

description:
Library name: 67F
sam67


title: 7F

description:
Library name: 7F
sam7


title: 63F

description:
Library name: 63F
sam63


title: 52F

description:
Library name: 52F
sam52


title: 53F

description:
Library name: 53F
sam53


title: 6F

description:
Library name: 6F
sam6


title: 55F

description:
Library name: 55F
sam55


title: 58F

description:
Library name: 58F
sam58


title: 56F

description:
Library name: 56F
sam56


title: 51F

description:
Library name: 51F
sam51


title: 467F

description:
Library name: 467F
sam467

source_name: Normal

value: Healthy Vol.

value: Control

value: Normal


title: 47F

description:
Library name: 47F
sam47


title: 48F

description:
Library name: 48F
sam48


title: 462F

description:
Library name: 462F
sam462


title: 464F

description:
Library name: 464F
sam464


title: 463F

description:
Library name: 463F
sam463


title: 57F

description:
Library name: 57F
sam57


title: 459F

description:
Library name: 459F
sam459


title: 5F

description:
Library name: 5F
sam5


title: 461F

description:
Library name: 461F
sam461


title: 458F

description:
Library name: 458F
sam458


title: 54F

description:
Library name: 54F
sam54


title: 451F

description:
Library name: 451F
sam451


title: 454F

description:
Library name: 454F
sam454


title: 453F

description:
Library name: 453F
sam453


title: 455F

description:
Library name: 455F
sam455


title: 456F

description:
Library name: 456F
sam456


title: 49F

description:
Library name: 49F
sam49


title: 43F

description:
Library name: 43F
sam43


title: 39F

description:
Library name: 39F
sam39


title: 36F

description:
Library name: 36F
sam36


title: 40F

description:
Library name: 40F
sam40


title: 35F

description:
Library name: 35F
sam35


title: 33F

description:
Library name: 33F
sam33


title: 34F

description:
Library name: 34F
sam34


title: 317F

description:
Library name: 317F
sam317


title: 452F

description:
Library name: 452F
sam452


title: 320F

description:
Library name: 320F
sam320


title: 319F

description:
Library name: 319F
sam319


title: 316F

description:
Library name: 316F
sam316


title: 318F

description:
Library name: 318F
sam318


title: 312F

description:
Library name: 312F
sam312


title: 32F

description:
Library name: 32F
sam32


title: 313F

description:
Library name: 313F
sam313


title: 310F

description:
Library name: 310F
sam310


title: 315F

description:
Library name: 315F
sam315


title: 314F

description:
Library name: 314F
sam314


title: 309F

description:
Library name: 309F
sam309


title: 311F

description:
Library name: 311F
sam311


title: 45F

description:
Library name: 45F
sam45


title: 31F

description:
Library name: 31F
sam31


title: 302F

description:
Library name: 302F
sam302


title: 305F

description:
Library name: 305F
sam305


title: 301F

description:
Library name: 301F
sam301


title: 304F

description:
Library name: 304F
sam304


title: 308F

description:
Library name: 308F
sam308


title: 303F

description:
Library name: 303F
sam303


title: 300F

description:
Library name: 300F
sam300


title: 296F

description:
Library name: 296F
sam296


title: 307F

description:
Library name: 307F
sam307


title: 299F

description:
Library name: 299F
sam299


title: 298F

description:
Library name: 298F
sam298


title: 294F

description:
Library name: 294F
sam294


title: 291F

description:
Library name: 291F
sam291


title: 293F

description:
Library name: 293F
sam293


title: 297F

description:
Library name: 297F
sam297


title: 292F

description:
Library name: 292F
sam292


title: 287F

description:
Library name: 287F
sam287


title: 288F

description:
Library name: 288F
sam288


title: 29F

description:
Library name: 29F
sam29


title: 290F

description:
Library name: 290F
sam290


title: 285F

description:
Library name: 285F
sam285


title: 283F

description:
Library name: 283F
sam283


title: 289F

description:
Library name: 289F
sam289


title: 286F

description:
Library name: 286F
sam286


title: 281F

description:
Library name: 281F
sam281


title: 279F

description:
Library name: 279F
sam279


title: 28F

description:
Library name: 28F
sam28


title: 280F

description:
Library name: 280F
sam280


title: 274F

description:
Library name: 274F
sam274


title: 295F

description:
Library name: 295F
sam295


title: 268F

description:
Library name: 268F
sam268


title: 270F

description:
Library name: 270F
sam270


title: 271F

description:
Library name: 271F
sam271


title: 269F

description:
Library name: 269F
sam269


title: 267F

description:
Library name: 267F
sam267


title: 273F

description:
Library name: 273F
sam273


title: 265F

description:
Library name: 265F
sam265


title: 264F

description:
Library name: 264F
sam264


title: 275F

description:
Library name: 275F
sam275


title: 243F

description:
Library name: 243F
sam243


title: 262F

description:
Library name: 262F
sam262


title: 239F

description:
Library name: 239F
sam239


title: 260F

description:
Library name: 260F
sam260


title: 25F

description:
Library name: 25F
sam25


title: 263F

description:
Library name: 263F
sam263


title: 257F

description:
Library name: 257F
sam257


title: 258F

description:
Library name: 258F
sam258


title: 236F

description:
Library name: 236F
sam236


title: 259F

description:
Library name: 259F
sam259


title: 276F

description:
Library name: 276F
sam276


title: 242F

description:
Library name: 242F
sam242


title: 24F

description:
Library name: 24F
sam24


title: 241F

description:
Library name: 241F
sam241


title: 27F

description:
Library name: 27F
sam27


title: 272F

description:
Library name: 272F
sam272


title: 277F

description:
Library name: 277F
sam277


title: 266F

description:
Library name: 266F
sam266


title: 235F

description:
Library name: 235F
sam235


title: 261F

description:
Library name: 261F
sam261


title: 23F

description:
Library name: 23F
sam23


title: 233F

description:
Library name: 233F
sam233


title: 223F

description:
Library name: 223F
sam223


title: 222F

description:
Library name: 222F
sam222


title: 231F

description:
Library name: 231F
sam231


title: 221F

description:
Library name: 221F
sam221


title: 217F

description:
Library name: 217F
sam217


title: 218F

description:
Library name: 218F
sam218


title: 212F

description:
Library name: 212F
sam212


title: 225F

description:
Library name: 225F
sam225


title: 209F

description:
Library name: 209F
sam209


title: 22F

description:
Library name: 22F
sam22


title: 232F

description:
Library name: 232F
sam232


title: 226F

description:
Library name: 226F
sam226


title: 208F

description:
Library name: 208F
sam208


title: 207F

description:
Library name: 207F
sam207


title: 213F

description:
Library name: 213F
sam213


title: 203F

description:
Library name: 203F
sam203


title: 211F

description:
Library name: 211F
sam211


title: 20F

description:
Library name: 20F
sam20


title: 210F

description:
Library name: 210F
sam210


title: 201F

description:
Library name: 201F
sam201


title: 220F

description:
Library name: 220F
sam220


title: 219F

description:
Library name: 219F
sam219


title: 215F

description:
Library name: 215F
sam215


title: 216F

description:
Library name: 216F
sam216


title: 205F

description:
Library name: 205F
sam205


title: 197F

description:
Library name: 197F
sam197


title: 194F

description:
Library name: 194F
sam194


title: 21F

description:
Library name: 21F
sam21


title: 195F

description:
Library name: 195F
sam195


title: 196F

description:
Library name: 196F
sam196


title: 204F

description:
Library name: 204F
sam204


title: 200F

description:
Library name: 200F
sam200


title: 191F

description:
Library name: 191F
sam191


title: 198F

description:
Library name: 198F
sam198


title: 206F

description:
Library name: 206F
sam206


title: 202F

description:
Library name: 202F
sam202


title: 199F

description:
Library name: 199F
sam199


title: 193F

description:
Library name: 193F
sam193


title: 189F

description:
Library name: 189F
sam189


title: 188F

description:
Library name: 188F
sam188


title: 186F

description:
Library name: 186F
sam186


title: 185F

description:
Library name: 185F
sam185


title: 187F

description:
Library name: 187F
sam187


title: 181F

description:
Library name: 181F
sam181


title: 184F

description:
Library name: 184F
sam184


title: 177F

description:
Library name: 177F
sam177


title: 179F

description:
Library name: 179F
sam179


title: 180F

description:
Library name: 180F
sam180


title: 178F

description:
Library name: 178F
sam178


title: 183F

description:
Library name: 183F
sam183


title: 19F

description:
Library name: 19F
sam19


title: 176F

description:
Library name: 176F
sam176


title: 174F

description:
Library name: 174F
sam174


title: 171F

description:
Library name: 171F
sam171


title: 175F

description:
Library name: 175F
sam175


title: 169F

description:
Library name: 169F
sam169


title: 167F

description:
Library name: 167F
sam167


title: 163F

description:
Library name: 163F
sam163


title: 173F

description:
Library name: 173F
sam173


title: 164F

description:
Library name: 164F
sam164


title: 172F

description:
Library name: 172F
sam172


title: 166F

description:
Library name: 166F
sam166


title: 162F

description:
Library name: 162F
sam162


title: 168F

description:
Library name: 168F
sam168


title: 165F

description:
Library name: 165F
sam165


title: 170F

description:
Library name: 170F
sam170


title: 159F

description:
Library name: 159F
sam159


title: 161F

description:
Library name: 161F
sam161


title: 16F

description:
Library name: 16F
sam16


title: 156F

description:
Library name: 156F
sam156


title: 160F

description:
Library name: 160F
sam160


title: 153F

description:
Library name: 153F
sam153


title: 155F

description:
Library name: 155F
sam155


title: 154F

description:
Library name: 154F
sam154


title: 151F

description:
Library name: 151F
sam151


title: 150F

description:
Library name: 150F
sam150


title: 15F

description:
Library name: 15F
sam15


title: 147F

description:
Library name: 147F
sam147


title: 148F

description:
Library name: 148F
sam148


title: 145F

description:
Library name: 145F
sam145


title: 12F

description:
Library name: 12F
sam12


title: 119F

description:
Library name: 119F
sam119


title: 111F

description:
Library name: 111F
sam111


title: 113F

description:
Library name: 113F
sam113


title: 144F

description:
Library name: 144F
sam144


title: 110F

description:
Library name: 110F
sam110


title: 11F

description:
Library name: 11F
sam11


title: 117F

description:
Library name: 117F
sam117


title: 115F

description:
Library name: 115F
sam115


title: 106F

description:
Library name: 106F
sam106


title: 152F

description:
Library name: 152F
sam152


title: 112F

description:
Library name: 112F
sam112


title: 102F

description:
Library name: 102F
sam102


title: 104F

description:
Library name: 104F
sam104


title: 143F

description:
Library name: 143F
sam143


title: 114F

description:
Library name: 114F
sam114


title: 107F

description:
Library name: 107F
sam107


title: 109F

description:
Library name: 109F
sam109


title: 105F

description:
Library name: 105F
sam105


title: Wildtype H929 replicate 2 at 24H

city: Boston

first: Mehmet

middle: Kemal

last: Samur

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

description: Library name: H929_Con_24_R2

data_processing:
Salmon quant from Salmon v0.12 with --validateMappings --seqBias --gcBias flags
Gencode V29 GTF file was used for Salmon Index
Assembly: GRCh38
Supplementary files format and content: txt file includes raw read counts from Salmon v0.12 with Gencode V29

growth_protocol: Passage two CAS-9 expressing NCI-H929 cells were grown in 10% RPMI media.

extract_protocol:
RNA-was isolated from control NCI-H929 and BCL7A KO NCI-H929 cells after 24 hr doxycycline induction  using All prep DNA/RNA Mini Kit from Qiagen inc
NEB strandaed poly-A selected RNA seq library prep kit was used based on compnay protocol.

treatment_protocol: CAS-9 expressing NCI-H929 cells were transduced with control and doxycycline inducible BCL7A KO (knock-out) constructs followed by puromycin selection for 3 days.After puromycin selection control NCI-H929 and BCL7A KO NCI-H929 were treated with 0.5 ug/ml doxycycline for 24 hours

value: cell line

value: B lymphocyte

value: WT


title: 100F

description:
Library name: 100F
sam100


title: Wildtype H929 replicate 1 at 24H

description: Library name: H929_Con_24_R1


title: H929 cell line with BCL7A KO replicate 1 at 24H

description: Library name: H929_BCL7A_KO_24_R1

value: BCL7A KO


title: H929 cell line with BCL7A KO replicate 2 at 24H

description: Library name: H929_BCL7A_KO_24_R2


title: Colonic biopsy: CM56

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description:
Library name: CM56
Colonic biopsy: CM56

data_processing:
Raw reads data were converted into FASTQ format and quality control was performed using the FASTQC software (Babraham Bioinformatics).
After trimming for adapters using trim_galore (Babraham Bioinformatics), mapping of the reads were obtained using the STAR program against human genome (hg38) and the quantification of genes were done using Partek Flow (v7.0.1) software using GENCODE V26 database
Assembly: Homo Sapiens genome hg38
Supplementary files format and content: read counts

source_name: Colonic biopsy

extract_protocol:
During endoscopy, at least two biopsies were collected from several segments of the colon (including sigmoid colon), fixed and routinely processed for histopathological assessment to confirm the diagnosis of MC and to exclude pathological alterations in control groups.
Sequencing libraries were prepared following the protocol included with the kit TruSeq Stranded mRNA Sample Preparation Guide (Part #15031047 Rev. E)

value: Colonic biopsy

value: LC


title: Colonic biopsy: CM92

description:
Library name: CM92
Colonic biopsy: CM92

value: H


title: Colonic biopsy: CM109_TR

description:
Library name: CM109_TR
Colonic biopsy: CM109_TR


title: Colonic biopsy: CM91

description:
Library name: CM91
Colonic biopsy: CM91


title: Colonic biopsy: CM36_TR

description:
Library name: CM36_TR
Colonic biopsy: CM36_TR


title: 103F

description:
Library name: 103F
sam103

value: Fat

value: Psoriasis

value: Week 12


title: Colonic biopsy: CM108_TR

description:
Library name: CM108_TR
Colonic biopsy: CM108_TR

value: IBS-D


title: Colonic biopsy: CM39_TR

description:
Library name: CM39_TR
Colonic biopsy: CM39_TR

value: CC


title: Colonic biopsy: CM43_TR

description:
Library name: CM43_TR
Colonic biopsy: CM43_TR


title: 101F

description:
Library name: 101F
sam101

value: Baseline

value: Lesional

value: Secukinumab


title: Colonic biopsy: CM40_TR

description:
Library name: CM40_TR
Colonic biopsy: CM40_TR


title: Colonic biopsy: CM111_TR

description:
Library name: CM111_TR
Colonic biopsy: CM111_TR


title: Colonic biopsy: CM21_TO

description:
Library name: CM21_TO
Colonic biopsy: CM21_TO


title: Colonic biopsy: CM42

description:
Library name: CM42
Colonic biopsy: CM42


title: Colonic biopsy: CM8

description:
Library name: CM8
Colonic biopsy: CM8


title: Colonic biopsy: CM95

description:
Library name: CM95
Colonic biopsy: CM95


title: Colonic biopsy: CM33_TR

description:
Library name: CM33_TR
Colonic biopsy: CM33_TR


title: Colonic biopsy: CM62

description:
Library name: CM62
Colonic biopsy: CM62


title: Colonic biopsy: CM42_TR

description:
Library name: CM42_TR
Colonic biopsy: CM42_TR


title: Colonic biopsy: CM17_TO

description:
Library name: CM17_TO
Colonic biopsy: CM17_TO


title: Colonic biopsy: CM117

description:
Library name: CM117
Colonic biopsy: CM117


title: Colonic biopsy: CM111

description:
Library name: CM111
Colonic biopsy: CM111


title: Colonic biopsy: CM32_TR

description:
Library name: CM32_TR
Colonic biopsy: CM32_TR


title: Colonic biopsy: CM65

description:
Library name: CM65
Colonic biopsy: CM65


title: Colonic biopsy: CM35_TR

description:
Library name: CM35_TR
Colonic biopsy: CM35_TR


title: Colonic biopsy: CM15

description:
Library name: CM15
Colonic biopsy: CM15


title: Colonic biopsy: CM20_TO

description:
Library name: CM20_TO
Colonic biopsy: CM20_TO


title: Colonic biopsy: CM38_TR

description:
Library name: CM38_TR
Colonic biopsy: CM38_TR


title: Colonic biopsy: CM29

description:
Library name: CM29
Colonic biopsy: CM29


title: Colonic biopsy: CM45_TR

description:
Library name: CM45_TR
Colonic biopsy: CM45_TR


title: Colonic biopsy: CM28

description:
Library name: CM28
Colonic biopsy: CM28


title: Colonic biopsy: CM64

description:
Library name: CM64
Colonic biopsy: CM64


title: Colonic biopsy: CM31

description:
Library name: CM31
Colonic biopsy: CM31


title: Colonic biopsy: CM98

description:
Library name: CM98
Colonic biopsy: CM98


title: Colonic biopsy: CM3

description:
Library name: CM3
Colonic biopsy: CM3


title: Colonic biopsy: CM16_TO

description:
Library name: CM16_TO
Colonic biopsy: CM16_TO


title: Colonic biopsy: CM14

description:
Library name: CM14
Colonic biopsy: CM14


title: Colonic biopsy: CM30

description:
Library name: CM30
Colonic biopsy: CM30


title: Colonic biopsy: CM89

description:
Library name: CM89
Colonic biopsy: CM89


title: Colonic biopsy: CM88

description:
Library name: CM88
Colonic biopsy: CM88


title: Colonic biopsy: CM87

description:
Library name: CM87
Colonic biopsy: CM87


title: Colonic biopsy: CM31_TR

description:
Library name: CM31_TR
Colonic biopsy: CM31_TR


title: Colonic biopsy: CM110_TR

description:
Library name: CM110_TR
Colonic biopsy: CM110_TR


title: Colonic biopsy: CM41_TR

description:
Library name: CM41_TR
Colonic biopsy: CM41_TR


title: Colonic biopsy: CM37_TR

description:
Library name: CM37_TR
Colonic biopsy: CM37_TR


title: ATAC-seq_RAD02

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

description: PE150 high throughout data

data_processing:
We used a publically available ATAC-Seq pipeline based on the official pipeline specification of ENCODE (https://github.com/kundajelab/atac-seq-pipeline).
Sam files were converted to Bam format using Samtools and used for peak calling.
MACS2 was used to call peaks and an initial threshold q-value of 0.1 was set as cutoff, using the Benjamini-Hochberg procedure for multiple-hypothesis correction.
Assembly: hg38/GRCh38
Supplementary files format and content: Normalized (per million reads) bigWig files were generated using the pipelines' MACS2 output.

source_name: Prostate

growth_protocol: Human normal prostate-derived stromal cells were routinely cultured in stromal complete media supplemented with 10% FBS, until a total number of approximately 50,000 was reached in each flask.

extract_protocol:
Following an Omni-ATAC protocol, cells were trypsinized and resuspended in 1 ml cold ATAC-Seq resuspension buffer, and centrigued at 500 rcf for 5 min in a pre-chilled fixed-angle centrifuge. After centrifugation, 900 ul of supernatant was aspirated, the remaining 100 ul of supernant was carefully taken to avoid the cell pellet. Pellets were then suspended in 50 ul ATAC-Seq RSB containing 0.1% NP40, 0.1% Tween-20 and 0.01% digitonin, with cell lysis incubated on ice for 3 min. After lysis, 1 ml of ATAC-Seq RSB containing 0.1% Tween-20 was added. Nuclei were then centrifuged for 10 min at 500 rcf at 4 C, with supernant removed and nuclei resuspended in 50 ul transposition mix.
Libraries were prepared according to Illumina's instructions accompanying the Nextera DNA Flex Library Prep Kit (FC-121-1030; Part# 1000000025416 v04). Briefly, nuclear pellets were subject to tagmentation by Bead-linked Transposomes (RLT), which were designed to tagment DNA with adapter sequences. Upon completion, tagmented products were cleaned up, and a pre-optimized PCR procedure was followed to amplify tagmented DNA. The resultant library of barcoded and amplified DNA was purified with a double-sided bead purification procedure. The library pool was quantified using a Bioanalyzer 2200 (Agilent) to assess size range of amplified DNA fragments and with a dsDNA fluorescent dye method, Quant-iT PicoGreen dsDNA Assay kit to quantify DNA fragments generated. ATAC libraries were pooled at equimolar concentrations and were sequenced multiplexed on the Illumina NovaSeq 6000 with 50-bp paired-ends.

treatment_protocol: To induce senescence, bleomycin (BLEO) was added to the media at 50 μg/ml, and cells were treated for 12 h before media change. Alternatively, cells were exposed to ionizing radiation (RAD) at a dose of 10 Gy. In each case, cells were allowed to stay in culture conditions for 7-10 d before collected for lysis.

value: Prostate

value: Stromal

value: wild type

value: RAD


title: Colonic biopsy: CM39

description:
Library name: CM39
Colonic biopsy: CM39


title: Colonic biopsy: CM34

description:
Library name: CM34
Colonic biopsy: CM34


title: ATAC-seq_RAD01

description: PE150 high throughout data


title: ATAC-seq_CTRL01

description: PE150 high throughout data

value: Naive


title: ATAC-seq_CTRL02

description: PE150 high throughout data


title: PSC27-RAD-2

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh19/hg19 whole genome using Bowtie2 (version 2.2.9) with the parameters: bowtie2 -end-to-end -very-sensitive -no-mixed -no-discordant - phred33 -I 10 -X 700.
Because a constant amount of pA-Tn5 was added to CUT&TAG reactions and brings along a fixed amount of E. coli DNA, we used bowtie2 with the parameters mentioned above to remove E. coli DNA and conduct normalization according to the CUT&TAG tutorial. CUT&TAG peaks were called using SEACR(1.3) with default parameters.
Assembly: GRCh19/hg19
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

growth_protocol: Normal human prostate-derived primary fibroblasts (PSC27) were routinely cultured in stromal complete media supplemented with 10% FBS.

extract_protocol:
Starting material cells were harvested under 3 different biological conditions: proliferating (CTRL), radiation-treated (RAD) and chemotherapeutically damaged (BLEO). CUT&Tag assay was performed as previously described. Briefly, 500,000 cells were washed and incubated with concanavalin A coated magnetic beads. Cell-magnetic beads complex were resuspended in Dig-wash Buffer, and then the primary antibody of CTCF was diluted 1:50 in Dig-Wash buffer and then incubated on a rotator overnight at 4 °C. The next day, cells were incubated with an appropriate secondary antibody (goat anti-rabbit) (1:100) in Dig-Wash buffer. Then, cells were incubated with pAG-Tn5 (1:200) in Dig-300 Buffer. For tagmentation, bead bound cells were resuspended in 50 μl of tagmentation buffer, with 1 μl of 10% SDS then added directly into the reaction to end the tagmentation. DNA was purified by 1.5 × Ampure XP beads. PCR cycling conditions: 72 °C for 5 min; 98 °C for 30 s; 12 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min. Libraries were sequenced (150-bp paired ends) by on the Illumina NovaSeq 6000.
Genomic DNA libraries were prepared for sequencing using standard Illumina protocols. One library was generated from each individual sample per treatment group.

treatment_protocol: PSC27 cells were maintained at 37 C as either consecutively proliferating cells (CTRL), subject to treatment by ionizing radiation (RAD) at a 10 Gy dose or chemotherapeutic drug bleomycin (BLEO) at 50 μg/ml.

value: Human primary fibroblast

value: Ionizing radiation


title: ATAC-seq_BLEO01

description: PE150 high throughout data

value: BLEO


title: PSC27-BLEO-1

value: Bleomycin


title: PSC27-CTRL-2

value: Control


title: PSC27-RAD-1


title: Colonic biopsy: CM59

description:
Library name: CM59
Colonic biopsy: CM59

value: Colonic biopsy


title: NK cytokine dex 3 bulk RNA-seq

city: Nanjing

first: Yuancheng

last: Li

state: JiangSu

address: No. 12 Jiangwangmiao Street

department: Institute of Dermatology

institute: Chinese Academy of Medicine Sciences and Peking Union Medical College

description: 10× Genomics

data_processing:
The scRNA-seq data demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The bulk RNA-seq data were processed  using the recommended CEL-Seq2 pipeline (https://github.com/yanailab/celseq2)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: blood

extract_protocol:
For bulk RNA-seq, RNA of sorted NK cells were extracted by trizol reagent
scRNA-seq libraries were constructed by 10 x genomics 3' kit, bulk RNA-seq libraries were constructed by CEL-Seq2 protocol

value: blood

value: PBMC

value: sorted CD56dim NK cell

value: NK cytokine dex


title: NK cytokine control 3 bulk RNA-seq

description: 10× Genomics

value: NK cytokine control


title: PSC27-CTRL-1


title: NK dex rep 3 bulk RNA-seq

description: 10× Genomics

value: NK dex


title: NK cytokine dex 1 bulk RNA-seq

description: 10× Genomics


title: NK cytokine control 1 bulk RNA-seq

description: 10× Genomics


title: NK control rep 3 bulk RNA-seq

description: 10× Genomics

value: NK control


title: NK cytokine dex 2 bulk RNA-seq

description: 10× Genomics


title: ATAC-seq_BLEO02

description: PE150 high throughout data

value: Prostate

value: Stromal


title: PSC27-BLEO-2


title: aMM tumor 3 scRNA-seq

description: 10× Genomics

source_name: skin

value: skin

value: skin cell

value: enriched CD45+ cells

tag: tissue type

value: aMM tumor


title: Colonic biopsy: CM99

description:
Library name: CM99
Colonic biopsy: CM99

value: H


title: NK control rep 2 bulk RNA-seq

description: 10× Genomics

tag: cell line


title: NK dex rep 2 bulk RNA-seq

description: 10× Genomics

tag: cell type


title: EMPD tumor 1 scRNA-seq

description: 10× Genomics

value: EMPD tumor


title: EMPD peri-tumor 2 scRNA-seq

description: 10× Genomics

value: EMPD peri-tumor


title: NK cytokine control 2 bulk RNA-seq

description: 10× Genomics


title: EMPD peri-tumor 3 scRNA-seq

description: 10× Genomics


title: cSCC tumor 1 scRNA-seq

description: 10× Genomics

value: cSCC tumor


title: EMPD peri-tumor 1 scRNA-seq

description: 10× Genomics


title: EMPD tumor 3 scRNA-seq

description: 10× Genomics